Query         gi|254781049|ref|YP_003065462.1| succinyl-CoA synthetase subunit beta [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 398
No_of_seqs    206 out of 1932
Neff          6.1 
Searched_HMMs 39220
Date          Mon May 30 06:50:53 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781049.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01016 sucCoAbeta succinyl- 100.0       0       0 1126.3  39.0  386    1-396     1-389 (389)
  2 PRK00696 sucC succinyl-CoA syn 100.0       0       0 1038.7  44.0  388    1-398     1-388 (388)
  3 COG0045 SucC Succinyl-CoA synt 100.0       0       0  970.9  42.5  384    1-397     1-386 (387)
  4 KOG1447 consensus              100.0       0       0  788.6  29.5  391    1-394    20-410 (412)
  5 KOG2799 consensus              100.0       0       0  765.2  18.4  393    1-396    23-422 (434)
  6 pfam08442 ATP-grasp_2 ATP-gras 100.0       0       0  458.0  21.6  201    2-212     1-201 (202)
  7 pfam00549 Ligase_CoA CoA-ligas 100.0 1.2E-27 3.1E-32  201.7  11.5  119  272-392     1-126 (128)
  8 KOG1254 consensus               99.7 4.4E-19 1.1E-23  145.4   1.2  313   37-373    76-464 (600)
  9 COG1042 Acyl-CoA synthetase (N  99.5 4.5E-14 1.2E-18  112.4   5.1  361    2-396    23-449 (598)
 10 COG1042 Acyl-CoA synthetase (N  99.5 4.6E-14 1.2E-18  112.3   4.6  117    2-148   470-586 (598)
 11 TIGR02717 AcCoA-syn-alpha acet  99.4 4.5E-12 1.1E-16   99.2  11.8  187  185-395   218-454 (457)
 12 TIGR01369 CPSaseII_lrg carbamo  99.4 1.5E-11 3.8E-16   95.8  11.9   95   10-130   133-227 (1089)
 13 pfam01071 GARS_A Phosphoribosy  99.3 3.1E-11   8E-16   93.7  12.4   99    6-127     4-102 (193)
 14 pfam02222 ATP-grasp ATP-grasp   99.3 5.4E-10 1.4E-14   85.5  14.8   88   12-128     1-88  (171)
 15 PRK02186 argininosuccinate lya  99.3 5.5E-10 1.4E-14   85.5  14.6   92    5-124   108-199 (892)
 16 PRK12815 carB carbamoyl phosph  99.2   1E-10 2.6E-15   90.3   8.4  116    9-154   133-248 (1068)
 17 pfam02786 CPSase_L_D2 Carbamoy  99.2 7.1E-10 1.8E-14   84.7  11.4  107    6-135     3-111 (211)
 18 PRK05294 carB carbamoyl phosph  99.1 2.6E-10 6.7E-15   87.6   8.1  139    9-180   133-278 (1063)
 19 PRK01372 ddl D-alanine--D-alan  99.1 1.4E-08 3.4E-13   76.3  16.0  166    5-223    99-265 (304)
 20 PRK09288 purT phosphoribosylgl  99.1   5E-09 1.3E-13   79.1  13.7   95    8-126   117-212 (395)
 21 TIGR00877 purD phosphoribosyla  99.1 1.2E-09   3E-14   83.3  10.3  211    8-265   112-346 (459)
 22 PRK00885 phosphoribosylamine--  99.1   3E-09 7.7E-14   80.6  11.6  199    7-253   105-307 (424)
 23 PRK13789 phosphoribosylamine--  99.1 2.7E-09 6.9E-14   80.9  10.8  212    7-265   111-328 (426)
 24 TIGR02068 cya_phycin_syn cyano  99.0 1.4E-09 3.7E-14   82.7   7.9  121    8-164   222-350 (876)
 25 PRK13790 phosphoribosylamine--  99.0 6.1E-09 1.5E-13   78.6  11.1  197    7-253   106-305 (415)
 26 COG0151 PurD Phosphoribosylami  99.0 6.6E-09 1.7E-13   78.3  10.8  195    7-253   106-308 (428)
 27 PRK07206 hypothetical protein;  99.0 2.4E-07 6.1E-12   68.1  17.6   97    5-123   109-208 (415)
 28 pfam07478 Dala_Dala_lig_C D-al  98.9 1.8E-07 4.5E-12   68.9  15.6  159   11-223     1-168 (201)
 29 PRK12767 carbamoyl phosphate s  98.9 1.3E-08 3.3E-13   76.4   8.4   92    5-129   112-204 (325)
 30 pfam08443 RimK RimK-like ATP-g  98.8 5.6E-08 1.4E-12   72.2  10.9   93    6-126     5-100 (190)
 31 PRK01966 ddl D-alanyl-alanine   98.8 5.8E-07 1.5E-11   65.5  15.9  166    5-224   133-308 (344)
 32 PRK05586 biotin carboxylase; V  98.8   9E-07 2.3E-11   64.3  16.8  107    6-135   117-225 (447)
 33 PRK08462 biotin carboxylase; V  98.8   1E-07 2.6E-12   70.6  11.4  107    6-135   119-227 (446)
 34 PRK08654 pyruvate carboxylase   98.8 4.1E-08 1.1E-12   73.1   9.4  167    6-212   117-292 (497)
 35 PRK07178 acetyl-CoA carboxylas  98.8   3E-07 7.7E-12   67.4  13.4  165    6-210   116-289 (471)
 36 PRK08591 acetyl-CoA carboxylas  98.8 3.8E-07 9.7E-12   66.8  13.8  107    6-135   117-225 (449)
 37 TIGR01369 CPSaseII_lrg carbamo  98.8 4.1E-08   1E-12   73.2   8.6  331    9-391   694-1088(1089)
 38 PRK06111 acetyl-CoA carboxylas  98.8 1.6E-06 4.1E-11   62.6  16.7  107    6-135   117-225 (449)
 39 TIGR00514 accC acetyl-CoA carb  98.8 1.2E-07 2.9E-12   70.2  10.3  106    7-135   118-226 (451)
 40 COG0458 CarB Carbamoylphosphat  98.7 2.2E-07 5.6E-12   68.3  11.0  101    7-134   119-219 (400)
 41 PRK08463 acetyl-CoA carboxylas  98.7 3.8E-06 9.7E-11   60.2  16.4  107    6-135   116-225 (478)
 42 TIGR02144 LysX_arch Lysine bio  98.7 7.9E-08   2E-12   71.2   7.2   81    7-113    91-173 (289)
 43 PRK06019 phosphoribosylaminoim  98.6 8.5E-07 2.2E-11   64.4  11.7   93    6-127   107-199 (377)
 44 TIGR02712 urea_carbox urea car  98.6 9.7E-07 2.5E-11   64.1  12.0  255    6-328   116-426 (1226)
 45 COG0439 AccC Biotin carboxylas  98.6 1.1E-06 2.7E-11   63.8  11.9  101    5-127   116-218 (449)
 46 PRK12999 pyruvate carboxylase;  98.6 9.6E-06 2.5E-10   57.5  16.4  108    6-136   121-230 (1147)
 47 TIGR01161 purK phosphoribosyla  98.6 9.7E-07 2.5E-11   64.1  11.1  121    5-162   103-227 (386)
 48 COG0026 PurK Phosphoribosylami  98.6 5.4E-06 1.4E-10   59.1  14.6  119    6-162   101-219 (375)
 49 TIGR01205 D_ala_D_alaTIGR D-al  98.6 1.3E-06 3.4E-11   63.1  10.7  153    5-198   150-316 (375)
 50 PRK12833 acetyl-CoA carboxylas  98.6 5.2E-06 1.3E-10   59.3  13.7  107    6-136   120-228 (458)
 51 PRK06395 phosphoribosylamine--  98.5 9.7E-07 2.5E-11   64.1   9.7  196    7-253   108-312 (435)
 52 KOG0237 consensus               98.5 1.2E-06 3.2E-11   63.4   9.9  106    7-134   111-216 (788)
 53 KOG0238 consensus               98.5 1.6E-05 4.1E-10   56.1  15.3  107    6-135   113-221 (670)
 54 COG4770 Acetyl/propionyl-CoA c  98.5 5.1E-05 1.3E-09   52.7  16.9  108    6-136   117-226 (645)
 55 PRK05294 carB carbamoyl phosph  98.4 0.00019 4.9E-09   48.9  24.0  329    9-393   673-1049(1063)
 56 PRK10446 ribosomal protein S6   98.4 8.6E-06 2.2E-10   57.8  12.2   80    6-113   101-181 (300)
 57 PRK12815 carB carbamoyl phosph  98.4   5E-05 1.3E-09   52.8  16.0  326    9-393   674-1049(1068)
 58 pfam02655 ATP-grasp_3 ATP-gras  98.4 2.4E-06   6E-11   61.5   9.0   80    5-127     4-83  (160)
 59 TIGR03103 trio_acet_GNAT GNAT-  98.2 1.2E-05   3E-10   56.9   9.2  109    8-148   301-415 (547)
 60 TIGR00768 rimK_fam alpha-L-glu  98.2 1.5E-05 3.8E-10   56.3   8.7   83    7-113   116-209 (321)
 61 PRK05784 phosphoribosylamine--  98.1 1.7E-05 4.3E-10   55.9   8.2  214    7-265   112-342 (485)
 62 COG0027 PurT Formate-dependent  98.0 3.2E-05 8.1E-10   54.1   7.7   84   13-120   123-206 (394)
 63 COG0189 RimK Glutathione synth  97.8  0.0003 7.6E-09   47.7  10.3   93    6-125   121-215 (318)
 64 PRK02471 bifunctional glutamat  97.8 0.00023 5.7E-09   48.5   8.9   89    6-123   491-583 (753)
 65 COG1038 PycA Pyruvate carboxyl  97.8  0.0016 4.2E-08   42.8  12.9  128    6-171   123-259 (1149)
 66 pfam06263 consensus             97.8  0.0011 2.7E-08   44.1  11.9  129  267-397   339-509 (514)
 67 TIGR01235 pyruv_carbox pyruvat  97.8 0.00062 1.6E-08   45.6  10.7  167    7-212   122-298 (1169)
 68 PRK06091 membrane protein FdrA  97.5  0.0029 7.4E-08   41.2  10.9  129  267-397   331-495 (555)
 69 PRK05678 succinyl-CoA syntheta  97.4  0.0059 1.5E-07   39.1  11.7  125  262-395   141-288 (289)
 70 PTZ00187 succinyl-CoA syntheta  97.3   0.005 1.3E-07   39.6  10.8  127  263-395   158-305 (309)
 71 COG1181 DdlA D-alanine-D-alani  97.3  0.0014 3.6E-08   43.3   7.3   94    5-127   104-201 (317)
 72 KOG0369 consensus               96.9   0.042 1.1E-06   33.5  13.0  106    7-135   150-257 (1176)
 73 KOG0370 consensus               96.7  0.0012   3E-08   43.8   2.6   90   13-130   507-596 (1435)
 74 PRK06849 hypothetical protein;  96.4   0.036 9.3E-07   34.0   8.6   95    8-135   120-214 (387)
 75 KOG0368 consensus               96.3   0.026 6.7E-07   34.9   7.6   88   23-137   223-310 (2196)
 76 cd07022 S49_Sppa_36K_type Sign  96.3   0.033 8.5E-07   34.2   8.1   24  178-201   146-169 (214)
 77 PRK13277 5-formaminoimidazole-  96.2   0.043 1.1E-06   33.5   8.4   97   10-135   129-225 (363)
 78 PRK13278 purP 5-formaminoimida  96.1    0.04   1E-06   33.7   7.7   94    9-135   126-219 (356)
 79 cd01540 PBP1_arabinose_binding  96.0    0.14 3.5E-06   30.2  11.9  107  282-393   152-266 (289)
 80 COG1759 5-formaminoimidazole-4  95.9   0.081 2.1E-06   31.7   8.7   95    9-134   129-223 (361)
 81 cd07014 S49_SppA Signal peptid  95.9   0.078   2E-06   31.8   8.4   71  297-370    16-89  (177)
 82 COG0074 SucD Succinyl-CoA synt  95.6     0.2   5E-06   29.1  11.5  132  257-395   134-289 (293)
 83 cd06287 PBP1_LacI_like_8 Ligan  95.6     0.2 5.1E-06   29.1  12.0  117  268-395   120-244 (269)
 84 TIGR01142 purT phosphoribosylg  95.6   0.075 1.9E-06   31.9   7.3  107   11-136   111-217 (407)
 85 cd07019 S49_SppA_1 Signal pept  95.2    0.19 4.7E-06   29.3   8.3   24  178-201   142-165 (211)
 86 cd06283 PBP1_RegR_EndR_KdgR_li  95.1    0.29 7.5E-06   28.0   9.5  105  281-395   138-244 (267)
 87 cd06300 PBP1_ABC_sugar_binding  95.1    0.29 7.5E-06   28.0  13.4  104  282-395   147-251 (272)
 88 pfam06263 consensus             95.0     0.3 7.6E-06   27.9  10.8  120  266-397   191-316 (514)
 89 cd07023 S49_Sppa_N_C Signal pe  94.9    0.17 4.2E-06   29.6   7.3   24  178-201   139-162 (208)
 90 COG3919 Predicted ATP-grasp en  94.8    0.08 2.1E-06   31.7   5.6   94   13-135   123-222 (415)
 91 cd06319 PBP1_ABC_sugar_binding  94.7    0.36 9.1E-06   27.4  14.5   85  302-395   166-252 (277)
 92 cd06318 PBP1_ABC_sugar_binding  94.6     0.4   1E-05   27.1  13.3   86  301-395   170-257 (282)
 93 cd06298 PBP1_CcpA_like Ligand-  94.5    0.41   1E-05   27.0   8.8  105  282-395   139-243 (268)
 94 cd06284 PBP1_LacI_like_6 Ligan  94.3    0.45 1.2E-05   26.7  10.0  104  283-395   138-242 (267)
 95 cd06321 PBP1_ABC_sugar_binding  94.2    0.46 1.2E-05   26.7  12.1   90  298-395   158-249 (271)
 96 cd06285 PBP1_LacI_like_7 Ligan  94.1    0.49 1.2E-05   26.5   8.8  103  284-395   138-241 (265)
 97 PRK06091 membrane protein FdrA  94.1    0.49 1.3E-05   26.5  10.6  121  266-397   193-318 (555)
 98 cd06292 PBP1_LacI_like_10 Liga  93.8    0.57 1.4E-05   26.1   9.3  105  281-395   143-247 (273)
 99 cd06291 PBP1_Qymf_like Ligand   93.6    0.59 1.5E-05   26.0  10.1  103  282-395   135-239 (265)
100 cd06313 PBP1_ABC_sugar_binding  93.6    0.61 1.6E-05   25.9  14.7   86  301-395   163-249 (272)
101 PRK10401 DNA-binding transcrip  93.4    0.64 1.6E-05   25.7   9.9  106  280-394   196-302 (346)
102 cd01539 PBP1_GGBP Periplasmic   93.4    0.65 1.7E-05   25.7  12.9   89  299-396   178-274 (303)
103 TIGR00706 SppA_dom signal pept  93.3    0.39   1E-05   27.2   6.6   22  179-200   150-171 (224)
104 cd06317 PBP1_ABC_sugar_binding  93.2    0.71 1.8E-05   25.5  13.5   88  299-395   164-254 (275)
105 PRK10355 xylF D-xylose transpo  93.1    0.71 1.8E-05   25.5   9.8   87  300-395   189-278 (330)
106 cd06308 PBP1_sensor_kinase_lik  93.1    0.71 1.8E-05   25.4  14.1   91  300-397   161-256 (270)
107 cd06270 PBP1_GalS_like Ligand   92.9    0.77   2E-05   25.2   9.8  104  283-395   139-243 (268)
108 cd06273 PBP1_GntR_like_1 This   92.8     0.8   2E-05   25.1   9.5  102  285-395   142-244 (268)
109 cd06289 PBP1_MalI_like Ligand-  92.8     0.8   2E-05   25.1   9.7   87  299-395   156-244 (268)
110 PRK04308 murD UDP-N-acetylmura  92.5    0.86 2.2E-05   24.9   8.3  103  284-397   299-412 (445)
111 cd06310 PBP1_ABC_sugar_binding  92.5    0.87 2.2E-05   24.9  13.6   85  301-394   163-249 (273)
112 PRK10423 transcriptional repre  92.3    0.92 2.4E-05   24.7   8.8  105  281-395   195-301 (327)
113 cd06311 PBP1_ABC_sugar_binding  92.3    0.93 2.4E-05   24.7  13.7   90  299-397   163-259 (274)
114 cd01537 PBP1_Repressors_Sugar_  92.2    0.93 2.4E-05   24.7  13.0   99  283-395   141-244 (264)
115 cd06286 PBP1_CcpB_like Ligand-  92.2    0.94 2.4E-05   24.6  10.3  103  282-395   136-239 (260)
116 cd01574 PBP1_LacI Ligand-bindi  92.2    0.94 2.4E-05   24.6   9.3   82  301-395   155-240 (264)
117 cd06294 PBP1_ycjW_transcriptio  91.9       1 2.6E-05   24.4  11.0  104  282-395   144-249 (270)
118 cd01575 PBP1_GntR Ligand-bindi  91.9       1 2.6E-05   24.4  12.4  103  282-394   138-242 (268)
119 cd06295 PBP1_CelR Ligand bindi  91.7     1.1 2.7E-05   24.3   9.0  103  283-395   148-252 (275)
120 cd06267 PBP1_LacI_sugar_bindin  91.7     1.1 2.7E-05   24.3   9.2  101  283-395   139-243 (264)
121 cd06275 PBP1_PurR Ligand-bindi  91.7     1.1 2.8E-05   24.2   8.2   83  301-395   158-244 (269)
122 cd06320 PBP1_allose_binding Pe  91.6     1.1 2.8E-05   24.2  11.6   88  299-395   160-249 (275)
123 PRK09701 D-allose transporter   91.4     1.1 2.9E-05   24.1  13.8   85  301-394   196-282 (311)
124 cd06271 PBP1_AglR_RafR_like Li  91.4     1.2 2.9E-05   24.1   9.1  104  283-395   143-247 (268)
125 cd06303 PBP1_LuxPQ_Quorum_Sens  91.3     1.2   3E-05   24.0  11.7   86  299-393   168-258 (280)
126 cd06293 PBP1_LacI_like_11 Liga  91.2     1.2 3.1E-05   23.9  11.0  103  282-394   138-242 (269)
127 cd06272 PBP1_hexuronate_repres  90.9     1.3 3.3E-05   23.7   9.2  103  283-395   134-238 (261)
128 cd01538 PBP1_ABC_xylose_bindin  90.8     1.3 3.4E-05   23.7  12.2   86  301-395   169-257 (288)
129 cd06296 PBP1_CatR_like Ligand-  90.8     1.3 3.4E-05   23.7   8.9  101  283-395   140-244 (270)
130 cd06301 PBP1_rhizopine_binding  90.5     1.4 3.5E-05   23.5  12.2   86  301-395   163-251 (272)
131 cd06316 PBP1_ABC_sugar_binding  90.3     1.5 3.7E-05   23.4  13.5   88  300-396   165-258 (294)
132 cd01542 PBP1_TreR_like Ligand-  90.2     1.5 3.8E-05   23.4   9.8  102  282-395   137-239 (259)
133 cd06297 PBP1_LacI_like_12 Liga  90.0     1.5 3.9E-05   23.3  10.7  102  282-395   141-244 (269)
134 cd06309 PBP1_YtfQ_like Peripla  89.8     1.6   4E-05   23.2  12.7   86  300-395   163-253 (273)
135 PRK10727 DNA-binding transcrip  89.7     1.6 4.1E-05   23.1   8.7  107  280-395   196-303 (342)
136 cd06274 PBP1_FruR Ligand bindi  89.5     1.7 4.2E-05   23.0  10.3  103  283-395   139-244 (264)
137 cd07018 S49_SppA_67K_type Sign  89.3     1.7 4.4E-05   22.9   7.5   24  178-201   152-175 (222)
138 PRK02472 murD UDP-N-acetylmura  89.3     1.7 4.4E-05   22.9   8.8   90  296-397   325-414 (450)
139 pfam00532 Peripla_BP_1 family.  89.2     1.7 4.4E-05   22.9  10.7  105  281-394   142-256 (281)
140 PRK03815 murD UDP-N-acetylmura  89.1     1.8 4.6E-05   22.8   8.7  106  282-397   252-368 (401)
141 cd06281 PBP1_LacI_like_5 Ligan  89.0     1.8 4.6E-05   22.8  11.1  102  283-395   139-242 (269)
142 cd06288 PBP1_sucrose_transcrip  88.4       2   5E-05   22.5   9.8   88  299-395   155-244 (269)
143 PRK10653 D-ribose transporter   88.3       2 5.1E-05   22.5  12.5   86  301-395   187-273 (295)
144 TIGR00705 SppA_67K signal pept  88.3       2 5.1E-05   22.5   7.2  251   75-364   117-404 (614)
145 PRK11303 DNA-binding transcrip  88.0     2.1 5.3E-05   22.4  10.8  103  281-395   200-304 (330)
146 cd06324 PBP1_ABC_sugar_binding  87.7     2.2 5.5E-05   22.3  14.5   79  301-388   182-264 (305)
147 PRK10703 DNA-binding transcrip  87.2     2.3 5.9E-05   22.0   9.0  106  280-395   198-305 (335)
148 cd06290 PBP1_LacI_like_9 Ligan  87.1     2.3   6E-05   22.0   8.5   85  301-395   156-242 (265)
149 pfam03709 OKR_DC_1_N Orn/Lys/A  87.1     1.8 4.7E-05   22.7   5.4   82  308-396    26-109 (111)
150 PRK02705 murD UDP-N-acetylmura  87.0     2.4 6.1E-05   22.0   9.0   91  296-397   328-420 (459)
151 cd06279 PBP1_LacI_like_3 Ligan  86.9     2.4 6.2E-05   21.9  10.5  102  282-395   155-260 (283)
152 PRK02006 murD UDP-N-acetylmura  86.7     2.5 6.4E-05   21.9   7.6   91  296-397   370-460 (501)
153 cd06302 PBP1_LsrB_Quorum_Sensi  86.6     2.5 6.4E-05   21.8  13.7  123  266-397   123-258 (298)
154 PRK11041 DNA-binding transcrip  86.1     2.7 6.8E-05   21.7  10.6  105  281-395   205-311 (341)
155 pfam02955 GSH-S_ATP Prokaryoti  85.9     2.7 6.9E-05   21.6  10.9   69   18-114    11-80  (176)
156 cd06282 PBP1_GntR_like_2 Ligan  85.6     2.8 7.1E-05   21.5   8.8  100  285-395   142-242 (266)
157 cd06323 PBP1_ribose_binding Pe  84.6     3.1 7.9E-05   21.2  12.5   84  303-395   163-247 (268)
158 pfam01740 STAS STAS domain. Th  84.5     2.7 6.9E-05   21.6   5.3   81  304-387    23-106 (106)
159 cd06305 PBP1_methylthioribose_  84.5     3.2   8E-05   21.2  10.6   86  303-395   163-252 (273)
160 COG1609 PurR Transcriptional r  84.0     3.3 8.4E-05   21.0  10.6  117  268-395   177-303 (333)
161 cd01545 PBP1_SalR Ligand-bindi  83.6     3.4 8.7E-05   21.0   9.2   85  301-394   159-244 (270)
162 cd01536 PBP1_ABC_sugar_binding  83.4     3.5 8.9E-05   20.9  11.1   86  301-395   161-248 (267)
163 cd06299 PBP1_LacI_like_13 Liga  83.0     3.6 9.2E-05   20.8  10.2   84  301-395   157-241 (265)
164 PRK10669 putative cation:proto  82.6     3.7 9.5E-05   20.7   8.5   89  291-396   460-548 (558)
165 cd01544 PBP1_GalR Ligand-bindi  82.1     3.9   1E-04   20.6   9.6  106  280-395   137-245 (270)
166 PRK10339 DNA-binding transcrip  81.4     4.1 0.00011   20.4   9.1  102  283-395   197-300 (327)
167 TIGR01124 ilvA_2Cterm threonin  81.0     3.6 9.3E-05   20.8   4.8   54   21-87     68-134 (508)
168 TIGR01859 fruc_bis_ald_ fructo  80.7     4.4 0.00011   20.2   5.1   41  161-202   254-299 (339)
169 cd06312 PBP1_ABC_sugar_binding  80.2     4.5 0.00012   20.1  10.5   82  305-395   167-250 (271)
170 TIGR01768 GGGP-family geranylg  79.8     3.2 8.1E-05   21.2   4.2   57  291-349   159-220 (242)
171 cd06322 PBP1_ABC_sugar_binding  79.0     4.9 0.00013   19.9  15.2   83  304-395   162-246 (267)
172 cd01543 PBP1_XylR Ligand-bindi  78.9       5 0.00013   19.9   9.8  106  281-395   129-238 (265)
173 KOG1255 consensus               77.9     5.3 0.00014   19.7   5.4  108  261-370   171-280 (329)
174 TIGR02086 IPMI_arch 3-isopropy  76.9     5.6 0.00014   19.5   4.7  165   10-208     6-198 (431)
175 PRK06241 phosphoenolpyruvate s  76.7     5.7 0.00015   19.5   9.9  110   11-130    25-198 (870)
176 cd06307 PBP1_uncharacterized_s  76.3     5.9 0.00015   19.4  14.3   85  301-395   166-252 (275)
177 PRK03803 murD UDP-N-acetylmura  75.5     6.2 0.00016   19.3   9.5   95  295-397   320-414 (448)
178 TIGR00097 HMP-P_kinase phospho  75.3     6.2 0.00016   19.2   7.4  111   74-197    50-165 (264)
179 TIGR01481 ccpA catabolite cont  72.4     7.3 0.00019   18.8   5.1   43  305-354   224-266 (332)
180 TIGR00470 sepS O-phosphoseryl-  72.4     3.8 9.6E-05   20.7   2.9   97  211-341   238-351 (558)
181 cd01391 Periplasmic_Binding_Pr  70.4     8.1 0.00021   18.5   7.8   72  284-365   147-222 (269)
182 PRK10949 protease 4; Provision  69.9     8.3 0.00021   18.4   7.1  247   75-366   130-410 (618)
183 cd06280 PBP1_LacI_like_4 Ligan  68.0       9 0.00023   18.2   8.7   83  304-395   155-238 (263)
184 cd06277 PBP1_LacI_like_1 Ligan  66.5     9.7 0.00025   18.0   9.5   79  305-395   164-243 (268)
185 pfam08886 GshA Glutamate-cyste  64.9      10 0.00026   17.8   4.5   29  115-144   108-137 (404)
186 KOG3432 consensus               64.8      10 0.00027   17.8   6.7   64  292-363    34-97  (121)
187 PRK01390 murD UDP-N-acetylmura  64.6      11 0.00027   17.7   8.3   87  296-396   332-418 (457)
188 PRK09526 lacI lac repressor; R  63.7      11 0.00028   17.6   9.9  101  280-395   201-306 (342)
189 TIGR01019 sucCoAalpha succinyl  62.3      12 0.00029   17.5   6.2  104  261-370   140-245 (288)
190 PTZ00294 glycerol kinase; Prov  61.7      12  0.0003   17.4   4.9   92  294-394   373-478 (510)
191 pfam10281 Ish1 Putative stress  61.6      10 0.00026   17.8   3.4   32    4-37      5-36  (38)
192 TIGR00417 speE spermidine synt  61.3     4.8 0.00012   20.0   1.6   51  106-161    59-109 (284)
193 PRK00683 murD UDP-N-acetylmura  60.5      12 0.00032   17.3   8.4  103  283-397   268-381 (418)
194 cd06278 PBP1_LacI_like_2 Ligan  60.4      12 0.00032   17.3  10.5  101  283-395   138-241 (266)
195 KOG1663 consensus               58.4     7.8  0.0002   18.6   2.3   28  309-336   208-235 (237)
196 cd01820 PAF_acetylesterase_lik  57.2      14 0.00036   16.9   6.4   19  201-219   165-183 (214)
197 PRK12412 pyridoxal kinase; Rev  57.1      14 0.00036   16.9   7.8   17  274-290   209-225 (268)
198 TIGR01320 mal_quin_oxido malat  56.5      14 0.00037   16.8   3.8   21   68-88    263-284 (487)
199 cd01541 PBP1_AraR Ligand-bindi  52.5      17 0.00043   16.4   9.8   82  304-395   166-249 (273)
200 TIGR02584 cas_NE0113 CRISPR-as  52.5      14 0.00034   17.0   2.7   67   60-143   134-200 (224)
201 TIGR02049 gshA_ferroox glutama  52.1      17 0.00043   16.4   3.6   75   21-114   237-319 (436)
202 PRK04531 acetylglutamate kinas  51.5      17 0.00044   16.3   6.5   60  333-395   345-412 (421)
203 TIGR01087 murD UDP-N-acetylmur  50.6      18 0.00046   16.2   7.6  109  279-397   317-442 (476)
204 TIGR00326 eubact_ribD riboflav  50.5      18 0.00046   16.2   3.4   37  308-346   305-341 (393)
205 PRK09585 anmK anhydro-N-acetyl  50.4     9.9 0.00025   17.9   1.8  119  271-392   181-335 (366)
206 pfam07364 DUF1485 Protein of u  49.9      18 0.00047   16.2   6.6   75  302-392   208-291 (292)
207 COG0821 gcpE 1-hydroxy-2-methy  49.7      18 0.00047   16.1   3.9   10  269-278   297-306 (361)
208 COG0069 GltB Glutamate synthas  49.0     4.2 0.00011   20.3  -0.3  117  229-345   274-396 (485)
209 COG0769 MurE UDP-N-acetylmuram  48.5      19 0.00049   16.0   7.6  100  293-397   333-438 (475)
210 TIGR00017 cmk cytidylate kinas  48.5      19 0.00049   16.0   3.8   76  139-240    83-165 (223)
211 PRK12483 threonine dehydratase  48.2      19  0.0005   16.0   5.2   13   74-86    139-151 (521)
212 pfam11379 DUF3182 Protein of u  46.5      21 0.00053   15.8   6.9   54   18-86    113-168 (355)
213 pfam03702 UPF0075 Uncharacteri  46.1      11 0.00027   17.7   1.4  119  271-392   180-332 (363)
214 PRK03562 glutathione-regulated  45.5      21 0.00055   15.7   8.1  111  257-395   420-530 (615)
215 PRK04169 geranylgeranylglycery  45.2      22 0.00055   15.7   3.6   50  290-345   154-206 (229)
216 pfam01990 ATP-synt_F ATP synth  45.1      22 0.00055   15.7   7.3   52  303-362    24-75  (92)
217 COG2115 XylA Xylose isomerase   44.7      14 0.00034   17.0   1.7  128  257-393   257-415 (438)
218 PRK09224 threonine dehydratase  44.5      22 0.00056   15.6   5.4   18   70-87    117-135 (504)
219 cd00616 AHBA_syn 3-amino-5-hyd  43.9      23 0.00058   15.6   6.1   14  339-352   282-295 (352)
220 pfam00462 Glutaredoxin Glutare  43.7      23 0.00058   15.5   3.9   43    6-52     13-56  (60)
221 PRK09084 aspartate kinase III;  43.4      23 0.00059   15.5   4.6   20  328-347   389-409 (447)
222 PRK03659 glutathione-regulated  43.0      23 0.00059   15.5  10.1  112  256-395   420-531 (602)
223 PRK10638 glutaredoxin 3; Provi  43.0      23 0.00059   15.5   4.0   46    6-54     16-61  (83)
224 TIGR03628 arch_S11P archaeal r  42.6      24  0.0006   15.4   5.4   47  337-383    50-105 (114)
225 cd07016 S14_ClpP_1 Caseinolyti  42.5      24  0.0006   15.4   8.0   14   26-39     15-28  (160)
226 cd02066 GRX_family Glutaredoxi  42.4      24 0.00061   15.4   3.6   45    6-53     14-58  (72)
227 PRK03806 murD UDP-N-acetylmura  42.3      24 0.00061   15.4   6.4   91  295-397   314-404 (438)
228 COG0771 MurD UDP-N-acetylmuram  42.2      24 0.00061   15.4   8.5  106  281-397   297-413 (448)
229 KOG2519 consensus               42.1      22 0.00057   15.6   2.5   27  294-320   305-331 (449)
230 PRK06253 O-phosphoseryl-tRNA s  41.8      24 0.00062   15.3   6.1   17  334-350   368-384 (527)
231 cd03419 GRX_GRXh_1_2_like Glut  41.5      23 0.00058   15.6   2.5   47    6-54     14-62  (82)
232 TIGR00612 ispG_gcpE 4-hydroxy-  41.1      13 0.00033   17.2   1.2   52  276-328   479-531 (633)
233 PRK10014 DNA-binding transcrip  41.1      25 0.00064   15.3   9.7  106  280-395   202-318 (342)
234 cd03027 GRX_DEP Glutaredoxin (  40.7      25 0.00064   15.2   3.4   46    6-54     15-60  (73)
235 PRK06382 threonine dehydratase  39.9      26 0.00066   15.2   5.4   25  266-290   293-317 (400)
236 PRK10936 periplasmic sensory p  39.8      26 0.00066   15.1  10.3  117  268-397   171-300 (340)
237 cd01844 SGNH_hydrolase_like_6   39.8      26 0.00066   15.1   5.1   28   15-42      5-34  (177)
238 cd03418 GRX_GRXb_1_3_like Glut  39.5      26 0.00067   15.1   4.2   34    6-39     14-47  (75)
239 pfam03411 Peptidase_M74 Penici  39.4      26 0.00067   15.1   4.4   52  306-360   124-181 (240)
240 TIGR00273 TIGR00273 iron-sulfu  39.4      26 0.00067   15.1  10.1  122   70-220    67-201 (450)
241 cd06306 PBP1_TorT-like TorT-li  38.8      27 0.00069   15.0  10.6   84  301-394   164-249 (268)
242 KOG3857 consensus               38.4      13 0.00034   17.1   0.9   37    7-43     89-131 (465)
243 PRK01077 cobyrinic acid a,c-di  38.3      27  0.0007   15.0   6.6   15   10-24     26-40  (451)
244 PRK09607 rps11p 30S ribosomal   38.3      28  0.0007   15.0   5.3   49  336-384    53-110 (129)
245 cd00394 Clp_protease_like Case  38.1      28 0.00071   15.0   6.4   11  189-199   113-123 (161)
246 PRK04663 murD UDP-N-acetylmura  37.8      28 0.00071   14.9   7.2   90  295-397   315-404 (438)
247 PRK08190 bifunctional enoyl-Co  37.7      18 0.00046   16.2   1.5   72  326-397   303-388 (465)
248 PRK06464 phosphoenolpyruvate s  37.6      16 0.00042   16.5   1.3   55   74-129   148-211 (794)
249 PRK08198 threonine dehydratase  37.5      28 0.00072   14.9   5.2   25  266-290   298-322 (406)
250 COG4789 EscV Type III secretor  36.8      15 0.00038   16.7   1.0   14    3-16     90-103 (689)
251 COG1646 Predicted phosphate-bi  36.4      29 0.00075   14.8   3.2   51  291-347   164-214 (240)
252 pfam08981 consensus             36.2      30 0.00075   14.8   7.0   17   29-45     15-31  (181)
253 PRK08526 threonine dehydratase  35.8      30 0.00077   14.7   5.3   24  267-290   296-319 (403)
254 COG1058 CinA Predicted nucleot  35.6      30 0.00077   14.7   5.9   63   10-77     28-95  (255)
255 pfam02195 ParBc ParB-like nucl  35.4      30 0.00078   14.7   3.9   55  342-397    26-89  (90)
256 PRK03995 hypothetical protein;  34.8      31 0.00079   14.6   5.3   40  340-379   219-262 (264)
257 PRK04690 murD UDP-N-acetylmura  34.4      32  0.0008   14.6   8.6   91  295-394   324-418 (468)
258 PTZ00317 malic enzyme; Provisi  34.1      32 0.00081   14.6   7.3   22  340-362   396-417 (570)
259 PRK05878 pyruvate phosphate di  33.8      22 0.00055   15.7   1.4   32  104-135   192-227 (529)
260 cd03364 TOPRIM_DnaG_primases T  33.7      32 0.00082   14.5   3.8   54  340-393     7-61  (79)
261 PRK08928 consensus              33.7      32 0.00082   14.5   5.8   25  304-328   358-382 (861)
262 pfam00411 Ribosomal_S11 Riboso  33.6      33 0.00083   14.5   5.9   49  335-383    45-94  (109)
263 TIGR03632 bact_S11 30S ribosom  33.4      33 0.00083   14.5   5.8   49  335-383    45-94  (108)
264 COG1879 RbsB ABC-type sugar tr  33.4      33 0.00084   14.5  12.5  120  267-395   159-286 (322)
265 PRK00536 speE spermidine synth  33.2      27  0.0007   15.0   1.8   39  120-160    65-103 (262)
266 CHL00041 rps11 ribosomal prote  32.3      34 0.00087   14.4   5.7   49  335-383    58-107 (116)
267 COG0281 SfcA Malic enzyme [Ene  32.2      34 0.00087   14.4   3.7   28  269-296   200-228 (432)
268 TIGR02903 spore_lon_C ATP-depe  31.7     3.3 8.3E-05   21.1  -3.1   58  294-351   480-546 (616)
269 PRK11660 putative sulfate tran  31.7      35 0.00089   14.3   8.7   84  304-393   476-565 (567)
270 PRK07334 threonine dehydratase  31.6      35 0.00089   14.3   5.1   23  268-290   294-316 (399)
271 PRK09492 treR trehalose repres  31.5      35  0.0009   14.3   9.8   98  281-395   197-295 (315)
272 pfam09840 DUF2067 Uncharacteri  31.5      35  0.0009   14.3   3.4   20  183-202   114-133 (190)
273 PRK13529 malate dehydrogenase;  31.3      35  0.0009   14.3   6.2   14   73-86    129-142 (563)
274 pfam01341 Glyco_hydro_6 Glycos  31.0      36 0.00091   14.2   8.0   67  292-358   154-230 (295)
275 COG0646 MetH Methionine syntha  31.0      36 0.00091   14.2   9.8  159  183-378    47-223 (311)
276 TIGR00962 atpA ATP synthase F1  30.9      22 0.00056   15.6   1.0   49   75-133   124-177 (520)
277 COG0272 Lig NAD-dependent DNA   30.2      37 0.00094   14.2   3.6   35    4-38    237-272 (667)
278 COG2759 MIS1 Formyltetrahydrof  30.2      37 0.00094   14.1   4.9   14  280-293   326-339 (554)
279 TIGR01418 PEP_synth phosphoeno  29.8      17 0.00044   16.3   0.3   95  275-371   564-673 (877)
280 pfam01949 DUF99 Protein of unk  29.0      39 0.00099   14.0   7.7   20  354-373   139-158 (185)
281 TIGR00644 recJ single-stranded  28.9      39 0.00099   14.0   7.1   14   73-86    422-435 (705)
282 COG2379 GckA Putative glycerat  28.9      17 0.00043   16.4   0.1   54  129-197   113-166 (422)
283 TIGR01746 Thioester-redct thio  28.8      39 0.00099   14.0   2.6   62  332-393   257-327 (405)
284 PRK02255 putrescine carbamoylt  28.8      39   0.001   14.0   6.7   15   31-45     61-75  (341)
285 COG0616 SppA Periplasmic serin  28.7      39   0.001   14.0   8.3   24  178-201   201-224 (317)
286 TIGR01828 pyru_phos_dikin pyru  28.7      27 0.00068   15.1   1.1   46  261-317   519-564 (920)
287 PRK05309 30S ribosomal protein  28.5      39   0.001   14.0   5.7   48  336-383    62-110 (126)
288 COG1405 SUA7 Transcription ini  28.4      25 0.00063   15.3   0.9   17  170-186   104-120 (285)
289 pfam02571 CbiJ Precorrin-6x re  28.4      40   0.001   13.9   5.3   62  288-359   162-223 (246)
290 pfam04223 CitF Citrate lyase,   28.1      40   0.001   13.9   6.9   66  282-349   216-284 (466)
291 PRK09466 metL bifunctional asp  27.6      41   0.001   13.9   4.4   23  293-315   419-448 (810)
292 TIGR01091 upp uracil phosphori  27.3      41  0.0011   13.8   4.8   33  260-292   117-157 (213)
293 cd03028 GRX_PICOT_like Glutare  27.1      42  0.0011   13.8   2.6   45    6-54     27-72  (90)
294 PRK09429 mepA penicillin-insen  26.9      42  0.0011   13.8   4.4   54  305-361   153-212 (270)
295 cd04258 AAK_AKiii-LysC-EC AAK_  26.7      42  0.0011   13.8   4.5   41  262-302   188-228 (292)
296 PRK12861 malic enzyme; Reviewe  26.5      43  0.0011   13.7   6.8   38  279-316   617-660 (762)
297 TIGR00575 dnlj DNA ligase, NAD  25.9      44  0.0011   13.7   4.2   36    3-38    240-279 (706)
298 TIGR00416 sms DNA repair prote  25.8      44  0.0011   13.6   3.8  163  183-357   219-422 (481)
299 PRK09902 hypothetical protein;  25.7      40   0.001   13.9   1.6   17  187-203   137-153 (216)
300 pfam00730 HhH-GPD HhH-GPD supe  25.7      42  0.0011   13.8   1.7   35    8-42     18-52  (144)
301 pfam06714 Gp5_OB Gp5 N-termina  24.6      46  0.0012   13.5   2.9   28  117-145    48-75  (144)
302 TIGR02181 GRX_bact glutaredoxi  24.5      47  0.0012   13.5   3.6   44    7-52     14-59  (82)
303 PRK00766 hypothetical protein;  24.4      47  0.0012   13.5   7.6   21  354-374   146-166 (194)
304 cd05147 RIO1_euk RIO kinase fa  24.1      47  0.0012   13.4   2.4   36  187-224   123-161 (190)
305 TIGR00593 pola DNA polymerase   23.5      48  0.0012   13.4   3.2   39    8-46     92-133 (1005)
306 pfam04414 tRNA_deacylase D-ami  22.9      50  0.0013   13.3   5.1   38  341-379   172-212 (214)
307 TIGR02665 molyb_mobA molybdopt  22.9      45  0.0011   13.6   1.4  120   48-218     4-136 (202)
308 TIGR02291 rimK_rel_E_lig alpha  22.8      50  0.0013   13.3   3.6   99    7-115    40-145 (320)
309 pfam01163 RIO1 RIO1 family. Th  22.7      50  0.0013   13.3   2.4   38  185-224   107-147 (186)
310 PRK06740 histidinol-phosphatas  22.4      51  0.0013   13.2   3.6   89  279-378   218-317 (338)
311 cd06314 PBP1_tmGBP Periplasmic  22.3      51  0.0013   13.2  10.9   84  303-395   161-246 (271)
312 TIGR03470 HpnH hopanoid biosyn  22.2      51  0.0013   13.2   4.2   71   26-126    59-133 (318)
313 PRK00286 xseA exodeoxyribonucl  22.2      51  0.0013   13.2  10.1   90  265-359   134-232 (443)
314 COG1486 CelF Alpha-galactosida  21.8      52  0.0013   13.1   5.1   39    7-53     51-89  (442)
315 pfam11094 UL11 Membrane-associ  21.6      53  0.0013   13.1   1.6   16  209-225    16-31  (39)
316 TIGR02392 rpoH_proteo alternat  21.5      17 0.00043   16.4  -1.0   22  163-184   139-160 (279)
317 cd08025 RNR_PFL_like_DUF711 Un  21.4      53  0.0014   13.1   2.0   23    7-29     55-77  (400)
318 PRK01368 murD UDP-N-acetylmura  21.3      53  0.0014   13.1   7.8   89  295-397   321-409 (450)
319 PRK09271 flavodoxin; Provision  21.0      54  0.0014   13.0   3.3   13   75-87     13-25  (160)
320 PRK03992 proteasome-activating  21.0      54  0.0014   13.0   3.9   49  130-178   126-191 (390)
321 PRK07679 pyrroline-5-carboxyla  20.7      28 0.00071   14.9  -0.0   38  359-397   234-271 (279)
322 cd05119 RIO RIO kinase family,  20.4      56  0.0014   13.0   2.3   37  187-225   120-159 (187)
323 cd02812 PcrB_like PcrB_like pr  20.4      56  0.0014   13.0   6.3   60  279-345   137-196 (219)
324 PRK11706 TDP-4-oxo-6-deoxy-D-g  20.3      56  0.0014   12.9   6.4   14  340-353   303-316 (375)
325 TIGR01063 gyrA DNA gyrase, A s  20.0      57  0.0014   12.9   1.5   37  100-141   550-586 (864)

No 1  
>TIGR01016 sucCoAbeta succinyl-CoA synthetase, beta subunit; InterPro: IPR005809   There are four different enzymes that share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. These enzymes are: ATP citrate-lyase (4.1.3.8 from EC) , the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues, catalyzes the formation of acetyl-CoA and oxaloacetate from citrate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. ATP-citrate lyase is a tetramer of identical subunits; Succinyl-CoA ligase (GDP-forming) (6.2.1.4 from EC)  is a mitochondrial enzyme that catalyzes the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. This enzyme is a dimer composed of an alpha and a beta subunits; Succinyl-CoA ligase (ADP-forming) (6.2.1.5 from EC)  is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP. It can also function in the other direction for anabolic purposes. This enzyme is a tetramer composed of two alpha and two beta subunits; and Malate-CoA ligase (6.2.1.9 from EC) (malyl-CoA synthetase) , is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. Malate-CoA ligase is composed of two different subunits.   This entry corresponds to a conserved region located in the first half of ATP citrate lyase and in the beta subunits of succinyl-CoA ligases and malate-CoA ligase. ; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=100.00  E-value=0  Score=1126.33  Aligned_cols=386  Identities=51%  Similarity=0.845  Sum_probs=382.7

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf             98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r    1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI   80 (398)
Q Consensus         1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~   80 (398)
                      |||||||||+||++||||||+|.+|+|++|+..++.++|...||||||||+||||||          |||++++|++|+.
T Consensus         1 M~LHEYqAK~if~~YGiPvp~g~v~~s~~e~~~~~~~~g~~~~VvKaQVhaGGRGKA----------GGv~~a~s~ee~~   70 (389)
T TIGR01016         1 MKLHEYQAKEIFAKYGIPVPEGEVATSVEEVEEIAEELGEGKVVVKAQVHAGGRGKA----------GGVKVAKSKEEAL   70 (389)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCCCEEECHHHHHHHHHHCCCCCEEEEEEEEECCCCCC----------CCEEEEECHHHHH
T ss_conf             986435589999847896788600416789999999707997899987732671121----------5768970879999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf             99998618765442122222443301103455565058999998347780489984478840245557483122033214
Q gi|254781049|r   81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID  160 (398)
Q Consensus        81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id  160 (398)
                      ++|.+|||+.+.|+||++.|++|++||||++++|.||||+|+++||+.++|++|+|++||||||++|+++||+|++.+||
T Consensus        71 ~~a~~llg~~l~t~Qt~~~g~~VnkiliE~~~~I~kEyY~s~v~DR~~~~pv~maS~eGGvdIEEvA~~~Pe~I~k~~id  150 (389)
T TIGR01016        71 KAAEKLLGKELKTFQTDPLGQPVNKILIEEKIDIDKEYYLSIVIDRSAKKPVIMASTEGGVDIEEVAEKSPEKIIKVAID  150 (389)
T ss_pred             HHHHHHHCCEEEEEECCCCCCEEEEEEECCCCCCCCEEEEEEEEEECCCCCEEEEECCCCCCHHHHHHCCCCCEEEEEEC
T ss_conf             99998708915786407888634478732677412001477999804787179970677841789952195716888717


Q ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHHHHHHH
Q ss_conf             44578957888788751988899885999999998999955975102326799059967994001321573556410278
Q gi|254781049|r  161 PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQ  240 (398)
Q Consensus       161 ~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~  240 (398)
                      |..++.+||+|.++++++|++..+.++.+++.+||++|.++|++|+||||||+|+||.++|||||+++||||+|||||+.
T Consensus       151 p~~~~~pYq~R~~a~~~~l~~~~~~~~~~i~~~Ly~~F~e~Da~L~EINPLViT~~G~L~alDAKl~~DDnALFRH~~l~  230 (389)
T TIGR01016       151 PLTGLLPYQARELAKKLGLEGELIKQVASIIKKLYQIFLEKDASLVEINPLVITKDGNLVALDAKLTIDDNALFRHPDLE  230 (389)
T ss_pred             CCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECCEEECCCCCEEEEEEECCCCCCHHCCCCCHH
T ss_conf             77777878999999970897057788999999999988753710254526368789888998332244655100671168


Q ss_pred             HHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf             63100015622245775398644228817999555036899999999658996248842788898999999999861998
Q gi|254781049|r  241 ELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSS  320 (398)
Q Consensus       241 ~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~  320 (398)
                      +|||++|+|++|.+|++.|||||+||||||||||||||||+|||+|+.|||+||||||||||||.|+|++||++|||||+
T Consensus       231 ~~~D~~~~~~~e~~A~~~gL~Yv~LdGnIGc~vNGAGLAMaTMDIiKl~GG~PANFLDvGGGA~~e~v~eA~~~vLsD~~  310 (389)
T TIGR01016       231 EMEDYTQEDQLEVEAKQLGLNYVKLDGNIGCMVNGAGLAMATMDIIKLYGGKPANFLDVGGGASEERVKEALKLVLSDKS  310 (389)
T ss_pred             HHCCCCCCCHHHHHHHHHCCCEEEECCCEEEECCCHHHHHHHHHHHHHHCCCCCEECCCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             76388877733799986188368854770797043567899999999718895302245878898999999898735998


Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC---CCEEEECCHHHHHHHHHHHHH
Q ss_conf             6589996358613289999999999997299987999748985899999999769---958994998999999999850
Q gi|254781049|r  321 VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG---LNVITAIDLDDAAQKIVHAVK  396 (398)
Q Consensus       321 vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g---~~~~~~~~~~~A~~~~v~~~k  396 (398)
                      ||+|||||||||||||.||+|||.|+++.+.++|+||||.|||+|+|++||+|||   +|+++++||++||+|+|++++
T Consensus       311 VKvvfiNIFGGI~RCD~vA~G~v~A~~~~~~~VP~VvRL~GTN~E~G~~iL~e~gkdr~ni~~~~sm~~aA~kaV~~~~  389 (389)
T TIGR01016       311 VKVVFINIFGGITRCDEVAKGLVEALKDVGVNVPVVVRLEGTNVEEGKKILQESGKDRLNIIFATSMEEAAEKAVELAK  389 (389)
T ss_pred             CEEEEEEECCCEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf             2089997068600187887889999831885368789815788788889999727677886322687889999999839


No 2  
>PRK00696 sucC succinyl-CoA synthetase subunit beta; Provisional
Probab=100.00  E-value=0  Score=1038.67  Aligned_cols=388  Identities=59%  Similarity=0.939  Sum_probs=385.4

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf             98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r    1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI   80 (398)
Q Consensus         1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~   80 (398)
                      |||||||||+||++||||||+|.+++|++|+.++++++++|+||||||||+||||||          ||||+++|++|+.
T Consensus         1 M~LhEyqaKell~~~gIpvp~g~v~~~~~ea~~~~~~l~~~~~VvKAQV~aGGRGKa----------GGVk~~~s~~ea~   70 (388)
T PRK00696          1 MNLHEYQAKELLAEYGVPVPRGYVAFTPEEAVEAAEELGGPVWVVKAQVHAGGRGKA----------GGVKVAKSKEEVR   70 (388)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHHCCCCEEEEEEECCCCCCCC----------CEEEEECCHHHHH
T ss_conf             963489999999986998999737799999999999829995899980545888868----------6079908999999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf             99998618765442122222443301103455565058999998347780489984478840245557483122033214
Q gi|254781049|r   81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID  160 (398)
Q Consensus        81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id  160 (398)
                      +.+++|||++|+|+||+++|++|++|||||++++.+|||+|+++||++++|++|+|.+||||||++|+++|++|++.++|
T Consensus        71 ~~a~~ilg~~lvT~QTg~~G~~V~~vlvee~~~i~~E~Ylsi~~DR~~~~~~~i~S~~GG~dIEevA~~~Pe~I~k~~id  150 (388)
T PRK00696         71 AAAEEILGKDLVTHQTGPEGQPVNRLLIEEGADIAKELYLSAVVDRATRRVVFMASTEGGMEIEEVAEETPEKIHKVAVD  150 (388)
T ss_pred             HHHHHHHCCCCCEECCCCCCCEEEEEEEEECCCHHHHEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHEEEEECC
T ss_conf             99999856774210158888444799987516612406899998647785799998887987999865291238999757


Q ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHHHHHHH
Q ss_conf             44578957888788751988899885999999998999955975102326799059967994001321573556410278
Q gi|254781049|r  161 PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQ  240 (398)
Q Consensus       161 ~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~  240 (398)
                      |..|++++++|.+++.+|++++...++.+++.+||++|.++||+|+|||||++|+||+++|||||++|||||+||||+|.
T Consensus       151 p~~gl~~~~~r~i~~~lgl~~~~~~~~~~ii~~Ly~~F~~~Da~LvEINPLv~t~dg~~ialDaKv~iDDNAlfR~~~i~  230 (388)
T PRK00696        151 PLVGLQPYQAREIAFKLGLPGEQVKQAVKIFMGLYKAFVEKDASLVEINPLVVTKDGDLLALDAKITFDDNALFRHPDIA  230 (388)
T ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEECCCEEECCCCCEEEEEEEEECCCCHHHCCHHHH
T ss_conf             77798999999999982999999999999999999999965974256124268689978998889841675233186667


Q ss_pred             HHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf             63100015622245775398644228817999555036899999999658996248842788898999999999861998
Q gi|254781049|r  241 ELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSS  320 (398)
Q Consensus       241 ~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~  320 (398)
                      ++||+++++|+|.+|+++|||||+||||||||||||||||||||+|+++||+||||||+||+|+.|+|++||+++++||+
T Consensus       231 ~~rd~~~ed~~E~~A~~~~lnyv~LdG~IG~mvNGAGLaMaTmD~i~~~Gg~pANFLDvGG~a~~e~v~~a~~ii~~d~~  310 (388)
T PRK00696        231 ALRDPSQEDPREAEASKFDLNYVALDGNIGCMVNGAGLAMATMDIIKLHGGEPANFLDVGGGATKERVTEAFKIILSDPN  310 (388)
T ss_pred             HCCCCCCCCHHHHHHHHCCCCEEEECCEEEEEECCCCCCCHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCC
T ss_conf             32687648978999988697359745769999747644413589999759985425634899889999999999866999


Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHCC
Q ss_conf             658999635861328999999999999729998799974898589999999976995899499899999999985069
Q gi|254781049|r  321 VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKGV  398 (398)
Q Consensus       321 vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~v  398 (398)
                      ||+|||||||||+|||+||+||++|+++.++++|+||||+|||+++|++||+++|+++++++||+|||+++|+++||.
T Consensus       311 vk~IliNIfGGI~rcd~vA~giv~A~~~~~~~~PiVvRl~Gtn~e~g~~iL~~sgl~i~~~~~l~eAa~~aV~~~~g~  388 (388)
T PRK00696        311 VKAILVNIFGGIMRCDVIAEGIVAAVKEVGVKVPLVVRLEGTNVELGKKILAESGLPIIAADSLMDAAQKVVAAVAGK  388 (388)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHCCC
T ss_conf             509999936882439999999999999649998789990678879999999978997487078999999999973489


No 3  
>COG0045 SucC Succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=100.00  E-value=0  Score=970.94  Aligned_cols=384  Identities=55%  Similarity=0.879  Sum_probs=377.8

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf             98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r    1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI   80 (398)
Q Consensus         1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~   80 (398)
                      |||||||||+||++||||||+|.+++|++|+..++.++|.++||+|||||+||||||          ||||+++|++|++
T Consensus         1 M~lhEYqaKelf~~~GiPvp~g~v~~s~eea~~~a~~lg~~~~VvKaQV~aGGRGKa----------GGVk~~~s~~ea~   70 (387)
T COG0045           1 MNLHEYQAKELFAKYGIPVPPGYVATSPEEAEEAAKELGGGPVVVKAQVHAGGRGKA----------GGVKLAKSPEEAK   70 (387)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCEEEECHHHHHHHHHHHCCCCEEEEEEEEECCCCCC----------CCEEEECCHHHHH
T ss_conf             967888899899972998999545408999999999818996799922530576666----------7668838989999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCC-EEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEEC
Q ss_conf             99998618765442122222443301103455565-05899999834778048998447884024555748312203321
Q gi|254781049|r   81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADIL-RELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLI  159 (398)
Q Consensus        81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~-~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~i  159 (398)
                      +++++|||++   +||+++|++|++||||+++++. +|||+|+++||+.++|++|+|++||||||++++++|++|++.++
T Consensus        71 ~~a~~~lg~~---~q~~~~G~~v~~vlvee~~~~~~~E~Ylsiv~DR~~~~p~~~~S~eGGmDIEeVa~~~PekI~~~~i  147 (387)
T COG0045          71 EAAEEILGKN---YQTDIKGEPVNKVLVEEAVDIIKKEYYLSIVLDRSSRRPVLMASTEGGMDIEEVAEKTPEKIVKVSV  147 (387)
T ss_pred             HHHHHHHCCC---CCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHEEEEEE
T ss_conf             9999984866---5457688454289997467776433799999973778379999667795189950028345268974


Q ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCC-CEEEEEEEEEECCCHHHHHHH
Q ss_conf             4445789578887887519888998859999999989999559751023267990599-679940013215735564102
Q gi|254781049|r  160 DPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNG-RLRVLDSKISFDDNALYRHLD  238 (398)
Q Consensus       160 d~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg-~vvAlDAKi~iDDnA~fR~~~  238 (398)
                      ||..|+++|++|.+++.+|+++....++++++.+||++|.++|++|+|||||++|+++ +++|||||++|||||+||||+
T Consensus       148 dp~~g~~~~~aR~la~~lgl~~~~~~~~~~ii~~ly~~f~~~Da~lvEINPLvvt~~~g~v~aLDaKi~~DdnAlfRHp~  227 (387)
T COG0045         148 DPLTGLRPYQARELAFKLGLEGELVKQVADIIKKLYKLFVEKDATLVEINPLVVTPDGGDVLALDAKITLDDNALFRHPD  227 (387)
T ss_pred             CCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCEEECCCCCEEEEEEEEECCCCCCCCCCC
T ss_conf             77668787799999997499878999999999999999997587678752508817998089976454036764346834


Q ss_pred             HHHHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCC
Q ss_conf             78631000156222457753986442288179995550368999999996589962488427888989999999998619
Q gi|254781049|r  239 IQELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSD  318 (398)
Q Consensus       239 ~~~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~  318 (398)
                      +.++||.++++|+|.+|++++||||+||||||||+|||||+|+|||+|+++||+||||||+||+||.|++++||++|++|
T Consensus       228 ~~~~~d~~~ed~~e~~a~~~~l~yV~LdG~IG~ivNGAGLaMaTmDii~~~Gg~PANFLDvGGgA~~e~v~~a~~~il~d  307 (387)
T COG0045         228 LAELRDESEEDPREAEASGYGLNYVELDGNIGCIVNGAGLAMATMDIVKLYGGKPANFLDVGGGATAERVKEAFKLILSD  307 (387)
T ss_pred             HHHHHCCCCCCHHHHHHHHCCCCEEEECCCEEEEECCHHHHHHHHHHHHHCCCCCCCEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             45553233358557876127875188638378996272699999999998089974144148999988999999998459


Q ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             9865899963586132899999999999972999879997489858999999997699589949989999999998506
Q gi|254781049|r  319 SSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       319 ~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      |+||+|||||||||||||.||+||++|+++.+.++|+||||.|||+|+|++||++||++++++++|++|++++|+++++
T Consensus       308 ~~vk~IfVNIfGGI~rcD~vA~GIi~Al~e~~~~vPlVVRL~GtN~e~Gk~iL~esg~~i~~~~~l~~aa~k~v~~~~~  386 (387)
T COG0045         308 PNVKAIFVNIFGGITRCDEVAEGIIAALKEVGVNVPLVVRLEGTNVEEGKRILAESGLNIIAADDLDEAAEKAVELAKG  386 (387)
T ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHHHC
T ss_conf             9854899997168675089999999999852988888998678878999999997399407624688999999998514


