Query         gi|254780710|ref|YP_003065123.1| diaminopimelate epimerase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 296
No_of_seqs    115 out of 2293
Neff          6.6 
Searched_HMMs 39220
Date          Sun May 29 20:59:39 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780710.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00450 dapF diaminopimelate  100.0       0       0  638.2  30.5  272    5-282     1-278 (278)
  2 TIGR00652 DapF diaminopimelate 100.0       0       0  638.5  26.8  271    6-280     1-293 (294)
  3 PRK13577 diaminopimelate epime 100.0       0       0  618.7  29.3  269    6-280     1-273 (281)
  4 COG0253 DapF Diaminopimelate e 100.0       0       0  589.0  27.8  268    6-281     1-272 (272)
  5 pfam01678 DAP_epimerase Diamin  99.9 1.6E-27 4.2E-32  201.3  11.4  116    8-125     1-120 (121)
  6 pfam01678 DAP_epimerase Diamin  99.9 7.1E-23 1.8E-27  170.7  10.6  113  161-274     4-121 (121)
  7 pfam02567 PhzC-PhzF Phenazine   99.6 4.1E-12 1.1E-16   99.7  23.4  255    8-277     4-280 (280)
  8 PRK10281 hypothetical protein;  99.5 2.8E-11 7.2E-16   94.2  22.1  262    8-281    11-299 (299)
  9 COG0384 Predicted epimerase, P  99.4 1.3E-09 3.3E-14   83.3  23.1  261    8-281    12-291 (291)
 10 KOG3033 consensus               99.2 5.8E-09 1.5E-13   79.0  16.5  262    8-281    13-286 (286)
 11 TIGR00654 PhzF_family phenazin  99.0 1.6E-07   4E-12   69.5  19.3  265    8-281    11-314 (314)
 12 PRK13969 proline racemase; Pro  98.8 2.6E-05 6.7E-10   54.9  23.3  266    3-285     4-326 (335)
 13 PRK13971 hydroxyproline-2-epim  98.7 2.9E-05 7.5E-10   54.5  20.2  273    1-285     1-324 (333)
 14 pfam05544 Pro_racemase Proline  98.7 1.9E-05 4.9E-10   55.8  19.0  259   10-285     3-318 (325)
 15 PRK13970 hydroxyproline-2-epim  98.5 3.4E-05 8.7E-10   54.1  17.7  263    4-285     2-302 (310)
 16 COG3938 Proline racemase [Amin  98.2 5.1E-05 1.3E-09   53.0  12.0  221    6-242     7-272 (341)
 17 pfam02567 PhzC-PhzF Phenazine   96.3     0.1 2.7E-06   31.2  11.3   93  162-262    10-105 (280)
 18 pfam04303 PrpF PrpF protein. P  95.9    0.16 4.2E-06   29.9  17.5  228   42-281    48-370 (371)
 19 COG0384 Predicted epimerase, P  93.4    0.68 1.7E-05   25.8  10.6   95  160-262    16-113 (291)
 20 PRK10281 hypothetical protein;  93.1    0.73 1.9E-05   25.6  11.3   91  162-260    17-110 (299)
 21 COG1903 CbiD Cobalamin biosynt  81.8     2.4   6E-05   22.2   4.1   43   41-91     32-75  (367)
 22 PRK00075 cbiD cobalt-precorrin  69.6     8.1 0.00021   18.7   4.1   10  117-126   116-125 (366)
 23 pfam10941 DUF2620 Protein of u  61.9     6.3 0.00016   19.4   2.3   34  222-255    49-82  (117)
 24 TIGR02065 ECX1 exosome complex  60.0     9.5 0.00024   18.2   3.0   33   47-87    103-135 (231)
 25 COG2828 Uncharacterized protei  49.2      19 0.00049   16.2   3.3   58  225-282   301-374 (378)
 26 TIGR01722 MMSDH methylmalonate  46.0      22 0.00055   15.9   3.6   73   12-105   161-247 (478)
 27 COG0059 IlvC Ketol-acid reduct  45.2      22 0.00057   15.8   4.8  101  169-277    80-203 (338)
 28 PRK10310 galactitol-specific P  42.0      14 0.00035   17.1   1.5   16  224-239     8-23  (94)
 29 TIGR01066 rplM_bact ribosomal   39.2      27  0.0007   15.2   3.7   30  231-260    30-59  (145)
 30 KOG1798 consensus               35.5      19 0.00048   16.3   1.3   13   64-76    930-942 (2173)
 31 cd05807 CBM20_CGTase CGTase, C  34.9      21 0.00054   15.9   1.5   35  193-230    58-97  (101)
 32 pfam02459 Adeno_terminal Adeno  34.3      30 0.00077   14.9   2.2   41  180-220   400-447 (548)
 33 cd05566 PTS_IIB_galactitol PTS  33.8      20 0.00051   16.1   1.2   15  224-238     6-20  (89)
 34 KOG1250 consensus               32.5      35 0.00089   14.5   2.8   28  227-254   322-353 (457)
 35 KOG1794 consensus               31.8      36 0.00091   14.4   3.6   46   30-80    104-149 (336)
 36 TIGR02219 phage_NlpC_fam putat  31.7      23 0.00058   15.7   1.2   37  216-262    54-91  (135)
 37 TIGR02639 ClpA ATP-dependent C  30.5      16 0.00042   16.7   0.3   13  164-177   595-607 (774)
 38 cd06221 sulfite_reductase_like  30.2      21 0.00055   15.9   0.9   21  208-233   217-237 (253)
 39 cd01775 CYR1_RA CYR1 is a fung  29.4      36 0.00091   14.4   1.9   17   61-77      2-18  (97)
 40 TIGR01415 trpB_rel pyridoxal-p  29.2      11 0.00028   17.8  -0.7   14   92-105   118-131 (426)
 41 PRK10815 sensor protein PhoQ;   28.9      40   0.001   14.1   7.6   76  181-259   380-473 (484)
 42 TIGR01362 KDO8P_synth 3-deoxy-  28.8      40   0.001   14.1   2.4   11  213-223   162-174 (279)
 43 TIGR02918 TIGR02918 conserved   28.3      33 0.00084   14.7   1.6   20   55-74    156-176 (511)
 44 TIGR00406 prmA ribosomal prote  27.9      32 0.00082   14.7   1.5   14  223-236   203-216 (330)
 45 cd05535 POLBc_epsilon DNA poly  26.6      38 0.00097   14.3   1.6   11   46-56    331-341 (621)
 46 TIGR03534 RF_mod_HemK protein-  26.5      34 0.00087   14.6   1.3   13   77-91     96-108 (251)
 47 PRK05270 galactose-1-phosphate  26.3      44  0.0011   13.8   4.2   59  113-173   143-227 (496)
 48 KOG2904 consensus               26.0      33 0.00085   14.6   1.2   12  249-260   275-286 (328)
 49 pfam02302 PTS_IIB PTS system,   25.8      40   0.001   14.2   1.6   17  223-239     4-20  (91)
 50 TIGR01123 ilvE_II branched-cha  25.6      19 0.00047   16.3  -0.1   17  214-230   261-278 (329)
 51 PRK08345 cytochrome-c3 hydroge  25.4      13 0.00034   17.2  -0.9   59   40-104    37-101 (292)
 52 COG2263 Predicted RNA methylas  25.1      37 0.00093   14.4   1.3   14   76-89     53-66  (198)
 53 COG1022 FAA1 Long-chain acyl-C  24.2      13 0.00032   17.4  -1.2   28  251-280   409-436 (613)
 54 TIGR01361 DAHP_synth_Bsub phos  24.0      49  0.0012   13.6   2.8   14  212-225   171-184 (262)
 55 TIGR02912 sulfite_red_C sulfit  24.0      25 0.00064   15.5   0.3   55  162-223   113-169 (323)
 56 PRK05225 ketol-acid reductoiso  23.7      49  0.0013   13.5   3.4   54  170-223   105-174 (489)
 57 COG2264 PrmA Ribosomal protein  23.3      48  0.0012   13.6   1.6   16  223-240   169-184 (300)
 58 COG3882 FkbH Predicted enzyme   23.3      50  0.0013   13.5   2.2   26   30-55    311-336 (574)
 59 PRK00517 prmA ribosomal protei  22.4      49  0.0012   13.6   1.5   18  222-241   168-185 (298)
 60 COG0043 UbiD 3-polyprenyl-4-hy  22.3      53  0.0013   13.3   2.6   95  197-293   162-276 (477)
 61 pfam06325 PrmA Ribosomal prote  22.2      50  0.0013   13.5   1.5   16  223-240   167-182 (294)
 62 cd00580 CHMI 5-carboxymethyl-2  21.9      49  0.0013   13.5   1.5   36  165-200     1-42  (113)
 63 cd05799 PGM2 This CD includes   21.7      54  0.0014   13.3   3.1   29   45-73     96-124 (487)
 64 KOG3480 consensus               21.6      30 0.00076   15.0   0.3   25   66-91     44-68  (90)
 65 KOG0697 consensus               21.6      54  0.0014   13.2   3.3   76   63-140   138-215 (379)
 66 TIGR01292 TRX_reduct thioredox  21.5      52  0.0013   13.4   1.5  126   79-237   184-319 (321)
 67 PRK10291 glyoxalase I; Provisi  21.5      55  0.0014   13.2   4.7   58  164-223    66-127 (129)
 68 PRK03124 S-adenosylmethionine   21.0      56  0.0014   13.2   5.3   66  190-257    47-119 (127)
 69 TIGR02630 xylose_isom_A xylose  21.0      35  0.0009   14.5   0.6  206   15-256   180-427 (437)
 70 KOG4042 consensus               20.7      28 0.00071   15.2  -0.0   70  188-260    82-152 (190)
 71 KOG0647 consensus               20.7      57  0.0014   13.1   3.9   13  159-171   170-182 (347)
 72 KOG1529 consensus               20.7      50  0.0013   13.5   1.3   48    6-53     39-93  (286)
 73 TIGR02177 PorB_KorB 2-oxoacid:  20.6      57  0.0014   13.1   4.0  116   77-226     7-134 (302)
 74 TIGR03533 L3_gln_methyl protei  20.6      57  0.0015   13.1   1.6   14  247-260   239-252 (284)
 75 PRK11805 N5-glutamine S-adenos  20.3      57  0.0015   13.1   1.5   13  247-259   251-263 (307)

No 1  
>PRK00450 dapF diaminopimelate epimerase; Provisional
Probab=100.00  E-value=0  Score=638.20  Aligned_cols=272  Identities=38%  Similarity=0.624  Sum_probs=246.8

Q ss_pred             C-CEEEEECCCCCCEEEEECCCCCCCCCHHHHHHHCCC-CCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHH
Q ss_conf             4-113785176773899947788878888899872035-67143558998258888866899997178762123320332
Q gi|254780710|r    5 M-VDFAKMEGIGNKILVIDMRGCHDNITSDAINALSTD-DNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMR   82 (296)
Q Consensus         5 m-i~F~Kmhg~GNDFiiiD~~~~~~~~~~~~i~~~~~~-~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~R   82 (296)
                      | |+|+||||+||||||+|.++....+++++++++|+| +||||||||+|++++++.+||+|+|||+|||+|+|||||+|
T Consensus         1 M~i~F~KmhG~GNDFiiid~~~~~~~~~~~~i~~lcdR~~GIGaDgll~i~~~~~~~~d~~m~ifN~DGS~AemCGNG~R   80 (278)
T PRK00450          1 MKMKFTKMHGLGNDFVVIDARDQDLTPTPELARALCDRHFGIGADGLLLVEPPPSPGADFRMRIFNADGSEAEMCGNGAR   80 (278)
T ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCHHHCCCCHHH
T ss_conf             93189999738982999979988789999999986256888688779999358898847899999399986752737899


Q ss_pred             HHHHHHHCC--CCCCEEEEEECCCCEEEEECCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEECCEEEE
Q ss_conf             231110013--576403798358837999857742774036877777768565656543443011057777402130999
Q gi|254780710|r   83 CVVRFLTSR--MKRKSFTFETIRGILVAKENRDGSISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVV  160 (296)
Q Consensus        83 c~a~yl~~~--~~~~~~~i~T~~g~~~~~~~~~~~v~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  160 (296)
                      |+|+||+++  ..+++++|+|.+|++.++...++.|+|+||.|+|.|++||+............     .......+++|
T Consensus        81 Cva~~l~~~~~~~~~~~~i~T~~G~~~~~~~~~~~i~V~MG~p~~~~~~ip~~~~~~~~~~~~~-----~~~~~~~~~~v  155 (278)
T PRK00450         81 CFARFVYDKGLTNKTEIRVETLAGIIELEVEDDGLVTVDMGEPRFEPAEIPFAAEAEKTYILEL-----QVGPTFECTAV  155 (278)
T ss_pred             HHHHHHHHCCCCCCCCEEEEECCCEEEEEEECCCEEEEECCCCCCCHHHCCCCCCCCCCCEEEC-----CCCCCEEEEEE
T ss_conf             9999999808888871899968953999992698199981587447755866554453201201-----46871479999


Q ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             55874279742557686888763100023323755551467997288728999804678766563235899999999817
Q gi|254780710|r  161 SMGNPHAIFFVEDDLYHYDLASFGNLLAKHPMFSEGVNLSIARVTSLESLDLRTWERGVGLTAACGSAACASVVASGCLH  240 (296)
Q Consensus       161 ~iGNPH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp~gvNV~fv~v~~~~~I~iRt~ERGvGeTlACGTGA~Asa~~~~~~~  240 (296)
                      +|||||||+||+ +++.+++.++|+.||+|++||+|+||+|++++++++|++||||||||||+||||||||||+++.+++
T Consensus       156 ~~GnPH~V~fv~-d~~~~~~~~~g~~i~~~~~Fp~g~NV~fv~v~~~~~i~vrt~ERGvGeTlACGTGa~Aaa~~a~~~g  234 (278)
T PRK00450        156 SMGNPHAVIFVD-DVDAAPVEELGPLLENHPRFPEGVNVGFVQVVDRDHIRLRVYERGVGETLACGTGACAAAVAAIRLG  234 (278)
T ss_pred             ECCCCEEEEEEC-CCCHHHHHHHCCHHCCCCCCCCCCEEEEEEEECCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHC
T ss_conf             559985999967-6012227664602013767878616999999069929999995268745255342889999999838


Q ss_pred             CCCC-CEEEECCCCEEEEEEEC-CCEEEEEECEEEEEEEEEEEC
Q ss_conf             8898-07999079579999958-981999946289998899841
Q gi|254780710|r  241 KTNR-AVSVKMLGGGLLIEWHD-NNHVFMTGEAKKEWEGKLDIK  282 (296)
Q Consensus       241 ~~~~-~v~V~~pGG~L~v~~~~-~~~i~l~Gpa~~vf~G~~~i~  282 (296)
                      ++++ +++|++|||.|.|+|.+ +++|+|+|||++||+|+++|.
T Consensus       235 ~~~~~~v~V~~~GG~L~V~~~~~~~~v~l~Gpa~~vf~G~i~~e  278 (278)
T PRK00450        235 LLDTEPVTVHLPGGTLTIEWKGDGDPVYMTGPATHVFDGEIDLE  278 (278)
T ss_pred             CCCCCEEEEECCCCEEEEEEECCCCEEEEECCCEEEEEEEEECC
T ss_conf             89994699996995799999889985999907799999999779


No 2  
>TIGR00652 DapF diaminopimelate epimerase; InterPro: IPR001653   Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see .   The lysine/diaminopimelic acid branch of the aspartate pathway produces the essential amino acid lysine via the intermediate meso-diaminopimelic acid (meso-DAP), which is also a vital cell wall component in Gram-negative bacteria . The production of dihydropicolinate from aspartate-semialdehyde controls flux into the lysine/diaminopimelic acid pathway. Three variants of this pathway exist, differing in how tetrahydropicolinate (formed by reduction of dihydropicolinate) is metabolised to meso-DAP. One variant, the most commonly found one in archaea and bacteria, uses primarily succinyl intermediates, while a second variant, found only in Bacillus, utilises primarily acetyl intermediates. In the third variant, found in some Gram-positive bacteria, a dehydrogenase converts tetrahydropicolinate directly to meso-DAP. In all variants meso-DAP is subsequently converted to lysine by a decarboxylase, or, in Gram-negative bacteria, assimilated into the cell wall. Evidence exists that a fourth, currently unknown, variant of this pathway may function in plants .   This entry represents diaminopimelate epimerase (5.1.1.7 from EC), which catalyses the isomerisation of L,L-dimaminopimelate to meso-DAP in the biosynthetic pathway leading from aspartate to lysine. It is a member of the broader family of PLP-independent amino acid racemases. This enzyme is a monomeric protein of about 30 kDa consisting of two domains which are homologus in structure though they share little sequence similarity . Each domain consists of mixed beta-sheets which fold into a barrel around the central helix. The active site cleft is formed from both domains and contains two conserved cysteines thought to function as the acid and base in the catalytic reaction . Other PLP-independent racemases such as glutamate racemase have been shown to share a similar structure and mechanism of catalysis.; GO: 0008837 diaminopimelate epimerase activity, 0009089 lysine biosynthetic process via diaminopimelate.
Probab=100.00  E-value=0  Score=638.46  Aligned_cols=271  Identities=34%  Similarity=0.620  Sum_probs=240.9

Q ss_pred             CEEEEECCCCCCEEEEECCC--CCCCCC---HHHHHHHCC-CCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCC
Q ss_conf             11378517677389994778--887888---889987203-567143558998258888866899997178762123320
Q gi|254780710|r    6 VDFAKMEGIGNKILVIDMRG--CHDNIT---SDAINALST-DDNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGN   79 (296)
Q Consensus         6 i~F~Kmhg~GNDFiiiD~~~--~~~~~~---~~~i~~~~~-~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGN   79 (296)
                      |.|+||||+||||||||.++  +.....   ++.++.+|+ ++|+||||+|+++||.+..+|++|+|||||||+|+||||
T Consensus         1 ~~F~KmhGlGNDFv~v~~~~eL~~~~~~~~kp~~~~~vc~r~~G~GaDG~i~v~~P~s~~~D~~~~iFNsDGS~A~mCGN   80 (294)
T TIGR00652         1 MEFSKMHGLGNDFVLVDEFDELAELVKEEEKPEFVRQVCDRHFGVGADGVIFVEPPGSPEADYKMRIFNSDGSEAEMCGN   80 (294)
T ss_pred             CEEEEEECCCCCEEEECCCHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCCCCCCCC
T ss_conf             92784321346579948904764421654338999999860481332527998569998863699999678980024766


Q ss_pred             HHHHHHHHHHCCC--CCCEEEEEECCCCEEEEECCCC----EEEECCCCCCCCHHHCCCCCCCCCCCCCE-EECCCCCCC
Q ss_conf             3322311100135--7640379835883799985774----27740368777777685656565434430-110577774
Q gi|254780710|r   80 GMRCVVRFLTSRM--KRKSFTFETIRGILVAKENRDG----SISVDMGEPILDWKLIPLARSFDKMDRDR-FHIGPVNHL  152 (296)
Q Consensus        80 G~Rc~a~yl~~~~--~~~~~~i~T~~g~~~~~~~~~~----~v~V~mG~p~~~~~~ip~~~~~~~~~~~~-~~~~~~~~~  152 (296)
                      |+||+|||++++.  .+++++|+|.+|.+.++...++    .|+||||.|.+..+.+|+....+...... +.....   
T Consensus        81 G~RC~~~f~~~~~~~~k~~~~v~T~~G~~~~~~~~~ng~v~~v~VdMG~p~~~~~~~p~~~~~~~~~~~~~~~~~~~---  157 (294)
T TIGR00652        81 GIRCFAKFVYEHGLVEKKDIRVETLAGVIKLEVEEENGAVAKVKVDMGEPKFKKEEIPLTDKVEKFEEPEVLLFGEV---  157 (294)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEEECCCEEEEEEEECCCEEEEEEEECCCCCCCHHCCCHHCCCCCCCCCCEEEEECC---
T ss_conf             78999999986223421106998617348999997288599999853775344100510015454554522431033---


Q ss_pred             EECCEEEEECCCCEEEEECCCC--CCHHHHHHHHHCCCCCCCC-CCCCCEEEEEECCCCEEEEEECCCC-CCCCCCCHHH
Q ss_conf             0213099955874279742557--6868887631000233237-5555146799728872899980467-8766563235
Q gi|254780710|r  153 FLRNPFVVSMGNPHAIFFVEDD--LYHYDLASFGNLLAKHPMF-SEGVNLSIARVTSLESLDLRTWERG-VGLTAACGSA  228 (296)
Q Consensus       153 ~~~~~~~v~iGNPH~Vi~v~d~--i~~~~l~~~g~~i~~~~~F-p~gvNV~fv~v~~~~~I~iRt~ERG-vGeTlACGTG  228 (296)
                      .....++|||||||||+||+ |  ++..++..+|+.||+|+.| |+||||+|+|++++++|++|||||| +|||+|||||
T Consensus       158 ~~~~~~~v~~GnPH~v~fv~-d~~~~~~~~~~lG~~~~~he~F~Peg~NV~Fv~~~~~~~i~~rtyERGV~G~T~ACGTG  236 (294)
T TIGR00652       158 QTLKLTAVDTGNPHLVVFVD-DLTVEGLDLTELGPLLEYHERFAPEGVNVNFVQVVGEDEIKLRTYERGVAGETLACGTG  236 (294)
T ss_pred             CEEEEEEEECCCCEEEEECC-CCCCCCCCHHHHHHHHHCCCCCCCCCEEEEEEEECCCCEEEEEEEEECCCCCCCCCCHH
T ss_conf             33799999659966999805-55646467567747765383557687238898976898899999880544554465147


Q ss_pred             HHHHHHHHHH--HCCCCCC-EEEECCCCEEEEEEECCC--EEEEEECEEEEEEEEEE
Q ss_conf             8999999998--1788980-799907957999995898--19999462899988998
Q gi|254780710|r  229 ACASVVASGC--LHKTNRA-VSVKMLGGGLLIEWHDNN--HVFMTGEAKKEWEGKLD  280 (296)
Q Consensus       229 A~Asa~~~~~--~~~~~~~-v~V~~pGG~L~v~~~~~~--~i~l~Gpa~~vf~G~~~  280 (296)
                      |||||+++.+  +++.+++ ++|+.|||.|.+.|.+++  ++||+|||++||+|.+.
T Consensus       237 a~A~a~aa~~~~~~~~~~~~~~V~~~gG~L~i~~~~~G~~~~ym~G~a~~V~~G~l~  293 (294)
T TIGR00652       237 ACASAIAAVKIGLGLTDKKAVTVHLPGGELEIEWKEDGKHRVYMTGPAVRVFDGELF  293 (294)
T ss_pred             HHHHHHHHHHHHCCCCCCCEEEEEECCCEEEEEEECCCCCEEEEEECEEEEEEEEEC
T ss_conf             999999998752045688616898169829999972885114687044688855653


No 3  
>PRK13577 diaminopimelate epimerase; Provisional
Probab=100.00  E-value=0  Score=618.68  Aligned_cols=269  Identities=29%  Similarity=0.463  Sum_probs=241.0

