Query gi|254780571|ref|YP_003064984.1| hypothetical protein CLIBASIA_02290 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 182 No_of_seqs 111 out of 492 Neff 8.9 Searched_HMMs 39220 Date Mon May 30 00:49:25 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780571.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG4961 TadG Flp pilus assembl 99.9 1.2E-20 3E-25 143.1 15.2 178 1-182 5-185 (185) 2 pfam07811 TadE TadE-like prote 98.9 5.1E-09 1.3E-13 73.0 5.9 43 17-59 1-43 (43) 3 COG3847 Flp Flp pilus assembly 97.8 0.00012 3E-09 46.8 7.1 36 4-39 1-36 (58) 4 pfam04964 Flp_Fap Flp/Fap pili 95.9 0.0095 2.4E-07 35.2 3.6 28 11-38 1-28 (47) 5 COG4655 Predicted membrane pro 95.6 0.11 2.7E-06 28.9 8.0 55 10-64 3-57 (565) 6 pfam04917 Shufflon_N Bacterial 94.6 0.2 5.1E-06 27.3 7.1 49 12-60 2-50 (356) 7 PRK10506 hypothetical protein; 93.4 0.39 9.9E-06 25.5 6.7 52 13-64 2-53 (155) 8 COG4970 FimT Tfp pilus assembl 90.8 1 2.6E-05 23.0 6.3 52 11-62 3-54 (181) 9 pfam05307 Bundlin Bundlin. Thi 89.5 0.79 2E-05 23.7 4.9 49 12-60 8-56 (97) 10 COG4966 PilW Tfp pilus assembl 85.3 0.56 1.4E-05 24.6 2.0 39 7-45 4-42 (318) 11 COG4537 ComGC Competence prote 77.2 2.7 6.8E-05 20.5 3.1 28 8-35 4-31 (107) 12 KOG3970 consensus 74.8 2 5.2E-05 21.2 2.0 12 128-139 184-195 (299) 13 COG1681 FlaB Archaeal flagelli 66.4 5 0.00013 18.9 2.5 53 14-66 1-55 (209) 14 pfam04021 Class_IIIsignal Clas 64.4 5.1 0.00013 18.8 2.2 22 15-36 1-22 (28) 15 PRK10913 dipeptide transporter 61.9 10 0.00027 16.9 4.3 32 3-36 18-49 (300) 16 TIGR01708 typeII_sec_gspH gene 59.4 7.1 0.00018 17.9 2.2 50 13-63 1-51 (175) 17 COG1991 Uncharacterized conser 56.8 0.75 1.9E-05 23.8 -3.1 30 7-36 4-33 (131) 18 COG2165 PulG Type II secretory 49.4 17 0.00043 15.7 7.4 49 13-61 5-53 (149) 19 PRK10332 hypothetical protein; 47.6 18 0.00046 15.5 5.6 54 12-65 5-58 (107) 20 pfam11688 DUF3285 Protein of u 38.5 25 0.00064 14.6 3.8 34 3-41 11-44 (45) 21 pfam12273 RCR Chitin synthesis 35.2 28 0.00072 14.3 2.2 16 22-37 4-19 (124) 22 TIGR01247 drrB daunorubicin re 35.1 25 0.00064 14.6 1.9 27 8-37 3-29 (240) 23 PRK08541 flagellin; Validated 34.0 30 0.00075 14.2 4.1 51 14-64 1-53 (212) 24 COG4726 PilX Tfp pilus assembl 32.6 31 0.00079 14.1 5.5 35 7-41 4-38 (196) 25 PRK10574 putative major pilin 28.4 37 0.00094 13.6 6.5 46 13-58 2-47 (146) 26 COG5605 Predicted small integr 27.6 38 0.00097 13.5 4.1 24 20-43 77-100 (115) 27 PRK09881 ATP-dependent peptide 24.3 44 0.0011 13.2 3.3 31 5-37 21-51 (296) 28 TIGR03061 pip_yhgE_Nterm YhgE/ 23.6 45 0.0012 13.1 3.4 27 8-34 3-29 (164) 29 KOG2856 consensus 22.2 48 0.0012 12.9 2.5 19 129-147 408-426 (472) No 1 >COG4961 TadG Flp pilus assembly protein TadG [Intracellular trafficking and secretion] Probab=99.87 E-value=1.2e-20 Score=143.06 Aligned_cols=178 Identities=13% Similarity=0.087 Sum_probs=114.7 Q ss_pred CHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH Q ss_conf 92479999975124455489999999999999999999999999999999999999999985288879788877999999 Q gi|254780571|r 1 MKCIKNYILRFLSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQETSINKQYLQGFENFLR 80 (182) Q Consensus 1 ~~~~~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~~~~~~~~~~~~~~~~~ 80 (182) +|..