Query         gi|254781095|ref|YP_003065508.1| UDP-N-acetylenolpyruvoylglucosamine reductase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 318
No_of_seqs    173 out of 2524
Neff          6.4 
Searched_HMMs 39220
Date          Mon May 30 04:34:02 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781095.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK13905 murB UDP-N-acetylenol 100.0       0       0  695.0  21.2  294   10-305     2-297 (298)
  2 PRK13906 murB UDP-N-acetylenol 100.0       0       0  689.0  23.0  304    1-310     1-306 (307)
  3 PRK12436 UDP-N-acetylenolpyruv 100.0       0       0  684.1  23.2  300    1-305     1-302 (305)
  4 COG0812 MurB UDP-N-acetylmuram 100.0       0       0  661.3  18.6  287   20-307     2-290 (291)
  5 PRK00046 murB UDP-N-acetylenol 100.0       0       0  645.7  19.7  285   20-305     2-342 (348)
  6 PRK13903 murB UDP-N-acetylenol 100.0       0       0  624.7  20.2  284   18-305    12-357 (359)
  7 PRK13904 murB UDP-N-acetylenol 100.0       0       0  590.0  17.2  257   21-303     1-257 (257)
  8 TIGR00179 murB UDP-N-acetyleno 100.0       0       0  342.6   9.7  277   27-304     1-327 (327)
  9 pfam02873 MurB_C UDP-N-acetyle 100.0 9.6E-38 2.4E-42  258.8   9.1  103  202-304     1-103 (103)
 10 PRK11230 glycolate oxidase sub  99.7 1.4E-16 3.7E-21  125.0   8.3  191    7-203    19-233 (499)
 11 pfam01565 FAD_binding_4 FAD bi  99.7 1.7E-16 4.4E-21  124.5   8.4  129   40-171     2-138 (138)
 12 COG0277 GlcD FAD/FMN-containin  99.6 1.5E-14 3.8E-19  112.3   8.0  157   36-202    29-208 (459)
 13 PRK11282 glcE glycolate oxidas  99.5 7.7E-14   2E-18  107.7   8.1  155   46-203     2-172 (351)
 14 TIGR00387 glcD glycolate oxida  99.3 6.2E-13 1.6E-17  102.0   2.9  155   42-202     1-176 (437)
 15 TIGR01678 FAD_lactone_ox sugar  99.2 2.1E-11 5.2E-16   92.4   5.6  152   36-200    12-185 (505)
 16 KOG1231 consensus               99.0 8.3E-10 2.1E-14   82.3   7.8  164   36-202    61-240 (505)
 17 KOG4730 consensus               99.0 6.3E-10 1.6E-14   83.0   5.8  158   37-202    48-219 (518)
 18 KOG1232 consensus               98.7 3.8E-08 9.6E-13   71.8   6.8  174   21-200    69-265 (511)
 19 TIGR01679 bact_FAD_ox FAD-link  98.6   1E-07 2.7E-12   69.0   7.0  151   40-199    13-177 (426)
 20 TIGR01677 pln_FAD_oxido plant-  98.6 3.8E-07 9.6E-12   65.5   8.1  166   34-207    34-229 (577)
 21 KOG1233 consensus               98.5   4E-07   1E-11   65.3   6.2  163   38-201   160-340 (613)
 22 TIGR02963 xanthine_xdhA xanthi  97.7 5.4E-05 1.4E-09   51.8   4.8  167   26-202   211-407 (515)
 23 pfam00941 FAD_binding_5 FAD bi  97.7 6.1E-05 1.5E-09   51.5   5.0  146   41-196     4-169 (171)
 24 PRK09971 xanthine dehydrogenas  97.4 0.00023 5.9E-09   47.9   4.2  148   40-196     5-172 (292)
 25 TIGR03195 4hydrxCoA_B 4-hydrox  97.1  0.0006 1.5E-08   45.2   4.1  150   42-196     7-211 (321)
 26 KOG0430 consensus               96.6  0.0042 1.1E-07   39.9   5.0  157   39-200   214-390 (1257)
 27 TIGR01676 GLDHase galactonolac  96.5  0.0039   1E-07   40.1   4.1  169   19-197    36-225 (541)
 28 COG1319 CoxM Aerobic-type carb  95.9  0.0042 1.1E-07   39.9   1.9  149   41-198     5-173 (284)
 29 TIGR03312 Se_sel_red_FAD proba  95.4   0.013 3.2E-07   36.8   2.9  143   40-196     2-154 (257)
 30 PRK09799 putative selenate red  94.3   0.036 9.3E-07   34.0   2.9  143   40-196     3-155 (258)
 31 TIGR03199 pucC xanthine dehydr  94.2    0.08   2E-06   31.8   4.4  138   45-196     1-157 (264)
 32 PRK11183 D-lactate dehydrogena  92.5    0.38 9.7E-06   27.5   5.6  123   20-145    19-154 (565)
 33 COG4630 XdhA Xanthine dehydrog  90.3    0.33 8.5E-06   27.9   3.5  162   27-199   191-371 (493)
 34 KOG1262 consensus               88.4    0.19 4.9E-06   29.4   1.1  101   93-200   113-228 (543)
 35 TIGR00130 frhD coenzyme F420-r  64.2     2.7 6.8E-05   22.2   0.8   91   64-182     1-99  (162)
 36 pfam01981 PTH2 Peptidyl-tRNA h  49.5      21 0.00053   16.6   3.4   38   30-67     42-80  (116)
 37 PTZ00139 succinate dehydrogena  48.9      21 0.00054   16.5   3.3   28   40-67     36-63  (622)
 38 PRK04322 peptidyl-tRNA hydrola  48.7      21 0.00054   16.5   4.4   38   30-67     42-80  (116)
 39 cd01824 Phospholipase_B_like P  46.5      23 0.00058   16.3   3.6   23  266-288   199-221 (288)
 40 PRK05675 sdhA succinate dehydr  45.3     5.4 0.00014   20.3  -0.3   22  115-136   206-229 (570)
 41 PRK10264 hydrogenase 1 maturat  44.9      11 0.00029   18.2   1.3   77   62-175     4-84  (195)
 42 cd02407 PTH2_family Peptidyl-t  43.4      25 0.00065   16.0   4.2   40   28-67     39-79  (115)
 43 PTZ00244 serine/threonine-prot  41.9      27 0.00069   15.8   3.6   48   30-82     45-95  (294)
 44 TIGR00090 TIGR00090 iojap homo  39.1      30 0.00076   15.6   3.8   39  257-296    54-92  (155)
 45 TIGR00140 hupD hydrogenase exp  39.0     6.8 0.00017   19.6  -0.5   53   64-121     1-55  (156)
 46 pfam00390 malic Malic enzyme,   38.4      30 0.00078   15.5   3.4   50   39-88     43-94  (182)
 47 pfam02731 SKIP_SNW SKIP/SNW do  37.6      23 0.00059   16.2   2.0   62  220-291    66-128 (158)
 48 PRK08401 L-aspartate oxidase;   37.6      31 0.00079   15.4   2.7   40   45-85    116-157 (464)
 49 LOAD_SKIP consensus             36.4      23 0.00059   16.2   1.9   62  220-291    70-132 (168)
 50 PRK07573 sdhA succinate dehydr  36.3      24  0.0006   16.2   1.9   88   40-129    35-127 (638)
 51 TIGR02587 TIGR02587 putative i  36.1      12  0.0003   18.1   0.3   24  128-154   110-133 (284)
 52 TIGR01008 rpsC_E_A ribosomal p  35.5      11 0.00029   18.2   0.2   73  113-194    97-181 (204)
 53 cd02430 PTH2 Peptidyl-tRNA hyd  31.4      39   0.001   14.8   4.7   37   30-66     41-78  (115)
 54 pfam08985 DUF1888 Domain of un  30.9      32 0.00081   15.4   1.8   23  151-174    69-91  (124)
 55 TIGR01048 lysA diaminopimelate  30.8      21 0.00055   16.4   1.0   19  105-123    59-77  (431)
 56 TIGR02082 metH methionine synt  30.7      41   0.001   14.7   2.8   32   37-69    162-203 (1265)
 57 COG2513 PrpB PEP phosphonomuta  30.6      19 0.00048   16.8   0.6   14  144-157   105-118 (289)
 58 TIGR00421 ubiX_pad polyprenyl   30.6      39 0.00099   14.8   2.2   23  275-297   154-176 (181)
 59 PRK07512 L-aspartate oxidase;   30.1      31  0.0008   15.4   1.7   27  103-129    72-98  (507)
 60 TIGR02687 TIGR02687 conserved   29.7      39   0.001   14.8   2.1   72   45-130   654-728 (911)
 61 cd02810 DHOD_DHPD_FMN Dihydroo  29.2      43  0.0011   14.5   2.4   24  270-293   218-241 (289)
 62 PTZ00306 NADH-dependent fumara  29.1      43  0.0011   14.5   3.2   92   38-131   409-509 (1167)
 63 TIGR01830 3oxo_ACP_reduc 3-oxo  28.5      13 0.00033   17.9  -0.5   82   35-129    46-132 (238)
 64 COG1775 HgdB Benzoyl-CoA reduc  28.0      45  0.0011   14.4   3.0   47  271-317   212-260 (379)
 65 TIGR03140 AhpF alkyl hydropero  27.6      46  0.0012   14.4   2.4   68  102-170   215-302 (515)
 66 COG1252 Ndh NADH dehydrogenase  27.5      46  0.0012   14.3   2.2   26   28-53    109-134 (405)
 67 KOG1342 consensus               27.1      47  0.0012   14.3   2.9   13  134-146   114-126 (425)
 68 pfam04283 CheF-arch Chemotaxis  26.1      49  0.0012   14.2   2.8   43  103-145    86-129 (220)
 69 TIGR00430 Q_tRNA_tgt queuine t  25.2      25 0.00065   16.0   0.5  134  157-314   141-291 (415)
 70 TIGR03004 ectoine_ehuC ectoine  25.1      16 0.00042   17.2  -0.5   21  132-152    80-101 (216)
 71 TIGR00072 hydrog_prot hydrogen  24.9      42  0.0011   14.6   1.6   92   62-182     2-99  (170)
 72 TIGR02143 trmA_only tRNA (urac  24.7      35  0.0009   15.1   1.1  199    5-235    75-296 (361)
 73 TIGR00314 cdhA CO dehydrogenas  24.6      32 0.00082   15.3   0.9   38   16-62    136-173 (795)
 74 COG2226 UbiE Methylase involve  24.5      52  0.0013   14.0   3.3   53   38-90     75-130 (238)
 75 pfam01786 AOX Alternative oxid  24.4      26 0.00066   15.9   0.4   16  126-141    59-74  (214)
 76 pfam09873 DUF2100 Uncharacteri  23.7      54  0.0014   13.9   3.0   18  188-205   130-147 (215)
 77 cd04906 ACT_ThrD-I_1 First of   23.5      25 0.00065   16.0   0.2   21  176-196    29-49  (85)
 78 TIGR02477 PFKA_PPi diphosphate  23.2      55  0.0014   13.9   2.9   29   45-73    151-182 (566)
 79 TIGR02207 lipid_A_htrB lipid A  23.1      27  0.0007   15.8   0.4   28  156-184   183-210 (308)
 80 TIGR01931 cysJ sulfite reducta  23.0      45  0.0012   14.4   1.4  114    4-121    82-214 (628)
 81 TIGR02309 HpaB-1 4-hydroxyphen  22.7      57  0.0014   13.8   4.6   62   21-88     47-112 (487)
 82 cd07560 Peptidase_S41_CPP C-te  22.6      57  0.0014   13.8   1.9   41   27-67     40-83  (211)
 83 COG4809 Archaeal ADP-dependent  22.6      55  0.0014   13.9   1.8   62  242-303   215-276 (466)
 84 PRK03971 putative deoxyhypusin  22.3      44  0.0011   14.5   1.3   67   43-118    43-113 (334)
 85 TIGR01826 CofD_related conserv  21.8      51  0.0013   14.1   1.5   74   38-121   165-253 (331)
 86 TIGR01494 ATPase_P-type ATPase  21.7      34 0.00087   15.2   0.6   55  197-251   279-343 (478)
 87 TIGR02627 rhamnulo_kin rhamnul  21.4      60  0.0015   13.6   2.3   66  202-279   342-410 (460)
 88 PTZ00239 serine/threonine prot  21.1      61  0.0016   13.6   4.0   47   31-82     37-86  (303)
 89 TIGR01929 menB naphthoate synt  20.7      62  0.0016   13.5   2.6   28   43-70     28-58  (278)
 90 PRK09754 phenylpropionate diox  20.3      63  0.0016   13.5   3.6   22  102-123   147-168 (400)
 91 PRK10872 relA GDP/GTP pyrophos  20.1      64  0.0016   13.4   2.4   30  156-185   404-436 (743)

No 1  
>PRK13905 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=100.00  E-value=0  Score=694.97  Aligned_cols=294  Identities=44%  Similarity=0.749  Sum_probs=283.3

Q ss_pred             HHHHHHHHCCEEEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCCEECCHHHHC
Q ss_conf             99998750662775488001522576614889999689899999999856-29989998475203660488402202211
Q gi|254781095|r   10 LRERGKQLRGKFQENFPLKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAGIRGVVLRLS   88 (318)
Q Consensus        10 l~~~~~~~~g~i~~n~~L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~~~G~vI~l~   88 (318)
                      +...+++++|+|++|+||++||||||||+|++|++|+|.+||.+++++++ +++|+++||+|||+||+|++|+|+||++.
T Consensus         2 ~~~~~~~~~g~i~~n~~Ls~~tt~~iGG~A~~~~~~~~~~~L~~~l~~~~~~~~p~~vlG~GSNlL~~D~g~~G~VI~l~   81 (298)
T PRK13905          2 LKLLLPLLRGRLLENEPLARYTWFKVGGPADYLFEPADIEDLAAFLKFLKENNIPVTVIGNGSNLLVRDGGIRGVVIRLG   81 (298)
T ss_pred             HHHHCCCCCCEEEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHHCCCCEEEECCCEEEEEECCCEEEEEEEEC
T ss_conf             43844413646980783665515120828789998699999999999788769988999270489781698622899953


Q ss_pred             CCCCCCEEEECCCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCEE
Q ss_conf             23443113302665123311221567777887520120003872566324311573215831345666434411232100
Q gi|254781095|r   89 NAGFSNIEVRNHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGANNCETSQYVVEVHGIDRKGNQH  168 (318)
Q Consensus        89 ~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAGayG~ei~d~i~~V~~~d~~g~~~  168 (318)
                      + .+..++..++ .++|+||+.|++|+++++++||+|||||+|||||||||++|||||||.||+|+|++|+++|.+|+++
T Consensus        82 ~-~~~~i~~~~~-~v~v~AG~~~~~lv~~~~~~gl~GlE~l~gIPGTvGgA~~mNaGayG~ei~d~l~~V~~~d~~g~~~  159 (298)
T PRK13905         82 K-GLNEIEVEGD-TVRAGAGAPLIKLARFAAEAGLSGLEFAAGIPGSVGGAVFMNAGAYGGETADVLVSVEVLDRDGEIK  159 (298)
T ss_pred             C-CCCEEEECCC-EEEEEECCCHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHCCCCCCHHHHHHEEEEEEEECCCCCEE
T ss_conf             7-6257998299-9999828988999999998599863999705846778976148977356666114489996999899


Q ss_pred             EECCCCCCCCCCCCCCCC-CCCEEEEECCCCCCCCCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHCC
Q ss_conf             001233443100232246-7620010023545654310012221001100015566704658897278985100026318
Q gi|254781095|r  169 VIPREQLKYQYRSSEITK-DLIITHVVLRGFPESQNIISAAIANVCHHRETVQPIKEKTGGSTFKNPTGHSAWQLIEKSG  247 (318)
Q Consensus       169 ~l~~~e~~f~YR~S~~~~-~~iIl~a~l~l~~~~~~~i~~~~~~~~~~R~~~qP~~~~s~GSvFkNP~~~~A~~LIe~~G  247 (318)
                      +++++||+|+||+|.|++ ++||++|+|++.+++++.++++|++++++|+++||.+.||||||||||++.+||||||+||
T Consensus       160 ~~~~~e~~f~YR~S~f~~~~~iIl~~~f~l~~~~~~~i~~~~~~~~~~R~~~qP~~~~~~GS~FKNP~~~~Ag~LIe~~G  239 (298)
T PRK13905        160 TLSNEELGFGYRHSALQEKGLIVLSATFRLEPGDPEAIRARMDELLAHREATQPLEYPSAGSVFKNPEGHFAGKLIDEAG  239 (298)
T ss_pred             EEEHHHCCCCCCCCCCCCCCCEEEEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHCC
T ss_conf             98747805133446778899479999999523997999999999998741337899994768364899860789999708


Q ss_pred             CCCCCCCCEEECCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEECCEEEEC
Q ss_conf             6882066778715677089968997999999999999999999847540042289621
Q gi|254781095|r  248 CRGLEFGGAKISELHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILLEWEIKRLGD  305 (318)
Q Consensus       248 lKG~~iG~a~vS~kHanfivN~g~ata~di~~Li~~v~~~V~~~~gi~Le~Ev~~iG~  305 (318)
                      |||+++|+|+||+||||||||.|+|||+|+++|+++||++|+++|||.||+||++||+
T Consensus       240 lKG~~iG~a~vS~kHanfivN~g~ata~dv~~L~~~i~~~V~~~~GI~Le~EV~iiG~  297 (298)
T PRK13905        240 LKGLRIGGAQVSEKHANFIINTGGATAADIEDLIELVQKTVKEKSGVELEWEVRIIGE  297 (298)
T ss_pred             CCCCEECCEEECCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEEEEEEECC
T ss_conf             7886587989834588589968999999999999999999999889760580188477


No 2  
>PRK13906 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=100.00  E-value=0  Score=688.97  Aligned_cols=304  Identities=33%  Similarity=0.548  Sum_probs=289.6

Q ss_pred             CCHHHHHHHHHHHHHHHCCEEEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCC
Q ss_conf             98579999999998750662775488001522576614889999689899999999856-29989998475203660488
Q gi|254781095|r    1 MIYGRISRLLRERGKQLRGKFQENFPLKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAG   79 (318)
Q Consensus         1 m~~~~~~~~l~~~~~~~~g~i~~n~~L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~   79 (318)
                      |+.+.|-..|+..++.  .+|+.|+||++||||||||+|++|++|++.+||.+++++++ +++|+++||+|||+||+|++
T Consensus         1 ~~~~~~~~~l~~~~p~--~ki~~n~~Ls~~tt~~iGG~A~~~~~p~~~~~l~~~~~~~~~~~ip~~vlG~GSNlLv~D~g   78 (307)
T PRK13906          1 MINKDIYQALQQLIPN--EKIKVDEPLKRYTYTKTGGNADFYITPTKNEEVQAVVKYAYQNEIPVTYLGNGSNIIIREGG   78 (307)
T ss_pred             CCCHHHHHHHHHHCCC--CCEECCCCCCCCCEEEECCEEEEEEEECCHHHHHHHHHHHHHCCCCEEEECCCEEEEEECCC
T ss_conf             9618999999986784--64672885665644127809789996499999999999898769978998270699896698


Q ss_pred             EECCHHHHCCCCCCCEEEECCCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCCCCCCEEEEEEEEEE
Q ss_conf             40220221123443113302665123311221567777887520120003872566324311573215831345666434
Q gi|254781095|r   80 IRGVVLRLSNAGFSNIEVRNHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGANNCETSQYVVEVH  159 (318)
Q Consensus        80 ~~G~vI~l~~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAGayG~ei~d~i~~V~  159 (318)
                      |+|+||++.  .+..++..++ .++|+||+.|++|++++.++||+|||||+|||||||||++|||||||.||+|+|++|+
T Consensus        79 ~~GiVI~l~--~~~~i~~~~~-~v~~~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTvGGAi~mNaGayG~ei~d~i~~v~  155 (307)
T PRK13906         79 IRGIVISLL--SLDHIEVSDD-AIIAGSGAAIIDVSRVARDYALTGLEFACGIPGSIGGAVYMNAGAYGGEVKDCIDYAL  155 (307)
T ss_pred             CCEEEEEEC--CCCEEEEECC-EEEEEECCCHHHHHHHHHHCCCCCCHHHCCCCCCHHHHHHCCCCCCCCCCEEEEEEEE
T ss_conf             032899955--6553996099-7999816818999999998698630333378833667754038978731133899999


Q ss_pred             EECCCCCEEEECCCCCCCCCCCCCCCCC-CCEEEEECCCCCCCCCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCC
Q ss_conf             4112321000012334431002322467-620010023545654310012221001100015566704658897278985
Q gi|254781095|r  160 GIDRKGNQHVIPREQLKYQYRSSEITKD-LIITHVVLRGFPESQNIISAAIANVCHHRETVQPIKEKTGGSTFKNPTGHS  238 (318)
Q Consensus       160 ~~d~~g~~~~l~~~e~~f~YR~S~~~~~-~iIl~a~l~l~~~~~~~i~~~~~~~~~~R~~~qP~~~~s~GSvFkNP~~~~  238 (318)
                      ++|.+|++++++++||+|+||+|.|+++ +||++|+|+|.++++++++++|+++.++|+++||...||||||||||++.+
T Consensus       156 ~~d~~g~~~~l~~~e~~f~YR~S~f~~~~~iIl~a~f~l~~~~~~~i~~~~~~~~~~R~~~qP~~~psaGS~FKNP~g~~  235 (307)
T PRK13906        156 CVNEQGSLIKLTTKELELDYRNSIIQKEHLVVLEAAFTLAPGKMTEIQAKMDDLTERRESKQPLEYPSCGSVFQRPPGHF  235 (307)
T ss_pred             EECCCCEEEEEECCCCEECCCCCCCCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH
T ss_conf             99589829998543111224667667688269999998657997999999999998764249866787550015999843


Q ss_pred             CHHHHHHCCCCCCCCCCEEECCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEECCEEEECCCCHH
Q ss_conf             100026318688206677871567708996899799999999999999999984754004228962168356
Q gi|254781095|r  239 AWQLIEKSGCRGLEFGGAKISELHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILLEWEIKRLGDFFDHQ  310 (318)
Q Consensus       239 A~~LIe~~GlKG~~iG~a~vS~kHanfivN~g~ata~di~~Li~~v~~~V~~~~gi~Le~Ev~~iG~f~~~~  310 (318)
                      ||+|||+|||||+++|+|+||+||||||||.|+|||+|+++|+++||++|+++|||+||+||++||++ |+|
T Consensus       236 Ag~LIe~~GlKG~~iG~a~VS~kHanfiVN~g~ata~di~~Li~~v~~~V~~k~GI~Le~EV~iiG~~-~~~  306 (307)
T PRK13906        236 AGKLIQDSNLQGHRIGGVEVSTKHAGFMVNVDNGTATDYENLIHYVQKTVKEKFGIELNREVRIIGEH-PKE  306 (307)
T ss_pred             HHHHHHHHCCCCCEECCEEECCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEECEEEECCC-CCC
T ss_conf             89999972979975649898235685899799999999999999999999998897505770976789-989


No 3  
>PRK12436 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=100.00  E-value=0  Score=684.13  Aligned_cols=300  Identities=30%  Similarity=0.504  Sum_probs=284.7

Q ss_pred             CCHHHHHHHHHHHHHHHCCEEEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCC
Q ss_conf             98579999999998750662775488001522576614889999689899999999856-29989998475203660488
Q gi|254781095|r    1 MIYGRISRLLRERGKQLRGKFQENFPLKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAG   79 (318)
Q Consensus         1 m~~~~~~~~l~~~~~~~~g~i~~n~~L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~   79 (318)
                      |....+.+.|.+.+++  |++++|+||++||||||||+|++|++|+|.+||.+++++++ +++|+++||+|||+||+|++
T Consensus         1 m~~~~~~~~l~~~~~~--g~i~~n~~L~~~tt~~IGG~A~~~~~~~~~~~L~~~~~~~~~~~~p~~vlG~GSNlL~~D~g   78 (305)
T PRK12436          1 MNMQEVYEYLSTVLPE--GHVKQDEMLKNHTHIKVGGKADVFVAPTNYDEIQEVIKYANKYNIPVTFLGNGSNVIIKDGG   78 (305)
T ss_pred             CCHHHHHHHHHHHCCC--CCEEECCCCCCCCCCCCCEEEEEEEEECCHHHHHHHHHHHHHCCCCEEEECCCEEEEEECCC
T ss_conf             9878999999976778--84670882665665344808649998699999999999888769977998272589785698


Q ss_pred             EECCHHHHCCCCCCCEEEECCCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCCCCCCEEEEEEEEEE
Q ss_conf             40220221123443113302665123311221567777887520120003872566324311573215831345666434
Q gi|254781095|r   80 IRGVVLRLSNAGFSNIEVRNHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGANNCETSQYVVEVH  159 (318)
Q Consensus        80 ~~G~vI~l~~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAGayG~ei~d~i~~V~  159 (318)
                      |+|+||++..  +..++..++ .++|+||+.|++|+++++++||+|+|||+|||||||||++|||||||.|++|++.+|+
T Consensus        79 ~~G~vI~l~~--~~~i~~~~~-~i~a~aG~~~~~l~~~a~~~gl~GlE~l~gIPGTVGGA~~mNaGayG~ei~~~l~~v~  155 (305)
T PRK12436         79 IRGITVSLIH--ITGVTVTGT-TIVAQCGAAIIDVSRIALDHNLTGLEFACGIPGSVGGALYMNAGAYGGEISFVLTEAV  155 (305)
T ss_pred             CCCEEEEEEE--ECEEEECCC-EEEEEECCCHHHHHHHHHHCCCCCCHHHCCCCCCHHHHHHCCCCCCCCCCEEEEEEEE
T ss_conf             0646999753--210685399-8999838868999999998698631323278843556741358999755315899999


Q ss_pred             EECCCCCEEEECCCCCCCCCCCCCCCCC-CCEEEEECCCCCCCCCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCC
Q ss_conf             4112321000012334431002322467-620010023545654310012221001100015566704658897278985
Q gi|254781095|r  160 GIDRKGNQHVIPREQLKYQYRSSEITKD-LIITHVVLRGFPESQNIISAAIANVCHHRETVQPIKEKTGGSTFKNPTGHS  238 (318)
Q Consensus       160 ~~d~~g~~~~l~~~e~~f~YR~S~~~~~-~iIl~a~l~l~~~~~~~i~~~~~~~~~~R~~~qP~~~~s~GSvFkNP~~~~  238 (318)
                      ++|.+|++++++++||+|+||+|.|+++ +||++|+|++.+++++.|++.|+++..+|+++||.+.||||||||||++.+
T Consensus       156 ~~~~~g~~~~~~~~e~~F~YR~S~f~~~~~iIl~~~f~l~~~~~~~i~~~~~~~~~~R~~~qP~~~psaGS~FKNP~~~~  235 (305)
T PRK12436        156 VMTGDGELRTLTKEAFEFGYRKSVFANNHYIILEARFELEEGVYEEIKAKMDDLTFKRESKQPLEYPSCGSVFKRPPNNF  235 (305)
T ss_pred             EECCCCCEEEECHHHCCCCCCCCCCCCCCEEEEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCC
T ss_conf             98078738997689917564567677887389999995367998999999999998651048876777562341899870


Q ss_pred             CHHHHHHCCCCCCCCCCEEECCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEECCEEEEC
Q ss_conf             1000263186882066778715677089968997999999999999999999847540042289621
Q gi|254781095|r  239 AWQLIEKSGCRGLEFGGAKISELHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILLEWEIKRLGD  305 (318)
Q Consensus       239 A~~LIe~~GlKG~~iG~a~vS~kHanfivN~g~ata~di~~Li~~v~~~V~~~~gi~Le~Ev~~iG~  305 (318)
                      ||||||+|||||+++|+|+||+||||||||.|+|||+||++|+++||++|+++|||.||+||++||+
T Consensus       236 Ag~LIe~~GlKG~~iG~a~vS~kHanfivN~g~Ata~Dv~~Li~~i~~~V~~~~gI~Le~Ev~iiGe  302 (305)
T PRK12436        236 AGKLIQESGLQGKRIGGVEVSLKHAGFMVNVDNGTAQDYIDLIHFVQKTVEEKFGVKLEREVRIIGE  302 (305)
T ss_pred             HHHHHHHHCCCCCEECCEEEECCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEEEEEEECC
T ss_conf             8999997187887163979860278389989998999999999999999999889750580188425


No 4  
>COG0812 MurB UDP-N-acetylmuramate dehydrogenase [Cell envelope biogenesis, outer membrane]
Probab=100.00  E-value=0  Score=661.33  Aligned_cols=287  Identities=42%  Similarity=0.641  Sum_probs=274.1

Q ss_pred             EEEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCCEECCHHHHCCCCCCCEEEE
Q ss_conf             2775488001522576614889999689899999999856-299899984752036604884022022112344311330
Q gi|254781095|r   20 KFQENFPLKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNIEVR   98 (318)
Q Consensus        20 ~i~~n~~L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i~~~   98 (318)
                      +++.++||++||||||||+|++++.|++++||.+++++++ .++|+++||+|||+||+|++++|+||.+.......++..
T Consensus         2 ~~~~~~~L~~~ttfriGg~A~~~~~~~~~e~l~~~~~~~~~~~~p~~ilG~GSNlLv~d~g~~gvvi~~~~~~~~~~~~~   81 (291)
T COG0812           2 RIKTNVPLKRYTTFRIGGPAEVLVEPRDIEELKAALKYAKAEDLPVLILGGGSNLLVRDGGIGGVVIKLGKLNFIEIEGD   81 (291)
T ss_pred             CCCCCCCCCCCEEEECCCCEEEEEECCCHHHHHHHHHHHHHCCCCEEEEECCCEEEEECCCCCEEEEECCCCCCEEEECC
T ss_conf             74457766663367628540279814899999999986442599879995671489954997669998045662245056


Q ss_pred             CCCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCEEEECCCCCCCC
Q ss_conf             26651233112215677778875201200038725663243115732158313456664344112321000012334431
Q gi|254781095|r   99 NHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGANNCETSQYVVEVHGIDRKGNQHVIPREQLKYQ  178 (318)
Q Consensus        99 ~~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAGayG~ei~d~i~~V~~~d~~g~~~~l~~~e~~f~  178 (318)
                      ++ .++|+||++|++|++++.++||+||||++|||||||||++|||||||.||+|++.+|+++|++|++++++++||+|+
T Consensus        82 ~~-~i~a~aG~~~~~l~~~~~~~gl~GlE~l~gIPGsvGgav~mNaGAyG~Ei~d~~~~v~~ld~~G~~~~l~~~el~f~  160 (291)
T COG0812          82 DG-LIEAGAGAPWHDLVRFALENGLSGLEFLAGIPGSVGGAVIMNAGAYGVEISDVLVSVEVLDRDGEVRWLSAEELGFG  160 (291)
T ss_pred             CC-EEEECCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCHHHHCCCCCCCCCHHEEEEEEEEECCCCCEEEEEHHHHCCC
T ss_conf             78-69990389679999999975972147661799541205530386254101211899999968997999888990964


Q ss_pred             CCCCCCCCC-CCEEEEECCCCCCCCCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHCCCCCCCCCCEE
Q ss_conf             002322467-6200100235456543100122210011000155667046588972789851000263186882066778
Q gi|254781095|r  179 YRSSEITKD-LIITHVVLRGFPESQNIISAAIANVCHHRETVQPIKEKTGGSTFKNPTGHSAWQLIEKSGCRGLEFGGAK  257 (318)
Q Consensus       179 YR~S~~~~~-~iIl~a~l~l~~~~~~~i~~~~~~~~~~R~~~qP~~~~s~GSvFkNP~~~~A~~LIe~~GlKG~~iG~a~  257 (318)
                      ||+|.|++. ++|++|+|+|.+++++.|.++|.++.+.|..+||.+.||||||||||++.+||||||+|||||+++|||+
T Consensus       161 YR~S~f~~~~~vvl~v~f~L~~~~~~~I~~~~~~ir~~R~~~qP~~~ps~GS~FKNP~~~~Ag~LIe~aGLKG~~iGgA~  240 (291)
T COG0812         161 YRTSPFKKEYLVVLSVEFKLTKGDPEDILAAMCAIRRRRELKQPIDLPSAGSFFKNPVGDFAGWLIEEAGLKGYRIGGAQ  240 (291)
T ss_pred             CCCCCCCCCCEEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEE
T ss_conf             56676787887999999987789989999999999985347999878998724219996457999997198887467888


