Query         gi|254781073|ref|YP_003065486.1| coproporphyrinogen III oxidase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 307
No_of_seqs    154 out of 1016
Neff          5.0 
Searched_HMMs 39220
Date          Mon May 30 04:07:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781073.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05330 coproporphyrinogen II 100.0       0       0  929.7  21.6  270   14-307     3-273 (297)
  2 pfam01218 Coprogen_oxidas Copr 100.0       0       0  917.8  21.1  264   20-307     2-271 (296)
  3 COG0408 HemF Coproporphyrinoge 100.0       0       0  908.5  19.1  272   13-307     2-279 (303)
  4 KOG1518 consensus              100.0       0       0  806.8  18.2  268   15-306    76-356 (382)
  5 TIGR02169 SMC_prok_A chromosom  63.2    0.61 1.6E-05   26.6  -2.7   72   25-130  1035-1106(1202)
  6 KOG0793 consensus               58.3      12 0.00031   18.3   3.3   58  192-249   868-931 (1004)
  7 TIGR02529 EutJ ethanolamine ut  56.9     6.2 0.00016   20.1   1.6   46   71-123    73-125 (240)
  8 pfam02961 BAF Barrier to autoi  52.3      14 0.00035   17.9   2.8   32  167-198    55-89  (89)
  9 TIGR00759 aceE 2-oxo-acid dehy  51.6     3.5 8.9E-05   21.8  -0.4   36  156-207   668-703 (905)
 10 COG3642 Mn2+-dependent serine/  50.1      16 0.00041   17.4   2.8   36  235-274   166-201 (204)
 11 pfam12268 DUF3612 Protein of u  44.3      11 0.00029   18.4   1.3   34  148-185    92-125 (178)
 12 pfam06319 DUF1052 Protein of u  41.2      15 0.00037   17.7   1.5   23  187-209    79-101 (158)
 13 TIGR01362 KDO8P_synth 3-deoxy-  39.9     8.9 0.00023   19.1   0.2   12  277-288   162-173 (279)
 14 COG5132 BUD31 Cell cycle contr  37.0      11 0.00028   18.5   0.3   56  222-284    11-70  (146)
 15 TIGR02539 SepCysS Sep-tRNA:Cys  34.8      16  0.0004   17.6   0.8   57  172-252   320-380 (381)
 16 KOG0738 consensus               34.1      37 0.00093   15.2   3.3   17   27-43     64-80  (491)
 17 pfam12138 Spherulin4 Spherulat  33.4      34 0.00088   15.3   2.4   31  189-219    82-113 (243)
 18 PHA00028 rep RNA replicase, be  32.9      38 0.00097   15.0   3.4   57  144-204   380-439 (561)
 19 COG2425 Uncharacterized protei  32.8      21 0.00053   16.8   1.1   14  144-157   226-239 (437)
 20 KOG4320 consensus               32.7      17 0.00042   17.4   0.6   23  115-137    99-121 (253)
 21 COG3354 FlaG Putative archaeal  32.3      37 0.00094   15.1   2.4   23   76-98     92-114 (154)
 22 pfam01125 G10 G10 protein.      32.2      38 0.00098   15.0   2.4   52  231-284    16-71  (145)
 23 TIGR02707 butyr_kinase butyrat  31.5      25 0.00064   16.2   1.4   67   25-108   152-219 (353)
 24 KOG4233 consensus               30.8      41   0.001   14.8   2.4   32  167-198    55-89  (90)
 25 COG1103 Archaea-specific pyrid  30.0     5.6 0.00014   20.4  -2.2   63  184-252   318-381 (382)
 26 PHA02087 hypothetical protein   28.3      34 0.00086   15.4   1.6   13  205-217    60-72  (83)
 27 TIGR01975 isoAsp_dipep beta-as  28.2      13 0.00032   18.1  -0.6   54  126-182   217-274 (391)
 28 KOG3410 consensus               27.7      33 0.00084   15.5   1.5   53  242-307    67-119 (120)
 29 PRK10997 yieM hypothetical pro  27.4      17 0.00043   17.3  -0.1   13  146-158   388-400 (484)
 30 PRK09491 rimI ribosomal-protei  26.7      30 0.00077   15.7   1.1   62  235-302    76-144 (144)
 31 KOG0175 consensus               26.1      34 0.00088   15.3   1.3   33  152-184   106-138 (285)
 32 KOG3404 consensus               25.8      22 0.00055   16.6   0.2   14  268-282    55-68  (145)
 33 TIGR01491 HAD-SF-IB-PSPlk Phos  25.3      45  0.0011   14.6   1.8   13  259-271    35-47  (203)
 34 pfam09433 HRP1 THO complex sub  25.2      52  0.0013   14.2   2.5   14  203-216   594-607 (725)
 35 PRK13272 treA trehalase; Provi  23.6      37 0.00095   15.1   1.1   64  145-220   316-392 (537)
 36 pfam04437 RINT1_TIP1 RINT-1 /   23.6      56  0.0014   14.0   4.5   28  175-202   243-272 (485)
 37 COG2075 RPL24A Ribosomal prote  22.6      56  0.0014   14.0   1.9   16   70-85     15-30  (66)
 38 TIGR01263 4HPPD 4-hydroxypheny  22.3      26 0.00067   16.1   0.1   35   74-112    43-83  (379)
 39 KOG3063 consensus               22.3      24 0.00061   16.4  -0.1   27   68-94     46-72  (301)
 40 TIGR00505 ribA GTP cyclohydrol  21.0      31 0.00078   15.7   0.3   11  201-211   108-119 (227)
 41 cd06182 CYPOR_like NADPH cytoc  20.6      64  0.0016   13.6   2.6   39  236-274   225-264 (267)
 42 KOG2305 consensus               20.5      41   0.001   14.8   0.8   15  121-135   138-154 (313)
 43 COG4829 CatC1 Muconolactone de  20.3      25 0.00063   16.2  -0.3   29  268-303    46-74  (98)

No 1  
>PRK05330 coproporphyrinogen III oxidase; Provisional
Probab=100.00  E-value=0  Score=929.67  Aligned_cols=270  Identities=46%  Similarity=0.866  Sum_probs=261.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEECCCEEEEEEEEEEE
Q ss_conf             69999999999999999999999996301022223445665125212317888887775048995059465368877763
Q gi|254781073|r   14 IEERKRISQRKFENLQSIICTEFEKLENEAHENSANRSPKIFTVKHWLRDKSQKEDLGGGRMATLCAGKVFEKAAVLVST   93 (307)
Q Consensus        14 ie~kk~~~~~wF~~LQd~Ic~~fE~lE~~~~~~~~~~~~~~F~~d~W~R~~g~~~~~GGG~s~VL~~G~VFEKaGVNfS~   93 (307)
                      +..++.++++||++||++||++||+||+.          ++|++|.|+|++|     |||+||||++|+||||||||||+
T Consensus         3 ~~~~~~~~~~~f~~LQ~~Ic~~~e~le~~----------~~F~~d~W~r~~g-----GGG~s~vl~~G~vFEKaGVN~S~   67 (297)
T PRK05330          3 MTPDKARVKAWLLGLQDRICAALEALDGP----------ARFVEDSWQRPEG-----GGGRSRVLRNGRVFEKAGVNFSH   67 (297)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCC----------CCEEECCCCCCCC-----CCCEEEEEECCCEEEEEEEEEEE
T ss_conf             76679999999999999999999975088----------8705046515899-----99738998489178850178998


Q ss_pred             EECCCHHHHHHHHHHCCCCCCCEEECEEEEEECCCCCCCHHHCCHHHEEECC-CCCCCCCCCCCCCCHHHCCCHHHHHHH
Q ss_conf             0035426776421110267651000002233136887440102302102024-312532001100000110432679999
Q gi|254781073|r   94 VYGDLSPDFKDQILGTTKNPYFWATGLSVIVHPYNPHVPAVHFNIRMIVTGA-YWFGGGIDLTPSLESRRHSYDPDVIFF  172 (307)
Q Consensus        94 V~G~~~p~~a~~i~g~~~~~~F~AtGiS~V~Hp~nP~vPt~H~N~R~f~~~~-~WFGGG~DLTP~~~~~~y~~~eD~~~f  172 (307)
                      |+|+++|+++.+++++.++++|||||||||+||+||+|||+|||+|||+|++ ||||||+||||+     |+++||+++|
T Consensus        68 V~G~~~p~~a~~~~~~~~~~~F~AtGiSlV~HP~NP~vPt~H~N~R~f~~~~~~WFGGG~DLTP~-----y~~~eD~~~f  142 (297)
T PRK05330         68 VHGEFLPPSATAHRPELAGRSFEATGVSLVAHPRNPYVPTVHMNVRFFKTGPVWWFGGGFDLTPY-----YPFEEDAVHF  142 (297)
T ss_pred             EECCCCHHHHHHCCCCCCCCCEEEECCEEEEECCCCCCCCCCCEEEEEECCCCCEECCCCCCCCC-----CCCHHHHHHH
T ss_conf             63568989997464545788706510126630478888630010589960576243576357777-----6867899999


Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99998403656733428999976787434532521234301010147866658967799999999999999999999875
Q gi|254781073|r  173 HNTLKEMCSQHAVANYTHYKEWCDRYFYLPHRQESRGIGGIFFDHLHSSPEMGGIDADFSFISAVGDCFIKLYPSLVRRN  252 (307)
Q Consensus       173 H~~~k~~Cd~~~~~~Y~~fKk~CD~YFylpHR~E~RGvGGIFFD~l~~~~~~~~~e~~f~f~~~vg~~fl~~y~~Iv~~r  252 (307)
                      |++||++||+|++++|++||||||+|||||||+|+|||||||||||++    ++||++|+|+++||++||++|+|||+||
T Consensus       143 H~~lK~~Cd~~~~~~Y~~fKk~CD~YFylpHR~E~RGiGGIFfD~l~~----~~~~~~f~f~~~vg~~fl~~Y~~Iv~kr  218 (297)
T PRK05330        143 HQTAKDACDPFGPDYYPRFKKWCDEYFYLKHRNEPRGIGGIFFDDLNS----GDFERDFAFTQAVGDAFLDAYLPIVERR  218 (297)
T ss_pred             HHHHHHHHHHHCHHHHHHHHHHHHHHCCCHHCCCCCCCCCEEHHHHCC----CCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999997639677799986404430010026554667143222046----2267779999999999999899999986


Q ss_pred             CCCCCCHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCHHHEEECCCCCCCCC
Q ss_conf             4799998999885420240112211110255357357888111411288878897
Q gi|254781073|r  253 YHHLFSEQDRQEQLIRRGRYAEFNLLYDKGTNFGFKTGGNVESILASMPPLVAWP  307 (307)
Q Consensus       253 ~~~~~~~~~k~~Ql~rRgRYvEFNL~yDRGT~FGL~t~gr~esIl~SlPp~~~Wp  307 (307)
                      ++++||++||+|||+||||||||||||||||+|||+||||||||||||||+|+|+
T Consensus       219 ~~~~~t~~~k~~Ql~rRGRYvEFNLlyDRGT~FGL~tggr~esILmSlPp~a~W~  273 (297)
T PRK05330        219 KDTPYGEREREFQLYRRGRYVEFNLVYDRGTLFGLQTGGRTESILMSLPPLVRWE  273 (297)
T ss_pred             CCCCCCHHHHHHHHHCCCEEEEEEEEEECCCEECCCCCCCHHHHHCCCCCCCEEC
T ss_conf             2587567888788751660389998864686003557996677420499877011


No 2  
>pfam01218 Coprogen_oxidas Coproporphyrinogen III oxidase.
Probab=100.00  E-value=0  Score=917.82  Aligned_cols=264  Identities=44%  Similarity=0.858  Sum_probs=256.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEECCCEEEEEEEEEEEEECCCH
Q ss_conf             99999999999999999996301022223445665125212317888887775048995059465368877763003542
Q gi|254781073|r   20 ISQRKFENLQSIICTEFEKLENEAHENSANRSPKIFTVKHWLRDKSQKEDLGGGRMATLCAGKVFEKAAVLVSTVYGDLS   99 (307)
Q Consensus        20 ~~~~wF~~LQd~Ic~~fE~lE~~~~~~~~~~~~~~F~~d~W~R~~g~~~~~GGG~s~VL~~G~VFEKaGVNfS~V~G~~~   99 (307)
                      ++++||++||++||++||+||++          ++|++|.|+|++|     |||+||||++|+||||||||||+|+|+++
T Consensus         2 ~~e~~f~~lQ~~Ic~~~e~le~~----------~~F~~d~W~r~~g-----GGG~s~vl~~G~vfEKagVN~S~V~G~~~   66 (296)
T pfam01218         2 RVEAYLLGLQDRICAALEAIDGG----------AKFVEDAWERPEG-----GGGRSRVLQDGNVFEKAGVNFSHVHGKLL   66 (296)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCC----------CCCEECCCCCCCC-----CCCEEEEEECCCEEEEEEEEEEEEEECCC
T ss_conf             68999999999999999975288----------8715326615899-----99738998089378850278999530278


Q ss_pred             HHHHHHHHHCCCCCCCEEECEEEEEECCCCCCCHHHCCHHHEEEC------CCCCCCCCCCCCCCCHHHCCCHHHHHHHH
Q ss_conf             677642111026765100000223313688744010230210202------43125320011000001104326799999
Q gi|254781073|r  100 PDFKDQILGTTKNPYFWATGLSVIVHPYNPHVPAVHFNIRMIVTG------AYWFGGGIDLTPSLESRRHSYDPDVIFFH  173 (307)
Q Consensus       100 p~~a~~i~g~~~~~~F~AtGiS~V~Hp~nP~vPt~H~N~R~f~~~------~~WFGGG~DLTP~~~~~~y~~~eD~~~fH  173 (307)
                      |+++.++++..++++|||||||||+||+||+|||+|||+|||++.      .||||||+|||||     |+++||+++||
T Consensus        67 p~~a~~~~~~~~~~~F~AtGiSlV~HP~NP~vPt~H~N~R~f~~~~~~~~~~wWFGGG~DLTP~-----y~~~eD~~~fH  141 (296)
T pfam01218        67 PASATAMRPELAGRPFQAMGVSLVIHPRNPYVPTVHANVRYFIAEKEGEEPVWWFGGGFDLTPY-----YGFEEDAVHFH  141 (296)
T ss_pred             HHHHHHCCCCCCCCCEEECCCEEEEECCCCCCCCEEEEEEEEEEECCCCCCCEEECCCCCCCCC-----CCCHHHHHHHH
T ss_conf             8899746433367760321222666427988763020068999745888764255465357777-----68778999999


Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99984036567334289999767874345325212343010101478666589677999999999999999999998754
Q gi|254781073|r  174 NTLKEMCSQHAVANYTHYKEWCDRYFYLPHRQESRGIGGIFFDHLHSSPEMGGIDADFSFISAVGDCFIKLYPSLVRRNY  253 (307)
Q Consensus       174 ~~~k~~Cd~~~~~~Y~~fKk~CD~YFylpHR~E~RGvGGIFFD~l~~~~~~~~~e~~f~f~~~vg~~fl~~y~~Iv~~r~  253 (307)
                      ++||++||+|+++||++||||||+|||||||+|+|||||||||||++    +++|++|+|+++||++||++|.|||+||+
T Consensus       142 ~~lK~~Cd~~~~~~Y~~fKk~CD~YFyipHR~E~RGiGGIFfD~l~~----~~~~~~f~f~~~vg~~fl~~Y~~Iv~kr~  217 (296)
T pfam01218       142 QTAKDACDPFGPDYYPRFKKWCDEYFYLKHRNEPRGVGGIFFDDLNE----GDFERSFAFVQSVGDAFLPAYLPIVERRK  217 (296)
T ss_pred             HHHHHHHHHHCHHHHHHHHHHHHHHCCHHHCCCCCCCCCEEHHHCCC----CCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999987628677899997756631213215554667144122046----35778999999999998888999999852


Q ss_pred             CCCCCHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCHHHEEECCCCCCCCC
Q ss_conf             799998999885420240112211110255357357888111411288878897
Q gi|254781073|r  254 HHLFSEQDRQEQLIRRGRYAEFNLLYDKGTNFGFKTGGNVESILASMPPLVAWP  307 (307)
Q Consensus       254 ~~~~~~~~k~~Ql~rRgRYvEFNL~yDRGT~FGL~t~gr~esIl~SlPp~~~Wp  307 (307)
                      +++||++||+|||+||||||||||||||||+|||+||||||||||||||+|+|.
T Consensus       218 ~~~~t~~~k~~Ql~rRGRYvEFNLlyDRGT~FGL~t~Gr~esILmSlPp~~~W~  271 (296)
T pfam01218       218 DTPYGEREREFQLYRRGRYVEFNLVYDRGTLFGLQTGGRTESILMSLPPLARWE  271 (296)
T ss_pred             CCCCCHHHHHHHHHHCCEEEEEEEEEECCCHHCCCCCCCCCEEEECCCCCCCCC
T ss_conf             587677888788760752479998863686110547996001344489877111


No 3  
>COG0408 HemF Coproporphyrinogen III oxidase [Coenzyme metabolism]
Probab=100.00  E-value=0  Score=908.49  Aligned_cols=272  Identities=47%  Similarity=0.902  Sum_probs=264.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEECCCEEEEEEEEEE
Q ss_conf             66999999999999999999999999630102222344566512521231788888777504899505946536887776
Q gi|254781073|r   13 DIEERKRISQRKFENLQSIICTEFEKLENEAHENSANRSPKIFTVKHWLRDKSQKEDLGGGRMATLCAGKVFEKAAVLVS   92 (307)
Q Consensus        13 ~ie~kk~~~~~wF~~LQd~Ic~~fE~lE~~~~~~~~~~~~~~F~~d~W~R~~g~~~~~GGG~s~VL~~G~VFEKaGVNfS   92 (307)
                      +++.+++.+++||++|||+||++||+||+++          +|.+|.|+|++++    |||++|||++|.||||+|||||
T Consensus         2 ~~~~~~~~~~~~~~~Lqd~Ic~~le~~dg~~----------~F~~d~W~r~~g~----GgG~~~vl~~G~vFEk~GVn~S   67 (303)
T COG0408           2 DIEPDKQAVKAWLLNLQDEICAALEALDGEA----------KFVEDSWQREEGG----GGGRSRVLMDGAVFEKGGVNFS   67 (303)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCE----------EEECCCCCCCCCC----CCCEEEEEECCCEEEECCCEEE
T ss_conf             8522899999999999999999998526640----------6740322246898----8872588722734663372158


