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Conserved domains on  [gi|77970313|gb|ABB11692|]
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Rhs family protein [Burkholderia lata]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RHS_core super family cl49306
RHS element core protein;
478-1298 1.40e-35

RHS element core protein;


The actual alignment was detected with superfamily member NF041261:

Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 148.23  E-value: 1.40e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   478 DGHIGKIVQTDHDGnvRRTVSLRYDQSGRIVEVVltDVDGRDTRiarYAYDTEN-CLTSYRNALDAISTYEYDAQRRMAR 556
Cdd:NF041261  348 AQHPGRMVAHRYAG--RPEMCYRYDDTGRVTEQL--NPAGLSYR---YQYEQDRiTITDSLNRREVLHTEGEGGLKRVVK 420

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   557 LAGANGYSFLYCYDSEGRC---VESAGQdrmwhvRFQYRPGR-----TIVTEGDGGRWTILYNEMGTITHVVDPYGGIAE 628
Cdd:NF041261  421 KEHADGSVTRSGYDAAGRLtaqTDAAGR------RTEYSLNVvsgdiTDITTPDGRETKFYYNDGNQLTSVTSPDGLESR 494

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   629 YVLDPSGRIVEEIDSGGRTLRWLYDARAgtigrldrfgnlwpnkDELPNLpnplAHHVPNAMRGLIWGEF-NVDNLTDTV 707
Cdd:NF041261  495 REYDEPGRLVSETSRSGETTRYRYDDPH----------------SELPAT----TTDATGSTKQMTWSRYgQLLAFTDCS 554

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   708 LLPQEIDHWAWGSATdAVARWPDERRQQR-DVAGRVIARTNISGHTERFEYDADDNLLLRFDQDGAATRYTRCSW-NLLA 785
Cdd:NF041261  555 GYQTRYEYDRFGQMT-AVHREEGISTYRRyDNRGQLTSVKDAQGRETRYEYNAAGDLTAVITPDGNRSETQYDAWgKAVS 633

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   786 SEENALGETIRYRYTSRrdVASVIDANGNESAYSYDFKKRMTSVTRHGRLRESYVYDGGDRLIEKRDGAGKWLLRFEigE 865
Cdd:NF041261  634 TTQGGLTRSMEYDAAGR--ITTLTNENGSHSTFLYDALDRLVQQRGFDGRTQRYHYDLTGKLTQSEDEGLVTLWHYD--E 709

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   866 NGLPRERTLASGSKHVYEYDRFGHLTKAS--TDAHEIT--RTFDNLGRRTSDKcdgLGVQHEYDGHrlgrttYLERFEVV 941
Cdd:NF041261  710 SDRITHRTVNGEPAEQWQYDEHGWLTDIShlSEGHRVAvhYGYDDKGRLTGER---QTVENPETGE------LLWQHETG 780

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   942 YTYTASGQSIR-TPGG--RTHCVQQGKDGRVLLRLANGTQACYMFDDVGRCTGRITWRTDSPAAFHRVT----------- 1007
Cdd:NF041261  781 HAYNEQGLANRvTPDSlpPVEWLTYGSGYLAGMKLGGTPLVEYTRDRLHRETVRSFGGAGSNAAYELTTaytpagqlqsq 860

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1008 ----------YEYSGAGELRRISDNQKgDTQYQYDRAHRLIGEMSSGWQA---CRYEYDPAGNLLALPTC-PMMQYTG-- 1071
Cdd:NF041261  861 hlnslvydrdYTWNDNGDLVRISGPRQ-TREYGYSATGRLTGVHTTAANLdirIPYATDPAGNRLPDPELhPDSTLTAwp 939

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1072 GNRLSTTSRGQYTYDERNHLSEEI---------AHDGRRTTYRYDSMDLLV---RVEWSDRHDAWTAEYDGLCRQV---- 1135
Cdd:NF041261  940 DNRIAEDAHYVYRYDEYGRLTEKTdripegvirTDDERTHHYHYDSQHRLVfytRIQHGEPLVESRYLYDPLGRRMakrv 1019

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1136 ------IAGTDNDS-----TVYYWDEDRLAA-QVDpggKVRVFVYVDEKSLVPFMFIDYPS-----------IDSPATSG 1192
Cdd:NF041261 1020 wrrerdLTGWMSLSrkpevTWYGWDGDRLTTvQTD---TTRIQTVYQPGSFTPLIRVETENgerakaqrrslAETLQQEG 1096

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1193 SE--YFVLFNQ--VGMPERIED------VSGRA-VWLA--------------------RKIHSYG--------VIEVAEG 1233
Cdd:NF041261 1097 SEngHGVVFPAelVRMLDRLEEeiradrVSEESrAWLAqcgltveqmarqvepeytpaRKLHLYHcdhrglplALISEEG 1176

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1234 NSL---EYD-----------------VRWPGHLFQRETGLHVNRFRSYNPMLGRYLQSDPVGHAGGGNLYTYSANPVVEV 1293
Cdd:NF041261 1177 NTAwqgEYDewgnllneenphhlqqpYRLPGQQYDEESGLYYNRNRYYDPLQGRYITQDPIGLKGGWNLYQYPLNPIRFI 1256


                  ....*
gi 77970313  1294 DVLGL 1298
Cdd:NF041261 1257 DPLGL 1261
PAAR_4 cd14740
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 93-213 1.38e-29

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of bacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). A few members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences as well as uncharacterized domains such as DUF4150. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes.


:

Pssm-ID: 269825  Cd Length: 121  Bit Score: 114.45  E-value: 1.38e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   93 PAATIGVPHLGTPHAH--SHPPSSGFPLPSVGATI--GSGCLSVLIGGIPAARVLDIGIAPTCGG-------ITPFFDIQ 161
Cdd:cd14740    1 PAARLGDPVVGDDIHIvlSPPGPVPTPLPHPGAGLivGGLSPTVLIGGMPAATVGSTAGNTPGGVpggpsvpPANPGTIV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 77970313  162 TGSSNTFIGGMRAARMGiDMTRHCNPMGhvghsggeaasAAEKGEEVASEAA 213
Cdd:cd14740   81 MGSSTVFINGKPAARMG-DMTATCNDPA-----------PAPVGTVVPPGAT 120
DUF6531 pfam20148
Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.
 339-412 1.10e-13

Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.


