Query         gi|254780858|ref|YP_003065271.1| NADH dehydrogenase I subunit F [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 425
No_of_seqs    156 out of 1693
Neff          5.4 
Searched_HMMs 39220
Date          Mon May 30 01:04:28 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780858.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01959 nuoF_fam NADH-quinon 100.0       0       0 1288.9  31.3  410    7-416     1-420 (420)
  2 PRK13596 NADH dehydrogenase I  100.0       0       0 1155.1  43.8  420    2-421     1-421 (426)
  3 PTZ00304 NADH dehydrogenase (u 100.0       0       0 1156.0  42.3  422    2-423    22-445 (483)
  4 COG1894 NuoF NADH:ubiquinone o 100.0       0       0 1143.0  38.6  415    1-418     5-422 (424)
  5 PRK11278 NADH dehydrogenase I  100.0       0       0 1123.9  42.8  415    8-425    15-434 (448)
  6 KOG2658 consensus              100.0       0       0  930.0  29.2  419    2-420    50-469 (478)
  7 TIGR01945 rnfC electron transp 100.0       0       0  433.3  19.6  318   34-413   118-441 (444)
  8 PRK05035 electron transport co 100.0       0       0  403.6  19.2  316   36-417   129-449 (725)
  9 pfam01512 Complex1_51K Respira 100.0       0       0  346.5  13.9  149   47-218     1-149 (150)
 10 COG4656 RnfC Predicted NADH:ub 100.0       0       0  330.4  22.5  330   16-415   101-433 (529)
 11 PRK05352 Na(+)-translocating N  99.9 1.1E-20 2.8E-25  159.4  13.8  297   35-413   111-445 (448)
 12 pfam10589 NADH_4Fe-4S NADH-ubi  99.5 5.6E-15 1.4E-19  121.0   3.3   46  330-375     1-46  (46)
 13 pfam10531 SLBB SLBB domain.     98.8 6.5E-09 1.7E-13   80.1   4.6   52  241-293     1-52  (52)
 14 TIGR01936 nqrA NADH:ubiquinone  97.0  0.0059 1.5E-07   39.9   8.1  230   37-337   112-357 (466)
 15 COG1726 NqrA Na+-transporting   96.6   0.052 1.3E-06   33.6  10.6  203   32-296   107-312 (447)
 16 TIGR03027 pepcterm_export puta  94.7    0.11 2.7E-06   31.5   5.8   80  240-326    79-163 (165)
 17 TIGR03028 EpsE polysaccharide   94.3    0.08   2E-06   32.3   4.6   43  241-285   164-206 (239)
 18 pfam05896 NQRA Na(+)-transloca  93.4    0.69 1.8E-05   25.9  10.8  144   35-224   110-255 (257)
 19 COG1596 Wza Periplasmic protei  93.0    0.11 2.8E-06   31.3   3.4   39  240-279   125-164 (239)
 20 TIGR03028 EpsE polysaccharide   91.8    0.36 9.2E-06   27.9   4.8   79  239-325    78-161 (239)
 21 pfam11973 NQRA_SLBB NQRA C-ter  91.7    0.36 9.1E-06   27.9   4.7   46  241-292     1-47  (51)
 22 TIGR00692 tdh L-threonine 3-de  86.2    0.19 4.8E-06   29.8  -0.0   25  111-135   179-203 (341)
 23 cd03008 TryX_like_RdCVF Trypar  80.8     1.1 2.7E-05   24.7   2.0   20  345-364    34-53  (146)
 24 KOG1145 consensus               76.1     6.2 0.00016   19.6   6.1   90  240-342   154-251 (683)
 25 COG1062 AdhC Zn-dependent alco  75.0    0.55 1.4E-05   26.6  -0.8   17  353-369   342-358 (366)
 26 TIGR02375 pseudoazurin pseudoa  73.9     1.9 4.8E-05   23.0   1.7   44  195-257    31-74  (123)
 27 PRK06964 DNA polymerase III su  70.0     4.2 0.00011   20.7   2.7   22   79-100    44-68  (342)
 28 KOG2501 consensus               69.1     1.8 4.5E-05   23.2   0.6   25  344-368    41-65  (157)
 29 TIGR02812 fadR_gamma fatty aci  66.0     3.2 8.2E-05   21.5   1.5   16  202-217    64-88  (275)
 30 COG3347 Uncharacterized conser  61.0      13 0.00032   17.5   4.5   34  376-409   363-396 (404)
 31 cd03009 TryX_like_TryX_NRX Try  58.3     6.8 0.00017   19.3   2.0   13   78-90     19-33  (131)
 32 PHA00330 putative replication   58.1       5 0.00013   20.1   1.3   14  128-141   105-118 (317)
 33 PRK07993 DNA polymerase III su  56.7      10 0.00026   18.1   2.7   82   79-183    47-133 (334)
 34 COG1064 AdhP Zn-dependent alco  56.7     3.1   8E-05   21.5   0.0   24   44-67    140-163 (339)
 35 PRK10083 putative dehydrogenas  54.2     4.7 0.00012   20.3   0.6   16  358-373   289-304 (339)
 36 COG0320 LipA Lipoate synthase   52.4     2.2 5.6E-05   22.6  -1.3  173  100-317   100-281 (306)
 37 COG1162 Predicted GTPases [Gen  49.9      19 0.00048   16.3   7.8  151   78-267    83-241 (301)
 38 PRK08699 DNA polymerase III su  48.8      14 0.00036   17.1   2.3   25  159-183   114-138 (325)
 39 cd03012 TlpA_like_DipZ_like Tl  48.4      16 0.00042   16.7   2.6   13   78-90     24-38  (126)
 40 TIGR03451 mycoS_dep_FDH mycoth  47.9     4.2 0.00011   20.7  -0.5   17  353-369   334-350 (358)
 41 PRK09880 L-idonate 5-dehydroge  47.1     5.9 0.00015   19.7   0.2   14  358-371   296-309 (343)
 42 cd02964 TryX_like_family Trypa  46.9      13 0.00033   17.4   1.9   13   78-90     18-32  (132)
 43 PRK05707 DNA polymerase III su  46.6      18 0.00046   16.4   2.6   82   79-183    45-131 (328)
 44 PRK03147 thiol-disulfide oxido  45.7      14 0.00035   17.2   1.9   10  238-247    95-104 (176)
 45 PRK12288 ribosome-associated G  44.2      23 0.00058   15.7   9.3   88  103-212   138-228 (344)
 46 PRK00098 ribosome-associated G  44.2      23 0.00059   15.7   9.3   87  104-212    98-185 (298)
 47 TIGR03201 dearomat_had 6-hydro  43.7     7.6 0.00019   18.9   0.3   17  354-370   325-341 (349)
 48 PRK08058 DNA polymerase III su  41.3      23 0.00059   15.7   2.5   25  159-183   111-135 (329)
 49 pfam04034 DUF367 Domain of unk  41.1      26 0.00065   15.4   2.9   36  188-223    46-82  (128)
 50 pfam01031 Dynamin_M Dynamin ce  40.6      26 0.00066   15.3   3.6   14  255-268   140-153 (295)
 51 TIGR01743 purR_Bsub pur operon  39.8      27 0.00068   15.3   3.6  102   95-217    12-122 (269)
 52 TIGR02418 acolac_catab acetola  39.5      13 0.00033   17.4   1.0   76  302-394   280-361 (553)
 53 KOG2453 consensus               39.0      15 0.00039   16.9   1.3   36  316-353   268-304 (507)
 54 KOG0633 consensus               38.6      28 0.00071   15.1   3.1   75  240-326   122-199 (375)
 55 TIGR00604 rad3 DNA repair heli  38.3      28 0.00072   15.1   4.8   80  308-387   266-359 (813)
 56 PRK05396 tdh L-threonine 3-deh  38.0      10 0.00026   18.1   0.3   18  352-369   315-332 (341)
 57 PRK05298 excinuclease ABC subu  36.6      28 0.00072   15.1   2.3   48  371-418   291-340 (657)
 58 TIGR00631 uvrb excinuclease AB  35.9     5.5 0.00014   19.9  -1.4   74  331-419   263-341 (667)
 59 TIGR01312 XylB xylulokinase; I  35.1     8.2 0.00021   18.7  -0.6  136  206-388   179-333 (494)
 60 TIGR02818 adh_III_F_hyde S-(hy  34.5     6.2 0.00016   19.5  -1.3   13  207-219   262-274 (368)
 61 TIGR01702 CO_DH_cata carbon-mo  34.4      32 0.00082   14.7   2.7  237   40-338   166-479 (647)
 62 pfam03431 RNA_replicase_B RNA   34.1      33 0.00083   14.7   2.6   68  315-382   325-427 (539)
 63 pfam08240 ADH_N Alcohol dehydr  33.7     9.2 0.00024   18.4  -0.5   17  343-359    64-80  (108)
 64 COG1312 UxuA D-mannonate dehyd  33.0      30 0.00076   14.9   2.0   29  190-222   212-240 (362)
 65 TIGR03599 YloV DAK2 domain fus  32.9      34 0.00087   14.5   3.0  282   16-386   140-427 (530)
 66 TIGR01068 thioredoxin thioredo  32.9      25 0.00063   15.5   1.5   49  338-390    20-69  (101)
 67 TIGR00385 dsbE periplasmic pro  32.9      23 0.00058   15.7   1.4   47   77-138    64-115 (175)
 68 TIGR01931 cysJ sulfite reducta  32.1      11 0.00029   17.7  -0.3   32  233-269   410-441 (628)
 69 PRK05481 lipoyl synthase; Prov  31.8      10 0.00026   18.1  -0.6  189   82-319    69-266 (289)
 70 PHA00028 rep RNA replicase, be  31.6      36 0.00091   14.4   2.7   76  317-392   333-444 (561)
 71 COG0556 UvrB Helicase subunit   31.6      11 0.00029   17.8  -0.4   47  371-417   290-338 (663)
 72 COG1461 Predicted kinase relat  31.5      36 0.00092   14.4   2.8  116  244-385   320-438 (542)
 73 pfam12395 DUF3658 Protein of u  31.3      36 0.00092   14.4   3.2   89   32-141     5-93  (111)
 74 PRK05354 arginine decarboxylas  31.1      36 0.00093   14.3   7.0  205   21-264    90-314 (634)
 75 TIGR01944 rnfB electron transp  29.9      13 0.00032   17.5  -0.4   68  311-386    21-94  (213)
 76 pfam01950 FBPase_3 Fructose-1,  29.5      39 0.00099   14.2   2.8  262    8-359    57-346 (364)
 77 TIGR02963 xanthine_xdhA xanthi  29.4      20  0.0005   16.2   0.5   30  354-385   452-481 (515)
 78 COG4152 ABC-type uncharacteriz  28.9      40   0.001   14.1   2.2   51  195-245    77-132 (300)
 79 TIGR02082 metH methionine synt  28.6      16 0.00041   16.7  -0.0   82  205-296   721-826 (1265)
 80 cd03011 TlpA_like_ScsD_MtbDsbE  28.6      25 0.00064   15.4   1.0   13   78-90     21-35  (123)
 81 pfam01799 Fer2_2 [2Fe-2S] bind  27.9      25 0.00064   15.4   0.9   20  331-351    13-32  (75)
 82 COG1829 Predicted archaeal kin  27.8      17 0.00043   16.6  -0.0   45  249-304   116-160 (283)
 83 TIGR01559 squal_synth farnesyl  27.7      35 0.00088   14.5   1.6   69   86-169    76-149 (350)
 84 TIGR01020 rpsE_arch ribosomal   27.6      22 0.00056   15.8   0.6   74  115-201    84-161 (220)
 85 KOG0910 consensus               27.5      40   0.001   14.1   1.8   20  346-365    71-90  (150)
 86 PRK13412 fkp bifunctional fuco  27.3      42  0.0011   13.9   2.2   14  114-127   225-238 (974)
 87 TIGR02708 L_lactate_ox L-lacta  26.9      43  0.0011   13.9   2.7  135  242-416   169-343 (368)
 88 pfam04363 DUF496 Protein of un  26.8      43  0.0011   13.9   5.7   41  372-419    32-72  (95)
 89 pfam06251 DUF1017 SLBB-domain   26.8      43  0.0011   13.9   7.9   91  240-342    73-169 (173)
 90 TIGR02707 butyr_kinase butyrat  26.8      17 0.00044   16.5  -0.1   62    2-81     17-86  (353)
 91 pfam09606 Med15 ARC105 or Med1  26.7      43  0.0011   13.8   3.3   13  376-388   737-749 (768)
 92 PRK03958 tRNA 2'-O-methylase;   26.5      44  0.0011   13.8   4.5   33  108-142    21-53  (175)
 93 TIGR02264 gmx_para_CXXCG Myxoc  26.3      41   0.001   14.0   1.7   16   43-58    129-144 (247)
 94 TIGR02723 phenyl_P_alpha pheny  26.3      44  0.0011   13.8   2.5   38  310-352   369-408 (485)
 95 PHA01735 hypothetical protein   26.2      44  0.0011   13.8   4.9   50  357-410    17-66  (76)
 96 smart00190 IL4_13 Interleukins  25.1      46  0.0012   13.6   4.1   66  331-424    72-138 (138)
 97 pfam06733 DEAD_2 DEAD_2. This   25.0      45  0.0012   13.7   1.8   24  317-340   139-162 (168)
 98 TIGR01929 menB naphthoate synt  24.7      28 0.00071   15.1   0.6   23  238-260    64-89  (278)
 99 PRK02287 hypothetical protein;  24.2      48  0.0012   13.5   2.9   38  186-223    83-121 (169)
100 pfam09795 Atg31 Autophagy-rela  24.2      45  0.0011   13.7   1.6   37   53-89     31-78  (159)
101 KOG1547 consensus               23.6      49  0.0013   13.5   2.5   13  154-166    42-54  (336)
102 TIGR00920 2A060605 3-hydroxy-3  23.6      49  0.0013   13.5   2.3   54   32-95    361-416 (988)
103 KOG1769 consensus               23.1      50  0.0013   13.4   4.5   58  242-299    23-80  (99)
104 pfam04722 Ssu72 Ssu72-like pro  23.1      50  0.0013   13.4   2.7   37  227-270    29-66  (193)
105 TIGR00276 TIGR00276 iron-sulfu  22.6      23 0.00059   15.6  -0.1   51   95-152    83-136 (297)
106 PRK12928 lipoyl synthase; Prov  22.5      13 0.00033   17.3  -1.4  187   82-318    77-273 (290)
107 COG1453 Predicted oxidoreducta  22.5      52  0.0013   13.3   6.4   72  344-415   297-387 (391)
108 PRK08445 hypothetical protein;  22.5      52  0.0013   13.3   3.3   18  408-425   320-337 (348)
109 TIGR01361 DAHP_synth_Bsub phos  22.4      39 0.00098   14.2   1.0   54  207-268    98-151 (262)
110 COG4032 Predicted thiamine-pyr  22.2      17 0.00043   16.6  -0.8   68  166-268    58-125 (172)
111 pfam03786 UxuA D-mannonate deh  21.8      53  0.0014   13.2   2.1   95  191-338   207-304 (350)
112 PRK13771 putative alcohol dehy  21.5      26 0.00066   15.4  -0.0   19  351-369   305-323 (332)
113 cd02949 TRX_NTR TRX domain, no  21.1      55  0.0014   13.1   1.9   19  346-364    23-41  (97)
114 TIGR00430 Q_tRNA_tgt queuine t  20.6      29 0.00073   15.1   0.0   67  327-418   346-412 (415)
115 TIGR01842 type_I_sec_PrtD type  20.5      56  0.0014   13.1   2.6   55   79-144   249-306 (556)
116 cd02950 TxlA TRX-like protein   20.5      52  0.0013   13.3   1.3   16   75-90     20-35  (142)
117 cd03010 TlpA_like_DsbE TlpA-li  20.4      29 0.00073   15.1  -0.0   13   78-90     26-40  (127)
118 cd02967 mauD Methylamine utili  20.0      55  0.0014   13.1   1.4   11  203-213    21-31  (114)

No 1  
>TIGR01959 nuoF_fam NADH-quinone oxidoreductase, F subunit; InterPro: IPR011537   This entry describes the F chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2. ; GO: 0010181 FMN binding, 0016651 oxidoreductase activity acting on NADH or NADPH, 0051287 NAD binding, 0051539 4 iron 4 sulfur cluster binding, 0006118 electron transport.
Probab=100.00  E-value=0  Score=1288.94  Aligned_cols=410  Identities=63%  Similarity=1.066  Sum_probs=402.3

Q ss_pred             HHHHHHCC-CCCCCHHHHHHCC---CHHHHHHHHHC--CHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCC-CCCEE
Q ss_conf             36755178-7677989999779---98999999826--989999999983977687571124556874235656-88619
Q gi|254780858|r    7 RIFTNLYG-LQGKSLSDSMSRG---HWDNVDKILEK--GRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCS-DRPHY   79 (425)
Q Consensus         7 r~~~~~~~-~~~~~l~~y~~~g---gy~~l~~~l~~--~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~-~~~~y   79 (425)
                      ++|+|++. .++++|++|.++|   ||++|+|+|++  +||+||++||+||||||||||||||.||+||||..+ .+|||
T Consensus         1 ~l~~~~~~D~~~~~L~~Y~~~gryrgY~~l~KaL~~~~~~ddii~~VK~SGLRGRGGAGFpTGlKWSFmPK~~sg~~pkY   80 (420)
T TIGR01959         1 VLTTNLDDDPESWTLEEYEKRGRYRGYDALRKALEEKMSPDDIIEEVKDSGLRGRGGAGFPTGLKWSFMPKDDSGPKPKY   80 (420)
T ss_pred             CCEEEEECCCCCCCHHHHHHCCCHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE
T ss_conf             95144324888510788963487024799999985267812588998743798788887643442233567878888536


Q ss_pred             EEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC-CCCCCC
Q ss_conf             9985767784860048999862589999999999971836389981555178999999999999868997767-678866
Q gi|254780858|r   80 LVVNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSN-SKLGYD  158 (425)
Q Consensus        80 vv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~-~~~g~~  158 (425)
                      |||||||+||||||||.||+++||+|||||+|+|||++|+++|||||+||..++++|++||+||+++||||+| ++||||
T Consensus        81 LvCNADE~EPGTcKDR~lm~~~PH~LIEGm~IaayA~ga~~gYiYiRGEf~~~~~~l~~Ai~EA~~~G~LGkNIlGsGFD  160 (420)
T TIGR01959        81 LVCNADEGEPGTCKDRDLMEFDPHQLIEGMIIAAYAIGAKRGYIYIRGEFIKEAENLEAAIAEAYAAGLLGKNILGSGFD  160 (420)
T ss_pred             EEEECCCCCCCCHHHHHHHHCCCCCEEHHHHHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             88727779777131489986288703057888778752531047861301678899999999999759820033788620


Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCC-CCCC
Q ss_conf             406997457510011078899863089998688899862278303785000289999999999605688863389-8774
Q gi|254780858|r  159 VDIIVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGR-ENNR  237 (425)
Q Consensus       159 ~~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~-~~~~  237 (425)
                      |||.||+||||||||||||||||||||||+||.||||||..|||||||+||||||||+||.||++|++||+++|. ++++
T Consensus       161 f~l~~H~GAGAYICGEETALleSLEGkrGqPRlKPPFPA~~GLYG~PT~iNNVETla~VP~I~~~G~~Wy~~~G~~~~~~  240 (420)
T TIGR01959       161 FELFVHRGAGAYICGEETALLESLEGKRGQPRLKPPFPAVFGLYGKPTVINNVETLASVPAILRRGADWYSKLGKSEKSP  240 (420)
T ss_pred             EEEEEECCCCCEECHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             57634338885050478974531057668455221787455566788436463233345788721689998507888888


Q ss_pred             CEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC
Q ss_conf             30476426788787268935898799999986155678711004898524565653210024563342201103873466
Q gi|254780858|r  238 GTKLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGT  317 (425)
Q Consensus       238 Gtkl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGs  317 (425)
                      |||||||||||+|||+||+||||||+||||+||||+++|++.||||||||.|+++|++++..+++||||+++++||||||
T Consensus       241 GtKLfs~SGhV~kPG~yE~plG~pl~ELledyAGG~r~G~~NLKaviPGGsS~P~L~~~~~~~~~MDydsl~~~GSmLGt  320 (420)
T TIGR01959       241 GTKLFSVSGHVNKPGNYELPLGIPLRELLEDYAGGVRGGWKNLKAVIPGGSSTPVLPAEEHLDVPMDYDSLAAAGSMLGT  320 (420)
T ss_pred             CCEEEEEEEEEECCCEEEEECCCCHHHHHHHHCCCCCCCCCCCCEEECCCCCCCCCCHHHHCCCCCCHHHHHHHHHCCCE
T ss_conf             85487531066579447700677689999986789888725454572687677761645540246677889864411220


Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCC-CCCCCCCHH
Q ss_conf             5179942865289999999999987627998852302899999999998289998999999999986223-666776502
Q gi|254780858|r  318 AAVIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEG-RTICALGDA  396 (425)
Q Consensus       318 g~iiV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~-~S~C~lG~~  396 (425)
                      |+|||||+++|||.++.++.+||+||||||||||||||.|+.+||+||.+|+|+++|||+|.+|++.|.+ .|||+||++
T Consensus       321 g~~iv~D~~tc~V~~~~Rl~~Fy~hESCGqCTPCREGt~W~~~il~rie~G~G~~~Did~L~~v~~~i~GG~TiCAlgda  400 (420)
T TIGR01959       321 GAVIVMDESTCIVKAVRRLSEFYAHESCGQCTPCREGTGWLVKILERIEEGEGKKEDIDLLLSVCKQIEGGKTICALGDA  400 (420)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCHH
T ss_conf             32687747834889999999973025787857875762459999999971789843589999997434889333678656


Q ss_pred             HHHHHHHHHHHCHHHHHHHH
Q ss_conf             47999999863889999998
Q gi|254780858|r  397 AAWPIQGLIKNFRPLIEERI  416 (425)
Q Consensus       397 a~~pv~s~l~~F~dEfe~hI  416 (425)
                      |+.||+|+|+||||||++||
T Consensus       401 Aa~P~~~~ikhFR~EFe~~i  420 (420)
T TIGR01959       401 AAWPVQSAIKHFRDEFEAHI  420 (420)
T ss_pred             HHHHHHHHHHHHHHHHHCCC
T ss_conf             65654778887789983379


No 2  
>PRK13596 NADH dehydrogenase I subunit F; Provisional
Probab=100.00  E-value=0  Score=1155.06  Aligned_cols=420  Identities=79%  Similarity=1.332  Sum_probs=413.5

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             62034367551787677989999779989999998269899999999839776875711245568742356568861999
Q gi|254780858|r    2 LTDQDRIFTNLYGLQGKSLSDSMSRGHWDNVDKILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLV   81 (425)
Q Consensus         2 ~~~~~r~~~~~~~~~~~~l~~y~~~ggy~~l~~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv   81 (425)
                      |+||+|||+|+++.++++|++|+++|||++|+|+++|+|++||++|++||||||||||||||+||+++++...+++||||
T Consensus         1 l~~~~ri~~n~~~~~~~~l~~y~~~GGy~~l~~~~~m~p~~vi~evk~SgLrGRGGAGFPtG~KW~~~~~~~~~~~~Yvv   80 (426)
T PRK13596          1 LKDKDRIFTNLYGLQDWSLKGAKARGDWDGTKAILDKGRDWIIEEMKASGLRGRGGAGFPTGLKWSFMPKESDGRPHYLV   80 (426)
T ss_pred             CCCCCHHHHHHCCCCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCCEEEE
T ss_conf             97213112101379999999999769999999999579999999999748888886636110247860313489962898


Q ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCCE
Q ss_conf             85767784860048999862589999999999971836389981555178999999999999868997767-67886640
Q gi|254780858|r   82 VNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSN-SKLGYDVD  160 (425)
Q Consensus        82 ~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~-~~~g~~~~  160 (425)
                      |||||+||||||||+||+++||+|||||+|++||+||+++|||||+||+.++++|++||+|++++|+||+| +++||+|+
T Consensus        81 ~NadEgEPGtfKDR~ll~~~Ph~viEG~~iaa~aigA~~~~iyiR~ey~~~~~~l~~Ai~ea~~~g~LG~nilgsg~~~~  160 (426)
T PRK13596         81 VNADESEPGTCKDRDILRHDPHKLIEGCLIASFAMGAHAAYIYIRGEFIREREALQAAIDEAYEAGLIGKNACGSGWDFD  160 (426)
T ss_pred             EECCCCCCCCCCCHHHHHCCCHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEE
T ss_conf             62688998640169988338188999999999983686489994524399999999999999983888765568887757


Q ss_pred             EEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEE
Q ss_conf             69974575100110788998630899986888998622783037850002899999999996056888633898774304
Q gi|254780858|r  161 IIVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTK  240 (425)
Q Consensus       161 i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtk  240 (425)
                      |+||+|+|+||||||||||+||||+|++||.|||||++.||||+||+||||||||+||+|+++|++||+++|+++++|||
T Consensus       161 i~v~~gaGaYIcGEetALl~slEG~rg~Pr~kPP~p~~~Gl~g~PT~VNNVETla~Vp~I~~~G~~wf~~~G~~~s~GTk  240 (426)
T PRK13596        161 IYVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPANMGLYGCPTTVNNVESIAVVPTILRRGAAWFASIGRPNNTGTK  240 (426)
T ss_pred             EEEEECCCCCEECCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             89741687412061899999841799999999998543676799844567889998999997038999728988899817


Q ss_pred             EEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEE
Q ss_conf             76426788787268935898799999986155678711004898524565653210024563342201103873466517
Q gi|254780858|r  241 LFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAV  320 (425)
Q Consensus       241 l~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~i  320 (425)
                      +|||||+|++|||||+|+||||+|||+++|||+.+|++++||||+||+|+++||+++++++|||||+++++|++||||+|
T Consensus       241 l~svsG~V~~PGvyE~p~G~~l~eli~~~~GG~~~G~~~~kav~pGG~S~~~l~~~~~~d~~ld~esl~~~Gs~LGsG~i  320 (426)
T PRK13596        241 LFCISGHVNKPCNVEEAMGIPFRELIEKHAGGVRGGWDNLLAVIPGGSSVPLIPAEQCEDAIMDFDSLRAVGSGLGTAGV  320 (426)
T ss_pred             EEEECCCCCCCCEEEECCCCCHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCHHHHHHCCCCCCCCEE
T ss_conf             99832663578269946887599999996388778876527998568877767888956577787889873877577501


Q ss_pred             EEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHH
Q ss_conf             99428652899999999999876279988523028999999999982899989999999999862236667765024799
Q gi|254780858|r  321 IVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAWP  400 (425)
Q Consensus       321 iV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~~S~C~lG~~a~~p  400 (425)
                      ||||+++|||++++++++||+|||||||||||+||+|+.++|++|.+|+++++|+++|.+++++|+++|+|+||+++++|
T Consensus       321 iV~d~~~~~v~~~~~~~~F~a~ESCGqCtPCReGt~~l~~il~ri~~G~g~~~Dld~L~~l~~~m~~~s~CgLG~~a~~p  400 (426)
T PRK13596        321 IVMDKSTDIIKAIARLSYFYKHESCGQCTPCREGTGWMWRVMERMVKGRAQKREIDMLLDVTKQIEGHTICALGDAAAWP  400 (426)
T ss_pred             EEECCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHH
T ss_conf             67489788999999999872447899998645159999999999983999989999999999855688658373210899


Q ss_pred             HHHHHHHCHHHHHHHHHHHCC
Q ss_conf             999986388999999865189
Q gi|254780858|r  401 IQGLIKNFRPLIEERIDQYHR  421 (425)
Q Consensus       401 v~s~l~~F~dEfe~hI~~~~r  421 (425)
                      |.|+|+|||+||++||++++|
T Consensus       401 v~S~l~~F~~Efe~~i~~~~~  421 (426)
T PRK13596        401 IQGLIRHFRPEIEERIDEYTR  421 (426)
T ss_pred             HHHHHHHHHHHHHHHHHHHCC
T ss_conf             999998679999999987153


No 3  
>PTZ00304 NADH dehydrogenase (ubiquinone); Provisional
Probab=100.00  E-value=0  Score=1155.98  Aligned_cols=422  Identities=64%  Similarity=1.155  Sum_probs=414.8

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCC-CCCCEEE
Q ss_conf             620343675517876779899997799899999982698999999998397768757112455687423565-6886199
Q gi|254780858|r    2 LTDQDRIFTNLYGLQGKSLSDSMSRGHWDNVDKILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVC-SDRPHYL   80 (425)
Q Consensus         2 ~~~~~r~~~~~~~~~~~~l~~y~~~ggy~~l~~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~-~~~~~yv   80 (425)
                      |+||||||+|+|+.++++|+..+++|+|...++++.++||+||++||+||||||||||||||+||+++++.. +++||||
T Consensus        22 l~d~drif~nlyg~~~~~l~~a~~rg~w~~tk~~~~~g~d~II~EvK~SGLRGRGGAGFPTG~KW~f~~~~~~~~kpkYl  101 (483)
T PTZ00304         22 LKDQDRIFTNLYNDFGTGIDSAERRGDWYRTKDILLKGHDWVINEIKASGLRGRGGAGFPSGLKWSFMPKKKPDGRPSYI  101 (483)
T ss_pred             CCCCCHHHHCCCCCCCCCHHHHHHCCCHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCCCCHHHCCCCCCCCCCEEE
T ss_conf             85313233301468883645688737958799999759699999999627888887746366642534466788985389


Q ss_pred             EEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCC
Q ss_conf             985767784860048999862589999999999971836389981555178999999999999868997767-6788664
Q gi|254780858|r   81 VVNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSN-SKLGYDV  159 (425)
Q Consensus        81 v~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~-~~~g~~~  159 (425)
                      ||||||+||||||||+||+++||+|||||+|++||+||+++|||||+||+.++++|++||+||+++|+||+| +++||+|
T Consensus       102 VcNaDEgEPGTfKDR~ile~dPH~lIEGmlIAa~AigA~~gyIYiRgEy~~~~~~L~~AI~eA~~~GlLG~nilGsg~~f  181 (483)
T PTZ00304        102 VVNGDESEPGTCKDREIMRHEPHKLVEGALIAGFAMRARYGYIYIRGEFYNEWRSVEKAIHEAYAKGYLGRNACGSGYDF  181 (483)
T ss_pred             EEECCCCCCCCCCCHHHHHHCHHHHHHHHHHHHHHHCCCEEEEEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCE
T ss_conf             99488898540358999842828899999999999688869999557569999999999999987574565456888764


Q ss_pred             EEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCE
Q ss_conf             06997457510011078899863089998688899862278303785000289999999999605688863389877430
Q gi|254780858|r  160 DIIVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGT  239 (425)
Q Consensus       160 ~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gt  239 (425)
                      +|+||+|+|+||||||||||+|||||||+||.|||||+++||||+||+||||||||+||.|+++|++||+++|+++++||
T Consensus       182 dI~v~~GAGAYICGEETALieSlEGkrG~PR~KPPfPa~~GL~g~PT~VNNVETlA~VP~Il~~Ga~wfas~G~~~s~GT  261 (483)
T PTZ00304        182 DLYTYRGAGAYICGEETAMISSIEGGPGKPRLKPPFPANVGLYGCPTTVTNCETVSVSPTILRRGPQWFASFGRKNNAGV  261 (483)
T ss_pred             EEEEEECCCCEEECHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHCCCCCCCCC
T ss_conf             68999668851746399999985799999999999875577579996333412387789999547399984798999981


Q ss_pred             EEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCE
Q ss_conf             47642678878726893589879999998615567871100489852456565321002456334220110387346651
Q gi|254780858|r  240 KLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAA  319 (425)
Q Consensus       240 kl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~  319 (425)
                      |+|||||+|++||+||+||||||+|||+++|||+.+|++++||||+||+|+++||++.+|+++||||+|+++||+||||+
T Consensus       262 KlfsvSG~V~~PGv~E~pmG~~LrelI~~~~GGv~~G~~~lkAv~pGG~S~~~lp~~~~d~~~mDfdsL~~~Gs~lGsG~  341 (483)
T PTZ00304        262 KLFCICGHVNRPCTVEEEMSIPLRDLIERHAGGVRGGWDNLLAVIPGGSSCPLIPKSICDNVLMDYDALKEAQTGLGTAA  341 (483)
T ss_pred             EEEEECCCCCCCEEEEECCCCCHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCCHHHCCCCCCCHHHHHHHCCCCCCEE
T ss_conf             26651366458805996489829999998679975873225999746866675897880766677588997277777537


Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             79942865289999999999987627998852302899999999998289998999999999986223666776502479
Q gi|254780858|r  320 VIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAW  399 (425)
Q Consensus       320 iiV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~~S~C~lG~~a~~  399 (425)
                      |||||+++|||++++++++||+|||||||||||+||.||.++|+||.+|+++++|+++|.+++++|.+.|+|+||++|++
T Consensus       342 vIV~d~~~~mv~~~~~~~~F~~~ESCGqCTPCReGT~wm~~il~ri~~G~g~~~did~L~~l~~~i~g~tiCaLG~aAa~  421 (483)
T PTZ00304        342 VIVMDKSTDLIAAIHRLSQFYAHESCGQCTPCREGSPWLEKMMKRFVHGNAKKEEIGTMLDVSKQLEGRTICALATAAAW  421 (483)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCH
T ss_conf             99986999999999999999607778899786172899999999997499988999999999964338710647766507


Q ss_pred             HHHHHHHHCHHHHHHHHHHHCCCC
Q ss_conf             999998638899999986518999
Q gi|254780858|r  400 PIQGLIKNFRPLIEERIDQYHRCN  423 (425)
Q Consensus       400 pv~s~l~~F~dEfe~hI~~~~rCp  423 (425)
                      ||+|+|+|||+|||+||++|+.++
T Consensus       422 Pv~s~ir~FR~e~E~~I~~~~~~~  445 (483)
T PTZ00304        422 PVQGLARHFTPLLEERIERYWEAN  445 (483)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             899999880899999999998609


