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Conserved domains on  [gi|1050396892|gb|OCT99081|]
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hypothetical protein XELAEV_18004872mg [Xenopus laevis]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 1027-1102 2.52e-37

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


:

Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 135.60  E-value: 2.52e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1050396892 1027 CVVLISNLPEGPMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLASK 1102
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 864-939 1.74e-27

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).


The actual alignment was detected with superfamily member cd12716:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 76  Bit Score: 107.48  E-value: 1.74e-27
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1050396892  864 TMIHVTNLPDSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMINNTRINLCLAGQ 939
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
PRK12678 super family cl36163
transcription termination factor Rho; Provisional
 1667-1896 7.84e-16

transcription termination factor Rho; Provisional


The actual alignment was detected with superfamily member PRK12678:

Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 83.80  E-value: 7.84e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1667 KGELSVTLT--LDSQKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSSPSESSNNLKSSAGSSQKKGGSRNVSSGSDKES 1744
Cdd:PRK12678    48 KGELIAAIKeaRGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQA 127

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1745 KFTQRSWERETRSSNKKDNRFRDDRSKEDRP-RDDRSKEERPRDDRSKEDRPRADRFKEDRPLDDRSKEERPRDDRSKED 1823
Cdd:PRK12678   128 RERRERGEAARRGAARKAGEGGEQPATEARAdAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRD 207

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1050396892 1824 RPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERskeDRPRDDRSKEERTRDDRAREDR 1896
Cdd:PRK12678   208 RREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDG---EGRGGRRGRRFRDRDRRGRRGG 277
Med15 super family cl26621
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 4-291 3.41e-12

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


The actual alignment was detected with superfamily member pfam09606:

Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 71.96  E-value: 3.41e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892    4 PRGGFPVQRQQQPGHPLLNQPNMNHPGMNLTGLNHPGMNLPNMNNPSlthpGMAPSGMNHPGMGhsGINQPGMNFNRMAH 83
Cdd:pfam09606  151 PGGQAGGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQQGPMG----GQMPPQMGVPGMP--GPADAGAQMGQQAQ 224

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892   84 PgmnQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQ-GGINPGGMNQGGMNQGdMGFHCEikGPGfaIRPH 162
Cdd:pfam09606  225 A---NGGMNPQQMGGAPNQVAMQQQQPQQQGQQSQLGMGINQMQQmPQGVGGGAGQGGPGQP-MGPPGQ--QPG--AMPN 296

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892  163 GMDPPGP----FLRGAPEPMGMKGM-----PLRAPMHGTPERPLG-------PQAFQQQRFGG--PSPVRPGPQRMQSHN 224
Cdd:pfam09606  297 VMSIGDQnnyqQQQTRQQQQQQGGNhpaahQQQMNQSVGQGGQVValgglnhLETWNPGNFGGlgANPMQRGQPGMMSSP 376

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1050396892  225 SDVAPGM------NLLMKQSPSDLLLGKDIPLHEPSrhvgnekqwePRGTFGHIPQPtGMKPVPSSQISDHQN 291
Cdd:pfam09606  377 SPVPGQQvrqvtpNQFMRQSPQPSVPSPQGPGSQPP----------QSHPGGMIPSP-ALIPSPSPQMSQQPA 438
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 1133-1206 1.14e-08

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


The actual alignment was detected with superfamily member cd12716:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 76  Bit Score: 53.94  E-value: 1.14e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1050396892 1133 VYLVDLPEKGYTESSVVCVGLRFGKVDHYAIFSNKRKAILHMCSASAAKAMHSFLTQYPCTIGENTVKSVLPSK 1206
Cdd:cd12716      3 VLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
PTZ00121 super family cl31754
MAEBL; Provisional
 1634-2136 7.16e-06

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 51.68  E-value: 7.16e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1634 VKSASEKSRDSSTDTKESLDKRNSGRTTKYNPQKGElsvtltldSQKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSSP 1713
Cdd:PTZ00121  1410 LKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKK--------ADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEE 1481

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1714 SESSNNLKSSAGSSQKKGGSRNVSSGSDKESKFTQRSWER----ETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDR 1789
Cdd:PTZ00121  1482 AKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAkkadEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAE 1561

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1790 SKEDRPRADRFKEDRPLDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKedrprddRSKEDRPR-DDLSKEDQDRPR 1868
Cdd:PTZ00121  1562 EKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAK-------KAEEAKIKaEELKKAEEEKKK 1634

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1869 DERSKEDRPRDDRSKEERTRDDRAREDRFKSSLTKQQRSSRSASHGKKSEKEQ---EDEFPFNLDEFVTVDEIVEEHGDA 1945
Cdd:PTZ00121  1635 VEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEkkaAEALKKEAEEAKKAEELKKKEAEE 1714

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1946 KKAEEQTDATYGINASR--KGKRKDNEpsplEAKKAKGRSPDPHvTKQDLSYVTLDEIVDEEDGTVGPQSNDSLGLAKE- 2022
Cdd:PTZ00121  1715 KKKAEELKKAEEENKIKaeEAKKEAEE----DKKKAEEAKKDEE-EKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEd 1789

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 2023 SKSLLTVDEVHAEVDQPSAKVPQGlmtldeiseeedGTRDSATTRAPLETPEDFVKEQLLTLDEVgGEEEEPITSESLSL 2102
Cdd:PTZ00121  1790 EKRRMEVDKKIKDIFDNFANIIEG------------GKEGNLVINDSKEMEDSAIKEVADSKNMQ-LEEADAFEKHKFNK 1856

                          490       500       510
                   ....*....|....*....|....*....|....*
gi 1050396892 2103 QATNPKDEENKAELN-DLDDKEIDLSKILEDPQVE 2136
Cdd:PTZ00121  1857 NNENGEDGNKEADFNkEKDLKEDDEEEIEEADEIE 1891
DUF6465 pfam20069
Family of unknown function (DUF6465); This family of proteins is functionally uncharacterized. ...
 944-1011 1.23e-04

Family of unknown function (DUF6465); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 117 and 173 amino acids in length. These proteins have a highly charged N-terminus.


:

Pssm-ID: 466279 [Multi-domain]  Cd Length: 130  Bit Score: 44.14  E-value: 1.23e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892  944 EKKDVTPASVAKTPVKTTTPPVNTAKAEAKTTKAEAKTTPKLDPKKGSANTKAARKAKVPDVIPPGFV 1011
Cdd:pfam20069    3 AKKAVAAAKAKAAKKAAKKAAKKKAAKKAKAAKAAKAAAKKAAAKKAAAKKTAAKKAKKAEVKEEVYV 70
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 2335-2369 2.10e-04

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


:

Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 40.31  E-value: 2.10e-04
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 1050396892  2335 QTGFFCELCSLFYINEPTKIKHCKSLRHYQSVEKH 2369
Cdd:smart00451    1 TGGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
rne super family cl35953
ribonuclease E; Reviewed
 1233-1394 5.03e-03

ribonuclease E; Reviewed


The actual alignment was detected with superfamily member PRK10811:

Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 42.33  E-value: 5.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1233 ETEEAQTADEMALKTLASNADSAAHNTFISTSIPVVAVIEPVVTclEEQSSAIEEESLTVVEQPSAVDEEAPaIMEEAPA 1312
Cdd:PRK10811   854 QVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEE--PVVVAEPQPEEVVVVETTHPEVIAAP-VTEQPQV 930

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1313 IMEEAPAIMEEAPVNMEEAQIPNEEATRLTNEEETGLASKEDMTLTNKEETFLTDKEETDQVEKEANEEEIYTIPKEETP 1392
Cdd:PRK10811   931 ITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEAT 1010


                   ..
gi 1050396892 1393 TF 1394
Cdd:PRK10811  1011 VE 1012
 
Name Accession Description Interval E-value
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 1027-1102 2.52e-37

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 135.60  E-value: 2.52e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1050396892 1027 CVVLISNLPEGPMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLASK 1102
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 864-939 1.74e-27

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 107.48  E-value: 1.74e-27
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1050396892  864 TMIHVTNLPDSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMINNTRINLCLAGQ 939
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 1667-1896 7.84e-16

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 83.80  E-value: 7.84e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1667 KGELSVTLT--LDSQKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSSPSESSNNLKSSAGSSQKKGGSRNVSSGSDKES 1744
Cdd:PRK12678    48 KGELIAAIKeaRGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQA 127

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1745 KFTQRSWERETRSSNKKDNRFRDDRSKEDRP-RDDRSKEERPRDDRSKEDRPRADRFKEDRPLDDRSKEERPRDDRSKED 1823
Cdd:PRK12678   128 RERRERGEAARRGAARKAGEGGEQPATEARAdAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRD 207

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1050396892 1824 RPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERskeDRPRDDRSKEERTRDDRAREDR 1896
Cdd:PRK12678   208 RREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDG---EGRGGRRGRRFRDRDRRGRRGG 277
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 4-291 3.41e-12

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 71.96  E-value: 3.41e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892    4 PRGGFPVQRQQQPGHPLLNQPNMNHPGMNLTGLNHPGMNLPNMNNPSlthpGMAPSGMNHPGMGhsGINQPGMNFNRMAH 83
Cdd:pfam09606  151 PGGQAGGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQQGPMG----GQMPPQMGVPGMP--GPADAGAQMGQQAQ 224

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892   84 PgmnQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQ-GGINPGGMNQGGMNQGdMGFHCEikGPGfaIRPH 162
Cdd:pfam09606  225 A---NGGMNPQQMGGAPNQVAMQQQQPQQQGQQSQLGMGINQMQQmPQGVGGGAGQGGPGQP-MGPPGQ--QPG--AMPN 296

