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Conserved domains on  [gi|1539234771|emb|VDY89376|]
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Rhs core protein with extension [Escherichia coli]

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;
569-1470 1.07e-51

RHS element core protein;


The actual alignment was detected with superfamily member NF041261:

Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 200.61  E-value: 1.07e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  569 LKLTYHASGYLKAIHRTDNGIQTLATYEQDARGRLTEAdarldyhlfyeydaadriiRWSDNDQtwSRFTYDEQGRCVTV 648
Cdd:NF041261   320 VRYTYTEAGELLAVYDRSNTQVRAFTYDAQHPGRMVAH-------------------RYAGRPE--MCYRYDDTGRVTEQ 378

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  649 TGAEGYyNATLDYGDGCTTVTDGKGIHRYYYDPDG----NILREEAPDGSTTTYEWDEFHHLLARHSPAGRVEKFEYNAA 724
Cdd:NF041261   379 LNPAGL-SYRYQYEQDRITITDSLNRREVLHTEGEgglkRVVKKEHADGSVTRSGYDAAGRLTAQTDAAGRRTEYSLNVV 457

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  725 QGQLSRYTAADGAEWQYCYDERGLLSNITDPAGQTWTQQCDERGLPVSLVSPQGEETRLAYTpqgllsgifrqderrlgi 804
Cdd:NF041261   458 SGDITDITTPDGRETKFYYNDGNQLTSVTSPDGLESRREYDEPGRLVSETSRSGETTRYRYD------------------ 519

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  805 eyDHHNrpetltdvmgrehhteysghDLPVKMRGPGGQSVRLQWQQHHKLSGLERAGTGAEGFRYDRHGNLLAYTDGNGV 884
Cdd:NF041261   520 --DPHS--------------------ELPATTTDATGSTKQMTWSRYGQLLAFTDCSGYQTRYEYDRFGQMTAVHREEGI 577

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  885 VWTMEYGPFDLPVARTDGEGHRWQYRYDKDTlQLTEVINPQGESYLYILDNCGRVTEERDwGGVVWRYRYDADGLCTARV 964
Cdd:NF041261   578 STYRRYDNRGQLTSVKDAQGRETRYEYNAAG-DLTAVITPDGNRSETQYDAWGKAVSTTQ-GGLTRSMEYDAAGRITTLT 655

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  965 --NGLEETILYgrDAAGRLAEVITPEGKTQ---------------------YAYDKSDRLTGIFSPDGTSQRTGYDERG- 1020
Cdd:NF041261   656 neNGSHSTFLY--DALDRLVQQRGFDGRTQryhydltgkltqsedeglvtlWHYDESDRITHRTVNGEPAEQWQYDEHGw 733

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1021 --RVNVTTQGRR-AIEYHYPDEHTvirciLPPEDERDRHPDESLL----KTTYRYNAAGELTEVI---LPGNETLT---- 1086
Cdd:NF041261   734 ltDISHLSEGHRvAVHYGYDDKGR-----LTGERQTVENPETGELlwqhETGHAYNEQGLANRVTpdsLPPVEWLTygsg 808

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1087 --------------FSRDEAGREVFR-----HSNRGFACEQGWNAAGQLTSQRAG--LFPEEATW---GGLV----PSLV 1138
Cdd:NF041261   809 ylagmklggtplveYTRDRLHRETVRsfggaGSNAAYELTTAYTPAGQLQSQHLNslVYDRDYTWndnGDLVrisgPRQT 888

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1139 REYRYDSAGNVSGV-TSREDYgrETRREYRLDRNGQV---------TAVTASGTGLGYGEGDESYGYDSCGylkaqsagr 1208
Cdd:NF041261   889 REYGYSATGRLTGVhTTAANL--DIRIPYATDPAGNRlpdpelhpdSTLTAWPDNRIAEDAHYVYRYDEYG--------- 957

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1209 hRISEETDQY-AGGHRLKQAGNTQYDYDAAGRMVSRTKHRDGyRPETErfrwdSRdqltgycsaqgelweYRHDASGRRT 1287
Cdd:NF041261   958 -RLTEKTDRIpEGVIRTDDERTHHYHYDSQHRLVFYTRIQHG-EPLVE-----SR---------------YLYDPLGRRM 1015

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1288 EKRCDRKKIRFT-------------YLWDGDSIAEIR---------------------EYRDDELYSVRH------LVFN 1327
Cdd:NF041261  1016 AKRVWRRERDLTgwmslsrkpevtwYGWDGDRLTTVQtdttriqtvyqpgsftplirvETENGERAKAQRrslaetLQQE 1095

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1328 GFE-------------LISQQFSRVRQPHPSV-APQWVTRTNHAVSDLT---------------------GRPLMLFNSE 1372
Cdd:NF041261  1096 GSEnghgvvfpaelvrMLDRLEEEIRADRVSEeSRAWLAQCGLTVEQMArqvepeytparklhlyhcdhrGLPLALISEE 1175

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1373 GKTVWQpGQTSLWGLALSlpadtdypdprgeldpEADPGLLY-----AGQWQDAESGLCYNRFRYYDPETGMYLVSDPLG 1447
Cdd:NF041261  1176 GNTAWQ-GEYDEWGNLLN----------------EENPHHLQqpyrlPGQQYDEESGLYYNRNRYYDPLQGRYITQDPIG 1238

                         1050      1060
                   ....*....|....*....|...
gi 1539234771 1448 LQGGEQTYRYVPNPCGYVDPSGL 1470
Cdd:NF041261  1239 LKGGWNLYQYPLNPIRFIDPLGL 1261
PAAR_RHS cd14742
proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement ...
 252-305 1.95e-24

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: 98.43  E-value: 1.95e-24
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1539234771  252 AGEDTALCDKENKPP-RIAQGSSNVFINNQPAARKGDKLECSAAIVEGSPDVFIG 305
Cdd:cd14742     32 AADSTVACSKHPPPPqLIAEGSETVFINGQPAARKGDKTTCSAVISEGSPNVFIG 86
DUF6531 pfam20148
Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.
 393-454 1.71e-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: 66.79  E-value: 1.71e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1539234771  393 DPVDPVTGAYCDERTDFTLGQTLPLSFTRFHSSVLPLHGLTGVGWSDSWSEY---------AWVREQGNRV 454
Cdd:pfam20148    2 DPVNVATGNKVLEETDFSLPGPLPLVWTRTYNSSSERDGPLGPGWSHPYDQRlelegdggvVYIDADGREV 72
YwqJ-deaminase super family cl24268
YwqJ-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily prototyped ...
 1505-1594 3.20e-03

YwqJ-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Bacillus YwqJ. Members of this family are present in a wide phyletic range of bacteria and a few basidiomycetes. Bacterial versions are predicted to function as toxins in bacterial polymorphic toxin systems.


