Query         gi|254780295|ref|YP_003064708.1| tRNA pseudouridine synthase A [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 247
No_of_seqs    126 out of 3058
Neff          7.3 
Searched_HMMs 13730
Date          Tue May 24 17:09:53 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780295.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 d1dj0a_ d.265.1.1 (A:) Pseudou 100.0       0       0  540.3  16.2  245    1-247     3-247 (264)
  2 d1u02a_ c.108.1.15 (A:) Trehal  39.8      10 0.00076   15.9   2.9   48    5-53      2-49  (229)
  3 d1l5aa1 c.43.1.2 (A:1-174) Vib  25.2      12 0.00085   15.6   1.1   24   61-84     24-47  (174)
  4 d2hh8a1 d.358.1.1 (A:7-133) Hy  22.2      14 0.00099   15.2   1.0   31  131-161    62-93  (127)
  5 d1q9ja1 c.43.1.2 (A:1-175) Pol  21.6      16  0.0012   14.7   1.3   22   63-84     27-48  (175)
  6 d1nbwa3 c.55.1.6 (A:406-607) A  16.8      29  0.0021   13.3   2.5  120   46-173    11-147 (202)
  7 d1e88a3 g.27.1.1 (A:1-41) Fibr  12.1      26  0.0019   13.5   0.4   11   47-57      2-12  (41)
  8 d1ixsa_ a.5.1.1 (A:) DNA helic  10.7      43  0.0031   12.3   2.4   39  185-223     9-47  (50)
  9 d1bs0a_ c.67.1.4 (A:) PLP-depe   8.2      55   0.004   11.7   1.5   52    8-59     41-116 (383)
 10 d2bwna1 c.67.1.4 (A:2-397) 5-a   7.8      57  0.0041   11.6   1.5   47   12-58     76-122 (396)

No 1  
>d1dj0a_ d.265.1.1 (A:) Pseudouridine synthase I TruA {Escherichia coli [TaxId: 562]}
Probab=100.00  E-value=0  Score=540.27  Aligned_cols=245  Identities=37%  Similarity=0.573  Sum_probs=239.4

Q ss_pred             CCEEEEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCHHHHHHHH
Q ss_conf             92299999971668720048753877889999999997099569997112138612223468864063211046899999
Q gi|254780295|r    1 MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALN   80 (247)
Q Consensus         1 M~r~~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~qv~~f~~~~~~~~~~~~~~lN   80 (247)
                      |.||++.|+||||+|+|||+||+.+||||+||+||.+++++++.+.+|||||+||||++||+||+++...+.+.+...||
T Consensus         3 ~~r~al~i~Y~Gt~f~G~Q~Q~~~~TVq~~Le~aL~~~~~~~~~~~~agRTD~GVhA~~qv~~~~~~~~~~~~~~~~~lN   82 (264)
T d1dj0a_           3 VYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVN   82 (264)
T ss_dssp             CEEEEEEEEECCTTSSCSCCTTCSSCHHHHHHHHHHHHHTSCCCEEESSCCCTTCEEEEEEEEEEESCCCCHHHHHHHHH
T ss_pred             CEEEEEEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCEEEEEEEEEECCCHHHHHHHCCCC
T ss_conf             47999999997997125758969979999999999996399738998402467733166799975122000111000001


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCEECCCCEEEEEEEEECCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHCCHHEEEECC
Q ss_conf             86188876543443226777550002100223556852443202333210244333335665565676520011001024
Q gi|254780295|r   81 AYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRS  160 (247)
Q Consensus        81 ~~L~~p~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~l~~a~~~l~G~HdF~~F~~  160 (247)
                      +.|  |+||+|+++.+|+++||||++|++|+|+|++.++..++++.+.+.|+...++|+++|++|++.|+|+|||++||+
T Consensus        83 ~~L--p~dI~i~~~~~v~~~F~aR~~a~~r~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~~~G~hdF~~F~~  160 (264)
T d1dj0a_          83 ANL--PGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRA  160 (264)
T ss_dssp             HTS--CTTEEEEEEEECCTTCCTTTTCCEEEEEEEEECSSSCCCTTTTSSEECCSCCCHHHHHHHHGGGCEEEECGGGCC
T ss_pred             CCC--CCCCCCCCCEECCCCCCCHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             234--423110000001665440033331243002013445663223321024677656888877763367541111211