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892  163 GMDPPGP----FLRGAPEPMGMKGM-----PLRAPMHGTPERPLG-------PQAFQQQRFGG--PSPVRPGPQRMQSHN 224
Cdd:pfam09606  297 VMSIGDQnnyqQQQTRQQQQQQGGNhpaahQQQMNQSVGQGGQVValgglnhLETWNPGNFGGlgANPMQRGQPGMMSSP 376

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1050396892  225 SDVAPGM------NLLMKQSPSDLLLGKDIPLHEPSrhvgnekqwePRGTFGHIPQPtGMKPVPSSQISDHQN 291
Cdd:pfam09606  377 SPVPGQQvrqvtpNQFMRQSPQPSVPSPQGPGSQPP----------QSHPGGMIPSP-ALIPSPSPQMSQQPA 438
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 1808-1900 4.77e-09

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 61.45  E-value: 4.77e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1808 DRSKEE-RPRDDRSKEDRPRDDRSKEDRPRDEH--------SKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPR 1878
Cdd:TIGR01642    6 DREREKsRGRDRDRSSERPRRRSRDRSRFRDRHrrsrersyREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85

                           90       100
                   ....*....|....*....|..
gi 1050396892 1879 DDRSKEERTRDDRAREDRFKSS 1900
Cdd:TIGR01642   86 RSIEQHRRRLRDRSPSNQWRKD 107
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 1133-1206 1.14e-08

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 53.94  E-value: 1.14e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1050396892 1133 VYLVDLPEKGYTESSVVCVGLRFGKVDHYAIFSNKRKAILHMCSASAAKAMHSFLTQYPCTIGENTVKSVLPSK 1206
Cdd:cd12716      3 VLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 862-927 2.25e-07

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 55.98  E-value: 2.25e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1050396892  862 PGTMIHVTNLPDsGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMI 927
Cdd:TIGR01649    1 PSPVVHVRNLPQ-DVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYI 65
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 1785-1891 8.25e-07

Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known.


Pssm-ID: 463734 [Multi-domain]  Cd Length: 98  Bit Score: 49.39  E-value: 8.25e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1785 PRDDRSKEDRPRADRFKEDRplDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDdlskEDQ 1864
Cdd:pfam12871    1 PRVSVLEDDLDEEEEEDEEE--DEEASDESERASLSRKRRSRSRRRSSTRDRSRSRSRSRSRDRRSRGTRDRR----RDR 74

                           90       100
                   ....*....|....*....|....*..
gi 1050396892 1865 DRPRDERSKEDRPRDDRSkeeRTRDDR 1891
Cdd:pfam12871   75 DRDRYRSLRSRSRDRSRD---RDRDRR 98
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 1722-1912 5.30e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.83  E-value: 5.30e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1722 SSAGSSQKKGGSRNVSSGSDKESKFTQRSWERETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDRSKEDRPRADRFK 1801
Cdd:NF033609   574 SNSDSGSDSGSDSTSDSGSDSASDSDSASDSDSASDSDSASDSDSASDSDSASDSDSASDSDSASDSDSDSDSDSDSDSD 653

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1802 EDRPLDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRDDR 1881
Cdd:NF033609   654 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 733

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1050396892 1882 SKEERTRDDRAREDRFKSSLTKQQRSSRSAS 1912
Cdd:NF033609   734 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 764
PTZ00121 PTZ00121
MAEBL; Provisional
 1634-2136 7.16e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 51.68  E-value: 7.16e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1634 VKSASEKSRDSSTDTKESLDKRNSGRTTKYNPQKGElsvtltldSQKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSSP 1713
Cdd:PTZ00121  1410 LKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKK--------ADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEE 1481

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1714 SESSNNLKSSAGSSQKKGGSRNVSSGSDKESKFTQRSWER----ETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDR 1789
Cdd:PTZ00121  1482 AKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAkkadEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAE 1561

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1790 SKEDRPRADRFKEDRPLDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKedrprddRSKEDRPR-DDLSKEDQDRPR 1868
Cdd:PTZ00121  1562 EKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAK-------KAEEAKIKaEELKKAEEEKKK 1634

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1869 DERSKEDRPRDDRSKEERTRDDRAREDRFKSSLTKQQRSSRSASHGKKSEKEQ---EDEFPFNLDEFVTVDEIVEEHGDA 1945
Cdd:PTZ00121  1635 VEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEkkaAEALKKEAEEAKKAEELKKKEAEE 1714

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1946 KKAEEQTDATYGINASR--KGKRKDNEpsplEAKKAKGRSPDPHvTKQDLSYVTLDEIVDEEDGTVGPQSNDSLGLAKE- 2022
Cdd:PTZ00121  1715 KKKAEELKKAEEENKIKaeEAKKEAEE----DKKKAEEAKKDEE-EKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEd 1789

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 2023 SKSLLTVDEVHAEVDQPSAKVPQGlmtldeiseeedGTRDSATTRAPLETPEDFVKEQLLTLDEVgGEEEEPITSESLSL 2102
Cdd:PTZ00121  1790 EKRRMEVDKKIKDIFDNFANIIEG------------GKEGNLVINDSKEMEDSAIKEVADSKNMQ-LEEADAFEKHKFNK 1856

                          490       500       510
                   ....*....|....*....|....*....|....*
gi 1050396892 2103 QATNPKDEENKAELN-DLDDKEIDLSKILEDPQVE 2136
Cdd:PTZ00121  1857 NNENGEDGNKEADFNkEKDLKEDDEEEIEEADEIE 1891
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 866-918 9.40e-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: 42.61  E-value: 9.40e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892  866 IHVTNLPdSGYTDQDILKIVQPFGKVCDILII-----RSKNEAFLETNFKEAAAAAVK 918
Cdd:pfam00076    1 LFVGNLP-PDTTEEDLKDLFSKFGPIKSIRLVrdetgRSKGFAFVEFEDEEDAEKAIE 57
DUF6465 pfam20069
Family of unknown function (DUF6465); This family of proteins is functionally uncharacterized. ...
 944-1011 1.23e-04

Family of unknown function (DUF6465); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 117 and 173 amino acids in length. These proteins have a highly charged N-terminus.


Pssm-ID: 466279 [Multi-domain]  Cd Length: 130  Bit Score: 44.14  E-value: 1.23e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892  944 EKKDVTPASVAKTPVKTTTPPVNTAKAEAKTTKAEAKTTPKLDPKKGSANTKAARKAKVPDVIPPGFV 1011
Cdd:pfam20069    3 AKKAVAAAKAKAAKKAAKKAAKKKAAKKAKAAKAAKAAAKKAAAKKAAAKKTAAKKAKKAEVKEEVYV 70
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 2335-2369 2.10e-04

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 40.31  E-value: 2.10e-04
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 1050396892  2335 QTGFFCELCSLFYINEPTKIKHCKSLRHYQSVEKH 2369
Cdd:smart00451    1 TGGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
MDN1 COG5271
Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal ...
 1754-2187 2.35e-04

Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis];


Pssm-ID: 444083 [Multi-domain]  Cd Length: 1028  Bit Score: 46.55  E-value: 2.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1754 ETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDRSKEDRPRADRFKEDRPLDDRSKEERPRDDRSKEDRPRDDRSKED 1833
Cdd:COG5271    382 DAAADEADAAADDSADDEEASADGGTSPTSDTDEEEEEADEDASAGETEDESTDVTSAEDDIATDEEADSLADEEEEAEA 461

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1834 RPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRDDRSKEERTRDDRAREDRFKSS-----------LT 1902
Cdd:COG5271    462 ELDTEEDTESAEEDADGDEATDEDDASDDGDEEEAEEDAEAEADSDELTAEETSADDGADTDAAADPedsdedaledeTE 541

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1903 KQQRSSRSASHGKKSEKEQEDEFPFNLDEFVTVDEIVEEHGDAKKAEEQTDATYGINASRKGKRKDNEPSPLEAKKAKGR 1982
Cdd:COG5271    542 GEENAPGSDQDADETDEPEATAEEDEPDEAEAETEDATENADADETEESADESEEAEASEDEAAEEEEADDDEADADADG 621

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1983 SPDPHVTKQDLSYVTLDEIVDEEDGTVGPQSNDSLGLAKESKSLLTVDEVHAEVDQPSAKVP-QGLMTLDEISEEEDGTR 2061
Cdd:COG5271    622 AADEEETEEEAAEDEAAEPETDASEAADEDADAETEAEASADESEEEAEDESETSSEDAEEDaDAAAAEASDDEEETEEA 701

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 2062 DSATTRAPLETPEDFVKEQLLTLDEVGGEEEEPITSESLSLQATNPKDEENKAELNDLDDKEIDLSKILE----DPQVED 2137
Cdd:COG5271    702 DEDAETASEEADAEEADTEADGTAEEAEEAAEEAESADEEAASLPDEADAEEEAEEAEEAEEDDADGLEEaleeEKADAE 781

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|
gi 1050396892 2138 QVTVDPKEQPLLTLDEVKGDDDTESIVDISFSEGNQFVTVDEIGEEEEDS 2187
Cdd:COG5271    782 EAATDEEAEAAAEEKEKVADEDQDTDEDALLDEAEADEEEDLDGEDEETA 831
III PHA00370
attachment protein
 80-147 3.31e-04

attachment protein


Pssm-ID: 164795 [Multi-domain]  Cd Length: 297  Bit Score: 45.29  E-value: 3.31e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892   80 RMAHPGMNQGGMNQGGMNQGGmNQGGMNQGGMNQGGmnQGGMNQGGMNQGGINPGGMNQGGMNQGDMG 147
Cdd:PHA00370    78 GSADKDGDGGGTGEGGSDTGG-DTGGGNTGGGSGGG--DTGGSGGGGSDGGGSEGGSTGKSLTKEGVG 142
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 1028-1185 2.16e-03

