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Conserved domains on  [gi|300797915|ref|NP_001178788|]
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RNA-binding protein 33 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHA03418 super family cl25519
hypothetical E4 protein; Provisional
 449-489 4.11e-04

hypothetical E4 protein; Provisional


The actual alignment was detected with superfamily member PHA03418:

Pssm-ID: 177646 [Multi-domain]  Cd Length: 230  Bit Score: 43.19  E-value: 4.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 300797915  449 VPLLPVPSQPRPAVGPQRFPGPPEFPQHTPGP--VPNSFNQPP 489
Cdd:PHA03418   33 LPLLPAPHHPNPQEDPDKNPSPPPDPPLTPRPpaQPNGHNKPP 75
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 436-727 1.48e-03

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.00  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  436 NPHFKGTVVTPVQVPLLP-VPSQPRPAVGPQRFPGPPEFPQHTPGP----VPNSFNQPPRLPLQDQWRAPPPPQE----- 505
Cdd:PHA03247 2700 DPPPPPPTPEPAPHALVSaTPLPPGPAAARQASPALPAAPAPPAVPagpaTPGGPARPARPPTTAGPPAPAPPAApaagp 2779

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  506 -----RDPFFLGVSGEPRFPSHLFLEQRSPPPPPPPPTLLNSSHPVPTQSPLPFTQPGPAFNQQGQqpvFPRERPVRPAL 580
Cdd:PHA03247 2780 prrltRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGP---PPPSLPLGGSV 2856

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  581 QPPGPVGilHFSQPGSATARPFIPPRQPfLPSPGQPFLPTHAQPNLQGPLHPPLPPPHQPQPQPQQPQQQPQHHQHQPPL 660
Cdd:PHA03247 2857 APGGDVR--RRPPSRSPAAKPAAPARPP-VRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPP 2933

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  661 QPPLQPPHQPPPQHQPPPQHQPQQHQHHHHLSAPPPPLMPMSQ---PQFRPHVQTAQPQSNSSRMQCTPR 727
Cdd:PHA03247 2934 PPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRfrvPQPAPSREAPASSTPPLTGHSLSR 3003
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 1152-1223 2.67e-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).


The actual alignment was detected with superfamily member cd12259:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 76  Bit Score: 37.68  E-value: 2.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915 1152 VVSVEGLSSSTTDVQLKSLLMSVGPIQSLQMLP--------QQRKAIAKFKEPAHALAFQqkfhrHMIDLSHINVALIVE 1223
Cdd:cd12259     1 VVQVTNVSPQATEEQMRTLFGFIGKIEELRLYPseddlapvLSKVCFVKYEDPEDVAVAL-----HLTNTVFIDRALIVI 75
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
 798-877 5.97e-03

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


:

Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 40.21  E-value: 5.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915   798 ASRSSQGKTDAKAKPLSPGAQPkEEAKAEAEFPDEDEETRLYRLKI----EEQKRLREEILKQKELRRQQQAGARKKELL 873
Cdd:TIGR02794   52 ANRIQQQKKPAAKKEQERQKKL-EQQAEEAEKQRAAEQARQKELEQraaaEKAAKQAEQAAKQAEEKQKQAEEAKAKQAA 130


                   ....
gi 300797915   874 ERLA 877
Cdd:TIGR02794  131 EAKA 134
MDN1 super family cl34967
Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal ...
 15-239 6.07e-03

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


The actual alignment was detected with superfamily member COG5271:

Pssm-ID: 444083 [Multi-domain]  Cd Length: 1028  Bit Score: 40.77  E-value: 6.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915   15 DDDFDQFDKPGAERSWRRrAADEDWDSELEDDLLGEDLLSGKKNQSDLSDEELNDDLLQSDNE--DEENFSSQGVTISLN 92
Cdd:COG5271   779 DAEEAATDEEAEAAAEEK-EKVADEDQDTDEDALLDEAEADEEEDLDGEDEETADEALEDIEAgiAEDDEEDDDAAAAKD 857

