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Conserved domains on  [gi|124358934|ref|NP_001019697|]
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la-related protein 4 isoform 1 [Mus musculus]

Protein Classification

RNA-binding protein; RNA-binding protein 43( domain architecture ID 10168999)

RNA-binding protein containing an RNA recognition motif (RRM)| RNA-binding protein 43 (RBM43) is an RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_LARP4 cd12707
RNA recognition motif (RRM) found in vertebrate La-related protein 4 (LARP4); This subgroup ...
 195-271 9.91e-53

RNA recognition motif (RRM) found in vertebrate La-related protein 4 (LARP4); This subgroup corresponds to the RRM of LARP4, a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP4 is structurally related to the La autoantigen. Like other La-related proteins (LARPs) family members, LARP4 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


:

Pssm-ID: 410106  Cd Length: 77  Bit Score: 176.40  E-value: 9.91e-53
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124358934 195 CIVILREIPETTPVEEVKALFKNENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAIN 271
Cdd:cd12707    1 CIIILREIPETTPVEEVKALFKNENCPKVISCEFAHNNNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAIN 77
LARP_4 cd08035
La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related ...
 116-190 6.24e-49

La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


:

Pssm-ID: 153404  Cd Length: 75  Bit Score: 165.99  E-value: 6.24e-49
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124358934 116 KECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVRP 190
Cdd:cd08035    1 RECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKVRP 75
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 319-716 1.91e-04

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.93  E-value: 1.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  319 PQSWSPSPAPYFETPLAPFPNGSFVNGFSSPGSYKTNAAAMNMGRPFPK-NRVKPHFRSSSGSEHSTEGSVSLGDGPLSR 397
Cdd:PHA03247 2609 RGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPApGRVSRPRRARRLGRAAQASSPPQRPRRRAA 2688

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  398 SSSRIFLSERHNPTVTGQQEQTYLPKEAPILQMeqngdfGRGRRTLFRGRRRRDDDRIPRPQPAATEAKA-PTPKFDLLA 476
Cdd:PHA03247 2689 RPTVGSLTSLADPPPPPPTPEPAPHALVSATPL------PPGPAAARQASPALPAAPAPPAVPAGPATPGgPARPARPPT 2762

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  477 TNFPPLP--------GSSSRVPDELGleNRMSDVVKGVCREKDSEDVRVSCPVPAEDGQTDCTSAPLSISPSPPCTAEPP 548
Cdd:PHA03247 2763 TAGPPAPappaapaaGPPRRLTRPAV--ASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPP 2840

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  549 VLSTTQQEQDQMEDSAVPKDtlnpvavPVSSPTATKPSPANTASPctsniNPPRAVALQEPRKLSYAEVCQKPPKEPSPV 628
Cdd:PHA03247 2841 PPPGPPPPSLPLGGSVAPGG-------DVRRRPPSRSPAAKPAAP-----ARPPVRRLARPAVSRSTESFALPPDQPERP 2908

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  629 LVQPLRELRSNAVSPTRNEENGAPEKPVEKPHEKPETRASKDHSGFRGNTIPRGAAGKIREQRRQFSHRATPQGVTRRNG 708
Cdd:PHA03247 2909 PQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREA 2988


                  ....*...
gi 124358934  709 KEQYVPPR 716
Cdd:PHA03247 2989 PASSTPPL 2996
 
Name Accession Description Interval E-value
RRM_LARP4 cd12707
RNA recognition motif (RRM) found in vertebrate La-related protein 4 (LARP4); This subgroup ...
 195-271 9.91e-53

RNA recognition motif (RRM) found in vertebrate La-related protein 4 (LARP4); This subgroup corresponds to the RRM of LARP4, a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP4 is structurally related to the La autoantigen. Like other La-related proteins (LARPs) family members, LARP4 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410106  Cd Length: 77  Bit Score: 176.40  E-value: 9.91e-53
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124358934 195 CIVILREIPETTPVEEVKALFKNENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAIN 271
Cdd:cd12707    1 CIIILREIPETTPVEEVKALFKNENCPKVISCEFAHNNNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAIN 77
LARP_4 cd08035
La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related ...
 116-190 6.24e-49

