Query         gi|254780616|ref|YP_003065029.1| F0F1 ATP synthase subunit gamma [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 294
No_of_seqs    111 out of 2347
Neff          7.8 
Searched_HMMs 13730
Date          Wed Jun  1 10:11:07 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780616.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 d2jdig1 c.49.2.1 (G:1-272) ATP 100.0       0       0  543.5  18.4  272    2-294     1-272 (272)
  2 d1fs0g_ c.49.2.1 (G:) ATP synt 100.0       0       0  412.8  22.2  230   19-255     1-230 (230)
  3 d1oaoc_ e.26.1.3 (C:) Bifuncti  76.1     1.4 0.00011   20.7   3.9   22   80-102   517-539 (729)
  4 d1t70a_ d.159.1.9 (A:) Putativ  47.5     1.5 0.00011   20.5  -0.4   13  162-174   158-170 (255)
  5 d1qw2a_ d.249.1.1 (A:) Hypothe  43.2       4 0.00029   17.9   1.2   39   81-130    32-72  (102)
  6 d1u55a_ d.278.1.1 (A:) Methyl-  34.6      12 0.00085   14.9   6.2   46   61-107   108-153 (188)
  7 d2pk8a1 d.274.1.1 (A:2-95) Hyp  26.3      16  0.0012   14.0   3.9   36   97-132     8-43  (94)
  8 d1sfea2 c.55.7.1 (A:12-92) Ada  23.5     8.3 0.00061   15.9   0.1   13   80-92     14-26  (81)
  9 d1ja1a2 c.23.5.2 (A:63-239) NA  21.8      20  0.0014   13.5   3.2   44   80-124    70-114 (177)
 10 d1kxpd3 a.126.1.1 (D:405-473)   19.0      18  0.0013   13.7   1.1   19   90-108     2-20  (69)

No 1  
>d2jdig1 c.49.2.1 (G:1-272) ATP synthase (F1-ATPase), gamma subunit {Cow (Bos taurus) [TaxId: 9913]}
Probab=100.00  E-value=0  Score=543.54  Aligned_cols=272  Identities=29%  Similarity=0.454  Sum_probs=237.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf             88799999999875689999999999999999999999830236999999999997301575442100024433343255
Q gi|254780616|r    2 TSLKEFKSRIHSVKETQKITEAMQLISVTKLRRAKEAIQNASSYQFHIKDFFMKCVVGEHFQEYPSPFVRGTGKDKVYLL   81 (294)
Q Consensus         2 ~~lk~ik~RI~sv~~~~KITkaMkmVA~skl~ka~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (294)
                      |||+|||+||+||++|+||||||+|||+|||||+|++++++|||+.....++.+            +.+..+...++.++
T Consensus         1 A~Lkeik~RI~Sv~~t~kITkAMkmVAasKlrkaq~~~~~~r~Y~~~~~~~~~~------------~~~~~~~~~~~~l~   68 (272)
T d2jdig1           1 ATLKDITRRLKSIKNIQKITKSMKMVAAAKYARAERELKPARVYGVGSLALYEK------------ADIKTPEDKKKHLI   68 (272)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-------------------------------CC
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCC------------CCCHHCCCCCCCEE
T ss_conf             986999999999879999999999999999999999998427658886886505------------32010134565116


Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHCCCCCCEEEEECCCCCCCCHHHHHHHHHHHH
Q ss_conf             31146424420011479999999876532038850388870403798510233320111114776640368899999765
Q gi|254780616|r   82 VICTAEKGLCGGFNAQIIRFARDRIKEFIAEGKEIKLLIIGRKGYEGLRKEFSSMIIDSIELSSKKGVDFVQAHGIARQI  161 (294)
Q Consensus        82 IvitSDrGLCG~~Ns~i~k~~~~~i~~~~~~~~~~~l~~vGkKg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~l  161 (294)
                      |||||||||||+||++|+|.+.+.+.+...++.++.++.+|+||.+++.+.+.......+.......+++..+..+...+
T Consensus        69 IvitSDrGLcG~fN~~iik~~~~~i~~~~~~~~~~~l~~~G~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~  148 (272)
T d2jdig1          69 IGVSSDRGLCGAIHSSVAKQMKSEAANLAAAGKEVKIIGVGDKIRSILHRTHSDQFLVTFKEVGRRPPTFGDASVIALEL  148 (272)
T ss_dssp             CCBCCSCCCSTTHHHHHC------------------CCCBSHHHHHHC----------CBCSCSSSCCCHHHHHHHHHHC
T ss_pred             EEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHCCCCEEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             99865777777764218999999988752168722898504302445553035212332200577775067789999999