No 4  
>COG1894 NuoF NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit [Energy production and conversion]
Probab=100.00  E-value=0  Score=1142.99  Aligned_cols=415  Identities=60%  Similarity=1.039  Sum_probs=407.2

Q ss_pred             CCCHHHH-HHHHHCCCCCCCHHHHHHCCCHHHHHHHH-HCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCE
Q ss_conf             9620343-67551787677989999779989999998-269899999999839776875711245568742356568861
Q gi|254780858|r    1 MLTDQDR-IFTNLYGLQGKSLSDSMSRGHWDNVDKIL-EKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPH   78 (425)
Q Consensus         1 ~~~~~~r-~~~~~~~~~~~~l~~y~~~ggy~~l~~~l-~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~   78 (425)
                      |+++|.| +|+|++..|+++|++|+++|||++|+|+| +|+|++||++||+||||||||||||||.||++++++.++. |
T Consensus         5 ~~~~~~r~~~~~~~~~~~~~l~~y~a~ggy~~l~kal~~m~p~~II~~Vk~SGLRGRGGAGFpTGlKWsfm~k~~~~~-k   83 (424)
T COG1894           5 FLKNQDRITFRNLGDPDPWSLDEYLARGGYEGLRKALTEMGPDEIIEEVKESGLRGRGGAGFPTGLKWSFMPKATSDQ-K   83 (424)
T ss_pred             CHHHHHHHHHHHCCCCCCCCHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCC-E
T ss_conf             010003579985579985549999854749999999986598999999987177777877787775211012478896-4


Q ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC-CCCCC
Q ss_conf             99985767784860048999862589999999999971836389981555178999999999999868997767-67886
Q gi|254780858|r   79 YLVVNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSN-SKLGY  157 (425)
Q Consensus        79 yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~-~~~g~  157 (425)
                      ||||||||+||||||||.||+++||++||||+|++||+||+++|||||+||+.++++|++||+||+++||||+| ++|||
T Consensus        84 ylvcNADE~ePGTfkDR~ime~dPH~LIEGm~IA~yA~gA~~~YiYiRgEy~~a~~~l~~AI~eA~~~GlLGknilGSgf  163 (424)
T COG1894          84 YLVCNADEGEPGTFKDRLIMEGDPHLLIEGMIIAAYAVGATKGYIYIRGEYPEAIERLQKAIEEAYAAGLLGKNILGSGF  163 (424)
T ss_pred             EEEEECCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             89984898997522137877059478888899999984453368997333099999999999999980856655568875


Q ss_pred             CCEEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCC
Q ss_conf             64069974575100110788998630899986888998622783037850002899999999996056888633898774
Q gi|254780858|r  158 DVDIIVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNR  237 (425)
Q Consensus       158 ~~~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~  237 (425)
                      +|+|.||.|+||||||||||||+||||||++||.|||||+..||||+||+||||||+|+||.|+++|++||+++|+++++
T Consensus       164 dfdl~vh~GAGAYICGEETALl~SLEGkrg~PR~KPPfPa~~GL~G~PT~INNVET~a~vP~Ii~~G~~wf~~~G~~~s~  243 (424)
T COG1894         164 DFDLYVHHGAGAYICGEETALLESLEGKRGQPRLKPPFPATSGLYGKPTVINNVETLANVPAIIRRGADWFRSIGKPNSR  243 (424)
T ss_pred             CEEEEEECCCCCEEECHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEECCHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             44899952776324052889888742778999999898644576689855402110020289998638999844888899


Q ss_pred             CEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC
Q ss_conf             30476426788787268935898799999986155678711004898524565653210024563342201103873466
Q gi|254780858|r  238 GTKLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGT  317 (425)
Q Consensus       238 Gtkl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGs  317 (425)
                      |||+|+|||+|+|||+||+|||||+||||+++|||+.+|+ ++||||+||||+++||.+.+| +|||||+++++||+|||
T Consensus       244 GTKlf~~sG~V~~pg~~E~pmG~tlrelie~~aGG~r~G~-~lKAv~pGG~s~~~l~~~~~d-~pmDydsl~~~gs~lGt  321 (424)
T COG1894         244 GTKLFSLSGHVKNPGLYEVPMGTTLRELIEDYAGGVRGGW-KLKAVQPGGPSGPCLPEELLD-TPMDYDSLAKAGSMLGT  321 (424)
T ss_pred             CCEEEEEECCCCCCCEEEECCCCCHHHHHHHHCCCCCCCC-EEEEEEECCCCCCCCCHHHHC-CCCCHHHHHHHCCCCCC
T ss_conf             8347886111268863772178859999999568867883-468996289876667888837-87677889860546676


Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             51799428652899999999999876279988523028999999999982899989999999999862236667765024
Q gi|254780858|r  318 AAVIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAA  397 (425)
Q Consensus       318 g~iiV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~~S~C~lG~~a  397 (425)
                      |+|||||+++|||++++++++||+|||||||||||+||.|+.++|+||.+|+++++|+++|.+++++|+..|+|+||++|
T Consensus       322 ggiiV~d~~~~mv~~~~~~~~F~~~ESCGkCtPCReGt~w~~~il~ri~~G~~~~~dl~~L~~l~~~i~g~s~CalG~~a  401 (424)
T COG1894         322 GGIIVMDDSTCMVKAARRLSEFYKHESCGKCTPCREGTGWMVRILERLVRGEGQPEDLDLLEDLCNQIKGKTFCALGDAA  401 (424)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCEEEECCCCC
T ss_conf             42899847500999999999985367688887866873789999999984888866799999997242774233227655


Q ss_pred             HHHHHHHHHHCHHHHHHHHHH
Q ss_conf             799999986388999999865
Q gi|254780858|r  398 AWPIQGLIKNFRPLIEERIDQ  418 (425)
Q Consensus       398 ~~pv~s~l~~F~dEfe~hI~~  418 (425)
                      ++||+|+|+||||||++||+.
T Consensus       402 ~~Pv~s~lr~Fr~E~~~~i~~  422 (424)
T COG1894         402 AWPVQSALRHFRDEFEAHIKV  422 (424)
T ss_pred             CHHHHHHHHHCHHHHHHHHCC
T ss_conf             046899998678999976304


No 5  
>PRK11278 NADH dehydrogenase I subunit F; Provisional
Probab=100.00  E-value=0  Score=1123.93  Aligned_cols=415  Identities=41%  Similarity=0.734  Sum_probs=403.7

Q ss_pred             HHHHHCCCCCCCHHHHHHCCCHHHHHHHHH-CCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCC
Q ss_conf             675517876779899997799899999982-6989999999983977687571124556874235656886199985767
Q gi|254780858|r    8 IFTNLYGLQGKSLSDSMSRGHWDNVDKILE-KGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLVVNADE   86 (425)
Q Consensus         8 ~~~~~~~~~~~~l~~y~~~ggy~~l~~~l~-~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv~N~~E   86 (425)
                      .|.|....||.+|++|+++|||++|+|+|+ |+|++|+++|++||||||||||||||+||+++++.....+|||||||||
T Consensus        15 ~~r~~~~~dp~~i~~Y~~~gGy~~l~kal~~m~p~evi~evk~SgLrGRGGAGFPtg~KW~~~~~~~~~~~kYvVcNadE   94 (448)
T PRK11278         15 TWRLRDDKQPVWLDEYRSKNGYEGARKALTGMSPDEIVNQVKDAGLKGRGGAGFSTGLKWSLMPKDESMNIRYLLCNADE   94 (448)
T ss_pred             CCCCCCCCCCCCHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCEEEEEECCC
T ss_conf             22336799987899998668799999998529999999999984887788674745313453114668996389996998


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCCEEEEEE
Q ss_conf             784860048999862589999999999971836389981555178999999999999868997767-6788664069974
Q gi|254780858|r   87 SEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSN-SKLGYDVDIIVHH  165 (425)
Q Consensus        87 ~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~-~~~g~~~~i~v~~  165 (425)
                      +||||||||+||+++||+|||||+|++||+||+++|||||+||+.++++|++||+|++++|+||+| ++++|+|+|+||+
T Consensus        95 gEPGtfKDR~lle~~Ph~viEGmiIaa~AigA~~~yIYiR~Ey~~~~~~l~~AI~ea~~~g~lG~nI~gsg~~~di~v~~  174 (448)
T PRK11278         95 MEPGTYKDRLLMEQLPHLLVEGMLISAFALKAYRGYIFLRGEYIEAAVNLRRAIAEATEAGLLGKNIMGTGFDFELFVHT  174 (448)
T ss_pred             CCCCCCCCHHHHHCCCHHHHHHHHHHHHHHCCCEEEEEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEE
T ss_conf             98443128998863956899999999999588648998265039999999999999997497776655777774579961


Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCC--CEEEEE
Q ss_conf             575100110788998630899986888998622783037850002899999999996056888633898774--304764
Q gi|254780858|r  166 GAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNR--GTKLFS  243 (425)
Q Consensus       166 g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~--Gtkl~t  243 (425)
                      |+|+||||||||||+||||+|++||.|||||+++||||+||+||||||||+||+|+++|++||+++|+++++  |||+||
T Consensus       175 GaGaYIcGEETALleSiEGkrg~PR~kPPfpa~~Gl~gkPT~VNNVETla~Vp~I~~~G~~wf~~~G~~~s~~~GTklfs  254 (448)
T PRK11278        175 GAGRYICGEETALINSLEGRRANPRSKPPFPATSGVWGKPTCVNNVETLCNVPAILANGVEWYQNISRGKSKDAGTKLMG  254 (448)
T ss_pred             CCCCEEECCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEE
T ss_conf             68722536299999984489998898999875467678984345699999899999863798874688889999827998


Q ss_pred             CCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEEEEE
Q ss_conf             26788787268935898799999986155678711004898524565653210024563342201103873466517994
Q gi|254780858|r  244 ISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAVIVM  323 (425)
Q Consensus       244 vsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~iiV~  323 (425)
                      |||+|+||||||+|+||||+|||+++|||+.+| +++|||++||+|+++|+++++| +||||+++.+.||+||||+||||
T Consensus       255 vSG~V~~PGvyEvp~G~tL~eli~~~~GG~~~G-~~~kav~pGG~sg~~l~~~~ld-~~ld~~sl~~~Gs~LGsG~viV~  332 (448)
T PRK11278        255 FSGRVKNPGLWELPFGTTAREILEDYAGGMRDG-LKFKAWQPGGAGTDFLTEAHLD-LPMEFESIGKAGSRLGTALAMAV  332 (448)
T ss_pred             ECCCCCCCCEEEECCCCCHHHHHHHHCCCCCCC-CCCEEEEECCCCCCCCCHHHHC-CCCCHHHHHHCCCCCCCEEEEEE
T ss_conf             236644684499459991999999838887899-5424997478777777988947-87786778644775344048983


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHH
Q ss_conf             286528999999999998762799885230289999999999828999899999999998622-3666776502479999
Q gi|254780858|r  324 DRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIE-GRTICALGDAAAWPIQ  402 (425)
Q Consensus       324 de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~-~~S~C~lG~~a~~pv~  402 (425)
                      |+++||+++++++++||+|||||||||||+||.|+.++|+||.+|+++++|+++|++++++|. ++|+|+||+++++||+
T Consensus       333 d~~~~~v~~~~~~~~F~~~ESCGqCtPCReGt~~l~~il~ri~~G~g~~~Dl~~L~~la~~m~~g~s~C~LG~~a~~Pv~  412 (448)
T PRK11278        333 DHEINMVSLVRNLEEFFARESCGWCTPCRDGLPWSVKILRALERGEGQPGDIETLEQLCRFLGPGKTFCAHAPGAVEPLQ  412 (448)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH
T ss_conf             68776999999999871568899998751719999999999984999989999999999874579610758533517999


Q ss_pred             HHHHHCHHHHHHHHHHHCCCCCC
Q ss_conf             99863889999998651899999
Q gi|254780858|r  403 GLIKNFRPLIEERIDQYHRCNFQ  425 (425)
Q Consensus       403 s~l~~F~dEfe~hI~~~~rCp~~  425 (425)
                      |+|++||+||++||++ ++||.+
T Consensus       413 s~l~~F~~EfeahI~~-~~~~~~  434 (448)
T PRK11278        413 SAIKYFREEFEAGIKQ-PFSNTH  434 (448)
T ss_pred             HHHHHHHHHHHHHHCC-CCCCCC
T ss_conf             9998779999998606-788765


No 6  
>KOG2658 consensus
Probab=100.00  E-value=0  Score=930.00  Aligned_cols=419  Identities=66%  Similarity=1.187  Sum_probs=414.4

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             62034367551787677989999779989999998269899999999839776875711245568742356568861999
Q gi|254780858|r    2 LTDQDRIFTNLYGLQGKSLSDSMSRGHWDNVDKILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLV   81 (425)
Q Consensus         2 ~~~~~r~~~~~~~~~~~~l~~y~~~ggy~~l~~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv   81 (425)
                      |+|++|||||+|+++++.|++.+++|+|..++.++..+|++|+++|++||||||||||||+|.||+++++..+++|||||
T Consensus        50 l~d~dRiFtNLygrhd~rlkgA~~rGdw~~tkEil~kg~~wI~~evk~SgLRGRGgaGFpsGlKw~fm~k~sd~rpk~lv  129 (478)
T KOG2658          50 LADEDRIFTNLYGRHDWRLKGALARGDWHKTKEILLKGPDWIVNEVKTSGLRGRGGAGFPSGLKWSFMNKPSDGRPKYLV  129 (478)
T ss_pred             CCCHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCEEHHCCCCCCCCCCEEE
T ss_conf             55411454555520106553135336567689998709499999877634556787788765410001478778973799


Q ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCCE
Q ss_conf             85767784860048999862589999999999971836389981555178999999999999868997767-67886640
Q gi|254780858|r   82 VNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSN-SKLGYDVD  160 (425)
Q Consensus        82 ~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~-~~~g~~~~  160 (425)
                      +|+||+||||||||.||+|+||++|||.+|++.+++|..+|||||++|.+..-.|++||.|||++||||+| .++|++||
T Consensus       130 VNadEgepGtcKDReilRHdPHKliEG~liagram~a~aayiyIR~efynEa~nlq~ai~eAY~agllGkn~cGtg~~fd  209 (478)
T KOG2658         130 VNADEGEPGTCKDREILRHDPHKLIEGCLIAGRAMGASAAYIYIRGEFYNEACNLQKAIIEAYAAGLLGKNACGTGYDFD  209 (478)
T ss_pred             EECCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHCCCCEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEE
T ss_conf             97888999756117876258077664443433210663258985004677887899999999984413554446775726


Q ss_pred             EEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEE
Q ss_conf             69974575100110788998630899986888998622783037850002899999999996056888633898774304
Q gi|254780858|r  161 IIVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTK  240 (425)
Q Consensus       161 i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtk  240 (425)
                      +.||+|+|+||||||||||+|||||.|.||.|||||+++|+||+||+|-||||+|++|.|++.|+.||.++|.+.+.|||
T Consensus       210 v~vhrGagaYicGEEtAlIesLeGk~gkPr~kppf~a~~G~Fg~Pt~V~NvETVav~PtI~rrG~~wfasfGR~~N~GTK  289 (478)
T KOG2658         210 VFVHRGAGAYICGEETALIESLEGKQGKPRLKPPFPADSGLFGCPTTVTNVETVAVSPTICRRGGKWFASFGRPRNRGTK  289 (478)
T ss_pred             EEEECCCCCEEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCHHHHHCCCHHHHHCCCCCCCCCE
T ss_conf             99953886333061889999860557998899998454552368722531023304408884365345541887788743


Q ss_pred             EEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEE
Q ss_conf             76426788787268935898799999986155678711004898524565653210024563342201103873466517
Q gi|254780858|r  241 LFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAV  320 (425)
Q Consensus       241 l~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~i  320 (425)
                      ||++||+|++|+++|.+|.+||+||||.||||+.+||+++-|++|||+|.++++++..+++.||||+|.+++|.||+|+|
T Consensus       290 Lf~iSG~Vn~PctVEeeMSiPlKdLIErhaGGV~GGWdnLlaiiPGG~stpli~kn~c~~vlmDFD~L~a~~S~lGtgav  369 (478)
T KOG2658         290 LFCISGHVNNPCTVEEEMSIPLKDLIERHAGGVRGGWDNLLAIIPGGSSTPLIPKNVCEQVLMDFDSLKAAQSGLGTGAV  369 (478)
T ss_pred             EEEECCCCCCCCCHHHHHCCCHHHHHHHHCCCCCCCHHHEEEECCCCCCCCCCCHHHHHHHHCCHHHHHHHHCCCCCEEE
T ss_conf             78743655897405777277389999984587436533214656699888771866675661146877766426873159


Q ss_pred             EEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHH
Q ss_conf             99428652899999999999876279988523028999999999982899989999999999862236667765024799
Q gi|254780858|r  321 IVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAWP  400 (425)
Q Consensus       321 iV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~~S~C~lG~~a~~p  400 (425)
                      ||||+++++++.+.++++||.|||||||||||+|+.|+.+++.|+.+|+++++++|+|-++++.|.+.++|+||+++++|
T Consensus       370 IVm~k~tdi~~~iarl~~FykhesC~qCt~CReG~~w~~~im~rfv~G~a~~~eid~~~e~~kqieghtiCalgd~aa~~  449 (478)
T KOG2658         370 IVMNKSTDIVKAIARLIKFYKHESCGQCTPCREGVEWLNEIMARFVDGQAHPSEIDMLFEISKQIEGHTICALGDSAAWP  449 (478)
T ss_pred             EEEECCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCC
T ss_conf             99707873999999999986236688787411125689999999752787889988999997543785345405554351


Q ss_pred             HHHHHHHCHHHHHHHHHHHC
Q ss_conf             99998638899999986518
Q gi|254780858|r  401 IQGLIKNFRPLIEERIDQYH  420 (425)
Q Consensus       401 v~s~l~~F~dEfe~hI~~~~  420 (425)
                      ++++++|||+|+|+++.+++
T Consensus       450 vqgliR~Fr~~ie~R~~~~a  469 (478)
T KOG2658         450 VQGLIRHFRPEIEERMKKRA  469 (478)
T ss_pred             HHHHHHHCCHHHHHHHHHHH
T ss_conf             57787757698999999998


No 7  
>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit; InterPro: IPR010208   The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation . A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized . This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase (IPR003667 from INTERPRO), but is distinct. This entry describes the C subunit.; GO: 0051539 4 iron 4 sulfur cluster binding, 0006118 electron transport, 0016020 membrane.
Probab=100.00  E-value=0  Score=433.27  Aligned_cols=318  Identities=22%  Similarity=0.363  Sum_probs=248.4

Q ss_pred             HHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99826989999999983977687571124556874235656886199985767784860048999862589999999999
Q gi|254780858|r   34 KILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLVVNADESEPGTCKDRDIMRHEPHTLIEGCVIAS  113 (425)
Q Consensus        34 ~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a  113 (425)
                      +.-++++++|++.|++|||+|+|||+||||+|++.-+   ..+.++||+||+|||||++.|+.||++++++||+|+.|.+
T Consensus       118 ~~~~l~~~~i~~~I~~AGIvGlGGAtFPthvKL~~pp---~~~~~~LIiNGAECEPYlT~DdrLMrEra~eI~~GI~I~~  194 (444)
T TIGR01945       118 DESSLSPEEILEKIRAAGIVGLGGATFPTHVKLNPPP---EKKVELLIINGAECEPYLTCDDRLMRERAEEIIQGIRILL  194 (444)
T ss_pred             CHHHCCHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCC---CCCCEEEEEECEECCCCCCCCCHHHHCCHHHHHHHHHHHH
T ss_conf             7331487999999997086556755201011038586---5521078980433386546142233317578999999999


Q ss_pred             HHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCC
Q ss_conf             97183638998155517899999999999986899776767886640699745751001107889986308999868889
Q gi|254780858|r  114 FAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAYICGEETALLESLEGKKGQPRLKP  193 (425)
Q Consensus       114 ~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kP  193 (425)
                      ++++.+++||+|+||+|+||++|++|+++..        ..   .-+|+|+..+..||+|-|++||++|+|+ -+|+.. 
T Consensus       195 ~~L~~~~~viGIEDNKpeAI~al~~a~~~~~--------~P---t~~i~v~vlpTkYPqGgEKQLI~~lTgr-eVPsG~-  261 (444)
T TIGR01945       195 KILGVKKVVIGIEDNKPEAIAALKKALEGYP--------KP---TKNIKVRVLPTKYPQGGEKQLIKALTGR-EVPSGG-  261 (444)
T ss_pred             HHHCCCEEEEEEECCCHHHHHHHHHHHHCCC--------CC---CCCEEEEEEECCCCCCHHHHHHHHHHCC-CCCCCC-
T ss_conf             9718986999865795799999999860278--------88---7754788841228986078899998345-078888-


Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCC-CCCCEEEEECCCCCHHHHHHHHHCC
Q ss_conf             986227830378500028999999999960568886338987743047642678-8787268935898799999986155
Q gi|254780858|r  194 PFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGH-VNYPCTVEESMSITFDELIEKHCGG  272 (425)
Q Consensus       194 P~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~-V~~Pg~~evp~Gt~l~eli~~~~GG  272 (425)
                       +|+++|+     ||+||.|+++|..++.+|...          -.|++||||+ |+||.||+|++|||+.+||+ +|||
T Consensus       262 -LP~d~Gv-----vvqNVGT~~Ai~~Av~~G~PL----------ieRvVTVtG~~i~~P~N~~v~IGTPV~~~l~-~cGg  324 (444)
T TIGR01945       262 -LPADIGV-----VVQNVGTAFAIKEAVVNGKPL----------IERVVTVTGDAIRRPKNLWVLIGTPVSDILA-HCGG  324 (444)
T ss_pred             -CCHHCCE-----EEECHHHHHHHHHHHHCCCCC----------EEEEEEEECCCCCCCCCEEEECCCCHHHHHH-HCCC
T ss_conf             -8312144-----456067899999998678961----------2566875141327887668855885799998-7187


Q ss_pred             CCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEEEEECCCCCHHHHHH-HHHHHHHHHHCCCCC-C
Q ss_conf             67871100489852456565321002456334220110387346651799428652899999-999999876279988-5
Q gi|254780858|r  273 IRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAVIVMDRSTDIIKAIW-RLSVFYKHESCGQCT-P  350 (425)
Q Consensus       273 ~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~iiV~de~~~iv~~~~-~~~~F~a~ESCGkCt-P  350 (425)
                      ..+...+   +++||||||+=-. +++ +|+          .-||.+|.+++..    ++.. +-.  -+-=+||+|. -
T Consensus       325 ~~~~~~r---~i~GGPMMG~al~-~~~-vPv----------~KGtsGiLal~~~----E~~~~~~~--~~CIRCg~Cv~~  383 (444)
T TIGR01945       325 FREKTER---LIMGGPMMGLALP-SLD-VPV----------TKGTSGILALDKE----ELTEPKPE--KPCIRCGKCVNV  383 (444)
T ss_pred             CCCCCCC---EEEECCCCCCCCC-CCC-CCE----------EECCCCEECCCCC----CCCCCCCC--CCCCCHHCCCCC
T ss_conf             7577887---5740786676578-888-667----------7225400035701----16787466--788440010155


Q ss_pred             CCCHH-HHHHHHHHHHHCCCCCHHHHHHHHHHH--HHHCCCCCCCCCHHHHHHHHHHHHHCHHHHH
Q ss_conf             23028-999999999982899989999999999--8622366677650247999999863889999
Q gi|254780858|r  351 CREGT-GWMMRVMERLVKGIAQKREIDLLYEVS--KNIEGRTICALGDAAAWPIQGLIKNFRPLIE  413 (425)
Q Consensus       351 CR~Gt-~~l~~il~~i~~G~a~~~Dl~~L~~la--~~i~~~S~C~lG~~a~~pv~s~l~~F~dEfe  413 (425)
                      |=.++ ++....+       +..++.|.+.+..  |=|..+ -|++--=|..|+...+|.=+.++.
T Consensus       384 CPm~L~P~~L~~~-------A~~~~~d~~~~~~L~DCIECG-~C~Y~CPs~iPLV~Y~R~aK~~~~  441 (444)
T TIGR01945       384 CPMGLLPQQLNWL-------AKADEFDEAAEHNLMDCIECG-SCSYVCPSNIPLVQYIRQAKAKLR  441 (444)
T ss_pred             CCCCCHHHHHHHH-------HHHHHHHHHHHCCCCEEEECC-CCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             6744227999987-------531016889963881466125-665428775258999988789861


No 8  
>PRK05035 electron transport complex protein RnfC; Provisional
Probab=100.00  E-value=0  Score=403.56  Aligned_cols=316  Identities=22%  Similarity=0.295  Sum_probs=242.5

Q ss_pred             HHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             82698999999998397768757112455687423565688619998576778486004899986258999999999997
Q gi|254780858|r   36 LEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLVVNADESEPGTCKDRDIMRHEPHTLIEGCVIASFA  115 (425)
Q Consensus        36 l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a  115 (425)
                      ..++++++++.|+++||+|+||||||||+||+.    ...++++||+||+|||||++.|+.||++.++.||+|+.|.+++
T Consensus       129 ~~~~~~el~~~I~~AGIvGlGGAgFPT~vKL~p----~~~~idtLIINgaECEPYIT~DdrLM~E~a~eIi~Gi~Il~~~  204 (725)
T PRK05035        129 RSLSREELIERIRQAGIAGLGGAGFPTAIKLQP----GGDKIETLIINGAECEPYITADDRLMRERADEILEGIRILAHI  204 (725)
T ss_pred             HHCCHHHHHHHHHHCCCCCCCCCCCCCHHHCCC----CCCCCCEEEECCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHH
T ss_conf             448999999999975943468888861131268----8887758997351356424016999988899999999999998


Q ss_pred             HCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             18363899815551789999999999998689977676788664069974575100110788998630899986888998
Q gi|254780858|r  116 IGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAYICGEETALLESLEGKKGQPRLKPPF  195 (425)
Q Consensus       116 ~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP~  195 (425)
                      +++++++|+|++|+|++|+.|++++...               -+|+|+..+..||+|.|+.||+.++|+. +|..+  +
T Consensus       205 l~~~~~iIgIEdNKPeAI~al~~a~~~~---------------~~i~V~~lptkYPqGgEKqLI~~lTGre-VP~G~--l  266 (725)
T PRK05035        205 LQPKEVLIGIEDNKPEAIAALRAALAGA---------------DDIRVRVIPTKYPSGGEKQLIQILTGKE-VPSGG--R  266 (725)
T ss_pred             HCCCEEEEEEECCCHHHHHHHHHHHCCC---------------CCEEEEECCCCCCCCHHHHHHHHHHCCC-CCCCC--C
T ss_conf             3998799998389899999999974669---------------9859998178799948999999994974-68999--8


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCC-CCCCEEEEECCCCCHHHHHHHHHCCCC
Q ss_conf             6227830378500028999999999960568886338987743047642678-878726893589879999998615567
Q gi|254780858|r  196 PANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGH-VNYPCTVEESMSITFDELIEKHCGGIR  274 (425)
Q Consensus       196 p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~-V~~Pg~~evp~Gt~l~eli~~~~GG~~  274 (425)
                      |+++|+     +|+||.|.++|...+.+|-...          .|++||||+ |++|+||+|++|||+++||+ +|||..
T Consensus       267 PadvGv-----vv~NVgTa~AI~~Av~~G~PLi----------eRvVTVTG~av~~P~N~~v~iGTPv~~Ll~-~~Gg~~  330 (725)
T PRK05035        267 PADIGV-----LMQNVGTAYAIKRAVIDGEPLI----------ERVVTLTGEAVARPGNVWARLGTPVRHLLN-QAGFKP  330 (725)
T ss_pred             CCCCCE-----EEECHHHHHHHHHHHHCCCCEE----------EEEEEEECCCCCCCCEEEEECCCCHHHHHH-HCCCCC
T ss_conf             765665-----9866899999999997499746----------899997467548997289979995999999-749988


Q ss_pred             CCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCC-CCCC
Q ss_conf             871100489852456565321002456334220110387346651799428652899999999999876279988-5230
Q gi|254780858|r  275 GGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAVIVMDRSTDIIKAIWRLSVFYKHESCGQCT-PCRE  353 (425)
Q Consensus       275 ~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~iiV~de~~~iv~~~~~~~~F~a~ESCGkCt-PCR~  353 (425)
                      +...+   |++||||||+--++ ++ .|+          .-||.+|++++.+.-....     .-...-.||+|. -|-.
T Consensus       331 ~~~~k---vImGGPMMG~~l~~-ld-vPV----------~K~Tn~ILa~~~~e~~~~~-----~e~~CIRCG~Cv~aCP~  390 (725)
T PRK05035        331 DADQR---VIMGGPMMGFTLPD-LD-VPV----------VKTTNCLLAPSATELPPPP-----PEQACIRCGACADACPA  390 (725)
T ss_pred             CCCCE---EEECCCCCCCCCCC-CC-CCC----------EECCEEEEECCHHHCCCCC-----CCCCCCCCCHHHHHCCC
T ss_conf             88875---88458975762788-99-870----------3054069962877748888-----88777525136763899


Q ss_pred             HH-HHHHHHHHHHHCCCCCHHHHHHHHHH--HHHHCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHH
Q ss_conf             28-99999999998289998999999999--986223666776502479999998638899999986
Q gi|254780858|r  354 GT-GWMMRVMERLVKGIAQKREIDLLYEV--SKNIEGRTICALGDAAAWPIQGLIKNFRPLIEERID  417 (425)
Q Consensus       354 Gt-~~l~~il~~i~~G~a~~~Dl~~L~~l--a~~i~~~S~C~lG~~a~~pv~s~l~~F~dEfe~hI~  417 (425)
                      ++ ++...-+   .+    ..|.+.+++.  .+=|. =..|.+---+..|+....++=+.|+.+.-+
T Consensus       391 ~LlPqqL~w~---ak----~~~~dka~~~~l~DCIE-CG~CaYVCPS~IPLVqYyR~aK~eI~~~~~  449 (725)
T PRK05035        391 SLLPQQLYWF---AK----AEEHDKAEEHNLFDCIE-CGACAYVCPSNIPLVQYYRQAKAEIRAIEQ  449 (725)
T ss_pred             CCCHHHHHHH---HH----CCCHHHHHHCCCCCCCC-CCCCCEECCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             7779999999---87----67799998679963600-287762689888489999999999999999


No 9  
>pfam01512 Complex1_51K Respiratory-chain NADH dehydrogenase 51 Kd subunit.
Probab=100.00  E-value=0  Score=346.46  Aligned_cols=149  Identities=46%  Similarity=0.724  Sum_probs=137.9

Q ss_pred             HHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEC
Q ss_conf             99839776875711245568742356568861999857677848600489998625899999999999718363899815
Q gi|254780858|r   47 VKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLVVNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVR  126 (425)
Q Consensus        47 v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir  126 (425)
                      |++|||+||||||||||+||+...+   ..++||||||+||||++|+||+||+++||+||||+.|+++++||++++||||
T Consensus         1 i~~agivG~GGAgFPt~~Kl~~~~~---~~~~~livN~~EcEP~~~~D~~lm~~~p~~vl~G~~i~~~a~ga~~~~I~I~   77 (150)
T pfam01512         1 IKEAGIVGRGGAGFPTHVKLSPPAD---KKIKYLIVNGAECEPGLTKDRRLMRERPHEIIEGILIAAYALGAKKGVIGIE   77 (150)
T ss_pred             CCCCCCCCCCCCCCCCHHHCCCCCC---CCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf             9401546676665300122346657---8997899967879843579823788758999999999999859898999982


Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             55178999999999999868997767678866406997457510011078899863089998688899862278303785
Q gi|254780858|r  127 GEFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPT  206 (425)
Q Consensus       127 ~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT  206 (425)
                      ++|++++++|++||++++..+            +|+|+.++++||||||++||++++|+ ..||.+|  |+++|+     
T Consensus        78 ~~~~~ai~~l~~ai~~~~~~~------------~i~V~~~~~~Yp~GeE~~Li~~l~Gr-~vP~~~~--P~~~G~-----  137 (150)
T pfam01512        78 DNKPEAIAALEKAIAEAPAAG------------DIEVVLLPGKYPCGEEKALIYSLTGR-EVPRGGL--PADVGV-----  137 (150)
T ss_pred             CCCHHHHHHHHHHHHHHHHCC------------CEEEEECCCCCCCCHHHHHHHHHHCC-CCCCCCC--CCCCCE-----
T ss_conf             688999999999999666639------------88999899867546799999998699-7798979--865785-----


Q ss_pred             CCCCHHHHHHHH
Q ss_conf             000289999999
Q gi|254780858|r  207 TVNNVESIAVVP  218 (425)
Q Consensus       207 ~V~NVeTla~v~  218 (425)
                      +||||||+++|+
T Consensus       138 vV~NVeT~~~V~  149 (150)
T pfam01512       138 VVNNVETLAAVP  149 (150)
T ss_pred             EEECHHHHHHCC
T ss_conf             998589984265


No 10 
>COG4656 RnfC Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion]
Probab=100.00  E-value=0  Score=330.41  Aligned_cols=330  Identities=22%  Similarity=0.341  Sum_probs=246.0

Q ss_pred             CCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCH
Q ss_conf             67798999977998999999826989999999983977687571124556874235656886199985767784860048
Q gi|254780858|r   16 QGKSLSDSMSRGHWDNVDKILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLVVNADESEPGTCKDR   95 (425)
Q Consensus        16 ~~~~l~~y~~~ggy~~l~~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv~N~~E~EPgt~kDr   95 (425)
                      ++.+.+.|...--.+.++   .++|+++++.|+++|++|.|||+||||+|+..-    ..+.+++|+||+||||++..|.
T Consensus       101 ~~d~~~~w~e~~p~~~~~---~~s~e~Lle~I~qAGIvg~gga~fpT~~Kl~~~----~~ki~~LIinaaecEp~~~~d~  173 (529)
T COG4656         101 QGDGLDQWIELQPIEDFE---GASPEELLEKIKQAGIVGLGGAGFPTAVKLQAG----CKKIETLIINAAECEPYITADD  173 (529)
T ss_pred             CCCCHHHHHHCCCCCCHH---HCCHHHHHHHHHHCCCCCCCCCCCCCHHHHCCC----CCCEEEEEEEHHCCCCCCCHHH
T ss_conf             575154442037774032---279999999999809564377778614442554----0300036663100576643768