Q ss_pred             ECCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEECCEEEECCC
Q ss_conf             71567708996899799999999999999999984754004228962168
Q gi|254781095|r  258 ISELHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILLEWEIKRLGDFF  307 (318)
Q Consensus       258 vS~kHanfivN~g~ata~di~~Li~~v~~~V~~~~gi~Le~Ev~~iG~f~  307 (318)
                      ||+||||||||.|+|||+|+++|+++||++|+++|||.||+||++||++.
T Consensus       241 vs~kHanflIN~g~ATa~Dv~~Li~~Vr~~V~e~fGi~LE~Ev~~Ig~~~  290 (291)
T COG0812         241 VSEKHANFLINTGNATAKDVLDLIEHVRQRVLEKFGIELEPEVKIIGESG  290 (291)
T ss_pred             ECHHHCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEEEEEEECCCC
T ss_conf             75422858997799869999999999999987853816412266514457


No 5  
>PRK00046 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=100.00  E-value=0  Score=645.73  Aligned_cols=285  Identities=28%  Similarity=0.385  Sum_probs=255.9

Q ss_pred             EEEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCCEECCHHHHCCCCCCCEEEE
Q ss_conf             2775488001522576614889999689899999999856-299899984752036604884022022112344311330
Q gi|254781095|r   20 KFQENFPLKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNIEVR   98 (318)
Q Consensus        20 ~i~~n~~L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i~~~   98 (318)
                      ++++|+||++||||||||+|++|++|+|.+||.+++++++ +++|+++||+|||+||+|+ |+|+||++..+++..++..
T Consensus         2 ~i~~n~~L~~~tt~riGG~A~~~~~p~~~~dL~~~~~~~~~~~~p~~ilG~GSNlL~~d~-~~g~VI~~~~~~~~~~~~~   80 (348)
T PRK00046          2 QLQMNHSLKPHNTFGIDARARHLVEAESEEQLLAALADARAAGLPVLVLGGGSNVLFTED-FDGTVLLNRIKGIEVVEDD   80 (348)
T ss_pred             CCCCCCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHHCCCCEEEEECCEEEEECCC-CCEEEEEECCCCCEEEEEC
T ss_conf             651688875564422580866999759999999999989877998899917268978379-8548999768984788633


Q ss_pred             CC-CCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEC-CCCCEEEECCCCCC
Q ss_conf             26-65123311221567777887520120003872566324311573215831345666434411-23210000123344
Q gi|254781095|r   99 NH-CEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGANNCETSQYVVEVHGID-RKGNQHVIPREQLK  176 (318)
Q Consensus        99 ~~-~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAGayG~ei~d~i~~V~~~d-~~g~~~~l~~~e~~  176 (318)
                      ++ ..++|+||+.|++|++++.++||+|+|||+|||||||||++|||||||.||+|+|++|+++| .+|++++++++||+
T Consensus        81 ~~~~~v~a~AG~~~~~lv~~~~~~gl~GlE~l~gIPGTVGGAv~mNaGayG~ei~d~i~sV~~~d~~~g~~~~~~~~e~~  160 (348)
T PRK00046         81 DDAWYLEVGAGENWHDLVEWTLQQGMPGLENLALIPGTVGAAPIQNIGAYGVELKDVCDYVEALDLATGELVRLTAAECR  160 (348)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHCCCCCHHHHCCCCCCHHHHHHHCCCCCCCCHHHEEEEEEEEECCCCEEEEECHHHCC
T ss_conf             98079999528978999999998698520545378823566875148757767420075999999579719997534605


Q ss_pred             CCCCCCCCCC----CCCEEEEECCCCCCCCC---------------------CCHHHHHHCCCCCCCC--CCCCCEEEEE
Q ss_conf             3100232246----76200100235456543---------------------1001222100110001--5566704658
Q gi|254781095|r  177 YQYRSSEITK----DLIITHVVLRGFPESQN---------------------IISAAIANVCHHRETV--QPIKEKTGGS  229 (318)
Q Consensus       177 f~YR~S~~~~----~~iIl~a~l~l~~~~~~---------------------~i~~~~~~~~~~R~~~--qP~~~~s~GS  229 (318)
                      |+||+|.|++    ++||++|+|+|.++.+.                     ..++.++.+++.|+++  ||...|||||
T Consensus       161 f~YR~S~fk~~~~~~~iI~sv~f~L~k~~~~~~~y~~l~~~~~~~~~~~~~~~~~~i~~~i~~~R~~k~p~P~~~pnaGS  240 (348)
T PRK00046        161 FGYRDSIFKHEYPDRFAITAVGFRLPKRWQPVLDYGDLRRELAARGIDPTTVTAQDVFDAVCAIRREKLPDPKVLGNAGS  240 (348)
T ss_pred             EECCCHHHHCCCCCCEEEEEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             21151244124689889999999866766555674899999975024546678999999999999733799554788664


Q ss_pred             EEECC-----------------------CC---CCCHHHHHHCCCCCCCCCCEEECCCCCEEEEECCCCCHHHHHHHHHH
Q ss_conf             89727-----------------------89---85100026318688206677871567708996899799999999999
Q gi|254781095|r  230 TFKNP-----------------------TG---HSAWQLIEKSGCRGLEFGGAKISELHCNFMINADNATGYDLEYLGEQ  283 (318)
Q Consensus       230 vFkNP-----------------------~~---~~A~~LIe~~GlKG~~iG~a~vS~kHanfivN~g~ata~di~~Li~~  283 (318)
                      |||||                       ++   .+||||||+|||||+++|||+||+||||||||.|+|||+||++|+++
T Consensus       241 ~FKNPi~~~~~~~~l~~~~p~~~~~~~~~g~~KvsAg~LIe~aGlKG~~iGga~VS~kHanfivN~g~Ata~Di~~Li~~  320 (348)
T PRK00046        241 FFKNPVVSAEQFEALLARFPDIVGYPQADGSVKLAAGWLIDQCGLKGFQIGGAAVHEQQALVLVNYGGATGADVLALARH  320 (348)
T ss_pred             EEECCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEECCEEECCCCCCEEEECCCCCHHHHHHHHHH
T ss_conf             33187655889998786478987655789862044899999818888703796985678878997999999999999999


Q ss_pred             HHHHHHHHHCCEEEECCEEEEC
Q ss_conf             9999999847540042289621
Q gi|254781095|r  284 VRKKVFNQSGILLEWEIKRLGD  305 (318)
Q Consensus       284 v~~~V~~~~gi~Le~Ev~~iG~  305 (318)
                      ||++|+++|||.||+||++||.
T Consensus       321 i~~~V~~~~GI~Le~Ev~iiG~  342 (348)
T PRK00046        321 IRQDVREKFGVELEPEPRFIGA  342 (348)
T ss_pred             HHHHHHHHHCCCCEEEEEEECC
T ss_conf             9999999889800461199788


No 6  
>PRK13903 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=100.00  E-value=0  Score=624.70  Aligned_cols=284  Identities=27%  Similarity=0.363  Sum_probs=252.5

Q ss_pred             CCEEEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCCEECCHHHHCCCCCCCEE
Q ss_conf             662775488001522576614889999689899999999856-2998999847520366048840220221123443113
Q gi|254781095|r   18 RGKFQENFPLKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNIE   96 (318)
Q Consensus        18 ~g~i~~n~~L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i~   96 (318)
                      .++|++|+||++||||||||+|++|++|+|++||.+++++++ +++|+++||+|||+||+|++|+|+||++..   ..++
T Consensus        12 ~~~I~~nv~L~~~tt~~iGG~A~~~~~p~~~~eL~~~l~~~~~~~~p~~ilG~GSNlL~~D~g~~g~VI~l~~---~~i~   88 (359)
T PRK13903         12 GAEVAEDVPLAPLTTLRVGGPARRLVTCTTTEQLVAAVRALDAAGEPLLVLGGGSNLVIADDGFDLTVVRIAT---SGIT   88 (359)
T ss_pred             CCEEECCCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHHCCCCEEEEECCEEEEEECCCCCEEEEEECC---CCEE
T ss_conf             8777679847766054328280399973999999999998887699889980622698806986449999768---8678


Q ss_pred             EECCCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC-CCCEEEECCCCC
Q ss_conf             3026651233112215677778875201200038725663243115732158313456664344112-321000012334
Q gi|254781095|r   97 VRNHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGANNCETSQYVVEVHGIDR-KGNQHVIPREQL  175 (318)
Q Consensus        97 ~~~~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAGayG~ei~d~i~~V~~~d~-~g~~~~l~~~e~  175 (318)
                      . ++..++|+||+.|++|++++.++||+|||||+|||||||||++|||||||.||+|+|++|+++|. +|++++++++||
T Consensus        89 ~-~~~~v~v~AG~~~~~lv~~~~~~gl~GlE~LagIPGtVGgA~~mNaGAyG~Ei~d~l~~V~~~d~~~g~~~~l~~~e~  167 (359)
T PRK13903         89 L-DGGLVRAEAGAVWDDVVARTVEAGLGGLECLSGIPGSAGATPVQNVGAYGAEVSDTITRVRLLDRRTGEVRWVSAAEL  167 (359)
T ss_pred             E-CCCEEEEEECCCHHHHHHHHHHCCCCCEEHHHCCCCCCCHHHEECCCCCCCCHHHHEEEEEEEECCCCCEEEEEHHHC
T ss_conf             6-698899984796899999999869851002305875402241355898876745511599999989994999725786


Q ss_pred             CCCCCCCCCCC--CCCEEEEECCCCCCCC--------------------CCCHHHHHHCCCCCCCCCCC------CCEEE
Q ss_conf             43100232246--7620010023545654--------------------31001222100110001556------67046
Q gi|254781095|r  176 KYQYRSSEITK--DLIITHVVLRGFPESQ--------------------NIISAAIANVCHHRETVQPI------KEKTG  227 (318)
Q Consensus       176 ~f~YR~S~~~~--~~iIl~a~l~l~~~~~--------------------~~i~~~~~~~~~~R~~~qP~------~~~s~  227 (318)
                      +|+||+|.|++  ++||++++|+|.+...                    ...++.++.+.+.|+++||.      +.|||
T Consensus       168 ~F~YR~S~fk~~~~~iIl~v~f~L~~~~~~~~~~y~~l~~~l~~~~~~~~~~~~i~~~v~~~R~~k~~~~~p~~~~~~sa  247 (359)
T PRK13903        168 GFGYRTSVLKHSDRAVVLEVEFALDPDGLSAPLRYGELARALGVEEGERVPPAAVREAVLALRAGKGMVLDPADHDTWSA  247 (359)
T ss_pred             EEECCCCCCCCCCCEEEEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             04202255566896899999999666767776558999999754247746999999999999985578889887777665


Q ss_pred             EEEEECCC----------------------------CCCCHHHHHHCCC-CC---CCCCCEEECCCCCEEEEECCCCCHH
Q ss_conf             58897278----------------------------9851000263186-88---2066778715677089968997999
Q gi|254781095|r  228 GSTFKNPT----------------------------GHSAWQLIEKSGC-RG---LEFGGAKISELHCNFMINADNATGY  275 (318)
Q Consensus       228 GSvFkNP~----------------------------~~~A~~LIe~~Gl-KG---~~iG~a~vS~kHanfivN~g~ata~  275 (318)
                      |||||||.                            ..+||||||+||| ||   .++|+|+||+||||||||.|+|||+
T Consensus       248 GS~FKNPi~~~~~~~~l~~~~~~~~~p~~~~~~~~~k~sAg~LId~aGl~KG~kg~~~G~a~VS~kHanfiVN~G~Ata~  327 (359)
T PRK13903        248 GSFFTNPVVTPAVAERLAARVGERPVPRYPAGPGGVKLSAAWLIERAGFGKGYPGAGAAPARLSTKHTLALTNRGGATAA  327 (359)
T ss_pred             CCEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCEEEEECCCCCCEEEECCCCCHH
T ss_conf             52013865327789988764045777764568875413289999984875566368731069877778589989999999


Q ss_pred             HHHHHHHHHHHHHHHHHCCEEEECCEEEEC
Q ss_conf             999999999999999847540042289621
Q gi|254781095|r  276 DLEYLGEQVRKKVFNQSGILLEWEIKRLGD  305 (318)
Q Consensus       276 di~~Li~~v~~~V~~~~gi~Le~Ev~~iG~  305 (318)
                      |+++|+++||++|+++|||+||+||++||.
T Consensus       328 Di~~L~~~ik~~V~~~~GI~Le~Ev~~iG~  357 (359)
T PRK13903        328 DVVALARTVRDGVRDVFGITLVPEPVLVGC  357 (359)
T ss_pred             HHHHHHHHHHHHHHHHHCCEEEECCEEEEC
T ss_conf             999999999999999889743677389731


No 7  
>PRK13904 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=100.00  E-value=0  Score=590.02  Aligned_cols=257  Identities=29%  Similarity=0.409  Sum_probs=231.4

Q ss_pred             EEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHCCCCEEEECCCCEEEEECCCEECCHHHHCCCCCCCEEEECC
Q ss_conf             77548800152257661488999968989999999985629989998475203660488402202211234431133026
Q gi|254781095|r   21 FQENFPLKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLPSDIPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNIEVRNH  100 (318)
Q Consensus        21 i~~n~~L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~~~~p~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i~~~~~  100 (318)
                      +++|+|||+||||||||||++|+.+.    +.      +...|+++||+|||+||+|++++++++.   ..+..++.++ 
T Consensus         1 ~~~~v~Ls~~Tt~kiGGpA~~~~~~~----~~------~~~~~~~ilG~GSNlLv~D~g~~~vvl~---~~~~~i~~~~-   66 (257)
T PRK13904          1 MEKIIDFSKYSSVKIGGPLEVLVLEQ----ID------DISQDGQLIGGANNLLISPNPKNLAILG---KNFDYIKIDG-   66 (257)
T ss_pred             CCCCCCCCCCCCCCCCCCEEEEEHHH----HH------HHCCCEEEEECEEEEEEECCCCCEEEEC---CCCCEEEECC-
T ss_conf             97524056767564160122336553----68------6199839990124899977993589986---8866499859-


Q ss_pred             CCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCEEEECCCCCCCCCC
Q ss_conf             65123311221567777887520120003872566324311573215831345666434411232100001233443100
Q gi|254781095|r  101 CEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGANNCETSQYVVEVHGIDRKGNQHVIPREQLKYQYR  180 (318)
Q Consensus       101 ~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAGayG~ei~d~i~~V~~~d~~g~~~~l~~~e~~f~YR  180 (318)
                      ..++|+||++|++|+++|.++||+|||||+|||||||||++|||||||.|++|+|++|++.+     .+++++||+|+||
T Consensus        67 ~~i~v~aG~~~~~l~~~a~~~gl~GlEfl~gIPGtvGGAv~mNAGayg~ei~d~l~~V~~~~-----~~~~~~e~~f~YR  141 (257)
T PRK13904         67 EHLEIGGATKSSKIFNYAKKNNLGGFEFLGKLPGTLGGLVKMNAGLKEYEIKNNLESICTNG-----GWILKEAIGFDYR  141 (257)
T ss_pred             CEEEEEECCCHHHHHHHHHHCCCCCCCEECCCCCCHHHHHHCCCCCCCHHHHHEEEEEEECC-----EEEEHHHCCCCCC
T ss_conf             99999717868999999998798652110278843555752317988166671089999876-----3998788785124


Q ss_pred             CCCCCCCCCEEEEECCCCCCCCCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHCCCCCCCCCCEEECC
Q ss_conf             23224676200100235456543100122210011000155667046588972789851000263186882066778715
Q gi|254781095|r  181 SSEITKDLIITHVVLRGFPESQNIISAAIANVCHHRETVQPIKEKTGGSTFKNPTGHSAWQLIEKSGCRGLEFGGAKISE  260 (318)
Q Consensus       181 ~S~~~~~~iIl~a~l~l~~~~~~~i~~~~~~~~~~R~~~qP~~~~s~GSvFkNP~~~~A~~LIe~~GlKG~~iG~a~vS~  260 (318)
                      +|.|+  .||++|+|++.++.++++.+.|+    .|+.+|| ..||||||||||++.+||+|||+|||||+++|+|+||+
T Consensus       142 ~S~~~--~iil~a~f~l~~~~~~~i~~~~~----~~r~~qP-~~ps~GS~FKNP~g~~Ag~LIe~~GlKG~~iG~a~vS~  214 (257)
T PRK13904        142 SSGIN--GVILEARFKKEHGFDEELLKALK----SMRKNQP-KGASFGSCFKNPKGDFAGRLIEAVGLKGYSIGDAGFSE  214 (257)
T ss_pred             CCCCC--CEEEEEEEEECCCCHHHHHHHHH----HHHHCCC-CCCCCCEEEECCCCCCHHHHHHHCCCCCCCCCCEEECC
T ss_conf             66888--68999999807899899999999----9986599-99985327568987626999986697657218989853


Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEECCEEE
Q ss_conf             6770899689979999999999999999998475400422896
Q gi|254781095|r  261 LHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILLEWEIKRL  303 (318)
Q Consensus       261 kHanfivN~g~ata~di~~Li~~v~~~V~~~~gi~Le~Ev~~i  303 (318)
                      ||||||||.|+|||+|+++||++||++|+++|||.||+||++|
T Consensus       215 kHaNfivN~g~Ata~Di~~Li~~v~~~V~~~~gI~Le~EV~ii  257 (257)
T PRK13904        215 EHANFLINLGGATFEDALDLIELAKKRVLEEFGINLEEEVKIL  257 (257)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             4787899899989999999999999999998898013788869


No 8  
>TIGR00179 murB UDP-N-acetylenolpyruvoylglucosamine reductase; InterPro: IPR003170   Members of this family are UDP-N-acetylenolpyruvoylglucosamine reductase enzymes, which are also called UDP-N-acetylmuramate dehydrogenases. This enzyme is responsible for the synthesis of UDP-N-acetylmuramic acid in bacterial cell wall biosynthesis and consequently provides an attractive target for the design of antibacterial agents.    The crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase in the presence of its substrate, enolpyruvyl-UDP-N-acetylglucosamine, has been solved to 2.7 A resolution. The structure reveals a novel flavin binding motif, shows a striking alignment of the flavin with the substrate, and suggests a catalytic mechanism for the reduction of this enol ether .  ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0009252 peptidoglycan biosynthetic process.
Probab=100.00  E-value=0  Score=342.57  Aligned_cols=277  Identities=34%  Similarity=0.548  Sum_probs=247.1

Q ss_pred             CCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCC-EECCHHHHCCCCCCCEEEECCCCCC
Q ss_conf             001522576614889999689899999999856-29989998475203660488-4022022112344311330266512
Q gi|254781095|r   27 LKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAG-IRGVVLRLSNAGFSNIEVRNHCEMI  104 (318)
Q Consensus        27 L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~-~~G~vI~l~~~~~~~i~~~~~~~i~  104 (318)
                      |+++||+++|++++++..|.+.+++..+..+.. .+.|+.++|.|||+++.|.+ +.++++.+. .........+...+.
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~g~n~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~   79 (327)
T TIGR00179         1 LAPFTTYKIGGNARLLVVPKSLEELVNVLDNAKEEDLPLLILGGGSNLLVLDEGKLGGVILNLG-YGLDHEEDEDGEYLT   79 (327)
T ss_pred             CCCCCEEECCCCCCEEEECCCHHHHHHHHHHHHHCCCCEEEEECCCCEEEECCCCHHHHHHHHH-HHHHHHCCCCCCEEE
T ss_conf             9864011037632012300234789999865542174146752465135414430003333333-200111035666677


Q ss_pred             CCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCCCCCCEEEEEEEEEEEE-CCCCCEEEECCCCCCCCCCCCC
Q ss_conf             331122156777788752012000387256632431157321583134566643441-1232100001233443100232
Q gi|254781095|r  105 VGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGANNCETSQYVVEVHGI-DRKGNQHVIPREQLKYQYRSSE  183 (318)
Q Consensus       105 v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAGayG~ei~d~i~~V~~~-d~~g~~~~l~~~e~~f~YR~S~  183 (318)
                      +++|..|..+..++.++++.|+||++++|||+||++.||+||||.++.+.+..++++ +.+|...++..++|.|+||.|.
T Consensus        80 ~~~g~~~~~~~~~~~~~~~~gl~~~~~~pg~~g~~~~~n~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~y~~~~  159 (327)
T TIGR00179        80 VGGGENWHKLVKYALKNGLSGLEFLAGLPGTLGGAVIMNAGAYGVELKEVLVKATVLELPDGKTEWLTNEQLGFGYRTSG  159 (327)
T ss_pred             ECCCCCHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEHHHHCCCCHHHH
T ss_conf             51554378999988633731014543055311320221034111347877765542014677523431112123200000


Q ss_pred             CCCC----C------CEEEEECCC-------CCCCCCCCHHHHHHCCCCCCCCCCCCCE----EEEEEEECC--CCC---
Q ss_conf             2467----6------200100235-------4565431001222100110001556670----465889727--898---
Q gi|254781095|r  184 ITKD----L------IITHVVLRG-------FPESQNIISAAIANVCHHRETVQPIKEK----TGGSTFKNP--TGH---  237 (318)
Q Consensus       184 ~~~~----~------iIl~a~l~l-------~~~~~~~i~~~~~~~~~~R~~~qP~~~~----s~GSvFkNP--~~~---  237 (318)
                      |++.    +      +++.+.+++       ...++..+...+......|..++|...|    ++||+||||  ...   
T Consensus       160 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~g~~g~~f~np~~~~~~~~  239 (327)
T TIGR00179       160 FQKKYGDRFAITAPGLVLKAELKLTLGFGDLEKDDPETITACQSFNKVCRKRTSPYPDPNENGNAGSFFKNPVVSPEHFE  239 (327)
T ss_pred             HHHHCCCCEEEEECCEEEEEHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf             12220363367750123420110024521011112134445555434555303677775323555541136555524689


Q ss_pred             ---------------------CCHHHHHHCCCCCCCCCCEEECCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEE
Q ss_conf             ---------------------51000263186882066778715677089968997999999999999999999847540
Q gi|254781095|r  238 ---------------------SAWQLIEKSGCRGLEFGGAKISELHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILL  296 (318)
Q Consensus       238 ---------------------~A~~LIe~~GlKG~~iG~a~vS~kHanfivN~g~ata~di~~Li~~v~~~V~~~~gi~L  296 (318)
                                           .++||||+|++||+++|++.++.+|+||++|.++|++.|+++|+.+++..|.++||+.|
T Consensus       240 ~~~~~~~~~p~~p~~dg~~~~~~g~~~~~~~l~g~~~gg~~~~~~~~~~~~n~~~~~~~~~~~l~~~~~~~~~~~~g~~~  319 (327)
T TIGR00179       240 ELLKHFPNLPNFPQADGSVKLAAGWLIEECGLKGYQIGGAAVSKEHANFLVNLGGAKAEDVLDLIEHVKAEVLEKYGILL  319 (327)
T ss_pred             HHHHHCCCCCCCCCCCCCEEHHHHHHHHHHCCCCEEECCCHHHHHHCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99863467777766565200133345554053511213301111002056753874246799999988887777623300


Q ss_pred             EECCEEEE
Q ss_conf             04228962
Q gi|254781095|r  297 EWEIKRLG  304 (318)
Q Consensus       297 e~Ev~~iG  304 (318)
                      ++||+++|
T Consensus       320 ~~~~~~~~  327 (327)
T TIGR00179       320 EPEVKFLG  327 (327)
T ss_pred             CCHHHHCC
T ss_conf             00121139


No 9  
>pfam02873 MurB_C UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain. Members of this family are UDP-N-acetylenolpyruvoylglucosamine reductase enzymes EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.
Probab=100.00  E-value=9.6e-38  Score=258.85  Aligned_cols=103  Identities=45%  Similarity=0.653  Sum_probs=101.3

Q ss_pred             CCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHCCCCCCCCCCEEECCCCCEEEEECCCCCHHHHHHHH
Q ss_conf             43100122210011000155667046588972789851000263186882066778715677089968997999999999
Q gi|254781095|r  202 QNIISAAIANVCHHRETVQPIKEKTGGSTFKNPTGHSAWQLIEKSGCRGLEFGGAKISELHCNFMINADNATGYDLEYLG  281 (318)
Q Consensus       202 ~~~i~~~~~~~~~~R~~~qP~~~~s~GSvFkNP~~~~A~~LIe~~GlKG~~iG~a~vS~kHanfivN~g~ata~di~~Li  281 (318)
                      |+.|+++|.++++.|+.+||...||||||||||++.+||||||+|||||+++|+|+||++|||||||.|+||++|+++|+
T Consensus         1 P~~I~~~m~~~~~~R~~~qP~~~~~~GS~FKNP~~~~Ag~LIe~~G~kG~~~G~a~vS~kHanfivN~g~ata~di~~l~   80 (103)
T pfam02873         1 PQQILKAMKKIRQTRKSTQPYKFPNAGSTFKNPEGFAAGWLIEEAGLKGYQIGGAQVSEKHANFIINTGNATAEDVVDLI   80 (103)
T ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHCCCCCCCCCEEEEECCCCEEEECCCCCHHHHHHHH
T ss_conf             98899999999998686996999987278559099739999999687988559988962567189968998999999999


Q ss_pred             HHHHHHHHHHHCCEEEECCEEEE
Q ss_conf             99999999984754004228962
Q gi|254781095|r  282 EQVRKKVFNQSGILLEWEIKRLG  304 (318)
Q Consensus       282 ~~v~~~V~~~~gi~Le~Ev~~iG  304 (318)
                      +.||+.|+++|||.||+||++||
T Consensus        81 ~~v~~~V~~~~gI~Le~Ev~iiG  103 (103)
T pfam02873        81 RHVRQTVFEKFGIWLEPEVKIIG  103 (103)
T ss_pred             HHHHHHHHHHHCCCCEEEEEEEC
T ss_conf             99999999988981256016309


No 10 
>PRK11230 glycolate oxidase subunit GlcD; Provisional
Probab=99.68  E-value=1.4e-16  Score=125.01  Aligned_cols=191  Identities=16%  Similarity=0.234  Sum_probs=138.2

Q ss_pred             HHHHHHHHHHHCC-EE-EECCCCCCCCCC---CCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECC-C
Q ss_conf             9999999875066-27-754880015225---76614889999689899999999856-2998999847520366048-8
Q gi|254781095|r    7 SRLLRERGKQLRG-KF-QENFPLKQITWF---RTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDA-G   79 (318)
Q Consensus         7 ~~~l~~~~~~~~g-~i-~~n~~L~~~tt~---rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~-~   79 (318)
                      ...+.++...+.. .+ ....+|..|.+=   ...+.+..++.|+|.+|+++++++|. +++|+.+-|+||++.-.-- .
T Consensus        19 ~~ll~~L~~~lg~~~Vl~~~~~l~~y~~D~~~~~~~~P~aVv~P~s~eeV~~iv~~a~~~~ipvvprGggTgL~Gga~p~   98 (499)
T PRK11230         19 TALLAALREHLPDLEILHTDEDLRPYECDGLSAYRTTPLLVVLPKQMEQVQALLAVCHRLRVPVVARGAGTGLSGGALPL   98 (499)
T ss_pred             HHHHHHHHHHCCCCCEECCHHHHHHHCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCC
T ss_conf             99999999767985188588897651357865566898889940999999999999998799099978983226581268


Q ss_pred             EECCHHHHCCCCCCCEEEEC-CCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHH-----HHHHHHHCCCCCC-----CC
Q ss_conf             40220221123443113302-6651233112215677778875201200038725-----6632431157321-----58
Q gi|254781095|r   80 IRGVVLRLSNAGFSNIEVRN-HCEMIVGARCSGKSLANSALRHGIGGFHFFYGIP-----GSIGGAAYMNAGA-----NN  148 (318)
Q Consensus        80 ~~G~vI~l~~~~~~~i~~~~-~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIP-----GTVGGAi~mNAGa-----yG  148 (318)
                      .+|+||++++++ ..++++. +..++|+||+.+.+|-+++.++||.    +---|     .||||.++.|||.     ||
T Consensus        99 ~~gIvl~l~rmn-~Ileid~~~~~v~VeaGv~~~~l~~~l~~~Gl~----~p~dP~S~~~~tIGG~iAtNAgG~~~~rYG  173 (499)
T PRK11230         99 EKGVLLVMARFN-RILDIDPVGRRARVQPGVRNLAISQAAAPHGLY----YAPDPSSQIACSIGGNVAENAGGVHCLKYG  173 (499)
T ss_pred             CCEEEEEECCCC-CEEEEECCCCEEEEECCCCHHHHHHHHHHCCCC----CCCCCCCCCCCCCCEEEECCCCCCCEEEEC
T ss_conf             982999800127-706882689979994581079999989866985----488987233552530773078786303315


Q ss_pred             CEEEEEEEEEEEECCCCCEEEECCCC---CCCCCCCCCCCCC---CCEEEEECCCCCCCCC
Q ss_conf             31345666434411232100001233---4431002322467---6200100235456543
Q gi|254781095|r  149 CETSQYVVEVHGIDRKGNQHVIPREQ---LKYQYRSSEITKD---LIITHVVLRGFPESQN  203 (318)
Q Consensus       149 ~ei~d~i~~V~~~d~~g~~~~l~~~e---~~f~YR~S~~~~~---~iIl~a~l~l~~~~~~  203 (318)
                      . +.|+|.+++++.++|++.++...-   -.|.-++-.+-.+   .||++|++++.|.++.
T Consensus       174 ~-trd~VlglevVlpdG~v~~~g~~~~~~~GydL~~LfiGSEGTLGIIT~a~LrL~p~P~~  233 (499)
T PRK11230        174 L-TVHNLLKVEILTLDGERLTLGSDALDSPGFDLLALFTGSEGMLGVVTEVTVKLLPKPPV  233 (499)
T ss_pred             C-HHHHHHCCEEEECCCCEECCCCCCCCCCCCCHHHHCCCCCCCEEEEEEEEEEEECCCCE
T ss_conf             6-89975104389368862115886678898477875357786238998999998747860


No 11 
>pfam01565 FAD_binding_4 FAD binding domain. This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidizes the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan.
Probab=99.68  E-value=1.7e-16  Score=124.47  Aligned_cols=129  Identities=27%  Similarity=0.412  Sum_probs=107.1

Q ss_pred             EEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCCEECCHHHHCCCCCCCE-EEE-CCCCCCCCCEEEHHHHHH
Q ss_conf             89999689899999999856-299899984752036604884022022112344311-330-266512331122156777
Q gi|254781095|r   40 EVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNI-EVR-NHCEMIVGARCSGKSLAN  116 (318)
Q Consensus        40 ~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i-~~~-~~~~i~v~AG~~~~~l~~  116 (318)
                      ..+++|+|++|+++++++++ +++|+.+.|+|+|.. .....++++|.+++  ++.+ +.+ ++..++|+||+.|.+|.+
T Consensus         2 ~~vv~P~s~~ev~~~v~~a~~~~~~v~~~g~G~~~~-~~~~~~gi~i~l~~--~~~i~~~d~~~~~v~v~aG~~~~~l~~   78 (138)
T pfam01565         2 AAVVRPESEEEVAAIVRLANEHGLPVLVRGGGSSLL-GDAVTGGVVLDLSR--LNGILEIDPENGTATVEAGVTLGDLVR   78 (138)
T ss_pred             CEEEECCCHHHHHHHHHHHHHCCCCEEEECCCEECC-CCCCCCEEEEECCC--CCCCEEEECCCCEEEEECCCCHHHHHH
T ss_conf             899990999999999999998699689988966727-98639959999568--997268853884899957809999999


