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Conserved domains on  [gi|46359779|gb|AAS88753|]
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At3g16980 [Arabidopsis thaliana]

Protein Classification

RNA_POL_M_15KD and Zn-ribbon_RPB9 domain-containing protein( domain architecture ID 13387809)

RNA_POL_M_15KD 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 ...
 64-113 9.43e-22

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: 80.76  E-value: 9.43e-22
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 46359779  64 SDPTLPRTKAVRCSKCQHREAVFFQA-TARGEEGMTLFFVCCnpNCGHRWR 113
Cdd:cd10508   1 QDPTLPRTEDHPCPKCGHNEAVFFQSqSRRAEEGMTLFYVCT--NCGHRWT 49
RPB9 super family cl34312
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 5-114 4.39e-17

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


The actual alignment was detected with superfamily member COG1594:

Pssm-ID: 441202 [Multi-domain]  Cd Length: 103  Bit Score: 70.36  E-value: 4.39e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46359779   5 KFCRECNNILYPKEDKeqkillYACRNCDHQEVADNSCVYRNEVHHSVSERTQILTDVASDPTLPRTKaVRCSKCQHREA 84
Cdd:COG1594   1 KFCPKCGSMMKPKDGV------LVCPKCGYEEPRDEEAEAKYVSTEEQEDKEIIVVEEEEVEGLPTTK-VICPKCGNDEA 73

                        90       100       110
                ....*....|....*....|....*....|.
gi 46359779  85 VFF-QATARGEEGMTLFFVCCNpnCGHRWRE 114
Cdd:COG1594  74 YWWlKQTRSADEPETRFFRCTK--CGHTWRE 102
 
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 ...
 64-113 9.43e-22

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: 80.76  E-value: 9.43e-22
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 46359779  64 SDPTLPRTKAVRCSKCQHREAVFFQA-TARGEEGMTLFFVCCnpNCGHRWR 113
Cdd:cd10508   1 QDPTLPRTEDHPCPKCGHNEAVFFQSqSRRAEEGMTLFYVCT--NCGHRWT 49
RPB9 COG1594
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 5-114 4.39e-17

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: 70.36  E-value: 4.39e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46359779   5 KFCRECNNILYPKEDKeqkillYACRNCDHQEVADNSCVYRNEVHHSVSERTQILTDVASDPTLPRTKaVRCSKCQHREA 84
Cdd:COG1594   1 KFCPKCGSMMKPKDGV------LVCPKCGYEEPRDEEAEAKYVSTEEQEDKEIIVVEEEEVEGLPTTK-VICPKCGNDEA 73

                        90       100       110
                ....*....|....*....|....*....|.
gi 46359779  85 VFF-QATARGEEGMTLFFVCCNpnCGHRWRE 114
Cdd:COG1594  74 YWWlKQTRSADEPETRFFRCTK--CGHTWRE 102
TFS_arch TIGR01384
transcription factor S, archaeal; This model describes archaeal transcription factor S, a ...
 5-114 1.37e-13

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: 61.39  E-value: 1.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46359779     5 KFCRECNNILYPKEDKeqkillYACRNCDHQE--VADNSCVYRNEVHHSVSERTQILTDVASdpTLPRTKaVRCSKCQHR 82
Cdd:TIGR01384   1 KFCPKCGSLMTPKNGV------YVCPSCGYEKekKPEDDYKVTEKVKHKIKETIIIREEDSE--TLPTTR-VECPKCGHK 71

                          90       100       110
                  ....*....|....*....|....*....|...
gi 46359779    83 EAVFF-QATARGEEGMTLFFVCcnPNCGHRWRE 114
Cdd:TIGR01384  72 EAYYWlLQTRRADEPETRFYKC--TKCGYVWRE 102
RPOL9 smart00661
RNA polymerase subunit 9;
5-58 1.86e-11

RNA polymerase subunit 9;


Pssm-ID: 197822  Cd Length: 52  Bit Score: 54.70  E-value: 1.86e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 46359779      5 KFCRECNNILYPKEDKEQKilLYACRNCDHQEVADNSCVYRNEVHHSVSERTQI 58
Cdd:smart00661   1 KFCPKCGNMLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
TFIIS_C pfam01096
Transcription factor S-II (TFIIS);
74-113 4.29e-10

Transcription factor S-II (TFIIS);


Pssm-ID: 426046  Cd Length: 39  Bit Score: 50.68  E-value: 4.29e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 46359779    74 VRCSKCQHREAVFFQA-TARGEEGMTLFFVCCnpNCGHRWR 113
Cdd:pfam01096   1 AKCPKCGNREAYFFQLqTRSADEPMTVFYVCT--KCGHRWR 39
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 76-114 9.33e-08

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: 44.63  E-value: 9.33e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 46359779     76 CSKCQHREAVFFQA-TARGEEGMTLFFVCCNpnCGHRWRE 114
Cdd:smart00440   3 CPKCGNREATFYQLqTRSADEPMTVFYVCTK--CGHHWRE 40
RNA_POL_M_15KD pfam02150
RNA polymerases M/15 Kd subunit;
4-39 2.20e-06

RNA polymerases M/15 Kd subunit;


Pssm-ID: 280336  Cd Length: 36  Bit Score: 41.30  E-value: 2.20e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 46359779     4 MKFCRECNNILYPKEDKEQKIllYACRNCDHQEVAD 39
Cdd:pfam02150   1 LIFCPKCGNLLLPTEDKLGSN--FECRQCGYEEPAD 34
 
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 ...
 64-113 9.43e-22

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: 80.76  E-value: 9.43e-22
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 46359779  64 SDPTLPRTKAVRCSKCQHREAVFFQA-TARGEEGMTLFFVCCnpNCGHRWR 113
Cdd:cd10508   1 QDPTLPRTEDHPCPKCGHNEAVFFQSqSRRAEEGMTLFYVCT--NCGHRWT 49
RPB9 COG1594
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 5-114 4.39e-17

