Query gi|254781211|ref|YP_003065624.1| hypothetical protein CLIBASIA_05590 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 234 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 23785 Date Wed Jun 1 01:49:15 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781211.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3fgh_A Transcription factor A, 37.3 16 0.00068 16.3 2.3 64 56-140 1-64 (67) 2 1v63_A Nucleolar transcription 27.0 30 0.0013 14.5 3.1 74 52-144 3-76 (101) 3 2k0d_X IMME7, colicin-E7 immun 21.8 38 0.0016 13.9 3.3 47 56-112 8-54 (101) 4 1unk_A Colicin E7; immunity pr 20.3 40 0.0017 13.7 2.9 45 58-112 3-47 (87) 5 3keo_A Redox-sensing transcrip 19.5 35 0.0015 14.1 1.4 15 92-106 158-172 (212) 6 1fr2_A Colicin E9 immunity pro 16.6 49 0.0021 13.2 4.1 44 58-112 3-46 (86) 7 1f6v_A DNA transposition prote 16.1 9.7 0.00041 17.7 -2.1 24 141-164 6-29 (91) 8 2cpy_A RNA-binding protein 12; 14.3 12 0.00049 17.2 -2.1 69 129-216 22-90 (114) 9 3h1q_A Ethanolamine utilizatio 10.7 72 0.003 12.1 1.2 32 60-91 90-121 (272) 10 2kng_A Protein LSR2; DNA-bindi 10.6 73 0.003 12.1 1.6 18 213-230 9-26 (55) No 1 >3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Probab=37.35 E-value=16 Score=16.29 Aligned_cols=64 Identities=16% Similarity=0.294 Sum_probs=40.8 Q ss_pred CCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHH Q ss_conf 89999832120038002014567898999886281578999999999983688778831136999999986507730234 Q gi|254781211|r 56 GEPKPPIEDYTLSCPDYVSEAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQFGASLEEERKLLQTKLGSDYETR 135 (234) Q Consensus 56 gepkppiedytlscpdyvseaevtahieafkeagvdarvaqkvvdklvdhgrkigeqfgasleeerkllqtklgsdyetr 135 (234) |.||.|.--|.+-|-+.. +.++....+ +-.+.||+.+-.--++|+.......-.+.+.- T Consensus 1 GkPKrP~say~~F~~~~r---------~~~~~~~p~------------e~~k~~~~~W~~ls~~eK~~y~~~a~~~~~~Y 59 (67) T 3fgh_A 1 GKPKRPRSAYNVYVAERF---------QEAKGDSPQ------------EKLKTVKENWKNLSDSEKELYIQHAKEDETRY 59 (67) T ss_dssp CCCCCCCCHHHHHHHHHH---------HHHCSSSHH------------HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHH---------HHHHHCCHH------------HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH T ss_conf 968799989999999999---------999850999------------99999999882099999999999999999999 Q ss_pred HHHHH Q ss_conf 77999 Q gi|254781211|r 136 EKDIA 140 (234) Q Consensus 136 ekdia 140 (234) +.+++ T Consensus 60 ~~e~~ 64 (67) T 3fgh_A 60 HNEMK 64 (67) T ss_dssp HHHHH T ss_pred HHHHH T ss_conf 99987 No 2 >1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1 Probab=27.01 E-value=30 Score=14.55 Aligned_cols=74 Identities=12% Similarity=0.263 Sum_probs=51.3 Q ss_pred HHHCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCC Q ss_conf 02118999983212003800201456789899988628157899999999998368877883113699999998650773 Q gi|254781211|r 52 TEEAGEPKPPIEDYTLSCPDYVSEAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQFGASLEEERKLLQTKLGSD 131 (234) Q Consensus 52 teeagepkppiedytlscpdyvseaevtahieafkeagvdarvaqkvvdklvdhgrkigeqfgasleeerkllqtklgsd 131 (234) +-..