Query gi|254780126|ref|YP_003064539.1| hypothetical protein CLIBASIA_00025 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 216 No_of_seqs 117 out of 177 Neff 5.9 Searched_HMMs 23785 Date Sun May 22 09:14:00 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780126.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1je5_A Helix-destabilizing pro 100.0 8.5E-35 3.6E-39 232.8 14.8 163 4-182 7-190 (206) 2 2x6u_A T-box transcription fac 32.3 17 0.00073 15.2 1.8 36 4-43 28-63 (203) 3 1xbr_A Protein (T protein); co 30.6 19 0.00082 14.9 1.8 36 4-43 24-59 (184) 4 1h6f_A T-box transcription fac 22.7 14 0.00059 15.8 -0.1 36 4-43 27-62 (193) 5 2j9c_A GLNK1, hypothetical nit 21.0 35 0.0015 13.3 4.5 54 2-58 31-84 (119) 6 2rp4_A Transcription factor P5 16.1 45 0.0019 12.6 4.3 36 21-61 15-50 (76) 7 3e8v_A Possible transglutamina 11.6 61 0.0026 11.8 4.3 50 118-170 5-56 (82) 8 2qn6_B Translation initiation 10.7 65 0.0027 11.7 5.0 29 28-58 50-79 (93) 9 2kel_A SVTR protein, uncharact 9.0 75 0.0032 11.3 2.8 33 27-59 9-49 (56) 10 2fym_A Enolase; RNA degradosom 8.8 77 0.0032 11.2 1.2 27 119-145 10-36 (431) No 1 >1je5_A Helix-destabilizing protein; OB-fold, beta barrel, DNA binding protein; 1.90A {Enterobacteria phage T7} SCOP: b.40.4.7 Probab=100.00 E-value=8.5e-35 Score=232.81 Aligned_cols=163 Identities=13% Similarity=0.203 Sum_probs=124.2 Q ss_pred EEEEEEE-ECCCCCCCCCCCCCCC--CCCCEEEEEEEECCCCHHH---HHHHHHHHHHHHHHH---HHHCCCCCCCCCCC Q ss_conf 6776899-8331278641123678--8662479999963787899---999999999998754---20002210013444 Q gi|254780126|r 4 LTVKGRL-SYPALDTKVRMKLPDG--SSVEHYGCDIVFPKADTKQ---INAVEACLKTAVTEI---FPNVSPDAFLSAVR 74 (216) Q Consensus 4 vt~kgr~-sYp~L~~P~~~~~~~g--~~~~kYs~~llipK~d~~~---~~~i~~AI~~a~~~~---~~~k~~~~~~~~~k 74 (216) .|++|++ +||||++||+.|...+ ..+.+|||+|+||++|++. +.+|+++++++.+.. +.++.+ T Consensus 7 ttp~G~a~~Y~~L~~PD~~f~~~~~~~~~g~Y~v~L~v~k~d~~a~~~~~~i~~~~~~a~~~~~~~~~~k~~-------- 78 (206) T 1je5_A 7 TSALGTAEPYAYIAKPDYGNEERGFGNPRGVYKVDLTIPNKDPRCQRMVDEIVKCHEEAYAAAVEEYEANPP-------- 78 (206) T ss_dssp ECCSEEECSSCEEEEEECCC---CCSCCSCEEEEEEEEETTSHHHHHHHHHHHHHHHHHHHHHHHHHHTSCC-------- T ss_pred CCCCCCEEECCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-------- T ss_conf 279833340553378874433234678896389999974761789999999999999999999987503654-------- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCC------------CCCCEEECCCCCCCCCCCCCCCCCCEEE Q ss_conf 4344665210175455555454456542277389930377------------7788368578747347677401540799 Q gi|254780126|r 75 SKSESRGVLRDGDAKIASSHKPENYTQTYTDSVYISAKNK------------YVQPLLVDRQAQPVSDPREVFYPGCWVI 142 (216) Q Consensus 75 ~~~~~k~plrDGD~~~~~~~~~~~~~e~~~g~~~i~a~~k------------~~kP~ivD~~~~~i~d~~~~iySGs~~k 142 (216) .....+.++++++... +++++++|.++|++++| +++|.|||++++||++. +.