Query         gi|255764509|ref|YP_003065434.2| hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 351
No_of_seqs    116 out of 668
Neff          5.8 
Searched_HMMs 39220
Date          Mon May 30 04:38:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764509.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam00368 HMG-CoA_red Hydroxym 100.0       0       0  843.9  38.0  334    1-345    36-370 (370)
  2 cd00643 HMG-CoA_reductase_clas 100.0       0       0  833.5  39.7  342    1-345    60-403 (403)
  3 cd00644 HMG-CoA_reductase_clas 100.0       0       0  778.3  33.1  317    1-347    43-380 (417)
  4 TIGR00920 2A060605 3-hydroxy-3 100.0       0       0  762.9  20.6  342    3-350   600-948 (988)
  5 cd00365 HMG-CoA_reductase Hydr 100.0       0       0  737.0  36.6  315    1-345    43-376 (376)
  6 KOG2480 consensus              100.0       0       0  682.6  30.8  343    2-350   238-585 (602)
  7 TIGR00533 HMG_CoA_R_NADP 3-hyd 100.0       0       0  672.7  29.4  342    2-345    68-419 (419)
  8 COG1257 HMG1 Hydroxymethylglut 100.0       0       0  674.2  27.5  320    1-345    61-396 (436)
  9 TIGR00532 HMG_CoA_R_NAD hydrox 100.0       0       0  593.6  22.1  313    1-344    67-401 (402)
 10 COG1257 HMG1 Hydroxymethylglut  99.1 7.3E-11 1.9E-15   87.4   3.9  124  214-349   272-415 (436)
 11 TIGR02248 mutH_TIGR DNA mismat  82.3     2.5 6.4E-05   21.4   4.3   69   58-126   121-191 (220)
 12 PRK09509 fieF ferrous iron eff  68.3     8.5 0.00022   18.0   9.3   64   94-157   216-279 (300)
 13 pfam01545 Cation_efflux Cation  67.7     8.8 0.00022   17.9   9.9   66   93-158   196-261 (273)
 14 COG0053 MMT1 Predicted Co/Zn/C  65.1     9.9 0.00025   17.6   8.8   71   92-162   216-286 (304)
 15 TIGR01162 purE phosphoribosyla  64.7     3.7 9.4E-05   20.3   1.6   53  263-323    93-148 (159)
 16 pfam09551 Spore_II_R Stage II   51.5      17 0.00043   16.2   4.5   58   77-136    39-113 (132)
 17 TIGR02837 spore_II_R stage II   44.8      11 0.00028   17.3   1.3   48   87-136    87-151 (172)
 18 pfam11281 DUF3083 Protein of u  41.9     5.5 0.00014   19.2  -0.6   91  182-279   162-270 (316)
 19 TIGR01415 trpB_rel pyridoxal-p  37.3      17 0.00044   16.1   1.3   36  109-145    75-112 (426)
 20 PTZ00186 heat shock 70 kDa pre  34.1      25 0.00065   15.0   1.8   48  106-154   220-269 (657)
 21 PRK05183 hscA chaperone protei  33.5      26 0.00067   14.9   1.8   22  276-297   336-358 (621)
 22 TIGR02350 prok_dnaK chaperone   32.5      33 0.00085   14.3   4.1   48  105-153   190-239 (598)
 23 TIGR01991 HscA Fe-S protein as  32.2      23 0.00059   15.3   1.3   53  233-299   313-366 (628)
 24 TIGR01826 CofD_related conserv  31.8      30 0.00075   14.6   1.8  122   19-164   117-265 (331)
 25 PRK13411 molecular chaperone D  31.5      30 0.00077   14.6   1.8   20  277-296   331-350 (655)
 26 TIGR03143 AhpF_homolog putativ  31.2      13 0.00034   16.8  -0.0   14  291-304   449-462 (555)
 27 PRK01433 hscA chaperone protei  31.1      31 0.00079   14.5   1.8   22  276-297   311-333 (595)
 28 CHL00094 dnaK heat shock prote  31.0      30 0.00078   14.5   1.8   21  277-297   332-353 (622)
 29 TIGR01506 ribC_arch riboflavin  30.5      36 0.00091   14.1   2.1   48  264-322    28-83  (152)
 30 COG0041 PurE Phosphoribosylcar  29.7      22 0.00057   15.4   0.9   38  264-301    97-135 (162)
 31 PRK13410 molecular chaperone D  29.3      35 0.00088   14.2   1.8   22  276-297   331-353 (719)
 32 TIGR02967 guan_deamin guanine   28.4      39 0.00099   13.9   2.2   43  257-299   282-332 (426)
 33 pfam00012 HSP70 Hsp70 protein.  27.9      37 0.00094   14.0   1.7   21  277-297   329-350 (598)
 34 PRK00290 dnaK molecular chaper  27.8      38 0.00096   14.0   1.8   22  277-298   332-354 (631)
 35 TIGR02484 CitB CitB domain pro  27.5     7.4 0.00019   18.4  -1.9   61  263-328   251-312 (392)
 36 KOG0100 consensus               27.3      38 0.00097   14.0   1.7   21  276-296   365-385 (663)
 37 TIGR01315 5C_CHO_kinase FGGY-f  26.7      23 0.00059   15.3   0.5   54  175-251   132-185 (574)
 38 TIGR02130 dapB_plant dihydrodi  25.3      20 0.00052   15.6   0.0   29  262-291    84-114 (275)
 39 pfam01177 Asp_Glu_race Asp/Glu  24.9      45  0.0011   13.5   3.8   88  141-245    93-182 (212)
 40 TIGR03452 mycothione_red mycot  24.7      18 0.00046   16.0  -0.3   16  294-312   399-414 (452)
 41 PTZ00052 thioredoxin reductase  24.6      19 0.00048   15.8  -0.2   10  236-245   308-317 (541)
 42 TIGR02885 spore_sigF RNA polym  23.1      13 0.00033   16.9  -1.4   10   29-38     66-75  (231)
 43 PRK06115 dihydrolipoamide dehy  22.5      26 0.00066   15.0   0.1   10  306-315   416-425 (466)
 44 TIGR02299 HpaE 5-carboxymethyl  21.4      16 0.00041   16.3  -1.1   16  177-192   363-378 (494)
 45 PRK12809 putative oxidoreducta  20.9     4.1  0.0001   20.0  -4.3   19  277-295   454-473 (639)
 46 TIGR02825 B4_12hDH leukotriene  20.4      55  0.0014   12.9   2.1   61  243-304    64-144 (327)
 47 PRK13930 rod shape-determining  20.2      56  0.0014   12.9   4.3   49  277-328   285-334 (336)

No 1  
>pfam00368 HMG-CoA_red Hydroxymethylglutaryl-coenzyme A reductase. The HMG-CoA reductases catalyse the conversion of HMG-CoA to mevalonate, which is the rate-limiting step in the synthesis of isoprenoids like cholesterol. Probably because of the critical role of this enzyme in cholesterol homeostasis, mammalian HMG-CoA reductase is heavily regulated at the transcriptional, translational, and post-translational levels.
Probab=100.00  E-value=0  Score=843.90  Aligned_cols=334  Identities=37%  Similarity=0.517  Sum_probs=323.0

Q ss_pred             CCCCCEEEEEEEEEEECCEEECCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEEEECCHH
Q ss_conf             97641037861127603756765136774788653034538999989999999559988999967922412599858977
Q gi|255764509|r    1 MHMKKVSSISMPMRWIGPMKITGNVIQDKVKVPLATYEYPLWHSVKRGAHISMLCPDGIRATLIDERMTRSIFFETENAE   80 (351)
Q Consensus         1 m~en~IG~~~lPlGia~~l~InG~~a~~~y~VPMATeE~SvVAAas~gak~~~~~sGG~~t~~~~~~m~r~~~f~~~~~~   80 (351)
                      ||||+||+++||+|||+||+|||+    +|+|||||||||||||+|||||++ +.+|||++++.++.|+|||+|.|++..
T Consensus        36 ~IEN~IG~~~lPlGvA~~l~InG~----~y~vPMAteE~svVAa~srgaK~~-~~~GG~~t~v~~~~m~~q~~~~f~~~~  110 (370)
T pfam00368        36 NIENVIGYVQVPLGVAGPLLINGK----EYYVPMATTEGALVASANRGAKAI-RASGGVTTRVLGDGMTRAPVFRFPSVR  110 (370)
T ss_pred             CCCEEEEEEECCEEEECCEEECCE----EEEEEEEECHHHHHHHHHHHHHHH-HHCCCEEEEECCCCEEEEEEEEECCHH
T ss_conf             645000034233236637799988----889877753888999998899999-856982999888866874799978734


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             89999976175099999997301578047888878738869999999732006721588999999999998679814897
Q gi|255764509|r   81 MALTALQEITLKKAEIARVIEQTSQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQWSYLHYGS  160 (351)
Q Consensus        81 ~a~~~~~~i~~~~~~i~~~a~~~sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~~~~~~~~  160 (351)
                      |+.+|..|+.+++++|+++||+++||||+++|+++..+++++|+|.|||||||||||||+|+|++|++|++++++.++++
T Consensus       111 ~~~~~~~~i~~~~~~i~~~a~~~srgggl~~i~~~~~~~~~~l~~~~dt~DAMGaNmvn~~~e~v~~~i~~~~~~~~~~~  190 (370)
T pfam00368       111 DAAEFKAWIEENFEEIKEAAESTSRHGGLQDIEPYIAGRMVYLRFIYDTGDAMGMNMVTKATEAACEFIEEEFPGMELLA  190 (370)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             19999999999999999998610578764799999708869999996213454206889999999999998689977999


Q ss_pred             ECCCCCHHHHHHHHHHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHH
Q ss_conf             34774312333554310377207999987569999757389999999887866565542200220216216677888887
Q gi|255764509|r  161 VSGNICSDKKATAINGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQKNLIGTFLAGGIRSANAHFANMLLAYYL  240 (351)
Q Consensus       161 ilsN~~tdkk~s~~n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~~~~~~a~t~NkgimNgI~Av~l  240 (351)
                      |+||||+|||+++.|++.+||+.|+|||+||.+++++.++++||++++ +.+.+.++..|+||++|||||||||||||||
T Consensus       191 IlsN~~tdKk~s~~n~~~grG~~V~A~~~i~~~~l~~~l~~~~e~~~~-i~~a~~~a~~d~~ra~t~NkgimNgI~Av~i  269 (370)
T pfam00368       191 LSGNLCTDKKPSAINWIEGRGKSVVAEAVIPAEVVEKVLKTTPEALVE-INTAKNLAGSALAGAIGFNAHAANGVAAVFI  269 (370)
T ss_pred             EECCCCCCCCHHHHEEECCCCEEEEEEEEECHHHHHHHCCCCHHHHHH-HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf             945765432201110004786399999999799996622999999999-9999999867661443124535878789985


Q ss_pred             HCCCCHHHHHHHCCCEEEEEEE-CCEEEEEEEECCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             6276378888640320256872-890899998056467730664468889999986086877887769889999999999
Q gi|255764509|r  241 ATGQDAANIVEGSQGLTYAKLH-DDSLYFSCTIPNLILGCVGNGKNIPAIKNNLTALGCIEERKTGDNARRLAAICAATV  319 (351)
Q Consensus       241 ATGnD~a~v~a~~~a~t~~~~~-~~~L~g~i~lPsl~vGtVGG~t~lp~~~~~l~ilg~~~~~~~~~~A~~La~iiAavg  319 (351)
                      |||||||+|+||+|+|+..+.. +++|++++|||||+||||||+|+||+||+||+||||.+++    ||++||+||||+|
T Consensus       270 ATGqD~ravea~aha~a~~~g~y~g~L~~sitlPsL~VGtVGGgt~lp~~~~~l~ilg~~g~~----~a~~La~IiAa~g  345 (370)
T pfam00368       270 ATGQDPAQVVESSHAITTMEGTYDGDLYGSVTLPSLEVGTVGGGTGLPTQRACLELLGVKGGG----NAKKLAEIIAAVV  345 (370)
T ss_pred             HCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCEEEECCCCCCCHHHHHHHHHHCCCCCC----CHHHHHHHHHHHH
T ss_conf             606967899877557332000458808999996671257405877686699999983999987----8999999999999


Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHCC
Q ss_conf             88899999988078868999987260
Q gi|255764509|r  320 LCGELSLLAAQTNPGELMEAHLRLER  345 (351)
Q Consensus       320 LAqnlaal~Al~t~G~iq~gHmkl~R  345 (351)
                      ||||||+|+||+++| ||+|||||+|
T Consensus       346 LA~nlsal~Al~t~g-iq~gHm~L~R  370 (370)
T pfam00368       346 LAGELSLLAALAAGH-LVKAHMKLGR  370 (370)
T ss_pred             HHHHHHHHHHHHHCC-HHHHHHHHCC
T ss_conf             998999999988273-7899987459


No 2  
>cd00643 HMG-CoA_reductase_classI Class I hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR). Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR), class I enzyme, homotetramer. Catalyzes the synthesis of coenzyme A and mevalonate in isoprenoid synthesis. In mammals this is the rate limiting committed step in cholesterol biosynthesis. Class I enzymes are found predominantly in eukaryotes and contain N-terminal membrane regions. With the exception of Archaeoglobus fulgidus, most archeae are assigned to class I, based on sequence similarity of the active site, even though they lack membrane regions. Yeast and human HMGR are divergent in their N-terminal regions, but are conserved in their active site. In contrast, human and bacterial HMGR differ in their active site architecture.
Probab=100.00  E-value=0  Score=833.52  Aligned_cols=342  Identities=41%  Similarity=0.602  Sum_probs=332.2

Q ss_pred             CCCCCEEEEEEEEEEECCEEECCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEEEECCHH
Q ss_conf             97641037861127603756765136774788653034538999989999999559988999967922412599858977
Q gi|255764509|r    1 MHMKKVSSISMPMRWIGPMKITGNVIQDKVKVPLATYEYPLWHSVKRGAHISMLCPDGIRATLIDERMTRSIFFETENAE   80 (351)
Q Consensus         1 m~en~IG~~~lPlGia~~l~InG~~a~~~y~VPMATeE~SvVAAas~gak~~~~~sGG~~t~~~~~~m~r~~~f~~~~~~   80 (351)
                      +|||+||+++||+|||+||+|||+|++++|+|||||||||||||+|||||+ ++.+|||++.+.++.|+|+|+|.|+|..
T Consensus        60 niEN~IG~~~vPlGvAgpl~InG~~a~~~y~VPmATtEgslVAS~srGak~-i~~~GG~~~~v~~d~MtRap~~~~~~~~  138 (403)
T cd00643          60 NIENVIGYVQVPVGVAGPLLINGEYAGGEFYVPMATTEGALVASTNRGCKA-INLSGGATTRVLGDGMTRAPVFRFPSAR  138 (403)
T ss_pred             CCCCEEEEEECCEEEECCEEECCCCCCCEEEEEEEECHHHHHHHHHHHHHH-HHHCCCEEEEEECCCCCCCCEEEECCHH
T ss_conf             765101256144256524487132367548985455366799998489999-9965985999936876387889959889


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             89999976175099999997301578047888878738869999999732006721588999999999998679814897
Q gi|255764509|r   81 MALTALQEITLKKAEIARVIEQTSQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQWSYLHYGS  160 (351)
Q Consensus        81 ~a~~~~~~i~~~~~~i~~~a~~~sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~~~~~~~~  160 (351)
                      ++.+|..|+.+|+++|++++|++||||+|++|++++.|++++|+|.|||+|||||||||+++|++|+||++++++.++++
T Consensus       139 ~a~~~~~wi~~~~~~i~~~a~stsr~g~L~~i~~~~~g~~v~lrf~~~TgDAMG~NMv~~~~e~~~~~i~~~~~~~~~~~  218 (403)
T cd00643         139 EAAEFKAWIEENFEAIKEVAESTSRHARLQSIKPYIAGRSVYLRFEYTTGDAMGMNMVTKATEAACDWIEENFPDMEVIS  218 (403)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCEEEEEEEEECCCHHHCHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             99999999986699999998475884368787756578889999998547233133779999999999998689976999