|-||+|.--|.|-|-++.... +..+.+ ..+-.+.||+.+-.--++|+.-......-+ T Consensus 3 ~~~~~p~KrP~~ay~lF~~e~r~~~---------~~~~~~----------~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~ 63 (101) T 1v63_A 3 SGSSGPKKPPMNGYQKFSQELLSNG---------ELNHLP----------LKERMVEIGSRWQRISQSQKEHYKKLAEEQ 63 (101) T ss_dssp CCCCSSCCCCSSSHHHHHHHHHHHC---------TTTTSC----------HHHHHHHHHHHHTTSCHHHHHHHHHHHHHH T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHH---------HCCCCC----------HHHHHHHHHHHHHHCCHHHHHHHHHHHHHH T ss_conf 9999989899989999999999987---------558989----------999999999998509999999999999999 Q ss_pred HHHHHHHHHHHHH Q ss_conf 0234779999975 Q gi|254781211|r 132 YETREKDIARYFR 144 (234) Q Consensus 132 yetrekdiaryfr 144 (234) -+..+..+..|-. T Consensus 64 k~~y~~e~~~y~~ 76 (101) T 1v63_A 64 QRQYKVHLDLWVK 76 (101) T ss_dssp HHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHH T ss_conf 9999999999985 No 3 >2k0d_X IMME7, colicin-E7 immunity protein; toxin inhibitor; NMR {Escherichia coli} Probab=21.82 E-value=38 Score=13.92 Aligned_cols=47 Identities=36% Similarity=0.489 Sum_probs=31.8 Q ss_pred CCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 899998321200380020145678989998862815789999999999836887788 Q gi|254781211|r 56 GEPKPPIEDYTLSCPDYVSEAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQ 112 (234) Q Consensus 56 gepkppiedytlscpdyvseaevtahieafkeagvdarvaqkvvdklvdhgrkigeq 112 (234) -+-|--|+||| |+|...-+..|-.+... ...+..|.|++|=.+|-|. T Consensus 8 ~elK~~isDYT--------E~EFl~fl~~i~~~~~~--~~e~~~d~L~~hF~~iteH 54 (101) T 2k0d_X 8 HELKNSISDYT--------EAEFVQLLKEIEKENVA--ATDDVLDVLLEHFVKITEH 54 (101) T ss_dssp -CCCSSGGGCB--------HHHHHHHHHHHHHHHHH--TCSHHHHHHHHHHHHHHCC T ss_pred HHHHHHHHHCC--------HHHHHHHHHHHHHCCCC--CHHHHHHHHHHHHHHHHCC T ss_conf 99986775518--------99999999999864677--5089999999999999708 No 4 >1unk_A Colicin E7; immunity protein, dimeric structure, RNAse active site; 1.80A {Escherichia coli} SCOP: a.28.2.1 PDB: 1mz8_A 1ayi_A 2jaz_A 2jb0_A 2jbg_A 7cei_A 1znv_A 1cei_A 1ujz_A 2erh_A Probab=20.32 E-value=40 Score=13.72 Aligned_cols=45 Identities=36% Similarity=0.494 Sum_probs=29.0 Q ss_pred CCCCCCCCEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9998321200380020145678989998862815789999999999836887788 Q gi|254781211|r 58 PKPPIEDYTLSCPDYVSEAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQ 112 (234) Q Consensus 58 pkppiedytlscpdyvseaevtahieafkeagvdarvaqkvvdklvdhgrkigeq 112 (234) -|--|+||| |+|...-+..|-++... -..+..|.|++|=.