Query gi|254780687|ref|YP_003065100.1| flagellar C-ring protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 318 No_of_seqs 160 out of 776 Neff 8.3 Searched_HMMs 13730 Date Wed Jun 1 09:02:44 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780687.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 d1o6aa_ b.139.1.1 (A:) Putativ 99.7 3.5E-17 2.6E-21 128.9 11.6 81 233-314 5-85 (87) 2 d1o9ya_ b.139.1.1 (A:) Structu 99.6 1.9E-15 1.4E-19 117.5 11.8 70 235-304 2-71 (71) 3 d1xkra_ d.252.1.1 (A:) Chemota 98.9 1.4E-06 1E-10 59.5 21.5 177 31-212 8-201 (205) 4 d1xkoa_ d.252.1.1 (A:) Chemota 96.4 0.028 2.1E-06 31.2 14.9 113 37-164 5-118 (153) 5 d1dzfa2 d.78.1.1 (A:144-215) E 28.9 13 0.00094 13.8 2.2 21 251-271 39-59 (72) 6 d1hmja_ d.78.1.1 (A:) RNA poly 26.7 14 0.001 13.5 1.8 19 252-270 33-51 (68) 7 d1wida_ b.142.1.2 (A:) DNA-bin 25.2 13 0.00095 13.7 1.4 28 246-273 72-99 (117) 8 d1eika_ d.78.1.1 (A:) RNA poly 22.1 15 0.0011 13.3 1.2 19 252-270 44-62 (77) 9 d1wpga1 b.82.7.1 (A:125-239) C 21.6 18 0.0013 12.9 2.3 19 258-276 20-38 (115) 10 d1nr9a_ d.177.1.1 (A:) Putativ 21.5 18 0.0013 12.9 3.6 20 253-272 177-196 (221) 11 d1s04a_ b.122.1.6 (A:) Hypothe 21.3 12 0.00088 14.0 0.6 37 223-268 7-43 (110) No 1 >d1o6aa_ b.139.1.1 (A:) Putative flagelar motor switch protein FliN {Thermotoga maritima [TaxId: 2336]} Probab=99.72 E-value=3.5e-17 Score=128.86 Aligned_cols=81 Identities=20% Similarity=0.295 Sum_probs=75.2 Q ss_pred HHHHHCEEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCEEEEEECCEEEEEEEEEEECCEEEEEEEECCCCHHHHHH Q ss_conf 99740800799998123430989945799978982578997389999999999999987889789999842581467888 Q gi|254780687|r 233 RKTYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITDRINFDQKSLK 312 (318) Q Consensus 233 ~~l~~~~v~i~a~Lg~~~l~l~dil~L~vGDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~~~AVrI~~~i~~~~~~l~ 312 (318) +.++++||+++|+||+++++++|+++|++||||+|+.+.+++++++|||+++|+|++|.+|+++||||++.+..+++ ++ T Consensus 5 ~~i~dipv~l~~~Lg~~~l~l~el~~L~~Gdvi~L~~~~~~~v~l~v~g~~~~~g~lg~~~~~~av~I~~~i~~~e~-~~ 83 (87) T d1o6aa_ 5 ELLLDIPLKVTVELGRTRMTLKRVLEMIHGSIIELDKLTGEPVDILVNGKLIARGEVVVIDENFGVRITEIVSPKER-LE 83 (87) T ss_dssp HHHTTCEEEEEEEEEEEEEEHHHHHHCCTTCEEEEEEETTCCEEEEETTEEEEEEEEEEETTEEEEEEEEECCHHHH-HH T ss_pred HHHCCCCEEEEEEEEEEEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEECCCHHH-HH T ss_conf 23326717999999300845999857999999991898999799999999999999999999999999981595899-88 Q ss_pred HH Q ss_conf 87 Q gi|254780687|r 313 NF 314 (318) Q Consensus 313 ~~ 314 (318) .