The actual alignment was detected with superfamily member pfam14431:

Pssm-ID: 373065  Cd Length: 134  Bit Score: 39.42  E-value: 3.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1505 SKLPRAVSAVVDKRTGKIYYG-ESGWPHPT-EIHPTLQN---NMP---SASKERWAI--ENCAEFKAVNEAL-------- 1566
Cdd:pfam14431   10 VRLPPDQAGVLDLQTGEYIRGvNPQYEKPGkDLHPLVQSrldELPgdgTAGHGRFAGgaGLHAEVQAVSNALydyearag 89

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1539234771 1567 ----KANAKISDLEVHTVLVKT----GEAFPMCKNC 1594
Cdd:pfam14431   90 erqaRAALDGLRIMVYTVRLPGtpegGTPFPPCPNC 125
 
Name Accession Description Interval E-value
RHS_core NF041261
RHS element core protein;
569-1470 1.07e-51

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 200.61  E-value: 1.07e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  569 LKLTYHASGYLKAIHRTDNGIQTLATYEQDARGRLTEAdarldyhlfyeydaadriiRWSDNDQtwSRFTYDEQGRCVTV 648
Cdd:NF041261   320 VRYTYTEAGELLAVYDRSNTQVRAFTYDAQHPGRMVAH-------------------RYAGRPE--MCYRYDDTGRVTEQ 378

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  649 TGAEGYyNATLDYGDGCTTVTDGKGIHRYYYDPDG----NILREEAPDGSTTTYEWDEFHHLLARHSPAGRVEKFEYNAA 724
Cdd:NF041261   379 LNPAGL-SYRYQYEQDRITITDSLNRREVLHTEGEgglkRVVKKEHADGSVTRSGYDAAGRLTAQTDAAGRRTEYSLNVV 457

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  725 QGQLSRYTAADGAEWQYCYDERGLLSNITDPAGQTWTQQCDERGLPVSLVSPQGEETRLAYTpqgllsgifrqderrlgi 804
Cdd:NF041261   458 SGDITDITTPDGRETKFYYNDGNQLTSVTSPDGLESRREYDEPGRLVSETSRSGETTRYRYD------------------ 519

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  805 eyDHHNrpetltdvmgrehhteysghDLPVKMRGPGGQSVRLQWQQHHKLSGLERAGTGAEGFRYDRHGNLLAYTDGNGV 884
Cdd:NF041261   520 --DPHS--------------------ELPATTTDATGSTKQMTWSRYGQLLAFTDCSGYQTRYEYDRFGQMTAVHREEGI 577

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  885 VWTMEYGPFDLPVARTDGEGHRWQYRYDKDTlQLTEVINPQGESYLYILDNCGRVTEERDwGGVVWRYRYDADGLCTARV 964
Cdd:NF041261   578 STYRRYDNRGQLTSVKDAQGRETRYEYNAAG-DLTAVITPDGNRSETQYDAWGKAVSTTQ-GGLTRSMEYDAAGRITTLT 655

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  965 --NGLEETILYgrDAAGRLAEVITPEGKTQ---------------------YAYDKSDRLTGIFSPDGTSQRTGYDERG- 1020
Cdd:NF041261   656 neNGSHSTFLY--DALDRLVQQRGFDGRTQryhydltgkltqsedeglvtlWHYDESDRITHRTVNGEPAEQWQYDEHGw 733

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1021 --RVNVTTQGRR-AIEYHYPDEHTvirciLPPEDERDRHPDESLL----KTTYRYNAAGELTEVI---LPGNETLT---- 1086
Cdd:NF041261   734 ltDISHLSEGHRvAVHYGYDDKGR-----LTGERQTVENPETGELlwqhETGHAYNEQGLANRVTpdsLPPVEWLTygsg 808

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1087 --------------FSRDEAGREVFR-----HSNRGFACEQGWNAAGQLTSQRAG--LFPEEATW---GGLV----PSLV 1138
Cdd:NF041261   809 ylagmklggtplveYTRDRLHRETVRsfggaGSNAAYELTTAYTPAGQLQSQHLNslVYDRDYTWndnGDLVrisgPRQT 888

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1139 REYRYDSAGNVSGV-TSREDYgrETRREYRLDRNGQV---------TAVTASGTGLGYGEGDESYGYDSCGylkaqsagr 1208
Cdd:NF041261   889 REYGYSATGRLTGVhTTAANL--DIRIPYATDPAGNRlpdpelhpdSTLTAWPDNRIAEDAHYVYRYDEYG--------- 957

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1209 hRISEETDQY-AGGHRLKQAGNTQYDYDAAGRMVSRTKHRDGyRPETErfrwdSRdqltgycsaqgelweYRHDASGRRT 1287
Cdd:NF041261   958 -RLTEKTDRIpEGVIRTDDERTHHYHYDSQHRLVFYTRIQHG-EPLVE-----SR---------------YLYDPLGRRM 1015

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1288 EKRCDRKKIRFT-------------YLWDGDSIAEIR---------------------EYRDDELYSVRH------LVFN 1327
Cdd:NF041261  1016 AKRVWRRERDLTgwmslsrkpevtwYGWDGDRLTTVQtdttriqtvyqpgsftplirvETENGERAKAQRrslaetLQQE 1095

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1328 GFE-------------LISQQFSRVRQPHPSV-APQWVTRTNHAVSDLT---------------------GRPLMLFNSE 1372
Cdd:NF041261  1096 GSEnghgvvfpaelvrMLDRLEEEIRADRVSEeSRAWLAQCGLTVEQMArqvepeytparklhlyhcdhrGLPLALISEE 1175

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1373 GKTVWQpGQTSLWGLALSlpadtdypdprgeldpEADPGLLY-----AGQWQDAESGLCYNRFRYYDPETGMYLVSDPLG 1447
Cdd:NF041261  1176 GNTAWQ-GEYDEWGNLLN----------------EENPHHLQqpyrlPGQQYDEESGLYYNRNRYYDPLQGRYITQDPIG 1238

                         1050      1060
                   ....*....|....*....|...
gi 1539234771 1448 LQGGEQTYRYVPNPCGYVDPSGL 1470
Cdd:NF041261  1239 LKGGWNLYQYPLNPIRFIDPLGL 1261
RhsA COG3209
Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction ...
 433-1471 1.36e-36

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


Pssm-ID: 442442 [Multi-domain]  Cd Length: 1103  Bit Score: 151.45  E-value: 1.36e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  433 TGVGWSDSWSEYAWVREQGNRVDIISLGATLNFAFDGESDTAVNPYHAQYILRRCDDYLELFDRNALSSRFFYDAFPGMR 512
Cdd:COG3209    134 GGTLGATAGSATTGSTDGGRGGVAVTGLAGGGASAYGLTLGGAAAGPATGVGTGAVTLATGLAGSALLALGSGAILGGLA 213

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  513 LRHPVTDDTSDDRLAHSPADRMYMLGGMSDTASNRITFERDSQYRITGVSHTDGIRLKLTYHASGYLKAIHRTDNGIQTL 592
Cdd:COG3209    214 GAYSGSATTATGTALGTPASVAATVTGSATGAAGAGAAVATAATTLGGTTGAGTGASGAGLDASTGTGGAGGSNAAATAG 293

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  593 ATYEQDARGRLTEADARLDYHLFYEYDAADRIIRWSDNDQTWSRFTYDEQGRCVTVTGAEGYYNATLDYGDGCTTVTDGK 672
Cdd:COG3209    294 GLGGAGLGSGGAGGGGTAGGTTTAAGTTGTAAVSGAADAGTTTTTGTGTGGTTTTVGGGGSLTLGGYGAAGGLTTSVGAG 373

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  673 GIHRYYYDPDGNILReeapDGSTTTYEWDEFHHLLARHSPAGRVEKFEYNAAQGQLSRYTAADGAEWQYcYDERGLLSNI 752
Cdd:COG3209    374 GGGSTSGSTTTVGGG----GTATGSGGGSSTTGVGAGTTTTSTTGGDGGPATAAGALTAGGTATGTGTG-GGGTTAGTDA 448

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  753 TDPAGQTWTQQCDERGLPVSLVSPQGEETRLAYTPQGLLSGIFRQDERRLGIEYDHHNRPETLTDVMGREHHTEYSGHDL 832
Cdd:COG3209    449 TTTTGGAGASGTLTTTGGAATGATTGGGTEAGTGGGTLTSGSAGATTLGTDTTLDDTLGGTTTTTAGARGLVVTTGTTLT 528

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  833 PVKMRGPGGQSVRLQWQQHHKLSGLERAGTGAEGFRYDRHGNLLAYTDGNGVVWTMEYGPFDLPVARTDGEGHRWQYRYD 912
Cdd:COG3209    529 LGTTTTATLSATDATGTGDTTTTGTVGTGTSTGTGGTGTVTTTGDGTGGASTTTGTTGGTATTTTVTTTTTTSTAGTTTT 608