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 43.27  E-value: 2.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1028 VVLISNLPEGpMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLASKFKDLK 1107
Cdd:TIGR01649    4 VVHVRNLPQD-VVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKR 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1108 DEERIFAyliEQSPCKITPSVYEEFVYLVDLpEKGYTESSvvcvglRFGKVDHYAIF--SNKRKAILHMCSA-SAAKAMH 1184
Cdd:TIGR01649   83 DGNSDFD---SAGPNKVLRVIVENPMYPITL-DVLYQIFN------PYGKVLRIVTFtkNNVFQALVEFESVnSAQHAKA 152


                   .
gi 1050396892 1185 S 1185
Cdd:TIGR01649  153 A 153
penta_MxKDx TIGR02953
pentapeptide MXKDX repeat protein; Members of this protein family are small bacterial proteins, ...
 57-111 2.72e-03

pentapeptide MXKDX repeat protein; Members of this protein family are small bacterial proteins, each with an N-terminal signal sequence followed by up to 11 imperfect repeats of a pentapeptide. The pentapeptide repeat usually follows the form Met-Xaa-Lys-Asp-Xaa.


Pssm-ID: 131998 [Multi-domain]  Cd Length: 75  Bit Score: 38.67  E-value: 2.72e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892   57 APSGMNHPGMGHSGINQPGMNFNRMAHPGMNQGGMNQGGMNQGGMNQGGMNQGGM 111
Cdd:TIGR02953   21 AQDAMKKDTMKKDAMGKDAMAKDAMSKDAMKKDAMKKDAMKKDGMKKDAMKKDAM 75
YdjI COG4260
Membrane protease subunit, stomatin/prohibitin family, contains C-terminal Zn-ribbon domain ...
 85-151 2.93e-03

Membrane protease subunit, stomatin/prohibitin family, contains C-terminal Zn-ribbon domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443402 [Multi-domain]  Cd Length: 337  Bit Score: 42.15  E-value: 2.93e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1050396892   85 GMNQGGMNQGGMNQGGMnqgGMNQgGMNQGGMNQGGMNQGGMNQGginPGGMNQGGMNQGDMGFHCE 151
Cdd:COG4260    252 AMEAAASNEGGAAGAGM---GMGM-GMAMGGMMAQALQQPGQPQQ---QQPAAAAAAPAQDPGKFCA 311
rne PRK10811
ribonuclease E; Reviewed
 1233-1394 5.03e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 42.33  E-value: 5.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1233 ETEEAQTADEMALKTLASNADSAAHNTFISTSIPVVAVIEPVVTclEEQSSAIEEESLTVVEQPSAVDEEAPaIMEEAPA 1312
Cdd:PRK10811   854 QVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEE--PVVVAEPQPEEVVVVETTHPEVIAAP-VTEQPQV 930

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1313 IMEEAPAIMEEAPVNMEEAQIPNEEATRLTNEEETGLASKEDMTLTNKEETFLTDKEETDQVEKEANEEEIYTIPKEETP 1392
Cdd:PRK10811   931 ITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEAT 1010


                   ..
gi 1050396892 1393 TF 1394
Cdd:PRK10811  1011 VE 1012
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 1636-1872 6.40e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 41.82  E-value: 6.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1636 SASEKSRDSSTDTKESLDKRNSGRTTKYNPQKGELSVTLTLDSQKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSspse 1715
Cdd:NF033609   640 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD---- 715

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1716 ssnnlkSSAGSSQKKGGSRNVSSGSDKESKFTQRSWERETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDRSKEDRP 1795
Cdd:NF033609   716 ------SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 789

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1050396892 1796 RADRFKEDRPLDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERS 1872
Cdd:NF033609   790 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSESDSNSDSES 866
 
Name Accession Description Interval E-value
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 1027-1102 2.52e-37

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 135.60  E-value: 2.52e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1050396892 1027 CVVLISNLPEGPMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLASK 1102
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 864-939 1.74e-27

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 107.48  E-value: 1.74e-27
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1050396892  864 TMIHVTNLPDSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMINNTRINLCLAGQ 939
Cdd:cd12716      1 CVVLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
 866-938 9.59e-18

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region.


Pssm-ID: 409870 [Multi-domain]  Cd Length: 76  Bit Score: 79.69  E-value: 9.59e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1050396892  866 IHVTNLPDSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMINNTRINLCLAG 938
Cdd:cd12436      3 LYLTGLPVSKYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGKKVKVSVSQ 75
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 1667-1896 7.84e-16

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 83.80  E-value: 7.84e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1667 KGELSVTLT--LDSQKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSSPSESSNNLKSSAGSSQKKGGSRNVSSGSDKES 1744
Cdd:PRK12678    48 KGELIAAIKeaRGGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQA 127

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1745 KFTQRSWERETRSSNKKDNRFRDDRSKEDRP-RDDRSKEERPRDDRSKEDRPRADRFKEDRPLDDRSKEERPRDDRSKED 1823
Cdd:PRK12678   128 RERRERGEAARRGAARKAGEGGEQPATEARAdAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRD 207

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1050396892 1824 RPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERskeDRPRDDRSKEERTRDDRAREDR 1896
Cdd:PRK12678   208 RREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDG---EGRGGRRGRRFRDRDRRGRRGG 277
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 866-932 1.18e-14

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.


Pssm-ID: 409855 [Multi-domain]  Cd Length: 74  Bit Score: 70.68  E-value: 1.18e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1050396892  866 IHVTNLPDSGyTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMINNTRI 932
Cdd:cd12421      2 VHIRNLPPDA-TEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRGRPV 67
RRM2_MATR3 cd12715
RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...
 865-939 1.61e-14

RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the RRM2 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.


Pssm-ID: 410114 [Multi-domain]  Cd Length: 80  Bit Score: 70.63  E-value: 1.61e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892  865 MIHVTNLPDSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMINNTRINLCLAGQ 939
Cdd:cd12715      2 VIHLSNLPHSGYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKPLWFQGRCVKVDLSQK 76
RRM_RBM20 cd12685
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily ...
 865-932 3.80e-14

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily corresponds to the RRM of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM). It contains only one copy of RNA-recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410086 [Multi-domain]  Cd Length: 76  Bit Score: 69.58  E-value: 3.80e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892  865 MIHVTNLPDSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMINNTRI 932
Cdd:cd12685      2 VVHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAYTEAAQAMVQYYQEKPAMINEEKL 69
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 4-291 3.41e-12

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 71.96  E-value: 3.41e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892    4 PRGGFPVQRQQQPGHPLLNQPNMNHPGMNLTGLNHPGMNLPNMNNPSlthpGMAPSGMNHPGMGhsGINQPGMNFNRMAH 83
Cdd:pfam09606  151 PGGQAGGMMQPSSGQPGSGTPNQMGPNGGPGQGQAGGMNGGQQGPMG----GQMPPQMGVPGMP--GPADAGAQMGQQAQ 224

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892   84 PgmnQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQ-GGINPGGMNQGGMNQGdMGFHCEikGPGfaIRPH 162
Cdd:pfam09606  225 A---NGGMNPQQMGGAPNQVAMQQQQPQQQGQQSQLGMGINQMQQmPQGVGGGAGQGGPGQP-MGPPGQ--QPG--AMPN 296

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892  163 GMDPPGP----FLRGAPEPMGMKGM-----PLRAPMHGTPERPLG-------PQAFQQQRFGG--PSPVRPGPQRMQSHN 224
Cdd:pfam09606  297 VMSIGDQnnyqQQQTRQQQQQQGGNhpaahQQQMNQSVGQGGQVValgglnhLETWNPGNFGGlgANPMQRGQPGMMSSP 376

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1050396892  225 SDVAPGM------NLLMKQSPSDLLLGKDIPLHEPSrhvgnekqwePRGTFGHIPQPtGMKPVPSSQISDHQN 291
Cdd:pfam09606  377 SPVPGQQvrqvtpNQFMRQSPQPSVPSPQGPGSQPP----------QSHPGGMIPSP-ALIPSPSPQMSQQPA 438
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 1731-1911 1.14e-10

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 66.85  E-value: 1.14e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1731 GGSRNVSSGSDKESKFTQRSWERETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDRSKEDRPRADRFKEDRPLDDRS 1810
Cdd:PRK12678    60 GGGAAAAAATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARR 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1811 KEERPRDDRSKEDRPRDDRSKEDRPRDEhsKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRDDRSKEERTRDD 1890
Cdd:PRK12678   140 GAARKAGEGGEQPATEARADAAERTEEE--ERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREE 217

                          170       180
                   ....*....|....*....|.
gi 1050396892 1891 RAREDRFKSSLTKQQRSSRSA 1911
Cdd:PRK12678   218 RGRRDGGDRRGRRRRRDRRDA 238
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 1679-1895 1.66e-10

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 66.47  E-value: 1.66e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1679 QKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSSPSESSNNLKSSAGSSQKKGGSRNVSSGSDKESKFTQRSWERETRSS 1758
Cdd:PRK12678    87 ARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEE 166

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1759 NKKDNRfRDDRSKEDRPRDDRSKEERPRDDRSKEDRpradrfkedrplDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDE 1838
Cdd:PRK12678   167 EERDER-RRRGDREDRQAEAERGERGRREERGRDGD------------DRDRRDRREQGDRREERGRRDGGDRRGRRRRR 233

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1050396892 1839 HSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRDDRSKEERTRDDRARED 1895
Cdd:PRK12678   234 DRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNEREPELRED 290
RRM1_PTBP1 cd12777
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...
 865-928 1.63e-09

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM1 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution.