Q ss_pred             ECCCCCHHHHHHHHHHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHH
Q ss_conf             34774312333554310377207999987569999757389999999887866565542200220216216677888887
Q gi|255764509|r  161 VSGNICSDKKATAINGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQKNLIGTFLAGGIRSANAHFANMLLAYYL  240 (351)
Q Consensus       161 ilsN~~tdkk~s~~n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~~~~~~a~t~NkgimNgI~Av~l  240 (351)
                      |+||||+|||++++|++.+|||+|+||+.||.++++++++++|+++.+.+..++.+++..++ ..++|+|+||||+|+||
T Consensus       219 i~gN~~tDKK~sa~n~~~gRGk~V~ae~~i~~~vv~~~l~~~~~~l~~~~~~k~~~gs~~ag-~~g~Nah~aN~i~Aifi  297 (403)
T cd00643         219 LSGNFCTDKKPSAINWIEGRGKSVVAEATIPREVVKEVLKTTPEALVEVNIAKNLIGSAMAG-SGGFNAHAANIVAAIFI  297 (403)
T ss_pred             EECCCCCCHHHHHHHHCCCCCEEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC-CCCCCCHHHHHHHHHHE
T ss_conf             84455431244445310257518998788759999988678999999999888877677604-67643006776667612


Q ss_pred             HCCCCHHHHHHHCCCEEEEEEE-CCEEEEEEEECCEEEEEECCCCCCHHHHHHHHHHCCCCCCC-CCCCHHHHHHHHHHH
Q ss_conf             6276378888640320256872-89089999805646773066446888999998608687788-776988999999999
Q gi|255764509|r  241 ATGQDAANIVEGSQGLTYAKLH-DDSLYFSCTIPNLILGCVGNGKNIPAIKNNLTALGCIEERK-TGDNARRLAAICAAT  318 (351)
Q Consensus       241 ATGnD~a~v~a~~~a~t~~~~~-~~~L~g~i~lPsl~vGtVGG~t~lp~~~~~l~ilg~~~~~~-~~~~A~~La~iiAav  318 (351)
                      |||||||+|+||+|++|+|+.. +|+||+++|||||+||||||||+||+||+||+||||+|.+. +.+||++||+||||+
T Consensus       298 ATGQD~A~v~ess~~~t~~e~~~~gdL~~svtlPsL~VGTVGGgT~lp~q~~~L~iLg~~g~~~~pg~~a~~LAeIiAa~  377 (403)
T cd00643         298 ATGQDAAQVVESSNCITTMELTADGDLYISVTMPSLEVGTVGGGTGLPTQRECLELLGCYGAGDEPGANARKLAEIVAAT  377 (403)
T ss_pred             ECCCCHHHHHHCCCEEEEEEECCCCCEEEEEEECCCEEEEECCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             04897799841132279999838995899998068257850687777779999998388889998454099999999999


Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHCC
Q ss_conf             988899999988078868999987260
Q gi|255764509|r  319 VLCGELSLLAAQTNPGELMEAHLRLER  345 (351)
Q Consensus       319 gLAqnlaal~Al~t~G~iq~gHmkl~R  345 (351)
                      +||||||+|+||++.+ ||+|||+|+|
T Consensus       378 ~LAgeLsll~Alat~~-~~~aHm~l~R  403 (403)
T cd00643         378 VLAGELSLLAALAAGH-LVRSHEKLGR  403 (403)
T ss_pred             HHHHHHHHHHHHHCCH-HHHHHHHHCC
T ss_conf             9998999999987075-8999997459


No 3  
>cd00644 HMG-CoA_reductase_classII Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR). Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR), class II, prokaryotic enzyme is a homodimer. Class II enzymes are found primarily in prokaryotes and Archaeoglobus fulgidus and are soluble as they lack the membrane region. Enzymes catalyze the synthesis of coenzyme A and mevalonate in isoprenoid synthesis. Bacteria, such as Pseudomonas mevalonii, which rely solely on mevalonate for their carbon source, catalyze the reverse reaction, using an NAD-dependent HMGR to deacetylate mevalonate into 3-hydroxy-3-methylglutaryl-CoA. Human and bacterial HMGR differ in their active site architecture.
Probab=100.00  E-value=0  Score=778.30  Aligned_cols=317  Identities=22%  Similarity=0.240  Sum_probs=298.5

Q ss_pred             CCCCCEEEEEEEEEEECCEEECCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEEEECCHH
Q ss_conf             97641037861127603756765136774788653034538999989999999559988999967922412599858977
Q gi|255764509|r    1 MHMKKVSSISMPMRWIGPMKITGNVIQDKVKVPLATYEYPLWHSVKRGAHISMLCPDGIRATLIDERMTRSIFFETENAE   80 (351)
Q Consensus         1 m~en~IG~~~lPlGia~~l~InG~~a~~~y~VPMATeE~SvVAAas~gak~~~~~sGG~~t~~~~~~m~r~~~f~~~~~~   80 (351)
                      ||||+||+|+||+|||+||+|||+    +|+|||||||||||||+|||||+| +.+|||++.+.++.|+||++|  .+..
T Consensus        43 mIENvIG~~~lPvGVA~n~lInGk----~y~VPMAtEE~SVVAAas~gaK~i-~~~GG~~t~v~~~~M~GqI~~--~~~~  115 (417)
T cd00644          43 MIENVIGTFSLPLGVATNFLVNGK----DYLVPMATEEPSVVAAASNAAKIA-RKSGGFKTSSSDRLMIGQIQL--VDVS  115 (417)
T ss_pred             HHHHCCEEECCCEEEECCEEECCE----EEEEEEEECHHHHHHHHHHHHHHH-HHCCCEEEEECCCCEEECEEE--CCCC
T ss_conf             022201133032001256589898----888645523238999997898999-867997999889937823286--7776


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHC-----CCCEEEEEEEEEEEC----CEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             89999976175099999997301-----578047888878738----869999999732006721588999999999998
Q gi|255764509|r   81 MALTALQEITLKKAEIARVIEQT-----SQFTRFLQLHSQIAG----NLLFLRLEFATGDASGHNMVTKAADAVMDWILS  151 (351)
Q Consensus        81 ~a~~~~~~i~~~~~~i~~~a~~~-----sr~ggl~~i~~~~~g----~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~  151 (351)
                      |+.++..|+.+++++|++.+|+.     +||||+++|+++..+    +|+++||.+||||||||||||+++|+++++|++
T Consensus       116 d~~~~~~~i~~~~~~i~~~An~~~~s~~kRGGGl~~i~~~~~~~~~~~~l~l~~~~dT~DAMGaNmvnt~~E~~a~~l~~  195 (417)
T cd00644         116 DPAKARAFILAHKDEILEIANEAHPSLVKRGGGARDIEVRVLDADLGDFLSVHLLVDTKDAMGANIVNTMLEAVAPLLEE  195 (417)
T ss_pred             CHHHHHHHHHHCHHHHHHHHHHHCHHHHHCCCCCEEEEEEEECCCCCCEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999985778899999752837786078812689998136679879999997206554317878999999999998


Q ss_pred             HCCCCEEEEECCCCCHHHHHHHHHHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHCCCCCH
Q ss_conf             67981489734774312333554310377207999987569999757389999999887866565542200220216216
Q gi|255764509|r  152 QWSYLHYGSVSGNICSDKKATAINGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQKNLIGTFLAGGIRSANAHF  231 (351)
Q Consensus       152 ~~~~~~~~~ilsN~~tdkk~s~~n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~~~~~~a~t~Nkgi  231 (351)
                      ++++..+++||||||+|++             |+|+|.||.+.+... ..+++++++.+..++.++..||||++||||||
T Consensus       196 ~~~~~~~~~IlSN~~~~~~-------------v~A~~~i~~~~l~~~-~~~g~~va~~i~~a~~~A~~d~yRA~ThNKGi  261 (417)
T cd00644         196 ITGGEVLLRILSNYATERL-------------VRAKVSIPVEALGTK-GGSGEEVAKKIALASAFAQVDPYRAATHNKGI  261 (417)
T ss_pred             HCCCCEEEEEECCCCCCCE-------------EEEEEEECHHHHCCC-CCCHHHHHHHHHHHHHHHHHCHHHHHHHCCCC
T ss_conf             7598569997434677775-------------789999729995545-77679999999999998600878888741420


Q ss_pred             HHHHHHHHHHCCCCHHHHHHHCCCE----------EEEEEECCEEEEEEEECCEEEEEECCCCCC-HHHHHHHHHHCCCC
Q ss_conf             6778888876276378888640320----------256872890899998056467730664468-88999998608687
Q gi|255764509|r  232 ANMLLAYYLATGQDAANIVEGSQGL----------TYAKLHDDSLYFSCTIPNLILGCVGNGKNI-PAIKNNLTALGCIE  300 (351)
Q Consensus       232 mNgI~Av~lATGnD~a~v~a~~~a~----------t~~~~~~~~L~g~i~lPsl~vGtVGG~t~l-p~~~~~l~ilg~~~  300 (351)
                      ||||||||||||||||+||+++|+|          |.|++++|+|+|++||| |+||||||+|++ |+||+||+||||  
T Consensus       262 mNgI~Av~iATGnD~ravEA~~HayAs~~G~y~~lt~~~~~~~~L~gsitlP-l~vGtVGG~t~~~P~~~~~l~iLgv--  338 (417)
T cd00644         262 MNGIDAVVLATGNDWRAVEAGAHAYAARSGQYRSLSTWEIDDGKLVGELELP-LAVGTVGGSTKVHPLAKLALKILGV--  338 (417)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCEEEECCCEEEEEEEEE-EEEEEECCCCCCCHHHHHHHHHHCC--
T ss_conf             3224677535157178888766577760697565531688398799999986-0446762667758648999997189--


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH-CCCC
Q ss_conf             7887769889999999999888999999880788689999872-6033
Q gi|255764509|r  301 ERKTGDNARRLAAICAATVLCGELSLLAAQTNPGELMEAHLRL-ERMH  347 (351)
Q Consensus       301 ~~~~~~~A~~La~iiAavgLAqnlaal~Al~t~G~iq~gHmkl-~R~~  347 (351)
                           +||++||+||||+||||||||||||+|+| ||+||||| .||-
T Consensus       339 -----~~A~~La~Iiaa~gLAqnlaal~ALat~g-iqkgHMkLh~rn~  380 (417)
T cd00644         339 -----PSAKELAEIIAAVGLAQNFAALRALATEG-IQKGHMKLHARNL  380 (417)
T ss_pred             -----CCHHHHHHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHH
T ss_conf             -----98999999999999999999999987477-5788999999999


No 4  
>TIGR00920 2A060605 3-hydroxy-3-methylglutaryl-coenzyme A reductase; InterPro: IPR004816   Synonym(s): 3-hydroxy-3-methylglutaryl-coenzyme A reductase, HMG-CoA reductase.    There are two distinct classes of hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase enzymes: class I consists of eukaryotic and most archaeal enzymes (1.1.1.34 from EC), while class II consists of prokaryotic enzymes (1.1.1.88 from EC) , .   Class I HMG-CoA reductases catalyse the NADP-dependent synthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). In vertebrates, membrane-bound HMG-CoA reductase is the rate-limiting enzyme in the biosynthesis of cholesterol and other isoprenoids. In plants, mevalonate is the precursor of all isoprenoid compounds . The reduction of HMG-CoA to mevalonate is regulated by feedback inhibition by sterols and non-sterol metabolites derived from mevalonate, including cholesterol. In archaea, HMG-CoA reductase is a cytoplasmic enzyme involved in the biosynthesis of the isoprenoids side chains of lipids . Class I HMG-CoA reductases consist of an N-terminal membrane domain (lacking in archaeal enzymes), and a C-terminal catalytic region. The catalytic region can be subdivided into three domains: an N-domain (N-terminal), a large L-domain, and a small S-domain (inserted within the L-domain). The L-domain binds the substrate, while the S-domain binds NADP.    Class II HMG-CoA reductases catalyse the reverse reaction of class I enzymes, namely the NAD-dependent synthesis of HMG-CoA from mevalonate and CoA . Some bacteria, such as Pseudomonas mevalonii, can use mevalonate as the sole carbon source. Class II enzymes lack a membrane domain. Their catalytic region is structurally related to that of class I enzymes, but it consists of only two domains: a large L-domain and a small S-domain (inserted within the L-domain). As with class I enzymes, the L-domain binds substrate, but the S-domain binds NAD (instead of NADP in class I).   This entry represents Metazoan class I HMG-CoA reductases, which are membrane-bound glycoproteins that remains in the endoplasmic reticulum after synthesis and glycosylation .; GO: 0004420 hydroxymethylglutaryl-CoA reductase (NADPH) activity, 0050661 NADP binding, 0008299 isoprenoid biosynthetic process, 0005789 endoplasmic reticulum membrane.
Probab=100.00  E-value=0  Score=762.88  Aligned_cols=342  Identities=36%  Similarity=0.564  Sum_probs=332.1

Q ss_pred             CCCEEEEEEEEEEECCEEECCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEEEECCHHHH
Q ss_conf             64103786112760375676513677478865303453899998999999955998899996792241259985897789
Q gi|255764509|r    3 MKKVSSISMPMRWIGPMKITGNVIQDKVKVPLATYEYPLWHSVKRGAHISMLCPDGIRATLIDERMTRSIFFETENAEMA   82 (351)
Q Consensus         3 en~IG~~~lPlGia~~l~InG~~a~~~y~VPMATeE~SvVAAas~gak~~~~~sGG~~t~~~~~~m~r~~~f~~~~~~~a   82 (351)
                      ||+|||++||+||||||+.||+    +|+|||||+||.||||-|||||. +...||++..+..++|||+|+++|++..++
T Consensus       600 ENViGYmPiPVGvAGPLlLDG~----~y~VPmATTEGcLVASTNRGcrA-l~~~GGv~S~v~~dGMTRGPvVRlP~~~~A  674 (988)
T TIGR00920       600 ENVIGYMPIPVGVAGPLLLDGK----EYQVPMATTEGCLVASTNRGCRA-LMLGGGVRSRVLADGMTRGPVVRLPSAARA  674 (988)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCC----EEEECCCHHCCHHHHHHHHHHHH-HHCCCCEEEEEEECCCCCCCCCCCCCHHHH
T ss_conf             0414521424555466102886----47745711013144213357898-641788389997058643650068875018


Q ss_pred             HHHHHHHH--HHHHHHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             99997617--5099999997301578047888878738869999999732006721588999999999998679814897
Q gi|255764509|r   83 LTALQEIT--LKKAEIARVIEQTSQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQWSYLHYGS  160 (351)
Q Consensus        83 ~~~~~~i~--~~~~~i~~~a~~~sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~~~~~~~~  160 (351)
                      .+.+.|++  ++|..||+.++||||+++|.+|+....|+++|+||.-.||||||+|||.+.+|.+-.++++.||+.++++
T Consensus       675 ae~k~Wle~penF~~iK~~FDSTSRFArL~~~h~~~aGR~LyiRF~a~TGDaMGMNMiSKgte~AL~~lq~~FPdm~Ils  754 (988)
T TIGR00920       675 AEVKAWLEVPENFAVIKDAFDSTSRFARLKKIHIAVAGRNLYIRFQAKTGDAMGMNMISKGTEQALAELQEVFPDMEILS  754 (988)
T ss_pred             HHHHHHHCCCCCHHHHHHCCCCCCHHHHHHHHHHEECCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             99988504843338885215764313555221000027640365453047866631022889999999875488808964


