Query gi|254780727|ref|YP_003065140.1| putative pilus assembly protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 474 No_of_seqs 232 out of 2174 Neff 7.2 Searched_HMMs 39220 Date Sun May 29 19:47:19 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780727.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG4964 CpaC Flp pilus assembl 100.0 0 0 633.4 34.4 427 36-474 21-455 (455) 2 TIGR02517 type_II_gspD general 100.0 0 0 412.0 23.1 238 183-421 405-689 (697) 3 TIGR02515 IV_pilus_PilQ type I 100.0 0 0 400.3 22.1 267 129-420 152-464 (464) 4 PRK10560 hofQ outer membrane p 100.0 0 0 383.2 29.3 278 117-420 100-384 (386) 5 PRK13568 hofQ putative outer m 100.0 0 0 379.0 28.8 278 117-420 97-384 (385) 6 PHA00019 phage assembly protei 100.0 0 0 377.5 29.5 275 118-421 141-427 (428) 7 COG1450 PulD Type II secretory 100.0 0 0 365.0 25.1 239 183-423 301-551 (587) 8 TIGR02519 pilus_MshL pilus (MS 100.0 0 0 333.1 22.3 258 138-419 3-311 (311) 9 TIGR02516 type_III_yscC type I 100.0 0 0 310.0 21.3 235 184-421 234-508 (508) 10 pfam00263 Secretin Bacterial t 100.0 1.4E-45 0 281.9 19.4 159 262-420 1-164 (164) 11 COG4796 HofQ Type II secretory 100.0 0 0 287.0 14.4 229 193-421 455-709 (709) 12 TIGR02520 pilus_B_mal_scr type 100.0 1.5E-32 3.9E-37 206.8 12.6 295 92-418 215-536 (536) 13 COG4796 HofQ Type II secretory 98.6 4.3E-07 1.1E-11 59.3 9.6 208 195-423 310-524 (709) 14 pfam04972 BON Putative phospho 97.4 0.00092 2.4E-08 40.0 7.3 60 121-191 2-63 (64) 15 PRK11023 hypothetical protein; 95.9 0.075 1.9E-06 29.0 8.5 90 77-168 70-178 (191) 16 PRK11023 hypothetical protein; 95.9 0.042 1.1E-06 30.4 7.0 51 132-193 66-116 (191) 17 PRK10568 periplasmic protein; 95.8 0.057 1.4E-06 29.7 7.5 95 84-190 86-202 (203) 18 COG2823 OsmY Predicted peripla 95.3 0.029 7.3E-07 31.4 4.5 51 130-191 145-195 (196) 19 PRK10568 periplasmic protein; 95.3 0.065 1.7E-06 29.3 6.3 48 134-192 78-125 (203) 20 PRK11198 hypothetical protein; 81.8 3.2 8.2E-05 19.5 5.1 77 119-209 26-104 (147) 21 pfam09911 DUF2140 Uncharacteri 66.3 8.2 0.00021 17.2 4.9 24 310-333 93-116 (187) 22 TIGR02268 TIGR02268 Myxococcus 62.7 9.6 0.00025 16.8 4.4 105 11-115 1-115 (308) 23 pfam06183 DinI DinI-like famil 60.3 11 0.00027 16.5 4.4 46 120-167 10-56 (65) 24 PRK13861 type IV secretion sys 57.4 12 0.0003 16.2 11.2 110 4-115 2-116 (293) 25 PRK11824 polynucleotide phosph 54.6 5.5 0.00014 18.2 1.0 62 356-417 583-644 (694) 26 KOG1249 consensus 52.6 13 0.00033 16.0 2.6 60 312-381 361-421 (572) 27 pfam03958 Secretin_N Bacterial 52.2 15 0.00037 15.7 6.3 49 116-167 7-62 (68) 28 pfam05046 Img2 Mitochondrial l 51.4 15 0.00038 15.6 6.3 48 105-152 23-73 (85) 29 pfam07788 DUF1626 Protein of u 49.5 9.4 0.00024 16.8 1.5 54 356-419 3-57 (70) 30 PRK00794 flbT flagellar biosyn 49.0 16 0.00042 15.4 3.1 34 359-394 5-38 (133) 31 PRK10838 spr putative outer me 49.0 16 0.00042 15.4 2.8 23 1-23 7-29 (188) 32 PRK13796 GTP-binding protein Y 48.6 17 0.00042 15.4 3.0 24 358-381 249-272 (367) 33 pfam09544 DUF2381 Protein of u 42.9 20 0.00052 14.9 6.2 94 18-111 4-104 (289) 34 pfam02368 Big_2 Bacterial Ig-l 40.6 22 0.00057 14.6 6.2 58 49-109 11-75 (79) 35 pfam07378 FlbT Flagellar prote 40.0 23 0.00058 14.6 3.0 35 359-394 2-36 (126) 36 COG4698 Uncharacterized protei 37.8 25 0.00063 14.4 3.5 20 314-333 105-124 (197) 37 pfam11492 Dicistro_VP4 Cricket 37.6 11 0.00028 16.5 0.3 16 386-401 25-40 (56) 38 pfam09133 SANTA SANTA (SANT As 35.0 21 0.00054 14.8 1.5 37 349-386 34-70 (93) 39 TIGR03597 GTPase_YqeH ribosome 34.8 28 0.0007 14.1 2.7 59 313-380 205-263 (360) 40 TIGR03591 polynuc_phos polyrib 33.5 16 0.00041 15.5 0.7 52 356-407 580-631 (684) 41 COG2982 AsmA Uncharacterized p 30.5 33 0.00083 13.7 2.0 73 1-74 1-76 (648) 42 PRK12696 flgH flagellar basal 27.5 37 0.00094 13.4 3.1 21 4-24 2-22 (238) 43 TIGR02186 alph_Pro_TM conserve 26.6 38 0.00098 13.3 3.3 107 8-149 1-109 (275) 44 COG1185 Pnp Polyribonucleotide 26.2 39 0.00099 13.2 1.8 46 356-401 581-626 (692) 45 PRK09915 putative outer membra 23.9 43 0.0011 13.0 3.9 27 5-31 3-29 (488) 46 smart00635 BID_2 Bacterial Ig- 23.8 44 0.0011 13.0 6.3 57 50-108 12-76 (81) 47 PHA02358 hypothetical protein 23.4 19 0.00048 15.1 -0.5 14 385-398 154-167 (194) 48 PRK10719 eutA reactivating fac 23.3 44 0.0011 12.9 1.9 60 116-175 61-121 (471) 49 pfam09796 QCR10 Ubiquinol-cyto 22.5 27 0.00069 14.1 0.2 15 387-401 42-56 (64) 50 PRK10503 multidrug efflux syst 21.5 48 0.0012 12.7 4.6 19 203-221 720-738 (1040) 51 COG1079 Uncharacterized ABC-ty 20.2 40 0.001 13.2 0.7 21 196-216 165-185 (304) No 1 >COG4964 CpaC Flp pilus assembly protein, secretin CpaC [Intracellular trafficking and secretion] Probab=100.00 E-value=0 Score=633.38 Aligned_cols=427 Identities=41% Similarity=0.658 Sum_probs=379.3 Q ss_pred CCCCCCCCCCCCCEEEEEECCEEEEECCCCHHHEEECCCCEEEEEECCCCEEEEEECCCCEEEEEEECCCCCEEEEEEEE Q ss_conf 33332234565402799507259995377633078537343799971698799995267227999988999778999873 Q gi|254780727|r 36 VINISDVEIGKGKKISIGLNKVIILQVPVDVQDVLVSDPTKADVVVHSPRTMYLFGKNVGQANVILIGHDGKQMLNLDIL 115 (474) Q Consensus 36 ~~~~~~~~~~~~~~l~l~~g~s~~l~~~~~~~rV~V~dp~Vadv~v~s~~~i~i~gk~~G~T~l~v~~~~g~~~~~~~v~ 115 (474) ......+.....+++.|..+++.++.++.++.+|+|+||+|||+..++++.+||+||++|+|++++|+++++.+..+++. T Consensus 21 ~~~i~~ss~~~~~t~~l~~~~~~~v~l~~~~~~i~Vg~p~iada~~~~~~~iyi~gk~~Gtt~v~~fg~~g~~~~~~~i~ 100 (455) T COG4964 21 VARIALSSASATKTLKLELGKSKTVVLPSDADDILVGDPNIADAVLLTDRSIYILGKSVGTTNVFVFGEEGRSIVSLDIE 100 (455) T ss_pred HHHHHHCCCCHHHEEEECCCCCEEEECCCCHHEEEECCCCHHCCCCCCCCEEEEEECCCCEEEEEEECCCCCCCCCCEEE T ss_conf 55410046641005761468735897246200168758202101304786499994378804789986888530220058 Q ss_pred CCCCHHHHHHHHHHHCCCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEE-EEECCCCC Q ss_conf 04541478999998578771699983894999997199999999999999861223455555665443035-54327772 Q gi|254780727|r 116 IERDIAHLEMTLRRFIADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMN-LLNIAGED 194 (474) Q Consensus 116 v~~d~~~l~~~l~~~~p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn-~l~v~~~~ 194 (474) |..|...+...+++.+|+++|+|...++.++++|+++++.+++++.++|++|.+.. +++| +++|.+++ T Consensus 101 v~~d~~~l~~~i~~~~P~s~i~V~~~~~~vvl~Gs~~~~~~a~~a~~ia~~~~g~~-----------e~~~s~~~v~~~~ 169 (455) T COG4964 101 VTRDTSGLGAPIRAVIPDSRIKVSSVNDRVVLSGSVRTAVDAESAVRIASQFLGGG-----------EVTNSLITVAGSQ 169 (455) T ss_pred EECCHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCHHHHHHHHHHHHCCCCCC-----------CEECCCEEECCCC T ss_conf 73485786546886488870489753785699875086898888776665017986-----------0441215761688 Q ss_pred EEEEEEEEEEEECHHHHHCCCEEEECCCCCCC--CCCCCCCCCCCCC-CCCCCCEEEEECCCCCHHHHHHHHHHCCCEEE Q ss_conf 27999999998500144226121001454336--4435455666666-66543033420377414311023773597589 Q gi|254780727|r 195 QVTLKVTIAEVRRDILKQIGFQHSITGSSSGP--SKSFAADFGGKFV-SEGGDFSVKGVLDRFSFETVLHALERATAIRT 271 (474) Q Consensus 195 QV~lev~i~EVs~~~~~~lGi~w~~~~~~~~~--~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~aL~~~g~a~i 271 (474) ||+|+|||+||+|+..++||++|+..+...+. ..+.......... ..+..+......++..+++.|+|||++|.+|+ T Consensus 170 QV~l~VrvvEVsr~v~k~LG~~~~~~g~~~g~~~~~g~~~~~~~~~~~~~g~~~G~l~~~n~~~~~~~i~Ale~~G~~r~ 249 (455) T COG4964 170 QVQLKVRVVEVSRSVLKQLGANLSARGGFSGGPVSFGALAVLGTGLGLEKGTTFGSLLSDNGVSIDAYINALEANGLART 249 (455) T ss_pred EEEEEEEEEEEEHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHHHHCCCCEEE T ss_conf 26899999998278898506206641131577541244445677545555544231036788350134033640885588 Q ss_pred EECCEEEEECCCEEEEEECCCEEEEECCCCCCCEEEEEEEEEEEEEEEEEEECCCEEEEEEEEEECCCCC----CCCCCC Q ss_conf 8422389875946757524730000013677620468988758999998981598499986123203445----555665 Q gi|254780727|r 272 LAEPTLTAISGQSASFTSGGQHLYKTVSSSTGATSVTTHDYGVVLHFTPTVLSPGRIGLRIQTEVSEPVI----GVNAGD 347 (474) Q Consensus 272 La~P~l~t~sgq~A~~~~G~e~pi~~~~~~~~~~~v~~~~~Gi~L~vtP~V~~~g~I~L~i~~evS~~~~----~~~~~~ 347 (474) ||+|+|+++|||+|+|++|||+|+|+..+.+++++|+||+||+.|.|+|+|+.++||.|++++|||+++. ..++.. T Consensus 250 LAePnL~a~SGe~AsFlaGGEfpip~~~d~~g~~TI~yk~fGv~L~ftPtVl~~gRI~L~v~peVSel~~~g~v~~~~~t 329 (455) T COG4964 250 LAEPNLTALSGETASFLAGGEFPIPVPDDKNGNVTIEYKEFGVGLTFTPTVLSNGRISLKVAPEVSELDYSGSVAVGGGT 329 (455) T ss_pred ECCCCEEEECCCCHHHHCCCEECCCCCCCCCCCEEEEEEECCCCEEEEEEEEECCEEEEEECCCCCCCCCCCCEEECCCC T ss_conf 51575223056400221376250356667788278999961665058617802877887644531246766757878823 Q ss_pred CCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEEEEEEECEECCCCCHHHC Q ss_conf 32167899999999858998999976653101321257112017612000165645521159999990515034686552 Q gi|254780727|r 348 MPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREETEIFIAATPFLVKPVAMRDL 427 (474) Q Consensus 348 ~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP~iV~p~~~~~~ 427 (474) +|.+++|+++|+|+|+|||||+||||+|++.....+++||||+|||||+||||++++++++||+|+||||+|+|.++.++ T Consensus 330 vP~~t~rradTtVeL~sGqSf~I~GL~qs~~~~~~~~vP~lG~iPIlGalFRs~~~~r~etELviIVTP~lVkP~~p~~~ 409 (455) T COG4964 330 VPGLTTRRADTTVELASGQSFVIGGLLQSNVRGAVDKVPGLGDIPILGALFRSKDFQRNETELVIIVTPYLVKPVAPGQL 409 (455) T ss_pred CCCEEEEEEEEEEEECCCCEEEEEEEEECCHHHHHHCCCCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCCCCCCHHHC T ss_conf 43158886001699058987999512101413466428887667502555422001567634899963551220685314 Q ss_pred CCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEC Q ss_conf 68754754776200011030023467776666666564334312769 Q gi|254780727|r 428 SRPDDHYSVEDDAKAFFFNRVNKIYGPKEASEVEGQNYKGAIGFIYK 474 (474) Q Consensus 428 ~~p~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~Gf~~~ 474 (474) ..|+|++.+++|...||+|+.++.|+.+.... ..+++.|..||+|+ T Consensus 410 ~~p~~~~t~~~d~~~~~~~~~~~v~~~~~g~~-~~~~~~g~~g~v~~ 455 (455) T COG4964 410 PAPPDDFTPASDPALYFLGNVNRVYGFPAGQT-DAARYGGAVGFVIK 455 (455) T ss_pred CCCCCCCCCCCCCCHHCCCCCCEEEECCCCCC-CCCCCCCCCCEEEC T ss_conf 58975668667721110355640476146765-56566763005769 No 2 >TIGR02517 type_II_gspD general secretion pathway protein D; InterPro: IPR013356 In Gram-negative bacteria, proteins that have first crossed the inner member by Sec-dependent protein transport can be exported across the outer membrane by type II secretion (also referred to as the main terminal branch of the general secretion pathway). Members of this family are general secretion pathway protein D. In Yersinia enterocolitica, a second member of this family is part of a novel second type II secretion system specifically associated with virulence (See ). This family is closely homologous to the type IV pilus outer membrane secretin PilQ (IPR013355 from INTERPRO) and to the type III secretion system pore YscC/HrcC (IPR003522 from INTERPRO).; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex, 0019867 outer membrane. Probab=100.00 E-value=0 Score=412.00 Aligned_cols=238 Identities=28% Similarity=0.424 Sum_probs=196.4 Q ss_pred CEEEEEECCCCCEEEEEEEEEEEECHHHHHCCCEEEECCCCCCCCCCCCC----------CCCC--CCCC---------- Q ss_conf 30355432777227999999998500144226121001454336443545----------5666--6666---------- Q gi|254780727|r 183 KVMNLLNIAGEDQVTLKVTIAEVRRDILKQIGFQHSITGSSSGPSKSFAA----------DFGG--KFVS---------- 240 (474) Q Consensus 183 ~vvn~l~v~~~~QV~lev~i~EVs~~~~~~lGi~w~~~~~~~~~~~~~~~----------~~~~--~~~~---------- 240 (474) .||.+|+++ +.||+||+.|+||+.+...+||++|...+........... ..+. ...