Query gi|254781148|ref|YP_003065561.1| hypothetical protein CLIBASIA_05275 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 69 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 33803 Date Wed Jun 1 22:55:06 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781148.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >3gxv_A Replicative DNA helica 95.3 0.016 4.7E-07 34.6 3.5 44 21-64 11-55 (123) 2 >2r6a_A DNAB helicase, replica 95.1 0.015 4.3E-07 34.8 2.7 52 13-64 6-58 (155) 3 >2q6t_A DNAB replication FORK 94.9 0.034 1E-06 32.8 4.2 47 18-64 7-55 (152) 4 >2r5u_A Replicative DNA helica 94.3 0.024 7.1E-07 33.6 2.1 44 21-64 31-75 (200) 5 >1b79_A DNAB helicase; hexamer 93.6 0.087 2.6E-06 30.6 4.0 47 19-65 19-66 (119) 6 >3bgw_A DNAB-like replicative 93.0 0.052 1.5E-06 31.8 2.0 49 15-64 9-57 (154) 7 >1bm9_A RTP, TER, replication 20.2 39 0.0011 16.2 1.0 15 50-64 50-64 (122) 8 >1vyi_A RNA polymerase alpha s 18.5 54 0.0016 15.4 1.4 33 3-42 22-54 (112) 9 >2wzl_A Phosphoprotein; viral 17.4 53 0.0016 15.5 1.1 32 4-42 209-240 (303) 10 >3ffr_A Phosphoserine aminotra 12.5 96 0.0028 14.0 1.4 29 37-65 7-35 (70) No 1 >>3gxv_A Replicative DNA helicase; hexameric helicase, primase, replication, ATP-binding, autocatalytic cleavage, DNA replication; 2.20A {Helicobacter pylori} PDB: 3gxv_D 3gxv_C (A:) Probab=95.33 E-value=0.016 Score=34.61 Aligned_cols=44 Identities=18% Similarity=0.306 Sum_probs=37.6 Q ss_pred EECHHHHHHHHHHHCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 710089998888706555-99998517762114789999998552 Q gi|254781148|r 21 IGLEQEILGSLLLKGNLQ-PIISFLDAQHFIDPIHSEVFRAITRK 64 (69) Q Consensus 21 igleqeilgslllkgnlq-piisfldaqhfidpihsevfraitrk 64 (69) +..||.+||++|..++.- -+...|...+|-+|.|..+|++|..- T Consensus 11 ~~aE~~lLg~ll~~~~~~~~v~~~L~~edF~~~~h~~If~~i~~l 55 (123) T 3gxv_A 11 QNIERIVLSGIVLANHKIEEVHSVLEPSDFYYPPNGLFFEIALKL 55 (123) T ss_dssp HHHHHHHHHHHHHSGGGHHHHHTTCCGGGCSSHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHH T ss_conf 999999999999697289999966899982989899999999999 No 2 >>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A (A:1-155) Probab=95.08 E-value=0.015 Score=34.78 Aligned_cols=52 Identities=25% Similarity=0.360 Sum_probs=42.9 Q ss_pred CCCEEEEEEECHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 5882898871008999888870655-599998517762114789999998552 Q gi|254781148|r 13 NNNSIYYFIGLEQEILGSLLLKGNL-QPIISFLDAQHFIDPIHSEVFRAITRK 64 (69) Q Consensus 13 nnnsiyyfigleqeilgslllkgnl-qpiisfldaqhfidpihsevfraitrk 64 (69) +++.+-|-+..|+.+||++|..... ..+.+.|.+.+|-+|.|..+|++|..- T Consensus 6 ~~~~~p~~~eaE~~lLg~ll~~~~~~~~v~~~L~~edF~~~~h~~If~ai~~l 58 (155) T 2r6a_A 6 SERIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRV 58 (155) T ss_dssp --CCCCCCHHHHHHHHHHHHHCGGGHHHHHHHCCGGGCSSHHHHHHHHHHHHH T ss_pred CCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHH T ss_conf 15899988999999999998596269999940598777998999999999999 No 3 >>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus} (A:1-152) Probab=94.94 E-value=0.034 Score=32.82 Aligned_cols=47 Identities=23% Similarity=0.420 Sum_probs=38.0 Q ss_pred EEEEECHHHHHHHHHHHCCHHH-HHHHH-HHHHHHHHHHHHHHHHHHHH Q ss_conf 9887100899988887065559-99985-17762114789999998552 Q gi|254781148|r 18 YYFIGLEQEILGSLLLKGNLQP-IISFL-DAQHFIDPIHSEVFRAITRK 64 (69) Q Consensus 18 yyfigleqeilgslllkgnlqp-iisfl-daqhfidpihsevfraitrk 64 (69) -+-+..