:

Pssm-ID: 466309 [Multi-domain]  Cd Length: 74  Bit Score: 67.56  E-value: 1.10e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 77970313    339 GEPISAVTGEVKNDFTDYETDETLPFIWGRHYCSGwNERNGAQGYGFRHAWQRELQL-LRTRAIYTDPRGTKYTF 412
Cdd:pfam20148    1 GDPVNVATGNKVLEETDFSLPGPLPLVWTRTYNSS-SERDGPLGPGWSHPYDQRLELeGDGGVVYIDADGREVTF 74
Mplasa_alph_rch super family cl37461
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 1340-1435 5.60e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


The actual alignment was detected with superfamily member TIGR04523:

Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 41.16  E-value: 5.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   1340 AERDAAIERMKREIENLEQEKKKLSLDEKNWYSYPETPET------KRLDAIRERVLELNDKIKNYPLVRDKTTEFPKGY 1413
Cdd:TIGR04523  606 EEKEKKISSLEKELEKAKKENEKLSSIIKNIKSKKNKLKQevkqikETIKEIRNKWPEIIKKIKESKTKIDDIIELMKDW 685

                           90       100
                   ....*....|....*....|..
gi 77970313   1414 LQSTHIEMIKRYTREGREGKLP 1435
Cdd:TIGR04523  686 LKELSLHYKKYITRMIRIKDLP 707
 
Name Accession Description Interval E-value
RHS_core NF041261
RHS element core protein;
478-1298 1.40e-35

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 148.23  E-value: 1.40e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   478 DGHIGKIVQTDHDGnvRRTVSLRYDQSGRIVEVVltDVDGRDTRiarYAYDTEN-CLTSYRNALDAISTYEYDAQRRMAR 556
Cdd:NF041261  348 AQHPGRMVAHRYAG--RPEMCYRYDDTGRVTEQL--NPAGLSYR---YQYEQDRiTITDSLNRREVLHTEGEGGLKRVVK 420

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   557 LAGANGYSFLYCYDSEGRC---VESAGQdrmwhvRFQYRPGR-----TIVTEGDGGRWTILYNEMGTITHVVDPYGGIAE 628
Cdd:NF041261  421 KEHADGSVTRSGYDAAGRLtaqTDAAGR------RTEYSLNVvsgdiTDITTPDGRETKFYYNDGNQLTSVTSPDGLESR 494

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   629 YVLDPSGRIVEEIDSGGRTLRWLYDARAgtigrldrfgnlwpnkDELPNLpnplAHHVPNAMRGLIWGEF-NVDNLTDTV 707
Cdd:NF041261  495 REYDEPGRLVSETSRSGETTRYRYDDPH----------------SELPAT----TTDATGSTKQMTWSRYgQLLAFTDCS 554

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   708 LLPQEIDHWAWGSATdAVARWPDERRQQR-DVAGRVIARTNISGHTERFEYDADDNLLLRFDQDGAATRYTRCSW-NLLA 785
Cdd:NF041261  555 GYQTRYEYDRFGQMT-AVHREEGISTYRRyDNRGQLTSVKDAQGRETRYEYNAAGDLTAVITPDGNRSETQYDAWgKAVS 633

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   786 SEENALGETIRYRYTSRrdVASVIDANGNESAYSYDFKKRMTSVTRHGRLRESYVYDGGDRLIEKRDGAGKWLLRFEigE 865
Cdd:NF041261  634 TTQGGLTRSMEYDAAGR--ITTLTNENGSHSTFLYDALDRLVQQRGFDGRTQRYHYDLTGKLTQSEDEGLVTLWHYD--E 709

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   866 NGLPRERTLASGSKHVYEYDRFGHLTKAS--TDAHEIT--RTFDNLGRRTSDKcdgLGVQHEYDGHrlgrttYLERFEVV 941
Cdd:NF041261  710 SDRITHRTVNGEPAEQWQYDEHGWLTDIShlSEGHRVAvhYGYDDKGRLTGER---QTVENPETGE------LLWQHETG 780

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   942 YTYTASGQSIR-TPGG--RTHCVQQGKDGRVLLRLANGTQACYMFDDVGRCTGRITWRTDSPAAFHRVT----------- 1007
Cdd:NF041261  781 HAYNEQGLANRvTPDSlpPVEWLTYGSGYLAGMKLGGTPLVEYTRDRLHRETVRSFGGAGSNAAYELTTaytpagqlqsq 860

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1008 ----------YEYSGAGELRRISDNQKgDTQYQYDRAHRLIGEMSSGWQA---CRYEYDPAGNLLALPTC-PMMQYTG-- 1071
Cdd:NF041261  861 hlnslvydrdYTWNDNGDLVRISGPRQ-TREYGYSATGRLTGVHTTAANLdirIPYATDPAGNRLPDPELhPDSTLTAwp 939

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1072 GNRLSTTSRGQYTYDERNHLSEEI---------AHDGRRTTYRYDSMDLLV---RVEWSDRHDAWTAEYDGLCRQV---- 1135
Cdd:NF041261  940 DNRIAEDAHYVYRYDEYGRLTEKTdripegvirTDDERTHHYHYDSQHRLVfytRIQHGEPLVESRYLYDPLGRRMakrv 1019

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1136 ------IAGTDNDS-----TVYYWDEDRLAA-QVDpggKVRVFVYVDEKSLVPFMFIDYPS-----------IDSPATSG 1192
Cdd:NF041261 1020 wrrerdLTGWMSLSrkpevTWYGWDGDRLTTvQTD---TTRIQTVYQPGSFTPLIRVETENgerakaqrrslAETLQQEG 1096

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1193 SE--YFVLFNQ--VGMPERIED------VSGRA-VWLA--------------------RKIHSYG--------VIEVAEG 1233
Cdd:NF041261 1097 SEngHGVVFPAelVRMLDRLEEeiradrVSEESrAWLAqcgltveqmarqvepeytpaRKLHLYHcdhrglplALISEEG 1176

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1234 NSL---EYD-----------------VRWPGHLFQRETGLHVNRFRSYNPMLGRYLQSDPVGHAGGGNLYTYSANPVVEV 1293
Cdd:NF041261 1177 NTAwqgEYDewgnllneenphhlqqpYRLPGQQYDEESGLYYNRNRYYDPLQGRYITQDPIGLKGGWNLYQYPLNPIRFI 1256


                  ....*
gi 77970313  1294 DVLGL 1298
Cdd:NF041261 1257 DPLGL 1261
RhsA COG3209
Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction ...
 398-1320 2.72e-35

Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction only];


Pssm-ID: 442442 [Multi-domain]  Cd Length: 1103  Bit Score: 147.21  E-value: 2.72e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  398 TRAIYTDPRGTKYTFSRNADGTYDGCCQGYSLEQIDSRRFFIRHEAAGDAEFERDAETALSVRCISHQRDRTQSLLRWRP 477
Cdd:COG3209  153 RGGVAVTGLAGGGASAYGLTLGGAAAGPATGVGTGAVTLATGLAGSALLALGSGAILGGLAGAYSGSATTATGTALGTPA 232

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  478 DGHIGKIVQTDHDGNVRRTVSLRYDQSGRIVEVVLTDVDGRDTRIARYAYDTENCLTSYRNALDAISTYEYDAQRRMARL 557
Cdd:COG3209  233 SVAATVTGSATGAAGAGAAVATAATTLGGTTGAGTGASGAGLDASTGTGGAGGSNAAATAGGLGGAGLGSGGAGGGGTAG 312

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  558 AGANGYSFLYCYDSEGRCVESAGQDRMWHVRFQYRPGRTIVTEGDGGRWTILYNEMGTITHVVDPYGGIAEYVLDPSGRI 637
Cdd:COG3209  313 GTTTAAGTTGTAAVSGAADAGTTTTTGTGTGGTTTTVGGGGSLTLGGYGAAGGLTTSVGAGGGGSTSGSTTTVGGGGTAT 392

