Query         gi|254781080|ref|YP_003065493.1| hypothetical protein CLIBASIA_04910 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 85
No_of_seqs    100 out of 205
Neff          3.6 
Searched_HMMs 39220
Date          Mon May 30 04:07:07 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781080.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK13694 hypothetical protein; 100.0 2.7E-33 6.8E-38  234.0  11.1   81    2-82      4-84  (84)
  2 pfam10073 DUF2312 Uncharacteri 100.0 1.2E-31 3.1E-36  223.4  10.7   74    8-81      1-74  (74)
  3 COG3750 Uncharacterized protei 100.0 1.5E-30 3.8E-35  216.5  10.5   82    1-82      4-85  (85)
  4 pfam07862 Nif11 Nitrogen fixat  81.8     2.5 6.4E-05   24.0   4.2   42    8-49      1-44  (49)
  5 pfam00038 Filament Intermediat  66.9      13 0.00033   19.4   6.0   51   10-60     10-62  (312)
  6 PRK02249 DNA primase large sub  62.3      16  0.0004   18.9   6.3   57   29-85    195-259 (333)
  7 pfam11126 Phage_DsbA Transcrip  62.2      16 0.00041   18.9   7.2   54   19-78     11-66  (69)
  8 pfam02787 CPSase_L_D3 Carbamoy  59.7      16 0.00041   18.9   4.1   59   15-83     38-99  (122)
  9 pfam07889 DUF1664 Protein of u  58.0      19 0.00048   18.4   5.8   52    6-57     59-114 (126)
 10 COG0178 UvrA Excinuclease ATPa  44.4      13 0.00033   19.5   1.6   21   29-49    699-722 (935)
 11 COG3040 Blc Bacterial lipocali  40.5      15 0.00038   19.1   1.4   21   31-51    146-166 (174)
 12 PRK10098 hypothetical protein;  39.9      36 0.00092   16.6   4.1   56    2-57      1-56  (350)
 13 PHA02244 ATPase-like protein    35.8      42  0.0011   16.2   3.9   42   15-56      5-46  (383)
 14 COG1392 Phosphate transport re  29.0      54  0.0014   15.5   5.7   48   10-57    146-195 (217)
 15 PRK00349 uvrA excinuclease ABC  26.2      38 0.00097   16.5   1.6   19   30-48    708-729 (944)
 16 pfam11572 DUF3234 Protein of u  25.7      44  0.0011   16.1   1.8   18   66-83     55-72  (102)
 17 pfam10910 DUF2744 Protein of u  25.3      63  0.0016   15.1   2.6   21   64-85    103-123 (125)
 18 TIGR02760 TraI_TIGR conjugativ  24.6      65  0.0017   15.0   2.9   49    5-53    261-333 (2193)
 19 COG0373 HemA Glutamyl-tRNA red  23.9      67  0.0017   14.9   4.1   28   29-56    112-139 (414)
 20 pfam05201 GlutR_N Glutamyl-tRN  22.4      71  0.0018   14.7   4.3   29   28-56    108-136 (150)
 21 COG4472 Uncharacterized protei  21.8      74  0.0019   14.7   5.2   52   25-80     15-85  (88)
 22 TIGR00630 uvra excinuclease AB  21.7      35  0.0009   16.7   0.7   19   30-48    738-759 (956)
 23 COG5113 UFD2 Ubiquitin fusion   21.5      66  0.0017   14.9   2.1   30   10-39    824-853 (929)
 24 cd04787 HTH_HMRTR_unk Helix-Tu  21.0      76  0.0019   14.6   4.1   34   39-72     51-84  (133)
 25 pfam09840 DUF2067 Uncharacteri  20.9      77   0.002   14.5   5.2   43   25-68    116-162 (190)
 26 PRK07093 para-aminobenzoate sy  20.2      79   0.002   14.4   2.8   25   60-84    165-189 (322)

No 1  
>PRK13694 hypothetical protein; Provisional
Probab=100.00  E-value=2.7e-33  Score=234.04  Aligned_cols=81  Identities=54%  Similarity=0.931  Sum_probs=78.8