La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153404  Cd Length: 75  Bit Score: 165.99  E-value: 6.24e-49
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124358934 116 KECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVRP 190
Cdd:cd08035    1 RECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKVRP 75
LA smart00715
Domain in the RNA-binding Lupus La protein; unknown function;
113-191 1.37e-35

Domain in the RNA-binding Lupus La protein; unknown function;


Pssm-ID: 128955 [Multi-domain]  Cd Length: 80  Bit Score: 128.89  E-value: 1.37e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934   113 EDLKECLKKQLEFCFSRENLSKDLYLISQMD-SDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVRPS 191
Cdd:smart00715   1 EELKQKIKKQVEYYFSDENLPRDKFLRKKMDkNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLKVRRR 80
La pfam05383
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ...
 119-175 6.42e-22

La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.


Pssm-ID: 461635  Cd Length: 59  Bit Score: 89.40  E-value: 6.42e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 124358934  119 LKKQLEFCFSRENLSKDLYLISQMDS--DQFVPIWTVANMEEIKKLTTNTDLILEVLRS 175
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKdpDGYVPISVIASFKRMKKLTTDIDLIAEALRE 59
PHA03247 PHA03247
large tegument protein UL36; Provisional
 319-716 1.91e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.93  E-value: 1.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  319 PQSWSPSPAPYFETPLAPFPNGSFVNGFSSPGSYKTNAAAMNMGRPFPK-NRVKPHFRSSSGSEHSTEGSVSLGDGPLSR 397
Cdd:PHA03247 2609 RGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPApGRVSRPRRARRLGRAAQASSPPQRPRRRAA 2688

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  398 SSSRIFLSERHNPTVTGQQEQTYLPKEAPILQMeqngdfGRGRRTLFRGRRRRDDDRIPRPQPAATEAKA-PTPKFDLLA 476
Cdd:PHA03247 2689 RPTVGSLTSLADPPPPPPTPEPAPHALVSATPL------PPGPAAARQASPALPAAPAPPAVPAGPATPGgPARPARPPT 2762

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  477 TNFPPLP--------GSSSRVPDELGleNRMSDVVKGVCREKDSEDVRVSCPVPAEDGQTDCTSAPLSISPSPPCTAEPP 548
Cdd:PHA03247 2763 TAGPPAPappaapaaGPPRRLTRPAV--ASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPP 2840

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  549 VLSTTQQEQDQMEDSAVPKDtlnpvavPVSSPTATKPSPANTASPctsniNPPRAVALQEPRKLSYAEVCQKPPKEPSPV 628
Cdd:PHA03247 2841 PPPGPPPPSLPLGGSVAPGG-------DVRRRPPSRSPAAKPAAP-----ARPPVRRLARPAVSRSTESFALPPDQPERP 2908

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  629 LVQPLRELRSNAVSPTRNEENGAPEKPVEKPHEKPETRASKDHSGFRGNTIPRGAAGKIREQRRQFSHRATPQGVTRRNG 708
Cdd:PHA03247 2909 PQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREA 2988


                  ....*...
gi 124358934  709 KEQYVPPR 716
Cdd:PHA03247 2989 PASSTPPL 2996
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 512-647 7.95e-04

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 42.98  E-value: 7.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  512 SEDVRVSCPVPAEDGQTDCTSAPLSISPSPPCTAEPPVlSTTQQEQDQMEDSAVPKDTLNPVAVPVSSPTATKPSPA--- 588
Cdd:pfam05109 451 STHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPV-TPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAvtt 529