Q ss_pred             HHHHHCCCCCCEEEEECCCCCCCCCCEEEEECCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             57650678750588620113443222044204788735422110036554322479967878999998999999999999
Q gi|254780616|r  162 TSLFTSNVFDLCFFIYSEFKSIIQQIPIISKIIPVDWSQDLEQKQQDILSVYRYESTLYSVLDDIVLRSISSRVFWIILE  241 (294)
Q Consensus       162 ~~~~~~~~~d~v~iiYn~f~s~~~q~p~~~~llP~~~~~~~~~~~~~~~~~~~~Ep~~~~il~~l~~~yl~~~l~~alle  241 (294)
                      ..  ..+++|+|+|+||+|+|+++|.|..++++|+++.       +.....|.|||+++++|+.|+|.|++++||+|++|
T Consensus       149 ~~--~~~~~d~v~i~y~~f~~~~~q~p~~~~l~p~~~~-------~~~~~~~~~~~~~~~vl~~l~~~yl~~~ly~a~~e  219 (272)
T d2jdig1         149 LN--SGYEFDEGSIIFNRFRSVISYKTEEKPIFSLDTI-------SSAESMSIYDDIDADVLRNYQEYSLANIIYYSLKE  219 (272)
T ss_dssp             ------------CCCCCEECSSSCEECC---------------------------------------HHHHHHHHHHHHH
T ss_pred             HH--HHHHCCEEEEEEECCCCCCCCCCEEECCCCCCCC-------CCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98--6642340379961245554122046416666630-------00000000134437899999999899999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999999999989999999999999998988988999998525319
Q gi|254780616|r  242 NKASEVGARITAMDNATRNAGQMVDNLVLSYNRQRQMRITTELIEIIAGAEVV  294 (294)
Q Consensus       242 s~aSE~aaRm~AM~~At~Na~~~i~~L~l~~Nk~RQ~~IT~El~EIisGaeAl  294 (294)
                      |+||||+|||+||++|||||+||+++|+++|||+||++||+||+|||||||||
T Consensus       220 s~aSE~aaRm~AM~~At~Na~eli~~L~~~yNr~RQ~~IT~El~EIv~GaeAl  272 (272)
T d2jdig1         220 STTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAAL  272 (272)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             89999999999999999849999999999999999999999999999778439


No 2  
>d1fs0g_ c.49.2.1 (G:) ATP synthase (F1-ATPase), gamma subunit {Escherichia coli [TaxId: 562]}
Probab=100.00  E-value=0  Score=412.76  Aligned_cols=230  Identities=23%  Similarity=0.419  Sum_probs=207.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHH
Q ss_conf             99999999999999999999983023699999999999730157544210002443334325531146424420011479
Q gi|254780616|r   19 KITEAMQLISVTKLRRAKEAIQNASSYQFHIKDFFMKCVVGEHFQEYPSPFVRGTGKDKVYLLVICTAEKGLCGGFNAQI   98 (294)
Q Consensus        19 KITkaMkmVA~skl~ka~~~~~~~~~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvitSDrGLCG~~Ns~i   98 (294)
                      ||||||||||+|||||+|++++++|||++.+.+++.++...  ..+..+|++.+++.+ +.++|||||||||||+||++|
T Consensus         1 KITkAMkmVAasKl~kaq~~~~~~r~Y~~~~~~~l~~l~~~--~~~~~~~~~~~~~~~-~~~~ivitSDrGLCG~~Ns~i   77 (230)
T d1fs0g_           1 KITKAMEMVAASKMRKSQDRMAASRPYAETMRKVIGHLAHG--NLEYKHPYLEDRDVK-RVGYLVVSTDRGLCGGLNINL   77 (230)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC------CCCGGGSCCCCS-EEEEEEECCSSSCSTTHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCC-EEEEEEEECCCCCCCCCCHHH
T ss_conf             96788999999999999999995250999999999999833--854346433478877-189999965853445531138


Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf             99999987653203885038887040379851023332011111477664036889999976557650678750588620
Q gi|254780616|r   99 IRFARDRIKEFIAEGKEIKLLIIGRKGYEGLRKEFSSMIIDSIELSSKKGVDFVQAHGIARQITSLFTSNVFDLCFFIYS  178 (294)
Q Consensus        99 ~k~~~~~i~~~~~~~~~~~l~~vGkKg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~l~~~~~~~~~d~v~iiYn  178 (294)
                      +|.+.+++++...+|.++.+++||+||.+|+++++.+.+..+....+  .+++.++..|++.+++.|.++++|+|+++||
T Consensus        78 ~k~~~~~~~~~~~~~~~~~~~~vGkk~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~i~~~~~~~~~~~~~d~v~iiYn  155 (230)
T d1fs0g_          78 FKKLLAEMKTWTDKGVQCDLAMIGSKGVSFFNSVGGNVVAQVTGMGD--NPSLSELIGPVKVMLQAYDEGRLDKLYIVSN  155 (230)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEESHHHHHHHHHHCCCEEEEECCCTT--CCCSHHHHHHHHHHHHHHHTTSCSCEEEEEE
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEEEEEHHHHHHCCCCEEEECCCCCC--CCCHHHHHHHHHHHHHHHHCCCCEEEEEEEC
T ss_conf             99999987665405873168875333325777428832431246766--7458889889999999886288338999952


Q ss_pred             CCCCCCCCCEEEEECCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11344322204420478873542211003655432247996787899999899999999999999999999999999
Q gi|254780616|r  179 EFKSIIQQIPIISKIIPVDWSQDLEQKQQDILSVYRYESTLYSVLDDIVLRSISSRVFWIILENKASEVGARITAMD  255 (294)
Q Consensus       179 ~f~s~~~q~p~~~~llP~~~~~~~~~~~~~~~~~~~~Ep~~~~il~~l~~~yl~~~l~~alles~aSE~aaRm~AM~  255 (294)
                      +|+|+++|+|+.+++||++.....  ......++|+|||+++++|++|+|+|++++||+|++||.||||+|||+||+
T Consensus       156 ~f~s~~~q~p~~~~llP~~~~~~~--~~~~~~~~~~fEP~~~~vl~~l~~~yl~~~ly~allEs~aSE~aARm~AM~  230 (230)
T d1fs0g_         156 KFINTMSQVPTISQLLPLPASDDD--DLKHKSWDYLYEPDPKALLDTLLRRYVESQVYQGVVENLASEQAARMVAMK  230 (230)
T ss_dssp             EEEETTEEEEEEEEEESCC---------CCCSCCCEEESCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCEEEEEECCCCCCCC--CCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             455534344122100023320012--234678885417899999999999999999999999999999999999668


No 3  
>d1oaoc_ e.26.1.3 (C:) Bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) alpha (ACS) subunit {Moorella thermoacetica [TaxId: 1525]}
Probab=76.12  E-value=1.4  Score=20.68  Aligned_cols=22  Identities=27%  Similarity=0.569  Sum_probs=12.3

Q ss_pred             EEEECCCCH-HHHHHHHHHHHHHH
Q ss_conf             553114642-44200114799999
Q gi|254780616|r   80 LLVICTAEK-GLCGGFNAQIIRFA  102 (294)
Q Consensus        80 ~~IvitSDr-GLCG~~Ns~i~k~~  102 (294)
                      +||| |.|| ||||++|=-=.|.+
T Consensus       517 VCvV-tPeR~gLCGAisWlD~kAa  539 (729)
T d1oaoc_         517 VCIV-TPERVGLCGAVSWLDAKAS  539 (729)
T ss_dssp             CEEE-BTTBCCTTSCCCHHHHHHH
T ss_pred             EEEE-CCCCCCCCCEEECCCCHHH
T ss_conf             4896-8986655450141030545


