Query gi|254781209|ref|YP_003065622.1| hypothetical protein CLIBASIA_05580 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 175 No_of_seqs 109 out of 402 Neff 7.9 Searched_HMMs 23785 Date Wed Jun 1 02:07:37 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781209.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3mc4_A WW/RSP5/WWP domain:bact 20.5 37 0.0016 13.4 4.4 18 122-139 65-82 (287) 2 2uwj_E Type III export protein 10.5 69 0.0029 11.8 2.2 40 116-155 14-58 (70) 3 2dam_A ETEA protein; KIAA0887, 7.5 92 0.0039 11.1 1.4 12 41-52 38-49 (67) 4 2gut_A ARC/mediator, positive 6.7 90 0.0038 11.1 0.1 30 113-142 5-38 (77) 5 2ixs_A SDAI restriction endonu 6.3 1.1E+02 0.0045 10.7 0.6 74 11-85 40-130 (323) 6 2joz_A Hypothetical protein YX 5.5 1.2E+02 0.005 10.4 2.7 30 64-93 50-79 (135) 7 3dvo_A Sgrair restriction enzy 5.5 1.2E+02 0.005 10.4 0.5 31 24-58 89-119 (338) 8 2hzm_A RNA polymerase II media 5.3 1.2E+02 0.0052 10.3 1.0 48 34-81 21-74 (212) 9 3mmp_G RNA-directed RNA polyme 4.5 1.4E+02 0.0058 10.0 3.4 43 4-48 31-80 (589) 10 3hrl_A Endonuclease-like prote 4.1 1.6E+02 0.0065 9.7 1.0 16 36-51 60-75 (104) No 1 >3mc4_A WW/RSP5/WWP domain:bacterial transferase hexapeptide repeat:serine O-acetyltransferase...; ssgcid, structural genomics; 1.95A {Brucella melitensis biovar abortus} Probab=20.54 E-value=37 Score=13.39 Aligned_cols=18 Identities=28% Similarity=0.351 Sum_probs=6.1 Q ss_pred HHHHHHHHHHHHHHHHCC Q ss_conf 999999999999577529 Q gi|254781209|r 122 QEAFALKLAGELCPPLIM 139 (175) Q Consensus 122 ~~~i~~~lA~~~A~~itg 139 (175) .++|+++||.+++.+... T Consensus 65 ~~ALs~~La~kL~~~~~~ 82 (287) T 3mc4_A 65 EEAVMHRIAERLGHPDVS 82 (287) T ss_dssp HHHHHHHHHHHHCCSSSC T ss_pred HHHHHHHHHHHHCCCCCC T ss_conf 999999999875883126 No 2 >2uwj_E Type III export protein PSCE; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa} Probab=10.47 E-value=69 Score=11.78 Aligned_cols=40 Identities=13% Similarity=0.036 Sum_probs=24.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHH-----HCCCHHHHHHHHHHHHHHH Q ss_conf 755999999999999999577-----5296899999999999999 Q gi|254781209|r 116 DCDPLYQEAFALKLAGELCPP-----LIMDDQMRSYLKGESERVL 155 (175) Q Consensus 116 ~~p~~f~~~i~~~lA~~~A~~-----itg~~~l~~~l~q~~~~~l 155 (175) .-+|.|++.|..+|-..++.- --|+.+..+.+++++...- T Consensus 14 gadp~~arel~~qL~qAl~~~Kr~l~rGg~~qqyq~wQqeAdAIE 58 (70) T 2uwj_E 14 VADGTHAAALRQRLQAALAECRRELARGACPERFQFLQQQARALE 58 (70) T ss_dssp SSSTHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH T ss_conf 588388999999999999999999980898899999999999999 No 3 >2dam_A ETEA protein; KIAA0887, UBA-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Probab=7.48 E-value=92 Score=11.06 Aligned_cols=12 Identities=17% Similarity=0.598 Sum_probs=8.7 Q ss_pred HHHHHHCCCCCE Q ss_conf 988640477511 Q gi|254781209|r 41 KGLLRSFSWSFA 52 (175) Q Consensus 41 ~~~L~~~~W~Fa 52 (175) +.+|..