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Conserved domains on  [gi|537141260|gb|ERE67850|]
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ethanolamine-phosphatecytidylyltransferase-like protein [Cricetulus griseus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PTZ00308 super family cl31425
ethanolamine-phosphate cytidylyltransferase; Provisional
284-624 7.72e-148

ethanolamine-phosphate cytidylyltransferase; Provisional


The actual alignment was detected with superfamily member PTZ00308:

Pssm-ID: 140329 [Multi-domain]  Cd Length: 353  Bit Score: 438.06  E-value: 7.72e-148
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCDFC 363
Cdd:PTZ00308  20 FDMLHFGHANALRQARALGDELFVGCHSDEEIMRNKGPPVMHQEERYEALRACKWVDEVVEGYPYTTRLEDLERLECDFV 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 364 VHGNDITLTVDGRDTYEEVKQAGRYRECKRTQGVSTTDLVGRMLLVTKAHHSSQEMSSEyreyadsfgkpphptpagdtL 443
Cdd:PTZ00308 100 VHGDDISVDLNGRNSYQEIIDAGKFKVVKRTEGISTTDLVGRMLLCTKSHLLKSVDEVQ--------------------L 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 444 SSEVSsqcpggqnPWTGVSQFLQTSQKIIQFASGKEPQPGETVIYVAGAFDLFHIGHVDFLEEVYKLAKrpYIIAGLHFD 523
Cdd:PTZ00308 160 ESSLF--------PYTPTSHCLTTSRKIVQFSNNRSPKPGDRIVYVDGSFDLFHIGHIRVLQKARELGD--YLIVGVHED 229
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 524 QEVNRYKGKNYPIMNLHERTLSVLACRYVSEVVIGAPYSVTAELLGHFKVDLVCHGKT-EIVPDRDGSDPYQEPKRRGIF 602
Cdd:PTZ00308 230 QVVNEQKGSNYPIMNLNERVLGVLSCRYVDEVVIGAPFDVTKEVIDSLHINVVVGGKFsDLVNEEGGSDPYEVPKAMGIF 309
                        330       340
                 ....*....|....*....|..
gi 537141260 603 RQIDSGSNLTTDLIVQRIIKNR 624
Cdd:PTZ00308 310 KEVDSGCDLTTDSIVDRVVKNR 331
SIR2 super family cl00195
SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which ...
44-219 5.64e-85

SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines.


The actual alignment was detected with superfamily member cd01410:

Pssm-ID: 444738  Cd Length: 206  Bit Score: 269.17  E-value: 5.64e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  44 DLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRTAISELHGNMYIEVCTSCVPNREYVRVFDvtertALHR 123
Cdd:cd01410   42 RFRRAEPTLTHMALVELERAGLLKFVISQNVDGLHLRSGLPREKLSELHGNMFIEVCKSCGPEYVRDDVVE-----TRGD 116
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 124 HQTGRTCHKCGTQLRDTIVHFGERGTLGqplNWEAATEAASKADTILCLGSSLKVlkkYPRLWCMTKPPSRRPKLYIVNL 203
Cdd:cd01410  117 KETGRRCHACGGILKDTIVDFGERLPPE---NWMGAAAAACRADLFLCLGTSLQV---TPAANLPLKAARAGGRLVIVNL 190
                        170
                 ....*....|....*.
gi 537141260 204 QWTPKDDWAALKLHGK 219
Cdd:cd01410  191 QPTPKDKLADLVIHGD 206
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
672-745 8.02e-51

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


:

Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 172.03  E-value: 8.02e-51
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12680    2 KLLVSNLDFGVSDADIKELFAEFGTLKKAAVHYDRSGRSLGTAEVVFERRADALKAMKQYNGVPLDGRPMKIQL 75
FoP_duplication super family cl16441
C-terminal duplication domain of Friend of PRMT1; Fop, or Friend of Prmt1, proteins are ...
798-818 6.23e-03

C-terminal duplication domain of Friend of PRMT1; Fop, or Friend of Prmt1, proteins are conserved from fungi and plants to vertebrates. There is little that is actually conserved except for this C-terminal LDXXLDAYM region where X is any amino acid). The Fop proteins themselves are nuclear proteins localized to regions with low levels of DAPI, with a punctate/speckle-like distribution. Fop is a chromatin-associated protein and it co-localizes with facultative heterochromatin. It is is critical for oestrogen-dependent gene activation.


The actual alignment was detected with superfamily member pfam13865:

Pssm-ID: 464005  Cd Length: 81  Bit Score: 36.57  E-value: 6.23e-03
                          10        20
                  ....*....|....*....|.
gi 537141260  798 SKQQLSAEELDAQLDAYNARM 818
Cdd:pfam13865  43 KKKPKTKEELDAELDEYMSPK 63
 
Name Accession Description Interval E-value
PTZ00308 PTZ00308
ethanolamine-phosphate cytidylyltransferase; Provisional
284-624 7.72e-148

ethanolamine-phosphate cytidylyltransferase; Provisional


Pssm-ID: 140329 [Multi-domain]  Cd Length: 353  Bit Score: 438.06  E-value: 7.72e-148
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCDFC 363
Cdd:PTZ00308  20 FDMLHFGHANALRQARALGDELFVGCHSDEEIMRNKGPPVMHQEERYEALRACKWVDEVVEGYPYTTRLEDLERLECDFV 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 364 VHGNDITLTVDGRDTYEEVKQAGRYRECKRTQGVSTTDLVGRMLLVTKAHHSSQEMSSEyreyadsfgkpphptpagdtL 443
Cdd:PTZ00308 100 VHGDDISVDLNGRNSYQEIIDAGKFKVVKRTEGISTTDLVGRMLLCTKSHLLKSVDEVQ--------------------L 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 444 SSEVSsqcpggqnPWTGVSQFLQTSQKIIQFASGKEPQPGETVIYVAGAFDLFHIGHVDFLEEVYKLAKrpYIIAGLHFD 523
Cdd:PTZ00308 160 ESSLF--------PYTPTSHCLTTSRKIVQFSNNRSPKPGDRIVYVDGSFDLFHIGHIRVLQKARELGD--YLIVGVHED 229
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 524 QEVNRYKGKNYPIMNLHERTLSVLACRYVSEVVIGAPYSVTAELLGHFKVDLVCHGKT-EIVPDRDGSDPYQEPKRRGIF 602
Cdd:PTZ00308 230 QVVNEQKGSNYPIMNLNERVLGVLSCRYVDEVVIGAPFDVTKEVIDSLHINVVVGGKFsDLVNEEGGSDPYEVPKAMGIF 309
                        330       340
                 ....*....|....*....|..
gi 537141260 603 RQIDSGSNLTTDLIVQRIIKNR 624
Cdd:PTZ00308 310 KEVDSGCDLTTDSIVDRVVKNR 331
SIRT7 cd01410
SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, ...
44-219 5.64e-85

SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.


Pssm-ID: 238701  Cd Length: 206  Bit Score: 269.17  E-value: 5.64e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  44 DLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRTAISELHGNMYIEVCTSCVPNREYVRVFDvtertALHR 123
Cdd:cd01410   42 RFRRAEPTLTHMALVELERAGLLKFVISQNVDGLHLRSGLPREKLSELHGNMFIEVCKSCGPEYVRDDVVE-----TRGD 116
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 124 HQTGRTCHKCGTQLRDTIVHFGERGTLGqplNWEAATEAASKADTILCLGSSLKVlkkYPRLWCMTKPPSRRPKLYIVNL 203
Cdd:cd01410  117 KETGRRCHACGGILKDTIVDFGERLPPE---NWMGAAAAACRADLFLCLGTSLQV---TPAANLPLKAARAGGRLVIVNL 190
                        170
                 ....*....|....*.
gi 537141260 204 QWTPKDDWAALKLHGK 219
Cdd:cd01410  191 QPTPKDKLADLVIHGD 206
CCT cd02174
CTP:phosphocholine cytidylyltransferase; CTP:phosphocholine cytidylyltransferase (CCT) ...
284-416 3.83e-84

CTP:phosphocholine cytidylyltransferase; CTP:phosphocholine cytidylyltransferase (CCT) catalyzes the condensation of CTP and phosphocholine to form CDP-choline as the rate-limiting and regulatory step in the CDP-choline pathway. CCT is unique in that its enzymatic activity is regulated by the extent of its association with membrane structures. A current model posts that the elastic stress of the bilayer curvature is sensed by CCT and this governs the degree of membrane association, thus providing a mechanism for both positive and negative regulation of activity.


Pssm-ID: 173925  Cd Length: 150  Bit Score: 264.81  E-value: 3.83e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMG--DYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCD 361
Cdd:cd02174   11 FDLFHYGHANALRQAKKLGpnDYLIVGVHSDEEIHKHKGPPVMTEEERYEAVRHCKWVDEVVEGAPYVTTPEFLDKYKCD 90
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 362 FCVHGNDITLTVDGRDTYEEVKQAGRYRECKRTQGVSTTDLVGRMLLVTKAHHSS 416
Cdd:cd02174   91 YVAHGDDIYLDADGEDCYQEVKDAGRFKEVKRTEGVSTTDLIGRILLDYRDYHRR 145
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
672-745 8.02e-51

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 172.03  E-value: 8.02e-51
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12680    2 KLLVSNLDFGVSDADIKELFAEFGTLKKAAVHYDRSGRSLGTAEVVFERRADALKAMKQYNGVPLDGRPMKIQL 75
CTP_transf_like pfam01467
Cytidylyltransferase-like; This family includes: Cholinephosphate cytidylyltransferase; ...
283-405 3.83e-32

Cytidylyltransferase-like; This family includes: Cholinephosphate cytidylyltransferase; glycerol-3-phosphate cytidylyltransferase. It also includes putative adenylyltransferases, and FAD synthases.


Pssm-ID: 396172 [Multi-domain]  Cd Length: 134  Bit Score: 121.27  E-value: 3.83e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  283 RYDMVHYGHSNQLRQARAMGDY-LIVGVHTDEEiAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCD 361
Cdd:pfam01467   5 TFDPIHLGHLRLLEQAKELFDEdLIVGVPSDEP-PHKLKRPLFSAEERLEMLELAKWVDEVIVVAPWELTRELLKELNPD 83
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 537141260  362 FCVHGNDITLTV--DGRDTYEEVKQAGRYR-----ECKRTQGVSTTDLVGR 405
Cdd:pfam01467  84 VLVIGADSLLDFwyELDEILGNVKLVVVVRpvffiPLKPTNGISSTDIRER 134
TagD COG0615
Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family [Cell wall/membrane ...
284-406 1.22e-31

Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family [Cell wall/membrane/envelope biogenesis]; Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis


Pssm-ID: 440380 [Multi-domain]  Cd Length: 131  Bit Score: 119.82  E-value: 1.22e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVpaaPYVTT--LETLDKYNCD 361
Cdd:COG0615    9 FDLLHPGHINLLKRAKALGDELIVGVATDEFVASKGRKPIIPEEQRKEIVEALKYVDEVI---LGEEWdkFEDIEEIKPD 85
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 537141260 362 FCVHGNDITLTVDG-RDTYEEVKQAGRYRECKRTQGVSTTDLVGRM 406
Cdd:COG0615   86 VIVLGDDWKGDFDFlKEELEKRGIGCEVVYLPRTEGISSTKIKKRI 131
PRK00481 PRK00481
NAD-dependent deacetylase; Provisional
26-231 1.80e-24

NAD-dependent deacetylase; Provisional


Pssm-ID: 234777  Cd Length: 242  Bit Score: 102.95  E-value: 1.80e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  26 PCLTQPFYLFSLlscsaADLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGlpRTAISELHGNMYIEVCTSCvp 105
Cdd:PRK00481  58 PELVWKFYNERR-----RQLLDAKPNAAHRALAELEKLGKLVTVITQNIDGLHERAG--SKNVIELHGSLLRARCTKC-- 128
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 106 NREYVRVFDVTERtalhrhqtGRTCHKCGTQLRDTIVHFGErgtlgqPLN---WEAATEAASKADTILCLGSSLKVlkkY 182
Cdd:PRK00481 129 GQTYDLDEYLKPE--------PPRCPKCGGILRPDVVLFGE------MLPelaIDEAYEALEEADLFIVIGTSLVV---Y 191
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 537141260 183 PRLWCMTKPPSRRPKLYIVNLQWTPKDDWAALKLHGKCDDVMQLLMDEL 231
Cdd:PRK00481 192 PAAGLPYEAREHGAKTVEINLEPTPLDSLFDLVIHGKAGEVVPELVEEL 240
SIR2 COG0846
NAD-dependent protein deacetylase, SIR2 family [Posttranslational modification, protein ...
43-229 3.93e-22

NAD-dependent protein deacetylase, SIR2 family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440607  Cd Length: 243  Bit Score: 96.38  E-value: 3.93e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  43 ADLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRtaISELHGNMYIEVCTSC---VPNREYVRVFdvtert 119
Cdd:COG0846   71 RLLRDAEPNAAHRALAELEKAGKLVFVITQNVDGLHQRAGSKN--VIELHGSLHRLRCTKCgkrYDLEDVLEDL------ 142
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 120 alhRHQTGRTCHKCGTQLRDTIVHFGERgtlGQPLNWEAATEAASKADTILCLGSSLKVlkkYP--RLWCMTKppSRRPK 197
Cdd:COG0846  143 ---EGELPPRCPKCGGLLRPDVVWFGEM---LPEEALERALEALAEADLFLVIGTSLVV---YPaaGLPEYAK--RAGAP 211
                        170       180       190
                 ....*....|....*....|....*....|..
gi 537141260 198 LYIVNLQWTPKDDWAALKLHGKCDDVMQLLMD 229
Cdd:COG0846  212 LVEINPEPTPLDSLADLVIRGDAGEVLPALVE 243
cyt_tran_rel TIGR00125
cytidyltransferase-like domain; Protein families that contain at least one copy of this domain ...
283-342 1.89e-21

cytidyltransferase-like domain; Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. Many of these proteins are known to use CTP or ATP and release pyrophosphate.


