Query         gi|254780763|ref|YP_003065176.1| hypothetical protein CLIBASIA_03260 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 107
No_of_seqs    107 out of 1265
Neff          6.1 
Searched_HMMs 39220
Date          Sun May 29 18:50:15 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780763.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00153 hypothetical protein; 100.0 1.8E-32 4.5E-37  228.1  15.4  105    1-107     3-107 (107)
  2 COG0718 Uncharacterized protei 100.0 1.9E-29 4.7E-34  208.9  14.4  102    1-104     4-105 (105)
  3 PRK03762 hypothetical protein; 100.0 2.1E-28 5.4E-33  202.2  14.4   94    3-98      2-95  (97)
  4 PRK00587 hypothetical protein;  99.9 2.6E-26 6.8E-31  188.9  13.8   98    3-103     2-99  (99)
  5 TIGR00103 TIGR00103 conserved   99.9   3E-26 7.6E-31  188.6  12.1  101    3-103    12-112 (112)
  6 pfam02575 DUF149 Uncharacteriz  99.9 2.3E-24 5.9E-29  176.6  13.0   92    8-100     1-92  (92)
  7 PRK00587 hypothetical protein;  94.9    0.28 7.1E-06   30.1   8.5   90    1-97      3-99  (99)
  8 PRK00153 hypothetical protein;  91.0    0.63 1.6E-05   27.9   5.4   93    9-107     4-103 (107)
  9 KOG3675 consensus               64.9     7.6 0.00019   21.0   3.2   52   21-72    266-317 (417)
 10 pfam11576 DUF3236 Protein of u  63.2      14 0.00035   19.4   4.2   49   32-82    103-151 (154)
 11 TIGR01352 tonB_Cterm TonB fami  56.0      21 0.00053   18.3   4.5   42   34-79     13-54  (81)
 12 pfam10437 Lip_prot_lig_C Bacte  41.6      35 0.00088   16.9   4.9   52   31-82     10-68  (85)
 13 TIGR00389 glyS_dimeric glycyl-  35.1      30 0.00076   17.3   2.3   50    9-63    407-457 (606)
 14 TIGR01202 bchC Chlorophyll syn  32.6      23 0.00058   18.0   1.3   15   93-107    46-60  (325)
 15 pfam07472 PA-IIL Fucose-bindin  32.2      35  0.0009   16.8   2.3   28   32-59     50-77  (107)
 16 TIGR01506 ribC_arch riboflavin  31.1      46  0.0012   16.1   2.7   58   36-99     79-142 (152)
 17 COG2968 Uncharacterized conser  30.4      52  0.0013   15.7   7.1   64   27-94    112-190 (243)
 18 PRK10718 hypothetical protein;  28.6      56  0.0014   15.5   3.0   49   30-79     85-134 (191)
 19 COG4572 ChaB Putative cation t  28.2      51  0.0013   15.8   2.5   24   59-82     13-36  (76)
 20 PRK05886 yajC preprotein trans  27.6      58  0.0015   15.4   5.2   53    7-60     21-73  (108)
 21 pfam05958 tRNA_U5-meth_tr tRNA  27.4      29 0.00075   17.3   1.2   52    9-60    181-233 (353)
 22 TIGR02063 RNase_R ribonuclease  27.3      59  0.0015   15.4   5.8   72    2-81    419-490 (755)
 23 PRK03822 lplA lipoate-protein   26.6      61  0.0015   15.3   8.5   56   29-84    255-317 (338)
 24 COG1422 Predicted membrane pro  26.2      61  0.0016   15.3   3.1   20    9-28     72-91  (201)
 25 PRK13259 regulatory protein Sp  26.2      61  0.0016   15.3   3.4   28   60-87     65-92  (94)
 26 pfam08714 Fae Formaldehyde-act  26.1      62  0.0016   15.2   4.0   38   43-83    101-138 (160)
 27 TIGR01377 soxA_mon sarcosine o  24.9      31 0.00078   17.2   0.9   33   22-54    168-201 (401)
 28 pfam10991 DUF2815 Protein of u  24.3      67  0.0017   15.0   3.7   41   59-107    36-76  (181)
 29 pfam08345 YscJ_FliF_C Flagella  24.2      58  0.0015   15.4   2.2   40   36-75     91-145 (162)
 30 COG0858 RbfA Ribosome-binding   23.7      69  0.0017   15.0   8.5   77    6-89      6-83  (118)
 31 PHA00431 internal virion prote  23.4      69  0.0018   14.9   5.4   58   25-84    658-715 (749)
 32 pfam07830 PP2C_C Protein serin  22.8      71  0.0018   14.9   3.6   51   53-105    12-68  (81)
 33 COG0810 TonB Periplasmic prote  22.4      73  0.0019   14.8   4.0   42   34-79    179-220 (244)
 34 TIGR03422 mito_frataxin fratax  21.6      75  0.0019   14.7   4.1   38   12-49     11-48  (97)
 35 TIGR00537 hemK_rel_arch methyl  21.1      19 0.00048   18.5  -0.8   34   27-60     23-58  (183)
 36 PRK05031 tRNA (uracil-5-)-meth  20.4      68  0.0017   15.0   1.9   50   10-59    192-242 (363)

No 1  
>PRK00153 hypothetical protein; Validated
Probab=100.00  E-value=1.8e-32  Score=228.11  Aligned_cols=105  Identities=43%  Similarity=0.736  Sum_probs=103.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             92179999999999999999999985308999976984999996483074688647882910068999999999999999
Q gi|254780763|r    1 MSNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHK   80 (107)
Q Consensus         1 M~nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~   80 (107)
                      |+||++||+|||+||++|+++|++|++.+|+|+|+||+|+||+||+++|++|+|||++++++|+++|||+|++|+|+|++
T Consensus         3 m~nm~~mmkqaq~mq~~~~~~q~el~~~~v~~~sg~glV~V~~nG~~~v~~i~Id~~ll~~~d~e~LedlI~~A~N~A~~   82 (107)
T PRK00153          3 MGNMANLMKQAQQMQEKMQKMQEELANKEVTGTAGGGLVTVTMTGKKEVVRVKIDPSVVDPEDVEMLEDLVAAAFNDALR   82 (107)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEEEECCCEEEEEEECHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             43599999999999999999999983758999987985999995495699999888986941599999999999999999


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             999999999999744899899999998
Q gi|254780763|r   81 KIEDLVATKTQEITEGLPIPPGLKFPF  107 (107)
Q Consensus        81 k~~~~~~~~m~~~tggl~lp~g~~lPf  107 (107)
                      ++++.++++|+++|||| +||||+ ||
T Consensus        83 ka~~~~~~~m~~~tgg~-~~PG~~-p~  107 (107)
T PRK00153         83 KADETTQEKMGALTGGL-LPPGFK-PF  107 (107)
T ss_pred             HHHHHHHHHHHHHHCCC-CCCCCC-CC
T ss_conf             99999999999984798-999999-98