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCHH
Q ss_conf             99986258999999999997183638998155517899999999999986899776767886640699745751001107
Q gi|254780858|r   96 DIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAYICGEE  175 (425)
Q Consensus        96 ~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Yi~GeE  175 (425)
                      +||.+.++.|++|+.|.++.+++++.+|+|+++||+++..++.++...               .+|.++..+..||.|.|
T Consensus       174 ~LM~e~a~eI~~Gi~il~~i~~~~~~vIaied~kp~ai~~l~~a~~~~---------------~~i~I~~lp~kYP~g~~  238 (529)
T COG4656         174 RLMREHAEEIVKGIQILRKILKPKEVVIAIEDNKPEAIAALRAALFGD---------------RDIKIHVLPTKYPSGGE  238 (529)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHCCC---------------CCEEEEECCCCCCCCHH
T ss_conf             999998999999999999751650479987459778899999974358---------------74499976777898218


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCC-CCCCEEE
Q ss_conf             889986308999868889986227830378500028999999999960568886338987743047642678-8787268
Q gi|254780858|r  176 TALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGH-VNYPCTV  254 (425)
Q Consensus       176 tali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~-V~~Pg~~  254 (425)
                      ..||..++|+. +|...  +|+++|+     +|+||+|+++|..++.+|...          -.|.+||+|+ |++|+++
T Consensus       239 k~li~~ltgr~-vP~g~--lp~~vgv-----lv~NV~T~~aV~~AIv~~~Pl----------ier~vTltG~av~~p~nv  300 (529)
T COG4656         239 KQLIKILTGRE-VPKGG--LPSDVGV-----LVQNVGTAYAVKRAIVDGKPL----------IERVVTLTGDAVKRPKNV  300 (529)
T ss_pred             HHHHHHHHCCC-CCCCC--CCCCCCE-----EEECHHHHHHHHHHHHCCCCE----------EEEEEEEECCCCCCCCEE
T ss_conf             88999974883-88888--8864457-----983558899999998659971----------799998514121688608


Q ss_pred             EECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEEEEECCCCCHHHHHH
Q ss_conf             93589879999998615567871100489852456565321002456334220110387346651799428652899999
Q gi|254780858|r  255 EESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAVIVMDRSTDIIKAIW  334 (425)
Q Consensus       255 evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~iiV~de~~~iv~~~~  334 (425)
                      +|++|||++++|+ .|||..+....   |++||||||+.-. .|| .|+          .-++.+++|.++.--.-....
T Consensus       301 ~VrIGTP~~~lL~-~~G~~~~~~~~---vi~gGPmmG~~l~-~ld-~PV----------tK~t~~Ll~~~~~e~~~~~~~  364 (529)
T COG4656         301 WVRIGTPVSQLLN-EAGGIDTKPYR---VIMGGPMMGFKLP-TLD-APV----------TKTTNGLLALTKKELLEPIKE  364 (529)
T ss_pred             EEECCCCHHHHHH-HCCCCCCCCCE---EEECCCCCCCCCC-CCC-CCE----------ECCCCEEEECCCCCCCCCCHH
T ss_conf             9977894999999-74897678751---7846875564144-567-764----------614443784373234663010


Q ss_pred             HHHHHHHHHHCCCCCCCCCHHH--HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCHHHH
Q ss_conf             9999998762799885230289--99999999982899989999999999862236667765024799999986388999
Q gi|254780858|r  335 RLSVFYKHESCGQCTPCREGTG--WMMRVMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAWPIQGLIKNFRPLI  412 (425)
Q Consensus       335 ~~~~F~a~ESCGkCtPCR~Gt~--~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~~S~C~lG~~a~~pv~s~l~~F~dEf  412 (425)
                      .        ||=+|.-|-.=.+  .+-..|.....+  ...|-.....+-+-+. -.+|+.---+..|+   .++|+.+.
T Consensus       365 q--------sCi~C~~C~d~CP~~Llp~ql~~~a~~--~~~~e~~~~~l~dCIE-Cg~Ca~vCPs~ipl---vq~~r~~K  430 (529)
T COG4656         365 Q--------SCIRCSLCADACPVNLLPQQLYWFAKG--EQHDEEEEHNLLDCIE-CGACAYVCPSNIPL---VQYFRQEK  430 (529)
T ss_pred             H--------CCCCHHHHHHHCCCCCCHHHHHHHHHH--HHHHHHHHHHHHHHHH-HCCCHHCCCCCCCH---HHHHHHHH
T ss_conf             1--------150477787747512588886677654--2456888877665255-07311007777888---99999999


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780858|r  413 EER  415 (425)
Q Consensus       413 e~h  415 (425)
                      ..-
T Consensus       431 a~i  433 (529)
T COG4656         431 AEI  433 (529)
T ss_pred             HHH
T ss_conf             999


No 11 
>PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional
Probab=99.86  E-value=1.1e-20  Score=159.44  Aligned_cols=297  Identities=17%  Similarity=0.233  Sum_probs=190.0

Q ss_pred             HHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98269899999999839776875711245568742356568861999857677848600489998625899999999999
Q gi|254780858|r   35 ILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLVVNADESEPGTCKDRDIMRHEPHTLIEGCVIASF  114 (425)
Q Consensus        35 ~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~  114 (425)
                      ..++++++|++.+.+||+    ++.|+|.- +..++ .+...|+.+++||.||||++..++++|+++...++.|+.+.++
T Consensus       111 ~~~ls~e~i~~~L~~sGl----w~~~rqRP-f~~ia-~p~~~P~~IfIna~d~~Pl~~d~~~il~~~~~~f~~Gi~iL~k  184 (448)
T PRK05352        111 LASLSREQVKENLLESGL----WTALRTRP-FSKVP-APDSTPRAIFVTAMDTNPLAADPEVIIAEQSEAFQAGLTVLAR  184 (448)
T ss_pred             HHHCCHHHHHHHHHHCCC----CCCCCCCC-CCCCC-CCCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             435699999999986698----62225645-55368-9878876599976568878889799998779999999999998


Q ss_pred             HHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             71836389981555178999999999999868997767678866406997457510011078899863089998688899
Q gi|254780858|r  115 AIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAYICGEETALLESLEGKKGQPRLKPP  194 (425)
Q Consensus       115 a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP  194 (425)
                      ... .+.++.+..+.......                      .-+++++..+|.||+|-+..+|+.|.           
T Consensus       185 Lt~-~~v~l~~~~~~~~~~~~----------------------~~~v~~~~~~GphPaG~~g~~Ih~i~-----------  230 (448)
T PRK05352        185 LTE-GKVHVCKADGAALPGEN----------------------LANVEVHEFAGPHPAGLVGTHIHFLD-----------  230 (448)
T ss_pred             HCC-CCEEEEECCCCCCCCCC----------------------CCCEEEEEECCCCCCCCHHHHEEEEC-----------
T ss_conf             618-97699954897654223----------------------57728998179899998132044676-----------


Q ss_pred             CCCCCCCCCCCCCC--CCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCC-CCCCEEEEECCCCCHHHHHHHHHC
Q ss_conf             86227830378500--028999999999960568886338987743047642678-878726893589879999998615
Q gi|254780858|r  195 FPANVGLYGCPTTV--NNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGH-VNYPCTVEESMSITFDELIEKHCG  271 (425)
Q Consensus       195 ~p~~~Gl~g~PT~V--~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~-V~~Pg~~evp~Gt~l~eli~~~~G  271 (425)
                       |+..|-     +|  -|++++++|...+..|.          ..-+|++||+|. |++|++|++.+|+++.+|+.   |
T Consensus       231 -Pi~~g~-----~VW~i~~qdVi~Ig~~~~~G~----------~~~~RvVtv~G~~v~~P~~~~t~iGa~v~~ll~---g  291 (448)
T PRK05352        231 -PVSAGK-----TVWTIGYQDVIAIGKLFLTGE----------LYTERVVALAGPAVKKPRLVRTRLGASLSELTA---G  291 (448)
T ss_pred             -CCCCCC-----EEEECCHHHHHHHHHHHHCCC----------CCCEEEEEEECCCCCCCCEEEEECCCCHHHHHC---C
T ss_conf             -888777-----469715888999999997498----------676589997368667883599968971999966---7


Q ss_pred             CCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEEEEECCCCC--HHHHH----------HHHHH-
Q ss_conf             567871100489852456565321002456334220110387346651799428652--89999----------99999-
Q gi|254780858|r  272 GIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAVIVMDRSTD--IIKAI----------WRLSV-  338 (425)
Q Consensus       272 G~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~iiV~de~~~--iv~~~----------~~~~~-  338 (425)
                      ....+..  + +|.||+++|.--...  +..|.|          -+..|.|+.|...  +..++          +-++. 
T Consensus       292 ~~~~~~~--R-iIsG~vL~G~~~~~~--~~~LG~----------y~~qvtvipe~~~~e~~Gw~~Pg~~k~S~~~~~~S~  356 (448)
T PRK05352        292 ELKAGEV--R-VISGSVLSGRTASGP--HAYLGR----------YHNQVSVLPEGREREFFGWLRPGSNKFSITRTYLSH  356 (448)
T ss_pred             CCCCCCE--E-EEECCCCCCEECCCC--CCCCCC----------CCCEEEEECCCCCHHCCCCCCCCCCCCCCCCEEEEH
T ss_conf             7777870--6-995676434151577--775345----------554226603787121101335788765412145400


Q ss_pred             HHH-H-----------H----HCCCCC---CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHH--HHHC-CCCCCCCCHH
Q ss_conf             998-7-----------6----279988---523028999999999982899989999999999--8622-3666776502
Q gi|254780858|r  339 FYK-H-----------E----SCGQCT---PCREGTGWMMRVMERLVKGIAQKREIDLLYEVS--KNIE-GRTICALGDA  396 (425)
Q Consensus       339 F~a-~-----------E----SCGkCt---PCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la--~~i~-~~S~C~lG~~  396 (425)
                      |+- .           |    -||.|-   |=..=-.+|.   ..+..     .|+|.++++.  +.+. +=++|.+-..
T Consensus       357 l~~~~~~~~~t~~nG~~Ra~I~~g~~e~v~P~di~P~qL~---ka~~~-----~d~e~~e~lGi~e~~eED~alcsyvCp  428 (448)
T PRK05352        357 LFKKKLFNFTTSTNGSERAMVPIGNYERVMPLDILPTLLL---RALIA-----GDTDEAQALGALELDEEDLALCTFVCP  428 (448)
T ss_pred             HCCCCCCCCCCCCCCCCCCEEECCHHHHHCCCCCCHHHHH---HHHHC-----CCHHHHHHCCCCCCCHHHCCEEEEECC
T ss_conf             1467767875666886443788674764278856899999---99870-----699999875990338536414645888


Q ss_pred             HHHHHHHHHHHCHHHHH
Q ss_conf             47999999863889999
Q gi|254780858|r  397 AAWPIQGLIKNFRPLIE  413 (425)
Q Consensus       397 a~~pv~s~l~~F~dEfe  413 (425)
                      +-..+.+.||.=-|.++
T Consensus       429 SK~e~~~i~r~~L~~~~  445 (448)
T PRK05352        429 GKYEYGPILRDCLDRIE  445 (448)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             61248999999999997


No 12 
>pfam10589 NADH_4Fe-4S NADH-ubiquinone oxidoreductase-F iron-sulfur binding region.
Probab=99.52  E-value=5.6e-15  Score=120.99  Aligned_cols=46  Identities=41%  Similarity=1.050  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             9999999999987627998852302899999999998289998999
Q gi|254780858|r  330 IKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREI  375 (425)
Q Consensus       330 v~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl  375 (425)
                      |++++++++||++||||||||||+||+|+.++|++|.+|+++++|+
T Consensus         1 v~~a~~~~~F~~~ESCGqC~PCR~Gt~~l~~~l~~i~~G~~~~~dl   46 (46)
T pfam10589         1 VAVARRLAEFFAHESCGKCTPCREGTKWLAEILDRIEEGKGTEEDL   46 (46)
T ss_pred             CHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCC
T ss_conf             9899999999751558999884051999999999998499982619


No 13 
>pfam10531 SLBB SLBB domain.
Probab=98.79  E-value=6.5e-09  Score=80.08  Aligned_cols=52  Identities=33%  Similarity=0.506  Sum_probs=44.2

Q ss_pred             EEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCC
Q ss_conf             76426788787268935898799999986155678711004898524565653
Q gi|254780858|r  241 LFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCL  293 (425)
Q Consensus       241 l~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l  293 (425)
                      +++|+|+|+||++||++.|||++|+|+.++|+...+ ..+|++++||++++++
T Consensus         1 ~v~V~G~V~~Pg~~~~~~G~~~~~~l~~aGG~~~~~-~~~~~~~~gG~~~~~~   52 (52)
T pfam10531         1 VVTVSGEVKRPGNYEVPIGTTLSDLIEQAGGLTDDA-RRLKRVIPGGPMMGIL   52 (52)
T ss_pred             CEEEEEEECCCEEEEECCCCCHHHHHHHHCCCCCCC-CCCCEEEECCCCCCCC
T ss_conf             999898977970799869799999999857998873-6211899798865649


No 14 
>TIGR01936 nqrA NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit; InterPro: IPR008703 This family consists of several bacterial Na^+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na^+-translocating NADH: ubiquinone oxidoreductase (Na^+-NQR) generates an electrochemical Na^+ potential driven by aerobic respiration .; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0006814 sodium ion transport.
Probab=96.97  E-value=0.0059  Score=39.89  Aligned_cols=230  Identities=14%  Similarity=0.167  Sum_probs=156.0

Q ss_pred             HCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCC--CCCCCEEEEEECCCCCCCCCCCHHHHHHHHH------HHHHH
Q ss_conf             269899999999839776875711245568742356--5688619998576778486004899986258------99999
Q gi|254780858|r   37 EKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKV--CSDRPHYLVVNADESEPGTCKDRDIMRHEPH------TLIEG  108 (425)
Q Consensus        37 ~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~--~~~~~~yvv~N~~E~EPgt~kDr~Ll~~~p~------~vieG  108 (425)
                      +++.++|.+.+.+|||=+.        .|-|.-.+.  +...|+=|=||+..-.|.+-.=..++...-.      .+.-|
T Consensus       112 ~Ls~~~~~~~l~~sGLw~~--------~k~RPFd~va~p~~~p~~iFi~a~Dt~Plap~~~~~~~~~s~~E~G~Y~f~~G  183 (466)
T TIGR01936       112 TLSAEQIKELLLESGLWTA--------LKQRPFDIVATPDSSPRDIFITAADTRPLAPDPEVVLAEFSEKEEGYYAFVAG  183 (466)
T ss_pred             HCCHHHHHHHHHHHHHHHH--------HHCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCEEEEECCCCCCCCHHHHHHH
T ss_conf             0378999999874005767--------65088888866888722057730057689988023352245543413566789


Q ss_pred             HHHHHHHHC-CCEEEEEE-CCCCHHHH-HHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCC
Q ss_conf             999999718-36389981-55517899-9999999999868997767678866406997457510011078899863089
Q gi|254780858|r  109 CVIASFAIG-AHCAFIYV-RGEFIRER-ESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAYICGEETALLESLEGK  185 (425)
Q Consensus       109 ~~i~a~a~g-A~~~~I~i-r~ey~~~~-~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Yi~GeEtali~sieG~  185 (425)
                      +...++..+ ..+.||.. ++.-...- +.+                      -.+++|...|-+|+|.-..+|+.+.  
T Consensus       184 ~~alakL~~G~~k~~~~~k~~~~~lP~~e~~----------------------~~~~~~~~~GPhPaG~~g~hIh~~~--  239 (466)
T TIGR01936       184 LDALAKLFTGSLKVHVCKKADRLSLPTQELL----------------------SNAEIHTVSGPHPAGLPGTHIHFIA--  239 (466)
T ss_pred             HHHHHHHHCCCCCEEEEEECCCCCCCCHHHC----------------------CCEEEEEEECCCCCCCCCEEEEEEC--
T ss_conf             9999987279964279970488757721210----------------------6615899526658986230345304--


Q ss_pred             CCCCCCCCCCCCCC-CCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCC-CCCC--EEEEECCCCC
Q ss_conf             99868889986227-830378500028999999999960568886338987743047642678-8787--2689358987
Q gi|254780858|r  186 KGQPRLKPPFPANV-GLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGH-VNYP--CTVEESMSIT  261 (425)
Q Consensus       186 r~~Pr~kPP~p~~~-Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~-V~~P--g~~evp~Gt~  261 (425)
                              |.-.+. -+|    - -|-.-+-+|..++..|.-|..          |+++++|. |+.|  ..+..-+|.+
T Consensus       240 --------Pi~~~~~~Vw----~-l~~qDvi~iG~LfltG~~~~~----------rviaLAG~~~~~~~RryVrt~~GA~  296 (466)
T TIGR01936       240 --------PIGAEKEVVW----T-LNYQDVIAIGKLFLTGELLTE----------RVIALAGPAVKKPLRRYVRTTKGAN  296 (466)
T ss_pred             --------CCCCCCCEEE----E-EEEEEEEEECCHHHCCEEEEE----------EEEEEECCCCCCCCCCEEEEECCCC
T ss_conf             --------3258863589----8-741132320102212243115----------6777306401113466278723776


Q ss_pred             HHHHHHHHHCCCC-CCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEEEEECCCCCHHHHHHHHH
Q ss_conf             9999998615567-871100489852456565321002456334220110387346651799428652899999999
Q gi|254780858|r  262 FDELIEKHCGGIR-GGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAVIVMDRSTDIIKAIWRLS  337 (425)
Q Consensus       262 l~eli~~~~GG~~-~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~iiV~de~~~iv~~~~~~~  337 (425)
                      |.+++..-  =+. ++..+   +|.|-+.+|-+-.++-+ +-|.   .+       +-.|.|+.+.++--+...+++
T Consensus       297 l~~l~~~~--~~~k~~~~r---~IsG~vLtG~~~~~~~~-PyLG---~r-------~~qisvl~eg~d~~E~F~~~~  357 (466)
T TIGR01936       297 LSQLLPGE--LTSKEGENR---LISGSVLTGRLAKKEEA-PYLG---RR-------DLQISVLPEGDDKRELFGWLR  357 (466)
T ss_pred             HHHHCCCC--CCCCCCCCE---EEECCCCCCCCCCCCCC-CCCC---CC-------CCEEEEECCCCCCHHHHHHHH
T ss_conf             68822433--553357725---88678776723366788-7265---20-------144666268797403466676


No 15 
>COG1726 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion]
Probab=96.61  E-value=0.052  Score=33.55  Aligned_cols=203  Identities=16%  Similarity=0.252  Sum_probs=131.0

Q ss_pred             HHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCC--CCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             9999826989999999983977687571124556874235--65688619998576778486004899986258999999
Q gi|254780858|r   32 VDKILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPK--VCSDRPHYLVVNADESEPGTCKDRDIMRHEPHTLIEGC  109 (425)
Q Consensus        32 l~~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~--~~~~~~~yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~  109 (425)
                      ++..-.++-++|...+.+|||-        |..|-+...+  .+...|+-+-+|+..-.|.+-.-...+........-|+
T Consensus       107 ~~~L~~l~~eeV~~~l~~sGLw--------talrtRPFsk~p~p~s~p~~iFvnamDt~Plaadp~vvi~~~s~~F~~Gl  178 (447)
T COG1726         107 LEQLAQLSLEEVRKNLIESGLW--------TALRTRPFSKVPAPDSTPRAIFVNAMDTNPLAADPEVVIAEFSEAFVVGL  178 (447)
T ss_pred             HHHHHHCCHHHHHHHHHHHHHH--------HHHHCCCCCCCCCCCCCHHHHEEECCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             8887222699999887760378--------88751888778899988066433301379899973869988888999899


Q ss_pred             HHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCCCC
Q ss_conf             99999718363899815551789999999999998689977676788664069974575100110788998630899986
Q gi|254780858|r  110 VIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAYICGEETALLESLEGKKGQP  189 (425)
Q Consensus       110 ~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Yi~GeEtali~sieG~r~~P  189 (425)
                      ...++..+-+  ++-.++.-..    +-+..                 .-.+++|.-.|-.|+|-..--|..|+      
T Consensus       179 ~vlsrL~~~k--~~vcka~~~~----~~~~~-----------------~~~~~~h~f~GPhPaGl~gtHIHfi~------  229 (447)
T COG1726         179 TVLSRLFGLK--HHVCKAAGTL----PPQEL-----------------LSNAHLHEFSGPHPAGLPGTHIHFIA------  229 (447)
T ss_pred             HHHHHHHCCE--EEEECCCCCC----CCHHH-----------------HCCEEEEECCCCCCCCCCCCEEEEEC------
T ss_conf             9999872661--8998056778----98122-----------------03503664268788898754057751------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCC-CCCCEEEEECCCCCHHHHHHH
Q ss_conf             8889986227830378500028999999999960568886338987743047642678-878726893589879999998
Q gi|254780858|r  190 RLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGH-VNYPCTVEESMSITFDELIEK  268 (425)
Q Consensus       190 r~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~-V~~Pg~~evp~Gt~l~eli~~  268 (425)
                          |.-+..=+|    - -|-.-+-+|..+...|--|          +.|++++.|. |++|-.+.-.+|.++.+|+. 
T Consensus       230 ----pv~~~k~Vw----~-inyQDViaIG~LF~tG~l~----------~erVvaLAGp~v~~prlvrT~~GAsls~L~~-  289 (447)
T COG1726         230 ----PVGATKVVW----T-INYQDVIAIGKLFLTGELL----------TERVVALAGPQVNKPRLVRTVLGASLSQLTA-  289 (447)
T ss_pred             ----CCCCCEEEE----E-EEHHHHHHHHHHHHCCEEE----------HHHHEECCCCCCCCCEEEEEECCCCHHHHCC-
T ss_conf             ----245752799----9-5235455535452113320----------3200100367778853798632677888501-


Q ss_pred             HHCCCCCCCCCEEEEEECCCCCCCCCCC
Q ss_conf             6155678711004898524565653210
Q gi|254780858|r  269 HCGGIRGGWDNLLAVIPGGSSVPCLPAG  296 (425)
Q Consensus       269 ~~GG~~~~~~~~kav~~GG~~~g~l~~~  296 (425)
                        +-..++..+   +|.|-+.+|-+...
T Consensus       290 --~~l~~g~nr---lISGsvL~G~~~~~  312 (447)
T COG1726         290 --GELKSGENR---LISGSVLTGRLAKG  312 (447)
T ss_pred             --CCCCCCCCE---EEECCCCCCCCCCC
T ss_conf             --355589721---88357556710168


No 16 
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=94.65  E-value=0.11  Score=31.47  Aligned_cols=80  Identities=18%  Similarity=0.189  Sum_probs=50.2

Q ss_pred             EEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCC-----CC
Q ss_conf             4764267887872689358987999999861556787110048985245656532100245633422011038-----73
Q gi|254780858|r  240 KLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMG-----SG  314 (425)
Q Consensus       240 kl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~G-----s~  314 (425)
                      +-++|.|.|++||.|.+.-++++-|.|. .|||+......-+..+.-...+.-      ...++|+.++-..|     -.
T Consensus        79 ~~V~V~G~V~~Pg~~~~~~~~tl~~al~-~AGG~~~~a~~~~i~i~R~~~g~~------~~~~vdl~~~l~~g~~~~n~~  151 (165)
T TIGR03027        79 EQIRVVGAAANPQALPYREGMTLLDVMI-AVGGLTDFADGNRAVIVRTVDGEQ------KQISVRLKDLIKDGDVTANVE  151 (165)
T ss_pred             EEEEEEEEECCCCEEECCCCCHHHHHHH-HCCCCCCCCCCCEEEEEEECCCCE------EEEEEEHHHHHHCCCCCCCCE
T ss_conf             7999981343782575488861999999-827998668875699999069977------999999999976698778947


Q ss_pred             CCCCEEEEECCC
Q ss_conf             466517994286
Q gi|254780858|r  315 LGTAAVIVMDRS  326 (425)
Q Consensus       315 LGsg~iiV~de~  326 (425)
                      |-.|-+|..+++
T Consensus       152 L~~GDvI~VP~s  163 (165)
T TIGR03027       152 LKPGDVLIIPES  163 (165)
T ss_pred             ECCCCEEEECCC
T ss_conf             589999998166


No 17 
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=94.30  E-value=0.08  Score=32.28  Aligned_cols=43  Identities=19%  Similarity=0.223  Sum_probs=34.1

Q ss_pred             EEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEE
Q ss_conf             764267887872689358987999999861556787110048985
Q gi|254780858|r  241 LFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIP  285 (425)
Q Consensus       241 l~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~  285 (425)
                      .+.|.|.|++||.|+..-++||.++|. .|||+..... .+.|.+
T Consensus       164 ~v~V~GeV~~Pg~y~~~~~~tl~~ai~-~AGG~~~~A~-~~~V~I  206 (239)
T TIGR03028       164 VFYIYGEVQRPGAYRLERNMTVMQALA-QGGGLTPRGT-ERGIRV  206 (239)
T ss_pred             EEEEECCCCCCEEEECCCCCCHHHHHH-HCCCCCCCCC-CCCEEE
T ss_conf             069943345650785389998999998-7469985446-684299


No 18 
>pfam05896 NQRA Na(+)-translocating NADH-quinone reductase subunit A (NQRA). This family consists of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration.
Probab=93.38  E-value=0.69  Score=25.95  Aligned_cols=144  Identities=13%  Similarity=0.140  Sum_probs=96.9

Q ss_pred             HHHCCHHHHHHHHHHCCCCCCCCCCCHHH--HHHHHCCCCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             98269899999999839776875711245--5687423565688619998576778486004899986258999999999
Q gi|254780858|r   35 ILEKGRDWIINEVKASGLRGRGGAGFSTG--MKWSFMPKVCSDRPHYLVVNADESEPGTCKDRDIMRHEPHTLIEGCVIA  112 (425)
Q Consensus        35 ~l~~~~~~ii~~v~~sgl~GrGGAgFPt~--~Kw~~~~~~~~~~~~yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~  112 (425)
                      .-.+++|+|.+.+.+||+-       |.=  +=++.++ .+...|+-+-+||...+|.+..=.++|+.+-..+-.|+.+.
T Consensus       110 ~~~ls~e~i~~~Ll~sGlW-------~~~rqRPf~~ia-~p~~~P~aIFIsa~dt~PLa~D~~~il~~~~~~F~~Gl~~L  181 (257)
T pfam05896       110 LSSLSREAVKENLLESGLW-------TALRTRPFSKVA-APDSTPKAIFVTAMDTNPLAADPEVIIAEQEEAFQAGLTAL  181 (257)
T ss_pred             HHHCCHHHHHHHHHHCCCH-------HHHHCCCCCCCC-CCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             3247999999999866970-------675426464569-99897787999803588888997999876599999999999


Q ss_pred             HHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCC
Q ss_conf             99718363899815551789999999999998689977676788664069974575100110788998630899986888
Q gi|254780858|r  113 SFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAYICGEETALLESLEGKKGQPRLK  192 (425)
Q Consensus       113 a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~k  192 (425)
                      .....- +.++.+..+.......                      .-+++++.-.|-||+|--...|+-|.         
T Consensus       182 ~kLt~g-~v~l~~~~~~~~~~~~----------------------~~~v~~~~f~GPHPAGnvG~hIh~i~---------  229 (257)
T pfam05896       182 SKLTDG-KVHVCKAPGAALPLAD----------------------LKGVELHEFSGPHPAGLVGTHIHFID---------  229 (257)
T ss_pred             HHHCCC-CEEEEECCCCCCCCCC----------------------CCCEEEEEECCCCCCCCHHHHEEECC---------
T ss_conf             997299-7799938998776556----------------------68769999559988978455123426---------


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHC
Q ss_conf             99862278303785000289999999999605
Q gi|254780858|r  193 PPFPANVGLYGCPTTVNNVESIAVVPTILRRG  224 (425)
Q Consensus       193 PP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G  224 (425)
                      |. -...=+|     .-|.+-+.++...+..|
T Consensus       230 Pi-n~~~~VW-----ti~~qdVi~IG~lf~tG  255 (257)
T pfam05896       230 PV-NAGKTVW-----TIGYQDVIAIGKLFLTG  255 (257)
T ss_pred             CC-CCCCEEE-----EECHHHHHHHHHHHHCC
T ss_conf             89-8886179-----97699999999998738


No 19 
>COG1596 Wza Periplasmic protein involved in polysaccharide export, contains    SLBB domain of b-grasp fold [Cell wall/membrane/envelope biogenesis]
Probab=93.01  E-value=0.11  Score=31.35  Aligned_cols=39  Identities=23%  Similarity=0.280  Sum_probs=33.4

Q ss_pred             EEEECCCCCCCCEEEEECC-CCCHHHHHHHHHCCCCCCCCC
Q ss_conf             4764267887872689358-987999999861556787110
Q gi|254780858|r  240 KLFSISGHVNYPCTVEESM-SITFDELIEKHCGGIRGGWDN  279 (425)
Q Consensus       240 kl~tvsG~V~~Pg~~evp~-Gt~l~eli~~~~GG~~~~~~~  279 (425)
                      +-+.|+|+|++||.|+..- |.++.+.|. .+||+.....+
T Consensus       125 ~~v~V~GeV~~PG~y~~~~~~~tv~~ai~-~AGG~~~~~~~  164 (239)
T COG1596         125 QKVFVSGEVKTPGQYPLTPRGLTVLDAIA-LAGGLTPRADK  164 (239)
T ss_pred             CEEEEECCCCCCCEEECCCCCCHHHHHHH-HCCCCCCCCCC
T ss_conf             35998466788837861566758999999-60798633222


No 20 
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=91.82  E-value=0.36  Score=27.86  Aligned_cols=79  Identities=18%  Similarity=0.274  Sum_probs=46.5

Q ss_pred             EEEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCC-----C
Q ss_conf             04764267887872689358987999999861556787110048985245656532100245633422011038-----7
Q gi|254780858|r  239 TKLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMG-----S  313 (425)
Q Consensus       239 tkl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~G-----s  313 (425)
                      +.-++|+|.|++||.|.+.-..++.+.|. .|||+......+. .+.--..+...     . ..+|+..+...|     -
T Consensus        78 ~~~V~V~G~V~~PG~y~l~~~~tl~~al~-~AGG~~~~~~~~~-~~~~~r~g~~~-----~-~~idl~~l~~~g~~~~ni  149 (239)
T TIGR03028        78 GQQVSVLGQVNRPGRYPLETAGRVSDVLA-LAGGVTPDGADVI-TLVREREGKIF-----R-KQIDFPALFNPGGDNENI  149 (239)
T ss_pred             CEEEEEECCCCCCEEEECCCCCHHHHHHH-HCCCCCCCCCCEE-EEEEEECCEEE-----E-EEECHHHHHHCCCCCCCE
T ss_conf             35899981334650788488762999999-7279997666237-99998799589-----9-886489985267765531


Q ss_pred             CCCCCEEEEECC
Q ss_conf             346651799428
Q gi|254780858|r  314 GLGTAAVIVMDR  325 (425)
Q Consensus       314 ~LGsg~iiV~de  325 (425)
                      .|-.|-+|.++.
T Consensus       150 ~L~~GD~I~V~~  161 (239)
T TIGR03028       150 LVAGGDIIYVDR  161 (239)
T ss_pred             ECCCCCEEEECC
T ss_conf             317999899726


No 21 
>pfam11973 NQRA_SLBB NQRA C-terminal domain. This family consists of the C-terminal domain of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration.
Probab=91.66  E-value=0.36  Score=27.90  Aligned_cols=46  Identities=26%  Similarity=0.489  Sum_probs=35.4

Q ss_pred             EEECCCC-CCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCC
Q ss_conf             7642678-878726893589879999998615567871100489852456565
Q gi|254780858|r  241 LFSISGH-VNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPC  292 (425)
Q Consensus       241 l~tvsG~-V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~  292 (425)
                      +++|+|. |++|..|+..+|.++.+|++   |-..++  ..+ +|.|.+..|-
T Consensus         1 vIal~G~~v~~P~y~~t~~Ga~i~~l~~---g~~~~~--~~R-iISG~vLtG~   47 (51)
T pfam11973         1 VVALAGPAVKKPRLVRTRLGASLSELLA---GELKEG--NVR-VISGSVLTGR   47 (51)
T ss_pred             CEEECCCCCCCCEEEEEECCCCHHHHHC---CCCCCC--CCE-EEECCCCCCC
T ss_conf             9886288889961899845977899866---676789--837-9978878675


No 22 
>TIGR00692 tdh L-threonine 3-dehydrogenase; InterPro: IPR004627   L-threonine 3-dehydrogenase (1.1.1.103 from EC) is a tetrameric, zinc-binding, NAD-dependent enzyme of threonine catabolism. It catalyses the conversion of L-threonine and NAD+ to L-2-amino-3-oxobutanoate and NADH. In Escherichia coli His-90 modulates substrate specificity and is believed part of the active site. Closely related proteins include sorbitol dehydrogenase, xylitol dehydrogenase, and benzyl alcohol dehydrogenase. Eukaryotic examples of this enzyme have been demonstrated experimentally but are not detected by this HMM. ; GO: 0008270 zinc ion binding, 0008743 L-threonine 3-dehydrogenase activity, 0006567 threonine catabolic process.
Probab=86.18  E-value=0.19  Score=29.77  Aligned_cols=25  Identities=20%  Similarity=0.212  Sum_probs=18.5