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  638 VEEIDSGGRTLRWLYDARAGTIGRLDRFGNLWPNKDELPNLPNPLAHHVPNAMRGLIWGEFNVDNLTDTVLLPQEIDHWA 717
Cdd:COG3209  393 GSGGGSSTTGVGAGTTTTSTTGGDGGPATAAGALTAGGTATGTGTGGGGTTAGTDATTTTGGAGASGTLTTTGGAATGAT 472

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  718 WGSATDAVARWPderrqqRDVAGRVIARTNISGHTERFEYDADDNLLLRFDQDGAATRYTRCSWNLLASEENALGETIRY 797
Cdd:COG3209  473 TGGGTEAGTGGG------TLTSGSAGATTLGTDTTLDDTLGGTTTTTAGARGLVVTTGTTLTLGTTTTATLSATDATGTG 546

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  798 RYTSRRDVASVIDANGNESAYSYDFKKRMTSVTRHGRLRESYVYDGGDRLIEKRDGAGKWLLRFEIGENGLPRERTLASG 877
Cdd:COG3209  547 DTTTTGTVGTGTSTGTGGTGTVTTTGDGTGGASTTTGTTGGTATTTTVTTTTTTSTAGTTTTTTSGYTRAGLTLTLGTGT 626

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  878 SKHVYEYDRFGHLTKASTDAHEITRTFDNLGRRTSDKCDGLGVQHEYDGHRLGRTTYLERFEVVYTYTASGQSIRTPGG- 956
Cdd:COG3209  627 ASGLERATASTGSTTGGTTGTGVTTTGTTTTRATGTTGTGTGVTAGLTTLATGGTTVGGGTGTTSTATTGATTGGTETGt 706

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  957 --RTHCVQQGKDGRVLLRLANGTQACYMFDDVGRCTGRITWRTDSPAAFHRVTYEYSGAGELRRISDNQK-----GDTQY 1029
Cdd:COG3209  707 tvTTLAGGTTTRLGTTTTGGGGGTTTDGTGTGGTTGTLTTTSTTTTTTAGALTYTYDALGRLTSETTPGGvtqgtYTTRY 786

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313 1030 QYDRAHRLIGEMSSGWQACRYEYDPAGNLLAlptcpmMQYTGGNRLSTTSRGQYTYDERNHL---SEEIAHDGRRTTYRY 1106
Cdd:COG3209  787 TYDALGRLTSVTYPDGETVTYTYDALGRLTS------VITVGSGGGTDLQDRTYTYDAAGNItsiTDALRAGTLTQTYTY 860

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313 1107 DSMDLLVRVEWSDRHDAWTaeYDGlCRQVIAGTDNDSTVYYWD-EDRLAAQVDPGGKVRVFVYvDEKSLVpfmfidypsi 1185
Cdd:COG3209  861 DALGRLTSATDPGTTESYT--YDA-NGNLTSRTDGGTTTYTYDaLGRLVSVTKPDGTTTTYTY-DALGHT---------- 926

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313 1186 dspatsgseyfvlfNQVGMPERIEDVSGRAVWLARkIHSYGVIEVAEGNSLEYDVRWPGHLFQRETGLHVNRFRSYNPML 1265
Cdd:COG3209  927 --------------DHLGSVRALTDASGQVVWRYD-YDPFGNLLAETSGAAANPLRFTGQEYDAETGLYYNGARYYDPAL 991

                        890       900       910       920       930
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 77970313 1266 GRYLQSDPVGHAGGGNLYTY-SANPVVEVDVLGLNAHVHGEDASEPSPEGPAVAGR 1320
Cdd:COG3209  992 GRFLSPDPIGLAGGLNLYAYvGNNPVNYVDPLGLAALLGTTGLGGGAGVGAGAAGG 1047
PAAR_4 cd14740
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 93-213 1.38e-29

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of bacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). A few members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences as well as uncharacterized domains such as DUF4150. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes.


Pssm-ID: 269825  Cd Length: 121  Bit Score: 114.45  E-value: 1.38e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   93 PAATIGVPHLGTPHAH--SHPPSSGFPLPSVGATI--GSGCLSVLIGGIPAARVLDIGIAPTCGG-------ITPFFDIQ 161
Cdd:cd14740    1 PAARLGDPVVGDDIHIvlSPPGPVPTPLPHPGAGLivGGLSPTVLIGGMPAATVGSTAGNTPGGVpggpsvpPANPGTIV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 77970313  162 TGSSNTFIGGMRAARMGiDMTRHCNPMGhvghsggeaasAAEKGEEVASEAA 213
Cdd:cd14740   81 MGSSTVFINGKPAARMG-DMTATCNDPA-----------PAPVGTVVPPGAT 120
Rhs_assc_core TIGR03696
RHS repeat-associated core domain; This model represents a conserved unique core sequence ...
 1225-1298 3.04e-18

RHS repeat-associated core domain; This model represents a conserved unique core sequence shared by large numbers of proteins. It is occasional in the Archaea Methanosarcina barkeri) but common in bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (pfam01839) class, and an RHS repeat (pfam05593) or YD repeat (TIGR01643). This class includes secreted bacterial insecticidal toxins and intercellular signalling proteins such as the teneurins in animals. The other class consists of uncharacterized proteins shorter than 400 amino acids, where this core domain of about 75 amino acids tends to occur in the N-terminal half. Over twenty such proteins are found in Pseudomonas putida alone; little sequence similarity or repeat structure is found among these proteins outside the region modeled by this domain.


Pssm-ID: 274730 [Multi-domain]  Cd Length: 77  Bit Score: 80.62  E-value: 3.04e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 77970313   1225 YGVIeVAEGNSLEYDVRWPGHLFQRETGLHVNRFRSYNPMLGRYLQSDPVGHAGGGNLYTY-SANPVVEVDVLGL 1298
Cdd:TIGR03696    4 YGEV-LSESGAAPNPLRFTGQYYDAETGLYYNGARYYDPELGRFLSPDPIGLGGGLNLYAYvGNNPVNWVDPLGL 77
DUF6531 pfam20148
Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.
 339-412 1.10e-13

Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.


Pssm-ID: 466309 [Multi-domain]  Cd Length: 74  Bit Score: 67.56  E-value: 1.10e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 77970313    339 GEPISAVTGEVKNDFTDYETDETLPFIWGRHYCSGwNERNGAQGYGFRHAWQRELQL-LRTRAIYTDPRGTKYTF 412
Cdd:pfam20148    1 GDPVNVATGNKVLEETDFSLPGPLPLVWTRTYNSS-SERDGPLGPGWSHPYDQRLELeGDGGVVYIDADGREVTF 74
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 119-182 2.13e-13

PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins.


