Query gi|254780937|ref|YP_003065350.1| DNA-directed RNA polymerase subunit omega [Candidatus Liberibacter asiaticus str. psy62] Match_columns 122 No_of_seqs 138 out of 474 Neff 4.1 Searched_HMMs 33803 Date Wed Jun 1 19:56:12 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780937.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 >2a6h_E RNA polymerase omega c 99.8 1.6E-21 4.6E-26 141.3 4.6 61 1-61 1-76 (77) 2 >3iyd_E DNA-directed RNA polym 99.8 1.6E-22 4.7E-27 146.8 -1.0 64 2-65 1-65 (90) 3 >3h0g_F DNA-directed RNA polym 97.3 0.00054 1.6E-08 42.5 5.5 47 14-60 75-122 (142) 4 >1twf_F ABC23, DNA-directed RN 97.2 0.00062 1.8E-08 42.1 5.5 47 14-60 85-132 (155) 5 >1qkl_A RPB6, DNA-directed RNA 97.1 0.00078 2.3E-08 41.6 4.9 47 14-60 57-104 (127) 6 >2waq_K DNA-directed RNA polym 96.7 0.0029 8.5E-08 38.4 5.3 46 15-60 2-50 (69) 7 >1i7d_A DNA topoisomerase III; 15.4 80 0.0024 13.3 2.8 57 19-75 19-80 (136) 8 >2gha_A Maltose ABC transporte 11.7 1E+02 0.0031 12.7 3.1 53 23-77 38-91 (98) 9 >3be7_A Zn-dependent arginine 11.6 1E+02 0.0031 12.7 3.3 44 16-59 23-68 (77) 10 >1h8b_A ACT-EF34, alpha-actini 11.1 1.1E+02 0.0032 12.6 1.8 38 44-81 10-57 (75) No 1 >>2a6h_E RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} (E:1-77) Probab=99.84 E-value=1.6e-21 Score=141.25 Aligned_cols=61 Identities=18% Similarity=0.322 Sum_probs=57.0 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC---------------CCCCCHHHHHHHHHCCCCCHH Q ss_conf 9600089985128789999999999999985788776774---------------468541156756540587999 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDV---------------GKDKNTVVALREIASGTLSPD 61 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~---------------~ndK~~ViALREIa~gki~~~ 61 (122) |+|.++++|++||+|||.||++||+|||||++|++|+++. +++|++++||+|||+|+|+++ T Consensus 1 M~~psid~ll~kv~srY~Lvi~aAKRArql~~g~~~~~~~~~~~~~~~~~~~~~~~~~Kpv~~Al~EIa~gkv~~~ 76 (77) T 2a6h_E 1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFG 76 (77) T ss_dssp -CCTTHHHHHHHSSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCCEEE T ss_pred CCCCCHHHHHHCCCCCEEEEHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCEEEC T ss_conf 9863577886224442244135389899998716985636965625564025567997588999999873735533 No 2 >>3iyd_E DNA-directed RNA polymerase subunit omega; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} (E:) Probab=99.83 E-value=1.6e-22 Score=146.84 Aligned_cols=64 Identities=44% Similarity=0.660 Sum_probs=59.8 Q ss_pred CEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCHHHHHHHHHCCCCCHHHHHH Q ss_conf 60008998512878999999999999998578877677-44685411567565405879999999 Q gi|254780937|r 2 ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVD-VGKDKNTVVALREIASGTLSPDDLEE 65 (122) Q Consensus 2 ARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~-~~ndK~~ViALREIa~gki~~~~l~e 65 (122) ||+||+|||++|+|||.||++||||||||+.|++|++. .+++|++++|||||++|||+++.+.+ T Consensus 1 Arptid~ll~~v~sRy~Lv~~aaKRARqL~~g~~p~v~~~~~~K~~~iAL~EIa~Gkv~~~~~~e 65 (90) T 3iyd_E 1 ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDV 65 (90) T ss_dssp CCSSSSSHHHHSSCSHHHHHHTTTTHHHHHHTCSTTCCSCTTSCCCCCBTTBCCCCCCSSCTTSC T ss_pred CCEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHCCH T ss_conf 91419999985477879999999999998749988767887896088999999908976787331 No 3 >>3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} (F:) Probab=97.27 E-value=0.00054 Score=42.47 Aligned_cols=47 Identities=17% Similarity=0.300 Sum_probs=42.6 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH Q ss_conf 7899999999999999857887767744685411-5675654058799 Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122) Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122) =.