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Conserved domains on  [gi|490282304|ref|WP_004178196|]
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MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Gammaproteobacteria]

Protein Classification

type IV secretory system conjugative DNA transfer family protein( domain architecture ID 11466229)

type IV secretory system conjugative DNA transfer family protein similar to Agrobacterium tumefaciens VirD4

CATH:  3.40.50.300
Gene Ontology:  GO:0005524|GO:0016887|GO:0016020
SCOP:  4004128

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
VirD4 COG3505
Type IV secretory pathway, VirD4 component, TraG/TraD family ATPase [Intracellular trafficking, ...
259-597 5.48e-28

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: 116.62  E-value: 5.48e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 259 NIQILGLPGSGKSVMATNALIRCVRDfGDAVVYFDPKGDAWAP--HVFRAHCPDFTLLDL-RPGKPAQLNLFRDLDQYA- 334
Cdd:COG3505    1 HVLVIGPTGSGKTVGLVIPNLTQLAR-GESVVVTDPKGDLAELtaGFRRRAGYDVYVFDPfDPERSHRWNPLDEIRDPAd 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 335 ---LKNLLIAGLNLGETGDvaDHYRISEQK----AAKLIAEqfPQGANIQQVLA-----------------------AAY 384
Cdd:COG3505   80 aqeLAEALIPALGGGGGGD--PFWREAARAllaaLILALAE--EGRRTLADVYRllsepeeelrellealpesphppVAD 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 385 ALPEALKKDVK-------GLITRLENVADLSVLQ--TDSGIDVAGIINGGGCLYVIGSMDDEAVIR-VQKMLFARCAQII 454
Cdd:COG3505  156 TLAAFLNAAEKtrssvlsTLASALELLSDPEVAAltSGSDFDLRDLIREKGTLYLVLPPDDLSTLApLLRLLLSQLIRAL 235
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 455 --IARDEFREWPHVSVMLDEIKYLLS-KYVLNALGTLRSRDCNLLLAHQSLGDFgqcgQDLPAEFVKTTVLDNTPIRWFY 531
Cdd:COG3505  236 lrRAERSGRLPRPVLLLLDEFANLGRlPSLETLLATGRGYGIRLVLILQSLAQL----EAIYGEEGAETILGNCGTKIFL 311
                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490282304 532 RAASLESAQWAAGQTGEirVDVERRRASREAGNVehisGDSfIQKEARPLFDVNTLQHLPDGFAVM 597
Cdd:COG3505  312 GVNDPETAEYLSELLGK--RTVERRSESRSRGSR----SRS-RSEQERPLLTPDELRRLPDGEAIV 370
 
Name Accession Description Interval E-value
VirD4 COG3505
Type IV secretory pathway, VirD4 component, TraG/TraD family ATPase [Intracellular trafficking, ...
259-597 5.48e-28

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: 116.62  E-value: 5.48e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 259 NIQILGLPGSGKSVMATNALIRCVRDfGDAVVYFDPKGDAWAP--HVFRAHCPDFTLLDL-RPGKPAQLNLFRDLDQYA- 334
Cdd:COG3505    1 HVLVIGPTGSGKTVGLVIPNLTQLAR-GESVVVTDPKGDLAELtaGFRRRAGYDVYVFDPfDPERSHRWNPLDEIRDPAd 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 335 ---LKNLLIAGLNLGETGDvaDHYRISEQK----AAKLIAEqfPQGANIQQVLA-----------------------AAY 384
Cdd:COG3505   80 aqeLAEALIPALGGGGGGD--PFWREAARAllaaLILALAE--EGRRTLADVYRllsepeeelrellealpesphppVAD 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 385 ALPEALKKDVK-------GLITRLENVADLSVLQ--TDSGIDVAGIINGGGCLYVIGSMDDEAVIR-VQKMLFARCAQII 454
Cdd:COG3505  156 TLAAFLNAAEKtrssvlsTLASALELLSDPEVAAltSGSDFDLRDLIREKGTLYLVLPPDDLSTLApLLRLLLSQLIRAL 235
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 455 --IARDEFREWPHVSVMLDEIKYLLS-KYVLNALGTLRSRDCNLLLAHQSLGDFgqcgQDLPAEFVKTTVLDNTPIRWFY 531
Cdd:COG3505  236 lrRAERSGRLPRPVLLLLDEFANLGRlPSLETLLATGRGYGIRLVLILQSLAQL----EAIYGEEGAETILGNCGTKIFL 311
                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490282304 532 RAASLESAQWAAGQTGEirVDVERRRASREAGNVehisGDSfIQKEARPLFDVNTLQHLPDGFAVM 597
Cdd:COG3505  312 GVNDPETAEYLSELLGK--RTVERRSESRSRGSR----SRS-RSEQERPLLTPDELRRLPDGEAIV 370
TrwB_AAD_bind pfam10412
Type IV secretion-system coupling protein DNA-binding domain; The plasmid conjugative coupling ...
262-607 3.22e-04

Type IV secretion-system coupling protein DNA-binding domain; The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export.


