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Conserved domains on  [gi|38505156|ref|NP_942016|]
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transcription elongation factor A protein 2 isoform b [Homo sapiens]

Protein Classification

transcription factor S-II family protein( domain architecture ID 1002377)

transcription factor S-II (TFS II) family protein similar to Drosophila melanogaster transcription elongation factor S-II, which is necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites

CATH:  2.20.25.10
Gene Ontology:  GO:0006351|GO:0003711|GO:0003677|GO:0008270
PubMed:  8855225

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFSII super family cl36890
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 1-272 6.99e-117

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


The actual alignment was detected with superfamily member TIGR01385:

Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 337.20  E-value: 6.99e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156     1 MDLLRELKAMPITLHLLQSTRVGMSVNALRKQSSDEeVIALAKSLIKSWKKLLDAsdaKARERGRGMPLPTSSR-DASEA 79
Cdd:TIGR01385  24 LDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNED-ISKLAKKIIKSWKKVVDK---NKSDHPGGNPEDKTTVgESVNS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156    80 PDPSRKRP----ELPRAPST-PRI--TTFPPVPVTCDAVRNKCREMLTAALQTDHDHVAIGADCERLSAQIEECIFRDVG 152
Cdd:TIGR01385 100 VKQEAKSQsdkiEQPKYVSSsPRNakNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPPQSIDPEAKAIQIEELKFNNLG 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156   153 NTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDELKEIRKAMTKEAIREHQMARTGGTQTDLF 232
Cdd:TIGR01385 180 TTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVTDLF 259

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 38505156   233 TCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWKFC 272
Cdd:TIGR01385 260 TCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKFC 299
 
Name Accession Description Interval E-value
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 1-272 6.99e-117

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 337.20  E-value: 6.99e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156     1 MDLLRELKAMPITLHLLQSTRVGMSVNALRKQSSDEeVIALAKSLIKSWKKLLDAsdaKARERGRGMPLPTSSR-DASEA 79
Cdd:TIGR01385  24 LDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNED-ISKLAKKIIKSWKKVVDK---NKSDHPGGNPEDKTTVgESVNS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156    80 PDPSRKRP----ELPRAPST-PRI--TTFPPVPVTCDAVRNKCREMLTAALQTDHDHVAIGADCERLSAQIEECIFRDVG 152
Cdd:TIGR01385 100 VKQEAKSQsdkiEQPKYVSSsPRNakNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPPQSIDPEAKAIQIEELKFNNLG 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156   153 NTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDELKEIRKAMTKEAIREHQMARTGGTQTDLF 232
Cdd:TIGR01385 180 TTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVTDLF 259

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 38505156   233 TCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWKFC 272
Cdd:TIGR01385 260 TCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKFC 299
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 107-219 3.16e-51

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 163.53  E-value: 3.16e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156   107 TCDAVRNKCREMLTAALQTDHDHvAIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAI 186
Cdd:pfam07500   1 TGDKVRDKCRELLYDALAKDSTE-ASEEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEI 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 38505156   187 TPQQIAVMTSEEMASDELKEIRKAMTKEAIREH 219
Cdd:pfam07500  80 SPEKLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
109-210 1.93e-47

Domain in the central regions of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 153.24  E-value: 1.93e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156    109 DAVRNKCREMLTAALQTDHDHVAIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITP 188
Cdd:smart00510   1 DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                           90       100
                   ....*....|....*....|..
gi 38505156    189 QQIAVMTSEEMASDELKEIRKA 210
Cdd:smart00510  81 EKLATMTAEELASAELKEKREK 102
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
 225-271 7.57e-27

domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins.


Pssm-ID: 259796  Cd Length: 47  Bit Score: 98.83  E-value: 7.57e-27
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 38505156 225 GGTQTDLFTCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWKF 271
Cdd:cd13749   1 EGTTTDLFKCGKCKKRKCTYYQLQTRSADEPMTTFVTCLNCGNRWKF 47
RPB9 COG1594
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 225-269 2.90e-08

DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441202 [Multi-domain]  Cd Length: 103  Bit Score: 50.72  E-value: 2.90e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 38505156 225 GGTQTDLFTCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRW 269
Cdd:COG1594  56 EGLPTTKVICPKCGNDEAYWWLKQTRSADEPETRFFRCTKCGHTW 100
PHA02998 PHA02998
RNA polymerase subunit; Provisional
 234-272 6.35e-05

RNA polymerase subunit; Provisional


Pssm-ID: 222958 [Multi-domain]  Cd Length: 195  Bit Score: 42.81  E-value: 6.35e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 38505156  234 CGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRW---KFC 272
Cdd:PHA02998 146 CPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFkppKFR 187
 
Name Accession Description Interval E-value
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 1-272 6.99e-117

transcription elongation factor S-II; This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.


