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Conserved domains on  [gi|33239445|ref|NP_003742|]
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eukaryotic translation initiation factor 3 subunit B isoform 1 [Homo sapiens]

Protein Classification

eukaryotic translation initiation factor 3 subunit B( domain architecture ID 12978583)

eukaryotic translation initiation factor 3 subunit B is an RNA-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis of a specialized repertoire of mRNAs and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome

CATH:  3.30.70.330
Gene Ontology:  GO:0003723|GO:0003743|GO:0031369|GO:0005852|GO:0006413
PubMed:  15853797|22278943|18515081
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG5354 super family cl34988
Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];
305-805 3.28e-101

Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];


The actual alignment was detected with superfamily member COG5354:

Pssm-ID: 227657 [Multi-domain]  Cd Length: 561  Bit Score: 324.52  E-value: 3.28e-101
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 305 QYSVIF-ESGDRTSIFWNDVKD-PVSIEERARWTETYVRWSPKGTYLATFHQRGIALWGGEKFKQIQRFSHQGVQLIDFS 382
Cdd:COG5354   1 MKSQFPlDYSAVISVFWNSQSEvIHTRFESENWPVAYVSESPLGTYLFSEHAAGVECWGGPSKAKLVRFRHPDVKYLDFS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 383 PCERYLVTFS---------PLMDTQDDPQaIIIWDILTGHKKRGFHCESSAH--WPIFKWSHDGKFFARMTLDTLSIYE- 450
Cdd:COG5354  81 PNEKYLVTWSrepiiepeiEISPFTSKNN-VFVWDIASGMIVFSFNGISQPYlgWPVLKFSIDDKYVARVVGSSLYIHEi 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 451 TPSMGLLDKKSLKISGIKDFSWSPGGN--IIAFWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVVDCKLHWQKNGDYLCV 528
Cdd:COG5354 160 TDNIEEHPFKNLRPVGILDFSISPEGNhdELAYWTPEKLNKPAMVRILSIPKNSVLVTKNLFKVSGVQLKWQVLGKYLLV 239

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 529 KVDRTPKG--TQGVVTNFEIFRMREKQVPVDVvEMKETIIAFAWEPNGSKFAVLHGEAPrISVSFYHVKNN--------- 597
Cdd:COG5354 240 LVMTHTKSnkSYFGESNLYLLRITERSIPVEK-DLKDPVHDFTWEPLSSRFAVISGYMP-ASVSVFDLRGNlrfyfpeqk 317

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 598 ---------GKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMN-------GALAFVDTS----------DCTVMNI--A 649
Cdd:COG5354 318 rntiffsphERYILFAGFDNLQGNIEIFDPAGRFKVAGAFNGLNtsycdwsPDGQFYDTDttseklrvdnSIKLWDVygA 397

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 650 EHYMASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQEQIKQIKKDLKKYSK 729
Cdd:COG5354 398 KVFELTNITWDPSGQYVTTSSSCPKHKVEHGYKIFKIAGALYPEEARGGFKNFAWRPEPPSKLTIESAKKYVKPSRHRFV 477

                       490       500       510       520       530       540       550
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 33239445 730 IFEQKDRLSQSKASKELVERRRTMMEDFRKYRKMAQELYMeQKNERlelrgGVDTDELDSNVDDwEEETIEFFVTE 805
Cdd:COG5354 478 PFEKAVIMEADSANRSSAPRKKELVEQWPEYSDEDKIRSL-LKKLR-----AIEALKERMRSGE-ELEVIQVNKIE 546
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
 184-264 6.67e-39

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: 138.87  E-value: 6.67e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 184 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFG--KITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 260
Cdd:cd12278   1 DSVVVVDGLPVVGEEKLEKLKKVLTKIFSKFGsgKIVGIYMPvDETGKTKGFAFVEYATPEEAKKAVKALNGYKLDKKHT 80


                ....
gi 33239445 261 FRVN 264
Cdd:cd12278  81 FAVN 84
PRK07764 super family cl35613
DNA polymerase III subunits gamma and tau; Validated
 4-161 4.04e-06

DNA polymerase III subunits gamma and tau; Validated


The actual alignment was detected with superfamily member PRK07764:

Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 50.37  E-value: 4.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445    4 AENVAVPEAAEERAEPGQQQPAAEPPPaegllrPAGPGAPEAAGTEASSEEVGIAEAGPESEVRTEPAAEAEAASGPSES 83
Cdd:PRK07764 600 PPAPASSGPPEEAARPAAPAAPAAPAA------PAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKA 673

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 33239445   84 PSPPAAEELPGSHAEPPVPAQGEAPGEQARDERSDSRAQAVSEDAGGNEGRAAEAEPRAlENGDADEPSFSDPEDFVD 161
Cdd:PRK07764 674 GGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPS-PAADDPVPLPPEPDDPPD 750
 