No 4  
>KOG1447 consensus
Probab=100.00  E-value=0  Score=788.57  Aligned_cols=391  Identities=47%  Similarity=0.735  Sum_probs=384.2

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf             98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r    1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI   80 (398)
Q Consensus         1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~   80 (398)
                      +||.|||||+||++||+.|.+..++++..|+.++++.++.|.+|+||||++|||||+.+....|   |||++.+++.++.
T Consensus        20 LNLqEfQSK~~l~k~Gv~vQ~F~Va~n~kea~E~~k~f~~~EyVvKAQILAGGRGKG~F~nG~K---GGVhiTk~k~~vl   96 (412)
T KOG1447          20 LNLQEFQSKEILSKNGVRVQRFFVADNAKEALEAAKRFNAKEYVVKAQILAGGRGKGVFNNGLK---GGVHITKDKNVVL   96 (412)
T ss_pred             CCHHHHHHHHHHHHCCEEEEEEEEECCCHHHHHHHHHCCCCCEEEEEEEEECCCCCCEECCCCC---CEEEEECCHHHHH
T ss_conf             1288766678898649058999970670778999985499223776443106765542447765---4068744874999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf             99998618765442122222443301103455565058999998347780489984478840245557483122033214
Q gi|254781049|r   81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID  160 (398)
Q Consensus        81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id  160 (398)
                      +.+++|+|++++|+||+..|.+|++|+|.+.++|.+|.||+|++||+..+|++++|++||||||.+|+++|++|.+.|+|
T Consensus        97 ~l~~qMIG~rL~TKQTpkeGv~VnKVMvAe~~dI~RETYLaiLmDRe~NGPVlvaSP~GGmDIEaVAe~tPE~Ifk~piD  176 (412)
T KOG1447          97 QLAKQMIGYRLATKQTPKEGVKVNKVMVAEALDISRETYLAILMDRECNGPVLVASPQGGMDIEAVAESTPELIFKEPID  176 (412)
T ss_pred             HHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCCCHHEEEEEEECCCCCCCEEEECCCCCCCHHHHHHHCHHHHCCCCCH
T ss_conf             99999874533204488556265558873003611240014355145689779856998865999865395765144620


Q ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHHHHHHH
Q ss_conf             44578957888788751988899885999999998999955975102326799059967994001321573556410278
Q gi|254781049|r  161 PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQ  240 (398)
Q Consensus       161 ~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~  240 (398)
                      ...++.+.++.+++..|+|.|....+.++-|.+||.+|..-|++.+|||||..|++|+++|+|||++|||||.|||+|++
T Consensus       177 I~~gi~esq~l~~Ak~L~F~G~l~~~aA~eI~kLY~LF~avDAtQvEiNPl~ET~~G~V~cvDAK~NFDDnA~fRQKdIF  256 (412)
T KOG1447         177 IFEGIKESQALRMAKNLGFVGPLKSQAADEITKLYNLFLAVDATQVEINPLGETPEGQVVCVDAKINFDDNAEFRQKDIF  256 (412)
T ss_pred             HCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHCCEE
T ss_conf             13688668899999844666707778999999999999651212787325665898608998501067841766423312


Q ss_pred             HHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf             63100015622245775398644228817999555036899999999658996248842788898999999999861998
Q gi|254781049|r  241 ELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSS  320 (398)
Q Consensus       241 ~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~  320 (398)
                      .+.+.++++|+|.+|.+++||||.|||||+|+||||||+|||||+|+++||+||||||+||+.+.+++++||+++++||+
T Consensus       257 amd~~eE~dPrEveAakynLnYigmDGNIaClVNGAGLAMATmDiIkLnGGePANFLDvGGgV~EdqV~~Af~ilTaDPk  336 (412)
T KOG1447         257 AMDDKEENDPREVEAAKYNLNYIGMDGNIACLVNGAGLAMATMDIIKLNGGEPANFLDVGGGVKEDQVYQAFKILTADPK  336 (412)
T ss_pred             ECCCCCCCCCHHHHHHHCCCCEEECCCCEEEEECCCHHHHHEEEEEEECCCCCCCEEECCCCCCHHHHHHHHHHHCCCCC
T ss_conf             10454435811334554474146316826888746314312010588549987530422676038899777643125884


Q ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHH
Q ss_conf             65899963586132899999999999972999879997489858999999997699589949989999999998
Q gi|254781049|r  321 VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHA  394 (398)
Q Consensus       321 vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~  394 (398)
                      ||+|||||||||++|..+|+||+.|+++++.++|+||||+|||.+++++||++||+|+.++.||++|++|+|..
T Consensus       337 Vk~iLvNiFGGIVNCAtIANGiv~A~~kl~LnVPlVVRLEGTNV~~A~~Ilk~SGLpI~tA~dLddAA~KAVas  410 (412)
T KOG1447         337 VKAILVNIFGGIVNCATIANGIVKACRKLELNVPLVVRLEGTNVQEAQKILKKSGLPITTAIDLDDAAKKAVAS  410 (412)
T ss_pred             EEEEEEEHHCCEEHHHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHC
T ss_conf             03999830046311476765799998862578757999757777899999873698502213367899977643


No 5  
>KOG2799 consensus
Probab=100.00  E-value=0  Score=765.17  Aligned_cols=393  Identities=46%  Similarity=0.737  Sum_probs=382.5

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf             98657999999998689888815747999999999872998699971213687656565567777777079958999999
Q gi|254781049|r    1 MNIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI   80 (398)
Q Consensus         1 M~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~   80 (398)
                      +.+|||++-+||++||+.+|++.++.|||||.++++++|...+|+|||+++|||||+.|+.   +-.|||+++.+|+|++
T Consensus        23 L~~hey~~~~ll~~~Gv~vp~g~vA~speEA~~~akklg~kdlVikAQ~lAgGRgKGtF~S---glkgGV~iVf~p~Eak   99 (434)
T KOG2799          23 LGIHEYRSAALLRKYGINVPLGYVAKSPEEAFAIAKKLGSKDLVIKAQVLAGGRGKGTFDS---GLKGGVKIVFSPQEAK   99 (434)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCC---CCCCCEEEEECHHHHH
T ss_conf             4689988999999718788877556887899999997088645997520105766677376---7678637976758888


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf             99998618765442122222443301103455565058999998347780489984478840245557483122033214
Q gi|254781049|r   81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID  160 (398)
Q Consensus        81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id  160 (398)
                      +.+.+|+|++|+|+||++.|+.|+.|+|.+.....+|+|+||++||.+.+|++++|.+||++||++++++|++|.+.|+|
T Consensus       100 ~va~qmiG~kLiTKQtG~~gk~c~~v~iC~Rk~~~~e~yFsil~dr~~k~pliIas~kgg~~ie~vae~~pdai~k~pi~  179 (434)
T KOG2799         100 AVASQMIGKKLITKQTGPAGKACSEVYICERKHTRAEYYFSILMDRHTKGPLIIASSKGGVNIEEVAEDTPDAIIKKPID  179 (434)
T ss_pred             HHHHHHHCCEEEEECCCCCCCCCCEEEEEEECCHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHCCCCHHCCCCC
T ss_conf             88997634020433347888843069985101305678899987304579779982457762898865582411104555


Q ss_pred             CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCC-CEEEEEEEEEECCCHHHHHHHH
Q ss_conf             445789578887887519888998859999999989999559751023267990599-6799400132157355641027
Q gi|254781049|r  161 PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNG-RLRVLDSKISFDDNALYRHLDI  239 (398)
Q Consensus       161 ~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg-~vvAlDAKi~iDDnA~fR~~~~  239 (398)
                      ...|+++.++..++..||++.....+..+.+.+||++|...|++++|||||+.+.++ +++|.|||+.+||||.|||.++
T Consensus       180 ~~~Gls~~~a~~v~~~lgfs~~~~~~a~~~~~kly~vf~~~dat~veinpl~e~t~d~~v~c~dak~~fd~na~fRq~~i  259 (434)
T KOG2799         180 NNTGLSPEIACLVADKLGFSPDGIRKAAKAVPKLYKVFHKSDATQVEINPLAEITSDHKVTCMDAKLNFDDNAAFRQKKI  259 (434)
T ss_pred             CCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCHHHCCCCCEEEECHHHHCCCCCHHHHHHHH
T ss_conf             66898888899998610889301799999999999998634642688522222156866661002323665578886455


Q ss_pred             HHHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCC
Q ss_conf             86310001562224577539864422881799955503689999999965899624884278889899999999986199
Q gi|254781049|r  240 QELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDS  319 (398)
Q Consensus       240 ~~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~  319 (398)
                      +.+||.+||||+|..|++++|||+.||||||||||||||+|||||+|+++||.||||||+||+|+.|.+.++|++|++||
T Consensus       260 F~~rd~~QEd~re~~aak~~ln~igldG~igC~vngaglamaTmdiiklhgg~panfldVGg~Atve~v~eaf~litsd~  339 (434)
T KOG2799         260 FLLRDLSQEDPREVTAAKVDLNYIGLDGNIGCLVNGAGLAMATMDIIKLHGGTPANFLDVGGGATVEQVREAFSLITSDK  339 (434)
T ss_pred             HHCCCHHHCCCHHHHHHHHCCCEECCCCCCCEEECCCHHHHHHEEEEEECCCCCCCEEEECCCCCHHHHHHHHHHHHCCH
T ss_conf             40036000484056687721000125776460004305543120024304899852144079876778988888872580


Q ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHH------HH
Q ss_conf             865899963586132899999999999972999879997489858999999997699589949989999999------99
Q gi|254781049|r  320 SVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKI------VH  393 (398)
Q Consensus       320 ~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~------v~  393 (398)
                      +|.+||+||||||+|||.+|.||+.|.+++..++|||+||+|||.+.|+.++.+||+.+.+++++++|++++      |+
T Consensus       340 kv~ailvnifGgi~rCDvia~Giv~aar~l~~~ipiv~rlqgt~v~~ak~~i~~sgmri~~~deldeaa~~~v~~S~ive  419 (434)
T KOG2799         340 KVMAILVNIFGGIMRCDVIAFGIVLAARELELNIPIVVRLQGTRVEAAKPIINTSGMRIRSFDELDEAAKKAVGGSTIVE  419 (434)
T ss_pred             HHHHHHHHHHCCEEECCCEECCHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHCCCEEEECHHHHHHHHHHCCCCHHHH
T ss_conf             49999999865720033010013356566523787899965776234146675257367741345688632216414988


Q ss_pred             HHH
Q ss_conf             850
Q gi|254781049|r  394 AVK  396 (398)
Q Consensus       394 ~~k  396 (398)
                      +++
T Consensus       420 la~  422 (434)
T KOG2799         420 LAS  422 (434)
T ss_pred             HHH
T ss_conf             766


No 6  
>pfam08442 ATP-grasp_2 ATP-grasp domain.
Probab=100.00  E-value=0  Score=458.03  Aligned_cols=201  Identities=48%  Similarity=0.740  Sum_probs=199.1

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf             86579999999986898888157479999999998729986999712136876565655677777770799589999999
Q gi|254781049|r    2 NIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS   81 (398)
Q Consensus         2 ~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~   81 (398)
                      ||||||||+||++||||||+|.+++|++||.+++++||+|+||+|||||+|||||+          |||++++|++|+++
T Consensus         1 nlhEyqaK~ll~~~gIpvp~g~~~~~~~ea~~~~~~l~~~~~VvKaQv~aGGRGKa----------GGVk~~~~~~ea~~   70 (202)
T pfam08442         1 NLHEYQAKEILAKYGVPVPRGEVAFSPEEAEEIAKKLGGKVYVVKAQVLAGGRGKA----------GGVKLAKSPEEAKE   70 (202)
T ss_pred             CCCHHHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCCEEEEEEEECCCCCCCC----------CEEEEECCHHHHHH
T ss_conf             95388999999985998999159699999999999809986999874235888767----------73899789999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf             99986187654421222224433011034555650589999983477804899844788402455574831220332144
Q gi|254781049|r   82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP  161 (398)
Q Consensus        82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~  161 (398)
                      ++++|||++|+|+||++.|++|++|||||++++.+|||+|+++||++++|++|+|.+||||||++|+++|++|.+.+|||
T Consensus        71 ~a~~~lg~~l~T~QTg~~G~~V~~vlvee~~~i~~E~Ylsi~~DR~~~~~~ii~S~~GG~dIEeVa~~~Pe~I~k~~id~  150 (202)
T pfam08442        71 AAKEMLGKNLVTKQTGPEGKPVNKVLVEEAVDIAREYYLSIVLDRASRGPVVIASSEGGVDIEEVAAKNPEAIIKVPIDP  150 (202)
T ss_pred             HHHHHCCCEEEEEECCCCCCEEEEEEEEECCCCCCEEEEEEEECCCCCCEEEEEECCCCCCHHHHHCCCHHHEEEEEECC
T ss_conf             99987297787550278896233899985154010079999975777844789726788509997300955729997187


Q ss_pred             CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEE
Q ss_conf             457895788878875198889988599999999899995597510232679
Q gi|254781049|r  162 LIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLI  212 (398)
Q Consensus       162 ~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLv  212 (398)
                      ..|++++++|++++.+|+++....++.+++.+||++|.++||+|+|||||+
T Consensus       151 ~~gl~~~~~r~~~~~lg~~~~~~~~~~~~i~~Ly~~f~~~Da~llEINPLV  201 (202)
T pfam08442       151 AKGLTPYQAREIAFKLGLEGELVKQAADIIKKLYKLFVEYDATLVEINPLV  201 (202)
T ss_pred             CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             879899999999998499989999999999999999996698289756887


No 7  
>pfam00549 Ligase_CoA CoA-ligase. This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilize ATP others use GTP.
Probab=99.95  E-value=1.2e-27  Score=201.73  Aligned_cols=119  Identities=38%  Similarity=0.598  Sum_probs=108.7

Q ss_pred             EECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             95550368999999996589962488427888-98999999999861998658999635861328999999999999729
Q gi|254781049|r  272 MVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVK  350 (398)
Q Consensus       272 ~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~  350 (398)
                      |+|||||+|+|||+++++|++|+||+|+||++ +.+.+.++|+++++||++|+||||+|+||.+||++|.++++|+++.+
T Consensus         1 ~~nGggL~~et~~~l~~~G~~~a~~ldiGGd~~~~~~~~e~l~~~~~Dp~tk~Ili~~~~G~g~~e~~A~~~v~a~~~~~   80 (128)
T pfam00549         1 LVNGGTLAMEAMDLIKLAGGGPHNFIDLGGDAFTPTTRIDALKLEAADPEVKVILLDIVLGYGACEDPAGGLLKAIKEAR   80 (128)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEEECCCHHHHHHHHHHHHHHHC
T ss_conf             94538699999999998599832588837999863379999999957888629999987743626999999999999846


Q ss_pred             -CCCCEEEECCCCCHHHH-----HHHHHHCCCCEEEECCHHHHHHHHH
Q ss_conf             -99879997489858999-----9999976995899499899999999
Q gi|254781049|r  351 -INIPLVMRLEGANVDIG-----NRLIAESGLNVITAIDLDDAAQKIV  392 (398)
Q Consensus       351 -~~~pivvRl~Gtn~~~g-----~~il~~~g~~~~~~~~~~~A~~~~v  392 (398)
                       .++|||+|+.|||++.+     .+.|.++|.+..  .+..+|+++|.
T Consensus        81 ~~~~PvVa~i~Gt~a~~~~~~ghagal~~~G~~~~--~sk~~A~~~Ag  126 (128)
T pfam00549        81 ARELPVVARVCGTEADPQGRSGQAKALAESGVLIA--SSNNQALRAAG  126 (128)
T ss_pred             CCCCCEEEEEEECCCCCCCCHHHHHHHHHCCCCCH--HHHHHHHHHCC
T ss_conf             99875899993026996553378789997799643--01999999769


No 8  
>KOG1254 consensus
Probab=99.73  E-value=4.4e-19  Score=145.40  Aligned_cols=313  Identities=17%  Similarity=0.088  Sum_probs=224.1

Q ss_pred             HCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCC--
Q ss_conf             729986999712136876565655677777770799589999999999861876544212222244330110345556--
Q gi|254781049|r   37 TLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADI--  114 (398)
Q Consensus        37 ~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~--  114 (398)
                      |+..-..|.|+..+++.|||.          |-|.+..+..+..++.+.+.+.+... + .-.| +...+.||+.+.+  
T Consensus        76 ~faS~rsv~k~~m~~~k~~ki----------~lvAiiAegvpe~~~~kl~~~a~~k~-~-~iiG-PaTvggVePg~fkig  142 (600)
T KOG1254          76 WFASTRSVAKPDMLALKRGKI----------GLVAIIAEGVPEADTRKLRAGAEVKG-V-GIIG-PATVGGVEPGVFKIG  142 (600)
T ss_pred             CHHHHHHHCCCHHHHHHCCCC----------CEEEEECCCCCHHHHHHHHHCCCCCC-C-EEEE-EEEECCCCCCCCCCC
T ss_conf             144434320334777635764----------18999715880778999874311236-3-6873-002211557865668


Q ss_pred             ----CEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC----CCHHHHHHHHHHCCCCHHHHHH
Q ss_conf             ----50589999983477804899844788402455574831220332144457----8957888788751988899885
Q gi|254781049|r  115 ----LRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG----VTSEDVASLCDMLELQGQARID  186 (398)
Q Consensus       115 ----~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g----l~~~~~~~l~~~lg~~~~~~~~  186 (398)
                          -.|+|+.+.++|...  ++.+|..|||++|+++..     .+...-|..+    -+.+-...+..++  +-.+...
T Consensus       143 nt~g~~dnil~~klyR~Gs--v~~vS~sGGmsnE~nn~i-----srtt~g~~egiaiggd~~pgSTl~dhi--~r~q~~~  213 (600)
T KOG1254         143 NTGGMMDNILNSKLYRPGS--VIYVSRSGGMSNELNNII-----SRTTDGPYEGIAIGGDRYPGSTLIDHI--PREQHDP  213 (600)
T ss_pred             CCCCCHHHHHHHCCCCCCC--EEEEECCCCCCHHHHHHH-----HHEECCCEEEEEECCCCCCCCHHHHHH--HHHHCCC
T ss_conf             8774245422110137865--799944788641221134-----401034113222056776681176520--3552367


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCC-------EEEECCCCC---EEEEEEEEEECCCHHHHHHH-HH----HHHCCCCCCHH
Q ss_conf             99999999899995597510232-------679905996---79940013215735564102-78----63100015622
Q gi|254781049|r  187 GGDLFPNLYKAFCDKDMSLLEIN-------PLIIMKNGR---LRVLDSKISFDDNALYRHLD-IQ----ELRDVSEEDSR  251 (398)
Q Consensus       187 ~~~ii~~L~~~f~e~Da~liEIN-------PLvvt~dg~---vvAlDAKi~iDDnA~fR~~~-~~----~~~d~~~~~~~  251 (398)
                      ..++|..|+.++-+.+.+++|+|       ||+.-.-|.   ++-+|.....|+.|.|-.-+ |.    .+|+--..-|.
T Consensus       214 ~vk~Iv~Lgevgg~~ey~~~e~~k~g~~tkPlVaw~~gtcA~~F~~evqfghagtaa~~~~eka~akn~al~~ag~~vpe  293 (600)
T KOG1254         214 LVKFIVVLGEVGGDEEYTFLEANKEGKITKPLVAWCIGTCADMFPLEVQFGHAGTAAFKNGEKAAAKNQALRDAGATVPE  293 (600)
T ss_pred             CCCEEEEEHHHCCCCEEEHHHHHHCCCCCCCEEEEECCCCCCCCCHHHHCCCCCHHHHCCHHHHHHCCHHHHHCCCCCCC
T ss_conf             01068873222663315454454147766887999467522024034421334122211156666403135541565763


Q ss_pred             ----------------------------------HHHHHHCCCCEEECCCCEEEEECCC-HHHHHHHHHHHHCCC--CCC
Q ss_conf             ----------------------------------2457753986442288179995550-368999999996589--962
Q gi|254781049|r  252 ----------------------------------EIEAKQHNLSYIALDGNIGCMVNGA-GLAMATMDIIKLYGG--APA  294 (398)
Q Consensus       252 ----------------------------------E~~A~~~~l~yv~LdG~Ig~~vnGa-GlamatmD~i~~~Gg--~pA  294 (398)
                                                        |-.+....|..+.-.|+|||++.|. |....+.|+....|.  +-+
T Consensus       294 sf~~l~~~i~~~~e~lv~~Grvvp~~Ev~pp~lp~d~saalklgllr~p~~i~t~Ia~~rGaeviYA~~p~~~~~a~elG  373 (600)
T KOG1254         294 SFDALGADIQETYEFLVPFGRVVPKTEVPPPGLPEDTSAALKLGLLRKPGRIWTSIAGGRGAEVIYADVPISLGYASELG  373 (600)
T ss_pred             CHHHHHHHHCCCHHCCCCCCEECCCCCCCCCCCCHHHHHHHHCCCCCCCCEEEEEECCCCCCEEEECCCHHHHHHHHHCC
T ss_conf             13344333234201115354454575579999871446676502305786389985179874036558605555676506


Q ss_pred             EEEECCCCCCHHHHHHHHHHHH-------CCCCCCEEEEECCCCHHHHHHHH---HHHHHHHHHCCC----CCCEEEECC
Q ss_conf             4884278889899999999986-------19986589996358613289999---999999997299----987999748
Q gi|254781049|r  295 NFLDVGGGADQDKVAAAFKIIT-------SDSSVKGILINIFGGIMRCDVLV---KGILSAVKEVKI----NIPLVMRLE  360 (398)
Q Consensus       295 NFlD~gG~a~~e~~~~a~~~il-------~~~~vk~iliNifGGI~~cd~vA---~gii~a~~~~~~----~~pivvRl~  360 (398)
                      |+..+||-+...++.++.+.++       .|-+.++.+  +.|||+++...+   .+|+.++.+.+.    .+-+.+|.-
T Consensus       374 ~gg~~Sllw~~~~lp~Ya~kfie~~~m~~aDhgp~Vsg--a~ntI~~~ra~kdl~sslv~gLltigdRfggald~aaR~f  451 (600)
T KOG1254         374 NGGVYSLLWFQRRLPQYARKFIEICTMLTADHGPAVSG--AGNTIANFRAGKDLFSSLVRGLLTIGDRFGGALDIAARRF  451 (600)
T ss_pred             CCCEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEE--CCCCEEEECCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHC
T ss_conf             66057144134411789999999884216898854674--1671687325899999999988551012143226998861


Q ss_pred             CCCHHHHHHHHHH
Q ss_conf             9858999999997
Q gi|254781049|r  361 GANVDIGNRLIAE  373 (398)
Q Consensus       361 Gtn~~~g~~il~~  373 (398)
                      |+|+++|+.-++.
T Consensus       452 ~~ayd~GL~~m~f  464 (600)
T KOG1254         452 GPAYDKGLAPMRF  464 (600)
T ss_pred             CHHHHCCCHHHHH
T ss_conf             8454346607887


No 9  
>COG1042 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]
Probab=99.47  E-value=4.5e-14  Score=112.36  Aligned_cols=361  Identities=16%  Similarity=0.120  Sum_probs=223.0

Q ss_pred             CCCHHHHHHHHHHCC----CCCCCCE------EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf             865799999999868----9888815------747999999999872998699971213687656565567777777079
Q gi|254781049|r    2 NIHEYQAKALLRKYN----VPVAKGV------VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVR   71 (398)
Q Consensus         2 ~L~EyqaK~lL~~~G----Ipvp~g~------~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~   71 (398)
                      ...+|+.++.|.+||    +||++..      .|.+.......+.++++++ |.+..         .+.+.|+...+||+
T Consensus        23 ~~vg~~i~~nL~~~g~g~i~PVnp~~~~v~G~~ay~s~~~lp~~~dlav~~-v~~~~---------~~~i~~~~~~kGv~   92 (598)
T COG1042          23 GKLGYEILRNLLEYGQGKIYPVNPKYDEVLGVKAYTSVADLPDAPDLAVIV-VPAKV---------VPEIVHELGEKGVK   92 (598)
T ss_pred             CHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCHHHHCCCCCCCEEEE-ECHHH---------HHHHHHHHCCCCCC
T ss_conf             215799999998568885574276532336631464075578887706898-52445---------68999872005873


Q ss_pred             E-ECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEE--EEEECCCCCEEEEEECCCCCCHHHHHH
Q ss_conf             9-5899999999998618765442122222443301103455565058999--998347780489984478840245557
Q gi|254781049|r   72 V-ESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLS--LLVDRTSGMVAFIASTQGGMDIEEVAK  148 (398)
Q Consensus        72 l-~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylg--i~~Dr~~~~~vii~S~~GGvdIE~va~  148 (398)
                      . +.......++.+++.  .+.+.+.. ....-...++.+++....+...+  .+.++.+..-   + .-|+..+++...
T Consensus        93 ~~i~is~gf~e~~~~~~--~~e~~~~~-~a~~~~~rligPn~~G~~~~~~glna~f~p~~~~~---~-~g~~afvsqsga  165 (598)
T COG1042          93 GAIVISAGFREAGEEGM--ELEKELVE-AARKYGMRIIGPNCLGLINPIIGLNATFDPVFGLG---R-GGGGAFVSQSGA  165 (598)
T ss_pred             EEEEECHHHHHHHHHHH--HHHHHHHH-HHHHCCCEEECCCCCCCCCCCCCCCCCCCCCCCCC---C-CCCEEEEEECHH
T ss_conf             58996245678877676--77889999-98855963862332453112236563126532334---7-887379995257


Q ss_pred             HCHHHHEEEECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHH--------HHHHHHHCCC-CCCCCCEEEECCCCC-
Q ss_conf             483122033214445789578887887519888998859999999--------9899995597-510232679905996-
Q gi|254781049|r  149 DYPQKIFKLLIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPN--------LYKAFCDKDM-SLLEINPLIIMKNGR-  218 (398)
Q Consensus       149 ~~p~~I~~~~id~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~--------L~~~f~e~Da-~liEINPLvvt~dg~-  218 (398)
                      -.   ..-.++....+    ..+...-.+|.  ....+..+++..        ...+|.|..- -...+||.-....++ 
T Consensus       166 v~---~~il~~~~~~~----~g~s~~vs~gn--~ad~~~~d~~~~~~~D~~tk~i~Ly~E~~~~~r~fl~~a~~~~~~kp  236 (598)
T COG1042         166 VS---FAILDWANEDG----MGFSIKVSLGN--AADRDESDLLEYLADDPRTKAIGLYIEGVKDGRKFLNAARAAERKKP  236 (598)
T ss_pred             HH---HHCCCHHHHCC----CCEEEEEEECC--HHHCCCHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHCCCC
T ss_conf             88---76165234268----75369996142--54338446677775276530799984254427999889998735787


Q ss_pred             EEEEEEEEEECCCHHH------------------HHHHHHHHHCCCCCCHHHH-HHHHCCCCEEECCC-CEEEEECCCHH
Q ss_conf             7994001321573556------------------4102786310001562224-57753986442288-17999555036
Q gi|254781049|r  219 LRVLDSKISFDDNALY------------------RHLDIQELRDVSEEDSREI-EAKQHNLSYIALDG-NIGCMVNGAGL  278 (398)
Q Consensus       219 vvAlDAKi~iDDnA~f------------------R~~~~~~~~d~~~~~~~E~-~A~~~~l~yv~LdG-~Ig~~vnGaGl  278 (398)
                      ++++|+..+.-....+                  ||-.+     ...++..|. ++.+....+..+.| ++..+.||+|.
T Consensus       237 ii~lk~gr~~~~akAa~shTgslag~~~~y~Aa~~~agv-----ir~~~~~elf~~~k~l~~~~~~~g~~~~ivtn~Gg~  311 (598)
T COG1042         237 IIALKAGRSEAGAKAAASHTGSLAGSDEAYDAAFKQAGV-----IRVESIEELFDAAKALSHQPPPAGDRVAIITNGGGP  311 (598)
T ss_pred             EEEEECCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHCCC-----EECCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCC
T ss_conf             799963478788899860261103642002798864072-----231674999999998624899987654789548876


Q ss_pred             HHHHHHHHHHCCCCC---------------------CEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEE-ECCCCHHHHH
Q ss_conf             899999999658996---------------------248842788898999999999861998658999-6358613289
Q gi|254781049|r  279 AMATMDIIKLYGGAP---------------------ANFLDVGGGADQDKVAAAFKIITSDSSVKGILI-NIFGGIMRCD  336 (398)
Q Consensus       279 amatmD~i~~~Gg~p---------------------ANFlD~gG~a~~e~~~~a~~~il~~~~vk~ili-NifGGI~~cd  336 (398)
                      +.-..|.+...|++.                     +|=+|+-|.++.++-.++++.++.++++..+++ .+.+..+--.
T Consensus       312 gvla~D~l~~~g~~l~~~~~~~~~~l~~~Lp~~~~~~NPvD~~~~a~~e~y~~~~~~~~~~~~~~~llvi~~~~~~~~~~  391 (598)
T COG1042         312 GVLAADALEERGLKLAELSEETIEKLRSRLPPHASVKNPVDLTGDADAERYKKTLEILLRDENVDALLVIVLPPASADPE  391 (598)
T ss_pred             CCCCHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCH
T ss_conf             53225579872887678998999999860695124468734206785788999999986065775589996378778841


Q ss_pred             HHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHH
Q ss_conf             999999999997299987-999748985899999999769958994998999999999850
Q gi|254781049|r  337 VLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVK  396 (398)
Q Consensus       337 ~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k  396 (398)
                      ..|+.|+.+ .....++| ++.-++|.+++.+.+++.+.|++.+  .+.+.|++....+++
T Consensus       392 ~~a~~~~~~-~~~~~~k~~v~~~~gg~~~~~~~~~l~~~gip~~--~~pe~a~~a~~~l~~  449 (598)
T COG1042         392 ETAEAIIRA-TAKKRGKPVVVSSMGGESSEKARRLLEEAGIPTY--PTPERAVKALSALAR  449 (598)
T ss_pred             HHHHHHHHH-HHHHCCCCEEEEECCCCCHHHHHHHHHHCCCCCC--CCHHHHHHHHHHHHH
T ss_conf             456788777-7661697659996677652667877641588766--680777889999998


No 10 
>COG1042 Acyl-CoA synthetase (NDP forming) [Energy production and conversion]
Probab=99.47  E-value=4.6e-14  Score=112.33  Aligned_cols=117  Identities=26%  Similarity=0.374  Sum_probs=103.2

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf             86579999999986898888157479999999998729986999712136876565655677777770799589999999
Q gi|254781049|r    2 NIHEYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS   81 (398)
Q Consensus         2 ~L~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~   81 (398)
                      .+.|+++|++++.|||++|++ ++.+++|+..+++.++      |.         .++++.||++.|||.+..+..++.+
T Consensus       470 ~~~~~e~~~~l~~~gi~~~~~-~~~~~~ea~~~a~~~~------Kl---------~s~~i~hksev~gv~l~~~~~~v~~  533 (598)
T COG1042         470 TLDEPEAKELLEAYGIPVPAT-IASTLDEAVHIAESIG------KL---------RSPDIDHKSEVGGVMLNRTADAVEK  533 (598)
T ss_pred             CCCCHHHHHHHHHHCCCCCCC-CCCCHHHHHHHHHHHH------HC---------CCCCCCHHHHCCCEEECCCHHHHHH
T ss_conf             157431455799846865654-5679899999999741------20---------4674211342166042673999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHH
Q ss_conf             9998618765442122222443301103455565058999998347780489984478840245557
Q gi|254781049|r   82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAK  148 (398)
Q Consensus        82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~  148 (398)
                      ++..++.+        +  ..+.+++||+|..  .|+++++..|+.|+ |+++++ +||+.+|.+-+
T Consensus       534 a~~~~~~~--------p--a~i~g~lvq~m~~--~E~~vgv~~dp~fg-p~i~~G-~Gg~~ve~l~d  586 (598)
T COG1042         534 AADDILAR--------P--ARIAGVLVQTMAK--LELIVGVKNDPTFG-PLILFG-EGGIEVEVLKD  586 (598)
T ss_pred             HHHHHHCC--------C--CHHHEEEHHHHHH--CCCEEECCCCCCCH-HHHHHC-CCCEEEEEECC
T ss_conf             99877506--------5--5002001576640--04122113888603-698853-78648884226


No 11 
>TIGR02717 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain; InterPro: IPR014089   This group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which they have been characterised , , . In most species this protein is bifunctional, existing as fused alpha-beta domains. In Pyrococcus and related species, however, the domains exist as separate polypeptides. This entry represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. One of these (along with its beta-domain partner) was characterised as ACS-II showing specificity for phenylacetyl-CoA . This entry excludes non-ACS-I paralogs. .
Probab=99.41  E-value=4.5e-12  Score=99.21  Aligned_cols=187  Identities=24%  Similarity=0.396  Sum_probs=134.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEE----EEE--------EEEEECCCHHHHHH------HHHHHHCCC
Q ss_conf             859999999989999559751023267990599679----940--------01321573556410------278631000
Q gi|254781049|r  185 IDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLR----VLD--------SKISFDDNALYRHL------DIQELRDVS  246 (398)
Q Consensus       185 ~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vv----AlD--------AKi~iDDnA~fR~~------~~~~~~d~~  246 (398)
                      .+-.+++.+...+-..        -|.++.+.|+=-    |.-        .-..+|  |.|||-      .+.+|.|.+
T Consensus       218 ~DG~~Fl~~A~~~s~~--------KPiv~lKsG~s~~GakAA~SHTGaLAGs~~~y~--aaf~q~G~iRa~~~~ELfd~A  287 (457)
T TIGR02717       218 KDGRKFLKTAKEISKK--------KPIVVLKSGTSEAGAKAASSHTGALAGSDEAYD--AAFKQAGVIRADSIEELFDLA  287 (457)
T ss_pred             CCHHHHHHHHHHHHHC--------CCEEEEECCCCHHHHHHHHHCCCHHHHHHHHHH--HHHCCCCEEEEECHHHHHHHH
T ss_conf             0416899998886305--------988999368883456765210231336689999--874301438870177889999


Q ss_pred             CCCHHHHHHHHCCCCEEEC--CC-CEEEEECCCHHHHHHHHHHHHCCCCCCEEE---------------------ECCC-
Q ss_conf             1562224577539864422--88-179995550368999999996589962488---------------------4278-
Q gi|254781049|r  247 EEDSREIEAKQHNLSYIAL--DG-NIGCMVNGAGLAMATMDIIKLYGGAPANFL---------------------DVGG-  301 (398)
Q Consensus       247 ~~~~~E~~A~~~~l~yv~L--dG-~Ig~~vnGaGlamatmD~i~~~Gg~pANFl---------------------D~gG-  301 (398)
                      +           -|++-.+  +| ||+++.||+|....|.|.+.++|.+-|+|.                     |+-| 
T Consensus       288 ~-----------~L~~~~~~~~g~~~~IiTN~GG~Gvia~D~~~~~Gl~L~~~~~~t~~~L~~~LP~~as~~NPVD~~Gs  356 (457)
T TIGR02717       288 R-----------LLSNQPLPPKGNRVAIITNAGGPGVIATDACEEVGLELAELSEKTKEKLRNILPPEASIKNPVDVLGS  356 (457)
T ss_pred             H-----------HHHCCCCCCCCCEEEEEECCCCHHHHHHHHHHHCCCEEECCCHHHHHHHHHHCCCCCCCCCCCEEEEC
T ss_conf             9-----------98358989988769999789616778765677749745558589999999747611477875125522


Q ss_pred             CCCHHHHHHHHHHHHCCCCCCEEEEECCCC--HHH-HHHHHHHHHHHHHHCCCC---CCEEE-ECCCCCHHHHHHHHHHC
Q ss_conf             889899999999986199865899963586--132-899999999999972999---87999-74898589999999976
Q gi|254781049|r  302 GADQDKVAAAFKIITSDSSVKGILINIFGG--IMR-CDVLVKGILSAVKEVKIN---IPLVM-RLEGANVDIGNRLIAES  374 (398)
Q Consensus       302 ~a~~e~~~~a~~~il~~~~vk~iliNifGG--I~~-cd~vA~gii~a~~~~~~~---~pivv-Rl~Gtn~~~g~~il~~~  374 (398)
                      .||+++-++++++++.|+||+++++ |+.-  .++ |++||++||+..++.+.+   +|+|+ -+.|..+..+.++|+++
T Consensus       357 DA~~~~Y~~~l~~v~eD~nVd~~~v-v~~~~a~~~~~~~va~~~~~~~~~~~~k~~~Kpvv~~~~gG~~~~~a~~~L~~~  435 (457)
T TIGR02717       357 DATAERYAKALKIVAEDENVDGVVV-VLTPTAMTDKPEEVAKGIIEVAKKSNEKKRDKPVVAGFVGGKSVKEAKRILEEN  435 (457)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCEEEE-EEECCCHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHC
T ss_conf             7898999999999834888888999-642530246799999988754303674212474489984673220156622315


Q ss_pred             CCCEEEECCHHHHHHHHHHHH
Q ss_conf             995899499899999999985
Q gi|254781049|r  375 GLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       375 g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      |+|.++  +-+.||+-.-.+-
T Consensus       436 giP~Y~--~Pe~AV~Al~~l~  454 (457)
T TIGR02717       436 GIPNYT--FPERAVKALSALY  454 (457)
T ss_pred             CCCCCC--CHHHHHHHHHHHH
T ss_conf             887647--9688999999861


No 12 
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275   Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC).   Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.   Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains .    This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=99.36  E-value=1.5e-11  Score=95.79  Aligned_cols=95  Identities=24%  Similarity=0.401  Sum_probs=44.3

Q ss_pred             HHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCC
Q ss_conf             99998689888815747999999999872998699971213687656565567777777079958999999999986187
Q gi|254781049|r   10 ALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGS   89 (398)
Q Consensus        10 ~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~   89 (398)
                      ++|++-|.|||++..++|.+||.++++++|||+ +|-+==-=||+|            ||  ++.|.+|+++-+++=|..
T Consensus       133 ~~M~ei~~pvp~S~~~~~~eEA~~~a~~~GyPv-iVRpAftLGG~G------------gG--iA~n~eEL~~~~~~aL~~  197 (1089)
T TIGR01369       133 EAMKEIGEPVPKSEIVHSVEEALKAAKEIGYPV-IVRPAFTLGGTG------------GG--IASNEEELKEIVERALSA  197 (1089)
T ss_pred             HHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EECCCHHCCCCC------------CC--EECCHHHHHHHHHHHHHH
T ss_conf             999973899881100278899999996268968-981003238899------------85--225778999999988630


Q ss_pred             CCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCC
Q ss_conf             65442122222443301103455565058999998347780
Q gi|254781049|r   90 TLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGM  130 (398)
Q Consensus        90 ~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~  130 (398)
                      .           ++++|||||-+.+.||+=.=+.+|+...+
T Consensus       198 S-----------pI~qvL~EkSl~GWKE~EYEVmRD~~dNC  227 (1089)
T TIGR01369       198 S-----------PINQVLVEKSLAGWKEIEYEVMRDSKDNC  227 (1089)
T ss_pred             C-----------CCCEEEEEEECCCCEEEEEEEEEECCCCE
T ss_conf             8-----------88557501100331788988986268788


No 13 
>pfam01071 GARS_A Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain. Phosphoribosylglycinamide synthetase catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam02786).
Probab=99.34  E-value=3.1e-11  Score=93.66  Aligned_cols=99  Identities=26%  Similarity=0.283  Sum_probs=80.9

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf             99999999868988881574799999999987299869997121368765656556777777707995899999999998
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIRE   85 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~   85 (398)
                      ..+|++|+++|||+|++..++|.+|+.++++++|||+ |||+--.+|+|              ||+++.|.+|+..++++
T Consensus         4 ~~~r~~l~~~gip~p~~~~~~~~~ea~~~~~~~g~P~-VvKp~~~~gs~--------------Gv~~v~~~~e~~~a~~~   68 (193)
T pfam01071         4 SFAKDFMKRHGIPTAEYETFTDPEEAKSYIREAGFPA-VVKADGLAAGK--------------GVIVAMDNEEAIKAVDE   68 (193)
T ss_pred             HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EEEECCCCCCC--------------CEEEECCHHHHHHHHHH
T ss_conf             9999999986989999078789999999999769988-99974346788--------------37995458999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf             618765442122222443301103455565058999998347
Q gi|254781049|r   86 ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT  127 (398)
Q Consensus        86 ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~  127 (398)
                      ++....       .+..-..|||||+++ +.|+-+....|..
T Consensus        69 ~~~~~~-------~~~~~~~vlvEefl~-G~E~sv~~~~dg~  102 (193)
T pfam01071        69 ILEQKK-------FGEAGEPVVIEEFLE-GEEVSVLAFVDGK  102 (193)
T ss_pred             HHHHCC-------CCCCCCCEEEEEECC-CCEEEEEEEEECC
T ss_conf             985230-------357899789987205-7165578984099


No 14 
>pfam02222 ATP-grasp ATP-grasp domain. This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity.
Probab=99.25  E-value=5.4e-10  Score=85.50  Aligned_cols=88  Identities=24%  Similarity=0.240  Sum_probs=70.0

Q ss_pred             HHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCC
Q ss_conf             99868988881574799999999987299869997121368765656556777777707995899999999998618765
Q gi|254781049|r   12 LRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTL   91 (398)
Q Consensus        12 L~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l   91 (398)
                      |++.|||+|++.+++|.+|+.++++++|||+ |||+- ..|.-|            .|+.++++.+|+.++.+...+   
T Consensus         1 l~~~Giptp~~~~i~~~~d~~~~~~~iGyP~-vvKp~-~~G~~g------------~G~~~v~~~~el~~a~~~~~~---   63 (171)
T pfam02222         1 LQKLGLPTPRFMAAESLEELIEAGQELGYPC-VLKAR-RGGYDG------------KGQYVVRSEADIPQAWEELGG---   63 (171)
T ss_pred             CHHCCCCCCCCEEECCHHHHHHHHHHCCCCE-EEEEC-CCCCCC------------CCCEEECCHHHHHHHHHHCCC---
T ss_conf             9020989999549899999999999709978-99961-102589------------852898899999999985589---


Q ss_pred             CCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCC
Q ss_conf             4421222224433011034555650589999983477
Q gi|254781049|r   92 ITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTS  128 (398)
Q Consensus        92 ~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~  128 (398)
                                  ..+++|+.++..+|+-+-..+|.+.
T Consensus        64 ------------~~~liE~~I~~~~Ei~~~~~r~~~g   88 (171)
T pfam02222        64 ------------GPVIVEEFVPFDKELSVLVVRSVDG   88 (171)
T ss_pred             ------------CCEEEEEECCCCEEEEEEEEECCCC
T ss_conf             ------------9579986046757999874344999


No 15 
>PRK02186 argininosuccinate lyase; Provisional
Probab=99.25  E-value=5.5e-10  Score=85.47  Aligned_cols=92  Identities=20%  Similarity=0.218  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             79999999986898888157479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR   84 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~   84 (398)
                      -+.-++.|.++|+|+|++.++++.+++..++.+||||+ |||+-..+|              .-||++|.|.+|+.+++.
T Consensus       108 K~~~Rq~L~~aGVp~P~~~lv~~~~e~~~aAa~IGfPv-VVKP~dgSG--------------S~GVrLc~s~aEL~e~~~  172 (892)
T PRK02186        108 KKRLARTLRDHGIDVPRTHALALDAVALDALDGLTYPV-VVKPRMGSG--------------SVGVRLCASVAEAAAHCA  172 (892)
T ss_pred             HHHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EECCCCCCC--------------CCCEEEECCHHHHHHHHH
T ss_conf             99999999966999995688358878999998479998-971688887--------------768587689999999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEE
Q ss_conf             8618765442122222443301103455565058999998
Q gi|254781049|r   85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLV  124 (398)
Q Consensus        85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~  124 (398)
                      .+.+..            ...+||||+++.. ||-+-...
T Consensus       173 ~l~~~r------------~~~vLVEEFieGp-EYSVEt~s  199 (892)
T PRK02186        173 ALRRAG------------TRAALVQAYVEGD-EYSVETLT  199 (892)
T ss_pred             HHHHCC------------CCCEEEEECCCCC-EEEEEEEE
T ss_conf             997154------------8866999715688-78999999


No 16 
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=99.19  E-value=1e-10  Score=90.32  Aligned_cols=116  Identities=19%  Similarity=0.348  Sum_probs=85.3

Q ss_pred             HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf             99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r    9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG   88 (398)
Q Consensus         9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg   88 (398)
                      ++++.+.|+|+|++..+++.+||..+++++|||+ ++.+--.-||||            ||  ++.|.+|+.+.+++-+.
T Consensus       133 ~~~m~~ig~~~~~s~~~~s~~ea~~~a~~ig~Pv-ivRps~~lGg~g------------~~--i~~n~~eL~~~~~~~~~  197 (1068)
T PRK12815        133 RALMKELGEPVPESEIVDSEEEALRFAEKIGFPI-IVRPAYTLGGDG------------GG--IAENEEELEQLARQGLQ  197 (1068)
T ss_pred             HHHHHHCCCCCCCCHHCCCHHHHHHHHHHCCCCE-EEEECCCCCCCC------------CE--EECCHHHHHHHHHHHHH
T ss_conf             9999976999997052199999999998669989-998361066896------------50--44599999999999996


Q ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHH
Q ss_conf             765442122222443301103455565058999998347780489984478840245557483122
Q gi|254781049|r   89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKI  154 (398)
Q Consensus        89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I  154 (398)
                      ..           +++.+|||+.+...+|+-+-+.+|.... .+++++.+   ++|.+.-.+-|.+
T Consensus       198 ~S-----------~~~~vlie~sl~gwkEie~ev~RD~~~n-~i~vc~mE---nidP~GIHTGDSi  248 (1068)
T PRK12815        198 AS-----------PIHQCLLEESIAGWKEIEYEVMRDRNDN-CVTVCNME---NIDPVGVHTGDSI  248 (1068)
T ss_pred             HC-----------CCCCEEEEHHCCCCEEEEEEEEEECCCC-EEEEEECC---CCCCCCCCCCCCC
T ss_conf             39-----------9985786501179769999999988989-79985412---3544543567745


No 17 
>pfam02786 CPSase_L_D2 Carbamoyl-phosphate synthase L chain, ATP binding domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117. The ATP binding domain (this one) has an ATP-grasp fold.
Probab=99.16  E-value=7.1e-10  Score=84.72  Aligned_cols=107  Identities=20%  Similarity=0.270  Sum_probs=81.3

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      ...|++|++.|||+|++.  .++|.+|+.+++++||||+ |||+- . ||-|+            |+.++++.+|+.+++
T Consensus         3 ~~~k~~l~~~GvP~~~~~~~~~~s~ee~~~~a~~iG~Pv-vvKp~-~-~g~g~------------G~~~v~~~~eL~~a~   67 (211)
T pfam02786         3 VLFKAAMKEAGVPTVPGTAGPVETEEEALAAAKEIGYPV-IIKAA-F-GGGGL------------GMGIARNEEELAELF   67 (211)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCE-EEECC-C-CCCCC------------CCEEEHHHHHHHHHH
T ss_conf             999999998698919987888799999999999859978-99737-7-78998------------751241277899999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             9861876544212222244330110345556505899999834778048998
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      ++.+...       .....-..+++|++++..+|+=+.+..|.... .+.++
T Consensus        68 ~~a~~~a-------~~~~~~~~vlvEe~i~g~~ei~v~v~~d~~~~-~~~~~  111 (211)
T pfam02786        68 ALALAEA-------PAAFGNPQVLVEKSLKGPKHIEYQVLRDAHGN-CITVC  111 (211)
T ss_pred             HHHHHHH-------HHCCCCCCEEEEECCCCCEEEEEEEEEECCCC-EEEEE
T ss_conf             9998751-------43169983899740477658999999827998-99999


No 18 
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=99.13  E-value=2.6e-10  Score=87.59  Aligned_cols=139  Identities=14%  Similarity=0.272  Sum_probs=91.9

Q ss_pred             HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf             99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r    9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG   88 (398)
Q Consensus         9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg   88 (398)
                      +++|.+.|+|+|++..++|.+||.++++++|||+ ++.+----||||-            |  ++.|.+|+.+....-+.
T Consensus       133 ~~~l~~i~~p~~~s~~~~s~~ea~~~a~~igyPv-ivRps~~LGG~g~------------~--i~~n~~eL~~~~~~~~~  197 (1063)
T PRK05294        133 KEAMKKIGLPVPRSGIAHTMEEALEVAEEIGYPV-IIRPSFTLGGTGG------------G--IAYNREELEEIVERGLD  197 (1063)
T ss_pred             HHHHHHCCCCCCCCHHCCCHHHHHHHHHHCCCCE-EEEECCCCCCCCC------------E--EECCHHHHHHHHHHHHH
T ss_conf             9999976999997253099999999998659988-9984421678764------------0--43499999999999996


Q ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCCHH
Q ss_conf             76544212222244330110345556505899999834778048998447884024555748312203321444578957
Q gi|254781049|r   89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSE  168 (398)
Q Consensus        89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~~~  168 (398)
                      ..           +++.+|||+.+...+|+-+-+.+|..... +++++.+   ++|.+.-.+-|.+..   -|...+++.
T Consensus       198 ~S-----------~~~qvLie~sl~gwkEie~ev~rD~~~n~-i~v~~mE---nidp~GIHtGDSi~v---aP~qTL~d~  259 (1063)
T PRK05294        198 LS-----------PTTEVLIEESLLGWKEYEMEVMRDKADNC-IIVCSIE---NIDPMGVHTGDSITV---APAQTLTDK  259 (1063)
T ss_pred             HC-----------CCCCEEEEHHCCCCEEEEEEEEEECCCCE-EEEEEEC---CCCCCCCCCCCCCEE---CCCCCCCHH
T ss_conf             19-----------99868966111798899999998189998-9995411---354564566672535---688658989


Q ss_pred             -------HHHHHHHHCCCC
Q ss_conf             -------888788751988
Q gi|254781049|r  169 -------DVASLCDMLELQ  180 (398)
Q Consensus       169 -------~~~~l~~~lg~~  180 (398)
                             .+.+++..||+.
T Consensus       260 e~q~lR~~a~kI~~~L~iv  278 (1063)
T PRK05294        260 EYQMLRDASIAILREIGVE  278 (1063)
T ss_pred             HHHHHHHHHHHHHHHCCCC
T ss_conf             9999999999999982957


No 19 
>PRK01372 ddl D-alanine--D-alanine ligase; Reviewed
Probab=99.10  E-value=1.4e-08  Score=76.30  Aligned_cols=166  Identities=23%  Similarity=0.249  Sum_probs=107.6

Q ss_pred             HHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             79999999986898888157479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR   84 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~   84 (398)
                      -+.+|++|+++|||+|++.+.+..++.......+++|+ +||+ ... |           |. =||.++++.+|+.++.+
T Consensus        99 K~~tK~i~~~~gI~tp~~~~~~~~~~~~~~~~~l~~P~-iVKP-~~~-G-----------SS-iGv~~V~~~~el~~ai~  163 (304)
T PRK01372         99 KLRTKLVWQAAGLPTAPWVVLTRAEDLLAAIDKLGLPL-VVKP-ARE-G-----------SS-VGVTKVKEADELPAALE  163 (304)
T ss_pred             HHHHHHHHHHCCCCCCCEEEECCCHHHHHHHHHHCCCE-EEEE-CCC-C-----------CC-CCEEEECCHHHHHHHHH
T ss_conf             89999999986999898499865313999987618987-9976-688-8-----------66-65389669889999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCC-CHHHHHHHCHHHHEEEECCCCC
Q ss_conf             861876544212222244330110345556505899999834778048998447884-0245557483122033214445
Q gi|254781049|r   85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGM-DIEEVAKDYPQKIFKLLIDPLI  163 (398)
Q Consensus        85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGv-dIE~va~~~p~~I~~~~id~~~  163 (398)
                      ..+..          +   +.+|||+.++. +|+-+++.-|+... ++-+. +.++. |-|.  +.++.           
T Consensus       164 ~a~~~----------~---~~vLvE~~I~G-rEitv~Vlg~~~lp-~~eI~-~~~~fyDy~a--KY~~~-----------  214 (304)
T PRK01372        164 LAFKY----------D---DEVLVEKYIKG-RELTVAVLGGKALP-VIRIV-PPGEFYDYEA--KYLAG-----------  214 (304)
T ss_pred             HHHHC----------C---CCCEEEEEECC-EEEEEEEECCCCCC-EEEEE-CCCCCCCHHH--CCCCC-----------
T ss_conf             98744----------8---86254502565-69999998997775-38994-5998757766--12557-----------


Q ss_pred             CCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEE
Q ss_conf             789578887887519888998859999999989999559751023267990599679940
Q gi|254781049|r  164 GVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLD  223 (398)
Q Consensus       164 gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlD  223 (398)
                           ..+. ..-..++.+..+.+.++..++|+++--.+..-++   +.++++|+++.+.
T Consensus       215 -----~s~~-~~Pa~l~~~~~~~i~~~a~~~~~aLg~~g~aRvD---f~~~~~g~~~~lE  265 (304)
T PRK01372        215 -----DTQY-LCPAGLPAELEAELQALALRAYKALGCRGWGRVD---FMLDEDGKPYLLE  265 (304)
T ss_pred             -----CCCE-ECCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEE---EEEECCCCEEEEE
T ss_conf             -----7411-0068999999999999999999984997369889---9990799789998


No 20 
>PRK09288 purT phosphoribosylglycinamide formyltransferase 2; Validated
Probab=99.10  E-value=5e-09  Score=79.14  Aligned_cols=95  Identities=21%  Similarity=0.200  Sum_probs=69.7

Q ss_pred             HHHHH-HHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             99999-98689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r    8 AKALL-RKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI   86 (398)
Q Consensus         8 aK~lL-~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i   86 (398)
                      -|+++ .++|||+|++..+++.+|+..+++++|||+ |+|+.  .|+-||            |+.+++|.+|+.++.+..
T Consensus       117 ~k~~~~~~lgIPt~~f~~v~s~~el~~~~~~lG~P~-vlK~~--~G~DGK------------Gq~~v~~~~dl~~a~~~a  181 (395)
T PRK09288        117 IRRLAAEELGLPTSPYRFADSLEELRAAVEEIGYPC-VVKPV--MSSSGK------------GQSVVRSPEDIEAAWEYA  181 (395)
T ss_pred             HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHHCCCE-EEECC--CCCCCC------------CEEEECCHHHHHHHHHHH
T ss_conf             999999746999999547089999999999829875-87224--157887------------528966878889999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEEC
Q ss_conf             1876544212222244330110345556505899999834
Q gi|254781049|r   87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDR  126 (398)
Q Consensus        87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr  126 (398)
                      +...        .+ ....+++|++++..+|+=+-+.++.
T Consensus       182 ~~~~--------~~-~~~~~ivE~~v~f~~E~Svi~aR~~  212 (395)
T PRK09288        182 QEGG--------RG-GAGRVIVEEFIDFDYEITLLTVRAV  212 (395)
T ss_pred             HHHC--------CC-CCCCEEEEEEECCCEEEEEEEEECC
T ss_conf             8507--------57-8970899888536179999999969


No 21 
>TIGR00877 purD phosphoribosylamine--glycine ligase; InterPro: IPR000115   Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase)  catalyzes the second step in the de novo biosynthesis of purine:  ATP + 5-phosphoribosylamine + glycine = ADP + P_i + 5'-phosphoribosylglycinamide  In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART.; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process.
Probab=99.10  E-value=1.2e-09  Score=83.28  Aligned_cols=211  Identities=24%  Similarity=0.297  Sum_probs=133.5

Q ss_pred             HHHHHHHCCCC-CCCCEEECCHHHHHHHHHHCCCC-EEEEECCCCCCCCCCCCCCCCCCCCCCEEEEE----CCHHHHHH
Q ss_conf             99999986898-88815747999999999872998-69997121368765656556777777707995----89999999
Q gi|254781049|r    8 AKALLRKYNVP-VAKGVVISSVHAAESAIKTLPGP-LYVVKSQIHAGGRGKGRFKELPADSKGGVRVE----SSLKSVIS   81 (398)
Q Consensus         8 aK~lL~~~GIp-vp~g~~a~s~~ea~~~a~~ig~p-~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~----~s~~ea~~   81 (398)
                      +|++|++|||| ++.+...++++||.+..++.+.| .+|||+.=||+|-              ||.++    .|.+||.+
T Consensus       112 aK~fm~~~gIPGta~Y~~Ft~~eea~~y~~~~g~PA~~VVKadGLAAGK--------------GV~V~Ge~L~~~eEA~~  177 (459)
T TIGR00877       112 AKDFMKRYGIPGTAEYEVFTDPEEAKSYIQEKGAPAEIVVKADGLAAGK--------------GVIVAGEQLKTNEEAIK  177 (459)
T ss_pred             HHHHHHHCCCCCCEEEECCCCHHHHHHHHHHCCCCCCEEEECCCCCCCC--------------CCEEECCCCCCHHHHHH
T ss_conf             9999996489832221000898999999984188974898056665798--------------62684760274789999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf             99986187654421222224433011034555650589999983477804899844788402455574831220332144
Q gi|254781049|r   82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP  161 (398)
Q Consensus        82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~  161 (398)
                      ++++||...    +-+..+   ++|+|||+++. .|+=+-.+.|..+--||..+  |          ++|.     -+|-
T Consensus       178 ~~~~~~~~~----~FG~a~---~~VVIEEfL~G-~E~S~~~~~DG~~v~Plp~a--Q----------DhKR-----~~eg  232 (459)
T TIGR00877       178 AVEEILEQK----AFGEAG---ERVVIEEFLEG-EEVSLLAFVDGKTVIPLPPA--Q----------DHKR-----ALEG  232 (459)
T ss_pred             HHHHHHHCC----CCCCCC---CCEEEEECCCC-CCEEEEEEECCCEEEECCCC--C----------CCCC-----CCCC
T ss_conf             999998547----656668---82589642488-00899999748667705421--5----------7650-----4668


Q ss_pred             CC-CC-----CHHHHHHHHHHCCCCHHH-HHHHHHHHHHHHHHHHHCC-----CCCCCCCEEEECCCCCEEEEEEEEEEC
Q ss_conf             45-78-----957888788751988899-8859999999989999559-----751023267990599679940013215
Q gi|254781049|r  162 LI-GV-----TSEDVASLCDMLELQGQA-RIDGGDLFPNLYKAFCDKD-----MSLLEINPLIIMKNGRLRVLDSKISFD  229 (398)
Q Consensus       162 ~~-gl-----~~~~~~~l~~~lg~~~~~-~~~~~~ii~~L~~~f~e~D-----a~liEINPLvvt~dg~vvAlDAKi~iD  229 (398)
                      .. |+     -.|--.+  ..|-+..+. .+....|++.--+.+.+-.     ..+..   |+++++|+.  |=-|| |+
T Consensus       233 D~~GpNTGGMGAYsP~p--hlL~~~~e~~~~~~~~I~~pt~~~l~~eG~~y~GvLYag---lMl~~~G~~--L~PkV-lE  304 (459)
T TIGR00877       233 DKKGPNTGGMGAYSPAP--HLLVFTEEVEKRIAEEIVEPTVKALRKEGTPYKGVLYAG---LMLTKEGGV--LVPKV-LE  304 (459)
T ss_pred             CCCCCCCCCCCCCCCCC--CCEECCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEE---EEEECCCCE--EEEEE-EE
T ss_conf             88788557863302787--844237178999987778999999985289724787413---899768988--64478-89


Q ss_pred             CCHHHHHHHHHHHHCCCC--CCHHHH--HHHHCCCC--EEEC
Q ss_conf             735564102786310001--562224--57753986--4422
Q gi|254781049|r  230 DNALYRHLDIQELRDVSE--EDSREI--EAKQHNLS--YIAL  265 (398)
Q Consensus       230 DnA~fR~~~~~~~~d~~~--~~~~E~--~A~~~~l~--yv~L  265 (398)
                      =|+.|==|+=.......+  .|-.|+  .+-+..|.  .+++
T Consensus       305 fN~RFGDPEtq~vL~lL~dqsdL~e~~~a~~eg~L~d~~~~~  346 (459)
T TIGR00877       305 FNVRFGDPETQAVLPLLKDQSDLLEVCLAAVEGKLDDSEVEL  346 (459)
T ss_pred             ECCCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCEEEE
T ss_conf             705278853444645423888889999998456665641124