Pssm-ID: 410169 [Multi-domain]  Cd Length: 81  Bit Score: 56.53  E-value: 1.63e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892  865 MIHVTNLPdSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVK-FSETTPVMIN 928
Cdd:cd12777      2 VIHVRKLP-NDVTEAEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNyYTSVTPVLRG 65
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 10-242 2.77e-09

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 62.72  E-value: 2.77e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892   10 VQRQQQPGHPLLNQPNMNHPGMNLTGLNHPGMNLPNMNNPSLTHPGmAPSG--MNHPGMGHSGINQPGMNFNRMAHPGMN 87
Cdd:pfam09606   62 QPQGGQGNGGMGGGQQGMPDPINALQNLAGQGTRPQMMGPMGPGPG-GPMGqqMGGPGTASNLLASLGRPQMPMGGAGFP 140

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892   88 QGGMNQGGMNQGGMNQGGMnQGGMNQGGmnQGGMNQGGMNQGGINP--GGMNQGGMN--QGDMGFHCEIKGPGFAIRPHG 163
Cdd:pfam09606  141 SQMSRVGRMQPGGQAGGMM-QPSSGQPG--SGTPNQMGPNGGPGQGqaGGMNGGQQGpmGGQMPPQMGVPGMPGPADAGA 217

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892  164 MDPPGPFLRGAPEPMGMKGMPLRAPMHGTPErplGPQAFQQQRFGGPSPVRPGPQRMQSHNSDVAPGMNL-LMKQSPSDL 242
Cdd:pfam09606  218 QMGQQAQANGGMNPQQMGGAPNQVAMQQQQP---QQQGQQSQLGMGINQMQQMPQGVGGGAGQGGPGQPMgPPGQQPGAM 294
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
 1028-1102 3.12e-09

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region.


Pssm-ID: 409870 [Multi-domain]  Cd Length: 76  Bit Score: 55.43  E-value: 3.12e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892 1028 VVLISNLPEGPMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLASK 1102
Cdd:cd12436      2 VLYLTGLPVSKYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGKKVKVSVSQK 76
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 1808-1900 4.77e-09

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 61.45  E-value: 4.77e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1808 DRSKEE-RPRDDRSKEDRPRDDRSKEDRPRDEH--------SKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPR 1878
Cdd:TIGR01642    6 DREREKsRGRDRDRSSERPRRRSRDRSRFRDRHrrsrersyREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSV 85

                           90       100
                   ....*....|....*....|..
gi 1050396892 1879 DDRSKEERTRDDRAREDRFKSS 1900
Cdd:TIGR01642   86 RSIEQHRRRLRDRSPSNQWRKD 107
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 1723-1906 4.81e-09

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 61.84  E-value: 4.81e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1723 SAGSSQKKGGSRNVSSGSDKESKFTQRSWERETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDRSKEdrprADRFKE 1802
Cdd:PRK12678    75 AAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARK----AGEGGE 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1803 DRPLDDRSkEERPRDDRSKEDRPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRprDDRS 1882
Cdd:PRK12678   151 QPATEARA-DAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDG--GDRR 227

                          170       180
                   ....*....|....*....|....
gi 1050396892 1883 KEERTRDDRAREDRFKSSLTKQQR 1906
Cdd:PRK12678   228 GRRRRRDRRDARGDDNREDRGDRD 251
Cytadhesin_P30 pfam07271
Cytadhesin P30/P32; This family consists of several Mycoplasma species specific Cytadhesin P32 ...
 2-120 8.91e-09

Cytadhesin P30/P32; This family consists of several Mycoplasma species specific Cytadhesin P32 and P30 proteins. P30 has been found to be membrane associated and localized on the tip organelle. It is thought that it is important in cytadherence and virulence. The N-terminus contains two predicted transmembrane helices followed by a long region of a short 6 residue proline rich repeat.


Pssm-ID: 429374 [Multi-domain]  Cd Length: 275  Bit Score: 59.21  E-value: 8.91e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892    2 FNP----RGGFPVQ--RQQQPG---HPLLNqPNMNHPGMNltglNHPGMN-LPNMNNPsltHPGMAPSGMNHPGMGHSGi 71
Cdd:pfam07271  161 FGPnpqqRIGFPMQpnMGMRPGfnqMPGMP-PNQMRPGFN----QMPGMPpRPGFPNP---MPNMQPRPGFRPQPGPMG- 231

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1050396892   72 NQPGMNFNrmaHPGMnqgGMNQGGMNQGGMNQ-GGMNqgGMNQGGMNQGG 120
Cdd:pfam07271  232 NRPGGGFP---HPGT---PMGPNRMPNPGMNQrPGMA--PPRPGFPPQNG 273
RRM1_2_NP220 cd12716
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); ...
 1133-1206 1.14e-08

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220); This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410115 [Multi-domain]  Cd Length: 76  Bit Score: 53.94  E-value: 1.14e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1050396892 1133 VYLVDLPEKGYTESSVVCVGLRFGKVDHYAIFSNKRKAILHMCSASAAKAMHSFLTQYPCTIGENTVKSVLPSK 1206
Cdd:cd12716      3 VLISNLPEKGYTVEEISNLAKPFGGVNDILILSSHKKAYLEMNFKEAVDSMVKYYETFPVLVGGKRLKISMAEK 76
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 1779-1891 1.76e-08

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 59.55  E-value: 1.76e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1779 RSKE-ERPRDDRSKEDR-PRADRFKE---DRPLDDRSKEERPRDDRSKEDRPRDD--RSKEDRPRD-EHSKEDRPRddRS 1850
Cdd:TIGR01622    3 RDRErERLRDSSSAGDRdRRRDKGRErsrDRSRDRERSRSRRRDRHRDRDYYRGRerRSRSRRPNRrYRPREKRRR--RG 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1050396892 1851 KEDRPRDDLskedqDRPRDERSKEDRPRDDRSKEERtRDDR 1891
Cdd:TIGR01622   81 DSYRRRRDD-----RRSRREKPRARDGTPEPLTEDE-RDRR 115
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 1768-1873 3.06e-08

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 58.75  E-value: 3.06e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1768 DRSKED-RPRDDRSKEERPRDDRSKEDRPRaDRFKEDRPlDDRSKEERPRDDRSKEDRPR--DDRSKEDRPRDEHSKEDR 1844
Cdd:TIGR01642    6 DREREKsRGRDRDRSSERPRRRSRDRSRFR-DRHRRSRE-RSYREDSRPRDRRRYDSRSPrsLRYSSVRRSRDRPRRRSR 83

                           90       100
                   ....*....|....*....|....*....
gi 1050396892 1845 PRDDRSKEDRPRDDLSKEDQDRPRDERSK 1873
Cdd:TIGR01642   84 SVRSIEQHRRRLRDRSPSNQWRKDDKKRS 112
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 1818-1937 4.74e-08

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 58.37  E-value: 4.74e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1818 DRSKED-RPRDDRSKEDRPRD-EHSK-EDRPRDDRSKEDRPRDDlskedqDRPRDERSKEDRPR--DDRSKEERTRDDRA 1892
Cdd:TIGR01642    6 DREREKsRGRDRDRSSERPRRrSRDRsRFRDRHRRSRERSYRED------SRPRDRRRYDSRSPrsLRYSSVRRSRDRPR 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1050396892 1893 REDRFKSSLTKQQRSSR--SASHGKKSEKEQEDEFPFNLDEFVTVDE 1937
Cdd:TIGR01642   80 RRSRSVRSIEQHRRRLRdrSPSNQWRKDDKKRSLWDIKPPGYELVTA 126
RRM_RBM20 cd12685
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily ...
 1133-1196 6.10e-08

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily corresponds to the RRM of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM). It contains only one copy of RNA-recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410086 [Multi-domain]  Cd Length: 76  Bit Score: 51.86  E-value: 6.10e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1050396892 1133 VYLVDLPEKGYTESSVVCVGLRFGKVDHYAIFSNKRKAILHMCSASAAKAMHSFLTQYPCTIGE 1196
Cdd:cd12685      3 VHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAYTEAAQAMVQYYQEKPAMINE 66
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 1756-1896 1.08e-07

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 57.24  E-value: 1.08e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1756 RSSNKKDNRFRDDRSKEDRPRDDRSKEERPRD---DRSKEDRPRADRFKEDRPLDDRSKEERPRDDRSKEdRPRDDRSKE 1832
Cdd:TIGR01622    1 RYRDRERERLRDSSSAGDRDRRRDKGRERSRDrsrDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRY-RPREKRRRR 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1050396892 1833 DRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQdrpRDERS-------KEDRPRDDR---SKEERTRDDRAREDR 1896
Cdd:TIGR01622   80 GDSYRRRRDDRRSRREKPRARDGTPEPLTEDE---RDRRTvfvqqlaARARERDLYeffSKVGKVRDVQIIKDR 150
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 16-237 1.20e-07

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 57.33  E-value: 1.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892   16 PGHPLLNQpnMNHPGMNLTGLNHPGMNLPNMNNPSLTHPGMAPSGM----NHPGMGHSGINQPGMNFNRMAHPGMNQGGM 91
Cdd:pfam09606  106 PGGPMGQQ--MGGPGTASNLLASLGRPQMPMGGAGFPSQMSRVGRMqpggQAGGMMQPSSGQPGSGTPNQMGPNGGPGQG 183

