Query gi|254780852|ref|YP_003065265.1| NADH dehydrogenase subunit A [Candidatus Liberibacter asiaticus str. psy62] Match_columns 121 No_of_seqs 117 out of 2581 Neff 6.3 Searched_HMMs 23785 Date Tue May 31 22:08:53 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780852.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3fy6_A Integron cassette prote 28.5 26 0.0011 15.1 2.2 13 107-119 82-94 (126) 2 2k9p_A Pheromone alpha factor 25.1 34 0.0014 14.5 5.4 36 5-40 15-50 (80) 3 1w8g_A YGGS, hypothetical UPF0 12.9 31 0.0013 14.7 -0.3 25 34-58 36-60 (234) 4 3cpg_A Uncharacterized protein 8.2 59 0.0025 13.3 -0.2 24 35-58 58-81 (282) 5 1paa_A Yeast transcription fac 8.1 70 0.0029 12.9 0.1 14 43-56 1-14 (30) 6 1sm7_A Recombinant IB pronapin 6.4 87 0.0037 12.4 -0.0 16 39-54 88-103 (109) 7 1ct5_A Protein (yeast hypothet 5.9 88 0.0037 12.3 -0.2 22 37-58 51-72 (256) 8 2jde_A Urokinase-type plasmino 5.3 1.1E+02 0.0048 11.8 0.0 17 38-54 4-20 (276) 9 3mk7_C Cytochrome C oxidase, C 5.3 1.5E+02 0.0062 11.1 7.3 77 5-82 1-77 (311) 10 1s6d_A Albumin 8; all helix, f 4.6 1.5E+02 0.0065 11.0 0.3 13 39-51 86-98 (103) No 1 >3fy6_A Integron cassette protein; novel, oyster POND, woodshole,USA, unknown function, structural genomics, PSI-2, protein structure initiative; 2.10A {Vibrio cholerae} Probab=28.54 E-value=26 Score=15.12 Aligned_cols=13 Identities=46% Similarity=0.831 Sum_probs=9.5 Q ss_pred HHHHHHHHHCCCC Q ss_conf 9999999835757 Q gi|254780852|r 107 VGFIYEWKKGALE 119 (121) Q Consensus 107 ~gl~yew~~G~L~ 119 (121) ---..|||||+|| T Consensus 82 qhawlewrkgald 94 (126) T 3fy6_A 82 QHAWLEWRKGALD 94 (126) T ss_dssp HHHHHHHHTTSSC T ss_pred HHHHHHHHHCCCC T ss_conf 9999999843665 No 2 >2k9p_A Pheromone alpha factor receptor; GPCR, micelle, structurral biology, fragment, G- protein coupled receptor, glycoprotein, membrane; NMR {Saccharomyces cerevisiae} Probab=25.14 E-value=34 Score=14.51 Aligned_cols=36 Identities=14% Similarity=0.231 Sum_probs=27.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHH Q ss_conf 653799999999999999999999997156789832 Q gi|254780852|r 5 LTSYAPILVFMAIASAIVIVLMISPFIVAFKSPDPE 40 (121) Q Consensus 5 ~~~y~~ili~~~~~~~~~~~~~~~s~~l~~~~~~~~ 40 (121) ...-....++..+.++.+..++.+.|+++++++.|. T Consensus 15 v~~~~~~aIv~GvriGaa~l~lii~w~isk~kkTPI 50 (80) T 2k9p_A 15 VNSTVTQAILFGVRSGAAALTLIVVWITSRSRKTPI 50 (80) T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCSCCCH T ss_pred HHHHHHEEHEEHHHHHHHHHHHHHHHHHHCCCCCCE T ss_conf 972423001001268899999999999963677988 No 3 >1w8g_A YGGS, hypothetical UPF0001 protein YGGS; structural genomics, hypothetical protein, putative enzyme with PLP-binding domain; HET: PLP ICT; 2.0A {Escherichia coli} Probab=12.92 E-value=31 Score=14.72 Aligned_cols=25 Identities=16% Similarity=0.278 Sum_probs=18.1 Q ss_pred CCCCCHHHHCHHHHHCHHCCCCCCC Q ss_conf 6789832417444313000434766 Q gi|254780852|r 34 FKSPDPEKLSTYECGFDPFDDARVK 58 (121) Q Consensus 34 ~~~~~~~K~s~yECGf~p~~~~~~~ 58 (121) +..