+ T Consensus 84 ~l 85 (87) T d1o6aa_ 84 LL 85 (87) T ss_dssp HH T ss_pred HH T ss_conf 64 No 2 >d1o9ya_ b.139.1.1 (A:) Structural protein HrcQ2, C-terminal domain {Pseudomonas syringae [TaxId: 317]} Probab=99.63 E-value=1.9e-15 Score=117.53 Aligned_cols=70 Identities=19% Similarity=0.200 Sum_probs=67.5 Q ss_pred HHHCEEEEEEEEEEEEECHHHHHCCCCCCEEECCCCCCCEEEEEECCEEEEEEEEEEECCEEEEEEEECC Q ss_conf 7408007999981234309899457999789825789973899999999999999878897899998425 Q gi|254780687|r 235 TYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITDRI 304 (318) Q Consensus 235 l~~~~v~i~a~Lg~~~l~l~dil~L~vGDVI~L~~~~~~~v~v~v~g~~~f~g~~G~~~~~~AVrI~~~i 304 (318) +.++|++++++||+++++++|+++|++||||+|++..+++|++++||+++|+|++|..|+++||||++.+ T Consensus 2 l~~i~v~l~~~lg~~~~~l~el~~L~~G~vl~l~~~~~~~V~l~v~g~~i~~G~l~~~~~~~av~It~li 71 (71) T d1o9ya_ 2 LDSLALDLTLRCGELRLTLAELRRLDAGTILEVTGISPGHATLCHGEQVVAEGELVDVEGRLGLQITRLV 71 (71) T ss_dssp CTTCEEEEEEEEEEEEEEHHHHHTCCTTCEEEECSSCTTEEEEEETTEEEEEEEEEEETTEEEEEEEEEC T ss_pred CCCEEEEEEEEEECCEEEHHHHHCCCCCCEEEECCCCCCCEEEEECCEEEEEEEEEEECCEEEEEEEEEC T ss_conf 5420689999992008389998535899999918778997999999889999999999999999999919 No 3 >d1xkra_ d.252.1.1 (A:) Chemotaxis protein CheC {Thermotoga maritima [TaxId: 2336]} Probab=98.88 E-value=1.4e-06 Score=59.47 Aligned_cols=177 Identities=11% Similarity=0.064 Sum_probs=131.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEEEHHHHHHCCCCC---EEEEEEE-CCCCCCEEEEEECHHHHHH Q ss_conf 99999999999999999999986298079986472566799897116886---3999997-3677833999988789999 Q gi|254780687|r 31 IEKISSSLGYLYKKFLPKIFKEKMDLDVDISYTSCQSGKFSHIIHSFKEN---FVFSQAS-LSSWSSNFFIGCSNNLVIT 106 (318) Q Consensus 31 ~~~~~~~~~e~~~r~l~~~l~~~~~~~v~v~~~~ve~~~~~e~i~~l~~p---~~~~i~~-~~pl~g~~ll~id~~l~~~ 106 (318) ..+.++++..--+...+++|+..++..|++++..++..++.++...+..+ .+..... ..++.|.+++.++..-+-. T Consensus 8 ~~D~l~Ei~NIg~G~AAtaLs~ll~~~v~l~vp~v~~~~~~e~~~~l~~~~~~~~~v~~~~~G~~~G~~ll~f~~~~a~~ 87 (205) T d1xkra_ 8 QKDLLKEIGNIGAGNAATAISYMINKKVEISVPNVEIVPISKVIFIAKDPEEIVVGVKMPVTGDIEGSVLLIMGTTVVKK 87 (205) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTSCEEEECCCEEEEEGGGGGGGSSCTTCEEEEEEEEEEESSCEEEEEEECHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECCEEEEEEHHHHHHHHCCCCCEEEEEEEEEEECCCEEEEEEECHHHHHH T ss_conf 99999999998888999999998599689877979997589999872786650899999866066648999988899999 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCHHHHHC-------HHH--HCCCCC Q ss_conf 99887278887666666565798999999999999999999985100273200000244311-------000--012478 Q gi|254780687|r 107 LLENLLGASHETIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYDIDY-------LKK--NTNRLS 177 (318) Q Consensus 107 lid~~lGG~g~~~~~~~~R~lT~iE~~l~~~i~~~~~~~l~~a~~~~~~~~~~~~~~~~~~~-------~~~--~~~~~p 177 (318) +++.