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Conserved domains on  [gi|651166787|ref|NP_001280561|]
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poly(A) polymerase alpha isoform 5 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PAP_central super family cl47902
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
1-113 2.82e-78

Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta- sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.


The actual alignment was detected with superfamily member pfam04928:

Pssm-ID: 461486 [Multi-domain]  Cd Length: 344  Bit Score: 248.20  E-value: 2.82e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787    1 MLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVS 80
Cdd:pfam04928 231 MLVARICQLYPNAAPSTLVSKFFRIFSQWKWPQPVLLKPIEEGPLQLRVWNPRINPSDRFHLMPIITPAYPSMNSTHNVS 310
                          90       100       110
                  ....*....|....*....|....*....|...
gi 651166787   81 VSTRMVMVEEFKQGLAITDEILLSKAEWSKLFE 113
Cdd:pfam04928 311 RSTLEVIKEEFKRGLEITDEIMLGKAPWKDLFE 343
PTZ00418 super family cl36559
Poly(A) polymerase; Provisional
1-317 8.99e-70

Poly(A) polymerase; Provisional


The actual alignment was detected with superfamily member PTZ00418:

Pssm-ID: 240410 [Multi-domain]  Cd Length: 593  Bit Score: 233.54  E-value: 8.99e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787   1 MLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECN-----LNLPVWDPRVNPSDRYHLMPIITPAYPQQNS 75
Cdd:PTZ00418 284 ILTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPnipglMNFKVWDPRVNPQDRAHLMPIITPAFPSMNS 363
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787  76 TYNVSVSTRMVMVEEFKQGLAITDEI-LLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGS 154
Cdd:PTZ00418 364 THNVTYTTKRVITEEFKRAHEIIKYIeKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKK 443
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787 155 LEknefiTLAHVNPQSFP-APKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKmFEVDMKI 233
Cdd:PTZ00418 444 LE-----TLNNLKIRPYPkFFKYQDDGWDYASSFFIGLVFFSKNVYNNSTFDLRYAIRDFVDIINNWPEMEK-YPDQIDI 517
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787 234 AAMHVKRKQlhqlLPNHVLQKKKkhstEGVKLTALNDSSLDLSMDSDNSMSVPSPTSATKTSPLNSSGSSQGrnSPAPAV 313
Cdd:PTZ00418 518 NIKYLKKSQ----LPAFVLSQTP----EEPVKTKANTKTNTSSATTSGQSGSSGSTSNSNSNESSPTMSSTE--LLNVSS 587

                 ....
gi 651166787 314 TAAS 317
Cdd:PTZ00418 588 TSTT 591
motB super family cl32828
flagellar motor protein MotB; Reviewed
251-396 6.88e-04

flagellar motor protein MotB; Reviewed


The actual alignment was detected with superfamily member PRK12799:

Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 42.01  E-value: 6.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787 251 VLQKKKKHSTEGvklTALNDSSLDL-------SMDSDNSMSV--PSPTSATKTS---PLNSSGSSQGRNSPAPaVTAASV 318
Cdd:PRK12799 263 VLNKQSQHDIEH---ENLDNRALDIekatglkQIDTHGTVPVaaVTPSSAVTQSsaiTPSSAAIPSPAVIPSS-VTTQSA 338
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 651166787 319 TNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPPPRSSGNAATSGNAATKIPTPI 396
Cdd:PRK12799 339 TTTQASAVALSSAGVLPSDVTLPGTVALPAAEPVNMQPQPMSTTETQQSSTGNITSTANGPTTSLPAAPASNIPVSPT 416
 
Name Accession Description Interval E-value
PAP_central pfam04928
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
1-113 2.82e-78

Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta- sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.