Q ss_pred             HHHHHHCCCEEEEEECCCCHHHHHH
Q ss_conf             9999718363899815551789999
Q gi|254780858|r  111 IASFAIGAHCAFIYVRGEFIRERES  135 (425)
Q Consensus       111 i~a~a~gA~~~~I~ir~ey~~~~~~  135 (425)
                      -+|++.||+..+|-=..||.....+
T Consensus       179 AVAKa~GA~~Vi~~d~neyRleLAk  203 (341)
T TIGR00692       179 AVAKAAGARNVIVIDKNEYRLELAK  203 (341)
T ss_pred             HHHHHHCCCEEEEECCCHHHHHHHH
T ss_conf             9987727840599658647999998


No 23 
>cd03008 TryX_like_RdCVF Tryparedoxin (TryX)-like family, Rod-derived cone viability factor (RdCVF) subfamily; RdCVF is a thioredoxin (TRX)-like protein specifically expressed in photoreceptors. RdCVF was isolated and identified as a factor that supports cone survival in retinal cultures. Cone photoreceptor loss is responsible for the visual handicap resulting from the inherited disease, retinitis pigmentosa. RdCVF shows 33% similarity to TRX but does not exhibit any detectable thiol oxidoreductase activity.
Probab=80.83  E-value=1.1  Score=24.70  Aligned_cols=20  Identities=10%  Similarity=0.032  Sum_probs=6.9

Q ss_pred             CCCCCCCCCHHHHHHHHHHH
Q ss_conf             79988523028999999999
Q gi|254780858|r  345 CGQCTPCREGTGWMMRVMER  364 (425)
Q Consensus       345 CGkCtPCR~Gt~~l~~il~~  364 (425)
                      +.+|.|||.=|+.|.+..++
T Consensus        34 A~WCpPCr~FTP~L~~fY~~   53 (146)
T cd03008          34 AVVSPQCQLFAPKLKDFFVR   53 (146)
T ss_pred             CCCCCHHHHHHHHHHHHHHH
T ss_conf             78681487677899999999


No 24 
>KOG1145 consensus
Probab=76.15  E-value=6.2  Score=19.55  Aligned_cols=90  Identities=16%  Similarity=0.210  Sum_probs=53.3

Q ss_pred             EEEECCCCCCCCEEEEECCCCCHHHHH------HHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCC--CCCCCHHHC
Q ss_conf             476426788787268935898799999------986155678711004898524565653210024563--342201103
Q gi|254780858|r  240 KLFSISGHVNYPCTVEESMSITFDELI------EKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAI--MDYDGLKEM  311 (425)
Q Consensus       240 kl~tvsG~V~~Pg~~evp~Gt~l~eli------~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~--ld~~~l~~~  311 (425)
                      -++||-|||.+-.       |||-|-+      ..-+||++..   +-|+.+.=|+|..++.  || +|  .-|..|++.
T Consensus       154 PVVTiMGHVDHGK-------TTLLD~lRks~VAA~E~GGITQh---IGAF~V~~p~G~~iTF--LD-TPGHaAF~aMRaR  220 (683)
T KOG1145         154 PVVTIMGHVDHGK-------TTLLDALRKSSVAAGEAGGITQH---IGAFTVTLPSGKSITF--LD-TPGHAAFSAMRAR  220 (683)
T ss_pred             CEEEEEECCCCCH-------HHHHHHHHHCCEEHHHCCCCCCE---ECEEEEECCCCCEEEE--EC-CCCHHHHHHHHHC
T ss_conf             8699860135770-------01998874072201323771000---0229996389977887--56-8747889999862


Q ss_pred             CCCCCCCEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf             8734665179942865289999999999987
Q gi|254780858|r  312 GSGLGTAAVIVMDRSTDIIKAIWRLSVFYKH  342 (425)
Q Consensus       312 Gs~LGsg~iiV~de~~~iv~~~~~~~~F~a~  342 (425)
                      |+..--=.|+|..-++-+-.++...+++...
T Consensus       221 GA~vtDIvVLVVAadDGVmpQT~EaIkhAk~  251 (683)
T KOG1145         221 GANVTDIVVLVVAADDGVMPQTLEAIKHAKS  251 (683)
T ss_pred             CCCCCCEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             6864447999997267756768999998876


No 25 
>COG1062 AdhC Zn-dependent alcohol dehydrogenases, class III [Energy production and conversion]
Probab=75.03  E-value=0.55  Score=26.61  Aligned_cols=17  Identities=6%  Similarity=-0.040  Sum_probs=8.1

Q ss_pred             CHHHHHHHHHHHHHCCC
Q ss_conf             02899999999998289
Q gi|254780858|r  353 EGTGWMMRVMERLVKGI  369 (425)
Q Consensus       353 ~Gt~~l~~il~~i~~G~  369 (425)
                      ..+..+.+-++.+.+|+
T Consensus       342 ~~Le~INeaf~~m~~G~  358 (366)
T COG1062         342 IPLEDINEAFDLMHEGK  358 (366)
T ss_pred             CCHHHHHHHHHHHHCCC
T ss_conf             76899999998764782


No 26 
>TIGR02375 pseudoazurin pseudoazurin; InterPro: IPR012745   Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related to plastocyanins. Several examples of pseudoazurin are encoded by a neighbouring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (IPR012746 from INTERPRO) of the same species.; GO: 0005507 copper ion binding.
Probab=73.92  E-value=1.9  Score=23.03  Aligned_cols=44  Identities=18%  Similarity=0.370  Sum_probs=31.9

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCCCCCCEEEEEC
Q ss_conf             862278303785000289999999999605688863389877430476426788787268935
Q gi|254780858|r  195 FPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGHVNYPCTVEES  257 (425)
Q Consensus       195 ~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~V~~Pg~~evp  257 (425)
                      .|+|.|        |||||   |..++-.|++.|++--.+.      ++|+  +..||||-+.
T Consensus        31 vPtDKG--------HNve~---iKgm~P~GA~~Fk~k~Ne~------~~vt--~~~eGvY~~k   74 (123)
T TIGR02375        31 VPTDKG--------HNVET---IKGMIPEGAEKFKSKINEE------YTVT--LTKEGVYGVK   74 (123)
T ss_pred             ECCCCC--------CCHHC---CCCCCCCCHHHCCCCCCCC------EEEE--EECCCEEEEE
T ss_conf             528887--------67000---0233652212102557875------5888--6148525885


No 27 
>PRK06964 DNA polymerase III subunit delta'; Validated
Probab=70.02  E-value=4.2  Score=20.70  Aligned_cols=22  Identities=27%  Similarity=0.486  Sum_probs=10.8

Q ss_pred             EEEE-E-CCCCCC-CCCCCHHHHHH
Q ss_conf             9998-5-767784-86004899986
Q gi|254780858|r   79 YLVV-N-ADESEP-GTCKDRDIMRH  100 (425)
Q Consensus        79 yvv~-N-~~E~EP-gt~kDr~Ll~~  100 (425)
                      ++.| | ..+++| |.|..-.++..
T Consensus        44 ~llC~~~~~~~~~Cg~C~sC~~~~~   68 (342)
T PRK06964         44 GLLCETPQPNGEPCGTCAACTWFAQ   68 (342)
T ss_pred             HHHCCCCCCCCCCCCCCHHHHHHHC
T ss_conf             9838999988897867777888862


No 28 
>KOG2501 consensus
Probab=69.10  E-value=1.8  Score=23.21  Aligned_cols=25  Identities=32%  Similarity=0.518  Sum_probs=14.4

Q ss_pred             HCCCCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             2799885230289999999999828
Q gi|254780858|r  344 SCGQCTPCREGTGWMMRVMERLVKG  368 (425)
Q Consensus       344 SCGkCtPCR~Gt~~l~~il~~i~~G  368 (425)
                      |.++|.|||.=|+.+.+..+++.+.
T Consensus        41 sA~wC~pCR~FTP~Lk~fYe~l~~~   65 (157)
T KOG2501          41 SAHWCPPCRDFTPILKDFYEELKDN   65 (157)
T ss_pred             EEEECCCHHHCCCHHHHHHHHHHHC
T ss_conf             8787783564886689999999736


No 29 
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178   Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=65.96  E-value=3.2  Score=21.45  Aligned_cols=16  Identities=44%  Similarity=0.657  Sum_probs=10.6

Q ss_pred             CCCCCCCCC---------HHHHHHH
Q ss_conf             037850002---------8999999
Q gi|254780858|r  202 YGCPTTVNN---------VESIAVV  217 (425)
Q Consensus       202 ~g~PT~V~N---------VeTla~v  217 (425)
                      +||||=|||         .|||+.+
T Consensus        64 HGKPTKVNnfWETSGLNILeTL~~L   88 (275)
T TIGR02812        64 HGKPTKVNNFWETSGLNILETLIRL   88 (275)
T ss_pred             CCCCCCCCCHHHCCCCCHHHHHHHH
T ss_conf             8899862762430273578999861


No 30 
>COG3347 Uncharacterized conserved protein [Function unknown]
Probab=60.99  E-value=13  Score=17.46  Aligned_cols=34  Identities=9%  Similarity=-0.034  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCH
Q ss_conf             9999999862236667765024799999986388
Q gi|254780858|r  376 DLLYEVSKNIEGRTICALGDAAAWPIQGLIKNFR  409 (425)
Q Consensus       376 ~~L~~la~~i~~~S~C~lG~~a~~pv~s~l~~F~  409 (425)
                      +.+.+....|++.+-|+-=+..++.=.--|+||+
T Consensus       363 d~~~~~i~v~~gA~~~g~~~~l~e~e~f~~EYW~  396 (404)
T COG3347         363 DLYEDAIAVVRGAEALGYYTPLSEAELFDMEYWD  396 (404)
T ss_pred             HHHHHHHHHHHCHHHHCCCCCCCHHHHCCCCCCC
T ss_conf             9999999985012343455567465521610165


No 31 
>cd03009 TryX_like_TryX_NRX Tryparedoxin (TryX)-like family, TryX and nucleoredoxin (NRX) subfamily; TryX and NRX are thioredoxin (TRX)-like protein disulfide oxidoreductases that alter the redox state of target proteins via the reversible oxidation of an active center CXXC motif. TryX is involved in the regulation of oxidative stress in parasitic trypanosomatids by reducing TryX peroxidase, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. TryX derives reducing equivalents from reduced trypanothione, a polyamine peptide conjugate unique to trypanosomatids, which is regenerated by the NADPH-dependent flavoprotein trypanothione reductase. Vertebrate NRX is a 400-amino acid nuclear protein with one redox active TRX domain containing a CPPC active site motif followed by one redox inactive TRX-like domain. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. Plant NRX, longer than the 
Probab=58.35  E-value=6.8  Score=19.26  Aligned_cols=13  Identities=15%  Similarity=0.039  Sum_probs=10.7

Q ss_pred             EEEEEE--CCCCCCC
Q ss_conf             199985--7677848
Q gi|254780858|r   78 HYLVVN--ADESEPG   90 (425)
Q Consensus        78 ~yvv~N--~~E~EPg   90 (425)
                      |||++|  |.-|.|.
T Consensus        19 K~vll~FWATWC~PC   33 (131)
T cd03009          19 KTVGLYFSASWCPPC   33 (131)
T ss_pred             CEEEEEEECCCCHHH
T ss_conf             889999987578666


No 32 
>PHA00330 putative replication initiation protein
Probab=58.12  E-value=5  Score=20.15  Aligned_cols=14  Identities=14%  Similarity=0.064  Sum_probs=6.9

Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             51789999999999
Q gi|254780858|r  128 EFIRERESLQAAVD  141 (425)
Q Consensus       128 ey~~~~~~l~~ai~  141 (425)
                      +...-+++|++.+.
T Consensus       105 ~~q~F~KRLRk~~~  118 (317)
T PHA00330        105 HIRLFIKRLREYID  118 (317)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             79999999998740


No 33 
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=56.69  E-value=10  Score=18.06  Aligned_cols=82  Identities=20%  Similarity=0.376  Sum_probs=41.9

Q ss_pred             EEEEECCCC-CC-CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCC---HHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             999857677-84-8600489998625899999999999718363899815551---789999999999998689977676
Q gi|254780858|r   79 YLVVNADES-EP-GTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEF---IRERESLQAAVDECYASGLLGSNS  153 (425)
Q Consensus        79 yvv~N~~E~-EP-gt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey---~~~~~~l~~ai~ea~~~g~lg~~~  153 (425)
                      ++.|-..++ +| |.|++-.++.+.-|-                =+..|..|+   .--|+.+|+.++........|.. 
T Consensus        47 ~llC~~~~~~~~Cg~C~~C~l~~~~~HP----------------D~~~i~pe~~~~~I~IdqIR~l~~~~~~~~~~g~~-  109 (334)
T PRK07993         47 YLLCQQPQGHKSCGHCRGCQLMQAGTHP----------------DYYTLTPEKGKSSLGVDAVREVTEKLYEHARLGGA-  109 (334)
T ss_pred             HHCCCCCCCCCCCCCCHHHHHHHCCCCC----------------CEEEECCCCCCCCCCHHHHHHHHHHHHHCCCCCCC-
T ss_conf             9818999999999999789998668999----------------84775342234559999999999998436656994-


Q ss_pred             CCCCCCEEEEEECCCCCCCCHHHHHHHHHC
Q ss_conf             788664069974575100110788998630
Q gi|254780858|r  154 KLGYDVDIIVHHGAGAYICGEETALLESLE  183 (425)
Q Consensus       154 ~~g~~~~i~v~~g~g~Yi~GeEtali~sie  183 (425)
                            .+.+...+.+.--.-..||+..+|
T Consensus       110 ------kV~iI~~Ae~mn~~AaNaLLKtLE  133 (334)
T PRK07993        110 ------KVVWLPDAALLTDAAANALLKTLE  133 (334)
T ss_pred             ------EEEEECCHHHHCHHHHHHHHHHHC
T ss_conf             ------799976677759999999998612


No 34 
>COG1064 AdhP Zn-dependent alcohol dehydrogenases [General function prediction only]
Probab=56.68  E-value=3.1  Score=21.52  Aligned_cols=24  Identities=17%  Similarity=0.091  Sum_probs=11.9

Q ss_pred             HHHHHHCCCCCCCCCCCHHHHHHH
Q ss_conf             999998397768757112455687
Q gi|254780858|r   44 INEVKASGLRGRGGAGFSTGMKWS   67 (425)
Q Consensus        44 i~~v~~sgl~GrGGAgFPt~~Kw~   67 (425)
                      ++....|-|.=.|.-.|-.-++|+
T Consensus       140 ~d~~~aApllCaGiT~y~alk~~~  163 (339)
T COG1064         140 LDLAEAAPLLCAGITTYRALKKAN  163 (339)
T ss_pred             CCHHHHHHHHCCEEEEEEEHHHCC
T ss_conf             986661154367005760046538


No 35 
>PRK10083 putative dehydrogenase; Provisional
Probab=54.23  E-value=4.7  Score=20.32  Aligned_cols=16  Identities=25%  Similarity=0.434  Sum_probs=7.2

Q ss_pred             HHHHHHHHHCCCCCHH
Q ss_conf             9999999982899989
Q gi|254780858|r  358 MMRVMERLVKGIAQKR  373 (425)
Q Consensus       358 l~~il~~i~~G~a~~~  373 (425)
                      ..++++-+.+|+-.++
T Consensus       289 ~~~~~~li~~g~i~~~  304 (339)
T PRK10083        289 FPVVIDWLAKGLIDPE  304 (339)
T ss_pred             HHHHHHHHHCCCCCHH
T ss_conf             9999999985999915


No 36 
>COG0320 LipA Lipoate synthase [Coenzyme metabolism]
Probab=52.36  E-value=2.2  Score=22.55  Aligned_cols=173  Identities=20%  Similarity=0.251  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEE--ECCCCHHH-HHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCHHH
Q ss_conf             6258999999999997183638998--15551789-99999999999868997767678866406997457510011078
Q gi|254780858|r  100 HEPHTLIEGCVIASFAIGAHCAFIY--VRGEFIRE-RESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAYICGEET  176 (425)
Q Consensus       100 ~~p~~vieG~~i~a~a~gA~~~~I~--ir~ey~~~-~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Yi~GeEt  176 (425)
                      +.|..|-|.+    ..+|-+..+|-  -||+-++. ...+-+.|+..++.+   +      ...|+|-..   =-.|.+.
T Consensus       100 ~EP~rvAeaV----~~mgLkyVViTsVdRDDL~DGGA~hfa~~i~~Ir~~~---P------~t~iEvL~P---DF~G~~~  163 (306)
T COG0320         100 DEPERVAEAV----KDMGLKYVVITSVDRDDLPDGGAQHFAECIRAIRELN---P------QTTIEVLTP---DFRGNDD  163 (306)
T ss_pred             CHHHHHHHHH----HHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHC---C------CCEEEEECC---CCCCCHH
T ss_conf             4278999999----9838986999753156665645689999999999639---9------964898386---5467899


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCC---CCCCEEEEECCCCCCCCEE
Q ss_conf             8998630899986888998622783037850002899999999996056888633898---7743047642678878726
Q gi|254780858|r  177 ALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRE---NNRGTKLFSISGHVNYPCT  253 (425)
Q Consensus       177 ali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~---~~~Gtkl~tvsG~V~~Pg~  253 (425)
                      +|-.-++-+           -++       .-|||||+.-+...++.|+...+++-.=   +.-+..++|=||       
T Consensus       164 al~~v~~~~-----------pdV-------~nHNvETVprL~~~VRp~A~Y~~SL~~L~~~k~~~P~i~TKSg-------  218 (306)
T COG0320         164 ALEIVADAG-----------PDV-------FNHNVETVPRLYPRVRPGATYERSLSLLERAKELGPDIPTKSG-------  218 (306)
T ss_pred             HHHHHHHCC-----------CCH-------HHCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCC-------
T ss_conf             999998369-----------611-------0045200001142568987688899999999985898631121-------


Q ss_pred             EEECCCCCHHHHHHHHHCCCCCCCCCEEEEEEC---CCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC
Q ss_conf             893589879999998615567871100489852---4565653210024563342201103873466
Q gi|254780858|r  254 VEESMSITFDELIEKHCGGIRGGWDNLLAVIPG---GSSVPCLPAGQMRGAIMDYDGLKEMGSGLGT  317 (425)
Q Consensus       254 ~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~G---G~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGs  317 (425)
                      .-+-+|-+..|+++...- +..-  .+..+-.|   -||..-+|...+- .|-.|+.+...+-.+|-
T Consensus       219 iMlGLGEt~~Ev~e~m~D-Lr~~--gvdilTiGQYlqPS~~HlpV~ryv-~PeeF~~~~~~a~~~GF  281 (306)
T COG0320         219 LMVGLGETDEEVIEVMDD-LRSA--GVDILTIGQYLQPSRKHLPVQRYV-TPEEFDELEEVAEEMGF  281 (306)
T ss_pred             EEEECCCCHHHHHHHHHH-HHHC--CCCEEEECCCCCCCCCCCCCEECC-CHHHHHHHHHHHHHCCC
T ss_conf             355057768999999999-9985--998997300147762458833211-88999999999997460


No 37 
>COG1162 Predicted GTPases [General function prediction only]
Probab=49.88  E-value=19  Score=16.27  Aligned_cols=151  Identities=18%  Similarity=0.283  Sum_probs=80.2

Q ss_pred             EEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHH-HHHHHCCCCCCCCCCC
Q ss_conf             199985767784860048999862589999999999971836389981555178999999999-9998689977676788
Q gi|254780858|r   78 HYLVVNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAV-DECYASGLLGSNSKLG  156 (425)
Q Consensus        78 ~yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai-~ea~~~g~lg~~~~~g  156 (425)
                      -.+|+-+.+-++-            -.+|+=.++++++-|++-.++-.+-+..+..+..+++. ...++.|+        
T Consensus        83 ~iiIvs~~~P~~~------------~~~ldR~Lv~ae~~gi~pvIvlnK~DL~~~~~~~~~~~~~~y~~~gy--------  142 (301)
T COG1162          83 AIIVVSLVDPDFN------------TNLLDRYLVLAEAGGIEPVIVLNKIDLLDDEEAAVKELLREYEDIGY--------  142 (301)
T ss_pred             EEEEEECCCCCCC------------HHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCE--------
T ss_conf             9999962689989------------88999999999776995799997533676167789999999986793--------


Q ss_pred             CCCEEEEEECCCCCCCCH-HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHH--HHHHHHHHHHHCHHHHHHCCC
Q ss_conf             664069974575100110-78899863089998688899862278303785000289--999999999605688863389
Q gi|254780858|r  157 YDVDIIVHHGAGAYICGE-ETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVE--SIAVVPTILRRGASWYSGFGR  233 (425)
Q Consensus       157 ~~~~i~v~~g~g~Yi~Ge-Etali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVe--Tla~v~~i~~~G~~~y~~~G~  233 (425)
                         ++.......    ++ -.+|.+.+.|+.-.      |--++|+ ||-|++|-.-  .-..+..|=.+     .+-|.
T Consensus       143 ---~v~~~s~~~----~~~~~~l~~~l~~~~sv------l~GqSGV-GKSSLiN~L~p~~~~~t~eIS~~-----~~rGk  203 (301)
T COG1162         143 ---PVLFVSAKN----GDGLEELAELLAGKITV------LLGQSGV-GKSTLINALLPELNQKTGEISEK-----LGRGR  203 (301)
T ss_pred             ---EEEEECCCC----CCCHHHHHHHHCCCEEE------EECCCCC-CHHHHHHHHCCHHHHHHHHHCCC-----CCCCC
T ss_conf             ---599953767----65589999975588499------9888877-69998874172121134421044-----78988


Q ss_pred             CCCCCEEEEEC--CCC-CCCCEEEEECC-CCCHHHHHH
Q ss_conf             87743047642--678-87872689358-987999999
Q gi|254780858|r  234 ENNRGTKLFSI--SGH-VNYPCTVEESM-SITFDELIE  267 (425)
Q Consensus       234 ~~~~Gtkl~tv--sG~-V~~Pg~~evp~-Gt~l~eli~  267 (425)
                      ..+.-++++.+  +|. +..||.-|+.+ ...-.+|..
T Consensus       204 HTTt~~~l~~l~~gG~iiDTPGf~~~~l~~~~~e~l~~  241 (301)
T COG1162         204 HTTTHVELFPLPGGGWIIDTPGFRSLGLAHLEPEDLVQ  241 (301)
T ss_pred             CCCCEEEEEECCCCCEEEECCCCCCCCCCCCCHHHHHH
T ss_conf             76324899983899889728997714745679999999


No 38 
>PRK08699 DNA polymerase III subunit delta'; Validated
Probab=48.77  E-value=14  Score=17.13  Aligned_cols=25  Identities=28%  Similarity=0.384  Sum_probs=14.8

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHC
Q ss_conf             4069974575100110788998630
Q gi|254780858|r  159 VDIIVHHGAGAYICGEETALLESLE  183 (425)
Q Consensus       159 ~~i~v~~g~g~Yi~GeEtali~sie  183 (425)
                      ..|.+...+.+.-.--..||+..+|
T Consensus       114 ~kV~ii~~ae~mn~~aaNaLLK~LE  138 (325)
T PRK08699        114 LRVILIHPAESMNVQAANSLLKVLE  138 (325)
T ss_pred             CEEEEECCHHHHCHHHHHHHHHHHC
T ss_conf             4699985777758999999999841


No 39 
>cd03012 TlpA_like_DipZ_like TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3.
Probab=48.39  E-value=16  Score=16.69  Aligned_cols=13  Identities=0%  Similarity=-0.090  Sum_probs=7.6

Q ss_pred             EEEEEE--CCCCCCC
Q ss_conf             199985--7677848
Q gi|254780858|r   78 HYLVVN--ADESEPG   90 (425)
Q Consensus        78 ~yvv~N--~~E~EPg   90 (425)
                      |+||+|  |.=|.|.
T Consensus        24 K~Vll~FWatwC~pC   38 (126)
T cd03012          24 KVVLLDFWTYCCINC   38 (126)
T ss_pred             CEEEEEEECCCCHHH
T ss_conf             989998722419378


No 40 
>TIGR03451 mycoS_dep_FDH mycothiol-dependent formaldehyde dehydrogenase. Members of this protein family are mycothiol-dependent formaldehyde dehydrogenase (EC 1.2.1.66). This protein is found, so far, only in the Actinobacteria (Mycobacterium sp., Streptomyces sp., Corynebacterium sp., and related species), where mycothione replaces glutathione.
Probab=47.88  E-value=4.2  Score=20.69  Aligned_cols=17  Identities=12%  Similarity=0.155  Sum_probs=7.6

Q ss_pred             CHHHHHHHHHHHHHCCC
Q ss_conf             02899999999998289
Q gi|254780858|r  353 EGTGWMMRVMERLVKGI  369 (425)
Q Consensus       353 ~Gt~~l~~il~~i~~G~  369 (425)
                      .....+.+.++++.+|+
T Consensus       334 ~~Le~~~eAfe~~~~g~  350 (358)
T TIGR03451       334 IGLDDVEEAFDKMHAGD  350 (358)
T ss_pred             EEHHHHHHHHHHHHCCC
T ss_conf             87999999999987799


No 41 
>PRK09880 L-idonate 5-dehydrogenase; Provisional
Probab=47.12  E-value=5.9  Score=19.69  Aligned_cols=14  Identities=14%  Similarity=0.335  Sum_probs=5.3

Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99999999828999
Q gi|254780858|r  358 MMRVMERLVKGIAQ  371 (425)
Q Consensus       358 l~~il~~i~~G~a~  371 (425)
                      ..+.++-+.+|+-.
T Consensus       296 ~~~~l~li~~g~i~  309 (343)
T PRK09880        296 FNTAVSWLANGVIN  309 (343)
T ss_pred             HHHHHHHHHCCCCC
T ss_conf             99999999859998


No 42 
>cd02964 TryX_like_family Tryparedoxin (TryX)-like family; composed of TryX and related proteins including nucleoredoxin (NRX), rod-derived cone viability factor (RdCVF) and the nematode homolog described as a 16-kD class of TRX. Most members of this family, except RdCVF, are protein disulfide oxidoreductases containing an active site CXXC motif, similar to TRX.
Probab=46.91  E-value=13  Score=17.38  Aligned_cols=13  Identities=15%  Similarity=0.039  Sum_probs=8.6

Q ss_pred             EEEEEE--CCCCCCC
Q ss_conf             199985--7677848
Q gi|254780858|r   78 HYLVVN--ADESEPG   90 (425)
Q Consensus        78 ~yvv~N--~~E~EPg   90 (425)
                      |||++|  |.=|-|.
T Consensus        18 K~vll~FWAsWC~pC   32 (132)
T cd02964          18 KTVGLYFSASWCPPC   32 (132)
T ss_pred             CEEEEEEECCCCHHH
T ss_conf             889999984568204


No 43 
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=46.65  E-value=18  Score=16.41  Aligned_cols=82  Identities=22%  Similarity=0.316  Sum_probs=41.5

Q ss_pred             EEEEEC-CCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCC---CHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             999857-67784-860048999862589999999999971836389981555---1789999999999998689977676
Q gi|254780858|r   79 YLVVNA-DESEP-GTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGE---FIRERESLQAAVDECYASGLLGSNS  153 (425)
Q Consensus        79 yvv~N~-~E~EP-gt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~e---y~~~~~~l~~ai~ea~~~g~lg~~~  153 (425)
                      ++.|.. ...+| |.|..=.++...-|-              +  ++.|..+   ..--|+.+++-++++......|.  
T Consensus        45 ~LlC~~~~~~~~Cg~C~sC~~~~~~~HP--------------D--~~~i~pe~~~~~I~IdqIR~l~~~~~~~~~~g~--  106 (328)
T PRK05707         45 FLLCEAPQGGGACGSCKGCQLLAAGSHP--------------D--NFVLEPEEADKPIKVDQVRELVSFVVQTAQLGG--  106 (328)
T ss_pred             HHHCCCCCCCCCCCCCHHHHHHHCCCCC--------------C--EEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCC--
T ss_conf             9848999998999888899998758999--------------8--799842666776979999999999831766789--


Q ss_pred             CCCCCCEEEEEECCCCCCCCHHHHHHHHHC
Q ss_conf             788664069974575100110788998630
Q gi|254780858|r  154 KLGYDVDIIVHHGAGAYICGEETALLESLE  183 (425)
Q Consensus       154 ~~g~~~~i~v~~g~g~Yi~GeEtali~sie  183 (425)
                           ..|.|...+.+--..-..||+..||
T Consensus       107 -----~KV~iI~~Ae~m~~~AaNALLKtLE  131 (328)
T PRK05707        107 -----RKVVLIEPAEAMNRNAANALLKSLE  131 (328)
T ss_pred             -----CEEEEEEHHHHHCHHHHHHHHHHHH
T ss_conf             -----5799950287738999999999850


No 44 
>PRK03147 thiol-disulfide oxidoreductase; Provisional
Probab=45.66  E-value=14  Score=17.20  Aligned_cols=10  Identities=10%  Similarity=0.461  Sum_probs=4.2

Q ss_pred             CEEEEECCCC
Q ss_conf             3047642678
Q gi|254780858|r  238 GTKLFSISGH  247 (425)
Q Consensus       238 Gtkl~tvsG~  247 (425)
                      |..++.|+-+
T Consensus        95 ~v~vi~i~~d  104 (176)
T PRK03147         95 GVEIIAVNVD  104 (176)
T ss_pred             CEEEEEECCC
T ss_conf             4478522078


No 45 
>PRK12288 ribosome-associated GTPase; Reviewed
Probab=44.21  E-value=23  Score=15.70  Aligned_cols=88  Identities=20%  Similarity=0.314  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCCC--HHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-EEEEEECCCCCCCCHHHHHH
Q ss_conf             899999999999718363899815551--789999999999998689977676788664-06997457510011078899
Q gi|254780858|r  103 HTLIEGCVIASFAIGAHCAFIYVRGEF--IRERESLQAAVDECYASGLLGSNSKLGYDV-DIIVHHGAGAYICGEETALL  179 (425)
Q Consensus       103 ~~vieG~~i~a~a~gA~~~~I~ir~ey--~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~-~i~v~~g~g~Yi~GeEtali  179 (425)
                      ..+||=.++++++.|.+-.++.=+-+-  ++....+++.++-.++.|+         .+ .+....+.|      =..|-
T Consensus       138 ~~liDRyLv~ae~~~I~pvIvlNK~DL~~~~~~~~~~~~l~~Y~~lGY---------~v~~~Sa~~~~g------l~~L~  202 (344)
T PRK12288        138 LNIIDRYLVACETLGIEPLIVLNKIDLLDDEERPFVNEQLDIYRNIGY---------RVLMVSSHTGEG------LEPLE  202 (344)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEECHHCCCHHHHHHHHHHHHHHHHCCC---------EEEEEECCCCCC------HHHHH
T ss_conf             789999999999869977999731440897789999999999986797---------399973688628------99999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             863089998688899862278303785000289
Q gi|254780858|r  180 ESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVE  212 (425)
Q Consensus       180 ~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVe  212 (425)
                      +.+.||.-.      |.-++|+ ||-|++|..-
T Consensus       203 ~~L~~ktsv------f~GqSGV-GKSSLiN~L~  228 (344)
T PRK12288        203 AALTGRISI------FVGQSGV-GKSSLINALL  228 (344)
T ss_pred             HHHCCCEEE------EEECCCC-CHHHHHHHCC
T ss_conf             987678599------9806876-7888876107


No 46 
>PRK00098 ribosome-associated GTPase; Reviewed
Probab=44.16  E-value=23  Score=15.69  Aligned_cols=87  Identities=18%  Similarity=0.276  Sum_probs=48.4

Q ss_pred             HHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC-CEEEEEECCCCCCCCHHHHHHHHH
Q ss_conf             9999999999971836389981555178999999999999868997767678866-406997457510011078899863
Q gi|254780858|r  104 TLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYD-VDIIVHHGAGAYICGEETALLESL  182 (425)
Q Consensus       104 ~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~-~~i~v~~g~g~Yi~GeEtali~si  182 (425)
                      ..||=.+++++.-|++-.++.=+-+-.+..+.++..++..+..|+         . +.+....+.|      -..|.+.+
T Consensus        98 ~~idR~Lv~a~~~~i~pvivlnK~DL~~~~~~~~~~~~~y~~~gy---------~v~~~S~~~~~g------~~~L~~~l  162 (298)
T PRK00098         98 DLLDRFLVLAEANDIKPIIVLNKIDLVDDLEEARERLALYRAIGY---------DVLELSAKEGPG------LDELKPLL  162 (298)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCC---------CEEEEECCCCCC------HHHHHHHH
T ss_conf             999999999998699589996424564779999999999987899---------789996899989------99999985


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCHH
Q ss_conf             089998688899862278303785000289
Q gi|254780858|r  183 EGKKGQPRLKPPFPANVGLYGCPTTVNNVE  212 (425)
Q Consensus       183 eG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVe  212 (425)
                      .||.-.      |--++|+ ||-|++|...
T Consensus       163 ~~k~sv------~~G~SGV-GKSSLiN~L~  185 (298)
T PRK00098        163 AGKVTV------LAGQSGV-GKSTLLNALV  185 (298)
T ss_pred             CCCEEE------EECCCCC-CHHHHHHHHC
T ss_conf             798699------9878988-7888887607


No 47 
>TIGR03201 dearomat_had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase. Members of this protein family are 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase, an enzyme in the anaerobic metabolism of aromatic enzymes by way of benzoyl-CoA, as seen in Thauera aromatica, Geobacter metallireducens, and Azoarcus sp. The experimentally characterized form from T. aromatica uses only NAD+, not NADP+. Note that Rhodopseudomonas palustris uses a different pathway to perform a similar degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Probab=43.66  E-value=7.6  Score=18.95  Aligned_cols=17  Identities=6%  Similarity=-0.140  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHHHHCCCC
Q ss_conf             28999999999982899
Q gi|254780858|r  354 GTGWMMRVMERLVKGIA  370 (425)
Q Consensus       354 Gt~~l~~il~~i~~G~a  370 (425)
                      ...++.+.++++.+|+.
T Consensus       325 pL~~~~eAf~~~~~gk~  341 (349)
T TIGR03201       325 PLDQIEHVFAAAHHHKL  341 (349)
T ss_pred             EHHHHHHHHHHHHCCCC
T ss_conf             19999999999977999