Q ss_pred             CCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             41243100899999999999999999999999999999987589879999999999618999999999999999998598
Q gi|254781080|r    2 IDNIQNVTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALGM   81 (85)
Q Consensus         2 ~~~~~~va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALGm   81 (85)
                      .+++++|++++||||||||||||+||++|++|||+|||||||+|||||+||+||++||+|+++|+|+|+||++|++||||
T Consensus         4 ~~~~~~va~~~Lr~fIERIErLeeEkk~i~~dikeVyaEAK~~GfD~K~mR~Iv~lRk~d~~er~E~ealLdlY~~ALGm   83 (84)
T PRK13694          4 DDDAEVVAKEQLRAYIERIERLEEEKKTISDDIKDVYAEAKGNGFDVKAMRTIIRLRKKDDDERAEQEAILELYMDALGM   83 (84)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             56302545999999999999999999989998999999988678868999999999838886898899999999998477


Q ss_pred             C
Q ss_conf             8
Q gi|254781080|r   82 L   82 (85)
Q Consensus        82 ~   82 (85)
                      +
T Consensus        84 ~   84 (84)
T PRK13694         84 I   84 (84)
T ss_pred             C
T ss_conf             9


No 2  
>pfam10073 DUF2312 Uncharacterized protein conserved in bacteria (DUF2312). Members of this family of hypothetical bacterial proteins have no known function.
Probab=99.97  E-value=1.2e-31  Score=223.43  Aligned_cols=74  Identities=58%  Similarity=0.932  Sum_probs=73.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             00899999999999999999999999999999987589879999999999618999999999999999998598
Q gi|254781080|r    8 VTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALGM   81 (85)
Q Consensus         8 va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALGm   81 (85)
                      |++++||||||||||||+||++|++|||||||||||+|||||+||+||++||+|+++|+|+|+||++|++||||
T Consensus         1 va~~~Lr~fIERIErLeeEkk~i~~dikeVyaEAK~~GfD~K~mR~ii~lRk~d~~er~E~e~ll~~Y~~ALGm   74 (74)
T pfam10073         1 VAADQLRQFIERIERLEEEKKDIADDIKDVYAEAKGNGFDTKALRQIIKLRKMDKDERAEQEAILELYKAALGM   74 (74)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             93888999999999899999979998999999987578869999999999818887898799999999987187


No 3  
>COG3750 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.97  E-value=1.5e-30  Score=216.50  Aligned_cols=82  Identities=55%  Similarity=0.895  Sum_probs=79.7

Q ss_pred             CCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94124310089999999999999999999999999999998758987999999999961899999999999999999859
Q gi|254781080|r    1 MIDNIQNVTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALG   80 (85)
Q Consensus         1 ~~~~~~~va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALG   80 (85)
                      .|+++.+++++|||+|||||||||+||++|++||||||+||||+|||+|++|+||++||+|.++|+|++++|++|+.|||
T Consensus         4 ~t~~s~tva~~QLrafIerIERlEeEk~~i~~dikdvy~eakg~GFDvKa~r~iirlrK~D~~er~EedAildlY~~aLg   83 (85)
T COG3750           4 ITSTSQTVAAGQLRAFIERIERLEEEKKTIADDIKDVYAEAKGHGFDVKAVRTIIRLRKLDKAERQEEDAILDLYMDALG   83 (85)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             35789999999999999999999999999988899999997637861999999999996038888888899999999854


Q ss_pred             CC
Q ss_conf             88
Q gi|254781080|r   81 ML   82 (85)
Q Consensus        81 m~   82 (85)
                      |.
T Consensus        84 ~~   85 (85)
T COG3750          84 MI   85 (85)
T ss_pred             CC
T ss_conf             79


No 4  
>pfam07862 Nif11 Nitrogen fixation protein of unknown function. This domain is found in the Cyanobacteria, and may be involved in nitrogen fixation, but no role has been assigned.
Probab=81.80  E-value=2.5  Score=24.01  Aligned_cols=42  Identities=21%  Similarity=0.504  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHCCCCHH
Q ss_conf             0089999999999999999999999--99999999875898799
Q gi|254781080|r    8 VTQDQLRTFIERLERLEEEKKLLTE--NIKDIYGEAKATGFDVK   49 (85)
Q Consensus         8 va~~~Lr~~IERIErLeeEkk~i~~--dikdVyaEAK~~GfD~K   49 (85)
                      .+.++|+.|++++..=..=...+..  +.-+|-+=|+..||+.-
T Consensus         1 MS~e~l~~Fl~~~~~d~~l~~~l~~~~~~~~vi~lA~~~Gf~~t   44 (49)
T pfam07862         1 MSEEQLKAFLEKVKSDPSLREQLKACSDAEEVVALAKEAGFEFT   44 (49)
T ss_pred             CCHHHHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHCCCCCC
T ss_conf             98999999999985399999999875999999999999599867