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf             56553332110331111233320011315888899999999999999976899888999998358821166636989847
Q gi|254780295|r  161 IHCQASSPIRTIDHFDVNSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY  240 (247)
Q Consensus       161 ~~~~~~~~~R~I~~~~v~~~~~~i~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~  240 (247)
                      .++..++++|++..+++.+.++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+++++....++|||+|||
T Consensus       161 ~~~~~~~~~r~i~~~~~~~~~~~i~i~i~g~sFL~~qVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~  240 (264)
T d1dj0a_         161 VQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLY  240 (264)
T ss_dssp             TTCCCSCCEEEEEEEEEEEETTEEEEEEEESCCCTTHHHHHHHHHHHHHTTSSCTTHHHHHHHHCCGGGSCCCCCSTTEE
T ss_pred             CCCCCCCCCCCCCCCCCEECCCEEEEEECHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCE
T ss_conf             45557774222211011014837998741037999999999999999976999999999998668856685644898878


Q ss_pred             EEEEEEC
Q ss_conf             6330439
Q gi|254780295|r  241 FDSVEYS  247 (247)
Q Consensus       241 L~~V~Y~  247 (247)
                      |++|+|.
T Consensus       241 L~~V~Y~  247 (264)
T d1dj0a_         241 LVAVDYP  247 (264)
T ss_dssp             EEEEECC
T ss_pred             ECCCCCC
T ss_conf             7555368


No 2  
>d1u02a_ c.108.1.15 (A:) Trehalose-6-phosphate phosphatase related protein {Archaeon Thermoplasma acidophilum [TaxId: 2303]}
Probab=39.77  E-value=10  Score=15.85  Aligned_cols=48  Identities=13%  Similarity=0.156  Sum_probs=33.5

Q ss_pred             EEEEEECCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCC
Q ss_conf             9999971668720048753877889999999997099569997112138
Q gi|254780295|r    5 CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDS   53 (247)
Q Consensus         5 ~~~i~YdGt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~   53 (247)
                      ++.+=+||| ...+..+|...++...+.++|.++...-.-++.+||+-.
T Consensus         2 Li~~DlDGT-L~~~~~~~~~~~i~~~~~~~l~~l~~~~~v~i~TGR~~~   49 (229)
T d1u02a_           2 LIFLDYDGT-LVPIIMNPEESYADAGLLSLISDLKERFDTYIVTGRSPE   49 (229)
T ss_dssp             EEEEECBTT-TBCCCSCGGGCCCCHHHHHHHHHHHHHSEEEEECSSCHH
T ss_pred             EEEEEECCC-CCCCCCCHHHCCCCHHHHHHHHHHHHCCCEEEECCCCHH
T ss_conf             899995577-789978965488999999999998509978999699879


No 3  
>d1l5aa1 c.43.1.2 (A:1-174) VibH {Vibrio cholerae [TaxId: 666]}
Probab=25.17  E-value=12  Score=15.56  Aligned_cols=24  Identities=17%  Similarity=0.199  Sum_probs=16.6

Q ss_pred             EEEEEECCCCCCHHHHHHHHHHHC
Q ss_conf             688640632110468999998618
Q gi|254780295|r   61 VAHFDLVREWVPVILCKALNAYLK   84 (247)
Q Consensus        61 v~~f~~~~~~~~~~~~~~lN~~L~   84 (247)
                      ...+.+..+++.+.+.++++..+.
T Consensus        24 ~~~~~i~g~ld~~~l~~A~~~l~~   47 (174)
T d1l5aa1          24 AHSLRLTGPLDTTLLLRALHLTVS   47 (174)
T ss_dssp             EEEEEEESSCCHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHH
T ss_conf             189998178799999999999997


No 4  
>d2hh8a1 d.358.1.1 (A:7-133) Hypothetical protein YdfO {Escherichia coli [TaxId: 562]}
Probab=22.24  E-value=14  Score=15.18  Aligned_cols=31  Identities=16%  Similarity=0.149  Sum_probs=24.1

Q ss_pred             CCCCCCCCHHHHHHHHHHH-HCCHHEEEECCC
Q ss_conf             2443333356655656765-200110010245
Q gi|254780295|r  131 WLIPKSLDCENMRIAAQHL-VGRHDFTTFRSI  161 (247)
Q Consensus       131 ~~~~~~lD~~~l~~a~~~l-~G~HdF~~F~~~  161 (247)
                      -.+....|.++++++++.. -|+.||.-||+.
T Consensus        62 ~~Va~~~n~~~i~~al~~~QaG~~~f~~Fc~~   93 (127)
T d2hh8a1          62 VSVKFSKDRHLIETTSNKLKSREITFQEYRRN   93 (127)
T ss_dssp             CCCCSCCCHHHHHHHHHHHHHTCCCHHHHHHH
T ss_pred             EEECCCCCHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf             78517589999999999986488659999999