Pssm-ID: 431268 [Multi-domain]  Cd Length: 386  Bit Score: 43.44  E-value: 3.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  262 ILGLPGSGKSVmATNALIRCVRDFGDAVVYFDPKGdAWAPHVFRAHCPdfTLLDLRPGKPAQLNLFRDLDQYalknllia 341
Cdd:pfam10412  20 IIGTTGSGKTQ-ALRGLLDQARARGDRAIIFDLTG-AFTERFYDPGRD--ILLNPLDARSPAWSPFAECKTP-------- 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  342 glnlgetgdvADHYRIseqkAAKLIAEQfPQGANIQQVLAAAYALPEALKKDVKglITRLENVADLSVLQTDSGIDVAGI 421
Cdd:pfam10412  88 ----------ADFAAI----AAALIPED-GGGSDPFWALAARTVLVDTLRALQR--TGRKTNAALLRALLTADLDELHEL 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  422 INGGGCLYVIGSMDDEAVIRVQKML--FARCAQIIIARDE---FREW-----------------------PHVSVMLD-E 472
Cdd:pfam10412 151 LAGTAAAPLTAPEAERTTASIRATLatNLRALRFLAPDGErfsIREWiteedpggwlfityradqraalrPLLSCWLDlA 230
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  473 IKYLLSK---------YVLNALGTLrSRDCNLLLAHQSLGDFGQC---------------GQDLPAefvktTVLDNTPIR 528
Cdd:pfam10412 231 IRALLSLppsrdrrlwFFLDELPAL-GRLPSLKDLLAEGRKFGGAvvlglqsiaqlreiyGEDGAQ-----TILSNCGTK 304
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  529 WFYRAASLESAQWAAGQTGEirVDVERRRASREAGNVEHISGDSF-IQKEARPLFDVNTLQHLPD--GFAV-MTGLGVAR 604
Cdd:pfam10412 305 LILRVSDGETAELCSDLLGD--REVERMDESLSYGANNSRDGVTLgRQRRVRPLVLPSEIMNLPRlhGYLKfPDGFPVAR 382

                  ...
gi 490282304  605 MAF 607
Cdd:pfam10412 383 VTL 385
TrwB_TraG_TraD_VirD4 cd01127
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are ...
259-299 3.25e-04

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: 41.44  E-value: 3.25e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 490282304 259 NIQILGLPGSGKSVMATNALIRcVRDFGDAVVYFDPKGDAW 299
Cdd:cd01127    1 NTLVLGTTGSGKTTSIVIPLLD-QAARGGSVIITDPKGELF 40
SXT_TraD TIGR03743
conjugative coupling factor TraD, SXT/TOL subfamily; Members of this protein family are the ...
240-298 6.77e-04

conjugative coupling factor TraD, SXT/TOL subfamily; Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274760 [Multi-domain]  Cd Length: 634  Bit Score: 42.65  E-value: 6.77e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 490282304  240 GKDEQGKPVLVPRDTwRKTNIQILGLPGSGKSVMATNALIRCVRDfGDAVVYFDPKGDA 298
Cdd:TIGR03743 160 GVEPKEEDVYLPLGH-RVGHTLVLGTTGVGKTRLAELLITQDIRR-GDVVIVIDPKGDA 216
 
Name Accession Description Interval E-value
VirD4 COG3505
Type IV secretory pathway, VirD4 component, TraG/TraD family ATPase [Intracellular trafficking, ...
259-597 5.48e-28