|+|..+.. ..++++.+...+..+.+.+..++-.+|+...+....+..|..... ... ...... T Consensus 88 l~~~L~g~~~~~-----~~~~~e~~~sal~EvgNIl~ga~l~~ls~~l~~~i~~s~P~~~~d~~~~i~~~~~~~~~~~~~ 162 (205) T d1xkra_ 88 ILEILTGRAPDN-----LLNLDEFSASALREIGNIMCGTYVSALADFLGFKIDTLPPQLVIDMISAIFAEASIEELEDNS 162 (205) T ss_dssp HHHHHHSCCCSC-----STTCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEECCCEEEEEEHHHHHHHHHHHHHSSCC T ss_pred HHHHHCCCCCCC-----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCEEEECCHHHHCCHHHHHHHCCCC T ss_conf 999856999776-----543037899999999999999999999998698776669978834635423536554302678 Q ss_pred CCEEEEEEEEEEECC----EEEEEEEEEEHHHHHHHHHH Q ss_conf 718999998866678----13799998504775256775 Q gi|254780687|r 178 NEFVTTINMNMTIEN----VASSFVLIIPQETLLKTTLI 212 (318) Q Consensus 178 ~e~vi~i~~~v~~~~----~~g~~~l~lP~~~l~~~~~~ 212 (318) ++.++++...+.+++ ..|.+.++.....+.....+ T Consensus 163 ~~~vl~i~t~~~~~~~~~~i~g~l~ll~~~~sl~~L~~~ 201 (205) T d1xkra_ 163 EDQIVFVETLLKVEEEEEPLTSYMMMIPKPGYLVKIFER 201 (205) T ss_dssp CCEEEEEEEEEEETTSSSCEEEEEEEEECTTHHHHHHHT T ss_pred CCEEEEEEEEEEECCCCCEEEEEEEECCCHHHHHHHHHH T ss_conf 875999999999637786378999991598999999997 No 4 >d1xkoa_ d.252.1.1 (A:) Chemotaxis protein CheX {Thermotoga maritima [TaxId: 2336]} Probab=96.41 E-value=0.028 Score=31.19 Aligned_cols=113 Identities=5% Similarity=0.023 Sum_probs=80.2 Q ss_pred HHHHHHHHHHHHHHHHHCCCEEEEEECCCEEEEHHHHHHCCCCCEEEEEEEC-CCCCCEEEEEECHHHHHHHHHHHHCCC Q ss_conf 9999999999999998629807998647256679989711688639999973-677833999988789999998872788 Q gi|254780687|r 37 SLGYLYKKFLPKIFKEKMDLDVDISYTSCQSGKFSHIIHSFKENFVFSQASL-SSWSSNFFIGCSNNLVITLLENLLGAS 115 (318) Q Consensus 37 ~~~e~~~r~l~~~l~~~~~~~v~v~~~~ve~~~~~e~i~~l~~p~~~~i~~~-~pl~g~~ll~id~~l~~~lid~~lGG~ 115 (318) .+-.-|.......|++.++..+......++.. ..+.+.+.+++.. .++.|..++.++..++..+++.|+||. T Consensus 5 e~in~f~~a~~~vl~~m~~~e~~~~~~~~~~~-------~~~~~~i~~~i~~~G~~~G~~~l~~~~~~a~~i~~~mlg~~ 77 (153) T d1xkoa_ 5 RIVNALIGSVYETIRDVLGIEPKTGKPSTVSH-------IEIPHSLVTVIGITGGIEGSLIYSFSSETALKVVSAMMGGM 77 (153) T ss_dssp HHHHHHHHHHHHHHHHHSCSCCEECCCEEESS-------CCCCCSEEEEEEEEESSCEEEEEEECHHHHHHHHHHHTTTC T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEC-------CCCCCCEEEEEEECCCCCEEEEEEECHHHHHHHHHHHHCCC