Pssm-ID: 428491  Cd Length: 71  Bit Score: 66.44  E-value: 2.13e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 77970313    119 PSVGATIGSGCLSVLIGGIPAARVLDIGIAPTCGGITPffdIQTGSSNTFIGGMRAARMGiDMT 182
Cdd:pfam05488    5 TSHGGVVITGSPTVLIGGKPAARVGDLVVCPPCGGGGP---IAEGSPTVLINGKPAAREG-DKT 64
RHS_core NF041261
RHS element core protein;
795-1114 2.95e-13

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 75.04  E-value: 2.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   795 IRYRYTSRRDVASVIDANGNE-SAYSYDFKKRMTSVTRH--GRLRESYVYDGGDRLIEKRDGAG---------------K 856
Cdd:NF041261  320 VRYTYTEAGELLAVYDRSNTQvRAFTYDAQHPGRMVAHRyaGRPEMCYRYDDTGRVTEQLNPAGlsyryqyeqdrititD 399

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   857 WLLRFEI----GENGLPR--ERTLASGSKHVYEYDRFGHLTkASTDAheitrtfdnLGRRTsdkcdglgvqhEYDGH--- 927
Cdd:NF041261  400 SLNRREVlhteGEGGLKRvvKKEHADGSVTRSGYDAAGRLT-AQTDA---------AGRRT-----------EYSLNvvs 458

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   928 -RLGRTTYLERFEVVYTYTASGQ--SIRTPGGRTHCVQQGKDGRVLLRLA-NGTQACYMFD-----------DVGRCTGR 992
Cdd:NF041261  459 gDITDITTPDGRETKFYYNDGNQltSVTSPDGLESRREYDEPGRLVSETSrSGETTRYRYDdphselpatttDATGSTKQ 538

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   993 ITW-RTDSPAAF-----HRVTYEYSGAGELRRISdNQKGDTQYQ-YDRAHRLIGEMSSGWQACRYEYDPAGNLLALPTC- 1064
Cdd:NF041261  539 MTWsRYGQLLAFtdcsgYQTRYEYDRFGQMTAVH-REEGISTYRrYDNRGQLTSVKDAQGRETRYEYNAAGDLTAVITPd 617

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 77970313  1065 ---PMMQYTGGNRLSTTSRGQYT----YDERNHLSEEIAHDGRRTTYRYDSMDLLVR 1114
Cdd:NF041261  618 gnrSETQYDAWGKAVSTTQGGLTrsmeYDAAGRITTLTNENGSHSTFLYDALDRLVQ 674
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 119-184 4.62e-12

Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 443280  Cd Length: 87  Bit Score: 63.30  E-value: 4.62e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 77970313  119 PSVGATIGSGCLSVLIGGIPAARVLDIGiapTCGGITPFFdIQTGSSNTFIGGMRAARMGiDMTRH 184
Cdd:COG4104   12 TSHGGPVISGSPTVLIGGRPAARVGDKV---SCPKHGPDT-IAEGSPTVLINGKPAARVG-DKTAC 72
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 1340-1435 5.60e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 41.16  E-value: 5.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   1340 AERDAAIERMKREIENLEQEKKKLSLDEKNWYSYPETPET------KRLDAIRERVLELNDKIKNYPLVRDKTTEFPKGY 1413
Cdd:TIGR04523  606 EEKEKKISSLEKELEKAKKENEKLSSIIKNIKSKKNKLKQevkqikETIKEIRNKWPEIIKKIKESKTKIDDIIELMKDW 685

                           90       100
                   ....*....|....*....|..
gi 77970313   1414 LQSTHIEMIKRYTREGREGKLP 1435
Cdd:TIGR04523  686 LKELSLHYKKYITRMIRIKDLP 707
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 1085-1115 5.67e-03

RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be involved in ligand binding. Note that this model may not find all the repeats in a protein and that it covers two RHS repeats. The 3D structure of an RHS-repeat-containing protein (the B and C components of an ABC toxin complex) has been determined. The RHS repeats form an extended strip of beta-sheet that spirals around to form a hollow shell, encapsulating the variable C-terminal domain.


Pssm-ID: 461685 [Multi-domain]  Cd Length: 37  Bit Score: 36.04  E-value: 5.67e-03
                           10        20        30
                   ....*....|....*....|....*....|.
gi 77970313   1085 YDERNHLSEEIAHDGRRTTYRYDSMDLLVRV 1115
Cdd:pfam05593    1 YDAAGRLTSVTDPDGRVTTYTYDAAGRLTAV 31
 
Name Accession Description Interval E-value
RHS_core NF041261
RHS element core protein;
478-1298 1.40e-35

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 148.23  E-value: 1.40e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   478 DGHIGKIVQTDHDGnvRRTVSLRYDQSGRIVEVVltDVDGRDTRiarYAYDTEN-CLTSYRNALDAISTYEYDAQRRMAR 556
Cdd:NF041261  348 AQHPGRMVAHRYAG--RPEMCYRYDDTGRVTEQL--NPAGLSYR---YQYEQDRiTITDSLNRREVLHTEGEGGLKRVVK 420

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   557 LAGANGYSFLYCYDSEGRC---VESAGQdrmwhvRFQYRPGR-----TIVTEGDGGRWTILYNEMGTITHVVDPYGGIAE 628
Cdd:NF041261  421 KEHADGSVTRSGYDAAGRLtaqTDAAGR------RTEYSLNVvsgdiTDITTPDGRETKFYYNDGNQLTSVTSPDGLESR 494

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   629 YVLDPSGRIVEEIDSGGRTLRWLYDARAgtigrldrfgnlwpnkDELPNLpnplAHHVPNAMRGLIWGEF-NVDNLTDTV 707
Cdd:NF041261  495 REYDEPGRLVSETSRSGETTRYRYDDPH----------------SELPAT----TTDATGSTKQMTWSRYgQLLAFTDCS 554

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   708 LLPQEIDHWAWGSATdAVARWPDERRQQR-DVAGRVIARTNISGHTERFEYDADDNLLLRFDQDGAATRYTRCSW-NLLA 785
Cdd:NF041261  555 GYQTRYEYDRFGQMT-AVHREEGISTYRRyDNRGQLTSVKDAQGRETRYEYNAAGDLTAVITPDGNRSETQYDAWgKAVS 633

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   786 SEENALGETIRYRYTSRrdVASVIDANGNESAYSYDFKKRMTSVTRHGRLRESYVYDGGDRLIEKRDGAGKWLLRFEigE 865
Cdd:NF041261  634 TTQGGLTRSMEYDAAGR--ITTLTNENGSHSTFLYDALDRLVQQRGFDGRTQRYHYDLTGKLTQSEDEGLVTLWHYD--E 709

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   866 NGLPRERTLASGSKHVYEYDRFGHLTKAS--TDAHEIT--RTFDNLGRRTSDKcdgLGVQHEYDGHrlgrttYLERFEVV 941
Cdd:NF041261  710 SDRITHRTVNGEPAEQWQYDEHGWLTDIShlSEGHRVAvhYGYDDKGRLTGER---QTVENPETGE------LLWQHETG 780

