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Conserved domains on  [gi|33620745|ref|NP_056969|]
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pre-mRNA cleavage complex 2 protein Pcf11 isoform 3 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 19-145 3.27e-59

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


:

Pssm-ID: 340779  Cd Length: 127  Bit Score: 199.33  E-value: 3.27e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   19 CRDYQSSLEDLTFNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGREYLTAFTKNLVA 98
Cdd:cd16982    1 VEEYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 33620745   99 TFICVFEKVDENTRKSLFKLRSTWDEIFPLKKLYALDVRVNSLDPAW 145
Cdd:cd16982   81 LFLDAYRLVDEKTRKKLEKLLNTWKTVFPNGKLLFPDEVLNKIERAL 127
gly_rich_SclB super family cl45768
LPXTG-anchored collagen-like adhesin Scl2/SclB; SclB (or Scl2 - streptococcal collagen-like ...
 1031-1173 7.85e-04

LPXTG-anchored collagen-like adhesin Scl2/SclB; SclB (or Scl2 - streptococcal collagen-like protein 2) is an LPXTG-anchored surface-anchored adhesin with a variable-length region of triple helix-forming collagen-like Gly-Xaa-Xaa repeats.


The actual alignment was detected with superfamily member NF038329:

Pssm-ID: 468478 [Multi-domain]  Cd Length: 440  Bit Score: 43.74  E-value: 7.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745  1031 FEGCHALRFDGQPGQPSLL-PRfdGLHGQPGPRFERtpGQPGPQRFDGPPGQQVQPRFDGvPQRFDGPQHQQAsrfdiPL 1109
Cdd:NF038329  107 DEGLQQLKGDGEKGEPGPAgPA--GPAGEQGPRGDR--GETGPAGPAGPPGPQGERGEKG-PAGPQGEAGPQG-----PA 176

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33620745  1110 GLQGTR-FDNHPSQRLESVSFNQTGPyNDPPGNAFNAPSQGLQFQRHEQIFDSPQGPNFNGPHGP 1173
Cdd:NF038329  177 GKDGEAgAKGPAGEKGPQGPRGETGP-AGEQGPAGPAGPDGEAGPAGEDGPAGPAGDGQQGPDGD 240
Mplasa_alph_rch super family cl37461
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 196-467 1.40e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


The actual alignment was detected with superfamily member TIGR04523:

Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 43.47  E-value: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    196 KNLTQE-QLIRQQLLAKQKQLLEL----QQKKLELE-LEQAKAQLAVSLSVQQETSNLgpgsAPSKLHVsqippmavkap 269
Cdd:TIGR04523  352 TNSESEnSEKQRELEEKQNEIEKLkkenQSYKQEIKnLESQINDLESKIQNQEKLNQQ----KDEQIKK----------- 416

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    270 hqvpVQSEKSRPgpSLQIQDLKGTNRDPRlnriSQHSHGKDQSHRKEFLMNTLNQSDTKTSKTIpSEKLNSSKQEKSKSg 349
Cdd:TIGR04523  417 ----LQQEKELL--EKEIERLKETIIKNN----SEIKDLTNQDSVKELIIKNLDNTRESLETQL-KVLSRSINKIKQNL- 484

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    350 eKITKKELDQLDSKSKSKSKSPSPLKNKLshtKDLKNQESESM-RLSDMNKRDPRLKKHLQDKTDGKDDDVKEKRKTAEK 428
Cdd:TIGR04523  485 -EQKQKELKSKEKELKKLNEEKKELEEKV---KDLTKKISSLKeKIEKLESEKKEKESKISDLEDELNKDDFELKKENLE 560

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 33620745    429 KDKDEHMKSSEhRLAGSRNKIINGIVQKQDTITE-ESEKQ 467
Cdd:TIGR04523  561 KEIDEKNKEIE-ELKQTQKSLKKKQEEKQELIDQkEKEKK 599
Innate_immun super family cl25893
Invertebrate innate immunity transcript family; The immune response of the purple sea urchin ...
 856-968 3.01e-03

Invertebrate innate immunity transcript family; The immune response of the purple sea urchin appears to be more complex than previously believed in that it uses immune-related gene families homologous to vertebrate Toll-like and NOD/NALP-like receptor families as well as C-type lectins and a rudimentary complement system. In addition, the species also produces this unusual family of mRNAs, also known as 185/333, which is strongly upregulated in response to pathogen challenge.