Q ss_pred             ECCCCCHHHHHHHHHHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHH
Q ss_conf             34774312333554310377207999987569999757389999999887866565542200220216216677888887
Q gi|255764509|r  161 VSGNICSDKKATAINGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQKNLIGTFLAGGIRSANAHFANMLLAYYL  240 (351)
Q Consensus       161 ilsN~~tdkk~s~~n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~~~~~~a~t~NkgimNgI~Av~l  240 (351)
                      +++|||||||+.++||+.||||+|..|++||.++++++||++.+.+.|.+..||.+|+++++.+.++|.|.+|-++||||
T Consensus       755 lSGNyCTDKKPAAiNWIeGRGK~VVcEA~ipA~~vr~VLKTs~~ALvdvNi~KNl~GSAmAGSIGG~NAHAANiVTAiyi  834 (988)
T TIGR00920       755 LSGNYCTDKKPAAINWIEGRGKSVVCEAIIPAKIVRSVLKTSAEALVDVNINKNLVGSAMAGSIGGFNAHAANIVTAIYI  834 (988)
T ss_pred             ECCCCCCCCCCCEEEEECCCCCCEEEEEECCHHHHHHHHCCCHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             03661568851101012168970698773463786455211078999851103862012100113156788889989986


Q ss_pred             HCCCCHHHHHHHCCCEEEEEE---ECCEEEEEEEECCEEEEEECCCCCCHHHHHHHHHHCCCCCC--CCCCCHHHHHHHH
Q ss_conf             627637888864032025687---28908999980564677306644688899999860868778--8776988999999
Q gi|255764509|r  241 ATGQDAANIVEGSQGLTYAKL---HDDSLYFSCTIPNLILGCVGNGKNIPAIKNNLTALGCIEER--KTGDNARRLAAIC  315 (351)
Q Consensus       241 ATGnD~a~v~a~~~a~t~~~~---~~~~L~g~i~lPsl~vGtVGG~t~lp~~~~~l~ilg~~~~~--~~~~~A~~La~ii  315 (351)
                      |||||+|+-..|+.|.|-+|.   +++|||.|+|||||.||||||||.||+|++||+||||.|..  .+++||++||+|+
T Consensus       835 AtGQDaAQNVgSSNC~TlME~~Gp~~~DLY~SCTMPSiEiGTVGGGT~LpPQ~ACL~MLGV~GA~~~~PG~NA~~LArIV  914 (988)
T TIGR00920       835 ATGQDAAQNVGSSNCMTLMEAWGPTGEDLYISCTMPSIEIGTVGGGTVLPPQSACLQMLGVRGANETRPGENAKQLARIV  914 (988)
T ss_pred             HCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCEEEEECCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             41787335201123233015788688860476047741442046766771478999740664556788735477761466


Q ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCC
Q ss_conf             99998889999998807886899998726033677
Q gi|255764509|r  316 AATVLCGELSLLAAQTNPGELMEAHLRLERMHLNG  350 (351)
Q Consensus       316 AavgLAqnlaal~Al~t~G~iq~gHmkl~R~~~~~  350 (351)
                      .+++||+|||++.||+. ||+.|+||||+|+.++-
T Consensus       915 C~TVmAGELSLMaALaa-GhLVKSHM~HNRS~i~~  948 (988)
T TIGR00920       915 CATVMAGELSLMAALAA-GHLVKSHMRHNRSSINL  948 (988)
T ss_pred             HHHHHHHHHHHHHHHHH-CCCCHHCCCCCCHHHCC
T ss_conf             55666768989999972-34101024002012200


No 5  
>cd00365 HMG-CoA_reductase Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR). Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR) is a tightly regulated enzyme, which catalyzes the synthesis of coenzyme A and mevalonate in isoprenoid synthesis. In mammals, this is the rate limiting committed step in cholesterol biosynthesis. Bacteria, such as Pseudomonas mevalonii, which rely solely on mevalonate for their carbon source, catalyze the reverse reaction, using an NAD-dependent HMGR to deacetylate mevalonate into 3-hydroxy-3-methylglutaryl-CoA. There are two classes of HMGR: class I enzymes which are found predominantly in eukaryotes and contain N-terminal membrane regions and class II enzymes which are found primarily in prokaryotes and are soluble as they lack the membrane region. With the exception of Archaeoglobus fulgidus, most archeae are assigned to class I, based on sequence similarity of the active site, even though they lack membrane regions. Yeast and human HMGR
Probab=100.00  E-value=0  Score=736.96  Aligned_cols=315  Identities=21%  Similarity=0.218  Sum_probs=282.2

Q ss_pred             CCCCCEEEEEEEEEEECCEEECCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEEEECCHH
Q ss_conf             97641037861127603756765136774788653034538999989999999559988999967922412599858977
Q gi|255764509|r    1 MHMKKVSSISMPMRWIGPMKITGNVIQDKVKVPLATYEYPLWHSVKRGAHISMLCPDGIRATLIDERMTRSIFFETENAE   80 (351)
Q Consensus         1 m~en~IG~~~lPlGia~~l~InG~~a~~~y~VPMATeE~SvVAAas~gak~~~~~sGG~~t~~~~~~m~r~~~f~~~~~~   80 (351)
                      ||||+||+++||+|||+||+|||+    +|+|||||||||||||+|||||+ ++.+|||++++.++.|+|||+|.|.+  
T Consensus        43 ~IEN~IG~~~lPlGvAg~l~InG~----~y~VPMATeE~SvVAa~srgaK~-~~~~GG~~~~v~~~~m~~q~~f~~~~--  115 (376)
T cd00365          43 MIENVIGTFELPYAVASNFQIDGR----DVLVPLVTEEPSIVAAASYMAKL-ARAGGGFTTSSSAPLMHAQVQIVLIQ--  115 (376)
T ss_pred             CCCCCCEEEECCEEEECCEEECCE----EEEEEEEECHHHHHHHHHHHHHH-HHHCCCEEEEECCCCEEEEEEEEECC--
T ss_conf             543011154322326547799884----77874674378899999889999-98279879998688579836999678--


Q ss_pred             HHHHHHHHHH-HHHHHHHHHHHHC-----CCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             8999997617-5099999997301-----578047888878738869999999732006721588999999999998679
Q gi|255764509|r   81 MALTALQEIT-LKKAEIARVIEQT-----SQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQWS  154 (351)
Q Consensus        81 ~a~~~~~~i~-~~~~~i~~~a~~~-----sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~~  154 (351)
                      |+.++..|+. +++++|++++|++     +||||+++|+++..+++++|+|.|||||||||||||+|+|++|++|+++++
T Consensus       116 d~~~~~~~~~~~~~~~i~~~a~~~~~~~~~rgGgl~~i~~~~~g~~v~l~~~~dtgDAMGaNmvn~~~E~v~~~i~~~~~  195 (376)
T cd00365         116 DPLNAKLSLLRSGKDEIIELANRKDQLLNSLGGGCRDIEVHTFGPMLVAHLIVDVGDAMGANMINTMAEAVAPLMEAYTG  195 (376)
T ss_pred             CHHHHHHHHHHHCHHHHHHHHHHHCHHHHHCCCEEEEEEEEEECCEEEEEEEEECHHHHCCHHHHHHHHHHHHHHHHHCC
T ss_conf             88999999987368999999973394667269617897867608789999997422332344889999999999998779


Q ss_pred             CCEE--EEECCCCCHHHHHHHHHHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHH-HHHHHHCCCHHHCCCCCH
Q ss_conf             8148--9734774312333554310377207999987569999757389999999887866-565542200220216216
Q gi|255764509|r  155 YLHY--GSVSGNICSDKKATAINGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQK-NLIGTFLAGGIRSANAHF  231 (351)
Q Consensus       155 ~~~~--~~ilsN~~tdkk~s~~n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~-~~~a~~~~~~a~t~Nkgi  231 (351)
                      +...  ..+++|             .+||+.|+||+.||.+.+++.+.+ +++.++.+.+. ..++..|+||++||||||
T Consensus       196 ~~~~~~~~~~~~-------------~~~g~~v~A~~~i~~~~l~~~~~~-~~~~~~~~~~~~~~~a~~d~~rA~thNkgi  261 (376)
T cd00365         196 GMQVRLRSLSNL-------------TGDGRLARAQARITPQQLETAEFS-GEAVIEGILDAYAFKAAVDSYRAATHNKGI  261 (376)
T ss_pred             CCHHHHEECCCC-------------CCCCEEEEEEEEEEHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             861523010434-------------568808999999819998441465-388999999999999753123024455531


Q ss_pred             HHHHHHHHHHCCCCHHHHHHHCCCE--------EEEEEE-CCEEEEEEEECCEEEEEECCCCCC-HHHHHHHHHHCCCCC
Q ss_conf             6778888876276378888640320--------256872-890899998056467730664468-889999986086877
Q gi|255764509|r  232 ANMLLAYYLATGQDAANIVEGSQGL--------TYAKLH-DDSLYFSCTIPNLILGCVGNGKNI-PAIKNNLTALGCIEE  301 (351)
Q Consensus       232 mNgI~Av~lATGnD~a~v~a~~~a~--------t~~~~~-~~~L~g~i~lPsl~vGtVGG~t~l-p~~~~~l~ilg~~~~  301 (351)
                      ||||||||||||||||+|++++|+|        |.|+.+ +++|+++++|| |+||||||+|++ |+||+||+||||   
T Consensus       262 mNgI~Av~iATGqD~raVea~~hayA~~~y~~lt~~~~~~~~~L~~sl~lP-l~VGtVGGgt~~~p~~~~~L~iLg~---  337 (376)
T cd00365         262 MNGVDPLIVACGQDWRAVEVGAHAYACRHYGSLTTWEKDNNGHLVITLEMS-MPVGLVGGATKTHPLAQASLRILGV---  337 (376)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEEEECCCEEEEEEEEC-CCEEEEECCCCCCHHHHHHHHHHCC---
T ss_conf             566788985607968899888647765046620389994796199999910-4247974788758889999997389---


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCC
Q ss_conf             88776988999999999988899999988078868999987260
Q gi|255764509|r  302 RKTGDNARRLAAICAATVLCGELSLLAAQTNPGELMEAHLRLER  345 (351)
Q Consensus       302 ~~~~~~A~~La~iiAavgLAqnlaal~Al~t~G~iq~gHmkl~R  345 (351)
                          ++|++|||||||+|||||||+|+||+|+| ||+|||||+.
T Consensus       338 ----~~A~~LaeIiAavgLA~nlsal~Al~t~g-iq~gHMkL~a  376 (376)
T cd00365         338 ----KTAQALARIAVAVGLAQNLGAMRALATEG-IQRGHMALHA  376 (376)
T ss_pred             ----CCHHHHHHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHCC
T ss_conf             ----78999999999999999999999988375-6788776329


No 6  
>KOG2480 consensus
Probab=100.00  E-value=0  Score=682.59  Aligned_cols=343  Identities=37%  Similarity=0.549  Sum_probs=333.4

Q ss_pred             CCCCEEEEEEEEEEECCEEECCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEEEECCHHH
Q ss_conf             76410378611276037567651367747886530345389999899999995599889999679224125998589778
Q gi|255764509|r    2 HMKKVSSISMPMRWIGPMKITGNVIQDKVKVPLATYEYPLWHSVKRGAHISMLCPDGIRATLIDERMTRSIFFETENAEM   81 (351)
Q Consensus         2 ~en~IG~~~lPlGia~~l~InG~~a~~~y~VPMATeE~SvVAAas~gak~~~~~sGG~~t~~~~~~m~r~~~f~~~~~~~   81 (351)
                      -||.|||++||+||||||++||+    +|+|||||+|+.||||.+||||. ++.+||.++.+.+++|+|+|++.|++..+
T Consensus       238 CENvIGY~piPVGVaGPLlldG~----~y~VPMATTEGaLVAStnRGcKa-I~a~GGa~sv~~~dGMTRgPvVRFps~~r  312 (602)
T KOG2480         238 CENVIGYMPIPVGVAGPLLLDGT----EYYVPMATTEGALVASTNRGCKA-INAGGGATSVLEKDGMTRGPVVRFPSARR  312 (602)
T ss_pred             HHCCCCCEECCCCCCCCEEECCE----EEEEEECCCCCHHHHHHCCCHHH-EECCCCEEEEEEECCCCCCCEEECCHHHH
T ss_conf             53334524312345365478785----88863003541236764025243-12478706899606743366354510777


Q ss_pred             HHHHHHHHH--HHHHHHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             999997617--509999999730157804788887873886999999973200672158899999999999867981489
Q gi|255764509|r   82 ALTALQEIT--LKKAEIARVIEQTSQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQWSYLHYG  159 (351)
Q Consensus        82 a~~~~~~i~--~~~~~i~~~a~~~sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~~~~~~~  159 (351)
                      +..+..|++  |+++.+++++|++||+++|++|++.+.|+.+|++|...||||||+|||.+.+|.+..++.++||+..++
T Consensus       313 A~~~k~WLe~~E~~~~lk~~FnstSRFaRLq~i~~~iaG~~lyiRF~~~TGDAMGMNMISKgve~~l~~l~~~fpdM~vi  392 (602)
T KOG2480         313 AAEAKIWLESPENQEVLKKAFNSTSRFARLQSIHTTIAGRNLYIRFCTSTGDAMGMNMISKGVENALRFLSEEFPDMQVI  392 (602)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHEEEEEEECCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEE
T ss_conf             78889886192668999998423113440100047851660389998225630000567888999999998748975589


Q ss_pred             EECCCCCHHHHHHHHHHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHH
Q ss_conf             73477431233355431037720799998756999975738999999988786656554220022021621667788888
Q gi|255764509|r  160 SVSGNICSDKKATAINGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQKNLIGTFLAGGIRSANAHFANMLLAYY  239 (351)
Q Consensus       160 ~ilsN~~tdkk~s~~n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~~~~~~a~t~NkgimNgI~Av~  239 (351)
                      +|++|||+|||+++.||+.||||+|.+|++||.++++++|+++++++++.+..++.+|+++++...++|.|.+|-++|||
T Consensus       393 ~iSGNyCtDKKpAAiNWieGRGKsVV~Ea~Ip~~vvr~VLkt~v~aLveln~~KnliGSAmAGSvGGfNAHAANiVtAvF  472 (602)
T KOG2480         393 SISGNYCTDKKPAAINWIEGRGKSVVAEATIPGEVVRKVLKTTVEALVELNILKNLIGSAMAGSVGGFNAHAANIVTAVF  472 (602)
T ss_pred             EECCCCCCCCCHHHHHHHCCCCCEEEEEEECCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf             85067446885676534406884689987545899999973499999988766643204540355672156788999999


Q ss_pred             HHCCCCHHHHHHHCCCEEEEEE-ECCEEEEEEEECCEEEEEECCCCCCHHHHHHHHHHCCCCCC--CCCCCHHHHHHHHH
Q ss_conf             7627637888864032025687-28908999980564677306644688899999860868778--87769889999999
Q gi|255764509|r  240 LATGQDAANIVEGSQGLTYAKL-HDDSLYFSCTIPNLILGCVGNGKNIPAIKNNLTALGCIEER--KTGDNARRLAAICA  316 (351)
Q Consensus       240 lATGnD~a~v~a~~~a~t~~~~-~~~~L~g~i~lPsl~vGtVGG~t~lp~~~~~l~ilg~~~~~--~~~~~A~~La~iiA  316 (351)
                      ||||||+++..+|++|.|.++. .|+||+.|++|||+.||||||||.|++|++||++|||.|+.  .+.+|||+||+|+|
T Consensus       473 lAtGQDpAQnVeSSnCiT~Me~~~d~DL~iSvtMPsIEVGTVGGGT~L~pQ~AcL~lLGv~G~~~~~PG~NarqLAriVa  552 (602)
T KOG2480         473 LATGQDPAQNVESSNCITLMEASTDGDLYISVTMPSIEVGTVGGGTVLEPQGACLDLLGVRGAHKTSPGDNARQLARIVA  552 (602)
T ss_pred             HHHCCCHHHHCCCCHHHHHHEECCCCCEEEEEECCCEEEEEECCCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             98279768811411035431004689758999605378886458652283788999836877787899736899999999


Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCC
Q ss_conf             9998889999998807886899998726033677
Q gi|255764509|r  317 ATVLCGELSLLAAQTNPGELMEAHLRLERMHLNG  350 (351)
Q Consensus       317 avgLAqnlaal~Al~t~G~iq~gHmkl~R~~~~~  350 (351)
                      +.+||+|||++.||++ |++.++||+|+|+..+.
T Consensus       553 aaVlAGELSLmaALAa-g~LVkSHM~~NRs~~~~  585 (602)
T KOG2480         553 AAVLAGELSLMAALAA-GHLVKSHMKLNRSSIAI  585 (602)
T ss_pred             HHHHHHHHHHHHHHHC-CHHHHHHHHHCCCCCCC
T ss_conf             9998738999998860-50789887636455678


No 7  
>TIGR00533 HMG_CoA_R_NADP 3-hydroxy-3-methylglutaryl Coenzyme A reductase; InterPro: IPR004554   Synonym(s): 3-hydroxy-3-methylglutaryl-coenzyme A reductase, HMG-CoA reductase.    There are two distinct classes of hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase enzymes: class I consists of eukaryotic and most archaeal enzymes (1.1.1.34 from EC), while class II consists of prokaryotic enzymes (1.1.1.88 from EC) , .   Class I HMG-CoA reductases catalyse the NADP-dependent synthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). In vertebrates, membrane-bound HMG-CoA reductase is the rate-limiting enzyme in the biosynthesis of cholesterol and other isoprenoids. In plants, mevalonate is the precursor of all isoprenoid compounds . The reduction of HMG-CoA to mevalonate is regulated by feedback inhibition by sterols and non-sterol metabolites derived from mevalonate, including cholesterol. In archaea, HMG-CoA reductase is a cytoplasmic enzyme involved in the biosynthesis of the isoprenoids side chains of lipids . Class I HMG-CoA reductases consist of an N-terminal membrane domain (lacking in archaeal enzymes), and a C-terminal catalytic region. The catalytic region can be subdivided into three domains: an N-domain (N-terminal), a large L-domain, and a small S-domain (inserted within the L-domain). The L-domain binds the substrate, while the S-domain binds NADP.    Class II HMG-CoA reductases catalyse the reverse reaction of class I enzymes, namely the NAD-dependent synthesis of HMG-CoA from mevalonate and CoA . Some bacteria, such as Pseudomonas mevalonii, can use mevalonate as the sole carbon source. Class II enzymes lack a membrane domain. Their catalytic region is structurally related to that of class I enzymes, but it consists of only two domains: a large L-domain and a small S-domain (inserted within the L-domain). As with class I enzymes, the L-domain binds substrate, but the S-domain binds NAD (instead of NADP in class I).   This entry represents the catalytic region found in class I HMG-CoA reductase enzymes (the eukaryotic enzymes contain an extra N-terminal domain not represented by this entry). ; GO: 0004420 hydroxymethylglutaryl-CoA reductase (NADPH) activity, 0050661 NADP binding, 0008299 isoprenoid biosynthetic process, 0016021 integral to membrane.
Probab=100.00  E-value=0  Score=672.67  Aligned_cols=342  Identities=38%  Similarity=0.583  Sum_probs=329.0

Q ss_pred             CCCCEEEEEEEEEEECCEEECCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEEEECCHHH
Q ss_conf             76410378611276037567651367747886530345389999899999995599889999679224125998589778
Q gi|255764509|r    2 HMKKVSSISMPMRWIGPMKITGNVIQDKVKVPLATYEYPLWHSVKRGAHISMLCPDGIRATLIDERMTRSIFFETENAEM   81 (351)
Q Consensus         2 ~en~IG~~~lPlGia~~l~InG~~a~~~y~VPMATeE~SvVAAas~gak~~~~~sGG~~t~~~~~~m~r~~~f~~~~~~~   81 (351)
                      +||.||+++||+|++|||+|||+|++++|||||||+|++||||++|||+. +++.||-++.+.+|.|+|+|++.+.++-+
T Consensus        68 ~EN~IG~~~iPlGv~GPL~i~Ge~a~~~yyiPlATtEGaLVAS~~RGC~~-I~~~GGAT~~~~~D~MTRaPv~r~~~~~~  146 (419)
T TIGR00533        68 IENVIGVVQIPLGVAGPLKIDGEYADGEYYIPLATTEGALVASVNRGCSV-ITKGGGATVRVTKDGMTRAPVVRTKSVVE  146 (419)
T ss_pred             CCCCCCEEECCCCEECCCEEECEECCCCEEECCCCCCHHHHHHHHHHHHH-HHCCCCCEEEEECCCCCCCCEECCHHHHH
T ss_conf             34534326257302345157120116515621211230677765432577-63689816998648743354231078998


Q ss_pred             HHHHHHHHH--HHHHHHHHHHHHCCCCEEEEEEE-EEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCC--C
Q ss_conf             999997617--50999999973015780478888-787388699999997320067215889999999999986798--1
Q gi|255764509|r   82 ALTALQEIT--LKKAEIARVIEQTSQFTRFLQLH-SQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQWSY--L  156 (351)
Q Consensus        82 a~~~~~~i~--~~~~~i~~~a~~~sr~ggl~~i~-~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~~~--~  156 (351)
                      +.+.+.|+.  |+++.|++.+|||+|||+|.+|+ .-+.|+++|.||.+.||||||+|||+.++|..++++.++++.  .
T Consensus       147 a~~~~~W~~seE~~~~ik~~~~ST~R~~~L~~I~P~~~aG~~ly~RF~~~TGDaMGMNMv~~a~E~al~~~~~E~~~E~~  226 (419)
T TIGR00533       147 ALKVREWIDSEENQNAIKEAAESTTRHGKLVKIEPILLAGDLLYPRFVTTTGDAMGMNMVTIATEKALKLLVEELGKEGI  226 (419)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCCCCEEEEEECCEEEECCCCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99877764011356899987403121004466340788556300010121575322257789999999999985133770


Q ss_pred             EE--EEECCCCCHHHHHHHHHHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHCCCCCHHHH
Q ss_conf             48--9734774312333554310377207999987569999757389999999887866565542200220216216677
Q gi|255764509|r  157 HY--GSVSGNICSDKKATAINGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQKNLIGTFLAGGIRSANAHFANM  234 (351)
Q Consensus       157 ~~--~~ilsN~~tdkk~s~~n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~~~~~~a~t~NkgimNg  234 (351)
                      ..  .++++|+|+||||++.||+.||||+|+||++||.+.++++||++++.+++.+..+|.++++.++...+||.|.+|-
T Consensus       227 ~V~~vavSGN~C~DKKPaa~NlIeGRGKSivAE~~~pg~~V~~~LK~~~~A~vE~N~~KNliGSA~agS~GGFNAH~AN~  306 (419)
T TIGR00533       227 EVKTVAVSGNLCTDKKPAAINLIEGRGKSIVAEVTIPGDVVEKVLKTTVSALVEVNIAKNLIGSAIAGSMGGFNAHYANI  306 (419)
T ss_pred             EEEEEEEECCCCCCCCCCCCCEECCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             79999863365647772212134178844899887365788766337678877657651035665530333056779999


Q ss_pred             HHHHHHHCCCCHHHHHHHCCCEEEEEE-ECCEEEEEEEECCEEEEEECCCCCCHHHHHHHHHHCCCCCC--CCCCCHHHH
Q ss_conf             888887627637888864032025687-28908999980564677306644688899999860868778--877698899
Q gi|255764509|r  235 LLAYYLATGQDAANIVEGSQGLTYAKL-HDDSLYFSCTIPNLILGCVGNGKNIPAIKNNLTALGCIEER--KTGDNARRL  311 (351)
Q Consensus       235 I~Av~lATGnD~a~v~a~~~a~t~~~~-~~~~L~g~i~lPsl~vGtVGG~t~lp~~~~~l~ilg~~~~~--~~~~~A~~L  311 (351)
                      |.|+|||||||.|++.|++.+.|-.+. .|||||++++||+++||||||||.|.+|++||+||||+|+.  .|..++++|
T Consensus       307 i~A~FLA~GQD~A~~VE~S~giT~~~~E~~GDL~~sV~lP~v~~gTvGGGT~lE~~~~~Ld~lGv~Gph~t~pg~~a~~~  386 (419)
T TIGR00533       307 IGAIFLATGQDEAHIVEGSLGITLAEVEVDGDLYFSVSLPDVPVGTVGGGTVLETQGECLDLLGVRGPHATEPGNKARKL  386 (419)
T ss_pred             HHHHHHHCCCCCHHEECCCCCEEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHHH
T ss_conf             99998741897012020122246554512784689987586102420698740525688886056789888865789999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCC
Q ss_conf             9999999988899999988078868999987260
Q gi|255764509|r  312 AAICAATVLCGELSLLAAQTNPGELMEAHLRLER  345 (351)
Q Consensus       312 a~iiAavgLAqnlaal~Al~t~G~iq~gHmkl~R  345 (351)
                      |+|+++..||+|||++.||+. ||+.|+||.|+|
T Consensus       387 A~Iv~~AVLAGELSL~~ALAA-GHL~~aH~~~~R  419 (419)
T TIGR00533       387 AEIVGAAVLAGELSLLGALAA-GHLVKAHSELGR  419 (419)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCC
T ss_conf             999999988878999999875-478886663169


No 8  
>COG1257 HMG1 Hydroxymethylglutaryl-CoA reductase [Lipid metabolism]
Probab=100.00  E-value=0  Score=674.22  Aligned_cols=320  Identities=30%  Similarity=0.421  Sum_probs=298.6

Q ss_pred             CCCCCEEEEEEEEEEECCEEECCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEEEECCHH
Q ss_conf             97641037861127603756765136774788653034538999989999999559988999967922412599858977
Q gi|255764509|r    1 MHMKKVSSISMPMRWIGPMKITGNVIQDKVKVPLATYEYPLWHSVKRGAHISMLCPDGIRATLIDERMTRSIFFETENAE   80 (351)
Q Consensus         1 m~en~IG~~~lPlGia~~l~InG~~a~~~y~VPMATeE~SvVAAas~gak~~~~~sGG~~t~~~~~~m~r~~~f~~~~~~   80 (351)
                      ||||+||+++||+||++||+|||+    +|+|||||||||||||+|||||+ ++++|||++++.++.|+|||+|.+.+..
T Consensus        61 ~iENvIG~~~lPlGia~~l~InG~----~Y~iPmATtEgalVAs~~rgaK~-i~~~GG~~~~~~~~~Mtr~~v~~~~~~~  135 (436)
T COG1257          61 NIENVIGTVQLPLGIAGPLLINGK----EYYIPMATTEGALVASASRGAKL-ITASGGATARVTEDGMTRQPVFRFVSLP  135 (436)
T ss_pred             HHHHHHCEEEEECCCCCCEEECCC----EEEEEEECCCHHHHHHHHHHHHH-HHHCCCCEEEEECCCCCCCCEEECCCHH
T ss_conf             655532236620133355488583----46876621513799998747899-9856992799834653355279437616


Q ss_pred             HHHHHHHHHH--HHHHHHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHC-CCCE
Q ss_conf             8999997617--509999999730157804788887873886999999973200672158899999999999867-9814
Q gi|255764509|r   81 MALTALQEIT--LKKAEIARVIEQTSQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQW-SYLH  157 (351)
Q Consensus        81 ~a~~~~~~i~--~~~~~i~~~a~~~sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~-~~~~  157 (351)
                      ++.+|..|++  ++++.+++.+++++||+++++|++...+++++++|.|||||||||||||+++|+++++|++++ ++.+
T Consensus       136 ~a~~~~~w~~~~e~~e~~k~~~~s~~~~~kl~~i~~~~~g~~l~l~~~~dT~DAMGmNMvn~~~E~v~~~i~~~~~~~~~  215 (436)
T COG1257         136 EAAKFAIWVKKKEIIELAKEAAPSTGRGGKLIHIEPFVEGNLLYLRFYVDTGDAMGMNMVNIATEAVAPFIEEETFGGAV  215 (436)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCEEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf             77888998502889999997522268764563456302475799999996340133478999999999999875267836


Q ss_pred             EEEECCCCCHHHHHHHHHHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHCCCCCHHHHHHH
Q ss_conf             89734774312333554310377207999987569999757389999999887866565542200220216216677888
Q gi|255764509|r  158 YGSVSGNICSDKKATAINGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQKNLIGTFLAGGIRSANAHFANMLLA  237 (351)
Q Consensus       158 ~~~ilsN~~tdkk~s~~n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~~~~~~a~t~NkgimNgI~A  237 (351)
                      +++|+||||+|||+++.|++.+|||.|.+|.++|.++++++++++++++++.            ||+.|||||+|||+++
T Consensus       216 ~~~issN~ctdkk~~a~~~~~grgk~v~ae~~~~~evv~~il~at~~a~~d~------------~rakt~~ggamnG~~g  283 (436)
T COG1257         216 LLAISSNLCTDKKPAAINSIEGRGKTVVAEATIPEEVVKKILKATPEAIVDV------------NRAKTLNGGAMNGIDG  283 (436)
T ss_pred             EEEEECCCCCCCCHHHEEEEEECCCEEECCCCCHHHHHHHHHHCCHHHHHHH------------HHHHHHHHHHHHHHHH
T ss_conf             9998245302445103478980363663344561999999984199877527------------8887633566510788


Q ss_pred             HHHHCCCCHHHHHHHCCCE-----------EEEEE-ECCEEEEEEEECCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf             8876276378888640320-----------25687-28908999980564677306644688899999860868778877
Q gi|255764509|r  238 YYLATGQDAANIVEGSQGL-----------TYAKL-HDDSLYFSCTIPNLILGCVGNGKNIPAIKNNLTALGCIEERKTG  305 (351)
Q Consensus       238 v~lATGnD~a~v~a~~~a~-----------t~~~~-~~~~L~g~i~lPsl~vGtVGG~t~lp~~~~~l~ilg~~~~~~~~  305 (351)
                      +.+|||||||+++.+.|.|           +|.+. ++++|++|+|||++.+|||||+|.+|+|++||+||||.      
T Consensus       284 fna~~aN~~~Ai~~a~gqdaA~~~e~s~~~t~~~~~~~~~L~~svtlP~~~vgt~Gggt~lp~q~~~l~ilGV~------  357 (436)
T COG1257         284 FNAHTANDVRAIEAATGQDAAQVGEYSPLITWMEDQRDGDLYGSVTLPSLVVGTGGGGTVLPTQREALKILGVA------  357 (436)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHCCCCCCEEEEEECCCCCEEEEEEECCCEEEEECCCCCCHHHHHHHHHHCCC------
T ss_conf             99887559999998707437751556774489996379807999980562367514887274389999982999------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH-CC
Q ss_conf             69889999999999888999999880788689999872-60
Q gi|255764509|r  306 DNARRLAAICAATVLCGELSLLAAQTNPGELMEAHLRL-ER  345 (351)
Q Consensus       306 ~~A~~La~iiAavgLAqnlaal~Al~t~G~iq~gHmkl-~R  345 (351)
                       ++.+|+.+++||||+|||++|++|+++| ||+|||+| ++
T Consensus       358 -ga~e~~~v~~~vgla~N~~alaalva~g-i~aGemsL~aa  396 (436)
T COG1257         358 -GAGELAGVLAAVGLAQNAAALAALVAEG-ILAGEMSLLAA  396 (436)
T ss_pred             -CCCCCHHHHCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHH
T ss_conf             -8643011220467223299999999989-87537899999


