Query         gi|254780299|ref|YP_003064712.1| acyl-CoA dehydrogenase protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 562
No_of_seqs    322 out of 5006
Neff          6.8 
Searched_HMMs 39220
Date          Sun May 29 16:56:11 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780299.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK11561 isovaleryl CoA dehydr 100.0       0       0 1095.8  51.6  528   19-556     3-534 (538)
  2 cd01154 AidB AidB. AidB is one 100.0       0       0  853.5  40.2  409   37-460     1-418 (418)
  3 cd01153 ACAD_fadE5 Putative ac 100.0       0       0  526.7  33.6  364   80-458    13-406 (407)
  4 cd01155 ACAD_FadE2 FadE2-like  100.0       0       0  517.6  32.4  353   81-460    19-394 (394)
  5 cd01161 VLCAD Very long chain  100.0       0       0  511.6  31.4  332  104-461    59-407 (409)
  6 KOG0137 consensus              100.0       0       0  498.5  30.7  462   53-545    64-558 (634)
  7 KOG0139 consensus              100.0       0       0  497.0  22.7  330   81-448    57-398 (398)
  8 TIGR03207 cyc_hxne_CoA_dh cycl 100.0       0       0  479.4  32.4  324  105-458    36-371 (372)
  9 PRK03354 crotonobetainyl-CoA d 100.0       0       0  480.7  29.9  339   81-461    26-378 (380)
 10 cd01162 IBD Isobutyryl-CoA deh 100.0       0       0  477.8  30.8  345   80-460    20-374 (375)
 11 cd01152 ACAD_fadE6_17_26 Putat 100.0       0       0  477.8  30.7  346   76-459    14-379 (380)
 12 cd01157 MCAD Medium chain acyl 100.0       0       0  473.0  32.7  344   79-459    19-376 (378)
 13 cd01151 GCD Glutaryl-CoA dehyd 100.0       0       0  478.0  28.4  326  105-460    48-382 (386)
 14 cd01156 IVD Isovaleryl-CoA deh 100.0       0       0  461.0  33.5  328  105-460    37-376 (376)
 15 cd01160 LCAD Long chain acyl-C 100.0       0       0  464.9  29.1  342   80-458    18-371 (372)
 16 KOG0140 consensus              100.0       0       0  465.3  25.6  340   78-459    45-403 (408)
 17 PRK12341 putative acyl-CoA deh 100.0       0       0  459.4  29.4  327  105-461    41-379 (383)
 18 TIGR03204 pimC_large pimeloyl- 100.0       0       0  454.9  28.8  347   78-459    21-393 (395)
 19 TIGR03203 pimD_small pimeloyl- 100.0       0       0  450.6  31.3  324  105-459    41-377 (378)
 20 KOG0141 consensus              100.0       0       0  466.8  17.8  330  104-461    77-420 (421)
 21 cd01158 SCAD/SBCAD Short chain 100.0       0       0  440.7  30.2  345   79-460    17-373 (373)
 22 COG1960 CaiA Acyl-CoA dehydrog 100.0       0       0  431.1  32.4  331  104-462    42-390 (393)
 23 cd00567 ACAD Acyl-CoA dehydrog 100.0       0       0  401.5  33.0  324  105-456    34-369 (369)
 24 cd01163 DszC Dibenzothiophene  100.0       0       0  387.9  30.1  330  105-458    26-372 (377)
 25 cd01159 NcnH Naphthocyclinone  100.0       0       0  364.5  30.3  320  105-459    26-369 (370)
 26 PRK13026 acyl-CoA dehydrogenas 100.0       0       0  341.7  36.8  371   33-451    57-461 (771)
 27 PRK09463 fadE acyl-CoA dehydro 100.0       0       0  339.8  35.4  370   33-451    58-462 (761)
 28 KOG0138 consensus              100.0       0       0  328.2  24.1  330   98-460    86-426 (432)
 29 KOG1469 consensus              100.0 2.4E-42       0  302.3  15.1  328   99-451    25-373 (392)
 30 cd01150 AXO Peroxisomal acyl-C 100.0 1.7E-34 4.3E-39  249.6  31.8  303  146-461    94-445 (610)
 31 pfam00441 Acyl-CoA_dh_1 Acyl-C 100.0 6.7E-33 1.7E-37  238.9  14.6  149  303-458     1-149 (150)
 32 KOG0135 consensus              100.0 1.2E-26   3E-31  197.0  19.2  310  134-458   105-462 (661)
 33 pfam08028 Acyl-CoA_dh_2 Acyl-C  99.9 3.5E-24   9E-29  180.3  12.9  130  318-447     1-133 (134)
 34 KOG0136 consensus               99.9 8.1E-22 2.1E-26  164.5  18.3  299  148-461   105-449 (670)
 35 pfam02770 Acyl-CoA_dh_M Acyl-C  99.5   1E-13 2.6E-18  110.1   5.6   51  199-250     1-52  (52)
 36 COG2368 Aromatic ring hydroxyl  98.4 0.00012 3.1E-09   49.2  17.3  256  191-456   140-431 (493)
 37 pfam02771 Acyl-CoA_dh_N Acyl-C  97.7 0.00011 2.9E-09   49.3   5.7   92   80-182    19-113 (113)
 38 KOG0137 consensus               95.8    0.11 2.8E-06   29.4   8.7   27  496-522   539-565 (634)
 39 pfam11794 HpaB_N 4-hydroxyphen  95.8    0.14 3.6E-06   28.6  14.7   75  191-266   133-221 (265)
 40 TIGR02309 HpaB-1 4-hydroxyphen  88.2     1.6 4.2E-05   21.5  10.8  218  196-426   149-400 (487)
 41 pfam03241 HpaB 4-hydroxyphenyl  88.0     1.7 4.3E-05   21.4   8.1   85  349-437    44-128 (205)
 42 TIGR01282 nifD nitrogenase mol  73.4     2.1 5.5E-05   20.7   1.9   69   10-85    267-338 (521)
 43 KOG0450 consensus               70.1     6.3 0.00016   17.5   3.7  109    1-124   201-311 (1017)
 44 TIGR01074 rep ATP-dependent DN  63.9     5.9 0.00015   17.7   2.5   30  415-444   516-546 (677)
 45 TIGR02093 P_ylase glycogen/sta  61.8     2.3 5.9E-05   20.4   0.1   17  163-179   365-382 (822)
 46 TIGR00972 3a0107s01c2 phosphat  61.6     4.9 0.00012   18.3   1.7   73  448-523   149-227 (248)
 47 pfam11859 DUF3379 Protein of u  60.7     9.7 0.00025   16.3   7.2   67  238-313   161-227 (232)
 48 TIGR02040 PpsR-CrtJ transcript  59.4     5.9 0.00015   17.7   1.8   22  331-352   290-311 (453)
 49 TIGR01862 N2-ase-Ialpha nitrog  58.4     3.5 8.9E-05   19.2   0.5   98    8-115   257-356 (510)
 50 pfam12186 AcylCoA_dehyd_C Acyl  57.3      11 0.00028   15.9   7.2   47  490-538    44-96  (114)
 51 COG5566 Uncharacterized conser  39.6      21 0.00053   14.1   5.7   43  407-449    62-106 (137)
 52 COG2087 CobU Adenosyl cobinami  39.2      13 0.00033   15.4   1.0   17  421-437   131-147 (175)
 53 TIGR00770 Dcu transporter, ana  38.6      21 0.00055   14.0   2.5   10   44-53     74-83  (447)
 54 cd03796 GT1_PIG-A_like This fa  38.5       9 0.00023   16.5   0.0   28  423-450   256-286 (398)
 55 pfam08877 MepB MepB protein. M  37.4      21 0.00054   14.0   1.8   55  234-289    49-103 (123)
 56 COG2704 DcuB Anaerobic C4-dica  35.0      24 0.00062   13.6   2.2   19  346-364   191-209 (436)
 57 TIGR01091 upp uracil phosphori  34.7      25 0.00063   13.6   1.9   11  154-164    84-94  (213)
 58 pfam05428 CRF-BP Corticotropin  33.9      14 0.00036   15.2   0.4   13  223-236   114-126 (311)
 59 pfam00289 CPSase_L_chain Carba  31.7      17 0.00043   14.7   0.5   32  414-447    73-105 (109)
 60 TIGR01919 hisA-trpF bifunction  31.5      11 0.00029   15.8  -0.4   47  218-266   132-179 (246)
 61 TIGR01960 ndhF3_CO2 NAD(P)H de  31.3      17 0.00044   14.6   0.6   16  419-434   384-399 (613)
 62 TIGR01132 pgm phosphoglucomuta  31.2      19 0.00049   14.2   0.8   78   58-143    56-135 (553)
 63 TIGR01075 uvrD DNA helicase II  29.8      29 0.00075   13.0   2.7   48  202-250   309-357 (741)
 64 PRK13795 hypothetical protein;  28.7      31 0.00078   12.9   2.4   20  342-361   273-292 (630)
 65 KOG2675 consensus               27.2      33 0.00083   12.7   8.1   50  207-258   310-359 (480)
 66 PRK05800 cobU adenosylcobinami  26.9      30 0.00076   13.0   1.1   17  421-437   127-143 (170)
 67 KOG1416 consensus               25.9      34 0.00088   12.6   1.4   18  533-550   410-427 (475)
 68 KOG1321 consensus               25.7      35 0.00088   12.6   4.1   27  205-235   169-195 (395)
 69 PRK13523 NADPH dehydrogenase N  25.7     9.4 0.00024   16.3  -1.6   12  101-112    81-92  (337)
 70 cd02930 DCR_FMN 2,4-dienoyl-Co  25.0      11 0.00028   15.9  -1.4   23   94-116    70-92  (353)
 71 PHA00728 hypothetical protein   25.0      30 0.00076   13.0   0.8   37   57-93     79-115 (153)
 72 cd02929 TMADH_HD_FMN Trimethyl  24.6      10 0.00026   16.1  -1.6   16   99-114    81-96  (370)
 73 cd04733 OYE_like_2_FMN Old yel  24.4      11 0.00028   15.9  -1.5   15  100-114    81-95  (338)
 74 cd04735 OYE_like_4_FMN Old yel  24.0      11 0.00028   15.9  -1.5   16   99-114    76-91  (353)
 75 TIGR02627 rhamnulo_kin rhamnul  23.8      32 0.00081   12.8   0.8   39    6-50     20-58  (460)
 76 cd04747 OYE_like_5_FMN Old yel  23.8      14 0.00035   15.3  -1.1   18   98-115    75-92  (361)
 77 COG1902 NemA NADH:flavin oxido  22.0      12 0.00031   15.6  -1.6   20  343-362   315-334 (363)
 78 KOG3581 consensus               21.5      26 0.00067   13.4  -0.0   28  208-236   196-225 (363)
 79 COG4815 Uncharacterized protei  21.4      42  0.0011   12.0   1.3   29  233-261    69-97  (145)
 80 cd02933 OYE_like_FMN Old yello  20.8      13 0.00033   15.5  -1.7   13  101-113    77-89  (338)
 81 COG2169 Ada Adenosine deaminas  20.7      43  0.0011   11.9   6.2   93  452-554    85-183 (187)
 82 cd03869 M14_CPX_like Peptidase  20.5      44  0.0011   11.9   1.3   22  222-245   265-287 (405)
 83 cd03867 M14_CPZ Peptidase M14-  20.3      44  0.0011   11.9   1.0   19  223-243   255-274 (395)
 84 TIGR01073 pcrA ATP-dependent D  20.0      45  0.0011   11.8   2.8   19  326-344   473-491 (811)

No 1  
>PRK11561 isovaleryl CoA dehydrogenase; Provisional
Probab=100.00  E-value=0  Score=1095.81  Aligned_cols=528  Identities=35%  Similarity=0.555  Sum_probs=501.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCEE
Q ss_conf             62110116788858998001678899999720-42110789999998501899999986343698462017998521365
Q gi|254780299|r   19 SDSLFALNQPPLFIGMNAYSSDSLLVALIANF-PSVVHKELELLGEYVLSCTAQELARMANYNTPQLHAYGPGGERWDKV   97 (562)
Q Consensus        19 ~~~~~~~nq~~~~~g~n~~~~D~~l~~~~~~~-~~~~~~~l~~~g~~~~~~~~~~~~~~a~~~~P~l~~~d~~G~r~d~v   97 (562)
                      ..||.|||||||+.|+|.|++|++|++++.++ ++|..++|..+|+.+||.++++|+++||+|||+|++||+||+|||+|
T Consensus         3 ~~TH~v~Nq~~~~~~~n~~~~D~~L~~a~~r~ga~~~~~~L~~~G~~~Gs~e~~e~~~~An~~~P~L~~~Dr~G~RiD~V   82 (538)
T PRK11561          3 WQTHTVFNQPIPLNNSNLFLSDGALCEAVTREGAGWDSDLLASIGQQLGTAESLELGRLANANPPELLRYDAQGQRLDDV   82 (538)
T ss_pred             CCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCCCCEEECCCCCCCCCCCE
T ss_conf             78732347999976876633588899999974777567999999998677999999998500898501508999867506


Q ss_pred             ECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCC-HHHHHHHHH
Q ss_conf             6688999999999967962033776666444763799999999983014453122135677899998508-788987301
Q gi|254780299|r   98 EFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSASMVALMTT-PRVHKDWAP  176 (562)
Q Consensus        98 ~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~a~~~L~~~-~e~~~~~lp  176 (562)
                      +|||+||+||+.++++|+|+++|+++.    ++++|+++++++||++|+|.|++||++||++++++|+.+ |++.+.|.|
T Consensus        83 e~hpawh~Lm~~~~~~g~~~~~w~~~~----~~g~~v~raA~~yL~~q~e~G~~CPltMT~aa~~~L~~~~p~~~~~~~~  158 (538)
T PRK11561         83 RFHPAWHLLMQGLCANRVHNLAWEEDA----RSGSFVARAARFMLHAQVEAGTLCPITMTFAATPLLLQMLPAPFQDWLT  158 (538)
T ss_pred             EECHHHHHHHHHHHHCCCCCCCCCCCC----CCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_conf             657899999999997686555655677----6551999999999851356466682248799999998618398999876


Q ss_pred             HHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEECCCCCEEEEEEECCCCCEEE
Q ss_conf             20010005442660015521235544588888786654302786489668984514686342115799970469961799
Q gi|254780299|r  177 KIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLSSPMSDAFIMLAQVEGRVGCF  256 (562)
Q Consensus       177 ~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~sa~~ad~~lVlArt~~Gls~F  256 (562)
                      +++|++||+++.|..+|.++++||+|||+||||||++++|+|+|.+||.|+|+|+|||+|+|+||+++|+||+++|+|||
T Consensus       159 ~l~s~~yD~~~~p~~~K~~~t~Gm~MTEkqGGSDV~an~T~A~~~~~g~YrL~G~KwF~Sa~~~D~~LvLAr~~gGLS~F  238 (538)
T PRK11561        159 PLLSDRYDSHLLPGGQKRGLLIGMGMTEKQGGSDVLSNTTRAERLADGSYRLVGHKWFFSVPQSDAHLVLAQAKGGLSCF  238 (538)
T ss_pred             HHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEEEEECCCCCHHEEEEEECCCCEEEE
T ss_conf             65335678122786202334432433257767641135259996699819999998885155500058886069955899


Q ss_pred             EEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98775898840347886304755456577279998690753007776579999997301333579999999999999999
Q gi|254780299|r  257 LVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFGFLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEAI  336 (562)
Q Consensus       257 lVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~  336 (562)
                      +||++.|||++|+|+|+|+|||+|+|++||+||+|+++.++|||++|+|+++|++|+|++|++++++++|+||+++.+|+
T Consensus       239 lvPr~~~DG~~N~i~i~RLKdKLG~rs~pSaEve~~gA~a~lvGeegrGv~~I~~M~n~TRl~~ai~sag~mRrAl~~A~  318 (538)
T PRK11561        239 FVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGEEGEGIRLILKMGGMTRFDCALGSHGLMRRAFSVAI  318 (538)
T ss_pred             EEEEECCCCCCCCEEEEEHHHHHCCCCCCEEEEEECCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             97503689997855774333321687688289998880799835788578999999999999999999999999999999


Q ss_pred             HHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99840462224235388889999999999999999999999887201110367776556799999999999999995699
Q gi|254780299|r  337 HYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVIAEAM  416 (562)
Q Consensus       337 ~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Ai  416 (562)
                      +|+++|++||++|++||+++++|+||.+++|++++++|+++..+|+. .++.+.+++|++||++|+|+||.+..++++||
T Consensus       319 ~~a~~R~aFG~~L~d~PLm~~~Ladm~le~eaa~aL~~rlA~a~d~~-~~~~e~a~~RllTpiaK~~~~k~a~~~~~Eam  397 (538)
T PRK11561        319 YHAHQRQVFGKPLIEQPLMRQVLSRMALQLEGQTALLFRLARAWDRR-ADAKEALWARLFTPAAKFVICKQGIPFVAEAM  397 (538)
T ss_pred             HHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99855750575353140599999999999999999999999974137-98678999999999999999712899999999


Q ss_pred             HHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHH--HHHHHHHCCC
Q ss_conf             88521300045518898500122322046222789999998312603799999999964254517789--9999873054
Q gi|254780299|r  417 ECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEKGTNLFEQLFSTLEQDLGSSGKKVI--TILRDSISLC  494 (562)
Q Consensus       417 qi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r~~~~~~~l~~~l~~~~g~~~~~~~--~~l~~~~~~~  494 (562)
                      |||||+||+||++++|+||||+||+|||||+|||||||+|++.|+|++++++++++....|..+..+.  +.++..+.. 
T Consensus       398 E~~GG~GYiEe~~~pRl~RdA~VnsIWEGT~NV~aLDvLRa~~r~p~~~~~~~~e~~~~~g~~~~~d~~~~~l~~~l~~-  476 (538)
T PRK11561        398 EVLGGIGYCEESELPRLYREMPVNSIWEGSGNIMCLDVLRVLNKQPGVYDLLSEAFVEVKGQDRHFDRAVRQLQQRLRK-  476 (538)
T ss_pred             HHHCCCEEECCCCCHHHHHCCCCCCEEECCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCC-
T ss_conf             9846825733785066775180413355677358999999871190389999999987328877899999999988548-


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             22137789999999999999999970857999999996400256554511434468899998
Q gi|254780299|r  495 KEDKGLARFLTEKIALASSAAALYRAGMNDIADVFLENRFLDNCHSTHCMLHGRFNAAHIID  556 (562)
Q Consensus       495 ~~~e~~AR~~~e~la~~~~aalL~r~a~~~va~af~~~Rl~~~~~~~~g~l~a~~d~~~~~~  556 (562)
                       +.|..+|+++++|++++|+++|+||++++|+++||++||+..++.   +||+..|...++.
T Consensus       477 -~~e~~ar~~~~~~a~~~qa~~l~r~~~~~va~afc~~rl~~~~~~---~~~~~~~~~~~~~  534 (538)
T PRK11561        477 -PAEEQGREITQQLFLLGCGAQMLRYASPPLAQAWCQMMLDTRGGV---RLSEQVQNDLLLR  534 (538)
T ss_pred             -CHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCC---CCCHHHHHHHHHH
T ss_conf             -607799999999999999999985099999999999971777982---3737777999987


No 2  
>cd01154 AidB AidB. AidB is one of several genes involved in the SOS adaptive response to DNA alkylation damage, whose expression is activated by the Ada protein. Its function has not been entirely elucidated; however, it is similar in sequence and function to acyl-CoA dehyrdogenases. It has been proposed that aidB directly destroys DNA alkylating agents such as nitrosoguanidines (nitrosated amides) or their reaction intermediates.
Probab=100.00  E-value=0  Score=853.53  Aligned_cols=409  Identities=41%  Similarity=0.631  Sum_probs=385.7

Q ss_pred             CCCCHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCC
Q ss_conf             01678899999720-42110789999998501899999986343698462017998521365668899999999996796
Q gi|254780299|r   37 YSSDSLLVALIANF-PSVVHKELELLGEYVLSCTAQELARMANYNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGL  115 (562)
Q Consensus        37 ~~~D~~l~~~~~~~-~~~~~~~l~~~g~~~~~~~~~~~~~~a~~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl  115 (562)
                      |++||+||++++++ +++++++|+++|+++++ ++++|++++|+|||+|++||+||+|+|+|++||+||++++.++++||
T Consensus         1 ~~~D~~L~~~l~~~~~~~~~~~l~~~G~~~~~-~~~~~~~~a~~~~P~l~~~d~~G~rid~v~~~~~~~~~~~~~~~~g~   79 (418)
T cd01154           1 YLDDPVLQQTLRYFGDPEEEPDLSRLGELAGG-ELYELARLADRNPPVLEMWDRWGRRVDRVWVHPAWHALMRRLIEEGV   79 (418)
T ss_pred             CCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHH-HHHHHHHHHCCCCCEEECCCCCCCCCCEEEECHHHHHHHHHHHHCCC
T ss_conf             99878899999985882202999999999879-99999987605898875658888868858828799999999997796


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHC-CHHHHHHHHHHHCCCCCCHHHCCCCCCC
Q ss_conf             203377666644476379999999998301445312213567789999850-8788987301200100054426600155
Q gi|254780299|r  116 HCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSASMVALMT-TPRVHKDWAPKIFSREYDPTNKAPMQKT  194 (562)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~a~~~L~~-~~e~~~~~lp~l~s~~~~~~~~~~~~k~  194 (562)
                      +++.|++...     ++++.+++..||++++|.|++||++||++++++|.. .+|..++|+|+++|++++         .
T Consensus        80 ~~~~~~~~~~-----~~~~~~~a~~~l~~~~~~g~~cp~~mT~ga~~~L~~~g~e~~k~~l~~l~s~~~~---------~  145 (418)
T cd01154          80 INIEDGPAGE-----GRRHVHFAAGYLLSDAAAGLLCPLTMTDAAVYALRKYGPEELKQYLPGLLSDRYK---------T  145 (418)
T ss_pred             CCCCCCCCCC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCC---------C
T ss_conf             1367887667-----8739999999999887776513999999999999970909999987875257854---------3


Q ss_pred             CCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEECCCCCEEEEEEECCC------CCEEEEEECCCCCCCCC
Q ss_conf             212355445888887866543027864896689845146863421157999704699------61799987758988403
Q gi|254780299|r  195 SVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLSSPMSDAFIMLAQVEG------RVGCFLVPRLLEDGSPN  268 (562)
Q Consensus       195 g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~sa~~ad~~lVlArt~~------Gls~FlVp~~~pgg~~n  268 (562)
                      +|+++|+||||++|||+++++|+|++++||.|+|||+|||||++++|+++|+|||++      |+|||+||++.|||++|
T Consensus       146 ~~~g~~~mTEp~~GSDv~~~~T~A~~~~~g~y~LnG~Kwf~s~~~ad~~lVlArt~~~~~g~~GiS~FlVP~~~~dg~~n  225 (418)
T cd01154         146 GLLGGTWMTEKQGGSDLGANETTAERSGGGVYRLNGHKWFASAPLADAALVLARPEGAPAGARGLSLFLVPRLLEDGTRN  225 (418)
T ss_pred             CCCCCCCCCCCCCCCCHHHHHEEEEECCCCEEEEEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCC
T ss_conf             31140247999844697763248998799979997899997781136899999947988887874589996316888868


Q ss_pred             CEEEEEECCCCCCCCCCEEEEEECCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             47886304755456577279998690753007776579999997301333579999999999999999998404622242
Q gi|254780299|r  269 GLCYQRLKNKIGNRSNATVELEFSNTFGFLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGI  348 (562)
Q Consensus       269 ~v~i~r~~~klG~r~~~t~ei~f~~~~~~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~  348 (562)
                      +|+|.++|+|+|+|++||+||+|+++.+++||++|+||++++.++|.+|+.++++++|+|++|+++|++||++|+|||+|
T Consensus       226 g~~i~rl~~KlG~r~~~t~el~f~~~~~~llG~~g~G~~~~~~~ln~~Rl~~a~~a~G~ar~al~~A~~YA~~R~~FG~p  305 (418)
T cd01154         226 GYRIRRLKDKLGTRSVATGEVEFDDAEAYLIGDEGKGIYYILEMLNISRLDNAVAALGIMRRALSEAYHYARHRRAFGKP  305 (418)
T ss_pred             CEEEECCCCCCCCCCCCEEEEEECCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             64851334776877687479998570264267545318999999888986405878999999999999874124347977


Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             35388889999999999999999999999887201110-36777655679999999999999999569988521300045
Q gi|254780299|r  349 LIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSR-SEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEE  427 (562)
Q Consensus       349 L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~-~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee  427 (562)
                      |++||+||++|++|.++++++++|+|++++.+|+.... +.+..++|+++|++|+|+|+.+.+++++|||+|||+||++|
T Consensus       306 i~~~~~v~~~La~m~~~~eaa~~l~~~~a~~~d~~~~~~~~~~~~~rl~t~iaK~~~~~~a~~~~~~amqi~GG~Gy~ee  385 (418)
T cd01154         306 LIDHPLMRRDLAEMEVDVEAATALTFRAARAFDRAAADKPVEAHMARLATPVAKLIACKRAAPVTSEAMEVFGGNGYLEE  385 (418)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             45369999999999999999999999999998436999767899888889999999999999999999997026013368


Q ss_pred             CHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf             518898500122322046222789999998312
Q gi|254780299|r  428 RSIARHYRESPANSILLGSGNAMVLDVLNLLEK  460 (562)
Q Consensus       428 ~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r  460 (562)
                      +|++|+|||++|++|||||+|||+||++|+|.|
T Consensus       386 ~~v~r~~RDa~i~~I~EGT~~Iq~ld~~Ral~k  418 (418)
T cd01154         386 WPVARLHREAQVTPIWEGTGNIQALDVLRVLVK  418 (418)
T ss_pred             CHHHHHHHHCCCCCEECCHHHHHHHHHHHHHCC
T ss_conf             369999974516611068999999999998529


No 3  
>cd01153 ACAD_fadE5 Putative acyl-CoA dehydrogenase (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position.
Probab=100.00  E-value=0  Score=526.75  Aligned_cols=364  Identities=23%  Similarity=0.368  Sum_probs=311.6

Q ss_pred             CCCEECCCCCCCCCCC--EEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHH
Q ss_conf             6984620179985213--65668899999999996796203377666644476379999999998301445312213567
Q gi|254780299|r   80 NTPQLHAYGPGGERWD--KVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVT  157 (562)
Q Consensus        80 ~~P~l~~~d~~G~r~d--~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt  157 (562)
                      -.|.-..+|+.+..+|  .+.|+|.++++++...+.||.++.+++++++.+.+  .........-++....+..+...+.
T Consensus        13 i~P~~~e~dr~~~~~~~~~~~~p~~~~e~~~~~~e~Gl~g~~vPee~GG~G~~--~~~~~~~~eel~r~~~~~~~~~~~~   90 (407)
T cd01153          13 LAPLNADGDREGPVFDDGRVVVPPPFKEALDAFAEAGWMALGVPEEYGGQGLP--ITVYSALAEIFSRGDAPLMYASGTQ   90 (407)
T ss_pred             CCCCCHHHHHCCCCCCCCCEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             35772878635771579832678269999999997798888989000999968--9999999999984748899999999


Q ss_pred             HHHHHHHH-CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEE
Q ss_conf             78999985-08788987301200100054426600155212355445888887866543027864896689845146863
Q gi|254780299|r  158 SASMVALM-TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLS  236 (562)
Q Consensus       158 ~~a~~~L~-~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~s  236 (562)
                      .++...+. ++++|+++|+|++.+++.             ++++++|||++|||+.+++|+|++++||.|+|||+|+|+|
T Consensus        91 ~~~~~i~~~Gt~eqk~~~Lp~i~~G~~-------------~~a~a~TEp~~GSd~~~~~T~A~~~gdG~~vlnG~K~~it  157 (407)
T cd01153          91 GAAATLLAHGTEAQREKWIPRLAEGEW-------------TGTMCLTEPDAGSDLGALRTKAVYQADGSWRINGVKRFIS  157 (407)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHCCCH-------------HEEEEECCCCCCCCCCCCEEEEEECCCCEEEEEEEEEEEE
T ss_conf             999999985999999998999968972-------------3498855897678845011255674897189961243352


Q ss_pred             CCC-CC----EEEEEEECCC------CCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEEEEECCCCCH
Q ss_conf             421-15----7999704699------617999877589884034788630475545657727999869075300777657
Q gi|254780299|r  237 SPM-SD----AFIMLAQVEG------RVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFGFLLGDLNVS  305 (562)
Q Consensus       237 a~~-ad----~~lVlArt~~------Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~~llG~~g~G  305 (562)
                      ++. ++    +++|+||+++      |+|+|+||++.||++.+++++.+.++|+|+|+++++++.|+||++.++|++|+|
T Consensus       158 ~g~~a~~~~~~~~v~art~~~~~~~~g~s~flVp~~~~~~~~~G~~v~~~~~~~G~rg~~~~~l~f~dv~v~llG~~g~G  237 (407)
T cd01153         158 AGEHDMSENIVHLVLARSEGAPPGVKGLSLFLVPKFLDDGERNGVTVARIEEKMGLHGSPTCELVFDNAKGELIGEEGMG  237 (407)
T ss_pred             CCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCCEEEEEECCCCCCCCCCCEEECCCCCEECCCCCCCCC
T ss_conf             13346635579999984589876766733676457567888797488301144477778840001356331233677754


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCC--------HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999997301333579999999999999999998404622242353888--------89999999999999999999999
Q gi|254780299|r  306 TGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPV--------MKRAIADIALDIAAATALSFRLA  377 (562)
Q Consensus       306 ~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~--------v~~~LAdm~~~~eaa~~l~~~~A  377 (562)
                      +++++..++.+|+.+++.++|+++++++.+++|+++|+|||+||.++|.        +|++|++|.+.+++++++.++++
T Consensus       238 ~~~~~~~l~~~R~~~aa~~lG~a~~al~~a~~ya~~R~~fg~pi~~~q~v~~~~~~~~~~~la~~~~~~e~~r~~~~~~a  317 (407)
T cd01153         238 LAQMFAMMNGARLGVGTQGTGLAEAAYLNALAYAKERKQGGDLIKAAPAVTIIHHPDVRRSLMTQKAYAEGSRALDLYTA  317 (407)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             77776333079999999999999999999999987777437611211320465149999999999999999999999999


Q ss_pred             HHHHCCCCCHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHH
Q ss_conf             887201110367-------7765567999999999999999956998852130004551889850012232204622278
Q gi|254780299|r  378 NSFDEAKSRSEE-------AAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAM  450 (562)
Q Consensus       378 ~~~D~~~~~~~~-------~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~  450 (562)
                      +..|.+.....+       .+.+.++++++|+++++.+.+++++|||+|||+||++|+|++|+|||+|+++||||||+||
T Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~a~~~~s~aK~~ase~a~~v~~~a~ql~GG~Gy~~e~~ler~~RDar~~~I~eGt~eIq  397 (407)
T cd01153         318 TVQDLAERKATEGEDRKALSALADLLTPVVKGFGSEAALEAVSDAIQVHGGSGYTREYPIEQYYRDARITTIYEGTTGIQ  397 (407)
T ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCHHHHH
T ss_conf             99875456655277888777767778899999999999999999999731276711689999999876357226699999


Q ss_pred             HHHHH-HHH
Q ss_conf             99999-983
Q gi|254780299|r  451 VLDVL-NLL  458 (562)
Q Consensus       451 aldv~-r~l  458 (562)
                      +++++ |.|
T Consensus       398 ~~~iigr~~  406 (407)
T cd01153         398 ALDLIGRKI  406 (407)
T ss_pred             HHHHHHHCC
T ss_conf             988798617


No 4  
>cd01155 ACAD_FadE2 FadE2-like Acyl-CoA dehydrogenase (ACAD). Acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACAD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. ACAD's are generally homotetramers and have an active site glutamate at a conserved position.
Probab=100.00  E-value=0  Score=517.59  Aligned_cols=353  Identities=17%  Similarity=0.159  Sum_probs=294.0

Q ss_pred             CCEECCCCCCCC-CCCE-EECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC---CCCCCCCHH
Q ss_conf             984620179985-2136-56688999999999967962033776666444763799999999983014---453122135
Q gi|254780299|r   81 TPQLHAYGPGGE-RWDK-VEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQL---EAGHLMSPS  155 (562)
Q Consensus        81 ~P~l~~~d~~G~-r~d~-v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~---~~g~~cp~~  155 (562)
                      .|.-..+|+... ..|. ...++-+++|++.+.+.||.++.+++++++.+.+  .+......+-++.+   ...+.|-..
T Consensus        19 ~P~~~e~~~~~~~~~~~~~~~~~~~~~l~~~~~~~G~~g~~~PeeyGG~G~~--~~~~~~~~Eel~r~~~~~~~~~~~~~   96 (394)
T cd01155          19 YPAEQEFLEYYAEGGDRWWTPPPIIEKLKAKAKAEGLWNLFLPEVSGLSGLT--NLEYAYLAEETGRSFFAPEVFNCQAP   96 (394)
T ss_pred             CCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHCCCCCC--HHHHHHHHHHHHHHCCCCCCCHHHHH
T ss_conf             4865888866511555311361479999999996797788998634899989--99999999999762634210010324


Q ss_pred             HHHHHHHHH--HCCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCC-CCCCHHHCCEEEEECCCCEEEECCEE
Q ss_conf             677899998--508788987301200100054426600155212355445888-88786654302786489668984514
Q gi|254780299|r  156 VTSASMVAL--MTTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKR-GGTDIAAITSQGQKISDGIYCLSGHK  232 (562)
Q Consensus       156 mt~~a~~~L--~~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~-~GSDv~~~~T~A~~~gdg~y~LnG~K  232 (562)
                      .+ +...+|  .+++||+++|||++++++.             +++++||||+ +|||+.+++|+|+++||+ |+|||+|
T Consensus        97 ~~-g~~~~l~~~Gteeqk~~~Lp~l~~Ge~-------------~~~~a~TEP~~agsD~~~~~T~A~~dgd~-~vlnG~K  161 (394)
T cd01155          97 DT-GNMEVLHRYGSEEQKKQWLEPLLDGKI-------------RSAFAMTEPDVASSDATNIECSIERDGDD-YVINGRK  161 (394)
T ss_pred             HH-HHHHHHHHHCCHHHHHHHHHHHHCCCH-------------HEEEEEECCCCCCCCHHHCEEEEEECCCE-EEEEEEE
T ss_conf             55-159999986999999998899847872-------------13888636987889678877898863998-9995379