+.+.+||+||++|++||||||++|+||+++++++|++.+++.++.+++|+++++|.++++...+..+. ..+.. T Consensus 5 ~~~~~~~~~rF~rdr~Ga~AVeFAlvap~ll~l~~g~ve~~~~~~~~~~l~~a~d~aara~~~~~~~~~~~~---~~~~~ 81 (185) T COG4961 5 RRGLRGLLRRFRRDRRGAAAVEFALVAPPLLLLVFGIVEFGIAFLAKQSLQNAADAAARAAARGLTTDAADL---DTIQA 81 (185) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHH---HHHHH T ss_conf 265799999887648768999999999999999999999999999999999999999999985076442025---67789 Q ss_pred HHHHCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCC-CCCCEEEEEEEEEEEE--ECCCCCCCCCCC Q ss_conf 8752347887389999999537885278960467877763565666677-9996799999999623--112233445367 Q gi|254780571|r 81 ATMYPYRTPNHSIIVTGYWLDNKQIVRKMWNWSSSNVKVEREDIPASIK-DASTFIVRAEVSINYR--TLVFSKILPDSL 157 (182) Q Consensus 81 ~~~~~~~~~~~~~~i~~~~~~~~~~~~v~~s~~~~~~~~~~~~~p~~~~-~~~~~~v~v~v~y~y~--p~~~~~~~~~~~ 157 (182) ....++............+.+......++|+....+..... ..+.... .....+..++..+.+. +.+..+...... T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~-~~~~~v~~~~~~~~~~~~~~~~~~~v~~~t~~~~~~~~ 160 (185) T COG4961 82 AATAFLNAIAPANAFLTVQSNTPSRGTVTVTANVADATLFD-TSQFTVTSAVTVSINLARGLVLVAVVPDLTGPGTSGSR 160 (185) T ss_pred HHHHHHHHHCCCCEEECCCCCCCCCEEEEEECCCCCCCCCC-CCCEEEEECCCCEEECCCCCCEEEEEECCCCCCCCCCC T ss_conf 99988875164220121322455640589601312343367-76358961454202012355305787323476445551 Q ss_pred CCCEEEEEEEEECCCCCCCEECCCC Q ss_conf 7847899899974753473425899 Q gi|254780571|r 158 KGDIVLRKVYYYRQRLGDQIVCRDC 182 (182) Q Consensus 158 ~~~~~l~~t~~~rpR~~~~i~c~~c 182 (182) ..++.+.++.++++|....++|.+| T Consensus 161 ~~~i~~~~~~~~~~~~~~~~~~~~~ 185 (185) T COG4961 161 SATIPVGATTLVRVRIDETITPGID 185 (185) T ss_pred EEEEECCCEEEEEECCCCCCCCCCC T ss_conf 2453114104675312311367899 No 2 >pfam07811 TadE TadE-like protein. The members of this family are similar to a region of the protein product of the bacterial tadE locus. In various bacterial species, the tad locus is closely linked to flp-like genes, which encode proteins required for the production of pili involved in adherence to surfaces. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria. All tad loci but TadA have putative transmembrane regions, and in fact the region in question is this family has a high proportion of hydrophobic amino acid residues. Probab=98.86 E-value=5.1e-09 Score=72.96 Aligned_cols=43 Identities=33% Similarity=0.564 Sum_probs=41.9 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5489999999999999999999999999999999999999999 Q gi|254780571|r 17 GVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGD 59 (182) Q Consensus 17 G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar 59 (182) |+++|||+|++|+|++++++++|++++++.++.+++|+++++| T Consensus 1 G~a~VEfalv~p~~l~l~~~~~~~~~~~~~~~~~~~Aa~~aaR 43 (43) T pfam07811 1 GAAAVEFALVLPVLLLLLFGIVELGRLFYARQVLQNAAREAAR 43 (43) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 9169999999999999999999999999999999999986749 No 3 >COG3847 Flp Flp pilus assembly protein, pilin Flp [Intracellular trafficking and secretion] Probab=97.76 E-value=0.00012 Score=46.75 Aligned_cols=36 Identities=28% Similarity=0.524 Sum_probs=30.1 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 799999751244554899999999999999999999 Q gi|254780571|r 4 IKNYILRFLSRENGVVAVEMAIILPILLLIYMAVYE 39 (182) Q Consensus 4 ~~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e 39 (182) |+..