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Conserved domains on  [gi|32564415|ref|NP_496464|]
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Mediator of RNA polymerase II transcription subunit 8 [Caenorhabditis elegans]

Protein Classification

mediator of RNA polymerase II transcription subunit 8 family protein( domain architecture ID 4230)

mediator of RNA polymerase II transcription subunit 8 (Med8) family protein is a component of the mediator complex, such as S. cerevisiae Med8 which binds to a TATA box-binding protein and to Med18 and Med20

Gene Ontology:  GO:0061629|GO:0016592
PubMed:  15175151|16263706|22579255

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Med8 super family cl10917
Mediator of RNA polymerase II transcription complex subunit 8; Arc32, or Med8, is one of the ...
 15-231 6.07e-17

Mediator of RNA polymerase II transcription complex subunit 8; Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex. The N-terminus of Med8 binds to the essential core Head part of Mediator and the C-terminus hinges to Med18 on the non-essential part of the Head that also includes Med20.


The actual alignment was detected with superfamily member pfam10232:

Pssm-ID: 463012  Cd Length: 230  Bit Score: 78.54  E-value: 6.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415    15 QGEPEKIAQATDMMIKRVTDAKKIIEELLQMLDLQEKCP-WPLMLEKFSTLASFMSSLQSSVRKSGMPHghedygqfLRS 93
Cdd:pfam10232   2 QREEKQLEASLEAIRQRLNDLKNSLASLIFKLENEYPLPnWPSLLDNFALISGQLTTLSKVLKSEKTPL--------LRN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415    94 HVLVTQRLQYEPDETLQRATQGRVMSWNHALVPEYLRTKPNPEMENEEGMLDGERSAKSADLVVRQIAAYNKNIEGLINH 173
Cdd:pfam10232  74 LVVLPLPLSPGRDEELARLTEGRVPVFSHDVVPDLLRTKLDPEVEPREAQLEARARNLGGEYTQKQIAGVNKVVTGLRRK 153

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 32564415   174 LNSV----DRMHTEAAIEKPTYNRDETAKIVKSILTGEGIRSQRTMAPAPPSSAP---MTTAPSS 231
Cdd:pfam10232 154 LSKAreewEEEEGSRGGIQQTSSGADTEALVAAVGFGKGLKPGVEFGISGPPPSGggmMGKLPSG 218
PAT1 super family cl37801
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 210-325 5.38e-06

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


The actual alignment was detected with superfamily member pfam09770:

Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 48.11  E-value: 5.38e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415   210 RSQRTMAPAPPSSAPMTtaPSSTGPSSSQPISGNQPEYQGSQLRQQLSGGQPQTSQAHLPMYSHHQQPQYSHQQPMNP-- 287
Cdd:pfam09770 204 RAQAKKPAQQPAPAPAQ--PPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPsi 281

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 32564415   288 -------QHHSPMTMMAPGQMIGHPiQQQRPPMHQMPPNMTIQRQ 325
Cdd:pfam09770 282 qpqaqqfHQQPPPVPVQPTQILQNP-NRLSAARVGYPQNPQPGVQ 325
 
Name Accession Description Interval E-value
Med8 pfam10232
Mediator of RNA polymerase II transcription complex subunit 8; Arc32, or Med8, is one of the ...
 15-231 6.07e-17

Mediator of RNA polymerase II transcription complex subunit 8; Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex. The N-terminus of Med8 binds to the essential core Head part of Mediator and the C-terminus hinges to Med18 on the non-essential part of the Head that also includes Med20.


Pssm-ID: 463012  Cd Length: 230  Bit Score: 78.54  E-value: 6.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415    15 QGEPEKIAQATDMMIKRVTDAKKIIEELLQMLDLQEKCP-WPLMLEKFSTLASFMSSLQSSVRKSGMPHghedygqfLRS 93
Cdd:pfam10232   2 QREEKQLEASLEAIRQRLNDLKNSLASLIFKLENEYPLPnWPSLLDNFALISGQLTTLSKVLKSEKTPL--------LRN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415    94 HVLVTQRLQYEPDETLQRATQGRVMSWNHALVPEYLRTKPNPEMENEEGMLDGERSAKSADLVVRQIAAYNKNIEGLINH 173
Cdd:pfam10232  74 LVVLPLPLSPGRDEELARLTEGRVPVFSHDVVPDLLRTKLDPEVEPREAQLEARARNLGGEYTQKQIAGVNKVVTGLRRK 153