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 124358934  589 ---NTASPCTSNINPPRAVALQEPRKLSYAEVCQKP-PKEPSPVL--VQPLRELRS---NAVSPTRNE 647
Cdd:pfam05109 530 ptpNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPtPNATIPTLgkTSPTSAVTTptpNATSPTVGE 597
RRM smart00360
RNA recognition motif;
197-263 2.20e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.19  E-value: 2.20e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124358934   197 VILREIPETTPVEEVKALFknENCPKVISCEFAHNSNW-------YITFQSDTDAQQAFKYLREevKTFQGKPI 263
Cdd:smart00360   2 LFVGNLPPDTTEEELRELF--SKFGKVESVRLVRDKETgkskgfaFVEFESEEDAEKALEALNG--KELDGRPL 71
LHP1 COG5193
La protein, small RNA-binding pol III transcript stabilizing protein and related ...
 120-176 5.74e-03

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];


Pssm-ID: 227520 [Multi-domain]  Cd Length: 438  Bit Score: 39.64  E-value: 5.74e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 124358934 120 KKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSS 176
Cdd:COG5193  275 KEQIEYYFSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEV 331
 
Name Accession Description Interval E-value
RRM_LARP4 cd12707
RNA recognition motif (RRM) found in vertebrate La-related protein 4 (LARP4); This subgroup ...
 195-271 9.91e-53

RNA recognition motif (RRM) found in vertebrate La-related protein 4 (LARP4); This subgroup corresponds to the RRM of LARP4, a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP4 is structurally related to the La autoantigen. Like other La-related proteins (LARPs) family members, LARP4 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410106  Cd Length: 77  Bit Score: 176.40  E-value: 9.91e-53
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124358934 195 CIVILREIPETTPVEEVKALFKNENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAIN 271
Cdd:cd12707    1 CIIILREIPETTPVEEVKALFKNENCPKVISCEFAHNNNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKAIN 77
LARP_4 cd08035
La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related ...
 116-190 6.24e-49

La RNA-binding domain of La-related protein 4; This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153404  Cd Length: 75  Bit Score: 165.99  E-value: 6.24e-49
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124358934 116 KECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVRP 190
Cdd:cd08035    1 RECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKVRP 75
LARP_4_5_like cd08031
La RNA-binding domain of proteins similar to La-related proteins 4 and 5; This domain is found ...
 116-190 4.42e-46

La RNA-binding domain of proteins similar to La-related proteins 4 and 5; This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153400  Cd Length: 75  Bit Score: 157.99  E-value: 4.42e-46
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124358934 116 KECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVRP 190
Cdd:cd08031    1 KELLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQVDEKGEKVRP 75
RRM_LARP4_5_like cd12430
RNA recognition motif (RRM) found in La-related protein 4 (LARP4), La-related protein 5 (LARP5 ...
 195-269 2.17e-45

RNA recognition motif (RRM) found in La-related protein 4 (LARP4), La-related protein 5 (LARP5 or LARP4B) and similar proteins; This subfamily corresponds to the RRM of LARP4 and LARP5. LARP4 is a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP5 is a cytosolic protein that co-sediments with polysomes and accumulates upon stress induction in cellular stress granules. It can interact with the cytosolic poly(A) binding protein 1 (PABPC1) and the receptor for activated C Kinase (RACK1), a component of the 40S ribosomal subunit. LARP5 may function as a stimulatory factor of translation through bridging mRNA factors of the 3' end with initiating ribosomes. Both, LARP4 and LARP5, are structurally related to the La autoantigen. Like other La-related proteins (LARPs) family members, LARP4 and LARP5 contain a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409864 [Multi-domain]  Cd Length: 76  Bit Score: 156.32  E-value: 2.17e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124358934 195 CIVILREIPETTPVEEVKALFKNENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKA 269
Cdd:cd12430    1 CIVILREIPESTPEEEVEALFSGQNCPKFTSCEFAINDSWYVTFESEEDAQEAYKYLREEVKTFNGKPIMARIKA 75
RRM_LARP5 cd12706
RNA recognition motif (RRM) found in vertebrate La-related protein 5 (LARP5 or LARP4B); This ...
 195-269 2.48e-41