Q ss_pred             HHHHHHC-CCHHCCCCHHHHHHHHHCCCCCCCCCE----EEEEEEEEEEECCCCCEEEEC
Q ss_conf             7887520-120003872566324311573215831----345666434411232100001
Q gi|254781095|r  117 SALRHGI-GGFHFFYGIPGSIGGAAYMNAGANNCE----TSQYVVEVHGIDRKGNQHVIP  171 (318)
Q Consensus       117 ~~~~~gl-~GlE~l~gIPGTVGGAi~mNAGayG~e----i~d~i~~V~~~d~~g~~~~l~  171 (318)
                      ++.++|+ .+.++.++.++||||++.+|++.++..    +.|+|.++++++++|++.+.+
T Consensus        79 ~l~~~g~~~~~~~~~~~~~tvGG~i~~~~~G~~~~~~G~~~d~v~~~~vV~~~G~iv~~s  138 (138)
T pfam01565        79 ALAAKGLLLGLEPGSGIPGTVGGAIATNGGGYGSEKYGLTRDNVLSLEVVLADGEVVRLS  138 (138)
T ss_pred             HHHHCCCEEEECCCCCCCCEEEEEECCCCCCCCCCCCCCHHHEEEEEEEECCCCCEEEEC
T ss_conf             999729988631676676203121248965567456464887489999996897199949


No 12 
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=99.56  E-value=1.5e-14  Score=112.29  Aligned_cols=157  Identities=26%  Similarity=0.333  Sum_probs=121.6

Q ss_pred             CCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEE---EECCCEECCHHHHCCCCCCCE-EEE-CCCCCCCCCEE
Q ss_conf             614889999689899999999856-299899984752036---604884022022112344311-330-26651233112
Q gi|254781095|r   36 GGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNIL---VRDAGIRGVVLRLSNAGFSNI-EVR-NHCEMIVGARC  109 (318)
Q Consensus        36 GG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil---~~D~~~~G~vI~l~~~~~~~i-~~~-~~~~i~v~AG~  109 (318)
                      .+.+...+.|++.+|+.+++++|. +++|+.+.|+||++-   +++ +  |++|++++  ++.+ +++ ++..++|+||+
T Consensus        29 ~~~p~~v~~p~s~~ev~~iv~~a~~~~~~v~prG~gt~~~g~~~~~-~--gvvl~l~~--mn~i~~iD~~~~~~~v~aGv  103 (459)
T COG0277          29 RGLPLAVVFPKSEEEVAAILRLANENGIPVVPRGGGTSLSGGAVPD-G--GVVLDLSR--LNRILEIDPEDGTATVQAGV  103 (459)
T ss_pred             CCCCCEEECCCCHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCC-C--EEEEECHH--CCCCEEECCCCCEEEECCCC
T ss_conf             6788658778999999999999997599089978997776773578-6--49998633--06865446889989985896


Q ss_pred             EHHHHHHHHHHHHCCCHHCCCCHH-----HHHHHHHCCCCCC-----CCCEEEEEEEEEEEECCCCCEEEECCCC----C
Q ss_conf             215677778875201200038725-----6632431157321-----5831345666434411232100001233----4
Q gi|254781095|r  110 SGKSLANSALRHGIGGFHFFYGIP-----GSIGGAAYMNAGA-----NNCETSQYVVEVHGIDRKGNQHVIPREQ----L  175 (318)
Q Consensus       110 ~~~~l~~~~~~~gl~GlE~l~gIP-----GTVGGAi~mNAGa-----yG~ei~d~i~~V~~~d~~g~~~~l~~~e----~  175 (318)
                      .+.++.+++.++||.    +...|     .||||++++|++.     ||. +.|+|.+++++.++|++.+....-    -
T Consensus       104 ~l~~l~~~l~~~Gl~----~p~~p~s~~~~tvGG~ia~~~~G~~~~~yG~-~~d~v~~l~vV~~~G~~~~~~~~~~k~~~  178 (459)
T COG0277         104 TLEDLEKALAPHGLF----LPVDPSSSGTATIGGNIATNAGGLRSLRYGL-TRDNVLGLRVVLPDGEILRLGRKLRKDNA  178 (459)
T ss_pred             CHHHHHHHHHHCCCC----CCCCCCCCCCCEEEEEECCCCCCCCCCCCCC-HHHEEEEEEEECCCCCEEECCCCCCCCCC
T ss_conf             889999999976982----4888875676568877147998834134676-63416579999089868971465567765


Q ss_pred             CCCCCCCCCC---CCCCEEEEECCCCCCCC
Q ss_conf             4310023224---67620010023545654
Q gi|254781095|r  176 KYQYRSSEIT---KDLIITHVVLRGFPESQ  202 (318)
Q Consensus       176 ~f~YR~S~~~---~~~iIl~a~l~l~~~~~  202 (318)
                      .|....-..-   .-.||++++|++.|..+
T Consensus       179 g~dl~~l~iGs~GtlGiit~~tl~l~p~p~  208 (459)
T COG0277         179 GYDLTALFVGSEGTLGIITEATLKLLPLPE  208 (459)
T ss_pred             CCHHHHHHCCCCCCCEEEEEEEEEEECCCC
T ss_conf             510477645587767689999999734886


No 13 
>PRK11282 glcE glycolate oxidase FAD binding subunit; Provisional
Probab=99.50  E-value=7.7e-14  Score=107.75  Aligned_cols=155  Identities=15%  Similarity=0.145  Sum_probs=113.0

Q ss_pred             CCHHHHHHHHHHH-HCCCCEEEECCCCEEEEECCCEECCHHHHCCCCCCCEEEEC-CCCCCCCCEEEHHHHHHHHHHHHC
Q ss_conf             8989999999985-62998999847520366048840220221123443113302-665123311221567777887520
Q gi|254781095|r   46 QDIHDLKYFLTLL-PSDIPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNIEVRN-HCEMIVGARCSGKSLANSALRHGI  123 (318)
Q Consensus        46 ~s~~el~~~l~~~-~~~~p~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i~~~~-~~~i~v~AG~~~~~l~~~~~~~gl  123 (318)
                      .+.+|+++++++| ++++|+.+-|+||++... ....|.||++++++ ..++++. +-.++|+||+.+.+|...+.++|+
T Consensus         2 ~~taev~e~Vr~A~~~~~pv~p~G~gT~~~~G-~~~~g~vl~l~rm~-~I~~~~~~d~~v~VeaGv~~~~L~~~la~~G~   79 (351)
T PRK11282          2 DISAALLERVRQAAADGTPLRIRGGGSKAFYG-RALAGEVLDTRAHR-GIVSYDPTELVITARAGTPLAELEAALAEAGQ   79 (351)
T ss_pred             CCHHHHHHHHHHHHHCCCCEEEECCCCCCCCC-CCCCCEEEECCCCC-CCEEECCCCCEEEECCCCCHHHHHHHHHHCCC
T ss_conf             61899999999999879928998999788878-89998598852468-71798588897999589819999999997088


Q ss_pred             C-CHHCCC-CHHHHHHHHHCCCCCC-----CCCEEEEEEEEEEEECCCCCEEEECCCC--CCCCCCCCCCC--CC---CC
Q ss_conf             1-200038-7256632431157321-----5831345666434411232100001233--44310023224--67---62
Q gi|254781095|r  124 G-GFHFFY-GIPGSIGGAAYMNAGA-----NNCETSQYVVEVHGIDRKGNQHVIPREQ--LKYQYRSSEIT--KD---LI  189 (318)
Q Consensus       124 ~-GlE~l~-gIPGTVGGAi~mNAGa-----yG~ei~d~i~~V~~~d~~g~~~~l~~~e--~~f~YR~S~~~--~~---~i  189 (318)
                      - .++-.+ +-=+||||.++.|||.     ||. +.|+|..++++..+|++.+.-..=  -.-+|--+.+-  .+   -|
T Consensus        80 ~l~~dPp~~~~~aTIGG~vAtNagG~r~~rYG~-tRD~VLGl~vVl~dG~vi~~Gg~~~KnvaGYDL~~L~vGSEGTLGv  158 (351)
T PRK11282         80 MLPFEPPHFGGGATVGGMVAAGLSGPRRPWAGA-VRDFVLGTRLINGRGEHLRFGGQVMKNVAGYDVSRLMAGSLGTLGV  158 (351)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCC-HHHHEEEEEEECCCCEEEEECCEECCCCCCCCHHHHHCCCCCCCEE
T ss_conf             224588777875434778882799742013588-8883754699878956996088024678775877874558750012


Q ss_pred             EEEEECCCCCCCCC
Q ss_conf             00100235456543
Q gi|254781095|r  190 ITHVVLRGFPESQN  203 (318)
Q Consensus       190 Il~a~l~l~~~~~~  203 (318)
                      |++++||+.|.+..
T Consensus       159 ITeatLrL~P~P~~  172 (351)
T PRK11282        159 LLEVSLKVLPRPRA  172 (351)
T ss_pred             EEEEEEEECCCCCC
T ss_conf             25889997478864


No 14 
>TIGR00387 glcD glycolate oxidase, subunit GlcD; InterPro: IPR004490 The glc locus of Escherichia coli encodes the subunits of glycolate oxidase and the glc regulator protein. The subunit GlcD is similar to that of several D-lactate dehydrogenases, including that of E. coli. Glycolate oxidase has been found to have some D-lactate dehydrogenase activity.; GO: 0008891 glycolate oxidase activity, 0009339 glycolate oxidase complex.
Probab=99.32  E-value=6.2e-13  Score=102.01  Aligned_cols=155  Identities=21%  Similarity=0.293  Sum_probs=117.0

Q ss_pred             EEEECCHHHHHHHHHHH-HCCCCEEEECCCCEEEEECCCE-ECCHHHHCCCCCCCEE-EEC-CCCCCCCCEEEHHHHHHH
Q ss_conf             99968989999999985-6299899984752036604884-0220221123443113-302-665123311221567777
Q gi|254781095|r   42 MFQPQDIHDLKYFLTLL-PSDIPITIVGLGSNILVRDAGI-RGVVLRLSNAGFSNIE-VRN-HCEMIVGARCSGKSLANS  117 (318)
Q Consensus        42 ~~~p~s~~el~~~l~~~-~~~~p~~iiG~GSNil~~D~~~-~G~vI~l~~~~~~~i~-~~~-~~~i~v~AG~~~~~l~~~  117 (318)
                      ++.|++.||+.++++.| ++++|+..-|.|||+--+-=.. .|+|+++. ..|+.|. ++. +.+.+|+.||...++.+.
T Consensus         1 Vv~P~n~eqv~~Ilk~C~e~ri~~vpRGaGTgLsGGalP~~ggl~lsv~-~~m~~ILeId~~n~~A~VqPGV~~~~~~~~   79 (437)
T TIGR00387         1 VVLPKNTEQVARILKLCHEHRIPIVPRGAGTGLSGGALPVEGGLVLSVF-KRMNKILEIDVVNLTAVVQPGVINLELEQA   79 (437)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCHHHHHH-HHHHHHHHCCCCCCEEEECCCEEHHHHHHH
T ss_conf             9788857899999998742787478526888776654256773023577-887676400478888987474013889999


Q ss_pred             HHHHHCCCHHCCCCHHH-----HHHHHHCCCCCC-----CCCEEEEEEEEEEEECCCCCEEE-ECCCC-CCCCCCCCCCC
Q ss_conf             88752012000387256-----632431157321-----58313456664344112321000-01233-44310023224
Q gi|254781095|r  118 ALRHGIGGFHFFYGIPG-----SIGGAAYMNAGA-----NNCETSQYVVEVHGIDRKGNQHV-IPREQ-LKYQYRSSEIT  185 (318)
Q Consensus       118 ~~~~gl~GlE~l~gIPG-----TVGGAi~mNAGa-----yG~ei~d~i~~V~~~d~~g~~~~-l~~~e-~~f~YR~S~~~  185 (318)
                      ..++||.    +.=-|+     ||||+|.-|||.     ||. +.|+|...+++.+||++.+ .++.- +.=||-=+.+-
T Consensus        80 V~~~~l~----YpPDPsS~~~~tiGGNiaENaGG~r~lKYG~-t~d~VlgLeVV~adGei~~~gg~~~kd~~GydLt~Lf  154 (437)
T TIGR00387        80 VEEHGLF----YPPDPSSQIVSTIGGNIAENAGGVRGLKYGT-TVDYVLGLEVVLADGEIIRIGGKTAKDVAGYDLTGLF  154 (437)
T ss_pred             HHHCCCC----CCCCHHHCCCCCCCCCCCCCCCCCHHHHHHH-HHHEEEEEEEECCCCHHHHHCCCCCCCCCCHHHHHHH
T ss_conf             8737872----4888011010004763003775301211011-2212333346636714321113414668862377788


Q ss_pred             --CC---CCEEEEECCCCCCCC
Q ss_conf             --67---620010023545654
Q gi|254781095|r  186 --KD---LIITHVVLRGFPESQ  202 (318)
Q Consensus       186 --~~---~iIl~a~l~l~~~~~  202 (318)
                        .+   -|++.+++|+-|.++
T Consensus       155 vGSEGtLGi~Te~tlKllpkPe  176 (437)
T TIGR00387       155 VGSEGTLGIVTEITLKLLPKPE  176 (437)
T ss_pred             HHCCCHHHHHHHHHHHHCCCCC
T ss_conf             7404157999989986306785


No 15 
>TIGR01678 FAD_lactone_ox sugar 1,4-lactone oxidases; InterPro: IPR010031   This entry identifies a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesising ascorbic acid or a derivative. These include L-gulonolactone oxidase (1.1.3.8 from EC) from rat and D-arabinono-1,4-lactone oxidase (1.1.3.37 from EC) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by IPR006093 from INTERPRO.; GO: 0016899 oxidoreductase activity acting on the CH-OH group of donors oxygen as acceptor, 0009058 biosynthetic process.
Probab=99.21  E-value=2.1e-11  Score=92.42  Aligned_cols=152  Identities=19%  Similarity=0.262  Sum_probs=115.5

Q ss_pred             CCEEEEEEEECCHHHHHHHHHHHHC-CCCEEEECCC---CEEEEECCCEECCHHHHCCCCCCCEEEE-C----CCCCCCC
Q ss_conf             6148899996898999999998562-9989998475---2036604884022022112344311330-2----6651233
Q gi|254781095|r   36 GGNAEVMFQPQDIHDLKYFLTLLPS-DIPITIVGLG---SNILVRDAGIRGVVLRLSNAGFSNIEVR-N----HCEMIVG  106 (318)
Q Consensus        36 GG~A~~~~~p~s~~el~~~l~~~~~-~~p~~iiG~G---SNil~~D~~~~G~vI~l~~~~~~~i~~~-~----~~~i~v~  106 (318)
                      +.....+++|+|+||+.+++..|+. +.++.++|+|   ||+.+.|+.    .|+|.+++ +.+..+ +    ...|||+
T Consensus        12 sa~pe~y~qP~s~eevrE~l~~Ar~~~Kk~~vVG~GHSPSdi~cTdg~----l~~ldkmn-kV~~fd~~Pelh~~~iTV~   86 (505)
T TIGR01678        12 SAKPEVYYQPKSVEEVREVLADAREAEKKVKVVGAGHSPSDIVCTDGF----LVSLDKMN-KVLKFDKEPELHKKDITVE   86 (505)
T ss_pred             ECCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCEECCCH----HEECCCCC-CEEEECCCCCCCCCCEEHH
T ss_conf             025355448972999999999987469838997577782321542602----10012245-1015527866322011165


Q ss_pred             CEEEHHHHHHHHHHHHCCCHHCCCCHH-HHHHHHHCCCCCCCCC-----EEEEEEEEEEEECCCCCEEEECCCCCCCCCC
Q ss_conf             112215677778875201200038725-6632431157321583-----1345666434411232100001233443100
Q gi|254781095|r  107 ARCSGKSLANSALRHGIGGFHFFYGIP-GSIGGAAYMNAGANNC-----ETSQYVVEVHGIDRKGNQHVIPREQLKYQYR  180 (318)
Q Consensus       107 AG~~~~~l~~~~~~~gl~GlE~l~gIP-GTVGGAi~mNAGayG~-----ei~d~i~~V~~~d~~g~~~~l~~~e~~f~YR  180 (318)
                      ||..+.+|-..+.++|++ +.+|--|- -||-|  +|-.|+||.     =++.++.+.+++..||++.+++++.=     
T Consensus        87 AGirlyql~e~L~~~Gys-~~~lGsiSe~sVaG--iistgtHgss~~Hg~l~~q~v~lti~~adGe~~~cs~e~~-----  158 (505)
T TIGR01678        87 AGIRLYQLQEILDEKGYS-LSNLGSISEVSVAG--IISTGTHGSSLKHGVLASQVVALTIMLADGEVLECSEERD-----  158 (505)
T ss_pred             HHHHHHHHHHHHHHCCCC-EECCCCCCCCEECC--EEECCCCCCCCCCCHHHHEEEEEEEEECCCCEEEECCCCC-----
T ss_conf             525686645897524871-00022100431211--5503746876533324403333456704775786022048-----


Q ss_pred             CCCCC-------CCCCEEEEECCCCCC
Q ss_conf             23224-------676200100235456
Q gi|254781095|r  181 SSEIT-------KDLIITHVVLRGFPE  200 (318)
Q Consensus       181 ~S~~~-------~~~iIl~a~l~l~~~  200 (318)
                      .-.|+       .=.||++++++--|+
T Consensus       159 ~dvF~AA~vslG~lGiIv~~Ti~vVP~  185 (505)
T TIGR01678       159 KDVFKAARVSLGALGIIVDVTIRVVPA  185 (505)
T ss_pred             HHHHHHHHHCCCCEEEEEEEEEEEECC
T ss_conf             568889864156247899998887336


No 16 
>KOG1231 consensus
Probab=99.05  E-value=8.3e-10  Score=82.27  Aligned_cols=164  Identities=19%  Similarity=0.201  Sum_probs=120.2

Q ss_pred             CCEEEEEEEECCHHHHHHHHHHHH-C--CCCEEEECCCCEEEEEC-CCEECCHHHHCCC-CCCCE--EEECCCCCCCCCE
Q ss_conf             614889999689899999999856-2--99899984752036604-8840220221123-44311--3302665123311
Q gi|254781095|r   36 GGNAEVMFQPQDIHDLKYFLTLLP-S--DIPITIVGLGSNILVRD-AGIRGVVLRLSNA-GFSNI--EVRNHCEMIVGAR  108 (318)
Q Consensus        36 GG~A~~~~~p~s~~el~~~l~~~~-~--~~p~~iiG~GSNil~~D-~~~~G~vI~l~~~-~~~~i--~~~~~~~i~v~AG  108 (318)
                      --+.....+|+|.+|+.++++.|. .  +.|+...|+|.-+=-.- .+-.|+||++... .+..+  -..++..+.|.||
T Consensus        61 ~~~P~aVL~P~S~edVs~ilk~~~~~~s~~pVaarG~GhSl~Gqa~a~~~GvvV~m~~~~~~~~~~~~~~~~~yvdV~~g  140 (505)
T KOG1231          61 QLPPLAVLFPSSVEDVSKILKHCNDYGSNFPVAARGGGHSLEGQALATRGGVVVCMDSSLLMKDVPVLVVDDLYVDVSAG  140 (505)
T ss_pred             CCCCEEEECCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCCCEEEEEEHHHCCCCCCEEECCCCEEEEECC
T ss_conf             78971687478789999999998626776326304786532575235789769998401026787324414624784078


Q ss_pred             EEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCCC------CCCEEEEEEEEEEEECCCCCEEEECCCCCCCCCCCC
Q ss_conf             22156777788752012000387256632431157321------583134566643441123210000123344310023
Q gi|254781095|r  109 CSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAGA------NNCETSQYVVEVHGIDRKGNQHVIPREQLKYQYRSS  182 (318)
Q Consensus       109 ~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAGa------yG~ei~d~i~~V~~~d~~g~~~~l~~~e~~f~YR~S  182 (318)
                      ..|-++.+++.+.||+-+-|.--.|-||||.++ |+|.      ||- ..++|.+.+++..+|++.+.+++ .+|..=+.
T Consensus       141 ~~Widll~~t~e~GL~p~swtDyl~ltVGGtls-nagiggqafRyGp-qi~NV~~LdVVtgkGeiv~cs~r-~n~~lf~~  217 (505)
T KOG1231         141 TLWIDLLDYTLEYGLSPFSWTDYLPLTVGGTLS-NAGIGGQAFRYGP-QISNVIELDVVTGKGEIVTCSKR-ANSNLFFL  217 (505)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCEEECCEEC-CCCCCCCEEECCC-HHHCEEEEEEECCCCCEEECCCC-CCCEEEEE
T ss_conf             008999999997398866767863202231641-6754653044265-01144788998179758963310-48401001


Q ss_pred             CCC---CCCCEEEEECCCCCCCC
Q ss_conf             224---67620010023545654
Q gi|254781095|r  183 EIT---KDLIITHVVLRGFPESQ  202 (318)
Q Consensus       183 ~~~---~~~iIl~a~l~l~~~~~  202 (318)
                      .+.   +-.||+.|+.++.+.++
T Consensus       218 vlGglGqfGIITrArI~le~aP~  240 (505)
T KOG1231         218 VLGGLGQFGIITRARIKLEPAPK  240 (505)
T ss_pred             EECCCCCEEEEEEEEEEECCCCC
T ss_conf             31367510158889997315886


No 17 
>KOG4730 consensus
Probab=99.01  E-value=6.3e-10  Score=83.01  Aligned_cols=158  Identities=20%  Similarity=0.259  Sum_probs=110.9

Q ss_pred             CEEEEEEEECCHHHHHHHHHHH-HCCCCEEEECCC---CEEEEECCCEECCHHHHCCCCCCCEEEEC-CCCCCCCCEEEH
Q ss_conf             1488999968989999999985-629989998475---20366048840220221123443113302-665123311221
Q gi|254781095|r   37 GNAEVMFQPQDIHDLKYFLTLL-PSDIPITIVGLG---SNILVRDAGIRGVVLRLSNAGFSNIEVRN-HCEMIVGARCSG  111 (318)
Q Consensus        37 G~A~~~~~p~s~~el~~~l~~~-~~~~p~~iiG~G---SNil~~D~~~~G~vI~l~~~~~~~i~~~~-~~~i~v~AG~~~  111 (318)
                      ..|..+..|++++||.++++.+ +++.++.+.|-|   |++.++|+    ..|++...+ ..++.+. ...++|+||+.+
T Consensus        48 c~aanv~yP~teaeL~~lVa~A~~a~~kirvVg~gHSp~~l~ctdg----~lisl~~ln-kVv~~dpe~~tvTV~aGirl  122 (518)
T KOG4730          48 CKAANVNYPKTEAELVELVAAATEAGKKIRVVGSGHSPSKLVCTDG----LLISLDKLN-KVVEFDPELKTVTVQAGIRL  122 (518)
T ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCEECCC----CEEEHHHHC-CCEEECCHHCEEEECCCCCH
T ss_conf             1120468998799999999999874865898515678776330465----477766632-31254730204771208289


Q ss_pred             HHHHHHHHHHHCCCHHCCCCHHH-HHHHHHCCCCCCCCCEEE--EEEEEEEE----ECCCCCEEEECCCC--CCCCCCCC
Q ss_conf             56777788752012000387256-632431157321583134--56664344----11232100001233--44310023
Q gi|254781095|r  112 KSLANSALRHGIGGFHFFYGIPG-SIGGAAYMNAGANNCETS--QYVVEVHG----IDRKGNQHVIPREQ--LKYQYRSS  182 (318)
Q Consensus       112 ~~l~~~~~~~gl~GlE~l~gIPG-TVGGAi~mNAGayG~ei~--d~i~~V~~----~d~~g~~~~l~~~e--~~f~YR~S  182 (318)
                      .+|...+.+.||+ |-++.-|-| ||||.  |-.||||...+  |++.++..    ...+|.+++++.+-  =.|.--..
T Consensus       123 rQLie~~~~~Gls-L~~~~si~e~sVgGi--i~TGaHGSS~~vH~~v~~i~~v~~~~~~~G~v~~Ls~e~dpe~F~AAkv  199 (518)
T KOG4730         123 RQLIEELAKLGLS-LPNAPSISEQSVGGI--ISTGAHGSSLWVHDYVSEIISVSPITPADGFVVVLSEEKDPELFNAAKV  199 (518)
T ss_pred             HHHHHHHHHCCCC-CCCCCCEECCEEEEE--EECCCCCCCCCCCCCCCEEEEEEEECCCCCEEEEECCCCCHHHHHHHHH
T ss_conf             9999999864845-567773202145127--7336688866437542226897430257823898016689888766561


Q ss_pred             CCCCCCCEEEEECCCCCCCC
Q ss_conf             22467620010023545654
Q gi|254781095|r  183 EITKDLIITHVVLRGFPESQ  202 (318)
Q Consensus       183 ~~~~~~iIl~a~l~l~~~~~  202 (318)
                      ++..=.||.+|+|++.|.-+
T Consensus       200 SLG~LGVIs~VTl~~vp~Fk  219 (518)
T KOG4730         200 SLGVLGVISQVTLSVVPAFK  219 (518)
T ss_pred             CCCCEEEEEEEEEEEEECCE
T ss_conf             45522689999999874300


No 18 
>KOG1232 consensus
Probab=98.72  E-value=3.8e-08  Score=71.79  Aligned_cols=174  Identities=16%  Similarity=0.213  Sum_probs=121.1

Q ss_pred             EEECCCCCCCCC--C-CCCCEEEEEEEECCHHHHHHHHHHHHC-CCCEEEECCCCEEEE-ECCCEECCHHHHCCCCCCCE
Q ss_conf             775488001522--5-766148899996898999999998562-998999847520366-04884022022112344311
Q gi|254781095|r   21 FQENFPLKQITW--F-RTGGNAEVMFQPQDIHDLKYFLTLLPS-DIPITIVGLGSNILV-RDAGIRGVVLRLSNAGFSNI   95 (318)
Q Consensus        21 i~~n~~L~~~tt--~-rvGG~A~~~~~p~s~~el~~~l~~~~~-~~p~~iiG~GSNil~-~D~~~~G~vI~l~~~~~~~i   95 (318)
                      ...-++|..||+  + +.-|+.+....|.|.+++.+++++|+. ++.+.+.|+-+-++- +---|+-+|+++..+  +.+
T Consensus        69 ~~~~edL~~~n~dwm~kyrG~sklvL~Pkst~eVS~ILkYCn~~kLAVVPQGGNTgLVGgSVPvfDEiVlsl~~m--NKi  146 (511)
T KOG1232          69 STDKEDLENFNTDWMKKYRGQSKLVLKPKSTEEVSAILKYCNDRKLAVVPQGGNTGLVGGSVPVFDEIVLSLGLM--NKI  146 (511)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHH--CCC
T ss_conf             568677754236789854687507865898899999998615050787347887665567631338886426654--352


Q ss_pred             EEECC--CCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHH--H--HHHHHHCCCCCC-----CCCEEEEEEEEEEEECCC
Q ss_conf             33026--651233112215677778875201200038725--6--632431157321-----583134566643441123
Q gi|254781095|r   96 EVRNH--CEMIVGARCSGKSLANSALRHGIGGFHFFYGIP--G--SIGGAAYMNAGA-----NNCETSQYVVEVHGIDRK  164 (318)
Q Consensus        96 ~~~~~--~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIP--G--TVGGAi~mNAGa-----yG~ei~d~i~~V~~~d~~  164 (318)
                      ..-|+  ..+.|.||+.+.++..++.++|+.   |-...+  |  .|||-++.|||.     ||. .--.|..++++.++
T Consensus       147 ~sfDevsGil~cdaG~ILen~d~~l~e~g~m---~PlDLgAKgsCqiGG~vsTnAGGlrllRYGs-LHgsvLGle~Vlp~  222 (511)
T KOG1232         147 LSFDEVSGILKCDAGVILENADNFLAEKGYM---FPLDLGAKGSCQIGGNVSTNAGGLRLLRYGS-LHGSVLGLEVVLPN  222 (511)
T ss_pred             CCCCCCCCEEEECCCEEEHHHHHHHHHCCCE---EEECCCCCCCCEECCEEECCCCCEEEEEECC-CCCCEEEEEEECCC
T ss_conf             3435555359953545742357789864935---5413787654234666421677557998635-34302346998479


Q ss_pred             CCEE----EECCCCCCCCCCCCCCCCC---CCEEEEECCCCCC
Q ss_conf             2100----0012334431002322467---6200100235456
Q gi|254781095|r  165 GNQH----VIPREQLKYQYRSSEITKD---LIITHVVLRGFPE  200 (318)
Q Consensus       165 g~~~----~l~~~e~~f~YR~S~~~~~---~iIl~a~l~l~~~  200 (318)
                      |++.    .+.++.-.+.-.+--+..+   .||+.+..-..|.
T Consensus       223 G~vl~~~~slRKDNTgydlkhLFIGSEGtlGVvT~vSil~~~k  265 (511)
T KOG1232         223 GTVLDLLSSLRKDNTGYDLKHLFIGSEGTLGVVTKVSILAPPK  265 (511)
T ss_pred             CCHHHHHHHHCCCCCCCCCHHHEECCCCEEEEEEEEEEEECCC
T ss_conf             7202535543446766651541314776146886679961599


No 19 
>TIGR01679 bact_FAD_ox FAD-linked oxidoreductase; InterPro: IPR010032   This entry identifies a family of bacterial oxidoreductases with covalently linked FAD, closely related to two different eukaryotic oxidases, L-gulonolactone oxidase (1.1.3.8 from EC) from rat and D-arabinono-1,4-lactone oxidase (1.1.3.37 from EC) from Saccharomyces cerevisiae..
Probab=98.64  E-value=1e-07  Score=69.00  Aligned_cols=151  Identities=21%  Similarity=0.247  Sum_probs=111.7

Q ss_pred             EEEEEECCHHHHHHHHHHHHC-CCCEEEECCCC---EEEEECCCEECCHHHHCCCCCCCEEEE-CCCCCCCCCEEEHHHH
Q ss_conf             899996898999999998562-99899984752---036604884022022112344311330-2665123311221567
Q gi|254781095|r   40 EVMFQPQDIHDLKYFLTLLPS-DIPITIVGLGS---NILVRDAGIRGVVLRLSNAGFSNIEVR-NHCEMIVGARCSGKSL  114 (318)
Q Consensus        40 ~~~~~p~s~~el~~~l~~~~~-~~p~~iiG~GS---Nil~~D~~~~G~vI~l~~~~~~~i~~~-~~~~i~v~AG~~~~~l  114 (318)
                      ...+.|.|+.||.++++-+.. +..++++|.|.   .|..+    +|++|+|.... ..++++ ....++|.||+.+.-|
T Consensus        13 ~ai~~P~degELad~~~~A~~pGervR~VGsGHSFT~la~t----dGt~~sl~~l~-g~v~~d~~~~~a~V~aGtrLgaL   87 (426)
T TIGR01679        13 SAIVAPKDEGELADVVKVAAKPGERVRAVGSGHSFTDLAKT----DGTLVSLEKLE-GVVDVDQQKDEAIVKAGTRLGAL   87 (426)
T ss_pred             CEECCCCCCHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCC----CCEEEECCCCC-EEEEECCCCCEEEEECCCCCCCH
T ss_conf             00117886014899999723889766544377650133366----86578731165-04300289886899506521404