Q ss_pred             CEEEEECCCCCCEEEEECCCCCCCCCHHHHHHHCCC-CCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHHHH
Q ss_conf             113785176773899947788878888899872035-6714355899825888886689999717876212332033223
Q gi|254780710|r    6 VDFAKMEGIGNKILVIDMRGCHDNITSDAINALSTD-DNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMRCV   84 (296)
Q Consensus         6 i~F~Kmhg~GNDFiiiD~~~~~~~~~~~~i~~~~~~-~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~Rc~   84 (296)
                      |+|+||||+||||||+|.++....+++++++++|+| +||||||||++.+ ++..+||+|+|||+|||+|+|||||+||+
T Consensus         1 i~F~Kmhg~GNDFiiid~~~~~~~~~~~~i~~lc~R~~GIGaDglli~~~-~~~~~d~~m~ifNaDGS~AemCGNG~RCv   79 (281)
T PRK13577          1 MQFYKYHALGNDYLVIDPRDFPFDLSAEAIRLICHRHFGVGSDGILFGPL-ASEGADFGLRIFNPDGSEAEKSGNGLRIF   79 (281)
T ss_pred             CCEEEEECCCCEEEEEECCCCCCCCCHHHHHHHHCCCCCCCCCEEEEECC-CCCCCCEEEEEECCCCCHHHCCCCHHHHH
T ss_conf             90877744998199997899878999999998647687857786999548-88887669999938988786373889999


Q ss_pred             HHHHHCC--CCCCEEEEEECCCCEEEEECCC-CEEEECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEECCEEEEE
Q ss_conf             1110013--5764037983588379998577-427740368777777685656565434430110577774021309995
Q gi|254780710|r   85 VRFLTSR--MKRKSFTFETIRGILVAKENRD-GSISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVVS  161 (296)
Q Consensus        85 a~yl~~~--~~~~~~~i~T~~g~~~~~~~~~-~~v~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  161 (296)
                      |+|++++  ..++.++|+|.+|.+.++..++ ..|+|+||.|.|.|.++|+...........+.+...    ...+++|+
T Consensus        80 a~~l~~~~~~~~~~~~i~T~~g~~~~~~~~~~~~i~V~mg~~~~~~~~ip~~~~~~~~~~~~~~~~~~----~~~~~~v~  155 (281)
T PRK13577         80 SRYLWDQGLVDDEPFTIETKGGVVECQVLDAGRTVTVEMGKVSFLSTDIPVAGEDREVLNEKLDVDGR----RLTYCAAT  155 (281)
T ss_pred             HHHHHHCCCCCCCCEEEEECCCEEEEEEECCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCC----EEEEEEEE
T ss_conf             99999758778971899978964899994699689998888766600175445554211304886893----57899982


Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             58742797425576868887631000233237555514679972887289998046787665632358999999998178
Q gi|254780710|r  162 MGNPHAIFFVEDDLYHYDLASFGNLLAKHPMFSEGVNLSIARVTSLESLDLRTWERGVGLTAACGSAACASVVASGCLHK  241 (296)
Q Consensus       162 iGNPH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp~gvNV~fv~v~~~~~I~iRt~ERGvGeTlACGTGA~Asa~~~~~~~~  241 (296)
                      |||||||+|++ +++..++.++|+.+++|+.||+|+||+|++++++++|++||||||||||+||||||||+|++++++++
T Consensus       156 iGNPH~V~~v~-~~~~~~~~~~g~~ie~~~~FP~g~NV~fv~~~~~~~I~~Rt~ERGvGeTlACGTGA~AaA~~~~~~g~  234 (281)
T PRK13577        156 IGNPHCVVLLD-EITEELARELGPLIETHPRFPNRTNVQFMKVIDRNTIQIEIWERGAGYTLASGSSSCAAAAVAHRLGL  234 (281)
T ss_pred             CCCCEEEEEEC-CCCHHHHHHCCCHHCCCCCCCCCEEEEEEEEECCCEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             49971999962-54245576418510034447898589999993599699999946787553435789999999998088


Q ss_pred             CCCCEEEECCCCEEEEEEECCCEEEEEECEEEEEEEEEE
Q ss_conf             898079990795799999589819999462899988998
Q gi|254780710|r  242 TNRAVSVKMLGGGLLIEWHDNNHVFMTGEAKKEWEGKLD  280 (296)
Q Consensus       242 ~~~~v~V~~pGG~L~v~~~~~~~i~l~Gpa~~vf~G~~~  280 (296)
                      ++++++|++|||.|.|+|.++++|+|+|||++||+|+++
T Consensus       235 ~~~~v~V~~~GG~L~v~~~~~~~v~ltGpa~~V~~G~i~  273 (281)
T PRK13577        235 CDSSITVHMPGGQIDIEIKDDFHVSMTGPVTKIAEGSLS  273 (281)
T ss_pred             CCCCEEEECCCCEEEEEECCCCEEEEECCCEEEEEEEEC
T ss_conf             999879994995899999379869999144999999999


No 4  
>COG0253 DapF Diaminopimelate epimerase [Amino acid transport and metabolism]
Probab=100.00  E-value=0  Score=589.01  Aligned_cols=268  Identities=40%  Similarity=0.696  Sum_probs=242.0

Q ss_pred             CEEEEECCCCCCEEEEECCCCCCCCCHHHHHHHCCCC-CCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHHHH
Q ss_conf             1137851767738999477888788888998720356-714355899825888886689999717876212332033223
Q gi|254780710|r    6 VDFAKMEGIGNKILVIDMRGCHDNITSDAINALSTDD-NTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMRCV   84 (296)
Q Consensus         6 i~F~Kmhg~GNDFiiiD~~~~~~~~~~~~i~~~~~~~-giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~Rc~   84 (296)
                      |+|+||||+||||||+|.++.....+++.++.+|+|+ ||||||+|+|++|.+..+|++|+|||+|||+|+|||||+||+
T Consensus         1 ~~F~KmhG~GNdfivvd~~~~~~~~~~~~a~~l~~r~~giGaDgvl~v~~p~s~~~d~~~rifN~DGS~ae~CGNG~Rc~   80 (272)
T COG0253           1 MEFSKMHGLGNDFIVVDEFDKKDEETPELARALCDRHFGIGADGVLFVEPPRSPGADFHLRIFNSDGSEAEMCGNGARCF   80 (272)
T ss_pred             CCEEEECCCCCCEEEEECCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCHHHHCCCHHHHH
T ss_conf             90677758898599993665334368999999865536857753999925888898789999967988776255699999


Q ss_pred             HHHHHCC--CCCCEEEEEECCCCEEEEECCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEECCEEEEEC
Q ss_conf             1110013--57640379835883799985774277403687777776856565654344301105777740213099955
Q gi|254780710|r   85 VRFLTSR--MKRKSFTFETIRGILVAKENRDGSISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVVSM  162 (296)
Q Consensus        85 a~yl~~~--~~~~~~~i~T~~g~~~~~~~~~~~v~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i  162 (296)
                      |+||+++  ..+++++|+|.+|++.++..+++.|+|+||.|.|.++.+|+...  .. ...+...    .....+++|+|
T Consensus        81 a~~l~~~~~~~~~~~~v~T~~G~~~~~~~~~~~v~VdMg~p~~~~~~ip~~~~--~~-~~~~~~~----~~~~~~~~vs~  153 (272)
T COG0253          81 ARFLAERGLVKKKEISVETLAGILKVKVHDDNTVSVDMGLPSFKPAEIPLLEE--KV-EEQYGLG----EETVTFYAVSM  153 (272)
T ss_pred             HHHHHHHCCCCCCCEEEEECCCEEEEEEEECCEEEEECCCCCCCCCCCCCHHH--HC-CCCCCCC----CCCEEEEEEEC
T ss_conf             99999853875751799952543899995087799986777526244772231--00-5510234----44204899966


Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             87427974255768688876310002332375555146799728872899980467876656323589999999981788
Q gi|254780710|r  163 GNPHAIFFVEDDLYHYDLASFGNLLAKHPMFSEGVNLSIARVTSLESLDLRTWERGVGLTAACGSAACASVVASGCLHKT  242 (296)
Q Consensus       163 GNPH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp~gvNV~fv~v~~~~~I~iRt~ERGvGeTlACGTGA~Asa~~~~~~~~~  242 (296)
                      ||||+|+||+ |++..++..+|+++++|+.||+|+||+|+|++++++|++||||||+|||+|||||||||++++.+++++
T Consensus       154 GnPH~V~~Vd-dv~~~~~~~~g~~l~~~~~Fp~~vNV~F~~v~~~~~i~lrv~ERG~G~T~ACGTGa~Aa~~~a~~~~~~  232 (272)
T COG0253         154 GNPHLVIFVD-DVETANLEELGPLLESHELFPEGVNVGFVQVLSRDAIRLRVYERGAGETLACGTGACAAAVVAARLGLL  232 (272)
T ss_pred             CCCEEEEEEC-CCCCCHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             9986999958-825233554234552375578842799999779992799993058830014651788999999981658


Q ss_pred             CCCEEEECCCCEEEEEEECCC-EEEEEECEEEEEEEEEEE
Q ss_conf             980799907957999995898-199994628999889984
Q gi|254780710|r  243 NRAVSVKMLGGGLLIEWHDNN-HVFMTGEAKKEWEGKLDI  281 (296)
Q Consensus       243 ~~~v~V~~pGG~L~v~~~~~~-~i~l~Gpa~~vf~G~~~i  281 (296)
                      +++++|++|||.|.|.|.+++ +++|+|||++||+|++.+
T Consensus       233 ~~~v~V~~pGG~L~i~~~~~g~~v~m~G~a~~v~~G~~~~  272 (272)
T COG0253         233 DRKVTVHLPGGTLEIEWKDDGKPVYMTGPATRVAEGKLYI  272 (272)
T ss_pred             CCCEEEECCCCEEEEEEECCCCEEEEEECEEEEEEEEECC
T ss_conf             9867999699749999986995299981579999108859


No 5  
>pfam01678 DAP_epimerase Diaminopimelate epimerase. Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family.
Probab=99.95  E-value=1.6e-27  Score=201.25  Aligned_cols=116  Identities=29%  Similarity=0.426  Sum_probs=103.1

Q ss_pred             EEEECCCCCCEEEEECCCCCCCCCHHHHHHHCCC-CCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCH-HHHHH
Q ss_conf             3785176773899947788878888899872035-671435589982588888668999971787621233203-32231
Q gi|254780710|r    8 FAKMEGIGNKILVIDMRGCHDNITSDAINALSTD-DNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNG-MRCVV   85 (296)
Q Consensus         8 F~Kmhg~GNDFiiiD~~~~~~~~~~~~i~~~~~~-~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG-~Rc~a   85 (296)
                      |.||||+|||||++|.++....++++.++++++| .++|+||+++++++.  ..+++|++||+|||+++||||| +||++
T Consensus         1 f~K~~G~gn~fi~vd~~~~~~~~~~~~~~~l~~r~~~~g~dnv~~v~~~~--~~~~~~ri~n~dg~et~aCGnGa~rc~a   78 (121)
T pfam01678         1 FAKMHGNPHDVVVVDDVEGANLLEPELGPALCHRHFFPGADNVLFVQVSG--ELDIKMRIFNRDGSETEACGNGAVACFA   78 (121)
T ss_pred             CCCEECCCCEEEEEECCCCCCCCCHHHHHHHHCCCCCCCCEEEEEEEECC--CCCEEEEEEECCCCHHHCCCCHHHHHHH
T ss_conf             97456899799999278777767888989865577799841489987168--8718999991899820235464799999


Q ss_pred             HHHHCC--CCCCEEEEEECCCCEEEEECCCCEEEECCCCCCC
Q ss_conf             110013--5764037983588379998577427740368777
Q gi|254780710|r   86 RFLTSR--MKRKSFTFETIRGILVAKENRDGSISVDMGEPIL  125 (296)
Q Consensus        86 ~yl~~~--~~~~~~~i~T~~g~~~~~~~~~~~v~V~mG~p~~  125 (296)
                      +|++++  ..++++.|+|.+|.+.++..+++.+.|+||+|.+
T Consensus        79 ~~~~~~~~~~~~~v~v~t~gG~l~v~~~~~~~v~v~~G~a~~  120 (121)
T pfam01678        79 AAVYLGGLVTKKPVLVETPGGDLEIEVKDDGHVIVMMGPAVL  120 (121)
T ss_pred             HHHHHCCCCCCCEEEEEECCEEEEEEEECCCCEEEEECCCEE
T ss_conf             999986998898799997991899999899989998358869


No 6  
>pfam01678 DAP_epimerase Diaminopimelate epimerase. Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family.
Probab=99.89  E-value=7.1e-23  Score=170.69  Aligned_cols=113  Identities=30%  Similarity=0.454  Sum_probs=97.8

Q ss_pred             ECCCCEEEEECCCCCCHHHH--HHHHHCCCCCCCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             55874279742557686888--7631000233237555514679972887289998046787665632358999999998
Q gi|254780710|r  161 SMGNPHAIFFVEDDLYHYDL--ASFGNLLAKHPMFSEGVNLSIARVTSLESLDLRTWERGVGLTAACGSAACASVVASGC  238 (296)
Q Consensus       161 ~iGNPH~Vi~v~d~i~~~~l--~~~g~~i~~~~~Fp~gvNV~fv~v~~~~~I~iRt~ERGvGeTlACGTGA~Asa~~~~~  238 (296)
                      ..||||++++++ +++..++  ..+++.+++++.||.++||.|++..++..+++|+||||.|||+||||||||+++++..
T Consensus         4 ~~G~gn~fi~vd-~~~~~~~~~~~~~~~l~~r~~~~g~dnv~~v~~~~~~~~~~ri~n~dg~et~aCGnGa~rc~a~~~~   82 (121)
T pfam01678         4 MHGNPHDVVVVD-DVEGANLLEPELGPALCHRHFFPGADNVLFVQVSGELDIKMRIFNRDGSETEACGNGAVACFAAAVY   82 (121)
T ss_pred             EECCCCEEEEEE-CCCCCCCCCHHHHHHHHCCCCCCCCEEEEEEEECCCCCEEEEEEECCCCHHHCCCCHHHHHHHHHHH
T ss_conf             568997999992-7877776788898986557779984148998716887189999918998202354647999999999


Q ss_pred             HCCC--CCCEEEECCCCEEEEEEECCCE-EEEEECEEEE
Q ss_conf             1788--9807999079579999958981-9999462899
Q gi|254780710|r  239 LHKT--NRAVSVKMLGGGLLIEWHDNNH-VFMTGEAKKE  274 (296)
Q Consensus       239 ~~~~--~~~v~V~~pGG~L~v~~~~~~~-i~l~Gpa~~v  274 (296)
                      .+..  +++++|+++||.|.++|.+++. +++.|||++|
T Consensus        83 ~~~~~~~~~v~v~t~gG~l~v~~~~~~~v~v~~G~a~~v  121 (121)
T pfam01678        83 LGGLVTKKPVLVETPGGDLEIEVKDDGHVIVMMGPAVLV  121 (121)
T ss_pred             HCCCCCCCEEEEEECCEEEEEEEECCCCEEEEECCCEEC
T ss_conf             869988987999979918999998999899983588699


No 7  
>pfam02567 PhzC-PhzF Phenazine biosynthesis-like protein. PhzC/PhzF is involved in dimerization of two 2,3-dihydro-3-oxo-anthranilic acid molecules to create PCA by P. fluorescens. This family also contains a putative thymidilate synthase from Mycobacterium tuberculosis, though there is no significant sequence similarity to pfam00303 members. This family appears to be distantly related to pfam01678, including containing a weak internal duplication. However members of this family do not contain the conserved cysteines that are hypothesized to be active site residues (Bateman A pers obs).
Probab=99.59  E-value=4.1e-12  Score=99.72  Aligned_cols=255  Identities=21%  Similarity=0.185  Sum_probs=164.8

Q ss_pred             EEEECCCCCCEEEE-ECCCCCCCCCHHHHHHHCCCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHH
Q ss_conf             37851767738999-47788878888899872035671435589982588888668999971787621233203322311
Q gi|254780710|r    8 FAKMEGIGNKILVI-DMRGCHDNITSDAINALSTDDNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMRCVVR   86 (296)
Q Consensus         8 F~Kmhg~GNDFiii-D~~~~~~~~~~~~i~~~~~~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~Rc~a~   86 (296)
                      |+.=--.||==-++ |    ...++.++.+.+++..+.  -=-.||.++.+...||++|||.+. .|-.+||-++-..++
T Consensus         4 Ft~~~f~GNPaaVv~~----~~~Ls~~~mQ~IA~e~n~--SETaFv~~~~~~~~~~~lR~FTP~-~Ev~fcGHaTlaaa~   76 (280)
T pfam02567         4 FTDSPFKGNPAAVVLD----ADELTDEEMQAIAAEFNL--SETAFVLPPSDEDADFRLRIFTPV-AEVPFCGHATLATAH   76 (280)
T ss_pred             CCCCCCCCCEEEEEEC----CCCCCHHHHHHHHHHHCC--CEEEEEECCCCCCCCEEEEEECCC-CCCCCCCCHHHHHHH
T ss_conf             7599998631799988----989999999999998799--658997058888773699996785-413556660589999


Q ss_pred             HHHCC--CCCCEEEEEECCCCEEEEECCC---CEEEECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEECCEEEEE
Q ss_conf             10013--5764037983588379998577---427740368777777685656565434430110577774021309995
Q gi|254780710|r   87 FLTSR--MKRKSFTFETIRGILVAKENRD---GSISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVVS  161 (296)
Q Consensus        87 yl~~~--~~~~~~~i~T~~g~~~~~~~~~---~~v~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  161 (296)
                      +|++.  .....+.++|.+|.+.++...+   ..+.+.|..|.+.+..++.......     ................++
T Consensus        77 ~L~~~~~~~~~~~~~~t~~G~l~v~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~~~~-----~~~~~~~~~~~~p~~~~~  151 (280)
T pfam02567        77 ALFEEGGNGNKTLELETLAGIVPVKLVEGDGGAEGAIEMNFPEFDLPAVSREDDALL-----LAGIGLEFHEALPIAVKS  151 (280)
T ss_pred             HHHHHCCCCCCEEEEECCEEEEEEEEECCCCCEEEEEEECCCCCCCCCCCHHHHHHH-----HHCCCCCCCCCCCEEEEE
T ss_conf             999837999987999937288999998158854899993799888767883555665-----416674202566628995


Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEE-E--EEECCCCEEEEEECCCCCC--CCCCCHHHHHHHHHHH
Q ss_conf             587427974255768688876310002332375555146-7--9972887289998046787--6656323589999999
Q gi|254780710|r  162 MGNPHAIFFVEDDLYHYDLASFGNLLAKHPMFSEGVNLS-I--ARVTSLESLDLRTWERGVG--LTAACGSAACASVVAS  236 (296)
Q Consensus       162 iGNPH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp~gvNV~-f--v~v~~~~~I~iRt~ERGvG--eTlACGTGA~Asa~~~  236 (296)
                      .|+||+++.++ +.+  .|..+-+-++....+..+..+. +  ....+...+..|.|--..|  |--+|||++||-+.+.
T Consensus       152 ~G~~~l~v~l~-~~~--~l~~~~pd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~FaP~~Gi~EDpaTGSA~~aLa~yl  228 (280)
T pfam02567       152 TGLWHVFVPLK-SLE--ALAALDPDLDAAIADCPDDGVIVGPAASAGSPRDYHARMFAPALGIVEDPATGSAAGALGAYL  228 (280)
T ss_pred             CCCCEEEEEEC-CHH--HHHHCCCCHHHHHHHCCCCEEEEEEECCCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             69977999969-999--998589997999845888679999961689875699981645679777676256579999999


Q ss_pred             HHHCCCCC--CEEEEC-----CCCEEEEEEECCC----EEEEEECEEEEEEE
Q ss_conf             98178898--079990-----7957999995898----19999462899988
Q gi|254780710|r  237 GCLHKTNR--AVSVKM-----LGGGLLIEWHDNN----HVFMTGEAKKEWEG  277 (296)
Q Consensus       237 ~~~~~~~~--~v~V~~-----pGG~L~v~~~~~~----~i~l~Gpa~~vf~G  277 (296)
                      ...+..+.  .+.+.+     .+|.|.+++..++    .|++.|.|..+.+|
T Consensus       229 ~~~~~~~~~~~~~i~QG~~~gR~g~i~v~~~~~~~~~~~V~vgG~av~v~~G  280 (280)
T pfam02567       229 SRHGNKPQFGNIAIRQGQASGRPGTLEVEVEGRGGRDVRVRVTGRAVTVMEG  280 (280)
T ss_pred             HHHCCCCCCCEEEEECCCCCCCCEEEEEEEEECCCCEEEEEEEEEEEEEEEC
T ss_conf             9846998774599988736089989999998279964589998189999879


No 8  
>PRK10281 hypothetical protein; Provisional
Probab=99.52  E-value=2.8e-11  Score=94.23  Aligned_cols=262  Identities=16%  Similarity=0.125  Sum_probs=155.3

Q ss_pred             EEEECCCCCCEEEEECCCCCCCCCHHHHHHHCCCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHHH
Q ss_conf             37851767738999477888788888998720356714355899825888886689999717876212332033223111
Q gi|254780710|r    8 FAKMEGIGNKILVIDMRGCHDNITSDAINALSTDDNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMRCVVRF   87 (296)
Q Consensus         8 F~Kmhg~GNDFiiiD~~~~~~~~~~~~i~~~~~~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~Rc~a~y   87 (296)
                      |+.=-=.||-=-++-   ....++.++.+.+++..+.  -=-.||.++.++..|+++|+|-+. .|-.+||-++-..++.
T Consensus        11 Ft~~~f~GNPaaVv~---~~~~L~~~~mq~IA~E~Nl--SETaFv~~~~~~~~~~~lR~FTP~-~Ev~fcGHaTlaa~~~   84 (299)
T PRK10281         11 FTSQPFRGNSAGVVL---PADGLSEAQMQLIARELGH--SETAFLLSSDDSSYDVRVRYFTPT-VEVPICGHATVAAHYV   84 (299)
T ss_pred             CCCCCCCCCEEEEEE---CCCCCCHHHHHHHHHHHCC--CEEEEEECCCCCCCCEEEEEECCC-CCCCCCCCHHHHHHHH
T ss_conf             649999962049997---8989899999999998799--559998057888771689997576-4145453067999999


Q ss_pred             HHCC--CCCCEEEEEECCCCEEEEECCCC---EEEECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEECCEEEEEC
Q ss_conf             0013--57640379835883799985774---277403687777776856565654344301105777740213099955
Q gi|254780710|r   88 LTSR--MKRKSFTFETIRGILVAKENRDG---SISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVVSM  162 (296)
Q Consensus        88 l~~~--~~~~~~~i~T~~g~~~~~~~~~~---~v~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i  162 (296)
                      +...  .....+.++|.+|.+.+.+..++   .+....+.|.+.+.   +.........+-+.+...+...-.....+++
T Consensus        85 l~~~~~~~~~~~~~~t~~G~l~v~v~~~~~~~~~~~~~~~p~~~~~---~~~~~~~~l~~algl~~~~i~~~~p~~~~~~  161 (299)
T PRK10281         85 RATVLGLGNCTVWQTTGAGKLPVDIEKENNDYRISMTQGTPEFEPP---LEGETRAAIINALGLTEDDILPGLPIQVAST  161 (299)
T ss_pred             HHHHCCCCCCEEEEECCCEEEEEEEEEECCEEEEEECCCCCCCCCC---CCCHHHHHHHHHHCCCHHHHCCCCCEEEEEC
T ss_conf             9972688995499981670799999950881699855898734699---8803299999873999689343798099975


Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCC--CCCE-E-EEEECCCCE--EEEEECCCCCC--CCCCCHHHHHHHHH
Q ss_conf             874279742557686888763100023323755--5514-6-799728872--89998046787--66563235899999
Q gi|254780710|r  163 GNPHAIFFVEDDLYHYDLASFGNLLAKHPMFSE--GVNL-S-IARVTSLES--LDLRTWERGVG--LTAACGSAACASVV  234 (296)
Q Consensus       163 GNPH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp~--gvNV-~-fv~v~~~~~--I~iRt~ERGvG--eTlACGTGA~Asa~  234 (296)
                      |.+|+++.++ +.+  .|..+-|-++....+..  +++- . |......+.  +..|.|--++|  |--+|||++||-+.
T Consensus       162 G~~~llv~l~-~~~--~l~~l~Pd~~~l~~l~~~~~~~g~~v~~~~~~~~~~~~~~R~FaP~~Gi~EDPaTGSA~~~La~  238 (299)
T PRK10281        162 GHSKVMIPLK-PEV--DLDALSPNLAALTAISKQIGCNGFFPFQIRPGKNEILTDGRMFSPAIGIVEDPVTGNANGPMGA  238 (299)
T ss_pred             CCCEEEEEEC-CHH--HHHHCCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCEEEEEECCCCCCCCCCCCCCHHHHHHHH
T ss_conf             9975999989-999--9973799989999878743963799999857887617999977665699756664321467799


Q ss_pred             HHHHHCCCCC-----CEEEEC-----CCCEEEEEEECC-C---EEEEEECEEEEEEEEEEE
Q ss_conf             9998178898-----079990-----795799999589-8---199994628999889984
Q gi|254780710|r  235 ASGCLHKTNR-----AVSVKM-----LGGGLLIEWHDN-N---HVFMTGEAKKEWEGKLDI  281 (296)
Q Consensus       235 ~~~~~~~~~~-----~v~V~~-----pGG~L~v~~~~~-~---~i~l~Gpa~~vf~G~~~i  281 (296)
                      +....++...     .+.+++     ..|.+.+++..+ +   .|++.|.|..|++|+|.|
T Consensus       239 yL~~~~~~~~~~~~~~~~~~QG~~~gR~s~i~v~v~~~~~~~~~V~vgG~av~v~~Ge~~i  299 (299)
T PRK10281        239 YLVHHNLLPHDGKVLRFKGHQGRALGRDGVIEVTVTIRDNQPEKVTISGQAVILFHAEWAI  299 (299)
T ss_pred             HHHHCCCCCCCCCCEEEEEEEEEECCCCEEEEEEEEECCCCEEEEEEEEEEEEEEEEEEEC
T ss_conf             9987585767777307999930164898489999996699766899988999999989989


No 9  
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=99.39  E-value=1.3e-09  Score=83.30  Aligned_cols=261  Identities=19%  Similarity=0.191  Sum_probs=165.5

Q ss_pred             EEEECCCCCCEEEEECCCCCCCCCHHHHHHHCCCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHHH
Q ss_conf             37851767738999477888788888998720356714355899825888886689999717876212332033223111
Q gi|254780710|r    8 FAKMEGIGNKILVIDMRGCHDNITSDAINALSTDDNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMRCVVRF   87 (296)
Q Consensus         8 F~Kmhg~GNDFiiiD~~~~~~~~~~~~i~~~~~~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~Rc~a~y   87 (296)
                      |+.=--.||---++.   ....++..+.+++++..+.  ---.||.++.++ +|+++|||-+++-. .+||-.+-..++.
T Consensus        12 Ft~~~~~GNp~aVv~---~a~~Lsd~~MQ~IA~e~n~--SET~Fv~~~~~~-~~~rlR~FTP~~Ev-pf~GHaTlga~~~   84 (291)
T COG0384          12 FTSKPFGGNPLAVVL---DADGLSDEQMQAIAREFNL--SETAFVLPPDDP-ADARLRIFTPTTEV-PFAGHATLGAAHV   84 (291)
T ss_pred             ECCCCCCCCCEEEEE---CCCCCCHHHHHHHHHHHCC--CEEEEECCCCCC-CCEEEEEECCCCCC-CCCCCHHHHHHHH
T ss_conf             337898998229981---8999999999999998499--616997278886-71489996787514-6688777999999


Q ss_pred             HHCC---CCCCEEEEEECCCCEEEEECCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEECCEEEEECCC
Q ss_conf             0013---5764037983588379998577427740368777777685656565434430110577774021309995587
Q gi|254780710|r   88 LTSR---MKRKSFTFETIRGILVAKENRDGSISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVVSMGN  164 (296)
Q Consensus        88 l~~~---~~~~~~~i~T~~g~~~~~~~~~~~v~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~iGN  164 (296)
                      +++.   .....+.++|.+|.+.+....++.- ..|..|.+.....+-. +...+ .+-+.+...+-.....+..+++|-
T Consensus        85 l~~~~~~~~~~~~~~e~~aG~v~i~~~~~~~~-~~~~~p~~~~~~~~~~-~~~~l-a~aLgL~~~~~~~~~~~~~~stG~  161 (291)
T COG0384          85 LAELGGLSNDTTLTLETKAGLVPVTVERGGGQ-AEFDLPQLPPPEEIEA-EPAEL-AEALGLEEDDLLPEHPPQVVSTGL  161 (291)
T ss_pred             HHHHCCCCCCCEEEEEECCCEEEEEEEECCCC-EEECCCCCCCCCCCCC-CHHHH-HHHCCCCHHHCCCCCCCEEEECCC
T ss_conf             99744888662499991467189999967883-3673688888666654-78999-987399947824246843750698


Q ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCCCCCC-CCCCEEEEE---ECCCCEEEEEECCCCC--CCCCCCHHHHHHHHHHHHH
Q ss_conf             427974255768688876310002332375-555146799---7288728999804678--7665632358999999998
Q gi|254780710|r  165 PHAIFFVEDDLYHYDLASFGNLLAKHPMFS-EGVNLSIAR---VTSLESLDLRTWERGV--GLTAACGSAACASVVASGC  238 (296)
Q Consensus       165 PH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp-~gvNV~fv~---v~~~~~I~iRt~ERGv--GeTlACGTGA~Asa~~~~~  238 (296)
                      ||+++.++ +.+.  +..+-+-.......+ .+.++-.+.   ...+..+..|-|==+.  -|--++||++|+-+.+...
T Consensus       162 ~~l~v~l~-s~~a--v~~~~pd~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~R~FaP~~Gi~EDPaTGSA~~~La~yl~~  238 (291)
T COG0384         162 PDLLVPLE-SLEA--LDALRPDFSALTELSAGGGGVYVFAREGAGAEADFHARMFAPGIGVVEDPATGSAAGALAAYLAK  238 (291)
T ss_pred             CEEEEEEC-CHHH--HHHCCCCHHHHHHHCCCCCCEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             61899918-8899--97669887998752336662599974057887758998135324887777764546589999998


Q ss_pred             HCCC--CCCEEEEC-----CCCEEEEEEECC---CEEEEEECEEEEEEEEEEE
Q ss_conf             1788--98079990-----795799999589---8199994628999889984
Q gi|254780710|r  239 LHKT--NRAVSVKM-----LGGGLLIEWHDN---NHVFMTGEAKKEWEGKLDI  281 (296)
Q Consensus       239 ~~~~--~~~v~V~~-----pGG~L~v~~~~~---~~i~l~Gpa~~vf~G~~~i  281 (296)
                      .+..  ..++.+++     ..|.|.+++...   ..|++.|.|..+++|++.|
T Consensus       239 ~~~~~~~~~~~~~QG~~~gR~s~i~~~~~~~~~~~~v~vgG~av~~~~g~l~l  291 (291)
T COG0384         239 HGGLPDKLRLLIEQGTELGRPSRIEVRVDEDGNKEAVRVGGRAVTVAEGELEL  291 (291)
T ss_pred             HCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCCEEEEEEEEEEEEEEEEEEC
T ss_conf             68888765389982323699848999996368814799811899987778819


No 10 
>KOG3033 consensus
Probab=99.17  E-value=5.8e-09  Score=78.99  Aligned_cols=262  Identities=18%  Similarity=0.244  Sum_probs=160.5

Q ss_pred             EEEECCCCCCEEEEECCCCCCCCCHHHHHHHCCCCCCCCCEEEEEECCC-CCCCCEEEEEEECCCCCCCCCCCHHHHHHH
Q ss_conf             3785176773899947788878888899872035671435589982588-888668999971787621233203322311
Q gi|254780710|r    8 FAKMEGIGNKILVIDMRGCHDNITSDAINALSTDDNTHFDQIMLIHDFQ-DASVDAFIRIINCDGSEVQSCGNGMRCVVR   86 (296)
Q Consensus         8 F~Kmhg~GNDFiiiD~~~~~~~~~~~~i~~~~~~~giG~Dgli~i~~~~-~~~~d~~m~~fN~DGS~A~mCGNG~Rc~a~   86 (296)
                      |++--=.||- ..+-... +...+.+..|.+++.+.+-=--  |+.|+. +...+|.+|.|-+ -+|-..||-++-.-|+
T Consensus        13 ft~~~f~gnp-aav~~l~-ene~d~e~Lq~iA~efNlSET~--Fl~pi~~~~~~~f~LRwFTp-~aEvplcGHaTLasah   87 (286)
T KOG3033          13 FTEKAFKGNP-AAVCFLE-ENERDDEYLQSIAAEFNLSETA--FLIPIGGKKCSRFSLRWFTP-TAEVPLCGHATLASAH   87 (286)
T ss_pred             EECCCCCCCC-CEEEECC-CCCCCHHHHHHHHHHHCCCCCE--EEECCCCCCCCCEEEEEECC-CCCCCCCCCCHHHHHH
T ss_conf             3132025996-1224222-3001699999998761864305--54337877555235787334-3337646761366778


Q ss_pred             HHHCC--CCCCEEEEEECCCCEEEEECCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEECCEEEEECCC
Q ss_conf             10013--5764037983588379998577427740368777777685656565434430110577774021309995587
Q gi|254780710|r   87 FLTSR--MKRKSFTFETIRGILVAKENRDGSISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVVSMGN  164 (296)
Q Consensus        87 yl~~~--~~~~~~~i~T~~g~~~~~~~~~~~v~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~iGN  164 (296)
                      -|..+  ...+++.++|.+|++.++.+..+.  ++|-.|.++...|-...+...+    +.. .....+.......-+++
T Consensus        88 vlf~~~~n~n~~l~f~t~sG~l~akrd~~~~--ieln~P~y~~~si~~~~~~~~~----fsk-a~~~~~i~dv~~~~~~~  160 (286)
T KOG3033          88 VLFNEIGNVNKELKFDTLSGILTAKRDELGS--IELNFPEYDTTSINISNELEGI----FSK-AEGPAFIFDVIKCVTPT  160 (286)
T ss_pred             HHHHHCCCCCCEEEEEEECCEEEEEECCCCC--EEECCCCCCCCCCCCCCHHHHH----HHH-HHCCCEECCCHHCCCCC
T ss_conf             8887526775159998411369998525651--6871675443144335067999----998-62875551511046898


Q ss_pred             C-EEEEECCCCCCHHHHHHHHHCCCCCCCCC-CCCCEEEEEECC-CCEEEEEECC--CCCCCCCCCHHHHHHHHHHHH-H
Q ss_conf             4-27974255768688876310002332375-555146799728-8728999804--678766563235899999999-8
Q gi|254780710|r  165 P-HAIFFVEDDLYHYDLASFGNLLAKHPMFS-EGVNLSIARVTS-LESLDLRTWE--RGVGLTAACGSAACASVVASG-C  238 (296)
Q Consensus       165 P-H~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp-~gvNV~fv~v~~-~~~I~iRt~E--RGvGeTlACGTGA~Asa~~~~-~  238 (296)
                      | -+++.+++.-..++++-.--.+..+..=| +++-|.|+--.+ +.....|-|-  -||.|--+||||.||.+-+-. .
T Consensus       161 p~~liVvl~~~~t~~elep~~~d~~di~~~p~~~~~v~~~g~~g~~~dy~~RyFAP~~GVnEDPvtGSa~caL~~yws~~  240 (286)
T KOG3033         161 PRKLIVVLDPWETVFELEPNRIDISDISTCPNNGMIVTFAGSSGSPYDYESRYFAPWVGVNEDPVTGSAHCALGPYWSLI  240 (286)
T ss_pred             CCEEEEEECCCCEEEECCHHHHHHHHHHCCCCCCEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCEEEEHHHHHHHH
T ss_conf             74599995783204634702422346542898724899766999987667651244004567888871456337779987


Q ss_pred             HCCCCC-CEEEE-CCCCEEEEEEECCC-EEEEEECEEEEEEEEEEE
Q ss_conf             178898-07999-07957999995898-199994628999889984
Q gi|254780710|r  239 LHKTNR-AVSVK-MLGGGLLIEWHDNN-HVFMTGEAKKEWEGKLDI  281 (296)
Q Consensus       239 ~~~~~~-~v~V~-~pGG~L~v~~~~~~-~i~l~Gpa~~vf~G~~~i  281 (296)
                      +++.+. ..... ..||.++++++++. .++|.|+|..|-+|++.+
T Consensus       241 ~~k~~~~afqas~~Rgg~~rv~l~~ea~rV~l~G~avtVl~G~i~v  286 (286)
T KOG3033         241 LGKKDFYAFQASPTRGGLFRVSLKKEAQRVILNGGAVTVLRGEILV  286 (286)
T ss_pred             CCCCCEEEEEECCCCCCEEEEEECCCCEEEEECCCCEEEEEEEEEC
T ss_conf             2842300010024678379999847760899549818998558859


No 11 
>TIGR00654 PhzF_family phenazine biosynthesis protein PhzF family; InterPro: IPR003719   Five genes, phzF, phzA, phzB, phzC and phzD, encode enzymes for phenazine biosynthesis in the biological control bacterium Pseudomonas chlororaphis (Pseudomonas aureofaciens). Protein PhzF is similar to 3-deoxy-D-arabino-heptulosonate-7-phosphate synthases of solanaceous plants. PhzC is responsible for the conversion of phenazine-I-carboxylic acid to 2-hydroxy-phenazine-I-carboxylic acid .; GO: 0003824 catalytic activity, 0009058 biosynthetic process.
Probab=99.04  E-value=1.6e-07  Score=69.51  Aligned_cols=265  Identities=17%  Similarity=0.167  Sum_probs=170.2

Q ss_pred             EEEECCCCCCEEEEECCCC-CCCCCHHHHHHHCCCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHH
Q ss_conf             3785176773899947788-878888899872035671435589982588888668999971787621233203322311
Q gi|254780710|r    8 FAKMEGIGNKILVIDMRGC-HDNITSDAINALSTDDNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMRCVVR   86 (296)
Q Consensus         8 F~Kmhg~GNDFiiiD~~~~-~~~~~~~~i~~~~~~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~Rc~a~   86 (296)
                      |+--=+-||---+|..-+. +.+++.++.++++++.|.  -=-.||.+|.++..|+++|||-+ ++|-.+||-.+=...+
T Consensus        11 FT~~pF~GNp~aV~~~~e~dene~s~~~mQ~IA~~~ny--SET~F~~~P~~~~~d~~LR~FTP-~~El~~aGHaTigs~y   87 (314)
T TIGR00654        11 FTSQPFKGNPAAVVLDAEDDENELSEEEMQLIAEEINY--SETAFLLKPVSEKADLRLRIFTP-KSELPFAGHATIGSLY   87 (314)
T ss_pred             EECCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHCC--CEEEEEECCCCCCCCEEEEEECC-CCCCCCCCCHHHHHHH
T ss_conf             74689898744887057687000587899999997188--40255317878766637887648-7534777864389999


Q ss_pred             HH--HCC---CCCCEEEEEECCCCEEEEECCC-C--EEEECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEE-CCE
Q ss_conf             10--013---5764037983588379998577-4--2774036877777768565656543443011057777402-130
Q gi|254780710|r   87 FL--TSR---MKRKSFTFETIRGILVAKENRD-G--SISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFL-RNP  157 (296)
Q Consensus        87 yl--~~~---~~~~~~~i~T~~g~~~~~~~~~-~--~v~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~-~~~  157 (296)
                      .+  .+.   ...+.+.+++..|.+.+++... +  .++..-+.|.|.++   ++.+...-..+-+.+..-+.... ...
T Consensus        88 ~~Gl~~~~~~~~~~t~~~~~~~G~~Pvti~~~~g~l~is~~~~~~~f~~~---~~~~~~~~l~~aLGLt~d~~~~~elpi  164 (314)
T TIGR00654        88 ALGLLEVTKLEVATTLVQEEKAGLVPVTIEEKDGQLRISLEQAAPDFEPK---LSGESRADLAKALGLTEDDFLKGELPI  164 (314)
T ss_pred             HHHHHCCCCCCCEEEEEEECCCCEEEEEEECCCCCEEEEEECCCCCCCCC---CCHHHHHHHHHHHCCCHHHHCCCCCCC
T ss_conf             87620057875102388703676056788615892788600258888889---876889999998387756816887660


Q ss_pred             EEEECCCCEEEEECCCCCC----HHHHHHHHHCCC---CCCCCCCCCCEEEEEECCCCE---EEEEECC-CCCC--CCCC
Q ss_conf             9995587427974255768----688876310002---332375555146799728872---8999804-6787--6656
Q gi|254780710|r  158 FVVSMGNPHAIFFVEDDLY----HYDLASFGNLLA---KHPMFSEGVNLSIARVTSLES---LDLRTWE-RGVG--LTAA  224 (296)
Q Consensus       158 ~~v~iGNPH~Vi~v~d~i~----~~~l~~~g~~i~---~~~~Fp~gvNV~fv~v~~~~~---I~iRt~E-RGvG--eTlA  224 (296)
                      .+.++|-+-+++.+++..+    .+|...+...+.   +.-.||-+..-.   ...++.   +..|-|= =+.|  |=-+
T Consensus       165 ~~~~tG~~~~~ipl~~~e~~~~~~P~~~~l~~~~~~~~~~gv~~~~~~~~---~~~~~~nkl~~gR~FasP~~gi~EDPv  241 (314)
T TIGR00654       165 QLLSTGLEFVVIPLKDEEALKKLSPDLKVLAELLKKLDKDGVYPFAPKKE---AAGKSDNKLLHGRMFASPVIGIVEDPV  241 (314)
T ss_pred             EEECCCCEEEEEECCCHHHHHHHCCCHHHHHHHHHCCCCCEEEECCCCCC---CCCCCCCHHHCCEEECCCCCCCEECCC
T ss_conf             45406753798851786998651788889999985078765886366776---788763101026000278776255572


Q ss_pred             CHHHHHHHHHHHHHHCCC--CCCEEEE----CCCC------EEEEEEE--CC--CEEEEEECEEEEEEEEEEE
Q ss_conf             323589999999981788--9807999----0795------7999995--89--8199994628999889984
Q gi|254780710|r  225 CGSAACASVVASGCLHKT--NRAVSVK----MLGG------GLLIEWH--DN--NHVFMTGEAKKEWEGKLDI  281 (296)
Q Consensus       225 CGTGA~Asa~~~~~~~~~--~~~v~V~----~pGG------~L~v~~~--~~--~~i~l~Gpa~~vf~G~~~i  281 (296)
                      ||||..|-+.++.-.+..  .+++.|.    -.|+      .+.+...  ++  ..+.++|-|+++++|.|+|
T Consensus       242 tG~g~~~lg~YL~~~~~~~~~h~~~i~rvkGhqG~~Lgr~g~~~~~v~~~~~~~~~v~iaG~Av~~~~~~~~~  314 (314)
T TIGR00654       242 TGSGSGALGAYLKHVLDNEKSHDITIERVKGHQGKALGRDGKLEVTVKKEGDNSEKVKIAGTAVLVIEGKLKI  314 (314)
T ss_pred             CCCCCHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEECCCCEEEEEEEEEEEEEEEEEECC
T ss_conf             1565367778898750686675348998505567301789618999994178847999977899875224519


No 12 
>PRK13969 proline racemase; Provisional
Probab=98.76  E-value=2.6e-05  Score=54.87  Aligned_cols=266  Identities=13%  Similarity=0.138  Sum_probs=141.7

Q ss_pred             CCCCEEEEECCCCCCEEEEE-CCCCCCCCCH-----------HHHH-HHCC-CCCC-CCCEEEEEECCCCCCCCEEEEEE
Q ss_conf             75411378517677389994-7788878888-----------8998-7203-5671-43558998258888866899997
Q gi|254780710|r    3 SSMVDFAKMEGIGNKILVID-MRGCHDNITS-----------DAIN-ALST-DDNT-HFDQIMLIHDFQDASVDAFIRII   67 (296)
Q Consensus         3 ~~mi~F~Kmhg~GNDFiiiD-~~~~~~~~~~-----------~~i~-~~~~-~~gi-G~Dgli~i~~~~~~~~d~~m~~f   67 (296)
                      +.+|+-.-||..|.=+=||- .......-+-           +.+| .|.. -+|- .-=|- +|.||.++.+|+-+-|+
T Consensus         4 ~~~i~~iD~Ht~GEP~RiV~~G~p~l~G~t~~ekr~~~~~~~D~lR~~Lm~EPRGh~~M~Ga-ll~pp~~~~Ad~Gvif~   82 (335)
T PRK13969          4 IKTIQTIESHTMGEPTRIVIGGLPKVPGKTMAEKMEYLEENNDSLRTMLMSEPRGHNDMFGA-IYTEPADETADLGIIFM   82 (335)
T ss_pred             CEEEEEEECCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEE-EEECCCCCCCCEEEEEE
T ss_conf             31788996557988757997398899999999999999866579999976089988761789-97089998888899999


Q ss_pred             ECCCCCCCCCCCHHHHHHHHHHCC--C----CCCEEEEEECCCCEEEEEC-CCCE-EEECC-CCCCCCHH-HCCCCCCCC
Q ss_conf             178762123320332231110013--5----7640379835883799985-7742-77403-68777777-685656565
Q gi|254780710|r   68 NCDGSEVQSCGNGMRCVVRFLTSR--M----KRKSFTFETIRGILVAKEN-RDGS-ISVDM-GEPILDWK-LIPLARSFD  137 (296)
Q Consensus        68 N~DGS~A~mCGNG~Rc~a~yl~~~--~----~~~~~~i~T~~g~~~~~~~-~~~~-v~V~m-G~p~~~~~-~ip~~~~~~  137 (296)
                      +++|-. .|||-|+=|++.+|.+.  .    +..++.|+|.+|++.++.. .+++ .+|.+ -.|+|..+ ++++..+  
T Consensus        83 ~~~gy~-~McGh~tI~~~t~lve~G~v~~~~p~t~v~ietPaGlV~a~~~~~~gkv~~V~f~nVPsf~~~~d~~v~vp--  159 (335)
T PRK13969         83 DGGGYL-NMCGHGSIGAATCAVEMGIVKVEEPYTNIKLEAPAGMINARVKVEDGKAKETSIVNVPAFLYKKDVEIDVP--  159 (335)
T ss_pred             ECCCCC-CCCCCCHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEEEECCCEEEEEEEEEECHHHHCCCEEECC--
T ss_conf             378677-54353278888899985971466896589998689529999999289502899997401464379689878--


