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Conserved domains on  [gi|673992131|gb|AIK60742|]
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type IV secretory system Conjugative DNA transfer family protein (plasmid) [Bacillus anthracis str. Vollum]

Protein Classification

DEAD/DEAH box helicase family protein( domain architecture ID 1000205)

DEAD/DEAH box helicase family protein such as a DEAD/DEAH box-containing ATP-dependent helicase, which catalyzes the unwinding of DNA or RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1-88 1.02e-12

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member pfam12696:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 125  Bit Score: 63.44  E-value: 1.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673992131    1 MLFNLVLQSYSQIEKLYDKEATE-IKDNCQNHIYIMSTNKDTIEEISHRAGHKTVIGKSSNESHLETDNKI-----TKNA 74
Cdd:pfam12696  30 ISLMLILQSIAQLEELYGKDGAEtILGNCNTKVFLGGGDEETAKYLSKLLGKYTVVSTTTSSSSSGSGGSGsssssSSQL 109

                          90
                  ....*....|....
gi 673992131   75 DQQRIISPERLAQF 88
Cdd:pfam12696 110 VGRPLLTPDELRRL 123
 
Name Accession Description Interval E-value
TraG-D_C pfam12696
TraM recognition site of TraD and TraG; This family includes both TraG and TraD as well as ...
 1-88 1.02e-12

TraM recognition site of TraD and TraG; This family includes both TraG and TraD as well as VirD4 proteins. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. This domain interacts with the relaxosome component TraM via the latter's tetramerization domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore.


Pssm-ID: 432726 [Multi-domain]  Cd Length: 125  Bit Score: 63.44  E-value: 1.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673992131    1 MLFNLVLQSYSQIEKLYDKEATE-IKDNCQNHIYIMSTNKDTIEEISHRAGHKTVIGKSSNESHLETDNKI-----TKNA 74
Cdd:pfam12696  30 ISLMLILQSIAQLEELYGKDGAEtILGNCNTKVFLGGGDEETAKYLSKLLGKYTVVSTTTSSSSSGSGGSGsssssSSQL 109

                          90
                  ....*....|....
gi 673992131   75 DQQRIISPERLAQF 88
Cdd:pfam12696 110 VGRPLLTPDELRRL 123
VirD4 COG3505
Type IV secretory pathway, VirD4 component, TraG/TraD family ATPase [Intracellular trafficking, ...
 3-127 1.00e-11

Type IV secretory pathway, VirD4 component, TraG/TraD family ATPase [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442728 [Multi-domain]  Cd Length: 402  Bit Score: 64.24  E-value: 1.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673992131   3 FNLVLQSYSQIEKLY-DKEATEIKDNCQNHIYIMSTNKDTIEEISHRAGHKTVIGKSSNESHleTDNKITKNADQQRIIS 81
Cdd:COG3505  279 LVLILQSLAQLEAIYgEEGAETILGNCGTKIFLGVNDPETAEYLSELLGKRTVERRSESRSR--GSRSRSRSEQERPLLT 356

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 673992131  82 PERLAQFIEGETLLLRALHRqDLKRKKVRAYPILNTRETSMPYRWQ 127
Cdd:COG3505  357 PDELRRLPDGEAIVLVRGGP-PIRAKKIRYYKDPEPAPAFEPRDAE 401
TrwB_TraG_TraD_VirD4 cd01127
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are ...
 1-36 9.76e-06

TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion (T4S) systems, versatile bacterial secretion systems mediating transport of protein and/or DNA. They are present in gram-negative and gram-positive bacteria, as well as archaea. They form hexameric rings and belong to the RecA-like NTPases superfamily, which also includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases.