The actual alignment was detected with superfamily member pfam12782:

Pssm-ID: 432781 [Multi-domain]  Cd Length: 291  Bit Score: 41.68  E-value: 3.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    856 FEGSPGGLRFEGP---GGQpVGGLRFEGHRGqpvGGLRFEG--PHGQPVGGLRFDNPRGqpvgglrfeGGHGPSGAAIR- 929
Cdd:pfam12782   42 FGGRPGGMQMGSPrqdGGQ-MGGRRFDGPES---GAPQMEGrrQNGGPMGGRRFDGPRF---------GGSRPDGAGGRp 108

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 33620745    930 FDGPHGQPGGGIRFEGPLLQQGVGM----RFEGpHGQSVAGLR 968
Cdd:pfam12782  109 FFGQGGRRGDGEEETDAAQQIGDGLggrgQFDG-HGRGHHGHR 150
PTZ00108 super family cl36510
DNA topoisomerase 2-like protein; Provisional
 374-616 5.96e-03

DNA topoisomerase 2-like protein; Provisional


The actual alignment was detected with superfamily member PTZ00108:

Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 41.57  E-value: 5.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   374 LKNKLSHTKDLKNQESESMRLSDMNKRDPRLKKHLQ---------------DKTDGKDDDVKEKRKTAEKKDKDEHMKSS 438
Cdd:PTZ00108 1111 LEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEveekeiakeqrlkskTKGKASKLRKPKLKKKEKKKKKSSADKSK 1190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   439 EHRLAGSRNKI------------INGIVQKQDTITEESEKQGTKPGRSSTRKRSRSRSPKSRSPIIhSPKRRDRRSPKRR 506
Cdd:PTZ00108 1191 KASVVGNSKRVdsdekrklddkpDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSED-NDEFSSDDLSKEG 1269

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   507 QRSMSPTSTPKAGKIRQSGAKQSHMEEFTPPSREDRNAKRSTKQDIRDPRRMKKTEEERPQETTNQhstKSGTEPKENVE 586
Cdd:PTZ00108 1270 KPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKK---KSKTRVKQASA 1346

                         250       260       270
                  ....*....|....*....|....*....|
gi 33620745   587 NwQSSKSAKRWKsgWEENKSLQQVDEHSKP 616
Cdd:PTZ00108 1347 S-QSSRLLRRPR--KKKSDSSSEDDDDSEV 1373
 
Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 19-145 3.27e-59

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340779  Cd Length: 127  Bit Score: 199.33  E-value: 3.27e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   19 CRDYQSSLEDLTFNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGREYLTAFTKNLVA 98
Cdd:cd16982    1 VEEYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 33620745   99 TFICVFEKVDENTRKSLFKLRSTWDEIFPLKKLYALDVRVNSLDPAW 145
Cdd:cd16982   81 LFLDAYRLVDEKTRKKLEKLLNTWKTVFPNGKLLFPDEVLNKIERAL 127
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
21-139 8.57e-34

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 126.62  E-value: 8.57e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745      21 DYQSSLEDLTfNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGREYLTAFTKNLVATF 100
Cdd:smart00582    1 AFEQKLESLN-NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVF 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*
gi 33620745     101 ICVFEKVDEN----TRKSLFKLRSTWDE--IFPLKKLYALDVRVN 139
Cdd:smart00582   80 QDALRRVLGAapeeLKKKIRRLLNIWEErgIFPPEVLRPLREKLN 124
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 26-127 5.31e-16

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 75.71  E-value: 5.31e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745     26 LEDLTfNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNV----GREYLTAFTKNLVATFI 101
Cdd:pfam04818    7 LSSLN-NSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSrkkgKSEFADAFEPVLPEAFA 85

                           90       100
                   ....*....|....*....|....*...
gi 33620745    102 CVFEKVDENTRKSLFKLRSTWDE--IFP 127
Cdd:pfam04818   86 SAYKKCDEKLKKKLERLLNIWEErnVFS 113
gly_rich_SclB NF038329
LPXTG-anchored collagen-like adhesin Scl2/SclB; SclB (or Scl2 - streptococcal collagen-like ...
 1031-1173 7.85e-04

LPXTG-anchored collagen-like adhesin Scl2/SclB; SclB (or Scl2 - streptococcal collagen-like protein 2) is an LPXTG-anchored surface-anchored adhesin with a variable-length region of triple helix-forming collagen-like Gly-Xaa-Xaa repeats.