No 48 
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=41.29  E-value=23  Score=15.66  Aligned_cols=25  Identities=20%  Similarity=0.254  Sum_probs=15.8

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHC
Q ss_conf             4069974575100110788998630
Q gi|254780858|r  159 VDIIVHHGAGAYICGEETALLESLE  183 (425)
Q Consensus       159 ~~i~v~~g~g~Yi~GeEtali~sie  183 (425)
                      ..|.|...+..-----.-||+..||
T Consensus       111 ~KV~II~~Ae~m~~~AaNALLKtLE  135 (329)
T PRK08058        111 KKVYIIEHADKMTASAANSLLKFLE  135 (329)
T ss_pred             CEEEEEECHHHHCHHHHHHHHHHHH
T ss_conf             6799973477629999999999864


No 49 
>pfam04034 DUF367 Domain of unknown function (DUF367).
Probab=41.06  E-value=26  Score=15.38  Aligned_cols=36  Identities=31%  Similarity=0.390  Sum_probs=26.8

Q ss_pred             CCCCCCCCCCCCCC-CCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             86888998622783-0378500028999999999960
Q gi|254780858|r  188 QPRLKPPFPANVGL-YGCPTTVNNVESIAVVPTILRR  223 (425)
Q Consensus       188 ~Pr~kPP~p~~~Gl-~g~PT~V~NVeTla~v~~i~~~  223 (425)
                      .+|.=|++-+---+ ||||.-.+.||-+|+--.|+-.
T Consensus        46 ~~R~LP~LvAaNPVNYGKP~kLs~vEAlAAaLyI~G~   82 (128)
T pfam04034        46 HERLLPFLVAANPVNYGKPCKLSCVEALAAALYIVGF   82 (128)
T ss_pred             CCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCC
T ss_conf             8766650432488666887621279999999999499


No 50 
>pfam01031 Dynamin_M Dynamin central region. This region lies between the GTPase domain, see pfam00350, and the pleckstrin homology (PH) domain, see pfam00169.
Probab=40.56  E-value=26  Score=15.33  Aligned_cols=14  Identities=14%  Similarity=0.057  Sum_probs=7.3

Q ss_pred             EECCCCCHHHHHHH
Q ss_conf             93589879999998
Q gi|254780858|r  255 EESMSITFDELIEK  268 (425)
Q Consensus       255 evp~Gt~l~eli~~  268 (425)
                      |+..|..++.++.+
T Consensus       140 el~ggarI~~iF~~  153 (295)
T pfam01031       140 ELSGGARIRYIFHE  153 (295)
T ss_pred             CCCCHHHHHHHHHH
T ss_conf             06621799999999


No 51 
>TIGR01743 purR_Bsub pur operon repressor; InterPro: IPR010078   This entry represents the pur operon repressor PurR of low-GC Gram-positive bacteria. This homodimeric repressor contains a large region homologous to phosphoribosyltransferases and is inhibited by 5-phosphoribosyl 1-pyrophosphate.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0016481 negative regulation of transcription, 0045982 negative regulation of purine base metabolic process.
Probab=39.85  E-value=27  Score=15.26  Aligned_cols=102  Identities=19%  Similarity=0.207  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCC---CCC
Q ss_conf             89998625899999999999718363899815551789999999999998689977676788664069974575---100
Q gi|254780858|r   95 RDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAG---AYI  171 (425)
Q Consensus        95 r~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g---~Yi  171 (425)
                      .+|+ ++||++| ++---+....+-|--|      .+-+.++++++++..        +|     .+..++|||   .||
T Consensus        12 ~~L~-~nP~kLi-~L~~F~d~y~~AKSsi------SEDi~I~~~~le~~~--------~G-----~~~T~~GAaGGv~Yi   70 (269)
T TIGR01743        12 KYLI-ENPNKLI-SLNKFSDKYESAKSSI------SEDIVIIKEVLEKFD--------IG-----KLETVPGAAGGVKYI   70 (269)
T ss_pred             HHHH-HCCEEEC-CCHHHHHHHHHHHCCH------HHHHHHHHHHHHHCC--------CC-----EEEEECCCCCCEEEE
T ss_conf             7774-2780102-7005787764211110------144899999850068--------86-----478614788970584


Q ss_pred             ----CCHHHHHHHHHCCCCCCC-CCCCC-CCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             ----110788998630899986-88899-86227830378500028999999
Q gi|254780858|r  172 ----CGEETALLESLEGKKGQP-RLKPP-FPANVGLYGCPTTVNNVESIAVV  217 (425)
Q Consensus       172 ----~GeEtali~sieG~r~~P-r~kPP-~p~~~Gl~g~PT~V~NVeTla~v  217 (425)
                          .-|..-.++.+--+-..| |.-|- |-.-.-+..+|.++.|+.-+-+-
T Consensus        71 P~~~~~~~~~fv~~l~~~l~~s~Ri~PGgflY~~Dll~~Psi~ski~~ila~  122 (269)
T TIGR01743        71 PEVSEKEAKEFVEELCEKLSESERILPGGFLYLTDLLFKPSILSKIGKILAS  122 (269)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             5646045688999999862288840377475553454178157778888754


No 52 
>TIGR02418 acolac_catab acetolactate synthase, catabolic; InterPro: IPR012782    Acetolactate synthase is a thiamin pyrophosphate-dependent enzyme that combines two molecules of pyruvate to yield 2-acetolactate with the release of CO2. It exists in two distinct forms that have different properties, though they are clearly related , . The biosynthetic form, found in plants, fungi and bacteria, is involved in the biosynthesis of branched-chain amino acids and contains non-catalytic FAD. The catabolic form is found only in some bacteria, participates in butanediol fermentation, and does not contain FAD.   This entry represents the catabolic form of acetolactate synthase, generally found in species that posses acetolactate decarboxylase, which is often encoded in the same operon. The enzyme is thought to be a homotetramer, though this has not conclusively been shown. Each monomer consists of three distinct domains, designated, starting from the N-terminus, as alpha, beta and gamma . The core of the alpha and gamma domains is a six-stranded parallel beta sheet surrounded by alpha helices, while the the beta domain forms a double Rossman fold. The thiamin pyrophosphate cofactor has an unusual conformation that has not been seen in other enzymes using this cofactor, including the biosynthetic form of acetolactate synthase. The active site is located in a funnel at the dimer interface, bordered by residues from all three domains.; GO: 0000287 magnesium ion binding, 0003984 acetolactate synthase activity, 0030976 thiamin pyrophosphate binding, 0050660 FAD binding.
Probab=39.53  E-value=13  Score=17.39  Aligned_cols=76  Identities=16%  Similarity=0.110  Sum_probs=44.5

Q ss_pred             CCCCCC-HHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH----HC-CCCCHHHH
Q ss_conf             334220-1103873466517994286528999999999998762799885230289999999999----82-89998999
Q gi|254780858|r  302 IMDYDG-LKEMGSGLGTAAVIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERL----VK-GIAQKREI  375 (425)
Q Consensus       302 ~ld~~~-l~~~Gs~LGsg~iiV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i----~~-G~a~~~Dl  375 (425)
                      |..||. ++-.+   .+.-||.+|..-  .++-.    .|        .|||+=..-+..-|+.|    .. -.-.++..
T Consensus       280 PIEYep~~WN~~---~~~~Iv~iD~~~--A~i~~----~y--------qP~~eLvGdia~tl~~l~~~~~~~~~L~~~~~  342 (553)
T TIGR02418       280 PIEYEPRNWNSE---LDATIVHIDVEP--AEIDN----NY--------QPDLELVGDIASTLDLLAERVEGFYELPEDAQ  342 (553)
T ss_pred             CEECCHHHCCCC---CCCEEEEEEEEE--EEHHH----CC--------CCCHHHHCCHHHHHHHHHHHHCCCCCCCHHHH
T ss_conf             503075544778---872068973144--21200----36--------86144325727779999586246610588899


Q ss_pred             HHHHHHHHHHCCCCCCCCC
Q ss_conf             9999999862236667765
Q gi|254780858|r  376 DLLYEVSKNIEGRTICALG  394 (425)
Q Consensus       376 ~~L~~la~~i~~~S~C~lG  394 (425)
                      +.|+++-..|...+.-.+-
T Consensus       343 ~~L~~l~~~~~~~~~~~~~  361 (553)
T TIGR02418       343 DILEDLKQQIEELDEVKAD  361 (553)
T ss_pred             HHHHHHHHHHHHHHCCCCC
T ss_conf             9999999999865317875


No 53 
>KOG2453 consensus
Probab=38.97  E-value=15  Score=16.89  Aligned_cols=36  Identities=28%  Similarity=0.517  Sum_probs=25.0

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHCCC-CCCCCC
Q ss_conf             66517994286528999999999998762799-885230
Q gi|254780858|r  316 GTAAVIVMDRSTDIIKAIWRLSVFYKHESCGQ-CTPCRE  353 (425)
Q Consensus       316 Gsg~iiV~de~~~iv~~~~~~~~F~a~ESCGk-CtPCR~  353 (425)
                      |.-+|||++|.+  +.++..-.-|.+--+.|| ||.||.
T Consensus       268 gnnaiiv~edad--l~lvvps~lfaavgtagqrctt~rr  304 (507)
T KOG2453         268 GNNAIIVNEDAD--LNLVVPSTLFAAVGTAGQRCTTTRR  304 (507)
T ss_pred             CCCEEEEECCCC--CEEEEHHHHHHHHCCCCCCHHHHHH
T ss_conf             983599852666--2143257899886255540146667


No 54 
>KOG0633 consensus
Probab=38.62  E-value=28  Score=15.13  Aligned_cols=75  Identities=9%  Similarity=0.254  Sum_probs=48.2

Q ss_pred             EEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEE---ECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCC
Q ss_conf             476426788787268935898799999986155678711004898---52456565321002456334220110387346
Q gi|254780858|r  240 KLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVI---PGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLG  316 (425)
Q Consensus       240 kl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~---~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LG  316 (425)
                      -+++|+..|+.-+|+.||+-..++-=++.++--.... .++|.++   ||-|.+.++..+++.++ |..          -
T Consensus       122 sMY~v~A~iNd~eVvkvpl~pdF~lnvdai~evl~~d-s~iK~~F~tSPgNPtg~~ik~~di~Ki-Le~----------p  189 (375)
T KOG0633         122 SMYVVDAAINDAEVVKVPLNPDFSLNVDAIAEVLELD-SKIKCIFLTSPGNPTGSIIKEDDILKI-LEM----------P  189 (375)
T ss_pred             EEEEEEEECCCCEEEEECCCCCCCCCHHHHHHHHHCC-CCCEEEEECCCCCCCCCCCCHHHHHHH-HHC----------C
T ss_conf             0589974037734798037887555699999998326-643289981798987330338899999-829----------8


Q ss_pred             CCEEEEECCC
Q ss_conf             6517994286
Q gi|254780858|r  317 TAAVIVMDRS  326 (425)
Q Consensus       317 sg~iiV~de~  326 (425)
                      +.+++|.||.
T Consensus       190 ~nglVVvDEA  199 (375)
T KOG0633         190 DNGLVVVDEA  199 (375)
T ss_pred             CCCEEEEEEE
T ss_conf             8837997500


No 55 
>TIGR00604 rad3 DNA repair helicase (rad3); InterPro: IPR013020   All proteins in this family for which functions are known are DNA-DNA helicases that function in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. .
Probab=38.28  E-value=28  Score=15.10  Aligned_cols=80  Identities=11%  Similarity=0.109  Sum_probs=51.4

Q ss_pred             HHHCCCCCCCC---EEEEECCCCCHHHHHHHHHH-HHHHHHCCCCCCCCCHHHHHHHHHHHHH-----CCCCCH-----H
Q ss_conf             11038734665---17994286528999999999-9987627998852302899999999998-----289998-----9
Q gi|254780858|r  308 LKEMGSGLGTA---AVIVMDRSTDIIKAIWRLSV-FYKHESCGQCTPCREGTGWMMRVMERLV-----KGIAQK-----R  373 (425)
Q Consensus       308 l~~~Gs~LGsg---~iiV~de~~~iv~~~~~~~~-F~a~ESCGkCtPCR~Gt~~l~~il~~i~-----~G~a~~-----~  373 (425)
                      =.+...-|..-   .||||||.+++.++....+. -..+=|=-.=--|..+...+.+.+..+.     +.+++.     .
T Consensus       266 r~~~~~~L~~dysdsIVifDEAHNl~n~~~s~~Srkl~~~s~~~~~~c~~~~~~~~~~~~~~~~~~~~~~d~~~GafGsa  345 (813)
T TIGR00604       266 RSALSLELKKDYSDSIVIFDEAHNLDNVCISSLSRKLSNISKRSLKRCSKEIAEYFEKIEERKLRLIREVDARKGAFGSA  345 (813)
T ss_pred             HHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH
T ss_conf             99987431001266258961225848999878646578613899999999999999889999999865137542402467


Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             99999999986223
Q gi|254780858|r  374 EIDLLYEVSKNIEG  387 (425)
Q Consensus       374 Dl~~L~~la~~i~~  387 (425)
                      -++.|..+...|+.
T Consensus       346 ~~~~l~~lv~~L~~  359 (813)
T TIGR00604       346 LLDELQKLVEGLKQ  359 (813)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             79999999989988


No 56 
>PRK05396 tdh L-threonine 3-dehydrogenase; Validated
Probab=37.99  E-value=10  Score=18.05  Aligned_cols=18  Identities=17%  Similarity=0.071  Sum_probs=8.1

Q ss_pred             CCHHHHHHHHHHHHHCCC
Q ss_conf             302899999999998289
Q gi|254780858|r  352 REGTGWMMRVMERLVKGI  369 (425)
Q Consensus       352 R~Gt~~l~~il~~i~~G~  369 (425)
                      +.....+.+.++.+.+|+
T Consensus       315 ~f~Lee~~eA~~~~~~g~  332 (341)
T PRK05396        315 RFPIDDFQKGFEAMRSGQ  332 (341)
T ss_pred             EEEHHHHHHHHHHHHCCC
T ss_conf             988999999999997799


No 57 
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=36.61  E-value=28  Score=15.11  Aligned_cols=48  Identities=23%  Similarity=0.279  Sum_probs=33.0

Q ss_pred             CHHHHHHHHHHH--HHHCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHH
Q ss_conf             989999999999--862236667765024799999986388999999865
Q gi|254780858|r  371 QKREIDLLYEVS--KNIEGRTICALGDAAAWPIQGLIKNFRPLIEERIDQ  418 (425)
Q Consensus       371 ~~~Dl~~L~~la--~~i~~~S~C~lG~~a~~pv~s~l~~F~dEfe~hI~~  418 (425)
                      +.-|+++|+++.  .-|..-|.---|+....|--++++|||++|--.|+.
T Consensus       291 T~yDlEMl~E~GyCsGIENYSRhl~gR~pGe~P~tLlDYfp~DfLl~iDE  340 (657)
T PRK05298        291 TRYDLEMLRELGYCSGIENYSRHLSGRAPGEPPPTLLDYFPDDFLLFIDE  340 (657)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCHHHHHCCCCEEEEECC
T ss_conf             88799999982877560121565069998878944887577565999832


No 58 
>TIGR00631 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 All proteins in this family for which functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0005737 cytoplasm, 0009380 excinuclease repair complex.
Probab=35.86  E-value=5.5  Score=19.91  Aligned_cols=74  Identities=19%  Similarity=0.231  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHH--HHHCCCCCCCCCHHHHHHHHHHHHHC
Q ss_conf             9999999999876279988523028999999999982899989999999999--86223666776502479999998638
Q gi|254780858|r  331 KAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVS--KNIEGRTICALGDAAAWPIQGLIKNF  408 (425)
Q Consensus       331 ~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la--~~i~~~S~C~lG~~a~~pv~s~l~~F  408 (425)
                      +-+..-++||..+  ||       .-...++-.|      |.-||++|+++.  .-|-.-|.=-=|+....|-.++++||
T Consensus       263 ~EL~eRl~~f~~~--~k-------llEaQRL~qR------T~yDLEMl~e~G~C~GIENYSRhl~GR~~GEpP~tLlDYF  327 (667)
T TIGR00631       263 KELEERLKYFEEQ--GK-------LLEAQRLKQR------TEYDLEMLREMGYCSGIENYSRHLSGRKPGEPPYTLLDYF  327 (667)
T ss_pred             HHHHHHHHHHHHC--CC-------HHHHHHHHHH------HHHHHHHHHHCCCCCCCCHHCCCCCCCCCCCCCCCHHHHC
T ss_conf             9999999999877--95-------1788889886------8877888750673377000000216777631596477650


Q ss_pred             ---HHHHHHHHHHH
Q ss_conf             ---89999998651
Q gi|254780858|r  409 ---RPLIEERIDQY  419 (425)
Q Consensus       409 ---~dEfe~hI~~~  419 (425)
                         |+||-=-|+..
T Consensus       328 ~gfP~DfLlviDES  341 (667)
T TIGR00631       328 IGFPEDFLLVIDES  341 (667)
T ss_pred             CCCCCCEEEEEEEC
T ss_conf             46886508988402


No 59 
>TIGR01312 XylB xylulokinase; InterPro: IPR006000   The ability to metabolise xylose, one of the most abundant sugars in nature, is dependent on its conversion to xylulose-5-phosphate, which then enters the non-oxidative pentose phosphate pathway . Xylulose-5-phosphate is produced from xylose by the sequential action of two enzymes; xylose isomerase, which converts xylose to xylulose, and xylulokinase, which subsequently phosphorylates xylulose.   This entry represents bacterial xylulokinase. In addition to its role in xylose metabolism this enzyme may also have a biosynthetic role. 1-deoxy-D-xylulose 5-phosphate serves as a precursor for the biosynthesis of the vitamins thiamine and pyridoxal and for the formation of isopentenyl pyrophosphate and dimethylallyl pyrophosphate via the nonmevalonate pathway of terpenoid biosynthesis. Xylulokinase catalyses the phosphorylation of 1-deoxy-D-xylulose at the hydroxy group of C-5 . This reaction therefore constitutes a potential salvage pathway for the generation of 1-deoxy-D-xylulose 5-phosphate from exogenous or endogenous 1-deoxy-D-xylulose as starting material for the biosynthesis of terpenoids, thiamine and pyridoxal. ; GO: 0004856 xylulokinase activity, 0005997 xylulose metabolic process.
Probab=35.09  E-value=8.2  Score=18.71  Aligned_cols=136  Identities=17%  Similarity=0.245  Sum_probs=88.3

Q ss_pred             CCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCC--CCCCEEEE--ECCCCCHHHHHHHHHCCCCCCCCCEE
Q ss_conf             500028999999999960568886338987743047642678--87872689--35898799999986155678711004
Q gi|254780858|r  206 TTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGH--VNYPCTVE--ESMSITFDELIEKHCGGIRGGWDNLL  281 (425)
Q Consensus       206 T~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~--V~~Pg~~e--vp~Gt~l~eli~~~~GG~~~~~~~~k  281 (425)
                      |+-.+|.+-.+=-.|+.+                  +.++++  -.=|-+||  -..|+-..|+-..+  |+..+..   
T Consensus       179 T~~fdV~~R~Ws~~~L~~------------------~~~~~~l~~~lP~l~e~~~~~G~~~~~~a~~~--Gl~~~v~---  235 (494)
T TIGR01312       179 TLWFDVKKRAWSKELLDA------------------LDLPLDLESLLPELIESSEVVGTVRPEVAARL--GLSAGVP---  235 (494)
T ss_pred             HHHHHHCCHHHHHHHHHH------------------HCCCCCCHHHCCEEECCCCCCCCCCHHHHHHC--CCCCCCE---
T ss_conf             665311002367999998------------------39898828859701478853027538999744--8999876---


Q ss_pred             EEEECCC--CCCCCCCCCCCC--CCCCCCCHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHH-----------HCC
Q ss_conf             8985245--656532100245--6334220110387346651799428652899999999999876-----------279
Q gi|254780858|r  282 AVIPGGS--SVPCLPAGQMRG--AIMDYDGLKEMGSGLGTAAVIVMDRSTDIIKAIWRLSVFYKHE-----------SCG  346 (425)
Q Consensus       282 av~~GG~--~~g~l~~~~ld~--~~ld~~~l~~~Gs~LGsg~iiV~de~~~iv~~~~~~~~F~a~E-----------SCG  346 (425)
                       |.-||.  +++-|.....+.  +.|          .|||.|++..-++....+-..++.-|++..           ||+
T Consensus       236 -V~~GGGDNA~gA~G~G~v~~G~~~~----------SlGTSGv~~a~~~~~~~dp~g~Vh~Fcha~P~~w~~m~vtLsat  304 (494)
T TIGR01312       236 -VAAGGGDNAAGAIGTGIVKPGDVTV----------SLGTSGVVYAVTDKPLPDPAGAVHGFCHALPGGWYPMGVTLSAT  304 (494)
T ss_pred             -EEECCHHHHHHHHCCCCCCCCCEEE----------EECCCCEEEEEECCCCCCCCCCCCEEECCCCCCCEEHHHHHHHH
T ss_conf             -8716277898985136226884178----------86354101001046667745661210005898713134556658


Q ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             988523028999999999982899989999999999862236
Q gi|254780858|r  347 QCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEGR  388 (425)
Q Consensus       347 kCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~~  388 (425)
                      -|      +.|+.+++..       ..|++.|.+.++...-+
T Consensus       305 ~~------l~w~~~l~~~-------~~~~~~l~~~~~~~~~G  333 (494)
T TIGR01312       305 SS------LEWFRELFGK-------SEDVEELNEEAEKSPPG  333 (494)
T ss_pred             HH------HHHHHHHHCC-------CCCHHHHHHHHHHCCCC
T ss_conf             89------9999996203-------46778999997527778


No 60 
>TIGR02818 adh_III_F_hyde S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase; InterPro: IPR014183   The members of this protein family show dual function. First, they remove formaldehyde, a toxic metabolite, by acting as S-(hydroxymethyl)glutathione dehydrogenase (1.1.1.284 from EC). S-(hydroxymethyl)glutathione can form spontaneously from formaldehyde and glutathione, and so this enzyme previously was designated glutathione-dependent formaldehyde dehydrogenase. These same proteins are also designated as class III alcohol dehydrogenases (1.1.1.1 from EC), i.e. alcohol dehydrogenases that do not require glutathione and they tend to show poor activity for ethanol among their various substrate alcohols..
Probab=34.53  E-value=6.2  Score=19.51  Aligned_cols=13  Identities=15%  Similarity=0.253  Sum_probs=5.5

Q ss_pred             CCCCHHHHHHHHH
Q ss_conf             0002899999999
Q gi|254780858|r  207 TVNNVESIAVVPT  219 (425)
Q Consensus       207 ~V~NVeTla~v~~  219 (425)
                      .|-||+.+-+.-.
T Consensus       262 ~~Gn~~~mr~ale  274 (368)
T TIGR02818       262 CIGNVNVMRAALE  274 (368)
T ss_pred             ECCHHHHHHHHHH
T ss_conf             1020789999987


No 61 
>TIGR01702 CO_DH_cata carbon-monoxide dehydrogenase, catalytic subunit; InterPro: IPR010047   This entry describes the Ni-containing carbon monoxide dehydrogenase (CODH) family (1.2.99.2 from EC). These enzymes reversibly oxidise CO to CO(2), and play key roles in the energy-yielding pathways of various autotrophic anaerobes, allowing these organisms to grow with CO as the sole carbon source . The active sites of these enzymes contain Ni-iron-sulphur (NiFeS) clusters. This family also includes the CODH subunit of bifunctional CODH/acetyl-CoA synthetase (CODH/ACS), which contains two Ni-containing active sites to catalyse the formation of acetyl-CoA from CO(2)-derived CO , .   CODH is related to hybrid cluster proteins (HCP, or prismane) (IPR010048 from INTERPRO), a complex whose activity is not yet fully described; the hybrid Fe-S cluster in HCPs is similar to the NiFeS cluster in CODH .; GO: 0016151 nickel ion binding, 0018492 carbon-monoxide dehydrogenase (acceptor) activity, 0051539 4 iron 4 sulfur cluster binding, 0006091 generation of precursor metabolites and energy, 0005737 cytoplasm.
Probab=34.45  E-value=32  Score=14.70  Aligned_cols=237  Identities=21%  Similarity=0.218  Sum_probs=114.7

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHH---
Q ss_conf             899999999839776875711245568742356568861999857677848--600489998625899999999999---
Q gi|254780858|r   40 RDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLVVNADESEPG--TCKDRDIMRHEPHTLIEGCVIASF---  114 (425)
Q Consensus        40 ~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv~N~~E~EPg--t~kDr~Ll~~~p~~vieG~~i~a~---  114 (425)
                      |+.=++.-++-||       ||.|.|-+... .-.   + =..|-| ++|-  +++   =|+=.-+..+.|.+++..   
T Consensus       166 ~~~R~e~~~~L~i-------lP~G~~~e~~~-~~~---~-t~tn~d-sdpv~L~~~---~Lrlgia~~~~g~~~~~~l~D  229 (647)
T TIGR01702       166 PEKRLEKWEKLGI-------LPGGIKAEVLD-AVS---K-TSTNLD-SDPVDLAVK---ALRLGIATGLTGQILAEELSD  229 (647)
T ss_pred             CCHHHHHHHHCCC-------CCCCHHHHHHH-HHH---H-HHCCCC-CCHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
T ss_conf             8413678763688-------77735689999-888---6-423789-877999999---999999999889999987536


Q ss_pred             ----------------HHCCCEEEEEECCCCHHHHHHHHHHH------HHHHHCC-CCCCC-CCCCCCCEEEEEECCCCC
Q ss_conf             ----------------71836389981555178999999999------9998689-97767-678866406997457510
Q gi|254780858|r  115 ----------------AIGAHCAFIYVRGEFIRERESLQAAV------DECYASG-LLGSN-SKLGYDVDIIVHHGAGAY  170 (425)
Q Consensus       115 ----------------a~gA~~~~I~ir~ey~~~~~~l~~ai------~ea~~~g-~lg~~-~~~g~~~~i~v~~g~g~Y  170 (425)
                                      .+.-+..=|.|.++.|..++.+.++.      ++|+++| --|-| .|               .
T Consensus       230 iLFGtP~p~~s~~~lgv~dP~~VNI~~~GH~P~l~~~l~~~A~~edi~~~Ak~AGaAkGi~ivG---------------~  294 (647)
T TIGR01702       230 ILFGTPQPVVSEADLGVLDPDYVNIVVNGHQPLLSEILIEAAKEEDIQDKAKAAGAAKGIKIVG---------------I  294 (647)
T ss_pred             HHCCCCCCEEEECCCEECCCCCEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHCCCCCCEEEE---------------E
T ss_conf             6538995268736762007676336883886468899999852856578999704778744778---------------7


Q ss_pred             CC-CHHHHHHHHHCCCCCCCCCCCCCC-CCCCCCCCCCCCCCHHHHHHH----------------HHHHHHCHHHHHHCC
Q ss_conf             01-107889986308999868889986-227830378500028999999----------------999960568886338
Q gi|254780858|r  171 IC-GEETALLESLEGKKGQPRLKPPFP-ANVGLYGCPTTVNNVESIAVV----------------PTILRRGASWYSGFG  232 (425)
Q Consensus       171 i~-GeEtali~sieG~r~~Pr~kPP~p-~~~Gl~g~PT~V~NVeTla~v----------------~~i~~~G~~~y~~~G  232 (425)
                      +| |.|      ++     -|.. .+| +=+|+     +=||.-+=..|                |.|=. =+       
T Consensus       295 ~CtGqe------~~-----~R~~-H~~EvFvG~-----~gN~~~~E~~iaTG~iD~~~~d~nC~~Psl~~-~A-------  349 (647)
T TIGR01702       295 ICTGQE------LL-----MRVG-HLPEVFVGL-----VGNWLSQELLIATGAIDAMVVDVNCTLPSLPA-VA-------  349 (647)
T ss_pred             EECCCH------HH-----HCCC-CCCCCHHHH-----HHHHHHHHHHHHCCCEEEEEEECCCCCCCCHH-HH-------
T ss_conf             740415------75-----3457-776210234-----75389898888416237766612588887146-77-------


Q ss_pred             CCCCCCEEEEECCCCCCCCEEEE-ECCCCCHH-----HHH----HHHHCCCCCC-CC-----CEE---EEEECCCCCC--
Q ss_conf             98774304764267887872689-35898799-----999----9861556787-11-----004---8985245656--
Q gi|254780858|r  233 RENNRGTKLFSISGHVNYPCTVE-ESMSITFD-----ELI----EKHCGGIRGG-WD-----NLL---AVIPGGSSVP--  291 (425)
Q Consensus       233 ~~~~~Gtkl~tvsG~V~~Pg~~e-vp~Gt~l~-----eli----~~~~GG~~~~-~~-----~~k---av~~GG~~~g--  291 (425)
                        +.-.|||+||+-.++-||+++ +|+-.-=+     ++|    |.|.-  +.. ..     ..|   -+++ |.|..  
T Consensus       350 --E~y~v~ii~vd~~~~~~Ga~~~i~y~~~~A~E~A~~iI~~AIeaFk~--R~~s~~~~~~~~~kG~~k~vv-GfS~Eal  424 (647)
T TIGR01702       350 --EKYHVKIITVDDLAKIKGADYKIPYDPEKAEETAKTIIEMAIEAFKE--RKESKQKVAIPKEKGKQKVVV-GFSEEAL  424 (647)
T ss_pred             --HHHCCEEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCCCCCEEEE-EECHHHH
T ss_conf             --36175378741000017700148988767889999999999997630--346788656540048621788-3077999


Q ss_pred             --CCCCCCCCCCCCCC-CCHHHCCC------CCCCCEEEEECCCCCHHHHHHHHHH
Q ss_conf             --53210024563342-20110387------3466517994286528999999999
Q gi|254780858|r  292 --CLPAGQMRGAIMDY-DGLKEMGS------GLGTAAVIVMDRSTDIIKAIWRLSV  338 (425)
Q Consensus       292 --~l~~~~ld~~~ld~-~~l~~~Gs------~LGsg~iiV~de~~~iv~~~~~~~~  338 (425)
                        +| ..++++-|+-. -++.+.|-      ..|+.-+-....|...|++++.+++
T Consensus       425 ~~~L-g~~~~~~P~~pLvd~I~~G~IkGVv~~vgCsnL~~~gqD~~~v~l~KELiK  479 (647)
T TIGR01702       425 VKAL-GGKLADDPLKPLVDLIAKGKIKGVVLLVGCSNLKNGGQDSSTVTLTKELIK  479 (647)
T ss_pred             HHHH-CCCCCCCCCCCHHHHHHCCCEEEEEEEEECCCCCCCCCCEEEEHHHHHHHH
T ss_conf             9972-464234754004554104741268899743036799940466313267530


No 62 
>pfam03431 RNA_replicase_B RNA replicase, beta-chain. This family is of Leviviridae RNA replicases. The replicase is also known as RNA dependent RNA polymerase.
Probab=34.05  E-value=33  Score=14.66  Aligned_cols=68  Identities=18%  Similarity=0.123  Sum_probs=33.2

Q ss_pred             CCCCEEEEECCC-CCHHHHHHHHHHHHH-----------------HHHCCCCC---------CCCCH---HHHHHHHHHH
Q ss_conf             466517994286-528999999999998-----------------76279988---------52302---8999999999
Q gi|254780858|r  315 LGTAAVIVMDRS-TDIIKAIWRLSVFYK-----------------HESCGQCT---------PCREG---TGWMMRVMER  364 (425)
Q Consensus       315 LGsg~iiV~de~-~~iv~~~~~~~~F~a-----------------~ESCGkCt---------PCR~G---t~~l~~il~~  364 (425)
                      +-++.|-|+.|| -++.+++..+++++.                 +|||||-.         .||.-   ...|..+|++
T Consensus       325 ~~~~~v~iYGDDII~ps~~~~~L~~vl~yvGF~pN~~KTF~~GpFRESCGkH~f~GvDVtPfYik~pi~~l~dlilvlN~  404 (539)
T pfam03431       325 GRTSDVGIYGDDIIVPTCAVPPLMEVLSYVGFTPNLKKTFTSGPFRESCGKHYFAGVDVTPFYIKRPIVSLPDLILVLNS  404 (539)
T ss_pred             CCCCEEEEECCCEEECHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCEEECCCCCCHHHHHHHHHH
T ss_conf             88750588437466322221899999988075468666435686144554543067777543655666788999999987


Q ss_pred             HH-----CCCCCHHHHHHHHHHH
Q ss_conf             98-----2899989999999999
Q gi|254780858|r  365 LV-----KGIAQKREIDLLYEVS  382 (425)
Q Consensus       365 i~-----~G~a~~~Dl~~L~~la  382 (425)
                      |.     +|-..++-+.......
T Consensus       405 i~rW~tv~Gi~dPr~~~v~~ky~  427 (539)
T pfam03431       405 IYRWGTVDGIWDPRLYPVYLKYR  427 (539)
T ss_pred             HCCCEECCCCCCCCHHHHHHHHH
T ss_conf             31501116732750668999998


No 63 
>pfam08240 ADH_N Alcohol dehydrogenase GroES-like domain. This is the catalytic domain of alcohol dehydrogenases. Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure.
Probab=33.69  E-value=9.2  Score=18.36  Aligned_cols=17  Identities=41%  Similarity=1.046  Sum_probs=12.6

