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 39220 Date Mon May 30 04:32:46 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780937.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK02756 DNA-directed RNA poly 100.0 7E-45 0 273.0 11.0 122 1-122 1-127 (128) 2 PRK01481 rpoZ DNA-directed RNA 100.0 6.9E-38 1.8E-42 233.7 8.1 86 1-86 1-88 (127) 3 PRK00392 rpoZ DNA-directed RNA 100.0 6.8E-34 1.7E-38 211.2 8.2 83 1-83 1-84 (87) 4 PRK04474 DNA-directed RNA poly 100.0 1.2E-32 3.2E-37 204.1 7.7 65 1-65 1-67 (99) 5 PRK04951 rpoZ DNA-directed RNA 100.0 2.4E-31 6.2E-36 196.9 8.1 73 1-73 1-74 (91) 6 PRK02128 DNA-directed RNA poly 100.0 2.8E-31 7.2E-36 196.5 7.0 65 1-66 1-65 (67) 7 PRK00425 rpoZ DNA-directed RNA 99.9 1.5E-23 3.7E-28 153.1 4.3 66 1-66 2-67 (69) 8 PRK02544 DNA-directed RNA poly 99.9 7E-23 1.8E-27 149.2 4.5 62 1-62 1-62 (98) 9 COG1758 RpoZ DNA-directed RNA 99.8 5.8E-20 1.5E-24 132.8 5.4 72 1-72 1-74 (74) 10 PRK02950 DNA-directed RNA poly 99.7 5.7E-18 1.5E-22 121.5 3.3 62 3-64 14-87 (89) 11 pfam01192 RNA_pol_Rpb6 RNA pol 99.6 6.1E-16 1.6E-20 110.1 3.2 55 7-61 1-56 (57) 12 PRK03853 DNA-directed RNA poly 99.5 3.5E-14 8.9E-19 100.2 3.9 59 7-65 10-71 (73) 13 PRK01814 rpoZ DNA-directed RNA 99.4 4E-14 1E-18 99.9 3.1 59 4-62 4-63 (67) 14 TIGR00690 rpoZ DNA-directed RN 98.9 6.3E-10 1.6E-14 76.2 3.0 63 1-63 1-71 (73) 15 PRK01099 rpoK DNA-directed RNA 96.7 0.0023 5.8E-08 39.3 4.2 46 15-60 32-80 (106) 16 PRK03721 rpoK DNA-directed RNA 95.9 0.012 3E-07 35.2 4.2 46 15-60 5-51 (57) 17 PRK01168 rpoK DNA-directed RNA 95.9 0.011 2.9E-07 35.4 4.1 46 15-60 4-51 (61) 18 KOG3405 consensus 94.6 0.044 1.1E-06 32.1 3.7 46 15-60 67-113 (136) 19 CHL00191 ycf61 DNA-directed RN 76.3 1.7 4.4E-05 23.1 2.0 57 6-62 15-71 (74) 20 PRK02753 DNA-directed RNA poly 75.8 2 5.2E-05 22.7 2.2 57 6-62 15-71 (74) 21 TIGR02315 ABC_phnC phosphonate 41.9 11 0.00028 18.6 0.9 46 8-57 138-205 (253) 22 PRK12876 ubiA prenyltransferas 26.2 34 0.00088 15.8 1.3 45 20-64 51-96 (299) 23 PRK12895 ubiA prenyltransferas 26.1 41 0.001 15.3 1.7 49 16-64 38-87 (286) 24 pfam08289 Flu_M1_C Influenza M 24.3 53 0.0013 14.7 2.0 64 13-76 18-85 (97) No 1 >PRK02756 DNA-directed RNA polymerase subunit omega; Provisional Probab=100.00 E-value=7e-45 Score=272.99 Aligned_cols=122 Identities=60% Similarity=0.864 Sum_probs=112.3 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCC Q ss_conf 96000899851287899999999999999857887767744685411567565405879999999999998411646657 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDEP 80 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e~~E~ 80 (122) |||||||||++||+|||+||++|++|||||+.|++|+|+++|||||||||||||+|+|+++.|++++|+++|+|++++|| T Consensus 1 MARvTVEDCl~kv~NRF~LVllAs~RArql~~G~~~~v~~dnDK~tViALREIA~~~i~~~~L~e~li~slQ~~~e~de~ 80 (128) T PRK02756 1 MARVTVEDCIDKVPNRFELVLLAAHRARQISAGAPLTVDRDNDKNPVVALREIADETISPEDLKEDLIHSLQKHVEVDEP 80 (128) T ss_pred CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCC T ss_conf 97233999887178778999999999999867999764866886612016876507768999999999997347888884 Q ss_pred CHHHHHHHHH-----CCCHHHCCCCCCCHHHHHHHHHHCCCCCCCCC Q ss_conf 8566676530-----25101101011498887865531168400279 Q gi|254780937|r 81 DSPTENSDFS-----WHKPEALSFGQMSEGDLLEGINNIVTPDKRDD 122 (122) Q Consensus 81 e~~~~~~~~~-----~~~~~~~~~~~~se~e~~~~~~~~i~p~k~~d 122 (122) +++....... ........