+ T Consensus 405 ~VI~~LD~r-R~QV~vEA~IvEvs~~~~~~~Gvqw~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~ 483 (697) T TIGR02517 405 EVIKQLDKR-RAQVLVEAIIVEVSLDDALELGVQWLIAGTGGTVGFGLVNGSTGAGNSGSLLGASASAINPDTAASKLLG 483 (697) T ss_pred HHHHHHCCC-CCCEEEEEEEEEEECCCCCCCCEEEEEECCCCEECCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHH T ss_conf 999983889-7664899999999708873220456761344120421204655555420001222336677741001101 Q ss_pred ----------CCCCCEEEEECCCCCHHHHHHHHHHCCCEEEEECCEEEEECCCEEEEEECCCEEEEECCCCC-----C-- Q ss_conf ----------65430334203774143110237735975898422389875946757524730000013677-----6-- Q gi|254780727|r 241 ----------EGGDFSVKGVLDRFSFETVLHALERATAIRTLAEPTLTAISGQSASFTSGGQHLYKTVSSST-----G-- 303 (474) Q Consensus 241 ----------~~~~~~~~~~~~~~~~~~~l~aL~~~g~a~iLa~P~l~t~sgq~A~~~~G~e~pi~~~~~~~-----~-- 303 (474) ....+.....+...+|.+.|+||++++..++||.|+|+|+|||+|+|.||+++||++.+... + T Consensus 484 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~Al~~~~~~NvLSTP~~lTlDN~eA~I~VGQ~VPv~tg~~~~Gt~~~~~~ 563 (697) T TIGR02517 484 SAGIGLLVTSSSTTSGVGGTGGIPNLGVLLNALKQDTGFNVLSTPSLLTLDNEEAEINVGQEVPVLTGSYNTGTGTGGTN 563 (697) T ss_pred HEECCCCCCEEEEEEEEEECCCCCEEEEEEEEECCCCCCCEEECCEEEEECCCEEEEEECCCCCCCCCEEEEEEEEECCC T ss_conf 10016650101212322100356234578875302657116877806763032146751767222365021155630545 Q ss_pred ---CEEEEEEEEEEEEEEEEEEE-CCCEEEEEEEEEECCCC----CCCCCCCCCEEEEEEEEEEEEECCCCEEEEEEEEE Q ss_conf ---20468988758999998981-59849998612320344----55556653216789999999985899899997665 Q gi|254780727|r 304 ---ATSVTTHDYGVVLHFTPTVL-SPGRIGLRIQTEVSEPV----IGVNAGDMPSYRVRKADTTVELPSGGTIVLAGLLK 375 (474) Q Consensus 304 ---~~~v~~~~~Gi~L~vtP~V~-~~g~I~L~i~~evS~~~----~~~~~~~~P~i~~R~~~T~V~l~~Get~vIgGL~~ 375 (474) ..++|||++|++|+|||+|. ++|.|.|+|.+|+|++. ........|.|++|+++|+|.++||||+|||||++ T Consensus 564 ~n~f~t~~r~~vG~~L~v~PqIn~eg~~v~L~I~Qevs~~~~~~~~~~~~~~~~~~nkR~i~t~v~V~dg~tvVLGGLi~ 643 (697) T TIGR02517 564 ANPFNTVERKDVGIKLKVTPQINGEGGTVRLEIYQEVSSVAPATGTVASAATGPTFNKREIKTSVLVDDGDTVVLGGLIQ 643 (697) T ss_pred CCEEEEEEEEEEEEEEEEEEEEECCCCEEEEEEEEEEECCCCCCCEEECCCCCCCEEEEEEEEEEEECCCCEEEEEEEEC T ss_conf 53143016887228998887783799869999986341333546412024577411114898899962798899866413 Q ss_pred EEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEEEEEEECEECCC Q ss_conf 3101321257112017612000165645521159999990515034 Q gi|254780727|r 376 DDIQQLKEGIPLLSKIPILGALFRNSRFNREETEIFIAATPFLVKP 421 (474) Q Consensus 376 ~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP~iV~p 421 (474) ++.+++.+|||+|||||+||+|||++...++||+|||||||||||- T Consensus 644 d~~~~~~~kvPlLGDIP~lG~LFr~~~~~~~KTNLmVFitP~Iir~ 689 (697) T TIGR02517 644 DKTSESVTKVPLLGDIPVLGRLFRSTTKERTKTNLMVFITPRIIRD 689 (697) T ss_pred CCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCEEEEEEECCEEECC T ss_conf 7510110134345785611011576673233316899960778779 No 3 >TIGR02515 IV_pilus_PilQ type IV pilus secretin PilQ; InterPro: IPR013355 A number of proteins homologous to PilQ are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also referred to as the main terminal branch of the general secretion pathway). Members of this family include PilQ itself, which is a component of the type IV pilus structure, from a number of species. In Haemophilus influenzae, the member of this family is associated with the uptake of exogenous DNA, rather than with formation of a type IV pilus - the surface structure required for this may be considered an unusual, incomplete type IV pilus structure.; GO: 0009297 pilus biogenesis, 0009306 protein secretion. Probab=100.00 E-value=0 Score=400.31 Aligned_cols=267 Identities=22% Similarity=0.387 Sum_probs=212.6 Q ss_pred HHC-CCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEEEEEEEC Q ss_conf 857-8771699983894999997199999999999999861223455555665443035543277722799999999850 Q gi|254780727|r 129 RFI-ADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIAGEDQVTLKVTIAEVRR 207 (474) Q Consensus 129 ~~~-p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~~~~QV~lev~i~EVs~ 207 (474) .++ |.++|.++...++++++.. +...+++.+ +|..|+++ .+||+||+||||++. T Consensus 152 ~~LS~RGSvt~D~RTN~Liv~D~---~~~l~~~r~---------------------li~~lD~P-v~QV~IEARIVea~~ 206 (464) T TIGR02515 152 AVLSERGSVTVDPRTNTLIVTDI---PEKLARIRE---------------------LIAELDIP-VKQVLIEARIVEATD 206 (464) T ss_pred HHCCCCCCEEEECCCCEEEEEEC---HHHHHHHHH---------------------HHHHCCCC-CCCEEEEEEEEEEEC T ss_conf 20389860897424253878621---578999999---------------------99961898-433899647999830 Q ss_pred HHHHHCCCEEEECCCCCCCCCCC---------------CCCC-----------------CCCCCCC------CCCCEEEE Q ss_conf 01442261210014543364435---------------4556-----------------6666666------54303342 Q gi|254780727|r 208 DILKQIGFQHSITGSSSGPSKSF---------------AADF-----------------GGKFVSE------GGDFSVKG 249 (474) Q Consensus 208 ~~~~~lGi~w~~~~~~~~~~~~~---------------~~~~-----------------~~~~~~~------~~~~~~~~ 249 (474) ++.|+||++|.........+... .+.. +...... +.++.+.. T Consensus 207 ~f~r~LGv~wG~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~nv~l~~~t~~~gsgGa~~~~~~~~~ 286 (464) T TIGR02515 207 SFARELGVRWGIADKTTNGNGTLGGIGSSTGTGATGVVSSTLAGGTMNPPIGDNLNVNLATATTAGGSGGAAAISFALGK 286 (464) T ss_pred CCCCCCEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH T ss_conf 61100606723435643246531013625666121642477877654777788763466356656544245788777654 Q ss_pred ECC-CCCHHHHHHHHHHCCCEEEEECCEEEEECCCEEEEEECCCEEEEECCCC----CCCEEEEEEEEEEEEEEEEEEEC Q ss_conf 037-7414311023773597589842238987594675752473000001367----76204689887589999989815 Q gi|254780727|r 250 VLD-RFSFETVLHALERATAIRTLAEPTLTAISGQSASFTSGGQHLYKTVSSS----TGATSVTTHDYGVVLHFTPTVLS 324 (474) Q Consensus 250 ~~~-~~~~~~~l~aL~~~g~a~iLa~P~l~t~sgq~A~~~~G~e~pi~~~~~~----~~~~~v~~~~~Gi~L~vtP~V~~ 324 (474) ... +..+++.|+|||++|.++|+|+|+|+|.|+++|+|..|.||||.+.++. .+.++|+||++=++|+|||+|.+ T Consensus 287 ~~~g~~~LdLELSAle~e~~~eiissPrv~T~d~~~A~I~qG~EIPY~~~s~~G~~~~~~~~v~FKeAvL~LeVTP~ITp 366 (464) T TIGR02515 287 LGSGGVLLDLELSALESEGKGEIISSPRVVTADNKKAKIEQGTEIPYQQTSSSGTGASSATSVEFKEAVLSLEVTPQITP 366 (464) T ss_pred HHCCCCHHHHHHHHHHHHCCCCEEECCEEEEECCCEEEEECCEEECEEEECCCCCCCCCEEEEEEEEEEEECCCCCEECC T ss_conf 40454014689999986188138765818720685557731546041898066200674217999998750531311656 Q ss_pred CCEEEEEEEEEECCCC--CCCCCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCC Q ss_conf 9849998612320344--55556653216789999999985899899997665310132125711201761200016564 Q gi|254780727|r 325 PGRIGLRIQTEVSEPV--IGVNAGDMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSR 402 (474) Q Consensus 325 ~g~I~L~i~~evS~~~--~~~~~~~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~ 402 (474) ||+|.|+|...=.+.. ......+.|.|++|++.|.|.++||||+||||.++++.++..+|||||||||+||+|||++. T Consensus 367 Dg~i~M~~~v~kd~~g~~~~~a~~~~~~I~k~ei~T~VlV~nGeTvViGGIY~~~~~~~~~kVPfLGDIP~lG~LFk~~~ 446 (464) T TIGR02515 367 DGRIIMDLKVSKDSPGAVVSQAGGGVPAIDKREINTQVLVKNGETVVIGGIYEQTQTNSVNKVPFLGDIPVLGNLFKKTA 446 (464) T ss_pred CCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEEEEEEECCCEEEEEEEEEEECCCCCCCCCEECCCCCEEHEEECCC T ss_conf 99389998871077875034678701504402677899972588899812898515644245511134560111011166 Q ss_pred CCCCEEEEEEEEECEECC Q ss_conf 552115999999051503 Q gi|254780727|r 403 FNREETEIFIAATPFLVK 420 (474) Q Consensus 403 ~~~~~tELvI~iTP~iV~ 420 (474) +++.|+||+||||||||. T Consensus 447 ~~~~K~ELLIFiTPri~~ 464 (464) T TIGR02515 447 KSDEKSELLIFITPRIVN 464 (464) T ss_pred CEEECEEEEEEECCEECC T ss_conf 311110431887565749 No 4 >PRK10560 hofQ outer membrane porin HofQ; Provisional Probab=100.00 E-value=0 Score=383.19 Aligned_cols=278 Identities=24% Similarity=0.374 Sum_probs=223.0 Q ss_pred CCCHHHHHHHHHHHCC-CCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCE Q ss_conf 4541478999998578-771699983894999997199999999999999861223455555665443035543277722 Q gi|254780727|r 117 ERDIAHLEMTLRRFIA-DSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIAGEDQ 195 (474) Q Consensus 117 ~~d~~~l~~~l~~~~p-~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~~~~Q 195 (474) ..+...+.+.++.++. ...|.++...++++++|+ +.+.+++.++ +..|+++. +| T Consensus 100 ya~~~~~~~~~~~~ls~~g~i~~d~~tN~liV~~t---~~~~~~i~~l---------------------i~~lD~~~-~Q 154 (386) T PRK10560 100 YADAGELAKAGEKLLSAKGSMTVDKRTNRLLLRDN---KTALSALEQW---------------------VAQMDLPV-GQ 154 (386) T ss_pred ECCHHHHHHHHHHHCCCCCEEEEECCCCEEEEECC---HHHHHHHHHH---------------------HHHHCCCC-CE T ss_conf 08999999765532267730999368887999749---9999999999---------------------99746767-77 Q ss_pred EEEEEEEEEEECHHHHHCCCEEEECCCCCCCCCCCCCCCCC----CCCCCCCCCEEEEECCCCCHHHHHHHHHHCCCEEE Q ss_conf 79999999985001442261210014543364435455666----66666543033420377414311023773597589 Q gi|254780727|r 196 VTLKVTIAEVRRDILKQIGFQHSITGSSSGPSKSFAADFGG----KFVSEGGDFSVKGVLDRFSFETVLHALERATAIRT 271 (474) Q Consensus 196 V~lev~i~EVs~~~~~~lGi~w~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~l~aL~~~g~a~i 271 (474) |+||++|+||++++.++||++|+..........+.....+. ...+...+++ .+..++..+.+.|+||+++|++++ T Consensus 155 V~Iea~IvEv~~~~~~~lGv~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~-~~~~~~~~l~~~l~aL~~~g~~~i 233 (386) T PRK10560 155 VELAAHIVTINEKSLRELGVKWTLADAQQAGGVGQVTTLGSDLSVATATTHVGFN-IGRINGRLLDLELSALEQKQQLDI 233 (386) T ss_pred EEEEEEEEEEECCCHHHHCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE-EECCCCHHHHHHHHHHHHCCCCEE T ss_conf 9999999999778338607223413466788646544446654455644543146-521363558886799873898439 Q ss_pred EECCEEEEECCCEEEEEECCCEEEEECCCCCCCEEEEEEEEEEEEEEEEEEECCCEEEEEEEEEECCCCC--CCCCCCCC Q ss_conf 8422389875946757524730000013677620468988758999998981598499986123203445--55566532 Q gi|254780727|r 272 LAEPTLTAISGQSASFTSGGQHLYKTVSSSTGATSVTTHDYGVVLHFTPTVLSPGRIGLRIQTEVSEPVI--GVNAGDMP 349 (474) Q Consensus 272 La~P~l~t~sgq~A~~~~G~e~pi~~~~~~~~~~~v~~~~~Gi~L~vtP~V~~~g~I~L~i~~evS~~~~--~~~~~~~P 349 (474) ||+|+++|+|||+|.|.+|.++||.+.++..+.++++|+++|+.|+|||+|.+||.|.|++.++.+.... .......| T Consensus 234 lS~P~i~t~~n~~A~I~vG~~ip~~~~~~~~~~t~~~~~~~gl~L~VtP~I~~dg~I~l~i~i~~~~~~~~~~~~~~~~~ 313 (386) T PRK10560 234 IASPRLLASHLQPASIKQGSEIPYQVSSGESGATSVEFKEAVLGMEVTPTVLQKGRIRLKLHISQNVPGQVLQQADGEVL 313 (386) T ss_pred EECCEEEEECCCEEEEECCEEEEEEECCCCCCCEEEEEEEEEEEEEEEEEECCCCEEEEEEEEEECCCCCCCCCCCCCCC T ss_conf 86787998379779998531998995147777325899997689999889988991999999974377620205787654 Q ss_pred EEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEEEEEEECEECC Q ss_conf 16789999999985899899997665310132125711201761200016564552115999999051503 Q gi|254780727|r 350 SYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREETEIFIAATPFLVK 420 (474) Q Consensus 350 ~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP~iV~ 420 (474) .+++|+++|+|.++||||++||||++++.++..+|||+|||||+||+|||+++.+++|+||+||||||||+ T Consensus 314 ~i~~r~~~T~v~v~dGetvviGGLi~~~~~~~~~~VP~LgdIP~lG~LF~~~~~~~~k~eLlIfItP~Iv~ 384 (386) T PRK10560 314 AIDKQEIETQVEVKSGETLALGGIFSRKNKSGQDSVPLLGDIPWFGQLFRHDGKEDERRELVVFITPRLVS 384 (386) T ss_pred CEEEEEEEEEEEECCCCEEEEEEEEEEEEEEEECCCCCCCCCCCCHHHHCCCCCCCCEEEEEEEEEEEEEC T ss_conf 15605998999992899999932788014455017715751212147507977757368999999718957 No 5 >PRK13568 hofQ putative outer membrane porin HofQ; Provisional Probab=100.00 E-value=0 Score=379.01 Aligned_cols=278 Identities=20% Similarity=0.306 Sum_probs=219.9 Q ss_pred CCCHHHHHHHHHHH-----CCCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECC Q ss_conf 45414789999985-----7877169998389499999719999999999999986122345555566544303554327 Q gi|254780727|r 117 ERDIAHLEMTLRRF-----IADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIA 191 (474) Q Consensus 117 ~~d~~~l~~~l~~~-----~p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~ 191 (474) ..