Pssm-ID: 468478 [Multi-domain]  Cd Length: 440  Bit Score: 43.74  E-value: 7.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745  1031 FEGCHALRFDGQPGQPSLL-PRfdGLHGQPGPRFERtpGQPGPQRFDGPPGQQVQPRFDGvPQRFDGPQHQQAsrfdiPL 1109
Cdd:NF038329  107 DEGLQQLKGDGEKGEPGPAgPA--GPAGEQGPRGDR--GETGPAGPAGPPGPQGERGEKG-PAGPQGEAGPQG-----PA 176

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33620745  1110 GLQGTR-FDNHPSQRLESVSFNQTGPyNDPPGNAFNAPSQGLQFQRHEQIFDSPQGPNFNGPHGP 1173
Cdd:NF038329  177 GKDGEAgAKGPAGEKGPQGPRGETGP-AGEQGPAGPAGPDGEAGPAGEDGPAGPAGDGQQGPDGD 240
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 196-467 1.40e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 43.47  E-value: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    196 KNLTQE-QLIRQQLLAKQKQLLEL----QQKKLELE-LEQAKAQLAVSLSVQQETSNLgpgsAPSKLHVsqippmavkap 269
Cdd:TIGR04523  352 TNSESEnSEKQRELEEKQNEIEKLkkenQSYKQEIKnLESQINDLESKIQNQEKLNQQ----KDEQIKK----------- 416

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    270 hqvpVQSEKSRPgpSLQIQDLKGTNRDPRlnriSQHSHGKDQSHRKEFLMNTLNQSDTKTSKTIpSEKLNSSKQEKSKSg 349
Cdd:TIGR04523  417 ----LQQEKELL--EKEIERLKETIIKNN----SEIKDLTNQDSVKELIIKNLDNTRESLETQL-KVLSRSINKIKQNL- 484

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    350 eKITKKELDQLDSKSKSKSKSPSPLKNKLshtKDLKNQESESM-RLSDMNKRDPRLKKHLQDKTDGKDDDVKEKRKTAEK 428
Cdd:TIGR04523  485 -EQKQKELKSKEKELKKLNEEKKELEEKV---KDLTKKISSLKeKIEKLESEKKEKESKISDLEDELNKDDFELKKENLE 560

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 33620745    429 KDKDEHMKSSEhRLAGSRNKIINGIVQKQDTITE-ESEKQ 467
Cdd:TIGR04523  561 KEIDEKNKEIE-ELKQTQKSLKKKQEEKQELIDQkEKEKK 599
Innate_immun pfam12782
Invertebrate innate immunity transcript family; The immune response of the purple sea urchin ...
 856-968 3.01e-03

Invertebrate innate immunity transcript family; The immune response of the purple sea urchin appears to be more complex than previously believed in that it uses immune-related gene families homologous to vertebrate Toll-like and NOD/NALP-like receptor families as well as C-type lectins and a rudimentary complement system. In addition, the species also produces this unusual family of mRNAs, also known as 185/333, which is strongly upregulated in response to pathogen challenge.


Pssm-ID: 432781 [Multi-domain]  Cd Length: 291  Bit Score: 41.68  E-value: 3.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    856 FEGSPGGLRFEGP---GGQpVGGLRFEGHRGqpvGGLRFEG--PHGQPVGGLRFDNPRGqpvgglrfeGGHGPSGAAIR- 929
Cdd:pfam12782   42 FGGRPGGMQMGSPrqdGGQ-MGGRRFDGPES---GAPQMEGrrQNGGPMGGRRFDGPRF---------GGSRPDGAGGRp 108

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 33620745    930 FDGPHGQPGGGIRFEGPLLQQGVGM----RFEGpHGQSVAGLR 968
Cdd:pfam12782  109 FFGQGGRRGDGEEETDAAQQIGDGLggrgQFDG-HGRGHHGHR 150
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 374-616 5.96e-03