|+|+-- T Consensus 38 r~iL~~H~WdlE 49 (67) T 2dam_A 38 RHTLEQHNWNIE 49 (67) T ss_dssp HHHHHHHTSCHH T ss_pred HHHHHHCCCCHH T ss_conf 999999188599 No 4 >2gut_A ARC/mediator, positive cofactor 2 glutamine/Q- rich-associated protein; KIX, 3 helical bundle, transcription; NMR {Homo sapiens} Probab=6.66 E-value=90 Score=11.12 Aligned_cols=30 Identities=3% Similarity=0.077 Sum_probs=19.0 Q ss_pred CHHHH-HHHHHHHHHHHHH---HHHHHHHCCCHH Q ss_conf 86675-5999999999999---999577529689 Q gi|254781209|r 113 PLSDC-DPLYQEAFALKLA---GELCPPLIMDDQ 142 (175) Q Consensus 113 ~~~~~-p~~f~~~i~~~lA---~~~A~~itg~~~ 142 (175) ++++| .|.|++.|+.++- ...+.+.+++.. T Consensus 5 ~d~dWrs~~FRq~Vi~kI~ea~~~~g~~~~kna~ 38 (77) T 2gut_A 5 QETDWRSTAFRQKLVSQIEDAMRKAGVAHSKSSK 38 (77) T ss_dssp CCSCTTSHHHHHHHHHHHHHHHHHHCCCCSSCHH T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHH T ss_conf 7466678789999999999999973899887899 No 5 >2ixs_A SDAI restriction endonuclease; hydrolase, domain architecture; HET: EPE; 2.0A {Streptomyces diastaticus} Probab=6.26 E-value=1.1e+02 Score=10.68 Aligned_cols=74 Identities=16% Similarity=0.185 Sum_probs=38.2 Q ss_pred HHHCCCCCCCCCCCCC-------HHHHHHHHH---------HHHHHHHHHHHC-CCCCEEEEEECCCCCCCCCCCEEEEC Q ss_conf 9971821124336889-------789999999---------679999886404-77511110000345677676504654 Q gi|254781209|r 11 LLKLGQRPLENWNERS-------LKADYCRLL---------LPPIHKGLLRSF-SWSFATQSMDLLPLYFTYNGELKYYI 73 (175) Q Consensus 11 L~~iG~~~I~sl~e~t-------~~A~~~~~~---------y~~~r~~~L~~~-~W~Fa~~r~~L~~~~~~~~~~~~y~l 73 (175) |.+++-.|-.+..+.+ +-...++.. .+++||..++.. ..+++.... -.+.-|++...+.|+| T Consensus 40 Lal~~lkp~~~W~~a~~~~~~~~~im~~~~~~ygk~YA~NTREtiR~~Tl~q~~~a~~~~~n~-d~p~~ptnSp~~~Y~L 118 (323) T 2ixs_A 40 LALAGLKPGDHWADSTTPRLGVQKIMDWSGAYWAKPYATGSREDFRKKTLRQWVDNGFAVLNP-DNLNIATNSQLNEYCL 118 (323) T ss_dssp HHHTTCCTTCBGGGCCCCCEEHHHHHHHHHHHSSCCCCGGGHHHHHHHTHHHHHHTTSEEECT-TCCSCCTTCTTCEEEE T ss_pred HHHCCCCCCCCHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCEEECC-CCCCCCCCCCCCCCCC T ss_conf 998189999965664186336209999999865976787775527888799998736027777-7899988899873506 Q ss_pred CCCCEEEEECCC Q ss_conf 855000232045 Q gi|254781209|r 74 PLKCLKVLNTSE 85 (175) Q Consensus 74 P~D~lrv~~v~~ 85 (175) ..+.+.++..+. T Consensus 119 ~~e~~~ll~~~g 130 (323) T 2ixs_A 119 SDEAAQAIRSYG 130 (323) T ss_dssp CHHHHHHHHHTT T ss_pred CHHHHHHHHHCC T ss_conf 899999998669 No 6 >2joz_A Hypothetical protein YXEF; structure, GFT, NESG, lipoprotein, structural genomics, PSI-2, protein structure initiative; NMR {Bacillus subtilis} SCOP: b.60.1.1 Probab=5.50 E-value=1.2e+02 Score=10.41 Aligned_cols=30 Identities=17% Similarity=0.303 Sum_probs=22.2 Q ss_pred CCCCCEEEECCCCCEEEEECCCCCCCCCCE Q ss_conf 767650465485500023204566312312 Q gi|254781209|r 64 TYNGELKYYIPLKCLKVLNTSEETQLRGRC 93 (175) Q Consensus 64 ~~~~~~~y~lP~D~lrv~~v~~~~~~~~~~ 93 (175) +-..+...++|.+..+|+..+-++.++... T Consensus 50 vi~grgev~~p~~aykvisq~tdgsiei~y 79 (135) T 2joz_A 50 VMEGRGEVQLPFMAYKVISQSTDGSIEIQY 79 (135) T ss_dssp EETTTEEEECCCEEEEEEECCSSSEEEEEE T ss_pred HHCCCCEECCCHHHHHHEECCCCCEEEEEE T ss_conf 221664021612545533026887189897 No 7 >3dvo_A Sgrair restriction enzyme; restriction enzyme/DNA complex; HET: DNA; 1.89A {Streptomyces griseus} PDB: 3dpg_A* 3dw9_A* Probab=5.47 E-value=1.2e+02 Score=10.40 Aligned_cols=31 Identities=16% Similarity=0.327 Sum_probs=21.9 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEC Q ss_conf 88978999999967999988640477511110000 Q gi|254781209|r 24 ERSLKADYCRLLLPPIHKGLLRSFSWSFATQSMDL 58 (175) Q Consensus 24 e~t~~A~~~~~~y~~~r~~~L~~~~W~Fa~~r~~L 58 (175) +.