Q ss_pred             CCCCCEEECCCCCCCEECCEEEEECCCCEEEEECC------CCCCHHHHHHHHHCCC---------CCCCCCCCCCEEEE
Q ss_conf             43443011057777402130999558742797425------5768688876310002---------33237555514679
Q gi|254780710|r  138 KMDRDRFHIGPVNHLFLRNPFVVSMGNPHAIFFVE------DDLYHYDLASFGNLLA---------KHPMFSEGVNLSIA  202 (296)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~~v~iGNPH~Vi~v~------d~i~~~~l~~~g~~i~---------~~~~Fp~gvNV~fv  202 (296)
                      ....  ..           .-...=||-=+++-.+      +.-+.-+|.++|..|+         .||..|..-.+.++
T Consensus       160 ~~G~--v~-----------vDiayGG~fyaiVd~~~lgl~l~~~~~~~l~~~g~~I~~a~~~~~~~~hP~~~~i~~i~~v  226 (335)
T PRK13969        160 DYGK--LT-----------LDISFGGSFFAMVDAEKVGIDISPANSQKLNDLGMKIVHAVNEQVEIKHPVLEHIKTVDLC  226 (335)
T ss_pred             CCCC--EE-----------EEEEECCEEEEEEEHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEE
T ss_conf             9775--79-----------9997266389998789939876832799999999999999986537879887777716899


Q ss_pred             EECCCCE-----E-EEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCC--CCEEEECCCCEE-EEEE------ECCCE--E
Q ss_conf             9728872-----8-999804678766563235899999999817889--807999079579-9999------58981--9
Q gi|254780710|r  203 RVTSLES-----L-DLRTWERGVGLTAACGSAACASVVASGCLHKTN--RAVSVKMLGGGL-LIEW------HDNNH--V  265 (296)
Q Consensus       203 ~v~~~~~-----I-~iRt~ERGvGeTlACGTGA~Asa~~~~~~~~~~--~~v~V~~pGG~L-~v~~------~~~~~--i  265 (296)
                      ...++..     . .+-+|=-|.=----||||.+|-.+..+..|++.  .+...+..=|.. ..+.      .+-.-  .
T Consensus       227 ~~~~~~~~~~~~~rn~vv~~~g~iDRSPcGTGtSARlA~l~a~G~l~~ge~~~~eSIiGs~F~~~i~~~t~~g~~~aVip  306 (335)
T PRK13969        227 EFYGPAKSEDADVQNVVVFGQGQVDRSPCGTGTSAKMALLYAQGKMKVGEEIVNESIICTKFKGKILEETKVGEYDGIIP  306 (335)
T ss_pred             EECCCCCCCCCCEEEEEEECCCCEECCCCCCCHHHHHHHHHHCCCCCCCCEEEEEECCCCEEEEEEEEEEEECCCCEEEE
T ss_conf             98079888887615689989982626887512899999999769977999099996028769999999999889587999


Q ss_pred             EEEECEEEEEEEEEEECCCC
Q ss_conf             99946289998899841320
Q gi|254780710|r  266 FMTGEAKKEWEGKLDIKTGK  285 (296)
Q Consensus       266 ~l~Gpa~~vf~G~~~i~~~~  285 (296)
                      ..+|.|-..-+.++-+...+
T Consensus       307 ~I~G~A~itG~~~~~~d~~D  326 (335)
T PRK13969        307 EITGSAYVTGFSQFLVDEED  326 (335)
T ss_pred             EEEEEEEEEEEEEEEECCCC
T ss_conf             99999999998899967999


No 13 
>PRK13971 hydroxyproline-2-epimerase; Provisional
Probab=98.67  E-value=2.9e-05  Score=54.55  Aligned_cols=273  Identities=15%  Similarity=0.121  Sum_probs=140.1

Q ss_pred             CCCCCCEEEEECCCCCCEEEEEC-CCCCCCCCHHH-----------HH-HHCC-CCCC-CCCEEEEEECCCCCCCCEEEE
Q ss_conf             98754113785176773899947-78887888889-----------98-7203-5671-435589982588888668999
Q gi|254780710|r    1 MQSSMVDFAKMEGIGNKILVIDM-RGCHDNITSDA-----------IN-ALST-DDNT-HFDQIMLIHDFQDASVDAFIR   65 (296)
Q Consensus         1 ~~~~mi~F~Kmhg~GNDFiiiD~-~~~~~~~~~~~-----------i~-~~~~-~~gi-G~Dgli~i~~~~~~~~d~~m~   65 (296)
                      |-..|+.-.-||..|.=+=||-. ......-+-..           +| .|+. -+|- .-=|- +|.||.++.+|+-+-
T Consensus         1 ~~~~~~~~ID~Ht~GEp~RII~~G~p~l~G~T~~ekr~~~~~~~D~lR~~Lm~EPRGh~~M~Ga-ll~pp~~~~Ad~Gvi   79 (333)
T PRK13971          1 MMRHTFFCIDGHTCGNPVRLVAGGGPLLEGATMSEKRAHFLREYDWIRTALMFEPRGHDMMSGS-ILYPPTRPDCDAAIL   79 (333)
T ss_pred             CCCCEEEEEECCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEE-EEECCCCCCCCEEEE
T ss_conf             9652689996568988768997088899998999999999875368999975678888741889-981899987888999


Q ss_pred             EEECCCCCCCCCCCHHHHHHHHHHCC--C---CCCEEEEEECCCCEEEEECCC-C-EEEECC-CCCCCCHH-HCCCCCCC
Q ss_conf             97178762123320332231110013--5---764037983588379998577-4-277403-68777777-68565656
Q gi|254780710|r   66 IINCDGSEVQSCGNGMRCVVRFLTSR--M---KRKSFTFETIRGILVAKENRD-G-SISVDM-GEPILDWK-LIPLARSF  136 (296)
Q Consensus        66 ~fN~DGS~A~mCGNG~Rc~a~yl~~~--~---~~~~~~i~T~~g~~~~~~~~~-~-~v~V~m-G~p~~~~~-~ip~~~~~  136 (296)
                      |++++|.. .|||-|+=|++.+|.+.  .   ....+.|+|.+|++.++...+ + ..+|.+ -.|+|... ++++..+ 
T Consensus        80 f~~~~gy~-~McGh~tI~~~t~lve~G~v~~~ep~~v~ietPaG~V~v~~~~~~gkv~~V~f~nVPsf~~~~d~~V~vp-  157 (333)
T PRK13971         80 FIETSGCL-PMCGHGTIGTVTAAIEEGLVTPKEPGKLTIDTPAGQVDIEYEQDGEKVESVRLTNVPSYLHAEDVEVEVP-  157 (333)
T ss_pred             EEECCCCC-CCCCCCHHEEEHHHHHCCCCCCCCCCEEEEECCCEEEEEEEEECCCEEEEEEEEEEEHHHHHCCCEEECC-
T ss_conf             99278776-6425430012226888598567898579986683689999998599288999996143574489689889-


Q ss_pred             CCCCCCEEECCCCCCCEECCEE-EEECCCCEEEEECCCCCCHHHHHHHHHCCCC---------CCCCCCCCCEEEEEECC
Q ss_conf             5434430110577774021309-9955874279742557686888763100023---------32375555146799728
Q gi|254780710|r  137 DKMDRDRFHIGPVNHLFLRNPF-VVSMGNPHAIFFVEDDLYHYDLASFGNLLAK---------HPMFSEGVNLSIARVTS  206 (296)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~-~v~iGNPH~Vi~v~d~i~~~~l~~~g~~i~~---------~~~Fp~gvNV~fv~v~~  206 (296)
                       ....  ...   +-.+-..+| +|+.  .++=+-+ +..+.-+|..+|..|+.         ||..|+---+.++...+
T Consensus       158 -g~G~--v~v---DiayGG~~yaiVda--~~~g~~l-~~~~~~~l~~~g~~ik~a~~~~~~~~hP~~~~i~~i~~v~~~~  228 (333)
T PRK13971        158 -GLGP--LKV---DVAYGGNFYAIVEP--QENFPGL-DHWSAADILAWSPVLRQALNEKYEFVHPDDPRIRGVSHVLWTG  228 (333)
T ss_pred             -CCCC--EEE---EEEECCEEEEEEEH--HHCCCCC-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEC
T ss_conf             -9775--789---99826648999867--8937776-8458999999999999999854577588887657604899955


Q ss_pred             CC-----E-EEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCC--CCEEEECCCCEE-E--E----EEECCCE--EEEEE
Q ss_conf             87-----2-8999804678766563235899999999817889--807999079579-9--9----9958981--99994
Q gi|254780710|r  207 LE-----S-LDLRTWERGVGLTAACGSAACASVVASGCLHKTN--RAVSVKMLGGGL-L--I----EWHDNNH--VFMTG  269 (296)
Q Consensus       207 ~~-----~-I~iRt~ERGvGeTlACGTGA~Asa~~~~~~~~~~--~~v~V~~pGG~L-~--v----~~~~~~~--i~l~G  269 (296)
                      +.     . =.+-+|--|.=----||||.+|-.+..+..|++.  .+..-++.=|.. .  +    ++.+..-  ...+|
T Consensus       229 ~~~~~~~~~rn~v~~~~g~iDRSPcGTGtsARlA~l~a~G~l~~ge~~~~eSIiGs~F~~~i~~~~~vg~~~aVip~I~G  308 (333)
T PRK13971        229 KPISPGADGRNAVFYGDKAIDRSPCGTGTSARMAQLAAKGKLKVGDEFVHESIIGSLFEGRVEAAATVGGRPAILPSIAG  308 (333)
T ss_pred             CCCCCCCCEEEEEEECCCCEECCCCCHHHHHHHHHHHHCCCCCCCCEEEEEECCCCEEEEEEEEEEEECCCCEEEEEEEE
T ss_conf             89887776168999699845448872518999999997799779985999842588099999999998992789999999


Q ss_pred             CEEEEEEEEEEECCCC
Q ss_conf             6289998899841320
Q gi|254780710|r  270 EAKKEWEGKLDIKTGK  285 (296)
Q Consensus       270 pa~~vf~G~~~i~~~~  285 (296)
                      .|-..-+.++-+...+
T Consensus       309 ~A~itG~~~f~~d~~D  324 (333)
T PRK13971        309 WARVTGHNTIFVDDRD  324 (333)
T ss_pred             EEEEEEEEEEEECCCC
T ss_conf             9999998899977999


No 14 
>pfam05544 Pro_racemase Proline racemase. This family consists of proline racemase (EC 5.1.1.4) proteins which catalyse the interconversion of L- and D-proline in bacteria. This family also contains several similar eukaryotic proteins including a sequence with B-cell mitogenic properties which has been characterized as a co-factor-independent proline racemase.
Probab=98.66  E-value=1.9e-05  Score=55.78  Aligned_cols=259  Identities=17%  Similarity=0.139  Sum_probs=136.9

Q ss_pred             EECCCCCCEEEEE-CCCCCCCCCH-----------HHHH-HHCCC-CCCC-CCEEEEEECCCCCCCCEEEEEEECCCCCC
Q ss_conf             8517677389994-7788878888-----------8998-72035-6714-35589982588888668999971787621
Q gi|254780710|r   10 KMEGIGNKILVID-MRGCHDNITS-----------DAIN-ALSTD-DNTH-FDQIMLIHDFQDASVDAFIRIINCDGSEV   74 (296)
Q Consensus        10 Kmhg~GNDFiiiD-~~~~~~~~~~-----------~~i~-~~~~~-~giG-~Dgli~i~~~~~~~~d~~m~~fN~DGS~A   74 (296)
                      -+|..|.=+=||- .......-+-           +.+| .|+.. +|-. -=|- +|.||.++.+|+-+-|++++|.. 
T Consensus         3 D~Ht~GEp~RiV~~G~p~l~G~T~~Ek~~~~~~~~D~lR~~Lm~EPRGh~~M~g~-ll~pp~~~~Ad~Gvif~~~~gy~-   80 (325)
T pfam05544         3 DSHTEGEPGRVVVGGVPPLPGATMAEKRRYFARDHDHLRRFLMFEPRGHDMMSGA-LLVPPKRPDADAGVIFMEPSGYL-   80 (325)
T ss_pred             EECCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEE-EECCCCCCCCCEEEEEEECCCCC-
T ss_conf             0116998768997187899999999999999874689999975189988750889-97089998877899998367566-


Q ss_pred             CCCCCHHHHHHHHHHCC--C----CCCEEEEEECCCCEEEEECC-CCE-EEECC-CCCCCCHH-HCCCCCCCCCCCCCEE
Q ss_conf             23320332231110013--5----76403798358837999857-742-77403-68777777-6856565654344301
Q gi|254780710|r   75 QSCGNGMRCVVRFLTSR--M----KRKSFTFETIRGILVAKENR-DGS-ISVDM-GEPILDWK-LIPLARSFDKMDRDRF  144 (296)
Q Consensus        75 ~mCGNG~Rc~a~yl~~~--~----~~~~~~i~T~~g~~~~~~~~-~~~-v~V~m-G~p~~~~~-~ip~~~~~~~~~~~~~  144 (296)
                      .|||-|+=|++.+|.+.  .    +..++.++|.+|++.++..- +++ .+|.+ ..|+|..+ ++++..+  ....  .
T Consensus        81 ~McGh~tI~~~t~lve~G~v~~~~~~t~v~ietPaGlV~a~~~~~~g~v~~Vsf~nVPSf~~~~d~~v~vp--g~G~--v  156 (325)
T pfam05544        81 PMCGHNTIGVVTVLLETGIVPPQEPETRLNLETPAGLVEARAECRDGKVERVSLRNVPSFVYALDVEVEVP--GLGR--V  156 (325)
T ss_pred             CCCCCCHHHHHHHHHHCCCCCCCCCCEEEEEECCCEEEEEEEEECCCCEEEEEEEEEECHHHHCCCEEECC--CCCC--E
T ss_conf             54253189999999987963468895379997894799999999699387999997431585479689789--9763--7


Q ss_pred             ECCCCCCCEECCEEEEECCCCEEEEECC------CCCCHHHHHHHHHCCC---------CCCCCCCCCCEEEEEECCCC-
Q ss_conf             1057777402130999558742797425------5768688876310002---------33237555514679972887-
Q gi|254780710|r  145 HIGPVNHLFLRNPFVVSMGNPHAIFFVE------DDLYHYDLASFGNLLA---------KHPMFSEGVNLSIARVTSLE-  208 (296)
Q Consensus       145 ~~~~~~~~~~~~~~~v~iGNPH~Vi~v~------d~i~~~~l~~~g~~i~---------~~~~Fp~gvNV~fv~v~~~~-  208 (296)
                                 ..-...=||-=+++-.+      +.-+..+|..+|.+|+         .||.-|+.--+.++...++. 
T Consensus       157 -----------~vDiayGG~~yaiVda~~lg~~l~~~~~~~L~~~g~~I~~a~~~~~~~~HP~~~~~~~i~~v~~~~~~~  225 (325)
T pfam05544       157 -----------RVDIAYGGNFYAIVDAEQLGFDIEPAEARELVAAGEKIRDALNEQLKVVHPENPDIRGVSHVQLTGPPT  225 (325)
T ss_pred             -----------EEEEEECCEEEEEEEHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCC
T ss_conf             -----------999985766899985899299768311999999999999999852687588888767057999946888


Q ss_pred             ----EEE-EEECCCCCCCCCCCHHHHHHHHHHHHHHCCCC--CCEEEECCCCE-EEEEEEC-----C-C--EEEEEECEE
Q ss_conf             ----289-99804678766563235899999999817889--80799907957-9999958-----9-8--199994628
Q gi|254780710|r  209 ----SLD-LRTWERGVGLTAACGSAACASVVASGCLHKTN--RAVSVKMLGGG-LLIEWHD-----N-N--HVFMTGEAK  272 (296)
Q Consensus       209 ----~I~-iRt~ERGvGeTlACGTGA~Asa~~~~~~~~~~--~~v~V~~pGG~-L~v~~~~-----~-~--~i~l~Gpa~  272 (296)
                          ..+ +-+|--|.=----||||.+|-.+..+..|++.  .+..-++.=|. -+.++.+     + .  ....+|.|-
T Consensus       226 ~~~~~~rn~v~~~~g~iDRSPcGTGTsArlA~l~a~G~l~~ge~~~~eSIiGs~F~~~i~~~t~vg~~~aVip~I~G~A~  305 (325)
T pfam05544       226 RAEGHARNAVIIGPGAIDRSPCGTGTSARMAQLHAKGKLKVGETFVHESIIGSEFEGRVEGETEVGGRPAIVPSISGRAW  305 (325)
T ss_pred             CCCCCEEEEEEECCCCEECCCCCHHHHHHHHHHHHCCCCCCCCEEEEEECCCCEEEEEEEEEEEECCCCEEEEEEEEEEE
T ss_conf             88875057999899836678862408999999997799779982999961287699999999898995779999999999


Q ss_pred             EEEEEEEEECCCC
Q ss_conf             9998899841320
Q gi|254780710|r  273 KEWEGKLDIKTGK  285 (296)
Q Consensus       273 ~vf~G~~~i~~~~  285 (296)
                      ..-+.++-+...+
T Consensus       306 itG~~~~~~d~~D  318 (325)
T pfam05544       306 ITGTNQLLLDPSD  318 (325)
T ss_pred             EEEEEEEEECCCC
T ss_conf             9998899977999


No 15 
>PRK13970 hydroxyproline-2-epimerase; Provisional
Probab=98.54  E-value=3.4e-05  Score=54.13  Aligned_cols=263  Identities=15%  Similarity=0.073  Sum_probs=140.0

Q ss_pred             CCCEEEEECCCCCCEEEE-ECCCCCCCCCH-----------HHHH-HHCCC-CCCCC-CEEEEEECCCCCCCCEEEEEEE
Q ss_conf             541137851767738999-47788878888-----------8998-72035-67143-5589982588888668999971
Q gi|254780710|r    4 SMVDFAKMEGIGNKILVI-DMRGCHDNITS-----------DAIN-ALSTD-DNTHF-DQIMLIHDFQDASVDAFIRIIN   68 (296)
Q Consensus         4 ~mi~F~Kmhg~GNDFiii-D~~~~~~~~~~-----------~~i~-~~~~~-~giG~-Dgli~i~~~~~~~~d~~m~~fN   68 (296)
                      .+|+-.-||..|+=+=|| +.......-+-           +.+| .|... +|-.. =|- +|.||.++.+|+-+-|++
T Consensus         2 r~i~~id~Ht~GEp~RiV~~G~p~l~G~T~~ekr~~~~~~~D~lR~~Lm~EPRGh~~M~Ga-ll~pp~~~~ad~Gvif~~   80 (310)
T PRK13970          2 KRIQIIDSHTGGEPTRLVVSGFPSLGGGTMAERRDVLAREHDRYRTACILEPRGSDVLVGA-LLCEPVSPDAAAGVIFFN   80 (310)
T ss_pred             CEEEEEECCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEE-EECCCCCCCCCEEEEEEE
T ss_conf             4799996147988758997088899999999999999976579999976288988751889-973899988778999981


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHCC--CCCCEEEEEECCCCEEEEECCCCEEEECCCCCCCCH-HHCCCCCCCCCCCCCEEE
Q ss_conf             78762123320332231110013--576403798358837999857742774036877777-768565656543443011
Q gi|254780710|r   69 CDGSEVQSCGNGMRCVVRFLTSR--MKRKSFTFETIRGILVAKENRDGSISVDMGEPILDW-KLIPLARSFDKMDRDRFH  145 (296)
Q Consensus        69 ~DGS~A~mCGNG~Rc~a~yl~~~--~~~~~~~i~T~~g~~~~~~~~~~~v~V~mG~p~~~~-~~ip~~~~~~~~~~~~~~  145 (296)
                      ++|-. .|||-|+=|++.+|.+.  .......++|.+|.+.++..++.+|++. ..|+|.. .++++..+  ....  ..
T Consensus        81 ~~gy~-~McGh~tI~~~t~l~e~G~v~p~~~~ietPaG~V~a~~~~~~~V~~~-nVpsf~~~~d~~v~vp--g~G~--v~  154 (310)
T PRK13970         81 NSGYL-GMCGHGTIGVVRTLHHMGRIGPGVHRIETPVGTVEATLHDDLSVSVR-NVLAYRHAKDVVVDVP--GYGP--VK  154 (310)
T ss_pred             CCCCC-CCCCCCEEEEEEHHHHCCCCCCCCEEEECCCCEEEEEEECCCEEEEE-EEEHHHHHCCCEEECC--CCCE--EE
T ss_conf             78777-75476344536065874876676178963783699999259989999-5600573279889868--9862--89


Q ss_pred             CCCCCCCEECCEEEEECCCCEEEE-----ECCCCCCHHHHHHHHHCCCCC-----CCCCCCCCEEEEEECCCC-EE---E
Q ss_conf             057777402130999558742797-----425576868887631000233-----237555514679972887-28---9
Q gi|254780710|r  146 IGPVNHLFLRNPFVVSMGNPHAIF-----FVEDDLYHYDLASFGNLLAKH-----PMFSEGVNLSIARVTSLE-SL---D  211 (296)
Q Consensus       146 ~~~~~~~~~~~~~~v~iGNPH~Vi-----~v~d~i~~~~l~~~g~~i~~~-----~~Fp~gvNV~fv~v~~~~-~I---~  211 (296)
                      .           -...=||-.+++     .+. .-+.-.|..++..++..     ..-|++..++.++....+ ..   .
T Consensus       155 v-----------DiayGG~fya~V~~~g~~~~-~~~~~~l~~~~~~ir~a~~~~~~~~~~~~~i~~v~~~~~~~~~~~rn  222 (310)
T PRK13970        155 G-----------DIAWGGNWFFLISDHGQRVA-GDNVAALTAYASAVRAGLERAGITGANGGEIDHIELFADDPEHDSRS  222 (310)
T ss_pred             E-----------EEEECCEEEEEECHHCCCCC-HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCCCCCCEE
T ss_conf             9-----------99706538999811067568-44699999999999999874598689888742389956898767128


Q ss_pred             EEECCCCCCCCCCCHHHHHHHHHHHHHHCCCC--CCEEEECCCCE-EEEEEEC-CCE--EEEEECEEEEEEEEEEECCCC
Q ss_conf             99804678766563235899999999817889--80799907957-9999958-981--999946289998899841320
Q gi|254780710|r  212 LRTWERGVGLTAACGSAACASVVASGCLHKTN--RAVSVKMLGGG-LLIEWHD-NNH--VFMTGEAKKEWEGKLDIKTGK  285 (296)
Q Consensus       212 iRt~ERGvGeTlACGTGA~Asa~~~~~~~~~~--~~v~V~~pGG~-L~v~~~~-~~~--i~l~Gpa~~vf~G~~~i~~~~  285 (296)
                      +-+|--|.=----||||.+|-.+..+..|++.  .+..-+..=|. ...+... .+.  ...+|.|-..-+.++-|...+
T Consensus       223 ~vv~~~~~vDRSPcGTGTSARlA~l~a~G~l~~ge~~~~eSiiGs~F~~~~~~~~~aViP~I~G~A~itG~~~~~~dp~D  302 (310)
T PRK13970        223 FVLCPGHAYDRSPCGTGTSAKLACLAADGKLAPGVVWRQASVIGSVFSASYAAAEGGIVPTIRGSAHLSAEATLLIEDDD  302 (310)
T ss_pred             EEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEEEECCCCEEEEEEECCCCEEEEEEEEEEEEEEEEEEEECCCC
T ss_conf             99969981045887632899999999749978998089996356649999985676299999889999998889956999


No 16 
>COG3938 Proline racemase [Amino acid transport and metabolism]
Probab=98.21  E-value=5.1e-05  Score=52.99  Aligned_cols=221  Identities=17%  Similarity=0.156  Sum_probs=125.1