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: 70.36  E-value: 4.39e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46359779   5 KFCRECNNILYPKEDKeqkillYACRNCDHQEVADNSCVYRNEVHHSVSERTQILTDVASDPTLPRTKaVRCSKCQHREA 84
Cdd:COG1594   1 KFCPKCGSMMKPKDGV------LVCPKCGYEEPRDEEAEAKYVSTEEQEDKEIIVVEEEEVEGLPTTK-VICPKCGNDEA 73

                        90       100       110
                ....*....|....*....|....*....|.
gi 46359779  85 VFF-QATARGEEGMTLFFVCCNpnCGHRWRE 114
Cdd:COG1594  74 YWWlKQTRSADEPETRFFRCTK--CGHTWRE 102
TFS_arch TIGR01384
transcription factor S, archaeal; This model describes archaeal transcription factor S, a ...
 5-114 1.37e-13

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: 61.39  E-value: 1.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46359779     5 KFCRECNNILYPKEDKeqkillYACRNCDHQE--VADNSCVYRNEVHHSVSERTQILTDVASdpTLPRTKaVRCSKCQHR 82
Cdd:TIGR01384   1 KFCPKCGSLMTPKNGV------YVCPSCGYEKekKPEDDYKVTEKVKHKIKETIIIREEDSE--TLPTTR-VECPKCGHK 71

                          90       100       110
                  ....*....|....*....|....*....|...
gi 46359779    83 EAVFF-QATARGEEGMTLFFVCcnPNCGHRWRE 114
Cdd:TIGR01384  72 EAYYWlLQTRRADEPETRFYKC--TKCGYVWRE 102
RPOL9 smart00661
RNA polymerase subunit 9;
5-58 1.86e-11

RNA polymerase subunit 9;


Pssm-ID: 197822  Cd Length: 52  Bit Score: 54.70  E-value: 1.86e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 46359779      5 KFCRECNNILYPKEDKEQKilLYACRNCDHQEVADNSCVYRNEVHHSVSERTQI 58
Cdd:smart00661   1 KFCPKCGNMLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
TFIIS_C pfam01096
Transcription factor S-II (TFIIS);
74-113 4.29e-10

Transcription factor S-II (TFIIS);


Pssm-ID: 426046  Cd Length: 39  Bit Score: 50.68  E-value: 4.29e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 46359779    74 VRCSKCQHREAVFFQA-TARGEEGMTLFFVCCnpNCGHRWR 113
Cdd:pfam01096   1 AKCPKCGNREAYFFQLqTRSADEPMTVFYVCT--KCGHRWR 39
Zn-ribbon cd00656
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 67-113 8.18e-09

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: 47.69  E-value: 8.18e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 46359779  67 TLPRTKaVRCSKCQHREAVFFQA-TARGEEGMTLFFVCCNpnCGHRWR 113
Cdd:cd00656   1 TLPTTD-RTCPKCGHDEAYWWMLqTRSADEPPTRFYKCTK--CGHTWR 45
Zn-ribbon_RPC11 cd10509
C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III; The C-terminal zinc ...
 74-114 1.23e-08

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: 47.20  E-value: 1.23e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 46359779  74 VRCSKCQHREAVFFQATAR-GEEGMTLFFVCCnpNCGHRWRE 114
Cdd:cd10509   7 ATCPKCGHNRAYFMQIQTRsADEPMTTFYKCC--KCGHQWRE 46
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 76-114 9.33e-08

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: 44.63  E-value: 9.33e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 46359779     76 CSKCQHREAVFFQA-TARGEEGMTLFFVCCNpnCGHRWRE 114
Cdd:smart00440   3 CPKCGNREATFYQLqTRSADEPMTVFYVCTK--CGHHWRE 40
Zn-ribbon_RPA12 cd10507
C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon ...
 75-114 4.03e-07

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: 43.35  E-value: 4.03e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 46359779  75 RCSKCQHREAVFFQATARG-EEGMTLFFVCcnPNCGHRWRE 114
Cdd:cd10507   8 KCPKCGHDEMTYSTLQLRSaDEGQTVFYEC--PKCGHRFSE 46
RNA_POL_M_15KD pfam02150
RNA polymerases M/15 Kd subunit;
4-39 2.20e-06

RNA polymerases M/15 Kd subunit;


Pssm-ID: 280336  Cd Length: 36  Bit Score: 41.30  E-value: 2.20e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 46359779     4 MKFCRECNNILYPKEDKEQKIllYACRNCDHQEVAD 39
Cdd:pfam02150   1 LIFCPKCGNLLLPTEDKLGSN--FECRQCGYEEPAD 34
Zn-ribbon_TFS cd10511
C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS); TFS is an archaeal ...
 67-114 3.84e-05

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: 38.10  E-value: 3.84e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 46359779  67 TLPRTKaVRCSKCQHREAVFF-QATARGEEGMTLFFVCcnPNCGHRWRE 114
Cdd:cd10511   1 TLPTTK-ITCPKCGHDEAYWWmVQTRSADEPPTRFYKC--TKCGHTWRE 46
Zn-ribbon_TFIIS cd13749
domain III/zinc ribbon domain of Transcription Factor IIS; TFIIS is a zinc-containing ...
 75-114 9.98e-04

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: 34.50  E-value: 9.98e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 46359779  75 RCSKCQHREAVFFQATAR-GEEGMTLFFVCCNpnCGHRWRE 114
Cdd:cd13749   9 KCGKCKKRKCTYYQLQTRsADEPMTTFVTCLN--CGNRWKF 47
 
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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