Query gi|254780946|ref|YP_003065359.1| hypothetical protein CLIBASIA_04225 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 98 No_of_seqs 114 out of 652 Neff 5.9 Searched_HMMs 23785 Date Wed Jun 1 00:14:50 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780946.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 2jr5_A UPF0350 protein VC_2471 99.9 3.8E-26 1.6E-30 170.6 9.7 86 6-92 4-89 (94) 2 1puz_A Conserved hypothetical 99.9 7E-26 2.9E-30 169.1 9.1 81 1-82 1-81 (82) 3 1x6i_A Hypothetical protein YG 99.9 4.4E-25 1.8E-29 164.5 9.1 81 8-89 8-88 (91) 4 3erm_A Uncharacterized conserv 33.0 25 0.0011 15.4 5.7 54 12-65 8-76 (91) 5 2da1_A Alpha-fetoprotein enhan 31.6 25 0.001 15.5 2.5 44 20-65 15-58 (70) 6 1x2m_A LAG1 longevity assuranc 28.0 31 0.0013 14.9 2.6 46 20-65 7-52 (64) 7 1xrx_A SEQA protein; protein f 23.1 36 0.0015 14.5 2.1 32 54-85 6-37 (50) 8 2dn0_A Zinc fingers and homeob 21.5 41 0.0017 14.2 3.0 46 18-65 14-59 (76) 9 2wvr_C DNA replication factor 18.8 20 0.00083 16.0 0.0 53 11-66 462-514 (546) 10 2wl8_A Peroxisomal biogenesis 18.5 48 0.002 13.8 4.9 39 10-52 28-66 (126) No 1 >2jr5_A UPF0350 protein VC_2471; structure, structural genomics, PSI, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Vibrio cholerae} Probab=99.93 E-value=3.8e-26 Score=170.63 Aligned_cols=86 Identities=23% Similarity=0.419 Sum_probs=81.7 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 99999999999740789999999999999820299999999999946891799999948899980675699999999998 Q gi|254780946|r 6 NLQCRKIVYRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGMEKPPEYLRTPIFKKIYDYYS 85 (98) Q Consensus 6 d~~~krl~~Rs~rRG~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~~~~p~~~~~~ii~~I~~f~~ 85 (98) ..+++||+||| ||||+|||+|||+|+++++++++++++.+|+.||+++|+|||+|++|+++||+...++++++|++|.. T Consensus 4 ~~~~~RL~wrs-RRG~kElDllL~~F~~~~~~~ls~~el~~fe~LL~~eD~dL~dwl~g~~~~~d~~~~~ii~kI~~~~~ 82 (94) T 2jr5_A 4 AEQKARIKWAC-RRGMLELDVVIMPFFEECFDSLTESEQDDFVALLESDDPDLFAWVMGHGRCENLGLAAMVDKIVAHNL 82 (94) T ss_dssp HHHHHHHHHHH-CCSSHHHHHTTTTHHHHHTTTCCHHHHHHHHHHHTSCCHHHHHHHHTCCCCSCHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH T ss_conf 79998999982-14459999969999999998699999999999980992999999958999998999999999999999 Q ss_pred HHHHHHH Q ss_conf 2277656 Q gi|254780946|r 86 NNLDRKN 92 (98) Q Consensus 86 ~~~~~~~ 92 (98) +++..+. T Consensus 83 ~k~~~~~ 89 (94) T 2jr5_A 83 SKVRLEH 89 (94) T ss_dssp HHHHHHC T ss_pred HHHHHHH T ss_conf 8640230 No 2 >1puz_A Conserved hypothetical protein; NMA1147, MR19, structural genomics, PSI, protein structure initiative; NMR {Neisseria meningitidis MC58} SCOP: a.218.1.1 Probab=99.93 E-value=7e-26 Score=169.12 Aligned_cols=81 Identities=31% Similarity=0.457 Sum_probs=78.5 Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHH Q ss_conf 98658999999999997407899999999999998202999999999999468917999999488999806756999999 Q gi|254780946|r 1 MKKNMNLQCRKIVYRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGMEKPPEYLRTPIFKKI 80 (98) Q Consensus 1 M~~~ld~~~krl~~Rs~rRG~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~~~~p~~~~~~ii~~I 80 (98) ||..-+.++|||+||| ||||+|+|+|||+|+++++++++++++.+|++||+++|+|||+|++|+++||+...++|+++| T Consensus 1 m~~~dd~~~krl~~rs-rRG~~ElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~g~~~~p~~~~~~ii~~I 79 (82) T 1puz_A 1 MMVFDDIAKRKIRFQT-RRGLLELDLIFGRFMEKEFEHLSDKELSEFSEILEFQDQELLALINGHSETDKGHLIPMLEKI 79 (82) T ss_dssp CCCCCHHHHHHHHHHS-CCSCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHTSCHHHHHHHHHTCSCCSCTTHHHHHHHH T ss_pred CCCCCHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHH T ss_conf 9746488998999994-132599999999999998987999999999999859909999999489999929999999998 Q ss_pred HH Q ss_conf 99 Q gi|254780946|r 81 YD 82 (98) Q Consensus 81 ~~ 82 (98) +. T Consensus 80 rk 81 (82) T 1puz_A 80 RR 81 (82) T