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Conserved domains on  [gi|41053969|ref|NP_956223|]
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tRNA (uracil-5-)-methyltransferase homolog A [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 200-609 1.08e-73

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


:

Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 240.85  E-value: 1.08e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 200 VPYEEQLMMKEKEVEGVLQKLAREIGnnnkamlpwlfvqkekhnkmcCPLEAIRPSPLQTGYRNKCEFVigVGADGEDRT 279
Cdd:COG2265  81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARLS--VRRTDGRLR 137

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 280 VGFrlgkYKGGS--------CAVVSPsettnvcsEAKRVVQCFQQFIRTTpyavyspETYEGHWRQLTVRTtrlkqtmam 351
Cdd:COG2265 138 LGF----YARGShelvdideCPLLDP--------ALNALLPALRELLAEL-------GARRGELRHLVVRA--------- 189

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 352 vffnpqklqekeleelkqnlgqyftegegkecavtslyfvrmgqrtsagtedlpcehvtGEEWIHEELLGLKFRISPHSF 431
Cdd:COG2265 190 -----------------------------------------------------------GRDYLTERLGGLTFRISPGSF 210

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 432 FQTNTPAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKA 511
Cdd:COG2265 211 FQVNPEQAEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDL 290

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 512 EDVFPTILnAVVSPNVtAIVDPPRAGLHSKVILAIRKAEhLKRLVYVACNAKAamnnFI-DLcrapsNRVRGAAFRPVKA 590
Cdd:COG2265 291 EEVLPELL-WGGRPDV-VVLDPPRAGAGPEVLEALAALG-PRRIVYVSCNPAT----LArDL-----ALLVEGGYRLEKV 358

                       410
                ....*....|....*....
gi 41053969 591 MAVDLFPQTMHCETILLFE 609
Cdd:COG2265 359 QPVDMFPHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 69-147 8.97e-45

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


:

Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 153.55  E-value: 8.97e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41053969  69 FTSEIYKVEIQNLPKYIGFNDLKKFLNKHGINPHKIKLLGRQKFAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLAKP 147
Cdd:cd12439   1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 200-609 1.08e-73

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 240.85  E-value: 1.08e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 200 VPYEEQLMMKEKEVEGVLQKLAREIGnnnkamlpwlfvqkekhnkmcCPLEAIRPSPLQTGYRNKCEFVigVGADGEDRT 279
Cdd:COG2265  81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARLS--VRRTDGRLR 137

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 280 VGFrlgkYKGGS--------CAVVSPsettnvcsEAKRVVQCFQQFIRTTpyavyspETYEGHWRQLTVRTtrlkqtmam 351
Cdd:COG2265 138 LGF----YARGShelvdideCPLLDP--------ALNALLPALRELLAEL-------GARRGELRHLVVRA--------- 189

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 352 vffnpqklqekeleelkqnlgqyftegegkecavtslyfvrmgqrtsagtedlpcehvtGEEWIHEELLGLKFRISPHSF 431
Cdd:COG2265 190 -----------------------------------------------------------GRDYLTERLGGLTFRISPGSF 210

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 432 FQTNTPAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKA 511
Cdd:COG2265 211 FQVNPEQAEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDL 290

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 512 EDVFPTILnAVVSPNVtAIVDPPRAGLHSKVILAIRKAEhLKRLVYVACNAKAamnnFI-DLcrapsNRVRGAAFRPVKA 590
Cdd:COG2265 291 EEVLPELL-WGGRPDV-VVLDPPRAGAGPEVLEALAALG-PRRIVYVSCNPAT----LArDL-----ALLVEGGYRLEKV 358

                       410
                ....*....|....*....
gi 41053969 591 MAVDLFPQTMHCETILLFE 609
Cdd:COG2265 359 QPVDMFPHTHHVESVALLE 377
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 200-603 4.92e-45

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 165.77  E-value: 4.92e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   200 VPYEEQLMMKEKEVEGVLQKLAreignnnkamlpwlfvqKEKHNKMCcPLEAIRPSPLqtGYRNKCEFVIGvgadgEDRT 279
Cdd:TIGR00479  72 LSYELQLRSKQQQVIALLERIG-----------------KFVSEPIE-DVPTIGDDPW--GYRNKARLSLG-----RSPS 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   280 VGFRLGKYKGGS--------CAVVSPSeTTNVCSEAKRVVQCFQqfirttpYAVYSPETYEGHWRQLTVRTTRLKQTMAM 351
Cdd:TIGR00479 127 GQLQAGFYQKGShdivdvkqCPVQAPA-LNALLPKVRAILENFG-------ASRYLEHKELGQARHGVLRIGRHTGELSS 198

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   352 VFFNPQKL---QEKELEELKQNLGQYFTEGEGKECAVTSLYFvrmGQRTsagtedlpcEHVTGEEWIHEELLGLKFRISP 428
Cdd:TIGR00479 199 VDRTALERfphKEELDLYLQPDSPDVKSICQNINPEKTNVIF---GEET---------EVIAGEMPIYDKSGDLSFTFSA 266

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   429 HSFFQTNTPAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLTNVEFHC 508
Cdd:TIGR00479 267 RDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYCGMGTFTLPLAKQAKSVVGVEGVPESVEKAQQNAELNGIANVTFYH 346

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   509 GKAEDVFPTILNAVVSPNVTaIVDPPRAGLHSKVILAIRKAEHlKRLVYVACNAKAAMNNFIDLCRapsnrvrgAAFRPV 588
Cdd:TIGR00479 347 GTLETVLPKQPWAGNGFDKV-LLDPPRKGCAAGVLRTIIKLKP-ERIVYVSCNPATLARDLEALCK--------AGYTIA 416

                         410
                  ....*....|....*
gi 41053969   589 KAMAVDLFPQTMHCE 603
Cdd:TIGR00479 417 RVQPVDMFPHTGHVE 431
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 69-147 8.97e-45

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 153.55  E-value: 8.97e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41053969  69 FTSEIYKVEIQNLPKYIGFNDLKKFLNKHGINPHKIKLLGRQKFAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLAKP 147
Cdd:cd12439   1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
410-610 5.09e-27

23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 111.88  E-value: 5.09e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  410 TGEEWIHEELLGLKFRISPHSFFQTNTPAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAV 489
Cdd:PRK03522 129 TEQQALPERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWVRELPPRSMWDLFCGVGGFGLHCATPGMQLTGIEISAEAI 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  490 KDAEANAKANGLTNVEFHCGKAEDVfptILNAVVSPNVtAIVDPPRAGLHSKVilairkAEHL-----KRLVYVACNAKA 564
Cdd:PRK03522 209 ACAKQSAAELGLTNVQFQALDSTQF---ATAQGEVPDL-VLVNPPRRGIGKEL------CDYLsqmapRFILYSSCNAQT 278

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 41053969  565 AMNnfiDLCRAPSnrvrgaaFRPVKAMAVDLFPQTMHCETILLFER 610
Cdd:PRK03522 279 MAK---DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
 401-611 3.96e-14