++.|++++++++++++.+|.+++| T Consensus 81 e~d~~~~~~~~~~~~~~~~~~~~~d~msEe~lLr~l~~~~~~~~~d~ 127 (128) T PRK02756 81 EPDTVPLLSSAGAAEDAEDDDVAFDRMSEEELLRGLEGLVPPEKDDD 127 (128) T ss_pred CHHHHHHHCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCCCCCCCCCC T ss_conf 15667651467777766644300100689999999873499765678 No 2 >PRK01481 rpoZ DNA-directed RNA polymerase subunit omega; Provisional Probab=100.00 E-value=6.9e-38 Score=233.74 Aligned_cols=86 Identities=37% Similarity=0.538 Sum_probs=77.8 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCC--CCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCC Q ss_conf 9600089985128789999999999999985788776--77446854115675654058799999999999984116466 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPT--VDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEID 78 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~--v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e~~ 78 (122) |||||||||++||||||+|||+|++|||||+.|+++. ++.+|||||||||||||+|+|+++.|++++|++||++.+++ T Consensus 1 MARVTVEDCl~kI~NRFeLVl~As~RARqL~~g~~~~~~~~~~nDK~tViALREIA~g~v~~e~Lke~lI~slQk~~~ie 80 (127) T PRK01481 1 MARITAEDCNKIIPDRFRLVVLATRYAKLLNYKVETNQIKKEKRDKPPVIALRRIAAGKVSVAQLEQDLINSLRTRTMIE 80 (127) T ss_pred CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEHHHHHHCCCCCHHHHHHHHHHHHHHCCCCC T ss_conf 97153999887377678999999999999854799886670006877530258877278899999999999987501147 Q ss_pred CCCHHHHH Q ss_conf 57856667 Q gi|254780937|r 79 EPDSPTEN 86 (122) Q Consensus 79 E~e~~~~~ 86 (122) ++.+..+. T Consensus 81 ~~~~~d~~ 88 (127) T PRK01481 81 PLVNQDES 88 (127) T ss_pred CCCCCHHH T ss_conf 31010023 No 3 >PRK00392 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed Probab=100.00 E-value=6.8e-34 Score=211.22 Aligned_cols=83 Identities=45% Similarity=0.637 Sum_probs=76.2 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCC Q ss_conf 9600089985128789999999999999985788-776774468541156756540587999999999999841164665 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGA-KPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQKHVEIDE 79 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~-~~~v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e~~E 79 (122) ||||||||||+||||||+||++|++|||||+.|+ +|+|+.+||||||+||||||+|+|+++.|.+..|...|+.....+ T Consensus 1 MARvTVEDCleki~NRF~LvllAs~RArql~~g~~~p~v~~~ndKptViALREIa~g~v~~~~L~e~~i~e~~~~~~~~e 80 (87) T PRK00392 1 MARVTVEDCLEHVDNRFELVMLSTKRARQLATGGKEPKVAWENDKPTVVALREIAEGLVDYEVIAQEEIVEDEPLFAAFE 80 (87) T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCC T ss_conf 98352999987079888999999999999984798875575368642045899882788999987999887775033245 Q ss_pred CCHH Q ss_conf 7856 Q gi|254780937|r 80 PDSP 83 (122) Q Consensus 80 ~e~~ 83 (122) ++.