Pssm-ID: 461486 [Multi-domain]  Cd Length: 344  Bit Score: 248.20  E-value: 2.82e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787    1 MLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVS 80
Cdd:pfam04928 231 MLVARICQLYPNAAPSTLVSKFFRIFSQWKWPQPVLLKPIEEGPLQLRVWNPRINPSDRFHLMPIITPAYPSMNSTHNVS 310
                          90       100       110
                  ....*....|....*....|....*....|...
gi 651166787   81 VSTRMVMVEEFKQGLAITDEILLSKAEWSKLFE 113
Cdd:pfam04928 311 RSTLEVIKEEFKRGLEITDEIMLGKAPWKDLFE 343
PTZ00418 PTZ00418
Poly(A) polymerase; Provisional
1-317 8.99e-70

Poly(A) polymerase; Provisional


Pssm-ID: 240410 [Multi-domain]  Cd Length: 593  Bit Score: 233.54  E-value: 8.99e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787   1 MLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECN-----LNLPVWDPRVNPSDRYHLMPIITPAYPQQNS 75
Cdd:PTZ00418 284 ILTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPnipglMNFKVWDPRVNPQDRAHLMPIITPAFPSMNS 363
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787  76 TYNVSVSTRMVMVEEFKQGLAITDEI-LLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGS 154
Cdd:PTZ00418 364 THNVTYTTKRVITEEFKRAHEIIKYIeKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKK 443
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787 155 LEknefiTLAHVNPQSFP-APKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKmFEVDMKI 233
Cdd:PTZ00418 444 LE-----TLNNLKIRPYPkFFKYQDDGWDYASSFFIGLVFFSKNVYNNSTFDLRYAIRDFVDIINNWPEMEK-YPDQIDI 517
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787 234 AAMHVKRKQlhqlLPNHVLQKKKkhstEGVKLTALNDSSLDLSMDSDNSMSVPSPTSATKTSPLNSSGSSQGrnSPAPAV 313
Cdd:PTZ00418 518 NIKYLKKSQ----LPAFVLSQTP----EEPVKTKANTKTNTSSATTSGQSGSSGSTSNSNSNESSPTMSSTE--LLNVSS 587

                 ....
gi 651166787 314 TAAS 317
Cdd:PTZ00418 588 TSTT 591
PAP_RNA-bind pfam04926
Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the ...
117-245 4.19e-32

Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding.


Pssm-ID: 461484  Cd Length: 177  Bit Score: 120.86  E-value: 4.19e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787  117 FFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSF------------------------- 171
Cdd:pfam04926   2 FFHKYKYYLQVVASSKTKEAHLKWSGLVESKLRLLVQKLERVPGIALAHPFPKGFervyvckteeeveavqqgslkyqvk 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787  172 ---------PAPKENPDKEE-------FRTMWVIGLVFKKtENSENLSVDLTYDIQSFTDTVYrqaiNSKMFEVD-MKIA 234
Cdd:pfam04926  82 grktitnatKVTDENKEDEGdegstkvYTTTFYIGLELDP-KAKGSKKLDISYPVQEFKNLCK----SWEKYDEEtMSIT 156
                         170
                  ....*....|.
gi 651166787  235 AMHVKRKQLHQ 245
Cdd:pfam04926 157 VRHVKNYDLPD 167
motB PRK12799
flagellar motor protein MotB; Reviewed
251-396 6.88e-04

flagellar motor protein MotB; Reviewed


Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 42.01  E-value: 6.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787 251 VLQKKKKHSTEGvklTALNDSSLDL-------SMDSDNSMSV--PSPTSATKTS---PLNSSGSSQGRNSPAPaVTAASV 318
Cdd:PRK12799 263 VLNKQSQHDIEH---ENLDNRALDIekatglkQIDTHGTVPVaaVTPSSAVTQSsaiTPSSAAIPSPAVIPSS-VTTQSA 338
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 651166787 319 TNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPPPRSSGNAATSGNAATKIPTPI 396
Cdd:PRK12799 339 TTTQASAVALSSAGVLPSDVTLPGTVALPAAEPVNMQPQPMSTTETQQSSTGNITSTANGPTTSLPAAPASNIPVSPT 416
 
Name Accession Description Interval E-value
PAP_central pfam04928
Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural ...
1-113 2.82e-78

Poly(A) polymerase central domain; The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta- sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.


