Query gi|254780549|ref|YP_003064962.1| signal peptide protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 271 No_of_seqs 140 out of 348 Neff 9.0 Searched_HMMs 23785 Date Tue May 31 19:46:55 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780549.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1lr0_A TOLA protein; domain-sw 99.9 1.4E-24 5.8E-29 158.1 10.9 94 171-271 23-121 (129) 2 1tol_A G3P - TOLA, protein (fu 99.7 4.5E-17 1.9E-21 115.3 8.5 88 172-270 126-215 (222) 3 2grx_C Protein TONB; beta barr 99.3 1.8E-13 7.5E-18 94.8 1.1 82 180-269 141-223 (229) 4 2k9k_A TONB2; metal transport; 97.9 1.4E-05 5.8E-10 49.8 4.7 76 189-269 26-105 (106) 5 1u07_A TONB protein; beta-hair 97.7 2.2E-05 9.2E-10 48.7 3.7 71 189-267 11-82 (90) 6 1bwv_A Rubisco, protein (ribul 22.5 2.4 0.0001 20.0 -4.0 60 209-270 407-481 (493) 7 1lgh_A LH II, B800/850, light 20.4 29 0.0012 13.8 1.2 21 6-26 26-46 (56) 8 2oa4_A SIR5; structure, struct 19.3 38 0.0016 13.1 2.7 52 209-261 13-72 (101) 9 1xrd_A LH-1, light-harvesting 17.4 43 0.0018 12.9 2.6 19 7-25 22-40 (52) 10 3kfu_F Aspartyl/glutamyl-tRNA( 15.5 48 0.002 12.6 7.9 78 165-243 149-227 (466) No 1 >1lr0_A TOLA protein; domain-swapping, TONB, protein transport; 1.91A {Pseudomonas aeruginosa} SCOP: d.212.1.1 Probab=99.92 E-value=1.4e-24 Score=158.10 Aligned_cols=94 Identities=16% Similarity=0.262 Sum_probs=83.6 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 00000789999999999622546565553752999999987998185335640588860589999999999999718898 Q gi|254780549|r 171 KRIPSQDAIAIVRNRVIANWNIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFR 250 (271) Q Consensus 171 ~~~~~~~~~~~ir~~I~~~w~~p~~~~~~~~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~ 250 (271) +..++.+|.++|+++|++||++|.+++ .++.|+|+|+|++||+|.+..++.+||+ +.||++|+|||.+|+||+ T Consensus 23 ~~~~~~~y~~~i~~~I~~~W~~P~~~~--~~~~v~v~i~l~~dG~v~~~~i~~sSG~-----~~~d~aa~~Av~ra~p~p 95 (129) T 1lr0_A 23 GSEVTGSLDDLIVNLVSQQWRRPPSAR--NGMSVEVLIEMLPDGTITNASVSRSSGD-----KPFDSSAVAAVRNVGRIP 95 (129) T ss_dssp HHHHHHHHHHHHHHHHHHHCCCCTTCC--TTCCEEEEEEECTTSBEEEEEEEECCSC-----HHHHHHHHHHHHHHCBCG T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCC--CCCEEEEEEEECCCCCEEEEEECCCCCC-----HHHHHHHHHHHHHHCCCC T ss_conf 588999999999999998468998778--8978999999989998987551027787-----589999999999852699 Q ss_pred C----CHHHHHH-CCEEEEEECHHHC Q ss_conf 8----8467761-2228997444009 Q gi|254780549|r 251 L----SPSTYKS-WRNITLFFVPSKM 271 (271) Q Consensus 251 ~----p~~~y~~-~~~~~~~F~p~~m 271 (271) . |++.