+ T Consensus 81 eE~~ 84 (87) T PRK00392 81 DESN 84 (87) T ss_pred CCCC T ss_conf 3101 No 4 >PRK04474 DNA-directed RNA polymerase subunit omega; Provisional Probab=99.97 E-value=1.2e-32 Score=204.13 Aligned_cols=65 Identities=49% Similarity=0.796 Sum_probs=61.8 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCC--CCCCCHHHHHHHHHCCCCCHHHHHH Q ss_conf 9600089985128789999999999999985788776774--4685411567565405879999999 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDV--GKDKNTVVALREIASGTLSPDDLEE 65 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~--~ndK~~ViALREIa~gki~~~~l~e 65 (122) ||||||||||+||||||+||++|++|||||+.|++|+|++ +|||||||||||||+|+|+.+.|.+ T Consensus 1 MARvTVEDCl~~i~NRF~Lvl~A~~RArql~~G~~p~v~~~~~~DKptViALREIa~g~v~~~~l~~ 67 (99) T PRK04474 1 MARITVEDCLEVVNNRFELVMMASKRARQLANGVQPLIENADASDKPTVMALREIAARRIDNALIDE 67 (99) T ss_pred CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEHHHHHHCCCCHHHHHH T ss_conf 9714399988617888899999999999986699970377544798723104887747678999989 No 5 >PRK04951 rpoZ DNA-directed RNA polymerase subunit omega; Validated Probab=99.97 E-value=2.4e-31 Score=196.86 Aligned_cols=73 Identities=42% Similarity=0.626 Sum_probs=66.7 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHH Q ss_conf 9600089985128789999999999999985-788776774468541156756540587999999999999841 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLS-QGAKPTVDVGKDKNTVVALREIASGTLSPDDLEEDFIHSLQK 73 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~-~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~~I~~lq~ 73 (122) ||||||||||+||+|||+||++|++|||||+ .|.+|+|+.+|||||||||||||+|+|+.+.|.+.-....+. T Consensus 1 MARvTVEDCl~~v~NRF~LVllAskRARql~~~g~~p~v~~~ndKptViALREIaeG~i~~~~l~~~~~~~~~e 74 (91) T PRK04951 1 MARVTVQDAVEKIGNRFDLILVAARRARQLQVGGKDPLVPEENDKPTVIALREIEEGLINNQILDARERQEQQE 74 (91) T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 98344999998478788999999999999982998884687589541345998884678999999889899999 No 6 >PRK02128 DNA-directed RNA polymerase subunit omega; Provisional Probab=99.97 E-value=2.8e-31 Score=196.49 Aligned_cols=65 Identities=51% Similarity=0.793 Sum_probs=62.6 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHH Q ss_conf 960008998512878999999999999998578877677446854115675654058799999999 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEED 66 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~ 66 (122) |||||||||+++|+|||+||++|++|||||..|++|+|+ +||||||+||||||+|+|+.+.|++. T Consensus 1 MARvTVEDCl~~i~NRF~Lvl~A~~Rarql~~G~~~~ve-~~dK~tViALREIa~g~v~~e~L~e~ 65 (67) T PRK02128 1 MARITVEDCLKQIPNRFELALAATYRARQLAQGHTPKIE-SRDKPTVVALREIAAGQVGLEMLKKV 65 (67) T ss_pred CCEEEHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCCHHHHHHHHCCCCHHHHHHC T ss_conf 982539998872798999999999999999669988656-68986221158878179799998417 No 7 >PRK00425 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed Probab=99.88 E-value=1.5e-23 Score=153.05 Aligned_cols=66 Identities=30% Similarity=0.568 Sum_probs=63.2 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHH Q ss_conf 960008998512878999999999999998578877677446854115675654058799999999 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLEED 66 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~l~e~ 66 (122) |..-||+||++||+|||.||++||+|||||..