Pssm-ID: 461486 [Multi-domain]  Cd Length: 344  Bit Score: 248.20  E-value: 2.82e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787    1 MLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVS 80
Cdd:pfam04928 231 MLVARICQLYPNAAPSTLVSKFFRIFSQWKWPQPVLLKPIEEGPLQLRVWNPRINPSDRFHLMPIITPAYPSMNSTHNVS 310
                          90       100       110
                  ....*....|....*....|....*....|...
gi 651166787   81 VSTRMVMVEEFKQGLAITDEILLSKAEWSKLFE 113
Cdd:pfam04928 311 RSTLEVIKEEFKRGLEITDEIMLGKAPWKDLFE 343
PTZ00418 PTZ00418
Poly(A) polymerase; Provisional
1-317 8.99e-70

Poly(A) polymerase; Provisional


Pssm-ID: 240410 [Multi-domain]  Cd Length: 593  Bit Score: 233.54  E-value: 8.99e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787   1 MLVARTCQLYPNAIASTLVHKFFLVFSKWEWPNPVLLKQPEECN-----LNLPVWDPRVNPSDRYHLMPIITPAYPQQNS 75
Cdd:PTZ00418 284 ILTARICQLYPNFAPSQLIHKFFRVYSIWNWKNPVLLCKIKEVPnipglMNFKVWDPRVNPQDRAHLMPIITPAFPSMNS 363
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787  76 TYNVSVSTRMVMVEEFKQGLAITDEI-LLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGS 154
Cdd:PTZ00418 364 THNVTYTTKRVITEEFKRAHEIIKYIeKNSENTWTNVLEPLDFFTSYKHFLVIQVYATNEHVHNKWEGWIESKIRFLIKK 443
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787 155 LEknefiTLAHVNPQSFP-APKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKmFEVDMKI 233
Cdd:PTZ00418 444 LE-----TLNNLKIRPYPkFFKYQDDGWDYASSFFIGLVFFSKNVYNNSTFDLRYAIRDFVDIINNWPEMEK-YPDQIDI 517
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787 234 AAMHVKRKQlhqlLPNHVLQKKKkhstEGVKLTALNDSSLDLSMDSDNSMSVPSPTSATKTSPLNSSGSSQGrnSPAPAV 313
Cdd:PTZ00418 518 NIKYLKKSQ----LPAFVLSQTP----EEPVKTKANTKTNTSSATTSGQSGSSGSTSNSNSNESSPTMSSTE--LLNVSS 587

                 ....
gi 651166787 314 TAAS 317
Cdd:PTZ00418 588 TSTT 591
PAP_RNA-bind pfam04926
Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the ...
117-245 4.19e-32

Poly(A) polymerase predicted RNA binding domain; Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding.


Pssm-ID: 461484  Cd Length: 177  Bit Score: 120.86  E-value: 4.19e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787  117 FFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSF------------------------- 171
Cdd:pfam04926   2 FFHKYKYYLQVVASSKTKEAHLKWSGLVESKLRLLVQKLERVPGIALAHPFPKGFervyvckteeeveavqqgslkyqvk 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787  172 ---------PAPKENPDKEE-------FRTMWVIGLVFKKtENSENLSVDLTYDIQSFTDTVYrqaiNSKMFEVD-MKIA 234
Cdd:pfam04926  82 grktitnatKVTDENKEDEGdegstkvYTTTFYIGLELDP-KAKGSKKLDISYPVQEFKNLCK----SWEKYDEEtMSIT 156
                         170
                  ....*....|.
gi 651166787  235 AMHVKRKQLHQ 245
Cdd:pfam04926 157 VRHVKNYDLPD 167
motB PRK12799
flagellar motor protein MotB; Reviewed
251-396 6.88e-04

flagellar motor protein MotB; Reviewed


Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 42.01  E-value: 6.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651166787 251 VLQKKKKHSTEGvklTALNDSSLDL-------SMDSDNSMSV--PSPTSATKTS---PLNSSGSSQGRNSPAPaVTAASV 318
Cdd:PRK12799 263 VLNKQSQHDIEH---ENLDNRALDIekatglkQIDTHGTVPVaaVTPSSAVTQSsaiTPSSAAIPSPAVIPSS-VTTQSA 338
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 651166787 319 TNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPPPRSSGNAATSGNAATKIPTPI 396
Cdd:PRK12799 339 TTTQASAVALSSAGVLPSDVTLPGTVALPAAEPVNMQPQPMSTTETQQSSTGNITSTANGPTTSLPAAPASNIPVSPT 416
 
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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