Pssm-ID: 410871 [Multi-domain]  Cd Length: 144  Bit Score: 44.52  E-value: 9.76e-06
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 673992131   1 MLFNLVLQSYSQIEKLYDKEATE-IKDNCQNHIYIMS 36
Cdd:cd01127  108 ISVVLILQSLAQLEAVYGKDGAQtILGNCNTKLYLGT 144
 
Name Accession Description Interval E-value
TraG-D_C pfam12696
TraM recognition site of TraD and TraG; This family includes both TraG and TraD as well as ...
 1-88 1.02e-12

TraM recognition site of TraD and TraG; This family includes both TraG and TraD as well as VirD4 proteins. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. This domain interacts with the relaxosome component TraM via the latter's tetramerization domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore.


Pssm-ID: 432726 [Multi-domain]  Cd Length: 125  Bit Score: 63.44  E-value: 1.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673992131    1 MLFNLVLQSYSQIEKLYDKEATE-IKDNCQNHIYIMSTNKDTIEEISHRAGHKTVIGKSSNESHLETDNKI-----TKNA 74
Cdd:pfam12696  30 ISLMLILQSIAQLEELYGKDGAEtILGNCNTKVFLGGGDEETAKYLSKLLGKYTVVSTTTSSSSSGSGGSGsssssSSQL 109

                          90
                  ....*....|....
gi 673992131   75 DQQRIISPERLAQF 88
Cdd:pfam12696 110 VGRPLLTPDELRRL 123
VirD4 COG3505
Type IV secretory pathway, VirD4 component, TraG/TraD family ATPase [Intracellular trafficking, ...
 3-127 1.00e-11

Type IV secretory pathway, VirD4 component, TraG/TraD family ATPase [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442728 [Multi-domain]  Cd Length: 402  Bit Score: 64.24  E-value: 1.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 673992131   3 FNLVLQSYSQIEKLY-DKEATEIKDNCQNHIYIMSTNKDTIEEISHRAGHKTVIGKSSNESHleTDNKITKNADQQRIIS 81
Cdd:COG3505  279 LVLILQSLAQLEAIYgEEGAETILGNCGTKIFLGVNDPETAEYLSELLGKRTVERRSESRSR--GSRSRSRSEQERPLLT 356

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 673992131  82 PERLAQFIEGETLLLRALHRqDLKRKKVRAYPILNTRETSMPYRWQ 127
Cdd:COG3505  357 PDELRRLPDGEAIVLVRGGP-PIRAKKIRYYKDPEPAPAFEPRDAE 401
TrwB_TraG_TraD_VirD4 cd01127
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are ...
 1-36 9.76e-06

TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion (T4S) systems, versatile bacterial secretion systems mediating transport of protein and/or DNA. They are present in gram-negative and gram-positive bacteria, as well as archaea. They form hexameric rings and belong to the RecA-like NTPases superfamily, which also includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases.


Pssm-ID: 410871 [Multi-domain]  Cd Length: 144  Bit Score: 44.52  E-value: 9.76e-06
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 673992131   1 MLFNLVLQSYSQIEKLYDKEATE-IKDNCQNHIYIMS 36
Cdd:cd01127  108 ISVVLILQSLAQLEAVYGKDGAQtILGNCNTKLYLGT 144
T4SS-DNA_transf pfam02534
Type IV secretory system Conjugative DNA transfer; These proteins contain a P-loop and ...
 1-76 8.76e-04

Type IV secretory system Conjugative DNA transfer; These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. The C-terminus of this domain interacts with the relaxosome component TraM via the latter's tetramerization domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore. The family contains a number of different DNA transfer proteins.


Pssm-ID: 367119 [Multi-domain]  Cd Length: 468  Bit Score: 40.47  E-value: 8.76e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 673992131    1 MLFNLVLQSYSQIEKLYDKE-ATEIKDNCQNHIYIMSTNK-DTIEEISHRAGHKTVIGKSSNEShleTDNKITKNADQ 76
Cdd:pfam02534 332 IRLTTICQSISQLKETYGGEgAKSILSNHAVVICFAASNDeETAKYISKLLGKTTVEVESSSKS---TDAKGSSRSRS 406
 
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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