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Conserved domains on  [gi|488035759|ref|WP_002107156|]
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MULTISPECIES: CarD family transcriptional regulator [Bacillus]

Protein Classification

CarD family transcriptional regulator( domain architecture ID 10003550)

CarD family transcriptional regulator similar to Mycobacterium RNA polymerase-binding transcription factor CarD, an essential RNA polymerase binding protein that plays an important role in reprogramming the transcription machinery under diverse stress conditions

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CdnL COG1329
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
2-152 1.29e-61

RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];


:

Pssm-ID: 440940 [Multi-domain]  Cd Length: 155  Bit Score: 186.49  E-value: 1.29e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488035759   2 FQIGDNIVYPMHGAGIIEAIEEKEFSGKKQQYYVIKMSISNMQVMIPMGKILSSSIRPVTDILALKHIIHIFQHGESDRL 81
Cdd:COG1329    1 FKVGDKVVYPMHGVGVIEAIEEKEIAGEKKEYYVLRFPYDDMTIMVPVDKAESVGLRPVISKEEVEKVLDVLKGRETVKP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488035759  82 LPWKQRYKVNTDKIKTGEIQEGAEVVRDLMRMKKEKALNTSEKKMLDNAHEFLISELGLIKGITENQIKSF 152
Cdd:COG1329   81 TNWSRRYREYEEKIKSGDIFEIAEVVRDLYRRDKEKKLSAGERKMLENARQLLVSELALALGIDEEEAEEL 151
 
Name Accession Description Interval E-value
CdnL COG1329
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
2-152 1.29e-61

RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];


Pssm-ID: 440940 [Multi-domain]  Cd Length: 155  Bit Score: 186.49  E-value: 1.29e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488035759   2 FQIGDNIVYPMHGAGIIEAIEEKEFSGKKQQYYVIKMSISNMQVMIPMGKILSSSIRPVTDILALKHIIHIFQHGESDRL 81
Cdd:COG1329    1 FKVGDKVVYPMHGVGVIEAIEEKEIAGEKKEYYVLRFPYDDMTIMVPVDKAESVGLRPVISKEEVEKVLDVLKGRETVKP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488035759  82 LPWKQRYKVNTDKIKTGEIQEGAEVVRDLMRMKKEKALNTSEKKMLDNAHEFLISELGLIKGITENQIKSF 152
Cdd:COG1329   81 TNWSRRYREYEEKIKSGDIFEIAEVVRDLYRRDKEKKLSAGERKMLENARQLLVSELALALGIDEEEAEEL 151
CarD_TRCF smart01058
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ...
 1-111 1.64e-31

CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase.


Pssm-ID: 215001 [Multi-domain]  Cd Length: 99  Bit Score: 108.31  E-value: 1.64e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488035759     1 MFQIGDNIVYPMHGAGIIEAIEEKEFSGKKQQYYVIKMSiSNMQVMIPMGKiLSSSIRPVTDILALKHIIHIFQHGEsdr 80
Cdd:smart01058   1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYA-GGDKLYVPVDN-LDLGSRYVGSEGEVEPVLDKLGGGS--- 75

                           90       100       110
                   ....*....|....*....|....*....|.
gi 488035759    81 llpWKQRYKvntdKIKTGEIQEGAEVVRDLM 111
Cdd:smart01058  76 ---WSKRKR----KAKSGIRDIAAELLRLYA 99
CarD_CdnL_TRCF pfam02559
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ...
 2-110 2.69e-19

CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain, CdnL. CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF (transcription-repair-coupling factor) proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. The family includes members otherwise referred to as CdnL, for CarD N-terminal like, which differ functionally from CarD. The TRCF domain mentioned above is the RNA polymerase-interacting domain or RID.


Pssm-ID: 460590 [Multi-domain]  Cd Length: 89  Bit Score: 77.10  E-value: 2.69e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488035759    2 FQIGDNIVYPMHGAGIIEAIEEKEfsgkKQQYYVIKMsISNMQVMIPMGKIlsSSIRPVTDILALKHIIHifqhgesdrl 81
Cdd:pfam02559   1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEY-AGGDKLYVPVDNL--DLIRKYISKGELDKLGD---------- 63

                          90       100
                  ....*....|....*....|....*....
gi 488035759   82 lpwKQRYKVNTDKIKTGEIQEGAEVVRDL 110
Cdd:pfam02559  64 ---GRRWRKYKEKLKSGDIEEAAELIKLY 89
 
Name Accession Description Interval E-value
CdnL COG1329
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
2-152 1.29e-61

RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];


Pssm-ID: 440940 [Multi-domain]  Cd Length: 155  Bit Score: 186.49  E-value: 1.29e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488035759   2 FQIGDNIVYPMHGAGIIEAIEEKEFSGKKQQYYVIKMSISNMQVMIPMGKILSSSIRPVTDILALKHIIHIFQHGESDRL 81
Cdd:COG1329    1 FKVGDKVVYPMHGVGVIEAIEEKEIAGEKKEYYVLRFPYDDMTIMVPVDKAESVGLRPVISKEEVEKVLDVLKGRETVKP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488035759  82 LPWKQRYKVNTDKIKTGEIQEGAEVVRDLMRMKKEKALNTSEKKMLDNAHEFLISELGLIKGITENQIKSF 152
Cdd:COG1329   81 TNWSRRYREYEEKIKSGDIFEIAEVVRDLYRRDKEKKLSAGERKMLENARQLLVSELALALGIDEEEAEEL 151
CarD_TRCF smart01058
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ...
 1-111 1.64e-31

CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase.


Pssm-ID: 215001 [Multi-domain]  Cd Length: 99  Bit Score: 108.31  E-value: 1.64e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488035759     1 MFQIGDNIVYPMHGAGIIEAIEEKEFSGKKQQYYVIKMSiSNMQVMIPMGKiLSSSIRPVTDILALKHIIHIFQHGEsdr 80
Cdd:smart01058   1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYA-GGDKLYVPVDN-LDLGSRYVGSEGEVEPVLDKLGGGS--- 75

                           90       100       110
                   ....*....|....*....|....*....|.
gi 488035759    81 llpWKQRYKvntdKIKTGEIQEGAEVVRDLM 111
Cdd:smart01058  76 ---WSKRKR----KAKSGIRDIAAELLRLYA 99
CarD_CdnL_TRCF pfam02559
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ...
 2-110 2.69e-19

CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain, CdnL. CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF (transcription-repair-coupling factor) proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. The family includes members otherwise referred to as CdnL, for CarD N-terminal like, which differ functionally from CarD. The TRCF domain mentioned above is the RNA polymerase-interacting domain or RID.


Pssm-ID: 460590 [Multi-domain]  Cd Length: 89  Bit Score: 77.10  E-value: 2.69e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488035759    2 FQIGDNIVYPMHGAGIIEAIEEKEfsgkKQQYYVIKMsISNMQVMIPMGKIlsSSIRPVTDILALKHIIHifqhgesdrl 81
Cdd:pfam02559   1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEY-AGGDKLYVPVDNL--DLIRKYISKGELDKLGD---------- 63

                          90       100
                  ....*....|....*....|....*....
gi 488035759   82 lpwKQRYKVNTDKIKTGEIQEGAEVVRDL 110
Cdd:pfam02559  64 ---GRRWRKYKEKLKSGDIEEAAELIKLY 89
 
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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