Q ss_pred             EEECCCHHHHHHHHHHCCCCCCCEEECEEEEEECCCCCCCHHHCCHHHEEECC------CCCCCCCCCCCCCCHHHCCCH
Q ss_conf             30035426776421110267651000002233136887440102302102024------312532001100000110432
Q gi|254781073|r   93 TVYGDLSPDFKDQILGTTKNPYFWATGLSVIVHPYNPHVPAVHFNIRMIVTGA------YWFGGGIDLTPSLESRRHSYD  166 (307)
Q Consensus        93 ~V~G~~~p~~a~~i~g~~~~~~F~AtGiS~V~Hp~nP~vPt~H~N~R~f~~~~------~WFGGG~DLTP~~~~~~y~~~  166 (307)
                      +|+|+++|+++++++++.++++|||||||||+||+||+|||+|||+|||+|.+      ||||||+||||+     |+++
T Consensus        68 ~V~G~~~P~~~~~~rp~~~g~~F~A~GiSlV~HP~NP~vPt~H~N~R~f~a~~~~~~~vwWFGGG~DLTP~-----y~~~  142 (303)
T COG0408          68 TVFGEFSPESATAMRPELAGRRFFATGISLVAHPKNPYVPTVHLNVRYFEAEKPGAEPVWWFGGGADLTPY-----YGFE  142 (303)
T ss_pred             EEECCCCCHHHHHCCCHHCCCCEEEEEEEEEEECCCCCCCCEEEEEEEEEEECCCCCCCEEECCCCCCCCC-----CCCH
T ss_conf             87446680787638830028863653116997258999874231478999745888754565477567545-----6623


Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             67999999998403656733428999976787434532521234301010147866658967799999999999999999
Q gi|254781073|r  167 PDVIFFHNTLKEMCSQHAVANYTHYKEWCDRYFYLPHRQESRGIGGIFFDHLHSSPEMGGIDADFSFISAVGDCFIKLYP  246 (307)
Q Consensus       167 eD~~~fH~~~k~~Cd~~~~~~Y~~fKk~CD~YFylpHR~E~RGvGGIFFD~l~~~~~~~~~e~~f~f~~~vg~~fl~~y~  246 (307)
                      ||++|||+++|.+||+|+.++||+||+|||||||||||||+|||||||||||++.    +|+.+|+|+++||++||++|+
T Consensus       143 eD~~hfH~~~k~aC~~~~~~~YprfK~WCDeYFyLkHR~E~RGiGGiFfD~l~~~----~~~~~Faf~qdvG~afl~aY~  218 (303)
T COG0408         143 EDAVHFHRAAKDACDPHGPEDYPRFKKWCDEYFYLKHRNEPRGIGGIFFDDLNEP----DFERDFAFTQDVGKAFLPAYL  218 (303)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHEEECCCCCCCCCCEEECCCCCCC----CHHHHHHHHHHHHHHHHHHHH
T ss_conf             6779999999997531782340688876355433014677777650531335678----989989999998777766437


Q ss_pred             HHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCHHHEEECCCCCCCCC
Q ss_conf             9998754799998999885420240112211110255357357888111411288878897
Q gi|254781073|r  247 SLVRRNYHHLFSEQDRQEQLIRRGRYAEFNLLYDKGTNFGFKTGGNVESILASMPPLVAWP  307 (307)
Q Consensus       247 ~Iv~~r~~~~~~~~~k~~Ql~rRgRYvEFNL~yDRGT~FGL~t~gr~esIl~SlPp~~~Wp  307 (307)
                      |||++|++++||++||+||||||||||||||||||||+||||||||+|||||||||+|+||
T Consensus       219 pIV~~r~~~~~te~er~fQl~RRGRYVEFNLvyDRGT~FGLqTgGr~ESILmSlPP~vrW~  279 (303)
T COG0408         219 PIVERRKNMPWTEREREFQLYRRGRYVEFNLVYDRGTLFGLQTGGRVESILMSLPPLVRWE  279 (303)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHCCCEEEEEEEEECCCEEEECCCCCHHHHHHCCCCCCCCC
T ss_conf             9998743899865677788886153379998874463675126973655764299534256


No 4  
>KOG1518 consensus
Probab=100.00  E-value=0  Score=806.83  Aligned_cols=268  Identities=43%  Similarity=0.810  Sum_probs=253.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEECCCEEEEEEEEEEEE
Q ss_conf             99999999999999999999999963010222234456651252123178888877750489950594653688777630
Q gi|254781073|r   15 EERKRISQRKFENLQSIICTEFEKLENEAHENSANRSPKIFTVKHWLRDKSQKEDLGGGRMATLCAGKVFEKAAVLVSTV   94 (307)
Q Consensus        15 e~kk~~~~~wF~~LQd~Ic~~fE~lE~~~~~~~~~~~~~~F~~d~W~R~~g~~~~~GGG~s~VL~~G~VFEKaGVNfS~V   94 (307)
                      +.-+.+.+...+..|.+||+++|++|+.          .+|.+|.|+|++|     |||+||||+||+||||||||+|.|
T Consensus        76 ~~ir~~mE~lI~~~Qaevc~aleaidgg----------~kF~~D~W~r~eG-----GgGiscVlQDG~vFEKaGVnvSVV  140 (382)
T KOG1518          76 SSIRAQMETLIREAQAEVCQALEAIDGG----------QKFKVDRWTRGEG-----GGGISCVLQDGNVFEKAGVNVSVV  140 (382)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCC----------CCCCEEEEECCCC-----CCCEEEEECCCCEEECCCCEEEEE
T ss_conf             7799999999999999999999874066----------5310222102789-----875279970687632177268999


Q ss_pred             ECCCHHHHHHHHHHCCC------CCCCEEECEEEEEECCCCCCCHHHCCHHHEEEC------CCCCCCCCCCCCCCCHHH
Q ss_conf             03542677642111026------765100000223313688744010230210202------431253200110000011
Q gi|254781073|r   95 YGDLSPDFKDQILGTTK------NPYFWATGLSVIVHPYNPHVPAVHFNIRMIVTG------AYWFGGGIDLTPSLESRR  162 (307)
Q Consensus        95 ~G~~~p~~a~~i~g~~~------~~~F~AtGiS~V~Hp~nP~vPt~H~N~R~f~~~------~~WFGGG~DLTP~~~~~~  162 (307)
                      +|.++|++..++++..+      ..+|+|+|||.||||+||++||+|+|||||+|.      .||||||+||||+     
T Consensus       141 ~G~l~p~Av~~mra~~k~lk~~~~lpFfA~GvS~ViHP~NPhaPT~HfNYRYFE~~~~dg~kqWWFGGG~DlTPs-----  215 (382)
T KOG1518         141 YGVLPPEAVQAMRARHKNLKPTGPLPFFAAGVSSVIHPKNPHAPTTHFNYRYFETENADGVKQWWFGGGADLTPS-----  215 (382)
T ss_pred             ECCCCHHHHHHHHHCCCCCCCCCCCCEEECCCEEEECCCCCCCCCEEEEEEEEEEECCCCCEEEEECCCCCCCHH-----
T ss_conf             444899999998722357777898754631520222268999873332026788754888377776578668715-----


Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             04326799999999840365673342899997678743453252123430101014786665896779999999999999
Q gi|254781073|r  163 HSYDPDVIFFHNTLKEMCSQHAVANYTHYKEWCDRYFYLPHRQESRGIGGIFFDHLHSSPEMGGIDADFSFISAVGDCFI  242 (307)
Q Consensus       163 y~~~eD~~~fH~~~k~~Cd~~~~~~Y~~fKk~CD~YFylpHR~E~RGvGGIFFD~l~~~~~~~~~e~~f~f~~~vg~~fl  242 (307)
                      |+++||++|||+.+|+|||+||+++||+||||||+||||+||+|+|||||||||||++.    |.|..|+||++|+.+|+
T Consensus       216 yl~eeD~~hFH~~~K~AcD~hdp~~YPrFKKWcDdYF~IkHR~E~RGiGGIFFDDld~~----d~ee~f~fv~~Ca~avv  291 (382)
T KOG1518         216 YLFEEDGKHFHQLHKEACDKHDPTFYPRFKKWCDDYFYIKHRKERRGIGGIFFDDLDEP----DPEELFSFVTDCARAVV  291 (382)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHEEEEECCCCCCCCCEECCCCCCC----CHHHHHHHHHHHHHHHC
T ss_conf             65334579999999987632497533567765123256420465456663522557888----99999999999887534


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCC-CHHHEEECCCCCCCC
Q ss_conf             9999999875479999899988542024011221111025535735788-811141128887889
Q gi|254781073|r  243 KLYPSLVRRNYHHLFSEQDRQEQLIRRGRYAEFNLLYDKGTNFGFKTGG-NVESILASMPPLVAW  306 (307)
Q Consensus       243 ~~y~~Iv~~r~~~~~~~~~k~~Ql~rRgRYvEFNL~yDRGT~FGL~t~g-r~esIl~SlPp~~~W  306 (307)
                      |+|+|||+||++++||+++|+||++||||||||||+|||||+|||+|.| |+||||||||..|+|
T Consensus       292 PsYipiv~krkdmeft~~ek~wQ~lRRGrYvEFNliYDRGT~FGL~tpgsRiESILmsLPlha~w  356 (382)
T KOG1518         292 PSYIPIVEKRKDMEFTEQEKQWQQLRRGRYVEFNLIYDRGTKFGLKTPGSRIESILMSLPLHASW  356 (382)
T ss_pred             CCCCHHHHHHCCCCCCHHHHHHHHHHCCCEEEEEEEEECCCEEECCCCCCHHHHHHHCCCCHHHH
T ss_conf             42204666505777674689999985053378999873574331347861067676436101102