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  913 KDTLQLTEVINPQGESYLYILDNCGRVTEERDWGGVVWRYRYDADGLCTARVNGLEETILYGRDAAGRLAEVITPEGKTQ 992
Cdd:COG3209    609 TTSGYTRAGLTLTLGTGTASGLERATASTGSTTGGTTGTGVTTTGTTTTRATGTTGTGTGVTAGLTTLATGGTTVGGGTG 688

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  993 YAYDKSDRLTGIFSPDGTSQRTGYDERGRVNVTTQGRRAIEYHYPDEHTVIRCILPPEDERDRHPDESLlkTTYRYNAAG 1072
Cdd:COG3209    689 TTSTATTGATTGGTETGTTVTTLAGGTTTRLGTTTTGGGGGTTTDGTGTGGTTGTLTTTSTTTTTTAGA--LTYTYDALG 766

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1073 ELTEVILPGNE-----TLTFSRDEAGREVFRHSNRGFACEQGWNAAGQLTSQRaglfpeEATWGGLVPSLVREYRYDSAG 1147
Cdd:COG3209    767 RLTSETTPGGVtqgtyTTRYTYDALGRLTSVTYPDGETVTYTYDALGRLTSVI------TVGSGGGTDLQDRTYTYDAAG 840

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1148 NVSGVTSREDYGRETRReYRLDRNGQVTAVTASGTGlgygegdesygydscgylkaqsagrhriseetdqyagghrlkqa 1227
Cdd:COG3209    841 NITSITDALRAGTLTQT-YTYDALGRLTSATDPGTT-------------------------------------------- 875

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1228 gnTQYDYDAAGRMVSRTkhrdgyRPETERFRWDSRDQLTGYCSAQGELWEYRHDASGrrtekrcdrkkirftylwdgdsi 1307
Cdd:COG3209    876 --ESYTYDANGNLTSRT------DGGTTTYTYDALGRLVSVTKPDGTTTTYTYDALG----------------------- 924

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1308 aeireyrddelysvrhlvfngfelisqqfsrvrqphpsvapqwvtrtnhaVSDLTGRPLMLFNSEGKTVWQpGQTSLWGL 1387
Cdd:COG3209    925 --------------------------------------------------HTDHLGSVRALTDASGQVVWR-YDYDPFGN 953

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1388 ALSLPADTDYPDPRgeldpeadpgllYAGQWQDAESGLCYNRFRYYDPETGMYLVSDPLGLQGGEQTYRYV-PNPCGYVD 1466
Cdd:COG3209    954 LLAETSGAAANPLR------------FTGQEYDAETGLYYNGARYYDPALGRFLSPDPIGLAGGLNLYAYVgNNPVNYVD 1021


                   ....*
gi 1539234771 1467 PSGLA 1471
Cdd:COG3209   1022 PLGLA 1026
PAAR_RHS cd14742
proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement ...
 252-305 1.95e-24

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: 98.43  E-value: 1.95e-24
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1539234771  252 AGEDTALCDKENKPP-RIAQGSSNVFINNQPAARKGDKLECSAAIVEGSPDVFIG 305
Cdd:cd14742     32 AADSTVACSKHPPPPqLIAEGSETVFINGQPAARKGDKTTCSAVISEGSPNVFIG 86
Rhs_assc_core TIGR03696
RHS repeat-associated core domain; This model represents a conserved unique core sequence ...
 1399-1470 1.16e-22

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: 92.95  E-value: 1.16e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1539234771 1399 DPRGELDPEADPG---LLYAGQWQDAESGLCYNRFRYYDPETGMYLVSDPLGLQGGEQTYRYVP-NPCGYVDPSGL 1470
Cdd:TIGR03696    2 DPYGEVLSESGAApnpLRFTGQYYDAETGLYYNGARYYDPELGRFLSPDPIGLGGGLNLYAYVGnNPVNWVDPLGL 77
RHS_core NF041261
RHS element core protein;
748-1288 5.93e-20

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 97.38  E-value: 5.93e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  748 LLSNITDPAGQTWT----QQCDERGLPVSLVSPQGEETRLAYTPQGLLSGIFRQDERRLGIEYDHHNR------PETLTD 817
Cdd:NF041261   208 VLTGMVDRFGRTLTfhreAAGDLAGEITGVTDGAGREFRLVLTTQAQRAEEARKQRTSSLSSPDGPRPlsssafPDTLPG 287

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  818 VM--GREHHTEYSG----HDLPVKMRGPGGQSVRLQWQQHHKLSGL-ERAGTGAEGFRYDRH--GNLLAYTDGNGVVWTM 888
Cdd:NF041261   288 GTeyGPDNGIRLSAvwltHDPAYPESLPAAPLVRYTYTEAGELLAVyDRSNTQVRAFTYDAQhpGRMVAHRYAGRPEMCY 367

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  889 EYGPFDLPVARTDGEGHRWQYRYDKDTLQLT------EVINPQGESYLyildncGRVTEERDWGGVVWRYRYDADGLCTA 962
Cdd:NF041261   368 RYDDTGRVTEQLNPAGLSYRYQYEQDRITITdslnrrEVLHTEGEGGL------KRVVKKEHADGSVTRSGYDAAGRLTA 441

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  963 RVNGLEETILYGRD-AAGRLAEVITPEGK-TQYAYDKSDRLTGIFSPDGTSQRTGYDERGR-VNVTTQGRRAIEYHYPDE 1039
Cdd:NF041261   442 QTDAAGRRTEYSLNvVSGDITDITTPDGReTKFYYNDGNQLTSVTSPDGLESRREYDEPGRlVSETSRSGETTRYRYDDP 521

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1040 HTVIRCILPpederdrhpDESLLKTTYRYNAAGELTEVILPGNETLTFSRDEAGREVFRHSNRGFACEQGWNAAGQLTSQ 1119
Cdd:NF041261   522 HSELPATTT---------DATGSTKQMTWSRYGQLLAFTDCSGYQTRYEYDRFGQMTAVHREEGISTYRRYDNRGQLTSV 592

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1120 RaglfpeeatwgglvpslvreyrydsagnvsgvtsrEDYGRETRREYrlDRNGQVTAVTASgtglgygEGDES-YGYDSC 1198
Cdd:NF041261   593 K-----------------------------------DAQGRETRYEY--NAAGDLTAVITP-------DGNRSeTQYDAW 628

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1199 GylKAQSAgrhriseetdqyagghrlKQAGNTQ-YDYDAAGRMVSRTkHRDGYRPEterFRWDSRDQLTGYCSAQGELWE 1277
Cdd:NF041261   629 G--KAVST------------------TQGGLTRsMEYDAAGRITTLT-NENGSHST---FLYDALDRLVQQRGFDGRTQR 684

                          570
                   ....*....|.
gi 1539234771 1278 YRHDASGRRTE 1288
Cdd:NF041261   685 YHYDLTGKLTQ 695
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 224-306 8.40e-16

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: 74.08  E-value: 8.40e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  224 FPAGPVLMEFATM-VGGRgeikkdvdfPEAGE-DTALCDKeNKPPRIAQGSSNVFINNQPAARKGDKLECSAAIVEGSPD 301
Cdd:COG4104     13 SHGGPVISGSPTVlIGGR---------PAARVgDKVSCPK-HGPDTIAEGSPTVLINGKPAARVGDKTACGGTIISGSPT 82


                   ....*
gi 1539234771  302 VFIGG 306
Cdd:COG4104     83 VLIGG 87
DUF6531 pfam20148
Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.
 393-454 1.71e-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: 66.79  E-value: 1.71e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1539234771  393 DPVDPVTGAYCDERTDFTLGQTLPLSFTRFHSSVLPLHGLTGVGWSDSWSEY---------AWVREQGNRV 454
Cdd:pfam20148    2 DPVNVATGNKVLEETDFSLPGPLPLVWTRTYNSSSERDGPLGPGWSHPYDQRlelegdggvVYIDADGREV 72
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 267-309 2.93e-09

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: 54.88  E-value: 2.93e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1539234771  267 RIAQGSSNVFINNQPAARKGDKLEC-----SAAIVEGSPDVFIGGEQV 309
Cdd:pfam05488   10 VVITGSPTVLIGGKPAARVGDLVVCppcggGGPIAEGSPTVLINGKPA 57
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 679-715 6.07e-06

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: 44.51  E-value: 6.07e-06
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1539234771  679 YDPDGNILREEAPDGSTTTYEWDEFHHLLARHSPAGR 715
Cdd:pfam05593    1 YDAAGRLTSVTDPDGRVTTYTYDAAGRLTAVTDPDGT 37
Bacuni_01323_like cd12871
Uncharacterized protein conserved in Bacteroidetes; A well-conserved family of 16-stranded ...
 634-753 3.44e-05

Uncharacterized protein conserved in Bacteroidetes; A well-conserved family of 16-stranded beta barrels resembling outer membrane porins. The interior of the barrels is mostly occupied by an insert with partially helical structure.


