Query gi|254780572|ref|YP_003064985.1| hypothetical protein CLIBASIA_02295 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 192 No_of_seqs 106 out of 485 Neff 8.8 Searched_HMMs 39220 Date Sun May 29 21:56:45 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780572.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-21 3.1E-26 126.5 13.6 152 2-168 5-157 (185) 2 pfam07811 TadE TadE-like prote 99.3 9.4E-12 2.4E-16 77.1 6.1 43 18-60 1-43 (43) 3 COG3847 Flp Flp pilus assembly 97.8 3.3E-05 8.4E-10 44.3 4.3 34 7-40 3-36 (58) 4 pfam04964 Flp_Fap Flp/Fap pili 96.6 0.002 5.1E-08 35.4 3.6 28 12-39 1-28 (47) 5 COG4655 Predicted membrane pro 95.4 0.017 4.4E-07 30.8 3.4 71 10-85 2-72 (565) 6 pfam04917 Shufflon_N Bacterial 94.2 0.3 7.6E-06 24.6 9.2 48 13-60 2-49 (356) 7 pfam05307 Bundlin Bundlin. Thi 93.5 0.24 6.1E-06 25.0 5.8 55 1-60 1-55 (97) 8 COG4966 PilW Tfp pilus assembl 83.1 2.2 5.7E-05 20.2 4.4 38 10-47 6-43 (318) 9 COG4537 ComGC Competence prote 81.8 1.6 4E-05 21.0 3.2 29 8-36 3-31 (107) 10 PRK10506 hypothetical protein; 81.4 3.3 8.3E-05 19.4 6.9 49 14-62 2-50 (155) 11 COG1681 FlaB Archaeal flagelli 69.6 4 0.0001 18.9 2.5 49 15-63 1-51 (209) 12 COG4970 FimT Tfp pilus assembl 69.5 7.2 0.00018 17.7 6.3 49 13-61 4-52 (181) 13 pfam04021 Class_IIIsignal Clas 69.0 3.5 9E-05 19.2 2.2 21 16-36 1-21 (28) 14 TIGR01708 typeII_sec_gspH gene 51.6 16 0.0004 15.9 3.2 50 14-64 1-51 (175) 15 COG1991 Uncharacterized conser 48.7 6.7 0.00017 17.8 0.7 27 11-37 7-33 (131) 16 pfam12273 RCR Chitin synthesis 37.1 28 0.00071 14.7 2.7 17 23-39 4-20 (124) 17 COG2165 PulG Type II secretory 35.8 29 0.00074 14.6 7.3 50 13-62 4-53 (149) 18 PRK11089 glucose-specific PTS 32.6 33 0.00085 14.3 3.9 14 1-14 1-14 (477) 19 TIGR01247 drrB daunorubicin re 28.3 30 0.00075 14.6 1.3 28 8-38 2-29 (240) 20 COG4726 PilX Tfp pilus assembl 22.3 53 0.0013 13.3 4.9 30 8-42 4-33 (196) 21 COG5605 Predicted small integr 20.7 57 0.0015 13.2 4.1 22 20-41 76-97 (115) 22 PRK08541 flagellin; Validated 20.7 57 0.0015 13.2 4.0 49 15-63 1-51 (212) 23 pfam09185 DUF1948 Domain of un 20.3 55 0.0014 13.2 1.4 30 13-42 2-31 (140) No 1 >COG4961 TadG Flp pilus assembly protein TadG [Intracellular trafficking and secretion] Probab=99.88 E-value=1.2e-21 Score=126.48 Aligned_cols=152 Identities=24% Similarity=0.282 Sum_probs=94.4 Q ss_pred CHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCHHHHHH Q ss_conf 03578988875202366459999999999999999999999999999999999999988874134457787-78899999 Q gi|254780572|r 2 RKKLLQGIRRSILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARKIRTGEISSKNT-HSLTEFRR 80 (192) Q Consensus 2 ~~~l~~~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~~~tg~~~~~~~-~~~~~~~~ 80 (192) ++.+....|||+|||+|++||||||++|+||+++||++|+|++++.++.+++|++.++|.+++++...... ....