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 74.01  E-value: 3.96e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   401 TEDLPcehVTGEEWIHEELLGlkfrisphSFFQTNTPAAEILYsavgEWA---QLDQDSTVLDVCCGTGTIGISLAKRVK 477
Cdd:pfam05958 160 DETLP---VAGREFIYRQVEN--------SFTQPNAAVNIKML----EWAcdvTQGSKGDLLELYCGNGNFSLALARNFR 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   478 KVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDvFPTILNAVVSPN------------VTAIVDPPRAGLHSKVILA 545
Cdd:pfam05958 225 KVLATEIAKPSVAAAQYNIAANNIDNVQIIRMSAEE-FTQAMNGVREFNrlkgidlksyncSTIFVDPPRAGLDPETLKL 303

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41053969   546 IRKAEhlkRLVYVACNAKAAMNNFIDLCRapSNRV-RGAAFrpvkamavDLFPQTMHCETILLFERV 611
Cdd:pfam05958 304 VQAYP---RILYISCNPETLCANLEQLSK--THRVeRFALF--------DQFPYTHHMECGVLLEKK 357
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 457-553 2.98e-09

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 54.74  E-value: 2.98e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 457 TVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDVFPtilNAVVSPNVtAIVDPPR 535
Cdd:cd02440   1 RVLDLGCGTGALALALASGpGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPP---EADESFDV-IISDPPL 76

                        90
                ....*....|....*....
gi 41053969 536 AGLHSKVILAIRKA-EHLK 553
Cdd:cd02440  77 HHLVEDLARFLEEArRLLK 95
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
80-150 3.52e-07

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 48.17  E-value: 3.52e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41053969  80 NLPKYIGFNDLKKFLNKHGiNPHKIKLL-----GRQK-FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLAKPKAD 150
Cdd:COG0724   8 NLPYSVTEEDLRELFSEYG-EVTSVKLItdretGRSRgFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83
RRM smart00360
RNA recognition motif;
78-142 1.12e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.43  E-value: 1.12e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969     78 IQNLPKYIGFNDLKKFLNKHG----INPHKIKLLGRQK-FAFVTFKNQEERDKAMKAVHGMQWKSNVLSV 142
Cdd:smart00360   4 VGNLPPDTTEEELRELFSKFGkvesVRLVRDKETGKSKgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 78-140 1.04e-05

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: 43.38  E-value: 1.04e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41053969    78 IQNLPKYIGFNDLKKFLNKHG----INPHKIKLLGRQKFAFVTFKNQEERDKAMKAVHGMQWKSNVL 140
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGpiksIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 62-160 5.35e-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: 46.34  E-value: 5.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969    62 RYIKEDLFTSEIYKVEIQNLPKYIGFNDLKKFLNKHG-INPHKIKLLGRQK---FAFVTFKNQEERDKAMKAVHG----M 133
Cdd:TIGR01628 167 KHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGeITSAAVMKDGSGRsrgFAFVNFEKHEDAAKAVEEMNGkkigL 246

                          90       100
                  ....*....|....*....|....*....
gi 41053969   134 QWKSNVLSVRLAKPKAD--PILKKRKQEE 160
Cdd:TIGR01628 247 AKEGKKLYVGRAQKRAEreAELRRKFEEL 275
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 200-609 1.08e-73

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 240.85  E-value: 1.08e-73
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 200 VPYEEQLMMKEKEVEGVLQKLAREIGnnnkamlpwlfvqkekhnkmcCPLEAIRPSPLQTGYRNKCEFVigVGADGEDRT 279
Cdd:COG2265  81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARLS--VRRTDGRLR 137

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 280 VGFrlgkYKGGS--------CAVVSPsettnvcsEAKRVVQCFQQFIRTTpyavyspETYEGHWRQLTVRTtrlkqtmam 351
Cdd:COG2265 138 LGF----YARGShelvdideCPLLDP--------ALNALLPALRELLAEL-------GARRGELRHLVVRA--------- 189

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 352 vffnpqklqekeleelkqnlgqyftegegkecavtslyfvrmgqrtsagtedlpcehvtGEEWIHEELLGLKFRISPHSF 431
Cdd:COG2265 190 -----------------------------------------------------------GRDYLTERLGGLTFRISPGSF 210

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 432 FQTNTPAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKA 511
Cdd:COG2265 211 FQVNPEQAEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDL 290

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 512 EDVFPTILnAVVSPNVtAIVDPPRAGLHSKVILAIRKAEhLKRLVYVACNAKAamnnFI-DLcrapsNRVRGAAFRPVKA 590
Cdd:COG2265 291 EEVLPELL-WGGRPDV-VVLDPPRAGAGPEVLEALAALG-PRRIVYVSCNPAT----LArDL-----ALLVEGGYRLEKV 358

                       410
                ....*....|....*....
gi 41053969 591 MAVDLFPQTMHCETILLFE 609
Cdd:COG2265 359 QPVDMFPHTHHVESVALLE 377
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 200-603 4.92e-45

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 165.77  E-value: 4.92e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   200 VPYEEQLMMKEKEVEGVLQKLAreignnnkamlpwlfvqKEKHNKMCcPLEAIRPSPLqtGYRNKCEFVIGvgadgEDRT 279
Cdd:TIGR00479  72 LSYELQLRSKQQQVIALLERIG-----------------KFVSEPIE-DVPTIGDDPW--GYRNKARLSLG-----RSPS 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   280 VGFRLGKYKGGS--------CAVVSPSeTTNVCSEAKRVVQCFQqfirttpYAVYSPETYEGHWRQLTVRTTRLKQTMAM 351
Cdd:TIGR00479 127 GQLQAGFYQKGShdivdvkqCPVQAPA-LNALLPKVRAILENFG-------ASRYLEHKELGQARHGVLRIGRHTGELSS 198

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   352 VFFNPQKL---QEKELEELKQNLGQYFTEGEGKECAVTSLYFvrmGQRTsagtedlpcEHVTGEEWIHEELLGLKFRISP 428
Cdd:TIGR00479 199 VDRTALERfphKEELDLYLQPDSPDVKSICQNINPEKTNVIF---GEET---------EVIAGEMPIYDKSGDLSFTFSA 266

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   429 HSFFQTNTPAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLTNVEFHC 508
Cdd:TIGR00479 267 RDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYCGMGTFTLPLAKQAKSVVGVEGVPESVEKAQQNAELNGIANVTFYH 346

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   509 GKAEDVFPTILNAVVSPNVTaIVDPPRAGLHSKVILAIRKAEHlKRLVYVACNAKAAMNNFIDLCRapsnrvrgAAFRPV 588
Cdd:TIGR00479 347 GTLETVLPKQPWAGNGFDKV-LLDPPRKGCAAGVLRTIIKLKP-ERIVYVSCNPATLARDLEALCK--------AGYTIA 416

                         410
                  ....*....|....*
gi 41053969   589 KAMAVDLFPQTMHCE 603
Cdd:TIGR00479 417 RVQPVDMFPHTGHVE 431
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 69-147 8.97e-45

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 153.55  E-value: 8.97e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41053969  69 FTSEIYKVEIQNLPKYIGFNDLKKFLNKHGINPHKIKLLGRQKFAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLAKP 147
Cdd:cd12439   1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
410-610 5.09e-27