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 41.57  E-value: 5.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   374 LKNKLSHTKDLKNQESESMRLSDMNKRDPRLKKHLQ---------------DKTDGKDDDVKEKRKTAEKKDKDEHMKSS 438
Cdd:PTZ00108 1111 LEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEveekeiakeqrlkskTKGKASKLRKPKLKKKEKKKKKSSADKSK 1190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   439 EHRLAGSRNKI------------INGIVQKQDTITEESEKQGTKPGRSSTRKRSRSRSPKSRSPIIhSPKRRDRRSPKRR 506
Cdd:PTZ00108 1191 KASVVGNSKRVdsdekrklddkpDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSED-NDEFSSDDLSKEG 1269

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   507 QRSMSPTSTPKAGKIRQSGAKQSHMEEFTPPSREDRNAKRSTKQDIRDPRRMKKTEEERPQETTNQhstKSGTEPKENVE 586
Cdd:PTZ00108 1270 KPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKK---KSKTRVKQASA 1346

                         250       260       270
                  ....*....|....*....|....*....|
gi 33620745   587 NwQSSKSAKRWKsgWEENKSLQQVDEHSKP 616
Cdd:PTZ00108 1347 S-QSSRLLRRPR--KKKSDSSSEDDDDSEV 1373
 
Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 19-145 3.27e-59

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340779  Cd Length: 127  Bit Score: 199.33  E-value: 3.27e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   19 CRDYQSSLEDLTFNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGREYLTAFTKNLVA 98
Cdd:cd16982    1 VEEYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 33620745   99 TFICVFEKVDENTRKSLFKLRSTWDEIFPLKKLYALDVRVNSLDPAW 145
Cdd:cd16982   81 LFLDAYRLVDEKTRKKLEKLLNTWKTVFPNGKLLFPDEVLNKIERAL 127
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
21-139 8.57e-34

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 126.62  E-value: 8.57e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745      21 DYQSSLEDLTfNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGREYLTAFTKNLVATF 100
Cdd:smart00582    1 AFEQKLESLN-NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVF 79

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*
gi 33620745     101 ICVFEKVDEN----TRKSLFKLRSTWDE--IFPLKKLYALDVRVN 139
Cdd:smart00582   80 QDALRRVLGAapeeLKKKIRRLLNIWEErgIFPPEVLRPLREKLN 124
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 20-124 4.11e-21

CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several eukaryotic RNA-processing factors including yeast proteins, Pcf11 and Nrd1, and vertebrate proteins, CTD-associated factors 8 (SCAF8) and Regulation of nuclear pre-mRNA domain-containing proteins (such as RPRD1 and RPRD2). Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340766  Cd Length: 123  Bit Score: 90.27  E-value: 4.11e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   20 RDYQSSLEDLTFNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGRE---YLTAFTKNL 96
Cdd:cd03562    1 KAFNSKLEELSDLSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRKgpeFTKDFSPVI 80

                         90       100
                 ....*....|....*....|....*...
gi 33620745   97 VATFICVFEKVDENTRKSLFKLRSTWDE 124
Cdd:cd03562   81 VELFKHVYSETDEDCKKKLGRVLSIWEE 108
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 26-127 5.31e-16

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 75.71  E-value: 5.31e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745     26 LEDLTfNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNV----GREYLTAFTKNLVATFI 101
Cdd:pfam04818    7 LSSLN-NSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSrkkgKSEFADAFEPVLPEAFA 85

                           90       100
                   ....*....|....*....|....*...
gi 33620745    102 CVFEKVDENTRKSLFKLRSTWDE--IFP 127
Cdd:pfam04818   86 SAYKKCDEKLKKKLERLLNIWEErnVFS 113
VHS_ENTH_ANTH cd00197
VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a ...
 24-122 1.11e-07

VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a VHS, CID, ENTH, or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The CTD-Interacting Domain (CID) is present in several RNA-processing factors and binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase II (RNAP II or Pol II). The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-Terminal Homology (ANTH) domain. VHS, ENTH, and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH and ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding.