Pssm-ID: 273592 [Multi-domain]  Cd Length: 299  Bit Score: 337.20  E-value: 6.99e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156     1 MDLLRELKAMPITLHLLQSTRVGMSVNALRKQSSDEeVIALAKSLIKSWKKLLDAsdaKARERGRGMPLPTSSR-DASEA 79
Cdd:TIGR01385  24 LDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNED-ISKLAKKIIKSWKKVVDK---NKSDHPGGNPEDKTTVgESVNS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156    80 PDPSRKRP----ELPRAPST-PRI--TTFPPVPVTCDAVRNKCREMLTAALQTDHDHVAIGADCERLSAQIEECIFRDVG 152
Cdd:TIGR01385 100 VKQEAKSQsdkiEQPKYVSSsPRNakNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPPQSIDPEAKAIQIEELKFNNLG 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156   153 NTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDELKEIRKAMTKEAIREHQMARTGGTQTDLF 232
Cdd:TIGR01385 180 TTEAAYKARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVTDLF 259

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 38505156   233 TCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWKFC 272
Cdd:TIGR01385 260 TCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWKFC 299
TFIIS_M pfam07500
Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase ...
 107-219 3.16e-51

Transcription factor S-II (TFIIS), central domain; Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity.


Pssm-ID: 462184  Cd Length: 112  Bit Score: 163.53  E-value: 3.16e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156   107 TCDAVRNKCREMLTAALQTDHDHvAIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAI 186
Cdd:pfam07500   1 TGDKVRDKCRELLYDALAKDSTE-ASEEDALELAVEIEEALFKKFGGTNKKYKNKIRSLLFNLKDKKNPDLRRRVLSGEI 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 38505156   187 TPQQIAVMTSEEMASDELKEIRKAMTKEAIREH 219
Cdd:pfam07500  80 SPEKLVTMSPEEMASEELKKEREKIEKEALKEA 112
TFS2M smart00510
Domain in the central regions of transcription elongation factor S-II (and elsewhere);
109-210 1.93e-47

Domain in the central regions of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 128786 [Multi-domain]  Cd Length: 102  Bit Score: 153.24  E-value: 1.93e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38505156    109 DAVRNKCREMLTAALQTDHDHVAIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKNPDLRRNVLCGAITP 188
Cdd:smart00510   1 DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80

                           90       100
                   ....*....|....*....|..
gi 38505156    189 QQIAVMTSEEMASDELKEIRKA 210
Cdd:smart00510  81 EKLATMTAEELASAELKEKREK 102
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
 225-271 7.57e-27

domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins.


Pssm-ID: 259796  Cd Length: 47  Bit Score: 98.83  E-value: 7.57e-27
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 38505156 225 GGTQTDLFTCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWKF 271
Cdd:cd13749   1 EGTTTDLFKCGKCKKRKCTYYQLQTRSADEPMTTFVTCLNCGNRWKF 47
TFIIS_C pfam01096
Transcription factor S-II (TFIIS);
232-270 1.99e-18

Transcription factor S-II (TFIIS);


Pssm-ID: 426046  Cd Length: 39  Bit Score: 76.49  E-value: 1.99e-18
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 38505156   232 FTCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWK 270
Cdd:pfam01096   1 AKCPKCGNREAYFFQLQTRSADEPMTVFYVCTKCGHRWR 39
TFIIS_I cd00183
N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a ...
 2-54 3.25e-18

N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme


Pssm-ID: 238107  Cd Length: 76  Bit Score: 76.96  E-value: 3.25e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 38505156   2 DLLRELKAMPITLHLLQSTRVGMSVNALRKqSSDEEVIALAKSLIKSWKKLLD 54
Cdd:cd00183  25 DLLRLLKKLPLTVEILKETRIGKKVNSLRK-HSNEKIRKLAKALIKSWKKLVD 76
Med26 pfam08711
TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is ...
 2-53 1.40e-16

TFIIS helical bundle-like domain; Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.


Pssm-ID: 462573 [Multi-domain]  Cd Length: 52  Bit Score: 71.78  E-value: 1.40e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 38505156     2 DLLRELKAMPITLHLLQSTRVGMSVNALRKQSSDEEVIALAKSLIKSWKKLL 53
Cdd:pfam08711   1 KLLKKLEKLPVTLELLKSTGIGKVVNKLRKHKENPEIKKLAKELVKKWKRLV 52
TFS2N smart00509
Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);
2-55 9.95e-16

Domain in the N-terminus of transcription elongation factor S-II (and elsewhere);


Pssm-ID: 197766 [Multi-domain]  Cd Length: 75  Bit Score: 70.03  E-value: 9.95e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 38505156      2 DLLRELKAMPITLHLLQSTRVGMSVNALRKqSSDEEVIALAKSLIKSWKKLLDA 55
Cdd:smart00509  23 DILKKLKKLPITVDLLEETRIGKKVNGLRK-HKNEEIRKLAKKLIKSWKKLVYS 75
Zn-ribbon cd00656
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 225-270 7.37e-15

C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.