No 5  
>pfam00038 Filament Intermediate filament protein.
Probab=66.86  E-value=13  Score=19.43  Aligned_cols=51  Identities=25%  Similarity=0.460  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH--HHHHHHHHC
Q ss_conf             899999999999999999999999999999987589879999--999999618
Q gi|254781080|r   10 QDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAI--KKILSLRKK   60 (85)
Q Consensus        10 ~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~l--r~IiklRk~   60 (85)
                      .++|-+||+++-.||.+-+.+..+|.....-....+-+++.+  ..+-.+|+.
T Consensus        10 N~Rla~YiekVr~LE~~N~~Le~~i~~~~~~~~~~~~~~~~~ye~el~~lr~~   62 (312)
T pfam00038        10 NDRLASYIDKVRFLEQQNKELEAKIEELRQKKSAEPSRLYSLYEQEIRELRKQ   62 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             99999999999999998999999999997076999998288899999999999


No 6  
>PRK02249 DNA primase large subunit; Validated
Probab=62.34  E-value=16  Score=18.90  Aligned_cols=57  Identities=26%  Similarity=0.307  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHHHHH--------CCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             999999999999875--------898799999999996189999999999999999985988679
Q gi|254781080|r   29 LLTENIKDIYGEAKA--------TGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALGMLKDE   85 (85)
Q Consensus        29 ~i~~dikdVyaEAK~--------~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALGm~~~~   85 (85)
                      ...+.|++.|++-..        .|-.|--|+.+|.--+.+.+---..--.|.+|+..+||..|+
T Consensus       195 ~~~~~i~~~~~~~~~~~~~~~~~~~~~PPCmk~~i~~l~~G~Nl~H~~Rf~Lasfl~~iG~~~d~  259 (333)
T PRK02249        195 PLLEEIREEYEKRKLETEFGEVTPGAFPPCMKALLSALQAGENLPHTARFAITSFLHNIGMDVDE  259 (333)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHH
T ss_conf             99999999999743103234226778980799999998669987717899999999976998899


No 7  
>pfam11126 Phage_DsbA Transcriptional regulator DsbA. DsbA is a double stranded binding protein found in bacteriophage T4 which is involved in transcriptional regulation. DsbA, along with other viral proteins, interacts with the host RNA polymerase core enzyme enabling initiation of transcription. DsbA acts as an enhancer protein of late genes in vitro. The protein consists of mainly alpha helices.
Probab=62.17  E-value=16  Score=18.88  Aligned_cols=54  Identities=22%  Similarity=0.343  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCC-HH-HHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999875898799999999996189-99-999999999999998
Q gi|254781080|r   19 RLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSLRKKD-EK-QWMEEEQILDVYLRA   78 (85)
Q Consensus        19 RIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~IiklRk~d-~~-er~E~e~iLd~Y~~A   78 (85)
                      +||...+-.|+|.+..|+=      -|.|+|...+.+++--++ .. .-+|.+-+.++|-..
T Consensus        11 ~ies~~e~iKdI~~~AK~E------~GvdgK~fnkl~klYHkq~R~~feae~~ev~elYd~i   66 (69)
T pfam11126        11 QIESYGELIKEIKNRAKEE------LGVDGKMFNKLFKLYHKQEREQFEAENDEVVELYDQI   66 (69)
T ss_pred             HHHHHHHHHHHHHHHHHHH------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9998998999999999998------3878899999999998865899998788899999998


