Query         gi|254780346|ref|YP_003064759.1| riboflavin synthase subunit beta [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 149
No_of_seqs    114 out of 1909
Neff          5.8 
Searched_HMMs 39220
Date          Sun May 29 15:13:28 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780346.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00061 ribH riboflavin synth 100.0       0       0  344.7  18.2  144    1-148     8-154 (154)
  2 PRK12419 riboflavin synthase s 100.0       0       0  340.7  17.6  141    4-148     9-155 (158)
  3 pfam00885 DMRL_synthase 6,7-di 100.0       0       0  332.0  17.6  139    5-147     3-144 (144)
  4 COG0054 RibH Riboflavin syntha 100.0       0       0  321.0  16.7  139    4-146    11-152 (152)
  5 TIGR00114 lumazine-synth 6,7-d 100.0       0       0  317.8  14.3  138    6-143     1-147 (148)
  6 KOG3243 consensus              100.0 2.4E-36 6.2E-41  245.9  13.2  136    5-144    17-156 (158)
  7 PRK06455 riboflavin synthase;   98.2 7.7E-05   2E-09   51.0  13.0  130    5-147     1-135 (155)
  8 COG1731 Archaeal riboflavin sy  97.8 0.00021 5.4E-09   48.3   8.8  129    5-143     1-131 (154)
  9 TIGR01506 ribC_arch riboflavin  97.7 0.00015 3.9E-09   49.2   6.9  116   23-145    14-131 (152)
 10 cd06284 PBP1_LacI_like_6 Ligan  96.7   0.029 7.3E-07   35.1  10.0  126    5-142   115-247 (267)
 11 cd06288 PBP1_sucrose_transcrip  96.6   0.035   9E-07   34.6   9.9  126    5-142   116-249 (269)
 12 cd06291 PBP1_Qymf_like Ligand   96.6    0.05 1.3E-06   33.6  10.3  126    5-142   112-244 (265)
 13 cd06271 PBP1_AglR_RafR_like Li  96.2   0.062 1.6E-06   33.0   9.3  125    6-142   121-252 (268)
 14 cd06270 PBP1_GalS_like Ligand   96.0    0.11 2.9E-06   31.4   9.6  122    6-142   117-248 (268)
 15 cd06294 PBP1_ycjW_transcriptio  96.0    0.16   4E-06   30.5  10.2  126    5-142   122-254 (270)
 16 cd01537 PBP1_Repressors_Sugar_  95.9    0.14 3.7E-06   30.8   9.8  126    5-142   118-249 (264)
 17 cd06296 PBP1_CatR_like Ligand-  95.8    0.11 2.8E-06   31.5   8.8  126    5-142   117-249 (270)
 18 cd06293 PBP1_LacI_like_11 Liga  95.6    0.22 5.7E-06   29.6   9.8  126    5-142   116-248 (269)
 19 PRK10703 DNA-binding transcrip  95.6    0.22 5.7E-06   29.6   9.6  123    5-142   178-310 (335)
 20 cd06275 PBP1_PurR Ligand-bindi  95.5    0.16 4.1E-06   30.5   8.8  126    5-142   117-249 (269)
 21 cd01545 PBP1_SalR Ligand-bindi  95.5    0.25 6.4E-06   29.3   9.9  123    5-142   118-250 (270)
 22 cd06267 PBP1_LacI_sugar_bindin  95.4    0.23 5.8E-06   29.5   9.3  126    5-142   116-248 (264)
 23 cd06290 PBP1_LacI_like_9 Ligan  95.3    0.15 3.8E-06   30.7   8.1  126    5-142   115-247 (265)
 24 cd06281 PBP1_LacI_like_5 Ligan  95.3    0.29 7.3E-06   28.9  10.1  123    5-142   116-247 (269)
 25 cd06286 PBP1_CcpB_like Ligand-  95.2    0.29 7.5E-06   28.9   9.7  123    5-142   114-244 (260)
 26 PRK10014 DNA-binding transcrip  95.2     0.3 7.8E-06   28.8  10.5  128    5-142   182-323 (342)
 27 cd06295 PBP1_CelR Ligand bindi  95.2    0.28 7.1E-06   29.0   9.1  126    5-142   125-257 (275)
 28 PRK10423 transcriptional repre  95.1    0.33 8.3E-06   28.6   9.4  102    6-119   175-277 (327)
 29 cd06285 PBP1_LacI_like_7 Ligan  94.9    0.23 5.8E-06   29.6   8.1  123    5-142   114-246 (265)
 30 PRK11041 DNA-binding transcrip  94.4     0.5 1.3E-05   27.4  10.4  121    6-141   185-315 (341)
 31 cd06325 PBP1_ABC_uncharacteriz  94.3    0.34 8.6E-06   28.5   7.8  116    5-142   131-250 (281)
 32 cd01575 PBP1_GntR Ligand-bindi  93.9    0.61 1.6E-05   26.9  10.4  126    5-142   116-248 (268)
 33 cd06279 PBP1_LacI_like_3 Ligan  93.8    0.64 1.6E-05   26.8  11.0  123    5-142   116-265 (283)
 34 PRK10401 DNA-binding transcrip  93.5    0.72 1.8E-05   26.4   9.0  103    6-120   177-280 (346)
 35 cd06287 PBP1_LacI_like_8 Ligan  93.4    0.74 1.9E-05   26.4  10.6  125    5-142   118-249 (269)
 36 cd01536 PBP1_ABC_sugar_binding  93.4    0.74 1.9E-05   26.4  10.7  123    6-142   122-253 (267)
 37 cd06289 PBP1_MalI_like Ligand-  93.4    0.75 1.9E-05   26.3   9.3  125    6-142   118-249 (268)
 38 COG1609 PurR Transcriptional r  93.1    0.83 2.1E-05   26.1  10.3  126    5-142   175-308 (333)
 39 PRK09526 lacI lac repressor; R  92.5       1 2.6E-05   25.5   9.2  125    5-142   181-311 (342)
 40 cd06273 PBP1_GntR_like_1 This   92.5       1 2.6E-05   25.5   9.8  125    6-142   117-249 (268)
 41 cd06272 PBP1_hexuronate_repres  92.4     1.1 2.7E-05   25.4  10.0  123    5-142   111-243 (261)
 42 cd06310 PBP1_ABC_sugar_binding  92.4     1.1 2.7E-05   25.4   8.2   35    7-41      1-35  (273)
 43 pfam00532 Peripla_BP_1 family.  92.2     1.1 2.8E-05   25.3   8.4   33    8-40    124-156 (281)
 44 cd01543 PBP1_XylR Ligand-bindi  91.9     1.2   3E-05   25.1  11.1  122    6-142   110-243 (265)
 45 cd06274 PBP1_FruR Ligand bindi  91.9     1.2   3E-05   25.1   8.8  124    5-142   116-249 (264)
 46 cd06298 PBP1_CcpA_like Ligand-  91.7     1.2 3.2E-05   25.0   9.3  122    5-142   116-248 (268)
 47 PRK10727 DNA-binding transcrip  91.7     1.2 3.2E-05   25.0   9.6  123    5-142   176-308 (342)
 48 cd06299 PBP1_LacI_like_13 Liga  91.6     1.3 3.3E-05   24.9   9.6  121    5-142   116-246 (265)
 49 cd06277 PBP1_LacI_like_1 Ligan  91.3     1.4 3.5E-05   24.7   9.7  124    5-142   118-248 (268)
 50 cd06280 PBP1_LacI_like_4 Ligan  91.2     1.4 3.6E-05   24.7  10.0  121    6-142   116-243 (263)
 51 cd06292 PBP1_LacI_like_10 Liga  91.0     1.5 3.7E-05   24.5   9.6  120    6-142   123-252 (273)
 52 cd06278 PBP1_LacI_like_2 Ligan  90.8     1.5 3.9E-05   24.4   9.8  124    5-142   115-246 (266)
 53 PRK10339 DNA-binding transcrip  90.7     1.6   4E-05   24.3   9.9  125    5-142   174-305 (327)
 54 PRK13337 putative lipid kinase  90.6     1.6   4E-05   24.3   7.1   92    4-113     1-93  (305)
 55 PRK11303 DNA-binding transcrip  90.6     1.6 4.1E-05   24.3  11.1  120    6-142   180-309 (330)
 56 PRK10936 periplasmic sensory p  89.8     1.6 4.2E-05   24.2   6.7   64    6-71     46-109 (340)
 57 pfam04392 ABC_sub_bind ABC tra  89.1     2.1 5.4E-05   23.5  10.6  116    5-142   130-249 (292)
 58 TIGR01481 ccpA catabolite cont  89.0     1.9 4.8E-05   23.9   6.5   97    5-117   177-279 (332)
 59 cd01574 PBP1_LacI Ligand-bindi  88.7     2.3 5.7E-05   23.4   9.6  122    5-142   116-245 (264)
 60 cd06308 PBP1_sensor_kinase_lik  88.4     2.3   6E-05   23.3  11.4  127    5-142   122-255 (270)
 61 COG1454 EutG Alcohol dehydroge  88.2     1.9 4.9E-05   23.8   6.1   62    5-73     29-94  (377)
 62 cd06317 PBP1_ABC_sugar_binding  87.8     2.5 6.5E-05   23.1  10.8  124    5-142   125-259 (275)
 63 cd06282 PBP1_GntR_like_2 Ligan  87.6     2.6 6.7E-05   23.0   9.8  123    5-142   116-247 (266)
 64 cd03132 GATase1_catalase Type   87.2    0.85 2.2E-05   26.0   3.8  107    6-124     2-113 (142)
 65 cd01544 PBP1_GalR Ligand-bindi  86.9     2.9 7.3E-05   22.7  10.4  124    6-142   113-250 (270)
 66 cd01542 PBP1_TreR_like Ligand-  86.8     2.9 7.4E-05   22.7  10.2  121    5-142   114-244 (259)
 67 PRK09423 gldA glycerol dehydro  86.3     3.1 7.9E-05   22.5   7.4   62    6-73     30-92  (366)
 68 cd06306 PBP1_TorT-like TorT-li  85.6     3.4 8.6E-05   22.3   7.1   87    7-108     1-87  (268)
 69 PRK09140 2-dehydro-3-deoxy-6-p  85.5     1.9 4.8E-05   23.9   4.8  106    5-122    10-124 (206)
 70 cd06321 PBP1_ABC_sugar_binding  85.2     3.5   9E-05   22.2  11.2  124    6-142   122-254 (271)
 71 cd06316 PBP1_ABC_sugar_binding  84.2     3.9 9.9E-05   21.9   9.1   63    7-72      1-63  (294)
 72 cd06297 PBP1_LacI_like_12 Liga  83.2     4.3 0.00011   21.7  10.5  111   17-142   131-249 (269)
 73 cd06283 PBP1_RegR_EndR_KdgR_li  82.4     4.6 0.00012   21.5   9.1  122    6-142   117-249 (267)
 74 cd06305 PBP1_methylthioribose_  82.2     4.7 0.00012   21.4   8.9   36    7-42      1-36  (273)
 75 PRK13805 bifunctional acetalde  80.5     5.3 0.00014   21.1   5.6   62    5-73    482-547 (862)
 76 PRK13055 putative lipid kinase  80.5     5.4 0.00014   21.1   8.9   89    4-113     1-94  (334)
 77 cd01541 PBP1_AraR Ligand-bindi  80.4     5.4 0.00014   21.0   9.9   35    7-41      1-35  (273)
 78 COG2984 ABC-type uncharacteriz  80.3     5.4 0.00014   21.0   8.4  116    6-142   160-278 (322)
 79 PRK09701 D-allose transporter   80.2     5.5 0.00014   21.0  10.4   89    5-107    24-112 (311)
 80 PRK05569 flavodoxin; Provision  79.3     5.5 0.00014   21.0   5.2  101    5-123     1-108 (141)
 81 cd01539 PBP1_GGBP Periplasmic   79.2     5.9 0.00015   20.8   9.4   33    7-39      1-33  (303)
 82 cd06314 PBP1_tmGBP Periplasmic  78.8     6.1 0.00015   20.7  11.1  123    5-142   120-251 (271)
 83 PRK05568 flavodoxin; Provision  78.3     5.6 0.00014   20.9   5.1   38    5-44      1-39  (142)
 84 cd06320 PBP1_allose_binding Pe  77.9     6.5 0.00016   20.6  11.8   63    7-71      1-63  (275)
 85 PRK08104 consensus              77.4     3.5 8.8E-05   22.2   3.8  104    6-122    16-128 (212)
 86 PRK07114 keto-hydroxyglutarate  77.3     3.1 7.9E-05   22.5   3.5   93   26-122    32-133 (223)
 87 pfam00465 Fe-ADH Iron-containi  76.9     6.9 0.00018   20.4   6.3   61    6-73     23-87  (312)
 88 PRK10310 galactitol-specific P  75.9     7.3 0.00019   20.2   6.3   84    4-122     1-88  (94)
 89 cd06302 PBP1_LsrB_Quorum_Sensi  75.5     7.5 0.00019   20.2  10.2  123    6-142   124-257 (298)
 90 PRK07580 Mg-protoporphyrin IX   73.8     4.3 0.00011   21.6   3.5   74   17-109    91-164 (230)
 91 cd06323 PBP1_ribose_binding Pe  73.1     8.6 0.00022   19.8  11.4   28    7-34    123-150 (268)
 92 PRK07053 glutamine amidotransf  72.9     8.7 0.00022   19.8   6.7  101    4-126     1-103 (235)
 93 PRK13411 molecular chaperone D  72.6     2.8 7.3E-05   22.8   2.3   89   16-113   303-400 (655)
 94 PRK06857 consensus              71.4     7.1 0.00018   20.3   4.2   88   27-122    29-125 (209)
 95 PRK09492 treR trehalose repres  70.6     9.8 0.00025   19.4   7.3   65    5-73     62-126 (315)
 96 PRK07455 keto-hydroxyglutarate  70.6     8.9 0.00023   19.7   4.5  102    7-121    15-125 (210)
 97 cd06309 PBP1_YtfQ_like Peripla  70.4     9.9 0.00025   19.4  11.7  125    5-142   124-258 (273)
 98 PRK06552 keto-hydroxyglutarate  70.2       9 0.00023   19.7   4.4   92   26-122    29-129 (209)
 99 cd06319 PBP1_ABC_sugar_binding  70.1      10 0.00026   19.4  12.1   32    7-38      1-32  (277)
100 COG0655 WrbA Multimeric flavod  70.1     8.4 0.00022   19.8   4.3   40    7-46      2-42  (207)
101 PRK13410 molecular chaperone D  69.0     5.7 0.00014   20.9   3.2   89   16-113   304-400 (719)
102 PRK08904 consensus              68.6     9.9 0.00025   19.4   4.4   88   27-122    27-123 (207)
103 PRK06015 keto-hydroxyglutarate  67.7      10 0.00026   19.4   4.3   89   26-122    31-128 (212)
104 PRK00290 dnaK molecular chaper  65.9     4.4 0.00011   21.6   2.1   89   16-113   304-400 (631)
105 cd06315 PBP1_ABC_sugar_binding  65.6      12 0.00032   18.8   6.2   84    6-106     1-85  (280)
106 PRK10714 undecaprenyl phosphat  65.5      12 0.00032   18.8   5.2   46    4-49      4-55  (324)
107 PRK09860 putative alcohol dehy  65.3      13 0.00032   18.8   6.4   62    5-73     31-96  (383)
108 pfam01081 Aldolase KDPG and KH  63.8      13 0.00034   18.6   5.0  102    8-122    11-121 (196)
109 cd01538 PBP1_ABC_xylose_bindin  63.8      13 0.00034   18.6   9.1   35    7-41      1-35  (288)
110 PRK10624 L-1,2-propanediol oxi  63.8      13 0.00034   18.6   6.3   62    5-73     29-94  (381)
111 TIGR02350 prok_dnaK chaperone   63.0     4.9 0.00012   21.3   1.9   69   16-84    301-377 (598)
112 cd01540 PBP1_arabinose_binding  62.7      14 0.00036   18.5   6.8   34    7-40      1-34  (289)
113 cd06300 PBP1_ABC_sugar_binding  60.6      15 0.00039   18.2   8.9  123    6-142   126-256 (272)
114 cd06301 PBP1_rhizopine_binding  60.1      16  0.0004   18.2  11.4  122    7-142   125-256 (272)
115 PTZ00009 heat shock 70 kDa pro  59.3     8.4 0.00022   19.8   2.6   92   17-113   309-409 (657)
116 PRK05718 keto-hydroxyglutarate  58.9      16 0.00042   18.1   6.2  102    8-122    18-128 (212)
117 PTZ00186 heat shock 70 kDa pre  56.3     2.9 7.4E-05   22.7  -0.2   87   18-113   331-425 (657)
118 pfam10087 DUF2325 Uncharacteri  56.2      18 0.00046   17.8   7.0   85   21-122     9-94  (96)
119 PRK13243 glyoxylate reductase;  54.7      17 0.00044   17.9   3.6   53    4-73      1-53  (333)
120 pfam00012 HSP70 Hsp70 protein.  54.6      13 0.00034   18.6   3.0   93   12-113   294-399 (598)
121 TIGR02021 BchM-ChlM magnesium   54.2      20  0.0005   17.6   5.2   88   17-123    82-171 (224)
122 TIGR01991 HscA Fe-S protein as  53.9      14 0.00036   18.4   3.0   59   20-78    319-385 (628)
123 pfam02514 CobN-Mg_chel CobN/Ma  53.3      20 0.00052   17.5   7.6  106    5-123    68-175 (1064)
124 COG2039 Pcp Pyrrolidone-carbox  53.1      17 0.00043   18.0   3.3   41   83-123   138-179 (207)
125 cd06322 PBP1_ABC_sugar_binding  52.5      21 0.00053   17.4  10.4  117    6-142   122-251 (267)
126 cd06318 PBP1_ABC_sugar_binding  52.3      21 0.00054   17.4   8.6   32    7-38      1-32  (282)
127 PRK10653 D-ribose transporter   51.9      21 0.00054   17.3  11.6   37    5-41     26-62  (295)
128 PRK05183 hscA chaperone protei  51.6      11 0.00027   19.2   2.1   89   17-112   310-406 (621)
129 PRK01433 hscA chaperone protei  51.4      12 0.00031   18.8   2.4   88   17-113   287-380 (595)
130 CHL00094 dnaK heat shock prote  51.2      16 0.00041   18.1   2.9   88   17-113   305-400 (622)
131 pfam00781 DAGK_cat Diacylglyce  50.7      22 0.00057   17.2   6.0   82   25-122    18-99  (127)
132 PRK13059 putative lipid kinase  48.5      24 0.00061   17.0   8.8   87    5-112     1-90  (294)
133 PRK08309 short chain dehydroge  46.7      26 0.00065   16.8   4.4   88    7-96     48-164 (182)
134 COG1597 LCB5 Sphingosine kinas  44.9      27  0.0007   16.7   7.0  100    4-123     1-101 (301)
135 PRK06490 glutamine amidotransf  44.5      28 0.00071   16.6   5.9  100    4-125    10-109 (243)
136 cd06307 PBP1_uncharacterized_s  43.9      28 0.00072   16.6   8.3   30    7-36      1-30  (275)
137 PRK00861 putative lipid kinase  42.8      30 0.00075   16.5   5.8   90    4-114     1-91  (296)
138 COG0400 Predicted esterase [Ge  40.8      32 0.00081   16.3   3.4   49    3-51    144-192 (207)
139 PRK08782 consensus              40.8      32 0.00081   16.3   6.0   87   27-121    34-129 (219)
140 PRK11914 diacylglycerol kinase  39.1      34 0.00086   16.1   7.2   90    3-112     4-94  (304)
141 KOG3857 consensus               39.1      34 0.00086   16.1   4.9   67    6-83     71-141 (465)
142 COG0800 Eda 2-keto-3-deoxy-6-p  38.8      29 0.00074   16.5   2.7   87   27-121    30-125 (211)
143 PRK00286 xseA exodeoxyribonucl  38.6      34 0.00087   16.1   9.4   89    5-110   135-233 (443)
144 COG1879 RbsB ABC-type sugar tr  38.6      34 0.00088   16.1   8.6   65    6-72     34-98  (322)
145 cd06334 PBP1_ABC_ligand_bindin  38.2      35 0.00089   16.0   7.6   65    3-74    138-204 (351)
146 TIGR01182 eda 2-dehydro-3-deox  37.1      36 0.00092   15.9   6.1   86   28-121    26-121 (205)
147 PRK02155 ppnK inorganic polyph  36.3      37 0.00095   15.8   4.5  103    1-122     1-116 (291)
148 PRK13054 lipid kinase; Reviewe  35.9      38 0.00096   15.8   9.3   92    4-114     3-94  (299)
149 PRK03767 TrpR binding protein   35.7      38 0.00097   15.8   4.8   40    5-45      1-41  (200)
150 PRK10161 transcriptional regul  33.7      41   0.001   15.6   7.8  118    4-146     1-122 (229)
151 cd01391 Periplasmic_Binding_Pr  33.6      41  0.0011   15.6   9.4   31    6-37    125-155 (269)
152 PRK09739 hypothetical protein;  33.0      42  0.0011   15.5   4.7   39    4-42      2-41  (201)
153 cd03817 GT1_UGDG_like This fam  31.9      44  0.0011   15.4   3.3   36    7-42      1-38  (374)
154 COG3364 Zn-ribbon containing p  31.1      14 0.00036   18.5   0.1   47    5-51      1-76  (112)
155 PRK10307 predicted glycosyl tr  30.2      47  0.0012   15.2   3.6   37    7-43      2-40  (415)
156 TIGR00504 pyro_pdase pyrrolido  30.0      47  0.0012   15.2   5.0   62   80-141   138-204 (220)
157 PRK00012 gatA aspartyl/glutamy  29.4      49  0.0012   15.1   5.2   44    3-46    255-301 (485)
158 cd00452 KDPG_aldolase KDPG and  28.6      50  0.0013   15.0   6.9  104    6-122     5-117 (190)
159 cd01741 GATase1_1 Subgroup of   28.0      51  0.0013   15.0   6.1   97    7-125     1-100 (188)
160 PRK00453 rpsF 30S ribosomal pr  27.7      52  0.0013   14.9   3.5   48    8-55      7-54  (95)
161 PRK02645 ppnK inorganic polyph  26.5      54  0.0014   14.8   5.2   99    4-122     2-112 (304)
162 PRK13057 putative lipid kinase  26.4      55  0.0014   14.8   8.3   73   22-115    13-85  (287)
163 pfam02601 Exonuc_VII_L Exonucl  26.1      56  0.0014   14.8   9.5   93    4-110    13-115 (295)
164 PRK07235 amidase; Provisional   25.3      57  0.0015   14.7   4.5   43    3-45    273-319 (504)
165 TIGR00707 argD acetylornithine  25.1      51  0.0013   15.0   2.0   21  125-145    97-117 (402)
166 PRK13689 hypothetical protein;  24.7      59  0.0015   14.6   3.1   29   11-39      3-31  (75)
167 PRK11574 hypothetical protein;  23.7      62  0.0016   14.5   2.5   94    4-106     1-103 (196)
168 cd06326 PBP1_STKc_like Type I   23.4      63  0.0016   14.5   7.4   63    4-73    135-199 (336)
169 cd03795 GT1_like_4 This family  23.2      63  0.0016   14.4   3.1   36    7-42      1-38  (357)
170 TIGR02040 PpsR-CrtJ transcript  22.8      25 0.00065   16.9   0.1   62   13-76     39-109 (453)
171 KOG1017 consensus               22.5      65  0.0017   14.3   3.1   34   79-114    88-124 (267)
172 pfam08967 DUF1884 Domain of un  22.4      65  0.0017   14.3   2.9   52   20-71     10-66  (85)
173 cd06311 PBP1_ABC_sugar_binding  22.0      67  0.0017   14.3  10.2  122    5-142   127-258 (274)
174 PRK11036 putative metallothion  21.8      67  0.0017   14.3   3.1   49   18-75     73-122 (256)
175 smart00851 MGS MGS-like domain  21.8      67  0.0017   14.3   3.8   68   26-106    21-89  (90)
176 cd04104 p47_IIGP_like p47 (47-  21.4      68  0.0017   14.2   5.1   77   42-129    58-134 (197)
177 pfam03358 FMN_red NADPH-depend  21.1      70  0.0018   14.2   4.4   37    7-43      2-39  (147)
178 cd06335 PBP1_ABC_ligand_bindin  21.0      70  0.0018   14.2   7.2   62    5-73    138-201 (347)
179 cd06313 PBP1_ABC_sugar_binding  20.5      71  0.0018   14.1  11.2  122    5-142   123-254 (272)
180 KOG3135 consensus               20.2      73  0.0019   14.0   4.4   43    5-48      1-43  (203)
181 TIGR02196 GlrX_YruB Glutaredox  20.1      73  0.0019   14.0   4.7   51   25-78     14-68  (79)

No 1  
>PRK00061 ribH riboflavin synthase subunit beta; Provisional
Probab=100.00  E-value=0  Score=344.69  Aligned_cols=144  Identities=33%  Similarity=0.561  Sum_probs=135.9

Q ss_pred             CCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC---EEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC
Q ss_conf             9665871799980312899999999999999987995---5555300144226999999863311378535665412000
Q gi|254780346|r    1 MEVFIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ---WSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMR   77 (149)
Q Consensus         1 m~~~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~---~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIk   77 (149)
                      ++-...||+||.|+||++|+++|++||.+.|.++|+.   +++++||||||||++++++++    +++|||+||||||||
T Consensus         8 ~~~~~~rI~IV~s~~n~~It~~L~~ga~~~L~~~g~~~~~i~~~~VPGa~EiP~a~~~l~~----~~~~DavIalG~VIk   83 (154)
T PRK00061          8 LDAKGLRIGIVVARFNDFITDALLEGAIDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAE----SGKYDAVIALGAVIR   83 (154)
T ss_pred             CCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHHH----CCCCCEEEEEEEEEE
T ss_conf             2688989999980385899999999999999985999312699987968889999999986----399887999999981


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             66524678999999999999974399705654255889999995065657456999999999999998636
Q gi|254780346|r   78 GKTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIELKKSLS  148 (149)
Q Consensus        78 GeT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~~l~  148 (149)
                      |||+|||+||++|++|||++|+++++||+||||||+|++||++|++++.+|||.|||+||++|++|+|+|.
T Consensus        84 GeT~H~d~I~~~v~~gl~~lsl~~~~PI~~GVLT~~n~~QA~~Ra~~~~~nkG~eaA~aal~Mi~l~~~l~  154 (154)
T PRK00061         84 GETPHFEYVANEVAKGLADVSLETGVPVAFGVLTTDTIEQAIERAGTKAGNKGAEAALAALEMANLLKALK  154 (154)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             89746899999999999999835798179985578998999998089877857999999999999999609


No 2  
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=100.00  E-value=0  Score=340.74  Aligned_cols=141  Identities=18%  Similarity=0.296  Sum_probs=131.7

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC---EEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             5871799980312899999999999999987995---5555300144226999999863311378535665412000665
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ---WSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~---~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      .-+||+||.|+||++|++.|++||.+.|.++|+.   +++++||||||||++++++++    +.+||++|||||||||||
T Consensus         9 ~~~riaIV~s~~n~~It~~Ll~ga~~~L~~~gv~~~~i~v~~VPGAfEiP~aa~~l~~----~~~~daiIalG~VIrGeT   84 (158)
T PRK12419          9 TPQRIAFVQARWHADIVDQAREGFVAEIAARGGAASQVDVFEVPGAFEIPLHAKTLAK----TGRYAAIVAAALVVDGGI   84 (158)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHHH----CCCCCEEEEEEEEECCCC
T ss_conf             8986999976775899999999999999985998554589982867899999999985----599988998878982897


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC---CCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             24678999999999999974399705654255889999995065---657456999999999999998636
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP---SHLDRGGCAARSALAMIELKKSLS  148 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~---~~~nkG~eaa~Aal~mi~l~~~l~  148 (149)
                      +||||||++|++|||++|+++++||+||||||+|.+||++|++.   +.+|||.|||+||++|++++|+|.
T Consensus        85 ~Hfd~V~~~v~~gl~~lsl~~~iPV~~GVLT~~n~eQA~eR~~~~~~~~~nKG~EaA~aalemi~l~~~Lr  155 (158)
T PRK12419         85 YRHEFVAQAVIDGLMQVQLETEVPVFSVVLTPHHFHESEEHQDFFRAHFVVKGAEAAHACADTLLSRERLR  155 (158)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             52478999999999999862498769998368988999998732136777668999999999999999851


No 3  
>pfam00885 DMRL_synthase 6,7-dimethyl-8-ribityllumazine synthase. This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function.
Probab=100.00  E-value=0  Score=332.00  Aligned_cols=139  Identities=34%  Similarity=0.580  Sum_probs=132.8

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC---EEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             871799980312899999999999999987995---55553001442269999998633113785356654120006652
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ---WSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~---~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      ..||+||.|+||++|+++|+++|.+.|.+.|+.   ++.++||||||||++++++++    +++|||+|+|||||||||+
T Consensus         3 ~~kI~IV~s~~n~~i~~~l~~~a~~~l~~~g~~~~~i~~~~VPGa~EiP~~~~~l~~----~~~~d~iIalG~VIkGeT~   78 (144)
T pfam00885         3 GLRIAIVVARFNADITDRLLEGALDALKRHGVSEEDIDVVRVPGAFELPLAAKKLAK----SGRYDAVVALGAVIRGGTY   78 (144)
T ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECCCHHHHHHHHHHHHH----CCCCCEEEEEEEEEECCCC
T ss_conf             988999980375999999999999999986999310589987968899999999986----4898879999999837984


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             467899999999999997439970565425588999999506565745699999999999999863
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIELKKSL  147 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~~l  147 (149)
                      |||+||++|++|||++++++++||+||||||+|++||++|++++++|||+|||+||++|++++|+|
T Consensus        79 H~e~I~~~v~~gl~~l~l~~~~PI~~gILt~~n~eQA~~R~~~~~~nkG~eaA~aal~m~~l~~~l  144 (144)
T pfam00885        79 HFDYVAQEVSRGLMQVSLETGVPVGFGVLTTDTFEQALERAGGKAGNKGAEAALAALEMANLLKKL  144 (144)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             899999999999999982679807998627899899999828988786899999999999998509


No 4  
>COG0054 RibH Riboflavin synthase beta-chain [Coenzyme metabolism]
Probab=100.00  E-value=0  Score=320.98  Aligned_cols=139  Identities=33%  Similarity=0.572  Sum_probs=132.1

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEE---EEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             587179998031289999999999999998799555---55300144226999999863311378535665412000665
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWS---SIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~---~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      .+.||+||.||||.+|+|.|++||.+.|+++|..++   +++|||+||||++++++++    +.+|||||+|||||||+|
T Consensus        11 ~~~riaIV~arfn~~I~d~ll~gA~~~l~~~G~~~~~i~vv~VPGa~EiPl~a~~La~----~~~yDAvv~lG~VIrG~T   86 (152)
T COG0054          11 KGLRIAIVVARFNDDITDALLEGAVDALKRHGADVDNIDVVRVPGAFEIPLAAKKLAR----TGKYDAVVALGAVIRGET   86 (152)
T ss_pred             CCCEEEEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHH----CCCCCEEEEEEEEEECCC
T ss_conf             7756999975432799999999999999982997445269982872326899999973----189566999646981797


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             246789999999999999743997056542558899999950656574569999999999999986
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIELKKS  146 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~~  146 (149)
                      +||||||+++++||+++|+++++||+|||||++|++||++|++.+.+|||.+||.||++|++++++
T Consensus        87 ~Hfd~Va~~~~~gl~~vsl~~~~PV~~GVLt~~~~eqA~~rag~~~gnkG~~Aa~aAlem~~l~~~  152 (152)
T COG0054          87 YHFDYVANEVARGLMDVSLETGVPVTFGVLTTDNIEQAIERAGTKAGNKGAEAAEAALEMANLLKK  152 (152)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             408999989999999988740997586623788699999872764444289999999999998619


No 5  
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex.
Probab=100.00  E-value=0  Score=317.82  Aligned_cols=138  Identities=31%  Similarity=0.511  Sum_probs=130.6

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH-CCCCCCEEEEEEEEECCCC
Q ss_conf             7179998031289999999999999998799555----5530014422699999986331-1378535665412000665
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT-RSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~-~~~~~D~vIaLG~VIkGeT   80 (149)
                      -||+||.||||.+|+|.|+++|.+.++.+|++.+    .+|||||||+|+++++++..+. ..++||+||+|||||||+|
T Consensus         1 ~rvg~v~ARFN~~It~~L~~gA~d~~~~~G~~~~~~i~~~~VPGafElP~~~~kL~~~~~klGkP~DAVi~LG~VIrG~T   80 (148)
T TIGR00114         1 VRVGIVIARFNRFITDKLLEGAIDALKRLGAEVDENIDVIRVPGAFELPLAVKKLAESGKKLGKPYDAVIALGAVIRGGT   80 (148)
T ss_pred             CEEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCEEEECCC
T ss_conf             92678771220689998999999999966895278635897068311268999998500201796335885114773796


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCC----CCHHHHHHHHHHHHHH
Q ss_conf             24678999999999999974399705654255889999995065657----4569999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHL----DRGGCAARSALAMIEL  143 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~----nkG~eaa~Aal~mi~l  143 (149)
                      +||||||+++++||+++++++++||+||||||+|+|||.+|++.+.+    |||.|||.++++|+++
T Consensus        81 ~HfeyV~~~A~~gia~~a~~~~~PV~fGilTt~~~eqA~~raG~~ag~sm~nkG~eaa~~a~e~~~~  147 (148)
T TIGR00114        81 PHFEYVADEAAKGIADLALDYDVPVIFGILTTETIEQAIERAGDKAGVSMENKGVEAAVKALEMAKL  147 (148)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHC
T ss_conf             6557777789999999998659877603328867999999601120121356679999999999850


No 6  
>KOG3243 consensus
Probab=100.00  E-value=2.4e-36  Score=245.88  Aligned_cols=136  Identities=24%  Similarity=0.420  Sum_probs=126.8

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE---EEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             8717999803128999999999999999879955---5553001442269999998633113785356654120006652
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQW---SSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~---~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      ..|++||++|||.-+++.|++||.++++++++..   ++.||||+||+|..++.+.+    +.+||++|++|++|||+|.
T Consensus        17 ~lR~~IvhARwN~vvi~~LvkGAiEtm~~~~V~eenI~ie~VPGS~Elp~g~~~~~~----r~~~daVi~IGvlIkGsTm   92 (158)
T KOG3243          17 GLRFAIVHARWNEVVIKLLVKGAIETMKKYSVREENIEIEWVPGSFELPVGAQNLGK----RGKFDAVICIGVLIKGSTM   92 (158)
T ss_pred             CEEEEEEEEHHHHHHHHHHHHHHHHHHHHHCCCHHCEEEEECCCCEECCHHHHHHHH----CCCCEEEEEEEEEEECCCH
T ss_conf             707999864467899999998899999982840226069972883564488886401----3675089887789706711


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCC-CCHHHHHHHHHHHHHHH
Q ss_conf             4678999999999999974399705654255889999995065657-45699999999999999
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHL-DRGGCAARSALAMIELK  144 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~-nkG~eaa~Aal~mi~l~  144 (149)
                      ||||||++++.|+|+++++.++|++||+|||.|+|||+.|++++.+ |+|.+++.||++|....
T Consensus        93 Hfeyis~s~~hglm~~~~~sgvPvIfGlLTc~~eeQAL~RaG~~~ghNhG~dwg~aAvEMa~kf  156 (158)
T KOG3243          93 HFEYISNSAAHGLMSASINSGVPVIFGLLTCEDEEQALNRAGGKAGHNHGADWGLAAVEMASKF  156 (158)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             0788877788777531135799779987554568999986123211246426788999999864


No 7  
>PRK06455 riboflavin synthase; Provisional
Probab=98.21  E-value=7.7e-05  Score=51.02  Aligned_cols=130  Identities=18%  Similarity=0.244  Sum_probs=92.5

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCC--CCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             8717999803128999999999999999879--95555530014422699999986331137853566541200066524
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRA--VQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~--~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      |.+|+|+-..|-.   -.|-.-|++.|++..  +.+..++|||.=.+|.++++++..    ..+|++++||-+  |.|+-
T Consensus         1 m~kiGi~DTTFaR---vdMg~~Aidel~~~~~~~~i~RyTVPGiKDlPvaakkLiee----~gCdiVmalGmp--G~~~~   71 (155)
T PRK06455          1 MKKIGIADTTFAR---VDMGSAAIDELRKLVPGAKIIRYTVPGIKDLPVAAKKLIEE----EGCDIVMALGMP--GPTEK   71 (155)
T ss_pred             CCEEEEECCCHHH---HHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHH----CCCCEEEECCCC--CCCCH
T ss_conf             9657873250222---21489999999973999638998179844467999999987----099789985776--87431