Name Accession Description Interval E-value
COG5354 COG5354
Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];
305-805 3.28e-101

Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];


Pssm-ID: 227657 [Multi-domain]  Cd Length: 561  Bit Score: 324.52  E-value: 3.28e-101
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 305 QYSVIF-ESGDRTSIFWNDVKD-PVSIEERARWTETYVRWSPKGTYLATFHQRGIALWGGEKFKQIQRFSHQGVQLIDFS 382
Cdd:COG5354   1 MKSQFPlDYSAVISVFWNSQSEvIHTRFESENWPVAYVSESPLGTYLFSEHAAGVECWGGPSKAKLVRFRHPDVKYLDFS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 383 PCERYLVTFS---------PLMDTQDDPQaIIIWDILTGHKKRGFHCESSAH--WPIFKWSHDGKFFARMTLDTLSIYE- 450
Cdd:COG5354  81 PNEKYLVTWSrepiiepeiEISPFTSKNN-VFVWDIASGMIVFSFNGISQPYlgWPVLKFSIDDKYVARVVGSSLYIHEi 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 451 TPSMGLLDKKSLKISGIKDFSWSPGGN--IIAFWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVVDCKLHWQKNGDYLCV 528
Cdd:COG5354 160 TDNIEEHPFKNLRPVGILDFSISPEGNhdELAYWTPEKLNKPAMVRILSIPKNSVLVTKNLFKVSGVQLKWQVLGKYLLV 239

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 529 KVDRTPKG--TQGVVTNFEIFRMREKQVPVDVvEMKETIIAFAWEPNGSKFAVLHGEAPrISVSFYHVKNN--------- 597
Cdd:COG5354 240 LVMTHTKSnkSYFGESNLYLLRITERSIPVEK-DLKDPVHDFTWEPLSSRFAVISGYMP-ASVSVFDLRGNlrfyfpeqk 317

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 598 ---------GKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMN-------GALAFVDTS----------DCTVMNI--A 649
Cdd:COG5354 318 rntiffsphERYILFAGFDNLQGNIEIFDPAGRFKVAGAFNGLNtsycdwsPDGQFYDTDttseklrvdnSIKLWDVygA 397

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 650 EHYMASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQEQIKQIKKDLKKYSK 729
Cdd:COG5354 398 KVFELTNITWDPSGQYVTTSSSCPKHKVEHGYKIFKIAGALYPEEARGGFKNFAWRPEPPSKLTIESAKKYVKPSRHRFV 477

                       490       500       510       520       530       540       550
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 33239445 730 IFEQKDRLSQSKASKELVERRRTMMEDFRKYRKMAQELYMeQKNERlelrgGVDTDELDSNVDDwEEETIEFFVTE 805
Cdd:COG5354 478 PFEKAVIMEADSANRSSAPRKKELVEQWPEYSDEDKIRSL-LKKLR-----AIEALKERMRSGE-ELEVIQVNKIE 546
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
 507-702 3.59e-85

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 462552 [Multi-domain]  Cd Length: 194  Bit Score: 269.14  E-value: 3.59e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   507 RNLFNVVDCKLHWQKNGDYLCVKVD-RTPKGTQGVVTNFEIFRMREKQVPVDVVEMKET--IIAFAWEPNGSKFAVLHGE 583
Cdd:pfam08662   1 KSFFKADKVQLKWNKNGTYLLVLTDtDVDKTGKSYYGETNLYLIGETGGPDCVVELDKEgpIHDVAWSPNGKEFAVIYGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   584 APRIsVSFYHVKnngkIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWDPTG 663
Cdd:pfam08662  81 MPAK-VSFFDLK----GNVIHSFGEQPRNTIFWSPFGRLVLLAGFGNLAGDIEFWDVVNKKKIATAEASNATLCEWSPDG 155

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 33239445   664 RYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQL 702
Cdd:pfam08662 156 RYFLTATTAPRLRVDNGFKIWHYNGALVYKYDFDELYQV 194
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
 184-264 6.67e-39

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: 138.87  E-value: 6.67e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 184 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFG--KITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 260
Cdd:cd12278   1 DSVVVVDGLPVVGEEKLEKLKKVLTKIFSKFGsgKIVGIYMPvDETGKTKGFAFVEYATPEEAKKAVKALNGYKLDKKHT 80


                ....
gi 33239445 261 FRVN 264
Cdd:cd12278  81 FAVN 84
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 187-256 4.71e-08