No 22 
>PRK00885 phosphoribosylamine--glycine ligase; Provisional
Probab=99.08  E-value=3e-09  Score=80.60  Aligned_cols=199  Identities=21%  Similarity=0.247  Sum_probs=121.0

Q ss_pred             HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI   86 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i   86 (398)
                      -+|+++++|+||++++...++.++|.+..++.++| +|+|+.=|++|.              ||.++.|.+|+.++.+++
T Consensus       105 faK~~m~~~~IPTa~~~~f~~~~~A~~~l~~~~~p-~VIKaDGLAaGK--------------GV~V~~~~~ea~~al~~i  169 (424)
T PRK00885        105 FAKDFMARYGIPTAAYEVFTDAEEAKAYLDEQGAP-IVVKADGLAAGK--------------GVVVAMTLEEAEAAVDDM  169 (424)
T ss_pred             HHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCC-EEEECCCCCCCC--------------CEEEECCHHHHHHHHHHH
T ss_conf             99999998298987548868999999999857998-899617656777--------------517637899999999998


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC-C
Q ss_conf             187654421222224433011034555650589999983477804899844788402455574831220332144457-8
Q gi|254781049|r   87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG-V  165 (398)
Q Consensus        87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g-l  165 (398)
                      |..+.    .+..|   ++|+|||++.. .|+=+-...|...-.|+-.+  +          ++ .++..-..-|..| +
T Consensus       170 ~~~~~----fg~ag---~~VvIEE~L~G-~E~S~~a~~DG~~~~~lp~a--q----------Dh-KR~~dgD~GPNTGGM  228 (424)
T PRK00885        170 LAGNK----FGDAG---ARVVIEEFLDG-EEASFFALVDGENVLPLPTA--Q----------DH-KRAGDGDTGPNTGGM  228 (424)
T ss_pred             HCCCC----CCCCC---CEEEEEECCCC-CEEEEEEEECCCCCCCCCCC--C----------CC-CCCCCCCCCCCCCCC
T ss_conf             50332----34568---72899970588-31799999789972647021--1----------47-505689999889988


Q ss_pred             CHHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHHHCCCCCCCC--CEEEECCCCCEEEEEEEEEECCCHHHHHHHHHHH
Q ss_conf             9578887887519888998859-999999989999559751023--2679905996799400132157355641027863
Q gi|254781049|r  166 TSEDVASLCDMLELQGQARIDG-GDLFPNLYKAFCDKDMSLLEI--NPLIIMKNGRLRVLDSKISFDDNALYRHLDIQEL  242 (398)
Q Consensus       166 ~~~~~~~l~~~lg~~~~~~~~~-~~ii~~L~~~f~e~Da~liEI--NPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~~~  242 (398)
                      -.+.-..     -+..+..+.+ .+++....+.+.+......=|  ==|.+|++| ..      .|.=|+.|=-|+...+
T Consensus       229 Ga~sP~p-----~~~~~~~~~i~~~Ii~pt~~~l~~eg~~y~GiLy~GlMit~~G-pk------VlEyN~RfGDPE~qvl  296 (424)
T PRK00885        229 GAYSPAP-----VVTEEVHDRVMEEIIEPTVKGMAAEGIPYTGVLYAGLMITKDG-PK------VIEFNCRFGDPETQVV  296 (424)
T ss_pred             CCCCCCC-----CCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEECCC-CE------EEEEECCCCCHHHHHH
T ss_conf             5667886-----7999999999998799999999857984799987799986797-55------8986313488588899


Q ss_pred             HCCCCCCHHHH
Q ss_conf             10001562224
Q gi|254781049|r  243 RDVSEEDSREI  253 (398)
Q Consensus       243 ~d~~~~~~~E~  253 (398)
                      ....+.|-.++
T Consensus       297 lp~L~~dl~~l  307 (424)
T PRK00885        297 LPRLKSDLVEL  307 (424)
T ss_pred             HHHCCCCHHHH
T ss_conf             87523619999


No 23 
>PRK13789 phosphoribosylamine--glycine ligase; Provisional
Probab=99.06  E-value=2.7e-09  Score=80.91  Aligned_cols=212  Identities=21%  Similarity=0.260  Sum_probs=123.5

Q ss_pred             HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI   86 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i   86 (398)
                      -+|+++++||||++++...++.++|.+..++.++|+ |||+.=||+|.              ||.++.+.+|+.++.++|
T Consensus       111 faK~fm~~~~IPTa~~~~f~~~~~A~~~l~~~~~P~-VIKaDGLAaGK--------------GV~V~~~~~eA~~al~~i  175 (426)
T PRK13789        111 FAKSLMKEAKIPTASYKTFTEYSSSLSYLESEMLPI-VIKADGLAAGK--------------GVTVATEKKMAKRALKEI  175 (426)
T ss_pred             HHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCCCCE-EEECCCCCCCC--------------CEEEECCHHHHHHHHHHH
T ss_conf             999999972999760157368999999998579988-99678768999--------------669539999999999997


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCC-CC
Q ss_conf             18765442122222443301103455565058999998347780489984478840245557483122033214445-78
Q gi|254781049|r   87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLI-GV  165 (398)
Q Consensus        87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~-gl  165 (398)
                      |....    -+..|   ++|+|||++.. .|+=+-...|...-  +.|-+.+          ++ .++..-..-|.. |+
T Consensus       176 ~~~~~----fg~ag---~~VvIEE~L~G-~E~S~~a~~dG~~~--~~lp~aQ----------Dh-KR~~dgD~GPNTGGM  234 (426)
T PRK13789        176 FKDKK----FGQSG---NQVVIEEFMEG-QEASIFAISDGDSY--FLLPAAQ----------DH-KRAFDGDQGPNTGGM  234 (426)
T ss_pred             HHHHH----HHCCC---CEEEEEECCCC-CCEEEEEEECCCEE--EECCCCC----------CC-CCCCCCCCCCCCCCC
T ss_conf             54423----30358---75999974589-84479999729977--8688644----------44-213379999999987


Q ss_pred             CHHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHHHHHCCCCCCCC--CEEEECCCCCEEEEEEEEEECCCHHHHHHHHHHH
Q ss_conf             95788878875198889988599-99999989999559751023--2679905996799400132157355641027863
Q gi|254781049|r  166 TSEDVASLCDMLELQGQARIDGG-DLFPNLYKAFCDKDMSLLEI--NPLIIMKNGRLRVLDSKISFDDNALYRHLDIQEL  242 (398)
Q Consensus       166 ~~~~~~~l~~~lg~~~~~~~~~~-~ii~~L~~~f~e~Da~liEI--NPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~~~  242 (398)
                      -.+--.     --+.....+.+. .++....+.+.+......=|  ==|.+|++|++..+      .=|+.|--|+...+
T Consensus       235 GaysP~-----p~~~~~~~~~i~~~ii~pt~~~l~~~g~~y~GvLy~GlMlt~~G~pkVl------EfN~RfGDPE~q~i  303 (426)
T PRK13789        235 GAYCPA-----PVITEAILQKVKERIFDPMFDDFRKKGHPYRGLLYAGLMISPEGEPKVV------EFNCRFGDPETQCV  303 (426)
T ss_pred             CCCCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCEEEE------EEEEECCCCHHHHH
T ss_conf             677778-----6689999999998604899999985899988676532899269976999------98853189168889


Q ss_pred             HCCCCCCHHHH--HHHHCCCCEEEC
Q ss_conf             10001562224--577539864422
Q gi|254781049|r  243 RDVSEEDSREI--EAKQHNLSYIAL  265 (398)
Q Consensus       243 ~d~~~~~~~E~--~A~~~~l~yv~L  265 (398)
                      ....+.|-.++  .+.+..|+-+.+
T Consensus       304 Lp~L~~dl~~~~~a~~~g~L~~~~~  328 (426)
T PRK13789        304 LAMLDGDLLELLYAASTGKIKVVNL  328 (426)
T ss_pred             HHHHHCCHHHHHHHHHHCCCCCCCC
T ss_conf             8874154999999997088664544


No 24 
>TIGR02068 cya_phycin_syn cyanophycin synthetase; InterPro: IPR011810    Cyanophycin is an insoluble storage polymer for carbon, nitrogen, and energy, found in most Cyanobacteria. The polymer has a backbone of L-aspartic acid, with most Asp side chain carboxyl groups attached to L-arginine. The polymer is made by this enzyme, cyanophycin synthetase, and degraded by cyanophycinase. Heterologously expressed cyanophycin synthetase in Escherichia coli produces a closely related, water-soluble polymer with some Arg replaced by Lys. It is unclear whether enzymes that produce soluble cyanophycin-like polymers in vivo in non-Cyanobacterial species should be designated as cyanophycin synthetase itself or as a related enzyme. Cyanophycin synthesis is analogous to polyhydroxyalkanoic acid (PHA) biosynthesis, except that PHA polymers lack nitrogen and may be made under nitrogen-limiting conditions .; GO: 0005524 ATP binding, 0016874 ligase activity, 0009059 macromolecule biosynthetic process.
Probab=99.01  E-value=1.4e-09  Score=82.70  Aligned_cols=121  Identities=27%  Similarity=0.354  Sum_probs=79.3

Q ss_pred             HHHHHHHCCCCCCCCEEECCHHHHHHHHHHCC-CCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEE-ECCHHHHHHHHHH
Q ss_conf             99999986898888157479999999998729-986999712136876565655677777770799-5899999999998
Q gi|254781049|r    8 AKALLRKYNVPVAKGVVISSVHAAESAIKTLP-GPLYVVKSQIHAGGRGKGRFKELPADSKGGVRV-ESSLKSVISDIRE   85 (398)
Q Consensus         8 aK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig-~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l-~~s~~ea~~~a~~   85 (398)
                      -|+||+.+|+|||+|.++.+.+||..+++++| ||+ |+|+-  =|-.||            ||.+ .+|.+|+..+++.
T Consensus       222 TK~iL~~~GvPVP~G~~~~~~~~a~~aa~~~GG~Pv-ViKP~--DGn~Gr------------Gv~~ni~~r~e~e~AY~~  286 (876)
T TIGR02068       222 TKKILKAAGVPVPEGTVVQSAEEAWEAAEDLGGYPV-VIKPY--DGNHGR------------GVTINIETRDEIESAYEA  286 (876)
T ss_pred             HHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCE-EEEEC--CCCCCC------------EEEECCCCHHHHHHHHHH
T ss_conf             999998478988887366778999999997189968-99517--799874------------378407774889999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEEC----CCC-CEEEEEECCCCCCHHHHHHHCHHHH-EEEEC
Q ss_conf             61876544212222244330110345556505899999834----778-0489984478840245557483122-03321
Q gi|254781049|r   86 ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDR----TSG-MVAFIASTQGGMDIEEVAKDYPQKI-FKLLI  159 (398)
Q Consensus        86 ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr----~~~-~~vii~S~~GGvdIE~va~~~p~~I-~~~~i  159 (398)
                      =-       +.   + ..+.|+||.++... ||=|=++-++    +.+ ++-+++  -|==-|||+       | ..+.-
T Consensus       287 A~-------~~---S-k~~~ViVEr~i~G~-dhRlLVVg~k~VAvA~R~PA~ViG--DG~hTi~eL-------iG~~~N~  345 (876)
T TIGR02068       287 AK-------EE---S-KTSEVIVERYIKGR-DHRLLVVGGKLVAVAERVPAHVIG--DGVHTIEEL-------IGEQINK  345 (876)
T ss_pred             HH-------HC---C-CCCEEEEEEEECCC-CEEEEEECCEEEEEECCCCCEEEC--CCCCHHHHH-------HHHHHCC
T ss_conf             98-------60---7-86606898764276-238999989689986188886883--872007664-------0576467


Q ss_pred             CCCCC
Q ss_conf             44457
Q gi|254781049|r  160 DPLIG  164 (398)
Q Consensus       160 d~~~g  164 (398)
                      ||..|
T Consensus       346 DP~RG  350 (876)
T TIGR02068       346 DPLRG  350 (876)
T ss_pred             CCCCC
T ss_conf             77888


No 25 
>PRK13790 phosphoribosylamine--glycine ligase; Provisional
Probab=99.01  E-value=6.1e-09  Score=78.59  Aligned_cols=197  Identities=22%  Similarity=0.264  Sum_probs=117.4

Q ss_pred             HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI   86 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i   86 (398)
                      -+|+++++||||++++..+++.++|.+..++.++|. |||+.=||+|.              ||.++.|.+|+.++.++|
T Consensus       106 faK~~m~~~~IPTa~~~~f~~~~~A~~~l~~~~~p~-VIKaDGLAaGK--------------GV~V~~~~~eA~~al~~i  170 (415)
T PRK13790        106 FAKKIMEKYNIPTADYKEVERKKDALTYIENCELPV-VVKKDGLAAGK--------------GVIIADTIEAARSAIEIM  170 (415)
T ss_pred             HHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EEECCCCCCCC--------------CEEEECCHHHHHHHHHHH
T ss_conf             999999982979777255087999999986179988-99668667899--------------569979999999999998


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCC
Q ss_conf             18765442122222443301103455565058999998347780489984478840245557483122033214445789
Q gi|254781049|r   87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVT  166 (398)
Q Consensus        87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~  166 (398)
                      |..+.       .|    .|+|||++.. .|+=+-...|....  +.+.+.         +.+     ++--.|-..|..
T Consensus       171 ~~~~~-------~g----~VvIEE~L~G-~E~S~~a~~DG~~~--~p~~~~---------aQD-----hKR~~dgD~GPN  222 (415)
T PRK13790        171 YGDEE-------EG----TVVFETFLEG-EEFSLMTFVNGDLA--VPFDCI---------AQD-----HKRAFDHDEGPN  222 (415)
T ss_pred             HCCCC-------CC----EEEEEEECCC-CCEEEEEEECCCEE--EECCCC---------CCC-----CCCCCCCCCCCC
T ss_conf             55554-------76----5999871578-63489999739979--957754---------321-----202468999999


Q ss_pred             HHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHHHCCCCCCCC--CEEEECCCCCEEEEEEEEEECCCHHHHHHHHHHHH
Q ss_conf             578887887519888998859-999999989999559751023--26799059967994001321573556410278631
Q gi|254781049|r  167 SEDVASLCDMLELQGQARIDG-GDLFPNLYKAFCDKDMSLLEI--NPLIIMKNGRLRVLDSKISFDDNALYRHLDIQELR  243 (398)
Q Consensus       167 ~~~~~~l~~~lg~~~~~~~~~-~~ii~~L~~~f~e~Da~liEI--NPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~~~~  243 (398)
                      .--.-...-.--++.+..+.+ ..++....+.+.+......=|  ==|.+|++| +..      |.=|+.|--|+...+.
T Consensus       223 TGGMGaysp~p~~~~~~~~~~~~~I~~p~~~~l~~eg~~y~GvLy~GlMlt~~G-pkV------lEyN~RfGDPE~q~iL  295 (415)
T PRK13790        223 TGGMGAYCPVPHISDDVLKLTNETIAQPIAKAMLNEGYQFFGVLYIGAILTKDG-PKV------IEFNARFGDPEAQVLL  295 (415)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCC-CEE------EEEEEECCCCHHHHHH
T ss_conf             998756677744698999999987089999999855998489988779986898-669------9987411892288898


Q ss_pred             CCCCCCHHHH
Q ss_conf             0001562224
Q gi|254781049|r  244 DVSEEDSREI  253 (398)
Q Consensus       244 d~~~~~~~E~  253 (398)
                      ...+.|-.|+
T Consensus       296 p~L~~Dl~~~  305 (415)
T PRK13790        296 SRMESDLMQH  305 (415)
T ss_pred             HHCCCHHHHH
T ss_conf             7605519999


No 26 
>COG0151 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]
Probab=99.00  E-value=6.6e-09  Score=78.34  Aligned_cols=195  Identities=23%  Similarity=0.263  Sum_probs=117.4

Q ss_pred             HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI   86 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i   86 (398)
                      -+|+++++||||++.+...+++++|.+..++.|.|+ |||+.=|++|.              ||+++.+.+|+.+++++|
T Consensus       106 faK~fm~k~~IPta~y~~f~~~e~a~ayi~~~g~pi-VVKadGLaaGK--------------GV~V~~~~eeA~~a~~~~  170 (428)
T COG0151         106 FAKDFMKKYGIPTAEYEVFTDPEEAKAYIDEKGAPI-VVKADGLAAGK--------------GVIVAMTLEEAEAAVDEM  170 (428)
T ss_pred             HHHHHHHHCCCCCCCCEECCCHHHHHHHHHHCCCCE-EEECCCCCCCC--------------CEEECCCHHHHHHHHHHH
T ss_conf             999999981999641110089899999999729988-99345446789--------------859827799999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC--
Q ss_conf             187654421222224433011034555650589999983477804899844788402455574831220332144457--
Q gi|254781049|r   87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG--  164 (398)
Q Consensus        87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g--  164 (398)
                      |....       -|....+|+|||+++. .|+=+=.+.|..+-.|+..+  +          ++     +--.|-..|  
T Consensus       171 l~~~~-------fg~~g~~VVIEEfL~G-eE~S~~a~~DG~~v~p~p~a--Q----------Dh-----Kra~dgD~GPN  225 (428)
T COG0151         171 LEGNA-------FGSAGARVVIEEFLDG-EEFSLQAFVDGKTVIPMPTA--Q----------DH-----KRAYDGDTGPN  225 (428)
T ss_pred             HHHCC-------CCCCCCCEEEEECCCC-EEEEEEEEECCCEEEECCCC--C----------CC-----CCCCCCCCCCC
T ss_conf             74000-------1478874899853346-17999999769867878531--4----------56-----43348998998


Q ss_pred             ---CCHHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHHHHHCCCCCCC--CCEEEECCCCCEEEEEEEEEECCCHHHHHHH
Q ss_conf             ---895788878875198889988599-9999998999955975102--3267990599679940013215735564102
Q gi|254781049|r  165 ---VTSEDVASLCDMLELQGQARIDGG-DLFPNLYKAFCDKDMSLLE--INPLIIMKNGRLRVLDSKISFDDNALYRHLD  238 (398)
Q Consensus       165 ---l~~~~~~~l~~~lg~~~~~~~~~~-~ii~~L~~~f~e~Da~liE--INPLvvt~dg~vvAlDAKi~iDDnA~fR~~~  238 (398)
                         +-.|.-..     =++.+..+... +++..-.+.+.+......=  --=|.+|++| ..      .|.=|+.|--|+
T Consensus       226 TGGMGaysp~P-----~~t~e~~~~~~~~Iv~ptv~gm~~EG~~f~GvLy~glMlt~~G-Pk------ViEfN~RFGDPE  293 (428)
T COG0151         226 TGGMGAYSPAP-----FITDEVVERAVEEIVEPTVEGMAKEGYPFRGVLYAGLMLTADG-PK------VIEFNARFGDPE  293 (428)
T ss_pred             CCCCCCCCCCC-----CCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCC-CE------EEEEECCCCCHH
T ss_conf             88877777988-----7998999999999999999999971898147887678982899-67------999856668835


Q ss_pred             HHHHHCCCCCCHHHH
Q ss_conf             786310001562224
Q gi|254781049|r  239 IQELRDVSEEDSREI  253 (398)
Q Consensus       239 ~~~~~d~~~~~~~E~  253 (398)
                      -.......+.|-.|+
T Consensus       294 tq~vL~~l~sdl~~~  308 (428)
T COG0151         294 TQVVLPLLESDLVEL  308 (428)
T ss_pred             HHHHHHHCCCCHHHH
T ss_conf             777787602609999


No 27 
>PRK07206 hypothetical protein; Provisional
Probab=98.96  E-value=2.4e-07  Score=68.09  Aligned_cols=97  Identities=20%  Similarity=0.233  Sum_probs=77.7

Q ss_pred             HHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHH---CCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf             799999999868988881574799999999987---29986999712136876565655677777770799589999999
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVVISSVHAAESAIKT---LPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS   81 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~---ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~   81 (398)
                      -|.-++.|++.|+|+|+...+++.+|+...+++   ++||+ |||+---+|.              -||++|.|.+|+++
T Consensus       109 K~~m~~~L~~aGl~~~~~~~~~~~~e~~~~~~~~~~~~~Pv-VvKP~~gagS--------------~gV~~c~~~~el~~  173 (415)
T PRK07206        109 KYEMINALANAGLPAIRQIDTADWEEASAWIRVNNLWDSPV-VIKPLESAGS--------------DGVFFCPDKQDAYH  173 (415)
T ss_pred             HHHHHHHHHHCCCCCCCEEECCCHHHHHHHHHHCCCCCCCE-EEECCCCCCC--------------CCEEEECCHHHHHH
T ss_conf             99999999975998553885299999999998605579998-9958999987--------------99899799999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEE
Q ss_conf             999861876544212222244330110345556505899999
Q gi|254781049|r   82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLL  123 (398)
Q Consensus        82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~  123 (398)
                      ++.+++++.-      ..|..-+.+||||+++ +.||.+-.+
T Consensus       174 a~~~i~~~~n------~~g~~~~~vLveEyl~-G~EysVe~v  208 (415)
T PRK07206        174 AFNAILGKAN------KLGLVNESVLVQEFLI-GTEYVVNTV  208 (415)
T ss_pred             HHHHHHCCCC------CCCCCCCCEEEEECCC-CCEEEEEEE
T ss_conf             9999856654------3578675388754146-857899999


No 28 
>pfam07478 Dala_Dala_lig_C D-ala D-ala ligase C-terminus. This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF).
Probab=98.92  E-value=1.8e-07  Score=68.95  Aligned_cols=159  Identities=21%  Similarity=0.285  Sum_probs=94.3

Q ss_pred             HHHHCCCCCCCCEEECCHH----HHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             9998689888815747999----999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r   11 LLRKYNVPVAKGVVISSVH----AAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI   86 (398)
Q Consensus        11 lL~~~GIpvp~g~~a~s~~----ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i   86 (398)
                      ||+++|||+|++.++++.+    ++.++..++|||+ |+|+-  .||-|            =||.+++|.+|+.++.+..
T Consensus         1 ll~~~Giptp~~~~v~~~~~~~~~~~~i~~~lg~P~-vvKP~--~~gss------------~Gv~~v~~~~el~~~i~~~   65 (201)
T pfam07478         1 LLKAAGIPVAPFIVLTREDWVLATIEKVEEKLGYPV-FVKPA--NLGSS------------VGISKVTSREELQSAIEEA   65 (201)
T ss_pred             CHHHCCCCCCCEEEEECCCCCHHHHHHHHHHCCCCE-EEEEC--CCCCC------------CCEEEECCHHHHHHHHHHH
T ss_conf             955659999990898253234357999998659988-99989--99986------------6879995846879999998


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE----ECCCCC-CHHHHHHHCHHHHEEEECCC
Q ss_conf             1876544212222244330110345556505899999834778048998----447884-02455574831220332144
Q gi|254781049|r   87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA----STQGGM-DIEEVAKDYPQKIFKLLIDP  161 (398)
Q Consensus        87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~----S~~GGv-dIE~va~~~p~~I~~~~id~  161 (398)
                      +...             +.+|||++++ ++|+-+++..|..   +.++.    ...+|+ +.+.-.  .+..  .     
T Consensus        66 ~~~~-------------~~vlVEefi~-G~E~~v~vl~~~~---~~~~~~~e~~~~~~~~~~~~k~--~~~~--~-----  119 (201)
T pfam07478        66 FQYD-------------NKVLIEEAIE-GREIECAVLGNED---LEVSPVGEIRLSGGFYDYEAKY--ILSS--A-----  119 (201)
T ss_pred             HHCC-------------CCEEEEECCC-CCEEEEEEEECCC---EEEEEEEEEECCCCEEEHHHEE--CCCC--C-----
T ss_conf             7459-------------8079998566-9679999970898---0898758994377502676801--3687--2-----


Q ss_pred             CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEE
Q ss_conf             45789578887887519888998859999999989999559751023267990599679940
Q gi|254781049|r  162 LIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLD  223 (398)
Q Consensus       162 ~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlD  223 (398)
                                ....-..++......+.++..+.+++.--.+..-+|.   .++++|+++.+.
T Consensus       120 ----------~~~~Pa~l~~~~~~~i~~~A~~~~~aLg~~g~~rvD~---~~d~~g~~~vlE  168 (201)
T pfam07478       120 ----------QIIVPADLPEEVEEQIQELALKAYKALGCRGLARIDF---FLTEDGEIYLNE  168 (201)
T ss_pred             ----------EEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEE---EECCCCCEEEEE
T ss_conf             ----------3761566859999999999999999848876057999---996899499999


No 29 
>PRK12767 carbamoyl phosphate synthase-like protein; Provisional
Probab=98.87  E-value=1.3e-08  Score=76.40  Aligned_cols=92  Identities=15%  Similarity=0.156  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHCCCCCCCCEEECCHHHHHH-HHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             79999999986898888157479999999-99872998699971213687656565567777777079958999999999
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVVISSVHAAES-AIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~-~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -+..+++|+++|||+|++...++.+++.. .+++++||+ |+|+-.-+|+              -|+.+++|.+|+..+.
T Consensus       112 K~~~~~~l~~~gip~P~t~~~~~~~~~~~~~~~~~~fP~-vvKP~~g~gs--------------~Gv~~i~~~~el~~~~  176 (325)
T PRK12767        112 KWLTYEFLKENGINTPKSYLPEDLEDLLKALAEELGFPL-IVKPRDGSGS--------------IGVFKVNNREELEFLL  176 (325)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCE-EEEECCCCCC--------------CCEEEECCHHHHHHHH
T ss_conf             999999999759998982055899999999986569966-9853567887--------------7549979999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCC
Q ss_conf             9861876544212222244330110345556505899999834778
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSG  129 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~  129 (398)
                      ++.                 ..++|||.++ ++||-+.+..|++..
T Consensus       177 ~~~-----------------~~~ivqe~i~-G~E~tvdv~~d~~g~  204 (325)
T PRK12767        177 RYN-----------------PNLIIQEFIE-GQEYTVDVLCDLNGE  204 (325)
T ss_pred             HHC-----------------CCEEEEECCC-CCEEEEEEEEECCCC
T ss_conf             748-----------------9749870348-988999999978999


No 30 
>pfam08443 RimK RimK-like ATP-grasp domain. This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK.
Probab=98.84  E-value=5.6e-08  Score=72.21  Aligned_cols=93  Identities=24%  Similarity=0.224  Sum_probs=71.5

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             999999998689888815747999999999872-9986999712136876565655677777770799589999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTL-PGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR   84 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~i-g~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~   84 (398)
                      +.+|++|+++|||+|++.++.+++++.+.++++ |||+ |+|+-  .|+.|+            ||.++++.+++.++.+
T Consensus         5 ~~tk~ll~~~Gip~P~~~~~~~~~~~~~~~~~~~g~Pv-VvKP~--~g~~g~------------gV~~v~~~~el~~~~~   69 (190)
T pfam08443         5 AKSHQLLAKHGIPVPNTGLAWSPEDAEKFIEQIKGFPV-VVKSV--FGSQGI------------GVFLAEDEQSLEQLLE   69 (190)
T ss_pred             HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCCCE-EEECC--CCCCCC------------CEEEEECHHHHHHHHH
T ss_conf             99999999879797998998899999999998089838-99678--899984------------5588606377778888


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCEEECCCCCC--CEEEEEEEEEEC
Q ss_conf             861876544212222244330110345556--505899999834
Q gi|254781049|r   85 EILGSTLITKQTGPTGSRVNCVYVEDGADI--LRELYLSLLVDR  126 (398)
Q Consensus        85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~--~~E~ylgi~~Dr  126 (398)
                      ......             ..+|+|++++.  .+|+=+.+.-+.
T Consensus        70 ~~~~~~-------------~~vlvqefI~~~~~~dirv~vi~~~  100 (190)
T pfam08443        70 AFKWLK-------------NQILVQEFIAEAGNRDIRCLVVGGE  100 (190)
T ss_pred             HHHHCC-------------CCEEEEEEEECCCCCEEEEEEECCC
T ss_conf             886348-------------7377555660478854899996063


No 31 
>PRK01966 ddl D-alanyl-alanine synthetase A; Reviewed
Probab=98.84  E-value=5.8e-07  Score=65.53  Aligned_cols=166  Identities=17%  Similarity=0.168  Sum_probs=101.4

Q ss_pred             HHHHHHHHHHCCCCCCCCEEECCHH---HHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH
Q ss_conf             7999999998689888815747999---9999998729986999712136876565655677777770799589999999
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVVISSVH---AAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS   81 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~a~s~~---ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~   81 (398)
                      -+.+|.+|+++|||+|++.+.+..+   ........+++|+ +||+ ...|            |. =||.++++.+|+.+
T Consensus       133 K~~tK~i~~~~gI~tp~~~~~~~~~~~~~~~~~~~~l~~P~-iVKP-~~~G------------SS-iGvs~v~~~~el~~  197 (344)
T PRK01966        133 KILTKRLLAAAGIPQAPYVVLTRSRREEAIAEVEEKLGLPV-FVKP-ANLG------------SS-VGISKVKNEEELEA  197 (344)
T ss_pred             HHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHCCCCE-EEEC-CCCC------------CC-CCEEEECCHHHHHH
T ss_conf             99999999987999898399816662345899998618987-9932-8996------------34-32599689999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf             99986187654421222224433011034555650589999983477804899844788402455574831220332144
Q gi|254781049|r   82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP  161 (398)
Q Consensus        82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~  161 (398)
                      +.+..+..          +   +.+||||+++ ++|+-+|+.-.  .+.|..+.  -+  +|.                +
T Consensus       198 ai~~a~~~----------~---~~vlvEefI~-GrE~tv~vl~~--~~~~~~l~--~~--Ei~----------------~  241 (344)
T PRK01966        198 ALDLAFEY----------D---RKVLVEQGIK-GREIECAVLGY--NDEPVASV--PG--EIV----------------K  241 (344)
T ss_pred             HHHHHHHC----------C---CCCEEECCCC-CEEEEEEEECC--CCCEEEEC--CE--EEC----------------C
T ss_conf             99999863----------9---7505751244-48999999748--99467731--15--871----------------7


Q ss_pred             CCCCCHHHHHHHH-------HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEE
Q ss_conf             4578957888788-------75198889988599999999899995597510232679905996799400
Q gi|254781049|r  162 LIGVTSEDVASLC-------DMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDS  224 (398)
Q Consensus       162 ~~gl~~~~~~~l~-------~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDA  224 (398)
                      ..++.+|+.....       .-..++.+..+.+.++..+.|++.--.+..-++.   .++++|+++.+..
T Consensus       242 ~~~fydy~~KY~~~~~~~~~~Pa~l~~~~~~~i~~~a~~~~~~lg~rg~~RiDf---~~d~~g~~y~lEv  308 (344)
T PRK01966        242 DNDFYDYEAKYIDDSGATLVIPADLSEELTEQIRELAIKAFKALGCSGLARVDF---FLTEDGEIYLNEI  308 (344)
T ss_pred             CCCCCCHHHCCCCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEE---EEECCCCEEEEEE
T ss_conf             987514888104689716966788999999999999999999819972798989---9908998899982


No 32 
>PRK05586 biotin carboxylase; Validated
Probab=98.83  E-value=9e-07  Score=64.29  Aligned_cols=107  Identities=24%  Similarity=0.410  Sum_probs=80.8

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -.+|++..+.|+|+.+|.  .+++.+++.++++++|||+ ++||-  +||-||            |.+++.+.+|+.+++
T Consensus       117 ~~ar~~a~~~gvPv~pg~~~~v~~~~ea~~~a~~iGyPv-~lKAa--~GGGGr------------Gmriv~~~~el~~~~  181 (447)
T PRK05586        117 SNAREIMKKAGVPVVPGSEGEIENEEEALKIAEEIGYPV-MVKAS--AGGGGR------------GIRIVRSEEELIKAF  181 (447)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEECC--CCCCCC------------EEEEECCHHHHHHHH
T ss_conf             999999998499765686888899999999998629823-76305--699977------------369989999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             9861876544212222244330110345556505899999834778048998
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      +.-..--    ++. -|  -..++||+.+...++.=+=+..|+... .+-++
T Consensus       182 ~~a~~ea----~~a-Fg--~~~v~vEk~i~~~RHIEVQvl~D~~Gn-~vhlg  225 (447)
T PRK05586        182 NTAKSEA----KAA-FG--DDSMYIEKFIENPRHIEFQILGDNYGN-VVHLG  225 (447)
T ss_pred             HHHHHHH----HHH-CC--CCCEEEEEECCCCCEEEEEEEECCCCC-EEEEE
T ss_conf             9999999----982-79--984688772478717999999707998-88840


No 33 
>PRK08462 biotin carboxylase; Validated
Probab=98.81  E-value=1e-07  Score=70.57  Aligned_cols=107  Identities=24%  Similarity=0.370  Sum_probs=81.5

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -.+|++..+.|+|+++|.  .+++.+|+.+++++||||+ +|||-  +||-||            |.+++.+.+|+.+++
T Consensus       119 ~~ar~~a~~~gvPvvpg~~~~v~~~~ea~~~a~~iGyPV-~lKas--~GGGGr------------Gmriv~~~~el~~~~  183 (446)
T PRK08462        119 SKAKQVMKRAGVPVIPGSDGALKSYEEAKKIAKEIGYPV-ILKAA--AGGGGR------------GMRVVEDESDLENLY  183 (446)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCE-EEEEC--CCCCCC------------EEEEECCHHHHHHHH
T ss_conf             989999998599806786787799999999999729956-87632--789987------------428957679999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             9861876544212222244330110345556505899999834778048998
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      ...-+.-.       .-..-..+++|+.+...+++=+-+..|+. |..+.++
T Consensus       184 ~~a~~ea~-------~~fg~~~v~vEk~i~~~rHIEvQvl~D~~-Gn~ihl~  227 (446)
T PRK08462        184 LAAESEAL-------SAFGDGTMYMEKFINNPRHIEVQILGDKH-GNVIHVG  227 (446)
T ss_pred             HHHHHHHH-------HHCCCCCEEEEEEECCCEEEEEEEEECCC-CCEEEEE
T ss_conf             99987788-------60588866999850355078999885289-9888853


No 34 
>PRK08654 pyruvate carboxylase subunit A; Validated
Probab=98.81  E-value=4.1e-08  Score=73.11  Aligned_cols=167  Identities=23%  Similarity=0.370  Sum_probs=101.5

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -.+|++..+.|+|+.+|.  .+++.+|+.+.+++||||+ ++||-  +||-||            |.+++.+.+|+.+++
T Consensus       117 ~~ar~la~~~gVPvvPG~~~~v~~~~ea~~~A~~IGyPV-~iKAs--~GGGGr------------GmriV~~~~eL~~~~  181 (497)
T PRK08654        117 INAKKLMKKAGVPVLPGTEEGIEDIEEAKEVAEEIGYPV-IIKAS--AGGGGI------------GMRVVYNEEELEEAI  181 (497)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEEC--CCCCCC------------CCEEEECCHHHHHHH
T ss_conf             999999998099868997566799999999998649845-87652--688888------------658996025689999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCC
Q ss_conf             98618765442122222443301103455565058999998347780489984478840245557483122033214445
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLI  163 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~  163 (398)
                      ..-..-    .+.. -|-  ..|+||+.+...+++=+-++.|.... .+-++...-  .|   -+.++..|   ...|.-
T Consensus       182 ~~a~~e----A~~~-fgd--~~v~iEk~i~~~RHIEVQvl~D~~Gn-vihlgeRdC--Si---QRr~QKvI---EeaPap  245 (497)
T PRK08654        182 ESTQSI----AQSA-FGD--STVFIEKYLEKPRHIEIQVLADKHGN-VIHLGDREC--SI---QRRHQKLI---EEAPSP  245 (497)
T ss_pred             HHHHHH----HHHH-CCC--CCEEEEEECCCCEEEEEEEEEECCCC-EEEECCEEC--CE---EECCCCEE---EECCCC
T ss_conf             999999----8874-599--84579884155537899999844797-867146023--43---62686369---978999


Q ss_pred             CCCHH-------HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEE
Q ss_conf             78957-------88878875198889988599999999899995597510232679
Q gi|254781049|r  164 GVTSE-------DVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLI  212 (398)
Q Consensus       164 gl~~~-------~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLv  212 (398)
                      .+++.       .+.+++..+|+.+....+|      ||   .+.+.-++|+||=+
T Consensus       246 ~l~~~~r~~m~~~Av~la~~vgY~gaGTVEF------l~---d~g~fyFlEmNtRl  292 (497)
T PRK08654        246 IMTPELRERMGEAAVKAAKAINYENAGTVEF------LY---SNGNFYFLEMNTRL  292 (497)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCEECCCEEEE------EE---ECCEEEEEEEECCC
T ss_conf             8988999999999999888734302332799------87---48839999612442


No 35 
>PRK07178 acetyl-CoA carboxylase; Validated
Probab=98.80  E-value=3e-07  Score=67.42  Aligned_cols=165  Identities=18%  Similarity=0.313  Sum_probs=101.5

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -.||++..+.|+|+.+|.  .+++.+|+.+.++++|||+ ++||  -+||-||            |.+++.+++|+.+.+
T Consensus       116 ~~ar~~a~~~gvPv~pgs~~~v~~~eea~~~A~~iGyPV-~lKA--a~GGGGr------------Gmrvv~~~~el~~~~  180 (471)
T PRK07178        116 TEARRSMIKAGVPVTPGSEGNLADIDEALAEAERIGYPV-MLKA--TSGGGGR------------GIRRCNSREELEQNF  180 (471)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEEECCCHHHHHHH
T ss_conf             989999998699826896886566999999998669815-8632--0268766------------449976605688999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCC
Q ss_conf             98618765442122222443301103455565058999998347780489984478840245557483122033214445
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLI  163 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~  163 (398)
                      +....--.       ....-..+++|+.+.-.++.=+-+.-|... ..+-++-..--  |.   +.+. ++.  ...|..
T Consensus       181 ~~~~~EA~-------~aFg~~~v~lEk~i~~~RHIEVQilgD~~G-nvihl~eRdCS--iQ---Rr~Q-KvI--EeaPa~  244 (471)
T PRK07178        181 PRVISEAT-------KAFGSAEVFLEKCIVNPKHIEVQILADSFG-NVVHLFERDCS--IQ---RRNQ-KLI--EIAPSP  244 (471)
T ss_pred             HHHHHHHH-------HHCCCCCEEEEEECCCCEEEEEEEEEECCC-CEEEEEEEECC--CC---CCCC-CEE--EECCCC
T ss_conf             99999999-------844997368766046762899999980789-88888412346--51---0787-327--876999


Q ss_pred             CCCHHH-------HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCE
Q ss_conf             789578-------88788751988899885999999998999955975102326
Q gi|254781049|r  164 GVTSED-------VASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINP  210 (398)
Q Consensus       164 gl~~~~-------~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINP  210 (398)
                      .+++..       +.+++..+|+.+.-..+|      |   +.+.+.-++|+||
T Consensus       245 ~l~~~~r~~l~~~A~~la~~v~Y~gaGTvEF------l---v~~~~~yFlEvNt  289 (471)
T PRK07178        245 QLTPEQRAYIGDLAVRAAKAVGYENAGTVEF------L---LADGEVYFMEMNT  289 (471)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCEEEEEEE------E---EECCCEEEEECCC
T ss_conf             8889999999889999999648650126999------9---8679479983246


No 36 
>PRK08591 acetyl-CoA carboxylase biotin carboxylase subunit; Validated
Probab=98.79  E-value=3.8e-07  Score=66.76  Aligned_cols=107  Identities=24%  Similarity=0.350  Sum_probs=79.4

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -.||++..+.|+|+.+|.  .+++++++...+++||||+ ++||  -+||-||            |.+++.+++|+.+++
T Consensus       117 ~~ar~~a~~agVPvvpgs~~~~~~~~ea~~~a~~iGyPv-~iKA--~~GGGGr------------Gmrvv~~~~el~~~~  181 (449)
T PRK08591        117 VTAKATMKKAGVPVVPGSDGPVDDEEEALAIAKEIGYPV-IIKA--TAGGGGR------------GMRVVRTEAELEKAF  181 (449)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------EEEEECCHHHHHHHH
T ss_conf             999999998399978887665568999999998749966-9885--2689877------------699985678999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             9861876544212222244330110345556505899999834778048998
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      ..--.--    +   .-.--..+++|+.++..+..=+=+.-|.. |..+-++
T Consensus       182 ~~~~~Ea----~---~aFg~~~v~iEk~i~~~RHIEVQilgD~~-Gn~vhl~  225 (449)
T PRK08591        182 SMARAEA----K---AAFGNPGVYMEKYLENPRHIEIQVLADGH-GNAIHLG  225 (449)
T ss_pred             HHHHHHH----H---HHCCCCCEEEEEECCCCCEEEEEEEECCC-CCEEECC
T ss_conf             9999999----9---73799856787712565367899986389-9889874


No 37 
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275   Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC).   Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.   Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains .    This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=98.78  E-value=4.1e-08  Score=73.16  Aligned_cols=331  Identities=18%  Similarity=0.235  Sum_probs=184.0

Q ss_pred             HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf             99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r    9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG   88 (398)
Q Consensus         9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg   88 (398)
                      -++|.+-|||=|++..++|.|||..+|++||||++|==+-|+. ||+-              .++.|.+|+.+..++-..
T Consensus       694 s~~l~~Lgi~QP~~~~a~s~eea~~~A~~iGYPvlvRPSYVLg-G~aM--------------~iv~~~eeL~~yl~~a~~  758 (1089)
T TIGR01369       694 SELLDELGIPQPEWKIATSVEEAKEFASEIGYPVLVRPSYVLG-GRAM--------------EIVYNEEELARYLEEAVE  758 (1089)
T ss_pred             HHHHHHCCCCCCCCCEECCHHHHHHHHHHCCCCEEECCCCCCC-CCCH--------------HEECCHHHHHHHHHHHHH
T ss_conf             9999715879898852728799999985469928981683003-3621--------------002678899999999997


Q ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCC--CHHHHHHHCHHHHEEEECCCCCCCC
Q ss_conf             76544212222244330110345556505899999834778048998447884--0245557483122033214445789
Q gi|254781049|r   89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGM--DIEEVAKDYPQKIFKLLIDPLIGVT  166 (398)
Q Consensus        89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGv--dIE~va~~~p~~I~~~~id~~~gl~  166 (398)
                      -.        ..   +-|||.++++.+.|+=+=.+-|-.  .+++     .|+  +||+-.-++=|...-.|-   ..++
T Consensus       759 ~S--------~~---~PVlidky~e~A~E~dVD~v~Dg~--~v~i-----~gI~EHiE~AGVHSGDs~~~~Pp---~~L~  817 (1089)
T TIGR01369       759 VS--------PE---HPVLIDKYLEDAVEIDVDAVSDGE--EVLI-----PGIMEHIEEAGVHSGDSTCVLPP---QTLS  817 (1089)
T ss_pred             HC--------CC---CCEEEEEECCCCEEEEEEEEEECC--EEEE-----EEHHHHHHHCCCCCCCHHHCCCC---CCCC
T ss_conf             20--------89---976988852888899998997288--4899-----62312342136761305311769---7778


Q ss_pred             HH-------HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-CCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHH--H-
Q ss_conf             57-------88878875198889988599999999899995-5975102326799059967994001321573556--4-
Q gi|254781049|r  167 SE-------DVASLCDMLELQGQARIDGGDLFPNLYKAFCD-KDMSLLEINPLIIMKNGRLRVLDSKISFDDNALY--R-  235 (398)
Q Consensus       167 ~~-------~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e-~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~f--R-  235 (398)
                      ..       ..+++|+.|.+.|--..||         +..+ .+.-.||.||= .   .|=+..=.|++==+=|..  | 
T Consensus       818 ~~~~~~i~~~~~~iA~~L~v~Gl~NiQf---------~~~~E~~~yVIE~NpR-A---SRtVPFvSKa~Gipl~~~A~~~  884 (1089)
T TIGR01369       818 EDIVKRIKDIVRKIAKELNVKGLFNIQF---------VVKDEGEVYVIEVNPR-A---SRTVPFVSKATGIPLAKLAVRV  884 (1089)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCEEEEE---------EEECCCCEEEEEECCC-C---CCCCCCEEEECCCCHHHHHHHH
T ss_conf             8999999999999998706607222455---------5616996799997174-2---0665413210378879999999


Q ss_pred             --HHHHHHHHC-C---CCCCHHHHHHHHCCCCEEECC-------------CCEEEEECCCHHHHHHHHHHHHCCC---CC
Q ss_conf             --102786310-0---015622245775398644228-------------8179995550368999999996589---96
Q gi|254781049|r  236 --HLDIQELRD-V---SEEDSREIEAKQHNLSYIALD-------------GNIGCMVNGAGLAMATMDIIKLYGG---AP  293 (398)
Q Consensus       236 --~~~~~~~~d-~---~~~~~~E~~A~~~~l~yv~Ld-------------G~Ig~~vnGaGlamatmD~i~~~Gg---~p  293 (398)
                        =.++.++-. .   .+..+.-.--|..-|+|.+|-             |.++|+.-=-..|.  .=.....|-   +.
T Consensus       885 ~~G~~l~~~~~~~gv~~~~~~~~vavK~~vFSF~kL~g~Dp~LGpEMkSTGEvmg~g~d~~~A~--~Ka~~~~~~~~p~k  962 (1089)
T TIGR01369       885 MLGKKLEELGKDLGVGKEKESKYVAVKVPVFSFSKLAGVDPVLGPEMKSTGEVMGIGRDLEEAF--LKAMLSSGNRIPKK  962 (1089)
T ss_pred             HHCCCCHHCCCCCCCCCCCCCCEEEEEEEECCCHHHCCCCEEECCCCCCCCEEEEECCCHHHHH--HHHHHHCCCCCCCC
T ss_conf             7088201027540112326887279964237712214887111775551322564127889999--99999818705788


Q ss_pred             CEEEECCCCCCHHHHHHHHHHHHC----------------CCCCCEEEEE-CCCCHH--HHHHHHHHHHHHHHHCCCCCC
Q ss_conf             248842788898999999999861----------------9986589996-358613--289999999999997299987
Q gi|254781049|r  294 ANFLDVGGGADQDKVAAAFKIITS----------------DSSVKGILIN-IFGGIM--RCDVLVKGILSAVKEVKINIP  354 (398)
Q Consensus       294 ANFlD~gG~a~~e~~~~a~~~il~----------------~~~vk~iliN-ifGGI~--~cd~vA~gii~a~~~~~~~~p  354 (398)
                      ..++=.++..+.+++...++.+..                +..++.-+|+ ++.+-.  .|.- -.-|.+.+++-+.+.=
T Consensus       963 g~~~~~~~d~dk~~~~~~a~~L~~~G~~~yat~gT~~~L~e~gi~~~~v~~~~e~~~~~~C~~-~p~~~~~~~~~~~~~v 1041 (1089)
T TIGR01369       963 GSVLLSVRDKDKEELLDLAKKLAEKGYKIYATEGTAKFLEEAGIKAEVVLKVSEGREDDDCEA-QPNILELIKNGEIELV 1041 (1089)
T ss_pred             CEEEEEECCCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHCCCCHHHEEEECCCCCCCCCCC-CHHHHHHHHHCCCEEE
T ss_conf             779998034434579999999986373788502026767651876332000037887888888-7158999970880699


Q ss_pred             EEEECCCC-------CHHHHHHHHH---HCCCCEEEECCHHHHHHHH
Q ss_conf             99974898-------5899999999---7699589949989999999
Q gi|254781049|r  355 LVMRLEGA-------NVDIGNRLIA---ESGLNVITAIDLDDAAQKI  391 (398)
Q Consensus       355 ivvRl~Gt-------n~~~g~~il~---~~g~~~~~~~~~~~A~~~~  391 (398)
                      |=.+-.|.       ....|.++.+   +.++|+++.-++-+|.-+|
T Consensus      1042 IN~~~~~~~~~~~~~~~~~gy~iRR~A~~~~vp~~t~~~~~~~~~~a 1088 (1089)
T TIGR01369      1042 INLTSKGKEGVLLRETATDGYKIRREAVDYGVPLITTLETAEAFLEA 1088 (1089)
T ss_pred             EECCCCCCCCEEECCCCCHHHHHHHHHHHCCCCEEECHHHHHHHHHH
T ss_conf             96578886631220245445899999996499778656899999980


No 38 
>PRK06111 acetyl-CoA carboxylase biotin carboxylase subunit; Validated
Probab=98.78  E-value=1.6e-06  Score=62.61  Aligned_cols=107  Identities=20%  Similarity=0.339  Sum_probs=78.5

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -.||++..+.|+|+.+|.  ..++++++...+++||||+ ++||  -+||-||            |.+++++.+|+.+++
T Consensus       117 ~~ar~~a~~~gvPvvPG~~~~~~~~~ea~~~a~~iGyPv-liKA--a~GGGGr------------Gmriv~~~~el~~~~  181 (449)
T PRK06111        117 IEARRAMQAAGVPVVPGITTALEDAEEAIAIARQIGYPV-MLKA--SAGGGGI------------GMQLVETEQELTKAF  181 (449)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEEECCHHHHHHHH
T ss_conf             999999998399855786777899999999998659802-6620--3589867------------208957999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             9861876544212222244330110345556505899999834778048998
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      ..--.. .   +. .-|  -..+++|+.++-.+..-+=+.-|. +|..+-++
T Consensus       182 ~~~~~e-A---~~-~Fg--~~~v~iEk~i~~~RHIEVQvl~D~-~Gn~vhlg  225 (449)
T PRK06111        182 ESNKKR-A---AN-FFG--NGEMYLEKYIEDARHIEIQLLADT-HGNTVYLW  225 (449)
T ss_pred             HHHHHH-H---HH-HCC--CCCEEEEEECCCCCEEEEEEEECC-CCCEEEEE
T ss_conf             999999-9---98-639--960255441357733799999706-88888830


No 39 
>TIGR00514 accC acetyl-CoA carboxylase, biotin carboxylase; InterPro: IPR004549   This family represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase (6.4.1.2 from EC) is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase (6.3.4.14 from EC), and two subunits of carboxyl transferase in a 2:2 complex. In the first step of long-chain fatty acid synthesis, biotin carboxylase catalyses the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-coA. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase). In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification.; GO: 0016874 ligase activity.
Probab=98.76  E-value=1.2e-07  Score=70.17  Aligned_cols=106  Identities=25%  Similarity=0.435  Sum_probs=82.2

Q ss_pred             HHHHHHHHCCCCCCCC--E-EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             9999999868988881--5-747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    7 QAKALLRKYNVPVAKG--V-VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g--~-~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -||+..++.|+|+-||  . ++.+.+|+...|++||||+ ++||-  +||=|+            |+|++++++|..+..
T Consensus       118 ~A~~~mKkaGVP~VPGS~GP~~~~~~e~~~~A~~IGyPv-~IKA~--AGGGGR------------GmR~vR~~~El~~~~  182 (451)
T TIGR00514       118 TAKETMKKAGVPVVPGSDGPLVEDEEEAVRIAKEIGYPV-IIKAT--AGGGGR------------GMRVVREEDELVKLI  182 (451)
T ss_pred             HHHHHHHHCCCCEECCCCCCCCCCHHHHHHHHHHCCCCE-EEEEE--CCCCCC------------EEEEECCHHHHHHHH
T ss_conf             999999748876623888863102788999997478968-99962--589972------------258862868999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             9861876544212222244330110345556505899999834778048998
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      +.       |++-...+..=..||+|++++--|..=+=|+=| .+|..+-++
T Consensus       183 ~~-------a~~EA~AAF~N~~VYiEKfienPRH~E~QVLAD-~~GN~vyLg  226 (451)
T TIGR00514       183 KA-------ARAEAAAAFNNDGVYIEKFIENPRHVEIQVLAD-KYGNVVYLG  226 (451)
T ss_pred             HH-------HHHHHHHCCCCCCEEEEEEECCCCEEEEEEEEC-CCCCEEEEC
T ss_conf             99-------999997402879627863336994079998751-788878971


No 40 
>COG0458 CarB Carbamoylphosphate synthase large subunit (split gene in MJ) [Amino acid transport and metabolism / Nucleotide transport and metabolism]
Probab=98.73  E-value=2.2e-07  Score=68.31  Aligned_cols=101  Identities=22%  Similarity=0.283  Sum_probs=82.4

Q ss_pred             HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI   86 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i   86 (398)
                      -.|+.|++.|+|+| +.++++.+++.+....+|||+ ++|+-.-.||.              |.-++.|.+|+.+.....
T Consensus       119 ~fke~m~eigi~~P-~~~~~~~~e~~~~~~~ig~Pv-IVrP~~~lGG~--------------G~~i~~n~eel~~~~~~~  182 (400)
T COG0458         119 LFKEAMREIGIPVP-SRIAHSVEEADEIADEIGYPV-IVKPSFGLGGS--------------GGGIAYNEEELEEIIEEG  182 (400)
T ss_pred             HHHHHHHHCCCCCC-CCCCCCHHHHHHHHHHCCCCE-EEECCCCCCCC--------------CEEEEECHHHHHHHHHHC
T ss_conf             99999998399988-412356777765576369977-98068578887--------------516871899999998732


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEE
Q ss_conf             187654421222224433011034555650589999983477804899
Q gi|254781049|r   87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFI  134 (398)
Q Consensus        87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii  134 (398)
                      +..           .+++.+|+|+.+...+|+..-+.+|......+..
T Consensus       183 l~~-----------s~~~~vl~eesi~G~ke~e~ev~rd~~~n~ivvc  219 (400)
T COG0458         183 LRA-----------SPVEEVLIEESIIGWKEFEYEVVRDGKDNCIVVC  219 (400)
T ss_pred             CCC-----------CCCCCCEEEEEECCCEEEEEEEEEECCCCEEEEE
T ss_conf             244-----------7642001244216856999999983799879998


No 41 
>PRK08463 acetyl-CoA carboxylase; Validated
Probab=98.70  E-value=3.8e-06  Score=60.18  Aligned_cols=107  Identities=19%  Similarity=0.295  Sum_probs=78.7

Q ss_pred             HHHHHHHHHCCCCCCCCE---EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf             999999998689888815---74799999999987299869997121368765656556777777707995899999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV---VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISD   82 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~---~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~   82 (398)
                      -+||++..+.|+||.+|.   ...+++++..+++++|||+ ++||  -+||-||            |.+++.+.+|+.+.
T Consensus       116 ~~Ar~~a~~~gVPvvpg~~~~~~~~~~~~~~~a~~iGyPv-~lKA--~~GGGGr------------Gmrvv~~~~el~~~  180 (478)
T PRK08463        116 NIARKLMAKNGIPIVPGTEKLNSESMEEIKIFARKIGYPV-ILKA--SGGGGGR------------GIRVVWKEEDLENA  180 (478)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------EEEEECCHHHHHHH
T ss_conf             9999999983998466767788767999999998659804-7840--3599987------------11785578999999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             99861876544212222244330110345556505899999834778048998
Q gi|254781049|r   83 IREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        83 a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      +.....--    +   .-.--..|++|+.+...+..=+-++-|.. |..+-++
T Consensus       181 ~~~a~~ea----~---~~Fg~~~v~iEk~i~~~RHiEVQvlgD~~-Gnvi~l~  225 (478)
T PRK08463        181 FESCKREA----K---AYFNNDEVFMEKYVVNPRHIEFQILGDNY-GNIIHLC  225 (478)
T ss_pred             HHHHHHHH----H---HHCCCCCEEEEEEECCCEEEEEEEEEECC-CCEEEEE
T ss_conf             99999999----9---84699854788750245178999986179-9788963


No 42 
>TIGR02144 LysX_arch Lysine biosynthesis enzyme LysX; InterPro: IPR011870    The family of proteins found in this family include the characterised LysX from Thermus thermophilus  which is part of a well-organised lysine biosynthesis gene cluster . LysX is believed to carry out an ATP-dependent acylation of the amino group of alpha-aminoadipate in the prokaryotic version of the fungal AAA lysine biosynthesis pathway. No species having a sequence in this family contains the elements of the more common diaminopimelate lysine biosythesis pathway, and none has been shown to be a lysine auxotroph. These sequences have mainly recieved the name of the related enzyme, "ribosomal protein S6 modification protein RimK". RimK has been characterised in Escherichia coli, and acts by ATP-dependent condensation of S6 with glutamate residues .; GO: 0003824 catalytic activity, 0005524 ATP binding, 0009085 lysine biosynthetic process.
Probab=98.67  E-value=7.9e-08  Score=71.24  Aligned_cols=81  Identities=26%  Similarity=0.278  Sum_probs=63.6

Q ss_pred             HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHH--HHH
Q ss_conf             999999986898888157479999999998729986999712136876565655677777770799589999999--999
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVIS--DIR   84 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~--~a~   84 (398)
                      -+.-.|+++|||+|++.++.+++.|..++++||||+ |+|+-+=|.||--+              +++|.+++..  ..+
T Consensus        91 ~T~~~L~~~gvP~P~t~~a~d~~~A~~~~e~lGYPv-V~KP~~GSWGRlV~--------------~~~d~~~~~~llEh~  155 (289)
T TIGR02144        91 FTTLKLAKAGVPTPRTYIAFDREAALKAAEELGYPV-VLKPVIGSWGRLVS--------------KIRDKDELESLLEHK  155 (289)
T ss_pred             HHHHHHHHCCCCCCCEEEEECHHHHHHHHHHCCCCE-EEECCCCCHHHHHH--------------HHCCHHHHHHHHHHH
T ss_conf             899999966788983589828689999999708988-97088884378876--------------403788988999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCEEECCCCC
Q ss_conf             86187654421222224433011034555
Q gi|254781049|r   85 EILGSTLITKQTGPTGSRVNCVYVEDGAD  113 (398)
Q Consensus        85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~  113 (398)
                      ++++.           ...+=.||||+++
T Consensus       156 e~~~~-----------~~~~~~y~QEfi~  173 (289)
T TIGR02144       156 EVLGG-----------SQLKLYYVQEFIN  173 (289)
T ss_pred             HHHCC-----------CCCCEEEEEEEEC
T ss_conf             98679-----------7633379998871


No 43 
>PRK06019 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed
Probab=98.64  E-value=8.5e-07  Score=64.44  Aligned_cols=93  Identities=26%  Similarity=0.298  Sum_probs=72.2

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf             99999999868988881574799999999987299869997121368765656556777777707995899999999998
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIRE   85 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~   85 (398)
                      +.=|++|++.|||+|++..++|.+|+..+.+++|||+ |+|+ ..-|=-||            |..+++|.+++.++...
T Consensus       107 ~~eK~~l~~lgiptapf~~v~s~~dl~~~~~~lg~P~-vlKt-~~~GYDGK------------Gq~~i~s~~dl~~a~~~  172 (377)
T PRK06019        107 LTEKQFLDELGIPVAPFALVDSAEDLDAAIADLGLPA-VLKT-RRGGYDGK------------GQWVLRSEADLDAAWAA  172 (377)
T ss_pred             HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EEEC-CCCCCCCC------------CCEEECCHHHHHHHHHH
T ss_conf             9999999976999888067189999999999729976-9951-33461887------------01897788899999986


Q ss_pred             HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf             618765442122222443301103455565058999998347
Q gi|254781049|r   86 ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT  127 (398)
Q Consensus        86 ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~  127 (398)
                      + +.              ..+++|++++..+|+=+-+.+|.+
T Consensus       173 l-~~--------------~~~i~E~~i~f~~ElSvivaR~~~  199 (377)
T PRK06019        173 L-GS--------------GPCILEEFVPFEREVSVIVARGRD  199 (377)
T ss_pred             C-CC--------------CCEEEEEEECCEEEEEEEEEECCC
T ss_conf             5-69--------------988999654351899999998489


No 44 
>TIGR02712 urea_carbox urea carboxylase; InterPro: IPR014084   Members of this family are ATP-dependent urea carboxylases, including characterised members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae (Baker's yeast). The allophanate hydrolase domain of the yeast enzyme is not included in this entry and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from O. sagaranensis was shown to be highly active on acetamide and formamide as well as urea..
Probab=98.64  E-value=9.7e-07  Score=64.08  Aligned_cols=255  Identities=20%  Similarity=0.222  Sum_probs=142.2