Q ss_pred             EEEECC---CCCEEEEEEECCC-------CCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCC--EEEEEECCEE---EE
Q ss_conf             686342---1157999704699-------6179998775898840347886304755456577--2799986907---53
Q gi|254780299|r  233 WFLSSP---MSDAFIMLAQVEG-------RVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNA--TVELEFSNTF---GF  297 (562)
Q Consensus       233 wf~sa~---~ad~~lVlArt~~-------Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~--t~ei~f~~~~---~~  297 (562)
                      ||||++   ++++++|+|||++       ++|+|+||++.||     +++.+..+|+|.+.++  ++++.|+||+   .+
T Consensus       162 ~~is~a~~a~a~~~~v~art~~~~~~~~~~~s~flV~~~~pG-----v~~~~~~~~~G~~~~~~g~~ev~fddv~VP~~~  236 (394)
T cd01155         162 WWSSGAGDPRCKIAIVMGRTDPDGAPRHRQQSMILVPMDTPG-----VTIIRPLSVFGYDDAPHGHAEITFDNVRVPASN  236 (394)
T ss_pred             EECCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEEEECCCCC-----EEECCCCCEECCCCCCCCCCEEEEEEECCCCEE
T ss_conf             711577566654799999606887777662689999726897-----462355421033478987423653123025210


Q ss_pred             EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00777657999999730133357999999999999999999840462224235388889999999999999999999999
Q gi|254780299|r  298 LLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLA  377 (562)
Q Consensus       298 llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A  377 (562)
                      +||++|+||++++..+|.+|+.+++.++|+++++++.+++|+++|+|||+||++||.||++|+||.++++++|+++++++
T Consensus       237 llG~~g~G~~~~~~~l~~~R~~~aa~~vG~a~~al~~a~~ya~~R~~fG~pi~~~q~v~~~ladm~~~ieaar~l~~~aa  316 (394)
T cd01155         237 LILGEGRGFEIAQGRLGPGRIHHCMRLIGAAERALELMCQRAVSREAFGKKLAQHGVVAHWIAKSRIEIEQARLLVLKAA  316 (394)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             13778861999998878999999999855048899888898761111797766489999999999999999999999999


Q ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHH
Q ss_conf             88720111036777655679999999999999999569988521300045518898500122322046222789999998
Q gi|254780299|r  378 NSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNL  457 (562)
Q Consensus       378 ~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~  457 (562)
                      +.+|++.+..     ++..++++|+++++.+.+++++|||+|||+||++|+|++|+|||+++++|||||++||.+.+.|.
T Consensus       317 ~~~D~~~~~~-----~~~~~a~aK~~ase~a~~va~~aiqi~Gg~G~~~e~~~~r~~Rdar~~~I~eGt~EI~r~iIar~  391 (394)
T cd01155         317 HMIDTVGNKA-----ARKEIAMIKVAAPRMALKIIDRAIQVHGAAGVSQDTPLANMYAWARTLRIADGPDEVHLRSIARM  391 (394)
T ss_pred             HHHHCCCCCH-----HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             9984799831-----69999999999999999999999996397300654699999998752774234999999999999


Q ss_pred             HCC
Q ss_conf             312
Q gi|254780299|r  458 LEK  460 (562)
Q Consensus       458 l~r  460 (562)
                      +-|
T Consensus       392 ~L~  394 (394)
T cd01155         392 ELK  394 (394)
T ss_pred             HHC
T ss_conf             859


No 5  
>cd01161 VLCAD Very long chain acyl-CoA dehydrogenase (VLCAD). VLCAD acyl-CoA dehydrogenases (ACAD), which is found in the mitochondria of eukaryotes and in some bacteria.  It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. VLCAD, which is a homodimer.
Probab=100.00  E-value=0  Score=511.63  Aligned_cols=332  Identities=20%  Similarity=0.276  Sum_probs=286.2

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHH--HHHHHH-HCCHHHHHHHHHHHCC
Q ss_conf             9999999967962033776666444763799999999983014453122135677--899998-5087889873012001
Q gi|254780299|r  104 HALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTS--ASMVAL-MTTPRVHKDWAPKIFS  180 (562)
Q Consensus       104 ~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~--~a~~~L-~~~~e~~~~~lp~l~s  180 (562)
                      +++++...+.||.++.+++++++.+.+  ++..+...+.++. ..+...++.++.  +..+.+ .+++||+++|+|++.+
T Consensus        59 ~e~~~~l~e~Gl~gl~vPee~GG~G~~--~~~~~~v~Eelg~-~~~~~~~~~~~~~~~~~~i~~~Gt~eqk~~~Lp~la~  135 (409)
T cd01161          59 RKTLTQLKELGLFGLQVPEEYGGLGLN--NTQYARLAEIVGM-DLGFSVTLGAHQSIGFKGILLFGTEAQKEKYLPKLAS  135 (409)
T ss_pred             HHHHHHHHHCCCCCCCCCHHHCCCCCC--HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHC
T ss_conf             999999997799889989323999989--9999999999977-7155799999999999999986999999999899967


Q ss_pred             CCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCC-EEEECCEEEEEE-CCCCCEEEEEEECC--------
Q ss_conf             00054426600155212355445888887866543027864896-689845146863-42115799970469--------
Q gi|254780299|r  181 REYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDG-IYCLSGHKWFLS-SPMSDAFIMLAQVE--------  250 (562)
Q Consensus       181 ~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg-~y~LnG~Kwf~s-a~~ad~~lVlArt~--------  250 (562)
                      ++.             ++++++|||++|||+.+++|+|++++|| +|+|||+|+|+| ++.+|+++|+|||+        
T Consensus       136 Ge~-------------~~a~a~tEp~aGsD~~~~~t~A~~~~dG~~~vLnG~K~~it~a~~Ad~~~V~Art~~~~~~~~~  202 (409)
T cd01161         136 GEW-------------IAAFALTEPSSGSDAASIRTTAVLSEDGKHYVLNGSKIWITNGGIADIFTVFAKTEVKDATGSV  202 (409)
T ss_pred             CCE-------------EEEEEECCCCCCCCHHCCCCEEEECCCCCEEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCC
T ss_conf             996-------------8999953898788600082058991899889999998676775638899999988877888776


Q ss_pred             -CCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEE---EEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             -961799987758988403478863047554565772799986907---5300777657999999730133357999999
Q gi|254780299|r  251 -GRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTF---GFLLGDLNVSTGPVEDMKILIYLDSAIMSVS  326 (562)
Q Consensus       251 -~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~---~~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G  326 (562)
                       +|+|+|+||++.||     +++.+.++|+|+|+++++++.|+||+   .++||++|+|++.++..++.+|+.+++.++|
T Consensus       203 ~~gis~flV~~~~pG-----v~~~~~~~~~G~r~~~~~~v~f~dv~VP~~~llG~~g~g~~~~~~~l~~~R~~~aa~~~G  277 (409)
T cd01161         203 KDKITAFIVERSFGG-----VTNGPPEKKMGIKGSNTAEVYFEDVKIPVENVLGEVGDGFKVAMNILNNGRFGMGAALIG  277 (409)
T ss_pred             CCCEEEEEEECCCCC-----CEECCCCCCCCCCCCCCCEEECCCCCCCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             687679999637898-----232575444577777762120230125555336667864021443106788888888889


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999984046222423538888999999999999999999999988720111036777655679999999999
Q gi|254780299|r  327 GMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCK  406 (562)
Q Consensus       327 ~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e  406 (562)
                      +++++++.+++|+++|+|||+||++||.||++|+||.++++++|+++|++++.+|++....     ..+.++++|++++|
T Consensus       278 ~a~~al~~a~~ya~~R~qFG~pI~~~q~vq~~ladm~~~~eaar~l~~~aa~~~d~~~~~~-----~~~~aa~aK~~ase  352 (409)
T cd01161         278 TMKRCIEKAVDYANNRKQFGKKIHEFGLIQEKLANMAILQYATESMAYMTSGNMDRGLKAE-----YQIEAAISKVFASE  352 (409)
T ss_pred             HHHHHHHHHHHHHHCCHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHHH
T ss_conf             9999999877787412304975001699999999999999999999999999986799965-----13999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCCC
Q ss_conf             9999995699885213000455188985001223220462227899999983126
Q gi|254780299|r  407 MAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEKG  461 (562)
Q Consensus       407 ~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r~  461 (562)
                      .+.+++++|||+|||+||++|+|++|+|||+++..|||||++||.+.+.|.+-|.
T Consensus       353 ~a~~va~~a~qi~GG~Gy~~e~~ver~~Rdar~~~I~eGt~ei~r~iIa~~~l~~  407 (409)
T cd01161         353 AAWLVVDEAIQIHGGMGFMREYGVERVLRDLRIFRIFEGTNEILRLFIALTGLQH  407 (409)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCEECCHHHHHHHHHHHHHHHH
T ss_conf             9999999999965760014556999999973784764778999999999999885


No 6  
>KOG0137 consensus
Probab=100.00  E-value=0  Score=498.54  Aligned_cols=462  Identities=21%  Similarity=0.260  Sum_probs=369.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCH
Q ss_conf             11078999999850189999998634369846201799852136566889999999999679620337766664447637
Q gi|254780299|r   53 VVHKELELLGEYVLSCTAQELARMANYNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQA  132 (562)
Q Consensus        53 ~~~~~l~~~g~~~~~~~~~~~~~~a~~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~  132 (562)
                      -+.+++-.+++..-++ ..+..+...--.|++-.-+.|++++|...  .-|+...+...+.|+.++.++.+++|.+... 
T Consensus        64 ~v~k~v~~yPev~~~e-~~~~~~~~~~pl~r~f~e~~d~~k~d~~~--~~~~~t~e~l~elG~fgl~v~~e~~G~G~~n-  139 (634)
T KOG0137          64 LVTKDVFPYPEVITSE-QKELLEQFVLPLERFFEEVNDSKKNDKLG--KIEETTLEALRELGLFGLQVPSEFDGLGFCN-  139 (634)
T ss_pred             HHHHHHCCCCCCCCHH-HHHHHHHHHHHHHHHHHCCCHHHHHHHHC--CCCHHHHHHHHHHCCEEECCCCCCCCCCCCH-
T ss_conf             2343315775658689-99998744425777641223043312312--5614579999970711520574247622345-


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCHHHHHHHHHH-----HHCCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCC
Q ss_conf             9999999998301445312213567789999-----85087889873012001000544266001552123554458888
Q gi|254780299|r  133 HKIRAARLYLMAQLEAGHLMSPSVTSASMVA-----LMTTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRG  207 (562)
Q Consensus       133 ~~~~~a~~~l~~~~~~g~~cp~~mt~~a~~~-----L~~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~  207 (562)
                        .++++.....++. -..|+++|+......     |.++++|+++|+|+|.|++.             ..+++||||..
T Consensus       140 --tq~arl~e~~~~~-D~~v~~tl~ahq~i~~k~l~lyGt~~Qk~kYL~~LaSg~~-------------~~A~altE~s~  203 (634)
T KOG0137         140 --TQYARLFEIVSVA-DLNVGVTLGAHQSIGLKGLLLYGTDEQKQKYLPKLASGKL-------------IAAFALTEPSS  203 (634)
T ss_pred             --HHHHHHHHCCCCC-CCCCEEEECCCHHHHEEEEEECCCHHHHHHHHHHHHCCCC-------------CCEEEEECCCC
T ss_conf             --8888776104310-1362046312321101222210887889887776515880-------------11379964788


Q ss_pred             CCCHHHCCEEEEECCC-CEEEECCEE-EEEECCCCCEEEEEEECC---------CCCEEEEEECCCCCCCCCCEEEEEEC
Q ss_conf             8786654302786489-668984514-686342115799970469---------96179998775898840347886304
Q gi|254780299|r  208 GTDIAAITSQGQKISD-GIYCLSGHK-WFLSSPMSDAFIMLAQVE---------GRVGCFLVPRLLEDGSPNGLCYQRLK  276 (562)
Q Consensus       208 GSDv~~~~T~A~~~gd-g~y~LnG~K-wf~sa~~ad~~lVlArt~---------~Gls~FlVp~~~pgg~~n~v~i~r~~  276 (562)
                      |||+++.+|+|+..+| ++|+|||.| ||+|++.+|+|+|+|+|+         +++|+|||+++..|     ++-.+.+
T Consensus       204 Gsdaas~~~~a~~s~dg~~y~LNG~Kiwisn~g~Adif~VfAqt~~~~~~g~~k~k~T~Flver~~~G-----vt~G~~e  278 (634)
T KOG0137         204 GSDAASGRTTATLSPDGKHYVLNGSKIWISNGGLADIFTVFAQTEVDPADGEVKRKITAFLVERDFGG-----VTNGPPE  278 (634)
T ss_pred             CCCCCCCEEEEEECCCCCEEEECCEEEEEECCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCC-----CCCCCCH
T ss_conf             76544443344664778757874725898668542013655125668987644674379998511158-----6689810


Q ss_pred             CCCCCCCCCEEEEEECCEE---EEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCC
Q ss_conf             7554565772799986907---5300777657999999730133357999999999999999999840462224235388
Q gi|254780299|r  277 NKIGNRSNATVELEFSNTF---GFLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQP  353 (562)
Q Consensus       277 ~klG~r~~~t~ei~f~~~~---~~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p  353 (562)
                      .|||++++.++++.|+++.   .++||++|+||+++++++|.+|+..++.++|.|+++++++.+|+..|.|||++|.++.
T Consensus       279 ~k~GiKgsnt~~v~f~~~ki~~envlG~~G~G~kva~nilnsgR~~~aaa~~G~mkr~I~~~~d~~~~rtQ~g~~L~~~~  358 (634)
T KOG0137         279 KKMGIKGSNTAEVHFEGVKIPIENVLGKPGDGFKVAMNILNSGRFGMAAALLGLMKRIIEEAADYATNRTQFGKKLHDFG  358 (634)
T ss_pred             HHHCCCCCCEEEEEECCCCCCHHHHCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCEECCCCHHHHH
T ss_conf             32056666424454101555188744898862699999871577660688899999999999998605510481511102


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             88999999999999999999999988720111036777655679999999999999999569988521300045518898
Q gi|254780299|r  354 VMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARH  433 (562)
Q Consensus       354 ~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl  433 (562)
                      ++|.++++|...+++..++.|-++..+|+.....     .++.++|.|+|++|.++.|+++++||+||+||++|+|+||+
T Consensus       359 l~q~k~~~m~~~~Ya~ESm~yl~sg~~D~~~a~d-----~~lEaai~Ki~a~e~a~~v~se~iqi~Gg~g~m~d~g~Er~  433 (634)
T KOG0137         359 LIQEKVAEMASKVYATESMLYLLSGLMDEVGAKD-----VQLEAAILKIFASEQAWAVVSEAIQIVGGMGYMRDTGLERL  433 (634)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEE-----EEEHHHHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCHHHH
T ss_conf             6899999999999999999999842445456615-----66147899998665799998864511055000356766777


Q ss_pred             HHCCHHHHHCCCCHHHHHHHHHHH-HCCCHHHHHHHHHHHHH-HCCCCHHHHHHHHHHHH----------CCCCCCHHHH
Q ss_conf             500122322046222789999998-31260379999999996-42545177899999873----------0542213778
Q gi|254780299|r  434 YRESPANSILLGSGNAMVLDVLNL-LEKGTNLFEQLFSTLEQ-DLGSSGKKVITILRDSI----------SLCKEDKGLA  501 (562)
Q Consensus       434 ~RDA~v~~I~EGt~~I~aldv~r~-l~r~~~~~~~l~~~l~~-~~g~~~~~~~~~l~~~~----------~~~~~~e~~A  501 (562)
                      +||++++.|||||++|+.|++++. +++.+..+......+.. ..+-......+ +++..          ...+.++..+
T Consensus       434 LRD~ri~~I~egtndvLrlfiAltg~q~ag~~l~~~~r~~kn~n~gli~~~~~~-~~~~~g~~~~~~ls~hvhpsL~~sa  512 (634)
T KOG0137         434 LRDARILRIFEGTNDVLRLFIALTGLQHAGKHLATGVRALKNANPGLIGGKVSR-LRSLRGPGTGLYLSEHVHPSLQDSA  512 (634)
T ss_pred             HHHHHEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHCCHHHH-HHHCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             654230122137506899999999877666788877777613772100221222-4431488766553123487899999


Q ss_pred             HHHHHHHHHHHHH--HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999999999--9999708579999999964002565545114
Q gi|254780299|r  502 RFLTEKIALASSA--AALYRAGMNDIADVFLENRFLDNCHSTHCML  545 (562)
Q Consensus       502 R~~~e~la~~~~a--alL~r~a~~~va~af~~~Rl~~~~~~~~g~l  545 (562)
                      ..+...+++..+.  .+|.+|+.+++.+++...||++.....|+|.
T Consensus       513 q~~e~~~~~~~~~Ve~ll~k~~k~iv~~q~~l~rlA~~~~~iYam~  558 (634)
T KOG0137         513 QKLESSLARFQQVVEKLLTKHGKGIVEEQSVLQRLANVAINIYAMV  558 (634)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999998853661478999999999999998887


No 7  
>KOG0139 consensus
Probab=100.00  E-value=0  Score=496.97  Aligned_cols=330  Identities=21%  Similarity=0.325  Sum_probs=285.9

Q ss_pred             CCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC--CCCCCCCHHHHH
Q ss_conf             984620179985213656688999999999967962033776666444763799999999983014--453122135677
Q gi|254780299|r   81 TPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQL--EAGHLMSPSVTS  158 (562)
Q Consensus        81 ~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~--~~g~~cp~~mt~  158 (562)
                      .|..+++|+.+      .|++.   ..+..++.||.++..++++++.+.-  +...++..+-.+-.  +.+..|-+.-|.
T Consensus        57 ~Plv~~mD~~~------~~~~~---v~k~~fe~Glmgv~vpeeyGGsG~d--f~~~~~v~EEisk~d~sv~~~v~v~ntL  125 (398)
T KOG0139          57 KPLVREMDRES------RYPAS---VIKGLFELGLMGVEVPEEYGGSGLD--FFAAAIVIEEISKVDASVGVIVDVQNTL  125 (398)
T ss_pred             CHHHHHHHHHC------CCCHH---HHHHHHHCCCCEEECCHHHCCCCHH--HHHHHHHHHHHHCCCCCCEEEEEECCCC
T ss_conf             56877631214------58999---9998765372036467665887144--9999999999843486510588731332


Q ss_pred             HHHHHHH-CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEE-EEEE
Q ss_conf             8999985-0878898730120010005442660015521235544588888786654302786489668984514-6863
Q gi|254780299|r  159 ASMVALM-TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHK-WFLS  236 (562)
Q Consensus       159 ~a~~~L~-~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~K-wf~s  236 (562)
                      -..+.++ +++||++.|+|++....              .++++++||++|||+.++.|+|+++||. |+|||+| |++|
T Consensus       126 ~~~~i~~fGteeqK~~~~P~~~~d~--------------vgsfAlSEpgaGSDa~A~~T~Ak~~Gd~-~viNGsKmWItN  190 (398)
T KOG0139         126 YLPLIIQFGTEEQKEKYLPKLTGDL--------------VGSFALSEPGAGSDAFALKTTAKKDGDD-YVINGSKMWITN  190 (398)
T ss_pred             CCHHHHHHCCHHHHHHHCCHHHCCC--------------CCEEEECCCCCCCCHHHHHHHHHHCCCE-EEEECCEEEECC
T ss_conf             3068887473988745334021031--------------1104543787876357766467535772-897343541038


Q ss_pred             CCCCCEEEEEEECC-----CCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHH
Q ss_conf             42115799970469-----9617999877589884034788630475545657727999869075---300777657999
Q gi|254780299|r  237 SPMSDAFIMLAQVE-----GRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGP  308 (562)
Q Consensus       237 a~~ad~~lVlArt~-----~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~  308 (562)
                      ++.++.++|+|.++     +|+|||+||++.||     +++.+.+||+|+|++.||.+.|+||++   ++||++|+|+++
T Consensus       191 ~~~A~~~lVfan~d~~~~~Kgit~fiV~rd~~G-----l~~~k~eDKLGmRaSsTcql~fedVrVpks~IlGe~G~Gyky  265 (398)
T KOG0139         191 AGEADWFLVFANADPSKGYKGITCFIVPRDTPG-----LSLGKKEDKLGMRASSTCQLHFEDVRVPKSSILGEYGKGYKY  265 (398)
T ss_pred             CCCCCEEEEEEECCHHHCCCCEEEEEEECCCCC-----CCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHCCCCCCCHHH
T ss_conf             643546899973684545576269996079887-----435884321366446544677414113504205677854489


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             99973013335799999999999999999984046222423538888999999999999999999999988720111036
Q gi|254780299|r  309 VEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSE  388 (562)
Q Consensus       309 i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~  388 (562)
                      .++.+|.+|+.++++.+|+++.|+++++.|+++|.|||++|.++|.+|++||+|++++|++|+|+|++|++.|++.+-..
T Consensus       266 Am~~Ln~gRIgi~AqmlglaQ~c~d~tI~Y~q~R~~FGk~l~d~Q~iQhqiA~~~teiEaaRlL~ynaAr~k~~G~pf~k  345 (398)
T KOG0139         266 AIEVLNAGRIGIGAQMLGLAQGCFDETIPYAQERLQFGKRLLDFQGLQHQIADMATEIEAARLLVYNAARMKDQGLPFVK  345 (398)
T ss_pred             HHHHCCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             98732753221046663577767876307899998845046667889999999999999999999999999875996478


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHH
Q ss_conf             777655679999999999999999569988521300045518898500122322046222
Q gi|254780299|r  389 EAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGN  448 (562)
Q Consensus       389 ~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~  448 (562)
                      |       ++|+|++++|.|..+++.|+|++||.||+.|+|+||+|||++|..|||||+|
T Consensus       346 e-------AAMAKl~ase~A~~~t~qCiq~lGG~Gyt~d~paek~yRDarI~~IyeGtsn  398 (398)
T KOG0139         346 E-------AAMAKLYASEVATKTTHQCIQWLGGVGYTKDFPAEKFYRDARIGEIYEGTSN  398 (398)
T ss_pred             H-------HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCEEEEEECCCCC
T ss_conf             9-------9999874215657789999999703472334618887533031014337789


No 8  
>TIGR03207 cyc_hxne_CoA_dh cyclohexanecarboxyl-CoA dehydrogenase. Cyclohex-1-ene-1carboxyl-CoA is an intermediate in the anaerobic degradation of benzoyl-CoA derived from varioius aromatic compounds, in Rhodopseudomonas palustris but not Thauera aromatica. The aliphatic compound cyclohexanecarboxylate, can be converted to the same intermediate in two steps. The first step is its ligation to coenzyme A. The second is the action of this enzyme, cyclohexanecarboxyl-CoA dehydrogenase.
Probab=100.00  E-value=0  Score=479.39  Aligned_cols=324  Identities=21%  Similarity=0.235  Sum_probs=281.3

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH--CCHHHHHHHHHHHCCCC
Q ss_conf             9999999679620337766664447637999999999830144531221356778999985--08788987301200100
Q gi|254780299|r  105 ALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSASMVALM--TTPRVHKDWAPKIFSRE  182 (562)
Q Consensus       105 ~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~a~~~L~--~~~e~~~~~lp~l~s~~  182 (562)
                      ++++...+.||.++.+++++++.+.  ..+..++...-++..+.+..+...++......|.  +++|++++|+|++.+++
T Consensus        36 e~~~~~~e~G~~gl~vPee~GG~G~--~~~~~~~v~Eelg~~~~~~~~~~~~~~~~~~~l~~~g~~e~k~~~L~~l~~G~  113 (372)
T TIGR03207        36 ELMRDMGEMGFIGPELPEEHGGLGM--GCLAAGVIHEQIARADLSMSYVNLLASLNGQILAQHARPEIAKPWLGQLIAGE  113 (372)
T ss_pred             HHHHHHHHCCCCCCCCCHHHCCCCC--CHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCC
T ss_conf             9999999779987899965689998--99999999999976276366899999999999998398999999879984998


Q ss_pred             CCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEE-CCCCCEEEEEEECC------CCCEE
Q ss_conf             054426600155212355445888887866543027864896689845146863-42115799970469------96179
Q gi|254780299|r  183 YDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLS-SPMSDAFIMLAQVE------GRVGC  255 (562)
Q Consensus       183 ~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~s-a~~ad~~lVlArt~------~Gls~  255 (562)
                      .             ++++++|||++|||+..++|+|++++|+ |+|||+|+|+| ++.+|+++|+|||+      .|+|+
T Consensus       114 ~-------------~~~~a~tEp~~Gsd~~~~~t~a~~~gd~-~~lnG~K~~it~a~~Ad~~~v~art~~~~~~~~g~s~  179 (372)
T TIGR03207       114 A-------------LFAIALTEPRGGSDAARLRLRAERDGDD-YVLNGEKTSISAADQADAAVVFARTGSEAEGARGISA  179 (372)
T ss_pred             E-------------EEEEEECCCCCCCCCCCCCEEEEEECCE-EEEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCEEE
T ss_conf             0-------------0699955897777613471499994898-9996424044578767689998631764468783478


Q ss_pred             EEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99877589884034788630475545657727999869075---300777657999999730133357999999999999
Q gi|254780299|r  256 FLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSL  332 (562)
Q Consensus       256 FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al  332 (562)
                      |+||++.||     ++..+ .+++|.|+++++++.|+||++   ++||++|+|+..++..++.+|+.+++.++|++++|+
T Consensus       180 ~lV~~~~~G-----v~~~~-~~~~g~r~~~~~~l~fddv~Vp~~~llG~~g~G~~~~~~~~~~~r~~~aa~~~G~a~~al  253 (372)
T TIGR03207       180 FLVPMDLPG-----ITRNR-FDCHGQRAIGRGSIFFENVRVPADHMLGNEGQGFVQVMQGFDFSRALIGLQVLAVARAAL  253 (372)
T ss_pred             EECCCCCCC-----CEEEC-CCCCCCCCCCCCEEEECCEEECHHHCCCCCCCHHHHHHHCCHHHHHHHCHHHHHHHHHHH
T ss_conf             832589998-----35525-446787777865167688756476437876642899975115899985866668999999


Q ss_pred             HHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999984046222423538888999999999999999999999988720111036777655679999999999999999
Q gi|254780299|r  333 AEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVI  412 (562)
Q Consensus       333 ~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~  412 (562)
                      +.+++|+++|+|||+||++||.||++|+||.++++++|+++|++++..|++.+...+       ++++|+++++.+.+++
T Consensus       254 ~~a~~y~~~R~qfG~~I~~~Q~v~~~ladm~~~ieaar~~~~~Aa~~~d~g~~~~~~-------aa~aK~~a~e~a~~~~  326 (372)
T TIGR03207       254 DETWRYVAERQAFGKPLSAFQGVSHPLADAETQVEAARLLCLQTLWLKDHGLPHTSE-------AAMCKWWAPKLAYDVI  326 (372)
T ss_pred             HHHHHHHHHHHCCCCCCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH-------HHHHHHHHHHHHHHHH
T ss_conf             999987640002796603159999999999999999999999999999688997699-------9999999999999999


Q ss_pred             HHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             5699885213000455188985001223220462227899999983
Q gi|254780299|r  413 AEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLL  458 (562)
Q Consensus       413 ~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l  458 (562)
                      ++|||+|||.||.++ |+||+|||+++++|||||++||.+.+.|-+
T Consensus       327 ~~a~qi~Gg~g~~~~-~~er~~Rdar~~~i~~Gt~ei~~~~i~r~~  371 (372)
T TIGR03207       327 HQCLLTHGHGGYDRG-DMEQRLRDVLGFQIGDGTAQIMKTIIARHR  371 (372)
T ss_pred             HHHHHHHCCHHHCCH-HHHHHHHHHHCCCCCCCHHHHHHHHHHHCC
T ss_conf             999998187664562-999999986578752059999999997306


No 9  
>PRK03354 crotonobetainyl-CoA dehydrogenase; Validated
Probab=100.00  E-value=0  Score=480.74  Aligned_cols=339  Identities=16%  Similarity=0.194  Sum_probs=288.6

Q ss_pred             CCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCH----HH
Q ss_conf             98462017998521365668899999999996796203377666644476379999999998301445312213----56
Q gi|254780299|r   81 TPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSP----SV  156 (562)
Q Consensus        81 ~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~----~m  156 (562)
                      +|+...+|+.+      .|++   ++++...+.||.++.+++++++.+.  ..+...+..+-++.    ..+|.    ++
T Consensus        26 ~~~~~~~d~~~------~~p~---~~~~~l~e~G~~~l~vpe~~GG~g~--~~~~~~~v~eelg~----~~~~~~~~~~~   90 (380)
T PRK03354         26 EAYFAECDRDS------VYPE---RFVKALADMGIDSLLIPEEHGGLDA--GFVTLAAVWMELGR----LGAPTYVLYQL   90 (380)
T ss_pred             CHHHHHHHHCC------CCCH---HHHHHHHHCCCCCCCCCHHHCCCCC--CHHHHHHHHHHHHH----HCCCHHHHHHH
T ss_conf             56799998618------9989---9999999779987689842289999--99999999999876----27837899999


Q ss_pred             HHHHHHHHH-CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEE
Q ss_conf             778999985-0878898730120010005442660015521235544588888786654302786489668984514686
Q gi|254780299|r  157 TSASMVALM-TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFL  235 (562)
Q Consensus       157 t~~a~~~L~-~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~  235 (562)
                      ..+..+++. ++++|+++|+|++.+++.             ++++++|||++|||+.+++|++++++| .|+|||+|+|+
T Consensus        91 ~~~~~~i~~~gs~eqk~~~L~~~~~G~~-------------~~~~a~tEp~~Gsd~~~~~t~a~~~~g-~~~lnG~K~~v  156 (380)
T PRK03354         91 PGGFNTFLREGTQEQIDKIMAFRGTGKQ-------------MWNSAITEPGAGSDVGSLKTTYTRRNG-KVYLNGSKCFI  156 (380)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHCCCH-------------HHEEEECCCCCCCCCCCCEEEEEEECC-EEEEEEEEECC
T ss_conf             9999999984999999987388728765-------------515543268777885556258998699-89997179666


Q ss_pred             E-CCCCCEEEEEEECCC-----CCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHH
Q ss_conf             3-421157999704699-----617999877589884034788630475545657727999869075---3007776579
Q gi|254780299|r  236 S-SPMSDAFIMLAQVEG-----RVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVST  306 (562)
Q Consensus       236 s-a~~ad~~lVlArt~~-----Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~  306 (562)
                      | ++.+|+++|+||++.     ++|+|+||++.||     |++.+. +|+|+|+++++++.|++|++   ++||++|+|+
T Consensus       157 t~a~~Ad~~~V~ar~~~~~~~~~~~~flV~~~~pG-----v~~~~~-~~~g~r~~~~~~l~fd~v~vp~~~llg~~g~g~  230 (380)
T PRK03354        157 TSSAYTPYIVVMARDGASPDKPVYTEWFVDMSKPG-----IKVTKL-EKLGLRMDSCCEITFDDVELDEKDMFGREGNGF  230 (380)
T ss_pred             CCCCCCCCEEEEEEECCCCCCCEEEEEEEECCCCC-----EEEEEC-CCCCCCCCCCCCCCCCCCCCCCEECCCCCCHHH
T ss_conf             67766880357766437899864678876569996-----698444-656877677653213440358300005557189


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99999730133357999999999999999999840462224235388889999999999999999999999887201110
Q gi|254780299|r  307 GPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSR  386 (562)
Q Consensus       307 ~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~  386 (562)
                      +.+...++.+|+.+++.++|+++++++.+++|+++|+|||+||++||.||++||||.+++++++++++++++.+|++...
T Consensus       231 ~~~~~~l~~~r~~~aa~~~G~a~~al~~a~~ya~~R~qfG~pi~~~q~vq~~lAdm~~~~e~ar~l~~~aa~~~d~g~~~  310 (380)
T PRK03354        231 NRVKEEFDHERFLVALTNYGTAMCAFEDAARYANQRVQFGEAIGRFQLIQEKFAHMAIKLNSMKNMLYEAAWKADNGTIT  310 (380)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99997021789999999877889999998665430332482365312389999999999999999999999998689997


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCCC
Q ss_conf             367776556799999999999999995699885213000455188985001223220462227899999983126
Q gi|254780299|r  387 SEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEKG  461 (562)
Q Consensus       387 ~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r~  461 (562)
                      ..+       ++++|+++++.+.+++++|||+|||+||++|+|++|+|||+++..|||||++||.+.+.|.+.|.
T Consensus       311 ~~~-------aa~aK~~a~e~a~~v~~~a~qi~GG~G~~~e~~l~r~~Rdar~~~i~~Gt~ei~~~~iar~~l~~  378 (380)
T PRK03354        311 SGD-------AAMCKYFCANAAFEVVDSAMQVLGGVGIAGNHRISRFWRDLRVDRVSGGSDEMQILTLGRAVLKQ  378 (380)
T ss_pred             HHH-------HHHHHHHHHHHHHHHHHHHHHHHCHHHHCCCHHHHHHHHHHHCCCEECCHHHHHHHHHHHHHHHH
T ss_conf             389-------99999999999999999999971607452558999999997341360778999999999999984


No 10 
>cd01162 IBD Isobutyryl-CoA dehydrogenase  (IBD) catalyzes the alpha, beta- dehydrogenation of short branched chain acyl-CoA intermediates in valine catabolism. It is predicted to be a homotetramer.
Probab=100.00  E-value=0  Score=477.82  Aligned_cols=345  Identities=19%  Similarity=0.240  Sum_probs=299.5

Q ss_pred             CCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             69846201799852136566889999999999679620337766664447637999999999830144531221356778
Q gi|254780299|r   80 NTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSA  159 (562)
Q Consensus        80 ~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~  159 (562)
                      ..|....+|+.+      .|++   ++++...+.||.++.+++++++.+.  ..+..+...+..+..+++....++++..
T Consensus        20 ~~p~a~~~d~~~------~~p~---e~~~~~~~~Gl~~~~vPee~GG~G~--~~~~~~~v~e~l~~~~~~~~~~~~~~~~   88 (375)
T cd01162          20 MAPHAADWDQKK------HFPV---DVLRKAAELGFGGIYIRDDVGGSGL--SRLDASIIFEALSTGCVSTAAYISIHNM   88 (375)
T ss_pred             CHHHHHHHHHCC------CCCH---HHHHHHHHCCCCCCCCCHHHCCCCC--CHHHHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             835499998649------9999---9999999779988889842389998--9999999999998856664359999999