Q ss_pred             HHCCCCCCCCCHHHHHH
Q ss_conf             62799885230289999
Q gi|254780858|r  343 ESCGQCTPCREGTGWMM  359 (425)
Q Consensus       343 ESCGkCtPCR~Gt~~l~  359 (425)
                      -+||.|..|+.|...+-
T Consensus        64 ~~Cg~C~~C~~G~~~~C   80 (108)
T pfam08240        64 IPCGKCAACREGRENLC   80 (108)
T ss_pred             CCCCCCHHHHCCCCCCC
T ss_conf             48998978959090208


No 64 
>COG1312 UxuA D-mannonate dehydratase [Carbohydrate transport and metabolism]
Probab=33.04  E-value=30  Score=14.94  Aligned_cols=29  Identities=24%  Similarity=0.624  Sum_probs=22.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             888998622783037850002899999999996
Q gi|254780858|r  190 RLKPPFPANVGLYGCPTTVNNVESIAVVPTILR  222 (425)
Q Consensus       190 r~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~  222 (425)
                      ..-||+|    +||-|-+|+|.|-+..+-.++.
T Consensus       212 PDDPP~p----i~GLpRIvst~ed~~~ll~~vd  240 (362)
T COG1312         212 PDDPPWP----IFGLPRIVSTIEDYQRLLEMVD  240 (362)
T ss_pred             CCCCCCC----CCCCCHHCCCHHHHHHHHHHCC
T ss_conf             9999844----4686133088999999997336


No 65 
>TIGR03599 YloV DAK2 domain fusion protein YloV. This model describes a protein family that contains an N-terminal DAK2 domain (pfam02734), so named because of similarity to the dihydroxyacetone kinase family family. The GTP-binding protein CgtA (a member of the obg family) is a bacterial GTPase associated with ribosome biogenesis, and it has a characteristic extension (TIGR03595) in certain lineages. This protein family described here was found, by the method of partial phylognetic profiling, to have a phylogenetic distribution strongly correlated to that of TIGR03595. This correlation implies some form of functional coupling.
Probab=32.95  E-value=34  Score=14.54  Aligned_cols=282  Identities=17%  Similarity=0.201  Sum_probs=130.0

Q ss_pred             CCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCH
Q ss_conf             67798999977998999999826989999999983977687571124556874235656886199985767784860048
Q gi|254780858|r   16 QGKSLSDSMSRGHWDNVDKILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLVVNADESEPGTCKDR   95 (425)
Q Consensus        16 ~~~~l~~y~~~ggy~~l~~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv~N~~E~EPgt~kDr   95 (425)
                      ...++.+.... -.+.-+++|..+|+ .+..++++|.+--||.||-.=..  -+...-.+.+  +-.+-.+-++-.. +.
T Consensus       140 ~~~~~~~~~~~-a~~~a~~aL~~TP~-~LpvLkeAGVVDAGg~Gl~~ile--g~~~~l~G~~--~~~~~~~~~~~~~-~~  212 (530)
T TIGR03599       140 EGDDLEEVMEA-AVEAAEKALARTPE-LLPVLKEAGVVDSGGQGLVVILE--GMLAALTGEP--IELAPYKPEPPEG-DE  212 (530)
T ss_pred             CCCCHHHHHHH-HHHHHHHHHHHCHH-HHHHHHHCCCCCCCHHHHHHHHH--HHHHHHCCCC--CCCCCCCCCCCCC-CC
T ss_conf             58999999999-99999999983867-66788866950774151999999--9999845998--7744455677642-22


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCEEEEE-ECCCCHHHHHHHHHHHHHHHHCCCCCCCC---CCCCCCEEEEEECCCCCC
Q ss_conf             99986258999999999997183638998-15551789999999999998689977676---788664069974575100
Q gi|254780858|r   96 DIMRHEPHTLIEGCVIASFAIGAHCAFIY-VRGEFIRERESLQAAVDECYASGLLGSNS---KLGYDVDIIVHHGAGAYI  171 (425)
Q Consensus        96 ~Ll~~~p~~vieG~~i~a~a~gA~~~~I~-ir~ey~~~~~~l~~ai~ea~~~g~lg~~~---~~g~~~~i~v~~g~g~Yi  171 (425)
                      .... .++.           ..-.=|.-| |+.......+.+++.+...      |..+   +.+--+.++||+--    
T Consensus       213 ~~~~-~~~~-----------~~~gYctefl~~~~~~~~~~~lr~~L~~~------GdSlvvv~~~~~~kVHvHT~~----  270 (530)
T TIGR03599       213 IASE-EHHD-----------IEFGYCTEFLVKLKDKFDEEKFRKELEKL------GDSLVVVGDDDLVKVHVHTND----  270 (530)
T ss_pred             CCCC-CCCC-----------CCCCEEEEEEEECCCCCCHHHHHHHHHHH------CCEEEEECCCCEEEEEEECCC----
T ss_conf             3455-6557-----------88564899999878757999999999973------985999757984999994199----


Q ss_pred             CCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC--CCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf             11078899863089998688899862278303785--0002899999999996056888633898774304764267887
Q gi|254780858|r  172 CGEETALLESLEGKKGQPRLKPPFPANVGLYGCPT--TVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGHVN  249 (425)
Q Consensus       172 ~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT--~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~V~  249 (425)
                         .-..|+..-              .   ||+++  -|.|-.-  +...++..          +     +--.-....+
T Consensus       271 ---pG~vle~~~--------------~---~G~l~~ikIenM~~--Q~~~~~~~----------~-----~~~~~~~~~~  313 (530)
T TIGR03599       271 ---PGLVLEYGQ--------------K---YGELIKIKIENMRE--QHEEILEG----------T-----SNEEKKKEEK  313 (530)
T ss_pred             ---HHHHHHHHH--------------H---HCCEEEEEEECCHH--HHHHHHCC----------C-----CCCCCCCCCC
T ss_conf             ---799999999--------------8---39367999815648--89876313----------5-----4344556667


Q ss_pred             CCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEEEEECCCCCH
Q ss_conf             87268935898799999986155678711004898524565653210024563342201103873466517994286528
Q gi|254780858|r  250 YPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAVIVMDRSTDI  329 (425)
Q Consensus       250 ~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~iiV~de~~~i  329 (425)
                      ..+++-|-.|--+.+++... |     ..   .|+.||..+-.- .+++.      +.+.    .++..-|+|++.+.++
T Consensus       314 ~~~vVAv~~G~Gl~~if~~~-G-----a~---~Vi~ggqt~NPS-t~dil------~Ai~----~~~a~~ViiLPNn~Ni  373 (530)
T TIGR03599       314 EYAIVAVAPGEGIAELFKSL-G-----AD---VVIEGGQTMNPS-TEDIL------KAIE----KVNAKNVFVLPNNKNI  373 (530)
T ss_pred             CEEEEEEECCHHHHHHHHHC-C-----CC---EEECCCCCCCCC-HHHHH------HHHH----HCCCCEEEEECCCCHH
T ss_conf             73999994584299999977-9-----96---996589989968-99999------9998----5798739994799108


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC
Q ss_conf             999999999998762799885230289999999999828999899999999998622
Q gi|254780858|r  330 IKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIE  386 (425)
Q Consensus       330 v~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~  386 (425)
                      +-.+.+..+....  -=.-.|+|-=.+-+..++. .......+++...|.+.+..++
T Consensus       374 ilaA~qaa~~~~k--~V~VipT~si~qgiaAl~~-fdp~~~~een~~~M~ea~~~v~  427 (530)
T TIGR03599       374 ILAAEQAAELADK--NVVVIPTKTIVQGLAALLV-FDPEASLEDNKEAMEEAIKAVR  427 (530)
T ss_pred             HHHHHHHHHHCCC--CEEEEECCCHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHCCC
T ss_conf             8999999874289--7899947988999999997-1878887899999999995597


No 66 
>TIGR01068 thioredoxin thioredoxin; InterPro: IPR005746 Thioredoxins , , ,  are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulphide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulphide and a dithiol. TR-S_2 + NADPH + H^+ -> TR-(SH)_2 + NADP^+ (1) trx-S_2 + TR-(SH)_2 -> trx-(SH)_2 + TR-S_2 (2) Protein-S_2 + trx-(SH)_2 -> Protein-(SH)_2 + trx-S_2 (3) In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide (steps 1 and 2). Reduced thioredoxin then directly reduces the disulphide in the substrate protein (step 3) . Protein disulphide isomerase (PDI), a resident foldase of the endoplasmic recticulum, is a multi-functional protein that catalyses the formation and isomerisation of disulphide bonds during protein folding , . PDI contains 2 redox active domains, near the N- and C-termini, that are similar to thioredoxin: both contribute to disulphide isomerase activity, but are functionally non-equivalent . Interestingly, a mutant PDI, with all 4 of the active cysteines replaced by serine, displays a low but detectable level of disulphide isomerase activity . Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity . A number of endoplasmic reticulum proteins that differ from the PDI major isozyme contain 2 (ERp60, ERp5) or 3 (ERp72 ) thioredoxin domains; all of them seem to be PDIs. 3D-structures have been determined for a number of thioredoxins . The molecule has a doubly-wound alternating alpha/beta fold, consisting of a 5-stranded parallel beta-sheet core, enclosed by 4 alpha-helices. The active site disulphide is located at the N-terminus of helix 2 in a short segment that is separated from the rest of the helix by a kink caused by a conserved proline. The 4-membered disulphide ring is located on the surface of the protein. A flat hydrophobic surface lies adjacent to the disulphide, which presumably facilitates interaction with other proteins.   One invariant feature of all thioredoxins is a cis-proline located in a loop preceding beta-strand 4. This residue is positioned in van der Waals contact with the active site cysteines and is important both for stability and function . Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase . Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0006662 glycerol ether metabolic process, 0045454 cell redox homeostasis.
Probab=32.87  E-value=25  Score=15.50  Aligned_cols=49  Identities=16%  Similarity=0.259  Sum_probs=27.0

Q ss_pred             HHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHCCCCC
Q ss_conf             99987627998852302899999999998289-998999999999986223666
Q gi|254780858|r  338 VFYKHESCGQCTPCREGTGWMMRVMERLVKGI-AQKREIDLLYEVSKNIEGRTI  390 (425)
Q Consensus       338 ~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~-a~~~Dl~~L~~la~~i~~~S~  390 (425)
                      .|+|    -+|.|||.=++-+.++-+.....- =-.=|.|.-.++|..-.-+||
T Consensus        20 DFWA----~WCGPCKm~aP~lee~a~e~~~~v~~~KlnvD~~~~~A~~ygi~SI   69 (101)
T TIGR01068        20 DFWA----PWCGPCKMIAPILEELAKEYEGKVKFVKLNVDENPDIAAKYGIRSI   69 (101)
T ss_pred             EEEC----CCCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHCCCCCC
T ss_conf             7435----9998734424688888754169746888534788341445285405


No 67 
>TIGR00385 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily; InterPro: IPR004799 Periplasmic protein thiol:disulphide oxidoreductase is involved in the biogenesis of c-type cytochromes as well as in disulphide bond formation in some periplasmic proteins. This group defines the DsbE subfamily.; GO: 0015036 disulfide oxidoreductase activity, 0017004 cytochrome complex assembly, 0030288 outer membrane-bounded periplasmic space.
Probab=32.86  E-value=23  Score=15.70  Aligned_cols=47  Identities=17%  Similarity=0.270  Sum_probs=22.0

Q ss_pred             CEEEEEE--CCCCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHCCCEEEEEE--CCCCHHHHHHHHH
Q ss_conf             6199985--76778486004-8999862589999999999971836389981--5551789999999
Q gi|254780858|r   77 PHYLVVN--ADESEPGTCKD-RDIMRHEPHTLIEGCVIASFAIGAHCAFIYV--RGEFIRERESLQA  138 (425)
Q Consensus        77 ~~yvv~N--~~E~EPgt~kD-r~Ll~~~p~~vieG~~i~a~a~gA~~~~I~i--r~ey~~~~~~l~~  138 (425)
                      .+.+.+|  |.=|=|  |+| |.+|.+=.   =+|          +==+|+|  ||+...|++-|.+
T Consensus        64 G~~~LlNVWAsWCp~--CraEHp~L~eLa---k~G----------rl~ivG~dYKD~~~~Al~~Lke  115 (175)
T TIGR00385        64 GKPVLLNVWASWCPP--CRAEHPYLNELA---KEG----------RLPIVGVDYKDQSQNALKFLKE  115 (175)
T ss_pred             CCEEEEEEEECCCCC--CHHCCHHHHHHH---HCC----------CCEEEEEECCCCCHHHHHHHHH
T ss_conf             960699884036888--310005789997---539----------7307886347884578888764


No 68 
>TIGR01931 cysJ sulfite reductase [NADPH] flavoprotein, alpha-component; InterPro: IPR010199   This entry describes an NADPH-dependent sulphite reductase flavoprotein subunit. Most members of the proteins of this entry are found in Cys biosynthesis gene clusters. The closest homologues are designated as subunits nitrate reductase.; GO: 0004783 sulfite reductase (NADPH) activity, 0000103 sulfate assimilation, 0019344 cysteine biosynthetic process.
Probab=32.07  E-value=11  Score=17.72  Aligned_cols=32  Identities=19%  Similarity=0.280  Sum_probs=15.3

Q ss_pred             CCCCCCEEEEECCCCCCCCEEEEECCCCCHHHHHHHH
Q ss_conf             9877430476426788787268935898799999986
Q gi|254780858|r  233 RENNRGTKLFSISGHVNYPCTVEESMSITFDELIEKH  269 (425)
Q Consensus       233 ~~~~~Gtkl~tvsG~V~~Pg~~evp~Gt~l~eli~~~  269 (425)
                      .|-.|  ||+|||-.-+.   ++=++.+|+..+.+++
T Consensus       410 RPL~P--RLYSIaSSq~e---v~dEVHlTVg~V~y~~  441 (628)
T TIGR01931       410 RPLTP--RLYSIASSQAE---VDDEVHLTVGVVRYEA  441 (628)
T ss_pred             CCCCC--CHHHHHHHHHH---CCCEEEEEEEEEEEEE
T ss_conf             77885--11218889865---6880688766889820


No 69 
>PRK05481 lipoyl synthase; Provisional
Probab=31.84  E-value=10  Score=18.09  Aligned_cols=189  Identities=18%  Similarity=0.198  Sum_probs=105.7

Q ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEE--ECCCCHHH-HHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             8576778486004899986258999999999997183638998--15551789-99999999999868997767678866
Q gi|254780858|r   82 VNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIY--VRGEFIRE-RESLQAAVDECYASGLLGSNSKLGYD  158 (425)
Q Consensus        82 ~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~--ir~ey~~~-~~~l~~ai~ea~~~g~lg~~~~~g~~  158 (425)
                      ||-+-+-|.     .+=.+.|..|-+.    ...+|-+.++|-  -||+-++. ...+-+.|.+.++..   +      +
T Consensus        69 C~V~tG~P~-----~~D~~EP~~vA~a----v~~m~Lk~vViTSV~RDDL~DgGA~hfa~~I~~Ir~~~---P------~  130 (289)
T PRK05481         69 CDVATGRPL-----PLDPDEPERVAEA----VARMGLKYVVITSVDRDDLPDGGAQHFAETIRAIRELS---P------G  130 (289)
T ss_pred             CCCCCCCCC-----CCCCHHHHHHHHH----HHHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHC---C------C
T ss_conf             407889989-----8870307999999----99828976999634166665655499999999998559---9------9


Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCC--
Q ss_conf             406997457510011078899863089998688899862278303785000289999999999605688863389877--
Q gi|254780858|r  159 VDIIVHHGAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENN--  236 (425)
Q Consensus       159 ~~i~v~~g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~--  236 (425)
                      ..|+|-..   =-.|...++|+.+---+  |        +  +     +-||+||+-.+...+|.++.+.+++..=+.  
T Consensus       131 ~~iEvLiP---DF~G~~~~~l~~v~~a~--P--------d--V-----~nHNiETV~rL~~~VRp~a~Y~rSL~vL~~~k  190 (289)
T PRK05481        131 TTIEVLIP---DFRGRKDAALEIVVAAP--P--------D--V-----FNHNLETVPRLYKRVRPGADYERSLELLKRAK  190 (289)
T ss_pred             CEEEECCC---CCCCCHHHHHHHHHHCC--H--------H--H-----HHCCHHHHHHHCCCCCCCCHHHHHHHHHHHHH
T ss_conf             77997072---11469999999998567--1--------7--7-----64351310443623388233899999999999


Q ss_pred             -CCEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECC---CCCCCCCCCCCCCCCCCCCCHHHCC
Q ss_conf             -430476426788787268935898799999986155678711004898524---5656532100245633422011038
Q gi|254780858|r  237 -RGTKLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGG---SSVPCLPAGQMRGAIMDYDGLKEMG  312 (425)
Q Consensus       237 -~Gtkl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG---~~~g~l~~~~ld~~~ld~~~l~~~G  312 (425)
                       ....++|=||       +-|-+|-+-.|+++.+.-=-..|   ..-+-.|-   |+-.-+|...+- .|-.|+.++..+
T Consensus       191 ~~~p~~~TKSg-------iMvGLGEt~eEv~~~~~DL~~~g---vdilTiGQYL~Ps~~hlpV~ryv-~P~eF~~~~~~a  259 (289)
T PRK05481        191 ELDPGIPTKSG-------LMVGLGETDEEVLEVMDDLRAHG---VDILTIGQYLQPSRKHLPVERYV-TPEEFDEYKEIA  259 (289)
T ss_pred             HHCCCCCEEEE-------EEEECCCCHHHHHHHHHHHHHCC---CCEEEECCCCCCCCCCCCCEECC-CHHHHHHHHHHH
T ss_conf             74899824135-------67755788999999999999819---98998340358886668843356-989999999999


Q ss_pred             CCCCCCE
Q ss_conf             7346651
Q gi|254780858|r  313 SGLGTAA  319 (425)
Q Consensus       313 s~LGsg~  319 (425)
                      -.+|--.
T Consensus       260 ~~~GF~~  266 (289)
T PRK05481        260 LELGFLH  266 (289)
T ss_pred             HHCCCCE
T ss_conf             9759967


No 70 
>PHA00028 rep RNA replicase, beta subunit
Probab=31.60  E-value=36  Score=14.39  Aligned_cols=76  Identities=16%  Similarity=0.157  Sum_probs=46.0

Q ss_pred             CCEEEEECCCC-CHHHHHHHHHHHHH-----------------HHHCCCCC---------CCC---CHHHHHHHHHHHHH
Q ss_conf             65179942865-28999999999998-----------------76279988---------523---02899999999998
Q gi|254780858|r  317 TAAVIVMDRST-DIIKAIWRLSVFYK-----------------HESCGQCT---------PCR---EGTGWMMRVMERLV  366 (425)
Q Consensus       317 sg~iiV~de~~-~iv~~~~~~~~F~a-----------------~ESCGkCt---------PCR---~Gt~~l~~il~~i~  366 (425)
                      .+.|-|+.||. +..+++..++++++                 +||||+--         .||   +....+..++++|.
T Consensus       333 ~~ti~VYGDDIIvps~~a~~li~vlsyvgF~pN~kKTF~~G~FRESCGaH~f~gvDVtPFYik~pi~~l~dlililN~l~  412 (561)
T PHA00028        333 PGTISVYGDDIIVPTEVAPPLINVLSYVGFMPNLKKTFWTGPFRESCGAHYFAGVDVTPFYIKRPLDNLPDLILILNSLR  412 (561)
T ss_pred             CCEEEEECCCEEEEHHHHHHHHHHHHHHCEECCCCCCCCCCCCHHHHHHHHCCCCCCCCEEECCCCCCHHHHHHHHHHHH
T ss_conf             97068965846731555188999998836004776643467624332032216756653586255468899999998631


Q ss_pred             -----CCCCCHHHHHHHHHHHHHHCCC-CCCC
Q ss_conf             -----2899989999999999862236-6677
Q gi|254780858|r  367 -----KGIAQKREIDLLYEVSKNIEGR-TICA  392 (425)
Q Consensus       367 -----~G~a~~~Dl~~L~~la~~i~~~-S~C~  392 (425)
                           +|-..+.-...-....+.++.. .+|+
T Consensus       413 ~W~~v~Gi~dPr~~~v~~ky~~liP~~~~i~~  444 (561)
T PHA00028        413 RWGTVTGISDPRLYPLYNKYRDLIPKTLVLPG  444 (561)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf             30124664673049999999986887462678


No 71 
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=31.57  E-value=11  Score=17.80  Aligned_cols=47  Identities=21%  Similarity=0.212  Sum_probs=26.9

Q ss_pred             CHHHHHHHHHHH--HHHCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHH
Q ss_conf             989999999999--86223666776502479999998638899999986
Q gi|254780858|r  371 QKREIDLLYEVS--KNIEGRTICALGDAAAWPIQGLIKNFRPLIEERID  417 (425)
Q Consensus       371 ~~~Dl~~L~~la--~~i~~~S~C~lG~~a~~pv~s~l~~F~dEfe~hI~  417 (425)
                      +.-|+++|+++.  .-+..-|.---|.....|-.++++|||++|--.|+
T Consensus       290 T~~DlEMl~e~G~C~GIENYSRhl~gr~~Ge~P~tL~DYfp~d~Ll~ID  338 (663)
T COG0556         290 TEYDLEMLRETGYCSGIENYSRHLTGRKPGEPPYTLFDYFPDDFLLFID  338 (663)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHHCCCCEEEEEE
T ss_conf             7753999998287766133356505899995798478858841389982


No 72 
>COG1461 Predicted kinase related to dihydroxyacetone kinase [General function prediction only]
Probab=31.51  E-value=36  Score=14.38  Aligned_cols=116  Identities=13%  Similarity=0.103  Sum_probs=66.1

Q ss_pred             CCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCEEEEE
Q ss_conf             26788787268935898799999986155678711004898524565653210024563342201103873466517994
Q gi|254780858|r  244 ISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTAAVIVM  323 (425)
Q Consensus       244 vsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg~iiV~  323 (425)
                      .+...+.-+++-|+.|--+.++++.++         ...|+.||..+-....+          -+.+.. ..++--++++
T Consensus       320 ~~~~~~~~~ivaV~~g~g~a~~f~~~G---------~~~vi~ggqt~nPSt~d----------iv~ai~-~~~a~~v~il  379 (542)
T COG1461         320 LKKETKDRGIVAVADGEGIADLFKSLG---------ADVVIEGGQTMNPSTDD----------IVEAIE-SVNAKNVFIL  379 (542)
T ss_pred             CCCCCCCCEEEEECCCCCHHHHHHHCC---------CCEEECCCCCCCCCHHH----------HHHHHH-HCCCCEEEEC
T ss_conf             233566737999459846899998669---------96894487656942899----------999999-7599758987


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCH---HHHHHHHHHHHHH
Q ss_conf             2865289999999999987627998852302899999999998289998---9999999999862
Q gi|254780858|r  324 DRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQK---REIDLLYEVSKNI  385 (425)
Q Consensus       324 de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~---~Dl~~L~~la~~i  385 (425)
                      ..+-.++-.+.+-++-+.+.  =.++|    |.-+.+.+.++..-+...   ++++.+.+....+
T Consensus       380 pnnkni~laa~~aa~~~~~~--v~vv~----t~t~~qglaAl~~f~~~~~~e~n~~~M~~al~~~  438 (542)
T COG1461         380 PNNKNIIMAAEQAAEAVDEN--VVVIP----TKTVPQGLAALLVFDPDQSLEDNKETMAEALKKV  438 (542)
T ss_pred             CCCHHHHHHHHHHHHHHCCC--EEEEE----CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             78525999789988874071--69983----2628877888750683456666699999998527


No 73 
>pfam12395 DUF3658 Protein of unknown function. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam08874. There are two completely conserved residues (D and R) that may be functionally important.
Probab=31.31  E-value=36  Score=14.36  Aligned_cols=89  Identities=10%  Similarity=0.044  Sum_probs=59.3

Q ss_pred             HHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99998269899999999839776875711245568742356568861999857677848600489998625899999999
Q gi|254780858|r   32 VDKILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHYLVVNADESEPGTCKDRDIMRHEPHTLIEGCVI  111 (425)
Q Consensus        32 l~~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i  111 (425)
                      +.++-..+.++.....++                |+...+.++. .+...-|---+-|..+=|.+|+++.+......+.+
T Consensus         5 ~~~~~~ls~~e~~~l~~e----------------W~~l~~~n~~-LR~w~~g~i~s~~ed~~D~~Il~~~~~~~~~a~rv   67 (111)
T pfam12395         5 LEEAKPLSVEERQRLAKE----------------WEELSNENAV-LRIWEDGKIVSVPEDYFDAFILEAATDEFQKAARV   67 (111)
T ss_pred             HHHCCCCCHHHHHHHHHH----------------HHHHHHCCCC-EEEEECCEEEEECHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             131298899999999999----------------9999818754-37878997887067876399996383544599999


Q ss_pred             HHHHHCCCEEEEEECCCCHHHHHHHHHHHH
Q ss_conf             999718363899815551789999999999
Q gi|254780858|r  112 ASFAIGAHCAFIYVRGEFIRERESLQAAVD  141 (425)
Q Consensus       112 ~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~  141 (425)
                      ++.++|..+  .+|-+.|  ..-++++-|+
T Consensus        68 Ig~v~g~~~--~~v~D~f--l~~Rir~Li~   93 (111)
T pfam12395        68 VGEVMGHLE--QLVGDTF--LEYRIRELIK   93 (111)
T ss_pred             HHHHHHHCC--CCCCHHH--HHHHHHHHHH
T ss_conf             999998667--7777899--9999999998


No 74 
>PRK05354 arginine decarboxylase; Provisional
Probab=31.07  E-value=36  Score=14.34  Aligned_cols=205  Identities=24%  Similarity=0.388  Sum_probs=97.4

Q ss_pred             HHHHHCCCHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCC--CCCCEEEEEECCCCCCCCCCCHHHH
Q ss_conf             99997799899999982698999999998397768757112455687423565--6886199985767784860048999
Q gi|254780858|r   21 SDSMSRGHWDNVDKILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVC--SDRPHYLVVNADESEPGTCKDRDIM   98 (425)
Q Consensus        21 ~~y~~~ggy~~l~~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~--~~~~~yvv~N~~E~EPgt~kDr~Ll   98 (425)
                      ++|-=.|.|++.=-+--.....|+++|-++|-.  =.-|+-+|-|=++++-.+  ......+||||       |||+..+
T Consensus        90 ~e~~Y~g~y~gVyPIKVNQ~r~VVeeI~~~G~~--~~~GLEAGSKpEL~a~la~~~~~~aliiCNG-------yKD~eyI  160 (634)
T PRK05354         90 EEYGYQGDYQGVYPIKVNQQRHVVEEIVASGKP--YNLGLEAGSKPELMAVLALANDPGSLIVCNG-------YKDREYI  160 (634)
T ss_pred             HHHCCCCCCCEECCEEECCHHHHHHHHHHHCCC--CCCCCCCCCHHHHHHHHHHCCCCCCEEEECC-------CCCHHHH
T ss_conf             982988866304223436528999999972765--6555535868999999862379995599568-------2769999


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEE-CCCCCC--CCHH
Q ss_conf             8625899999999999718363899815551789999999999998689977676788664069974-575100--1107
Q gi|254780858|r   99 RHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHH-GAGAYI--CGEE  175 (425)
Q Consensus        99 ~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~-g~g~Yi--~GeE  175 (425)
                      +-        +++ +.-+ -++++|-|+  .+...+.   -|+.+++.+. -+.+|    +.+++.. |.|..-  .||.
T Consensus       161 ~L--------Al~-a~kl-G~~v~iViE--k~~EL~~---il~~a~~l~v-~P~iG----vR~kL~s~gsGkW~~SgGd~  220 (634)
T PRK05354        161 RL--------ALI-GRKL-GHKVFIVIE--KLSELEL---ILEEAKELGV-KPRLG----VRARLASQGSGKWQSSGGEK  220 (634)
T ss_pred             HH--------HHH-HHHC-CCCEEEEEC--CHHHHHH---HHHHHHHCCC-CCCEE----EEEEECCCCCCCCCCCCCCC
T ss_conf             99--------999-9976-996699974--6899999---9999997499-98505----79986256576106778741


Q ss_pred             -------HHHHHHHCCCC--CCC-CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECC
Q ss_conf             -------88998630899--986-88899862278303785000289999999999605688863389877430476426
Q gi|254780858|r  176 -------TALLESLEGKK--GQP-RLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSIS  245 (425)
Q Consensus       176 -------tali~sieG~r--~~P-r~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvs  245 (425)
                             +.+++.++--+  ++. +.+ =+-.-.|     .-+.|+.+   |...+++.+--|..+-.-..+ -+.+-|.
T Consensus       221 sKFGLs~~eil~~v~~Lk~~~~ld~L~-LLHfHiG-----SQI~~I~~---ik~av~Ea~r~Y~eL~~~Ga~-i~ylDvG  290 (634)
T PRK05354        221 SKFGLSATEILEAVERLREAGLLDCLQ-LLHFHLG-----SQIANIRD---IKTAVREAARIYVELRKLGAP-IKYLDVG  290 (634)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCHHHHH-HHEECCC-----CCCCCHHH---HHHHHHHHHHHHHHHHHCCCC-CEEEEEC
T ss_conf             215888999999999988658453243-3113245-----55534999---999999999999999975898-5178515


Q ss_pred             CC--CCCCE---EEEECCCCCHHH
Q ss_conf             78--87872---689358987999
Q gi|254780858|r  246 GH--VNYPC---TVEESMSITFDE  264 (425)
Q Consensus       246 G~--V~~Pg---~~evp~Gt~l~e  264 (425)
                      |-  |.--|   ....-+..++.|
T Consensus       291 GGLgVDYdGs~s~~~~S~NYsl~E  314 (634)
T PRK05354        291 GGLGVDYDGTRSQSDSSVNYSLQE  314 (634)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             862667677665886676769999


No 75 
>TIGR01944 rnfB electron transport complex, RnfABCDGE type, B subunit; InterPro: IPR010207   The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This entry describes the B subunit.; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding, 0006118 electron transport.
Probab=29.95  E-value=13  Score=17.47  Aligned_cols=68  Identities=22%  Similarity=0.256  Sum_probs=34.0

Q ss_pred             CCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHC-CCCCHH-----HHHHHHHHHHH
Q ss_conf             387346651799428652899999999999876279988523028999999999982-899989-----99999999986
Q gi|254780858|r  311 MGSGLGTAAVIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVK-GIAQKR-----EIDLLYEVSKN  384 (425)
Q Consensus       311 ~Gs~LGsg~iiV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~-G~a~~~-----Dl~~L~~la~~  384 (425)
                      .|..||..++..-=+++.+|+.+-.++=-.+   ||||.     -+=-.=.-+.|.+ |++.-.     --+.++.||+.
T Consensus        21 ~G~~LGyaa~~F~v~~dp~ve~id~lLPQTQ---CGqCG-----ypGC~PYAeAia~NGea~In~C~PGG~a~~~~lA~~   92 (213)
T TIGR01944        21 LGAILGYAAMRFHVEADPIVERIDALLPQTQ---CGQCG-----YPGCRPYAEAIAENGEALINKCPPGGEAVILKLAEL   92 (213)
T ss_pred             HHHHHHHHHHHCCCCCCCHHHHHHHHCCCCC---CCCCC-----CCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             8787756532113888878999986477554---64678-----887415899998607877878888707899999998


Q ss_pred             HC
Q ss_conf             22
Q gi|254780858|r  385 IE  386 (425)
Q Consensus       385 i~  386 (425)
                      |.
T Consensus        93 L~   94 (213)
T TIGR01944        93 LG   94 (213)
T ss_pred             HC
T ss_conf             38


No 76 
>pfam01950 FBPase_3 Fructose-1,6-bisphosphatase. This is a family of bacterial and archaeal fructose-1,6-bisphosphatases (FBPases). FBPase catalyses the hydrolysis of D-fructose-1,6-bisphosphate (FBP) to D-fructose-6-phosphate (F6P) and orthophosphate and is an essential regulatory enzyme in the glyconeogenic pathway.
Probab=29.51  E-value=39  Score=14.16  Aligned_cols=262  Identities=20%  Similarity=0.295  Sum_probs=118.3

Q ss_pred             HHHHHCCCCCCCHHHHHHCCCHHHHHHHHHCC--------HHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEE
Q ss_conf             67551787677989999779989999998269--------8999999998397768757112455687423565688619
Q gi|254780858|r    8 IFTNLYGLQGKSLSDSMSRGHWDNVDKILEKG--------RDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCSDRPHY   79 (425)
Q Consensus         8 ~~~~~~~~~~~~l~~y~~~ggy~~l~~~l~~~--------~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~~~~~y   79 (425)
                      |.|...+.|...++.--    |++..++-+..        -++++..--.-+++|+|    |---.+++.-+ ++  +..
T Consensus        57 imTH~~G~dn~eiH~LA----W~aF~~~tevAK~l~LYGAGQDLL~DaFSGNvkGmG----PgvAEmEf~ER-~s--EP~  125 (364)
T pfam01950        57 IMTHTKGVDNEEIHKLA----WDAFMAATEVAKELKLYGAGQDLLKDAFSGNVKGMG----PGVAEMEFEER-PS--EPF  125 (364)
T ss_pred             EEECCCCCCCHHHHHHH----HHHHHHHHHHHHHHCCCCCCCHHHHCCCCCCCCCCC----CCEEEEEECCC-CC--CCE
T ss_conf             67436678967899999----999999999998716544660343023576626778----74268872257-88--867


Q ss_pred             EEEECCCCCCCCCCC-HHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             998576778486004-8999862589999999999971836389981555178999999999999868997767678866
Q gi|254780858|r   80 LVVNADESEPGTCKD-RDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSNSKLGYD  158 (425)
Q Consensus        80 vv~N~~E~EPgt~kD-r~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~  158 (425)
                      +|--+|-+|||.|.= -|.|-.+|..-. |++                                      +.+++..||.
T Consensus       126 ivF~aDKTePGAfNlPlY~~FaDPfnt~-GLv--------------------------------------idp~mh~Gf~  166 (364)
T pfam01950       126 IVFAADKTEPGAFNLPLYKMFADPFNTA-GLV--------------------------------------IDPSMHEGFR  166 (364)
T ss_pred             EEEEECCCCCCCCCCHHHHHHCCCCCCC-CEE--------------------------------------ECCCCCCCEE
T ss_conf             9998538888733216788752855676-504--------------------------------------3700026715