++.. T Consensus 5 ~~~~~~~~~rF~rdr~Ga~AVeFAlvap~ll~l~~g~ve~~~~~~~~~~l~~a~d~aara~~~~~~~~~~~~~~~~~~~~ 84 (185) T COG4961 5 RRGLRGLLRRFRRDRRGAAAVEFALVAPPLLLLVFGIVEFGIAFLAKQSLQNAADAAARAAARGLTTDAADLDTIQAAAT 84 (185) T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH T ss_conf 26579999988764876899999999999999999999999999999999999999999998507644202567789999 Q ss_pred HHHHHHHHHCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEECCCH Q ss_conf 99864211003344432233315898651268432553465555667766556676534689997189999999801000 Q gi|254780572|r 81 VFCNDLRVLFNCSENEIGRPYDLYLDVKQIKSLQEITETVPRKDKSDSSSEIDDRNFSFHPGGPSTYNVLRAYYHWPLFT 160 (192) Q Consensus 81 ~i~~~~~~~~~~~~~~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~iv~v~v~y~~~~~~ 160 (192) ..|+.......+............++...... ..... +.......+..+..+...+..+.++.+. T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~--~~~~~-------------~~~~~~v~~~~~~~~~~~~~~~~~~~v~ 149 (185) T COG4961 85 AFLNAIAPANAFLTVQSNTPSRGTVTVTANVA--DATLF-------------DTSQFTVTSAVTVSINLARGLVLVAVVP 149 (185) T ss_pred HHHHHHCCCCEEECCCCCCCCCEEEEEECCCC--CCCCC-------------CCCCEEEEECCCCEEECCCCCCEEEEEE T ss_conf 88875164220121322455640589601312--34336-------------7763589614542020123553057873 Q ss_pred HHHHHHHH Q ss_conf 01355554 Q gi|254780572|r 161 DLMRQYIS 168 (192) Q Consensus 161 p~~~~~l~ 168 (192) ++.++... T Consensus 150 ~~t~~~~~ 157 (185) T COG4961 150 DLTGPGTS 157 (185) T ss_pred CCCCCCCC T ss_conf 23476445 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=99.26 E-value=9.4e-12 Score=77.07 Aligned_cols=43 Identities=40% Similarity=0.657 Sum_probs=42.2 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6459999999999999999999999999999999999999988 Q gi|254780572|r 18 GAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVAR 60 (192) Q Consensus 18 G~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR 60 (192) |+++|||++++|+|++++++++|+|+++++++.+++|+++++| 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=3.3e-05 Score=44.35 Aligned_cols=34 Identities=24% Similarity=0.314 Sum_probs=28.3 Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9888752023664599999999999999999999 Q gi|254780572|r 7 QGIRRSILIREGAVAIEFAILVMPYFMLVFAILE 40 (192) Q Consensus 7 ~~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E 40 (192) +.++||+|||+|+++||.+|++-+.-+.+.+.+. T Consensus 3 ~~~~rF~rDE~GAtaiEYglia~lIav~ii~~~~ 36 (58) T COG3847 3 KLLRRFLRDEDGATAIEYGLIAALIAVVIIAGGS 36 (58) T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7899997745651899999999999999999999 No 4 >pfam04964 Flp_Fap Flp/Fap pilin component. Probab=96.63 E-value=0.002 Score=35.42 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=22.7 Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5202366459999999999999999999 Q gi|254780572|r 12 SILIREGAVAIEFAILVMPYFMLVFAIL 39 (192) Q Consensus 12 ~~~d~rG~aaVEFAlv~p~ll~l~~g~~ 39 (192) |+|||+|++|||.+|++-+.-+.+.+.. 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=95.35 E-value=0.017 Score=30.76 Aligned_cols=71 Identities=10% Similarity=0.020 Sum_probs=53.8 Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH Q ss_conf 8752023664599999999999999999999999999999999999999888741344577877889999999864 Q gi|254780572|r 10 RRSILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARKIRTGEISSKNTHSLTEFRRVFCND 85 (192) Q Consensus 10 rr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~~~tg~~~~~~~~~~~~~~~~i~~~ 85 (192) ..|.|.+|+.+-|--|+.+|+.+..+.-.+|.|+++..++.||+.++.+|-... +.