Pssm-ID: 340764  Cd Length: 115  Bit Score: 51.66  E-value: 1.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   24 SSLEDLTFN-----SKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGREYLTAFTKNLVA 98
Cdd:cd00197    3 KTVEKATSNenmgpDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVASNDFA 82

                         90       100       110
                 ....*....|....*....|....*....|.
gi 33620745   99 TFICVFEK-------VDENTRKSLFKLRSTW 122
Cdd:cd00197   83 VELLKFDKsgllgddVSTNVREKAIELVQLW 113
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 33-132 5.27e-06

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; This subfamily includes SR-related and CTD-associated factors 8 (SCAF8) and 4 (SCAF4), and similar proteins. SCAF4 is also called Splicing factor arginine serine rich 15 (SFRS15). Members may play roles in mRNA processing. Both SCAF4 and SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340780  Cd Length: 131  Bit Score: 47.22  E-value: 5.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   33 SKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGREYLTA-------FTKNLVATFICVFe 105
Cdd:cd16983   18 SKSKINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQYGKEkdvyaprFAKNLSKTFLNLL- 96

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 33620745  106 KVDENTRKSLFKLRSTW--------DEIFPLKKLY 132
Cdd:cd16983   97 KCPEKDKPKVKRVLNLWqkngvfpkEIIQPLLDAA 131
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 23-124 1.11e-05

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; Regulation of nuclear pre-mRNA domain-containing protein 1A (RPRD1A) is also called Cyclin-dependent kinase inhibitor 2B-related protein or p15INK4B-related protein (P15RS). RPRD1A is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A form homodimers and heterodimers with RPRD1B through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340808  Cd Length: 128  Bit Score: 46.57  E-value: 1.11e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   23 QSSLEDLTfNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNV---GREYLTAFTKNLVAT 99
Cdd:cd17011    7 EKKLSELS-NSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSkrkGPEFTKDFAPVIVEA 85

                         90       100
                 ....*....|....*....|....*
gi 33620745  100 FICVFEKVDENTRKSLFKLRSTWDE 124
Cdd:cd17011   86 FKHVSSETDESCKKHLGRVLSIWEE 110
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 23-124 9.02e-05

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; Regulation of nuclear pre-mRNA domain-containing protein 1B (RPRD1B) is also called Cell cycle-related and expression-elevated protein in tumor (CREPT). RPRD1B is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1B form homodimers and heterodimers with RPRD1A through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. RPRD1B is highly expressed during tumorigenesis and in endometrial cancer, has been shown to promote tumor growth by accelerating the cell cycle. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340809  Cd Length: 129  Bit Score: 43.84  E-value: 9.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   23 QSSLEDLTfNSKPHINMLTILAEENLPFAKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNVGR---EYLTAFTKNLVAT 99
Cdd:cd17012    8 EKKLSELS-NSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRkgpEFTREFESVLVDA 86

                         90       100
                 ....*....|....*....|....*
gi 33620745  100 FICVFEKVDENTRKSLFKLRSTWDE 124
Cdd:cd17012   87 FSHVAREADEGCKKPLERLLNIWQE 111
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 51-127 1.35e-04

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340778  Cd Length: 125  Bit Score: 43.34  E-value: 1.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   51 AKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNV----GREYLTAFTKNLVATFICVFEKVDENTRKSLFKLRSTWDE-- 124
Cdd:cd16981   32 AKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSrrkgAPEFVEAFKKVLPEALALVRSEGDESVRKKVLRVLNIWEErn 111


                 ...
gi 33620745  125 IFP 127
Cdd:cd16981  112 VFG 114
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 51-140 2.77e-04

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and similar proteins; This subfamily contains Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A) and 1B (RPRD1B) from jawed vertebrates, CID domain-containing protein 1 (CIDS1 or cids-1) from Caenorhabditis elegans, and similar proteins. RPRD1A and RPRD1B are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains. Both associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. The function of CIDS1 is not yet known. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340799  Cd Length: 128  Bit Score: 42.25  E-value: 2.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   51 AKEIVSLIEAQTAKAPSSEKLPVMYLMDSIVKNV---GREYLTAFTKNLVATFICVFEKVDENTRKSLFKLRSTWDE--I 125
Cdd:cd17002   34 AKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSrkkGPEFTKEFAPVLEDAFKHVAKLTDSEVLKALERILNIWKErqV 113

                         90
                 ....*....|....*
gi 33620745  126 FPLKKLYALDVRVNS 140
Cdd:cd17002  114 YEKDFIEQLRAALRK 128
gly_rich_SclB NF038329
LPXTG-anchored collagen-like adhesin Scl2/SclB; SclB (or Scl2 - streptococcal collagen-like ...
 1031-1173 7.85e-04

LPXTG-anchored collagen-like adhesin Scl2/SclB; SclB (or Scl2 - streptococcal collagen-like protein 2) is an LPXTG-anchored surface-anchored adhesin with a variable-length region of triple helix-forming collagen-like Gly-Xaa-Xaa repeats.


