Query gi|254780514|ref|YP_003064927.1| type II restriction endonuclease [Candidatus Liberibacter asiaticus str. psy62] Match_columns 110 No_of_seqs 7 out of 9 Neff 1.7 Searched_HMMs 23785 Date Tue May 31 21:22:34 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780514.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 2gb7_A R.ECL18KI; ECL18KI-DNA 99.4 1.7E-13 7E-18 98.8 5.8 71 17-91 67-137 (305) 2 3bm3_A PSPGI restriction endon 99.3 1.3E-12 5.5E-17 93.6 2.6 87 1-91 31-117 (272) 3 1na6_A Ecorii, restriction end 97.7 8.9E-06 3.7E-10 53.6 2.0 33 59-91 251-283 (404) 4 2p9x_A Hypothetical protein PH 71.4 2.8 0.00012 21.3 3.2 25 39-63 48-74 (99) 5 1x1q_A Tryptophan synthase bet 28.0 30 0.0012 15.4 2.4 34 33-66 55-88 (418) 6 1xsz_A Guanine nucleotide exch 21.5 38 0.0016 14.7 2.0 76 15-92 64-148 (356) 7 2fz0_A R-snare NYV1P, V-snare 21.3 32 0.0014 15.1 1.5 41 14-54 97-138 (149) 8 1r8s_E ARNO; protein transport 20.3 41 0.0017 14.6 1.9 78 12-91 63-149 (203) 9 2r09_A Cytohesin-3; autoinhibi 19.8 37 0.0016 14.8 1.6 81 11-93 64-153 (347) 10 1qop_B Tryptophan synthase bet 16.1 58 0.0024 13.7 2.7 34 33-66 33-66 (396) No 1 >2gb7_A R.ECL18KI; ECL18KI-DNA complex, type II restriction endonuclease, nucleotide flipping, base extrusion, hydrolase/DNA complex; HET: DNA; 1.70A {Enterobacter cloacae} PDB: 2fqz_A* Probab=99.42 E-value=1.7e-13 Score=98.82 Aligned_cols=71 Identities=30% Similarity=0.327 Sum_probs=65.9 Q ss_pred CHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 369999999996379642001579999999963212011044576310322355433045799999999739999 Q gi|254780514|r 17 VPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTF 91 (110) Q Consensus 17 tPK~ll~~llselin~~t~K~~e~~etir~~~gdY~~~i~P~iy~l~lsntqsrrsrag~~fe~iiY~~Yn~~t~ 91 (110) .-+.+..++++.++|.+.+|++.+.++|+++|++|+. +||.|++|++|||+||||+.||.+|.+++..+.. T Consensus 67 ~E~~~~~~~ls~~~d~~~~k~~~v~~~i~~~~~~~~d----~i~~L~lSv~QsRkSRAG~sfE~hle~if~~~GI 137 (305) T 2gb7_A 67 FEKEFTTRMLSYLIDEERIKDMSPYDAIRDFTMEYPT----HIYDLALSNTQSRRSRAGKEFESILELLMMGAGI 137 (305) T ss_dssp HHHHHHHHHHHTTCCHHHHTTSCHHHHHHHHHHHCHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCH----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC T ss_conf 8488899999853102110103699999877315818----9999998888746620204299999999997398 No 2 >3bm3_A PSPGI restriction endonuclease; endonuclease-DNA complex, restriction enzyme, PSPGI, base flipping, hydrolase/DNA complex; HET: DNA MSE CIT; 1.70A {Pyrococcus SP} Probab=99.26 E-value=1.3e-12 Score=93.56 Aligned_cols=87 Identities=18% Similarity=0.182 Sum_probs=76.3 Q ss_pred CCHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 95259999997764103699999999963796420015799999999632120110445763103223554330457999 Q gi|254780514|r 1 MQFNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEY 80 (110) Q Consensus 1 ~qFN~ii~~~i~k~~EtPK~ll~~llselin~~t~K~~e~~etir~~~gdY~~~i~P~iy~l~lsntqsrrsrag~~fe~ 80 (110) ++||++|+|.++| .|+|+.++...+.. ..+....+.+....+.+|++|.++.+|+ +.+.