-...+....+.+.++ T Consensus 2 ~g~~r~~rs~~gvltal~~~lal~~l~l~VD~G~l~leqR~LQ~~ADlAAiaAA-----s~~~~~~~Av~~sf~~n 72 (565) T COG4655 2 NGWPRRQRSMVGVLTALFVPLALATLLLGVDYGYLYLEQRELQRVADLAAIAAA-----SNLDDAEQAVQTSFTQN 72 (565) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEHHHHHHHHHHHHHHHH-----HHCCCHHHHHHHHHHHC T ss_conf 842376766778999999999999886502201244117878887769988877-----62798889999999866 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=94.17 E-value=0.3 Score=24.55 Aligned_cols=48 Identities=13% Similarity=0.153 Sum_probs=37.5 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 202366459999999999999999999999999999999999999988 Q gi|254780572|r 13 ILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVAR 60 (192) Q Consensus 13 ~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR 60 (192) +|+.||.+.+|..+++.++.+++++.+++-.-......-+.+++...+ T Consensus 2 r~~~kGf~LlE~~~~L~I~~~~~~~~~~~~~~~~~~~~~q~aA~q~~~ 49 (356) T pfam04917 2 KKTDKGVSLLEVGAVLLIVVMVIPKVAENIEDYLNNVRWQNAAEHANT 49 (356) T ss_pred CEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 120344308999999999999999999999989999999999999999 No 7 >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=93.50 E-value=0.24 Score=25.03 Aligned_cols=55 Identities=16% Similarity=0.124 Sum_probs=45.0 Q ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 903578988875202366459999999999999999999999999999999999999988 Q gi|254780572|r 1 MRKKLLQGIRRSILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVAR 60 (192) Q Consensus 1 m~~~l~~~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR 60 (192) |..++.+ .+-|+|.+.+|-++|+-+--.++.|++-+=......++.|+|..+.+- T Consensus 1 ~~~~~~n-----kK~~kGlsLiE~~mVLal~A~vIAGvf~YY~saq~snK~q~Ai~ei~s 55 (97) T pfam05307 1 MVSKIMN-----KKYEKGLSLIESAMVLALAATVTAGVMFYYQSASDSNKAQNAISEVMS 55 (97) T ss_pred CCHHHHH-----HHHHCCCHHHHHHHHHHHHHHHHHHHHEEHHHHHHHHHHHHHHHHHHH T ss_conf 9337530-----667525219999999999999997751030745663799999999999 No 8 >COG4966 PilW Tfp pilus assembly protein PilW [Cell motility and secretion / Intracellular trafficking and secretion] Probab=83.13 E-value=2.2 Score=20.19 Aligned_cols=38 Identities=21% Similarity=0.227 Sum_probs=29.6 Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 87520236645999999999999999999999999999 Q gi|254780572|r 10 RRSILIREGAVAIEFAILVMPYFMLVFAILEISLSFTA 47 (192) Q Consensus 10 rr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~ 47 (192) ++..|++||.+.|||-+.+.+=++++.+++.+-+.... T Consensus 6 ~~~~rrqrG~SLIELMIallIglivL~av~s~y~~sr~ 43 (318) T COG4966 6 RARPRRQRGFSLIELMIALLIGLIVLLAVGSLYLSSRQ 43 (318) T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHEEEEHHH T ss_conf 35545557743999999999999999977630343567 No 9 >COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion] Probab=81.85 E-value=1.6 Score=20.97 Aligned_cols=29 Identities=14% Similarity=0.360 Sum_probs=21.9 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 88875202366459999999999999999 Q gi|254780572|r 8 GIRRSILIREGAVAIEFAILVMPYFMLVF 36 (192) Q Consensus 8 ~lrr~~~d~rG~aaVEFAlv~p~ll~l~~ 36 (192) .+..++++++|-+.||+-+|+.+.-.