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   942 YTYTASGQSIR-TPGG--RTHCVQQGKDGRVLLRLANGTQACYMFDDVGRCTGRITWRTDSPAAFHRVT----------- 1007
Cdd:NF041261  781 HAYNEQGLANRvTPDSlpPVEWLTYGSGYLAGMKLGGTPLVEYTRDRLHRETVRSFGGAGSNAAYELTTaytpagqlqsq 860

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1008 ----------YEYSGAGELRRISDNQKgDTQYQYDRAHRLIGEMSSGWQA---CRYEYDPAGNLLALPTC-PMMQYTG-- 1071
Cdd:NF041261  861 hlnslvydrdYTWNDNGDLVRISGPRQ-TREYGYSATGRLTGVHTTAANLdirIPYATDPAGNRLPDPELhPDSTLTAwp 939

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1072 GNRLSTTSRGQYTYDERNHLSEEI---------AHDGRRTTYRYDSMDLLV---RVEWSDRHDAWTAEYDGLCRQV---- 1135
Cdd:NF041261  940 DNRIAEDAHYVYRYDEYGRLTEKTdripegvirTDDERTHHYHYDSQHRLVfytRIQHGEPLVESRYLYDPLGRRMakrv 1019

                         730       740       750       760       770       780       790       800
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1136 ------IAGTDNDS-----TVYYWDEDRLAA-QVDpggKVRVFVYVDEKSLVPFMFIDYPS-----------IDSPATSG 1192
Cdd:NF041261 1020 wrrerdLTGWMSLSrkpevTWYGWDGDRLTTvQTD---TTRIQTVYQPGSFTPLIRVETENgerakaqrrslAETLQQEG 1096

                         810       820       830       840       850       860       870       880
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1193 SE--YFVLFNQ--VGMPERIED------VSGRA-VWLA--------------------RKIHSYG--------VIEVAEG 1233
Cdd:NF041261 1097 SEngHGVVFPAelVRMLDRLEEeiradrVSEESrAWLAqcgltveqmarqvepeytpaRKLHLYHcdhrglplALISEEG 1176

                         890       900       910       920       930       940       950       960
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  1234 NSL---EYD-----------------VRWPGHLFQRETGLHVNRFRSYNPMLGRYLQSDPVGHAGGGNLYTYSANPVVEV 1293
Cdd:NF041261 1177 NTAwqgEYDewgnllneenphhlqqpYRLPGQQYDEESGLYYNRNRYYDPLQGRYITQDPIGLKGGWNLYQYPLNPIRFI 1256


                  ....*
gi 77970313  1294 DVLGL 1298
Cdd:NF041261 1257 DPLGL 1261
RhsA COG3209
Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction ...
 398-1320 2.72e-35

Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction only];


Pssm-ID: 442442 [Multi-domain]  Cd Length: 1103  Bit Score: 147.21  E-value: 2.72e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  398 TRAIYTDPRGTKYTFSRNADGTYDGCCQGYSLEQIDSRRFFIRHEAAGDAEFERDAETALSVRCISHQRDRTQSLLRWRP 477
Cdd:COG3209  153 RGGVAVTGLAGGGASAYGLTLGGAAAGPATGVGTGAVTLATGLAGSALLALGSGAILGGLAGAYSGSATTATGTALGTPA 232

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  478 DGHIGKIVQTDHDGNVRRTVSLRYDQSGRIVEVVLTDVDGRDTRIARYAYDTENCLTSYRNALDAISTYEYDAQRRMARL 557
Cdd:COG3209  233 SVAATVTGSATGAAGAGAAVATAATTLGGTTGAGTGASGAGLDASTGTGGAGGSNAAATAGGLGGAGLGSGGAGGGGTAG 312

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  558 AGANGYSFLYCYDSEGRCVESAGQDRMWHVRFQYRPGRTIVTEGDGGRWTILYNEMGTITHVVDPYGGIAEYVLDPSGRI 637
Cdd:COG3209  313 GTTTAAGTTGTAAVSGAADAGTTTTTGTGTGGTTTTVGGGGSLTLGGYGAAGGLTTSVGAGGGGSTSGSTTTVGGGGTAT 392

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  638 VEEIDSGGRTLRWLYDARAGTIGRLDRFGNLWPNKDELPNLPNPLAHHVPNAMRGLIWGEFNVDNLTDTVLLPQEIDHWA 717
Cdd:COG3209  393 GSGGGSSTTGVGAGTTTTSTTGGDGGPATAAGALTAGGTATGTGTGGGGTTAGTDATTTTGGAGASGTLTTTGGAATGAT 472

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  718 WGSATDAVARWPderrqqRDVAGRVIARTNISGHTERFEYDADDNLLLRFDQDGAATRYTRCSWNLLASEENALGETIRY 797
Cdd:COG3209  473 TGGGTEAGTGGG------TLTSGSAGATTLGTDTTLDDTLGGTTTTTAGARGLVVTTGTTLTLGTTTTATLSATDATGTG 546

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  798 RYTSRRDVASVIDANGNESAYSYDFKKRMTSVTRHGRLRESYVYDGGDRLIEKRDGAGKWLLRFEIGENGLPRERTLASG 877
Cdd:COG3209  547 DTTTTGTVGTGTSTGTGGTGTVTTTGDGTGGASTTTGTTGGTATTTTVTTTTTTSTAGTTTTTTSGYTRAGLTLTLGTGT 626

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  878 SKHVYEYDRFGHLTKASTDAHEITRTFDNLGRRTSDKCDGLGVQHEYDGHRLGRTTYLERFEVVYTYTASGQSIRTPGG- 956
Cdd:COG3209  627 ASGLERATASTGSTTGGTTGTGVTTTGTTTTRATGTTGTGTGVTAGLTTLATGGTTVGGGTGTTSTATTGATTGGTETGt 706

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  957 --RTHCVQQGKDGRVLLRLANGTQACYMFDDVGRCTGRITWRTDSPAAFHRVTYEYSGAGELRRISDNQK-----GDTQY 1029
Cdd:COG3209  707 tvTTLAGGTTTRLGTTTTGGGGGTTTDGTGTGGTTGTLTTTSTTTTTTAGALTYTYDALGRLTSETTPGGvtqgtYTTRY 786

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313 1030 QYDRAHRLIGEMSSGWQACRYEYDPAGNLLAlptcpmMQYTGGNRLSTTSRGQYTYDERNHL---SEEIAHDGRRTTYRY 1106
Cdd:COG3209  787 TYDALGRLTSVTYPDGETVTYTYDALGRLTS------VITVGSGGGTDLQDRTYTYDAAGNItsiTDALRAGTLTQTYTY 860

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313 1107 DSMDLLVRVEWSDRHDAWTaeYDGlCRQVIAGTDNDSTVYYWD-EDRLAAQVDPGGKVRVFVYvDEKSLVpfmfidypsi 1185
Cdd:COG3209  861 DALGRLTSATDPGTTESYT--YDA-NGNLTSRTDGGTTTYTYDaLGRLVSVTKPDGTTTTYTY-DALGHT---------- 926

                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313 1186 dspatsgseyfvlfNQVGMPERIEDVSGRAVWLARkIHSYGVIEVAEGNSLEYDVRWPGHLFQRETGLHVNRFRSYNPML 1265
Cdd:COG3209  927 --------------DHLGSVRALTDASGQVVWRYD-YDPFGNLLAETSGAAANPLRFTGQEYDAETGLYYNGARYYDPAL 991

                        890       900       910       920       930
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 77970313 1266 GRYLQSDPVGHAGGGNLYTY-SANPVVEVDVLGLNAHVHGEDASEPSPEGPAVAGR 1320
Cdd:COG3209  992 GRFLSPDPIGLAGGLNLYAYvGNNPVNYVDPLGLAALLGTTGLGGGAGVGAGAAGG 1047
PAAR_4 cd14740
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 93-213 1.38e-29

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of bacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). A few members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences as well as uncharacterized domains such as DUF4150. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes.