No 8  
>pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.
Probab=59.74  E-value=16  Score=18.87  Aligned_cols=59  Identities=27%  Similarity=0.376  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999999999999999---9999999998758987999999999961899999999999999999859886
Q gi|254781080|r   15 TFIERLERLEEEKKLLT---ENIKDIYGEAKATGFDVKAIKKILSLRKKDEKQWMEEEQILDVYLRALGMLK   83 (85)
Q Consensus        15 ~~IERIErLeeEkk~i~---~dikdVyaEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iLd~Y~~ALGm~~   83 (85)
                      =|+++|+++-+--+.|.   .--++.+-+||..||--+-+-++.   ..+..+       .--++..+|+.|
T Consensus        38 wFL~~i~~Iv~~e~~l~~~~~~~~~~l~~aK~~GFSD~~IA~l~---~~~e~~-------Ir~~R~~~~i~P   99 (122)
T pfam02787        38 WFLEKIKEIVELEKELKKGDPLSDDLLLKAKKLGFSDAQIAKLL---GVTEEE-------VRKLRKELGIRP   99 (122)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHH---CCCHHH-------HHHHHHHCCCCC
T ss_conf             99999999999999998548999999999999499989999883---986999-------999999879912


No 9  
>pfam07889 DUF1664 Protein of unknown function (DUF1664). The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=57.98  E-value=19  Score=18.42  Aligned_cols=52  Identities=25%  Similarity=0.351  Sum_probs=39.4

Q ss_pred             HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCHHHHHHHHHH
Q ss_conf             31008999999999999999999999999999999875----89879999999999
Q gi|254781080|r    6 QNVTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKA----TGFDVKAIKKILSL   57 (85)
Q Consensus         6 ~~va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~----~GfD~K~lr~Iikl   57 (85)
                      -..+.-+|-+.|+++-.=-+|-++|+..+++=-.|+++    -|||++.++++|.-
T Consensus        59 l~~tKrhLsqRI~~vd~kld~~~eis~~i~~eV~e~~~~~~~i~~D~~~v~~~v~~  114 (126)
T pfam07889        59 IAATKKHLSQRIDNLDDKLDEQKEISESTRDEVTEIREDLSNIGEDVKSVQQAVEG  114 (126)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999998873532199999999999999999996499887699999999998


No 10 
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=44.38  E-value=13  Score=19.45  Aligned_cols=21  Identities=29%  Similarity=0.613  Sum_probs=16.5

Q ss_pred             HHHHHHHHHHH---HHHHCCCCHH
Q ss_conf             99999999999---9875898799
Q gi|254781080|r   29 LLTENIKDIYG---EAKATGFDVK   49 (85)
Q Consensus        29 ~i~~dikdVya---EAK~~GfD~K   49 (85)
                      .+.++|++.||   |||.+||.+-
T Consensus       699 g~Fd~IR~lFA~tpeAK~rGyk~g  722 (935)
T COG0178         699 GVFDDIRELFAGTPEAKARGYKPG  722 (935)
T ss_pred             CCHHHHHHHHHHCHHHHHCCCCCC
T ss_conf             243789999820939897399865


No 11 
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=40.48  E-value=15  Score=19.07  Aligned_cols=21  Identities=38%  Similarity=0.600  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHCCCCHHHH
Q ss_conf             999999999987589879999
Q gi|254781080|r   31 TENIKDIYGEAKATGFDVKAI   51 (85)
Q Consensus        31 ~~dikdVyaEAK~~GfD~K~l   51 (85)
                      .+..+...++||..|||+..+
T Consensus       146 ~~~~~~ml~~ak~~Gfdv~~l  166 (174)
T COG3040         146 QETLKRMLEIAKRRGFDVSKL  166 (174)
T ss_pred             HHHHHHHHHHHHHCCCCCCEE
T ss_conf             899999999999718774236


No 12 
>PRK10098 hypothetical protein; Provisional
Probab=39.90  E-value=36  Score=16.62  Aligned_cols=56  Identities=18%  Similarity=0.257  Sum_probs=42.3

Q ss_pred             CCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             41243100899999999999999999999999999999987589879999999999
Q gi|254781080|r    2 IDNIQNVTQDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILSL   57 (85)
Q Consensus         2 ~~~~~~va~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~Iikl   57 (85)
                      |++...++.++|++|+.++=.---=-..-+..+-|+.-+|--+|.+..=+..+...
T Consensus         1 m~~~~ri~~~~l~~~~~~~~~~~G~~~~~A~~vA~~Lv~adl~G~~SHGv~rl~~Y   56 (350)
T PRK10098          1 MESGHRIDAQTLHSFVQALWRQAGSEEREAKLVADHLVAANLAGHDSHGVGMIPSY   56 (350)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
T ss_conf             98767438999999999999985999999999999999998288604439899999