ss_dssp HH T ss_pred HC T ss_conf 70 No 3 >1x6i_A Hypothetical protein YGFY; structural genomics, transcriptional regulation, structure 2 function project, S2F, unknown function; 1.20A {Escherichia coli} PDB: 1x6j_A Probab=99.92 E-value=4.4e-25 Score=164.50 Aligned_cols=81 Identities=27% Similarity=0.450 Sum_probs=77.0 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 99999999974078999999999999982029999999999994689179999994889998067569999999999822 Q gi|254780946|r 8 QCRKIVYRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGMEKPPEYLRTPIFKKIYDYYSNN 87 (98) Q Consensus 8 ~~krl~~Rs~rRG~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~~~~p~~~~~~ii~~I~~f~~~~ 87 (98) +++||+||| ||||+|||++|++|+++++++++++++.+|++||+++|+|||+|++|+++||+....+++++|++|.+++ T Consensus 8 ~k~rL~wr~-RRG~kElDllL~~F~~~~~~~ls~~el~~fe~LL~~~D~dL~~wl~~~~~~~d~~~~~ii~~I~~~~~~~ 86 (91) T 1x6i_A 8 NKARIHWAC-RRGMRELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELEMMVRLIQTRNRER 86 (91) T ss_dssp CHHHHHHHT-CCSSHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHTSCHHHHHHHHTTSSBCSSHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHC T ss_conf 699999982-1443999998999999999869999999999998498199999994899999899999999999987725 Q ss_pred HH Q ss_conf 77 Q gi|254780946|r 88 LD 89 (98) Q Consensus 88 ~~ 89 (98) .. T Consensus 87 g~ 88 (91) T 1x6i_A 87 GP 88 (91) T ss_dssp SC T ss_pred CC T ss_conf 88 No 4 >3erm_A Uncharacterized conserved protein; APC85034, ppspto1197, seudomonas syringae PV. tomato STR. DC3000, structural genomics, PSI-2; HET: MSE; 2.45A {Pseudomonas syringae PV} Probab=32.96 E-value=25 Score=15.43 Aligned_cols=54 Identities=15% Similarity=0.097 Sum_probs=41.2 Q ss_pred HHHHHHHCC---------------HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 999997407---------------899999999999998202999999999999468917999999488 Q gi|254780946|r 12 IVYRCWRRG---------------TREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGM 65 (98) Q Consensus 12 l~~Rs~rRG---------------~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~ 65 (98) ++|.|-|-| |+|+-=-|..|+......+++.+...+--+|..+-..+...+-|+ T Consensus 8 ~~yvv~R~g~mtF~sKKEADAyDKMLdlAd~L~~~L~~~~~~ldE~q~E~L~l~LA~~Kd~l~~~lkgk 76 (91) T 3erm_A 8 TLYRSTRDLETTFVDRKLADAHDQMLELAELLTDVLIKNVPGLSEKHAEDASIYMAKNRAVFAAAFKNN 76 (91) T ss_dssp -------------CHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHTTHHHHHHHHHSC T ss_pred EEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 999997079614465888878999999999999999847899888899999999997799999998579 No 5 >2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Probab=31.63 E-value=25 Score=15.50 Aligned_cols=44 Identities=9% Similarity=0.112 Sum_probs=36.0 Q ss_pred CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 7899999999999998202999999999999468917999999488 Q gi|254780946|r 20 GTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGM 65 (98) Q Consensus 20 G~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~ 65 (98) .-..+++|-.-|..+.++ +.+++..+...+.++...+-.|+.++ T Consensus 15 t~~q~~~Le~~F~~~~~P--~~~~~~~La~~~~l~~~qV~~WF~Nr 58 (70) T 2da1_A 15 TDDQLRVLRQYFDINNSP--SEEQIKEMADKSGLPQKVIKHWFRNT 58 (70) T ss_dssp CHHHHHHHHHHHHHCSSC--CTTHHHHHHHHHCCCHHHHHHHHHHH T ss_pred CHHHHHHHHHHHHHCCCC--CHHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 999999999999975998--99999999999791999988977988 No 6 >1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Probab=27.97 E-value=31 Score=14.93 Aligned_cols=46 Identities=20% Similarity=0.284 Sum_probs=34.6 Q ss_pred CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 7899999999999998202999999999999468917999999488 Q gi|254780946|r 20 GTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGM 65 (98) Q Consensus 20 G~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~ 65 (98) ++.|---+|..++...-...+..+...+...+.++...+-.