No 5  
>TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression .    This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent ..
Probab=63.23  E-value=0.61  Score=26.63  Aligned_cols=72  Identities=19%  Similarity=0.320  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEEEEEECCCEEEEEEEEEEEEECCCHHHHHH
Q ss_conf             99999999999999630102222344566512521231788888777504899505946536887776300354267764
Q gi|254781073|r   25 FENLQSIICTEFEKLENEAHENSANRSPKIFTVKHWLRDKSQKEDLGGGRMATLCAGKVFEKAAVLVSTVYGDLSPDFKD  104 (307)
Q Consensus        25 F~~LQd~Ic~~fE~lE~~~~~~~~~~~~~~F~~d~W~R~~g~~~~~GGG~s~VL~~G~VFEKaGVNfS~V~G~~~p~~a~  104 (307)
                      +..-+..|-..++.+|....                               .|.+  .+|+..--||+.|++.++|+=..
T Consensus      1035 L~~Er~~i~~rI~~~e~~Kr-------------------------------~~F~--~aF~~IN~~f~~iF~~LSP~G~g 1081 (1202)
T TIGR02169      1035 LEEEREEILERIEEYEKKKR-------------------------------EVFM--EAFEAINENFKEIFAELSPGGTG 1081 (1202)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-------------------------------HHHH--HHHHHHHHHHHHHHHHHCCCCCE
T ss_conf             99989999999999887889-------------------------------9999--99999999999999853889824


Q ss_pred             HHHHCCCCCCCEEECEEEEEECCCCC
Q ss_conf             21110267651000002233136887
Q gi|254781073|r  105 QILGTTKNPYFWATGLSVIVHPYNPH  130 (307)
Q Consensus       105 ~i~g~~~~~~F~AtGiS~V~Hp~nP~  130 (307)
                      ..-=..-+-|| +.||-|++||++=-
T Consensus      1082 ~L~Le~PdDPF-~GGl~l~a~P~~K~ 1106 (1202)
T TIGR02169      1082 ELILENPDDPF-AGGLELKAKPKGKP 1106 (1202)
T ss_pred             EEECCCCCCCC-CCCCEEEEEECCCC
T ss_conf             65435888743-68717888737885


No 6  
>KOG0793 consensus
Probab=58.26  E-value=12  Score=18.26  Aligned_cols=58  Identities=19%  Similarity=0.431  Sum_probs=33.4

Q ss_pred             HHHHHHH----HHHHHH--CCCCCCCCEEHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9976787----434532--521234301010147866658967799999999999999999999
Q gi|254781073|r  192 KEWCDRY----FYLPHR--QESRGIGGIFFDHLHSSPEMGGIDADFSFISAVGDCFIKLYPSLV  249 (307)
Q Consensus       192 Kk~CD~Y----FylpHR--~E~RGvGGIFFD~l~~~~~~~~~e~~f~f~~~vg~~fl~~y~~Iv  249 (307)
                      --|||+|    |||+.-  +|+|-|--..|=-+....-...--..++|-+.|-++|-.---|||
T Consensus       868 HIWceDfLVRSFYLKNlqtseTRTvTQFHfLSWp~egvPasarslLdFRRKVNK~YRGRScpIi  931 (1004)
T KOG0793         868 HIWCEDFLVRSFYLKNLQTSETRTVTQFHFLSWPDEGVPASARSLLDFRRKVNKCYRGRSCPII  931 (1004)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf             4303467899999853133552135544541254568863137899999885242157778669


No 7  
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein; InterPro: IPR013366    Salmonella typhimurium is capable of growth on ethanolamine as a sole source of carbon nitrogen and energy . During growth on this compound the cells form a multimolecular structure known as a metabolosome, which is similar to the carboxysome used by some photosynthetic bacteria to fix CO2, and is thought to contain the enzymes needed to metabolise this compound to acetyl-CoA. The metabolosome is not directly involved in the biochemistry of ethanolamine utilization - instead its role is thought to be to concentrate the enzymes involved in this process, while also protecting the cell from the build-up of toxic intermediates . The genes involved in growth on ethanolamine are encoded in a 17-gene operon known as the ethanolamine utilization (eut) operon. EutJ shows similarity to chaperonins and may play a role in assembly of the metabolosme , though it is not necessary for growth on this compound..
Probab=56.85  E-value=6.2  Score=20.13  Aligned_cols=46  Identities=24%  Similarity=0.387  Sum_probs=31.6

Q ss_pred             CCEEEEEEECCCEEEEEEEEEEEEECCCHHHHHHHHHHC-------CCCCCCEEECEEEE
Q ss_conf             750489950594653688777630035426776421110-------26765100000223
Q gi|254781073|r   71 GGGRMATLCAGKVFEKAAVLVSTVYGDLSPDFKDQILGT-------TKNPYFWATGLSVI  123 (307)
Q Consensus        71 GGG~s~VL~~G~VFEKaGVNfS~V~G~~~p~~a~~i~g~-------~~~~~F~AtGiS~V  123 (307)
                      ++|-.+++-  +|+|-||..+++|-=  -|.+++.....       ..+.   -||||++
T Consensus        73 ~~~~~k~~v--NV~EsAG~eV~~V~D--EPTAAa~vL~i~nG~VVDvGGG---TTGiSI~  125 (240)
T TIGR02529        73 EEGDVKVIV--NVVESAGIEVLKVLD--EPTAAAAVLQIKNGAVVDVGGG---TTGISIL  125 (240)
T ss_pred             CCCCEEEEE--EEEECCCEEEEEEEC--CHHHHHHHHCCCCCEEEEECCC---CEEEEEE
T ss_conf             889758999--987225615766514--2789998728857279984788---0335799


No 8  
>pfam02961 BAF Barrier to autointegration factor. The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration.
Probab=52.33  E-value=14  Score=17.88  Aligned_cols=32  Identities=34%  Similarity=0.728  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHH
Q ss_conf             679999999984036567---33428999976787
Q gi|254781073|r  167 PDVIFFHNTLKEMCSQHA---VANYTHYKEWCDRY  198 (307)
Q Consensus       167 eD~~~fH~~~k~~Cd~~~---~~~Y~~fKk~CD~Y  198 (307)
                      .|-..|-.-+|++|....   .+-|.-.|.|||+.
T Consensus        55 kde~~F~~Wlk~~~gAn~kQa~dcy~cLkeWCd~F   89 (89)
T pfam02961        55 KDEELFKEWLKDTCGANAKQARDCYNCLKEWCSCF   89 (89)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             64999999999980888889988999999998629


No 9  
>TIGR00759 aceE 2-oxo-acid dehydrogenase E1 component, homodimeric type; InterPro: IPR004660   Most members of this family are pyruvate dehydrogenase complex, E1 component. It includes a counterexample from Pseudomonas putida, MdeB, that is active as an E1 component of an alpha-ketoglutarate dehydrogenase complex rather than a pyruvate dehydrogenase complex. The second pyruvate dehydrogenase complex E1 protein from Alcaligenes eutrophus, PdhE, complements an aceE mutant of Escherichia coli but is not part of a pyruvate dehydrogenase complex operon, is more similar to the Pseudomonas putida MdeB than to E. coli AceE, and may have also have a different primary specificity. ; GO: 0016491 oxidoreductase activity.
Probab=51.60  E-value=3.5  Score=21.75  Aligned_cols=36  Identities=19%  Similarity=0.520  Sum_probs=29.4

Q ss_pred             CCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             0000011043267999999998403656733428999976787434532521
Q gi|254781073|r  156 PSLESRRHSYDPDVIFFHNTLKEMCSQHAVANYTHYKEWCDRYFYLPHRQES  207 (307)
Q Consensus       156 P~~~~~~y~~~eD~~~fH~~~k~~Cd~~~~~~Y~~fKk~CD~YFylpHR~E~  207 (307)
                      |+     |-|+ =++-++..++.+|-.-          .||.||||.=-||.
T Consensus       668 Pa-----FAyE-vAVI~~~Gl~RMy~E~----------qed~FyY~Tv~NE~  703 (905)
T TIGR00759       668 PA-----FAYE-VAVIMEDGLRRMYGEK----------QEDVFYYVTVLNEN  703 (905)
T ss_pred             CC-----HHHH-HHHHHHHHHHHHCCCC----------CCCEEEEEEEECCC
T ss_conf             51-----0233-6787877897323667----------44224766450578


No 10 
>COG3642 Mn2+-dependent serine/threonine protein kinase [Signal transduction mechanisms]
Probab=50.13  E-value=16  Score=17.44  Aligned_cols=36  Identities=25%  Similarity=0.358  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHH
Q ss_conf             9999999999999998754799998999885420240112
Q gi|254781073|r  235 SAVGDCFIKLYPSLVRRNYHHLFSEQDRQEQLIRRGRYAE  274 (307)
Q Consensus       235 ~~vg~~fl~~y~~Iv~~r~~~~~~~~~k~~Ql~rRgRYvE  274 (307)
                      ..+-..|+..|...+....    .-.++---.-+||||||
T Consensus       166 e~l~~~f~~gY~~~~~~~~----~Vl~~~~eIr~RgRYve  201 (204)
T COG3642         166 EELFAAFLEGYREEFGEAK----EVLERLEEIRLRGRYVE  201 (204)
T ss_pred             HHHHHHHHHHHHHHHCCHH----HHHHHHHHHHHHCCCCC
T ss_conf             9999999999998750289----99999999997233000


No 11 
>pfam12268 DUF3612 Protein of unknown function (DUF3612). This domain family is found in bacteria, and is approximately 180 amino acids in length. The family is found in association with pfam01381.
Probab=44.32  E-value=11  Score=18.41  Aligned_cols=34  Identities=29%  Similarity=0.572  Sum_probs=25.9

Q ss_pred             CCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             25320011000001104326799999999840365673
Q gi|254781073|r  148 FGGGIDLTPSLESRRHSYDPDVIFFHNTLKEMCSQHAV  185 (307)
Q Consensus       148 FGGG~DLTP~~~~~~y~~~eD~~~fH~~~k~~Cd~~~~  185 (307)
                      .--|.||.|.++.+.    -|+..--+.+|+.|-+.+.
T Consensus        92 lcaGIDLnPAi~aQG----~Da~~ia~~lk~~Cv~~gG  125 (178)
T pfam12268        92 LCAGIDLNPAIEAQG----GDALALAQELKSACVSNGG  125 (178)
T ss_pred             EEECCCCCHHHHHCC----CCHHHHHHHHHHHHHHCCC
T ss_conf             884235534676448----8999999999999983799