Q ss_pred             HHHHHHHHCCCHHCCCCH-HHHHHHHHCCCCCCCC-----CEEEEEEEEEEEECCCCCEEEECCCC---CCCCCCCCCCC
Q ss_conf             777887520120003872-5663243115732158-----31345666434411232100001233---44310023224
Q gi|254781095|r  115 ANSALRHGIGGFHFFYGI-PGSIGGAAYMNAGANN-----CETSQYVVEVHGIDRKGNQHVIPREQ---LKYQYRSSEIT  185 (318)
Q Consensus       115 ~~~~~~~gl~GlE~l~gI-PGTVGGAi~mNAGayG-----~ei~d~i~~V~~~d~~g~~~~l~~~e---~~f~YR~S~~~  185 (318)
                      --.+++.|+ ||+|+-.| |=+||||+..-.  ||     ..+.-.|+++++++..|++.-++..+   +-.+-|=| +-
T Consensus        88 gp~La~~g~-gL~N~gDid~QsigGAlgTAT--HGtG~~~~a~h~~~~~lrlVt~~Gkv~d~~~~~d~~~~~AarVs-lG  163 (426)
T TIGR01679        88 GPLLAEKGR-GLENLGDIDKQSIGGALGTAT--HGTGVKLQALHARVVSLRLVTASGKVLDLSEADDQDIYLAARVS-LG  163 (426)
T ss_pred             HHHHHHHCC-CCCCCCCCCHHHHHHHHHHCC--CCCCCCCCCCCEEEEEEEEECCCCCEEECCCCCCHHHHHHHHHH-HH
T ss_conf             589997514-566778866013211101021--57886333542067899998588707875568787799999888-64


Q ss_pred             CCCCEEEEECCCCC
Q ss_conf             67620010023545
Q gi|254781095|r  186 KDLIITHVVLRGFP  199 (318)
Q Consensus       186 ~~~iIl~a~l~l~~  199 (318)
                      -=.||..|+|+..+
T Consensus       164 AlGViSqVtl~t~a  177 (426)
T TIGR01679       164 ALGVISQVTLRTVA  177 (426)
T ss_pred             HHCHHHEEEECCCC
T ss_conf             30101001101254


No 20 
>TIGR01677 pln_FAD_oxido plant-specific FAD-dependent oxidoreductase; InterPro: IPR010030   This entry identifies a family of uncharacterised plant-specific FAD-dependent oxidoreductases. At least seven distinct members are found in Arabidopsis thaliana. The family shows considerable sequence similarity to three different enzymes of ascorbic acid biosynthesis: L-galactono-1,4-lactone dehydrogenase (1.3.2.3 from EC) from higher plants, D-arabinono-1,4-lactone oxidase (1.1.3.37 from EC) from Saccharomyces cerevisiae, and L-gulonolactone oxidase (1.1.3.8 from EC) from mouse, as well as to a bacterial sorbitol oxidase. The class of compound acted on by members of this family is unknown..
Probab=98.56  E-value=3.8e-07  Score=65.48  Aligned_cols=166  Identities=18%  Similarity=0.226  Sum_probs=118.0

Q ss_pred             CCCCEEEEEEEECCHHHHHHHHHHH-HCCCCEEEECCCCEEE----EE-CCCE---ECCHHHHCCCCCCC-EEEEC-CCC
Q ss_conf             7661488999968989999999985-6299899984752036----60-4884---02202211234431-13302-665
Q gi|254781095|r   34 RTGGNAEVMFQPQDIHDLKYFLTLL-PSDIPITIVGLGSNIL----VR-DAGI---RGVVLRLSNAGFSN-IEVRN-HCE  102 (318)
Q Consensus        34 rvGG~A~~~~~p~s~~el~~~l~~~-~~~~p~~iiG~GSNil----~~-D~~~---~G~vI~l~~~~~~~-i~~~~-~~~  102 (318)
                      |---+|...+.|.|++||..++..+ .++.|+.+.-+=|-.|    .+ ++.-   .+++|+.++  ++. |.++. .-+
T Consensus        34 R~tC~aAav~YP~tE~dlv~~VA~A~~~g~k~kv~t~ySHsIpkLaCpG~Gs~G~as~LlIST~~--ln~vv~vdA~~~t  111 (577)
T TIGR01677        34 RSTCRAAAVAYPKTEEDLVKVVADATAKGLKVKVVTRYSHSIPKLACPGDGSDGEASALLISTKR--LNRVVAVDAEAMT  111 (577)
T ss_pred             CCCCCHHCCCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCEEECCCCCCCCHHHHHHHHHH--HCCEEEECCCCEE
T ss_conf             45464211448767689999999998468935898123144664015688886102344332556--1864787033126


Q ss_pred             CCCCCEEEHHHHHHHHHHHHCCCHHCCCCHH---H-HHHHHHCCCCCCCC-------CEEEEEEEEEEEECC----CC--
Q ss_conf             1233112215677778875201200038725---6-63243115732158-------313456664344112----32--
Q gi|254781095|r  103 MIVGARCSGKSLANSALRHGIGGFHFFYGIP---G-SIGGAAYMNAGANN-------CETSQYVVEVHGIDR----KG--  165 (318)
Q Consensus       103 i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIP---G-TVGGAi~mNAGayG-------~ei~d~i~~V~~~d~----~g--  165 (318)
                      |||+||++|.+|+..+...||+    |--=|   | ||||.+-  .|+||       +.+=|+|..++++-|    ||  
T Consensus       112 vTvdSG~~LR~lI~~a~~~Gla----L~~APYWeGlsvGGl~s--TGaHGSSlwGkGsAVHdyVv~~rlV~PA~~~dGfA  185 (577)
T TIGR01677       112 VTVDSGVSLRELIEEAEKAGLA----LPYAPYWEGLSVGGLLS--TGAHGSSLWGKGSAVHDYVVGIRLVVPASAADGFA  185 (577)
T ss_pred             EEECCCCCHHHHHHHHHHCCCC----CCCCCCCCCCEECCCCC--CCCCCCCCCCCCCCEEEEEEEEEEECCCCCCCCEE
T ss_conf             7630487678999998644643----46786403402243001--57433232268973222577667413688777536


Q ss_pred             CEEEECCCC--CCCCCCCCCCCCCCCEEEEECCCCCCCCCCCHH
Q ss_conf             100001233--443100232246762001002354565431001
Q gi|254781095|r  166 NQHVIPREQ--LKYQYRSSEITKDLIITHVVLRGFPESQNIISA  207 (318)
Q Consensus       166 ~~~~l~~~e--~~f~YR~S~~~~~~iIl~a~l~l~~~~~~~i~~  207 (318)
                      +++.|+.-+  -.|.==.-++-==.||..|+|.|.|.=+..+.-
T Consensus       186 Kv~~L~~~~~d~~lnAakVSLGvLGVIS~VtL~L~p~FKRSvtY  229 (577)
T TIGR01677       186 KVVVLEEGDDDALLNAAKVSLGVLGVISKVTLALEPLFKRSVTY  229 (577)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCEEEEEEEEECCCCCCEEEE
T ss_conf             77770578583256566555100201335664316774520322


No 21 
>KOG1233 consensus
Probab=98.47  E-value=4e-07  Score=65.30  Aligned_cols=163  Identities=17%  Similarity=0.171  Sum_probs=120.2

Q ss_pred             EEEEEEEECCHHHHHHHHHHH-HCCCCEEEECCCC---EEEEECCCEECCHHHHCCCCCCCEEEECCC--CCCCCCEEEH
Q ss_conf             488999968989999999985-6299899984752---036604884022022112344311330266--5123311221
Q gi|254781095|r   38 NAEVMFQPQDIHDLKYFLTLL-PSDIPITIVGLGS---NILVRDAGIRGVVLRLSNAGFSNIEVRNHC--EMIVGARCSG  111 (318)
Q Consensus        38 ~A~~~~~p~s~~el~~~l~~~-~~~~p~~iiG~GS---Nil~~D~~~~G~vI~l~~~~~~~i~~~~~~--~i~v~AG~~~  111 (318)
                      ..+.++.|+..+|+.++++.+ +++.-+.++|+|+   |-|-....-.-.+|+|....++.+-..++.  +..++||..-
T Consensus       160 iPDiVvWP~chdevVkiv~lA~khN~~iiPiGGGTSVs~al~cP~~E~R~iislDtsqmnriLWidreNLT~~~eaGIvG  239 (613)
T KOG1233         160 IPDIVVWPKCHDEVVKIVELAMKHNCAIIPIGGGTSVSNALDCPETEKRAIISLDTSQMNRILWIDRENLTCRAEAGIVG  239 (613)
T ss_pred             CCCEEECCCCHHHHHHHHHHHHHCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECHHHHHHEEEECCCCCEEEEECCCCH
T ss_conf             88557636623899999988854676999747964013531488654405897027752021685356616998537420


Q ss_pred             HHHHHHHHHHHCC-CHHCCCCHHHHHHHHHCCCCC-----CCCCEEEEEEEEEEEECCCCCEEE---ECCCCCCCCCCCC
Q ss_conf             5677778875201-200038725663243115732-----158313456664344112321000---0123344310023
Q gi|254781095|r  112 KSLANSALRHGIG-GFHFFYGIPGSIGGAAYMNAG-----ANNCETSQYVVEVHGIDRKGNQHV---IPREQLKYQYRSS  182 (318)
Q Consensus       112 ~~l~~~~~~~gl~-GlE~l~gIPGTVGGAi~mNAG-----ayG~ei~d~i~~V~~~d~~g~~~~---l~~~e~~f~YR~S  182 (318)
                      .+|-+.+.+.|++ |-|-=+-==.|+||.+..-|.     -||. |-|.|..+..+.+.|.+..   .++-.+.-+.-+-
T Consensus       240 Q~LERqL~~~G~t~GHEPDS~EFSTlGGWVsTRASGMKKN~YGN-IEDLVVh~~mVtP~Giiek~Cq~PRmS~GPDihh~  318 (613)
T KOG1233         240 QSLERQLNKKGFTCGHEPDSIEFSTLGGWVSTRASGMKKNKYGN-IEDLVVHLNMVTPKGIIEKQCQVPRMSSGPDIHHI  318 (613)
T ss_pred             HHHHHHHHHCCCCCCCCCCCEEEECCCCEEEECCCCCCCCCCCC-HHHHEEEEEEECCCCHHHHHHCCCCCCCCCCCCEE
T ss_conf             77999986448644789884655313431221012232244578-66716789863574221344068755579983048


Q ss_pred             CCCCC---CCEEEEECCCCCCC
Q ss_conf             22467---62001002354565
Q gi|254781095|r  183 EITKD---LIITHVVLRGFPES  201 (318)
Q Consensus       183 ~~~~~---~iIl~a~l~l~~~~  201 (318)
                      ++..+   .+|+.++++..|-+
T Consensus       319 IlGSEGTLGVitEvtiKirPiP  340 (613)
T KOG1233         319 ILGSEGTLGVITEVTIKIRPIP  340 (613)
T ss_pred             EECCCCCEEEEEEEEEEEEECH
T ss_conf             7416762267888999875363


No 22 
>TIGR02963 xanthine_xdhA xanthine dehydrogenase, small subunit; InterPro: IPR014307   Members of this protein are the small subunit (or, in eukaryotes, the N-terminal domain) of xanthine dehydrogenase, an enzyme of purine catabolism via urate. The small subunit contains both an FAD and a 2Fe-2S cofactor. Aldehyde oxidase (retinal oxidase) appears to have arisen as a neofunctionalisation among xanthine dehydrogenases in eukaryotes. ; GO: 0004854 xanthine dehydrogenase activity, 0004855 xanthine oxidase activity, 0050660 FAD binding.
Probab=97.72  E-value=5.4e-05  Score=51.82  Aligned_cols=167  Identities=17%  Similarity=0.270  Sum_probs=112.8

Q ss_pred             CCCCCCCCCCCCEEEEE--EEECCHHHHHHHHHHHHCCCCEEEECCCCEE-E-EEC--CCEECCHHHHCC-CCCCCEEEE
Q ss_conf             80015225766148899--9968989999999985629989998475203-6-604--884022022112-344311330
Q gi|254781095|r   26 PLKQITWFRTGGNAEVM--FQPQDIHDLKYFLTLLPSDIPITIVGLGSNI-L-VRD--AGIRGVVLRLSN-AGFSNIEVR   98 (318)
Q Consensus        26 ~L~~~tt~rvGG~A~~~--~~p~s~~el~~~l~~~~~~~p~~iiG~GSNi-l-~~D--~~~~G~vI~l~~-~~~~~i~~~   98 (318)
                      .+.+.-|..+....+-+  +.|.|.+||+++....+   .-.|+-|++-+ | |.-  ..++ .+|.++. ..++.|+..
T Consensus       211 ~~~~~~~~~l~~~~~~~~W~~P~t~~dLA~l~~a~P---~ArivAGsTDVGLWVTk~~R~L~-~~i~~g~v~EL~~i~~~  286 (515)
T TIGR02963       211 ALRAGETVELNSGGERFTWIAPTTLDDLAALKAAHP---KARIVAGSTDVGLWVTKQMRDLP-DVIYVGQVAELKRIEET  286 (515)
T ss_pred             HHCCCCCEEEECCCCCEEEEECCCHHHHHHHHHHCC---CCEEEECCEEHHHHHHHHHHHHH-CCCCCCCCHHHCEEEEC
T ss_conf             644798489841786158870688899999997289---95899646004668856421121-11025684321101334


Q ss_pred             CCCCCCCCCEEEHHHHHHHHHHH--HCC----------C-HHCCCCHH----HHHHHHHCCCCCCCCCEEEEE---E--E
Q ss_conf             26651233112215677778875--201----------2-00038725----663243115732158313456---6--6
Q gi|254781095|r   99 NHCEMIVGARCSGKSLANSALRH--GIG----------G-FHFFYGIP----GSIGGAAYMNAGANNCETSQY---V--V  156 (318)
Q Consensus        99 ~~~~i~v~AG~~~~~l~~~~~~~--gl~----------G-lE~l~gIP----GTVGGAi~mNAGayG~ei~d~---i--~  156 (318)
                      ++ .|+.|||+++.+.-..+.++  .|.          - +.++++.|    |||||-| ||+..    |+|.   |  .
T Consensus       287 ~~-~i~iGA~v~l~~a~~~L~~~~P~l~~~T~~Fq~~~el~~RfAs~QiRN~GTlGGNI-ANGSP----IGD~pP~LIAL  360 (515)
T TIGR02963       287 DD-GIEIGAGVTLTDAYAALAERYPELGAKTRLFQAALELLRRFASLQIRNAGTLGGNI-ANGSP----IGDSPPALIAL  360 (515)
T ss_pred             CC-EEEEECCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC-CCCCC----CCCCCHHHHHC
T ss_conf             87-26982488888999999872422013478899999999986889732011013642-26687----66678378713


Q ss_pred             EEEEECCCCC-EEEECCCCCCCCCCCCCCCCCCCEEEEECCCCCCCC
Q ss_conf             4344112321-000012334431002322467620010023545654
Q gi|254781095|r  157 EVHGIDRKGN-QHVIPREQLKYQYRSSEITKDLIITHVVLRGFPESQ  202 (318)
Q Consensus       157 ~V~~~d~~g~-~~~l~~~e~~f~YR~S~~~~~~iIl~a~l~l~~~~~  202 (318)
                      ..++..+.|+ .+++.=||+..+|+....+...+|.++.+-..+.+.
T Consensus       361 GA~l~LR~G~~~R~lpLEdfFi~Y~k~~~~pgEFve~~~vP~~~~~~  407 (515)
T TIGR02963       361 GATLTLRKGETRRTLPLEDFFIDYGKQDRQPGEFVEALRVPTAAPDE  407 (515)
T ss_pred             CCEEEEECCCCCCCCHHHHHHHHHHHEECCCCCEEEEEEECCCCCCC
T ss_conf             98799970775232117777467202010355078888730479970


No 23 
>pfam00941 FAD_binding_5 FAD binding domain in molybdopterin dehydrogenase.
Probab=97.71  E-value=6.1e-05  Score=51.52  Aligned_cols=146  Identities=17%  Similarity=0.231  Sum_probs=95.8

Q ss_pred             EEEEECCHHHHHHHHHHHHCCCCEEEECCCCEEEEE--CCC-EECCHHHHCC-CCCCCEEEECCCCCCCCCEEEHHHHHH
Q ss_conf             999968989999999985629989998475203660--488-4022022112-344311330266512331122156777
Q gi|254781095|r   41 VMFQPQDIHDLKYFLTLLPSDIPITIVGLGSNILVR--DAG-IRGVVLRLSN-AGFSNIEVRNHCEMIVGARCSGKSLAN  116 (318)
Q Consensus        41 ~~~~p~s~~el~~~l~~~~~~~p~~iiG~GSNil~~--D~~-~~G~vI~l~~-~~~~~i~~~~~~~i~v~AG~~~~~l~~  116 (318)
                      .|+.|+|.+|+.+++...   -...++.+|+.++..  .+. -+..+|.+.+ ..++.++..++ .+++||++.+.++..
T Consensus         4 ~y~~P~sl~ea~~ll~~~---~~a~ilAGGTdl~~~~~~~~~~~~~lIdl~~I~eL~~I~~~~~-~l~IGA~vt~~~l~~   79 (171)
T pfam00941         4 TYYRPASLEEALALLAKG---PDAKLVAGGTSLGPEMKLRLARPPVLIDINGIPELRGIEETGD-GLEIGAAVTLTELID   79 (171)
T ss_pred             EEECCCCHHHHHHHHHHC---CCCEEEECCCHHHHHHHCCCCCCCEEEEHHHCCCCCEEEEECC-EEEEEEEEEHHHHHH
T ss_conf             597789999999999669---9988997476289997437689885998567787653898199-899933216999763


Q ss_pred             H-HHHHHCCCH----HCCCCHH----HHHHHHHCCCCCCCCCEEEEEE-------EEEEEECCCCCEEEECCCCCCCCCC
Q ss_conf             7-887520120----0038725----6632431157321583134566-------6434411232100001233443100
Q gi|254781095|r  117 S-ALRHGIGGF----HFFYGIP----GSIGGAAYMNAGANNCETSQYV-------VEVHGIDRKGNQHVIPREQLKYQYR  180 (318)
Q Consensus       117 ~-~~~~gl~Gl----E~l~gIP----GTVGGAi~mNAGayG~ei~d~i-------~~V~~~d~~g~~~~l~~~e~~f~YR  180 (318)
                      . .....+..|    ...++..    |||||.++ ||-    -.+|..       -.|++...+| .++++-+|+--+|+
T Consensus        80 ~~~~~~~~p~l~~a~~~ia~~qIRn~aTiGGni~-~a~----p~~D~~~~Llal~A~v~l~~~~g-~R~v~~~dF~~g~~  153 (171)
T pfam00941        80 SPLVAEVFPALAEALRKIASPQIRNVATIGGNIA-NAS----PISDLPPALLALDATVELRSPEG-RRTVPLEDFFLGYR  153 (171)
T ss_pred             CHHHHHHHHHHHHHHHHCCCHHHEEEEEECCEEC-CCC----CCCCHHHHHHHHCCEEEEECCCC-EEEEEHHHHCCCCC
T ss_conf             9666656499999987138975745777624310-366----65324599997385999986995-29989999467734


Q ss_pred             CCCCCCCCCEEEEECC
Q ss_conf             2322467620010023
Q gi|254781095|r  181 SSEITKDLIITHVVLR  196 (318)
Q Consensus       181 ~S~~~~~~iIl~a~l~  196 (318)
                      .+.++++.+++++.+-
T Consensus       154 ~t~l~~~Eii~~I~iP  169 (171)
T pfam00941       154 KTDLEPGELLTAVRIP  169 (171)
T ss_pred             CCCCCCCCEEEEEECC
T ss_conf             4046988759999856


No 24 
>PRK09971 xanthine dehydrogenase subunit XdhB; Provisional
Probab=97.37  E-value=0.00023  Score=47.86  Aligned_cols=148  Identities=13%  Similarity=0.209  Sum_probs=95.3

Q ss_pred             EEEEEECCHHHHHHHHHHHHCCCCEEEECCCCEEEEE--CC-CEECCHHHHCCC-CCCCEEEECCCCCCCCCEEEHHHHH
Q ss_conf             8999968989999999985629989998475203660--48-840220221123-4431133026651233112215677
Q gi|254781095|r   40 EVMFQPQDIHDLKYFLTLLPSDIPITIVGLGSNILVR--DA-GIRGVVLRLSNA-GFSNIEVRNHCEMIVGARCSGKSLA  115 (318)
Q Consensus        40 ~~~~~p~s~~el~~~l~~~~~~~p~~iiG~GSNil~~--D~-~~~G~vI~l~~~-~~~~i~~~~~~~i~v~AG~~~~~l~  115 (318)
                      +.|+.|+|.+|..+++...+   ...++.+|+.++..  .+ .-+..+|.+.+- .+..++..++..++.||.+.+.++.
T Consensus         5 ~~Y~~P~sl~eA~~ll~~~~---~a~ilAGGTdL~~~~~~~~~~~~~lIdi~~I~eL~~I~~~~dg~l~IGA~vT~~el~   81 (292)
T PRK09971          5 AEYHEAATLADAIELLADNP---QAKLIAGGTDVLIQLHHHNDRYRHLVDIRNIAELRGITLAEDGSIRIGAATTFTQII   81 (292)
T ss_pred             CCEECCCCHHHHHHHHHHCC---CCEEEECCCHHHHHHHCCCCCCCEEEECCCCHHHCCEEECCCCCEEEEECCCHHHHH
T ss_conf             54728899999999984199---987996373189998568899885888357825457788799839997067289875


Q ss_pred             HHH-HHHHCCCHHCC---CCHH-----HHHHHHHCCCCCCCCCEEEEEE-------EEEEEECCCCCEEEECCCCCCCCC
Q ss_conf             778-87520120003---8725-----6632431157321583134566-------643441123210000123344310
Q gi|254781095|r  116 NSA-LRHGIGGFHFF---YGIP-----GSIGGAAYMNAGANNCETSQYV-------VEVHGIDRKGNQHVIPREQLKYQY  179 (318)
Q Consensus       116 ~~~-~~~gl~GlE~l---~gIP-----GTVGGAi~mNAGayG~ei~d~i-------~~V~~~d~~g~~~~l~~~e~~f~Y  179 (318)
                      ... .+..+..|-..   .+=|     |||||.++...     -.+|..       -.|++...+| .++++-+|+--+|
T Consensus        82 ~~~~i~~~~p~L~~a~~~ig~~qIRN~aTiGGni~~a~-----p~~D~~p~LlaldA~v~i~s~~g-~R~ipl~dF~~g~  155 (292)
T PRK09971         82 EDPIVQRHLPALAEAAVSIGGPQIRNVATIGGNICNGA-----TSADSATPLFALDAKLELHSPNG-VRFVPINGFYTGP  155 (292)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCC-----CCCHHHHHHHHHHCEEEEECCCC-CEECCHHHHCCCC
T ss_conf             19688866669999999738996702414366544678-----75016799999640468973899-7733389962575


Q ss_pred             CCCCCCCCCCEEEEECC
Q ss_conf             02322467620010023
Q gi|254781095|r  180 RSSEITKDLIITHVVLR  196 (318)
Q Consensus       180 R~S~~~~~~iIl~a~l~  196 (318)
                      +.+.++++.+++++.+.
T Consensus       156 ~~t~l~~~Eil~~I~ip  172 (292)
T PRK09971        156 GKVSLEHDEILVAFHIP  172 (292)
T ss_pred             CCCCCCCCCEEEEEEEC
T ss_conf             53335775369999974


No 25 
>TIGR03195 4hydrxCoA_B 4-hydroxybenzoyl-CoA reductase, beta subunit. This model represents the second largest chain, beta, of the enzyme 4-hydroxybenzoyl-CoA reductase. In species capable of degrading various aromatic compounds by way of benzoyl-CoA, this enzyme can convert 4-hydroxybenzoyl-CoA to benzoyl-CoA.
Probab=97.12  E-value=0.0006  Score=45.23  Aligned_cols=150  Identities=15%  Similarity=0.232  Sum_probs=95.5

Q ss_pred             EEEECCHHHHHHHHHHHHCCCCEEEECCCCEEEE--ECC-CEECCHHHHCC-CCCCCEEEECCCCCCCCCEEEHHHHHHH
Q ss_conf             9996898999999998562998999847520366--048-84022022112-3443113302665123311221567777
Q gi|254781095|r   42 MFQPQDIHDLKYFLTLLPSDIPITIVGLGSNILV--RDA-GIRGVVLRLSN-AGFSNIEVRNHCEMIVGARCSGKSLANS  117 (318)
Q Consensus        42 ~~~p~s~~el~~~l~~~~~~~p~~iiG~GSNil~--~D~-~~~G~vI~l~~-~~~~~i~~~~~~~i~v~AG~~~~~l~~~  117 (318)
                      |+.|.|.+|..+++...+   .-.+|.+|+.++.  ..+ ..+..+|.+++ ..+..|+..++ .++.||++.+.++...
T Consensus         7 y~rP~sl~eAl~lL~~~~---~a~~lAGGTdL~~~~~~~~~~p~~lIdl~~I~eL~~I~~~~~-~l~IGA~vt~~~l~~~   82 (321)
T TIGR03195         7 TLRPASLADAVAALAAHP---AARPLAGGTDLLPNLRRGLGQPETLVDLTGIDEIAQLSTLAD-GLRIGAGVTLAALAED   82 (321)
T ss_pred             EECCCCHHHHHHHHHHCC---CCEEEECCCCHHHHHHCCCCCCCEEEECCCCCCCCEEEECCC-EEEECCCCCHHHHHHC
T ss_conf             328999999999986099---988997420299998557789985898788856470787699-3999134448887759


Q ss_pred             -HHHHHCCCHHC---CCCHH-----HHHHHHHCCCCCCC------------------CCE---------------EEEEE
Q ss_conf             -88752012000---38725-----66324311573215------------------831---------------34566
Q gi|254781095|r  118 -ALRHGIGGFHF---FYGIP-----GSIGGAAYMNAGAN------------------NCE---------------TSQYV  155 (318)
Q Consensus       118 -~~~~gl~GlE~---l~gIP-----GTVGGAi~mNAGay------------------G~e---------------i~d~i  155 (318)
                       .....+..|--   ..+=|     |||||.++++..||                  +++               .+|..
T Consensus        83 ~~v~~~~P~L~~a~~~igspqIRn~gTiGGNl~~~~rc~yy~~~~~~r~~~~~c~~~~g~~~~~~p~~~~~~Asp~~D~~  162 (321)
T TIGR03195        83 ALVRTRWPALAQAARAVAGPTHRAAATLGGNLCLDTRCIYYNQSEWWRSGNGYCLKYRGDKCHVAPKSDRCYAAFSGDVA  162 (321)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHCCEEECCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             78787749999999974889770732202432345652001441111478874334567521123565544468841047


Q ss_pred             -------EEEEEECCCCCEEEECCCCCCC--CCCCCCCCCCCCEEEEECC
Q ss_conf             -------6434411232100001233443--1002322467620010023
Q gi|254781095|r  156 -------VEVHGIDRKGNQHVIPREQLKY--QYRSSEITKDLIITHVVLR  196 (318)
Q Consensus       156 -------~~V~~~d~~g~~~~l~~~e~~f--~YR~S~~~~~~iIl~a~l~  196 (318)
                             -.|++...+| .++++-+|+..  +|+.+.++.+.+++++.+.
T Consensus       163 p~LlaL~A~v~l~s~~G-~R~ip~~dFf~~~G~~~t~L~~~Ellt~I~iP  211 (321)
T TIGR03195       163 PALLVLDAEAEIVGPAG-VRRVPLAELYVEDGAAHLTLEPGEVLAAVRVP  211 (321)
T ss_pred             HHHHHCCCEEEEECCCC-CEEEEHHHHCCCCCCCEECCCCCCEEEEEECC
T ss_conf             89997198999985997-39989899300528531215888379999815


No 26 
>KOG0430 consensus
Probab=96.61  E-value=0.0042  Score=39.89  Aligned_cols=157  Identities=17%  Similarity=0.179  Sum_probs=88.3

Q ss_pred             EEEEEEECCHHHHHHHHHHHHCCCCEEEECCCCEEEEEC-CCEECCHHHHCC-CCCCCEEEECCCCCCCCCEEEHHHHHH
Q ss_conf             889999689899999999856299899984752036604-884022022112-344311330266512331122156777
Q gi|254781095|r   39 AEVMFQPQDIHDLKYFLTLLPSDIPITIVGLGSNILVRD-AGIRGVVLRLSN-AGFSNIEVRNHCEMIVGARCSGKSLAN  116 (318)
Q Consensus        39 A~~~~~p~s~~el~~~l~~~~~~~p~~iiG~GSNil~~D-~~~~G~vI~l~~-~~~~~i~~~~~~~i~v~AG~~~~~l~~  116 (318)
                      --.++.|.|.+||.+++.  +...-.++.|+-+-=+-.+ ..++. .|.... +.+..+.. ++..++.||++++.+...
T Consensus       214 ~~~W~~P~sl~eL~~~~~--~~~~~~Lv~GNT~~gv~~r~~~~~~-~Id~~~v~el~~~~~-~~~gi~lGa~~sls~~~~  289 (1257)
T KOG0430         214 GIRWYWPVSLEELFELKA--NKPDAKLVAGNTAHGVYRRSPDYQK-FIDVSGVPELKALNV-DDNGLELGAALSLSETME  289 (1257)
T ss_pred             CCEEECCCCHHHHHHHHH--CCCCEEEEECCCCCEEEECCCCCCC-EECHHCCCHHHCCCC-CCCCEEECCCCCHHHHHH
T ss_conf             717867566999999985--2864389852533158851688761-354300841210356-877418755243999999


Q ss_pred             HHHHHH-CCC----------HHCCCCHH----HHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCEEEEC--CCCCC-CC
Q ss_conf             788752-012----------00038725----66324311573215831345666434411232100001--23344-31
Q gi|254781095|r  117 SALRHG-IGG----------FHFFYGIP----GSIGGAAYMNAGANNCETSQYVVEVHGIDRKGNQHVIP--REQLK-YQ  178 (318)
Q Consensus       117 ~~~~~g-l~G----------lE~l~gIP----GTVGGAi~mNAGayG~ei~d~i~~V~~~d~~g~~~~l~--~~e~~-f~  178 (318)
                      .+.+.- +.|          ++|.++.|    ||+||.+++-+... .-++|......+.|..-.+..-.  -++.. -+
T Consensus       290 ~l~~~~~~~~~~~~~~~~~hl~~~A~~~IRN~ati~GnI~~~~~~~-~f~SDl~~~l~a~~a~v~~~~~~~~~~~~~l~~  368 (1257)
T KOG0430         290 LLRKLVKRPGFEYFKALWEHLKWFANVQIRNVGTIGGNICTKAQSP-EFPSDLFILLEALDAKVTILNNSGDLEKVFLEE  368 (1257)
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHCCCCEECCCCCCCEEEECCCCC-CCCHHHHHHHHHHCCEEEEEECCCCCCEEEHHH
T ss_conf             9999870728889999999998750500002210034166426787-785067889876236899860688621453866


Q ss_pred             CCCCCCCCCCCEEEEECCCCCC
Q ss_conf             0023224676200100235456
Q gi|254781095|r  179 YRSSEITKDLIITHVVLRGFPE  200 (318)
Q Consensus       179 YR~S~~~~~~iIl~a~l~l~~~  200 (318)
                      ||.+.+..+.|++++.+...+.
T Consensus       369 y~~~~l~~~~illsv~ip~~~~  390 (1257)
T KOG0430         369 YLGSSLGAKEILLSVVLPASRK  390 (1257)
T ss_pred             HHCCCCCCCEEEEEEECCCCHH
T ss_conf             6446567230789997267389


No 27 
>TIGR01676 GLDHase galactonolactone dehydrogenase; InterPro: IPR010029   This entry identifies L-galactono-gamma-lactone dehydrogenase 1.3.2.3 from EC. This enzyme performs the final step in ascorbic acid biosynthesis in higher plants. The protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD..
Probab=96.45  E-value=0.0039  Score=40.06  Aligned_cols=169  Identities=22%  Similarity=0.296  Sum_probs=108.9

