Query gi|254780990|ref|YP_003065403.1| hypothetical protein CLIBASIA_04455 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 66 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 23785 Date Tue May 31 23:23:51 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780990.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3do5_A HOM, homoserine dehydro 12.1 93 0.0039 14.0 3.1 61 4-66 233-293 (327) 2 1np3_A Ketol-acid reductoisome 9.0 1.2E+02 0.0051 13.4 2.0 40 1-41 77-116 (338) 3 3pvi_A Protein (pvuii endonucl 8.7 76 0.0032 14.4 0.5 16 51-66 90-105 (157) 4 3ksk_A Type-2 restriction enzy 5.1 1.6E+02 0.0067 12.8 0.6 14 52-65 250-263 (324) 5 2qj2_A Hepatocyte growth facto 4.2 2E+02 0.0082 12.3 0.6 12 17-28 61-72 (184) 6 3kks_A Integrase, IN; beta-str 3.9 2.5E+02 0.011 11.8 0.9 10 32-41 3-12 (152) 7 1h95_A CSD, Y-box binding prot 3.5 1.4E+02 0.0058 13.1 -0.7 12 2-13 24-35 (79) 8 2k5n_A Putative cold-shock pro 3.4 1.5E+02 0.0063 12.9 -0.6 11 2-13 18-28 (74) 9 3lk3_T Carmil homolog, leucine 3.3 2E+02 0.0083 12.3 -0.1 16 6-21 60-75 (115) 10 3hn4_A Hepatocyte growth facto 3.2 2.4E+02 0.01 11.9 0.3 13 48-60 10-22 (264) No 1 >3do5_A HOM, homoserine dehydrogenase; NP_069768.1, putative homoserine dehydrogenase, structural genomics, joint center for structural genomics; 2.20A {Archaeoglobus fulgidus} Probab=12.13 E-value=93 Score=13.99 Aligned_cols=61 Identities=20% Similarity=0.198 Sum_probs=42.8 Q ss_pred CCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEEEEHHHHHCCCCCCCCCCCCEEEEEC Q ss_conf 456434567775545413895218986502221345441052210076520002463465429 Q gi|254780990|r 4 VPDDGIDDLFEEDLFQYDANKSELVLISSLWSIDFFEINCALLRRRHPINKYEKTDNFFALYT 66 (66) Q Consensus 4 vpddgiddlfeedlfqydankselvlisslwsidffeincallrrrhpinkyektdnffalyt 66 (66) |+-.||+.+..+|+-+-.....-+-++.+..... ..+.-.++-..||.. -..++|.+.++| T Consensus 233 v~~~gi~~~~~~~~~~a~~~g~~lrlv~~~~~~~-~~V~~~~v~~~~pla-~~g~~N~v~i~t 293 (327) T 3do5_A 233 VEVTGITQITPEAFQVAAEKGYTIRLIAEVSREK-LKVSPRLVPFHHPLA-IKGTMNAAMFKT 293 (327) T ss_dssp SEECCSTTCCHHHHHHHHTTTEEEEEEEEESSSC-EEEEEEEEETTSGGG-CCSSCEEEEEEE T ss_pred HCCCCCCCCCHHHHHHHHHCCCEEEEEEEEECCE-EEEEEEEECCCCCCE-ECCCCEEEEEEE T ss_conf 0415854468899999986497799987852766-999999967999713-789855999984 No 2 >1np3_A Ketol-acid reductoisomerase; A DEEP figure-OF-eight knot, C-terminal alpha-helical domain, oxidoreductase; 2.00A {Pseudomonas aeruginosa} SCOP: a.100.1.2 c.2.1.6 Probab=8.99 E-value=1.2e+02 Score=13.38 Aligned_cols=40 Identities=23% Similarity=0.383 Sum_probs=29.8 Q ss_pred CEECCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCEEEEEE Q ss_conf 93345643456777554541389521898650222134544 Q gi|254780990|r 1 MFLVPDDGIDDLFEEDLFQYDANKSELVLISSLWSIDFFEI 41 (66) Q Consensus 1 mflvpddgiddlfeedlfqydankselvlisslwsidffei 41 (66) |+|+||...