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: 50.69  E-value: 4.71e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 33239445   187 IVVDNVPQvgpdrlEKLKNVIHKIFSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:pfam00076   1 LFVGNLPP------DTTEEDLKDLFSKFGPIKSiRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELG 65
RRM smart00360
RNA recognition motif;
207-259 4.79e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.67  E-value: 4.79e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 33239445    207 IHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH 259
Cdd:smart00360  16 LRELFSKFGKVESVRLVrdKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRP 70
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 4-161 4.04e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 50.37  E-value: 4.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445    4 AENVAVPEAAEERAEPGQQQPAAEPPPaegllrPAGPGAPEAAGTEASSEEVGIAEAGPESEVRTEPAAEAEAASGPSES 83
Cdd:PRK07764 600 PPAPASSGPPEEAARPAAPAAPAAPAA------PAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKA 673

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 33239445   84 PSPPAAEELPGSHAEPPVPAQGEAPGEQARDERSDSRAQAVSEDAGGNEGRAAEAEPRAlENGDADEPSFSDPEDFVD 161
Cdd:PRK07764 674 GGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPS-PAADDPVPLPPEPDDPPD 750
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 189-256 6.73e-04

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: 43.26  E-value: 6.73e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   189 VDNV-PQVGPDRLEKLknvihkiFSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:TIGR01628 183 VKNLdPSVNEDKLREL-------FAKFGEITSaAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIG 245
FimV COG3170
Type IV pilus assembly protein FimV [Cell motility, Extracellular structures];
4-181 9.25e-04

Type IV pilus assembly protein FimV [Cell motility, Extracellular structures];


Pssm-ID: 442403 [Multi-domain]  Cd Length: 508  Bit Score: 42.47  E-value: 9.25e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   4 AENVAVPEAAEERAEPGQQQPAAEPPPAEGLLRPAGPGAPEAAG-------TEASSEEVGIAEAGPESEVRTEPAAEAEA 76
Cdd:COG3170 225 AQSADWAAYRARLAAAVEPAPAAAAPAAPPAAAAAAGPVPAAAEdtlspevTAAAAAEEADALPEAAAELAERLAALEAQ 304

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445  77 ASGPSESPSPPAAEelPGSHAEPPVPAQGEAPGEQARDERSDSRAQAVSEDAGGNEG-RAAEAEPRALENGDADEPSFSD 155
Cdd:COG3170 305 LAELQRLLALKNPA--PAAAVSAPAAAAAAATVEAAAPAAAAQPAAAAPAPALDNPLlLAGLLRRRKAEADEVDPVAEAD 382

                       170       180
                ....*....|....*....|....*..
gi 33239445 156 -PEDFVDDVSEEELLGDVLKDRPQEAD 181
Cdd:COG3170 383 vYLAYGRDDQAEEILKEALASEPERLD 409
 
Name Accession Description Interval E-value
COG5354 COG5354
Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];
305-805 3.28e-101

Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];


Pssm-ID: 227657 [Multi-domain]  Cd Length: 561  Bit Score: 324.52  E-value: 3.28e-101
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 305 QYSVIF-ESGDRTSIFWNDVKD-PVSIEERARWTETYVRWSPKGTYLATFHQRGIALWGGEKFKQIQRFSHQGVQLIDFS 382
Cdd:COG5354   1 MKSQFPlDYSAVISVFWNSQSEvIHTRFESENWPVAYVSESPLGTYLFSEHAAGVECWGGPSKAKLVRFRHPDVKYLDFS 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 383 PCERYLVTFS---------PLMDTQDDPQaIIIWDILTGHKKRGFHCESSAH--WPIFKWSHDGKFFARMTLDTLSIYE- 450
Cdd:COG5354  81 PNEKYLVTWSrepiiepeiEISPFTSKNN-VFVWDIASGMIVFSFNGISQPYlgWPVLKFSIDDKYVARVVGSSLYIHEi 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 451 TPSMGLLDKKSLKISGIKDFSWSPGGN--IIAFWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVVDCKLHWQKNGDYLCV 528
Cdd:COG5354 160 TDNIEEHPFKNLRPVGILDFSISPEGNhdELAYWTPEKLNKPAMVRILSIPKNSVLVTKNLFKVSGVQLKWQVLGKYLLV 239

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 529 KVDRTPKG--TQGVVTNFEIFRMREKQVPVDVvEMKETIIAFAWEPNGSKFAVLHGEAPrISVSFYHVKNN--------- 597
Cdd:COG5354 240 LVMTHTKSnkSYFGESNLYLLRITERSIPVEK-DLKDPVHDFTWEPLSSRFAVISGYMP-ASVSVFDLRGNlrfyfpeqk 317

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 598 ---------GKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMN-------GALAFVDTS----------DCTVMNI--A 649
Cdd:COG5354 318 rntiffsphERYILFAGFDNLQGNIEIFDPAGRFKVAGAFNGLNtsycdwsPDGQFYDTDttseklrvdnSIKLWDVygA 397