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCC---CHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             6789999999999999743997056542558---8999999506565745699999999999999863
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVD---SEQQAFDRVSPSHLDRGGCAARSALAMIELKKSL  147 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~---n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~~l  147 (149)
                      ..+-..+.+.||+.+++.+++-|+---.--+   +++...+-+    .|+-+|-|.-++.|+.--+.|
T Consensus        72 DK~~a~~aS~GLi~~Ql~T~kHIieVfVHEDEa~d~keL~~la----~~RareHa~N~v~ll~~p~~L  135 (155)
T PRK06455         72 DKYSAHEASIGLIMAQLMTNKHIIEVFVHEDEAKDEKELKELA----EDRAREHAENLVKLLFKPEAL  135 (155)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCHHHHHHHH----HHHHHHHHHHHHHHHHCHHHH
T ss_conf             4788999978999999982885899987144568989999999----999999999999998696988


No 8  
>COG1731 Archaeal riboflavin synthase [Coenzyme metabolism]
Probab=97.79  E-value=0.00021  Score=48.28  Aligned_cols=129  Identities=19%  Similarity=0.210  Sum_probs=87.7

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHC--CCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             871799980312899999999999999987--995555530014422699999986331137853566541200066524
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSR--AVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~--~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      |.+|+|+-..|-.   -.|=.-|.+.|++.  |+++..++|||.-.+|.++++++..    .-+|++++||-+  |.|.-
T Consensus         1 ~~kvGiaDTTFaR---vdMg~vai~~lk~~~~~~~i~R~TVPGIKdlpvaakrLiee----eGCd~Vi~lG~~--G~t~~   71 (154)
T COG1731           1 MTKVGIADTTFAR---VDMGSVAIDELKKLLPGIKIKRYTVPGIKDLPVAAKRLIEE----EGCDIVIALGWV--GPTEK   71 (154)
T ss_pred             CCEEEEECCCEEE---ECCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHH----CCCCEEEECCCC--CCCHH
T ss_conf             9625541350123---20147799999963899834886279844375899998876----188489983676--85014


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             6789999999999999743997056542558899999950656574569999999999999
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIEL  143 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l  143 (149)
                      ..+-..+.+-||+.+++-+++-|+---.-- ++...++-...=..|+-+|-|+-++.|+.-
T Consensus        72 Dk~~~~~aS~GLi~~QlmTn~hiidV~VHE-DEa~dekeL~~la~~RareHa~Nlv~ll~~  131 (154)
T COG1731          72 DKYSYLAASIGLIMAQLMTNKHIIDVTVHE-DEAEDEKELKELAVDRAREHAENLVKLLFK  131 (154)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEEEEEC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             579999985689999998087489999604-454798999999999999999999999868


No 9  
>TIGR01506 ribC_arch riboflavin synthase; InterPro: IPR006399   These archaeal proteins, bacterial riboflavin biosynthesis alpha chain, catalyze the final step in riboflavin biosynthesis. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain. ; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process.
Probab=97.70  E-value=0.00015  Score=49.17  Aligned_cols=116  Identities=17%  Similarity=0.261  Sum_probs=87.1

Q ss_pred             HHHHHHHHHHHC--CCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999987--995555530014422699999986331137853566541200066524678999999999999974
Q gi|254780346|r   23 LFEGCVNVLHSR--AVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSIN  100 (149)
Q Consensus        23 ll~ga~~~l~~~--~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~  100 (149)
                      |=.-|.+.|+++  ++.+...+|||.=++|.|+++++.-.    =+|.||+||-+  |.+.-+.+=....+-||..+++=
T Consensus        14 MG~~AideLr~~~~gi~i~R~TVPGIKDLP~AaKklleE~----GCe~VitLGwv--G~~ekDklsy~~aS~GLi~vqlm   87 (152)
T TIGR01506        14 MGKVAIDELRKKLAGIKIVRRTVPGIKDLPVAAKKLLEEK----GCEIVITLGWV--GREEKDKLSYLAASVGLIIVQLM   87 (152)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHCCC----CCCEEEECCCC--CCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             0067899876425896357510689504467887641216----88558866889--96024788999887888654321


Q ss_pred             CCCCCEEEEECCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             399705654255889999995065657456999999999999998
Q gi|254780346|r  101 GSLPIGNGIVVVDSEQQAFDRVSPSHLDRGGCAARSALAMIELKK  145 (149)
Q Consensus       101 ~~~PI~~gILt~~n~~QA~~R~~~~~~nkG~eaa~Aal~mi~l~~  145 (149)
                      +|+-|+-- ---|+++.+.+--..=..|+-+|=|+-++.|+.-=.
T Consensus        88 Tnk~vidV-tvHEDEaedpeeL~~~A~nRaReHa~Nl~~ll~~p~  131 (152)
T TIGR01506        88 TNKHVIDV-TVHEDEAEDPEELKVVAENRAREHARNLVALLVEPD  131 (152)
T ss_pred             CCCEEEEE-EEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             08788888-753586678678898874556689999999860783


No 10 
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=96.74  E-value=0.029  Score=35.13  Aligned_cols=126  Identities=17%  Similarity=0.144  Sum_probs=87.7

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             8717999803128999999999999999879955555-300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      ..||+++.+......+..-.+|+.+.+++++..++.. .++|.+..-.+.+.+.+-.....++||++|.          .
T Consensus       115 ~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------n  184 (267)
T cd06284         115 HRRIALITGPRDNPLARDRLEGYRQALAEAGLPADEELIQEGDFSLESGYAAARRLLALPDRPTAIFCF----------S  184 (267)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C
T ss_conf             976999628888725999999999999983998551277327876777889999999659999802657----------8


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             7899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+..  ..+|=-..|++.++.+.+.--.-      .....-|.+|++.++++++
T Consensus       185 D~~A~g~~~~l~~~g--~~vP~di~vigfd~~~~~~~~~p~lttv~~~~~~~g~~a~~~ll~~i~  247 (267)
T cd06284         185 DEMAIGAISALKELG--LRVPEDISVVGFDDIDFARMTTPPLTTIRQPRYEIGRTAAELLLDIIE  247 (267)
T ss_pred             CHHHHHHHHHHHHCC--CCCCCEEEEEEECCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             688999999999839--999962799987784899824898339985999999999999999976


No 11 
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=96.63  E-value=0.035  Score=34.55  Aligned_cols=126  Identities=15%  Similarity=0.149  Sum_probs=85.6

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             8717999803128999999999999999879955555-300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -.||+.+.+.-+...+..-..|+.+.+.++|.+++.. ..++.++.-.+.+.+.+-.....++||++|.          .
T Consensus       116 ~~~i~~i~~~~~~~~~~~R~~gf~~a~~~~~i~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~dai~~~----------~  185 (269)
T cd06288         116 HRRIAFINGEPWMLAAKDRLKGYRQALAEAGIPFDPDLVVHGDWSADDGYEAAAALLDLDDRPTAIFCG----------N  185 (269)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEECCC----------C
T ss_conf             875578748988757999999999999976998664224126776677777779998558998610147----------7


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC-------CCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950656-------57456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS-------HLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~-------~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+.  ...+|=-..|++-+|.+.+-+...++       ...-|..|++..+++++
T Consensus       186 d~~A~g~~~~l~~~--gi~vP~di~iigfD~~~~~~~~~~P~lTti~q~~~~~g~~A~~~l~~~i~  249 (269)
T cd06288         186 DRMAMGAYQALLER--GLRIPQDVSVVGFDNQEIIAEHLRPPLTTVALPHYEMGRWAVELLLDGIE  249 (269)
T ss_pred             HHHHHHHHHHHHHC--CCCCCCCEEEEEECCCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             89999999999985--99999988999988868999637899649980999999999999999975


No 12 
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription
Probab=96.57  E-value=0.05  Score=33.61  Aligned_cols=126  Identities=16%  Similarity=0.116  Sum_probs=82.5

Q ss_pred             CCEEEEEEECHHHHH-HHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             871799980312899-9999999999999879955555300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENL-SAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i-~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -.||+++.+...... ...=+.|+.+.++++|.+.+.+.+++.+......+.+.+-.....++||++|.          .
T Consensus       112 hr~I~~i~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ai~~~----------n  181 (265)
T cd06291         112 CKHIAHIGGPNNTVSPTNLRYEGFLDVLKENGLEVRIIEIQENFDDAEKKEEIKELLEEYPDIDGIFAS----------N  181 (265)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEECC----------C
T ss_conf             964999966888874899999999999997699960899768898699999999998559998843216----------6


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             7899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+++.+..+  .+|==..|++-+|.+.+.--.-      .....-|..|++.++++++
T Consensus       182 D~~A~g~~~al~~~g~--~vP~disvigfDd~~~~~~~~p~LTtv~~~~~~~g~~A~~~Ll~~i~  244 (265)
T cd06291         182 DLTAILVLKEAQQRGI--RVPEDLQIIGYDGTKLTRLYTPELTTIRQPIEEIAKTAVDLLIKQIE  244 (265)
T ss_pred             HHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             8999999999998199--99998699998880999843999559973999999999999999965


No 13 
>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the represso
Probab=96.25  E-value=0.062  Score=33.04  Aligned_cols=125  Identities=11%  Similarity=0.041  Sum_probs=80.1

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             7179998031289999999999999998799555553-001442269999998633113785356654120006652467
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      .||+++.+.-.......-+.|+.+.+.++|.+.+..+ .+|.+......+.+.+-.....++||++|.          .|
T Consensus       121 ~~I~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~p~Ai~~~----------nD  190 (268)
T cd06271         121 RRIALLNPPEDLTFAQHRRAGYRRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIVCS----------SE  190 (268)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CH
T ss_conf             74875488754607999999999999983999771136506875777999999999659998689977----------77


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             89999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      .++-.+.+.+.+..  ..+|=-..|++-+|.+.+.--.      ......-|..|++-.+++++
T Consensus       191 ~~A~g~l~~l~~~g--~~vP~DisvigfD~~~~~~~~~p~LTti~~~~~~~g~~A~~~Ll~~i~  252 (268)
T cd06271         191 LMALGVLAALAEAG--LRPGRDVSVVGFDDSPPLLFFSPPLTTVRSDLRAAGRRLAELLLARIA  252 (268)
T ss_pred             HHHHHHHHHHHHCC--CCCCCCEEEEEECCCHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             99999999999829--998999799997882899827898089980999999999999999977


No 14 
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=96.00  E-value=0.11  Score=31.42  Aligned_cols=122  Identities=16%  Similarity=0.188  Sum_probs=79.9

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHH---HHHHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             717999803128999999999999999879955555-3001442269---999998633113785356654120006652
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPA---AVSMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~---a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      .||+++.+.........-+.|+.+.+.++|...+.. .+.|.|..-.   +++.++   ....++||++|.         
T Consensus       117 ~~i~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll---~~~~~~~ai~~~---------  184 (268)
T cd06270         117 RKIACITGPLTKEDARLRLQGYRDALAEAGIALDESLIIEGDFTEEGGYAAMQELL---ARGAPFTAVFCA---------  184 (268)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHH---HCCCCCCEEEEC---------
T ss_conf             83898459888831999999999999985999780047616776788999889999---569998745533---------


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             46789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                       .|.++-.+.+.+.+..+  .+|==..|++-+|.+.+.-=.      ......-|.+|++.++++++
T Consensus       185 -nD~~A~g~~~~l~~~g~--~vP~disvigfdd~~~~~~~~P~LTti~~~~~~~g~~A~~~Ll~~i~  248 (268)
T cd06270         185 -NDEMAAGAISALREHGI--SVPQDVSIIGFDDVLLARYLYPKLTTVHYPIEEMAQMAAKLALQLVY  248 (268)
T ss_pred             -CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             -77999999999998299--99997699998986899714899549964999999999999999974


No 15 
>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=95.97  E-value=0.16  Score=30.55  Aligned_cols=126  Identities=13%  Similarity=0.070  Sum_probs=78.2

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEH-HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             871799980312899999999999999987995555530-0144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVT-PGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~V-PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -.||+++.+.-+...+..=++|+.+.+.++|...+..++ .+.|......+.+.+-.....++||++|.          .
T Consensus       122 hr~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~tai~~~----------n  191 (270)
T cd06294         122 HKKIAFVGGDLDLEVTQDRLQGYKQALEDHGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIVAT----------D  191 (270)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C
T ss_conf             956999818998658999999999999986999773333137766788999999998469998489987----------7


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+++.+..  ..+|=-..|++-++...+.--.      ......-|+.|++.++++++
T Consensus       192 D~~A~g~~~al~~~g--~~iP~disvvgfDd~~~~~~~~P~LTtv~q~~~~~G~~A~~~Ll~~i~  254 (270)
T cd06294         192 DLLALGVLKVLNELG--LKVPEDLSIIGFNNSILSELAHPPLTSVDINPRELGYEAAELLIDLIE  254 (270)
T ss_pred             HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             499999999999839--999998499998972899842898179973999999999999999966


No 16 
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain.  The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=95.92  E-value=0.14  Score=30.78  Aligned_cols=126  Identities=13%  Similarity=0.108  Sum_probs=68.3

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      ..||+++...-.......-.+|+.+.+.+++.......+++.+....+.+.+.+......++||+++.          .|
T Consensus       118 ~~~i~~i~~~~~~~~~~~R~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~dai~~~----------~d  187 (264)
T cd01537         118 HRRIALLAGPLGSSTARERVAGFKDALKEAGPIEIVLVQEGDWDAEKGYQAAEELLTAHPDPTAIFAA----------ND  187 (264)
T ss_pred             CCCEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEC----------CH
T ss_conf             86245304887770699999999999997799985379957999899999999998508997699989----------86


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                      .++..+.+.+.+..+  .+|==..|++.+|...+....-      .....-|..|++.++++++
T Consensus       188 ~~A~gv~~al~~~g~--~ip~di~ivg~d~~~~~~~~~p~ltti~~~~~~~g~~a~~~l~~~i~  249 (264)
T cd01537         188 DMALGALRALREAGL--RVPDDISVIGFDGTPEALLAGPPLTTVRQPPDELGRAAVELLLELLN  249 (264)
T ss_pred             HHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             999999999997499--99998399999974999971998299983999999999999999965


No 17 
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=95.78  E-value=0.11  Score=31.52  Aligned_cols=126  Identities=16%  Similarity=0.080  Sum_probs=82.6

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             871799980312899999999999999987995555-5300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -+||+++...-+......-+.|+.+.+.++|.+.+. ...+|.|....+.+.+.+-.....++||++|.          .
T Consensus       117 ~~~I~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~~aii~~----------~  186 (270)
T cd06296         117 HRRIGFITGPPDLLCSRARLDGYRAALAEAGIPVDPALVREGDFSTESGFRAAAELLALPERPTAIFAG----------N  186 (270)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHEEECCCHHHHHHHHHHHHHHCCCCCCCEEEC----------C
T ss_conf             972888459988655999999999999986999885553306501789999999999549988620347----------8


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+..  ..+|=-..|++-+|...+.--.      ......-|..|++.++++++
T Consensus       187 D~~A~g~~~~l~~~g--i~vP~di~iigfd~~~~~~~~~p~lttI~~~~~~~g~~a~~~ll~~i~  249 (270)
T cd06296         187 DLMALGVYEAARERG--LRIPEDLSVVGFDDLPEARWVSPPLTTVRQPLREMGRAAVRLLLRLIE  249 (270)
T ss_pred             CHHHHHHHHHHHHCC--CCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             689999999999869--999998879997887899852898389982999999999999999965


No 18 
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=95.61  E-value=0.22  Score=29.60  Aligned_cols=126  Identities=14%  Similarity=-0.002  Sum_probs=79.2

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             87179998031289999999999999998799555553-00144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -.||+++.+.-....+..-++|+++.+.+++...+..+ ..|.+..-..-+.+........++||++|.          .
T Consensus       116 ~~~I~~i~~~~~~~~~~~R~~G~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av~~~----------n  185 (269)
T cd06293         116 HRRIAFVGGPDALISARERYAGYREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPTAIFAA----------S  185 (269)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C
T ss_conf             983899548877633999999999999976999993489955631135999999998479998589968----------8


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             7899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+..  ..+|=-.+|++-+|.+.+..-.-      .....-|.+|++..+++++
T Consensus       186 D~~A~g~l~~l~~~g--i~vP~disiigfd~~~~~~~~~P~lTti~q~~~~ig~~A~~~Ll~~i~  248 (269)
T cd06293         186 DEIAIGLLEVLRERG--LSIPGDMSLVGFDDVGPAHLFAPPLTTIRQPVRELGRRAVALLLATLW  248 (269)
T ss_pred             HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             599999999999849--999996599988880999830898489965999999999999999845


No 19 
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=95.55  E-value=0.22  Score=29.61  Aligned_cols=123  Identities=12%  Similarity=0.118  Sum_probs=77.8

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             8717999803128999999999999999879955555-30014422699---9999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      -.||+++.+..+......-++|+.+.+.++|...+.- .+.|.|+....   ++.++   .....++|++|.        
T Consensus       178 hr~Ia~i~~~~~~~~~~~R~~gf~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll---~~~~~ptAi~~~--------  246 (335)
T PRK10703        178 HRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKVPEEWIVQGDFEPESGYEAMQQIL---SQEHRPTAVFCG--------  246 (335)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCHHEEEECCCCHHHHHHHHHHHH---HCCCCCCEEEEC--------
T ss_conf             986999958876521789999999999985999881328965788588999999999---569998668968--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             2467899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+++.+..  ..+|==..|++-+|...+.--.-      ......|..|++..+++++
T Consensus       247 --nD~~A~g~~~~l~~~g--~~VP~DisvigfDd~~~~~~~~P~LTtv~~~~~~~g~~A~~~Ll~~i~  310 (335)
T PRK10703        247 --GDIMAMGAICAADEMG--LRVPQDISVIGYDNVRNARYFTPALTTIHQPKDRLGETAFNMLLDRIV  310 (335)
T ss_pred             --CHHHHHHHHHHHHHCC--CCCCCCEEEEEECCCHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             --7599999999999719--999997499998882899825898279982999999999999999961


No 20 
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a 
Probab=95.52  E-value=0.16  Score=30.50  Aligned_cols=126  Identities=11%  Similarity=0.039  Sum_probs=76.8

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             87179998031289999999999999998799555553-00144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      ..||+++...........-+.|+.+.+.+++.+....+ +.|-++..-+.+.+.+-.....++||++|.          .
T Consensus       117 ~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~i~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~~aii~~----------~  186 (269)
T cd06275         117 HRRIGCITGPLEKAPAQQRLAGFRRAMAEAGLPVNPGWIVEGDFECEGGYEAMQRLLAQPKRPTAVFCG----------N  186 (269)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHCCCCCEEECC----------C
T ss_conf             971775569977716999999999999985999765550367777688999999999708996612318----------7


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++..+.+.+.+..+  .+|==..|.+.++...+.--.      ......-|..|++-++++++
T Consensus       187 d~~A~g~~~~l~~~gi--~vP~di~vvgfd~~~~~~~~~p~ltti~q~~~~~g~~a~~~L~~~i~  249 (269)
T cd06275         187 DLMAMGALCAAQEAGL--RVPQDLSIIGYDDIELARYFSPPLTTIHQPKDRLGELAVNMLLERIK  249 (269)
T ss_pred             HHHHHHHHHHHHHCCC--CCCCCCEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             4999999999998088--78998679987787999833898589961999999999999999966


No 21 
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=95.45  E-value=0.25  Score=29.27  Aligned_cols=123  Identities=16%  Similarity=0.108  Sum_probs=80.0

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHH--HHHHHHH-HHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             871799980312899999999999999987995555-53001--4422699-9999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPG--VLEIPAA-VSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPG--a~EiP~a-~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      ..||+++...-.......-++|+.+.+.++|...+. ..++|  ++|-... ++.++.   ...+++|++|.        
T Consensus       118 ~~~I~~i~g~~~~~~~~~R~~Gf~~a~~~~gi~~~~~~i~~~~~s~~~~~~~~~~ll~---~~~~~tai~~~--------  186 (270)
T cd01545         118 HRRIAFIAGPPDHRASAERLEGYRDALAEAGLPLDPELVAQGDFTFESGLEAAEALLA---LPDRPTAIFAS--------  186 (270)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCHHHHHHHHHHHH---CCCCCCEEEEC--------
T ss_conf             9659993699777369999999999999839997721220265310269999999985---59998589978--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             246789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+.+.+..+  .+|==..|++-+|...+.--+      .-....-|..|++..++.++
T Consensus       187 --nD~~A~g~~~~l~~~g~--~iP~dvsiigfD~~~~~~~~~P~LTti~q~~~~~g~~A~~~Ll~~i~  250 (270)
T cd01545         187 --NDDMAAGVLAVAHRRGL--RVPDDLSVVGFDDTPIATTIWPPLTTVRQPIAEMARAAAELLIARLR  250 (270)
T ss_pred             --CHHHHHHHHHHHHHHCC--CCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             --88999999999998189--99998699998885999835898249971999999999999999956


No 22 
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily.  In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=95.41  E-value=0.23  Score=29.54  Aligned_cols=126  Identities=17%  Similarity=0.103  Sum_probs=76.2

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             8717999803128999999999999999879955555-300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      .+||+++...-.......-.+|+.+.+++++...... ..++.+....+.+.+.+-.....++||++|.          .
T Consensus       116 ~~~i~~i~~~~~~~~~~~R~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------~  185 (264)
T cd06267         116 HRRIAFIGGPPDLSTARERLEGYREALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIFAA----------N  185 (264)
T ss_pred             CCCEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCHHEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C
T ss_conf             885689638987706999999999999986999885307527897799999999999659999899878----------8


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+..  ..+|=-.+|++.+|...+.--.      ......-|..|++.++++++
T Consensus       186 D~~A~g~~~~l~~~g--~~iP~di~Iig~d~~~~~~~~~p~lttv~~~~~~ig~~a~~~l~~~i~  248 (264)
T cd06267         186 DLMAIGALRALRELG--LRVPEDVSVVGFDDIPLAELLTPPLTTVRQPIEEMGRAAAELLLERIE  248 (264)
T ss_pred             HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             799999999999829--999997799999984898534899479990999999999999999965


No 23 
>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=95.33  E-value=0.15  Score=30.71  Aligned_cols=126  Identities=16%  Similarity=0.124  Sum_probs=76.2

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             871799980312899999999999999987995555-5300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -.||+++...-....+..-..|+.+.++++|...+. ..++|.+....+.+.+.+......++||++|.          .
T Consensus       115 ~~~i~~i~~~~~~~~~~~R~~Gf~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------n  184 (265)
T cd06290         115 HRRIAHITGPRGHIDARDRLAGYRKALEEAGLEVQPDLIVQGDFEEESGLEAVEELLQRGPDFTAIFAA----------N  184 (265)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHEECCCCCCHHHHHHHHHHHHHCCCCCCCEEC----------C
T ss_conf             986556048878701999999999999986999988883416677178999999999719998842105----------7


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+++.+..  ..+|==..|++-+|...+.-=+      .....--|..|++..+++++
T Consensus       185 D~~A~g~~~~~~~~g--~~vP~di~vigfD~~~~~~~~~p~ltti~~~~~~~G~~A~~~L~~~i~  247 (265)
T cd06290         185 DQTAYGARLALYRRG--LRVPEDVSLIGFDDLPLSAYTTPPLTTVRQPIEEMGQIAARALLALIN  247 (265)
T ss_pred             HHHHHHHHHHHHHHC--CCCCCCEEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             899999999999809--999998799999987899732898289995999999999999999975


No 24 
>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=95.28  E-value=0.29  Score=28.92  Aligned_cols=123  Identities=11%  Similarity=0.034  Sum_probs=77.4

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE--EEHHHHHHHHHH-HHHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             871799980312899999999999999987995555--530014422699-99998633113785356654120006652
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS--IVTPGVLEIPAA-VSMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~--i~VPGa~EiP~a-~~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      -+||+++....+...+..-++|+.+.+.++|...+.  +...+..+-.+. +..++   ....++||++|.         
T Consensus       116 ~~~I~~i~~~~~~~~~~~R~~G~~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~ll---~~~~~p~ai~~~---------  183 (269)
T cd06281         116 HRRIALVGGGSNTRPGRERLEGYKAAFAAAGLPPDPALVRLSTPAASGFDATRALL---ALPDRPTAIIAG---------  183 (269)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCHHHHHHHHHHHH---HCCCCCCEEEEC---------
T ss_conf             98668980788776799999999999997799999439977997489999999998---079999656512---------


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             46789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                       .|.++-.+.+.+.+.  ...+|=-..|++.+|...+.-=.      ......-|..|++..+++++
T Consensus       184 -~d~~A~g~l~~l~~~--g~~VP~disviGfD~~~~~~~~~P~LTTi~~~~~~~g~~A~~~Ll~~i~  247 (269)
T cd06281         184 -GTQVLVGVLRALREA--GLRIPRDLSVISIGDSDLAELMDPPITALRRDREAVGRTAAELMLDRLE  247 (269)
T ss_pred             -CHHHHHHHHHHHHHC--CCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             -338899999999981--9999998699998887999835899679974999999999999999966


No 25 
>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. CcpB is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.
Probab=95.24  E-value=0.29  Score=28.85  Aligned_cols=123  Identities=13%  Similarity=0.004  Sum_probs=81.2

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHH--HHHHHHHH-HHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             87179998031289999999999999998799555553-001--44226999-999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPG--VLEIPAAV-SMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPG--a~EiP~a~-~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      -.||+++.+.-+...+..-.+|+.+.+.++|...+.-+ ..+  .+|-...+ +.++   ....++||++|.        
T Consensus       114 ~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~---~~~~~p~ai~~~--------  182 (260)
T cd06286         114 YRKIAYCIGRKKSLNSQSRKKAYKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLL---KMKDRPDAIFTG--------  182 (260)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHH---HCCCCCCEEEEC--------
T ss_conf             973999938988704999999999999977999773036446520667999999998---449998736736--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH----CCCCCCCHHHHHHHHHHHHH
Q ss_conf             246789999999999999743997056542558899999950----65657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV----SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~----~~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+.+.+.  ...+|=-..|++.++..-+..-.    ......-|++|++..+++++
T Consensus       183 --nd~~A~g~~~al~~~--g~~vP~di~vigfdd~~~~~~p~lTtv~~~~~~~g~~A~~~ll~~i~  244 (260)
T cd06286         183 --SDEVAAGIITEAKKQ--GIRVPEDLAIIGFDNQPISELLGITTIDQPVKELGEKAFELLLNQLE  244 (260)
T ss_pred             --CHHHHHHHHHHHHHC--CCCCCCCEEEEEECCHHHHCCCCCCEEECCHHHHHHHHHHHHHHHHC
T ss_conf             --899999999999972--99999976999989849982899758935999999999999999976


No 26 
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=95.20  E-value=0.3  Score=28.76  Aligned_cols=128  Identities=12%  Similarity=0.024  Sum_probs=78.2

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             87179998031289999999999999998799555553-00144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -.||+.+.+.-.......-+.|..+.|.++|.+.+.-+ +.+.++-..+.+.+.+-.....+++|++|          ..
T Consensus       182 hr~Ia~i~~~~~~~~~~~R~~gf~~al~~~~l~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~tAi~c----------~~  251 (342)
T PRK10014        182 HQRIAWLGGQSSSLTRAERVGGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVVC----------YN  251 (342)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEE----------EC
T ss_conf             98699995788863399999999999997699988334896689789999999999836999718999----------67


Q ss_pred             HHHHHHHHHHHHHHHHHCC-------CCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             7899999999999997439-------97056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGS-------LPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~-------~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+..++.+..++-.       +|=-..|++.+|...+..-.      ......-|..|++..+++++
T Consensus       252 D~~A~g~~~~l~~~g~~v~~d~~~~~ip~~vsIigfdd~~~~~~~~P~LTtv~~~~~~ig~~a~~~Ll~~i~  323 (342)
T PRK10014        252 ETIAMGAWFGLLRAGRQSGESGVDRYFEQQVALAAFTDVPEAELDDPPLTWASTPAREIGRTLADRMMQRIT  323 (342)
T ss_pred             HHHHHHHHHHHHHHCHHCCCCCCCCCCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             899999999999958221755333478985899998884888625898569983999999999999999966


No 27 
>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn chang
Probab=95.18  E-value=0.28  Score=29.00  Aligned_cols=126  Identities=16%  Similarity=0.152  Sum_probs=73.0

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             8717999803128999999999999999879955555-300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -++|+++.+.-.......-+.|+.+.+.+++...+.. .+++.|..-.+.+.+.+-.....++||++|.          .
T Consensus       125 ~~~I~~i~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------n  194 (275)
T cd06295         125 RRRIAFLGGPQDMPEGEERLEGYREALAEAGLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFAA----------S  194 (275)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C
T ss_conf             987987058866726999999999999986999994179965776687999988898549998703414----------7


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+..  ..+|=-..|++.++.+.+.-=.      ......-|..|++.++++++
T Consensus       195 D~~A~g~~~~~~~~g--~~iP~disIigfd~~~~~~~~~P~LTtI~~~~~~ig~~A~~~Ll~~i~  257 (275)
T cd06295         195 DLMALGALRALREAG--RRVPEDVAVVGFDDIPLAAYADPPLTTVRQDIEEAGRLLVDLLLALIA  257 (275)
T ss_pred             CHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             587899999999749--998985699996786899834898699980999999999999999967


No 28 
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=95.09  E-value=0.33  Score=28.57  Aligned_cols=102  Identities=12%  Similarity=0.146  Sum_probs=40.6

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             71799980312899999999999999987995555-53001442269999998633113785356654120006652467
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      .||+++.+.........=++|+.+.+.++|..... ..+.|.|+.....+.+.+-.....++||++|.          .|
T Consensus       175 r~I~~i~~~~~~~~~~~R~~gf~~al~~~gl~~~~~~~~~~~~~~~~g~~~~~~ll~~~~~ptAi~~~----------nD  244 (327)
T PRK10423        175 TRIACITGPLDKTPARLRLEGYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLAHPLRPQAVFTG----------ND  244 (327)
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CC
T ss_conf             74999668876617999999999999985999884369960467378999999998479999845517----------80


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHH
Q ss_conf             89999999999999743997056542558899999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAF  119 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~  119 (149)
                      .++-.+.+++.+..  ..+|==..|++.+|...+.
T Consensus       245 ~~A~g~~~al~~~g--~~iP~DisvigfDd~~~~~  277 (327)
T PRK10423        245 AMAVGVYQALYQAG--LQVPQDIAVIGYDDIELAS  277 (327)
T ss_pred             HHHHHHHHHHHHCC--CCCCCCEEEEEECCCHHHH
T ss_conf             99999999999869--9999975999975828998


No 29 
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=94.91  E-value=0.23  Score=29.56  Aligned_cols=123  Identities=13%  Similarity=0.085  Sum_probs=77.5

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             87179998031289999999999999998799555553-0014422699---9999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      ..||+++...-+......-..|+.+.+.++|.+....+ +.+.+..-..   ++.++   ....++||++|.        
T Consensus       114 ~~~i~~l~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l---~~~~~~~ai~~~--------  182 (265)
T cd06285         114 HRRIAVLAGPDYASTARDRLAGFRAALAEAGIEVPPERIVYSGFDIEGGEAAAEKLL---RSDSPPTAIFAV--------  182 (265)
T ss_pred             CCCEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHEECCCCCHHHHHHHHHHHH---HCCCCCCCEECC--------
T ss_conf             865875478877705999999999999986999875660136621556999999998---569998810037--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             246789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+.+.+..  ..+|=-..|++-+|...+..=.      .-....-|+.|++..+++++
T Consensus       183 --nD~~A~g~~~~l~~~g--~~iP~di~iigfd~~~~~~~~~p~LTti~q~~~~ig~~A~~~ll~~i~  246 (265)
T cd06285         183 --NDFAAIGVMGAARDRG--LRVPDDVALVGYNDIPLVARLPVPLTTVRSPFHQIGRTALRLLLETIA  246 (265)
T ss_pred             --CHHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             --8899999999999859--999998799998782899707899579972999999999999999847


No 30 
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=94.36  E-value=0.5  Score=27.45  Aligned_cols=121  Identities=16%  Similarity=0.091  Sum_probs=59.1

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHH--HHHH-HHHHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             7179998031289999999999999998799555553-00144--2269-999998633113785356654120006652
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVL--EIPA-AVSMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~--EiP~-a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      .||+.+.+..+....+.-++|+.+.+.++|++.+.-+ +.|.|  |-.. +++.++   .....+||++|.         
T Consensus       185 r~I~~i~~~~~~~~~~~R~~G~~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll---~~~~~ptAi~~~---------  252 (341)
T PRK11041        185 KRIACIAGPEEMPLCHYRLQGYVQALRRCGITVDPQYIARGDFTFEAGAKAMQQLL---ELPQPPTAVFCH---------  252 (341)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHH---HCCCCCCEEEEC---------
T ss_conf             76999968987768999999999999986999991048954676799999999999---559998579876---------


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHH
Q ss_conf             46789999999999999743997056542558899999950------6565745699999999999
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMI  141 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi  141 (149)
                       .|.++-.+.+++.+..  ..+|==..|++.+|...+.--.      ......-|..|++-.++++
T Consensus       253 -nD~~A~g~l~al~~~G--l~VP~DisViGfdd~~~~~~~~P~LTTV~~~~~~~g~~A~~~L~~~i  315 (341)
T PRK11041        253 -SDVMALGALSQAKRQG--LKVPQDLSIIGFDNIDLAQFCDPPLTTIAQPRYEIGREAMLLLLDQL  315 (341)
T ss_pred             -CHHHHHHHHHHHHHHC--CCCCCCEEEEEECCHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHH
T ss_conf             -7799999999999718--98999659999888389852699836998199999999999999996


No 31 
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=94.33  E-value=0.34  Score=28.48  Aligned_cols=116  Identities=10%  Similarity=0.088  Sum_probs=77.6

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      .+||++++..=.. -....++..++...+.|+++....|+..-|++.+++.+.      .+.|++...       |+.  
T Consensus       131 ~k~igvlyn~~e~-ns~~~~~~~~~~a~~~Gi~v~~~~v~~~~ei~~a~~~l~------~~~Dal~~~-------~d~--  194 (281)
T cd06325         131 AKTVGVLYNPSEA-NSVVQVKELKKAAAKLGIEVVEATVSSSNDVQQAAQSLA------GKVDAIYVP-------TDN--  194 (281)
T ss_pred             CCEEEEEECCCCC-CHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHH------HCCCEEEEE-------CCC--
T ss_conf             8589999579986-569999999999997698899994598889999999756------258999991-------881--


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH----CCCCCCCHHHHHHHHHHHHH
Q ss_conf             89999999999999743997056542558899999950----65657456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV----SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~----~~~~~nkG~eaa~Aal~mi~  142 (149)
                      ++. +....+.+++.++.+|+..+     +..+...-+    +.+..+-|+.+|+-+.+.++
T Consensus       195 ~v~-s~~~~i~~~a~~~~iPv~~~-----~~~~v~~G~L~s~g~~~~~~G~~aa~~a~rIL~  250 (281)
T cd06325         195 TVA-SAMEAVVKVANEAKIPVIAS-----DDDMVKRGGLATYGIDYYELGRQTGKMAAKILK  250 (281)
T ss_pred             HHH-HHHHHHHHHHHHCCCCEEEC-----CHHHHHCCCEEEECCCHHHHHHHHHHHHHHHHC
T ss_conf             277-79999999998749988936-----778861672799827899999999999999978


No 32 
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, 
Probab=93.90  E-value=0.61  Score=26.87  Aligned_cols=126  Identities=17%  Similarity=0.102  Sum_probs=78.9

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEH-HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             871799980312899999999999999987995555530-0144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVT-PGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~V-PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -.||+++...-....+..-+.|+.+.+.++|......+. .+.+......+.+-+-.....++||++|.          .
T Consensus       116 ~~~i~~i~~~~~~~~~~~R~~G~~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~dai~~~----------n  185 (268)
T cd01575         116 YRRIGFLGARMDDTRAQQRLEGFRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFCS----------N  185 (268)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C
T ss_conf             976999848988736999999999999976989880899548998899999999999569998379987----------8


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+..  ..+|==..|++.+|...+.-=.      ......-|..|++.++++++
T Consensus       186 D~~A~g~~~~l~~~g--~~iP~disvigfdd~~~~~~~~p~ltti~~~~~~~g~~a~~~l~~~i~  248 (268)
T cd01575         186 DDLALGALFECQRRG--ISVPEDIAIAGFGDLEIAAALPPALTTVRTPRREIGRRAAELLLARLA  248 (268)
T ss_pred             HHHHHHHHHHHHHHC--CCCCCCEEEEEECCHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             899999999999838--999997799998973899616899679996999999999999999976


No 33 
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=93.80  E-value=0.64  Score=26.76  Aligned_cols=123  Identities=19%  Similarity=0.178  Sum_probs=76.1