Q ss_pred             HHHHHHHHHCCCCCCCC-EEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             99999999868988881-57479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKG-VVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR   84 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g-~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~   84 (398)
                      |-|.+|=.+.|+|..+| -+..|.+||..+|++||||+ +|||=  |||=|=            |-..|.|.+|+.+++.
T Consensus       116 HtAR~lA~~aGVPL~PGTgLL~sl~eA~~~A~~IGYPV-MlKST--AGGGGI------------Gl~~c~~~~eL~~aFe  180 (1226)
T TIGR02712       116 HTARELAEAAGVPLLPGTGLLESLDEALEAAKEIGYPV-MLKST--AGGGGI------------GLQKCDNAAELAEAFE  180 (1226)
T ss_pred             HHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCE-EEEEC--CCCCCC------------CCCCCCCHHHHHHHHH
T ss_conf             56899999668898885155877999999986469954-79870--787652------------4511189899999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC
Q ss_conf             86187654421222224433011034555650589999983477804899844788402455574831220332144457
Q gi|254781049|r   85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG  164 (398)
Q Consensus        85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g  164 (398)
                      .-  +++-     ..-.-=.+|.+|.+|+.+|..=+=|.=|.. |+.+.++-.    |= ++=+.++..|--+|-+    
T Consensus       181 ~V--krlg-----~~~F~daGVFlErfv~~ARHvEVQifGDG~-G~v~aLGeR----DC-SLQRRNQKVvEETPAP----  243 (1226)
T TIGR02712       181 TV--KRLG-----ESFFGDAGVFLERFVENARHVEVQIFGDGK-GKVVALGER----DC-SLQRRNQKVVEETPAP----  243 (1226)
T ss_pred             HH--HHHH-----HHCCCCCCEEHHHHHCCCCEEEEEEEECCC-CCEEEEECC----CC-CCCCCCCCEEEECCCC----
T ss_conf             98--9988-----632363514340320378428998752697-336997116----75-4444566558727746----


Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH------------H--HCCCCCCCCCEEEECCCC---CEEEEE----
Q ss_conf             8957888788751988899885999999998999------------9--559751023267990599---679940----
Q gi|254781049|r  165 VTSEDVASLCDMLELQGQARIDGGDLFPNLYKAF------------C--DKDMSLLEINPLIIMKNG---RLRVLD----  223 (398)
Q Consensus       165 l~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f------------~--e~Da~liEINPLvvt~dg---~vvAlD----  223 (398)
                                   +|+.+....+.+-..+|.+..            .  .-++..+|+|-=.-.+.+   .|.=||    
T Consensus       244 -------------~LP~~~R~~L~~AA~~Lg~~V~YrSAGTVEFiYD~~~d~FYFLEVNTRLQVEHPvTE~VtGlDLVEW  310 (1226)
T TIGR02712       244 -------------NLPEETRAALLAAAEKLGEAVNYRSAGTVEFIYDEARDEFYFLEVNTRLQVEHPVTEMVTGLDLVEW  310 (1226)
T ss_pred             -------------CCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCEEEEEECCCCCCCCCCEEEEECCHHHHH
T ss_conf             -------------8648999999999999999718763760477402210871211323411133573017846408989


Q ss_pred             -EEEEECCCHHHHHHHHHHHHCC-----CC-------CCHHHHHHHH----CC-C----------CEEECCCCEEEEECC
Q ss_conf             -0132157355641027863100-----01-------5622245775----39-8----------644228817999555
Q gi|254781049|r  224 -SKISFDDNALYRHLDIQELRDV-----SE-------EDSREIEAKQ----HN-L----------SYIALDGNIGCMVNG  275 (398)
Q Consensus       224 -AKi~iDDnA~fR~~~~~~~~d~-----~~-------~~~~E~~A~~----~~-l----------~yv~LdG~Ig~~vnG  275 (398)
                       -|+.=+     ..|++.++.-.     .+       +-..|..++.    .| |          .-++.|++|-     
T Consensus       311 M~r~AAg-----~~p~~~~~~~~~~~~l~p~G~aiEaRvYAEnP~k~F~PSpG~Lt~V~FP~~~G~~~RvDTWV~-----  380 (1226)
T TIGR02712       311 MVRIAAG-----ELPDFDSLNIEIFDNLTPRGAAIEARVYAENPAKNFQPSPGLLTEVQFPDDGGKAVRVDTWVE-----  380 (1226)
T ss_pred             HHHHHCC-----CCCCHHHCCCCCCCCCCCCEEEEEEEEEEECCCCCCCCCCCEEEEEECCCCCCCEEEEECEEC-----
T ss_conf             9997168-----888852443000357887503899998440776777269860688772788895378702112-----


Q ss_pred             CHHHHHHHHHHHHCCCCCCEEEE------CCCCCCHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf             03689999999965899624884------278889899999999986199865899963
Q gi|254781049|r  276 AGLAMATMDIIKLYGGAPANFLD------VGGGADQDKVAAAFKIITSDSSVKGILINI  328 (398)
Q Consensus       276 aGlamatmD~i~~~Gg~pANFlD------~gG~a~~e~~~~a~~~il~~~~vk~iliNi  328 (398)
                                   .|-+-.-|-|      |--+++++.....|.-=|..-+|.+|.=|+
T Consensus       381 -------------~Gtevsp~YDPmlAKiIv~g~~R~~A~~kL~~AL~~T~v~Gi~TNL  426 (1226)
T TIGR02712       381 -------------TGTEVSPEYDPMLAKIIVHGKDREDAIAKLSQALDETRVYGIETNL  426 (1226)
T ss_pred             -------------CCCEECCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCEEEEECH
T ss_conf             -------------7835677658742446643679789999999887301012354247


No 45 
>COG0439 AccC Biotin carboxylase [Lipid metabolism]
Probab=98.63  E-value=1.1e-06  Score=63.78  Aligned_cols=101  Identities=25%  Similarity=0.350  Sum_probs=75.4

Q ss_pred             HHHHHHHHHHCCCCCCCCEE--ECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf             79999999986898888157--4799999999987299869997121368765656556777777707995899999999
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVV--ISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISD   82 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~--a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~   82 (398)
                      -+.+|+++.+.|+|+|++.-  ..+.+|+.+.+++||||+ +||+---.|||              |+++|.+.+|+.++
T Consensus       116 K~~ar~~~~~aGVP~vpgs~~~~~~~ee~~~~a~~iGyPV-ivKa~~GgGg~--------------G~r~v~~~~el~~a  180 (449)
T COG0439         116 KITARRLMAKAGVPVVPGSDGAVADNEEALAIAEEIGYPV-IVKAAAGGGGR--------------GMRVVRNEEELEAA  180 (449)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEECCCCCCC--------------CEEEECCHHHHHHH
T ss_conf             8999999997499958997877688899999998719978-99977889965--------------47997999999999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf             998618765442122222443301103455565058999998347
Q gi|254781049|r   83 IREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT  127 (398)
Q Consensus        83 a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~  127 (398)
                      +....+-.-    .- -|.  ..+++|+.+...+-.-+-+.-|..
T Consensus       181 ~~~~~~ea~----~~-fg~--~~v~iEk~i~~~rhievqv~gD~~  218 (449)
T COG0439         181 FEAARGEAE----AA-FGN--PRVYLEKFIEGPRHIEVQVLGDGH  218 (449)
T ss_pred             HHHHHHHHH----HH-CCC--CCEEEEEECCCCCEEEEEEEECCC
T ss_conf             999998888----75-589--727863410588468999987686


No 46 
>PRK12999 pyruvate carboxylase; Reviewed
Probab=98.61  E-value=9.6e-06  Score=57.51  Aligned_cols=108  Identities=24%  Similarity=0.332  Sum_probs=79.9

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -+||++-.+.|+|+.+|.  .+++.+++.+.++++|||+ .+||-  +||-|+            |.+++.+.+|+.+++
T Consensus       121 ~~ar~~a~~~gvPvvpgs~~~~~~~~~~~~~a~~iGyPv-~iKA~--~GGGGr------------Gmrvv~~~~~l~~~~  185 (1147)
T PRK12999        121 VAARNAAIKAGVPVIPGTEGPIDDLEEALEFAEEIGYPL-MLKAS--AGGGGR------------GMRIVRSEEELEEAF  185 (1147)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEEC--CCCCCC------------CEEEECCHHHHHHHH
T ss_conf             999999998398988898998899999999998719978-99977--789805------------148958989999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEE
Q ss_conf             98618765442122222443301103455565058999998347780489984
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIAS  136 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S  136 (398)
                      ..--+- -   +   .-.--..+++|+.+...+..-+-|+-|. +|..+-++-
T Consensus       186 ~~a~~E-A---~---~aFG~~~v~~Ek~i~~~rHiEvQilgD~-~Gnvvhl~e  230 (1147)
T PRK12999        186 ERAKRE-A---K---AAFGNDEVYLEKYVENPRHIEVQILGDK-HGNVVHLYE  230 (1147)
T ss_pred             HHHHHH-H---H---HHCCCCCEEEEEECCCCCEEEEEEEECC-CCCEEEECC
T ss_conf             999999-9---9---8369975688550367864799999628-898887147


No 47 
>TIGR01161 purK phosphoribosylaminoimidazole carboxylase, ATPase subunit; InterPro: IPR005875    Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This family represents PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, which catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP.    PurK belongs to the ATP grasp superfamily of C-N ligase enzymes. Each subunit of PurK is composed of three domains (A, B, and C). The B domain contains a flexible, glycine-rich loop (B loop, T123-G130) that is disordered in the sulphate-PurK structure and becomes ordered in the MgADP-PurK structure. MgADP is wedged between the B and C domains, as with all members of the ATP grasp superfamily. Other enzymes in this superfamily contain a conserved Omega loop proposed to interact with the B loop, define the specificity of their nonnucleotide substrate, and protect the acyl phosphate intermediate formed from this substrate. PurK contains a minimal Omega loop without conserved residues. In the reaction catalyzed by PurK, carboxyphosphate is the putative acyl phosphate intermediate. The sulphate of the sulphate ion-liganded PurK interacts electrostatically with Arg 242 and the backbone amide group of Asn 245, components of the J loop of the C domain. This sulphate may reveal the location of the carboxyphosphate binding site. Conserved residues within the C-terminus of the C domain define a pocket that is proposed to bind AIR in collaboration with an N-terminal strand loop helix motif in the A domain (P loop, G8-L1). The P loop is proposed to bind the phosphate of AIR on the basis of similar binding sites observed in PurN and PurE and proposed in PurD and PurT, four other enzymes in the purine pathway .; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process, 0009320 phosphoribosylaminoimidazole carboxylase complex.
Probab=98.60  E-value=9.7e-07  Score=64.08  Aligned_cols=121  Identities=22%  Similarity=0.278  Sum_probs=85.0

Q ss_pred             HHHHHHHHHHCCCCCCCCEEEC--CHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf             7999999998689888815747--99999999987299869997121368765656556777777707995899999999
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVVIS--SVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISD   82 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~a~--s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~   82 (398)
                      =|.=|++|.++|+|||++.++.  +.++......++|+|+ |||+-=+       +=      |-=|..++++.+++.++
T Consensus       103 k~~qK~~L~~~g~~vp~f~~~~~~~~~~~~~~~~~~g~p~-VlK~~~g-------GY------DGrGq~~i~~~~~~~~~  168 (386)
T TIGR01161       103 KLTQKQFLQKLGLPVPPFVVIEIKDEEELDSALQELGFPV-VLKARRG-------GY------DGRGQFVIKSEADLPQA  168 (386)
T ss_pred             HHHHHHHHHHCCCCCCCCCEEECCCHHHHHHHHHHCCCCE-EEEEEEC-------CC------CCCCCEEECCHHHHHHH
T ss_conf             5899999996689988412022368425789998739847-9984206-------52------77310897474328899


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHH--HHEEEECC
Q ss_conf             9986187654421222224433011034555650589999983477804899844788402455574831--22033214
Q gi|254781049|r   83 IREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQ--KIFKLLID  160 (398)
Q Consensus        83 a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~--~I~~~~id  160 (398)
                      ++.+-...             ..++||++|+..+|+=+=+.++  ..+-+..+ +-    +|-+   ..|  -|.+..+-
T Consensus       169 ~~~~~~~~-------------~~~~~E~fV~F~~Elsv~vaR~--~~G~~~~Y-P~----ven~---~~ddagIl~~~~a  225 (386)
T TIGR01161       169 LKELGDKE-------------EELIVEEFVPFERELSVIVARS--ADGEIAFY-PV----VENI---HQDDAGILRLVVA  225 (386)
T ss_pred             HHHCCCCC-------------EEEEEEECCCCCEEEEEEEEEC--CCCCEEEC-CC----EEEE---EECCCCEEEEEEE
T ss_conf             98528884-------------0589852356200699999977--89748882-86----1235---6527787789863


Q ss_pred             CC
Q ss_conf             44
Q gi|254781049|r  161 PL  162 (398)
Q Consensus       161 ~~  162 (398)
                      |.
T Consensus       226 PA  227 (386)
T TIGR01161       226 PA  227 (386)
T ss_pred             CC
T ss_conf             37


No 48 
>COG0026 PurK Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and metabolism]
Probab=98.59  E-value=5.4e-06  Score=59.14  Aligned_cols=119  Identities=24%  Similarity=0.246  Sum_probs=77.1

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHH
Q ss_conf             99999999868988881574799999999987299869997121368765656556777777707995899999999998
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIRE   85 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~   85 (398)
                      +.=|++|.+.|||||++.++++.+|+..++.++|+|. |+|.-- -|=-|            -|..++++.++....+..
T Consensus       101 ~~eK~~l~~~Gi~va~~~~v~~~~el~~~~~~~g~p~-VlKtr~-gGYDG------------kGQ~~i~~~~~~~~~~~~  166 (375)
T COG0026         101 LVEKQFLDKAGLPVAPFQVVDSAEELDAAAADLGFPA-VLKTRR-GGYDG------------KGQWRIRSDADLELRAAG  166 (375)
T ss_pred             HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCCCE-EEEECC-CCCCC------------CCEEEEECCCCCHHHHHH
T ss_conf             9999999976999998278579889999999759956-998322-65668------------870894070102356766


Q ss_pred             HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCC
Q ss_conf             61876544212222244330110345556505899999834778048998447884024555748312203321444
Q gi|254781049|r   86 ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPL  162 (398)
Q Consensus        86 ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~  162 (398)
                      ..           .+   ...++|++++..+|+  |+..-|+..+-+..+-.     .|.+   +.+-|....+-|.
T Consensus       167 ~~-----------~~---~~~vlE~fV~F~~Ei--Svi~aR~~~G~~~~yP~-----~eN~---h~~gIl~~siaPa  219 (375)
T COG0026         167 LA-----------EG---GVPVLEEFVPFEREI--SVIVARSNDGEVAFYPV-----AENV---HRNGILRTSIAPA  219 (375)
T ss_pred             HH-----------CC---CCEEEEEECCCCEEE--EEEEEECCCCCEEEECC-----CCEE---EECCEEEEEEECC
T ss_conf             51-----------36---863688603566489--99999858997898066-----2101---3367899997237


No 49 
>TIGR01205 D_ala_D_alaTIGR D-alanine--D-alanine ligase; InterPro: IPR005905    D-alanine--D-alanine ligase (6.3.2.4 from EC) is a bacterial enzyme involved in cell-wall biosynthesis. It participates in forming UDP-N-acetylmuramoyl pentapeptide, the peptidoglycan precursor. These enzymes are proteins of 300 to 360 amino acids containing many conserved regions. The N-terminal Gly-rich region could be involved in ATP-binding.    This family of enzymes represent chromosomal versions of species not specifically resistant to glycopeptide antibiotics such as vancomycin. The mechanism of glycopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). This model attempts to exclude the VanA/VanB and VanC subfamilies while capturing most other D-Ala-D-Ala ligases above the trusted cut-off. However, changes in small numbers of amino acids, as demonstrated crystallographically, can alter specificity. In chlamydial species, this enzyme is found as a fusion protein with UDP-N-acetylmuramate--alanine ligase. ; GO: 0008716 D-alanine-D-alanine ligase activity, 0009252 peptidoglycan biosynthetic process, 0005737 cytoplasm.
Probab=98.55  E-value=1.3e-06  Score=63.14  Aligned_cols=153  Identities=20%  Similarity=0.191  Sum_probs=98.8

Q ss_pred             HHHHHHHHHHCCCCCCCCEEE--CCHHHHH-------HHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf             799999999868988881574--7999999-------9998729986999712136876565655677777770799589
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVVI--SSVHAAE-------SAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESS   75 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~a--~s~~ea~-------~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s   75 (398)
                      =+-.|.++++.|||+|++...  .+.....       ....++|||+ +||+- +            -.|.. ||..+.+
T Consensus       150 K~~tK~~~~~~Glp~~~y~~l~~~~~~~~~~~~~~~~~~~~~lg~P~-~VKPa-~------------~GSSv-G~~~V~~  214 (375)
T TIGR01205       150 KLLTKLLLKSLGLPTPDYAVLRRKERSSEDEAECENVAVLEKLGFPV-FVKPA-R------------EGSSV-GISKVKS  214 (375)
T ss_pred             HHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCE-EEEEC-C------------CCCEE-EEEEECC
T ss_conf             89999999875797447046750454456134689999998368978-99734-6------------77757-7898467


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCC---CCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHH
Q ss_conf             999999999861876544212222244330110345---55650589999983477804899844788402455574831
Q gi|254781049|r   76 LKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDG---ADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQ  152 (398)
Q Consensus        76 ~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~---v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~  152 (398)
                      .+|+..+.+.-|...             ++|+||++   +. .+|+=+|++-+-. .-|.+  |. ++. +      .++
T Consensus       215 ~~eL~~a~~~Af~~d-------------~~v~vE~~~~~i~-grEl~v~~L~~~~-~lp~~--~~-~~~-~------~~~  269 (375)
T TIGR01205       215 EEELEAALDEAFKYD-------------ERVIVEEFKQRIK-GRELEVSILGNEE-ALPII--SI-VPE-I------EPD  269 (375)
T ss_pred             HHHHHHHHHHHHCCC-------------CEEEEEECCCCCC-CCEEEEEEEECCC-CCEEE--EC-CCC-C------CCC
T ss_conf             789999999861559-------------6599981114789-8526898870797-43245--40-675-3------567


Q ss_pred             HHEEEECCCCCCCCHHH-HHHHHHH-CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             22033214445789578-8878875-1988899885999999998999
Q gi|254781049|r  153 KIFKLLIDPLIGVTSED-VASLCDM-LELQGQARIDGGDLFPNLYKAF  198 (398)
Q Consensus       153 ~I~~~~id~~~gl~~~~-~~~l~~~-lg~~~~~~~~~~~ii~~L~~~f  198 (398)
                      -. ..-.|-........ .+.+... .+++.+..+.+.++..+.|+..
T Consensus       270 g~-~~FYDY~~KY~~~~g~~~~~pa~~~L~~~~~~~i~~~a~~ay~~~  316 (375)
T TIGR01205       270 GG-SDFYDYEAKYLDGDGTEYVIPAPAGLDEELEEKIKELALKAYKAL  316 (375)
T ss_pred             CC-CEECCHHHCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             67-600002114277887326515656788899999999999999840


No 50 
>PRK12833 acetyl-CoA carboxylase biotin carboxylase subunit; Provisional
Probab=98.55  E-value=5.2e-06  Score=59.27  Aligned_cols=107  Identities=24%  Similarity=0.358  Sum_probs=77.6

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -++|++..+.|+|+.+|.  .+++.+++...+++||||+ ++||-  +||-||            |.+++.+.+|+.+.+
T Consensus       120 ~~ar~~a~~~gvPvvpgs~~~v~~~~ea~~~a~~iGyPv-~iKAs--~GGGGr------------Gmriv~~~~el~~~~  184 (458)
T PRK12833        120 ARARETARRAGVPTVPGSDGVVASLDAALEVAARIGYPV-MIKAA--AGGGGR------------GIRVAHDAAQLAAEL  184 (458)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHH-HHHHC--CCCCCC------------CEEEECCCCCHHHHH
T ss_conf             999999998499966896676677999999998659754-21332--589987------------107952641148999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEE
Q ss_conf             98618765442122222443301103455565058999998347780489984
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIAS  136 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S  136 (398)
                      ..--..-    +   .-..-..+++|+.++..+++=+=+.-|.. + .+-++.
T Consensus       185 ~~a~~ea----~---~~Fg~~~v~iEk~i~~~RHIEVQvl~D~~-~-~vhl~e  228 (458)
T PRK12833        185 PLAQREA----Q---AAFGDGGVYLERFIARARHIEVQILGDGE-N-VVHLFE  228 (458)
T ss_pred             HHHHHHH----H---HHCCCCCEEEEEECCCCEEEEEEEEECCC-C-EEEEEE
T ss_conf             9999999----9---72699764787613675079999985478-7-699850


No 51 
>PRK06395 phosphoribosylamine--glycine ligase; Provisional
Probab=98.54  E-value=9.7e-07  Score=64.08  Aligned_cols=196  Identities=21%  Similarity=0.199  Sum_probs=108.1

Q ss_pred             HHHHHHHHCCCC-CCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEC----CHHHHHH
Q ss_conf             999999986898-88815747999999999872998699971213687656565567777777079958----9999999
Q gi|254781049|r    7 QAKALLRKYNVP-VAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVES----SLKSVIS   81 (398)
Q Consensus         7 qaK~lL~~~GIp-vp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~----s~~ea~~   81 (398)
                      -+|+++++|||| ++++..+.+.+++.......++|+ |||+.-|++|  |            ||.++.    +.+++.+
T Consensus       108 FaK~fm~~~~IP~ta~~~~~~~~~ea~~~~~~~~~pi-VIKadGLAaG--K------------GV~V~~~~~~~~~ea~~  172 (435)
T PRK06395        108 FMRYLMERHNIPGNINFNACFSEKDAARDYITSMKDV-AVKPIGLTGG--K------------GVKVTGEQLNSVDEAIR  172 (435)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEECCCCCC--C------------CEEEECCCHHHHHHHHH
T ss_conf             8999999809985664532399999999999709984-8973422578--9------------64895585778999999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf             99986187654421222224433011034555650589999983477804899844788402455574831220332144
Q gi|254781049|r   82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP  161 (398)
Q Consensus        82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~  161 (398)
                      .+.+++..          +   ..|+|||++. +.|+=+....|...-.|+-.  .+          ++ .++..-.--|
T Consensus       173 ~~~~~~~~----------~---~~vvIEE~L~-G~E~S~~a~~dG~~~~~lp~--aq----------Dh-KR~~dgD~GP  225 (435)
T PRK06395        173 YAIEILDR----------D---GVVLIEKKMT-GEEFSLQAFSDGKHLSFMPI--VQ----------DY-KRAYEGDHGP  225 (435)
T ss_pred             HHHHHHHC----------C---CEEEEEEEEE-CCEEEEEEEECCCEEEECCC--CC----------CC-CCCCCCCCCC
T ss_conf             99988734----------8---8599999984-41689999976995585873--01----------25-3344799999


Q ss_pred             CC-CCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCC---CCCCEEEECCCCCEEEEEEEEEECCCHHHHHH
Q ss_conf             45-789578887887519888998859999999989999559751---02326799059967994001321573556410
Q gi|254781049|r  162 LI-GVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSL---LEINPLIIMKNGRLRVLDSKISFDDNALYRHL  237 (398)
Q Consensus       162 ~~-gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~l---iEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~  237 (398)
                      .. |+-.+.-.....- -+.....+....++....+...+.....   +=+. |.+|++| +..      |.=|+.|--|
T Consensus       226 NTGGMGaysp~~~~~p-~l~~~~~e~~~~Ii~pti~~l~~eg~~y~GvLy~G-lMit~~g-pkV------lEyN~RfGDP  296 (435)
T PRK06395        226 NTGGMGSISDRDFSLP-FLSKDAPERAKHILNDIIRAMKDENNPFKGIMYGQ-FMDTPNG-VKV------IEINARFADP  296 (435)
T ss_pred             CCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEE-EEEECCC-CEE------EEEEECCCCC
T ss_conf             9998745688888874-32778999999999999999996499708998778-9850899-648------9986203880


Q ss_pred             HHHHHHCCCCCCHHHH
Q ss_conf             2786310001562224
Q gi|254781049|r  238 DIQELRDVSEEDSREI  253 (398)
Q Consensus       238 ~~~~~~d~~~~~~~E~  253 (398)
                      +..-+....+.|-.|+
T Consensus       297 E~QviLp~L~~Dl~~l  312 (435)
T PRK06395        297 EGINVLYLLKSDFVET  312 (435)
T ss_pred             HHHHHHHHHCCCHHHH
T ss_conf             6888877600529999


No 52 
>KOG0237 consensus
Probab=98.53  E-value=1.2e-06  Score=63.38  Aligned_cols=106  Identities=24%  Similarity=0.241  Sum_probs=82.4

Q ss_pred             HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             99999998689888815747999999999872998699971213687656565567777777079958999999999986
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI   86 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i   86 (398)
                      -+|+++.+||||+.++...+++++|....+..++|.+|+||.=+|-|              -||.+.+|.+|+.++.++|
T Consensus       111 fsK~fm~r~~IPTA~y~~ft~~e~a~sfi~~~~~~~~ViKAdGLAAG--------------KGViv~~~~~EA~eAv~sI  176 (788)
T KOG0237         111 FSKDFMHRHNIPTAKYKTFTDPEEAKSFIQSATDKALVIKADGLAAG--------------KGVIVAKSKEEAFEAVDSI  176 (788)
T ss_pred             HHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCCCCCEEEEECCCCCC--------------CCEEEECCHHHHHHHHHHH
T ss_conf             89988986399832026407879989999848985648960552457--------------7157405479999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEE
Q ss_conf             187654421222224433011034555650589999983477804899
Q gi|254781049|r   87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFI  134 (398)
Q Consensus        87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii  134 (398)
                      |...    +-+..|+   +|.|||..+...=-.|.+ .|..+..++..
T Consensus       177 l~~~----~fg~AG~---tvViEE~LEGeEvS~laf-tDG~s~~~mp~  216 (788)
T KOG0237         177 LVKK----VFGSAGK---TVVIEELLEGEEVSFLAF-TDGYSVRPLPP  216 (788)
T ss_pred             HHHH----HHCCCCC---EEEHHHHCCCCEEEEEEE-ECCCCCCCCCC
T ss_conf             8544----4135664---586112307625789998-55730233885


No 53 
>KOG0238 consensus
Probab=98.51  E-value=1.6e-05  Score=56.07  Aligned_cols=107  Identities=21%  Similarity=0.310  Sum_probs=81.2

Q ss_pred             HHHHHHHHHCCCCCCCC--EEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             99999999868988881--5747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKG--VVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g--~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      ..||++.++.|+|+-+|  ....+.+++.+.+.+||||+ .+||  -+||-||            |-+++.+++|..+..
T Consensus       113 ~~sk~im~~AgVp~vpG~~g~~qs~e~~~~~a~eIgyPv-MiKa--~~GGGGk------------GMria~~~~ef~~~~  177 (670)
T KOG0238         113 STSKQIMKAAGVPLVPGYHGEDQSDEEAKKVAREIGYPV-MIKA--TAGGGGK------------GMRIAWSEEEFEEGL  177 (670)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEEECCHHHHHHHH
T ss_conf             778999986499613685643266799999998619857-9995--1578876------------317514868899999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             9861876544212222244330110345556505899999834778048998
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      +.-       .|...+-.--.++|+|.+++--+..-+-++-| .+|..+-++
T Consensus       178 ~~a-------k~Ea~~sFGdd~~llEkfi~npRHiEvQv~gD-~hGnav~l~  221 (670)
T KOG0238         178 ESA-------KQEAAKSFGDDGMLLEKFIDNPRHIEVQVFGD-KHGNAVHLG  221 (670)
T ss_pred             HHH-------HHHHHHHCCCCHHHHHHHCCCCCEEEEEEEEC-CCCCEEEEC
T ss_conf             988-------88887631864110777636875489999734-777688850


No 54 
>COG4770 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]
Probab=98.46  E-value=5.1e-05  Score=52.74  Aligned_cols=108  Identities=23%  Similarity=0.362  Sum_probs=79.9

Q ss_pred             HHHHHHHHHCCCCCCCCEE--ECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             9999999986898888157--47999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVV--ISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~--a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -.||.+..+.|+|+-+|..  +.+.+++...+.+||||+ .+||  -+||-||            |.|++.+++|+.+..
T Consensus       117 ~~AK~l~~~AgVp~VPG~~g~~qd~~~~~~~A~eiGyPV-lIKA--saGGGGK------------GMRvv~~~~e~~e~l  181 (645)
T COG4770         117 IAAKKLAAEAGVPTVPGYHGPIQDAAELVAIAEEIGYPV-LIKA--SAGGGGK------------GMRVVETPEEFAEAL  181 (645)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEEECCHHHHHHHH
T ss_conf             999999997499806897874458999999998639858-9996--3689977------------537626889999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEE
Q ss_conf             98618765442122222443301103455565058999998347780489984
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIAS  136 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S  136 (398)
                      ..-- +.    -+..-|  =..++||..++--+..-+-+.-| ++|..+.++-
T Consensus       182 ~sar-rE----A~asFG--ddrv~iEkyl~~PRHIEiQV~aD-~HGNvv~LgE  226 (645)
T COG4770         182 ESAR-RE----AKASFG--DDRVFIEKYLDKPRHIEIQVFAD-QHGNVVHLGE  226 (645)
T ss_pred             HHHH-HH----HHHHCC--CCEEEHHHHCCCCCEEEEEEEEC-CCCCEEEEEC
T ss_conf             9999-99----885048--86476245517874489999862-7787888632


No 55 
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=98.45  E-value=0.00019  Score=48.94  Aligned_cols=329  Identities=19%  Similarity=0.178  Sum_probs=176.2

Q ss_pred             HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf             99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r    9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG   88 (398)
Q Consensus         9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg   88 (398)
                      +++|.+.||+.|++..++|.+||.++++++|||++|=-+-|+ ||||              -.++.|.+|+.....+.+.
T Consensus       673 ~~~l~~l~i~qp~~~~a~s~~ea~~~a~~iGyPvlvRPSyVL-GG~~--------------M~iv~~~~eL~~yl~~a~~  737 (1063)
T PRK05294        673 QKLLEKLGIKQPPNGTATSVEEALEIAEEIGYPVLVRPSYVL-GGRA--------------MEIVYDEEELERYMREAVK  737 (1063)
T ss_pred             HHHHHHCCCCCCCCCEECCHHHHHHHHHHCCCCEEECCCCCC-CCCC--------------EEEECCHHHHHHHHHHHHH
T ss_conf             999986599999970766899999999864986684343102-5771--------------4785699999999999986


Q ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCCHH
Q ss_conf             76544212222244330110345556505899999834778048998447884024555748312203321444578957
Q gi|254781049|r   89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSE  168 (398)
Q Consensus        89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~~~  168 (398)
                      -       . .   -+.|||.+++...+|+=+-...|..   -+++.+-.  =+||.-.-.+-|.+...   |...++..
T Consensus       738 v-------s-~---~~pvlIdkfl~ga~E~eVDai~Dg~---~v~I~gIm--EHIE~AGVHSGDS~~V~---Pp~~Ls~~  798 (1063)
T PRK05294        738 V-------S-P---DHPVLIDRFLEDAIEVDVDAICDGE---DVLIGGIM--EHIEEAGVHSGDSACSL---PPYTLSEE  798 (1063)
T ss_pred             H-------C-C---CCCEEEEHHHHHCHHHHHHEEECCC---EEEEEEEE--EECCCCCCCCCCCEEEE---CCCCCCHH
T ss_conf             3-------8-9---9977863543202454430231488---48999987--20014575667842881---68558999


Q ss_pred             HHH-------HHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHH-----H
Q ss_conf             888-------7887519888998859999999989999559751023267990599679940013215735564-----1
Q gi|254781049|r  169 DVA-------SLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYR-----H  236 (398)
Q Consensus       169 ~~~-------~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR-----~  236 (398)
                      ..+       +++..|++.|-...||         +..+.+.-.+|+||=+    .+=++.=+|.+==+=|..-     -
T Consensus       799 ~~~~i~~~t~~ia~~l~v~G~~NiQf---------~vk~~~vyVIE~NpRa----SRtvPfvSKatg~pl~~iAtk~~lG  865 (1063)
T PRK05294        799 IIDEIREQTKKLALELNVVGLMNVQF---------AVKDDEVYVIEVNPRA----SRTVPFVSKATGVPLAKIAARVMLG  865 (1063)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEE---------EECCCEEEEEEECCCC----CCCCHHHHHHCCCCHHHHHHHHHCC
T ss_conf             99999999999998556666420335---------5409838999944744----4530445764199799999999829


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCCEEECCC----------CEE-EEECCCHHHHHHHHHHHHCCCCC----CEEEECCC
Q ss_conf             0278631000156222457753986442288----------179-99555036899999999658996----24884278
Q gi|254781049|r  237 LDIQELRDVSEEDSREIEAKQHNLSYIALDG----------NIG-CMVNGAGLAMATMDIIKLYGGAP----ANFLDVGG  301 (398)
Q Consensus       237 ~~~~~~~d~~~~~~~E~~A~~~~l~yv~LdG----------~Ig-~~vnGaGlamatmD~i~~~Gg~p----ANFlD~gG  301 (398)
                      ..+.++.......+.-.--+..-++|-+|.|          ..| +|+-|--+..|..-.....|.+-    .=|+-++.
T Consensus       866 ~~l~~l~~~~~~~~~~v~VK~pvFsf~k~~g~d~~LGpEMkSTGEVmg~g~~~~eAl~Ka~~aag~~iP~~G~v~iSv~d  945 (1063)
T PRK05294        866 KKLAELGYTKEIIPPHVSVKEAVFPFNKFPGVDPLLGPEMKSTGEVMGIDRTFGEAFAKAQLAAGNRLPTSGTVLVSVRD  945 (1063)
T ss_pred             CCHHHCCCCCCCCCCCEEEECCCCCHHHCCCCCCCCCCCCCCCCCCEEECCCHHHHHHHHHHHCCCCCCCCCEEEEEECC
T ss_conf             97344278877888828997564874334999988787724343415734999999999998669988988879999424


Q ss_pred             CCCHHHHHHHHHHH----------------HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC--CCCC
Q ss_conf             88989999999998----------------61998658999635861328999999999999729998799974--8985
Q gi|254781049|r  302 GADQDKVAAAFKII----------------TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL--EGAN  363 (398)
Q Consensus       302 ~a~~e~~~~a~~~i----------------l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl--~Gtn  363 (398)
                      . +.+.+....+.+                |.+.++++-.|+-..-      --.-|++.+++.+++  +|+-.  ....
T Consensus       946 ~-dK~~~~~~a~~l~~lGf~i~AT~GTa~~L~~~GI~~~~V~Kv~e------~~p~i~d~i~~~~I~--lVINt~~~~~~ 1016 (1063)
T PRK05294        946 R-DKEEVVELAKRLLELGFKILATEGTAKFLEEAGIPVELVNKVHE------GRPHIVDLIKNGEID--LVINTPEGRQA 1016 (1063)
T ss_pred             C-CHHHHHHHHHHHHHCCCEEEECHHHHHHHHHCCCCEEEECCCCC------CCCCHHHHHHCCCEE--EEEECCCCCCC
T ss_conf             2-57999999999997699899841789999976991599646578------992599999769826--99979999877


Q ss_pred             HHHHHHHH---HHCCCCEEEECCHHHHHHHHHH
Q ss_conf             89999999---9769958994998999999999
Q gi|254781049|r  364 VDIGNRLI---AESGLNVITAIDLDDAAQKIVH  393 (398)
Q Consensus       364 ~~~g~~il---~~~g~~~~~~~~~~~A~~~~v~  393 (398)
                      ...|.+|-   -+.++|+++.-+.-+|+-++.+
T Consensus      1017 ~~dg~~IRR~Av~~~IP~~Tsl~~A~a~v~al~ 1049 (1063)
T PRK05294       1017 IRDGFSIRRAALEYKVPYITTLAGARAAAEAIE 1049 (1063)
T ss_pred             CCCCHHHHHHHHHHCCCEEECHHHHHHHHHHHH
T ss_conf             776299999999709998967999999999999


No 56 
>PRK10446 ribosomal protein S6 modification protein; Provisional
Probab=98.42  E-value=8.6e-06  Score=57.82  Aligned_cols=80  Identities=20%  Similarity=0.258  Sum_probs=61.3

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             999999998689888815747999999999872-9986999712136876565655677777770799589999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTL-PGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR   84 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~i-g~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~   84 (398)
                      +.+-++|+++|||+|+..++.+++++.++.+.+ |+| +|+|.  +.|-.|+            ||.++++.+++....+
T Consensus       101 l~t~qlL~~~gip~P~T~~~~~~~~~~~~i~~~gg~P-vViKp--l~Gs~G~------------GV~l~e~~~~~~~i~~  165 (300)
T PRK10446        101 LRSMQLLARQGIDLPVTGIAHSPDDTSDLIDMVGGAP-LVVKL--VEGTQGI------------GVVLAETRQAAESVID  165 (300)
T ss_pred             HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCCC-EEEEE--CCCCCCC------------CEEEEECHHHHHHHHH
T ss_conf             9999999875979998898369999999999808997-89996--7898860------------3699737899999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCEEECCCCC
Q ss_conf             86187654421222224433011034555
Q gi|254781049|r   85 EILGSTLITKQTGPTGSRVNCVYVEDGAD  113 (398)
Q Consensus        85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~  113 (398)
                      .+.+..             ..+|++|+++
T Consensus       166 ~~~~~~-------------~~~~iQeyI~  181 (300)
T PRK10446        166 AFRGLN-------------AHILVQEYIK  181 (300)
T ss_pred             HHHHCC-------------CCEEEEEECC
T ss_conf             886228-------------7377522025


No 57 
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=98.42  E-value=5e-05  Score=52.78  Aligned_cols=326  Identities=18%  Similarity=0.201  Sum_probs=164.3

Q ss_pred             HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf             99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r    9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG   88 (398)
Q Consensus         9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg   88 (398)
                      +++|.+.||+.|++..++|.+||.++++++|||++|=-+-|+ |||+-              .++.|.+|+....++-..
T Consensus       674 ~~ll~~l~i~~p~~~~~~~~~ea~~~a~~iGyPvlvRPSyvL-gG~~m--------------~iv~~~~eL~~y~~~a~~  738 (1068)
T PRK12815        674 YQLLDELGLPHVPGLTATSEEEALAFAKRIGYPVLIRPSYVI-GGQGM--------------AVVYDEPALEAYLEENVQ  738 (1068)
T ss_pred             HHHHHHCCCCCCCCCEECCHHHHHHHHHHCCCCEEECCCCCC-CCCEE--------------EEECCHHHHHHHHHHHCC
T ss_conf             999997389999963545667999999864997784244335-77423--------------897599999999985157


Q ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCCHH
Q ss_conf             76544212222244330110345556505899999834778048998447884024555748312203321444578957
Q gi|254781049|r   89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSE  168 (398)
Q Consensus        89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~~~  168 (398)
                                   ..+.|||.++++ ++|+=+-...|..  ..++-+..+   +||+-.-.+-|.+...   |...++..
T Consensus       739 -------------~~~pvlIdkfl~-g~E~evDai~Dg~--~v~I~gImE---HIE~AGVHSGDS~~v~---Pp~~Ls~~  796 (1068)
T PRK12815        739 -------------QLYPILIDQFID-GKEYEVDAISDGE--DVTIPGIIE---HIEQAGVHSGDSIAVL---PPQSLSPE  796 (1068)
T ss_pred             -------------CCCCEEEEECCC-CCEEEEEEEECCC--CEEEEEEEE---CHHHCCCCCCCCEEEE---CCCCCCHH
T ss_conf             -------------888556230005-4046889996499--559999642---1131466568854883---89878999


Q ss_pred             HHH-------HHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHH--H---H
Q ss_conf             888-------788751988899885999999998999955975102326799059967994001321573556--4---1
Q gi|254781049|r  169 DVA-------SLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALY--R---H  236 (398)
Q Consensus       169 ~~~-------~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~f--R---~  236 (398)
                      ..+       +++..|++.|-...+++         ..+.+.-.+|+||=+    .+=++.=+|.+==+=|..  |   -
T Consensus       797 ~~~~i~~~t~kia~~L~v~Gl~NiQfa---------vk~~~vyVIEvNpRA----SRTvPFvSKatG~pl~~iAtkvmlG  863 (1068)
T PRK12815        797 QQAKIRDQAIKIAKKLGFRGIMNIQFL---------LAGDEIYVLEVNPRA----SRTVPFVSKATGVPLAKLATKVLLG  863 (1068)
T ss_pred             HHHHHHHHHHHHHHHCEEECCEEEEEE---------EECCEEEEEEEECCC----CCCHHHHHHHCCCCHHHHHHHHHCC
T ss_conf             999999999999964835451269999---------979989999961875----5432667873298899999999849


Q ss_pred             HHHHHHHCCCCCCH-HHH-HHHHCCCCEEECC-------------CCEEEEECCCHHHHHHHHHHHHCCCC-C---CEEE
Q ss_conf             02786310001562-224-5775398644228-------------81799955503689999999965899-6---2488
Q gi|254781049|r  237 LDIQELRDVSEEDS-REI-EAKQHNLSYIALD-------------GNIGCMVNGAGLAMATMDIIKLYGGA-P---ANFL  297 (398)
Q Consensus       237 ~~~~~~~d~~~~~~-~E~-~A~~~~l~yv~Ld-------------G~Ig~~vnGaGlamatmD~i~~~Gg~-p---ANFl  297 (398)
                      ..+.++..+....| .+. --+..=++|-+|.             |.+  |+-|.-+..|..-.....|.+ |   .=|+
T Consensus       864 ~~L~~l~~~~~~~p~~~~~~VK~pvFsf~k~~g~d~~LGpEMkSTGEV--mgig~~~~eA~~Ka~~aag~~lP~~G~vfi  941 (1068)
T PRK12815        864 KSLAELGYPNELWPGSNFIHVKMPVFSFLRYPGVDNTLGPEMKSTGEV--MGIDKDLESALYKGYAASDLHIPTYGTIFI  941 (1068)
T ss_pred             CCHHHCCCCCCCCCCCCCEEEECCCCCHHHCCCCCCCCCCCCCCCCCC--EEECCCHHHHHHHHHHHCCCCCCCCCEEEE
T ss_conf             975662886555778882899835487444389998778884223231--562499999999999966998898988999


Q ss_pred             ECCCCCCHHHHHHHHHHH----------------HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf             427888989999999998----------------6199865899963586132899999999999972999879997489
Q gi|254781049|r  298 DVGGGADQDKVAAAFKII----------------TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG  361 (398)
Q Consensus       298 D~gG~a~~e~~~~a~~~i----------------l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G  361 (398)
                      -++- .+.+.+....+.+                |...++.+-.||-..--      -.-|++.+++.++.+-+......
T Consensus       942 Sv~d-~DK~~~~~~a~~l~~lGf~i~AT~GTa~~L~~~GI~~~~V~Kv~eg------~p~i~d~i~~~~i~lViNt~~g~ 1014 (1068)
T PRK12815        942 SVRD-EDKEAVAELARRFEQLGFKLLATEGTANWLAEEGITTGVVEKVQEG------SPSLLERIKQHRIVLVVNTSLSD 1014 (1068)
T ss_pred             EECC-CCHHHHHHHHHHHHHCCCEEEECHHHHHHHHHCCCEEEEEECCCCC------CCCHHHHHHCCCEEEEEECCCCC
T ss_conf             9610-0178999999999987998998658999999779836997136789------81299998679857999799998


Q ss_pred             CCHHHHHHHH---HHCCCCEEEECCHHHHHHHHHH
Q ss_conf             8589999999---9769958994998999999999
Q gi|254781049|r  362 ANVDIGNRLI---AESGLNVITAIDLDDAAQKIVH  393 (398)
Q Consensus       362 tn~~~g~~il---~~~g~~~~~~~~~~~A~~~~v~  393 (398)
                      .....|.+|-   -+.++|+++.-+.-+|.-++.+
T Consensus      1015 ~~~~D~~~IRr~Av~~~IP~~Ttl~~A~a~v~al~ 1049 (1068)
T PRK12815       1015 SASEDAIKIRDEALTTHIPVFTSLETAQAFLDVLE 1049 (1068)
T ss_pred             CCCCCHHHHHHHHHHHCCCEEECHHHHHHHHHHHH
T ss_conf             76654399999999829988927999999999999


No 58 
>pfam02655 ATP-grasp_3 ATP-grasp domain. No functional information or experimental verification of function is known in this family. This family appears to be an ATP-grasp domain (Pers. obs. A Bateman).
Probab=98.41  E-value=2.4e-06  Score=61.54  Aligned_cols=80  Identities=21%  Similarity=0.232  Sum_probs=59.5

Q ss_pred             HHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             79999999986898888157479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR   84 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~   84 (398)
                      -|..+++|+++|||+|+.....++++       +.+|+ |+|+-.-+|||              ||.++++.+++.... 
T Consensus         4 K~~t~~~l~~~gip~P~~~~~~~~~~-------~~~P~-VvKP~~g~gs~--------------Gv~~v~~~~~l~~~~-   60 (160)
T pfam02655         4 KLKTYKALKNAGVPTPETLSAEEPTE-------EEKKY-IVKPRDGCGGE--------------GVRFVENGREDEEFI-   60 (160)
T ss_pred             HHHHHHHHHHCCCCCCCEEECCCHHH-------CCCCE-EEECCCCCCCC--------------CEEEEECHHHHHHHC-
T ss_conf             89999999987959999986578235-------59989-99808989873--------------189994899986532-


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf             8618765442122222443301103455565058999998347
Q gi|254781049|r   85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT  127 (398)
Q Consensus        85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~  127 (398)
                                         ..+++||+++ +.|+=+++..|..
T Consensus        61 -------------------~~~liqe~i~-G~e~sv~~l~~~~   83 (160)
T pfam02655        61 -------------------ENVIIQEFIE-GEPLSVSLLSDGE   83 (160)
T ss_pred             -------------------CCEEEEEEEE-CCEEEEEEEEECC
T ss_conf             -------------------5658874794-4423899999899


No 59 
>TIGR03103 trio_acet_GNAT GNAT-family acetyltransferase TIGR03103. Members of this protein family belong to the GNAT family of acetyltransferases. Each is part of a conserved three-gene cassette sparsely distributed across at least twenty different species known so far, including alpha, beta, and gamma Proteobacteria, Mycobacterium, and Prosthecochloris, which is a member of the Chlorobi. The other two members of the cassette are a probable protease and an asparagine synthetase family protein.
Probab=98.23  E-value=1.2e-05  Score=56.92  Aligned_cols=109  Identities=18%  Similarity=0.213  Sum_probs=72.2

Q ss_pred             HHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEE-ECCHHHHHHHHHHH
Q ss_conf             99999986898888157479999999998729986999712136876565655677777770799-58999999999986
Q gi|254781049|r    8 AKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRV-ESSLKSVISDIREI   86 (398)
Q Consensus         8 aK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l-~~s~~ea~~~a~~i   86 (398)
                      .|+||++.|+|||.++++.+.+++.+++.+.| |+ |||+.  -|-.||            ||-+ ..|.+++..++..-
T Consensus       301 T~rll~~AG~~VP~~~~~~~~~~~~~fl~~~G-~V-VVKP~--dGnqGr------------GVtvnl~t~eev~~A~~~A  364 (547)
T TIGR03103       301 TRRLVSEAGLQVPEQQLAGNGEAVEAFLAEHG-AV-VVKPV--RGEQGK------------GISVDVRTPDDLEAAIAKA  364 (547)
T ss_pred             HHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCC-CE-EECCC--CCCCCC------------CEEECCCCHHHHHHHHHHH
T ss_conf             99999973998999745699899999998739-99-97768--788886------------1587259999999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEEC----CCC-CEEEEEECCCCCCHHHHHH
Q ss_conf             1876544212222244330110345556505899999834----778-0489984478840245557
Q gi|254781049|r   87 LGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDR----TSG-MVAFIASTQGGMDIEEVAK  148 (398)
Q Consensus        87 lg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr----~~~-~~vii~S~~GGvdIE~va~  148 (398)
                                   -.....|+||++++.. +|=+=+.-++    ..+ ++-+++  -|=-.|+++-+
T Consensus       365 -------------~~~~~~VIVE~fi~G~-D~RlLVIggkVVAAA~R~Pa~VvG--DG~sTI~eLIe  415 (547)
T TIGR03103       365 -------------RQFCDRVLLERYVPGE-DLRLVVIDFEVVAAAVRRPPEVIG--DGRSSIRDLIE  415 (547)
T ss_pred             -------------HHHCCCEEEEEEECCC-CEEEEEECCEEEEEECCCCCEEEE--CCHHHHHHHHH
T ss_conf             -------------9759957999840697-169999999999998147967984--86620999984


No 60 
>TIGR00768 rimK_fam alpha-L-glutamate ligases, RimK family; InterPro: IPR004666   Escherichia coli RimK adds additional Glu residues to the native Glu-Glu C-terminus of ribosomal protein S6. Mutation of the Glu-Glu terminus to Lys-Glu blocked addition. S6 has the C-terminal sequence Glu-Glu in few species, suggesting the homolog of rimK may have a function other than S6 modification in those species. However, most species having a member of this protein subfamily do not have an S6 homolog ending in Glu-Glu.; GO: 0006464 protein modification process.
Probab=98.17  E-value=1.5e-05  Score=56.25  Aligned_cols=83  Identities=22%  Similarity=0.290  Sum_probs=61.6

Q ss_pred             HHHHHHHHCCCCCCCCEEEC--------CHHHHHHHHHHCC---CCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf             99999998689888815747--------9999999998729---986999712136876565655677777770799589
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVIS--------SVHAAESAIKTLP---GPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESS   75 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~--------s~~ea~~~a~~ig---~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s   75 (398)
                      -+-.+|+++|||+|++.++.        ++++|...++++|   ||. |+|+-.  |-+|+            +|-++++
T Consensus       116 ~s~~~L~~~G~P~P~~~~~~PqnfDReW~~~~a~~~ie~~g~lEfP~-V~Kp~~--GS~G~------------~V~l~~D  180 (321)
T TIGR00768       116 LSHQLLAKAGVPLPRTGVAGPQNFDREWSPEEALKLIEEIGQLEFPV-VLKPVF--GSWGR------------LVSLARD  180 (321)
T ss_pred             HHHHHHHHCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHCCCCCCE-EEECCC--CCCCC------------EEEEEEC
T ss_conf             99999995868987335736632243589889999998731764245-871785--63542------------6898506


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCC
Q ss_conf             99999999986187654421222224433011034555
Q gi|254781049|r   76 LKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGAD  113 (398)
Q Consensus        76 ~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~  113 (398)
                      ..++.......       ++.  +|..-+.+||+|.++
T Consensus       181 ~~~~~~~~e~~-------~~~--~~~~~~~~~~QeyI~  209 (321)
T TIGR00768       181 KQAAETLLEHF-------EQL--NGPQYKVFLVQEYIK  209 (321)
T ss_pred             HHHHHHHHHHH-------HHH--CCCCCCEEEEEEEEC
T ss_conf             78999999999-------721--883323578872011


No 61 
>PRK05784 phosphoribosylamine--glycine ligase; Provisional
Probab=98.13  E-value=1.7e-05  Score=55.93  Aligned_cols=214  Identities=19%  Similarity=0.172  Sum_probs=105.0

Q ss_pred             HHHHHHHHCCCC-CCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECC-HHHHHH---
Q ss_conf             999999986898-888157479999999998729986999712136876565655677777770799589-999999---
Q gi|254781049|r    7 QAKALLRKYNVP-VAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESS-LKSVIS---   81 (398)
Q Consensus         7 qaK~lL~~~GIp-vp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s-~~ea~~---   81 (398)
                      -+|+++++|||| ++++...++.++|.+..+..+ | +|||+.=||+|.              ||.++.+ .+.+.+   
T Consensus       112 FaK~fm~~~~IPtta~~~~f~~~~~A~~~l~~~~-p-iVIKaDGLAaGK--------------GV~V~~~~~~~~~~~~~  175 (485)
T PRK05784        112 FARSLMWKYGIPGRLRYGVFKDVEEAYSFAEYGG-S-VAIKPARQAGGK--------------GVKVIYDLQAYLSNEKD  175 (485)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCC-C-EEEECCHHCCCC--------------CEEEECCCHHHHHHHHH
T ss_conf             9999999728996640121389999999986489-8-499211330678--------------51882272777777899


Q ss_pred             -----HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEE
Q ss_conf             -----999861876544212222244330110345556505899999834778048998447884024555748312203
Q gi|254781049|r   82 -----DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFK  156 (398)
Q Consensus        82 -----~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~  156 (398)
                           .+.+++...   ..   -|.--++|+|||++. +.|+=+-...|...-  +.|.+.+          ++ .++..
T Consensus       176 e~~~~~~~~~~~~~---~~---fg~ag~~VvIEEfL~-G~E~S~~a~~DG~~~--~~lp~aQ----------Dh-KR~~d  235 (485)
T PRK05784        176 EVLTKGAEEIKEQL---AS---YRDVEEKILVEEKVD-GVEYTVQVLTDGESV--FPLPPVQ----------DN-PHAYE  235 (485)
T ss_pred             HHHHHHHHHHHHHH---HH---HCCCCCEEEEEECCC-CCEEEEEEEEECCEE--EECCCCC----------CC-CCCCC
T ss_conf             99999999999876---54---324687099996446-817999999829969--9892220----------57-65568


Q ss_pred             EECCCCCC-CCHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHH-HCCCCCCC--CCEEEECCCCCEEEEEEEEEECCC
Q ss_conf             32144457-89578887887519-888998859999999989999-55975102--326799059967994001321573
Q gi|254781049|r  157 LLIDPLIG-VTSEDVASLCDMLE-LQGQARIDGGDLFPNLYKAFC-DKDMSLLE--INPLIIMKNGRLRVLDSKISFDDN  231 (398)
Q Consensus       157 ~~id~~~g-l~~~~~~~l~~~lg-~~~~~~~~~~~ii~~L~~~f~-e~Da~liE--INPLvvt~dg~vvAlDAKi~iDDn  231 (398)
                      -..-|..| +-.|--...  .+. +.........+++....+... +......=  -==|.+|++| ...      +.=|
T Consensus       236 gD~GPNTGGMGAysP~~~--~~P~l~~~~~~~~~~Ii~pti~~l~~e~g~~y~GvLY~GlMit~~G-PkV------lEfN  306 (485)
T PRK05784        236 YGIGPETGGMGSVSGPGE--LLPFIEEEEYEEAVEIVKATVEAIRKETGERYVGVLSGQMMLTALG-PTV------IEYY  306 (485)
T ss_pred             CCCCCCCCCCEECCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCC-CEE------EEEE
T ss_conf             999989998700678766--7754479999999874899999998616997278887678861898-489------9996


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHH--HHHHCCCCEEEC
Q ss_conf             5564102786310001562224--577539864422
Q gi|254781049|r  232 ALYRHLDIQELRDVSEEDSREI--EAKQHNLSYIAL  265 (398)
Q Consensus       232 A~fR~~~~~~~~d~~~~~~~E~--~A~~~~l~yv~L  265 (398)
                      +.|--|+...+....+.|-.++  .+.+..|+-+++
T Consensus       307 ~RfGDPEtQ~iLp~L~sDl~~l~~a~~~g~L~~~~~  342 (485)
T PRK05784        307 SRLGDPEALNALYLYEGDFYELFELAATGKLHKAER  342 (485)
T ss_pred             CCCCCCHHHHHHHHHHCCHHHHHHHHHCCCCCCCCE
T ss_conf             887883388899874263999999998199887870


No 62 
>COG0027 PurT Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]
Probab=98.01  E-value=3.2e-05  Score=54.08  Aligned_cols=84  Identities=25%  Similarity=0.295  Sum_probs=62.9

Q ss_pred             HHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCC
Q ss_conf             98689888815747999999999872998699971213687656565567777777079958999999999986187654
Q gi|254781049|r   13 RKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLI   92 (398)
Q Consensus        13 ~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~   92 (398)
                      .+.|+|+.++..++|.+|...++..||||+ |+|+-+-+-|.|..              ++++++++..+-+.-      
T Consensus       123 eeLglpTs~Y~fa~s~~e~~~a~~~iGfPc-vvKPvMSSSGkGqs--------------vv~~~e~ve~AW~~A------  181 (394)
T COG0027         123 EELGLPTSKYRFADSLEELRAAVEKIGFPC-VVKPVMSSSGKGQS--------------VVRSPEDVEKAWEYA------  181 (394)
T ss_pred             HHHCCCCCCCCCCCCHHHHHHHHHHCCCCE-ECCCCCCCCCCCCE--------------EECCHHHHHHHHHHH------
T ss_conf             972999766321355999999999749970-21332026889821--------------435987889999999------


Q ss_pred             CCCCCCCCCCCCCEEECCCCCCCEEEEE
Q ss_conf             4212222244330110345556505899
Q gi|254781049|r   93 TKQTGPTGSRVNCVYVEDGADILRELYL  120 (398)
Q Consensus        93 t~qt~~~G~~v~~vLVEe~v~~~~E~yl  120 (398)
                        |.+..|. -.+|.||++++++-|.-+
T Consensus       182 --~~g~R~~-~~RVIVE~fv~fd~EITl  206 (394)
T COG0027         182 --QQGGRGG-SGRVIVEEFVKFDFEITL  206 (394)
T ss_pred             --HHCCCCC-CCCEEEEEEECCEEEEEE
T ss_conf             --7547888-871899987323279999


No 63 
>COG0189 RimK Glutathione synthase/Ribosomal protein S6 modification enzyme (glutaminyl transferase) [Coenzyme metabolism / Translation, ribosomal structure and biogenesis]
Probab=97.85  E-value=0.0003  Score=47.69  Aligned_cols=93  Identities=22%  Similarity=0.248  Sum_probs=64.4

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHH-HHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHH-HHHHHH
Q ss_conf             99999999868988881574799999-9999872998699971213687656565567777777079958999-999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAA-ESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLK-SVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea-~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~-ea~~~a   83 (398)
                      ..+-++|+..|+|+|+..++.+++++ ...++.+|+|+ |+|+---+|||              ||.++++.+ ++.+..
T Consensus       121 ~~~~~~l~~~~ipvP~T~i~~~~~~~~~~~~~~~g~pv-VlKp~~Gs~G~--------------gV~~v~~~d~~l~~~~  185 (318)
T COG0189         121 LYTTQLLAKAGIPVPPTLITRDPDEAAEFVAEHLGFPV-VLKPLDGSGGR--------------GVFLVEDADPELLSLL  185 (318)
T ss_pred             HHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCCCE-EEEECCCCCCC--------------CEEEECCCCHHHHHHH
T ss_conf             99999999659999986896584788999997468988-99647888866--------------5599437765699999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEE
Q ss_conf             986187654421222224433011034555650589999983
Q gi|254781049|r   84 REILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVD  125 (398)
Q Consensus        84 ~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~D  125 (398)
                      ..+.+..            -+.++++|+++....-+..+++.
T Consensus       186 e~~~~~~------------~~~~ivQeyi~~~~~~~rrivv~  215 (318)
T COG0189         186 ETLTQEG------------RKLIIVQEYIPKAKRDDRRVLVG  215 (318)
T ss_pred             HHHHCCC------------CCEEEEECCCCCCCCCEEEEEEE
T ss_conf             9863455------------64298620347677873999998


No 64 
>PRK02471 bifunctional glutamate--cysteine ligase/glutathione synthetase; Provisional
Probab=97.79  E-value=0.00023  Score=48.49  Aligned_cols=89  Identities=21%  Similarity=0.244  Sum_probs=62.4