RNA recognition motif (RRM) found in vertebrate La-related protein 5 (LARP5 or LARP4B); This subgroup corresponds to the RRM of LARP5, a cytosolic protein that co-sediments with polysomes and accumulates upon stress induction in cellular stress granules. It can interact with the cytosolic poly(A) binding protein 1 (PABPC1) and the receptor for activated C Kinase (RACK1), a component of the 40S ribosomal subunit. LARP5 may function as a stimulatory factor of translation through bridging mRNA factors of the 3' end with initiating ribosomes. Like other La-related proteins (LARPs) family members, LARP5 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410105  Cd Length: 77  Bit Score: 145.19  E-value: 2.48e-41
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124358934 195 CIVILREIPETTPVEEVKALFKNENCPKVISCEFAHNSNWYITFQSDTDAQQAFKYLREEVKTFQGKPIMARIKA 269
Cdd:cd12706    1 CIVILREVPESTPIEEVEALFKGDNLPKFINCEFAYNDNWFITFESEADAQQAYKYLREEVKTFQGKPIKARIKA 75
LA smart00715
Domain in the RNA-binding Lupus La protein; unknown function;
113-191 1.37e-35

Domain in the RNA-binding Lupus La protein; unknown function;


Pssm-ID: 128955 [Multi-domain]  Cd Length: 80  Bit Score: 128.89  E-value: 1.37e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934   113 EDLKECLKKQLEFCFSRENLSKDLYLISQMD-SDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVRPS 191
Cdd:smart00715   1 EELKQKIKKQVEYYFSDENLPRDKFLRKKMDkNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLKVRRR 80
LARP_5 cd08036
La RNA-binding domain of La-related protein 5; This domain is found in vertebrate La-related ...
 116-190 7.59e-34

La RNA-binding domain of La-related protein 5; This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153405  Cd Length: 75  Bit Score: 123.98  E-value: 7.59e-34
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124358934 116 KECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVRP 190
Cdd:cd08036    1 RELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEKVRP 75
LAM cd07323
LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins ...
 116-190 5.56e-30

LA motif RNA-binding domain; This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153396  Cd Length: 75  Bit Score: 113.01  E-value: 5.56e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124358934 116 KECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVRP 190
Cdd:cd07323    1 LEKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTKVRR 75
La pfam05383
La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well ...
 119-175 6.42e-22

La domain; This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.


Pssm-ID: 461635  Cd Length: 59  Bit Score: 89.40  E-value: 6.42e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 124358934  119 LKKQLEFCFSRENLSKDLYLISQMDS--DQFVPIWTVANMEEIKKLTTNTDLILEVLRS 175
Cdd:pfam05383   1 IKKQVEYYFSDENLPKDKFLRKQMDKdpDGYVPISVIASFKRMKKLTTDIDLIAEALRE 59
LARP_1_2 cd08034
La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in ...
 116-189 1.25e-16

La RNA-binding domain proteins similar to La-related proteins 1 and 2; This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153403  Cd Length: 73  Bit Score: 74.77  E-value: 1.25e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124358934 116 KECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDekGEKVR 189
Cdd:cd08034    1 KEYIKKQIEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELV--DEKVR 72
LARP_2 cd08038
La RNA-binding domain of La-related protein 2; This domain is found in vertebrate La-related ...
 116-184 3.01e-15

La RNA-binding domain of La-related protein 2; This domain is found in vertebrate La-related protein 2 (LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153407  Cd Length: 73  Bit Score: 71.14  E-value: 3.01e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934 116 KECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQ-VDEK 184
Cdd:cd08038    1 KEYIKRQIEYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEVEiVDQK 70
LARP_6 cd08033
La RNA-binding domain of La-related protein 6; This domain is found in animal and plant ...
 119-189 2.89e-14