Pssm-ID: 214015 [Multi-domain]  Cd Length: 231  Bit Score: 47.03  E-value: 3.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  634 WSRFTYDEQGRCVTVTGAEGYYNA------TLDYGDGCTTVTD--GKGIHRYYYDPDGNILREEAPD-GSTTTYEWDefh 704
Cdd:cd12871     18 EYTFEYDADGRLTSITTTQEGEAEeityttTITYEPNVITVTDdgGKTVSTYTLNEKGYVTSCTETEyGKGQLRTYT--- 94

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1539234771  705 hllarhspagrvekFEYNaAQGQLSRYTAADGAEWQYC---YDERGLLSNIT 753
Cdd:cd12871     95 --------------FTYN-ADGQLTKIVESIGTEYSTItitWNNGDIVSIST 131
YwqJ-deaminase pfam14431
YwqJ-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily prototyped ...
 1505-1594 3.20e-03

YwqJ-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Bacillus YwqJ. Members of this family are present in a wide phyletic range of bacteria and a few basidiomycetes. Bacterial versions are predicted to function as toxins in bacterial polymorphic toxin systems.


Pssm-ID: 373065  Cd Length: 134  Bit Score: 39.42  E-value: 3.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1505 SKLPRAVSAVVDKRTGKIYYG-ESGWPHPT-EIHPTLQN---NMP---SASKERWAI--ENCAEFKAVNEAL-------- 1566
Cdd:pfam14431   10 VRLPPDQAGVLDLQTGEYIRGvNPQYEKPGkDLHPLVQSrldELPgdgTAGHGRFAGgaGLHAEVQAVSNALydyearag 89

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1539234771 1567 ----KANAKISDLEVHTVLVKT----GEAFPMCKNC 1594
Cdd:pfam14431   90 erqaRAALDGLRIMVYTVRLPGtpegGTPFPPCPNC 125
 
Name Accession Description Interval E-value
RHS_core NF041261
RHS element core protein;
569-1470 1.07e-51

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 200.61  E-value: 1.07e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  569 LKLTYHASGYLKAIHRTDNGIQTLATYEQDARGRLTEAdarldyhlfyeydaadriiRWSDNDQtwSRFTYDEQGRCVTV 648
Cdd:NF041261   320 VRYTYTEAGELLAVYDRSNTQVRAFTYDAQHPGRMVAH-------------------RYAGRPE--MCYRYDDTGRVTEQ 378

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  649 TGAEGYyNATLDYGDGCTTVTDGKGIHRYYYDPDG----NILREEAPDGSTTTYEWDEFHHLLARHSPAGRVEKFEYNAA 724
Cdd:NF041261   379 LNPAGL-SYRYQYEQDRITITDSLNRREVLHTEGEgglkRVVKKEHADGSVTRSGYDAAGRLTAQTDAAGRRTEYSLNVV 457

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  725 QGQLSRYTAADGAEWQYCYDERGLLSNITDPAGQTWTQQCDERGLPVSLVSPQGEETRLAYTpqgllsgifrqderrlgi 804
Cdd:NF041261   458 SGDITDITTPDGRETKFYYNDGNQLTSVTSPDGLESRREYDEPGRLVSETSRSGETTRYRYD------------------ 519

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  805 eyDHHNrpetltdvmgrehhteysghDLPVKMRGPGGQSVRLQWQQHHKLSGLERAGTGAEGFRYDRHGNLLAYTDGNGV 884
Cdd:NF041261   520 --DPHS--------------------ELPATTTDATGSTKQMTWSRYGQLLAFTDCSGYQTRYEYDRFGQMTAVHREEGI 577

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  885 VWTMEYGPFDLPVARTDGEGHRWQYRYDKDTlQLTEVINPQGESYLYILDNCGRVTEERDwGGVVWRYRYDADGLCTARV 964
Cdd:NF041261   578 STYRRYDNRGQLTSVKDAQGRETRYEYNAAG-DLTAVITPDGNRSETQYDAWGKAVSTTQ-GGLTRSMEYDAAGRITTLT 655

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  965 --NGLEETILYgrDAAGRLAEVITPEGKTQ---------------------YAYDKSDRLTGIFSPDGTSQRTGYDERG- 1020
Cdd:NF041261   656 neNGSHSTFLY--DALDRLVQQRGFDGRTQryhydltgkltqsedeglvtlWHYDESDRITHRTVNGEPAEQWQYDEHGw 733

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1021 --RVNVTTQGRR-AIEYHYPDEHTvirciLPPEDERDRHPDESLL----KTTYRYNAAGELTEVI---LPGNETLT---- 1086
Cdd:NF041261   734 ltDISHLSEGHRvAVHYGYDDKGR-----LTGERQTVENPETGELlwqhETGHAYNEQGLANRVTpdsLPPVEWLTygsg 808

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1087 --------------FSRDEAGREVFR-----HSNRGFACEQGWNAAGQLTSQRAG--LFPEEATW---GGLV----PSLV 1138
Cdd:NF041261   809 ylagmklggtplveYTRDRLHRETVRsfggaGSNAAYELTTAYTPAGQLQSQHLNslVYDRDYTWndnGDLVrisgPRQT 888

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1139 REYRYDSAGNVSGV-TSREDYgrETRREYRLDRNGQV---------TAVTASGTGLGYGEGDESYGYDSCGylkaqsagr 1208
Cdd:NF041261   889 REYGYSATGRLTGVhTTAANL--DIRIPYATDPAGNRlpdpelhpdSTLTAWPDNRIAEDAHYVYRYDEYG--------- 957

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1209 hRISEETDQY-AGGHRLKQAGNTQYDYDAAGRMVSRTKHRDGyRPETErfrwdSRdqltgycsaqgelweYRHDASGRRT 1287
Cdd:NF041261   958 -RLTEKTDRIpEGVIRTDDERTHHYHYDSQHRLVFYTRIQHG-EPLVE-----SR---------------YLYDPLGRRM 1015

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1288 EKRCDRKKIRFT-------------YLWDGDSIAEIR---------------------EYRDDELYSVRH------LVFN 1327
Cdd:NF041261  1016 AKRVWRRERDLTgwmslsrkpevtwYGWDGDRLTTVQtdttriqtvyqpgsftplirvETENGERAKAQRrslaetLQQE 1095

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1328 GFE-------------LISQQFSRVRQPHPSV-APQWVTRTNHAVSDLT---------------------GRPLMLFNSE 1372
Cdd:NF041261  1096 GSEnghgvvfpaelvrMLDRLEEEIRADRVSEeSRAWLAQCGLTVEQMArqvepeytparklhlyhcdhrGLPLALISEE 1175

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1373 GKTVWQpGQTSLWGLALSlpadtdypdprgeldpEADPGLLY-----AGQWQDAESGLCYNRFRYYDPETGMYLVSDPLG 1447
Cdd:NF041261  1176 GNTAWQ-GEYDEWGNLLN----------------EENPHHLQqpyrlPGQQYDEESGLYYNRNRYYDPLQGRYITQDPIG 1238