++..+...++.. .+...|.++...++++++|. +.+.+++.++ +..|+++ T Consensus 97 ~~~~~~~~~~~~~~~~~~~s~~g~v~~d~~tNsliV~~~---~~~~~~i~~l---------------------i~~LD~~ 152 (385) T PRK13568 97 YANAEQVADSLDPLQGGLLSPLGSVVADKRTNTLLIRDT---PASLALLKNW---------------------LIEMDLP 152 (385) T ss_pred CCCHHHHHHHHHHCCCCCCCCCCEEEECCCCCEEEEECC---HHHHHHHHHH---------------------HHHHCCC T ss_conf 288999999876502653356630898576777999639---9999999999---------------------9974565 Q ss_pred CCCEEEEEEEEEEEECHHHHHCCCEEEECCCCCCCCCCCC---CCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHCCC Q ss_conf 7722799999999850014422612100145433644354---5566666666543033420377414311023773597 Q gi|254780727|r 192 GEDQVTLKVTIAEVRRDILKQIGFQHSITGSSSGPSKSFA---ADFGGKFVSEGGDFSVKGVLDRFSFETVLHALERATA 268 (474) Q Consensus 192 ~~~QV~lev~i~EVs~~~~~~lGi~w~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~aL~~~g~ 268 (474) . +||+||++|+||++++.++||++|.......+...... .+........+.++. .+..++..+.+.|+||+++|+ T Consensus 153 ~-~QV~Iea~IvEvs~~~~~~lGv~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~-~~~~~~~~l~~~l~aL~~~g~ 230 (385) T PRK13568 153 L-QQVQLSAHIVTISSEDLQELGVRWGMGEGKGNTALRINDFNVNLPLPNSAASVGFH-VARIGGRLLELELSALEQENQ 230 (385) T ss_pred C-CEEEEEEEEEEEECCCHHHCCEEEEECCCCCCCCEECCCCCCCCCCCCCCCCCCEE-EEECCCHHHHHHHHHHHHCCC T ss_conf 5-65999999999835714750656650258886413236643356677753334337-642162768899789874898 Q ss_pred EEEEECCEEEEECCCEEEEEECCCEEEEECCCCCCCEEEEEEEEEEEEEEEEEEECCCEEEEEEEEEECCCC--CCCCCC Q ss_conf 589842238987594675752473000001367762046898875899999898159849998612320344--555566 Q gi|254780727|r 269 IRTLAEPTLTAISGQSASFTSGGQHLYKTVSSSTGATSVTTHDYGVVLHFTPTVLSPGRIGLRIQTEVSEPV--IGVNAG 346 (474) Q Consensus 269 a~iLa~P~l~t~sgq~A~~~~G~e~pi~~~~~~~~~~~v~~~~~Gi~L~vtP~V~~~g~I~L~i~~evS~~~--~~~~~~ 346 (474) +++||+|+|+|+|||+|.|.+|.++||.+.++..+.++++|+++|+.|+|||+|.+||.|.|++.++.+... ...... T Consensus 231 ~~vlS~P~i~t~nn~~A~I~vG~~vp~~~~~~~~~~~~~~~~~~gl~L~VtP~I~~dg~I~l~i~i~~~~~~~~~~~~~~ 310 (385) T PRK13568 231 VDIIASPRLITSHQQTASIKQGSDIPYTVSRGKKEAAAIEFKEAVLGMEVTPKILRNGKIILDLKISQNMPGITIKRGES 310 (385) T ss_pred CEEEECCEEEEECCCEEEEECCCEEEEEEEECCCCCEEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCCCCCCCCC T ss_conf 35961684899779638997687899998607877404789876688999878868995899999874367620024777 Q ss_pred CCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEEEEEEECEECC Q ss_conf 53216789999999985899899997665310132125711201761200016564552115999999051503 Q gi|254780727|r 347 DMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREETEIFIAATPFLVK 420 (474) Q Consensus 347 ~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP~iV~ 420 (474) ..|.+++|+++|+|.++||||++||||++++.+++.+|||||||||+||+|||+++.+++|+||+||||||||+ T Consensus 311 ~~~~i~~r~~~T~v~v~dG~tvviGGli~~~~~~~~~~VP~LgdIP~iG~LF~~~~~~~~k~ELlIfITP~Ii~ 384 (385) T PRK13568 311 EMLLIDKQEIKTQVTVNDGETIVLGGIFQQKKRQSVNKVPLLADIPLLGAMFRQDTQQQSRRELVIFITPKLIS 384 (385) T ss_pred CCCEEEEEEEEEEEEECCCCEEEEEEEEECCEEEEECCCCCCCCCCCCHHHHCCCCCCCCEEEEEEEEEEEEEC T ss_conf 76405506999999994899999903788213103007705853444416507977757468999999849945 No 6 >PHA00019 phage assembly protein Probab=100.00 E-value=0 Score=377.46 Aligned_cols=275 Identities=22% Similarity=0.341 Sum_probs=218.6 Q ss_pred CCHHHHHHHHHHHC-----CCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCC Q ss_conf 54147899999857-----8771699983894999997199999999999999861223455555665443035543277 Q gi|254780727|r 118 RDIAHLEMTLRRFI-----ADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIAG 192 (474) Q Consensus 118 ~d~~~l~~~l~~~~-----p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~~ 192 (474) ..+.++...++..+ +...+.+++..++++++|+ +.+.+++.++ ++.|+++ T Consensus 141 ~~a~~~~~~l~~~~~~~~~~~g~v~~D~rtNsliv~~t---~~~~~~i~~l---------------------I~~LD~~- 195 (428) T PHA00019 141 VRASDLLPLVKIFVKSNGAPGGSVTDLPGTNSLVVSGS---ASQLPALADF---------------------ISAIDVP- 195 (428) T ss_pred CCHHHHHHHHHHHHCCCCCCCCEEEECCCCCEEEEECC---HHHHHHHHHH---------------------HHHHCCC- T ss_conf 68999999998764336788832898488677999969---9999999999---------------------9984766- Q ss_pred CCEEEEEEEEEEEECHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHCCCEEEE Q ss_conf 72279999999985001442261210014543364435455666666665430334203774143110237735975898 Q gi|254780727|r 193 EDQVTLKVTIAEVRRDILKQIGFQHSITGSSSGPSKSFAADFGGKFVSEGGDFSVKGVLDRFSFETVLHALERATAIRTL 272 (474) Q Consensus 193 ~~QV~lev~i~EVs~~~~~~lGi~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~aL~~~g~a~iL 272 (474) ++||+||++|+|++++...++|+.|.........+.......++.....++. .+.+++..+++.|+||+++|++++| T Consensus 196 ~~QV~IEa~Ivev~~~~~~~~g~~~g~~~g~~~~~~~~~~~~~~~l~~~~~~---~g~~~~~~l~~~l~aLe~~g~~~il 272 (428) T PHA00019 196 RRQVLIEALIFETSLGDGVDLSFAAGLASGGKVAGGFNTARLTTVLSSAGGS---FGIFNGNVLGLSVKALENSSNSRVL 272 (428) T ss_pred CCEEEEEEEEEEEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC---EEEECCCCHHHHHHHHHHCCCCEEE T ss_conf 6248999999997136562310321566686211354455444434345640---3441462076656888737885396 Q ss_pred ECCEEEEECCCEEEEEECCCEEEEECCC-------CCCCEEEEEEEEEEEEEEEEEEECCCEEEEEEEEEECCCCCCCCC Q ss_conf 4223898759467575247300000136-------776204689887589999989815984999861232034455556 Q gi|254780727|r 273 AEPTLTAISGQSASFTSGGQHLYKTVSS-------STGATSVTTHDYGVVLHFTPTVLSPGRIGLRIQTEVSEPVIGVNA 345 (474) Q Consensus 273 a~P~l~t~sgq~A~~~~G~e~pi~~~~~-------~~~~~~v~~~~~Gi~L~vtP~V~~~g~I~L~i~~evS~~~~~~~~ 345 (474) |+|+|+|+|||+|+|.+|.++||.+... ++..++++|+++|++|+|||+|.+||+|.|++++++|++...... T Consensus 273 S~P~i~t~dn~~A~I~~G~~vp~~t~~~~~~~~~~~~~~~t~~~~d~gl~L~VtP~I~~d~~I~L~i~~~~s~~~~~~~~ 352 (428) T PHA00019 273 SRPRILTLSGQSGYISVGQNVPFVTGRVTGEAANVNNPFQTIERKDVGVSLEVTPVVMGDGQLVLDIDTKADSLSDSTIA 352 (428) T ss_pred ECCEEEEECCCEEEEEECCEEEEEEEEECCCCCCCCCCCEEEEEEEEEEEEEEEEEECCCCCEEEEEEEEECCCCCCCCC T ss_conf 07668996596589980447988975413432236876047999997799999999968994999999863354555556 Q ss_pred CCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEEEEEEECEECCC Q ss_conf 6532167899999999858998999976653101321257112017612000165645521159999990515034 Q gi|254780727|r 346 GDMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREETEIFIAATPFLVKP 421 (474) Q Consensus 346 ~~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP~iV~p 421 (474) .. |.+++|+++|+|.++||||+|||||++++.++..+|||+|||||+||+|||+++.+++|+||+||||||||+. T Consensus 353 ~~-~~i~~r~~~T~v~v~dGetvVIGGl~~~~~~~~~~~VP~LgdIP~lG~LFk~~~~~~~k~ELlIfITP~Iir~ 427 (428) T PHA00019 353 SD-IITNQRSLQTTVQVKDGQTLLLGGLISSNNTDGDSSVPFLSKIPLIGWLFRSKSDSNEQRTLYVLLTARVIKA 427 (428) T ss_pred CC-CCCCCEEEEEEEEECCCCEEEEEEEEEEEEEEECCCCCCCCCCCCCHHHHCCCCCCCCEEEEEEEEEEEEEEC T ss_conf 78-5431079989999848999999768782110131277368644101265179777673689999990299734 No 7 >COG1450 PulD Type II secretory pathway, component PulD [Cell motility and secretion / Intracellular trafficking and secretion] Probab=100.00 E-value=0 Score=364.99 Aligned_cols=239 Identities=26% Similarity=0.424 Sum_probs=193.1 Q ss_pred CEEEEEECCCCCEEEEEEEEEEEECHHHHHCCCEEEECCCCCCCCCCCCCCCCCCC---CCCCCCCEEE-EECCCCCHHH Q ss_conf 30355432777227999999998500144226121001454336443545566666---6665430334-2037741431 Q gi|254780727|r 183 KVMNLLNIAGEDQVTLKVTIAEVRRDILKQIGFQHSITGSSSGPSKSFAADFGGKF---VSEGGDFSVK-GVLDRFSFET 258 (474) Q Consensus 183 ~vvn~l~v~~~~QV~lev~i~EVs~~~~~~lGi~w~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~~~~~~~~~~ 258 (474) .++..|+++ ++||.||+.|+||+.++..++|++|...+...+.........+... ...+..+... ...+..+|.+ T Consensus 301 ~lI~~LD~~-~~QV~Iea~Ivevs~~~~~~lGv~W~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~a 379 (587) T COG1450 301 ELIEKLDVR-PKQVEIEASIVEVSLNDLEQLGVNWSALNSGGGKVGNTNSSLGNAGLSGGALAGLVSGINTGAGKSNFDA 379 (587) T ss_pred HHHHHHCCC-CCEEEEEEEEEEEECCCHHHHCCCCHHHCCCCCCEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCHHH T ss_conf 999975567-5269999999995267136639300521776772430221021577676533333344453446532999 Q ss_pred HHHHHHHCCCEEEEECCEEEEECCCEEEEEECCCEEEEE-----CCCCCCCEEEEEEEEEEEEEEEEEEECCCEEEEEEE Q ss_conf 102377359758984223898759467575247300000-----136776204689887589999989815984999861 Q gi|254780727|r 259 VLHALERATAIRTLAEPTLTAISGQSASFTSGGQHLYKT-----VSSSTGATSVTTHDYGVVLHFTPTVLSPGRIGLRIQ 333 (474) Q Consensus 259 ~l~aL~~~g~a~iLa~P~l~t~sgq~A~~~~G~e~pi~~-----~~~~~~~~~v~~~~~Gi~L~vtP~V~~~g~I~L~i~ 333 (474) .|+||++++++++||+|+|+|+||++|.|.+|.++| .+ ...++...+++|+++|+.|+|||+|.++|++.|+|+ T Consensus 380 ~inaL~~~~~~~VlS~Psl~tlnN~~A~i~VGq~vp-~~~~~~~~~~g~~~~~~~~~~~Gv~LkVtP~I~~~~~v~L~Ie 458 (587) T COG1450 380 LINALSQNGDANVLSTPSLLTLNNQQAIIDVGQDVP-QTGTSYTKVTGEKTATLERIDVGVMLKVTPRINDDGRVLLDIE 458 (587) T ss_pred HHHHHHHCCCCEEEECCEEEEECCCCEEEECCCCCC-CCEEEEEECCCCEEEEEEEEEEEEEEEEEEEECCCCEEEEEEE T ss_conf 998987658947973788998248607987675346-6137998357843445778872079998778848985899984 Q ss_pred EEECCCCCC---CCCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEE Q ss_conf 232034455---55665321678999999998589989999766531013212571120176120001656455211599 Q gi|254780727|r 334 TEVSEPVIG---VNAGDMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREETEI 410 (474) Q Consensus 334 ~evS~~~~~---~~~~~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tEL 410 (474) +|+|+.... .+....|.+++|+++|.+.++||||++||||++++.++..+|||||||||+||+|||++..+++++|| T Consensus 459 qevs~~~~~~~~~~~~~~p~~~~r~I~T~v~v~dG~slvlGGLi~d~~s~s~skVP~LGdIP~iG~LFr~t~~~~~kt~l 538 (587) T COG1450 459 QEVSSVATSDSVTSNDPLPTTNKREITTEVRVKDGDSLLLGGLIQDKQSDSVSKVPFLGDIPLIGSLFRSTSKTRKKTEL 538 (587) T ss_pred CCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEECCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCEEEE T ss_conf 15545566654335687863531463579994689999981376525242013886676564311442462000232899 Q ss_pred EEEEECEECCCCC Q ss_conf 9999051503468 Q gi|254780727|r 411 FIAATPFLVKPVA 423 (474) Q Consensus 411 vI~iTP~iV~p~~ 423 (474) +|||||++|+... T Consensus 539 ~~fI~P~ii~~~~ 551 (587) T COG1450 539 MFFITPRIIRSPA 551 (587) T ss_pred EEEEEEEEECCCH T ss_conf 9998879925803 No 8 >TIGR02519 pilus_MshL pilus (MSHA type) biogenesis protein MshL; InterPro: IPR013358 Proteins containing this region are predicted secretins, that is, outer membrane pore proteins associated with delivery of proteins from the periplasm to the outside of the cell. Related proteins include the GspD type II secretion family, the YscC/HrcC family type III secretion family, and the PilQ type IV pilus formation family. These proteins are found in gene clusters associated with MSHA (mannose-sensitive hemagglutinin) and related pili, and appear to be the secretin of this pilus system.. Probab=100.00 E-value=0 Score=333.09 Aligned_cols=258 Identities=25% Similarity=0.341 Sum_probs=197.5 Q ss_pred EEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEEEEEEECHHHHHCCCEE Q ss_conf 99838949999971999999999999998612234555556654430355432777227999999998500144226121 Q gi|254780727|r 138 VEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIAGEDQVTLKVTIAEVRRDILKQIGFQH 217 (474) Q Consensus 138 v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~~~~QV~lev~i~EVs~~~~~~lGi~w 217 (474) ++...+.+.+++. +.+.+++.+..+.+- -+..+||.||++|+||++++.++.