No 12 
>pfam06319 DUF1052 Protein of unknown function (DUF1052). This family consists of several bacterial proteins of unknown function.
Probab=41.17  E-value=15  Score=17.72  Aligned_cols=23  Identities=26%  Similarity=0.663  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             42899997678743453252123
Q gi|254781073|r  187 NYTHYKEWCDRYFYLPHRQESRG  209 (307)
Q Consensus       187 ~Y~~fKk~CD~YFylpHR~E~RG  209 (307)
                      -.+.|-.|||.|||--+-+=+..
T Consensus        79 KW~~Yl~~CDrfffAV~~~fP~d  101 (158)
T pfam06319        79 KWPEYRLHCDRLFFATHPDVPLE  101 (158)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             61678999887875168899802


No 13 
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase; InterPro: IPR006269   These sequences describe 2-dehydro-3-deoxyphosphooctonate aldolase. Alternate names include 3-deoxy-d-manno-octulosonic acid 8-phosphate and KDO-8 phosphate synthetase. It catalyzes the aldol condensation of phosphoenolpyruvate with D-arabinose 5-phosphate.   phosphoenolpyruvate + D-arabinose 5-phosphate + H_2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate    In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide. ; GO: 0008676 3-deoxy-8-phosphooctulonate synthase activity, 0008152 metabolic process, 0005737 cytoplasm.
Probab=39.85  E-value=8.9  Score=19.11  Aligned_cols=12  Identities=50%  Similarity=1.176  Sum_probs=8.7

Q ss_pred             HHHCCCCCCCCC
Q ss_conf             111025535735
Q gi|254781073|r  277 LLYDKGTNFGFK  288 (307)
Q Consensus       277 L~yDRGT~FGL~  288 (307)
                      ||.+|||.||-+
T Consensus       162 ~lcERG~~FGYn  173 (279)
T TIGR01362       162 LLCERGTSFGYN  173 (279)
T ss_pred             EEEECCCCCCCC
T ss_conf             586178888887


No 14 
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=37.01  E-value=11  Score=18.49  Aligned_cols=56  Identities=21%  Similarity=0.297  Sum_probs=28.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHH---HHHH-CCCCCHHHHHHHHCCCCC
Q ss_conf             66589677999999999999999999998754799998999---8854-202401122111102553
Q gi|254781073|r  222 PEMGGIDADFSFISAVGDCFIKLYPSLVRRNYHHLFSEQDR---QEQL-IRRGRYAEFNLLYDKGTN  284 (307)
Q Consensus       222 ~~~~~~e~~f~f~~~vg~~fl~~y~~Iv~~r~~~~~~~~~k---~~Ql-~rRgRYvEFNL~yDRGT~  284 (307)
                      +.++.||+.--++.+.-...-+     +++.+..+ +..|.   -||| ..|.||+ +||-|-||..
T Consensus        11 p~PdgFeki~ptL~~fe~~mRq-----aen~~~~~-sk~E~lwpIfQLHHQRSRYI-Y~LyyKR~aI   70 (146)
T COG5132          11 PAPDGFEKIRPTLEKFEAEMRQ-----AENAPLAP-SKPENLWPIFQLHHQRSRYI-YNLYYKRGAI   70 (146)
T ss_pred             CCCCCHHHHCCHHHHHHHHHHH-----HHCCCCCC-CCHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
T ss_conf             9996354524359999999998-----75277789-97677669999987655788-8878655167


No 15 
>TIGR02539 SepCysS Sep-tRNA:Cys-tRNA synthase; InterPro: IPR013375   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 .    Many archaeal species lack cysteinyl-tRNA synthetase, an essential enzyme that provides Cys-tRNA(Cys) in other organisms. Instead, in a two step pathway, tRNA-Cys is acylated with O-phosphoserine (Sep) to form Sep-tRNA(Cys), which is subsequently converted to Cys-tRNA(Cys) . This pathway is also thought to function as the sole route of cysteine biosynthesis in these organisms. Several other archaeal species use both this pathway and direct tRNA(Cys) aminoacylation to synthesize Cys-tRNA(Cys), but this pathway appears to be the only route for cysteine biosynthesis. Proteins in this entry catalyse the second step in this pathway using pyridoxal phosphate and a sulphur donor to synthesize Cys from Sep while attached to the tRNA..
Probab=34.81  E-value=16  Score=17.55  Aligned_cols=57  Identities=23%  Similarity=0.343  Sum_probs=34.5

Q ss_pred             HHHHHHHHCCCCCHH---HHHHHHHHHHHHHHHHHHCCCCCCCCEEHHCCCCCCCCCCH-HHHHHHHHHHHHHHHHHHHH
Q ss_conf             999998403656733---42899997678743453252123430101014786665896-77999999999999999999
Q gi|254781073|r  172 FHNTLKEMCSQHAVA---NYTHYKEWCDRYFYLPHRQESRGIGGIFFDHLHSSPEMGGI-DADFSFISAVGDCFIKLYPS  247 (307)
Q Consensus       172 fH~~~k~~Cd~~~~~---~Y~~fKk~CD~YFylpHR~E~RGvGGIFFD~l~~~~~~~~~-e~~f~f~~~vg~~fl~~y~~  247 (307)
                      ||..+++.    .+.   +|.+.||              |||.||      ....+.-+ -..|-+.++=-..+.+|+.+
T Consensus       320 f~Eia~~~----kr~GyFLY~ELKk--------------Rgi~GI------~~G~Tk~~K~SvYGL~~Eqv~~Vv~sf~e  375 (381)
T TIGR02539       320 FHEIAKKH----KRRGYFLYEELKK--------------RGIVGI------RSGQTKEIKLSVYGLTKEQVEYVVDSFKE  375 (381)
T ss_pred             CHHHHCCC----CCCCCCHHHHHHH--------------CCCEEC------CCCCCEEEEEEEECCCCCHHHHHHHHHHH
T ss_conf             01341448----7977640566531--------------583001------78874277643312752114444678999


Q ss_pred             HHHHH
Q ss_conf             99875
Q gi|254781073|r  248 LVRRN  252 (307)
Q Consensus       248 Iv~~r  252 (307)
                      |+++.
T Consensus       376 I~e~~  380 (381)
T TIGR02539       376 IVEEY  380 (381)
T ss_pred             HHHHC
T ss_conf             99854


No 16 
>KOG0738 consensus
Probab=34.07  E-value=37  Score=15.16  Aligned_cols=17  Identities=18%  Similarity=0.358  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHHHHC
Q ss_conf             99999999999963010
Q gi|254781073|r   27 NLQSIICTEFEKLENEA   43 (307)
Q Consensus        27 ~LQd~Ic~~fE~lE~~~   43 (307)
                      .+-++|...++.++-..
T Consensus        64 e~vk~i~~~~~~~~~a~   80 (491)
T KOG0738          64 ELVKQIVRDLRDLKEAS   80 (491)
T ss_pred             HHHHHHHHHHHHHCCCC
T ss_conf             99999987788612102


No 17 
>pfam12138 Spherulin4 Spherulation-specific family 4. This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 250 and 398 amino acids in length. There is a conserved NPG sequence motif and there are two completely conserved G residues that may be functionally important. Starvation will often induce spherulation - the production of spores - and this process may involve DNA-methylation. Changes in the methylation of spherulin4 are associated with the formation of spherules, but these changes are probably transient. Methylation of the gene accompanies its transcriptional activation, and spherulin4 mRNA is only detectable in late spherulating cultures and mature spherules. It is a spherulation-specific protein.
Probab=33.38  E-value=34  Score=15.33  Aligned_cols=31  Identities=26%  Similarity=0.404  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHHHCC-CCCCCCEEHHCCC
Q ss_conf             899997678743453252-1234301010147
Q gi|254781073|r  189 THYKEWCDRYFYLPHRQE-SRGIGGIFFDHLH  219 (307)
Q Consensus       189 ~~fKk~CD~YFylpHR~E-~RGvGGIFFD~l~  219 (307)
                      ..-++.-|.|.-.+-+-+ .=+|+|||||..-
T Consensus        82 ~~v~~di~~y~~W~~~~~~~~~v~GiF~DE~p  113 (243)
T pfam12138        82 SEVLADIDTYAGWPSQSATGYGVDGIFLDETP  113 (243)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEECCCC
T ss_conf             99998799985155405756344438962687


No 18 
>PHA00028 rep RNA replicase, beta subunit
Probab=32.88  E-value=38  Score=15.04  Aligned_cols=57  Identities=30%  Similarity=0.540  Sum_probs=41.1

Q ss_pred             CCCCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             243125320011000001104326799999999840365---6733428999976787434532
Q gi|254781073|r  144 GAYWFGGGIDLTPSLESRRHSYDPDVIFFHNTLKEMCSQ---HAVANYTHYKEWCDRYFYLPHR  204 (307)
Q Consensus       144 ~~~WFGGG~DLTP~~~~~~y~~~eD~~~fH~~~k~~Cd~---~~~~~Y~~fKk~CD~YFylpHR  204 (307)
                      ++.||- |.|.||++..+.--...|....-+.++-.-+.   -++-+|+-+.|-||   .||-.
T Consensus       380 GaH~f~-gvDVtPFYik~pi~~l~dlililN~l~~W~~v~Gi~dPr~~~v~~ky~~---liP~~  439 (561)
T PHA00028        380 GAHYFA-GVDVTPFYIKRPLDNLPDLILILNSLRRWGTVTGISDPRLYPLYNKYRD---LIPKT  439 (561)
T ss_pred             HHHHCC-CCCCCCEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH---HCCCC
T ss_conf             032216-7566535862554688999999986313012466467304999999998---68874