                         1050      1060
                   ....*....|....*....|...
gi 1539234771 1448 LQGGEQTYRYVPNPCGYVDPSGL 1470
Cdd:NF041261  1239 LKGGWNLYQYPLNPIRFIDPLGL 1261
RhsA COG3209
Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction ...
 433-1471 1.36e-36

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


Pssm-ID: 442442 [Multi-domain]  Cd Length: 1103  Bit Score: 151.45  E-value: 1.36e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  433 TGVGWSDSWSEYAWVREQGNRVDIISLGATLNFAFDGESDTAVNPYHAQYILRRCDDYLELFDRNALSSRFFYDAFPGMR 512
Cdd:COG3209    134 GGTLGATAGSATTGSTDGGRGGVAVTGLAGGGASAYGLTLGGAAAGPATGVGTGAVTLATGLAGSALLALGSGAILGGLA 213

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  513 LRHPVTDDTSDDRLAHSPADRMYMLGGMSDTASNRITFERDSQYRITGVSHTDGIRLKLTYHASGYLKAIHRTDNGIQTL 592
Cdd:COG3209    214 GAYSGSATTATGTALGTPASVAATVTGSATGAAGAGAAVATAATTLGGTTGAGTGASGAGLDASTGTGGAGGSNAAATAG 293

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  593 ATYEQDARGRLTEADARLDYHLFYEYDAADRIIRWSDNDQTWSRFTYDEQGRCVTVTGAEGYYNATLDYGDGCTTVTDGK 672
Cdd:COG3209    294 GLGGAGLGSGGAGGGGTAGGTTTAAGTTGTAAVSGAADAGTTTTTGTGTGGTTTTVGGGGSLTLGGYGAAGGLTTSVGAG 373

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  673 GIHRYYYDPDGNILReeapDGSTTTYEWDEFHHLLARHSPAGRVEKFEYNAAQGQLSRYTAADGAEWQYcYDERGLLSNI 752
Cdd:COG3209    374 GGGSTSGSTTTVGGG----GTATGSGGGSSTTGVGAGTTTTSTTGGDGGPATAAGALTAGGTATGTGTG-GGGTTAGTDA 448

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  753 TDPAGQTWTQQCDERGLPVSLVSPQGEETRLAYTPQGLLSGIFRQDERRLGIEYDHHNRPETLTDVMGREHHTEYSGHDL 832
Cdd:COG3209    449 TTTTGGAGASGTLTTTGGAATGATTGGGTEAGTGGGTLTSGSAGATTLGTDTTLDDTLGGTTTTTAGARGLVVTTGTTLT 528

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  833 PVKMRGPGGQSVRLQWQQHHKLSGLERAGTGAEGFRYDRHGNLLAYTDGNGVVWTMEYGPFDLPVARTDGEGHRWQYRYD 912
Cdd:COG3209    529 LGTTTTATLSATDATGTGDTTTTGTVGTGTSTGTGGTGTVTTTGDGTGGASTTTGTTGGTATTTTVTTTTTTSTAGTTTT 608

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  913 KDTLQLTEVINPQGESYLYILDNCGRVTEERDWGGVVWRYRYDADGLCTARVNGLEETILYGRDAAGRLAEVITPEGKTQ 992
Cdd:COG3209    609 TTSGYTRAGLTLTLGTGTASGLERATASTGSTTGGTTGTGVTTTGTTTTRATGTTGTGTGVTAGLTTLATGGTTVGGGTG 688

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  993 YAYDKSDRLTGIFSPDGTSQRTGYDERGRVNVTTQGRRAIEYHYPDEHTVIRCILPPEDERDRHPDESLlkTTYRYNAAG 1072
Cdd:COG3209    689 TTSTATTGATTGGTETGTTVTTLAGGTTTRLGTTTTGGGGGTTTDGTGTGGTTGTLTTTSTTTTTTAGA--LTYTYDALG 766

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1073 ELTEVILPGNE-----TLTFSRDEAGREVFRHSNRGFACEQGWNAAGQLTSQRaglfpeEATWGGLVPSLVREYRYDSAG 1147
Cdd:COG3209    767 RLTSETTPGGVtqgtyTTRYTYDALGRLTSVTYPDGETVTYTYDALGRLTSVI------TVGSGGGTDLQDRTYTYDAAG 840

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1148 NVSGVTSREDYGRETRReYRLDRNGQVTAVTASGTGlgygegdesygydscgylkaqsagrhriseetdqyagghrlkqa 1227
Cdd:COG3209    841 NITSITDALRAGTLTQT-YTYDALGRLTSATDPGTT-------------------------------------------- 875

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1228 gnTQYDYDAAGRMVSRTkhrdgyRPETERFRWDSRDQLTGYCSAQGELWEYRHDASGrrtekrcdrkkirftylwdgdsi 1307
Cdd:COG3209    876 --ESYTYDANGNLTSRT------DGGTTTYTYDALGRLVSVTKPDGTTTTYTYDALG----------------------- 924

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1308 aeireyrddelysvrhlvfngfelisqqfsrvrqphpsvapqwvtrtnhaVSDLTGRPLMLFNSEGKTVWQpGQTSLWGL 1387
Cdd:COG3209    925 --------------------------------------------------HTDHLGSVRALTDASGQVVWR-YDYDPFGN 953

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1388 ALSLPADTDYPDPRgeldpeadpgllYAGQWQDAESGLCYNRFRYYDPETGMYLVSDPLGLQGGEQTYRYV-PNPCGYVD 1466
Cdd:COG3209    954 LLAETSGAAANPLR------------FTGQEYDAETGLYYNGARYYDPALGRFLSPDPIGLAGGLNLYAYVgNNPVNYVD 1021


                   ....*
gi 1539234771 1467 PSGLA 1471
Cdd:COG3209   1022 PLGLA 1026
PAAR_RHS cd14742
proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement ...
 252-305 1.95e-24

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: 98.43  E-value: 1.95e-24
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1539234771  252 AGEDTALCDKENKPP-RIAQGSSNVFINNQPAARKGDKLECSAAIVEGSPDVFIG 305
Cdd:cd14742     32 AADSTVACSKHPPPPqLIAEGSETVFINGQPAARKGDKTTCSAVISEGSPNVFIG 86
Rhs_assc_core TIGR03696
RHS repeat-associated core domain; This model represents a conserved unique core sequence ...
 1399-1470 1.16e-22

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: 92.95  E-value: 1.16e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1539234771 1399 DPRGELDPEADPG---LLYAGQWQDAESGLCYNRFRYYDPETGMYLVSDPLGLQGGEQTYRYVP-NPCGYVDPSGL 1470
Cdd:TIGR03696    2 DPYGEVLSESGAApnpLRFTGQYYDAETGLYYNGARYYDPELGRFLSPDPIGLGGGLNLYAYVGnNPVNWVDPLGL 77
RHS_core NF041261
RHS element core protein;
748-1288 5.93e-20

RHS element core protein;


Pssm-ID: 469161 [Multi-domain]  Cd Length: 1261  Bit Score: 97.38  E-value: 5.93e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  748 LLSNITDPAGQTWT----QQCDERGLPVSLVSPQGEETRLAYTPQGLLSGIFRQDERRLGIEYDHHNR------PETLTD 817
Cdd:NF041261   208 VLTGMVDRFGRTLTfhreAAGDLAGEITGVTDGAGREFRLVLTTQAQRAEEARKQRTSSLSSPDGPRPlsssafPDTLPG 287

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  818 VM--GREHHTEYSG----HDLPVKMRGPGGQSVRLQWQQHHKLSGL-ERAGTGAEGFRYDRH--GNLLAYTDGNGVVWTM 888
Cdd:NF041261   288 GTeyGPDNGIRLSAvwltHDPAYPESLPAAPLVRYTYTEAGELLAVyDRSNTQVRAFTYDAQhpGRMVAHRYAGRPEMCY 367