T ss_conf 99999999999999998599842388546622-------56788789999961464279999988999999999983899 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCHH Q ss_conf 8766666656579899999999999999999998510027320000024 Q gi|254780687|r 116 HETIPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFY 164 (318) Q Consensus 116 g~~~~~~~~R~lT~iE~~l~~~i~~~~~~~l~~a~~~~~~~~~~~~~~~ 164 (318) .. .++.+.....+..+.+.+++.....++.. +....+..|. T Consensus 78 ~~-------~~~~e~~~da~~E~~NiI~G~~~~~l~~~-g~~i~~s~P~ 118 (153) T d1xkoa_ 78 EY-------NQLDELALSAIGELGNMTAGKLAMKLEHL-GKHVDITPPT 118 (153) T ss_dssp CC-------CSCCHHHHHHHHHHHHHHHHHHHHHCCC----CEEECCCE T ss_pred CC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCEEEECCCE T ss_conf 87-------40778899999999999999999999867-9869844997 No 5 >d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Probab=28.90 E-value=13 Score=13.78 Aligned_cols=21 Identities=19% Similarity=0.373 Sum_probs=16.6 Q ss_pred ECHHHHHCCCCCCEEECCCCC Q ss_conf 309899457999789825789 Q gi|254780687|r 251 TTLKDVVTLKIGQVIPFLHRE 271 (318) Q Consensus 251 l~l~dil~L~vGDVI~L~~~~ 271 (318) =++...+++++|||+.+.+.- T Consensus 39 DPva~~~g~~~GdvikI~R~s 59 (72) T d1dzfa2 39 DPVALYLGLKRGEVVKIIRKS 59 (72) T ss_dssp CHHHHHHTCCTTCEEEEECTT T ss_pred CHHHHHCCCCCCCEEEEEECC T ss_conf 973561188889789999758 No 6 >d1hmja_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Probab=26.73 E-value=14 Score=13.53 Aligned_cols=19 Identities=16% Similarity=0.342 Sum_probs=15.2 Q ss_pred CHHHHHCCCCCCEEECCCC Q ss_conf 0989945799978982578 Q gi|254780687|r 252 TLKDVVTLKIGQVIPFLHR 270 (318) Q Consensus 252 ~l~dil~L~vGDVI~L~~~ 270 (318) |+...+++++|||+.+.+. T Consensus 33 Pva~~~g~k~GdvvkI~R~ 51 (68) T d1hmja_ 33 PVIQEIGAKEGDVVRVIRK 51 (68) T ss_pred HHHHHHCCCCCCEEEEEEC T ss_conf 8789819999958999975 No 7 >d1wida_ b.142.1.2 (A:) DNA-binding protein RAV1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Probab=25.18 E-value=13 Score=13.74 Aligned_cols=28 Identities=14% Similarity=0.252 Sum_probs=19.4 Q ss_pred EEEEEECHHHHHCCCCCCEEECCCCCCC Q ss_conf 8123430989945799978982578997 Q gi|254780687|r 246 INLKKTTLKDVVTLKIGQVIPFLHREKT 273 (318) Q Consensus 246 Lg~~~l~l~dil~L~vGDVI~L~~~~~~ 273 (318) ++.-......-.+|++||+|-|.....