Q ss_pred             CEEEECCCCCC--CCC--C-C-CCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEECCCCEEEEECCCE----ECCHHHH
Q ss_conf             62775488001--522--5-7-6614889999689899999999856-299899984752036604884----0220221
Q gi|254781095|r   19 GKFQENFPLKQ--ITW--F-R-TGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIVGLGSNILVRDAGI----RGVVLRL   87 (318)
Q Consensus        19 g~i~~n~~L~~--~tt--~-r-vGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~iiG~GSNil~~D~~~----~G~vI~l   87 (318)
                      .++.+..||-+  ||-  | + -.-..+.|..|+++++|..+++.++ ....+..+|.|-    +..|+    -|+| .+
T Consensus        36 aq~fryaPlP~dlhtvsnWsGthev~tr~f~qPe~~e~le~~vk~anekk~r~rPvGsGl----sPnGiGl~r~Gmv-n~  110 (541)
T TIGR01676        36 AQLFRYAPLPEDLHTVSNWSGTHEVLTRVFLQPEDLEELEQVVKTANEKKARVRPVGSGL----SPNGIGLSRLGMV-NL  110 (541)
T ss_pred             HHEEECCCCCHHHHHHHCCCCCCEEEHEEECCHHHHHHHHHHHHHHHHHHCCCCCCCCCC----CCCCCCHHHHHHH-HH
T ss_conf             111330688412222202455300000000371568999999975442101113113677----8655322356788-89


Q ss_pred             CCCCCCCEEEE-CCCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHH-HHHHHHHCCCCCCCC-----CEEEEEEEEEEE
Q ss_conf             12344311330-26651233112215677778875201200038725-663243115732158-----313456664344
Q gi|254781095|r   88 SNAGFSNIEVR-NHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIP-GSIGGAAYMNAGANN-----CETSQYVVEVHG  160 (318)
Q Consensus        88 ~~~~~~~i~~~-~~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIP-GTVGGAi~mNAGayG-----~ei~d~i~~V~~  160 (318)
                      ..+. ..+.++ +...++|+||+...+|+....+.|++ |.+++.|- -.|||-+-  .||||     --|-+.+.+...
T Consensus       111 almd-~vl~vd~ekk~v~vqaGirvqqlvd~ikeyG~t-lqnfasireqqiGGi~q--vGahGtGaklPPideqvi~mkl  186 (541)
T TIGR01676       111 ALMD-KVLEVDKEKKRVRVQAGIRVQQLVDAIKEYGLT-LQNFASIREQQIGGIVQ--VGAHGTGAKLPPIDEQVIAMKL  186 (541)
T ss_pred             HHHH-HHHHHHCCCCEEEEEECCHHHHHHHHHHHHCCH-HHHHHHHHHHCCCCEEE--ECCCCCCCCCCCCCCCEEEEEE
T ss_conf             9888-887530234578884062166888778862303-55555543310464688--6554567768863200144454


Q ss_pred             ECC-CCCEEEECCCC--CCCCCCCCCCCCCCCEEEEECCC
Q ss_conf             112-32100001233--44310023224676200100235
Q gi|254781095|r  161 IDR-KGNQHVIPREQ--LKYQYRSSEITKDLIITHVVLRG  197 (318)
Q Consensus       161 ~d~-~g~~~~l~~~e--~~f~YR~S~~~~~~iIl~a~l~l  197 (318)
                      +.+ +|.+..-...|  +.|=-|. -+..-.+|..++|+-
T Consensus       187 vtPakGtieis~~kdPelf~larC-GlGGlGvvaevtlqC  225 (541)
T TIGR01676       187 VTPAKGTIEISKEKDPELFYLARC-GLGGLGVVAEVTLQC  225 (541)
T ss_pred             ECCCCCEEEECCCCCCCEEEEECC-CCCCCCEEEEEHHHH
T ss_conf             136775066326788644543102-776441000000122


No 28 
>COG1319 CoxM Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM/CutM homologs [Energy production and conversion]
Probab=95.90  E-value=0.0042  Score=39.89  Aligned_cols=149  Identities=17%  Similarity=0.214  Sum_probs=86.9

Q ss_pred             EEEEECCHHHHHHHHHHHHCCCCEEEECCCCEEEE-ECCCE--ECCHHHHCCCC-CCCEEEECCCCCCCCCEEEHHHHHH
Q ss_conf             99996898999999998562998999847520366-04884--02202211234-4311330266512331122156777
Q gi|254781095|r   41 VMFQPQDIHDLKYFLTLLPSDIPITIVGLGSNILV-RDAGI--RGVVLRLSNAG-FSNIEVRNHCEMIVGARCSGKSLAN  116 (318)
Q Consensus        41 ~~~~p~s~~el~~~l~~~~~~~p~~iiG~GSNil~-~D~~~--~G~vI~l~~~~-~~~i~~~~~~~i~v~AG~~~~~l~~  116 (318)
                      .|+.|.|.+|...+++..  . ...+|++|+|++- .+.+.  +..++.+.... ...+...++..++.||-+.+.++.+
T Consensus         5 ~y~rp~Sv~eA~~ll~~~--~-~a~~laGGt~L~~~~k~~~~~p~~lVdI~~l~~~~~~~~~~g~~l~IGA~vt~~ei~~   81 (284)
T COG1319           5 EYYRPASVEEALNLLARA--P-DAKYLAGGTDLLPLMKLGIERPDHLVDINGLDELLGIVTTEGGSLRIGALVTLTEIAR   81 (284)
T ss_pred             EEECCCCHHHHHHHHHHC--C-CCEEEECCCHHHHHHHCCCCCCCEEEEECCCHHHHCEEEECCCEEEEEECCCHHHHHH
T ss_conf             897779999999999748--8-8589407633788764556882407982387045156860698799941252799774


Q ss_pred             HH-HHHHCCCH---HCCCCHH-----HHHHHHHCCCCCCCCCEEEEEEE-------EEEEECCCCCEEEECCCCCCCCCC
Q ss_conf             78-87520120---0038725-----66324311573215831345666-------434411232100001233443100
Q gi|254781095|r  117 SA-LRHGIGGF---HFFYGIP-----GSIGGAAYMNAGANNCETSQYVV-------EVHGIDRKGNQHVIPREQLKYQYR  180 (318)
Q Consensus       117 ~~-~~~gl~Gl---E~l~gIP-----GTVGGAi~mNAGayG~ei~d~i~-------~V~~~d~~g~~~~l~~~e~~f~YR  180 (318)
                      .. .+.-+..|   ....+=|     ||+||.++-+.     ..+|...       .|.+..+.| .++++-+++.-+=.
T Consensus        82 ~~~~~~~~p~L~ea~~~ia~~qvRN~aTiGGn~c~a~-----p~aD~~~aLlaLdA~v~~~~~~g-~r~i~~~~f~~~p~  155 (284)
T COG1319          82 HPAVRRIPPALSEAASAIASPQVRNRATIGGNLCNAD-----PAADLAPALLALDAEVEIRSPGG-ERTIPIEDFFRGPG  155 (284)
T ss_pred             CHHHHHHCHHHHHHHHHHCCHHHCCEEEECCHHCCCC-----CCHHHHHHHHHCCCEEEEECCCC-CEEEEHHHHHCCCC
T ss_conf             9433421559999998735854411044233110378-----81466899997498899960786-38988799641966


Q ss_pred             CCCCCCCCCEEEEECCCC
Q ss_conf             232246762001002354
Q gi|254781095|r  181 SSEITKDLIITHVVLRGF  198 (318)
Q Consensus       181 ~S~~~~~~iIl~a~l~l~  198 (318)
                      .+.+.+..+|+.+.|...
T Consensus       156 ~t~l~~gelit~v~lP~~  173 (284)
T COG1319         156 ETALEPGELITAVILPPP  173 (284)
T ss_pred             CCCCCCCCEEEEEECCCC
T ss_conf             313578707999976897


No 29 
>TIGR03312 Se_sel_red_FAD probable selenate reductase, FAD-binding subunit. This protein is suggested by Bebien, et al., to be the FAD-binding subunit of a molydbopterin-containing selenate reductase. Our comparative genomics suggests it to be a subunit of a selenium-dependent molybdenum hydroxylase for an unknown substrate.
Probab=95.43  E-value=0.013  Score=36.85  Aligned_cols=143  Identities=17%  Similarity=0.181  Sum_probs=77.9

Q ss_pred             EEEEEECCHHHHHHHHHHHHCCCCEEEECCCCEEEEEC-CCEECCHHHHCCCCCCCEEEECCCCCCCCCEEEHHHHHHHH
Q ss_conf             89999689899999999856299899984752036604-88402202211234431133026651233112215677778
Q gi|254781095|r   40 EVMFQPQDIHDLKYFLTLLPSDIPITIVGLGSNILVRD-AGIRGVVLRLSNAGFSNIEVRNHCEMIVGARCSGKSLANSA  118 (318)
Q Consensus        40 ~~~~~p~s~~el~~~l~~~~~~~p~~iiG~GSNil~~D-~~~~G~vI~l~~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~  118 (318)
                      +.|+.|+|.+|..+++...  .-.-.+++|||-+...- ...+.+.|.+....++.++..++ .++.||.+.+.++...-
T Consensus         2 ~eY~rP~sl~EA~~lL~~~--~~~a~ilaGGtdL~~~~~~~~~~~~i~l~~~~L~~I~~~~~-~l~IGA~~t~~~l~~~~   78 (257)
T TIGR03312         2 EQFFRPESTIQALELKKRH--TGVAVWFAGGSKLNATPTRTDKKVAISLDKLALDKIELQGG-ALHIGAMCHLQSLIDNE   78 (257)
T ss_pred             CCCCCCCCHHHHHHHHHHC--CCCCEEECCCCCHHHHHCCCCCCEEEECCCCCCCCEEECCC-EEEECCCCCHHHHHHCC
T ss_conf             7621889899999999768--99888973785745333477774367726037560897699-99995418099996494


Q ss_pred             HHH-HCCCHHCCCCHH-----HHHHHHHCCCCCCCCCEEEEEEEEEEEECCC---CCEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf             875-201200038725-----6632431157321583134566643441123---2100001233443100232246762
Q gi|254781095|r  119 LRH-GIGGFHFFYGIP-----GSIGGAAYMNAGANNCETSQYVVEVHGIDRK---GNQHVIPREQLKYQYRSSEITKDLI  189 (318)
Q Consensus       119 ~~~-gl~GlE~l~gIP-----GTVGGAi~mNAGayG~ei~d~i~~V~~~d~~---g~~~~l~~~e~~f~YR~S~~~~~~i  189 (318)
                      .-. .|.-.--..+=|     |||||.++ ||-.    .+|..--...+|..   +.-++++-+|+--+||      +.+
T Consensus        79 ~~~~~L~~a~~~i~~~qIRN~gTiGGnla-~a~P----~aD~~p~LlAl~A~v~l~~~~~ip~~dF~~g~~------~Ei  147 (257)
T TIGR03312        79 LTPAALKEALGFVYSRHIRNQATIGGEIA-AFQS----ESLLLPVLLALKATVVLANASQMDIEDYLASEQ------REL  147 (257)
T ss_pred             CCHHHHHHHHHHHCCHHHCCCEEEEEEEC-CCCC----CHHHHHHHHHCCCEEEECCCCEEEHHHHHCCCC------CEE
T ss_conf             42389999998655786512104434621-5787----358899999749899985896887999707899------808


Q ss_pred             EEEEECC
Q ss_conf             0010023
Q gi|254781095|r  190 ITHVVLR  196 (318)
Q Consensus       190 Il~a~l~  196 (318)
                      ++++.+.
T Consensus       148 l~~I~iP  154 (257)
T TIGR03312       148 IVEVIIP  154 (257)
T ss_pred             EEEEEEC
T ss_conf             9999964


No 30 
>PRK09799 putative selenate reductase subunit YgfM; Provisional
Probab=94.35  E-value=0.036  Score=33.96  Aligned_cols=143  Identities=15%  Similarity=0.187  Sum_probs=74.9

Q ss_pred             EEEEEECCHHHHHHHHHHHHCCCCEEEECCCCEEEEECC-CEECCHHHHCCCCCCCEEEECCCCCCCCCEEEHHHHHHHH
Q ss_conf             899996898999999998562998999847520366048-8402202211234431133026651233112215677778
Q gi|254781095|r   40 EVMFQPQDIHDLKYFLTLLPSDIPITIVGLGSNILVRDA-GIRGVVLRLSNAGFSNIEVRNHCEMIVGARCSGKSLANSA  118 (318)
Q Consensus        40 ~~~~~p~s~~el~~~l~~~~~~~p~~iiG~GSNil~~D~-~~~G~vI~l~~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~  118 (318)
                      +-|+.|+|.+|..+++...  .-.-.++++||-+..... ..+.+.|.+....+..++..++ .++.||.+.+.++....
T Consensus         3 ~eY~rP~Sl~EA~~lL~~~--~~~a~~laGGt~L~~~~~~~~~~~~i~l~~ieL~~I~~~~~-~l~IGA~~t~~~l~~~~   79 (258)
T PRK09799          3 EQFFRPDSVEQALELKRRY--QDEAVWFAGGSKLNATPTRTDKKIAISLQDLELDWIDWDNG-ALRIGAMSRLQPLRDAR   79 (258)
T ss_pred             CCCCCCCCHHHHHHHHHHC--CCCCEEECCCCCHHHHHCCCCCCEEEECCCCCCCEEEECCC-EEEECCCCCHHHHHHCC
T ss_conf             5435979899999999768--99878974887465453366773478725367560897599-99994538299997584


Q ss_pred             HHH-HCCCHHCCCCHH-----HHHHHHHCCCCCCCCCEEEEEEEEEEEECCC---CCEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf             875-201200038725-----6632431157321583134566643441123---2100001233443100232246762
Q gi|254781095|r  119 LRH-GIGGFHFFYGIP-----GSIGGAAYMNAGANNCETSQYVVEVHGIDRK---GNQHVIPREQLKYQYRSSEITKDLI  189 (318)
Q Consensus       119 ~~~-gl~GlE~l~gIP-----GTVGGAi~mNAGayG~ei~d~i~~V~~~d~~---g~~~~l~~~e~~f~YR~S~~~~~~i  189 (318)
                      .-. .|.-.--..+=|     |||||.++ |+-.    .+|.+--...+|..   +.-.+++-+|+--++      ++.+
T Consensus        80 ~~~~~L~~a~~~i~s~qIRN~gTiGGnia-~a~p----~aD~~p~LlAl~A~v~~~~~~~ip~~dF~~g~------~~El  148 (258)
T PRK09799         80 FIPAALREALGFVYSRHVRNQSTIGGEIA-ARQE----ESVLLPVLLALDAELVFGNGETLSIEDYLACP------CDRL  148 (258)
T ss_pred             CCHHHHHHHHHHHCCHHHCCCEEEEEEEC-CCCC----CHHHHHHHHHCCCEEEECCCCEEEHHHHHCCC------CCEE
T ss_conf             21589999998646886604204532521-5788----52468999867989997689688799984799------9818


Q ss_pred             EEEEECC
Q ss_conf             0010023
Q gi|254781095|r  190 ITHVVLR  196 (318)
Q Consensus       190 Il~a~l~  196 (318)
                      ++++.+.
T Consensus       149 l~~I~ip  155 (258)
T PRK09799        149 LTEIIIK  155 (258)
T ss_pred             EEEEEEC
T ss_conf             9999963


No 31 
>TIGR03199 pucC xanthine dehydrogenase C subunit. This gene has been characterized in B. subtilis as the FAD binding-subunit of xanthine dehydrogenase (pucC), acting in conjunction with pucD, the molybdopterin-binding subunit and pucE, the FeS-binding subunit.
Probab=94.21  E-value=0.08  Score=31.79  Aligned_cols=138  Identities=15%  Similarity=0.252  Sum_probs=76.2

Q ss_pred             ECCHHHHHHHHHHHHCCCCEEEECCCCEEEEE--CCCE--ECCHHHHCC-CCCCCEEEECCCCCCCCCEEEHHHHHHH-H
Q ss_conf             68989999999985629989998475203660--4884--022022112-3443113302665123311221567777-8
Q gi|254781095|r   45 PQDIHDLKYFLTLLPSDIPITIVGLGSNILVR--DAGI--RGVVLRLSN-AGFSNIEVRNHCEMIVGARCSGKSLANS-A  118 (318)
Q Consensus        45 p~s~~el~~~l~~~~~~~p~~iiG~GSNil~~--D~~~--~G~vI~l~~-~~~~~i~~~~~~~i~v~AG~~~~~l~~~-~  118 (318)
                      |+|.+|+.+++...+ +  -.++++|+-+.+.  .+.+  +..+|.+.+ ..++.|+..++ .++.||.+.+.++.+. .
T Consensus         1 P~sl~Eal~ll~~~~-~--a~~laGGt~l~~~~~~~~~~~p~~lIdl~~I~eL~~I~~~~~-~l~IGA~vt~~~i~~~~~   76 (264)
T TIGR03199         1 PAALDEAWSLLEKAP-D--STFVSGSTLLQLQWEKGTLPMKQHLVSLEGIDELKGISTSDT-HVSIGALTTLNECRKNPL   76 (264)
T ss_pred             CCCHHHHHHHHHHCC-C--CEEEECCCHHHHHHHCCCCCCCCEEEECCCCCCCCCEEECCC-EEEEEECCCHHHHHHCHH
T ss_conf             999899999997599-9--979978750077673276578873897799800135897799-799952681999752978


Q ss_pred             HHHHCCCHHCC---CCHH-----HHHHHHHCCCCCCCCCEEEEEEE-----EEEEECCCCCEEEECCCCCCCCCCCCCCC
Q ss_conf             87520120003---8725-----66324311573215831345666-----43441123210000123344310023224
Q gi|254781095|r  119 LRHGIGGFHFF---YGIP-----GSIGGAAYMNAGANNCETSQYVV-----EVHGIDRKGNQHVIPREQLKYQYRSSEIT  185 (318)
Q Consensus       119 ~~~gl~GlE~l---~gIP-----GTVGGAi~mNAGayG~ei~d~i~-----~V~~~d~~g~~~~l~~~e~~f~YR~S~~~  185 (318)
                      .+..+..|--+   .|=|     |||||.++..++       |..-     ..++.-..+...+.+-++   .|+...+.
T Consensus        77 i~~~~p~L~~a~~~ig~~qIRN~gTiGGnia~~~~-------D~~p~Llal~A~v~~~~~~~~~~p~~~---f~~~~~~~  146 (264)
T TIGR03199        77 IKRALPCFVDAASAIAAPGVRNRATIGGNIASGIG-------DFIPALLVLGAELIVYQKELIRLPLGA---WLSEEDFK  146 (264)
T ss_pred             HHHHCHHHHHHHHHHCCHHHEEEEEECCCCCCCCC-------CHHHHHHHCCCEEEEECCCCEEEEHHH---HHHHCCCC
T ss_conf             88777699999987488632311465451257875-------477999975998999469708965788---66440478


Q ss_pred             CCCCEEEEECC
Q ss_conf             67620010023
Q gi|254781095|r  186 KDLIITHVVLR  196 (318)
Q Consensus       186 ~~~iIl~a~l~  196 (318)
                      .+.+++++.+.
T Consensus       147 ~~eii~~i~i~  157 (264)
T TIGR03199       147 PTAIVTRVIIG  157 (264)
T ss_pred             CCCEEEEEEEE
T ss_conf             77579999981


No 32 
>PRK11183 D-lactate dehydrogenase; Provisional
Probab=92.46  E-value=0.38  Score=27.51  Aligned_cols=123  Identities=18%  Similarity=0.172  Sum_probs=79.1

Q ss_pred             EEEECCCCCCCCC-CCCC-CEEEEEEEECCHHHHHHHHHHH-HCCCCEEEECCCCEEE-----EECC-CEE-CCHHHHCC
Q ss_conf             2775488001522-5766-1488999968989999999985-6299899984752036-----6048-840-22022112
Q gi|254781095|r   20 KFQENFPLKQITW-FRTG-GNAEVMFQPQDIHDLKYFLTLL-PSDIPITIVGLGSNIL-----VRDA-GIR-GVVLRLSN   89 (318)
Q Consensus        20 ~i~~n~~L~~~tt-~rvG-G~A~~~~~p~s~~el~~~l~~~-~~~~p~~iiG~GSNil-----~~D~-~~~-G~vI~l~~   89 (318)
                      .+.......+|.+ ||.| |.|-.+++|.|.-|+-++++.| +++  ..||=-++|+=     .+++ +|+ .+|| ++.
T Consensus        19 vlt~~~~t~~y~~G~R~G~G~alaVv~P~tL~e~W~vl~~cv~~~--~iiimQAaNTGLTgGStP~g~dYDR~ivi-int   95 (565)
T PRK11183         19 VLTDPAKTERYRKGFRSGQGDALAVVFPGTLLELWRVLQACVEAD--KIIIMQAANTGLTGGSTPNGNDYDRDIVI-IST   95 (565)
T ss_pred             EECCHHHCCCHHCCEECCCCCEEEEECCCCHHHHHHHHHHHHHCC--EEEEECCCCCCCCCCCCCCCCCCCCCEEE-EEC
T ss_conf             514744310011230116861789976852999999999999669--48997355668888889998888888799-971


Q ss_pred             CCCCCEEEE-CCCCCCCCCEEEHHHHHHHHHHHHCCC--HHCCCCHHHHHHHHHCCCCC
Q ss_conf             344311330-266512331122156777788752012--00038725663243115732
Q gi|254781095|r   90 AGFSNIEVR-NHCEMIVGARCSGKSLANSALRHGIGG--FHFFYGIPGSIGGAAYMNAG  145 (318)
Q Consensus        90 ~~~~~i~~~-~~~~i~v~AG~~~~~l~~~~~~~gl~G--lE~l~gIPGTVGGAi~mNAG  145 (318)
                      +.++.|... +..++.+-+|..+.+|-+.+...|..-  .=--+.|-.||=|.|+-|.|
T Consensus        96 ~r~~~i~li~~g~qvv~lpG~tL~~Le~~L~p~~RepHSviGSscigasv~gGvcnnSG  154 (565)
T PRK11183         96 LRLDKIQLLNNGKQVLCLPGTTLYQLEKALKPLGREPHSVIGSSCIGASVIGGICNNSG  154 (565)
T ss_pred             CCCCCEEECCCCCEEEECCCCCHHHHHHHHHHCCCCCCHHHCCCCCCCHHEEEEECCCC
T ss_conf             43264688268877998289779999998665189983110434336520122454886


No 33 
>COG4630 XdhA Xanthine dehydrogenase, iron-sulfur cluster and FAD-binding subunit A [Nucleotide transport and metabolism]
Probab=90.31  E-value=0.33  Score=27.87  Aligned_cols=162  Identities=18%  Similarity=0.230  Sum_probs=95.1

Q ss_pred             CCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHCCCCEEEECCCCEE--EEEC--CCEECCHHHHCC-CCCCCEEEECCC
Q ss_conf             00152257661488999968989999999985629989998475203--6604--884022022112-344311330266
Q gi|254781095|r   27 LKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLPSDIPITIVGLGSNI--LVRD--AGIRGVVLRLSN-AGFSNIEVRNHC  101 (318)
Q Consensus        27 L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~~~~p~~iiG~GSNi--l~~D--~~~~G~vI~l~~-~~~~~i~~~~~~  101 (318)
                      +.+--+.-+++-++-|+.|.+.+|+.+++...+   ...++-+++.+  -+..  ..+ ..||-+.. ..+..|+..++ 
T Consensus       191 ~~~~e~v~~~~~~~r~~~P~~l~D~a~l~aa~P---~AtivAGsTDvgLwVtk~mr~l-~~vi~v~~l~eL~~i~~~~~-  265 (493)
T COG4630         191 LRDTETVEVGSGDDRFIVPATLADFADLLAAHP---GATIVAGSTDVGLWVTKQMRDL-NPVIFVGHLAELRRIEVSTG-  265 (493)
T ss_pred             CCCCCEEEECCCCCEEEEECCHHHHHHHHHHCC---CCEEEECCCCHHHHHHHHHHHC-CCEEEECCHHHHHEEEECCC-
T ss_conf             568867985489850673153888999986299---9779805750436788887505-87699656364430553588-


Q ss_pred             CCCCCCEEEHHHHHHHHHHHHCCCHH----CCCCH----HHHHHHHHCCCCCCCCCEEEEE-----EEEEEEECCCC-CE
Q ss_conf             51233112215677778875201200----03872----5663243115732158313456-----66434411232-10
Q gi|254781095|r  102 EMIVGARCSGKSLANSALRHGIGGFH----FFYGI----PGSIGGAAYMNAGANNCETSQY-----VVEVHGIDRKG-NQ  167 (318)
Q Consensus       102 ~i~v~AG~~~~~l~~~~~~~gl~GlE----~l~gI----PGTVGGAi~mNAGayG~ei~d~-----i~~V~~~d~~g-~~  167 (318)
                      .++.|||+++.+.-+.+..+= --|-    -+.|-    -||+||.+. |    |+-|.|.     -...++...+| .-
T Consensus       266 ~l~iGAgvt~t~a~~~la~~~-P~l~~L~~r~gg~qvRN~gTlGGNIa-n----gSPIGDtPPaLIALgA~ltLr~g~~~  339 (493)
T COG4630         266 GLEIGAGVTYTQAYRALAGRY-PALGELWDRFGGEQVRNMGTLGGNIA-N----GSPIGDTPPALIALGATLTLRSGDGR  339 (493)
T ss_pred             CEEECCCCCHHHHHHHHHHHC-CHHHHHHHHHCCHHHHCCCCCCCCCC-C----CCCCCCCCCHHHHCCCEEEEEECCCC
T ss_conf             189766763999999987417-33899999850055302444356556-8----88688998124430768999846986


Q ss_pred             EEECCCCCCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             00012334431002322467620010023545
Q gi|254781095|r  168 HVIPREQLKYQYRSSEITKDLIITHVVLRGFP  199 (318)
Q Consensus       168 ~~l~~~e~~f~YR~S~~~~~~iIl~a~l~l~~  199 (318)
                      ++++-+|+..+|+....+...+|-++..-+..
T Consensus       340 RtlPLe~~Fi~Y~kqdr~pGEfVe~v~vP~~~  371 (493)
T COG4630         340 RTLPLEDYFIAYGKQDRQPGEFVEAVRVPLPA  371 (493)
T ss_pred             CCCCHHHHHHHHHHHCCCCCHHHHHEECCCCC
T ss_conf             44338999998624126763014324357788


No 34 
>KOG1262 consensus
Probab=88.44  E-value=0.19  Score=29.41  Aligned_cols=101  Identities=12%  Similarity=0.115  Sum_probs=67.0

Q ss_pred             CCEEEEC-CCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHH----HHHHHHHCCCCC----C--CCCEEEEEEEEEEEE
Q ss_conf             3113302-6651233112215677778875201200038725----663243115732----1--583134566643441
Q gi|254781095|r   93 SNIEVRN-HCEMIVGARCSGKSLANSALRHGIGGFHFFYGIP----GSIGGAAYMNAG----A--NNCETSQYVVEVHGI  161 (318)
Q Consensus        93 ~~i~~~~-~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIP----GTVGGAi~mNAG----a--yG~ei~d~i~~V~~~  161 (318)
                      +.++.+. ..+++|+.++...++++++...|++    |+-.|    -||||.+. ..|    +  ||- +.+.+.+-+++
T Consensus       113 dILeld~ekmtvrvEP~Vtmgqis~~lip~g~t----LaV~~EldDlTvGGLin-G~Gies~ShkyGl-fq~~~~aYEvV  186 (543)
T KOG1262         113 DILELDEEKMTVRVEPLVTMGQISKFLIPKGYT----LAVLPELDDLTVGGLIN-GVGIESSSHKYGL-FQHICTAYEVV  186 (543)
T ss_pred             HHHHCCHHCCEEEECCCCCHHHHHHHHCCCCCE----EEEECCCCCCEECCEEE-ECCCCCCCCHHHH-HHHHHHEEEEE
T ss_conf             777603200269834876598887775247731----43112346512323332-0122245402255-88654205899


Q ss_pred             CCCCCEEEECCC----CCCCCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             123210000123----344310023224676200100235456
Q gi|254781095|r  162 DRKGNQHVIPRE----QLKYQYRSSEITKDLIITHVVLRGFPE  200 (318)
Q Consensus       162 d~~g~~~~l~~~----e~~f~YR~S~~~~~~iIl~a~l~l~~~  200 (318)
                      ..+|++.+..++    |+.|+--+|.= .-...++|++++-|.
T Consensus       187 ladGelv~~t~dne~sdLfyaiPWSqG-TlgfLVaatiriIkv  228 (543)
T KOG1262         187 LADGELVRVTPDNEHSDLFYAIPWSQG-TLGFLVAATIRIIKV  228 (543)
T ss_pred             ECCCEEEEECCCCCCCCEEEECCCCCC-CHHEEEEEEEEEEEC
T ss_conf             628728983278666732797454467-120033317889963


No 35 
>TIGR00130 frhD coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit).; InterPro: IPR004411   This group of sequence are classed as unassigned endopeptidases belonging to the MEROPS peptidase family A31 (HybD endopeptidase family, clan AE). The sequences in this family represent the delta subunit, frhD, of the nickel-containing 8-hydroxy-5-deazaflavin reducing hydrogenase otherwise known as coenzyme F420-reducing hydrogenase. The delta subunit is not part of the active FRH heterotrimer, which contains three known subunits, alpha, beta, and gamma. The alpha subunit contains the metallo centre, which binds nickel. When nickel binds to the metallo centre the alpha subunit is processed to the active enzyme by cleavage at a conserved site near the C-terminus. This entry contains the archaeal hydrogenase maturation endopeptidases of family A31 that are thought to be responsible for these cleavages . At present there is no direct evidence to support there classification as peptidases. ; GO: 0008233 peptidase activity, 0006464 protein modification process.
Probab=64.21  E-value=2.7  Score=22.16  Aligned_cols=91  Identities=25%  Similarity=0.370  Sum_probs=56.3

Q ss_pred             EEEECCCCEEEEECCCEECCHHH-HCCCCCCCEEEECCCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCC
Q ss_conf             99984752036604884022022-11234431133026651233112215677778875201200038725663243115
Q gi|254781095|r   64 ITIVGLGSNILVRDAGIRGVVLR-LSNAGFSNIEVRNHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAYM  142 (318)
Q Consensus        64 ~~iiG~GSNil~~D~~~~G~vI~-l~~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~m  142 (318)
                      ++|+|=| |+||.|.||---||. |.+..+...-...++.-..-||+.-.+++.+.....                    
T Consensus         1 IlvlGcG-N~LfgDDGfG~~Vi~~L~k~~~~~~il~~~~v~~~DAGtgg~~l~~~l~~e~--------------------   59 (162)
T TIGR00130         1 ILVLGCG-NILFGDDGFGLEVIEKLKKLELDKLILKKENVEVIDAGTGGFDLVNTLVDEE--------------------   59 (162)
T ss_pred             CEEEEEC-CHHCCCCCCCHHHHHHHHHHCCCCCCCCCCCCEEEECCCCHHHHHEECCCCC--------------------
T ss_conf             9688663-6001368885766677764126600103378479976755456532100346--------------------


Q ss_pred             CCCCCCCEEEEEEEEEEEECC---CCCEEEECCCCCC----CCCCCC
Q ss_conf             732158313456664344112---3210000123344----310023
Q gi|254781095|r  143 NAGANNCETSQYVVEVHGIDR---KGNQHVIPREQLK----YQYRSS  182 (318)
Q Consensus       143 NAGayG~ei~d~i~~V~~~d~---~g~~~~l~~~e~~----f~YR~S  182 (318)
                             +-.+-+.=|.++|.   -|+++++..+|+-    +.|+-|
T Consensus        60 -------~~~kKiiiVD~i~fg~~PG~~~k~~v~~lpnna~k~~~~~   99 (162)
T TIGR00130        60 -------EKLKKIIIVDAIDFGLEPGTVKKIEVEELPNNALKKYLID   99 (162)
T ss_pred             -------CCCCEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCEEC
T ss_conf             -------8757689998870767986377615420666667863101