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915   93 TTSGIVTSFELSDNTNDQSGEQESEYEQGDDELAYHKPEEQELYTQEYPEEGQYEGHDTELTEDQIEYGDEPEEEQLYSD 172
Cdd:COG5271   858 VDADLDLDADLAADEHEAEEAQEAETDADADADAGEADSSGESSAAAEDDDAAEDADSDDGANDEDDDDDAEEERKDAEE 937

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 300797915  173 -----EVLDIEINEPLDEFTDEEYLQAYGGQQGLQVREDCEAEDDLDEITDSQVASETHEGGMETLELQKDI 239
Cdd:COG5271   938 delgaAEDDLDALALDEAGDEESDDAAADDAGDDSLADDDEALADAADDAEADDSELDASESTGEAEGDEDD 1009
 
Name Accession Description Interval E-value
PHA03418 PHA03418
hypothetical E4 protein; Provisional
 449-489 4.11e-04

hypothetical E4 protein; Provisional


Pssm-ID: 177646 [Multi-domain]  Cd Length: 230  Bit Score: 43.19  E-value: 4.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 300797915  449 VPLLPVPSQPRPAVGPQRFPGPPEFPQHTPGP--VPNSFNQPP 489
Cdd:PHA03418   33 LPLLPAPHHPNPQEDPDKNPSPPPDPPLTPRPpaQPNGHNKPP 75
PHA03247 PHA03247
large tegument protein UL36; Provisional
 436-727 1.48e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.00  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  436 NPHFKGTVVTPVQVPLLP-VPSQPRPAVGPQRFPGPPEFPQHTPGP----VPNSFNQPPRLPLQDQWRAPPPPQE----- 505
Cdd:PHA03247 2700 DPPPPPPTPEPAPHALVSaTPLPPGPAAARQASPALPAAPAPPAVPagpaTPGGPARPARPPTTAGPPAPAPPAApaagp 2779

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  506 -----RDPFFLGVSGEPRFPSHLFLEQRSPPPPPPPPTLLNSSHPVPTQSPLPFTQPGPAFNQQGQqpvFPRERPVRPAL 580
Cdd:PHA03247 2780 prrltRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGP---PPPSLPLGGSV 2856

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  581 QPPGPVGilHFSQPGSATARPFIPPRQPfLPSPGQPFLPTHAQPNLQGPLHPPLPPPHQPQPQPQQPQQQPQHHQHQPPL 660
Cdd:PHA03247 2857 APGGDVR--RRPPSRSPAAKPAAPARPP-VRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPP 2933

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  661 QPPLQPPHQPPPQHQPPPQHQPQQHQHHHHLSAPPPPLMPMSQ---PQFRPHVQTAQPQSNSSRMQCTPR 727
Cdd:PHA03247 2934 PPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRfrvPQPAPSREAPASSTPPLTGHSLSR 3003
RRM_SRSF11_SREK1 cd12259
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), ...
 1152-1223 2.67e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable.


Pssm-ID: 409704 [Multi-domain]  Cd Length: 76  Bit Score: 37.68  E-value: 2.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915 1152 VVSVEGLSSSTTDVQLKSLLMSVGPIQSLQMLP--------QQRKAIAKFKEPAHALAFQqkfhrHMIDLSHINVALIVE 1223
Cdd:cd12259     1 VVQVTNVSPQATEEQMRTLFGFIGKIEELRLYPseddlapvLSKVCFVKYEDPEDVAVAL-----HLTNTVFIDRALIVI 75
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
 798-877 5.97e-03

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 40.21  E-value: 5.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915   798 ASRSSQGKTDAKAKPLSPGAQPkEEAKAEAEFPDEDEETRLYRLKI----EEQKRLREEILKQKELRRQQQAGARKKELL 873
Cdd:TIGR02794   52 ANRIQQQKKPAAKKEQERQKKL-EQQAEEAEKQRAAEQARQKELEQraaaEKAAKQAEQAAKQAEEKQKQAEEAKAKQAA 130


