Query gi|254781072|ref|YP_003065485.1| hypothetical protein CLIBASIA_04870 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 190 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 23785 Date Wed Jun 1 00:24:46 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781072.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 2gsv_A Hypothetical protein YV 80.9 2.1 8.8E-05 22.4 4.7 48 89-140 26-73 (80) 2 2kp7_A Crossover junction endo 26.2 31 0.0013 14.4 5.3 71 25-98 6-83 (87) 3 2asw_A Hypothetical protein AF 26.1 31 0.0013 14.4 2.2 50 93-142 5-56 (56) 4 3lb6_A Interleukin-13, IL-13; 16.1 49 0.0021 13.0 2.0 17 135-151 27-43 (132) 5 3bpo_A Interleukin 13; IL4, IL 15.4 51 0.0021 12.9 2.1 11 90-100 97-107 (127) 6 2cpg_A REPA protein, transcrip 14.6 53 0.0022 12.7 3.2 27 98-135 15-41 (45) 7 1e8o_B SRP14, signal recogniti 12.8 60 0.0025 12.4 2.1 18 33-50 4-21 (106) 8 1u84_A Hypothetical protein; s 11.1 68 0.0028 12.0 2.5 59 100-163 16-76 (90) 9 1q1v_A DEK protein; winged-hel 11.0 68 0.0029 12.0 2.5 18 130-147 51-68 (70) 10 1jy2_P Fibrinogen gamma-B chai 10.0 65 0.0027 12.2 0.6 19 9-27 4-22 (48) No 1 >2gsv_A Hypothetical protein YVFG; alpha-helical protein, structural genomics, PSI, protein structure initiative; 1.90A {Bacillus subtilis} SCOP: a.23.7.1 PDB: 2js1_A Probab=80.86 E-value=2.1 Score=22.44 Aligned_cols=48 Identities=33% Similarity=0.531 Sum_probs=38.6 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHEEHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999951567102019999999999999888999999999 Q gi|254781072|r 89 YFKALTKYYKSVVAELREFGLGKSAIEIEEITKAVDTLTRAYNEYKKEIREL 140 (190) Q Consensus 89 yfkaltkyyksvvaelrefglgksaieieeitkavdtltrayneykkeirel 140 (190) -..|+..||+|||..|-.-.|.|.|.-|.. ...|..|||.-++|-..| T Consensus 26 KIhAmNaYYrsVvstlvqDqltKNA~vlkR----iqHLdEAYqKVk~ee~~~ 73 (80) T 2gsv_A 26 KIHAMNSYYRSVVSTLVQDQLTKNAVVLKR----IQHLDEAYNKVKRGESKL 73 (80) T ss_dssp HHHHHHHHHHHHHHHHHHCSSSCHHHHHHH----HHHHHHHHHHHHHC---- T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHH T ss_conf 999999999999999999999730799999----999999999998888754 No 2 >2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour suppressor, DNA damage, DNA recombination, DNA repair, hydrolase, magnesium; NMR {Mus musculus} Probab=26.22 E-value=31 Score=14.40 Aligned_cols=71 Identities=17% Similarity=0.031 Sum_probs=40.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HC---CCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 222044444399999999999999998776666554455533----11---36978634655465687889999999999 Q gi|254781072|r 25 QIRSKESVINKEFVTKVEELYEKAQKAHKKRDKVYGAYDKVS----SH---KKSPKELSKAFYIDFRTELKYFKALTKYY 97 (190) Q Consensus 25 qirskesvinkefvtkveelyekaqkahkkrdkvygaydkvs----sh---kkspkelskafyidfrtelkyfkaltkyy 97 (190) ++|.--|-.|..|+.-++++.+.++.-. ++..-+|.+.- ++ -.|++++..-=.|.-+.--+.-.-|.