||.++ T Consensus 7 ~t~~~~~iLe~~f~~~~~~P~~~~~~~La~~lgl~~~qV~~WF~Nr 52 (64) T 1x2m_A 7 GTAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQR 52 (64) T ss_dssp CSSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHH T ss_pred CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHCCHHH T ss_conf 9858999999999885899299999999999498989988805854 No 7 >1xrx_A SEQA protein; protein filament, LEFT-handed helix, DNA replication inhibitor; 2.15A {Escherichia coli} SCOP: a.43.1.7 Probab=23.05 E-value=36 Score=14.54 Aligned_cols=32 Identities=13% Similarity=0.313 Sum_probs=22.6 Q ss_pred CCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 91799999948899980675699999999998 Q gi|254780946|r 54 DDSNLFKWFTGMEKPPEYLRTPIFKKIYDYYS 85 (98) Q Consensus 54 ~D~dL~~wl~~~~~~p~~~~~~ii~~I~~f~~ 85 (98) -|.|||.++..+..--.+--..|++++.++.. T Consensus 6 vDeeLYryIAs~T~~IGESASdILRRlL~~~~ 37 (50) T 1xrx_A 6 VDDELYSYIASHTKHIGESASDILRRMLKFSA 37 (50) T ss_dssp ECHHHHHHHHTTCSSTTCCHHHHHHHHHTC-- T ss_pred ECHHHHHHHHHHHHHHCCCHHHHHHHHHCCCC T ss_conf 11999999998765632479999999976986 No 8 >2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Probab=21.48 E-value=41 Score=14.20 Aligned_cols=46 Identities=17% Similarity=0.391 Sum_probs=36.9 Q ss_pred HCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 407899999999999998202999999999999468917999999488 Q gi|254780946|r 18 RRGTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGM 65 (98) Q Consensus 18 rRG~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~ 65 (98) +..--.+.+|-.-|..+.++ +..+...+...+.++-..+-.||.++ T Consensus 14 ~~t~~Ql~~Le~~f~~~~~P--~~~~~~~LA~~~gl~~~~V~~WF~nr 59 (76) T 2dn0_A 14 KKSHEQLSALKGSFCRNQFP--GQSEVEHLTKVTGLSTREVRKWFSDR 59 (76) T ss_dssp CCCHHHHHHHHHHHHHSSSC--CSHHHHHHHHHHCCCHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHHHHCCCC--CHHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 89999999999999986899--99999999999497999999989988 No 9 >2wvr_C DNA replication factor CDT1; DNA replication license, DNA replication inhibitor, phosphoprotein, UBL conjugation, DNA-binding, polymorphism; HET: DNA; 3.30A {Homo sapiens} PDB: 2klo_A* Probab=18.85 E-value=20 Score=16.05 Aligned_cols=53 Identities=15% Similarity=0.180 Sum_probs=43.6 Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHCCC Q ss_conf 99999974078999999999999982029999999999994689179999994889 Q gi|254780946|r 11 KIVYRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIEEDDSNLFKWFTGME 66 (98) Q Consensus 11 rl~~Rs~rRG~kElDllL~~F~~~~~~~l~~~el~~f~~LL~~~D~dL~~wl~~~~ 66 (98) +.+|.+.+++...|..|+..+.+.+...++..++....+||..--+ +||.-.. T Consensus 462 ~~~f~~~~~~~~~~~~~~~~~~~s~~~~~~~~e~~~~l~~l~~~~p---~w~~~~~ 514 (546) T 2wvr_C 462 RSVFVSERKPALSMEVACARMVGSCCTIMSPGEMEKHLLLLSELLP---DWLSLHR 514 (546) T ss_dssp -------------------------------------------------------- T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCC---HHEEEEE T ss_conf 9998642466422999999999851565899999999999987583---5359863 No 10 >2wl8_A Peroxisomal biogenesis factor 19; protein transport, biogenesis disorder, zellweger syndrome, membrane, prenylation; 2.05A {Homo sapiens} Probab=18.55 E-value=48 Score=13.82 Aligned_cols=39 Identities=8% Similarity=0.176 Sum_probs=33.5 Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC Q ss_conf 9999999740789999999999999820299999999999946 Q gi|254780946|r 10 RKIVYRCWRRGTREMDLILGSFVDHFILELSSVELTMLESIIE 52 (98) Q Consensus 10 krl~~Rs~rRG~kElDllL~~F~~~~~~~l~~~el~~f~~LL~ 52 (98) |-+.|.. |||+.-=+.+|++.+-.+++.++...|+.=.+ T Consensus 28 KevLYeP----mKel~~kyP~WL~~n~~~ls~ed~~rY~kQ~~ 66 (126) T 2wl8_A 28 KDVLYPS----LKEITEKYPEWLQSHRESLPPEQFEKYQEQHS 66 (126) T ss_dssp HHHHHHH----HHHHHTTHHHHHHHHGGGSCHHHHHHHHHHHH T ss_pred HHHHHCC----HHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHH T ss_conf 6452411----99999876199986767699999999999999 Done!