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCC-EEEE---ECCHHHHHH
Q ss_conf             999999998689888815747999999999872998699971213687656565567777777-0799---589999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKG-GVRV---ESSLKSVIS   81 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~G-GV~l---~~s~~ea~~   81 (398)
                      .-+|++|+++|+|||+|.-.++.++|.++...+.....|||+.        .       +.-| ||-+   ..|.++..+
T Consensus       491 ~vtK~vl~~~g~~vp~g~~~~~~~~a~~~~~~~~~k~ivvKpk--------s-------tn~g~gi~if~~~~~~~~~~~  555 (753)
T PRK02471        491 VVTKKILAEAGFPVPAGDEFTSLEEALADYSLFEDKAIVVKPK--------S-------TNFGLGISIFKEVASLEDYQK  555 (753)
T ss_pred             HHHHHHHHHCCCCCCCCCEECCHHHHHHHHHHHCCCCEEECCC--------C-------CCCCCCEEEECCCCCHHHHHH
T ss_conf             9999999985998999874078999999999867996686807--------7-------778776598348999899999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEE
Q ss_conf             999861876544212222244330110345556505899999
Q gi|254781049|r   82 DIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLL  123 (398)
Q Consensus        82 ~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~  123 (398)
                      +.+.-+.-.             +.|+||++++. +||=+=+.
T Consensus       556 A~~~af~~d-------------~~VlVE~~i~G-~dyR~lVI  583 (753)
T PRK02471        556 ALEIAFKED-------------SSVLVEEFIVG-TEYRFFVL  583 (753)
T ss_pred             HHHHHHHCC-------------CEEEEEEEECC-CCEEEEEE
T ss_conf             999998569-------------81899973168-70699999


No 65 
>COG1038 PycA Pyruvate carboxylase [Energy production and conversion]
Probab=97.76  E-value=0.0016  Score=42.81  Aligned_cols=128  Identities=23%  Similarity=0.319  Sum_probs=86.0

Q ss_pred             HHHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf             999999998689888815--747999999999872998699971213687656565567777777079958999999999
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDI   83 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a   83 (398)
                      -.|+.+-.+.|+||-++.  .+.+.+|+.+.++++|||+ .+||----||||              -+++.+.+++.+.+
T Consensus       123 v~Ar~~A~~agvPvipgt~~~~~~~ee~~~fa~~~gyPv-miKA~~GGGGRG--------------MR~vr~~~~l~~~~  187 (1149)
T COG1038         123 VKARNAAIKAGVPVIPGTDGPIETIEEALEFAEEYGYPV-MIKAAAGGGGRG--------------MRVVRSEADLAEAF  187 (1149)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEECCCCCCCC--------------EEEECCHHHHHHHH
T ss_conf             889999997599855699998212999999998669858-999714798665--------------26625888999999


Q ss_pred             HH-------HCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEE
Q ss_conf             98-------61876544212222244330110345556505899999834778048998447884024555748312203
Q gi|254781049|r   84 RE-------ILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFK  156 (398)
Q Consensus        84 ~~-------ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~  156 (398)
                      .+       -||+              ..|+||..++-.+..-+-|+-| ..|.++-++-  ---.|.   +.++..   
T Consensus       188 ~~AksEAkaAFG~--------------~eVyvEk~ve~pkHIEVQiLgD-~~GnvvHLfE--RDCSvQ---RRhQKV---  244 (1149)
T COG1038         188 ERAKSEAKAAFGN--------------DEVYVEKLVENPKHIEVQILGD-THGNVVHLFE--RDCSVQ---RRHQKV---  244 (1149)
T ss_pred             HHHHHHHHHHCCC--------------CCEEHHHHHCCCCEEEEEEEEC-CCCCEEEEEE--CCCCHH---HCCCEE---
T ss_conf             9988999974189--------------8066565524865268998605-7787888862--355331---014403---


Q ss_pred             EECCCCCCCCHHHHH
Q ss_conf             321444578957888
Q gi|254781049|r  157 LLIDPLIGVTSEDVA  171 (398)
Q Consensus       157 ~~id~~~gl~~~~~~  171 (398)
                      +.+.|...+++..-.
T Consensus       245 VE~APa~~L~~~~R~  259 (1149)
T COG1038         245 VEVAPAPYLSPELRD  259 (1149)
T ss_pred             EEECCCCCCCHHHHH
T ss_conf             785688889999999


No 66 
>pfam06263 consensus
Probab=97.75  E-value=0.0011  Score=44.06  Aligned_cols=129  Identities=17%  Similarity=0.186  Sum_probs=85.9

Q ss_pred             CCEEEEECCCHHHHHHHHHHHHCCC--------------------CCCEEEECCCCC----------CHHHHHHHHHHHH
Q ss_conf             8179995550368999999996589--------------------962488427888----------9899999999986
Q gi|254781049|r  267 GNIGCMVNGAGLAMATMDIIKLYGG--------------------APANFLDVGGGA----------DQDKVAAAFKIIT  316 (398)
Q Consensus       267 G~Ig~~vnGaGlamatmD~i~~~Gg--------------------~pANFlD~gG~a----------~~e~~~~a~~~il  316 (398)
                      +.|-=+-.|+-|+=-.|=++....+                    .--.|+|+|-..          +++.=.+.+.--.
T Consensus       339 ~~irGLysGGTLa~EA~~l~~~~l~~~~sn~~~~g~~~L~d~~~s~gH~iiDlGDD~fT~GRPHPMIDPs~R~e~i~~~a  418 (514)
T pfam06263       339 KYIRGLYSGGTLADEAAMLLSEALGDVYSNIPLEGEMLLANIDKSQGHTIIDLGDDMFTVGRPHPMIDPTLRNERILQEA  418 (514)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCHHCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             74899954715999999999986087667888873002576333589568866774345789978868478999999971


Q ss_pred             CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHC-------CCCCCEEEECCCCC-----HHHHHHHHHHCCCCEEEECCH
Q ss_conf             199865899963586132899999999999972-------99987999748985-----899999999769958994998
Q gi|254781049|r  317 SDSSVKGILINIFGGIMRCDVLVKGILSAVKEV-------KINIPLVMRLEGAN-----VDIGNRLIAESGLNVITAIDL  384 (398)
Q Consensus       317 ~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~-------~~~~pivvRl~Gtn-----~~~g~~il~~~g~~~~~~~~~  384 (398)
                      .||.+-+||+-+-=|-=...+.|..++.|+++.       +..+++|+-.+||.     .++..+.|+++|  +..+++-
T Consensus       419 ~Dp~v~VILlDvVLGyGah~DPag~L~paI~~a~~~a~~~gr~l~vvatV~GT~~DPQ~~~~Q~~~L~~AG--v~V~~SN  496 (514)
T pfam06263       419 ADPEVAVILLDVVLGYGAHADPAGELLPAIEEARAIAKADGRELAVIATVCGTEADPQGRSEQIKILEEAG--VLVVSSN  496 (514)
T ss_pred             CCCCCEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCHHHHHHHHHHCC--EEEECCC
T ss_conf             49972289998532268999848999999999998887538970899997388989748999999999789--5997585


Q ss_pred             HHHHHHHHHHHHC
Q ss_conf             9999999998506
Q gi|254781049|r  385 DDAAQKIVHAVKG  397 (398)
Q Consensus       385 ~~A~~~~v~~~k~  397 (398)
                      .+|++.|.+++|.
T Consensus       497 a~A~~~A~~l~~~  509 (514)
T pfam06263       497 AQAVRLAKKIAKL  509 (514)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999987


No 67 
>TIGR01235 pyruv_carbox pyruvate carboxylase; InterPro: IPR005930    In the postabsorptive state, blood glucose concentration is kept constant by a combination of glycogenolysis and gluconeogenesis. During prolonged fasting, when hepatic glycogen is exhausted, gluconeogenesis becomes the only source of plasma glucose. Gluconeogenesis (the production of new glucose molecules) occurs mainly in liver and, to a small extent, in kidneys.    Pyruvate carboxylase (6.4.1.1 from EC), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate, thus playing a crucial role in gluconeogenesis.  ATP + pyruvate + HCO3- = ADP + phosphate + oxaloacetate  Most well characterised forms of active enzyme consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain.; GO: 0004736 pyruvate carboxylase activity, 0006094 gluconeogenesis, 0005737 cytoplasm.
Probab=97.75  E-value=0.00062  Score=45.60  Aligned_cols=167  Identities=23%  Similarity=0.332  Sum_probs=100.1

Q ss_pred             HHHHHHHHCCCCCCCC--EEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             9999999868988881--57479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r    7 QAKALLRKYNVPVAKG--VVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR   84 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g--~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~   84 (398)
                      .|.++=.+.||||-||  -.++|.+|+...++..|||+ ++||=-=-||||              -|++++.+|+.++++
T Consensus       122 ~AR~~A~~aGvPvvPgt~Gp~~t~eev~~f~~~~GYPv-i~KAs~GGGGRG--------------MRvvR~~~dv~~~~~  186 (1169)
T TIGR01235       122 AARNLAIKAGVPVVPGTDGPVETLEEVLDFAKAIGYPV-IIKASYGGGGRG--------------MRVVRSEEDVADAFQ  186 (1169)
T ss_pred             HHHHHHHHCCCCEECCCCCCHHHHHHHHHHHHHCCCCE-EEEECCCCCCCC--------------CEEECCHHHHHHHHH
T ss_conf             99988887788763688687525999999997569958-987216889720--------------168607567999988


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCC
Q ss_conf             86187654421222224433011034555650589999983477804899844788402455574831220332144457
Q gi|254781049|r   85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIG  164 (398)
Q Consensus        85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~g  164 (398)
                      += .+.-.+    .=|.  ..++||+.++-.|..=+=++-| ..|.+|=+|=.  -=.   |-+.++..   +.+.|..-
T Consensus       187 rA-~sEA~A----AFGn--d~~yvEklie~pkHiEvQ~LGD-~~GNVVHLFER--DCS---VQRRhQKV---vE~APA~~  250 (1169)
T TIGR01235       187 RA-KSEAKA----AFGN--DEVYVEKLIERPKHIEVQLLGD-KHGNVVHLFER--DCS---VQRRHQKV---VEVAPAPS  250 (1169)
T ss_pred             HH-HHHHHH----CCCC--CEEEEEEECCCCCEEEEEEEEC-CCCCEEEEEEC--CCC---CEEECCEE---EEECCCCC
T ss_conf             87-688731----0489--8069851024882078987634-88987888750--776---20005507---88678877


Q ss_pred             CCHHHH-------HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCEEE
Q ss_conf             895788-------8788751988899885999999998999955-97510232679
Q gi|254781049|r  165 VTSEDV-------ASLCDMLELQGQARIDGGDLFPNLYKAFCDK-DMSLLEINPLI  212 (398)
Q Consensus       165 l~~~~~-------~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~-Da~liEINPLv  212 (398)
                      |+++.-       -+||+..|+.+.--.+|      |..  .+. .+-.|||||=+
T Consensus       251 Ls~e~Rd~~~~~AvkLAk~~nY~nAGTvEF------L~d--~~~G~FYFIEvNpRi  298 (1169)
T TIGR01235       251 LSREVRDEIAEYAVKLAKEVNYINAGTVEF------LVD--NDTGKFYFIEVNPRI  298 (1169)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCEEE------EEE--CCCCCEEEEEECCCE
T ss_conf             888899999999999987428988872488------555--488937789988800


No 68 
>PRK06091 membrane protein FdrA; Validated
Probab=97.48  E-value=0.0029  Score=41.19  Aligned_cols=129  Identities=14%  Similarity=0.182  Sum_probs=81.7

Q ss_pred             CCEEEEECCCHHHHHHHHHHHHCCCCC---------------CEEEECCCCC----------CHHHHHHHHHHHHCCCCC
Q ss_conf             817999555036899999999658996---------------2488427888----------989999999998619986
Q gi|254781049|r  267 GNIGCMVNGAGLAMATMDIIKLYGGAP---------------ANFLDVGGGA----------DQDKVAAAFKIITSDSSV  321 (398)
Q Consensus       267 G~Ig~~vnGaGlamatmD~i~~~Gg~p---------------ANFlD~gG~a----------~~e~~~~a~~~il~~~~v  321 (398)
                      +.|-=+-.|+-|+=-.|=++...-+-|               -.|+|+|-..          +++.=.+.+.--..||.+
T Consensus       331 ~~irGLysGGTLa~EA~~ll~~~l~~~~~~~~~~g~~l~s~gH~iiDlGDD~fT~GRPHPMIDPs~R~e~i~~~a~Dp~v  410 (555)
T PRK06091        331 GFICGLYTGGTLAAEAAGLLAGHLGVEADDEHHHGMMLDADGHQIIDLGDDFYTVGRPHPMIDPTLRNQLIADLGAKPQV  410 (555)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC
T ss_conf             73799953712999999999987099888533544111058956986577423578988886827799999997349972


Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHH------CCCCCCEEEECCCCC-----HHHHHHHHHHCCCCEEEECCHHHHHHH
Q ss_conf             589996358613289999999999997------299987999748985-----899999999769958994998999999
Q gi|254781049|r  322 KGILINIFGGIMRCDVLVKGILSAVKE------VKINIPLVMRLEGAN-----VDIGNRLIAESGLNVITAIDLDDAAQK  390 (398)
Q Consensus       322 k~iliNifGGI~~cd~vA~gii~a~~~------~~~~~pivvRl~Gtn-----~~~g~~il~~~g~~~~~~~~~~~A~~~  390 (398)
                      -+||+-+-=|.=...+.|..++.|+++      -+..+++|+-..||.     .++..+.|+++|  +..+++-.+|++.
T Consensus       411 ~VILlDvVLGyGah~DPag~L~paI~~a~~a~~~gr~l~vVa~V~GT~~DPQ~~~~Q~~~L~~AG--v~V~~SNa~A~~~  488 (555)
T PRK06091        411 RVLLLDVVIGFGATADPAASLVSAWQKACAARSDNQPLYAIATVTGTERDPQCRSQQIATLEDAG--IAVVSSLPEATLL  488 (555)
T ss_pred             EEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCHHHHHHHHHHCC--EEEECCCHHHHHH
T ss_conf             28999875326899984899999999999755338963899998078889738999999999689--5997573999999


Q ss_pred             HHHHHHC
Q ss_conf             9998506
Q gi|254781049|r  391 IVHAVKG  397 (398)
Q Consensus       391 ~v~~~k~  397 (398)
                      |+++.+.
T Consensus       489 A~~l~~~  495 (555)
T PRK06091        489 AAALIRP  495 (555)
T ss_pred             HHHHHCC
T ss_conf             9997088


No 69 
>PRK05678 succinyl-CoA synthetase subunit alpha; Validated
Probab=97.40  E-value=0.0059  Score=39.14  Aligned_cols=125  Identities=16%  Similarity=0.306  Sum_probs=92.6

Q ss_pred             EEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCH-HHHHHHHHHHHCCCCCCEEEEECCCCHHHH--HHH
Q ss_conf             44228817999555036899999999658996248842788898-999999999861998658999635861328--999
Q gi|254781049|r  262 YIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQ-DKVAAAFKIITSDSSVKGILINIFGGIMRC--DVL  338 (398)
Q Consensus       262 yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~-e~~~~a~~~il~~~~vk~iliNifGGI~~c--d~v  338 (398)
                      ++-..|+||++..-++|+-..+|.+...|.=-.-+.-+||.+-. ......++.+..||+.|+|++  +|-|--.  ...
T Consensus       141 ~~~~pG~VgiiSrSGtLtye~~~~l~~~g~G~S~~VgiGgD~i~G~~f~d~L~~f~~Dp~T~~Ivl--iGEiGG~~E~~a  218 (289)
T PRK05678        141 HIHKKGRVGIVSRSGTLTYEAVAQLTDLGLGQSTCVGIGGDPINGTNFIDVLKAFEEDPETDAIVM--IGEIGGSAEEEA  218 (289)
T ss_pred             CCCCCCCEEEEECCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHCCCCCCEEEE--EECCCCHHHHHH
T ss_conf             247798689997776579999999997698669898527887678449999999742977327999--975598799999


Q ss_pred             HHHHHHHHHHCCCCCCEEEECCCCCHHHHHH--------------------HHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             9999999997299987999748985899999--------------------99976995899499899999999985
Q gi|254781049|r  339 VKGILSAVKEVKINIPLVMRLEGANVDIGNR--------------------LIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       339 A~gii~a~~~~~~~~pivvRl~Gtn~~~g~~--------------------il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      |+-    .++ ++++|||.-..|..+-+|++                    -|+++|+.  .+++..+-.+..-+..
T Consensus       219 a~~----i~~-~~~KPVva~iaG~~AP~gk~mGHAGAIi~~~~gta~~K~~al~~aGv~--Va~~p~~i~~~~~~~l  288 (289)
T PRK05678        219 AEW----IKA-NVTKPVVGYIAGVTAPPGKRMGHAGAIISGGKGTAEEKIEALEAAGVK--VARSPSEIGKTLKEVL  288 (289)
T ss_pred             HHH----HHH-CCCCCEEEEEECCCCCCCCCCCCCCEECCCCCCCHHHHHHHHHHCCCE--ECCCHHHHHHHHHHHH
T ss_conf             999----985-589967999951458999723321222048988899999999987797--5799999999999984


No 70 
>PTZ00187 succinyl-CoA synthetase alpha subunit; Provisional
Probab=97.34  E-value=0.005  Score=39.64  Aligned_cols=127  Identities=17%  Similarity=0.320  Sum_probs=95.5

Q ss_pred             EECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             42288179995550368999999996589962488427888-98999999999861998658999635861328999999
Q gi|254781049|r  263 IALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKG  341 (398)
Q Consensus       263 v~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~g  341 (398)
                      +--.|+||++...+.|+--..+.+...|.=.--..-+||.+ .-....+++++...||+.|+|++  .|-|=-.++  +-
T Consensus       158 i~~pG~VGivSRSGTLTyE~~~~lt~~G~GqSt~VgIGGDpi~Gt~f~d~L~~f~~D~~T~aIVl--iGEIGG~~E--e~  233 (309)
T PTZ00187        158 IHQKGKIGIVSRSGTLTYEAVAQTTAVGLGQSTCVGIGGDPFNGTNFIDCLKLFLNDPETEGIIL--IGEIGGTAE--EE  233 (309)
T ss_pred             HCCCCCEEEEECCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCHHHHHHHHHCCCCCCEEEE--EECCCCHHH--HH
T ss_conf             55788358994477528999999986698669999846987589789999999862957658999--816598699--99


Q ss_pred             HHHHHHHCCCCCCEEEECCCCCHHHHHHH--------------------HHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             99999972999879997489858999999--------------------9976995899499899999999985
Q gi|254781049|r  342 ILSAVKEVKINIPLVMRLEGANVDIGNRL--------------------IAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       342 ii~a~~~~~~~~pivvRl~Gtn~~~g~~i--------------------l~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      ..+.+++...++|+|.-+.|..+-.|+++                    |+++|++  .+++..+-.+...++.
T Consensus       234 aA~~Ik~~~~~KPVva~IAG~~AP~gkrmGHAGAIi~~~~gta~~K~~al~~AGv~--Va~~p~ei~~~v~~~l  305 (309)
T PTZ00187        234 AADWIKNNPTKKPVVSFIAGITAPPGRRMGHAGAIVSGGKGTAKGKIEALRAAGVT--VSKSPAQLGKTMAEVM  305 (309)
T ss_pred             HHHHHHHCCCCCCEEEEEEECCCCCCCCCCCHHEEECCCCCCHHHHHHHHHHCCCE--ECCCHHHHHHHHHHHH
T ss_conf             99999966999988999812568999704320001028988899999999988698--7899999999999999


No 71 
>COG1181 DdlA D-alanine-D-alanine ligase and related ATP-grasp enzymes [Cell envelope biogenesis, outer membrane]
Probab=97.27  E-value=0.0014  Score=43.25  Aligned_cols=94  Identities=22%  Similarity=0.202  Sum_probs=65.2

Q ss_pred             HHHHHHHHHHCCCCCCCCEEECC----HHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH
Q ss_conf             79999999986898888157479----99999999872998699971213687656565567777777079958999999
Q gi|254781049|r    5 EYQAKALLRKYNVPVAKGVVISS----VHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVI   80 (398)
Q Consensus         5 EyqaK~lL~~~GIpvp~g~~a~s----~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~   80 (398)
                      -...|.+++..|+|+++....+.    ..........++||+ +||.-     |.        .| .=|+..+++.+|..
T Consensus       104 k~~~K~~~~~~g~~~a~~~~~~~~~~~~~~~e~~~~~l~~p~-~Vkp~-----~~--------gS-Svg~~~v~~~~d~~  168 (317)
T COG1181         104 KIVTKRLFKAEGLPVAPYVALTRDEYSSVIVEEVEEGLGFPL-FVKPA-----RE--------GS-SVGRSPVNVEGDLQ  168 (317)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHCCCCHHHHHHHHHCCCCCCE-EEECC-----CC--------EE-EEEEEECCEECCHH
T ss_conf             999988998678651235675334520478887741468878-99858-----73--------11-36799883504369


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECC
Q ss_conf             99998618765442122222443301103455565058999998347
Q gi|254781049|r   81 SDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRT  127 (398)
Q Consensus        81 ~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~  127 (398)
                      .+.+..+...             +.+++|+.+. .+|+-+++..+..
T Consensus       169 ~~~e~a~~~d-------------~~vl~e~~~~-~rei~v~vl~~~~  201 (317)
T COG1181         169 SALELAFKYD-------------RDVLREQGIT-GREIEVGVLGNDY  201 (317)
T ss_pred             HHHHHHHHHC-------------CCCEECCCCC-CCEEEEEECCCCC
T ss_conf             9999999847-------------8512003776-6558986358865


No 72 
>KOG0369 consensus
Probab=96.87  E-value=0.042  Score=33.51  Aligned_cols=106  Identities=27%  Similarity=0.377  Sum_probs=74.5

Q ss_pred             HHHHHHHHCCCCCCCCE--EECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH
Q ss_conf             99999998689888815--7479999999998729986999712136876565655677777770799589999999999
Q gi|254781049|r    7 QAKALLRKYNVPVAKGV--VISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIR   84 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~--~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~   84 (398)
                      .|..+--+.|+||-+|-  -+++.+||.+.+++.|+|+ .+||----||||              .+++.+.+++.+.++
T Consensus       150 ~AR~~Ai~agVpvVPGTpgPitt~~EA~eF~k~yG~Pv-I~KAAyGGGGRG--------------mRvVr~~e~vee~f~  214 (1176)
T KOG0369         150 AARAIAIEAGVPVVPGTPGPITTVEEALEFVKEYGLPV-IIKAAYGGGGRG--------------MRVVRSGEDVEEAFQ  214 (1176)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE-EEEECCCCCCCC--------------EEEEECHHHHHHHHH
T ss_conf             88899997199715899997542999999998619838-996101689764--------------377502556999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             861876544212222244330110345556505899999834778048998
Q gi|254781049|r   85 EILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        85 ~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      .--+--    ++. -|  --.+.||.+++--+..-+-++-| ..|.++-++
T Consensus       215 Ra~SEA----~aa-FG--nG~~FvEkF~ekPrHIEvQllgD-~~GNvvHLy  257 (1176)
T KOG0369         215 RAYSEA----LAA-FG--NGTLFVEKFLEKPRHIEVQLLGD-KHGNVVHLY  257 (1176)
T ss_pred             HHHHHH----HHH-CC--CCEEEHHHHHCCCCEEEEEEECC-CCCCEEEEE
T ss_conf             888999----986-17--86153786625865268987213-568789876


No 73 
>KOG0370 consensus
Probab=96.67  E-value=0.0012  Score=43.77  Aligned_cols=90  Identities=19%  Similarity=0.258  Sum_probs=55.2

Q ss_pred             HHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCC
Q ss_conf             98689888815747999999999872998699971213687656565567777777079958999999999986187654
Q gi|254781049|r   13 RKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLI   92 (398)
Q Consensus        13 ~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~   92 (398)
                      .+.+.++.++..+++.+||.++++.+|||+ ++.+----||-|-+              +++|.+|+.+-+.+-|.++  
T Consensus       507 ~ei~e~ia~s~a~~sie~al~aae~l~ypv-ivRaayalgglgSg--------------fa~n~eeL~~l~~~a~a~s--  569 (1435)
T KOG0370         507 NEINEKIAPSEAVSTIEEALEAAERLGYPV-IVRAAYALGGLGSG--------------FANNEEELQDLAAQALALS--  569 (1435)
T ss_pred             HHHCCCCCCHHHHHHHHHHHHHHHHCCCHH-HHHHHHHHCCCCCC--------------CCCCHHHHHHHHHHCCCCC--
T ss_conf             763150562566767999998888628289-99999985376643--------------3444899999976431258--


Q ss_pred             CCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCC
Q ss_conf             42122222443301103455565058999998347780
Q gi|254781049|r   93 TKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGM  130 (398)
Q Consensus        93 t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~  130 (398)
                                 .++|||+.....+|.-.-+++|.-..+
T Consensus       570 -----------~QilvekSlkGwkevEyevvrDa~~nc  596 (1435)
T KOG0370         570 -----------PQILVEKSLKGWKEVEYEVVRDAYDNC  596 (1435)
T ss_pred             -----------CEEEEHHHHCCCCCEEEEEEECCCCCH
T ss_conf             -----------615422332443434899980200040


No 74 
>PRK06849 hypothetical protein; Provisional
Probab=96.35  E-value=0.036  Score=33.95  Aligned_cols=95  Identities=15%  Similarity=0.087  Sum_probs=58.1

Q ss_pred             HHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHC
Q ss_conf             99999986898888157479999999998729986999712136876565655677777770799589999999999861
Q gi|254781049|r    8 AKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREIL   87 (398)
Q Consensus         8 aK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~il   87 (398)
                      --++..+.|+|+|++.++++++++......-.++++|+|+ +  .+|+.           .+|....+.+++..    + 
T Consensus       120 F~~~a~~lGl~vP~T~~i~s~edv~~~~~~~~~~~~ilKP-v--~~~~~-----------~~v~~~~~~~~l~~----l-  180 (387)
T PRK06849        120 FIQQARSLGLSAPKTYLITDPEAIINFDFKTPHTPYVLKP-I--YSRFV-----------RRVDLTKTKAAVLK----L-  180 (387)
T ss_pred             HHHHHHHCCCCCCCEEEECCHHHHHHHHHCCCCCCEEECC-C--CCCCC-----------CEEEECCCHHHHHC----C-
T ss_conf             9999997499999889818999998655336689789823-7--66653-----------33652159778615----8-


Q ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             876544212222244330110345556505899999834778048998
Q gi|254781049|r   88 GSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        88 g~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                        ++ +.+        +.++++|.++...-++.++..+   |.++...
T Consensus       181 --~~-s~~--------~p~v~Qe~I~G~~~ct~al~~~---Gkv~A~~  214 (387)
T PRK06849        181 --PI-SHK--------SPWIMQEFIPGQEYCSYSIVRS---GELRAHS  214 (387)
T ss_pred             --CC-CCC--------CCEEEEEECCCCEEEEEEEEEC---CEEEEEE
T ss_conf             --87-667--------9828998716967589999789---9999999


No 75 
>KOG0368 consensus
Probab=96.31  E-value=0.026  Score=34.90  Aligned_cols=88  Identities=24%  Similarity=0.365  Sum_probs=64.7

Q ss_pred             EEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             57479999999998729986999712136876565655677777770799589999999999861876544212222244
Q gi|254781049|r   23 VVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSR  102 (398)
Q Consensus        23 ~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~  102 (398)
                      ..+.+++|+.++++.||||+ .+||  --||-||            |++-|.|.++....+++..+-        -.|-+
T Consensus       223 acv~~~eegLeaae~IGfPv-MIKA--SEGGGGK------------GIRkv~n~ddF~~lf~qv~~E--------vPGSP  279 (2196)
T KOG0368         223 ACVRNVEEGLEAAEKIGFPV-MIKA--SEGGGGK------------GIRKVENEDDFKALFKQVQNE--------VPGSP  279 (2196)
T ss_pred             HHCCCHHHHHHHHHHCCCCE-EEEE--CCCCCCC------------CEEECCCHHHHHHHHHHHHHH--------CCCCC
T ss_conf             43088889999998629836-9995--4578976------------613045667899999999855--------89995


Q ss_pred             CCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEEC
Q ss_conf             33011034555650589999983477804899844
Q gi|254781049|r  103 VNCVYVEDGADILRELYLSLLVDRTSGMVAFIAST  137 (398)
Q Consensus       103 v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~  137 (398)
                         +.+-+-++..+.+-+-++-| +.|..+-++|.
T Consensus       280 ---IFlMK~a~~ARHlEVQlLaD-qYGn~IsLfgR  310 (2196)
T KOG0368         280 ---IFLMKLADQARHLEVQLLAD-QYGNVISLFGR  310 (2196)
T ss_pred             ---EEHHHHCCCCCEEEEEHHHH-HHCCEEEEECC
T ss_conf             ---55200336754021002245-30878777436


No 76 
>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.
Probab=96.29  E-value=0.033  Score=34.21  Aligned_cols=24  Identities=25%  Similarity=0.267  Sum_probs=16.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             988899885999999998999955
Q gi|254781049|r  178 ELQGQARIDGGDLFPNLYKAFCDK  201 (398)
Q Consensus       178 g~~~~~~~~~~~ii~~L~~~f~e~  201 (398)
                      .++.+..+.+...+..+|+.|.+.
T Consensus       146 ~~s~e~~~~~q~~ld~~~~~F~~~  169 (214)
T cd07022         146 PLSDEARARLQAEVDALYAMFVAA  169 (214)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             568899999999999999999999


No 77 
>PRK13277 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein; Provisional
Probab=96.25  E-value=0.043  Score=33.47  Aligned_cols=97  Identities=13%  Similarity=0.218  Sum_probs=66.2

Q ss_pred             HHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCC
Q ss_conf             99998689888815747999999999872998699971213687656565567777777079958999999999986187
Q gi|254781049|r   10 ALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGS   89 (398)
Q Consensus        10 ~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~   89 (398)
                      .||.+.|||.|+  ...+|+|       |..|+ .||-+=-.|+-|+            |--+++|++|..+.+++++..
T Consensus       129 ~LLe~Agi~~Pk--~~~~Pee-------IDr~V-IVK~~gAkg~~gr------------GyF~a~s~~ef~~k~~~li~~  186 (363)
T PRK13277        129 RLLEKAGIPRPR--TFKPPEE-------IDRPV-IVKLPEAKRRLER------------GFFIAASYKDFYEKSERLIKQ  186 (363)
T ss_pred             HHHHHCCCCCCC--CCCCHHH-------CCCCE-EEEECCCCCCCCC------------EEEEECCHHHHHHHHHHHHHC
T ss_conf             999867999870--0599666-------78526-9974567787763------------589967989999999999875


Q ss_pred             CCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             6544212222244330110345556505899999834778048998
Q gi|254781049|r   90 TLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        90 ~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      -+++.      .-++...|||.+-. --||+-...+|-.+..=+++
T Consensus       187 G~I~~------e~l~~~~IeEyv~G-~~~~~~fFySpl~~~lEllg  225 (363)
T PRK13277        187 GVIDR------EDLEKARIEEYVIG-AHFNFNYFYSPIRDRVELLG  225 (363)
T ss_pred             CCCCH------HHCCCCEEEEEECC-CEEEEEECCCCCCCCEEEEE
T ss_conf             87572------21444378998437-64665210253237503663


No 78 
>PRK13278 purP 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase; Provisional
Probab=96.11  E-value=0.04  Score=33.71  Aligned_cols=94  Identities=18%  Similarity=0.280  Sum_probs=65.1

Q ss_pred             HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf             99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r    9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG   88 (398)
Q Consensus         9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg   88 (398)
                      .+||.+.|||.|+  ...+|+|       |..|+ .||.|=-.||||              --+++|++|..+.+++++.
T Consensus       126 ~~lLe~Agi~~Pk--~~~~Pee-------IDr~V-IVK~~gAkggrG--------------yF~a~s~~ef~~k~~~l~~  181 (356)
T PRK13278        126 RKLLEGAGIRIPR--KYEDPED-------IDGPV-IVKLPGAKGGRG--------------YFIASSPEEFWEKIDRLKE  181 (356)
T ss_pred             HHHHHHCCCCCCE--ECCCHHH-------CCCCE-EEEECCCCCCCE--------------EEEECCHHHHHHHHHHHHH
T ss_conf             9999867999871--1589555-------78526-997467777745--------------8995798999999999886


Q ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEE
Q ss_conf             76544212222244330110345556505899999834778048998
Q gi|254781049|r   89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus        89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~  135 (398)
                      .-++.        ..+...|||.+-. --+|+....+|-.+..=+++
T Consensus       182 ~g~i~--------d~~~~~IeEyv~G-~~~~~~yFySpl~~~lEllg  219 (356)
T PRK13278        182 KGLIE--------DVEKYIIQEYVVG-VPYYIHYFYSPIKNRLELLG  219 (356)
T ss_pred             CCCCC--------CCCCCEEEEEECC-CEEEHHHCCCCCCCCEEEEE
T ss_conf             27545--------5544279998347-41231220352006613663


No 79 
>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=96.02  E-value=0.14  Score=30.18  Aligned_cols=107  Identities=19%  Similarity=0.183  Sum_probs=68.3

Q ss_pred             HHHHHHHCCCCCCEEEEC-CCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC--CCEEE
Q ss_conf             999999658996248842-78889899999999-986199865899963586132899999999999972999--87999
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDV-GGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN--IPLVM  357 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~-gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~--~pivv  357 (398)
                      ..|.++..|.+..+.++. -++.+.++-+++++ +|.++|+++.++|     +...|.+|.|.++|+++.+.+  ..++|
T Consensus       152 f~~~l~~~g~p~~~vv~~~~~~~~~~~a~~~~~~~L~a~pdi~~~~i-----~a~ND~mAlGA~~Al~~aGl~~~~v~vv  226 (289)
T cd01540         152 ALEALKAPGFPEANIFQAPQKTTDTEGAFDAAASTLTKNPNVKNWII-----YGLNDETVLGAVRATEQSGIAAADVIGV  226 (289)
T ss_pred             HHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEE-----EECCCHHHHHHHHHHHHCCCCCCCEEEE
T ss_conf             99999635999607998456886699999999999975899884399-----9779668899999999749988976999


Q ss_pred             ECCCCCHHHHHHHHHHCCCCEEEECCHH----HHHHHHHH
Q ss_conf             7489858999999997699589949989----99999999
Q gi|254781049|r  358 RLEGANVDIGNRLIAESGLNVITAIDLD----DAAQKIVH  393 (398)
Q Consensus       358 Rl~Gtn~~~g~~il~~~g~~~~~~~~~~----~A~~~~v~  393 (398)
                      -+.|+..-...--..++++--....+-.    .|++.+++
T Consensus       227 gidg~~~~~~~~~~~~~~~~atv~Q~p~~~G~~av~~~~~  266 (289)
T cd01540         227 GINGSDAADEESKKQPTGFYGTVLISPTNHGYITAQNLYE  266 (289)
T ss_pred             EEECCCHHHHHHHCCCCCEEEEEEECHHHHHHHHHHHHHH
T ss_conf             9728825999974336764899950889999999999999


No 80 
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl    5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and    metabolism]
Probab=95.95  E-value=0.081  Score=31.67  Aligned_cols=95  Identities=20%  Similarity=0.284  Sum_probs=65.5

Q ss_pred             HHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf             99999868988881574799999999987299869997121368765656556777777707995899999999998618
Q gi|254781049|r    9 KALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG   88 (398)
Q Consensus         9 K~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg   88 (398)
                      .+||.+.||++|+  ..++|+|       |..|+ .||-+---||||              --++.|++|..+.+++++.
T Consensus       129 ~~lLekAgi~~P~--~~~~Pee-------Idr~V-iVK~pgAkggRG--------------yFiA~s~eef~ek~erl~~  184 (361)
T COG1759         129 YKLLEKAGLRIPK--KYKSPEE-------IDRPV-IVKLPGAKGGRG--------------YFIASSPEEFYEKAERLLK  184 (361)
T ss_pred             HHHHHHCCCCCCC--CCCCHHH-------CCCCE-EEECCCCCCCCE--------------EEEECCHHHHHHHHHHHHH
T ss_conf             9999974999885--6699678-------68736-985577667743--------------7997698999999999987


Q ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEE
Q ss_conf             7654421222224433011034555650589999983477804899
Q gi|254781049|r   89 STLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFI  134 (398)
Q Consensus        89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii  134 (398)
                      ..++|..      ..+...|||.+- +.-||+.....+-....=++
T Consensus       185 ~gvi~~E------dlkna~IeEYv~-G~~f~~~yFyS~i~~~lEl~  223 (361)
T COG1759         185 RGVITEE------DLKNARIEEYVV-GAPFYFHYFYSPIKDRLELL  223 (361)
T ss_pred             CCCCCHH------HHHHCEEEEEEE-CCCEEEEEEECCCCCCEEEE
T ss_conf             2876534------432135447750-66013455202345704576


No 81 
>cd07014 S49_SppA Signal peptide peptidase A. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is an intramembrane enzyme found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be ClpP-like serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain, cleaving peptide bonds in the plane of the lipid bilayer. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal p
Probab=95.90  E-value=0.078  Score=31.77  Aligned_cols=71  Identities=23%  Similarity=0.336  Sum_probs=51.0

Q ss_pred             EECCCCCCHHHHHHHHHHHHCCCCCCEEEEEC--CCCHH-HHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH
Q ss_conf             84278889899999999986199865899963--58613-2899999999999972999879997489858999999
Q gi|254781049|r  297 LDVGGGADQDKVAAAFKIITSDSSVKGILINI--FGGIM-RCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRL  370 (398)
Q Consensus       297 lD~gG~a~~e~~~~a~~~il~~~~vk~iliNi--fGGI~-~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i  370 (398)
                      .+..|+.+.+.+.+.++-...||+||+|++.|  .||-+ -|+.+++.|-+ +++  .++|+++-+.+.-+.-|--+
T Consensus        16 ~~~~g~~~~~~i~~~l~~a~~d~~vkaIvL~InSPGGs~~~s~~i~~~I~~-~r~--~~KPV~a~~~~~aASg~Y~i   89 (177)
T cd07014          16 SDTQGNVSGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAA-ARA--AGKPVVASGGGNAASGGYWI   89 (177)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHH-HHH--CCCCEEEEECCCCCCHHHHH
T ss_conf             888887169999999999951999628999961898188999999999999-886--59989999778562057787


No 82 
>COG0074 SucD Succinyl-CoA synthetase, alpha subunit [Energy production and conversion]
Probab=95.63  E-value=0.2  Score=29.14  Aligned_cols=132  Identities=17%  Similarity=0.317  Sum_probs=93.8

Q ss_pred             HCCC--CEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEEEECCCCHH
Q ss_conf             5398--6442288179995550368999999996589962488427888-989999999998619986589996358613
Q gi|254781049|r  257 QHNL--SYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGILINIFGGIM  333 (398)
Q Consensus       257 ~~~l--~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~iliNifGGI~  333 (398)
                      +.|+  +++-..|+||++.--+.|+--....+...|.-----.-+||.+ .-.....+++++..||..++|.+  .|-|-
T Consensus       134 kiGimp~~i~~~G~IGiVSrSGTLTyE~~~qlt~~G~GqS~~IGiGGDpi~Gt~fid~L~~fe~Dp~T~~ivm--iGEiG  211 (293)
T COG0074         134 KIGIMPGNIYKPGNIGIVSRSGTLTYEAVSQLTEAGLGQSTAIGIGGDPIPGTSFIDALEMFEADPETEAIVM--IGEIG  211 (293)
T ss_pred             EEEECHHHHCCCCCEEEEECCCCHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCHHHHHHHHHCCCCCEEEEE--EECCC
T ss_conf             3510523405788569996686639999999976388558999857887688159999998645867407999--92679


Q ss_pred             -HHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH--------------------HHHCCCCEEEECCHHHHHHHHH
Q ss_conf             -2899999999999972999879997489858999999--------------------9976995899499899999999
Q gi|254781049|r  334 -RCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRL--------------------IAESGLNVITAIDLDDAAQKIV  392 (398)
Q Consensus       334 -~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i--------------------l~~~g~~~~~~~~~~~A~~~~v  392 (398)
                       ..+..|--.|++   .-..+|+|.-+.|.-+.+|+++                    |+++|.++  .+++.+-.+...
T Consensus       212 G~aEe~AA~~i~~---~~~~KPVVa~iaG~tap~gkrmGhaGaiv~~~~gta~~Ki~al~~aGv~v--~etp~~l~~~l~  286 (293)
T COG0074         212 GPAEEEAAEYIKA---NATRKPVVAYIAGRTAPEGKRMGHAGAIVSGGKGTAESKIAALEAAGVKV--AETPAELGELLL  286 (293)
T ss_pred             CCHHHHHHHHHHH---HCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCEE--CCCHHHHHHHHH
T ss_conf             9389999999996---34689869998436798233012103433078765899999999759741--179999999999


Q ss_pred             HHH
Q ss_conf             985
Q gi|254781049|r  393 HAV  395 (398)
Q Consensus       393 ~~~  395 (398)
                      +..
T Consensus       287 ~vl  289 (293)
T COG0074         287 EVL  289 (293)
T ss_pred             HHH
T ss_conf             986


No 83 
>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=95.60  E-value=0.2  Score=29.08  Aligned_cols=117  Identities=20%  Similarity=0.231  Sum_probs=72.7

Q ss_pred             CEEEEECCCHHHH------HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf             1799955503689------999999965899624884278889899999999986-199865899963586132899999
Q gi|254781049|r  268 NIGCMVNGAGLAM------ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVK  340 (398)
Q Consensus       268 ~Ig~~vnGaGlam------atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~  340 (398)
                      +|+++..-.....      .+.+....+|..|.. ..+....+.+.-+++++-++ ..|.+.+||       ...|.+|-
T Consensus       120 rIa~i~g~~~~~~~~~R~~gy~~a~~~~gl~~~~-~~~~~~~~~~~g~~a~~~ll~~~~~~~AI~-------~~nD~~A~  191 (269)
T cd06287         120 QIALIVGSARRNSYLEAEAAYRAFAAEHGMPPVV-LRVDEAGGEEAGYAACAQLLAQHPDLDALC-------VPVDAFAV  191 (269)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCE-EEECCCCCHHHHHHHHHHHHCCCCCCCEEE-------EECHHHHH
T ss_conf             7999968986758999999999999877999847-997688985999999999971799997799-------82799999


Q ss_pred             HHHHHHHHCCCCCCEEEECCC-CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             999999972999879997489-8589999999976995899499899999999985
Q gi|254781049|r  341 GILSAVKEVKINIPLVMRLEG-ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       341 gii~a~~~~~~~~pivvRl~G-tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      |+++|+++.++++|==+.+-| .+...+ + +....+.- ...+.++..++++++.
T Consensus       192 g~l~al~~~Gl~VP~DvsVvgfdD~~~a-~-~~~P~LTt-V~qp~~e~G~~A~~lL  244 (269)
T cd06287         192 GAVRAATELGRAVPDQLRVVTRYDGLRA-R-TSEPPLTA-VDLHLDEVAEQAVDLL  244 (269)
T ss_pred             HHHHHHHHHCCCCCCCCEEEEECCCHHH-H-CCCCCCEE-EEECHHHHHHHHHHHH
T ss_conf             9999999858877987669981592897-3-45888548-9719999999999999


No 84 
>TIGR01142 purT phosphoribosylglycinamide formyltransferase 2; InterPro: IPR005862    The formation of isosinate, a precursor of adenylate and guanylate, from 5-phosphoribosyl 1-pyrophosphate in the de novo purine biosynthesis pathway is basically composed of 10 steps of reactions . Phosphoribosylglycinamide formyltransferase 2 (2.1.2 from EC) is an alternative enzyme to phosphoribosylglycinamide formyltransferase that catalyzes the third step in the de novo purine biosynthesis pathway. ; GO: 0016742 hydroxymethyl- formyl- and related transferase activity, 0009113 purine base biosynthetic process.
Probab=95.58  E-value=0.075  Score=31.86  Aligned_cols=107  Identities=20%  Similarity=0.190  Sum_probs=76.3

Q ss_pred             HHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCC
Q ss_conf             99986898888157479999999998729986999712136876565655677777770799589999999999861876
Q gi|254781049|r   11 LLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGST   90 (398)
Q Consensus        11 lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~   90 (398)
                      ...+.|+|+.++..+++.++.......+|+|+ ++|+-.-+.|+|..              ++++++++..+-+.-.|..
T Consensus       111 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~g~p~-~~~p~~~~~g~g~~--------------~~~~~~~~~~~w~~~~g~~  175 (407)
T TIGR01142       111 AAEELGLPTAPYEFADSLEELREAVEKIGFPC-VVKPVLSSSGKGQS--------------VVRGPEDLEKAWEYAKGHQ  175 (407)
T ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCC-EEHHHHCCCCCCCE--------------EECCHHHHHHHHHHHHCCC
T ss_conf             67763254220011101788999998607750-00122114666530--------------0047345678876650431


Q ss_pred             CCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEE
Q ss_conf             5442122222443301103455565058999998347780489984
Q gi|254781049|r   91 LITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIAS  136 (398)
Q Consensus        91 l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S  136 (398)
                      +   |.+..|. -.++++|+.++...|.-+-....-...+++..++
T Consensus       176 ~---~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  217 (407)
T TIGR01142       176 V---QEGGRGG-AGRVIVEEFIDFDYEITLLTVRAVDGNGPLTTFC  217 (407)
T ss_pred             C---CCCCCCC-CCCEEEEECCCCHHHHHHHEEEECCCCCCEEEEC
T ss_conf             0---1134555-5624552001310211000000027777501101


No 85 
>cd07019 S49_SppA_1 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppAs in this subfamily are found in all three domains of life and are involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-te
Probab=95.21  E-value=0.19  Score=29.29  Aligned_cols=24  Identities=25%  Similarity=0.187  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             988899885999999998999955
Q gi|254781049|r  178 ELQGQARIDGGDLFPNLYKAFCDK  201 (398)
Q Consensus       178 g~~~~~~~~~~~ii~~L~~~f~e~  201 (398)
                      .++++....+...+..+|+.|.+.
T Consensus       142 ~lt~e~r~~~q~~vd~~~~~F~~~  165 (211)
T cd07019         142 ALPPEAQLGLQLSIENGYKRFITL  165 (211)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999


No 86 
>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=95.07  E-value=0.29  Score=27.98  Aligned_cols=105  Identities=16%  Similarity=0.238  Sum_probs=64.7

Q ss_pred             HHHHHHHHCCCCC-CEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             9999999658996-24884278889899999999986-199865899963586132899999999999972999879997
Q gi|254781049|r  281 ATMDIIKLYGGAP-ANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR  358 (398)
Q Consensus       281 atmD~i~~~Gg~p-ANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR  358 (398)
                      ...+.++.+|... -.+.+. +..+.+..+++++-++ .+|.+.+|+       ...|.+|.|+++++++.+.++|==+.
T Consensus       138 g~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~aii-------~~~D~~A~g~~~~l~~~g~~vP~dis  209 (267)
T cd06283         138 GFKEALAEHGIGVNEELIEI-DDEDADELDERLRQLLNKPKKKTAIF-------AANGLILLEVLKALKELGIRIPEDVG  209 (267)
T ss_pred             HHHHHHHHCCCCCCCEEEEE-CCCCHHHHHHHHHHHHHCCCCCCEEC-------CCCCHHHHHHHHHHHHCCCCCCCCCE
T ss_conf             99999997599765148983-35426779999999984799986420-------37709999999999982998898766


Q ss_pred             CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             4898589999999976995899499899999999985
Q gi|254781049|r  359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      .-|-+-..--+.+ ...+.- ...+..+..+++|++.
T Consensus       210 Vvg~dd~~~~~~~-~p~lTt-v~~~~~~~g~~av~~l  244 (267)
T cd06283         210 LIGFDDTEWAELI-GPGITT-IAQPTYEMGKTAAELL  244 (267)
T ss_pred             EEEECCHHHHHHC-CCCCEE-EECCHHHHHHHHHHHH
T ss_conf             8853886999842-999539-9839999999999999


No 87 
>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=95.07  E-value=0.29  Score=27.98  Aligned_cols=104  Identities=22%  Similarity=0.221  Sum_probs=65.2

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHH-HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             9999996589962488427888989999999998-619986589996358613289999999999997299987999748
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKII-TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~i-l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      .+|.+..+++- ---...-|+.+.++-++.++-+ .++|++++||-|        |..|.|.++|+++.+.+.|+++=-.
T Consensus       147 f~~~l~~~p~i-~iv~~~~~~~~~~~a~~~~~~~L~~~pdid~I~~~--------d~~a~Ga~~Al~~aG~~~~~~~g~~  217 (272)
T cd06300         147 AKEVLKEYPGI-KIVGEVYGDWDQAVAQKAVADFLASNPDVDGIWTQ--------GGDAVGAVQAFEQAGRDIPPVTGED  217 (272)
T ss_pred             HHHHHHHCCCE-EEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEC--------CCCHHHHHHHHHHCCCCCCEEEEEC
T ss_conf             99998641424-88655448888899999999999868996099977--------8218999999996699988699975


Q ss_pred             CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             98589999999976995899499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      ++ ......++++.++....+.+-.+-.+.+|+.+
T Consensus       218 ~~-~~~~~~~~~~g~~~a~~~q~p~~~G~~av~~a  251 (272)
T cd06300         218 EN-GFLRWRLWKDKGLKGIAISNPPGQSAAALRAA  251 (272)
T ss_pred             CC-HHHHHHHHCCCCEEEEEECCHHHHHHHHHHHH
T ss_conf             95-78999983489759999708599999999999


No 88 
>pfam06263 consensus
Probab=95.04  E-value=0.3  Score=27.92  Aligned_cols=120  Identities=28%  Similarity=0.379  Sum_probs=94.5

Q ss_pred             CCCEEEEEC-CCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHH-----HHHHHHHHHCCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             881799955-503689999999965899624884278889899-----99999998619986589996358613289999
Q gi|254781049|r  266 DGNIGCMVN-GAGLAMATMDIIKLYGGAPANFLDVGGGADQDK-----VAAAFKIITSDSSVKGILINIFGGIMRCDVLV  339 (398)
Q Consensus       266 dG~Ig~~vn-GaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~-----~~~a~~~il~~~~vk~iliNifGGI~~cd~vA  339 (398)
                      .|+||+++. |-|+- --+=+|..+|+---+-+-+||-.=.+.     +..+++.+..||..++|.+ |  .=--+..|+
T Consensus       191 ~G~IGiVgASGTG~Q-Evt~~Id~~G~GVshaIGtGGRDLs~eVGGisml~al~aL~~Dp~T~vIvl-I--SKPPa~eV~  266 (514)
T pfam06263       191 RGDIGVVGASGTGIQ-EVTVIIDRLGGGISQAIGTGGRDLSAEVGGIMMLDALDALEQDEETKVIVL-I--SKPPAPEVA  266 (514)
T ss_pred             CCCCEEEECCCCCHH-HHHHHHHHHCCCEEEEECCCCCHHHHHHCCHHHHHHHHHHHCCCCCEEEEE-E--CCCCCHHHH
T ss_conf             787117851664467-899999871787322203677402577534689999999855998329999-6--589978999


Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             9999999972999879997489858999999997699589949989999999998506
Q gi|254781049|r  340 KGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       340 ~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      +-|++.++.  ..+|+|+-+-|.+.+.-    .+  -+++++.+++||++++|.++++
T Consensus       267 ~kVl~~~~~--~~KPVV~~FLG~~~~~~----~~--~nv~~a~tL~eAA~~Av~l~~~  316 (514)
T pfam06263       267 EKILELLKA--SGKPVVVLFLGGDPTER----RE--GNVTFATTLEDAAQKAVALSNG  316 (514)
T ss_pred             HHHHHHHHH--CCCCEEEEEECCCCCCC----CC--CCEEECCCHHHHHHHHHHHHCC
T ss_conf             999999984--29988999847998545----66--8825236789999999997168


No 89 
>cd07023 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad 
Probab=94.90  E-value=0.17  Score=29.62  Aligned_cols=24  Identities=25%  Similarity=0.353  Sum_probs=18.5

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             988899885999999998999955
Q gi|254781049|r  178 ELQGQARIDGGDLFPNLYKAFCDK  201 (398)
Q Consensus       178 g~~~~~~~~~~~ii~~L~~~f~e~  201 (398)
                      .++.+..+.+...+..+|+.|.+.
T Consensus       139 ~~s~e~~~~~~~~ld~~~~~F~~~  162 (208)
T cd07023         139 PLTEEERAILQALVDDIYDQFVDV  162 (208)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999999999999999999


No 90 
>COG3919 Predicted ATP-grasp enzyme [General function prediction only]
Probab=94.82  E-value=0.08  Score=31.68  Aligned_cols=94  Identities=17%  Similarity=0.129  Sum_probs=56.5

Q ss_pred             HHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCC----CCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCC
Q ss_conf             9868988881574799999999987299869997121----368765656556777777707995899999999998618
Q gi|254781049|r   13 RKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQI----HAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILG   88 (398)
Q Consensus        13 ~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV----~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg   88 (398)
                      .++|+|+|+...++|..++  .+.++.+|+ .+|+-.    |.=+|.|+             ..+.+.+|.+.+...--+
T Consensus       123 ~elgl~~P~Ty~v~S~~d~--~~~el~FPv-ILKP~mgg~~~~~araKa-------------~~a~d~ee~k~a~~~a~e  186 (415)
T COG3919         123 EELGLPYPKTYLVNSEIDT--LVDELTFPV-ILKPGMGGSVHFEARAKA-------------FTAADNEEMKLALHRAYE  186 (415)
T ss_pred             HHHCCCCCCEEEECCHHHH--HHHHEEEEE-EECCCCCCCCEEEHHHHE-------------EECCCHHHHHHHHHHHHH
T ss_conf             9819997606772314432--123144038-861788875100101001-------------431677999999999887


Q ss_pred             CCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEE--EEEECCCCCEEEEE
Q ss_conf             765442122222443301103455565058999--99834778048998
Q gi|254781049|r   89 STLITKQTGPTGSRVNCVYVEDGADILRELYLS--LLVDRTSGMVAFIA  135 (398)
Q Consensus        89 ~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylg--i~~Dr~~~~~vii~  135 (398)
                                .+ -...+.|+|+++.+-|=-.+  ...|  .+.|+.++
T Consensus       187 ----------ei-gpDnvvvQe~IPGGgE~qfsyaAlw~--~g~pvaef  222 (415)
T COG3919         187 ----------EI-GPDNVVVQEFIPGGGENQFSYAALWD--KGHPVAEF  222 (415)
T ss_pred             ----------HC-CCCCEEEEEECCCCCCCCCHHHHHHH--CCCCHHHH
T ss_conf             ----------43-99725887705799822320988985--79834644


No 91 
>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=94.74  E-value=0.36  Score=27.41  Aligned_cols=85  Identities=12%  Similarity=0.095  Sum_probs=55.8

Q ss_pred             CCCHHHHHH-HHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCC-CEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf             889899999-9999861998658999635861328999999999999729998-79997489858999999997699589
Q gi|254781049|r  302 GADQDKVAA-AFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINI-PLVMRLEGANVDIGNRLIAESGLNVI  379 (398)
Q Consensus       302 ~a~~e~~~~-a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~-pivvRl~Gtn~~~g~~il~~~g~~~~  379 (398)
                      +.+.+..++ +-+++.++|++++||.       ..|.+|.|.++|+++.+.+- ..++=..|+  .++.+.+++-.+...
T Consensus       166 ~~~~~~~~~~~~~~L~~~p~i~ai~~-------~~d~~a~Ga~~a~~~~G~~~~i~vvg~D~~--~~~~~~i~~G~~~~t  236 (277)
T cd06319         166 DFSYQETFDYTNDLLTANPDIRAIWL-------QGSDRYQGALDAIATAGKTGKVLLICFDAE--PEFIELLKSGALVGA  236 (277)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEECCCC--HHHHHHHHCCCCEEE
T ss_conf             99999999999999973899768996-------698899999999997599998589963797--999999875993699


Q ss_pred             EECCHHHHHHHHHHHH
Q ss_conf             9499899999999985
Q gi|254781049|r  380 TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       380 ~~~~~~~A~~~~v~~~  395 (398)
                      ...+..+-..++++.+
T Consensus       237 v~q~p~~~G~~av~~~  252 (277)
T cd06319         237 GMQQPFLMGERAVETV  252 (277)
T ss_pred             EECCHHHHHHHHHHHH
T ss_conf             9649999999999999


No 92 
>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=94.55  E-value=0.4  Score=27.13  Aligned_cols=86  Identities=15%  Similarity=0.151  Sum_probs=60.7

Q ss_pred             CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf             8889899999999-986199865899963586132899999999999972999-87999748985899999999769958
Q gi|254781049|r  301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNV  378 (398)
Q Consensus       301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~  378 (398)
                      |..+.+.-+++++ ++.++|++++||-       .-|.+|.|.++|+++.+.. ...|+=..|+  .++++.+++-.+..
T Consensus       170 ~~~~~~~a~~~~~~~L~~~p~i~~i~~-------~nD~~a~Ga~~Al~~~G~~~~v~vvG~D~~--~~~~~~i~~g~~~~  240 (282)
T cd06318         170 GDWTREGGLKAMEDLLVAHPDINVVYS-------ENDDMALGAMRVLAEAGKTDDVKVAAADGQ--KEALALIKGGKYGA  240 (282)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCCEE
T ss_conf             897799999999999975899709998-------896799999999996699998299998988--99999998399649


Q ss_pred             EEECCHHHHHHHHHHHH
Q ss_conf             99499899999999985
Q gi|254781049|r  379 ITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       379 ~~~~~~~~A~~~~v~~~  395 (398)
                      ....+.....+.+|+++
T Consensus       241 tv~q~p~~~G~~av~~~  257 (282)
T cd06318         241 TALNDPDLVARTAVEVA  257 (282)
T ss_pred             EEECCHHHHHHHHHHHH
T ss_conf             99349999999999999


No 93 
>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=94.48  E-value=0.41  Score=27.03  Aligned_cols=105  Identities=14%  Similarity=0.106  Sum_probs=64.0

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf             99999965899624884278889899999999986199865899963586132899999999999972999879997489
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG  361 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G  361 (398)
                      ..+.+..+|.++-+-.-.-+..+.+.-+++++-+++++++.+|+.       ..|.+|.|+++++++.+.++|==+.+-|
T Consensus       139 f~~a~~~~g~~~~~~~i~~~~~~~~~~~~~~~~l~~~~~~~ai~~-------~nD~~A~g~l~~l~~~g~~vP~disvig  211 (268)
T cd06298         139 YKEALSEANIEFDESLIFEGDYTYESGYELAEELLEDGKPTAAFV-------TDDELAIGILNAAQDAGLKVPEDFEIIG  211 (268)
T ss_pred             HHHHHHHCCCCCCHHHEECCCHHHHHHHHHHHHHHHCCCCCEEEE-------CCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             999999849997601200354037789999999983699978996-------6879999999999974999998749999


Q ss_pred             CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             8589999999976995899499899999999985
Q gi|254781049|r  362 ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       362 tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      -.-..--+ +-...+.. ...+..+..+.|+++.
T Consensus       212 fDd~~~a~-~~~P~LTt-v~~~~~~~G~~A~~~l  243 (268)
T cd06298         212 FNNTKLAS-MVRPQLTS-VTQPLYDIGAVAMRLL  243 (268)
T ss_pred             ECCHHHHH-CCCCCCEE-EECCHHHHHHHHHHHH
T ss_conf             78818997-14899769-9729999999999999


No 94 
>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=94.27  E-value=0.45  Score=26.73  Aligned_cols=104  Identities=15%  Similarity=0.095  Sum_probs=64.5

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf             9999965899624884278889899999999986-199865899963586132899999999999972999879997489
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG  361 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G  361 (398)
                      ++.++.+|..+-...-..+..+.+..+++++-++ ..+++.+|+       ...|.+|.|+++++++.+.++|==+.+-|
T Consensus       138 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~~~~l~~~g~~vP~di~vig  210 (267)
T cd06284         138 RQALAEAGLPADEELIQEGDFSLESGYAAARRLLALPDRPTAIF-------CFSDEMAIGAISALKELGLRVPEDISVVG  210 (267)
T ss_pred             HHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCEEEEEE
T ss_conf             99999839985512773278767778899999996599998026-------57868899999999983999996279998


Q ss_pred             CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             8589999999976995899499899999999985
Q gi|254781049|r  362 ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       362 tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      -+-..--+++ ...+.. ...+..+..++|+++.
T Consensus       211 fd~~~~~~~~-~p~ltt-v~~~~~~~g~~a~~~l  242 (267)
T cd06284         211 FDDIDFARMT-TPPLTT-IRQPRYEIGRTAAELL  242 (267)
T ss_pred             ECCHHHHHHC-CCCCEE-EEECHHHHHHHHHHHH
T ss_conf             7784899824-898339-9859999999999999