+|++|+|+||||++||. T Consensus 31 ~n~~e~l~r~~~k-~~~~~~i~pdr~l~--~~~e~e~elf~~~E~~i~~~~l~~gF~~-~~l~~Sv~nrRKSRAGksfE~ 106 (272) T 3bm3_A 31 LNVDELLDRLFEK-DESGEVITPSRIAK--MLEEKAFEIYKEYEKQVREAYLSAGYSR-EKLEQSFQQARFSRGGKAFEI 106 (272) T ss_dssp HTHHHHHHTTTSB-CTTSCBCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHTTCCH-HHHHHHHHHHHHHHHHHHHHH T ss_pred CCCHHHHHHHHHC-CCCCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHCCCCH-HHHHHHHHHHHHCCCCHHHHH T ss_conf 6811777877522-77756678578999--9998888999999999999987158754-788888877654144155999 Q ss_pred HHHHHHHHHHH Q ss_conf 99999739999 Q gi|254780514|r 81 IIYSLYNINTF 91 (110) Q Consensus 81 iiY~~Yn~~t~ 91 (110) +++.|++.+.+ T Consensus 107 hle~if~~~GI 117 (272) T 3bm3_A 107 IFTKLLNKFGI 117 (272) T ss_dssp HHHHHHHHHTC T ss_pred HHHHHHHHCCC T ss_conf 99999997598 No 3 >1na6_A Ecorii, restriction endonuclease ecorii; site-specific restriction, mutation, replication, hydrolase; 2.10A {Escherichia coli} SCOP: b.142.1.1 c.52.1.22 PDB: 3hqg_A 3hqf_A Probab=97.73 E-value=8.9e-06 Score=53.56 Aligned_cols=33 Identities=21% Similarity=0.315 Sum_probs=29.4 Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 576310322355433045799999999739999 Q gi|254780514|r 59 LYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTF 91 (110) Q Consensus 59 iy~l~lsntqsrrsrag~~fe~iiY~~Yn~~t~ 91 (110) +..+.||++|+|+||||++||.+++.|++.+.. T Consensus 251 Fi~~slSv~nrRKSRAGksfE~hle~if~~~gi 283 (404) T 1na6_A 251 FIALANSVSNRRKSRAGKSLELHLEHLFIEHGL 283 (404) T ss_dssp HHHHHHHHHHHHHHHSSSHHHHHHHHHHHTSSC T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCC T ss_conf 999887777766630315599999999997599 No 4 >2p9x_A Hypothetical protein PH0832; NPPSFA, national project on protein structural and functional analyses; 1.65A {Pyrococcus horikoshii OT3} Probab=71.39 E-value=2.8 Score=21.34 Aligned_cols=25 Identities=20% Similarity=0.482 Sum_probs=18.4 Q ss_pred HHHHHHHHHHHHHHCCC--CHHHHHHH Q ss_conf 79999999963212011--04457631 Q gi|254780514|r 39 FFHNTLTKKFGDYMSKI--TPYLYEWV 63 (110) Q Consensus 39 e~~etir~~~gdY~~~i--~P~iy~l~ 63 (110) -|.++|.+.+|||++|. |-+||.+. T Consensus 48 kFkeaV~~LFGEysarllem~ii~~l~ 74 (99) T 2p9x_A 48 KFKEAVSKLFGEYSARLLEMVIISKLK 74 (99) T ss_dssp HHHHHHHHHHCHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999899999999999999 No 5 >1x1q_A Tryptophan synthase beta chain; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; 2.50A {Thermus thermophilus HB8} Probab=28.00 E-value=30 Score=15.38 Aligned_cols=34 Identities=18% Similarity=0.243 Sum_probs=29.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 4200157999999996321201104457631032 Q gi|254780514|r 33 KTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSN 66 (110) Q Consensus 33 ~t~K~~e~~etir~~~gdY~~~i~P~iy~l~lsn 66 (110) +-.++.+|.+.++...-+|.||-+|-++.-.||. T Consensus 55 ~~~~~~~f~~~~~~~~~~~~grPTPL~~a~rLs~ 88 (418) T 1x1q_A 55 EAKKDPAFLEELDHYLRQFAGRPTPLYHAKRLSE 88 (418) T ss_dssp HHHHCHHHHHHHHHHHHHTTCCSCCEEECHHHHH T ss_pred HHHCCHHHHHHHHHHHHHCCCCCCCCEEHHHHHH T ss_conf 9966989999999998753899973348376697 No 6 >1xsz_A Guanine nucleotide exchange protein; ARF guanine nucleotide exchange factor, signaling protein; 1.41A {Legionella pneumophila} SCOP: a.118.3.1 d.129.9.1 PDB: 1xt0_B Probab=21.53 E-value=38 Score=14.71 Aligned_cols=76 