No 2  
>COG0718 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.97  E-value=1.9e-29  Score=208.92  Aligned_cols=102  Identities=46%  Similarity=0.734  Sum_probs=99.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             92179999999999999999999985308999976984999996483074688647882910068999999999999999
Q gi|254780763|r    1 MSNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHK   80 (107)
Q Consensus         1 M~nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~   80 (107)
                      |+||+.|++|||+||++|+++|++|++.+|+|+||||+|+|++||+++|++|+|||++++|+|+|+|||||++|+|+|.+
T Consensus         4 ~~~~~~l~kqaqqmQ~~~~~~Q~ela~~ev~g~aggGlVtV~~~G~~ev~~v~Idp~l~dpeD~E~LeDLi~aA~ndA~~   83 (105)
T COG0718           4 MMDMQKLMKQAQQMQKKMQKMQEELAQKEVTGKAGGGLVTVTINGKGEVKSVEIDPSLLDPEDKEMLEDLILAAFNDAKK   83 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEECCCCEEEEEEECCCCEEEEEECHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             13099999999999999999999998527765227847999994796478887287875964188999999999999999


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             999999999999744899899999
Q gi|254780763|r   81 KIEDLVATKTQEITEGLPIPPGLK  104 (107)
Q Consensus        81 k~~~~~~~~m~~~tggl~lp~g~~  104 (107)
                      ++++..+++|+++|+||+ | ||+
T Consensus        84 kv~e~~~e~m~~~t~gm~-P-G~~  105 (105)
T COG0718          84 KVEETRKEKMGALTGGMP-P-GFK  105 (105)
T ss_pred             HHHHHHHHHHHHHHCCCC-C-CCC
T ss_conf             999999999998645489-9-999


No 3  
>PRK03762 hypothetical protein; Provisional
Probab=99.96  E-value=2.1e-28  Score=202.23  Aligned_cols=94  Identities=31%  Similarity=0.453  Sum_probs=92.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             17999999999999999999998530899997698499999648307468864788291006899999999999999999
Q gi|254780763|r    3 NIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKI   82 (107)
Q Consensus         3 nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~   82 (107)
                      ||++||+|||+||++|+++|++|++.+|+|+||||+|+|++||+++|++|+|||+++  +|+|+|||||++|+|+|++++
T Consensus         2 d~~~mmkqaq~mQ~km~~~Qeel~~~~v~g~sGGGlVkV~~nGk~ev~~i~IDp~l~--eD~emLeDLI~aA~NdA~~k~   79 (97)
T PRK03762          2 DFSKMGEMLEQMQEKAKQLEEENANTEFTAKSGGGLVSVSANGKGEIIDISIDDSLL--EDKESLQILLISAINDVLKMV   79 (97)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEEEECCCEEEEEEECHHHC--CCHHHHHHHHHHHHHHHHHHH
T ss_conf             889999999999999999999984879999974967999995573089999887880--768799999999999999999


Q ss_pred             HHHHHHHHHHHHCCCC
Q ss_conf             9999999999744899
Q gi|254780763|r   83 EDLVATKTQEITEGLP   98 (107)
Q Consensus        83 ~~~~~~~m~~~tggl~   98 (107)
                      ++.++++|+++||||+
T Consensus        80 ~~~~~~~m~~~tgGmg   95 (97)
T PRK03762         80 EENRKNLAFNMLGGFG   95 (97)
T ss_pred             HHHHHHHHHHHHCCCC
T ss_conf             9999999998757788


No 4  
>PRK00587 hypothetical protein; Provisional
Probab=99.94  E-value=2.6e-26  Score=188.90  Aligned_cols=98  Identities=18%  Similarity=0.218  Sum_probs=93.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             17999999999999999999998530899997698499999648307468864788291006899999999999999999
Q gi|254780763|r    3 NIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKI   82 (107)
Q Consensus         3 nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~   82 (107)
                      ||++||+|||+||++|.+.|++|++.+|++++ ||+|+|++||+++|++|+|||++++|+|+|+|||||++|+|+|++++
T Consensus         2 Nm~~mmkQaqkMQ~~m~~~Qeel~~~~~~~s~-gG~V~v~~nG~~ei~~i~I~pe~VDPeD~EmLeDLi~aAvNeAl~~v   80 (99)
T PRK00587          2 NFQKLAQQLKKMQNTMEKKQKEFEEKEFDFDY-KKYILIKIKGNLNIEKIEINKELIDPEDKETLQDMLREAINEAISIT   80 (99)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEC-CCEEEEEEECCEEEEEEEECHHCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             88999999999999999999999737888855-98799999678469998727001694218899999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCC
Q ss_conf             999999999974489989999
Q gi|254780763|r   83 EDLVATKTQEITEGLPIPPGL  103 (107)
Q Consensus        83 ~~~~~~~m~~~tggl~lp~g~  103 (107)
                      ++...+.|++.++++  |+||
T Consensus        81 ~~~~~~~m~~~m~~~--tG~f   99 (99)
T PRK00587         81 CKERDAIMNSTIPKG--TGLF   99 (99)
T ss_pred             HHHHHHHHHHHCCCC--CCCC
T ss_conf             999999998663788--8999


No 5  
>TIGR00103 TIGR00103 conserved hypothetical protein TIGR00103; InterPro: IPR004401   The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta . YbaB is co-transcribed with recR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain..
Probab=99.94  E-value=3e-26  Score=188.56  Aligned_cols=101  Identities=43%  Similarity=0.656  Sum_probs=99.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             17999999999999999999998530899997698499999648307468864788291006899999999999999999
Q gi|254780763|r    3 NIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKI   82 (107)
Q Consensus         3 nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~   82 (107)
                      |+.+||+|||+||.+++.+|+|++..+|+|.||+|+|+|+++|++++++|.|||++++++|+++||++|.+|+|+|++++
T Consensus        12 ~l~~~m~~a~~~q~~~~~l~eE~~~~~~~gksG~GlV~v~~~G~~~~~~~~Id~~l~d~~D~~~Le~~i~~A~NdA~~~v   91 (112)
T TIGR00103        12 NLGELMKQAQKVQEKMKKLQEEIAKLEVTGKSGAGLVTVTINGNLELKSIEIDPSLLDPEDKEALEDLITEALNDAVKKV   91 (112)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHEECCCCCCCEEEEEEECCCCCEEEECCHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             79999999999999899999888721316423773578886368652021035533286664889999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCC
Q ss_conf             999999999974489989999
Q gi|254780763|r   83 EDLVATKTQEITEGLPIPPGL  103 (107)
Q Consensus        83 ~~~~~~~m~~~tggl~lp~g~  103 (107)
                      ++..+++|..++.+||+||||
T Consensus        92 ~e~~~~kM~~~~~~l~~~PGl  112 (112)
T TIGR00103        92 KEKYKEKMALVTKGLPLVPGL  112 (112)
T ss_pred             HHHHHHHHHHHHHHCCCCCCC
T ss_conf             999988899999752789899