|...-...||||...+|+.|.| T Consensus 36 K~~~~e~I~~a~~~G~r~fGENrvQ 60 (234) T 1w8g_A 36 KTKPASAIAEAIDAGQRQFGENYVQ 60 (234) T ss_dssp TTSCHHHHHHHHHTTCCEEEESSHH T ss_pred CCCCHHHHHHHHHCCCCCCCCCCHH T ss_conf 9989999999998699714687418 No 4 >3cpg_A Uncharacterized protein; unknown protein, TIM barrel, monomer, structural genomics, PSI-2, protein structure initiative; 1.71A {Bifidobacterium adolescentis ATCC15703} Probab=8.19 E-value=59 Score=13.27 Aligned_cols=24 Identities=13% Similarity=0.199 Sum_probs=17.5 Q ss_pred CCCCHHHHCHHHHHCHHCCCCCCC Q ss_conf 789832417444313000434766 Q gi|254780852|r 35 KSPDPEKLSTYECGFDPFDDARVK 58 (121) Q Consensus 35 ~~~~~~K~s~yECGf~p~~~~~~~ 58 (121) ..+-.+-...||||...+|+.|.| T Consensus 58 ~~p~e~I~~a~~~G~r~FGENrvQ 81 (282) T 3cpg_A 58 TRDIGEIMAAIDAGVRMIGENRPQ 81 (282) T ss_dssp TCCHHHHHHHHHTTCCCEEESCHH T ss_pred CCCHHHHHHHHHCCCCCCCCCCHH T ss_conf 989999999998699703687089 No 5 >1paa_A Yeast transcription factor ADR1; transcription regulation; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 Probab=8.09 E-value=70 Score=12.86 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=8.8 Q ss_pred CHHHHHCHHCCCCC Q ss_conf 74443130004347 Q gi|254780852|r 43 STYECGFDPFDDAR 56 (121) Q Consensus 43 s~yECGf~p~~~~~ 56 (121) .||+||+-.-.-+| T Consensus 1 KPf~C~~C~R~FaR 14 (30) T 1paa_A 1 KAYACGLCNRAFTR 14 (30) T ss_dssp CCSBCTTTCCBCSS T ss_pred CCCCCCCCCCHHHH T ss_conf 98343534351348 No 6 >1sm7_A Recombinant IB pronapin; all alpha-helix, right-handed superhelix, plant protein; NMR {Brassica napus} Probab=6.45 E-value=87 Score=12.36 Aligned_cols=16 Identities=13% Similarity=0.152 Sum_probs=12.8 Q ss_pred HHHHCHHHHHCHHCCC Q ss_conf 3241744431300043 Q gi|254780852|r 39 PEKLSTYECGFDPFDD 54 (121) Q Consensus 39 ~~K~s~yECGf~p~~~ 54 (121) ..|+.|..||.+|++. T Consensus 88 ~Ak~LP~~C~i~p~~~ 103 (109) T 1sm7_A 88 IAKNLPNVCNMKQIGT 103 (109) T ss_dssp TTSSHHHHSCCCSSCS T ss_pred HHHHCCCCCCCCCCCC T ss_conf 9985713039798888 No 7 >1ct5_A Protein (yeast hypothetical protein, selenoMet); TIM barrel, pyridoxal-5'-phosphate, selenomethionine, MAD, structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces cerevisiae} SCOP: c.1.6.2 PDB: 1b54_A* Probab=5.95 E-value=88 Score=12.34 Aligned_cols=22 Identities=23% Similarity=0.475 Sum_probs=11.9 Q ss_pred CCHHHHCHHHHHCHHCCCCCCC Q ss_conf 9832417444313000434766 Q gi|254780852|r 37 PDPEKLSTYECGFDPFDDARVK 58 (121) Q Consensus 37 ~~~~K~s~yECGf~p~~~~~~~ 58 (121) +-.