|++ T Consensus 3 ~~~k~~~~~kgFTLvEMLiVLlIISiLlL 31 (107) T COG4537 3 KMKKFLKHKKGFTLVEMLIVLLIISILLL 31 (107) T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHH T ss_conf 67777776326259999999999999999 No 10 >PRK10506 hypothetical protein; Provisional Probab=81.41 E-value=3.3 Score=19.37 Aligned_cols=49 Identities=14% Similarity=-0.044 Sum_probs=34.9 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0236645999999999999999999999999999999999999998887 Q gi|254780572|r 14 LIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARKI 62 (192) Q Consensus 14 ~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~~ 62 (192) ++|+|-+.||.-+++-++-+|....+--=.....++.|..++++....+ T Consensus 2 ~~q~GFTLiEllvvi~ii~il~~~a~p~~~~~~q~~~L~~~a~~l~~fL 50 (155) T PRK10506 2 KKQRGYTLIETLVAMTLVVILSAWGLYGWQYWQQQQRLWQTAQQLRDFL 50 (155) T ss_pred CCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8556627999999999999999887777999999999999999999999 No 11 >COG1681 FlaB Archaeal flagellins [Cell motility and secretion] Probab=69.55 E-value=4 Score=18.94 Aligned_cols=49 Identities=18% Similarity=0.171 Sum_probs=36.6 Q ss_pred CCCCHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 23664599999999999999--99999999999999999999999988874 Q gi|254780572|r 15 IREGAVAIEFAILVMPYFML--VFAILEISLSFTAGQLFESAAYDVARKIR 63 (192) Q Consensus 15 d~rG~aaVEFAlv~p~ll~l--~~g~~E~g~~~~~~~~l~~A~~~aaR~~~ 63 (192) ||||..=+|=++|+..|.++ +++-+=++...|.+++-+...+++.+.+. T Consensus 1 ~rrG~~GIgtlIVfIAmVlVAAVaA~VlInt~g~lqQKa~~tg~e~t~qvs 51 (209) T COG1681 1 DRRGATGIGTLIVFIAMVLVAAVAAYVLINTGGFLQQKAKATGEEGTQQVS 51 (209) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEHHHHHHHHHHHHEEE T ss_conf 984110432899999999999999999865342022456777565451300 No 12 >COG4970 FimT Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion] Probab=69.52 E-value=7.2 Score=17.66 Aligned_cols=49 Identities=18% Similarity=0.120 Sum_probs=37.6 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2023664599999999999999999999999999999999999999888 Q gi|254780572|r 13 ILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARK 61 (192) Q Consensus 13 ~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~ 61 (192) +++.+|.+.+|.-+++-++-+|..-.+--....+..+.+++++.+-+-. T Consensus 4 r~~~rGfTL~ELliviAIlAIla~~A~P~fs~~i~~~rl~s~a~eL~a~ 52 (181) T COG4970 4 RSRTRGFTLLELLIVLAILAILAVIAAPNFSQWIRSQRLRSAADELAAA 52 (181) T ss_pred CCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 4146750499999999999999998510088887787898899999999 No 13 >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=68.99 E-value=3.5 Score=19.20 Aligned_cols=21 Identities=19% Similarity=0.716 Sum_probs=16.4 Q ss_pred CCCHHHHHHHHHHHHHHHHHH Q ss_conf 366459999999999999999 Q gi|254780572|r 16 REGAVAIEFAILVMPYFMLVF 36 (192) Q Consensus 16 ~rG~aaVEFAlv~p~ll~l~~ 36 (192) +||+.++||.++.-.+++... T Consensus 1 ~kGQ~SlE~~lLi~~vlv~~~ 21 (28) T pfam04021 1 KKGQISLEFLLLILAVLVVAI 21 (28) T ss_pred CCCEEEHHHHHHHHHHHHHHH T ss_conf 986543999999999999997 No 14 >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=51.58 E-value=16 Score=15.94 Aligned_cols=50 Identities=24% Similarity=0.287 Sum_probs=39.2 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH Q ss_conf 02366459999999999999999999999999-9999999999999888741 Q gi|254780572|r 14 LIREGAVAIEFAILVMPYFMLVFAILEISLSF-TAGQLFESAAYDVARKIRT 64 (192) Q Consensus 14 ~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~-~~~~~l~~A~~~aaR~~~t 64 (192) +.