                   ....
gi 300797915   874 ERLA 877
Cdd:TIGR02794  131 EAKA 134
MDN1 COG5271
Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal ...
 15-239 6.07e-03

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: 40.77  E-value: 6.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915   15 DDDFDQFDKPGAERSWRRrAADEDWDSELEDDLLGEDLLSGKKNQSDLSDEELNDDLLQSDNE--DEENFSSQGVTISLN 92
Cdd:COG5271   779 DAEEAATDEEAEAAAEEK-EKVADEDQDTDEDALLDEAEADEEEDLDGEDEETADEALEDIEAgiAEDDEEDDDAAAAKD 857

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915   93 TTSGIVTSFELSDNTNDQSGEQESEYEQGDDELAYHKPEEQELYTQEYPEEGQYEGHDTELTEDQIEYGDEPEEEQLYSD 172
Cdd:COG5271   858 VDADLDLDADLAADEHEAEEAQEAETDADADADAGEADSSGESSAAAEDDDAAEDADSDDGANDEDDDDDAEEERKDAEE 937

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 300797915  173 -----EVLDIEINEPLDEFTDEEYLQAYGGQQGLQVREDCEAEDDLDEITDSQVASETHEGGMETLELQKDI 239
Cdd:COG5271   938 delgaAEDDLDALALDEAGDEESDDAAADDAGDDSLADDDEALADAADDAEADDSELDASESTGEAEGDEDD 1009
 
Name Accession Description Interval E-value
PHA03418 PHA03418
hypothetical E4 protein; Provisional
 449-489 4.11e-04

hypothetical E4 protein; Provisional


Pssm-ID: 177646 [Multi-domain]  Cd Length: 230  Bit Score: 43.19  E-value: 4.11e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 300797915  449 VPLLPVPSQPRPAVGPQRFPGPPEFPQHTPGP--VPNSFNQPP 489
Cdd:PHA03418   33 LPLLPAPHHPNPQEDPDKNPSPPPDPPLTPRPpaQPNGHNKPP 75
PHA03247 PHA03247
large tegument protein UL36; Provisional
 436-727 1.48e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.00  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  436 NPHFKGTVVTPVQVPLLP-VPSQPRPAVGPQRFPGPPEFPQHTPGP----VPNSFNQPPRLPLQDQWRAPPPPQE----- 505
Cdd:PHA03247 2700 DPPPPPPTPEPAPHALVSaTPLPPGPAAARQASPALPAAPAPPAVPagpaTPGGPARPARPPTTAGPPAPAPPAApaagp 2779

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  506 -----RDPFFLGVSGEPRFPSHLFLEQRSPPPPPPPPTLLNSSHPVPTQSPLPFTQPGPAFNQQGQqpvFPRERPVRPAL 580
Cdd:PHA03247 2780 prrltRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGP---PPPSLPLGGSV 2856

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  581 QPPGPVGilHFSQPGSATARPFIPPRQPfLPSPGQPFLPTHAQPNLQGPLHPPLPPPHQPQPQPQQPQQQPQHHQHQPPL 660
Cdd:PHA03247 2857 APGGDVR--RRPPSRSPAAKPAAPARPP-VRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPP 2933

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  661 QPPLQPPHQPPPQHQPPPQHQPQQHQHHHHLSAPPPPLMPMSQ---PQFRPHVQTAQPQSNSSRMQCTPR 727
Cdd:PHA03247 2934 PPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRfrvPQPAPSREAPASSTPPLTGHSLSR 3003
dnaA PRK14086
chromosomal replication initiator protein DnaA;
454-616 2.54e-03