|||| T Consensus 3 iN~~~G~l~~~A~---p~~~~~V~~yl~~l~---------------------~~~~rQV~ie~~ileV~L~D~~~~GiDW 58 (311) T TIGR02519 3 INKEAGLLTVRAT---PAQIRRVEEYLESLK---------------------ERIHRQVLIEAKILEVTLSDNYQQGIDW 58 (311) T ss_pred CCCCCCEEEEEEC---HHHHHHHHHHHHHHH---------------------HHCCCCEEEEEEEEEEEECCCCEECCCH T ss_conf 4777357999852---589999999999988---------------------8508638999799999857880015128 Q ss_pred EECCCCCCCCCCCCCC------CCCCCCC----------------CCCCCEEEEECCCCCHHHHHHHHHHCCCEEEEECC Q ss_conf 0014543364435455------6666666----------------65430334203774143110237735975898422 Q gi|254780727|r 218 SITGSSSGPSKSFAAD------FGGKFVS----------------EGGDFSVKGVLDRFSFETVLHALERATAIRTLAEP 275 (474) Q Consensus 218 ~~~~~~~~~~~~~~~~------~~~~~~~----------------~~~~~~~~~~~~~~~~~~~l~aL~~~g~a~iLa~P 275 (474) +.............+. .++.+.+ .+.+....-..++..|.+.++||.++|++++||+| T Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~sg~~~l~~i~~~~~~~G~A~G~G~~i~~a~Gsf~~~v~~L~~~G~~~VLSnP 138 (311) T TIGR02519 59 SNFNGSLLGRYKLGGAATSNDSSGNIFSSGLGFLDNISLPTTVNGAAAGLGSNISIANGSFDAIVNFLATFGDVKVLSNP 138 (311) T ss_pred HHHHCCCCCHHCCCCCEEECCCCCCCCCCCCCCHHHCCCCCCCCEEEEECCCEEEEECCHHHHHHHHHHHCCCEEEEECC T ss_conf 99630221010578620313557740557765510334222341244321522674035488999999962973673177 Q ss_pred EEEEECCCEEEEEECCCEEEEECCCC-------CC-CE-------EEEEEEEEEEEEEEEEEECCCEEEEEEEEEECCCC Q ss_conf 38987594675752473000001367-------76-20-------46898875899999898159849998612320344 Q gi|254780727|r 276 TLTAISGQSASFTSGGQHLYKTVSSS-------TG-AT-------SVTTHDYGVVLHFTPTVLSPGRIGLRIQTEVSEPV 340 (474) Q Consensus 276 ~l~t~sgq~A~~~~G~e~pi~~~~~~-------~~-~~-------~v~~~~~Gi~L~vtP~V~~~g~I~L~i~~evS~~~ 340 (474) +|+|+|||+|-|+||..+.|.+.... .+ ++ .+.....|+.|+|||.|.+||+|.|+|+|.+|+.. T Consensus 139 k~~a~NnQ~A~isVG~~~~Y~~~~~~~Gss~~~~ggtt~~~~~~~~~~s~f~G~~l~VtP~I~dDg~v~L~v~P~~s~v~ 218 (311) T TIGR02519 139 KVMALNNQPAVISVGDSITYVTEISSTGSSTTTSGGTTSTASSDVEVDSVFSGIVLGVTPQIKDDGKVILNVHPSISEVK 218 (311) T ss_pred EEEEECCCEEEEEECCEEEEEEEEEEECCCCCCCCCCEEEEEEEEEECCEEEEEEECCCCEEECCCEEEEEEECCEEEEE T ss_conf 28853585789993461368987786424356888640355442357735401261420028618879999842287787 Q ss_pred CC-------------C-CCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCC Q ss_conf 55-------------5-566532167899999999858998999976653101321257112017612000165645521 Q gi|254780727|r 341 IG-------------V-NAGDMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNRE 406 (474) Q Consensus 341 ~~-------------~-~~~~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~ 406 (474) .. . .....|.+.+|+++|+|+++|||++||||||+++.++..+|+|+|||||+||+||+++.+.++ T Consensus 219 ~~~~Ge~~~~~~~~~~g~~~~lP~~~~Ke~ss~~~~~~G~~~vlGGLi~~~~s~~~~~~P~LgdiP~lG~LF~~~~~~~~ 298 (311) T TIGR02519 219 PQKDGESLELIEVGNEGAEVALPEISVKEMSSVVRVKDGDTVVLGGLIDKKKSNTKSGLPLLGDIPGLGYLFSYKSKSKK 298 (311) T ss_pred ECCCCCCCCCCCCCCCCCEECCCCEEEEEEEEEEEECCCCEEEEEEEECCCCCCCCCCCCCCCCCCEEEEECCCCCCCCE T ss_conf 30267641001357767524077023323567999517979997134236501311355531147634331277513521 Q ss_pred EEEEEEEEECEEC Q ss_conf 1599999905150 Q gi|254780727|r 407 ETEIFIAATPFLV 419 (474) Q Consensus 407 ~tELvI~iTP~iV 419 (474) ++|||||++|+|| T Consensus 299 ~~ElVI~l~P~v~ 311 (311) T TIGR02519 299 KTELVIILRPSVV 311 (311) T ss_pred EEEEEEEECCEEC T ss_conf 3689999133669 No 9 >TIGR02516 type_III_yscC type III secretion outer membrane pore, YscC/HrcC family; InterPro: IPR003522 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia . The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself , type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. This family aids in the structural assembly of the invasion complex . Another characteristic of this family is its ability to form a channel through the outer bacterial membrane, allowing secretion to take place. Members include the Salmonella InvG and SpiA gene, the Shigella MxiD, and the Yersinia Kim5 and YscC proteins. Plant pathogen members include the Hypersensitivity Response (HR) genes of Burkholderia and Erwinia.; GO: 0009306 protein secretion. Probab=100.00 E-value=0 Score=310.04 Aligned_cols=235 Identities=22% Similarity=0.380 Sum_probs=192.2 Q ss_pred EEEEEECCCCCEEEEEEEEEEEECHHHHHCCCEEEECCCCCCCCCCCCCC-------------CC----------CCCCC Q ss_conf 03554327772279999999985001442261210014543364435455-------------66----------66666 Q gi|254780727|r 184 VMNLLNIAGEDQVTLKVTIAEVRRDILKQIGFQHSITGSSSGPSKSFAAD-------------FG----------GKFVS 240 (474) Q Consensus 184 vvn~l~v~~~~QV~lev~i~EVs~~~~~~lGi~w~~~~~~~~~~~~~~~~-------------~~----------~~~~~ 240 (474) +|..|+++ ++||.|++.|+||+++++++||+||++..+..+...++... ++ +...+ T Consensus 234 LI~~LD~~-~~~iEi~~~I~Did~~~L~~LGvdW~~~~~~g~~~~g~~~~~~~~Y~GGqinPffGT~~l~g~av~s~~a~ 312 (508) T TIGR02516 234 LIQQLDVP-PRLIEISASIIDIDADDLSQLGVDWRATLGAGDKQTGFGKTSQDDYDGGQINPFFGTDKLTGLAVVSAGAS 312 (508) T ss_pred HHHHHCCC-CCEEEEEEEEEEECCCCHHHCCCEEEEEEECCCCEEEEEECCCCCCCCCEECCCCCCCCCCCCCCCCCHHC T ss_conf 99971864-43078999999714784256271069997179837987641578778863344425565678644573020 Q ss_pred CCCCCEEEEECCCCCHHHHHHHHHHCCCEEEEECCEEEEECCCEEEEEECCCEEEEECCCCCCCEEEEEEEEEEEEEEEE Q ss_conf 65430334203774143110237735975898422389875946757524730000013677620468988758999998 Q gi|254780727|r 241 EGGDFSVKGVLDRFSFETVLHALERATAIRTLAEPTLTAISGQSASFTSGGQHLYKTVSSSTGATSVTTHDYGVVLHFTP 320 (474) Q Consensus 241 ~~~~~~~~~~~~~~~~~~~l~aL~~~g~a~iLa~P~l~t~sgq~A~~~~G~e~pi~~~~~~~~~~~v~~~~~Gi~L~vtP 320 (474) .+...+.....+...|-+.++|||++|.|+|+|+|.++|++|.+|.|-.-.+|++... +......+..++|+.|.||| T Consensus 313 ~~~~~s~~~~~~~~~f~arvnALe~~~~A~ivs~P~vlTleN~~Av~D~~~TfY~kv~--Ge~~a~L~~vt~GT~LRVtP 390 (508) T TIGR02516 313 LGATGSSIVTSDGDYFLARVNALEQNGKAKIVSRPSVLTLENVQAVLDNNRTFYVKVS--GERVADLESVTAGTLLRVTP 390 (508) T ss_pred CCCEEEEEEEECCHHHHHHHHHHHCCCEEEEEEEEEEEEECCCCEEECCCCEEEEEEE--EEEEEEEECEEEEEEEEEEE T ss_conf 6830789886262033432212520773799984169986483148328726999998--88899850246533677603 Q ss_pred EEEC-CC---------EEEEEEEEEECC-----CCCCCCCC--CCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCC Q ss_conf 9815-98---------499986123203-----44555566--5321678999999998589989999766531013212 Q gi|254780727|r 321 TVLS-PG---------RIGLRIQTEVSE-----PVIGVNAG--DMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKE 383 (474) Q Consensus 321 ~V~~-~g---------~I~L~i~~evS~-----~~~~~~~~--~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~ 383 (474) +|.. +| +|.|.|+.|--+ ...+.... .+|.++.-+++|...+..|||++|||+++|+..+..+ T Consensus 391 r~~~d~g~~~tGkr~~~i~L~v~IeDGq~~~~~s~~~~~~dnn~lP~i~~t~i~TqA~v~~GqSLLiGGy~~D~~~~~~~ 470 (508) T TIGR02516 391 RVIEDGGAKSTGKRVEQIKLNVDIEDGQQKTTTSLTTSTVDNNALPEIKRTEISTQARVGHGQSLLIGGYIRDEKADSLD 470 (508) T ss_pred EEEECCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEECCCCCCC T ss_conf 88746989645724578999988751888857777777202444884226504479992588058875254322241115 Q ss_pred CCCCEECCCCEEECCCCCCCCCCEEEEEEEEECEECCC Q ss_conf 57112017612000165645521159999990515034 Q gi|254780727|r 384 GIPLLSKIPILGALFRNSRFNREETEIFIAATPFLVKP 421 (474) Q Consensus 384 ~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP~iV~p 421 (474) |||+|||||+||.|||++++++++.|-|++|+||+|++ T Consensus 471 ~iP~Lg~IPllG~LFr~~~~~~~~~vRLFLi~P~~v~~ 508 (508) T TIGR02516 471 GIPLLGDIPLLGALFRSTSKEKSRVVRLFLITPKIVRD 508 (508) T ss_pred CCCCCCCCCCCCCCCCCEEECCCEEEEEEEECCEECCC T ss_conf 78410255710553221241444069999740557389 No 10 >pfam00263 Secretin Bacterial type II and III secretion system protein. Probab=100.00 E-value=1.4e-45 Score=281.86 Aligned_cols=159 Identities=36% Similarity=0.557 Sum_probs=146.8 Q ss_pred HHHHCCCEEEEECCEEEEECCCEEEEEECCCEEEEECCCC---CCCEEEEEEEEEEEEEEEEEEECCCEEEEEEEEEECC Q ss_conf 3773597589842238987594675752473000001367---7620468988758999998981598499986123203 Q gi|254780727|r 262 ALERATAIRTLAEPTLTAISGQSASFTSGGQHLYKTVSSS---TGATSVTTHDYGVVLHFTPTVLSPGRIGLRIQTEVSE 338 (474) Q Consensus 262 aL~~~g~a~iLa~P~l~t~sgq~A~~~~G~e~pi~~~~~~---~~~~~v~~~~~Gi~L~vtP~V~~~g~I~L~i~~evS~ 338 (474) ||+++|.+++|++|+|+++||++|.|.+|+++||++.... ....+++|+++|+.|+|+|+|.+||+|.|++++++|+ T Consensus 1 AL~~~g~~~ils~P~i~t~~g~~a~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~G~~L~VtP~I~~~~~V~L~i~~~~s~ 80 (164) T pfam00263 1 ALEQNGNAKVLSSPSLLTLNNQEASILVGQEVPYPTSSTSGNGTTTVEIKYIDAGLSLEVTPRVTDDGTITLEINPEVSS 80 (164) T ss_pred CCCCCCCCEEEECCEEEEECCCEEEEECCEEEEEEEEEECCCCEEEEEEEEEEEEEEEEEEEEECCCCEEEEEEEEEEEE T ss_conf 94305981899789899989999999973499968998528872888999999879999999994499799999999810 Q ss_pred CCCCC--CCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEEEEEEEC Q ss_conf 44555--5665321678999999998589989999766531013212571120176120001656455211599999905 Q gi|254780727|r 339 PVIGV--NAGDMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREETEIFIAATP 416 (474) Q Consensus 339 ~~~~~--~~~~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP 416 (474) +.... .....|.+++|+++|+|.+++|||++||||++++.+++.+|||+|||||+||+||++++++++++||+||||| T Consensus 81 ~~~~~~~~~~~~P~~~~r~~~t~v~l~~Get~vlgGl~~~~~~~~~~gvP~L~~iP~lG~lF~~~~~~~~~~el~i~ItP 160 (164) T pfam00263 81 LDGSNAVTGGGVPTINTREVTTTVRVRDGQTLVLGGLIQEEDSESVSKVPLLGDIPLLGALFRSTSKSKEKTELLIFITP 160 (164) T ss_pred CCCCCCCCCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEEEEEEECCCCCCCCCCHHHHCCCCCCCCCEEEEEEEEEE T ss_conf 23321245677863898999999999799799996288983610314361574061104541886573537999999995 Q ss_pred EECC Q ss_conf 1503 Q gi|254780727|r 417 FLVK 420 (474) Q Consensus 417 ~iV~ 420 (474) |||+ T Consensus 161 ~ii~ 164 (164) T pfam00263 161 RIVR 164 (164) T ss_pred EECC T ss_conf 9919 No 11 >COG4796 HofQ Type II secretory pathway, component HofQ [Intracellular trafficking and secretion] Probab=100.00 E-value=0 Score=287.01 Aligned_cols=229 Identities=25% Similarity=0.370 Sum_probs=191.5 Q ss_pred CCEEEEEEEEEEEECHHHHHCCCEEEECCCCCCC----------CCC-----------CCCCCCCCCCCC-CCCCEEEEE Q ss_conf 7227999999998500144226121001454336----------443-----------545566666666-543033420 Q gi|254780727|r 193 EDQVTLKVTIAEVRRDILKQIGFQHSITGSSSGP----------SKS-----------FAADFGGKFVSE-GGDFSVKGV 250 (474) Q Consensus 193 ~~QV~lev~i~EVs~~~~~~lGi~w~~~~~~~~~----------~~~-----------~~~~~~~~~~~~-~~~~~~~~~ 250 (474) ..||+++.+++++.++.++++|+.|......... +.. +..++.....+. ...+.+... T Consensus 455 ~~qv~i~a~ivtv~~~~~~elgv~~gl~~~~~~~~~~~~~l~~~~~~~~d~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 534 (709) T COG4796 455 VNQVIIEARIVTVLKLSLRELGVLWGLIQTTDRELGGIGALGRLFFSQGDNAVKNEIVLNITLPVTTPTVGSITLGFARI 534 (709) T ss_pred HHHEEEEEEEEEEEECCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCEEEEEC T ss_conf 45606775456775235765555763112355555677632345433467752244214303577566657651331100 Q ss_pred CCCCCHHHHHHHHHHCCCEEEEECCEEEEECCCEEEEEECCCEEEEECCCCCC--CEEEEEEEEEEEEEEEEEEECCCEE Q ss_conf 37741431102377359758984223898759467575247300000136776--2046898875899999898159849 Q gi|254780727|r 251 LDRFSFETVLHALERATAIRTLAEPTLTAISGQSASFTSGGQHLYKTVSSSTG--ATSVTTHDYGVVLHFTPTVLSPGRI 328 (474) Q Consensus 251 ~~~~~~~~~l~aL~~~g~a~iLa~P~l~t~sgq~A~~~~G~e~pi~~~~~~~~--~~~v~~~~~Gi~L~vtP~V~~~g~I 328 (474) ++...+.+-|+|++++++++++++|++.|.++++|++..|.|+||...+.+.+ .++++|++.++.|.+||+|.