No 95 
>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=94.23  E-value=0.46  Score=26.68  Aligned_cols=90  Identities=20%  Similarity=0.188  Sum_probs=59.9

Q ss_pred             ECCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCC
Q ss_conf             4278889899999999-986199865899963586132899999999999972999879997489858999999997699
Q gi|254781049|r  298 DVGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGL  376 (398)
Q Consensus       298 D~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~  376 (398)
                      ...|..+.+.-+++++ ++.++|++++||-       .-|.+|.|.++|+++.+.+.+.++-..|...-. ..+....+.
T Consensus       158 ~~~~~~~~~~~~~~~~~ll~~~p~~~aifa-------~nD~~A~Ga~~a~~~~G~~~i~ivg~dg~~~~~-~~~~~~~~~  229 (271)
T cd06321         158 DQNGKGSRDGGLRVMQGLLTRFPKLDGVFA-------INDPTAIGADLAAKQAGRNDIKITSVDGAPDAE-KAILSGNSL  229 (271)
T ss_pred             EECCCCCHHHHHHHHHHHHHCCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCHHHH-HHHHCCCCC
T ss_conf             722887899999999999850886778997-------786899999999997597999899996967999-998669997


Q ss_pred             C-EEEECCHHHHHHHHHHHH
Q ss_conf             5-899499899999999985
Q gi|254781049|r  377 N-VITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       377 ~-~~~~~~~~~A~~~~v~~~  395 (398)
                      - -....+..+..+++++++
T Consensus       230 ~~~tv~Q~~~~mG~~av~~l  249 (271)
T cd06321         230 IIATAAQDPRAMARKAVEIG  249 (271)
T ss_pred             CEEEEECCHHHHHHHHHHHH
T ss_conf             27998489999999999999


No 96 
>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=94.11  E-value=0.49  Score=26.51  Aligned_cols=103  Identities=17%  Similarity=0.105  Sum_probs=62.0

Q ss_pred             HHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCC
Q ss_conf             999965899624884278889899999999986-1998658999635861328999999999999729998799974898
Q gi|254781049|r  284 DIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGA  362 (398)
Q Consensus       284 D~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gt  362 (398)
                      +.+..+|-+.....-+.+..+.+..+++++-++ +++.+.+||       ...|.+|.|+++++++.+.++|==+.+-|-
T Consensus       138 ~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~~~~l~~~g~~iP~di~iigf  210 (265)
T cd06285         138 AALAEAGIEVPPERIVYSGFDIEGGEAAAEKLLRSDSPPTAIF-------AVNDFAAIGVMGAARDRGLRVPDDVALVGY  210 (265)
T ss_pred             HHHHHCCCCCCHHHEECCCCCHHHHHHHHHHHHHCCCCCCCEE-------CCCHHHHHHHHHHHHHCCCCCCCCEEEEEE
T ss_conf             9999869998756601366215569999999985699988100-------378899999999999859999998799998


Q ss_pred             CHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             589999999976995899499899999999985
Q gi|254781049|r  363 NVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       363 n~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      +--.-.+.+. ..+.. ...+..+-+++|+++.
T Consensus       211 d~~~~~~~~~-p~LTt-i~q~~~~ig~~A~~~l  241 (265)
T cd06285         211 NDIPLVARLP-VPLTT-VRSPFHQIGRTALRLL  241 (265)
T ss_pred             CCHHHHHHCC-CCCEE-EECCHHHHHHHHHHHH
T ss_conf             7828997078-99579-9729999999999999


No 97 
>PRK06091 membrane protein FdrA; Validated
Probab=94.10  E-value=0.49  Score=26.50  Aligned_cols=121  Identities=21%  Similarity=0.257  Sum_probs=93.8

Q ss_pred             CCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHH-----HHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHH
Q ss_conf             881799955503689999999965899624884278889899-----999999986199865899963586132899999
Q gi|254781049|r  266 DGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDK-----VAAAFKIITSDSSVKGILINIFGGIMRCDVLVK  340 (398)
Q Consensus       266 dG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~-----~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~  340 (398)
                      .|+||+++.-+--.=--+=+|..+|+---+-+-+||-.=.+.     +..+++.+..||..++|.+ |  .=--+..|++
T Consensus       193 ~G~IGIVgASGTG~QEvs~~Id~~G~GVshaIGtGGRDLs~eVGGis~l~al~aL~~Dp~T~vIvl-I--SKPPa~eV~~  269 (555)
T PRK06091        193 EGNIGVIGASGTGIQELCSQIALAGEGITHAIGLGGRDLSREVGGISALTALEMLSADEKSEVLAF-V--SKPPAEAVRL  269 (555)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHCCCEEEEECCCCCHHHHHHCCHHHHHHHHHHHCCCCCEEEEE-E--CCCCCHHHHH
T ss_conf             887127951665466899999871787322203777402567533789999999855998329999-6--5899789999


Q ss_pred             HHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             999999972999879997489858999999997699589949989999999998506
Q gi|254781049|r  341 GILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       341 gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      -|++.++.  ..+|+|+-+-|.+.+..    .+  -+++++.+++||++++|.+++.
T Consensus       270 kVl~~~~~--~~KPVV~~FLG~~p~~~----~e--~~~~~a~tL~eaA~~Av~l~~~  318 (555)
T PRK06091        270 KIINAMKA--TGKPVVALFLGYTPAVA----RE--ENVWFASTLDEAARLACLLSRV  318 (555)
T ss_pred             HHHHHHHH--CCCCEEEEEECCCCCCC----CC--CCEEHHHHHHHHHHHHHHHCCC
T ss_conf             99999984--29988999727997656----76--7641244299999998744055


No 98 
>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=93.75  E-value=0.57  Score=26.09  Aligned_cols=105  Identities=14%  Similarity=0.147  Sum_probs=69.0

Q ss_pred             HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             99999996589962488427888989999999998619986589996358613289999999999997299987999748
Q gi|254781049|r  281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      ...+.++.+|..+-...-..+..+.+.-+++++-+++.+ ..+||       +..|.+|.|+++++++.+.++|==+.+-
T Consensus       143 G~~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~l~~~-~~ai~-------~~nD~~A~g~~~~l~~~g~~ip~di~Vi  214 (273)
T cd06292         143 GFRAALEEAGLEPPEALVARGMFSVEGGQAAAVELLGSG-PTAIV-------AASDLMALGAIRAARRRGLRVPEDVSVV  214 (273)
T ss_pred             HHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCC-CCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             999999984999771489716777788999999997479-96577-------4585999999999998399899965999


Q ss_pred             CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             98589999999976995899499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      |-+-..-.+++ ...+. ....+.++..++|+++.
T Consensus       215 gfD~~~~~~~~-~p~LT-tI~q~~~~~g~~a~~~l  247 (273)
T cd06292         215 GYDDSALMAFT-DPPLT-TVRQPVEEMAAAAVDRL  247 (273)
T ss_pred             EECCHHHHHHC-CCCCE-EEECCHHHHHHHHHHHH
T ss_conf             99985899815-89967-99959999999999999


No 99 
>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=93.64  E-value=0.59  Score=25.96  Aligned_cols=103  Identities=15%  Similarity=0.229  Sum_probs=64.7

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHH-HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             9999996589962488427888989999999998-619986589996358613289999999999997299987999748
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKII-TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~i-l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      ..+.++.+|.++. ...+.+..+.+..+++++-+ .+.|++.+||       ...|.+|-|+++++++.+.++|==+.+-
T Consensus       135 f~~al~~~g~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ai~-------~~nD~~A~g~~~al~~~g~~vP~disvi  206 (265)
T cd06291         135 FLDVLKENGLEVR-IIEIQENFDDAEKKEEIKELLEEYPDIDGIF-------ASNDLTAILVLKEAQQRGIRVPEDLQII  206 (265)
T ss_pred             HHHHHHHCCCCCE-EEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------CCCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             9999997699960-8997688986999999999985599988432-------1668999999999998199999986999


Q ss_pred             CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             9858999999997699589-9499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      |-+-.   .+.+...-++. ...+..+..++|+++.
T Consensus       207 gfDd~---~~~~~~~p~LTtv~~~~~~~g~~A~~~L  239 (265)
T cd06291         207 GYDGT---KLTRLYTPELTTIRQPIEEIAKTAVDLL  239 (265)
T ss_pred             EECCH---HHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             98880---9998439995599739999999999999


No 100
>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=93.57  E-value=0.61  Score=25.88  Aligned_cols=86  Identities=10%  Similarity=0.089  Sum_probs=64.4

Q ss_pred             CCCCHHHHHHHHHH-HHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf             88898999999999-86199865899963586132899999999999972999879997489858999999997699589
Q gi|254781049|r  301 GGADQDKVAAAFKI-ITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI  379 (398)
Q Consensus       301 G~a~~e~~~~a~~~-il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~  379 (398)
                      ++.+.++..+.++- +.++|++++||       ...|.+|.|.++|+++.+.+.-+|+-..|+.+  +++.+++-.+...
T Consensus       163 ~~~~~~~a~~~~~~~L~~~pdid~I~-------~~nD~~a~Ga~~Al~~aG~~~v~v~g~Dg~~~--~l~~I~~G~~~at  233 (272)
T cd06313         163 ANWDVSKAARIWETWLTKYPQLDGAF-------CHNDSMALAAYQIMKAAGRTKIVIGGVDGDPP--AIQAVSDGRMVAT  233 (272)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCEEEEECCCHH--HHHHHHCCCCEEE
T ss_conf             68768999999999996499987899-------88847789999999976999868999789999--9999985991899


Q ss_pred             EECCHHHHHHHHHHHH
Q ss_conf             9499899999999985
Q gi|254781049|r  380 TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       380 ~~~~~~~A~~~~v~~~  395 (398)
                      ...+..+-.+.+|+.+
T Consensus       234 v~q~~~~~G~~av~~a  249 (272)
T cd06313         234 VRNPACRIHGGAIAAG  249 (272)
T ss_pred             EECCHHHHHHHHHHHH
T ss_conf             8069999999999999


No 101
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=93.42  E-value=0.64  Score=25.73  Aligned_cols=106  Identities=18%  Similarity=0.179  Sum_probs=69.8

Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             9999999965899624884278889899999999986-199865899963586132899999999999972999879997
Q gi|254781049|r  280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR  358 (398)
Q Consensus       280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR  358 (398)
                      ....+.+..+|..+..-+=.-+..+.+.-++++.-++ .++.+.+||       ...|.+|-|+++++++.++++|==+.
T Consensus       196 ~G~~~al~~~gl~~~~~~v~~~~~~~~~~~~~~~~ll~~~~~~tAi~-------~~nD~~A~g~l~al~~~Gl~VP~Dis  268 (346)
T PRK10401        196 AGWLSALKEQGIIPPESWIGTGTPDMQGGEAAMVELLGRNLQLTAVF-------AYNDNMAAGALTALKDNGIAIPLHLS  268 (346)
T ss_pred             HHHHHHHHHCCCCCCHHEEEECCCCHHHHHHHHHHHHHCCCCCCCCE-------ECCHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             99999999849998701487268757889999999981599988614-------44889999999999985998998728


Q ss_pred             CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHH
Q ss_conf             489858999999997699589949989999999998
Q gi|254781049|r  359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHA  394 (398)
Q Consensus       359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~  394 (398)
                      +-|-+-.. .--+-...|.-+ ..+.++..+.|+++
T Consensus       269 ViGfDd~~-~a~~~~P~LTTV-~~p~~~mg~~Av~l  302 (346)
T PRK10401        269 IIGFDDIP-IARYTDPQLTTV-RYPIASMAKLATEL  302 (346)
T ss_pred             EEEECCHH-HHHCCCCCCCEE-ECCHHHHHHHHHHH
T ss_conf             99989808-985289998769-60999999999999


No 102
>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=93.39  E-value=0.65  Score=25.69  Aligned_cols=89  Identities=12%  Similarity=0.134  Sum_probs=65.3

Q ss_pred             CCCCCCHHHHHHHHHHHH-CCC-CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC------CCEEEECCCCCHHHHHHH
Q ss_conf             278889899999999986-199-865899963586132899999999999972999------879997489858999999
Q gi|254781049|r  299 VGGGADQDKVAAAFKIIT-SDS-SVKGILINIFGGIMRCDVLVKGILSAVKEVKIN------IPLVMRLEGANVDIGNRL  370 (398)
Q Consensus       299 ~gG~a~~e~~~~a~~~il-~~~-~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~------~pivvRl~Gtn~~~g~~i  370 (398)
                      .-+..+.+.-++.++-+| +.| ++++||       ...|.+|.|.++|+++.+.+      ...|+-..|+.  ++++.
T Consensus       178 ~~~~w~~~~a~~~~e~~L~~~~d~id~I~-------a~ND~mAlGA~~Al~~aG~~~~~~~~~I~VvG~Dg~~--~~l~a  248 (303)
T cd01539         178 DTANWDRAQAKDKMDALLLKYGDKIEAVI-------ANNDAMALGAIEALQKYGYNKGDKSKNIPVVGVDALP--EALEL  248 (303)
T ss_pred             EECCCCHHHHHHHHHHHHHHCCCCEEEEE-------ECCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCH--HHHHH
T ss_conf             71687889999999999985899735999-------7894779999999997598766678886799867999--99999


Q ss_pred             HHHCCCCEEEECCHHHHHHHHHHHHH
Q ss_conf             99769958994998999999999850
Q gi|254781049|r  371 IAESGLNVITAIDLDDAAQKIVHAVK  396 (398)
Q Consensus       371 l~~~g~~~~~~~~~~~A~~~~v~~~k  396 (398)
                      +++-.+......+..+-.+.+|+++.
T Consensus       249 I~~G~~~aTv~Q~p~~~g~~av~~a~  274 (303)
T cd01539         249 IKKGSMTGTVLNDPKGQAEAIYNLGM  274 (303)
T ss_pred             HHCCCCEEEEECCHHHHHHHHHHHHH
T ss_conf             98399889995699999999999999


No 103
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type; InterPro: IPR004635   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. This group of sequences represent both long and short forms of the bacterial SppA and homologs found in the archaea and plants.   Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signaling function.  During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . ; GO: 0008233 peptidase activity, 0006508 proteolysis.
Probab=93.27  E-value=0.39  Score=27.16  Aligned_cols=22  Identities=23%  Similarity=0.255  Sum_probs=13.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8889988599999999899995
Q gi|254781049|r  179 LQGQARIDGGDLFPNLYKAFCD  200 (398)
Q Consensus       179 ~~~~~~~~~~~ii~~L~~~f~e  200 (398)
                      +.++...-+..+|..-|+.|++
T Consensus       150 lt~eE~~~lQ~~v~~~Y~~F~~  171 (224)
T TIGR00706       150 LTPEERKILQSLVNESYEQFVQ  171 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6299999999988888757899


No 104
>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=93.17  E-value=0.71  Score=25.47  Aligned_cols=88  Identities=15%  Similarity=0.200  Sum_probs=60.8

Q ss_pred             CCCCCCHHHHHHHHHHHH-C-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCC
Q ss_conf             278889899999999986-1-99865899963586132899999999999972999-87999748985899999999769
Q gi|254781049|r  299 VGGGADQDKVAAAFKIIT-S-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESG  375 (398)
Q Consensus       299 ~gG~a~~e~~~~a~~~il-~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g  375 (398)
                      .-++.+.+..++.++-+| + .+.+++||       ...|.+|.|.++|+++.+.+ ...|+=..|+  .++.+.+++-.
T Consensus       164 ~~~~~~~~~a~~~~~~lL~~~~~~i~~I~-------~~nd~~a~Ga~~Al~~~G~~~~v~vvg~d~~--~~~~~~i~~G~  234 (275)
T cd06317         164 QPADWDREKAQVAMEALITKFGDDIDGVY-------AGDDNMARGALNAAKEAGLAGGIVIVGANNF--AVGYEAIRAGK  234 (275)
T ss_pred             EECCCCHHHHHHHHHHHHHHCCCCCCEEE-------CCCCHHHHHHHHHHHHCCCCCCCEEEEECCC--HHHHHHHHCCC
T ss_conf             74147789999999999873457533440-------5895789999999997499899879987980--99999998599


Q ss_pred             CCEEEECCHHHHHHHHHHHH
Q ss_conf             95899499899999999985
Q gi|254781049|r  376 LNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       376 ~~~~~~~~~~~A~~~~v~~~  395 (398)
                      +......+.......+++++
T Consensus       235 ~~~tv~q~p~~~G~~av~~~  254 (275)
T cd06317         235 YYGTIYQSPVDDGEAALQTA  254 (275)
T ss_pred             CEEEEECCHHHHHHHHHHHH
T ss_conf             83999259999999999999


No 105
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=93.15  E-value=0.71  Score=25.45  Aligned_cols=87  Identities=8%  Similarity=0.095  Sum_probs=64.2

Q ss_pred             CCCCCHHHHHHHHHH-HHCCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCC
Q ss_conf             788898999999999-861998-65899963586132899999999999972999-879997489858999999997699
Q gi|254781049|r  300 GGGADQDKVAAAFKI-ITSDSS-VKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGL  376 (398)
Q Consensus       300 gG~a~~e~~~~a~~~-il~~~~-vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~  376 (398)
                      .++.++++-.+.++- +.++|+ +++||       ..-|.+|.|.++|+++.+.. ...|+=..|+.  ++.+.+++-.+
T Consensus       189 ~~~w~~~~A~~~me~~L~a~~~~id~V~-------a~ND~mAlGA~~Al~~aG~~~~v~V~G~Dg~~--~al~~I~~G~~  259 (330)
T PRK10355        189 VDGWLPENALKIMENALTANNNKIDAVV-------ASNDATAGGAIQALSAQGLSGKVAISGQDADL--AAIKRIVAGTQ  259 (330)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEEE-------ECCCCHHHHHHHHHHHCCCCCCCEEECCCCCH--HHHHHHHCCCE
T ss_conf             5642288999999999960998516999-------89971489999999966999997699027998--99999974962


Q ss_pred             CEEEECCHHHHHHHHHHHH
Q ss_conf             5899499899999999985
Q gi|254781049|r  377 NVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       377 ~~~~~~~~~~A~~~~v~~~  395 (398)
                      ....+.+..+-++.+++++
T Consensus       260 ~~Tv~q~~~~~g~~ave~a  278 (330)
T PRK10355        260 TMTVYKPITKLANTAAEIA  278 (330)
T ss_pred             EEEEECCHHHHHHHHHHHH
T ss_conf             8998379999999999999


No 106
>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=93.13  E-value=0.71  Score=25.44  Aligned_cols=91  Identities=12%  Similarity=0.150  Sum_probs=61.3

Q ss_pred             CCCCCHHHHHHHHHHH-HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCC-HHHHHHHHHHCCC
Q ss_conf             7888989999999998-6199865899963586132899999999999972999-87999748985-8999999997699
Q gi|254781049|r  300 GGGADQDKVAAAFKII-TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGAN-VDIGNRLIAESGL  376 (398)
Q Consensus       300 gG~a~~e~~~~a~~~i-l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn-~~~g~~il~~~g~  376 (398)
                      -|..+.+..+++++-+ .++|.+++||       ..-|.+|.|.++|+++.+.. .-.|+-..|+. ..++.+.+++--+
T Consensus       161 ~~~~~~~~a~~~~~~~L~~~pdi~aI~-------a~nD~~A~Ga~~Al~~aG~~~~i~vvg~D~~~~~~~~l~~i~~g~~  233 (270)
T cd06308         161 DGDWLKEKAEEKMEELLQANPDIDLVY-------AHNDPMALGAYLAAKRAGREKEIKFIGIDGLPGPGGGIEAVRDGEL  233 (270)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHCCCC
T ss_conf             176679999999999985088888899-------7786589999999997699999589988899336999999873861


Q ss_pred             CEEEE-CCH-HHHHHHHHHHHHC
Q ss_conf             58994-998-9999999998506
Q gi|254781049|r  377 NVITA-IDL-DDAAQKIVHAVKG  397 (398)
Q Consensus       377 ~~~~~-~~~-~~A~~~~v~~~k~  397 (398)
                      ..... ..+ ..|++.++.+.+|
T Consensus       234 ~~t~~~p~~G~~av~~a~~~l~G  256 (270)
T cd06308         234 DATFLYPTGGKEAIEVAMKILNG  256 (270)
T ss_pred             EEEEECHHHHHHHHHHHHHHHCC
T ss_conf             69998837899999999999777


No 107
>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=92.91  E-value=0.77  Score=25.23  Aligned_cols=104  Identities=18%  Similarity=0.214  Sum_probs=61.6

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf             9999965899624884278889899999999986-199865899963586132899999999999972999879997489
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG  361 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G  361 (398)
                      .+.+..+|.++..-.-+-+..+.+.-+++++-++ +.|++.+||       +.-|.+|-|+++++++.+.++|==+.+-|
T Consensus       139 ~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~~~~~ai~-------~~nD~~A~g~~~~l~~~g~~vP~disvig  211 (268)
T cd06270         139 RDALAEAGIALDESLIIEGDFTEEGGYAAMQELLARGAPFTAVF-------CANDEMAAGAISALREHGISVPQDVSIIG  211 (268)
T ss_pred             HHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             99999859997800476167767889998899995699987455-------33779999999999982999999769999


Q ss_pred             CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             8589999999976995899499899999999985
Q gi|254781049|r  362 ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       362 tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      -+-..--+++ ...+.. ...+.++..++|+++.
T Consensus       212 fdd~~~~~~~-~P~LTt-i~~~~~~~g~~A~~~L  243 (268)
T cd06270         212 FDDVLLARYL-YPKLTT-VHYPIEEMAQMAAKLA  243 (268)
T ss_pred             ECCHHHHHHC-CCCCEE-EECCHHHHHHHHHHHH
T ss_conf             8986899714-899549-9649999999999999


No 108
>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=92.78  E-value=0.8  Score=25.11  Aligned_cols=102  Identities=14%  Similarity=0.173  Sum_probs=61.7

Q ss_pred             HHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCC
Q ss_conf             999658996248842788898999999999861-9986589996358613289999999999997299987999748985
Q gi|254781049|r  285 IIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGAN  363 (398)
Q Consensus       285 ~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn  363 (398)
                      .+..+|...-...-..+..+.+.-+++++-++. .++..+||       +..|.+|.|+++++++.+.++|==+.+-|-.
T Consensus       142 al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nd~~A~g~i~~l~~~g~~iP~disvigfd  214 (268)
T cd06273         142 ALAEAGLELPELWQVEAPYSIADGRAALRQLLEQPPRPTAVI-------CGNDVLALGALYEARRLGLSVPEDLSIVGFD  214 (268)
T ss_pred             HHHHHCCCCCHHHEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEEEC
T ss_conf             999809998714203157898999999999984799984899-------7787999999999996399999967999999


Q ss_pred             HHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             89999999976995899499899999999985
Q gi|254781049|r  364 VDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       364 ~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      -..-.+++. ..+.. ...+.++..++|+++.
T Consensus       215 ~~~~~~~~~-p~lTt-i~~~~~~~g~~a~~~L  244 (268)
T cd06273         215 DIDGSAELE-PALTT-VRVPAREIGRIAAEAL  244 (268)
T ss_pred             CHHHHHHHC-CCCEE-EEECHHHHHHHHHHHH
T ss_conf             828898418-99479-9919999999999999


No 109
>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=92.76  E-value=0.8  Score=25.10  Aligned_cols=87  Identities=13%  Similarity=0.115  Sum_probs=56.9

Q ss_pred             CCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             2788898999999999861-998658999635861328999999999999729998799974898589999999976995
Q gi|254781049|r  299 VGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLN  377 (398)
Q Consensus       299 ~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~  377 (398)
                      +-+..+.+.-+.+++-++. +|.+.+|+       +..|.+|-|+++|+++.+.++|==+.+-|.+-.   .+..-..-+
T Consensus       156 ~~~~~~~~~~~~~~~~~l~~~~~~~aii-------~~~D~~A~g~l~~l~~~gi~vp~disiigfd~~---~~~~~~~p~  225 (268)
T cd06289         156 VEGPPSRQGGAEAVAQLLDLPPRPTAIV-------CFNDLVAFGAMSGLRRAGLTPGRDIAVVGFDDV---AEAALATPA  225 (268)
T ss_pred             ECCCCCHHHHHHHHHHHHHCCCCCCEEC-------CCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCH---HHHHHCCCC
T ss_conf             3168865569999999984699986203-------576899999999999849999985499995787---899722897


Q ss_pred             EE-EECCHHHHHHHHHHHH
Q ss_conf             89-9499899999999985
Q gi|254781049|r  378 VI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       378 ~~-~~~~~~~A~~~~v~~~  395 (398)
                      +. ...+..+..++|+++.
T Consensus       226 ltti~~~~~~~g~~a~~~l  244 (268)
T cd06289         226 LTTVSTDPREIGRRAAELL  244 (268)
T ss_pred             EEEEEECHHHHHHHHHHHH
T ss_conf             1699849999999999999


No 110
>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=92.54  E-value=0.86  Score=24.91  Aligned_cols=103  Identities=21%  Similarity=0.303  Sum_probs=68.9

Q ss_pred             HHHHHCCCCC-----------CEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999658996-----------24884278889899999999986199865899963586132899999999999972999
Q gi|254781049|r  284 DIIKLYGGAP-----------ANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN  352 (398)
Q Consensus       284 D~i~~~Gg~p-----------ANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~  352 (398)
                      +.++.|-|-|           -.|.|=+=+++.+.+..|++-+ .  + +.+|  |.||..+-.+... +.+.+++.   
T Consensus       299 ~aL~~F~Gl~hR~E~v~~~~GV~~iNDSKaTn~~at~~Al~~~-~--~-~i~l--I~GG~~Kg~d~~~-l~~~~~~~---  368 (445)
T PRK04308        299 EHVKTFQGLPHRVEKIGEKNGVVFIDDSKGTNVGATAAAIAGL-Q--N-PLFV--ILGGMGKGQDFTP-LRDALAGK---  368 (445)
T ss_pred             HHHHHCCCCCCCEEEEEEECCEEEEECCCCCCHHHHHHHHHHC-C--C-CEEE--EECCCCCCCCHHH-HHHHHHHH---
T ss_conf             9987579999862899864898898079888889999999827-7--9-7799--9767667778699-99998752---


Q ss_pred             CCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             879997489858999999997699589949989999999998506
Q gi|254781049|r  353 IPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       353 ~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      +. -+-+-|.+.+.=.+.|+.+++++..+++|++|+++|.++++.
T Consensus       369 ~~-~v~~~G~~~~~i~~~l~~~~~~~~~~~~l~~Av~~a~~~a~~  412 (445)
T PRK04308        369 AK-GVFLIGVDAPQIRRDLDGCGLNLTDCATLEEAVQTAYAQAEA  412 (445)
T ss_pred             CE-EEEEECCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHCCC
T ss_conf             56-999989799999998863798558768799999999974889


No 111
>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=92.49  E-value=0.87  Score=24.87  Aligned_cols=85  Identities=14%  Similarity=0.119  Sum_probs=55.8

Q ss_pred             CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf             8889899999999-98619986589996358613289999999999997299987-999748985899999999769958
Q gi|254781049|r  301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGLNV  378 (398)
Q Consensus       301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~~~  378 (398)
                      +..+.+..++.++ ++.++|++++||.       .+|.+|.|.++|+++.+.+-. .|+=..++  .+..+.+++--+..
T Consensus       163 ~~~~~~~~~~~~~~~L~~~pdi~ai~~-------~nd~~a~ga~~al~~~g~~~~i~vvg~D~~--~~~~~~i~~G~i~~  233 (273)
T cd06310         163 SDSDYAKALDITEDLLTANPDLKGIFG-------ANEGSAVGAARAVRQAGKAGKVKVVGFDAS--PEQIDALREGVIQA  233 (273)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCCEE
T ss_conf             652489999999999975898757984-------384899999999997799999399998986--99999998599859


Q ss_pred             EEECCHHHHHHHHHHH
Q ss_conf             9949989999999998
Q gi|254781049|r  379 ITAIDLDDAAQKIVHA  394 (398)
Q Consensus       379 ~~~~~~~~A~~~~v~~  394 (398)
                      ....+-.+-...+|++
T Consensus       234 tv~q~p~~~G~~av~~  249 (273)
T cd06310         234 LVVQNPYKMGYLGVKT  249 (273)
T ss_pred             EECCCHHHHHHHHHHH
T ss_conf             9818999999999999


No 112
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=92.27  E-value=0.92  Score=24.69  Aligned_cols=105  Identities=11%  Similarity=0.114  Sum_probs=69.6

Q ss_pred             HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             9999999658996248842788898999999999861-998658999635861328999999999999729998799974
Q gi|254781049|r  281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL  359 (398)
Q Consensus       281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl  359 (398)
                      ...+.+..+|.....-..+-+..+.+.-+++++-+++ .+.+.+||       ...|.+|.|+++|+++.++++|==+.+
T Consensus       195 gf~~al~~~gl~~~~~~~~~~~~~~~~g~~~~~~ll~~~~~ptAi~-------~~nD~~A~g~~~al~~~g~~iP~Disv  267 (327)
T PRK10423        195 GYRAAMKRAGLNIPDGYEVTGDFEFNGGFDAMQQLLAHPLRPQAVF-------TGNDAMAVGVYQALYQAGLQVPQDIAV  267 (327)
T ss_pred             HHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEE
T ss_conf             9999999859998843699604673789999999984799998455-------178099999999999869999997599


Q ss_pred             CCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             89858999999997699589-9499899999999985
Q gi|254781049|r  360 EGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       360 ~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      -|-+-.   .+.+-..-++. ...+.++..+.|+++.
T Consensus       268 igfDd~---~~~~~~~P~LTTv~~~~~~~g~~A~~~L  301 (327)
T PRK10423        268 IGYDDI---ELASYMTPPLTTIHQPKDELGELAIDVL  301 (327)
T ss_pred             EEECCC---HHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             997582---8998269993799839999999999999


No 113
>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=92.26  E-value=0.93  Score=24.68  Aligned_cols=90  Identities=16%  Similarity=0.220  Sum_probs=58.3

Q ss_pred             CCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCC-
Q ss_conf             278889899999999-986199865899963586132899999999999972999-87999748985899999999769-
Q gi|254781049|r  299 VGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESG-  375 (398)
Q Consensus       299 ~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g-  375 (398)
                      .-|+.+.+.-.+.++ +|.++|++++||       ...|.+|.|.++|+++.+.+ .++++=..|+.  ++.+.+++-. 
T Consensus       163 ~~~~~~~~~a~~~~~~~L~~~pdi~~If-------a~nD~ma~Ga~~Al~~aG~~~~~~vvG~Dg~~--~~~~~i~~G~~  233 (274)
T cd06311         163 QYANWNRDDAFSVMQDLLTKFPKIDAVW-------AHDDDMAVGVLAAIKQAGRTDIKFVVGGAGSK--DMIKMIMDGDP  233 (274)
T ss_pred             ECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCCCHHHHHHHHHHHCCCCCCCEEEEECCCH--HHHHHHHCCCC
T ss_conf             0387568999999999984388888899-------88980589999999976999997899965998--99999976997


Q ss_pred             -CCEEEECC---HHHHHHHHHHHHHC
Q ss_conf             -95899499---89999999998506
Q gi|254781049|r  376 -LNVITAID---LDDAAQKIVHAVKG  397 (398)
Q Consensus       376 -~~~~~~~~---~~~A~~~~v~~~k~  397 (398)
                       +......+   .-.|++.++.+.+|
T Consensus       234 ~~~atv~~~p~~~~~Av~~a~~~l~G  259 (274)
T cd06311         234 LIPADVLYPPSMIASAIDLTVALFQG  259 (274)
T ss_pred             EEEEEEECCHHHHHHHHHHHHHHHCC
T ss_conf             48999808999999999999999779


No 114
>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=92.25  E-value=0.93  Score=24.68  Aligned_cols=99  Identities=20%  Similarity=0.257  Sum_probs=60.2

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHH-HCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEE
Q ss_conf             999996589962488427888989999999998-619986589996358613289999999999997299987---9997
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKII-TSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMR  358 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~i-l~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvR  358 (398)
                      .+.+..+|..+..+... +..+.+..++.++-+ .+.|++.+|+       ...|.+|.|+++++++.+.++|   -|+-
T Consensus       141 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~dai~-------~~~d~~A~gv~~al~~~g~~ip~di~ivg  212 (264)
T cd01537         141 KDALKEAGPIEIVLVQE-GDWDAEKGYQAAEELLTAHPDPTAIF-------AANDDMALGALRALREAGLRVPDDISVIG  212 (264)
T ss_pred             HHHHHHCCCCCCEEEEE-CCCCHHHHHHHHHHHHHHCCCCEEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             99999779998537995-79998999999999985089976999-------89869999999999974999999839999


Q ss_pred             CCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             489858999999997699589-9499899999999985
Q gi|254781049|r  359 LEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       359 l~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      ..++  ....    ..+-++. ...+.++..+.++++.
T Consensus       213 ~d~~--~~~~----~~~p~ltti~~~~~~~g~~a~~~l  244 (264)
T cd01537         213 FDGT--PEAL----LAGPPLTTVRQPPDELGRAAVELL  244 (264)
T ss_pred             ECCH--HHHH----HHCCCEEEEECCHHHHHHHHHHHH
T ss_conf             9974--9999----719982999839999999999999


No 115
>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=92.21  E-value=0.94  Score=24.65  Aligned_cols=103  Identities=15%  Similarity=0.187  Sum_probs=63.7

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             999999658996248842788898999999999861-9986589996358613289999999999997299987999748
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      ..+.+..+|..+-.-+-+.+..+.+.-+++++.+++ .+++.++|       +..|.+|.|+++|+++.+.++|==+.+-
T Consensus       136 f~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~p~ai~-------~~nd~~A~g~~~al~~~g~~vP~di~vi  208 (260)
T cd06286         136 YKDALEEYGLTPDEEWIFEGCFTIEDGERIGHQLLKMKDRPDAIF-------TGSDEVAAGIITEAKKQGIRVPEDLAII  208 (260)
T ss_pred             HHHHHHHCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             999999779997730364465206679999999984499987367-------3689999999999997299999976999


Q ss_pred             CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             98589999999976995899499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      |-+-..   +-+...+.. ...+..+..+.|+++.
T Consensus       209 gfdd~~---~~~~p~lTt-v~~~~~~~g~~A~~~l  239 (260)
T cd06286         209 GFDNQP---ISELLGITT-IDQPVKELGEKAFELL  239 (260)
T ss_pred             EECCHH---HHCCCCCCE-EECCHHHHHHHHHHHH
T ss_conf             989849---982899758-9359999999999999


No 116
>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=92.20  E-value=0.94  Score=24.64  Aligned_cols=82  Identities=15%  Similarity=0.188  Sum_probs=56.1

Q ss_pred             CCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             888989999999998619986589996358613289999999999997299987---99974898589999999976995
Q gi|254781049|r  301 GGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRLEGANVDIGNRLIAESGLN  377 (398)
Q Consensus       301 G~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl~Gtn~~~g~~il~~~g~~  377 (398)
                      |..+.+.-+++++.++++|.+.+|+.       .-|.+|.|+++++++.+.++|   -|+-+.++-.      .....-+
T Consensus       155 ~~~~~~~~~~~~~~l~~~~~~~aii~-------~~D~~A~g~i~~l~~~g~~iP~di~iigfd~~~~------~~~~~p~  221 (264)
T cd01574         155 GDWSAESGYRAGRELLREGDPTAVFA-------ANDQMALGVLRALHELGLRVPDDVSVVGFDDIPE------SAYFIPP  221 (264)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCEEEE-------CCHHHHHHHHHHHHHHCCCCCCCCEEEEECCCHH------HHHCCCC
T ss_conf             68997999999999983799968963-------6429999999999982998898847998688178------8950898


Q ss_pred             EE-EECCHHHHHHHHHHHH
Q ss_conf             89-9499899999999985
Q gi|254781049|r  378 VI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       378 ~~-~~~~~~~A~~~~v~~~  395 (398)
                      +. ...+..+..+.|+++.
T Consensus       222 lTtI~~~~~~~g~~A~~~l  240 (264)
T cd01574         222 LTTVRQDFAALGRRAVELL  240 (264)
T ss_pred             EEEEEECHHHHHHHHHHHH
T ss_conf             5899819999999999999


No 117
>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=91.87  E-value=1  Score=24.39  Aligned_cols=104  Identities=14%  Similarity=0.141  Sum_probs=68.7

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             999999658996248842788898999999999861-9986589996358613289999999999997299987999748
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      ..+.++.+|..+-...-+.+..+.+.-+++++-+++ ++.+.+||       ...|.+|.|+++|+++.+.++|==+.+-
T Consensus       144 f~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~tai~-------~~nD~~A~g~~~al~~~g~~iP~disvv  216 (270)
T cd06294         144 YKQALEDHGIPDRNEVIISLDFSEEGGYKALKKLLEQHPRPTAIV-------ATDDLLALGVLKVLNELGLKVPEDLSII  216 (270)
T ss_pred             HHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             999999869997733331377667889999999984699984899-------8774999999999998399999984999


Q ss_pred             CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             9858999999997699589-9499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      |-+-.   .+.+-..-++. ...+.++..++|+++.
T Consensus       217 gfDd~---~~~~~~~P~LTtv~q~~~~~G~~A~~~L  249 (270)
T cd06294         217 GFNNS---ILSELAHPPLTSVDINPRELGYEAAELL  249 (270)
T ss_pred             EECCH---HHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             98972---8998428981799739999999999999


No 118
>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=91.85  E-value=1  Score=24.38  Aligned_cols=103  Identities=10%  Similarity=0.055  Sum_probs=65.5

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             99999965899624884278889899999999986-19986589996358613289999999999997299987999748
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      ..+.++.+|..+.......+..+.+.-+++++-++ +.|++++||.       ..|.+|.|+++++++.++++|==+.+-
T Consensus       138 ~~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~dai~~-------~nD~~A~g~~~~l~~~g~~iP~disvi  210 (268)
T cd01575         138 FRAALRAAGLDPPLVVTTPEPSSFALGRELLAELLARWPDLDAVFC-------SNDDLALGALFECQRRGISVPEDIAIA  210 (268)
T ss_pred             HHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEE-------CCHHHHHHHHHHHHHHCCCCCCCEEEE
T ss_conf             9999997698988089954899889999999999956999837998-------788999999999998389999977999


Q ss_pred             CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHH
Q ss_conf             9858999999997699589-949989999999998
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHA  394 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~  394 (398)
                      |-+-.   .+.+-..-++. ...+..+..++|+++
T Consensus       211 gfdd~---~~~~~~~p~ltti~~~~~~~g~~a~~~  242 (268)
T cd01575         211 GFGDL---EIAAALPPALTTVRTPRREIGRRAAEL  242 (268)
T ss_pred             EECCH---HHHHCCCCCCEEEEECHHHHHHHHHHH
T ss_conf             98973---899616899679996999999999999


No 119
>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=91.72  E-value=1.1  Score=24.29  Aligned_cols=103  Identities=17%  Similarity=0.212  Sum_probs=67.0

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf             99999658996248842788898999999999861-99865899963586132899999999999972999879997489
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG  361 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G  361 (398)
                      .+.+..+|..+-.+.-+.+.-+.+..+++++-++. .|+.++||.       .-|.+|.|+++++++.+.++|==+.+-|
T Consensus       148 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~~-------~nD~~A~g~~~~~~~~g~~iP~disIig  220 (275)
T cd06295         148 REALAEAGLPLDPRLVAPGDFTEESGRAAMRALLERGPDFDAVFA-------ASDLMALGALRALREAGRRVPEDVAVVG  220 (275)
T ss_pred             HHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             999998699999417996577668799998889854999870341-------4758789999999974999898569999


Q ss_pred             CCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             858999999997699589-9499899999999985
Q gi|254781049|r  362 ANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       362 tn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      -+-.   .+.+-..-++. ...+..+..++|+++.
T Consensus       221 fd~~---~~~~~~~P~LTtI~~~~~~ig~~A~~~L  252 (275)
T cd06295         221 FDDI---PLAAYADPPLTTVRQDIEEAGRLLVDLL  252 (275)
T ss_pred             ECCH---HHHHHCCCCEEEEEECHHHHHHHHHHHH
T ss_conf             6786---8998348986999809999999999999


No 120
>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=91.68  E-value=1.1  Score=24.26  Aligned_cols=101  Identities=16%  Similarity=0.232  Sum_probs=60.4

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCE---EEE
Q ss_conf             9999965899624884278889899999999986-199865899963586132899999999999972999879---997
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPL---VMR  358 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pi---vvR  358 (398)
                      .+.++.+|.+.-...-..+..+.+..+++++-++ +.|++.+||       +..|.+|.|+++++++.+.++|=   |+-
T Consensus       139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~~D~~A~g~~~~l~~~g~~iP~di~Iig  211 (264)
T cd06267         139 REALEEAGIPLDEELIVEGDFSEESGYEAARELLASGERPTAIF-------AANDLMAIGALRALRELGLRVPEDVSVVG  211 (264)
T ss_pred             HHHHHHCCCCCCHHEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             99999869998853075278977999999999996599998998-------78879999999999982999999779999


Q ss_pred             CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             4898589999999976995899499899999999985
Q gi|254781049|r  359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      ..++  +. .+. -...+.- ...+..+..++|+++.
T Consensus       212 ~d~~--~~-~~~-~~p~ltt-v~~~~~~ig~~a~~~l  243 (264)
T cd06267         212 FDDI--PL-AEL-LTPPLTT-VRQPIEEMGRAAAELL  243 (264)
T ss_pred             ECCH--HH-HHC-CCCCCEE-EEECHHHHHHHHHHHH
T ss_conf             9984--89-853-4899479-9909999999999999


No 121
>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=91.65  E-value=1.1  Score=24.24  Aligned_cols=83  Identities=14%  Similarity=0.252  Sum_probs=54.9

Q ss_pred             CCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCHHHHHHHHHHCCC
Q ss_conf             8889899999999986-19986589996358613289999999999997299987---9997489858999999997699
Q gi|254781049|r  301 GGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRLEGANVDIGNRLIAESGL  376 (398)
Q Consensus       301 G~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl~Gtn~~~g~~il~~~g~  376 (398)
                      +..+.+..+++++-++ ..+.+.+|+       +..|.+|.|+++++++.++++|   -|+=..++...   +++. ..+
T Consensus       158 ~~~~~~~~~~~~~~~l~~~~~~~aii-------~~~d~~A~g~~~~l~~~gi~vP~di~vvgfd~~~~~---~~~~-p~l  226 (269)
T cd06275         158 GDFECEGGYEAMQRLLAQPKRPTAVF-------CGNDLMAMGALCAAQEAGLRVPQDLSIIGYDDIELA---RYFS-PPL  226 (269)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEE-------CCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCHHHH---HHCC-CCE
T ss_conf             77776889999999997089966123-------187499999999999808878998679987787999---8338-985


Q ss_pred             CEEEECCHHHHHHHHHHHH
Q ss_conf             5899499899999999985
Q gi|254781049|r  377 NVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       377 ~~~~~~~~~~A~~~~v~~~  395 (398)
                      .. ...+..+..+.|+++.
T Consensus       227 tt-i~q~~~~~g~~a~~~L  244 (269)
T cd06275         227 TT-IHQPKDRLGELAVNML  244 (269)
T ss_pred             EE-EECCHHHHHHHHHHHH
T ss_conf             89-9619999999999999


No 122
>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=91.65  E-value=1.1  Score=24.24  Aligned_cols=88  Identities=17%  Similarity=0.175  Sum_probs=59.0

Q ss_pred             CCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCC
Q ss_conf             278889899999999-98619986589996358613289999999999997299987-9997489858999999997699
Q gi|254781049|r  299 VGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGL  376 (398)
Q Consensus       299 ~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~  376 (398)
                      .-+..+.+.-+++++ ++.++|++++||.       ..|.+|.|.++|+++.+..-. .|+=..|+  .++++.+++-.+
T Consensus       160 ~~~~~~~~~~~~~~~~~L~~~pd~~ai~~-------~nD~~A~Ga~~al~~~g~~~di~vvG~D~~--~~~~~~i~~g~~  230 (275)
T cd06320         160 QPADWDREKAYDVATTILQRNPDLKAIYC-------NNDTMALGVVEAVKNAGKQGKVLVVGTDGI--PEAYKSIRAGEL  230 (275)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCC
T ss_conf             15530389999999998862876677996-------698899999999997699998299998976--999999864996


Q ss_pred             CEEEECCHHHHHHHHHHHH
Q ss_conf             5899499899999999985
Q gi|254781049|r  377 NVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       377 ~~~~~~~~~~A~~~~v~~~  395 (398)
                      ......+..+..+.+++++
T Consensus       231 ~~tv~q~~~~~G~~av~~l  249 (275)
T cd06320         231 TATVDSFPALIGEVAMEVM  249 (275)
T ss_pred             EEEECCCHHHHHHHHHHHH
T ss_conf             6998179999999999999


No 123
>PRK09701 D-allose transporter subunit; Provisional
Probab=91.41  E-value=1.1  Score=24.08  Aligned_cols=85  Identities=15%  Similarity=0.222  Sum_probs=59.2

Q ss_pred             CCCCHHHHHHH-HHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf             88898999999-99986199865899963586132899999999999972999-87999748985899999999769958
Q gi|254781049|r  301 GGADQDKVAAA-FKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNV  378 (398)
Q Consensus       301 G~a~~e~~~~a-~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~  378 (398)
                      +..+.++-++. -.++.++|++++||-       ..|.+|-|.++|+++.+.+ .-.++-..|+.+  +.+.+++-.+..
T Consensus       196 ~~~d~~~a~~~~~~~L~a~Pdi~~I~~-------~nd~~a~Ga~~Al~~aG~~~~i~vvG~D~~~~--~~~~I~~G~i~a  266 (311)
T PRK09701        196 ADWDRIKALDVATNVLQRNPNIKAIYC-------ANDTMAMGVAQAVANAGKTGKVLVVGTDGIPE--ARKMVEAGQMTA  266 (311)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEEECCCHH--HHHHHHCCCCEE
T ss_conf             776587799999999954999768997-------79726899999999669999839999789999--999998598279


Q ss_pred             EEECCHHHHHHHHHHH
Q ss_conf             9949989999999998
Q gi|254781049|r  379 ITAIDLDDAAQKIVHA  394 (398)
Q Consensus       379 ~~~~~~~~A~~~~v~~  394 (398)
                      ....+-.+.-.++|+.
T Consensus       267 tv~Q~P~~~G~~av~~  282 (311)
T PRK09701        267 TVAQNPADIGATGLKL  282 (311)
T ss_pred             EEEECHHHHHHHHHHH
T ss_conf             9973999999999999


No 124
>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=91.40  E-value=1.2  Score=24.07  Aligned_cols=104  Identities=15%  Similarity=0.132  Sum_probs=61.7

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf             9999965899624884278889899999999986-199865899963586132899999999999972999879997489
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG  361 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G  361 (398)
                      .+.++.+|.++-...-+-+..+.+.-+++++-++ +.+++.+||       +..|.+|.|+++++++.+.++|==+.+-|
T Consensus       143 ~~al~~~gl~~~~~~~~~~~~~~~~~~~~~~~ll~~~~~p~Ai~-------~~nD~~A~g~l~~l~~~g~~vP~Disvig  215 (268)
T cd06271         143 RRALAEAGLPLDPALIVSGDMTEEGGYAAAAELLALPDRPTAIV-------CSSELMALGVLAALAEAGLRPGRDVSVVG  215 (268)
T ss_pred             HHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             99999839997711365068757779999999996599986899-------77779999999999982999899979999


Q ss_pred             CCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             8589999999976995899499899999999985
Q gi|254781049|r  362 ANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       362 tn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      -.-..--+++ ...+.. ...+.++..++|+++.
T Consensus       216 fD~~~~~~~~-~p~LTt-i~~~~~~~g~~A~~~L  247 (268)
T cd06271         216 FDDSPPLLFF-SPPLTT-VRSDLRAAGRRLAELL  247 (268)
T ss_pred             ECCCHHHHHC-CCCEEE-EECCHHHHHHHHHHHH
T ss_conf             7882899827-898089-9809999999999999


No 125
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ:  LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate 
Probab=91.29  E-value=1.2  Score=24.00  Aligned_cols=86  Identities=19%  Similarity=0.143  Sum_probs=62.9

Q ss_pred             CCCCCCHHHHHHHHHH-HHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCC
Q ss_conf             2788898999999999-86199865899963586132899999999999972999-879997489858999999997699
Q gi|254781049|r  299 VGGGADQDKVAAAFKI-ITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGL  376 (398)
Q Consensus       299 ~gG~a~~e~~~~a~~~-il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~  376 (398)
                      .-|..++++-+++.+- +.++|++++||       ...|.+|.|.++|+++.+.. .-+|+-..|+-.+  .+.+++-.+
T Consensus       168 ~~~~~~r~~a~~~a~~~L~~~Pdi~~I~-------a~nd~mAlGa~~Al~~ag~~~~i~vvG~dg~~~~--l~ai~~G~l  238 (280)
T cd06303         168 FYTDATRQKAYQATSDILSNNPDVDFIY-------ACSTDIALGASDALKELGREDDILINGWGGGSAE--LDAIQQGEL  238 (280)
T ss_pred             ECCCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCEEEEEECCCHHH--HHHHHCCCC
T ss_conf             5277668999999999998698930999-------7894578999999997398788799972799999--999984998


Q ss_pred             CEEE---ECCHHHHHHHHHH
Q ss_conf             5899---4998999999999
Q gi|254781049|r  377 NVIT---AIDLDDAAQKIVH  393 (398)
Q Consensus       377 ~~~~---~~~~~~A~~~~v~  393 (398)
                      ....   -+|+--|+.-|+.
T Consensus       239 ~aTv~r~~dd~g~~~aeaik  258 (280)
T cd06303         239 DVTVMRMNDDTGVAMAEAIK  258 (280)
T ss_pred             EEEEEECCCCHHHHHHHHHH
T ss_conf             58984026642199999999


No 126
>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=91.21  E-value=1.2  Score=23.95  Aligned_cols=103  Identities=14%  Similarity=0.048  Sum_probs=64.8

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             99999965899624884278889899999999986-19986589996358613289999999999997299987999748
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      ..+.+..+|...-.-.-+-|..+.+.-+++++-++ .+++..++|       +..|.+|-|+.+++++.++++|==+.+-
T Consensus       138 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~av~-------~~nD~~A~g~l~~l~~~gi~vP~disii  210 (269)
T cd06293         138 YREALAEAHIPEVPEYVCFGDYTREFGRAAAAQLLARGDPPTAIF-------AASDEIAIGLLEVLRERGLSIPGDMSLV  210 (269)
T ss_pred             HHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             999999769999934899556311359999999984799985899-------6885999999999998499999965999


Q ss_pred             CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHH
Q ss_conf             9858999999997699589-949989999999998
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHA  394 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~  394 (398)
                      |-+-.   .+.+...-++. ...+.++..++|+++
T Consensus       211 gfd~~---~~~~~~~P~lTti~q~~~~ig~~A~~~  242 (269)
T cd06293         211 GFDDV---GPAHLFAPPLTTIRQPVRELGRRAVAL  242 (269)
T ss_pred             EECCH---HHHHHCCCCEEEEECCHHHHHHHHHHH
T ss_conf             88880---999830898489965999999999999


No 127
>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=90.85  E-value=1.3  Score=23.73  Aligned_cols=103  Identities=17%  Similarity=0.195  Sum_probs=61.0

Q ss_pred             HHHHHHCCCCCC-EEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             999996589962-48842788898999999999861-9986589996358613289999999999997299987999748
Q gi|254781049|r  283 MDIIKLYGGAPA-NFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       283 mD~i~~~Gg~pA-NFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      .+.+..+|.... .+.. .+..+.+.-+++++-+++ .+.+.+||       ...|.+|.|+++++++.+.++|==+.+-
T Consensus       134 ~~al~~~g~~~~~~~i~-~~~~~~~~~~~~~~~ll~~~~~p~Ai~-------~~nD~~A~g~~~~l~~~g~~vP~dvsvi  205 (261)
T cd06272         134 LETCDENGISISDSHID-VDGLSAEGGDNAAKKLLKESDLPTAII-------CGSYDIALGVLSALNKQGISIPEDIEII  205 (261)
T ss_pred             HHHHHHCCCCCCCEEEE-ECCCHHHHHHHHHHHHHHCCCCCCCEE-------ECCHHHHHHHHHHHHHHCCCCCCCEEEE
T ss_conf             99999859985513898-303103679999999985278986101-------2768999999999998099999955999


Q ss_pred             CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             98589999999976995899499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      |-+-..-.+++. ..+.- ...+.++..++|+++.
T Consensus       206 GfDd~~~~~~~~-P~LTt-v~q~~~~ig~~A~~~L  238 (261)
T cd06272         206 SYDNIPQMAIID-PPLTA-VDVPIEEIAKKSLELL  238 (261)
T ss_pred             EECCCHHHHHHC-CCCEE-EEECHHHHHHHHHHHH
T ss_conf             988818899509-98479-9809999999999999


No 128
>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=90.78  E-value=1.3  Score=23.69  Aligned_cols=86  Identities=16%  Similarity=0.183  Sum_probs=60.1

Q ss_pred             CCCCHHHHHHHHHHHH-CCC-CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             8889899999999986-199-865899963586132899999999999972999-8799974898589999999976995
Q gi|254781049|r  301 GGADQDKVAAAFKIIT-SDS-SVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLN  377 (398)
Q Consensus       301 G~a~~e~~~~a~~~il-~~~-~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~  377 (398)
                      ++.+.+.-++.++-+| +.| ++++||       ...|.+|.|.++|+++.+.. ...|+=..|+.  ++++.+++-.+.
T Consensus       169 ~~~~~~~a~~~~~~~L~~~~~~i~aI~-------a~nD~~A~Ga~~Al~~aG~~~~v~vvG~Dg~~--~~l~~I~~G~~~  239 (288)
T cd01538         169 PDWDPETAQKRMENALTANYNKVDGVL-------AANDGTAGGAIAALKAAGLAGKPPVTGQDAEL--AAVQRIVEGTQT  239 (288)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCEEEECCCCH--HHHHHHHCCCCE
T ss_conf             785778899999999984655575898-------55856779999999974999987398359989--999999739825


Q ss_pred             EEEECCHHHHHHHHHHHH
Q ss_conf             899499899999999985
Q gi|254781049|r  378 VITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       378 ~~~~~~~~~A~~~~v~~~  395 (398)
                      .....+..+-..++|+++
T Consensus       240 ~tv~Q~p~~~G~~av~~a  257 (288)
T cd01538         240 MTVYKDIRELAEAAAELA  257 (288)
T ss_pred             EEEECCHHHHHHHHHHHH
T ss_conf             999559999999999999


No 129
>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=90.77  E-value=1.3  Score=23.68  Aligned_cols=101  Identities=16%  Similarity=0.168  Sum_probs=61.1

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEE
Q ss_conf             99999658996248842788898999999999861-9986589996358613289999999999997299987---9997
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMR  358 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvR  358 (398)
                      .+.+..+|..+-.-.-+-|..+.+..+++++-++. ++++.+|+       +..|.+|-|+++++++.++++|   -|+=
T Consensus       140 ~~a~~~~~~~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~~aii-------~~~D~~A~g~~~~l~~~gi~vP~di~iig  212 (270)
T cd06296         140 RAALAEAGIPVDPALVREGDFSTESGFRAAAELLALPERPTAIF-------AGNDLMALGVYEAARERGLRIPEDLSVVG  212 (270)
T ss_pred             HHHHHHCCCCCCHHHEEECCCHHHHHHHHHHHHHHCCCCCCCEE-------ECCCHHHHHHHHHHHHCCCCCCCCCEEEE
T ss_conf             99999869998855533065017899999999995499886203-------47868999999999986999999887999


Q ss_pred             CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             4898589999999976995899499899999999985
Q gi|254781049|r  359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      ..++..-   +++ ...+.. ...+..+..++|+++.
T Consensus       213 fd~~~~~---~~~-~p~ltt-I~~~~~~~g~~a~~~l  244 (270)
T cd06296         213 FDDLPEA---RWV-SPPLTT-VRQPLREMGRAAVRLL  244 (270)
T ss_pred             ECCHHHH---HHC-CCCEEE-EEECHHHHHHHHHHHH
T ss_conf             7887899---852-898389-9829999999999999


No 130
>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=90.53  E-value=1.4  Score=23.54  Aligned_cols=86  Identities=13%  Similarity=0.172  Sum_probs=54.8

Q ss_pred             CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCC-C-EEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             8889899999999-9861998658999635861328999999999999729998-7-99974898589999999976995
Q gi|254781049|r  301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINI-P-LVMRLEGANVDIGNRLIAESGLN  377 (398)
Q Consensus       301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~-p-ivvRl~Gtn~~~g~~il~~~g~~  377 (398)
                      |..+.+..++.++ ++.++|++++||-       .-|.+|-|.++|+++.+..- . .|+=..|+  .++.+.+++-.+.
T Consensus       163 ~~~~~~~a~~~~~~~L~~~~~~~aI~~-------~nd~~a~Ga~~al~~~g~~~~~i~v~G~D~~--~~~~~~i~~g~~~  233 (272)
T cd06301         163 ANWSRAEAMDLMENWLSSGGKIDAVVA-------NNDEMALGAIMALKAAGKSDKDVPVAGIDGT--PDALAAVKKGDLD  233 (272)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCCEEEEEECCC--HHHHHHHHCCCCE
T ss_conf             312357899999999983677787995-------5827899999999986989998799998985--9999998749976


Q ss_pred             EEEECCHHHHHHHHHHHH
Q ss_conf             899499899999999985
Q gi|254781049|r  378 VITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       378 ~~~~~~~~~A~~~~v~~~  395 (398)
                      .....+..+-.+.+|+++
T Consensus       234 ~tv~q~~~~~G~~av~~~  251 (272)
T cd06301         234 VTVFQDAKGQGAGALDAA  251 (272)
T ss_pred             EEEECCHHHHHHHHHHHH
T ss_conf             998069999999999999


No 131
>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=90.28  E-value=1.5  Score=23.40  Aligned_cols=88  Identities=17%  Similarity=0.220  Sum_probs=53.5

Q ss_pred             CCCCCHHHHHHH-HHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCC
Q ss_conf             788898999999-99986199865899963586132899999999999972999-8799974898589999999976995
Q gi|254781049|r  300 GGGADQDKVAAA-FKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLN  377 (398)
Q Consensus       300 gG~a~~e~~~~a-~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~  377 (398)
                      -+..+.++..+. -.++.++|++++||-       ..|.+|.|.++|+++.+.+ ++|+ -..+ ..+.+.+++++--+.
T Consensus       165 ~~~~~~~~a~~~~~~~L~~~Pdi~~I~~-------~nd~~a~Ga~~Al~~aG~~~v~iv-g~d~-g~~~~~~~i~~G~~~  235 (294)
T cd06316         165 KGIDGPSKAEDIANAMLTQNPDLKGIYA-------VWDVPAEGVIAALRAAGRDDIKVT-TVDL-GLNVALDMAKGGNVA  235 (294)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEE-EEEC-CCHHHHHHHHCCCCE
T ss_conf             3888889999999999973999888998-------686365999999998199983799-9958-968999999779977


Q ss_pred             EEEECCHH----HHHHHHHHHHH
Q ss_conf             89949989----99999999850
Q gi|254781049|r  378 VITAIDLD----DAAQKIVHAVK  396 (398)
Q Consensus       378 ~~~~~~~~----~A~~~~v~~~k  396 (398)
                      .....+-.    .+++.++.+.+
T Consensus       236 atv~q~p~~~G~~~v~~a~~~l~  258 (294)
T cd06316         236 GIGAQRPYDQGVAEARLAALALI  258 (294)
T ss_pred             EEEEECHHHHHHHHHHHHHHHHC
T ss_conf             99983889999999999999977


No 132
>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=90.18  E-value=1.5  Score=23.35  Aligned_cols=102  Identities=16%  Similarity=0.276  Sum_probs=64.2

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf             99999965899624884278889899999999986199865899963586132899999999999972999879997489
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG  361 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G  361 (398)
                      ..+.+..+|.++..+..  +..+.+.-+++++-+++...+.+||       ..-|.+|.|+++++++.+.++|==+.+-|
T Consensus       137 ~~~al~~~g~~~~~~~~--~~~~~~~~~~~~~~ll~~~~~~Ai~-------~~nD~~A~g~~~~l~~~g~~vP~Disvig  207 (259)
T cd01542         137 YLDALKEHGICPPNIVE--TDFSYESAYEAAQELLEPQPPDAIV-------CATDTIALGAMKYLQELGRRIPEDISVAG  207 (259)
T ss_pred             HHHHHHHCCCCCCEEEE--CCCCHHHHHHHHHHHHHCCCCCCEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             99999976999635996--5787778999999997457998324-------34589999999999981999999869999