No 19 
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=32.81  E-value=21  Score=16.76  Aligned_cols=14  Identities=21%  Similarity=0.126  Sum_probs=8.7

Q ss_pred             CCCCCCCCCCCCCC
Q ss_conf             24312532001100
Q gi|254781073|r  144 GAYWFGGGIDLTPS  157 (307)
Q Consensus       144 ~~~WFGGG~DLTP~  157 (307)
                      +..|+++=.+|-|.
T Consensus       226 ~i~~~~~l~~Llp~  239 (437)
T COG2425         226 GITQSDDLLRLLPI  239 (437)
T ss_pred             CHHHCCHHHCCCCH
T ss_conf             20001044314907


No 20 
>KOG4320 consensus
Probab=32.70  E-value=17  Score=17.37  Aligned_cols=23  Identities=30%  Similarity=0.205  Sum_probs=21.2

Q ss_pred             CEEECEEEEEECCCCCCCHHHCC
Q ss_conf             10000022331368874401023
Q gi|254781073|r  115 FWATGLSVIVHPYNPHVPAVHFN  137 (307)
Q Consensus       115 F~AtGiS~V~Hp~nP~vPt~H~N  137 (307)
                      +-|.|+|+|+|-.-+.++.+|+-
T Consensus        99 ~aalgl~vVaNfQet~i~~VH~~  121 (253)
T KOG4320          99 AAALGLSVVANFQETAIRIVHDI  121 (253)
T ss_pred             HHHHHHEEEEECCCCCCHHHHHH
T ss_conf             99853013450545430222323


No 21 
>COG3354 FlaG Putative archaeal flagellar protein G [Cell motility and secretion]
Probab=32.30  E-value=37  Score=15.14  Aligned_cols=23  Identities=26%  Similarity=0.371  Sum_probs=20.4

Q ss_pred             EEEECCCEEEEEEEEEEEEECCC
Q ss_conf             99505946536887776300354
Q gi|254781073|r   76 ATLCAGKVFEKAAVLVSTVYGDL   98 (307)
Q Consensus        76 ~VL~~G~VFEKaGVNfS~V~G~~   98 (307)
                      -||-||++.+++.|+|++|-|.-
T Consensus        92 tVliDG~iv~~a~~~~~~~~gs~  114 (154)
T COG3354          92 TVLIDGNIVTPAYVTFTSVNGSS  114 (154)
T ss_pred             EEEECCCEECCCEEEEEECCCCE
T ss_conf             99985858235237999439975


No 22 
>pfam01125 G10 G10 protein.
Probab=32.22  E-value=38  Score=15.02  Aligned_cols=52  Identities=17%  Similarity=0.210  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH---HH-CCCCCHHHHHHHHCCCCC
Q ss_conf             9999999999999999999875479999899988---54-202401122111102553
Q gi|254781073|r  231 FSFISAVGDCFIKLYPSLVRRNYHHLFSEQDRQE---QL-IRRGRYAEFNLLYDKGTN  284 (307)
Q Consensus       231 f~f~~~vg~~fl~~y~~Iv~~r~~~~~~~~~k~~---Ql-~rRgRYvEFNL~yDRGT~  284 (307)
                      |+.++++-..|-.-...+...-.. .=...|-.|   |+ ..|.||| |+|-|.|-..
T Consensus        16 ~~~Ie~tL~e~~~kmr~a~~~~~~-~k~k~e~lWpI~rI~hqrsRYI-ydlyYk~k~I   71 (145)
T pfam01125        16 FDKIEPTLDEFEAKMRDAENEPHE-GKRKKEALWPIFRIHHQRSRYI-YDLYYKRKAI   71 (145)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHH
T ss_conf             888789999999999998618877-7775621006899876661899-9999888676


No 23 
>TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245   This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm.
Probab=31.46  E-value=25  Score=16.22  Aligned_cols=67  Identities=22%  Similarity=0.202  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEE-EEEECCCEEEEEEEEEEEEECCCHHHHH
Q ss_conf             999999999999996301022223445665125212317888887775048-9950594653688777630035426776
Q gi|254781073|r   25 FENLQSIICTEFEKLENEAHENSANRSPKIFTVKHWLRDKSQKEDLGGGRM-ATLCAGKVFEKAAVLVSTVYGDLSPDFK  103 (307)
Q Consensus        25 F~~LQd~Ic~~fE~lE~~~~~~~~~~~~~~F~~d~W~R~~g~~~~~GGG~s-~VL~~G~VFEKaGVNfS~V~G~~~p~~a  103 (307)
                      |.-|-..-|+.=-+-|....     ...-.|+.-+          .|||+| -+-++|+|++  -+|==.=-|.|+|+.+
T Consensus       152 fHALNqKAvARr~A~e~gK~-----YE~~N~ivaH----------lGGGISvaAH~~Gr~vD--VNNALdGeGPFSPERs  214 (353)
T TIGR02707       152 FHALNQKAVARRIAKELGKR-----YEEMNLIVAH----------LGGGISVAAHRKGRVVD--VNNALDGEGPFSPERS  214 (353)
T ss_pred             HHHHHHHHHHHHHHHHCCCC-----CCCCCEEEEE----------CCCCCEEEEECCCCEEE--EECCCCCCCCCCCCCC
T ss_conf             44433889999999972896-----0044548998----------28870341454861799--7347784329387545


Q ss_pred             HHHHH
Q ss_conf             42111
Q gi|254781073|r  104 DQILG  108 (307)
Q Consensus       104 ~~i~g  108 (307)
                      -..|-
T Consensus       215 G~LP~  219 (353)
T TIGR02707       215 GTLPL  219 (353)
T ss_pred             CCCCH
T ss_conf             65658


No 24 
>KOG4233 consensus
Probab=30.80  E-value=41  Score=14.84  Aligned_cols=32  Identities=34%  Similarity=0.728  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHH
Q ss_conf             6799999999840365---6733428999976787
Q gi|254781073|r  167 PDVIFFHNTLKEMCSQ---HAVANYTHYKEWCDRY  198 (307)
Q Consensus       167 eD~~~fH~~~k~~Cd~---~~~~~Y~~fKk~CD~Y  198 (307)
                      -|-..|..=+|.+|..   +..+-|.-.+.|||.+
T Consensus        55 KdE~lF~~Wlk~~~gat~~~a~~~~~CL~eWc~~F   89 (90)
T KOG4233          55 KDEDLFQEWLKETCGATAKQAQDCFNCLNEWCDCF   89 (90)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             66999999999982844888999998899999975


No 25 
>COG1103 Archaea-specific pyridoxal phosphate-dependent enzymes [General function prediction only]
Probab=29.98  E-value=5.6  Score=20.44  Aligned_cols=63  Identities=11%  Similarity=0.110  Sum_probs=32.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHCCCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             73342899997678743453252123430101014786665896-7799999999999999999999875
Q gi|254781073|r  184 AVANYTHYKEWCDRYFYLPHRQESRGIGGIFFDHLHSSPEMGGI-DADFSFISAVGDCFIKLYPSLVRRN  252 (307)
Q Consensus       184 ~~~~Y~~fKk~CD~YFylpHR~E~RGvGGIFFD~l~~~~~~~~~-e~~f~f~~~vg~~fl~~y~~Iv~~r  252 (307)
                      .+.+|.--||---.-|||=+-=..|||.||==--      ...+ -..+-+..+-.+...+++.+|+++.
T Consensus       318 tp~f~eIakk~~r~gyFlY~ELK~RgI~GI~~G~------Tk~~K~svyGl~~Eqve~V~~afkeI~eky  381 (382)
T COG1103         318 TPVFHEIAKKHKRKGYFLYEELKKRGIHGIQPGQ------TKYFKLSVYGLSWEQVEYVVDAFKEIAEKY  381 (382)
T ss_pred             CCHHHHHHHHCCCCCEEEHHHHHHCCCCCCCCCC------EEEEEEEEECCCHHHHHHHHHHHHHHHHHC
T ss_conf             7128999875767854668988765866506675------137888750577999999999999999861


No 26 
>PHA02087 hypothetical protein
Probab=28.26  E-value=34  Score=15.39  Aligned_cols=13  Identities=62%  Similarity=0.902  Sum_probs=8.1

Q ss_pred             CCCCCCCCEEHHC
Q ss_conf             5212343010101
Q gi|254781073|r  205 QESRGIGGIFFDH  217 (307)
Q Consensus       205 ~E~RGvGGIFFD~  217 (307)
                      -|.-|-|||-||+
T Consensus        60 pe~~ggggi~fdd   72 (83)
T PHA02087         60 PESEGGGGITFDD   72 (83)
T ss_pred             CCCCCCCCEEECC
T ss_conf             7346898603564


No 27 
>TIGR01975 isoAsp_dipep beta-aspartyl peptidase; InterPro: IPR010229   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of proteins include metallopeptidases belonging to the MEROPS peptidase family M38 (clan MJ, beta-aspartyl dipeptidase family). This entry includes the beta-aspartyl dipeptidase from Escherichia coli, (3.4.19.5 from EC, IadA), which degrades isoaspartyl dipeptides and may unblock degradation of proteins that cannot be repaired. This entry also describes closely related proteins from other species (e.g. Clostridium perfringens, Thermoanaerobacter tengcongensis) that may have an equivalent in function. This family shows homology to dihydroorotases. The L-isoaspartyl derivative of Asp arises non-enzymatically over time as a form of protein damage. In this isomerisation, the connectivity of the polypeptide changes to pass through the beta-carboxyl of the side chain. Much but not all of this damage can be repaired by protein-L-isoaspartate (D-aspartate) O-methyltransferase..
Probab=28.18  E-value=13  Score=18.13  Aligned_cols=54  Identities=26%  Similarity=0.374  Sum_probs=37.2