-+++++++.++=...+-|. .|.=.+|.|-.| T Consensus 77 ~~L~pD~~q~~~y~~~i~p~l~~g~~l~-faHGf~i~~~~i 116 (338) T 1np3_A 77 MILTPDEFQGRLYKEEIEPNLKKGATLA-FAHGFSIHYNQV 116 (338) T ss_dssp EECSCHHHHHHHHHHHTGGGCCTTCEEE-ESCCHHHHTTSS T ss_pred EEECCHHHHHHHHHHHHHHHCCCCCEEE-ECCCCEEEECCE T ss_conf 6508877779999876664358887798-625540420330 No 3 >3pvi_A Protein (pvuii endonuclease); complex (restriction endonuclease/DNA), mutant, protein/DNA, hydrolase/DNA complex; HET: DNA; 1.59A {Proteus vulgaris} SCOP: c.52.1.6 PDB: 1eyu_A* 1f0o_A 1pvi_A* 1ni0_A 1k0z_A 1h56_A 1pvu_A 2pvi_A* Probab=8.68 E-value=76 Score=14.42 Aligned_cols=16 Identities=38% Similarity=0.636 Sum_probs=13.5 Q ss_pred CCCCCCCCCCEEEEEC Q ss_conf 6520002463465429 Q gi|254780990|r 51 PINKYEKTDNFFALYT 66 (66) Q Consensus 51 pinkyektdnffalyt 66 (66) -|.||.|.|-+||.|. T Consensus 90 Ii~KYRkV~WiFA~y~ 105 (157) T 3pvi_A 90 IIAKYRQVPWIFAIYR 105 (157) T ss_dssp HHHHHHTSCEEEEEEE T ss_pred HHHHHHCCCEEEEEEC T ss_conf 9988735776876534 No 4 >3ksk_A Type-2 restriction enzyme pvuii; single chain restriction endonuclease, DNA-binding protein, endonuclease, hydrolase, magnesium, metal-binding; 2.35A {Proteus vulgaris} Probab=5.10 E-value=1.6e+02 Score=12.79 Aligned_cols=14 Identities=43% Similarity=0.793 Sum_probs=7.0 Q ss_pred CCCCCCCCCEEEEE Q ss_conf 52000246346542 Q gi|254780990|r 52 INKYEKTDNFFALY 65 (66) Q Consensus 52 inkyektdnffaly 65 (66) |.||.|.|-+||.| T Consensus 250 i~KYRkV~WiFA~y 263 (324) T 3ksk_A 250 IAKYRQVPWIFAIY 263 (324) T ss_dssp HHHHTTSCEEEEEE T ss_pred HHHHHCCCEEEEEE T ss_conf 98763577688752 No 5 >2qj2_A Hepatocyte growth factor; HGF/SF, hormone/growth factor; 1.81A {Homo sapiens} SCOP: g.10.1.1 g.14.1.1 PDB: 1nk1_A 3mkp_A* 1gmn_A* 1gmo_A* 1bht_A* 1gp9_A* 2qj4_A Probab=4.24 E-value=2e+02 Score=12.33 Aligned_cols=12 Identities=17% Similarity=0.506 Sum_probs=4.7 Q ss_pred HHHHCCCCCEEE Q ss_conf 454138952189 Q gi|254780990|r 17 LFQYDANKSELV 28 (66) Q Consensus 17 lfqydankselv 28 (66) -|+|+.....-+ T Consensus 61 aF~~~~~~~~C~ 72 (184) T 2qj2_A 61 AFVFDKARKQCL 72 (184) T ss_dssp EEEEETTTTEEE T ss_pred CCCCCCCCCCEE T ss_conf 243157457048 No 6 >3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding protein; 2.20A {Bovine immunodeficiency virus R29} PDB: 3kkr_A Probab=3.85 E-value=2.5e+02 Score=11.78 Aligned_cols=10 Identities=30% Similarity=0.624 Sum_probs=4.0 Q ss_pred ECCCEEEEEE Q ss_conf 0222134544 Q gi|254780990|r 32 SLWSIDFFEI 41 (66) Q Consensus 32 slwsidffei 41 (66) -+|.