Identities=12% Similarity=0.118 Sum_probs=39.3 Q ss_pred HCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH--HCC---CCH----HHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 1036999999999637964200157999999996321--201---104----4576310322355433045799999999 Q gi|254780514|r 15 YEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDY--MSK---ITP----YLYEWVLSNTQSRRSRDGQEFEYIIYSL 85 (110) Q Consensus 15 ~EtPK~ll~~llselin~~t~K~~e~~etir~~~gdY--~~~---i~P----~iy~l~lsntqsrrsrag~~fe~iiY~~ 85 (110) +-.|+++-.+++.+.++..+++++.+.+++|.+++.. ||+ |-. |--.++..|...-.|.+ .--.+.||+ T Consensus 64 Lg~~~~~n~~vL~~yv~~fdF~g~~id~ALR~fL~~f~LPgEaQ~IDRile~Fa~rY~~~Np~~f~s~D--~~yiLaySi 141 (356) T 1xsz_A 64 LSSPEAENQQVLKAFTSQMNFNGQSFVEGLRTFLKTFKLPGEAQKIDRLVQSFSGAYFQQNPDVVSNAD--AAYLLAFQT 141 (356) T ss_dssp HTCCSHHHHHHHHHHHHTSCCTTSCHHHHHHHHHHTSCBCSSHHHHHHHHHHHHHHHHHHCTTTSSSHH--HHHHHHHHH T ss_pred HCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC--HHHHHHHHH T ss_conf 579976799999999985797899589999999984768970799999999999999985988789802--899999999 Q ss_pred HHHHHHH Q ss_conf 7399999 Q gi|254780514|r 86 YNINTFV 92 (110) Q Consensus 86 Yn~~t~~ 92 (110) -=|||=. T Consensus 142 ImLnTDl 148 (356) T 1xsz_A 142 IMLNTDL 148 (356) T ss_dssp HHHHHHH T ss_pred HHHCCCC T ss_conf 9963202 No 7 >2fz0_A R-snare NYV1P, V-snare component of the vacuolar snare complex involved in vesicle fusion; inhibits...; snare protein, longin domain; NMR {Saccharomyces cerevisiae} Probab=21.29 E-value=32 Score=15.15 Aligned_cols=41 Identities=12% Similarity=0.322 Sum_probs=29.4 Q ss_pred HHCCHHHHHHHHHHHHCCHHH-HHHHHHHHHHHHHHHHHHCC Q ss_conf 410369999999996379642-00157999999996321201 Q gi|254780514|r 14 NYEVPKMLITELSTELFNLKT-ANQNFFHNTLTKKFGDYMSK 54 (110) Q Consensus 14 ~~EtPK~ll~~llselin~~t-~K~~e~~etir~~~gdY~~~ 54 (110) ..++||-|--++|++|-.++. ..++++..-+..+.-.+-++ T Consensus 97 ~~dvPKILPiRlLSeLK~~~~~~~De~L~~~v~~ild~FH~E 138 (149) T 2fz0_A 97 LVDIPKILPIRILSGLQEYESNATNELLSSHVGQILDSFHEE 138 (149) T ss_dssp ETTSCSSHHHHHHHHHTTSSCCCSTTTHHHHHHHHHHHHHHH T ss_pred ECCCCCCCCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 358864021788755135667998899999999999999999 No 8 >1r8s_E ARNO; protein transport/exchange factor; HET: GDP; 1.46A {Homo sapiens} SCOP: a.118.3.1 PDB: 1r8m_E* 1r8q_E* 1s9d_E* 1pbv_A 1bc9_A Probab=20.27 E-value=41 Score=14.56 Aligned_cols=78 Identities=15% Similarity=0.138 Sum_probs=38.8 Q ss_pred HHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH--HCC---CCH----HHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 7641036999999999637964200157999999996321--201---104----4576310322355433045799999 Q gi|254780514|r 12 SNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDY--MSK---ITP----YLYEWVLSNTQSRRSRDGQEFEYII 82 (110) Q Consensus 12 ~k~~EtPK~ll~~llselin~~t~K~~e~~etir~~~gdY--~~~---i~P----~iy~l~lsntqsrrsrag~~fe~ii 82 (110) |..+.-|+.+-.+++.+-++.-+++++.+.+|+|.+|+.. ||+ |-- +--.|+..|...-.+ -..--.