Pssm-ID: 468478 [Multi-domain]  Cd Length: 440  Bit Score: 43.74  E-value: 7.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745  1031 FEGCHALRFDGQPGQPSLL-PRfdGLHGQPGPRFERtpGQPGPQRFDGPPGQQVQPRFDGvPQRFDGPQHQQAsrfdiPL 1109
Cdd:NF038329  107 DEGLQQLKGDGEKGEPGPAgPA--GPAGEQGPRGDR--GETGPAGPAGPPGPQGERGEKG-PAGPQGEAGPQG-----PA 176

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33620745  1110 GLQGTR-FDNHPSQRLESVSFNQTGPyNDPPGNAFNAPSQGLQFQRHEQIFDSPQGPNFNGPHGP 1173
Cdd:NF038329  177 GKDGEAgAKGPAGEKGPQGPRGETGP-AGEQGPAGPAGPDGEAGPAGEDGPAGPAGDGQQGPDGD 240
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 51-133 1.20e-03

CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar proteins; Yeast transcription termination factor Rtt103 is a CID (CTD-Interacting Domain) containing protein that functions in DNA damage response. It associates with sites of DNA breaks and is essential for recovery from DNA double strand breaks in the chromosome. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). Rtt103 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340800  Cd Length: 127  Bit Score: 40.67  E-value: 1.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   51 AKEIVSLIEAQTAKAP--SSEKLPVMYLMDSIV-----KNVGrEYLTAFTKNLVATFICVFEKVDENTRKSLFKLRSTWD 123
Cdd:cd17003   32 ADEIAEIWSDYLLKSSvnSRRKLLLIYLANDVVqqakaKKKT-EFIDAFSKVLPEVLEKIYPSLPSDIKKKIKRVVNVWK 110

                         90
                 ....*....|....*
gi 33620745  124 E--IFP---LKKLYA 133
Cdd:cd17003  111 QrqIFSkdvIDDIEE 125
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 196-467 1.40e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 43.47  E-value: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    196 KNLTQE-QLIRQQLLAKQKQLLEL----QQKKLELE-LEQAKAQLAVSLSVQQETSNLgpgsAPSKLHVsqippmavkap 269
Cdd:TIGR04523  352 TNSESEnSEKQRELEEKQNEIEKLkkenQSYKQEIKnLESQINDLESKIQNQEKLNQQ----KDEQIKK----------- 416

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    270 hqvpVQSEKSRPgpSLQIQDLKGTNRDPRlnriSQHSHGKDQSHRKEFLMNTLNQSDTKTSKTIpSEKLNSSKQEKSKSg 349
Cdd:TIGR04523  417 ----LQQEKELL--EKEIERLKETIIKNN----SEIKDLTNQDSVKELIIKNLDNTRESLETQL-KVLSRSINKIKQNL- 484

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    350 eKITKKELDQLDSKSKSKSKSPSPLKNKLshtKDLKNQESESM-RLSDMNKRDPRLKKHLQDKTDGKDDDVKEKRKTAEK 428
Cdd:TIGR04523  485 -EQKQKELKSKEKELKKLNEEKKELEEKV---KDLTKKISSLKeKIEKLESEKKEKESKISDLEDELNKDDFELKKENLE 560

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 33620745    429 KDKDEHMKSSEhRLAGSRNKIINGIVQKQDTITE-ESEKQ 467
Cdd:TIGR04523  561 KEIDEKNKEIE-ELKQTQKSLKKKQEEKQELIDQkEKEKK 599
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 195-445 2.35e-03