Pssm-ID: 272920 [Multi-domain]  Cd Length: 66  Bit Score: 88.52  E-value: 1.89e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  283 RYDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEV 342
Cdd:TIGR00125   7 TFDPFHLGHLDLLERAKELFDELIVGVGSDQFVNPLKGEPVFSLEERLEMLKALKYVDEV 66
SIR2 pfam02146
Sir2 family; This region is characteriztic of Silent information regulator 2 (Sir2) proteins, ...
26-179 1.75e-18

Sir2 family; This region is characteriztic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organization and DNA damage repair processes.i


Pssm-ID: 426621  Cd Length: 179  Bit Score: 83.84  E-value: 1.75e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260   26 PCLTQPFYLFSLLsCSAADLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRtaISELHGNMYIEVCTSCVP 105
Cdd:pfam02146  38 PELVWDPEPFYNI-ARELLPGEAQPNPAHYFIAKLEDKGKLLRLITQNIDGLHERAGSKK--VVELHGSFAKARCVSCHQ 114
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260  106 NREYVRVFDVTErtalhRHQTGRtCHKCGTQLRDTIVHFGErgtlGQPLNWEAATEAASKADTILCLGSSLKVL 179
Cdd:pfam02146 115 KYTGETLYERIR-----PEKVPH-CPQCGGLLKPDIVFFGE----NLPDKFHRAYEDLEEADLLIVIGTSLKVY 178
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
672-743 9.65e-18

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 78.60  E-value: 9.65e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDReTGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKV 75
RRM smart00360
RNA recognition motif;
672-743 6.85e-17

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 75.71  E-value: 6.85e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260   672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
673-741 1.07e-12

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 63.79  E-value: 1.07e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260  673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 741
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
673-755 2.93e-09

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 60.59  E-value: 2.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLvtSQIDT 752
Cdd:TIGR01628 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL--AQRKE 365

                  ...
gi 537141260  753 QRR 755
Cdd:TIGR01628 366 QRR 368
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
672-773 1.19e-05

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 45.80  E-value: 1.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTsqi 750
Cdd:PLN03134  36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDReTGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN--- 112
                         90       100
                 ....*....|....*....|...
gi 537141260 751 dtQRRPAQSINRGGMTRNRGSGT 773
Cdd:PLN03134 113 --DRPSAPRAYGGGGGYSGGGGG 133
FoP_duplication pfam13865
C-terminal duplication domain of Friend of PRMT1; Fop, or Friend of Prmt1, proteins are ...
798-818 6.23e-03

C-terminal duplication domain of Friend of PRMT1; Fop, or Friend of Prmt1, proteins are conserved from fungi and plants to vertebrates. There is little that is actually conserved except for this C-terminal LDXXLDAYM region where X is any amino acid). The Fop proteins themselves are nuclear proteins localized to regions with low levels of DAPI, with a punctate/speckle-like distribution. Fop is a chromatin-associated protein and it co-localizes with facultative heterochromatin. It is is critical for oestrogen-dependent gene activation.


Pssm-ID: 464005  Cd Length: 81  Bit Score: 36.57  E-value: 6.23e-03
                          10        20
                  ....*....|....*....|.
gi 537141260  798 SKQQLSAEELDAQLDAYNARM 818
Cdd:pfam13865  43 KKKPKTKEELDAELDEYMSPK 63
 
Name Accession Description Interval E-value
PTZ00308 PTZ00308
ethanolamine-phosphate cytidylyltransferase; Provisional
284-624 7.72e-148

ethanolamine-phosphate cytidylyltransferase; Provisional


Pssm-ID: 140329 [Multi-domain]  Cd Length: 353  Bit Score: 438.06  E-value: 7.72e-148
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCDFC 363
Cdd:PTZ00308  20 FDMLHFGHANALRQARALGDELFVGCHSDEEIMRNKGPPVMHQEERYEALRACKWVDEVVEGYPYTTRLEDLERLECDFV 99
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 364 VHGNDITLTVDGRDTYEEVKQAGRYRECKRTQGVSTTDLVGRMLLVTKAHHSSQEMSSEyreyadsfgkpphptpagdtL 443
Cdd:PTZ00308 100 VHGDDISVDLNGRNSYQEIIDAGKFKVVKRTEGISTTDLVGRMLLCTKSHLLKSVDEVQ--------------------L 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 444 SSEVSsqcpggqnPWTGVSQFLQTSQKIIQFASGKEPQPGETVIYVAGAFDLFHIGHVDFLEEVYKLAKrpYIIAGLHFD 523
Cdd:PTZ00308 160 ESSLF--------PYTPTSHCLTTSRKIVQFSNNRSPKPGDRIVYVDGSFDLFHIGHIRVLQKARELGD--YLIVGVHED 229
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 524 QEVNRYKGKNYPIMNLHERTLSVLACRYVSEVVIGAPYSVTAELLGHFKVDLVCHGKT-EIVPDRDGSDPYQEPKRRGIF 602
Cdd:PTZ00308 230 QVVNEQKGSNYPIMNLNERVLGVLSCRYVDEVVIGAPFDVTKEVIDSLHINVVVGGKFsDLVNEEGGSDPYEVPKAMGIF 309
                        330       340
                 ....*....|....*....|..
gi 537141260 603 RQIDSGSNLTTDLIVQRIIKNR 624
Cdd:PTZ00308 310 KEVDSGCDLTTDSIVDRVVKNR 331
PLN02406 PLN02406
ethanolamine-phosphate cytidylyltransferase
284-623 3.61e-107

ethanolamine-phosphate cytidylyltransferase


Pssm-ID: 215227 [Multi-domain]  Cd Length: 418  Bit Score: 335.50  E-value: 3.61e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETL----DKYN 359
Cdd:PLN02406  62 FDMMHYGHANALRQARALGDELVVGVVSDEEIIANKGPPVTPMHERMIMVSGVKWVDEVIPDAPYAITEEFMnklfNEYN 141
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 360 CDFCVHGNDITLTVDGRDTYEEVKQAGRYRECKRTQGVSTTDLVGRMLLVTKAH--HSSQEMSSEYREYADSFGKPPHPt 437
Cdd:PLN02406 142 IDYIIHGDDPCLLPDGTDAYALAKKAGRYKQIKRTEGVSSTDIVGRMLLCVRERsiSDSHNHSSLQRQFSHGHSQFEDG- 220
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 438 pagdtlssevssqcpgGQNPWTGVSQFLQTSQKIIQFASGKEPQPGETVIYVAGAFDLFHIGHVDFLEEVYKLAKrpYII 517
Cdd:PLN02406 221 ----------------GSGSGTRVSHFLPTSRRIVQFSNGKGPGPDARIVYIDGAFDLFHAGHVEILRLARALGD--FLL 282
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 518 AGLHFDQEVNRYKGKNYPIMNLHERTLSVLACRYVSEVVIGAPYSVTAELLGHFKVDLVCHGK-TEIVPDRDG-SDPYQE 595
Cdd:PLN02406 283 VGIHTDQTVSAHRGAHRPIMNLHERSLSVLACRYVDEVIIGAPWEVSKDMITTFNISLVVHGTvAENNDFLKGeDDPYAV 362
                        330       340
                 ....*....|....*....|....*...
gi 537141260 596 PKRRGIFRQIDSGSNLTTDLIVQRIIKN 623
Cdd:PLN02406 363 PKSMGIFQVLESPLDITTSTIIRRIVAN 390
SIRT7 cd01410
SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, ...
44-219 5.64e-85

SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.


Pssm-ID: 238701  Cd Length: 206  Bit Score: 269.17  E-value: 5.64e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  44 DLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRTAISELHGNMYIEVCTSCVPNREYVRVFDvtertALHR 123
Cdd:cd01410   42 RFRRAEPTLTHMALVELERAGLLKFVISQNVDGLHLRSGLPREKLSELHGNMFIEVCKSCGPEYVRDDVVE-----TRGD 116
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 124 HQTGRTCHKCGTQLRDTIVHFGERGTLGqplNWEAATEAASKADTILCLGSSLKVlkkYPRLWCMTKPPSRRPKLYIVNL 203
Cdd:cd01410  117 KETGRRCHACGGILKDTIVDFGERLPPE---NWMGAAAAACRADLFLCLGTSLQV---TPAANLPLKAARAGGRLVIVNL 190
                        170
                 ....*....|....*.
gi 537141260 204 QWTPKDDWAALKLHGK 219
Cdd:cd01410  191 QPTPKDKLADLVIHGD 206
CCT cd02174
CTP:phosphocholine cytidylyltransferase; CTP:phosphocholine cytidylyltransferase (CCT) ...
284-416 3.83e-84

CTP:phosphocholine cytidylyltransferase; CTP:phosphocholine cytidylyltransferase (CCT) catalyzes the condensation of CTP and phosphocholine to form CDP-choline as the rate-limiting and regulatory step in the CDP-choline pathway. CCT is unique in that its enzymatic activity is regulated by the extent of its association with membrane structures. A current model posts that the elastic stress of the bilayer curvature is sensed by CCT and this governs the degree of membrane association, thus providing a mechanism for both positive and negative regulation of activity.


Pssm-ID: 173925  Cd Length: 150  Bit Score: 264.81  E-value: 3.83e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMG--DYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCD 361
Cdd:cd02174   11 FDLFHYGHANALRQAKKLGpnDYLIVGVHSDEEIHKHKGPPVMTEEERYEAVRHCKWVDEVVEGAPYVTTPEFLDKYKCD 90
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 362 FCVHGNDITLTVDGRDTYEEVKQAGRYRECKRTQGVSTTDLVGRMLLVTKAHHSS 416
Cdd:cd02174   91 YVAHGDDIYLDADGEDCYQEVKDAGRFKEVKRTEGVSTTDLIGRILLDYRDYHRR 145
ECT cd02173
CTP:phosphoethanolamine cytidylyltransferase (ECT); CTP:phosphoethanolamine ...
483-624 3.44e-83

CTP:phosphoethanolamine cytidylyltransferase (ECT); CTP:phosphoethanolamine cytidylyltransferase (ECT) catalyzes the conversion of phosphoethanolamine to CDP-ethanolamine as part of the CDP-ethanolamine biosynthesis pathway. ECT expression in hepatocytes is localized predominantly to areas of the cytoplasm that are rich in rough endoplasmic reticulum. Several ECTs, including yeast and human ECT, have large repetitive sequences located within their N- and C-termini.


Pssm-ID: 173924  Cd Length: 152  Bit Score: 262.20  E-value: 3.44e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 483 GETVIYVAGAFDLFHIGHVDFLEEVYKLakRPYIIAGLHFDQEVNRYKGKNYPIMNLHERTLSVLACRYVSEVVIGAPYS 562
Cdd:cd02173    1 GDKVVYVDGAFDLFHIGHIEFLEKAREL--GDYLIVGVHDDQTVNEYKGSNYPIMNLHERVLSVLACRYVDEVVIGAPYV 78
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 563 VTAELLGHFKVDLVCHGKTEIVPD-RDGSDPYQEPKRRGIFRQIDSGSNLTTDLIVQRIIKNR 624
Cdd:cd02173   79 ITKELIEHFKIDVVVHGKTEETPDsLDGEDPYAVPKEMGIFKEIDSGSDLTTRDIVNRIIKNR 141
SIR2-fam cd01407
SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze ...
47-219 5.99e-55

SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.


Pssm-ID: 238698  Cd Length: 218  Bit Score: 188.93  E-value: 5.99e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  47 EAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRtaISELHGNMYIEVCTSCvpNREYVRVFDVtertALHRHQT 126
Cdd:cd01407   61 NAQPNPAHRALAELERKGKLKRVITQNVDGLHQRAGSPK--VIELHGSLFRVRCTKC--GKEYPRDELQ----ADIDREE 132
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 127 GRTCHKCGTQLRDTIVHFGERGtlgqPLNWEAATEAASKADTILCLGSSLKVlkkYPRLWCMTKPPSRRPKLYIVNLQWT 206
Cdd:cd01407  133 VPRCPKCGGLLRPDVVFFGESL----PEELDEAAEALAKADLLLVIGTSLQV---YPAAGLPLYAPERGAPVVIINLEPT 205
                        170
                 ....*....|...
gi 537141260 207 PKDDWAALKLHGK 219
Cdd:cd01407  206 PADRKADLVILGD 218
RRM_THOC4 cd12680
RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This ...
672-745 8.02e-51

RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins; This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes.


Pssm-ID: 410081 [Multi-domain]  Cd Length: 75  Bit Score: 172.03  E-value: 8.02e-51
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12680    2 KLLVSNLDFGVSDADIKELFAEFGTLKKAAVHYDRSGRSLGTAEVVFERRADALKAMKQYNGVPLDGRPMKIQL 75
cytidylyltransferase cd02170
cytidylyltransferase; The cytidylyltransferase family includes cholinephosphate ...
284-409 2.25e-47

cytidylyltransferase; The cytidylyltransferase family includes cholinephosphate cytidylyltransferase (CCT), glycerol-3-phosphate cytidylyltransferase, RafE and phosphoethanolamine cytidylyltransferase (ECT). All enzymes catalyze the transfer of a cytidylyl group from CTP to various substrates.


Pssm-ID: 173921 [Multi-domain]  Cd Length: 136  Bit Score: 164.77  E-value: 2.25e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNcDFC 363
Cdd:cd02170   10 FDIIHPGHIRFLEEAKKLGDYLIVGVARDETVAKIKRRPILPEEQRAEVVEALKYVDEVILGHPWSYFKPLEELKP-DVI 88
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 537141260 364 VHGNDITLTVDGRDTYEEVKQAGRYREC--KRTQGVSTTDLVGRMLLV 409
Cdd:cd02170   89 VLGDDQKNGVDEEEVYEELKKRGKVIEVprKKTEGISSSDIIKRILEL 136
SIR2 cd00296
SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which ...
47-219 1.25e-43

SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines.


Pssm-ID: 238184 [Multi-domain]  Cd Length: 222  Bit Score: 157.51  E-value: 1.25e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  47 EAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRTAISELHGNMYIEVCTSCVPNREYVRVFDVTERtalhrhqt 126
Cdd:cd00296   63 DAKPNPAHRALAELERKGKLKRIITQNVDGLHERAGSRRNRVIELHGSLDRVRCTSCGKEYPRDEVLEREKP-------- 134
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 127 gRTCHKCGTQLRDTIVHFGERGTLGqplNWEAATEAASKADTILCLGSSLKVlkkYPRLWCMTKPPSRRPKLYIVNLQWT 206
Cdd:cd00296  135 -PRCPKCGGLLRPDVVDFGEALPKE---WFDRALEALLEADLVLVIGTSLTV---YPAARLLLRAPERGAPVVIINREPT 207
                        170
                 ....*....|....*
gi 537141260 207 PKDDW--AALKLHGK 219
Cdd:cd00296  208 PADALkkADLVILGD 222
CCT cd02174
CTP:phosphocholine cytidylyltransferase; CTP:phosphocholine cytidylyltransferase (CCT) ...
487-623 9.28e-36

CTP:phosphocholine cytidylyltransferase; CTP:phosphocholine cytidylyltransferase (CCT) catalyzes the condensation of CTP and phosphocholine to form CDP-choline as the rate-limiting and regulatory step in the CDP-choline pathway. CCT is unique in that its enzymatic activity is regulated by the extent of its association with membrane structures. A current model posts that the elastic stress of the bilayer curvature is sensed by CCT and this governs the degree of membrane association, thus providing a mechanism for both positive and negative regulation of activity.