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  889 EYGPFDLPVARTDGEGHRWQYRYDKDTLQLT------EVINPQGESYLyildncGRVTEERDWGGVVWRYRYDADGLCTA 962
Cdd:NF041261   368 RYDDTGRVTEQLNPAGLSYRYQYEQDRITITdslnrrEVLHTEGEGGL------KRVVKKEHADGSVTRSGYDAAGRLTA 441

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  963 RVNGLEETILYGRD-AAGRLAEVITPEGK-TQYAYDKSDRLTGIFSPDGTSQRTGYDERGR-VNVTTQGRRAIEYHYPDE 1039
Cdd:NF041261   442 QTDAAGRRTEYSLNvVSGDITDITTPDGReTKFYYNDGNQLTSVTSPDGLESRREYDEPGRlVSETSRSGETTRYRYDDP 521

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1040 HTVIRCILPpederdrhpDESLLKTTYRYNAAGELTEVILPGNETLTFSRDEAGREVFRHSNRGFACEQGWNAAGQLTSQ 1119
Cdd:NF041261   522 HSELPATTT---------DATGSTKQMTWSRYGQLLAFTDCSGYQTRYEYDRFGQMTAVHREEGISTYRRYDNRGQLTSV 592

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1120 RaglfpeeatwgglvpslvreyrydsagnvsgvtsrEDYGRETRREYrlDRNGQVTAVTASgtglgygEGDES-YGYDSC 1198
Cdd:NF041261   593 K-----------------------------------DAQGRETRYEY--NAAGDLTAVITP-------DGNRSeTQYDAW 628

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1199 GylKAQSAgrhriseetdqyagghrlKQAGNTQ-YDYDAAGRMVSRTkHRDGYRPEterFRWDSRDQLTGYCSAQGELWE 1277
Cdd:NF041261   629 G--KAVST------------------TQGGLTRsMEYDAAGRITTLT-NENGSHST---FLYDALDRLVQQRGFDGRTQR 684

                          570
                   ....*....|.
gi 1539234771 1278 YRHDASGRRTE 1288
Cdd:NF041261   685 YHYDLTGKLTQ 695
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 224-306 8.40e-16

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: 74.08  E-value: 8.40e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  224 FPAGPVLMEFATM-VGGRgeikkdvdfPEAGE-DTALCDKeNKPPRIAQGSSNVFINNQPAARKGDKLECSAAIVEGSPD 301
Cdd:COG4104     13 SHGGPVISGSPTVlIGGR---------PAARVgDKVSCPK-HGPDTIAEGSPTVLINGKPAARVGDKTACGGTIISGSPT 82


                   ....*
gi 1539234771  302 VFIGG 306
Cdd:COG4104     83 VLIGG 87
RhsA COG3209
Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction ...
 389-787 5.50e-14

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


Pssm-ID: 442442 [Multi-domain]  Cd Length: 1103  Bit Score: 77.49  E-value: 5.50e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  389 RWVTDPVDPVTGAYCDERTDFTLGQTLPLSFTRFHSSVLPLHGLTGVGWSDSWSEYAWVREQGNRVDIISLGATLNFAFD 468
Cdd:COG3209    550 TTGTVGTGTSTGTGGTGTVTTTGDGTGGASTTTGTTGGTATTTTVTTTTTTSTAGTTTTTTSGYTRAGLTLTLGTGTASG 629

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  469 GESDTAVNPYHAQYILRRCDDYLELFDRNALSSRFFYDAFPGMRLRHPVTDDTSDDRLAHSPADRMYMLGGMSDTASNRI 548
Cdd:COG3209    630 LERATASTGSTTGGTTGTGVTTTGTTTTRATGTTGTGTGVTAGLTTLATGGTTVGGGTGTTSTATTGATTGGTETGTTVT 709

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  549 TFERDSQYRITGVSHTDGIRLKLTYHASGYLKAI----HRTDNGIQTLATYEQDARGRLTEADARL-----DYHLFYEYD 619
Cdd:COG3209    710 TLAGGTTTRLGTTTTGGGGGTTTDGTGTGGTTGTltttSTTTTTTAGALTYTYDALGRLTSETTPGgvtqgTYTTRYTYD 789

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  620 AADRIIRWSDNDQTWSRFTYDEQGRCVTVTGAEGYYNATLDYgdgcttvtdgkgiHRYYYDPDGNILREE---APDGSTT 696
Cdd:COG3209    790 ALGRLTSVTYPDGETVTYTYDALGRLTSVITVGSGGGTDLQD-------------RTYTYDAAGNITSITdalRAGTLTQ 856

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  697 TYEWDEFHHLLARHSPaGRVEKFEYNAAqGQLSRYTaaDGAEWQYCYDERGLLSNITDPAGQTWT------QQCDERGLP 770
Cdd:COG3209    857 TYTYDALGRLTSATDP-GTTESYTYDAN-GNLTSRT--DGGTTTYTYDALGRLVSVTKPDGTTTTytydalGHTDHLGSV 932

                          410
                   ....*....|....*...
gi 1539234771  771 VSLVSPQGEET-RLAYTP 787
Cdd:COG3209    933 RALTDASGQVVwRYDYDP 950
DUF6531 pfam20148
Domain of unknown function (DUF6531); This putative domain is found in a range of RHS proteins.
 393-454 1.71e-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: 66.79  E-value: 1.71e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1539234771  393 DPVDPVTGAYCDERTDFTLGQTLPLSFTRFHSSVLPLHGLTGVGWSDSWSEY---------AWVREQGNRV 454
Cdd:pfam20148    2 DPVNVATGNKVLEETDFSLPGPLPLVWTRTYNSSSERDGPLGPGWSHPYDQRlelegdggvVYIDADGREV 72
RhsA COG3209
Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction ...
 391-915 3.66e-13

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


Pssm-ID: 442442 [Multi-domain]  Cd Length: 1103  Bit Score: 74.79  E-value: 3.66e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  391 VTDPVDPVTGAYCDERTDFTLGQTLPLSFTRFHSSVLPLHGLTGVGWSDSWSEYAWVREQGNRVDIISLGATLNFAFDGE 470
Cdd:COG3209    486 LTSGSAGATTLGTDTTLDDTLGGTTTTTAGARGLVVTTGTTLTLGTTTTATLSATDATGTGDTTTTGTVGTGTSTGTGGT 565

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  471 SDTAVNPYHAQYILRRCDDYLELFDRNALSSRFFYDAFPGMRLRHPVTDDTSDDRLAHSPADRMYMLGGMSDTASNRITF 550
Cdd:COG3209    566 GTVTTTGDGTGGASTTTGTTGGTATTTTVTTTTTTSTAGTTTTTTSGYTRAGLTLTLGTGTASGLERATASTGSTTGGTT 645

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  551 ERDSQYRITGVSHTDGIRLKLTYHASGYLKAIHRTDNGIQTLATYEQDARGRLTEADARLDYHLFYEYDAADRIIRWSDN 630
Cdd:COG3209    646 GTGVTTTGTTTTRATGTTGTGTGVTAGLTTLATGGTTVGGGTGTTSTATTGATTGGTETGTTVTTLAGGTTTRLGTTTTG 725

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  631 DQTWSRFTYDEQGRCVTVTGAEGYYNATLDYGDgcttvtdgkgihRYYYDPDGNILREEAPDGS-----TTTYEWDEFHH 705
Cdd:COG3209    726 GGGGTTTDGTGTGGTTGTLTTTSTTTTTTAGAL------------TYTYDALGRLTSETTPGGVtqgtyTTRYTYDALGR 793

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  706 LLARHSPAGRVEKFEYNAAqGQLSR------YTAADGAEWQYCYDERGLLSNITDPAGQTWTQQCderglpvslvspqge 779
Cdd:COG3209    794 LTSVTYPDGETVTYTYDAL-GRLTSvitvgsGGGTDLQDRTYTYDAAGNITSITDALRAGTLTQT--------------- 857