Q ss_pred             CCEEEEEEE-----------------CHHHHHHHHHHHHHHHHHHHCCCCEEEEE--HHHHHHHHH---HHHHHHHHHHC
Q ss_conf             871799980-----------------31289999999999999998799555553--001442269---99999863311
Q gi|254780346|r    5 IPHVLIIEA-----------------RFYENLSAMLFEGCVNVLHSRAVQWSSIV--TPGVLEIPA---AVSMVMNAKTR   62 (149)
Q Consensus         5 ~~kI~IV~s-----------------~~~~~i~~~ll~ga~~~l~~~~~~~~~i~--VPGa~EiP~---a~~~~~~~~~~   62 (149)
                      -+||+++..                 .........=++|+.+.+.++|...+..+  -.|.+....   +++.++.   .
T Consensus       116 h~~Ia~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~~G~~~al~~~gl~~~~~~i~~~~~~~~~~g~~~~~~ll~---~  192 (283)
T cd06279         116 HRRIGILGLRLGRDRNTGRVTDERLASATFSVARERLEGYLEALEEAGIDISDVPIWEIPENDRASGEEAARELLD---A  192 (283)
T ss_pred             CCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHHHHH---C
T ss_conf             9869999524556654443221013664247799999999999998599977205784599999999999999995---5


Q ss_pred             CCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC-----CCCCCHHHHHHHH
Q ss_conf             37853566541200066524678999999999999974399705654255889999995065-----6574569999999
Q gi|254780346|r   63 SVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP-----SHLDRGGCAARSA  137 (149)
Q Consensus        63 ~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~-----~~~nkG~eaa~Aa  137 (149)
                      ..++||++|.          .|.++-.+.+++.+..  ..+|==..|++-+|...|..+-.-     ....-|..|++-.
T Consensus       193 ~~~ptai~~~----------nD~~A~g~~~~l~~~G--i~VP~DvsviGfDd~~~a~~~P~LTTI~q~~~~~G~~A~~~L  260 (283)
T cd06279         193 SPRPTAILCM----------SDVLALGALQVARELG--LRVPEDLSVVGFDGIPEARLRPGLTTVRQPSEEKGRLAARLL  260 (283)
T ss_pred             CCCCCEEEEC----------CHHHHHHHHHHHHHHC--CCCCCCEEEEEECCCHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             9999669857----------7299999999999818--999996599958988899458997089619999999999999


Q ss_pred             HHHHH
Q ss_conf             99999
Q gi|254780346|r  138 LAMIE  142 (149)
Q Consensus       138 l~mi~  142 (149)
                      +++++
T Consensus       261 l~~i~  265 (283)
T cd06279         261 LDLLE  265 (283)
T ss_pred             HHHHC
T ss_conf             99964


No 34 
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=93.51  E-value=0.72  Score=26.45  Aligned_cols=103  Identities=14%  Similarity=0.121  Sum_probs=59.5

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             7179998031289999999999999998799555553-001442269999998633113785356654120006652467
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      .||+++.+.........-.+|+.+.+.++|...+..+ ..|.+......+.+..-.....++||++|.          .|
T Consensus       177 rrI~~i~~~~~~~~~~~R~~G~~~al~~~gl~~~~~~v~~~~~~~~~~~~~~~~ll~~~~~~tAi~~~----------nD  246 (346)
T PRK10401        177 QRIGYLSSSHGIEDDAMRKAGWLSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRNLQLTAVFAY----------ND  246 (346)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCHHEEEECCCCHHHHHHHHHHHHHCCCCCCCCEEC----------CH
T ss_conf             82899947988716899999999999984999870148726875788999999998159998861444----------88


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHH
Q ss_conf             899999999999997439970565425588999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFD  120 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~  120 (149)
                      .++-.+.+++.+..  ..+|==..|++-+|...+.-
T Consensus       247 ~~A~g~l~al~~~G--l~VP~DisViGfDd~~~a~~  280 (346)
T PRK10401        247 NMAAGALTALKDNG--IAIPLHLSIIGFDDIPIARY  280 (346)
T ss_pred             HHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHC
T ss_conf             99999999999859--98998728999898089852


No 35 
>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=93.45  E-value=0.74  Score=26.39  Aligned_cols=125  Identities=13%  Similarity=0.027  Sum_probs=80.8

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      -.||+++.+.-.......-..|..+.+.++|.+...+++++.+.-....+...+-.....++||++|.          .|
T Consensus       118 hrrIa~i~g~~~~~~~~~R~~gy~~a~~~~gl~~~~~~~~~~~~~~~g~~a~~~ll~~~~~~~AI~~~----------nD  187 (269)
T cd06287         118 ARQIALIVGSARRNSYLEAEAAYRAFAAEHGMPPVVLRVDEAGGEEAGYAACAQLLAQHPDLDALCVP----------VD  187 (269)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHHHCCCCCCCEEEEE----------CH
T ss_conf             98799996898675899999999999987799984799768898599999999997179999779982----------79


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC-------CCCCHHHHHHHHHHHHH
Q ss_conf             89999999999999743997056542558899999950656-------57456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS-------HLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~-------~~nkG~eaa~Aal~mi~  142 (149)
                      .++-.+.+++.+..+  .+|==..|++.++...+.- ..+.       ...-|++|++-+++.++
T Consensus       188 ~~A~g~l~al~~~Gl--~VP~DvsVvgfdD~~~a~~-~~P~LTtV~qp~~e~G~~A~~lLl~~i~  249 (269)
T cd06287         188 AFAVGAVRAATELGR--AVPDQLRVVTRYDGLRART-SEPPLTAVDLHLDEVAEQAVDLLFAHLE  249 (269)
T ss_pred             HHHHHHHHHHHHHCC--CCCCCCEEEEECCCHHHHC-CCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             999999999998588--7798766998159289734-5888548971999999999999999966


No 36 
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=93.43  E-value=0.74  Score=26.37  Aligned_cols=123  Identities=18%  Similarity=0.131  Sum_probs=51.3

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHH
Q ss_conf             71799980312899999999999999987995555530014422699999986331137853566541200066524678
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDV   85 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~   85 (149)
                      .||+++.+.-....+..=++|+.+.|++++-.......++.+....+.+.+-+-.....++|+++|.          .|.
T Consensus       122 ~~i~~i~g~~~~~~~~~R~~Gf~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------nd~  191 (267)
T cd01536         122 GKVAIIEGPPGSSNAQERVKGFRDALKEYPDIEIVAVQDGNWDREKALQAMEDLLQANPDIDAIFAA----------NDS  191 (267)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHCCCCCHHHHHHHHHHHHHCCCCCEEEEEC----------CCH
T ss_conf             4799954899886899999999999984558662022200110257889999776417986299971----------649


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC---------CCCCCCHHHHHHHHHHHHH
Q ss_conf             99999999999997439970565425588999999506---------5657456999999999999
Q gi|254780346|r   86 IAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS---------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        86 I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~---------~~~~nkG~eaa~Aal~mi~  142 (149)
                      ++-.+.+++.+    .++|=-..|++.++...+.....         .....-|+.|++.++++++
T Consensus       192 ~a~g~~~al~~----~g~~~di~viG~D~~~~~~~~~~~~~~lttv~q~~~~~G~~a~~~l~~~i~  253 (267)
T cd01536         192 MALGAVAALKA----AGRKGDVKIVGVDGSPEALAAIKEGGILATVAQDPYTQGYLAVEAAVKLLK  253 (267)
T ss_pred             HHHHHHHHHHH----CCCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             99999999997----699999399998983999999855996599927999999999999999976


No 37 
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=93.39  E-value=0.75  Score=26.33  Aligned_cols=125  Identities=16%  Similarity=0.106  Sum_probs=52.1

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             7179998031289999999999999998799555553-001442269999998633113785356654120006652467
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      +||+++...-.......-.+|+.+.+.+++...+..+ .++-+..-...+.+.+-.....++||++|.          .|
T Consensus       118 ~~i~~i~~~~~~~~~~~R~~Gf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~aii~~----------~D  187 (268)
T cd06289         118 RRIAFIGGLEDSSTRRERLAGYRAALAEAGLPFDSELVVEGPPSRQGGAEAVAQLLDLPPRPTAIVCF----------ND  187 (268)
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEECCC----------CH
T ss_conf             70999528988706999999999999976998664345316886556999999998469998620357----------68


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             89999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      .++-.+.+++.+..+  .+|==..|++.++..++.--.      .-....-|..|++.++++++
T Consensus       188 ~~A~g~l~~l~~~gi--~vp~disiigfd~~~~~~~~~p~ltti~~~~~~~g~~a~~~l~~~i~  249 (268)
T cd06289         188 LVAFGAMSGLRRAGL--TPGRDIAVVGFDDVAEAALATPALTTVSTDPREIGRRAAELLLRRIA  249 (268)
T ss_pred             HHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             999999999998499--99985499995787899722897169984999999999999999976


No 38 
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=93.10  E-value=0.83  Score=26.05  Aligned_cols=126  Identities=17%  Similarity=0.143  Sum_probs=78.4

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE-EEEEHHHHHHHHHHHHHHHHHHHCCCC-CCEEEEEEEEECCCCCH
Q ss_conf             8717999803128999999999999999879955-555300144226999999863311378-53566541200066524
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQW-SSIVTPGVLEIPAAVSMVMNAKTRSVT-YDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~-~~i~VPGa~EiP~a~~~~~~~~~~~~~-~D~vIaLG~VIkGeT~H   82 (149)
                      -.||+++...-....+..-++|..+.+.++|... +....+|.|..-...+.+.+-.....+ +||++|.          
T Consensus       175 ~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~i~~~~~~~~~g~~~~~~ll~~~~~~ptAif~~----------  244 (333)
T COG1609         175 HRRIAFIGGPLDSSASRERLEGYRAALREAGLPINPEWIVEGDFSEESGYEAAERLLARGEPRPTAIFCA----------  244 (333)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCCEEEEC----------
T ss_conf             9859999679877218999999999999759997742366167887899999999985489999789987----------


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             67899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                      .|.++-.+.+.+.+..+.  +|==..|++-+|.+.+.--.-      ......|++|++..+++++
T Consensus       245 nD~~Alg~l~~~~~~g~~--vP~disviGfDd~~~~~~~~P~LTTv~~~~~~~G~~A~~~Ll~~i~  308 (333)
T COG1609         245 NDLMALGALRALRELGLR--VPEDLSVIGFDDIELARFLTPPLTTVRQPIEELGRRAAELLLERIN  308 (333)
T ss_pred             CCHHHHHHHHHHHHCCCC--CCCCEEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             809999999999980899--9987899998884776515898069950999999999999998743


No 39 
>PRK09526 lacI lac repressor; Reviewed
Probab=92.49  E-value=1  Score=25.53  Aligned_cols=125  Identities=11%  Similarity=0.136  Sum_probs=72.9

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      ..||+++.+..+...+..=+.|+.+.+.+++.....+ ..|-|+..-..+.+.+-.....++||++|.          .|
T Consensus       181 hr~I~~i~~~~~~~~~~~R~~Gf~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~l~~~~~ptai~~~----------~D  249 (342)
T PRK09526        181 HQQIALLAGPLSSVSARLRLAGWLEYLTRNQLSPIAV-REGDWSAMSGYQQTLQMLNEGPVFTAVLVA----------ND  249 (342)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEE-EECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CH
T ss_conf             9759999589766009999999999999779896169-956898789999999998369999758756----------77


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             89999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      .++-.+.+.+.+.  ...+|==..|++-++..-+.--.      ......-|..|++.++++++
T Consensus       250 ~~A~g~i~~l~~~--g~~vP~DisIigfDd~~~~~~~~P~LTtv~~p~~~ig~~A~~~Ll~~i~  311 (342)
T PRK09526        250 QMALGVLRALHES--GLRVPGDISVIGYDDTEDSSYFIPPLTTIKQDFRLLGKEAVDRLLSLSD  311 (342)
T ss_pred             HHHHHHHHHHHHH--CCCCCCCEEEEEECCCHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             9999999999980--9999997499998980899824898089981999999999999999865


No 40 
>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational
Probab=92.48  E-value=1  Score=25.53  Aligned_cols=125  Identities=15%  Similarity=0.088  Sum_probs=69.0

Q ss_pred             CEEEEEEEC-HHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             717999803-1289999999999999998799555553-00144226999999863311378535665412000665246
Q gi|254780346|r    6 PHVLIIEAR-FYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         6 ~kI~IV~s~-~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      +||+++.+. -....+..-+.|+.+.+.++|......+ ..+.|..-.+.+.+.+......++||++|.          .
T Consensus       117 ~~i~~i~~~~~~~~~~~~R~~gf~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~~----------n  186 (268)
T cd06273         117 RRIAMIFGPTQGNDRARARRAGVRAALAEAGLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVICG----------N  186 (268)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHEEECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C
T ss_conf             747999468777778999999999999980999871420315789899999999998479998489977----------8


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+..  ..+|=-..|++-+|..-+.--.      ......-|.+|++.++++++
T Consensus       187 d~~A~g~i~~l~~~g--~~iP~disvigfd~~~~~~~~~p~lTti~~~~~~~g~~a~~~L~~~i~  249 (268)
T cd06273         187 DVLALGALYEARRLG--LSVPEDLSIVGFDDIDGSAELEPALTTVRVPAREIGRIAAEALLALLG  249 (268)
T ss_pred             HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHHCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             799999999999639--999996799999982889841899479991999999999999999966


No 41 
>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor 
Probab=92.35  E-value=1.1  Score=25.43  Aligned_cols=123  Identities=17%  Similarity=0.037  Sum_probs=75.1

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE--EEHH-HHHHHH-HHHHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             871799980312899999999999999987995555--5300-144226-999999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS--IVTP-GVLEIP-AAVSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~--i~VP-Ga~EiP-~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      -.||+++...-...-...-..|+.+.+.++|...+.  +... -.++-. .+++.+++   ...++||++|.        
T Consensus       111 ~~~i~~i~~~~~~~~~~~R~~gf~~al~~~g~~~~~~~i~~~~~~~~~~~~~~~~ll~---~~~~p~Ai~~~--------  179 (261)
T cd06272         111 HKKIAYIGDLSLDRRQRKRFKGFLETCDENGISISDSHIDVDGLSAEGGDNAAKKLLK---ESDLPTAIICG--------  179 (261)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCHHHHHHHHHHHHHH---CCCCCCCEEEC--------
T ss_conf             9828996698887359999999999999859985513898303103679999999985---27898610127--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             2467899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+++.+.  ...+|==..|++-+|...+.--.-      .....-|+.|++..+++++
T Consensus       180 --nD~~A~g~~~~l~~~--g~~vP~dvsviGfDd~~~~~~~~P~LTtv~q~~~~ig~~A~~~L~~~i~  243 (261)
T cd06272         180 --SYDIALGVLSALNKQ--GISIPEDIEIISYDNIPQMAIIDPPLTAVDVPIEEIAKKSLELLLKLIT  243 (261)
T ss_pred             --CHHHHHHHHHHHHHH--CCCCCCCEEEEEECCCHHHHHHCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             --689999999999980--9999995599998881889950998479980999999999999999964


No 42 
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=92.35  E-value=1.1  Score=25.43  Aligned_cols=35  Identities=6%  Similarity=0.032  Sum_probs=19.8

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             17999803128999999999999999879955555
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI   41 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i   41 (149)
                      ||++|...-..+.-..+.+|+.+..++.|+++...
T Consensus         1 kIg~i~~~~~npf~~~v~~G~e~aA~~~G~~v~~~   35 (273)
T cd06310           1 KIALVPKGTTSDFWQAVKAGAEAAAKELGVKVTFQ   35 (273)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             98999599998599999999999999809989997


No 43 
>pfam00532 Peripla_BP_1 family. This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356).
Probab=92.16  E-value=1.1  Score=25.29  Aligned_cols=33  Identities=6%  Similarity=0.038  Sum_probs=16.0

Q ss_pred             EEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             799980312899999999999999987995555
Q gi|254780346|r    8 VLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS   40 (149)
Q Consensus         8 I~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~   40 (149)
                      |+++.+.-+......-++|+.+.|.++|.+.+.
T Consensus       124 i~~~~~~~~~~~~~~R~~Gf~~al~~~g~~~~~  156 (281)
T pfam00532       124 IAVMAGPASALTARERVQGFMAALAAAGREVKI  156 (281)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             477307876507899999999999975999982


No 44 
>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=91.94  E-value=1.2  Score=25.13  Aligned_cols=122  Identities=14%  Similarity=0.037  Sum_probs=77.0

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-----HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             7179998031289999999999999998799555553-----00144226999999863311378535665412000665
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-----TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-----VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      .||+.+ +.-....+..-..|+.+.+.++|++...+.     .+..++-  +.+.+.+......+++|++|.        
T Consensus       110 r~I~~i-g~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~~~--~~~~l~~~l~~~~~ptAi~~~--------  178 (265)
T cd01543         110 RHFAFY-GLPGARWSDEREEAFRQLVAEAGYECSFFYRGLSTDAQSWEE--EQEELAQWLQSLPKPVGIFAC--------  178 (265)
T ss_pred             CEEEEE-CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHH--HHHHHHHHHHCCCCCEEEEEC--------
T ss_conf             749998-999880699999999999997799976341245446753999--999999998359998399988--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC-------CCCCCHHHHHHHHHHHHH
Q ss_conf             24678999999999999974399705654255889999995065-------657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP-------SHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~-------~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+++.+..+  .+|==.+|++-+|...+-+-+.+       .....|.+||+..+++++
T Consensus       179 --nD~~A~g~l~~l~~~Gi--~VP~disViGfD~~~~~~~~~~P~LTtV~q~~~~mG~~Aa~lL~~~i~  243 (265)
T cd01543         179 --TDARARQLLEACRRAGI--AVPEEVAVLGVDNDELICELSRPPLSSVEQNAERIGYEAAKLLDRLMR  243 (265)
T ss_pred             --CHHHHHHHHHHHHHHHC--CCCCCEEEEEECCCHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHHC
T ss_conf             --36999999999998322--577755999982868889527999733962999999999999999967


No 45 
>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type I periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor
Probab=91.92  E-value=1.2  Score=25.11  Aligned_cols=124  Identities=13%  Similarity=-0.039  Sum_probs=78.3

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHHHHHHHHHH---HHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             87179998031289999999999999998799555553-00144226999---999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPGVLEIPAAV---SMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPGa~EiP~a~---~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      -.||+++.+......+..-+.|+.+.+.++|...+..+ ..+.|......   ..++..  ....+||++|.        
T Consensus       116 hr~I~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~i~~~~~~~~~g~~~~~~~l~~--~~~~p~ai~~~--------  185 (264)
T cd06274         116 PEEVLFLGGLPELSPSRERLAGFRQALADAGLPVQPDWIYAEGYSPESGYQLMAELLAR--LGRLPRALFTT--------  185 (264)
T ss_pred             CCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHH--CCCCCCCCCCC--------
T ss_conf             96699976898773099999999999997799877407982688878999999999986--56887422017--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             2467899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+.+.+..+  .+|==..|++-+|...|.--.-      -....-|.+|++-.+++++
T Consensus       186 --nd~~a~g~l~~l~~~g~--~vP~disvvgfDd~~~a~~~~p~LTtv~q~~~~~g~~A~~lLl~~i~  249 (264)
T cd06274         186 --SYTLLEGVLRFLRERPG--LAPSDLRIATFDDHPLLDFLPFPVHSVPQDHEALAEAAFELALAALG  249 (264)
T ss_pred             --CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             --69999999999998599--99998799998986899737999769967999999999999999867


No 46 
>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.
Probab=91.75  E-value=1.2  Score=25.00  Aligned_cols=122  Identities=13%  Similarity=0.141  Sum_probs=76.0

Q ss_pred             CCEEEEEEECHHHHH-HHHHHHHHHHHHHHCCCCEEE--E-EHHHHHHHHHHH-HHHHHHHHCCCCCCEEEEEEEEECCC
Q ss_conf             871799980312899-999999999999987995555--5-300144226999-99986331137853566541200066
Q gi|254780346|r    5 IPHVLIIEARFYENL-SAMLFEGCVNVLHSRAVQWSS--I-VTPGVLEIPAAV-SMVMNAKTRSVTYDGIIVLGVVMRGK   79 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i-~~~ll~ga~~~l~~~~~~~~~--i-~VPGa~EiP~a~-~~~~~~~~~~~~~D~vIaLG~VIkGe   79 (149)
                      -.||+++...+.... .+.-++|+.+.+.++|.....  + .....++-...+ +.++    ...++||++|.       
T Consensus       116 ~~~I~~i~~~~~~~~~~~~R~~gf~~a~~~~g~~~~~~~i~~~~~~~~~~~~~~~~l~----~~~~~~ai~~~-------  184 (268)
T cd06298         116 HKKIAFISGPLEDSINGDERLAGYKEALSEANIEFDESLIFEGDYTYESGYELAEELL----EDGKPTAAFVT-------  184 (268)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHEECCCHHHHHHHHHHHHHH----HCCCCCEEEEC-------
T ss_conf             9669999678777625999999999999984999760120035403778999999998----36999789966-------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             5246789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   80 TAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        80 T~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                         .|.++-.+.+.+.+..+  .+|=-..|++.++.+-|.--.      ......-|+.|++..+++++
T Consensus       185 ---nD~~A~g~l~~l~~~g~--~vP~disvigfDd~~~a~~~~P~LTtv~~~~~~~G~~A~~~l~~~i~  248 (268)
T cd06298         185 ---DDELAIGILNAAQDAGL--KVPEDFEIIGFNNTKLASMVRPQLTSVTQPLYDIGAVAMRLLTKLMN  248 (268)
T ss_pred             ---CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             ---87999999999997499--99987499997881899714899769972999999999999999966


No 47 
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=91.71  E-value=1.2  Score=24.97  Aligned_cols=123  Identities=15%  Similarity=0.119  Sum_probs=71.8

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHH---HHHHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             871799980312899999999999999987995555-5300144226---999999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIP---AAVSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP---~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      -.||+++.+.........-++|+.+.+.++|...+. +...+.+.--   .++..++.   ...+++|++|.        
T Consensus       176 hr~Ia~i~~~~~~~~~~~R~~g~~~al~~~gl~~~~~~i~~~~~~~~~~~~~~~~ll~---~~~~~tAi~~~--------  244 (342)
T PRK10727        176 HTRIGYLCSNHSISDAEDRLQGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLG---RGRNFTAVACY--------  244 (342)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHH---CCCCCCCCEEC--------
T ss_conf             9759999689888359999999999999769999820588157877889999999985---59997741554--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             246789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+++.+..+  .+|==..|++-+|...+.--.      .......|..|++-++++++
T Consensus       245 --nD~~A~g~l~al~~~Gl--~VP~DisViGfDd~~~~~~~~P~LTTV~~p~~e~g~~A~~lLl~~i~  308 (342)
T PRK10727        245 --NDSMAAGAMGVLNDNGI--DVPGEISLIGFDDVLVSRYVRPRLTTVRYPIVTMATQAAELALALAD  308 (342)
T ss_pred             --CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             --69999999999998299--99998699988971898648899858977999999999999999855


No 48 
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia.  This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=91.57  E-value=1.3  Score=24.88  Aligned_cols=121  Identities=12%  Similarity=0.010  Sum_probs=74.7

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHH---HHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             8717999803128999999999999999879955555-300144226999---999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAV---SMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~---~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      -.||+++.+.-.......-++|+.+.+.+++...+.. ...+.+......   +.++     ...+|+++|.        
T Consensus       116 ~~~i~~i~~~~~~~~~~~R~~gf~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l-----~~~p~ai~~~--------  182 (265)
T cd06299         116 HKKIGYISGPQDTSTGRERLEAFRQACASLGLEVNEDLVVLGGYSQESGYAGATKLL-----DQGATAIIAG--------  182 (265)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCHHHHHHHHHHHH-----HCCCCEEECC--------
T ss_conf             983886048988756999999999999976999993059984035578999999999-----6399854506--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             2467899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+.+.+.  ...+|=-..|++.+|.+.+.-..-      .....-|.+|++.++++++
T Consensus       183 --nD~~A~g~~~~l~~~--g~~vP~dvsvvgfd~~~~~~~~~p~lTTv~~~~~~~g~~A~~~L~~~i~  246 (265)
T cd06299         183 --DSMMTIGAIRAIHDA--GLVIGEDISLIGFDDLPVFRLQTPPLTVIDQQVEQMGKRAVDMLLSLIA  246 (265)
T ss_pred             --CCHHHHHHHHHHHHH--CCCCCCCEEEEEECCHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             --858899999999983--8999993499999975889853998399980999999999999999962


No 49 
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=91.27  E-value=1.4  Score=24.69  Aligned_cols=124  Identities=12%  Similarity=0.096  Sum_probs=72.8

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             8717999803128999999999999999879955555-300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -.||+++....+..-...-+.|+.+.+.++|.+.+.. ...+..+.-..+..++..  ....++|++|.          .
T Consensus       118 hr~I~~i~~~~~~~~~~~R~~Gf~~al~~~gl~~~~~~~~~~~~~~~~~~~~~~~~--~~~~ptAi~~~----------n  185 (268)
T cd06277         118 HRKIGFVGDPLYSPSFEERYEGYKKALLDHGIPFNEDYDITEKEEDEEDIGKFIDE--LKPLPTAFFCS----------N  185 (268)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHH--CCCCCCEEEEC----------C
T ss_conf             98369972788881299999999999998599998224662587779999999984--78899879968----------8


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+..  ..+|==..|++.+|.+.+.--.      ......-|++|++..+++++
T Consensus       186 D~~A~g~~~~l~~~g--~~vP~Disivgfdd~~~~~~~~P~LTtv~~~~~~~G~~A~~~Ll~~i~  248 (268)
T cd06277         186 DGVAFLLIKVLKEMG--IRVPEDVSVIGFDDIEYATIFTPPLTTVRVDKEEMGKLAVKRLLEKLE  248 (268)
T ss_pred             HHHHHHHHHHHHHCC--CCCCCCCEEEEECCHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             599999999999859--999986289997887899844898089992999999999999999966


No 50 
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=91.25  E-value=1.4  Score=24.68  Aligned_cols=121  Identities=8%  Similarity=0.004  Sum_probs=77.8

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH-HHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             71799980312899999999999999987995555530014422699-99998633113785356654120006652467
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA-VSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a-~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      .||+.+.+.-. .....-+.|+.+.+.++|.+.+..+++-..|--.. +..++   ....++||++|.          .|
T Consensus       116 r~I~~l~g~~~-~~~~~R~~Gf~~al~~~gi~~~~~~~~~~~~~~~~~~~~~l---~~~~~~~ai~~~----------nD  181 (263)
T cd06280         116 RRIGGLFGNAS-TTGAERRAGYEDAMRRHGLAPDARFVAPTAEAAEAALAAWL---AAPERPEALVAS----------NG  181 (263)
T ss_pred             CEEEEEECCCC-CCHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHHHHHHHHH---HCCCCCCEEEEC----------CH
T ss_conf             66999938998-43999999999999976999763782487678999999998---279999789967----------88


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             89999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      .++-.+.+++.+..  ..+|==..|++-+|...+.--.      .-....-|.+|++-.+++++
T Consensus       182 ~~A~g~l~~l~~~g--~~vP~disviGfDd~~~a~~~~P~LTTv~~~~~~~g~~A~~~Ll~~i~  243 (263)
T cd06280         182 LLLLGALRAVRAAG--LRIPQDLALAGFDNDPWTELVGPGITVIEQPVEEIGRAAMSLLLERLA  243 (263)
T ss_pred             HHHHHHHHHHHHHC--CCCCCCCEEEEECCHHHHHCCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             99999999999848--999998789997785888617999779980999999999999999966


No 51 
>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=91.02  E-value=1.5  Score=24.54  Aligned_cols=120  Identities=12%  Similarity=-0.005  Sum_probs=72.3

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE---EHHHHHHHHHHH-HHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             717999803128999999999999999879955555---300144226999-9998633113785356654120006652
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI---VTPGVLEIPAAV-SMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i---~VPGa~EiP~a~-~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      .||+++...-....+..-+.|+.+.+++++...+..   ..+...|..... ..++     +.++||++|.         
T Consensus       123 ~~i~~i~~~~~~~~~~~R~~G~~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l-----~~~~~ai~~~---------  188 (273)
T cd06292         123 RRIGFASGPGRTVPRRRKIAGFRAALEEAGLEPPEALVARGMFSVEGGQAAAVELL-----GSGPTAIVAA---------  188 (273)
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHH-----HCCCCEEEEC---------
T ss_conf             80899517877715999999999999984999771489716777788999999997-----4799657745---------


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             467899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                       .|.++-.+.+.+.+.  ...+|==..|++.+|...+.--.-      ......|..|++..+++++
T Consensus       189 -nD~~A~g~~~~l~~~--g~~ip~di~VigfD~~~~~~~~~p~LTtI~q~~~~~g~~a~~~ll~~i~  252 (273)
T cd06292         189 -SDLMALGAIRAARRR--GLRVPEDVSVVGYDDSALMAFTDPPLTTVRQPVEEMAAAAVDRLMARID  252 (273)
T ss_pred             -CCHHHHHHHHHHHHC--CCCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             -859999999999983--9989996599999985899815899679995999999999999999966


No 52 
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=90.84  E-value=1.5  Score=24.43  Aligned_cols=124  Identities=15%  Similarity=-0.023  Sum_probs=74.7

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEH-HHHHHHHH-HHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             871799980312899999999999999987995555530-01442269-9999986331137853566541200066524
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVT-PGVLEIPA-AVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~V-PGa~EiP~-a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      -+||+++.+.-+......=++|+.+.|.++|.+...+.. +..+|-.. +.+.++   ....++||++|.          
T Consensus       115 h~~I~~i~~~~~~~~~~~R~~G~~~al~~~gl~~~~~~~~~~~~~~g~~~~~~ll---~~~~~ptAi~~~----------  181 (266)
T cd06278         115 CRRIAFIGGPADTSTSRERERGFRDALAAAGVPVVVEEAGDYSYEGGYEAARRLL---ASRPRPDAIFCA----------  181 (266)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHHHHHHH---HCCCCCCCCEEC----------
T ss_conf             9889999688888149999999999999869994389818999899999999998---459998862507----------


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             67899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                      -|.++-.+.+.+.+ .+...+|==..|++-+|.+.+.--.-      .....-|+.|++..+++++
T Consensus       182 nD~~A~g~l~~l~~-~~g~~vP~disvvgfD~~~~~~~~~p~LTtv~~~~~~~g~~A~~~Ll~~i~  246 (266)
T cd06278         182 NDLLAIGVMDAARQ-EGGLRVPEDVSVIGFDDIPMAAWPSYQLTTVRQPVDRMAEEAVDLLEARIE  246 (266)
T ss_pred             CHHHHHHHHHHHHH-HCCCCCCCCEEEEEECCHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             78999999999997-358888886699987880898544998489983999999999999999971


No 53 
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=90.69  E-value=1.6  Score=24.35  Aligned_cols=125  Identities=12%  Similarity=0.028  Sum_probs=72.7

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC-EEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             871799980312899999999999999987995-5555300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ-WSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~-~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      -.||+++.+.-+....+.-..|..+.+...+.. .+.++ .|.|......+....-......+||++|.          .
T Consensus       174 ~r~I~~i~~~~~~~~~~~R~~~~~~~~~~~~~~~~~~i~-~~~~~~~~g~~~~~~ll~~~~~p~ai~~~----------n  242 (327)
T PRK10339        174 VNRIGFIGGEDEPGKADIREVAFAEYGRLKQVVREEDIW-RGGFSSSSGYELAKQMLAREDYPKALFVA----------S  242 (327)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCHHHEE-ECCCCHHHHHHHHHHHHHCCCCCCEEEEC----------C
T ss_conf             983999957887644999999999999875999737558-66898699999999998469999748977----------7


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             7899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                      |.++-.+.+.+.+..  ..+|==.+|++.+|...+.--.-      .....-|.+|++-.++.++
T Consensus       243 D~~A~g~l~al~~~g--i~VP~DisVigfdd~~~~~~~~P~LTtv~~~~~~~g~~Av~~Ll~~i~  305 (327)
T PRK10339        243 DSIAIGVLRAIHERG--LNIPQDISLISVNDIPTARFTFPPLSTVRIHSEMMGSQGVNLLYEKAR  305 (327)
T ss_pred             HHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             799999999999829--999997599998973889833899569986999999999999999973


No 54 
>PRK13337 putative lipid kinase; Reviewed
Probab=90.62  E-value=1.6  Score=24.34  Aligned_cols=92  Identities=20%  Similarity=0.186  Sum_probs=53.5

Q ss_pred             CCCEEEEEEECH-HHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             587179998031-2899999999999999987995555530014422699999986331137853566541200066524
Q gi|254780346|r    4 FIPHVLIIEARF-YENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         4 ~~~kI~IV~s~~-~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      ||+|+++|+-.. -+.-..+.++...+.|.+++++++...+.+.-+.--.++..     ....||.+|+.|    ||=. 
T Consensus         1 mmkr~~~I~NP~sG~g~~~~~~~~i~~~l~~~g~~~~~~~T~~~g~a~~~a~~~-----~~~~~d~vv~~G----GDGT-   70 (305)
T PRK13337          1 MMKRARIIYNPTSGRELFKKNLPDVLQKLEQAGYETSAHATTGPGDATLAARQA-----AERNFDLVIAAG----GDGT-   70 (305)
T ss_pred             CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHH-----HHCCCCEEEEEE----CCHH-
T ss_conf             984599999975688646778999999999879969999827802899999998-----777999899995----7628-


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             6789999999999999743997056542558
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                          -+++.+|++..    +.....|||-..
T Consensus        71 ----v~evvngl~~~----~~~~~lgiiP~G   93 (305)
T PRK13337         71 ----LNEVVNGLAEK----ENRPKLGIIPVG   93 (305)
T ss_pred             ----HHHHHHHHHCC----CCCCEEEEEECC
T ss_conf             ----99999998558----998628997078


No 55 
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=90.57  E-value=1.6  Score=24.28  Aligned_cols=120  Identities=14%  Similarity=0.060  Sum_probs=63.7

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             71799980312899999999999999987995555530014422699---999986331137853566541200066524
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      .||+++.+.-.......-..|+.+.+.++|.+.+.++. +.|..-..   ++.++   .....+||++|.          
T Consensus       180 rrI~~i~~~~~~~~~~~R~~Gf~~al~~~g~~~~~~~~-~~~~~~~g~~~~~~ll---~~~~~p~Ai~~~----------  245 (330)
T PRK11303        180 ESILLLGALPELSVSFLREQGFRQALKDDPREVHFLYA-ESFSREAGAQLFEKWL---ETHGMPDALFTT----------  245 (330)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC-CCCCHHHHHHHHHHHH---HCCCCCCEEEEC----------
T ss_conf             97999968975637999999999999967998059964-8899899999999998---379999779974----------


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC-------CCCCHHHHHHHHHHHHH
Q ss_conf             6789999999999999743997056542558899999950656-------57456999999999999
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS-------HLDRGGCAARSALAMIE  142 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~-------~~nkG~eaa~Aal~mi~  142 (149)
                      -|.++-.+.+++.+..+  .+|==..|++-+|.+.+.- ..+.       ...-|..|++-++++++
T Consensus       246 nD~~A~g~l~al~~~g~--~VP~DvsvigfDd~~~~~~-~~p~LTtv~q~~~~~g~~A~~~Ll~~i~  309 (330)
T PRK11303        246 SYTLLQGVLDVLLERPG--KLPSDLAIATFGDNELLDF-LPCPVNAVAQQHRLIAERALELALAALD  309 (330)
T ss_pred             CHHHHHHHHHHHHHCCC--CCCCCEEEEEECCHHHHHC-CCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             89999999999998599--9999759999996288971-7999729967999999999999999965


No 56 
>PRK10936 periplasmic sensory protein associated with the TorRS two-component regulatory system; Provisional
Probab=89.81  E-value=1.6  Score=24.25  Aligned_cols=64  Identities=9%  Similarity=0.070  Sum_probs=52.2

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             717999803128999999999999999879955555300144226999999863311378535665
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIV   71 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIa   71 (149)
                      -||+++........=..+-.|+.+..++.|++..++..+|-.++.-=.+.+-+.-  ..++||++.
T Consensus        46 ~ki~~~~p~lkd~yW~~v~~G~~~~Ak~lGv~l~v~~a~~~~d~~~Q~~qie~~i--~~~vDAIil  109 (340)
T PRK10936         46 WKLCALYPHLKDSYWLSVNYGLVQEAKRLGVDLKVLEAGGYYNLATQQQQLEQCV--AWGADAILL  109 (340)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHH--HCCCCEEEE
T ss_conf             1799980688886999999999999998098699985899889999999999999--759999998


No 57 
>pfam04392 ABC_sub_bind ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.
Probab=89.06  E-value=2.1  Score=23.55  Aligned_cols=116  Identities=15%  Similarity=0.149  Sum_probs=76.6

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      .+||+++++.-... ...+++..++.+.+.|++.....|+..=|++.+.+.+.      .+.|+++.+       ++++ 
T Consensus       130 ~k~igviyn~~e~~-s~~~~~~~~~~a~~~gi~l~~~~v~~~~ei~~a~~~l~------~~~Dal~i~-------~d~~-  194 (292)
T pfam04392       130 VKSIGVYYSPSEAN-SVSLVEEIKKYAKKSGIKVVEASVPSSNDVPSAMSSMA------GKVDAIFIP-------TDNL-  194 (292)
T ss_pred             CCEEEEEECCCCCC-HHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHH------CCCCEEEEE-------CCCC-
T ss_conf             85899995799865-79999999999997699899996688667999999743------289889993-------7810-