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892   92 NQGGMNQG-GMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGINPGGMNQGGMNQGD----MGFHCEIKGPGFAIRPHGMDP 166
Cdd:pfam09606  184 QAGGMNGGqQGPMGGQMPPQMGVPGMPGPADAGAQMGQQAQANGGMNPQQMGGAPnqvaMQQQQPQQQGQQSQLGMGINQ 263

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050396892  167 PGPFLRGAP--EPMGMKGMPLRAPMHGTPERPLG-----PQAFQQQRfggpspVRPGPQRMQSHNSDVAPG-MNLLMKQ 237
Cdd:pfam09606  264 MQQMPQGVGggAGQGGPGQPMGPPGQQPGAMPNVmsigdQNNYQQQQ------TRQQQQQQGGNHPAAHQQqMNQSVGQ 336
RRM1_PTBP1_like cd12688
RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
 865-928 1.27e-07

RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM1 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and functions at several aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein and negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410089 [Multi-domain]  Cd Length: 81  Bit Score: 51.16  E-value: 1.27e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892  865 MIHVTNLPdSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVK-FSETTPVMIN 928
Cdd:cd12688      2 VLHIRKLP-CDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMATEEAAVTMVNyYTPVTPHLRS 65
RRM_RBM20 cd12685
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily ...
 1028-1102 1.32e-07

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20); This subfamily corresponds to the RRM of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM). It contains only one copy of RNA-recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410086 [Multi-domain]  Cd Length: 76  Bit Score: 50.70  E-value: 1.32e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892 1028 VVLISNLPEGPMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLASK 1102
Cdd:cd12685      2 VVHICNLPEGSCTENDVINLGLPFGKVTNYILMRSTNQAFLEMAYTEAAQAMVQYYQEKPAMINEEKLLIRMSKR 76
RRM1_PTBP2 cd12778
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 ...
 865-928 1.38e-07

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM1 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410170 [Multi-domain]  Cd Length: 82  Bit Score: 51.22  E-value: 1.38e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892  865 MIHVTNLPDSgYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVK-FSETTPVMIN 928
Cdd:cd12778      3 VLHIRKLPGE-VTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNyYTAVTPHLRN 66
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 1732-1850 1.72e-07

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 56.47  E-value: 1.72e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1732 GSRNVSSGSDKESKFTQRSWERETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDD--RSKEDRPRadrfKEDRPLDDR 1809
Cdd:TIGR01622    1 RYRDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRerRSRSRRPN----RRYRPREKR 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1050396892 1810 SKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKEDRpRDDRS 1850
Cdd:TIGR01622   77 RRRGDSYRRRRDDRRSRREKPRARDGTPEPLTEDE-RDRRT 116
RRM1_hnRNPL_like cd12689
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 862-929 1.88e-07

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410090 [Multi-domain]  Cd Length: 80  Bit Score: 50.35  E-value: 1.88e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892  862 PGTMIHVTNLPDsGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMINN 929
Cdd:cd12689      1 PSPVVHVRGLSE-HVTEADLVEALQNFGPISYVTMMPKKRQALVEFEDIEGAKACVNYAQQNPIYVGG 67
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 862-927 2.25e-07

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 55.98  E-value: 2.25e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1050396892  862 PGTMIHVTNLPDsGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMI 927
Cdd:TIGR01649    1 PSPVVHVRNLPQ-DVVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYI 65
RRM1_ROD1 cd12779
RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This ...
 860-929 2.47e-07

RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM1 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein that negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities.


Pssm-ID: 410171 [Multi-domain]  Cd Length: 90  Bit Score: 50.41  E-value: 2.47e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892  860 SNPGTMIHVTNLPdSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMINN 929
Cdd:cd12779      2 CSPSRVLHIRKIP-NDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMASEEAAVTMVNYYTTVTPHLRN 70
RRM1_MATR3 cd12714
RNA recognition motif 1 (RRM1) found in vertebrate matrin-3; This subgroup corresponds to the ...
 865-927 2.69e-07

RNA recognition motif 1 (RRM1) found in vertebrate matrin-3; This subgroup corresponds to the RRM1 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.


Pssm-ID: 410113 [Multi-domain]  Cd Length: 76  Bit Score: 49.93  E-value: 2.69e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1050396892  865 MIHVTNLPDSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETTPVMI 927
Cdd:cd12714      2 VVHIMDFQRGKNLRYQLLQLAEPFGIITNHLILNKINEAFIEMATTEEAQAAVDYYMTTPALV 64
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 1809-1924 3.11e-07

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 55.70  E-value: 3.11e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1809 RSKE-ERPRDDRSKEDRPRDdrskedRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRdDRSKEERT 1887
Cdd:TIGR01622    3 RDRErERLRDSSSAGDRDRR------RDKGRERSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPN-RRYRPREK 75

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1050396892 1888 RDDRAREDRFKSSLTKQQRSSRSASHGKKsEKEQEDE 1924
Cdd:TIGR01622   76 RRRRGDSYRRRRDDRRSRREKPRARDGTP-EPLTEDE 111
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
 864-943 4.51e-07

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 49.20  E-value: 4.51e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892  864 TMIHVTNLPdSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVkfsettpVMINNTRINlclaGQKVEC 943
Cdd:cd12354      1 TTVYVGNIT-KGLTEALLQQTFSPFGQILEVRVFPDKGYAFIRFDSHEAATHAI-------VSVNGTIIN----GQAVKC 68
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 1834-1926 5.24e-07

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 54.93  E-value: 5.24e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1834 RPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRDDRSKEERTRdDRAREDRFKSSLTKQQRSSRSASH 1913
Cdd:TIGR01622    1 RYRDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYR-GRERRSRSRRPNRRYRPREKRRRR 79

                           90
                   ....*....|...
gi 1050396892 1914 GKKSEKEQEDEFP 1926
Cdd:TIGR01622   80 GDSYRRRRDDRRS 92
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 1785-1891 8.25e-07

Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known.


Pssm-ID: 463734 [Multi-domain]  Cd Length: 98  Bit Score: 49.39  E-value: 8.25e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1785 PRDDRSKEDRPRADRFKEDRplDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDdlskEDQ 1864
Cdd:pfam12871    1 PRVSVLEDDLDEEEEEDEEE--DEEASDESERASLSRKRRSRSRRRSSTRDRSRSRSRSRSRDRRSRGTRDRR----RDR 74

                           90       100
                   ....*....|....*....|....*..
gi 1050396892 1865 DRPRDERSKEDRPRDDRSkeeRTRDDR 1891
Cdd:pfam12871   75 DRDRYRSLRSRSRDRSRD---RDRDRR 98
RRM2_MATR3 cd12715
RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...
 1028-1106 9.90e-07

RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the RRM2 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.


Pssm-ID: 410114 [Multi-domain]  Cd Length: 80  Bit Score: 48.68  E-value: 9.90e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050396892 1028 VVLISNLPEGPMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLASKFKDL 1106
Cdd:cd12715      2 VIHLSNLPHSGYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAMVDHCKKKPLWFQGRCVKVDLSQKYKTL 80
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 1766-1924 1.84e-06

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 53.37  E-value: 1.84e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1766 RDDRSKEDRPRDDRSKEERPRDDRSKEDRPRADRFKEDRPLDDRSKEERPRDDRSKEDRpRDDRSKEDRPRDEHSKEDRP 1845
Cdd:PRK12678    80 AARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAAR-RGAARKAGEGGEQPATEARA 158

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050396892 1846 RDDRSKEDRPRDDLSKEDQDRPRDERSkEDRPRDDRSKEERTRDDRAREDRFKSSLTKQQRSSRSASHGKKSEKEQEDE 1924
Cdd:PRK12678   159 DAAERTEEEERDERRRRGDREDRQAEA-ERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRR 236
RRM1_2_MATR3_like cd12436
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; ...
 1133-1206 2.21e-06

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins; This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region.


Pssm-ID: 409870 [Multi-domain]  Cd Length: 76  Bit Score: 47.34  E-value: 2.21e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1050396892 1133 VYLVDLPEKGYTESSVVCVGLRFGKVDHYAIFSNKRKAILHMCSASAAKAMHSFLTQYPCTIGENTVKSVLPSK 1206
Cdd:cd12436      3 LYLTGLPVSKYSEEDVLKLAEPFGKVNNVLLIRSKREAFIEMETAEDAQAMLSYCKTKPITIKGKKVKVSVSQK 76
PTZ00121 PTZ00121
MAEBL; Provisional
 1740-1979 2.25e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 53.61  E-value: 2.25e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1740 SDKESKFTQRSWERETRSSNKKDNRFRDDRSKED-RPRDDRSKEE---RPRDDRSKEDRPRAD---RFKEDRPLDDRSKE 1812
Cdd:PTZ00121  1075 SYKDFDFDAKEDNRADEATEEAFGKAEEAKKTETgKAEEARKAEEakkKAEDARKAEEARKAEdarKAEEARKAEDAKRV 1154

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1813 ERPRddRSKEDRprddRSKEDRPRDEHSKEDRPRddRSKEDRPRDDLSKEDQDRprdeRSKEDRPRDDRSKEERTRddRA 1892
Cdd:PTZ00121  1155 EIAR--KAEDAR----KAEEARKAEDAKKAEAAR--KAEEVRKAEELRKAEDAR----KAEAARKAEEERKAEEAR--KA 1220