|++|+|+.+++||+++|||||++|+|+++.+++. T Consensus 2 M~~Psid~ll~kvdsrY~LV~~aAKRARqL~~g~~plv~~~~~Kpv~iALeEI~~gkvt~e~~~eG 67 (69) T PRK00425 2 MINPSIVDLLEKVDDRYSLVILTAKRARQIIAGDEKLVDIESNKPLTIAINEVDQGLVTYERPEEG 67 (69) T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCEEECCCCC T ss_conf 877879999984578424689999999998759976668878860879999998599645406555 No 8 >PRK02544 DNA-directed RNA polymerase subunit omega; Provisional Probab=99.87 E-value=7e-23 Score=149.20 Aligned_cols=62 Identities=34% Similarity=0.553 Sum_probs=60.0 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHH Q ss_conf 96000899851287899999999999999857887767744685411567565405879999 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDD 62 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~ 62 (122) |++.||++||+||+|||.||++||+|||||..|++|+++++++|++++||||||.|+|..+. T Consensus 1 Ml~PSId~Ll~KVdSrYsLVilAaKRARqL~~Ga~Pt~~~ds~K~t~~ALeEIaaG~V~idP 62 (98) T PRK02544 1 MLKPSIDTLLDKVPSKYSLVILQAKRAHELEAGATPTQEFKSVKSTLQALEEIESGNVVIHP 62 (98) T ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCEEECC T ss_conf 98677999998558701568899989999865898765445765799999999839814489 No 9 >COG1758 RpoZ DNA-directed RNA polymerase, subunit K/omega [Transcription] Probab=99.80 E-value=5.8e-20 Score=132.77 Aligned_cols=72 Identities=54% Similarity=0.770 Sum_probs=65.0 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCC--CCCHHHHHHHHHCCCCCHHHHHHHHHHHHH Q ss_conf 960008998512878999999999999998578877677446--854115675654058799999999999984 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGK--DKNTVVALREIASGTLSPDDLEEDFIHSLQ 72 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~n--dK~~ViALREIa~gki~~~~l~e~~I~~lq 72 (122) |+|+|+++|+++++|||+||++|++|||||+.|++++++.+. +|++++|||||++|+|.++.+.+....+.| T Consensus 1 m~~~~~~~l~~~~~~ryelv~~aa~RA~Ql~~ga~~~~~~~~~~~kpv~iAl~Ei~~g~i~~~i~~~~~~~~~~ 74 (74) T COG1758 1 MARPTIEDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKIPIEILRELLIHSLQ 74 (74) T ss_pred CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHCCCCC T ss_conf 98567999862035788999999999999983999765563336784899999998299782101122210239 No 10 >PRK02950 DNA-directed RNA polymerase subunit omega; Provisional Probab=99.70 E-value=5.7e-18 Score=121.53 Aligned_cols=62 Identities=31% Similarity=0.586 Sum_probs=54.2 Q ss_pred EEEHHHHHCCCCCHHHHHHHHHHHHHHHHC-----------CCCCCCCCCC-CCCHHHHHHHHHCCCCCHHHHH Q ss_conf 000899851287899999999999999857-----------8877677446-8541156756540587999999 Q gi|254780937|r 3 RTTVEDCIDKVDNRFLLVLLASHRTRHLSQ-----------GAKPTVDVGK-DKNTVVALREIASGTLSPDDLE 64 (122) Q Consensus 3 RvTvEdcl~kv~nrf~LVllAa~RArql~~-----------G~~~~v~~~n-dK~~ViALREIa~gki~~~~l~ 64 (122) --.++|||+||+|||.||++||||||||++ +..|+|+..+ +||.+||||||++|+|+.+.+. T Consensus 14 ~P~id~Ll~kvdsky~LVi~aakRARqin~Y~~qL~eGl~e~vgPlV~~~~~~KPLsIAlrEI~eg~l~~e~~e 87 (89) T PRK02950 14 NPPIDELLDRVDSKYALVIYAAKRARQINDYYNQLGEGLLEYVGPLVEPGLQEKPLSIALREINADLLTAEHTE 87 (89) T ss_pred CCCHHHHHHHCCCCEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEHHHHHHCCCCCCCCCC T ss_conf 88899999854871100468788898888888886011003478855677788861113999876886441356 No 11 >pfam01192 RNA_pol_Rpb6 RNA polymerase Rpb6. Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly. Probab=99.59 E-value=6.1e-16 Score=110.10 Aligned_cols=55 Identities=40% Similarity=0.601 Sum_probs=51.0 Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCHHHHHHHHHCCCCCHH Q ss_conf 9985128789999999999999985788776774468-541156756540587999 Q gi|254780937|r 7 EDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKD-KNTVVALREIASGTLSPD 61 (122) Q Consensus 7 Edcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~nd-K~~ViALREIa~gki~~~ 61 (122) |+|+.++.|||+||+++++|||||+.|++|+|+.+++ ||+++|||||++|+|.++ T Consensus 1 e~l~~~~~nryel~~~~a~RA~Ql~~ga~~~v~~~~~~kp~~iAl~Ei~~g~i~~~ 56 (57) T pfam01192 1 ERLTSKYLNRYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPE 56 (57) T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEECCCCCCCHHHHHHHHHHCCCCCCC T ss_conf 98677763799999999999999985998725577897889999999992899999 No 12 >PRK03853 DNA-directed RNA polymerase subunit omega; Provisional Probab=99.46 E-value=3.5e-14 Score=100.23 Aligned_cols=59 Identities=41% Similarity=0.625 Sum_probs=52.4 Q ss_pred HHHHCCCCC-HHHHHHHHHHHHHHHHCCCCCCCCCC--CCCCHHHHHHHHHCCCCCHHHHHH Q ss_conf 998512878-99999999999999857887767744--685411567565405879999999 Q gi|254780937|r 7 EDCIDKVDN-RFLLVLLASHRTRHLSQGAKPTVDVG--KDKNTVVALREIASGTLSPDDLEE 65 (122) Q Consensus 7 Edcl~kv~n-rf~LVllAa~RArql~~G~~~~v~~~--ndK~~ViALREIa~gki~~~~l~e 65 (122) ...|++|+| ||.|+++.++||+||+.|+.|+|+.+ +.|++.|||+|||+|||.++.+.+ T Consensus 10 aKALe~v~~DRY~Ls~~vakRa~qLanGA~PLv~~d~~k~K~tdIAL~EIAeGKI~le~i~e 71 (73) T PRK03853 10 AKALKNVGNDRYKLSLLVFKRAEQLANGAKPLVDMDPKKHKLADIALREIAEGKIDLERIVE 71 (73) T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEC T ss_conf 99998728608999999999999986688642246845554899999999817520134201 No 13 >PRK01814 rpoZ DNA-directed RNA polymerase subunit omega; Validated Probab=99.44 E-value=4e-14 Score=99.86 Aligned_cols=59 Identities=25% Similarity=0.350 Sum_probs=52.1 Q ss_pred EEHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCC-CCCHHHHHHHHHCCCCCHHH Q ss_conf 008998512878999999999999998578877677446-85411567565405879999 Q gi|254780937|r 4 TTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGK-DKNTVVALREIASGTLSPDD 62 (122) Q Consensus 4 vTvEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~n-dK~~ViALREIa~gki~~~~ 62 (122) -.+.+.++||+|||.||.+||||||||..|.+++++.-. .|++-+||.||++|+|+++. T Consensus 4 PSiD~Ll~kvdSkYsLV~~AaKRAreL~~~~~~~l~~~~S~K~Vg~ALEEI~ag~lt~~p 63 (67) T PRK01814 4 PSIDSLLTKIDSKYTLVTVAAKRAREMQLANNCVVEKPVSHKCVGKALEEIDAEALSYVP 63 (67) T ss_pred CCHHHHHHHCCCCEEEHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEECC T ss_conf 779999986278413313777788997618854233576667099999999849536257 No 14 >TIGR00690 rpoZ DNA-directed RNA polymerase, omega subunit; InterPro: IPR003716 Bacterial DNA-dependent RNA polymerase (RNAP) has the core composition of alpha(2)-beta-beta'-omega, where omega is the smallest of the subunits. The omega subunit is required to promote RNAP assembly by acting like a chaperone to maintain beta' in the correct conformation and to recruit it