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH----CCCCCCCHHHHHHHHHHHHH
Q ss_conf             89999999999999743997056542558899999950----65657456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV----SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~----~~~~~nkG~eaa~Aal~mi~  142 (149)
                       +. +....+.+++.++++|+...     +..+...-+    +.+..+-|++||+=+.++++
T Consensus       195 -v~-s~~~~i~~~a~~~kiPv~~~-----~~~~V~~Gal~s~g~~~~~~G~~aa~~a~rIL~  249 (292)
T pfam04392       195 -IA-SAFTAVLQEANKAKIPVITS-----DTSSVERGACAAVGVDYKQIGVQAANIVAKILK  249 (292)
T ss_pred             -HH-HHHHHHHHHHHHCCCCEEEC-----CHHHHHCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             -78-89999999999749998957-----788884796799946999999999999999978


No 58 
>TIGR01481 ccpA catabolite control protein A; InterPro: IPR006377   Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [e.g. acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription.
Probab=89.02  E-value=1.9  Score=23.89  Aligned_cols=97  Identities=8%  Similarity=0.267  Sum_probs=73.6

Q ss_pred             CCEEEEEEECHHHHHH-HHHHHHHHHHHHHCCCCEEE-EEHHH--HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             8717999803128999-99999999999987995555-53001--44226999999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEARFYENLS-AMLFEGCVNVLHSRAVQWSS-IVTPG--VLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~-~~ll~ga~~~l~~~~~~~~~-i~VPG--a~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      .++|++|..+..+.|- +--+.|-++.|++.|++++. .-.-|  +|.--+.+..-+  ...+.+++|++|.        
T Consensus       177 hK~iAfv~G~L~~~~N~~~~l~GykE~L~~~gI~~~e~L~~~~~YsY~~G~K~~~~l--~~s~p~~tAv~v~--------  246 (332)
T TIGR01481       177 HKKIAFVSGSLSDSVNGEVRLEGYKEALKKAGIAYEEDLVIEAKYSYDAGVKLAAEL--LESSPKITAVVVA--------  246 (332)
T ss_pred             CCEEEEEECCCCCCCCCEECCCHHHHHHHHCCCCCCCCEEEECCCCCHHHHHHHHHH--HHCCCCCCEEEEC--------
T ss_conf             826888736757110452013304678873687414221330455504469999999--8538996589981--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHC--CCCCEEEEECCCCHHH
Q ss_conf             246789999999999999743--9970565425588999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSING--SLPIGNGIVVVDSEQQ  117 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~--~~PI~~gILt~~n~~Q  117 (149)
                            +++-+=|+++-+++.  ++|==+.|+|-+|..-
T Consensus       247 ------~DE~A~G~lnaa~D~Gi~VPeDLevitsnnt~l  279 (332)
T TIGR01481       247 ------DDELAIGILNAALDAGIKVPEDLEVITSNNTKL  279 (332)
T ss_pred             ------CHHHHHHHHHHHHHCCCCCCCCCEEECCCCCEE
T ss_conf             ------828899999999857898876456741066023


No 59 
>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=88.67  E-value=2.3  Score=23.39  Aligned_cols=122  Identities=16%  Similarity=0.099  Sum_probs=74.2

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEH-HHHHHHHH-HHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             871799980312899999999999999987995555530-01442269-9999986331137853566541200066524
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVT-PGVLEIPA-AVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~V-PGa~EiP~-a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      -++|+++.+.-+......-.+|+.+.+.+++.+...+.. ....|--+ +.+.++    ...++||++|-          
T Consensus       116 ~~~i~~i~~~~~~~~~~~R~~G~~~al~~~~i~~~~~~~~~~~~~~~~~~~~~l~----~~~~~~aii~~----------  181 (264)
T cd01574         116 HRTIAHVAGPEEWLSARARLAGWRAALEAAGIAPPPVLEGDWSAESGYRAGRELL----REGDPTAVFAA----------  181 (264)
T ss_pred             CCCEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCCHHHHHHHHHHHH----HCCCCCEEEEC----------
T ss_conf             9827325899777579999999999999869897448866899799999999998----37999689636----------


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             6789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                      .|.++-.+.+.+.+..+  .+|==..|++-+|...+.--.      .-....-|.+|++.++++++
T Consensus       182 ~D~~A~g~i~~l~~~g~--~iP~di~iigfd~~~~~~~~~p~lTtI~~~~~~~g~~A~~~l~~~i~  245 (264)
T cd01574         182 NDQMALGVLRALHELGL--RVPDDVSVVGFDDIPESAYFIPPLTTVRQDFAALGRRAVELLLALLE  245 (264)
T ss_pred             CHHHHHHHHHHHHHHCC--CCCCCCEEEEECCCHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             42999999999998299--88988479986881788950898589981999999999999999976


No 60 
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=88.40  E-value=2.3  Score=23.27  Aligned_cols=127  Identities=12%  Similarity=-0.020  Sum_probs=68.8

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      ..||+++...-....+..-.+|+.+.|+++.--..+...+|-|..-.+.+..-+-.....++|++.|.          .|
T Consensus       122 ~~~i~~i~G~~~~~~~~~R~~Gf~~~l~~~~~~~vv~~~~~~~~~~~a~~~~~~~L~~~pdi~aI~a~----------nD  191 (270)
T cd06308         122 KGNILEIWGLEGSSPAIERHDGFKEALSKYPKIKIVAQQDGDWLKEKAEEKMEELLQANPDIDLVYAH----------ND  191 (270)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEC----------CC
T ss_conf             85499962799985499999999999986689524668617667999999999998508888889977----------86


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC-------CCCHHHHHHHHHHHHH
Q ss_conf             899999999999997439970565425588999999506565-------7456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH-------LDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~-------~nkG~eaa~Aal~mi~  142 (149)
                      ..+-.+.+++.+.....+++|. |+=......++++-.....       .-.|+.|+++++.+++
T Consensus       192 ~~A~Ga~~Al~~aG~~~~i~vv-g~D~~~~~~~~l~~i~~g~~~~t~~~p~~G~~av~~a~~~l~  255 (270)
T cd06308         192 PMALGAYLAAKRAGREKEIKFI-GIDGLPGPGGGIEAVRDGELDATFLYPTGGKEAIEVAMKILN  255 (270)
T ss_pred             HHHHHHHHHHHHCCCCCCCEEE-EECCCCCHHHHHHHHHCCCCEEEEECHHHHHHHHHHHHHHHC
T ss_conf             5899999999976999995899-888993369999998738616999883789999999999977


No 61 
>COG1454 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]
Probab=88.16  E-value=1.9  Score=23.80  Aligned_cols=62  Identities=19%  Similarity=0.282  Sum_probs=42.5

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHH---HHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             87179998031289999999999999998799555553-001---4422699999986331137853566541
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPG---VLEIPAAVSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPG---a~EiP~a~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      .+|.+||..+.  -..-.+++...+.|++.++++.++. |++   .=++-.+++.     .+..++|.+|+||
T Consensus        29 ~~r~liVTd~~--~~~~g~~~~v~~~L~~~~i~~~if~~v~p~P~~~~v~~~~~~-----~~~~~~D~iIalG   94 (377)
T COG1454          29 AKRALIVTDRG--LAKLGLLDKVLDSLDAAGIEYEVFDEVEPEPTIETVEAGAEV-----AREFGPDTIIALG   94 (377)
T ss_pred             CCCEEEEECCC--CCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHH-----HHHCCCCEEEEEC
T ss_conf             87159997986--311066999999987449828995688999988899999999-----9816999899977


No 62 
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=87.84  E-value=2.5  Score=23.06  Aligned_cols=124  Identities=14%  Similarity=0.200  Sum_probs=75.0

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHC-CCCCCEEEEEEEEECCCCCH
Q ss_conf             8717999803128999999999999999879955555-300144226999999863311-37853566541200066524
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTR-SVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~-~~~~D~vIaLG~VIkGeT~H   82 (149)
                      +.+|+++...-.......-.+|+.+.|.+.+-+++.+ .+++-|....+.+..-+-... ..+.|++++          +
T Consensus       125 ~~~v~~i~g~~~~~~~~~R~~Gf~~~l~~~~~~i~iv~~~~~~~~~~~a~~~~~~lL~~~~~~i~~I~~----------~  194 (275)
T cd06317         125 KGQIVVIAGQPGNGTAIERQKGFEDELAEVCPGVEVLDTQPADWDREKAQVAMEALITKFGDDIDGVYA----------G  194 (275)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEEC----------C
T ss_conf             961799937999859999999999999985887569888741477899999999998734575334405----------8


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH
Q ss_conf             67899999999999997439970565425588999999506565---------7456999999999999
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE  142 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~  142 (149)
                      .|..+-.+.+++.+..++.+++| .|   .+...++++......         ..-|+.+++.++++++
T Consensus       195 nd~~a~Ga~~Al~~~G~~~~v~v-vg---~d~~~~~~~~i~~G~~~~tv~q~p~~~G~~av~~~~~~l~  259 (275)
T cd06317         195 DDNMARGALNAAKEAGLAGGIVI-VG---ANNFAVGYEAIRAGKYYGTIYQSPVDDGEAALQTAMDVLN  259 (275)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCEE-EE---ECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             95789999999997499899879-98---7980999999985998399925999999999999999977


No 63 
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=87.57  E-value=2.6  Score=22.96  Aligned_cols=123  Identities=19%  Similarity=0.176  Sum_probs=72.0

Q ss_pred             CCEEEEEEECHHH-HHHHHHHHHHHHHHHHCCCCEE-EEEHHHHHHH-HHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             8717999803128-9999999999999998799555-5530014422-69999998633113785356654120006652
Q gi|254780346|r    5 IPHVLIIEARFYE-NLSAMLFEGCVNVLHSRAVQWS-SIVTPGVLEI-PAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         5 ~~kI~IV~s~~~~-~i~~~ll~ga~~~l~~~~~~~~-~i~VPGa~Ei-P~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      ..||+++...++. +....-.+|+.+.+.+++.+.. .+..+...+- -..+..++   ....++||++|.         
T Consensus       116 ~~~i~~i~~~~~~~~~~~~R~~Gf~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~~~~~~~ai~~~---------  183 (266)
T cd06282         116 HRRIAMLAGRLAASDRARQRYAGYRAAMRAAGLAPLPPVEIPFNTAALPSALLALL---TAHPAPTAIFCS---------  183 (266)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEECCCHHHHHHHHHHHH---HCCCCCCEEEEC---------
T ss_conf             95699997778888689999999999999869997617993487268999999998---379998479853---------


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             46789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                       .|.++-.+.+++.+..  ..+|=-..|++-+|...+.--.      .-....-|..|++.++++++
T Consensus       184 -nD~~A~g~l~al~~~g--~~vP~disIigfd~~~~~~~~~P~lTti~q~~~~~g~~A~~~l~~~i~  247 (266)
T cd06282         184 -NDLLALAVIRALRRLG--LRVPDDLSVVGFDGIAIGRLLTPPLATVAQPNRDIGRQAVQRLLARIA  247 (266)
T ss_pred             -CCHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHCCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             -8889999999999849--999998499998970899707999679986999999999999999977


No 64 
>cd03132 GATase1_catalase Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Catalase catalyzes the dismutation of hydrogen peroxide (H2O2) to water and oxygen. This group includes the large catalases: Neurospora crassa Catalase-1 and Catalase-3 and, Escherichia coli HP-II.  This GATase1-like domain has an essential role in HP-II catalase activity.  However, it lacks enzymatic activity and the catalytic triad typical of GATase1 domains. Catalase-1 and -3 are homotetrameric, HP-II is homohexameric. It has been proposed that this domain may facilitate the folding and oligomerization process. The interface between this GATase1-like domain of HP-II and the core of the subunit forms part of a channel which provides access to the deeply buried catalase active sites of HPII.  Catalase-1 is associated with non-growing cells; C
Probab=87.25  E-value=0.85  Score=26.00  Aligned_cols=107  Identities=18%  Similarity=0.194  Sum_probs=64.2

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-HHH----HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             7179998031289999999999999998799555553-001----44226999999863311378535665412000665
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-TPG----VLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-VPG----a~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      .||+|..+.   ...+.-+...++.|.+.|+.++++- -.|    .-.-+..++.-+. ...+..|||++..|    |..
T Consensus         2 rkVaiLv~d---g~~~~e~~~~~~al~~aG~~v~via~~~g~v~~~~g~~~~vd~t~~-~~~s~~fDAvvipg----G~~   73 (142)
T cd03132           2 RKVGILVAD---GVDAAELSALKAALKAAGANVKVVAPTLGGVVDSDGKTLEVDQTYA-GAPSVLFDAVVVPG----GAE   73 (142)
T ss_pred             CEEEEEECC---CCCHHHHHHHHHHHHHCCCEEEEEECCCCCEECCCCCEEECCEEEC-CCCHHHCCEEEECC----CCC
T ss_conf             889999669---9888999999999998899899995798707758998880544353-68964713688438----877


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC
Q ss_conf             24678999999999999974399705654255889999995065
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP  124 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~  124 (149)
                      .-..+-.+.-+..+.+=+.+|++||+.-    ..-.+.++.++.
T Consensus        74 ~~~~L~~~~~~~~fv~eay~h~KpI~a~----~~~~~lL~~agi  113 (142)
T cd03132          74 AAFALAPSGRALHFVTEAFKHGKPIGAV----GEGSDLLEAAGI  113 (142)
T ss_pred             CHHHHCCCHHHHHHHHHHHHCCCEEEEE----CCHHHHHHHCCC
T ss_conf             9888644867999999999769979993----772999997697


No 65 
>cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold.  Hence, they are structurally homologous to the periplasmic sugar bindi
Probab=86.95  E-value=2.9  Score=22.74  Aligned_cols=124  Identities=10%  Similarity=0.069  Sum_probs=75.7

Q ss_pred             CEEEEEEE-----CHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEEC
Q ss_conf             71799980-----312899999999999999987995555530014422699---9999863311378535665412000
Q gi|254780346|r    6 PHVLIIEA-----RFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMR   77 (149)
Q Consensus         6 ~kI~IV~s-----~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIk   77 (149)
                      .||+.+.+     ..+....+.=+.|..+.+.++|.........|.|.....   ++.+++.. ....+||++|.     
T Consensus       113 r~I~~i~g~~~~~~~~~~~~~~R~~Gy~~al~~~g~~~~~~~~~~~~~~~~g~~~~~~~l~~~-~~~~ptAi~~~-----  186 (270)
T cd01544         113 TRIGFIGGEEKTTDGHEYIEDPRETAFREYMKEKGLYDPELIYIGDFTVESGYQLMKEALKSL-GDNLPTAFFIA-----  186 (270)
T ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCHHHHHHHHHHHHHCC-CCCCCCEEEEC-----
T ss_conf             869999577667751225689999999999998599996449966899799999999999728-87899789982-----


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH------CCCCCCCHHHHHHHHHHHHH
Q ss_conf             665246789999999999999743997056542558899999950------65657456999999999999
Q gi|254780346|r   78 GKTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV------SPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        78 GeT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~------~~~~~nkG~eaa~Aal~mi~  142 (149)
                           .|.++-.+.+++.+..  ..+|==..|++.+|..-+.--.      .-.....|.+|++.+++.++
T Consensus       187 -----nD~~A~g~l~~l~~~g--l~VP~DisviGfDd~~~~~~~~P~LTTV~q~~~~iG~~A~~~Ll~~i~  250 (270)
T cd01544         187 -----SDPMAIGALRALQEAG--IKVPEDVSVISFNDIEVAKYVSPPLSTVKIDTEEMGETAVDLLLERIN  250 (270)
T ss_pred             -----CCHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             -----3188999999999879--988776599997780789826899369982999999999999999961


No 66 
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=86.82  E-value=2.9  Score=22.70  Aligned_cols=121  Identities=16%  Similarity=0.142  Sum_probs=73.3

Q ss_pred             CCEEEEEEEC-HHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             8717999803-12899999999999999987995555530014422699---9999863311378535665412000665
Q gi|254780346|r    5 IPHVLIIEAR-FYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         5 ~~kI~IV~s~-~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      -.||+++... .+......=+.|..+.+.++|.+...+. .+.|....+   ++.+++    ..++||++|.        
T Consensus       114 hr~I~~i~~~~~~~~~~~~R~~G~~~al~~~g~~~~~~~-~~~~~~~~~~~~~~~ll~----~~~~~Ai~~~--------  180 (259)
T cd01542         114 HKNIAYLGVSESDIAVGILRKQGYLDALKEHGICPPNIV-ETDFSYESAYEAAQELLE----PQPPDAIVCA--------  180 (259)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEE-ECCCCHHHHHHHHHHHHH----CCCCCCEEEC--------
T ss_conf             985999955865606799999999999997699963599-657877789999999974----5799832434--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             2467899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+++.+..  ..+|==..|++-+|...+.--.-      .....-|+.|++.++++++
T Consensus       181 --nD~~A~g~~~~l~~~g--~~vP~Disvigfdd~~~~~~~~P~LTtv~q~~~~~G~~A~~~Ll~~i~  244 (259)
T cd01542         181 --TDTIALGAMKYLQELG--RRIPEDISVAGFGGYELSSVVTPSLTTVDFGYKEAGKKAAELLLQLIE  244 (259)
T ss_pred             --CHHHHHHHHHHHHHCC--CCCCCCEEEEEECCHHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             --5899999999999819--999998699998982999826899789995999999999999999966


No 67 
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=86.31  E-value=3.1  Score=22.53  Aligned_cols=62  Identities=16%  Similarity=0.159  Sum_probs=30.4

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH-HHHHHHHHHCCCCCCEEEEEE
Q ss_conf             71799980312899999999999999987995555530014422699-999986331137853566541
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA-VSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a-~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      +|++||...   ...+.+.+...+.|++.|+++....++|  |.+.. ++...+ ..+..++|.||++|
T Consensus        30 ~r~liVtd~---~~~~~~~~~v~~~L~~~gi~~~~~~~~~--~pt~~~v~~~~~-~~~~~~~D~IiavG   92 (366)
T PRK09423         30 KRALLIADE---FVLGIVGDTVEASLKDAGLDVVFEVFNG--ECSDNEIDRLVA-IAEENGCDVIIGIG   92 (366)
T ss_pred             CEEEEEECC---HHHHHHHHHHHHHHHHCCCEEEEEECCC--CCCHHHHHHHHH-HHHHCCCCEEEEEC
T ss_conf             958999895---2899899999999986798699973389--999999999999-99864999899937


No 68 
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=85.56  E-value=3.4  Score=22.30  Aligned_cols=87  Identities=10%  Similarity=0.132  Sum_probs=54.4

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHH
Q ss_conf             17999803128999999999999999879955555300144226999999863311378535665412000665246789
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVI   86 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I   86 (149)
                      ||+++........=..+.+|+.+..++.|+++..+..+|-..+.-=++.+-+  .....+||+|.-       ..-.+-+
T Consensus         1 ki~v~~~~l~npfw~~~~~Ga~~aA~e~G~~v~~~~~~~~~d~~~Qi~~ie~--~i~~gvDaIii~-------p~d~~al   71 (268)
T cd06306           1 KLCVLYPHLKDAYWLSVNYGMVEEAKRLGVSLKLLEAGGYPNLAKQIAQLED--CAAWGADAILLG-------AVSPDGL   71 (268)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHH--HHHCCCCEEEEC-------CCCHHHH
T ss_conf             9899957889879999999999999996997999958999999999999999--998399999986-------7986777


Q ss_pred             HHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             9999999999997439970565
Q gi|254780346|r   87 AHAVTRGLVDLSINGSLPIGNG  108 (149)
Q Consensus        87 ~~~v~~gl~~lsl~~~~PI~~g  108 (149)
                           ..+.+. .+.++||+.-
T Consensus        72 -----~~~~~a-~~agIPVV~~   87 (268)
T cd06306          72 -----NEILQQ-VAASIPVIAL   87 (268)
T ss_pred             -----HHHHHH-HHCCCEEEEE
T ss_conf             -----899999-9869829999


No 69 
>PRK09140 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed
Probab=85.48  E-value=1.9  Score=23.87  Aligned_cols=106  Identities=10%  Similarity=0.180  Sum_probs=72.3

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE-EE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             8717999803128999999999999999879955-55-530014422699999986331137853566541200066524
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQW-SS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~-~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      .+=|+|+.+.-.++.     ....+.|.+.|+.. |+ .++|+++|+   ++.+-+    ...-+..|-.|.|...|+-+
T Consensus        10 ~plvaIlR~~~~~~a-----~~~~~al~~~Gi~~iEVTl~tp~a~~~---I~~l~~----~~~~~~~iGAGTVlt~e~~~   77 (206)
T PRK09140         10 LPLIAILRGITPDEA-----LAHVGALIEAGFRAIEIPLNSPDPFDS---IAALVK----ALGDDALIGAGTVLSPEQVD   77 (206)
T ss_pred             CCEEEEEECCCHHHH-----HHHHHHHHHCCCCEEEEECCCCCHHHH---HHHHHH----HCCCCEEEEEEECCCHHHHH
T ss_conf             997999958999999-----999999998699889991799769999---999999----67986599862046799999


Q ss_pred             HHH-------HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             678-------9999999999999743997056542558899999950
Q gi|254780346|r   83 CDV-------IAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        83 ~e~-------I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                      .-.       ||-.....+.+.+.++++|.+-|++|+....||+++-
T Consensus        78 ~ai~aGA~FiVSP~~~~~vi~~a~~~~i~~iPG~~TPsEi~~A~~~G  124 (206)
T PRK09140         78 RLADAGGRLIVTPNIDPEVIRRAVAYGMTVMPGVATPTEAFAALRAG  124 (206)
T ss_pred             HHHHCCCCEEECCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCC
T ss_conf             99985999999999989999999982996527859999999999859


No 70 
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=85.15  E-value=3.5  Score=22.18  Aligned_cols=124  Identities=12%  Similarity=0.045  Sum_probs=65.8

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCC-CCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             717999803128999999999999999879-9555553001442269999998633113785356654120006652467
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRA-VQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~-~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      .+|+++...-.....+ -++|+++.|.++. .........|.+....+.+..-+-.....++||++|.          .|
T Consensus       122 ~~i~~~~g~~~~~~~~-R~~G~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~p~~~aifa~----------nD  190 (271)
T cd06321         122 GNVAILNGPPVSAVLD-RVAGCKAALAKYPGIKLLSDDQNGKGSRDGGLRVMQGLLTRFPKLDGVFAI----------ND  190 (271)
T ss_pred             EEEEEECCCCCHHHHH-HHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CC
T ss_conf             0799975998535999-999999999877997688767228878999999999998508867789977----------86


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC--------CCCCCHHHHHHHHHHHHH
Q ss_conf             8999999999999974399705654255889999995065--------657456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP--------SHLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~--------~~~nkG~eaa~Aal~mi~  142 (149)
                      ..+-.+.+++.+...  +.|...|+-..++..+++.+-.+        ....-|+.|++.++++++
T Consensus       191 ~~A~Ga~~a~~~~G~--~~i~ivg~dg~~~~~~~~~~~~~~~~~tv~Q~~~~mG~~av~~l~~~i~  254 (271)
T cd06321         191 PTAIGADLAAKQAGR--NDIKITSVDGAPDAEKAILSGNSLIIATAAQDPRAMARKAVEIGYDILN  254 (271)
T ss_pred             HHHHHHHHHHHHCCC--CCCEEEEEECCHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             899999999997597--9998999969679999986699972799848999999999999999977


No 71 
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=84.22  E-value=3.9  Score=21.92  Aligned_cols=63  Identities=14%  Similarity=0.098  Sum_probs=35.7

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEE
Q ss_conf             179998031289999999999999998799555553001442269999998633113785356654
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVL   72 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaL   72 (149)
                      ||++|...-+.+.-..|.+|+++..++.|++... ..++-+...--++.+-+..  ...+|+++..
T Consensus         1 kia~v~~~~~n~f~~~~~~Ga~~aA~~lG~~v~~-~~da~~d~~~Q~~~i~~~I--~~gvDaIii~   63 (294)
T cd06316           1 KAAIVMHTSGSDWSNAQVRGAKDEFAKLGIEVVA-TTDAQFDPAKQVADIETTI--SQKPDIIISI   63 (294)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEE-ECCCCCCHHHHHHHHHHHH--HCCCCEEEEE
T ss_conf             9899957889989999999999999983998999-6699889999999999999--8599999993


No 72 
>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs. Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal  HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=83.20  E-value=4.3  Score=21.66  Aligned_cols=111  Identities=14%  Similarity=0.068  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEE-EEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             899999999999999987995555-530014422699---9999863311378535665412000665246789999999
Q gi|254780346|r   17 ENLSAMLFEGCVNVLHSRAVQWSS-IVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTR   92 (149)
Q Consensus        17 ~~i~~~ll~ga~~~l~~~~~~~~~-i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~   92 (149)
                      ......-++|+.+.|+++|..++. ....|.+.....   ++.++   ....++||++|.          .|.++-.+.+
T Consensus       131 ~~~~~~R~~Gf~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~ll---~~~~~p~Ai~~~----------nD~~A~g~l~  197 (269)
T cd06297         131 RTVFAERRAGFQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLL---EKASPPLAVFAS----------ADQQALGALQ  197 (269)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHH---HCCCCCCEEEEC----------CHHHHHHHHH
T ss_conf             268999999999999982998662234137863656999999998---369998589989----------7899999999


Q ss_pred             HHHHHHHHCCCCCEEEEECCCCHHHHHHHHC----CCCCCCHHHHHHHHHHHHH
Q ss_conf             9999997439970565425588999999506----5657456999999999999
Q gi|254780346|r   93 GLVDLSINGSLPIGNGIVVVDSEQQAFDRVS----PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        93 gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~----~~~~nkG~eaa~Aal~mi~  142 (149)
                      ++.+.  ...+|==..|++-+|...+..-+-    .....-|+.|++..+++++
T Consensus       198 ~l~~~--Gi~vP~DisviGfDd~~~a~~~~LTTv~q~~~~~G~~A~~~Ll~~i~  249 (269)
T cd06297         198 EAVEL--GLTVGEDVRVVGFDDHPFAREAGLSTLAQPVEAMGARAAQLLLERLE  249 (269)
T ss_pred             HHHHC--CCCCCCCEEEEEECCHHHHHCCCCCEEECCHHHHHHHHHHHHHHHHC
T ss_conf             99983--99889966999989848972489867963999999999999999966


No 73 
>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA b
Probab=82.43  E-value=4.6  Score=21.48  Aligned_cols=122  Identities=19%  Similarity=0.205  Sum_probs=69.0

Q ss_pred             CEEEEEEECHHHHHH-HHHHHHHHHHHHHCCCCEEE--EEHHH--HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCC
Q ss_conf             717999803128999-99999999999987995555--53001--44226999999863311378535665412000665
Q gi|254780346|r    6 PHVLIIEARFYENLS-AMLFEGCVNVLHSRAVQWSS--IVTPG--VLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKT   80 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~-~~ll~ga~~~l~~~~~~~~~--i~VPG--a~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT   80 (149)
                      .||+++.......-+ ..-.+|+.+.+.+++.....  +..++  .-+...+++.+++   ...++||++|.        
T Consensus       117 ~~i~~i~~~~~~~~~~~~R~~g~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~---~~~~~~aii~~--------  185 (267)
T cd06283         117 ERILFVTEPLDEISPRMERYEGFKEALAEHGIGVNEELIEIDDEDADELDERLRQLLN---KPKKKTAIFAA--------  185 (267)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHH---CCCCCCEECCC--------
T ss_conf             7299995687788379999999999999759976514898335426779999999984---79998642037--------


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC------CCCCCCHHHHHHHHHHHHH
Q ss_conf             2467899999999999997439970565425588999999506------5657456999999999999
Q gi|254780346|r   81 AHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS------PSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        81 ~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~------~~~~nkG~eaa~Aal~mi~  142 (149)
                        .|.++-.+.+.+.+..  ..+|=-..|.+.++.+++.--.-      .....-|+.|++.++++++
T Consensus       186 --~D~~A~g~~~~l~~~g--~~vP~disVvg~dd~~~~~~~~p~lTtv~~~~~~~g~~av~~l~~~i~  249 (267)
T cd06283         186 --NGLILLEVLKALKELG--IRIPEDVGLIGFDDTEWAELIGPGITTIAQPTYEMGKTAAELLLERIE  249 (267)
T ss_pred             --CCHHHHHHHHHHHHCC--CCCCCCCEEEEECCHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             --7099999999999829--988987668853886999842999539983999999999999999977


No 74 
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=82.23  E-value=4.7  Score=21.43  Aligned_cols=36  Identities=3%  Similarity=-0.028  Sum_probs=24.2

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             179998031289999999999999998799555553
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV   42 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~   42 (149)
                      ||++|......+.-..+.+|+++..++.|++.....
T Consensus         1 kIa~~~~~~~~~f~~~~~~G~~~~A~~~G~~~~v~d   36 (273)
T cd06305           1 RIAVVRYGGSGDFDQAYLAGTKAEAEALGGDLRVYD   36 (273)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             989997178897999999999999997499899973


No 75 
>PRK13805 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional
Probab=80.54  E-value=5.3  Score=21.07  Aligned_cols=62  Identities=21%  Similarity=0.290  Sum_probs=41.2

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-H---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             87179998031289999999999999998799555553-0---014422699999986331137853566541
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-T---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      .+|.+||.-++-.  .-++++...+.|++.|++++++. |   |-.-.+--.++.+     +..++|.+|+||
T Consensus       482 ~kralIVTD~~~~--~~G~vd~v~~~L~~~gi~~~vFd~V~pdPt~~~V~~G~~~~-----~~~~~D~IIalG  547 (862)
T PRK13805        482 KKRAFIVTDRGMV--ELGYVDKVTDVLRANGVETEVFSEVEPDPTLSTVRKGAELM-----RSFKPDTIIALG  547 (862)
T ss_pred             CCEEEEECCHHHH--HCCCHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHH-----HHCCCCEEEEEC
T ss_conf             9779998785187--67889999999998698399966989993979999999999-----864999999947


No 76 
>PRK13055 putative lipid kinase; Reviewed
Probab=80.50  E-value=5.4  Score=21.06  Aligned_cols=89  Identities=15%  Similarity=0.172  Sum_probs=55.5

Q ss_pred             CCCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEH---HH-HHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECC
Q ss_conf             5871799980312-899999999999999987995555530---01-442269999998633113785356654120006
Q gi|254780346|r    4 FIPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVT---PG-VLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRG   78 (149)
Q Consensus         4 ~~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~V---PG-a~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkG   78 (149)
                      ||+|+++|+=..= ..-..+.+....+.|.+.+++...+..   || +.++       .+ .+....||.+|+.|    |
T Consensus         1 MmKr~~lIvNP~SG~g~~~~~~~~i~~~L~~~g~e~~~~~tt~~~~~a~~~-------a~-~a~~~g~d~Iva~G----G   68 (334)
T PRK13055          1 MQKRARLIYNPTSGQEIMKKNVADILDILEQAGYETSAFQTTPEPNSAKNE-------AR-RAAKAGFDLIIAAG----G   68 (334)
T ss_pred             CCEEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEECCCCHHHHH-------HH-HHHHCCCCEEEEEC----C
T ss_conf             970699999987789757889999999999869859999944178579999-------99-87657998999987----7


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             65246789999999999999743997056542558
Q gi|254780346|r   79 KTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        79 eT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                      |=.     -++|.+|++    ..+.|...|||.+.
T Consensus        69 DGT-----inevvngl~----~~~~~~~LgiIP~G   94 (334)
T PRK13055         69 DGT-----INEVVNGIA----PLEKRPKMAIIPAG   94 (334)
T ss_pred             CCH-----HHHHHHHHH----CCCCCCEEEEEECC
T ss_conf             608-----999999873----46999718998077


No 77 
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=80.36  E-value=5.4  Score=21.03  Aligned_cols=35  Identities=11%  Similarity=0.171  Sum_probs=20.0

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             17999803128999999999999999879955555
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI   41 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i   41 (149)
                      +|++|..+.....-..+++|..+.+.++|+..-..
T Consensus         1 ~IGvivp~l~n~ff~~~~~gi~~~~~~~gy~~li~   35 (273)
T cd01541           1 NIGVITTYISDYIFPSIIRGIESVLSEKGYSLLLA   35 (273)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             98999588765799999999999999869989999


No 78 
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=80.31  E-value=5.4  Score=21.02  Aligned_cols=116  Identities=16%  Similarity=0.198  Sum_probs=68.7

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHH
Q ss_conf             71799980312899999999999999987995555530014422699999986331137853566541200066524678
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDV   85 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~   85 (149)
                      ++|.++++. .++-+..+++..+..+..+|+++-...+|-+-|+|.+.+-+.      ++.|++...       |   |.
T Consensus       160 k~Igv~Y~p-~E~ns~~l~eelk~~A~~~Gl~vve~~v~~~ndi~~a~~~l~------g~~d~i~~p-------~---dn  222 (322)
T COG2984         160 KSIGVLYNP-GEANSVSLVEELKKEARKAGLEVVEAAVTSVNDIPRAVQALL------GKVDVIYIP-------T---DN  222 (322)
T ss_pred             EEEEEEECC-CCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHHHC------CCCCEEEEE-------C---CH
T ss_conf             069999579-886608999999999987798899983476320089999734------787679986-------6---06


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCC---HHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf             99999999999997439970565425588---9999995065657456999999999999
Q gi|254780346|r   86 IAHAVTRGLVDLSINGSLPIGNGIVVVDS---EQQAFDRVSPSHLDRGGCAARSALAMIE  142 (149)
Q Consensus        86 I~~~v~~gl~~lsl~~~~PI~~gILt~~n---~~QA~~R~~~~~~nkG~eaa~Aal~mi~  142 (149)
                      -..+....+...+.+.++|++.    .++   ++-|..-++.+..+-|.+++.-+.++++
T Consensus       223 ~i~s~~~~l~~~a~~~kiPli~----sd~~~V~~Ga~aA~gvdy~~~G~qtg~~v~~ILk  278 (322)
T COG2984         223 LIVSAIESLLQVANKAKIPLIA----SDTSSVKEGALAALGVDYKDLGKQTGEMVVKILK  278 (322)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEC----CCHHHHHCCCCEEECCCHHHHHHHHHHHHHHHHC
T ss_conf             7788899999998870897354----7778876686036606799988999999999976


No 79 
>PRK09701 D-allose transporter subunit; Provisional
Probab=80.22  E-value=5.5  Score=21.00  Aligned_cols=89  Identities=9%  Similarity=0.085  Sum_probs=56.0

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      ..+|++|...+....-..+.+|+.+..++.|++++.+..|.--....=++.+-+.  ....+||++.--.          
T Consensus        24 ~~~iavi~k~~~npf~~~~~~Ga~~aAk~~G~~v~v~~~~~~~D~~~Qi~~Ie~~--I~~gvdaIii~p~----------   91 (311)
T PRK09701         24 AAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFASPSEGDFQSQLQLFEDL--SNKNYKGIAFAPL----------   91 (311)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHHH--HHCCCCEEEEECC----------
T ss_conf             6849999688899899999999999999869979999279878999999999999--9759999999189----------


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             89999999999999743997056
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGN  107 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~  107 (149)
                        .........+-..+.++||+.
T Consensus        92 --d~~a~~~~i~~A~~aGIpVV~  112 (311)
T PRK09701         92 --SSVNLVMPVARAWKKGIYLVN  112 (311)
T ss_pred             --CHHHHHHHHHHHHHCCCCEEE
T ss_conf             --877889999999977991896


No 80 
>PRK05569 flavodoxin; Provisional
Probab=79.25  E-value=5.5  Score=21.01  Aligned_cols=101  Identities=14%  Similarity=0.017  Sum_probs=58.8

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      |+||+||+.+-| .=|+.|-+...+.+.+.|++++...+.   +.+  ...++       ++|+ |++||    -|.+.+
T Consensus         1 M~Kv~IvY~S~~-GnTe~mA~~IaeG~~~~G~ev~v~~~~---~~~--~~di~-------~~d~-i~~Gs----pT~~~~   62 (141)
T PRK05569          1 MKKVSIIYWSCG-GNVEVLANTIADGAKEAGAEVTIKHVA---DAK--VEDVL-------EADA-VAFGS----PSMDNN   62 (141)
T ss_pred             CCEEEEEEECCC-CHHHHHHHHHHHHHHHCCCEEEEEECC---CCC--HHHHH-------HCCE-EEEEC----CCCCCC
T ss_conf             974999998996-089999999999999769819999842---399--88997-------1890-59905----455888