+-...||||...+|+.|.| T Consensus 51 ~~~~I~~~~~~G~~~fGENrvQ 72 (256) T 1ct5_A 51 PASDIQILYDHGVREFGENYVQ 72 (256) T ss_dssp CHHHHHHHHHHTCCEEEECCHH T ss_pred CHHHHHHHHHCCCCCCCCCHHH T ss_conf 9999999998699624686599 No 8 >2jde_A Urokinase-type plasminogen activator; plasminogen activation, EGF-like domain, blood coagulation, inhibitor complex, UPA, kringle, zymogen; 2.2A {Homo sapiens} PDB: 2vnt_A* Probab=5.30 E-value=1.1e+02 Score=11.75 Aligned_cols=17 Identities=18% Similarity=0.548 Sum_probs=10.5 Q ss_pred CHHHHCHHHHHCHHCCC Q ss_conf 83241744431300043 Q gi|254780852|r 38 DPEKLSTYECGFDPFDD 54 (121) Q Consensus 38 ~~~K~s~yECGf~p~~~ 54 (121) .+.-..++|||..|... T Consensus 4 ~~~~~~~~~CG~~~~~p 20 (276) T 2jde_A 4 SPPEELKFQCGQKTLRP 20 (276) T ss_dssp ----------------- T ss_pred CCCCCCCCCCCCCCCCC T ss_conf 98855777989937899 No 9 >3mk7_C Cytochrome C oxidase, CBB3-type, subunit P; TM helices, oxidoreductase; HET: HEM HEC FC6; 3.20A {Pseudomonas stutzeri} Probab=5.26 E-value=1.5e+02 Score=11.15 Aligned_cols=77 Identities=12% Similarity=0.199 Sum_probs=0.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCHHHHHCHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 653799999999999999999999997156789832417444313000434766524799999999998759999979 Q gi|254780852|r 5 LTSYAPILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVLFVIFDLEIAFLFP 82 (121) Q Consensus 5 ~~~y~~ili~~~~~~~~~~~~~~~s~~l~~~~~~~~K~s~yECGf~p~~~~~~~Fsi~fyliallFliFDvEiv~l~P 82 (121) |+.|+++.+ .++.++....+..+-...+++++..+...+=+--.|-+++-..|.+-=....-..=++|-+=-.++|| T Consensus 1 ~~~fw~~~i-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~h~~Dgi~E~~np~P~ww~~~f~~tiv~~~~Y~~~yp 77 (311) T 3mk7_C 1 MSTFWSGYI-ALLTLGTIVALFWLIFATRKGESAGTTDQTMGHAFDGIEEYDNPLPRWWFLLFIGTLVFGILYLVLYP 77 (311) T ss_dssp CCHHHHHHH-HHHHHHHHHHHHHHHHHTTTTCCSSCCCCCCSCCBTTBCBCCCCCCHHHHHHHHHHHHHHHHHHHHST T ss_pred CCCHHHHHH-HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 975379999-99999999999999999981578887777468877781010389978999999999999999999953 No 10 >1s6d_A Albumin 8; all helix, folded LEAF, right-handed superhelix, disulphide rich, plant protein; NMR {Helianthus annuus} SCOP: a.52.1.3 Probab=4.61 E-value=1.5e+02 Score=11.04 Aligned_cols=13 Identities=15% Similarity=0.191 Sum_probs=0.0 Q ss_pred HHHHCHHHHHCHH Q ss_conf 3241744431300 Q gi|254780852|r 39 PEKLSTYECGFDP 51 (121) Q Consensus 39 ~~K~s~yECGf~p 51 (121) ..|+.|..||.+| T Consensus 86 ~Ak~LPs~C~i~P 98 (103) T 1s6d_A 86 MAHNLPIECNLMS 98 (103) T ss_dssp HHHHHHHHTTSSS T ss_pred HHHHCHHHCCCCC T ss_conf 9985737329897 Done!