Pssm-ID: 173925  Cd Length: 150  Bit Score: 132.31  E-value: 9.28e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 487 IYVAGAFDLFHIGHVDFLEEVYKLAKRPYIIAGLHFDQEVNRYKGKnyPIMNLHERTLSVLACRYVSEVVIGAPYSVTAE 566
Cdd:cd02174    5 VYVDGCFDLFHYGHANALRQAKKLGPNDYLIVGVHSDEEIHKHKGP--PVMTEEERYEAVRHCKWVDEVVEGAPYVTTPE 82
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 567 LLGHFKVDLVCHGKtEIVPDRDGSDPYQEPKRRGIFRQI---DSGSnlTTDlIVQRIIKN 623
Cdd:cd02174   83 FLDKYKCDYVAHGD-DIYLDADGEDCYQEVKDAGRFKEVkrtEGVS--TTD-LIGRILLD 138
PLN02413 PLN02413
choline-phosphate cytidylyltransferase
254-407 1.02e-34

choline-phosphate cytidylyltransferase


Pssm-ID: 215229  Cd Length: 294  Bit Score: 134.30  E-value: 1.02e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 254 AGEEGAYVTVKATVPPPDLVGRTLGGGIsrYDMVHYGHSNQLRQARAM--GDYLIVGVHTDEEIAKHKGPPVFTQEERYK 331
Cdd:PLN02413   8 STAAASSGSATPSSSPSDRPVRVYADGI--YDLFHFGHARSLEQAKKLfpNTYLLVGCCNDELTHKYKGKTVMTEDERYE 85
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 332 MVQAIKWVDEVVPAAPYVTTLETLDKYNCDFCVHgnDITLTVD----GRDTYEEVKQAGRYRECKRTQGVSTTDLVGRML 407
Cdd:PLN02413  86 SLRHCKWVDEVIPDAPWVITQEFLDKHRIDYVAH--DALPYADasgaGKDVYEFVKKIGKFKETKRTDGISTSDIIMRIV 163
CTP_transf_like pfam01467
Cytidylyltransferase-like; This family includes: Cholinephosphate cytidylyltransferase; ...
283-405 3.83e-32

Cytidylyltransferase-like; This family includes: Cholinephosphate cytidylyltransferase; glycerol-3-phosphate cytidylyltransferase. It also includes putative adenylyltransferases, and FAD synthases.


Pssm-ID: 396172 [Multi-domain]  Cd Length: 134  Bit Score: 121.27  E-value: 3.83e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  283 RYDMVHYGHSNQLRQARAMGDY-LIVGVHTDEEiAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCD 361
Cdd:pfam01467   5 TFDPIHLGHLRLLEQAKELFDEdLIVGVPSDEP-PHKLKRPLFSAEERLEMLELAKWVDEVIVVAPWELTRELLKELNPD 83
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 537141260  362 FCVHGNDITLTV--DGRDTYEEVKQAGRYR-----ECKRTQGVSTTDLVGR 405
Cdd:pfam01467  84 VLVIGADSLLDFwyELDEILGNVKLVVVVRpvffiPLKPTNGISSTDIRER 134
TagD COG0615
Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family [Cell wall/membrane ...
284-406 1.22e-31

Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family [Cell wall/membrane/envelope biogenesis]; Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis


Pssm-ID: 440380 [Multi-domain]  Cd Length: 131  Bit Score: 119.82  E-value: 1.22e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVpaaPYVTT--LETLDKYNCD 361
Cdd:COG0615    9 FDLLHPGHINLLKRAKALGDELIVGVATDEFVASKGRKPIIPEEQRKEIVEALKYVDEVI---LGEEWdkFEDIEEIKPD 85
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 537141260 362 FCVHGNDITLTVDG-RDTYEEVKQAGRYRECKRTQGVSTTDLVGRM 406
Cdd:COG0615   86 VIVLGDDWKGDFDFlKEELEKRGIGCEVVYLPRTEGISSTKIKKRI 131
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
672-745 2.30e-31

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 116.91  E-value: 2.30e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12418    2 RVRVSNLHPDVTEEDLRELFGRVGPVKSVKINYDRSGRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKVEL 75
ECT cd02173
CTP:phosphoethanolamine cytidylyltransferase (ECT); CTP:phosphoethanolamine ...
284-407 2.44e-28

CTP:phosphoethanolamine cytidylyltransferase (ECT); CTP:phosphoethanolamine cytidylyltransferase (ECT) catalyzes the conversion of phosphoethanolamine to CDP-ethanolamine as part of the CDP-ethanolamine biosynthesis pathway. ECT expression in hepatocytes is localized predominantly to areas of the cytoplasm that are rich in rough endoplasmic reticulum. Several ECTs, including yeast and human ECT, have large repetitive sequences located within their N- and C-termini.


Pssm-ID: 173924  Cd Length: 152  Bit Score: 111.20  E-value: 2.44e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGP--PVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCD 361
Cdd:cd02173   11 FDLFHIGHIEFLEKARELGDYLIVGVHDDQTVNEYKGSnyPIMNLHERVLSVLACRYVDEVVIGAPYVITKELIEHFKID 90
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 537141260 362 FCVHG--NDITLTVDGRDTYEEVKQAGRYRECKRTQGVSTTDLVGRML 407
Cdd:cd02173   91 VVVHGktEETPDSLDGEDPYAVPKEMGIFKEIDSGSDLTTRDIVNRII 138
PRK00481 PRK00481
NAD-dependent deacetylase; Provisional
26-231 1.80e-24

NAD-dependent deacetylase; Provisional


Pssm-ID: 234777  Cd Length: 242  Bit Score: 102.95  E-value: 1.80e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  26 PCLTQPFYLFSLlscsaADLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGlpRTAISELHGNMYIEVCTSCvp 105
Cdd:PRK00481  58 PELVWKFYNERR-----RQLLDAKPNAAHRALAELEKLGKLVTVITQNIDGLHERAG--SKNVIELHGSLLRARCTKC-- 128
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 106 NREYVRVFDVTERtalhrhqtGRTCHKCGTQLRDTIVHFGErgtlgqPLN---WEAATEAASKADTILCLGSSLKVlkkY 182
Cdd:PRK00481 129 GQTYDLDEYLKPE--------PPRCPKCGGILRPDVVLFGE------MLPelaIDEAYEALEEADLFIVIGTSLVV---Y 191
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 537141260 183 PRLWCMTKPPSRRPKLYIVNLQWTPKDDWAALKLHGKCDDVMQLLMDEL 231
Cdd:PRK00481 192 PAAGLPYEAREHGAKTVEINLEPTPLDSLFDLVIHGKAGEVVPELVEEL 240
cytidylyltransferase cd02170
cytidylyltransferase; The cytidylyltransferase family includes cholinephosphate ...
484-622 6.04e-24

cytidylyltransferase; The cytidylyltransferase family includes cholinephosphate cytidylyltransferase (CCT), glycerol-3-phosphate cytidylyltransferase, RafE and phosphoethanolamine cytidylyltransferase (ECT). All enzymes catalyze the transfer of a cytidylyl group from CTP to various substrates.


Pssm-ID: 173921 [Multi-domain]  Cd Length: 136  Bit Score: 98.13  E-value: 6.04e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 484 ETVIYVAGAFDLFHIGHVDFLEEVYKLAKrpYIIAGLHFDQEVNRYKGKnyPIMNLHERTLSVLACRYVSEVVIGAPYSV 563
Cdd:cd02170    1 MKRVYAAGTFDIIHPGHIRFLEEAKKLGD--YLIVGVARDETVAKIKRR--PILPEEQRAEVVEALKYVDEVILGHPWSY 76
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 564 TAELLgHFKVDLVCHGKTEIVPDrDGSDPYQEPKRRGIFRQI--DSGSNLTTDLIVQRIIK 622
Cdd:cd02170   77 FKPLE-ELKPDVIVLGDDQKNGV-DEEEVYEELKKRGKVIEVprKKTEGISSSDIIKRILE 135
PTZ00308 PTZ00308
ethanolamine-phosphate cytidylyltransferase; Provisional
481-621 6.43e-24

ethanolamine-phosphate cytidylyltransferase; Provisional


Pssm-ID: 140329 [Multi-domain]  Cd Length: 353  Bit Score: 104.10  E-value: 6.43e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 481 QPGETVIYVAGAFDLFHIGHVDFLEEVYKLAKRpyIIAGLHFDQEVNRYKGKnyPIMNLHERTLSVLACRYVSEVVIGAP 560
Cdd:PTZ00308   8 KPGTIRVWVDGCFDMLHFGHANALRQARALGDE--LFVGCHSDEEIMRNKGP--PVMHQEERYEALRACKWVDEVVEGYP 83
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 561 YSVTAELLGHFKVDLVCHGKtEIVPDRDGSDPYQEPKRRGIFRQIDSGSNLTTDLIVQRII 621
Cdd:PTZ00308  84 YTTRLEDLERLECDFVVHGD-DISVDLNGRNSYQEIIDAGKFKVVKRTEGISTTDLVGRML 143
SIR2 COG0846
NAD-dependent protein deacetylase, SIR2 family [Posttranslational modification, protein ...
43-229 3.93e-22

NAD-dependent protein deacetylase, SIR2 family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440607  Cd Length: 243  Bit Score: 96.38  E-value: 3.93e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  43 ADLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRtaISELHGNMYIEVCTSC---VPNREYVRVFdvtert 119
Cdd:COG0846   71 RLLRDAEPNAAHRALAELEKAGKLVFVITQNVDGLHQRAGSKN--VIELHGSLHRLRCTKCgkrYDLEDVLEDL------ 142
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 120 alhRHQTGRTCHKCGTQLRDTIVHFGERgtlGQPLNWEAATEAASKADTILCLGSSLKVlkkYP--RLWCMTKppSRRPK 197
Cdd:COG0846  143 ---EGELPPRCPKCGGLLRPDVVWFGEM---LPEEALERALEALAEADLFLVIGTSLVV---YPaaGLPEYAK--RAGAP 211
                        170       180       190
                 ....*....|....*....|....*....|..
gi 537141260 198 LYIVNLQWTPKDDWAALKLHGKCDDVMQLLMD 229
Cdd:COG0846  212 LVEINPEPTPLDSLADLVIRGDAGEVLPALVE 243
SIR2_Af2 cd01413
SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, ...
45-219 1.47e-21

SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.


Pssm-ID: 238704  Cd Length: 222  Bit Score: 93.97  E-value: 1.47e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  45 LSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRtaISELHGNMYIEVCTSCvpNREYvrvfDVTERTALHRH 124
Cdd:cd01413   63 LLEAQPNKAHYFLAELEKQGIIKAIITQNIDGLHQRAGSKN--VIELHGTLQTAYCVNC--GSKY----DLEEVKYAKKH 134
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 125 QTGRtCHKCGTQLRDTIVHFGErgTLGQPLnWEAATEAASKADTILCLGSSLKVlkkYP--RLWCMTKppSRRPKLYIVN 202
Cdd:cd01413  135 EVPR-CPKCGGIIRPDVVLFGE--PLPQAL-LREAIEAAKEADLFIVLGSSLVV---YPanLLPLIAK--ENGAKLVIVN 205
                        170
                 ....*....|....*..
gi 537141260 203 LQWTPKDDWAALKLHGK 219
Cdd:cd01413  206 ADETPFDYIADLVIQDK 222
cyt_tran_rel TIGR00125
cytidyltransferase-like domain; Protein families that contain at least one copy of this domain ...
283-342 1.89e-21

cytidyltransferase-like domain; Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. Many of these proteins are known to use CTP or ATP and release pyrophosphate.


Pssm-ID: 272920 [Multi-domain]  Cd Length: 66  Bit Score: 88.52  E-value: 1.89e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  283 RYDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEV 342
Cdd:TIGR00125   7 TFDPFHLGHLDLLERAKELFDELIVGVGSDQFVNPLKGEPVFSLEERLEMLKALKYVDEV 66
SIRT5_Af1_CobB cd01412
SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human ...
44-228 9.88e-21

SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.