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 650 EHYMASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQEQIKQIKKDLKKYSK 729
Cdd:COG5354 398 KVFELTNITWDPSGQYVTTSSSCPKHKVEHGYKIFKIAGALYPEEARGGFKNFAWRPEPPSKLTIESAKKYVKPSRHRFV 477

                       490       500       510       520       530       540       550
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 33239445 730 IFEQKDRLSQSKASKELVERRRTMMEDFRKYRKMAQELYMeQKNERlelrgGVDTDELDSNVDDwEEETIEFFVTE 805
Cdd:COG5354 478 PFEKAVIMEADSANRSSAPRKKELVEQWPEYSDEDKIRSL-LKKLR-----AIEALKERMRSGE-ELEVIQVNKIE 546
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
 507-702 3.59e-85

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 462552 [Multi-domain]  Cd Length: 194  Bit Score: 269.14  E-value: 3.59e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   507 RNLFNVVDCKLHWQKNGDYLCVKVD-RTPKGTQGVVTNFEIFRMREKQVPVDVVEMKET--IIAFAWEPNGSKFAVLHGE 583
Cdd:pfam08662   1 KSFFKADKVQLKWNKNGTYLLVLTDtDVDKTGKSYYGETNLYLIGETGGPDCVVELDKEgpIHDVAWSPNGKEFAVIYGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   584 APRIsVSFYHVKnngkIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWDPTG 663
Cdd:pfam08662  81 MPAK-VSFFDLK----GNVIHSFGEQPRNTIFWSPFGRLVLLAGFGNLAGDIEFWDVVNKKKIATAEASNATLCEWSPDG 155

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 33239445   664 RYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQL 702
Cdd:pfam08662 156 RYFLTATTAPRLRVDNGFKIWHYNGALVYKYDFDELYQV 194
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
 184-264 6.67e-39

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: 138.87  E-value: 6.67e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 184 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFG--KITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 260
Cdd:cd12278   1 DSVVVVDGLPVVGEEKLEKLKKVLTKIFSKFGsgKIVGIYMPvDETGKTKGFAFVEYATPEEAKKAVKALNGYKLDKKHT 80


                ....
gi 33239445 261 FRVN 264
Cdd:cd12278  81 FAVN 84
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 187-264 2.49e-08

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: 51.51  E-value: 2.49e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 33239445 187 IVVDNVPQvgpdrlEKLKNVIHKIFSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKqHTFRVN 264
Cdd:cd00590   1 LFVGNLPP------DTTEEDLRELFSKFGEVVSvRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGG-RPLKVS 72
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 187-256 4.71e-08

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: 50.69  E-value: 4.71e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 33239445   187 IVVDNVPQvgpdrlEKLKNVIHKIFSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:pfam00076   1 LFVGNLPP------DTTEEDLKDLFSKFGPIKSiRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELG 65
RRM smart00360
RNA recognition motif;
207-259 4.79e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.67  E-value: 4.79e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 33239445    207 IHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH 259
Cdd:smart00360  16 LRELFSKFGKVESVRLVrdKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRP 70
WD40 COG2319
WD40 repeat [General function prediction only];
312-506 9.44e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 55.30  E-value: 9.44e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 312 SGDRTSIFWndvkDPVSIEERARWTE-----TYVRWSPKGTYLAT-FHQRGIALWGGEKFKQIQRFS-HQG-VQLIDFSP 383
Cdd:COG2319 139 SADGTVRLW----DLATGKLLRTLTGhsgavTSVAFSPDGKLLASgSDDGTVRLWDLATGKLLRTLTgHTGaVRSVAFSP 214

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 384 CERYLVTFSplmdtqdDPQAIIIWDILTGHKKRGFHCESSAHWPIfKWSHDGKFFARMTLD-TLSIYETPSMGLLDKKSL 462
Cdd:COG2319 215 DGKLLASGS-------ADGTVRLWDLATGKLLRTLTGHSGSVRSV-AFSPDGRLLASGSADgTVRLWDLATGELLRTLTG 286

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 33239445 463 KISGIKDFSWSPGGNIIAFwVPEDKdipaRVTLMQLPTRQEIRV 506
Cdd:COG2319 287 HSGGVNSVAFSPDGKLLAS-GSDDG----TVRLWDLATGKLLRT 325
WD40 COG2319
WD40 repeat [General function prediction only];
312-480 1.10e-07

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 54.92  E-value: 1.10e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 312 SGDRTSIFWN-DVKDPVSIEERARWTETYVRWSPKGTYLATFHQRG-IALWGGEKFKQIQRFSHQ--GVQLIDFSPCERY 387
Cdd:COG2319 223 SADGTVRLWDlATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGtVRLWDLATGELLRTLTGHsgGVNSVAFSPDGKL 302