|||||++| T Consensus 79 k~~~~k~~~~~~~~~~-------p~~~e~~G~~~fk~K~Ka~~~~~k~g~~~~~~P~v~D~~~~~l~~~-~~i~~Gs~~~ 150 (206) T 1je5_A 79 AVARGKKPLKPYEGDM-------PFFDNGDGTTTFKFKCYASFQDKKTKETKHINLVVVDSKGKKMEDV-PIIGGGSKLK 150 (206) T ss_dssp -------CCCCCBCCC-------SEEECSSSEEEEEEEEESEEECTTTCCEEECCCCEECTTSCBCSSC-CCCCTTCEEE T ss_pred CCCCCCCCCCCCCCCC-------CCCCCCCCCEEEEEEEEEEEECCCCCCCCCCCCEEECCCCCCCCCC-CCCCCCCEEE T ss_conf 4442335777765668-------8653658748999998667411556775555870796989898886-6035786899 Q ss_pred EEEEEEEEECCCCCCEEEEEEECEEEEEECCCCCCCCCCC Q ss_conf 9999998640788531169997407997248755566665 Q gi|254780126|r 143 AKLNIGAYELDPYKTKGFSCTLTGVQFFKHDERWGASPKS 182 (216) Q Consensus 143 v~~~~~pY~~~~~~gkGVs~~L~~VQ~i~dgE~~GG~~~~ 182 (216) |+++++||.++++.|+||+|+|++||+|+++|+.||+..+ T Consensus 151 v~~~~~py~~~~~~g~Gvsl~L~~VQv~~~~e~~~g~~~~ 190 (206) T 1je5_A 151 VKYSLVPYKWNTAVGASVKLQLESVMLVELATFGGGEDDW 190 (206) T ss_dssp EEEEEEEECCCSSCCBEEEEEEEEEEEEECCC------CC T ss_pred EEEEEEEEEECCCCCEEEEEEECEEEEEECCCCCCCCCCC T ss_conf 9999987886598863899883669998712567877666 No 2 >2x6u_A T-box transcription factor TBX5; developmental protein, DNA-binding, HOLT-ORAM-syndrome, IG-fold, nuclear protein, repressor; HET: PE4; 1.90A {Homo sapiens} PDB: 2x6v_A* Probab=32.31 E-value=17 Score=15.20 Aligned_cols=36 Identities=22% Similarity=0.287 Sum_probs=23.8 Q ss_pred EEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEECCCCH Q ss_conf 6776899833127864112367886624799999637878 Q gi|254780126|r 4 LTVKGRLSYPALDTKVRMKLPDGSSVEHYGCDIVFPKADT 43 (216) Q Consensus 4 vt~kgr~sYp~L~~P~~~~~~~g~~~~kYs~~llipK~d~ 43 (216) ||..||-.||.|. ++..+-+ -..+|++.|-|-.-|. T Consensus 28 ITk~GRrmFP~l~--~~vsGLd--p~~~Y~v~l~~~~~d~ 63 (203) T 2x6u_A 28 ITKAGRRMFPSYK--VKVTGLN--PKTKYILLMDIVPADD 63 (203) T ss_dssp CBSSCEECSSCCE--EEEESCC--SSSEEEEEEEEEEEEE T ss_pred ECCCCEECCCCEE--EEEECCC--CCCCEEEEEEEEECCC T ss_conf 8458741477529--9996888--6754689999898777 No 3 >1xbr_A Protein (T protein); complex (transcription factor/DNA), transcription factor, DNA-binding protein, transcription/DNA complex; HET: DNA; 2.50A {Xenopus laevis} SCOP: b.2.5.4 Probab=30.58 E-value=19 Score=14.90 Aligned_cols=36 Identities=33% Similarity=0.426 Sum_probs=24.5 Q ss_pred EEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEECCCCH Q ss_conf 6776899833127864112367886624799999637878 Q gi|254780126|r 4 LTVKGRLSYPALDTKVRMKLPDGSSVEHYGCDIVFPKADT 43 (216) Q Consensus 4 vt~kgr~sYp~L~~P~~~~~~~g~~~~kYs~~llipK~d~ 43 (216) ||..||-.||.|. +...+=+ -..+|++.|-|..-|. T Consensus 24 ITk~GRrmFP~l~--~~vsGLd--p~~~Y~v~l~~~~~D~ 59 (184) T 1xbr_A 24 VTKNGRRMFPVLK--VSMSGLD--PNAMYTVLLDFVAADN 59 (184) T ss_dssp CBTTCEECSSCCE--EEEECSC--TTSEEEEEEEEEESSS T ss_pred EECCCCCCCCCEE--EEEECCC--CCCCEEEEEEEEECCC T ss_conf 9158725687249--9997889--5645699999998567 No 4 >1h6f_A T-box transcription factor TBX3; transcription factor, TBX3, T-box transcription factor; 1.7A {Homo sapiens} SCOP: b.2.5.4 Probab=22.72 E-value=14 Score=15.78 Aligned_cols=36 Identities=28% Similarity=0.302 Sum_probs=24.4 Q ss_pred EEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEECCCCH Q ss_conf 6776899833127864112367886624799999637878 Q gi|254780126|r 4 LTVKGRLSYPALDTKVRMKLPDGSSVEHYGCDIVFPKADT 43 (216) Q Consensus 4 vt~kgr~sYp~L~~P~~~~~~~g~~~~kYs~~llipK~d~ 43 (216) ||..