||+..-+-.-||.||+.|++++|+..+...|+ ||..|...|+|.+ T Consensus 75 lTkyE~ARilG~RAlQis~gAp~~v~~~~~tdPl~IA~~El~~~~iP~ 122 (142) T 3h0g_F 75 MTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPL 122 (142) T ss_dssp CCHHHHHHHHHHHHHHHHTCCCCCSCCCSCCCTTHHHHHHHHTTCCCC T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE T ss_conf 129899999999999997799825657888699999999998499877 No 4 >>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} (F:) Probab=97.23 E-value=0.00062 Score=42.11 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=42.7 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH Q ss_conf 7899999999999999857887767744685411-5675654058799 Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122) Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122) =.||+..-+-.-||.||+.|++++|+..+.-.|+ ||..|...|+|.+ T Consensus 85 lTkyE~aRi~g~RalQis~~ap~~v~~~~~~dpl~iA~~El~~~~ip~ 132 (155) T 1twf_F 85 MTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPL 132 (155) T ss_dssp CCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCE T ss_pred HHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE T ss_conf 319999999999999997799825657888799999999998399877 No 5 >>1qkl_A RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide; transcription; NMR {Homo sapiens} (A:) Probab=97.10 E-value=0.00078 Score=41.56 Aligned_cols=47 Identities=11% Similarity=0.244 Sum_probs=42.5 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH Q ss_conf 7899999999999999857887767744685411-5675654058799 Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122) Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122) =.||+..-+-.-||.||+.|++++|+..+.-.|+ ||..|...|+|.+ T Consensus 57 lTkyE~ARilG~RAlQis~gAp~~v~~~~~~dpl~IA~~El~~~~iP~ 104 (127) T 1qkl_A 57 MTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPI 104 (127) T ss_dssp CCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCE T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE T ss_conf 219899999999999985699844668888799999999998399877 No 6 >>2waq_K DNA-directed RNA polymerase RPO6 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_I 2pmz_K 3hkz_K (K:27-95) Probab=96.74 E-value=0.0029 Score=38.38 Aligned_cols=46 Identities=24% Similarity=0.338 Sum_probs=39.7 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCC---CCHHHHHHHHHCCCCCH Q ss_conf 89999999999999985788776774468---54115675654058799 Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKD---KNTVVALREIASGTLSP 60 (122) Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~nd---K~~ViALREIa~gki~~ 60 (122) .||+-.-+-.-||.||+.|++++|+.++. -|..||..|...|+|.+ T Consensus 2 TkyE~ARIiG~RAlQismgAp~li~~~~~~~~dPl~IA~~El~~~~iP~ 50 (69) T 2waq_K 2 TRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPI 50 (69) T ss_dssp CHHHHHHHHHHHHHHHTTTCCCTTCCCSSSCCSSSHHHHHHHHTTCSCE T ss_pred CHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHCCCCCE T ss_conf 5999999999999999779985787787788799999999998199877 No 7 >>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex, single-stranded DNA, isomerase/DNA complex; HET: DNA; 2.05A {Escherichia coli} (A:153-193,A:565-659) Probab=15.44 E-value=80 Score=13.32 Aligned_cols=57 Identities=12% Similarity=0.090 Sum_probs=33.9 Q ss_pred HHHHHHHHHHHHHCCCC-CCCCCCCC-CCHH---HHHHHHHCCCCCHHHHHHHHHHHHHHCC Q ss_conf 99999999999857887-76774468-5411---5675654058799999999999984116 Q gi|254780937|r 19 LVLLASHRTRHLSQGAK-PTVDVGKD-KNTV---VALREIASGTLSPDDLEEDFIHSLQKHV 75 (122) Q Consensus 19 LVllAa~RArql~~G~~-~~v~~~nd-K~~V---iALREIa~gki~~~~l~e~~I~~lq~~~ 75 (122) ||=+-.