+|+ T Consensus 6 ~~r~~Ps~~N~lfi~~L~e~~~~~~~k~---~k~~~aY~kA~~sLk~~p~~I~s~~~l~~l~GIG~~i~~ki~e~L~~yc 82 (87) T 2kp7_A 6 SVRPLPVCPNPLFVRWLTEWRDEAASRG---RHTRFVFQKALRSLQRYPLPLRSGKEAKILQHFGDRLCRMLDEKLKQHL 82 (87) T ss_dssp --CCCCCSCCCHHHHHHHHHHHHHHHHT---CTTHHHHHHHHHHHHHCCSCCCSHHHHHTCTTTCHHHHHHHHHHHHHHH T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHCC---CHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHH T ss_conf 8899999988999999999999998707---3579999999999997899888899997279977899999999999999 Q ss_pred H Q ss_conf 9 Q gi|254781072|r 98 K 98 (190) Q Consensus 98 k 98 (190) + T Consensus 83 ~ 83 (87) T 2kp7_A 83 A 83 (87) T ss_dssp H T ss_pred H T ss_conf 8 No 3 >2asw_A Hypothetical protein AF1503; homodimer, parallel coiled-coil, complementary X-DA packing, unknown function; NMR {Archaeoglobus fulgidus} SCOP: a.274.1.1 PDB: 2asx_A Probab=26.10 E-value=31 Score=14.40 Aligned_cols=50 Identities=10% Similarity=0.248 Sum_probs=29.0 Q ss_pred HHHHHHHHHHHHHHCCCCCHHEEHHHHH--HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999515671020199999--9999999988899999999999 Q gi|254781072|r 93 LTKYYKSVVAELREFGLGKSAIEIEEIT--KAVDTLTRAYNEYKKEIRELIE 142 (190) Q Consensus 93 ltkyyksvvaelrefglgksaieieeit--kavdtltrayneykkeirelie 142 (190) +++--..+....++.+-|.-...+.+.. .-+..|.+++|.....++++|+ T Consensus 5 I~~Pl~~l~~~~~~i~~Gd~~~~i~~~~~~dEig~La~~fn~M~~~l~~~ie 56 (56) T 2asw_A 5 ITRPIIELSNTADKIAEGNLEAEVPHQNRADEIGILAKSIERLRRSLKVAME 56 (56) T ss_dssp HHHHHHHHHHHHHHHHTTCTTCCCTTTTCCSHHHHHHHHHHHHHHHHHHHHC T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 9999999999999998799988379899965999999999999999999739 No 4 >3lb6_A Interleukin-13, IL-13; cytokine, decoy, decoy receptor, glycoprotein; HET: MLY NAG; 3.05A {Homo sapiens} PDB: 3lb6_B* Probab=16.14 E-value=49 Score=12.99 Aligned_cols=17 Identities=41% Similarity=0.714 Sum_probs=12.4 Q ss_pred HHHHHHHHHHHHHCHHC Q ss_conf 99999999999712102 Q gi|254781072|r 135 KEIRELIEEFIELGFDQ 151 (190) Q Consensus 135 keirelieefielgfdq 151 (190) ++.+|||||...+.-+| T Consensus 27 ~aLkELIeeLvnitqnq 43 (132) T 3lb6_A 27 TALRELIEELVNITQNQ 43 (132) T ss_dssp HHHHHHHHHHHHHHHSC T ss_pred HHHHHHHHHHHHCCCCC T ss_conf 88999999998606556 No 5 >3bpo_A Interleukin 13; IL4, IL13, IL4R, IL13R, cytokine, alternative splicing, glycoprotein, immune response, membrane; HET: NAG; 3.00A {Homo sapiens} PDB: 1ijz_A 1ik0_A 3g6d_A 3l5w_I 3l5x_A* 3l5y_A 1ga3_A Probab=15.39 E-value=51 Score=12.86 Aligned_cols=11 Identities=27% Similarity=0.199 Sum_probs=4.7 Q ss_pred HHHHHHHHHHH Q ss_conf 99999999999 Q gi|254781072|r 90 FKALTKYYKSV 100 (190) Q Consensus 90 fkaltkyyksv 100 (190) .|.|-.|++.+ T Consensus 97 vK~LL~~~r~~ 107 (127) T 3bpo_A 97 VKDLLLHLKKL 107 (127) T ss_dssp HHHHHHHHHHH T ss_pred HHHHHHHHHHH T ss_conf 99999999999 No 6 >2cpg_A REPA protein, transcriptional repressor COPG; DNA-binding protein, plasmid, gene regulation; 1.60A {Streptococcus agalactiae} SCOP: a.43.1.3 PDB: 1b01_A* 1ea4_A* Probab=14.64 E-value=53 Score=12.73 Aligned_cols=27 Identities=41% Similarity=0.621 Sum_probs=16.6 Q ss_pred HHHHHHHHHCCCCCHHEEHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999515671020199999999999998889999 Q gi|254781072|r 98 KSVVAELREFGLGKSAIEIEEITKAVDTLTRAYNEYKK 135 (190) Q Consensus 98 ksvvaelrefglgksaieieeitkavdtltrayneykk 135 (190) +..----+|-||.|||+ ++-|..