Pssm-ID: 269825  Cd Length: 121  Bit Score: 114.45  E-value: 1.38e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   93 PAATIGVPHLGTPHAH--SHPPSSGFPLPSVGATI--GSGCLSVLIGGIPAARVLDIGIAPTCGG-------ITPFFDIQ 161
Cdd:cd14740    1 PAARLGDPVVGDDIHIvlSPPGPVPTPLPHPGAGLivGGLSPTVLIGGMPAATVGSTAGNTPGGVpggpsvpPANPGTIV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 77970313  162 TGSSNTFIGGMRAARMGiDMTRHCNPMGhvghsggeaasAAEKGEEVASEAA 213
Cdd:cd14740   81 MGSSTVFINGKPAARMG-DMTATCNDPA-----------PAPVGTVVPPGAT 120
Rhs_assc_core TIGR03696
RHS repeat-associated core domain; This model represents a conserved unique core sequence ...
 1225-1298 3.04e-18

RHS repeat-associated core domain; This model represents a conserved unique core sequence shared by large numbers of proteins. It is occasional in the Archaea Methanosarcina barkeri) but common in bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (pfam01839) class, and an RHS repeat (pfam05593) or YD repeat (TIGR01643). This class includes secreted bacterial insecticidal toxins and intercellular signalling proteins such as the teneurins in animals. The other class consists of uncharacterized proteins shorter than 400 amino acids, where this core domain of about 75 amino acids tends to occur in the N-terminal half. Over twenty such proteins are found in Pseudomonas putida alone; little sequence similarity or repeat structure is found among these proteins outside the region modeled by this domain.


Pssm-ID: 274730 [Multi-domain]  Cd Length: 77  Bit Score: 80.62  E-value: 3.04e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 77970313   1225 YGVIeVAEGNSLEYDVRWPGHLFQRETGLHVNRFRSYNPMLGRYLQSDPVGHAGGGNLYTY-SANPVVEVDVLGL 1298
Cdd:TIGR03696    4 YGEV-LSESGAAPNPLRFTGQYYDAETGLYYNGARYYDPELGRFLSPDPIGLGGGLNLYAYvGNNPVNWVDPLGL 77
DUF6531 pfam20148
Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.
 339-412 1.10e-13

Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.


Pssm-ID: 466309 [Multi-domain]  Cd Length: 74  Bit Score: 67.56  E-value: 1.10e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 77970313    339 GEPISAVTGEVKNDFTDYETDETLPFIWGRHYCSGwNERNGAQGYGFRHAWQRELQL-LRTRAIYTDPRGTKYTF 412
Cdd:pfam20148    1 GDPVNVATGNKVLEETDFSLPGPLPLVWTRTYNSS-SERDGPLGPGWSHPYDQRLELeGDGGVVYIDADGREVTF 74
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 119-182 2.13e-13

PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins.


Pssm-ID: 428491  Cd Length: 71  Bit Score: 66.44  E-value: 2.13e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 77970313    119 PSVGATIGSGCLSVLIGGIPAARVLDIGIAPTCGGITPffdIQTGSSNTFIGGMRAARMGiDMT 182
Cdd:pfam05488    5 TSHGGVVITGSPTVLIGGKPAARVGDLVVCPPCGGGGP---IAEGSPTVLINGKPAAREG-DKT 64
RHS_core NF041261
RHS element core protein;
795-1114 2.95e-13

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 75.04  E-value: 2.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   795 IRYRYTSRRDVASVIDANGNE-SAYSYDFKKRMTSVTRH--GRLRESYVYDGGDRLIEKRDGAG---------------K 856
Cdd:NF041261  320 VRYTYTEAGELLAVYDRSNTQvRAFTYDAQHPGRMVAHRyaGRPEMCYRYDDTGRVTEQLNPAGlsyryqyeqdrititD 399

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   857 WLLRFEI----GENGLPR--ERTLASGSKHVYEYDRFGHLTkASTDAheitrtfdnLGRRTsdkcdglgvqhEYDGH--- 927
Cdd:NF041261  400 SLNRREVlhteGEGGLKRvvKKEHADGSVTRSGYDAAGRLT-AQTDA---------AGRRT-----------EYSLNvvs 458

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   928 -RLGRTTYLERFEVVYTYTASGQ--SIRTPGGRTHCVQQGKDGRVLLRLA-NGTQACYMFD-----------DVGRCTGR 992
Cdd:NF041261  459 gDITDITTPDGRETKFYYNDGNQltSVTSPDGLESRREYDEPGRLVSETSrSGETTRYRYDdphselpatttDATGSTKQ 538

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   993 ITW-RTDSPAAF-----HRVTYEYSGAGELRRISdNQKGDTQYQ-YDRAHRLIGEMSSGWQACRYEYDPAGNLLALPTC- 1064
Cdd:NF041261  539 MTWsRYGQLLAFtdcsgYQTRYEYDRFGQMTAVH-REEGISTYRrYDNRGQLTSVKDAQGRETRYEYNAAGDLTAVITPd 617

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 77970313  1065 ---PMMQYTGGNRLSTTSRGQYT----YDERNHLSEEIAHDGRRTTYRYDSMDLLVR 1114
Cdd:NF041261  618 gnrSETQYDAWGKAVSTTQGGLTrsmeYDAAGRITTLTNENGSHSTFLYDALDRLVQ 674
PAAR_2 cd14738
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 93-184 7.54e-13

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269823  Cd Length: 94  Bit Score: 65.73  E-value: 7.54e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   93 PAATIGvphlgtpHAHSHPPSSGFPLPSVGATI-GSGCLSVLIGGIPAARVLDIGIaptCGGitPFFDIQTGSSNTFIGG 171
Cdd:cd14738    1 PAARIG-------DMHVCPMVVTGPVPHVGGPIvGPGPTTVLIGGLPAARVGDMCV---CVG--PPDTIVQGSSTVLIGG 68

                         90
                 ....*....|...
gi 77970313  172 MRAARMGiDMTRH 184
Cdd:cd14738   69 KPAARMG-DSTAH 80
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 119-184 4.62e-12

Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 443280  Cd Length: 87  Bit Score: 63.30  E-value: 4.62e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 77970313  119 PSVGATIGSGCLSVLIGGIPAARVLDIGiapTCGGITPFFdIQTGSSNTFIGGMRAARMGiDMTRH 184
Cdd:COG4104   12 TSHGGPVISGSPTVLIGGRPAARVGDKV---SCPKHGPDT-IAEGSPTVLINGKPAARVG-DKTAC 72
PAAR_5 cd14741
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 93-182 5.90e-11

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family in bacteria as well as some archaea, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269826  Cd Length: 95  Bit Score: 60.48  E-value: 5.90e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   93 PAATIGVPhlgTPHahshppssGFPLpsvgaTIGSGCLSVLIGGIPAARVL-DIGIAPTCGGITPFFD--IQTGSSNTFI 169
Cdd:cd14741    2 PAARIGDS---TAH--------GGPL-----TPGPGSPNVLIGGFPAWRAGgDGHVCPLVTGPVPHVGgvVAAGSTTVLI 65

                         90
                 ....*....|...
gi 77970313  170 GGMRAARMGiDMT 182
Cdd:cd14741   66 NGLPAARMG-DMI 77
PAAR_like cd14671
proline-alanine-alanine-arginine (PAAR) repeat superfamily; This domain is found in the PAAR ...
 93-184 1.33e-10

proline-alanine-alanine-arginine (PAAR) repeat superfamily; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat superfamily, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. The PAAR-repeat proteins form a diverse superfamily with several subgroups extended both N- and C-terminally by domains with various predicted functions; the termini are exposed to solution, and do not distort the VgrG binding site. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269821  Cd Length: 77  Bit Score: 58.87  E-value: 1.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   93 PAAtigVPHLGTPHAHSHPPSSGFPlpsvgatigsgclSVLIGGIPAARVLDIGIAPTCGGItpffdIQTGSSNTFIGGM 172
Cdd:cd14671    1 PAA---RVGDPTAHTPGGPVISGSP-------------NVFINGRPAARVGDVGDHPGGGNA-----IVSGSGTVFINGK 59

                         90
                 ....*....|..
gi 77970313  173 RAARMGiDMTRH 184
Cdd:cd14671   60 PAARVG-DRTSC 70
RhsA COG3209
Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction ...
 343-861 6.37e-08

Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction only];


Pssm-ID: 442442 [Multi-domain]  Cd Length: 1103  Bit Score: 57.84  E-value: 6.37e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  343 SAVTGEVKNDFTDYETDETLPFIWGRHYCSGWNERNGAQGYGFRHAWQRELQLLRTRAIYTDPRGTKYTFSRNADGTYDG 422
Cdd:COG3209  470 GATTGGGTEAGTGGGTLTSGSAGATTLGTDTTLDDTLGGTTTTTAGARGLVVTTGTTLTLGTTTTATLSATDATGTGDTT 549

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  423 CCQGYSLEQIDSRRFFIRHEAAGDAEFERDAETALSVRCISHQRDRTQSLLRWRPDGHIGKIVQTDHDGNVRRTVSLRYD 502
Cdd:COG3209  550 TTGTVGTGTSTGTGGTGTVTTTGDGTGGASTTTGTTGGTATTTTVTTTTTTSTAGTTTTTTSGYTRAGLTLTLGTGTASG 629

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  503 QSGRIVEVVL----TDVDGRDTRIARYAYDTENCLTSYRNALDAISTYEYDAQRRMARLAGANGYSFLYCYDSEGRCVES 578
Cdd:COG3209  630 LERATASTGSttggTTGTGVTTTGTTTTRATGTTGTGTGVTAGLTTLATGGTTVGGGTGTTSTATTGATTGGTETGTTVT 709

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  579 AGQDRMWHVRFQYRPGRTIVTEGDGGRWTILYNEMGTITHVVDPYGGIAEYVLDPSGRIVEEIDSGG-----RTLRWLYD 653
Cdd:COG3209  710 TLAGGTTTRLGTTTTGGGGGTTTDGTGTGGTTGTLTTTSTTTTTTAGALTYTYDALGRLTSETTPGGvtqgtYTTRYTYD 789

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  654 ARagtiGRLDRFgnLWPNKDELPNLPNPLahhvpnamrGLIWGEFNVDNLTDTVLLPQEIDHWAWG---SATDAVARWPD 730
Cdd:COG3209  790 AL----GRLTSV--TYPDGETVTYTYDAL---------GRLTSVITVGSGGGTDLQDRTYTYDAAGnitSITDALRAGTL 854

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  731 ERRQQRDVAGRVIARTNiSGHTERFEYDADDNLLLRfdQDGAATRYTRCSWNLLASEENALGETIRYRYtsrrDVASVID 810
Cdd:COG3209  855 TQTYTYDALGRLTSATD-PGTTESYTYDANGNLTSR--TDGGTTTYTYDALGRLVSVTKPDGTTTTYTY----DALGHTD 927

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|.
gi 77970313  811 ANGNESAysydfkkrmtSVTRHGRLRESYVYDGGDRLIEKRDGAGKWLLRF 861
Cdd:COG3209  928 HLGSVRA----------LTDASGQVVWRYDYDPFGNLLAETSGAAANPLRF 968
PAAR_3 cd14739
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 91-170 8.58e-08

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269824  Cd Length: 90  Bit Score: 51.21  E-value: 8.58e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   91 GMPAATIGVPHLGT--PHAHsHPPSSGFPlpsvgatigSGCLSVLIGGIPAARVLDigiAPTCGGItpffdIQTGSSNTF 168
Cdd:cd14739   27 GMPAAVVGDMHACVipPPPA-HPPASPFP---------PGSATVLIGGRPAARVGD---ACGCGAT-----IVVGAPTVL 88


                 ..
gi 77970313  169 IG 170
Cdd:cd14739   89 IG 90
PAAR_CT_1 cd14743
proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension; This domain is found ...
 117-184 2.07e-05

proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Some members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences as well as uncharacterized domains. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes.


Pssm-ID: 269828  Cd Length: 78  Bit Score: 44.21  E-value: 2.07e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 77970313  117 PLPSVGATIGSGCLSVLIGGIPAARVLDigiAPTCGGItpffdIQTGSSNTFIGGMRAARMGiDMTRH 184
Cdd:cd14743   12 PLPGHGSTPIGSSSADFFDGLPAARVGD---KTSCGAT-----IVSGSINVLINGKPAAVLG-STTSH 70
PAAR_5 cd14741
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 91-156 2.63e-05

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family in bacteria as well as some archaea, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269826  Cd Length: 95  Bit Score: 44.31  E-value: 2.63e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 77970313   91 GMPAATIGVphlgtpHAHSHPPSSGfPLPSVGATIGSGCLSVLIGGIPAARvldIGIAPTCGGITP 156
Cdd:cd14741   29 GFPAWRAGG------DGHVCPLVTG-PVPHVGGVVAAGSTTVLINGLPAAR---MGDMIVEGGPPN 84
PAAR_RHS cd14742
proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement ...
 123-182 9.59e-05

proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement hotspot (Rhs) extensions; This PAAR (proline-alanine-alanine-arginine) repeat subfamily, which forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS), contains C- and N-terminal domain extensions. These include Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences at the C-terminal, and various predicted functions at N- and C-terminal extensions. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes.