La RNA-binding domain of La-related protein 6; This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153402  Cd Length: 77  Bit Score: 68.08  E-value: 2.89e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124358934 119 LKKQLEFCFSRENLSKDLYLISQM--DSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVR 189
Cdd:cd08033    4 IVKQVEYYFSDENLLKDAFLLKHVrrNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKKVR 76
LARP_1 cd08037
La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related ...
 116-184 8.75e-13

La RNA-binding domain of La-related protein 1; This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153406  Cd Length: 73  Bit Score: 63.77  E-value: 8.75e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934 116 KECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQ-VDEK 184
Cdd:cd08037    1 KDYIKRQIEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSKVVEiIDMK 70
LA_like_fungal cd08029
La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in ...
 121-189 2.76e-10

La-motif domain of fungal proteins similar to the La autoantigen; This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153398  Cd Length: 76  Bit Score: 56.93  E-value: 2.76e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124358934 121 KQLEFCFSRENLSKDLYL--ISQMDSDQFVPIWTVAN---MEEIKKLttntDLILEVLRSSPMVQVDEKGEKVR 189
Cdd:cd08029    6 KQVEFYFSDSNLPTDKFLwtLTGGSNNGWVPIKTIASfkrMRRFQPL----EAVVEALRESELLEVSEDGENVR 75
LARP_7 cd08032
La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key ...
 119-189 5.90e-10

La RNA-binding domain of La-related protein 7; LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.


Pssm-ID: 153401  Cd Length: 82  Bit Score: 56.10  E-value: 5.90e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124358934 119 LKKQLEFCFSRENLSKDLYLISQMDS--DQFVPIWTVANMEEIKKLTTNTDLILEVLRSSPMVQVDEKGEKVR 189
Cdd:cd08032    9 IAKQVDFWFGDVNLHKDRFLREQIEKsrDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRIR 81
LARP_3 cd08028
La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the ...
 114-189 5.84e-09

La RNA-binding domain of La-related protein 3; This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).


Pssm-ID: 153397  Cd Length: 82  Bit Score: 53.46  E-value: 5.84e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124358934 114 DLKECLKKQLEFCFSRENLSKDLYLISQM-DSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSS--PMVQVDEKGEKVR 189
Cdd:cd08028    3 DLEKKIIRQIEYYFGDFNLPRDKFLKEQIkEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSksGLIEVSEDKTKIR 81
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 197-266 4.22e-05

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: 42.27  E-value: 4.22e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124358934 197 VILREIPETTPVEEVKALFknENCPKVISCEFAHNSNW------YITFQSDTDAQQAFKYLREevKTFQGKPIMAR 266
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELF--SKFGEVVSVRIVRDRDGkskgfaFVEFESPEDAEKALEALNG--TELGGRPLKVS 72
LA_like_plant cd08030
La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant ...
 115-189 9.13e-05

La-motif domain of plant proteins similar to the La autoantigen; This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.


Pssm-ID: 153399  Cd Length: 90  Bit Score: 41.61  E-value: 9.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934 115 LKECLKKQLEFCFSRENLSKDLYLISQM--DSDQFVPIWTVANMEEIKKL---------TTNTDLILEV---LRSSPMVQ 180
Cdd:cd08030    1 TKEKVLRQVEFYFSDSNLPRDDFLLEEVeeDPDGMVSLALICSFSRMRSLlglgggkpeDVPEDTLKAVaeaLRTSTLLK 80


                 ....*....
gi 124358934 181 VDEKGEKVR 189
Cdd:cd08030   81 VSEDGKRVG 89
PHA03247 PHA03247
large tegument protein UL36; Provisional
 319-716 1.91e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.93  E-value: 1.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  319 PQSWSPSPAPYFETPLAPFPNGSFVNGFSSPGSYKTNAAAMNMGRPFPK-NRVKPHFRSSSGSEHSTEGSVSLGDGPLSR 397
Cdd:PHA03247 2609 RGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPApGRVSRPRRARRLGRAAQASSPPQRPRRRAA 2688

