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Conserved domains on  [gi|1028909941|pdb|5IYD|I]
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Chain I, DNA-directed RNA polymerase II subunit RPB9

Protein Classification

RPOL9 and Zn-ribbon_RPB9 domain-containing protein( domain architecture ID 10652808)

RPOL9 and Zn-ribbon_RPB9 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Zn-ribbon_RPB9 cd10508
C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon ...
 74-124 1.37e-27

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: 95.78  E-value: 1.37e-27
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
5IYD_I       74 QDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTapHCGHRWT 124
Cdd:cd10508   1 QDPTLPRTEDHPCPKCGHNEAVFFQSQSRRAEEGMTLFYVCT--NCGHRWT 49
RPOL9 smart00661
RNA polymerase subunit 9;
15-68 1.95e-17

RNA polymerase subunit 9;


:

Pssm-ID: 197822  Cd Length: 52  Bit Score: 70.11  E-value: 1.95e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
5IYD_I          15 RFCQECNNMLYPKEDKENRilLYACRNCDYQQEADNSCIYVNKITHEVDELTQI 68
Cdd:smart00661   1 KFCPKCGNMLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
 
Name Accession Description Interval E-value
Zn-ribbon_RPB9 cd10508
C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon ...
 74-124 1.37e-27

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: 95.78  E-value: 1.37e-27
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
5IYD_I       74 QDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTapHCGHRWT 124
Cdd:cd10508   1 QDPTLPRTEDHPCPKCGHNEAVFFQSQSRRAEEGMTLFYVCT--NCGHRWT 49
RPOL9 smart00661
RNA polymerase subunit 9;
15-68 1.95e-17

RNA polymerase subunit 9;


Pssm-ID: 197822  Cd Length: 52  Bit Score: 70.11  E-value: 1.95e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
5IYD_I          15 RFCQECNNMLYPKEDKENRilLYACRNCDYQQEADNSCIYVNKITHEVDELTQI 68
Cdd:smart00661   1 KFCPKCGNMLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 84-125 1.83e-10

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: 51.95  E-value: 1.83e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
5IYD_I          84 HPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTapHCGHRWTE 125
Cdd:smart00440   1 AECPKCGNREATFYQLQTRSADEPMTVFYVCT--KCGHHWRE 40
RNA_POL_M_15KD pfam02150
RNA polymerases M/15 Kd subunit;
14-49 6.20e-10

RNA polymerases M/15 Kd subunit;


Pssm-ID: 280336  Cd Length: 36  Bit Score: 50.55  E-value: 6.20e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
5IYD_I         14 IRFCQECNNMLYPKEDKENRIllYACRNCDYQQEAD 49
Cdd:pfam02150   1 LIFCPKCGNLLLPTEDKLGSN--FECRQCGYEEPAD 34
TFIIS_C pfam01096
Transcription factor S-II (TFIIS);
84-124 1.25e-09

Transcription factor S-II (TFIIS);


Pssm-ID: 426046  Cd Length: 39  Bit Score: 49.91  E-value: 1.25e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
5IYD_I         84 HPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAphCGHRWT 124
Cdd:pfam01096   1 AKCPKCGNREAYFFQLQTRSADEPMTVFYVCTK--CGHRWR 39
gpA1 COG5525
Phage terminase, large subunit GpA [Mobilome: prophages, transposons];
84-125 1.39e-03

Phage terminase, large subunit GpA [Mobilome: prophages, transposons];


Pssm-ID: 444276 [Multi-domain]  Cd Length: 635  Bit Score: 36.85  E-value: 1.39e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
5IYD_I       84 HPCQKCGHK-----EAVFFQSHSARAEDAmrlYYVCtaPHCGHRWTE 125
Cdd:COG5525 233 VPCPHCGEEqeltwENLKWDKDPEAPETA---HYVC--PHCGCVIEE 274
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 86-123 3.18e-03

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: 35.97  E-value: 3.18e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
5IYD_I         86 CQKCGHKEAVFFQSHSARAEDAMRLYYVCTAphCGHRW 123
Cdd:TIGR01385 261 CGKCKQKKCTYYQLQTRSADEPMTTFVTCEE--CGNRW 296
AccD COG0777
Acetyl-CoA carboxylase beta subunit [Lipid transport and metabolism]; Acetyl-CoA carboxylase ...
 17-44 8.13e-03

Acetyl-CoA carboxylase beta subunit [Lipid transport and metabolism]; Acetyl-CoA carboxylase beta subunit is part of the Pathway/BioSystem: Fatty acid biosynthesis


Pssm-ID: 440540 [Multi-domain]  Cd Length: 280  Bit Score: 34.65  E-value: 8.13e-03
                        10        20
                ....*....|....*....|....*...
5IYD_I       17 CQECNNMLYPKEDKENrilLYACRNCDY 44
Cdd:COG0777  28 CPSCGEILYRKELEEN---LYVCPKCGH 52
 
Name Accession Description Interval E-value
Zn-ribbon_RPB9 cd10508
C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon ...
 74-124 1.37e-27