No 6  
>pfam02575 DUF149 Uncharacterized BCR, YbaB family COG0718.
Probab=99.92  E-value=2.3e-24  Score=176.58  Aligned_cols=92  Identities=45%  Similarity=0.688  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999853089999769849999964830746886478829100689999999999999999999999
Q gi|254780763|r    8 VGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIEDLVA   87 (107)
Q Consensus         8 lkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~~~~   87 (107)
                      |+|||+||++|+++|++|++.+|+|+|++|+|+|++||+++|++|+|||++++ +|+++|+|+|++|||+|++++++.++
T Consensus         1 ~~qaq~mq~~~~~~q~el~~~~~~~~s~~g~V~v~~~G~~~v~~i~Id~~l~~-~d~e~Ledli~~A~n~A~~~a~~~~~   79 (92)
T pfam02575         1 MKQAQQMQEKMEKAQEELANKEVEGTSGGGLVKVTVNGKGEVKDVEIDPELLD-EDKEMLEDLIVAAINDALKKAEELAK   79 (92)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEEECCCCEEEEEEECHHHHC-CCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             95899999999999999727499999889839999826847999999889963-88999999999999999999999999


Q ss_pred             HHHHHHHCCCCCC
Q ss_conf             9999974489989
Q gi|254780763|r   88 TKTQEITEGLPIP  100 (107)
Q Consensus        88 ~~m~~~tggl~lp  100 (107)
                      ++|+++||||++|
T Consensus        80 ~~m~~~~gg~~~p   92 (92)
T pfam02575        80 EEMGKLTGGLNLP   92 (92)
T ss_pred             HHHHHHHCCCCCC
T ss_conf             9999983699999


No 7  
>PRK00587 hypothetical protein; Provisional
Probab=94.92  E-value=0.28  Score=30.14  Aligned_cols=90  Identities=14%  Similarity=0.145  Sum_probs=57.2

Q ss_pred             CCCHHHHHHHHH----HHHHHHHHHHHHHH---HEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHH
Q ss_conf             921799999999----99999999999985---30899997698499999648307468864788291006899999999
Q gi|254780763|r    1 MSNIMKMVGQFK----EIQGKMEKMKESIT---SLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIA   73 (107)
Q Consensus         1 M~nm~~llkqaq----~mq~~m~~~q~eL~---~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~   73 (107)
                      |.+|..-.++.|    +.|+.+.+.  ++.   .--|++..-|..--+.++=+-++++=+ |++.|    .+.+-..|-.
T Consensus         3 m~~mmkQaqkMQ~~m~~~Qeel~~~--~~~~s~gG~V~v~~nG~~ei~~i~I~pe~VDPe-D~EmL----eDLi~aAvNe   75 (99)
T PRK00587          3 FQKLAQQLKKMQNTMEKKQKEFEEK--EFDFDYKKYILIKIKGNLNIEKIEINKELIDPE-DKETL----QDMLREAINE   75 (99)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHC--EEEEECCCEEEEEEECCEEEEEEEECHHCCCCC-CHHHH----HHHHHHHHHH
T ss_conf             8999999999999999999999737--888855987999996784699987270016942-18899----9999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             999999999999999999974489
Q gi|254780763|r   74 AHSDAHKKIEDLVATKTQEITEGL   97 (107)
Q Consensus        74 A~N~A~~k~~~~~~~~m~~~tggl   97 (107)
                      |+..+-++.++.+.+.|+++|||+
T Consensus        76 Al~~v~~~~~~~m~~~m~~~tG~f   99 (99)
T PRK00587         76 AISITCKERDAIMNSTIPKGTGLF   99 (99)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             999999999999986637888999


No 8  
>PRK00153 hypothetical protein; Validated
Probab=90.95  E-value=0.63  Score=27.87  Aligned_cols=93  Identities=15%  Similarity=0.171  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHH--HCC-CCHHHHH----HHHHHHHHHHHHHH
Q ss_conf             9999999999999999853089999769849999964830746886478--829-1006899----99999999999999
Q gi|254780763|r    9 GQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRS--LLF-EDNVEIL----EDLIIAAHSDAHKK   81 (107)
Q Consensus         9 kqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~--~l~-~~d~e~L----edli~~A~N~A~~k   81 (107)
                      +..++|-++++++|+++++..-+-..    .+|+.+-.+..+.|.++-.  +++ .-|.+.|    .+.+-..+-.|+.+
T Consensus         4 ~nm~~mmkqaq~mq~~~~~~q~el~~----~~v~~~sg~glV~V~~nG~~~v~~i~Id~~ll~~~d~e~LedlI~~A~N~   79 (107)
T PRK00153          4 GNMANLMKQAQQMQEKMQKMQEELAN----KEVTGTAGGGLVTVTMTGKKEVVRVKIDPSVVDPEDVEMLEDLVAAAFND   79 (107)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHC----CEEEEEECCCEEEEEEECCCEEEEEEECHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             35999999999999999999999837----58999987985999995495699999888986941599999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             99999999999744899899999998
Q gi|254780763|r   82 IEDLVATKTQEITEGLPIPPGLKFPF  107 (107)
Q Consensus        82 ~~~~~~~~m~~~tggl~lp~g~~lPf  107 (107)
                      +-+.+++.+.+-...  +.+||++|-
T Consensus        80 A~~ka~~~~~~~m~~--~tgg~~~PG  103 (107)
T PRK00153         80 ALRKADETTQEKMGA--LTGGLLPPG  103 (107)
T ss_pred             HHHHHHHHHHHHHHH--HHCCCCCCC
T ss_conf             999999999999999--847989999


No 9  
>KOG3675 consensus
Probab=64.88  E-value=7.6  Score=21.02  Aligned_cols=52  Identities=23%  Similarity=0.280  Sum_probs=42.3

Q ss_pred             HHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHH
Q ss_conf             9999853089999769849999964830746886478829100689999999
Q gi|254780763|r   21 MKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLII   72 (107)
Q Consensus        21 ~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~   72 (107)
                      ++.++--+.|--++|.|+|+++.|-...=..|++|.+.++......|++-+.
T Consensus       266 ~~ARfvi~kv~lEageglvkie~T~g~Dd~~vrLDrSkI~svG~pal~~FL~  317 (417)
T KOG3675         266 MRARFVIMKVLLEAGEGLVKIEPTTGSDDARVRLDRSKIDSVGRPALEDFLR  317 (417)
T ss_pred             HHHHHHHEEHHHHHCCCEEEEEECCCCCCEEEEECHHHHHHCCCHHHHHHHH
T ss_conf             3201001012677558827861047886447882166553047177999999