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 388 LVTFSplmdtqDDpQAIIIWDILTGHKKRGFHCESSAHWPIfKWSHDGKFFARMTLD-TLSIYETPSMGLLDKKSLKISG 466
Cdd:COG2319 303 LASGS------DD-GTVRLWDLATGKLLRTLTGHTGAVRSV-AFSPDGKTLASGSDDgTVRLWDLATGELLRTLTGHTGA 374

                       170
                ....*....|....
gi 33239445 467 IKDFSWSPGGNIIA 480
Cdd:COG2319 375 VTSVAFSPDGRTLA 388
WD40 COG2319
WD40 repeat [General function prediction only];
340-480 1.49e-07

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 54.53  E-value: 1.49e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 340 VRWSPKGTYLATFHQ-RGIALWGGEKFKQIQRFSHQG--VQLIDFSPCERYLVTFSplmdtqDDpQAIIIWDILTGHKKR 416
Cdd:COG2319 210 VAFSPDGKLLASGSAdGTVRLWDLATGKLLRTLTGHSgsVRSVAFSPDGRLLASGS------AD-GTVRLWDLATGELLR 282

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33239445 417 GFHCESSAHWPIfKWSHDGKFFARMTLD-TLSIYETPSMGLLDKKSLKISGIKDFSWSPGGNIIA 480
Cdd:COG2319 283 TLTGHSGGVNSV-AFSPDGKLLASGSDDgTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLA 346
WD40 COG2319
WD40 repeat [General function prediction only];
340-480 8.61e-07

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 52.22  E-value: 8.61e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 340 VRWSPKGTYLATFHQ-RGIALWGGEKFKQIQRFS-HQG-VQLIDFSPCERYLVTFSplmdtqDDpQAIIIWDILTGHKKR 416
Cdd:COG2319 126 VAFSPDGKTLASGSAdGTVRLWDLATGKLLRTLTgHSGaVTSVAFSPDGKLLASGS------DD-GTVRLWDLATGKLLR 198

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33239445 417 GFHCESSAHWPIfKWSHDGKFFARMTLD-TLSIYETPSMGLLDKKSLKISGIKDFSWSPGGNIIA 480
Cdd:COG2319 199 TLTGHTGAVRSV-AFSPDGKLLASGSADgTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLA 262
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 4-161 4.04e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 50.37  E-value: 4.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445    4 AENVAVPEAAEERAEPGQQQPAAEPPPaegllrPAGPGAPEAAGTEASSEEVGIAEAGPESEVRTEPAAEAEAASGPSES 83
Cdd:PRK07764 600 PPAPASSGPPEEAARPAAPAAPAAPAA------PAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKA 673

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 33239445   84 PSPPAAEELPGSHAEPPVPAQGEAPGEQARDERSDSRAQAVSEDAGGNEGRAAEAEPRAlENGDADEPSFSDPEDFVD 161
Cdd:PRK07764 674 GGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPS-PAADDPVPLPPEPDDPPD 750
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
 207-264 1.87e-05

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 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: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 43.43  E-value: 1.87e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 207 IHKIFSKFGKITN-DFYPE-EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHtFRVN 264
Cdd:cd12371  17 IKSVFEAFGKIKScSLAPDpETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQY-LRVG 75
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 6-141 2.61e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 48.06  E-value: 2.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445    6 NVAVPEAAEERAEPGQQQPAAEPPPAEGLLRPAGPGAPEAAGTEAsseevgiAEAGPESEVRTEPAAEAEAASGPSESPS 85
Cdd:PRK07764 386 GVAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQ-------PAPAPAPAPAPPSPAGNAPAGGAPSPPP 458

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 33239445   86 PPAAEELPGShAEPPVPAQGEAPGEQARDERSDSRAQAVSEDAGGNEGRAAEAEPR 141
Cdd:PRK07764 459 AAAPSAQPAP-APAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAATLR 513
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
 187-264 3.44e-05

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: 42.89  E-value: 3.44e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 187 IVVDNVPQVGPDrlEKLKNvihkIFSKFGKITNdF---YPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQhTFRV 263
Cdd:cd12671   9 VFVGNIPYEATE--EQLKD----IFSEVGPVVS-FrlvYDRETGKPKGYGFCEYQDQETALSAMRNLNGYELNGR-ALRV 80


                .
gi 33239445 264 N 264
Cdd:cd12671  81 D 81
PRK12495 PRK12495
hypothetical protein; Provisional
 3-141 4.26e-05

hypothetical protein; Provisional


Pssm-ID: 183558 [Multi-domain]  Cd Length: 226  Bit Score: 45.63  E-value: 4.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445    3 DAENVAVPEAAEERAEPGQ-QQPAAEPPPAEGlLRPAGPGAPEAAGTEASSEEVGI-AEAGPESEVRTEPAAEAEAASGP 80
Cdd:PRK12495  80 DGAEATAPSDAGSQASPDDdAQPAAEAEAADQ-SAPPEASSTSATDEAATDPPATAaARDGPTPDPTAQPATPDERRSPR 158