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  780 etrLAYTPQGLLSGIfRQDERRLGIEYDHHNRpeTLTDVMGREHHTEYSGHDLPVKMRGPGGQSVRLQWqqhhklsgler 859
Cdd:COG3209    858 ---YTYDALGRLTSA-TDPGTTESYTYDANGN--LTSRTDGGTTTYTYDALGRLVSVTKPDGTTTTYTY----------- 920

                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1539234771  860 agtGAEGFrYDRHGNLLAYTDGNG-VVWTMEYGPFDLPVARTDGEG---HRWQ-YRYDKDT 915
Cdd:COG3209    921 ---DALGH-TDHLGSVRALTDASGqVVWRYDYDPFGNLLAETSGAAanpLRFTgQEYDAET 977
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 260-309 1.10e-11

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: 62.14  E-value: 1.10e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1539234771  260 DKENKPPRIAQGSSNVFINNQPAARKGDKLECS----AAIVEGSPDVFIGGEQV 309
Cdd:COG4104     10 DKTSHGGPVISGSPTVLIGGRPAARVGDKVSCPkhgpDTIAEGSPTVLINGKPA 63
PAAR_1 cd14737
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 260-305 1.85e-09

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: 56.13  E-value: 1.85e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1539234771  260 DKENKPP---RIAQGSSNVFINNQPAARKGDKLECSAAIVEGSPDVFIG 305
Cdd:cd14737     46 TCPKHPPhggVIASGSSTVFINGKPAARVGDPVSCGGTVAGGSPNVFIG 94
PAAR_like cd14671
proline-alanine-alanine-arginine (PAAR) repeat superfamily; This domain is found in the PAAR ...
 268-310 2.47e-09

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: 55.41  E-value: 2.47e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1539234771  268 IAQGSSNVFINNQPAARKGDKLEC---SAAIVEGSPDVFIGGEQVT 310
Cdd:cd14671     17 VISGSPNVFINGRPAARVGDVGDHpggGNAIVSGSGTVFINGKPAA 62
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 267-309 2.93e-09

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: 54.88  E-value: 2.93e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1539234771  267 RIAQGSSNVFINNQPAARKGDKLEC-----SAAIVEGSPDVFIGGEQV 309
Cdd:pfam05488   10 VVITGSPTVLIGGKPAARVGDLVVCppcggGGPIAEGSPTVLINGKPA 57
PAAR_like cd14671
proline-alanine-alanine-arginine (PAAR) repeat superfamily; This domain is found in the PAAR ...
 265-298 3.35e-09

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: 55.02  E-value: 3.35e-09
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1539234771  265 PPRIAQGSSNVFINNQPAARKGDKLECSAAIVEG 298
Cdd:cd14671     44 GNAIVSGSGTVFINGKPAARVGDRTSCGGVIVSG 77
PAAR_2 cd14738
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 255-305 6.54e-09

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: 54.56  E-value: 6.54e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1539234771  255 DTALCdkeNKPP-RIAQGSSNVFINNQPAARKGDKLECSAAIVEGSPDVFIG 305
Cdd:cd14738     46 DMCVC---VGPPdTIVQGSSTVLIGGKPAARMGDSTAHGGVIVSGVPTVLIG 94
PAAR_motif pfam05488
PAAR motif; This motif is found usually in pairs in a family of bacterial membrane proteins. ...
 255-296 1.29e-08

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: 52.96  E-value: 1.29e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1539234771  255 DTALCDKENKPPRIAQGSSNVFINNQPAARKGDKLECSAAIV 296
Cdd:pfam05488   30 DLVVCPPCGGGGPIAEGSPTVLINGKPAAREGDKTACGATLI 71
PAAR_CT_1 cd14743
proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension; This domain is found ...
 255-312 1.46e-08

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: 53.07  E-value: 1.46e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1539234771  255 DTALCDKENKPPRIAQGSSNVFINNQPAARKGDKLECSAAIVEGSPDVFIGGEQVTYL 312
Cdd:cd14743      7 DPHACPLPGHGSTPIGSSSADFFDGLPAARVGDKTSCGATIVSGSINVLINGKPAAVL 64
PAAR_2 cd14738
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 266-306 7.70e-07

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: 48.78  E-value: 7.70e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1539234771  266 PRIAQGSSNVFINNQPAARKGDKLECSA---AIVEGSPDVFIGG 306
Cdd:cd14738     25 PIVGPGPTTVLIGGLPAARVGDMCVCVGppdTIVQGSSTVLIGG 68
PAAR_1 cd14737
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 265-309 7.83e-07

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: 48.82  E-value: 7.83e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1539234771  265 PPR-IAQGSSNVFINNQPAARKGDKLE---C------SAAIVEGSPDVFIGGEQV 309
Cdd:cd14737     17 PPTpVIAGSPDVTVNGKPVLRQGDALAphtCpkhpphGGVIASGSSTVFINGKPA 71
YD_repeat_2x TIGR01643
YD repeat (two copies); This model describes two tandem copies of a 21-residue extracellular ...
 679-720 9.04e-07

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: 46.81  E-value: 9.04e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1539234771  679 YDPDGNILREEAPDGSTTTYEWDEFHHLLARHSPAGRVEKFE 720
Cdd:TIGR01643    1 YDAAGRLTGSTDADGTTTRYTYDAAGRLVEITDADGGSTRYE 42
PAAR_5 cd14741
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 252-304 1.46e-06

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: 48.16  E-value: 1.46e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1539234771  252 AGEDTALCDKENKPPR-----IAQGSSNVFINNQPAARKGDKLECSAA---IVEGSPDVFI 304
Cdd:cd14741     35 AGGDGHVCPLVTGPVPhvggvVAAGSTTVLINGLPAARMGDMIVEGGPpntIAMGAPTVLI 95
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 679-715 6.07e-06

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: 44.51  E-value: 6.07e-06
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1539234771  679 YDPDGNILREEAPDGSTTTYEWDEFHHLLARHSPAGR 715
Cdd:pfam05593    1 YDAAGRLTSVTDPDGRVTTYTYDAAGRLTAVTDPDGT 37
PAAR_3 cd14739
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 264-305 6.20e-06

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: 46.20  E-value: 6.20e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1539234771  264 KPPRIAQ--------GSSNVFINNQPAARKGDKLECSAAIVEGSPDVFIG 305
Cdd:cd14739     41 IPPPPAHppaspfppGSATVLIGGRPAARVGDACGCGATIVVGAPTVLIG 90
Bacuni_01323_like cd12871
Uncharacterized protein conserved in Bacteroidetes; A well-conserved family of 16-stranded ...
 634-753 3.44e-05

Uncharacterized protein conserved in Bacteroidetes; A well-conserved family of 16-stranded beta barrels resembling outer membrane porins. The interior of the barrels is mostly occupied by an insert with partially helical structure.


Pssm-ID: 214015 [Multi-domain]  Cd Length: 231  Bit Score: 47.03  E-value: 3.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771  634 WSRFTYDEQGRCVTVTGAEGYYNA------TLDYGDGCTTVTD--GKGIHRYYYDPDGNILREEAPD-GSTTTYEWDefh 704
Cdd:cd12871     18 EYTFEYDADGRLTSITTTQEGEAEeityttTITYEPNVITVTDdgGKTVSTYTLNEKGYVTSCTETEyGKGQLRTYT--- 94

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1539234771  705 hllarhspagrvekFEYNaAQGQLSRYTAADGAEWQYC---YDERGLLSNIT 753
Cdd:cd12871     95 --------------FTYN-ADGQLTKIVESIGTEYSTItitWNNGDIVSIST 131
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 743-779 5.86e-05

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: 41.43  E-value: 5.86e-05
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1539234771  743 YDERGLLSNITDPAGQTWTQQCDERGLPVSLVSPQGE 779
Cdd:pfam05593    1 YDAAGRLTSVTDPDGRVTTYTYDAAGRLTAVTDPDGT 37
YD_repeat_2x TIGR01643
YD repeat (two copies); This model describes two tandem copies of a 21-residue extracellular ...
 553-593 7.64e-05