No 9  
>TIGR00532 HMG_CoA_R_NAD hydroxymethylglutaryl-CoA reductase, degradative; InterPro: IPR004553   Synonym(s): 3-hydroxy-3-methylglutaryl-coenzyme A reductase, HMG-CoA reductase.    There are two distinct classes of hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase enzymes: class I consists of eukaryotic and most archaeal enzymes (1.1.1.34 from EC), while class II consists of prokaryotic enzymes (1.1.1.88 from EC) , .   Class I HMG-CoA reductases catalyse the NADP-dependent synthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA). In vertebrates, membrane-bound HMG-CoA reductase is the rate-limiting enzyme in the biosynthesis of cholesterol and other isoprenoids. In plants, mevalonate is the precursor of all isoprenoid compounds . The reduction of HMG-CoA to mevalonate is regulated by feedback inhibition by sterols and non-sterol metabolites derived from mevalonate, including cholesterol. In archaea, HMG-CoA reductase is a cytoplasmic enzyme involved in the biosynthesis of the isoprenoids side chains of lipids . Class I HMG-CoA reductases consist of an N-terminal membrane domain (lacking in archaeal enzymes), and a C-terminal catalytic region. The catalytic region can be subdivided into three domains: an N-domain (N-terminal), a large L-domain, and a small S-domain (inserted within the L-domain). The L-domain binds the substrate, while the S-domain binds NADP.    Class II HMG-CoA reductases catalyse the reverse reaction of class I enzymes, namely the NAD-dependent synthesis of HMG-CoA from mevalonate and CoA . Some bacteria, such as Pseudomonas mevalonii, can use mevalonate as the sole carbon source. Class II enzymes lack a membrane domain. Their catalytic region is structurally related to that of class I enzymes, but it consists of only two domains: a large L-domain and a small S-domain (inserted within the L-domain). As with class I enzymes, the L-domain binds substrate, but the S-domain binds NAD (instead of NADP in class I).    This entry represents class II HMG-CoA reductases, as well as some class I enzymes from archaea. This family was built from two class II NAD-dependent enzymes from organisms closely related to Pseudomonas mevalonii, a bacterium that can use mevalonate as its sole carbon source. Some archaeal HMG-CoA reductases were found to be of bacterial origin .    This family is occasionally found together with a thiolase (IPR002155 from INTERPRO) to form a putative bifunctional acetyl-CoA acetyltransferase/HMG-CoA reductase protein .; GO: 0016616 oxidoreductase activity acting on the CH-OH group of donors NAD or NADP as acceptor, 0050662 coenzyme binding, 0015936 coenzyme A metabolic process.
Probab=100.00  E-value=0  Score=593.56  Aligned_cols=313  Identities=20%  Similarity=0.195  Sum_probs=274.3

Q ss_pred             CCCCCEEEEEEEEEEECCEEECCCCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEE-EECCH
Q ss_conf             97641037861127603756765136774788653034538999989999999559988999967922412599-85897
Q gi|255764509|r    1 MHMKKVSSISMPMRWIGPMKITGNVIQDKVKVPLATYEYPLWHSVKRGAHISMLCPDGIRATLIDERMTRSIFF-ETENA   79 (351)
Q Consensus         1 m~en~IG~~~lPlGia~~l~InG~~a~~~y~VPMATeE~SvVAAas~gak~~~~~sGG~~t~~~~~~m~r~~~f-~~~~~   79 (351)
                      ||||.||++++|+||+.||+||||    +|.+||||||||||||+|++||++ ..+||+++.-..-.|++|+|. .+.++
T Consensus        67 MIEN~IG~l~lP~GI~~Nl~I~GK----~Y~~P~A~EE~SVVAA~~~AA~~~-~~~~~~~~~~~~~~~~Gqiq~~~~~~~  141 (402)
T TIGR00532        67 MIENVIGYLELPLGIVKNLKIDGK----DYLLPIAIEESSVVAALSFAAKIL-READLFYSLYEVLLIIGQIQVIKLKSE  141 (402)
T ss_pred             HHHHEEEEEECCHHHHHHCEECCC----EEECCEEECCHHHHHHHHHHHHHH-HHCCCCEEECEEEEEEEEEEEEEECCH
T ss_conf             342000012032134410223483----231320103236999999999999-745871320102245521567875273


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-----CCCCEEEEEEEEEEEC----CEEEEEEEEEECCCCCCHHHHHHHHHHHHHHH
Q ss_conf             78999997617509999999730-----1578047888878738----86999999973200672158899999999999
Q gi|255764509|r   80 EMALTALQEITLKKAEIARVIEQ-----TSQFTRFLQLHSQIAG----NLLFLRLEFATGDASGHNMVTKAADAVMDWIL  150 (351)
Q Consensus        80 ~~a~~~~~~i~~~~~~i~~~a~~-----~sr~ggl~~i~~~~~g----~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~  150 (351)
                      .++.   ..+...+|+|++.+|.     ..||||++++++++++    .+..|++++|||||||||.+|++||.|+++|+
T Consensus       142 ~~~~---~~~~~~~D~I~~~~~~~~~~l~~~GGG~~~~~~Rvi~~~~~~~~~~~~~VD~~DAMGAN~~N~~~E~VA~FI~  218 (402)
T TIGR00532       142 KDLK---KIVLDLKDKIKERIEELLTNLVNLGGGFKDLEARVIDIKELKILKLNLIVDVKDAMGANLLNSIAEKVAEFIE  218 (402)
T ss_pred             HHHH---HHHHHCCCHHHHHHHHHHHHHHHCCCCEEEHHHHEEEEEECCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf             3556---6765236157778756326777458971341131010110246899999853301011268788877666675


Q ss_pred             HHCCCCEEEEECCCCCHHHHHHHHHHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHCCCCC
Q ss_conf             86798148973477431233355431037720799998756999975738999999988786656554220022021621
Q gi|255764509|r  151 SQWSYLHYGSVSGNICSDKKATAINGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQKNLIGTFLAGGIRSANAH  230 (351)
Q Consensus       151 ~~~~~~~~~~ilsN~~tdkk~s~~n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~~~~~~a~t~Nkg  230 (351)
                      .++|++++++|+||..++..+.+      |-+.+.-.-.     .   -+-+.-.+++.+...+-++.+++.|++|||||
T Consensus       219 ~~~G~~~~L~~~SN~~~~~ta~A------R~~~~F~~~~-----~---G~E~sWn~~~~I~L~~~~~~~~~~R~~T~NKG  284 (402)
T TIGR00532       219 LIFGYKVVLKVLSNLIAEFTAKA------RAKLVFDKLL-----I---GKEDSWNLVKKIELIYAIAAADEERAVTNNKG  284 (402)
T ss_pred             HHCCCEEEEEEECHHHHHHHHHH------HHHEEECCCC-----C---CCCCHHHHHHHHHHHHHHHHCCCCCHHHCCCC
T ss_conf             54286688753004788777650------1111101036-----8---98504788878888777743162001122785


Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHCCCE----------EEEE-EECCEEEEEEEECCEEEEEECCCCCC-HHHHHHHHHHCC
Q ss_conf             66778888876276378888640320----------2568-72890899998056467730664468-889999986086
Q gi|255764509|r  231 FANMLLAYYLATGQDAANIVEGSQGL----------TYAK-LHDDSLYFSCTIPNLILGCVGNGKNI-PAIKNNLTALGC  298 (351)
Q Consensus       231 imNgI~Av~lATGnD~a~v~a~~~a~----------t~~~-~~~~~L~g~i~lPsl~vGtVGG~t~l-p~~~~~l~ilg~  298 (351)
                      |||||+|++||||||+|++|+|+|.|          |+++ ..++.|+|+||+| |.|||.||.|+. |.++.+||||+|
T Consensus       285 IMNGI~~~~~AT~ND~RA~EA~~H~yA~~~GkY~PL~~y~v~~~~~LVG~IEIP-l~VG~~GG~~~~N~~~~~SlKIl~V  363 (402)
T TIGR00532       285 IMNGISALMLATFNDFRALEASVHKYAAKSGKYKPLSKYEVDRDNALVGEIEIP-LAVGVKGGVIKVNELAKLSLKILNV  363 (402)
T ss_pred             CHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCEEEEEECC-CCCCCCCCEEEECHHHHHHHHHHCC
T ss_conf             122257787531662567775444565437653664305662378425448624-0126316704433377766676055


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHC
Q ss_conf             8778877698899999999998889999998807886899998726
Q gi|255764509|r  299 IEERKTGDNARRLAAICAATVLCGELSLLAAQTNPGELMEAHLRLE  344 (351)
Q Consensus       299 ~~~~~~~~~A~~La~iiAavgLAqnlaal~Al~t~G~iq~gHmkl~  344 (351)
                             .++.||+.|.+|+||||||||||||+++| ||+|||+|+
T Consensus       364 -------N~~~El~~~~~~~GLA~NFAALRALA~~G-IQ~GHM~LH  401 (402)
T TIGR00532       364 -------NSKEELIRVLAALGLASNFAALRALAFEG-IQKGHMRLH  401 (402)
T ss_pred             -------CCHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCC
T ss_conf             -------77889999999851677899999988515-221410206


No 10 
>COG1257 HMG1 Hydroxymethylglutaryl-CoA reductase [Lipid metabolism]
Probab=99.09  E-value=7.3e-11  Score=87.40  Aligned_cols=124  Identities=38%  Similarity=0.359  Sum_probs=81.2

Q ss_pred             HHHHHHCCCHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHC---CC---------EEEEEEE--CCEEEEEE-EECC----
Q ss_conf             5655422002202162166778888876276378888640---32---------0256872--89089999-8056----
Q gi|255764509|r  214 NLIGTFLAGGIRSANAHFANMLLAYYLATGQDAANIVEGS---QG---------LTYAKLH--DDSLYFSC-TIPN----  274 (351)
Q Consensus       214 ~~~a~~~~~~a~t~NkgimNgI~Av~lATGnD~a~v~a~~---~a---------~t~~~~~--~~~L~g~i-~lPs----  274 (351)
                      ++.+.++.+.. ++|.|.+|-+.|+++|||||.+++.+++   .-         |....+.  ...-.|.. .+|.    
T Consensus       272 t~~ggamnG~~-gfna~~aN~~~Ai~~a~gqdaA~~~e~s~~~t~~~~~~~~~L~~svtlP~~~vgt~Gggt~lp~q~~~  350 (436)
T COG1257         272 TLNGGAMNGID-GFNAHTANDVRAIEAATGQDAAQVGEYSPLITWMEDQRDGDLYGSVTLPSLVVGTGGGGTVLPTQREA  350 (436)
T ss_pred             HHHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCHHHHCCCCCCEEEEEECCCCCEEEEEEECCCEEEEECCCCCCHHHHHH
T ss_conf             63356651078-89988755999999870743775155677448999637980799998056236751488727438999


Q ss_pred             E-EEEEECCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCC
Q ss_conf             4-67730664468889999986086877887769889999999999888999999880788689999872603367
Q gi|255764509|r  275 L-ILGCVGNGKNIPAIKNNLTALGCIEERKTGDNARRLAAICAATVLCGELSLLAAQTNPGELMEAHLRLERMHLN  349 (351)
Q Consensus       275 l-~vGtVGG~t~lp~~~~~l~ilg~~~~~~~~~~A~~La~iiAavgLAqnlaal~Al~t~G~iq~gHmkl~R~~~~  349 (351)
                      | .+|+-|++.       --.++-+-++   ..|+..|++|+++..|+++++++.+++. ++.-++|.+|+|...+
T Consensus       351 l~ilGV~ga~e-------~~~v~~~vgl---a~N~~alaalva~gi~aGemsL~aal~A-~~lg~ah~el~r~~~~  415 (436)
T COG1257         351 LKILGVAGAGE-------LAGVLAAVGL---AQNAAALAALVAEGILAGEMSLLAALAA-GHLGAAHDELGRVVER  415 (436)
T ss_pred             HHHHCCCCCCC-------CHHHHCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_conf             99829998643-------0112204672---2329999999998987537899999987-7765668877389876


No 11 
>TIGR02248 mutH_TIGR DNA mismatch repair endonuclease MutH; InterPro: IPR004230 MutS, MutL and MutH are the three essential proteins for initiation of methyl-directed DNA mismatch repair to correct mistakes made during DNA replication in Escherichia coli. MutH cleaves a newly synthesized and unmethylated daughter strand 5' to the sequence d(GATC) in a hemi-methylated duplex. Activation of MutH requires the recognition of a DNA mismatch by MutS and MutL .; GO: 0004519 endonuclease activity, 0006304 DNA modification.
Probab=82.31  E-value=2.5  Score=21.36  Aligned_cols=69  Identities=19%  Similarity=0.118  Sum_probs=48.9

Q ss_pred             CEEEEEECCCEEEEEEEEECCHHHHHHHHHHHHHHHHHH-HHHHH-HCCCCEEEEEEEEEEECCEEEEEEE
Q ss_conf             889999679224125998589778999997617509999-99973-0157804788887873886999999
Q gi|255764509|r   58 GIRATLIDERMTRSIFFETENAEMALTALQEITLKKAEI-ARVIE-QTSQFTRFLQLHSQIAGNLLFLRLE  126 (351)
Q Consensus        58 G~~t~~~~~~m~r~~~f~~~~~~~a~~~~~~i~~~~~~i-~~~a~-~~sr~ggl~~i~~~~~g~~v~l~~~  126 (351)
                      |-+.-.+.+...|.|.|.-.+..+-..+++.=+|-.|.| +...+ =|+|||.++++.+......+..+++
T Consensus       121 G~R~ipl~~r~vG~p~lW~p~~~~~~~Lk~DWEElMdLIvlGkve~itarhGevLQ~rpKaaN~~a~t~~I  191 (220)
T TIGR02248       121 GERHIPLLERRVGEPLLWEPSSEQERQLKQDWEELMDLIVLGKVEKITARHGEVLQLRPKAANSKALTKFI  191 (220)
T ss_pred             CCCEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCEEEECCCCCCCEEEEEEE
T ss_conf             24011103451477300598979999887537998878883313223341154010062000461110011


No 12 
>PRK09509 fieF ferrous iron efflux protein F; Reviewed
Probab=68.32  E-value=8.5  Score=18.01  Aligned_cols=64  Identities=17%  Similarity=0.196  Sum_probs=48.2

Q ss_pred             HHHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             9999997301578047888878738869999999732006721588999999999998679814
Q gi|255764509|r   94 AEIARVIEQTSQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQWSYLH  157 (351)
Q Consensus        94 ~~i~~~a~~~sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~~~~~  157 (351)
                      ++|++++.+...--++.++.++..|+++++++.+...+-|=---.-.++|.+-+.|++.+|...
T Consensus       216 ~~I~~~i~~~~gV~~vh~lr~r~~G~~~~vd~hI~v~~~lsv~eaH~I~~~ve~~i~~~~~~~~  279 (300)
T PRK09509        216 QEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQLHLEMEDNLPLVQAHMVADQVEQALLRRFPGSD  279 (300)
T ss_pred             HHHHHHHHCCCCCCCCEEEEEEEECCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999999728898770268989858929999999989799899999999999999997679981