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: 95.78  E-value: 1.37e-27
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
5IYD_I       74 QDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTapHCGHRWT 124
Cdd:cd10508   1 QDPTLPRTEDHPCPKCGHNEAVFFQSQSRRAEEGMTLFYVCT--NCGHRWT 49
RPOL9 smart00661
RNA polymerase subunit 9;
15-68 1.95e-17

RNA polymerase subunit 9;


Pssm-ID: 197822  Cd Length: 52  Bit Score: 70.11  E-value: 1.95e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
5IYD_I          15 RFCQECNNMLYPKEDKENRilLYACRNCDYQQEADNSCIYVNKITHEVDELTQI 68
Cdd:smart00661   1 KFCPKCGNMLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 84-125 1.83e-10

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: 51.95  E-value: 1.83e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
5IYD_I          84 HPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTapHCGHRWTE 125
Cdd:smart00440   1 AECPKCGNREATFYQLQTRSADEPMTVFYVCT--KCGHHWRE 40
RNA_POL_M_15KD pfam02150
RNA polymerases M/15 Kd subunit;
14-49 6.20e-10

RNA polymerases M/15 Kd subunit;


Pssm-ID: 280336  Cd Length: 36  Bit Score: 50.55  E-value: 6.20e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
5IYD_I         14 IRFCQECNNMLYPKEDKENRIllYACRNCDYQQEAD 49
Cdd:pfam02150   1 LIFCPKCGNLLLPTEDKLGSN--FECRQCGYEEPAD 34
TFIIS_C pfam01096
Transcription factor S-II (TFIIS);
84-124 1.25e-09

Transcription factor S-II (TFIIS);


Pssm-ID: 426046  Cd Length: 39  Bit Score: 49.91  E-value: 1.25e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
5IYD_I         84 HPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAphCGHRWT 124
Cdd:pfam01096   1 AKCPKCGNREAYFFQLQTRSADEPMTVFYVCTK--CGHRWR 39
Zn-ribbon cd00656
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 77-124 1.94e-07

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: 44.23  E-value: 1.94e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
5IYD_I       77 TLPRTEDHpCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAphCGHRWT 124
Cdd:cd00656   1 TLPTTDRT-CPKCGHDEAYWWMLQTRSADEPPTRFYKCTK--CGHTWR 45
Zn-ribbon_RPC11 cd10509
C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III; The C-terminal zinc ...
 85-125 1.69e-05

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: 39.49  E-value: 1.69e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
5IYD_I       85 PCQKCGHKEAVFFQSHSARAEDAMRLYYVCTapHCGHRWTE 125
Cdd:cd10509   8 TCPKCGHNRAYFMQIQTRSADEPMTTFYKCC--KCGHQWRE 46
Zn-ribbon_RPA12 cd10507
C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon ...
 83-125 1.28e-04

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: 37.18  E-value: 1.28e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
5IYD_I       83 DHPCQKCGHKEAVF--FQSHSarAEDAMRLYYVCtaPHCGHRWTE 125
Cdd:cd10507   6 EEKCPKCGHDEMTYstLQLRS--ADEGQTVFYEC--PKCGHRFSE 46
gpA1 COG5525
Phage terminase, large subunit GpA [Mobilome: prophages, transposons];
84-125 1.39e-03

Phage terminase, large subunit GpA [Mobilome: prophages, transposons];


Pssm-ID: 444276 [Multi-domain]  Cd Length: 635  Bit Score: 36.85  E-value: 1.39e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
5IYD_I       84 HPCQKCGHK-----EAVFFQSHSARAEDAmrlYYVCtaPHCGHRWTE 125
Cdd:COG5525 233 VPCPHCGEEqeltwENLKWDKDPEAPETA---HYVC--PHCGCVIEE 274
Zn-ribbon_TFS cd10511
C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS); TFS is an archaeal ...
 77-125 2.59e-03

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: 33.86  E-value: 2.59e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
5IYD_I       77 TLPRTEDHpCQKCGHKEAVFFQSHSARAEDAMRLYYVCTapHCGHRWTE 125
Cdd:cd10511   1 TLPTTKIT-CPKCGHDEAYWWMVQTRSADEPPTRFYKCT--KCGHTWRE 46
TFSII TIGR01385
transcription elongation factor S-II; This model represents eukaryotic transcription ...
 86-123 3.18e-03

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: 35.97  E-value: 3.18e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
5IYD_I         86 CQKCGHKEAVFFQSHSARAEDAMRLYYVCTAphCGHRW 123
Cdd:TIGR01385 261 CGKCKQKKCTYYQLQTRSADEPMTTFVTCEE--CGNRW 296
AccD COG0777
Acetyl-CoA carboxylase beta subunit [Lipid transport and metabolism]; Acetyl-CoA carboxylase ...
 17-44 8.13e-03

Acetyl-CoA carboxylase beta subunit [Lipid transport and metabolism]; Acetyl-CoA carboxylase beta subunit is part of the Pathway/BioSystem: Fatty acid biosynthesis


Pssm-ID: 440540 [Multi-domain]  Cd Length: 280  Bit Score: 34.65  E-value: 8.13e-03
                        10        20
                ....*....|....*....|....*...
5IYD_I       17 CQECNNMLYPKEDKENrilLYACRNCDY 44
Cdd:COG0777  28 CPSCGEILYRKELEEN---LYVCPKCGH 52
 
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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