Pssm-ID: 259791  Cd Length: 45  Bit Score: 66.95  E-value: 7.37e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 38505156 225 GGTQTDlFTCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWK 270
Cdd:cd00656   1 TLPTTD-RTCPKCGHDEAYWWMLQTRSADEPPTRFYKCTKCGHTWR 45
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 232-271 8.60e-15

C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.


Pssm-ID: 128717 [Multi-domain]  Cd Length: 40  Bit Score: 66.58  E-value: 8.60e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 38505156    232 FTCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWKF 271
Cdd:smart00440   1 AECPKCGNREATFYQLQTRSADEPMTVFYVCTKCGHHWRE 40
Zn-ribbon_RPC11 cd10509
C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III; The C-terminal zinc ...
 233-270 6.30e-11

C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III; The C-terminal zinc ribbon domain (C-ribbon) of subunit C11 (Zn-ribbon_RPC11) in RNA polymerase (Pol) III is required for intrinsic transcript cleavage. RPC11 is also involved in Pol III termination. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPC11 has strong homology to RPB9 of Pol II and RPA12 of Pol I. Zn-ribbon_RPC11 is homologous to Pol II elongation factor TFIIS domain III. C11 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259794  Cd Length: 46  Bit Score: 56.44  E-value: 6.30e-11
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 38505156 233 TCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWK 270
Cdd:cd10509   8 TCPKCGHNRAYFMQIQTRSADEPMTTFYKCCKCGHQWR 45
Zn-ribbon_TFS cd10511
C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS); TFS is an archaeal ...
 229-270 7.64e-09

C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS); TFS is an archaeal protein that stimulates the intrinsic cleavage activity of archaeal RNA polymerase. TFS C-terminal domain shows sequence similarity to the homologous C-terminal zinc ribbon domain of subunits A12.2, Rpb9, and C11 in eukaryotic RNA Polymerases (Pol) I, II, and III, respectively and domain III of TFIIS. TFS is not a subunit of archaeal RNA polymerase even though its domains arrangement is similar to A12.2, Rpb9, and C1. TFS is a transcription factor with a similar function to eukaryotic TFIIS. TFS has external cleavage induction activity and improves the fidelity of transcription. TFS has two zinc-binding domains.


Pssm-ID: 259795  Cd Length: 47  Bit Score: 50.43  E-value: 7.64e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 38505156 229 TDLFTCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWK 270
Cdd:cd10511   4 TTKITCPKCGHDEAYWWMVQTRSADEPPTRFYKCTKCGHTWR 45
RPB9 COG1594
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 225-269 2.90e-08

DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441202 [Multi-domain]  Cd Length: 103  Bit Score: 50.72  E-value: 2.90e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 38505156 225 GGTQTDLFTCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRW 269
Cdd:COG1594  56 EGLPTTKVICPKCGNDEAYWWLKQTRSADEPETRFFRCTKCGHTW 100
Zn-ribbon_RPA12 cd10507
C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon ...
 233-270 7.35e-08

C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259792  Cd Length: 47  Bit Score: 47.97  E-value: 7.35e-08
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 38505156 233 TCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWK 270
Cdd:cd10507   8 KCPKCGHDEMTYSTLQLRSADEGQTVFYECPKCGHRFS 45
Zn-ribbon_RPB9 cd10508
C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon ...
 229-270 6.73e-06

C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon domain (C-ribbon) of subunit B9 (Zn-ribbon_RPB9) in RNA polymerase (Pol) II is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPB9 have strong homology to RPA12 of Pol I and RPC11 of Pol III subunits but its intrinsic cleavage activity is weaker for Pol II. Zn-ribbon_RPB9 is homologous to Pol II elongation factor TFIIS domain III. The very weak cleavage activity of Pol II is stimulated by TFIIS. RPB9 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259793  Cd Length: 49  Bit Score: 42.24  E-value: 6.73e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 38505156 229 TDLFTCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWK 270
Cdd:cd10508   8 TEDHPCPKCGHNEAVFFQSQSRRAEEGMTLFYVCTNCGHRWT 49
TFS_arch TIGR01384
transcription factor S, archaeal; This model describes archaeal transcription factor S, a ...
 233-270 1.04e-05

transcription factor S, archaeal; This model describes archaeal transcription factor S, a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae. [Transcription, Transcription factors]


Pssm-ID: 130451 [Multi-domain]  Cd Length: 104  Bit Score: 43.29  E-value: 1.04e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 38505156   233 TCGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRWK 270
Cdd:TIGR01384  64 ECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR 101
PHA02998 PHA02998
RNA polymerase subunit; Provisional
 234-272 6.35e-05

RNA polymerase subunit; Provisional


Pssm-ID: 222958 [Multi-domain]  Cd Length: 195  Bit Score: 42.81  E-value: 6.35e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 38505156  234 CGKCRKKNCTYTQVQTRSSDEPMTTFVVCNECGNRW---KFC 272
Cdd:PHA02998 146 CPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFkppKFR 187
 
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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