No 13 
>pfam01545 Cation_efflux Cation efflux family. Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells.
Probab=67.68  E-value=8.8  Score=17.93  Aligned_cols=66  Identities=11%  Similarity=0.115  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             999999973015780478888787388699999997320067215889999999999986798148
Q gi|255764509|r   93 KAEIARVIEQTSQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQWSYLHY  158 (351)
Q Consensus        93 ~~~i~~~a~~~sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~~~~~~  158 (351)
                      .+++.+..+....--++.++..+..|+.+++++.+...+.|--.-.....+.+-+.+++.+|+...
T Consensus       196 ~~~i~~~i~~~~~v~~v~~~~~~~~G~~~~v~v~i~v~~~~~~~~~~~i~~~i~~~l~~~~~~i~~  261 (273)
T pfam01545       196 VDKIRKALEALPGVLGVHDLRVWKSGPTLLVEIHIEVDPDLTVEEAHEIADEIEKALKEKFPGIVH  261 (273)
T ss_pred             HHHHHHHHHCCCCCEEEEEEEEEEECCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf             999999996389950343579999689599999999899998999999999999999986899886


No 14 
>COG0053 MMT1 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=65.10  E-value=9.9  Score=17.62  Aligned_cols=71  Identities=13%  Similarity=0.185  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             09999999730157804788887873886999999973200672158899999999999867981489734
Q gi|255764509|r   92 KKAEIARVIEQTSQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILSQWSYLHYGSVS  162 (351)
Q Consensus        92 ~~~~i~~~a~~~sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~~~~~~~~~~il  162 (351)
                      ..++++++..+...--++.++.++..|+.+++++.+...+.|-.--.-.+++.+.+.|++.++......|.
T Consensus       216 ~~~~i~~~i~~~~~V~~v~~lr~R~~G~~~~id~~i~v~~~ls~~eah~I~~~ie~~i~~~~~~~~~v~Ih  286 (304)
T COG0053         216 DLEKIRAIILSVPGVKGVHDLRTRKSGSRIFIDVHIEVDPDLSLEEAHEIADEVEKRIKKEFPKVADVTIH  286 (304)
T ss_pred             HHHHHHHHHHCCCCCCCCHHEEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             99999999846645523010156665887999999971999988889999999999999756877528999


No 15 
>TIGR01162 purE phosphoribosylaminoimidazole carboxylase, catalytic subunit; InterPro: IPR000031   Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain . The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme .; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process, 0009320 phosphoribosylaminoimidazole carboxylase complex.
Probab=64.67  E-value=3.7  Score=20.30  Aligned_cols=53  Identities=19%  Similarity=0.066  Sum_probs=39.3

Q ss_pred             CCEEEEEEEECC-EEEEEECCCCC--CHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             890899998056-46773066446--88899999860868778877698899999999998889
Q gi|255764509|r  263 DDSLYFSCTIPN-LILGCVGNGKN--IPAIKNNLTALGCIEERKTGDNARRLAAICAATVLCGE  323 (351)
Q Consensus       263 ~~~L~g~i~lPs-l~vGtVGG~t~--lp~~~~~l~ilg~~~~~~~~~~A~~La~iiAavgLAqn  323 (351)
                      -|.|+=++-||+ +||+||+=+-.  -..+-.+.+||+.+.        .+|++=+...=..+.
T Consensus        93 ~DSLlSiVQMP~GvPVATvaig~aGA~NAAllAa~ILa~~~--------~~l~~kl~~~~~~~~  148 (159)
T TIGR01162        93 LDSLLSIVQMPAGVPVATVAIGNAGAKNAALLAAQILAIKD--------PELAEKLKEYRENQK  148 (159)
T ss_pred             HHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCC--------HHHHHHHHHHHHHHH
T ss_conf             13544543075897465300371327889999999972689--------889999999999999


No 16 
>pfam09551 Spore_II_R Stage II sporulation protein R (spore_II_R). SpoIIR is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation.
Probab=51.54  E-value=17  Score=16.18  Aligned_cols=58  Identities=22%  Similarity=0.247  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHC-CCCEEEEEEE----------------EEEECCEEEEEEEEEECCCCCCH
Q ss_conf             897789999976175099999997301-5780478888----------------78738869999999732006721
Q gi|255764509|r   77 ENAEMALTALQEITLKKAEIARVIEQT-SQFTRFLQLH----------------SQIAGNLLFLRLEFATGDASGHN  136 (351)
Q Consensus        77 ~~~~~a~~~~~~i~~~~~~i~~~a~~~-sr~ggl~~i~----------------~~~~g~~v~l~~~~dt~DAMGaN  136 (351)
                      .+..+..+...|+.+|.++|.++|+.+ .+-|.--+++                +...|+|--|+  +.-|++-|+|
T Consensus        39 ~~~~s~~ea~~~i~~~l~eIe~~a~~~l~~~G~~y~v~v~~~~~~FPtK~YG~~~~PaG~YeAlr--I~IG~g~G~N  113 (132)
T pfam09551        39 EDSKSIEEARRVIKENLPEIEEIAEKVIKEEGYDYPVKVELGKFSFPTKLYGNITLPAGEYEALR--ITIGEGEGAN  113 (132)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCEECCCCCEEEEE--EEECCCCCCC
T ss_conf             55999999999999716999999999999858998669999877589864277751487468999--9942757762


No 17 
>TIGR02837 spore_II_R stage II sporulation protein R; InterPro: IPR014202    This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation , ..
Probab=44.84  E-value=11  Score=17.29  Aligned_cols=48  Identities=23%  Similarity=0.343  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHHHHC-CCCEEEEEEEEEE----------------ECCEEEEEEEEEECCCCCCH
Q ss_conf             76175099999997301-5780478888787----------------38869999999732006721
Q gi|255764509|r   87 QEITLKKAEIARVIEQT-SQFTRFLQLHSQI----------------AGNLLFLRLEFATGDASGHN  136 (351)
Q Consensus        87 ~~i~~~~~~i~~~a~~~-sr~ggl~~i~~~~----------------~g~~v~l~~~~dt~DAMGaN  136 (351)
                      .-|.++-.+|.++|+++ +.-|--.++++..                .|.|=-+++  .-||+-|+|
T Consensus        87 ~~i~~~l~eI~~iA~~~~~~~G~~y~v~v~l~~~~FPtK~YGn~vlPaG~Y~A~rI--liG~g~G~N  151 (172)
T TIGR02837        87 RVIKENLPEIEKIAESVIKKEGADYKVRVELGKVSFPTKLYGNIVLPAGKYEALRI--LIGEGEGAN  151 (172)
T ss_pred             HHHHHCCCCHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCCCCCCCEEEEEE--EEECCCCCC
T ss_conf             99985181278999999996489832677652345686444441155873278777--874569875


No 18 
>pfam11281 DUF3083 Protein of unknown function (DUF3083). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=41.92  E-value=5.5  Score=19.22  Aligned_cols=91  Identities=14%  Similarity=0.068  Sum_probs=38.5

Q ss_pred             CEEEEEEEECHHHHHHHHCC-CHH---HHHHHHHHHHHHHHHCCCHHHCCCCC--HHHHHHHHHHHCCCCHHHHH-----
Q ss_conf             07999987569999757389-999---99988786656554220022021621--66778888876276378888-----
Q gi|255764509|r  182 KNFVAEITINRAICQKYLRT-SPE---KIILLNTQKNLIGTFLAGGIRSANAH--FANMLLAYYLATGQDAANIV-----  250 (351)
Q Consensus       182 ~~V~Ae~~i~~~~~~~~l~~-~~e---~~~~~~~~~~~~a~~~~~~a~t~Nkg--imNgI~Av~lATGnD~a~v~-----  250 (351)
                      -+|++..-+.+++.+..+.- .++   .+.+++.... +.....+   ..|.+  |+||...++=-.--|--...     
T Consensus       162 tYatv~lPl~R~lk~~~~~e~~~~dy~~lYq~l~D~F-~~a~~~~---qL~~~AmvANGl~PlVRns~~e~v~~~~Elqm  237 (316)
T pfam11281       162 TYATVSLPLSRRLKQQVLPETNSQDYGPLYQKLEDAF-IQAAKKK---QLNRVAMVANGLTPLVRNSKDENVDGTGELQM  237 (316)
T ss_pred             EEEEEECHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-HHHHHHC---CCCEEEEEECCCCCEEECCCCCCCCCCCCEEE
T ss_conf             6999961223899986164458640078999999999-9998754---34402345458753364363122345661578


Q ss_pred             -------HHCCCEEEEEEECCEEEEEEEECCEEEEE
Q ss_conf             -------64032025687289089999805646773
Q gi|255764509|r  251 -------EGSQGLTYAKLHDDSLYFSCTIPNLILGC  279 (351)
Q Consensus       251 -------a~~~a~t~~~~~~~~L~g~i~lPsl~vGt  279 (351)
                             +..+-+..|  +.+.|+-++.+- +.-|-
T Consensus       238 lgfdp~~~~~q~~~~W--~~~~LVdtv~fv-~~A~~  270 (316)
T pfam11281       238 LGFDPNAEEPQYIGHW--DADKLVDTVYFV-FVAGK  270 (316)
T ss_pred             EECCCCCCCCCHHHCC--CCCHHEEEEEEE-EEECC
T ss_conf             8528775652044302--500103578999-99657


No 19 
>TIGR01415 trpB_rel pyridoxal-phosphate dependent TrpB-like enzyme; InterPro: IPR006316   These sequences represent a family of pyridoxal-phosphate dependent enzymes that are closely related to the beta subunit of tryptophan synthase. ; GO: 0004834 tryptophan synthase activity, 0030170 pyridoxal phosphate binding, 0000162 tryptophan biosynthetic process.
Probab=37.25  E-value=17  Score=16.07  Aligned_cols=36  Identities=11%  Similarity=0.147  Sum_probs=23.5

Q ss_pred             EEEEEEEEECCE--EEEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf             788887873886--9999999732006721588999999
Q gi|255764509|r  109 FLQLHSQIAGNL--LFLRLEFATGDASGHNMVTKAADAV  145 (351)
Q Consensus       109 l~~i~~~~~g~~--v~l~~~~dt~DAMGaNmvnt~~E~v  145 (351)
                      .+.++-. +|.-  +-+++...-----|.--+||+.=++
T Consensus        75 A~~LEe~-Lgt~gr~rIyyK~E~~~~tGSHK~NTA~AqA  112 (426)
T TIGR01415        75 AKGLEEL-LGTPGRARIYYKYESVSPTGSHKINTAIAQA  112 (426)
T ss_pred             HHHHHHH-HCCCCEEEEEEEECCCCCCCCCCHHHHHHHH
T ss_conf             5444786-2899527898740575778885244799999


No 20 
>PTZ00186 heat shock 70 kDa precursor protein; Provisional
Probab=34.08  E-value=25  Score=15.04  Aligned_cols=48  Identities=8%  Similarity=0.081  Sum_probs=24.0

Q ss_pred             CEEEEEEEEEEECCEEEEEEEEEECCCC--CCHHHHHHHHHHHHHHHHHCC
Q ss_conf             8047888878738869999999732006--721588999999999998679
Q gi|255764509|r  106 FTRFLQLHSQIAGNLLFLRLEFATGDAS--GHNMVTKAADAVMDWILSQWS  154 (351)
Q Consensus       106 ~ggl~~i~~~~~g~~v~l~~~~dt~DAM--GaNmvnt~~E~v~~~i~~~~~  154 (351)
                      |||-.|+..-...+- .+.+.-..||..  |.++=+...+.++..+.+..+
T Consensus       220 GGGTfDVSIl~~~~g-~feVlat~GD~~LGG~DfD~~i~~~~~~~f~~~~~  269 (657)
T PTZ00186        220 GGGTFDISVLEIAGG-VFEVKATNGDTHLGGEDFDLALSDYILEEFRKTSG  269 (657)
T ss_pred             CCCEEEEEEEEEECC-EEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             996178899999788-68998446887767689999999999999988639


No 21 
>PRK05183 hscA chaperone protein HscA; Provisional
Probab=33.54  E-value=26  Score=14.94  Aligned_cols=22  Identities=18%  Similarity=0.440  Sum_probs=15.8

Q ss_pred             EEEEECCCCCCHHHHHHHH-HHC
Q ss_conf             6773066446888999998-608
Q gi|255764509|r  276 ILGCVGNGKNIPAIKNNLT-ALG  297 (351)
Q Consensus       276 ~vGtVGG~t~lp~~~~~l~-ilg  297 (351)
                      .|=.|||+|+.|..|..++ .+|
T Consensus       336 ~ViLVGGSTRiP~Vq~~v~~~Fg  358 (621)
T PRK05183        336 EVVMVGGSTRVPLVREAVGEFFG  358 (621)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHC
T ss_conf             99992885456689999999859


No 22 
>TIGR02350 prok_dnaK chaperone protein DnaK; InterPro: IPR012725    Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes, the grpE protein is a co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.    Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for the Mycoplasma sequence) found clustered with other genes of this systems. This entry excludes DnaK homologues that are not DnaK itself, such as the heat shock cognate protein HscA (IPR010236 from INTERPRO). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of DnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; the lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=32.51  E-value=33  Score=14.31  Aligned_cols=48  Identities=13%  Similarity=0.102  Sum_probs=36.4

Q ss_pred             CCEEEEEEEEEEECCEEEEEEEEEECCCC--CCHHHHHHHHHHHHHHHHHC
Q ss_conf             78047888878738869999999732006--72158899999999999867
Q gi|255764509|r  105 QFTRFLQLHSQIAGNLLFLRLEFATGDAS--GHNMVTKAADAVMDWILSQW  153 (351)
Q Consensus       105 r~ggl~~i~~~~~g~~v~l~~~~dt~DAM--GaNmvnt~~E~v~~~i~~~~  153 (351)
                      -|||--||..-.+|+- .+.+.-.-||..  |-||=+.+.+.+...+....
T Consensus       190 LGGGTFDvSILe~gdG-~feV~sT~GDt~LGGdDFD~~Iidwl~~~fk~~~  239 (598)
T TIGR02350       190 LGGGTFDVSILEIGDG-VFEVKSTAGDTHLGGDDFDERIIDWLADEFKKEE  239 (598)
T ss_pred             CCCCCEEEEEEEECCC-EEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             5888324688875686-8999851688878752057999999999988763


No 23 
>TIGR01991 HscA Fe-S protein assembly chaperone HscA; InterPro: IPR010236   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents the HscA chaperone protein from the SUF system. HscA (or Hsc66) is a specialised bacterial Hsp70-class molecular chaperone that participates in the assembly of iron-sulphur cluster proteins. HscA resembles DnaK, but belongs to a separate clade. HscA interacts with IscU, which is believed to serve as a template for Fe-S cluster formation. The HscA-IscU interaction is facilitated by the J-type co-chaperone protein HscB (or Hsc20), which binds to both HscA and IscU, bringing them into contact with each other. HscA recognises a conserved LPPVK sequence motif at positions 99-103 of IscU .; GO: 0005524 ATP binding, 0016887 ATPase activity, 0051082 unfolded protein binding, 0016226 iron-sulfur cluster assembly.
Probab=32.21  E-value=23  Score=15.29  Aligned_cols=53  Identities=13%  Similarity=0.181  Sum_probs=30.2

Q ss_pred             HHHHHHHHHCCCCHHHHHHHCCCEEEEEEECCEEEEEEEECCEEEEEECCCCCCHHHHHHH-HHHCCC
Q ss_conf             7788888762763788886403202568728908999980564677306644688899999-860868
Q gi|255764509|r  233 NMLLAYYLATGQDAANIVEGSQGLTYAKLHDDSLYFSCTIPNLILGCVGNGKNIPAIKNNL-TALGCI  299 (351)
Q Consensus       233 NgI~Av~lATGnD~a~v~a~~~a~t~~~~~~~~L~g~i~lPsl~vGtVGG~t~lp~~~~~l-~ilg~~  299 (351)
                      |-|++++-=|+.-.|..      +-..=++.+.+        ..|=-|||+|+.|.+|... ++.||.
T Consensus       313 ~li~~LV~rtl~~crrA------lkDaGV~~~e~--------~~VvmVGGSTRvp~Vr~~VaelFg~~  366 (628)
T TIGR01991       313 ELIEPLVKRTLLPCRRA------LKDAGVEKEEV--------KGVVMVGGSTRVPKVREAVAELFGRE  366 (628)
T ss_pred             HHHHHHHHHHHHHHHHH------HHHCCCCHHHC--------CEEEEECCCCCHHHHHHHHHHHHCCC
T ss_conf             89999998521678888------87527883253--------26578626546167999998863778


