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 23785 Date Tue May 31 22:49:12 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780937.hhm -d /home/congqian_1/database/pdb/pdb70.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3lu0_E DNA-directed RNA polyme 100.0 1.4E-30 6.1E-35 191.3 1.7 64 1-64 1-65 (91) 2 3h0g_F DNA-directed RNA polyme 97.6 9.9E-05 4.2E-09 45.7 5.5 47 14-60 75-122 (142) 3 1twf_F ABC23, DNA-directed RNA 97.5 0.00011 4.7E-09 45.5 5.5 47 14-60 85-132 (155) 4 1qkl_A RPB6, DNA-directed RNA 97.5 0.00012 5.1E-09 45.3 4.9 47 14-60 57-104 (127) 5 2waq_K DNA-directed RNA polyme 97.1 0.00058 2.4E-08 41.4 5.3 47 14-60 27-76 (95) 6 2a6h_E RNA polymerase omega ch 96.7 0.0029 1.2E-07 37.5 6.0 60 1-60 1-75 (99) 7 2p0l_A Lipoate-protein ligase 26.9 32 0.0013 14.7 5.2 40 41-80 212-251 (288) 8 2kxh_B Peptide of FAR upstream 14.4 58 0.0024 13.3 1.5 19 11-32 4-22 (31) 9 1ekz_A DSRBDIII, maternal effe 12.2 70 0.0029 12.8 1.6 18 39-56 2-19 (76) 10 2kvu_A MKL/myocardin-like prot 9.3 89 0.0038 12.2 1.1 46 33-78 17-63 (75) No 1 >3lu0_E DNA-directed RNA polymerase subunit omega; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_E* Probab=99.96 E-value=1.4e-30 Score=191.28 Aligned_cols=64 Identities=47% Similarity=0.733 Sum_probs=60.8 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCHHHHHHHHHCCCCCHHHHH Q ss_conf 9600089985128789999999999999985788-776774468541156756540587999999 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGA-KPTVDVGKDKNTVVALREIASGTLSPDDLE 64 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~-~~~v~~~ndK~~ViALREIa~gki~~~~l~ 64 (122) ||||||||||+||+|||.||++||||||||+.|+ +|+++.+||||+|+||||||+|||+++.+. T Consensus 1 MARvtVEDcl~kv~nRy~LV~lAakRARql~~g~~~~~~~~~~~K~~viALrEIa~gki~~~~l~ 65 (91) T 3lu0_E 1 MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILD 65 (91) T ss_dssp -CCTTHHHHHHHSSSHHHHHHHHHHHHHHHHHTCCCSCCSSSCCCSSCCSHHHHHSSSCEEESSS T ss_pred CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHCC T ss_conf 97132999988547796999999999999984898886787689607899999990897677623 No 2 >3h0g_F DNA-directed RNA polymerases I, II, and III subunit rpabc2; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Probab=97.57 E-value=9.9e-05 Score=45.74 Aligned_cols=47 Identities=17% Similarity=0.300 Sum_probs=42.1 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~ariiG~Ra~Qi~~ga~~~i~~~~~~d~~~IA~~El~~~kiP~ 122 (142) T 3h0g_F 75 MTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPL 122 (142) T ss_dssp CCHHHHHHHHHHHHHHHHTCCCCCSCCCSCCCTTHHHHHHHHTTCCCC T ss_pred HHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE T ss_conf 319899999999999997799844647888699999999998499877 No 3 >1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F 1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F* 1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F 1y77_F* ... Probab=97.54 E-value=0.00011 Score=45.46 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=41.9 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~ariiG~Ra~Qis~ga~~~v~~~~~~d~~~IA~~El~~~kiP~ 132 (155) T 1twf_F 85 MTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPL 132 (155) T ss_dssp CCHHHHHHHHHHHHHHHHTTCCCSSCCSSCCSHHHHHHHHHHTTCCCE T ss_pred HHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE T ss_conf 319999999999999997799825647888799999999998499877 No 4 >1qkl_A RPB6, DNA-directed RNA polymerase II 14.4 KD polypeptide; transcription; NMR {Homo sapiens} SCOP: a.143.1.2 Probab=97.47 E-value=0.00012 Score=45.27 Aligned_cols=47 Identities=11% Similarity=0.244 Sum_probs=41.1 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~Ra~Qi~~ga~~~i~~~~~~d~~~IA~~EL~~kkiPf 104 (127) T 1qkl_A 57 MTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPI 104 (127) T ss_dssp CCHHHHHHHHHHHHHHHHHSCCSSSCSSSSCSSSHHHHHHHHHTCCCE T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCE T ss_conf 219999999999999996699944457888799999999998399877 No 5 >2waq_K DNA-directed RNA polymerase RPO6 subunit; multi-subunit, transcription; 3.35A {Sulfolobus shibatae} PDB: 2wb1_I 2pmz_K 3hkz_K Probab=97.14 E-value=0.00058 Score=41.43 Aligned_cols=47 Identities=23% Similarity=0.335 Sum_probs=39.2 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCC--CCH-HHHHHHHHCCCCCH Q ss_conf 789999999999999985788776774468--541-15675654058799 Q gi|254780937|r 14 DNRFLLVLLASHRTRHLSQGAKPTVDVGKD--KNT-VVALREIASGTLSP 60 (122) Q Consensus 14 ~nrf~LVllAa~RArql~~G~~~~v~~~nd--K~~-ViALREIa~gki~~ 60 (122) =++|+..-+-+-||.||+.|++|+|+..+. -++ .||.+|.-.|++-+ T Consensus 27 LTKYE~aRIIG~Ra~QLs~GA~p~I~~~~~~~~d~~~IA~~EL~~~kiPf 76 (95) T 2waq_K 27 LTRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPI 76 (95) T ss_dssp CCHHHHHHHHHHHHHHHTTTCCCTTCCCSSSCCSSSHHHHHHHHTTCSCE T ss_pred CCHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHCCCCCE T ss_conf 06989999998999999779985786788788799999999998399887 No 6 >2a6h_E RNA polymerase omega chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.143.1.1 PDB: 1smy_E* 1zyr_E* 1iw7_E* 2a69_E* 2a6e_E 2a68_E* 2be5_E* 2cw0_E 3dxj_E* 2o5i_E 2o5j_E* 2ppb_E* 3eql_E* 1ynj_K* 1i6v_E* 1l9u_E 1l9z_E 1hqm_E* 1ynn_K* Probab=96.72 E-value=0.0029 Score=37.49 Aligned_cols=60 Identities=27% Similarity=0.464 Sum_probs=45.0 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHH-HHCCCCCC-CCCC------------CCCCHH-HHHHHHHCCCCCH Q ss_conf 96000899851287899999999999999-85788776-7744------------685411-5675654058799 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRH-LSQGAKPT-VDVG------------KDKNTV-VALREIASGTLSP 60 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArq-l~~G~~~~-v~~~------------ndK~~V-iALREIa~gki~~ 60 (122) ||---+.-.+.-.+|||.|.++.++||-| |.+|.+-+ ++.+ .|-|+| +|.+|..-|++.. T Consensus 1 MAe~g~DtLl~ltDSkYrLsvvvakRA~QlLr~g~~ntvL~p~e~p~~~tleg~~~dpN~vt~AMkEL~tGrL~~ 75 (99) T 2a6h_E 1 MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAETWAMKELLTGRLVF 75 (99) T ss_dssp -CCTTHHHHHHHSSSHHHHHHHHHHHHHHHHHTCTTCCSCCSSSCCCCSSSSGGGTSSCSHHHHHHHHTTTCCEE T ss_pred CCCCCHHHHHHHCCCCEEEEHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCEEE T ss_conf 986247788740444235522538989999871798564796662456402455789747899999987274553 No 7 >2p0l_A Lipoate-protein ligase