+|-|. T Consensus 3 lK~~isDYT--------E~EFl~fl~~i~~~~~~--~~e~~~d~l~~hF~~iteH 47 (87) T 1unk_A 3 LKNSISDYT--------EAEFVQLLKEIEKENVA--ATDDVLDVLLEHFVKITEH 47 (87) T ss_dssp CCCSGGGSC--------HHHHHHHHHHHHHHHHS--SCCHHHHHHHHHHHHHHCC T ss_pred CCCCCCCCC--------HHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHCCC T ss_conf 330126379--------99999999999974787--6188999999999997049 No 5 >3keo_A Redox-sensing transcriptional repressor REX; DNA binding protein, winged helix, rossmann fold, NAD+; HET: NAD; 1.50A {Streptococcus agalactiae serogroup iiiorganism_taxid} PDB: 3keq_A* 3ket_A* Probab=19.51 E-value=35 Score=14.14 Aligned_cols=15 Identities=47% Similarity=0.558 Sum_probs=6.1 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 789999999999836 Q gi|254781211|r 92 ARVAQKVVDKLVDHG 106 (234) Q Consensus 92 arvaqkvvdklvdhg 106 (234) +..||.|.|.||+.| T Consensus 158 ~~~AQ~vad~Lv~~G 172 (212) T 3keo_A 158 STEAQEVADILVKAG 172 (212) T ss_dssp GGGHHHHHHHHHHHT T ss_pred HHHHHHHHHHHHHHC T ss_conf 789999999999829 No 6 >1fr2_A Colicin E9 immunity protein; protein-protein complex, zinc containing enzyme, HNH-motif, immune system; 1.60A {Escherichia coli} SCOP: a.28.2.1 PDB: 1e0h_A 1emv_A 1imp_A 1imq_A 2k5x_A 2vln_A 2vlp_A 2vlq_A 2vlo_A 2gzf_A 2gzg_A 2gzi_A 2gyk_A 2gzj_A 2gze_A 1bxi_A 3gkl_C 3gjn_A Probab=16.57 E-value=49 Score=13.17 Aligned_cols=44 Identities=32% Similarity=0.385 Sum_probs=31.1 Q ss_pred CCCCCCCCEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9998321200380020145678989998862815789999999999836887788 Q gi|254781211|r 58 PKPPIEDYTLSCPDYVSEAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQ 112 (234) Q Consensus 58 pkppiedytlscpdyvseaevtahieafkeagvdarvaqkvvdklvdhgrkigeq 112 (234) -|--|+||| |+|...-+..|-++.... ....|.||+|=.+|-|. T Consensus 3 lK~~i~DYT--------E~EFl~fl~~i~~~~~~~---e~~~~~lv~hF~~iteH 46 (86) T 1fr2_A 3 LKHSISDYT--------EAEFLQLVTTICNADTSS---EEELVKLVTHFAEMTEH 46 (86) T ss_dssp CCSCGGGSB--------HHHHHHHHHHHHTTCSSS---HHHHHHHHHHHHHHHCC T ss_pred CCCCCCCCC--------HHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHCCC T ss_conf 221015379--------999999999999668987---99999999999997259 No 7 >1f6v_A DNA transposition protein; MU phage, recombination, ATPase, DNA binding, high salt, solution structure, DNA binding protein; HET: DNA; NMR {Enterobacteria phage MU} SCOP: a.49.1.1 Probab=16.12 E-value=9.7 Score=17.75 Aligned_cols=24 Identities=21% Similarity=0.400 Sum_probs=17.6 Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 997530388147999998632256 Q gi|254781211|r 141 RYFRKEKIPDNDVQSLISAWGFEK 164 (234) Q Consensus 141 ryfrkekipdndvqslisawgfek 164 (234) +-.+..|--.+||++++.|||.