||-.||.|. ++..+-+. ..+|++.|-|..-|. T Consensus 27 vTk~GRrmFP~l~--~~vsGLdp--~~~Y~v~l~~~~~D~ 62 (193) T 1h6f_A 27 ITKSGRRMFPPFK--VRCSGLDK--KAKYILLMDIIAADD 62 (193) T ss_dssp CCTTCBCCSSCCE--EEEESCCS--SSEEEEEEEEEEEEE T ss_pred EECCCCCCCCCEE--EEEECCCC--CCEEEEEEEEEECCC T ss_conf 9158732477128--99868895--751689999998748 No 5 >2j9c_A GLNK1, hypothetical nitrogen regulatory PII-like protein MJ0059; EM single particle, nitrogen metabolism, signalling, transcription; HET: ATP; 1.30A {Methanococcus jannaschii} PDB: 2j9d_A* 2j9e_A* 2j9d_E* Probab=21.03 E-value=35 Score=13.32 Aligned_cols=54 Identities=15% Similarity=0.062 Sum_probs=31.1 Q ss_pred CEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHH Q ss_conf 336776899833127864112367886624799999637878999999999999987 Q gi|254780126|r 2 QKLTVKGRLSYPALDTKVRMKLPDGSSVEHYGCDIVFPKADTKQINAVEACLKTAVT 58 (216) Q Consensus 2 ~kvt~kgr~sYp~L~~P~~~~~~~g~~~~kYs~~llipK~d~~~~~~i~~AI~~a~~ 58 (216) +-..+.||-+.+....-+.--.......||+.+.++++.++.+ ++-++|..+.. T Consensus 31 Tv~~v~G~G~~~~~~~~~~~~~~~~~~~~k~~leivv~d~~ve---~vv~aI~~aa~ 84 (119) T 2j9c_A 31 TVSEVKGRGVQGGIVERYRGREYIVDLIPKVKIELVVKEEDVD---NVIDIICENAR 84 (119) T ss_dssp EEEEEEEECCSSSSCCEETTEECSSSCEEEEEEEEEEEGGGHH---HHHHHHHHHHC T ss_pred EEEEEEECCCCCCCCEEECCCEEEECCCCEEEEEEEECHHHHH---HHHHHHHHHHC T ss_conf 9996564178888521431412452205469999998878899---99999999835 No 6 >2rp4_A Transcription factor P53; DMP53, oligomerization domain, tetramerizaiton domain, nucleus; NMR {Drosophila melanogaster} Probab=16.08 E-value=45 Score=12.63 Aligned_cols=36 Identities=28% Similarity=0.573 Sum_probs=25.9 Q ss_pred CCCCCCCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 12367886624799999637878999999999999987542 Q gi|254780126|r 21 MKLPDGSSVEHYGCDIVFPKADTKQINAVEACLKTAVTEIF 61 (216) Q Consensus 21 ~~~~~g~~~~kYs~~llipK~d~~~~~~i~~AI~~a~~~~~ 61 (216) .-..+|+ |.+.|..||.+- .+.-|+-.|++++.+.. T Consensus 15 srt~dGd----YrL~itcp~Ke~-LlqSIEgmi~~~A~~vL 50 (76) T 2rp4_A 15 SRTPDGD----YRLAITCPNKEW-LLQSIEGMIKEAAAEVL 50 (76) T ss_dssp ECCTTTB----EEEEEEESCHHH-HHHHHHHHHHHHHHHHH T ss_pred EECCCCC----EEEEEECCCHHH-HHHHHHHHHHHHHHHHH T ss_conf 5436996----579987075999-99999999999999998 No 7 >3e8v_A Possible transglutaminase-family protein; structural genomics, unknown function, PSI-2, protein structure initiative; 2.40A {Bacteroides fragilis nctc 9343} Probab=11.61 E-value=61 Score=11.84 Aligned_cols=50 Identities=16% Similarity=0.132 Sum_probs=31.8 Q ss_pred CEEECCCCCCCCCCC--CCCCCCCEEEEEEEEEEEECCCCCCEEEEEEECEEEEE Q ss_conf 836857874734767--74015407999999998640788531169997407997 Q gi|254780126|r 118 PLLVDRQAQPVSDPR--EVFYPGCWVIAKLNIGAYELDPYKTKGFSCTLTGVQFF 170 (216) Q Consensus 118 P~ivD~~~~~i~d~~--~~iySGs~~kv~~~~~pY~~~~~~gkGVs~~L~~VQ~i 170 (216) ..