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 42.65  E-value: 2.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    195 QKNLTQEQLIRQQLLAKQKQLLELQQKKLELELEQAKAQLAVsLSVQQETSNLGPGSAPSKLHVSQIPPMAVKAP--HQV 272
Cdd:TIGR00618  237 QTQQSHAYLTQKREAQEEQLKKQQLLKQLRARIEELRAQEAV-LEETQERINRARKAAPLAAHIKAVTQIEQQAQriHTE 315

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    273 PVQSEKSR-----PGPSLQIQDLKGTNRDPRLNRI-SQHSHGKDQsHRKEFLMntLNQSDTKTSKTIPSEKLNSSKqEKS 346
Cdd:TIGR00618  316 LQSKMRSRakllmKRAAHVKQQSSIEEQRRLLQTLhSQEIHIRDA-HEVATSI--REISCQQHTLTQHIHTLQQQK-TTL 391

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    347 KSGEKITKKELDQLDSKS---KSKSKSPSPLKNKLSHTK----------DLKNQ------ESESMRLSDMNKRDPRLKKH 407
Cdd:TIGR00618  392 TQKLQSLCKELDILQREQatiDTRTSAFRDLQGQLAHAKkqqelqqryaELCAAaitctaQCEKLEKIHLQESAQSLKER 471

                          250       260       270
                   ....*....|....*....|....*....|....*...
gi 33620745    408 LQDKTDGKDDDVKEKRKTAEKKDKDEHMKSSEHRLAGS 445
Cdd:TIGR00618  472 EQQLQTKEQIHLQETRKKAVVLARLLELQEEPCPLCGS 509
Innate_immun pfam12782
Invertebrate innate immunity transcript family; The immune response of the purple sea urchin ...
 856-968 3.01e-03

Invertebrate innate immunity transcript family; The immune response of the purple sea urchin appears to be more complex than previously believed in that it uses immune-related gene families homologous to vertebrate Toll-like and NOD/NALP-like receptor families as well as C-type lectins and a rudimentary complement system. In addition, the species also produces this unusual family of mRNAs, also known as 185/333, which is strongly upregulated in response to pathogen challenge.


Pssm-ID: 432781 [Multi-domain]  Cd Length: 291  Bit Score: 41.68  E-value: 3.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745    856 FEGSPGGLRFEGP---GGQpVGGLRFEGHRGqpvGGLRFEG--PHGQPVGGLRFDNPRGqpvgglrfeGGHGPSGAAIR- 929
Cdd:pfam12782   42 FGGRPGGMQMGSPrqdGGQ-MGGRRFDGPES---GAPQMEGrrQNGGPMGGRRFDGPRF---------GGSRPDGAGGRp 108

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 33620745    930 FDGPHGQPGGGIRFEGPLLQQGVGM----RFEGpHGQSVAGLR 968
Cdd:pfam12782  109 FFGQGGRRGDGEEETDAAQQIGDGLggrgQFDG-HGRGHHGHR 150
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 374-616 5.96e-03

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 41.57  E-value: 5.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   374 LKNKLSHTKDLKNQESESMRLSDMNKRDPRLKKHLQ---------------DKTDGKDDDVKEKRKTAEKKDKDEHMKSS 438
Cdd:PTZ00108 1111 LEKKEKELEKLKNTTPKDMWLEDLDKFEEALEEQEEveekeiakeqrlkskTKGKASKLRKPKLKKKEKKKKKSSADKSK 1190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   439 EHRLAGSRNKI------------INGIVQKQDTITEESEKQGTKPGRSSTRKRSRSRSPKSRSPIIhSPKRRDRRSPKRR 506
Cdd:PTZ00108 1191 KASVVGNSKRVdsdekrklddkpDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSED-NDEFSSDDLSKEG 1269

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33620745   507 QRSMSPTSTPKAGKIRQSGAKQSHMEEFTPPSREDRNAKRSTKQDIRDPRRMKKTEEERPQETTNQhstKSGTEPKENVE 586
Cdd:PTZ00108 1270 KPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKK---KSKTRVKQASA 1346

                         250       260       270
                  ....*....|....*....|....*....|
gi 33620745   587 NwQSSKSAKRWKsgWEENKSLQQVDEHSKP 616
Cdd:PTZ00108 1347 S-QSSRLLRRPR--KKKSDSSSEDDDDSEV 1373
 
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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