No 10 
>pfam11576 DUF3236 Protein of unknown function (DUF3236). This family of proteins with unknown function appears to be restricted to Methanobacteria.
Probab=63.17  E-value=14  Score=19.42  Aligned_cols=49  Identities=18%  Similarity=0.310  Sum_probs=40.5

Q ss_pred             EEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             997698499999648307468864788291006899999999999999999
Q gi|254780763|r   32 GNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKI   82 (107)
Q Consensus        32 g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~   82 (107)
                      |--|.|-.-|.|++++.++.-.++|+-+=  .++.+++.+..-.++|++++
T Consensus       103 GvPGSGSmLvimD~kgRiLTaslSPs~ii--Hk~~ie~~v~~E~~eAL~ri  151 (154)
T pfam11576       103 GVPGSGSMLVIMDSKGRILTAALSPSHVI--HKKSIEEAVELELEEALERI  151 (154)
T ss_pred             CCCCCCCEEEEECCCCCEEEECCCCHHHH--HCCCHHHHHHHHHHHHHHHH
T ss_conf             58987637999838876875137912643--00449999999999999983


No 11 
>TIGR01352 tonB_Cterm TonB family C-terminal domain; InterPro: IPR006260   The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria . Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm.    Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins .    The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores . An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin .    To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane. ; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space.
Probab=56.02  E-value=21  Score=18.28  Aligned_cols=42  Identities=19%  Similarity=0.283  Sum_probs=31.6

Q ss_pred             ECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             7698499999648307468864788291006899999999999999
Q gi|254780763|r   34 AGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAH   79 (107)
Q Consensus        34 sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~   79 (107)
                      .|-=.|+++++-+|.|.+++|..+    .....|....+.|+..+-
T Consensus        13 ~G~V~v~~~v~~~G~v~~~~v~~S----sg~~~lD~~Al~a~~~~~   54 (81)
T TIGR01352        13 EGTVVVRFTVDASGRVTSVRVLKS----SGNRALDRAALEAVRKAR   54 (81)
T ss_pred             CCEEEEEEEECCCCCEEEEEEECC----CCCHHHHHHHHHHHHHCC
T ss_conf             656899998689983557888305----798788799999998500


No 12 
>pfam10437 Lip_prot_lig_C Bacterial lipoate protein ligase C-terminus. This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C-terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with the domain BPL_LipA_LipB pfam03099, further upstream. This C-terminal domain is more stable than the BPL_LipA_LipB and the hypothesis is that the C-terminal domain has a role in recognising the lipoyl domain and/or transferring the lipoyl group onto it from the lipoyl-AMP intermediate. C-terminal fragments of length 172 to 193 amino acid residues are observed in the eubacterial enzymes whereas in their archaeal counterparts the C-terminal segment is significantly smaller, ranging in size from 87 to 107 amino acid residues.
Probab=41.59  E-value=35  Score=16.86  Aligned_cols=52  Identities=27%  Similarity=0.330  Sum_probs=39.7

Q ss_pred             EEEECCCEEEEEEE-CCCCEEEEEECHHHCCCCHHHHHHHHHH------HHHHHHHHHH
Q ss_conf             99976984999996-4830746886478829100689999999------9999999999
Q gi|254780763|r   31 EGNAGGGMVSVRIN-GKNMLTGVKIDRSLLFEDNVEILEDLII------AAHSDAHKKI   82 (107)
Q Consensus        31 ~g~sg~g~V~V~~~-G~~~i~~i~Id~~~l~~~d~e~Ledli~------~A~N~A~~k~   82 (107)
                      +..-.+|.|.+.++ =++.|++++|--+++.+.|.+.|+..+.      +++.+++...
T Consensus        10 ~~rf~~G~ve~~l~V~~G~I~~iki~gDf~~~~~i~~le~~L~G~~y~~~~i~~~L~~~   68 (85)
T pfam10437        10 DKRFPWGTIEVHLNVEKGKIKDIKIFGDFLGPGDLEELEEKLIGVKYDKEAIKKALNEI   68 (85)
T ss_pred             EEECCCCEEEEEEEECCCEEEEEEEECCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHC
T ss_conf             34748847999999738999899998456983549999998679986999999999849


No 13 
>TIGR00389 glyS_dimeric glycyl-tRNA synthetase; InterPro: IPR002315   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   In eubacteria, glycyl-tRNA synthetase (6.1.1.14 from EC) is an alpha2/beta2 tetramer composed of 2 different subunits , , . In some eubacteria, in archaea and eukaryota, glycyl-tRNA synthetase is an alpha2 dimer, this family. It belongs to class IIc and is one of the most complex synthetases. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha (see IPR002310 from INTERPRO) and beta subunits (see IPR002311 from INTERPRO) also lack significant sequence similarity. However, they are translated from a single mRNA , and a single chain glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain .   The sequence and crystal structure of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, shows that each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel beta-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA synthetase due to the conserved nature of the class II active site , .; GO: 0000166 nucleotide binding, 0004820 glycine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006426 glycyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=35.12  E-value=30  Score=17.28  Aligned_cols=50  Identities=20%  Similarity=0.382  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHH-HHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCH
Q ss_conf             9999999999999-999853089999769849999964830746886478829100
Q gi|254780763|r    9 GQFKEIQGKMEKM-KESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDN   63 (107)
Q Consensus         9 kqaq~mq~~m~~~-q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d   63 (107)
                      ++|+++..-+..+ |.+|......... +|.+++.++|    ..++|+++++.=.+
T Consensus       407 kdAk~ies~L~~lse~dl~~~~~~l~~-~G~f~~~~dG----~~ve~~~~~v~i~~  457 (606)
T TIGR00389       407 KDAKKIESALENLSEDDLEEVEKELDE-EGKFIIEVDG----KEVEILKDLVEIKE  457 (606)
T ss_pred             CHHHHHHHHHHHCCHHHHHHHHHHHHC-CCEEEEEECC----EEEEECHHHEEEEE
T ss_conf             117899999973287478999998634-9869999858----18987121242666