Q ss_pred             HHHH-HH---HHHHHHHHHHCCCCCEEEEECCC---CHHHHHHHHC
Q ss_conf             8999-99---99999999743997056542558---8999999506
Q gi|254780346|r   85 VIAH-AV---TRGLVDLSINGSLPIGNGIVVVD---SEQQAFDRVS  123 (149)
Q Consensus        85 ~I~~-~v---~~gl~~lsl~~~~PI~~gILt~~---n~~QA~~R~~  123 (149)
                      .+-+ .+   ...+..+.++..+-..||--.-.   ...+..+|..
T Consensus        63 ~~~~~~~~~~l~~l~~~~~~~K~~a~FGSyGW~~Ge~~~~~~~~l~  108 (141)
T PRK05569         63 NIEQEEMAPFLDQFKLTPNENKKCILFGSYGWDNGEFMKLWKDRMK  108 (141)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf             7771769999999853455898899996677886469999999999


No 81 
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=79.25  E-value=5.9  Score=20.81  Aligned_cols=33  Identities=3%  Similarity=0.108  Sum_probs=15.0

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             179998031289999999999999998799555
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWS   39 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~   39 (149)
                      ||+++...+....-..|.+|+.+..++.|.+++
T Consensus         1 kIGv~~~~~~npF~~~~~~g~e~~a~e~g~~v~   33 (303)
T cd01539           1 KIGVFLYKFDDTFISLVRKNLEDIQKENGGKVE   33 (303)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEE
T ss_conf             989996488998999999999999998599579


No 82 
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=78.78  E-value=6.1  Score=20.72  Aligned_cols=123  Identities=12%  Similarity=0.089  Sum_probs=72.3

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      ..+++++.......-...-.+|+.+.|+++++++-.+ ..+.++.+-+.+.+-.......+.|++++..          +
T Consensus       120 ~g~v~i~~g~~~~~~~~~R~~Gf~~~l~~~~~~iv~~-~~~~~~~~~a~~~~~~~L~~~pdi~~i~~~~----------~  188 (271)
T cd06314         120 GGKVAIFVGSLGADNAKERIQGIKDAIKDSKIEIVDT-RGDEEDFAKAKSNAEDALNAHPDLKCMFGLY----------A  188 (271)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEE-ECCCCCHHHHHHHHHHHHHHCCCCCEEEEEC----------C
T ss_conf             9869999458998789999999999996258579875-1577638899999999997589987899808----------8


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH
Q ss_conf             899999999999997439970565425588999999506565---------7456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~  142 (149)
                      ..+..+.+++.+......+.    |.+.+...++.+......         -.-|+.+.+++.+.++
T Consensus       189 ~~a~ga~~Al~~~g~~~~i~----vvg~D~~~~~~~~i~~G~i~~tv~Q~p~~~G~~av~~~~~~l~  251 (271)
T cd06314         189 YNGPAIAEAVKAAGKLGKVK----IVGFDEDPDTLQGVKEGTIQGTVVQRPYQMGYLSVTVLAALLK  251 (271)
T ss_pred             CCHHHHHHHHHHHCCCCCCE----EEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             51699999999847589967----9987898999999982998599838999999999999999976


No 83 
>PRK05568 flavodoxin; Provisional
Probab=78.29  E-value=5.6  Score=20.92  Aligned_cols=38  Identities=5%  Similarity=-0.032  Sum_probs=30.5

Q ss_pred             CCEEEEEE-ECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHH
Q ss_conf             87179998-03128999999999999999879955555300
Q gi|254780346|r    5 IPHVLIIE-ARFYENLSAMLFEGCVNVLHSRAVQWSSIVTP   44 (149)
Q Consensus         5 ~~kI~IV~-s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VP   44 (149)
                      |+||+||+ |.|.+  |+.|-+--.+.+.+.|++++...+.
T Consensus         1 M~kv~IvY~S~~Gn--Te~mA~~Iaegl~~~Gv~V~~~~~~   39 (142)
T PRK05568          1 MKKLNIIYWSGTGN--TEAMANLIAEGAKENGLEVKLLNVS   39 (142)
T ss_pred             CCEEEEEEECCCCH--HHHHHHHHHHHHHHCCCEEEEEEEC
T ss_conf             97299999899854--9999999999998669839999800


No 84 
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily.  Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=77.87  E-value=6.5  Score=20.55  Aligned_cols=63  Identities=16%  Similarity=0.160  Sum_probs=34.6

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             17999803128999999999999999879955555300144226999999863311378535665
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIV   71 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIa   71 (149)
                      ||++|...+....-..+.+|+.+..+++|+.+.....++-.+..--.+.+-.  .....+||+|.
T Consensus         1 kIGviv~~~~npf~~~~~~g~e~~a~~~G~~v~v~~~~~~~d~~~q~~~i~~--~i~~~vdgii~   63 (275)
T cd06320           1 KYGVVLKTLSNEFWRSLKEGYENEAKKLGVSVDIQAAPSEGDQQGQLSIAEN--MINKGYKGLLF   63 (275)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHH--HHHCCCCEEEE
T ss_conf             9899948998889999999999999974998999968997589999999999--99749987987


No 85 
>PRK08104 consensus
Probab=77.43  E-value=3.5  Score=22.24  Aligned_cols=104  Identities=20%  Similarity=0.226  Sum_probs=70.3

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             717999803128999999999999999879955555--300144226999999863311378535665412000665246
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      +=|.|+..+ ..+-..    ...+.|.+.|+..-.|  +.|+++|.-   +.+.+     .-+|.+|-.|.|+.-|+-+.
T Consensus        16 ~iipVir~~-~~~~a~----~la~al~~gGi~~iEiTlrt~~a~~~I---~~l~~-----~~p~~~vGaGTV~~~e~~~~   82 (212)
T PRK08104         16 PVVPVIVIN-KLEHAV----PLAKALVAGGVRVLEVTLRTPCALEAI---RAIAK-----EVPEAIVGAGTVLNPQQLAE   82 (212)
T ss_pred             CEEEEEECC-CHHHHH----HHHHHHHHCCCCEEEEECCCCHHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHH
T ss_conf             868999779-999999----999999987998899968881499999---99998-----68985685420267999999


Q ss_pred             HH-------HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             78-------9999999999999743997056542558899999950
Q gi|254780346|r   84 DV-------IAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        84 e~-------I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                      -.       ||-.....+.+.+.++++|.+=|+.|+....||++.-
T Consensus        83 ai~aGA~FiVSP~~~~~v~~~a~~~~i~~iPGv~TpsEi~~A~~~G  128 (212)
T PRK08104         83 VTEAGAQFAISPGLTEELLKAATEGTIPLIPGISTVSELMLGMDYG  128 (212)
T ss_pred             HHHCCCCEEECCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHCC
T ss_conf             9985999998489999999999982997656769999999999879


No 86 
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=77.30  E-value=3.1  Score=22.52  Aligned_cols=93  Identities=13%  Similarity=0.037  Sum_probs=66.8

Q ss_pred             HHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHH
Q ss_conf             9999999879955555--3001442269999998633113785356654120006652467-------899999999999
Q gi|254780346|r   26 GCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVD   96 (149)
Q Consensus        26 ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~   96 (149)
                      ...+.|.+.|+..-.|  +.|+++|.-..+.+...    ...+|..|-.|.|+.-++-+--       .||-.....+.+
T Consensus        32 ~~a~aL~~gGi~~iEiTlrt~~a~~~i~~l~~~~~----~~~p~~~iGaGTVl~~~~~~~a~~aGA~FiVSP~~~~~v~~  107 (223)
T PRK07114         32 KVVKACYDGGVRAFEFTNRGDFAHEVFGELVKYAA----KECPEMILGVGSIVDAATAALYIQLGANFVVGPLFNEDIAK  107 (223)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHH----HHCCCCEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHH
T ss_conf             99999998899889995889658999999999998----66898089655188999999999859989999999999999


Q ss_pred             HHHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             99743997056542558899999950
Q gi|254780346|r   97 LSINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        97 lsl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                      ...++++|.+-|+.|+....+|++.-
T Consensus       108 ~~~~~~~~~iPGv~TptEi~~A~~~G  133 (223)
T PRK07114        108 VCNRRKIPYSPGCGSVSEIGFAEELG  133 (223)
T ss_pred             HHHHCCCCCCCCCCCHHHHHHHHHCC
T ss_conf             99983997537319999999999879


No 87 
>pfam00465 Fe-ADH Iron-containing alcohol dehydrogenase.
Probab=76.91  E-value=6.9  Score=20.39  Aligned_cols=61  Identities=20%  Similarity=0.279  Sum_probs=39.1

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-H---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             7179998031289999999999999998799555553-0---014422699999986331137853566541
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-T---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      +|++||.++.-.  ...+++...+.|++.++++..+. +   |-.-++--+++.     .+..++|.||++|
T Consensus        23 ~r~llVt~~~~~--~~g~~~~l~~~L~~~~~~~~~~~~v~~~p~~~~v~~~~~~-----~~~~~~D~IIaiG   87 (312)
T pfam00465        23 ARALIVTDPSLK--KLGLLDRVLDSLEEAGIEVVVFDGVEPNPTLEEVDEAAAA-----AREEGADVIIAVG   87 (312)
T ss_pred             CEEEEEECCCHH--HCCHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHH-----HHHCCCCEEEECC
T ss_conf             979999895856--6763999999999749949998582799999999999999-----9964998999808


No 88 
>PRK10310 galactitol-specific PTS system component IIB; Provisional
Probab=75.95  E-value=7.3  Score=20.23  Aligned_cols=84  Identities=13%  Similarity=0.078  Sum_probs=53.3

Q ss_pred             CCCEEEEEEECHHHHHHHHHHH-HHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             5871799980312899999999-999999987995555530014422699999986331137853566541200066524
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFE-GCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~-ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      |++||++.+..==.  |..+.. -..+.++++|++++...++ .-|+|          ...+.+|.+|...-+       
T Consensus         1 MkKkIlVACGsGIA--TSTvva~kv~~~~~e~gi~v~i~Q~~-i~ev~----------~~~~~~DlivtTt~~-------   60 (94)
T PRK10310          1 MKRKIIVACGGAVA--TSTMAAEEIKELCQSHNIPVELIQCR-VNEIE----------TYMDGVHLICTTARV-------   60 (94)
T ss_pred             CCCEEEEECCCCHH--HHHHHHHHHHHHHHHCCCEEEEEEEE-HHHHH----------HCCCCCCEEEEECCC-------
T ss_conf             99559998588375--99999999999999859806899974-78755----------416897789992253-------


Q ss_pred             HHHHHHHHHHHHHHHHHHC-CCCCEEEE--ECCCCHHHHHHHH
Q ss_conf             6789999999999999743-99705654--2558899999950
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSING-SLPIGNGI--VVVDSEQQAFDRV  122 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~-~~PI~~gI--Lt~~n~~QA~~R~  122 (149)
                                     .-++ ++|+++|+  ||==++++.++..
T Consensus        61 ---------------~~~~g~iPvi~g~~fLTGiG~d~~~~~I   88 (94)
T PRK10310         61 ---------------DRSFGDIPLVHGMPFVSGVGIEALQNKI   88 (94)
T ss_pred             ---------------CCCCCCCCEEECCCCCCCCCHHHHHHHH
T ss_conf             ---------------7765888779634200037889999999


No 89 
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily.  LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=75.51  E-value=7.5  Score=20.15  Aligned_cols=123  Identities=14%  Similarity=0.091  Sum_probs=62.3

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC-EEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             71799980312899999999999999987995-5555-300144226999999863311378535665412000665246
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ-WSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~-~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      .+|+++...-...-...-.+|+.+.+++.+.+ .+++ ..++-+...-+.+..-.-.....+.|++++.          .
T Consensus       124 g~v~i~~g~~~~~~~~~R~~g~~~~l~~~~~~~~~vv~~~~~~~~~~~a~~~~~~~L~~~Pdi~~I~~~----------n  193 (298)
T cd06302         124 GEYAIFVGSLTATNQNAWIDAAKAYQKEKYYPMLELVDRQYGDDDADKSYQTAQELLKAYPDLKGIIGP----------T  193 (298)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEC----------C
T ss_conf             958999858898679999999999986348998799986137874899999999999759991299978----------9


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH
Q ss_conf             7899999999999997439970565425588999999506565---------7456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~  142 (149)
                      +..+..+.++|.+..++..+. +.|.   +...++.+......         -.-|+.++++++++++
T Consensus       194 d~~a~Ga~~Al~~aG~~~~V~-vvG~---D~~~~~~~~I~~G~i~atv~Q~P~~~G~~av~~a~~~~~  257 (298)
T cd06302         194 SVGIPGAARAVEEAGLKGKVA-VTGL---GLPNQMAPYVKSGAVKEFALWNPADLGYAAVYVAKALLE  257 (298)
T ss_pred             CHHHHHHHHHHHHCCCCCCEE-EEEE---CCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             816999999999679999859-9996---887999999985982699984999999999999999977


No 90 
>PRK07580 Mg-protoporphyrin IX methyl transferase; Validated
Probab=73.76  E-value=4.3  Score=21.63  Aligned_cols=74  Identities=16%  Similarity=0.147  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf             89999999999999998799555553001442269999998633113785356654120006652467899999999999
Q gi|254780346|r   17 ENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVD   96 (149)
Q Consensus        17 ~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~   96 (149)
                      -||+..|++-|.+...+.|....+-+..|-+|-.            .+.||.|+|+.++|     ||.-  ......|..
T Consensus        91 vDiS~~mi~~A~~Ra~~~g~~~~v~F~~gDle~~------------~G~FD~Vv~mdvLi-----HYp~--~d~~~~l~~  151 (230)
T PRK07580         91 SDISPQMVEEARERAPEAGLDGNITFEVGDLESL------------LGSFDTVVCLDVLI-----HYPQ--EDAERMLAH  151 (230)
T ss_pred             EECCHHHHHHHHHHHHHHCCCCCCEEEECCCCCC------------CCCCCCHHHCCCEE-----ECCH--HHHHHHHHH
T ss_conf             8389999999997558627876753896676545------------79866023337155-----4578--899999999


Q ss_pred             HHHHCCCCCEEEE
Q ss_conf             9974399705654
Q gi|254780346|r   97 LSINGSLPIGNGI  109 (149)
Q Consensus        97 lsl~~~~PI~~gI  109 (149)
                      ++-..+-.++|-.
T Consensus       152 la~~~~~~~ifTf  164 (230)
T PRK07580        152 LASLTRGSLIFTF  164 (230)
T ss_pred             HHHCCCCEEEEEE
T ss_conf             9725588599996


No 91 
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=73.08  E-value=8.6  Score=19.78  Aligned_cols=28  Identities=11%  Similarity=-0.015  Sum_probs=12.2

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHC
Q ss_conf             1799980312899999999999999987
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSR   34 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~   34 (149)
                      ||+++.+.....-...-.+|+.+.++++
T Consensus       123 ~i~~~~g~~~~~~~~~R~~gf~~a~~~~  150 (268)
T cd06323         123 KVVELQGIPGASAARERGKGFHEVVDKY  150 (268)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             6999638999858999999999999877


No 92 
>PRK07053 glutamine amidotransferase; Provisional
Probab=72.92  E-value=8.7  Score=19.76  Aligned_cols=101  Identities=18%  Similarity=0.149  Sum_probs=63.8

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHH-HHHHHHHHHHHHHCCCCCCEEEEEEEEECC-CCC
Q ss_conf             587179998031289999999999999998799555553001442-269999998633113785356654120006-652
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLE-IPAAVSMVMNAKTRSVTYDGIIVLGVVMRG-KTA   81 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~E-iP~a~~~~~~~~~~~~~~D~vIaLG~VIkG-eT~   81 (149)
                      ||+||+|+.-.-.+.-     .-..+.|.+.|+.++.+.+. .-+ +|          .....||++|.+|-=--- |++
T Consensus         1 mmk~ilvlqH~~~E~p-----G~i~~~l~~~g~~~~~~~~~-~~~~~p----------~~~~~~d~livlGGpms~~d~~   64 (235)
T PRK07053          1 MMKTAVAIRHVAFEDL-----GSFEQVLGERGYRVRYVDVG-VDDLEV----------LDALEPDLLVVLGGPIGVYDDA   64 (235)
T ss_pred             CCCEEEEEECCCCCCC-----HHHHHHHHHCCCEEEEEECC-CCCCCC----------CCCCCCCEEEEECCCCCCCCCC
T ss_conf             9953999968998898-----69999999789959999678-898899----------9966679999938998988776


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC
Q ss_conf             467899999999999997439970565425588999999506565
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH  126 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~  126 (149)
                      -|-++.+  -..+++-.++.++|+.=-=|.    .|.+.++-+..
T Consensus        65 ~~Pwl~~--e~~lIr~a~~~~~PvLGIClG----~QLlA~AlGG~  103 (235)
T PRK07053         65 LYPFLAP--EIALLRQRLAAGLPTLGICLG----AQLIARALGAR  103 (235)
T ss_pred             CCCCHHH--HHHHHHHHHHCCCCEEEECHH----HHHHHHHHCCE
T ss_conf             6855899--999999999869988998473----89999970977


No 93 
>PRK13411 molecular chaperone DnaK; Provisional
Probab=72.61  E-value=2.8  Score=22.76  Aligned_cols=89  Identities=21%  Similarity=0.259  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH-----CCCCCCEEEEEEEEECCCCCHHHHH
Q ss_conf             289999999999999998799555----5530014422699999986331-----1378535665412000665246789
Q gi|254780346|r   16 YENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT-----RSVTYDGIIVLGVVMRGKTAHCDVI   86 (149)
Q Consensus        16 ~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~-----~~~~~D~vIaLG~VIkGeT~H~e~I   86 (149)
                      ..++.++.++-+.+.|++.+...+    ++-|=|+-.+|..-+.+-+...     .+-++|-.||+|+-|+|..--    
T Consensus       303 ~~~L~~rt~~pv~~aL~dA~l~~~dId~ViLVGGSTRIP~Vq~~v~~~F~gk~~~~~iNPDEaVA~GAAiqa~iL~----  378 (655)
T PRK13411        303 AKDLVEATIEPVQQALKDAGLTPEDIDRIILVGGSTRIPAVQEAIQQFFGGKQPDRSVNPDEAVALGAAIQAGVLG----  378 (655)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHC----
T ss_conf             9999999998899999980998311789999888146579999999982899888897821689886999888753----


Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             999999999999743997056542558
Q gi|254780346|r   87 AHAVTRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        87 ~~~v~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                       ..    ..++.+---+|...||=|..
T Consensus       379 -g~----~~d~~llDV~PlsLGiet~g  400 (655)
T PRK13411        379 -GE----VKDLLLLDVTPLSLGIETLG  400 (655)
T ss_pred             -CC----CCCEEEEEECCCEEEEEECC
T ss_conf             -77----55438998427236889769


No 94 
>PRK06857 consensus
Probab=71.41  E-value=7.1  Score=20.29  Aligned_cols=88  Identities=15%  Similarity=0.152  Sum_probs=64.9

Q ss_pred             HHHHHHHCCCCEEE--EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHH-------HHHHHHHHHHHH
Q ss_conf             99999987995555--530014422699999986331137853566541200066524678-------999999999999
Q gi|254780346|r   27 CVNVLHSRAVQWSS--IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDV-------IAHAVTRGLVDL   97 (149)
Q Consensus        27 a~~~l~~~~~~~~~--i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~-------I~~~v~~gl~~l   97 (149)
                      ..+.|.+.|+..-.  .+.|+++|.-   +.+.+     ..+|.+|-.|.|...|+-+.=.       ||-.....+.+.
T Consensus        29 ~~~al~~gGi~~iEiTlrt~~a~~~I---~~l~~-----~~p~~~vGaGTV~~~e~~~~a~~aGA~FiVSP~~~~~v~~~  100 (209)
T PRK06857         29 LAKVLAENGLPVAEITFRSAAAAEAI---RLLRE-----AYPDMLIGAGTVLTPEQVDAAKEAGADFIVSPGFNPNTVKY  100 (209)
T ss_pred             HHHHHHHCCCCEEEEECCCCCHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHHHHCCCCEEECCCCCHHHHHH
T ss_conf             99999987998899958993299999---99997-----58994899993767999999998399999908999999999


Q ss_pred             HHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             9743997056542558899999950
Q gi|254780346|r   98 SINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        98 sl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                      +.++++|.+=|+.|+....+|++.-
T Consensus       101 a~~~~i~~iPGv~TpsEi~~A~~~G  125 (209)
T PRK06857        101 CQQLNIPIVPGVNNPSLVEQALEMG  125 (209)
T ss_pred             HHHCCCCEECCCCCHHHHHHHHHCC
T ss_conf             9974996547879999999999879


No 95 
>PRK09492 treR trehalose repressor; Provisional
Probab=70.61  E-value=9.8  Score=19.43  Aligned_cols=65  Identities=15%  Similarity=0.142  Sum_probs=33.3

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             871799980312899999999999999987995555530014422699999986331137853566541
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      .+.|++|..++.......++.+..+.+.++|+..-.....+.-+.   .+..++. -...++||+|..|
T Consensus        62 t~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy~~~i~~~~~~~~~---~~~~~~~-l~~~~vdGiIl~~  126 (315)
T PRK09492         62 DKVVGIIVSRLDSPSENLAVQTMLPAFYQQGYDPIIMESQFSPQL---VNEHLGV-LRRRNVDGVILFG  126 (315)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCHHH---HHHHHHH-HHHCCCCEEEEEC
T ss_conf             864666226778836789999999999974981899946899799---9999999-9967989899968


No 96 
>PRK07455 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=70.59  E-value=8.9  Score=19.70  Aligned_cols=102  Identities=16%  Similarity=0.158  Sum_probs=69.3

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             17999803128999999999999999879955555--3001442269999998633113785356654120006652467
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      =|.|+...=.+ -.    ....+.|.+.|+..-.|  +.|+++|.-   +.+.+     .-.|..|-.|.|..-|+-+.-
T Consensus        15 vi~Vlr~~~~~-~a----~~~~~al~~gGi~~iEiTl~t~~a~~~I---~~l~~-----~~p~~~iGaGTV~~~e~~~~a   81 (210)
T PRK07455         15 AIAVIRAPDLE-LG----LQMAEAVAAGGMRLIEITWNSDQPAELI---SQLRE-----KLPECIIGTGTLLTLEDLEEA   81 (210)
T ss_pred             EEEEEECCCHH-HH----HHHHHHHHHCCCCEEEEECCCCCHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHH
T ss_conf             79999759999-99----9999999987998899968998899999---99998-----789968988818789999999


Q ss_pred             -------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHH
Q ss_conf             -------8999999999999974399705654255889999995
Q gi|254780346|r   85 -------VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDR  121 (149)
Q Consensus        85 -------~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R  121 (149)
                             .||-.....+.+.+.++++|.+-|+.|+....+|++.
T Consensus        82 ~~aGA~FiVSP~~~~~vi~~a~~~~i~~iPGv~TpsEi~~A~~~  125 (210)
T PRK07455         82 IAAGAQFCFTPHVDLELIQAAVAADIPIIPGALTPTEIVTAWQA  125 (210)
T ss_pred             HHCCCCEEECCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHC
T ss_conf             98699999868888999999998299765886999999999986


No 97 
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=70.43  E-value=9.9  Score=19.41  Aligned_cols=125  Identities=10%  Similarity=0.077  Sum_probs=73.7

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCC-CCCCEEEEEEEEECCCCCH
Q ss_conf             8717999803128999999999999999879955555-3001442269999998633113-7853566541200066524
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRS-VTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~-~~~D~vIaLG~VIkGeT~H   82 (149)
                      ..+|+++........+..-.+|+.+.|.++. ..+.+ ..+|-|.-..+.+.+-...... .++|+++|.          
T Consensus       124 ~~~i~~i~g~~~~~~~~~R~~Gf~~~l~~~~-~~~iv~~~~~~~~~~~~~~~~~~~L~~~p~~i~ai~~~----------  192 (273)
T cd06309         124 KGNIVELQGTVGSSVAIDRKKGFAEVIKKYP-NMKIVASQTGDFTRAKGKEVMEALLKAHGDDIDAVYAH----------  192 (273)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHCC-CCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCEEEEC----------
T ss_conf             8079998289898599999999999998789-98676541234688999999999997278888889867----------


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC--------CCCHHHHHHHHHHHHH
Q ss_conf             67899999999999997439970565425588999999506565--------7456999999999999
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH--------LDRGGCAARSALAMIE  142 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~--------~nkG~eaa~Aal~mi~  142 (149)
                      .|.++-.+.+++.+..++  +|=-..|.+.++..+++++.....        -.-|+.|+++++++++
T Consensus       193 nd~~a~Ga~~al~~~G~~--~~~di~ivg~D~~~~~~~~i~~g~l~~~~~~~p~~G~~Av~~l~~~l~  258 (273)
T cd06309         193 NDEMALGAIQAIKAAGKK--PGKDIKIVSIDGTKDAFQAMADGKLNATVECNPLFGPLAFDTLEKYLA  258 (273)
T ss_pred             CCHHHHHHHHHHHHCCCC--CCCCEEEEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHC
T ss_conf             857999999999983999--999869999899999999987699719997839999999999999977


No 98 
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=70.18  E-value=9  Score=19.68  Aligned_cols=92  Identities=13%  Similarity=0.119  Sum_probs=66.2

Q ss_pred             HHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHH
Q ss_conf             9999999879955555--3001442269999998633113785356654120006652467-------899999999999
Q gi|254780346|r   26 GCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVD   96 (149)
Q Consensus        26 ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~   96 (149)
                      ...+.|.+.|+..-.|  +.|+++|.-   +.+.++  ....+|..|-.|.|+.-|+-+.=       .||-.....+.+
T Consensus        29 ~~~~al~~gGi~~iEITl~tp~a~~~i---~~l~~~--~~~~p~~~iGaGTV~~~e~~~~a~~aGA~FiVSP~~~~~v~~  103 (209)
T PRK06552         29 KISLAVIKGGIKAIEVTYTNPFASEVI---KELVER--YKDDPEVLIGAGTVLDAVTARQAILAGAQFIVSPSFNRETAK  103 (209)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCHHHHH---HHHHHH--HCCCCCEEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHH
T ss_conf             999999987998899967897599999---999998--177998189887274899999999859988976999899999


Q ss_pred             HHHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             99743997056542558899999950
Q gi|254780346|r   97 LSINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        97 lsl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                      .+.++++|.+-|+.|+....+|++.-
T Consensus       104 ~a~~~~i~~iPG~~TpsEi~~A~~~G  129 (209)
T PRK06552        104 ICNRYQIPYLPGCMTVTEIVTALEAG  129 (209)
T ss_pred             HHHHCCCCEECCCCCHHHHHHHHHCC
T ss_conf             99985996417979999999999869


No 99 
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=70.11  E-value=10  Score=19.37  Aligned_cols=32  Identities=6%  Similarity=0.002  Sum_probs=15.8

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             17999803128999999999999999879955
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQW   38 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~   38 (149)
                      ||++|..+.....-..+.+|+.+.+++.|++.
T Consensus         1 kIg~vv~~~~npF~~~~~~G~~~~a~~~G~~~   32 (277)
T cd06319           1 QIAYIVSDLRIPFWQIMGRGVKSKAKALGYDA   32 (277)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEE
T ss_conf             98999189998699999999999999729989


No 100
>COG0655 WrbA Multimeric flavodoxin WrbA [General function prediction only]
Probab=70.07  E-value=8.4  Score=19.83  Aligned_cols=40  Identities=18%  Similarity=0.098  Sum_probs=33.1

Q ss_pred             EEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHHHH
Q ss_conf             1799980312-899999999999999987995555530014
Q gi|254780346|r    7 HVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTPGV   46 (149)
Q Consensus         7 kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa   46 (149)
                      |+..|...+| ..-+..|++.+.+.+++.|++.+.+.+|+-
T Consensus         2 ki~~I~gs~r~~G~t~~l~~~~~~g~~~~G~E~~~i~v~~~   42 (207)
T COG0655           2 KILGINGSPRSNGNTAKLAEAVLEGAEEAGAEVEIIRLPEK   42 (207)
T ss_pred             EEEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEEECCC
T ss_conf             07899982699874999999999999864985899984788


No 101
>PRK13410 molecular chaperone DnaK; Provisional
Probab=68.96  E-value=5.7  Score=20.91  Aligned_cols=89  Identities=13%  Similarity=0.244  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHH
Q ss_conf             289999999999999998799555----5530014422699999986331----13785356654120006652467899
Q gi|254780346|r   16 YENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIA   87 (149)
Q Consensus        16 ~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~   87 (149)
                      ..++.++.++-+.+.|.++++..+    ++-|=|+--+|..-+.+-+...    .+-++|-+||+||-|++....-+   
T Consensus       304 ~~~L~~Rt~~pv~~aL~dAgl~~~dId~VILVGGSTRIP~Vq~~V~e~FGkep~~~iNPDEaVA~GAAiQA~iLsg~---  380 (719)
T PRK13410        304 CGDLVSRLRRPVKRALKDAGLSPVQIDEVVLVGGSTRMPMVKQLVRSLIDREPNQNVNPDEVVAVGAAIQAGILAGE---  380 (719)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCC---
T ss_conf             99999999999999999838994141399997882554889999999849997888997177503188864310477---


Q ss_pred             HHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             99999999999743997056542558
Q gi|254780346|r   88 HAVTRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        88 ~~v~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                            +.++-|---+|...||=|..
T Consensus       381 ------~~d~lllDVtPlSLGiet~g  400 (719)
T PRK13410        381 ------VKDILLLDVTPLSLGLETIG  400 (719)
T ss_pred             ------CCCEEEEEEECCCEEEEECC
T ss_conf             ------56538897315635898618


No 102
>PRK08904 consensus
Probab=68.56  E-value=9.9  Score=19.41  Aligned_cols=88  Identities=16%  Similarity=0.188  Sum_probs=64.8

Q ss_pred             HHHHHHHCCCCEEE--EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHHH
Q ss_conf             99999987995555--53001442269999998633113785356654120006652467-------8999999999999
Q gi|254780346|r   27 CVNVLHSRAVQWSS--IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVDL   97 (149)
Q Consensus        27 a~~~l~~~~~~~~~--i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~l   97 (149)
                      ..+.|.+.|+..-.  .+.|+++|.-   +.+.+     .-+|.+|-.|.|...++-+.=       .||-.....+.+.
T Consensus        27 ~a~al~~~Gi~~iEiTlrtp~a~~~i---~~l~~-----~~p~~~vGaGTVl~~e~~~~a~~aGA~FiVSP~~~~~v~~~   98 (207)
T PRK08904         27 LSRALVEGGIPTLEITLRTPVGLDAI---RLIAK-----EVPNAIVGAGTVTNPEQLKAVEDAGAVFAISPGLHESLAKA   98 (207)
T ss_pred             HHHHHHHCCCCEEEEECCCCHHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHHHHCCCCEEECCCCCHHHHHH
T ss_conf             99999987998899957991399999---99998-----68987685531368999999998499999848998999999


Q ss_pred             HHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             9743997056542558899999950
Q gi|254780346|r   98 SINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        98 sl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                      ..++++|.+=|+.|+....+|++.-
T Consensus        99 a~~~~i~~iPGv~TpsEi~~A~~~G  123 (207)
T PRK08904         99 GHNSGIPLIPGVATPGEIQLALEHG  123 (207)
T ss_pred             HHHCCCCEECCCCCHHHHHHHHHCC
T ss_conf             9983997657869999999999879


No 103
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=67.75  E-value=10  Score=19.36  Aligned_cols=89  Identities=15%  Similarity=0.184  Sum_probs=64.1

Q ss_pred             HHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHH
Q ss_conf             9999999879955555--3001442269999998633113785356654120006652467-------899999999999
Q gi|254780346|r   26 GCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVD   96 (149)
Q Consensus        26 ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~   96 (149)
                      ...+.|.+.|+..-.|  +.|+++|.-   +.+.+     .-+|.+|-.|.|...|+-+.=       .||-.....+.+
T Consensus        31 ~~~~al~~gGi~~iEITlrt~~a~~~I---~~l~~-----~~p~~~vGaGTVl~~e~~~~a~~aGA~FiVSP~~~~~v~~  102 (212)
T PRK06015         31 PLARALARGGLPAIEITLRTPAALDAI---RAVAA-----EVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLA  102 (212)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHHHHCCCCEEECCCCCHHHHH
T ss_conf             999999987998899968995199999---99998-----6999679542115699999999849989985899999999


Q ss_pred             HHHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             99743997056542558899999950
Q gi|254780346|r   97 LSINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        97 lsl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                      .+.+.++|.+=|+.|+....+|++.-
T Consensus       103 ~a~~~~i~~iPGv~TpsEi~~A~~~G  128 (212)
T PRK06015        103 AANDSDVPLLPGAITPSEVMALREEG  128 (212)
T ss_pred             HHHHCCCCEECCCCCHHHHHHHHHCC
T ss_conf             99983997737869999999999879


No 104
>PRK00290 dnaK molecular chaperone DnaK; Provisional
Probab=65.93  E-value=4.4  Score=21.61  Aligned_cols=89  Identities=21%  Similarity=0.340  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHH
Q ss_conf             289999999999999998799555----5530014422699999986331----13785356654120006652467899
Q gi|254780346|r   16 YENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIA   87 (149)
Q Consensus        16 ~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~   87 (149)
                      ..++.++.+.-+.+.|.+.+...+    ++-|=|+--+|..-+.+-+...    .+-++|-.||+|+-|+|.----    
T Consensus       304 ~~~l~~r~~~~v~~aL~~A~l~~~dId~ViLVGGsTRiP~Vq~~v~~~Fgk~~~~~inPDeaVA~GAAiqa~iLsg----  379 (631)
T PRK00290        304 TEDLVERTIEPCRQALKDAGLSVSDIDEVILVGGSTRMPAVQELVKEFFGKEPNKGVNPDEVVAVGAAIQGGVLAG----  379 (631)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCC----
T ss_conf             9999999999999999980898222159999178245679999999996889777969126899879999988638----


Q ss_pred             HHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             99999999999743997056542558
Q gi|254780346|r   88 HAVTRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        88 ~~v~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                       .    +.++-|---+|...||=|..
T Consensus       380 -~----~~d~~LlDVtPlSLGiet~g  400 (631)
T PRK00290        380 -D----VKDVLLLDVTPLSLGIETLG  400 (631)
T ss_pred             -C----CCCCEEEECCCCCEEEEECC
T ss_conf             -7----66736896034531378639


No 105
>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=65.57  E-value=12  Score=18.80  Aligned_cols=84  Identities=15%  Similarity=0.155  Sum_probs=56.6

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHH-HHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             71799980312899999999999999987995555530014422-69999998633113785356654120006652467
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEI-PAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~Ei-P~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      |+|.+|.|..+..-.-.+.+|+++..+..|.+..+++--|.-+- --+++..     ...+.||+|.-|.      +   
T Consensus         1 k~i~~va~~l~n~g~~~v~~G~~eaA~~lGw~v~v~D~~g~~~~~~~~i~~a-----i~~k~D~Iii~~~------D---   66 (280)
T cd06315           1 KNIIFVASDLKNGGILGVGEGVREAAKAIGWNLRILDGRGSEAGQAAALNQA-----IALKPDGIVLGGV------D---   66 (280)
T ss_pred             CEEEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHH-----HHCCCCEEEECCC------C---
T ss_conf             9399998726687415498899999997598799988999999999999999-----9639999999982------9---


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCE
Q ss_conf             8999999999999974399705
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIG  106 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~  106 (149)
                        +.++...|.... +-++|++
T Consensus        67 --~~~~~~~l~~A~-~agIPvv   85 (280)
T cd06315          67 --AAELQAELELAQ-KAGIPVV   85 (280)
T ss_pred             --HHHHHHHHHHHH-HCCCCEE
T ss_conf             --788789999999-8799789


No 106
>PRK10714 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional
Probab=65.48  E-value=12  Score=18.79  Aligned_cols=46  Identities=13%  Similarity=0.132  Sum_probs=36.7

Q ss_pred             CCCEEEEEEECHHHHH-HHHHHHHHHHHHHHCCCCEEEEEH-----HHHHHH
Q ss_conf             5871799980312899-999999999999987995555530-----014422
Q gi|254780346|r    4 FIPHVLIIEARFYENL-SAMLFEGCVNVLHSRAVQWSSIVT-----PGVLEI   49 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i-~~~ll~ga~~~l~~~~~~~~~i~V-----PGa~Ei   49 (149)
                      -|+||.||..-||++= ...+++...+.+...+.+++.+.|     -+++|+
T Consensus         4 pmkkiSIViP~yNEe~~i~~~~~~~~~~l~~~~~~~EiI~VDDgS~D~T~~~   55 (324)
T PRK10714          4 PIKKVSVVIPVYNEQESLPELIRRTTAACESLGKEYEILLIDDGSSDNSAEM   55 (324)
T ss_pred             CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHH
T ss_conf             9986999980177787799999999999986799989999989998677999


No 107
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=65.29  E-value=13  Score=18.76  Aligned_cols=62  Identities=18%  Similarity=0.276  Sum_probs=41.4

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-H---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             87179998031289999999999999998799555553-0---014422699999986331137853566541
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-T---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      .+|++||....-.  -..+++...+.|.+.|+.+.++. |   |-.-.+--+++..     +..++|.+|++|
T Consensus        31 ~k~~lvvt~~~~~--~~g~~~~v~~~L~~~gi~~~~f~~V~~nP~~~~v~~~~~~~-----r~~~~D~ivavG   96 (383)
T PRK09860         31 FTRTLIVTDNMLT--KLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLL-----KENNCDSVISLG   96 (383)
T ss_pred             CCEEEEECCCCHH--HCCHHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHH-----HHCCCCEEEEEC
T ss_conf             9879998284566--57469999999987699589968952796999999999999-----873999999938