No 36 
>pfam01981 PTH2 Peptidyl-tRNA hydrolase PTH2. Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.
Probab=49.46  E-value=21  Score=16.56  Aligned_cols=38  Identities=8%  Similarity=0.253  Sum_probs=31.2

Q ss_pred             CCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEE
Q ss_conf             522576614889999689899999999856-29989998
Q gi|254781095|r   30 ITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIV   67 (318)
Q Consensus        30 ~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~ii   67 (318)
                      +..|.-.|.++......|+++|.++.+.++ .++|+.++
T Consensus        42 ~~~W~~~G~~KIvlkv~de~~L~~l~~~a~~~gl~~~~V   80 (116)
T pfam01981        42 LKAWEREGQKKIVLKVNSEEELLELKEKAKSLGLPTSLI   80 (116)
T ss_pred             HHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             999997799679997299999999999999849966999


No 37 
>PTZ00139 succinate dehydrogenase (flavoprotein) subunit; Provisional
Probab=48.90  E-value=21  Score=16.50  Aligned_cols=28  Identities=14%  Similarity=0.069  Sum_probs=11.2

Q ss_pred             EEEEEECCHHHHHHHHHHHHCCCCEEEE
Q ss_conf             8999968989999999985629989998
Q gi|254781095|r   40 EVMFQPQDIHDLKYFLTLLPSDIPITIV   67 (318)
Q Consensus        40 ~~~~~p~s~~el~~~l~~~~~~~p~~ii   67 (318)
                      |.++.=.-..-|...+..++.+.++.+|
T Consensus        36 DVlVIGsG~AGL~AAi~a~~~G~~V~ll   63 (622)
T PTZ00139         36 DAVVVGAGGAGLRAALGLSESGYKTACI   63 (622)
T ss_pred             CEEEECCCHHHHHHHHHHHHCCCCEEEE
T ss_conf             8799996699999999999769908999


No 38 
>PRK04322 peptidyl-tRNA hydrolase; Provisional
Probab=48.68  E-value=21  Score=16.48  Aligned_cols=38  Identities=11%  Similarity=0.211  Sum_probs=31.2

Q ss_pred             CCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEE
Q ss_conf             522576614889999689899999999856-29989998
Q gi|254781095|r   30 ITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIV   67 (318)
Q Consensus        30 ~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~ii   67 (318)
                      +..|.-+|.++......|+++|.++.+.++ .++|..++
T Consensus        42 ~~~W~~~G~~KIvlkv~~e~~L~~l~~~a~~~gl~~~~V   80 (116)
T PRK04322         42 FEEWLNEGQKKVVLKVNSEEELLELKKKAERLGLPTALI   80 (116)
T ss_pred             HHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             999995799479998599999999999999879968999


No 39 
>cd01824 Phospholipase_B_like Phospholipase-B_like. This subgroup of the SGNH-family of lipolytic enzymes may have both esterase and phospholipase-A/lysophospholipase activity.  It's members may be involved in the conversion of phosphatidylcholine to fatty acids and glycerophosphocholine, perhaps in the context of dietary lipid uptake. Members may be membrane proteins. The tertiary fold of the SGNH-hydrolases is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; Its active site closely resembles two of the three components of typical Ser-His-Asp(Glu) triad from other serine hydrolases.
Probab=46.51  E-value=23  Score=16.27  Aligned_cols=23  Identities=13%  Similarity=0.251  Sum_probs=11.0

Q ss_pred             EEECCCCCHHHHHHHHHHHHHHH
Q ss_conf             99689979999999999999999
Q gi|254781095|r  266 MINADNATGYDLEYLGEQVRKKV  288 (318)
Q Consensus       266 ivN~g~ata~di~~Li~~v~~~V  288 (318)
                      +.+....+-+++.+++...++..
T Consensus       199 l~~~~~~~~~~~~~~~~~~q~~~  221 (288)
T cd01824         199 LLGPTENSYQDLKKFYKEYQNEV  221 (288)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             57887033999999999999999


No 40 
>PRK05675 sdhA succinate dehydrogenase flavoprotein subunit; Reviewed
Probab=45.26  E-value=5.4  Score=20.26  Aligned_cols=22  Identities=27%  Similarity=0.404  Sum_probs=13.1

Q ss_pred             HHHHHHHH--CCCHHCCCCHHHHH
Q ss_conf             77788752--01200038725663
Q gi|254781095|r  115 ANSALRHG--IGGFHFFYGIPGSI  136 (318)
Q Consensus       115 ~~~~~~~g--l~GlE~l~gIPGTV  136 (318)
                      ...+.+.|  |..+||.--.|..+
T Consensus       206 ~amA~raGA~l~dmEfiQfhPT~l  229 (570)
T PRK05675        206 VGMALRAGVPVQDIEMWQFHPTGI  229 (570)
T ss_pred             HHHHHHCCCCCCCCHHHEEECCCC
T ss_conf             999998798464831715731322


No 41 
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=44.88  E-value=11  Score=18.23  Aligned_cols=77  Identities=23%  Similarity=0.332  Sum_probs=41.8

Q ss_pred             CCEEEECCCCEEEEECCCEECCHHH-HCCCCCCCEEEECCCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHH
Q ss_conf             9899984752036604884022022-112344311330266512331122156777788752012000387256632431
Q gi|254781095|r   62 IPITIVGLGSNILVRDAGIRGVVLR-LSNAGFSNIEVRNHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAA  140 (318)
Q Consensus        62 ~p~~iiG~GSNil~~D~~~~G~vI~-l~~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi  140 (318)
                      .++.|+|-| |+|++|+|+---++. |. .++.   ..+.. -.+..|+.--+|..+..+                    
T Consensus         4 ~rIlVLGiG-NiL~~DEG~GV~~v~~L~-~~~~---~p~~V-~liDGGT~G~~Ll~~le~--------------------   57 (195)
T PRK10264          4 QRVVVMGLG-NLLWADEGFGVRVAERLY-AHYH---WPEEV-EIVDGGTQGLNLLGYVES--------------------   57 (195)
T ss_pred             CEEEEEECC-CCCCCCCCHHHHHHHHHH-HHCC---CCCCC-EEEECCCCHHHHHHHHHC--------------------
T ss_conf             618999127-311235738999999999-8568---99882-898445319999999842--------------------


Q ss_pred             CCCCCCCCCEEEEEEEEEEEEC---CCCCEEEECCCCC
Q ss_conf             1573215831345666434411---2321000012334
Q gi|254781095|r  141 YMNAGANNCETSQYVVEVHGID---RKGNQHVIPREQL  175 (318)
Q Consensus       141 ~mNAGayG~ei~d~i~~V~~~d---~~g~~~~l~~~e~  175 (318)
                                 .|.+.=|+.++   +-|+++.+..+|+
T Consensus        58 -----------~d~LIvvDAV~~g~~PGtv~~~~~dev   84 (195)
T PRK10264         58 -----------ASHLLILDAIDYGLEPGTLRTYAGERI   84 (195)
T ss_pred             -----------CCEEEEEECCCCCCCCCEEEEEECCCC
T ss_conf             -----------997999846537999975999714304


No 42 
>cd02407 PTH2_family Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes.
Probab=43.45  E-value=25  Score=15.98  Aligned_cols=40  Identities=10%  Similarity=0.208  Sum_probs=32.9

Q ss_pred             CCCCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEE
Q ss_conf             01522576614889999689899999999856-29989998
Q gi|254781095|r   28 KQITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIV   67 (318)
Q Consensus        28 ~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~ii   67 (318)
                      .-+..|..+|.++......|+++|.++.+.++ .++|+.++
T Consensus        39 ~~~~~W~~~g~~KIvlkv~~e~~L~~l~~~a~~~~l~~~~v   79 (115)
T cd02407          39 TLLRAWELEGQKKVVLKVPSEEELLELAKKAKELGLPHSLI   79 (115)
T ss_pred             HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             99999871899559996799999999999999879988999


No 43 
>PTZ00244 serine/threonine-protein phosphatase PP1; Provisional
Probab=41.92  E-value=27  Score=15.83  Aligned_cols=48  Identities=15%  Similarity=0.064  Sum_probs=28.9

Q ss_pred             CCCCCCCCEEEEEEEEC-CHHHHHHHHHHH--HCCCCEEEECCCCEEEEECCCEEC
Q ss_conf             52257661488999968-989999999985--629989998475203660488402
Q gi|254781095|r   30 ITWFRTGGNAEVMFQPQ-DIHDLKYFLTLL--PSDIPITIVGLGSNILVRDAGIRG   82 (318)
Q Consensus        30 ~tt~rvGG~A~~~~~p~-s~~el~~~l~~~--~~~~p~~iiG~GSNil~~D~~~~G   82 (318)
                      =+-+++-+|.-.+-..+ ...||.++++..  +...++..||.     .-|.|..+
T Consensus        45 p~ll~i~~Pv~VvGDiHGq~~DLl~if~~~G~P~~~~YlFLGD-----YVDRG~~S   95 (294)
T PTZ00244         45 PMLLEIRPPVRVCGDTHGQYYDLLRIFEKCGFPPYSNYLFLGD-----YVDRGKHS   95 (294)
T ss_pred             CCEEEECCCEEEEEECCCCHHHHHHHHHHCCCCCCCCEEECCC-----CCCCCCCC
T ss_conf             9858857997999889999899999999749998656882155-----35777653


No 44 
>TIGR00090 TIGR00090 iojap homolog; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear..
Probab=39.10  E-value=30  Score=15.55  Aligned_cols=39  Identities=18%  Similarity=0.324  Sum_probs=31.3

Q ss_pred             EECCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEE
Q ss_conf             8715677089968997999999999999999999847540
Q gi|254781095|r  257 KISELHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILL  296 (318)
Q Consensus       257 ~vS~kHanfivN~g~ata~di~~Li~~v~~~V~~~~gi~L  296 (318)
                      .+|----+|||.+|. |...+..+++.+++.+++-+|+..
T Consensus        54 ~~s~l~d~~iICTG~-S~~qV~aiaD~~~~~~~~~hG~~~   92 (155)
T TIGR00090        54 GVSYLADYFIICTGT-SSKQVLAIADNIKKQLKEAHGLLP   92 (155)
T ss_pred             CCCEEECCCEEEECC-HHHHHHHHHHHHHHHHHHHCCEEE
T ss_conf             874211220333067-278999999999999998668222


No 45 
>TIGR00140 hupD hydrogenase expression/formation protein; InterPro: IPR004419   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of metallopeptidases belong to the MEROPS peptidase family A31 (HybD endopeptidase family, clan AE). The family contains the HyaD and HybD endopeptidases and their homologues. ; GO: 0046872 metal ion binding, 0016485 protein processing.
Probab=39.02  E-value=6.8  Score=19.62  Aligned_cols=53  Identities=30%  Similarity=0.429  Sum_probs=28.2

Q ss_pred             EEEECCCCEEEEECCCEECCHHHHCCCCCCCEEEEC--CCCCCCCCEEEHHHHHHHHHHH
Q ss_conf             999847520366048840220221123443113302--6651233112215677778875
Q gi|254781095|r   64 ITIVGLGSNILVRDAGIRGVVLRLSNAGFSNIEVRN--HCEMIVGARCSGKSLANSALRH  121 (318)
Q Consensus        64 ~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i~~~~--~~~i~v~AG~~~~~l~~~~~~~  121 (318)
                      +.|+|=| |+|.+|+|| |+  |.-..--..-+..+  .++ ..-.|+.--.|..+..+.
T Consensus         1 IlvLGiG-NiLwaDEG~-GV--R~vE~L~~~Y~f~~p~~V~-~lDGGT~G~~L~~~~~~~   55 (156)
T TIGR00140         1 ILVLGIG-NILWADEGF-GV--RLVEALQERYEFPDPHNVT-LLDGGTQGLYLLGLIEEA   55 (156)
T ss_pred             CEEEEEH-HHHHHHHHH-HH--HHHHHHHHCCCCCCCCEEE-EEECHHHHHHHHHHHHHC
T ss_conf             9685020-555742104-68--8999988404598996248-983535788999998737


No 46 
>pfam00390 malic Malic enzyme, N-terminal domain.
Probab=38.38  E-value=30  Score=15.48  Aligned_cols=50  Identities=20%  Similarity=0.317  Sum_probs=37.1

Q ss_pred             EEEEEEECCHHHHHHHHHHH-HCCCCEEEECCCCEEE-EECCCEECCHHHHC
Q ss_conf             88999968989999999985-6299899984752036-60488402202211
Q gi|254781095|r   39 AEVMFQPQDIHDLKYFLTLL-PSDIPITIVGLGSNIL-VRDAGIRGVVLRLS   88 (318)
Q Consensus        39 A~~~~~p~s~~el~~~l~~~-~~~~p~~iiG~GSNil-~~D~~~~G~vI~l~   88 (318)
                      --.|+.+++...+.++++-. ..++.+.++-.|+.+| +.|-|..|+-|..+
T Consensus        43 ~Glyis~~d~g~i~~~l~nwp~~~v~~iVVTDGerILGLGDlG~~Gm~I~iG   94 (182)
T pfam00390        43 RGLYTSIGNLGKIKDILKNWPEEDVRVIVVTDGERILGLGDLGVAGMPIMEG   94 (182)
T ss_pred             CEEEEECCCHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHH
T ss_conf             6589702665689999982885673599985673014667656576502445


No 47 
>pfam02731 SKIP_SNW SKIP/SNW domain. This domain is found in chromatin proteins.
Probab=37.61  E-value=23  Score=16.22  Aligned_cols=62  Identities=23%  Similarity=0.275  Sum_probs=36.5

Q ss_pred             CCCCCEEEEEEEECCCCCCCHHHHHHCCCCCCCCCCEEECCCCCEEEEECCCCCHHHHHHHHH-HHHHHHHHH
Q ss_conf             556670465889727898510002631868820667787156770899689979999999999-999999998
Q gi|254781095|r  220 QPIKEKTGGSTFKNPTGHSAWQLIEKSGCRGLEFGGAKISELHCNFMINADNATGYDLEYLGE-QVRKKVFNQ  291 (318)
Q Consensus       220 qP~~~~s~GSvFkNP~~~~A~~LIe~~GlKG~~iG~a~vS~kHanfivN~g~ata~di~~Li~-~v~~~V~~~  291 (318)
                      +-++.|.|=|-.|||.|+.-. |-.++--.|...-++.|         |.+-|.-++.|.+++ .+++.|..+
T Consensus        66 ~~WkIPp~ISNWKN~kGytIp-LDKRlaadgrglq~~~i---------NdkFa~lseAL~~Aer~AReev~~R  128 (158)
T pfam02731        66 EDWKIPPAISNWKNPKGYTIP-LDKRVAADGRGLQDVEI---------NDKFAKLSEALYIADRKAREEVRQR  128 (158)
T ss_pred             HCCCCCCCCCCCCCCCCCEEC-CHHHHHHCCCCCCCCCC---------CHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             716799875677288886407-05777642687777763---------1579999999999999999999999


No 48 
>PRK08401 L-aspartate oxidase; Provisional
Probab=37.58  E-value=31  Score=15.42  Aligned_cols=40  Identities=18%  Similarity=0.278  Sum_probs=17.3

Q ss_pred             ECCHHHHHHHHH-HHHC-CCCEEEECCCCEEEEECCCEECCHH
Q ss_conf             689899999999-8562-9989998475203660488402202
Q gi|254781095|r   45 PQDIHDLKYFLT-LLPS-DIPITIVGLGSNILVRDAGIRGVVL   85 (318)
Q Consensus        45 p~s~~el~~~l~-~~~~-~~p~~iiG~GSNil~~D~~~~G~vI   85 (318)
                      ..+-.++...+. .++. ++++ +-+--..+++.|+-..|+.+
T Consensus       116 ~~tG~~i~~~L~~~~~~~~v~~-~~~~~~~l~~~dg~v~Gv~~  157 (464)
T PRK08401        116 NETGKHLIPILEKHARELGVNF-IRGFAEELAIKNGKAYGVFL  157 (464)
T ss_pred             CCCHHHHHHHHHHHHHHCCCEE-EHHHHHHHEEECCEEEEEEE
T ss_conf             7658999999999999739857-86765757022898999998


No 49 
>LOAD_SKIP consensus
Probab=36.36  E-value=23  Score=16.23  Aligned_cols=62  Identities=23%  Similarity=0.254  Sum_probs=37.1

Q ss_pred             CCCCCEEEEEEEECCCCCCCHHHHHHCCCCCCCCCCEEECCCCCEEEEECCCCCHHHHHHHHH-HHHHHHHHH
Q ss_conf             556670465889727898510002631868820667787156770899689979999999999-999999998
Q gi|254781095|r  220 QPIKEKTGGSTFKNPTGHSAWQLIEKSGCRGLEFGGAKISELHCNFMINADNATGYDLEYLGE-QVRKKVFNQ  291 (318)
Q Consensus       220 qP~~~~s~GSvFkNP~~~~A~~LIe~~GlKG~~iG~a~vS~kHanfivN~g~ata~di~~Li~-~v~~~V~~~  291 (318)
                      +-++.|.|=|-.|||.|+.-. |-.++.--|...-++.|++++         |.-++.|.+++ .+++.|..+
T Consensus        70 ~~WkIPp~ISNWKN~kGyTIp-LDKRlaadgRglq~v~iNdkF---------a~lseAL~~Aer~AREev~~R  132 (168)
T LOAD_SKIP        70 NDWKIPPCVSNWKNPKGYTIP-LDKRLAADGRGLQDVEINDNF---------AKLSEALYIAEKKAREEVRAR  132 (168)
T ss_pred             HCCCCCCCCCCCCCCCCCCCC-CHHHHHHCCCCCCCCCHHHHH---------HHHHHHHHHHHHHHHHHHHHH
T ss_conf             707799875677388885207-057765237787753142679---------999999999999999999999


No 50 
>PRK07573 sdhA succinate dehydrogenase flavoprotein subunit; Reviewed
Probab=36.26  E-value=24  Score=16.19  Aligned_cols=88  Identities=8%  Similarity=-0.015  Sum_probs=50.7

Q ss_pred             EEEEEECCHHHHHHHHHHHHCCCCEEEE-----CCCCEEEEECCCEECCHHHHCCCCCCCEEEECCCCCCCCCEEEHHHH
Q ss_conf             8999968989999999985629989998-----47520366048840220221123443113302665123311221567
Q gi|254781095|r   40 EVMFQPQDIHDLKYFLTLLPSDIPITIV-----GLGSNILVRDAGIRGVVLRLSNAGFSNIEVRNHCEMIVGARCSGKSL  114 (318)
Q Consensus        40 ~~~~~p~s~~el~~~l~~~~~~~p~~ii-----G~GSNil~~D~~~~G~vI~l~~~~~~~i~~~~~~~i~v~AG~~~~~l  114 (318)
                      |+++.=.-..-|...++.++.+.++.++     ..+||.....+|+....-.. ... +.++..=..++.+|+|...+++
T Consensus        35 DVlVIGsG~AGL~AAi~aa~~G~~V~vl~~~~~~~~snS~~AqGGInAa~~~~-~~~-DS~e~H~~DTlkaG~gl~d~~~  112 (638)
T PRK07573         35 DIIVVGTGLAGASAAATLGELGYNVKVFCYQDSPRRAHSIAAQGGINAAKNYQ-NDG-DSVYRLFYDTVKGGDFRAREAN  112 (638)
T ss_pred             CEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHCCCC-CCC-CCHHHHHHHHHHHHCCCCCHHH
T ss_conf             88999966999999999997499569999228999620888755567404689-999-8989999999986278774999


Q ss_pred             HHHHHHHHCCCHHCC
Q ss_conf             777887520120003
Q gi|254781095|r  115 ANSALRHGIGGFHFF  129 (318)
Q Consensus       115 ~~~~~~~gl~GlE~l  129 (318)
                      ++.+++++-.-+++|
T Consensus       113 V~~l~~~ap~~I~~L  127 (638)
T PRK07573        113 VYRLAEVSVNIIDQC  127 (638)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999889999999


No 51 
>TIGR02587 TIGR02587 putative integral membrane protein TIGR02587; InterPro: IPR013416    This entry is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighbourhood. Proteins containing this entry appear to span the membrane seven times..
Probab=36.15  E-value=12  Score=18.09  Aligned_cols=24  Identities=25%  Similarity=0.376  Sum_probs=15.2

Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCEEEEE
Q ss_conf             038725663243115732158313456
Q gi|254781095|r  128 FFYGIPGSIGGAAYMNAGANNCETSQY  154 (318)
Q Consensus       128 ~l~gIPGTVGGAi~mNAGayG~ei~d~  154 (318)
                      -+-++|+|+|.++.   .++=++..|.
T Consensus       110 a~~~VP~slGa~La---r~qLG~~~~~  133 (284)
T TIGR02587       110 ALQGVPASLGAALA---RQQLGDTNDN  133 (284)
T ss_pred             HEECCCHHHHHHHH---HHHCCCCCCC
T ss_conf             20026367999998---7626788877


No 52 
>TIGR01008 rpsC_E_A ribosomal protein S3; InterPro: IPR005703   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 S3 is one of the proteins from the small ribosomal subunit. This family describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=35.47  E-value=11  Score=18.16  Aligned_cols=73  Identities=15%  Similarity=0.206  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHC----CCHHCCCCHHHHHHHHHCCCCCCCCCEEE--EEEEEEEE--EC-CCCCEEE--ECCCC-CCCCCC
Q ss_conf             67777887520----12000387256632431157321583134--56664344--11-2321000--01233-443100
Q gi|254781095|r  113 SLANSALRHGI----GGFHFFYGIPGSIGGAAYMNAGANNCETS--QYVVEVHG--ID-RKGNQHV--IPREQ-LKYQYR  180 (318)
Q Consensus       113 ~l~~~~~~~gl----~GlE~l~gIPGTVGGAi~mNAGayG~ei~--d~i~~V~~--~d-~~g~~~~--l~~~e-~~f~YR  180 (318)
                      .....+.++||    .++.++.-         +|||||-|+|+.  ==|.+-+.  .- .+|.+..  -+.++ .+=+|+
T Consensus        97 ~~iA~~LeRG~hFRRaAY~~~rr---------iM~aGAkGvEv~iSGKL~~eRAr~~KF~~G~~~k~G~Pa~~lV~~g~a  167 (204)
T TIGR01008        97 EKIARSLERGLHFRRAAYTAVRR---------IMEAGAKGVEVTISGKLTGERARTEKFAAGYLKKSGEPAEELVDKGFA  167 (204)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHH---------HHHCCCCEEEEEEECCHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHH
T ss_conf             99999984534778999999999---------982569527999827417877875210178489813876888776644


Q ss_pred             CCCCCCCCCEEEEE
Q ss_conf             23224676200100
Q gi|254781095|r  181 SSEITKDLIITHVV  194 (318)
Q Consensus       181 ~S~~~~~~iIl~a~  194 (318)
                      +-.+++.-+=+.|.
T Consensus       168 ~a~~k~GVlGV~V~  181 (204)
T TIGR01008       168 IALLKLGVLGVKVK  181 (204)
T ss_pred             EEECCCCEEEEEEE
T ss_conf             01148970226888


No 53 
>cd02430 PTH2 Peptidyl-tRNA hydrolase, type 2 (PTH2). Peptidyl-tRNA hydrolase (PTH) activity releases tRNA from the premature translation termination product peptidyl-tRNA, therefore allowing the tRNA and peptide to be reused in protein synthesis. PTH2 is present in archaea and eukaryotes.
Probab=31.44  E-value=39  Score=14.78  Aligned_cols=37  Identities=8%  Similarity=0.231  Sum_probs=30.2

Q ss_pred             CCCCCCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEE
Q ss_conf             522576614889999689899999999856-2998999
Q gi|254781095|r   30 ITWFRTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITI   66 (318)
Q Consensus        30 ~tt~rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~i   66 (318)
                      +..|.-+|.++......|+++|.++...++ .++|+.+
T Consensus        41 ~~~W~~~G~~KIvlkv~~e~~l~~l~~~a~~~~l~~~~   78 (115)
T cd02430          41 LRAWEREGQKKIVLKVNSEEELLELKKKAKSLGLPTSL   78 (115)
T ss_pred             HHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEE
T ss_conf             99999679956999779999999999999987997899


No 54 
>pfam08985 DUF1888 Domain of unknown function (DUF1888). This domain is found in a set of hypothetical bacterial proteins.
Probab=30.90  E-value=32  Score=15.38  Aligned_cols=23  Identities=9%  Similarity=-0.025  Sum_probs=12.1

Q ss_pred             EEEEEEEEEEECCCCCEEEECCCC
Q ss_conf             345666434411232100001233
Q gi|254781095|r  151 TSQYVVEVHGIDRKGNQHVIPREQ  174 (318)
Q Consensus       151 i~d~i~~V~~~d~~g~~~~l~~~e  174 (318)
                      +-.+|.+|++- .||....+-..|
T Consensus        69 fD~iIdaVtis-~dG~~l~LvD~D   91 (124)
T pfam08985        69 FDRVIDAVTLS-SDGTLAQLVDLD   91 (124)
T ss_pred             CCCEEEEEEEC-CCCEEEEEEECC
T ss_conf             31307679983-797089999657


No 55 
>TIGR01048 lysA diaminopimelate decarboxylase; InterPro: IPR002986   Pyridoxal-dependent decarboxylases that act on ornithine-, lysine-, arginine- and related substrates can be classified into different families on the basis of sequence similarity , . One of these families includes ornithine decarboxylase (ODC), which catalyses the transformation of ornithine into putrescine; prokaryotic diaminopimelic acid decarboxylase (DAPDC), which catalyses the conversion of diaminopimelic acid into lysine, the final step of lysine biosynthesis; Pseudomonas syringae pv. tabaci protein, tabA, which is probably involved in tabtoxin biosynthesis and is similar to DAPDC; and bacterial and plant biosynthetic arginine decarboxylase (ADC), which catalyses the transformation of arginine into agmatine, the first step in putrescine synthesis from arginine.   Although these proteins, which are known collectively as group IV decarboxylases , probably share a common evolutionary origin, their levels of sequence similarity are low, being confined to a few short conserved regions. These conserved motifs suggest a common structural arrangement for positioning of substrate and the cofactor pyridoxal 5'-phosphate among bacterial DAP decarboxylases, eukaryotic ornithine decarboxylases and arginine decarboxylases .   The structure of bacterial diaminopimelate decarboxylase has been determined . ; GO: 0008836 diaminopimelate decarboxylase activity, 0009089 lysine biosynthetic process via diaminopimelate.
Probab=30.84  E-value=21  Score=16.44  Aligned_cols=19  Identities=16%  Similarity=-0.041  Sum_probs=10.0

Q ss_pred             CCCEEEHHHHHHHHHHHHC
Q ss_conf             3311221567777887520
Q gi|254781095|r  105 VGARCSGKSLANSALRHGI  123 (318)
Q Consensus       105 v~AG~~~~~l~~~~~~~gl  123 (318)
                      |-=..+...+.+.+++.|+
T Consensus        59 A~KAn~Nl~~~~~la~~G~   77 (431)
T TIGR01048        59 AVKANSNLALLRLLAELGS   77 (431)
T ss_pred             EHHHHCCHHHHHHHHHCCC
T ss_conf             4314076889999996388


No 56 
>TIGR02082 metH methionine synthase; InterPro: IPR011822   Vitamin B12 dependent methionine synthase 2.1.1.13 from EC (5-methyltetrahydrofolate--homocysteine S-methyltransferase) catalyses the conversion of 5-methyltetrahydrofolate and L-homocysteine to tetrahydrofolate and L-methionine as the final step in de novo methionine biosynthesis. The enzyme requires methylcobalamin as a cofactor. In humans, defects in this enzyme are the cause of autosomal recessive inherited methylcobalamin deficiency (CBLG), which causes mental retardation, macrocytic anemia and homocystinuria. Mild deficiencies in activity may result in mild hyperhomocysteinemia, and mutations in the enzyme may be involved in tumorigenesis. Vitamin B12 dependent methionine synthase is found in prokaryotes and eukaryotes, but in prokaryotes the cofactor is cobalamin.   This enzyme is a large protein composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and tetrahydrofolate , the third module binds the B12 cofactor , and the C-terminal module (activation domain) binds S-adenosylmethionine. The activation domain is essential for the reductive activation of the enzyme. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain . The activation domain adopts an unusual alpha/beta fold.Recent studies suggest that this enzyme exists as an ensemble of conformations with equilibria dependent on the oxidation and methylation state of the cobalamin and on the concentrations of substrates or products .; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0050897 cobalt ion binding, 0009086 methionine biosynthetic process.
Probab=30.66  E-value=41  Score=14.70  Aligned_cols=32  Identities=22%  Similarity=0.433  Sum_probs=14.2

Q ss_pred             CEEEEEEEECCHHHHHH---HHH-----HHHC--CCCEEEECC
Q ss_conf             14889999689899999---999-----8562--998999847
Q gi|254781095|r   37 GNAEVMFQPQDIHDLKY---FLT-----LLPS--DIPITIVGL   69 (318)
Q Consensus        37 G~A~~~~~p~s~~el~~---~l~-----~~~~--~~p~~iiG~   69 (318)
                      |=||.+. ++|+-|+.+   ++-     |.+.  .+|+++=|-
T Consensus       162 GGvDllL-iET~fDtLnaKAAlfA~~~~F~~~g~~lPi~iSGt  203 (1265)
T TIGR02082       162 GGVDLLL-IETVFDTLNAKAALFAAETVFEEKGRELPIMISGT  203 (1265)
T ss_pred             CCCHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
T ss_conf             2603547-74799999999999999999997289787688602


No 57 
>COG2513 PrpB PEP phosphonomutase and related enzymes [Carbohydrate transport and metabolism]
Probab=30.64  E-value=19  Score=16.82  Aligned_cols=14  Identities=29%  Similarity=0.221  Sum_probs=9.2

Q ss_pred             CCCCCCEEEEEEEE
Q ss_conf             32158313456664
Q gi|254781095|r  144 AGANNCETSQYVVE  157 (318)
Q Consensus       144 AGayG~ei~d~i~~  157 (318)
                      ||+-|..|-|.+..
T Consensus       105 aG~agi~iEDq~~p  118 (289)
T COG2513         105 AGAAGIHIEDQVGP  118 (289)
T ss_pred             CCCCEEEEEECCCC
T ss_conf             58626645322550


No 58 
>TIGR00421 ubiX_pad polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases; InterPro: IPR004507   This family contains flavoproteins, which are aromatic acid decarboxylases. An example is the Saccharomyces cerevisiae gene, PAD1 that encodes phenylacrylic acid decarboxylase. Mutations of this gene are viable and confer resistance to cinnamic acid. ; GO: 0016831 carboxy-lyase activity.
Probab=30.62  E-value=39  Score=14.82  Aligned_cols=23  Identities=26%  Similarity=0.277  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCEEE
Q ss_conf             99999999999999998475400
Q gi|254781095|r  275 YDLEYLGEQVRKKVFNQSGILLE  297 (318)
Q Consensus       275 ~di~~Li~~v~~~V~~~~gi~Le  297 (318)
                      +.+.+|++++-.+|.+.+||+..
T Consensus       154 kS~~Dl~~~~VgR~LD~lGI~~d  176 (181)
T TIGR00421       154 KSVEDLIDFIVGRVLDQLGIEND  176 (181)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             88788986779877776244378


No 59 
>PRK07512 L-aspartate oxidase; Provisional
Probab=30.08  E-value=31  Score=15.42  Aligned_cols=27  Identities=11%  Similarity=0.138  Sum_probs=11.4