+||+| T Consensus 535 ~~~~~L~leLsA~e~~~~~~ilasPrlit~~~~~A~I~~G~eip~~~~s~~~~~t~~~v~f~~a~l~l~VtP~I~~d~~i 614 (709) T COG4796 535 GGGPLLDLELSALEQEGRAKILASPRLITANGEPASIKQGTEIPYQVASGGGGGTITSVEFKEAVLGLEVTPRITPDGRI 614 (709) T ss_pred CCCCCCCEECCHHHHCCCCCCCCCCEEEECCCCCEEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCCEECCEECCCCCE T ss_conf 68721033045023406876315881374378741522676466153146777656675301122341443235689967 Q ss_pred EEEEEEEECCCCCCCC--CCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCC Q ss_conf 9986123203445555--66532167899999999858998999976653101321257112017612000165645521 Q gi|254780727|r 329 GLRIQTEVSEPVIGVN--AGDMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNRE 406 (474) Q Consensus 329 ~L~i~~evS~~~~~~~--~~~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~ 406 (474) .|++.+..+++..... ...+|.+++|++.|.+.++||||++|||.+++...++.+|||+|||||+||+|||++.+... T Consensus 615 ~L~~~~~~~~p~~~~~~~~~~i~~i~~~ei~t~v~v~~G~TvvlgGi~~~~~~~t~skVPlLgdiP~iG~lFr~~~~~~~ 694 (709) T COG4796 615 FLDLFVTQDSPGQVQVIGVGEIPLISKQEINTQVIVKNGETVVLGGIFQEADRSTVSKVPLLGDIPVIGALFRTTTKTTE 694 (709) T ss_pred EEEEEEEECCCCCEEECCCCCCCCCCHHHHCCCCEECCCCEEEEECEEEECCCCCCCCCCCCCCCCCCHHHHHCCCCCCC T ss_conf 98743351277734432677522124656055524316957997021440566764556515546410334201355566 Q ss_pred EEEEEEEEECEECCC Q ss_conf 159999990515034 Q gi|254780727|r 407 ETEIFIAATPFLVKP 421 (474) Q Consensus 407 ~tELvI~iTP~iV~p 421 (474) ++||+||+||+++.| T Consensus 695 rrEl~IfiTP~i~~~ 709 (709) T COG4796 695 RRELLIFITPRIIEP 709 (709) T ss_pred CCCEEEEECCCCCCC T ss_conf 663258825756789 No 12 >TIGR02520 pilus_B_mal_scr type IVB pilus formation outer membrane protein, R64 PilN family; InterPro: IPR013359 Several related protein families encode outer membrane pore proteins for type II secretion, type III secretion, and type IV pilus formation. Proteins in this entry appear to be secretins for pilus formation, although they are quite different from PilQ. Members include the PilN lipoprotein of the plasmid R64 thin pilus, a type IV pilus. Some proteins may be examples of bundle-forming pilus B (bfpB).. Probab=100.00 E-value=1.5e-32 Score=206.82 Aligned_cols=295 Identities=17% Similarity=0.220 Sum_probs=214.9 Q ss_pred CCCCEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHC---CCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHH Q ss_conf 2672279999889997789998730454147899999857---8771699983894999997199999999999999861 Q gi|254780727|r 92 KNVGQANVILIGHDGKQMLNLDILIERDIAHLEMTLRRFI---ADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFL 168 (474) Q Consensus 92 k~~G~T~l~v~~~~g~~~~~~~v~v~~d~~~l~~~l~~~~---p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~ 168 (474) -..|+|-|..-+ ....-..+...| .+++++.+++++ |..++......+.+.++.. |+..+|+ +.|. T Consensus 215 ~GsGttGltans-tq~tav~~~~sv---~~di~~~v~aMlS~~P~G~~~lS~sTG~L~VtD~---P~VL~Rv----~~Y~ 283 (536) T TIGR02520 215 AGSGTTGLTANS-TQSTAVKLKSSV---LNDIQKSVKAMLSSSPEGSLVLSRSTGSLAVTDS---PEVLDRV----ASYI 283 (536) T ss_pred CCCCCCCCCCCC-CCEEEEEEEHHH---HHHHHHHHEEEECCCCCCCEEEECCCEEEEEEEC---CCHHHHH----HHHH T ss_conf 777534521146-640578750134---5433110201204699840687605406899406---6468899----9999 Q ss_pred CCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEEEEEEECHHHHHCCCEEEECCCCCC--CCCCCCCCCCCCCCCCCCCCE Q ss_conf 223455555665443035543277722799999999850014422612100145433--644354556666666654303 Q gi|254780727|r 169 SQSGRNQYANSSSKKVMNLLNIAGEDQVTLKVTIAEVRRDILKQIGFQHSITGSSSG--PSKSFAADFGGKFVSEGGDFS 246 (474) Q Consensus 169 ~~~~~~~~~~~~~~~vvn~l~v~~~~QV~lev~i~EVs~~~~~~lGi~w~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~ 246 (474) +.......+||.|.|+|+||+++..+|+|+||+..+.... .+........+.......... T Consensus 284 -----------------~~~N~~l~rqV~LnV~v~~v~~~~~dq~~vdW~~vYK~~~~r~GLs~~n~~~g~s~~~~a~~s 346 (536) T TIGR02520 284 -----------------DSQNRRLTRQVLLNVKVLSVSFKDSDQYGVDWSLVYKSLSRRIGLSLANKVAGTSTAATAGSS 346 (536) T ss_pred -----------------HHHCCCCCCEEEEEEEEEEEEECCCCCCEEEEEEEEEEEECEECCCCCCCCCCCCCCCCCCEE T ss_conf -----------------850501130489889999988447764030004476654021134215766774100455406 Q ss_pred EEEE---CCCCCHHHHHHHHHHCCCEEEEECCEEEEECCCEEEEEECCCEEEEECCCCCCCE------EEE--EEEEEEE Q ss_conf 3420---3774143110237735975898422389875946757524730000013677620------468--9887589 Q gi|254780727|r 247 VKGV---LDRFSFETVLHALERATAIRTLAEPTLTAISGQSASFTSGGQHLYKTVSSSTGAT------SVT--THDYGVV 315 (474) Q Consensus 247 ~~~~---~~~~~~~~~l~aL~~~g~a~iLa~P~l~t~sgq~A~~~~G~e~pi~~~~~~~~~~------~v~--~~~~Gi~ 315 (474) .... .-...-.++|+||+++|+++++.+|.+||+|.|+|-|+++++.-|.-...++.+. .+| ....|+. T Consensus 347 a~i~~~~s~F~Gs~~li~ALs~QG~vs~v~~~svTTlNlqp~P~QvA~q~~YlaS~stt~t~~vGsst~l~Pa~vTtGfn 426 (536) T TIGR02520 347 AAIDVVKSPFAGSTLLIRALSEQGKVSVVTSPSVTTLNLQPVPVQVATQTGYLASVSTTSTANVGSSTSLEPATVTTGFN 426 (536) T ss_pred EEEECCCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCEEECCEEEEEEEEECCCCCCCCCEEECCCCEECCCCH T ss_conf 67744668615327999998407918674146644004776556886736999864111267744101034870345620 Q ss_pred EEEEEEEECCCEEEEEEEEEECCCC------CCCC-----CCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCC Q ss_conf 9999898159849998612320344------5555-----6653216789999999985899899997665310132125 Q gi|254780727|r 316 LHFTPTVLSPGRIGLRIQTEVSEPV------IGVN-----AGDMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEG 384 (474) Q Consensus 316 L~vtP~V~~~g~I~L~i~~evS~~~------~~~~-----~~~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~ 384 (474) |.+.|.|.+++.|.|+++..+|+.. .... -.+.|.+..|.+.-.|.||+|||+||.|+-+.+++.++.| T Consensus 427 M~LLP~i~d~~~ilLqf~~s~S~~~~L~~~~s~~~~sGl~~vq~p~~d~r~~~~kV~LksG~TLv~sGye~~~~~~d~~G 506 (536) T TIGR02520 427 MTLLPKILDDGDILLQFSISLSDLAELKKFTSKEGGSGLAKVQTPDVDLRNFSQKVALKSGETLVLSGYEERNDTADREG 506 (536) T ss_pred HHHHHHHHCCCCEEEEEEECCCCHHHHHEECCCCCCCCEEEEECCCCHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCC T ss_conf 12123663288466876405688447310024567853158741760077553341168897668813257775644244 Q ss_pred CCCEECCCCEEECCCCCCCCCCEEEEEEEEECEE Q ss_conf 7112017612000165645521159999990515 Q gi|254780727|r 385 IPLLSKIPILGALFRNSRFNREETEIFIAATPFL 418 (474) Q Consensus 385 vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP~i 418 (474) + |=-|.=. |-+++..++++.-|||+|||-+ T Consensus 507 ~-G~p~~~~---lGGs~~~~~~~~~lvvlvTPv~ 536 (536) T TIGR02520 507 V-GDPDVIV---LGGSRESERDHEVLVVLVTPVV 536 (536) T ss_pred C-CCCCEEE---ECCCCCCCCCCCEEEEEECCCC T ss_conf 7-7722256---3476446556607999866889 No 13 >COG4796 HofQ Type II secretory pathway, component HofQ [Intracellular trafficking and secretion] Probab=98.62 E-value=4.3e-07 Score=59.35 Aligned_cols=208 Identities=18% Similarity=0.138 Sum_probs=144.7 Q ss_pred EEEEEEEEEEEECHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHCCCEEEEEC Q ss_conf 27999999998500144226121001454336443545566666666543033420377414311023773597589842 Q gi|254780727|r 195 QVTLKVTIAEVRRDILKQIGFQHSITGSSSGPSKSFAADFGGKFVSEGGDFSVKGVLDRFSFETVLHALERATAIRTLAE 274 (474) Q Consensus 195 QV~lev~i~EVs~~~~~~lGi~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~aL~~~g~a~iLa~ 274 (474) .++++..+.|+.+..+.++++ |.......... ..+...-..+ ..........+....++ .....+.+++ T Consensus 310 n~v~~~~V~~~~tl~L~dvp~-~~q~L~l~l~~------~~~l~~~~~~--~v~~i~~~~~~~~~~~~--~~~~~~~~a~ 378 (709) T COG4796 310 NLVLEDEVLGTLTLRLTDVPI-WPQALDLVLRS------AKGLDLRKHG--NVVRIGPSSELNKNERA--ELEATNLIAN 378 (709) T ss_pred CEEEECCCCEEEEEECCCCCC-HHHHHHHHHHC------CCCEEECCCC--CEEEEECCCHHHHHHHH--HHHHHHHHCC T ss_conf 414220001167752345873-56677775311------5550133688--56896054355554565--5300233316 Q ss_pred CEEEEECCCEEEEEECCCEEEEECCCCCCCEEEEEEEEEEEEEEEEEEECCCEEEEEEEEEECCC----CCCCCCCCCC- Q ss_conf 23898759467575247300000136776204689887589999989815984999861232034----4555566532- Q gi|254780727|r 275 PTLTAISGQSASFTSGGQHLYKTVSSSTGATSVTTHDYGVVLHFTPTVLSPGRIGLRIQTEVSEP----VIGVNAGDMP- 349 (474) Q Consensus 275 P~l~t~sgq~A~~~~G~e~pi~~~~~~~~~~~v~~~~~Gi~L~vtP~V~~~g~I~L~i~~evS~~----~~~~~~~~~P- 349 (474) |++-+.+...+-.+++...|. .......+...-|.+. .|.+.|.+..|++..+.+..++++. ........+| T Consensus 379 ~~~~~~~~~~~l~y~~~~~~~-~~~a~s~~~g~~~~~~--~ls~~~sv~~D~~tn~~~i~d~~~~i~~i~~~~~~~d~p~ 455 (709) T COG4796 379 PRIRLRNKEKALIYAGAAEPF-LSLATSLTTGGVYNDV--LLSVRGSVTFDNRTNILLILDVPSIIQQIRTLVAQIDIPV 455 (709) T ss_pred CCCCCHHHHHHHHHCCCCCCH-HHHCCCCCCCCCCCCC--CCCCCCCEEECCCCCEEEEECCHHHHHHHHHHHHHCCCCH T ss_conf 331112344444413567620-0000003567544553--2333673556277766896073889999974201116754 Q ss_pred --EEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEEEEEEECEECCCCC Q ss_conf --16789999999985899899997665310132125711201761200016564552115999999051503468 Q gi|254780727|r 350 --SYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREETEIFIAATPFLVKPVA 423 (474) Q Consensus 350 --~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP~iV~p~~ 423 (474) .+-++++.|.....++|.-+..|+++.+... ++++|.+|.+|-+......++|.+.=++|++..|.. T Consensus 456 ~qv~i~a~ivtv~~~~~~elgv~~gl~~~~~~~-------~~~~~~l~~~~~~~~d~~~~~~~~l~~~~~~~~~~~ 524 (709) T COG4796 456 NQVIIEARIVTVLKLSLRELGVLWGLIQTTDRE-------LGGIGALGRLFFSQGDNAVKNEIVLNITLPVTTPTV 524 (709) T ss_pred HHEEEEEEEEEEEECCCCCCCEEEEECCCCCCC-------CCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCC T ss_conf 560677545677523576555576311235555-------567763234543346775224421430357756665 No 14 >pfam04972 BON Putative phospholipid-binding domain. This domain is found in a family of osmotic shock protection proteins. It is also found in some Secretins and a group of potential haemolysins. Its likely function is attachment to phospholipid membranes. Probab=97.37 E-value=0.00092 Score=40.04 Aligned_cols=60 Identities=25% Similarity=0.378 Sum_probs=50.1 Q ss_pred HHHHHHHHH--HCCCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECC Q ss_conf 478999998--57877169998389499999719999999999999986122345555566544303554327 Q gi|254780727|r 121 AHLEMTLRR--FIADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIA 191 (474) Q Consensus 121 ~~l~~~l~~--~~p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~ 191 (474) ..++..|.. .++..+|++...++.++|+|.|.+..+++++.++|+.+.+. .+|.|.|.+. T Consensus 2 ~~i~~~l~~~~~~~~~~I~V~v~~g~V~L~G~v~s~~~~~~a~~~a~~~~Gv-----------~~V~n~l~v~ 63 (64) T pfam04972 2 AKVKAALLADPGLPASDIKVTVENGVVTLSGTVDSEEEKEKAEEIARNVKGV-----------KKVVNEITVR 63 (64) T ss_pred HHHHHHHHCCCCCCCCCEEEEEECCEEEEEEECCCHHHHHHHHHHHHCCCCC-----------CEEEEEEEEE T ss_conf 7899988349899857169999896999999859999999999999669698-----------5899617992 No 15 >PRK11023 hypothetical protein; Provisional Probab=95.94 E-value=0.075 Score=28.99 Aligned_cols=90 Identities=20% Similarity=0.331 Sum_probs=55.6 Q ss_pred EEEEECCCCEEEEEECCCCEE-----EEEEECCCCCEEEEEEEECCCCHH--------HHHHHHH------HHCCCCCEE Q ss_conf 799971698799995267227-----999988999778999873045414--------7899999------857877169 Q gi|254780727|r 77 ADVVVHSPRTMYLFGKNVGQA-----NVILIGHDGKQMLNLDILIERDIA--------HLEMTLR------RFIADSNIR 137 (474) Q Consensus 77 adv~v~s~~~i~i~gk~~G~T-----~l~v~~~~g~~~~~~~v~v~~d~~--------~l~~~l~------~~~p~~~i~ 137 (474) .++.+.+ +.++|+|.-+=.. .-++|.-+|=.-...++.+....+ -+...++ .-++..+++ T Consensus 70 I~v~v~n-g~VLLtGqV~~~~~k~~a~~ia~~~~gVr~V~Nei~V~~~~s~~~~a~D~~Ittkvk~~ll~~~~v~s~~ik 148 (191) T PRK11023 70 INVTAYQ-GKVLLIGQSPNAELSARAKQIAMGVEGVTEVYNEIRQGQPIGLGQASKDTWITTKVRSQLLTSDSVKSSNVK 148 (191) T ss_pred EEEEEEC-CEEEEEEEECCHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCEEECHHHHHHHHHHHHHCCCCCCCEEE T ss_conf 9999977-899999997999999999999846688428999999668876442200298999999998737797763789 Q ss_pred EEEECCEEEEEEEECCHHHHHHHHHHHHHHH Q ss_conf 9983894999997199999999999999861 Q gi|254780727|r 138 VEMVSDTVVLHGMVRTIQDSQRAVELSETFL 168 (474) Q Consensus 138 v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~ 168 (474) |...++.++|-|.