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 33239445   81 SEspsppaaeelPGSHAEPPVPAQGEAPGEQARDERSDSRAQAVSEDAggneGRAAEAE-PR 141
Cdd:PRK12495 159 QR----------PPVSGEPPTPSTPDAHVAGTLQAARESLVETLARFA----RRAAATDdPR 206
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
 207-255 9.21e-05

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: 41.35  E-value: 9.21e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 33239445 207 IHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL 255
Cdd:cd12398  17 LKEIFSEVGPVVSFrlVTDRETGKPKGYGFCEFRDAETALSAVRNLNGYEL 67
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
 199-258 1.18e-04

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: 41.00  E-value: 1.18e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 33239445 199 RLEKL-KNV----IHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 258
Cdd:cd12365   2 HVGKLtRNVtkdhLKEIFSVYGTVKNVDLPidREPNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQ 68
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 207-252 2.37e-04

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: 40.02  E-value: 2.37e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 33239445 207 IHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADG 252
Cdd:cd12316  16 LRELFEAFGKISEVHIPldKQTKRSKGFAFVLFVIPEDAVKAYQELDG 63
PHA03169 PHA03169
hypothetical protein; Provisional
 16-184 2.73e-04

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 44.19  E-value: 2.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   16 RAEPGQQQPAAEPPPAE----GLLRPAGPGAPEAAGTE-ASSEEVGIAEAGPESEVRTEPAAEAEAASGPsespsppaae 90
Cdd:PHA03169  61 VAEQGHRQTESDTETAEesrhGEKEERGQGGPSGSGSEsVGSPTPSPSGSAEELASGLSPENTSGSSPES---------- 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   91 elPGSHAEPPVPAQGEAPGEQARDERSD-SRAQAVSEDAGGN--------EGRAAEAEPRALENGDADEPSFSDPEdfvD 161
Cdd:PHA03169 131 --PASHSPPPSPPSHPGPHEPAPPESHNpSPNQQPSSFLQPShedspeepEPPTSEPEPDSPGPPQSETPTSSPPP---Q 205

                        170       180
                 ....*....|....*....|...
gi 33239445  162 DVSEEEllGDVLKDRPQEADGID 184
Cdd:PHA03169 206 SPPDEP--GEPQSPTPQQAPSPN 226
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 2-145 2.92e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.59  E-value: 2.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445    2 QDAENVAVPEAAEERAEPGQQQPAAEPPPAEgllrpagpgAPEAAGTEASSEEVGIAEAGPESEVRTEPAAEAEAASGPS 81
Cdd:PRK07764 409 APAPAAAAPAAAAAPAPAAAPQPAPAPAPAP---------APPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAA 479

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 33239445   82 ESPSPPAAeelPGSHAEPPVPAQGEAPGEQARDERSDSRAQAVSEDAGGNEGRAAEA---EPRALEN 145
Cdd:PRK07764 480 PAPAPPAA---PAPAAAPAAPAAPAAPAGADDAATLRERWPEILAAVPKRSRKTWAIllpEATVLGV 543
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
 201-264 5.00e-04

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: 39.43  E-value: 5.00e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 33239445 201 EKLKNVihkiFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQhTFRVN 264
Cdd:cd12399  13 EQLKSL----FGQFGAVFDVKLPmdRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGR-TIRVN 73
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
7-156 5.12e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 43.68  E-value: 5.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445    7 VAVPEAAEERAEPGQQQPAAEPPPAEGLLRPAGPGAPEAAGTEASSEEVGIAEAGPESEVRTEPAAEAEAASGpsespsp 86
Cdd:PRK07003 449 VPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDA------- 521

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   87 paaeelPGSHAEPPVPAQGEAPGEQARDERSDSRAQA----------VSEDAGGNEGRAAE--AEPRALENGDADEPSFS 154
Cdd:PRK07003 522 ------PAAAAPPAPEARPPTPAAAAPAARAGGAAAAldvlrnagmrVSSDRGARAAAAAKpaAAPAAAPKPAAPRVAVQ 595


                 ..
gi 33239445  155 DP 156
Cdd:PRK07003 596 VP 597
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 187-265 6.29e-04

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: 39.07  E-value: 6.29e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445 187 IVVDNVP-QVGPDRLeklknviHKIFSKFGKIT-----NDFypeEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHt 260
Cdd:cd21608   2 LYVGNLSwDTTEDDL-------RDLFSEFGEVEsakviTDR---ETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRS- 70


                ....*
gi 33239445 261 FRVNL 265
Cdd:cd21608  71 IVVNE 75
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 189-256 6.73e-04