Q ss_pred             CEEEEECCCCCCEEEEECCCCCC-CCC-HHHHHHHCC------------CCCCCCCEEEEEECCCCCCCCEEEEEEECCC
Q ss_conf             11378517677389994778887-888-889987203------------5671435589982588888668999971787
Q gi|254780710|r    6 VDFAKMEGIGNKILVIDMRGCHD-NIT-SDAINALST------------DDNTHFDQIMLIHDFQDASVDAFIRIINCDG   71 (296)
Q Consensus         6 i~F~Kmhg~GNDFiiiD~~~~~~-~~~-~~~i~~~~~------------~~giG~Dgli~i~~~~~~~~d~~m~~fN~DG   71 (296)
                      +.-.--|..||-==+|-.-.... ..+ -++.+.+.+            -+|--+--.=+|.||+.+.+|+-+.|++++|
T Consensus         7 i~~id~HteGe~grvV~GG~p~~pg~tm~Eq~~~~~~d~d~lR~~l~~EPRG~~~~~~~lL~Pp~~pda~aa~ii~eps~   86 (341)
T COG3938           7 IHCIDCHTEGEPGRVVVGGVPPLPGATMWEQRRWFARDHDWLRNFLMFEPRGHDFRSGNLLVPPKRPDADAAVIIMEPSG   86 (341)
T ss_pred             EEEECCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCHHHHHHHHEECCCCCCCEEEEEECCCCCCCCCEEEEEECCCC
T ss_conf             99970246886344897687898987689998887406488877632377887511566863899987657999974689


Q ss_pred             CCCCCCCCHHHHHHHHHHCC--C----CCCEEEEEECCCCEEEEEC-CCCE---EEECCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             62123320332231110013--5----7640379835883799985-7742---77403687777776856565654344
Q gi|254780710|r   72 SEVQSCGNGMRCVVRFLTSR--M----KRKSFTFETIRGILVAKEN-RDGS---ISVDMGEPILDWKLIPLARSFDKMDR  141 (296)
Q Consensus        72 S~A~mCGNG~Rc~a~yl~~~--~----~~~~~~i~T~~g~~~~~~~-~~~~---v~V~mG~p~~~~~~ip~~~~~~~~~~  141 (296)
                      .-. |||.|+=|++--|.+.  .    +...+.++|.+|.+.++.. .+++   |++.+ .|+|..+.- ++.+.+.+. 
T Consensus        87 ~~p-MsGsntIc~~T~lle~G~v~m~eP~t~l~letP~GlV~~~a~crdGk~E~V~l~N-vPsf~~~ld-~~vevpglG-  162 (341)
T COG3938          87 CLP-MSGSNTICVVTVLLESGLVPMQEPETVLRLETPAGLVEATAECRDGKVERVRLRN-VPSFLHRLD-ASVEVPGLG-  162 (341)
T ss_pred             CCC-CCCCCCHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEEECCCCEEEEEEEC-CHHHHHHCC-CEEECCCCC-
T ss_conf             987-6788826465678875876577885379985688579999971488288999973-566686638-757657762-


Q ss_pred             CEEECCCCCCCEECCEEEEECCCCEEEEECC------CCCCHHHHHHHHHCCCC---------CCCCCCCCCEEEEEECC
Q ss_conf             3011057777402130999558742797425------57686888763100023---------32375555146799728
Q gi|254780710|r  142 DRFHIGPVNHLFLRNPFVVSMGNPHAIFFVE------DDLYHYDLASFGNLLAK---------HPMFSEGVNLSIARVTS  206 (296)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~v~iGNPH~Vi~v~------d~i~~~~l~~~g~~i~~---------~~~Fp~gvNV~fv~v~~  206 (296)
                       .+...           ...-||--+++-.+      ++-++-+|..++..|++         ||-+|+---|+|++..+
T Consensus       163 -~l~vD-----------iAYGG~~yaiVd~~~~g~~l~~~~A~~L~~~g~~i~~a~n~~~~f~HPe~p~i~~~s~~~~~~  230 (341)
T COG3938         163 -RLTVD-----------IAYGGNFYAIVDAQANGFDLAPDEAGELVALGVKIRQALNEQLDFVHPENPDIRGVSHCQFAG  230 (341)
T ss_pred             -EEEEE-----------EEECCEEEEEEEHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEC
T ss_conf             -58899-----------740755799981688176658632688988679999987521475488887657445899807


Q ss_pred             C-----CEEEEEECCCCC-CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             8-----728999804678-76656323589999999981788
Q gi|254780710|r  207 L-----ESLDLRTWERGV-GLTAACGSAACASVVASGCLHKT  242 (296)
Q Consensus       207 ~-----~~I~iRt~ERGv-GeTlACGTGA~Asa~~~~~~~~~  242 (296)
                      +     ..++--|+=+.- =----||||..|--+.++..|+.
T Consensus       231 ~~~~~~~~~Rnav~~~p~~~DRSPcGTGtSArmA~L~AkGkl  272 (341)
T COG3938         231 PPVRPGADLRNAVFYGPKAIDRSPCGTGTSARMAVLHAKGKL  272 (341)
T ss_pred             CCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCC
T ss_conf             876767555413897887545588877506778998745775


No 17 
>pfam02567 PhzC-PhzF Phenazine biosynthesis-like protein. PhzC/PhzF is involved in dimerization of two 2,3-dihydro-3-oxo-anthranilic acid molecules to create PCA by P. fluorescens. This family also contains a putative thymidilate synthase from Mycobacterium tuberculosis, though there is no significant sequence similarity to pfam00303 members. This family appears to be distantly related to pfam01678, including containing a weak internal duplication. However members of this family do not contain the conserved cysteines that are hypothesized to be active site residues (Bateman A pers obs).
Probab=96.28  E-value=0.1  Score=31.16  Aligned_cols=93  Identities=17%  Similarity=0.232  Sum_probs=71.4

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEEC--CCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             58742797425576868887631000233237555514679972--8872899980467876656323589999999981
Q gi|254780710|r  162 MGNPHAIFFVEDDLYHYDLASFGNLLAKHPMFSEGVNLSIARVT--SLESLDLRTWERGVGLTAACGSAACASVVASGCL  239 (296)
Q Consensus       162 iGNPH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp~gvNV~fv~v~--~~~~I~iRt~ERGvGeTlACGTGA~Asa~~~~~~  239 (296)
                      -|||=+|++..+.+.......+++.+...+       .-|+...  +....++|.|=- .+|=.=||-+..|++.+....
T Consensus        10 ~GNPaaVv~~~~~Ls~~~mQ~IA~e~n~SE-------TaFv~~~~~~~~~~~lR~FTP-~~Ev~fcGHaTlaaa~~L~~~   81 (280)
T pfam02567        10 KGNPAAVVLDADELTDEEMQAIAAEFNLSE-------TAFVLPPSDEDADFRLRIFTP-VAEVPFCGHATLATAHALFEE   81 (280)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCE-------EEEEECCCCCCCCEEEEEECC-CCCCCCCCCHHHHHHHHHHHH
T ss_conf             863179998898999999999999879965-------899705888877369999678-541355666058999999983


Q ss_pred             CCCC-CCEEEECCCCEEEEEEECC
Q ss_conf             7889-8079990795799999589
Q gi|254780710|r  240 HKTN-RAVSVKMLGGGLLIEWHDN  262 (296)
Q Consensus       240 ~~~~-~~v~V~~pGG~L~v~~~~~  262 (296)
                      +... ..++.+++.|.|.|++..+
T Consensus        82 ~~~~~~~~~~~t~~G~l~v~~~~~  105 (280)
T pfam02567        82 GGNGNKTLELETLAGIVPVKLVEG  105 (280)
T ss_pred             CCCCCCEEEEECCEEEEEEEEECC
T ss_conf             799998799993728899999815


No 18 
>pfam04303 PrpF PrpF protein. PrpF is a protein found in the 2-methylcitrate pathway. It is structurally similar to DAP epimerase and proline racemase. This protein is likely to acts to isomerize trans-aconitate to cis-aconitate.
Probab=95.86  E-value=0.16  Score=29.85  Aligned_cols=228  Identities=15%  Similarity=0.122  Sum_probs=116.0

Q ss_pred             CCCCC-----CEEEEEECCCCCCCCEEEEEE-----ECCCCCCCCCCCHHHHHHHHHHCC--C----CCCEEEE-EECCC
Q ss_conf             67143-----558998258888866899997-----178762123320332231110013--5----7640379-83588
Q gi|254780710|r   42 DNTHF-----DQIMLIHDFQDASVDAFIRII-----NCDGSEVQSCGNGMRCVVRFLTSR--M----KRKSFTF-ETIRG  104 (296)
Q Consensus        42 ~giG~-----Dgli~i~~~~~~~~d~~m~~f-----N~DGS~A~mCGNG~Rc~a~yl~~~--~----~~~~~~i-~T~~g  104 (296)
                      .|+|.     --+-+|.++..+.+|..+.|-     .+-=.-+.+|||=+-.++-|+.++  .    .....+| .|..+
T Consensus        48 DGlGG~~s~tSKvaIv~~s~~~~~DVdY~F~QV~v~~~~VD~~~NCGN~~saVgpfAie~GlV~~~~~~t~VrI~n~NT~  127 (371)
T pfam04303        48 DGIGGGNSSTSKVAIISKSSTPDHDVDYLFGQVSIDEQFVDWSGNCGNLSAAVGPFAIEAGLVPARIPVTAVRIWNVNTG  127 (371)
T ss_pred             CCCCCCCCCCCEEEEEECCCCCCCCEEEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCC
T ss_conf             77778777664399994688899741688999864685343678864455401457876396426899789999984789


Q ss_pred             C-EEEE-ECCCCEEEEC----C-CCCCCC---------------HHHCCCCCCCCCCCCCEEECCCCCCCEECCEEEEEC
Q ss_conf             3-7999-8577427740----3-687777---------------776856565654344301105777740213099955
Q gi|254780710|r  105 I-LVAK-ENRDGSISVD----M-GEPILD---------------WKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVVSM  162 (296)
Q Consensus       105 ~-~~~~-~~~~~~v~V~----m-G~p~~~---------------~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i  162 (296)
                      . +.+. ...++.+..+    + |.|-..               -+..|--...+.     +...   . .....++|+.
T Consensus       128 ~~i~~~v~~~~G~~~~~Gd~~I~GVpGt~a~I~l~F~~p~Gs~TG~LlPTGn~~D~-----i~~~---g-g~i~vT~IDa  198 (371)
T pfam04303       128 KTIEAHVPTPNGQVQYDGDFEIDGVPGPGAPIALTFLDAAGDGTGALFPTGNLIDT-----LDVP---G-GTVEVTCIDA  198 (371)
T ss_pred             CEEEEEEECCCCCCCCCCCEECCCCCCCCCCCEECCCCCCCCCCCCCCCCCCEEEE-----EECC---C-CEEEEEEEEC
T ss_conf             87999996689941335873427756788851521578556668887999980379-----9728---9-6299999956


Q ss_pred             CCCEEEEECCC----------CCCH-HHHHHHHHCCCC-----------------CCCCCCCCCEEEEEEC---------
Q ss_conf             87427974255----------7686-888763100023-----------------3237555514679972---------
Q gi|254780710|r  163 GNPHAIFFVED----------DLYH-YDLASFGNLLAK-----------------HPMFSEGVNLSIARVT---------  205 (296)
Q Consensus       163 GNPH~Vi~v~d----------~i~~-~~l~~~g~~i~~-----------------~~~Fp~gvNV~fv~v~---------  205 (296)
                      |||-+.+-.+|          ++++ ..|...=..||.                 .+..|   -+.|+.--         
T Consensus       199 a~P~Vfv~A~dlGltG~E~p~el~a~~~ll~rlE~IR~~aa~~MGl~~d~~~a~~~~~iP---Ki~lVs~P~~y~~~~G~  275 (371)
T pfam04303       199 AIPMVFVEAESLGYTGTELAEEINADPQLLARFETLRAAAALRMGLIGDVEDMVLRQHTP---KPAFVSPPEDYKASGGK  275 (371)
T ss_pred             CCCEEEEEHHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHCCCCCC---EEEEEECCCCCCCCCCC
T ss_conf             883899888994998201277662499999999999999999716789967850568998---69999588546567883


Q ss_pred             ----CCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHC---------CCCCCEEEECCCCEEEEEEE--C-CCE---EE
Q ss_conf             ----88728999804678766563235899999999817---------88980799907957999995--8-981---99
Q gi|254780710|r  206 ----SLESLDLRTWERGVGLTAACGSAACASVVASGCLH---------KTNRAVSVKMLGGGLLIEWH--D-NNH---VF  266 (296)
Q Consensus       206 ----~~~~I~iRt~ERGvGeTlACGTGA~Asa~~~~~~~---------~~~~~v~V~~pGG~L~v~~~--~-~~~---i~  266 (296)
                          ++-.|..|.|=-|.=..-==.|||+|.++++..-|         .....++|..|.|.+.|...  + ++.   .-
T Consensus       276 ~~~~~~~Di~~R~fs~~~~H~a~~vTgavcla~Aa~i~GTV~~~~~~~~~~~~v~I~HPsG~i~v~~~~~~~~~~v~~a~  355 (371)
T pfam04303       276 WVSAVEIDLLVRAFSMGKLHHALAGTGAVAIATAAAVPGTLVNLAAGGGERTVVRFGHPSGTLDVGAEATQQDGTVLRAI  355 (371)
T ss_pred             CCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCEEEEECCCEEEEEEEEEECCCCCEEEEE
T ss_conf             52255567899980341002133367899999998279957898606799855999679817999999756899589999


Q ss_pred             EEECEEEEEEEEEEE
Q ss_conf             994628999889984
Q gi|254780710|r  267 MTGEAKKEWEGKLDI  281 (296)
Q Consensus       267 l~Gpa~~vf~G~~~i  281 (296)
                      +.-.|..+|+|++.+
T Consensus       356 v~RTAR~Lm~G~V~v  370 (371)
T pfam04303       356 ISRTARRLMEGWVRV  370 (371)
T ss_pred             EEECCHHHCCEEEEC
T ss_conf             996013425377969


No 19 
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=93.36  E-value=0.68  Score=25.79  Aligned_cols=95  Identities=14%  Similarity=0.134  Sum_probs=68.1

Q ss_pred             EECCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCC-EEEEEECCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             9558742797425576868887631000233237555514679972887-289998046787665632358999999998
Q gi|254780710|r  160 VSMGNPHAIFFVEDDLYHYDLASFGNLLAKHPMFSEGVNLSIARVTSLE-SLDLRTWERGVGLTAACGSAACASVVASGC  238 (296)
Q Consensus       160 v~iGNPH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp~gvNV~fv~v~~~~-~I~iRt~ERGvGeTlACGTGA~Asa~~~~~  238 (296)
                      -..|||=.|+.-.+.+....+..+++.+..++       .-|+...++. ..++|.|-=....-+ ||-.+.||+.+...
T Consensus        16 ~~~GNp~aVv~~a~~Lsd~~MQ~IA~e~n~SE-------T~Fv~~~~~~~~~rlR~FTP~~Evpf-~GHaTlga~~~l~~   87 (291)
T COG0384          16 PFGGNPLAVVLDADGLSDEQMQAIAREFNLSE-------TAFVLPPDDPADARLRIFTPTTEVPF-AGHATLGAAHVLAE   87 (291)
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHCCCE-------EEEECCCCCCCCEEEEEECCCCCCCC-CCCHHHHHHHHHHH
T ss_conf             98998229981899999999999999849961-------69972788867148999678751466-88777999999997


Q ss_pred             HCC-CC-CCEEEECCCCEEEEEEECC
Q ss_conf             178-89-8079990795799999589
Q gi|254780710|r  239 LHK-TN-RAVSVKMLGGGLLIEWHDN  262 (296)
Q Consensus       239 ~~~-~~-~~v~V~~pGG~L~v~~~~~  262 (296)
                      ++. .. ..+..+..-|.+.+.....
T Consensus        88 ~~~~~~~~~~~~e~~aG~v~i~~~~~  113 (291)
T COG0384          88 LGGLSNDTTLTLETKAGLVPVTVERG  113 (291)
T ss_pred             HCCCCCCCEEEEEECCCEEEEEEEEC
T ss_conf             44888662499991467189999967


No 20 
>PRK10281 hypothetical protein; Provisional
Probab=93.13  E-value=0.73  Score=25.57  Aligned_cols=91  Identities=15%  Similarity=0.156  Sum_probs=52.5

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEECCC--CEEEEEECCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             5874279742557686888763100023323755551467997288--72899980467876656323589999999981
Q gi|254780710|r  162 MGNPHAIFFVEDDLYHYDLASFGNLLAKHPMFSEGVNLSIARVTSL--ESLDLRTWERGVGLTAACGSAACASVVASGCL  239 (296)
Q Consensus       162 iGNPH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp~gvNV~fv~v~~~--~~I~iRt~ERGvGeTlACGTGA~Asa~~~~~~  239 (296)
                      -|||=+|++..+.+.......+++.+.-++       --|+...+.  ...++|.|==. .|--=||-...|++++....
T Consensus        17 ~GNPaaVv~~~~~L~~~~mq~IA~E~NlSE-------TaFv~~~~~~~~~~~lR~FTP~-~Ev~fcGHaTlaa~~~l~~~   88 (299)
T PRK10281         17 RGNSAGVVLPADGLSEAQMQLIARELGHSE-------TAFLLSSDDSSYDVRVRYFTPT-VEVPICGHATVAAHYVRATV   88 (299)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCE-------EEEEECCCCCCCCEEEEEECCC-CCCCCCCCHHHHHHHHHHHH
T ss_conf             962049997898989999999999879955-------9998057888771689997576-41454530679999999972


Q ss_pred             CCC-CCCEEEECCCCEEEEEEE
Q ss_conf             788-980799907957999995
Q gi|254780710|r  240 HKT-NRAVSVKMLGGGLLIEWH  260 (296)
Q Consensus       240 ~~~-~~~v~V~~pGG~L~v~~~  260 (296)
                      +.. +..+.-....|.|.|.+.
T Consensus        89 ~~~~~~~~~~~t~~G~l~v~v~  110 (299)
T PRK10281         89 LGLGNCTVWQTTGAGKLPVDIE  110 (299)
T ss_pred             CCCCCCEEEEECCCEEEEEEEE
T ss_conf             6889954999816707999999


No 21 
>COG1903 CbiD Cobalamin biosynthesis protein CbiD [Coenzyme metabolism]
Probab=81.76  E-value=2.4  Score=22.22  Aligned_cols=43  Identities=12%  Similarity=0.088  Sum_probs=20.6

Q ss_pred             CCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHHHH-HHHHHCC
Q ss_conf             56714355899825888886689999717876212332033223-1110013
Q gi|254780710|r   41 DDNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMRCV-VRFLTSR   91 (296)
Q Consensus        41 ~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~Rc~-a~yl~~~   91 (296)
                      .+|.-.|.+-+..|... .....+++       .+.++|..||. -|+.-|+
T Consensus        32 ~~g~~~~~V~V~tP~G~-~lev~ve~-------~~~~~~~a~A~v~K~~GDd   75 (367)
T COG1903          32 LNGEKVDTVKVPTPAGI-RLEVPVEV-------VEKGGNFARAAVRKDAGDD   75 (367)
T ss_pred             HCCCCCEEEEECCCCCC-EEEEEEEE-------EEECCCCEEEEEECCCCCC
T ss_conf             54982306984168873-68999898-------8722783589997278999


No 22 
>PRK00075 cbiD cobalt-precorrin-6A synthase; Reviewed
Probab=69.56  E-value=8.1  Score=18.69  Aligned_cols=10  Identities=30%  Similarity=0.836  Sum_probs=4.9

Q ss_pred             EECCCCCCCC
Q ss_conf             7403687777
Q gi|254780710|r  117 SVDMGEPILD  126 (296)
Q Consensus       117 ~V~mG~p~~~  126 (296)
                      .+..|.|..+
T Consensus       116 ~~~vGepAIN  125 (366)
T PRK00075        116 GLPVGEPAIN  125 (366)
T ss_pred             CCCCCCCCCC
T ss_conf             7999974249


No 23 
>pfam10941 DUF2620 Protein of unknown function DUF2620. This is a bacterial family of proteins with unknown function.
Probab=61.86  E-value=6.3  Score=19.41  Aligned_cols=34  Identities=15%  Similarity=0.293  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCEE
Q ss_conf             6563235899999999817889807999079579
Q gi|254780710|r  222 TAACGSAACASVVASGCLHKTNRAVSVKMLGGGL  255 (296)
Q Consensus       222 TlACGTGA~Asa~~~~~~~~~~~~v~V~~pGG~L  255 (296)
                      --||-||+=++...+..+-.-++..+|.+||...
T Consensus        49 iGACnTGgGgALamAIallG~~~C~Tvs~pg~~~   82 (117)
T pfam10941        49 IGACNTGAGGALAMAIAILGKDKCATIAMPGKPP   82 (117)
T ss_pred             EEECCCCCCHHHHHHHHHHCCCCEEEEECCCCCC
T ss_conf             6644789619999999994846357855699999


No 24 
>TIGR02065 ECX1 exosome complex exonuclease 1; InterPro: IPR011807   The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate.   PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) , as well as in archaeal and eukaryotic RNA exosomes , , the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber . Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel , .   This entry represents a family of archaeal proteins that are orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt .; GO: 0016896 exoribonuclease activity producing 5'-phosphomonoesters, 0000178 exosome (RNase complex).
Probab=60.02  E-value=9.5  Score=18.25  Aligned_cols=33  Identities=24%  Similarity=0.665  Sum_probs=22.2

Q ss_pred             CEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHHH
Q ss_conf             55899825888886689999717876212332033223111
Q gi|254780710|r   47 DQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMRCVVRF   87 (296)
Q Consensus        47 Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~Rc~a~y   87 (296)
                      .--|+++.-+-...|.|+++-.|||        |+||++--
T Consensus       103 epai~~E~fPRt~IDVF~EvLQADa--------GTR~Aglt  135 (231)
T TIGR02065       103 EPAILLEQFPRTAIDVFVEVLQADA--------GTRCAGLT  135 (231)
T ss_pred             CCEEEEECCCCCCCEEEEEEEECCC--------CHHHHHHH
T ss_conf             3101322388950105789985276--------50478899


No 25 
>COG2828 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.20  E-value=19  Score=16.20  Aligned_cols=58  Identities=21%  Similarity=0.248  Sum_probs=38.6

Q ss_pred             CHHHHHHHHHHHHHHC----------CCCCCEEEECCCCEEEEEEEC---CC---EEEEEECEEEEEEEEEEEC
Q ss_conf             3235899999999817----------889807999079579999958---98---1999946289998899841
Q gi|254780710|r  225 CGSAACASVVASGCLH----------KTNRAVSVKMLGGGLLIEWHD---NN---HVFMTGEAKKEWEGKLDIK  282 (296)
Q Consensus       225 CGTGA~Asa~~~~~~~----------~~~~~v~V~~pGG~L~v~~~~---~~---~i~l~Gpa~~vf~G~~~i~  282 (296)
                      -||||.|.+-++..-|          -..+.|++.-|.|.|.|....   ++   ...|.-.|...|||.+...
T Consensus       301 ~~TgAvaiatA~a~pGtv~~~la~~~g~~~~V~~~HPSG~l~v~~~~~~~~~tv~~a~~~RtAR~lmeG~V~~p  374 (378)
T COG2828         301 AGTGAVAIATAAAVPGTVLVNLAAGGGERKNVRFEHPSGTLDVGLEAEGQDGTVTRASMSRTARKLMEGWVRVP  374 (378)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHCCCCCCCEEEEECCCCCEEEEEEECCCCCCEEEEEEEHHHHHHHCCEEECC
T ss_conf             65448876676626881787765268866138853798727775555268872788875313456525268547


