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!