Q ss_pred             CCCCCCCHHHCC--HHHEEECC--CCCCCCCCCCCCCCHHHCCCHHHHHHHHHHHHHHCCC
Q ss_conf             368874401023--02102024--3125320011000001104326799999999840365
Q gi|254781073|r  126 PYNPHVPAVHFN--IRMIVTGA--YWFGGGIDLTPSLESRRHSYDPDVIFFHNTLKEMCSQ  182 (307)
Q Consensus       126 p~nP~vPt~H~N--~R~f~~~~--~WFGGG~DLTP~~~~~~y~~~eD~~~fH~~~k~~Cd~  182 (307)
                      |-|-++|| |||  .-.||.+-  .--||=.|||-+....  ..+|-.+.=-..+|.+.++
T Consensus       217 Pi~q~lPT-H~nR~~~LFE~g~~fa~~GG~iDlTss~~p~--~~~egev~p~eGlk~~l~~  274 (391)
T TIGR01975       217 PITQFLPT-HINRNRELFEAGLEFAKKGGTIDLTSSIDPQ--FRKEGEVKPAEGLKKLLEA  274 (391)
T ss_pred             CCCCCCCC-CCCCCHHHHHHHHHHHHCCCEEEEECCCCCC--CCCCCCCCHHHHHHHHHHC
T ss_conf             70025577-6476756899999999739808760278887--5535543767899999963


No 28 
>KOG3410 consensus
Probab=27.69  E-value=33  Score=15.47  Aligned_cols=53  Identities=17%  Similarity=0.132  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCHHHEEECCCCCCCCC
Q ss_conf             999999998754799998999885420240112211110255357357888111411288878897
Q gi|254781073|r  242 IKLYPSLVRRNYHHLFSEQDRQEQLIRRGRYAEFNLLYDKGTNFGFKTGGNVESILASMPPLVAWP  307 (307)
Q Consensus       242 l~~y~~Iv~~r~~~~~~~~~k~~Ql~rRgRYvEFNL~yDRGT~FGL~t~gr~esIl~SlPp~~~Wp  307 (307)
                      +++|+.........+.-.--++.+..-|-|--+||+..|-=|-+++.             |-|+||
T Consensus        67 T~Ae~~~e~~qe~~~~kril~~a~ktHk~rve~~n~~Ld~~tEh~di-------------pKvsw~  119 (120)
T KOG3410          67 TKAELRFEKVQEKRPCKRILKEAGKTHKERVEKFNRHLDEMTEHFDI-------------PKVSWT  119 (120)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-------------CCCCCC
T ss_conf             37788889999866999999998767899999999988612402476-------------678999


No 29 
>PRK10997 yieM hypothetical protein; Provisional
Probab=27.43  E-value=17  Score=17.34  Aligned_cols=13  Identities=54%  Similarity=0.886  Sum_probs=9.6

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             3125320011000
Q gi|254781073|r  146 YWFGGGIDLTPSL  158 (307)
Q Consensus       146 ~WFGGG~DLTP~~  158 (307)
                      .=|+||.|+.|++
T Consensus       388 ~sF~GGTD~~~~L  400 (484)
T PRK10997        388 QSFRGGTDLAPCL  400 (484)
T ss_pred             CCCCCCCCHHHHH
T ss_conf             8888984579999


No 30 
>PRK09491 rimI ribosomal-protein-alanine N-acetyltransferase; Provisional
Probab=26.66  E-value=30  Score=15.70  Aligned_cols=62  Identities=8%  Similarity=0.170  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCC-----CCCHHHHHHHHCCCCCHHHHHHHHCCCCCCCC--CCCCCHHHEEECCCC
Q ss_conf             999999999999999875479-----99989998854202401122111102553573--578881114112888
Q gi|254781073|r  235 SAVGDCFIKLYPSLVRRNYHH-----LFSEQDRQEQLIRRGRYAEFNLLYDKGTNFGF--KTGGNVESILASMPP  302 (307)
Q Consensus       235 ~~vg~~fl~~y~~Iv~~r~~~-----~~~~~~k~~Ql~rRgRYvEFNL~yDRGT~FGL--~t~gr~esIl~SlPp  302 (307)
                      +.+|...+.........+.-.     --..++....||++==+.   -+   |..=+-  ...||-++|+||||-
T Consensus        76 ~G~g~~Ll~~~~~~~~~~g~~~i~LEVr~sN~~A~~lY~k~GF~---~~---g~R~~YY~~~dg~EDAiiM~l~L  144 (144)
T PRK09491         76 QGLGRALLEHLIDELEKRGVATLWLEVRASNAAAIALYESLGFN---EV---TIRRNYYPTADGREDAIIMALPL  144 (144)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHCCCE---EE---CEECCCCCCCCCCCCCEEEECCC
T ss_conf             89799999999999998799799999957878999999988998---91---78878568978990216886279


No 31 
>KOG0175 consensus
Probab=26.09  E-value=34  Score=15.33  Aligned_cols=33  Identities=24%  Similarity=0.441  Sum_probs=27.6

Q ss_pred             CCCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             001100000110432679999999984036567
Q gi|254781073|r  152 IDLTPSLESRRHSYDPDVIFFHNTLKEMCSQHA  184 (307)
Q Consensus       152 ~DLTP~~~~~~y~~~eD~~~fH~~~k~~Cd~~~  184 (307)
                      .+++||+....-.-..||.+|++.|-.-|-.|.
T Consensus       106 IeIn~ylLGTmAGgAADCqfWer~L~kecRL~e  138 (285)
T KOG0175         106 IEINPYLLGTMAGGAADCQFWERVLAKECRLHE  138 (285)
T ss_pred             EEECHHHHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             640614310024751456899999998877898


No 32 
>KOG3404 consensus
Probab=25.83  E-value=22  Score=16.64  Aligned_cols=14  Identities=36%  Similarity=0.940  Sum_probs=5.9

Q ss_pred             CCCCHHHHHHHHCCC
Q ss_conf             024011221111025
Q gi|254781073|r  268 RRGRYAEFNLLYDKG  282 (307)
Q Consensus       268 rRgRYvEFNL~yDRG  282 (307)
                      .|.||+ |+|-|-|+
T Consensus        55 QrsRYi-YdlyykR~   68 (145)
T KOG3404          55 QRSRYI-YDLYYKRK   68 (145)
T ss_pred             HHHHHH-HHHHHHHH
T ss_conf             423668-88888788


No 33 
>TIGR01491 HAD-SF-IB-PSPlk Phosphoserine phosphatase-like hydrolase, archaeal; InterPro: IPR006386   This group of sequences belong to the IB subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences are all from archaeal species. The phylogenetically closest group of sequences to these are phosphoserine phosphatases. As there are no known archaeal phosphoserine phosphatases, it seems likely that this group of sequences represent the archaeal branch of PSPase..
Probab=25.35  E-value=45  Score=14.58  Aligned_cols=13  Identities=15%  Similarity=0.365  Sum_probs=5.0

Q ss_pred             HHHHHHHHCCCCC
Q ss_conf             8999885420240
Q gi|254781073|r  259 EQDRQEQLIRRGR  271 (307)
Q Consensus       259 ~~~k~~Ql~rRgR  271 (307)
                      +.+|.+.|+++|+
T Consensus        35 ~A~kn~elf~~G~   47 (203)
T TIGR01491        35 LAKKNAELFESGS   47 (203)
T ss_pred             HHHHHHHHHHCCC
T ss_conf             5678789873596


No 34 
>pfam09433 HRP1 THO complex subunit HPR1. The THO complex plays a role in coupling transcription elongation to mRNA export. It is composed of subunits THP2, HPR1, THO2 and MFT1.
Probab=25.21  E-value=52  Score=14.19  Aligned_cols=14  Identities=29%  Similarity=0.655  Sum_probs=5.6

Q ss_pred             HHCCCCCCCCEEHH
Q ss_conf             32521234301010
Q gi|254781073|r  203 HRQESRGIGGIFFD  216 (307)
Q Consensus       203 HR~E~RGvGGIFFD  216 (307)
                      --+|.-||-|+|=+
T Consensus       594 kVdE~tGi~GLF~e  607 (725)
T pfam09433       594 KVDEKTGLAGLFDE  607 (725)
T ss_pred             CCCCCCCCCCCCCH
T ss_conf             76610143213684


No 35 
>PRK13272 treA trehalase; Provisional
Probab=23.63  E-value=37  Score=15.12  Aligned_cols=64  Identities=20%  Similarity=0.246  Sum_probs=38.6

Q ss_pred             CCCCCCCC-------------CCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             43125320-------------01100000110432679999999984036567334289999767874345325212343
Q gi|254781073|r  145 AYWFGGGI-------------DLTPSLESRRHSYDPDVIFFHNTLKEMCSQHAVANYTHYKEWCDRYFYLPHRQESRGIG  211 (307)
Q Consensus       145 ~~WFGGG~-------------DLTP~~~~~~y~~~eD~~~fH~~~k~~Cd~~~~~~Y~~fKk~CD~YFylpHR~E~RGvG  211 (307)
                      .=||+.|.             ||+-.+    |..+.+...++....+.|...=.....+.++.-++|++-    |.    
T Consensus       316 SRW~~d~~~L~tI~T~~IiPVDLNalL----y~~E~~lA~~~~~~~~~~~~~y~~~A~~R~~aI~~~LWn----e~----  383 (537)
T PRK13272        316 SRWLADGRELATIRTTAIVPIDLNSLL----YHLERTLAQACASSGAACSQDYAALAQQRKQAIDAHLWN----PA----  383 (537)
T ss_pred             CCCCCCCCCCCCCCCCEECEECHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCC----CC----
T ss_conf             233567865243330221436589999----999999999998658467999999999999999997628----87----