+..|.++..+++.+..+++ |||+.+...| T Consensus 89 dsnakakvagdifeivssavm----wncaarwnsl 119 (338) T 3dvo_A 89 DSNAKAKVAGDIFEIVSSAVM----WNCAARWNSL 119 (338) T ss_dssp CHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHH T ss_pred CCCCHHHHCCCHHHHHHHHHH----HHHHHHHHHH T ss_conf 565212320009999899999----9888764201 No 8 >2hzm_A RNA polymerase II mediator complex subunit 20; beta barrel, channel, transcription; 2.40A {Saccharomyces cerevisiae} PDB: 2hzs_A Probab=5.27 E-value=1.2e+02 Score=10.33 Aligned_cols=48 Identities=8% Similarity=0.027 Sum_probs=23.9 Q ss_pred HHHHHHHHHHHH-HCCCCCEEEEEECCCCC-CCC--C--CCEEEECCCCCEEEE Q ss_conf 996799998864-04775111100003456-776--7--650465485500023 Q gi|254781209|r 34 LLLPPIHKGLLR-SFSWSFATQSMDLLPLY-FTY--N--GELKYYIPLKCLKVL 81 (175) Q Consensus 34 ~~y~~~r~~~L~-~~~W~Fa~~r~~L~~~~-~~~--~--~~~~y~lP~D~lrv~ 81 (175) .+-|....+++. ...|+|..|--..++-. |.. . |+-++..|.++.-++ T Consensus 21 qFhD~LSneL~t~~gkWSfefK~fR~~~~niP~~~SK~LyTlt~s~~~~~t~lI 74 (212) T 2hzm_A 21 ELKDALSNSILSVRDPWSIDFRTYRCSIKNLPADVSKLMYSITFHHHGRQTVLI 74 (212) T ss_dssp HHHHHHGGGCCEECCCEEEEEEEEEECSCCC----CCEEEEEEEESSSEEEEEE T ss_pred HHHHHHHHHHHHHCCCCEEEEEEHHCCCCCCCHHHHHHEEEEECCCCCCEEEEE T ss_conf 999998766655157652897810057677985342023685125689704998 No 9 >3mmp_G RNA-directed RNA polymerase beta chain; RDRP,HOST-factor complex, translation, transferase; HET: PXN; 2.50A {Enterobacteria phage qbeta} Probab=4.53 E-value=1.4e+02 Score=10.02 Aligned_cols=43 Identities=26% Similarity=0.353 Sum_probs=0.0 Q ss_pred HHHHHHHHHHCCCCCCCCCCC-------CCHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999999718211243368-------897899999996799998864047 Q gi|254781209|r 4 LEICNWALLKLGQRPLENWNE-------RSLKADYCRLLLPPIHKGLLRSFS 48 (175) Q Consensus 4 l~i~N~aL~~iG~~~I~sl~e-------~t~~A~~~~~~y~~~r~~~L~~~~ 48 (175) ++|+|--|...|..|.+|-++ -.-.+...+.-| .|.++|..|+ T Consensus 31 ~siandl~~a~~~~~~~s~e~ci~~~p~~~~~~d~fr~~Y--Lr~eilsK~~ 80 (589) T 3mmp_G 31 LSIANDLLLAYGQSPFNSEAECISFSPRFDGTPDDFRINY--LKAEIMSKYD 80 (589) T ss_dssp HHHHHHHHHHTTCCCCSSHHHHHSCCCCSCSCHHHHHHHH--HHHHHTTTCS T ss_pred HHHHHHHHHHCCCCCCCCHHHHHCCCCCCCCCHHHHHHHH--HHHHHHHCCC T ss_conf 5678889997398877758887257987788842778999--9999986188 No 10 >3hrl_A Endonuclease-like protein; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 1.95A {Neisseria gonorrhoeae fa 1090} Probab=4.11 E-value=1.6e+02 Score=9.72 Aligned_cols=16 Identities=13% Similarity=0.187 Sum_probs=0.0 Q ss_pred HHHHHHHHHHHCCCCC Q ss_conf 6799998864047751 Q gi|254781209|r 36 LPPIHKGLLRSFSWSF 51 (175) Q Consensus 36 y~~~r~~~L~~~~W~F 51 (175) .|..|+..|+.+||.+ T Consensus 60 ~D~~Rd~~L~~~Gw~V 75 (104) T 3hrl_A 60 YDHARTVYLNSLGFTV 75 (104) T ss_dssp CCHHHHHHHHHTTCEE T ss_pred HHHHHHHHHHHCCCEE T ss_conf 3899999999899989 Done!