|+. ||+|+|+|+|++| T Consensus 96 ~p~~~p~~~y~~~~r~i~l~F~Ped~ 121 (129) T 1lr0_A 96 EMQQLPRATFDSLYRQRRIIFKPEDL 121 (129) T ss_dssp GGGGSCHHHHHHHTSEEEEEECHHHH T ss_pred CCCCCCHHHHHHHEEEEEEEECHHHC T ss_conf 99877977874400677899882133 No 2 >1tol_A G3P - TOLA, protein (fusion protein consisting of minor coat protein, glycine rich linker, TOLA,...; bacteriophage M13, phage infection; 1.85A {Enterobacteria phage M13} SCOP: b.37.1.1 d.212.1.1 PDB: 1s62_A Probab=99.70 E-value=4.5e-17 Score=115.28 Aligned_cols=88 Identities=16% Similarity=0.238 Sum_probs=72.9 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 00007899999999996225465655537529999999879981853356405888605899999999999997188988 Q gi|254780549|r 172 RIPSQDAIAIVRNRVIANWNIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFRL 251 (271) Q Consensus 172 ~~~~~~~~~~ir~~I~~~w~~p~~~~~~~~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~~ 251 (271) ......|...|+++|+++|.+|.+.+ +.+|+|+|+|.+||+|+++.. +||+ ..||++|+|||.+ .+||. T Consensus 126 ~a~i~~Y~~~I~a~I~~~~~~p~~~~---Gk~~~V~I~l~pdG~V~~V~~--sSGd-----~alD~AA~~AVr~-a~fP~ 194 (222) T 1tol_A 126 GADINNYAGQIKSAIESKFYDASSYA---GKTCTLRIKLAPDGMLLDIKP--EGGD-----PALCQAALAAAKL-AKIPK 194 (222) T ss_dssp CHHHHHHHHHHHHHHHTTCTTGGGGT---TCCEEEEEEECTTSCEEEEEE--EEEC-----HHHHHHHHHHHHH-CCCCC T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCC---CCEEEEEEEECCCCEEEEEEE--CCCC-----HHHHHHHHHHHHH-CCCCC T ss_conf 36688899999999986268985458---998999999889972987463--6899-----8999999999984-78998 Q ss_pred CH--HHHHHCCEEEEEECHHH Q ss_conf 84--67761222899744400 Q gi|254780549|r 252 SP--STYKSWRNITLFFVPSK 270 (271) Q Consensus 252 p~--~~y~~~~~~~~~F~p~~ 270 (271) || +.|+.||+|.|+|+|+. T Consensus 195 pp~~~vye~fr~i~l~F~Ps~ 215 (222) T 1tol_A 195 PPSQAVYEVFKNAPLDFKPAA 215 (222) T ss_dssp CSCHHHHHHHTTCEEEEECCC T ss_pred CCCHHHHHHHEEEEEEECCCC T ss_conf 997678665166248988887 No 3 >2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex, inter-protein beta sheet, protein-protein, metal transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A {Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A Probab=99.32 E-value=1.8e-13 Score=94.78 Aligned_cols=82 Identities=15% Similarity=0.124 Sum_probs=63.5 Q ss_pred HHHHHHHHHHCCCCCCCCCCC-CEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH Q ss_conf 999999996225465655537-5299999998799818533564058886058999999999999971889888467761 Q gi|254780549|r 180 AIVRNRVIANWNIPSDFKRFK-KLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFRLSPSTYKS 258 (271) Q Consensus 180 ~~ir~~I~~~w~~p~~~~~~~-~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~~p~~~y~~ 258 (271) ..++..+..+|.||..++..+ ++.|+|.|.|+.||+|.+..++.+||.. +||++|++||.+..