+ +..+++++.++|+.-. T Consensus 149 V~teng~VyLmG~v-t~~E~~~av~iAr~v~ 178 (191) T PRK11023 149 VTTENGEVFLLGLV-TQREAKAAADIASRVS 178 (191) T ss_pred EEEECCEEEEEEEC-CHHHHHHHHHHHHCCC T ss_conf 99999899999967-9999999999986399 No 16 >PRK11023 hypothetical protein; Provisional Probab=95.88 E-value=0.042 Score=30.44 Aligned_cols=51 Identities=20% Similarity=0.197 Sum_probs=41.4 Q ss_pred CCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCC Q ss_conf 87716999838949999971999999999999998612234555556654430355432777 Q gi|254780727|r 132 ADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIAGE 193 (474) Q Consensus 132 p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~~~ 193 (474) ...+|.+...++.+.|.|+|++++..+++.+++....+- .+|.|.|+|..+ T Consensus 66 ~~~~I~v~v~ng~VLLtGqV~~~~~k~~a~~ia~~~~gV-----------r~V~Nei~V~~~ 116 (191) T PRK11023 66 KEARINVTAYQGKVLLIGQSPNAELSARAKQIAMGVEGV-----------TEVYNEIRQGQP 116 (191) T ss_pred CCCEEEEEEECCEEEEEEEECCHHHHHHHHHHHHCCCCC-----------EEEEEEEEECCC T ss_conf 460899999778999999979999999999998466884-----------289999996688 No 17 >PRK10568 periplasmic protein; Provisional Probab=95.84 E-value=0.057 Score=29.68 Aligned_cols=95 Identities=21% Similarity=0.279 Sum_probs=57.5 Q ss_pred CCEEEEEECCCCEE-----EEEEECCCCCEEEEEEEECCC-----------CHHHHHHHHHH------HCCCCCEEEEEE Q ss_conf 98799995267227-----999988999778999873045-----------41478999998------578771699983 Q gi|254780727|r 84 PRTMYLFGKNVGQA-----NVILIGHDGKQMLNLDILIER-----------DIAHLEMTLRR------FIADSNIRVEMV 141 (474) Q Consensus 84 ~~~i~i~gk~~G~T-----~l~v~~~~g~~~~~~~v~v~~-----------d~~~l~~~l~~------~~p~~~i~v~~~ 141 (474) ...++|.|.-+-.. .-++|.-.|=.-...++.|.. |. .+...++. .++..+|+|+.. T Consensus 86 ~G~VlLsG~V~s~~~k~~A~~iA~~V~GV~~V~NeL~V~~~~~~s~~~~a~D~-~ITtkvKa~Ll~d~~v~s~~i~V~T~ 164 (203) T PRK10568 86 QKVVTLSGFVESQAQAEEAVKVAKGVEGVTSVSDKLHVRDAKEGSVKGYAGDT-ATTSEIKAKLLADDIVPSRKVKVETT 164 (203) T ss_pred CCEEEEEEECCCHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCCCCCCHH-HHHHHHHHHHHCCCCCCCEEEEEEEE T ss_conf 58899974069999999999998528982388766897058886501236509-99999999863178877258899996 Q ss_pred CCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEC Q ss_conf 8949999971999999999999998612234555556654430355432 Q gi|254780727|r 142 SDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNI 190 (474) Q Consensus 142 ~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v 190 (474) ++.+.|.|.|.+..+++++.++|+...+- .+|.|.|.| T Consensus 165 nGvV~L~G~V~s~~E~~rA~~iAr~V~GV-----------k~V~N~l~V 202 (203) T PRK10568 165 DGVVQLSGTVDSQAQSDRAESIAKAVDGV-----------KSVKNDLKV 202 (203) T ss_pred CEEEEEEEEECCHHHHHHHHHHHHCCCCC-----------EEEEEEEEE T ss_conf 53999999989999999999998549996-----------088876898 No 18 >COG2823 OsmY Predicted periplasmic or secreted lipoprotein [General function prediction only] Probab=95.34 E-value=0.029 Score=31.39 Aligned_cols=51 Identities=35% Similarity=0.479 Sum_probs=41.4 Q ss_pred HCCCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECC Q ss_conf 57877169998389499999719999999999999986122345555566544303554327 Q gi|254780727|r 130 FIADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIA 191 (474) Q Consensus 130 ~~p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~ 191 (474) .++.++|+|...++.+.|.|.|++..++++|.++|....+- .+|+|.+++. T Consensus 145 ~v~s~~IkV~t~~g~V~L~G~V~s~~e~~~A~~~A~~v~GV-----------k~V~~~l~i~ 195 (196) T COG2823 145 NVKSSNIKVETENGEVYLSGLVDSQEEAERAEEIASKVSGV-----------KKVVNDLKIK 195 (196) T ss_pred CCCCCEEEEEEECCEEEEEEEECCHHHHHHHHHHHHCCCCH-----------HHHHHHHCCC T ss_conf 78730489999898999987748999999999998629778-----------8886444406 No 19 >PRK10568 periplasmic protein; Provisional Probab=95.33 E-value=0.065 Score=29.33 Aligned_cols=48 Identities=21% Similarity=0.337 Sum_probs=40.3 Q ss_pred CCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCC Q ss_conf 71699983894999997199999999999999861223455555665443035543277 Q gi|254780727|r 134 SNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIAG 192 (474) Q Consensus 134 ~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~~ 192 (474) .+|.|+..++.+.|+|.|++..++.+|.++|...-+- ..|.|.|+|+. T Consensus 78 ~~I~V~t~~G~VlLsG~V~s~~~k~~A~~iA~~V~GV-----------~~V~NeL~V~~ 125 (203) T PRK10568 78 TDISVKTDQKVVTLSGFVESQAQAEEAVKVAKGVEGV-----------TSVSDKLHVRD 125 (203) T ss_pred CEEEEEEECCEEEEEEECCCHHHHHHHHHHHHCCCCC-----------EEEEEEEEECC T ss_conf 1379999658899974069999999999998528982-----------38876689705 No 20 >PRK11198 hypothetical protein; Provisional Probab=81.78 E-value=3.2 Score=19.52 Aligned_cols=77 Identities=8% Similarity=0.085 Sum_probs=50.3 Q ss_pred CHHHHHHHHHHHC-CCCCEE-EEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCEE Q ss_conf 4147899999857-877169-99838949999971999999999999998612234555556654430355432777227 Q gi|254780727|r 119 DIAHLEMTLRRFI-ADSNIR-VEMVSDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQYANSSSKKVMNLLNIAGEDQV 196 (474) Q Consensus 119 d~~~l~~~l~~~~-p~~~i~-v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~vvn~l~v~~~~QV 196 (474) ....+...|..+- |..+.. +..-++++.++|.+.+.+..+++.-.+....+- .+|-+.+.|..+. T Consensus 26 ~a~~l~~~i~~~gl~~~~~~~~~~~~~~v~vsG~a~~q~~~EKiila~GNv~Gv-----------~~V~d~~~v~~~~-- 92 (147) T PRK11198 26 AADALKEHISKTGLPGADLVVVQVGDGKATVSGDAASQEAKEKIILAVGNIQGV-----------ASVDDQVKVATPA-- 92 (147) T ss_pred HHHHHHHHHHHCCCCCCCCEEEEECCCEEEEEEECCCHHHHHHHHEECCCCCCH-----------HHHCCCCCCCCCC-- T ss_conf 899999999983999778548985698699962008988874372100260253-----------3312565347999-- Q ss_pred EEEEEEEEEECHH Q ss_conf 9999999985001 Q gi|254780727|r 197 TLKVTIAEVRRDI 209 (474) Q Consensus 197 ~lev~i~EVs~~~ 209 (474) -+.+++.|.+-+ T Consensus 93 -~e~~~YtVq~GD 104 (147) T PRK11198 93 -PESQFYTVKSGD 104 (147) T ss_pred -CCCCEEEECCCC T ss_conf -998578979899 No 21 >pfam09911 DUF2140 Uncharacterized protein conserved in bacteria (DUF2140). This domain, found in various hypothetical prokaryotic proteins, has no known function. Probab=66.34 E-value=8.2 Score=17.17 Aligned_cols=24 Identities=29% Similarity=0.494 Sum_probs=17.5 Q ss_pred EEEEEEEEEEEEEECCCEEEEEEE Q ss_conf 887589999989815984999861 Q gi|254780727|r 310 HDYGVVLHFTPTVLSPGRIGLRIQ 333 (474) Q Consensus 310 ~~~Gi~L~vtP~V~~~g~I~L~i~ 333 (474) .++-+.|.|.|.|.+||.|.|+.. T Consensus 93 ~~V~~~l~F~P~V~~nGnv~Lk~~ 116 (187) T pfam09911 93 SKVPLYIYFEPTVLKNGNVLLKAK 116 (187) T ss_pred EEEEEEEEEEEEECCCCCEEEEEC T ss_conf 246489998159816998999856 No 22 >TIGR02268 TIGR02268 Myxococcus xanthus paralogous family TIGR02268; InterPro: IPR011754 This family consists of at least 8 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown.. Probab=62.65 E-value=9.6 Score=16.76 Aligned_cols=105 Identities=8% Similarity=0.055 Sum_probs=67.8 Q ss_pred HHHHHHHHHHHHHCCCCCCC-CCCCCCCCCCCCCCC--CCCEEEEEECCEEEEECCCCHHHEEECCCCEE-EEEEC--CC Q ss_conf 99999998545411465455-434643333223456--54027995072599953776330785373437-99971--69 Q gi|254780727|r 11 MMSIFLFSSNPSVAKLPPIK-EANAAVINISDVEIG--KGKKISIGLNKVIILQVPVDVQDVLVSDPTKA-DVVVH--SP 84 (474) Q Consensus 11 ~~~~~L~~~~~~~a~~~~~~-~~~~~~~~~~~~~~~--~~~~l~l~~g~s~~l~~~~~~~rV~V~dp~Va-dv~v~--s~ 84 (474) ++.++|++..+..|++++++ ...-..+.+.....+ +-..+.+.-|-+..+.|+.++.+--+.-+.-- -.+.+ +. T Consensus 1 ~~~~lLl~~~A~~AQp~at~r~~~~Rrv~v~a~~~~a~p~P~vr~~pg~~T~l~FD~~~~~~~~~~eg~eGRF~~~Dv~e 80 (308) T TIGR02268 1 LAAVLLLAGAAAEAQPSATARARRVRRVEVSAAAAGAEPPPEVRVAPGVSTTLLFDAPINREKLLLEGSEGRFRRLDVTE 80 (308) T ss_pred CHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEECCCCEEEEECCCCCCHHHCCCCCCCCCEEEECCCC T ss_conf 36411027164103876445885447988647643478997778769811788707744631436776557478851674 Q ss_pred CEEEEEEC----CCCEEEEEEECCCCCEEEEEEEE Q ss_conf 87999952----67227999988999778999873 Q gi|254780727|r 85 RTMYLFGK----NVGQANVILIGHDGKQMLNLDIL 115 (474) Q Consensus 85 ~~i~i~gk----~~G~T~l~v~~~~g~~~~~~~v~ 115 (474) ..|+|... .-+...|.++..||..+...... T Consensus 81 ~~L~LvP~~~~~~geR~~L~VrF~DGavP~rA~l~ 115 (308) T TIGR02268 81 EHLILVPSEALPEGERLELTVRFADGAVPARAVLE 115 (308) T ss_pred CEEEEECCCCCCCCCCEEEEEEECCCCCHHHHHHH T ss_conf 07888266202778710689986253203344332 No 23 >pfam06183 DinI DinI-like family. This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity. The structure of DinI is known. Probab=60.26 E-value=11 Score=16.51 Aligned_cols=46 Identities=17% Similarity=0.314 Sum_probs=35.2 Q ss_pred HHHHHHHHHHHCCCCCEEEEEEC-CEEEEEEEECCHHHHHHHHHHHHHH Q ss_conf 14789999985787716999838-9499999719999999999999986 Q gi|254780727|r 120 IAHLEMTLRRFIADSNIRVEMVS-DTVVLHGMVRTIQDSQRAVELSETF 167 (474) Q Consensus 120 ~~~l~~~l~~~~p~~~i~v~~~~-~~vvl~G~v~~~~~~~~~~~ia~~~ 167 (474) ..+|.+.|+..||+..|+|.... +.+-+.|..+ .+.+++.++.+.. T Consensus 10 ~~EL~kRl~~~fPd~~V~Vr~~s~n~l~v~g~~k--~dK~~i~eiLqE~ 56 (65) T pfam06183 10 QNELTKRIQSLYPDTVVSVRKGSANGLSVTGAAK--DDKERIMEILQET 56 (65) T ss_pred HHHHHHHHHHHCCCCEEEEEECCCCCEEECCCCH--HHHHHHHHHHHHH T ss_conf 9999998653389957987105679705438774--0399999999999 No 24 >PRK13861 type IV secretion system protein VirB9; Provisional Probab=57.37 E-value=12 Score=16.22 Aligned_cols=110 Identities=12% Similarity=0.218 Sum_probs=61.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCEEEEECC--CCHHHEEECCCCEEEEEE Q ss_conf 578999999999998545411465455434643333223456540279950725999537--763307853734379997 Q gi|254780727|r 4 LQRTFFTMMSIFLFSSNPSVAKLPPIKEANAAVINISDVEIGKGKKISIGLNKVIILQVP--VDVQDVLVSDPTKADVVV 81 (474) Q Consensus 4 ~~r~~~~~~~~~L~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~g~s~~l~~~--~~~~rV~V~dp~Vadv~v 81 (474) ||+.+.+++++++++..+.++..|.... .+..+..+.=...-.-.+.-..|.+..|.|. |.+..+.+||+.=-++.. T Consensus 2 mk~l~~~~~~~l~~~~~a~A~~~P~~s~-~D~Riq~v~Ynp~~V~~V~~~~G~~T~I~F~~dE~I~~v~~Gd~~~W~v~~ 80 (293) T PRK13861 2 IKKLFLTLACLLFAAIGALAEDTPAAGK-LDPRMRYLAYNPDQVVRLSTAVGATLVVTFGANETVTAVAVSNSKDLAALP 80 (293) T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCEEEEECCCCEEEEEEECCEEEEEEECCCCEEEEECCCCCCCEEEEC T ss_conf 0899999999998612667875698888-897717988088888999998746999998899879986158820148962 Q ss_pred CCCCEEEEEECCC-CEEEEEEE-CCC-CCEEEEEEEE Q ss_conf 1698799995267-22799998-899-9778999873 Q gi|254780727|r 82 HSPRTMYLFGKNV-GQANVILI-GHD-GKQMLNLDIL 115 (474) Q Consensus 82 ~s~~~i~i~gk~~-G~T~l~v~-~~~-g~~~~~~~v~ 115 (474) ..|.+++-.+.. -.|++.+. ..+ ++-.+.+++. T Consensus 81 -~gN~lfiKP~~~~~~tn~~v~T~~~~~kr~y~f~l~ 116 (293) T PRK13861 81 -RGNYLFFKASQVLPPQPVVVLTASDAGMRRYVFSIS 116 (293) T ss_pred -CCCEEEEEECCCCCCCCEEEEECCCCCEEEEEEEEE T ss_conf -787799966677899841898316788289999998 No 25 >PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Probab=54.60 E-value=5.5 Score=18.19 Aligned_cols=62 Identities=16% Similarity=0.284 Sum_probs=43.7 Q ss_pred EEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEEEEEEEEECE Q ss_conf 99999985899899997665310132125711201761200016564552115999999051 Q gi|254780727|r 356 ADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREETEIFIAATPF 417 (474) Q Consensus 356 ~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~tELvI~iTP~ 417 (474) ...++.+.|..++-|.+--++........|=.+-.-|-+|..|..+=..-.