+- T Consensus 6 kr~~i~k~kk~Di~Ai~~AWgv~d 29 (91) T 1f6v_A 6 KRTAINKTKKADVKAIADAWQING 29 (91) T ss_dssp CTTCCSSCSGGGTTHHHHSSTTSS T ss_pred HHHCCCCCCHHHHHHHHHHHCCCC T ss_conf 113015898899999999918998 No 8 >2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Probab=14.29 E-value=12 Score=17.22 Aligned_cols=69 Identities=14% Similarity=0.287 Sum_probs=45.7 Q ss_pred CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHHHCCCCCC Q ss_conf 77302347799999753038814799999863225677799998751121123310221245214432288862784300 Q gi|254781211|r 129 GSDYETREKDIARYFRKEKIPDNDVQSLISAWGFEKTFNFFDRYAQQNKESSTGDTFVRSEGSQEADRDFDKVFNTPDFG 208 (234) Q Consensus 129 gsdyetrekdiaryfrkekipdndvqslisawgfektfnffdryaqqnkesstgdtfvrsegsqeadrdfdkvfntpdfg 208 (234) +-.|.+.+.||..+|..-.+..+.|.-+. + ..-.++|.-||.-+-..+|.+-.. .|...|+ T Consensus 22 nLp~~~t~~di~~~F~~~g~~~~~v~~~~------------~-----~~g~~~G~afV~F~~~e~a~~Al~--~n~~~i~ 82 (114) T 2cpy_A 22 NIPFSITKMDVLQFLEGIPVDENAVHVLV------------D-----NNGQGLGQALVQFKNEDDARKSER--LHRKKLN 82 (114) T ss_dssp SCCTTSCHHHHHHHTTTSCCCSTTEEECC------------C-----TTSSCSSCEEEECSSHHHHHHHGG--GCSEEET T ss_pred CCCCCCCHHHHHHHHHHHCCCCEEEEEEE------------C-----CCCCEEEEEEEEECCHHHHHHHHH--CCCCCCC T ss_conf 99998989999999887198307899988------------9-----999870389999899999999985--3998299 Q ss_pred HHHHCCCH Q ss_conf 33312646 Q gi|254781211|r 209 SRVLSGDK 216 (234) Q Consensus 209 srvlsgdk 216 (234) .|.+.-.. T Consensus 83 gr~i~v~~ 90 (114) T 2cpy_A 83 GREAFVHV 90 (114) T ss_dssp TEEEEEEE T ss_pred CEEEEEEE T ss_conf 99999999 No 9 >3h1q_A Ethanolamine utilization protein EUTJ; structural genomics, PSI-2, protein structure initiative; HET: ATP; 2.80A {Carboxydothermus hydrogenoformans z-2901} Probab=10.73 E-value=72 Score=12.09 Aligned_cols=32 Identities=13% Similarity=0.083 Sum_probs=28.0 Q ss_pred CCCCCCEECCCHHHHHHHHHHHHHHHHHCCHH Q ss_conf 98321200380020145678989998862815 Q gi|254781211|r 60 PPIEDYTLSCPDYVSEAEVTAHIEAFKEAGVD 91 (234) Q Consensus 60 ppiedytlscpdyvseaevtahieafkeagvd 91 (234) .++.+-.+++|-|.++.+-.|-.+|.+.||.+ T Consensus 90 ~~i~~~vi~VP~~~t~~~r~ai~~aa~~AGl~ 121 (272) T 3h1q_A 90 SELFQAATAIPPGTVGRNAEACGHVVAGAGLE 121 (272) T ss_dssp SCCCEEEEECCSCC---CTTHHHHHHHHTTCE T ss_pred CCCCCEEEEECCCCCHHHHHHHHHHHHHCCCC T ss_conf 98886899989989989999999999985997 No 10 >2kng_A Protein LSR2; DNA-binding domain, immune response, DNA binding protein; NMR {Mycobacterium tuberculosis} Probab=10.63 E-value=73 Score=12.07 Aligned_cols=18 Identities=28% Similarity=0.726 Sum_probs=12.3 Q ss_pred CCCHHHHHHHHHHHHHHH Q ss_conf 264678899999986544 Q gi|254781211|r 213 SGDKEATKTLRQWAEKQA 230 (234) Q Consensus 213 sgdkeatktlrqwaekqa 230 (234) ..|++-++.+|.||..+. T Consensus 9 ~~dr~~~~~IR~WAr~~G 26 (55) T 2kng_A 9 AIDREQSAAIREWARRNG 26 (55) T ss_dssp CCSSTHHHHHHHHHHHTT T ss_pred CCCHHHHHHHHHHHHHCC T ss_conf 866353799999999938 Done!