+|||+|||+|+++||.+|++-+.=+.+.+.+. T Consensus 1 m~~~~~rF~rDE~GAtaiEYglia~lIav~ii~~~~ 36 (58) T COG3847 1 MKKLLRRFLRDEDGATAIEYGLIAALIAVVIIAGGS 36 (58) T ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 917899997745651899999999999999999999 No 4 >pfam04964 Flp_Fap Flp/Fap pilin component. Probab=95.87 E-value=0.0095 Score=35.24 Aligned_cols=28 Identities=29% Similarity=0.579 Sum_probs=22.5 Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5124455489999999999999999999 Q gi|254780571|r 11 FLSRENGVVAVEMAIILPILLLIYMAVY 38 (182) Q Consensus 11 f~rd~~G~aaVEFAli~P~ll~ll~~~~ 38 (182) |+|||+|++|||.+|++-+.=+.+.+.+ T Consensus 1 F~kde~GaTAIEYgLIaalIav~iI~~~ 28 (47) T pfam04964 1 FLKDESGATAIEYGLIAALIAVVIIAYV 28 (47) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 9656564159999999999999999999 No 5 >COG4655 Predicted membrane protein [Function unknown] Probab=95.56 E-value=0.11 Score=28.90 Aligned_cols=55 Identities=22% Similarity=0.303 Sum_probs=46.6 Q ss_pred HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 7512445548999999999999999999999999999999999999999998528 Q gi|254780571|r 10 RFLSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQE 64 (182) Q Consensus 10 rf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~ 64 (182) -|+|.+|+.+-|--|+.+|+.+..+.-.+|+|+.+..++.+++.++-+|--.+.. T Consensus 3 g~~r~~rs~~gvltal~~~lal~~l~l~VD~G~l~leqR~LQ~~ADlAAiaAAs~ 57 (565) T COG4655 3 GWPRRQRSMVGVLTALFVPLALATLLLGVDYGYLYLEQRELQRVADLAAIAAASN 57 (565) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEHHHHHHHHHHHHHHHHHH T ss_conf 4237676677899999999999988650220124411787888776998887762 No 6 >pfam04917 Shufflon_N Bacterial shufflon protein, N-terminal constant region. This family represents the high-similarity N-terminal 'constant region' shared by shufflon proteins. Probab=94.58 E-value=0.2 Score=27.27 Aligned_cols=49 Identities=22% Similarity=0.266 Sum_probs=40.2 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1244554899999999999999999999999999999999999999999 Q gi|254780571|r 12 LSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDM 60 (182) Q Consensus 12 ~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~ 60 (182) ||..||.+++|..+.+-++.+++++.+++-.-.......+.+++.+.++ T Consensus 2 r~~~kGf~LlE~~~~L~I~~~~~~~~~~~~~~~~~~~~~q~aA~q~~~v 50 (356) T pfam04917 2 KKTDKGVSLLEVGAVLLIVVMVIPKVAENIEDYLNNVRWQNAAEHANTY 50 (356) T ss_pred CEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 1203443089999999999999999999999899999999999999999 No 7 >PRK10506 hypothetical protein; Provisional Probab=93.40 E-value=0.39 Score=25.54 Aligned_cols=52 Identities=12% Similarity=0.173 Sum_probs=45.4 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 2445548999999999999999999999999999999999999999998528 Q gi|254780571|r 13 SRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQE 64 (182) Q Consensus 13 rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~ 64 (182) +.|+|.+.||+-+++-++-++....+--..-...+++|..++++...++.