Query gi|254780854|ref|YP_003065267.1| NADH dehydrogenase subunit C [Candidatus Liberibacter asiaticus str. psy62] Match_columns 202 No_of_seqs 224 out of 1237 Neff 5.9 Searched_HMMs 23785 Date Tue May 31 22:44:09 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780854.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3i9v_5 NADH-quinone oxidoreduc 100.0 0 0 406.3 7.5 177 8-192 3-203 (207) 2 3mcr_A NADH dehydrogenase, sub 100.0 0 0 304.8 9.1 129 4-132 83-213 (213) 3 3ech_C 25-MER fragent of prote 21.5 11 0.00047 17.8 -0.8 12 113-124 13-24 (26) 4 2fhm_A Probable acylphosphatas 20.2 45 0.0019 14.1 4.9 57 16-76 30-90 (91) 5 1kr7_A Neural globin, mini-hem 13.6 19 0.0008 16.4 -1.2 23 118-143 10-32 (110) 6 2a0m_A Arginase superfamily pr 13.5 65 0.0027 13.1 1.7 29 119-147 139-169 (316) 7 2zjr_I 50S ribosomal protein L 13.3 40 0.0017 14.4 0.4 33 136-175 46-80 (156) 8 1bl1_A Parathyroid hormone rec 13.2 13 0.00054 17.4 -2.1 15 110-124 10-24 (31) 9 3d33_A Domain of unknown funct 13.2 38 0.0016 14.5 0.3 18 158-175 18-36 (108) 10 3m1r_A Formimidoylglutamase; s 12.4 71 0.003 12.9 1.8 30 117-146 144-174 (322) No 1 >3i9v_5 NADH-quinone oxidoreductase subunit 5; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_5* 3iam_5* 3ias_5* 3m9s_5* Probab=100.00 E-value=0 Score=406.29 Aligned_cols=177 Identities=32% Similarity=0.554 Sum_probs=157.4 Q ss_pred HHHHHHHHCCCCEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCC----CCCCEEEEEEEEECC- Q ss_conf 999999861531145798479599998689899999998718789801475132568877----778579999966157- Q gi|254780854|r 8 LGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLS----RSNRFDVVYHFLSPK- 82 (202) Q Consensus 8 L~~~L~~~l~~~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~----~~~RFeVvY~LlS~~- 82 (202) |.+.|++.+...+.......|+++|.|+++++.+++++||+ ++|++|+|||||||++ +++||+|||||+|++ T Consensus 3 le~~l~e~~~~~~~~e~~~~g~l~i~V~~e~l~~v~~~Lk~---~gf~~L~dit~vD~~~~~~~~~~rf~vvY~l~S~~~ 79 (207) T 3i9v_5 3 LERVLEEARAKGYPIEDNGLGNLWVVLPRERFKEEMAHYKA---MGFNFLADIVGLDYLTYPDPRPERFAVVYELVSLPG 79 (207) T ss_dssp THHHHHHHHHTTCCCCBCTTSCBEEECCHHHHHHHHHHHHH---TTCCCEEEEEEEECTTCSSCCSSSEEEEEEECCCTT T ss_pred HHHHHHHHHHCCCCEEECCCCCEEEEECHHHHHHHHHHHHH---CCCCCEEEEEEEECCCCCCCCCCEEEEEEEEECCCC T ss_conf 89999986643672002458838999839999999999986---899928788848278776787875899999744655 Q ss_pred ----CCCEEEEEEEECCC-CEEECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCC----CCC Q ss_conf ----52059982120578-501012233025531011210113827356798767788998987871133778----984 Q gi|254780854|r 83 ----YNRRLRVKIAVAEG-KSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPV----TGF 153 (202) Q Consensus 83 ----~n~ri~Vk~~v~e~-~~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPl----tG~ 153 (202) .|.||+||+.++++ +.||||++|||||||+|||+||||||.