Pssm-ID: 269827  Cd Length: 86  Bit Score: 42.58  E-value: 9.59e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313  123 ATIGSGCLSVLIGGIPAARVLDIGIAPTCGGITPFFdIQTGSSNTFIGGMRAARMGIDMT 182
Cdd:cd14742   13 GTITSGSPNVFINGKPAARAADSTVACSKHPPPPQL-IAEGSETVFINGQPAARKGDKTT 71
YD_repeat_2x TIGR01643
YD repeat (two copies); This model describes two tandem copies of a 21-residue extracellular ...
 737-777 2.46e-04

YD repeat (two copies); This model describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin.


Pssm-ID: 273728 [Multi-domain]  Cd Length: 42  Bit Score: 39.88  E-value: 2.46e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 77970313    737 DVAGRVIARTNISGHTERFEYDADDNLLLRFDQDGAATRYT 777
Cdd:TIGR01643    2 DAAGRLTGSTDADGTTTRYTYDAAGRLVEITDADGGSTRYE 42
PAAR_CT_2 cd14744
proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This ...
 120-178 3.66e-04

proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly beta- and gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Most members contain C-terminal domain extensions corresponding to several uncharacterized domains such as S-type pyocin, DUF2235, DUF2345 and cytotoxic proteins. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes.


Pssm-ID: 269829  Cd Length: 78  Bit Score: 40.62  E-value: 3.66e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 77970313  120 SVGATIGSGCLSVLIGGIPAARVLDIGIAPTCGGITPffdIQTGSSNTFIGGMRAARMG 178
Cdd:cd14744   11 THGGVVISGSSTFTIDGRPVARVGDKVTCPKCKGTGP---IVEGGPTFTVDGRPVALDG 66
PAAR_3 cd14739
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 122-178 3.96e-04

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269824  Cd Length: 90  Bit Score: 40.80  E-value: 3.96e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 77970313  122 GATIGSGCLSVLIGGIPAARVLDIGIA--PTCGGITPFFDIQTGSSNTFIGGMRAARMG 178
Cdd:cd14739   13 GTITGPGVPTVLIGGMPAAVVGDMHACviPPPPAHPPASPFPPGSATVLIGGRPAARVG 71
PAAR_2 cd14738
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 91-170 4.45e-04

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269823  Cd Length: 94  Bit Score: 40.69  E-value: 4.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   91 GMPAATIGVPHLGTPhahshPPSsgfplpsvgaTIGSGCLSVLIGGIPAARVLDigiapTC--GGItpffdIQTGSSNTF 168
Cdd:cd14738   38 GLPAARVGDMCVCVG-----PPD----------TIVQGSSTVLIGGKPAARMGD-----STahGGV-----IVSGVPTVL 92


                 ..
gi 77970313  169 IG 170
Cdd:cd14738   93 IG 94
PAAR_1 cd14737
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 88-170 4.61e-04

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269822  Cd Length: 94  Bit Score: 40.73  E-value: 4.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   88 KMPGMPAATIGVPHlgTPHAHS-HPPSSGfplpsvgaTIGSGCLSVLIGGIPAARVLDigiAPTCGGItpffdIQTGSSN 166
Cdd:cd14737   29 TVNGKPVLRQGDAL--APHTCPkHPPHGG--------VIASGSSTVFINGKPAARVGD---PVSCGGT-----VAGGSPN 90


                 ....
gi 77970313  167 TFIG 170
Cdd:cd14737   91 VFIG 94
PAAR_1 cd14737
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 92-178 6.00e-04

proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli.


Pssm-ID: 269822  Cd Length: 94  Bit Score: 40.34  E-value: 6.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   92 MPAATIGvpHLGTPHahshppsSGFPlPSVGATiGSGclSVLIGGIPAARVLDIgIAPTCGGITPFFD--IQTGSSNTFI 169
Cdd:cd14737    1 PAAARLG--DICTGH-------GGFP-PTPVIA-GSP--DVTVNGKPVLRQGDA-LAPHTCPKHPPHGgvIASGSSTVFI 66


                 ....*....
gi 77970313  170 GGMRAARMG 178
Cdd:cd14737   67 NGKPAARVG 75
PAAR_CT_1 cd14743
proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension; This domain is found ...
 93-164 6.77e-04

proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension; This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Some members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences as well as uncharacterized domains. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes.


Pssm-ID: 269828  Cd Length: 78  Bit Score: 39.98  E-value: 6.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   93 PAATIGVPHLGTPHAHSHPPSSGFP------LP--------SVGATIGSGCLSVLIGGIPAARVldiGIAPTCGGItpff 158
Cdd:cd14743    1 PAARVGDPHACPLPGHGSTPIGSSSadffdgLPaarvgdktSCGATIVSGSINVLINGKPAAVL---GSTTSHGGV---- 73


                 ....*.
gi 77970313  159 dIQTGS 164
Cdd:cd14743   74 -VIGGS 78
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 91-153 2.73e-03

PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins.


Pssm-ID: 428491  Cd Length: 71  Bit Score: 37.93  E-value: 2.73e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 77970313     91 GMPAATIGVPHLGTPHAHSHPpssgfplpsvgatIGSGCLSVLIGGIPAARVLDIgiaPTCGG 153
Cdd:pfam05488   22 GKPAARVGDLVVCPPCGGGGP-------------IAEGSPTVLINGKPAAREGDK---TACGA 68
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 1340-1435 5.60e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 41.16  E-value: 5.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 77970313   1340 AERDAAIERMKREIENLEQEKKKLSLDEKNWYSYPETPET------KRLDAIRERVLELNDKIKNYPLVRDKTTEFPKGY 1413
Cdd:TIGR04523  606 EEKEKKISSLEKELEKAKKENEKLSSIIKNIKSKKNKLKQevkqikETIKEIRNKWPEIIKKIKESKTKIDDIIELMKDW 685

                           90       100
                   ....*....|....*....|..
gi 77970313   1414 LQSTHIEMIKRYTREGREGKLP 1435
Cdd:TIGR04523  686 LKELSLHYKKYITRMIRIKDLP 707
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 1085-1115 5.67e-03

RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be involved in ligand binding. Note that this model may not find all the repeats in a protein and that it covers two RHS repeats. The 3D structure of an RHS-repeat-containing protein (the B and C components of an ABC toxin complex) has been determined. The RHS repeats form an extended strip of beta-sheet that spirals around to form a hollow shell, encapsulating the variable C-terminal domain.


Pssm-ID: 461685 [Multi-domain]  Cd Length: 37  Bit Score: 36.04  E-value: 5.67e-03
                           10        20        30
                   ....*....|....*....|....*....|.
gi 77970313   1085 YDERNHLSEEIAHDGRRTTYRYDSMDLLVRV 1115
Cdd:pfam05593    1 YDAAGRLTSVTDPDGRVTTYTYDAAGRLTAV 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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