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: 116.62  E-value: 5.48e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 259 NIQILGLPGSGKSVMATNALIRCVRDfGDAVVYFDPKGDAWAP--HVFRAHCPDFTLLDL-RPGKPAQLNLFRDLDQYA- 334
Cdd:COG3505    1 HVLVIGPTGSGKTVGLVIPNLTQLAR-GESVVVTDPKGDLAELtaGFRRRAGYDVYVFDPfDPERSHRWNPLDEIRDPAd 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 335 ---LKNLLIAGLNLGETGDvaDHYRISEQK----AAKLIAEqfPQGANIQQVLA-----------------------AAY 384
Cdd:COG3505   80 aqeLAEALIPALGGGGGGD--PFWREAARAllaaLILALAE--EGRRTLADVYRllsepeeelrellealpesphppVAD 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 385 ALPEALKKDVK-------GLITRLENVADLSVLQ--TDSGIDVAGIINGGGCLYVIGSMDDEAVIR-VQKMLFARCAQII 454
Cdd:COG3505  156 TLAAFLNAAEKtrssvlsTLASALELLSDPEVAAltSGSDFDLRDLIREKGTLYLVLPPDDLSTLApLLRLLLSQLIRAL 235
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 455 --IARDEFREWPHVSVMLDEIKYLLS-KYVLNALGTLRSRDCNLLLAHQSLGDFgqcgQDLPAEFVKTTVLDNTPIRWFY 531
Cdd:COG3505  236 lrRAERSGRLPRPVLLLLDEFANLGRlPSLETLLATGRGYGIRLVLILQSLAQL----EAIYGEEGAETILGNCGTKIFL 311
                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490282304 532 RAASLESAQWAAGQTGEirVDVERRRASREAGNVehisGDSfIQKEARPLFDVNTLQHLPDGFAVM 597
Cdd:COG3505  312 GVNDPETAEYLSELLGK--RTVERRSESRSRGSR----SRS-RSEQERPLLTPDELRRLPDGEAIV 370
VirB4 COG3451
Type IV secretory pathway, VirB4 component [Intracellular trafficking, secretion, and ...
222-542 1.14e-09

Type IV secretory pathway, VirB4 component [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 442674 [Multi-domain]  Cd Length: 546  Bit Score: 61.12  E-value: 1.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 222 ALADFSSEQARQEQAVFLGKDEQGKPVLVprDTWRKT---NIQILGLPGSGKSVmATNALIRCVRDFGDAVVYFDPKGDa 298
Cdd:COG3451  168 ALFPFHSFELGDPWGIYLLNTRSGTPVFF--DFHDGLdngNTLILGPSGSGKSF-LLKLLLLQLLRYGARIVIFDPGGS- 243
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 299 wAPHVFRAHcpDFTLLDLRPGKPAQLNLFRDLDQYALKNLL---IAGLNLGETGDVADhyrisEQKAAkliaeqfpqgan 375
Cdd:COG3451  244 -YEILVRAL--GGTYIDLSPGSPTGLNPFDLEDTEEKRDFLlelLELLLGREGEPLTP-----EERAA------------ 303
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 376 IQQVLAAAYA-LPEALKKDVKGLITRLENVADLSVLQ------TDSGIDvAGIINGGGCL---------YVIGSMDDEAV 439
Cdd:COG3451  304 IDRAVRALYRrADPEERTTLSDLYELLKEQPEAKDLAarlepyTKGGSY-GWLFDGPTNLdlsdarfvvFDLTELLDNPE 382
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 440 IR--VQKMLFARCAQIIIARDEFREwphVSVMLDEIKYLLS-----KYVLNALGTLRSRDCNLLLAHQSLGDFgqcgqdL 512
Cdd:COG3451  383 LRppVLLYLLHRIWNRLRKNNDGRP---TLIVIDEAWLLLDnpafaEFLEEWLKTLRKYNGAVIFATQSVEDF------L 453
                        330       340       350
                 ....*....|....*....|....*....|
gi 490282304 513 PAEfVKTTVLDNTPIRWFYRAASLESAQWA 542
Cdd:COG3451  454 SSP-IAEAIIENSATKILLPQPKADIEDYA 482
HerA COG0433
Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase ...
215-509 6.19e-09

Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase domains [Replication, recombination and repair];


Pssm-ID: 440202 [Multi-domain]  Cd Length: 388  Bit Score: 58.47  E-value: 6.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 215 GEPVPVnALADFSSEQARQEQAVFLGKDEQ-GKPVLVPRDTWRKTNIQILGLPGSGKSVMATNALIRCVRDfGDAVVYFD 293
Cdd:COG0433    5 GSPVYL-ADDEELEELLGDGGGILIGKLLSpGVPVYLDLDKLLNRHILILGATGSGKSNTLQVLLEELSRA-GVPVLVFD 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 294 PKGDAWAPHVFRAHCPDFTLLDLRPGKPAQLNlFRDLDQ--YALKNLLIAGLNLGET--GDVADHYRISEQKAAK----- 364
Cdd:COG0433   83 PHGEYSGLAEPGAERADVGVFDPGAGRPLPIN-PWDLFAtaSELGPLLLSRLDLNDTqrGVLREALRLADDKGLLlldlk 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 365 -LIAEqfpqganIQQVLAAAYALPEALKKDVKGLITRLENVADLSVLQTDSGIDVAGIINGGGCLYVI--GSMDDEA--- 438
Cdd:COG0433  162 dLIAL-------LEEGEELGEEYGNVSAASAGALLRRLESLESADGLFGEPGLDLEDLLRTDGRVTVIdlSGLPEELqst 234
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304 439 -VIRVQKMLFArcAQIIIARDEFREWPHVsVMLDEIKYLLSKYVLNALGTL-------RSRDCNLLLAHQSLGDF----- 505
Cdd:COG0433  235 fVLWLLRELFE--ARPEVGDADDRKLPLV-LVIDEAHLLAPAAPSALLEILeriaregRKFGVGLILATQRPSDIdedvl 311

                 ....
gi 490282304 506 GQCG 509
Cdd:COG0433  312 SQLG 315
TrwB_AAD_bind pfam10412
Type IV secretion-system coupling protein DNA-binding domain; The plasmid conjugative coupling ...
262-607 3.22e-04

Type IV secretion-system coupling protein DNA-binding domain; The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export.