Pssm-ID: 238703  Cd Length: 224  Bit Score: 91.50  E-value: 9.88e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  44 DLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGlpRTAISELHGNMYIEVCTSCvpnrEYVRVFDVTE-RTALH 122
Cdd:cd01412   58 KALRAQPNPAHLALAELERRLPNVLLITQNVDGLHERAG--SRNVIELHGSLFRVRCSSC----GYVGENNEEIpEEELP 131
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 123 RhqtgrtCHKCGTQLRDTIVHFGERgtlgQPLNWEAATEAASKADTILCLGSSLKVlkkYPRLWCMTKPPSRRPKLYIVN 202
Cdd:cd01412  132 R------CPKCGGLLRPGVVWFGES----LPLALLEAVEALAKADLFLVIGTSGVV---YPAAGLPEEAKERGARVIEIN 198
                        170       180
                 ....*....|....*....|....*.
gi 537141260 203 LQWTPKDDWAALKLHGKCDDVMQLLM 228
Cdd:cd01412  199 PEPTPLSPIADFAFRGKAGEVLPALL 224
PLN02413 PLN02413
choline-phosphate cytidylyltransferase
475-623 3.81e-20

choline-phosphate cytidylyltransferase


Pssm-ID: 215229  Cd Length: 294  Bit Score: 91.93  E-value: 3.81e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 475 ASGKEPQPGETVIYVAGAFDLFHIGHVDFLEEVYKLAKRPYIIAGLHFDQEVNRYKGKNypIMNLHERTLSVLACRYVSE 554
Cdd:PLN02413  18 TPSSSPSDRPVRVYADGIYDLFHFGHARSLEQAKKLFPNTYLLVGCCNDELTHKYKGKT--VMTEDERYESLRHCKWVDE 95
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 555 VVIGAPYSVTAELLGHFKVDLVCHgktEIVPDRD----GSDPYQEPKRRGIFRQIDSGSNLTTDLIVQRIIKN 623
Cdd:PLN02413  96 VIPDAPWVITQEFLDKHRIDYVAH---DALPYADasgaGKDVYEFVKKIGKFKETKRTDGISTSDIIMRIVKD 165
PRK14138 PRK14138
NAD-dependent deacetylase; Provisional
45-233 1.38e-18

NAD-dependent deacetylase; Provisional


Pssm-ID: 172627 [Multi-domain]  Cd Length: 244  Bit Score: 86.03  E-value: 1.38e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  45 LSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRtaISELHGNMYIEVCTSCVPNREYVRVFDVTERTALHRh 124
Cdd:PRK14138  69 MLEAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQKAGSKK--VIELHGNVEEYYCVRCGKRYTVEDVIEKLEKSDVPR- 145
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 125 qtgrtCHKCGTQLRDTIVHFGERgtlgqpLNWEAATEA---ASKADTILCLGSSLKVlkkYPRLWCMTKPPSRRPKLYIV 201
Cdd:PRK14138 146 -----CDDCSGLIRPNIVFFGEA------LPQDALREAirlSSKASLMIVMGSSLVV---YPAAELPLITVRSGGKLVIV 211
                        170       180       190
                 ....*....|....*....|....*....|..
gi 537141260 202 NLQWTPKDDWAALKLHGKCDDVMQLLMDELGL 233
Cdd:PRK14138 212 NLGETPLDDIATLKYNMDVVEFANRVMSEGGI 243
SIR2 pfam02146
Sir2 family; This region is characteriztic of Silent information regulator 2 (Sir2) proteins, ...
26-179 1.75e-18

Sir2 family; This region is characteriztic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organization and DNA damage repair processes.i


Pssm-ID: 426621  Cd Length: 179  Bit Score: 83.84  E-value: 1.75e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260   26 PCLTQPFYLFSLLsCSAADLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRtaISELHGNMYIEVCTSCVP 105
Cdd:pfam02146  38 PELVWDPEPFYNI-ARELLPGEAQPNPAHYFIAKLEDKGKLLRLITQNIDGLHERAGSKK--VVELHGSFAKARCVSCHQ 114
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260  106 NREYVRVFDVTErtalhRHQTGRtCHKCGTQLRDTIVHFGErgtlGQPLNWEAATEAASKADTILCLGSSLKVL 179
Cdd:pfam02146 115 KYTGETLYERIR-----PEKVPH-CPQCGGLLKPDIVFFGE----NLPDKFHRAYEDLEEADLLIVIGTSLKVY 178
SIRT4 cd01409
SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and ...
46-224 2.75e-18

SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.


Pssm-ID: 238700  Cd Length: 260  Bit Score: 85.43  E-value: 2.75e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  46 SEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGlpRTAISELHGNMYIEVCTSC---VPNREYVRVF--------D 114
Cdd:cd01409   69 SAAQPNAAHRALAALEAAGRLHGLITQNVDGLHTKAG--SRNVVELHGSLHRVVCLSCgfrTPRAELQDRLealnpgfaE 146
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 115 VTERTA------LHRHQTGR----TCHKCGTQLRDTIVHFGE---RGTLgqplnwEAATEAASKADTILCLGSSLKVLKK 181
Cdd:cd01409  147 QAAGQApdgdvdLEDEQVAGfrvpECERCGGVLKPDVVFFGEnvpRDRV------VTAAARLAEADALLVLGSSLMVYSG 220
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 537141260 182 YpRLwCMTKPPSRRPkLYIVNLQWTPKDDWAALKLHGKCDDVM 224
Cdd:cd01409  221 Y-RF-VLAAAEAGLP-IAIVNIGPTRADHLATLKVDARCGEVL 260
G3P_Cytidylyltransferase cd02171
glycerol-3-phosphate cytidylyltransferase; Glycerol-3-phosphate cytidylyltransferase, ...
284-402 2.86e-18

glycerol-3-phosphate cytidylyltransferase; Glycerol-3-phosphate cytidylyltransferase,(CDP-glycerol pyrophosphorylase). Glycerol-3-phosphate cytidyltransferase acts in pathways of teichoic acid biosynthesis. Teichoic acids are substituted polymers, linked by phosphodiester bonds, of glycerol, ribitol, etc. An example is poly(glycerol phosphate), the major teichoic acid of the Bacillus subtilis cell wall. Most, but not all, species encoding proteins in this family are Gram-positive bacteria. A closely related protein assigned a different function experimentally is a human ethanolamine-phosphate cytidylyltransferase.


Pssm-ID: 173922 [Multi-domain]  Cd Length: 129  Bit Score: 81.76  E-value: 2.86e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCDFC 363
Cdd:cd02171   10 FDLLHIGHLNLLERAKALGDKLIVAVSTDEFNAGKGKKAVIPYEQRAEILESIRYVDLVIPETNWEQKIEDIKKYNVDVF 89
                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 537141260 364 VHGNDITLTVDGRDTYEEVKqagrYREckRTQGVSTTDL 402
Cdd:cd02171   90 VMGDDWEGKFDFLKEYCEVV----YLP--RTKGISSTQL 122
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
673-744 6.53e-18

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 78.48  E-value: 6.53e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
672-743 9.65e-18

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 78.60  E-value: 9.65e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDReTGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKV 75
RRM smart00360
RNA recognition motif;
672-743 6.85e-17

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 75.71  E-value: 6.85e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260   672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKeTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SKAR cd12681
RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; ...
672-745 1.53e-16

RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410082 [Multi-domain]  Cd Length: 69  Bit Score: 74.62  E-value: 1.53e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVhydrsgRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12681    2 RLTVSNLHPSVTEDDIVELFSVIGALKRARL------VRPGVAEVVYVRREDAITAIKKYNNRELDGQPMKCKL 69
cyt_tran_rel TIGR00125
cytidyltransferase-like domain; Protein families that contain at least one copy of this domain ...
486-555 1.95e-14

cytidyltransferase-like domain; Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. Many of these proteins are known to use CTP or ATP and release pyrophosphate.


Pssm-ID: 272920 [Multi-domain]  Cd Length: 66  Bit Score: 68.49  E-value: 1.95e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  486 VIYVAGAFDLFHIGHVDFLEEVYKLAkrPYIIAGLHFDQEVNRYKGKnyPIMNLHERTLSVLACRYVSEV 555
Cdd:TIGR00125   1 RVIFVGTFDPFHLGHLDLLERAKELF--DELIVGVGSDQFVNPLKGE--PVFSLEERLEMLKALKYVDEV 66
SIR2H cd01411
SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species ...
48-183 3.31e-14

SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.


Pssm-ID: 238702  Cd Length: 225  Bit Score: 72.78  E-value: 3.31e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  48 AEPTLTHMSITRLHEQKLVQhVVSQNCDGLHLRSGlPRTAIsELHGNMYIEVCTSC---VPNREYVRVFdvtertalhrh 124
Cdd:cd01411   72 AKPNIIHQKMAELEKMGLKA-VITQNIDGLHQKAG-SKNVV-EFHGSLYRIYCTVCgktVDWEEYLKSP----------- 137
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 125 qtgrTCHKCGTQLRDTIVHFGErgtlgqPLNWEA---ATEAASKADTILCLGSSLKVlkkYP 183
Cdd:cd01411  138 ----YHAKCGGVIRPDIVLYEE------MLNESVieeAIQAIEKADLLVIVGTSFVV---YP 186
TagD COG0615
Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family [Cell wall/membrane ...
485-558 3.34e-14

Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family [Cell wall/membrane/envelope biogenesis]; Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis


Pssm-ID: 440380 [Multi-domain]  Cd Length: 131  Bit Score: 70.13  E-value: 3.34e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 485 TVIYVAGAFDLFHIGHVDFLEEVYKLAKrpYIIAGLHFDqEVNRYKGKNyPIMNLHERTLSVLACRYVSEVVIG 558
Cdd:COG0615    1 KRVITYGTFDLLHPGHINLLKRAKALGD--ELIVGVATD-EFVASKGRK-PIIPEEQRKEIVEALKYVDEVILG 70
PLN02406 PLN02406
ethanolamine-phosphate cytidylyltransferase
487-621 3.54e-14

ethanolamine-phosphate cytidylyltransferase


Pssm-ID: 215227 [Multi-domain]  Cd Length: 418  Bit Score: 75.49  E-value: 3.54e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 487 IYVAGAFDLFHIGHVDFLEEVYKLAKRpyIIAGLHFDQEVNRYKGKnyPIMNLHERTLSVLACRYVSEVVIGAPYSVTAE 566
Cdd:PLN02406  56 VYMDGCFDMMHYGHANALRQARALGDE--LVVGVVSDEEIIANKGP--PVTPMHERMIMVSGVKWVDEVIPDAPYAITEE 131
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 567 ----LLGHFKVDLVCHGKTE-IVPdrDGSDPYQEPKRRGIFRQIDSGSNLTTDLIVQRII 621
Cdd:PLN02406 132 fmnkLFNEYNIDYIIHGDDPcLLP--DGTDAYALAKKAGRYKQIKRTEGVSSTDIVGRML 189
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
672-740 4.29e-14

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 67.96  E-value: 4.29e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRP 740
Cdd:cd12414    1 RLIVRNLPFKCTEDDLKKLFSKFGKVLEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRP 69
SIRT1 cd01408
SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and ...
30-226 6.15e-14

SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.


Pssm-ID: 238699  Cd Length: 235  Bit Score: 72.28  E-value: 6.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  30 QPFYLFsllscsAADL--SEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRTAISELHGNMYIEVCTSC---V 104
Cdd:cd01408   53 RPFYAL------AKELypGQFKPSVAHYFIKLLEDKGLLLRNYTQNIDTLERVAGVPDDRIIEAHGSFATAHCIKCkhkY 126
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 105 PNREYvrvfdvteRTALHRHQTGRtCHKCGTQLRDTIVHFGErgTLGQPLNwEAATEAASKADTILCLGSSLKVlkkYPR 184
Cdd:cd01408  127 PGDWM--------REDIFNQEVPK-CPRCGGLVKPDIVFFGE--SLPSRFF-SHMEEDKEEADLLIVIGTSLKV---APF 191
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 537141260 185 LWCMTKPPSRRPKLYI-----VNLQWTPKDdwaaLKLHGKCDD-VMQL 226
Cdd:cd01408  192 ASLPSRVPSEVPRVLInrepvGHLGKRPFD----VALLGDCDDgVREL 235
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
672-743 1.00e-13

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 66.81  E-value: 1.00e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd21608    1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVITDReTGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVV 73
PRK05333 PRK05333
NAD-dependent protein deacetylase;
48-233 7.83e-13

NAD-dependent protein deacetylase;


Pssm-ID: 235415  Cd Length: 285  Bit Score: 69.71  E-value: 7.83e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  48 AEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGlpRTAISELHGNMYIEVCTSC--VPNREYVRVFDVTERTALHRHQ 125
Cdd:PRK05333  81 AQPNAAHHALARLGAAGRIERLVTQNVDGLHQRAG--SRDVIELHGRLDGVRCMGCgaRHPRAEIQHVLEAANPEWLALE 158
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 126 TGRT-------------------CHKCGTQLRDTIVHFGE-----RGtlgqplnwEAATEAASKADTILCLGSSLKVLKK 181
Cdd:PRK05333 159 AAPApdgdadlewaafdhfrvpaCPACGGILKPDVVFFGEnvpreRV--------AAARAALDAADAVLVVGSSLMVYSG 230
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 537141260 182 YpRlWCMTKPPSRRPkLYIVNLQWTPKDDWAALKLHGKCDDVMQLLMDELGL 233
Cdd:PRK05333 231 Y-R-FCVWAAQQGKP-IAALNLGRTRADPLLTLKVEASCAQALAALVARLGL 279
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
673-741 1.07e-12

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 63.79  E-value: 1.07e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260  673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 741
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
RRM_YRA1_MLO3 cd12267
RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA ...
672-746 2.42e-12

RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins; This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p.


Pssm-ID: 409711 [Multi-domain]  Cd Length: 78  Bit Score: 62.82  E-value: 2.42e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 672 KLLVSNLDFGVSDADIQELFA-EFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG-RPMNIQLV 746
Cdd:cd12267    2 KVIVSNLPKDVTEAQIREYFVsQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDKFNGRLDDGnRKMKVEVV 78
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
672-745 3.25e-12

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 62.61  E-value: 3.25e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12413    1 TLFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKgKDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVEL 75
RfaE_N cd02172
N-terminal domain of RfaE; RfaE is a protein involved in the biosynthesis of ...
284-368 3.41e-12

N-terminal domain of RfaE; RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in Escherichia coli, and separate proteins in other organisms. Domain I is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (this family) adds ADP to yield ADP-D-glycero-D-manno-heptose .


Pssm-ID: 173923 [Multi-domain]  Cd Length: 144  Bit Score: 64.74  E-value: 3.41e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVQAIKWVDEVVpAAPYVTTLETLDKYNCDFC 363
Cdd:cd02172   13 FDLLHPGHVRHLQAARSLGDILVVSLTSDRYVNKGPGRPIFPEDLRAEVLAALGFVDYVV-LFDNPTALEIIDALQPNIY 91

                 ....*
gi 537141260 364 VHGND 368
Cdd:cd02172   92 VKGGD 96
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
673-749 9.76e-12

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 61.10  E-value: 9.76e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQ 749
Cdd:cd12284    1 LYVGSLHFNITEDMLRGIFEPFGKIEFVQLQKDPeTGRSKGYGFIQFRDAEDAKKALEQLNGFELAGRPMKVGHVTER 78
RRM2_MYEF2 cd12660
RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This ...
673-745 1.72e-11

RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410061 [Multi-domain]  Cd Length: 76  Bit Score: 60.42  E-value: 1.72e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12660    3 IFVANLDFKVGWKKLKEVFSMAGTVKRADIKEDKDGKSRGMGTVTFEQAIEAVQAISMFNGQFLFDRPMHVKM 75
CTP_transf_like pfam01467
Cytidylyltransferase-like; This family includes: Cholinephosphate cytidylyltransferase; ...
488-579 3.61e-11

Cytidylyltransferase-like; This family includes: Cholinephosphate cytidylyltransferase; glycerol-3-phosphate cytidylyltransferase. It also includes putative adenylyltransferases, and FAD synthases.