to the alpha(2)beta subassembly to form a functional core enzyme .; GO: 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=98.92 E-value=6.3e-10 Score=76.24 Aligned_cols=63 Identities=46% Similarity=0.653 Sum_probs=59.2 Q ss_pred CCEEEHHHHHCCCCCHHHHHHHHHHHHHHHH------CCCCCCCC--CCCCCCHHHHHHHHHCCCCCHHHH Q ss_conf 9600089985128789999999999999985------78877677--446854115675654058799999 Q gi|254780937|r 1 MARTTVEDCIDKVDNRFLLVLLASHRTRHLS------QGAKPTVD--VGKDKNTVVALREIASGTLSPDDL 63 (122) Q Consensus 1 MARvTvEdcl~kv~nrf~LVllAa~RArql~------~G~~~~v~--~~ndK~~ViALREIa~gki~~~~l 63 (122) |++.++++|+.++++||.|++++++|++++. .|..+.++ ..++|++++||++|++|+++.... T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~ 71 (73) T TIGR00690 1 MARPPIDDLLEKVDSRYSLVLLAAKRARQLLVYYQLGEGEDLLVPPGEESDKPLGIALREIAAGKLKVELL 71 (73) T ss_pred CCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 98752667875326401345665567777777653034410021000000013567776654111100001 No 15 >PRK01099 rpoK DNA-directed RNA polymerase subunit K; Provisional Probab=96.70 E-value=0.0023 Score=39.31 Aligned_cols=46 Identities=22% Similarity=0.460 Sum_probs=39.0 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCC--CCC-HHHHHHHHHCCCCCH Q ss_conf 8999999999999998578877677446--854-115675654058799 Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGK--DKN-TVVALREIASGTLSP 60 (122) Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~n--dK~-~ViALREIa~gki~~ 60 (122) .+|+-.-+-..||.||+.|++|+|+.++ .-. -.||..|.-.++|-+ T Consensus 32 TKYEkarIiG~RA~Qi~~GA~p~I~i~~~~~~D~~~IA~~EL~qkkIPf 80 (106) T PRK01099 32 TKYEIARIIGARALQLAMGAQPLIDIRELGSTDPVLIAEEELRRGLLDF 80 (106) T ss_pred HHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHCCCCE T ss_conf 3889999998999998679996686787888688999999998399977 No 16 >PRK03721 rpoK DNA-directed RNA polymerase subunit K; Provisional Probab=95.90 E-value=0.012 Score=35.25 Aligned_cols=46 Identities=22% Similarity=0.331 Sum_probs=39.2 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH Q ss_conf 899999999999999857887767744685411-5675654058799 Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122) Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122) +||+-.-.-.-||-||+-|++++|+....-.|+ ||..|.-.|+|-+ T Consensus 5 TryEkARIiGaRALQIsmGAPvli~~~~~~dpl~IA~~El~~~~iPi 51 (57) T PRK03721 5 TRFEKARIIGARALQIAMGAPVLIDVPEGITPLEAAILEFEKGVIPI 51 (57) T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHCCCCCE T ss_conf 27799998859999987599857718898798999999998699745 No 17 >PRK01168 rpoK DNA-directed RNA polymerase subunit K; Provisional Probab=95.90 E-value=0.011 Score=35.39 Aligned_cols=46 Identities=17% Similarity=0.309 Sum_probs=38.6 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCH-HHHHHHHHCCCCCH Q ss_conf 89999999999999985788776774468-541-15675654058799 Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKD-KNT-VVALREIASGTLSP 60 (122) Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~nd-K~~-ViALREIa~gki~~ 60 (122) .||+-.-+-.-||.||+.|++++|+..++ ..| -||..|.-.