No 108
>pfam01081 Aldolase KDPG and KHG aldolase. This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate aldolase (KDPG-aldolase)
Probab=63.79  E-value=13  Score=18.59  Aligned_cols=102  Identities=15%  Similarity=0.206  Sum_probs=67.8

Q ss_pred             EEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-
Q ss_conf             7999803128999999999999999879955555--3001442269999998633113785356654120006652467-
Q gi|254780346|r    8 VLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-   84 (149)
Q Consensus         8 I~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-   84 (149)
                      |.|+... ..+-..    ...+.|.+.|+..-.+  +.|+++|.-   +.+.+     ...|..|-.|.|..-|+-+-= 
T Consensus        11 ipV~r~~-~~~~a~----~~~~al~~~Gi~~iEiTl~t~~a~~~I---~~l~~-----~~p~~~iGaGTV~~~e~~~~a~   77 (196)
T pfam01081        11 VPVIVIK-DKEDAL----PLAEALAAGGIRVLEVTLRTPCALDAI---RLLRK-----NRPDALVGAGTVLNAQQLAEAA   77 (196)
T ss_pred             EEEEECC-CHHHHH----HHHHHHHHCCCCEEEEECCCHHHHHHH---HHHHH-----HCCCCEEEEEECCCHHHHHHHH
T ss_conf             9999779-999999----999999987998899947982799999---99996-----4999679998376899999999


Q ss_pred             ------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             ------89999999999999743997056542558899999950
Q gi|254780346|r   85 ------VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        85 ------~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                            .||-.....+.+.+.++++|.+=|+.|+....||++.-
T Consensus        78 ~aGA~FivSP~~~~~v~~~a~~~~i~~iPGv~TpsEi~~A~~~G  121 (196)
T pfam01081        78 EAGAQFVVSPGLTADLLKHAVDVKIPLIPGVSTPSEIMLGLDLG  121 (196)
T ss_pred             HCCCCEEECCCCHHHHHHHHHHCCCCEECCCCCHHHHHHHHHCC
T ss_conf             74999999787639999999973996637859999999999879


No 109
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=63.76  E-value=13  Score=18.59  Aligned_cols=35  Identities=6%  Similarity=-0.222  Sum_probs=17.1

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             17999803128999999999999999879955555
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI   41 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i   41 (149)
                      ||+++..+...+.=..+.+|+.+..++.|++....
T Consensus         1 kIGv~vp~l~n~ff~~~~~g~e~~A~e~G~~v~~~   35 (288)
T cd01538           1 KIGLSLPTKTEERWIRDRPNFEAALKELGAEVIVQ   35 (288)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             98999079889799999999999999769989997


No 110
>PRK10624 L-1,2-propanediol oxidoreductase; Provisional
Probab=63.76  E-value=13  Score=18.59  Aligned_cols=62  Identities=11%  Similarity=0.221  Sum_probs=41.9

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE-H---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             87179998031289999999999999998799555553-0---014422699999986331137853566541
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV-T---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~-V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      .+|++||..+.-.+  ..+++...+.|++.++.+.++. |   |-.=.+--+++.+     +....|.||++|
T Consensus        29 ~k~~lvvtd~~~~k--~g~~~~v~~~L~~~~i~~~vf~~v~pnP~~~~V~~~~~~~-----r~~~~D~IiavG   94 (381)
T PRK10624         29 YHKALIVTDKTLVQ--CGVVAKVTDKLDAAGLAYEIYDGVKPNPTISVVKEGLEVF-----QASGADYLIAIG   94 (381)
T ss_pred             CCEEEEEECCCHHH--CCHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHH-----HHCCCCEEEEEC
T ss_conf             98799996965455--6369999999987698399988925898999999999999-----864999899808


No 111
>TIGR02350 prok_dnaK chaperone protein DnaK; InterPro: IPR012725    Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes, the grpE protein is a co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.    Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for the Mycoplasma sequence) found clustered with other genes of this systems. This entry excludes DnaK homologues that are not DnaK itself, such as the heat shock cognate protein HscA (IPR010236 from INTERPRO). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of DnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; the lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=63.04  E-value=4.9  Score=21.30  Aligned_cols=69  Identities=23%  Similarity=0.300  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHH----HCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             289999999999999998799555----553001442269999998633----113785356654120006652467
Q gi|254780346|r   16 YENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAK----TRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus        16 ~~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~----~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      -.++.++...-+...|.+++...+    ++-|=|+=-+|.+-+.+-...    .++-+||-+||+|+-|+|.--.-|
T Consensus       301 ~~dLv~~~~~p~~~aL~DA~l~~~~I~~v~LVGG~TRiP~V~~~V~~~~GK~p~~~vNPDEvVAiGAAiQgGVL~Gd  377 (598)
T TIGR02350       301 TADLVERTKEPVRQALKDAGLSASDIDEVILVGGSTRIPAVQELVKEFFGKEPNKSVNPDEVVAIGAAIQGGVLKGD  377 (598)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             99999998999999997537884366668985588412489999998729887888880588888788875431787


No 112
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=62.66  E-value=14  Score=18.46  Aligned_cols=34  Identities=6%  Similarity=-0.082  Sum_probs=18.0

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             1799980312899999999999999987995555
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS   40 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~   40 (149)
                      ||+++....+...=..|.+|+++..++.|++...
T Consensus         1 KIg~~~~tl~npff~~~~~g~~~~A~e~G~~l~~   34 (289)
T cd01540           1 KIGFIVKQPEEPWFQTEWKFAKKAAKEKGFTVVK   34 (289)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEE
T ss_conf             9899958998839999999999999984987999


No 113
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=60.63  E-value=15  Score=18.24  Aligned_cols=123  Identities=15%  Similarity=0.091  Sum_probs=65.4

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             717999803128999999999999999879955555-3001442269999998633113785356654120006652467
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      .+|+++...-....+..-.+|+.+.|.+++ .++++ ..+|-|....+.+..-.......+.|++++-      +    +
T Consensus       126 g~i~~i~G~~~~~~~~~R~~Gf~~~l~~~p-~i~iv~~~~~~~~~~~a~~~~~~~L~~~pdid~I~~~------d----~  194 (272)
T cd06300         126 GNVLVVRGLAGHPVDEDRYAGAKEVLKEYP-GIKIVGEVYGDWDQAVAQKAVADFLASNPDVDGIWTQ------G----G  194 (272)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHHHCC-CEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEC------C----C
T ss_conf             763899448898499999999999986414-2488655448888899999999999868996099977------8----2


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCC-------CCCCCHHHHHHHHHHHHH
Q ss_conf             8999999999999974399705654255889999995065-------657456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSP-------SHLDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~-------~~~nkG~eaa~Aal~mi~  142 (149)
                       .+-.+.+++.+...  ..|+..|.-..........+-+.       +...-|+.|+++++++++
T Consensus       195 -~a~Ga~~Al~~aG~--~~~~~~g~~~~~~~~~~~~~~g~~~a~~~q~p~~~G~~av~~a~~~l~  256 (272)
T cd06300         195 -DAVGAVQAFEQAGR--DIPPVTGEDENGFLRWRLWKDKGLKGIAISNPPGQSAAALRAAVQALE  256 (272)
T ss_pred             -CHHHHHHHHHHCCC--CCCEEEEECCCHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             -18999999996699--988699975957899998348975999970859999999999999977


No 114
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=60.15  E-value=16  Score=18.19  Aligned_cols=122  Identities=15%  Similarity=0.127  Sum_probs=50.7

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHH
Q ss_conf             17999803128999999999999999879955555-30014422699999986331137853566541200066524678
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDV   85 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~   85 (149)
                      +|+++...-.......-.+|+.+.|.++. ..+.+ ..+|-|....+.+.+-+-.....+.|++++.          .|.
T Consensus       125 ~v~~i~g~~~~~~~~~R~~Gf~~~l~~~~-~~~iv~~~~~~~~~~~a~~~~~~~L~~~~~~~aI~~~----------nd~  193 (272)
T cd06301         125 NVAILMGPLGQSAQIDRTKGVEEVLAKYP-DIKVVEEQTANWSRAEAMDLMENWLSSGGKIDAVVAN----------NDE  193 (272)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHHCC-CCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCEEEEC----------CCH
T ss_conf             18973589997689999999999998789-9658876313123578999999999836777879955----------827


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH
Q ss_conf             99999999999997439970565425588999999506565---------7456999999999999
Q gi|254780346|r   86 IAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE  142 (149)
Q Consensus        86 I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~  142 (149)
                      .+-.+.++|.+..+.   |=-..|.+.+...++.+......         ..-|+.|++.++++++
T Consensus       194 ~a~Ga~~al~~~g~~---~~~i~v~G~D~~~~~~~~i~~g~~~~tv~q~~~~~G~~av~~~~~~l~  256 (272)
T cd06301         194 MALGAIMALKAAGKS---DKDVPVAGIDGTPDALAAVKKGDLDVTVFQDAKGQGAGALDAALKLAK  256 (272)
T ss_pred             HHHHHHHHHHHCCCC---CCCEEEEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             899999999986989---998799998985999999874997699806999999999999999977


No 115
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=59.34  E-value=8.4  Score=19.83  Aligned_cols=92  Identities=14%  Similarity=0.221  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH-----CCCCCCEEEEEEEEECCCCCHHHHHH
Q ss_conf             89999999999999998799555----5530014422699999986331-----13785356654120006652467899
Q gi|254780346|r   17 ENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT-----RSVTYDGIIVLGVVMRGKTAHCDVIA   87 (149)
Q Consensus        17 ~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~-----~~~~~D~vIaLG~VIkGeT~H~e~I~   87 (149)
                      .++.++.+.-+.+.|++.++..+    ++-|=|+-.+|..-+.+-+...     .+-++|-.||+||-+++...-     
T Consensus       309 ~~l~~r~~~~i~~aL~~a~l~~~dId~ViLVGGsTRiP~Vq~~l~~~f~gk~~~~~iNpDEaVA~GAAiqaa~Ls-----  383 (657)
T PTZ00009        309 GDLFRSTLQPVEKVLQDAKMDKRSVHDVVLVGGSTRIPKVQSLISDFFNGKELNKSINPDEAVAYGAAVQAAILT-----  383 (657)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHC-----
T ss_conf             999998999999999973799525149998088146768999999981898888897831466654899999871-----


Q ss_pred             HHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             99999999999743997056542558
Q gi|254780346|r   88 HAVTRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        88 ~~v~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                      ..-.....++.+.--+|+..||=|..
T Consensus       384 g~~~~~v~~~~l~Dv~PlslGie~~g  409 (657)
T PTZ00009        384 GGQSKQTQGLLLLDVAPLSLGLETAG  409 (657)
T ss_pred             CCCCCCCCEEEEEECCCEEEEEEECC
T ss_conf             89655412368996164047888659


No 116
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=58.89  E-value=16  Score=18.05  Aligned_cols=102  Identities=17%  Similarity=0.199  Sum_probs=68.6

Q ss_pred             EEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-
Q ss_conf             7999803128999999999999999879955555--3001442269999998633113785356654120006652467-
Q gi|254780346|r    8 VLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-   84 (149)
Q Consensus         8 I~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-   84 (149)
                      |.||.. -..+-...+    .+.|.+.|+..-.|  +.|+++|.   ++.+.+     .-.|..|-.|.|...|+-+.= 
T Consensus        18 i~Vlr~-~~~~~a~~i----~~al~~gGi~~iEiTl~tp~a~~~---I~~l~~-----~~p~~~vGaGTV~~~e~~~~a~   84 (212)
T PRK05718         18 VPVIVI-NKLEDAVPL----AKALVAGGLPVLEVTLRTPAALEA---IRAIRK-----EVPEALIGAGTVLNPEQLAQAI   84 (212)
T ss_pred             EEEEEC-CCHHHHHHH----HHHHHHCCCCEEEEECCCCHHHHH---HHHHHH-----HCCCCEEEEEEECCHHHHHHHH
T ss_conf             999974-899999999----999998799789995789619999---999997-----5898179653313488999999


Q ss_pred             ------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             ------89999999999999743997056542558899999950
Q gi|254780346|r   85 ------VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        85 ------~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                            .||-.....+.+.+.+.++|.+=|+.|+....+|++.-
T Consensus        85 ~aGA~FiVSP~~~~~v~~~a~~~~i~~iPGv~TpsEi~~A~~~G  128 (212)
T PRK05718         85 EAGAQFIVSPGLTPPLLKACQDGPIPLIPGVNTPSELMLAMELG  128 (212)
T ss_pred             HCCCCEEECCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHCC
T ss_conf             84998998489989999999981997657869999999999879


No 117
>PTZ00186 heat shock 70 kDa precursor protein; Provisional
Probab=56.34  E-value=2.9  Score=22.72  Aligned_cols=87  Identities=21%  Similarity=0.316  Sum_probs=54.4

Q ss_pred             HHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHHHH
Q ss_conf             9999999999999998799555----5530014422699999986331----1378535665412000665246789999
Q gi|254780346|r   18 NLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIAHA   89 (149)
Q Consensus        18 ~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~~~   89 (149)
                      ++.++.+.-+.+.|++.++..+    ++-|=|+--+|..-+++-+...    .+-++|-.||+|+-|.|.--.-+     
T Consensus       331 ~Ll~rt~~~v~~aL~dAgl~~~dId~VILVGGSTRIP~Vq~~l~~~Fgkep~~~iNPDEaVA~GAAiqa~iL~g~-----  405 (657)
T PTZ00186        331 RLIERSIAPCKQCMKDAGVELKEINDVVLVGGMTRMPKVVEEVKKFFQKDPFRGVNPDEAVALGAATLGGVLRGD-----  405 (657)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCC-----
T ss_conf             999999999999999818998780089995784154799999999858997779791189999899988876387-----


Q ss_pred             HHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             999999999743997056542558
Q gi|254780346|r   90 VTRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        90 v~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                          ..++-|---+|...||=|..
T Consensus       406 ----~~~~~LlDVtPlSLGiet~g  425 (657)
T PTZ00186        406 ----VKGLVLLDVTPLSLGIETLG  425 (657)
T ss_pred             ----CCCEEEEEEECCEEEEEECC
T ss_conf             ----55348998555517999718


No 118
>pfam10087 DUF2325 Uncharacterized protein conserved in bacteria (DUF2325). Members of this family of hypothetical bacterial proteins have no known function.
Probab=56.17  E-value=18  Score=17.77  Aligned_cols=85  Identities=13%  Similarity=0.105  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999987995555530014422699999986331137853566541200066524678999999999999974
Q gi|254780346|r   21 AMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSIN  100 (149)
Q Consensus        21 ~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~  100 (149)
                      +.++....+.+++.|++....+  |..+=. . +.+ .  ..-.+.|.||++          -|+|++..+.-+.+..=+
T Consensus         9 ~~~~~~~~~~~~~~G~~~~~h~--~g~~~~-~-~~l-~--~~i~~aDlVI~~----------td~vsH~~~~~vK~~akk   71 (96)
T pfam10087         9 DDRLGHYRKLLEKYGGEFIVHD--GGREKK-K-KKI-P--ALLKKADLVIVF----------TDCVSHDAMWRVKEEAKK   71 (96)
T ss_pred             HHHHHHHHHHHHHCCCEEEEEC--CCCCCH-H-HHH-H--HCCCCCCEEEEE----------CCCCCHHHHHHHHHHHHH
T ss_conf             5678999999998399899965--898733-5-567-7--505898889997----------176687999999999998


Q ss_pred             CCCCCEEEE-ECCCCHHHHHHHH
Q ss_conf             399705654-2558899999950
Q gi|254780346|r  101 GSLPIGNGI-VVVDSEQQAFDRV  122 (149)
Q Consensus       101 ~~~PI~~gI-Lt~~n~~QA~~R~  122 (149)
                      +++|+.+.= =...+..++++|.
T Consensus        72 ~~~p~v~~~s~s~~~l~~~l~~~   94 (96)
T pfam10087        72 RGIPVVFSRSRSLSALERALARL   94 (96)
T ss_pred             HCCCEEEECCCCHHHHHHHHHHH
T ss_conf             49978997687499999999996


No 119
>PRK13243 glyoxylate reductase; Reviewed
Probab=54.68  E-value=17  Score=17.92  Aligned_cols=53  Identities=15%  Similarity=0.291  Sum_probs=26.0

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             5871799980312899999999999999987995555530014422699999986331137853566541
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      |+|||+|.. +.+        +.+.+.|+++ ++++...-+..  ++.  +.+++   .-.++|++|+.+
T Consensus         1 Mk~Kvlvt~-~i~--------~~~~~~L~~~-~~v~~~~~~~~--~~~--~~l~~---~i~~~d~li~~~   53 (333)
T PRK13243          1 MKPRVFITR-EIP--------ENGIEMLEEH-FEVEVWEDERE--IPR--EVLLE---KVKDVDALVTML   53 (333)
T ss_pred             CCCEEEEEC-CCC--------HHHHHHHHHC-CCEEEECCCCC--CCH--HHHHH---HHCCCCEEEECC
T ss_conf             997899969-889--------9999999717-95999269999--999--99999---867982999858


No 120
>pfam00012 HSP70 Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region.
Probab=54.59  E-value=13  Score=18.63  Aligned_cols=93  Identities=22%  Similarity=0.324  Sum_probs=53.3

Q ss_pred             EECHHH---HHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCC-
Q ss_conf             803128---9999999999999998799555----5530014422699999986331----137853566541200066-
Q gi|254780346|r   12 EARFYE---NLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGK-   79 (149)
Q Consensus        12 ~s~~~~---~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGe-   79 (149)
                      .++|.+   ++.+++.+-+.+.|.+.++..+    ++-|=|+--+|..-+.+-+...    .+-++|-.||.||-+++. 
T Consensus       294 R~eFE~l~~~l~~r~~~~i~~~L~~a~l~~~dId~ViLvGGssRiP~Vq~~l~~~fg~~~~~~inpdeaVa~GAA~~aa~  373 (598)
T pfam00012       294 RAKFEELCADLFERTLEPVEKALKDAKLSKSEIDEVVLVGGSTRIPAVQELVKEFFGKEPSKTVNPDEAVAIGAAVQAGV  373 (598)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             99999999999999999998789872899545125786188656768999999986899666868531423308999987


Q ss_pred             -CCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             -5246789999999999999743997056542558
Q gi|254780346|r   80 -TAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        80 -T~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                       +..|.         ..++.+.--+|...||-+..
T Consensus       374 ls~~~~---------v~~~~~~Dv~p~slgi~~~~  399 (598)
T pfam00012       374 LSGTFD---------VKDVLLLDVTPLSLGIETLG  399 (598)
T ss_pred             HCCCCC---------CCCEEEEEECCCEEEEEECC
T ss_conf             578764---------56528998547358999818


No 121
>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase; InterPro: IPR010251   Chlorophyll and bacteriochlorophyll are essential photosynthetic pigments involved in oxygenic and non-oxygenic photosythesis respectively. They are both synthesised from protoporphyrin IX in complex pathways which share many common steps. The second committed step in both pathways is the methylation of magnesium protoporphyrin IX, catalysed by magnesium protoporphyrin O-methyltransferase with S-adenosyl methionine (SAM) as the methyl donor , , .Sequence alignments suggest that the protein contains the characteristic seven-stranded beta-sheet fold found in other SAM-dependent methyltransferases.   This entry represents magnesium protoporphyrin O-methyltransferase from cyanobacteria and plants, where it is known as ChlM, and from other photosynthetic bacteria, where it is known as BchM.; GO: 0046406 magnesium protoporphyrin IX methyltransferase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process.
Probab=54.17  E-value=20  Score=17.57  Aligned_cols=88  Identities=10%  Similarity=0.073  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCC-CCCCEEEEEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             8999999999999999879955555-3001442269999998633113-7853566541200066524678999999999
Q gi|254780346|r   17 ENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRS-VTYDGIIVLGVVMRGKTAHCDVIAHAVTRGL   94 (149)
Q Consensus        17 ~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~-~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl   94 (149)
                      -||+++|++-|.+.....+.....+ .+-|.+|=            .. ++||.|||+=++|-       |=.+.....|
T Consensus        82 ~DIS~~mv~~A~~r~~~~~~~~nl~~FeV~Dl~s------------~~~G~fD~VV~mDvlIH-------Yp~~d~~~~l  142 (224)
T TIGR02021        82 VDISEQMVELARERAEKEDEAGNLVEFEVNDLES------------LELGKFDAVVAMDVLIH-------YPAEDIAKAL  142 (224)
T ss_pred             EHHHHHHHHHHHHHCCCCCCCCCCCEEEECCHHH------------HCCCCCCEEEEEHHHHH-------CCHHHHHHHH
T ss_conf             2376899999986210021016700354530444------------13898555675212232-------0222279999


Q ss_pred             HHHHHHCCCCCEEEEECCCCHHHHHHHHC
Q ss_conf             99997439970565425588999999506
Q gi|254780346|r   95 VDLSINGSLPIGNGIVVVDSEQQAFDRVS  123 (149)
Q Consensus        95 ~~lsl~~~~PI~~gILt~~n~~QA~~R~~  123 (149)
                      .+|.-..+-|++|-.=--.+.=.++.+.|
T Consensus       143 ~~Laslt~~~~~ftfAP~T~~l~~~~~IG  171 (224)
T TIGR02021       143 EHLASLTKERVIFTFAPKTAYLAFLKAIG  171 (224)
T ss_pred             HHHHHHHCCCEEEEECCCCHHHHHHHHHH
T ss_conf             99887435864898678767899999851


No 122
>TIGR01991 HscA Fe-S protein assembly chaperone HscA; InterPro: IPR010236   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents the HscA chaperone protein from the SUF system. HscA (or Hsc66) is a specialised bacterial Hsp70-class molecular chaperone that participates in the assembly of iron-sulphur cluster proteins. HscA resembles DnaK, but belongs to a separate clade. HscA interacts with IscU, which is believed to serve as a template for Fe-S cluster formation. The HscA-IscU interaction is facilitated by the J-type co-chaperone protein HscB (or Hsc20), which binds to both HscA and IscU, bringing them into contact with each other. HscA recognises a conserved LPPVK sequence motif at positions 99-103 of IscU .; GO: 0005524 ATP binding, 0016887 ATPase activity, 0051082 unfolded protein binding, 0016226 iron-sulfur cluster assembly.
Probab=53.91  E-value=14  Score=18.44  Aligned_cols=59  Identities=17%  Similarity=0.294  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHHC----CCCCCEEEEEEEEECC
Q ss_conf             99999999999998799555----55300144226999999863311----3785356654120006
Q gi|254780346|r   20 SAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKTR----SVTYDGIIVLGVVMRG   78 (149)
Q Consensus        20 ~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~~----~~~~D~vIaLG~VIkG   78 (149)
                      +.+=+..|...|++.|++.+    +|-|=||=-+|-+=+.+..-...    +-+||-|||||.-|+-
T Consensus       319 V~rtl~~crrAlkDaGV~~~e~~~VvmVGGSTRvp~Vr~~VaelFg~~PL~~ldPD~VVAlGAAiQA  385 (628)
T TIGR01991       319 VKRTLLPCRRALKDAGVEKEEVKGVVMVGGSTRVPKVREAVAELFGREPLTDLDPDKVVALGAAIQA  385 (628)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             9852167888887527883253265786265461679999988637787888875142465589987


No 123
>pfam02514 CobN-Mg_chel CobN/Magnesium Chelatase. This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN is implicated in the conversion of hydrogenobyrinic acid a,c-diamide to cobyrinic acid. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis.
Probab=53.33  E-value=20  Score=17.49  Aligned_cols=106  Identities=20%  Similarity=0.221  Sum_probs=60.0

Q ss_pred             CCEEEEEEECHHHHHH-HHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE-EEECCCCCH
Q ss_conf             8717999803128999-99999999999987995555530014422699999986331137853566541-200066524
Q gi|254780346|r    5 IPHVLIIEARFYENLS-AMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG-VVMRGKTAH   82 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~-~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG-~VIkGeT~H   82 (149)
                      .|.|+|+.-+-|--=. -..++.-.+.|.+.|+++-.++++  .+..-++...+... .....|++|.+- .-+.|... 
T Consensus        68 ~p~Vgilfyr~~~~~g~~~~idali~~Le~~G~nvipvf~~--~~~~~~~~~~~~~~-~~~~vd~iI~~~~F~l~~~~~-  143 (1064)
T pfam02514        68 APTVGILFYRSYLLAGDTAHIDALIRALEARGLNVIPVFSD--LDSREAVRDFFFRD-GEPKVDAIINLTGFSLVGGPA-  143 (1064)
T ss_pred             CCEEEEEECHHHHHCCCCHHHHHHHHHHHHCCCEEEEEEEC--CCCCHHHHHHHHHC-CCCCCCEEEECCCCCCCCCCC-
T ss_conf             98799996555664398489999999999789969999945--75509999999847-998873899738423668882-


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC
Q ss_conf             67899999999999997439970565425588999999506
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS  123 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~  123 (149)
                              .++.--+ -+.++|+..+|.........|+.+.
T Consensus       144 --------~~~~~~l-~~lnVPvl~~i~~~~~s~~~W~~s~  175 (1064)
T pfam02514       144 --------ENGVELL-KKLDVPVLQAIPLYFQSREEWEASS  175 (1064)
T ss_pred             --------HHHHHHH-HHCCCCEEEEEECCCCCHHHHHHCC
T ss_conf             --------1677899-8779988997525899999997388


No 124
>COG2039 Pcp Pyrrolidone-carboxylate peptidase (N-terminal pyroglutamyl peptidase) [Posttranslational modification, protein turnover, chaperones]
Probab=53.11  E-value=17  Score=17.96  Aligned_cols=41  Identities=20%  Similarity=0.261  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCC-CHHHHHHHHC
Q ss_conf             6789999999999999743997056542558-8999999506
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVD-SEQQAFDRVS  123 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~-n~~QA~~R~~  123 (149)
                      --|+||.++.+++...-+++-|+-.|-+-+. +.+||..+-+
T Consensus       138 GTyvCNhvmY~~l~~~~~~~~~~~~GFiHvPy~peqa~~~~~  179 (207)
T COG2039         138 GTYVCNHVMYGLLHHLAKKGPPVRAGFIHVPYLPEQAARKPN  179 (207)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHCCCC
T ss_conf             142247899999999997488876515760678899817999


No 125
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=52.52  E-value=21  Score=17.41  Aligned_cols=117  Identities=15%  Similarity=0.160  Sum_probs=53.8

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHH---HHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             71799980312899999999999999987995555530014422699---999986331137853566541200066524
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAA---VSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a---~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      .+|+++...-.... ..=++|+.+.|.++. ..+.+.+...+..+-+   .+.++.   ...++||++|.          
T Consensus       122 ~~i~~i~~~~~~~~-~~R~~Gf~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~~L~---~~p~~~aI~~~----------  186 (267)
T cd06322         122 GQVAIIDYPTVQSV-VDRVRGFKEALADYP-NIKIVAVQPGITRAEALTAAQNILQ---ANPDLDGIFAF----------  186 (267)
T ss_pred             CEEEEEECCCCHHH-HHHHHHHHHHHHHCC-CCEEEEEECCCCHHHHHHHHHHHHH---HCCCCCEEEEC----------
T ss_conf             45999917997369-999999999999779-9469998357887999999999986---28777489981----------


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH---CCC-------CCCCHHHHHHHHHHHHH
Q ss_conf             6789999999999999743997056542558899999950---656-------57456999999999999
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV---SPS-------HLDRGGCAARSALAMIE  142 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~---~~~-------~~nkG~eaa~Aal~mi~  142 (149)
                      .|.++-.+.+++.+..++ ++    .|++.++..+|..-.   ++.       ...-|+.|++.++++++
T Consensus       187 nD~~A~Ga~~al~~~g~~-di----~vvGfD~~~~a~~~i~~~~p~~ttv~Q~~~~~G~~av~~l~~~i~  251 (267)
T cd06322         187 GDDAALGAVSAIKAAGRD-NV----KVIGFDGMPEARKAVDGEPPFVAVIRQYPDQMGKKAIDAAADVLN  251 (267)
T ss_pred             CCHHHHHHHHHHHHCCCC-CC----EEEEECCCHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             879999999999975999-98----899994949999999708987899968999999999999999977


No 126
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=52.26  E-value=21  Score=17.38  Aligned_cols=32  Identities=9%  Similarity=-0.001  Sum_probs=16.2

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             17999803128999999999999999879955
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAVQW   38 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~   38 (149)
                      ||+++........-..+.+|+.+..++.|++.
T Consensus         1 kIG~~~~~~~npf~~~~~~g~~~~a~~~G~~v   32 (282)
T cd06318           1 KIGFSQYTLNSPFFAALTEAAKAHAKALGYEL   32 (282)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCCEE
T ss_conf             98999489989799999999999999729999


No 127
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=51.86  E-value=21  Score=17.34  Aligned_cols=37  Identities=5%  Similarity=0.069  Sum_probs=26.3

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             8717999803128999999999999999879955555
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI   41 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i   41 (149)
                      .+-|++|........-..+++|+.+.++++|++.-..
T Consensus        26 ~~TIgvivp~i~npff~~v~~gie~~a~~~Gy~l~v~   62 (295)
T PRK10653         26 KDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVL   62 (295)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             9979999489879799999999999999769989998


No 128
>PRK05183 hscA chaperone protein HscA; Provisional
Probab=51.58  E-value=11  Score=19.24  Aligned_cols=89  Identities=17%  Similarity=0.254  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCEE----EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHHH
Q ss_conf             89999999999999998799555----5530014422699999986331----137853566541200066524678999
Q gi|254780346|r   17 ENLSAMLFEGCVNVLHSRAVQWS----SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIAH   88 (149)
Q Consensus        17 ~~i~~~ll~ga~~~l~~~~~~~~----~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~~   88 (149)
                      .++.++.+.-+...|+++++..+    ++-|=|+--+|..-+.+-+...    .+-++|-+||+|+-|.+.--     +.
T Consensus       310 ~~L~~rt~~~v~~aL~dA~l~~~dId~ViLVGGSTRiP~Vq~~v~~~Fgk~~~~~inPDeaVA~GAAiQa~iL-----~g  384 (621)
T PRK05183        310 APLVKRTLLACRRALRDAGVEADEVLEVVMVGGSTRVPLVREAVGEFFGRTPLTSIDPDKVVALGAAIQADIL-----AG  384 (621)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHCEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHH-----CC
T ss_conf             9999999999999998713683002099992885456689999999859896668990168887699999986-----28


Q ss_pred             HHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             999999999974399705654255
Q gi|254780346|r   89 AVTRGLVDLSINGSLPIGNGIVVV  112 (149)
Q Consensus        89 ~v~~gl~~lsl~~~~PI~~gILt~  112 (149)
                      ...  ..++-+---+|...||=|.
T Consensus       385 ~~~--~~~~lllDV~PlSLGIEt~  406 (621)
T PRK05183        385 NKP--DSDMLLLDVIPLSLGLETM  406 (621)
T ss_pred             CCC--CCCEEEEEECCCCEEEEEC
T ss_conf             976--6706999612541356862


No 129
>PRK01433 hscA chaperone protein HscA; Provisional
Probab=51.43  E-value=12  Score=18.81  Aligned_cols=88  Identities=14%  Similarity=0.168  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCC-E-EEEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHHHHH
Q ss_conf             899999999999999987995-5-55530014422699999986331----13785356654120006652467899999
Q gi|254780346|r   17 ENLSAMLFEGCVNVLHSRAVQ-W-SSIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIAHAV   90 (149)
Q Consensus        17 ~~i~~~ll~ga~~~l~~~~~~-~-~~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~~~v   90 (149)
                      .++.++.++-+.+.|.+.+.+ + +++-|=|+--+|..-+.+-+...    .+-++|-+||+|+-|.+..-     +.. 
T Consensus       287 ~~L~~r~~~~v~~~L~~a~~~dId~ViLVGGsTRiP~Vq~~l~~~Fg~~~~~~inPDEaVA~GAAiqa~~L-----~~~-  360 (595)
T PRK01433        287 LPLVERTINIAQECLEQAGNPNIDGVILVGGATRIPLIKDELYKAFKVDILSDIDPDKAVVWGAALQAENL-----IAP-  360 (595)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH-----CCC-
T ss_conf             99999999999999997693535548996785545899999999858997789784789999899987764-----377-


Q ss_pred             HHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             99999999743997056542558
Q gi|254780346|r   91 TRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        91 ~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                         ..++-+---+|...||=|..
T Consensus       361 ---~~~~~llDV~PlSLGiEt~g  380 (595)
T PRK01433        361 ---HTNSLLIDVVPLSLGMELYG  380 (595)
T ss_pred             ---CCCEEEEEECCCCEEEEECC
T ss_conf             ---66539999517636899749


No 130
>CHL00094 dnaK heat shock protein 70
Probab=51.21  E-value=16  Score=18.12  Aligned_cols=88  Identities=18%  Similarity=0.255  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCE---E-EEEHHHHHHHHHHHHHHHHHHH----CCCCCCEEEEEEEEECCCCCHHHHHHH
Q ss_conf             8999999999999999879955---5-5530014422699999986331----137853566541200066524678999
Q gi|254780346|r   17 ENLSAMLFEGCVNVLHSRAVQW---S-SIVTPGVLEIPAAVSMVMNAKT----RSVTYDGIIVLGVVMRGKTAHCDVIAH   88 (149)
Q Consensus        17 ~~i~~~ll~ga~~~l~~~~~~~---~-~i~VPGa~EiP~a~~~~~~~~~----~~~~~D~vIaLG~VIkGeT~H~e~I~~   88 (149)
                      .++.++..+-+.+.|.+.++..   + ++-|=|+-.+|..-+.+-+...    .+-++|-.||+||-|++...     +.
T Consensus       305 ~~l~~r~~~~v~~~L~~a~l~~~dId~ViLVGGstRiP~V~~~l~~~fgk~~~~~inpDeaVA~GAAiqa~~l-----s~  379 (622)
T CHL00094        305 SDLIDRCRIPVENALKDAKLDKSDIDEVVLVGGSTRIPAIQELVKSLLGKDPNQSVNPDEVVAIGAAIQAGVL-----AG  379 (622)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHCEEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH-----CC
T ss_conf             9999999999999999819998894399993881256789999999858996779681589999899986765-----48


Q ss_pred             HHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             9999999999743997056542558
Q gi|254780346|r   89 AVTRGLVDLSINGSLPIGNGIVVVD  113 (149)
Q Consensus        89 ~v~~gl~~lsl~~~~PI~~gILt~~  113 (149)
                          ...++.+.--+|...||=|..
T Consensus       380 ----~~~~~~l~Dv~PlslGie~~g  400 (622)
T CHL00094        380 ----EVKDILLLDVTPLSLGVETLG  400 (622)
T ss_pred             ----CCCCEEEEEEECCCEEEEECC
T ss_conf             ----655359999844517889729


No 131
>pfam00781 DAGK_cat Diacylglycerol kinase catalytic domain. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologues. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family.
Probab=50.72  E-value=22  Score=17.23  Aligned_cols=82  Identities=18%  Similarity=0.157  Sum_probs=49.0

Q ss_pred             HHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999999879955555300144226999999863311378535665412000665246789999999999999743997
Q gi|254780346|r   25 EGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSINGSLP  104 (149)
Q Consensus        25 ~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~P  104 (149)
                      +.+.+.|.+.+..++.+.+.+.-...    .+.........+|.+++.|    ||=     --+++.+||+........|
T Consensus        18 ~~i~~~l~~~~~~~~~~~t~~~~~~~----~~~~~~~~~~~~d~vv~~G----GDG-----Tv~evvngl~~~~~~~~~p   84 (127)
T pfam00781        18 DKVLEKLRKALNEAQVFETEEGGPAV----ALELARALGDFKDLVVVAG----GDG-----TVNEVLNGLAGREDRLKPP   84 (127)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCHHH----HHHHHHHHCCCCCEEEEEC----CCC-----HHHHHHHHHHHCCCCCCCC
T ss_conf             99999999879975999989888799----9999985235888899988----975-----7999999997468877897


Q ss_pred             CEEEEECCCCHHHHHHHH
Q ss_conf             056542558899999950
Q gi|254780346|r  105 IGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus       105 I~~gILt~~n~~QA~~R~  122 (149)
                        .|||-.-+-.. +.|+
T Consensus        85 --lgiIP~GTgNd-fa~~   99 (127)
T pfam00781        85 --LGIIPLGTGND-FARA   99 (127)
T ss_pred             --EEEECCCCHHH-HHHH
T ss_conf             --89924876758-9998


No 132
>PRK13059 putative lipid kinase; Reviewed
Probab=48.50  E-value=24  Score=17.01  Aligned_cols=87  Identities=20%  Similarity=0.243  Sum_probs=50.2