+. T Consensus 2 ~~q~GFTLiEllvvi~ii~il~~~a~p~~~~~~q~~~L~~~a~~l~~fL~~~ 53 (155) T PRK10506 2 KKQRGYTLIETLVAMTLVVILSAWGLYGWQYWQQQQRLWQTAQQLRDFLLYL 53 (155) T ss_pred CCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8556627999999999999999887777999999999999999999999999 No 8 >COG4970 FimT Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion] Probab=90.82 E-value=1 Score=23.04 Aligned_cols=52 Identities=25% Similarity=0.350 Sum_probs=44.2 Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5124455489999999999999999999999999999999999999999985 Q gi|254780571|r 11 FLSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVA 62 (182) Q Consensus 11 f~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~ 62 (182) +|+..+|...+|+-+++-++=+|..-.+-.+.-....+++.+++++.+-.+. T Consensus 3 ~r~~~rGfTL~ELliviAIlAIla~~A~P~fs~~i~~~rl~s~a~eL~a~l~ 54 (181) T COG4970 3 FRSRTRGFTLLELLIVLAILAILAVIAAPNFSQWIRSQRLRSAADELAAALQ 54 (181) T ss_pred CCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 5414675049999999999999999851008888778789889999999999 No 9 >pfam05307 Bundlin Bundlin. This family consists of several bundlin proteins from E. coli. Bundlin is a type IV pilin protein that is the only known structural component of enteropathogenic Escherichia coli bundle-forming pili (BFP). BFP play a role in virulence, antigenicity, autoaggregation, and localized adherence to epithelial cells. Probab=89.53 E-value=0.79 Score=23.68 Aligned_cols=49 Identities=16% Similarity=0.108 Sum_probs=41.5 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1244554899999999999999999999999999999999999999999 Q gi|254780571|r 12 LSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDM 60 (182) Q Consensus 12 ~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~ 60 (182) ++-|+|.+.||-++++-+--.++.|++-+-.-....++.++|..+.+-. T Consensus 8 kK~~kGlsLiE~~mVLal~A~vIAGvf~YY~saq~snK~q~Ai~ei~s~ 56 (97) T pfam05307 8 KKYEKGLSLIESAMVLALAATVTAGVMFYYQSASDSNKAQNAISEVMSA 56 (97) T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHEEHHHHHHHHHHHHHHHHHHHH T ss_conf 6675252199999999999999977510307456637999999999999 No 10 >COG4966 PilW Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion] Probab=85.27 E-value=0.56 Score=24.59 Aligned_cols=39 Identities=23% Similarity=0.220 Sum_probs=29.0 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999751244554899999999999999999999999999 Q gi|254780571|r 7 YILRFLSRENGVVAVEMAIILPILLLIYMAVYEITMLYT 45 (182) Q Consensus 7 ~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~ 45 (182) +.+...|.++|.+.||+-+-+.+=++++.+++.+.+... T Consensus 4 ~~~~~~rrqrG~SLIELMIallIglivL~av~s~y~~sr 42 (318) T COG4966 4 HRRARPRRQRGFSLIELMIALLIGLIVLLAVGSLYLSSR 42 (318) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHEEEEHH T ss_conf 443554555774399999999999999997763034356 No 11 >COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion] Probab=77.18 E-value=2.7 Score=20.49 Aligned_cols=28 Identities=32% Similarity=0.647 Sum_probs=19.7 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 9975124455489999999999999999 Q gi|254780571|r 8 ILRFLSRENGVVAVEMAIILPILLLIYM 35 (182) Q Consensus 8 lrrf~rd~~G~aaVEFAli~P~ll~ll~ 35 (182) +..|+++++|-..||+-|++.