+++-++ .. T Consensus 141 ~~~~~~~~~~~~yp~~A~r~~~~G~v~V~f~I~~~G~V~~v~i~~SSG~~-----~LD~aAl~avrr~~f~P~~~---~~ 212 (229) T 2grx_C 141 SGPRALSRNQPQYPARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPAN-----MFEREVKNAMRRWRYEPGKP---GS 212 (229) T ss_dssp -------CCCCCCCHHHHHHTCCEEECEEEECCTTSCCEEEEECCCSSST-----TSHHHHHHHTTSCCCCTTCC---CS T ss_pred CCHHHHHCCCCCCCHHHHHCCCCCEEEEEEEECCCCCEEEEEEEECCCCH-----HHHHHHHHHHHHCCCCCCCC---CC T ss_conf 15477743387770999976898779999998289989688998668965-----89999999999677889987---87 Q ss_pred CCEEEEEECHH Q ss_conf 22289974440 Q gi|254780549|r 259 WRNITLFFVPS 269 (271) Q Consensus 259 ~~~~~~~F~p~ 269 (271) |-.+.|.|+-+ T Consensus 213 ~~~v~i~F~L~ 223 (229) T 2grx_C 213 GIVVNILFKIN 223 (229) T ss_dssp CEECCEEECCC T ss_pred CEEEEEEEEEC T ss_conf 65998999989 No 4 >2k9k_A TONB2; metal transport; NMR {Listonella anguillarum} Probab=97.85 E-value=1.4e-05 Score=49.84 Aligned_cols=76 Identities=17% Similarity=0.074 Sum_probs=55.6 Q ss_pred HCCCCCCCCCCC-CEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHH---HHHCCEEEE Q ss_conf 225465655537-5299999998799818533564058886058999999999999971889888467---761222899 Q gi|254780549|r 189 NWNIPSDFKRFK-KLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFRLSPST---YKSWRNITL 264 (271) Q Consensus 189 ~w~~p~~~~~~~-~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~~p~~~---y~~~~~~~~ 264 (271) ...||..+...+ .+.|+|+|.++.||.|.+..++.+++.. .|+++|++||.+....|-..+. -..|..+.+ T Consensus 26 ~P~YP~~A~~~gieG~V~v~f~I~~~G~v~~~~v~~ss~~~-----~fd~aa~~av~~~~f~P~~~~G~pv~~~~~~~~i 100 (106) T 2k9k_A 26 EPVYPSRALKRGVEGFVTLSFTIDTTGKAVDINVVDANPKR-----MFEREAMQALKKWKYQPQIVDGKAIEQPGQTVTV 100 (106) T ss_dssp SCCCCSHHHHHCCCCEEEEEEEEETTTEEEEEEEEEESSSS-----SSHHHHHHHHHHCCCCCCCCSSCCSCEEEEEEEE T ss_pred CCCCCHHHHHCCCEEEEEEEEEEECCCCEEEEEEEECCCCH-----HHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEEE T ss_conf 99997999975990499999999289989888998647938-----8999999999976778888098576578799989 Q ss_pred EECHH Q ss_conf 74440 Q gi|254780549|r 265 FFVPS 269 (271) Q Consensus 265 ~F~p~ 269 (271) +|+-. T Consensus 101 ~F~L~ 105 (106) T 2k9k_A 101 EFKIA 105 (106) T ss_dssp ECCCC T ss_pred EEEEC T ss_conf 99973 No 5 >1u07_A TONB protein; beta-hairpin, protein transport; 1.13A {Escherichia coli} SCOP: d.212.1.2 PDB: 2gsk_B* 1ihr_A 1qxx_A Probab=97.70 E-value=2.2e-05 Score=48.72 Aligned_cols=71 Identities=15% Similarity=0.183 Sum_probs=50.7 Q ss_pred HCCCCCCCCCCC-CEEEEEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCEEEEEEC Q ss_conf 225465655537-5299999998799818533564058886058999999999999971889888467761222899744 Q gi|254780549|r 189 NWNIPSDFKRFK-KLRVKMHFQLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVIKSQAFRLSPSTYKSWRNITLFFV 267 (271) Q Consensus 189 ~w~~p~~~~~~~-~~~v~v~i~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~~~~p~~~p~~~y~~~~~~~~~F~ 267 (271) .+.||..+...+ .+.|.|+|.++.||+|....++.++|.. .|+++|++|+.+....+-.+ ..+-.+.