Q ss_pred             CCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHH--HHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             871799980312-8999999999999999879955555300--1442269999998633113785356654120006652
Q gi|254780346|r    5 IPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTP--GVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         5 ~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VP--Ga~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      |+|+++|+=.-= ..=..+.++...+.|.++++++..+..+  ++.+.  +.+      +....||.+|+.|    ||=.
T Consensus         1 Mkk~~~I~NP~sG~g~~~~~~~~i~~~l~~~~~~~~~~~t~~~~~~~~--a~~------~~~~~~d~vv~~G----GDGT   68 (294)
T PRK13059          1 MKKVKFIYNPYSGENAIISELDKVIEIHQKYGYLVVPYRISLGCDLKE--AFK------DIDESYKYILIAG----GDGT   68 (294)
T ss_pred             CCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEECCCHHHH--HHH------HHHCCCCEEEEEE----CCCH
T ss_conf             977999999766886668899999999997798899998535608999--999------8874898899995----6788


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             4678999999999999974399705654255
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVV  112 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~  112 (149)
                           -++|.+|++..  +.++|  .|||-.
T Consensus        69 -----inevvngl~~~--~~~~~--lgiiP~   90 (294)
T PRK13059         69 -----VDNVVNAMKKL--NIDIP--IGILPV   90 (294)
T ss_pred             -----HHHHHHHHHHC--CCCCC--EEEEEC
T ss_conf             -----99999999856--99985--799826


No 133
>PRK08309 short chain dehydrogenase; Provisional
Probab=46.74  E-value=26  Score=16.85  Aligned_cols=88  Identities=6%  Similarity=0.112  Sum_probs=42.9

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCC-CCEEEEEHH-HHHHHHHH-HHHHHHH----------------------HH
Q ss_conf             17999803128999999999999999879-955555300-14422699-9999863----------------------31
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRA-VQWSSIVTP-GVLEIPAA-VSMVMNA----------------------KT   61 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~-~~~~~i~VP-Ga~EiP~a-~~~~~~~----------------------~~   61 (149)
                      +|--+..+|+.  .+.|-..-.+++++.| ++.-+.|+- .+=+-+.+ ++.+...                      +.
T Consensus        48 ~i~~l~~DY~d--~~~l~~~l~~ai~q~Gp~dl~VaWiHssa~~al~~v~~~l~~~~~~~~l~HVlGS~~~~~~~~~e~~  125 (182)
T PRK08309         48 SITCLPLDYHD--DDAVKLAIKRTIEQNGPITLAVAWIHSSAKDALSVVCRELDLSSETYRLFHVLGSPAKASRIASEKI  125 (182)
T ss_pred             CEEEEECCCCC--HHHHHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCC
T ss_conf             32578746488--6999999999996189856899998357224599999998548998169999468778653510002


Q ss_pred             CCCCCCEE-EEEEEEECCCCCH---HHHHHHHHHHHHHH
Q ss_conf             13785356-6541200066524---67899999999999
Q gi|254780346|r   62 RSVTYDGI-IVLGVVMRGKTAH---CDVIAHAVTRGLVD   96 (149)
Q Consensus        62 ~~~~~D~v-IaLG~VIkGeT~H---~e~I~~~v~~gl~~   96 (149)
                      .....+-. |.||.++.|+...   .|-||+.|..++..
T Consensus       126 ~~~~~~y~~ViLGFv~e~~~sRWLTHeEIS~GVi~Ai~~  164 (182)
T PRK08309        126 GPLRCSYRRVILGFILEDTYSRWLTHEEISDGVIKAIES  164 (182)
T ss_pred             CCCCCCEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHC
T ss_conf             335786288998889718864146458999999999865


No 134
>COG1597 LCB5 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]
Probab=44.93  E-value=27  Score=16.67  Aligned_cols=100  Identities=21%  Similarity=0.221  Sum_probs=59.9

Q ss_pred             CCCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             5871799980312-899999999999999987995555530014422699999986331137853566541200066524
Q gi|254780346|r    4 FIPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         4 ~~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      +|+|+.++.-... ....+..+..+.+.|.+.+.+.....+-..=+..-.++.+     ....||.+|+.|    |    
T Consensus         1 ~~~~~~~i~Np~sG~~~~~~~~~~~~~~l~~~g~~~~~~~t~~~g~a~~~a~~a-----~~~~~D~via~G----G----   67 (301)
T COG1597           1 RMKKALLIYNPTSGKGKAKKLLREVEELLEEAGHELSVRVTEEAGDAIEIAREA-----AVEGYDTVIAAG----G----   67 (301)
T ss_pred             CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHCCEEEEEEECCCHHHHHHHHHH-----HHCCCCEEEEEC----C----
T ss_conf             995289998887765005777999999999728646999703752299999998-----645898899963----4----


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHC
Q ss_conf             67899999999999997439970565425588999999506
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVS  123 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~  123 (149)
                       |=.-++|++||..    ...|. .|||-+-+.. .+.|+-
T Consensus        68 -DGTv~evingl~~----~~~~~-LgilP~GT~N-dfAr~L  101 (301)
T COG1597          68 -DGTVNEVANGLAG----TDDPP-LGILPGGTAN-DFARAL  101 (301)
T ss_pred             -CCHHHHHHHHHHC----CCCCC-EEEECCCCHH-HHHHHC
T ss_conf             -8879999988733----79981-7993486577-889985


No 135
>PRK06490 glutamine amidotransferase; Provisional
Probab=44.47  E-value=28  Score=16.63  Aligned_cols=100  Identities=13%  Similarity=0.074  Sum_probs=65.7

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             58717999803128999999999999999879955555300144226999999863311378535665412000665246
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      .++||+||.-.=.+.-     .-..+.|.+.|++.++++..---++|-          .-..|||+|.+|-=.- -.+-+
T Consensus        10 ~~k~vLviqH~~~e~p-----G~i~~~L~~~G~~~~i~r~~~gd~lP~----------~l~~~dglvVlGGpms-a~D~~   73 (243)
T PRK06490         10 DKRPILIVLHQERSTP-----GRVGQLLRERGYPLDIRRPRLGDPLPE----------TLEDHAGAVIFGGPMS-ANDPD   73 (243)
T ss_pred             CCCCEEEEECCCCCCC-----HHHHHHHHHCCCEEEEEECCCCCCCCC----------CCCCCCEEEEECCCCC-CCCCC
T ss_conf             8985799966899997-----299999997898589996789998999----------7546058999289999-89987


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC
Q ss_conf             789999999999999743997056542558899999950656
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS  125 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~  125 (149)
                      .++..+.  .+.+-.++.++|+.-==|.    .|.+.|+-+.
T Consensus        74 p~l~~e~--~~I~~~l~~~~P~LGICLG----aQLlA~alGg  109 (243)
T PRK06490         74 DFIRREI--DWISVPLKENKPFLGICLG----AQMLARHLGA  109 (243)
T ss_pred             CHHHHHH--HHHHHHHHCCCCEEEECHH----HHHHHHHHCC
T ss_conf             1799999--9999999869988998884----9999998398


No 136
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=43.90  E-value=28  Score=16.57  Aligned_cols=30  Identities=3%  Similarity=-0.165  Sum_probs=16.5

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             179998031289999999999999998799
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRAV   36 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~   36 (149)
                      ||+++..+.+...-..+.+|+.+..++.+.
T Consensus         1 kIgvv~~~~~npF~~~i~~Gie~aa~~~~~   30 (275)
T cd06307           1 RLGFLLPKGSNAFYRELAAALEAAAAAFPD   30 (275)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCCC
T ss_conf             989995799996999999999999986568


No 137
>PRK00861 putative lipid kinase; Reviewed
Probab=42.76  E-value=30  Score=16.47  Aligned_cols=90  Identities=14%  Similarity=0.153  Sum_probs=45.1

Q ss_pred             CCCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             5871799980312-899999999999999987995555530014422699999986331137853566541200066524
Q gi|254780346|r    4 FIPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         4 ~~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      |++|+++|+=..= ..-....+....+.|. .+++++++.+...-+..    .+.+. +....||.+|+.|    ||=. 
T Consensus         1 M~kr~~~IvNP~aG~g~~~~~~~~i~~~l~-~~~~~~v~~T~~~~~a~----~la~~-a~~~~~d~vv~~G----GDGT-   69 (296)
T PRK00861          1 MTRSACLIFNPVAGQGNPEVDLALIRAILQ-PEMDLDIYLTTPEIGAD----ALAQE-AVERGAELIIASG----GDGT-   69 (296)
T ss_pred             CCEEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEEEECCCCCHH----HHHHH-HHHCCCCEEEEEC----CHHH-
T ss_conf             970799999867899864657999999997-29968999957888699----99999-9867998999988----8189-


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEECCCC
Q ss_conf             67899999999999997439970565425588
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIGNGIVVVDS  114 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n  114 (149)
                          -++|.++++    ..++|  .||+-..|
T Consensus        70 ----v~ev~~gl~----~~~~~--lgiiP~GT   91 (296)
T PRK00861         70 ----ISAVAGALI----GTDIP--LGIIPRGT   91 (296)
T ss_pred             ----HHHHHHHHC----CCCCC--EEEEECCC
T ss_conf             ----999997533----58961--69980766


No 138
>COG0400 Predicted esterase [General function prediction only]
Probab=40.81  E-value=32  Score=16.28  Aligned_cols=49  Identities=16%  Similarity=0.082  Sum_probs=23.7

Q ss_pred             CCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHH
Q ss_conf             6587179998031289999999999999998799555553001442269
Q gi|254780346|r    3 VFIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPA   51 (149)
Q Consensus         3 ~~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~   51 (149)
                      +...+|++.....-+-+--.+-..+.+.|...|.+++..+.++.-|||.
T Consensus       144 ~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~~~~GH~i~~  192 (207)
T COG0400         144 LAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRWHEGGHEIPP  192 (207)
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCH
T ss_conf             4797288714676884688899999999998199779998368886899


No 139
>PRK08782 consensus
Probab=40.79  E-value=32  Score=16.28  Aligned_cols=87  Identities=14%  Similarity=0.148  Sum_probs=63.1

Q ss_pred             HHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHHH
Q ss_conf             999999879955555--3001442269999998633113785356654120006652467-------8999999999999
Q gi|254780346|r   27 CVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVDL   97 (149)
Q Consensus        27 a~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~l   97 (149)
                      ..+.|.+.|+..-.|  +.|+++|+-   +.+.+     ..+|..+-.|.|+..|+-+.=       .||-.....+.+.
T Consensus        34 ~~eal~~gGi~~iEiTlrt~~a~~~i---~~l~~-----~~p~~~vGaGTV~~~e~~~~a~~aGA~FiVSP~~~~~v~~~  105 (219)
T PRK08782         34 VADALLEGGLPAIELTLRTPVAIEAL---AMLKR-----ELPNIVIGAGTVLSERQLRQSVDAGADFLVTPGTPAPLARL  105 (219)
T ss_pred             HHHHHHHCCCCEEEEECCCCHHHHHH---HHHHH-----HCCCCEEEEEEECCHHHHHHHHHCCCCEEECCCCCHHHHHH
T ss_conf             99999987998799967993399999---99998-----68994799997058999999998499899878997999999


Q ss_pred             HHHCCCCCEEEEECCCCHHHHHHH
Q ss_conf             974399705654255889999995
Q gi|254780346|r   98 SINGSLPIGNGIVVVDSEQQAFDR  121 (149)
Q Consensus        98 sl~~~~PI~~gILt~~n~~QA~~R  121 (149)
                      +.+.++|.+-|+.|+....+|++.
T Consensus       106 a~~~~i~~iPGv~TpSEi~~A~~~  129 (219)
T PRK08782        106 LADAPIPAVPGAATPTELLTLMGL  129 (219)
T ss_pred             HHHCCCCEECCCCCHHHHHHHHHC
T ss_conf             998199764785999999999987


No 140
>PRK11914 diacylglycerol kinase; Reviewed
Probab=39.10  E-value=34  Score=16.11  Aligned_cols=90  Identities=20%  Similarity=0.262  Sum_probs=50.8

Q ss_pred             CCCCEEEEEEECHH-HHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             65871799980312-89999999999999998799555553001442269999998633113785356654120006652
Q gi|254780346|r    3 VFIPHVLIIEARFY-ENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         3 ~~~~kI~IV~s~~~-~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      ..|+|+++|+=..= ..-..+..+...+.|.+.+++++....-+.-+.-    .+.+. +....||.+|+.|    ||=.
T Consensus         4 ~~m~kv~vIvNP~aG~g~~~~~~~~i~~~l~~~g~~~~~~~t~~~~~a~----~la~~-a~~~g~d~vv~~G----GDGT   74 (304)
T PRK11914          4 HEIGKVTVLTNPLSGHGAAPHAAERAIARLHHRGVDVVEIVGTDAHHAR----HLVAA-ALAKGTDALVVVG----GDGV   74 (304)
T ss_pred             CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH----HHHHH-HHHCCCCEEEEEE----CCHH
T ss_conf             4586699999977799856889999999999879909999327878999----99998-8864996999995----6259


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             4678999999999999974399705654255
Q gi|254780346|r   82 HCDVIAHAVTRGLVDLSINGSLPIGNGIVVV  112 (149)
Q Consensus        82 H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~  112 (149)
                           -+++.+++.    +.++|  .||+-.
T Consensus        75 -----v~ev~~~l~----~~~~p--lgiiP~   94 (304)
T PRK11914         75 -----ISNALQVLA----GTDIP--LGIIPA   94 (304)
T ss_pred             -----HHHHHHHHC----CCCCE--EEEECC
T ss_conf             -----889876413----57860--899638


No 141
>KOG3857 consensus
Probab=39.07  E-value=34  Score=16.11  Aligned_cols=67  Identities=18%  Similarity=0.313  Sum_probs=40.1

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEE---H-HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC
Q ss_conf             7179998031289999999999999998799555553---0-01442269999998633113785356654120006652
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIV---T-PGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTA   81 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~---V-PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~   81 (149)
                      +|.++|.-.=-  +--.+.+-+++.|.+.++++++++   + |-.=-.-.+++.     +++..||.+|++|    |...
T Consensus        71 Kk~llvTDkni--~~~~~~~~a~~~L~~~~I~~~vyD~v~~ePtv~s~~~alef-----ak~~~fDs~vaiG----GGSa  139 (465)
T KOG3857          71 KKTLLVTDKNI--AKLGLVKVAQDSLEENGINVEVYDKVQPEPTVGSVTAALEF-----AKKKNFDSFVAIG----GGSA  139 (465)
T ss_pred             CCEEEEECCCH--HHCCCHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHH-----HHHCCCCEEEEEC----CCCH
T ss_conf             42589607774--44141789999999759816972476479862349999999-----8733665589876----8504


Q ss_pred             HH
Q ss_conf             46
Q gi|254780346|r   82 HC   83 (149)
Q Consensus        82 H~   83 (149)
                      |.
T Consensus       140 ~D  141 (465)
T KOG3857         140 HD  141 (465)
T ss_pred             HH
T ss_conf             55


No 142
>COG0800 Eda 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]
Probab=38.77  E-value=29  Score=16.51  Aligned_cols=87  Identities=15%  Similarity=0.178  Sum_probs=60.6

Q ss_pred             HHHHHHHCCCCE-EE-EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH-------HHHHHHHHHHHHH
Q ss_conf             999999879955-55-53001442269999998633113785356654120006652467-------8999999999999
Q gi|254780346|r   27 CVNVLHSRAVQW-SS-IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVDL   97 (149)
Q Consensus        27 a~~~l~~~~~~~-~~-i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~l   97 (149)
                      ..+.|-+.|+.. ++ .++|.++|.--.+...        ..+++|--|.|..-++-.--       .||-.....+.+.
T Consensus        30 ~a~Ali~gGi~~IEITl~sp~a~e~I~~l~~~--------~p~~lIGAGTVL~~~q~~~a~~aGa~fiVsP~~~~ev~~~  101 (211)
T COG0800          30 LAKALIEGGIPAIEITLRTPAALEAIRALAKE--------FPEALIGAGTVLNPEQARQAIAAGAQFIVSPGLNPEVAKA  101 (211)
T ss_pred             HHHHHHHCCCCEEEEECCCCCHHHHHHHHHHH--------CCCCEECCCCCCCHHHHHHHHHCCCCEEECCCCCHHHHHH
T ss_conf             99999976987699964798789999999986--------7465882455669999999998599789899999999999


Q ss_pred             HHHCCCCCEEEEECCCCHHHHHHH
Q ss_conf             974399705654255889999995
Q gi|254780346|r   98 SINGSLPIGNGIVVVDSEQQAFDR  121 (149)
Q Consensus        98 sl~~~~PI~~gILt~~n~~QA~~R  121 (149)
                      ..++++|++=|+.|+--..+|++.
T Consensus       102 a~~~~ip~~PG~~TptEi~~Ale~  125 (211)
T COG0800         102 ANRYGIPYIPGVATPTEIMAALEL  125 (211)
T ss_pred             HHHCCCCCCCCCCCHHHHHHHHHC
T ss_conf             986799636887998999999980


No 143
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=38.62  E-value=34  Score=16.07  Aligned_cols=89  Identities=20%  Similarity=0.238  Sum_probs=54.7

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCC--CEEEE--EHHHH---HHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC
Q ss_conf             87179998031289999999999999998799--55555--30014---4226999999863311378535665412000
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAV--QWSSI--VTPGV---LEIPAAVSMVMNAKTRSVTYDGIIVLGVVMR   77 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~--~~~~i--~VPGa---~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIk   77 (149)
                      -.||+||.|.     +-.-+......+.+..-  ++..+  .|-|.   -||--+++.+    ....+||.+|    |+|
T Consensus       135 P~~IgvITS~-----tgAa~~Di~~~~~~R~p~~~i~l~p~~VQG~~A~~~I~~ai~~~----~~~~~~DvII----i~R  201 (443)
T PRK00286        135 PKRIGVITSP-----TGAAIRDILTVLSRRFPSVEVIIYPTLVQGEGAAASIVEAIERA----NARGEVDVLI----VAR  201 (443)
T ss_pred             CCEEEEEECC-----CHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHHHHH----HHHCCCCEEE----EEC
T ss_conf             5579998368-----43899999999850499659999814562654799999999998----5224888899----936


Q ss_pred             CCCCHHHHHH---HHHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             6652467899---99999999999743997056542
Q gi|254780346|r   78 GKTAHCDVIA---HAVTRGLVDLSINGSLPIGNGIV  110 (149)
Q Consensus        78 GeT~H~e~I~---~~v~~gl~~lsl~~~~PI~~gIL  110 (149)
                      |.=+--|+-|   ..+++++    .+..+||+.||=
T Consensus       202 GGGS~eDL~~FNdE~varaI----~~s~iPVISaIG  233 (443)
T PRK00286        202 GGGSLEDLWAFNDEAVARAI----AASKIPVISAVG  233 (443)
T ss_pred             CCCCHHHHHHCCCHHHHHHH----HHCCCCEEECCC
T ss_conf             87888897651879999999----848997895146


No 144
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=38.61  E-value=34  Score=16.07  Aligned_cols=65  Identities=8%  Similarity=0.113  Sum_probs=45.2

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEE
Q ss_conf             7179998031289999999999999998799555553001442269999998633113785356654
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVL   72 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaL   72 (149)
                      .+|+++...-.......|.+|+.+..++.|.......+++-+..+.-++.+-+.  ...++|+++.-
T Consensus        34 ~~i~~~~~~~~~~f~~~~~~g~~~~a~~~g~~~~~~~~~~~~d~~~Q~~~i~~~--ia~~~daIiv~   98 (322)
T COG1879          34 KTIGVVVPTLGNPFFQAVRKGAEAAAKKLGVVVAVVIADAQNDVAKQIAQIEDL--IAQGVDAIIIN   98 (322)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHH--HHCCCCEEEEE
T ss_conf             879999477888189999999999998649955897157888819999999999--85599889992


No 145
>cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=38.25  E-value=35  Score=16.03  Aligned_cols=65  Identities=11%  Similarity=0.031  Sum_probs=45.5

Q ss_pred             CCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE--EEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE
Q ss_conf             65871799980312899999999999999987995555--5300144226999999863311378535665412
Q gi|254780346|r    3 VFIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS--IVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGV   74 (149)
Q Consensus         3 ~~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~--i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~   74 (149)
                      +..+||++|...+  +......+.+.+.+++.|+++-.  ..-||.-+.-..+.++.     ..++|+++..|.
T Consensus       138 ~~~kkva~v~~d~--~~G~~~~~~~~~~~~~~G~~vv~~~~~~~~~~Dft~~l~~i~-----~a~pD~V~~~~~  204 (351)
T cd06334         138 LKGKKIALVYHDS--PFGKEPIEALKALAEKLGFEVVLEPVPPPGPNDQKAQWLQIR-----RSGPDYVILWGW  204 (351)
T ss_pred             CCCCEEEEEECCC--HHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCHHHHHHHHH-----HCCCCEEEEECC
T ss_conf             4887899995686--276899999999999769979888806999835899999999-----769899999377


No 146
>TIGR01182 eda 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related . They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=37.12  E-value=36  Score=15.92  Aligned_cols=86  Identities=17%  Similarity=0.222  Sum_probs=61.3

Q ss_pred             HHHHHHCCCCE-EE-EEHHHHHHHHHHHHHHHHHHHCCCCC-CEEEEEEEEECCCCCHHH-------HHHHHHHHHHHHH
Q ss_conf             99999879955-55-53001442269999998633113785-356654120006652467-------8999999999999
Q gi|254780346|r   28 VNVLHSRAVQW-SS-IVTPGVLEIPAAVSMVMNAKTRSVTY-DGIIVLGVVMRGKTAHCD-------VIAHAVTRGLVDL   97 (149)
Q Consensus        28 ~~~l~~~~~~~-~~-i~VPGa~EiP~a~~~~~~~~~~~~~~-D~vIaLG~VIkGeT~H~e-------~I~~~v~~gl~~l   97 (149)
                      .+.|-+-|+.. |+ +++|.+.|.=-   .+ +    ...+ |..|--|.|+.=|.-.-=       .||=.+..-|.+.
T Consensus        26 A~aL~egG~~~~EvTlRT~~A~~aI~---~l-~----~~~P~~~~iGAGTVL~~~Q~~~A~~AGA~F~vSPG~~p~l~~~   97 (205)
T TIGR01182        26 AKALIEGGLRVLEVTLRTPVALEAIR---AL-R----KEVPKDALIGAGTVLNPEQLRQAVAAGAQFIVSPGLTPELAKH   97 (205)
T ss_pred             HHHHHHCCCEEEEEEECCCCHHHHHH---HH-H----HHCCCCCEECCCCCCCHHHHHHHHHCCCCEEECCCCCHHHHHH
T ss_conf             99998679808988514721689999---99-9----7282334871676489899999997089578769788899999


Q ss_pred             HHHCCCCCEEEEECCCCHHHHHHH
Q ss_conf             974399705654255889999995
Q gi|254780346|r   98 SINGSLPIGNGIVVVDSEQQAFDR  121 (149)
Q Consensus        98 sl~~~~PI~~gILt~~n~~QA~~R  121 (149)
                      ..++++|++=||.|+--.+||+++
T Consensus        98 ~~~~~~P~iPGV~tpsEi~~Al~~  121 (205)
T TIGR01182        98 AKDKGIPIIPGVATPSEIMLALEL  121 (205)
T ss_pred             HHHCCCCEECCCCCHHHHHHHHHC
T ss_conf             850888121777687899999875


No 147
>PRK02155 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=36.33  E-value=37  Score=15.84  Aligned_cols=103  Identities=18%  Similarity=0.155  Sum_probs=59.9

Q ss_pred             CCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EH---HHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEE
Q ss_conf             96658717999803128999999999999999879955555-30---014422699999986331137853566541200
Q gi|254780346|r    1 MEVFIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VT---PGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVM   76 (149)
Q Consensus         1 m~~~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~V---PGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VI   76 (149)
                      |.-.-+||+||.. .+..-+..++....+.|.++|+++-.- .+   .|.=+.|..     .......+.|-+|++|   
T Consensus         1 M~~~fk~Vgiv~k-~~~~~~~~~~~~l~~~L~~~g~~v~~e~~~a~~~~~~~~~~~-----~~~~~~~~~Dlvi~lG---   71 (291)
T PRK02155          1 MGSQFRTVALVGR-YQTPGIAEPLEALAACIAKRGFEVVFEADTARNTGLTGYPAL-----TPAEIGARADVAVVLG---   71 (291)
T ss_pred             CCCCCCEEEEEEC-CCCHHHHHHHHHHHHHHHHCCCEEEEEHHHHHHCCCCCCCCC-----CHHHHCCCCCEEEEEC---
T ss_conf             9987989999914-898689999999999999788999995557776399887747-----9799463767899976---


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCCCE------EEEECCC---CHHHHHHHH
Q ss_conf             066524678999999999999974399705------6542558---899999950
Q gi|254780346|r   77 RGKTAHCDVIAHAVTRGLVDLSINGSLPIG------NGIVVVD---SEQQAFDRV  122 (149)
Q Consensus        77 kGeT~H~e~I~~~v~~gl~~lsl~~~~PI~------~gILt~~---n~~QA~~R~  122 (149)
                       ||         .+.-...+....+++||.      .|-||.-   +.++++++.
T Consensus        72 -GD---------GTlL~~a~~~~~~~~PilGiN~G~lGFLt~~~~~~~~~~l~~i  116 (291)
T PRK02155         72 -GD---------GTMLGIGRQLAPYGTPLIGINHGRLGFITDIPLSDMQEALPPM  116 (291)
T ss_pred             -CC---------HHHHHHHHHHHCCCCCEEEEECCCEEECCCCCHHHHHHHHHHH
T ss_conf             -78---------8999999987115996899854751340688778899999999


No 148
>PRK13054 lipid kinase; Reviewed
Probab=35.93  E-value=38  Score=15.80  Aligned_cols=92  Identities=17%  Similarity=0.198  Sum_probs=52.3

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             58717999803128999999999999999879955555300144226999999863311378535665412000665246
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      |++-.+||...-  . ..+-+..+.+.|.+.++++++..+-..-+    +..+.+. +....||.+|+.|    ||=   
T Consensus         3 ~~k~lli~N~~~--~-g~~~~~~~~~~l~~~~~~~~~~~T~~~gd----a~~la~~-a~~~g~d~vv~~G----GDG---   67 (299)
T PRK13054          3 FPKSLLILNGKS--A-GNEELREAVGLLREEGHTLHVRVTWEKGD----AARYVEE-ALALGVATVIAGG----GDG---   67 (299)
T ss_pred             CCEEEEEECCCC--C-CHHHHHHHHHHHHHCCCEEEEEECCCCCH----HHHHHHH-HHHCCCCEEEEEC----CCH---
T ss_conf             856999981700--0-50689999999997698799996489745----9999999-9877998999987----722---


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCC
Q ss_conf             7899999999999997439970565425588
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDS  114 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n  114 (149)
                        --++|.+||++..  ...+...|||-.-+
T Consensus        68 --Tv~evvngl~~~~--~~~~~~LgiiP~GT   94 (299)
T PRK13054         68 --TLNEVATALAQLE--GDDRPSLGILPLGT   94 (299)
T ss_pred             --HHHHHHHHHHHCC--CCCCCEEEEECCCC
T ss_conf             --9999999997478--87786399963875


No 149
>PRK03767 TrpR binding protein WrbA; Provisional
Probab=35.71  E-value=38  Score=15.78  Aligned_cols=40  Identities=13%  Similarity=0.173  Sum_probs=26.1

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHH-CCCCEEEEEHHH
Q ss_conf             87179998031289999999999999998-799555553001
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHS-RAVQWSSIVTPG   45 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~-~~~~~~~i~VPG   45 (149)
                      |+||+||.-+=| .-+..|-+...+-..+ .|++....+||-
T Consensus         1 M~kI~IvyyS~~-G~t~~lA~~ia~Ga~~~~G~ev~l~~v~e   41 (200)
T PRK03767          1 MAKVLVLYYSMY-GHIETMAEAVAEGAREVAGAEVTIKRVPE   41 (200)
T ss_pred             CCCEEEEEECCC-CHHHHHHHHHHHHHHHCCCCEEEEEECCC
T ss_conf             970899993899-88999999999766551797799985556


No 150
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=33.75  E-value=41  Score=15.59  Aligned_cols=118  Identities=13%  Similarity=0.101  Sum_probs=60.5

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             58717999803128999999999999999879955555300144226999999863311378535665412000665246
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      |++||+||.-+-      .+.+.-...|...|+++...     ....-+.+.+     ....||.+|. -.-.- +.+=+
T Consensus         1 M~~kILiVEDd~------~l~~~l~~~L~~~g~~v~~a-----~~g~~a~~~l-----~~~~~Dliil-Di~lP-~~dG~   62 (229)
T PRK10161          1 MARRILVVEDEA------PIREMVCFVLEQNGFQPVEA-----EDYDSAVNQL-----NEPWPDLILL-DWMLP-GGSGI   62 (229)
T ss_pred             CCCCEEEEECCH------HHHHHHHHHHHHCCCEEEEE-----CCHHHHHHHH-----HCCCCCEEEE-ECCCC-CCCCH
T ss_conf             997199995999------99999999999779999998-----9999999998-----5289989999-78998-87633


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH----CCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             789999999999999743997056542558899999950----656574569999999999999986
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV----SPSHLDRGGCAARSALAMIELKKS  146 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~----~~~~~nkG~eaa~Aal~mi~l~~~  146 (149)
                      +     +++.|.+-+...++||++  ||..+.++-.-++    .....-|--+...=..++-.+.|+
T Consensus        63 ~-----~~~~ir~~~~~~~~PII~--lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~aRi~a~lrR  122 (229)
T PRK10161         63 Q-----FIKHLKRESMTRDIPVVM--LTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR  122 (229)
T ss_pred             H-----HHHHHHHCCCCCCCCEEE--EECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf             5-----878877502468975899--95566657799998769876520899989999999999712


No 151
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=33.57  E-value=41  Score=15.57  Aligned_cols=31  Identities=16%  Similarity=0.133  Sum_probs=14.3

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             71799980312899999999999999987995
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ   37 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~   37 (149)
                      .||+++..... .......+|+.+.+++++.+
T Consensus       125 ~~i~~i~~~~~-~~~~~r~~g~~~~~~~~g~~  155 (269)
T cd01391         125 KRVALIYGDDG-AYGRERLEGFKAALKKAGIE  155 (269)
T ss_pred             CEEEEECCCCC-HHHHHHHHHHHHHHHHCCCC
T ss_conf             61699737985-77999999999999986998


No 152
>PRK09739 hypothetical protein; Provisional
Probab=32.97  E-value=42  Score=15.51  Aligned_cols=39  Identities=13%  Similarity=0.123  Sum_probs=28.0

Q ss_pred             CCCEEEEEEECHHH-HHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             58717999803128-9999999999999998799555553
Q gi|254780346|r    4 FIPHVLIIEARFYE-NLSAMLFEGCVNVLHSRAVQWSSIV   42 (149)
Q Consensus         4 ~~~kI~IV~s~~~~-~i~~~ll~ga~~~l~~~~~~~~~i~   42 (149)
                      .++||+||.+-=++ -.+..|.+.+.+.|.+.|.++++++
T Consensus         2 ~~kkiLIV~aHP~~~S~~~ala~~~~~~l~~~GheV~v~D   41 (201)
T PRK09739          2 QSERIYLVWAHPRHDSLTAKVADAIHQRAQERGIQVTELD   41 (201)
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             9777999973899865689999999999998799599997


No 153
>cd03817 GT1_UGDG_like This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1,2-diacylglycerol forming 3-D-glucosyl-1,2-diacylglycerol.
Probab=31.89  E-value=44  Score=15.40  Aligned_cols=36  Identities=11%  Similarity=0.137  Sum_probs=25.9

Q ss_pred             EEEEEEECHHHHH--HHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             1799980312899--99999999999998799555553
Q gi|254780346|r    7 HVLIIEARFYENL--SAMLFEGCVNVLHSRAVQWSSIV   42 (149)
Q Consensus         7 kI~IV~s~~~~~i--~~~ll~ga~~~l~~~~~~~~~i~   42 (149)
                      ||+||...|++.+  +......-.+.|.+.|.++.++.
T Consensus         1 kIaivt~~y~P~~GG~~~~~~~La~~L~~~GheV~Vit   38 (374)
T cd03817           1 KIGIFTDTYLPQVNGVATSIRRLAEELEKRGHEVYVVA   38 (374)
T ss_pred             CEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             98999589899998099999999999997799899997


No 154
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=31.15  E-value=14  Score=18.45  Aligned_cols=47  Identities=23%  Similarity=0.396  Sum_probs=25.4

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHH---------------------------HHHHHHCCCCEEEEE--HHHHHHHHH
Q ss_conf             87179998031289999999999---------------------------999998799555553--001442269
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGC---------------------------VNVLHSRAVQWSSIV--TPGVLEIPA   51 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga---------------------------~~~l~~~~~~~~~i~--VPGa~EiP~   51 (149)
                      |++..+=...-|++-...|+.||                           .+...+.|-.++.|.  -||.|||-+
T Consensus         1 MpH~CtrCG~vf~~g~~~il~GCp~CG~nkF~yv~~e~rpa~~e~~d~~vrde~~a~ge~ietIrI~~pG~YeiNl   76 (112)
T COG3364           1 MPHQCTRCGEVFDDGSEEILSGCPKCGCNKFLYVPEEKRPAVAEAADPEVRDEDGAQGEPIETIRILRPGVYEINL   76 (112)
T ss_pred             CCCEECCCCCCCCCCCHHHHCCCCCCCCHHEEECCCCCCCCHHHHCCCCCCCHHHCCCCCCEEEEEECCCEEEEEH
T ss_conf             9752140445636512998815720163114763444563114441876641122036750489994496489744


No 155
>PRK10307 predicted glycosyl transferase; Provisional
Probab=30.15  E-value=47  Score=15.22  Aligned_cols=37  Identities=14%  Similarity=0.186  Sum_probs=28.3

Q ss_pred             EEEEEEECHHHHHH--HHHHHHHHHHHHHCCCCEEEEEH
Q ss_conf             17999803128999--99999999999987995555530
Q gi|254780346|r    7 HVLIIEARFYENLS--AMLFEGCVNVLHSRAVQWSSIVT   43 (149)
Q Consensus         7 kI~IV~s~~~~~i~--~~ll~ga~~~l~~~~~~~~~i~V   43 (149)
                      ||++|...|++++.  ......-.+.|.+.|.+++++..
T Consensus         2 rIl~vs~~y~P~~~G~~~~~~~La~~L~~~GheV~Vit~   40 (415)
T PRK10307          2 KILVYGINYAPELTGIGKYTGEMAEWLAARGHEVRVITA   40 (415)
T ss_pred             EEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             899985848997887999999999999978998999977


No 156
>TIGR00504 pyro_pdase pyrrolidone-carboxylate peptidase; InterPro: IPR000816   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad .    This group of cysteine peptidases belong to MEROPS peptidase family C15 (pyroglutamyl peptidase I, clan CF). The type example being pyroglutamyl peptidase I of Bacillus amyloliquefaciens.    Pyroglutamyl/pyrrolidone carboxyl peptidase (Pcp or PYRase) is an exopeptidase that hydrolytically removes the pGlu from pGlu-peptides or pGlu-proteins , . PYRase has been found in prokaryotes and eukaryotes where at least two different classes have been characterised: the first containing bacterial and animal type I PYRases, and the second containing animal type II and serum PYRases. Type I and bacterial PYRases are soluble enzymes, while type II PYRases are membrane-bound. The primary application of PYRase has been its utilisation for protein or peptide sequencing, and bacterial diagnosis . The conserved residues Cys-144 and His-168 have been identified by inhibition and mutagenesis studies , .; GO: 0004219 pyroglutamyl-peptidase I activity, 0006508 proteolysis.
Probab=30.00  E-value=47  Score=15.20  Aligned_cols=62  Identities=18%  Similarity=0.213  Sum_probs=43.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC-CHHHHHHH---HCCCC-CCCHHHHHHHHHHHH
Q ss_conf             5246789999999999999743997056542558-89999995---06565-745699999999999
Q gi|254780346|r   80 TAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVD-SEQQAFDR---VSPSH-LDRGGCAARSALAMI  141 (149)
Q Consensus        80 T~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~-n~~QA~~R---~~~~~-~nkG~eaa~Aal~mi  141 (149)
                      -.=--||||.++.++++-.-+++.|+.-|=+=+. .-+|+.+.   ..++- .+--..+.++|++.+
T Consensus       138 ~tAGTFvCN~~~Yl~lh~~A~~G~p~raGFIHvPy~P~q~~~~~nl~~PSmSld~~v~Gv~~Ai~~A  204 (220)
T TIGR00504       138 YTAGTFVCNYLMYLLLHHLAQKGLPVRAGFIHVPYLPEQVAEKKNLNVPSMSLDTAVAGVEIAIETA  204 (220)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             3534789999999999987405897112014438871344300358897378999999999999998


No 157
>PRK00012 gatA aspartyl/glutamyl-tRNA amidotransferase subunit A; Reviewed
Probab=29.38  E-value=49  Score=15.13  Aligned_cols=44  Identities=14%  Similarity=0.094  Sum_probs=30.9