No 13 
>PHA02244 ATPase-like protein
Probab=35.84  E-value=42  Score=16.22  Aligned_cols=42  Identities=31%  Similarity=0.415  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             999999999999999999999999998758987999999999
Q gi|254781080|r   15 TFIERLERLEEEKKLLTENIKDIYGEAKATGFDVKAIKKILS   56 (85)
Q Consensus        15 ~~IERIErLeeEkk~i~~dikdVyaEAK~~GfD~K~lr~Iik   56 (85)
                      .-||+.|||-|..-.-.-|..|-..|-.|+-|.-.++-.|+.
T Consensus         5 dsie~lerlveqqmettkdladklgeknsnpyeqaiid~i~~   46 (383)
T PHA02244          5 DSIEGLERLVEQQMETTKDLADKLGEKNSNPYEQAIIDAIRE   46 (383)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf             578999999999888889999984334699278999999998


No 14 
>COG1392 Phosphate transport regulator (distant homolog of PhoU) [Inorganic ion transport and metabolism]
Probab=29.04  E-value=54  Score=15.51  Aligned_cols=48  Identities=23%  Similarity=0.265  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHHHH
Q ss_conf             899999999999999999999999999999987589--879999999999
Q gi|254781080|r   10 QDQLRTFIERLERLEEEKKLLTENIKDIYGEAKATG--FDVKAIKKILSL   57 (85)
Q Consensus        10 ~~~Lr~~IERIErLeeEkk~i~~dikdVyaEAK~~G--fD~K~lr~Iikl   57 (85)
                      ..++..++..|+++|.+-..+....-...-......  .+.-.+++|+..
T Consensus       146 ~~~~~~i~~eI~~~E~e~D~i~~~l~k~Lf~~e~~~~~~~~~~~~~i~~~  195 (217)
T COG1392         146 ADRLLEIIKEIEALEHECDDIQRELLKKLFSLETEINPIDVIILKEIIEK  195 (217)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             78899999999998887149999999999723245125899999999999


No 15 
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=26.18  E-value=38  Score=16.48  Aligned_cols=19  Identities=32%  Similarity=0.719  Sum_probs=9.2

Q ss_pred             HHHHHHHHHH---HHHHCCCCH
Q ss_conf             9999999999---987589879
Q gi|254781080|r   30 LTENIKDIYG---EAKATGFDV   48 (85)
Q Consensus        30 i~~dikdVya---EAK~~GfD~   48 (85)
                      +.++|+..||   +||.+||.+
T Consensus       708 ~~d~IR~lFA~~~~ak~rg~~~  729 (944)
T PRK00349        708 VFDPIRELFAGTPEAKARGYKP  729 (944)
T ss_pred             CHHHHHHHHHCCHHHHHHCCCC
T ss_conf             5799999984194879709997


No 16 
>pfam11572 DUF3234 Protein of unknown function (DUF3234). This bacterial family of proteins has no known function. Some members in this family of proteins are annotated as TTHA0547 however this cannot be confirmed.
Probab=25.75  E-value=44  Score=16.08  Aligned_cols=18  Identities=44%  Similarity=0.868  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHHCCCC
Q ss_conf             999999999999859886
Q gi|254781080|r   66 MEEEQILDVYLRALGMLK   83 (85)
Q Consensus        66 ~E~e~iLd~Y~~ALGm~~   83 (85)
                      .|--++-+.|+.||||+.
T Consensus        55 LE~~ALKEafL~ALG~L~   72 (102)
T pfam11572        55 LESRALKEAFLRALGMLQ   72 (102)
T ss_pred             HHHHHHHHHHHHHHHHCC
T ss_conf             457888999999975404


No 17 
>pfam10910 DUF2744 Protein of unknown function (DUF2744). This is a viral family of proteins with unknown function.
Probab=25.28  E-value=63  Score=15.08  Aligned_cols=21  Identities=33%  Similarity=0.550  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             9999999999999985988679
Q gi|254781080|r   64 QWMEEEQILDVYLRALGMLKDE   85 (85)
Q Consensus        64 er~E~e~iLd~Y~~ALGm~~~~   85 (85)
                      ..+|++++|+.|+ .||+++++
T Consensus       103 t~qe~~a~l~q~r-~lg~i~d~  123 (125)
T pfam10910       103 TQQEQRAQLEQYR-ELGLIPDE  123 (125)
T ss_pred             CCHHHHHHHHHHH-HHCCCCCC
T ss_conf             3698999999999-83766778


