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!