Q ss_pred             CEEHHCCCC
Q ss_conf             010101478
Q gi|254781073|r  212 GIFFDHLHS  220 (307)
Q Consensus       212 GIFFD~l~~  220 (307)
                      |+||||=-.
T Consensus       384 G~~~DYd~~  392 (537)
T PRK13272        384 GYYADYDWQ  392 (537)
T ss_pred             CEEEECCCC
T ss_conf             804420046


No 36 
>pfam04437 RINT1_TIP1 RINT-1 / TIP-1 family. This family includes RINT-1, a Rad50 interacting protein which participates in radiation induced checkpoint control, as well as the TIP-1 protein from yeast that seems to be involved in a complex with Sec20p that is required for golgi transport.
Probab=23.58  E-value=56  Score=13.99  Aligned_cols=28  Identities=32%  Similarity=0.718  Sum_probs=18.7

Q ss_pred             HHHHHCCCCCHHH--HHHHHHHHHHHHHHH
Q ss_conf             9984036567334--289999767874345
Q gi|254781073|r  175 TLKEMCSQHAVAN--YTHYKEWCDRYFYLP  202 (307)
Q Consensus       175 ~~k~~Cd~~~~~~--Y~~fKk~CD~YFylp  202 (307)
                      .+..+|-.++...  ....+.|||+.|||-
T Consensus       243 ~l~~~~~~lnsa~yi~~~L~eWs~~v~Fle  272 (485)
T pfam04437       243 ELERTCRKLNAANYLESKLKDWSDDVFFLE  272 (485)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCEEHH
T ss_conf             399999998359999999998557763121


No 37 
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=22.63  E-value=56  Score=13.95  Aligned_cols=16  Identities=38%  Similarity=0.434  Sum_probs=13.5

Q ss_pred             CCCEEEEEEECCCEEE
Q ss_conf             7750489950594653
Q gi|254781073|r   70 LGGGRMATLCAGKVFE   85 (307)
Q Consensus        70 ~GGG~s~VL~~G~VFE   85 (307)
                      -|-|+|.|..||.||=
T Consensus        15 PGtG~m~Vr~Dg~v~~   30 (66)
T COG2075          15 PGTGIMYVRNDGKVLR   30 (66)
T ss_pred             CCCEEEEEECCCEEEE
T ss_conf             9942799955983999


No 38 
>TIGR01263 4HPPD 4-hydroxyphenylpyruvate dioxygenase; InterPro: IPR005956    4-hydroxyphenylpyruvate dioxygenase (1.13.11.27 from EC) oxidizes 4-hydroxyphenylpyruvate, a tyrosine and phenylalanine catabolite, to homogentisate. Homogentisate can undergo a further non-enzymatic oxidation and polymerization into brown pigments that protect some bacterial species from light. A similar process occurs spontaneously in blood and is hemolytic . In some bacterial species, this enzyme has been studied as a hemolysin.; GO: 0003868 4-hydroxyphenylpyruvate dioxygenase activity, 0009072 aromatic amino acid family metabolic process.
Probab=22.31  E-value=26  Score=16.07  Aligned_cols=35  Identities=14%  Similarity=0.204  Sum_probs=16.4

Q ss_pred             EEEEEECCCEEEEEEEEEEEEECCC------HHHHHHHHHHCCCC
Q ss_conf             4899505946536887776300354------26776421110267
Q gi|254781073|r   74 RMATLCAGKVFEKAAVLVSTVYGDL------SPDFKDQILGTTKN  112 (307)
Q Consensus        74 ~s~VL~~G~VFEKaGVNfS~V~G~~------~p~~a~~i~g~~~~  112 (307)
                      .+-++++|+|    -.=+|......      ...++..+.+..++
T Consensus        43 ~~~~~rqG~i----~fv~~~~~~~~~~~~~~~~~f~~~HGdgv~d   83 (379)
T TIGR01263        43 ASTVYRQGQI----NFVVTAELSSDTTTASEAADFAAKHGDGVKD   83 (379)
T ss_pred             EEEEEECCEE----EEEEECCCCCCCHHHHHHHHHHHHCCCCHHH
T ss_conf             6999993759----9998457788851256999999757882312


No 39 
>KOG3063 consensus
Probab=22.25  E-value=24  Score=16.36  Aligned_cols=27  Identities=22%  Similarity=0.327  Sum_probs=19.9

Q ss_pred             CCCCCEEEEEEECCCEEEEEEEEEEEE
Q ss_conf             877750489950594653688777630
Q gi|254781073|r   68 EDLGGGRMATLCAGKVFEKAAVLVSTV   94 (307)
Q Consensus        68 ~~~GGG~s~VL~~G~VFEKaGVNfS~V   94 (307)
                      ...+|-.+.-+.+|+-+|--||-++-|
T Consensus        46 Etv~G~V~l~lk~gkkleH~Gikiefi   72 (301)
T KOG3063          46 ETVSGKVNLRLKDGKKLEHQGIKIEFI   72 (301)
T ss_pred             CEEEEEEEEEECCCCCCCCCCEEEEEE
T ss_conf             753018999974786111276489999


No 40 
>TIGR00505 ribA GTP cyclohydrolase II; InterPro: IPR000926   GTP cyclohydrolase II catalyses the first committed step in the biosynthesis of riboflavin. The enzyme converts GTP and water to formate, 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)- pyrimidine and pyrophosphate, and requires magnesium as a cofactor. It is sometimes found as a bifunctional enzyme with 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP_synthase) IPR000422 from INTERPRO. ; GO: 0003935 GTP cyclohydrolase II activity, 0009231 riboflavin biosynthetic process.
Probab=20.99  E-value=31  Score=15.65  Aligned_cols=11  Identities=64%  Similarity=0.942  Sum_probs=8.3

Q ss_pred             HHHH-CCCCCCC
Q ss_conf             4532-5212343
Q gi|254781073|r  201 LPHR-QESRGIG  211 (307)
Q Consensus       201 lpHR-~E~RGvG  211 (307)
                      |=|| +|=||||
T Consensus       108 iY~RG~EGRGIG  119 (227)
T TIGR00505       108 IYLRGQEGRGIG  119 (227)
T ss_pred             EEECCCCCCCCC
T ss_conf             970376677623


No 41 
>cd06182 CYPOR_like NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPOR has a C-terminal ferredoxin reducatase (FNR)- like FAD and NAD binding module, an FMN-binding domain, and an additional conecting domain (inserted within the FAD binding region) that orients the FNR and FMN binding domains. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria and participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-t
Probab=20.62  E-value=64  Score=13.61  Aligned_cols=39  Identities=15%  Similarity=0.146  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCHHHHHHH-HCCCCCHHH
Q ss_conf             999999999999998754799998999885-420240112
Q gi|254781073|r  236 AVGDCFIKLYPSLVRRNYHHLFSEQDRQEQ-LIRRGRYAE  274 (307)
Q Consensus       236 ~vg~~fl~~y~~Iv~~r~~~~~~~~~k~~Q-l~rRgRYvE  274 (307)
                      .++..+..+...|+.+.....-.+.+.-++ |.+.|||+|
T Consensus       225 ~M~~~V~~~l~~il~~~g~~~~~~A~~~l~~l~~~gRY~~  264 (267)
T cd06182         225 SMAKDVEDALVKIIAKAGGVDESDAEEYLKELEDEGRYVE  264 (267)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             1068999999999998479999999999999998698666


No 42 
>KOG2305 consensus
Probab=20.48  E-value=41  Score=14.85  Aligned_cols=15  Identities=40%  Similarity=0.937  Sum_probs=10.7

Q ss_pred             EEEEECCCC--CCCHHH
Q ss_conf             223313688--744010
Q gi|254781073|r  121 SVIVHPYNP--HVPAVH  135 (307)
Q Consensus       121 S~V~Hp~nP--~vPt~H  135 (307)
                      -+|+||.||  ++|-+.
T Consensus       138 ~lvaHPvNPPyfiPLvE  154 (313)
T KOG2305         138 CLVAHPVNPPYFIPLVE  154 (313)
T ss_pred             EEEECCCCCCCCCCHHE
T ss_conf             25745799974120110


No 43 
>COG4829 CatC1 Muconolactone delta-isomerase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.34  E-value=25  Score=16.25  Aligned_cols=29  Identities=41%  Similarity=0.843  Sum_probs=19.9

Q ss_pred             CCCCHHHHHHHHCCCCCCCCCCCCCHHHEEECCCCC
Q ss_conf             024011221111025535735788811141128887
Q gi|254781073|r  268 RRGRYAEFNLLYDKGTNFGFKTGGNVESILASMPPL  303 (307)
Q Consensus       268 rRgRYvEFNL~yDRGT~FGL~t~gr~esIl~SlPp~  303 (307)
                      +-|-|+-+.       +|-+.++|-.+.||.||||-
T Consensus        46 ~~Geyanys-------lFd~dd~~eLh~~L~~~P~f   74 (98)
T COG4829          46 RPGEYANYS-------LFDADDNGELHQLLASMPPF   74 (98)
T ss_pred             CCCCCCCEE-------EECCCCHHHHHHHHHCCCCC
T ss_conf             143102311-------23078617899999629986


Done!