No 26 
>TIGR01722 MMSDH methylmalonate-semialdehyde dehydrogenase; InterPro: IPR010061   These proteins are involved in valine catabolism, methylmalonate-semialdehyde dehydrogenase catalyzes the irreversible NAD+- and CoA-dependent oxidative decarboxylation of methylmalonate semialdehyde to propionyl-CoA. Methylmalonate-semialdehyde dehydrogenase has been characterised in both prokaryotes ,  and eukaryotes , functioning as a mammalian tetramer and a bacterial homodimer. Although similar in monomeric molecular mass and enzymatic activity, the N-terminal sequence in Pseudomonas aeruginosa does not correspond with the N-terminal sequence predicted for rat liver. Sequence homology to a variety of prokaryotic and eukaryotic aldehyde dehydrogenases places MMSDH in the aldehyde dehydrogenase (NAD+) superfamily making MMSDH's CoA requirement unique among known ALDHs. Methylmalonate semialdehyde dehydrogenase is closely related to betaine aldehyde dehydrogenase, 2-hydroxymuconic semialdehyde dehydrogenase, and class 1 and 2 aldehyde dehydrogenase .    In Bacillus, a highly homologous protein to methylmalonic acid semialdehyde dehydrogenase, groups out from the main MMSDH clade with Listeria and Sulfolobus. This Bacillus protein has been suggested to be located in an iol operon and/or involved in myo-inositol catabolism, converting malonic semialdehyde to acetyl CoA ad CO2 . The preceding enzymes responsible for valine catabolism are present in Bacillus, Listeria, and Sulfolobus.; GO: 0004491 methylmalonate-semialdehyde dehydrogenase (acylating) activity, 0006573 valine metabolic process.
Probab=46.01  E-value=22  Score=15.89  Aligned_cols=73  Identities=15%  Similarity=0.257  Sum_probs=38.8

Q ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHCC---CCCCCCCEEEEE-----------ECCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf             17677389994778887888889987203---567143558998-----------2588888668999971787621233
Q gi|254780710|r   12 EGIGNKILVIDMRGCHDNITSDAINALST---DDNTHFDQIMLI-----------HDFQDASVDAFIRIINCDGSEVQSC   77 (296)
Q Consensus        12 hg~GNDFiiiD~~~~~~~~~~~~i~~~~~---~~giG~Dgli~i-----------~~~~~~~~d~~m~~fN~DGS~A~mC   77 (296)
                      =.|||-||+     ++.+-.|..--+++.   +-|. -||+|-|           .++++-.+   +-|-   ||.    
T Consensus       161 iaCGNtF~l-----KPSE~vP~a~v~lAeLf~eaGa-PdGvlnvvHG~k~aVd~ll~HPdvKA---vSFV---GS~----  224 (478)
T TIGR01722       161 IACGNTFVL-----KPSEKVPSAAVKLAELFSEAGA-PDGVLNVVHGDKEAVDRLLEHPDVKA---VSFV---GSV----  224 (478)
T ss_pred             HHHCCCEEC-----CCCCCCHHHHHHHHHHHHHCCC-CCCEEEEEECCHHHHHHHHCCCCEEE---EEEC---CCH----
T ss_conf             984661023-----7767675789999999986579-98716866187478777616897147---8521---512----


Q ss_pred             CCHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             2033223111001357640379835883
Q gi|254780710|r   78 GNGMRCVVRFLTSRMKRKSFTFETIRGI  105 (296)
Q Consensus        78 GNG~Rc~a~yl~~~~~~~~~~i~T~~g~  105 (296)
                           -+++|+++.-....=++|...|-
T Consensus       225 -----~~g~Yi~~tgsahgKRVQa~~GA  247 (478)
T TIGR01722       225 -----AVGRYIYETGSAHGKRVQALAGA  247 (478)
T ss_pred             -----HHHHHHHHHCCCCCCEEEECCCC
T ss_conf             -----46656632023478743203577


No 27 
>COG0059 IlvC Ketol-acid reductoisomerase [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=45.22  E-value=22  Score=15.81  Aligned_cols=101  Identities=16%  Similarity=0.240  Sum_probs=58.7

Q ss_pred             EECCCCCCHHHHH-HHHHCCCCC--CCCCCCCCEEEEEECCCCEEEE-------------EECCCCCC-CCC------CC
Q ss_conf             7425576868887-631000233--2375555146799728872899-------------98046787-665------63
Q gi|254780710|r  169 FFVEDDLYHYDLA-SFGNLLAKH--PMFSEGVNLSIARVTSLESLDL-------------RTWERGVG-LTA------AC  225 (296)
Q Consensus       169 i~v~d~i~~~~l~-~~g~~i~~~--~~Fp~gvNV~fv~v~~~~~I~i-------------Rt~ERGvG-eTl------AC  225 (296)
                      +...|.+...-.+ ++.|.|+..  -.|.-|.||+|-++.-+..+.+             |+|.+|-| .+|      +.
T Consensus        80 ~L~PDe~q~~vy~~~I~p~Lk~G~aL~FaHGfNihf~~i~ppkdvdV~MVAPKgPG~~VR~~y~~G~GvP~LiAV~qD~s  159 (338)
T COG0059          80 ILLPDEQQKEVYEKEIAPNLKEGAALGFAHGFNIHFGLIVPPKDVDVIMVAPKGPGHLVRREYKEGFGVPALIAVHQDAS  159 (338)
T ss_pred             EECCHHHHHHHHHHHHHHHHCCCCEEEECCCCCEECCCCCCCCCCCEEEECCCCCCHHHHHHHHCCCCCEEEEEEEECCC
T ss_conf             81865467899998743452278667762655311330337766718998389996789999873699516999986688


Q ss_pred             HHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCEEEEEECEEEEEEE
Q ss_conf             2358999999998178898079990795799999589819999462899988
Q gi|254780710|r  226 GSAACASVVASGCLHKTNRAVSVKMLGGGLLIEWHDNNHVFMTGEAKKEWEG  277 (296)
Q Consensus       226 GTGA~Asa~~~~~~~~~~~~v~V~~pGG~L~v~~~~~~~i~l~Gpa~~vf~G  277 (296)
                      |.+--=|...+.-.|.        .++|.+.+.+.+.-+-.|-|.-...+-|
T Consensus       160 G~a~~~Ala~AkgiGg--------~RaGvieTTFkeEtetDLfGEQ~vLcGg  203 (338)
T COG0059         160 GKALDIALAYAKGIGG--------TRAGVIETTFKEETETDLFGEQAVLCGG  203 (338)
T ss_pred             CCHHHHHHHHHHHCCC--------CCCCEEEEEEHHHHHHCCCCCHHHHHHH
T ss_conf             5099999999976188--------7631476420876640111121112007


No 28 
>PRK10310 galactitol-specific PTS system component IIB; Provisional
Probab=41.97  E-value=14  Score=17.14  Aligned_cols=16  Identities=38%  Similarity=0.642  Sum_probs=10.2

Q ss_pred             CCHHHHHHHHHHHHHH
Q ss_conf             6323589999999981
Q gi|254780710|r  224 ACGSAACASVVASGCL  239 (296)
Q Consensus       224 ACGTGA~Asa~~~~~~  239 (296)
                      |||||.+-|.+++.+.
T Consensus         8 ACGsGIATSTvva~kv   23 (94)
T PRK10310          8 ACGGAVATSTMAAEEI   23 (94)
T ss_pred             ECCCCHHHHHHHHHHH
T ss_conf             8588375999999999


No 29 
>TIGR01066 rplM_bact ribosomal protein L13; InterPro: IPR005823   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    Ribosomal protein L13 is one of the proteins from the large ribosomal subunit . In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. This entry represents ribosomal protein L13 from bacteria, mitochondria and chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=39.23  E-value=27  Score=15.21  Aligned_cols=30  Identities=23%  Similarity=0.083  Sum_probs=9.8

Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCEEEEEEE
Q ss_conf             999999981788980799907957999995
Q gi|254780710|r  231 ASVVASGCLHKTNRAVSVKMLGGGLLIEWH  260 (296)
Q Consensus       231 Asa~~~~~~~~~~~~v~V~~pGG~L~v~~~  260 (296)
                      ||.+|..++|+--..-+=++..|+=-|.+|
T Consensus        30 A~~vA~~LRGKHKp~YTP~~D~GD~VIvIN   59 (145)
T TIGR01066        30 ASEVAKLLRGKHKPTYTPHVDCGDYVIVIN   59 (145)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCEEEEEE
T ss_conf             898999843788884347861487269970


No 30 
>KOG1798 consensus
Probab=35.49  E-value=19  Score=16.27  Aligned_cols=13  Identities=31%  Similarity=0.360  Sum_probs=4.8

Q ss_pred             EEEEECCCCCCCC
Q ss_conf             9997178762123
Q gi|254780710|r   64 IRIINCDGSEVQS   76 (296)
Q Consensus        64 m~~fN~DGS~A~m   76 (296)
                      +-+||.|||.||+
T Consensus       930 YAVFN~DGsLAEL  942 (2173)
T KOG1798         930 YAVFNEDGSLAEL  942 (2173)
T ss_pred             EEEECCCCCHHHH
T ss_conf             5786578855442


No 31 
>cd05807 CBM20_CGTase CGTase, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. CGTase, also known as cyclodextrin glycosyltransferase and cyclodextrin glucanotransferase, catalyzes the formation of various cyclodextrins (alpha-1,4-glucans) from starch. CGTase has, in addition to its C-terminal CBM20 domain, an N-terminal catalytic domain belonging to glycosyl hydrolase family 13 and an IPT domain of unknown function. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific
Probab=34.90  E-value=21  Score=15.92  Aligned_cols=35  Identities=14%  Similarity=0.379  Sum_probs=22.5

Q ss_pred             CCCCCCEEE--EEECCCCEEEEEECCCCCCC---CCCCHHHHH
Q ss_conf             755551467--99728872899980467876---656323589
Q gi|254780710|r  193 FSEGVNLSI--ARVTSLESLDLRTWERGVGL---TAACGSAAC  230 (296)
Q Consensus       193 Fp~gvNV~f--v~v~~~~~I~iRt~ERGvGe---TlACGTGA~  230 (296)
                      .|.|..++|  +.+.+.+++   +||-|...   |-+||||++
T Consensus        58 lpag~~~eyK~v~~~~~g~v---~WE~g~Nr~~t~P~~gt~tv   97 (101)
T cd05807          58 VPAGTTIEFKFIKKNGDNTV---TWESGSNHTYTAPSSTTGTI   97 (101)
T ss_pred             ECCCCCEEEEEEEECCCCCE---EEECCCCEEEECCCCCCEEE
T ss_conf             67999599999999689988---98579996697889966799


No 32 
>pfam02459 Adeno_terminal Adenoviral DNA terminal protein. This protein is covalently attached to the terminii of replicating DNA in vivo.
Probab=34.33  E-value=30  Score=14.93  Aligned_cols=41  Identities=29%  Similarity=0.365  Sum_probs=28.5

Q ss_pred             HHHHHHCCCCCCCCCCCCCEEEEEECCC------CEEEEEEC-CCCCC
Q ss_conf             8763100023323755551467997288------72899980-46787
Q gi|254780710|r  180 LASFGNLLAKHPMFSEGVNLSIARVTSL------ESLDLRTW-ERGVG  220 (296)
Q Consensus       180 l~~~g~~i~~~~~Fp~gvNV~fv~v~~~------~~I~iRt~-ERGvG  220 (296)
                      |..+...++.+..|.--|+++++||+=+      ..+.-||| |+|..
T Consensus       400 L~YL~~~L~~~~~f~R~V~ln~~QVimrgRd~~G~~vysRVW~e~~~~  447 (548)
T pfam02459       400 LNYLHAHLRLNRPFRRYVELNLAQVIMRGRDENGEVVYSRVWNENGNN  447 (548)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEECCCCCC
T ss_conf             999999997308888860310578999985488878788630568877


No 33 
>cd05566 PTS_IIB_galactitol PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS).  In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and
Probab=33.80  E-value=20  Score=16.11  Aligned_cols=15  Identities=33%  Similarity=0.625  Sum_probs=6.6

Q ss_pred             CCHHHHHHHHHHHHH
Q ss_conf             632358999999998
Q gi|254780710|r  224 ACGSAACASVVASGC  238 (296)
Q Consensus       224 ACGTGA~Asa~~~~~  238 (296)
                      |||||..-|.+++.+
T Consensus         6 aCGsGiaTSt~v~~k   20 (89)
T cd05566           6 ACGTGVATSTVVASK   20 (89)
T ss_pred             ECCCCCHHHHHHHHH
T ss_conf             989970399999999


No 34 
>KOG1250 consensus
Probab=32.52  E-value=35  Score=14.52  Aligned_cols=28  Identities=25%  Similarity=0.234  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHCCC----CCCEEEECCCCE
Q ss_conf             3589999999981788----980799907957
Q gi|254780710|r  227 SAACASVVASGCLHKT----NRAVSVKMLGGG  254 (296)
Q Consensus       227 TGA~Asa~~~~~~~~~----~~~v~V~~pGG~  254 (296)
                      -+|||+++++...++.    +..+.....||.
T Consensus       322 EpAgaaaLaai~~~~~~~lk~~~vv~ilsG~n  353 (457)
T KOG1250         322 EPAGAAALAAIYSGKLNHLKGKKVVSILSGGN  353 (457)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCCEEEEECCCCC
T ss_conf             36249889999705655667760776513688


No 35 
>KOG1794 consensus
Probab=31.78  E-value=36  Score=14.44  Aligned_cols=46  Identities=35%  Similarity=0.396  Sum_probs=26.9

Q ss_pred             CCHHHHHHHCCCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCH
Q ss_conf             888899872035671435589982588888668999971787621233203
Q gi|254780710|r   30 ITSDAINALSTDDNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNG   80 (296)
Q Consensus        30 ~~~~~i~~~~~~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG   80 (296)
                      ++.+++-.+...+--+-.|+++|-     +.+..-+.+|+|||++.--|=|
T Consensus       104 v~sDa~~sl~a~t~g~~~GiVLia-----GTgs~crl~~~DGs~~~~ggwg  149 (336)
T KOG1794         104 VTSDADGSLAAATPGGEGGIVLIA-----GTGSNCRLVNPDGSEKGAGGWG  149 (336)
T ss_pred             EEHHHHHHHHHCCCCCCCCEEEEE-----CCCCEEEEECCCCCCCCCCCCC
T ss_conf             611577787524877778679995-----3785048888988826799887


No 36 
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family; InterPro: IPR011929    Members of this family show sequence similarity to members of the NlpC/P60 family, described by Anantharaman and Aravind . The NlpC/P60 family includes a number of characterised bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes..
Probab=31.68  E-value=23  Score=15.72  Aligned_cols=37  Identities=22%  Similarity=0.267  Sum_probs=19.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCCCCC-EEEECCCCEEEEEEECC
Q ss_conf             467876656323589999999981788980-79990795799999589
Q gi|254780710|r  216 ERGVGLTAACGSAACASVVASGCLHKTNRA-VSVKMLGGGLLIEWHDN  262 (296)
Q Consensus       216 ERGvGeTlACGTGA~Asa~~~~~~~~~~~~-v~V~~pGG~L~v~~~~~  262 (296)
                      |+|.||||.          .+..++++.-+ ..--+||=.|..+|+++
T Consensus        54 E~G~~e~L~----------~Aa~R~lv~~pG~~~~qpGDlLlFRw~~G   91 (135)
T TIGR02219        54 EVGGGELLL----------EAALRHLVAVPGLEAAQPGDLLLFRWRPG   91 (135)
T ss_pred             CCCCCHHHH----------HHHHHHHCCCCCCCCCCCCCEEEECCCCC
T ss_conf             148883688----------88865512578888788876677715524


No 37 
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461    Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=30.49  E-value=16  Score=16.67  Aligned_cols=13  Identities=23%  Similarity=0.828  Sum_probs=7.0

Q ss_pred             CCEEEEECCCCCCH
Q ss_conf             74279742557686
Q gi|254780710|r  164 NPHAIFFVEDDLYH  177 (296)
Q Consensus       164 NPH~Vi~v~d~i~~  177 (296)
                      |||||+.. |.|++
T Consensus       595 ~P~cVLLL-DEIEK  607 (774)
T TIGR02639       595 HPHCVLLL-DEIEK  607 (774)
T ss_pred             CCCEEEHH-HHHHH
T ss_conf             88535423-46666


No 38 
>cd06221 sulfite_reductase_like Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is linked to ferredoxin and reduces NH2OH and SeO3 at a lesser rate than it's normal substate SO3(2-). Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+.
Probab=30.23  E-value=21  Score=15.90  Aligned_cols=21  Identities=24%  Similarity=0.484  Sum_probs=12.8

Q ss_pred             CEEEEEECCCCCCCCCCCHHHHHHHH
Q ss_conf             72899980467876656323589999
Q gi|254780710|r  208 ESLDLRTWERGVGLTAACGSAACASV  233 (296)
Q Consensus       208 ~~I~iRt~ERGvGeTlACGTGA~Asa  233 (296)
                      .+|.+-.=||     ++||.|+|.+=
T Consensus       217 e~I~vSle~~-----M~CG~G~C~~C  237 (253)
T cd06221         217 EQIWVSLERR-----MKCGVGKCGHC  237 (253)
T ss_pred             HEEEEECCCC-----CCCCCEECCCC
T ss_conf             0079931553-----66836054872


No 39 
>cd01775 CYR1_RA CYR1 is a fungal adenylate cyclase with at least four domains, an N-terminal RA (Ras association) domain, a middle leucine-rich repeat domain, a catalytic domain.   The N-terminal RA domain of CYR1 post-translationally modifies a small GTPase called Ras. The Ras-CYR1 pathway has been implicated in the transduction of a glucose-triggered signal to an intracellular environment where a protein phosphorylation cascade is initiated by cyclic AMP.
Probab=29.42  E-value=36  Score=14.45  Aligned_cols=17  Identities=24%  Similarity=0.346  Sum_probs=14.0

Q ss_pred             CEEEEEEECCCCCCCCC
Q ss_conf             68999971787621233
Q gi|254780710|r   61 DAFIRIINCDGSEVQSC   77 (296)
Q Consensus        61 d~~m~~fN~DGS~A~mC   77 (296)
                      .|++++|++|||-+...
T Consensus         2 ~y~IRIfr~D~Tf~tls   18 (97)
T cd01775           2 SYCIRVFRSDGTFTTLS   18 (97)
T ss_pred             CEEEEEEECCCCEEEEE
T ss_conf             74899994499489997


No 40 
>TIGR01415 trpB_rel pyridoxal-phosphate dependent TrpB-like enzyme; InterPro: IPR006316   These sequences represent a family of pyridoxal-phosphate dependent enzymes that are closely related to the beta subunit of tryptophan synthase. ; GO: 0004834 tryptophan synthase activity, 0030170 pyridoxal phosphate binding, 0000162 tryptophan biosynthetic process.
Probab=29.24  E-value=11  Score=17.79  Aligned_cols=14  Identities=29%  Similarity=0.116  Sum_probs=6.2

Q ss_pred             CCCCEEEEEECCCC
Q ss_conf             57640379835883
Q gi|254780710|r   92 MKRKSFTFETIRGI  105 (296)
Q Consensus        92 ~~~~~~~i~T~~g~  105 (296)
                      -+.++++-||.+|.
T Consensus       118 ~G~k~l~TETGAGQ  131 (426)
T TIGR01415       118 EGAKRLVTETGAGQ  131 (426)
T ss_pred             CCCEEEECCCCCCH
T ss_conf             48437432368864


No 41 
>PRK10815 sensor protein PhoQ; Provisional
Probab=28.91  E-value=40  Score=14.13  Aligned_cols=76  Identities=22%  Similarity=0.226  Sum_probs=40.0

Q ss_pred             HHHHHCCCCCCCC-CCCCCEEEEEECCCCEEEEE---------------ECCCCC-CCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             7631000233237-55551467997288728999---------------804678-766563235899999999817889
Q gi|254780710|r  181 ASFGNLLAKHPMF-SEGVNLSIARVTSLESLDLR---------------TWERGV-GLTAACGSAACASVVASGCLHKTN  243 (296)
Q Consensus       181 ~~~g~~i~~~~~F-p~gvNV~fv~v~~~~~I~iR---------------t~ERGv-GeTlACGTGA~Asa~~~~~~~~~~  243 (296)
                      ..++.+++|.--+ |+++.|..-+  +.+.+.+.               +|||+. +.|..-|||- .-+++.......+
T Consensus       380 ~~l~NLldNAikys~~~v~I~~~~--~~~~~~I~V~D~GpGIp~e~~~~IFeRF~R~d~~r~GsGL-GLaIvk~Iv~~hg  456 (484)
T PRK10815        380 EVMGNVLDNACKYCLEFVEISARQ--TDEHLHIVVEDDGPGIPESKRELIFDRGQRVDTLRPGQGV-GLAVAREITEQYE  456 (484)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEE--ECCEEEEEEEECCCCCCHHHHHHHCCCCCCCCCCCCCCCH-HHHHHHHHHHHCC
T ss_conf             999999999997288867999999--6999999999739999989998624688779999998576-7999999999889


Q ss_pred             CCEEE-ECCCCEEEEEE
Q ss_conf             80799-90795799999
Q gi|254780710|r  244 RAVSV-KMLGGGLLIEW  259 (296)
Q Consensus       244 ~~v~V-~~pGG~L~v~~  259 (296)
                      -.+++ ..|+|.+.+++
T Consensus       457 G~I~l~~s~~gG~~f~I  473 (484)
T PRK10815        457 GKIVASESPLGGARMEV  473 (484)
T ss_pred             CEEEEEECCCCCEEEEE
T ss_conf             98999956999248999


No 42 
>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=28.83  E-value=40  Score=14.12  Aligned_cols=11  Identities=36%  Similarity=0.522  Sum_probs=6.8

Q ss_pred             EECCCCC--CCCC
Q ss_conf             9804678--7665
Q gi|254780710|r  213 RTWERGV--GLTA  223 (296)
Q Consensus       213 Rt~ERGv--GeTl  223 (296)
                      -.=|||+  ||+.
T Consensus       162 ~lcERG~~FGYnn  174 (279)
T TIGR01362       162 LLCERGTSFGYNN  174 (279)
T ss_pred             EEEECCCCCCCCC
T ss_conf             5861788888875


No 43 
>TIGR02918 TIGR02918 conserved hypothetical protein TIGR02918; InterPro: IPR014267   Members of this entry are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus..
Probab=28.33  E-value=33  Score=14.68  Aligned_cols=20  Identities=25%  Similarity=0.250  Sum_probs=12.0

Q ss_pred             CCCCCCCEEE-EEEECCCCCC
Q ss_conf             8888866899-9971787621
Q gi|254780710|r   55 FQDASVDAFI-RIINCDGSEV   74 (296)
Q Consensus        55 ~~~~~~d~~m-~~fN~DGS~A   74 (296)
                      |.++.+...| +|||-|||.|
T Consensus       156 P~Dn~A~LY~R~FYNEDGSIA  176 (511)
T TIGR02918       156 PADNKAKLYQRTFYNEDGSIA  176 (511)
T ss_pred             CCCCCCEEEECEEECCCCCHH
T ss_conf             767985471011242588343