+.=.+++ T Consensus 4 ~~k~~~~~kgFTLvEMLiVLlIISiLlL 31 (107) T COG4537 4 MKKFLKHKKGFTLVEMLIVLLIISILLL 31 (107) T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHH T ss_conf 7777776326259999999999999999 No 12 >KOG3970 consensus Probab=74.78 E-value=2 Score=21.20 Aligned_cols=12 Identities=0% Similarity=-0.111 Sum_probs=4.4 Q ss_pred CCCCCCEEEEEE Q ss_conf 779996799999 Q gi|254780571|r 128 IKDASTFIVRAE 139 (182) Q Consensus 128 ~~~~~~~~v~v~ 139 (182) ...++..++..+ T Consensus 184 ~~sp~h~V~~m~ 195 (299) T KOG3970 184 YSSPNHDVTFMR 195 (299) T ss_pred CCCCCCCEEEEC T ss_conf 878997047633 No 13 >COG1681 FlaB Archaeal flagellins [Cell motility and secretion] Probab=66.37 E-value=5 Score=18.86 Aligned_cols=53 Identities=13% Similarity=0.095 Sum_probs=40.2 Q ss_pred CCCCHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 445548999999999--99999999999999999999999999999999852888 Q gi|254780571|r 14 RENGVVAVEMAIILP--ILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQETS 66 (182) Q Consensus 14 d~~G~aaVEFAli~P--~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~~~ 66 (182) ||||..-||-+|++- +|..-.++.+-++..+|.+|+-+..-+++.+.++.+-. T Consensus 1 ~rrG~~GIgtlIVfIAmVlVAAVaA~VlInt~g~lqQKa~~tg~e~t~qvsSgi~ 55 (209) T COG1681 1 DRRGATGIGTLIVFIAMVLVAAVAAYVLINTGGFLQQKAKATGEEGTQQVSSGIE 55 (209) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEHHHHHHHHHHHHEEECCEE T ss_conf 9841104328999999999999999998653420224567775654513003359 No 14 >pfam04021 Class_IIIsignal Class III signal peptide. This family of archaeal proteins contains. an amino terminal motif QXSXEXXXL that has been suggested to be part of a class III signal sequence. With the Q being the +1 residue of the signal peptidase cleavage site. Two members of this family are cleaved by a type IV pilin-like signal peptidase. Probab=64.37 E-value=5.1 Score=18.80 Aligned_cols=22 Identities=14% Similarity=0.495 Sum_probs=17.0 Q ss_pred CCCHHHHHHHHHHHHHHHHHHH Q ss_conf 4554899999999999999999 Q gi|254780571|r 15 ENGVVAVEMAIILPILLLIYMA 36 (182) Q Consensus 15 ~~G~aaVEFAli~P~ll~ll~~ 36 (182) +||+.++||.++.-.+++.... T Consensus 1 ~kGQ~SlE~~lLi~~vlv~~~i 22 (28) T pfam04021 1 KKGQISLEFLLLILAVLVVAII 22 (28) T ss_pred CCCEEEHHHHHHHHHHHHHHHH T ss_conf 9865439999999999999977 No 15 >PRK10913 dipeptide transporter; Provisional Probab=61.89 E-value=10 Score=16.91 Aligned_cols=32 Identities=13% Similarity=0.318 Sum_probs=20.5 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 4799999751244554899999999999999999 Q gi|254780571|r 3 CIKNYILRFLSRENGVVAVEMAIILPILLLIYMA 36 (182) Q Consensus 3 ~~~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~ 36 (182) -++..+|||+||+.+ .+-+++++-++++-+|+ T Consensus 18 p~~~~w~r~~r~~~a--~~g~~il~~~~l~alfa 49 (300) T PRK10913 18 PLQEFWHYFKRNKGA--VVGLVYVVIVLFIAIFA 49 (300) T ss_pred HHHHHHHHHHHCHHH--HHHHHHHHHHHHHHHHH T ss_conf 899999998538799--99999999999999999 No 16 >TIGR01708 typeII_sec_gspH general secretion pathway protein H; InterPro: IPR010053 This entry represents GspH, protein H of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex. Probab=59.39 E-value=7.1 Score=17.94 Aligned_cols=50 Identities=16% Similarity=0.290 Sum_probs=38.7 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHC Q ss_conf 24455489999999999999999999999999-9999999999999999852 Q gi|254780571|r 13 SRENGVVAVEMAIILPILLLIYMAVYEITMLY-TLSKRLTRFASHMGDMVAQ 63 (182) Q Consensus 13 rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~-~~~~~l~~A~~~~ar~~~~ 63 (182) +.