|+|-+ T Consensus 4 TryEkARIiGaRAlQIsmGAP~li~~~~~~~Dpl~IA~~El~~~~iPi 51 (61) T PRK01168 4 TKFEKARIIGARALQIAMGAPVIIDIPKNIIDPVDIAMIEFENNVIPI 51 (61) T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHCCCCCE T ss_conf 068999998599999876998378188887698999999998699877 No 18 >KOG3405 consensus Probab=94.55 E-value=0.044 Score=32.08 Aligned_cols=46 Identities=13% Similarity=0.281 Sum_probs=41.2 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHH-HHHHHHHCCCCCH Q ss_conf 899999999999999857887767744685411-5675654058799 Q gi|254780937|r 15 NRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTV-VALREIASGTLSP 60 (122) Q Consensus 15 nrf~LVllAa~RArql~~G~~~~v~~~ndK~~V-iALREIa~gki~~ 60 (122) .+|+--.+-.-||-||+-|++++|+-++.-+|. ||..|.+..||-+ T Consensus 67 TKYErArvLGtRAlQIsm~APvmVeLegETdPL~IAmkEL~qkKIP~ 113 (136) T KOG3405 67 TKYERARVLGTRALQISMNAPVMVELEGETDPLEIAMKELKQKKIPF 113 (136) T ss_pred HHHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHCCCCE T ss_conf 37778776647778875389728851787788999999986365866 No 19 >CHL00191 ycf61 DNA-directed RNA polymerase subunit omega; Provisional Probab=76.28 E-value=1.7 Score=23.07 Aligned_cols=57 Identities=14% Similarity=0.207 Sum_probs=44.4 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHH Q ss_conf 899851287899999999999999857887767744685411567565405879999 Q gi|254780937|r 6 VEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDD 62 (122) Q Consensus 6 vEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~ 62 (122) .|..+..-.|||.+++-.|+||++-..-.--.++-..=||++=|.-|..++.--++- T Consensus 15 ~E~Li~aasNRY~iTVqVAnRAKrrRyed~d~~dd~~~KPv~RAIiEMsDEl~qPei 71 (74) T CHL00191 15 SEELLNAASNRYKITVQVANRAKRRRYEDFDLLEDPSIKPIIRAILEMVDEINQPEI 71 (74) T ss_pred HHHHHHHHCCCEEEHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCC T ss_conf 999998513544643798678887410200244553433899999997220367521 No 20 >PRK02753 DNA-directed RNA polymerase subunit omega; Provisional Probab=75.81 E-value=2 Score=22.67 Aligned_cols=57 Identities=16% Similarity=0.191 Sum_probs=43.6 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHH Q ss_conf 899851287899999999999999857887767744685411567565405879999 Q gi|254780937|r 6 VEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDD 62 (122) Q Consensus 6 vEdcl~kv~nrf~LVllAa~RArql~~G~~~~v~~~ndK~~ViALREIa~gki~~~~ 62 (122) .|..+..-.|||.+++-.|+||++-..-.--.++-..-||++=|.-|..++.--++- T Consensus 15 aE~Li~aasNRY~iTVqVA~RAKrrRyed~d~~dd~~~KPv~RAIiEMsDEl~qPei 71 (74) T PRK02753 15 AESLIRASSNRYRITVQVANRAKRRRYEDFDNLEDSMMKPVQRAIIEMSDELTQPEI 71 (74) T ss_pred HHHHHHHHCCCEEEHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCC T ss_conf 999998504544634898778887411200355543433899999997120367401 No 21 >TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein; InterPro: IPR012693 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.; GO: 0005524 ATP binding, 0015416 phosphonate transmembrane-transporting ATPase activity, 0015716 phosphonate transport, 0016020 membrane. Probab=41.90 E-value=11 Score=18.58 Aligned_cols=46 Identities=26% Similarity=0.330 Sum_probs=31.5 Q ss_pred HHHCCCCCHHHHHHHHHHHHHHHHCCC--------------------CCC--CCCCCCCCHHHHHHHHHCCC Q ss_conf 985128789999999999999985788--------------------776--77446854115675654058 Q gi|254780937|r 8 DCIDKVDNRFLLVLLASHRTRHLSQGA--------------------KPT--VDVGKDKNTVVALREIASGT 57 (122) Q Consensus 8 dcl~kv~nrf~LVllAa~RArql~~G~--------------------~~~--v~~~ndK~~ViALREIa~gk 57 (122) .