+.|-+.||.-+|+. ++.|+-+++-.++.- +....|+..+++-++.+++ T Consensus 1 ~r~~GFtLiElLvVl~-i~gL~aa~~~~~l~~~~~~~~l~~~a~rl~~~l~~ 51 (175) T TIGR01708 1 HRQSGFTLIELLVVLA-IMGLVAAAAALSLDSASGTKELDQAAQRLAAELRL 51 (175) T ss_pred CCCCCCCHHHHHHHHH-HHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH T ss_conf 9877510889999999-99999999961167788862178999999999999 No 15 >COG1991 Uncharacterized conserved protein [Function unknown] Probab=48.69 E-value=6.7 Score=17.80 Aligned_cols=27 Identities=22% Similarity=0.530 Sum_probs=21.6 Q ss_pred HHHCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 752023664599999999999999999 Q gi|254780572|r 11 RSILIREGAVAIEFAILVMPYFMLVFA 37 (192) Q Consensus 11 r~~~d~rG~aaVEFAlv~p~ll~l~~g 37 (192) .+..+.||+...||.|++|..++.... T Consensus 7 ~~~~~nkgQiSLEf~Ll~l~ivla~~i 33 (131) T COG1991 7 KIILSNKGQISLEFSLLLLAIVLAASI 33 (131) T ss_pred EEEECCCCCEEEEHHHHHHHHHHHHHH T ss_conf 542246662564138999999997312 No 16 >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=37.10 E-value=28 Score=14.72 Aligned_cols=17 Identities=29% Similarity=0.610 Sum_probs=9.3 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999 Q gi|254780572|r 23 EFAILVMPYFMLVFAIL 39 (192) Q Consensus 23 EFAlv~p~ll~l~~g~~ 39 (192) =||+++..+|+++|+++ T Consensus 4 ~fav~i~~~~i~~f~~~ 20 (124) T pfam12273 4 LFAIFIIALLILFFLTA 20 (124) T ss_pred EHHHHHHHHHHHHHHHH T ss_conf 08999999999999999 No 17 >COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion] Probab=35.83 E-value=29 Score=14.62 Aligned_cols=50 Identities=18% Similarity=0.048 Sum_probs=33.6 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 20236645999999999999999999999999999999999999998887 Q gi|254780572|r 13 ILIREGAVAIEFAILVMPYFMLVFAILEISLSFTAGQLFESAAYDVARKI 62 (192) Q Consensus 13 ~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g~~~~~~~~l~~A~~~aaR~~ 62 (192) .+.|||-+.+|.-+++.++-++...++---.....+...+.+.....+.+ T Consensus 4 ~~~qrGFTLiElLVvl~Iigil~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 53 (149) T COG2165 4 MKKQRGFTLIELLVVLAIIGILAALALPSLQGSIDKAKRLEAAQQALRVI 53 (149) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 41456738999999999999999999999999889999999999999999 No 18 >PRK11089 glucose-specific PTS system IIBC components; Provisional Probab=32.59 E-value=33 Score=14.33 Aligned_cols=14 Identities=14% Similarity=0.133 Sum_probs=5.3 Q ss_pred CCHHHHHHHHHHHC Q ss_conf 90357898887520 Q gi|254780572|r 1 MRKKLLQGIRRSIL 14 (192) Q Consensus 1 m~~~l~~~lrr~~~ 14 (192) |++++++.+.||.| T Consensus 1 m~~~~~~~lQk~gk 14 (477) T PRK11089 1 MFKNAFANLQKVGK 14 (477) T ss_pred CHHHHHHHHHHHHH T ss_conf 92669999999677 No 19 >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=28.27 E-value=30 Score=14.59 Aligned_cols=28 Identities=25% Similarity=0.364 Sum_probs=16.9 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 8887520236645999999999999999999 Q gi|254780572|r 8 GIRRSILIREGAVAIEFAILVMPYFMLVFAI 38 (192) Q Consensus 8 ~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~ 38 (192) .