+.|-+.||+-+++ +++.|+.+++-.++-- +....|++.++..++.... T Consensus 1 ~r~~GFtLiElLvVl-~i~gL~aa~~~~~l~~~~~~~~l~~~a~rl~~~l~~ 51 (175) T TIGR01708 1 HRQSGFTLIELLVVL-AIMGLVAAAAALSLDSASGTKELDQAAQRLAAELRL 51 (175) T ss_pred CCCCCCCHHHHHHHH-HHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 987751088999999-999999999961167788862178999999999999 No 17 >COG1991 Uncharacterized conserved protein [Function unknown] Probab=56.75 E-value=0.75 Score=23.79 Aligned_cols=30 Identities=20% Similarity=0.486 Sum_probs=23.3 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 999751244554899999999999999999 Q gi|254780571|r 7 YILRFLSRENGVVAVEMAIILPILLLIYMA 36 (182) Q Consensus 7 ~lrrf~rd~~G~aaVEFAli~P~ll~ll~~ 36 (182) ++..+..+.+|+...||.|++|+.++.... T Consensus 4 ~i~~~~~~nkgQiSLEf~Ll~l~ivla~~i 33 (131) T COG1991 4 YITKIILSNKGQISLEFSLLLLAIVLAASI 33 (131) T ss_pred EEEEEEECCCCCEEEEHHHHHHHHHHHHHH T ss_conf 662542246662564138999999997312 No 18 >COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion] Probab=49.37 E-value=17 Score=15.66 Aligned_cols=49 Identities=10% Similarity=0.122 Sum_probs=31.8 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2445548999999999999999999999999999999999999999998 Q gi|254780571|r 13 SRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMV 61 (182) Q Consensus 13 rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~ 61 (182) +.|+|-+.||.-+++-++=++...++--.......+....+.....+.+ T Consensus 5 ~~qrGFTLiElLVvl~Iigil~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 53 (149) T COG2165 5 KKQRGFTLIELLVVLAIIGILAALALPSLQGSIDKAKRLEAAQQALRVI 53 (149) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 1456738999999999999999999999999889999999999999999 No 19 >PRK10332 hypothetical protein; Provisional Probab=47.57 E-value=18 Score=15.49 Aligned_cols=54 Identities=15% Similarity=0.103 Sum_probs=35.1 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 124455489999999999999999999999999999999999999999985288 Q gi|254780571|r 12 LSRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQET 65 (182) Q Consensus 12 ~rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~~ 65 (182) .++++|-+..|.-+.+.+|.+.+.|...+-.+....=....=-+++=|++-+.. T Consensus 5 l~~Q~GFSLpEvlvA~lLf~isl~aL~~Yqq~L~~sf~~~~Q~rQ~Wr~a~qq~ 58 (107) T PRK10332 5 LKNQRGFSLPEVLLAMVLMVMIVTALSGYQRTLMNSFASRNQYQQLWRHAWQQT 58 (107) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 213678872999999999999999999999999999999999999999999861 No 20 >pfam11688 DUF3285 Protein of unknown function (DUF3285). This family of proteins with unknown function appears to be restricted to Cyanobacteria. Probab=38.47 E-value=25 Score=14.63 Aligned_cols=34 Identities=12% Similarity=0.192 Sum_probs=26.6 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 479999975124455489999999999999999999999 Q gi|254780571|r 3 CIKNYILRFLSRENGVVAVEMAIILPILLLIYMAVYEIT 41 (182) Q Consensus 3 ~~~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~ 41 (182) +|||+.