Q ss_pred             CCCCCEEEHHHHHHHHHHHHCCCHHCC
Q ss_conf             123311221567777887520120003
Q gi|254781095|r  103 MIVGARCSGKSLANSALRHGIGGFHFF  129 (318)
Q Consensus       103 i~v~AG~~~~~l~~~~~~~gl~GlE~l  129 (318)
                      +.+|.|...+++++..++++...++||
T Consensus        72 l~aG~gl~d~~~v~~l~~~a~~~i~~L   98 (507)
T PRK07512         72 LAAGAGLCDEAVARRIAAEAPAAIEDL   98 (507)
T ss_pred             HHHCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             996478788999999999899999999


No 60 
>TIGR02687 TIGR02687 conserved hypothetical protein TIGR02687; InterPro: IPR014060   Members of this family are uncharacterised proteins sporadically distributed in bacteria and archaea, about 880 amino acids in length. Proteins in this entry are encoded by genes that are repeatedly found upstream of another uncharacterised gene which encodes proteins of about 470 amino acids in length (see IPR014061 from INTERPRO)..
Probab=29.68  E-value=39  Score=14.80  Aligned_cols=72  Identities=21%  Similarity=0.259  Sum_probs=38.3

Q ss_pred             ECCHHHHHHHHHHHHCCCCEEEECCCCEEEE-ECCCEECCHHHHCCCCCCCEEEECCCCCCCCCEE-EHHHHHHHHHH-H
Q ss_conf             6898999999998562998999847520366-0488402202211234431133026651233112-21567777887-5
Q gi|254781095|r   45 PQDIHDLKYFLTLLPSDIPITIVGLGSNILV-RDAGIRGVVLRLSNAGFSNIEVRNHCEMIVGARC-SGKSLANSALR-H  121 (318)
Q Consensus        45 p~s~~el~~~l~~~~~~~p~~iiG~GSNil~-~D~~~~G~vI~l~~~~~~~i~~~~~~~i~v~AG~-~~~~l~~~~~~-~  121 (318)
                      -+++.||.+++++.-..      =+|||+|| +|.||   +-+  .   ..++..|...+-+..-- .+..--||..- +
T Consensus       654 ~eai~eL~~Lv~~l~~r------ln~~~ilVTADHGF---lYq--~---~~l~~~Dk~~~~~~~~~r~l~~~kRFiLgd~  719 (911)
T TIGR02687       654 EEAIVELKKLVKKLINR------LNGTNILVTADHGF---LYQ--E---DPLEEADKSALDAKPESRILKAKKRFILGDK  719 (911)
T ss_pred             HHHHHHHHHHHHHHHCC------CCCCEEEEECCCCH---HHH--H---HHHHHCCCCEEECCCCCCEECCCCCEEECCC
T ss_conf             99999999999998411------14574588415561---445--3---1354277502110377522016576775055


Q ss_pred             HCCCHHCCC
Q ss_conf             201200038
Q gi|254781095|r  122 GIGGFHFFY  130 (318)
Q Consensus       122 gl~GlE~l~  130 (318)
                      +|+--.++.
T Consensus       720 ~L~~~~~~~  728 (911)
T TIGR02687       720 GLAEEDSLW  728 (911)
T ss_pred             CCCCCCCCC
T ss_conf             778774202


No 61 
>cd02810 DHOD_DHPD_FMN Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain.  DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of
Probab=29.25  E-value=43  Score=14.55  Aligned_cols=24  Identities=8%  Similarity=0.045  Sum_probs=12.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             997999999999999999999847
Q gi|254781095|r  270 DNATGYDLEYLGEQVRKKVFNQSG  293 (318)
Q Consensus       270 g~ata~di~~Li~~v~~~V~~~~g  293 (318)
                      |+=|...+..+.-..-..+++..+
T Consensus       218 gGlSG~~i~~~al~~v~~~~~~~~  241 (289)
T cd02810         218 GGLSGAPIRPLALRWVARLAARLQ  241 (289)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             523662778899999999999749


No 62 
>PTZ00306 NADH-dependent fumarate reductase; Provisional
Probab=29.07  E-value=43  Score=14.53  Aligned_cols=92  Identities=11%  Similarity=0.116  Sum_probs=47.3

Q ss_pred             EEEEEEEECCHHHHHHHHHHHHCCCCEEEECC----CCEEEEECCCEECCHHHHCCCCCCCEEEE----CCCCCCCCCEE
Q ss_conf             48899996898999999998562998999847----52036604884022022112344311330----26651233112
Q gi|254781095|r   38 NAEVMFQPQDIHDLKYFLTLLPSDIPITIVGL----GSNILVRDAGIRGVVLRLSNAGFSNIEVR----NHCEMIVGARC  109 (318)
Q Consensus        38 ~A~~~~~p~s~~el~~~l~~~~~~~p~~iiG~----GSNil~~D~~~~G~vI~l~~~~~~~i~~~----~~~~i~v~AG~  109 (318)
                      |++..+.=.--.-|.+.++..+.+.++.+|=.    |=|.+.+.+|++|.--+.-..  ..|.+.    -+.++..|-|-
T Consensus       409 P~rVIVVGsGlAGLSAAIeA~e~GakVVLLEKmp~lGGNS~KASSGINgAgT~~Qk~--~GI~DS~ElF~~DTlKSGkG~  486 (1167)
T PTZ00306        409 PARVIVVGGGLAGCSAAIEAASCGAQVILLEKEAKLGGNSAKATSGINGWGTRAQAK--QDVLDGGKFFERDTHLSGKGG  486 (1167)
T ss_pred             CCCEEEECCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHCCCCCCCCCHHHHH--HCCCCCHHHHHHHHHHHCCCC
T ss_conf             986899897579999999999779957999578988874003315736689777897--099888889999988733789


Q ss_pred             E-HHHHHHHHHHHHCCCHHCCCC
Q ss_conf             2-156777788752012000387
Q gi|254781095|r  110 S-GKSLANSALRHGIGGFHFFYG  131 (318)
Q Consensus       110 ~-~~~l~~~~~~~gl~GlE~l~g  131 (318)
                      . .+.|++.+.++....+|||..
T Consensus       487 n~DPeLVr~La~~SadAIeWL~e  509 (1167)
T PTZ00306        487 HCDPGLVKTLSVKSADAISWLSS  509 (1167)
T ss_pred             CCCHHHHHHHHHCCHHHHHHHHH
T ss_conf             99979999999734889999998


No 63 
>TIGR01830 3oxo_ACP_reduc 3-oxoacyl-(acyl-carrier-protein) reductase; InterPro: IPR011284   This entry represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis found in many plant and bacterial species. This enzyme is involved in type II fatty acid biosynthesis, where the individual metabolic transformations are carried out by different enzymes rather than by a single enzyme as occurs in type I fatty acid biosynthesis .   Structural studies show that the enzyme is a tetramer which forms a typical Rossman fold , . Unlike other members of the short-chain dehydrogenase/reductase superfamily, the enzyme undergoes a marked conformational change upon binding of the NADP(H)cofactor. This conformational change aligns the side chains of the catalytic triad at the active site in an active conformation and increases the affinity of the enzyme for its substrate.; GO: 0004316 3-oxoacyl-[acyl-carrier-protein] reductase activity, 0051287 NAD binding, 0006633 fatty acid biosynthetic process.
Probab=28.46  E-value=13  Score=17.85  Aligned_cols=82  Identities=20%  Similarity=0.310  Sum_probs=43.4

Q ss_pred             CCCEEEEE-EEECCHHHHHHHHHHH-HC-CCCEEEECCCCEEEEECCCE--ECCHHHHCCCCCCCEEEECCCCCCCCCEE
Q ss_conf             66148899-9968989999999985-62-99899984752036604884--02202211234431133026651233112
Q gi|254781095|r   35 TGGNAEVM-FQPQDIHDLKYFLTLL-PS-DIPITIVGLGSNILVRDAGI--RGVVLRLSNAGFSNIEVRNHCEMIVGARC  109 (318)
Q Consensus        35 vGG~A~~~-~~p~s~~el~~~l~~~-~~-~~p~~iiG~GSNil~~D~~~--~G~vI~l~~~~~~~i~~~~~~~i~v~AG~  109 (318)
                      -|+.|..+ +...+.|++.++++.+ ++ ++         .+|+.-.|+  |++.++++...|+.+-  +-+ | -++=-
T Consensus        46 ~G~~a~~~~~dvs~~~~~~~~~~~~~~~~Gi---------DiLVNNAGITrD~Ll~RMk~edWd~Vi--~~N-L-~g~F~  112 (238)
T TIGR01830        46 LGVKAAGVVLDVSDREDVKALVEEAEEELGI---------DILVNNAGITRDNLLMRMKEEDWDAVI--NVN-L-KGVFN  112 (238)
T ss_pred             CCCEEEEEEECCCCHHHHHHHHHHHHHHHCC---------EEEEECCCCCCCCHHCCCCHHHHHHHH--HHH-H-HHHHH
T ss_conf             6975999960388889999999999998299---------089978741343010048855689999--861-2-66878


Q ss_pred             EHHHHHHHHHHHHCCCHHCC
Q ss_conf             21567777887520120003
Q gi|254781095|r  110 SGKSLANSALRHGIGGFHFF  129 (318)
Q Consensus       110 ~~~~l~~~~~~~gl~GlE~l  129 (318)
                      ......+.+.++-.+=.=+.
T Consensus       113 ~t~~v~~~M~K~R~GrIINi  132 (238)
T TIGR01830       113 LTQAVLRPMIKQRSGRIINI  132 (238)
T ss_pred             HHHHHHHHHHHHCCCCEEEE
T ss_conf             88998898875067434861


No 64 
>COG1775 HgdB Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]
Probab=28.02  E-value=45  Score=14.41  Aligned_cols=47  Identities=30%  Similarity=0.247  Sum_probs=28.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCC-EEEECCEEEECCCC-HHHHHHHCC
Q ss_conf             979999999999999999998475-40042289621683-568886325
Q gi|254781095|r  271 NATGYDLEYLGEQVRKKVFNQSGI-LLEWEIKRLGDFFD-HQIVDATKI  317 (318)
Q Consensus       271 ~ata~di~~Li~~v~~~V~~~~gi-~Le~Ev~~iG~f~~-~~~~~~~~~  317 (318)
                      .+...++..|++.++++|.+-.|. .|-.++++++++-+ -++++-+|.
T Consensus       212 d~~~~~l~~l~eelekr~~eg~~~Ri~~~g~p~~~~~~~v~~~~e~~~~  260 (379)
T COG1775         212 DAFIEELEELIEELEKRVEEGEGPRILITGIPILGDNPKVWEILEEVGE  260 (379)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCHHHHHHHHCC
T ss_conf             8899999999999998786068865885067555788646588875145


No 65 
>TIGR03140 AhpF alkyl hydroperoxide reductase, F subunit. This enzyme is the partner of the peroxiredoxin (alkyl hydroperoxide reductase) AhpC which contains the peroxide-reactive cysteine. AhpF contains the reductant (NAD(P)H) binding domain (pfam00070) and presumably acts to resolve the disulfide which forms after oxidation of the active site cysteine in AphC. This proteins contains two paired conserved cysteine motifs, CxxCP and CxHCDGP.
Probab=27.64  E-value=46  Score=14.37  Aligned_cols=68  Identities=19%  Similarity=0.272  Sum_probs=42.0

Q ss_pred             CCCCCCEEEHHHHHHHHHHHHCC----------------CHHCCCCHHHHHHHHHCCC----CCCCCCEEEEEEEEEEEE
Q ss_conf             51233112215677778875201----------------2000387256632431157----321583134566643441
Q gi|254781095|r  102 EMIVGARCSGKSLANSALRHGIG----------------GFHFFYGIPGSIGGAAYMN----AGANNCETSQYVVEVHGI  161 (318)
Q Consensus       102 ~i~v~AG~~~~~l~~~~~~~gl~----------------GlE~l~gIPGTVGGAi~mN----AGayG~ei~d~i~~V~~~  161 (318)
                      .+.+|+|-.--.-+-|+++.||.                ..|++.|+|.+-|--+..+    |-.||.++... ..|.-+
T Consensus       215 viIIGgGPAGlsAAIYaaR~gl~t~vi~~~~GGqv~~t~~IeNypG~~~i~G~eL~~~~~~qa~~~gv~~~~~-~~v~~i  293 (515)
T TIGR03140       215 VLVVGGGPAGAAAAIYAARKGLRTAMVAERIGGQVKDTVGIENLISVPYTTGSQLAANLEEHIKQYPIDLMEN-QRAKKI  293 (515)
T ss_pred             EEEECCCHHHHHHHHHHHHCCCCEEEEECCCCCCCEECCCEEECCCCCCCCHHHHHHHHHHHHHHCCCEEEEC-CEEEEE
T ss_conf             8998967899999999997799769992487753130346004489877757999999999999749689913-369999


Q ss_pred             CCCCCEEEE
Q ss_conf             123210000
Q gi|254781095|r  162 DRKGNQHVI  170 (318)
Q Consensus       162 d~~g~~~~l  170 (318)
                      +.++..+.+
T Consensus       294 ~~~~~~~~v  302 (515)
T TIGR03140       294 ETEDGLIVV  302 (515)
T ss_pred             ECCCCCEEE
T ss_conf             727981899


No 66 
>COG1252 Ndh NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]
Probab=27.47  E-value=46  Score=14.35  Aligned_cols=26  Identities=23%  Similarity=0.362  Sum_probs=18.3

Q ss_pred             CCCCCCCCCCEEEEEEEECCHHHHHH
Q ss_conf             01522576614889999689899999
Q gi|254781095|r   28 KQITWFRTGGNAEVMFQPQDIHDLKY   53 (318)
Q Consensus        28 ~~~tt~rvGG~A~~~~~p~s~~el~~   53 (318)
                      +..++|++-|-+++-+..++.+|-.+
T Consensus       109 s~~~~fgi~G~~E~a~~lks~edA~~  134 (405)
T COG1252         109 SETNYFGIPGAAEYAFGLKTLEDALR  134 (405)
T ss_pred             CCCCCCCCCCHHHHCCCCCCHHHHHH
T ss_conf             76676899787870777788999999


No 67 
>KOG1342 consensus
Probab=27.06  E-value=47  Score=14.30  Aligned_cols=13  Identities=38%  Similarity=0.647  Sum_probs=6.8

Q ss_pred             HHHHHHHCCCCCC
Q ss_conf             6632431157321
Q gi|254781095|r  134 GSIGGAAYMNAGA  146 (318)
Q Consensus       134 GTVGGAi~mNAGa  146 (318)
                      ||+.||..-|-|.
T Consensus       114 gSl~aa~kLn~~~  126 (425)
T KOG1342         114 GSLNAAQKLNRGE  126 (425)
T ss_pred             CCHHHHHHHCCCC
T ss_conf             4359999737777


No 68 
>pfam04283 CheF-arch Chemotaxis signal transduction system protein F from archaea. This is a family of proteins that are archaea-specific components of the bacterial-like chemotaxis signal transduction system of archaea. In H. salinarum, the CheF proteins interact with the chemotaxis proteins CheY, CheD and CheC2 as well as the flagella-accessory proteins FlaCE and FlaD, and are essential for any tactic response. CheF probably functions at the interface between the bacterial-like chemotaxis signal transduction system and the archaeal flagellar apparatus.
Probab=26.15  E-value=49  Score=14.20  Aligned_cols=43  Identities=12%  Similarity=0.228  Sum_probs=35.8

Q ss_pred             CCCCCEEE-HHHHHHHHHHHHCCCHHCCCCHHHHHHHHHCCCCC
Q ss_conf             12331122-15677778875201200038725663243115732
Q gi|254781095|r  103 MIVGARCS-GKSLANSALRHGIGGFHFFYGIPGSIGGAAYMNAG  145 (318)
Q Consensus       103 i~v~AG~~-~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~mNAG  145 (318)
                      +.+.++.. ...+...+.+.-|-|-+-+.--|..+||.+-|++-
T Consensus        86 ~~i~~~~~~i~~F~~~lF~alLng~~v~v~hpAi~GGvV~~d~~  129 (220)
T pfam04283        86 VLISPGDSTIDTFETKLFKALLDGTEVLVLHPAIVGGVVSTDSK  129 (220)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHCCEEEEEECCCEECCEECCCCC
T ss_conf             99967930789999999998408848999746101754057883


No 69 
>TIGR00430 Q_tRNA_tgt queuine tRNA-ribosyltransferase; InterPro: IPR004803   The queuine tRNA-ribosyltransferase (tgt) 2.4.2.29 from EC catalyzes an exchange for the guanine base at position 34 of many tRNAs; this nucleotide is subsequently modified to queuosine. The archaea have a closely related enzyme (IPR004804 from INTERPRO) that catalyses a base exchange for guanine at position 15 in some tRNAs, a site that is subsequently converted to the archaeal-specific modified base archaeosine (7-formamidino-7-deazaguanosine), while Archaeoglobus fulgidus has both enzymes. ; GO: 0008479 queuine tRNA-ribosyltransferase activity, 0008616 queuosine biosynthetic process.
Probab=25.24  E-value=25  Score=15.98  Aligned_cols=134  Identities=22%  Similarity=0.278  Sum_probs=71.1

Q ss_pred             EEEEECC-CCCEEEECCCC-CCCCCCCCCCCCCCCEEEE-ECCCCCCCCCCCHHHHHHCCCCCCC----CCCCC--CEEE
Q ss_conf             4344112-32100001233-4431002322467620010-0235456543100122210011000----15566--7046
Q gi|254781095|r  157 EVHGIDR-KGNQHVIPREQ-LKYQYRSSEITKDLIITHV-VLRGFPESQNIISAAIANVCHHRET----VQPIK--EKTG  227 (318)
Q Consensus       157 ~V~~~d~-~g~~~~l~~~e-~~f~YR~S~~~~~~iIl~a-~l~l~~~~~~~i~~~~~~~~~~R~~----~qP~~--~~s~  227 (318)
                      .|..=++ ||....++++. ++..|-   |..| ||-.- ...-.+.+.+..++.++...+|-+.    .+-.+  ..++
T Consensus       141 GV~Fk~p~dG~~~~ltPek~~~IQ~~---LGSD-IiM~fDeC~p~~ad~~~~~~s~~rt~rWA~~~l~~~~~~~~G~~~~  216 (415)
T TIGR00430       141 GVHFKSPIDGSKIFLTPEKSMEIQYA---LGSD-IIMAFDECTPYPADYDYAEKSTERTLRWAERCLEAHDRRKEGNKQA  216 (415)
T ss_pred             CEEECCCCCCCEEEECHHHHHHHHHH---HCCC-EEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             60435788887020185789999986---2897-7987026887886578999999987999999998620247887775


Q ss_pred             ------EEEEECCCCCCCHHHHHHCCCCCCCCCCE-EECCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEECC
Q ss_conf             ------58897278985100026318688206677-87156770899689979999999999999999998475400422
Q gi|254781095|r  228 ------GSTFKNPTGHSAWQLIEKSGCRGLEFGGA-KISELHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILLEWEI  300 (318)
Q Consensus       228 ------GSvFkNP~~~~A~~LIe~~GlKG~~iG~a-~vS~kHanfivN~g~ata~di~~Li~~v~~~V~~~~gi~Le~Ev  300 (318)
                            |++|++--..||-.||+ .|+-||-|||. .|            |-+.+++++.++++-=.       ..+.=+
T Consensus       217 LFgIvQGg~y~dLR~~S~~~L~~-~df~GYAIGGLisV------------GEp~~~m~~il~~~~PL-------lP~dKP  276 (415)
T TIGR00430       217 LFGIVQGGTYEDLRSQSAKGLIE-LDFPGYAIGGLISV------------GEPKDDMLRILEHTAPL-------LPKDKP  276 (415)
T ss_pred             EEEEEECCHHHHHHHHHHHHHHH-CCCCCCEEECEEEC------------CCCHHHHHHHHHHHHCC-------CCCCCC
T ss_conf             34687073048889999999986-18895045032412------------58889988899875035-------777688


Q ss_pred             EEE-ECCCCHHHHHH
Q ss_conf             896-21683568886
Q gi|254781095|r  301 KRL-GDFFDHQIVDA  314 (318)
Q Consensus       301 ~~i-G~f~~~~~~~~  314 (318)
                      |++ |=-.++.++||
T Consensus       277 RYLMGvG~p~~l~~a  291 (415)
T TIGR00430       277 RYLMGVGTPEDLLDA  291 (415)
T ss_pred             CCCCCCCCHHHHHHH
T ss_conf             402054888999999


No 70 
>TIGR03004 ectoine_ehuC ectoine/hydroxyectoine ABC transporter, permease protein EhuC; InterPro: IPR014342   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    Members of this entry are presumed to act as permease subunits of ectoine ABC transporters. Operons containing this gene also contain other genes of the ABC transporter and are typically found next to either ectoine utilization or ectoine biosynthesis operons. Permease subunits EhuC and EhuD are homologues..
Probab=25.05  E-value=16  Score=17.19  Aligned_cols=21  Identities=29%  Similarity=0.305  Sum_probs=14.6

Q ss_pred             HHHHHHH-HHCCCCCCCCCEEE
Q ss_conf             2566324-31157321583134
Q gi|254781095|r  132 IPGSIGG-AAYMNAGANNCETS  152 (318)
Q Consensus       132 IPGTVGG-Ai~mNAGayG~ei~  152 (318)
                      -|=|+|= ++..|+||||-||.
T Consensus        80 ~P~t~gv~~Lglh~GaYGAEiv  101 (216)
T TIGR03004        80 DPLTVGVLALGLHVGAYGAEIV  101 (216)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHH
T ss_conf             5189999999973265016888


No 71 
>TIGR00072 hydrog_prot hydrogenase maturation protease; InterPro: IPR000671   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised . More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin  and archaean preflagellin have been described , .   Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure.   Metalloproteases are the most diverse of the four main types of protease, with more than 30 families identified to date . In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as abXHEbbHbc, where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . At one step of this process, after nickel incorporation, each hydrogenase isoenzyme is processed by proteolytic cleavage at the C-terminal end by the corresponding hydrogenase maturation endopeptidase . For example, Escherichia coli HycI is involved in processing of pre-HycE (the large subunit of hydrogenase 3) , ; HybD is involved in processing of pre-HybC (the large subunit of hydrogenase 2) ; and HyaD is assumed to be involved in processing of the large subunit of hydrogenase 1. This group represents metallopeptidases of the MEROPS peptidase family A31 (HybD endopeptidase family, clan AE).   The cleavage site is after a His or an Arg, liberating a short peptide , . This cleavage occurs only in the presence of nickel, and the endopeptidase probably uses the metal in the large subunit of [NiFe]-hydrogenases as a recognition motif . There is no direct evidence for the active site or substrate-binding site, but there are predictions based on an available structure .   Nomenclature note: the following names are used in different organisms for members of this group: HycI, HybD, HyaD, HoxM, HoxW, HupD, HynC, HupM, VhoD, VhtD . Gene/protein names are sometimes used interchangeably to designate various "hydrogenase cluster" proteins unrelated to each other in various organisms. For example, the following names are used for members of this group, but also for unrelated proteins: HupD is used in Azotobacter chroococcum and Anabaena sp. to designate an unrelated hydrogenase maturation factor; HydD is used to designate hydrogenase structural genes in Thermococcus litoralis, Pyrococcus abyssi, and other species.; GO: 0008047 enzyme activator activity, 0008233 peptidase activity.
Probab=24.88  E-value=42  Score=14.63  Aligned_cols=92  Identities=18%  Similarity=0.214  Sum_probs=51.1

Q ss_pred             CCEEEECCCCEEEEECCCEECCHHHHCCCCCCCEEEECCCCCCCCCEEEHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHC
Q ss_conf             98999847520366048840220221123443113302665123311221567777887520120003872566324311
Q gi|254781095|r   62 IPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNIEVRNHCEMIVGARCSGKSLANSALRHGIGGFHFFYGIPGSIGGAAY  141 (318)
Q Consensus        62 ~p~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~~~~gl~GlE~l~gIPGTVGGAi~  141 (318)
                      .++.|+|=| |+|+.|+||---|+..-.+.+..-+ ..++.....||+.-.+|........++                 
T Consensus         2 ~~ilvlG~G-N~L~gDDG~G~~v~e~l~~~~~~p~-~~~nv~~iDgGt~g~~l~~~l~~~~~~-----------------   62 (170)
T TIGR00072         2 KRILVLGVG-NILFGDDGFGVRVAEKLKKRFELPE-NIKNVEVIDGGTGGLDLLGLLEEADPK-----------------   62 (170)
T ss_pred             CCEEEEEEC-CCCCCCCCCCHHHHHHHHHHHCCCC-CCCEEEEEECCCCCHHHHHHHHHCCCC-----------------
T ss_conf             707899754-8330567657889999999740666-687289980665786678877415885-----------------


Q ss_pred             CCCCCCCCEEEEEEEEEEEEC-C-CCCEEEEC-CCCCCC---CCCCC
Q ss_conf             573215831345666434411-2-32100001-233443---10023
Q gi|254781095|r  142 MNAGANNCETSQYVVEVHGID-R-KGNQHVIP-REQLKY---QYRSS  182 (318)
Q Consensus       142 mNAGayG~ei~d~i~~V~~~d-~-~g~~~~l~-~~e~~f---~YR~S  182 (318)
                                .=.|..+--+. . -|+++.+. ++++.=   .|.-|
T Consensus        63 ----------~~iivDA~~~~~~~pG~v~~i~~~d~~p~~~~~~~~s   99 (170)
T TIGR00072        63 ----------KVIIVDAIDFGSLEPGTVRIIEVEDEIPNFLKAKKMS   99 (170)
T ss_pred             ----------EEEEEEEEECCCCCCCEEEEEECCCHHHHHHCCCCCC
T ss_conf             ----------7899977756898987589973210346752213565


No 72 
>TIGR02143 trmA_only tRNA (uracil-5-)-methyltransferase; InterPro: IPR011869    This family consists exclusively of proteins believed to act as tRNA (uracil-5-)-methyltransferase. All members of this entry belong to the Proteobacteria. ; GO: 0009021 tRNA (uracil-5-)-methyltransferase activity, 0008033 tRNA processing.
Probab=24.66  E-value=35  Score=15.09  Aligned_cols=199  Identities=16%  Similarity=0.190  Sum_probs=98.7

Q ss_pred             HHHHHHHHHHHHHCCEEEECCCCCC-------CCCCCCCCEEEEEEEECCHHHH----HHHHHH-HH-CCCCEEEECCCC
Q ss_conf             9999999998750662775488001-------5225766148899996898999----999998-56-299899984752
Q gi|254781095|r    5 RISRLLRERGKQLRGKFQENFPLKQ-------ITWFRTGGNAEVMFQPQDIHDL----KYFLTL-LP-SDIPITIVGLGS   71 (318)
Q Consensus         5 ~~~~~l~~~~~~~~g~i~~n~~L~~-------~tt~rvGG~A~~~~~p~s~~el----~~~l~~-~~-~~~p~~iiG~GS   71 (318)
                      +|.++...+...++    .+..|+.       +||+.=.-..-.+| =+..+|-    +..|+. .+ .+..+-+||+-+
T Consensus        75 ~IN~lM~~L~~~~~----~~~~L~~KLFqvdfLsTLsg~~~vsLlY-Hk~Ldd~W~~~A~~L~~~L~~~~l~v~lIGRa~  149 (361)
T TIGR02143        75 LINRLMPALIAALK----QNEALRHKLFQVDFLSTLSGEILVSLLY-HKQLDDEWRQAAEALKDKLRAQGLDVNLIGRAR  149 (361)
T ss_pred             HHHHHHHHHHHHHH----HCHHHHHHCEEHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECC
T ss_conf             99999999999984----0667540012202566457888857750-677217899999999999863478568997336


Q ss_pred             E--EEEECCCEECCHHHHCCCCCCCEEEECCCCCCCCCEEEHHHHHHHHHHH--HCCC---HHCCCCHHHHHHHHHCCCC
Q ss_conf             0--3660488402202211234431133026651233112215677778875--2012---0003872566324311573
Q gi|254781095|r   72 N--ILVRDAGIRGVVLRLSNAGFSNIEVRNHCEMIVGARCSGKSLANSALRH--GIGG---FHFFYGIPGSIGGAAYMNA  144 (318)
Q Consensus        72 N--il~~D~~~~G~vI~l~~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~~~~--gl~G---lE~l~gIPGTVGGAi~mNA  144 (318)
                      -  +++. ..|=-=.+.+..+.+..-..  ++-.+=.=|....+...||.+-  +..|   ||-.+|         .   
T Consensus       150 k~Ki~l~-~DYv~E~L~V~gr~~~YrQ~--E~sFtQPNa~vn~kMLeWA~~~~~~~~g~DLLELYCG---------N---  214 (361)
T TIGR02143       150 KKKIVLD-RDYVDETLPVNGREFIYRQV--ENSFTQPNAAVNQKMLEWALEVTQNSKGMDLLELYCG---------N---  214 (361)
T ss_pred             CCEEEEE-CCCEEEEECCCCEEEEEEEC--CCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEECC---------C---
T ss_conf             8655510-35303662038807899863--7872475189999999999998358888720100026---------7---


Q ss_pred             CCCCCEEEEEEEEEEEECCCCCEEEECCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCHHHHHHCCCCCCCCC-C--
Q ss_conf             2158313456664344112321000012334431002322467620010023545654310012221001100015-5--
Q gi|254781095|r  145 GANNCETSQYVVEVHGIDRKGNQHVIPREQLKYQYRSSEITKDLIITHVVLRGFPESQNIISAAIANVCHHRETVQ-P--  221 (318)
Q Consensus       145 GayG~ei~d~i~~V~~~d~~g~~~~l~~~e~~f~YR~S~~~~~~iIl~a~l~l~~~~~~~i~~~~~~~~~~R~~~q-P--  221 (318)
                      |=|---.+.....|.+       .+++|..++++--+-...  . |--+  ++-.-+.++..++|...+.-|+.+. -  
T Consensus       215 GNFsLaLA~~f~rVLA-------TEiaK~SV~aAq~Ni~~N--~-idNv--~i~RlSAEEft~A~~~~R~F~RL~d~gId  282 (361)
T TIGR02143       215 GNFSLALAQNFERVLA-------TEIAKPSVNAAQYNIAAN--K-IDNV--QIIRLSAEEFTEAMNGVREFRRLKDGGID  282 (361)
T ss_pred             CCCHHHHHHHHHHHHH-------HHCCCCCHHHHHHHHHCC--C-CCCE--EHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             5310445653334554-------302402479999998717--9-8831--01023279999986037765465668863


Q ss_pred             CCCEEEEEEEECCC
Q ss_conf             66704658897278
Q gi|254781095|r  222 IKEKTGGSTFKNPT  235 (318)
Q Consensus       222 ~~~~s~GSvFkNP~  235 (318)
                      ++-.+|++||.+||
T Consensus       283 L~~Y~f~tiFVDPP  296 (361)
T TIGR02143       283 LKSYNFNTIFVDPP  296 (361)
T ss_pred             CCCCCCCEEEECCC
T ss_conf             34202560267798


No 73 
>TIGR00314 cdhA CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit; InterPro: IPR004460 Acetyl-CoA decarbonylase/synthase (ACDS) is a multienzyme complex (carbon monoxide dehydrogenase is a synonym). The ACDS complex carries out an unusual reaction involving the reversible cleavage and synthesis of acetyl-CoA in methanogens. The family contains the 4Fe-4S ferredoxin domain [C-x(2)-C-x(2)-C-x(3)-C-[PEG]] between residues 448-462 of the model.; GO: 0018492 carbon-monoxide dehydrogenase (acceptor) activity, 0006084 acetyl-CoA metabolic process.
Probab=24.55  E-value=32  Score=15.34  Aligned_cols=38  Identities=21%  Similarity=0.392  Sum_probs=22.2

