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Conserved domains on  [gi|1240364309|gb|PAV76258|]
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hypothetical protein WR25_02177 [Diploscapter pachys]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPOL9 smart00661
RNA polymerase subunit 9;
14-67 8.24e-18

RNA polymerase subunit 9;


:

Pssm-ID: 197822  Cd Length: 52  Bit Score: 74.34  E-value: 8.24e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1240364309   14 KFCPECNNMLYPKEDKEHRqlLYACRNCDHKQVSDNPCIYVNKLMHEVDELTQI 67
Cdd:smart00661   1 KFCPKCGNMLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
Zn-ribbon_RPB9 cd10508
C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon ...
 73-108 1.82e-15

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: 68.05  E-value: 1.82e-15
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1240364309  73 HDPTLPKTEDHPCKKCGHGLAVFFQAQSRRAEQMLR 108
Cdd:cd10508     1 QDPTLPRTEDHPCPKCGHNEAVFFQSQSRRAEEGMT 36
Robl_LC7 smart00960
Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and ...
 126-196 1.58e-06

Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.


:

Pssm-ID: 214939  Cd Length: 88  Bit Score: 44.88  E-value: 1.58e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1240364309  126 GSLLANRDGLILASVGLS--DVNVYGSLLAGIWDTFDRTGDNsASREELKDTVVMCEDGMIAAQRVANMLIAI 196
Cdd:smart00960  16 GALVVSRDGLLLASSGLSddDAERLAALAAGLLSLAERAARE-LGEGELRQLRIEGEKGEVLITPAGDALLAV 87
 
Name Accession Description Interval E-value
RPOL9 smart00661
RNA polymerase subunit 9;
14-67 8.24e-18

RNA polymerase subunit 9;


Pssm-ID: 197822  Cd Length: 52  Bit Score: 74.34  E-value: 8.24e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1240364309   14 KFCPECNNMLYPKEDKEHRqlLYACRNCDHKQVSDNPCIYVNKLMHEVDELTQI 67
Cdd:smart00661   1 KFCPKCGNMLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
Zn-ribbon_RPB9 cd10508
C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon ...
 73-108 1.82e-15

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: 68.05  E-value: 1.82e-15
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1240364309  73 HDPTLPKTEDHPCKKCGHGLAVFFQAQSRRAEQMLR 108
Cdd:cd10508     1 QDPTLPRTEDHPCPKCGHNEAVFFQSQSRRAEEGMT 36
RPB9 COG1594
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 14-105 9.40e-14

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: 64.97  E-value: 9.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1240364309  14 KFCPECNNMLYPKEDKehrqllYACRNCDHKQVSDNPC--IYVNKLMHEVDELTQIVADVihDPTLPKTEDHpCKKCGHG 91
Cdd:COG1594     1 KFCPKCGSMMKPKDGV------LVCPKCGYEEPRDEEAeaKYVSTEEQEDKEIIVVEEEE--VEGLPTTKVI-CPKCGND 71

                          90
                  ....*....|....
gi 1240364309  92 LAVFFQAQSRRAEQ 105
Cdd:COG1594    72 EAYWWLKQTRSADE 85
RNA_POL_M_15KD pfam02150
RNA polymerases M/15 Kd subunit;
13-50 4.25e-09

RNA polymerases M/15 Kd subunit;


Pssm-ID: 280336  Cd Length: 36  Bit Score: 50.55  E-value: 4.25e-09
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1240364309  13 IKFCPECNNMLYPKEDKEHRQllYACRNCDHKQVSDNP 50
Cdd:pfam02150   1 LIFCPKCGNLLLPTEDKLGSN--FECRQCGYEEPADQF 36
Robl_LC7 smart00960
Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and ...
 126-196 1.58e-06

Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.