Pssm-ID: 396172 [Multi-domain]  Cd Length: 134  Bit Score: 61.57  E-value: 3.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  488 YVAGAFDLFHIGHVDFLEEVYKLAKRPyIIAGLHFDQEVNRYKgknYPIMNLHERTLSVLACRYVSEVVIGAPYSVTAEL 567
Cdd:pfam01467   1 LFGGTFDPIHLGHLRLLEQAKELFDED-LIVGVPSDEPPHKLK---RPLFSAEERLEMLELAKWVDEVIVVAPWELTREL 76
                          90
                  ....*....|..
gi 537141260  568 LGHFKVDLVCHG 579
Cdd:pfam01467  77 LKELNPDVLVIG 88
RfaE_N cd02172
N-terminal domain of RfaE; RfaE is a protein involved in the biosynthesis of ...
481-588 1.78e-10

N-terminal domain of RfaE; RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in Escherichia coli, and separate proteins in other organisms. Domain I is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (this family) adds ADP to yield ADP-D-glycero-D-manno-heptose .


Pssm-ID: 173923 [Multi-domain]  Cd Length: 144  Bit Score: 59.74  E-value: 1.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 481 QPGETVIYVAGAFDLFHIGHVDFLEEVYKLAKRpyIIAGLHFDQEVNryKGKNYPIMNLHERTLSVLACRYVSEVVIgAP 560
Cdd:cd02172    1 QRGKTVVLCHGVFDLLHPGHVRHLQAARSLGDI--LVVSLTSDRYVN--KGPGRPIFPEDLRAEVLAALGFVDYVVL-FD 75
                         90       100
                 ....*....|....*....|....*...
gi 537141260 561 YSVTAELLGHFKVDLVCHGKTEIVPDRD 588
Cdd:cd02172   76 NPTALEIIDALQPNIYVKGGDYENPEND 103
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
672-745 2.42e-10

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 57.44  E-value: 2.42e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12447    1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARVITDRgSGRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINVDF 75
RRM2_HRB1_GBP2 cd21606
RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, ...
673-739 2.95e-10

RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410185 [Multi-domain]  Cd Length: 75  Bit Score: 56.99  E-value: 2.95e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd21606    4 VFIANLPYSINWQALKDMFKECGDVLRADVELDYNGRSRGFGTVIYATEEEMHRAIDTFNGYELEGR 70
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
673-745 4.88e-10

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 56.45  E-value: 4.88e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYN------GVPLDGRPMNIQL 745
Cdd:cd12415    3 VFIRNLSFDTTEEDLKEFFSKFGEVKYARIVLDKdTGHSKGTAFVQFKTKESADKCIEAANdesedgGLVLDGRKLIVSL 82
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
672-743 5.26e-10

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 56.47  E-value: 5.26e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12412    4 RIFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRAGVSKGYGFVTFETQEDAEKIQKWGANLVFKGKKLNV 75
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
672-745 6.07e-10

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 56.18  E-value: 6.07e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12392    4 KLFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRNGKPKGLAYVEYENEADASQAVLKTDGTEIKDHTISVAI 77
PTZ00408 PTZ00408
NAD-dependent deacetylase; Provisional
42-183 6.17e-10

NAD-dependent deacetylase; Provisional


Pssm-ID: 240405  Cd Length: 242  Bit Score: 60.61  E-value: 6.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  42 AADLSEAEPTLTHMSITRLHEQ----KLVqhVVSQNCDGLHLRSGlpRTAISELHGNMyIEVCtsCVPNReyvRVFDVTE 117
Cdd:PTZ00408  62 ALLSSSVKPNKAHFALAKLEREyrggKVV--VVTQNVDNLHERAG--STHVLHMHGEL-LKVR--CTATG---HVFDWTE 131
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 118 RTAlhrHQTGRtCHKCG--TQLRDTIVHFGErgtlgQPLNWEAATEAASKADTILCLGSSLKVlkkYP 183
Cdd:PTZ00408 132 DVV---HGSSR-CKCCGcvGTLRPHIVWFGE-----MPLYMDEIESVMSKTDLFVAVGTSGNV---YP 187
RRM2_hnRNPM_like cd12386
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
675-745 1.16e-09

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409820 [Multi-domain]  Cd Length: 74  Bit Score: 55.06  E-value: 1.16e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12386    3 VANLDYKVGWKKLKEVFKLAGKVVRADIREDKDGKSRGMGVVQFEHPIEAVQAISMFNGQMLFDRPMRVKM 73
RRM2_hnRNPM cd12659
RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
673-745 1.28e-09

RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410060 [Multi-domain]  Cd Length: 76  Bit Score: 55.44  E-value: 1.28e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12659    3 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFNGQLLFDRPMHVKM 75
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
675-740 1.45e-09

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 55.31  E-value: 1.45e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRP 740
Cdd:cd12363    6 VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQqTGRSRGFGFVYFESVEDAKEAKERLNGQEIDGRR 72
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
672-743 2.29e-09

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 54.27  E-value: 2.29e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLkkAAVHY---DRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12316    1 RLFVRNLPFTATEDELRELFEAFGKI--SEVHIpldKQTKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLHV 73
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
673-755 2.93e-09

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 60.59  E-value: 2.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLvtSQIDT 752
Cdd:TIGR01628 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL--AQRKE 365

                  ...
gi 537141260  753 QRR 755
Cdd:TIGR01628 366 QRR 368
rfaE_dom_II TIGR02199
rfaE bifunctional protein, domain II; RfaE is a protein involved in the biosynthesis of ...
483-579 4.05e-09

rfaE bifunctional protein, domain II; RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in E. coli, and separate proteins in some other genome. Domain I (TIGR02198) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (this family) adds ADP to yield ADP-D-glycero-D-manno-heptose. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]


Pssm-ID: 131254 [Multi-domain]  Cd Length: 144  Bit Score: 55.77  E-value: 4.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  483 GETVIYVAGAFDLFHIGHVDFLEEVYKLAKRpyIIAGLHFDQEVNRYKGKNYPIMNLHERT--LSVLACryVSEVVI--- 557
Cdd:TIGR02199  10 GKKIVFTNGCFDILHAGHVSYLQQARALGDR--LVVGVNSDASVKRLKGETRPINPEEDRAevLAALSS--VDYVVIfde 85
                          90       100
                  ....*....|....*....|..
gi 537141260  558 GAPysvtAELLGHFKVDLVCHG 579
Cdd:TIGR02199  86 DTP----EELIGELKPDILVKG 103
RRM_TRA2A cd12642
RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and ...
675-743 4.32e-09

RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins; This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 410047 [Multi-domain]  Cd Length: 84  Bit Score: 53.84  E-value: 4.32e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12642    9 VFGLSLYTTERDLREVFSRYGPLAGVNVVYDqRTGRSRGFAFVYFERIDDSKEAMERANGMELDGRRIRV 78
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
672-745 6.83e-09

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 53.04  E-value: 6.83e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12381    3 NLYVKNLDDTIDDEKLREEFSPFGTITSAKVMTDEGGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVAL 76
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
672-739 8.05e-09

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 53.25  E-value: 8.05e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12449    2 KLFVGGLSFDTNEQSLEEVFSKYGQISEVVVVKDReTQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGR 70
PRK11316 PRK11316
bifunctional D-glycero-beta-D-manno-heptose-7-phosphate kinase/D-glycero-beta-D-manno-heptose ...
284-344 1.29e-08

bifunctional D-glycero-beta-D-manno-heptose-7-phosphate kinase/D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase HldE;


Pssm-ID: 183085 [Multi-domain]  Cd Length: 473  Bit Score: 58.30  E-value: 1.29e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 284 YDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGP--PVFTQEERYKMVQAIKWVDEVVP 344
Cdd:PRK11316 349 FDILHAGHVSYLANARKLGDRLIVAVNSDASVKRLKGEgrPVNPLEQRMAVLAALEAVDWVVP 411
PTZ00409 PTZ00409
Sir2 (Silent Information Regulator) protein; Provisional
47-178 1.30e-08

Sir2 (Silent Information Regulator) protein; Provisional


Pssm-ID: 173599 [Multi-domain]  Cd Length: 271  Bit Score: 56.85  E-value: 1.30e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  47 EAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGlpRTAISELHGNMYIEVCTSCvpnREYVRVFDVT-ERTALHRHQ 125
Cdd:PTZ00409  89 EIELNPGHVALSTLESLGYLKFVVTQNVDGLHEESG--NTKVIPLHGSVFEARCCTC---RKTIQLNKIMlQKTSHFMHQ 163
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 537141260 126 TGRTChKCGTQLRDTIVHFGErgtlGQPLNW-EAATEAASKADTILCLGSSLKV 178
Cdd:PTZ00409 164 LPPEC-PCGGIFKPNVILFGE----VIPKSLlKQAEKEIDKCDLLLVVGTSSSV 212
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
675-741 1.44e-08

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 52.18  E-value: 1.44e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 741
Cdd:cd12380    6 VKNFGEDVDDDELKELFEKYGKITSAKVMKDDSGKSKGFGFVNFENHEAAQKAVEELNGKELNGKKL 72
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
675-741 1.93e-08

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 51.84  E-value: 1.93e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQyNGVPLDGRPM 741
Cdd:cd12391    4 VSNLDYSVPEDKIREIFSGCGEITDVRLVKNYKGKSKGYCYVEFKDEESAQKALKL-DRQPVEGRPM 69
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
673-745 2.66e-08

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 51.63  E-value: 2.66e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMkQYNGVPLDGRPMNIQL 745
Cdd:cd12450    2 LFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDRdDGRSKGFGHVEFASAESAQKAL-EKSGQDLGGREIRLDL 74
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
672-749 2.79e-08

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 51.71  E-value: 2.79e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 672 KLLVSNLDFGVSDAD-IQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQ 749
Cdd:cd12675    2 KLIIRNLPWSIKKPVhLKKLFGRYGKVVEATIPRKKGGKLSGFAFVTMKGRKNAEEALESVNGLEIDGRPVAVDWAVSK 80
RRM_RBM7 cd12592
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily ...
673-744 3.62e-08

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7); This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus.


Pssm-ID: 410005 [Multi-domain]  Cd Length: 75  Bit Score: 50.98  E-value: 3.62e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12592    4 LFVGNLDTKVTEELLFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIKLYGRPLKIQ 75
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
672-745 4.92e-08

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 50.72  E-value: 4.92e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAV---HYDRSGRS-LGTADVHFERKADALKAMkQYNGVPLDGRPMNIQL 745
Cdd:cd12298    2 EIRVRNLDFELDEEALRGIFEKFGEIESINIpkkQKNRKGRHnNGFAFVTFEDADSAESAL-QLNGTLLDNRKISVSL 78
RRM1_I_PABPs cd12378
RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily ...
673-743 6.88e-08

RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409812 [Multi-domain]  Cd Length: 80  Bit Score: 50.32  E-value: 6.88e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12378    2 LYVGDLHPDVTEAMLYEKFSPAGPVLSIRVCRDAvTRRSLGYAYVNFQQPADAERALDTLNFDVIKGKPIRI 73
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
672-744 7.65e-08

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 49.92  E-value: 7.65e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAV--HYdrsgrslgtADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12343    1 KIFVGNLPDAATSEELRALFEKYGKVTECDIvkNY---------AFVHMEKEEDAEDAIKALNGYEFMGSRINVE 66
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
673-739 7.89e-08

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 50.70  E-value: 7.89e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12236    4 LFVARLSYDTTESKLRREFEKYGPIKRVRLVRDkKTGKSRGYAFIEFEHERDMKAAYKHADGKKIDGR 71
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
675-739 1.06e-07

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 49.59  E-value: 1.06e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12393    6 VSNLPFSLTNNDLHQIFSKYGKVVKVTILKDKETRkSKGVAFVLFLDRESAHNAVRAMNNKELFGR 71
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
673-738 1.11e-07

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 55.20  E-value: 1.11e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260  673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG 738
Cdd:TIGR01628 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGL 246
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
675-733 1.20e-07

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 49.43  E-value: 1.20e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNG 733
Cdd:cd12408    4 VTNLSEDATEEDLRELFRPFGPISRVYLAKDKeTGQSKGFAFVTFETREDAERAIEKLNG 63
RRM_RBM24_RBM38_like cd12384
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar ...
672-745 1.44e-07

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409818 [Multi-domain]  Cd Length: 76  Bit Score: 49.29  E-value: 1.44e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVpLDGRPMNIQL 745
Cdd:cd12384    2 KIFVGGLPYHTTDDSLREYFEQFGEIEEAVVITDRqTGKSRGYGFVTMADREAAERACKDPNPI-IDGRKANVNL 75
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
673-747 1.51e-07

RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410031 [Multi-domain]  Cd Length: 80  Bit Score: 49.42  E-value: 1.51e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 747
Cdd:cd12619    4 IFVGDLSPEVTDAALFNAFSDFPSCSDARVMWDqKTGRSRGYGFVSFRSQQDAQNAINSMNGKWLGSRPIRCNWAT 79
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
673-731 2.08e-07

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 49.73  E-value: 2.08e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 731
Cdd:cd12676    4 LFVRNLPFDATEDELYSHFSQFGPLKYARVVKDPaTGRSKGTAFVKFKNKEDADNCLSAA 63
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
672-747 2.26e-07

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 48.93  E-value: 2.26e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGrSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 747
Cdd:cd12407    2 RLHVSNIPFRFRDPDLRQMFGQFGTILDVEIIFNERG-SKGFGFVTFANSADADRAREKLNGTVVEGRKIEVNNAT 76
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
672-745 2.75e-07

RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins; This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409843 [Multi-domain]  Cd Length: 84  Bit Score: 48.81  E-value: 2.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTL----KKAAVHYDRSG--RSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12409    1 RVYISNLSYSTTEEELEELLKDYKPVsvliPSYTVRGFRSRkhRPLGIAYAEFSSVEEAEKVVKDLNGKVFKGRKLFVKL 80
RRM5_MRD1 cd12570
RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 ...
672-744 2.78e-07

RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 241014 [Multi-domain]  Cd Length: 76  Bit Score: 48.66  E-value: 2.78e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAV--HYDRSGRslGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12570    2 KILVKNLPFEATKKDVRTLFSSYGQLKSVRVpkKFDQSAR--GFAFVEFSTAKEALNAMNALKDTHLLGRRLVLQ 74
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
675-739 2.86e-07

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 48.44  E-value: 2.86e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRsGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd21605    6 VGNLPFDCTWEDLKDHFSQVGEVIRADIVTSR-GRHRGMGTVEFTNKEDVDRAISKFDHTMFMGR 69
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
672-753 2.94e-07

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 53.77  E-value: 2.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQI 750
Cdd:TIGR01622 216 RLYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDpETGRSKGYGFIQFRDAEQAKEALEKMNGFELAGRPIKVGLGNDFT 295

                  ...
gi 537141260  751 DTQ 753
Cdd:TIGR01622 296 PES 298
RRM_TRA2B cd12641
RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and ...
673-749 4.18e-07

RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins; This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes.