23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 111.88  E-value: 5.09e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  410 TGEEWIHEELLGLKFRISPHSFFQTNTPAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAV 489
Cdd:PRK03522 129 TEQQALPERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWVRELPPRSMWDLFCGVGGFGLHCATPGMQLTGIEISAEAI 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  490 KDAEANAKANGLTNVEFHCGKAEDVfptILNAVVSPNVtAIVDPPRAGLHSKVilairkAEHL-----KRLVYVACNAKA 564
Cdd:PRK03522 209 ACAKQSAAELGLTNVQFQALDSTQF---ATAQGEVPDL-VLVNPPRRGIGKEL------CDYLsqmapRFILYSSCNAQT 278

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 41053969  565 AMNnfiDLCRAPSnrvrgaaFRPVKAMAVDLFPQTMHCETILLFER 610
Cdd:PRK03522 279 MAK---DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
421-610 3.83e-23

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 102.54  E-value: 3.83e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  421 GLKFRISPHSFFQTNTPAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANG 500
Cdd:PRK13168 264 GLRLAFSPRDFIQVNAQVNQKMVARALEWLDPQPGDRVLDLFCGLGNFTLPLARQAAEVVGVEGVEAMVERARENARRNG 343

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  501 LTNVEFHCGKAEDVFPTIL------NAVvspnvtaIVDPPRAGlhskvilAIRKAEHL-----KRLVYVACNakaamnnf 569
Cdd:PRK13168 344 LDNVTFYHANLEEDFTDQPwalggfDKV-------LLDPPRAG-------AAEVMQALaklgpKRIVYVSCN-------- 401

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 41053969  570 idlcraPSNRVRGAA------FRPVKAMAVDLFPQTMHCETILLFER 610
Cdd:PRK13168 402 ------PATLARDAGvlveagYRLKRAGMLDMFPHTGHVESMALFER 442
PRK09328 PRK09328
N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
 405-515 4.89e-16

N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional


Pssm-ID: 236467 [Multi-domain]  Cd Length: 275  Bit Score: 78.67  E-value: 4.89e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  405 PCEHVTGEEwiheELLGLKFRISPHSF---FQTntpaaEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVK--KV 479
Cdd:PRK09328  65 PLQYILGEA----EFWGLDFKVSPGVLiprPET-----EELVEWALEALLLKEPLRVLDLGTGSGAIALALAKERPdaEV 135

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 41053969  480 IGIELCQEAVKDAEANAKANGLTNVEFHCGkaeDVF 515
Cdd:PRK09328 136 TAVDISPEALAVARRNAKHGLGARVEFLQG---DWF 168
HemK COG2890
Methylase of polypeptide chain release factors [Translation, ribosomal structure and ...
 405-515 1.28e-14

Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442135 [Multi-domain]  Cd Length: 282  Bit Score: 74.42  E-value: 1.28e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 405 PCEHVTGEEWIHeellGLKFRISPHSF---FQTntpaaEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVK--KV 479
Cdd:COG2890  69 PLAYILGEAEFY----GLEFKVDPGVLiprPET-----EELVELALALLPAGAPPRVLDLGTGSGAIALALAKERPdaRV 139

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 41053969 480 IGIELCQEAVKDAEANAKANGLTN-VEFHCGkaeDVF 515
Cdd:COG2890 140 TAVDISPDALAVARRNAERLGLEDrVRFLQG---DLF 173
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
 401-611 3.96e-14

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 74.01  E-value: 3.96e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   401 TEDLPcehVTGEEWIHEELLGlkfrisphSFFQTNTPAAEILYsavgEWA---QLDQDSTVLDVCCGTGTIGISLAKRVK 477
Cdd:pfam05958 160 DETLP---VAGREFIYRQVEN--------SFTQPNAAVNIKML----EWAcdvTQGSKGDLLELYCGNGNFSLALARNFR 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   478 KVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDvFPTILNAVVSPN------------VTAIVDPPRAGLHSKVILA 545
Cdd:pfam05958 225 KVLATEIAKPSVAAAQYNIAANNIDNVQIIRMSAEE-FTQAMNGVREFNrlkgidlksyncSTIFVDPPRAGLDPETLKL 303

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41053969   546 IRKAEhlkRLVYVACNAKAAMNNFIDLCRapSNRV-RGAAFrpvkamavDLFPQTMHCETILLFERV 611
Cdd:pfam05958 304 VQAYP---RILYISCNPETLCANLEQLSK--THRVeRFALF--------DQFPYTHHMECGVLLEKK 357
PRK05031 PRK05031
tRNA (uracil-5-)-methyltransferase; Validated
 408-610 6.93e-14

tRNA (uracil-5-)-methyltransferase; Validated


Pssm-ID: 235332  Cd Length: 362  Bit Score: 73.32  E-value: 6.93e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  408 HVTGEEWIHEEL----LGLKFRISPHSFFQTNTPAAE-ILysavgEWAqLD--QDST--VLDVCCGTGTIGISLAKRVKK 478
Cdd:PRK05031 157 IVLDQDYVDERLpvagREFIYRQVENSFTQPNAAVNEkML-----EWA-LDatKGSKgdLLELYCGNGNFTLALARNFRR 230

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  479 VIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDvFPTILNAVVSPNV------------TAIVDPPRAGLHSKVILAI 546
Cdd:PRK05031 231 VLATEISKPSVAAAQYNIAANGIDNVQIIRMSAEE-FTQAMNGVREFNRlkgidlksynfsTIFVDPPRAGLDDETLKLV 309

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41053969  547 RKAEhlkRLVYVACNAKAAMNNFIDLCRapSNRV-RGAAFrpvkamavDLFPQTMHCETILLFER 610
Cdd:PRK05031 310 QAYE---RILYISCNPETLCENLETLSQ--THKVeRFALF--------DQFPYTHHMECGVLLEK 361
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 458-534 5.44e-13

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 64.89  E-value: 5.44e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   458 VLDVCCGTGTIGISLAKRVK-KVIGIELCQEAVKDAEANAKANGLtNVEFHCGKAEDvFPTILN---AVVSPNVTAIVDP 533
Cdd:pfam13649   1 VLDLGCGTGRLTLALARRGGaRVTGVDLSPEMLERARERAAEAGL-NVEFVQGDAED-LPFPDGsfdLVVSSGVLHHLPD 78


                  .
gi 41053969   534 P 534
Cdd:pfam13649  79 P 79
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 457-559 3.69e-12

16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 65.60  E-value: 3.69e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 457 TVLDVCCGTGTIGISLAKR--VKKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKA-EDVFPTILNAVVSpNvtaivdP 533
Cdd:COG2813  52 RVLDLGCGYGVIGLALAKRnpEARVTLVDVNARAVELARANAAANGLENVEVLWSDGlSGVPDGSFDLILS-N------P 124

                        90       100       110
                ....*....|....*....|....*....|....
gi 41053969 534 P-RAGL--HSKVILA-IRKA-EHLK---RLVYVA 559
Cdd:COG2813 125 PfHAGRavDKEVAHAlIADAaRHLRpggELWLVA 158
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 442-536 1.04e-11

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 62.70  E-value: 1.04e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 442 LYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLtNVEFHCGKAEDV-FPT-IL 519
Cdd:COG2226  10 GREALLAALGLRPGARVLDLGCGTGRLALALAERGARVTGVDISPEMLELARERAAEAGL-NVEFVVGDAEDLpFPDgSF 88