Q ss_pred             HHCCEEEECCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHCCC
Q ss_conf             50662775488001522576614889999689899999999856299
Q gi|254781095|r   16 QLRGKFQENFPLKQITWFRTGGNAEVMFQPQDIHDLKYFLTLLPSDI   62 (318)
Q Consensus        16 ~~~g~i~~n~~L~~~tt~rvGG~A~~~~~p~s~~el~~~l~~~~~~~   62 (318)
                      +|.+.+....|+.+.-+    |     +.|+|..||.+++.|++.++
T Consensus       136 DLG~~v~~eAPi~rtv~----G-----ikPkTLgDL~~~L~YaEeqi  173 (795)
T TIGR00314       136 DLGSEVDVEAPITRTVT----G-----IKPKTLGDLREALDYAEEQI  173 (795)
T ss_pred             CCCCCCCEECCHHHEEC----C-----CCCCCHHHHHHHHHHHHHHH
T ss_conf             46888524466222020----4-----67787789999999988888


No 74 
>COG2226 UbiE Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]
Probab=24.46  E-value=52  Score=14.00  Aligned_cols=53  Identities=17%  Similarity=0.073  Sum_probs=23.1

Q ss_pred             EEEEEEEECCHHHHHHHHHHHHC-C-C-CEEEECCCCEEEEECCCEECCHHHHCCC
Q ss_conf             48899996898999999998562-9-9-8999847520366048840220221123
Q gi|254781095|r   38 NAEVMFQPQDIHDLKYFLTLLPS-D-I-PITIVGLGSNILVRDAGIRGVVLRLSNA   90 (318)
Q Consensus        38 ~A~~~~~p~s~~el~~~l~~~~~-~-~-p~~iiG~GSNil~~D~~~~G~vI~l~~~   90 (318)
                      +++....=-|..-|....+.++. + . =-++.|...|+-|+|..||-+.+..+..
T Consensus        75 ~g~v~~~D~s~~ML~~a~~k~~~~~~~~i~fv~~dAe~LPf~D~sFD~vt~~fglr  130 (238)
T COG2226          75 TGEVVGLDISESMLEVAREKLKKKGVQNVEFVVGDAENLPFPDNSFDAVTISFGLR  130 (238)
T ss_pred             CCEEEEEECCHHHHHHHHHHHHCCCCCCEEEEEECHHHCCCCCCCCCEEEEEEHHH
T ss_conf             84499997999999999987432476632799705654988887658898651235


No 75 
>pfam01786 AOX Alternative oxidase. The alternative oxidase is used as a second terminal oxidase in the mitochondria, electrons are transfered directly from reduced ubiquinol to oxygen forming water. This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process. In rice the transcript levels of the alternative oxidase are increased by low temperature.
Probab=24.40  E-value=26  Score=15.94  Aligned_cols=16  Identities=31%  Similarity=0.692  Sum_probs=13.9

Q ss_pred             HHCCCCHHHHHHHHHC
Q ss_conf             0003872566324311
Q gi|254781095|r  126 FHFFYGIPGSIGGAAY  141 (318)
Q Consensus       126 lE~l~gIPGTVGGAi~  141 (318)
                      ||-.+|+||-|||.+.
T Consensus        59 LETVAgVPgmV~gm~~   74 (214)
T pfam01786        59 LETVAGVPGMVGGMLR   74 (214)
T ss_pred             HHHHCCCCHHHHHHHH
T ss_conf             2121268717899999


No 76 
>pfam09873 DUF2100 Uncharacterized protein conserved in archaea (DUF2100). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=23.66  E-value=54  Score=13.91  Aligned_cols=18  Identities=28%  Similarity=-0.029  Sum_probs=7.4

Q ss_pred             CCEEEEECCCCCCCCCCC
Q ss_conf             620010023545654310
Q gi|254781095|r  188 LIITHVVLRGFPESQNII  205 (318)
Q Consensus       188 ~iIl~a~l~l~~~~~~~i  205 (318)
                      .=|+++.=-|.+.|+..|
T Consensus       130 lnIv~TeG~L~~EDmk~I  147 (215)
T pfam09873       130 LNIVSTEGPLEIEDMRII  147 (215)
T ss_pred             CCEEECCCCCCHHHHHHH
T ss_conf             435634887778999873


No 77 
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.50  E-value=25  Score=15.99  Aligned_cols=21  Identities=19%  Similarity=0.387  Sum_probs=10.7

Q ss_pred             CCCCCCCCCCCCCCEEEEECC
Q ss_conf             431002322467620010023
Q gi|254781095|r  176 KYQYRSSEITKDLIITHVVLR  196 (318)
Q Consensus       176 ~f~YR~S~~~~~~iIl~a~l~  196 (318)
                      .|.||.+.-..-.|.+++.+.
T Consensus        29 EF~YR~~~~~~A~V~vGi~~~   49 (85)
T cd04906          29 EFNYRYADEKDAHIFVGVSVA   49 (85)
T ss_pred             EEEEECCCCCCEEEEEEEEEC
T ss_conf             357743787637999998727


No 78 
>TIGR02477 PFKA_PPi diphosphate--fructose-6-phosphate 1-phosphotransferase; InterPro: IPR011183    Diphosphate--fructose-6-phosphate 1-phosphotransferase catalyses the addition of phosphate from diphosphate (PPi) to fructose 6-phosphate to give fructose 1,6-bisphosphate (2.7.1.90 from EC). The enzyme is also known as pyrophosphate-dependent phosphofructokinase. The usage of PPi-dependent enzymes in glycolysis presumably frees up ATP for other processes . IPR012828 from INTERPRO represents the ATP-dependent 6-phosphofructokinase enzyme contained within Phosphofructokinase. This entry contains primarily bacterial, plant alpha, and plant beta sequences. These may be dimeric nonallosteric enzymes (bacteria) or allosteric heterotetramers (plants) .   For additional information please see , , , .; GO: 0005524 ATP binding, 0047334 diphosphate-fructose-6-phosphate 1-phosphotransferase activity, 0006096 glycolysis, 0005945 6-phosphofructokinase complex.
Probab=23.23  E-value=55  Score=13.85  Aligned_cols=29  Identities=17%  Similarity=0.165  Sum_probs=12.7

Q ss_pred             ECCHHHHHHHHHHHH-CCCC-EEEE-CCCCEE
Q ss_conf             689899999999856-2998-9998-475203
Q gi|254781095|r   45 PQDIHDLKYFLTLLP-SDIP-ITIV-GLGSNI   73 (318)
Q Consensus        45 p~s~~el~~~l~~~~-~~~p-~~ii-G~GSNi   73 (318)
                      .+|+|+..++++.++ .++. +.|| |..||+
T Consensus       151 I~T~Eq~~~al~~~k~l~LdgLVIIGGDdSNT  182 (566)
T TIGR02477       151 IETEEQFAKALETAKKLKLDGLVIIGGDDSNT  182 (566)
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEEEECCCCCHH
T ss_conf             56888999999998760896489974798679


No 79 
>TIGR02207 lipid_A_htrB lipid A biosynthesis lauroyl (or palmitoleoyl) acyltransferase; InterPro: IPR011920   Bacterial lipopolysachharides (LPS) are glycolipids that make up the outer monolayer of the outer membranes of most Gram-negative bacteria. Though LPS moleculesare variable, they all show the same general features: an outer polysaccharide which is attached to the lipid component, termed lipid A . The polysaccharide component consists of a variable repeat-structure polysaccharide known as the O-antigen, and a highly conserved short core oligosaccharide which connects the O-antigen to lipid A. Lipid A is a glucosamine-based phospholipid that makes up the membrane anchor region of LPS . The structure of lipid A is relatively invariant between species, presumably reflecting its fundamental role in membrane integrity. Recognition of lipid A by the innate immune system can lead to a response even at picomolar levels. In some genera, such as Neisseria and Haemophilus, lipooligosaccharides (LOS) are the predominant glycolipids . These are analogous to LPS except that they lack O-antigens, with the LOS oligosaccharide structures limited to 10 saccharide units.    This entry represents a narrow clade of acyltransferases, nearly all of which transfer a lauroyl group to KDO2-lipid IV-A, a lipid A precursor; these proteins are termed lipid A biosynthesis lauroyl acyltransferase, HtrB. An exception is a closely related paralog of Escherichia coli HtrB, LpxP, which acts in cold shock conditions by transferring a palmitoleoyl rather than lauroyl group to the lipid A precursor. Members of this family are homologous to the family of acyltransferases responsible for the next step in lipid A biosynthesis .; GO: 0016747 transferase activity transferring groups other than amino-acyl groups, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=23.14  E-value=27  Score=15.77  Aligned_cols=28  Identities=14%  Similarity=0.153  Sum_probs=21.4

Q ss_pred             EEEEEECCCCCEEEECCCCCCCCCCCCCC
Q ss_conf             64344112321000012334431002322
Q gi|254781095|r  156 VEVHGIDRKGNQHVIPREQLKYQYRSSEI  184 (318)
Q Consensus       156 ~~V~~~d~~g~~~~l~~~e~~f~YR~S~~  184 (318)
                      .++-=...+|++.|..+|. +||+|+|.|
T Consensus       183 r~m~~~Lk~Ge~~WYAPDh-DYG~k~SVF  210 (308)
T TIGR02207       183 RGMIKALKNGERIWYAPDH-DYGRKSSVF  210 (308)
T ss_pred             HHHHHHHCCCCEEEECCCC-CCCCCCCEE
T ss_conf             8999860489727855874-638698543


No 80 
>TIGR01931 cysJ sulfite reductase [NADPH] flavoprotein, alpha-component; InterPro: IPR010199   This entry describes an NADPH-dependent sulphite reductase flavoprotein subunit. Most members of the proteins of this entry are found in Cys biosynthesis gene clusters. The closest homologues are designated as subunits nitrate reductase.; GO: 0004783 sulfite reductase (NADPH) activity, 0000103 sulfate assimilation, 0019344 cysteine biosynthetic process.
Probab=22.98  E-value=45  Score=14.40  Aligned_cols=114  Identities=13%  Similarity=0.163  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHHHHHCCEEEECCCCCCCCCCCCCCEEEEEEEECC------HHHHHHHHHH-----HH--CCCCEEEECCC
Q ss_conf             79999999998750662775488001522576614889999689------8999999998-----56--29989998475
Q gi|254781095|r    4 GRISRLLRERGKQLRGKFQENFPLKQITWFRTGGNAEVMFQPQD------IHDLKYFLTL-----LP--SDIPITIVGLG   70 (318)
Q Consensus         4 ~~~~~~l~~~~~~~~g~i~~n~~L~~~tt~rvGG~A~~~~~p~s------~~el~~~l~~-----~~--~~~p~~iiG~G   70 (318)
                      .++.+.|.+.+..- |.--+=+++..|..=.+-..-.+++...|      .||-..+.+|     ++  .++.|-|+|-|
T Consensus        82 r~~A~~l~~~l~~~-g~~V~l~~~~dYk~k~lk~E~~L~lv~STqGEGEPPeeA~~lhkFL~skkAPkL~~L~ysVlgLG  160 (628)
T TIGR01931        82 RRLAKALAEKLEAA-GLSVRLVSADDYKFKQLKSERLLLLVISTQGEGEPPEEAISLHKFLHSKKAPKLENLRYSVLGLG  160 (628)
T ss_pred             HHHHHHHHHHHHHC-CCEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCEEEECCC
T ss_conf             89999999999865-98388961026883201045178999853689896378999999871688878865324443036


Q ss_pred             --CEEEEECCC--EECCHHHHCCCCCCCEEEE--CCCCCCCCCEEEHHHHHHHHHHH
Q ss_conf             --203660488--4022022112344311330--26651233112215677778875
Q gi|254781095|r   71 --SNILVRDAG--IRGVVLRLSNAGFSNIEVR--NHCEMIVGARCSGKSLANSALRH  121 (318)
Q Consensus        71 --SNil~~D~~--~~G~vI~l~~~~~~~i~~~--~~~~i~v~AG~~~~~l~~~~~~~  121 (318)
                        |==.|...|  ||   =+|...+-+.+...  -+.....-|..+..++...+.++
T Consensus       161 D~SY~~FCQ~GKdFD---~Rl~ELGG~rLlpRvDaD~dy~~~A~~W~~~vL~~l~~~  214 (628)
T TIGR01931       161 DSSYEFFCQTGKDFD---KRLEELGGKRLLPRVDADVDYDAAAAEWRADVLTALKEK  214 (628)
T ss_pred             CCCHHHHHHHHHHHH---HHHHHCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             446045203157888---899861630001112046445576888899999997564


No 81 
>TIGR02309 HpaB-1 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component; InterPro: IPR012687    This entry represents the monooxygenase found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Deinococcus, Thermus and Oceanobacillus. Phylogenetic trees support inclusion of the Bacillus halodurans sequence although the complete 4-hydroxyphenylacetic acid degradation pathway may not exist in that organism. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein, HpaC. This family of sequences is a member of a larger subfamily of monooxygenases HpaB..
Probab=22.66  E-value=57  Score=13.78  Aligned_cols=62  Identities=19%  Similarity=0.274  Sum_probs=48.9

Q ss_pred             EEECCCCCCCCCCCCCC--EEEEEEEECCHHHHHHHHHHHH--CCCCEEEECCCCEEEEECCCEECCHHHHC
Q ss_conf             77548800152257661--4889999689899999999856--29989998475203660488402202211
Q gi|254781095|r   21 FQENFPLKQITWFRTGG--NAEVMFQPQDIHDLKYFLTLLP--SDIPITIVGLGSNILVRDAGIRGVVLRLS   88 (318)
Q Consensus        21 i~~n~~L~~~tt~rvGG--~A~~~~~p~s~~el~~~l~~~~--~~~p~~iiG~GSNil~~D~~~~G~vI~l~   88 (318)
                      ++-+.+++..-|+--+|  .++-|..|+|+|||...-+..+  .++..=++|+      +..+.+..|....
T Consensus        47 LQ~~~~~k~~lTye~~Gkr~~~sFm~P~TkedL~~r~ea~~~wa~~~lG~mGR------sPDYlNa~VMa~~  112 (487)
T TIGR02309        47 LQYEKDLKEVLTYEEEGKRYSKSFMVPKTKEDLKERAEAYKLWADITLGLMGR------SPDYLNAEVMAAE  112 (487)
T ss_pred             HCCCCCCCCEECCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCC------CCHHHHHHHHHHH
T ss_conf             11675444241466788610012147567689999999999981488665457------8523016999888


No 82 
>cd07560 Peptidase_S41_CPP C-terminal processing peptidase; serine protease family S41. The C-terminal processing peptidase (CPP, EC 3.4.21.102) also known as tail-specific protease (tsp), the photosystem II D1 C-terminal processing protease (D1P), and other related S41 protease family members are present in this CD. CPP is synthesized as a precursor form with a carboxyl-terminal extension. It specifically recognizes a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. The C-terminal carboxylate group is essential, and proteins where this group is amidated are not substrates. This family of proteases contains the PDZ domain that promotes protein-protein interactions and is important for substrate recognition. The active site consists of a serine/lysine catalytic dyad. The bacterial CCP-1 is believed to be important for the degradation of incorrectl
Probab=22.62  E-value=57  Score=13.78  Aligned_cols=41  Identities=20%  Similarity=0.178  Sum_probs=22.1

Q ss_pred             CCCCCCC--CCCCEEEEEEEECCHHHHHHHHHHHH-CCCCEEEE
Q ss_conf             0015225--76614889999689899999999856-29989998
Q gi|254781095|r   27 LKQITWF--RTGGNAEVMFQPQDIHDLKYFLTLLP-SDIPITIV   67 (318)
Q Consensus        27 L~~~tt~--rvGG~A~~~~~p~s~~el~~~l~~~~-~~~p~~ii   67 (318)
                      +-+||+|  .||=.-=.-+...+.+|+.+.++.++ .+.+=+||
T Consensus        40 ~DPyS~Y~~~IGyI~i~~F~~~t~~~~~~al~~l~~~g~~glIl   83 (211)
T cd07560          40 LDPYSRYLTPIGYIRITSFSENTAEELKKALKELKKQGMKGLIL   83 (211)
T ss_pred             CCCCHHCCCCEEEEEEEEECCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             29850116963999942556521999999999999769967999


No 83 
>COG4809 Archaeal ADP-dependent phosphofructokinase/glucokinase [Carbohydrate transport and metabolism]
Probab=22.62  E-value=55  Score=13.86  Aligned_cols=62  Identities=18%  Similarity=0.006  Sum_probs=49.7

Q ss_pred             HHHHCCCCCCCCCCEEECCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCEEEECCEEE
Q ss_conf             02631868820667787156770899689979999999999999999998475400422896
Q gi|254781095|r  242 LIEKSGCRGLEFGGAKISELHCNFMINADNATGYDLEYLGEQVRKKVFNQSGILLEWEIKRL  303 (318)
Q Consensus       242 LIe~~GlKG~~iG~a~vS~kHanfivN~g~ata~di~~Li~~v~~~V~~~~gi~Le~Ev~~i  303 (318)
                      +.+.+.=-+.++.||.+|--|+.--.+.++.|+.++++.....-+.-++.-+|+...|.-.+
T Consensus       215 ~~~~l~~i~~~vDgaiiSGyq~l~eey~dg~t~~~yle~s~e~i~~lk~~~~irvHlEfas~  276 (466)
T COG4809         215 IREFLDEIAKEVDGAIISGYQGLKEEYSDGSTYKYYLERSREDIKALKDRENIRVHLEFASI  276 (466)
T ss_pred             HHHHHHHHHHHCCEEEEECHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             99999987654130112012666666379971889999999999997424463699985223


No 84 
>PRK03971 putative deoxyhypusine synthase; Provisional
Probab=22.30  E-value=44  Score=14.46  Aligned_cols=67  Identities=13%  Similarity=0.227  Sum_probs=34.5

Q ss_pred             EEECCHHHHHHHHHHH----HCCCCEEEECCCCEEEEECCCEECCHHHHCCCCCCCEEEECCCCCCCCCEEEHHHHHHHH
Q ss_conf             9968989999999985----629989998475203660488402202211234431133026651233112215677778
Q gi|254781095|r   43 FQPQDIHDLKYFLTLL----PSDIPITIVGLGSNILVRDAGIRGVVLRLSNAGFSNIEVRNHCEMIVGARCSGKSLANSA  118 (318)
Q Consensus        43 ~~p~s~~el~~~l~~~----~~~~p~~iiG~GSNil~~D~~~~G~vI~l~~~~~~~i~~~~~~~i~v~AG~~~~~l~~~~  118 (318)
                      +..++..+-.++.+-.    +..--..+||--||++-  .|.++++..|-+.++.  .    ..++-+|+. -+++.+.+
T Consensus        43 Fqa~~Lg~A~~i~~~m~e~~~~~~~tifL~~tg~mis--aGlr~ii~~Li~~~~V--D----~iVtTgg~i-~hDi~~~l  113 (334)
T PRK03971         43 FQATHLGKAVKIWKKIEEKRKNEEATVFLGYTSNIVS--SGLREIIAYLVKEKKV--D----VIVTTAGGI-EEDFIKCL  113 (334)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCC--HHHHHHHHHHHHHCCE--E----EEEECCCCH-HHHHHHHH
T ss_conf             1178899999999999875057886699975431002--2179999999982862--0----898058861-88999985


No 85 
>TIGR01826 CofD_related conserved hypothetical protein; InterPro: IPR010119   This entry represents a subfamily of conserved hypothetical proteins that forms a sister group to the family of CofD, (IPR010115 from INTERPRO), LPPG:Fo 2-phospho-L-lactate transferase, an enzyme of cytochrome F420 biosynthesis..
Probab=21.84  E-value=51  Score=14.05  Aligned_cols=74  Identities=24%  Similarity=0.385  Sum_probs=45.2

Q ss_pred             EEEEEEEE--CCHHHH-HHHHHHHH-CCCCEEEECCCC-------EEEEECCCEECCHHHHCCCCCCCEEEECCCCCCCC
Q ss_conf             48899996--898999-99999856-299899984752-------03660488402202211234431133026651233
Q gi|254781095|r   38 NAEVMFQP--QDIHDL-KYFLTLLP-SDIPITIVGLGS-------NILVRDAGIRGVVLRLSNAGFSNIEVRNHCEMIVG  106 (318)
Q Consensus        38 ~A~~~~~p--~s~~el-~~~l~~~~-~~~p~~iiG~GS-------Nil~~D~~~~G~vI~l~~~~~~~i~~~~~~~i~v~  106 (318)
                      .-+.|.+|  ++.+-+ .+++...+ ++  ..|||=||       |+|+++  +.-.+...+.   ..+.+.|   +--+
T Consensus       165 i~rv~LePal~~~~a~a~eAv~aI~eAD--lIilGPGSLyTSI~PnLLvp~--i~~A~~~s~A---~kvYV~N---lmtq  234 (331)
T TIGR01826       165 IERVRLEPALEDVKALAREAVEAIREAD--LIILGPGSLYTSIIPNLLVPE--IAEALRESKA---PKVYVCN---LMTQ  234 (331)
T ss_pred             EEEEEECCCCCCCCCCCHHHHHHHHHCC--EEEECCCHHHHHHHHHHHHHH--HHHHHHHCCC---CEEEEEC---CCCC
T ss_conf             0488833678884875158999996669--278777245777424321678--9999972899---8999733---5668


Q ss_pred             C----EEEHHHHHHHHHHH
Q ss_conf             1----12215677778875
Q gi|254781095|r  107 A----RCSGKSLANSALRH  121 (318)
Q Consensus       107 A----G~~~~~l~~~~~~~  121 (318)
                      .    +-+..+=+.++.++
T Consensus       235 pGET~~~~~~dHv~~l~~h  253 (331)
T TIGR01826       235 PGETDGFSVEDHVKALHRH  253 (331)
T ss_pred             CCCCCCCCHHHHHHHHHHH
T ss_conf             8866477289999999986


No 86 
>TIGR01494 ATPase_P-type ATPase, P-type (transporting), HAD superfamily, subfamily IC; InterPro: IPR001757   ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , .  F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.   P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H^+, Na^+, K^+, Mg^2+, Ca^2+, Ag^+ and Ag^2+, Zn^2+, Co^2+, Pb^2+, Ni^2+, Cd^2+, Cu^+ and Cu^2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.    This entry represents the several classes of P-type ATPases, including those that transport K^+ (3.6.3.12 from EC), Mg^2+ (3.6.3.2 from EC), Cd^2+ (3.6.3.3 from EC), Cu ^2+ (3.6.3.4 from EC), Zn^2+ (3.6.3.5 from EC), Na^+ (3.6.3.7 from EC), Ca^2+ (3.6.3.8 from EC), Na^+/K^+ (3.6.3.9 from EC), and H^+/K^+ (3.6.3.10 from EC). These P-ATPases are found in both prokaryotes and eukaryotes.   More information about this protein can be found at Protein of the Month: ATP Synthases . ; GO: 0005524 ATP binding, 0015662 ATPase activity coupled to transmembrane movement of ions phosphorylative mechanism, 0006810 transport, 0016020 membrane.
Probab=21.68  E-value=34  Score=15.17  Aligned_cols=55  Identities=15%  Similarity=0.176  Sum_probs=29.1

Q ss_pred             CCCCCCCCCHHHHHHCCCCCCCCCCCCCE----------EEEEEEECCCCCCCHHHHHHCCCCCC
Q ss_conf             54565431001222100110001556670----------46588972789851000263186882
Q gi|254781095|r  197 GFPESQNIISAAIANVCHHRETVQPIKEK----------TGGSTFKNPTGHSAWQLIEKSGCRGL  251 (318)
Q Consensus       197 l~~~~~~~i~~~~~~~~~~R~~~qP~~~~----------s~GSvFkNP~~~~A~~LIe~~GlKG~  251 (318)
                      ..++.++.+.+....+.++-+...-.+.+          -+.=.|.||.-..+.+.|+.+-=.|.
T Consensus       279 ~~KGa~~~~~~~~~~~~~~~~~~~~~G~R~l~~a~~~~~lG~~~~~D~lr~~~~~~i~~L~~agi  343 (478)
T TIGR01494       279 YVKGAPEVILERCSDTEEHLEELASEGLRTLAVAYKEELLGLTAIEDPLREDVKETIEELKRAGI  343 (478)
T ss_pred             EECCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECEEEEEEEEECCCCCCHHHHHHHHHHCCC
T ss_conf             87183467899888899998876317870899998060789999734577726899999986599


No 87 
>TIGR02627 rhamnulo_kin rhamnulokinase; InterPro: IPR013449    Rhamnulokinase (2.7.1.5 from EC) is an enzyme that catalyzes the second step in rhamnose catabolism.; GO: 0008993 rhamnulokinase activity, 0019301 rhamnose catabolic process.
Probab=21.41  E-value=60  Score=13.62  Aligned_cols=66  Identities=20%  Similarity=0.219  Sum_probs=28.4

Q ss_pred             CCCCHHHHHHCCCCCCCCCCCCCE---EEEEEEECCCCCCCHHHHHHCCCCCCCCCCEEECCCCCEEEEECCCCCHHHHH
Q ss_conf             431001222100110001556670---46588972789851000263186882066778715677089968997999999
Q gi|254781095|r  202 QNIISAAIANVCHHRETVQPIKEK---TGGSTFKNPTGHSAWQLIEKSGCRGLEFGGAKISELHCNFMINADNATGYDLE  278 (318)
Q Consensus       202 ~~~i~~~~~~~~~~R~~~qP~~~~---s~GSvFkNP~~~~A~~LIe~~GlKG~~iG~a~vS~kHanfivN~g~ata~di~  278 (318)
                      |+..-++++.+|  |+..||...-   =|=|+|-=---.++-.+-|-+.|+|..|-.        .+|  .||+|-..++
T Consensus       342 P~~M~~eI~~yC--REt~Q~vP~s~aeLArCiFdSLAl~Y~~~~~~l~~l~g~~i~~--------LhI--VGGGs~n~~L  409 (460)
T TIGR02627       342 PENMVEEIQAYC--RETNQPVPESDAELARCIFDSLALLYRQVLLELAELRGKPISQ--------LHI--VGGGSQNAFL  409 (460)
T ss_pred             CHHHHHHHHHHH--HHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCE--------EEE--ECCCHHHHHH
T ss_conf             654799999975--4237889996556888788889999999999987302688551--------468--6175144466


Q ss_pred             H
Q ss_conf             9
Q gi|254781095|r  279 Y  279 (318)
Q Consensus       279 ~  279 (318)
                      +
T Consensus       410 N  410 (460)
T TIGR02627       410 N  410 (460)
T ss_pred             H
T ss_conf             7


No 88 
>PTZ00239 serine/threonine protein phosphatase 2A; Provisional
Probab=21.12  E-value=61  Score=13.59  Aligned_cols=47  Identities=13%  Similarity=0.057  Sum_probs=28.0

Q ss_pred             CCCCCCCEEEEEEEEC-CHHHHHHHHHHH--HCCCCEEEECCCCEEEEECCCEEC
Q ss_conf             2257661488999968-989999999985--629989998475203660488402
Q gi|254781095|r   31 TWFRTGGNAEVMFQPQ-DIHDLKYFLTLL--PSDIPITIVGLGSNILVRDAGIRG   82 (318)
Q Consensus        31 tt~rvGG~A~~~~~p~-s~~el~~~l~~~--~~~~p~~iiG~GSNil~~D~~~~G   82 (318)
                      |-+++.+|.-.+-..+ ...||..+.+..  ....++..+|.     +-|.|-.+
T Consensus        37 ~ll~i~~Pv~VvGDiHGq~~DLl~if~~~G~p~~~~YlFLGD-----YVDRG~~s   86 (303)
T PTZ00239         37 NVQPVKAPVNVCGDIHGQFYDLQALMKEGGDIPEHNYIFIGD-----FVDRGYNS   86 (303)
T ss_pred             CEEEECCCEEEEEECCCCHHHHHHHHHHCCCCCCCCEEECCC-----CCCCCCCC
T ss_conf             758857997999447889899999999739998665884786-----32678874


No 89 
>TIGR01929 menB naphthoate synthase; InterPro: IPR010198   This entry represents an enzyme, naphthoate synthase , MenB or dihydroxynaphthoic acid synthetase), which is involved in the fifth step of the menaquinone biosynthesis pathway. Menaquinone (vitamin K2), is an essential quinone used in electron-transfer pathways serving as the major electron carrier during anaerobic growth. In the bacterium, the biosynthetic pathway in bacteria typically comprises 6-7 steps . Together with o-succinylbenzoate-CoA ligase (menE IPR010192 from INTERPRO),MenB takes 2-succinylbenzoate and converts it into 1,4-di-hydroxy-2-naphthoic acid (DHNA) , , , . The conversion of o-succinylbenzoate-CoA ligase to DHNA is mediated by the enzyme DHNA synthase, which is encoded by menB .   The protein structure of naphthoate synthase has been expressed in Escherichia coli, purified and crystallized, and found to have fold characteristics of the crotonase family of enzymes, which is notable for the presence of several highly flexible regions around the active site. The C-terminal region of the protein may play a critical role both in completion of the binding pocket and in stabilisation of the hexamer, suggesting a link between oligomerization and catalytic activity .   Included in this entry are two enzymes from Arabidopsis thaliana and one from Staphylococcus aureus, which are identified as putative enoyl-CoA hydratase/isomerases. These enzymes group with the naphthoate synthases when building a tree and when doing BLAST searches.; GO: 0008935 naphthoate synthase activity, 0009234 menaquinone biosynthetic process.
Probab=20.65  E-value=62  Score=13.52  Aligned_cols=28  Identities=29%  Similarity=0.554  Sum_probs=22.7

Q ss_pred             EEECCHHHHHHHHHHHHC--CCCEEEE-CCC
Q ss_conf             996898999999998562--9989998-475
Q gi|254781095|r   43 FQPQDIHDLKYFLTLLPS--DIPITIV-GLG   70 (318)
Q Consensus        43 ~~p~s~~el~~~l~~~~~--~~p~~ii-G~G   70 (318)
                      +.|+|++||.+++..++.  ++=+.|| |.|
T Consensus        28 FRP~T~~E~~~al~~aR~~~~iGVv~LtG~G   58 (278)
T TIGR01929        28 FRPRTVDEIIRALDDAREDPDIGVVILTGAG   58 (278)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCCCEEEEECCC
T ss_conf             7800489999999971379996279861767


No 90 
>PRK09754 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional
Probab=20.30  E-value=63  Score=13.48  Aligned_cols=22  Identities=41%  Similarity=0.409  Sum_probs=13.5

Q ss_pred             CCCCCCEEEHHHHHHHHHHHHC
Q ss_conf             5123311221567777887520
Q gi|254781095|r  102 EMIVGARCSGKSLANSALRHGI  123 (318)
Q Consensus       102 ~i~v~AG~~~~~l~~~~~~~gl  123 (318)
                      .+.+|+|..--+++..+.+.|.
T Consensus       147 vvVIGgG~IGlE~A~~l~~~G~  168 (400)
T PRK09754        147 VVIVGAGTIGLELAASATQRRC  168 (400)
T ss_pred             EEEECCCHHHHHHHHHHHHCCC
T ss_conf             9998855899999999997599


No 91 
>PRK10872 relA GDP/GTP pyrophosphokinase; Provisional
Probab=20.06  E-value=64  Score=13.45  Aligned_cols=30  Identities=23%  Similarity=0.388  Sum_probs=24.6

Q ss_pred             EEEEEECCCCCEEEECCCC--CCCCCC-CCCCC
Q ss_conf             6434411232100001233--443100-23224
Q gi|254781095|r  156 VEVHGIDRKGNQHVIPREQ--LKYQYR-SSEIT  185 (318)
Q Consensus       156 ~~V~~~d~~g~~~~l~~~e--~~f~YR-~S~~~  185 (318)
                      ..|-+|.|+|++..|++..  ++|+|+ ||...
T Consensus       404 d~VyVFTPkGdvi~LP~GaTplDFAYaIHTevG  436 (743)
T PRK10872        404 DRVYVFTPKGDVVDLPAGSTPLDFAYHIHSDVG  436 (743)
T ss_pred             CEEEEECCCCCEEECCCCCEEEHHHHHHCCCCH
T ss_conf             649998899877987999723031354347303


Done!