No 44 
>TIGR00406 prmA ribosomal protein L11 methyltransferase; InterPro: IPR004498 Ribosomal protein L11 methyltransferase (2.1.1 from EC) is required for the methylation of ribosomal protein L11. It forms a bifunctional operon in Escherichia coli with panF (pantothenate transport).; GO: 0008276 protein methyltransferase activity, 0006479 protein amino acid methylation.
Probab=27.92  E-value=32  Score=14.73  Aligned_cols=14  Identities=21%  Similarity=0.418  Sum_probs=9.0

Q ss_pred             CCCHHHHHHHHHHH
Q ss_conf             56323589999999
Q gi|254780710|r  223 AACGSAACASVVAS  236 (296)
Q Consensus       223 lACGTGA~Asa~~~  236 (296)
                      ..||||-.|-|++.
T Consensus       203 ~GCGSGIL~IAa~~  216 (330)
T TIGR00406       203 VGCGSGILSIAALK  216 (330)
T ss_pred             ECCCHHHHHHHHHH
T ss_conf             12671789999997


No 45 
>cd05535 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Probab=26.58  E-value=38  Score=14.26  Aligned_cols=11  Identities=27%  Similarity=0.042  Sum_probs=5.9

Q ss_pred             CCEEEEEECCC
Q ss_conf             35589982588
Q gi|254780710|r   46 FDQIMLIHDFQ   56 (296)
Q Consensus        46 ~Dgli~i~~~~   56 (296)
                      -||+-.+.|..
T Consensus       331 TDGIWC~LP~s  341 (621)
T cd05535         331 TDGIWCILPKS  341 (621)
T ss_pred             CCCEEEECCCC
T ss_conf             88746866667


No 46 
>TIGR03534 RF_mod_HemK protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK, a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. However, the family is diverse enough that even many members of the seed alignment do not score above the seed alignment, which was set high enough to exclude all instances of PrmB.
Probab=26.45  E-value=34  Score=14.58  Aligned_cols=13  Identities=23%  Similarity=0.460  Sum_probs=5.4

Q ss_pred             CCCHHHHHHHHHHCC
Q ss_conf             320332231110013
Q gi|254780710|r   77 CGNGMRCVVRFLTSR   91 (296)
Q Consensus        77 CGNG~Rc~a~yl~~~   91 (296)
                      ||.|  |++--+...
T Consensus        96 tGSG--~I~i~la~~  108 (251)
T TIGR03534        96 TGSG--AIALALAKE  108 (251)
T ss_pred             CCHH--HHHHHHHHH
T ss_conf             6716--999999996


No 47 
>PRK05270 galactose-1-phosphate uridylyltransferase; Provisional
Probab=26.32  E-value=44  Score=13.83  Aligned_cols=59  Identities=27%  Similarity=0.392  Sum_probs=32.2

Q ss_pred             CCEEEECCCCCCCCHHHCCCCCCCCCCCCC--------------------------EEECCCCCCCEECCEEEEECCCCE
Q ss_conf             742774036877777768565656543443--------------------------011057777402130999558742
Q gi|254780710|r  113 DGSISVDMGEPILDWKLIPLARSFDKMDRD--------------------------RFHIGPVNHLFLRNPFVVSMGNPH  166 (296)
Q Consensus       113 ~~~v~V~mG~p~~~~~~ip~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~~~v~iGNPH  166 (296)
                      +-.|++++-+|-.+++.|-.++...+..-.                          .+.+......+..++|+-.  |-|
T Consensus       143 ~LeITINLSKPEKDPk~IAaak~~~~s~YPkC~LC~ENEGY~Gr~nhPAR~NhRiI~~~L~ge~W~fQYSPYaYy--nEH  220 (496)
T PRK05270        143 DLEITINLSKPEKDPKAIAAAKNAKASSYPKCLLCMENEGYAGRLNHPARSNHRIIRVTLGGESWGFQYSPYAYF--NEH  220 (496)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEECCCCEE--ECE
T ss_conf             569998656888999999998617778998433543046756778898655752676752897014674541054--123


Q ss_pred             EEEECCC
Q ss_conf             7974255
Q gi|254780710|r  167 AIFFVED  173 (296)
Q Consensus       167 ~Vi~v~d  173 (296)
                      ||+|-++
T Consensus       221 cIvl~~~  227 (496)
T PRK05270        221 CIFLSEK  227 (496)
T ss_pred             EEEECCC
T ss_conf             6886586


No 48 
>KOG2904 consensus
Probab=26.00  E-value=33  Score=14.63  Aligned_cols=12  Identities=25%  Similarity=0.055  Sum_probs=5.4

Q ss_pred             ECCCCEEEEEEE
Q ss_conf             907957999995
Q gi|254780710|r  249 KMLGGGLLIEWH  260 (296)
Q Consensus       249 ~~pGG~L~v~~~  260 (296)
                      -.|||.+..+..
T Consensus       275 Lq~gg~~~le~~  286 (328)
T KOG2904         275 LQPGGFEQLELV  286 (328)
T ss_pred             CCCCCEEEEEEC
T ss_conf             566885889733


No 49 
>pfam02302 PTS_IIB PTS system, Lactose/Cellobiose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This family also contains the fructose specific IIB subunit.
Probab=25.82  E-value=40  Score=14.15  Aligned_cols=17  Identities=35%  Similarity=0.704  Sum_probs=9.2

Q ss_pred             CCCHHHHHHHHHHHHHH
Q ss_conf             56323589999999981
Q gi|254780710|r  223 AACGSAACASVVASGCL  239 (296)
Q Consensus       223 lACGTGA~Asa~~~~~~  239 (296)
                      .+||||...|..++.++
T Consensus         4 ~~C~~G~atS~m~a~~l   20 (91)
T pfam02302         4 TACGAGMATSLMAAEAL   20 (91)
T ss_pred             EECCCHHHHHHHHHHHH
T ss_conf             88876376999999999


No 50 
>TIGR01123 ilvE_II branched-chain amino acid aminotransferase; InterPro: IPR005786   Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped  into subfamilies.   One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C-terminus side of the PlP-lysine.    Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE) (2.6.1.42 from EC). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family less similar to the DAAT family. ; GO: 0004084 branched-chain-amino-acid transaminase activity, 0009081 branched chain family amino acid metabolic process.
Probab=25.64  E-value=19  Score=16.32  Aligned_cols=17  Identities=41%  Similarity=0.556  Sum_probs=12.5

Q ss_pred             ECCCCC-CCCCCCHHHHH
Q ss_conf             804678-76656323589
Q gi|254780710|r  214 TWERGV-GLTAACGSAAC  230 (296)
Q Consensus       214 t~ERGv-GeTlACGTGA~  230 (296)
                      --|+|. -|-.||||.|.
T Consensus       261 ~~~~G~~tEvfacGTAAV  278 (329)
T TIGR01123       261 AVEAGAITEVFACGTAAV  278 (329)
T ss_pred             HHHCCCCEEEECCCCCEE
T ss_conf             765451101001186148


No 51 
>PRK08345 cytochrome-c3 hydrogenase subunit gamma; Provisional
Probab=25.40  E-value=13  Score=17.23  Aligned_cols=59  Identities=12%  Similarity=-0.015  Sum_probs=27.4

Q ss_pred             CCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCC--C----CCCCCHHHHHHHHHHCCCCCCEEEEEECCC
Q ss_conf             3567143558998258888866899997178762--1----233203322311100135764037983588
Q gi|254780710|r   40 TDDNTHFDQIMLIHDFQDASVDAFIRIINCDGSE--V----QSCGNGMRCVVRFLTSRMKRKSFTFETIRG  104 (296)
Q Consensus        40 ~~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~--A----~mCGNG~Rc~a~yl~~~~~~~~~~i~T~~g  104 (296)
                      ++...-.-|++.|.-+.....  -+-|.++|-.+  -    ..-|.|++-+    .+....+.+.+.-.-|
T Consensus        37 ~~f~~~PGQFv~v~v~g~ge~--PiSi~~~~~~~g~l~~~~r~vG~~T~~L----~~lk~Gd~l~v~GPlG  101 (292)
T PRK08345         37 ESFTFKPGQFVQVTIPGVGEV--PISICSSPTRKGFFELCIRRAGRVTTVV----HRLKEGDIVGVRGPYG  101 (292)
T ss_pred             CCCCCCCCCEEEEEECCCCCC--CEEEECCCCCCCEEEEEEEEECHHHHHH----HCCCCCCEEEEEECCC
T ss_conf             458608998599996899961--0587156888998999998218699999----6289999999972357


No 52 
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=25.12  E-value=37  Score=14.38  Aligned_cols=14  Identities=21%  Similarity=0.358  Sum_probs=9.1

Q ss_pred             CCCCHHHHHHHHHH
Q ss_conf             33203322311100
Q gi|254780710|r   76 SCGNGMRCVVRFLT   89 (296)
Q Consensus        76 mCGNG~Rc~a~yl~   89 (296)
                      =||+|.-.++.+++
T Consensus        53 G~GTG~La~ga~~l   66 (198)
T COG2263          53 GAGTGILAIGAALL   66 (198)
T ss_pred             CCCCCHHHHHHHHC
T ss_conf             78847889999862


No 53 
>COG1022 FAA1 Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]
Probab=24.21  E-value=13  Score=17.40  Aligned_cols=28  Identities=14%  Similarity=0.281  Sum_probs=22.7

Q ss_pred             CCCEEEEEEECCCEEEEEECEEEEEEEEEE
Q ss_conf             795799999589819999462899988998
Q gi|254780710|r  251 LGGGLLIEWHDNNHVFMTGEAKKEWEGKLD  280 (296)
Q Consensus       251 pGG~L~v~~~~~~~i~l~Gpa~~vf~G~~~  280 (296)
                      |....++++.++++|++.||..  ++|.++
T Consensus       409 p~p~~evKI~d~GEilVRG~~V--m~GYyk  436 (613)
T COG1022         409 PLPGIEVKIADDGEILVRGPNV--MKGYYK  436 (613)
T ss_pred             CCCCCEEEECCCCEEEEECCHH--CCHHCC
T ss_conf             3788569983674489816412--102208


No 54 
>TIGR01361 DAHP_synth_Bsub phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006268   These sequences are one of at least three types of phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase). This enzyme catalyzes the first of 7 steps in the biosynthesis of chorismate, that last common precursor of all three aromatic amino acids and of PABA, ubiquinone and menaquinone. Some members of this family, including an experimentally characterised member from Bacillus subtilis, are bifunctional, with a chorismate mutase domain N-terminal to this region. The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis.; GO: 0016832 aldehyde-lyase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=24.02  E-value=49  Score=13.55  Aligned_cols=14  Identities=29%  Similarity=0.377  Sum_probs=7.8

Q ss_pred             EEECCCCCCCCCCC
Q ss_conf             99804678766563
Q gi|254780710|r  212 LRTWERGVGLTAAC  225 (296)
Q Consensus       212 iRt~ERGvGeTlAC  225 (296)
                      +||||.=.=.||==
T Consensus       171 IRTfE~~TR~TLD~  184 (262)
T TIGR01361       171 IRTFEKSTRNTLDL  184 (262)
T ss_pred             CCCCCCHHHHHHHH
T ss_conf             56763002453337


No 55 
>TIGR02912 sulfite_red_C sulfite reductase, subunit C; InterPro: IPR014261    This entry represents subunit C, one of the three subunits of the anaerobic sulphite reductase of Salmonella, and close homologues from various Clostridium species, where the three-gene neighbourhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substrates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulphite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulphide gas from sulphite..
Probab=23.97  E-value=25  Score=15.46  Aligned_cols=55  Identities=25%  Similarity=0.445  Sum_probs=36.7

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEEC-CCCEEEEEECCCCC-CCCC
Q ss_conf             58742797425576868887631000233237555514679972-88728999804678-7665
Q gi|254780710|r  162 MGNPHAIFFVEDDLYHYDLASFGNLLAKHPMFSEGVNLSIARVT-SLESLDLRTWERGV-GLTA  223 (296)
Q Consensus       162 iGNPH~Vi~v~d~i~~~~l~~~g~~i~~~~~Fp~gvNV~fv~v~-~~~~I~iRt~ERGv-GeTl  223 (296)
                      +||.=|-      ..+.+-..+++.||+ -.||.-.-|-.+-+= ..+.+++|--.=|. |-|.
T Consensus       113 ~GN~vC~------~an~~Tt~~a~riEK-~vfP~dyH~K~~l~GCPNDC~Ka~M~D~GI~G~t~  169 (323)
T TIGR02912       113 IGNRVCP------FANYDTTKFAKRIEK-AVFPNDYHLKIALTGCPNDCAKARMHDFGIIGMTE  169 (323)
T ss_pred             CCCCCCC------CCCCCHHHHHHHHHH-HCCCCCCEEEEEEECCCCHHHHCCHHHCCEECCCC
T ss_conf             3776276------656547789888654-21888751899987488712330020131432545


No 56 
>PRK05225 ketol-acid reductoisomerase; Validated
Probab=23.69  E-value=49  Score=13.51  Aligned_cols=54  Identities=17%  Similarity=0.233  Sum_probs=33.2

Q ss_pred             ECCCCCCHHHHHHHHHCCCCC--CCCCCCCCEEEEEECCCCEEEE-------------EECCCCCC-CCC
Q ss_conf             425576868887631000233--2375555146799728872899-------------98046787-665
Q gi|254780710|r  170 FVEDDLYHYDLASFGNLLAKH--PMFSEGVNLSIARVTSLESLDL-------------RTWERGVG-LTA  223 (296)
Q Consensus       170 ~v~d~i~~~~l~~~g~~i~~~--~~Fp~gvNV~fv~v~~~~~I~i-------------Rt~ERGvG-eTl  223 (296)
                      ...|.....-...+.|.+...  -.|.-|.|+.|-.+.-+.-|.+             |+|.||-| .||
T Consensus       105 LtPD~q~~~v~~~i~p~mk~g~~L~faHGfnI~~~~i~~r~di~V~MvAPK~PG~~VR~~y~~G~GvP~L  174 (489)
T PRK05225        105 LTPDKQHSDVVRAVQPLMKQGAALGYSHGFNIVEEGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTL  174 (489)
T ss_pred             ECCCCCHHHHHHHHHHHHCCCCEEEECCCCEEEECCCCCCCCCEEEEECCCCCCHHHHHHHHCCCCCCEE
T ss_conf             0885514899999987612677211145650553123168886389975899964899998627997449


No 57 
>COG2264 PrmA Ribosomal protein L11 methylase [Translation, ribosomal structure and biogenesis]
Probab=23.29  E-value=48  Score=13.61  Aligned_cols=16  Identities=38%  Similarity=0.592  Sum_probs=9.1

Q ss_pred             CCCHHHHHHHHHHHHHHC
Q ss_conf             563235899999999817
Q gi|254780710|r  223 AACGSAACASVVASGCLH  240 (296)
Q Consensus       223 lACGTGA~Asa~~~~~~~  240 (296)
                      +.||||-.|  +++.++|
T Consensus       169 vGcGSGILa--IAa~kLG  184 (300)
T COG2264         169 VGCGSGILA--IAAAKLG  184 (300)
T ss_pred             ECCCHHHHH--HHHHHCC
T ss_conf             267815999--9999819


No 58 
>COG3882 FkbH Predicted enzyme involved in methoxymalonyl-ACP biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.27  E-value=50  Score=13.46  Aligned_cols=26  Identities=19%  Similarity=0.328  Sum_probs=17.2

Q ss_pred             CCHHHHHHHCCCCCCCCCEEEEEECC
Q ss_conf             88889987203567143558998258
Q gi|254780710|r   30 ITSDAINALSTDDNTHFDQIMLIHDF   55 (296)
Q Consensus        30 ~~~~~i~~~~~~~giG~Dgli~i~~~   55 (296)
                      ...+.++++|.+-++|.|-++|+.+.
T Consensus       311 ~K~eNirkIAkklNlg~dSmvFiDD~  336 (574)
T COG3882         311 PKAENIRKIAKKLNLGLDSMVFIDDN  336 (574)
T ss_pred             CCHHHHHHHHHHHCCCCCCEEEECCC
T ss_conf             41556999999828886404772488


No 59 
>PRK00517 prmA ribosomal protein L11 methyltransferase; Reviewed
Probab=22.38  E-value=49  Score=13.56  Aligned_cols=18  Identities=33%  Similarity=0.429  Sum_probs=11.8

Q ss_pred             CCCCHHHHHHHHHHHHHHCC
Q ss_conf             65632358999999998178
Q gi|254780710|r  222 TAACGSAACASVVASGCLHK  241 (296)
Q Consensus       222 TlACGTGA~Asa~~~~~~~~  241 (296)
                      -..||||..|-  ++.++|.
T Consensus       168 DvG~GSGILaI--aA~klGa  185 (298)
T PRK00517        168 DVGCGSGILAI--AAAKLGA  185 (298)
T ss_pred             EECCCCHHHHH--HHHHCCC
T ss_conf             71577069999--9997499


No 60 
>COG0043 UbiD 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases [Coenzyme metabolism]
Probab=22.30  E-value=53  Score=13.34  Aligned_cols=95  Identities=22%  Similarity=0.188  Sum_probs=47.7

Q ss_pred             CCEEEE--EECCCCEEEEEECC-CCC----------CC----CCCCHHHHHHHHHHHHHH--CCCCCCEEEECCCCEEEE
Q ss_conf             514679--97288728999804-678----------76----656323589999999981--788980799907957999
Q gi|254780710|r  197 VNLSIA--RVTSLESLDLRTWE-RGV----------GL----TAACGSAACASVVASGCL--HKTNRAVSVKMLGGGLLI  257 (296)
Q Consensus       197 vNV~fv--~v~~~~~I~iRt~E-RGv----------Ge----TlACGTGA~Asa~~~~~~--~~~~~~v~V~~pGG~L~v  257 (296)
                      .|++++  |+++++++-+|.-- ||-          |+    +.+=|.=-.....++.-+  +.-+-...=...|+.+.+
T Consensus       162 ~NlgiyR~qv~~~~~l~~~~~~hr~~~~~~~~a~~~g~~lpvAv~iG~dP~~~laA~~plP~gvsE~~fAg~l~g~~~~v  241 (477)
T COG0043         162 RNLGIYRMQVLGKNKLAMRWVPHRHGALHLRKAEERGEPLPVAVAIGADPATILAAATPLPYGVSELEFAGALRGEPLEV  241 (477)
T ss_pred             CCCEEEEEEEECCCEEEEEEEECCCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHCCCCCCCCCCHHHHHHHHCCCCEEE
T ss_conf             66517889995487589997745647999999998378874699967998998721377998956999888862795458


Q ss_pred             EEECCCEEEEEECEEEEEEEEEEECCCCCC-CCCCCC
Q ss_conf             995898199994628999889984132000-148874
Q gi|254780710|r  258 EWHDNNHVFMTGEAKKEWEGKLDIKTGKWI-KKNEDD  293 (296)
Q Consensus       258 ~~~~~~~i~l~Gpa~~vf~G~~~i~~~~~~-~~~~~~  293 (296)
                      .--..+.+..--.|++|.||.+...  +.. ++++-|
T Consensus       242 vk~~~~~l~VPa~aEiVlEG~i~~~--e~~~EGPFGD  276 (477)
T COG0043         242 VKCDTNGLPVPADAEIVLEGYIDPE--ERAPEGPFGD  276 (477)
T ss_pred             EEECCCCCCCCCCCEEEEEEEECCC--CCCCCCCCCC
T ss_conf             9826878515678759999997787--5026788505


No 61 
>pfam06325 PrmA Ribosomal protein L11 methyltransferase (PrmA). This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences.
Probab=22.23  E-value=50  Score=13.47  Aligned_cols=16  Identities=38%  Similarity=0.389  Sum_probs=10.9

Q ss_pred             CCCHHHHHHHHHHHHHHC
Q ss_conf             563235899999999817
Q gi|254780710|r  223 AACGSAACASVVASGCLH  240 (296)
Q Consensus       223 lACGTGA~Asa~~~~~~~  240 (296)
                      ..||||..|-  ++.++|
T Consensus       167 ~GcGSGILaI--aA~klG  182 (294)
T pfam06325       167 VGCGSGILAI--AALKLG  182 (294)
T ss_pred             ECCCHHHHHH--HHHHCC
T ss_conf             0565089999--999759


No 62 
>cd00580 CHMI 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the homoprotocatechuate pathway, one of the microbial meta-fission pathways that degrade aromatic carbon sources to citric acid cycle intermediates.  Despite the structural similarity of CHMI with 4-oxalocrotonate tautomerase (4-OT) and macrophage migration inhibitory factor (MIF), there is no significant sequence similarity among these protein families, and therefore, they are not combined in one hierarchy.
Probab=21.86  E-value=49  Score=13.52  Aligned_cols=36  Identities=22%  Similarity=0.401  Sum_probs=20.8

Q ss_pred             CEEEEECCCCCCH-HHHHH----HHHCCCCCCCCCC-CCCEE
Q ss_conf             4279742557686-88876----3100023323755-55146
Q gi|254780710|r  165 PHAIFFVEDDLYH-YDLAS----FGNLLAKHPMFSE-GVNLS  200 (296)
Q Consensus       165 PH~Vi~v~d~i~~-~~l~~----~g~~i~~~~~Fp~-gvNV~  200 (296)
                      ||+++.-+++++. .++..    +...+-....||. ++-+=
T Consensus         1 PH~iiEyS~nL~~~~d~~~l~~~l~~~~~~sg~F~~~~iK~R   42 (113)
T cd00580           1 PHLIIEYSANLEGRADIPELLRALHDALVASGLFPLGGIKVR   42 (113)
T ss_pred             CCEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEE
T ss_conf             909999378800037999999999999996699885464886


No 63 
>cd05799 PGM2 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. PGM2L1 is thought to catalyze the 1,3-bisphosphoglycerate-dependent synthesis of glucose 1,6-bisphosphate and other aldose-bisphosphates that serve as cofactors for several sugar phosphomutases and possibly also as regulators of glycolytic enzymes. PGM2 and PGM2L1 belong to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/ph
Probab=21.70  E-value=54  Score=13.26  Aligned_cols=29  Identities=14%  Similarity=0.091  Sum_probs=23.4

Q ss_pred             CCCEEEEEECCCCCCCCEEEEEEECCCCC
Q ss_conf             43558998258888866899997178762
Q gi|254780710|r   45 HFDQIMLIHDFQDASVDAFIRIINCDGSE   73 (296)
Q Consensus        45 G~Dgli~i~~~~~~~~d~~m~~fN~DGS~   73 (296)
                      ++|+-+.|.-+.++..+--++||++||.+
T Consensus        96 ~a~~GImITASHNP~~~NGiK~~~~~G~~  124 (487)
T cd05799          96 GADAGIMITASHNPKEYNGYKVYWEDGAQ  124 (487)
T ss_pred             CCCEEEEEECCCCCCCCCCEEEECCCCCC
T ss_conf             99857999348997522777987799984


No 64 
>KOG3480 consensus
Probab=21.62  E-value=30  Score=14.95  Aligned_cols=25  Identities=20%  Similarity=0.288  Sum_probs=13.5

Q ss_pred             EEECCCCCCCCCCCHHHHHHHHHHCC
Q ss_conf             97178762123320332231110013
Q gi|254780710|r   66 IINCDGSEVQSCGNGMRCVVRFLTSR   91 (296)
Q Consensus        66 ~fN~DGS~A~mCGNG~Rc~a~yl~~~   91 (296)
                      |.-+|=+..|+|= ==||||+|+.-+
T Consensus        44 y~EaeLtKGE~~C-iDRCVaKy~~~n   68 (90)
T KOG3480          44 YKEAELTKGESVC-IDRCVAKYLDVN   68 (90)
T ss_pred             CCCCCCCCCHHHH-HHHHHHHHHHHH
T ss_conf             3600025751668-999999999999