Pssm-ID: 410046 [Multi-domain]  Cd Length: 87  Bit Score: 48.46  E-value: 4.18e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQ 749
Cdd:cd12641   10 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQqSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 87
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
673-744 4.37e-07

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 47.93  E-value: 4.37e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12365    1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVDLPIDRePNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 73
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
673-755 4.92e-07

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 53.27  E-value: 4.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPmnIQLVTSQID 751
Cdd:TIGR01628   3 LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSvTRRSLGYGYVNFQNPADAERALETMNFKRLGGKP--IRIMWSQRD 80

                  ....
gi 537141260  752 TQRR 755
Cdd:TIGR01628  81 PSLR 84
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
672-743 7.15e-07

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 47.41  E-value: 7.15e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12566    4 RLFLRNLPYSTKEDDLQKLFSKFGEVSEVHVPIDkKTKKSKGFAYVLFLDPEDAVQAYNELDGKVFQGRLIHI 76
PRK11316 PRK11316
bifunctional D-glycero-beta-D-manno-heptose-7-phosphate kinase/D-glycero-beta-D-manno-heptose ...
483-548 1.23e-06

bifunctional D-glycero-beta-D-manno-heptose-7-phosphate kinase/D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase HldE;


Pssm-ID: 183085 [Multi-domain]  Cd Length: 473  Bit Score: 51.75  E-value: 1.23e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260 483 GETVIYVAGAFDLFHIGHVDFLEEVYKLAKRpyIIAGLHFDQEVNRYKGKNYPIMNLhERTLSVLA 548
Cdd:PRK11316 339 GEKIVMTNGCFDILHAGHVSYLANARKLGDR--LIVAVNSDASVKRLKGEGRPVNPL-EQRMAVLA 401
G3P_Cytidylyltransferase cd02171
glycerol-3-phosphate cytidylyltransferase; Glycerol-3-phosphate cytidylyltransferase, ...
484-580 1.23e-06

glycerol-3-phosphate cytidylyltransferase; Glycerol-3-phosphate cytidylyltransferase,(CDP-glycerol pyrophosphorylase). Glycerol-3-phosphate cytidyltransferase acts in pathways of teichoic acid biosynthesis. Teichoic acids are substituted polymers, linked by phosphodiester bonds, of glycerol, ribitol, etc. An example is poly(glycerol phosphate), the major teichoic acid of the Bacillus subtilis cell wall. Most, but not all, species encoding proteins in this family are Gram-positive bacteria. A closely related protein assigned a different function experimentally is a human ethanolamine-phosphate cytidylyltransferase.


Pssm-ID: 173922 [Multi-domain]  Cd Length: 129  Bit Score: 48.25  E-value: 1.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 484 ETVIYVAGAFDLFHIGHVDFLEEVYKLAKrpYIIAGLHFDqEVNRYKGKNyPIMNLHERTLSVLACRYVSEVVIGAPYSV 563
Cdd:cd02171    1 MKVVITYGTFDLLHIGHLNLLERAKALGD--KLIVAVSTD-EFNAGKGKK-AVIPYEQRAEILESIRYVDLVIPETNWEQ 76
                         90
                 ....*....|....*..
gi 537141260 564 TAELLGHFKVDLVCHGK 580
Cdd:cd02171   77 KIEDIKKYNVDVFVMGD 93
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
673-745 1.35e-06

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 46.47  E-value: 1.35e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDrsgrslgTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12251    4 LYVRNLMLSTTEEKLRELFSEYGKVERVKKIKD-------YAFVHFEERDDAVKAMEEMNGKELEGSEIEVSL 69
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
673-743 1.41e-06

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 46.75  E-value: 1.41e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLK---KAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd21619    4 IYVGNIDMTINEDALEKIFSRYGQVEsvrRPPIHTDKADRTTGFGFIKYTDAESAERAMQQADGILLGRRRLVV 77
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
672-743 1.62e-06

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 46.64  E-value: 1.62e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd21609    1 RLYVGNIPRNVTSEELAKIFEEAGTVEIAEVMYDRyTGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKV 73
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
673-745 1.87e-06

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 46.45  E-value: 1.87e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKA--AVHYDRSGR--SLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12318    3 LFVKNLNFKTTEEALKKHFEKCGPIRSVtiAKKKDPKGPllSMGYGFVEFKSPEAAQKALKQLQGTVLDGHALELKI 79
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
673-739 1.87e-06

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 46.30  E-value: 1.87e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12674    3 LFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDpETKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGH 70
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
672-739 1.96e-06

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 46.23  E-value: 1.96e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12353    1 HIFVGDLSPEIETEDLKEAFAPFGEISDARVVKDtQTGKSKGYGFVSFVKKEDAENAIQGMNGQWLGGR 69
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
672-739 2.04e-06

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 46.07  E-value: 2.04e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12320    2 KLIVKNVPFEATRKEIRELFSPFGQLKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHLYGR 69
RRM2_p54nrb_like cd12333
RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
673-732 2.09e-06

RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409770 [Multi-domain]  Cd Length: 80  Bit Score: 46.15  E-value: 2.09e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 732
Cdd:cd12333    2 LRVKNLSPYVSNELLEQAFSQFGDVERAVVIVDDRGRSTGEGIVEFSRKPGAQAALKRCS 61
RRM_BOULE cd12673
RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of ...
672-743 2.14e-06

RNA recognition motif (RRM) found in protein BOULE; This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410074 [Multi-domain]  Cd Length: 81  Bit Score: 46.41  E-value: 2.14e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12673    4 RIFVGGIDFKTNENDLRKFFAQYGSVKEVKIVNDRAGVSKGYGFITFETQEDAQKILQEAEKLNYKDKKLNI 75
RRM1_PES4_MIP6 cd21601
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
673-743 2.17e-06

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410180 [Multi-domain]  Cd Length: 80  Bit Score: 46.19  E-value: 2.17e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd21601    3 LFIGDLDKDVTEEMLRDIFSKYKSLVSVKICLDsETKKSLGYGYLNFSDKEDAEKAIEEFNYTPIFGKEVRI 74
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
673-740 2.62e-06

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 46.07  E-value: 2.62e-06
                         10        20        30        40        50        60
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gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRP 740
Cdd:cd12324    9 IFVTGVHEEAQEEDIHDKFAEFGEIKNLHLNLDRrTGFVKGYALVEYETKKEAQAAIEGLNGKELLGQT 77
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
673-744 2.73e-06

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 45.72  E-value: 2.73e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12311    1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRyTRESRGFAFVRFYDKRDAEDAIDAMDGAELDGRELRVQ 73
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
673-745 3.08e-06

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 45.40  E-value: 3.08e-06
                         10        20        30        40        50        60        70
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gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDrsgrslgTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12494    4 LFVRNLATTVTEEILEKTFSQFGKLERVKKLKD-------YAFVHFEDRDAAVKAMDEMNGKEVEGEEIEIVL 69
RRM4_RBM12_like cd12514
RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
673-739 4.07e-06

RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.


Pssm-ID: 409936 [Multi-domain]  Cd Length: 73  Bit Score: 45.10  E-value: 4.07e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAaVH--YDRSGRSLGTADVHFERKADALKAMKqYNGVPLDGR 739
Cdd:cd12514    2 IRITNLPYDATPVDIQRFFEDHGVRPED-VHllRNKKGRGNGEALVTFKSEGDAREVLK-LNGKKLGKR 68
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
673-743 4.22e-06

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 45.20  E-value: 4.22e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12399    1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDReTKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRV 72
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
672-733 5.73e-06

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 44.92  E-value: 5.73e-06
                         10        20        30        40        50        60
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gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQYNG 733
Cdd:cd12361    1 KLFVGMIPKTASEEDVRPLFEQFGNIEEVQILRDKQtGQSKGCAFVTFSTREEALRAIEALHN 63
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
673-744 6.08e-06

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 44.60  E-value: 6.08e-06
                         10        20        30        40        50        60        70
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gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12336    4 LFVGNLDPRVTEEILYELFLQAGPLEGVKIPKDPNGKPKNFAFVTFKHEVSVPYAIQLLNGIRLFGREIRIK 75
RRM2_SECp43_like cd12345
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
673-747 6.80e-06

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409781 [Multi-domain]  Cd Length: 80  Bit Score: 44.57  E-value: 6.80e-06
                         10        20        30        40        50        60        70
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gi 537141260 673 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 747
Cdd:cd12345    4 LFVGDLAPDVTDYQLYETFsARYPSVRGAKVVMDPvTGRSKGYGFVRFGDESEQDRALTEMQGVYLGSRPIRVSPAT 80
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
673-740 6.82e-06

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 44.74  E-value: 6.82e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKaaVH---YDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRP 740
Cdd:cd12397    1 LFVGNLSFETTEEDLRKHFAPAGKIRK--VRmatFEDSGKCKGFAFVDFKEIESATNAVKGPINHSLNGRD 69
RRM2_PSF cd12590
RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB) ...
673-730 7.98e-06

RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF); This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules.


Pssm-ID: 410003 [Multi-domain]  Cd Length: 80  Bit Score: 44.61  E-value: 7.98e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 730
Cdd:cd12590    2 LSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFER 59
RRM2_Bruno_like cd12636
RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar ...
672-732 8.15e-06

RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar proteins; This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region.


Pssm-ID: 410044 [Multi-domain]  Cd Length: 81  Bit Score: 44.48  E-value: 8.15e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 732
Cdd:cd12636    3 KLFVGMLSKKCNESDVRIMFSPYGSIEECTVLRDQNGKSRGCAFVTFTSRQCAVNAIKAMH 63
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
675-740 9.29e-06

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 44.43  E-value: 9.29e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRP 740
Cdd:cd12398    5 VGNIPYDATEEQLKEIFSEVGPVVSFRLVTDReTGKPKGYGFCEFRDAETALSAVRNLNGYELNGRP 71
RRM2_RAVER cd12389
RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
673-739 1.02e-05

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409823 [Multi-domain]  Cd Length: 77  Bit Score: 44.23  E-value: 1.02e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKA-AVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12389    2 LCVTNLPLSFTEEQFEELVRPYGNVERCfLVYSEVTGESKGYGFVEYTSKESAIRAKNQLHGRQIGGR 69
RRM3_hnRNPH_CRSF1_like cd12506
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H ...
678-730 1.10e-05

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins; This subfamily corresponds to the RRM3 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. For instance, members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity.


Pssm-ID: 409929 [Multi-domain]  Cd Length: 75  Bit Score: 43.90  E-value: 1.10e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 678 LDFGVSDADIQELFAefgTLKKAAVH--YDRSGRSLGTADVHFERKADALKAMKQ 730
Cdd:cd12506    8 LPYRATENDIFEFFS---PLNPVNVRirYNKDGRATGEADVEFATHEDAVAAMSK 59
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
672-773 1.19e-05

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 45.80  E-value: 1.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTsqi 750
Cdd:PLN03134  36 KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDReTGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN--- 112
                         90       100
                 ....*....|....*....|...
gi 537141260 751 dtQRRPAQSINRGGMTRNRGSGT 773
Cdd:PLN03134 113 --DRPSAPRAYGGGGGYSGGGGG 133
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
675-739 1.43e-05

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 48.65  E-value: 1.43e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260  675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:TIGR01628  93 VKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDK 157
RRM3_ACF cd12498
RNA recognition motif 3 (RRM3) found in vertebrate APOBEC-1 complementation factor (ACF); This ...
673-745 1.61e-05

RNA recognition motif 3 (RRM3) found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 409921 [Multi-domain]  Cd Length: 83  Bit Score: 43.76  E-value: 1.61e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQElfaEFGTLKKAAVhyDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12498   11 LYVRNLMLSTTEETIEK---EFSNIKPGAV--ERVKKIRDYAFVHFYNREDAVNAMNALNGKVIDGSPIEVTL 78
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
672-747 1.73e-05

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 43.55  E-value: 1.73e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 747
Cdd:cd12382    3 KLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDReTNKSRGFAFVTFESPADAKDAARDMNGKELDGKAIKVEQAT 79
PTZ00410 PTZ00410
NAD-dependent SIR2; Provisional
50-191 1.78e-05

NAD-dependent SIR2; Provisional


Pssm-ID: 185600  Cd Length: 349  Bit Score: 47.94  E-value: 1.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  50 PTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLPRTAISELHGNMYIEVCTSC-VPnreyvrvFDVTERTALHRHQTGR 128
Cdd:PTZ00410 100 PTAVHHFIRLLADEGRLLRCCTQNIDGLERAAGVPPSLLVEAHGSFSAASCIEChTP-------YDIEQAYLEARSGKVP 172
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 129 TCHKCGTQLRDTIVHFGErgtlGQPLNWEAATEAASKADTILCLGSSLKVlKKYPRLWCMTKP 191
Cdd:PTZ00410 173 HCSTCGGIVKPDVVFFGE----NLPDAFFNVHHDIPEAELLLIIGTSLQV-HPFALLACVVPK 230
RRM2_CoAA cd12609
RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator ...
672-745 1.89e-05

RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410021 [Multi-domain]  Cd Length: 68  Bit Score: 43.30  E-value: 1.89e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDrsgrslgTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12609    2 KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKD-------YAFVHMEREEEALAAIEALNGKEVKGRRINVEL 68
RRM_RBM11 cd12593
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily ...
673-744 2.23e-05

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11); This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 410006 [Multi-domain]  Cd Length: 75  Bit Score: 43.25  E-value: 2.23e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12593    4 VFVGNLHSNVNEEILYELFLQAGPLTKVTIAKDKEGKPKSFGFVCFKHAESVPYAIALLNGIRLYGRPIKLQ 75
RRM_NCBP2 cd12240
RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar ...
673-745 2.83e-05

RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins; This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC.


Pssm-ID: 409686 [Multi-domain]  Cd Length: 78  Bit Score: 42.94  E-value: 2.83e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRS-LGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12240    1 LYVGNLSFYTTEEQIYELFSKCGDIKRIIMGLDKFKKTpCGFCFVEYYSREDAENAVKYLNGTKLDDRIIRVDW 74
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
672-727 4.19e-05

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus.


Pssm-ID: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 42.51  E-value: 4.19e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKA 727
Cdd:cd12579    1 KLFVGGLKGDVGEGDLVEHFSQFGTVEKVEVIADKdTGKKRGFGFVYFEDHDSADKA 57
RRM5_RBM12_like cd12515
RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; ...
675-745 4.35e-05

RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins; This subfamily corresponds to the RRM5 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear.