                        90
                ....*....|....*...
gi 41053969 520 NAVVSPNV-TAIVDPPRA 536
Cdd:COG2226  89 DLVISSFVlHHLPDPERA 106
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 437-513 1.21e-11

SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only];


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 64.17  E-value: 1.21e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41053969 437 PAAEILYSAVgewAQLDQDSTVLDVCCGTGTIGISLAKRVK-KVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAED 513
Cdd:COG0500  12 PGLAALLALL---ERLPKGGRVLDLGCGTGRNLLALAARFGgRVIGIDLSPEAIALARARAAKAGLGNVEFLVADLAE 86
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 449-509 1.59e-11

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 64.40  E-value: 1.59e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41053969 449 WAQLDQDSTVLDVCCGTGTIGISLAKRVK--KVIGIELCQEAVKDAEANAKANGLTN-VEFHCG 509
Cdd:COG4123  32 FAPVKKGGRVLDLGTGTGVIALMLAQRSPgaRITGVEIQPEAAELARRNVALNGLEDrITVIHG 95
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 452-513 3.72e-10

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 58.58  E-value: 3.72e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41053969   452 LDQDSTVLDVCCGTGTIGISLAKRV---KKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAED 513
Cdd:pfam13847   1 IDKGMRVLDLGCGTGHLSFELAEELgpnAEVVGIDISEEAIEKARENAQKLGFDNVEFEQGDIEE 65
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
 458-553 5.16e-10

Methyltransferase small domain; This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.


Pssm-ID: 428349 [Multi-domain]  Cd Length: 170  Bit Score: 58.76  E-value: 5.16e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   458 VLDVCCGTGTIGISLAKRVKKVIgIELCQE---AVKDAEANAKANGLTNVEFHCGKA-EDVFPTILNAVVSpnvtaivDP 533
Cdd:pfam05175  35 VLDLGCGAGVLGAALAKESPDAE-LTMVDInarALESARENLAANGLENGEVVASDVySGVEDGKFDLIIS-------NP 106

                          90       100
                  ....*....|....*....|....*
gi 41053969   534 P-RAGLHSKVILA---IRKA-EHLK 553
Cdd:pfam05175 107 PfHAGLATTYNVAqrfIADAkRHLR 131
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 450-514 2.88e-09

2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis


Pssm-ID: 441829 [Multi-domain]  Cd Length: 126  Bit Score: 55.41  E-value: 2.88e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41053969 450 AQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKAnglTNVEFHCGKAEDV 514
Cdd:COG2227  20 RLLPAGGRVLDVGCGTGRLALALARRGADVTGVDISPEALEIARERAAE---LNVDFVQGDLEDL 81
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 457-553 2.98e-09

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 54.74  E-value: 2.98e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 457 TVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDVFPtilNAVVSPNVtAIVDPPR 535
Cdd:cd02440   1 RVLDLGCGTGALALALASGpGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPP---EADESFDV-IISDPPL 76

                        90
                ....*....|....*....
gi 41053969 536 AGLHSKVILAIRKA-EHLK 553
Cdd:cd02440  77 HHLVEDLARFLEEArRLLK 95
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 450-534 5.47e-09

tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440663 [Multi-domain]  Cd Length: 172  Bit Score: 55.73  E-value: 5.47e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 450 AQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDVfptilnAVVSPNVTA 529
Cdd:COG1041  22 AGAKEGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPKMVEGARENLEHYGYEDADVIRGDARDL------PLADESVDA 95


                ....*.
gi 41053969 530 IV-DPP 534
Cdd:COG1041  96 IVtDPP 101
CobL COG2242
Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part ...
 451-518 1.69e-08

Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 441843 [Multi-domain]  Cd Length: 403  Bit Score: 57.10  E-value: 1.69e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 451 QLDQDSTVLDVCCGTGTIGISLAKRVK--KVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDVFPTI 518
Cdd:COG2242 244 ALRPGDVLWDIGAGSGSVSIEAARLAPggRVYAIERDPERAALIRANARRFGVPNVEVVEGEAPEALADL 313
PRK08317 PRK08317
hypothetical protein; Provisional
 436-536 5.44e-08

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 54.17  E-value: 5.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  436 TPAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVK---KVIGIELCQEAVKDAeANAKANGLTNVEFHCGKAE 512
Cdd:PRK08317   1 LPDFRRYRARTFELLAVQPGDRVLDVGCGPGNDARELARRVGpegRVVGIDRSEAMLALA-KERAAGLGPNVEFVRGDAD 79

                         90       100
                 ....*....|....*....|....*..
gi 41053969  513 DV-FPT-ILNAVVSPNVTA-IVDPPRA 536
Cdd:PRK08317  80 GLpFPDgSFDAVRSDRVLQhLEDPARA 106
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 437-517 6.87e-08

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 52.24  E-value: 6.87e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 437 PAAEILYSAVGEWAQLDQDSTVLDVCCGTGTIGISLAKRVK-KVIGIELCQEAVKDAEANAKANGLTN-VEFHCGKAEDV 514
Cdd:COG2230  34 EAQEAKLDLILRKLGLKPGMRVLDIGCGWGGLALYLARRYGvRVTGVTLSPEQLEYARERAAEAGLADrVEVRLADYRDL 113


                ...
gi 41053969 515 FPT 517
Cdd:COG2230 114 PAD 116
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
433-556 8.54e-08

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 52.98  E-value: 8.54e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 433 QTNTP---AAEILYSAvgeWAQLD-QDSTVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGlTNVEFH 507
Cdd:COG2263  23 QYPTPaelAAELLHLA---YLRGDiEGKTVLDLGCGTGMLAIGAALLgAKKVVGVDIDPEALEIARENAERLG-VRVDFI 98

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 508 CGKAEDVFPTILNAVVSPN-----VTAIVDPP---RAGLHSKVILAIRKA---EHLKRLV 556
Cdd:COG2263  99 RADVTRIPLGGSVDTVVMNppfgaQRRHADRPfleKALEIAAVIYSIHNAgslDFVERFA 158
PRK14968 PRK14968
putative methyltransferase; Provisional
 457-506 9.91e-08

putative methyltransferase; Provisional


Pssm-ID: 237872 [Multi-domain]  Cd Length: 188  Bit Score: 52.59  E-value: 9.91e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 41053969  457 TVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLTN--VEF 506
Cdd:PRK14968  26 RVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNngVEV 77
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 76-143 1.42e-07

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: 48.82  E-value: 1.42e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41053969  76 VEIQNLPKYIGFNDLKKFLNKHGiNPHKIKLL----GRQK-FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVR 143
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFG-EVVSVRIVrdrdGKSKgFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
MenG_MenH_UbiE TIGR01934
ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of ...
 448-513 1.63e-07

ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of methyltransferases involved in the biosynthesis of menaquinone and ubiqinone. Some members such as the UbiE enzyme from E. coli are believed to act in both pathways, while others may act in only the menaquinone pathway. These methyltransferases are members of the UbiE/CoQ family of methyltransferases (pfam01209) which also contains ubiquinone methyltransferases and other methyltransferases. Members of this clade include a wide distribution of bacteria and eukaryotes, but no archaea. An outgroup for this clade is provided by the phosphatidylethanolamine methyltransferase (EC 2.1.1.17) from Rhodobacter sphaeroides. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]