|+|++++|..+.. ..||.-....-..++ | .+.++-..++++++.+-+- T Consensus 5 V~V~d~~G~PV~gA~V~FkvyNYAEfy~va~~--~-TD~~G~a~lt~G~Gdmlv~ 56 (82) T 3e8v_A 5 VLVTDAEGQPVADATVEFKVYNYAEFYTVATK--H-TDRSGHASLTAGKGDMLVW 56 (82) T ss_dssp EEEECTTSCBCTTCEEEEEEEETTEEEEEEEE--E-CCTTSEEEEECCSEEEEEE T ss_pred EEEECCCCCCCCCCEEEEEEECHHHEEEEEEE--E-ECCCCEEEEEECCCCEEEE T ss_conf 99995899998999999999602752672012--8-8788609999558759999 No 8 >2qn6_B Translation initiation factor 2 alpha subunit; initiation of translation, GTP-binding, nucleotide-binding, protein biosynthesis; HET: GDP; 2.15A {Sulfolobus solfataricus P2} SCOP: d.58.51.1 PDB: 2qmu_B* Probab=10.73 E-value=65 Score=11.66 Aligned_cols=29 Identities=17% Similarity=0.346 Sum_probs=19.3 Q ss_pred CCCEEEEEEEECCCCHHHH-HHHHHHHHHHHH Q ss_conf 6624799999637878999-999999999987 Q gi|254780126|r 28 SVEHYGCDIVFPKADTKQI-NAVEACLKTAVT 58 (216) Q Consensus 28 ~~~kYs~~llipK~d~~~~-~~i~~AI~~a~~ 58 (216) +.|+|.+++.-+ |.++. ..++++++.+.+ T Consensus 50 gaP~Yri~v~a~--D~k~ae~~l~~a~~~i~~ 79 (93) T 2qn6_B 50 GAPRYRVDVVGT--NPKEASEALNQIISNLIK 79 (93) T ss_dssp STTEEEEEEEES--CHHHHHHHHHHHHHHHHH T ss_pred CCCEEEEEEEEC--CHHHHHHHHHHHHHHHHH T ss_conf 698189999937--999999999999999999 No 9 >2kel_A SVTR protein, uncharacterized protein 56B; homodimer, ribbon-helix-helix, transcription repressor; NMR {Sulfolobus islandicus rod-shaped VIRUS1} Probab=9.04 E-value=75 Score=11.27 Aligned_cols=33 Identities=12% Similarity=0.179 Sum_probs=0.0 Q ss_pred CCCCEEEEEEEECCCCHHHHH--------HHHHHHHHHHHH Q ss_conf 866247999996378789999--------999999999875 Q gi|254780126|r 27 SSVEHYGCDIVFPKADTKQIN--------AVEACLKTAVTE 59 (216) Q Consensus 27 ~~~~kYs~~llipK~d~~~~~--------~i~~AI~~a~~~ 59 (216) +++.|-+--|.|||+-...++ +|..+|.+|+++ T Consensus 9 ~~~~K~~FGI~~~K~LKTRLKiYCA~N~~~i~~~I~EAi~E 49 (56) T 2kel_A 9 KKKQKAVFGIYMDKDLKTRLKVYCAKNNLQLTQAIEEAIKE 49 (56) T ss_dssp --CCEEEEEEEEEHHHHHHHHHHHHHSCCCHHHHHHHHHHH T ss_pred HHHHHEEEEEEECHHHHHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 76542346667164575565552123648799999999999 No 10 >2fym_A Enolase; RNA degradosome, enolase, lyase; 1.60A {Escherichia coli} SCOP: c.1.11.1 d.54.1.1 PDB: 1e9i_A 3h8a_A Probab=8.79 E-value=77 Score=11.21 Aligned_cols=27 Identities=15% Similarity=0.215 Sum_probs=0.0 Q ss_pred EEECCCCCCCCCCCCCCCCCCEEEEEE Q ss_conf 368578747347677401540799999 Q gi|254780126|r 119 LLVDRQAQPVSDPREVFYPGCWVIAKL 145 (216) Q Consensus 119 ~ivD~~~~~i~d~~~~iySGs~~kv~~ 145 (216) .|+|+.|+|..+.+-....|..+|+++ T Consensus 10 ~IlDSRG~PTvEvev~~~~g~~gra~~ 36 (431) T 2fym_A 10 EIIDSRGNPTVEAEVHLEGGFVGMAAA 36 (431) T ss_dssp EEECTTSCEEEEEEEEETTSCEEEEEC T ss_pred EEECCCCCCEEEEEEEECCCCEEEEEC T ss_conf 997689982599999988997899966 Done!