Q ss_pred             C-CHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             8-589999999976995899499899999999985
Q gi|254781049|r  362 A-NVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       362 t-n~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      - |.+.+ +++ ...+.. ...+..+..++|+++.
T Consensus       208 fdd~~~~-~~~-~P~LTt-v~q~~~~~G~~A~~~L  239 (259)
T cd01542         208 FGGYELS-SVV-TPSLTT-VDFGYKEAGKKAAELL  239 (259)
T ss_pred             ECCHHHH-HHC-CCCCEE-EEECHHHHHHHHHHHH
T ss_conf             8982999-826-899789-9959999999999999


No 133
>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=90.05  E-value=1.5  Score=23.28  Aligned_cols=102  Identities=15%  Similarity=0.148  Sum_probs=65.8

Q ss_pred             HHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             999999658996248842788898999999999861-9986589996358613289999999999997299987999748
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      ..+.++.+|.....-+-+.+..+.+.-+++++-+++ .+.+.+||       .-.|.+|-|+++++++.++++|==+.+-
T Consensus       141 f~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~ll~~~~~p~Ai~-------~~nD~~A~g~l~~l~~~Gi~vP~Disvi  213 (269)
T cd06297         141 FQQALKDAGRPFSPDLLAITDHSEEGGRLAMRHLLEKASPPLAVF-------ASADQQALGALQEAVELGLTVGEDVRVV  213 (269)
T ss_pred             HHHHHHHCCCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             999999829986622341378636569999999983699985899-------8978999999999998399889966999


Q ss_pred             CCCH-HHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             9858-9999999976995899499899999999985
Q gi|254781049|r  361 GANV-DIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~-~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      |-+- +.+    +..+|... ..+..+..++|+++.
T Consensus       214 GfDd~~~a----~~~~LTTv-~q~~~~~G~~A~~~L  244 (269)
T cd06297         214 GFDDHPFA----REAGLSTL-AQPVEAMGARAAQLL  244 (269)
T ss_pred             EECCHHHH----HCCCCCEE-ECCHHHHHHHHHHHH
T ss_conf             98984897----24898679-639999999999999


No 134
>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=89.79  E-value=1.6  Score=23.15  Aligned_cols=86  Identities=12%  Similarity=0.182  Sum_probs=58.8

Q ss_pred             CCCCCHHHHHHHHHHHH-CCC-CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCHHHHHHHHHHC
Q ss_conf             78889899999999986-199-86589996358613289999999999997299987---99974898589999999976
Q gi|254781049|r  300 GGGADQDKVAAAFKIIT-SDS-SVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRLEGANVDIGNRLIAES  374 (398)
Q Consensus       300 gG~a~~e~~~~a~~~il-~~~-~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl~Gtn~~~g~~il~~~  374 (398)
                      .|..+.+.-+++++-+| ++| .+++||       ..-|.+|.|.++|+++.+.++|   .|+-..|+  .++.+.+++-
T Consensus       163 ~~~~~~~~~~~~~~~~L~~~p~~i~ai~-------~~nd~~a~Ga~~al~~~G~~~~~di~ivg~D~~--~~~~~~i~~g  233 (273)
T cd06309         163 TGDFTRAKGKEVMEALLKAHGDDIDAVY-------AHNDEMALGAIQAIKAAGKKPGKDIKIVSIDGT--KDAFQAMADG  233 (273)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCC--HHHHHHHHCC
T ss_conf             2346889999999999972788888898-------678579999999999839999998699998999--9999998769


Q ss_pred             CCCEEEECCHHHHHHHHHHHH
Q ss_conf             995899499899999999985
Q gi|254781049|r  375 GLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       375 g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      .+......+-. ..+++|+++
T Consensus       234 ~l~~~~~~~p~-~G~~Av~~l  253 (273)
T cd06309         234 KLNATVECNPL-FGPLAFDTL  253 (273)
T ss_pred             CCEEEEECCHH-HHHHHHHHH
T ss_conf             97199978399-999999999


No 135
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=89.67  E-value=1.6  Score=23.09  Aligned_cols=107  Identities=14%  Similarity=0.152  Sum_probs=69.2

Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             99999999658996248842788898999999999861-99865899963586132899999999999972999879997
Q gi|254781049|r  280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR  358 (398)
Q Consensus       280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR  358 (398)
                      -...+.+..+|..+-..+=.-+..+.+.-+++++-+++ .+.+.+||       .-.|.+|-|+++|+++.++++|==+.
T Consensus       196 ~g~~~al~~~gl~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~tAi~-------~~nD~~A~g~l~al~~~Gl~VP~Dis  268 (342)
T PRK10727        196 QGYYDALAESGIPANDRLVTFGEPDESGGEQAMTELLGRGRNFTAVA-------CYNDSMAAGAMGVLNDNGIDVPGEIS  268 (342)
T ss_pred             HHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCCCE-------ECCHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             99999999769999820588157877889999999985599977415-------54699999999999982999999869


Q ss_pred             CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             4898589999999976995899499899999999985
Q gi|254781049|r  359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      +-|-+--.--+. -...|.- ...+.++..+.|+++.
T Consensus       269 ViGfDd~~~~~~-~~P~LTT-V~~p~~e~g~~A~~lL  303 (342)
T PRK10727        269 LIGFDDVLVSRY-VRPRLTT-VRYPIVTMATQAAELA  303 (342)
T ss_pred             EEEECCHHHHHC-CCCCCEE-EECCHHHHHHHHHHHH
T ss_conf             998897189864-8899858-9779999999999999


No 136
>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=89.54  E-value=1.7  Score=23.03  Aligned_cols=103  Identities=12%  Similarity=0.044  Sum_probs=64.0

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             9999965899624884278889899999999986-1998-6589996358613289999999999997299987999748
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSS-VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~-vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      .+.+..+|.....-+-+.+..+.+.-+++++-++ +.+. ..+||       +..|.+|.|+++++++.+.++|==+.+-
T Consensus       139 ~~al~~~g~~~~~~~i~~~~~~~~~g~~~~~~~l~~~~~~p~ai~-------~~nd~~a~g~l~~l~~~g~~vP~disvv  211 (264)
T cd06274         139 RQALADAGLPVQPDWIYAEGYSPESGYQLMAELLARLGRLPRALF-------TTSYTLLEGVLRFLRERPGLAPSDLRIA  211 (264)
T ss_pred             HHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCC-------CCCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             999997799877407982688878999999999986568874220-------1769999999999998599999987999


Q ss_pred             CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             9858999999997699589-9499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      |-.-.   .+.+-...++. ...+.++.+++|+++.
T Consensus       212 gfDd~---~~a~~~~p~LTtv~q~~~~~g~~A~~lL  244 (264)
T cd06274         212 TFDDH---PLLDFLPFPVHSVPQDHEALAEAAFELA  244 (264)
T ss_pred             EECCH---HHHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             98986---8997379997699679999999999999


No 137
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=89.32  E-value=1.7  Score=22.92  Aligned_cols=24  Identities=17%  Similarity=0.378  Sum_probs=18.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             988899885999999998999955
Q gi|254781049|r  178 ELQGQARIDGGDLFPNLYKAFCDK  201 (398)
Q Consensus       178 g~~~~~~~~~~~ii~~L~~~f~e~  201 (398)
                      .++.+..+.+..++..+|+.|.+.
T Consensus       152 ~~s~e~re~~~~~l~~~~~~f~~~  175 (222)
T cd07018         152 DMSPEAREQTQALLDSLWDQYLAD  175 (222)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             658999999999999999999999


No 138
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=89.31  E-value=1.7  Score=22.92  Aligned_cols=90  Identities=17%  Similarity=0.252  Sum_probs=59.3

Q ss_pred             EEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC
Q ss_conf             88427888989999999998619986589996358613289999999999997299987999748985899999999769
Q gi|254781049|r  296 FLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG  375 (398)
Q Consensus       296 FlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g  375 (398)
                      |.|=+=.++.+.+..|++-. . .  +.+|  |.||..+-....+ +...++.    +.-++ +-|.+.+.=.+.+++.+
T Consensus       325 ~iNDSKaTN~~at~~Al~~~-~-~--~iil--I~GG~~Kg~d~~~-l~~~~~~----vk~v~-~~G~~~~~i~~~~~~~~  392 (450)
T PRK02472        325 FYNDSKATNILATQKALSGF-N-Q--PVIL--LAGGLDRGNEFDE-LIPYLKN----VKAMV-VFGETAPKLARAANKAG  392 (450)
T ss_pred             EEECCCCCCHHHHHHHHHCC-C-C--CEEE--EEECCCCCCCHHH-HHHHHHC----CCEEE-EECCCHHHHHHHHHHCC
T ss_conf             98268888999999998458-9-9--8799--9915556888799-9999737----68999-96889999999997379


Q ss_pred             CCEEEECCHHHHHHHHHHHHHC
Q ss_conf             9589949989999999998506
Q gi|254781049|r  376 LNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       376 ~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      ++++.+++|++|+++|.+.++.
T Consensus       393 ~~~~~~~~l~~Av~~a~~~a~~  414 (450)
T PRK02472        393 ITIVEADNVEDAVPKAYALSEP  414 (450)
T ss_pred             CEEEECCCHHHHHHHHHHHCCC
T ss_conf             7189879999999999985889


No 139
>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=89.23  E-value=1.7  Score=22.88  Aligned_cols=105  Identities=19%  Similarity=0.176  Sum_probs=67.4

Q ss_pred             HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCC-CCCCE---
Q ss_conf             999999965899624884278889899999999986-1998658999635861328999999999999729-99879---
Q gi|254781049|r  281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVK-INIPL---  355 (398)
Q Consensus       281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~-~~~pi---  355 (398)
                      ...+.++.+|.......=..|..+.+.-+++++-++ +.|.+.+||       ...|.+|-|.++++++.+ .++|=   
T Consensus       142 Gf~~al~~~g~~~~~~~~~~~~~~~~~g~~~~~~ll~~~~~~~Ai~-------~~nD~~A~G~~~al~~~G~~~vP~dv~  214 (281)
T pfam00532       142 GFMAALAAAGREVKIYHVATGDNDIPDAALAANAMLVSHPTIDAIV-------AMNDEAAMGAVRALLKQGRVKIPDIVG  214 (281)
T ss_pred             HHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEE-------ECCHHHHHHHHHHHHHCCCCCCCCHHC
T ss_conf             9999999759999820688368888999999999985499960999-------758799999999999829997883112


Q ss_pred             -----EEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHH
Q ss_conf             -----997489858999999997699589949989999999998
Q gi|254781049|r  356 -----VMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHA  394 (398)
Q Consensus       356 -----vvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~  394 (398)
                           |+-..|.....--.+ -...|.- ...+.++..++|+++
T Consensus       215 i~~~svvg~d~~~~~~~~~~-~~P~LTT-V~qp~~~mG~~A~~~  256 (281)
T pfam00532       215 IGINSVVGFDGLSKAQDTGL-YLSPLTV-IQLPRQLLGIKASDM  256 (281)
T ss_pred             CCCCCEEEEECCCHHHHHHC-CCCCCEE-EECCHHHHHHHHHHH
T ss_conf             57776699908832566503-8998437-955999999999999


No 140
>PRK03815 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=89.06  E-value=1.8  Score=22.80  Aligned_cols=106  Identities=19%  Similarity=0.177  Sum_probs=67.1

Q ss_pred             HHHHHHHCCCCC---C--------EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999658996---2--------48842788898999999999861998658999635861328999999999999729
Q gi|254781049|r  282 TMDIIKLYGGAP---A--------NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVK  350 (398)
Q Consensus       282 tmD~i~~~Gg~p---A--------NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~  350 (398)
                      ..+.++.+.|-|   -        .|.|=+=+++.+.+..|++-. .++  +.+|  |.||..+-.+..+ +.+.+++. 
T Consensus       252 ~~~~l~~F~gl~HRlE~v~~~~gv~fiNDSKATN~~At~~Al~~~-~~~--~iil--I~GG~~Kg~d~~~-L~~~i~~~-  324 (401)
T PRK03815        252 DYERLNAFVIEAHKLEEFRDKQGRLWVDDSKATNIDATIQALKRY-KDK--KIHL--ILGGDDKGVDLTP-LFEELKNF-  324 (401)
T ss_pred             HHHHHHHCCCCCCCEEEEEEECCEEEECCCCCCCHHHHHHHHHHC-CCC--CEEE--EECCCCCCCCHHH-HHHHHHHH-
T ss_conf             899998489988853899984898996688789889999999837-678--6799--9637655678799-99997640-


Q ss_pred             CCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             99879997489858999999997699589949989999999998506
Q gi|254781049|r  351 INIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       351 ~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                        + .-+-+-|.+.+.=.+.+++.+++++.+++|++|++.|-+.++.
T Consensus       325 --~-~~v~~~G~~~~~i~~~~~~~~~~~~~~~~l~eAv~~a~~~a~~  368 (401)
T PRK03815        325 --D-IEIYAIGSNAEKILALAKEFNIKAQKCEFLEKAVNEIKKVLKQ  368 (401)
T ss_pred             --C-EEEEEECCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHCCC
T ss_conf             --5-6999987899999999875698469828699999999985789


No 141
>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=88.96  E-value=1.8  Score=22.76  Aligned_cols=102  Identities=13%  Similarity=0.071  Sum_probs=60.8

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC
Q ss_conf             9999965899624884278889899999999986-199865899963586132899999999999972999879997489
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG  361 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G  361 (398)
                      .+.+..+|..+-...-..+. +.+..+++++-++ ..+.+.+||       ...|.+|.|+++++++.+.++|==+.+-|
T Consensus       139 ~~al~~~g~~~~~~~~~~~~-~~~~~~~~~~~ll~~~~~p~ai~-------~~~d~~A~g~l~~l~~~g~~VP~disviG  210 (269)
T cd06281         139 KAAFAAAGLPPDPALVRLST-PAASGFDATRALLALPDRPTAII-------AGGTQVLVGVLRALREAGLRIPRDLSVIS  210 (269)
T ss_pred             HHHHHHCCCCCCCEEEECCC-CHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEE
T ss_conf             99999779999943997799-74899999999980799996565-------12338899999999981999999869999


Q ss_pred             CCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             858999999997699589-9499899999999985
Q gi|254781049|r  362 ANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       362 tn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      -+-..   +.+...-++. ...+..+..++|+++.
T Consensus       211 fD~~~---~~~~~~P~LTTi~~~~~~~g~~A~~~L  242 (269)
T cd06281         211 IGDSD---LAELMDPPITALRRDREAVGRTAAELM  242 (269)
T ss_pred             ECCHH---HHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             88879---998358996799749999999999999


No 142
>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=88.42  E-value=2  Score=22.53  Aligned_cols=88  Identities=20%  Similarity=0.214  Sum_probs=54.9

Q ss_pred             CCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCC-CHHHHHHHHHHCCC
Q ss_conf             2788898999999999861-998658999635861328999999999999729998799974898-58999999997699
Q gi|254781049|r  299 VGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGA-NVDIGNRLIAESGL  376 (398)
Q Consensus       299 ~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gt-n~~~g~~il~~~g~  376 (398)
                      +-+..+.+..+++++-+++ .+++.+||       ...|.+|-|+++++++.+.++|==+.+-|- |.+...+.+. .++
T Consensus       155 ~~~~~~~~~~~~~~~~ll~~~~~~dai~-------~~~d~~A~g~~~~l~~~gi~vP~di~iigfD~~~~~~~~~~-P~l  226 (269)
T cd06288         155 VHGDWSADDGYEAAAALLDLDDRPTAIF-------CGNDRMAMGAYQALLERGLRIPQDVSVVGFDNQEIIAEHLR-PPL  226 (269)
T ss_pred             ECCCCCHHHHHHHHHHHHHCCCCCCEEC-------CCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHCC-CCC
T ss_conf             1267766777777799985589986101-------47789999999999985999999889999888689996378-996


Q ss_pred             CEEEECCHHHHHHHHHHHH
Q ss_conf             5899499899999999985
Q gi|254781049|r  377 NVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       377 ~~~~~~~~~~A~~~~v~~~  395 (398)
                      ..+ ..+.++..++|+++.
T Consensus       227 Tti-~q~~~~~g~~A~~~l  244 (269)
T cd06288         227 TTV-ALPHYEMGRWAVELL  244 (269)
T ss_pred             EEE-EECHHHHHHHHHHHH
T ss_conf             499-809999999999999


No 143
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=88.31  E-value=2  Score=22.48  Aligned_cols=86  Identities=19%  Similarity=0.270  Sum_probs=58.6

Q ss_pred             CCCCHHHHHHHHHH-HHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf             88898999999999-86199865899963586132899999999999972999879997489858999999997699589
Q gi|254781049|r  301 GGADQDKVAAAFKI-ITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI  379 (398)
Q Consensus       301 G~a~~e~~~~a~~~-il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~  379 (398)
                      +..+.+.-+++++- +.++|++++||-       ..|.+|-|.++|+++.+++-..|+=..|+.  ++...+++.-+...
T Consensus       187 ~~~~~~~g~~~~~~lL~~~p~~~aIf~-------~nD~~A~Ga~~al~~~G~~di~vvGfD~~~--~~~~~i~~g~~~~T  257 (295)
T PRK10653        187 ADFDRTKGLNVMQNLLTAHPDVQAVFA-------QNDEMALGALRALQTAGKSDVMVVGFDGTP--DGEKAVNDGKLAAT  257 (295)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEECCCH--HHHHHHHCCCCEEE
T ss_conf             777899999999999960899778997-------797799999999998099983999289987--99999774996299


Q ss_pred             EECCHHHHHHHHHHHH
Q ss_conf             9499899999999985
Q gi|254781049|r  380 TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       380 ~~~~~~~A~~~~v~~~  395 (398)
                      ...+..+-.+.+|+++
T Consensus       258 v~Q~~~~~G~~av~~l  273 (295)
T PRK10653        258 IAQQPDQIGAKGVETA  273 (295)
T ss_pred             EECCHHHHHHHHHHHH
T ss_conf             9279999999999999


No 144
>TIGR00705 SppA_67K signal peptide peptidase SppA, 67K type; InterPro: IPR004634   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain.   Signal peptides of secretory proteins seem to serve at least two important biological functions. First, they are required for protein targeting to and translocation across membranes, such as the eubacterial plasma membrane and the endoplasmic reticular membrane of eukaryotes. Second, in addition to their role as determinants for protein targeting and translocation, certain signal peptides have a signalling function.  During or shortly after pre-protein translocation, the signal peptide is removed by signal peptidases. The integral membrane protein, SppA (protease IV), of Escherichia coli was shown experimentally to degrade signal peptides. The member of this family from Bacillus subtilis has only been shown to be required for efficient processing of pre-proteins under conditions of hyper-secretion . These enzymes have a molecular mass around 67 kDa and a duplication such that the N-terminal half shares extensive homology with the C-terminal half and was shown in E. coli to form homotetramers. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both. ; GO: 0009003 signal peptidase activity, 0006465 signal peptide processing, 0016021 integral to membrane.
Probab=88.31  E-value=2  Score=22.48  Aligned_cols=251  Identities=18%  Similarity=0.256  Sum_probs=124.4

Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHC---H
Q ss_conf             9999999999861876544212222244330110345556505899999834778048998447884024555748---3
Q gi|254781049|r   75 SLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDY---P  151 (398)
Q Consensus        75 s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~---p  151 (398)
                      +..++..+..+-       +|   .|++|   ++----.-.-.|||+-+=|.      |+.++.|+|||.=.+.++   .
T Consensus       117 ~l~~~~~AL~~F-------k~---SgKpv---~ay~~nYS~~~YYLAsfAd~------I~L~p~G~Vdl~Gl~~~~Lfy~  177 (614)
T TIGR00705       117 ALSEIGKALSEF-------KD---SGKPV---YAYGENYSQGQYYLASFADE------ILLNPMGSVDLHGLATETLFYK  177 (614)
T ss_pred             CHHHHHHHHHHH-------HH---CCCEE---EEEECCCCCHHHHHHHHHHH------HHCCCCCCEECCCCCCCCCCHH
T ss_conf             279889999999-------85---69908---99852534023688765402------4036887245035244764088


Q ss_pred             HHHEEEECCC---CCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC----CCCCCCCCEEEECCCCCEEEEEE
Q ss_conf             1220332144---4578957888788751988899885999999998999955----97510232679905996799400
Q gi|254781049|r  152 QKIFKLLIDP---LIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDK----DMSLLEINPLIIMKNGRLRVLDS  224 (398)
Q Consensus       152 ~~I~~~~id~---~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~----Da~liEINPLvvt~dg~vvAlDA  224 (398)
                      ..+-|..|.+   -.|-..-.+..+.+. .++++........+-.||+-|+..    -..-++-.-++-..++ .+..|-
T Consensus       178 ~~l~K~~v~~~~~rvG~YKgavEpF~R~-d~SPe~r~~~q~~l~~lWq~YL~~Va~NRsl~~~~~~~~~~a~~-~L~~l~  255 (614)
T TIGR00705       178 GMLDKLGVSVHVFRVGTYKGAVEPFLRE-DMSPEARENQQRWLGELWQNYLSSVAENRSLAIPKEQVLPSAQG-LLEALK  255 (614)
T ss_pred             HHHHHHCCCCCEEEEECCCCCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCHHH-HHHHHH
T ss_conf             7997612862168962102421423555-66888899999999999988888887031135708760211212-467877


Q ss_pred             EEEECCCHHH-HHHHH-HHHH---CCCCCCHHHHH--HHHCCCCEEEC----------------CCCEEEEECCCHHHHH
Q ss_conf             1321573556-41027-8631---00015622245--77539864422----------------8817999555036899
Q gi|254781049|r  225 KISFDDNALY-RHLDI-QELR---DVSEEDSREIE--AKQHNLSYIAL----------------DGNIGCMVNGAGLAMA  281 (398)
Q Consensus       225 Ki~iDDnA~f-R~~~~-~~~~---d~~~~~~~E~~--A~~~~l~yv~L----------------dG~Ig~~vnGaGlama  281 (398)
                      |..=| .|.+ .+.++ ....   +..-..+.+.+  -.+...++|.|                +-.||++ |=+|    
T Consensus       256 ~~~g~-~~~~a~~~~lV~~~~~~~~~~~~l~~~~e~~~~d~~~~~i~l~dY~~~~~~r~E~~~~~~~iaiv-~~~G----  329 (614)
T TIGR00705       256 KLKGD-LAKYALEEKLVTAVVSQAEVEKALKELFEEDEEDKEKRLISLDDYARKRPQRLENYDVDDKIAIV-YLEG----  329 (614)
T ss_pred             HHCCH-HHHHHHHHHHHHHHHHHCCCCCCCHHHCCCCCCCCHHCCCCHHHHHHCCHHHHHHCCCCCCEEEE-EEEC----
T ss_conf             51354-78999876578998735175310444448872310003211466520132354422798816999-7006----


Q ss_pred             HHHHHHHCCCCCCEEEECCCC-CCHHHHHHHHHHHHCCCCCCEEE--EECCCCHHHHHH-HHHHHHHHHHHCCCCCCEEE
Q ss_conf             999999658996248842788-89899999999986199865899--963586132899-99999999997299987999
Q gi|254781049|r  282 TMDIIKLYGGAPANFLDVGGG-ADQDKVAAAFKIITSDSSVKGIL--INIFGGIMRCDV-LVKGILSAVKEVKINIPLVM  357 (398)
Q Consensus       282 tmD~i~~~Gg~pANFlD~gG~-a~~e~~~~a~~~il~~~~vk~il--iNifGGI~~cd~-vA~gii~a~~~~~~~~pivv  357 (398)
                                .-+|==|.-++ +-.+++.+-++...+||+||+|.  ||=-||=+..-+ |=+-+ ..++..+ ++||||
T Consensus       330 ----------~I~~G~~t~~nG~ggD~~a~lLr~a~~D~~iKAvvLRinSPGGsv~Ase~IR~e~-~~~~~~G-kKPViv  397 (614)
T TIGR00705       330 ----------SIVDGRDTEENGVGGDTVAALLRKARSDPDIKAVVLRINSPGGSVFASEIIRREL-ERLQARG-KKPVIV  397 (614)
T ss_pred             ----------CEECCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEHHHHHHHHH-HHHHHCC-CCCEEE
T ss_conf             ----------4235775667860036799999987079981289988638986342878999999-9998268-997898


Q ss_pred             ECCCCCH
Q ss_conf             7489858
Q gi|254781049|r  358 RLEGANV  364 (398)
Q Consensus       358 Rl~Gtn~  364 (398)
                      -|.+--+
T Consensus       398 SMG~~AA  404 (614)
T TIGR00705       398 SMGAMAA  404 (614)
T ss_pred             ECCHHHH
T ss_conf             4350232


No 145
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=88.05  E-value=2.1  Score=22.37  Aligned_cols=103  Identities=13%  Similarity=0.066  Sum_probs=69.1

Q ss_pred             HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             9999999658996248842788898999999999861-998658999635861328999999999999729998799974
Q gi|254781049|r  281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL  359 (398)
Q Consensus       281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl  359 (398)
                      ...+.+..+|.++- + -+++..+.+.-+++++-+++ .+...+||       ...|.+|.|+++++++.++++|==+.+
T Consensus       200 Gf~~al~~~g~~~~-~-~~~~~~~~~~g~~~~~~ll~~~~~p~Ai~-------~~nD~~A~g~l~al~~~g~~VP~Dvsv  270 (330)
T PRK11303        200 GFRQALKDDPREVH-F-LYAESFSREAGAQLFEKWLETHGMPDALF-------TTSYTLLQGVLDVLLERPGKLPSDLAI  270 (330)
T ss_pred             HHHHHHHHCCCCEE-E-EECCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEE
T ss_conf             99999996799805-9-96488998999999999983799997799-------748999999999999859999997599


Q ss_pred             CCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             89858999999997699589-9499899999999985
Q gi|254781049|r  360 EGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       360 ~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      -|-+-.   .+..-...++. ...+.++.+++|+++.
T Consensus       271 igfDd~---~~~~~~~p~LTtv~q~~~~~g~~A~~~L  304 (330)
T PRK11303        271 ATFGDN---ELLDFLPCPVNAVAQQHRLIAERALELA  304 (330)
T ss_pred             EEECCH---HHHHCCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             999962---8897179997299679999999999999


No 146
>cd06324 PBP1_ABC_sugar_binding_like_13 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 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=87.74  E-value=2.2  Score=22.26  Aligned_cols=79  Identities=19%  Similarity=0.149  Sum_probs=54.9

Q ss_pred             CCCCHHHHHHHHHH-HHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCHHHHHHHHHHCCC
Q ss_conf             88898999999999-8619986589996358613289999999999997299987---9997489858999999997699
Q gi|254781049|r  301 GGADQDKVAAAFKI-ITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRLEGANVDIGNRLIAESGL  376 (398)
Q Consensus       301 G~a~~e~~~~a~~~-il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl~Gtn~~~g~~il~~~g~  376 (398)
                      ++.+.++-+++++- |.++|++++||       ...|.+|.|.++|+++.+.+.|   .|+-..|+  .++.+.+++-.+
T Consensus       182 ~~~~~~~a~~~~~~lL~~~Pdi~aI~-------~~ND~mAlGAv~Al~~aG~~~~~dv~IvG~Dg~--~~~~~~I~~G~~  252 (305)
T cd06324         182 AGWSEDEAYEQAENLLKRYPDVRLIW-------AANDQMAFGALRAAKEAGRKPGRDVLFGGVNWS--PEALRAIKDGRL  252 (305)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEEEEECCC--HHHHHHHHCCCE
T ss_conf             89878999999999997399998899-------788578999999999749987998899970698--999999984980


Q ss_pred             CEEEECCHHHHH
Q ss_conf             589949989999
Q gi|254781049|r  377 NVITAIDLDDAA  388 (398)
Q Consensus       377 ~~~~~~~~~~A~  388 (398)
                      ............
T Consensus       253 ~~t~~~~~~~g~  264 (305)
T cd06324         253 SVSAGGHFTEGG  264 (305)
T ss_pred             EEEECCCHHHHH
T ss_conf             699728888999


No 147
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=87.19  E-value=2.3  Score=22.05  Aligned_cols=106  Identities=12%  Similarity=0.089  Sum_probs=67.4

Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             99999999658996248842788898999999999861-99865899963586132899999999999972999879997
Q gi|254781049|r  280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR  358 (398)
Q Consensus       280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR  358 (398)
                      -...+.+..+|...-.-.=+-|..+.+.-+++++-++. .+.+.+||       ...|.+|-|+++++++.++++|==+.
T Consensus       198 ~gf~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~~~ptAi~-------~~nD~~A~g~~~~l~~~g~~VP~Dis  270 (335)
T PRK10703        198 AGFMKAMEEANIKVPEEWIVQGDFEPESGYEAMQQILSQEHRPTAVF-------CGGDIMAMGAICAADEMGLRVPQDIS  270 (335)
T ss_pred             HHHHHHHHHCCCCCCHHEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEE
T ss_conf             99999999859998813289657885889999999995699986689-------68759999999999971999999749


Q ss_pred             CCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             489858999999997699589-9499899999999985
Q gi|254781049|r  359 LEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       359 l~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      +-|-+-..   +.+...-++. ...+.++..+.|+++.
T Consensus       271 vigfDd~~---~~~~~~P~LTtv~~~~~~~g~~A~~~L  305 (335)
T PRK10703        271 VIGYDNVR---NARYFTPALTTIHQPKDRLGETAFNML  305 (335)
T ss_pred             EEEECCCH---HHHHCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             99988828---998258982799829999999999999


No 148
>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=87.14  E-value=2.3  Score=22.03  Aligned_cols=85  Identities=15%  Similarity=0.162  Sum_probs=50.8

Q ss_pred             CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf             8889899999999-986199865899963586132899999999999972999879997489858999999997699589
Q gi|254781049|r  301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI  379 (398)
Q Consensus       301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~  379 (398)
                      |..+.+.-+++++ ++.+.|.+.+||       +..|.+|.|+++++++.+.++|==+.+-|-+-.   .+..-..-++.
T Consensus       156 ~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~~~~~~~~g~~vP~di~vigfD~~---~~~~~~~p~lt  225 (265)
T cd06290         156 GDFEEESGLEAVEELLQRGPDFTAIF-------AANDQTAYGARLALYRRGLRVPEDVSLIGFDDL---PLSAYTTPPLT  225 (265)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCCE-------ECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCH---HHHHHCCCCEE
T ss_conf             66771789999999997199988421-------057899999999999809999998799999987---89973289828


Q ss_pred             -EECCHHHHHHHHHHHH
Q ss_conf             -9499899999999985
Q gi|254781049|r  380 -TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       380 -~~~~~~~A~~~~v~~~  395 (398)
                       ...+..+..++|+++.
T Consensus       226 ti~~~~~~~G~~A~~~L  242 (265)
T cd06290         226 TVRQPIEEMGQIAARAL  242 (265)
T ss_pred             EEEECHHHHHHHHHHHH
T ss_conf             99959999999999999


No 149
>pfam03709 OKR_DC_1_N Orn/Lys/Arg decarboxylase, N-terminal domain. This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure.
Probab=87.06  E-value=1.8  Score=22.73  Aligned_cols=82  Identities=15%  Similarity=0.287  Sum_probs=57.0

Q ss_pred             HHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC-CCHHHHHHHHHHC-CCCEEEECCHH
Q ss_conf             999999986199865899963586132899999999999972999879997489-8589999999976-99589949989
Q gi|254781049|r  308 VAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG-ANVDIGNRLIAES-GLNVITAIDLD  385 (398)
Q Consensus       308 ~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G-tn~~~g~~il~~~-g~~~~~~~~~~  385 (398)
                      ...+..++-+++++-++++.+       |+...++++.+++.+.++||++=-.- +.++.-...|+.. |+=-...++-+
T Consensus        26 ~~d~~~~~~~~~~i~avil~~-------~~~~~~ll~~ir~~n~~lPvFl~~~~~~~~~vp~~~l~~i~gfi~l~edt~~   98 (111)
T pfam03709        26 TDDLLSLIETFTDIAAVVLSW-------DDEARGLLDEIRRRNFDLPVFLLAETRTSEDVPLDVLREIDGFIELFEDTPE   98 (111)
T ss_pred             HHHHHHHHHHCCCCCEEEEEE-------CHHHHHHHHHHHHHCCCCCEEEEECHHHHHCCCHHHHHHHHHHHHHHCCCHH
T ss_conf             899999998387876899984-------6068999999997478999898844125750999999988786736568989


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999850
Q gi|254781049|r  386 DAAQKIVHAVK  396 (398)
Q Consensus       386 ~A~~~~v~~~k  396 (398)
                      .-++++...++
T Consensus        99 fia~~I~~aa~  109 (111)
T pfam03709        99 FIARQIEAAAR  109 (111)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999986


No 150
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=87.04  E-value=2.4  Score=22.00  Aligned_cols=91  Identities=22%  Similarity=0.265  Sum_probs=60.9

Q ss_pred             EEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC
Q ss_conf             88427888989999999998619986589996358613289999999999997299987999748985899999999769
Q gi|254781049|r  296 FLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG  375 (398)
Q Consensus       296 FlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g  375 (398)
                      |.|=+=+++.+.+..|++-.   ++ +.||  |.||..+-.+..+ +...+++   ++.- |-+-|.+.+.=.+.+++++
T Consensus       328 fiNDSKaTN~~a~~~Al~~~---~~-~iil--I~GG~~K~~d~~~-l~~~~~~---~v~~-v~~~G~~~~~i~~~l~~~~  396 (459)
T PRK02705        328 FINDSKATNYDAAEVGLKAV---PG-PIIL--IAGGEAKQGDDSA-WLKQIKA---KAAA-VLLFGEAAPELAQLLQESG  396 (459)
T ss_pred             EECCCCCCCHHHHHHHHHHC---CC-CEEE--EECCCCCCCCHHH-HHHHHHH---CCEE-EEEECCCHHHHHHHHHHCC
T ss_conf             97278788989999999828---99-8699--9567666787399-9999864---0619-9998989999999997369


Q ss_pred             C--CEEEECCHHHHHHHHHHHHHC
Q ss_conf             9--589949989999999998506
Q gi|254781049|r  376 L--NVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       376 ~--~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      +  ++..+++|++|+++|.++++.
T Consensus       397 ~~~~~~~~~~l~~Av~~a~~~a~~  420 (459)
T PRK02705        397 YTGEIEIVETLDEAVNRAFELAKE  420 (459)
T ss_pred             CCCCEEECCCHHHHHHHHHHHHHC
T ss_conf             987769859999999999998765


No 151
>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=86.89  E-value=2.4  Score=21.94  Aligned_cols=102  Identities=15%  Similarity=0.231  Sum_probs=64.0

Q ss_pred             HHHHHHHCCCCCCE--EEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             99999965899624--8842788898999999999861-99865899963586132899999999999972999879997
Q gi|254781049|r  282 TMDIIKLYGGAPAN--FLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMR  358 (398)
Q Consensus       282 tmD~i~~~Gg~pAN--FlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvR  358 (398)
                      ..+.+..+|..+-.  ..+ .|..+.+..+++++-+++ .+++.+||       ...|.+|-|+++++++.++++|==+.
T Consensus       155 ~~~al~~~gl~~~~~~i~~-~~~~~~~~g~~~~~~ll~~~~~ptai~-------~~nD~~A~g~~~~l~~~Gi~VP~Dvs  226 (283)
T cd06279         155 YLEALEEAGIDISDVPIWE-IPENDRASGEEAARELLDASPRPTAIL-------CMSDVLALGALQVARELGLRVPEDLS  226 (283)
T ss_pred             HHHHHHHCCCCCCCEEEEE-CCCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf             9999998599977205784-599999999999999995599996698-------57729999999999981899999659


Q ss_pred             CCCCC-HHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             48985-89999999976995899499899999999985
Q gi|254781049|r  359 LEGAN-VDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       359 l~Gtn-~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      +-|-+ .+.+  .+ ...+..+ ..+..+..+.|+++.
T Consensus       227 viGfDd~~~a--~~-~P~LTTI-~q~~~~~G~~A~~~L  260 (283)
T cd06279         227 VVGFDGIPEA--RL-RPGLTTV-RQPSEEKGRLAARLL  260 (283)
T ss_pred             EEEECCCHHH--HC-CCCCEEE-ECCHHHHHHHHHHHH
T ss_conf             9958988899--45-8997089-619999999999999


No 152
>PRK02006 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=86.65  E-value=2.5  Score=21.86  Aligned_cols=91  Identities=19%  Similarity=0.285  Sum_probs=61.5

Q ss_pred             EEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC
Q ss_conf             88427888989999999998619986589996358613289999999999997299987999748985899999999769
Q gi|254781049|r  296 FLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG  375 (398)
Q Consensus       296 FlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g  375 (398)
                      |-|=+=+++.+.+..|++-.  ++  +.+|  |.||..+-.+... +.+.+++.   +.-++ +-|.+.+.=.+.+.+++
T Consensus       370 ~iNDSKaTN~~at~~Al~s~--~~--~iil--I~GG~~K~~d~~~-L~~~~~~~---~k~vi-l~G~~~~~i~~~l~~~~  438 (501)
T PRK02006        370 YVDDSKGTNVGATVAALDGL--AQ--RVVL--IAGGDGKGQDFSP-LAAPVARW---ARAVV-LIGRDAPAIRAALADTG  438 (501)
T ss_pred             EECCCCCCCHHHHHHHHHHC--CC--CEEE--EEECCCCCCCHHH-HHHHHHHH---CEEEE-EECCCHHHHHHHHHCCC
T ss_conf             97378778989999999707--89--7499--9805777779799-99999853---70999-98989999999975179


Q ss_pred             CCEEEECCHHHHHHHHHHHHHC
Q ss_conf             9589949989999999998506
Q gi|254781049|r  376 LNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       376 ~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      ++++.+.+|++|+++|.++++.
T Consensus       439 ~~~~~~~~l~~Av~~a~~~a~~  460 (501)
T PRK02006        439 VPLVDAATLEEAVRAAAELAQP  460 (501)
T ss_pred             CEEEECCCHHHHHHHHHHHCCC
T ss_conf             8079859999999999975789


No 153
>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=86.56  E-value=2.5  Score=21.83  Aligned_cols=123  Identities=17%  Similarity=0.136  Sum_probs=69.7

Q ss_pred             CCCEEEEECCCHHHHH------HHHHHHHCCCCCCEEEE-CCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHH
Q ss_conf             8817999555036899------99999965899624884-278889899999999-986199865899963586132899
Q gi|254781049|r  266 DGNIGCMVNGAGLAMA------TMDIIKLYGGAPANFLD-VGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDV  337 (398)
Q Consensus       266 dG~Ig~~vnGaGlama------tmD~i~~~Gg~pANFlD-~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~  337 (398)
                      .|+|.++..-.|-.-.      ..|.++..+..--.-.+ .-+..+.++.++.++ ++.++|++++||       ...|.
T Consensus       123 ~g~v~i~~g~~~~~~~~~R~~g~~~~l~~~~~~~~~vv~~~~~~~~~~~a~~~~~~~L~~~Pdi~~I~-------~~nd~  195 (298)
T cd06302         123 KGEYAIFVGSLTATNQNAWIDAAKAYQKEKYYPMLELVDRQYGDDDADKSYQTAQELLKAYPDLKGII-------GPTSV  195 (298)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEE-------ECCCH
T ss_conf             99589998588986799999999999863489987999861378748999999999997599912999-------78981


Q ss_pred             HHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCCCEEEECCHHH----HHHHHHHHHHC
Q ss_conf             99999999997299987-99974898589999999976995899499899----99999998506
Q gi|254781049|r  338 LVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGLNVITAIDLDD----AAQKIVHAVKG  397 (398)
Q Consensus       338 vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~----A~~~~v~~~k~  397 (398)
                      +|.|.++|+++.+.+-. .|+=..++  +++.+.+++-.+......+-..    |++.++++.+|
T Consensus       196 ~a~Ga~~Al~~aG~~~~V~vvG~D~~--~~~~~~I~~G~i~atv~Q~P~~~G~~av~~a~~~~~G  258 (298)
T cd06302         196 GIPGAARAVEEAGLKGKVAVTGLGLP--NQMAPYVKSGAVKEFALWNPADLGYAAVYVAKALLEG  258 (298)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHHHCC
T ss_conf             69999999996799998599996887--9999999859826999849999999999999999779


No 154
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=86.10  E-value=2.7  Score=21.67  Aligned_cols=105  Identities=14%  Similarity=0.121  Sum_probs=67.5

Q ss_pred             HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC-CCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             9999999658996248842788898999999999861-998658999635861328999999999999729998799974
Q gi|254781049|r  281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS-DSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL  359 (398)
Q Consensus       281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~-~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl  359 (398)
                      ...+.+..+|...-.-.-+-|..+.+.-+++++-++. .+.+.+||       ...|.+|-|+++++++.++++|==+.+
T Consensus       205 G~~~al~~~gl~~~~~~i~~~~~~~~~g~~~~~~ll~~~~~ptAi~-------~~nD~~A~g~l~al~~~Gl~VP~DisV  277 (341)
T PRK11041        205 GYVQALRRCGITVDPQYIARGDFTFEAGAKAMQQLLELPQPPTAVF-------CHSDVMALGALSQAKRQGLKVPQDLSI  277 (341)
T ss_pred             HHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCEEE
T ss_conf             9999999869999910489546767999999999995599985798-------767799999999999718989996599


Q ss_pred             CCCCHHHHHHHHHHCCCCEEE-ECCHHHHHHHHHHHH
Q ss_conf             898589999999976995899-499899999999985
Q gi|254781049|r  360 EGANVDIGNRLIAESGLNVIT-AIDLDDAAQKIVHAV  395 (398)
Q Consensus       360 ~Gtn~~~g~~il~~~g~~~~~-~~~~~~A~~~~v~~~  395 (398)
                      -|-+-..   +.+-..-++.+ ..+.++..+.|+++.
T Consensus       278 iGfdd~~---~~~~~~P~LTTV~~~~~~~g~~A~~~L  311 (341)
T PRK11041        278 IGFDNID---LAQFCDPPLTTIAQPRYEIGREAMLLL  311 (341)
T ss_pred             EEECCHH---HHHCCCCCEEEEECCHHHHHHHHHHHH
T ss_conf             9988838---985269983699819999999999999


No 155
>pfam02955 GSH-S_ATP Prokaryotic glutathione synthetase, ATP-grasp domain.
Probab=85.92  E-value=2.7  Score=21.62  Aligned_cols=69  Identities=12%  Similarity=0.087  Sum_probs=42.1

Q ss_pred             CCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEE-EECCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             888815747999999999872998699971213687656565567777777079-9589999999999861876544212
Q gi|254781049|r   18 PVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVR-VESSLKSVISDIREILGSTLITKQT   96 (398)
Q Consensus        18 pvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~-l~~s~~ea~~~a~~ilg~~l~t~qt   96 (398)
                      -+|+..++++++++.+..+..+ + +|+|+---+|||              ||. +..+...+....+.+..        
T Consensus        11 ~~P~T~vt~~~~~i~~f~~~~g-~-vVvKPl~Gs~G~--------------GV~~i~~~~~~~~~i~e~~~~--------   66 (176)
T pfam02955        11 LIPPTLVTRDKEEIRAFLEEHG-D-IILKPLDGMGGA--------------GVFRIKKDDPNLNVILETLTQ--------   66 (176)
T ss_pred             CCCCEEEECCHHHHHHHHHHCC-C-EEEEECCCCCCC--------------CEEEECCCCHHHHHHHHHHHH--------
T ss_conf             0869479889999999999779-8-999957888876--------------759954783558999999984--------


Q ss_pred             CCCCCCCCCEEECCCCCC
Q ss_conf             222244330110345556
Q gi|254781049|r   97 GPTGSRVNCVYVEDGADI  114 (398)
Q Consensus        97 ~~~G~~v~~vLVEe~v~~  114 (398)
                        .+.  ..++++|+++.
T Consensus        67 --~~~--~~ii~QeyI~~   80 (176)
T pfam02955        67 --YGR--RPVMAQRYLPE   80 (176)
T ss_pred             --CCC--CCEEEEECCCC
T ss_conf             --688--83986431376


No 156
>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=85.65  E-value=2.8  Score=21.53  Aligned_cols=100  Identities=17%  Similarity=0.252  Sum_probs=54.3

Q ss_pred             HHHHCCCCCCEEEECCCCCCHHHHHHH-HHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCC
Q ss_conf             999658996248842788898999999-9998619986589996358613289999999999997299987999748985
Q gi|254781049|r  285 IIKLYGGAPANFLDVGGGADQDKVAAA-FKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGAN  363 (398)
Q Consensus       285 ~i~~~Gg~pANFlD~gG~a~~e~~~~a-~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn  363 (398)
                      .+..+|.++-.......  +.+..+++ .+++.+++.+.+||       ..-|.+|-|+++|+++.+.++|==+.+-|-+
T Consensus       142 a~~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~l~al~~~g~~vP~disIigfd  212 (266)
T cd06282         142 AMRAAGLAPLPPVEIPF--NTAALPSALLALLTAHPAPTAIF-------CSNDLLALAVIRALRRLGLRVPDDLSVVGFD  212 (266)
T ss_pred             HHHHCCCCCCCEEEECC--CHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCCEEEEEEC
T ss_conf             99986999761799348--72689999999983799984798-------5388899999999998499999984999989


Q ss_pred             HHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             89999999976995899499899999999985
Q gi|254781049|r  364 VDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       364 ~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      -..--++ -...+.. ...+.++..+.|+++.
T Consensus       213 ~~~~~~~-~~P~lTt-i~q~~~~~g~~A~~~l  242 (266)
T cd06282         213 GIAIGRL-LTPPLAT-VAQPNRDIGRQAVQRL  242 (266)
T ss_pred             CHHHHHC-CCCCCEE-EECCHHHHHHHHHHHH
T ss_conf             7089970-7999679-9869999999999999


No 157
>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=84.63  E-value=3.1  Score=21.23  Aligned_cols=84  Identities=17%  Similarity=0.219  Sum_probs=56.4

Q ss_pred             CCHHHHHHHH-HHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEE
Q ss_conf             8989999999-998619986589996358613289999999999997299987999748985899999999769958994
Q gi|254781049|r  303 ADQDKVAAAF-KIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITA  381 (398)
Q Consensus       303 a~~e~~~~a~-~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~  381 (398)
                      .+.+.-+++. +++.++|++++||       ...|.+|.|.++|+++.+++-.-|+=..++...  ...+...-+-....
T Consensus       163 ~~~~~~~~~~~~lL~~~~~~~aI~-------~~nD~~A~ga~~al~~~g~~di~viGfD~~~~~--~~~~~~~~~~~Ti~  233 (268)
T cd06323         163 FDRAKGLNVMENILQAHPDIKGVF-------AQNDEMALGAIEALKAAGKDDVKVVGFDGTPDA--LKAIKAGKMAATVA  233 (268)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEEE-------ECCCHHHHHHHHHHHHHCCCCEEEEEECCCHHH--HHHHHCCCCEEEEE
T ss_conf             027999999999986298885899-------778399999999999709998299988898899--99744599439990


Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             99899999999985
Q gi|254781049|r  382 IDLDDAAQKIVHAV  395 (398)
Q Consensus       382 ~~~~~A~~~~v~~~  395 (398)
                      .+..+..++++++.
T Consensus       234 q~~~~~g~~av~~l  247 (268)
T cd06323         234 QQPALMGRLAVETA  247 (268)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             79999999999999


No 158
>pfam01740 STAS STAS domain. The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function.
Probab=84.55  E-value=2.7  Score=21.62  Aligned_cols=81  Identities=15%  Similarity=0.315  Sum_probs=52.3

Q ss_pred             CHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHH-HHCCCCCCEEEECCCCCHHHHHHHHHHCCCC--EEE
Q ss_conf             9899999999986199865899963586132899999999999-9729998799974898589999999976995--899
Q gi|254781049|r  304 DQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAV-KEVKINIPLVMRLEGANVDIGNRLIAESGLN--VIT  380 (398)
Q Consensus       304 ~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~-~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~--~~~  380 (398)
                      +.+...+.+.-.+..+.++.+.++ |.++...|-.+-+.+..+ ++.. +.-+-+.+.|.+.+. +++++.+|+.  +..
T Consensus        23 ~a~~~~~~l~~~~~~~~~~~vvlD-~~~v~~iDssgl~~l~~~~~~~~-~~g~~l~l~~~~~~v-~~~l~~~gl~~~~~i   99 (106)
T pfam01740        23 NAEAFRERLLRAIEEGEIRHVILD-LSGVPFIDSSGLGALLELYKELR-RRGVELVLVGPSPEV-RRTLEKTGLDDIIGI   99 (106)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEEE-EECCCCCCCHHHHHHHHHHHHHH-HCCCEEEEECCCHHH-HHHHHHHCCCCEECC
T ss_conf             999999999999865899789999-70898889029999999999999-769909997699899-999998099866446


Q ss_pred             ECCHHHH
Q ss_conf             4998999
Q gi|254781049|r  381 AIDLDDA  387 (398)
Q Consensus       381 ~~~~~~A  387 (398)
                      +.+.++|
T Consensus       100 ~~s~~eA  106 (106)
T pfam01740       100 FPTVEEA  106 (106)
T ss_pred             CCCHHHC
T ss_conf             4995659


No 159
>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=84.48  E-value=3.2  Score=21.19  Aligned_cols=86  Identities=16%  Similarity=0.050  Sum_probs=51.5

Q ss_pred             CCHHHHHH-HHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHH-CC-CCE
Q ss_conf             89899999-99998619986589996358613289999999999997299987-9997489858999999997-69-958
Q gi|254781049|r  303 ADQDKVAA-AFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAE-SG-LNV  378 (398)
Q Consensus       303 a~~e~~~~-a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~-~g-~~~  378 (398)
                      .+.+..+. ...++.++|+.+...|     +...|.+|.|.++|+++.+.+-. .|+=..|+.  +..+.+++ .| +..
T Consensus       163 ~~~~~~~~~~~~~L~~~pd~~~~ai-----~~~nd~~a~Ga~~Al~~~G~~~~v~v~G~D~~~--~~~~~i~~~~g~~~a  235 (273)
T cd06305         163 NTAQDAAAQVEAVLKKYPKGGIDAI-----WAAWDEFAKGAKQALDEAGRTDEIKIYGVDISP--EDLQLMREPDSPWVA  235 (273)
T ss_pred             CHHHHHHHHHHHHHHHCCCCCEEEE-----EECCCHHHHHHHHHHHHCCCCCCCEEEEECCCH--HHHHHHHCCCCCEEE
T ss_conf             6399999999999973888762799-----935857899999999976999994899978998--999999727995599


Q ss_pred             EEECCHHHHHHHHHHHH
Q ss_conf             99499899999999985
Q gi|254781049|r  379 ITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       379 ~~~~~~~~A~~~~v~~~  395 (398)
                      ....+..+-.+.+|+.+
T Consensus       236 tv~Q~p~~~G~~av~~~  252 (273)
T cd06305         236 TAAQDPALIGKVAVRNV  252 (273)
T ss_pred             EEECCHHHHHHHHHHHH
T ss_conf             99479999999999999


No 160
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=83.97  E-value=3.3  Score=21.04  Aligned_cols=117  Identities=13%  Similarity=0.155  Sum_probs=73.1

Q ss_pred             CEEEEECCC-HHH-----HHHHHHHHHCCCCC-CEEEECCCCCCHHHHHHHHHHHHCCC-C-CCEEEEECCCCHHHHHHH
Q ss_conf             179995550-368-----99999999658996-24884278889899999999986199-8-658999635861328999
Q gi|254781049|r  268 NIGCMVNGA-GLA-----MATMDIIKLYGGAP-ANFLDVGGGADQDKVAAAFKIITSDS-S-VKGILINIFGGIMRCDVL  338 (398)
Q Consensus       268 ~Ig~~vnGa-Gla-----matmD~i~~~Gg~p-ANFlD~gG~a~~e~~~~a~~~il~~~-~-vk~iliNifGGI~~cd~v  338 (398)
                      +|+++..+. ..+     ....+....+|..+ ..+. .-|..+.+.-+++++-++... . +.+||       ...|.+
T Consensus       177 ~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~~~~~i-~~~~~~~~~g~~~~~~ll~~~~~~ptAif-------~~nD~~  248 (333)
T COG1609         177 RIAFIGGPLDSSASRERLEGYRAALREAGLPINPEWI-VEGDFSEESGYEAAERLLARGEPRPTAIF-------CANDLM  248 (333)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCEE-EECCCCHHHHHHHHHHHHHCCCCCCCEEE-------ECCCHH
T ss_conf             5999967987721899999999999975999774236-61678878999999999854899997899-------878099


Q ss_pred             HHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             99999999972999879997489858999999997699589-9499899999999985
Q gi|254781049|r  339 VKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       339 A~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      |.|+++++++.++++|==+.+-|-+-.   .+-+-..-++. ...+..+..++|+++.
T Consensus       249 Alg~l~~~~~~g~~vP~disviGfDd~---~~~~~~~P~LTTv~~~~~~~G~~A~~~L  303 (333)
T COG1609         249 ALGALRALRELGLRVPEDLSVIGFDDI---ELARFLTPPLTTVRQPIEELGRRAAELL  303 (333)
T ss_pred             HHHHHHHHHHCCCCCCCCEEEEEECCH---HHHHHCCCCEEEEECCHHHHHHHHHHHH
T ss_conf             999999999808999987899998884---7765158980699509999999999999


No 161
>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=83.64  E-value=3.4  Score=20.96  Aligned_cols=85  Identities=13%  Similarity=0.117  Sum_probs=51.4

Q ss_pred             CCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE
Q ss_conf             8889899999999986-199865899963586132899999999999972999879997489858999999997699589
Q gi|254781049|r  301 GGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI  379 (398)
Q Consensus       301 G~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~  379 (398)
                      |.-+.+.-+++.+.++ .+++..+||       +..|.+|.|+++++++.+.++|==|.+-|-+-..-.+++ ...+.. 
T Consensus       159 ~~~s~~~~~~~~~~ll~~~~~~tai~-------~~nD~~A~g~~~~l~~~g~~iP~dvsiigfD~~~~~~~~-~P~LTt-  229 (270)
T cd01545         159 GDFTFESGLEAAEALLALPDRPTAIF-------ASNDDMAAGVLAVAHRRGLRVPDDLSVVGFDDTPIATTI-WPPLTT-  229 (270)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHHHHC-CCCCEE-
T ss_conf             65310269999999985599985899-------788899999999999818999998699998885999835-898249-


Q ss_pred             EECCHHHHHHHHHHH
Q ss_conf             949989999999998
Q gi|254781049|r  380 TAIDLDDAAQKIVHA  394 (398)
Q Consensus       380 ~~~~~~~A~~~~v~~  394 (398)
                      ...+..+..++|++.
T Consensus       230 i~q~~~~~g~~A~~~  244 (270)
T cd01545         230 VRQPIAEMARAAAEL  244 (270)
T ss_pred             EECCHHHHHHHHHHH
T ss_conf             971999999999999


No 162
>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=83.44  E-value=3.5  Score=20.91  Aligned_cols=86  Identities=20%  Similarity=0.245  Sum_probs=55.6

Q ss_pred             CCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf             8889899999999986-19986589996358613289999999999997299987-999748985899999999769958
Q gi|254781049|r  301 GGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP-LVMRLEGANVDIGNRLIAESGLNV  378 (398)
Q Consensus       301 G~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p-ivvRl~Gtn~~~g~~il~~~g~~~  378 (398)
                      +..+.+..+++++-++ +.|++.+||       +.-|.+|.|+++|+++.+.+-. -|+=..++  ++....+.+..+-.
T Consensus       161 ~~~~~~~~~~~~~~~l~~~~~~~ai~-------~~nd~~a~g~~~al~~~g~~~di~viG~D~~--~~~~~~~~~~~~lt  231 (267)
T cd01536         161 GNWDREKALQAMEDLLQANPDIDAIF-------AANDSMALGAVAALKAAGRKGDVKIVGVDGS--PEALAAIKEGGILA  231 (267)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCEEEE-------ECCCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCCEE
T ss_conf             01102578899997764179862999-------7164999999999997699999399998983--99999985599659


Q ss_pred             EEECCHHHHHHHHHHHH
Q ss_conf             99499899999999985
Q gi|254781049|r  379 ITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       379 ~~~~~~~~A~~~~v~~~  395 (398)
                      ....+..+..++++++.
T Consensus       232 tv~q~~~~~G~~a~~~l  248 (267)
T cd01536         232 TVAQDPYTQGYLAVEAA  248 (267)
T ss_pred             EEECCHHHHHHHHHHHH
T ss_conf             99279999999999999


No 163
>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=83.04  E-value=3.6  Score=20.80  Aligned_cols=84  Identities=13%  Similarity=0.167  Sum_probs=54.5

Q ss_pred             CCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEE
Q ss_conf             88898999999999861998658999635861328999999999999729998799974898589999999976995899
Q gi|254781049|r  301 GGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVIT  380 (398)
Q Consensus       301 G~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~  380 (398)
                      +..+.+.-+.+++.+++. ++.+||       ...|.+|.|+++++++.+.++|==+.+-|-+-.+   +.....-++.+
T Consensus       157 ~~~~~~~~~~~~~~~l~~-~p~ai~-------~~nD~~A~g~~~~l~~~g~~vP~dvsvvgfd~~~---~~~~~~p~lTT  225 (265)
T cd06299         157 GGYSQESGYAGATKLLDQ-GATAII-------AGDSMMTIGAIRAIHDAGLVIGEDISLIGFDDLP---VFRLQTPPLTV  225 (265)
T ss_pred             ECCCHHHHHHHHHHHHHC-CCCEEE-------CCCCHHHHHHHHHHHHHCCCCCCCEEEEEECCHH---HHHHCCCCEEE
T ss_conf             403557899999999963-998545-------0685889999999998389999934999999758---89853998399


Q ss_pred             -ECCHHHHHHHHHHHH
Q ss_conf             -499899999999985
Q gi|254781049|r  381 -AIDLDDAAQKIVHAV  395 (398)
Q Consensus       381 -~~~~~~A~~~~v~~~  395 (398)
                       ..+..+..+.|+++.
T Consensus       226 v~~~~~~~g~~A~~~L  241 (265)
T cd06299         226 IDQQVEQMGKRAVDML  241 (265)
T ss_pred             EECCHHHHHHHHHHHH
T ss_conf             9809999999999999


No 164
>PRK10669 putative cation:proton antiport protein; Provisional
Probab=82.62  E-value=3.7  Score=20.70  Aligned_cols=89  Identities=18%  Similarity=0.292  Sum_probs=58.1

Q ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH
Q ss_conf             99624884278889899999999986199865899963586132899999999999972999879997489858999999
Q gi|254781049|r  291 GAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRL  370 (398)
Q Consensus       291 g~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i  370 (398)
                      |.|+=|    |.++.+.+-++..+    .+.|.+.+-+     .-+.-+.-++...++..+++||++|-.   .++-.+.
T Consensus       460 g~~v~~----GDa~~~~~L~~agi----~~A~~vvit~-----~d~~~~~~iv~~~r~~~p~~~IiaRa~---~~~~~~~  523 (558)
T PRK10669        460 GIRAVL----GNAANEEIMQLAHL----DCARWLLLTI-----PNGYEAGEIVASAREKNPDIEIIARAH---YDDEVAY  523 (558)
T ss_pred             CCEEEE----ECCCCHHHHHHCCC----CCCCEEEEEE-----CCHHHHHHHHHHHHHHCCCCEEEEEEC---CHHHHHH
T ss_conf             997999----78998899985791----3249999981-----988999999999998786986999979---8999999


Q ss_pred             HHHCCCCEEEECCHHHHHHHHHHHHH
Q ss_conf             99769958994998999999999850
Q gi|254781049|r  371 IAESGLNVITAIDLDDAAQKIVHAVK  396 (398)
Q Consensus       371 l~~~g~~~~~~~~~~~A~~~~v~~~k  396 (398)
                      |++.|.+.... +-.|++++.+++..
T Consensus       524 L~~aGA~~VV~-~~~e~a~~m~e~l~  548 (558)
T PRK10669        524 ITERGANQVVM-GEREIARTMLELLE  548 (558)
T ss_pred             HHHCCCCEEEC-CHHHHHHHHHHHHC
T ss_conf             99779998989-37899999999857