Pssm-ID: 273884 [Multi-domain]  Cd Length: 223  Bit Score: 52.26  E-value: 1.63e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41053969   448 EWAQLDQDSTVLDVCCGTGTIGISLAKRV---KKVIGIELCQEAVkdAEANAKANGLTNVEFHCGKAED 513
Cdd:TIGR01934  33 KLIGVFKGQKVLDVACGTGDLAIELAKSApdrGKVTGVDFSSEML--EVAKKKSELPLNIEFIQADAEA 99
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
80-150 3.52e-07

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 48.17  E-value: 3.52e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41053969  80 NLPKYIGFNDLKKFLNKHGiNPHKIKLL-----GRQK-FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLAKPKAD 150
Cdd:COG0724   8 NLPYSVTEEDLRELFSEYG-EVTSVKLItdretGRSRgFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83
COG4976 COG4976
Predicted methyltransferase, contains TPR repeat [General function prediction only];
453-509 4.21e-07

Predicted methyltransferase, contains TPR repeat [General function prediction only];


Pssm-ID: 444001 [Multi-domain]  Cd Length: 181  Bit Score: 50.38  E-value: 4.21e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 41053969 453 DQDSTVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVkdAEANAKANGltnVEFHCG 509
Cdd:COG4976  45 GPFGRVLDLGCGTGLLGEALRPRGYRLTGVDLSEEML--AKAREKGVY---DRLLVA 96
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 448-513 4.27e-07

bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE;


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 51.31  E-value: 4.27e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  448 EWAQLDQDSTVLDVCCGTGTIGISLAKRVKK---VIGIELCQEAVKDAEANAKANGL-TNVEFHCGKAED 513
Cdd:PRK00216  45 KWLGVRPGDKVLDLACGTGDLAIALAKAVGKtgeVVGLDFSEGMLAVGREKLRDLGLsGNVEFVQGDAEA 114
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
454-516 9.45e-07

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 47.51  E-value: 9.45e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41053969 454 QDSTVLDVCCGTGTIGISLAKRVK--KVIGIELCQEAVkdaeANAKANgLTNVEFHCGKAEDVFP 516
Cdd:COG4106   1 PPRRVLDLGCGTGRLTALLAERFPgaRVTGVDLSPEML----ARARAR-LPNVRFVVADLRDLDP 60
RRM smart00360
RNA recognition motif;
78-142 1.12e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.43  E-value: 1.12e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969     78 IQNLPKYIGFNDLKKFLNKHG----INPHKIKLLGRQK-FAFVTFKNQEERDKAMKAVHGMQWKSNVLSV 142
Cdd:smart00360   4 VGNLPPDTTEEELRELFSKFGkvesVRLVRDKETGKSKgFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
PCMT pfam01135
Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT);
448-509 1.25e-06

Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT);


Pssm-ID: 395902 [Multi-domain]  Cd Length: 205  Bit Score: 49.67  E-value: 1.25e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41053969   448 EWAQLDQDSTVLDVCCGTGTIGISLA---KRVKKVIGIELCQEAVKDAEANAKANGLTNVEFHCG 509
Cdd:pfam01135  67 ELLELKPGMRVLEIGSGSGYLTACFArmvGEVGRVVSIEHIPELVEIARRNLEKLGLENVIVVVG 131
Ubie_methyltran pfam01209
ubiE/COQ5 methyltransferase family;
456-512 1.77e-06

ubiE/COQ5 methyltransferase family;


Pssm-ID: 395966 [Multi-domain]  Cd Length: 228  Bit Score: 49.36  E-value: 1.77e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   456 STVLDVCCGTGTIGISLAKRVK---KVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAE 512
Cdd:pfam01209  44 NKFLDVAGGTGDWTFGLSDSAGssgKVVGLDINENMLKEGEKKAKEEGKYNIEFLQGNAE 103
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 402-534 3.29e-06

23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure and biogenesis]; 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440709 [Multi-domain]  Cd Length: 392  Bit Score: 49.79  E-value: 3.29e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 402 EDLPCE--HVTGEE----WIHEEllGLKFRISPHS-----FF--QTNTPAAeilysaVGEWAQldqDSTVLDVCCGTGTI 468
Cdd:COG1092 162 EGLPQYegVLYGEApeevEVEEN--GLKFLVDLTDgqktgLFldQRENRAR------VAELAK---GKRVLNLFSYTGGF 230

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 469 GISLAKR-VKKVIGIELCQEAVKDAEANAKANGLT-NVEFHCGkaeDVFPTILNAVVSPNV--TAIVDPP 534
Cdd:COG1092 231 SVHAAAGgAKSVTSVDLSATALEWAKENAALNGLDdRHEFVQA---DAFDWLRELAREGERfdLIILDPP 297
RRM_MTHFSD cd12270
RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase ...
 76-146 3.72e-06

RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins; This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear.


Pssm-ID: 409713 [Multi-domain]  Cd Length: 72  Bit Score: 45.00  E-value: 3.72e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41053969  76 VEIQNLPKYIGFNDLKKFLNKHGINPHKIKLLGRQKFAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLAK 146
Cdd:cd12270   2 VYVGNIPRSVRVSDLKSALRERGINPLRITWQGARGKAFLHYSDMADADSAVSSLQGLRIGGNTLTVELAK 72
hemK_fam TIGR00536
HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme ...
 402-507 4.99e-06

HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase. Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain. [Protein fate, Protein modification and repair]


Pssm-ID: 273125 [Multi-domain]  Cd Length: 284  Bit Score: 48.50  E-value: 4.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   402 EDLPCEHVTGEEWiheeLLGLKFRISPHSFFQTntPAAEILYSAvgEWAQLDQDST---VLDVCCGTGTIGISLA--KRV 476
Cdd:TIGR00536  67 KGVPVAYLLGSKE----FYGLEFFVNEHVLIPR--PETEELVEK--ALASLISQPPilhILDLGTGSGCIALALAyeFPN 138

                          90       100       110
                  ....*....|....*....|....*....|..
gi 41053969   477 KKVIGIELCQEAVKDAEANAKANGLT-NVEFH 507
Cdd:TIGR00536 139 AEVIAVDISPDALAVAEENAEKNQLEhRVEFI 170
PrmA COG2264
Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis];
448-513 9.96e-06

Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441865 [Multi-domain]  Cd Length: 284  Bit Score: 47.48  E-value: 9.96e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 448 EW--AQLDQDSTVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGLTN-VEFHCGKAED 513
Cdd:COG2264 140 EAleKLLKPGKTVLDVGCGSGILAIAAAKLgAKRVLAVDIDPVAVEAARENAELNGVEDrIEVVLGDLLE 209
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 78-140 1.04e-05

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: 43.38  E-value: 1.04e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41053969    78 IQNLPKYIGFNDLKKFLNKHG----INPHKIKLLGRQKFAFVTFKNQEERDKAMKAVHGMQWKSNVL 140
Cdd:pfam00076   3 VGNLPPDTTEEDLKDLFSKFGpiksIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 459-516 2.75e-05