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: 43.26  E-value: 6.73e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   189 VDNV-PQVGPDRLEKLknvihkiFSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:TIGR01628 183 VKNLdPSVNEDKLREL-------FAKFGEITSaAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIG 245
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
 210-263 8.15e-04

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 39.11  E-value: 8.15e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 33239445 210 IFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQhTFRV 263
Cdd:cd12411  29 VFSQYGEIVDINLVrdKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGR-TIRV 83
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
 207-255 9.20e-04

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: 38.66  E-value: 9.20e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 33239445 207 IHKIFSKFGKITNDFYPEED----GKTKGYIFLEYASPAHAVDAVKNADGYKL 255
Cdd:cd21619  18 LEKIFSRYGQVESVRRPPIHtdkaDRTTGFGFIKYTDAESAERAMQQADGILL 70
FimV COG3170
Type IV pilus assembly protein FimV [Cell motility, Extracellular structures];
4-181 9.25e-04

Type IV pilus assembly protein FimV [Cell motility, Extracellular structures];


Pssm-ID: 442403 [Multi-domain]  Cd Length: 508  Bit Score: 42.47  E-value: 9.25e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   4 AENVAVPEAAEERAEPGQQQPAAEPPPAEGLLRPAGPGAPEAAG-------TEASSEEVGIAEAGPESEVRTEPAAEAEA 76
Cdd:COG3170 225 AQSADWAAYRARLAAAVEPAPAAAAPAAPPAAAAAAGPVPAAAEdtlspevTAAAAAEEADALPEAAAELAERLAALEAQ 304

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445  77 ASGPSESPSPPAAEelPGSHAEPPVPAQGEAPGEQARDERSDSRAQAVSEDAGGNEG-RAAEAEPRALENGDADEPSFSD 155
Cdd:COG3170 305 LAELQRLLALKNPA--PAAAVSAPAAAAAAATVEAAAPAAAAQPAAAAPAPALDNPLlLAGLLRRRKAEADEVDPVAEAD 382

                       170       180
                ....*....|....*....|....*..
gi 33239445 156 -PEDFVDDVSEEELLGDVLKDRPQEAD 181
Cdd:COG3170 383 vYLAYGRDDQAEEILKEALASEPERLD 409
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
 315-392 9.71e-04

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 462552 [Multi-domain]  Cd Length: 194  Bit Score: 41.10  E-value: 9.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   315 RTSIFWNDVKDPVSIEERARWTetyVRWSPKGTY--LATFH--QRGIALWGGEKFKQIQRFSHQGVQLIDFSPCERYLVT 390
Cdd:pfam08662  84 KVSFFDLKGNVIHSFGEQPRNT---IFWSPFGRLvlLAGFGnlAGDIEFWDVVNKKKIATAEASNATLCEWSPDGRYFLT 160


                  ..
gi 33239445   391 FS 392
Cdd:pfam08662 161 AT 162
RRM3_RBM19 cd12567
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
 207-252 1.12e-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: 38.53  E-value: 1.12e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 33239445 207 IHKIFSKFGKITNDFYPEED--GKTKGYIFLEYASPAHAVDAVKNADG 252
Cdd:cd12567  19 LEKLFSKYGPLSEVHFPIDSltKKPKGFAFVTYMIPEHAVKAYAELDG 66
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
 206-265 1.14e-03

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 38.36  E-value: 1.14e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 33239445 206 VIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQhTFRVNL 265
Cdd:cd12347  14 VLHAAFIPFGDIVDIQIPldYETEKHRGFAFVEFEEAEDAAAAIDNMNESELFGR-TIRVNL 74
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
 206-256 1.40e-03

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: 38.15  E-value: 1.40e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 33239445 206 VIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:cd12382  17 ALEAVFGKYGRIVEVLLmkDRETNKSRGFAFVTFESPADAKDAARDMNGKELD 69
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
 209-256 1.53e-03

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: 37.98  E-value: 1.53e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 33239445 209 KIFSKFGKI-------TNDfyPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:cd12318  19 KHFEKCGPIrsvtiakKKD--PKGPLLSMGYGFVEFKSPEAAQKALKQLQGTVLD 71
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
 189-256 1.70e-03

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: 37.63  E-value: 1.70e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 33239445 189 VDNVP-QVGPDRLEKLknvihkiFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:cd12311   3 VDNLTyRTTPDDLRRV-------FEKYGEVGDVYIPRDryTRESRGFAFVRFYDKRDAEDAIDAMDGAELD 66
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 207-256 2.61e-03

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: 37.15  E-value: 2.61e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 33239445 207 IHKIFSKFGKITNDFYPE-EDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:cd12414  16 LKKLFSKFGKVLEVTIPKkPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIK 66
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
 189-256 2.78e-03