-|+--|..|.. ..|-|=.+ .-|- -.|.+|+.|+.+.+.+.+.+-..++..+ T Consensus 19 l~G~N~tR~~t~~~~~~~~svGRL~~p~~TA~wE~~Ld~Ia~G~~~~~~fl~~~~~~~~~~v 80 (136) T 1i7d_A 19 LYGINMTRAYTILGRNAGYQGVLATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLI 80 (136) T ss_dssp HHHHHHHHHHHHHHHTTTCCSCCHHSTHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHH T ss_pred HCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH T ss_conf 71743008999876630566664369889999999999998699989999999999999999 No 8 >>2gha_A Maltose ABC transporter, periplasmic maltose- binding protein; periplasmic binding protein, MBP, maltotriose, sugar binding protein; HET: MLR; 1.60A {Thermotoga maritima MSB8} PDB: 2ghb_A 2fnc_A* (A:155-206,A:337-382) Probab=11.73 E-value=1e+02 Score=12.70 Aligned_cols=53 Identities=11% Similarity=0.156 Sum_probs=35.3 Q ss_pred HHHHHHHH-HCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCC Q ss_conf 99999998-57887767744685411567565405879999999999998411646 Q gi|254780937|r 23 ASHRTRHL-SQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEI 77 (122) Q Consensus 23 Aa~RArql-~~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e~ 77 (122) +......+ ..|.-|+-+. =.|---||-=|+.||.+++.--+++|+..+.+++. T Consensus 38 g~~~i~~l~~~g~~pM~~V--W~p~~~Al~~i~~gk~~p~~al~~AV~~Ik~~I~~ 91 (98) T 2gha_A 38 GVKLLKRLVDEGILDMAAV--WAAMNDALNLVVNGKATVEEALKNAVERIKAQIQG 91 (98) T ss_dssp HHHHHHHHHHTTSSCGGGT--HHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHC- T ss_pred HHHHHHHHHHHCCCCHHHH--HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCC T ss_conf 9999998765026788999--99999999999859899999999999999999737 No 9 >>3be7_A Zn-dependent arginine carboxypeptidase; unknown source, amidohydrolase, sargasso SEA, structural genomics, protein structure initiative, PSI; HET: ARG; 2.30A {Unidentified} (A:60-136) Probab=11.57 E-value=1e+02 Score=12.67 Aligned_cols=44 Identities=16% Similarity=0.259 Sum_probs=30.2 Q ss_pred HHHHHHHHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHH-HHCCCCC Q ss_conf 9999999999999985-788776774468541156756-5405879 Q gi|254780937|r 16 RFLLVLLASHRTRHLS-QGAKPTVDVGKDKNTVVALRE-IASGTLS 59 (122) Q Consensus 16 rf~LVllAa~RArql~-~G~~~~v~~~ndK~~ViALRE-Ia~gki~ 59 (122) .-...+.|.+.|++.. .|-...-+....-..+++||+ |..|+|. T Consensus 23 ~~~~~~~~~~~a~~~L~~GvTTvRd~G~~~~~~~~lr~~i~~G~i~ 68 (77) T 3be7_A 23 SHMGTVWGVVNAEKTLMAGFTTVRNVGAANYADVSVRDAIERGVIN 68 (77) T ss_dssp THHHHHHHHHHHHHHHTTTEEEEEECCCSTTHHHHHHHHHHTTSSC T ss_pred HHHHHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCCCCCCC T ss_conf 4688887753012210356530102100223221211112333322 No 10 >>1h8b_A ACT-EF34, alpha-actinin 2, skeletal muscle isoform; structural protein, Z-DISK structural complex; NMR {Homo sapiens} (A:) Probab=11.12 E-value=1.1e+02 Score=12.58 Aligned_cols=38 Identities=13% Similarity=0.278 Sum_probs=23.4 Q ss_pred CCHHHHHHHHHCCC--CCHHHHHHHH--------HHHHHHCCCCCCCC Q ss_conf 54115675654058--7999999999--------99984116466578 Q gi|254780937|r 44 KNTVVALREIASGT--LSPDDLEEDF--------IHSLQKHVEIDEPD 81 (122) Q Consensus 44 K~~ViALREIa~gk--i~~~~l~e~~--------I~~lq~~~e~~E~e 81 (122) ..+.-|.|.+|+|| |+.++|+..+ |..++.+...+... T Consensus 10 Eqv~~sFr~lA~gKpYIT~~eLr~~L~peqaeyc~~~M~~y~~p~~~~ 57 (75) T 1h8b_A 10 EQVIASFRILASDKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVP 57 (75) T ss_dssp HHHHHHHHHHTTSCSSBCHHHHHHHSCHHHHHHHHHHSCSCCCSSCCT T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC T ss_conf 999888765305885105999986589178899998684556999885 Done!