||+ |+.|.-+|.+||-||+.|- ||. .|+.+.+.+-=.||.|..++ T Consensus 138 ~~L~----rVGl~~~A~~RaD~LSGGQQQRVaIARAL~Q~P~lILADEPiASLDP~~s~~VMd~lk~In~e~ 205 (253) T TIGR02315 138 SLLE----RVGLADKAYQRADQLSGGQQQRVAIARALAQQPKLILADEPIASLDPKTSKQVMDYLKRINKED 205 (253) T ss_pred HHHH----HCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHC T ss_conf 8765----2387889865213215851168999986368995897048843367567899999999988776 No 22 >PRK12876 ubiA prenyltransferase; Reviewed Probab=26.21 E-value=34 Score=15.77 Aligned_cols=45 Identities=20% Similarity=0.009 Sum_probs=33.2 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCC-CCHHHHHHHHHCCCCCHHHHH Q ss_conf 999999999985788776774468-541156756540587999999 Q gi|254780937|r 20 VLLASHRTRHLSQGAKPTVDVGKD-KNTVVALREIASGTLSPDDLE 64 (122) Q Consensus 20 VllAa~RArql~~G~~~~v~~~nd-K~~ViALREIa~gki~~~~l~ 64 (122) +.+|.--||--.-+-.-.+|++=| |||=.+-|.++.|+|+..+-. T Consensus 51 ~~~a~v~aRsagm~~Nr~~Dr~iD~~npRT~~Rpl~~G~is~~~a~ 96 (299) T PRK12876 51 GGSAFFCARTVGIIVNQIIDRAIDKKNPRTSKRVLPAKLLSINFSW 96 (299) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH T ss_conf 9999999978985999862415478997778998878887998999 No 23 >PRK12895 ubiA prenyltransferase; Reviewed Probab=26.06 E-value=41 Score=15.34 Aligned_cols=49 Identities=18% Similarity=0.199 Sum_probs=37.7 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCC-CCHHHHHHHHHCCCCCHHHHH Q ss_conf 9999999999999985788776774468-541156756540587999999 Q gi|254780937|r 16 RFLLVLLASHRTRHLSQGAKPTVDVGKD-KNTVVALREIASGTLSPDDLE 64 (122) Q Consensus 16 rf~LVllAa~RArql~~G~~~~v~~~nd-K~~ViALREIa~gki~~~~l~ 64 (122) ++-++++++==+|--.-.-.-.+|+|=| ||+=.+-|.++.|+|+..+-. T Consensus 38 ~l~l~~lg~v~~Rsagc~iNdi~DrdiD~~v~RTk~RpL~sG~is~~eA~ 87 (286) T PRK12895 38 KILLILIAAVSARTSAMSINRIEGLRYDMINPRKKDWALVSGRIKMREAI 87 (286) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHH T ss_conf 99999999999989998999870604345798889997988897999999 No 24 >pfam08289 Flu_M1_C Influenza Matrix protein (M1) C-terminal domain. This region is thought to be a second domain of the M1 matrix protein. Probab=24.30 E-value=53 Score=14.72 Aligned_cols=64 Identities=11% Similarity=0.264 Sum_probs=37.7 Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCC---CCCC-CCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCC Q ss_conf 87899999999999999857887767---7446-8541156756540587999999999999841164 Q gi|254780937|r 13 VDNRFLLVLLASHRTRHLSQGAKPTV---DVGK-DKNTVVALREIASGTLSPDDLEEDFIHSLQKHVE 76 (122) Q Consensus 13 v~nrf~LVllAa~RArql~~G~~~~v---~~~n-dK~~ViALREIa~gki~~~~l~e~~I~~lq~~~e 76 (122) -.||.-|-.-.+|--.|....++--- +... -..-|-|+|-|+..--+-..|+.++++.||.|+. T Consensus 18 hE~rMVlAstTAKaMeqmagsseqaaeamevA~qarqmv~amRtiGt~p~~~~gl~ddl~EnLqayqk 85 (97) T pfam08289 18 HEMQMVLAMNTAKAMEGMAGSSEKAADAMELAEEAQQMIGALRSIGAHPKNGAGIAKDLLENLKAYQK 85 (97) T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 67789998757999998525547689999999999999999998437988741058999999999998 Done!