No 14 
>TIGR01202 bchC Chlorophyll synthesis pathway, bchC; InterPro: IPR005903   Some prokaryotes, such as the purple and green sulphur bacteria, gain energy from a mode of photosynthesis that does not generate oxygen, and is inhibited by its presence , . These organisms do not include chlorophylls in their photosynthetic pigments, but instead use closely related molecules known as bacteriochlorophylls. Like chlorophylls, bacteriochlorophylls are tetrapyroles with a five-membered ring structure, differing in the side chains and hydration state of the ring structure. These alterations in structure determine what light wavelengths can be harvested by the organism .   Bacteriochlorophyll a is a photosynthetic pigment found in many of the purple bacteria. It is synthesised from protoporphyrin IX in a series of reactions including magnesium-chelation, methyl transfer, ring formation, vinyl-group reduction protochlorophyllide reduction, and finally phytol addition . This entry represents 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide a dehydrogenase, the enzyme catalysing the penultimate step in light-independent bacteriochlorophyll a biosynthesis .; GO: 0016491 oxidoreductase activity, 0030494 bacteriochlorophyll biosynthetic process.
Probab=32.61  E-value=23  Score=18.01  Aligned_cols=15  Identities=27%  Similarity=0.625  Sum_probs=12.4

Q ss_pred             HHCCCCCCCCCCCCC
Q ss_conf             744899899999998
Q gi|254780763|r   93 ITEGLPIPPGLKFPF  107 (107)
Q Consensus        93 ~tggl~lp~g~~lPf  107 (107)
                      .+|-||=||||-+||
T Consensus        46 ~~G~~P~fPGmgyPl   60 (325)
T TIGR01202        46 WNGLMPPFPGMGYPL   60 (325)
T ss_pred             HCCCCCCCCCCCCCC
T ss_conf             558985347776788


No 15 
>pfam07472 PA-IIL Fucose-binding lectin II (PA-IIL). In Pseudomonas aeruginosa the fucose-binding lectin II (PA-IIL) contributes to the pathogenic virulence of the bacterium. PA-IIL functions as a tetramer when binding fucose. Each monomer is comprised of a nine-stranded, antiparallel beta-sandwich arrangement and contains two calcium cations that mediate the binding of fucose in a recognition mode unique among carbohydrate-protein interactions.
Probab=32.22  E-value=35  Score=16.79  Aligned_cols=28  Identities=18%  Similarity=0.266  Sum_probs=21.6

Q ss_pred             EEECCCEEEEEEECCCCEEEEEECHHHC
Q ss_conf             9976984999996483074688647882
Q gi|254780763|r   32 GNAGGGMVSVRINGKNMLTGVKIDRSLL   59 (107)
Q Consensus        32 g~sg~g~V~V~~~G~~~i~~i~Id~~~l   59 (107)
                      -.||.|.|+|.+.++++...+.-....|
T Consensus        50 l~Sg~GkVriev~~nGkps~l~s~q~~l   77 (107)
T pfam07472        50 LNSGTGKVRIEVIANGKPSKLRSRQVTL   77 (107)
T ss_pred             EECCCCEEEEEEEECCCCCCCEEEECCC
T ss_conf             8569972999998389424410011013


No 16 
>TIGR01506 ribC_arch riboflavin synthase; InterPro: IPR006399   These archaeal proteins, bacterial riboflavin biosynthesis alpha chain, catalyze the final step in riboflavin biosynthesis. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain. ; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process.
Probab=31.13  E-value=46  Score=16.09  Aligned_cols=58  Identities=17%  Similarity=0.311  Sum_probs=42.9

Q ss_pred             CCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH-----HH-HHHHHCCCCC
Q ss_conf             9849999964830746886478829100689999999999999999999999-----99-9997448998
Q gi|254780763|r   36 GGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIEDLVA-----TK-TQEITEGLPI   99 (107)
Q Consensus        36 ~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~~~~-----~~-m~~~tggl~l   99 (107)
                      =|||-|.+=-+..|++|+|-++  ..+|+   +.|-+-|.|.|-+-++....     .+ +.+.+| +++
T Consensus        79 ~GLi~vqlmTnk~vidVtvHED--Eaedp---eeL~~~A~nRaReHa~Nl~~ll~~p~raL~k~AG-~Gl  142 (152)
T TIGR01506        79 VGLIIVQLMTNKHVIDVTVHED--EAEDP---EELKVVAENRAREHARNLVALLVEPDRALVKEAG-MGL  142 (152)
T ss_pred             HHHHHHHHHCCCEEEEEEEECC--CCCCH---HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCC-CCC
T ss_conf             8886543210878888875358--66786---7889887455668999999986078357554206-877


No 17 
>COG2968 Uncharacterized conserved protein [Function unknown]
Probab=30.36  E-value=52  Score=15.72  Aligned_cols=64  Identities=20%  Similarity=0.264  Sum_probs=46.9

Q ss_pred             HEEEEEEECCCEEEEEEE---------------CCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             308999976984999996---------------48307468864788291006899999999999999999999999999
Q gi|254780763|r   27 SLEAEGNAGGGMVSVRIN---------------GKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIEDLVATKTQ   91 (107)
Q Consensus        27 ~~~v~g~sg~g~V~V~~~---------------G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~~~~~~m~   91 (107)
                      ..+++|..+..-|.|++.               |--+|-+|.+.   ++.+ ....++...+|+-||..|++...+.-.-
T Consensus       112 ~~~ltGY~asn~v~V~v~dl~klg~ilD~av~~Ganqi~gisf~---~~d~-~a~~~~Ar~~Av~dA~~kA~~lA~a~gv  187 (243)
T COG2968         112 EPELTGYRASNTVEVTVRDLDKLGELLDEAVKAGANQINGISFG---VDDP-EAAVQQARKAAVADAIAKAQALASALGV  187 (243)
T ss_pred             CCEEEEEEEEEEEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEE---ECCH-HHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             83489998542699998126678799999997575545864675---3887-9999999999999999999999986187


Q ss_pred             HHH
Q ss_conf             974
Q gi|254780763|r   92 EIT   94 (107)
Q Consensus        92 ~~t   94 (107)
                      ++.
T Consensus       188 ~l~  190 (243)
T COG2968         188 KLG  190 (243)
T ss_pred             CCC
T ss_conf             423


No 18 
>PRK10718 hypothetical protein; Provisional
Probab=28.58  E-value=56  Score=15.53  Aligned_cols=49  Identities=18%  Similarity=0.108  Sum_probs=30.5

Q ss_pred             EEEEECCCEEEEEEECC-CCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99997698499999648-307468864788291006899999999999999
Q gi|254780763|r   30 AEGNAGGGMVSVRINGK-NMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAH   79 (107)
Q Consensus        30 v~g~sg~g~V~V~~~G~-~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~   79 (107)
                      |++-. ++.|+++++|+ ++|.+|++.++-+...-.-.+-...-+-|.+|.
T Consensus        85 fqA~k-~d~V~lvi~G~kgtV~rI~V~D~~i~t~wG~~IGtpFs~lY~KAf  134 (191)
T PRK10718         85 FEAMK-GDQVAMVINGQQGTVSRIDVLDSDIPTAWGVKIGTPFSDLYSKAF  134 (191)
T ss_pred             EEECC-CCEEEEEEECCCCEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             85417-881899996688639999985555441125403771688777663