Q ss_pred             CCCCEEEEEEECHHHH---HHHHHHHHHHHHHHHCCCCEEEEEHHHH
Q ss_conf             6587179998031289---9999999999999987995555530014
Q gi|254780346|r    3 VFIPHVLIIEARFYEN---LSAMLFEGCVNVLHSRAVQWSSIVTPGV   46 (149)
Q Consensus         3 ~~~~kI~IV~s~~~~~---i~~~ll~ga~~~l~~~~~~~~~i~VPGa   46 (149)
                      +...||+++...|...   -+...++.+.+.|++.|+++..+..|..
T Consensus       255 ~~~lrIgv~~~~~~~~~d~~v~~a~~~a~~~L~~~G~~v~ei~~p~~  301 (485)
T PRK00012        255 LKGLKIGVPKEYFGEGLDPEVKEAVEAAIKVLKDLGAEIVEVSLPHT  301 (485)
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCH
T ss_conf             66767997110025778999999999999999977988999448666


No 158
>cd00452 KDPG_aldolase KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase,  is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.
Probab=28.55  E-value=50  Score=15.05  Aligned_cols=104  Identities=17%  Similarity=0.233  Sum_probs=67.4

Q ss_pred             CEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             717999803128999999999999999879955555--300144226999999863311378535665412000665246
Q gi|254780346|r    6 PHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         6 ~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      +-|.|+...= .+-.    ....+.|.+.|+..-.|  +.|+++|.-   +.+.+    . -.|..|-.|.|...++-+.
T Consensus         5 ~iiaVlr~~~-~~~a----~~~~~al~~~Gi~~iEitl~t~~a~~~i---~~l~~----~-~~~~~iGaGTV~~~~~~~~   71 (190)
T cd00452           5 PLVAVLRGDD-AEDA----LALAEALIEGGIRAIEITLRTPGALEAI---RALRK----E-FPEALIGAGTVLTPEQADA   71 (190)
T ss_pred             CEEEEEECCC-HHHH----HHHHHHHHHCCCCEEEEECCCCHHHHHH---HHHHH----H-CCCCEEEECCCCCHHHHHH
T ss_conf             7799997799-9999----9999999986998899967880299999---99998----6-8980896523477999999


Q ss_pred             H-------HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             7-------89999999999999743997056542558899999950
Q gi|254780346|r   84 D-------VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV  122 (149)
Q Consensus        84 e-------~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~  122 (149)
                      =       .||-.....+.+.+.++++|.+-|+.|+....||++.-
T Consensus        72 a~~aGa~FivsP~~~~~v~~~a~~~~~~~iPGv~TpsEi~~A~~~G  117 (190)
T cd00452          72 AIAAGAQFIVSPGLDPEVVKAANRAGIPLLPGVATPTEIMQALELG  117 (190)
T ss_pred             HHHCCCCEEECCCCCHHHHHHHHHCCCCEECCCCCHHHHHHHHHCC
T ss_conf             9985998997377999999999982996657879999999999879


No 159
>cd01741 GATase1_1 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the glutaminase active site. In this subgroup this triad is conserved. GATase activity can be found in a range of biosynthetic enzymes, including: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase , anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides, as in glutamine 
Probab=27.99  E-value=51  Score=14.98  Aligned_cols=97  Identities=15%  Similarity=0.199  Sum_probs=51.6

Q ss_pred             EEEEEEECHHHHHHHHHHHHHHHHHHHCC---CCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             17999803128999999999999999879---955555300144226999999863311378535665412000665246
Q gi|254780346|r    7 HVLIIEARFYENLSAMLFEGCVNVLHSRA---VQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         7 kI~IV~s~~~~~i~~~ll~ga~~~l~~~~---~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      ||+|+...-.+.     .....+.|.+.+   ++++.+.+...-.+|           .-.+|||+|..|.=--=+++-+
T Consensus         1 ~i~il~~~~~~~-----~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dgvii~Gg~~~~~~~~~   64 (188)
T cd01741           1 RILILQHDTPEG-----PGLFEDLLREAGAETIEIDVVDVYAGELLP-----------DLDDYDGLVILGGPMSVDEDDY   64 (188)
T ss_pred             CEEEEECCCCCC-----CHHHHHHHHHCCCCCEEEEEEECCCCCCCC-----------CHHHCCEEEEECCCCCCCCCCC
T ss_conf             989997799999-----748999999669984689999666698997-----------8444088999699877786788


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCC
Q ss_conf             789999999999999743997056542558899999950656
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPS  125 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~  125 (149)
                      ..+.+  ...+.+-.++.++|+.-==+    -.|.+.++-+.
T Consensus        65 pwi~~--~~~~i~~~~~~~~PilGIC~----G~Qlla~alGg  100 (188)
T cd01741          65 PWLKK--LKELIRQALAAGKPVLGICL----GHQLLARALGG  100 (188)
T ss_pred             HHHHH--HHHHHHHHHHCCCCEEEECH----HHHHHHHHCCC
T ss_conf             66999--99999999987999999846----89999998399


No 160
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=27.67  E-value=52  Score=14.95  Aligned_cols=48  Identities=15%  Similarity=0.172  Sum_probs=40.7

Q ss_pred             EEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHH
Q ss_conf             799980312899999999999999987995555530014422699999
Q gi|254780346|r    8 VLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSM   55 (149)
Q Consensus         8 I~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~   55 (149)
                      +.|+.+...++-.+.+++...+.+.+.|..+..+...|--.+++.++.
T Consensus         7 ~~il~p~l~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k   54 (95)
T PRK00453          7 VFILRPDLSEEQVKALVERYKGVITKNGGEIHKVEDWGRRRLAYPINK   54 (95)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEECC
T ss_conf             999889999899999999999999979988999850212004423066


No 161
>PRK02645 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=26.54  E-value=54  Score=14.82  Aligned_cols=99  Identities=19%  Similarity=0.209  Sum_probs=60.2

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCH
Q ss_conf             58717999803128999999999999999879955555-30014422699999986331137853566541200066524
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAH   82 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H   82 (149)
                      .++||+|| ++..+.....+.....+.|.+.|+++-.. ..++..++|.-    ..  ....+.|-+|+||    |    
T Consensus         2 ~lk~VlIV-~k~~~~~A~~~a~~l~~~L~~rGi~v~~~~~~~~~~~~~~~----~~--~~~~~~Dlvi~lG----G----   66 (304)
T PRK02645          2 QLKLVIIA-YKAGSPQAKEAAERCAKQLEARGIKVLMGPSGPKDNPYPVF----LA--SAEELPDLAIVLG----G----   66 (304)
T ss_pred             CCCEEEEE-ECCCCHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCC----CC--CCCCCCCEEEEEC----C----
T ss_conf             74599999-85899999999999999999888999984443444777620----01--4466888999978----6----


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCE-------EEEECC-C---CHHHHHHHH
Q ss_conf             678999999999999974399705-------654255-8---899999950
Q gi|254780346|r   83 CDVIAHAVTRGLVDLSINGSLPIG-------NGIVVV-D---SEQQAFDRV  122 (149)
Q Consensus        83 ~e~I~~~v~~gl~~lsl~~~~PI~-------~gILt~-~---n~~QA~~R~  122 (149)
                           +.+.-...+....+++||.       .|-||- .   ..++++++.
T Consensus        67 -----DGT~L~aar~~~~~~iPilGiN~~G~lGFLte~~~~~~~~~~l~~l  112 (304)
T PRK02645         67 -----DGTVLAAARHLAPHDIPILSFNVGGHLGFLTHPRDLLQDESVWDRL  112 (304)
T ss_pred             -----CHHHHHHHHHHCCCCCCEEEEECCCEEEEECCCCCCCCHHHHHHHH
T ss_conf             -----8899999998542699889982486469716764221178999999


No 162
>PRK13057 putative lipid kinase; Reviewed
Probab=26.35  E-value=55  Score=14.80  Aligned_cols=73  Identities=21%  Similarity=0.261  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999879955555300144226999999863311378535665412000665246789999999999999743
Q gi|254780346|r   22 MLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSING  101 (149)
Q Consensus        22 ~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~  101 (149)
                      .....+...|.+.|++++.......-+.-    .++++.  ...||.+|+.|    ||     =--++++++++    ++
T Consensus        13 ~~~~~~~~~l~~~g~~~~~~~T~~~g~a~----~~~~~~--~~~~d~vv~~G----GD-----GTv~ev~~gl~----~~   73 (287)
T PRK13057         13 AALGAARAALEAAGLELVEPHPESPADLS----EVIEAH--ADGVDLVIVGG----GD-----GTLNAAAPALV----ET   73 (287)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCCHHHHH----HHHHHH--HCCCCEEEEEC----CH-----HHHHHHHHHHC----CC
T ss_conf             31999999999879979999549878999----999998--66999899988----58-----99999999860----57


Q ss_pred             CCCCEEEEECCCCH
Q ss_conf             99705654255889
Q gi|254780346|r  102 SLPIGNGIVVVDSE  115 (149)
Q Consensus       102 ~~PI~~gILt~~n~  115 (149)
                      ++|  .|||-.-|-
T Consensus        74 ~~~--lgiiP~GTg   85 (287)
T PRK13057         74 GLP--LGILPLGTA   85 (287)
T ss_pred             CCC--EEEECCCCH
T ss_conf             983--699738864


No 163
>pfam02601 Exonuc_VII_L Exonuclease VII, large subunit. This family consist of exonuclease VII, large subunit EC:3.1.11.6 This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones.
Probab=26.06  E-value=56  Score=14.77  Aligned_cols=93  Identities=18%  Similarity=0.355  Sum_probs=55.6

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCC--EEEE--EHHHH---HHHHHHHHHHHHHHHCCCCCCEEEEEEEEE
Q ss_conf             5871799980312899999999999999987995--5555--30014---422699999986331137853566541200
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQ--WSSI--VTPGV---LEIPAAVSMVMNAKTRSVTYDGIIVLGVVM   76 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~--~~~i--~VPGa---~EiP~a~~~~~~~~~~~~~~D~vIaLG~VI   76 (149)
                      +-.||+||.|.     +-.-+......+.+....  +..+  .|-|.   -||--+++.+-. .....+||.+|    |+
T Consensus        13 ~p~~IgvITS~-----~gAa~~Di~~~~~~r~p~~~i~l~p~~VQG~~a~~~I~~ai~~~~~-~~~~~~~Dvii----i~   82 (295)
T pfam02601        13 FPKRIAVITSA-----TGAAYQDFLRTARRRGPLVEIEIYPTLVQGDGAAESIVSALERANE-RETALDYDVIV----II   82 (295)
T ss_pred             CCCEEEEEECC-----CCHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHH-CCCCCCCCEEE----EE
T ss_conf             99989998489-----4089999999999819996799947357650489999999999984-68989983899----95


Q ss_pred             CCCCCHHHHHH---HHHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             06652467899---99999999999743997056542
Q gi|254780346|r   77 RGKTAHCDVIA---HAVTRGLVDLSINGSLPIGNGIV  110 (149)
Q Consensus        77 kGeT~H~e~I~---~~v~~gl~~lsl~~~~PI~~gIL  110 (149)
                      ||.=+--|+-|   ..+++.+.    +..+||+.||=
T Consensus        83 RGGGS~eDL~~FN~e~laraI~----~~~iPvisaIG  115 (295)
T pfam02601        83 RGGGSKEDLWVFNDEELARAIA----NSPIPVITGIG  115 (295)
T ss_pred             CCCCCHHHHHHCCHHHHHHHHH----HCCCCEEECCC
T ss_conf             7868889874558899999998----38998780678


No 164
>PRK07235 amidase; Provisional
Probab=25.33  E-value=57  Score=14.69  Aligned_cols=43  Identities=14%  Similarity=0.039  Sum_probs=32.8

Q ss_pred             CCCCEEEEEEECHH----HHHHHHHHHHHHHHHHHCCCCEEEEEHHH
Q ss_conf             65871799980312----89999999999999998799555553001
Q gi|254780346|r    3 VFIPHVLIIEARFY----ENLSAMLFEGCVNVLHSRAVQWSSIVTPG   45 (149)
Q Consensus         3 ~~~~kI~IV~s~~~----~~i~~~ll~ga~~~l~~~~~~~~~i~VPG   45 (149)
                      +...||+|+...|.    +.-++..++.+.+.|.+.|+.++.+.+|-
T Consensus       273 ~~~lrIGv~~~~~~~~~~d~~v~~av~~a~~~L~~~Ga~V~ev~~P~  319 (504)
T PRK07235        273 VKGLKIGVLREGFGLPNSEPEVDEAVRAAAERLESLGATVEEVSIPW  319 (504)
T ss_pred             CCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf             44563443033458888889999999999999986698589844850


No 165
>TIGR00707 argD acetylornithine and succinylornithine aminotransferases; InterPro: IPR004636   This family of proteins, for which ornithine aminotransferases form an outgroup, consists mostly of proteins designated acetylornithine aminotransferase. However, the two very closely related members from Escherichia coli are assigned different enzymatic activities. One is acetylornithine aminotransferase (2.6.1.11 from EC), ArgD, an enzyme of arginine biosynthesis, while another is succinylornithine aminotransferase, an enzyme of the arginine succinyltransferase pathway, an ammonia-generating pathway of arginine catabolism . Members of this family may also act on ornithine, like ornithine aminotransferase (2.6.1.13 from EC)  and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (2.6.1.17 from EC, DapC, an enzyme of lysine biosynthesis) . ; GO: 0008483 transaminase activity, 0006525 arginine metabolic process.
Probab=25.11  E-value=51  Score=15.01  Aligned_cols=21  Identities=19%  Similarity=0.154  Sum_probs=14.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHH
Q ss_conf             657456999999999999998
Q gi|254780346|r  125 SHLDRGGCAARSALAMIELKK  145 (149)
Q Consensus       125 ~~~nkG~eaa~Aal~mi~l~~  145 (149)
                      -.+|=|.||-.|||++++..-
T Consensus        97 FFCNSGaEAnEAAlKlARk~~  117 (402)
T TIGR00707        97 FFCNSGAEANEAALKLARKYT  117 (402)
T ss_pred             EEECCHHHHHHHHHHHHHHHH
T ss_conf             751474789999999989864


No 166
>PRK13689 hypothetical protein; Provisional
Probab=24.65  E-value=59  Score=14.61  Aligned_cols=29  Identities=10%  Similarity=0.197  Sum_probs=26.2

Q ss_pred             EEECHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             98031289999999999999998799555
Q gi|254780346|r   11 IEARFYENLSAMLFEGCVNVLHSRAVQWS   39 (149)
Q Consensus        11 V~s~~~~~i~~~ll~ga~~~l~~~~~~~~   39 (149)
                      +.|+|..+-++.++..-...|+++++..|
T Consensus         3 i~SKYs~~qvE~il~el~~vLeKH~Ap~D   31 (75)
T PRK13689          3 QQSKYSDEQVEQLLAELLAVLEKHKAPTD   31 (75)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             53202389999999999999986599941


No 167
>PRK11574 hypothetical protein; Provisional
Probab=23.71  E-value=62  Score=14.50  Aligned_cols=94  Identities=10%  Similarity=0.042  Sum_probs=55.2

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE--------EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEE
Q ss_conf             58717999803128999999999999999879955555--------3001442269999998633113785356654120
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI--------VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVV   75 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i--------~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~V   75 (149)
                      |.+|++|..+.=.+|+-   .-...+.|.+.|+++...        .|.|+.-+...+...+..- ...+||+++-=|  
T Consensus         1 M~kk~LV~lA~GfEEiE---a~~~vDvLRRagi~V~~asv~~~~~~~v~gs~gi~i~aD~~l~~v-~~~~yD~ivlPG--   74 (196)
T PRK11574          1 MSASALVCLAPGSEETE---AVTTIDLLVRGGIKVTTASVASDGNLTITCSRGVKLLADAPLVEV-ADGEYDVIVLPG--   74 (196)
T ss_pred             CCCEEEEECCCCCCHHH---HHHHHHHHHHCCCEEEEEEECCCCCCEEEECCCCEEECCCCHHHC-CCCCCCEEECCC--
T ss_conf             98569999169850212---518999997779849999853899737994799789578677777-825588899178--


Q ss_pred             ECCCCCHHHHHH-HHHHHHHHHHHHHCCCCCE
Q ss_conf             006652467899-9999999999974399705
Q gi|254780346|r   76 MRGKTAHCDVIA-HAVTRGLVDLSINGSLPIG  106 (149)
Q Consensus        76 IkGeT~H~e~I~-~~v~~gl~~lsl~~~~PI~  106 (149)
                         ..+-.+... ++....+.+-..+.+++|.
T Consensus        75 ---G~~ga~~L~~~~~v~~~lk~~~~~gK~iA  103 (196)
T PRK11574         75 ---GIKGAECFRDSPLLVETVKQFHRSGRIVA  103 (196)
T ss_pred             ---CCHHHHHHHHCHHHHHHHHHHHHCCCEEE
T ss_conf             ---80379998739899999999998799199


No 168
>cd06326 PBP1_STKc_like Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins. The type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins, some of which contain a conserved catalytic serine/threonine protein kinase (STKc) domain in the N-terminal region. Members of this group are sequence-similar to the branched-chain amino acid ABC transporter leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=23.37  E-value=63  Score=14.45  Aligned_cols=63  Identities=13%  Similarity=0.222  Sum_probs=43.9

Q ss_pred             CCCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEE-EEE-HHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             587179998031289999999999999998799555-553-0014422699999986331137853566541
Q gi|254780346|r    4 FIPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWS-SIV-TPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         4 ~~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~-~i~-VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      ..+|++|+..+  .+....+.+.+.+.+++.|.++- ... -||.-+.-..+.++.     ..++|+++..|
T Consensus       135 g~kkvavl~~d--~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~Dfs~~l~~i~-----~~~pD~v~~~~  199 (336)
T cd06326         135 GLKRIAVFYQD--DAFGKDGLAGVEKALAARGLKPVATASYERNTADVAAAVAQLA-----AARPQAVIMVG  199 (336)
T ss_pred             CCCEEEEEECC--CHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHH-----HCCCCEEEEEC
T ss_conf             99759999358--7588999999999999779937999986899877799999998-----47979999927


No 169
>cd03795 GT1_like_4 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP-linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=23.19  E-value=63  Score=14.43  Aligned_cols=36  Identities=11%  Similarity=0.162  Sum_probs=26.7

Q ss_pred             EEEEEEECHHHHH--HHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             1799980312899--99999999999998799555553
Q gi|254780346|r    7 HVLIIEARFYENL--SAMLFEGCVNVLHSRAVQWSSIV   42 (149)
Q Consensus         7 kI~IV~s~~~~~i--~~~ll~ga~~~l~~~~~~~~~i~   42 (149)
                      ||++|...|++++  ++..+..-.+.|.+.|.++.++.
T Consensus         1 kIL~i~~~f~P~~GG~e~~~~~L~~~L~~~Gh~V~v~~   38 (357)
T cd03795           1 RVLHVGKFYPPDRGGIEQVIRDLAEGLAARGIEVAVLC   38 (357)
T ss_pred             CEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             99999382899898299999999999997799899998


No 170
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR; InterPro: IPR011785    This entry represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor . These proteins contain a Helix-Turn-Helix motif of the "fis" type..
Probab=22.76  E-value=25  Score=16.88  Aligned_cols=62  Identities=21%  Similarity=0.263  Sum_probs=39.2

Q ss_pred             ECHHHHHHHHHHHHHHHHHHHCCCC--------EEEEEHHHHHHHHHHHHHHHHHHH-CCCCCCEEEEEEEEE
Q ss_conf             0312899999999999999987995--------555530014422699999986331-137853566541200
Q gi|254780346|r   13 ARFYENLSAMLFEGCVNVLHSRAVQ--------WSSIVTPGVLEIPAAVSMVMNAKT-RSVTYDGIIVLGVVM   76 (149)
Q Consensus        13 s~~~~~i~~~ll~ga~~~l~~~~~~--------~~~i~VPGa~EiP~a~~~~~~~~~-~~~~~D~vIaLG~VI   76 (149)
                      -+|++-+++.=.+-+...|.+..-+        ...+-.|+.+|+|.-.  .+-... ..++..+++++|==.
T Consensus        39 ~~w~ei~~~es~~k~~~~l~~a~~~g~~a~r~~~~~~~~P~~~ElP~~F--~~~~L~~sdGk~~~vLa~GrdL  109 (453)
T TIGR02040        39 RRWEEIVTEESKEKVEALLSEAKRTGVGAVRVELNRFVLPSDLELPMEF--VLVRLGASDGKDEGVLALGRDL  109 (453)
T ss_pred             CCHHHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCEEE--EEECCCCCCCCCCCEEEECCCC
T ss_conf             8444413577899999999714688885777766541179997244034--6761678788887358884652


No 171
>KOG1017 consensus
Probab=22.46  E-value=65  Score=14.34  Aligned_cols=34  Identities=24%  Similarity=0.361  Sum_probs=14.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH---CCCCCEEEEECCCC
Q ss_conf             6524678999999999999974---39970565425588
Q gi|254780346|r   79 KTAHCDVIAHAVTRGLVDLSIN---GSLPIGNGIVVVDS  114 (149)
Q Consensus        79 eT~H~e~I~~~v~~gl~~lsl~---~~~PI~~gILt~~n  114 (149)
                      .|.|-||+-+  ++-|++|-++   +.+|-.-+-.|+.+
T Consensus        88 st~rsDF~F~--ADRLiRLViEE~LNqLPytec~VtTPT  124 (267)
T KOG1017          88 STNRSDFVFN--ADRLIRLVIEECLNQLPYTECTVTTPT  124 (267)
T ss_pred             CCCCCCEEEE--HHHHHHHHHHHHHHCCCCCCEEEECCC
T ss_conf             6864343660--888999999988622885320542688


No 172
>pfam08967 DUF1884 Domain of unknown function (DUF1884). This domain is found in a set of hypothetical bacterial proteins. It shows similarity to the N-terminus of ATP-synthase.
Probab=22.41  E-value=65  Score=14.34  Aligned_cols=52  Identities=21%  Similarity=0.239  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEEEH-HHHHHH-HHHHHHHHHHHH---CCCCCCEEEE
Q ss_conf             999999999999987995555530-014422-699999986331---1378535665
Q gi|254780346|r   20 SAMLFEGCVNVLHSRAVQWSSIVT-PGVLEI-PAAVSMVMNAKT---RSVTYDGIIV   71 (149)
Q Consensus        20 ~~~ll~ga~~~l~~~~~~~~~i~V-PGa~Ei-P~a~~~~~~~~~---~~~~~D~vIa   71 (149)
                      +-..++.+.+.|+.-|++.|++-| |+++|- +--+-.+.+-+-   .---+||+|+
T Consensus        10 il~~ie~~inELk~eG~ePDiiL~G~e~~efl~e~~l~~~~lkv~~ieELG~DAVv~   66 (85)
T pfam08967        10 ILEIIEEKINELKMEGFEPDIILVGPEFYEFLSEDFLKVSNLKVYIIEELGSDAVIA   66 (85)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHCCEEEEHHHCCCCEEEE
T ss_conf             999999999999865899876998489998813888876186688787618851897


No 173
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=22.00  E-value=67  Score=14.29  Aligned_cols=122  Identities=8%  Similarity=0.020  Sum_probs=72.6

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHH
Q ss_conf             87179998031289999999999999998799555553001442269999998633113785356654120006652467
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCD   84 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e   84 (149)
                      ..||+++.+.= ...+..-.+|+.+.++++++++ +-..+|-|+--.+.+.+-+-.....+.|++.+.          .|
T Consensus       127 ~g~v~il~G~~-~~~~~~R~~Gf~~~l~~~~i~v-v~~~~~~~~~~~a~~~~~~~L~~~pdi~~Ifa~----------nD  194 (274)
T cd06311         127 NGNIVVLRGIP-TPIDNERVDAFDAAIAKYPIKI-LDRQYANWNRDDAFSVMQDLLTKFPKIDAVWAH----------DD  194 (274)
T ss_pred             CCCEEEEECCC-CCHHHHHHHHHHHHHHHCCCEE-EEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEC----------CC
T ss_conf             78579996899-8457999999999998779889-985038756899999999998438888889988----------98


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHH-CCCC---------CCCHHHHHHHHHHHHH
Q ss_conf             89999999999999743997056542558899999950-6565---------7456999999999999
Q gi|254780346|r   85 VIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRV-SPSH---------LDRGGCAARSALAMIE  142 (149)
Q Consensus        85 ~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~-~~~~---------~nkG~eaa~Aal~mi~  142 (149)
                      -.+-.+.++|.+.... +.+++.|.   +-..++.+.. .++.         ..-|+.|++.++++++
T Consensus       195 ~ma~Ga~~Al~~aG~~-~~~~vvG~---Dg~~~~~~~i~~G~~~~~atv~~~p~~~~~Av~~a~~~l~  258 (274)
T cd06311         195 DMAVGVLAAIKQAGRT-DIKFVVGG---AGSKDMIKMIMDGDPLIPADVLYPPSMIASAIDLTVALFQ  258 (274)
T ss_pred             CHHHHHHHHHHHCCCC-CCCEEEEE---CCCHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHHHHHHC
T ss_conf             0589999999976999-99789996---5998999999769974899980899999999999999977


No 174
>PRK11036 putative metallothionein SmtA; Provisional
Probab=21.82  E-value=67  Score=14.26  Aligned_cols=49  Identities=16%  Similarity=0.150  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEHHHHH-HHHHHHHHHHHHHHCCCCCCEEEEEEEE
Q ss_conf             999999999999999879955555300144-2269999998633113785356654120
Q gi|254780346|r   18 NLSAMLFEGCVNVLHSRAVQWSSIVTPGVL-EIPAAVSMVMNAKTRSVTYDGIIVLGVV   75 (149)
Q Consensus        18 ~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~-EiP~a~~~~~~~~~~~~~~D~vIaLG~V   75 (149)
                      |++..|++.|+..+.+.|+....-++-+.. +++-.         ....||.|+|.+++
T Consensus        73 D~S~~mL~~A~~~a~~~gv~~~~~~v~~~~q~l~~~---------~~~~fDlVlcHaVL  122 (256)
T PRK11036         73 DLSAEMIQRAKQAAEAKGVSDNMQFIHCAAQDIAQH---------LETPVDLILFHAVL  122 (256)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHH---------CCCCCCEEEEEHHH
T ss_conf             699999999999988649661279885689988542---------36886678651367


No 175
>smart00851 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site PUBMED:10526357.
Probab=21.81  E-value=67  Score=14.26  Aligned_cols=68  Identities=18%  Similarity=0.182  Sum_probs=37.1

Q ss_pred             HHHHHHHHCCCCEEEEEHHHHHH-HHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99999998799555553001442-26999999863311378535665412000665246789999999999999743997
Q gi|254780346|r   26 GCVNVLHSRAVQWSSIVTPGVLE-IPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSINGSLP  104 (149)
Q Consensus        26 ga~~~l~~~~~~~~~i~VPGa~E-iP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~P  104 (149)
                      |..+.|+++|+++..+ +|-..| .|-..+++     ..+++|.||..-       +.+.-....-...+.+.++++++|
T Consensus        21 GTa~~L~~~Gi~v~~l-~~ki~~g~~~i~~~i-----~~~~IdlVInt~-------~~~~~~~~~d~~~iRr~a~~~~Ip   87 (90)
T smart00851       21 GTAKFLREAGLPVKTL-HPKVHGGILAILDLI-----KNGEIDLVINTL-------YPLGAQPHEDGKALRRAAENIDIP   87 (90)
T ss_pred             HHHHHHHHCCCCCEEE-ECCCCCCCCCHHHHH-----CCCCEEEEEEEC-------CCCCCHHHHCCCCHHHHHHCCCCC
T ss_conf             5899999759971043-024435610489981-----978879999846-------876323653588899998808988


Q ss_pred             CE
Q ss_conf             05
Q gi|254780346|r  105 IG  106 (149)
Q Consensus       105 I~  106 (149)
                      ..
T Consensus        88 ~~   89 (90)
T smart00851       88 GA   89 (90)
T ss_pred             CC
T ss_conf             70


No 176
>cd04104 p47_IIGP_like p47 (47-kDa) family.  The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1.  They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens.  p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma).  ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis.  TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro.  IRG-47 is involved in resistance to T. gondii infection.  LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections.  IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues.  In macrophages, IIGP1 interacts with hook3, a microtubule binding protei
Probab=21.41  E-value=68  Score=14.21  Aligned_cols=77  Identities=14%  Similarity=0.090  Sum_probs=43.0

Q ss_pred             EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHH
Q ss_conf             30014422699999986331137853566541200066524678999999999999974399705654255889999995
Q gi|254780346|r   42 VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHCDVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDR  121 (149)
Q Consensus        42 ~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R  121 (149)
                      +.||+=-.-+..+..++.. .-.+||.||.+      -...|..---    .|...--+.++|.-+-.=-+++.-++..|
T Consensus        58 DlPG~Gt~~f~~~~Yl~~~-~~~~yD~fiii------ss~rf~~nd~----~la~~i~~~gK~fyfVRsK~D~dl~n~~~  126 (197)
T cd04104          58 DLPGIGSTAFPPDDYLEEM-KFSEYDFFIII------SSTRFSSNDV----KLAKAIQCMGKKFYFVRTKVDRDLSNEQR  126 (197)
T ss_pred             CCCCCCCCCCCHHHHHHHC-CCCCCCEEEEE------ECCCCCHHHH----HHHHHHHHCCCCEEEEEECCCCCCCHHHH
T ss_conf             2899998765989999865-85545789998------3886414269----99999998099289998612140005663


Q ss_pred             HCCCCCCC
Q ss_conf             06565745
Q gi|254780346|r  122 VSPSHLDR  129 (149)
Q Consensus       122 ~~~~~~nk  129 (149)
                      +.+..-|+
T Consensus       127 ~~p~~f~~  134 (197)
T cd04104         127 SKPRSFNR  134 (197)
T ss_pred             CCCCCCCH
T ss_conf             78766599


No 177
>pfam03358 FMN_red NADPH-dependent FMN reductase.
Probab=21.06  E-value=70  Score=14.17  Aligned_cols=37  Identities=16%  Similarity=0.133  Sum_probs=28.8

Q ss_pred             EEEEEEECHHH-HHHHHHHHHHHHHHHHCCCCEEEEEH
Q ss_conf             17999803128-99999999999999987995555530
Q gi|254780346|r    7 HVLIIEARFYE-NLSAMLFEGCVNVLHSRAVQWSSIVT   43 (149)
Q Consensus         7 kI~IV~s~~~~-~i~~~ll~ga~~~l~~~~~~~~~i~V   43 (149)
                      ||+++.++-.+ -.+..|.+-+.+.|.+.|.+.+.++.
T Consensus         2 kil~i~GS~r~~s~t~~l~~~~~~~l~~~g~e~~~idl   39 (147)
T pfam03358         2 KILVISGSPRKGSNTRKLAEWAAELLEEAGAEVELIDL   39 (147)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             79999767998876999999999998776992599632


No 178
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=20.99  E-value=70  Score=14.16  Aligned_cols=62  Identities=15%  Similarity=0.145  Sum_probs=43.3

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEE-E-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
Q ss_conf             871799980312899999999999999987995555-5-30014422699999986331137853566541
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSS-I-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLG   73 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~-i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG   73 (149)
                      .+|++|+...  .+....+.+++.+.+++.|.++-. . .-||.-+.-..+.++.     ..++|+|+..|
T Consensus       138 ~kkvai~~~d--~~~G~~~~~~~~~~~~~~G~~vv~~~~~~~~~~Df~~~l~~i~-----~~~pD~V~~~~  201 (347)
T cd06335         138 FKKVALLLDN--TGWGRSNRKDLTAALAARGLKPVAVEWFNWGDKDMTAQLLRAK-----AAGADAIIIVG  201 (347)
T ss_pred             CCEEEEEEEC--CHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCCHHHHHHHHH-----HCCCCEEEEEC
T ss_conf             8669999707--6366899999999998659867578840799834899999998-----66999999947


No 179
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=20.55  E-value=71  Score=14.10  Aligned_cols=122  Identities=16%  Similarity=0.160  Sum_probs=67.6

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEE-EHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCCHH
Q ss_conf             8717999803128999999999999999879955555-300144226999999863311378535665412000665246
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSI-VTPGVLEIPAAVSMVMNAKTRSVTYDGIIVLGVVMRGKTAHC   83 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i-~VPGa~EiP~a~~~~~~~~~~~~~~D~vIaLG~VIkGeT~H~   83 (149)
                      ..+|+++...-.....+.-.+|+.+.+++. -.++++ ..|+-|..--+.+..-.-.....+.|++++          |.
T Consensus       123 ~g~v~ii~g~~~~~~~~~R~~Gf~~~l~~~-~~i~vv~~~~~~~~~~~a~~~~~~~L~~~pdid~I~~----------~n  191 (272)
T cd06313         123 KGKIAMLQGALGHTGAQGRAQGFNDVIKKY-PDIEVVDEQPANWDVSKAARIWETWLTKYPQLDGAFC----------HN  191 (272)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHC-CCCEEEEEEECCCCHHHHHHHHHHHHHHCCCCCEEEE----------CC
T ss_conf             972999847988689999999999999877-9919999862687689999999999964999878998----------88


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHCCCC---------CCCHHHHHHHHHHHHH
Q ss_conf             7899999999999997439970565425588999999506565---------7456999999999999
Q gi|254780346|r   84 DVIAHAVTRGLVDLSINGSLPIGNGIVVVDSEQQAFDRVSPSH---------LDRGGCAARSALAMIE  142 (149)
Q Consensus        84 e~I~~~v~~gl~~lsl~~~~PI~~gILt~~n~~QA~~R~~~~~---------~nkG~eaa~Aal~mi~  142 (149)
                      |..+-.+.+++.... ..++.    |.+.+...++++......         -.-|+.+++++++.++
T Consensus       192 D~~a~Ga~~Al~~aG-~~~v~----v~g~Dg~~~~l~~I~~G~~~atv~q~~~~~G~~av~~a~~~~~  254 (272)
T cd06313         192 DSMALAAYQIMKAAG-RTKIV----IGGVDGDPPAIQAVSDGRMVATVRNPACRIHGGAIAAGVRIVR  254 (272)
T ss_pred             CHHHHHHHHHHHHCC-CCCCE----EEEECCCHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHC
T ss_conf             477899999999769-99868----9997899999999985991899806999999999999999976


No 180
>KOG3135 consensus
Probab=20.16  E-value=73  Score=14.05  Aligned_cols=43  Identities=23%  Similarity=0.241  Sum_probs=29.6

Q ss_pred             CCEEEEEEECHHHHHHHHHHHHHHHHHHHCCCCEEEEEHHHHHH
Q ss_conf             87179998031289999999999999998799555553001442
Q gi|254780346|r    5 IPHVLIIEARFYENLSAMLFEGCVNVLHSRAVQWSSIVTPGVLE   48 (149)
Q Consensus         5 ~~kI~IV~s~~~~~i~~~ll~ga~~~l~~~~~~~~~i~VPGa~E   48 (149)
                      |+||+||.=+.|..| +.|-+.-++-.+..+-+-+...||..+-
T Consensus         1 ~~kv~iv~ys~yghv-~~lAe~~kkGie~a~geA~i~qVpEtl~   43 (203)
T KOG3135           1 MPKVAIVIYSTYGHV-AKLAEAEKKGIESAGGEATIYQVPETLS   43 (203)
T ss_pred             CCEEEEEEEECCCHH-HHHHHHHHHHHHCCCCEEEEEECCCCCC
T ss_conf             963899999802289-9999999700330698168997655168


No 181
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family; InterPro: IPR011911   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon . Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system..
Probab=20.07  E-value=73  Score=14.04  Aligned_cols=51  Identities=16%  Similarity=0.089  Sum_probs=33.6

Q ss_pred             HHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHHHHH-CCCCCCEE---EEEEEEECC
Q ss_conf             9999999987995555530014422699999986331-13785356---654120006
Q gi|254780346|r   25 EGCVNVLHSRAVQWSSIVTPGVLEIPAAVSMVMNAKT-RSVTYDGI---IVLGVVMRG   78 (149)
Q Consensus        25 ~ga~~~l~~~~~~~~~i~VPGa~EiP~a~~~~~~~~~-~~~~~D~v---IaLG~VIkG   78 (149)
                      ..|++.|..+|++++.+.|-   .=+.|.+.+++... ..+-+-.+   |.=+-||.|
T Consensus        14 ~~aK~yL~~~gv~f~~~dV~---~d~~A~~~~~k~~gG~~gVPv~vsGdi~~~~i~~G   68 (79)
T TIGR02196        14 KKAKEYLTSKGVAFEEIDVE---KDSAAREELLKKLGGQRGVPVIVSGDIGTHKIIVG   68 (79)
T ss_pred             HHHHHHHHHCCCCEEEECCC---CCHHHHHHHHHHHCCCCCCCEEEECCCCCCEEEEE
T ss_conf             89999999549945763433---69788999999838985455576342379724870


Done!