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 43.04  E-value: 2.75e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 41053969   459 LDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLTnveFHCGKAEDV-FP 516
Cdd:pfam08241   1 LDVGCGTGLLTELLARLGARVTGVDISPEMLELAREKAPREGLT---FVVGDAEDLpFP 56
MenG_heptapren TIGR02752
demethylmenaquinone methyltransferase; MenG is a generic term for a methyltransferase that ...
 456-511 3.22e-05

demethylmenaquinone methyltransferase; MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]


Pssm-ID: 131799  Cd Length: 231  Bit Score: 45.57  E-value: 3.22e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 41053969   456 STVLDVCCGTGTIGISLAKRV---KKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKA 511
Cdd:TIGR02752  47 TSALDVCCGTADWSIALAEAVgpeGHVIGLDFSENMLSVGRQKVKDAGLHNVELVHGNA 105
Cons_hypoth95 pfam03602
Conserved hypothetical protein 95;
449-558 3.60e-05

Conserved hypothetical protein 95;


Pssm-ID: 427391 [Multi-domain]  Cd Length: 179  Bit Score: 44.92  E-value: 3.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   449 WAQLDQDSTVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGLTNVEFhcgkAEDVFPTILNAVVSPNV 527
Cdd:pfam03602  36 LAPYIEGARVLDLFAGSGALGLEALSRgAKRVTLVEKDKRAVQILKENLQLLGLPGAVL----VMDALLALLRLAGKGPV 111

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 41053969   528 TAIV--DPP-RAGLHSKVILAIRKAEHLKR--LVYV 558
Cdd:pfam03602 112 FDIVflDPPyAKGLIEEVLDLLAEKGWLKPnaLIYV 147
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 78-145 4.65e-05

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: 41.78  E-value: 4.65e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 41053969  78 IQNLPKYIGFNDLKKFLNKHG-INPHKIKLLGRQK---FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLA 145
Cdd:cd12565   5 VKNLPKYVTEKRLKEHFSKKGeITDVKVMRTKDGKsrrFGFIGFKSEEEAQKAVKYFNKTFIDTSKISVEFA 76
Pcm COG2518
Protein-L-isoaspartate O-methyltransferase [Posttranslational modification, protein turnover, ...
 448-509 5.19e-05

Protein-L-isoaspartate O-methyltransferase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442008 [Multi-domain]  Cd Length: 197  Bit Score: 44.69  E-value: 5.19e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41053969 448 EWAQLDQDSTVLDVccGTGTiGIS---LAKRVKKVIGIELCQEAVKDAEANAKANGLTNVEFHCG 509
Cdd:COG2518  60 EALDLKPGDRVLEI--GTGS-GYQaavLARLAGRVYSVERDPELAERARERLAALGYDNVTVRVG 121
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 62-160 5.35e-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: 46.34  E-value: 5.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969    62 RYIKEDLFTSEIYKVEIQNLPKYIGFNDLKKFLNKHG-INPHKIKLLGRQK---FAFVTFKNQEERDKAMKAVHG----M 133
Cdd:TIGR01628 167 KHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGeITSAAVMKDGSGRsrgFAFVNFEKHEDAAKAVEEMNGkkigL 246

                          90       100
                  ....*....|....*....|....*....
gi 41053969   134 QWKSNVLSVRLAKPKAD--PILKKRKQEE 160
Cdd:TIGR01628 247 AKEGKKLYVGRAQKRAEreAELRRKFEEL 275
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 454-571 7.70e-05

16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA G966 N2-methylase RsmD is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440505 [Multi-domain]  Cd Length: 183  Bit Score: 43.92  E-value: 7.70e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 454 QDSTVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGLT-NVEFHCGKAEDVFPTILNA---VVspnvt 528
Cdd:COG0742  41 EGARVLDLFAGSGALGLEALSRgAASVVFVEKDRKAAAVIRKNLEKLGLEdRARVIRGDALRFLKRLAGEpfdLV----- 115

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 41053969 529 aIVDPP-RAGLHSKVILAIRKAEHLKR--LVYVACNAKAAMNNFID 571
Cdd:COG0742 116 -FLDPPyAKGLLEKALELLAENGLLAPggLIVVEHSKREELPELPA 160
arsM PRK11873
arsenite methyltransferase;
450-513 8.15e-05

arsenite methyltransferase;


Pssm-ID: 237007 [Multi-domain]  Cd Length: 272  Bit Score: 44.94  E-value: 8.15e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41053969  450 AQLDQDSTVLDVCCGTGTIGISLAKRVK---KVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAED 513
Cdd:PRK11873  73 AELKPGETVLDLGSGGGFDCFLAARRVGptgKVIGVDMTPEMLAKARANARKAGYTNVEFRLGEIEA 139
PRK07402 PRK07402
precorrin-6Y C5,15-methyltransferase subunit CbiT;
451-518 9.07e-05

precorrin-6Y C5,15-methyltransferase subunit CbiT;


Pssm-ID: 180961  Cd Length: 196  Bit Score: 43.83  E-value: 9.07e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  451 QLDQDSTVLDVCCGTGTIGISLAKRVKK--VIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDVFPTI 518
Cdd:PRK07402  37 RLEPDSVLWDIGAGTGTIPVEAGLLCPKgrVIAIERDEEVVNLIRRNCDRFGVKNVEVIEGSAPECLAQL 106
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
 78-142 1.35e-04

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: 40.70  E-value: 1.35e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41053969  78 IQNLPKYIGFNDLKKFLNKHG--INPhKI----KLLGRQKFAFVTFKNQEERDKAMKAVHGMQWKSNVLSV 142
Cdd:cd12417   4 ISGLSDTTKAADLKKIFSKYGkvVSA-KVvtsaRTPGSRCYGYVTMASVEEADLCIKSLNKTELHGRVITV 73
trmB PRK00121
tRNA (guanine-N(7)-)-methyltransferase; Reviewed
 425-515 2.24e-04

tRNA (guanine-N(7)-)-methyltransferase; Reviewed


Pssm-ID: 234649  Cd Length: 202  Bit Score: 42.84  E-value: 2.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  425 RISPHSFFQTNTPAAEILYsAVGEWAQL--DQDSTVLDVCCGTGTigiSLAKRVKK-----VIGIELCQEAVKDAEANAK 497
Cdd:PRK00121  10 RLTKGQQRAIEELWPRLSP-APLDWAELfgNDAPIHLEIGFGKGE---FLVEMAKAnpdinFIGIEVHEPGVGKALKKIE 85

                         90
                 ....*....|....*...
gi 41053969  498 ANGLTNVEFHCGKAEDVF 515
Cdd:PRK00121  86 EEGLTNLRLLCGDAVEVL 103
Trm5 COG2520
tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 ...
 457-514 2.54e-04

tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 N-methylase Trm5 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 442010 [Multi-domain]  Cd Length: 333  Bit Score: 43.70  E-value: 2.54e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 457 TVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGL-TNVEFHCGKAEDV 514
Cdd:COG2520 183 RVLDMFAGVGPFSIPIAKRsGAKVVAIDINPDAVEYLKENIRLNKVeDRVTPILGDAREV 242
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 78-146 2.75e-04

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: 39.98  E-value: 2.75e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  78 IQNLPKYIGFNDLKKFLNKHGinphKIKLL-------GRQK-----FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLA 145
Cdd:cd12355   4 IGNLDPRLTEYHLLKLLSKYG----KIKKFdflfhktGPLKgqprgYCFVTFETKEEAEKAIECLNGKLALGKKLVVRWA 79