|+.+||++++..+.-. +++.+ .+.+|-+|.|..+|++|..- T Consensus 7 p~~~~aE~~vLg~ll~~~~~~~~~~~~ll~~e~F~~~~h~~If~ai~~l 55 (152) T 2q6t_A 7 PHSLEAEQSVLGSILLDSDVMDEVEGLLPSPEAFYAEAHRKIYAAMQAL 55 (152) T ss_dssp CCCHHHHHHHHHHHHHCGGGHHHHHHHCCSGGGCSSHHHHHHHHHHHHH T ss_pred CCCHHHHHHHHHHHHCCHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHH T ss_conf 9889999999999985964899999875886534888899999999999 No 4 >>2r5u_A Replicative DNA helicase; DNAB, primase, replication, ATP-binding, autocatalytic cleavage, DNA replication, DNA-binding, endonuclease; 1.90A {Mycobacterium tuberculosis} (A:) Probab=94.25 E-value=0.024 Score=33.61 Aligned_cols=44 Identities=30% Similarity=0.523 Sum_probs=38.4 Q ss_pred EECHHHHHHHHHHHCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 7100899988887065559-9998517762114789999998552 Q gi|254781148|r 21 IGLEQEILGSLLLKGNLQP-IISFLDAQHFIDPIHSEVFRAITRK 64 (69) Q Consensus 21 igleqeilgslllkgnlqp-iisfldaqhfidpihsevfraitrk 64 (69) +-.|+.+||++|+....-+ +...|.+.+|-+|.|..+|++|..- T Consensus 31 ~~aE~~vLg~ll~~p~~~~~v~~~L~~edF~~~~h~~If~~i~~l 75 (200) T 2r5u_A 31 LAAEQSVLGGMLLSKDAIADVLERLRPGDFYRPAHQNVYDAILDL 75 (200) T ss_dssp HHHHHHHHHHHHHCHHHHHHHHTTCCTTCCSSHHHHHHHHHHHHH T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHH T ss_conf 999999999999387279999985899874739999999999999 No 5 >>1b79_A DNAB helicase; hexamer, DNA replication; 2.30A {Escherichia coli} (A:) Probab=93.60 E-value=0.087 Score=30.57 Aligned_cols=47 Identities=26% Similarity=0.364 Sum_probs=39.5 Q ss_pred EEEECHHHHHHHHHHHCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 887100899988887065559-99985177621147899999985522 Q gi|254781148|r 19 YFIGLEQEILGSLLLKGNLQP-IISFLDAQHFIDPIHSEVFRAITRKT 65 (69) Q Consensus 19 yfigleqeilgslllkgnlqp-iisfldaqhfidpihsevfraitrkt 65 (69) |-+-.|+-+||++|...+.-. ++..|...+|-+|.|..+|++|..-- T Consensus 19 ~~~~aE~~vLg~ll~~~~~~~~v~~~L~~edF~~~~h~~If~~i~~l~ 66 (119) T 1b79_A 19 HSIEAEQSVLGGLMLDNERWDDVAERVVADDFYTRPHRHIFTEMARLQ 66 (119) T ss_dssp CHHHHHHHHHHHHHHCGGGHHHHHTTCCGGGSSSHHHHHHHHHHHHHH T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHCCHHHHHHHHHHHHHH T ss_conf 988999999999994940899999765999827498999999999985 No 6 >>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1} (A:1-154) Probab=92.97 E-value=0.052 Score=31.80 Aligned_cols=49 Identities=24% Similarity=0.297 Sum_probs=40.2 Q ss_pred CEEEEEEECHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 82898871008999888870655599998517762114789999998552 Q gi|254781148|r 15 NSIYYFIGLEQEILGSLLLKGNLQPIISFLDAQHFIDPIHSEVFRAITRK 64 (69) Q Consensus 15 nsiyyfigleqeilgslllkgnlqpiisfldaqhfidpihsevfraitrk 64 (69) +..-|=+..|+.+||++|.....-.-+ +|...+|-+|.|..+|++|..