A; PFAM, lopoate-protein ligase A, structural genomics, protein structure initiative, PSI-2; 2.04A {Streptococcus agalactiae COH1} SCOP: d.104.1.3 Probab=26.89 E-value=32 Score=14.74 Aligned_cols=40 Identities=15% Similarity=0.209 Sum_probs=31.9 Q ss_pred CCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCC Q ss_conf 4685411567565405879999999999998411646657 Q gi|254780937|r 41 GKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDEP 80 (122) Q Consensus 41 ~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e~~E~ 80 (122) +.+...|..|+++....++.+.+.+.++..+++.-...++ T Consensus 212 ~~~~~~vtsL~~~lg~~~t~eev~~~l~~~~~~~~~~~~~ 251 (288) T 2p0l_A 212 NVDPEIMANLSDLLDCPMTVEDVIDRMLISLKQVGFNDRL 251 (288) T ss_dssp CCCTTSBCCHHHHTTCCCCHHHHHHHHHHHHHHHTCCEEE T ss_pred CCCHHHEEEHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCC T ss_conf 7552002459997299999999999999999986576642 No 8 >2kxh_B Peptide of FAR upstream element-binding protein 1; RRM, FIR, FBP, protein-protein complex, protein binding; NMR {Homo sapiens} Probab=14.36 E-value=58 Score=13.27 Aligned_cols=19 Identities=26% Similarity=0.396 Sum_probs=12.5 Q ss_pred CCCCCHHHHHHHHHHHHHHHHC Q ss_conf 1287899999999999999857 Q gi|254780937|r 11 DKVDNRFLLVLLASHRTRHLSQ 32 (122) Q Consensus 11 ~kv~nrf~LVllAa~RArql~~ 32 (122) ..|+..|. -|-+|||||.. T Consensus 4 gyvndafk---dalqrarqiaa 22 (31) T 2kxh_B 4 GYVNDAFK---DALQRARQIAA 22 (31) T ss_dssp SSCSSHHH---HHHHHHHHHHH T ss_pred HHHHHHHH---HHHHHHHHHHH T ss_conf 03558999---99999999999 No 9 >1ekz_A DSRBDIII, maternal effect protein (staufen); structure, protein/RNA, protein DSRBD, RNA hairpin; NMR {Drosophila melanogaster} SCOP: d.50.1.1 PDB: 1stu_A Probab=12.22 E-value=70 Score=12.79 Aligned_cols=18 Identities=28% Similarity=0.447 Sum_probs=13.2 Q ss_pred CCCCCCCHHHHHHHHHCC Q ss_conf 744685411567565405 Q gi|254780937|r 39 DVGKDKNTVVALREIASG 56 (122) Q Consensus 39 ~~~ndK~~ViALREIa~g 56 (122) +..+.|+||..|.|++-. T Consensus 2 ~~~~~k~pvs~L~E~~qk 19 (76) T 1ekz_A 2 DEGDKKSPISQVHEIGIK 19 (76) T ss_dssp CCCCCSCHHHHHHHHHHH T ss_pred CCCCCCCHHHHHHHHHHH T ss_conf 877788977999999996 No 10 >2kvu_A MKL/myocardin-like protein 1; SAP motif, DNA/RNA binding, structural genomics, northeast structural genomics consortium (NESG), PSI-2; NMR {Homo sapiens} PDB: 2kw9_A Probab=9.32 E-value=89 Score=12.20 Aligned_cols=46 Identities=15% Similarity=0.191 Sum_probs=31.7 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHC-CCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 88776774468541156756540-58799999999999984116466 Q gi|254780937|r 33 GAKPTVDVGKDKNTVVALREIAS-GTLSPDDLEEDFIHSLQKHVEID 78 (122) Q Consensus 33 G~~~~v~~~ndK~~ViALREIa~-gki~~~~l~e~~I~~lq~~~e~~ 78 (122) |.+...+.+=.|=+|..||++-. -.+.+...+..||.+|+.+.+.. T Consensus 17 ~~p~~~p~~l~~mtV~eLK~~lk~rgL~vsG~KaeLI~RL~~~~~~~ 63 (75) T 2kvu_A 17 GKPGALPANLDDMKVAELKQELKLRSLPVSGTKTELIERLRAYQDQI 63 (75) T ss_dssp SSCSSCCTTTTTSCHHHHHHHHHHTTCCCCSCHHHHHHHHHHHHHTT T ss_pred CCCCCCHHHHHHCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCC T ss_conf 99986735498894999999999869898878899999999999741 Done!