+|||.|.|+=++. .++-|++.+++||. T Consensus 2 elKRF~R~rsRi~g---si~nPL~WLifFG~ 29 (240) T TIGR01247 2 ELKRFIRSRSRIVG---SILNPLLWLIFFGK 29 (240) T ss_pred CCCHHHCCHHHHHH---HHHHHHHHHHHHHH T ss_conf 64223023578999---89768999999700 No 20 >COG4726 PilX Tfp pilus assembly protein PilX [Cell motility and secretion / Intracellular trafficking and secretion] Probab=22.26 E-value=53 Score=13.33 Aligned_cols=30 Identities=20% Similarity=0.310 Sum_probs=16.1 Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 88875202366459999999999999999999999 Q gi|254780572|r 8 GIRRSILIREGAVAIEFAILVMPYFMLVFAILEIS 42 (192) Q Consensus 8 ~lrr~~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g 42 (192) +.+|..|.|||.+.| ..++++++++++-++ T Consensus 4 m~~r~~r~qRG~~Li-----vvL~~LvvltLl~l~ 33 (196) T COG4726 4 MLIRGSRRQRGFALI-----VVLMVLVVLTLLGLA 33 (196) T ss_pred CCCCCCCCCCCEEEH-----HHHHHHHHHHHHHHH T ss_conf 667876456764738-----999999999999999 No 21 >COG5605 Predicted small integral membrane protein [Function unknown] Probab=20.66 E-value=57 Score=13.15 Aligned_cols=22 Identities=36% Similarity=0.798 Sum_probs=15.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5999999999999999999999 Q gi|254780572|r 20 VAIEFAILVMPYFMLVFAILEI 41 (192) Q Consensus 20 aaVEFAlv~p~ll~l~~g~~E~ 41 (192) -|.-.|+++||+++++|-..-. T Consensus 76 lal~yaiilppllvlvfv~lmv 97 (115) T COG5605 76 LALVYAIILPPLLVLVFVVLMV 97 (115) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999850799999999999 No 22 >PRK08541 flagellin; Validated Probab=20.66 E-value=57 Score=13.15 Aligned_cols=49 Identities=20% Similarity=0.255 Sum_probs=29.9 Q ss_pred CCCCHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 23664599999999999999--99999999999999999999999988874 Q gi|254780572|r 15 IREGAVAIEFAILVMPYFML--VFAILEISLSFTAGQLFESAAYDVARKIR 63 (192) Q Consensus 15 d~rG~aaVEFAlv~p~ll~l--~~g~~E~g~~~~~~~~l~~A~~~aaR~~~ 63 (192) +|||+.=+|=++|+..|+++ +++-+=++-..+-+++-+...+++...+. T Consensus 1 ~kkG~~GigtlIVfIAmVlVAAvaa~Vli~t~g~lqqka~~tg~~s~~qva 51 (212) T PRK08541 1 MKKGAVGIGTLIVFIAMVLVAAVAASVLINTSGYLQQKASATGRETTQQVA 51 (212) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHEECCHHHHHHHHHHHHHHHHHHHH T ss_conf 975302420899999999999987752322114555777776565788651 No 23 >pfam09185 DUF1948 Domain of unknown function (DUF1948). Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central alpha-helix surrounded by five others, in a NusB-like fold. Their function has not, as yet, been determined. Probab=20.27 E-value=55 Score=13.23 Aligned_cols=30 Identities=7% Similarity=0.119 Sum_probs=18.7 Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 202366459999999999999999999999 Q gi|254780572|r 13 ILIREGAVAIEFAILVMPYFMLVFAILEIS 42 (192) Q Consensus 13 ~~d~rG~aaVEFAlv~p~ll~l~~g~~E~g 42 (192) .|.||-.|.|||.+.+..|+---.-.++.. T Consensus 2 trtqrriaivefifa~lfflpk~ad~iqa~ 31 (140) T pfam09185 2 TRTQRRIAIVEFIFALLFFLPKEADQIQAA 31 (140) T ss_pred CCHHHHHHHHHHHHHHHHHCCCCHHHHHHH T ss_conf 522455779999999999774518899999 Done!