No 19 
>COG4572 ChaB Putative cation transport regulator [General function prediction only]
Probab=28.22  E-value=51  Score=15.78  Aligned_cols=24  Identities=17%  Similarity=0.113  Sum_probs=18.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             291006899999999999999999
Q gi|254780763|r   59 LFEDNVEILEDLIIAAHSDAHKKI   82 (107)
Q Consensus        59 l~~~d~e~Ledli~~A~N~A~~k~   82 (107)
                      +..--++.++|++.+|||-|++.-
T Consensus        13 vr~~lp~haqdiy~~afnsA~e~y   36 (76)
T COG4572          13 VRHQLPSHAQDIYKAAFNSAWEQY   36 (76)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999917999999999999887663


No 20 
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=27.61  E-value=58  Score=15.42  Aligned_cols=53  Identities=8%  Similarity=0.088  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCC
Q ss_conf             999999999999999999853089999769849999964830746886478829
Q gi|254780763|r    7 MVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLF   60 (107)
Q Consensus         7 llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~   60 (107)
                      |++..|+-|++.+++|..|..-.-...++| +.-.+..-.-+...++|.|-..-
T Consensus        21 ~iRpQkKrqk~~~~m~~sL~~Gd~VvT~~G-l~GtV~~v~dd~v~lEiApGv~v   73 (108)
T PRK05886         21 ASRRQRKAMQATIDLHESLQPGDRVHTTSG-LQATIVGITDDTVDLEIAPGVVT   73 (108)
T ss_pred             HCCHHHHHHHHHHHHHHHCCCCCEEEECCC-CEEEEEEECCCEEEEEECCCCEE
T ss_conf             316899999999999983689998997898-28999997188799997699589


No 21 
>pfam05958 tRNA_U5-meth_tr tRNA (Uracil-5-)-methyltransferase. This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalysed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.
Probab=27.40  E-value=29  Score=17.30  Aligned_cols=52  Identities=10%  Similarity=0.024  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECC-CCEEEEEECHHHCC
Q ss_conf             99999999999999998530899997698499999648-30746886478829
Q gi|254780763|r    9 GQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGK-NMLTGVKIDRSLLF   60 (107)
Q Consensus         9 kqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~-~~i~~i~Id~~~l~   60 (107)
                      .++++|.+.+.+.=..-....++..||-|.++..+..+ .+|..|+|+++++.
T Consensus       181 ~~~~~l~~~a~~~~~~~~~~vlDlYcG~Gtfsl~lA~~~~~V~GvE~~~~AV~  233 (353)
T pfam05958       181 AVNIKMLEWACEVTQGSKGDLLELYCGNGNFSLALAQNFRRVLATEIAKPSVN  233 (353)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCEEEEEECCHHHHH
T ss_conf             99999999999986268995899846888888999864787999962599999


No 22 
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805    This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=27.30  E-value=59  Score=15.39  Aligned_cols=72  Identities=8%  Similarity=0.197  Sum_probs=59.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             21799999999999999999999853089999769849999964830746886478829100689999999999999999
Q gi|254780763|r    2 SNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKK   81 (107)
Q Consensus         2 ~nm~~llkqaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k   81 (107)
                      .+|.++++.+.++.+-+.+..++=..+.|+-+=    ++|+++=+|++++|.+-..-..   --++|+.-++| |.|...
T Consensus       419 ~~~~~~l~~~~~L~~~L~~~R~~rG~IdFd~~E----~k~ilDe~G~~~~I~~~~R~~A---~klIEefM~~A-Ne~vA~  490 (755)
T TIGR02063       419 APLKEMLKNLEELYKILRKKRKKRGAIDFDSKE----AKIILDENGKPIDIVPRERGDA---HKLIEEFMIVA-NETVAE  490 (755)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC----CEEEECCCCEEEEEEEEECCCC---CHHHHHHHHHH-HHHHHH
T ss_conf             115777998999999999877651881237764----1799878842899898413332---22368889999-999999


No 23 
>PRK03822 lplA lipoate-protein ligase A; Provisional
Probab=26.58  E-value=61  Score=15.31  Aligned_cols=56  Identities=16%  Similarity=0.070  Sum_probs=45.5

Q ss_pred             EEEEEECCCEEEEEEEC-CCCEEEEEECHHHCCCCHHHHHHHHH------HHHHHHHHHHHHH
Q ss_conf             89999769849999964-83074688647882910068999999------9999999999999
Q gi|254780763|r   29 EAEGNAGGGMVSVRING-KNMLTGVKIDRSLLFEDNVEILEDLI------IAAHSDAHKKIED   84 (107)
Q Consensus        29 ~v~g~sg~g~V~V~~~G-~~~i~~i~Id~~~l~~~d~e~Ledli------~~A~N~A~~k~~~   84 (107)
                      +.+..-..|.|.+-++- ++.|++++|--+++.+.+.+.|+..+      ..|+.++++...-
T Consensus       255 ~~~~rf~~G~ve~~l~V~~G~I~~~ki~gDff~~~~i~~le~~L~G~~y~~~~i~~~l~~l~~  317 (338)
T PRK03822        255 LLDERFTWGGVELHFDVEKGHITRAQIFTDSLNPAPLEALAGRLQGCLYRADALQQECEALIV  317 (338)
T ss_pred             EEEEECCCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             533553673699999982898989999866899425999999856997789999999998764


No 24 
>COG1422 Predicted membrane protein [Function unknown]
Probab=26.24  E-value=61  Score=15.27  Aligned_cols=20  Identities=20%  Similarity=0.386  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHE
Q ss_conf             99999999999999998530
Q gi|254780763|r    9 GQFKEIQGKMEKMKESITSL   28 (107)
Q Consensus         9 kqaq~mq~~m~~~q~eL~~~   28 (107)
                      ++.+++|+.|++.|++.++.
T Consensus        72 ekm~~~qk~m~efq~e~~eA   91 (201)
T COG1422          72 EKMKELQKMMKEFQKEFREA   91 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999


No 25 
>PRK13259 regulatory protein SpoVG; Reviewed
Probab=26.24  E-value=61  Score=15.27  Aligned_cols=28  Identities=18%  Similarity=0.127  Sum_probs=21.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9100689999999999999999999999
Q gi|254780763|r   60 FEDNVEILEDLIIAAHSDAHKKIEDLVA   87 (107)
Q Consensus        60 ~~~d~e~Ledli~~A~N~A~~k~~~~~~   87 (107)
                      +++=.+.|++.|+.||++++.+..+...
T Consensus        65 t~e~R~~i~~aVl~aY~e~le~~~e~~~   92 (94)
T PRK13259         65 NSDTREKIQDAILKEYEREGELEEEEEE   92 (94)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCHHHC
T ss_conf             9899999999999999987734713340