No 18 
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI; InterPro: IPR014129   This entry represents TraI, which is a component of the relaxosome complex. In the process of conjugative plasmid transfer the relaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein ..
Probab=24.58  E-value=65  Score=15.00  Aligned_cols=49  Identities=27%  Similarity=0.398  Sum_probs=30.8

Q ss_pred             HHHCCHHHHHHHHHHHHHHHHHHHH------------------------HHHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             4310089999999999999999999------------------------999999999998758987999999
Q gi|254781080|r    5 IQNVTQDQLRTFIERLERLEEEKKL------------------------LTENIKDIYGEAKATGFDVKAIKK   53 (85)
Q Consensus         5 ~~~va~~~Lr~~IERIErLeeEkk~------------------------i~~dikdVyaEAK~~GfD~K~lr~   53 (85)
                      +.||+-.-|.+|=.|=+.+++.-..                        -..-..+...++|+.|||+..+.+
T Consensus       261 I~GvPe~~~~afS~R~~qI~~~~~E~G~~sakard~AAl~TR~~K~~~d~~~l~~~W~~~~K~~GFD~~~~v~  333 (2193)
T TIGR02760       261 IEGVPEEVLTAFSKRRQQIDEAVKEKGTSSAKARDVAALDTRKSKTYIDDETLMEKWQQEIKDLGFDISALVA  333 (2193)
T ss_pred             CCCCCHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             4778745776530178999997310376118899998863276875058789989999998644888899999


No 19 
>COG0373 HemA Glutamyl-tRNA reductase [Coenzyme metabolism]
Probab=23.93  E-value=67  Score=14.92  Aligned_cols=28  Identities=21%  Similarity=0.425  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             9999999999998758987999999999
Q gi|254781080|r   29 LLTENIKDIYGEAKATGFDVKAIKKILS   56 (85)
Q Consensus        29 ~i~~dikdVyaEAK~~GfD~K~lr~Iik   56 (85)
                      .|..++|+-|+.|+.+|+-.+.+..+..
T Consensus       112 QILGQVK~Ay~~a~~~g~~g~~L~~lFq  139 (414)
T COG0373         112 QILGQVKDAYAKAQENGTLGKVLNRLFQ  139 (414)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             9999999999999981985289999999


No 20 
>pfam05201 GlutR_N Glutamyl-tRNAGlu reductase, N-terminal domain.
Probab=22.41  E-value=71  Score=14.74  Aligned_cols=29  Identities=17%  Similarity=0.337  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             99999999999998758987999999999
Q gi|254781080|r   28 KLLTENIKDIYGEAKATGFDVKAIKKILS   56 (85)
Q Consensus        28 k~i~~dikdVyaEAK~~GfD~K~lr~Iik   56 (85)
                      ..|..++|+-|..|+..|+-.+.|..++.
T Consensus       108 ~qIlgQvK~A~~~a~~~g~~g~~L~~lf~  136 (150)
T pfam05201       108 PQILGQVKEAYELAREAGTVGKILNRLFQ  136 (150)
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             89999999999999982984489999999


No 21 
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.77  E-value=74  Score=14.65  Aligned_cols=52  Identities=27%  Similarity=0.624  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH-------------------HHHHCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999999875898799999999-------------------9961899999999999999999859
Q gi|254781080|r   25 EEKKLLTENIKDIYGEAKATGFDVKAIKKIL-------------------SLRKKDEKQWMEEEQILDVYLRALG   80 (85)
Q Consensus        25 eEkk~i~~dikdVyaEAK~~GfD~K~lr~Ii-------------------klRk~d~~er~E~e~iLd~Y~~ALG   80 (85)
                      ..++++.+-..+||.--+..||.|  +.|||                   .+||.+.++.-|  .++-.|+.--|
T Consensus        15 ~~~~~v~e~L~~VY~sL~ekGYNp--iNQiVGYllSGDPaYIpr~ndARn~IRk~eRDeIvE--Elvk~YLk~~~   85 (88)
T COG4472          15 SDKKDVKETLNDVYNSLEEKGYNP--INQIVGYLLSGDPAYIPRYNDARNQIRKLERDEIVE--ELVKYYLKGNG   85 (88)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCH--HHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHH--HHHHHHHHHCC
T ss_conf             708899999999999998727872--877884401489644676210899999874889999--99999985157