Q ss_pred             HHHHHH--CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEE-
Q ss_conf             999985--08788987301200100054426600155212355445888887866543027864896689845146863-
Q gi|254780299|r  160 SMVALM--TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLS-  236 (562)
Q Consensus       160 a~~~L~--~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~s-  236 (562)
                      +...|.  ++++|+++|+|++.+++.             ..++++|||++|||+.+++|+|++++|+ |+|||+|+|+| 
T Consensus        89 ~~~~l~~~g~~~qk~~~l~~i~~g~~-------------~~~~a~tEp~~Gsd~~~~~t~a~~~g~~-~~lnG~K~~it~  154 (375)
T cd01162          89 CAWMIDSFGNDEQRERFLPDLCTMEK-------------LASYCLTEPGSGSDAAALRTRAVREGDH-YVLNGSKAFISG  154 (375)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHCCCC-------------EEEEEECCCCCCCCCCCCEEEEEEECCE-EEEEEEEEECCC
T ss_conf             99999984999999998799847983-------------0488732788888754543599996998-999325850344


Q ss_pred             CCCCCEEEEEEECC----CCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEE---EEEECCCCCHHHHH
Q ss_conf             42115799970469----961799987758988403478863047554565772799986907---53007776579999
Q gi|254780299|r  237 SPMSDAFIMLAQVE----GRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTF---GFLLGDLNVSTGPV  309 (562)
Q Consensus       237 a~~ad~~lVlArt~----~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~---~~llG~~g~G~~~i  309 (562)
                      ++.+|+++|+||++    .|+++|+||++.||     +++.+.++|+|+|+++++++.|+||+   .++||++|+|+..+
T Consensus       155 a~~Ad~~~v~ar~~~~~~~g~~~flV~~~~pG-----v~~~~~~~~~G~~~~~~~~l~fd~v~Vp~~~~lg~~g~g~~~~  229 (375)
T cd01162         155 AGDSDVYVVMARTGGEGPKGISCFVVEKGTPG-----LSFGANEKKMGWNAQPTRAVIFEDCRVPVENRLGGEGQGFGIA  229 (375)
T ss_pred             CCCCCEEEEEEEECCCCCCEEEEEEECCCCCC-----CCCCCCCCCCCCCCCCCEEEEECCCCCCHHHCCCCCCCHHHHH
T ss_conf             66665268998527887642589975279988-----6124311345667788405750452235554068766069999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             99730133357999999999999999999840462224235388889999999999999999999999887201110367
Q gi|254780299|r  310 EDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEE  389 (562)
Q Consensus       310 ~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~  389 (562)
                      +..++.+|+.+++.++|+++++++.+++|+++|+|||+||++||.+|++|+||.+++++++++++++++.+|++.+... 
T Consensus       230 ~~~l~~~rl~~aa~~~G~a~~al~~a~~ya~~R~~fg~pi~~~q~vq~~ladm~~~~~aar~l~~~aa~~~d~~~~~~~-  308 (375)
T cd01162         230 MAGLNGGRLNIASCSLGAAQAALDLARAYLEERKQFGKPLADFQALQFKLADMATELVASRLMVRRAASALDRGDPDAV-  308 (375)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH-
T ss_conf             9877899999898789999999999999988788629850049999999999999999999999999999867997679-


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf             77655679999999999999999569988521300045518898500122322046222789999998312
Q gi|254780299|r  390 AAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEK  460 (562)
Q Consensus       390 ~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r  460 (562)
                           ..++++|+++++.+.+++++|||+|||+||++|+|++|+|||++++.|||||++||.+.+.|.+-+
T Consensus       309 -----~~~~~aK~~~s~~a~~v~~~a~qi~Gg~G~~~e~~l~r~~Rdar~~~i~~Gt~ei~r~~iar~il~  374 (375)
T cd01162         309 -----KLCAMAKRFATDECFDVANQALQLHGGYGYLKDYPVEQYVRDLRVHQILEGTNEIMRLIIARALLT  374 (375)
T ss_pred             -----HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCHHHHHHHHHCCCEECCCHHHHHHHHHHHHHHC
T ss_conf             -----999999999999999999999996473554157589999987178415088799999999999859


No 11 
>cd01152 ACAD_fadE6_17_26 Putative acyl-CoA dehydrogenase (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position.
Probab=100.00  E-value=0  Score=477.77  Aligned_cols=346  Identities=17%  Similarity=0.197  Sum_probs=292.7

Q ss_pred             HHHHCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHH
Q ss_conf             63436984620179985213656688999999999967962033776666444763799999999983014453122135
Q gi|254780299|r   76 MANYNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPS  155 (562)
Q Consensus        76 ~a~~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~  155 (562)
                      .+++.+|....+++.+.+.+. ++++.|.+   ...+.||.++.+++++++.+.  .++.......-++..+..+....+
T Consensus        14 ~~~~i~P~~~~~~~~~~~~~~-~~~~~~~~---~l~e~Gl~gl~vPe~~GG~G~--~~~~~~~v~Eelgr~~~~~~~~~~   87 (380)
T cd01152          14 LAAHLPPELREESALGYREGR-EDRRRWQR---ALAAAGWAAPGWPKEYGGRGA--SLMEQLIFREEMAAAGAPVPFNQI   87 (380)
T ss_pred             HHHHCCCCCCHHHHCCCCCCC-CCHHHHHH---HHHHCCCCCCCCCCCCCCCCC--CHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             997688865305635777643-32799999---999679787588824499999--999999999999975897427999


Q ss_pred             HHHHHHHHHH--CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEE
Q ss_conf             6778999985--08788987301200100054426600155212355445888887866543027864896689845146
Q gi|254780299|r  156 VTSASMVALM--TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKW  233 (562)
Q Consensus       156 mt~~a~~~L~--~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kw  233 (562)
                      +.....+.|.  ++++|+++|+|++.+++.             +.++++|||++|||+.+++|+|++++|+ |+|||+|+
T Consensus        88 ~~~~~~~~l~~~gs~eqk~~~L~~l~~G~~-------------~~a~a~TEp~~GSd~~~~~T~A~~~g~~-~vlnG~K~  153 (380)
T cd01152          88 GIDLAGPTILAYGTDEQKRRFLPPILSGEE-------------IWCQGFSEPGAGSDLAGLRTRAVRDGDD-WVVNGQKI  153 (380)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHCCCH-------------HEEEEECCCCCCCCCHHCEEEEEEECCE-EEEEEEEE
T ss_conf             999999999987999999999999958982-------------0498847998877502084599996998-99974641


Q ss_pred             EEE-CCCCCEEEEEEECC------CCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCC
Q ss_conf             863-42115799970469------9617999877589884034788630475545657727999869075---3007776
Q gi|254780299|r  234 FLS-SPMSDAFIMLAQVE------GRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLN  303 (562)
Q Consensus       234 f~s-a~~ad~~lVlArt~------~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g  303 (562)
                      |+| ++.+|+++|+|||+      +|+|+|+||++.||     |++.+.++++|  ++.++++.|+||++   ++||++|
T Consensus       154 ~it~a~~Ad~~~v~art~~~~~~~~gis~flV~~~~pG-----v~~~~~~~~~g--~~~~~~i~fd~v~Vp~~~llG~~g  226 (380)
T cd01152         154 WTSGAHYADWAWLLVRTDPEAPKHRGISILLVDMDSPG-----VTVRPIRSING--GEFFNEVFLDDVRVPDANRVGEVN  226 (380)
T ss_pred             CCCCHHHCCCCCEEEECCCCCCCCCCEEEEEECCCCCC-----CEEECEEECCC--CCCCEEEEECCEEECHHHCCCCCC
T ss_conf             33340004544401202887666686267852279998-----44621032368--877224767773203121478888


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             57999999730133357999999999999999999840462224235388889999999999999999999999887201
Q gi|254780299|r  304 VSTGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEA  383 (562)
Q Consensus       304 ~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~  383 (562)
                      +|+++++.+++.+|+.++    |.+..+++.+++|+++|.+||+||++||.||++|++|.+++++++++++++++.+|++
T Consensus       227 ~G~~~~~~~l~~~R~~~~----g~a~~~~~~a~~~a~~r~~~G~pl~~~q~vq~~la~m~~~iea~r~l~~~aa~~~d~g  302 (380)
T cd01152         227 DGWKVAMTTLNFERVSIG----GSAATFFELLLARLLLLTRDGRPLIDDPLVRQRLARLEAEAEALRLLVFRLASALAAG  302 (380)
T ss_pred             HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             599999999999999999----9998766366899999986378755689999999999999999999999999999778


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCH--------HHHHHHCCHHHHHCCCCHHHHHHHHH
Q ss_conf             1103677765567999999999999999956998852130004551--------88985001223220462227899999
Q gi|254780299|r  384 KSRSEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERS--------IARHYRESPANSILLGSGNAMVLDVL  455 (562)
Q Consensus       384 ~~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~--------leRl~RDA~v~~I~EGt~~I~aldv~  455 (562)
                      .+...       .++++|+++++.+.+++++|||+|||.||++|+|        ++|+|||+|+++|||||++||.+.+.
T Consensus       303 ~~~~~-------~~a~aK~~a~e~a~~v~~~a~qi~Gg~G~~~~~~~~~~~~~~~er~~Rdar~~~I~eGt~ei~~~~Ia  375 (380)
T cd01152         303 KPPGA-------EASIAKLFGSELAQELAELALELLGTAALLRDPAPGAELAGRWEADYLRSRATTIYGGTSEIQRNIIA  375 (380)
T ss_pred             CCCCH-------HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf             89836-------89999999999999999999998082522566766331002999999752078551309999999999


Q ss_pred             HHHC
Q ss_conf             9831
Q gi|254780299|r  456 NLLE  459 (562)
Q Consensus       456 r~l~  459 (562)
                      |.+.
T Consensus       376 r~ll  379 (380)
T cd01152         376 ERLL  379 (380)
T ss_pred             HHHC
T ss_conf             8851


No 12 
>cd01157 MCAD Medium chain acyl-CoA dehydrogenase (MCAD). MCADs are mitochondrial beta-oxidation enzymes, which catalyze the alpha,beta dehydrogenation of the corresponding medium chain acyl-CoA by FAD, which becomes reduced. The reduced form of MCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. MCAD is a  homotetramer.
Probab=100.00  E-value=0  Score=472.97  Aligned_cols=344  Identities=18%  Similarity=0.206  Sum_probs=296.1

Q ss_pred             HCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHH
Q ss_conf             36984620179985213656688999999999967962033776666444763799999999983014453122135677
Q gi|254780299|r   79 YNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTS  158 (562)
Q Consensus        79 ~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~  158 (562)
                      +.+|....+|+.|      .|+.   ++++...+.||.++.+++++++.+.+  .+.......-.+..+.++..++.++.
T Consensus        19 ~i~p~a~~~d~~~------~~p~---~~~~~l~e~Gl~~~~vPee~GG~G~~--~~~~~~v~eela~~~~~~~~~~~~~~   87 (378)
T cd01157          19 EIIPVAAEYDKSG------EYPW---PLIKRAWELGLMNTHIPEDCGGLGLG--TFDTCLITEELAYGCTGVQTAIEANS   87 (378)
T ss_pred             HCHHHHHHHHHCC------CCCH---HHHHHHHHCCCCCCCCCHHHCCCCCC--HHHHHHHHHHHHHHCCCCCCCCHHHH
T ss_conf             5826599998639------9999---99999997789878998534999999--99999999999751865331012779


Q ss_pred             H-HHHHH-HCCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEE
Q ss_conf             8-99998-508788987301200100054426600155212355445888887866543027864896689845146863
Q gi|254780299|r  159 A-SMVAL-MTTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLS  236 (562)
Q Consensus       159 ~-a~~~L-~~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~s  236 (562)
                      . ..+++ .++++|+++|+|++.+++             .++++++|||++|||+.+++|+|++++|+ |+|||+|+|+|
T Consensus        88 l~~~~l~~~g~~~qk~~~L~~l~~G~-------------~~~~~a~tEp~~Gsd~~~~~t~a~~~gd~-~~lnG~K~~vt  153 (378)
T cd01157          88 LGQMPVIISGNDEQKKKYLGRMTEEP-------------LMCAYCVTEPGAGSDVAGIKTKAEKKGDE-YIINGQKMWIT  153 (378)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHCCC-------------CEEEEEECCCCCCCCCCCCCCEEEEECCE-EEEEEEEECCC
T ss_conf             99999998499999999879984898-------------51798743788777644572279996898-99902774345


Q ss_pred             -CCCCCEEEEEEECC--------CCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCC
Q ss_conf             -42115799970469--------9617999877589884034788630475545657727999869075---30077765
Q gi|254780299|r  237 -SPMSDAFIMLAQVE--------GRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNV  304 (562)
Q Consensus       237 -a~~ad~~lVlArt~--------~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~  304 (562)
                       ++.+|+++|+||++        +++++|+||++.||     |++.+.++++|+|+++++++.|+||++   ++||.+|+
T Consensus       154 ~a~~Ad~~~v~ar~~~~~~~~~~~~~~~flV~~~~pG-----v~~~~~~~~~G~r~~~~~~v~f~dv~vp~~~~lg~~g~  228 (378)
T cd01157         154 NGGKANWYFLLARSDPDPKCPASKAFTGFIVEADTPG-----IQPGRKELNMGQRCSDTRGITFEDVRVPKENVLIGEGA  228 (378)
T ss_pred             CCCCCCEEEEEEEECCCCCCCCCCEEEEEEECCCCCC-----CCCCCCCCCCCCCCCCCCEEEEEEECCCCHHCCCCCCC
T ss_conf             5666762479988468876677760699996367888-----75455002336544674227898641570303678764


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             79999997301333579999999999999999998404622242353888899999999999999999999998872011
Q gi|254780299|r  305 STGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAK  384 (562)
Q Consensus       305 G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~  384 (562)
                      |++.++..++.+|+.+++.++|+++++++.+++|+++|+|||+||++||.+|++|+||.+++++++.+++++++.+|++.
T Consensus       229 g~~~~~~~l~~~r~~~aa~~~G~a~~~l~~a~~ya~~R~~fG~pi~~~q~vq~~lad~~~~le~ar~l~~~aa~~~d~g~  308 (378)
T cd01157         229 GFKIAMGAFDKTRPPVAAGAVGLAQRALDEATKYALERKTFGKLIAEHQAVSFMLADMAMKVELARLAYQRAAWEVDSGR  308 (378)
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             58998761068899887877889999999988877767643977442999999999999999999999999999997899


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHC
Q ss_conf             103677765567999999999999999956998852130004551889850012232204622278999999831
Q gi|254780299|r  385 SRSEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLE  459 (562)
Q Consensus       385 ~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~  459 (562)
                      ...       ..++++|+++++.+.+++++|||+|||+||++|+|++|+|||+++.+|||||++||.+.+.|.+-
T Consensus       309 ~~~-------~~~a~aK~~a~e~a~~v~~~a~q~~Gg~G~~~e~~l~r~~Rdar~~~i~~Gt~ei~r~~iar~ll  376 (378)
T cd01157         309 RNT-------YYASIAKAFAADIANQLATDAVQIFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISREHL  376 (378)
T ss_pred             CCH-------HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             972-------89999999999999999999999817501066668999998625560606789999999999985


No 13 
>cd01151 GCD Glutaryl-CoA dehydrogenase (GCD). GCD is an acyl-CoA dehydrogenase, which catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and carbon dioxide in the catabolism of lysine, hydroxylysine, and tryptophan. It uses electron transfer flavoprotein (ETF) as an electron acceptor. GCD is a homotetramer. GCD deficiency leads to a severe neurological disorder in humans.
Probab=100.00  E-value=0  Score=478.05  Aligned_cols=326  Identities=21%  Similarity=0.254  Sum_probs=282.3

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHH-HHHHHH-H-CCHHHHHHHHHHHCCC
Q ss_conf             999999967962033776666444763799999999983014453122135677-899998-5-0878898730120010
Q gi|254780299|r  105 ALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTS-ASMVAL-M-TTPRVHKDWAPKIFSR  181 (562)
Q Consensus       105 ~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~-~a~~~L-~-~~~e~~~~~lp~l~s~  181 (562)
                      ++++...+.||.++. ++++++.  +...+..++...-++..+.++.+.+.+.. .....| . ++++|+++|+|++.++
T Consensus        48 ~~~~~l~e~G~~g~~-peeyGG~--G~~~~~~~~v~eel~~~~~~~~~~~~~~~~l~~~~l~~~gt~~qk~~~Lp~l~~G  124 (386)
T cd01151          48 KIIEEMGELGLLGAT-IKGYGCA--GLSSVAYGLIAREVERVDSGYRSFMSVQSSLVMLPIYDFGSEEQKQKYLPKLASG  124 (386)
T ss_pred             HHHHHHHHCCCCCCC-HHHHCCC--CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCC
T ss_conf             999999976998788-3310899--9999999999999987477631099999899999999849999999758531599


Q ss_pred             CCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEE-ECCCCCEEEEEEECC--CCCEEEEE
Q ss_conf             005442660015521235544588888786654302786489668984514686-342115799970469--96179998
Q gi|254780299|r  182 EYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFL-SSPMSDAFIMLAQVE--GRVGCFLV  258 (562)
Q Consensus       182 ~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~-sa~~ad~~lVlArt~--~Gls~FlV  258 (562)
                      +.             +.++++|||++|||+.+++|+|++++|+ |+|||+|+|+ +++.+|+++|+||++  +++++|+|
T Consensus       125 ~~-------------~~a~a~tEp~~Gsd~~~~~t~a~~~g~~-~vlnG~K~~it~a~~Ad~~lv~ar~~~~~~~~~flV  190 (386)
T cd01151         125 EL-------------IGCFGLTEPNHGSDPGGMETRARKDGGG-YKLNGSKTWITNSPIADVFVVWARNDETGKIRGFIL  190 (386)
T ss_pred             CE-------------EEEEEECCCCCCCCCCCCEEEEEECCCE-EEEEEEEECCCCCCCCCEEEEEEECCCCCCCEEEEE
T ss_conf             98-------------9999832898887600082699986985-999878506655544553136643168877538998


Q ss_pred             ECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             77589884034788630475545657727999869075---300777657999999730133357999999999999999
Q gi|254780299|r  259 PRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEA  335 (562)
Q Consensus       259 p~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A  335 (562)
                      |++.||     |++.++++|+|+|+++++++.|++|++   +++++ ++|+..++..++.+|+.+++.++|+++++++.+
T Consensus       191 ~~~~~G-----v~~~~~~~~~g~r~~~~~~l~fd~v~Vp~~~~l~~-~~g~~~~~~~l~~~R~~~aa~~~G~a~~ald~a  264 (386)
T cd01151         191 ERGMKG-----LSAPKIQGKFSLRASITGEIVMDNVFVPEENLLPG-AEGLRGPFKCLNNARYGIAWGALGAAEDCYHTA  264 (386)
T ss_pred             ECCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             679887-----51244002345556776221247862509980362-166899999999888663241159999999988


Q ss_pred             HHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99984046222423538888999999999999999999999988720111036777655679999999999999999569
Q gi|254780299|r  336 IHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVIAEA  415 (562)
Q Consensus       336 ~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~~~A  415 (562)
                      ++|+++|+|||+||++||.||++||||.++++++++++|++++..|++.....       .++++|+++|+.+.+++++|
T Consensus       265 ~~ya~~R~qFG~pI~~~q~vq~~ladm~~~le~ar~~~~~aa~~~d~g~~~~~-------~as~aK~~ase~a~~v~~~a  337 (386)
T cd01151         265 RQYVLDRKQFGRPLAAFQLVQKKLADMLTEIALGLLACLRVGRLKDQGKATPE-------QISLLKRNNCGKALEIARTA  337 (386)
T ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH-------HHHHHHHHHHHHHHHHHHHH
T ss_conf             87788888559810018999999999999999999999999999967999779-------99999999999999999999


Q ss_pred             HHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf             988521300045518898500122322046222789999998312
Q gi|254780299|r  416 MECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEK  460 (562)
Q Consensus       416 iqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r  460 (562)
                      ||+|||+||++|+|++|+|||++++.|||||++||.+.+.|.+..
T Consensus       338 ~Qi~GG~G~~~e~~~~r~~Rdar~~~i~eGt~ev~r~~iar~l~G  382 (386)
T cd01151         338 REMLGGNGISDEYHIIRHMVNLESVNTYEGTHDIHALILGRAITG  382 (386)
T ss_pred             HHHCCCHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             996521533423789999999826352278799999999999758


No 14 
>cd01156 IVD Isovaleryl-CoA dehydrogenase (IVD) is an is an acyl-CoA dehydrogenase, which catalyzes the third step in leucine catabolism, the conversion of isovaleryl-CoA (3-methylbutyryl-CoA) into 3-methylcrotonyl-CoA. IVD is a homotetramer and has the greatest affinity for small branched chain substrates.
Probab=100.00  E-value=0  Score=461.02  Aligned_cols=328  Identities=20%  Similarity=0.251  Sum_probs=286.4

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHH-HHHHHHH-H-CCHHHHHHHHHHHCCC
Q ss_conf             99999996796203377666644476379999999998301445312213567-7899998-5-0878898730120010
Q gi|254780299|r  105 ALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVT-SASMVAL-M-TTPRVHKDWAPKIFSR  181 (562)
Q Consensus       105 ~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt-~~a~~~L-~-~~~e~~~~~lp~l~s~  181 (562)
                      ++++...+.||.++.+++++++.+.  +++..+...+-.+...++...+..+. ..++..| + ++++++++|+|+++++
T Consensus        37 ~~~~~l~e~Gl~~~~vPee~GG~g~--~~~~~~~v~e~lg~~~~~~~~~~~~~~~~~~~~l~~~g~~~q~~~~l~~l~~G  114 (376)
T cd01156          37 DLWRKMGKLGLLGITAPEEYGGSGM--GYLAHVIIMEEISRASGSVALSYGAHSNLCINQIYRNGSAAQKEKYLPKLISG  114 (376)
T ss_pred             HHHHHHHHCCCCCCCCCHHHCCCCC--CHHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC
T ss_conf             9999999779988889965699998--89999999999986367555122276788999999849999999998998479


Q ss_pred             CCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEE-CCCCCEEEEEEECCC-----CCEE
Q ss_conf             0054426600155212355445888887866543027864896689845146863-421157999704699-----6179
Q gi|254780299|r  182 EYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLS-SPMSDAFIMLAQVEG-----RVGC  255 (562)
Q Consensus       182 ~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~s-a~~ad~~lVlArt~~-----Gls~  255 (562)
                      +.             ++++++|||++|||+.++.|+|++++|+ |+|||+|+|+| ++.+|+++|+||++.     |+++
T Consensus       115 ~~-------------~~~~a~tEp~~Gsd~~~~~t~a~~~~~~-~~lnG~K~~v~~~~~Ad~~~v~ar~~~~~~~~gi~~  180 (376)
T cd01156         115 EH-------------IGALAMSEPNAGSDVVSMKLRAEKKGDR-YVLNGSKMWITNGPDADTLVVYAKTDPSAGAHGITA  180 (376)
T ss_pred             CE-------------EEEECCCCCCCCCCHHCCEEEEEEECCE-EEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCEEE
T ss_conf             85-------------5430468999887512075799981998-999516723221212543578862167667576269


Q ss_pred             EEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99877589884034788630475545657727999869075---300777657999999730133357999999999999
Q gi|254780299|r  256 FLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSL  332 (562)
Q Consensus       256 FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al  332 (562)
                      |+||+..||     +++.+.++|+|+|+++++++.|+||++   ++||++|+|++.++..++.+|+.+++.++|++++++
T Consensus       181 flV~~~~~G-----v~~~~~~~~~G~r~~~~~~v~fd~v~vp~~~llg~~~~g~~~~~~~l~~~r~~~aa~~~G~a~~al  255 (376)
T cd01156         181 FIVEKGMPG-----FSRAQKLDKLGMRGSNTCELVFEDCEVPEENILGGENKGVYVLMSGLDYERLVLAGGPIGIMQAAL  255 (376)
T ss_pred             EEEECCCCC-----CCCCCCCCCCCCCCCCCEEEEECCEECCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998406898-----620465455567778861687154441667615864406999987135778886665544457776


Q ss_pred             HHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999984046222423538888999999999999999999999988720111036777655679999999999999999
Q gi|254780299|r  333 AEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVI  412 (562)
Q Consensus       333 ~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~  412 (562)
                      +.+++|+++|+|||+||++||.+|++|+||.+++++++++++++++.+|.+.....       ..+.+|+++++.+.+++
T Consensus       256 ~~a~~ya~~R~qfG~~i~~~q~iq~~lad~~~~~e~ar~~~~~aa~~~d~~~~~~~-------~~a~ak~~~~e~a~~~a  328 (376)
T cd01156         256 DVAIPYAHQRKQFGQPIGEFQLVQGKLADMYTRLNASRSYLYTVAKACDRGNMDPK-------DAAGVILYAAEKATQVA  328 (376)
T ss_pred             HHHHHHHHHHHHCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH-------HHHHHHHHHHHHHHHHH
T ss_conf             77777788898719850106999999999999999999999999999867999889-------99999999999999999


Q ss_pred             HHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf             569988521300045518898500122322046222789999998312
Q gi|254780299|r  413 AEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEK  460 (562)
Q Consensus       413 ~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r  460 (562)
                      ++|||+|||+||++|+|++|+|||+++.+|+|||++||.+.+.|.+-|
T Consensus       329 ~~a~q~~Gg~G~~~e~~~~r~~Rdar~~~i~~Gt~ei~r~~ia~~ll~  376 (376)
T cd01156         329 LDAIQILGGNGYINDYPTGRLLRDAKLYEIGAGTSEIRRMVIGRELFK  376 (376)
T ss_pred             HHHHHHCCCHHHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf             999996274312267489999987106723066899999999999609


No 15 
>cd01160 LCAD Long chain acyl-CoA dehydrogenase (LCAD) is acyl-CoA dehydrogenases (ACAD), which is found in the mitochondria of eukaryotes and in some prokaryotes.  It catalyzes the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of LCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. LCAD is a homodimer.
Probab=100.00  E-value=0  Score=464.94  Aligned_cols=342  Identities=23%  Similarity=0.286  Sum_probs=289.5

Q ss_pred             CCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             69846201799852136566889999999999679620337766664447637999999999830144531221356778
Q gi|254780299|r   80 NTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSA  159 (562)
Q Consensus        80 ~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~  159 (562)
                      ..|....+|+.|.      |++   ++++...+.||.++.++.++++.+.  ..+......+-.+.......+....+..
T Consensus        18 ~~p~~~~~d~~~~------~p~---~~~~~l~~~G~~~~~vPe~~GG~G~--~~~~~~~v~eel~~~~~~~~~~~~~~~~   86 (372)
T cd01160          18 VAPFHHEWEKAGE------VPR---EVWRKAGEQGLLGVGFPEEYGGIGG--DLLSAAVLWEELARAGGSGPGLSLHTDI   86 (372)
T ss_pred             CCHHHHHHHHCCC------CCH---HHHHHHHHCCCCCCCCCHHHCCCCC--CHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             8245999987499------999---9999999779988899954589997--8999999999998867631299999999


Q ss_pred             HHHHHH--CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEE-
Q ss_conf             999985--08788987301200100054426600155212355445888887866543027864896689845146863-
Q gi|254780299|r  160 SMVALM--TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLS-  236 (562)
Q Consensus       160 a~~~L~--~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~s-  236 (562)
                      ..+.|.  ++++++++|+|++.+++.             ++++++|||++|||+.+++|+|++++|+ |+|||+|+|+| 
T Consensus        87 ~~~~l~~~g~~~qk~~~l~~~~~G~~-------------~~~~a~tEp~~Gsd~~~~~t~a~~~g~~-~~lnG~K~~vs~  152 (372)
T cd01160          87 VSPYITRAGSPEQKERVLPQMVAGKK-------------IGAIAMTEPGAGSDLQGIRTTARKDGDH-YVLNGSKTFITN  152 (372)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHCCCE-------------EEEEEECCCCCCCCCCCCCEEEEEECCE-EEEEEEEECCCC
T ss_conf             99999984999999999899967996-------------9999843898888756564189996998-999326704544


Q ss_pred             CCCCCEEEEEEECC------CCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHH
Q ss_conf             42115799970469------9617999877589884034788630475545657727999869075---30077765799
Q gi|254780299|r  237 SPMSDAFIMLAQVE------GRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTG  307 (562)
Q Consensus       237 a~~ad~~lVlArt~------~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~  307 (562)
                      ++.+|+++|+||++      +|+++|+||++.||     |++.+.++++|+++++++++.|+||++   ++||++|+|++
T Consensus       153 a~~Ad~~~v~a~~~~~~~~~~g~~~~lV~~~~~G-----v~~~~~~~~~G~~~~~~~~v~f~~v~Vp~~~~lg~~~~g~~  227 (372)
T cd01160         153 GMLADVVIVVARTGGEARGAGGISLFLVERGTPG-----FSRGRKLKKMGWKAQDTAELFFDDCRVPAENLLGEENKGFY  227 (372)
T ss_pred             CCCCCCCEEEEEECCCCCCCCCEEEEEECCCCCC-----CCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHH
T ss_conf             3456640366652047777784488975168998-----70146545457534665500367668562003687462799


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf             99997301333579999999999999999998404622242353888899999999999999999999998872011103
Q gi|254780299|r  308 PVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRS  387 (562)
Q Consensus       308 ~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~  387 (562)
                      .++..++.+|+.+++.++|+++++++.+++|+++|+|||+||.+||.||++|++|.+++++++++++++++..|.+....
T Consensus       228 ~~~~~l~~~r~~~aa~~~G~a~~al~~a~~y~~~R~~fG~~i~~~q~i~~~la~~~~~~~~ar~l~~~aa~~~d~g~~~~  307 (372)
T cd01160         228 YLMQNLPQERLLIAAGALAAAEFMLEETRNYVKQRKAFGKTLAQLQVVRHKIAELATKVAVTRAFLDNCAWRHEQGRLDV  307 (372)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH
T ss_conf             99985688899887652026899999999999877632992542899999999999999999999999999997799977


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             67776556799999999999999995699885213000455188985001223220462227899999983
Q gi|254780299|r  388 EEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLL  458 (562)
Q Consensus       388 ~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l  458 (562)
                      .       .++++|+++++.+.+++++|||+|||+||+.|+|++|+|||+++.+|||||++||.+.+.|.+
T Consensus       308 ~-------~a~~aK~~~~e~a~~~~~~a~q~~Gg~G~~~e~~~~r~~Rda~~~~i~~Gt~ev~~~~ia~~l  371 (372)
T cd01160         308 A-------EASMAKYWATELQNRVAYECVQLHGGWGYMREYPIARAYRDARVQPIYGGTTEIMKELISRQM  371 (372)
T ss_pred             H-------HHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
T ss_conf             9-------999999999999999999999962852212564899999861777551768999999999973


No 16 
>KOG0140 consensus
Probab=100.00  E-value=0  Score=465.32  Aligned_cols=340  Identities=19%  Similarity=0.249  Sum_probs=295.6

Q ss_pred             HHCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHH
Q ss_conf             43698462017998521365668899999999996796203377666644476379999999998301445312213567
Q gi|254780299|r   78 NYNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVT  157 (562)
Q Consensus        78 ~~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt  157 (562)
                      +.--|....||..|      +|+   .++++.+.+.|+.+.-.+..+++.+  ...+....-++     +....|.-++|
T Consensus        45 ~e~~P~aae~Dk~g------e~P---~~iirkA~~lG~~~~~ip~~~GG~G--ls~l~t~lI~E-----~LayGCtg~~~  108 (408)
T KOG0140          45 DEMIPNAAEYDKSG------EFP---WEIIRKAHELGFMNTYIPEDYGGLG--LSRLDTCLIFE-----ALAYGCTGIQT  108 (408)
T ss_pred             HHHCCCHHHHCCCC------CCC---HHHHHHHHHCCCCCCCCCCCCCCCC--CHHHHHHHHHH-----HHHCCCHHHHH
T ss_conf             76253054314367------776---8999999872667654750138877--01477899999-----99736466778


Q ss_pred             HHHHH------H-HHCCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECC
Q ss_conf             78999------9-8508788987301200100054426600155212355445888887866543027864896689845
Q gi|254780299|r  158 SASMV------A-LMTTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSG  230 (562)
Q Consensus       158 ~~a~~------~-L~~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG  230 (562)
                      ...+.      + +.+++||+++|+|+|+...             ...+.++|||++||||++++|+|++.|| +|+|||
T Consensus       109 ~I~~~~l~~~pi~~~gneeqKkk~lg~l~~~p-------------~~asYcvTEPgAGSDvagikTka~KkGD-eYiiNG  174 (408)
T KOG0140         109 AISIHNLAAWPIILSGNEEQKKKYLGRLAEEP-------------KVASYCVTEPGAGSDVAGIKTKAEKKGD-EYIING  174 (408)
T ss_pred             HHHCCCHHHHHEHHCCCHHHHHHHHHHHHCCH-------------HHHHHHCCCCCCCCCHHHHHHHHHHCCC-EEEECC
T ss_conf             87334334422211286888876535554031-------------4544100588987641443124453487-799747


Q ss_pred             EE-EEEECCCCCEEEEEEECCC--------CCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EE
Q ss_conf             14-6863421157999704699--------617999877589884034788630475545657727999869075---30
Q gi|254780299|r  231 HK-WFLSSPMSDAFIMLAQVEG--------RVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FL  298 (562)
Q Consensus       231 ~K-wf~sa~~ad~~lVlArt~~--------Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~l  298 (562)
                      +| |+++++.+++++|+||+++        ++++|+|+.++||     ++.++-+++||.|+++|--+.|+||++   |.
T Consensus       175 sKawItg~G~anwyfVlaRtd~~pk~p~~Kaft~fiVe~dTpG-----lt~GkKE~nmGqr~sdTR~itFEDvrVP~~Nv  249 (408)
T KOG0140         175 SKAWITGAGHANWYFVLARTDPDPKTPAGKAFTAFIVEGDTPG-----LTRGKKEKNMGQRCSDTRGITFEDVRVPKENV  249 (408)
T ss_pred             CEEEEECCCCCCEEEEEEECCCCCCCCCCCCEEEEEEECCCCC-----CCCCHHHHCCCCCCCCCCEEEEEECCCCHHCC
T ss_conf             3356506874536999984489999998763589998089977-----67671331246557887503664135530011


Q ss_pred             ECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             07776579999997301333579999999999999999998404622242353888899999999999999999999998
Q gi|254780299|r  299 LGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLAN  378 (562)
Q Consensus       299 lG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~  378 (562)
                      ||.+|.||++++..++.+|..++++++|++.||++++.+|+.+|++||+||++||.+|.+||||++.+|.+|++++++|+
T Consensus       250 lg~~G~GFkvAm~~fd~tRp~vAa~alG~A~r~ld~a~ky~~eRK~FG~~iA~hQ~vqF~LAdMA~~le~aRL~~~~aa~  329 (408)
T KOG0140         250 LGAPGAGFKVAMGGFDKTRPNVAAGALGLAQRCLDEATKYALERKAFGTPIANHQAVQFMLADMAINLELARLMTRNAAW  329 (408)
T ss_pred             CCCCCCCCEEHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             26898640100212258887514454678899999999999989874867021045787799998789999999998899


Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             87201110367776556799999999999999995699885213000455188985001223220462227899999983
Q gi|254780299|r  379 SFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLL  458 (562)
Q Consensus       379 ~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l  458 (562)
                      .+|++.+..       ...+|+|.++++.+..++..|+|+|||+||..|||+++++||++|.+|||||++||.+.+.|.|
T Consensus       330 evd~~r~~s-------y~aSiAK~fA~D~an~~at~AvQifGG~Gfn~eYpVeklmRDaki~QIyEGTsqiqRlvIsR~l  402 (408)
T KOG0140         330 EVDNGRRNS-------YYASIAKLFATDTANQAATNAVQIFGGNGFNKEYPVEKLMRDAKIYQIYEGTSQIQRLVISRSL  402 (408)
T ss_pred             HHHCCCCCH-------HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_conf             862688612-------7899999875205889987778754467756446699997441466766443899999999999


Q ss_pred             C
Q ss_conf             1
Q gi|254780299|r  459 E  459 (562)
Q Consensus       459 ~  459 (562)
                      -
T Consensus       403 l  403 (408)
T KOG0140         403 L  403 (408)
T ss_pred             H
T ss_conf             9


No 17 
>PRK12341 putative acyl-CoA dehydrogenase; Provisional
Probab=100.00  E-value=0  Score=459.38  Aligned_cols=327  Identities=19%  Similarity=0.210  Sum_probs=277.7

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHH-HCCHHHHHHHHHHHCC-CC
Q ss_conf             999999967962033776666444763799999999983014453122135677899998-5087889873012001-00
Q gi|254780299|r  105 ALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSASMVAL-MTTPRVHKDWAPKIFS-RE  182 (562)
Q Consensus       105 ~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~a~~~L-~~~~e~~~~~lp~l~s-~~  182 (562)
                      ++++...+.||.++.+++++|+.+  ..++......+-.+.......+ +++...+..++ .++++++++|++.++. ++
T Consensus        41 ~~~~~l~e~Gl~~l~vPee~GG~G--~~~~~~~~v~eelg~~~~~~~~-~~~~~~~~~i~~~gs~eq~~~~l~~~l~~G~  117 (383)
T PRK12341         41 EFMRALADNGISMLGVPEEFGGIP--ADYVTQMLALMEVSKCGAPAFL-ITNGQCIHSMRRFGSAEQLRKTAESTLETGD  117 (383)
T ss_pred             HHHHHHHHCCCCCCCCCHHHCCCC--CCHHHHHHHHHHHHHHCCCCCC-CCHHHHHHHHHHHCCHHHHHHHHHHHHHCCC
T ss_conf             999999977888879985458999--8899999999999873677654-3179999999997899999998568872787


Q ss_pred             CCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEE-CCCCCEEEEEEECCC------CCEE
Q ss_conf             054426600155212355445888887866543027864896689845146863-421157999704699------6179
Q gi|254780299|r  183 YDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLS-SPMSDAFIMLAQVEG------RVGC  255 (562)
Q Consensus       183 ~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~s-a~~ad~~lVlArt~~------Gls~  255 (562)
                                   ..+++++|||++|||+.+++|+|++++| .|+|||+|+|+| ++.+|+++|+||+++      |+|+
T Consensus       118 -------------~~~~~a~tEp~~Gsd~~~~~tta~~~~~-~~~lnG~K~~it~a~~Ad~~~v~ar~~~~~~~~~gis~  183 (383)
T PRK12341        118 -------------PAYALALTEPGAGSDNNSATTTYTRKNG-KVYINGQKTFITGAKEYPYMLVLARDPQPKDPKKAFTL  183 (383)
T ss_pred             -------------EEEEEEECCCCCCCCHHHCEEEEEEECC-EEEEECEECCCCCCCCCCEEEEEECCCCCCCCCCEEEE
T ss_conf             -------------5799982488877871226257886399-99995635474555568789999535888887654899


Q ss_pred             EEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99877589884034788630475545657727999869075---300777657999999730133357999999999999
Q gi|254780299|r  256 FLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSL  332 (562)
Q Consensus       256 FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al  332 (562)
                      |+||++.||     |++.+ .+++|.|+++++++.|+||++   ++||++|+|+..++..++.+|+.+++.++|++++++
T Consensus       184 flV~~~~pG-----v~v~~-~~~~g~~~~~~~~v~f~dv~Vp~~~~lg~~g~g~~~~~~~l~~~rl~~aa~~~G~a~~al  257 (383)
T PRK12341        184 WWVDSSKPG-----IKINP-LHKIGWHMLSTCEVYLDNVEVEESDLVGEEGMGFLNVMYNFEMERLINAARSTGFAECAF  257 (383)
T ss_pred             EEEECCCCC-----EEEEC-CCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998569996-----48704-645688765202342354223611146766728999999776889999998850557667


Q ss_pred             HHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999984046222423538888999999999999999999999988720111036777655679999999999999999
Q gi|254780299|r  333 AEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVI  412 (562)
Q Consensus       333 ~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~  412 (562)
                      +.+++|+++|+|||+||++||.||++|+||.+++++++++++++++..|++.+..       ..++++|+++++.+.+++
T Consensus       258 ~~a~~ya~~R~qfG~pi~~~Q~vq~~lad~~~~~e~ar~l~~~aa~~~d~~~~~~-------~~aa~aK~~a~e~a~~v~  330 (383)
T PRK12341        258 EDAARYANQRIAFGKPIGHNQMIQEKLALMAIKIENMRNMVLKVAWQADNGQSLR-------TSAALAKLYCARTAMEVI  330 (383)
T ss_pred             HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH-------HHHHHHHHHHHHHHHHHH
T ss_conf             7653457888861985003899999999999999999999999999986899953-------799999999999999999


Q ss_pred             HHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCCC
Q ss_conf             5699885213000455188985001223220462227899999983126
Q gi|254780299|r  413 AEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEKG  461 (562)
Q Consensus       413 ~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r~  461 (562)
                      ++|||+|||+||++|+|++|+|||+++++|||||++||.+.+.|.+-|+
T Consensus       331 ~~a~qi~Gg~G~~~e~~~~r~~Rdar~~~I~~Gt~ei~~~~ia~~vl~~  379 (383)
T PRK12341        331 DDAIQIMGGLGYTDEARVSRFWRDVRCERIGGGTDEIMIYVAGRQILKD  379 (383)
T ss_pred             HHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             9999963850104554999999984161751778999999999999998


No 18 
>TIGR03204 pimC_large pimeloyl-CoA dehydrogenase, large subunit. Members of this protein family are the PimC proteins of species such as Rhodopseudomonas palustris and Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Especially relevant is pimeloyl-CoA, basis of the gene symbol, as it is a catabolite of benzoyl-CoA degradation, which occurs in Rhodopseudomonas palustris.
Probab=100.00  E-value=0  Score=454.92  Aligned_cols=347  Identities=15%  Similarity=0.131  Sum_probs=270.1

Q ss_pred             HHCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHH
Q ss_conf             43698462017998521365668899999999996796203377666644476379999999998301445312213567
Q gi|254780299|r   78 NYNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVT  157 (562)
Q Consensus        78 ~~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt  157 (562)
                      ++.+|..+.++..|+..    .++...+.++...+.||.++.|++++++.+.  ..+...+..+-++..........+++
T Consensus        21 ~~v~p~~~~~~~~~~~~----~~~~~~~~~~~l~~~G~~~~~~PeeyGG~G~--~~~~~~iv~EEl~~~~~~~~~~~~~~   94 (395)
T TIGR03204        21 DNVPADTRQKLVEGRHL----TKDEMVTWWRILNKKGWGVSHWPKQYGGTGW--TSVQHYIFNEELQSAPAPQPLAFGVS   94 (395)
T ss_pred             HHCCHHHHHHHHCCCCC----CHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC--CHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             74981144687436788----8588999999999668998999824399998--89999999999735597188999999


Q ss_pred             HHHHHHH-H-CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEE
Q ss_conf             7899998-5-0878898730120010005442660015521235544588888786654302786489668984514686
Q gi|254780299|r  158 SASMVAL-M-TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFL  235 (562)
Q Consensus       158 ~~a~~~L-~-~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~  235 (562)
                      . +.++| . +++|||++|||++++++.             ++++++|||++|||+++++|+|+++|| +|+|||+|+||
T Consensus        95 ~-~~~~i~~~GteeqK~~~Lp~l~~G~~-------------~~~~a~tEP~aGSD~~~~~T~A~~~gd-~~vinG~K~~i  159 (395)
T TIGR03204        95 M-VGPVIYTFGNEEQKKRFLPRIANVDD-------------WWCQGFSEPGSGSDLASLKTKAEKKGD-KWIINGQKTWT  159 (395)
T ss_pred             H-HHHHHHHHCCHHHHHHHHHHHHCCCH-------------HHEEEECCCCCCCCCCCCCEEEEECCC-EEEEEEEECCC
T ss_conf             9-99999986989999998899848767-------------766652589888870025657873499-89999674372


Q ss_pred             E-CCCCCEEEEEEECC------CCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCH
Q ss_conf             3-42115799970469------9617999877589884034788630475545657727999869075---300777657
Q gi|254780299|r  236 S-SPMSDAFIMLAQVE------GRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVS  305 (562)
Q Consensus       236 s-a~~ad~~lVlArt~------~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G  305 (562)
                      | ++.||+++|+|||+      +|+|+|+||++.||     +++.+++.++|  +++++++.|+||++   ++||++|+|
T Consensus       160 t~a~~Ad~~~v~art~~~~~~~~Gis~flV~~~~~G-----~~v~~~~~~~g--~~~~~~v~f~dv~VP~~~llG~~g~G  232 (395)
T TIGR03204       160 TLAQHADWIFCLCRTDPTAKKQMGISFILVDMKSKG-----ITVRPIQTIDG--GVEVNEVFFDDVEVPYENLVGEENKG  232 (395)
T ss_pred             CCCCCCCCEEEEEECCCCCCCCCCCEEEECCCCCCC-----EEECCCCCCCC--CCCCCCCCCCCCCCCHHHCCCCCCCH
T ss_conf             678635520133301687777787123202478997-----37454303577--66645202576201533036877847


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999973013335799999999999999999984046222423538888999999999999999999999988720111
Q gi|254780299|r  306 TGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKS  385 (562)
Q Consensus       306 ~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~  385 (562)
                      |++++..++.+|+.++  ++|+++++++.+++|+++|+|||+||++||.||++||+|.+++++++.+.++++........
T Consensus       233 ~~~~~~~l~~~R~~~a--~~G~a~~al~~a~~ya~~R~~fG~pi~~~q~i~~~lA~m~~~~~a~~l~~~~~~~~~~~~~~  310 (395)
T TIGR03204       233 WDYAKFLLGNERTGIA--RVGVSKERIRRIKDLAAKVESGGKPVIEDAKFREKLAAVEIELKALELTQLRVVADEGKHGK  310 (395)
T ss_pred             HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999998999999999--99999999999999999998579651209999999999999999999999999999887469


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----------CCCCCCC----HHHHHHHCCHHHHHCCCCHHHHH
Q ss_conf             036777655679999999999999999569988521----------3000455----18898500122322046222789
Q gi|254780299|r  386 RSEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGG----------SGYIEER----SIARHYRESPANSILLGSGNAMV  451 (562)
Q Consensus       386 ~~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG----------~Gy~ee~----~leRl~RDA~v~~I~EGt~~I~a  451 (562)
                      ..     .....+++|+++++.+..+++.+||++|+          .||.+..    +++|.|||+++.+||||||+||.
T Consensus       311 ~~-----~~~~~s~~K~~ase~~~~~~~~a~qi~G~~~~~~~ihG~~g~~~~~~~~~~i~r~yrd~r~~~I~eGTsEIqr  385 (395)
T TIGR03204       311 GK-----PNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHGDDGSNEAMDWTAQIAPSYFNNRKVSIYGGSNEIQR  385 (395)
T ss_pred             CC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHH
T ss_conf             99-----8699999999999999999999999854210023113667623556657899999986467736543999999


Q ss_pred             HHHHHHHC
Q ss_conf             99999831
Q gi|254780299|r  452 LDVLNLLE  459 (562)
Q Consensus       452 ldv~r~l~  459 (562)
                      +.+.|.+.
T Consensus       386 ~iIAr~lL  393 (395)
T TIGR03204       386 NIIAKAVL  393 (395)
T ss_pred             HHHHHHHC
T ss_conf             99999861


No 19 
>TIGR03203 pimD_small pimeloyl-CoA dehydrogenase, small subunit. Members of this protein family are the PimD proteins of species such as Rhodopseudomonas palustris, Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Especially relevant is pimeloyl-CoA, basis of the gene symbol, as it is a catabolite of benzoyl-CoA degradation, which occurs in Rhodopseudomonas palustris.
Probab=100.00  E-value=0  Score=450.64  Aligned_cols=324  Identities=16%  Similarity=0.160  Sum_probs=272.6

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHH-HHHHHH--CCHHHHHHHHHHHCCC
Q ss_conf             9999999679620337766664447637999999999830144531221356778-999985--0878898730120010
Q gi|254780299|r  105 ALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSA-SMVALM--TTPRVHKDWAPKIFSR  181 (562)
Q Consensus       105 ~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~-a~~~L~--~~~e~~~~~lp~l~s~  181 (562)
                      ++++...+.||.++.+++++++.+.+  .+...+...-.+-  .....|...|.. +...|.  ++++|+++|+|+++++
T Consensus        41 ~lw~~lae~G~~gl~ipEe~GG~G~~--~~~~~~v~Eelgr--~~~~~p~~~~~~~~~~~l~~~g~~~qk~~~Lp~l~~G  116 (378)
T TIGR03203        41 AVWGKLAEQGLLGLPFSEADGGFGAG--SVETMIVMEALGK--ALVLEPYLATVVIGGGFLRHAGSAAQKAAHLPGIIDG  116 (378)
T ss_pred             HHHHHHHHCCCCCCCCCHHHCCCCCC--HHHHHHHHHHHHH--HCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC
T ss_conf             99999997799876898655999947--9999999999987--5652788889999999999839999999766998389


Q ss_pred             CCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEE-CCCCCEEEEEEECC------CCCE
Q ss_conf             0054426600155212355445888887866543027864896689845146863-42115799970469------9617
Q gi|254780299|r  182 EYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLS-SPMSDAFIMLAQVE------GRVG  254 (562)
Q Consensus       182 ~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~s-a~~ad~~lVlArt~------~Gls  254 (562)
                      +.             +.++++|||++|||+.+++|+|++++|+ |+|||+|+|++ +..+|+++|+||++      +|+|
T Consensus       117 ~~-------------~~a~a~tEp~~gsd~~~~~t~a~~~gd~-~vlnG~K~~i~~~~~Ad~~lv~a~t~~~~~~~~gi~  182 (378)
T TIGR03203       117 SK-------------TFAFAQLEKNSRYDLGDVSTTAKKTGDG-WVIDGEKFVVLNGETADTLIVTARTKGARRDRTGIG  182 (378)
T ss_pred             CE-------------EEEEEECCCCCCCCHHHCEEEEEECCCE-EEECCCCCEEECCCCCCEEEEEEECCCCCCCCCCEE
T ss_conf             93-------------4798724888887612174599981882-797287301432666768999997788667778427


Q ss_pred             EEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999877589884034788630475545657727999869075---30077765799999973013335799999999999
Q gi|254780299|r  255 CFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVS  331 (562)
Q Consensus       255 ~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~a  331 (562)
                      +|+||++.||     +++.+...+.|.+   ++++.|++|++   ++||++++|++.+...++.+|+.+++.++|+++++
T Consensus       183 ~flV~~~~~G-----v~~~~~~~~~g~~---~~~v~f~~v~V~~~~~lg~~~~g~~~~~~~l~~~r~~~aa~a~G~a~~a  254 (378)
T TIGR03203       183 VFLVPAGAKG-----VTIKGYPTQDGLH---AADITFTGVVVGADAAIGDPENALPLIERVVDDARAALCAEAVGLMDES  254 (378)
T ss_pred             EEEEECCCCC-----EEECCCCCCCCCC---CCCCCCCCCCCCHHHEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9986068996-----1455603656765---4444577830236650276324899999999998999999997799999


Q ss_pred             HHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999998404622242353888899999999999999999999998872011103677765567999999999999999
Q gi|254780299|r  332 LAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAV  411 (562)
Q Consensus       332 l~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v  411 (562)
                      ++.+++|+++|+|||+||++||.||++||||.+++|++|+++|.+++..|........     ..++++|+++++.+.++
T Consensus       255 l~~av~Ya~~R~qFGrpIg~fQaIqh~lAdm~~~~e~ar~l~~~aa~a~~~~~~~~~~-----~~~a~AK~~a~eaa~~v  329 (378)
T TIGR03203       255 LKTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVAVEQARSMAMFATMASDFDDAKERA-----NAIAAAKVQIGKSLKFV  329 (378)
T ss_pred             HHHHHHHHHHCEECCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH-----HHHHHHHHHHHHHHHHH
T ss_conf             9999999861806880557524899999999999999999999999998714981249-----99999999999999999


Q ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHC
Q ss_conf             956998852130004551889850012232204622278999999831
Q gi|254780299|r  412 IAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLE  459 (562)
Q Consensus       412 ~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~  459 (562)
                      +++|+|+|||+||++|||++|+|||++++.|++||++++..-+.++++
T Consensus       330 a~~aiQihGG~G~t~E~~~~~~~Rra~~~~~~~G~~~~h~~ria~a~g  377 (378)
T TIGR03203       330 GQQSIQLHGGIGMTMEAKIGHYFKRLTMIEHTFGDTDFHLSRVSAAGG  377 (378)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf             999999865896960388999999999999861989999999998768


No 20 
>KOG0141 consensus
Probab=100.00  E-value=0  Score=466.80  Aligned_cols=330  Identities=21%  Similarity=0.306  Sum_probs=289.3

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHH-HHHHHH--HCCHHHHHHHHHHHCC
Q ss_conf             9999999967962033776666444763799999999983014453122135677-899998--5087889873012001
Q gi|254780299|r  104 HALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTS-ASMVAL--MTTPRVHKDWAPKIFS  180 (562)
Q Consensus       104 ~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~-~a~~~L--~~~~e~~~~~lp~l~s  180 (562)
                      ++.++..-+.|++++.-+.++++.+  +..+.+++..+-.+-++.++.-...... -++--|  .+++||+++|+|+|+|
T Consensus        77 r~~WkklG~~gllGita~~~~GG~G--~~y~~h~ivmEE~sra~g~v~lsygaHSnlcinqlvrnGseeQkekylPkl~s  154 (421)
T KOG0141          77 REFWKKLGKQGLLGITAPEEYGGSG--GGYLSHCIVMEEISRASGGVALSYGAHSNLCINQLVRNGSEEQKEKYLPKLIS  154 (421)
T ss_pred             HHHHHHHHHCCCCCCCCHHHHCCCC--HHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
T ss_conf             9999996445745214616628875--30788999999987652785655321121589998826989998754045505


Q ss_pred             CCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEE-EEEECCCCCEEEEEEECC-------CC
Q ss_conf             0005442660015521235544588888786654302786489668984514-686342115799970469-------96
Q gi|254780299|r  181 REYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHK-WFLSSPMSDAFIMLAQVE-------GR  252 (562)
Q Consensus       181 ~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~K-wf~sa~~ad~~lVlArt~-------~G  252 (562)
                      +++             +++.+||||++||||.+++++|+++||+ |+|||.| |++++|++|+.+|.|+|+       .|
T Consensus       155 Ge~-------------iGalAMsEp~AGSDvv~mK~~Aek~g~~-yiLNGsK~witNG~~advliVyAkTd~~a~~~~hG  220 (421)
T KOG0141         155 GEH-------------IGALAMSEPGAGSDVVSMKLKAEKKGDD-YILNGSKFWITNGPDADVLIVYAKTDHSAVPPSHG  220 (421)
T ss_pred             CCC-------------CCEEEECCCCCCCCCCEEEEECEECCCC-EEECCCEEEEECCCCCCEEEEEEECCCCCCCCCCC
T ss_conf             450-------------0203324899987401124100105883-78617479871698775799998238888997676


Q ss_pred             CEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEE---EEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1799987758988403478863047554565772799986907---5300777657999999730133357999999999
Q gi|254780299|r  253 VGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTF---GFLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMR  329 (562)
Q Consensus       253 ls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~---~~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar  329 (562)
                      ||+|+|++..||     ++..+--||||+|++.|||+.|+|++   .+++|++|+|+.++|..+..+|+.++.+.+|+|+
T Consensus       221 It~FiVEkgm~G-----Fs~~~KLdKlGmrgsdTcELvFed~~vpas~ilg~enkGvYvlMsgLd~ERLvla~gplglmq  295 (421)
T KOG0141         221 ITAFIVEKGMPG-----FSTAQKLDKLGMRGSDTCELVFEDCKVPASNILGEENKGVYVLMSGLDLERLVLAAGPLGLMQ  295 (421)
T ss_pred             EEEEEECCCCCC-----CCCCHHHHHHCCCCCCCHHEEHHHCCCCHHHHCCCCCCEEEEEECCCCHHHHHHCCCCHHHHH
T ss_conf             179997178865-----320124576347777603200643368578742867864899943787667433268569999


Q ss_pred             HHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999984046222423538888999999999999999999999988720111036777655679999999999999
Q gi|254780299|r  330 VSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAP  409 (562)
Q Consensus       330 ~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~  409 (562)
                      .+++++..|+++|++||++|.+||++|.+||||++.+-++|+.+|.+++..|.+.-++.+       .+.+|+|++|.+.
T Consensus       296 a~~d~~~~Y~~qR~afgk~ig~fQ~~QgklAdmyT~l~a~Rsyvy~va~~~d~g~~~~kd-------cag~il~aaE~~t  368 (421)
T KOG0141         296 AALDETFPYAHQRKAFGKKIGHFQLLQGKLADMYTTLCASRSYVYNVARACDAGNVDPKD-------CAGVILYAAEKAT  368 (421)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH-------HHHHHHHHHHHHH
T ss_conf             999875668999998587105789887689999999999999999999986638998455-------1010005865657


Q ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCCC
Q ss_conf             9995699885213000455188985001223220462227899999983126
Q gi|254780299|r  410 AVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEKG  461 (562)
Q Consensus       410 ~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r~  461 (562)
                      .|+.+|+|||||+||+.|||+.|+||||++..|+-||++|..+-+.|.+.++
T Consensus       369 qVald~iQ~~GGnGYineyp~gr~lrDAklyeIgaGTsEirr~lIgRel~~e  420 (421)
T KOG0141         369 QVALDAIQCLGGNGYINEYPTGRLLRDAKLYEIGAGTSEIRRLLIGRELNKE  420 (421)
T ss_pred             HHHHHHHHHCCCCCCCCCCCHHHHHHHCEEEECCCCHHHHHHHHHHHHHHCC
T ss_conf             9998888532676300346114665314334525874999999998776025


No 21 
>cd01158 SCAD/SBCAD Short chain acyl-CoA dehydrogenase (SCAD). SCAD is a mitochondrial beta-oxidation enzyme. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of SCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis.  This subgroup also contains the eukaryotic short/branched chain acyl-CoA dehydrogenase(SBCAD), the bacterial butyryl-CoA dehydorgenase(BCAD) and 2-methylbutyryl-CoA dehydrogenase, which is involved in isoleucine catabolism.  These enzymes are homotetramers.
Probab=100.00  E-value=0  Score=440.69  Aligned_cols=345  Identities=23%  Similarity=0.297  Sum_probs=292.7

Q ss_pred             HCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHH
Q ss_conf             36984620179985213656688999999999967962033776666444763799999999983014453122135677
Q gi|254780299|r   79 YNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTS  158 (562)
Q Consensus        79 ~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~  158 (562)
                      +..|+...+|+.|      .|++   ++++...+.||.++.+++++++.+.+  ++..+....-.+..+......+++..
T Consensus        17 ~~~p~a~~~d~~~------~~p~---~~~~~l~~~G~~~l~~P~~~GG~g~~--~~~~~~~~e~l~~~~~~~~~~~~~~~   85 (373)
T cd01158          17 EIAPLAAEMDEKG------EFPR---EVIKEMAELGLMGIPIPEEYGGAGLD--FLAYAIAIEELAKVDASVAVIVSVHN   85 (373)
T ss_pred             HCHHHHHHHHHCC------CCCH---HHHHHHHHCCCCCCCCCHHHCCCCCC--HHHHHHHHHHHHHHCCCCCEEEHHHH
T ss_conf             6847899998659------9999---99999998799877999323999999--99999999999865766664304878


Q ss_pred             --HHHHHHH-CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEE
Q ss_conf             --8999985-0878898730120010005442660015521235544588888786654302786489668984514686
Q gi|254780299|r  159 --ASMVALM-TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFL  235 (562)
Q Consensus       159 --~a~~~L~-~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~  235 (562)
                        .+..++. ++++++++|+|++.+++.             +.++++|||.+|||+..++|+|++++|| |+|||+|+|+
T Consensus        86 ~~~~~~l~~~g~~~~~~~~l~~~~~G~~-------------~~~~a~sEp~~Gsd~~~~~t~a~~~~~g-~~lnG~K~~v  151 (373)
T cd01158          86 SLGANPIIKFGTEEQKKKYLPPLATGEK-------------IGAFALSEPGAGSDAAALKTTAKKDGDD-YVLNGSKMWI  151 (373)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHCCCE-------------EEEEEECCCCCCCCCCCCCEEEEEECCE-EEEEEEEECC
T ss_conf             9999999983999999998899957994-------------7998733898888744452399997999-9998577065


Q ss_pred             E-CCCCCEEEEEEECCC-----CCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHH
Q ss_conf             3-421157999704699-----617999877589884034788630475545657727999869075---3007776579
Q gi|254780299|r  236 S-SPMSDAFIMLAQVEG-----RVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVST  306 (562)
Q Consensus       236 s-a~~ad~~lVlArt~~-----Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~  306 (562)
                      | ++.+|+++|+|++++     |+++|+||++.||     +++.+.++++|+++++++++.|+||++   ++||++|+|+
T Consensus       152 s~a~~Ad~~lv~a~~~~~~~~~g~~~~lv~~~~~G-----v~i~~~~~~~G~~~~~~~~~~f~~v~Vp~~~~lg~~g~g~  226 (373)
T cd01158         152 TNGGEADFYIVFAVTDPSKGYRGITAFIVERDTPG-----LSVGKKEDKLGIRGSSTTELIFEDVRVPKENILGEEGEGF  226 (373)
T ss_pred             CCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCC-----CEECCCCCCCCCCCCCCCCEECCCEEECHHHCCCCCCCHH
T ss_conf             45556774147665168777672589962267888-----6305765444676666650005652776353378878279


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99999730133357999999999999999999840462224235388889999999999999999999999887201110
Q gi|254780299|r  307 GPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSR  386 (562)
Q Consensus       307 ~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~  386 (562)
                      ..++..++.+|+.+++.++|+++++++.+++|+++|+|||+||.+||.+|++|++|.+++++++++++++++..|.+.+.
T Consensus       227 ~~~~~~l~~~r~~~aa~~~G~a~~al~~a~~ya~~R~~fG~pi~~~q~v~~~la~~~~~l~~ar~l~~~aa~~~d~~~~~  306 (373)
T cd01158         227 KIAMQTLDGGRIGIAAQALGIAQAALDAAVDYAKERKQFGKPIADFQGIQFKLADMATEIEAARLLTYKAARLKDNGEPF  306 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99987537789998898764658878999999886775299720589999999999999999999999999999779994


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf             36777655679999999999999999569988521300045518898500122322046222789999998312
Q gi|254780299|r  387 SEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEK  460 (562)
Q Consensus       387 ~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r  460 (562)
                      ..+       ++++|+++++.+.+++++|||++||.||++|+|++|+|||+++.+|+|||++||.+.+.|.+.|
T Consensus       307 ~~~-------aa~aK~~a~~~a~~~~~~a~q~~Gg~G~~~~~~l~r~~Rda~~~~i~~Gt~ev~r~~i~~~~l~  373 (373)
T cd01158         307 IKE-------AAMAKLFASEVAMRVTTDAVQIFGGYGYTKDYPVERYYRDAKITEIYEGTSEIQRLVIAKHLLK  373 (373)
T ss_pred             HHH-------HHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHC
T ss_conf             699-------9999999999999999999998084543267789999986056636177799999999999729


No 22 
>COG1960 CaiA Acyl-CoA dehydrogenases [Lipid metabolism]
Probab=100.00  E-value=0  Score=431.11  Aligned_cols=331  Identities=25%  Similarity=0.334  Sum_probs=288.8

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHH----HH--HCCHHHHHHHHHH
Q ss_conf             99999999679620337766664447637999999999830144531221356778999----98--5087889873012
Q gi|254780299|r  104 HALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSASMV----AL--MTTPRVHKDWAPK  177 (562)
Q Consensus       104 ~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~a~~----~L--~~~~e~~~~~lp~  177 (562)
                      .++++...+.|+.++.|+.++++.  +.......+..+.++..+.+..+.+.++.....    .+  .++++++++|+|+
T Consensus        42 ~~~~~~l~~~G~~~~~~p~e~GG~--~~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~q~~~~l~~  119 (393)
T COG1960          42 RELLRALAEAGLLGLTIPEEYGGL--GLSPLEQAAVLEELARADAGGALALGLTHGGLGALAPTILRFGTEEQKRRYLPR  119 (393)
T ss_pred             HHHHHHHHHCCCCCCCCCHHHCCC--CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             999999997698667899666898--865456999999999866023367888888888766554206889999875266


Q ss_pred             HCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCC-EEEEECCCCEEEECCEEEEEEC-CCCCEEEEEEECCC----
Q ss_conf             00100054426600155212355445888887866543-0278648966898451468634-21157999704699----
Q gi|254780299|r  178 IFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAIT-SQGQKISDGIYCLSGHKWFLSS-PMSDAFIMLAQVEG----  251 (562)
Q Consensus       178 l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~-T~A~~~gdg~y~LnG~Kwf~sa-~~ad~~lVlArt~~----  251 (562)
                      +.+++             ++.++++|||++|||+.++. |++++.+++ |+|||+|||||+ +.+|+++|+||+++    
T Consensus       120 ~~~G~-------------~~~~~~~tEp~~Gsd~~~~~~t~a~~~~g~-~~lnG~K~~is~~~~ad~~~v~Ar~~~~~~~  185 (393)
T COG1960         120 LASGE-------------LIGAFALTEPGAGSDLASLRTTAAVRDDGD-YVLNGQKIWISNAPVADWLLVLARTDPAPGK  185 (393)
T ss_pred             HHCCC-------------HHHEEEECCCCCCCCCCCCCCEEEEECCCC-EEEEEEEEEECCCCCCCEEEEEEECCCCCCC
T ss_conf             52444-------------142235157877775323562499975996-8997378876688777779999865876666


Q ss_pred             --CCEEEEEECC-CCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             --6179998775-89884034788630475545657727999869075---30077765799999973013335799999
Q gi|254780299|r  252 --RVGCFLVPRL-LEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIYLDSAIMSV  325 (562)
Q Consensus       252 --Gls~FlVp~~-~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~Rl~~a~~~~  325 (562)
                        |+|+|+||++ .||     +++.+++++.|+++++|+++.|+||++   ++||++|+|+..++..++.+|+.+++.++
T Consensus       186 ~~gis~flV~~~~~~G-----v~~~~~~~~~G~r~~~~~~v~f~~v~vp~~~lig~~~~g~~~~~~~l~~~r~~~aa~~~  260 (393)
T COG1960         186 HKGISLFLVPKDLTPG-----VSVGPILKKMGLRGSATGEVFFDDVRVPAENLLGEEGDGFKIAMETLNVERLGIAAQAL  260 (393)
T ss_pred             CCCEEEEEEECCCCCC-----EEEECCCCCCCCCCCCCEEEEECCEECCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             6752699987688997-----28625545567677861589976623428860677786299999989888999999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998404622242353888899999999999999999999998872011103677765567999999999
Q gi|254780299|r  326 SGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCC  405 (562)
Q Consensus       326 G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~  405 (562)
                      |++++|++.+++|+++|++||++|++||.+|++|++|.+++++++++++++++..|.+...       ...++++|++++
T Consensus       261 G~a~~al~~a~~ya~~R~~fg~~i~~~~~vq~~la~~~~~~~a~r~~~~~aa~~~d~~~~~-------~~~~~~aK~~~~  333 (393)
T COG1960         261 GIAEAALEEAVAYARERKQFGRPIADFQLVQFKLADMAAELEAARLLVLRAAELADAGDDA-------GAEAAMAKLFAT  333 (393)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH-------HHHHHHHHHHHH
T ss_conf             9999999999999998564188632278999999999999999999999998876445524-------789999999999


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCCCH
Q ss_conf             999999956998852130004551889850012232204622278999999831260
Q gi|254780299|r  406 KMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEKGT  462 (562)
Q Consensus       406 e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r~~  462 (562)
                      +.+..+++++||+|||+||+.|+|++|+|||+++++|||||++||.+++.+.+.+.+
T Consensus       334 ~~~~~v~~~a~q~~Gg~g~~~e~~i~r~~rda~~~~i~~Gt~~i~~~~i~~~l~~~~  390 (393)
T COG1960         334 EAALEVADEAVQVHGGYGYTEEYPVERYYRDARILRIYEGTSEIQRLIIARRLLGLP  390 (393)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCC
T ss_conf             999999999999539421057864999998734553146769999999999972554


No 23 
>cd00567 ACAD Acyl-CoA dehydrogenase (ACAD). Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast,  AXO catalyzes a different  oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium  (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities.  The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD
Probab=100.00  E-value=0  Score=401.52  Aligned_cols=324  Identities=27%  Similarity=0.317  Sum_probs=283.1