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  398 SSSRIFLSERHNPTVTGQQEQTYLPKEAPILQMeqngdfGRGRRTLFRGRRRRDDDRIPRPQPAATEAKA-PTPKFDLLA 476
Cdd:PHA03247 2689 RPTVGSLTSLADPPPPPPTPEPAPHALVSATPL------PPGPAAARQASPALPAAPAPPAVPAGPATPGgPARPARPPT 2762

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  477 TNFPPLP--------GSSSRVPDELGleNRMSDVVKGVCREKDSEDVRVSCPVPAEDGQTDCTSAPLSISPSPPCTAEPP 548
Cdd:PHA03247 2763 TAGPPAPappaapaaGPPRRLTRPAV--ASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPP 2840

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  549 VLSTTQQEQDQMEDSAVPKDtlnpvavPVSSPTATKPSPANTASPctsniNPPRAVALQEPRKLSYAEVCQKPPKEPSPV 628
Cdd:PHA03247 2841 PPPGPPPPSLPLGGSVAPGG-------DVRRRPPSRSPAAKPAAP-----ARPPVRRLARPAVSRSTESFALPPDQPERP 2908

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  629 LVQPLRELRSNAVSPTRNEENGAPEKPVEKPHEKPETRASKDHSGFRGNTIPRGAAGKIREQRRQFSHRATPQGVTRRNG 708
Cdd:PHA03247 2909 PQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREA 2988


                  ....*...
gi 124358934  709 KEQYVPPR 716
Cdd:PHA03247 2989 PASSTPPL 2996
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 512-647 7.95e-04

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 42.98  E-value: 7.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934  512 SEDVRVSCPVPAEDGQTDCTSAPLSISPSPPCTAEPPVlSTTQQEQDQMEDSAVPKDTLNPVAVPVSSPTATKPSPA--- 588
Cdd:pfam05109 451 STHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPV-TPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAvtt 529

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 124358934  589 ---NTASPCTSNINPPRAVALQEPRKLSYAEVCQKP-PKEPSPVL--VQPLRELRS---NAVSPTRNE 647
Cdd:pfam05109 530 ptpNATSPTLGKTSPTSAVTTPTPNATSPTPAVTTPtPNATIPTLgkTSPTSAVTTptpNATSPTVGE 597
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
517-670 1.25e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 42.17  E-value: 1.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934 517 VSCPVPAEDGQTDCTSAPLSISPSPPCTAEPPVLSTTQQEQDQ-----MEDSAVPKDTLNPVAVPVSSPTAT-KPSPANT 590
Cdd:PRK12323 382 VAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPArrspaPEALAAARQASARGPGGAPAPAPApAAAPAAA 461

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124358934 591 ASPCTSNINPPRAVALQEPRKLSYAevcqkPPKEPSPVLVQPLRELRSNAVSPTRNEENGAPEKPVEKPHEKPETRASKD 670
Cdd:PRK12323 462 ARPAAAGPRPVAAAAAAAPARAAPA-----AAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDD 536
RRM smart00360
RNA recognition motif;
197-263 2.20e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.19  E-value: 2.20e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124358934   197 VILREIPETTPVEEVKALFknENCPKVISCEFAHNSNW-------YITFQSDTDAQQAFKYLREevKTFQGKPI 263
Cdd:smart00360   2 LFVGNLPPDTTEEELRELF--SKFGKVESVRLVRDKETgkskgfaFVEFESEEDAEKALEALNG--KELDGRPL 71
LHP1 COG5193
La protein, small RNA-binding pol III transcript stabilizing protein and related ...
 120-176 5.74e-03

La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis];


Pssm-ID: 227520 [Multi-domain]  Cd Length: 438  Bit Score: 39.64  E-value: 5.74e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 124358934 120 KKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEEIKKLTTNTDLILEVLRSS 176
Cdd:COG5193  275 KEQIEYYFSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEV 331
 
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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