|+|||||||||+|++|+|||||||||| ||| T Consensus 80 ~~~~~~~rv~vk~~v~~~~p~ipSi~~i~p~A~w~ERE~~DmfGi~f~ghpdlrril~~~~~~g~PLRKDfpl~~~~~~~ 159 (207) T 3i9v_5 80 WKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYDLFGIVFEGHPDLRKILTPEDLEGHPLRKDYPLGETPTLF 159 (207) T ss_dssp SSSCCCCCEEEEEEECSSCCBCCCCTTTCSTHHHHHHHHHHTSCCBCTTCSCCCCCSSCTTCCSCTTSTTSCCCCCCEEC T ss_pred CCCCCCEEEEEEEECCCCCCCCCCEECCCCCCCCCCEEEEEECCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 66677608999984676567667710305799812322026127676799998454588899989877674688866652 Q ss_pred EEEEE----------CHHHCEEECCCCEEEEHHHCCCCCCCCCCCCCCC Q ss_conf 47887----------6211513126642202221276656323453345 Q gi|254780854|r 154 VELHY----------DDKVKKVVYRPVELMQEHRDYDFLSPWEGVNSLF 192 (202) Q Consensus 154 ~evry----------d~~~k~v~~epv~l~q~~r~f~~~spwe~~~~~~ 192 (202) +|+|| +..+++|+|+|+.+.|+||+ +|+|++++. T Consensus 160 ~e~~~~~p~~~r~~~~~~~~~~~~~~~~~~~~~r~-----~~~~~~~~~ 203 (207) T 3i9v_5 160 REGRYIIPAEFRAALTGKDPGLTFYKGGSRKGYRS-----LWADLKKAR 203 (207) T ss_dssp TTSCEECGGGTCCSCCSSCCCSSSCCCGGGSCCCC-----CC------- T ss_pred EEEEECCCCCCCCCCCCCCCCCEEECCCCCCCCCC-----HHCCCHHHH T ss_conf 46675586424444456565411301553635304-----111601320 No 2 >3mcr_A NADH dehydrogenase, subunit C; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.65A {Thermobifida fusca} Probab=100.00 E-value=0 Score=304.75 Aligned_cols=129 Identities=33% Similarity=0.641 Sum_probs=117.8 Q ss_pred HHHHHHHHHHHHCCCCEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCC-CCEEEEEEEEECC Q ss_conf 799999999986153114579847959999868989999999871878980147513256887777-8579999966157 Q gi|254780854|r 4 KIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRS-NRFDVVYHFLSPK 82 (202) Q Consensus 4 ~L~~L~~~L~~~l~~~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~-~RFeVvY~LlS~~ 82 (202) .|+++.+.+...|+++|+++++.+|+++|.|++++|.++|++||+++.|+|++|+||||||||++. .||++||||+|++ T Consensus 83 ~L~~~~~~~~~~~~~aI~~vvv~rGeltl~V~~e~L~~V~~~LKdd~~l~Fe~L~dltgVDype~~~~rf~vVYhL~S~~ 162 (213) T 3mcr_A 83 ALERSLKEIGTPYDTAISRVVVDRGEITFHVQREHLLDVATRLRDDPALRFELCLGVTGVHYPEDEGNELHAVYALRSIT 162 (213) T ss_dssp HHHHHHHHTTCCHHHHEEEEEEETTEEEEEECGGGHHHHHHHHHHCTTTCCCEEEEEEEEECTTSTTCCEEEEEEEEETT T ss_pred HHHHHHHHHHCHHHHHHEEEEEECCEEEEEECHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCCCCEEEEEEEECCC T ss_conf 99999987301032130389998998999985999999999996288999763100200716765688358999830366 Q ss_pred CCCEEEEEEEECCCC-EEECCCCCEECCCCEECCCHHHCCCEECCCCCCCC Q ss_conf 520599821205785-01012233025531011210113827356798767 Q gi|254780854|r 83 YNRRLRVKIAVAEGK-SVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRR 132 (202) Q Consensus 83 ~n~ri~Vk~~v~e~~-~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRR 132 (202) +|.||+||+.++++. .||||++|||+|||||||+||||||.