Q ss_pred             CEEEEEECCCC---CCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCC
Q ss_conf             40699745751---001107889986308999868889986227830378500028999999999960568886338987
Q gi|254780858|r  159 VDIIVHHGAGA---YICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGREN  235 (425)
Q Consensus       159 ~~i~v~~g~g~---Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~  235 (425)
                      |+|.=+. .+.   +-|=||+--|.++-|-.+.=-.|-=++-.-   |.+-.|..++-|.+++-       .|  .|..+
T Consensus       167 FeV~Dv~-~~k~i~l~~Pee~Ydllalig~~~RyvIk~V~~k~~---ge~aav~St~RL~~iAG-------~Y--vGKDD  233 (364)
T pfam01950       167 FEVLDVI-EHKKIELSTPEEMYDLLALIGAPGRYVIKRVYRRSD---GEIAAVVSTERLNLIAG-------KY--VGKDD  233 (364)
T ss_pred             EEEEECC-CCEEEEECCCHHHHHHHHHHCCCCCEEEEEEEECCC---CCEEEEEEHHHHHHHCC-------EE--CCCCC
T ss_conf             8999713-662787429168889999847987368999875589---97679976667776417-------11--07888


Q ss_pred             CCCEEEEECCCCCCCCEEEEECCCC-CHHHHHHHH------HCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCC-
Q ss_conf             7430476426788787268935898-799999986------15567871100489852456565321002456334220-
Q gi|254780858|r  236 NRGTKLFSISGHVNYPCTVEESMSI-TFDELIEKH------CGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMDYDG-  307 (425)
Q Consensus       236 ~~Gtkl~tvsG~V~~Pg~~evp~Gt-~l~eli~~~------~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~-  307 (425)
                      .              -.++...-|. .+.|++|-+      +|.|++. +       -||.|++   ..-+-.+.-|+. 
T Consensus       234 P--------------V~iVR~Q~gfPA~gEvlepFa~phlV~GwmRGS-H-------~gPlMPV---~~~~a~~trfdgp  288 (364)
T pfam01950       234 P--------------VAIVRAQSGFPAVGEVLEPFAFPHLVAGWMRGS-H-------NGPLMPV---PLNDAVPTRFDGP  288 (364)
T ss_pred             C--------------EEEEEECCCCCCHHHHHHCCCCCCCCCCCCCCC-C-------CCCCCCE---ECCCCCCCCCCCC
T ss_conf             6--------------699985688996455441244651113434565-6-------7863311---1366775467899


Q ss_pred             --HHHCCCCCCCCEEE----EECCCCCHHHHHHHHHHHHHHH--HCCCCCCCCCHHHHHH
Q ss_conf             --11038734665179----9428652899999999999876--2799885230289999
Q gi|254780858|r  308 --LKEMGSGLGTAAVI----VMDRSTDIIKAIWRLSVFYKHE--SCGQCTPCREGTGWMM  359 (425)
Q Consensus       308 --l~~~Gs~LGsg~ii----V~de~~~iv~~~~~~~~F~a~E--SCGkCtPCR~Gt~~l~  359 (425)
                        +.+.|..+-.|-++    .||+  .-.|.+++.+..-+.+  +-|---|-|.....|.
T Consensus       289 PrV~algFql~~GkL~GP~D~Fdd--pafD~~R~~a~~~A~~mRr~Gpf~PhrLp~~emE  346 (364)
T pfam01950       289 PRVIALGFQLHEGKLIGPVDMFDD--PAFDYARRKALEIADYIRRQGPFEPHRLPPEEME  346 (364)
T ss_pred             CEEEEEEEEEECCEECCCCCCCCC--CCHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHH
T ss_conf             768888888617887476224577--3237999999999999996499876658978802


No 77 
>TIGR02963 xanthine_xdhA xanthine dehydrogenase, small subunit; InterPro: IPR014307   Members of this protein are the small subunit (or, in eukaryotes, the N-terminal domain) of xanthine dehydrogenase, an enzyme of purine catabolism via urate. The small subunit contains both an FAD and a 2Fe-2S cofactor. Aldehyde oxidase (retinal oxidase) appears to have arisen as a neofunctionalisation among xanthine dehydrogenases in eukaryotes. ; GO: 0004854 xanthine dehydrogenase activity, 0004855 xanthine oxidase activity, 0050660 FAD binding.
Probab=29.44  E-value=20  Score=16.17  Aligned_cols=30  Identities=10%  Similarity=-0.012  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             28999999999982899989999999999862
Q gi|254780858|r  354 GTGWMMRVMERLVKGIAQKREIDLLYEVSKNI  385 (425)
Q Consensus       354 Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i  385 (425)
                      +|++-+.-.++...|+  +.|-+.++.-...+
T Consensus       452 ATPKRA~~~EaaL~G~--~W~~~~~~~A~~aL  481 (515)
T TIGR02963       452 ATPKRAAAVEAALLGK--PWDEATVEAAMAAL  481 (515)
T ss_pred             CHHHHHHHHHHHHCCC--CCCHHHHHHHHHHH
T ss_conf             5115699999985388--53379999999999


No 78 
>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=28.95  E-value=40  Score=14.10  Aligned_cols=51  Identities=20%  Similarity=0.363  Sum_probs=26.9

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHH-----HHHHHHCHHHHHHCCCCCCCCEEEEECC
Q ss_conf             86227830378500028999999-----9999605688863389877430476426
Q gi|254780858|r  195 FPANVGLYGCPTTVNNVESIAVV-----PTILRRGASWYSGFGRENNRGTKLFSIS  245 (425)
Q Consensus       195 ~p~~~Gl~g~PT~V~NVeTla~v-----~~i~~~G~~~y~~~G~~~~~Gtkl~tvs  245 (425)
                      +|.+.|||.+-|+..-+--||-+     ..|-..=..|..++.....+.-|+=++|
T Consensus        77 LPEERGLy~k~tv~dql~yla~LkGm~~~e~~~~~~~wLer~~i~~~~~~kIk~LS  132 (300)
T COG4152          77 LPEERGLYPKMTVEDQLKYLAELKGMPKAEIQKKLQAWLERLEIVGKKTKKIKELS  132 (300)
T ss_pred             CHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHH
T ss_conf             81540667567199999999986499689999999999996065654442477753


No 79 
>TIGR02082 metH methionine synthase; InterPro: IPR011822   Vitamin B12 dependent methionine synthase 2.1.1.13 from EC (5-methyltetrahydrofolate--homocysteine S-methyltransferase) catalyses the conversion of 5-methyltetrahydrofolate and L-homocysteine to tetrahydrofolate and L-methionine as the final step in de novo methionine biosynthesis. The enzyme requires methylcobalamin as a cofactor. In humans, defects in this enzyme are the cause of autosomal recessive inherited methylcobalamin deficiency (CBLG), which causes mental retardation, macrocytic anemia and homocystinuria. Mild deficiencies in activity may result in mild hyperhomocysteinemia, and mutations in the enzyme may be involved in tumorigenesis. Vitamin B12 dependent methionine synthase is found in prokaryotes and eukaryotes, but in prokaryotes the cofactor is cobalamin.   This enzyme is a large protein composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and tetrahydrofolate , the third module binds the B12 cofactor , and the C-terminal module (activation domain) binds S-adenosylmethionine. The activation domain is essential for the reductive activation of the enzyme. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain . The activation domain adopts an unusual alpha/beta fold.Recent studies suggest that this enzyme exists as an ensemble of conformations with equilibria dependent on the oxidation and methylation state of the cobalamin and on the concentrations of substrates or products .; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0050897 cobalt ion binding, 0009086 methionine biosynthetic process.
Probab=28.64  E-value=16  Score=16.75  Aligned_cols=82  Identities=15%  Similarity=0.257  Sum_probs=39.4

Q ss_pred             CCCCCCHHHHH-HH----HHHHHHCHHHHHHCC----CCCCCCEEEE-ECCCCCCCC-----------EEEE-ECCC--C
Q ss_conf             85000289999-99----999960568886338----9877430476-426788787-----------2689-3589--8
Q gi|254780858|r  205 PTTVNNVESIA-VV----PTILRRGASWYSGFG----RENNRGTKLF-SISGHVNYP-----------CTVE-ESMS--I  260 (425)
Q Consensus       205 PT~V~NVeTla-~v----~~i~~~G~~~y~~~G----~~~~~Gtkl~-tvsG~V~~P-----------g~~e-vp~G--t  260 (425)
                      |=||.-.++|- +|    |++=+...+-----|    ...+.||-++ ||=|||--=           .+|| |-+|  +
T Consensus       721 PqVvkSArVMK~AVayL~P~me~~~~~~rvlnGtvee~~~~~G~~vlATVKGDVHDIGKNiV~vvLscNgY~VvdLGvm~  800 (1265)
T TIGR02082       721 PQVVKSARVMKKAVAYLEPYMEKEKSEDRVLNGTVEEEDSSKGKIVLATVKGDVHDIGKNIVGVVLSCNGYEVVDLGVMV  800 (1265)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCCCCCCEECCEECCCCCCCCEEEEEEECCCEECCCCCEEEEEEECCCEEEEECCCCC
T ss_conf             11367689999998406764553000485020300134588875899984475510265233268707884898635258


Q ss_pred             CHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCC
Q ss_conf             799999986155678711004898524565653210
Q gi|254780858|r  261 TFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAG  296 (425)
Q Consensus       261 ~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~  296 (425)
                      |...||+.+        ++.+|=++|  ++|.|+++
T Consensus       801 P~e~IL~~A--------~~~~AD~Ig--lSGLitpS  826 (1265)
T TIGR02082       801 PVEKILEAA--------KDHNADVIG--LSGLITPS  826 (1265)
T ss_pred             CHHHHHHHH--------HHCCCCEEE--ECCCCHHH
T ss_conf             856899999--------843898998--45655012


No 80 
>cd03011 TlpA_like_ScsD_MtbDsbE TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif. The Salmonella typhimurium ScsD is a thioredoxin-like protein which confers copper tolerance to copper-sensitive mutants of E. coli. MtbDsbE has been characterized as an oxidase in vitro, catalyzing the disulfide bond formation of substrates like hirudin. The reduced form of MtbDsbE is more stable than its oxidized form, consistent with an oxidase function. This is in contrast to the function of DsbE from gram-negative bacteria which is a specific reductase of apocytochrome c.
Probab=28.55  E-value=25  Score=15.42  Aligned_cols=13  Identities=15%  Similarity=-0.074  Sum_probs=7.9

Q ss_pred             EEEEEE--CCCCCCC
Q ss_conf             199985--7677848
Q gi|254780858|r   78 HYLVVN--ADESEPG   90 (425)
Q Consensus        78 ~yvv~N--~~E~EPg   90 (425)
                      |++|+|  |.=|.|.
T Consensus        21 k~vvl~FWAtWC~pC   35 (123)
T cd03011          21 KPVLVYFWATWCPVC   35 (123)
T ss_pred             CEEEEEEECCCCCCH
T ss_conf             989999993878136


No 81 
>pfam01799 Fer2_2 [2Fe-2S] binding domain.
Probab=27.91  E-value=25  Score=15.44  Aligned_cols=20  Identities=25%  Similarity=0.398  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHHHHCCCCCCC
Q ss_conf             999999999987627998852
Q gi|254780858|r  331 KAIWRLSVFYKHESCGQCTPC  351 (425)
Q Consensus       331 ~~~~~~~~F~a~ESCGkCtPC  351 (425)
                      .+-..|.+..+-+ ||.|||-
T Consensus        13 ~vQ~af~~~~~~Q-CGfCtPG   32 (75)
T pfam01799        13 PVQQAFIEHGAVQ-CGYCTPG   32 (75)
T ss_pred             HHHHHHHHHCCCC-CCCCCHH
T ss_conf             9999999918970-7887504


No 82 
>COG1829 Predicted archaeal kinase (sugar kinase superfamily) [General function prediction only]
Probab=27.79  E-value=17  Score=16.59  Aligned_cols=45  Identities=16%  Similarity=0.217  Sum_probs=32.0

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCC
Q ss_conf             78726893589879999998615567871100489852456565321002456334
Q gi|254780858|r  249 NYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMRGAIMD  304 (425)
Q Consensus       249 ~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~~~ld  304 (425)
                      +..-+-||..||-|.|++.+++||+.=  +    +-+|+|.-+.     .|.+|+|
T Consensus       116 ~~AH~aEV~~gtGLGDVvAq~~GGlVi--R----~~pG~Pg~~~-----vd~Ip~~  160 (283)
T COG1829         116 RIAHVAEVENGTGLGDVVAQYTGGLVI--R----VKPGGPGEGE-----VDRIPVP  160 (283)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHCCCEEE--E----ECCCCCCEEE-----EEEEECC
T ss_conf             988899987178704788875085799--8----3189998578-----9886048


No 83 
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase; InterPro: IPR006449   This family of sequences describe farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs lack the C-terminal predicted transmembrane region universally conserved among members of this family and therefore are not included in this group.    These enzymes catalyse the formation of squalene by the reductive dimerisation of two farnesyl diphosphate molecules in a two-step reaction. This reaction occurs at the final branch point of the isoprenoid biosynthesis pathway, and is the first committed step in cholesterol biosynthesis.  2 farnesyl diphosphate ---> presqualene diphosphate ---> squalene    The human enzyme (P37268 from SWISSPROT) is a membrane-bound monomer which folds as a single domain . A large channel surrounded by five alpha helices runs through the centre of the protein. One end of this channel is exposed to solvent, while the other is completely enclosed and surrounded by hydrophobic residues. The two half reactions occur at different active sites in this channel. The first half reaction occurs at one end of the channel, then the intermediate is thought to move into the enclosed pocket where the second half reaction occurs. ; GO: 0004310 farnesyl-diphosphate farnesyltransferase activity, 0008610 lipid biosynthetic process, 0016021 integral to membrane.
Probab=27.68  E-value=35  Score=14.48  Aligned_cols=69  Identities=23%  Similarity=0.286  Sum_probs=41.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCC-----CCCCCCCE
Q ss_conf             7784860048999862589999999999971836389981555178999999999999868997767-----67886640
Q gi|254780858|r   86 ESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDECYASGLLGSN-----SKLGYDVD  160 (425)
Q Consensus        86 E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~ea~~~g~lg~~-----~~~g~~~~  160 (425)
                      |+.|- -|||.||+.-|+-.+|              |.=++.+|.+.|+-+.+--..=.+......+     ..|--++|
T Consensus        76 ~s~P~-~~dr~lL~~F~~v~~e--------------F~~L~~~YQevI~dIT~rMG~GMA~f~~~~~~n~ngv~Tv~dyD  140 (350)
T TIGR01559        76 ESDPN-EKDRQLLDDFPVVSLE--------------FLKLKPKYQEVIADITKRMGNGMADFVLKEVTNENGVDTVEDYD  140 (350)
T ss_pred             CCCCC-HHHHHHHHHHHHHHHH--------------HHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHC
T ss_conf             88386-6677775420279998--------------73278543268999877611247888630466765200187626


Q ss_pred             EEEEECCCC
Q ss_conf             699745751
Q gi|254780858|r  161 IIVHHGAGA  169 (425)
Q Consensus       161 i~v~~g~g~  169 (425)
                      ..-|.+||-
T Consensus       141 ~YCHYVAGl  149 (350)
T TIGR01559       141 KYCHYVAGL  149 (350)
T ss_pred             CCCCEEEEE
T ss_conf             767266424


No 84 
>TIGR01020 rpsE_arch ribosomal protein S5; InterPro: IPR005711   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=27.61  E-value=22  Score=15.80  Aligned_cols=74  Identities=23%  Similarity=0.489  Sum_probs=49.3

Q ss_pred             HHCCCEEEEEECC-CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCC--CCCHHHHHHHHHCCCCCCCCC
Q ss_conf             7183638998155-5178999999999999868997767678866406997457510--011078899863089998688
Q gi|254780858|r  115 AIGAHCAFIYVRG-EFIRERESLQAAVDECYASGLLGSNSKLGYDVDIIVHHGAGAY--ICGEETALLESLEGKKGQPRL  191 (425)
Q Consensus       115 a~gA~~~~I~ir~-ey~~~~~~l~~ai~ea~~~g~lg~~~~~g~~~~i~v~~g~g~Y--i~GeEtali~sieG~r~~Pr~  191 (425)
                      +||-+.||+++=- .-.+-.-++++||..|.            +++ |.|++|=|.-  -||++..+=-..+||-|=.+.
T Consensus        84 vVGn~dGYVGlG~gkA~eV~~AIrKAI~~AK------------lnI-i~VrRGCGsWec~cG~pHsvPfkV~Gk~GSV~V  150 (220)
T TIGR01020        84 VVGNRDGYVGLGKGKAKEVAPAIRKAINNAK------------LNI-IPVRRGCGSWECGCGRPHSVPFKVSGKSGSVRV  150 (220)
T ss_pred             EEECCCCCEEECCCCCCHHHHHHHHHHHHCC------------CCE-EEEECCCCCCCCCCCCCCCCCEEEEECCCEEEE
T ss_conf             9857898176234631003468999997247------------143-566405676346578885334565000004899


Q ss_pred             CC-CCCCCCCC
Q ss_conf             89-98622783
Q gi|254780858|r  192 KP-PFPANVGL  201 (425)
Q Consensus       192 kP-P~p~~~Gl  201 (425)
                      +- |=|-=.||
T Consensus       151 ~LiPAP~G~GL  161 (220)
T TIGR01020       151 RLIPAPKGVGL  161 (220)
T ss_pred             EEECCCCCCEE
T ss_conf             98749996238


No 85 
>KOG0910 consensus
Probab=27.52  E-value=40  Score=14.10  Aligned_cols=20  Identities=15%  Similarity=0.385  Sum_probs=12.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHH
Q ss_conf             99885230289999999999
Q gi|254780858|r  346 GQCTPCREGTGWMMRVMERL  365 (425)
Q Consensus       346 GkCtPCR~Gt~~l~~il~~i  365 (425)
                      -+|.|||.=.+++.++....
T Consensus        71 ~WCgPCk~l~P~l~~~~~~~   90 (150)
T KOG0910          71 EWCGPCKMLGPILEELVSEY   90 (150)
T ss_pred             CCCCCHHHHHHHHHHHHHHH
T ss_conf             75743767469999987753


No 86 
>PRK13412 fkp bifunctional fucokinase/L-fucose-1-P-guanylyltransferase; Provisional
Probab=27.30  E-value=42  Score=13.91  Aligned_cols=14  Identities=0%  Similarity=-0.109  Sum_probs=5.4

Q ss_pred             HHHCCCEEEEEECC
Q ss_conf             97183638998155
Q gi|254780858|r  114 FAIGAHCAFIYVRG  127 (425)
Q Consensus       114 ~a~gA~~~~I~ir~  127 (425)
                      +..--+.|++.+++
T Consensus       225 ~~~llD~Giw~ls~  238 (974)
T PRK13412        225 HLFLMDIGIWLLSD  238 (974)
T ss_pred             CCEEEEEEEEEECC
T ss_conf             96400005999884


No 87 
>TIGR02708 L_lactate_ox L-lactate oxidase; InterPro: IPR014080   Members of this entry oxidize L-lactate to pyruvate, reducing molecular oxygen to hydrogen peroxide. The enzyme is known in Aerococcus viridans, Streptococcus iniae, and some strains of Streptococcus pyogenes where it appears to contribute to virulence..
Probab=26.92  E-value=43  Score=13.87  Aligned_cols=135  Identities=16%  Similarity=0.220  Sum_probs=87.7

Q ss_pred             EECCCC--CCCCEEEEECCCCCHHHH-----------------------------HHHHHC------CCCCCCCCEEEEE
Q ss_conf             642678--878726893589879999-----------------------------998615------5678711004898
Q gi|254780858|r  242 FSISGH--VNYPCTVEESMSITFDEL-----------------------------IEKHCG------GIRGGWDNLLAVI  284 (425)
Q Consensus       242 ~tvsG~--V~~Pg~~evp~Gt~l~el-----------------------------i~~~~G------G~~~~~~~~kav~  284 (425)
                      -||+|+  +.+-.-+--|+|+|+=+-                             |-.|.|      |+.-.. .....+
T Consensus       169 aTV~GNR~~D~~N~FVfP~GMPIV~~YL~G~~~G~s~~~vY~~aKQ~lsprDiE~IA~ySGLPVyVKG~Q~~E-D~~~al  247 (368)
T TIGR02708       169 ATVGGNREVDKRNGFVFPVGMPIVQEYLPGEGAGKSLDYVYKSAKQKLSPRDIEEIAAYSGLPVYVKGPQCPE-DADRAL  247 (368)
T ss_pred             CCCCCCCCCCCCCCEEECCCCCHHHHCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCCEEEECCCCHH-HHHHHH
T ss_conf             6335774413558736115560333107887677406666655411578100899972179836860788866-899999


Q ss_pred             ECCCCCCCC---CCCCCCCCCCCCCCHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             524565653---21002456334220110387346651799428652899999999999876279988523028999999
Q gi|254780858|r  285 PGGSSVPCL---PAGQMRGAIMDYDGLKEMGSGLGTAAVIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRV  361 (425)
Q Consensus       285 ~GG~~~g~l---~~~~ld~~~ld~~~l~~~Gs~LGsg~iiV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~i  361 (425)
                      --|.||=|+   ..++|+..|-.||+|.+.--.+----=||||-                            |.+|...+
T Consensus       248 ~AGASGIWV~NHG~RQl~~~PaaFD~L~~vAE~V~~rVPIVFDS----------------------------GvRRG~Hv  299 (368)
T TIGR02708       248 KAGASGIWVTNHGGRQLDGGPAAFDSLQEVAEAVDKRVPIVFDS----------------------------GVRRGQHV  299 (368)
T ss_pred             HCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEC----------------------------CCCCHHHH
T ss_conf             72886257604775023678752000699999852855668508----------------------------84325789


Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHH
Q ss_conf             9999828999899999999998622366677650247999999863889999998
Q gi|254780858|r  362 MERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAWPIQGLIKNFRPLIEERI  416 (425)
Q Consensus       362 l~~i~~G~a~~~Dl~~L~~la~~i~~~S~C~lG~~a~~pv~s~l~~F~dEfe~hI  416 (425)
                      ++.|.+|-    ||   .    .+..-.+-||.-+...=+.+.+++|.+|++.=+
T Consensus       300 ~KALASGA----D~---V----AlGRPv~yGLAlGG~~G~~~V~~~l~~~L~~VM  343 (368)
T TIGR02708       300 FKALASGA----DL---V----ALGRPVIYGLALGGSVGARQVLEYLNKELKRVM  343 (368)
T ss_pred             HHHHHCCC----CE---E----ECCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99872356----44---3----013235666550102218999999998877776


No 88 
>pfam04363 DUF496 Protein of unknown function (DUF496).
Probab=26.84  E-value=43  Score=13.86  Aligned_cols=41  Identities=27%  Similarity=0.431  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCHHHHHHHHHHH
Q ss_conf             899999999998622366677650247999999863889999998651
Q gi|254780858|r  372 KREIDLLYEVSKNIEGRTICALGDAAAWPIQGLIKNFRPLIEERIDQY  419 (425)
Q Consensus       372 ~~Dl~~L~~la~~i~~~S~C~lG~~a~~pv~s~l~~F~dEfe~hI~~~  419 (425)
                      ..-+.+|..+.++++..       ++..-+...+.+.+++||.+|+++
T Consensus        32 qKRV~LL~NL~~YI~~~-------Ms~e~i~~II~nMr~DYEdRVDDy   72 (95)
T pfam04363        32 QKRVLLLDNLLDYIKPD-------MSIEEIRAIIENMRDDYEDRVDDY   72 (95)
T ss_pred             HHHHHHHHHHHHHCCCC-------CCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999998899986799-------989999999998786788746788


No 89 
>pfam06251 DUF1017 SLBB-domain like (DUF1017). This family of uncharacterized bacterial proteins contains a central beta-grasp like domain related to the SLBB domain.
Probab=26.82  E-value=43  Score=13.85  Aligned_cols=91  Identities=14%  Similarity=0.230  Sum_probs=48.8

Q ss_pred             EEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCC-CCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCC
Q ss_conf             4764267887872689358987999999861556787-110048985245656532100245633422011038734665
Q gi|254780858|r  240 KLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGG-WDNLLAVIPGGSSVPCLPAGQMRGAIMDYDGLKEMGSGLGTA  318 (425)
Q Consensus       240 kl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~-~~~~kav~~GG~~~g~l~~~~ld~~~ld~~~l~~~Gs~LGsg  318 (425)
                      .-++|.|.|.+|+.+...-|.++.+-|+. +|...+. ...+--+++-|-..-. +..-+..        ..  ..+--|
T Consensus        73 ~~V~V~G~V~~~~~~~~~~~~~v~dYl~~-~g~~~~Ad~s~~~VIqPdG~v~~~-~va~Wn~--------~~--~~~~PG  140 (173)
T pfam06251        73 TTVTLLGAVSQPGNVPWQPGASVKDYLKS-AGLLSGADKSYVWVIQPDGRAQKH-PVAYWNR--------QH--QEIAPG  140 (173)
T ss_pred             CEEEEEECCCCCCEEECCCCCCHHHHHHH-CCCCCCCCCCEEEEEECCCEEEEC-CCEECCC--------CC--CCCCCC
T ss_conf             88999965689740331699999999983-797566885407999179708885-5020036--------87--778999


Q ss_pred             EEEEE--CCC---CCHHHHHHHHHHHHHH
Q ss_conf             17994--286---5289999999999987
Q gi|254780858|r  319 AVIVM--DRS---TDIIKAIWRLSVFYKH  342 (425)
Q Consensus       319 ~iiV~--de~---~~iv~~~~~~~~F~a~  342 (425)
                      ++|++  +++   .+..++...+++..++
T Consensus       141 s~I~Vpf~~~~l~~~~~~Ln~~I~~lL~~  169 (173)
T pfam06251       141 ATIYVGFSDSSLPDDYSNLNEDIVELLRN  169 (173)
T ss_pred             CEEEEECCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             89998467333682387899999999985


No 90 
>TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245   This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm.
Probab=26.76  E-value=17  Score=16.50  Aligned_cols=62  Identities=19%  Similarity=0.336  Sum_probs=41.6

Q ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHCC--------CCCCCCCCCHHHHHHHHCCCCC
Q ss_conf             62034367551787677989999779989999998269899999999839--------7768757112455687423565
Q gi|254780858|r    2 LTDQDRIFTNLYGLQGKSLSDSMSRGHWDNVDKILEKGRDWIINEVKASG--------LRGRGGAGFSTGMKWSFMPKVC   73 (425)
Q Consensus         2 ~~~~~r~~~~~~~~~~~~l~~y~~~ggy~~l~~~l~~~~~~ii~~v~~sg--------l~GrGGAgFPt~~Kw~~~~~~~   73 (425)
                      |.|+.-||......+..-|..|..-=..--+|      .+-|++.+++.|        ++||||          ++...+
T Consensus        17 f~de~~~~~~tlrH~~eEL~~f~~v~dQfeFR------~~~i~~~L~e~Gi~~~~l~AvVgRGG----------LLkPi~   80 (353)
T TIGR02707        17 FEDEKPLFEETLRHSVEELAKFKNVIDQFEFR------KQVILEVLEEKGINISKLDAVVGRGG----------LLKPIE   80 (353)
T ss_pred             EECCEEEEEECCCCCHHHHHCCCCEEECHHHH------HHHHHHHHHHCCCCHHHEEEEEECCC----------CCCCCC
T ss_conf             65780678644625878730566402112689------99999998740887124315797277----------023338


Q ss_pred             CCCCEEEE
Q ss_conf             68861999
Q gi|254780858|r   74 SDRPHYLV   81 (425)
Q Consensus        74 ~~~~~yvv   81 (425)
                      ++.  |+|
T Consensus        81 GGT--Y~V   86 (353)
T TIGR02707        81 GGT--YLV   86 (353)
T ss_pred             CCE--EEE
T ss_conf             960--477


No 91 
>pfam09606 Med15 ARC105 or Med15 subunit of Mediator complex non-fungal. The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.
Probab=26.68  E-value=43  Score=13.84  Aligned_cols=13  Identities=15%  Similarity=0.153  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHCCC
Q ss_conf             9999999862236
Q gi|254780858|r  376 DLLYEVSKNIEGR  388 (425)
Q Consensus       376 ~~L~~la~~i~~~  388 (425)
                      ++|..|...++..
T Consensus       737 ~lLntWe~svrQa  749 (768)
T pfam09606       737 HLLNTWEMSVRQA  749 (768)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999987


No 92 
>PRK03958 tRNA 2'-O-methylase; Reviewed
Probab=26.51  E-value=44  Score=13.82  Aligned_cols=33  Identities=21%  Similarity=0.217  Sum_probs=24.1

Q ss_pred             HHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHH
Q ss_conf             99999997183638998155517899999999999
Q gi|254780858|r  108 GCVIASFAIGAHCAFIYVRGEFIRERESLQAAVDE  142 (425)
Q Consensus       108 G~~i~a~a~gA~~~~I~ir~ey~~~~~~l~~ai~e  142 (425)
                      -..+.|+|+||++.++.  ++-+...+.++.-.+.
T Consensus        21 Hv~LtaRAfGA~~i~l~--~~D~~~~etv~~V~~r   53 (175)
T PRK03958         21 HVGLTARALGADKILFA--SEDEHVKESVEDIVER   53 (175)
T ss_pred             HHHHHHHHHCCCEEEEC--CCCHHHHHHHHHHHHH
T ss_conf             88898887268767876--8876689999999986


No 93 
>TIGR02264 gmx_para_CXXCG Myxococcus xanthus double-CXXCG motif paralogous family; InterPro: IPR011750   This entry consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment..
Probab=26.30  E-value=41  Score=14.00  Aligned_cols=16  Identities=38%  Similarity=0.767  Sum_probs=5.7

Q ss_pred             HHHHHHHCCCCCCCCC
Q ss_conf             9999998397768757
Q gi|254780858|r   43 IINEVKASGLRGRGGA   58 (425)
Q Consensus        43 ii~~v~~sgl~GrGGA   58 (425)
                      -+|.++++|+||+-||
T Consensus       129 ALE~L~~~GvRGL~Ga  144 (247)
T TIGR02264       129 ALERLRAAGVRGLQGA  144 (247)
T ss_pred             HHHHHHHHHCCCCCCC
T ss_conf             9999987413444567


No 94 
>TIGR02723 phenyl_P_alpha phenylphosphate carboxylase, alpha subunit; InterPro: IPR014095   Members of this protein family are the alpha subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This alpha subunit is homologous to the beta subunit and, more broadly, to UbiD family decarboxylases..
Probab=26.27  E-value=44  Score=13.79  Aligned_cols=38  Identities=39%  Similarity=0.644  Sum_probs=29.1

Q ss_pred             HCCCCCCC--CEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             03873466--51799428652899999999999876279988523
Q gi|254780858|r  310 EMGSGLGT--AAVIVMDRSTDIIKAIWRLSVFYKHESCGQCTPCR  352 (425)
Q Consensus       310 ~~Gs~LGs--g~iiV~de~~~iv~~~~~~~~F~a~ESCGkCtPCR  352 (425)
                      +.||.||-  .-++|.||.+++..+-.-+-.|     |-+|-|=|
T Consensus       369 afGsklGPWfhmvmvvddqtdifnWdevyhaf-----CtrCnPer  408 (485)
T TIGR02723       369 AFGSKLGPWFHMVMVVDDQTDIFNWDEVYHAF-----CTRCNPER  408 (485)
T ss_pred             HHCCCCCCEEEEEEEEECCCCCCCHHHHHHHH-----HCCCCCCC
T ss_conf             63143576178999980764301134455454-----22457545


No 95 
>PHA01735 hypothetical protein
Probab=26.17  E-value=44  Score=13.78  Aligned_cols=50  Identities=14%  Similarity=0.179  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCHH
Q ss_conf             999999999828999899999999998622366677650247999999863889
Q gi|254780858|r  357 WMMRVMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAWPIQGLIKNFRP  410 (425)
Q Consensus       357 ~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~~S~C~lG~~a~~pv~s~l~~F~d  410 (425)
                      ...+++.||.+|+++..||....++..   ...|-+... -.+|+..+...-|+
T Consensus        17 lt~ell~rIksGeAttaDL~aA~~~LK---dN~I~gva~-egsPL~~La~~lP~   66 (76)
T PHA01735         17 LTNELLSRIKSGEATTADLRAACDWLK---SNDITGVAV-DGSPLAKLAGLMPQ   66 (76)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHH---HCCCCEEEC-CCCHHHHHHHHCCC
T ss_conf             999999986078887999999999999---879662367-99869999875899


No 96 
>smart00190 IL4_13 Interleukins 4 and 13. Interleukins-4 and -13 are cytokines involved in inflammatory and immune responses. IL-4 stimulates B and T cells.
Probab=25.11  E-value=46  Score=13.65  Aligned_cols=66  Identities=21%  Similarity=0.470  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCHH
Q ss_conf             99999999998762799885230289999999999828999899999999998622366677650247999999863889
Q gi|254780858|r  331 KAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAWPIQGLIKNFRP  410 (425)
Q Consensus       331 ~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~~S~C~lG~~a~~pv~s~l~~F~d  410 (425)
                      .++..+.+||.+ +|       .+..+..+.|+|...+                |....-|..-.    .-.+.++.|=+
T Consensus        72 rA~~vLr~~y~~-~~-------s~i~r~lr~L~r~l~~----------------~a~~~~c~v~e----~~~TtlkdFLe  123 (138)
T smart00190       72 RALKVLRNFYFH-NC-------SAILKTLRKLDRNCSG----------------LASQTSCTVNE----AKDTTLADFLE  123 (138)
T ss_pred             HHHHHHHHHHHH-HH-------HHHHHHHHHHHHCCCC----------------CCCCCCCCCCC----CCHHHHHHHHH
T ss_conf             999999999883-10-------7999999999720322----------------46789878542----10558999999