No 5  
>d1q9ja1 c.43.1.2 (A:1-175) Polyketide synthase associated protein 5, PapA5 {Mycobacterium tuberculosis [TaxId: 1773]}
Probab=21.64  E-value=16  Score=14.70  Aligned_cols=22  Identities=23%  Similarity=0.143  Sum_probs=14.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHC
Q ss_conf             8640632110468999998618
Q gi|254780295|r   63 HFDLVREWVPVILCKALNAYLK   84 (247)
Q Consensus        63 ~f~~~~~~~~~~~~~~lN~~L~   84 (247)
                      .+.++..++.+.+..+++....
T Consensus        27 ~~~l~g~ld~~~l~~A~~~lv~   48 (175)
T d1q9ja1          27 TIQLRGVIDVDALSDAFDALLE   48 (175)
T ss_dssp             EEEEESCCCHHHHHHHHHHHHH
T ss_pred             EEEECCCCCHHHHHHHHHHHHH
T ss_conf             9998588899999999999999


No 6  
>d1nbwa3 c.55.1.6 (A:406-607) ATPase domain of the glycerol dehydratase reactivase alpha subunit {Klebsiella pneumoniae [TaxId: 573]}
Probab=16.78  E-value=29  Score=13.30  Aligned_cols=120  Identities=20%  Similarity=0.241  Sum_probs=63.1

Q ss_pred             EECCCCCC-CCEEEEEEEEEEECCCCCCHHHHHHHHHHHCCC-----CCCCCCCCCCCCCCCCCEECCCCEEEEEEEEEC
Q ss_conf             97112138-612223468864063211046899999861888-----765434432267775500021002235568524
Q gi|254780295|r   46 HGAGRTDS-GVHALRQVAHFDLVREWVPVILCKALNAYLKIS-----DTISILNLSIVDKQFHARFSAIRRSYLYRIITR  119 (247)
Q Consensus        46 ~~a~RTD~-GVhA~~qv~~f~~~~~~~~~~~~~~lN~~L~~p-----~~Irv~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~  119 (247)
                      .|+|-||+ ..++.|++..+.+..-  -+-+...+|+.|-++     ++|+-.-..+|..-||.|+---.+    .+...
T Consensus        11 lG~GStDasii~~~g~v~avhlAGA--G~mVTmlI~~eLGl~d~~lAE~IKkyPlakVEslf~irhEdG~v----~Ff~~   84 (202)
T d1nbwa3          11 LGAGSTDAAIVNAEGQITAVHLAGA--GNMVSLLIKTELGLEDLSLAEAIKKYPLAKVESLFSIRHENGAV----EFFRE   84 (202)
T ss_dssp             ECSSEEEEEEECSSSCEEEEEEECC--HHHHHHHHHHHHTCSCHHHHHHHHHSCEEEECSSSEEEETTSCE----EECSS
T ss_pred             CCCCCCCHHHCCCCCCEEEEEECCC--CHHHHHHHHHHHCCCCHHHHHHHHHCCHHHHCCCEEEEECCCCE----EEECC
T ss_conf             3898533544067885899996277--31649999987289957899987326244413433788517826----87158


Q ss_pred             CCCCHHHHHHCCC-------CCCCCCHHHHH---HHHHH-HHCCHHEEEECCCCCCCCCCCCCCC
Q ss_conf             4320233321024-------43333356655---65676-5200110010245655333211033
Q gi|254780295|r  120 QAPLALEKGRAWL-------IPKSLDCENMR---IAAQH-LVGRHDFTTFRSIHCQASSPIRTID  173 (247)
Q Consensus       120 ~~~~~~~~~~~~~-------~~~~lD~~~l~---~a~~~-l~G~HdF~~F~~~~~~~~~~~R~I~  173 (247)
                      +.++......+..       ++..+.+++.+   ..+|. ..=+.-.+++....+  ...+|.|.
T Consensus        85 pl~p~~farvv~~~~~~lvP~~~~~~~Ekir~vR~~aK~~vfvtNa~RaL~~vsp--~gnir~i~  147 (202)
T d1nbwa3          85 ALSPAVFAKVVYIKEGELVPIDNASPLEKIRLVRRQAKEKVFVTNCLRALRQVSP--GGSIRDIA  147 (202)
T ss_dssp             CCCGGGTTCEEEEETTEEEEECCSSCHHHHHHHHHHHHHHHHHHHHHHHHSSSST--TCCSTTCC
T ss_pred             CCCHHHEEEEEEECCCCEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CCCCCCCC
T ss_conf             9995790689995379535358855589999999987567479989999860499--88867776