|+||||||| T Consensus 163 ~n~rIrlkv~v~~~dP~IPSI~~I~psAnW~ERE~yDMFGI~F~GHPdLrR 213 (213) T 3mcr_A 163 HNYEIRLEVSCPDSDPHIPSIVSVYPTNDWHEREAWDFFGIIFDGHPALTR 213 (213) T ss_dssp TTEEEEEEEEECTTSCEEECCTTTCTTHHHHHHHHHHHHCCEEETCGGGC- T ss_pred CCCEEEEEECCCCCCCCCCEEHHHCCCCCHHHHHHHHCCCEEECCCCCCCC T ss_conf 661368860346688968704210257677688776136801788998889 No 3 >3ech_C 25-MER fragent of protein ARMR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} Probab=21.49 E-value=11 Score=17.79 Aligned_cols=12 Identities=50% Similarity=1.287 Sum_probs=9.4 Q ss_pred ECCCHHHCCCEE Q ss_conf 112101138273 Q gi|254780854|r 113 EREVWDMYGIFF 124 (202) Q Consensus 113 ERE~~DmfGI~F 124 (202) -|.+||+||-.| T Consensus 13 rrnawdlygehf 24 (26) T 3ech_C 13 RRNAWDLYGEHF 24 (26) T ss_dssp HHTHHHHHHSCC T ss_pred HHHHHHHHHHHC T ss_conf 860898725231 No 4 >2fhm_A Probable acylphosphatase; hydrolase; NMR {Bacillus subtilis} PDB: 2hlt_A 2hlu_A 3br8_A Probab=20.18 E-value=45 Score=14.10 Aligned_cols=57 Identities=23% Similarity=0.337 Sum_probs=34.1 Q ss_pred CCCCEEEEEEECC--CEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCC--CCCCCCCCCEEEEE Q ss_conf 1531145798479--5999986898999999987187898014751325--68877778579999 Q gi|254780854|r 16 FSGSVRFAVNSVG--ELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCG--VDFLSRSNRFDVVY 76 (202) Q Consensus 16 l~~~I~~~~~~~~--el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDIta--VDyp~~~~RFeVvY 76 (202) +.+.+.+.. .| ++.+.-+.+.+..++..|+..+ .......++. .+.......|++.| T Consensus 30 l~G~V~N~~--dG~Vei~~~G~~~~i~~f~~~l~~gp--~~a~V~~v~~~~~~~~~~~~~F~I~~ 90 (91) T 2fhm_A 30 LAGWVKNRD--DGRVEILAEGPENALQSFVEAVKNGS--PFSKVTDISVTESRSLEGHHRFSIVY 90 (91) T ss_dssp CEEEEEECT--TSCEEEEEEECHHHHHHHHHHHHTTC--SSSEEEEEEEEEECCCCCCCSEEECC T ss_pred CEEEEEECC--CCCEEEEEECCHHHHHHHHHHHHHCC--CCCEEEEEEEEECCCCCCCCCEEEEE T ss_conf 889999999--99899999859999999999997699--98889999999858888999859936 No 5 >1kr7_A Neural globin, mini-hemoglobin; nerve tissue, protein cavities, oxygen transport, oxygen storage/transport complex; HET: HEM; 1.50A {Cerebratulus lacteus} SCOP: a.1.1.4 PDB: 1v07_A* 2vyz_A* 2vyy_A* Probab=13.63 E-value=19 Score=16.36 Aligned_cols=23 Identities=30% Similarity=0.741 Sum_probs=18.0 Q ss_pred HHCCCEECCCCCCCCCCCCCCCCCCC Q ss_conf 11382735679876778899898787 Q gi|254780854|r 118 DMYGIFFEGHPDLRRILTDYGFEGHP 143 (202) Q Consensus 118 DmfGI~F~gHPdlRRiL~d~~feGhP 143 (202) |||.-.|+-||+.|++.. |.|.+ T Consensus 10 ~ff~~LF~~~P~~~~~F~---f~~~~ 32 (110) T 1kr7_A 10 DFYQELFKAHPEYQNKFG---FKGVA 32 (110) T ss_dssp HHHHHHHHHCGGGGGGST---TTTCC T ss_pred HHHHHHHHHCHHHHHHCC---CCCCC T ss_conf 999999998957897678---87885 No 6 >2a0m_A Arginase superfamily protein; structural genomics, PSI, protein structure initiative, structural genomics of pathogenic protozoa consortium; 1.60A {Trypanosoma cruzi} SCOP: c.42.1.1 Probab=13.48 E-value=65 Score=13.09 Aligned_cols=29 Identities=34% Similarity=0.462 Sum_probs=19.6 Q ss_pred HCC-CEECCCCCCCCCCCCCCC-CCCCCCCC Q ss_conf 138-273567987677889989-87871133 Q gi|254780854|r 119 MYG-IFFEGHPDLRRILTDYGF-EGHPLRKD 147 (202) Q Consensus 119 mfG-I~F~gHPdlRRiL~d~~f-eGhPLRKD 147 (202) .+| |.|+.|+|+|.-..+..+ .