No 26 
>pfam08714 Fae Formaldehyde-activating enzyme (Fae). Formaldehyde-activating enzyme is an enzyme required for energy metabolism and formaldehyde detoxification. It catalyses the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin.
Probab=26.08  E-value=62  Score=15.25  Aligned_cols=38  Identities=16%  Similarity=0.052  Sum_probs=28.4

Q ss_pred             EECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             96483074688647882910068999999999999999999
Q gi|254780763|r   43 INGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIE   83 (107)
Q Consensus        43 ~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~   83 (107)
                      .+--.-|.+|.|+|++.   |...|.+.=-+|...|++++-
T Consensus       101 a~dl~iiv~V~i~p~a~---D~~kiy~~Ny~ATk~AI~rAm  138 (160)
T pfam08714       101 ADDLVIIVSVFIHPEAL---DDKKIYRYNYEATKLAIKRAM  138 (160)
T ss_pred             HCCEEEEEEEECCCCCC---CHHHHHHHHHHHHHHHHHHHH
T ss_conf             03479999997183303---689999999999999999998


No 27 
>TIGR01377 soxA_mon sarcosine oxidase, monomeric form; InterPro: IPR006281   This set of sequences describe the alpha subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate .    Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the monomeric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process.
Probab=24.92  E-value=31  Score=17.19  Aligned_cols=33  Identities=12%  Similarity=0.310  Sum_probs=23.7

Q ss_pred             HHHHHHEEEEEEECCCEEEEEEEC-CCCEEEEEE
Q ss_conf             999853089999769849999964-830746886
Q gi|254780763|r   22 KESITSLEAEGNAGGGMVSVRING-KNMLTGVKI   54 (107)
Q Consensus        22 q~eL~~~~v~g~sg~g~V~V~~~G-~~~i~~i~I   54 (107)
                      .+.+.+++.+|+||+++|+|+.+. +++-+++-|
T Consensus       168 ~~kV~~i~~~GesGe~~vt~kt~~~sy~a~~lvv  201 (401)
T TIGR01377       168 GTKVVEIKPDGESGELLVTVKTTKDSYQAKKLVV  201 (401)
T ss_pred             CCEEEEEEECCCCCCCEEEEEEECCEEECCEEEE
T ss_conf             8603665426767895489997277032135789


No 28 
>pfam10991 DUF2815 Protein of unknown function (DUF2815). This is a phage related family of proteins with unknown function.
Probab=24.29  E-value=67  Score=15.04  Aligned_cols=41  Identities=29%  Similarity=0.298  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             2910068999999999999999999999999999744899899999998
Q gi|254780763|r   59 LFEDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGLPIPPGLKFPF  107 (107)
Q Consensus        59 l~~~d~e~Ledli~~A~N~A~~k~~~~~~~~m~~~tggl~lp~g~~lPf  107 (107)
                      +.+.|..+     +.+|+.|++.+.+....+  +.. |-.+|+.+++|+
T Consensus        36 ipK~d~~t-----i~~I~~AI~~a~~~~~~~--k~~-g~~~~~~~k~pl   76 (181)
T pfam10991        36 IPKSDTET-----IKAIKAAIKAAAEEGWGK--KAD-GKKIPATLKTPL   76 (181)
T ss_pred             ECCCCHHH-----HHHHHHHHHHHHHHHHHH--HCC-CCCCCCCCCCCC
T ss_conf             85798899-----999999999999875410--035-772576565631


No 29 
>pfam08345 YscJ_FliF_C Flagellar M-ring protein C-terminal. This domain is found in bacterial flagellar M-ring (FliF) proteins together with the YscJ/FliF domain (pfam01514).
Probab=24.17  E-value=58  Score=15.41  Aligned_cols=40  Identities=13%  Similarity=0.172  Sum_probs=21.3

Q ss_pred             CCEEEEEEECCCCEEEEEE----CH-----------HHCCCCHHHHHHHHHHHHH
Q ss_conf             9849999964830746886----47-----------8829100689999999999
Q gi|254780763|r   36 GGMVSVRINGKNMLTGVKI----DR-----------SLLFEDNVEILEDLIIAAH   75 (107)
Q Consensus        36 ~g~V~V~~~G~~~i~~i~I----d~-----------~~l~~~d~e~Ledli~~A~   75 (107)
                      +..++.+...-+.|.++.+    |.           .-++++..+.|++||..|+
T Consensus        91 ~~~~~~~~~~~G~I~rlsvaV~vd~~~~~~~~~~~~~~~s~ee~~~i~~lV~~Ai  145 (162)
T pfam08345        91 SRTVRHTVQAPGKIKRLSVAVVVDGVYVVADGKAAYVPRSPEELAQIEALVKSAV  145 (162)
T ss_pred             CCEEEEEECCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             7489999818981777899999856423677853346679999999999999960


No 30 
>COG0858 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis]
Probab=23.70  E-value=69  Score=14.97  Aligned_cols=77  Identities=16%  Similarity=0.107  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHHH-HHHHHHHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999-99999853089999769849999964830746886478829100689999999999999999999
Q gi|254780763|r    6 KMVGQFKEIQGKME-KMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIED   84 (107)
Q Consensus         6 ~llkqaq~mq~~m~-~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~   84 (107)
                      -..+-++++|..+. -+|.++..-.+..-.   ...|.++++...-.|.+++=-   ++ +.-.+-+++|+|.|-.-.+.
T Consensus         6 R~~rv~e~i~~~l~~il~~eikDprl~~~~---Vt~V~vS~Dl~~A~Vyvt~l~---~~-~~~~~~~~~~L~~A~g~ir~   78 (118)
T COG0858           6 RAKRVAEQIQKELAEILQREIKDPRLGLVT---VTDVEVSKDLSHAKVYVTVLG---DE-ESSKAEILAALNKAKGFIRS   78 (118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCEE---EEEEEECCCCCEEEEEEEECC---CC-HHHHHHHHHHHHHHHHHHHH
T ss_conf             889999999999999999875497768668---889998799755899996267---74-22289999999996999999


Q ss_pred             HHHHH
Q ss_conf             99999
Q gi|254780763|r   85 LVATK   89 (107)
Q Consensus        85 ~~~~~   89 (107)
                      .....
T Consensus        79 ~l~~~   83 (118)
T COG0858          79 ELGKR   83 (118)
T ss_pred             HHHHH
T ss_conf             99985


No 31 
>PHA00431 internal virion protein C
Probab=23.40  E-value=69  Score=14.93  Aligned_cols=58  Identities=21%  Similarity=0.236  Sum_probs=41.8