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1893 REDRFKSSLTKQQRSSRSASHGKKSEKEQEDEFPFNLDEFVTVDEI-------VEEHGDA---KKAEEQTDATYGINASR 1962
Cdd:PTZ00121  1221 EDAKKAEAVKKAEEAKKDAEEAKKAEEERNNEEIRKFEEARMAHFArrqaaikAEEARKAdelKKAEEKKKADEAKKAEE 1300

                          250
                   ....*....|....*..
gi 1050396892 1963 KGKRKDNEPSPLEAKKA 1979
Cdd:PTZ00121  1301 KKKADEAKKKAEEAKKA 1317
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 1833-1928 2.27e-06

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 52.97  E-value: 2.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1833 DRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPR-DDRSKEERTRDDRA----REDRFKSSLTKQQRS 1907
Cdd:TIGR01642    2 DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYReDSRPRDRRRYDSRSprslRYSSVRRSRDRPRRR 81

                           90       100
                   ....*....|....*....|.
gi 1050396892 1908 SRSASHGKKSEKEQEDEFPFN 1928
Cdd:TIGR01642   82 SRSVRSIEQHRRRLRDRSPSN 102
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 1768-1924 3.57e-06

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 52.21  E-value: 3.57e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1768 DRSKEDRPRDDRSKEERPRDDRSKEDRPRADRFKEDRPLDDRSKEERPRDDrskEDRPRDDRSKEDRPRDEHSKEDRPRD 1847
Cdd:PRK12678    68 ATPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEA---ASAPEAAQARERRERGEAARRGAARK 144

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1848 -DRSKEDRPRDDLSKEDQDRPRDERSKE--DRPRDDRsKEERTRDDRAREDRFKSSLTKQQRSSRSASHGKKSEKEQEDE 1924
Cdd:PRK12678   145 aGEGGEQPATEARADAAERTEEEERDERrrRGDREDR-QAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDG 223
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 1028-1092 5.11e-06

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.


Pssm-ID: 409855 [Multi-domain]  Cd Length: 74  Bit Score: 46.41  E-value: 5.11e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892 1028 VVLISNLPEgPMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGG 1092
Cdd:cd12421      1 VVHIRNLPP-DATEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRG 64
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 1722-1912 5.30e-06

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 51.83  E-value: 5.30e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1722 SSAGSSQKKGGSRNVSSGSDKESKFTQRSWERETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDRSKEDRPRADRFK 1801
Cdd:NF033609   574 SNSDSGSDSGSDSTSDSGSDSASDSDSASDSDSASDSDSASDSDSASDSDSASDSDSASDSDSASDSDSDSDSDSDSDSD 653

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1802 EDRPLDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRDDR 1881
Cdd:NF033609   654 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 733

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1050396892 1882 SKEERTRDDRAREDRFKSSLTKQQRSSRSAS 1912
Cdd:NF033609   734 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDS 764
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 1635-1859 6.58e-06

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 51.44  E-value: 6.58e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1635 KSASEKSRDSSTDTKESLDKRNSGRTTKYNPQKGELSVTLTLDSQKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSSPS 1714
Cdd:PRK12678    69 TPAAPAAAARRAARAAAAARQAEQPAAEAAAAKAEAAPAARAAAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEG 148

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1715 ESSNNLKSSAGSSQKKGGSRNVSS---GSDKESKFTQRSWERETRSSNKKDNrfRDDRSKEDRPRDDRSKEERPRDDRSK 1791
Cdd:PRK12678   149 GEQPATEARADAAERTEEEERDERrrrGDREDRQAEAERGERGRREERGRDG--DDRDRRDRREQGDRREERGRRDGGDR 226

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1050396892 1792 EDRPRADRFKEDRplDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDE-HSKEDRPRDDRSKEDRPRDDL 1859
Cdd:PRK12678   227 RGRRRRRDRRDAR--GDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRrGRRGGDGGNEREPELREDDVL 293
PTZ00121 PTZ00121
MAEBL; Provisional
 1634-2136 7.16e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 51.68  E-value: 7.16e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1634 VKSASEKSRDSSTDTKESLDKRNSGRTTKYNPQKGElsvtltldSQKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSSP 1713
Cdd:PTZ00121  1410 LKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKK--------ADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEE 1481

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1714 SESSNNLKSSAGSSQKKGGSRNVSSGSDKESKFTQRSWER----ETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDR 1789
Cdd:PTZ00121  1482 AKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAkkadEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAE 1561

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1790 SKEDRPRADRFKEDRPLDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKedrprddRSKEDRPR-DDLSKEDQDRPR 1868
Cdd:PTZ00121  1562 EKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAK-------KAEEAKIKaEELKKAEEEKKK 1634

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1869 DERSKEDRPRDDRSKEERTRDDRAREDRFKSSLTKQQRSSRSASHGKKSEKEQ---EDEFPFNLDEFVTVDEIVEEHGDA 1945
Cdd:PTZ00121  1635 VEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEkkaAEALKKEAEEAKKAEELKKKEAEE 1714

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1946 KKAEEQTDATYGINASR--KGKRKDNEpsplEAKKAKGRSPDPHvTKQDLSYVTLDEIVDEEDGTVGPQSNDSLGLAKE- 2022
Cdd:PTZ00121  1715 KKKAEELKKAEEENKIKaeEAKKEAEE----DKKKAEEAKKDEE-EKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEd 1789

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 2023 SKSLLTVDEVHAEVDQPSAKVPQGlmtldeiseeedGTRDSATTRAPLETPEDFVKEQLLTLDEVgGEEEEPITSESLSL 2102
Cdd:PTZ00121  1790 EKRRMEVDKKIKDIFDNFANIIEG------------GKEGNLVINDSKEMEDSAIKEVADSKNMQ-LEEADAFEKHKFNK 1856

                          490       500       510
                   ....*....|....*....|....*....|....*
gi 1050396892 2103 QATNPKDEENKAELN-DLDDKEIDLSKILEDPQVE 2136
Cdd:PTZ00121  1857 NNENGEDGNKEADFNkEKDLKEDDEEEIEEADEIE 1891
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 1824-1931 7.69e-06

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 51.07  E-value: 7.69e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1824 RPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRdDRSKEERTRDDRAREDRFKSSLTK 1903
Cdd:TIGR01622    1 RYRDRERERLRDSSSAGDRDRRRDKGRERSRDRSRDRERSRSRRRDRHRDRDYYR-GRERRSRSRRPNRRYRPREKRRRR 79

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1050396892 1904 QQRSSR---SASHGKKSEKEqEDEFPFNLDE 1931
Cdd:TIGR01622   80 GDSYRRrrdDRRSRREKPRA-RDGTPEPLTE 109
RRM2_MATR3 cd12715
RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the ...
 1133-1183 1.31e-05

RNA recognition motif 2 (RRM2) found in vertebrate matrin-3; This subgroup corresponds to the RRM2 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1.


Pssm-ID: 410114 [Multi-domain]  Cd Length: 80  Bit Score: 45.21  E-value: 1.31e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1050396892 1133 VYLVDLPEKGYTESSVVCVGLRFGKVDHYAIFSNKRKAILHMCSASAAKAM 1183
Cdd:cd12715      3 IHLSNLPHSGYSDAAVLKLAEPYGKVKNYILMRMKNQAFLEMESREDAMAM 53
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 1795-1896 1.71e-05

Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known.


Pssm-ID: 463734 [Multi-domain]  Cd Length: 98  Bit Score: 45.54  E-value: 1.71e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1795 PRADRFKEDrpLDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRderske 1874
Cdd:pfam12871    1 PRVSVLEDD--LDEEEEEDEEEDEEASDESERASLSRKRRSRSRRRSSTRDRSRSRSRSRSRDRRSRGTRDRRR------ 72

                           90       100
                   ....*....|....*....|....*.
gi 1050396892 1875 DRPRD-DRSKEERTRD---DRAREDR 1896
Cdd:pfam12871   73 DRDRDrYRSLRSRSRDrsrDRDRDRR 98
RRM1_PTBPH3 cd12687
RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 ...
 865-923 3.05e-05

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subfamily corresponds to the RRM1 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410088 [Multi-domain]  Cd Length: 75  Bit Score: 44.09  E-value: 3.05e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1050396892  865 MIHVTNLpDSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAVKFSETT 923
Cdd:cd12687      2 VLHVRNV-GHEISENDLLQLAQPFGVVTKLVMLRAKNQALLQMQDVSAAISALQFYTSV 59
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 1727-1838 4.94e-05

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


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 48.38  E-value: 4.94e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1727 SQKKGGSRNVSSGSDKE---SKFTQRSWEREtRSSNKKDNRFRDDRSKEDRPRDdRSKEERPRDDRSKEdRPRADRFKED 1803
Cdd:TIGR01622    4 DRERERLRDSSSAGDRDrrrDKGRERSRDRS-RDRERSRSRRRDRHRDRDYYRG-RERRSRSRRPNRRY-RPREKRRRRG 80

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1050396892 1804 RPLDDRSKEERPRDDRSKEDRPRDDRSKEDRpRDE 1838
Cdd:TIGR01622   81 DSYRRRRDDRRSRREKPRARDGTPEPLTEDE-RDR 114
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 866-918 9.40e-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: 42.61  E-value: 9.40e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892  866 IHVTNLPdSGYTDQDILKIVQPFGKVCDILII-----RSKNEAFLETNFKEAAAAAVK 918
Cdd:pfam00076    1 LFVGNLP-PDTTEEDLKDLFSKFGPIKSIRLVrdetgRSKGFAFVEFEDEEDAEKAIE 57
DUF6465 pfam20069
Family of unknown function (DUF6465); This family of proteins is functionally uncharacterized. ...
 944-1011 1.23e-04

Family of unknown function (DUF6465); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 117 and 173 amino acids in length. These proteins have a highly charged N-terminus.