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 32564415   174 LNSV----DRMHTEAAIEKPTYNRDETAKIVKSILTGEGIRSQRTMAPAPPSSAP---MTTAPSS 231
Cdd:pfam10232 154 LSKAreewEEEEGSRGGIQQTSSGADTEALVAAVGFGKGLKPGVEFGISGPPPSGggmMGKLPSG 218
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 210-325 5.38e-06

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 48.11  E-value: 5.38e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415   210 RSQRTMAPAPPSSAPMTtaPSSTGPSSSQPISGNQPEYQGSQLRQQLSGGQPQTSQAHLPMYSHHQQPQYSHQQPMNP-- 287
Cdd:pfam09770 204 RAQAKKPAQQPAPAPAQ--PPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPsi 281

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 32564415   288 -------QHHSPMTMMAPGQMIGHPiQQQRPPMHQMPPNMTIQRQ 325
Cdd:pfam09770 282 qpqaqqfHQQPPPVPVQPTQILQNP-NRLSAARVGYPQNPQPGVQ 325
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 213-323 1.59e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 40.18  E-value: 1.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415   213 RTMAPAPPSSAPMTTA---PSSTGPSSSQPISGNQPEYQGSQlrQQLSGGQPQTSQAHLPMYSHHQQPQYSHQQPMNPQH 289
Cdd:TIGR01628 379 QPRMRQLPMGSPMGGAmgqPPYYGQGPQQQFNGQPLGWPRMS--MMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQK 456

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 32564415   290 HSPMTMMAPGQMIGHPIQQQRP-----PMHQMPPNMTIQ 323
Cdd:TIGR01628 457 PPMQPVMYPPNYQSLPLSQDLPqpqstASQGGQNKKLAQ 495
SP4_N cd22536
N-terminal domain of transcription factor Specificity Protein (SP) 4; Specificity Proteins ...
 203-316 4.88e-03

N-terminal domain of transcription factor Specificity Protein (SP) 4; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. Human SP4 is a risk gene of multiple psychiatric disorders including schizophrenia, bipolar disorder, and major depression. SP4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP4.


Pssm-ID: 411773 [Multi-domain]  Cd Length: 623  Bit Score: 38.75  E-value: 4.88e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415 203 ILTGEGIRSQRTMAPAPPSSAPMTTAPSSTGPSSSQPISGNQP-EYQGSQLRQQLSGGQPQTSQAHLPMYShHQQPQYSH 281
Cdd:cd22536 277 VSTPITTASVSTMPESPSSSTTCTTTASTSLTSSDTLVSSAETgQYASTAASSERTEEEPQTSAAESEAQS-SSQLQSNG 355

                        90       100       110
                ....*....|....*....|....*....|....*
gi 32564415 282 QQPMNPQHHSPMTMMAPGQMIGHPIQQQRPPMHQM 316
Cdd:cd22536 356 LQNVQDQSNSLQQVQIVGQPILQQIQIQQPQQQII 390
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 212-314 9.59e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 37.76  E-value: 9.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415   212 QRTMAPAPPSSAPMTTAPSSTGPSSSQPISGNQPEYQGSQLRQQLSGGQPQTSQAHlPMYSHH--QQPQYSHQQPM--NP 287
Cdd:PRK10263  398 QQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQ-STFAPQstYQTEQTYQQPAaqEP 476

                          90       100       110
                  ....*....|....*....|....*....|.
gi 32564415   288 QHHSPMTMMAPGQMIGHPIQQQ----RPPMH 314
Cdd:PRK10263  477 LYQQPQPVEQQPVVEPEPVVEEtkpaRPPLY 507
 
Name Accession Description Interval E-value
Med8 pfam10232
Mediator of RNA polymerase II transcription complex subunit 8; Arc32, or Med8, is one of the ...
 15-231 6.07e-17

Mediator of RNA polymerase II transcription complex subunit 8; Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex. The N-terminus of Med8 binds to the essential core Head part of Mediator and the C-terminus hinges to Med18 on the non-essential part of the Head that also includes Med20.