No 4  
>d1t70a_ d.159.1.9 (A:) Putative phosphatase DR1281 {Deinococcus radiodurans [TaxId: 1299]}
Probab=47.49  E-value=1.5  Score=20.52  Aligned_cols=13  Identities=0%  Similarity=-0.079  Sum_probs=5.4

Q ss_pred             HHHHHCCCCCCEE
Q ss_conf             5765067875058
Q gi|254780616|r  162 TSLFTSNVFDLCF  174 (294)
Q Consensus       162 ~~~~~~~~~d~v~  174 (294)
                      +-+|..|.+..|.
T Consensus       158 ~g~~ldGrvsav~  170 (255)
T d1t70a_         158 MGWHLAGRVAAVI  170 (255)
T ss_dssp             HHHHHTTSSSEEE
T ss_pred             HHHHHCCCEEEEE
T ss_conf             8853437679998


No 5  
>d1qw2a_ d.249.1.1 (A:) Hypothetical protein Ta1206 {Archaeon Thermoplasma acidophilum [TaxId: 2303]}
Probab=43.25  E-value=4  Score=17.86  Aligned_cols=39  Identities=23%  Similarity=0.449  Sum_probs=25.3

Q ss_pred             EEECCCCHHH--HHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECHHHHHHH
Q ss_conf             5311464244--2001147999999987653203885038887040379851
Q gi|254780616|r   81 LVICTAEKGL--CGGFNAQIIRFARDRIKEFIAEGKEIKLLIIGRKGYEGLR  130 (294)
Q Consensus        81 ~IvitSDrGL--CG~~Ns~i~k~~~~~i~~~~~~~~~~~l~~vGkKg~~~~~  130 (294)
                      ++++++|+|+  ||.+|-..+..       +    ..+...+.|=+-.+-+-
T Consensus        32 Ll~i~~~~G~imCG~ldV~~~~k-------~----g~~A~rv~GV~TiedlL   72 (102)
T d1qw2a_          32 LLFIKGSKGYAMCGYLNMETSNK-------V----GDIAVRVMGVKTLDDML   72 (102)
T ss_dssp             EEEEECSSCEEECTTCCHHHHHH-------T----TCCEEECCSCCSHHHHH
T ss_pred             EEEEECCCCEEEECCCCHHHHHH-------C----CCEEEEEEEECCHHHHH
T ss_conf             99998288489964334899863-------5----88059997004499984


No 6  
>d1u55a_ d.278.1.1 (A:) Methyl-accepting chemotaxis protein {Thermoanaerobacter tengcongensis [TaxId: 119072]}
Probab=34.58  E-value=12  Score=14.91  Aligned_cols=46  Identities=9%  Similarity=0.049  Sum_probs=31.4

Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             57544210002443334325531146424420011479999999876
Q gi|254780616|r   61 HFQEYPSPFVRGTGKDKVYLLVICTAEKGLCGGFNAQIIRFARDRIK  107 (294)
Q Consensus        61 ~~~~~~~~~~~~~~~~~~~~~IvitSDrGLCG~~Ns~i~k~~~~~i~  107 (294)
                      .+.+...|.+.-.......+.+...|.|||| .|-..+++.+-++..
T Consensus       108 ~yp~~~~P~f~~~~~~~~~l~l~Y~S~R~l~-~~~~Gli~g~A~~f~  153 (188)
T d1u55a_         108 MIKGATPPRLIAKPVAKDAIEMEYVSKRKMY-DYFLGLIEGSSKFFK  153 (188)
T ss_dssp             TSTTCCCCBCCEEEEETTEEEEEEEETTCCH-HHHHHHHHHHHHHHT
T ss_pred             HCCCCCCCEEEEEECCCCEEEEEEEECCCHH-HHHHHHHHHHHHHHC
T ss_conf             3889989957999878998999999579838-999999999999959