No 24 
>TIGR01826 CofD_related conserved hypothetical protein; InterPro: IPR010119   This entry represents a subfamily of conserved hypothetical proteins that forms a sister group to the family of CofD, (IPR010115 from INTERPRO), LPPG:Fo 2-phospho-L-lactate transferase, an enzyme of cytochrome F420 biosynthesis..
Probab=31.77  E-value=30  Score=14.63  Aligned_cols=122  Identities=13%  Similarity=0.169  Sum_probs=57.6

Q ss_pred             EEECCCCCCCCEEEEEEEHHHHHHHHH---HHHH---HHHHHCCCCEEEE-EECCCE-EEEEEEEE--CCHHHH-HHHHH
Q ss_conf             567651367747886530345389999---8999---9999559988999-967922-41259985--897789-99997
Q gi|255764509|r   19 MKITGNVIQDKVKVPLATYEYPLWHSV---KRGA---HISMLCPDGIRAT-LIDERM-TRSIFFET--ENAEMA-LTALQ   87 (351)
Q Consensus        19 l~InG~~a~~~y~VPMATeE~SvVAAa---s~ga---k~~~~~sGG~~t~-~~~~~m-~r~~~f~~--~~~~~a-~~~~~   87 (351)
                      |.|+|+      .+||...--.|+|-+   -.|-   . .   .|=.... .....- ++-+.+.-  +|+.-. .+...
T Consensus       117 L~v~G~------vlP~~~~~v~L~A~~Gle~DG~mfr~-V---~GE~~I~e~~~~~~Pi~rv~LePal~~~~a~a~eAv~  186 (331)
T TIGR01826       117 LKVKGR------VLPMTEHPVQLVAEFGLEEDGRMFRV-V---RGESNIPELKKGGKPIERVRLEPALEDVKALAREAVE  186 (331)
T ss_pred             HCCCCC------EEECCCCCCCEEEEECCCCCCCEEEE-E---ECCEEEEHHHCCCCCEEEEEECCCCCCCCCCCHHHHH
T ss_conf             356552------54068875431143050449948999-8---4552100402588880488833678884875158999


Q ss_pred             HHHHHHH----------------HHHHHHHHCCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             6175099----------------999997301578047888878738869999999732006721588999999999998
Q gi|255764509|r   88 EITLKKA----------------EIARVIEQTSQFTRFLQLHSQIAGNLLFLRLEFATGDASGHNMVTKAADAVMDWILS  151 (351)
Q Consensus        88 ~i~~~~~----------------~i~~~a~~~sr~ggl~~i~~~~~g~~v~l~~~~dt~DAMGaNmvnt~~E~v~~~i~~  151 (351)
                      .|++=--                .+.++++...+ -+...        -++..+.=..|++-|--.     |.=-++|.+
T Consensus       187 aI~eADlIilGPGSLyTSI~PnLLvp~i~~A~~~-s~A~k--------vYV~NlmtqpGET~~~~~-----~dHv~~l~~  252 (331)
T TIGR01826       187 AIREADLIILGPGSLYTSIIPNLLVPEIAEALRE-SKAPK--------VYVCNLMTQPGETDGFSV-----EDHVKALHR  252 (331)
T ss_pred             HHHHCCEEEECCCHHHHHHHHHHHHHHHHHHHHH-CCCCE--------EEEECCCCCCCCCCCCCH-----HHHHHHHHH
T ss_conf             9966692787772457774243216789999972-89989--------997335668886647728-----999999998


Q ss_pred             HCCCCEEEEECCC
Q ss_conf             6798148973477
Q gi|255764509|r  152 QWSYLHYGSVSGN  164 (351)
Q Consensus       152 ~~~~~~~~~ilsN  164 (351)
                      +.+....-.++-|
T Consensus       253 h~G~~~iD~Vlvn  265 (331)
T TIGR01826       253 HLGKPFIDVVLVN  265 (331)
T ss_pred             HCCCCCCCEEEEC
T ss_conf             6689834478717


No 25 
>PRK13411 molecular chaperone DnaK; Provisional
Probab=31.51  E-value=30  Score=14.57  Aligned_cols=20  Identities=25%  Similarity=0.531  Sum_probs=15.2

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q ss_conf             77306644688899999860
Q gi|255764509|r  277 LGCVGNGKNIPAIKNNLTAL  296 (351)
Q Consensus       277 vGtVGG~t~lp~~~~~l~il  296 (351)
                      |=.|||+|+.|..|..++=+
T Consensus       331 ViLVGGSTRIP~Vq~~v~~~  350 (655)
T PRK13411        331 IILVGGSTRIPAVQEAIQQF  350 (655)
T ss_pred             EEEECCCCCCHHHHHHHHHH
T ss_conf             99988814657999999998


No 26 
>TIGR03143 AhpF_homolog putative alkyl hydroperoxide reductase F subunit. This family of thioredoxin reductase homologs is found adjacent to alkylhydroperoxide reductase C subunit predominantly in cases where there is only one C subunit in the genome and that genome is lacking the F subunit partner (also a thioredcxin reductase homolog) that is usually found (TIGR03140).
Probab=31.25  E-value=13  Score=16.76  Aligned_cols=14  Identities=7%  Similarity=-0.071  Sum_probs=7.2

Q ss_pred             HHHHHHCCCCCCCC
Q ss_conf             99986086877887
Q gi|255764509|r  291 NNLTALGCIEERKT  304 (351)
Q Consensus       291 ~~l~ilg~~~~~~~  304 (351)
                      .-|.++++.|++++
T Consensus       449 ~vlal~~~~g~~~~  462 (555)
T TIGR03143       449 FILALYNAAGPGQP  462 (555)
T ss_pred             HHHHHHHCCCCCCC
T ss_conf             99999853799989


No 27 
>PRK01433 hscA chaperone protein HscA; Provisional
Probab=31.14  E-value=31  Score=14.49  Aligned_cols=22  Identities=36%  Similarity=0.436  Sum_probs=15.8

Q ss_pred             EEEEECCCCCCHHHHHHHH-HHC
Q ss_conf             6773066446888999998-608
Q gi|255764509|r  276 ILGCVGNGKNIPAIKNNLT-ALG  297 (351)
Q Consensus       276 ~vGtVGG~t~lp~~~~~l~-ilg  297 (351)
                      .|=-|||+|+.|..|..++ ..|
T Consensus       311 ~ViLVGGsTRiP~Vq~~l~~~Fg  333 (595)
T PRK01433        311 GVILVGGATRIPLIKDELYKAFK  333 (595)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHC
T ss_conf             48996785545899999999858


No 28 
>CHL00094 dnaK heat shock protein 70
Probab=31.00  E-value=30  Score=14.54  Aligned_cols=21  Identities=38%  Similarity=0.586  Sum_probs=14.1

Q ss_pred             EEEECCCCCCHHHHHHHH-HHC
Q ss_conf             773066446888999998-608
Q gi|255764509|r  277 LGCVGNGKNIPAIKNNLT-ALG  297 (351)
Q Consensus       277 vGtVGG~t~lp~~~~~l~-ilg  297 (351)
                      |=.|||+|++|..|..++ ..|
T Consensus       332 ViLVGGstRiP~V~~~l~~~fg  353 (622)
T CHL00094        332 VVLVGGSTRIPAIQELVKSLLG  353 (622)
T ss_pred             EEEECCCCCCHHHHHHHHHHHC
T ss_conf             9993881256789999999858


No 29 
>TIGR01506 ribC_arch riboflavin synthase; InterPro: IPR006399   These archaeal proteins, bacterial riboflavin biosynthesis alpha chain, catalyze the final step in riboflavin biosynthesis. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain. ; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process.
Probab=30.49  E-value=36  Score=14.10  Aligned_cols=48  Identities=23%  Similarity=0.329  Sum_probs=27.9

Q ss_pred             CEEEEEEEECCEEEEEECCCCC-CHHH-HHHHHHHCCCC------CCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             9089999805646773066446-8889-99998608687------7887769889999999999888
Q gi|255764509|r  264 DSLYFSCTIPNLILGCVGNGKN-IPAI-KNNLTALGCIE------ERKTGDNARRLAAICAATVLCG  322 (351)
Q Consensus       264 ~~L~g~i~lPsl~vGtVGG~t~-lp~~-~~~l~ilg~~~------~~~~~~~A~~La~iiAavgLAq  322 (351)
                      +.=+..-|.|         |++ ||.+ |--|+=.||..      .|.  ..+.+|+-+.||+||.+
T Consensus        28 gi~i~R~TVP---------GIKDLP~AaKklleE~GCe~VitLGwvG~--~ekDklsy~~aS~GLi~   83 (152)
T TIGR01506        28 GIKIVRRTVP---------GIKDLPVAAKKLLEEKGCEIVITLGWVGR--EEKDKLSYLAASVGLII   83 (152)
T ss_pred             CCCEEEEECC---------CCCCCHHHHHHHHCCCCCCEEEECCCCCC--CHHHHHHHHHHHHHHHH
T ss_conf             9635751068---------95044678876412168855886688996--02478899988788865


No 30 
>COG0041 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]
Probab=29.70  E-value=22  Score=15.38  Aligned_cols=38  Identities=21%  Similarity=0.195  Sum_probs=30.3

Q ss_pred             CEEEEEEEEC-CEEEEEECCCCCCHHHHHHHHHHCCCCC
Q ss_conf             9089999805-6467730664468889999986086877
Q gi|255764509|r  264 DSLYFSCTIP-NLILGCVGNGKNIPAIKNNLTALGCIEE  301 (351)
Q Consensus       264 ~~L~g~i~lP-sl~vGtVGG~t~lp~~~~~l~ilg~~~~  301 (351)
                      |.|+-.+.|| .+||+||+=+-.-...-.+.+||+.+.+
T Consensus        97 DSL~SiVQMP~GiPVaTvaIg~a~NAallAa~iLa~~d~  135 (162)
T COG0041          97 DSLLSIVQMPAGVPVATVAIGNAANAALLAAQILAIKDP  135 (162)
T ss_pred             HHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHHHCCCCH
T ss_conf             877887218999736887606133189999999837998


No 31 
>PRK13410 molecular chaperone DnaK; Provisional
Probab=29.28  E-value=35  Score=14.20  Aligned_cols=22  Identities=18%  Similarity=0.363  Sum_probs=15.8

Q ss_pred             EEEEECCCCCCHHHHHHH-HHHC
Q ss_conf             677306644688899999-8608
Q gi|255764509|r  276 ILGCVGNGKNIPAIKNNL-TALG  297 (351)
Q Consensus       276 ~vGtVGG~t~lp~~~~~l-~ilg  297 (351)
                      .|=.|||+|+.|..|..+ ++.|
T Consensus       331 ~VILVGGSTRIP~Vq~~V~e~FG  353 (719)
T PRK13410        331 EVVLVGGSTRMPMVKQLVRSLID  353 (719)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHC
T ss_conf             99997882554889999999849


No 32 
>TIGR02967 guan_deamin guanine deaminase; InterPro: IPR014311   This entry describes guanine deaminase, which hydrolyzes guanine to xanthine and ammonia. Xanthine can then be converted to urate by xanthine dehydrogenase. In some bacteria, the guanine deaminase gene is found near the xdhABC genes for xanthine dehydrogenase. Non-homologous forms of guanine deaminase also exist, as well as more distantly related homologs which are not included in this entry. .
Probab=28.38  E-value=39  Score=13.87  Aligned_cols=43  Identities=16%  Similarity=0.160  Sum_probs=27.0

Q ss_pred             EEEEEECC--EEEEE-EEEC-CEEEEE-ECCCCC---CHHHHHHHHHHCCC
Q ss_conf             25687289--08999-9805-646773-066446---88899999860868
Q gi|255764509|r  257 TYAKLHDD--SLYFS-CTIP-NLILGC-VGNGKN---IPAIKNNLTALGCI  299 (351)
Q Consensus       257 t~~~~~~~--~L~g~-i~lP-sl~vGt-VGG~t~---lp~~~~~l~ilg~~  299 (351)
                      +....-.|  +|.-. ...+ .+-+|| |||||+   |-+-+++.|++...
T Consensus       282 SNLFLGSGlF~L~~a~~~~~v~vGlGTDvGgGtSfSmL~t~~eAyKv~ql~  332 (426)
T TIGR02967       282 SNLFLGSGLFDLKKAVLEHGVRVGLGTDVGGGTSFSMLQTLNEAYKVSQLQ  332 (426)
T ss_pred             HHHHHHHHCCCHHHHHHHCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             444653302446999975797587740665245478999999999997416


No 33 
>pfam00012 HSP70 Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region.
Probab=27.94  E-value=37  Score=14.03  Aligned_cols=21  Identities=29%  Similarity=0.523  Sum_probs=14.7

Q ss_pred             EEEECCCCCCHHHHHHHH-HHC
Q ss_conf             773066446888999998-608
Q gi|255764509|r  277 LGCVGNGKNIPAIKNNLT-ALG  297 (351)
Q Consensus       277 vGtVGG~t~lp~~~~~l~-ilg  297 (351)
                      |=.|||+|++|..|..++ .+|
T Consensus       329 ViLvGGssRiP~Vq~~l~~~fg  350 (598)
T pfam00012       329 VVLVGGSTRIPAVQELVKEFFG  350 (598)
T ss_pred             EEECCCCCCCHHHHHHHHHHHC
T ss_conf             7861886567689999999868


No 34 
>PRK00290 dnaK molecular chaperone DnaK; Provisional
Probab=27.77  E-value=38  Score=13.97  Aligned_cols=22  Identities=23%  Similarity=0.416  Sum_probs=15.7

Q ss_pred             EEEECCCCCCHHHHHHHH-HHCC
Q ss_conf             773066446888999998-6086
Q gi|255764509|r  277 LGCVGNGKNIPAIKNNLT-ALGC  298 (351)
Q Consensus       277 vGtVGG~t~lp~~~~~l~-ilg~  298 (351)
                      |=.|||+|+.|..|.-++ .+|.
T Consensus       332 ViLVGGsTRiP~Vq~~v~~~Fgk  354 (631)
T PRK00290        332 VILVGGSTRMPAVQELVKEFFGK  354 (631)
T ss_pred             EEEECCCCCCHHHHHHHHHHHCC
T ss_conf             99917824567999999999688


No 35 
>TIGR02484 CitB CitB domain protein; InterPro: IPR012830   This entry identifies proteins that are decribed as citrate utilization protein B, restricted to the proteobacteria. CitB  has been identified in Salmonella and Escherichia coli as the signal transduction component of a two-component system for citrate in which CitA acts as a citrate transporter.   This domain is also a C-terminal domain in the Rhodobacter capsulatus CobZ gene, which in most other species exists as the separate CitB gene adjacent to CobZ. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene ) and is complemented by the characterised precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate..
Probab=27.54  E-value=7.4  Score=18.39  Aligned_cols=61  Identities=28%  Similarity=0.312  Sum_probs=33.1