++|. T Consensus 11 ~P~YP~~A~~~g~eG~v~v~f~I~~~G~v~~~~v~~s~~~~-----~fd~aa~~av~~~~f~P~~~---~~~~~v~i~F~ 82 (90) T 1u07_A 11 QPQYPARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPAN-----MFEREVKNAMRRWRYEPGKP---GSGIVVNILFK 82 (90) T ss_dssp CCCCCHHHHHHTCCEEEEEEEEECTTSCEEEEEEEEEESSS-----SSHHHHHHHHTTCEECTTCC---EEEEEEEEEEE T ss_pred CCCCCHHHHHCCCEEEEEEEEEEECCCCEEEEEEEECCCCH-----HHHHHHHHHHHHCCCCCCCC---CCCEEEEEEEE T ss_conf 99886999977993489999999599989799999888976-----89999999998587889997---88889999999 No 6 >1bwv_A Rubisco, protein (ribulose bisphosphate carboxylase); carbon dioxide fixation, complex (rubisco/reaction intermediate); HET: KCX CAP; 2.40A {Galdieria partita} SCOP: c.1.14.1 d.58.9.1 PDB: 1iwa_A 1bxn_A Probab=22.54 E-value=2.4 Score=19.99 Aligned_cols=60 Identities=15% Similarity=0.209 Sum_probs=32.5 Q ss_pred EECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHH--------------HH-CCCCCCHHHHHHCCEEEEEECHHH Q ss_conf 987998185335640588860589999999999999--------------71-889888467761222899744400 Q gi|254780549|r 209 QLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVI--------------KS-QAFRLSPSTYKSWRNITLFFVPSK 270 (271) Q Consensus 209 ~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~--------------~~-~p~~~p~~~y~~~~~~~~~F~p~~ 270 (271) .|+-.|-+.|.|- +...+-..+|.+-|+++.|+. .+ .--+-+..--+.|++|.|+|+.-+ T Consensus 407 il~~GGGi~GHP~--G~aaGa~A~RqA~EA~v~~~~~~~~~a~eg~e~l~e~Ak~~~eL~~Ale~Wg~i~f~~~~~~ 481 (493) T 1bwv_A 407 VLQFGGGTIGHPD--GIQAGATANRVALEAMILARNENRDYLTEGPEILREAAKTCGALRTALDLWKDITFNYTSTD 481 (493) T ss_dssp EEECSHHHHTCTT--CHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHCHHHHHHHHHHTTCCCCCCCSS T ss_pred EEECCCCCCCCCC--CHHHHHHHHHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHCCHHHHHHHHHHCCCEEECCCCC T ss_conf 9976875237985--65889999999999999733410445542549999997529899999998667367335787 No 7 >1lgh_A LH II, B800/850, light harvesting complex II; bacteriochlorophyll, dexter energy transfer, foerster exciton transfer mechanism; HET: BCL LYC DET HTO; 2.40A {Phaeospirillum molischianum} SCOP: f.3.1.1 Probab=20.37 E-value=29 Score=13.80 Aligned_cols=21 Identities=19% Similarity=0.309 Sum_probs=15.1 Q ss_pred HHHHHHHHHHHHHHHHHHHCC Q ss_conf 699999999999999987175 Q gi|254780549|r 6 GLAISMILHVMFLLLLYFNFN 26 (271) Q Consensus 6 gL~lSi~lH~~li~l~~f~~~ 26 (271) -++..+.+|+.++.+-.|+|- T Consensus 26 v~v~ai~VH~~vlslpg~~w~ 46 (56) T 1lgh_A 26 ATVVAIAVHAAVLAAPGFNWI 46 (56) T ss_dssp HHHHHHHHHHHHHHSGGGCHH T ss_pred HHHHHHHHHHHHHHCCCCHHH T ss_conf 999999999998706771088 No 8 >2oa4_A SIR5; structure, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Silicibacter pomeroyi} SCOP: a.4.12.3 Probab=19.32 E-value=38 Score=13.14 Aligned_cols=52 Identities=17% Similarity=0.266 Sum_probs=30.1 Q ss_pred EECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHH--------HHCCCCCCHHHHHHCCE Q ss_conf 987998185335640588860589999999999999--------71889888467761222 Q gi|254780549|r 209 QLNQKGFVLGKINVDVVGGTELVRRMLRENARKAVI--------KSQAFRLSPSTYKSWRN 261 (271) Q Consensus 209 ~l~~~G~v~~~~~~~~~~~~~~~~~~~~~~a~rAi~--------~~~p~~~p~~~y~~~~~ 261 (271) ...