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 42.12  E-value: 2.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  454 VPSQPRPAVGPQRFPGPPEFPQHTPGPVPNSFNQPPRLPLQDQWRAPPPPQErdpfflgvsgEPRFPSHlflEQRSPPPP 533
Cdd:PRK14086  127 DDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPRAADDYGWQQQRLGFPPRA----------PYASPAS---YAPEQERD 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915  534 PPPPTLLNSSHPVPTQSPlpfTQPGPAFNQQGQQpvfPRERPVRpalqPPGPVGILHFSQPGSATARPFIPPRQPFLPSP 613
Cdd:PRK14086  194 REPYDAGRPEYDQRRRDY---DHPRPDWDRPRRD---RTDRPEP----PPGAGHVHRGGPGPPERDDAPVVPIRPSAPGP 263


                  ....*
gi 300797915  614 --GQP 616
Cdd:PRK14086  264 laAQP 268
RRM_SRSF11_SREK1 cd12259
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), ...
 1152-1223 2.67e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable.


Pssm-ID: 409704 [Multi-domain]  Cd Length: 76  Bit Score: 37.68  E-value: 2.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915 1152 VVSVEGLSSSTTDVQLKSLLMSVGPIQSLQMLP--------QQRKAIAKFKEPAHALAFQqkfhrHMIDLSHINVALIVE 1223
Cdd:cd12259     1 VVQVTNVSPQATEEQMRTLFGFIGKIEELRLYPseddlapvLSKVCFVKYEDPEDVAVAL-----HLTNTVFIDRALIVI 75
RRM1_hnRNPL_like cd12689
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 1151-1195 2.68e-03

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: 38.02  E-value: 2.68e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 300797915 1151 CVVSVEGLSSSTTDVQLKSLLMSVGPIQSLQMLPQQRKAIAKFKE 1195
Cdd:cd12689     3 PVVHVRGLSEHVTEADLVEALQNFGPISYVTMMPKKRQALVEFED 47
tolA_full TIGR02794
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ...
 798-877 5.97e-03

TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis]


Pssm-ID: 274303 [Multi-domain]  Cd Length: 346  Bit Score: 40.21  E-value: 5.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915   798 ASRSSQGKTDAKAKPLSPGAQPkEEAKAEAEFPDEDEETRLYRLKI----EEQKRLREEILKQKELRRQQQAGARKKELL 873
Cdd:TIGR02794   52 ANRIQQQKKPAAKKEQERQKKL-EQQAEEAEKQRAAEQARQKELEQraaaEKAAKQAEQAAKQAEEKQKQAEEAKAKQAA 130


                   ....
gi 300797915   874 ERLA 877
Cdd:TIGR02794  131 EAKA 134
MDN1 COG5271
Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal ...
 15-239 6.07e-03

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: 40.77  E-value: 6.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915   15 DDDFDQFDKPGAERSWRRrAADEDWDSELEDDLLGEDLLSGKKNQSDLSDEELNDDLLQSDNE--DEENFSSQGVTISLN 92
Cdd:COG5271   779 DAEEAATDEEAEAAAEEK-EKVADEDQDTDEDALLDEAEADEEEDLDGEDEETADEALEDIEAgiAEDDEEDDDAAAAKD 857

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 300797915   93 TTSGIVTSFELSDNTNDQSGEQESEYEQGDDELAYHKPEEQELYTQEYPEEGQYEGHDTELTEDQIEYGDEPEEEQLYSD 172
Cdd:COG5271   858 VDADLDLDADLAADEHEAEEAQEAETDADADADAGEADSSGESSAAAEDDDAAEDADSDDGANDEDDDDDAEEERKDAEE 937

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 300797915  173 -----EVLDIEINEPLDEFTDEEYLQAYGGQQGLQVREDCEAEDDLDEITDSQVASETHEGGMETLELQKDI 239
Cdd:COG5271   938 delgaAEDDLDALALDEAGDEESDDAAADDAGDDSLADDDEALADAADDAEADDSELDASESTGEAEGDEDD 1009
 
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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