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: 37.15  E-value: 2.78e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 33239445 189 VDNVPQ-VGPDRLEKLknvihkiFSKFGKITN-----DfypeEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:cd12380   6 VKNFGEdVDDDELKEL-------FEKYGKITSakvmkD----DSGKSKGFGFVNFENHEAAQKAVEELNGKELN 68
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 8-179 3.34e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.12  E-value: 3.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445    8 AVPEAAEERAEPGQQQPAAEPPPAEGL---LRPAGPGAPEAAGTEASSEEV----GIAEAGPESEVRTEPAAEAEAASGP 80
Cdd:PRK07764 640 SAAPAPGVAAPEHHPKHVAVPDASDGGdgwPAKAGGAAPAAPPPAPAPAAPaapaGAAPAQPAPAPAATPPAGQADDPAA 719

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   81 SESPSPPAAEELPGS-------HAEPPVPAQGEAPGEQARDERSDSRAQAVSeDAGGNEGRAAEAEPRALENGDADEPSF 153
Cdd:PRK07764 720 QPPQAAQGASAPSPAaddpvplPPEPDDPPDPAGAPAQPPPPPAPAPAAAPA-AAPPPSPPSEEEEMAEDDAPSMDDEDR 798

                        170       180
                 ....*....|....*....|....*.
gi 33239445  154 SDPEDFVDDVSEEELLGDVLKDRPQE 179
Cdd:PRK07764 799 RDAEEVAMELLEEELGAKKIEEFAAD 824
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 8-184 3.76e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.74  E-value: 3.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445    8 AVPEAAEERAEPGQQQPAAEPPPAEGLLRP---AGPGAPEAAGTEASSEEVGIAEAGPESEVRTEPAAEAEAASGPSESP 84
Cdd:PRK07764 616 AAPAAPAAPAAPAPAGAAAAPAEASAAPAPgvaAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAG 695

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33239445   85 SPPAAEELPGSHAEPPVPAQGEAP----GEQARDERSDSRAQAV------------------SEDAGGNEGRAAEAEPRA 142
Cdd:PRK07764 696 AAPAQPAPAPAATPPAGQADDPAAqppqAAQGASAPSPAADDPVplppepddppdpagapaqPPPPPAPAPAAAPAAAPP 775

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 33239445  143 LENGDADEPSFSDPEDFVDD-------VSEEELLGDVLKDRPQEADGID 184
Cdd:PRK07764 776 PSPPSEEEEMAEDDAPSMDDedrrdaeEVAMELLEEELGAKKIEEFAAD 824
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 198-259 5.04e-03

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 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: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 36.83  E-value: 5.04e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33239445 198 DRLEK-LKNV--IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH 259
Cdd:cd12390   8 DRLPKdFRDGseLRKLFSQVGKPTFCQLAMGNGVPRGFAFVEFASAEDAEEAQQLLNGHDLQGSP 72
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
 209-253 5.13e-03

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: 36.63  E-value: 5.13e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 33239445 209 KIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGY 253
Cdd:cd12566  21 KLFSKFGEVSEVHVPidKKTKKSKGFAYVLFLDPEDAVQAYNELDGK 67
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
 207-255 5.60e-03

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: 36.82  E-value: 5.60e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 33239445 207 IHKIFSKFGKITNdFYPEEDGKT---KGYIFLEYASPAHAVDAVKNADGYKL 255
Cdd:cd12324  23 IHDKFAEFGEIKN-LHLNLDRRTgfvKGYALVEYETKKEAQAAIEGLNGKEL 73
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 209-252 6.04e-03

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: 36.51  E-value: 6.04e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 33239445 209 KIFSKFGKITN-DFY-----PEEdGKTKGYIFLEYASPAHAVDAVKNADG 252
Cdd:cd12355  18 KLLSKYGKIKKfDFLfhktgPLK-GQPRGYCFVTFETKEEAEKAIECLNG 66
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
 207-265 7.18e-03

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 35.88  E-value: 7.18e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 33239445 207 IHKIFSKFGKITN---DFYPeedgKTKGYIFLEYASPAHAVDAVKNADGYKLDKqHTFRVNL 265
Cdd:cd12599  16 VEDLFSKYGPVVSidlKIPP----RPPAYAFVEFEDARDAEDAIRGRDGYDFDG-HRLRVEL 72
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
 207-256 8.90e-03

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: 36.06  E-value: 8.90e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 33239445 207 IHKIFSKFGKITNDF--YPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 256
Cdd:cd12236  18 LRREFEKYGPIKRVRlvRDKKTGKSRGYAFIEFEHERDMKAAYKHADGKKID 69
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
 201-252 9.55e-03

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: 35.71  E-value: 9.55e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 33239445 201 EKLKnvihKIFSKFGKITN-DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADG 252
Cdd:cd12381  16 EKLR----EEFSPFGTITSaKVMTDEGGRSKGFGFVCFSSPEEATKAVTEMNG 64
 
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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