|+ .|.+...|.|.+.-|+.++.++.-++ T Consensus 11 AMRNMVRK-----g~~SL~HF~LT~~gll~~lv~la~l~ 44 (45) T pfam11688 11 AMRNMVRK-----GGKSLLHFGLTALGLLGFLVLIAYLG 44 (45) T ss_pred HHHHHHHH-----CCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999980-----68400568999999999999999952 No 21 >pfam12273 RCR Chitin synthesis regulation, resistance to Congo red. RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5. Probab=35.21 E-value=28 Score=14.32 Aligned_cols=16 Identities=25% Similarity=0.515 Sum_probs=8.7 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999999999999999 Q gi|254780571|r 22 EMAIILPILLLIYMAV 37 (182) Q Consensus 22 EFAli~P~ll~ll~~~ 37 (182) -|||++..+|+++|+. T Consensus 4 ~fav~i~~~~i~~f~~ 19 (124) T pfam12273 4 LFAIFIIALLILFFLT 19 (124) T ss_pred EHHHHHHHHHHHHHHH T ss_conf 0899999999999999 No 22 >TIGR01247 drrB daunorubicin resistance ABC transporter membrane protein; InterPro: IPR005942 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents the Daunorubicin resistance ABC transporter membrane protein, which is associated with the effux of the drug daunorubicin and found in bacteria and archaea. It functions as an ATP dependent antiporter. In eukaryotes proteins of similar function include p-glyco-proteins and a multidrug resistance protein.. Probab=35.11 E-value=25 Score=14.61 Aligned_cols=27 Identities=26% Similarity=0.555 Sum_probs=17.4 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 997512445548999999999999999999 Q gi|254780571|r 8 ILRFLSRENGVVAVEMAIILPILLLIYMAV 37 (182) Q Consensus 8 lrrf~rd~~G~aaVEFAli~P~ll~ll~~~ 37 (182) +|||.|.+.=+ ==.++-|++.+++||. T Consensus 3 lKRF~R~rsRi---~gsi~nPL~WLifFG~ 29 (240) T TIGR01247 3 LKRFIRSRSRI---VGSILNPLLWLIFFGK 29 (240) T ss_pred CCHHHCCHHHH---HHHHHHHHHHHHHHHH T ss_conf 42230235789---9989768999999700 No 23 >PRK08541 flagellin; Validated Probab=34.04 E-value=30 Score=14.20 Aligned_cols=51 Identities=18% Similarity=0.176 Sum_probs=37.2 Q ss_pred CCCCHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 44554899999999--9999999999999999999999999999999998528 Q gi|254780571|r 14 RENGVVAVEMAIIL--PILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQE 64 (182) Q Consensus 14 d~~G~aaVEFAli~--P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~ar~~~~~ 64 (182) ++||+.-||-+|++ .+|..-+++.+=+.-.++.+++.+...++..+.++.+ T Consensus 1 ~kkG~~GigtlIVfIAmVlVAAvaa~Vli~t~g~lqqka~~tg~~s~~qvasg 53 (212) T PRK08541 1 MKKGAVGIGTLIVFIAMVLVAAVAASVLINTSGYLQQKASATGRETTQQVASG 53 (212) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHEECCHHHHHHHHHHHHHHHHHHHHCC T ss_conf 97530242089999999999998775232211455577777656578865155 No 24 >COG4726 PilX Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion] Probab=32.62 E-value=31 Score=14.06 Aligned_cols=35 Identities=20% Similarity=0.331 Sum_probs=19.9 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99975124455489999999999999999999999 Q gi|254780571|r 7 YILRFLSRENGVVAVEMAIILPILLLIYMAVYEIT 41 (182) Q Consensus 7 ~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~~e~~ 41 (182) +.+|-.|.|||.+.|---+++.++-++-++.