Pssm-ID: 466279 [Multi-domain]  Cd Length: 130  Bit Score: 44.14  E-value: 1.23e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892  944 EKKDVTPASVAKTPVKTTTPPVNTAKAEAKTTKAEAKTTPKLDPKKGSANTKAARKAKVPDVIPPGFV 1011
Cdd:pfam20069    3 AKKAVAAAKAKAAKKAAKKAAKKKAAKKAKAAKAAKAAAKKAAAKKAAAKKTAAKKAKKAEVKEEVYV 70
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 1745-1867 1.82e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 46.81  E-value: 1.82e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1745 KFTQRSWER-ETRSSNKKDNRFRDDRSKEDRPRDdRSKEERPRdDRSKEDRPRaDRFKEDrplddrsKEERPRDDRSKED 1823
Cdd:TIGR01642    3 EEPDREREKsRGRDRDRSSERPRRRSRDRSRFRD-RHRRSRER-SYREDSRPR-DRRRYD-------SRSPRSLRYSSVR 72

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1050396892 1824 RPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQ-DRP 1867
Cdd:TIGR01642   73 RSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLwDIK 117
ZnF_U1 smart00451
U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ...
 2335-2369 2.10e-04

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.


Pssm-ID: 197732 [Multi-domain]  Cd Length: 35  Bit Score: 40.31  E-value: 2.10e-04
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 1050396892  2335 QTGFFCELCSLFYINEPTKIKHCKSLRHYQSVEKH 2369
Cdd:smart00451    1 TGGFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR 35
MDN1 COG5271
Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal ...
 1754-2187 2.35e-04

Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis];


Pssm-ID: 444083 [Multi-domain]  Cd Length: 1028  Bit Score: 46.55  E-value: 2.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1754 ETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDRSKEDRPRADRFKEDRPLDDRSKEERPRDDRSKEDRPRDDRSKED 1833
Cdd:COG5271    382 DAAADEADAAADDSADDEEASADGGTSPTSDTDEEEEEADEDASAGETEDESTDVTSAEDDIATDEEADSLADEEEEAEA 461

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1834 RPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRDDRSKEERTRDDRAREDRFKSS-----------LT 1902
Cdd:COG5271    462 ELDTEEDTESAEEDADGDEATDEDDASDDGDEEEAEEDAEAEADSDELTAEETSADDGADTDAAADPedsdedaledeTE 541

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1903 KQQRSSRSASHGKKSEKEQEDEFPFNLDEFVTVDEIVEEHGDAKKAEEQTDATYGINASRKGKRKDNEPSPLEAKKAKGR 1982
Cdd:COG5271    542 GEENAPGSDQDADETDEPEATAEEDEPDEAEAETEDATENADADETEESADESEEAEASEDEAAEEEEADDDEADADADG 621

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1983 SPDPHVTKQDLSYVTLDEIVDEEDGTVGPQSNDSLGLAKESKSLLTVDEVHAEVDQPSAKVP-QGLMTLDEISEEEDGTR 2061
Cdd:COG5271    622 AADEEETEEEAAEDEAAEPETDASEAADEDADAETEAEASADESEEEAEDESETSSEDAEEDaDAAAAEASDDEEETEEA 701

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 2062 DSATTRAPLETPEDFVKEQLLTLDEVGGEEEEPITSESLSLQATNPKDEENKAELNDLDDKEIDLSKILE----DPQVED 2137
Cdd:COG5271    702 DEDAETASEEADAEEADTEADGTAEEAEEAAEEAESADEEAASLPDEADAEEEAEEAEEAEEDDADGLEEaleeEKADAE 781

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|
gi 1050396892 2138 QVTVDPKEQPLLTLDEVKGDDDTESIVDISFSEGNQFVTVDEIGEEEEDS 2187
Cdd:COG5271    782 EAATDEEAEAAAEEKEKVADEDQDTDEDALLDEAEADEEEDLDGEDEETA 831
III PHA00370
attachment protein
 80-147 3.31e-04

attachment protein


Pssm-ID: 164795 [Multi-domain]  Cd Length: 297  Bit Score: 45.29  E-value: 3.31e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892   80 RMAHPGMNQGGMNQGGMNQGGmNQGGMNQGGMNQGGmnQGGMNQGGMNQGGINPGGMNQGGMNQGDMG 147
Cdd:PHA00370    78 GSADKDGDGGGTGEGGSDTGG-DTGGGNTGGGSGGG--DTGGSGGGGSDGGGSEGGSTGKSLTKEGVG 142
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 1752-1858 3.42e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 45.65  E-value: 3.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1752 ERETRSSNKKDNRFRDDRSKEDRPR-----DDRSKEERPRDDRSKED-RPRaDRFKED---RPLDDRSKEERPRDDRSKE 1822
Cdd:TIGR01642    3 EEPDREREKSRGRDRDRSSERPRRRsrdrsRFRDRHRRSRERSYREDsRPR-DRRRYDsrsPRSLRYSSVRRSRDRPRRR 81

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1050396892 1823 DRPRDDRSKE-DRPRDEHSKEDRPRDD--RSKEDRPRDD 1858
Cdd:TIGR01642   82 SRSVRSIEQHrRRLRDRSPSNQWRKDDkkRSLWDIKPPG 120
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
 864-934 3.65e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 41.01  E-value: 3.65e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1050396892  864 TMIHVTNLPDSGYTDQDILKIVQPFGKVCDILIIRSKNEAFLETNFKEAAAAAvkFSETTPVMiNNTRINL 934
Cdd:cd12257      2 TTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKA--YRSPEAVF-NNRFIKV 69
RRM1_PTBPH3 cd12687
RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 ...
 1039-1094 4.43e-04

RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3); This subfamily corresponds to the RRM1 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410088 [Multi-domain]  Cd Length: 75  Bit Score: 41.01  E-value: 4.43e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1050396892 1039 MTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFY-DVFPSNMGGNV 1094
Cdd:cd12687     12 ISENDLLQLAQPFGVVTKLVMLRAKNQALLQMQDVSAAISALQFYtSVQPSIRGRNV 68
PHA02896 PHA02896
A-type inclusion like protein; Provisional
 1741-1930 6.58e-04

A-type inclusion like protein; Provisional


Pssm-ID: 165222  Cd Length: 616  Bit Score: 45.02  E-value: 6.58e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1741 DKESKFTQRSWEREtRSSNKKDNRF---RDDRSKEDRPRDDRSKEERPRDDRSKEDR---PRADRFKEDRPLDDRSKEER 1814
Cdd:PHA02896   412 DEAPILNRRHGQMD-DKYDKRDHRYknnKYDIYDDESPRYKYKDDDYDDNDDNDDDHiipKKANNLEDAKDFEDEMMDAI 490

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1815 PRDDRSkedrPRDDRSKEDR--PRDEHSKE-DRPRDDRSKEDRPRDDLSKEDQDRPRDERSKEDRPRDDRSKEERTRDDR 1891
Cdd:PHA02896   491 ADDDYT----PKSIRNRRNGylLKDEDRYYyDRGHRNLGAEKDPEKPHPDKDEEYPEDKDKSDDDRLNDADKAMRKLEAD 566

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1050396892 1892 AREDRFKSSLTKQQRSSRSASHGKKsekeQEDEFPFNLD 1930
Cdd:PHA02896   567 GFGDRYRKIKEKMDNLEDDYDDLRK----HAIELPKKLD 601
RRM_DNAJC17 cd12429
RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17; The CD ...
 852-918 7.30e-04

RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17; The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding.


Pssm-ID: 409863 [Multi-domain]  Cd Length: 74  Bit Score: 40.33  E-value: 7.30e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1050396892  852 PLLKFKNKSNPGtmihvtnlpDSGYTDQDILKIVQPFGKVCDILIIRSKN-EAFLETNFKEAAAAAVK 918
Cdd:cd12429      1 PRLKVKWKSKKG---------NGGYSEEELRKIFSKYGPVSDVVISSKKKgSAIVEFATVVAADAAVE 59
RRM1_PTBP2 cd12778
RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 ...
 1028-1107 1.32e-03

RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM1 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410170 [Multi-domain]  Cd Length: 82  Bit Score: 39.66  E-value: 1.32e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1028 VVLISNLPeGPMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLaSKFKDLK 1107
Cdd:cd12778      3 VLHIRKLP-GEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYTAVTPHLRNQPIYIQY-SNHKELK 80
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 1754-1836 1.37e-03

Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known.