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH--CCHHHHHHHHHHHCCCC
Q ss_conf             9999999679620337766664447637999999999830144531221356778999985--08788987301200100
Q gi|254780299|r  105 ALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSASMVALM--TTPRVHKDWAPKIFSRE  182 (562)
Q Consensus       105 ~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~a~~~L~--~~~e~~~~~lp~l~s~~  182 (562)
                      ++++...+.||..+..+..+++.+...  . ..+........+....+++.++......|.  ++++++++|++++.+++
T Consensus        34 ~~~~~l~~~Gl~~~~~p~~~GG~~~~~--~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~l~~~~~g~  110 (369)
T cd00567          34 ELLAELGLLGLLGPTVPGGYGGGGLDL--L-ELAIEEELARADAAAALLLLGTLLGAALLLAYGTEEQKERYLPPLASGE  110 (369)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCH--H-HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCC
T ss_conf             999999984899679861249998469--9-9999999977674069999999999999998399999999989984899


Q ss_pred             CCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEEC-CCCCEEEEEEECCC------CCEE
Q ss_conf             0544266001552123554458888878665430278648966898451468634-21157999704699------6179
Q gi|254780299|r  183 YDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLSS-PMSDAFIMLAQVEG------RVGC  255 (562)
Q Consensus       183 ~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~sa-~~ad~~lVlArt~~------Gls~  255 (562)
                                   +++++++|||.+|||+...+|+|++++|| |+|||+|+|+|+ +.+|+++|+|++++      |+++
T Consensus       111 -------------~~~~~a~sE~~~g~~~~~~~t~a~~~~gg-~~l~G~k~~~s~~~~ad~~~v~a~~~~~~~~~~~~~~  176 (369)
T cd00567         111 -------------AIAAFALTEPGAGSDLAGIRTTARKDGDG-YVLNGRKIFISNGGDADLFIVLARTDEEGPGHRGISA  176 (369)
T ss_pred             -------------EEEEEEECCCCCCCCCCCEEEEEEEECCE-EEEEEEEEEECCCCCCCCCEEEEEECCCCCCCCCEEE
T ss_conf             -------------38999725898788855414699997998-9999999986220026751688751687678885689


Q ss_pred             EEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99877589884034788630475545657727999869075---300777657999999730133357999999999999
Q gi|254780299|r  256 FLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSL  332 (562)
Q Consensus       256 FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al  332 (562)
                      |+||+..||     +++.+.++++|+|+++++.+.|+++++   ++||.++.+++.+...++..|+.+++.++|++++++
T Consensus       177 ~lv~~~~~g-----v~~~~~~~~~G~r~t~s~~v~~~~v~Vp~~~~l~~~~~~~~~~~~~~~~~~~~~aa~~lG~a~~al  251 (369)
T cd00567         177 FLVPADTPG-----VTVGRIWDKMGMRGSGTGELVFDDVRVPEDNLLGEEGGGFELAMKGLNVGRLLLAAVALGAARAAL  251 (369)
T ss_pred             EEEECCCCC-----EEEEECCCCCCCCCCCCCCCEECCEEECHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999516896-----688631355677654444211056787636503641037999998557779999999987778769


Q ss_pred             HHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999984046222423538888999999999999999999999988720111036777655679999999999999999
Q gi|254780299|r  333 AEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVI  412 (562)
Q Consensus       333 ~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~  412 (562)
                      +.+++|+++|++||+||+++|.+|++|++|.+++++++++++++++.+|.+...      .+..++++|+++++.+.+++
T Consensus       252 ~~~~~~~~~R~~~g~~l~~~~~v~~~la~~~~~~~~a~~~~~~aa~~~d~~~~~------~~~~~~~aK~~a~~~a~~~~  325 (369)
T cd00567         252 DEAVEYAKQRKQFGKPLAEFQAVQFKLADMAAELEAARLLLYRAAWLLDQGPDE------ARLEAAMAKLFATEAAREVA  325 (369)
T ss_pred             HHHHHHHHHCCCCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC------CHHHHHHHHHHHHHHHHHHH
T ss_conf             999999873523797044099999999999999999999999999999779986------47999999999999999999


Q ss_pred             HHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHH
Q ss_conf             56998852130004551889850012232204622278999999
Q gi|254780299|r  413 AEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLN  456 (562)
Q Consensus       413 ~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r  456 (562)
                      ++++|++||.||++|+|++|+|||+++.+|||||++|+.+.++|
T Consensus       326 ~~~~~~~Gg~g~~~~~~l~r~~Rdar~~~~~~G~~~~~~~~~~~  369 (369)
T cd00567         326 DLAMQIHGGRGYSREYPVERYLRDARAARIAEGTAEIQRLIIAR  369 (369)
T ss_pred             HHHHHHHCHHHHCCCCHHHHHHHHHHCCEECCCHHHHHHHHHCC
T ss_conf             99999728787666868999999863151516889999998677


No 24 
>cd01163 DszC Dibenzothiophene (DBT) desulfurization enzyme C (DszC). DszC is a flavin reductase dependent enzyme, which catalyzes the first two steps of DBT desulfurization in mesophilic bacteria. DszC converts DBT to DBT-sulfoxide, which is then converted to DBT-sulfone. Bacteria with this enzyme are candidates for the removal of organic sulfur compounds from fossil fuels, which pollute the environment. An equivalent enzyme tdsC, is found in thermophilic bacteria. This alignment also contains a closely related uncharacterized subgroup.
Probab=100.00  E-value=0  Score=387.88  Aligned_cols=330  Identities=18%  Similarity=0.170  Sum_probs=274.2

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH--CCHHHHHHHHHHHCCCC
Q ss_conf             9999999679620337766664447637999999999830144531221356778999985--08788987301200100
Q gi|254780299|r  105 ALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSASMVALM--TTPRVHKDWAPKIFSRE  182 (562)
Q Consensus       105 ~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~a~~~L~--~~~e~~~~~lp~l~s~~  182 (562)
                      +.++.+.+.||.++..++++++.+.+  .+.......-.+..+.++...+.++.+.+..|.  ++++++++|+|++.+++
T Consensus        26 e~~~~l~e~Gl~gl~vP~~~GG~g~~--~~~~~~v~eela~~~~s~a~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~g~  103 (377)
T cd01163          26 EEVALLRQSGLGTLRVPKEYGGLGAS--LPDLYEVVRELAAADSNIAQALRAHFGFVEALLLAGPEQFRKRWFGRVLNGW  103 (377)
T ss_pred             HHHHHHHHCCCCCCCCCHHHCCCCCC--HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCC
T ss_conf             99999997799887989323999999--9999999999987685589999874248999998097999998668873798


Q ss_pred             CCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEEC-CCCCEEEEEEECCCC-CEEEEEEC
Q ss_conf             0544266001552123554458888878665430278648966898451468634-211579997046996-17999877
Q gi|254780299|r  183 YDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLSS-PMSDAFIMLAQVEGR-VGCFLVPR  260 (562)
Q Consensus       183 ~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~sa-~~ad~~lVlArt~~G-ls~FlVp~  260 (562)
                                    +.+.++|||. |||.....|++++++|+ |+|||+|+|+|+ +.+|+++|.|++++| .++|+||+
T Consensus       104 --------------~~~~a~te~g-~~~~~~~~t~a~~~~gg-~~lnG~K~fiS~~~~Ad~~~v~a~~~~g~~~~~lv~~  167 (377)
T cd01163         104 --------------IFGNAVSERG-SVRPGTFLTATVRDGGG-YVLNGKKFYSTGALFSDWVTVSALDEEGKLVFAAVPT  167 (377)
T ss_pred             --------------EEECCCCCCC-CCCCCCCCEEEEEECCE-EEEEEEEECCCCCCCCCEEEEEEEECCCCEEEEEEEC
T ss_conf             --------------6213568877-76500041489973998-9998468524798658689999995599707999977


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             589884034788630475545657727999869075---30077765799999973013335799999999999999999
Q gi|254780299|r  261 LLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEAIH  337 (562)
Q Consensus       261 ~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~  337 (562)
                      +.||     |++.+.++|+|+|+++|+++.|+||++   +++|+++.++..+. .+...|+..++.++|++++|++.+++
T Consensus       168 ~~~G-----v~i~~~~~~~G~rgs~s~~l~fddv~Vp~~~llg~~~~~~~~~~-~~~~~~~~~aa~~lG~a~~Ald~a~~  241 (377)
T cd01163         168 DRPG-----ITVVDDWDGFGQRLTASGTVTFDNVRVEPDEVLPRPNAPDRGTL-LTAIYQLVLAAVLAGIARAALDDAVA  241 (377)
T ss_pred             CCCC-----CCCCCCCCCCCCCCCCCEEEEECCEEECHHHCCCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9988-----73577632246777874179855467069991687763888988-54899999999999999999999999


Q ss_pred             HHHHCCCC-----CCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-----CHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98404622-----2423538888999999999999999999999988720111-----0367776556799999999999
Q gi|254780299|r  338 YARRRHVS-----GGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKS-----RSEEAAYARIMAPITKYWCCKM  407 (562)
Q Consensus       338 yA~~R~~f-----G~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~-----~~~~~a~arl~t~iaK~~~~e~  407 (562)
                      |+++|+++     +.+++++|.+|++|++|.+++++++++++++++.+|....     .+.+...+++.++++|++++|.
T Consensus       242 ya~~R~r~~~~~~~~~~~~~~~vq~~la~~~~~~~aar~l~~~aa~~~d~~~~~~~~~~~~~~~~~~~~~a~aK~~ase~  321 (377)
T cd01163         242 YVRSRTRPWIHSGAESARDDPYVQQVVGDLAARLHAAEALVLQAARALDAAAAAGTALTAEARGEAALAVAAAKVVVTRL  321 (377)
T ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99973120256753321356999999999999999999999999999988643355456445576799999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             999995699885213000455188985001223220462227899999983
Q gi|254780299|r  408 APAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLL  458 (562)
Q Consensus       408 a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l  458 (562)
                      +.++++++||++||+||++|+|+||+|||+|+.++++.++.|++...-++|
T Consensus       322 a~~v~~~a~qi~GG~G~~~~~~leR~~RDar~~~~h~p~~~~~~~~~~~~~  372 (377)
T cd01163         322 ALDATSRLFEVGGASATAREHNLDRHWRNARTHTLHNPVIYKERAVGDYAL  372 (377)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
T ss_conf             999999999998299977583599999977656104889999999999997


No 25 
>cd01159 NcnH Naphthocyclinone hydroxylase (NcnH). Naphthocyclinone is an aromatic polyketide and an antibiotic, which is active against Gram-positive bacteria.  Polyketides are secondary metabolites, which have important biological functions such as antitumor, immunosupressive or antibiotic activities. NcnH is a hydroxylase involved in the biosynthesis of naphthocyclinone and possibly other polyketides.
Probab=100.00  E-value=0  Score=364.46  Aligned_cols=320  Identities=16%  Similarity=0.126  Sum_probs=242.6

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH-CCHHHHHHHHHHHCCCCC
Q ss_conf             9999999679620337766664447637999999999830144531221356778999985-087889873012001000
Q gi|254780299|r  105 ALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSASMVALM-TTPRVHKDWAPKIFSREY  183 (562)
Q Consensus       105 ~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~a~~~L~-~~~e~~~~~lp~l~s~~~  183 (562)
                      ++++...+.||.++..++++++.+...  +.......-.+..+.+......+.......+. ..++.++++...      
T Consensus        26 e~~~~l~e~Gl~gl~vP~e~GG~G~~~--~~~~~v~eela~~~~s~a~~~~~~~~~~~~~~~~~~~~~~~~~~~------   97 (370)
T cd01159          26 EVVRALREIGFFRMFVPKRYGGLEGDF--AEFAEAIATLAEACGSAAWVASIVATHSRMLAAFPPEAQEEVWGD------   97 (370)
T ss_pred             HHHHHHHHCCCCCCCCCHHHCCCCCCH--HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCC------
T ss_conf             999999987999879885459999899--999999999998772589999999899999987699999987357------


Q ss_pred             CHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEEC-CCCCEEEEEEECCC-----CCEEEE
Q ss_conf             544266001552123554458888878665430278648966898451468634-21157999704699-----617999
Q gi|254780299|r  184 DPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLSS-PMSDAFIMLAQVEG-----RVGCFL  257 (562)
Q Consensus       184 ~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~sa-~~ad~~lVlArt~~-----Gls~Fl  257 (562)
                                         .++..+++.....++|++++|| |+|||+|+|||+ +.+|+++|+|++++     +++.|+
T Consensus        98 -------------------~~~~~~~~~~~~~~~A~~~~~g-yvlnG~K~fiS~a~~Ad~~~v~a~~~~~~~~~~~~~~~  157 (370)
T cd01159          98 -------------------GPDTLLAGSYAPGGRAERVDGG-YRVSGTWPFASGCDHADWILVGAIVEDDDGGPLPRAFV  157 (370)
T ss_pred             -------------------CCCCCCCCCCCCCCEEEEECCE-EEEEEEEECCCCCCCCCEEEEEEEECCCCCCCCEEEEE
T ss_conf             -------------------8653132566777527997999-99973685446887678899999975667887469999


Q ss_pred             EECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEEC------CCCCH---HHHHHHHHHHHHHHHHHHHH
Q ss_conf             877589884034788630475545657727999869075---3007------77657---99999973013335799999
Q gi|254780299|r  258 VPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLG------DLNVS---TGPVEDMKILIYLDSAIMSV  325 (562)
Q Consensus       258 Vp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG------~~g~G---~~~i~~~l~~~Rl~~a~~~~  325 (562)
                      ||+.       ++++.+.++|+|+|+++|+++.|+||.+   ++++      ..+.+   ....+.++...++.+++.++
T Consensus       158 v~~~-------g~~i~~~~~~~G~r~t~s~~v~~~dv~VP~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~aa~~l  230 (370)
T cd01159         158 VPRA-------EYEIVDTWHVVGLRGTGSNTVVVDDVFVPEHRTLTAGDMMAGDGPGGSTPVYRMPLRQVFPLSFAAVSL  230 (370)
T ss_pred             EECC-------CEEECCCCCCCCCCCCCCCCCEECCEECCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7068-------368887778786887888665047745459984664422245653002588898898999999999999


Q ss_pred             HHHHHHHHHHHHHHHHCCC---CCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH-HHHHHHHHHHHHH
Q ss_conf             9999999999999840462---22423538888999999999999999999999988720111036-7776556799999
Q gi|254780299|r  326 SGMRVSLAEAIHYARRRHV---SGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSE-EAAYARIMAPITK  401 (562)
Q Consensus       326 G~ar~al~~A~~yA~~R~~---fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~-~~a~arl~t~iaK  401 (562)
                      |++++|++.+++|+++|+|   ||+||.++|.||++|++|.+++++++++++++++.+|++..... .....+....++|
T Consensus       231 Gia~~al~~a~~ya~~R~q~~~fg~~i~~~q~vq~~la~m~~~l~aar~l~~~aa~~~d~~~~~~~~~~~~~~~~~~~ak  310 (370)
T cd01159         231 GAAEGALAEFLELAGKRVRQYGAAVKMAEAPITQLRLAEAAAELDAARAFLERATRDLWAHALAGGPIDVEERARIRRDA  310 (370)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             99999999999999846525457887555899999999999999999999999999999767437889999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCH-HHHHHHHHHHHC
Q ss_conf             9999999999956998852130004551889850012232204622-278999999831
Q gi|254780299|r  402 YWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSG-NAMVLDVLNLLE  459 (562)
Q Consensus       402 ~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~-~I~aldv~r~l~  459 (562)
                      .++++.+.++++.+||++||+||++|+|+||+|||+|+..|+|||+ +|+.+.+.|.+.
T Consensus       311 ~~a~e~a~~v~~~a~q~~Gg~g~~~~~pleR~~RD~R~~~~h~g~~~e~~~~~igra~l  369 (370)
T cd01159         311 AYAAKLSAEAVDRLFHAAGGSALYTASPLQRIWRDIHAAAQHAALNPETAAEAYGRALL  369 (370)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf             99999999999999998739998016269999999858872776789999999999961


No 26 
>PRK13026 acyl-CoA dehydrogenase; Reviewed
Probab=100.00  E-value=0  Score=341.73  Aligned_cols=371  Identities=14%  Similarity=0.147  Sum_probs=289.9

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHH
Q ss_conf             99800167889999972042110789999998501899999986343698462017998521365668899999999996
Q gi|254780299|r   33 GMNAYSSDSLLVALIANFPSVVHKELELLGEYVLSCTAQELARMANYNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIH  112 (562)
Q Consensus        33 g~n~~~~D~~l~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~a~~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~  112 (562)
                      +-+.|...|-.+.++..-.+...++=..|   . ..+..++....|...=...          +-+.+|   +.++...+
T Consensus        57 d~elF~G~Pdw~~l~~~~~~~Lt~eEqaf---l-d~~v~~lc~m~ddw~i~~~----------~~dlp~---e~w~~~k~  119 (771)
T PRK13026         57 EGELFRGKPDWQKLHSYPKPTLTAEEQAF---I-DNQVETLLSMLDDFDIVHN----------RKDLPP---EVWDYLKK  119 (771)
T ss_pred             EHHHCCCCCCHHHHHCCCCCCCCHHHHHH---H-CCHHHHHHHHHHHHHHHHH----------HCCCCH---HHHHHHHH
T ss_conf             42130899889999538988899899977---3-4799999986126764411----------144999---99999997


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHH-HHCCC-CCC--CCCCHHHHHHHHHHHH--CCHHHHHHHHHHHCCCCCCHH
Q ss_conf             79620337766664447637999999999-83014-453--1221356778999985--087889873012001000544
Q gi|254780299|r  113 DGLHCSIWDRSFEPVVRKQAHKIRAARLY-LMAQL-EAG--HLMSPSVTSASMVALM--TTPRVHKDWAPKIFSREYDPT  186 (562)
Q Consensus       113 ~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~-l~~~~-~~g--~~cp~~mt~~a~~~L~--~~~e~~~~~lp~l~s~~~~~~  186 (562)
                      +|..++..+.+|++.  +.+...+..... +.+.+ ..+  ++-|-+.  |-..+|.  +++|||++|||+|.++++   
T Consensus       120 ~~ffgmiIpkeyGG~--~fS~~a~s~v~~ki~s~s~~~avtvmvpNSL--GpgeLL~~yGTeeQK~~yLPrLA~Ge~---  192 (771)
T PRK13026        120 EGFFALIIPKEYGGK--AFSAYANSTIVSKIATRSVSAAVTVMVPNSL--GPGELLTHYGTQEQKDYWLPRLADGTE---  192 (771)
T ss_pred             CCCEEEEECHHHCCC--CCCHHHHHHHHHHHHHCCCCCEEEEECCCCC--CHHHHHHHCCCHHHHHHHHHCCCCCCE---
T ss_conf             794589821644886--5688899999999983262011466246766--838999870889998633220046774---


Q ss_pred             HCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEE-----CCCC--EEEECCEE-EEEECCCCCEEEEEEEC-C-------
Q ss_conf             2660015521235544588888786654302786-----4896--68984514-68634211579997046-9-------
Q gi|254780299|r  187 NKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQK-----ISDG--IYCLSGHK-WFLSSPMSDAFIMLAQV-E-------  250 (562)
Q Consensus       187 ~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~-----~gdg--~y~LnG~K-wf~sa~~ad~~lVlArt-~-------  250 (562)
                                +.||+||||.+|||.+++.++++.     +|+.  +|+|||.| |+|++|.|+++-+..+. |       
T Consensus       193 ----------IpcFaLTeP~aGSDA~~~~d~gvv~~~~~dG~~~lg~~Ln~~KryITlapvAtviglafk~~DPd~llg~  262 (771)
T PRK13026        193 ----------IPCFALTGPEAGSDAGAIPDTGIVCKGEFEGEEVLGLRLTWDKRYITLAPVATVLGLAFKLRDPDGLLGD  262 (771)
T ss_pred             ----------EEECCCCCCCCCCCCCCCCCEEEEEECCCCCCEEEEEEEEEEEEEEECCCCCEEEEEEEECCCCHHHCCC
T ss_conf             ----------0022258998888744687506985024467448999987778777448752189999870276121267


Q ss_pred             ---CCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEEC---CCCCHHHHHHHHHHHHH-HHH
Q ss_conf             ---9617999877589884034788630475545657727999869075---3007---77657999999730133-357
Q gi|254780299|r  251 ---GRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLG---DLNVSTGPVEDMKILIY-LDS  320 (562)
Q Consensus       251 ---~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG---~~g~G~~~i~~~l~~~R-l~~  320 (562)
                         .||||||||+++||     +++.+.++++|.... ++.+.++||..   ++||   +.|+||+..++.++.+| +++
T Consensus       263 ~~~~GIT~aLvp~~~pG-----v~iG~rh~plg~~f~-ng~~~g~dV~IP~d~iiGG~~~~G~Gw~mlmecL~~GRgIsL  336 (771)
T PRK13026        263 KKELGITCALIPTDHPG-----VEIGRRHNPLGMAFM-NGTTRGKDVFIPLDWIIGGPDYAGRGWRMLVECLSAGRGISL  336 (771)
T ss_pred             CCCCCEEEEEECCCCCC-----CEECCCCCCCCCCCC-CCCEEEEEEEEEHHHCCCCCHHCCCHHHHHHHHHHCCCCCCH
T ss_conf             76565378981589998-----240255377657767-896155688963676148702028539999999721454235


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             99999999999999999984046222423538888999999999999999999999988720111036777655679999
Q gi|254780299|r  321 AIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPIT  400 (562)
Q Consensus       321 a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~ia  400 (562)
                      .+.++|.++.|++.+..||+.|+|||+||++|+.||.+||+|....+.+.+....++..+|++..+.       +.++|+
T Consensus       337 pA~~~g~ak~a~~~~~aYA~~R~QFg~PIg~FegIqekLA~ma~~tY~~~A~~~~t~~~ld~g~kPs-------V~sAi~  409 (771)
T PRK13026        337 PALGTASGHMATKTTGAYAYVRRQFGMPIGQFEGVQEALARIAGNTYLLEAARRLTTTGLDLGVKPS-------VVTAIA  409 (771)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH-------HHHHHH
T ss_conf             3544899999999999999999982895785323899999999999999999999998885699823-------999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHHHCCHHHHHCCCCHHHHH
Q ss_conf             999999999999569988521300045--518898500122322046222789
Q gi|254780299|r  401 KYWCCKMAPAVIAEAMECIGGSGYIEE--RSIARHYRESPANSILLGSGNAMV  451 (562)
Q Consensus       401 K~~~~e~a~~v~~~Aiqi~GG~Gy~ee--~~leRl~RDA~v~~I~EGt~~I~a  451 (562)
                      ||.++|.+..++.++|.||||.|.+..  +-+.+.|.-+||.-.-||. ||+.
T Consensus       410 Ky~~Te~~R~~~~~aMDi~gG~~I~~Gp~N~l~~~Y~~~PI~ITVEGA-NILT  461 (771)
T PRK13026        410 KYHMTELGRTVVNDAMDIHAGKAIQLGPKNYLGHPYMAVPIAITVEGA-NILT  461 (771)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHCCCCCCEEEECCCH-HHHH
T ss_conf             998889999998764223058710147614654101569756722508-8888


No 27 
>PRK09463 fadE acyl-CoA dehydrogenase; Reviewed
Probab=100.00  E-value=0  Score=339.84  Aligned_cols=370  Identities=16%  Similarity=0.174  Sum_probs=289.3

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHH
Q ss_conf             99800167889999972042110789999998501899999986343698462017998521365668899999999996
Q gi|254780299|r   33 GMNAYSSDSLLVALIANFPSVVHKELELLGEYVLSCTAQELARMANYNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIH  112 (562)
Q Consensus        33 g~n~~~~D~~l~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~a~~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~  112 (562)
                      +-+.|...|-.+.++..-.+...+|=..|   . ..+..++....|...=...          .-+.+|   +.++...+
T Consensus        58 ~~~lf~G~pdw~~l~~~~~~~Lt~eEqaF---l-d~~v~~lc~m~ddw~i~~~----------~~dlp~---~~w~~~k~  120 (761)
T PRK09463         58 EGELFSGKPDWKKLLNYPKPTLTAEEQAF---L-DGPVEELCRMVDDWQITHE----------LADLPP---EVWQFIKE  120 (761)
T ss_pred             EHHHHCCCCCHHHHHCCCCCCCCHHHHHH---H-CCHHHHHHHHHHHHHHHHH----------HCCCCH---HHHHHHHH
T ss_conf             44040899889999548977589999977---4-3789999986017875400----------145999---99999997


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHH-HHHCCC-CCCCC--CCHHHHHHHHHHHH--CCHHHHHHHHHHHCCCCCCHH
Q ss_conf             7962033776666444763799999999-983014-45312--21356778999985--087889873012001000544
Q gi|254780299|r  113 DGLHCSIWDRSFEPVVRKQAHKIRAARL-YLMAQL-EAGHL--MSPSVTSASMVALM--TTPRVHKDWAPKIFSREYDPT  186 (562)
Q Consensus       113 ~Gl~~~~~~~~~~~~~~~~~~~~~~a~~-~l~~~~-~~g~~--cp~~mt~~a~~~L~--~~~e~~~~~lp~l~s~~~~~~  186 (562)
                      +|..++..+.+|++.  +.+...+.... .+.+.+ ..++.  -|-+.  |-..+|.  +++|||++|||+|.++++   
T Consensus       121 ~~ffgmiIpkeyGGl--~fs~~a~s~v~~kias~s~~~avtvmvpNSL--GpgeLL~~yGTeeQK~~yLPrLA~Ge~---  193 (761)
T PRK09463        121 HGFFGMIIPKEYGGL--EFSAYAHSRVLQKLASRSGTLAVTVMVPNSL--GPGELLLHYGTDEQKDHYLPRLARGEE---  193 (761)
T ss_pred             CCCEEEEECHHHCCC--CCCHHHHHHHHHHHHCCCCCCEEEEECCCCC--CHHHHHHHHCCHHHHHHHCCCCCCCCC---
T ss_conf             792489812643897--6788999999999972585422788337887--869999882889998633211036773---


Q ss_pred             HCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEE-----CCCCEEE---ECCEE-EEEECCCCCEEEEEEECC-------
Q ss_conf             2660015521235544588888786654302786-----4896689---84514-686342115799970469-------
Q gi|254780299|r  187 NKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQK-----ISDGIYC---LSGHK-WFLSSPMSDAFIMLAQVE-------  250 (562)
Q Consensus       187 ~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~-----~gdg~y~---LnG~K-wf~sa~~ad~~lVlArt~-------  250 (562)
                                +.||+||||.+|||.+++.++++.     +|++ |+   |||.| |+|.+|.++++.+..++.       
T Consensus       194 ----------IpcFaLTeP~AGSDA~s~~d~gvv~~~~~~G~~-~lg~~Ln~~KryITlapvAtv~glafk~~DP~~llg  262 (761)
T PRK09463        194 ----------IPCFALTSPEAGSDAGSIPDTGVVCKGEWEGEE-VLGMRLTWNKRYITLAPVATVLGLAFKLYDPDGLLG  262 (761)
T ss_pred             ----------CCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCC-EEEEEEEEEEEEEECCCCCCEEEEEEECCCCCCCCC
T ss_conf             ----------103204899888874458762488534225761-699997667778854875417999997468621247


Q ss_pred             ----CCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCC---CCHHHHHHHHHHHHH-HH
Q ss_conf             ----9617999877589884034788630475545657727999869075---300777---657999999730133-35
Q gi|254780299|r  251 ----GRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDL---NVSTGPVEDMKILIY-LD  319 (562)
Q Consensus       251 ----~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~---g~G~~~i~~~l~~~R-l~  319 (562)
                          .||||||||+++||     +++.+.++++|.... ++.+..+||..   ++||++   |+||+..++.++.+| ++
T Consensus       263 ~~~~~GIT~aLip~~~pG-----v~iG~rh~plg~~F~-Ngp~~g~dV~VP~d~iIGg~~~~G~Gw~mlme~L~~GR~Is  336 (761)
T PRK09463        263 DKEDLGITCALIPTDTPG-----VEIGRRHFPLNVPFQ-NGPTRGKDVFIPLDYIIGGPKMAGQGWRMLMECLSVGRGIS  336 (761)
T ss_pred             CCCCCCEEEEEECCCCCC-----CEECCCCCCCCCCCC-CCCEECCCEEECHHHHCCCCCCCCCCHHHHHHHHCCCCCCC
T ss_conf             776566258871289998-----340465586767657-88524451685188804884235860999999871576524


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             79999999999999999998404622242353888899999999999999999999998872011103677765567999
Q gi|254780299|r  320 SAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPI  399 (562)
Q Consensus       320 ~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~i  399 (562)
                      +.+.++|.++.++..+..||+.|+|||+||++|+.||.+||+|....+.+.+....++..+|++..+.       +.++|
T Consensus       337 LpA~a~G~ak~a~~~a~aYA~~RkQFg~PIg~FegIqekLA~ma~~tY~~~A~~~~t~~~~d~g~kPs-------v~sAi  409 (761)
T PRK09463        337 LPSNSTGGAKLAALATGAYARIRRQFKLPIGKFEGVEEPLARIAGNAYLMDAARTLTTAAVDLGEKPS-------VISAI  409 (761)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH-------HHHHH
T ss_conf             00545689999999999999989884886454556899999999999999999999999986799951-------89999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHHHCCHHHHHCCCCHHHHH
Q ss_conf             9999999999999569988521300045--518898500122322046222789
Q gi|254780299|r  400 TKYWCCKMAPAVIAEAMECIGGSGYIEE--RSIARHYRESPANSILLGSGNAMV  451 (562)
Q Consensus       400 aK~~~~e~a~~v~~~Aiqi~GG~Gy~ee--~~leRl~RDA~v~~I~EGt~~I~a  451 (562)
                      +||.++|++..++.++|.||||.|.+..  +-+.+.|.-+||.-.-||. ||+.
T Consensus       410 ~K~~~Te~~r~~~~~aMDi~gG~~I~~Gp~N~l~~~Y~~~Pi~ITVEGA-NILT  462 (761)
T PRK09463        410 AKYHLTERGRQVINDAMDIHGGKGICLGPNNYLARAYQAAPIAITVEGA-NILT  462 (761)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHHHHCCCCEEEEECCH-HHHH
T ss_conf             9999889999887663000468743137720442221258857885417-8888


No 28 
>KOG0138 consensus
Probab=100.00  E-value=0  Score=328.20  Aligned_cols=330  Identities=19%  Similarity=0.226  Sum_probs=270.3

Q ss_pred             ECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-HHCCCCCCCCCCHHHHH--HHHH-HHHCCHHHHHH
Q ss_conf             66889999999999679620337766664447637999999999-83014453122135677--8999-98508788987
Q gi|254780299|r   98 EFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLY-LMAQLEAGHLMSPSVTS--ASMV-ALMTTPRVHKD  173 (562)
Q Consensus        98 ~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~-l~~~~~~g~~cp~~mt~--~a~~-~L~~~~e~~~~  173 (562)
                      +|++   +++...-+.|+.+-++    .+++.++...+.+...- -..-++.+.---++...  +.-+ .+-++++|+++
T Consensus        86 ~F~~---~i~pemGsmGvlG~ti----kGYGCaG~S~vaygl~~rEveRVDs~yrs~~sVqsSL~m~~Iy~~GSE~Qkqk  158 (432)
T KOG0138          86 VFDR---EIIPEMGSMGVLGPTI----KGYGCAGVSSVAYGLLAREVERVDSGYRSAMSVQSSLVMGPIYAYGSEEQKQK  158 (432)
T ss_pred             CCCH---HHHHHHHCCCCCCCCC----CCCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             4885---4423432133356765----57677744778889999999886320103213353342546865177888764


Q ss_pred             HHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCCC-EEEECCEE-EEEECCCCCEEEEEEEC--
Q ss_conf             301200100054426600155212355445888887866543027864896-68984514-68634211579997046--
Q gi|254780299|r  174 WAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISDG-IYCLSGHK-WFLSSPMSDAFIMLAQV--  249 (562)
Q Consensus       174 ~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gdg-~y~LnG~K-wf~sa~~ad~~lVlArt--  249 (562)
                      |+|.|.++.             .++++++|||++|||.+.+.|+|+.+..+ .|.|||+| |++|.|.+|+++|+||.  
T Consensus       159 YlPslA~g~-------------~igcfgLTEPn~GSdpsgmeT~At~~e~~ktyklNGsKtWI~nsp~aDl~vvwAr~~t  225 (432)
T KOG0138         159 YLPSLAKGK-------------LIGCFGLTEPNHGSDPSGMETRATYDESNKTYKLNGSKTWITNSPMADLFVVWARCET  225 (432)
T ss_pred             HHHHHHCCC-------------EEEEEECCCCCCCCCCCCCCCEEEECCCCCEEEECCEEEEECCCCCCCEEEEEEECCC
T ss_conf             223553276-------------5458731478889896666523577268855897780234337863205799874156


Q ss_pred             CCCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99617999877589884034788630475545657727999869075---300777657999999730133357999999
Q gi|254780299|r  250 EGRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIYLDSAIMSVS  326 (562)
Q Consensus       250 ~~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~Rl~~a~~~~G  326 (562)
                      ++.+--|+|+|+.+|     ++..+++.|++.|.++|+.+-.++|++   +++ +.-.+|.--+..+|.+|++++++.+|
T Consensus       226 ~n~I~GFi~~k~~~G-----L~apkI~gK~sLRas~tG~Ilmd~V~VPeE~~L-Pg~~s~qgpf~cLnnaR~giAWg~lG  299 (432)
T KOG0138         226 DNKIRGFILEKGMRG-----LSAPKIEGKFSLRASATGMILMDGVEVPEENLL-PGASSLQGPFGCLNNARYGIAWGALG  299 (432)
T ss_pred             CCCEEEEEEECCCCC-----CCCCCCCCEEEEEECCCCCEEECCCCCCHHHCC-CCCCCCCCCHHHHHHHHHHEEEHHCH
T ss_conf             783446887068887-----767776870566651567556448757724218-88311378365553334410100020


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999984046222423538888999999999999999999999988720111036777655679999999999
Q gi|254780299|r  327 GMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCK  406 (562)
Q Consensus       327 ~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e  406 (562)
                      +++.|++.|..|..+|+|||+||+.+|++|.+|+||-.++.....+++++.++.|++...+..       +++.|.|.|-
T Consensus       300 ase~c~~~arqY~ldRkQFG~PLAanQL~Q~Kladmltei~lgl~~clrl~rLkd~g~~tp~q-------iSl~Krn~~g  372 (432)
T KOG0138         300 ASEFCLHTARQYTLDRKQFGRPLAANQLIQKKLADMLTEITLGLQACLRLGRLKDQGKATPEQ-------ISLLKRNNCG  372 (432)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH-------HHHHHHCCCH
T ss_conf             678999999999888887587126778999999999999999999888762114215688466-------6787630521