Q ss_pred             HHHEEEEEEECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             853089999769849999964830746886478829100689999999999999999999
Q gi|254780763|r   25 ITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIED   84 (107)
Q Consensus        25 L~~~~v~g~sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~   84 (107)
                      +.+...+....||-| +.++-.+. +.|.+|++++...=.+.-+.+--+|.+.|++.+.+
T Consensus       658 v~n~ql~~~~qgg~I-~lmd~TG~-Vrvr~d~ell~~~y~e~Q~~~~e~a~e~alkd~nk  715 (749)
T PHA00431        658 VTNKQLTVYTQGGSI-YLMDTTGQ-VRVRYDKELLSKVYRENQQKLAEEAREKALKDVNK  715 (749)
T ss_pred             CCCCEEEEEECCCEE-EEECCCCC-EEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             436625888449738-99738884-68997799999999999999999999999863101


No 32 
>pfam07830 PP2C_C Protein serine/threonine phosphatase 2C, C-terminal domain. Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain.
Probab=22.85  E-value=71  Score=14.86  Aligned_cols=51  Identities=12%  Similarity=0.245  Sum_probs=30.8

Q ss_pred             EECHHHCCCCHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHC-CC-CCCCCCCC
Q ss_conf             86478829100689999999999999999999----99999999744-89-98999999
Q gi|254780763|r   53 KIDRSLLFEDNVEILEDLIIAAHSDAHKKIED----LVATKTQEITE-GL-PIPPGLKF  105 (107)
Q Consensus        53 ~Id~~~l~~~d~e~Ledli~~A~N~A~~k~~~----~~~~~m~~~tg-gl-~lp~g~~l  105 (107)
                      +.+++++..+  .-|+..|..-+.+.+++...    .-..-|..+.. ++ +||||-.|
T Consensus        12 kv~~EAv~kE--~eLd~~le~~v~Eii~~~~~~~~~dl~~vm~~La~e~Ip~LPPGGGl   68 (81)
T pfam07830        12 KVSEEAVKKE--AELDKYLEQRVEEIIEKSSEDGVPDLLHVMKTLASEDIPGLPPGGGL   68 (81)
T ss_pred             CCCHHHHHHH--HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCCCH
T ss_conf             9999999999--99999999999999997254575229999999875578999999469


No 33 
>COG0810 TonB Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]
Probab=22.39  E-value=73  Score=14.80  Aligned_cols=42  Identities=19%  Similarity=0.205  Sum_probs=31.3

Q ss_pred             ECCCEEEEEEECCCCEEEEEECHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             7698499999648307468864788291006899999999999999
Q gi|254780763|r   34 AGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAH   79 (107)
Q Consensus        34 sg~g~V~V~~~G~~~i~~i~Id~~~l~~~d~e~Ledli~~A~N~A~   79 (107)
                      .|-=.|+++++-+|.|.+++|-.+    .....|....+.|++.+.
T Consensus       179 ~G~V~V~f~i~~~G~v~~v~v~~S----Sg~~~lD~aal~air~~~  220 (244)
T COG0810         179 EGTVKVKFTIDPDGNVTNVRVLKS----SGSPALDRAALEAIRKWR  220 (244)
T ss_pred             CCEEEEEEEECCCCCEEEEEEEEC----CCCHHHHHHHHHHHHHHC
T ss_conf             406999999899997845788623----896788899999999725


No 34 
>TIGR03422 mito_frataxin frataxin. Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately.
Probab=21.58  E-value=75  Score=14.70  Aligned_cols=38  Identities=16%  Similarity=0.318  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECCCCE
Q ss_conf             99999999999998530899997698499999648307
Q gi|254780763|r   12 KEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNML   49 (107)
Q Consensus        12 q~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~~~i   49 (107)
                      ..+...+.+..+......++....+|.+++++.+.+++
T Consensus        11 ~~ie~~le~~~d~~~~~d~D~~~~~gvLti~~~~~~~~   48 (97)
T TIGR03422        11 DHLLDKLEELGESRPDLDFDVEYSSGVLTLELPSVGTY   48 (97)
T ss_pred             HHHHHHHHHHHCCCCCCCEEEECCCCEEEEEECCCCEE
T ss_conf             99999999752214565621133698799998899789


No 35 
>TIGR00537 hemK_rel_arch methylase, putative; InterPro: IPR004557   These proteins exhibit homology to the Saccharomyces cerevisiae (yeast) ORF YDR140w (FYV9). No known function has been described for this yeast ORF though the null mutant is viable and exhibits K1 killer toxin hypersensitivity. Members of this entry are weakly related to the yeast ORF YNL063w which is a putative S-adenosyl-methionine-dependent methyltransferase . Members of this entry are found in archaeal, bacterial and eukaryotic lineages.; GO: 0008168 methyltransferase activity.
Probab=21.08  E-value=19  Score=18.53  Aligned_cols=34  Identities=24%  Similarity=0.290  Sum_probs=30.3

Q ss_pred             HEEEEEEECCCEEEEEEECCCC--EEEEEECHHHCC
Q ss_conf             3089999769849999964830--746886478829
Q gi|254780763|r   27 SLEAEGNAGGGMVSVRINGKNM--LTGVKIDRSLLF   60 (107)
Q Consensus        27 ~~~v~g~sg~g~V~V~~~G~~~--i~~i~Id~~~l~   60 (107)
                      ....|.-+|-|+|.+-+.+++.  |+.+.|+|-+..
T Consensus        23 deVlEiG~GtGlvair~~~Kg~k~i~~tDinP~Avk   58 (183)
T TIGR00537        23 DEVLEIGAGTGLVAIRLKEKGKKKILTTDINPFAVK   58 (183)
T ss_pred             CEEEEEECCHHHHHHHHHCCCCCEEEEEECCHHHHH
T ss_conf             528997168048999985158820788636879999


No 36 
>PRK05031 tRNA (uracil-5-)-methyltransferase; Validated
Probab=20.42  E-value=68  Score=14.98  Aligned_cols=50  Identities=8%  Similarity=0.043  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHHHHHEEEEEEECCCEEEEEEECC-CCEEEEEECHHHC
Q ss_conf             9999999999999998530899997698499999648-3074688647882
Q gi|254780763|r   10 QFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGK-NMLTGVKIDRSLL   59 (107)
Q Consensus        10 qaq~mq~~m~~~q~eL~~~~v~g~sg~g~V~V~~~G~-~~i~~i~Id~~~l   59 (107)
                      ++++|-+.+.+.=..-....++..||-|.++..+... .+|..|+|+++.+
T Consensus       192 ~~e~l~~~a~~~~~~~~~~vlDLYcG~Gtfsl~LA~~~~~V~gVE~~~~aV  242 (363)
T PRK05031        192 VNEKMLEWALDATKGSKGDLLELYCGNGNFTLALARNFRRVLATEISKPSV  242 (363)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCEEEEEECCHHHH
T ss_conf             999999999997613898289860586642699886268799995389999


Done!