+-=-+|-+-|- T Consensus 583 tg~~Idi~ddG~v~i~~~~~~~~~~A~~~I~~i~~~~evG~iy~g~V~~i~~fGafve~~pg 644 (694) T PRK11824 583 TGAKIDIEDDGTVKIAASDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEILPG 644 (694) T ss_pred HCCEEEEECCCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEECEEEEEECCC T ss_conf 89889996891799998999999999999998457685897799999999844189996799 No 26 >KOG1249 consensus Probab=52.57 E-value=13 Score=16.03 Aligned_cols=60 Identities=33% Similarity=0.437 Sum_probs=34.8 Q ss_pred EEEEEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCEEEEEEEE-EEEEECCCCEEEEEEEEEEEECCC Q ss_conf 7589999989815984999861232034455556653216789999-999985899899997665310132 Q gi|254780727|r 312 YGVVLHFTPTVLSPGRIGLRIQTEVSEPVIGVNAGDMPSYRVRKAD-TTVELPSGGTIVLAGLLKDDIQQL 381 (474) Q Consensus 312 ~Gi~L~vtP~V~~~g~I~L~i~~evS~~~~~~~~~~~P~i~~R~~~-T~V~l~~Get~vIgGL~~~~~~~~ 381 (474) .|=.+-=||=++.+++|...+..| |. ... .| +|++. -++.++.|+|+.||||.+-+.-+. T Consensus 361 ~~~w~YDTPG~~~~~q~~~llt~e--El-~~v----~p---~~~lrprtf~vkpG~sl~iGGl~RLDilqa 421 (572) T KOG1249 361 RGAWLYDTPGVLNPNQILSLLTSE--EL-LNV----TP---RRVLRPRTFRVKPGYSLFIGGLVRLDILQA 421 (572) T ss_pred CCCEEECCCCCCCHHHHHHHCCHH--HH-HHC----CC---CCCCCCCEEECCCCCEEEEEEEEEEEHHHC T ss_conf 652551588756754654341687--76-314----73---110166127737884799710578653340 No 27 >pfam03958 Secretin_N Bacterial type II/III secretion system short domain. This is a short, often repeated, domain found in bacterial type II/III secretory system proteins. All previous NolW-like domains fall into this family. Probab=52.20 E-value=15 Score=15.72 Aligned_cols=49 Identities=12% Similarity=0.225 Sum_probs=36.0 Q ss_pred CCCCHHHHHHHHHHHC-------CCCCEEEEEECCEEEEEEEECCHHHHHHHHHHHHHH Q ss_conf 0454147899999857-------877169998389499999719999999999999986 Q gi|254780727|r 116 IERDIAHLEMTLRRFI-------ADSNIRVEMVSDTVVLHGMVRTIQDSQRAVELSETF 167 (474) Q Consensus 116 v~~d~~~l~~~l~~~~-------p~~~i~v~~~~~~vvl~G~v~~~~~~~~~~~ia~~~ 167 (474) ...++.++...|+.++ +...+.+++..++++++|. +...+++.++.+.. T Consensus 7 ~~~~a~~l~~~L~~~~~~~~~~~~~~~v~~~~~~n~liv~g~---~~~~~~v~~li~~l 62 (68) T pfam03958 7 KYASAEDLASALRALLGGSGLLSKRGSVVADPRTNSLIVSGP---PEYVERIRQLIKQL 62 (68) T ss_pred ECCCHHHHHHHHHHHCCCCCCCCCCCEEEEECCCCEEEEECC---HHHHHHHHHHHHHH T ss_conf 476599999999985366555689836999688777999829---99999999999985 No 28 >pfam05046 Img2 Mitochondrial large subunit ribosomal protein (Img2). This family of proteins have been identified as part of the mitochondrial large ribosomal subunit in yeast. Probab=51.38 E-value=15 Score=15.65 Aligned_cols=48 Identities=27% Similarity=0.401 Sum_probs=37.5 Q ss_pred CCCEEEEEEEECCCCHHHHHHHHHHHCCC---CCEEEEEECCEEEEEEEEC Q ss_conf 99778999873045414789999985787---7169998389499999719 Q gi|254780727|r 105 DGKQMLNLDILIERDIAHLEMTLRRFIAD---SNIRVEMVSDTVVLHGMVR 152 (474) Q Consensus 105 ~g~~~~~~~v~v~~d~~~l~~~l~~~~p~---~~i~v~~~~~~vvl~G~v~ 152 (474) .|....+.--.+..|..+|++.|++.++. ..+.|.+..+.+.++|... T Consensus 23 ~g~~~~T~IRkI~GDi~~L~~dL~~~L~~~~~~~~~V~e~~g~i~ikG~~~ 73 (85) T pfam05046 23 GGTKIITEIRKIEGDIWALRRDLREFLGEIPKIDVRVNELSGKIEIKGDRV 73 (85) T ss_pred CCCEEEEEEEEECCCHHHHHHHHHHHHHHCCCCCEEEEEECCEEEEECCCH T ss_conf 993879999857176999999999987213688718997338999907568 No 29 >pfam07788 DUF1626 Protein of unknown function (DUF1626). This is a family consisting of sequences from hypothetical proteins of unknown function expressed by certain species of archaebacteria. One member is thought to be similar to tropomyosin. Probab=49.47 E-value=9.4 Score=16.81 Aligned_cols=54 Identities=15% Similarity=0.218 Sum_probs=28.6 Q ss_pred EEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCEE-EEEEEEECEEC Q ss_conf 99999985899899997665310132125711201761200016564552115-99999905150 Q gi|254780727|r 356 ADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREET-EIFIAATPFLV 419 (474) Q Consensus 356 ~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~t-ELvI~iTP~iV 419 (474) ++--+-++||.++++- ...+.++ ||++++..--.--.+..+++ .-+|+|||.+= T Consensus 3 VE~DviikdG~~ilvE------ikSs~~r----~Dv~~~~rK~~~Yek~~grk~~rlivItP~id 57 (70) T pfam07788 3 VELDVVVKDGVHILVE------IKSSLSR----GDLAVIKRKGELYEKAKGRKVDRLIVVTPFID 57 (70) T ss_pred EEEEEEEECCCEEEEE------EECCCCH----HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCC T ss_conf 3799999779599999------8436862----33599999999999986887762899846659 No 30 >PRK00794 flbT flagellar biosynthesis repressor FlbT; Reviewed Probab=48.99 E-value=16 Score=15.42 Aligned_cols=34 Identities=24% Similarity=0.347 Sum_probs=20.9 Q ss_pred EEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCE Q ss_conf 999858998999976653101321257112017612 Q gi|254780727|r 359 TVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPIL 394 (474) Q Consensus 359 ~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPil 394 (474) .++||+||-++|+|-.=.+. ....+=++.|.|+| T Consensus 5 kl~LKpgERi~INGAVi~nd--rr~~l~i~n~a~iL 38 (133) T PRK00794 5 VLSLKPGERIFINGAVLRND--RKVRLELLNDATFL 38 (133) T ss_pred EEEECCCCEEEECCEEEECC--CEEEEEEEECCCCH T ss_conf 79856998899848499828--80589997067010 No 31 >PRK10838 spr putative outer membrane lipoprotein; Provisional Probab=48.96 E-value=16 Score=15.42 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=18.0 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 93357899999999999854541 Q gi|254780727|r 1 MRYLQRTFFTMMSIFLFSSNPSV 23 (474) Q Consensus 1 ~~~~~r~~~~~~~~~L~~~~~~~ 23 (474) ||++-|.+++.+++.|++++... T Consensus 7 ~r~~l~~~~~~~~~~~l~ac~~~ 29 (188) T PRK10838 7 LRYILRGIPAIAVAVLLSACSSN 29 (188) T ss_pred HHHHHHHHHHHHHHHHHHHHCCC T ss_conf 99999871799999988863389 No 32 >PRK13796 GTP-binding protein YqeH; Provisional Probab=48.57 E-value=17 Score=15.38 Aligned_cols=24 Identities=29% Similarity=0.286 Sum_probs=19.5 Q ss_pred EEEEECCCCEEEEEEEEEEEECCC Q ss_conf 999985899899997665310132 Q gi|254780727|r 358 TTVELPSGGTIVLAGLLKDDIQQL 381 (474) Q Consensus 358 T~V~l~~Get~vIgGL~~~~~~~~ 381 (474) -+..+++|||+.||||.+-+..+. T Consensus 249 ~t~~l~~gqslfigGL~RiD~~~g 272 (367) T PRK13796 249 KTYQLNEEQTLFLGGLARFDYVSG 272 (367) T ss_pred EEEEECCCCEEEEEEEEEEEEECC T ss_conf 079967985899800899999538 No 33 >pfam09544 DUF2381 Protein of unknown function (DUF2381). This family consists of at least 8 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown. Probab=42.90 E-value=20 Score=14.86 Aligned_cols=94 Identities=15% Similarity=0.156 Sum_probs=51.8 Q ss_pred HHHHHHCCCCC-CCCCCCCCCCCCCCCCCCCCEEEEEECCEEEEECCCCHHH--EEECCCCEEEEEECCCCEEEEEECC- Q ss_conf 85454114654-5543464333322345654027995072599953776330--7853734379997169879999526- Q gi|254780727|r 18 SSNPSVAKLPP-IKEANAAVINISDVEIGKGKKISIGLNKVIILQVPVDVQD--VLVSDPTKADVVVHSPRTMYLFGKN- 93 (474) Q Consensus 18 ~~~~~~a~~~~-~~~~~~~~~~~~~~~~~~~~~l~l~~g~s~~l~~~~~~~r--V~V~dp~Vadv~v~s~~~i~i~gk~- 93 (474) ...++.|..++ ........+........+...+.+.-|.+.++-|+.++.+ +.+-+..--...-...+.+.|.... T Consensus 4 ~~~~A~Aq~~~~~~~~~~R~i~l~~~~~~p~peV~Vapg~~T~llFdapi~~~~~~~egr~Rf~~vd~g~~~l~L~p~~~ 83 (289) T pfam09544 4 WGTAARAQPAPPAREPRVRRVTLSAGPAEPPPEVRVAPGVPTVLLFDAPIRRETLTVEGRGRFRVVDVGERTLILVPVED 83 (289) T ss_pred CCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEECCCCCEEEEECCCCCCCCEEECCCCEEEEECCCCCEEEEEECCC T ss_conf 05500037787656541357994378889896699769961699846755646236725445897126775799988432 Q ss_pred --CC-EEEEEEECCCCCEEEE Q ss_conf --72-2799998899977899 Q gi|254780727|r 94 --VG-QANVILIGHDGKQMLN 111 (474) Q Consensus 94 --~G-~T~l~v~~~~g~~~~~ 111 (474) +| .-.|.+...+|..+.+ T Consensus 84 L~~gERl~L~V~F~DG~~P~~ 104 (289) T pfam09544 84 LAEGERLELTVRFADGAAPAR 104 (289) T ss_pred CCCCCCEEEEEEECCCCCCCC T ss_conf 688873579999747887632 No 34 >pfam02368 Big_2 Bacterial Ig-like domain (group 2). This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial and phage surface proteins such as intimins. Probab=40.55 E-value=22 Score=14.65 Aligned_cols=58 Identities=19% Similarity=0.115 Sum_probs=41.2 Q ss_pred EEEEEECCEEEEEC---CCCH----HHEEECCCCEEEEEECCCCEEEEEECCCCEEEEEEECCCCCEE Q ss_conf 27995072599953---7763----3078537343799971698799995267227999988999778 Q gi|254780727|r 49 KISIGLNKVIILQV---PVDV----QDVLVSDPTKADVVVHSPRTMYLFGKNVGQANVILIGHDGKQM 109 (474) Q Consensus 49 ~l~l~~g~s~~l~~---~~~~----~rV~V~dp~Vadv~v~s~~~i~i~gk~~G~T~l~v~~~~g~~~ 109 (474) .+.|.+|.+..+.. |.+. -.-.-+||+||.+.. ..-.+.|.++|++++.+...+|... T Consensus 11 ~~~l~~G~t~ql~a~~~p~~a~~~~vtw~Ssn~~vAtVd~---~~G~Vta~~~G~a~Itat~~d~~~~ 75 (79) T pfam02368 11 VASLLKGATLQLGATVLPSDASNGKVTWSSSNTSIATVSG---STGLVTALAKGTATITATSGDNQSA 75 (79) T ss_pred CCEEECCCEEEEEEEEEECCCCCCEEEEEECCCCEEEEEC---CCCEEEEEECEEEEEEEEECCCCEE T ss_conf 3289049879999999846678855999989999899989---9888999827189999996999868 No 35 >pfam07378 FlbT Flagellar protein FlbT. This family consists of several FlbT proteins. FlbT is a post-transcriptional regulator of flagellin. FlbT is associated with the 5' untranslated region (UTR) of fljK (25 kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolish FlbT association and result in increased mRNA stability. It is therefore thought that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR. Probab=40.01 E-value=23 Score=14.60 Aligned_cols=35 Identities=20% Similarity=0.408 Sum_probs=18.1 Q ss_pred EEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCE Q ss_conf 999858998999976653101321257112017612 Q gi|254780727|r 359 TVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPIL 394 (474) Q Consensus 359 ~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPil 394 (474) .++||+||-++|+|-.=.+. .....+=++++.|+| T Consensus 2 kl~LKp~Eri~INGAVi~Ng-drr~~l~i~n~a~iL 36 (126) T pfam07378 2 KLSLKPGERIIINGAVIRNG-DRRSRLEIENDAPIL 36 (126) T ss_pred EEEECCCCEEEECCEEEEEC-CCCEEEEEECCCCEE T ss_conf 35607998899858588707-973489996178131 No 36 >COG4698 Uncharacterized protein conserved in bacteria [Function unknown] Probab=37.77 E-value=25 Score=14.39 Aligned_cols=20 Identities=40% Similarity=0.690 Sum_probs=13.3 Q ss_pred EEEEEEEEEECCCEEEEEEE Q ss_conf 89999989815984999861 Q gi|254780727|r 314 VVLHFTPTVLSPGRIGLRIQ 333 (474) Q Consensus 314 i~L~vtP~V~~~g~I~L~i~ 333 (474) +-+.|.|+|.+||.|.|.+. T Consensus 105 l~I~f~P~v~~NG~i~L~V~ 124 (197) T COG4698 105 LYIYFEPTVLQNGDIELSVT 124 (197) T ss_pred EEEEECCEEECCCCEEEEEE T ss_conf 79997415613896899988 No 37 >pfam11492 Dicistro_VP4 Cricket paralysis virus, VP4. This is a family of minor capsid proteins, known as VP4, from the dicistroviridae. The dicistroviridae is a group of small, RNA-containing viruses that are closely structurally related to the picornaviridae. VP4 is a short, extended polypeptide chain found within the viral capsid, at the interface between the external protein shell and packaged RNA genome. Probab=37.57 E-value=11 Score=16.45 Aligned_cols=16 Identities=31% Similarity=0.702 Sum_probs=12.3 Q ss_pred CCEECCCCEEECCCCC Q ss_conf 1120176120001656 Q gi|254780727|r 386 PLLSKIPILGALFRNS 401 (474) Q Consensus 386 P~LgdIPilG~LF~s~ 401 (474) -.|.+||+||..|+-. T Consensus 25 ~~ls~IPvig~~aka~ 40 (56) T pfam11492 25 SALSSIPVIGNIAKAT 40 (56) T ss_pred HHCCCCCCCCCHHHHH T ss_conf 6601686012101048 No 38 >pfam09133 SANTA SANTA (SANT Associated). The SANTA domain (SANT Associated domain) is approximately 90 amino acids in length and is conserved in Eukaryota. It is sometimes found in association with the SANT domain (pfam00249, also known as Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha- helixes. Many conserved hydrophobic residues are present which implying a possible role in protein-protein interactions. Probab=35.03 E-value=21 Score=14.78 Aligned_cols=37 Identities=35% Similarity=0.466 Sum_probs=27.0 Q ss_pred CEEEEEEEEEEEEECCCCEEEEEEEEEEEECCCCCCCC Q ss_conf 21678999999998589989999766531013212571 Q gi|254780727|r 349 PSYRVRKADTTVELPSGGTIVLAGLLKDDIQQLKEGIP 386 (474) Q Consensus 349 P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP 386 (474) -.