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCC
Q ss_conf             999999569988521300045518898500122322046222789999998312
Q gi|254780299|r  407 MAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEK  460 (562)
Q Consensus       407 ~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r  460 (562)
                      .+.+++..+-+++||+|...||.+.|++-|--....||||.+|.+|.+.|++..
T Consensus       373 KaleiAr~~RdmLGgNGI~deyhv~rh~~nLE~vnTYEGThDihaLilGRaiTG  426 (432)
T KOG0138         373 KALEIARQARDMLGGNGISDEYHVIRHAMNLEAVNTYEGTHDIHALILGRAITG  426 (432)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCEECCCCCCHHHHHHHHHHHHH
T ss_conf             489999999987457762268999998747520110345304777765113320


No 29 
>KOG1469 consensus
Probab=100.00  E-value=2.4e-42  Score=302.30  Aligned_cols=328  Identities=17%  Similarity=0.187  Sum_probs=275.5

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCC--CC-CCCCHHHHHHHHHHH--HCCHHHHHH
Q ss_conf             6889999999999679620337766664447637999999999830144--53-122135677899998--508788987
Q gi|254780299|r   99 FHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLE--AG-HLMSPSVTSASMVAL--MTTPRVHKD  173 (562)
Q Consensus        99 ~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~--~g-~~cp~~mt~~a~~~L--~~~~e~~~~  173 (562)
                      .||-...|++.+..+|++++..+....-++.+..++.-+...+++.-+-  +- +-|-.-=| |-..+|  .+++||+.+
T Consensus        25 ~~p~iekLKE~aK~eGlWNLFlp~~~qkyg~GLtnveYa~icElmGrs~~APeVfNC~APDT-GNMEvl~rYGseeQks~  103 (392)
T KOG1469          25 KPPVIEKLKEMAKVEGLWNLFLPAVSQKYGAGLTNVEYAHICELMGRSFFAPEVFNCQAPDT-GNMEVLHRYGSEEQKSQ  103 (392)
T ss_pred             CCCHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCHHCCCCCCCC-CCEEEHHHHCCHHHHHH
T ss_conf             98158899998875026775407888764267540159999998563413610025789998-87564124178888765


Q ss_pred             HHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCC-CCCCHHHCCEEEEECCCCEEEECCEEEEEEC---CCCCEEEEEEEC
Q ss_conf             301200100054426600155212355445888-8878665430278648966898451468634---211579997046
Q gi|254780299|r  174 WAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKR-GGTDIAAITSQGQKISDGIYCLSGHKWFLSS---PMSDAFIMLAQV  249 (562)
Q Consensus       174 ~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~-~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~sa---~~ad~~lVlArt  249 (562)
                      ||-+|+.++             +.+||+||||+ +.||..+++..-++++| .|+|||+|||+|+   |.|.+.+++.+|
T Consensus       104 WL~PLLeG~-------------irScFaMTEP~VASSDATNIe~SI~r~~~-~YvINg~KWw~sga~~PkCrv~i~mGkt  169 (392)
T KOG1469         104 WLIPLLEGN-------------IRSCFAMTEPDVASSDATNIECSIRRDGD-SYVINGKKWWISGAGDPKCRIAIFMGKT  169 (392)
T ss_pred             HHHHHHCCC-------------CEEEEEECCCCCCCCCCCCCEEEEEECCC-EEEEECCEEEECCCCCCCEEEEEEEECC
T ss_conf             768876377-------------02467605886335666640588997287-7898061456527999862799997046


Q ss_pred             CC-------CCEEEEEECCCCCCCCCCEEEEEECCCCCCCCC--CEEEEEECCEEE---EEECCCCCHHHHHHHHHHHHH
Q ss_conf             99-------617999877589884034788630475545657--727999869075---300777657999999730133
Q gi|254780299|r  250 EG-------RVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSN--ATVELEFSNTFG---FLLGDLNVSTGPVEDMKILIY  317 (562)
Q Consensus       250 ~~-------Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~--~t~ei~f~~~~~---~llG~~g~G~~~i~~~l~~~R  317 (562)
                      +.       ..|+.|||+++||     |.|.|.-..+|.--.  +..|+.|++|++   |++-.+|+||.+....+...|
T Consensus       170 ~~~~~~rhkQqSmiLVpM~TpG-----vkiiRpltVfG~~DapgGH~Ei~F~~VrVP~~NmlLGeGrGFEIaQGRLGPGR  244 (392)
T KOG1469         170 DNTSASRHKQQSMILVPMNTPG-----VKIIRPLTVFGYTDAPGGHFEIHFENVRVPATNMLLGEGRGFEIAQGRLGPGR  244 (392)
T ss_pred             CCCCCCHHHCCCEEEEECCCCC-----EEEEEEEEEECCCCCCCCCCEEEEEEEEEECCCEEECCCCCCEEECCCCCCCH
T ss_conf             8775661022417998558997-----26752014641346899862688777874134456417876254126668737


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             35799999999999999999984046222423538888999999999999999999999988720111036777655679
Q gi|254780299|r  318 LDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMA  397 (562)
Q Consensus       318 l~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t  397 (562)
                      ++.++.-+|.++|+++...+.+.+|.+|||+|.+|..+.+.||+..+++|.+|+|++++|..+|...+..     ++...
T Consensus       245 iHHcMRliG~aERal~lm~~R~~sRiaFgk~l~q~~s~~~diA~sRveiEqaRLLvLkAAh~mD~~G~k~-----Ak~~i  319 (392)
T KOG1469         245 IHHCMRLIGLAERALQLMKERALSRIAFGKKLVQHGSVAHDIAESRVEIEQARLLVLKAAHSMDTLGNKG-----AKKEI  319 (392)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH-----HHHHE
T ss_conf             8899998617899999999998878773543554023999999877676652443423666665206423-----42120


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHH
Q ss_conf             999999999999999569988521300045518898500122322046222789
Q gi|254780299|r  398 PITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMV  451 (562)
Q Consensus       398 ~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~a  451 (562)
                      +++|..+..++..+.+.|||++||.|...++|+.++|--++++.|-.|..++..
T Consensus       320 AMiKv~AP~ma~kilD~AiQ~~G~aG~s~~~~la~l~~~~r~lriadgPd~vhL  373 (392)
T KOG1469         320 AMIKVAAPNMASKILDRAIQVQGGAGVSSDTPLANLYAIARVLRIADGPDEVHL  373 (392)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEEECCCCCCCCH
T ss_conf             023311717789999999997367777889643578777654772268874006


No 30 
>cd01150 AXO Peroxisomal acyl-CoA oxidases (AXO) catalyze the first set in the peroxisomal fatty acid beta-oxidation, the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. In a second oxidative half-reaction, the reduced FAD is reoxidized by molecular oxygen. AXO is generally a homodimer, but it has been reported to form a different type of oligomer in yeast. There are several subtypes of AXO's, based on substrate specificity. Palmitoyl-CoA oxidase acts on straight-chain fatty acids and prostanoids; whereas, the closely related Trihydroxycoprostanoly-CoA oxidase has the greatest activity for  2-methyl branched side chains of bile precursors. Pristanoyl-CoA oxidase, acts on 2-methyl branched fatty acids.  AXO has an additional domain, C-terminal to the region with similarity to acyl-CoA dehydrogenases, which is included in this alignment.
Probab=100.00  E-value=1.7e-34  Score=249.58  Aligned_cols=303  Identities=17%  Similarity=0.139  Sum_probs=245.2

Q ss_pred             CCCCCCCCHHHHHHH-HHHHH--CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECC
Q ss_conf             445312213567789-99985--087889873012001000544266001552123554458888878665430278648
Q gi|254780299|r  146 LEAGHLMSPSVTSAS-MVALM--TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKIS  222 (562)
Q Consensus       146 ~~~g~~cp~~mt~~a-~~~L~--~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~g  222 (562)
                      .+....-|+.+..+. .++|.  +++|+.++|+|+..+.+             +++++++||-.+||||++++|||+-|.
T Consensus        94 ~d~~~~~~~~vh~~mF~~tI~~lGT~eq~~~wl~~~~~~~-------------i~G~yaqTELGHGSnv~gleTTAtyD~  160 (610)
T cd01150          94 YDLSLGAKLGLHLGLFGNAIKNLGTDEHQDYWLQGANNLE-------------IIGCFAQTELGHGSNLQGLETTATYDP  160 (610)
T ss_pred             CCCCCCEEEEEHHHHHHHHHHHHCCHHHHHHHHHHHHCCC-------------EEEEEEECCCCCCCCCCCCEEEEEECC
T ss_conf             4811150134308769999986089999999986885386-------------220110002344444567544899868


Q ss_pred             C-CEEEEC-----CEEEEEEC-C-CCCEEEEEEEC--C---CCCEEEEEECCCCCC--CCCCEEEEEECCCCCCCCCCEE
Q ss_conf             9-668984-----51468634-2-11579997046--9---961799987758988--4034788630475545657727
Q gi|254780299|r  223 D-GIYCLS-----GHKWFLSS-P-MSDAFIMLAQV--E---GRVGCFLVPRLLEDG--SPNGLCYQRLKNKIGNRSNATV  287 (562)
Q Consensus       223 d-g~y~Ln-----G~Kwf~sa-~-~ad~~lVlArt--~---~Gls~FlVp~~~pgg--~~n~v~i~r~~~klG~r~~~t~  287 (562)
                      . ++|+||     ..|||+.+ + .|.+.+|+||.  +   .|+..|+||-+.++.  ..+||+|+.+-.|+|..+..++
T Consensus       161 ~t~EFVinTPt~~A~KwW~G~lg~~athavV~AqL~i~gk~~Gvh~FvVpIRd~~th~~lPGV~vGDiG~K~G~ngvDNG  240 (610)
T cd01150         161 LTQEFVINTPDFTATKWWPGNLGKTATHAVVFAQLITPGKNHGLHAFIVPIRDPKTHQPLPGVTVGDIGPKMGLNGVDNG  240 (610)
T ss_pred             CCCEEEECCCCCCCEEECCCCCCCCCCEEEEEEEEEECCCCCCCCEEEEEECCCCCCCCCCCCEECCCCCCCCCCCCCCE
T ss_conf             88978878999123225466533567779999999889823441248987357887888999666247665686777761


Q ss_pred             EEEECCEEE---EEE----------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-
Q ss_conf             999869075---300----------------777657999999730133357999999999999999999840462224-
Q gi|254780299|r  288 ELEFSNTFG---FLL----------------GDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGG-  347 (562)
Q Consensus       288 ei~f~~~~~---~ll----------------G~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~-  347 (562)
                      .+.|++|+.   +||                ..+...+..|+..+...|+.+...+...+.+|+-+|+.|+..|+|||. 
T Consensus       241 ~l~FdnvRIPR~nmL~r~~~V~~dG~y~~~~~~~~~~y~~ml~~~~~gR~~i~~~~~~~l~~a~tIAiRYs~vRrQf~~~  320 (610)
T cd01150         241 FLQFRNVRIPRENLLNRFGDVSPDGTYVSPFKDPNKRYGAMLGTRSGGRVGLIYDAAMSLKKAATIAIRYSAVRRQFGPK  320 (610)
T ss_pred             EEEECEEECCHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEECCCC
T ss_conf             78844363167998764083589986657888666789999999971077899999999999999999987303014899


Q ss_pred             ------CHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ------2353888899999999999999999999998872011-----10367776556799999999999999995699
Q gi|254780299|r  348 ------ILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAK-----SRSEEAAYARIMAPITKYWCCKMAPAVIAEAM  416 (562)
Q Consensus       348 ------~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~-----~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Ai  416 (562)
                            ||+++|..|++|--+-+...+.......+...+++..     .+...-...-.+++..|.++|..+...+.+|-
T Consensus       321 ~~~~E~~iidY~tqQ~rLlP~LA~ayA~~~~~~~l~~~~~~~~~~~~~~~~~~l~elHalssglKa~~Tw~a~~~ie~cR  400 (610)
T cd01150         321 PSDPEVQILDYQLQQYRLFPQLAAAYAFHFAAKSLVEMYHEIIKELLQGNSELLAELHALSAGLKAVATWTAAQGIQECR  400 (610)
T ss_pred             CCCCCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99974223022978988799999999999999999999999998773377456789999999999998999999999999


Q ss_pred             HHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCCC
Q ss_conf             885213000455188985001223220462227899999983126
Q gi|254780299|r  417 ECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEKG  461 (562)
Q Consensus       417 qi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r~  461 (562)
                      |.+||+||...+.++.++-|.-++..|||-|+|+.+-+.|.|.|.
T Consensus       401 ~aCGGhGy~~~sgl~~l~~d~~~~~TyEGDN~VL~qQ~ar~Llk~  445 (610)
T cd01150         401 EACGGHGYLAMNRLPTLRDDNDPFCTYEGDNTVLLQQTANYLLKK  445 (610)
T ss_pred             HHCCCCCCHHHCCCHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             744775423223723555246754320200999999999999999


No 31 
>pfam00441 Acyl-CoA_dh_1 Acyl-CoA dehydrogenase, C-terminal domain. C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle.
Probab=100.00  E-value=6.7e-33  Score=238.87  Aligned_cols=149  Identities=28%  Similarity=0.347  Sum_probs=142.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             65799999973013335799999999999999999984046222423538888999999999999999999999988720
Q gi|254780299|r  303 NVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDE  382 (562)
Q Consensus       303 g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~  382 (562)
                      |+||++++..++++|+.+++.++|.++++++++++|+++|++||+||+++|.||++|++|.+++++++++++++++.+|+
T Consensus         1 G~G~~~~~~~L~~eR~~~a~~~~g~~~~~l~~~~~~a~~R~~~G~~l~~~~~vq~~la~~~~~~~~~r~~~~~a~~~~~~   80 (150)
T pfam00441         1 GRGFAVAMETLNHERLLIAAAALGLARRALDEAIEYARQRKAFGRPLIDFQLIRHKLADMAAELEAARLLVYRAAEALDA   80 (150)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC
T ss_conf             97299999999999999999999999999999999712301599718756999999886307999999999999999985


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             1110367776556799999999999999995699885213000455188985001223220462227899999983
Q gi|254780299|r  383 AKSRSEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLL  458 (562)
Q Consensus       383 ~~~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l  458 (562)
                      +.....       .++++|+++|+.+.++++.|+|++||.||++|+|++|+|||+++.+|||||++||...+.|.+
T Consensus        81 ~~~~~~-------~~s~~K~~~te~~~~~~~~a~~l~G~~G~~~~~~~~r~~rdar~~~I~~Gt~ei~r~iia~~~  149 (150)
T pfam00441        81 GGPDPA-------EAAMAKLYASELAQEVADLAMQLLGGYGYSREYPLERLYRDARVLRIGEGTSEIQRNIIARRL  149 (150)
T ss_pred             CCCCHH-------HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf             999579-------999999999999999999999863866047787999999988287102888999999999986


No 32 
>KOG0135 consensus
Probab=99.95  E-value=1.2e-26  Score=196.95  Aligned_cols=310  Identities=17%  Similarity=0.164  Sum_probs=234.3

Q ss_pred             HHHHHHHHHHCCCCCCCCCCHHHH----HHHHHHHHCCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCC
Q ss_conf             999999998301445312213567----7899998508788987301200100054426600155212355445888887
Q gi|254780299|r  134 KIRAARLYLMAQLEAGHLMSPSVT----SASMVALMTTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGT  209 (562)
Q Consensus       134 ~~~~a~~~l~~~~~~g~~cp~~mt----~~a~~~L~~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GS  209 (562)
                      ...++.+......+.++.--+...    .+++..+ ++..-. +|+.+.-..+             ..+|++|||-.+||
T Consensus       105 ~k~~al~E~lg~yd~sls~K~~lh~~lfg~AV~~~-GT~rH~-~yi~~~~n~e-------------v~gcfamTEl~HGS  169 (661)
T KOG0135         105 LKKFALTEALGIYDQSLSAKLGLHFLLFGNAVKSM-GTKRHH-DYIQKTENYE-------------VKGCFAMTELGHGS  169 (661)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-CCHHHH-HHHHHHHCCE-------------EEEEEEEEEECCCC
T ss_conf             88999999985227112265644453363788851-528789-9986332122-------------45457876414776


Q ss_pred             CHHHCCEEEEECC-CCEEEECC-----EEEEE-ECC-CCCEEEEEEEC-----CCCCEEEEEECCCCC--CCCCCEEEEE
Q ss_conf             8665430278648-96689845-----14686-342-11579997046-----996179998775898--8403478863
Q gi|254780299|r  210 DIAAITSQGQKIS-DGIYCLSG-----HKWFL-SSP-MSDAFIMLAQV-----EGRVGCFLVPRLLED--GSPNGLCYQR  274 (562)
Q Consensus       210 Dv~~~~T~A~~~g-dg~y~LnG-----~Kwf~-sa~-~ad~~lVlArt-----~~Gls~FlVp~~~pg--g~~n~v~i~r  274 (562)
                      ++.+++|+|+-|+ .++++||-     .|||+ +++ .+.+.+|+|+.     +.|+..|+||-+.|+  -+.+||+|+.
T Consensus       170 Nt~~I~TtatyDP~t~EfVinTP~~~A~K~WiGn~a~~athavvfa~L~~~g~n~G~H~FiiqIRdpkT~~t~PgV~igD  249 (661)
T KOG0135         170 NTKGIQTTATYDPTTEEFVINTPDFSAIKCWIGNAAKHATHAVVFAQLHVPGQNHGLHGFIIQIRDPKTLQTLPGVRIGD  249 (661)
T ss_pred             CCCCEEEEEEECCCCCEEEECCCCHHHHHHHHCCCCCCCEEEEEEEEEEECCCCCCEEEEEEEEECCCCCCCCCCCEECC
T ss_conf             64531455412698772675489688888875032235247999888653686673125888840563357799826310


Q ss_pred             ECCCCCCCCCCEEEEEECCEEE---EEE----------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0475545657727999869075---300----------------777657999999730133357999999999999999
Q gi|254780299|r  275 LKNKIGNRSNATVELEFSNTFG---FLL----------------GDLNVSTGPVEDMKILIYLDSAIMSVSGMRVSLAEA  335 (562)
Q Consensus       275 ~~~klG~r~~~t~ei~f~~~~~---~ll----------------G~~g~G~~~i~~~l~~~Rl~~a~~~~G~ar~al~~A  335 (562)
                      .-+|.|.++...+.+.|++++.   +||                -++++-|-.++..+..+|++++..+++.+.-++.+|
T Consensus       250 ~G~K~GlnGVDNG~l~F~nvRIPRenLLNr~gDVtpDG~YvSs~k~~~qrfgA~L~~Ls~GRvgIa~~ai~~lkla~tIA  329 (661)
T KOG0135         250 CGHKIGLNGVDNGFLWFDNVRIPRENLLNRFGDVTPDGKYVSSFKDPSQRFGASLGSLSSGRVGIASSAIGALKLALTIA  329 (661)
T ss_pred             CCCCCCCCCCCCCEEEEECCCCCHHHHHHHCCCCCCCCEEECCCCCHHHHHCHHHCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             33312656665754898425585688865215768997045367886566341230345522699999998888778776


Q ss_pred             HHHHHHCCCCCC-------CHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH---HHHHHHHHHHHHHHHH
Q ss_conf             999840462224-------235388889999999999999999999999887201110367---7765567999999999
Q gi|254780299|r  336 IHYARRRHVSGG-------ILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEE---AAYARIMAPITKYWCC  405 (562)
Q Consensus       336 ~~yA~~R~~fG~-------~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~---~a~arl~t~iaK~~~~  405 (562)
                      +.|...|+|||.       ||.|+|..|++|.-+-+...+.....-.+...+++-.....+   .+-...+++-.|.+++
T Consensus       330 IRYS~sRRQFGP~~~geEv~iLeYp~qQ~RL~P~LAaaya~~fas~~l~~~y~E~~~~~~~~~n~keiHALsSg~K~~~T  409 (661)
T KOG0135         330 IRYSLSRRQFGPTKNGEEVPILEYPSQQYRLLPYLAAAYALSFASKYLVMIYVERTPRTNEGVNSKEIHALSSGLKPVAT  409 (661)
T ss_pred             HHHHHHHHHHCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHH
T ss_conf             66687686508877998332453415788878999999999999999999999886621023203678998844530454


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             99999995699885213000455188985001223220462227899999983
Q gi|254780299|r  406 KMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLL  458 (562)
Q Consensus       406 e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l  458 (562)
                      ....+...+|-|+.||+||+.++-+..+=-|--++..|||-|||+-..+.+.|
T Consensus       410 W~~~~~LqecREAcGGhGYl~~nRlg~Lr~D~D~~~TfEGDNnVLlQqvsn~L  462 (661)
T KOG0135         410 WHNMRALQECREACGGHGYLQENRLGQLRDDHDPFQTFEGDNNVLLQQVSNAL  462 (661)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCEEECCCEEHHHHHHHHH
T ss_conf             76577999999871660088887744455678855420067520799999999


No 33 
>pfam08028 Acyl-CoA_dh_2 Acyl-CoA dehydrogenase, C-terminal domain.
Probab=99.92  E-value=3.5e-24  Score=180.31  Aligned_cols=130  Identities=25%  Similarity=0.304  Sum_probs=116.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCC--CCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH-HHHHHH
Q ss_conf             357999999999999999999840462--22423538888999999999999999999999988720111036-777655
Q gi|254780299|r  318 LDSAIMSVSGMRVSLAEAIHYARRRHV--SGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSE-EAAYAR  394 (562)
Q Consensus       318 l~~a~~~~G~ar~al~~A~~yA~~R~~--fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~-~~a~ar  394 (562)
                      |++++.++|++++|++++++|+++|++  ||+||.++|.+|.+|++|.+++++++++++++++.+|+...... .....+
T Consensus         1 lgiaA~~lG~a~~ald~~~~~~~~R~~~~~g~~l~~~~~~q~~la~~~~~l~aar~~~~~~a~~~~~~~~~g~~~~~~~~   80 (134)
T pfam08028         1 LGFAAPALGAARGALAAFIERARERVRAYGGAPLAEDPATQTRLAEAAAEIDAARLLLERAADRIWAHADRGDEVTPEER   80 (134)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf             95999999999999999999997176666886699777899999999999999999999999999975653776999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHHHCCCCH
Q ss_conf             67999999999999999956998852130004551889850012232204622
Q gi|254780299|r  395 IMAPITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANSILLGSG  447 (562)
Q Consensus       395 l~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~I~EGt~  447 (562)
                      ..+.++|.++++.+.+++++++|++||.||.+++|++|+|||+++.+|+||++
T Consensus        81 ~~~~~~k~~a~~~a~~v~~~~~~~~Gg~g~~~~~~~~R~~RD~r~~~~H~~~~  133 (134)
T pfam08028        81 ARARRDAALAAELAVAAVDRLFRAAGGSALFKDSPLQRFWRDAHAGAAHAGLD  133 (134)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999999999999999738531668983999999998999727789


No 34 
>KOG0136 consensus
Probab=99.90  E-value=8.1e-22  Score=164.46  Aligned_cols=299  Identities=15%  Similarity=0.130  Sum_probs=224.9

Q ss_pred             CCCCCCHHHHHHH-HHHHH--CCHHHHHHHHHHHCCCCCCHHHCCCCCCCCCEEEEECCCCCCCCCHHHCCEEEEECCC-
Q ss_conf             5312213567789-99985--0878898730120010005442660015521235544588888786654302786489-
Q gi|254780299|r  148 AGHLMSPSVTSAS-MVALM--TTPRVHKDWAPKIFSREYDPTNKAPMQKTSVAIGLGLTEKRGGTDIAAITSQGQKISD-  223 (562)
Q Consensus       148 ~g~~cp~~mt~~a-~~~L~--~~~e~~~~~lp~l~s~~~~~~~~~~~~k~g~~~~~~lTEp~~GSDv~~~~T~A~~~gd-  223 (562)
                      ..-..|+....+. +++|+  +++||.++|+++-...+             ++++.+.||-++||.++.++|+|+-|.. 
T Consensus       105 ~~~~~pl~lH~~MFvp~l~~q~t~EQ~~~Wl~~a~~~~-------------IiGtYAQTElGHGTnl~~LET~AtyD~~T  171 (670)
T KOG0136         105 GQEGHPLALHYGMFVPTLKGQGTDEQQEKWLSRALNME-------------IIGTYAQTELGHGTNLRGLETTATYDPKT  171 (670)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCE-------------EEEEEHHHHHCCCCCCCCCCEEEEECCCC
T ss_conf             77884255546564677614899999999997510561-------------78751323423442111430022235776


Q ss_pred             CEEEEC-----CEEEEEEC--CCCCEEEEEEEC--C---CCCEEEEEECCCCC--CCCCCEEEEEECCCCCCCCCCEEEE
Q ss_conf             668984-----51468634--211579997046--9---96179998775898--8403478863047554565772799
Q gi|254780299|r  224 GIYCLS-----GHKWFLSS--PMSDAFIMLAQV--E---GRVGCFLVPRLLED--GSPNGLCYQRLKNKIGNRSNATVEL  289 (562)
Q Consensus       224 g~y~Ln-----G~Kwf~sa--~~ad~~lVlArt--~---~Gls~FlVp~~~pg--g~~n~v~i~r~~~klG~r~~~t~ei  289 (562)
                      .+++||     ..|||..+  ..+.+.+|+|+.  .   -|+-.|+||-+.++  ....||.|+.+-.|||..+...+.+
T Consensus       172 ~eFVl~TPt~ta~KWWPGgLG~ssnhAvV~AqL~~~gk~~G~h~FiV~lRd~~th~pL~Gi~iGDIG~Kmg~ng~dNGfL  251 (670)
T KOG0136         172 QEFVLNTPTLTATKWWPGGLGKSSNHAVVVAQLITKGKCYGPHPFIVQLRDEDTHKPLPGITVGDIGPKMGFNGVDNGFL  251 (670)
T ss_pred             CEEEECCCCCCEECCCCCCCCCCCCHHEEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCEECCCCCCCCCCCCCCCEE
T ss_conf             64884589743002468766553320201245556461114540589723754467999974067776546667766511


Q ss_pred             EECCEEE---EEE------CCCCCHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-------C
Q ss_conf             9869075---300------7776579999-----99730133357999999999999999999840462224-------2
Q gi|254780299|r  290 EFSNTFG---FLL------GDLNVSTGPV-----EDMKILIYLDSAIMSVSGMRVSLAEAIHYARRRHVSGG-------I  348 (562)
Q Consensus       290 ~f~~~~~---~ll------G~~g~G~~~i-----~~~l~~~Rl~~a~~~~G~ar~al~~A~~yA~~R~~fG~-------~  348 (562)
                      .|++++.   +++      -+.|...+--     ...+-..|-.+.....-....|.-+|+.|+.-|+|+.-       .
T Consensus       252 ~f~nvRIPR~nmLmr~~kV~~dGtyv~p~~~~l~Y~tMv~vRs~mv~d~a~~La~A~tIAtRYSaVRRQ~~i~pg~~E~q  331 (670)
T KOG0136         252 GFDNVRIPRTNMLMRHAKVEPDGTYVKPPHPKLGYGTMVYVRSLMVMDQARFLAKAATIATRYSAVRRQSEIRPGQPEVQ  331 (670)
T ss_pred             EECCEEECHHHHHHHHHEECCCCCCCCCCCCCCCEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCE
T ss_conf             02236615276420111116787705788541330136998504687799999998999999888761268899998853


Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH-------HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             3538888999999999999999999999988-------720111036777655679999999999999999569988521
Q gi|254780299|r  349 LIDQPVMKRAIADIALDIAAATALSFRLANS-------FDEAKSRSEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGG  421 (562)
Q Consensus       349 L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~-------~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG  421 (562)
                      |+|||..|.+|--.-+...|-+.....+-+.       ++++.-  ..-+-+-.+++-.|..+|..+..-+++|-+.+||
T Consensus       332 IlDyqTQQ~rlFP~LA~ayAf~~~g~~l~~~Y~~~~~~l~~g~~--s~LpeLHaLS~gLKa~~T~~~~~GIE~~R~aCGG  409 (670)
T KOG0136         332 ILDYQTQQYRLFPQLARAYAFRFVGEELWELYEDVLKELENGNF--SRLPELHALSAGLKAVVTWDTAQGIEQCRLACGG  409 (670)
T ss_pred             EEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH--HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             53126378787588878998899899999999999998846882--2244778877656788666566279999986277


Q ss_pred             CCCCCCCHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHCCC
Q ss_conf             3000455188985001223220462227899999983126
Q gi|254780299|r  422 SGYIEERSIARHYRESPANSILLGSGNAMVLDVLNLLEKG  461 (562)
Q Consensus       422 ~Gy~ee~~leRl~RDA~v~~I~EGt~~I~aldv~r~l~r~  461 (562)
                      +||..-+.++-+|-.+-..-.|||-|.||-|.++|.|.|.
T Consensus       410 HGYs~~Sglp~iY~~~v~~CTYEGEN~VmlLQ~ARfLmKs  449 (670)
T KOG0136         410 HGYSQASGLPEIYGVAVGACTYEGENTVLLLQVARFLVKS  449 (670)
T ss_pred             CCCHHHCCCCCCEEEEEEEEEEECCCEEEHHHHHHHHHHH
T ss_conf             5405442896201420013222236343138999999999


No 35 
>pfam02770 Acyl-CoA_dh_M Acyl-CoA dehydrogenase, middle domain. Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold.
Probab=99.45  E-value=1e-13  Score=110.12  Aligned_cols=51  Identities=29%  Similarity=0.703  Sum_probs=46.9

Q ss_pred             EEECCCCCCCCCHHHCCEEEEECCCCEEEECCEEEEEE-CCCCCEEEEEEECC
Q ss_conf             55445888887866543027864896689845146863-42115799970469
Q gi|254780299|r  199 GLGLTEKRGGTDIAAITSQGQKISDGIYCLSGHKWFLS-SPMSDAFIMLAQVE  250 (562)
Q Consensus       199 ~~~lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~s-a~~ad~~lVlArt~  250 (562)
                      +++||||++|||+.+++|+|++++|+ |+|||+|||++ ++.+|+++|+|||+
T Consensus         1 a~a~TEp~~GsD~~~~~T~A~~~g~~-~~lnG~K~~it~~~~a~~~~v~art~   52 (52)
T pfam02770         1 AFALTEPGAGSDLASLETTAERDGDG-WVLNGRKWWITNAALADLALVLARTG   52 (52)
T ss_pred             CEEECCCCCCCCHHHCEEEEEEECCE-EEEEEEEEEECCCCCCCEEEEEEEEC
T ss_conf             96986899788647598899996999-99999999576931469999999849


No 36 
>COG2368 Aromatic ring hydroxylase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=98.39  E-value=0.00012  Score=49.21  Aligned_cols=256  Identities=17%  Similarity=0.163  Sum_probs=139.6

Q ss_pred             CCCCCCEEEEECCCCCCCCCHHHCCE-------EE-EECCCCEEEECCEEEEEE-CCCCCEEEEE-EEC--CC--C-CEE
Q ss_conf             01552123554458888878665430-------27-864896689845146863-4211579997-046--99--6-179
Q gi|254780299|r  191 MQKTSVAIGLGLTEKRGGTDIAAITS-------QG-QKISDGIYCLSGHKWFLS-SPMSDAFIML-AQV--EG--R-VGC  255 (562)
Q Consensus       191 ~~k~g~~~~~~lTEp~~GSDv~~~~T-------~A-~~~gdg~y~LnG~Kwf~s-a~~ad~~lVl-Art--~~--G-ls~  255 (562)
                      .+|+....+-+||-|++-=.-...+-       +- ++.+|| -++.|-|-.+| ++.+|..+|+ .+.  ++  . --.
T Consensus       140 vqk~DL~~~hA~tdpk~dRsk~p~e~~dpdiyvrVvee~~dG-IVVrGAK~~aT~~a~tdei~V~Pt~~~~~~d~dfAv~  218 (493)
T COG2368         140 VQKNDLALTHAITDPKGDRSKRPSEQKDPDIYVRVVEETEDG-IVVRGAKALATGSALTDEIFVLPTRSMQEDDKDFAVA  218 (493)
T ss_pred             HHHCCCEEEECEECCCCCCCCCHHHCCCCCEEEEEEEEECCC-EEEECHHHHHCCCCCCCEEEEEECCCCCCCCCCEEEE
T ss_conf             985283452000158866778833356877269999970495-6997767772266411238984134467888864899


Q ss_pred             EEEECCCCCCCC---CCEEEEEE-C-CCCC----CCC-CCEEEEEECCEEE-----EEECCCC--CHHHHHHHHHHHHHH
Q ss_conf             998775898840---34788630-4-7554----565-7727999869075-----3007776--579999997301333
Q gi|254780299|r  256 FLVPRLLEDGSP---NGLCYQRL-K-NKIG----NRS-NATVELEFSNTFG-----FLLGDLN--VSTGPVEDMKILIYL  318 (562)
Q Consensus       256 FlVp~~~pgg~~---n~v~i~r~-~-~klG----~r~-~~t~ei~f~~~~~-----~llG~~g--~G~~~i~~~l~~~Rl  318 (562)
                      |.+|.++||.+.   +.+...+- + ....    .|. ...+.+.||+|.+     .+.++.-  ..+.......++.|.
T Consensus       219 FaiP~dt~GvK~i~r~s~~~~~~~~~g~fd~plssrfde~dailVfDdVfVPWERVf~y~d~~~~~~~~~~~~Fa~~~~~  298 (493)
T COG2368         219 FAIPMDTEGVKFICRRSYELGRGAEGGPFDYPLSSRFDENDAILVFDDVFVPWERVFIYRDLERAYAWYAVSGFARLHRQ  298 (493)
T ss_pred             EECCCCCCCEEEEECCCCHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHEEEECCHHHHHHHHHHHHHHHHHHH
T ss_conf             97006998628993376123214678987886555545675189962652532551562468988778888879887441


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             57999999999999999999840462224235388889999999999999999999999887201110367776556799
Q gi|254780299|r  319 DSAIMSVSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAP  398 (562)
Q Consensus       319 ~~a~~~~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~  398 (562)
                      ..+..-.+....-+-.+..-++.     --+.+++.||.+|++|.+..|.+.++...++..-.+.....--.  -...+.
T Consensus       299 q~~~~k~~k~d~i~G~~~~~~~~-----~Gv~~~~hIq~kl~Emi~~~e~~~al~~Aa~~~a~~~~~G~~~P--n~~~~n  371 (493)
T COG2368         299 QAVGRKAVKLDFILGAAYLIAET-----NGVEEFRHIQEKLGEMIALLELMWALSDAAAEEAQKNPNGAWLP--NPAYAN  371 (493)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-----HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEC--CHHHHH
T ss_conf             12334577999999999999986-----38411155899999999999999999999875034588885514--789975