Q ss_pred             HHHHHHHH-HCCCCC
Q ss_conf             99999865-189999
Q gi|254780858|r  411 LIEERIDQ-YHRCNF  424 (425)
Q Consensus       411 Efe~hI~~-~~rCp~  424 (425)
                      ....++++ |.+|+|
T Consensus       124 ~Lk~imq~ky~k~~~  138 (138)
T smart00190      124 RLKSIMREKYSKGSF  138 (138)
T ss_pred             HHHHHHHHHHHCCCC
T ss_conf             999999998614689


No 97 
>pfam06733 DEAD_2 DEAD_2. This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast.
Probab=25.00  E-value=45  Score=13.71  Aligned_cols=24  Identities=13%  Similarity=0.249  Sum_probs=20.4

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             651799428652899999999999
Q gi|254780858|r  317 TAAVIVMDRSTDIIKAIWRLSVFY  340 (425)
Q Consensus       317 sg~iiV~de~~~iv~~~~~~~~F~  340 (425)
                      .+.|+||||..++.+++...+.|.
T Consensus       139 ~~~IvI~DEAHNl~~~~~~~~S~~  162 (168)
T pfam06733       139 KNSIVIFDEAHNIEDVCISSLSFE  162 (168)
T ss_pred             CCEEEEEECCCCHHHHHHHHCCCE
T ss_conf             884999988137599999961876


No 98 
>TIGR01929 menB naphthoate synthase; InterPro: IPR010198   This entry represents an enzyme, naphthoate synthase , MenB or dihydroxynaphthoic acid synthetase), which is involved in the fifth step of the menaquinone biosynthesis pathway. Menaquinone (vitamin K2), is an essential quinone used in electron-transfer pathways serving as the major electron carrier during anaerobic growth. In the bacterium, the biosynthetic pathway in bacteria typically comprises 6-7 steps . Together with o-succinylbenzoate-CoA ligase (menE IPR010192 from INTERPRO),MenB takes 2-succinylbenzoate and converts it into 1,4-di-hydroxy-2-naphthoic acid (DHNA) , , , . The conversion of o-succinylbenzoate-CoA ligase to DHNA is mediated by the enzyme DHNA synthase, which is encoded by menB .   The protein structure of naphthoate synthase has been expressed in Escherichia coli, purified and crystallized, and found to have fold characteristics of the crotonase family of enzymes, which is notable for the presence of several highly flexible regions around the active site. The C-terminal region of the protein may play a critical role both in completion of the binding pocket and in stabilisation of the hexamer, suggesting a link between oligomerization and catalytic activity .   Included in this entry are two enzymes from Arabidopsis thaliana and one from Staphylococcus aureus, which are identified as putative enoyl-CoA hydratase/isomerases. These enzymes group with the naphthoate synthases when building a tree and when doing BLAST searches.; GO: 0008935 naphthoate synthase activity, 0009234 menaquinone biosynthetic process.
Probab=24.71  E-value=28  Score=15.13  Aligned_cols=23  Identities=17%  Similarity=0.296  Sum_probs=10.5

Q ss_pred             CEEEEECCCC--CCCCEE-EEECCCC
Q ss_conf             3047642678--878726-8935898
Q gi|254780858|r  238 GTKLFSISGH--VNYPCT-VEESMSI  260 (425)
Q Consensus       238 Gtkl~tvsG~--V~~Pg~-~evp~Gt  260 (425)
                      |.|=||+.||  |+--.= |.=.-|.
T Consensus        64 G~~AFCsGGDQ~irg~~GgY~d~~G~   89 (278)
T TIGR01929        64 GDKAFCSGGDQKIRGKSGGYIDESGV   89 (278)
T ss_pred             CCEEEEECCCEEEECCCCCEECCCCC
T ss_conf             87126536852375587753557872


No 99 
>PRK02287 hypothetical protein; Provisional
Probab=24.24  E-value=48  Score=13.54  Aligned_cols=38  Identities=34%  Similarity=0.400  Sum_probs=27.3

Q ss_pred             CCCCCCCCCC-CCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             9986888998-6227830378500028999999999960
Q gi|254780858|r  186 KGQPRLKPPF-PANVGLYGCPTTVNNVESIAVVPTILRR  223 (425)
Q Consensus       186 r~~Pr~kPP~-p~~~Gl~g~PT~V~NVeTla~v~~i~~~  223 (425)
                      ++..|.=|++ ++.-==||||.-.+-||-+|+--.|+-.
T Consensus        83 ~~~~R~LP~LvAaNPVNYGkP~kLs~vEAlAAaLyI~G~  121 (169)
T PRK02287         83 AGNHRRLPFLLAANPVNYGKPCKLSSVEAFAAALYILGY  121 (169)
T ss_pred             CCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCC
T ss_conf             687666650312488666887621279999999999499


No 100
>pfam09795 Atg31 Autophagy-related protein 31. Autophagy is an intracellular degradation system that responds to nutrient starvation. Cis1/Atg31 has been shown to be required for autophagosome formation in Saccharomyces cerevisiae. It interacts with Atg17.
Probab=24.18  E-value=45  Score=13.74  Aligned_cols=37  Identities=27%  Similarity=0.407  Sum_probs=22.9

Q ss_pred             CCCCCCCCHHHHHHHHCCCC-----------CCCCCEEEEEECCCCCC
Q ss_conf             76875711245568742356-----------56886199985767784
Q gi|254780858|r   53 RGRGGAGFSTGMKWSFMPKV-----------CSDRPHYLVVNADESEP   89 (425)
Q Consensus        53 ~GrGGAgFPt~~Kw~~~~~~-----------~~~~~~yvv~N~~E~EP   89 (425)
                      -|-++|=|||-+|+=|-...           ..+-.-++|++.+|+--
T Consensus        31 ~g~~~~MFpTnIKYIFEDDdd~~~d~~~~~~~~~ieNVIIV~lDesg~   78 (159)
T pfam09795        31 TGSENTMFPTNIKYIFEDDDDSQHDSDDLEINTDIENVIIVDLDESGS   78 (159)
T ss_pred             CCCCCEECCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEECCCCCC
T ss_conf             787651310130589617874456632013357854489997168874


No 101
>KOG1547 consensus
Probab=23.61  E-value=49  Score=13.46  Aligned_cols=13  Identities=38%  Similarity=0.669  Sum_probs=7.5

Q ss_pred             CCCCCCEEEEEEC
Q ss_conf             7886640699745
Q gi|254780858|r  154 KLGYDVDIIVHHG  166 (425)
Q Consensus       154 ~~g~~~~i~v~~g  166 (425)
                      +.||+|+|-|+-.
T Consensus        42 k~GF~FNIMVVgq   54 (336)
T KOG1547          42 KTGFDFNIMVVGQ   54 (336)
T ss_pred             HCCCCEEEEEEEC
T ss_conf             6267257999806


No 102
>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=23.60  E-value=49  Score=13.46  Aligned_cols=54  Identities=17%  Similarity=0.298  Sum_probs=38.6

Q ss_pred             HHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCC-CCCEEEEEECCCCC-CCCCCCH
Q ss_conf             9999826989999999983977687571124556874235656-88619998576778-4860048
Q gi|254780858|r   32 VDKILEKGRDWIINEVKASGLRGRGGAGFSTGMKWSFMPKVCS-DRPHYLVVNADESE-PGTCKDR   95 (425)
Q Consensus        32 l~~~l~~~~~~ii~~v~~sgl~GrGGAgFPt~~Kw~~~~~~~~-~~~~yvv~N~~E~E-Pgt~kDr   95 (425)
                      ++|.++|+-|.|+-.+-.          +-..+||-+..+... ...+.=+.||++== |....++
T Consensus       361 ~~r~~~m~~~~i~t~~~~----------~~l~vkyiFf~~~~tyPe~t~sl~~G~~vv~P~~~~~~  416 (988)
T TIGR00920       361 LSRLLTMDLDYIVTLILA----------IVLAVKYIFFSQRETYPESTVSLKNGDPVVNPVSDQKK  416 (988)
T ss_pred             HHHCCCCCHHHHHHHHHH----------HHHHHHHHCCCCCCCCCCCCEEEECCCEEECCCCCHHH
T ss_conf             961378558899999999----------98876431005634377441354048510278986124


No 103
>KOG1769 consensus
Probab=23.14  E-value=50  Score=13.40  Aligned_cols=58  Identities=9%  Similarity=0.130  Sum_probs=43.9

Q ss_pred             EECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCC
Q ss_conf             6426788787268935898799999986155678711004898524565653210024
Q gi|254780858|r  242 FSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGGSSVPCLPAGQMR  299 (425)
Q Consensus       242 ~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG~~~g~l~~~~ld  299 (425)
                      +-|.|+=..--+|.|...|||+.|.+.||--.--.++.|+.++-|-+...-=++++|+
T Consensus        23 LKV~gqd~~~~~Fkikr~t~LkKLM~aYc~r~Gl~~~s~RFlfdG~rI~~~~TP~~L~   80 (99)
T KOG1769          23 LKVKGQDGSVVVFKIKRHTPLKKLMKAYCERQGLSMNSLRFLFDGQRIRETHTPADLE   80 (99)
T ss_pred             EEEECCCCCEEEEEEECCCHHHHHHHHHHHHCCCCCCEEEEEECCEECCCCCCHHHHC
T ss_conf             8983478978999962388599999999997199642489998880867888934518


No 104
>pfam04722 Ssu72 Ssu72-like protein. The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs.
Probab=23.07  E-value=50  Score=13.39  Aligned_cols=37  Identities=16%  Similarity=0.369  Sum_probs=26.8

Q ss_pred             HHHHCCCCCCCCEEEEECCCC-CCCCEEEEECCCCCHHHHHHHHH
Q ss_conf             886338987743047642678-87872689358987999999861
Q gi|254780858|r  227 WYSGFGRENNRGTKLFSISGH-VNYPCTVEESMSITFDELIEKHC  270 (425)
Q Consensus       227 ~y~~~G~~~~~Gtkl~tvsG~-V~~Pg~~evp~Gt~l~eli~~~~  270 (425)
                      .-+++|+..     .+-+-|. ..+|.+|+  +|||..++-+++-
T Consensus        29 ~V~SfGTGs-----~VkLPGps~d~PnvY~--FgT~Y~~iy~dL~   66 (193)
T pfam04722        29 NVRSFGTGS-----AVKLPGPSIDKPNVYD--FGTPYDEIYNDLE   66 (193)
T ss_pred             CEEECCCCC-----CCCCCCCCCCCCCCCC--CCCCHHHHHHHHH
T ss_conf             657406897-----4348899899986414--8998999999999


No 105
>TIGR00276 TIGR00276 iron-sulfur cluster binding protein, putative; InterPro: IPR004453 This is a family of putative iron-sulphur cluster binding proteins. These proteins contain the 4Fe-4S ferredoxins iron-sulphur binding domain..
Probab=22.60  E-value=23  Score=15.65  Aligned_cols=51  Identities=18%  Similarity=0.201  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHH---HHHHHHHHHHHHHCCCCCCC
Q ss_conf             89998625899999999999718363899815551789---99999999999868997767
Q gi|254780858|r   95 RDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFIRE---RESLQAAVDECYASGLLGSN  152 (425)
Q Consensus        95 r~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~~~---~~~l~~ai~ea~~~g~lg~~  152 (425)
                      +..|+..=...|+-++--+...-..+.++       +.   -...++|++|..-.|+.|+|
T Consensus        83 h~~L~~~l~~~L~~~~~~~~~~~~~~~~v-------D~hWr~~~~~~a~A~~AG~Gw~GkN  136 (297)
T TIGR00276        83 HDVLTFKLSDALEEELYQAVPILASKVLV-------DLHWRGPISEKALAERAGIGWVGKN  136 (297)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCE-------ECCCCCCCCCCHHHHHCCCCEEEEC
T ss_conf             99999999999988655320443445411-------0122232012179985799615420


No 106
>PRK12928 lipoyl synthase; Provisional
Probab=22.51  E-value=13  Score=17.35  Aligned_cols=187  Identities=20%  Similarity=0.241  Sum_probs=102.6

Q ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEE--CCCCHHH-HHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             85767784860048999862589999999999971836389981--5551789-99999999999868997767678866
Q gi|254780858|r   82 VNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYV--RGEFIRE-RESLQAAVDECYASGLLGSNSKLGYD  158 (425)
Q Consensus        82 ~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~i--r~ey~~~-~~~l~~ai~ea~~~g~lg~~~~~g~~  158 (425)
                      ||-+-+-|..     +=.+.|..|-+.+    ..+|-+.++|--  ||+-++. ...+.+.|++.++..   +      +
T Consensus        77 C~V~tg~P~~-----lD~~EP~rvA~av----~~m~LkyvVITSV~RDDL~DgGA~hfa~~I~~Ir~~~---P------~  138 (290)
T PRK12928         77 CQVAKGRPMP-----LDPDEPERVAEAV----AALGLRYVVLTSVARDDLPDGGAAHFVATIAAIRARN---P------G  138 (290)
T ss_pred             CCCCCCCCCC-----CCHHHHHHHHHHH----HHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHC---C------C
T ss_conf             1553799898-----9803479999999----9838976898412367886645299999999998459---9------8


Q ss_pred             CEEEEEECCCCCCCCH-HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCC-
Q ss_conf             4069974575100110-78899863089998688899862278303785000289999999999605688863389877-
Q gi|254780858|r  159 VDIIVHHGAGAYICGE-ETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENN-  236 (425)
Q Consensus       159 ~~i~v~~g~g~Yi~Ge-Etali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~-  236 (425)
                      ..|+|-..   =-.|. |.||=.-++-+          | +  +     +-||+||+-.+...+|.++...+++..=+. 
T Consensus       139 ~~iEvLiP---DF~G~~~~al~~v~~a~----------p-d--V-----~nHNiETV~rL~~~VRp~A~Y~rSL~vL~~a  197 (290)
T PRK12928        139 TGIEVLTP---DFWGGVARALATVLAAK----------P-D--C-----FNHNLETVPRLQKAVRRGADYQRSLDLLARA  197 (290)
T ss_pred             CEEEEECH---HHCCCHHHHHHHHHHCC----------C-H--H-----HHCCCCCCHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             67997071---11368789999998468----------5-4--6-----5455012043171248855089999999999


Q ss_pred             --CCEEEEECCCCCCCCEEEEECCCCCHHHHHHHHHCCCCCCCCCEEEEEECC---CCCCCCCCCCCCCCCCCCCCHHHC
Q ss_conf             --430476426788787268935898799999986155678711004898524---565653210024563342201103
Q gi|254780858|r  237 --RGTKLFSISGHVNYPCTVEESMSITFDELIEKHCGGIRGGWDNLLAVIPGG---SSVPCLPAGQMRGAIMDYDGLKEM  311 (425)
Q Consensus       237 --~Gtkl~tvsG~V~~Pg~~evp~Gt~l~eli~~~~GG~~~~~~~~kav~~GG---~~~g~l~~~~ld~~~ld~~~l~~~  311 (425)
                        ....++|=||       +-|-+|-+-.|+++.+--=-..|   ..-+-.|-   |+-.-+|...+- .|-.|+.++..
T Consensus       198 k~~~~~i~TKSg-------iMvGLGEt~eEv~~~~~DLr~~g---vdilTiGQYL~Ps~~h~pV~ryv-~P~eF~~~~~~  266 (290)
T PRK12928        198 KELAPGIPTKSG-------LMLGLGETEDEVIETLRDLRAVD---CDRLTIGQYLRPSLAHLPVQRYW-TPEEFEALGQI  266 (290)
T ss_pred             HHHCCCCEEEEE-------EEEECCCCHHHHHHHHHHHHHCC---CCEEEECCCCCCCCCCCCCEECC-CHHHHHHHHHH
T ss_conf             973888524134-------58860588999999999999819---98998240258886668833356-98999999999


Q ss_pred             CCCCCCC
Q ss_conf             8734665
Q gi|254780858|r  312 GSGLGTA  318 (425)
Q Consensus       312 Gs~LGsg  318 (425)
                      +-.+|--
T Consensus       267 a~~~GF~  273 (290)
T PRK12928        267 ARELGFK  273 (290)
T ss_pred             HHHCCCC
T ss_conf             9976996


No 107
>COG1453 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]
Probab=22.50  E-value=52  Score=13.32  Aligned_cols=72  Identities=14%  Similarity=0.107  Sum_probs=43.7

Q ss_pred             HCCCCCCCCCH--HHHHHHHHHHHHCCCCCHHHHHHHHHHHHH------H-CCCCC----------CCCCHHHHHHHHHH
Q ss_conf             27998852302--899999999998289998999999999986------2-23666----------77650247999999
Q gi|254780858|r  344 SCGQCTPCREG--TGWMMRVMERLVKGIAQKREIDLLYEVSKN------I-EGRTI----------CALGDAAAWPIQGL  404 (425)
Q Consensus       344 SCGkCtPCR~G--t~~l~~il~~i~~G~a~~~Dl~~L~~la~~------i-~~~S~----------C~lG~~a~~pv~s~  404 (425)
                      .|..|.||-.|  .+...++++.+....-....--....+...      . ..+|-          |......+..++.+
T Consensus       297 ~C~yC~PCP~gInIP~~f~lyN~~~~~~~~~~~~~~Y~~l~~~~~~~~~~~g~as~CieCgqCl~~CPq~l~Ip~~Lk~v  376 (391)
T COG1453         297 GCRYCLPCPSGINIPEIFRLYNLAVAFDDVDYAKFRYNMLENGGHWFPGPKGKASDCIECGQCLEKCPQHLDIPELLKEV  376 (391)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCHHHHHHHH
T ss_conf             25414769888776889999888886245023588999984567567887442245634331533499758678999999


Q ss_pred             HHHCHHHHHHH
Q ss_conf             86388999999
Q gi|254780858|r  405 IKNFRPLIEER  415 (425)
Q Consensus       405 l~~F~dEfe~h  415 (425)
                      -+.|..+--++
T Consensus       377 ~~~leg~~~~~  387 (391)
T COG1453         377 HEELEGEDLER  387 (391)
T ss_pred             HHHHCCHHHHH
T ss_conf             99961057888


No 108
>PRK08445 hypothetical protein; Provisional
Probab=22.45  E-value=52  Score=13.31  Aligned_cols=18  Identities=11%  Similarity=-0.014  Sum_probs=10.7

Q ss_pred             CHHHHHHHHHHHCCCCCC
Q ss_conf             889999998651899999
Q gi|254780858|r  408 FRPLIEERIDQYHRCNFQ  425 (425)
Q Consensus       408 F~dEfe~hI~~~~rCp~~  425 (425)
                      -++|+.+.|++.+|-|-|
T Consensus       320 ~~~~l~~lI~~aG~~P~e  337 (348)
T PRK08445        320 NQAEMIELIKDIGEVPAK  337 (348)
T ss_pred             CHHHHHHHHHHCCCCEEE
T ss_conf             999999999985998632


No 109
>TIGR01361 DAHP_synth_Bsub phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006268   These sequences are one of at least three types of phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase). This enzyme catalyzes the first of 7 steps in the biosynthesis of chorismate, that last common precursor of all three aromatic amino acids and of PABA, ubiquinone and menaquinone. Some members of this family, including an experimentally characterised member from Bacillus subtilis, are bifunctional, with a chorismate mutase domain N-terminal to this region. The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis.; GO: 0016832 aldehyde-lyase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=22.38  E-value=39  Score=14.17  Aligned_cols=54  Identities=28%  Similarity=0.403  Sum_probs=45.6

Q ss_pred             CCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCCCCCCEEEEECCCCCHHHHHHH
Q ss_conf             00028999999999960568886338987743047642678878726893589879999998
Q gi|254780858|r  207 TVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGHVNYPCTVEESMSITFDELIEK  268 (425)
Q Consensus       207 ~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~V~~Pg~~evp~Gt~l~eli~~  268 (425)
                      -..++|.++....|++-|+---+++        .|+.--|..++|-+..=-||-|+.|.|+.
T Consensus        98 d~~d~e~~~~y~D~lQiGARNmQNF--------~LL~~vG~~~KPVLLKRG~~aTi~EwL~A  151 (262)
T TIGR01361        98 DPRDVEIVAEYADILQIGARNMQNF--------ELLKEVGKQGKPVLLKRGMGATIEEWLEA  151 (262)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCH--------HHHHHHHHCCCCEEEECCCCHHHHHHHHH
T ss_conf             6256777876511342225412256--------99999722379755307721589999999


No 110
>COG4032 Predicted thiamine-pyrophosphate-binding protein [General function prediction only]
Probab=22.25  E-value=17  Score=16.56  Aligned_cols=68  Identities=25%  Similarity=0.310  Sum_probs=41.2

Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECC
Q ss_conf             57510011078899863089998688899862278303785000289999999999605688863389877430476426
Q gi|254780858|r  166 GAGAYICGEETALLESLEGKKGQPRLKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSIS  245 (425)
Q Consensus       166 g~g~Yi~GeEtali~sieG~r~~Pr~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvs  245 (425)
                      -+|+|.+|+.+|++--                ..|+      =|.|--++.+.          .   +-+-|-+.++|--
T Consensus        58 cAGa~lAGkk~ailmQ----------------nsGl------GNsiNal~SL~----------~---ty~iPl~ml~ShR  102 (172)
T COG4032          58 CAGAYLAGKKPAILMQ----------------NSGL------GNSINALASLY----------V---TYKIPLLMLASHR  102 (172)
T ss_pred             EHHHHHCCCCCEEEEE----------------CCCC------CHHHHHHHHHH----------H---HHCCCHHHHHHCC
T ss_conf             0245542899679884----------------3673------16899999999----------8---7422355520113


Q ss_pred             CCCCCCEEEEECCCCCHHHHHHH
Q ss_conf             78878726893589879999998
Q gi|254780858|r  246 GHVNYPCTVEESMSITFDELIEK  268 (425)
Q Consensus       246 G~V~~Pg~~evp~Gt~l~eli~~  268 (425)
                      |..+.----.||||--+-++++.
T Consensus       103 G~~~E~i~AQVpmGr~~~kiLe~  125 (172)
T COG4032         103 GVLKEGIEAQVPMGRALPKILEG  125 (172)
T ss_pred             CHHHCCCCCCCCCCHHHHHHHHH
T ss_conf             41303773136421215899965


No 111
>pfam03786 UxuA D-mannonate dehydratase (UxuA). UxuA (this family) and UxuB are required for hexuronate degradation.
Probab=21.79  E-value=53  Score=13.23  Aligned_cols=95  Identities=21%  Similarity=0.390  Sum_probs=50.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCCCEEEEECCCCC-CCCEEEEECCCCCHHHHHHHH
Q ss_conf             8899862278303785000289999999999605688863389877430476426788-787268935898799999986
Q gi|254780858|r  191 LKPPFPANVGLYGCPTTVNNVESIAVVPTILRRGASWYSGFGRENNRGTKLFSISGHV-NYPCTVEESMSITFDELIEKH  269 (425)
Q Consensus       191 ~kPP~p~~~Gl~g~PT~V~NVeTla~v~~i~~~G~~~y~~~G~~~~~Gtkl~tvsG~V-~~Pg~~evp~Gt~l~eli~~~  269 (425)
                      --||+|    +||-|-+|+|.|-+..+-.++.          .+.+ |-. | -+|.. .+|       +--+-++|..+
T Consensus       207 DDPP~~----l~GlPRI~s~~ed~~~ll~~v~----------Sp~N-Git-f-C~GSlg~~~-------~nDl~~~ir~f  262 (350)
T pfam03786       207 DDPPWP----IFGLPRIVTNIEDYQRLLELVD----------SPYN-GIT-L-CTGSYGARP-------DNDLPEMIREF  262 (350)
T ss_pred             CCCCCC----CCCCCEECCCHHHHHHHHHHCC----------CCCC-CEE-E-ECCCCCCCC-------CCCHHHHHHHH
T ss_conf             999855----5787633189999999998479----------9412-678-7-114566788-------89999999998


Q ss_pred             HCCCCCCCCCEEEEEECCCCCCCCCCCCCCC--CCCCCCCHHHCCCCCCCCEEEEECCCCCHHHHHHHHHH
Q ss_conf             1556787110048985245656532100245--63342201103873466517994286528999999999
Q gi|254780858|r  270 CGGIRGGWDNLLAVIPGGSSVPCLPAGQMRG--AIMDYDGLKEMGSGLGTAAVIVMDRSTDIIKAIWRLSV  338 (425)
Q Consensus       270 ~GG~~~~~~~~kav~~GG~~~g~l~~~~ld~--~~ld~~~l~~~Gs~LGsg~iiV~de~~~iv~~~~~~~~  338 (425)
                      ++       ++-.|..          +....  .+-+|   .+.      .   ..+-++||+++++.+.+
T Consensus       263 ~~-------RI~FvH~----------RnV~~~~~~~~F---~E~------~---hl~G~~DM~~v~kal~~  304 (350)
T pfam03786       263 AD-------RIYFAHL----------RNIKREEGPKDF---YET------A---HLEGSTDMASVMKAYHE  304 (350)
T ss_pred             HC-------CCCEEEE----------ECCCCCCCCCCE---EEC------C---CCCCCCHHHHHHHHHHH
T ss_conf             43-------1024543----------011135899984---753------6---66788309999999998


No 112
>PRK13771 putative alcohol dehydrogenase; Provisional
Probab=21.51  E-value=26  Score=15.35  Aligned_cols=19  Identities=11%  Similarity=-0.034  Sum_probs=9.1

Q ss_pred             CCCHHHHHHHHHHHHHCCC
Q ss_conf             2302899999999998289
Q gi|254780858|r  351 CREGTGWMMRVMERLVKGI  369 (425)
Q Consensus       351 CR~Gt~~l~~il~~i~~G~  369 (425)
                      .+....++.+.++++.+|+
T Consensus       305 ~~~~l~~~~~A~~~l~~~~  323 (332)
T PRK13771        305 GHVSLSDIDKALEMLKDKS  323 (332)
T ss_pred             EEEEHHHHHHHHHHHHCCC
T ss_conf             7982899999999997799


No 113
>cd02949 TRX_NTR TRX domain, novel NADPH thioredoxin reductase (NTR) family; composed of fusion proteins found only in oxygenic photosynthetic organisms containing both TRX and NTR domains. The TRX domain functions as a protein disulfide reductase via the reversible oxidation of an active center dithiol present in a CXXC motif, while the NTR domain functions as a reductant to oxidized TRX. The fusion protein is  bifunctional, showing both TRX and NTR activities, but it is not an independent NTR/TRX system. In plants, the protein is found exclusively in shoots and mature leaves and is localized in the chloroplast. It is involved in plant protection against oxidative stress.
Probab=21.06  E-value=55  Score=13.13  Aligned_cols=19  Identities=26%  Similarity=0.651  Sum_probs=8.0

Q ss_pred             CCCCCCCCHHHHHHHHHHH
Q ss_conf             9988523028999999999
Q gi|254780858|r  346 GQCTPCREGTGWMMRVMER  364 (425)
Q Consensus       346 GkCtPCR~Gt~~l~~il~~  364 (425)
                      -+|.|||.=.+.+.++.++
T Consensus        23 ~wCgpCk~l~P~l~~la~e   41 (97)
T cd02949          23 PTCGPCRTLKPILNKVIDE   41 (97)
T ss_pred             CCCCCHHHHHHHHHHHHHH
T ss_conf             9985656426999999998


No 114
>TIGR00430 Q_tRNA_tgt queuine tRNA-ribosyltransferase; InterPro: IPR004803   The queuine tRNA-ribosyltransferase (tgt) 2.4.2.29 from EC catalyzes an exchange for the guanine base at position 34 of many tRNAs; this nucleotide is subsequently modified to queuosine. The archaea have a closely related enzyme (IPR004804 from INTERPRO) that catalyses a base exchange for guanine at position 15 in some tRNAs, a site that is subsequently converted to the archaeal-specific modified base archaeosine (7-formamidino-7-deazaguanosine), while Archaeoglobus fulgidus has both enzymes. ; GO: 0008479 queuine tRNA-ribosyltransferase activity, 0008616 queuosine biosynthetic process.
Probab=20.58  E-value=29  Score=15.05  Aligned_cols=67  Identities=10%  Similarity=0.062  Sum_probs=36.1

Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             52899999999999876279988523028999999999982899989999999999862236667765024799999986
Q gi|254780858|r  327 TDIIKAIWRLSVFYKHESCGQCTPCREGTGWMMRVMERLVKGIAQKREIDLLYEVSKNIEGRTICALGDAAAWPIQGLIK  406 (425)
Q Consensus       327 ~~iv~~~~~~~~F~a~ESCGkCtPCR~Gt~~l~~il~~i~~G~a~~~Dl~~L~~la~~i~~~S~C~lG~~a~~pv~s~l~  406 (425)
                      .|.==+.++|.+-|-+.           +.+..|+|--+..   +...|.-+.+|.+.++.+           ....-+.
T Consensus       346 ~C~Cy~Ck~YSRAYL~H-----------L~r~~EllG~rL~---s~HNl~f~~rL~~~iR~A-----------I~~d~f~  400 (415)
T TIGR00430       346 ECDCYTCKNYSRAYLRH-----------LIRAKELLGARLA---SLHNLHFLLRLMEKIRQA-----------ILEDRFL  400 (415)
T ss_pred             CCCCCCCCCHHHHHHHH-----------HHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH-----------HHCCCCC
T ss_conf             77763144112789878-----------8863179999997---788999999999999887-----------5368733


Q ss_pred             HCHHHHHHHHHH
Q ss_conf             388999999865
Q gi|254780858|r  407 NFRPLIEERIDQ  418 (425)
Q Consensus       407 ~F~dEfe~hI~~  418 (425)
                      .|+.||-+....
T Consensus       401 ~F~~~f~~~~g~  412 (415)
T TIGR00430       401 SFREEFLEKYGE  412 (415)
T ss_pred             CHHHHHHHHCCC
T ss_conf             058999997257


No 115
>TIGR01842 type_I_sec_PrtD type I secretion system ATPase; InterPro: IPR010128   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0015031 protein transport, 0016021 integral to membrane.
Probab=20.54  E-value=56  Score=13.06  Aligned_cols=55  Identities=20%  Similarity=0.295  Sum_probs=33.8

Q ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCH---HHHHHHHHHHHHHH
Q ss_conf             9998576778486004899986258999999999997183638998155517---89999999999998
Q gi|254780858|r   79 YLVVNADESEPGTCKDRDIMRHEPHTLIEGCVIASFAIGAHCAFIYVRGEFI---RERESLQAAVDECY  144 (425)
Q Consensus        79 yvv~N~~E~EPgt~kDr~Ll~~~p~~vieG~~i~a~a~gA~~~~I~ir~ey~---~~~~~l~~ai~ea~  144 (425)
                      |+++.+...|           -.|=.+|-|-+|.++|++-=+..|..=..|-   .+++++++=+++..
T Consensus       249 ~Lai~ghsa~-----------it~G~mIAgSIl~GRaLaPid~aI~~Wk~~~~Ar~ay~Rl~~ll~~~p  306 (556)
T TIGR01842       249 YLAIDGHSAE-----------ITPGMMIAGSILVGRALAPIDGAIGGWKQFSAARQAYKRLNELLAEYP  306 (556)
T ss_pred             EEEECCCCCC-----------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             0323035441-----------573137888899977841077888888889999999999999998578


No 116
>cd02950 TxlA TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation  of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport.
Probab=20.52  E-value=52  Score=13.31  Aligned_cols=16  Identities=19%  Similarity=0.163  Sum_probs=8.9

Q ss_pred             CCCEEEEEECCCCCCC
Q ss_conf             8861999857677848
Q gi|254780858|r   75 DRPHYLVVNADESEPG   90 (425)
Q Consensus        75 ~~~~yvv~N~~E~EPg   90 (425)
                      ++|-.|---|+=|+|.
T Consensus        20 gKPvlVdFyA~WC~~C   35 (142)
T cd02950          20 GKPTLVEFYADWCTVC   35 (142)
T ss_pred             CCCEEEEEECCCCHHH
T ss_conf             9978999989989778


No 117
>cd03010 TlpA_like_DsbE TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c maturation (Ccm) factor with a redox active CXXC motif. Assembly of cytochrome c requires the ligation of heme to reduced thiols of the apocytochrome. In bacteria, this assembly occurs in the periplasm. The reductase activity of DsbE in the oxidizing environment of the periplasm is crucial in the maturation of cytochrome c.
Probab=20.42  E-value=29  Score=15.05  Aligned_cols=13  Identities=23%  Similarity=0.238  Sum_probs=8.2

Q ss_pred             EEEEEE--CCCCCCC
Q ss_conf             199985--7677848
Q gi|254780858|r   78 HYLVVN--ADESEPG   90 (425)
Q Consensus        78 ~yvv~N--~~E~EPg   90 (425)
                      |+||+|  |.=|.|.
T Consensus        26 k~vvl~FWAtWC~pC   40 (127)
T cd03010          26 KPYLLNVWASWCAPC   40 (127)
T ss_pred             CEEEEEEECCCCHHH
T ss_conf             989999998958668


No 118
>cd02967 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.
Probab=20.02  E-value=55  Score=13.12  Aligned_cols=11  Identities=27%  Similarity=0.341  Sum_probs=4.3

Q ss_pred             CCCCCCCCHHH
Q ss_conf             37850002899
Q gi|254780858|r  203 GCPTTVNNVES  213 (425)
Q Consensus       203 g~PT~V~NVeT  213 (425)
                      |||+++|=..|
T Consensus        21 gk~vll~Fwat   31 (114)
T cd02967          21 GRPTLLFFLSP   31 (114)
T ss_pred             CCEEEEEEECC
T ss_conf             98499999789


Done!