Pssm-ID: 463734 [Multi-domain]  Cd Length: 98  Bit Score: 40.14  E-value: 1.37e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1754 ETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDRSKEDRPRADRFKEDRPLDDRSKE-ERPRDDRSKEDRPRDDRSKE 1832
Cdd:pfam12871   15 EEDEEEDEEASDESERASLSRKRRSRSRRRSSTRDRSRSRSRSRSRDRRSRGTRDRRRDrDRDRYRSLRSRSRDRSRDRD 94


                   ....
gi 1050396892 1833 DRPR 1836
Cdd:pfam12871   95 RDRR 98
RRM1_3_MRN1 cd12261
RNA recognition motif 1 (RRM1) and 3 (RRM3) found in RNA-binding protein MRN1 and similar ...
 866-934 1.73e-03

RNA recognition motif 1 (RRM1) and 3 (RRM3) found in RNA-binding protein MRN1 and similar proteins; This subfamily corresponds to the RRM1 and RRM3 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 240707 [Multi-domain]  Cd Length: 73  Bit Score: 39.12  E-value: 1.73e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892  866 IHVTNLPDsGYTDQDILKIVQPfGKVCDILIIRSKNEAFLeTNFKEAAAAA-VKFSETTPVMINNTRINL 934
Cdd:cd12261      3 VYLGNLPE-DTTIRDILSAIRG-GPLESIKLLPTKNSATV-SFLDEAAAEAfYAYARNNGFYINGKRIKV 69
hnRNP-L_PTB TIGR01649
hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ...
 1028-1185 2.16e-03

hnRNP-L/PTB/hephaestus splicing factor family; Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).


Pssm-ID: 273733 [Multi-domain]  Cd Length: 481  Bit Score: 43.27  E-value: 2.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1028 VVLISNLPEGpMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLASKFKDLK 1107
Cdd:TIGR01649    4 VVHVRNLPQD-VVEADLVEALIPFGPVSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKR 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1108 DEERIFAyliEQSPCKITPSVYEEFVYLVDLpEKGYTESSvvcvglRFGKVDHYAIF--SNKRKAILHMCSA-SAAKAMH 1184
Cdd:TIGR01649   83 DGNSDFD---SAGPNKVLRVIVENPMYPITL-DVLYQIFN------PYGKVLRIVTFtkNNVFQALVEFESVnSAQHAKA 152


                   .
gi 1050396892 1185 S 1185
Cdd:TIGR01649  153 A 153
RRM1_PTBP1_like cd12688
RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
 1028-1107 2.45e-03

RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM1 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and functions at several aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein and negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410089 [Multi-domain]  Cd Length: 81  Bit Score: 38.83  E-value: 2.45e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1028 VVLISNLPeGPMTVEELSNLAKPFGGVNDIIIISTHRKALLELSSKNSVDSMIKFYDVFPSNMGGNVLSISLaSKFKDLK 1107
Cdd:cd12688      2 VLHIRKLP-CDVTEAEVISLGLPFGKVTNLLMLKGKNQAFLEMATEEAAVTMVNYYTPVTPHLRSQPIYIQY-SNHKELK 79
penta_MxKDx TIGR02953
pentapeptide MXKDX repeat protein; Members of this protein family are small bacterial proteins, ...
 57-111 2.72e-03

pentapeptide MXKDX repeat protein; Members of this protein family are small bacterial proteins, each with an N-terminal signal sequence followed by up to 11 imperfect repeats of a pentapeptide. The pentapeptide repeat usually follows the form Met-Xaa-Lys-Asp-Xaa.


Pssm-ID: 131998 [Multi-domain]  Cd Length: 75  Bit Score: 38.67  E-value: 2.72e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892   57 APSGMNHPGMGHSGINQPGMNFNRMAHPGMNQGGMNQGGMNQGGMNQGGMNQGGM 111
Cdd:TIGR02953   21 AQDAMKKDTMKKDAMGKDAMAKDAMSKDAMKKDAMKKDAMKKDGMKKDAMKKDAM 75
YdjI COG4260
Membrane protease subunit, stomatin/prohibitin family, contains C-terminal Zn-ribbon domain ...
 85-151 2.93e-03

Membrane protease subunit, stomatin/prohibitin family, contains C-terminal Zn-ribbon domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443402 [Multi-domain]  Cd Length: 337  Bit Score: 42.15  E-value: 2.93e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1050396892   85 GMNQGGMNQGGMNQGGMnqgGMNQgGMNQGGMNQGGMNQGGMNQGginPGGMNQGGMNQGDMGFHCE 151
Cdd:COG4260    252 AMEAAASNEGGAAGAGM---GMGM-GMAMGGMMAQALQQPGQPQQ---QQPAAAAAAPAQDPGKFCA 311
penta_MxKDx TIGR02953
pentapeptide MXKDX repeat protein; Members of this protein family are small bacterial proteins, ...
 93-146 4.18e-03

pentapeptide MXKDX repeat protein; Members of this protein family are small bacterial proteins, each with an N-terminal signal sequence followed by up to 11 imperfect repeats of a pentapeptide. The pentapeptide repeat usually follows the form Met-Xaa-Lys-Asp-Xaa.


Pssm-ID: 131998 [Multi-domain]  Cd Length: 75  Bit Score: 37.90  E-value: 4.18e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1050396892   93 QGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGINPGGMNQGGMNQGDM 146
Cdd:TIGR02953   22 QDAMKKDTMKKDAMGKDAMAKDAMSKDAMKKDAMKKDAMKKDGMKKDAMKKDAM 75
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 1029-1098 4.32e-03

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: 38.03  E-value: 4.32e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1050396892 1029 VLISNLPEGpMTVEELSNLAKPFGGVNDIIIISTHRK-----ALLELSSKNSVDSMIKFYDVFpsNMGGNVLSIS 1098
Cdd:cd00590      1 LFVGNLPPD-TTEEDLRELFSKFGEVVSVRIVRDRDGkskgfAFVEFESPEDAEKALEALNGT--ELGGRPLKVS 72
rne PRK10811
ribonuclease E; Reviewed
 1233-1394 5.03e-03

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 42.33  E-value: 5.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1233 ETEEAQTADEMALKTLASNADSAAHNTFISTSIPVVAVIEPVVTclEEQSSAIEEESLTVVEQPSAVDEEAPaIMEEAPA 1312
Cdd:PRK10811   854 QVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEE--PVVVAEPQPEEVVVVETTHPEVIAAP-VTEQPQV 930

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1313 IMEEAPAIMEEAPVNMEEAQIPNEEATRLTNEEETGLASKEDMTLTNKEETFLTDKEETDQVEKEANEEEIYTIPKEETP 1392
Cdd:PRK10811   931 ITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEAT 1010


                   ..
gi 1050396892 1393 TF 1394
Cdd:PRK10811  1011 VE 1012
MSCRAMM_ClfA NF033609
MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial ...
 1636-1872 6.40e-03

MSCRAMM family adhesin clumping factor ClfA; Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.


Pssm-ID: 468110 [Multi-domain]  Cd Length: 934  Bit Score: 41.82  E-value: 6.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1636 SASEKSRDSSTDTKESLDKRNSGRTTKYNPQKGELSVTLTLDSQKGSKLDTRKKPSADRGSTGRESSTPKSNSNRSspse 1715
Cdd:NF033609   640 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD---- 715

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1716 ssnnlkSSAGSSQKKGGSRNVSSGSDKESKFTQRSWERETRSSNKKDNRFRDDRSKEDRPRDDRSKEERPRDDRSKEDRP 1795
Cdd:NF033609   716 ------SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSD 789

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1050396892 1796 RADRFKEDRPLDDRSKEERPRDDRSKEDRPRDDRSKEDRPRDEHSKEDRPRDDRSKEDRPRDDLSKEDQDRPRDERS 1872
Cdd:NF033609   790 SDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSESDSNSDSES 866
penta_MxKDx TIGR02953
pentapeptide MXKDX repeat protein; Members of this protein family are small bacterial proteins, ...
 73-126 6.44e-03

pentapeptide MXKDX repeat protein; Members of this protein family are small bacterial proteins, each with an N-terminal signal sequence followed by up to 11 imperfect repeats of a pentapeptide. The pentapeptide repeat usually follows the form Met-Xaa-Lys-Asp-Xaa.


Pssm-ID: 131998 [Multi-domain]  Cd Length: 75  Bit Score: 37.52  E-value: 6.44e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1050396892   73 QPGMNFNRMAHPGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGMNQGGM 126
Cdd:TIGR02953   22 QDAMKKDTMKKDAMGKDAMAKDAMSKDAMKKDAMKKDAMKKDGMKKDAMKKDAM 75
DUF4670 pfam15709
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ...
 1770-1931 7.12e-03

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.


Pssm-ID: 464815 [Multi-domain]  Cd Length: 522  Bit Score: 41.48  E-value: 7.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1770 SKEDRPRDDRSKEERPRDDRSKEDRpraDRFKEDRPLDDRSKEERPRDDRSKEDRprddRSKEDRPRDEHSKEDRPRDDR 1849
Cdd:pfam15709  311 SEEERSEEDPSKALLEKREQEKASR---DRLRAERAEMRRLEVERKRREQEEQRR----LQQEQLERAEKMREELELEQQ 383

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1050396892 1850 SKEDRPRddLSKEDQDRPRDERSKEDRPRDDRSKEERTRDDRAREDRFKSSLTKQQRSSRSASHGKKSEKEQEDEFPFNL 1929
Cdd:pfam15709  384 RRFEEIR--LRKQRLEEERQRQEEEERKQRLQLQAAQERARQQQEEFRRKLQELQRKKQQEEAERAEAEKQRQKELEMQL 461


                   ..
gi 1050396892 1930 DE 1931
Cdd:pfam15709  462 AE 463
RRM1_PTBP1_hnRNPL_like cd12421
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 1144-1199 9.55e-03

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM.


Pssm-ID: 409855 [Multi-domain]  Cd Length: 74  Bit Score: 37.17  E-value: 9.55e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1050396892 1144 TESSVVCVGLRFGKVDHYAIFSNKRKAILHMCSASAAKAMHSFLTQYPCTIGENTV 1199
Cdd:cd12421     12 TEADLVALGLPFGKVTNVLLLKGKNQALVEMEDVESASSMVNYYTTVPPLIRGRPV 67
 
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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