No 22 
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602   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).  During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=21.65  E-value=35  Score=16.70  Aligned_cols=19  Identities=32%  Similarity=0.751  Sum_probs=11.8

Q ss_pred             HHHHHHHHHH---HHHHCCCCH
Q ss_conf             9999999999---987589879
Q gi|254781080|r   30 LTENIKDIYG---EAKATGFDV   48 (85)
Q Consensus        30 i~~dikdVya---EAK~~GfD~   48 (85)
                      +.++||+.||   |||.+||.+
T Consensus       738 vFd~IR~LFA~~PeAk~RGY~~  759 (956)
T TIGR00630       738 VFDEIRELFAETPEAKARGYKP  759 (956)
T ss_pred             CCHHHHHHHHCCCHHHHCCCCC
T ss_conf             4305777640585378738899


No 23 
>COG5113 UFD2 Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones]
Probab=21.55  E-value=66  Score=14.94  Aligned_cols=30  Identities=30%  Similarity=0.544  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             899999999999999999999999999999
Q gi|254781080|r   10 QDQLRTFIERLERLEEEKKLLTENIKDIYG   39 (85)
Q Consensus        10 ~~~Lr~~IERIErLeeEkk~i~~dikdVya   39 (85)
                      -+.||+||.|.|..+--++.=.+|.-||-.
T Consensus       824 IE~l~~f~nr~E~~r~~ea~EeED~GDvPD  853 (929)
T COG5113         824 IEELRSFINRLEKVRVIEAVEEEDMGDVPD  853 (929)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCH
T ss_conf             999999999998989887522332168956


No 24 
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=21.01  E-value=76  Score=14.55  Aligned_cols=34  Identities=29%  Similarity=0.394  Sum_probs=22.4

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             9987589879999999999618999999999999
Q gi|254781080|r   39 GEAKATGFDVKAIKKILSLRKKDEKQWMEEEQIL   72 (85)
Q Consensus        39 aEAK~~GfD~K~lr~IiklRk~d~~er~E~e~iL   72 (85)
                      ..++..||..+-||+++.++..++....+-..+|
T Consensus        51 ~~~r~~G~sL~eIr~ll~l~~~~~~~~~~~~~ll   84 (133)
T cd04787          51 LSARQLGFSLKDIKEILSHADQGESPCPMVRRLI   84 (133)
T ss_pred             HHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             9999869999999999988737999789999999


No 25 
>pfam09840 DUF2067 Uncharacterized protein conserved in archaea (DUF2067). This domain, found in various archaeal proteins, has no known function.
Probab=20.90  E-value=77  Score=14.54  Aligned_cols=43  Identities=26%  Similarity=0.380  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH----HHCCHHHHHHH
Q ss_conf             999999999999999987589879999999999----61899999999
Q gi|254781080|r   25 EEKKLLTENIKDIYGEAKATGFDVKAIKKILSL----RKKDEKQWMEE   68 (85)
Q Consensus        25 eEkk~i~~dikdVyaEAK~~GfD~K~lr~Iikl----Rk~d~~er~E~   68 (85)
                      +|.-.+...+.++|+|+...-.-++ +|.+|..    ..+||++.-|.
T Consensus       116 eev~e~~~~L~eiy~ei~~~~lt~~-~k~vv~~~s~~~g~~~~evie~  162 (190)
T pfam09840       116 EEVVEVARELSEIYKELRFQPLTTK-AKRVVVAASYATGKDPDDAIEE  162 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHH-HHHHHHEEHHHHCCCHHHHHHH
T ss_conf             9999999999999999854766765-6645311034618998999999


No 26 
>PRK07093 para-aminobenzoate synthase component I; Validated
Probab=20.18  E-value=79  Score=14.44  Aligned_cols=25  Identities=32%  Similarity=0.546  Sum_probs=22.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             8999999999999999998598867
Q gi|254781080|r   60 KDEKQWMEEEQILDVYLRALGMLKD   84 (85)
Q Consensus        60 ~d~~er~E~e~iLd~Y~~ALGm~~~   84 (85)
                      .|+-+++|+-+|.|+-+.-||+.++
T Consensus       165 ~d~Ke~aEh~MIVDL~RNDL~~va~  189 (322)
T PRK07093        165 NDEKEFAEHATIVDLMRNDLSMVAT  189 (322)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             2938789999999999868772387


Done!