+-.. T Consensus 4 m~~r~~r~qRG~~LivvL~~LvvltLl~l~~~r~~ 38 (196) T COG4726 4 MLIRGSRRQRGFALIVVLMVLVVLTLLGLAAARSV 38 (196) T ss_pred CCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHHH T ss_conf 66787645676473899999999999999999999 No 25 >PRK10574 putative major pilin subunit; Provisional Probab=28.39 E-value=37 Score=13.62 Aligned_cols=46 Identities=13% Similarity=0.239 Sum_probs=25.9 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2445548999999999999999999999999999999999999999 Q gi|254780571|r 13 SRENGVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMG 58 (182) Q Consensus 13 rd~~G~aaVEFAli~P~ll~ll~~~~e~~~~~~~~~~l~~A~~~~a 58 (182) .+|+|...||.-++.-++=.|..-.+-.-.-+..+.++..+...++ T Consensus 2 ~~q~gftLiElmivvaii~il~~ia~p~y~~y~~~a~~~~~l~~~~ 47 (146) T PRK10574 2 TKQRGFTLIELMVVIGIIAILSAIGIPAYQNYLRKAALTDMLQTFV 47 (146) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7556816589999999999999999999999999999999999878 No 26 >COG5605 Predicted small integral membrane protein [Function unknown] Probab=27.60 E-value=38 Score=13.54 Aligned_cols=24 Identities=38% Similarity=0.509 Sum_probs=17.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999 Q gi|254780571|r 20 AVEMAIILPILLLIYMAVYEITML 43 (182) Q Consensus 20 aVEFAli~P~ll~ll~~~~e~~~~ 43 (182) |.-.|++.|+++++.|...-.+.+ T Consensus 77 al~yaiilppllvlvfv~lmv~ea 100 (115) T COG5605 77 ALVYAIILPPLLVLVFVVLMVAEA 100 (115) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999850799999999999985 No 27 >PRK09881 ATP-dependent peptide transporter membrane subunit; Provisional Probab=24.32 E-value=44 Score=13.17 Aligned_cols=31 Identities=16% Similarity=0.239 Sum_probs=16.9 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 999997512445548999999999999999999 Q gi|254780571|r 5 KNYILRFLSRENGVVAVEMAIILPILLLIYMAV 37 (182) Q Consensus 5 ~~~lrrf~rd~~G~aaVEFAli~P~ll~ll~~~ 37 (182) .++++|||||..+. +-+.+++.++++.+|+- T Consensus 21 ~~~~~~~~r~~~a~--~g~~il~~~~l~ai~~p 51 (296) T PRK09881 21 AKLVWMLKGSPLTV--TGAVIIVLMLLMMIFSP 51 (296) T ss_pred HHHHHHHHHCHHHH--HHHHHHHHHHHHHHHHH T ss_conf 19999983188999--99999999999999999 No 28 >TIGR03061 pip_yhgE_Nterm YhgE/Pip N-terminal domain. This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057. Probab=23.56 E-value=45 Score=13.08 Aligned_cols=27 Identities=15% Similarity=0.176 Sum_probs=14.7 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 997512445548999999999999999 Q gi|254780571|r 8 ILRFLSRENGVVAVEMAIILPILLLIY 34 (182) Q Consensus 8 lrrf~rd~~G~aaVEFAli~P~ll~ll 34 (182) |||++|..--..++=..+++|+|+..+ T Consensus 3 ~k~~~~~~~~~~~~~~~~liP~ly~~~ 29 (164) T TIGR03061 3 LKRLRKNKLLRIALIAIMLIPLLYGGL 29 (164) T ss_pred HHHHHHCCHHHHHHHHHHHHHHHHHHH T ss_conf 788763828999999999999999999 No 29 >KOG2856 consensus Probab=22.17 E-value=48 Score=12.91 Aligned_cols=19 Identities=16% Similarity=0.146 Sum_probs=13.1 Q ss_pred CCCCCEEEEEEEEEEEEEC Q ss_conf 7999679999999962311 Q gi|254780571|r 129 KDASTFIVRAEVSINYRTL 147 (182) Q Consensus 129 ~~~~~~~v~v~v~y~y~p~ 147 (182) ...+...|.|++-|+|.+- T Consensus 408 ~a~~g~~v~vraLYDY~gq 426 (472) T KOG2856 408 DAKGGDFVRVRALYDYAGQ 426 (472) T ss_pred CCCCCCEEEEEEEECCCCC T ss_conf 2347751567764125764 Done!