No 7  
>d2pk8a1 d.274.1.1 (A:2-95) Hypothetical protein PF0899 {Pyrococcus furiosus [TaxId: 2261]}
Probab=26.27  E-value=16  Score=14.02  Aligned_cols=36  Identities=19%  Similarity=0.436  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHCC
Q ss_conf             799999998765320388503888704037985102
Q gi|254780616|r   97 QIIRFARDRIKEFIAEGKEIKLLIIGRKGYEGLRKE  132 (294)
Q Consensus        97 ~i~k~~~~~i~~~~~~~~~~~l~~vGkKg~~~~~~~  132 (294)
                      .++....+.+.+++.+|-+..++.+|.-++.|++..
T Consensus         8 riL~~ie~~inELk~dG~ePDiiL~G~e~~ef~~~~   43 (94)
T d2pk8a1           8 RILGEIEEKMNELKMDGFNPDIILFGREAYNFLSNL   43 (94)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCCEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEECHHHHHHHHHH
T ss_conf             999999999999986589987699748999999999


No 8  
>d1sfea2 c.55.7.1 (A:12-92) Ada DNA repair protein {Escherichia coli [TaxId: 562]}
Probab=23.49  E-value=8.3  Score=15.86  Aligned_cols=13  Identities=23%  Similarity=0.779  Sum_probs=9.6

Q ss_pred             EEEECCCCHHHHH
Q ss_conf             5531146424420
Q gi|254780616|r   80 LLVICTAEKGLCG   92 (294)
Q Consensus        80 ~~IvitSDrGLCG   92 (294)
                      -+++..|++|+|+
T Consensus        14 ~llvaat~~Glc~   26 (81)
T d1sfea2          14 RCLVAESERGICA   26 (81)
T ss_dssp             EEEEEECSSSEEE
T ss_pred             EEEEEECCCCEEE
T ss_conf             0899984893899


No 9  
>d1ja1a2 c.23.5.2 (A:63-239) NADPH-cytochrome p450 reductase, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}
Probab=21.76  E-value=20  Score=13.47  Aligned_cols=44  Identities=23%  Similarity=0.240  Sum_probs=18.8

Q ss_pred             EEEECCCCHHHHHHHHHHHHHHHHHHHHHH-HHCCCCEEEEEEECH
Q ss_conf             553114642442001147999999987653-203885038887040
Q gi|254780616|r   80 LLVICTAEKGLCGGFNAQIIRFARDRIKEF-IAEGKEIKLLIIGRK  124 (294)
Q Consensus        80 ~~IvitSDrGLCG~~Ns~i~k~~~~~i~~~-~~~~~~~~l~~vGkK  124 (294)
                      ++|+++|--|- |.+..+.-+....+.+.. .-.+..+.|+..|.+
T Consensus        70 ~~i~~~ST~g~-G~~P~n~~~F~~~L~~~~~~l~~~~yaVfGlGds  114 (177)
T d1ja1a2          70 LVVFCMATYGE-GDPTDNAQDFYDWLQETDVDLTGVKFAVFGLGNK  114 (177)
T ss_dssp             EEEEEEEEETT-TEECGGGHHHHHHHHHCCCCCTTCEEEEEEEECS
T ss_pred             EEEEEEECCCC-CCCCHHHHHHHHHHHHCCCCCCCCEEEEEECCCC
T ss_conf             69999824579-9987769999998873120235753788825885


No 10 
>d1kxpd3 a.126.1.1 (D:405-473) Vitamin D binding protein {Human (Homo sapiens) [TaxId: 9606]}
Probab=19.02  E-value=18  Score=13.66  Aligned_cols=19  Identities=16%  Similarity=0.506  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             4200114799999998765
Q gi|254780616|r   90 LCGGFNAQIIRFARDRIKE  108 (294)
Q Consensus        90 LCG~~Ns~i~k~~~~~i~~  108 (294)
                      |||.|+.+-+-..+..+.+
T Consensus         2 LC~dYse~tFte~kkkL~e   20 (69)
T d1kxpd3           2 LCADYSENTFTEYKKKLAE   20 (69)
T ss_dssp             HTTTTTTSCHHHHHHHHHH
T ss_pred             CHHHHHHCCHHHHHHHHHH
T ss_conf             1033312309999999999


Done!