                .
gi 41053969 146 K 146
Cdd:cd12355  80 H 80
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
 76-145 5.12e-04

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: 39.03  E-value: 5.12e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41053969  76 VEIQNLPKYIGFNDLKKFLNKHG----INPHKIKLLGRQK-FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLA 145
Cdd:cd12408   2 IRVTNLSEDATEEDLRELFRPFGpisrVYLAKDKETGQSKgFAFVTFETREDAERAIEKLNGFGYDNLILSVEWA 76
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 75-145 5.64e-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: 38.69  E-value: 5.64e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41053969  75 KVEIQNLPKYIGFNDLKKFLNKHG-INPHKI---KLLGRQK-FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLA 145
Cdd:cd21608   1 KLYVGNLSWDTTEDDLRDLFSEFGeVESAKVitdRETGRSRgFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76
PRK14967 PRK14967
putative methyltransferase; Provisional
 452-537 5.68e-04

putative methyltransferase; Provisional


Pssm-ID: 184931 [Multi-domain]  Cd Length: 223  Bit Score: 41.58  E-value: 5.68e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  452 LDQDSTVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGLTnVEFHCGKAEDVFPTI-LNAVVS--PNV 527
Cdd:PRK14967  34 LGPGRRVLDLCTGSGALAVAAAAAgAGSVTAVDISRRAVRSARLNALLAGVD-VDVRRGDWARAVEFRpFDVVVSnpPYV 112

                         90
                 ....*....|.
gi 41053969  528 -TAIVDPPRAG 537
Cdd:PRK14967 113 pAPPDAPPSRG 123
Methyltransf_4 pfam02390
Putative methyltransferase; This is a family of putative methyltransferases. The aligned ...
 454-519 5.96e-04

Putative methyltransferase; This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity.


Pssm-ID: 367068  Cd Length: 173  Bit Score: 41.12  E-value: 5.96e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41053969   454 QDSTVLDVCCGTGTIGISLAKRV--KKVIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDVFPTIL 519
Cdd:pfam02390   1 DAPVFLEIGCGMGGFLVAMAKANpdKNFIGIEIRVPGVAKALKKIDALGLQNLRILCGNALDVLPNYF 68
COG4076 COG4076
Predicted RNA methylase [General function prediction only];
455-517 6.75e-04

Predicted RNA methylase [General function prediction only];


Pssm-ID: 443253 [Multi-domain]  Cd Length: 230  Bit Score: 41.56  E-value: 6.75e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41053969 455 DSTVLDVCCGTGTIGIsLAKR--VKKVIGIELCQEAVKDAEANAKANGLT-NVEFHCGKAEDV-FPT 517
Cdd:COG4076  36 GDVVLDIGTGSGLLSM-LAARagAKKVYAVEVNPDIAAVARRIIAANGLSdRITVINADATDLdLPE 101
RRM1_RBM40_like cd12238
RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 78-142 7.13e-04

RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM1 of 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 repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), 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.


Pssm-ID: 409684 [Multi-domain]  Cd Length: 73  Bit Score: 38.39  E-value: 7.13e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41053969  78 IQNLPKYIGFNDLKKFLNKHGInpHKIKLLGRQKF----AFVTFKNQEERDKAMKAVHGMQWKSNVLSV 142
Cdd:cd12238   4 VRHLPPELSEDDKEDLLKHFGA--TSVRVMKRRGKlkhtAFATFDNEQAASKALSRLHQLKILGKRLVV 70
RRM2_HRB1_GBP2 cd21606
RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, ...
 74-143 7.20e-04

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: 38.50  E-value: 7.20e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41053969  74 YKVEIQNLPKYIGFNDLKKFLNKHGINPH-KIKLLGRQK---FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVR 143
Cdd:cd21606   2 YEVFIANLPYSINWQALKDMFKECGDVLRaDVELDYNGRsrgFGTVIYATEEEMHRAIDTFNGYELEGRVLEVK 75
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 76-128 8.04e-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: 38.31  E-value: 8.04e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 41053969  76 VEIQNLPKYIGFNDLKKFLNKHGINPHKIKLLGRQKF-----AFVTFKNQEERDKAMK 128
Cdd:cd12254   2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGrptgeAYVEFASEEDAQRALR 59
RRM1_RRT5 cd12409
RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) ...
 75-147 8.43e-04

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: 38.41  E-value: 8.43e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  75 KVEIQNLPKYIGFNDLKKFLNKHG-----INPHKIKLLGRQK-----FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRL 144
Cdd:cd12409   1 RVYISNLSYSTTEEELEELLKDYKpvsvlIPSYTVRGFRSRKhrplgIAYAEFSSVEEAEKVVKDLNGKVFKGRKLFVKL 80


                ...
gi 41053969 145 AKP 147
Cdd:cd12409  81 HVP 83
ksgA PRK14896
16S ribosomal RNA methyltransferase A;
448-524 8.73e-04

16S ribosomal RNA methyltransferase A;


Pssm-ID: 237852 [Multi-domain]  Cd Length: 258  Bit Score: 41.43  E-value: 8.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969  448 EWAQLDQDSTVLDVCCGTGTIGISLAKRVKKVIGIELcqeavkD----AEANAKANGLTNVEFHCGKAEDV-FPTiLNAV 522
Cdd:PRK14896  23 EYAEDTDGDPVLEIGPGKGALTDELAKRAKKVYAIEL------DprlaEFLRDDEIAAGNVEIIEGDALKVdLPE-FNKV 95


                 ..
gi 41053969  523 VS 524
Cdd:PRK14896  96 VS 97
prmA PRK00517
50S ribosomal protein L11 methyltransferase;
448-506 1.11e-03

50S ribosomal protein L11 methyltransferase;


Pssm-ID: 234786 [Multi-domain]  Cd Length: 250  Bit Score: 40.91  E-value: 1.11e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 41053969  448 EW--AQLDQDSTVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGLTNVEF 506
Cdd:PRK00517 111 EAleKLVLPGKTVLDVGCGSGILAIAAAKLgAKKVLAVDIDPQAVEAARENAELNGVELNVY 172
TrmB COG0220
tRNA G46 N7-methylase TrmB [Translation, ribosomal structure and biogenesis]; tRNA G46 ...
 443-524 1.22e-03

tRNA G46 N7-methylase TrmB [Translation, ribosomal structure and biogenesis]; tRNA G46 N7-methylase TrmB is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439990  Cd Length: 204  Bit Score: 40.51  E-value: 1.22e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 443 YSAVGEWAQL--DQDSTVLDVCCGTGTigiSLAKRVKK-----VIGIELCQEAVKDAEANAKANGLTNVEFHCGKAEDVF 515
Cdd:COG0220  19 LKGPLDWAELfgNDAPLVLEIGFGKGE---FLVELAAAnpdinFIGIEVHEPGVAKALKKAEEEGLTNVRLLRGDAVELL 95