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCHHHH----HCCCCHHHHHHHHHH
Q ss_conf             9999999999999956998852130004551889850012232----204622278999999
Q gi|254780299|r  399 ITKYWCCKMAPAVIAEAMECIGGSGYIEERSIARHYRESPANS----ILLGSGNAMVLDVLN  456 (562)
Q Consensus       399 iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~~leRl~RDA~v~~----I~EGt~~I~aldv~r  456 (562)
                      +.|.+..+.-.++.....++.||.=.+--+  ++=+++-.+-.    -.-|++|+-+.+-+|
T Consensus       372 ~~r~~~~~~~~~~~~~l~~i~gg~~i~lPS--~~D~~n~e~~~~l~kYlrg~~~~~aeeR~k  431 (493)
T COG2368         372 VGRVYAPKAYPRIKEILQDISGGGIITLPS--AEDLFNPEIRPYLDKYLRGSANVDAEERLK  431 (493)
T ss_pred             HHHHHCCCCHHHHHHHHHHHHCCCEEECCC--HHHHCCCHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf             687752212288999999973586563673--665219155688999982447998999999


No 37 
>pfam02771 Acyl-CoA_dh_N Acyl-CoA dehydrogenase, N-terminal domain. The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain.
Probab=97.65  E-value=0.00011  Score=49.33  Aligned_cols=92  Identities=21%  Similarity=0.167  Sum_probs=58.3

Q ss_pred             CCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             69846201799852136566889999999999679620337766664447637999999999830144531221356778
Q gi|254780299|r   80 NTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSFEPVVRKQAHKIRAARLYLMAQLEAGHLMSPSVTSA  159 (562)
Q Consensus        80 ~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~g~~cp~~mt~~  159 (562)
                      .+|+...+|..+      .+++   ++++.+.+.||.++.|+..+++.+  ...+...+...-++.++.+....+.+..+
T Consensus        19 l~p~~~~~d~~~------~~p~---~~~~~l~~~G~~~~~~P~~~GG~g--~~~~~~~~~~ee~~~~~~~~~~~~~~~~~   87 (113)
T pfam02771        19 VAPHAAEWDEEG------EFPR---ELWRKLGELGLLGLTIPEEYGGAG--LDYLEYALVAEELARADASVGLALSVHSS   87 (113)
T ss_pred             CHHHHHHHHHCC------CCCH---HHHHHHHHCCCCEEECCHHHCCCC--CCHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             822499998769------9999---999999986998150763118999--99999999999998607836899997788


Q ss_pred             -HHHHHH--CCHHHHHHHHHHHCCCC
Q ss_conf             -999985--08788987301200100
Q gi|254780299|r  160 -SMVALM--TTPRVHKDWAPKIFSRE  182 (562)
Q Consensus       160 -a~~~L~--~~~e~~~~~lp~l~s~~  182 (562)
                       +..+|.  ++++|+++|||++++++
T Consensus        88 ~~~~~l~~~gs~~qk~r~Lp~l~~Ge  113 (113)
T pfam02771        88 LVAPPILRFGTEEQKEKYLPKLASGE  113 (113)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHCCCC
T ss_conf             67999999896999998839872899


No 38 
>KOG0137 consensus
Probab=95.77  E-value=0.11  Score=29.37  Aligned_cols=27  Identities=11%  Similarity=0.075  Sum_probs=15.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             213778999999999999999997085
Q gi|254780299|r  496 EDKGLARFLTEKIALASSAAALYRAGM  522 (562)
Q Consensus       496 ~~e~~AR~~~e~la~~~~aalL~r~a~  522 (562)
                      +.....+++++-...++.-++.+.++.
T Consensus       539 ~~q~~l~rlA~~~~~iYam~a~isRAS  565 (634)
T KOG0137         539 EEQSVLQRLANVAINIYAMVAVISRAS  565 (634)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             789999999999999988875466656


No 39 
>pfam11794 HpaB_N 4-hydroxyphenylacetate 3-hydroxylase N terminal. HpaB encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli. HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC, which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis.
Probab=95.76  E-value=0.14  Score=28.58  Aligned_cols=75  Identities=16%  Similarity=0.242  Sum_probs=47.1

Q ss_pred             CCCCCCEEEEECCCCCCCCCHHH------CCEEEE-ECCCCEEEECCEEEE-EECCCCCEEEEEEEC---C--CCC-EEE
Q ss_conf             01552123554458888878665------430278-648966898451468-634211579997046---9--961-799
Q gi|254780299|r  191 MQKTSVAIGLGLTEKRGGTDIAA------ITSQGQ-KISDGIYCLSGHKWF-LSSPMSDAFIMLAQV---E--GRV-GCF  256 (562)
Q Consensus       191 ~~k~g~~~~~~lTEp~~GSDv~~------~~T~A~-~~gdg~y~LnG~Kwf-~sa~~ad~~lVlArt---~--~Gl-s~F  256 (562)
                      .+++.+..+-+||-|++-=....      +-.+-+ +..|| -+|+|-|-. |.++.+|-.+|+--.   +  +.. -.|
T Consensus       133 ~~~nDl~~~~a~~dPq~dRs~~p~q~d~d~~l~Vvee~~dG-IvVrGAK~~~T~a~~a~ei~V~p~~~~~~~d~dyAv~f  211 (265)
T pfam11794       133 AQENDLYLTHAITDPKGDRSKPPHQEDPDVYVHVVEETDDG-IVVRGAKALATGAAIADEIFVMPTRAMPEEDKDYAVAF  211 (265)
T ss_pred             HHHHCCEEEEEEECCCCCCCCCHHHCCCCCEEEEEEECCCC-EEEECHHHHHCCCCCCCEEEEEECCCCCCCCCCEEEEE
T ss_conf             99709553545337987788771125887468999974896-89978677523675346189973588998886668999


Q ss_pred             EEECCCCCCC
Q ss_conf             9877589884
Q gi|254780299|r  257 LVPRLLEDGS  266 (562)
Q Consensus       257 lVp~~~pgg~  266 (562)
                      .||.++||.+
T Consensus       212 avP~ntpGlk  221 (265)
T pfam11794       212 AVPMDAPGLK  221 (265)
T ss_pred             EEECCCCCEE
T ss_conf             9766999708


No 40 
>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=88.20  E-value=1.6  Score=21.46  Aligned_cols=218  Identities=17%  Similarity=0.246  Sum_probs=116.7

Q ss_pred             CEEEEECCCCCC-CCCH------HHCCE-EEEECCCCEEEECCEEEEEEC-CCCCEEEEEEEC------C-CCCEE-EEE
Q ss_conf             123554458888-8786------65430-278648966898451468634-211579997046------9-96179-998
Q gi|254780299|r  196 VAIGLGLTEKRG-GTDI------AAITS-QGQKISDGIYCLSGHKWFLSS-PMSDAFIMLAQV------E-GRVGC-FLV  258 (562)
Q Consensus       196 ~~~~~~lTEp~~-GSDv------~~~~T-~A~~~gdg~y~LnG~Kwf~sa-~~ad~~lVlArt------~-~Gls~-FlV  258 (562)
                      +..+-+||.||- -|-.      .-+.- .-++.++| -++.|-.-..|- +.+|=++|+=-|      + +.-|+ |-+
T Consensus       149 l~lTHaL~nPQVNRak~~seqpDpyialgvVe~td~G-viVrGaRm~AT~pGiaDEiliFPSTvlk~ga~k~~YalaFai  227 (487)
T TIGR02309       149 LSLTHALTNPQVNRAKIASEQPDPYIALGVVEKTDDG-VIVRGARMLATLPGIADEILIFPSTVLKSGAEKDRYALAFAI  227 (487)
T ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEECCCE-EEECCHHHHCCCCCCCCEEEECCHHHHHCCCCCCCHHHHHCC
T ss_conf             0023321166522234767766785100247764860-597272873332242235566550342047887710321125


Q ss_pred             ECCCCCCC---CCCEEEEEE--CCCCCCCCC-CEEEEEECCEE-----EEEECCC---CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             77589884---034788630--475545657-72799986907-----5300777---6579999997301333579999
Q gi|254780299|r  259 PRLLEDGS---PNGLCYQRL--KNKIGNRSN-ATVELEFSNTF-----GFLLGDL---NVSTGPVEDMKILIYLDSAIMS  324 (562)
Q Consensus       259 p~~~pgg~---~n~v~i~r~--~~klG~r~~-~t~ei~f~~~~-----~~llG~~---g~G~~~i~~~l~~~Rl~~a~~~  324 (562)
                      |..+||..   |..+..++-  -+-+|.|.- .-|.|.||||-     ..+|+..   |+.+.. ...+++.--.+-+--
T Consensus       228 ptnTPGL~f~cRE~~d~G~~pfDhPlsSrfeE~Da~ViFDdVLVPWeRiFiL~dvElcN~AyA~-T~Av~HMahQVvalk  306 (487)
T TIGR02309       228 PTNTPGLRFLCRESLDVGKDPFDHPLSSRFEEQDALVIFDDVLVPWERIFILEDVELCNKAYAE-TDAVVHMAHQVVALK  306 (487)
T ss_pred             CCCCCCCCEEECCCCCCCCCCCCCCCCCEEECCCEEEEECCCCCCCCEEEEECCHHHHHHHHHH-CCHHHHHHHHHHHHH
T ss_conf             4678886401015533685787788544022364178763733771005530211334101222-123655677777666


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHH
Q ss_conf             999999999999998404622242353888899999999999999999999998872011---10367776556799999
Q gi|254780299|r  325 VSGMRVSLAEAIHYARRRHVSGGILIDQPVMKRAIADIALDIAAATALSFRLANSFDEAK---SRSEEAAYARIMAPITK  401 (562)
Q Consensus       325 ~G~ar~al~~A~~yA~~R~~fG~~L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~---~~~~~~a~arl~t~iaK  401 (562)
                      ++=.+.-|-.+..-+.     +--+.-||.||.+.+|+-+.+|.++++.+++-.......   -.++-.+     .-.|.
T Consensus       307 iAKtEafLGva~~~~~-----~IG~dgfqHV~~KiaEIi~~LE~Mka~~~~Aee~Ak~n~yG~mtPdr~a-----LdaAR  376 (487)
T TIGR02309       307 IAKTEAFLGVALKLVD-----SIGADGFQHVQDKIAEIIVALEAMKAFLVKAEEEAKENRYGLMTPDREA-----LDAAR  376 (487)
T ss_pred             HHHHHHHHHHHHHHHH-----HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHH-----HHHHH
T ss_conf             7778889999999985-----4078840336778999999999889999999862674663455774434-----55554


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             9999999999956998852130004
Q gi|254780299|r  402 YWCCKMAPAVIAEAMECIGGSGYIE  426 (562)
Q Consensus       402 ~~~~e~a~~v~~~Aiqi~GG~Gy~e  426 (562)
                      -|=...-.+ ..|-+|++|..|.+.
T Consensus       377 N~yPr~ypR-l~EiL~~lGASGli~  400 (487)
T TIGR02309       377 NYYPRVYPR-LAEILRLLGASGLIT  400 (487)
T ss_pred             HHCCCCCHH-HHHHHHHHCCCCCCC
T ss_conf             100001200-899999836245022


No 41 
>pfam03241 HpaB 4-hydroxyphenylacetate 3-hydroxylase C terminal. HpaB encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli. HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC, which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis.
Probab=88.03  E-value=1.7  Score=21.39  Aligned_cols=85  Identities=8%  Similarity=0.090  Sum_probs=56.7

Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             35388889999999999999999999999887201110367776556799999999999999995699885213000455
Q gi|254780299|r  349 LIDQPVMKRAIADIALDIAAATALSFRLANSFDEAKSRSEEAAYARIMAPITKYWCCKMAPAVIAEAMECIGGSGYIEER  428 (562)
Q Consensus       349 L~~~p~v~~~LAdm~~~~eaa~~l~~~~A~~~D~~~~~~~~~a~arl~t~iaK~~~~e~a~~v~~~Aiqi~GG~Gy~ee~  428 (562)
                      +.++|.||.+|++|....|..+++...+...-...+...-  .--+..+-.+|.+.++.-.+++....++.||. .+. .
T Consensus        44 ~~~~~~Vqekl~Eli~~~e~~~a~~~aa~~~a~~~~~G~~--~P~~~~~~a~r~~~~~~y~~~~~il~~l~gg~-li~-l  119 (205)
T pfam03241        44 VDKFPHVQEKLGELIALRELFRALLIAAEAEAEKDPNGAY--LPNLLLLNAGRVLAPELYPRIVEILRDLGGGG-LIT-L  119 (205)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCE--EECHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-EEE-C
T ss_conf             6645169999999999999999999999974965999855--40788999999998876999999999981779-335-7


Q ss_pred             HHHHHHHCC
Q ss_conf             188985001
Q gi|254780299|r  429 SIARHYRES  437 (562)
Q Consensus       429 ~leRl~RDA  437 (562)
                      |-+.=|.+.
T Consensus       120 Ps~~Df~np  128 (205)
T pfam03241       120 PSEADFANP  128 (205)
T ss_pred             CCHHHHCCH
T ss_conf             897884694


No 42 
>TIGR01282 nifD nitrogenase molybdenum-iron protein alpha chain; InterPro: IPR005972    The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene , . Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes . It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I .; GO: 0016163 nitrogenase activity, 0009399 nitrogen fixation, 0016612 molybdenum-iron nitrogenase complex.
Probab=73.42  E-value=2.1  Score=20.66  Aligned_cols=69  Identities=14%  Similarity=0.258  Sum_probs=42.2

Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHH---HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEC
Q ss_conf             202457887621101167888589980016788---9999972042110789999998501899999986343698462
Q gi|254780299|r   10 LAMNQVHQPSDSLFALNQPPLFIGMNAYSSDSL---LVALIANFPSVVHKELELLGEYVLSCTAQELARMANYNTPQLH   85 (562)
Q Consensus        10 ~~~~~~~~~~~~~~~~nq~~~~~g~n~~~~D~~---l~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~a~~~~P~l~   85 (562)
                      ++|||+++.=.+.++.    |...+|+|=.+..   |+++++.|   .++++.+-.|.|..++........+++.|+|.
T Consensus       267 RSmNYi~~~MEekYGi----PW~e~NFfGp~~i~~sLR~iA~~F---Dd~~i~~~~E~VIA~y~~~~~~~i~~yr~rl~  338 (521)
T TIGR01282       267 RSMNYISRHMEEKYGI----PWMEYNFFGPTKIAESLRKIAEFF---DDPEIKEKAEEVIAKYQPQVDAVIAKYRPRLE  338 (521)
T ss_pred             CCHHHHHHHHHHHCCC----CCEEEECCCHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             4366887787865089----836873348468999999998546---96678888889999888999999999987424


No 43 
>KOG0450 consensus
Probab=70.08  E-value=6.3  Score=17.51  Aligned_cols=109  Identities=20%  Similarity=0.180  Sum_probs=54.8

Q ss_pred             CCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCC--CHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             96878766320245788762110116788858998001678899999720421--1078999999850189999998634
Q gi|254780299|r    1 MTLREIYRRLAMNQVHQPSDSLFALNQPPLFIGMNAYSSDSLLVALIANFPSV--VHKELELLGEYVLSCTAQELARMAN   78 (562)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~nq~~~~~g~n~~~~D~~l~~~~~~~~~~--~~~~l~~~g~~~~~~~~~~~~~~a~   78 (562)
                      ||||||-+||.+.+-......-+-.|   .+.-.||.     .+++-...+-.  .+..-.-|..++=|  ..=...++.
T Consensus       201 ltLreIl~rlE~~YC~~igvEfmhI~---~~eqcnWi-----r~k~EtP~~~q~s~e~k~~il~RL~~s--t~FE~FLa~  270 (1017)
T KOG0450         201 LTLREILRRLEKAYCGSIGVEFMHIN---DLEQCNWI-----RQKFETPGPMQYSHEQKRVILDRLTRS--TRFEEFLAT  270 (1017)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEEEEC---CHHHHHHH-----HHHCCCCCCCCCCHHHHHHHHHHHHHH--HHHHHHHHH
T ss_conf             52999999999876324305788608---57772799-----986369985115778899999998876--479999865


Q ss_pred             HCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             3698462017998521365668899999999996796203377666
Q gi|254780299|r   79 YNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIWDRSF  124 (562)
Q Consensus        79 ~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~~~~~  124 (562)
                      +. |.-+.|.-.|..    ..-|+-|++.+.+.+.|+-++..--++
T Consensus       271 Kw-~seKRFGLEGcE----~lIP~mK~iiDrS~elGVe~iviGMpH  311 (1017)
T KOG0450         271 KW-PSEKRFGLEGCE----VLIPAMKTIIDRSSELGVESIVIGMPH  311 (1017)
T ss_pred             HC-CCCCCCCCCCHH----HHHHHHHHHHHHHHHCCCHHEEECCCC
T ss_conf             08-852013655325----450678988623544180215733776


No 44 
>TIGR01074 rep ATP-dependent DNA helicase Rep; InterPro: IPR005752    RepA hexameric DNA helicase contain ATP-binding domains similar to those seen in monomeric helicases but which are arranged in a ring. There is compelling evidence to suggest that a single ssDNA molecule passes through the centre of the hexameric ring. Activity of the enzyme is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilizing the duplex and separating the two strands in an active process  ; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=63.92  E-value=5.9  Score=17.71  Aligned_cols=30  Identities=10%  Similarity=0.049  Sum_probs=13.7

Q ss_pred             HHHHHCCCCCCCC-CHHHHHHHCCHHHHHCC
Q ss_conf             9988521300045-51889850012232204
Q gi|254780299|r  415 AMECIGGSGYIEE-RSIARHYRESPANSILL  444 (562)
Q Consensus       415 Aiqi~GG~Gy~ee-~~leRl~RDA~v~~I~E  444 (562)
                      --+.+=|.|.-+. -.+.++..---+..+-|
T Consensus       516 ~~~~L~~~e~~~~~m~l~~~v~~ltLrd~lE  546 (677)
T TIGR01074       516 LKEMLEGDEEDGPEMNLEQVVQRLTLRDMLE  546 (677)
T ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             9998417888852346899999998754641


No 45 
>TIGR02093 P_ylase glycogen/starch/alpha-glucan phosphorylases; InterPro: IPR011833   The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site . The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'.   Proteins in this entry are glycosyltransferases with phosphorylase activities. Members use phosphate to break alpha 1,4 linkages between pairs of glucose residues at the end of long glucose polymers, releasing alpha-D-glucose 1-phosphate. The nomenclature convention is to preface the name according to the natural substrate, as in glycogen phosphorylase, starch phosphorylase, maltodextrin phosphorylase, etc.   The main role of glycogen phosphorylase (GPase) is to provide phosphorylated glucose molecules (G-1-P) . GPase is a highly regulated allosteric enzyme. The net effect of the regulatory site allows the enzyme to operate at a variety of rates; the enzyme is not simply regulated as "on" or "off", but rather it can be thought of being set to operate at an ideal rate based on changing conditions at in the cell. The most important allosteric effector is the phosphate molecule covalently attached to Ser14. This switches GPase from the b (inactive) state to the a (active) state. Upon phosphorylation, GPase attains about 800f its Vmax. When the enzyme is not phosphorylated, GPase activity is practically non-existent at low AMP levels .    There is some apparent controversy as to the structure of GPase. All sources agree that the enzyme is multimeric, but there is apparent controversy as to the enzyme being a tetramer or a dimer. Apparently, GPase (in the a form) forms tetramers in the crystal form. The consensus seems to be that 'regardless of the a or b form, GPase functions as a dimer in vivo . The GPase monomer is best described as consisting of two domains, an N-terminal domain and a C-terminal domain . The C-terminal domain is often referred to as the catalytic domain. It consists of a beta-sheet core surrounded by layers of helical segments . The vitamin cofactor pyridoxal phosphate (PLP) is covalently attached to the amino acid backbone. The N-terminal domain also consists of a central beta-sheet core and is surrounded by layers of helical segments. The N-terminal domain contains different allosteric effector sites to regulate the enzyme.   Bacterial phosphorylases follow the same catalytic mechanisms as their plant and animal counterparts, but differ considerably in terms of their substrate specificity and regulation. The catalytic domains are highly conserved while the regulatory sites are only poorly conserved. For maltodextrin phosphorylase from Escherichia coli the physiological role of the enzyme in the utilisation of maltidextrins is known in detail; that of all the other bacterial phosphorylases is still unclear. Roles in regulatuon of endogenous glycogen metabolism in periods of starvation, and sporulation, stress response or quick adaptation to changing environments are possible .; GO: 0004645 phosphorylase activity, 0030170 pyridoxal phosphate binding, 0005975 carbohydrate metabolic process.
Probab=61.78  E-value=2.3  Score=20.44  Aligned_cols=17  Identities=18%  Similarity=0.278  Sum_probs=7.8

Q ss_pred             HHHC-CHHHHHHHHHHHC
Q ss_conf             9850-8788987301200
Q gi|254780299|r  163 ALMT-TPRVHKDWAPKIF  179 (562)
Q Consensus       163 ~L~~-~~e~~~~~lp~l~  179 (562)
                      +|+. +-.++++.||+++
T Consensus       365 ALE~Wp~~Lf~~LLPRhl  382 (822)
T TIGR02093       365 ALEKWPVDLFEKLLPRHL  382 (822)
T ss_pred             HHCCCCHHHHHHHHHHHH
T ss_conf             531289779987636699


No 46 
>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein; InterPro: IPR005670   This is a family of phosphate transport system permease proteins.; GO: 0005315 inorganic phosphate transmembrane transporter activity, 0015114 phosphate transmembrane transporter activity, 0006817 phosphate transport, 0016020 membrane.
Probab=61.63  E-value=4.9  Score=18.27  Aligned_cols=73  Identities=14%  Similarity=0.128  Sum_probs=53.9

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCC------CCCCHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             2789999998312603799999999964254517789999987305------4221377899999999999999999708
Q gi|254780299|r  448 NAMVLDVLNLLEKGTNLFEQLFSTLEQDLGSSGKKVITILRDSISL------CKEDKGLARFLTEKIALASSAAALYRAG  521 (562)
Q Consensus       448 ~I~aldv~r~l~r~~~~~~~l~~~l~~~~g~~~~~~~~~l~~~~~~------~~~~e~~AR~~~e~la~~~~aalL~r~a  521 (562)
                      .-|+|-++|+|.=+|+.+  |++|...++.|.+-.-.+.+-..+..      -.-.-.+|.++.++.|.-+.|. |++++
T Consensus       149 QQQRLCIARalA~ePeVl--LlDEPTSALDPIaT~~IEeLi~eLk~~YTivIVTHnMqQA~RiSD~tAFF~~G~-LvE~G  225 (248)
T TIGR00972       149 QQQRLCIARALAVEPEVL--LLDEPTSALDPIATGKIEELIQELKKKYTIVIVTHNMQQAARISDRTAFFYDGE-LVEYG  225 (248)
T ss_pred             HHHHHHHHHHHHCCCCEE--CCCCCCCCCCHHHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHHHHHHCCE-EEEEC
T ss_conf             889999998752488521--057888757877899999999987652979988177567899999998865672-57407


Q ss_pred             CH
Q ss_conf             57
Q gi|254780299|r  522 MN  523 (562)
Q Consensus       522 ~~  523 (562)
                      +.
T Consensus       226 ~T  227 (248)
T TIGR00972       226 DT  227 (248)
T ss_pred             CH
T ss_conf             81


No 47 
>pfam11859 DUF3379 Protein of unknown function (DUF3379). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 234 to 251 amino acids in length.
Probab=60.73  E-value=9.7  Score=16.25  Aligned_cols=67  Identities=13%  Similarity=0.175  Sum_probs=41.9

Q ss_pred             CCCCEEEEEEECCCCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEEEECCEEEEEECCCCCHHHHHHHHH
Q ss_conf             2115799970469961799987758988403478863047554565772799986907530077765799999973
Q gi|254780299|r  238 PMSDAFIMLAQVEGRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVELEFSNTFGFLLGDLNVSTGPVEDMK  313 (562)
Q Consensus       238 ~~ad~~lVlArt~~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei~f~~~~~~llG~~g~G~~~i~~~l  313 (562)
                      +.-.+|+|+---.|.+++|+||...+-      ....--++-|+.+   --+...++..-|||+.|.-+..+..-+
T Consensus       161 g~~sLHlV~qg~~GkVTlFivP~~~~~------~~~~~F~d~~~~G---~~~~~~~a~~ilVge~~~dl~~v~~~i  227 (232)
T pfam11859       161 GVKSLHLVFQGEQGKVTLFIVPIESRM------VLEEAFADNGYEG---IIFPTGDASLILVGEKGEDLDKVKKKI  227 (232)
T ss_pred             CCCEEEEEEECCCCCEEEEEECCCCCC------CHHHHHCCCCCEE---EEEECCCEEEEEECCCCCCHHHHHHHH
T ss_conf             974368999648887899992175421------1566523677427---778638747999806620579999998


No 48 
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR; InterPro: IPR011785    This entry represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor . These proteins contain a Helix-Turn-Helix motif of the "fis" type..
Probab=59.41  E-value=5.9  Score=17.71  Aligned_cols=22  Identities=18%  Similarity=0.234  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHCCCCCCCHHHC
Q ss_conf             9999999984046222423538
Q gi|254780299|r  331 SLAEAIHYARRRHVSGGILIDQ  352 (562)
Q Consensus       331 al~~A~~yA~~R~~fG~~L~~~  352 (562)
                      +|-+-++-...-..-|+.|.++
T Consensus       290 aFl~l~~~ss~~~v~G~~L~~w  311 (453)
T TIGR02040       290 AFLELVEVSSKEAVRGRTLDRW  311 (453)
T ss_pred             HHHHHHHHCCHHHHCCCCHHHH
T ss_conf             9998987177545313323554


No 49 
>TIGR01862 N2-ase-Ialpha nitrogenase component I, alpha chain; InterPro: IPR010143   This entry represents all three varieties (Fe-Fe, Mo-Fe and V-Fe) of the component I alpha chain of nitrogenase.   Nitrogenase (1.18.6.1 from EC)  is the enzyme system responsible for biological nitrogen fixation. Nitrogenase is an oligomeric complex which consists of two components: component 2 is an homodimer of an iron-sulphur protein, while component 1 which contains the active site for the reduction of nitrogen to ammonia exists in three different forms: the molybdenum-iron containing protein (MoFe) is a hetero-tetramer consisting of two pairs of alpha (nifD) and beta (nifK) subunits; the vanadium-iron containing protein (VFe) is a hexamer of two pairs each of alpha (vnfD), beta (vnfK), and delta (vnfG) subunits; the third form seems to only contain iron and is a hexamer composed of alpha (anfD), beta (anfK), and delta (anfG) subunits. The alpha and beta chains of the three types of component 1 are evolutionary related and they are also related to proteins nifE and nifN, which are most probably involved in the iron-molybdenum cofactor biosynthesis .; GO: 0016163 nitrogenase activity, 0051536 iron-sulfur cluster binding, 0009399 nitrogen fixation.
Probab=58.43  E-value=3.5  Score=19.25  Aligned_cols=98  Identities=14%  Similarity=0.182  Sum_probs=63.2

Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCC
Q ss_conf             63202457887621101167888589980016788999997204211078999999850189999998634369846201
Q gi|254780299|r    8 RRLAMNQVHQPSDSLFALNQPPLFIGMNAYSSDSLLVALIANFPSVVHKELELLGEYVLSCTAQELARMANYNTPQLHAY   87 (562)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~nq~~~~~g~n~~~~D~~l~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~a~~~~P~l~~~   87 (562)
                      =.++|||.++.-.+.-+.    |..+.|+|=.+.....+-+-..-+-++++.+=++.+..+++.+|...-+.+.|+|+  
T Consensus       257 C~RS~nYIa~~le~rYGI----P~~~~dffG~~~~~e~LR~I~~~Fg~~eI~~r~EevIae~~a~w~p~ld~yKerL~--  330 (510)
T TIGR01862       257 CARSANYIANELEERYGI----PWLKIDFFGFEYIAESLRAIAAFFGDSEIEKRAEEVIAEEIAKWKPELDYYKERLQ--  330 (510)
T ss_pred             ECCHHHHHHHHHHHCCCC----CEEEECCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHC--
T ss_conf             014057999985530787----53775465703789989999964588542268888778744210412454113114--


Q ss_pred             CCCCCCCCEEEC--CHHHHHHHHHHHHCCC
Q ss_conf             799852136566--8899999999996796
Q gi|254780299|r   88 GPGGERWDKVEF--HPAWHALLRRSIHDGL  115 (562)
Q Consensus        88 d~~G~r~d~v~~--~p~~~~l~~~~~~~Gl  115 (562)
                         |+|+ .|..  +-.||-..-..-+.|+
T Consensus       331 ---GK~v-~ly~GG~r~wH~~~~~~~~lG~  356 (510)
T TIGR01862       331 ---GKRV-CLYVGGSRLWHWIKSLEEDLGV  356 (510)
T ss_pred             ---CCEE-EEECCCCCHHHHHHHHHHHCCC
T ss_conf             ---9889-9975888001111257776394


No 50 
>pfam12186 AcylCoA_dehyd_C Acyl-CoA dehydrogenase C terminal. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam02770, pfam00441, pfam02771. There is a conserved ARRL sequence motif. The C terminal domain is an alpha helical domain. The flavin ring of Acyl-CoA dehydrogenase is buried in the crevice between the two alpha helical domains and the beta-sheet domain of one subunit, and the adenosine pyrophosphate moiety is stretched into the subunit junction of a neighbouring subunit, composed of two C terminal domains.
Probab=57.34  E-value=11  Score=15.88  Aligned_cols=47  Identities=23%  Similarity=0.132  Sum_probs=33.7

Q ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHH------HHHHHHHHHHHHHH
Q ss_conf             73054221377899999999999999999708579------99999996400256
Q gi|254780299|r  490 SISLCKEDKGLARFLTEKIALASSAAALYRAGMND------IADVFLENRFLDNC  538 (562)
Q Consensus       490 ~~~~~~~~e~~AR~~~e~la~~~~aalL~r~a~~~------va~af~~~Rl~~~~  538 (562)
                      ...+.+-....||+++|..+.+..+-||++.+..+      .|+.|+  |++..-
T Consensus        44 e~~nqe~~DF~ARRL~eMaa~iims~LLl~dA~kapelF~kSA~VY~--~~ae~e   96 (114)
T pfam12186        44 EAKDQELLDFQARRLVEMAAHIIMGHLLLQDANKDEDLFRKSAEVYL--RYAEAE   96 (114)
T ss_pred             HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH--HHHHHH
T ss_conf             74175999999999999999999999999987458888988699999--998998


No 51 
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=39.59  E-value=21  Score=14.06  Aligned_cols=43  Identities=26%  Similarity=0.256  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCC--CHHHHHHHCCHHHHHCCCCHHH
Q ss_conf             999999569988521300045--5188985001223220462227
Q gi|254780299|r  407 MAPAVIAEAMECIGGSGYIEE--RSIARHYRESPANSILLGSGNA  449 (562)
Q Consensus       407 ~a~~v~~~Aiqi~GG~Gy~ee--~~leRl~RDA~v~~I~EGt~~I  449 (562)
                      .+..++-.-|+-+||.+|---  -.+-+-.||..+.+=|+|.|-+
T Consensus        62 ~alk~v~~l~~y~GGrsfYlP~G~s~r~t~Rn~~ifsd~dG~n~~  106 (137)
T COG5566          62 LALKLVFKLMEYGGGRSFYLPKGDSIRATLRNKQIFSDFDGSNYV  106 (137)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHCCCCCHH
T ss_conf             089999999997398158831756899999989999760776389


No 52 
>COG2087 CobU Adenosyl cobinamide kinase/adenosyl cobinamide phosphate guanylyltransferase [Coenzyme metabolism]
Probab=39.24  E-value=13  Score=15.41  Aligned_cols=17  Identities=29%  Similarity=0.616  Sum_probs=14.6

Q ss_pred             CCCCCCCCHHHHHHHCC
Q ss_conf             13000455188985001
Q gi|254780299|r  421 GSGYIEERSIARHYRES  437 (562)
Q Consensus       421 G~Gy~ee~~leRl~RDA  437 (562)
                      |.|.+-++++.|+|||.
T Consensus       131 G~GiVPe~~l~R~fRD~  147 (175)
T COG2087         131 GLGIVPEYRLGRLFRDI  147 (175)
T ss_pred             CCCCCCCCHHHHHHHHH
T ss_conf             47768583666799998


No 53 
>TIGR00770 Dcu transporter, anaerobic C4-dicarboxylate uptake (Dcu) family; InterPro: IPR004668   These proteins are members of the C4-Dicarboxylate Uptake (Dcu) family. Most proteins in this family are predicted to have 12 GES predicted transmembrane regions; however the one member whose membrane topology has been experimentally determined has 10 transmembrane regions, with both the N- and C-termini localized to the periplasm . The DcuA and DcuB proteins are involved in the transport of aspartate, malate, fumarate and succinate in many species , , , and are thought to function as antiporters with any two of these substrates. Since DcuA is encoded in an operon with the gene for aspartase, and DcuB is encoded in an operon with the gene for fumarase, their physiological functions may be to catalyze aspartate:fumarate and fumarate:malate exchange during the anaerobic utilization of aspartate and fumarate, respectively . The Escherichia coli DcuA and DcuB proteins have very different expression patterns . DcuA is constitutively expressed; DcuB is strongly induced anaerobically by FNR and C4-dicarboxylates, while it is repressed by nitrate and subject to CRP-mediated catabolite repression.; GO: 0015556 C4-dicarboxylate transmembrane transporter activity, 0015740 C4-dicarboxylate transport, 0016021 integral to membrane.
Probab=38.59  E-value=21  Score=13.96  Aligned_cols=10  Identities=20%  Similarity=0.258  Sum_probs=5.1

Q ss_pred             HHHHHHCCCC
Q ss_conf             9999720421
Q gi|254780299|r   44 VALIANFPSV   53 (562)
Q Consensus        44 ~~~~~~~~~~   53 (562)
                      +++||+.|..
T Consensus        74 EKlLRrnPK~   83 (447)
T TIGR00770        74 EKLLRRNPKY   83 (447)
T ss_pred             HHHHCCCCCE
T ss_conf             8974169973


No 54 
>cd03796 GT1_PIG-A_like This family is most closely related to the GT1 family of glycosyltransferases. Phosphatidylinositol glycan-class A (PIG-A), an X-linked gene in humans, is necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, a very early intermediate in glycosyl phosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is an important cellular structure that facilitates the attachment of many proteins to cell surfaces. Somatic mutations in PIG-A have been associated with Paroxysmal Nocturnal Hemoglobinuria (PNH), an acquired hematological disorder.
Probab=38.46  E-value=9  Score=16.49  Aligned_cols=28  Identities=11%  Similarity=0.064  Sum_probs=14.5