+|+..+ T Consensus 3 h~W~~D~t~~ 12 (152) T 3kks_A 3 HLWQMDNTHW 12 (152) T ss_dssp CEEEEEEEEE T ss_pred CEEEEEEEEE T ss_conf 1000516266 No 7 >1h95_A CSD, Y-box binding protein; translation factor, transcription factor, OB-fold, 5- stranded anti-parallel beta-barrel, single stranded DNA binding; NMR {Homo sapiens} SCOP: b.40.4.5 Probab=3.50 E-value=1.4e+02 Score=13.12 Aligned_cols=12 Identities=33% Similarity=0.739 Sum_probs=0.0 Q ss_pred EECCCCCHHHHH Q ss_conf 334564345677 Q gi|254780990|r 2 FLVPDDGIDDLF 13 (66) Q Consensus 2 flvpddgiddlf 13 (66) |..||||-.|+| T Consensus 24 FI~~ddg~~DvF 35 (79) T 1h95_A 24 FINRNDTKEDVF 35 (79) T ss_dssp EEEEGGGTEEEE T ss_pred EEEECCCCEEEE T ss_conf 998589970499 No 8 >2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB fold, structural genomics, protein structure initiative; NMR {Pectobacterium atrosepticum} Probab=3.36 E-value=1.5e+02 Score=12.92 Aligned_cols=11 Identities=27% Similarity=0.869 Sum_probs=0.0 Q ss_pred EECCCCCHHHHH Q ss_conf 334564345677 Q gi|254780990|r 2 FLVPDDGIDDLF 13 (66) Q Consensus 2 flvpddgiddlf 13 (66) |+.++|| +|+| T Consensus 18 FI~~~~G-~DvF 28 (74) T 2k5n_A 18 FIKDENG-DNRY 28 (74) T ss_dssp EEEESSS-CEEE T ss_pred EEEECCC-CCEE T ss_conf 9874699-8399 No 9 >3lk3_T Carmil homolog, leucine-rich repeat-containing protein 16A; CAPZ, actin filaments, uncapping, actin-filament regulators, protein-protein complex; 2.68A {Homo sapiens} Probab=3.27 E-value=2e+02 Score=12.31 Aligned_cols=16 Identities=31% Similarity=0.848 Sum_probs=0.0 Q ss_pred CCCHHHHHHHHHHHHC Q ss_conf 6434567775545413 Q gi|254780990|r 6 DDGIDDLFEEDLFQYD 21 (66) Q Consensus 6 ddgiddlfeedlfqyd 21 (66) |.|+|+.|..-+.+.| T Consensus 60 dEGld~FFskkv~~~~ 75 (115) T 3lk3_T 60 DEGVDEFFTKKVTKMD 75 (115) T ss_dssp CTTHHHHTTCCCC--- T ss_pred CCCHHHHHHCCCCCCC T ss_conf 2357867530324465 No 10 >3hn4_A Hepatocyte growth factor; HGF/SF, hormone/growth factor, alternative splicing, disulfi glycoprotein, kringle, serine protease homol hormone; HET: EPE; 2.60A {Homo sapiens} Probab=3.17 E-value=2.4e+02 Score=11.87 Aligned_cols=13 Identities=31% Similarity=0.733 Sum_probs=0.0 Q ss_pred HCCCCCCCCCCCC Q ss_conf 0076520002463 Q gi|254780990|r 48 RRHPINKYEKTDN 60 (66) Q Consensus 48 rrhpinkyektdn 60 (66) +|.|++.|.||++ T Consensus 10 ~~~~l~~~~~~~~ 22 (264) T 3hn4_A 10 RRNTIHEFKKSAK 22 (264) T ss_dssp CCCCGGGEEEEEE T ss_pred CCCHHHHHHHCCC T ss_conf 6455777642478 Done!