Pssm-ID: 409937 [Multi-domain]  Cd Length: 75  Bit Score: 42.21  E-value: 4.35e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRpmNIQL 745
Cdd:cd12515    5 MRNLPFKATIEDILDFFYGYRVIPDSVsIRYNDDGQPTGDARVAFPSPREARRAVRELNNRPLGGR--KVKL 74
RRM2_NCL cd12404
RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to ...
673-741 4.81e-05

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.


Pssm-ID: 409838 [Multi-domain]  Cd Length: 77  Bit Score: 42.42  E-value: 4.81e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKkaaVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 741
Cdd:cd12404    6 LFVKNLPYSTTQDELKEVFEDAVDIR---IPMGRDGRSKGIAYIEFKSEAEAEKALEEKQGTEVDGRSI 71
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
672-754 4.95e-05

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 42.30  E-value: 4.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGvpldgrpmniqlvtSQID 751
Cdd:cd12564    2 RLIVKNLPSSITEDRLRKLFSAFGTITDVQLKYTKDGKFRRFGFVGFKSEEEAQKALKHFNN--------------SFID 67

                 ...
gi 537141260 752 TQR 754
Cdd:cd12564   68 TSR 70
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
673-743 5.77e-05

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 41.90  E-value: 5.77e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDrsgrslgTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12495    4 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMDEMNGKDLEGENIEI 67
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
672-739 5.97e-05

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 41.90  E-value: 5.97e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG----RSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12355    1 RLWIGNLDPRLTEYHLLKLLSKYGKIKKFDFLFHKTGplkgQPRGYCFVTFETKEEAEKAIECLNGKLALGK 72
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
673-739 6.69e-05

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 41.84  E-value: 6.69e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRslGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12241    5 LYVRNLPYKISSEELYDLFGKYGAIRQIRIGNTKETR--GTAFVVYEDIFDAKNACDHLSGFNVCNR 69
RRM2_Hu_like cd12376
RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
673-745 8.11e-05

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 240822 [Multi-domain]  Cd Length: 79  Bit Score: 41.84  E-value: 8.11e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGV-PLDG-RPMNIQL 745
Cdd:cd12376    3 LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQlTGVSRGVGFIRFDKRIEAEEAIKGLNGQkPEGAsEPITVKF 78
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
673-736 8.49e-05

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 41.62  E-value: 8.49e-05
                         10        20        30        40        50        60
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gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPL 736
Cdd:cd12650    3 LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKvTGQSLGYGFVNYVDPSDAEKAINTLNGLRL 67
RRM2_I_PABPs cd12379
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This ...
675-739 1.01e-04

RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409813 [Multi-domain]  Cd Length: 77  Bit Score: 41.41  E-value: 1.01e-04
                         10        20        30        40        50        60
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gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12379    7 IKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAERAIEKVNGMLLNGK 71
RRM2_HuR cd12773
RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup ...
673-748 1.07e-04

RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410166 [Multi-domain]  Cd Length: 84  Bit Score: 41.44  E-value: 1.07e-04
                         10        20        30        40        50        60        70
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gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNG--VPLDGRPMNIQLVTS 748
Cdd:cd12773    3 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQaTGLSRGVAFIRFDKRSEAEEAITNFNGhkPPGSSEPITVKFAAN 81
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
672-744 1.10e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 41.44  E-value: 1.10e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 672 KLLVSNLDFGVSDADIQELFA---EFGTLKKAAVHYD--RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12239    3 RLYVKNLSKRVSEKDLKYIFGrfvDSSSEEKNMFDIRlmTEGRMKGQAFITFPSEELAEKALNLTNGYVLHGKPMVVQ 80
RRM3_GRSF1 cd12733
RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; ...
678-728 1.17e-04

RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins; This subgroup corresponds to the RRM3 of G-rich sequence factor 1 (GRSF-1), a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity.


Pssm-ID: 410132 [Multi-domain]  Cd Length: 75  Bit Score: 41.29  E-value: 1.17e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 537141260 678 LDFGVSDADIQELFAEFgTLKKAAVHYDRSGRSLGTADVHFERKADALKAM 728
Cdd:cd12733    8 LPFQANGQDIINFFAPL-KPVRITMEYGPDGKATGEADVHFASHEDAVAAM 57
RRM2_SXL cd12651
RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
673-745 1.18e-04

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 410054 [Multi-domain]  Cd Length: 81  Bit Score: 41.42  E-value: 1.18e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12651    5 LYVTNLPRTITEDELDTIFGAYGNIVQKNLLRDKLtGRPRGVAFVRYDKREEAQAAISALNGTIPEGGTQPLSV 78
RRM_CFIm68_CFIm59 cd12372
RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or ...
673-741 1.27e-04

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.


Pssm-ID: 409807 [Multi-domain]  Cd Length: 76  Bit Score: 41.15  E-value: 1.27e-04
                         10        20        30        40        50        60        70
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gi 537141260 673 LLVSNLDFGVSDADIQELFAEFG--TLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 741
Cdd:cd12372    1 LYVGNLQWWTTDEDLEGACASFGvvDVKEIKFFEHKaNGKSKGYAYVEFASPAAAAAVKEKLEKREFNGRPC 72
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
673-744 1.34e-04

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 41.11  E-value: 1.34e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKkaAVHYdrSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12524    4 LFVRNINSSVEDEELRALFEQFGEIR--TLYT--ACKHRGFIMVSYYDIRAAQSAKRALQGTELGGRKLDIH 71
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
672-748 1.37e-04

RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409817 [Multi-domain]  Cd Length: 83  Bit Score: 41.11  E-value: 1.37e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPmnIQLVTS 748
Cdd:cd12383    8 RIFCGDLGNEVTDEVLARAFSKYPSFQKAKVIRDkRTGKSKGYGFVSFKDPNDYLKALREMNGKYVGNRP--IKLRKS 83
RRM2_TIA1 cd12618
RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
673-741 1.45e-04

RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410030 [Multi-domain]  Cd Length: 78  Bit Score: 41.14  E-value: 1.45e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 741
Cdd:cd12618    5 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDmATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 74
RRM3_NCL cd12405
RNA recognition motif 3 (RRM3) found in vertebrate nucleolin; This subfamily corresponds to ...
673-745 1.60e-04

RNA recognition motif 3 (RRM3) found in vertebrate nucleolin; This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.


Pssm-ID: 409839 [Multi-domain]  Cd Length: 72  Bit Score: 40.63  E-value: 1.60e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAavhyDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12405    4 LVVNNLSYSATEESLQSVFEKATSIRIP----QNNGRPKGYAFVEFESVEDAKEALESCNNTEIEGRSIRLEF 72
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
673-745 1.64e-04

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 44.99  E-value: 1.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260  673 LLVSNLDFGVSDADIQELFAEFgtlKKAAVhyDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:TIGR01648 236 LYVRNLMTTTTEEIIEKSFSEF---KPGKV--ERVKKIRDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL 303
RRM2_PHIP1 cd12272
RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting ...
675-743 1.69e-04

RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409715 [Multi-domain]  Cd Length: 73  Bit Score: 40.46  E-value: 1.69e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKqYNGVPLDGRPMNI 743
Cdd:cd12272    4 IGNLAWDIDEDDLRELFAECCEITNVRLHTDKeTGEFKGYGHVEFADEESLDAALK-LAGTKLCGRPIRV 72
RRM_PPIL4 cd12235
RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and ...
673-739 1.69e-04

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 409681 [Multi-domain]  Cd Length: 83  Bit Score: 40.72  E-value: 1.69e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12235    6 LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKkTGDSLQYAFIEFETKESCEEAYFKMDNVLIDDR 73
RRM3_Crp79_Mug28 cd21622
RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
673-734 1.73e-04

RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the three RRM motif.


Pssm-ID: 410201 [Multi-domain]  Cd Length: 92  Bit Score: 41.20  E-value: 1.73e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 673 LLVSNLDFGV--SDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMKQYNGV 734
Cdd:cd21622    6 LFVKNLDDTVitNKEDLEQLFSPFGQIVSSYlATYPGTGISKGFGFVAFSKPEDAAKAKETLNGV 70
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
672-745 1.99e-04

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 40.46  E-value: 1.99e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRsgrslGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12340    1 RLFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDS-----NFAFVEFEELEDAIRAKDSVHGRVLNNEPLYVTY 69
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
673-743 2.00e-04

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 40.74  E-value: 2.00e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS----GRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12223    4 LYVGNLPPSVTEEVLLREFGRFGPLASVKIMWPRTeeerRRNRNCGFVAFMSRADAERAMRELNGKDVMGYELKL 78
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
675-744 2.07e-04

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 40.39  E-value: 2.07e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKkaAVH---YDRSGRSLGTADVHFERKADALKAMkQYNGVPLDGRPMNIQ 744
Cdd:cd12271    3 VGGIPYYSTEAEIRSYFSSCGEVR--SVDlmrFPDSGNFRGIAFITFKTEEAAKRAL-ALDGEMLGNRFLKVE 72
RRM_CNOT4 cd12438
RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) ...
688-748 2.29e-04

RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T


Pssm-ID: 409872 [Multi-domain]  Cd Length: 98  Bit Score: 40.97  E-value: 2.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 688 QELFAEFGTLKKAAV----HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS 748
Cdd:cd12438   26 PEYFGQYGKIKKIVInrstSYAGSQGPSASAYVTYSRKEDALRAIQAVDGFVLDGRTLKASFGTT 90
RRM2_PSP1 cd12589
RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1); This ...
673-730 2.66e-04

RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1); This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410002 [Multi-domain]  Cd Length: 80  Bit Score: 40.36  E-value: 2.66e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 730
Cdd:cd12589    2 LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPPARKALER 59
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
673-740 2.91e-04

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 40.08  E-value: 2.91e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRP 740
Cdd:cd12448    1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTDReTGQPKGFGYVDFSTIDSAEAAIDALGGEYIDGRP 69
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
673-733 2.95e-04

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 40.08  E-value: 2.95e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNG 733
Cdd:cd12375    2 LIVNYLPQSMTQEELRSLFGAIGPIESCKLVRDKiTGQSLGYGFVNYRDPNDARKAINTLNG 63
RRM1_RIM4_like cd12453
RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; ...
673-746 2.95e-04

RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins; This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1.


Pssm-ID: 409887 [Multi-domain]  Cd Length: 86  Bit Score: 40.47  E-value: 2.95e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQ----ELFAEFGTLKKAAVHYDRSGRSLgtADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 746
Cdd:cd12453    5 LFVASLSSARSDEELCaavtNHFSKWGELLNVKVLKDWSNRPY--AFVQYTNTEDAKNALVNGHNTLLDGRHLRVEKA 80
RRM4_RBM19_RRM3_MRD1 cd12317
RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
673-736 3.03e-04

RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 (RRM3) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409756 [Multi-domain]  Cd Length: 72  Bit Score: 39.93  E-value: 3.03e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSgrslgTADVHFERKADALKAM-----KQYNGVPL 736
Cdd:cd12317    3 ILVKNLPFGATEEELRELFEKFGTLGRLLLPPSRT-----IALVEFLEPQDARRAFkklayKRFKHVPL 66
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
673-740 3.70e-04

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 39.47  E-value: 3.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGtLKKAAVH--YDRSGRSLGTADVHFERKADALKAMKQYNGVpLDGRP 740
Cdd:cd12254    2 VRLRGLPFSATEEDIRDFFSGLD-IPPDGIHivYDDDGRPTGEAYVEFASEEDAQRALRRHKGK-MGGRY 69
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
673-744 3.70e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 39.52  E-value: 3.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMkQYNGVPLDGRPMNIQ 744
Cdd:cd12283    2 VFVMQLSLKARERDLYEFFSKAGKVRDVRLIMDRnSRRSKGVAYVEFYDVESVPLAL-ALTGQRLLGQPIMVQ 73
PRK00777 PRK00777
pantetheine-phosphate adenylyltransferase;
277-348 3.90e-04

pantetheine-phosphate adenylyltransferase;


Pssm-ID: 234834  Cd Length: 153  Bit Score: 41.74  E-value: 3.90e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 277 LGGgisRYDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVFTQEERYKMVqaIKWVDEVVPAAPY 348
Cdd:PRK00777   6 VGG---TFDPLHDGHRALLRKAFELGKRVTIGLTSDEFAKSYKKHKVRPYEVRLKNL--KKFLKAVEYDREY 72
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
673-748 4.04e-04

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 39.80  E-value: 4.04e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS 748
Cdd:cd12671    9 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDReTGKPKGYGFCEYQDQETALSAMRNLNGYELNGRALRVDNAAS 85
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
673-744 4.14e-04

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 39.44  E-value: 4.14e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260 673 LLVSNLDFGVSDADIQ----ELFAEFGTLKKAAVHYDRSGRslGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12246    2 LYINNLNEKIKKDELKrslyALFSQFGPVLDIVASKSLKMR--GQAFVVFKDVESATNALRALQGFPFYGKPMRIQ 75
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
672-747 4.16e-04

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 39.61  E-value: 4.16e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFErKADALKAMKQYNGVPLDGRPMNIQLVT 747
Cdd:cd12330    1 KIFVGGLAPDVTEEEFKEYFEQFGTVVDAVVMLDHdTGRSRGFGFVTFD-SESAVEKVLSKGFHELGGKKVEVKRAT 76
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
673-743 4.28e-04

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 39.61  E-value: 4.28e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLkkaavHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12346    4 VFVGGLDPNVTEEDLRVLFGPFGEI-----VYVKIPPGKGCGFVQFVNRASAEAAIQKLQGTPIGGSRIRL 69
RRM2_p54nrb cd12591
RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein ...
673-728 5.12e-04

RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb); This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410004 [Multi-domain]  Cd Length: 80  Bit Score: 39.51  E-value: 5.12e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAM 728
Cdd:cd12591    2 LTVKNLPQFVSNELLEEAFSVFGQVERAVVIVDDRGRPTGKGIVEFSGKPAARKAL 57
RRM_DAZL cd12672
RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; ...
673-730 7.37e-04

RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins; This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 410073 [Multi-domain]  Cd Length: 82  Bit Score: 39.00  E-value: 7.37e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 730
Cdd:cd12672    8 VFVGGIDIRMDENEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYDDVDIQKIVES 65
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
687-737 8.04e-04

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.