                ....*....
gi 41053969 516 PTILNAVVS 524
Cdd:COG0220  96 ELFPDGSLD 104
Gcd14 COG2519
tRNA A58 N-methylase Trm61 [Translation, ribosomal structure and biogenesis]; tRNA A58 ...
 455-516 1.51e-03

tRNA A58 N-methylase Trm61 [Translation, ribosomal structure and biogenesis]; tRNA A58 N-methylase Trm61 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 442009 [Multi-domain]  Cd Length: 249  Bit Score: 40.53  E-value: 1.51e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41053969 455 DSTVLDVCCGTGTIGISLAKRVK---KVIGIELCQEAVKDAEANAKANGLT-NVEFHCGKAEDVFP 516
Cdd:COG2519  92 GARVLEAGTGSGALTLALARAVGpegKVYSYERREDFAEIARKNLERFGLPdNVELKLGDIREGID 157
COG2521 COG2521
Predicted archaeal methyltransferase [General function prediction only];
457-538 1.70e-03

Predicted archaeal methyltransferase [General function prediction only];


Pssm-ID: 442011 [Multi-domain]  Cd Length: 285  Bit Score: 40.66  E-value: 1.70e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969 457 TVLDVCCGTGTIGISLAKR-VKKVIGIELCQEAVKDAEANAKANGLTN--VEFHCGKAEDVFPTILNAvvspNVTAIV-D 532
Cdd:COG2521 135 RVLDTCTGLGYTAIEALKRgAREVITVEKDPNVLELAELNPWSRELANerIKIILGDASEVIKTFPDE----SFDAIIhD 210


                ....*.
gi 41053969 533 PPRAGL 538
Cdd:COG2521 211 PPRFSL 216
PRK07580 PRK07580
Mg-protoporphyrin IX methyl transferase; Validated
 448-514 1.74e-03

Mg-protoporphyrin IX methyl transferase; Validated


Pssm-ID: 236059 [Multi-domain]  Cd Length: 230  Bit Score: 40.21  E-value: 1.74e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41053969  448 EWAQLDQD---STVLDVCCGTGTIGISLAKRVKKVIGIELCQEAVKDAEANAKANGLT-NVEFHCGKAEDV 514
Cdd:PRK07580  54 SWLPADGDltgLRILDAGCGVGSLSIPLARRGAKVVASDISPQMVEEARERAPEAGLAgNITFEVGDLESL 124
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 112-148 2.65e-03

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: 37.19  E-value: 2.65e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 41053969 112 FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLAKPK 148
Cdd:cd12413  43 FGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79
PRK13943 PRK13943
protein-L-isoaspartate O-methyltransferase; Provisional
 448-509 3.12e-03

protein-L-isoaspartate O-methyltransferase; Provisional


Pssm-ID: 237568 [Multi-domain]  Cd Length: 322  Bit Score: 40.21  E-value: 3.12e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41053969  448 EWAQLDQDSTVLDVCCGTGTIGISLAKRVKK---VIGIELCQEAVKDAEANAKANGLTNVEFHCG 509
Cdd:PRK13943  74 EWVGLDKGMRVLEIGGGTGYNAAVMSRVVGEkglVVSVEYSRKICEIAKRNVRRLGIENVIFVCG 138
RRM1_VICKZ cd12358
RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds ...
 78-148 3.73e-03

RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found 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: 240804 [Multi-domain]  Cd Length: 73  Bit Score: 36.58  E-value: 3.73e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41053969  78 IQNLPKYIGFNDLKKFLNKHGINPHKIkLLGRQKFAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLAKPK 148
Cdd:cd12358   3 IGNLSSDVNESDLRQLFEEHKIPVSSV-LVKKGGYAFVDCPDQSWADKAIEKLNGKILQGKVIEVEHSVPK 72
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 112-147 5.03e-03

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: 36.07  E-value: 5.03e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 41053969 112 FAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLAKP 147
Cdd:cd12251  37 YAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLAKP 72
RRM2_La_like cd12292
RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 ...
 75-142 5.31e-03

RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins; This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409734 [Multi-domain]  Cd Length: 74  Bit Score: 36.14  E-value: 5.31e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41053969  75 KVEIQNLPKYIGFNDLKKFLNKHGINPHkIKLLGRQKFAFVTFKNQEERDKAMKAVHG---MQWKSNVLSV 142
Cdd:cd12292   3 ILKITGIGPSVSRDDLKELFKQFGEVEY-VDFTPGDDEGHVRFKTSEAAQKARDAYTGkleLNGKEWKLEI 72
PrmA pfam06325
Ribosomal protein L11 methyltransferase (PrmA); This family consists of several Ribosomal ...
 448-556 6.52e-03

Ribosomal protein L11 methyltransferase (PrmA); This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences.


Pssm-ID: 428888 [Multi-domain]  Cd Length: 294  Bit Score: 38.79  E-value: 6.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   448 EW--AQLDQDSTVLDVCCGTGTIGISLAK-RVKKVIGIELCQEAVKDAEANAKANGLTNvEFHCGKAEDVFPTILNAVVS 524
Cdd:pfam06325 153 EAleRLVKPGESVLDVGCGSGILAIAALKlGAKKVVGVDIDPVAVRAAKENAELNGVEA-RLEVYLPGDLPKEKADVVVA 231

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 41053969   525 pNvtaivdppraglhskvILA---IRKAEHLKRLV 556
Cdd:pfam06325 232 -N----------------ILAdplIELAPDIYALV 249
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 75-129 6.52e-03

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: 36.08  E-value: 6.52e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41053969  75 KVEIQNLPKYIGFNDLKKFLNKHG------INPHKIKLLGRQK--FAFVTFKNQEERDKAMKA 129
Cdd:cd12298   2 EIRVRNLDFELDEEALRGIFEKFGeiesinIPKKQKNRKGRHNngFAFVTFEDADSAESALQL 64
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 78-145 6.91e-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: 35.61  E-value: 6.91e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41053969  78 IQNLPKYIGFNDLKKFLNKHG--------INPHKiKLLGrqkFAFVTFKNQEERDKAMKAVHGMQWKSNVLSVRLA 145
Cdd:cd12414   4 VRNLPFKCTEDDLKKLFSKFGkvlevtipKKPDG-KLRG---FAFVQFTNVADAAKAIKGMNGKKIKGRPVAVDWA 75
Methyltransf_12 pfam08242
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 459-538 8.84e-03

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 400515 [Multi-domain]  Cd Length: 98  Bit Score: 36.19  E-value: 8.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41053969   459 LDVCCGTGTIGISLAKRVK--KVIGIELCQEAVKDAEANAKANGL---TNVEFHCGKAEDVFPTILNAVVSPNVTAIVDP 533
Cdd:pfam08242   1 LEIGCGTGTLLRALLEALPglEYTGLDISPAALEAARERLAALGLlnaVRVELFQLDLGELDPGSFDVVVASNVLHHLAD 80


                  ....*
gi 41053969   534 PRAGL 538
Cdd:pfam08242  81 PRAVL 85
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 70-136 9.00e-03

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: 35.67  E-value: 9.00e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 41053969  70 TSEIYkveIQNLPKYIGFNDLK----KFLNKHGINPHK--IKLL--GRQKF-AFVTFKNQEERDKAMKAVHGMQWK 136
Cdd:cd12239   1 SNRLY---VKNLSKRVSEKDLKyifgRFVDSSSEEKNMfdIRLMteGRMKGqAFITFPSEELAEKALNLTNGYVLH 73
 
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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