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCC-HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             890899998056467730664468-889999986086877887769889999999999888999999
Q gi|255764509|r  263 DDSLYFSCTIPNLILGCVGNGKNI-PAIKNNLTALGCIEERKTGDNARRLAAICAATVLCGELSLLA  328 (351)
Q Consensus       263 ~~~L~g~i~lPsl~vGtVGG~t~l-p~~~~~l~ilg~~~~~~~~~~A~~La~iiAavgLAqnlaal~  328 (351)
                      ..-=|+-+++| ..+|||||-+=. .++-..    +.+..-++.|+-|..+..=..-.|-.-|..+.
T Consensus       251 ~~APYp~~slP-V~LG~vGGv~m~vG~aGL~----~L~~~~r~ePa~r~~~~l~~d~~l~~~L~~~a  312 (392)
T TIGR02484       251 REAPYPLLSLP-VILGTVGGVMMVVGAAGLW----GLREKARPEPAVRALARLGMDRLLLLALVLVA  312 (392)
T ss_pred             CCCCCCCCCCH-HHHHHHHHHHHHHHHHHHH----HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             45788742001-5755678999999999999----99974487877321787649999999999998


No 36 
>KOG0100 consensus
Probab=27.31  E-value=38  Score=13.95  Aligned_cols=21  Identities=24%  Similarity=0.411  Sum_probs=14.9

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             677306644688899999860
Q gi|255764509|r  276 ILGCVGNGKNIPAIKNNLTAL  296 (351)
Q Consensus       276 ~vGtVGG~t~lp~~~~~l~il  296 (351)
                      .+=.|||+|++|.+++-|+=.
T Consensus       365 eiVLVGGsTrIPKvQqllk~f  385 (663)
T KOG0100         365 EIVLVGGSTRIPKVQQLLKDF  385 (663)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
T ss_conf             389954865682699999998


No 37 
>TIGR01315 5C_CHO_kinase FGGY-family pentulose kinase; InterPro: IPR006003    The enzymes for catabolism of the pentitols D-arabinitol and ribitol include NAD-dependent pentose dehydrogenase (dalD and rbtD), ATP-dependent pentulose kinases (dalK and rbtK) and a pentose-specific ion symporter (dalT and rbtT). Of the two kinases (19.3 0dentity), DalK (487 aa) belongs to the family of short D-xylulokinases and RbtK (D-ribulokinase; 535 aa) to the family of long kinases . .
Probab=26.73  E-value=23  Score=15.29  Aligned_cols=54  Identities=15%  Similarity=0.184  Sum_probs=30.2

Q ss_pred             HHCCCCCCEEEEEEEECHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             31037720799998756999975738999999988786656554220022021621667788888762763788886
Q gi|255764509|r  175 NGIMGRGKNFVAEITINRAICQKYLRTSPEKIILLNTQKNLIGTFLAGGIRSANAHFANMLLAYYLATGQDAANIVE  251 (351)
Q Consensus       175 n~~~~rG~~V~Ae~~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~~~~~~a~t~NkgimNgI~Av~lATGnD~a~v~a  251 (351)
                      +++.|   +++.|..||.=+=   ||-.--+..+...+-.++.-++++                 +|||.|.|.+=.
T Consensus       132 ~YVGG---k~S~EME~PK~LW---LK~Nmp~~~~~~~~fFDL~DfLTw-----------------rATG~~~RS~Cs  185 (574)
T TIGR01315       132 KYVGG---KVSLEMEVPKVLW---LKENMPEEYEAAGKFFDLADFLTW-----------------RATGKEIRSLCS  185 (574)
T ss_pred             HCCCC---EECCCCCCCHHHH---HHCCCCHHHHHHCCCCCCHHHHHH-----------------HHCCCCCCCEEE
T ss_conf             11587---1211114533676---521331677620202443344667-----------------642554330321


No 38 
>TIGR02130 dapB_plant dihydrodipicolinate reductase; InterPro: IPR011859    This narrow family includes genes from Arabidopsis and Fibrobacter succinogenes (which probably recieved the gene from a plant via lateral gene transfer). The sequences are distantly related to the dihydrodipicolinate reductases from archaea. In Fibrobacter this gene is the only candidate DHPR in the genome..
Probab=25.27  E-value=20  Score=15.64  Aligned_cols=29  Identities=17%  Similarity=0.630  Sum_probs=18.5

Q ss_pred             ECCEEEEEEEECCEEEEEECCC-CCC-HHHHH
Q ss_conf             2890899998056467730664-468-88999
Q gi|255764509|r  262 HDDSLYFSCTIPNLILGCVGNG-KNI-PAIKN  291 (351)
Q Consensus       262 ~~~~L~g~i~lPsl~vGtVGG~-t~l-p~~~~  291 (351)
                      +|-.||+...+| -..||-||- ++| .++.+
T Consensus        84 DNA~lY~K~~~P-FVMGTTGGDR~~L~K~V~~  114 (275)
T TIGR02130        84 DNAELYVKVKVP-FVMGTTGGDREALAKLVED  114 (275)
T ss_pred             CCHHHHCCCCCC-EEECCCCCHHHHHHHHHHH
T ss_conf             203520023576-4653787418999999875


No 39 
>pfam01177 Asp_Glu_race Asp/Glu/Hydantoin racemase. This family contains aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase.
Probab=24.94  E-value=45  Score=13.48  Aligned_cols=88  Identities=10%  Similarity=-0.057  Sum_probs=44.4

Q ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHCCCCCCEEEEEE--EECHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             999999999986798148973477431233355431037720799998--756999975738999999988786656554
Q gi|255764509|r  141 AADAVMDWILSQWSYLHYGSVSGNICSDKKATAINGIMGRGKNFVAEI--TINRAICQKYLRTSPEKIILLNTQKNLIGT  218 (351)
Q Consensus       141 ~~E~v~~~i~~~~~~~~~~~ilsN~~tdkk~s~~n~~~~rG~~V~Ae~--~i~~~~~~~~l~~~~e~~~~~~~~~~~~a~  218 (351)
                      +.+++...++. .+ ...+.+++-|.+.+.....+++..+|..+...-  ..-.+.. +.-+.+++..........   .
T Consensus        93 ~~~a~~~a~~~-~~-~~ri~vl~t~~t~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~---~  166 (212)
T pfam01177        93 IVEAALKALAL-LG-AKRVGVLATYGTIVSGLYQELLAEAGIEVVAPAIRLGIVEVL-ELGRIEEASVEALAAALE---R  166 (212)
T ss_pred             HHHHHHHHHHH-CC-CCEEEEEECCHHHHHHHHHHHHHHCCCCEEECCCCCCCHHHH-HHCCCCHHHHHHHHHHHH---H
T ss_conf             47899999997-18-980899956424437999999997599278524355325599-928999999999999998---8


Q ss_pred             HCCCHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf             220022021621667788888762763
Q gi|255764509|r  219 FLAGGIRSANAHFANMLLAYYLATGQD  245 (351)
Q Consensus       219 ~~~~~a~t~NkgimNgI~Av~lATGnD  245 (351)
                      .           .-+++|+++|+|-+=
T Consensus       167 ~-----------~~~~~d~ivLgCT~l  182 (212)
T pfam01177       167 L-----------AEDGADAVILGCTEL  182 (212)
T ss_pred             H-----------HHCCCCEEEECCCCH
T ss_conf             7-----------528989999858882


No 40 
>TIGR03452 mycothione_red mycothione reductase. Mycothiol, a glutathione analog in Mycobacterium tuberculosis and related species, can form a disulfide-linked dimer called mycothione. This enzyme can reduce mycothione to regenerate two mycothiol molecules. The enzyme shows some sequence similarity to glutathione-disulfide reductase, trypanothione-disulfide reductase, and dihydrolipoamide dehydrogenase. The characterized protein from M. tuberculosis, a homodimer, has FAD as a cofactor, one per monomer, and uses NADPH as a substrate.
Probab=24.70  E-value=18  Score=15.98  Aligned_cols=16  Identities=25%  Similarity=0.140  Sum_probs=6.4

Q ss_pred             HHHCCCCCCCCCCCHHHHH
Q ss_conf             8608687788776988999
Q gi|255764509|r  294 TALGCIEERKTGDNARRLA  312 (351)
Q Consensus       294 ~ilg~~~~~~~~~~A~~La  312 (351)
                      +|||+.--+   ++|.||-
T Consensus       399 ~ILG~~ivG---~~A~ElI  414 (452)
T TIGR03452       399 KLLGAHIIG---PQASSLI  414 (452)
T ss_pred             EEEEEEEEC---CCHHHHH
T ss_conf             799999989---9999999


No 41 
>PTZ00052 thioredoxin reductase; Provisional
Probab=24.62  E-value=19  Score=15.84  Aligned_cols=10  Identities=30%  Similarity=0.301  Sum_probs=4.7

Q ss_pred             HHHHHHCCCC
Q ss_conf             8888762763
Q gi|255764509|r  236 LAYYLATGQD  245 (351)
Q Consensus       236 ~Av~lATGnD  245 (351)
                      |.+++|+|--
T Consensus       308 d~vLvA~GR~  317 (541)
T PTZ00052        308 DTVLYATGRK  317 (541)
T ss_pred             EEEEEECCCC
T ss_conf             2899922655


No 42 
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=23.07  E-value=13  Score=16.91  Aligned_cols=10  Identities=30%  Similarity=0.355  Sum_probs=5.9

Q ss_pred             CEEEEEEEHH
Q ss_conf             4788653034
Q gi|255764509|r   29 KVKVPLATYE   38 (351)
Q Consensus        29 ~y~VPMATeE   38 (351)
                      +|.|||=.=|
T Consensus        66 TYAVPmI~GE   75 (231)
T TIGR02885        66 TYAVPMIMGE   75 (231)
T ss_pred             ECCCCHHHHH
T ss_conf             2122202212


No 43 
>PRK06115 dihydrolipoamide dehydrogenase; Reviewed
Probab=22.46  E-value=26  Score=14.99  Aligned_cols=10  Identities=0%  Similarity=-0.014  Sum_probs=4.1

Q ss_pred             CCHHHHHHHH
Q ss_conf             6988999999
Q gi|255764509|r  306 DNARRLAAIC  315 (351)
Q Consensus       306 ~~A~~La~ii  315 (351)
                      ++|.||...+
T Consensus       416 ~~A~elI~~~  425 (466)
T PRK06115        416 PSVSEMIGEF  425 (466)
T ss_pred             CCHHHHHHHH
T ss_conf             9999999999


No 44 
>TIGR02299 HpaE 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase; InterPro: IPR011985    This entry represents the dehydrogenase responsible for the conversion of 5-carboxymethyl-2-hydroxymuconate semialdehyde to 5-carboxymethyl-2-hydroxymuconate (a tricarboxylic acid). This is the step in the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate following the oxidative opening of the aromatic ring ..
Probab=21.45  E-value=16  Score=16.27  Aligned_cols=16  Identities=19%  Similarity=0.447  Sum_probs=7.3

Q ss_pred             CCCCCCEEEEEEEECH
Q ss_conf             0377207999987569
Q gi|255764509|r  177 IMGRGKNFVAEITINR  192 (351)
Q Consensus       177 ~~~rG~~V~Ae~~i~~  192 (351)
                      ..+||.+|...+.+..
T Consensus       363 ~~~~GNYv~PT~f~~~  378 (494)
T TIGR02299       363 ELGRGNYVLPTVFTDA  378 (494)
T ss_pred             CCCCCCEEECEEEECC
T ss_conf             4687942503488888


No 45 
>PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed
Probab=20.95  E-value=4.1  Score=20.03  Aligned_cols=19  Identities=11%  Similarity=0.441  Sum_probs=8.3

Q ss_pred             EEEECCC-CCCHHHHHHHHH
Q ss_conf             7730664-468889999986
Q gi|255764509|r  277 LGCVGNG-KNIPAIKNNLTA  295 (351)
Q Consensus       277 vGtVGG~-t~lp~~~~~l~i  295 (351)
                      |-++||| |..-.++.++++
T Consensus       454 VVVIGGGntAmDcaRTA~Rl  473 (639)
T PRK12809        454 VVVLGGGDTTMDCLRTSIRL  473 (639)
T ss_pred             EEEECCCCHHHHHHHHHHHC
T ss_conf             99989982189999999983


No 46 
>TIGR02825 B4_12hDH leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase; InterPro: IPR014190   Leukotriene B4 12-hydroxydehydrogenase is an NADP-dependent enzyme of arachidonic acid metabolism, responsible for converting leukotriene B4 to the much less active metabolite 12-oxo-leukotriene B4. The BRENDA database lists leukotriene B4 12-hydroxydehydrogenase as one of the synonyms of 2-alkenal reductase (1.3.1.74 from EC), while 1.3.1.48 from EC is 15-oxoprostaglandin 13-reductase..
Probab=20.40  E-value=55  Score=12.92  Aligned_cols=61  Identities=30%  Similarity=0.396  Sum_probs=36.7

Q ss_pred             CCCHHHHHHHC-------------CCEEEEEEECCE------EEEEEEEC-CEEEEEECCCCCCHHHHHHHHHHCCCCCC
Q ss_conf             76378888640-------------320256872890------89999805-64677306644688899999860868778
Q gi|255764509|r  243 GQDAANIVEGS-------------QGLTYAKLHDDS------LYFSCTIP-NLILGCVGNGKNIPAIKNNLTALGCIEER  302 (351)
Q Consensus       243 GnD~a~v~a~~-------------~a~t~~~~~~~~------L~g~i~lP-sl~vGtVGG~t~lp~~~~~l~ilg~~~~~  302 (351)
                      ||..+.|.++.             .+++.-.+.||.      ..+-=++| ||++||||= -++...---|+|-|++++.
T Consensus        64 G~qva~vveskn~a~P~Gt~v~a~~GW~~hsisdG~~l~kl~~eWPd~~PlslalGtvGm-PG~tayfGll~iCG~k~G~  142 (327)
T TIGR02825        64 GQQVARVVESKNSALPKGTIVLASSGWTSHSISDGKDLEKLLTEWPDTLPLSLALGTVGM-PGLTAYFGLLEICGVKGGE  142 (327)
T ss_pred             HHHHHHHHHHCCCCCCCCEEEEECCCCCEEEECCCHHHHHHHHCCCCCCCHHHHHCCCCC-CHHHHHHHHHHHCCCCCCC
T ss_conf             778887763124467754178740676200000420123322116652431221003464-0578887677750466687


Q ss_pred             CC
Q ss_conf             87
Q gi|255764509|r  303 KT  304 (351)
Q Consensus       303 ~~  304 (351)
                      ..
T Consensus       143 tv  144 (327)
T TIGR02825       143 TV  144 (327)
T ss_pred             EE
T ss_conf             57


No 47 
>PRK13930 rod shape-determining protein MreB; Provisional
Probab=20.20  E-value=56  Score=12.89  Aligned_cols=49  Identities=12%  Similarity=0.091  Sum_probs=29.1

Q ss_pred             EEEECCCCCCHHHHHHH-HHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             77306644688899999-86086877887769889999999999888999999
Q gi|255764509|r  277 LGCVGNGKNIPAIKNNL-TALGCIEERKTGDNARRLAAICAATVLCGELSLLA  328 (351)
Q Consensus       277 vGtVGG~t~lp~~~~~l-~ilg~~~~~~~~~~A~~La~iiAavgLAqnlaal~  328 (351)
                      |=-|||+|++|..++-+ +.+|..-.-  .+| -+.+-...|.=+++|+-+++
T Consensus       285 IiLvGGsSriP~i~~~l~e~~g~~v~~--~~~-P~~aVA~GAAi~~~~~~~~~  334 (336)
T PRK13930        285 IVLTGGGALLRGLDKLLSEETGLPVHI--AED-PLTCVARGTGKALENLDKLR  334 (336)
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCCC--CCC-HHHHHHHHHHHHHHCHHHHC
T ss_conf             999877455147999999997839888--988-77799999999985878642


Done!