|||+++..--+-.. +.....-.---++.+||. .|.-|.+.++-|..|.. T Consensus 13 v~~pdG~~~t~adlP~~-~trRWvA~RKa~VV~aV~~G~~S~~EAcrrY~LS~eEf~~W~~ 72 (101) T 2oa4_A 13 VTLPDGSIMTRADLPPA-NTRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVS 72 (101) T ss_dssp EECSSSCEEETTSSCCS-CCSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHH T ss_pred EECCCCCCCCCCCCCCC-CCEEECHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 46899981301129996-5603269999999999983845799999883999999999999 No 9 >1xrd_A LH-1, light-harvesting protein B-880, alpha chain; membrane spanning helix, pigment binding, photosynthesis, membrane protein; NMR {Rhodospirillum rubrum} SCOP: f.3.1.1 Probab=17.43 E-value=43 Score=12.88 Aligned_cols=19 Identities=21% Similarity=0.621 Sum_probs=12.5 Q ss_pred HHHHHHHHHHHHHHHHHHC Q ss_conf 9999999999999998717 Q gi|254780549|r 7 LAISMILHVMFLLLLYFNF 25 (271) Q Consensus 7 L~lSi~lH~~li~l~~f~~ 25 (271) +++.+.+|.+++.--.||| T Consensus 22 ~~LAl~IHfiLLSt~rfNW 40 (52) T 1xrd_A 22 FVLALLIHFILLSTERFNW 40 (52) T ss_dssp HHHHHHHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCCCCCC T ss_conf 9999999999744676565 No 10 >3kfu_F Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase; ASPRS, gatcab, ATP-binding, aminoacyl-tRNA synthetase, ligas nucleotide-binding, protein biosynthesis, ligase-RNA comple; HET: H2U 5MU PSU; 3.00A {Thermus thermophilus} Probab=15.48 E-value=48 Score=12.60 Aligned_cols=78 Identities=15% Similarity=0.073 Sum_probs=0.0 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEECCCCEEEEEEEECCCCCC-HHHHHHHHHHHHHHH Q ss_conf 1110000000078999999999962254656555375299999998799818533564058886-058999999999999 Q gi|254780549|r 165 VEKSSRKRIPSQDAIAIVRNRVIANWNIPSDFKRFKKLRVKMHFQLNQKGFVLGKINVDVVGGT-ELVRRMLRENARKAV 243 (271) Q Consensus 165 ~~~~~~~~~~~~~~~~~ir~~I~~~w~~p~~~~~~~~~~v~v~i~l~~~G~v~~~~~~~~~~~~-~~~~~~~~~~a~rAi 243 (271) ..+.-........|...|+.-++-.-.-..++.. +.++|.++|++.+.|.-.|.++-.++-+| ....++..--+.|-+ T Consensus 149 TePd~~s~~eA~~~~~~L~~ilr~lgvsd~~mee-GslR~DvNVSir~~g~~~g~RvEiKNlNS~~~v~kAIeyEi~RQ~ 227 (466) T 3kfu_F 149 TEPDLKTPEEARLFLQRIQALVQTLGISDASPEE-GKLRADVNVSVRRVGEPLGTKVEIKNLNSFKSVQRALEYEIRRQT 227 (466) T ss_dssp ECTTBCCHHHHHHHHHHHHHHHHHHTSBCCCGGG-TCEEEEEEEEECCSSSSCCCCEEEEEECCHHHHHHHHHHHHHHHH T ss_pred ECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC-CCCCCCCCEEECCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHH T ss_conf 0478688999999999999999970877675113-614146505641478877765775166554689999999999999 Done!