+ T Consensus 72 l~~GW~~Fv~~~~Lk~GD~~~F~~~~~~ 99 (117) T d1wida_ 72 LTKGWSRFVKEKNLRAGDVVSFSRSNGQ 99 (117) T ss_dssp EESSHHHHHHHTTCCTTCEEEEEECCSS T ss_pred EECCHHHHHHHCCCCCCCEEEEEEEECC T ss_conf 7457799888749997999999998189 No 8 >d1eika_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase subunit H) {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Probab=22.06 E-value=15 Score=13.35 Aligned_cols=19 Identities=11% Similarity=0.420 Sum_probs=13.6 Q ss_pred CHHHHHCCCCCCEEECCCC Q ss_conf 0989945799978982578 Q gi|254780687|r 252 TLKDVVTLKIGQVIPFLHR 270 (318) Q Consensus 252 ~l~dil~L~vGDVI~L~~~ 270 (318) |+...+++++|||+.+.++ T Consensus 44 Pva~~~g~k~GdvvkI~R~ 62 (77) T d1eika_ 44 PVAKAIGAKRGDIVKIIRK 62 (77) T ss_dssp HHHHGGGCCTTCEEEEEEE T ss_pred HHHHHHCCCCCCEEEEEEC T ss_conf 7245107868857999975 No 9 >d1wpga1 b.82.7.1 (A:125-239) Calcium ATPase, transduction domain A {Rabbit (Oryctolagus cuniculus) [TaxId: 9986]} Probab=21.60 E-value=18 Score=12.90 Aligned_cols=19 Identities=16% Similarity=0.160 Sum_probs=7.6 Q ss_pred CCCCCCEEECCCCCCCEEE Q ss_conf 5799978982578997389 Q gi|254780687|r 258 TLKIGQVIPFLHREKTCAI 276 (318) Q Consensus 258 ~L~vGDVI~L~~~~~~~v~ 276 (318) +|-|||+|.+.....-|+| T Consensus 20 eLv~GDiv~l~~G~~vPaD 38 (115) T d1wpga1 20 DIVPGDIVEVAVGDKVPAD 38 (115) T ss_dssp GCCTTCEEEEETTCBCCSE T ss_pred HCCCCCEEEECCCCEEEEC T ss_conf 9889989999999999515 No 10 >d1nr9a_ d.177.1.1 (A:) Putative isomerase YcgM {Escherichia coli [TaxId: 562]} Probab=21.47 E-value=18 Score=12.88 Aligned_cols=20 Identities=25% Similarity=0.302 Sum_probs=15.6 Q ss_pred HHHHHCCCCCCEEECCCCCC Q ss_conf 98994579997898257899 Q gi|254780687|r 253 LKDVVTLKIGQVIPFLHREK 272 (318) Q Consensus 253 l~dil~L~vGDVI~L~~~~~ 272 (318) +.+.+.|.+||+|-...+.. T Consensus 177 lS~~~tL~pGDiI~TGTP~G 196 (221) T d1nr9a_ 177 MSKFFTLKAGDVVLTGTPDG 196 (221) T ss_dssp HTTTSCBCTTCEEECCCCSC T ss_pred HHCCCEECCCCEEECCCCCC T ss_conf 84799789997899589898 No 11 >d1s04a_ b.122.1.6 (A:) Hypothetical protein PF0455 {Pyrococcus furiosus [TaxId: 2261]} Probab=21.30 E-value=12 Score=13.97 Aligned_cols=37 Identities=16% Similarity=0.262 Sum_probs=23.0 Q ss_pred CCHHHHHHHHHHHHHCEEEEEEEEEEEEECHHHHHCCCCCCEEECC Q ss_conf 7989999999997408007999981234309899457999789825 Q gi|254780687|r 223 QSEDLIDPFARKTYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFL 268 (318) Q Consensus 223 ~~~~~~~~l~~~l~~~~v~i~a~Lg~~~l~l~dil~L~vGDVI~L~ 268 (318) ..+.|-..+......+++.+ .=++...+++||.|.+. T Consensus 7 L~~~~F~~Ik~G~K~IE~Rl---------~d~kr~~ik~GD~I~F~ 43 (110) T d1s04a_ 7 LQEEFLELIKLRKKKIEGRL---------YDEKRRQIKPGDVISFE 43 (110) T ss_dssp CCHHHHHHHHHTTSSCCCCC---------CCHHHHHCCSSSCEEET T ss_pred CCCCHHHHHHCCCCEEEEEE---------CHHHHHHCCCCCEEEEE T ss_conf 57015799876897899980---------65668638999999994 Done!