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: 41.42  E-value: 7.64e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1539234771  553 DSQYRITGVSHTDGIRLKLTYHASGYLKAIHRTDNGIQTLA 593
Cdd:TIGR01643    2 DAAGRLTGSTDADGTTTRYTYDAAGRLVEITDADGGSTRYE 42
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 869-904 8.51e-05

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: 41.05  E-value: 8.51e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1539234771  869 YDRHGNLLAYTDGNGVVWTMEYGPFDLPVARTDGEG 904
Cdd:pfam05593    1 YDAAGRLTSVTDPDGRVTTYTYDAAGRLTAVTDPDG 36
YD_repeat_2x TIGR01643
YD repeat (two copies); This model describes two tandem copies of a 21-residue extracellular ...
 976-1014 2.28e-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: 40.27  E-value: 2.28e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1539234771  976 DAAGRLAEVITPEGK-TQYAYDKSDRLTGIFSPDGTSQRT 1014
Cdd:TIGR01643    2 DAAGRLTGSTDADGTtTRYTYDAAGRLVEITDADGGSTRY 41
PAAR_CT_2 cd14744
proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This ...
 267-309 2.93e-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: 41.00  E-value: 2.93e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1539234771  267 RIAQGSSNVFINNQPAARKGDKLECSA-----AIVEGSPDVFIGGEQV 309
Cdd:cd14744     15 VVISGSSTFTIDGRPVARVGDKVTCPKckgtgPIVEGGPTFTVDGRPV 62
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 618-653 3.24e-04

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: 39.50  E-value: 3.24e-04
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1539234771  618 YDAADRIIRWSDNDQTWSRFTYDEQGRCVTVTGAEG 653
Cdd:pfam05593    1 YDAAGRLTSVTDPDGRVTTYTYDAAGRLTAVTDPDG 36
YD_repeat_2x TIGR01643
YD repeat (two copies); This model describes two tandem copies of a 21-residue extracellular ...
 721-760 3.65e-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: 39.50  E-value: 3.65e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1539234771  721 YNAaQGQLSRYTAADGAEWQYCYDERGLLSNITDPAGQTW 760
Cdd:TIGR01643    1 YDA-AGRLTGSTDADGTTTRYTYDAAGRLVEITDADGGST 39
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 721-758 4.44e-04

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: 39.12  E-value: 4.44e-04
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1539234771  721 YNAAqGQLSRYTAADGAEWQYCYDERGLLSNITDPAGQ 758
Cdd:pfam05593    1 YDAA-GRLTSVTDPDGRVTTYTYDAAGRLTAVTDPDGT 37
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 976-1010 6.02e-04

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: 38.73  E-value: 6.02e-04
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1539234771  976 DAAGRLAEVITPEGK-TQYAYDKSDRLTGIFSPDGT 1010
Cdd:pfam05593    2 DAAGRLTSVTDPDGRvTTYTYDAAGRLTAVTDPDGT 37
PAAR_4 cd14740
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 265-306 6.63e-04

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: 41.26  E-value: 6.63e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1539234771  265 PPRIAQGSSNVFINNQPAARKGDKLEC---------------SAAIVEGSPDVFIGG 306
Cdd:cd14740     34 GLIVGGLSPTVLIGGMPAATVGSTAGNtpggvpggpsvppanPGTIVMGSSTVFING 90
PAAR COG4104
Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular ...
 280-306 9.43e-04

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: 39.80  E-value: 9.43e-04
                           10        20
                   ....*....|....*....|....*..
gi 1539234771  280 QPAARKGDKLECSAAIVEGSPDVFIGG 306
Cdd:COG4104      3 KPAARLGDKTSHGGPVISGSPTVLIGG 29
YD_repeat_2x TIGR01643
YD repeat (two copies); This model describes two tandem copies of a 21-residue extracellular ...
 869-909 1.06e-03

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: 38.34  E-value: 1.06e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1539234771  869 YDRHGNLLAYTDGNGVVWTMEYGPFDLPVARTDGEGHRWQY 909
Cdd:TIGR01643    1 YDAAGRLTGSTDADGTTTRYTYDAAGRLVEITDADGGSTRY 41
PAAR_CT_1 cd14743
proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension; This domain is found ...
 268-299 1.63e-03

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: 38.82  E-value: 1.63e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1539234771  268 IAQGSSNVFINNQPAARKGDKLECSAAIVEGS 299
Cdd:cd14743     47 IVSGSINVLINGKPAAVLGSTTSHGGVVIGGS 78
PAAR_RHS cd14742
proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement ...
 281-309 1.85e-03

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: 38.72  E-value: 1.85e-03
                           10        20
                   ....*....|....*....|....*....
gi 1539234771  281 PAARKGDKLECSAAIVEGSPDVFIGGEQV 309
Cdd:cd14742      1 PAARVGDPIAHTGTITSGSPNVFINGKPA 29
PAAR_4 cd14740
proline-alanine-alanine-arginine (PAAR) domain; This domain is found in the PAAR ...
 263-287 2.26e-03

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: 39.72  E-value: 2.26e-03
                           10        20
                   ....*....|....*....|....*
gi 1539234771  263 NKPPRIAQGSSNVFINNQPAARKGD 287
Cdd:cd14740     74 ANPGTIVMGSSTVFINGKPAARMGD 98
YwqJ-deaminase pfam14431
YwqJ-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily prototyped ...
 1505-1594 3.20e-03

YwqJ-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Bacillus YwqJ. Members of this family are present in a wide phyletic range of bacteria and a few basidiomycetes. Bacterial versions are predicted to function as toxins in bacterial polymorphic toxin systems.


Pssm-ID: 373065  Cd Length: 134  Bit Score: 39.42  E-value: 3.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1539234771 1505 SKLPRAVSAVVDKRTGKIYYG-ESGWPHPT-EIHPTLQN---NMP---SASKERWAI--ENCAEFKAVNEAL-------- 1566
Cdd:pfam14431   10 VRLPPDQAGVLDLQTGEYIRGvNPQYEKPGkDLHPLVQSrldELPgdgTAGHGRFAGgaGLHAEVQAVSNALydyearag 89

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1539234771 1567 ----KANAKISDLEVHTVLVKT----GEAFPMCKNC 1594
Cdd:pfam14431   90 erqaRAALDGLRIMVYTVRLPGtpegGTPFPPCPNC 125
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 954-989 3.65e-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: 36.42  E-value: 3.65e-03
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1539234771  954 YDADGLCTARVNGLEETILYGRDAAGRLAEVITPEG 989
Cdd:pfam05593    1 YDAAGRLTSVTDPDGRVTTYTYDAAGRLTAVTDPDG 36
PAAR_CT_2 cd14744
proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension; This ...
 255-291 6.07e-03

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: 37.15  E-value: 6.07e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1539234771  255 DTALCDKENKPPRIAQGSSNVFINNQPAARKGDKLEC 291
Cdd:cd14744     35 DKVTCPKCKGTGPIVEGGPTFTVDGRPVALDGDRVAC 71
YD_repeat_2x TIGR01643
YD repeat (two copies); This model describes two tandem copies of a 21-residue extracellular ...
 700-741 8.44e-03

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: 35.64  E-value: 8.44e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1539234771  700 WDEFHHLLARHSPAGRVEKFEYNaAQGQLSRYTAADGAEWQY 741
Cdd:TIGR01643    1 YDAAGRLTGSTDADGTTTRYTYD-AAGRLVEITDADGGSTRY 41
RHS_repeat pfam05593
RHS Repeat; RHS proteins contain extended repeat regions. These repeats often appear to be ...
 995-1026 9.57e-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: 35.27  E-value: 9.57e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1539234771  995 YDKSDRLTGIFSPDGTSQRTGYDERGRVNVTT 1026
Cdd:pfam05593    1 YDAAGRLTSVTDPDGRVTTYTYDAAGRLTAVT 32
 
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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