- T Consensus 9 ~~~p~~~eaE~~vLg~ll~~~~~~~~i-~L~~edF~~~~h~~If~~i~~l 57 (154) T 3bgw_A 9 TVMLYNEYAEQAVLGSILTEPELIKEC-PLTPEHFSPGKHFNIYFTMQDL 57 (154) T ss_dssp -----CHHHHHHHHHHHHHSTTHHHHS-CCCGGGSCTTHHHHHHHHHHHH T ss_pred CCCCCCHHHHHHHHHHHHCCHHHHHHC-EECHHHCCCHHHHHHHHHHHHH T ss_conf 688899999999999998797456441-0087888888999999999999 No 7 >>1bm9_A RTP, TER, replication terminator protein; DNA-binding protein, contrahelicase; 2.00A {Bacillus subtilis} (A:) Probab=20.17 E-value=39 Score=16.18 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=11.9 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 114789999998552 Q gi|254781148|r 50 IDPIHSEVFRAITRK 64 (69) Q Consensus 50 idpihsevfraitrk 64 (69) ..|-||||+||...- T Consensus 50 y~P~hsEiYraLHeL 64 (122) T 1bm9_A 50 FKPNHTEVYRSLHEL 64 (122) T ss_dssp CCCCHHHHHHHHHHH T ss_pred CCCCHHHHHHHHHHH T ss_conf 899778999999999 No 8 >>1vyi_A RNA polymerase alpha subunit; transferase, replication, transcription, RNA-directed RNA polymerase, phosphorylation; HET: GOL; 1.5A {Rabies virus} (A:) Probab=18.51 E-value=54 Score=15.39 Aligned_cols=33 Identities=39% Similarity=0.520 Sum_probs=19.9 Q ss_pred CHHHHHHHCCCCCEEEEEEECHHHHHHHHHHHCCHHHHHH Q ss_conf 0256776214588289887100899988887065559999 Q gi|254781148|r 3 SDFSKKYYSRNNNSIYYFIGLEQEILGSLLLKGNLQPIIS 42 (69) Q Consensus 3 sdfskkyysrnnnsiyyfigleqeilgslllkgnlqpiis 42 (69) ..|||||--....|--+.-..|| ||-||..|+. T Consensus 22 ESfSKkYkFPSrSSGIFL~NFEQ-------LKmNLDdIVk 54 (112) T 1vyi_A 22 ESFSKKYKFPSRSSGIFLYNFEQ-------LKMNLDDIVK 54 (112) T ss_dssp HTTTCCEEEEBTTSCEEEECGGG-------GCCCHHHHHH T ss_pred HHHHHCCCCCCCCCCEEEECHHH-------HHCCHHHHHH T ss_conf 98645046887777467761898-------7456899999 No 9 >>2wzl_A Phosphoprotein; viral protein, rabies, virion, chaperone, RNA replication, nucleoprotein; 2.10A {Mokola virus} (A:) Probab=17.37 E-value=53 Score=15.45 Aligned_cols=32 Identities=41% Similarity=0.523 Sum_probs=19.7 Q ss_pred HHHHHHHCCCCCEEEEEEECHHHHHHHHHHHCCHHHHHH Q ss_conf 256776214588289887100899988887065559999 Q gi|254781148|r 4 DFSKKYYSRNNNSIYYFIGLEQEILGSLLLKGNLQPIIS 42 (69) Q Consensus 4 dfskkyysrnnnsiyyfigleqeilgslllkgnlqpiis 42 (69) -|||||---...|--+.-..|| ||-||.-|+. T Consensus 209 SFSKKYKFPSRSSGIFL~NFEQ-------LKMNLDDIVk 240 (303) T 2wzl_A 209 SFSKKYKFPSRSSGIFLWNFEQ-------LKMNLDDIVK 240 (303) T ss_dssp TTTCCEEEEBSSSSEEEECGGG-------GCCCHHHHHH T ss_pred HHCCCCCCCCCCCCEEEECHHH-------HCCCHHHHHH T ss_conf 7412567887766445544887-------5255899999 No 10 >>3ffr_A Phosphoserine aminotransferase SERC; YP_677612.1, structural genomics, joint center for structural genomics, JCSG; HET: LLP MSE P33; 1.75A {Cytophaga hutchinsonii atcc 33406} (A:14-58,A:241-265) Probab=12.55 E-value=96 Score=14.03 Aligned_cols=29 Identities=21% Similarity=0.199 Sum_probs=19.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 55999985177621147899999985522 Q gi|254781148|r 37 LQPIISFLDAQHFIDPIHSEVFRAITRKT 65 (69) Q Consensus 37 lqpiisfldaqhfidpihsevfraitrkt 65 (69) -|-+++++|.|--.-.-.|.+||.|-.-+ T Consensus 7 ~QHl~Tald~qigsISHRSk~f~diyK~t 35 (70) T 3ffr_A 7 RQHXITALDEKIGVISHRSKKFEEVYKTA 35 (70) T ss_dssp HHHHHHHHHTTTTTSCTTSHHHHHHHHHH T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHHH T ss_conf 99999987744898777788999999999 Done!