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!