Pssm-ID: 463012  Cd Length: 230  Bit Score: 78.54  E-value: 6.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415    15 QGEPEKIAQATDMMIKRVTDAKKIIEELLQMLDLQEKCP-WPLMLEKFSTLASFMSSLQSSVRKSGMPHghedygqfLRS 93
Cdd:pfam10232   2 QREEKQLEASLEAIRQRLNDLKNSLASLIFKLENEYPLPnWPSLLDNFALISGQLTTLSKVLKSEKTPL--------LRN 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415    94 HVLVTQRLQYEPDETLQRATQGRVMSWNHALVPEYLRTKPNPEMENEEGMLDGERSAKSADLVVRQIAAYNKNIEGLINH 173
Cdd:pfam10232  74 LVVLPLPLSPGRDEELARLTEGRVPVFSHDVVPDLLRTKLDPEVEPREAQLEARARNLGGEYTQKQIAGVNKVVTGLRRK 153

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 32564415   174 LNSV----DRMHTEAAIEKPTYNRDETAKIVKSILTGEGIRSQRTMAPAPPSSAP---MTTAPSS 231
Cdd:pfam10232 154 LSKAreewEEEEGSRGGIQQTSSGADTEALVAAVGFGKGLKPGVEFGISGPPPSGggmMGKLPSG 218
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 210-325 5.38e-06

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 48.11  E-value: 5.38e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415   210 RSQRTMAPAPPSSAPMTtaPSSTGPSSSQPISGNQPEYQGSQLRQQLSGGQPQTSQAHLPMYSHHQQPQYSHQQPMNP-- 287
Cdd:pfam09770 204 RAQAKKPAQQPAPAPAQ--PPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQRPQSPQPDPAQPsi 281

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 32564415   288 -------QHHSPMTMMAPGQMIGHPiQQQRPPMHQMPPNMTIQRQ 325
Cdd:pfam09770 282 qpqaqqfHQQPPPVPVQPTQILQNP-NRLSAARVGYPQNPQPGVQ 325
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 213-323 1.59e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 40.18  E-value: 1.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415   213 RTMAPAPPSSAPMTTA---PSSTGPSSSQPISGNQPEYQGSQlrQQLSGGQPQTSQAHLPMYSHHQQPQYSHQQPMNPQH 289
Cdd:TIGR01628 379 QPRMRQLPMGSPMGGAmgqPPYYGQGPQQQFNGQPLGWPRMS--MMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQK 456

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 32564415   290 HSPMTMMAPGQMIGHPIQQQRP-----PMHQMPPNMTIQ 323
Cdd:TIGR01628 457 PPMQPVMYPPNYQSLPLSQDLPqpqstASQGGQNKKLAQ 495
SP4_N cd22536
N-terminal domain of transcription factor Specificity Protein (SP) 4; Specificity Proteins ...
 203-316 4.88e-03

N-terminal domain of transcription factor Specificity Protein (SP) 4; Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. Human SP4 is a risk gene of multiple psychiatric disorders including schizophrenia, bipolar disorder, and major depression. SP4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP4.


Pssm-ID: 411773 [Multi-domain]  Cd Length: 623  Bit Score: 38.75  E-value: 4.88e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415 203 ILTGEGIRSQRTMAPAPPSSAPMTTAPSSTGPSSSQPISGNQP-EYQGSQLRQQLSGGQPQTSQAHLPMYShHQQPQYSH 281
Cdd:cd22536 277 VSTPITTASVSTMPESPSSSTTCTTTASTSLTSSDTLVSSAETgQYASTAASSERTEEEPQTSAAESEAQS-SSQLQSNG 355

                        90       100       110
                ....*....|....*....|....*....|....*
gi 32564415 282 QQPMNPQHHSPMTMMAPGQMIGHPIQQQRPPMHQM 316
Cdd:cd22536 356 LQNVQDQSNSLQQVQIVGQPILQQIQIQQPQQQII 390
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 250-319 6.72e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 38.25  E-value: 6.72e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 32564415   250 SQLRQQLSGGQPQTSQAHL--PMYSHHQQPQYSHQQPMnpqhhspmtMMAPGQMIGHPIQQQRP----PMHQMPPN 319
Cdd:TIGR01628 369 AHLQDQFMQLQPRMRQLPMgsPMGGAMGQPPYYGQGPQ---------QQFNGQPLGWPRMSMMPtpmgPGGPLRPN 435
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 212-314 9.59e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 37.76  E-value: 9.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 32564415   212 QRTMAPAPPSSAPMTTAPSSTGPSSSQPISGNQPEYQGSQLRQQLSGGQPQTSQAHlPMYSHH--QQPQYSHQQPM--NP 287
Cdd:PRK10263  398 QQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQ-STFAPQstYQTEQTYQQPAaqEP 476

                          90       100       110
                  ....*....|....*....|....*....|.
gi 32564415   288 QHHSPMTMMAPGQMIGHPIQQQ----RPPMH 314
Cdd:PRK10263  477 LYQQPQPVEQQPVVEPEPVVEEtkpaRPPLY 507
 
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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