|-|+|+= T Consensus 139 ~i~vI~~DAH~D~~~~~~~~~~~~g~~~~~~ 169 (316) T 2a0m_A 139 DVGVINVDSHLDVRPPLQDGRVHSGTPFRQL 169 (316) T ss_dssp CCEEEEECSSCCCCCCCTTSCCCTTCHHHHH T ss_pred CEEEEEECCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 5479983466354666779888899751211 No 7 >2zjr_I 50S ribosomal protein L15; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.12.1.1 PDB: 1nwx_J* 1nwy_J* 1sm1_J* 1xbp_J* 2zjp_I* 2zjq_I 1nkw_J 3cf5_I* 3dll_I* 1pnu_J 1pny_J 1vor_M 1vou_M 1vow_M 1voy_M 1vp0_M Probab=13.28 E-value=40 Score=14.39 Aligned_cols=33 Identities=33% Similarity=0.444 Sum_probs=24.8 Q ss_pred CCCCCC--CCCCCCCCCCCCEEEEECHHHCEEECCCCEEEEH Q ss_conf 998987--8711337789844788762115131266422022 Q gi|254780854|r 136 DYGFEG--HPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQE 175 (202) Q Consensus 136 d~~feG--hPLRKDFPltG~~evryd~~~k~v~~epv~l~q~ 175 (202) .-+||| .||-+=+|--||.-. +..|++|+|.+= T Consensus 46 ~~~feGGq~Pl~rr~PKrGF~~~-------~~~~~~vnl~~L 80 (156) T 2zjr_I 46 GAFFEGGRSRLIARLPKRGFNNV-------GTTYEVVKLSQL 80 (156) T ss_dssp CCSCSCCSSSSTTTSCCCCCCCC-------CCCCCEECHHHH T ss_pred CCCCCCCCCCCEEECCCCCCCCC-------CCEEEEEEHHHH T ss_conf 88524686561330674588876-------641678887883 No 8 >1bl1_A Parathyroid hormone receptor; micelle structures, calciotropic hormones, structures; NMR {Homo sapiens} SCOP: j.15.1.1 Probab=13.20 E-value=13 Score=17.38 Aligned_cols=15 Identities=40% Similarity=0.736 Sum_probs=10.3 Q ss_pred CCEECCCHHHCCCEE Q ss_conf 310112101138273 Q gi|254780854|r 110 DWFEREVWDMYGIFF 124 (202) Q Consensus 110 ~W~ERE~~DmfGI~F 124 (202) .--|||+||-.|..+ T Consensus 10 et~erevfdrl~liy 24 (31) T 1bl1_A 10 ETREREVFDRLGMIY 24 (31) T ss_dssp SCCHHHHHHSSHHHH T ss_pred CCHHHHHHHHHHEEE T ss_conf 415888887601156 No 9 >3d33_A Domain of unknown function with AN immunoglobulin-like beta-sandwich fold; YP_001297618.1; HET: MSE; 1.70A {Bacteroides vulgatus atcc 8482} Probab=13.15 E-value=38 Score=14.52 Aligned_cols=18 Identities=17% Similarity=0.595 Sum_probs=6.5 Q ss_pred ECHHHCEEE-CCCCEEEEH Q ss_conf 762115131-266422022 Q gi|254780854|r 158 YDDKVKKVV-YRPVELMQE 175 (202) Q Consensus 158 yd~~~k~v~-~epv~l~q~ 175 (202) .|+.+++++ .-|+....+ T Consensus 18 w~~~~rs~~~~~Pi~a~Id 36 (108) T 3d33_A 18 WDDPIRSAATNCPITVFTD 36 (108) T ss_dssp CCC-------CCSEEEEEE T ss_pred CCCCCEECCCCCCCEEEEE T ss_conf 2688163388999599997 No 10 >3m1r_A Formimidoylglutamase; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; HET: CAC; 2.20A {Bacillus subtilis} Probab=12.35 E-value=71 Score=12.89 Aligned_cols=30 Identities=23% Similarity=0.428 Sum_probs=18.1 Q ss_pred HHHCCCE-ECCCCCCCCCCCCCCCCCCCCCC Q ss_conf 0113827-35679876778899898787113 Q gi|254780854|r 117 WDMYGIF-FEGHPDLRRILTDYGFEGHPLRK 146 (202) Q Consensus 117 ~DmfGI~-F~gHPdlRRiL~d~~feGhPLRK 146 (202) +.-+||. |+.|+|+|.--...-..|.|++. T Consensus 144 ~~~i~vI~~DAH~Dl~~~~~~~~~~~~~~~~ 174 (322) T 3m1r_A 144 KGTTAVIQFDAHHDVRNTEDGGPTNGTPFRR 174 (322) T ss_dssp HCSEEEEEECSSCCCCCSSCC--CTTCHHHH T ss_pred CCCEEEEEEECCCCCCCCCCCCCCCCHHHHH T ss_conf 7973699954675545476898576027899 Done!