Pssm-ID: 214939  Cd Length: 88  Bit Score: 44.88  E-value: 1.58e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1240364309  126 GSLLANRDGLILASVGLS--DVNVYGSLLAGIWDTFDRTGDNsASREELKDTVVMCEDGMIAAQRVANMLIAI 196
Cdd:smart00960  16 GALVVSRDGLLLASSGLSddDAERLAALAAGLLSLAERAARE-LGEGELRQLRIEGEKGEVLITPAGDALLAV 87
COG2018 COG2018
Predicted regulator of Ras-like GTPase activity, Roadblock/LC7/MglB family [Signal ...
 108-223 8.57e-06

Predicted regulator of Ras-like GTPase activity, Roadblock/LC7/MglB family [Signal transduction mechanisms];


Pssm-ID: 441621  Cd Length: 123  Bit Score: 43.68  E-value: 8.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1240364309 108 RQKALVEVLKQ--ANSDEIYGSLLANRDGLILASVGLS---DVNVYGSLLAGIWDTFDRTGDnSASREELKDTVVMCEDG 182
Cdd:COG2018     2 QAEKLDWLLDDlvERVPGVRGAVLVSADGLLIASSLGLdddDAERLAAMAAGLLSLARRAAR-ELGAGEVEQVVVEGERG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1240364309 183 MIAAQRV-ANMLIAIKASRNAPLGTVRSRLSALAKYLEEPLS 223
Cdd:COG2018    81 YLLVTAAgDGAVLAVLADPDADLGLVRYEMRRLAERLGELLT 122
Robl_LC7 pfam03259
Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and ...
 115-198 9.59e-05

Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.


Pssm-ID: 397386  Cd Length: 91  Bit Score: 39.92  E-value: 9.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1240364309 115 VLKQANSDEIYGSLLANRDGLILASVGL--SDVNVYGSLLAGIWDTFDRTGDNSASrEELKDTVVMCEDGMIAAQRVAN- 191
Cdd:pfam03259   6 LDLLQRVPGVRGALVVSKDGLVIASSTLdnDDADHLAALASGLLSAAKGAARDLGS-GELRQLLIEGKKGELYLTPAGEg 84


                  ....*..
gi 1240364309 192 MLIAIKA 198
Cdd:pfam03259  85 ALLVVLA 91
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 83-106 5.41e-04

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: 36.54  E-value: 5.41e-04
                           10        20
                   ....*....|....*....|....
gi 1240364309   83 HPCKKCGHGLAVFFQAQSRRAEQM 106
Cdd:smart00440   1 AECPKCGNREATFYQLQTRSADEP 24
 
Name Accession Description Interval E-value
RPOL9 smart00661
RNA polymerase subunit 9;
14-67 8.24e-18

RNA polymerase subunit 9;


Pssm-ID: 197822  Cd Length: 52  Bit Score: 74.34  E-value: 8.24e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1240364309   14 KFCPECNNMLYPKEDKEHRqlLYACRNCDHKQVSDNPCIYVNKLMHEVDELTQI 67
Cdd:smart00661   1 KFCPKCGNMLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
Zn-ribbon_RPB9 cd10508
C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon ...
 73-108 1.82e-15

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: 68.05  E-value: 1.82e-15
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1240364309  73 HDPTLPKTEDHPCKKCGHGLAVFFQAQSRRAEQMLR 108
Cdd:cd10508     1 QDPTLPRTEDHPCPKCGHNEAVFFQSQSRRAEEGMT 36
RPB9 COG1594
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 14-105 9.40e-14

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: 64.97  E-value: 9.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1240364309  14 KFCPECNNMLYPKEDKehrqllYACRNCDHKQVSDNPC--IYVNKLMHEVDELTQIVADVihDPTLPKTEDHpCKKCGHG 91
Cdd:COG1594     1 KFCPKCGSMMKPKDGV------LVCPKCGYEEPRDEEAeaKYVSTEEQEDKEIIVVEEEE--VEGLPTTKVI-CPKCGND 71