No 65 
>KOG0697 consensus
Probab=21.59  E-value=54  Score=13.24  Aligned_cols=76  Identities=21%  Similarity=0.305  Sum_probs=43.5

Q ss_pred             EEEEEECCCCCCCCCCCHHHHHHHHHHCC-CCCCEEEEEECCCCEEE-EECCCCEEEECCCCCCCCHHHCCCCCCCCCCC
Q ss_conf             99997178762123320332231110013-57640379835883799-98577427740368777777685656565434
Q gi|254780710|r   63 FIRIINCDGSEVQSCGNGMRCVVRFLTSR-MKRKSFTFETIRGILVA-KENRDGSISVDMGEPILDWKLIPLARSFDKMD  140 (296)
Q Consensus        63 ~m~~fN~DGS~A~mCGNG~Rc~a~yl~~~-~~~~~~~i~T~~g~~~~-~~~~~~~v~V~mG~p~~~~~~ip~~~~~~~~~  140 (296)
                      +.-|.|.--|+|-.|+||.-|++--=.+- .++..-+|+--.|-+-. ++++.-.|+-.+|  .++.+.+|-..+.+++.
T Consensus       138 h~y~~NcGDSRavl~rng~~~f~TqDHKP~~p~EkeRIqnAGGSVMIqRvNGsLAVSRAlG--DydyK~v~~kgp~eQlV  215 (379)
T KOG0697         138 HIYIINCGDSRAVLCRNGEVVFSTQDHKPYLPKEKERIQNAGGSVMIQRVNGSLAVSRALG--DYDYKNVPGKGPTEQLV  215 (379)
T ss_pred             EEEEEECCCCHHHEECCCCEEEECCCCCCCCHHHHHHHHCCCCEEEEEEECCEEEEEHHCC--CCCCCCCCCCCCHHCCC
T ss_conf             6999964762120015882577515788888678899755897389998546253103306--75424588889220246


No 66 
>TIGR01292 TRX_reduct thioredoxin-disulfide reductase; InterPro: IPR005982    Reactive oxygen species (ROS) are known mediators of intracellular signaling cascades. Excessive production of ROS may, however, lead to oxidative stress, loss of cell function, and ultimately apoptosis or necrosis. A balance between oxidant and antioxidant intracellular systems is hence vital for cell function, regulation, and adaptation to diverse growth conditions. Thioredoxin reductase in conjunction with thioredoxin is a ubiquitous oxidoreductase system with antioxidant and redox regulatory roles. Thioredoxin reductase (1.8.1.9 from EC) reduces oxidised thioredoxin in the presence of NADPH. Reduced thioredoxin serves as an electron donor for thioredoxin peroxidase which consequently reduces H_2O_2 to H_2O. In mammals, extracellular forms of Trx also have cytokine-like effects. Mammalian TrxR has a highly reactive active site selenocysteine residue resulting in a profound reductive capacity, reducing several substrates in addition to Trx .; GO: 0004791 thioredoxin-disulfide reductase activity, 0019430 removal of superoxide radicals, 0005737 cytoplasm.
Probab=21.53  E-value=52  Score=13.38  Aligned_cols=126  Identities=13%  Similarity=0.119  Sum_probs=54.2

Q ss_pred             CHHHHHHHHHHCCC-CCC--EEEEEECCCCEEEEECCCCEE-EECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEE
Q ss_conf             03322311100135-764--037983588379998577427-74036877777768565656543443011057777402
Q gi|254780710|r   79 NGMRCVVRFLTSRM-KRK--SFTFETIRGILVAKENRDGSI-SVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFL  154 (296)
Q Consensus        79 NG~Rc~a~yl~~~~-~~~--~~~i~T~~g~~~~~~~~~~~v-~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~  154 (296)
                      +.+|| .+.+.|+. +..  .+.|.+..-+.+..=+....| +|.+-.             ..+-...         ...
T Consensus       184 d~fRA-~k~~~~r~~~~~eG~I~~l~n~~v~Ei~G~~~~~V~~v~i~N-------------~~t~e~~---------~l~  240 (321)
T TIGR01292       184 DKFRA-EKILLDRLKKNPEGKIEFLWNSTVEEIVGDNSKKVESVKIKN-------------TVTGEEE---------ELK  240 (321)
T ss_pred             CCCCC-CHHHHHHHHHCCCCCEEEECCCEEEEEECCCCEEEEEEEEEE-------------CCCCEEE---------EEE
T ss_conf             86363-289998998378987899648689999617831553358996-------------2388488---------998


Q ss_pred             CCEEEEECCCCEEEEECCCCCCHHHHHHHHHCCCCCC-CCCCCCCEEEEE----ECCC-CEEEEEECCCCCCCCCCCHHH
Q ss_conf             1309995587427974255768688876310002332-375555146799----7288-728999804678766563235
Q gi|254780710|r  155 RNPFVVSMGNPHAIFFVEDDLYHYDLASFGNLLAKHP-MFSEGVNLSIAR----VTSL-ESLDLRTWERGVGLTAACGSA  228 (296)
Q Consensus       155 ~~~~~v~iGNPH~Vi~v~d~i~~~~l~~~g~~i~~~~-~Fp~gvNV~fv~----v~~~-~~I~iRt~ERGvGeTlACGTG  228 (296)
                      -++.++.+|--=..=|+++ ....++.+-|=.+-... --...|||.=+-    +.++ ..=++-|         |||+|
T Consensus       241 vdGvF~aIG~~P~t~~~~~-~G~~~~D~~GyI~t~~~~Gn~~~Tsv~GvFAAGDv~~kW~~rQ~vT---------Aag~G  310 (321)
T TIGR01292       241 VDGVFIAIGHEPNTELLKG-LGLLELDEGGYIVTDEGLGNTMRTSVPGVFAAGDVRDKWGFRQAVT---------AAGDG  310 (321)
T ss_pred             ECEEEEEECCCCCHHHHHC-CCCEEECCCCCEEECCCCCCEEECCCCCEEEEEEEECCCCCEEEEE---------EECHH
T ss_conf             4447898412032057650-7834676998688617548612306686897304406886137678---------70006


Q ss_pred             HHHHHHHHH
Q ss_conf             899999999
Q gi|254780710|r  229 ACASVVASG  237 (296)
Q Consensus       229 A~Asa~~~~  237 (296)
                      +.||.-+..
T Consensus       311 ~~AA~~a~~  319 (321)
T TIGR01292       311 CIAALSAER  319 (321)
T ss_pred             HHHHHHHHH
T ss_conf             899999987


No 67 
>PRK10291 glyoxalase I; Provisional
Probab=21.49  E-value=55  Score=13.23  Aligned_cols=58  Identities=16%  Similarity=0.149  Sum_probs=35.7

Q ss_pred             CCEEEEECCCCCCHH--HHHHHHHCCCCCC-CCCCCCCEEEEEECCCCEEEEEECCCCC-CCCC
Q ss_conf             742797425576868--8876310002332-3755551467997288728999804678-7665
Q gi|254780710|r  164 NPHAIFFVEDDLYHY--DLASFGNLLAKHP-MFSEGVNLSIARVTSLESLDLRTWERGV-GLTA  223 (296)
Q Consensus       164 NPH~Vi~v~d~i~~~--~l~~~g~~i~~~~-~Fp~gvNV~fv~v~~~~~I~iRt~ERGv-GeTl  223 (296)
                      --|+.+-|+ |+++.  .|.+.|-.+...+ -.+.| ...++-+.+++=..+...||+- |.+|
T Consensus        66 ~gHiA~~Vd-Di~~~~~~l~~~G~~v~~~~~~~~~g-~~~~aFv~DPDGy~IElie~~~~g~~~  127 (129)
T PRK10291         66 YGHIALSVD-NAAEACEKIRQNGGNVTREAGPVKGG-TTVIAFVEDPDGYKIELIEEKDAGRGL  127 (129)
T ss_pred             EEEEEEEEC-CHHHHHHHHHHCCCCEEECCCCCCCC-CEEEEEEECCCCCEEEEEECCCCCCCC
T ss_conf             789999819-99999999997499043567678999-558999999999889999878630111


No 68 
>PRK03124 S-adenosylmethionine decarboxylase proenzyme; Provisional
Probab=21.04  E-value=56  Score=13.17  Aligned_cols=66  Identities=26%  Similarity=0.348  Sum_probs=36.2

Q ss_pred             CCCCCCCCCEEEEEECCCCEEEEEEC-CCCC-C-CCCCCHHHH---HHHHHHHHHHCCCCCCEEEECCC-CEEEE
Q ss_conf             32375555146799728872899980-4678-7-665632358---99999999817889807999079-57999
Q gi|254780710|r  190 HPMFSEGVNLSIARVTSLESLDLRTW-ERGV-G-LTAACGSAA---CASVVASGCLHKTNRAVSVKMLG-GGLLI  257 (296)
Q Consensus       190 ~~~Fp~gvNV~fv~v~~~~~I~iRt~-ERGv-G-eTlACGTGA---~Asa~~~~~~~~~~~~v~V~~pG-G~L~v  257 (296)
                      |++-|+|  |.-+-+++..+|.+-|| |+|. - --..||..+   .|.-+....++-...+++....| |.+.|
T Consensus        47 h~F~P~G--vT~v~lLaESHisiHTwPE~g~aavDiftCg~~~~P~~a~~~L~~~lk~~~~~~~~~~RG~~~~~~  119 (127)
T PRK03124         47 HKFAPQG--VSGVVVISESHLTIHTWPEHGYAAVDVFTCGDRVDPWDAANYIAEGLNAKTREAIELPRGVGPFPV  119 (127)
T ss_pred             EECCCCC--EEEEEEEECCEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCC
T ss_conf             8659996--899999402168999667688599999945999999999999999859892799998189867526


No 69 
>TIGR02630 xylose_isom_A xylose isomerase; InterPro: IPR013452    Xylose isomerase (5.3.1.5 from EC) is an enzyme which interconverts D-xylose and D-xylulose.; GO: 0009045 xylose isomerase activity.
Probab=20.97  E-value=35  Score=14.47  Aligned_cols=206  Identities=17%  Similarity=0.222  Sum_probs=93.3

Q ss_pred             CCCEEEEECCCCC-CCCCHHHHHHH---------CC--CCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCCCCCCCHHH
Q ss_conf             7738999477888-78888899872---------03--567143558998258888866899997178762123320332
Q gi|254780710|r   15 GNKILVIDMRGCH-DNITSDAINAL---------ST--DDNTHFDQIMLIHDFQDASVDAFIRIINCDGSEVQSCGNGMR   82 (296)
Q Consensus        15 GNDFiiiD~~~~~-~~~~~~~i~~~---------~~--~~giG~Dgli~i~~~~~~~~d~~m~~fN~DGS~A~mCGNG~R   82 (296)
                      |.-||..=.|+-. ..|..+..+.+         +.  .+-|||+|-++|+|.+.++.-=|   |.-|-..         
T Consensus       180 GENYVFWGGREGYetLLNTD~~~Eld~lArF~~mAvdYa~~IGF~G~fLIEPKPkEPTKHQ---YDfDaAT---------  247 (437)
T TIGR02630       180 GENYVFWGGREGYETLLNTDMKLELDHLARFLQMAVDYAKKIGFKGQFLIEPKPKEPTKHQ---YDFDAAT---------  247 (437)
T ss_pred             CCCCEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC---CCHHHHH---------
T ss_conf             8862431753033214452177899999889999999988468998441167631218887---7067999---------


Q ss_pred             HHHHHHHCCCCCCE--EEEEECCCCEEEE-------E---C-CCCEEEECCCCCCCCHHHCCCCCCCCCC--------CC
Q ss_conf             23111001357640--3798358837999-------8---5-7742774036877777768565656543--------44
Q gi|254780710|r   83 CVVRFLTSRMKRKS--FTFETIRGILVAK-------E---N-RDGSISVDMGEPILDWKLIPLARSFDKM--------DR  141 (296)
Q Consensus        83 c~a~yl~~~~~~~~--~~i~T~~g~~~~~-------~---~-~~~~v~V~mG~p~~~~~~ip~~~~~~~~--------~~  141 (296)
                       +--||.+.-..+.  +.||+..-.+...       .   . -=|+|=.|=|-+.+.|-.--...+..++        ..
T Consensus       248 -~~~FL~~ygL~~~FKlNiEaNHAtLAGHTF~HEL~~A~~~g~LGSiDAN~GD~LlGWDTDqFPtd~y~~tlaMyevl~~  326 (437)
T TIGR02630       248 -VIAFLKKYGLDKDFKLNIEANHATLAGHTFEHELRVARDNGLLGSIDANQGDLLLGWDTDQFPTDVYETTLAMYEVLKN  326 (437)
T ss_pred             -HHHHHHHHCCCCCCEEEEEHHHHHHHCCCHHHHHHHHHHCCCCCCEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC
T ss_conf             -9999987289655223110211554022248899999981993020004788755655114767678999999999971


Q ss_pred             CEEECCCCCCCEECCEEEEECCCCEEEEECCCCCCHHHHH--HHH------HCCCCC-CCCCCCCCEEEEEECCCCEEEE
Q ss_conf             3011057777402130999558742797425576868887--631------000233-2375555146799728872899
Q gi|254780710|r  142 DRFHIGPVNHLFLRNPFVVSMGNPHAIFFVEDDLYHYDLA--SFG------NLLAKH-PMFSEGVNLSIARVTSLESLDL  212 (296)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~v~iGNPH~Vi~v~d~i~~~~l~--~~g------~~i~~~-~~Fp~gvNV~fv~v~~~~~I~i  212 (296)
                      ..+..+.+|+.-              =+. ..+.+..||-  +|+      +-|+.. .+-.+|   .+-+++..   |-
T Consensus       327 GGl~~GGlNFDA--------------KvR-R~S~~~~DLf~aHIaGMDtfA~GLk~A~~l~~dg---~L~~~~~~---RY  385 (437)
T TIGR02630       327 GGLTTGGLNFDA--------------KVR-RESFDPEDLFLAHIAGMDTFARGLKVAAKLLEDG---FLDKIVAE---RY  385 (437)
T ss_pred             CCCCCCCCCCCC--------------CCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CHHHHHHH---HC
T ss_conf             786688866543--------------557-6788533577676889999999999999987248---42268997---51


Q ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCEEE
Q ss_conf             98046787665632358999999998178898079990795799
Q gi|254780710|r  213 RTWERGVGLTAACGSAACASVVASGCLHKTNRAVSVKMLGGGLL  256 (296)
Q Consensus       213 Rt~ERGvGeTlACGTGA~Asa~~~~~~~~~~~~v~V~~pGG~L~  256 (296)
                      ..|.-|+|--..-|....+..... .+.+-+. +.+..+.|.++
T Consensus       386 ~s~~~g~G~~I~~G~~~l~~L~~y-a~~~~~~-~~~~~~SGrqE  427 (437)
T TIGR02630       386 SSFNSGIGAEIEAGKTDLESLEKY-ALEKGDD-LEPENKSGRQE  427 (437)
T ss_pred             CCCCCHHHHHHHHCCCCHHHHHHH-HHCCCCC-EEEECCCCHHH
T ss_conf             442513468887147888899999-8278985-21212872578


No 70 
>KOG4042 consensus
Probab=20.74  E-value=28  Score=15.17  Aligned_cols=70  Identities=16%  Similarity=0.196  Sum_probs=44.0

Q ss_pred             CCCCCCCCCCCEEEEEECCCCEEEEEEC-CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEE
Q ss_conf             2332375555146799728872899980-467876656323589999999981788980799907957999995
Q gi|254780710|r  188 AKHPMFSEGVNLSIARVTSLESLDLRTW-ERGVGLTAACGSAACASVVASGCLHKTNRAVSVKMLGGGLLIEWH  260 (296)
Q Consensus       188 ~~~~~Fp~gvNV~fv~v~~~~~I~iRt~-ERGvGeTlACGTGA~Asa~~~~~~~~~~~~v~V~~pGG~L~v~~~  260 (296)
                      -.+..|.-|.-++-.++-+++-|...-| +|||-.|-.|--|||+...-.-  . +...+.|+-.-+.-++...
T Consensus        82 Gt~NvFeVgc~s~A~kvGd~NVieskayvg~gv~vssgC~vGA~c~v~~~q--~-lpent~vYga~~L~R~~~~  152 (190)
T KOG4042          82 GTWNVFEVGCKSSAKKVGDRNVIESKAYVGDGVSVSSGCSVGAKCTVFSHQ--N-LPENTSVYGATNLSRTTKT  152 (190)
T ss_pred             ECCCEEEEECHHHHHHHCCCCEEEEEEEECCCCEECCCCEECCCEEEECCC--C-CCCCCEEECCCCCCCEECC
T ss_conf             236358861233455516765476666864994872796541405771103--4-6975168721340100027


No 71 
>KOG0647 consensus
Probab=20.74  E-value=57  Score=13.13  Aligned_cols=13  Identities=23%  Similarity=0.391  Sum_probs=8.7

Q ss_pred             EEECCCCEEEEEC
Q ss_conf             9955874279742
Q gi|254780710|r  159 VVSMGNPHAIFFV  171 (296)
Q Consensus       159 ~v~iGNPH~Vi~v  171 (296)
                      .|.+++.|++++-
T Consensus       170 vVata~r~i~vyn  182 (347)
T KOG0647         170 VVATAERHIAVYN  182 (347)
T ss_pred             EEEECCCCEEEEE
T ss_conf             7884577279998


No 72 
>KOG1529 consensus
Probab=20.67  E-value=50  Score=13.50  Aligned_cols=48  Identities=10%  Similarity=0.161  Sum_probs=25.0

Q ss_pred             CEEEEECCCCCCEEEEECCCC-----CC-CCCHHHHHHHCCCCCCCC-CEEEEEE
Q ss_conf             113785176773899947788-----87-888889987203567143-5589982
Q gi|254780710|r    6 VDFAKMEGIGNKILVIDMRGC-----HD-NITSDAINALSTDDNTHF-DQIMLIH   53 (296)
Q Consensus         6 i~F~Kmhg~GNDFiiiD~~~~-----~~-~~~~~~i~~~~~~~giG~-Dgli~i~   53 (296)
                      ..|.-.|--|=+|+-+|.-..     +. ..+.+.....+++-|++- |.+++-.
T Consensus        39 ~e~~~~hipga~~fdld~~~~~s~~~~~~lp~~e~Fa~y~~~lGi~n~d~vViYd   93 (286)
T KOG1529          39 FEFLERHIPGASHFDLDIISYPSSPYRHMLPTAEHFAEYASRLGVDNGDHVVIYD   93 (286)
T ss_pred             HHHHHCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEEC
T ss_conf             3344316898515421123467886644476078999999862989997699973


No 73 
>TIGR02177 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family; InterPro: IPR011896    A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This entry describes the beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes..
Probab=20.61  E-value=57  Score=13.11  Aligned_cols=116  Identities=18%  Similarity=0.228  Sum_probs=61.7

Q ss_pred             CCC-HHHHHHHHHHCCCCCCEEEEEECCCCEEEEECCCCEEEECCCCCCCCHHHCCCCCCCCCCCCCEEECCCCCCCEEC
Q ss_conf             320-3322311100135764037983588379998577427740368777777685656565434430110577774021
Q gi|254780710|r   77 CGN-GMRCVVRFLTSRMKRKSFTFETIRGILVAKENRDGSISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLR  155 (296)
Q Consensus        77 CGN-G~Rc~a~yl~~~~~~~~~~i~T~~g~~~~~~~~~~~v~V~mG~p~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~  155 (296)
                      ||| |++-+-+=+..++..+.-++-+.+|+=.+..... -|.|++=. .+.=+.+|++..                    
T Consensus         7 CGDFGIL~AL~~AL~EL~LdP~qvvVVSGIGCS~ktPh-Y~n~~g~h-~LHGRA~P~A~G--------------------   64 (302)
T TIGR02177         7 CGDFGILSALQKALAELNLDPEQVVVVSGIGCSAKTPH-YVNVNGFH-GLHGRALPVATG--------------------   64 (302)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCC-CCCCCCCC-CCCCCCCHHHHH--------------------
T ss_conf             88677899999999862889852799813131134773-00136645-233563101101--------------------


Q ss_pred             CEEEEECCCCEEEEECCC---CCCHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCEEE-------EEECCCCC-CCCCC
Q ss_conf             309995587427974255---76868887631000233237555514679972887289-------99804678-76656
Q gi|254780710|r  156 NPFVVSMGNPHAIFFVED---DLYHYDLASFGNLLAKHPMFSEGVNLSIARVTSLESLD-------LRTWERGV-GLTAA  224 (296)
Q Consensus       156 ~~~~v~iGNPH~Vi~v~d---~i~~~~l~~~g~~i~~~~~Fp~gvNV~fv~v~~~~~I~-------iRt~ERGv-GeTlA  224 (296)
                          |=+=|||+-+.|.-   |.-.+=..++=...|        =|+++..++.+|+++       -=|-.+|+ =.+++
T Consensus        65 ----~KlANP~L~Viv~GGDGD~~GIG~~Hfva~gR--------RN~dIt~l~~DN~VYGLTKGQAsPTl~~G~kTk~lp  132 (302)
T TIGR02177        65 ----IKLANPKLKVIVVGGDGDLYGIGGNHFVAAGR--------RNVDITVLVHDNQVYGLTKGQASPTLLKGVKTKSLP  132 (302)
T ss_pred             ----HHHCCCCCEEEEEECCCCCHHHHHHHHHHHHC--------CCCCCEEEEECCEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf             ----20108984689860686410110577875411--------478824884247054666553452146871042335


Q ss_pred             CH
Q ss_conf             32
Q gi|254780710|r  225 CG  226 (296)
Q Consensus       225 CG  226 (296)
                      -|
T Consensus       133 ~p  134 (302)
T TIGR02177       133 YP  134 (302)
T ss_pred             CC
T ss_conf             78


No 74 
>TIGR03533 L3_gln_methyl protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific. Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors.
Probab=20.58  E-value=57  Score=13.11  Aligned_cols=14  Identities=21%  Similarity=0.088  Sum_probs=7.8

Q ss_pred             EEECCCCEEEEEEE
Q ss_conf             99907957999995
Q gi|254780710|r  247 SVKMLGGGLLIEWH  260 (296)
Q Consensus       247 ~V~~pGG~L~v~~~  260 (296)
                      ..-.|||.|.+++-
T Consensus       239 ~~L~pgG~l~lEiG  252 (284)
T TIGR03533       239 DHLNENGVLVVEVG  252 (284)
T ss_pred             HHCCCCCEEEEEEC
T ss_conf             84256978999979


No 75 
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=20.31  E-value=57  Score=13.11  Aligned_cols=13  Identities=23%  Similarity=0.079  Sum_probs=7.4

Q ss_pred             EEECCCCEEEEEE
Q ss_conf             9990795799999
Q gi|254780710|r  247 SVKMLGGGLLIEW  259 (296)
Q Consensus       247 ~V~~pGG~L~v~~  259 (296)
                      ..-.|||.|.+++
T Consensus       251 ~~L~pgG~L~~Ei  263 (307)
T PRK11805        251 DYLTEDGVLVCEV  263 (307)
T ss_pred             HHCCCCCEEEEEE
T ss_conf             7447696899997


Done!