Pssm-ID: 409720 [Multi-domain]  Cd Length: 84  Bit Score: 39.10  E-value: 8.04e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 537141260 687 IQELFAEFGTLKKAAVHY--DRSGRSLGTADVHFERKADALKAMKQYNGVPLD 737
Cdd:cd12278   24 LTKIFSKFGSGKIVGIYMpvDETGKTKGFAFVEYATPEEAKKAVKALNGYKLD 76
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
673-745 8.26e-04

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 38.71  E-value: 8.26e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADAL-KAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12226    2 LFVGGLSPSITEDDLERRFSRFGTVSDVEIIRKKDAPDRGFAYIDLRTSEAALqKCLSTLNGVKWKGSRLKIQL 75
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
672-745 8.44e-04

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 38.50  E-value: 8.44e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLgtADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12338    1 RIYVGNLPGDIRERDIEDLFYKYGPILAIDLKNRRRGPPF--AFVEFEDPRDAEDAIRGRDGYDFDGYRLRVEF 72
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
673-744 9.39e-04

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 38.37  E-value: 9.39e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12362    1 LFVYHLPNEFTDQDLYQLFAPFGNVVSAKVFVDKnTGRSKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLKVQ 73
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
673-764 1.05e-03

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 42.60  E-value: 1.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260  673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFeRKADALKAMKQYNGVPLDGRPMNIQLvtSQID 751
Cdd:TIGR01622 117 VFVQQLAARARERDLYEFFSKVGKVRDVQIIKDRnSRRSKGVGYVEF-YDVDSVQAALALTGQKLLGIPVIVQL--SEAE 193
                          90
                  ....*....|...
gi 537141260  752 TQRRPAQSINRGG 764
Cdd:TIGR01622 194 KNRAARAATETSG 206
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
672-745 1.23e-03

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 38.25  E-value: 1.23e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAV--HYdrsgrslgtADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12608    2 KIFVGNVDEDTSQEELSALFEPYGAVLSCAVmkQF---------AFVHMRGEAAADRAIRELNGRELHGRALVVEE 68
RRM1_RBM19_MRD1 cd12315
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple ...
672-746 1.24e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409754 [Multi-domain]  Cd Length: 81  Bit Score: 38.29  E-value: 1.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEF-----GTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV 746
Cdd:cd12315    2 RLIVKNLPLSLDEDQFRRLFSQKckdigLTITDCKLLTKSGGVSRRFGFVGFKDEEDAQKAKEFFNGTYFRTSKVTVEFS 81
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
673-740 1.29e-03

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 39.22  E-value: 1.29e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNG---VPLDGRP 740
Cdd:cd21615   21 LFVGRLDYSLTELELQKKFSKFGEIEKIRIVRDkETGKSRGYAFIVFKSESDAKNAFKEGNGlrgLKINDRT 92
RRM2_VICKZ cd12359
RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds ...
672-738 1.38e-03

RNA recognition motif 2 (RRM2) found in the VICKZ family proteins; This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 409794 [Multi-domain]  Cd Length: 76  Bit Score: 38.12  E-value: 1.38e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSgrSLGTADVHFERKADALKAMKQYNGVPLDG 738
Cdd:cd12359    2 KIQIRNIPPHARWEDLDSLLSTYGTVENCEQVNTKS--ETATVNVTYESPEQAQQAVNKLNGYQYEG 66
RRM3_hnRNPM_like cd12387
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
673-744 1.42e-03

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409821 [Multi-domain]  Cd Length: 71  Bit Score: 37.95  E-value: 1.42e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDrSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12387    1 IFVRNLPFDYTWQKLKDKFKDCGHVTFASIKME-NGKSKGCGTVRFDSPEDAENACRMMNGSKQSGREIDVR 71
RRM1_SF3B4 cd12334
RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
673-741 1.47e-03

RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409771 [Multi-domain]  Cd Length: 74  Bit Score: 37.97  E-value: 1.47e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKaaVHY--DR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM 741
Cdd:cd12334    1 VYVGNLDEKVTEELLWELFIQAGPVVN--VHMpkDRvTQQHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPI 70
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
672-739 1.62e-03

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 37.78  E-value: 1.62e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12370    2 RVYVGSIYFELGEDTIRQAFAPFGPIKSIDMSWDPvTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGR 70
RRM3_HRB1_GBP2 cd21607
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...
673-743 1.67e-03

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410186 [Multi-domain]  Cd Length: 79  Bit Score: 38.07  E-value: 1.67e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd21607    5 IYCSNLPLSTAESDLYDLFETIGKVNNAELKYDETGDPTGSAVVEYENLDDADVCISKLNNYNYGGCDLKI 75
RRM6_RBM19 cd12571
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
672-729 2.00e-03

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409985 [Multi-domain]  Cd Length: 79  Bit Score: 37.79  E-value: 2.00e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAV--HYDRSGRSLGTADVHFERKADALKAMK 729
Cdd:cd12571    2 KILVRNIPFQATVKEVRELFSTFGELKTVRLpkKMGGTGQHRGFGFVDFITKQDAKRAFD 61
RRM2_SECp43 cd12612
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43); ...
673-749 2.11e-03

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43); This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region.


Pssm-ID: 410024 [Multi-domain]  Cd Length: 82  Bit Score: 37.74  E-value: 2.11e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 673 LLVSNLDFGVSDADIQELFAE-FGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVP-LDGRPMNIQLVTSQ 749
Cdd:cd12612    4 LFVGDLTPEVDDGMLYEFFLKrYPSCKGAKVVLDQLGNSRGYGFVRFSDENEQKRALTECQGASgLGGKPIRLSVAIPK 82
RRM2_RBM4 cd12607
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
672-744 2.64e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410019 [Multi-domain]  Cd Length: 67  Bit Score: 37.25  E-value: 2.64e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDrsgrslgTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12607    2 KLHVGNISSSCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAMEAIRGLDNTEFQGKRMHVQ 67
RRM2_TIAR cd12617
RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup ...
673-747 2.89e-03

RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410029 [Multi-domain]  Cd Length: 80  Bit Score: 37.28  E-value: 2.89e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 747
Cdd:cd12617    4 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMAtGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWAT 79
RRM3_RBM19 cd12567
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
672-743 3.19e-03

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409983 [Multi-domain]  Cd Length: 79  Bit Score: 37.37  E-value: 3.19e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLkkAAVHY--DR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 743
Cdd:cd12567    4 RLFVRNLPYTCTEEDLEKLFSKYGPL--SEVHFpiDSlTKKPKGFAFVTYMIPEHAVKAYAELDGTVFQGRLLHL 76
RRM3_MYEF2 cd12662
RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This ...
672-745 3.22e-03

RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410063 [Multi-domain]  Cd Length: 77  Bit Score: 37.26  E-value: 3.22e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDrSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12662    1 QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME-NGKSKGCGTVRFDSPESAEKACRLMNGIKISGREIDVRL 73
RRM1_p54nrb cd12588
RNA recognition motif 1 (RRM1) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein ...
672-745 3.33e-03

RNA recognition motif 1 (RRM1) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb); This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus.


Pssm-ID: 410001 [Multi-domain]  Cd Length: 71  Bit Score: 36.85  E-value: 3.33e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRsgrslGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12588    3 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF 71
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
673-744 3.47e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 37.35  E-value: 3.47e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12312    3 LFVRNVADDTRPDDLRREFGRYGPIVDVYIPLDfYTRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQ 75
RRM2_Hu cd12652
RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to ...
673-738 4.36e-03

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410055 [Multi-domain]  Cd Length: 79  Bit Score: 36.92  E-value: 4.36e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQYNGVPLDG 738
Cdd:cd12652    3 LYVSGLPKTMTQKELEQLFSQFGRIITSRILCDNVtGLSRGVGFIRFDKRVEAERAIKALNGTIPPG 69
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
675-744 4.59e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 36.71  E-value: 4.59e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQyNGVPLDGRPMNIQ 744
Cdd:cd12395    4 VGNLPFDIEEEELRKHFEDCGDVEAVRIVRDReTGIGKGFGYVLFKDKDSVDLALKL-NGSKLRGRKLRVK 73
RRM4_RBM12 cd12749
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12 (RBM12) and similar proteins; ...
675-747 4.83e-03

RNA recognition motif 4 (RRM4) found in RNA-binding protein 12 (RBM12) and similar proteins; This subgroup corresponds to the RRM4 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear.


Pssm-ID: 410143 [Multi-domain]  Cd Length: 88  Bit Score: 37.10  E-value: 4.83e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260 675 VSNLDFGVSDADIQELFAEFGtLKKAAVHY--DRSGRSLGTADVHFERKADALKAMKQYNGvPLDGRPMNIQLVT 747
Cdd:cd12749    4 ISNIPYNITKKDVLQFLEGIG-LDENSVQVlvDNNGQGLGQALVQFKSEDDARKAERLHRK-KLNGRDAFLHLVT 76
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
672-739 4.94e-03

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 36.46  E-value: 4.94e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12417    1 NLWISGLSDTTKAADLKKIFSKYGKVVSAKVVTSaRTPGSRCYGYVTMASVEEADLCIKSLNKTELHGR 69
RRM4_RBM12B cd12748
RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins; ...
675-729 5.48e-03

RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins; This subgroup corresponds to the RRM4 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear.


Pssm-ID: 410142 [Multi-domain]  Cd Length: 76  Bit Score: 36.61  E-value: 5.48e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 537141260 675 VSNLDFGVSDADIQELFAEFgTLKKAAVH--YDRSGRSLGTADVHFERKADALKAMK 729
Cdd:cd12748    5 VRNLPFDVTKVEVQDFFEGF-ALAEDDIIllYDDKGVGLGEALVKFKSEEEAMKAER 60
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
673-744 5.69e-03

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 36.08  E-value: 5.69e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKaaVHYDRSGRSLGTadVHFERKADALKAMKQYNGVPLDGRPMNIQ 744
Cdd:cd12276    4 LLVFNLDAPVSNDELKSLFSKFGEIKE--IRPTPDKPSQKF--VEFYDVRDAEAALDGLNGRELLGGKLKVA 71
FoP_duplication pfam13865
C-terminal duplication domain of Friend of PRMT1; Fop, or Friend of Prmt1, proteins are ...
798-818 6.23e-03

C-terminal duplication domain of Friend of PRMT1; Fop, or Friend of Prmt1, proteins are conserved from fungi and plants to vertebrates. There is little that is actually conserved except for this C-terminal LDXXLDAYM region where X is any amino acid). The Fop proteins themselves are nuclear proteins localized to regions with low levels of DAPI, with a punctate/speckle-like distribution. Fop is a chromatin-associated protein and it co-localizes with facultative heterochromatin. It is is critical for oestrogen-dependent gene activation.


Pssm-ID: 464005  Cd Length: 81  Bit Score: 36.57  E-value: 6.23e-03
                          10        20
                  ....*....|....*....|.
gi 537141260  798 SKQQLSAEELDAQLDAYNARM 818
Cdd:pfam13865  43 KKKPKTKEELDAELDEYMSPK 63
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
675-743 6.25e-03

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 36.13  E-value: 6.25e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 675 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMkQYNGVPLDGRPMNI 743
Cdd:cd12306    4 VGNVDYGTTPEELQAHFKSCGTINRVTILCDKfTGQPKGFAYIEFVDKSSVENAL-LLNESEFRGRQIKV 72
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
672-739 6.45e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 36.07  E-value: 6.45e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVhydrSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 739
Cdd:cd12373    1 KVYVGNLGPRVTKRELEDAFEKYGPLRNVWV----ARNPPGFAFVEFEDPRDAEDAVRALDGRRICGS 64
RRM3_hnRNPM cd12661
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
672-745 6.77e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410062 [Multi-domain]  Cd Length: 77  Bit Score: 36.39  E-value: 6.77e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDrSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12661    1 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVRFESPEVAERACRMMNGIKLNGREIDVRI 73
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
672-745 6.86e-03

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 36.00  E-value: 6.86e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 745
Cdd:cd12565    2 RIIVKNLPKYVTEKRLKEHFSKKGEITDVKVMRTKDGKSRRFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEF 75
RRM2_CELF3_4_5_6 cd12635
RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, ...
672-733 7.45e-03

RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins; This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region.


Pssm-ID: 410043 [Multi-domain]  Cd Length: 81  Bit Score: 36.24  E-value: 7.45e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537141260 672 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNG 733
Cdd:cd12635    3 KLFVGMLGKQQSEDDVRRLFEPFGSIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHG 64
RRM2_Crp79_Mug28 cd21621
RNA recognition motif 2 (RRM2) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
673-741 7.47e-03

RNA recognition motif 2 (RRM2) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410200 [Multi-domain]  Cd Length: 74  Bit Score: 36.15  E-value: 7.47e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 537141260 673 LLVSNLDFGVSDADIQELFAEFGTLKKAAV--HYDRSGRSLGtaDVHFERKADALKAMKQYNGVPLDGRPM 741
Cdd:cd21621    1 LTVLNLPTDMTPKDLYNLFSEHGKVEGTAInqVPDNRGRRYG--EVAMNSYEDCQKALEYFNGYVYKGYIL 69
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
673-736 8.02e-03

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 39.54  E-value: 8.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537141260  673 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQYNGVPL 736
Cdd:TIGR01661   6 LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVtGQSLGYGFVNYVRPEDAEKAVNSLNGLRL 70
PRK01170 PRK01170
bifunctional pantetheine-phosphate adenylyltransferase/NTP phosphatase;
275-334 9.74e-03

bifunctional pantetheine-phosphate adenylyltransferase/NTP phosphatase;


Pssm-ID: 234912 [Multi-domain]  Cd Length: 322  Bit Score: 39.03  E-value: 9.74e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 537141260 275 RTLGGGIsrYDMVHYGHSNQLRQARAMGDYLIVGVHTDEEIAKHKGPPVfTQEERYKMVQ 334
Cdd:PRK01170   2 ITVVGGT--FSKLHKGHKALLKKAIETGDEVVIGLTSDEYVRKNKVYPI-PYEDRKRKLE 58
PRK07143 PRK07143
hypothetical protein; Provisional
470-542 9.77e-03

hypothetical protein; Provisional


Pssm-ID: 235946 [Multi-domain]  Cd Length: 279  Bit Score: 38.83  E-value: 9.77e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 537141260 470 KIIQFAsgKEPQPGETVIYVAGAFDLFHIGHVdfleEVYKLAKRP-YIIAGLHFDQEVNRYKGKNYPIMNLHER 542
Cdd:PRK07143   3 KVYTFP--LKNFKFEKPTFVLGGFESFHLGHL----ELFKKAKESnDEIVIVIFKNPENLPKNTNKKFSDLNSR 70
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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