No 7  
>d1e88a3 g.27.1.1 (A:1-41) Fibronectin {Human (Homo sapiens) [TaxId: 9606]}
Probab=12.14  E-value=26  Score=13.54  Aligned_cols=11  Identities=55%  Similarity=0.516  Sum_probs=8.0

Q ss_pred             ECCCCCCCCEE
Q ss_conf             71121386122
Q gi|254780295|r   47 GAGRTDSGVHA   57 (247)
Q Consensus        47 ~a~RTD~GVhA   57 (247)
                      |..+||.||.-
T Consensus         2 G~C~Td~Gv~Y   12 (41)
T d1e88a3           2 GHCVTDSGVVY   12 (41)
T ss_dssp             CCEEETTTEEE
T ss_pred             CCCCCCCCEEE
T ss_conf             85574687577


No 8  
>d1ixsa_ a.5.1.1 (A:) DNA helicase RuvA subunit, C-terminal domain {Thermus thermophilus [TaxId: 274]}
Probab=10.72  E-value=43  Score=12.27  Aligned_cols=39  Identities=21%  Similarity=0.185  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             113158888999999999999999768998889999983
Q gi|254780295|r  185 EIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQ  223 (247)
Q Consensus       185 ~i~i~g~~FL~~mVR~mVG~li~v~~g~~~~~~i~~~L~  223 (247)
                      ..-+.+=||--.|||..|.-+++-.-+.-..+-|+..|.
T Consensus         9 ~~AL~aLGFrE~QvRsvVaell~~nP~a~aq~lIr~aL~   47 (50)
T d1ixsa_           9 VMALAALGFKEAQARAVVLDLLAQNPKARAQDLIKEALK   47 (50)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHCTTCCHHHHHHHHHT
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             999999642178999999999871954239999999986


No 9  
>d1bs0a_ c.67.1.4 (A:) PLP-dependent acyl-CoA synthase (8-amino-7-oxonanoate synthase, AONS) {Escherichia coli [TaxId: 562]}
Probab=8.15  E-value=55  Score=11.67  Aligned_cols=52  Identities=10%  Similarity=0.157  Sum_probs=35.1

Q ss_pred             EEECCCCCEEEEECC------------------------CCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEE
Q ss_conf             997166872004875------------------------3877889999999997099569997112138612223
Q gi|254780295|r    8 IEYNGSGYFGWQRQK------------------------NGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR   59 (247)
Q Consensus         8 i~YdGt~y~G~q~Q~------------------------~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~~   59 (247)
                      +-+.+++|-|+...|                        +...+..+||+.|..+++.+-.+..+|=+.+...+..
T Consensus        41 l~f~s~dYLGl~~~p~v~~a~~~a~~~~G~~~~~sr~~~g~~~~~~~lE~~LA~~~g~e~al~~~SG~~an~~~i~  116 (383)
T d1bs0a_          41 LNFSSNDYLGLSHHPQIIRAWQQGAEQFGIGSGGSGHVSGYSVVHQALEEELAEWLGYSRALLFISGFAANQAVIA  116 (383)
T ss_dssp             EECSCCCTTSGGGCHHHHHHHHHHHHHHCSCCCSBTTTTCCCHHHHHHHHHHHHHHTCSEEEEESCHHHHHHHHHH
T ss_pred             EEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHH
T ss_conf             9987653026678989999999999983898876553467406899999999875199835886044224677787


No 10 
>d2bwna1 c.67.1.4 (A:2-397) 5-aminolevulinate synthase {Rhodobacter capsulatus [TaxId: 1061]}
Probab=7.78  E-value=57  Score=11.57  Aligned_cols=47  Identities=13%  Similarity=0.089  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEE
Q ss_conf             66872004875387788999999999709956999711213861222
Q gi|254780295|r   12 GSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHAL   58 (247)
Q Consensus        12 Gt~y~G~q~Q~~~~TVq~~le~aL~~~~~~~~~~~~a~RTD~GVhA~   58 (247)
                      |++..|...-.+...+..+||+.|.++++.+-.+..+|=.++++.+.
T Consensus        76 G~gs~~Sr~~~G~~~~h~~LE~~lA~~~g~e~all~~sG~~An~~~i  122 (396)
T d2bwna1          76 GAGSGGTRNISGTTAYHRRLEAEIAGLHQKEAALVFSSAYNANDATL  122 (396)
T ss_dssp             CSCCCSBTTTBCCBHHHHHHHHHHHHHTTCSEEEEESCHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHH
T ss_conf             89864552445874499999999999749985155401137788899


Done!