Q ss_pred             CCCCCCHHHHHHHCCHH---HHHCCCCHHHH
Q ss_conf             00045518898500122---32204622278
Q gi|254780299|r  423 GYIEERSIARHYRESPA---NSILLGSGNAM  450 (562)
Q Consensus       423 Gy~ee~~leRl~RDA~v---~~I~EGt~~I~  450 (562)
                      |++.+..+..+|+.|-|   -+.+||-+.+.
T Consensus       256 G~v~~~~l~~~~~~aDvfv~PS~~Egfglv~  286 (398)
T cd03796         256 GAVPHERVRDVLVQGHIFLNTSLTEAFCIAI  286 (398)
T ss_pred             CCCCHHHHHHHHHHHHEEECCCCCCCCCHHH
T ss_conf             8885677788887744212765424666799


No 55 
>pfam08877 MepB MepB protein. MepB is a functionally uncharacterized protein in the mepRAB gene cluster of Staphylococcus aureus.
Probab=37.41  E-value=21  Score=14.00  Aligned_cols=55  Identities=20%  Similarity=0.190  Sum_probs=34.1

Q ss_pred             EEECCCCCEEEEEEECCCCCEEEEEECCCCCCCCCCEEEEEECCCCCCCCCCEEEE
Q ss_conf             86342115799970469961799987758988403478863047554565772799
Q gi|254780299|r  234 FLSSPMSDAFIMLAQVEGRVGCFLVPRLLEDGSPNGLCYQRLKNKIGNRSNATVEL  289 (562)
Q Consensus       234 f~sa~~ad~~lVlArt~~Gls~FlVp~~~pgg~~n~v~i~r~~~klG~r~~~t~ei  289 (562)
                      |......|.++|....++..+.|+.|+..- ....=++...-+.|||.|-=|.-..
T Consensus        49 f~~~d~~d~lvI~v~d~~~~G~FiFpk~~L-~~kgIlss~~~~GK~a~RVYPpW~~  103 (123)
T pfam08877        49 FDYDDAPDLLIIVVIDDNRRGQFIFPKEVL-IEKGILSSDGSKGKMAFRVYPSWCT  103 (123)
T ss_pred             CCCCCCCCEEEEEEECCCEEEEEEEEHHHH-HHCCCEECCCCCCEEEEEECCCCCC
T ss_conf             743347897999997289067799039999-7679510489887048887898657


No 56 
>COG2704 DcuB Anaerobic C4-dicarboxylate transporter [General function prediction only]
Probab=35.01  E-value=24  Score=13.59  Aligned_cols=19  Identities=21%  Similarity=0.377  Sum_probs=9.1

Q ss_pred             CCCHHHCCCHHHHHHHHHH
Q ss_conf             2423538888999999999
Q gi|254780299|r  346 GGILIDQPVMKRAIADIAL  364 (562)
Q Consensus       346 G~~L~~~p~v~~~LAdm~~  364 (562)
                      ||.|.+.|-.|++|.|=..
T Consensus       191 gkeL~~Dp~yq~RL~~~~~  209 (436)
T COG2704         191 GKELDDDPEYQKRLSEGLI  209 (436)
T ss_pred             CCCCCCCHHHHHHHHCCCC
T ss_conf             2534579889998627653


No 57 
>TIGR01091 upp uracil phosphoribosyltransferase; InterPro: IPR005765    The enzyme uracil phosphoribosyltransferase (UPRT, 2.4.2.9 from EC) catalyzes conversion of uracil to uridine 5'-monophosphate utilizing 5'-phosphoribosyl--1-pyrophosphate (PRPP).  UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate  ; GO: 0004845 uracil phosphoribosyltransferase activity, 0006223 uracil salvage.
Probab=34.66  E-value=25  Score=13.55  Aligned_cols=11  Identities=0%  Similarity=0.075  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHH
Q ss_conf             35677899998
Q gi|254780299|r  154 PSVTSASMVAL  164 (562)
Q Consensus       154 ~~mt~~a~~~L  164 (562)
                      +.|.+|...++
T Consensus        84 Lgm~dG~~~~~   94 (213)
T TIGR01091        84 LGMVDGVLKLI   94 (213)
T ss_pred             HHHHHHHHHHC
T ss_conf             68999999848


No 58 
>pfam05428 CRF-BP Corticotropin-releasing factor binding protein (CRF-BP). This family consists of several eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP). Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development.
Probab=33.89  E-value=14  Score=15.20  Aligned_cols=13  Identities=46%  Similarity=0.682  Sum_probs=10.2

Q ss_pred             CCEEEECCEEEEEE
Q ss_conf             96689845146863
Q gi|254780299|r  223 DGIYCLSGHKWFLS  236 (562)
Q Consensus       223 dg~y~LnG~Kwf~s  236 (562)
                      || |+|||+|.-.+
T Consensus       114 DG-W~LkGEkFPs~  126 (311)
T pfam05428       114 DG-WELKGEKFPSS  126 (311)
T ss_pred             EE-EEECCCCCCCC
T ss_conf             61-08846688484


No 59 
>pfam00289 CPSase_L_chain Carbamoyl-phosphate synthase L chain, N-terminal domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117.
Probab=31.72  E-value=17  Score=14.66  Aligned_cols=32  Identities=19%  Similarity=0.350  Sum_probs=23.6

Q ss_pred             HHHHHHCCCCCCCCCH-HHHHHHCCHHHHHCCCCH
Q ss_conf             6998852130004551-889850012232204622
Q gi|254780299|r  414 EAMECIGGSGYIEERS-IARHYRESPANSILLGSG  447 (562)
Q Consensus       414 ~Aiqi~GG~Gy~ee~~-leRl~RDA~v~~I~EGt~  447 (562)
                      .+.-+|+|+|++.|++ +++...|+  .-+|=|++
T Consensus        73 ~~~aihpGyGflsEn~~fa~~~~~~--Gi~fiGPs  105 (109)
T pfam00289        73 GADAIHPGYGFLSENAEFAEACEKA--GITFIGPS  105 (109)
T ss_pred             CCCEEECCCCCCCCCHHHHHHHHHC--CCEEECCC
T ss_conf             8896877976233599999999988--89899958


No 60 
>TIGR01919 hisA-trpF bifunctional HisA/TrpF protein; InterPro: IPR010188   This entry represents a bifunctional protein possessing both hisA (1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase) and trpF (N-(5'phosphoribosyl)anthranilate isomerase) activities . Thus, it is involved in both the histidine and tryptophan biosynthetic pathways. Enzymes with this property have been described only in the Actinobacteria (High-GC Gram-positive). The enzyme is closely related to the monofunctional HisA proteins and in Actinobacteria, the classical monofunctional TrpF is generally absent.; GO: 0003949 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity, 0004640 phosphoribosylanthranilate isomerase activity, 0000105 histidine biosynthetic process, 0000162 tryptophan biosynthetic process, 0005737 cytoplasm.
Probab=31.50  E-value=11  Score=15.80  Aligned_cols=47  Identities=21%  Similarity=0.393  Sum_probs=34.8

Q ss_pred             EEECCCCEEEECCEEEEEECCCCCEEEEEEECC-CCCEEEEEECCCCCCC
Q ss_conf             786489668984514686342115799970469-9617999877589884
Q gi|254780299|r  218 GQKISDGIYCLSGHKWFLSSPMSDAFIMLAQVE-GRVGCFLVPRLLEDGS  266 (562)
Q Consensus       218 A~~~gdg~y~LnG~Kwf~sa~~ad~~lVlArt~-~Gls~FlVp~~~pgg~  266 (562)
                      +++..||+|++.|.=|...+++  .|=|+-|.| .|-|=|+|--...||+
T Consensus       132 ~V~~~DGeh~l~g~GW~~dGGD--Lwevl~~LDS~GCsRfVVTDv~KDG~  179 (246)
T TIGR01919       132 DVRLIDGEHRLRGRGWESDGGD--LWEVLERLDSEGCSRFVVTDVAKDGT  179 (246)
T ss_pred             EEEEECCCEEEECCCCCCCCCC--HHHHHHHHCCCCCCCEEEEECCCCCC
T ss_conf             7898738566604675578862--89999874348854037850123786


No 61 
>TIGR01960 ndhF3_CO2 NAD(P)H dehydrogenase, subunit NdhF3 family; InterPro: IPR010217   This family represents NAD(P)H dehydrogenase subunit 5, or ndhF. It is restricted to two paralogs in each completed cyanobacterial genome, in which several subtypes of ndhF are found. Included in this family is NdhF3, shown to play a role in high-affinity CO2 uptake in Synechococcus sp. PCC7002. In all cases, neighbouring genes include a paralog of ndhD but do include other NAD(P)H dehydrogenase subunits. Instead, genes related to C02 uptake tend to be found nearby.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport.
Probab=31.27  E-value=17  Score=14.56  Aligned_cols=16  Identities=19%  Similarity=0.534  Sum_probs=6.7

Q ss_pred             HCCCCCCCCCHHHHHH
Q ss_conf             5213000455188985
Q gi|254780299|r  419 IGGSGYIEERSIARHY  434 (562)
Q Consensus       419 ~GG~Gy~ee~~leRl~  434 (562)
                      .|+.|.+-=.|+.-++
T Consensus       384 VGsagLia~~PLG~FW  399 (613)
T TIGR01960       384 VGSAGLIALPPLGSFW  399 (613)
T ss_pred             HHHHHHHHHCCHHHHH
T ss_conf             9967998745312589


No 62 
>TIGR01132 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific; InterPro: IPR005852    Phosphoglucomutase, alpha-D-glucose phosphate-specific () links the anaerobic or aerobic glycolysis of glucose-6-phosphate and glucose-1-phosphate produced by various glycan phosphorylases by catalysing the transfer of a phosphate group between C-1 and C-6 of glucose .     Alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.; GO: 0004614 phosphoglucomutase activity, 0005975 carbohydrate metabolic process.
Probab=31.18  E-value=19  Score=14.25  Aligned_cols=78  Identities=8%  Similarity=-0.010  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCC--CCCCCCCCCCCHHHH
Q ss_conf             999999850189999998634369846201799852136566889999999999679620337--766664447637999
Q gi|254780299|r   58 LELLGEYVLSCTAQELARMANYNTPQLHAYGPGGERWDKVEFHPAWHALLRRSIHDGLHCSIW--DRSFEPVVRKQAHKI  135 (562)
Q Consensus        58 l~~~g~~~~~~~~~~~~~~a~~~~P~l~~~d~~G~r~d~v~~~p~~~~l~~~~~~~Gl~~~~~--~~~~~~~~~~~~~~~  135 (562)
                      +.+.=-++..+-+.|....--.--|.....|.++      ---|+|....+.+..+|+....-  .+..++  -|.+-+-
T Consensus        56 FNE~HILAi~QAv~~~R~~~G~TGP~y~G~DtHa------LSEPA~~s~LEVLaAN~v~~~v~tat~~~ry--TPTPavS  127 (553)
T TIGR01132        56 FNEAHILAITQAVVDYRAAQGITGPLYIGKDTHA------LSEPAFVSALEVLAANQVEVIVQTATENNRY--TPTPAVS  127 (553)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCC------CCHHHHHHHHHHHHHCCEEEEEEECCCCCCC--CCCHHHH
T ss_conf             6647899999999999972782035111677542------5406899999998746725888402247888--8964665


Q ss_pred             HHHHHHHH
Q ss_conf             99999983
Q gi|254780299|r  136 RAARLYLM  143 (562)
Q Consensus       136 ~~a~~~l~  143 (562)
                      +++..|--
T Consensus       128 ~AILtyN~  135 (553)
T TIGR01132       128 HAILTYNK  135 (553)
T ss_pred             HHHHHHCC
T ss_conf             78874126


No 63 
>TIGR01075 uvrD DNA helicase II; InterPro: IPR005753    The SOS response is required for efficient nucleotide excision repair (NER) of the major ultraviolet light (UV) induced DNA lesions. The expression of three NER genes, uvrA, uvrB, and uvrD, is upregulated as part of the SOS response. UvrD differs from the others in that it is not involved in lesion recognition but rather in promoting the post-incision steps of NER, including turnover of the UvrBC incision complex . The form of the UvrD helicase with optimal helicase activity is oligomeric with at least two sites for binding the DNA substrate, where one site contacts regions of the 3'-ssDNA tail that are distal from the single-stranded/double-stranded DNA junction.; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=29.80  E-value=29  Score=13.03  Aligned_cols=48  Identities=17%  Similarity=0.194  Sum_probs=24.1

Q ss_pred             CCCCCCCCCHHHCCEEEEECCCCEEEECCEE-EEEECCCCCEEEEEEECC
Q ss_conf             4588888786654302786489668984514-686342115799970469
Q gi|254780299|r  202 LTEKRGGTDIAAITSQGQKISDGIYCLSGHK-WFLSSPMSDAFIMLAQVE  250 (562)
Q Consensus       202 lTEp~~GSDv~~~~T~A~~~gdg~y~LnG~K-wf~sa~~ad~~lVlArt~  250 (562)
                      =||-..|-.+.-=...-+-|+- .|+++-.| |--.++.-+-+-||=|..
T Consensus       309 wT~g~~Ge~i~~YsAfneLdEA-rFvv~~~~~w~~~GG~l~e~AvLYRsN  357 (741)
T TIGR01075       309 WTDGEVGEPISLYSAFNELDEA-RFVVSRIKAWQREGGALDEIAVLYRSN  357 (741)
T ss_pred             ECCCCCCCCEEEEECCCHHHHH-HHHHHHHHHHHHCCCCCCCEEEEECCC
T ss_conf             1345678702576513413789-999999999986589641365663255


No 64 
>PRK13795 hypothetical protein; Provisional
Probab=28.69  E-value=31  Score=12.90  Aligned_cols=20  Identities=5%  Similarity=0.116  Sum_probs=10.5

Q ss_pred             CCCCCCCHHHCCCHHHHHHH
Q ss_conf             46222423538888999999
Q gi|254780299|r  342 RHVSGGILIDQPVMKRAIAD  361 (562)
Q Consensus       342 R~~fG~~L~~~p~v~~~LAd  361 (562)
                      ...|...=.+||-...-.-+
T Consensus       273 ~~~f~dTglEfPeT~e~v~~  292 (630)
T PRK13795        273 KAFFNNTGLEFPETVENVKE  292 (630)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             89995077676469999999


No 65 
>KOG2675 consensus
Probab=27.23  E-value=33  Score=12.73  Aligned_cols=50  Identities=14%  Similarity=0.332  Sum_probs=28.1

Q ss_pred             CCCCHHHCCEEEEECCCCEEEECCEEEEEECCCCCEEEEEEECCCCCEEEEE
Q ss_conf             8878665430278648966898451468634211579997046996179998
Q gi|254780299|r  207 GGTDIAAITSQGQKISDGIYCLSGHKWFLSSPMSDAFIMLAQVEGRVGCFLV  258 (562)
Q Consensus       207 ~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~sa~~ad~~lVlArt~~Gls~FlV  258 (562)
                      ++|-+.- .+..++.+. .-.|-|.|||+-+-.-+--+|+--++..-|.|+-
T Consensus       310 ~~~~Psk-~~~~~k~pp-~~ELeGkkW~VEnq~~~~~~Vi~~~e~kqsvyIy  359 (480)
T KOG2675         310 GSSSPSK-SAAPKKKPP-VKELEGKKWRVENQENNKNLVIDDAELKQSVYIY  359 (480)
T ss_pred             CCCCCCC-CCCCCCCCC-EEEECCCEEEEEECCCCCCEEEEECCCCCEEEEE
T ss_conf             8888765-556777997-0363164568860037765166642454248998


No 66 
>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated
Probab=26.89  E-value=30  Score=12.98  Aligned_cols=17  Identities=29%  Similarity=0.679  Sum_probs=13.4

Q ss_pred             CCCCCCCCHHHHHHHCC
Q ss_conf             13000455188985001
Q gi|254780299|r  421 GSGYIEERSIARHYRES  437 (562)
Q Consensus       421 G~Gy~ee~~leRl~RDA  437 (562)
                      |.|++-++++.|.|||.
T Consensus       127 G~Givp~~~~~R~frd~  143 (170)
T PRK05800        127 GMGIVPEYRLGRRFRDI  143 (170)
T ss_pred             CCCCCCCCHHHHHHHHH
T ss_conf             77788998799999999


No 67 
>KOG1416 consensus
Probab=25.86  E-value=34  Score=12.57  Aligned_cols=18  Identities=11%  Similarity=0.065  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHCCCCCC
Q ss_conf             400256554511434468
Q gi|254780299|r  533 RFLDNCHSTHCMLHGRFN  550 (562)
Q Consensus       533 Rl~~~~~~~~g~l~a~~d  550 (562)
                      +|-..|.+.|-.||.|.-
T Consensus       410 ~ite~wlR~YQVLP~RtH  427 (475)
T KOG1416         410 SITETWLRPYQVLPDRTH  427 (475)
T ss_pred             EECHHHCCCEEECCCCCC
T ss_conf             502423531010577788


No 68 
>KOG1321 consensus
Probab=25.68  E-value=35  Score=12.55  Aligned_cols=27  Identities=19%  Similarity=0.314  Sum_probs=16.2

Q ss_pred             CCCCCCHHHCCEEEEECCCCEEEECCEEEEE
Q ss_conf             8888786654302786489668984514686
Q gi|254780299|r  205 KRGGTDIAAITSQGQKISDGIYCLSGHKWFL  235 (562)
Q Consensus       205 p~~GSDv~~~~T~A~~~gdg~y~LnG~Kwf~  235 (562)
                      ...||.+..+.+.-+.+  |  ...+-||-+
T Consensus       169 sTsGSSln~l~r~~r~~--~--~~~~~~wsi  195 (395)
T KOG1321         169 STSGSSLNELWRQFRED--G--YERDIKWSI  195 (395)
T ss_pred             ECCCCCHHHHHHHHHHC--C--CCCCCCEEE
T ss_conf             15764299999999844--7--656881586


No 69 
>PRK13523 NADPH dehydrogenase NamA; Provisional
Probab=25.66  E-value=9.4  Score=16.34  Aligned_cols=12  Identities=17%  Similarity=0.105  Sum_probs=4.1

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             899999999996
Q gi|254780299|r  101 PAWHALLRRSIH  112 (562)
Q Consensus       101 p~~~~l~~~~~~  112 (562)
                      |+|+++-+...+
T Consensus        81 ~~~~~l~~avh~   92 (337)
T PRK13523         81 EGLHKLVTFIHD   92 (337)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999975


No 70 
>cd02930 DCR_FMN 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain.  DCR in E. coli  is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the flavin and iron-sulfur cofactors. Metabolism of unsaturated fatty acids requires auxiliary enzymes in addition to those used in b-oxidation. After a given number of cycles through the b-oxidation pathway, those unsaturated fatty acyl-CoAs with double bonds at even-numbered carbon positions contain 2-trans, 4-cis double bonds that can not be modified by enoyl-CoA hydratase. DCR utilizes NADPH to remove the C4-C5 double bond. DCR can catalyze the reduction of both natural fatty acids with cis double bonds, as well as substrates containing trans double bonds. The reaction is initiated by hybrid transfer from NADPH to FAD, which in turn transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. The fully reduced FMN provi
Probab=25.05  E-value=11  Score=15.87  Aligned_cols=23  Identities=4%  Similarity=-0.022  Sum_probs=14.4

Q ss_pred             CCEEECCHHHHHHHHHHHHCCCC
Q ss_conf             13656688999999999967962
Q gi|254780299|r   94 WDKVEFHPAWHALLRRSIHDGLH  116 (562)
Q Consensus        94 ~d~v~~~p~~~~l~~~~~~~Gl~  116 (562)
                      ++.-+.-|+|+++-+...++|-.
T Consensus        70 i~~d~~i~~~k~l~~~vH~~G~~   92 (353)
T cd02930          70 LNSPRQAAGHRLITDAVHAEGGK   92 (353)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCE
T ss_conf             27999999999999999976997


No 71 
>PHA00728 hypothetical protein
Probab=25.00  E-value=30  Score=13.00  Aligned_cols=37  Identities=30%  Similarity=0.288  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCC
Q ss_conf             8999999850189999998634369846201799852
Q gi|254780299|r   57 ELELLGEYVLSCTAQELARMANYNTPQLHAYGPGGER   93 (562)
Q Consensus        57 ~l~~~g~~~~~~~~~~~~~~a~~~~P~l~~~d~~G~r   93 (562)
                      ++.++-.+.|.+.+.|++..|++-..+|+.-...|+|
T Consensus        79 EfarLP~YFgEePv~ELae~A~kLKHYLVSKgGrGRR  115 (153)
T PHA00728         79 EFARLPAYFGEEPVVELAQFADKLKHYLVSKGGRGRR  115 (153)
T ss_pred             HHHHCHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf             8852455407751789999999988886345887416


No 72 
>cd02929 TMADH_HD_FMN Trimethylamine dehydrogenase (TMADH) and histamine dehydrogenase (HD) FMN-binding domain.  TMADH is an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. The protein forms a symetrical dimer with each subunit containing one 4Fe-4S cluster and one FMN cofactor.  It contains a unique flavin, in the form of a 6-S-cysteinyl FMN  which is bent by ~25 degrees along the N5-N10 axis of the flavin isoalloxazine ring. This modification of the conformation of the flavin is thought to facilitate catalysis.The closely related histamine dehydrogenase catalyzes oxidative deamination of histamine.
Probab=24.60  E-value=10  Score=16.11  Aligned_cols=16  Identities=13%  Similarity=-0.039  Sum_probs=7.5

Q ss_pred             CCHHHHHHHHHHHHCC
Q ss_conf             6889999999999679
Q gi|254780299|r   99 FHPAWHALLRRSIHDG  114 (562)
Q Consensus        99 ~~p~~~~l~~~~~~~G  114 (562)
                      +-|+|+++-+...++|
T Consensus        81 ~i~~~k~l~d~vH~~G   96 (370)
T cd02929          81 DIRNLAAMTDAVHKHG   96 (370)
T ss_pred             HHHHHHHHHHHHHHCC
T ss_conf             9999999999999669


No 73 
>cd04733 OYE_like_2_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 2.  Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction.  Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=24.42  E-value=11  Score=15.95  Aligned_cols=15  Identities=13%  Similarity=0.182  Sum_probs=7.7

Q ss_pred             CHHHHHHHHHHHHCC
Q ss_conf             889999999999679
Q gi|254780299|r  100 HPAWHALLRRSIHDG  114 (562)
Q Consensus       100 ~p~~~~l~~~~~~~G  114 (562)
                      -|+|+++-+...++|
T Consensus        81 i~~~k~l~d~vh~~g   95 (338)
T cd04733          81 LEAFREWAAAAKANG   95 (338)
T ss_pred             HHHHHHHHHHHHHCC
T ss_conf             999999999998569


No 74 
>cd04735 OYE_like_4_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 4.  Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction.  Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=24.04  E-value=11  Score=15.86  Aligned_cols=16  Identities=19%  Similarity=0.160  Sum_probs=7.9

Q ss_pred             CCHHHHHHHHHHHHCC
Q ss_conf             6889999999999679
Q gi|254780299|r   99 FHPAWHALLRRSIHDG  114 (562)
Q Consensus        99 ~~p~~~~l~~~~~~~G  114 (562)
                      +-|+|+++-+...++|
T Consensus        76 ~i~~~k~l~~avH~~G   91 (353)
T cd04735          76 DIPGLRKLAQAIKSKG   91 (353)
T ss_pred             HHHHHHHHHHHHHHCC
T ss_conf             9999999999998579


No 75 
>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=23.80  E-value=32  Score=12.80  Aligned_cols=39  Identities=18%  Similarity=0.280  Sum_probs=27.4

Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHC
Q ss_conf             766320245788762110116788858998001678899999720
Q gi|254780299|r    6 IYRRLAMNQVHQPSDSLFALNQPPLFIGMNAYSSDSLLVALIANF   50 (562)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~nq~~~~~g~n~~~~D~~l~~~~~~~   50 (562)
                      =++.|..-++||.+      ||.-..-|+..|+.|...++++.-+
T Consensus        20 ~~~~L~L~EiHRF~------N~l~~~dg~~~WDid~l~~~I~~GL   58 (460)
T TIGR02627        20 ETQKLTLEEIHRFK------NQLVSQDGHECWDIDALEQEILIGL   58 (460)
T ss_pred             CCCCEEEEEEEEEC------CEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf             33113466675421------6016568875342999999999999


No 76 
>cd04747 OYE_like_5_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 5.  Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction.  Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=23.77  E-value=14  Score=15.27  Aligned_cols=18  Identities=11%  Similarity=0.285  Sum_probs=9.3

Q ss_pred             ECCHHHHHHHHHHHHCCC
Q ss_conf             668899999999996796
Q gi|254780299|r   98 EFHPAWHALLRRSIHDGL  115 (562)
Q Consensus        98 ~~~p~~~~l~~~~~~~Gl  115 (562)
                      ++-|+|+++-+...++|-
T Consensus        75 ~~i~~~r~la~avH~~G~   92 (361)
T cd04747          75 DALAGWKKVVDEVHAAGG   92 (361)
T ss_pred             HHHHHHHHHHHHHHHCCC
T ss_conf             999999999999997699


No 77 
>COG1902 NemA NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]
Probab=22.01  E-value=12  Score=15.62  Aligned_cols=20  Identities=15%  Similarity=0.137  Sum_probs=12.4

Q ss_pred             CCCCCCHHHCCCHHHHHHHH
Q ss_conf             62224235388889999999
Q gi|254780299|r  343 HVSGGILIDQPVMKRAIADI  362 (562)
Q Consensus       343 ~~fG~~L~~~p~v~~~LAdm  362 (562)
                      ..+|++++..|..-.++.+-
T Consensus       315 Va~gR~~ladP~~v~k~~~g  334 (363)
T COG1902         315 VAMGRPFLADPDLVLKAAEG  334 (363)
T ss_pred             EEECHHHHCCCCHHHHHHCC
T ss_conf             87263665092089999737


No 78 
>KOG3581 consensus
Probab=21.49  E-value=26  Score=13.37  Aligned_cols=28  Identities=29%  Similarity=0.375  Sum_probs=15.4

Q ss_pred             CCCH--HHCCEEEEECCCCEEEECCEEEEEE
Q ss_conf             8786--6543027864896689845146863
Q gi|254780299|r  208 GTDI--AAITSQGQKISDGIYCLSGHKWFLS  236 (562)
Q Consensus       208 GSDv--~~~~T~A~~~gdg~y~LnG~Kwf~s  236 (562)
                      ||-.  +++..+--|++-|-| .|-.|.|.-
T Consensus       196 gdr~L~aa~a~r~WP~gRGI~-hN~~KtFLv  225 (363)
T KOG3581         196 GDRLLQAAGAARDWPDGRGIF-HNDNKTFLV  225 (363)
T ss_pred             CCHHHHHCCCCCCCCCCCCEE-ECCCCEEEE
T ss_conf             688887563201498666324-558853899


No 79 
>COG4815 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.37  E-value=42  Score=12.00  Aligned_cols=29  Identities=24%  Similarity=0.307  Sum_probs=22.8

Q ss_pred             EEEECCCCCEEEEEEECCCCCEEEEEECC
Q ss_conf             68634211579997046996179998775
Q gi|254780299|r  233 WFLSSPMSDAFIMLAQVEGRVGCFLVPRL  261 (562)
Q Consensus       233 wf~sa~~ad~~lVlArt~~Gls~FlVp~~  261 (562)
                      -|.+.+.||..+++.+.+.--++|..|+.
T Consensus        69 Pfs~~~~a~~LlI~V~de~~~G~F~Fpre   97 (145)
T COG4815          69 PFSDDGMAAGLLIFVIDEVLRGVFRFPRE   97 (145)
T ss_pred             CCCCCCCCCEEEEEEECCCCCEEEECCHH
T ss_conf             98821003705999981652316871488


No 80 
>cd02933 OYE_like_FMN Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction.  Members of OYE family include 12-oxophytodienoate reductase, pentaerythritol tetranitrate reductase, morphinone reductase, and related enzymes.
Probab=20.77  E-value=13  Score=15.47  Aligned_cols=13  Identities=8%  Similarity=0.271  Sum_probs=4.7

Q ss_pred             HHHHHHHHHHHHC
Q ss_conf             8999999999967
Q gi|254780299|r  101 PAWHALLRRSIHD  113 (562)
Q Consensus       101 p~~~~l~~~~~~~  113 (562)
                      |+|+++-+...++
T Consensus        77 ~~~~~l~~~vh~~   89 (338)
T cd02933          77 EGWKKVTDAVHAK   89 (338)
T ss_pred             HHHHHHHHHHHHC
T ss_conf             9999999999855


No 81 
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=20.72  E-value=43  Score=11.92  Aligned_cols=93  Identities=19%  Similarity=0.311  Sum_probs=47.0

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99999831260379999999996425451778999998730542213778999999999999999997085799999999
Q gi|254780299|r  452 LDVLNLLEKGTNLFEQLFSTLEQDLGSSGKKVITILRDSISLCKEDKGLARFLTEKIALASSAAALYRAGMNDIADVFLE  531 (562)
Q Consensus       452 ldv~r~l~r~~~~~~~l~~~l~~~~g~~~~~~~~~l~~~~~~~~~~e~~AR~~~e~la~~~~aalL~r~a~~~va~af~~  531 (562)
                      ..+.+.+...+  -..+++++...++-.........+....+.+..-+.++++.       .+..++.++. .|-++-+.
T Consensus        85 ~~a~~~ie~~~--~~~~le~la~~lg~sp~~~~R~FK~~~G~Tp~~ya~a~R~~-------~a~~~L~~g~-sv~~a~~d  154 (187)
T COG2169          85 ATACRLIEQNP--EKRWLEELADELGVSPSTLHRLFKAITGMTPKEYARARRMG-------RARKQLRMGA-SVTDAQID  154 (187)
T ss_pred             HHHHHHHHCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHH-------HHHHHHHCCC-CHHHHHHH
T ss_conf             99999998188--74638999999678959999999998389999999999999-------9999973788-63589998


Q ss_pred             ------HHHHHHHHHHHHHCCCCCCHHHH
Q ss_conf             ------64002565545114344688999
Q gi|254780299|r  532 ------NRFLDNCHSTHCMLHGRFNAAHI  554 (562)
Q Consensus       532 ------~Rl~~~~~~~~g~l~a~~d~~~~  554 (562)
                            ++.-..-...+||-|..++..++
T Consensus       155 aGf~s~s~F~~af~~~~G~~P~~~r~~~~  183 (187)
T COG2169         155 AGFESSSRFYDAFSKILGMTPTKFRHGGI  183 (187)
T ss_pred             HCCCCHHHHHHHHHHHCCCCHHHHHHHCC
T ss_conf             27887688999999872998788876033


No 82 
>cd03869 M14_CPX_like Peptidase M14-like domain of carboxypeptidase (CP)-like protein X (CPX), CPX forms a distinct subgroup of the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Proteins belonging to this subgroup include CP-like protein X1 (CPX1), CP-like protein X2 (CPX2),  and aortic CP-like protein (ACLP) and its isoform adipocyte enhancer binding protein-1 (AEBP1). AEBP1 is a truncated form of ACLP, which may arise from alternative splicing of the gene. These proteins are inactive towards standard CP substrates because they lack one or more critical active site and substrate-binding residues that are necessary for activity. They may function as binding proteins rather than as active CPs or display catalytic activity toward other substrates.  Pro
Probab=20.47  E-value=44  Score=11.88  Aligned_cols=22  Identities=27%  Similarity=0.678  Sum_probs=16.4

Q ss_pred             CCCEEEECCEEEE-EECCCCCEEEE
Q ss_conf             8966898451468-63421157999
Q gi|254780299|r  222 SDGIYCLSGHKWF-LSSPMSDAFIM  245 (562)
Q Consensus       222 gdg~y~LnG~Kwf-~sa~~ad~~lV  245 (562)
                      .||  +.||-+|+ +++++.|+.-+
T Consensus       265 ~~G--ItNGA~WY~v~GgMQD~nY~  287 (405)
T cd03869         265 EDG--IINGASWHTVAGSMNDFSYL  287 (405)
T ss_pred             CCC--EECCCEEECCCCCCCCCCCC
T ss_conf             787--06042532156762102422


No 83 
>cd03867 M14_CPZ Peptidase M14-like domain of carboxypeptidase (CP) Z (CPZ), CPZ belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPZ is a secreted Zn-dependent enzyme whose biological function is largely unknown. Unlike other members of the N/E subfamily, CPZ has a bipartite structure, which consists of an N-terminal cysteine-rich domain (CRD) whose sequence is similar to Wnt-binding proteins, and a C-terminal CP catalytic domain that removes C-terminal Arg residues from substrates. CPZ is enriched in the extracellular matrix and is widely distributed during early embryogenesis.  That the CRD of CPZ can bind to Wnt4 suggests that CPZ plays a role in Wnt signaling.
Probab=20.32  E-value=44  Score=11.86  Aligned_cols=19  Identities=37%  Similarity=0.779  Sum_probs=15.4

Q ss_pred             CCEEEECCEEEE-EECCCCCEE
Q ss_conf             966898451468-634211579
Q gi|254780299|r  223 DGIYCLSGHKWF-LSSPMSDAF  243 (562)
Q Consensus       223 dg~y~LnG~Kwf-~sa~~ad~~  243 (562)
                      ||  +.||-+|+ +++++.|+.
T Consensus       255 ~G--ItNGA~WY~v~GgMQD~n  274 (395)
T cd03867         255 GG--IINGAEWYSFSGGMSDFN  274 (395)
T ss_pred             CC--EECCCEEEECCCCCHHHH
T ss_conf             87--053515540467600343


No 84 
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA; InterPro: IPR005751    The DNA helicase PcrA is found mainly in Gram-positive bacteria and belongs to a superfamily of helicases, together with Rep and UvrD helicases from Escherichia coli. The action of the 3'5' bacterial DNA helicase is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilising the duplex and separating the two strands in an active process .; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=20.03  E-value=45  Score=11.82  Aligned_cols=19  Identities=21%  Similarity=0.095  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999840462
Q gi|254780299|r  326 SGMRVSLAEAIHYARRRHV  344 (562)
Q Consensus       326 G~ar~al~~A~~yA~~R~~  344 (562)
                      |+...+++.-..||.++..
T Consensus       473 GiG~~s~~~~~~~a~~~~i  491 (811)
T TIGR01073       473 GIGASSLEKIRSYALELNI  491 (811)
T ss_pred             CCCHHHHHHHHHHHHHCCC
T ss_conf             6446789999999986088


Done!