|.+|-..++++-.||-++.|.|.+.. .....+|.| T Consensus 34 ~~IvkR~~~~~l~T~dG~~~~L~G~in~-~~~~~nGfs 70 (93) T pfam09133 34 NFIVKRHSSTTLETVDGITYVLVGFIDR-SRMLKNGFP 70 (93) T ss_pred HHHHEEECCCEEEECCCEEEEEECCCCH-HHHHHCCCC T ss_conf 5541001243799258709999465688-889885999 No 39 >TIGR03597 GTPase_YqeH ribosome biogenesis GTPase YqeH. This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli. Probab=34.85 E-value=28 Score=14.11 Aligned_cols=59 Identities=20% Similarity=0.260 Sum_probs=32.4 Q ss_pred EEEEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEECC Q ss_conf 58999998981598499986123203445555665321678999999998589989999766531013 Q gi|254780727|r 313 GVVLHFTPTVLSPGRIGLRIQTEVSEPVIGVNAGDMPSYRVRKADTTVELPSGGTIVLAGLLKDDIQQ 380 (474) Q Consensus 313 Gi~L~vtP~V~~~g~I~L~i~~evS~~~~~~~~~~~P~i~~R~~~T~V~l~~Get~vIgGL~~~~~~~ 380 (474) |..+-=||=+..++++.-.+.++ +... -.|. ++--.-+..+++|||+.||||.+-+.-+ T Consensus 205 ~~~i~DTPGi~~~~q~~~~L~~~--~lk~-----i~p~--k~i~p~t~~l~~gqslfiGGL~rid~~~ 263 (360) T TIGR03597 205 GHSLYDTPGIINSHQMAHYLDKK--DLKY-----ITPK--KEIKPKTYQLNPNQTLFLGGLARFDYLK 263 (360) T ss_pred CCEEECCCCCCCHHHHHHHCCHH--HHHH-----CCCC--CCCCCEEEEECCCCEEEECCEEEEEEEC T ss_conf 95574577655742755544998--8742-----1776--5106527897897289993389999814 No 40 >TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family). Probab=33.46 E-value=16 Score=15.45 Aligned_cols=52 Identities=12% Similarity=0.228 Sum_probs=39.1 Q ss_pred EEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCCCCCCCE Q ss_conf 9999998589989999766531013212571120176120001656455211 Q gi|254780727|r 356 ADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNSRFNREE 407 (474) Q Consensus 356 ~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~~~~~~~ 407 (474) ...++.+.|..++-|.+--++........|=.+-.-|-+|..|..+=..-.+ T Consensus 580 tg~~I~i~ddG~v~i~~~~~~~~~~A~~~I~~~~~~~evG~~y~g~V~~i~~ 631 (684) T TIGR03591 580 TGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMD 631 (684) T ss_pred HCCEEEEECCCEEEEEECCHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEE T ss_conf 8988998589089999899999999999999851668589779999999984 No 41 >COG2982 AsmA Uncharacterized protein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane] Probab=30.51 E-value=33 Score=13.69 Aligned_cols=73 Identities=21% Similarity=0.309 Sum_probs=37.8 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC-CCCCEEEE--EECCEEEEECCCCHHHEEECCC Q ss_conf 93357899999999999854541146545543464333322345-65402799--5072599953776330785373 Q gi|254780727|r 1 MRYLQRTFFTMMSIFLFSSNPSVAKLPPIKEANAAVINISDVEI-GKGKKISI--GLNKVIILQVPVDVQDVLVSDP 74 (474) Q Consensus 1 ~~~~~r~~~~~~~~~L~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~l~l--~~g~s~~l~~~~~~~rV~V~dp 74 (474) ||.|+|++..++++.++..+...+-.+-..+ ............ ...+.+.+ .++-+.--...-...++.+++| T Consensus 1 ~~~~~~~l~~~l~~~i~~ia~~~~~~~lf~p-N~~k~~i~q~v~a~t~~~l~i~Gdi~w~~~P~~~v~l~d~tLs~~ 76 (648) T COG2982 1 MRRMRKVLVSLLGILILVIALLAAVLPLFDP-NDFKDTIVQQVSAATGRPLAINGDLGWRLWPWPSVILEDITLSNP 76 (648) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCEECCCCEECCC T ss_conf 9307788999999999999999998652682-200089999999985896466167644227765025034263488 No 42 >PRK12696 flgH flagellar basal body L-ring protein; Reviewed Probab=27.45 E-value=37 Score=13.37 Aligned_cols=21 Identities=10% Similarity=0.262 Sum_probs=15.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHC Q ss_conf 578999999999998545411 Q gi|254780727|r 4 LQRTFFTMMSIFLFSSNPSVA 24 (474) Q Consensus 4 ~~r~~~~~~~~~L~~~~~~~a 24 (474) |+|.+..++++++++.+.+.. T Consensus 2 m~~~l~~~~~~~~L~GC~~~~ 22 (238) T PRK12696 2 IRKLLAASCAVLLLSGCNAAR 22 (238) T ss_pred HHHHHHHHHHHHHHHCCCCCC T ss_conf 589999999999951656888 No 43 >TIGR02186 alph_Pro_TM conserved hypothetical protein; InterPro: IPR011734 This family consists of predicted transmembrane proteins of about 270 amino acids. Members are found, so far, only among the Alphaproteobacteria and only once in each genome.. Probab=26.64 E-value=38 Score=13.29 Aligned_cols=107 Identities=12% Similarity=0.099 Sum_probs=59.3 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCEEEEECCCCHHHEEECCCCEEEEEECCCCEE Q ss_conf 99999999998545411465455434643333223456540279950725999537763307853734379997169879 Q gi|254780727|r 8 FFTMMSIFLFSSNPSVAKLPPIKEANAAVINISDVEIGKGKKISIGLNKVIILQVPVDVQDVLVSDPTKADVVVHSPRTM 87 (474) Q Consensus 8 ~~~~~~~~L~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~g~s~~l~~~~~~~rV~V~dp~Vadv~v~s~~~i 87 (474) +.+++++.|+.+..+.+..+.++-..-+ .....+.....++| .|-+++.+|+=..--+..++ T Consensus 1 ~r~Lla~~lv~~~g~~a~~a~aQ~~~~a-lPPGPQ~~p~~E~l-----------------eig~St~~i~itsnF~G~~L 62 (275) T TIGR02186 1 LRALLAAVLVLLLGAAATVAAAQVLELA-LPPGPQVRPLEERL-----------------EIGVSTEEIAITSNFRGADL 62 (275) T ss_pred CCHHHHHHHHHHHCCCCCCHHHCCCCCC-CCCCCCCCCCCEEE-----------------EEEEECCEEEECCCCCCCCE T ss_conf 9447899999863002476224264102-77778888743016-----------------88653575651568898760 Q ss_pred EEEECCCCEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEECC--EEEEEE Q ss_conf 99952672279999889997789998730454147899999857877169998389--499999 Q gi|254780727|r 88 YLFGKNVGQANVILIGHDGKQMLNLDILIERDIAHLEMTLRRFIADSNIRVEMVSD--TVVLHG 149 (474) Q Consensus 88 ~i~gk~~G~T~l~v~~~~g~~~~~~~v~v~~d~~~l~~~l~~~~p~~~i~v~~~~~--~vvl~G 149 (474) -|||--.+...+.. +. ..||+.|.-. =|..++.|+.+.. .|++-- T Consensus 63 tlFGa~~~~d~~~~--~~----g~YdivV~l~-----------GP~~~~vvRkKeR~~GiWiNt 109 (275) T TIGR02186 63 TLFGALDNADPLLL--AQ----GKYDIVVTLE-----------GPRDDMVVRKKERVFGIWINT 109 (275) T ss_pred EEEECCCCCCCCHH--HC----CCCCEEEEEE-----------CCCCCCEEEEECCEEEEEECC T ss_conf 78601266330167--53----6953799975-----------787771361210276577615 No 44 >COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Probab=26.22 E-value=39 Score=13.24 Aligned_cols=46 Identities=15% Similarity=0.351 Sum_probs=25.9 Q ss_pred EEEEEEECCCCEEEEEEEEEEEECCCCCCCCCEECCCCEEECCCCC Q ss_conf 9999998589989999766531013212571120176120001656 Q gi|254780727|r 356 ADTTVELPSGGTIVLAGLLKDDIQQLKEGIPLLSKIPILGALFRNS 401 (474) Q Consensus 356 ~~T~V~l~~Get~vIgGL~~~~~~~~~~~vP~LgdIPilG~LF~s~ 401 (474) ....+.+.+-.|+-|++--.+.....+..+-.+-.-+-+|..|..+ T Consensus 581 tg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~ 626 (692) T COG1185 581 TGVKIDIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGT 626 (692) T ss_pred HCCEEEECCCCCEEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEE T ss_conf 4767984589858999565688899999999987431015289988 No 45 >PRK09915 putative outer membrane efflux protein MdtP; Provisional Probab=23.92 E-value=43 Score=12.98 Aligned_cols=27 Identities=7% Similarity=0.205 Sum_probs=17.8 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 789999999999985454114654554 Q gi|254780727|r 5 QRTFFTMMSIFLFSSNPSVAKLPPIKE 31 (474) Q Consensus 5 ~r~~~~~~~~~L~~~~~~~a~~~~~~~ 31 (474) -|.|++++.|.++++....++|...+. T Consensus 3 ~~~~~r~~~~~~l~~~~lLagC~~~p~ 29 (488) T PRK09915 3 NRQLSRLLLCSILGSTTLISGCALVRK 29 (488) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 157769999999999999752668999 No 46 >smart00635 BID_2 Bacterial Ig-like domain 2. Probab=23.75 E-value=44 Score=12.96 Aligned_cols=57 Identities=21% Similarity=0.276 Sum_probs=37.9 Q ss_pred EEEEECCEEEEEC---CCCH-----HHEEECCCCEEEEEECCCCEEEEEECCCCEEEEEEECCCCCE Q ss_conf 7995072599953---7763-----307853734379997169879999526722799998899977 Q gi|254780727|r 50 ISIGLNKVIILQV---PVDV-----QDVLVSDPTKADVVVHSPRTMYLFGKNVGQANVILIGHDGKQ 108 (474) Q Consensus 50 l~l~~g~s~~l~~---~~~~-----~rV~V~dp~Vadv~v~s~~~i~i~gk~~G~T~l~v~~~~g~~ 108 (474) +.|..|.+..+.. |... -+...+||+||.+. +.+.+.+.|.++|.+++.+...++.. T Consensus 12 ~~l~~G~t~~l~a~~~p~~a~~~~~vtw~Ssn~~vAtV~--~~~G~~vta~~~G~atItat~~dg~~ 76 (81) T smart00635 12 ASVKKGLTLQLTATVTPSSAKVTGKVTWTSSNPSVATVV--NASGLVVTAVAAGTATITATSGDGSS 76 (81) T ss_pred CEECCCCEEEEEEEECCCCCCCCCCEEEEECCCCEEEEE--CCCCEEEEEEECCEEEEEEEECCCCC T ss_conf 627149889999998046667686269980899789998--69982999980426899999168973 No 47 >PHA02358 hypothetical protein Probab=23.38 E-value=19 Score=15.09 Aligned_cols=14 Identities=43% Similarity=0.686 Sum_probs=9.4 Q ss_pred CCCEECCCCEEECC Q ss_conf 71120176120001 Q gi|254780727|r 385 IPLLSKIPILGALF 398 (474) Q Consensus 385 vP~LgdIPilG~LF 398 (474) .|.|+.||++|||- T Consensus 154 aPa~s~IP~VGWva 167 (194) T PHA02358 154 APALSSIPFVGWVA 167 (194) T ss_pred CCHHHCCCHHHHHH T ss_conf 20320797078899 No 48 >PRK10719 eutA reactivating factor for ethanolamine ammonia lyase; Provisional Probab=23.31 E-value=44 Score=12.91 Aligned_cols=60 Identities=13% Similarity=0.059 Sum_probs=47.0 Q ss_pred CCCCHHHHHHHHHHHCCCCCEEEEEE-CCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 04541478999998578771699983-8949999971999999999999998612234555 Q gi|254780727|r 116 IERDIAHLEMTLRRFIADSNIRVEMV-SDTVVLHGMVRTIQDSQRAVELSETFLSQSGRNQ 175 (474) Q Consensus 116 v~~d~~~l~~~l~~~~p~~~i~v~~~-~~~vvl~G~v~~~~~~~~~~~ia~~~~~~~~~~~ 175 (474) ...|...+++.+.+.+..+.++-+.. .+.++++|....-+.+..+.+....+.++-.... T Consensus 61 ~~ID~~~i~~~i~~qy~~Agi~p~dI~tGAVIITGEtaRk~NA~~i~~~ls~~aGdFVvAT 121 (471) T PRK10719 61 GGIDEAAIKELIEEQYQAAGIAPESIDSGAVIITGETARKENARPVVMALSGSAGDFVVAT 121 (471) T ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCEEEEE T ss_conf 7327999999999999984999888763409996455524349999999887569779971 No 49 >pfam09796 QCR10 Ubiquinol-cytochrome-c reductase complex subunit (QCR10). The QCR10 family of proteins are a component of the ubiquinol-cytochrome c reductase complex (also known as complex III or cytochrome b-c1 complex). This complex is located on the inner mitochondrial membrane and it couples electron transfer from ubiquinol to cytochrome. This subunit (QCR10) is required for stable association of the iron-sulfur protein with the complex. Probab=22.47 E-value=27 Score=14.15 Aligned_cols=15 Identities=33% Similarity=0.868 Sum_probs=10.1 Q ss_pred CEECCCCEEECCCCC Q ss_conf 120176120001656 Q gi|254780727|r 387 LLSKIPILGALFRNS 401 (474) Q Consensus 387 ~LgdIPilG~LF~s~ 401 (474) +|.+||++|.-|..+ T Consensus 42 il~KIP~~g~~~~~~ 56 (64) T pfam09796 42 ILQKIPVFGSYWERE 56 (64) T ss_pred HHHHCCCCCCHHCCC T ss_conf 987277543100347 No 50 >PRK10503 multidrug efflux system subunit MdtB; Provisional Probab=21.54 E-value=48 Score=12.70 Aligned_cols=19 Identities=21% Similarity=0.331 Sum_probs=12.2 Q ss_pred EEEECHHHHHCCCEEEECC Q ss_conf 9985001442261210014 Q gi|254780727|r 203 AEVRRDILKQIGFQHSITG 221 (474) Q Consensus 203 ~EVs~~~~~~lGi~w~~~~ 221 (474) ++++++...++|++-.... T Consensus 720 i~idr~~a~~~Glt~~~v~ 738 (1040) T PRK10503 720 VNVDRDSASRLGISMADVD 738 (1040) T ss_pred EECCHHHHHHCCCCHHHHH T ss_conf 8448888986699878876 No 51 >COG1079 Uncharacterized ABC-type transport system, permease component [General function prediction only] Probab=20.22 E-value=40 Score=13.16 Aligned_cols=21 Identities=10% Similarity=0.194 Sum_probs=9.2 Q ss_pred EEEEEEEEEEECHHHHHCCCE Q ss_conf 799999999850014422612 Q gi|254780727|r 196 VTLKVTIAEVRRDILKQIGFQ 216 (474) Q Consensus 196 V~lev~i~EVs~~~~~~lGi~ 216 (474) .-++.|-+--+-...+..|+| T Consensus 165 ~GL~lravGE~P~aad~~Gi~ 185 (304) T COG1079 165 FGLRLRAVGENPAAADAMGIN 185 (304) T ss_pred CCEEEEEECCCHHHHHHCCCC T ss_conf 466999826982678867987 Done!