+. T Consensus 63 geyLg~~~~~~~~vL~~y~~~fdf~~~~i~~ALR~~l~~f~LpgEsQ~IdRile~Fa~~Y~~~Np~~f~~--~d~v~~la 140 (203) T 1r8s_E 63 GDYLGEREELNLAVLHAFVDLHEFTDLNLVQALRQFLWSFRLPGKAQKIDRMMEAFAQRYCLCNPGVFQS--TDTCYVLS 140 (203) T ss_dssp HHHHTCCSHHHHHHHHHHHHTCCCTTCCHHHHHHHHHHSSCCCSSHHHHHHHHHHHHHHHHHHSTTSSSC--HHHHHHHH T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC--HHHHHHHH T ss_conf 9997146568999999998846978996999999999845189718999999999999999749876788--33899999 Q ss_pred HHHHHHHHH Q ss_conf 999739999 Q gi|254780514|r 83 YSLYNINTF 91 (110) Q Consensus 83 Y~~Yn~~t~ 91 (110) ||+-=|||= T Consensus 141 ~slimLnTd 149 (203) T 1r8s_E 141 YSVIMLNTD 149 (203) T ss_dssp HHHHHHHHH T ss_pred HHHHHHHHH T ss_conf 999999876 No 9 >2r09_A Cytohesin-3; autoinhibition, GRP1, PIP3, ARF, 3-phosphoinositide, pleckstrin homology domain, coiled coil, guanine-nucleotide releasing factor; HET: 4IP PGE PE5; 1.90A {Mus musculus} SCOP: a.118.3.1 b.55.1.1 PDB: 2r0d_A* Probab=19.83 E-value=37 Score=14.78 Aligned_cols=81 Identities=10% Similarity=0.124 Sum_probs=44.1 Q ss_pred HHHHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH--HCC------CC-HHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 77641036999999999637964200157999999996321--201------10-4457631032235543304579999 Q gi|254780514|r 11 ISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGDY--MSK------IT-PYLYEWVLSNTQSRRSRDGQEFEYI 81 (110) Q Consensus 11 i~k~~EtPK~ll~~llselin~~t~K~~e~~etir~~~gdY--~~~------i~-P~iy~l~lsntqsrrsrag~~fe~i 81 (110) ||..+..|+++-.+++.+-++.-+++++.+.+|+|.++... ||+ |+ -|--.++..|...-.+ -..-..+ T Consensus 64 ig~~l~~~~~~~~~vl~~y~~~~~f~~~~~~~alR~~l~~~~lpgE~q~idril~~Fs~~y~~~N~~~~~~--~d~~~~l 141 (347) T 2r09_A 64 IGDYLGERDDFNIKVLQAFVELHEFADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCNPGVFQS--TDTCYVL 141 (347) T ss_dssp HHHHHHCCSHHHHHHHHHHHHTSCCTTCCHHHHHHHHTTSCCCCSSHHHHHHHHHHHHHHHHHHSTTSSSC--HHHHHHH T ss_pred HHHHHCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC--CCHHHHH T ss_conf 99996799658999999999753738997999999999856898738999999999988898749786668--4731029 Q ss_pred HHHHHHHHHHHH Q ss_conf 999973999999 Q gi|254780514|r 82 IYSLYNINTFVT 93 (110) Q Consensus 82 iY~~Yn~~t~~~ 93 (110) .|++--+||-.. T Consensus 142 ~~s~imLntdlh 153 (347) T 2r09_A 142 SFAIIMLNTSLH 153 (347) T ss_dssp HHHHHHHHHHHH T ss_pred HHHHHHHHHHCC T ss_conf 999999850202 No 10 >1qop_B Tryptophan synthase beta chain; lyase, carbon-oxygen lyase, tryptophan biosynthesis, pyridoxal phosphate; HET: IPL PLP; 1.4A {Salmonella typhimurium} SCOP: c.79.1.1 PDB: 1k7e_B* 1k7f_B* 1kfb_B* 1k3u_B* 1tjp_B* 1wbj_B* 2cli_B* 2clk_B* 2cll_B* 2j9x_B* 3cep_B* 1kfc_B* 1k8x_B* 1kfj_B* 1kfk_B* 2rh9_B* 2rhg_B* 2j9y_B* 1cw2_B* 1a5s_B* ... Probab=16.09 E-value=58 Score=13.68 Aligned_cols=34 Identities=9% Similarity=0.125 Sum_probs=28.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCC Q ss_conf 4200157999999996321201104457631032 Q gi|254780514|r 33 KTANQNFFHNTLTKKFGDYMSKITPYLYEWVLSN 66 (110) Q Consensus 33 ~t~K~~e~~etir~~~gdY~~~i~P~iy~l~lsn 66 (110) +..++.+|.+-++...-+|.||-+|-++.-.||. T Consensus 33 ~~~~~~~f~~~~~~~~~~~~grpTPL~~~~~Ls~ 66 (396) T 1qop_B 33 SAQKDPEFQAQFADLLKNYAGRPTALTKCQNITA 66 (396) T ss_dssp HHHTCHHHHHHHHHHHHHTTCCSCCEEECHHHHT T ss_pred HHHCCHHHHHHHHHHHHHCCCCCCHHHEHHHHHH T ss_conf 9961989999999998744899966766485556 Done!