                          90
                  ....*....|....
gi 1240364309  92 LAVFFQAQSRRAEQ 105
Cdd:COG1594    72 EAYWWLKQTRSADE 85
RNA_POL_M_15KD pfam02150
RNA polymerases M/15 Kd subunit;
13-50 4.25e-09

RNA polymerases M/15 Kd subunit;


Pssm-ID: 280336  Cd Length: 36  Bit Score: 50.55  E-value: 4.25e-09
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1240364309  13 IKFCPECNNMLYPKEDKEHRQllYACRNCDHKQVSDNP 50
Cdd:pfam02150   1 LIFCPKCGNLLLPTEDKLGSN--FECRQCGYEEPADQF 36
Robl_LC7 smart00960
Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and ...
 126-196 1.58e-06

Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.


Pssm-ID: 214939  Cd Length: 88  Bit Score: 44.88  E-value: 1.58e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1240364309  126 GSLLANRDGLILASVGLS--DVNVYGSLLAGIWDTFDRTGDNsASREELKDTVVMCEDGMIAAQRVANMLIAI 196
Cdd:smart00960  16 GALVVSRDGLLLASSGLSddDAERLAALAAGLLSLAERAARE-LGEGELRQLRIEGEKGEVLITPAGDALLAV 87
COG2018 COG2018
Predicted regulator of Ras-like GTPase activity, Roadblock/LC7/MglB family [Signal ...
 108-223 8.57e-06

Predicted regulator of Ras-like GTPase activity, Roadblock/LC7/MglB family [Signal transduction mechanisms];


Pssm-ID: 441621  Cd Length: 123  Bit Score: 43.68  E-value: 8.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1240364309 108 RQKALVEVLKQ--ANSDEIYGSLLANRDGLILASVGLS---DVNVYGSLLAGIWDTFDRTGDnSASREELKDTVVMCEDG 182
Cdd:COG2018     2 QAEKLDWLLDDlvERVPGVRGAVLVSADGLLIASSLGLdddDAERLAAMAAGLLSLARRAAR-ELGAGEVEQVVVEGERG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1240364309 183 MIAAQRV-ANMLIAIKASRNAPLGTVRSRLSALAKYLEEPLS 223
Cdd:COG2018    81 YLLVTAAgDGAVLAVLADPDADLGLVRYEMRRLAERLGELLT 122
Robl_LC7 pfam03259
Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and ...
 115-198 9.59e-05

Roadblock/LC7 domain; This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.


Pssm-ID: 397386  Cd Length: 91  Bit Score: 39.92  E-value: 9.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1240364309 115 VLKQANSDEIYGSLLANRDGLILASVGL--SDVNVYGSLLAGIWDTFDRTGDNSASrEELKDTVVMCEDGMIAAQRVAN- 191
Cdd:pfam03259   6 LDLLQRVPGVRGALVVSKDGLVIASSTLdnDDADHLAALASGLLSAAKGAARDLGS-GELRQLLIEGKKGELYLTPAGEg 84


                  ....*..
gi 1240364309 192 MLIAIKA 198
Cdd:pfam03259  85 ALLVVLA 91
ZnF_C2C2 smart00440
C2C2 Zinc finger; Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and ...
 83-106 5.41e-04

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: 36.54  E-value: 5.41e-04
                           10        20
                   ....*....|....*....|....
gi 1240364309   83 HPCKKCGHGLAVFFQAQSRRAEQM 106
Cdd:smart00440   1 AECPKCGNREATFYQLQTRSADEP 24
Zn-ribbon_RPC11 cd10509
C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III; The C-terminal zinc ...
 78-106 6.41e-03

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: 33.71  E-value: 6.41e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1240364309  78 PKTEDhPCKKCGHGLAVFFQAQSRRA-EQM 106
Cdd:cd10509     3 DKTEA-TCPKCGHNRAYFMQIQTRSAdEPM 31
 
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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