Pssm-ID: 431268 [Multi-domain]  Cd Length: 386  Bit Score: 43.44  E-value: 3.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  262 ILGLPGSGKSVmATNALIRCVRDFGDAVVYFDPKGdAWAPHVFRAHCPdfTLLDLRPGKPAQLNLFRDLDQYalknllia 341
Cdd:pfam10412  20 IIGTTGSGKTQ-ALRGLLDQARARGDRAIIFDLTG-AFTERFYDPGRD--ILLNPLDARSPAWSPFAECKTP-------- 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  342 glnlgetgdvADHYRIseqkAAKLIAEQfPQGANIQQVLAAAYALPEALKKDVKglITRLENVADLSVLQTDSGIDVAGI 421
Cdd:pfam10412  88 ----------ADFAAI----AAALIPED-GGGSDPFWALAARTVLVDTLRALQR--TGRKTNAALLRALLTADLDELHEL 150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  422 INGGGCLYVIGSMDDEAVIRVQKML--FARCAQIIIARDE---FREW-----------------------PHVSVMLD-E 472
Cdd:pfam10412 151 LAGTAAAPLTAPEAERTTASIRATLatNLRALRFLAPDGErfsIREWiteedpggwlfityradqraalrPLLSCWLDlA 230
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  473 IKYLLSK---------YVLNALGTLrSRDCNLLLAHQSLGDFGQC---------------GQDLPAefvktTVLDNTPIR 528
Cdd:pfam10412 231 IRALLSLppsrdrrlwFFLDELPAL-GRLPSLKDLLAEGRKFGGAvvlglqsiaqlreiyGEDGAQ-----TILSNCGTK 304
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  529 WFYRAASLESAQWAAGQTGEirVDVERRRASREAGNVEHISGDSF-IQKEARPLFDVNTLQHLPD--GFAV-MTGLGVAR 604
Cdd:pfam10412 305 LILRVSDGETAELCSDLLGD--REVERMDESLSYGANNSRDGVTLgRQRRVRPLVLPSEIMNLPRlhGYLKfPDGFPVAR 382

                  ...
gi 490282304  605 MAF 607
Cdd:pfam10412 383 VTL 385
TrwB_TraG_TraD_VirD4 cd01127
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are ...
259-299 3.25e-04

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: 41.44  E-value: 3.25e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 490282304 259 NIQILGLPGSGKSVMATNALIRcVRDFGDAVVYFDPKGDAW 299
Cdd:cd01127    1 NTLVLGTTGSGKTTSIVIPLLD-QAARGGSVIITDPKGELF 40
SXT_TraD TIGR03743
conjugative coupling factor TraD, SXT/TOL subfamily; Members of this protein family are the ...
240-298 6.77e-04

conjugative coupling factor TraD, SXT/TOL subfamily; Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains. [Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274760 [Multi-domain]  Cd Length: 634  Bit Score: 42.65  E-value: 6.77e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 490282304  240 GKDEQGKPVLVPRDTwRKTNIQILGLPGSGKSVMATNALIRCVRDfGDAVVYFDPKGDA 298
Cdd:TIGR03743 160 GVEPKEEDVYLPLGH-RVGHTLVLGTTGVGKTRLAELLITQDIRR-GDVVIVIDPKGDA 216
TraG-D_C pfam12696
TraM recognition site of TraD and TraG; This family includes both TraG and TraD as well as ...
465-591 1.36e-03

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: 39.17  E-value: 1.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490282304  465 HVSVMLDE---IKYLLSkyVLNALGTLRSRDCNLLLAHQSLGDfgqcGQDLPAEFVKTTVLDNTPIRWFYRAASLESAQW 541
Cdd:pfam12696   1 PVLFVLDEfanLGKIPD--LEKLISTGRSRGISLMLILQSIAQ----LEELYGKDGAETILGNCNTKVFLGGGDEETAKY 74
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 490282304  542 AAGQTGEIRVDVERRRASREAGNVEHISGDSFIQKEARPLFDVNTLQHLP 591
Cdd:pfam12696  75 LSKLLGKYTVVSTTTSSSSSGSGGSGSSSSSSSQLVGRPLLTPDELRRLP 124
 
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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