+|++ T Consensus 15 ~~L~~~akekGlSKSal-----------ltvALe~y~k 41 (45) T 2cpg_A 15 ENLEKMAREMGLSKSAM-----------ISVALENYKK 41 (45) T ss_dssp HHHHHHHHHHTCCHHHH-----------HHHHHHHHHH T ss_pred HHHHHHHHHCCCCHHHH-----------HHHHHHHHHH T ss_conf 99999999748519999-----------9999999872 No 7 >1e8o_B SRP14, signal recognition particle 14 kDa protein; ALU ribonucleoprotein particle, protein recognition of AN RNA U-turn, translational control; HET: GDP; 3.20A {Homo sapiens} SCOP: d.49.1.1 PDB: 1e8s_B 1ry1_D* Probab=12.83 E-value=60 Score=12.39 Aligned_cols=18 Identities=22% Similarity=0.589 Sum_probs=14.9 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 439999999999999999 Q gi|254781072|r 33 INKEFVTKVEELYEKAQK 50 (190) Q Consensus 33 inkefvtkveelyekaqk 50 (190) -|.+|.+++.+||+++.. T Consensus 4 ~nd~FL~~Lt~Lf~~~k~ 21 (106) T 1e8o_B 4 ESEQFLTELTRLFQKCRT 21 (106) T ss_dssp CHHHHHHHHHHHHHHHTT T ss_pred CHHHHHHHHHHHHHHCCC T ss_conf 738999999999985676 No 8 >1u84_A Hypothetical protein; structural genomics, protein structure initiative, MCSG, PSI midwest center for structural genomics; 1.60A {Geobacillus stearothermophilus} SCOP: a.230.1.1 Probab=11.07 E-value=68 Score=12.02 Aligned_cols=59 Identities=24% Similarity=0.345 Sum_probs=38.5 Q ss_pred HHHHHHHCCCCCHHEE--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCCCCCCCHHHHHH Q ss_conf 9999995156710201--999999999999988899999999999999712102330101246788 Q gi|254781072|r 100 VVAELREFGLGKSAIE--IEEITKAVDTLTRAYNEYKKEIRELIEEFIELGFDQCDECDLCSEKAD 163 (190) Q Consensus 100 vvaelrefglgksaie--ieeitkavdtltrayneykkeirelieefielgfdqcdecdlcsekad 163 (190) .++..--||+|...-+ +.+|..||-... --+++-+-|....+..|+++---.-|-+.|. T Consensus 16 ~i~~WDPf~~G~d~YetE~~dvv~av~~~d-----d~~~LA~~IQ~Iye~SFee~~P~e~C~k~A~ 76 (90) T 1u84_A 16 WIGAWDPFGLGKDAYDVEAASVLQAVYETE-----DARTLAARIQSIYEFAFDEPIPFPHCLKLAR 76 (90) T ss_dssp HHHHHCTTSSCGGGGHHHHHHHHHHHTTCS-----CHHHHHHHHHHHHHHHHSSCCCHHHHHHHHH T ss_pred HHHCCCCCCCCCCCCCHHHHHHHHHHHHCC-----CHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 998069877897645437999999999418-----8899999999999987413476899999999 No 9 >1q1v_A DEK protein; winged-helix motif, DNA binding protein; NMR {Homo sapiens} SCOP: a.159.4.1 Probab=11.01 E-value=68 Score=12.00 Aligned_cols=18 Identities=33% Similarity=0.473 Sum_probs=13.2 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 889999999999999971 Q gi|254781072|r 130 YNEYKKEIRELIEEFIEL 147 (190) Q Consensus 130 yneykkeirelieefiel 147 (190) ..++|..|+++|++|+-+ T Consensus 51 Ls~rK~~I~~~I~~~Ls~ 68 (70) T 1q1v_A 51 LTERKDFIKTTVKELISL 68 (70) T ss_dssp CSHHHHHHHHHHHHHHHS T ss_pred CHHHHHHHHHHHHHHHHC T ss_conf 388999999999999844 No 10 >1jy2_P Fibrinogen gamma-B chain; fragment E, disulfide bonds, asymmetry, coiled- coil, beta-sheet, blood clotting; 1.40A {Bos taurus} SCOP: h.1.8.1 PDB: 1jy3_P 2a45_I* Probab=10.05 E-value=65 Score=12.15 Aligned_cols=19 Identities=32% Similarity=0.541 Sum_probs=13.4 Q ss_pred CCCCCCCCCCHHHHHHHHH Q ss_conf 7751218620000234222 Q gi|254781072|r 9 NNDTSKIPDAKFGSFLQIR 27 (190) Q Consensus 9 nndtskipdakfgsflqir 27 (190) +.|.--|||..||||-.-. T Consensus 4 t~~ncCild~rFGsYCPTT 22 (48) T 1jy2_P 4 TRDNCCILDERFGSYCPTT 22 (48) T ss_dssp -CCSSCCSBTTTBCEEECH T ss_pred CCCCCCCCCCCCCCCCCCC T ss_conf 6465414751013769851 Done!