No 165
>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=82.05  E-value=3.9  Score=20.56  Aligned_cols=106  Identities=16%  Similarity=0.161  Sum_probs=67.9

Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCC---CCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             999999996589962488427888989999999998619---98658999635861328999999999999729998799
Q gi|254781049|r  280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSD---SSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLV  356 (398)
Q Consensus       280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~---~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~piv  356 (398)
                      -...+.+..+|.....+. +.|..+.+.-+++++-+++.   ..+.+||       +..|.+|.|+++++++.++++|==
T Consensus       137 ~Gy~~al~~~g~~~~~~~-~~~~~~~~~g~~~~~~~l~~~~~~~ptAi~-------~~nD~~A~g~l~~l~~~gl~VP~D  208 (270)
T cd01544         137 TAFREYMKEKGLYDPELI-YIGDFTVESGYQLMKEALKSLGDNLPTAFF-------IASDPMAIGALRALQEAGIKVPED  208 (270)
T ss_pred             HHHHHHHHHCCCCCCCEE-EECCCCHHHHHHHHHHHHHCCCCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCCC
T ss_conf             999999998599996449-966899799999999999728878997899-------823188999999999879988776


Q ss_pred             EECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             974898589999999976995899499899999999985
Q gi|254781049|r  357 MRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       357 vRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      +.+-|-.-..-.+++ ...+.. ...+..+-.++|+++.
T Consensus       209 isviGfDd~~~~~~~-~P~LTT-V~q~~~~iG~~A~~~L  245 (270)
T cd01544         209 VSVISFNDIEVAKYV-SPPLST-VKIDTEEMGETAVDLL  245 (270)
T ss_pred             EEEEEECCHHHHHHC-CCCCEE-EECCHHHHHHHHHHHH
T ss_conf             599997780789826-899369-9829999999999999


No 166
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=81.36  E-value=4.1  Score=20.40  Aligned_cols=102  Identities=19%  Similarity=0.190  Sum_probs=61.1

Q ss_pred             HHHHHHCCC-CCCEEEECCCCCCHHHHHHHHHHHHCCCC-CCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             999996589-96248842788898999999999861998-6589996358613289999999999997299987999748
Q gi|254781049|r  283 MDIIKLYGG-APANFLDVGGGADQDKVAAAFKIITSDSS-VKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       283 mD~i~~~Gg-~pANFlD~gG~a~~e~~~~a~~~il~~~~-vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                      .+.....|. .+.+..  -|..+.+.-+++.+-++..+. ..+||       ..+|.+|-|+++++++.++++|==+.+-
T Consensus       197 ~~~~~~~~~~~~~~i~--~~~~~~~~g~~~~~~ll~~~~~p~ai~-------~~nD~~A~g~l~al~~~gi~VP~DisVi  267 (327)
T PRK10339        197 AEYGRLKQVVREEDIW--RGGFSSSSGYELAKQMLAREDYPKALF-------VASDSIAIGVLRAIHERGLNIPQDISLI  267 (327)
T ss_pred             HHHHHHCCCCCHHHEE--ECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             9999875999737558--668986999999999984699997489-------7777999999999998299999975999


Q ss_pred             CCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             98589999999976995899499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      |-+-..--+++ ...+.. ...+.++..+.||++.
T Consensus       268 gfdd~~~~~~~-~P~LTt-v~~~~~~~g~~Av~~L  300 (327)
T PRK10339        268 SVNDIPTARFT-FPPLST-VRIHSEMMGSQGVNLL  300 (327)
T ss_pred             EECCHHHHHHC-CCCCEE-EECCHHHHHHHHHHHH
T ss_conf             98973889833-899569-9869999999999999


No 167
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic; InterPro: IPR005787    Serine and threonine dehydratases ,  are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown  that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue.    This family describes a form of threonine dehydratase, with two copies of the threonine dehydratase C-terminal domain IPR001721 from INTERPRO. Members with known function participate in isoleucine biosynthesis and are inhibited by isoleucine.; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process.
Probab=80.97  E-value=3.6  Score=20.77  Aligned_cols=54  Identities=15%  Similarity=0.169  Sum_probs=31.2

Q ss_pred             CCEEECCH-HH---HHHHHHHCCCCEEE--------EECCCCCCCCCCCCCCCCCCCCCCEEEE-ECCHHHHHHHHHHHC
Q ss_conf             81574799-99---99999872998699--------9712136876565655677777770799-589999999999861
Q gi|254781049|r   21 KGVVISSV-HA---AESAIKTLPGPLYV--------VKSQIHAGGRGKGRFKELPADSKGGVRV-ESSLKSVISDIREIL   87 (398)
Q Consensus        21 ~g~~a~s~-~e---a~~~a~~ig~p~~V--------vKaQV~aGgRGKa~~~~~hk~~~GGV~l-~~s~~ea~~~a~~il   87 (398)
                      +|++|-|+ +.   ..-.+++||-+-+.        ||.|-             -|+.-|-|.| -.|-+||...|.++-
T Consensus        68 ~GVIaASAGNHAQGVAlsa~~LG~~A~IVMP~tTP~IKV~A-------------Vk~~GgeVvLhG~~y~~A~~~A~eL~  134 (508)
T TIGR01124        68 RGVIAASAGNHAQGVALSAEKLGLKAVIVMPETTPDIKVDA-------------VKAFGGEVVLHGDNYDDAKDHAIELA  134 (508)
T ss_pred             CCEEECCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCHHH-------------EECCCCEEEEECCCHHHHHHHHHHHH
T ss_conf             82012024545789987663179726987888882200120-------------31269879973798579999999999


No 168
>TIGR01859 fruc_bis_ald_ fructose-1,6-bisphosphate aldolase, class II; InterPro: IPR011289   Fructose-1,6-bisphosphate (FBP) aldolases reversibly cleave FBP to two triose phosphates, glycerone phophate and D-glyceraldehyde 3-phosphate. They play a key role in both glycolysis (FBP cleavage) and gluconeogenesis (FBP synthesis). These enzymes can be divide into two classes based on their mode of catalysis. Class I FBP aldolases form a Schiff-base intermediate between glycerone phophate and an active site lysine residue, while the class II enzymes use a divalent cation such as Zn(2+) for catalysis .   This entry represents class II FBP aldolases found in Gram-positive bacteria, a variety of Gram-negative baceria, and amitochondriate protists. These enzymes are homotetramers where each momomer forms a TIM barrel fold .; GO: 0004332 fructose-bisphosphate aldolase activity, 0008270 zinc ion binding, 0006096 glycolysis, 0030388 fructose 16-bisphosphate metabolic process.
Probab=80.67  E-value=4.4  Score=20.25  Aligned_cols=41  Identities=17%  Similarity=0.266  Sum_probs=17.5

Q ss_pred             CCCCCCHHHHHHHHHHCCC-----CHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             4457895788878875198-----88998859999999989999559
Q gi|254781049|r  161 PLIGVTSEDVASLCDMLEL-----QGQARIDGGDLFPNLYKAFCDKD  202 (398)
Q Consensus       161 ~~~gl~~~~~~~l~~~lg~-----~~~~~~~~~~ii~~L~~~f~e~D  202 (398)
                      -..|++..++++.+. ||.     .-+....|..-++++.+=|...|
T Consensus       254 ds~GIP~e~ikkAi~-lGiaKiNidTe~riAf~~~~R~~l~dy~a~d  299 (339)
T TIGR01859       254 DSKGIPEEQIKKAIK-LGIAKINIDTECRIAFTAAIRKVLEDYEAKD  299 (339)
T ss_pred             CCCCCCHHHHHHHHH-CCCCEEEECCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             777686789999997-2914176581678999999999984114355


No 169
>cd06312 PBP1_ABC_sugar_binding_like_4 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=80.20  E-value=4.5  Score=20.15  Aligned_cols=82  Identities=10%  Similarity=-0.006  Sum_probs=58.6

Q ss_pred             HHHHHHH-HHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEEC
Q ss_conf             8999999-99986199865899963586132899999999999972999-879997489858999999997699589949
Q gi|254781049|r  305 QDKVAAA-FKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAI  382 (398)
Q Consensus       305 ~e~~~~a-~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~  382 (398)
                      .+...+. -.++.++|++++||       ...|.+|.|.++|+++.+.+ .-.|+=..++.  +..+.+++-.+......
T Consensus       167 ~~~a~~~~~~~L~~~pdi~~I~-------~~nd~~a~ga~~Al~~ag~~~~i~vvg~D~~~--~~~~~i~~G~i~~tv~Q  237 (271)
T cd06312         167 PTEVASRIAAYLRANPDVDAVL-------TLGAPSAAPAAKALKQAGLKGKVKLGGFDLSP--ATLQAIKAGYIQFAIDQ  237 (271)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEE-------ECCCHHHHHHHHHHHHCCCCCCEEEEEECCCH--HHHHHHHCCCCEEEEEC
T ss_conf             9999999999998498988899-------88967899999999966999985999988999--99999986995599958


Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             9899999999985
Q gi|254781049|r  383 DLDDAAQKIVHAV  395 (398)
Q Consensus       383 ~~~~A~~~~v~~~  395 (398)
                      +-.+--.++|+..
T Consensus       238 ~p~~~Gy~aV~~l  250 (271)
T cd06312         238 QPYLQGYLPVSLL  250 (271)
T ss_pred             CHHHHHHHHHHHH
T ss_conf             9999999999999


No 170
>TIGR01768 GGGP-family geranylgeranylglyceryl phosphate synthase family protein; InterPro: IPR008205   This family contains prokaryotic proteins that are related to pcrB. Staphylococcus aureus chromosomal gene pcrA encodes a protein with significant similarity (40 0dentity) to two Escherichia coli helicases: the helicase II encoded by the uvrD gene and the Rep helicase. PcrB gene seems to belong to an operon containing at least one other gene, pcrBA, downstream from pcrB . The PcrB proteins often contain an FMN binding site although the function of these proteins is still unknown..
Probab=79.75  E-value=3.2  Score=21.16  Aligned_cols=57  Identities=26%  Similarity=0.376  Sum_probs=44.2

Q ss_pred             CCCCEEEECCCCCCH---HHHHHHHHHHHCC--CCCCEEEEECCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             996248842788898---9999999998619--9865899963586132899999999999972
Q gi|254781049|r  291 GAPANFLDVGGGADQ---DKVAAAFKIITSD--SSVKGILINIFGGIMRCDVLVKGILSAVKEV  349 (398)
Q Consensus       291 g~pANFlD~gG~a~~---e~~~~a~~~il~~--~~vk~iliNifGGI~~cd~vA~gii~a~~~~  349 (398)
                      +=|==||++||++..   ..+-...|-++++  -.-+..|  ++||-.|+-+.|+-++.|.-+.
T Consensus       159 g~~~~YLEagsgap~pvpPE~va~vk~v~~~aGyGGe~~L--~vGGGIRs~E~A~~~a~AgAD~  220 (242)
T TIGR01768       159 GMPIIYLEAGSGAPEPVPPELVAEVKKVLDKAGYGGEVKL--IVGGGIRSVEKARKLAEAGADV  220 (242)
T ss_pred             CCCEEEEECCCCCCCCCCHHHHHHHHHHHHCCCCCCCEEE--EEECCCCCHHHHHHHHHCCCCE
T ss_conf             9968999637875479745899999987410478863257--8407647889999995345989


No 171
>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=78.98  E-value=4.9  Score=19.90  Aligned_cols=83  Identities=19%  Similarity=0.229  Sum_probs=55.8

Q ss_pred             CHHHHH-HHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCE-EEE
Q ss_conf             989999-999998619986589996358613289999999999997299987999748985899999999769958-994
Q gi|254781049|r  304 DQDKVA-AAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNV-ITA  381 (398)
Q Consensus       304 ~~e~~~-~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~-~~~  381 (398)
                      +.+.-. .+-+++.++|++++||-       .-|.+|.|.++|+++.+.+-.-|+-..|+  .+++..++..+... ...
T Consensus       162 ~~~~~~~~~~~~L~~~p~~~aI~~-------~nD~~A~Ga~~al~~~g~~di~vvGfD~~--~~a~~~i~~~~p~~ttv~  232 (267)
T cd06322         162 TRAEALTAAQNILQANPDLDGIFA-------FGDDAALGAVSAIKAAGRDNVKVIGFDGM--PEARKAVDGEPPFVAVIR  232 (267)
T ss_pred             CHHHHHHHHHHHHHHCCCCCEEEE-------CCCHHHHHHHHHHHHCCCCCCEEEEECCC--HHHHHHHHHCCCCEEEEE
T ss_conf             879999999999862877748998-------18799999999999759999889999494--999999970898789996


Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             99899999999985
Q gi|254781049|r  382 IDLDDAAQKIVHAV  395 (398)
Q Consensus       382 ~~~~~A~~~~v~~~  395 (398)
                      .+..+-.+++++++
T Consensus       233 Q~~~~~G~~av~~l  246 (267)
T cd06322         233 QYPDQMGKKAIDAA  246 (267)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             89999999999999


No 172
>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=78.89  E-value=5  Score=19.88  Aligned_cols=106  Identities=12%  Similarity=0.097  Sum_probs=62.2

Q ss_pred             HHHHHHHHCCCCCC--EEEECCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEE
Q ss_conf             99999996589962--4884278889899999999-98619986589996358613289999999999997299987999
Q gi|254781049|r  281 ATMDIIKLYGGAPA--NFLDVGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVM  357 (398)
Q Consensus       281 atmD~i~~~Gg~pA--NFlD~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivv  357 (398)
                      ...+.+..+|.++-  .+.+.-...+.+...+.+. .+.+.|+..+||.       ..|.+|-|+++++++.++++|==+
T Consensus       129 Gf~~al~~~g~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~ptAi~~-------~nD~~A~g~l~~l~~~Gi~VP~di  201 (265)
T cd01543         129 AFRQLVAEAGYECSFFYRGLSTDAQSWEEEQEELAQWLQSLPKPVGIFA-------CTDARARQLLEACRRAGIAVPEEV  201 (265)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEE-------CCHHHHHHHHHHHHHHHCCCCCCE
T ss_conf             9999999779997634124544675399999999999835999839998-------836999999999998322577755


Q ss_pred             ECCCCC-HHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             748985-89999999976995899499899999999985
Q gi|254781049|r  358 RLEGAN-VDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       358 Rl~Gtn-~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      .+-|-+ ......+. ...+.- ...+.++..++|+++.
T Consensus       202 sViGfD~~~~~~~~~-~P~LTt-V~q~~~~mG~~Aa~lL  238 (265)
T cd01543         202 AVLGVDNDELICELS-RPPLSS-VEQNAERIGYEAAKLL  238 (265)
T ss_pred             EEEEECCCHHHHHHC-CCCCCE-EEECHHHHHHHHHHHH
T ss_conf             999982868889527-999733-9629999999999999


No 173
>KOG1255 consensus
Probab=77.89  E-value=5.3  Score=19.69  Aligned_cols=108  Identities=19%  Similarity=0.328  Sum_probs=67.4

Q ss_pred             CEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEE-EECCCCHHHHHHH
Q ss_conf             6442288179995550368999999996589962488427888-9899999999986199865899-9635861328999
Q gi|254781049|r  261 SYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGIL-INIFGGIMRCDVL  338 (398)
Q Consensus       261 ~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~il-iNifGGI~~cd~v  338 (398)
                      .++.-.|.||++.--+-|+--..-.-...|.-..-..-+||.| +-..-..++++.|.||..++|. |-=.||  ..++-
T Consensus       171 g~Ihk~G~IGIVSRSGTLTYEaVhQTT~vglGQslcvGiGGDpFnGT~FID~L~vFl~D~~t~GIiliGEIGG--~AEe~  248 (329)
T KOG1255         171 GHIHKRGKIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTNFIDCLEVFLEDPETEGIILIGEIGG--SAEEE  248 (329)
T ss_pred             CCCCCCCEEEEEECCCCEEEHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHCCCCCCEEEEEECCCC--HHHHH
T ss_conf             1146686268996587246004012041356634688614788899648999998825856341799961477--14688


Q ss_pred             HHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH
Q ss_conf             99999999972999879997489858999999
Q gi|254781049|r  339 VKGILSAVKEVKINIPLVMRLEGANVDIGNRL  370 (398)
Q Consensus       339 A~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i  370 (398)
                      |--.++....-...+|+|--+.|.-+-.|+|+
T Consensus       249 AA~flk~~nSg~~~kPVvsFIAG~tAppGrRM  280 (329)
T KOG1255         249 AAEFLKEYNSGSTAKPVVSFIAGVTAPPGRRM  280 (329)
T ss_pred             HHHHHHHHCCCCCCCCEEEEEECCCCCCCCCC
T ss_conf             99999984158988864578514657986534


No 174
>TIGR02086 IPMI_arch 3-isopropylmalate dehydratase, large subunit; InterPro: IPR011826   3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus .    This entry represents the large subunit of 3-isopropylmalate dehydratase (LeuC), as well as homoaconitase enzymes, from prokaryotes. Homoaconitase, aconitase and 3-isopropylmalate dehydratase have similar overall structures and domain organisation . All are dehydratases that bind a [4Fe-4S]-cluster.   Information about related proteins can be found at Protein of the Month: Aconitase .; GO: 0003861 3-isopropylmalate dehydratase activity, 0051539 4 iron 4 sulfur cluster binding, 0009098 leucine biosynthetic process.
Probab=76.87  E-value=5.6  Score=19.53  Aligned_cols=165  Identities=19%  Similarity=0.167  Sum_probs=101.4

Q ss_pred             HHHHHC-CCCCCCCEEEC-----------CHHHHHHHHHHCC---CCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf             999986-89888815747-----------9999999998729---98699971213687656565567777777079958
Q gi|254781049|r   10 ALLRKY-NVPVAKGVVIS-----------SVHAAESAIKTLP---GPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVES   74 (398)
Q Consensus        10 ~lL~~~-GIpvp~g~~a~-----------s~~ea~~~a~~ig---~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~   74 (398)
                      +||++. |-+|-+|.++.           |.--+.+..++++   +|.-|.+.|       |+..-+=|..-.--|+.++
T Consensus         6 KILS~kvG~~V~aGE~V~v~VD~am~hDGt~p~~i~~l~~~g~rGG~~~v~~p~-------k~v~~fDH~~P~~~v~~A~   78 (431)
T TIGR02086         6 KILSEKVGRPVEAGEIVEVEVDLAMAHDGTGPLAIKALRELGERGGMAKVEDPE-------KIVIVFDHVVPAPTVEAAE   78 (431)
T ss_pred             HHHHHHCCCCCCCCCEEEEECCEEEEECCCHHHHHHHHHHHHHCCCCCCCCCCC-------EEEEEEECCCCCCCHHHHH
T ss_conf             888985679878865799702599996487178999999997347867664686-------4899982688996567788


Q ss_pred             CHHHHHHHHHHHCCCCCCC-CCCCCCCCCCCCEEECC-CCCCCEEEEEEE-EEECCCCCEEEEEECCCCCCHH------H
Q ss_conf             9999999999861876544-21222224433011034-555650589999-9834778048998447884024------5
Q gi|254781049|r   75 SLKSVISDIREILGSTLIT-KQTGPTGSRVNCVYVED-GADILRELYLSL-LVDRTSGMVAFIASTQGGMDIE------E  145 (398)
Q Consensus        75 s~~ea~~~a~~ilg~~l~t-~qt~~~G~~v~~vLVEe-~v~~~~E~ylgi-~~Dr~~~~~vii~S~~GGvdIE------~  145 (398)
                      ...+.+++++++   .|.. .+.+ .| .+++||+|+ .+...+ +.+|- ...+..|..-.++.+.|+.|+=      +
T Consensus        79 ~Q~~~REF~K~~---gI~~f~~~g-~G-IcHQ~L~E~Gya~PG~-vvvG~DSHT~T~GA~GAFA~GmGATDvA~a~~~G~  152 (431)
T TIGR02086        79 LQKEIREFAKRH---GIKVFFDVG-EG-ICHQVLVEKGYAEPGM-VVVGADSHTCTSGALGAFATGMGATDVAIALATGK  152 (431)
T ss_pred             HHHHHHHHHHHC---CCCEEEECC-CE-EEEEEEEECCCCCCCE-EEEECCCCCCHHHCHHHEEECCCHHHHHHHHHHCC
T ss_conf             778999888766---870599879-80-2778865306247761-89952677400000023042578689999998286


Q ss_pred             HHHHCHHHHEEEECC--CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCC--CCC
Q ss_conf             557483122033214--445789578887887519888998859999999989999559751--023
Q gi|254781049|r  146 VAKDYPQKIFKLLID--PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDKDMSL--LEI  208 (398)
Q Consensus       146 va~~~p~~I~~~~id--~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~Da~l--iEI  208 (398)
                      .|-+-|+.|. +.++  |....+                    .+|++.++.+.+..-.++.  +|+
T Consensus       153 ~W~~VPe~~~-V~~~G~l~~~v~--------------------AKDv~L~~~~~lg~~gatY~a~E~  198 (431)
T TIGR02086       153 TWLKVPESIK-VVVEGKLEEGVT--------------------AKDVALEIVGELGADGATYMAIEF  198 (431)
T ss_pred             CEEECCEEEE-EEEEECCCCCEE--------------------HHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             1364580899-998721698602--------------------248898999984878764016987


No 175
>PRK06241 phosphoenolpyruvate synthase; Validated
Probab=76.71  E-value=5.7  Score=19.48  Aligned_cols=110  Identities=17%  Similarity=0.148  Sum_probs=59.9

Q ss_pred             HHHHCCCCCCCCEEECCHH---------------------------------------------------HHHHHHHHCC
Q ss_conf             9998689888815747999---------------------------------------------------9999998729
Q gi|254781049|r   11 LLRKYNVPVAKGVVISSVH---------------------------------------------------AAESAIKTLP   39 (398)
Q Consensus        11 lL~~~GIpvp~g~~a~s~~---------------------------------------------------ea~~~a~~ig   39 (398)
                      -|.+.|+|||+|.++++..                                                   +...+...++
T Consensus        25 ~l~~~G~pVP~gfvit~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~~~~p~~~~~~i~~~~~~~~  104 (870)
T PRK06241         25 ELSKAGIPVPEGFCVTTEAYKKFIESNEELDELLDQLTLLKREDREQIGEISKKIREVIRAIEIPEDIKEAIAAALSKFG  104 (870)
T ss_pred             HHHHCCCCCCCCEEEHHHHHHHHHHCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC
T ss_conf             99978899999687519999999980885689999997267765777999999999999828998899999999999827


Q ss_pred             --CCEEEEECCCCCCCCCCCCCCCCCCCCCCEEE--E-ECCHHHHHHHHHHHCCCC----CCCCCCCCCCCC----CCCE
Q ss_conf             --98699971213687656565567777777079--9-589999999999861876----544212222244----3301
Q gi|254781049|r   40 --GPLYVVKSQIHAGGRGKGRFKELPADSKGGVR--V-ESSLKSVISDIREILGST----LITKQTGPTGSR----VNCV  106 (398)
Q Consensus        40 --~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~--l-~~s~~ea~~~a~~ilg~~----l~t~qt~~~G~~----v~~v  106 (398)
                        .|+ .|.+--.       ..+....|..|---  + +...+++.++.++.+.+-    .+... ...|..    --.|
T Consensus       105 ~~~~~-aVRSSa~-------~ED~~~~sfAGq~dt~L~v~~~~~l~~ai~~c~aS~~~~ra~~YR-~~~~~~~~~~~maV  175 (870)
T PRK06241        105 EDHAY-AVRSSAT-------AEDLPTASFAGQQDTYLNVIGKEAILQHIRKCWASLFTDRAVIYR-LQNGFDHRKVSMSV  175 (870)
T ss_pred             CCCCE-EEECCCC-------CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHH-HHCCCCHHHHCCEE
T ss_conf             99878-9967661-------247977773544112068899899999999999706889999999-98499917744057


Q ss_pred             EECCCCCCCEEEEEEEEEECCCCC
Q ss_conf             103455565058999998347780
Q gi|254781049|r  107 YVEDGADILRELYLSLLVDRTSGM  130 (398)
Q Consensus       107 LVEe~v~~~~E~ylgi~~Dr~~~~  130 (398)
                      +|++|++... -=+.++.||.++.
T Consensus       176 vVQ~Mv~~~~-sGV~FT~dP~tg~  198 (870)
T PRK06241        176 VVQKMVFPEA-SGILFTADPVTGN  198 (870)
T ss_pred             EEEECCCCCC-CEEEEECCCCCCC
T ss_conf             8885114764-2699977888899


No 176
>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=76.28  E-value=5.9  Score=19.41  Aligned_cols=85  Identities=16%  Similarity=0.235  Sum_probs=57.2

Q ss_pred             CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf             8889899999999-986199865899963586132899999999999972999-87999748985899999999769958
Q gi|254781049|r  301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNV  378 (398)
Q Consensus       301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~  378 (398)
                      +..+.+.-+++++ ++.++|++++||..  ++     .++ |+++|+++.+.. ...+|=..++  .+..+.|++-.+..
T Consensus       166 ~~~~~~~a~~~~~~lL~~~Pdi~ai~~~--~~-----~~~-ga~~Al~~~g~~~~v~vvg~D~~--~~~~~~l~~G~i~a  235 (275)
T cd06307         166 GLDDPARAYEATRKLLARHPDLVGIYNA--GG-----GNR-GVIRALREAGRAGKVVFVGHELT--PETRAALRDGTIDA  235 (275)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEEC--CC-----CHH-HHHHHHHHCCCCCCEEEEECCCC--HHHHHHHHCCCCEE
T ss_conf             7886599999999999749996299984--87-----169-99999997399998699962799--89999998198379


Q ss_pred             EEECCHHHHHHHHHHHH
Q ss_conf             99499899999999985
Q gi|254781049|r  379 ITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       379 ~~~~~~~~A~~~~v~~~  395 (398)
                      ....+-.+-.+++|+++
T Consensus       236 ~v~Q~P~~~G~~Av~~l  252 (275)
T cd06307         236 VIDQDPGHLARSAVRVL  252 (275)
T ss_pred             EEECCHHHHHHHHHHHH
T ss_conf             99359999999999999


No 177
>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=75.51  E-value=6.2  Score=19.27  Aligned_cols=95  Identities=17%  Similarity=0.260  Sum_probs=59.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHC
Q ss_conf             48842788898999999999861998658999635861328999999999999729998799974898589999999976
Q gi|254781049|r  295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAES  374 (398)
Q Consensus       295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~  374 (398)
                      -|.|=+=+++.+.+..|++-+.+...=+.||  |.||..+-.+..+ +.+.+.+   ++.-++ +-|...+.=.+.+.+ 
T Consensus       320 ~fiNDSKaTN~~at~~Al~~~~~~~~~~iil--I~GG~~K~~d~~~-l~~~~~~---~v~~v~-l~G~~~~~i~~~l~~-  391 (448)
T PRK03803        320 RYYNDSKGTNVGATLAAIEGLGADIEGKLVL--IAGGQGKGADFSE-LREPVAK---YCRAVV-LIGRDAELIEQALGD-  391 (448)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEE--EECCCCCCCCHHH-HHHHHHH---CCEEEE-EECCCHHHHHHHHCC-
T ss_conf             9996899899789999999646523686899--9378666668799-9999973---660999-979599999997506-


Q ss_pred             CCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             99589949989999999998506
Q gi|254781049|r  375 GLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       375 g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      ..+++.+.+|++|++.|.+.++.
T Consensus       392 ~~~~~~~~~l~~Av~~a~~~a~~  414 (448)
T PRK03803        392 AVPLVRAATLEEAVTQAAELAQP  414 (448)
T ss_pred             CCCEEECCCHHHHHHHHHHHCCC
T ss_conf             89879949999999999985789


No 178
>TIGR00097 HMP-P_kinase phosphomethylpyrimidine kinase; InterPro: IPR004399 Phosphomethylpyrimidine kinase (2.7.4.7 from EC), also known as HMP-phosphate kinase, catalyses the phosphorylation of HMP-P to HMP-PP in the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine during the biosynthesis of thiamine.; GO: 0008972 phosphomethylpyrimidine kinase activity, 0009228 thiamin biosynthetic process.
Probab=75.30  E-value=6.2  Score=19.24  Aligned_cols=111  Identities=19%  Similarity=0.172  Sum_probs=49.1

Q ss_pred             CCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEE--EEEEECCCCCEEEEEECCCCCCHHHHHHHCH
Q ss_conf             89999999999861876544212222244330110345556505899--9998347780489984478840245557483
Q gi|254781049|r   74 SSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYL--SLLVDRTSGMVAFIASTQGGMDIEEVAKDYP  151 (398)
Q Consensus        74 ~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~yl--gi~~Dr~~~~~vii~S~~GGvdIE~va~~~p  151 (398)
                      -.|+-+.+-.+..+. .+ ..+.-.-|...+.=+||-=+.--+||=+  -+++|     |||+ |.-|....++-+-.  
T Consensus        50 ipp~~V~aQl~aV~~-D~-~~~a~KtGML~saeIve~Va~~l~~y~~~~~~VvD-----PVMV-AksG~~Ll~~~a~~--  119 (264)
T TIGR00097        50 IPPDFVEAQLDAVLS-DI-KVDAVKTGMLASAEIVEAVAKKLREYDVQIPIVVD-----PVMV-AKSGAALLEEEAVE--  119 (264)
T ss_pred             CCHHHHHHHHHHHHH-CC-CCCEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEC-----CCEE-ECCCCCCCCHHHHH--
T ss_conf             587799999999861-08-96558862456707778667765404883038976-----7216-52875465478999--


Q ss_pred             HHHEEE--ECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHH-HH
Q ss_conf             122033--21444578957888788751988899885999999998-99
Q gi|254781049|r  152 QKIFKL--LIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLY-KA  197 (398)
Q Consensus       152 ~~I~~~--~id~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~-~~  197 (398)
                       .+++.  |+-...-+..+++..|+..  .+-+..+++.+-.++|+ ++
T Consensus       120 -~l~~~LLP~A~~~TPN~pEAe~L~g~--~~I~~~~dm~~AAk~l~~~l  165 (264)
T TIGR00097       120 -ALKKRLLPLATLVTPNLPEAEALLGA--TKIRTEEDMIKAAKKLREEL  165 (264)
T ss_pred             -HHHHHHCCCEEEECCCHHHHHHHCCC--CCCCCHHHHHHHHHHHHHHH
T ss_conf             -99997387114306897999998089--66589899999999998851


No 179
>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=72.44  E-value=7.3  Score=18.79  Aligned_cols=43  Identities=26%  Similarity=0.444  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             89999999998619986589996358613289999999999997299987
Q gi|254781049|r  305 QDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP  354 (398)
Q Consensus       305 ~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p  354 (398)
                      .+-++-.-++.-+.|++.+||+       --|++|=||++|.-+.++++|
T Consensus       224 ~~G~K~~~~l~~s~p~~tAv~v-------~~DE~A~G~lnaa~D~Gi~VP  266 (332)
T TIGR01481       224 DAGVKLAAELLESSPKITAVVV-------ADDELAIGILNAALDAGIKVP  266 (332)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEE-------CCHHHHHHHHHHHHHCCCCCC
T ss_conf             4469999999853899658998-------182889999999985789887


No 180
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase; InterPro: IPR005246   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   All known phenylalanyl-tRNA synthetases, excepting a monomeric mitochondrial form, have an alpha 2 beta 2 heterotetrameric structure. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains but is longer and of unknown function; more generally, it resembles class 2 aminoacyl tRNA ligases. .
Probab=72.38  E-value=3.8  Score=20.68  Aligned_cols=97  Identities=21%  Similarity=0.247  Sum_probs=50.2

Q ss_pred             EEECCCCCEEEEEEEEEECC-----CHHHHHHHHHHHH---------CCCCCCHHHHHHHHCCCC--EEE-CCCCEEEEE
Q ss_conf             79905996799400132157-----3556410278631---------000156222457753986--442-288179995
Q gi|254781049|r  211 LIIMKNGRLRVLDSKISFDD-----NALYRHLDIQELR---------DVSEEDSREIEAKQHNLS--YIA-LDGNIGCMV  273 (398)
Q Consensus       211 Lvvt~dg~vvAlDAKi~iDD-----nA~fR~~~~~~~~---------d~~~~~~~E~~A~~~~l~--yv~-LdG~Ig~~v  273 (398)
                      |.-.-+-.+|.+|--+.+||     .+|-+|--+..+|         ...+++..|+.|=.--|.  -.+ -||+|=+  
T Consensus       238 LmtYhSASCVvVdeevsvDdGKaVAEgLL~qfGF~~FrFrpDEKkSKYYiP~TQTEVyAyHPkL~GsstkysdeWiEv--  315 (558)
T TIGR00470       238 LMTYHSASCVVVDEEVSVDDGKAVAEGLLEQFGFEKFRFRPDEKKSKYYIPDTQTEVYAYHPKLKGSSTKYSDEWIEV--  315 (558)
T ss_pred             CCCEEEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEE--
T ss_conf             011345466785771243642688999998708544750576464543578885056776264566644104764798--


Q ss_pred             CCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             55036899999999658996248842788898999999999861998658999635861328999999
Q gi|254781049|r  274 NGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKG  341 (398)
Q Consensus       274 nGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~g  341 (398)
                                          |.|.=|+-.|            |+.=++..=..|..=|+=|-.+|=.|
T Consensus       316 --------------------ATFG~YSPiA------------La~Y~Id~pVMNLGlGVERlAMIlyg  351 (558)
T TIGR00470       316 --------------------ATFGVYSPIA------------LAKYDIDVPVMNLGLGVERLAMILYG  351 (558)
T ss_pred             --------------------EECCCCHHHH------------HHHCCCCCCEEECCCHHHHHHHHHHC
T ss_conf             --------------------7434310467------------74168496522256318767877814


No 181
>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=70.42  E-value=8.1  Score=18.50  Aligned_cols=72  Identities=17%  Similarity=0.259  Sum_probs=40.6

Q ss_pred             HHHHHCCCCCCEEEECCCCCCH-HHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---EEEEC
Q ss_conf             9999658996248842788898-9999999998619986589996358613289999999999997299987---99974
Q gi|254781049|r  284 DIIKLYGGAPANFLDVGGGADQ-DKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---LVMRL  359 (398)
Q Consensus       284 D~i~~~Gg~pANFlD~gG~a~~-e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---ivvRl  359 (398)
                      +.++.+|.+.......  ..+. +....+.+++.+.+++++|+       ..+|.+|.|+++++++.+++ |   -|+=.
T Consensus       147 ~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~l~~~~~~~ai~-------~~~d~~a~g~~~a~~~~G~~-p~d~~iig~  216 (269)
T cd01391         147 AALKKAGIEVVAIEYG--DLDTEKGFQALLQLLKAAPKPDAIF-------ACNDEMAAGALKAAREAGLT-PGDISIIGF  216 (269)
T ss_pred             HHHHHCCCCEEEEEEE--CCCCCHHHHHHHHHHHHCCCCEEEE-------ECCHHHHHHHHHHHHHCCCC-CCCEEEEEE
T ss_conf             9999869986799971--3432148999999986189973999-------88889999999999986989-476599817


Q ss_pred             CCCCHH
Q ss_conf             898589
Q gi|254781049|r  360 EGANVD  365 (398)
Q Consensus       360 ~Gtn~~  365 (398)
                      .++...
T Consensus       217 d~~~~~  222 (269)
T cd01391         217 DGSPAA  222 (269)
T ss_pred             CCCHHH
T ss_conf             898899


No 182
>PRK10949 protease 4; Provisional
Probab=69.87  E-value=8.3  Score=18.42  Aligned_cols=247  Identities=19%  Similarity=0.275  Sum_probs=114.1

Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCH---
Q ss_conf             99999999998618765442122222443301103455565058999998347780489984478840245557483---
Q gi|254781049|r   75 SLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYP---  151 (398)
Q Consensus        75 s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p---  151 (398)
                      +.+|++++..+.       +   ..|++|-.  .-+. -....|||+-.-|.     +.| .+.|+|++.-.+...+   
T Consensus       130 ~l~eI~~AL~~F-------K---~SGK~ViA--y~d~-ysq~~YyLAS~AD~-----I~L-~P~G~v~l~Gl~~~~~y~K  190 (618)
T PRK10949        130 SMQYIGKALREF-------R---DSGKPVYA--VGDN-YSQGQYYLASFANK-----IWL-SPQGVVDLHGFATNGLYYK  190 (618)
T ss_pred             HHHHHHHHHHHH-------H---HHCCEEEE--EECC-CCCCCEEEEEECCE-----EEE-CCCCEEEEECCCHHHHHHH
T ss_conf             999999999999-------9---81993999--9667-78530102110777-----898-8996687866301177899


Q ss_pred             HHHEEEECCCCC-CCCHH--HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC-----CCCCCCCCEEEE--------C-
Q ss_conf             122033214445-78957--888788751988899885999999998999955-----975102326799--------0-
Q gi|254781049|r  152 QKIFKLLIDPLI-GVTSE--DVASLCDMLELQGQARIDGGDLFPNLYKAFCDK-----DMSLLEINPLII--------M-  214 (398)
Q Consensus       152 ~~I~~~~id~~~-gl~~~--~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~-----Da~liEINPLvv--------t-  214 (398)
                      +.+-+..|.+.. ..-.|  ....+.. -.++.+..++...++..||+-|.+.     ..+.-+++|..-        . 
T Consensus       191 ~lLdKlgI~~~vfrvG~YKSAvEpf~r-~~MS~e~re~~~~~l~~lw~~~~~~Ia~~R~l~~~~l~~~~~~~~~~l~~~~  269 (618)
T PRK10949        191 SLLDKLKVSTHVFRVGTYKSAVEPFIR-DDMSPAAREADSRWIGELWQNYLNTVAANRQITPQQLFPGAQGILEGLTKVG  269 (618)
T ss_pred             HHHHHCCCEEEEEEECCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             999974982899981375674651114-4599999999999999999999999998659997897777999999998708


Q ss_pred             CCCCEEEEEEEEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCEEEC-----------CCCEEEEECCCHHHHHHH
Q ss_conf             599679940013215735564102786310001562224577539864422-----------881799955503689999
Q gi|254781049|r  215 KNGRLRVLDSKISFDDNALYRHLDIQELRDVSEEDSREIEAKQHNLSYIAL-----------DGNIGCMVNGAGLAMATM  283 (398)
Q Consensus       215 ~dg~vvAlDAKi~iDDnA~fR~~~~~~~~d~~~~~~~E~~A~~~~l~yv~L-----------dG~Ig~~vnGaGlamatm  283 (398)
                      .+..-.|++.++ +| .-.+|..-...+.+....+..     +.++++|.+           ...|+++..=+...    
T Consensus       270 g~~a~~Al~~gL-VD-~l~~~~e~~~~l~~~~g~~~~-----~~~~~~is~~~y~~~~~~~~~~~IAVI~a~G~Iv----  338 (618)
T PRK10949        270 GDTAKYALDNKL-VD-ALASSAEIEKALTKAFGWSKT-----DKNYRAISIYDYALKTPADTGGQIAVIFANGAIM----  338 (618)
T ss_pred             CCHHHHHHHCCC-CC-CCCCHHHHHHHHHHHHCCCCC-----CCCCCEECHHHHCCCCCCCCCCEEEEEEEEEEEE----
T ss_conf             840999987699-85-467688999999998488743-----5675443287723236887798389999687685----


Q ss_pred             HHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEE--EECCCCHHH-HHHHHHHHHHHHHHCCCCCCEEEECC
Q ss_conf             999965899624884278889899999999986199865899--963586132-89999999999997299987999748
Q gi|254781049|r  284 DIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGIL--INIFGGIMR-CDVLVKGILSAVKEVKINIPLVMRLE  360 (398)
Q Consensus       284 D~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~il--iNifGGI~~-cd~vA~gii~a~~~~~~~~pivvRl~  360 (398)
                           -|-.+      .|....+.+.+.++-.-.|++||+|.  ||=-||=+- .|.|-+-|.. ++  +.++||||-|.
T Consensus       339 -----~G~~~------~g~ig~dt~~~~lr~a~~D~~VKAvVLRVnSPGGSa~ASE~I~~el~~-lk--~~gKPVVvSMG  404 (618)
T PRK10949        339 -----DGEET------PGNVGGDTTAAQIRDARLDPKVKAIVLRVNSPGGSVTASEVIRAELAA-AR--AAGKPVVVSMG  404 (618)
T ss_pred             -----CCCCC------CCCCCHHHHHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHHH-HH--HCCCCEEEEEC
T ss_conf             -----48887------886655899999999730867228999985899866789999999999-98--44997999970


Q ss_pred             CCCHHH
Q ss_conf             985899
Q gi|254781049|r  361 GANVDI  366 (398)
Q Consensus       361 Gtn~~~  366 (398)
                      +.-+.-
T Consensus       405 ~vAASG  410 (618)
T PRK10949        405 GMAASG  410 (618)
T ss_pred             CCCCCC
T ss_conf             101566


No 183
>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=68.02  E-value=9  Score=18.17  Aligned_cols=83  Identities=18%  Similarity=0.304  Sum_probs=50.3

Q ss_pred             CHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEEC
Q ss_conf             9899999999986-199865899963586132899999999999972999879997489858999999997699589949
Q gi|254781049|r  304 DQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAI  382 (398)
Q Consensus       304 ~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~  382 (398)
                      +.+.-++++.-++ +.+.+.+||       +..|.+|.|+++++++.++++|==+.+-|-+-..--+++ ...+.- ...
T Consensus       155 ~~~~~~~~~~~~l~~~~~~~ai~-------~~nD~~A~g~l~~l~~~g~~vP~disviGfDd~~~a~~~-~P~LTT-v~~  225 (263)
T cd06280         155 TAEAAEAALAAWLAAPERPEALV-------ASNGLLLLGALRAVRAAGLRIPQDLALAGFDNDPWTELV-GPGITV-IEQ  225 (263)
T ss_pred             CHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCCEEEEECCHHHHHCC-CCCCEE-EEE
T ss_conf             76789999999982799997899-------678899999999999848999998789997785888617-999779-980


Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             9899999999985
Q gi|254781049|r  383 DLDDAAQKIVHAV  395 (398)
Q Consensus       383 ~~~~A~~~~v~~~  395 (398)
                      +.++..+.|+++.
T Consensus       226 ~~~~~g~~A~~~L  238 (263)
T cd06280         226 PVEEIGRAAMSLL  238 (263)
T ss_pred             CHHHHHHHHHHHH
T ss_conf             9999999999999


No 184
>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=66.51  E-value=9.7  Score=17.98  Aligned_cols=79  Identities=10%  Similarity=0.119  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEE-EECC
Q ss_conf             899999999986199865899963586132899999999999972999879997489858999999997699589-9499
Q gi|254781049|r  305 QDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVI-TAID  383 (398)
Q Consensus       305 ~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~-~~~~  383 (398)
                      .+...+.++.+  ++...+||       +..|.+|.|+++++++.++++|==+.+-|-+-..   +.+-..-++. ...+
T Consensus       164 ~~~~~~~~~~~--~~~ptAi~-------~~nD~~A~g~~~~l~~~g~~vP~Disivgfdd~~---~~~~~~P~LTtv~~~  231 (268)
T cd06277         164 EEDIGKFIDEL--KPLPTAFF-------CSNDGVAFLLIKVLKEMGIRVPEDVSVIGFDDIE---YATIFTPPLTTVRVD  231 (268)
T ss_pred             HHHHHHHHHHC--CCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCCEEEEECCHH---HHHHCCCCEEEEEEC
T ss_conf             99999999847--88998799-------6885999999999998599999862899978878---998448980899929


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             899999999985
Q gi|254781049|r  384 LDDAAQKIVHAV  395 (398)
Q Consensus       384 ~~~A~~~~v~~~  395 (398)
                      ..+..+.|+++.
T Consensus       232 ~~~~G~~A~~~L  243 (268)
T cd06277         232 KEEMGKLAVKRL  243 (268)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 185
>pfam08886 GshA Glutamate-cysteine ligase. This is a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase.
Probab=64.92  E-value=10  Score=17.78  Aligned_cols=29  Identities=14%  Similarity=0.142  Sum_probs=12.8

Q ss_pred             CEEEEEEEEEECCCCCEEEEEECCCC-CCHH
Q ss_conf             50589999983477804899844788-4024
Q gi|254781049|r  115 LRELYLSLLVDRTSGMVAFIASTQGG-MDIE  144 (398)
Q Consensus       115 ~~E~ylgi~~Dr~~~~~vii~S~~GG-vdIE  144 (398)
                      +-+..+|-. ||+...|..+-+..|. +.+|
T Consensus       108 G~~VrvGs~-~pei~~~~~~~~~~g~~l~le  137 (404)
T pfam08886       108 GLNVRIGSL-DPEITEPTTLELPNGDTLTLE  137 (404)
T ss_pred             CCEEEEECC-CCCCCCCEEEECCCCCEEEEE
T ss_conf             966996078-701268656755899756788


No 186
>KOG3432 consensus
Probab=64.79  E-value=10  Score=17.77  Aligned_cols=64  Identities=25%  Similarity=0.384  Sum_probs=52.5

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCC
Q ss_conf             962488427888989999999998619986589996358613289999999999997299987999748985
Q gi|254781049|r  292 APANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGAN  363 (398)
Q Consensus       292 ~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn  363 (398)
                      .--||+=+--..|.+.+..+|+-.++.+.+-.||||        +.+|+-|-..+......+|-|.-+.--+
T Consensus        34 r~~Nf~vv~~~Tt~~eiedaF~~f~~RdDIaIiLIn--------q~~Ae~iR~~vD~h~~~vPAvLeIpSKd   97 (121)
T KOG3432          34 REPNFLVVDSKTTVEEIEDAFKSFTARDDIAIILIN--------QFIAEMIRDRVDAHTQAVPAVLEIPSKD   97 (121)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHCCCCCEEEEEEH--------HHHHHHHHHHHHHCCCCCCEEEEECCCC
T ss_conf             898889995568989999999863345675898773--------8899999999874034677368825878


No 187
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=64.58  E-value=11  Score=17.74  Aligned_cols=87  Identities=13%  Similarity=0.110  Sum_probs=54.9

Q ss_pred             EEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCC
Q ss_conf             88427888989999999998619986589996358613289999999999997299987999748985899999999769
Q gi|254781049|r  296 FLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESG  375 (398)
Q Consensus       296 FlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g  375 (398)
                      |.|=+=+++.+.+..|++-.   ++  .+|  |.||..+-.+... +...++    ++.-++- -|-..++=.+.|++. 
T Consensus       332 ~iNDSKaTN~~at~~Al~s~---~~--i~l--I~GG~~K~~d~~~-l~~~~~----~v~~~~l-iG~~~~~~~~~l~~~-  397 (457)
T PRK01390        332 FVNDSKATNADAAAPALSSF---PN--IYW--IAGGKPKAGGIES-LAPFFP----RIAKAYL-IGEAAEEFAATLGGA-  397 (457)
T ss_pred             EECCCCCCCHHHHHHHHHCC---CC--EEE--EECCCCCCCCHHH-HHHHHH----CCCEEEE-ECCCHHHHHHHHHCC-
T ss_conf             85377678989999999737---88--599--9450478889799-999874----3359999-898889999987367-


Q ss_pred             CCEEEECCHHHHHHHHHHHHH
Q ss_conf             958994998999999999850
Q gi|254781049|r  376 LNVITAIDLDDAAQKIVHAVK  396 (398)
Q Consensus       376 ~~~~~~~~~~~A~~~~v~~~k  396 (398)
                      .++..+.+|++|++.|+..++
T Consensus       398 ~~~~~~~~l~~av~~a~~~a~  418 (457)
T PRK01390        398 VPYEISGTLEAAVAAAARDAA  418 (457)
T ss_pred             CCEEECCCHHHHHHHHHHHHH
T ss_conf             987985989999999999998


No 188
>PRK09526 lacI lac repressor; Reviewed
Probab=63.74  E-value=11  Score=17.64  Aligned_cols=101  Identities=12%  Similarity=0.100  Sum_probs=63.3

Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCC---E
Q ss_conf             9999999965899624884278889899999999986-19986589996358613289999999999997299987---9
Q gi|254781049|r  280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIP---L  355 (398)
Q Consensus       280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~p---i  355 (398)
                      ....+.++.+|..|-.-+  -+..+.+.-+++++-++ ..++..+||       ...|.+|-|+++++++.++++|   -
T Consensus       201 ~Gf~~~~~~~~l~~~~~~--~~~~~~~~~~~~~~~~l~~~~~ptai~-------~~~D~~A~g~i~~l~~~g~~vP~Dis  271 (342)
T PRK09526        201 AGWLEYLTRNQLSPIAVR--EGDWSAMSGYQQTLQMLNEGPVFTAVL-------VANDQMALGVLRALHESGLRVPGDIS  271 (342)
T ss_pred             HHHHHHHHHCCCCCCEEE--ECCCCHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf             999999997798961699--568987899999999983699997587-------56779999999999980999999749


Q ss_pred             EEECCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             997489858999999997699589-9499899999999985
Q gi|254781049|r  356 VMRLEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       356 vvRl~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      |+=..++.      +.+-..-++. ...+.++.++.|+++.
T Consensus       272 IigfDd~~------~~~~~~P~LTtv~~p~~~ig~~A~~~L  306 (342)
T PRK09526        272 VIGYDDTE------DSSYFIPPLTTIKQDFRLLGKEAVDRL  306 (342)
T ss_pred             EEEECCCH------HHHHCCCCEEEEEECHHHHHHHHHHHH
T ss_conf             99989808------998248980899819999999999999


No 189
>TIGR01019 sucCoAalpha succinyl-CoA synthetase, alpha subunit; InterPro: IPR005810   There are four different enzymes that share a similar catalytic mechanism which involves the phosphorylation by ATP (or GTP) of a specific histidine residue in the active site. These enzymes are: ATP citrate-lyase (4.1.3.8 from EC) , the primary enzyme responsible for the synthesis of cytosolic acetyl-CoA in many tissues, catalyzes the formation of acetyl-CoA and oxaloacetate from citrate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. ATP-citrate lyase is a tetramer of identical subunits; Succinyl-CoA ligase (GDP-forming) (6.2.1.4 from EC)  is a mitochondrial enzyme that catalyzes the substrate level phosphorylation step of the tricarboxylic acid cycle: the formation of succinyl-CoA from succinate with a concomitant hydrolysis of GTP to GDP and phosphate. This enzyme is a dimer composed of an alpha and a beta subunits; Succinyl-CoA ligase (ADP-forming) (6.2.1.5 from EC)  is a bacterial enzyme that during aerobic metabolism functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP. It can also function in the other direction for anabolic purposes. This enzyme is a tetramer composed of two alpha and two beta subunits; and Malate-CoA ligase (6.2.1.9 from EC) (malyl-CoA synthetase) , is a bacterial enzyme that forms malyl-CoA from malate and CoA with the concomitant hydrolysis of ATP to ADP and phosphate. Malate-CoA ligase is composed of two different subunits.   This entry corresponds to two regions, a glycine-rich conserved region, located in the second half of ATP citrate lyase and in the alpha subunits of succinyl-CoA ligases and malate-CoA ligase; and the active site phosphorylated histidine residue, which is located some 50 residues to the C-terminal of the first region.  ; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=62.33  E-value=12  Score=17.48  Aligned_cols=104  Identities=16%  Similarity=0.312  Sum_probs=76.8

Q ss_pred             CEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCC-CHHHHHHHHHHHHCCCCCCEEEEECCCCHH-HHHHH
Q ss_conf             6442288179995550368999999996589962488427888-989999999998619986589996358613-28999
Q gi|254781049|r  261 SYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGA-DQDKVAAAFKIITSDSSVKGILINIFGGIM-RCDVL  338 (398)
Q Consensus       261 ~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a-~~e~~~~a~~~il~~~~vk~iliNifGGI~-~cd~v  338 (398)
                      .|+...|++|++...+-|+.-.+-.+...|.-.....-+||.+ +.......++....||..+.+++  .|-|- ..+.-
T Consensus       140 ~~~~~~g~~g~~~~~g~l~~~~~~~~~~~g~g~~~~~g~ggdp~~g~~~~~~~~~~~~d~~~~~~~~--~g~~gg~~~~~  217 (288)
T TIGR01019       140 GHIHKPGNVGLVSRSGTLTYEAVWQLTEAGFGQSTCVGIGGDPVNGTSFVDVLELFEEDPETEAVVL--IGEIGGSAEEE  217 (288)
T ss_pred             CEEECCCCCEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHHHHHHHCCCCCEEEEE--EECCCCCHHHH
T ss_conf             0010356400442354125777887764126620144136654455227888987514766505888--62147850367


Q ss_pred             HHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH
Q ss_conf             99999999972999879997489858999999
Q gi|254781049|r  339 VKGILSAVKEVKINIPLVMRLEGANVDIGNRL  370 (398)
Q Consensus       339 A~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i  370 (398)
                      |.-.++    ...+.|++--+.|...-.|+++
T Consensus       218 ~~~~~~----~~~~~p~~~~~~g~~~p~g~~~  245 (288)
T TIGR01019       218 AADFIK----ENLSKPVVGFIAGLTAPPGKRL  245 (288)
T ss_pred             HHHHHH----HHCCCCHHHHHCCCCCCCCCCC
T ss_conf             899987----5214421111102346754323


No 190
>PTZ00294 glycerol kinase; Provisional
Probab=61.68  E-value=12  Score=17.40  Aligned_cols=92  Identities=13%  Similarity=0.173  Sum_probs=57.5

Q ss_pred             CEEEECCCCCCHHHHHHHH------------HHHHCCC--CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             2488427888989999999------------9986199--8658999635861328999999999999729998799974
Q gi|254781049|r  294 ANFLDVGGGADQDKVAAAF------------KIITSDS--SVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL  359 (398)
Q Consensus       294 ANFlD~gG~a~~e~~~~a~------------~~il~~~--~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl  359 (398)
                      +.|+-++-..+...+++|+            +.+..+.  +++.|.  +.||.++-+..-+=+.+.+     ++||.+--
T Consensus       373 g~~~Gl~~~~~~~~i~RAvlEgia~~~r~~~e~l~~~~G~~~~~I~--~~GG~a~s~lw~Qi~ADv~-----g~pV~~~~  445 (510)
T PTZ00294        373 GTIVGMTYKTTRAHIIRAALEAIALQLNDVVLAMKRDSGIELNSLR--VDGGLTKNKLLMQIQADIL-----GVKLEVPE  445 (510)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEE--EECCCHHCHHHHHHHHHHH-----CCEEEECC
T ss_conf             2224888889999999999998999999999999986099978799--9778323899999999965-----98479468


Q ss_pred             CCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHH
Q ss_conf             89858999999997699589949989999999998
Q gi|254781049|r  360 EGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHA  394 (398)
Q Consensus       360 ~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~  394 (398)
                      .....-.|-.|+.-.+..++  .|++||+++.+..
T Consensus       446 ~~e~~alGaAilAavg~G~~--~s~~eA~~~~~~~  478 (510)
T PTZ00294        446 MHETTALGAALCAGLAAGVW--TSLEEVKALSRRE  478 (510)
T ss_pred             CCCHHHHHHHHHHHHHHCCC--CCHHHHHHHCCCC
T ss_conf             88708999999999981989--9999999747778


No 191
>pfam10281 Ish1 Putative stress-responsive nuclear envelope protein. This family of proteins found in fungi is a putative stress-responsive nuclear envelope protein Ish1.
Probab=61.64  E-value=10  Score=17.79  Aligned_cols=32  Identities=13%  Similarity=0.185  Sum_probs=25.3

Q ss_pred             CHHHHHHHHHHCCCCCCCCEEECCHHHHHHHHHH
Q ss_conf             5799999999868988881574799999999987
Q gi|254781049|r    4 HEYQAKALLRKYNVPVAKGVVISSVHAAESAIKT   37 (398)
Q Consensus         4 ~EyqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~   37 (398)
                      .+-|-|+.|.+||||+|+..-  +-++..+.+.+
T Consensus         5 s~~~Lk~wL~~~gi~~~~~~~--~rd~Ll~~a~~   36 (38)
T pfam10281         5 SDSDLKEWLDSHGIPVPQKAA--TRDELLALARK   36 (38)
T ss_pred             CHHHHHHHHHHCCCCCCCCHH--HHHHHHHHHHH
T ss_conf             488999999984997897136--89999999986


No 192
>TIGR00417 speE spermidine synthase; InterPro: IPR001045 Synonym(s): Spermidine aminopropyltransferase   A group of polyamine biosynthetic enzymes involved in the fifth (last) step in the biosynthesis of spermidine from arginine and methionine which includes; spermidine synthase (), spermine synthase () and putrescine N-methyltransferase () .   The Thermotoga maritima spermidine synthase monomer consists of two domains: an N-terminal domain composed of six beta-strands, and a Rossmann-like C- terminal domain . The larger C-terminal catalytic core domain consists of a seven-stranded beta-sheet flanked by nine alpha helices. This domain resembles a topology observed in a number of nucleotide and dinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)- dependent methyltransferase (MTases) . ; GO: 0003824 catalytic activity.
Probab=61.33  E-value=4.8  Score=19.99  Aligned_cols=51  Identities=20%  Similarity=0.160  Sum_probs=39.0

Q ss_pred             EEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECCC
Q ss_conf             11034555650589999983477804899844788402455574831220332144
Q gi|254781049|r  106 VYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDP  161 (398)
Q Consensus       106 vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~  161 (398)
                      +.=.||+.|     +.+.--++-++++++|++-|||-=|-+-.++-+.+.-+.||-
T Consensus        59 F~YhEMi~H-----vpL~~H~NPk~VLvIGGGDGG~lREV~KH~sVE~~~lVdID~  109 (284)
T TIGR00417        59 FIYHEMIAH-----VPLFAHPNPKKVLVIGGGDGGVLREVVKHKSVEKATLVDIDE  109 (284)
T ss_pred             HHHHHHHHH-----HHHHCCCCCCEEEEEECCCCCEEEEEEECCCCCEEEEEECCH
T ss_conf             356789987-----565368988547899638884687887559816799997274


No 193
>PRK00683 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=60.48  E-value=12  Score=17.27  Aligned_cols=103  Identities=14%  Similarity=0.250  Sum_probs=61.3

Q ss_pred             HHHHHHCCCCCC-----------EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf             999996589962-----------488427888989999999998619986589996358613289999999999997299
Q gi|254781049|r  283 MDIIKLYGGAPA-----------NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKI  351 (398)
Q Consensus       283 mD~i~~~Gg~pA-----------NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~  351 (398)
                      .+.++.|.|-|-           .|.|=+=+++.+.+..|++-.-  .  +.||  |.||..+-.+... +...+++   
T Consensus       268 ~~al~~F~glpHR~E~v~~~~Gv~fiNDSKaTN~~a~~~AL~s~~--~--~iil--I~GG~~K~~d~~~-L~~~~~~---  337 (418)
T PRK00683        268 LEAVATFEKPPHRMEYLGEKDGVHYINDSKATTVSAVEKALLAVG--K--DVIV--ILGGRNKGGDFPS-LLPVLRQ---  337 (418)
T ss_pred             HHHHHHCCCCCCCEEEEEEECCCEEECCCCCCCHHHHHHHHHHCC--C--CCEE--EECCCCCCCCHHH-HHHHHHH---
T ss_conf             999973488411136888817823763776789899999998567--8--8589--9757876678699-9999863---


Q ss_pred             CCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             9879997489858999999997699589949989999999998506
Q gi|254781049|r  352 NIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       352 ~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      ++.-++=+ |...++=.+.+++ .+++..+.+|++|+..|.++++.
T Consensus       338 ~vk~v~~~-G~~~~~i~~~l~~-~~~~~~~~~l~eAv~~a~~~a~~  381 (418)
T PRK00683        338 TAKHVVAM-GECRQEIAQALSE-KFPLTVVKDLQEAVSCAQEIAQP  381 (418)
T ss_pred             CCCEEEEE-CCCHHHHHHHHHC-CCCEEECCCHHHHHHHHHHHCCC
T ss_conf             18499996-8899999998756-99879859899999999984789


No 194
>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=60.41  E-value=12  Score=17.26  Aligned_cols=101  Identities=17%  Similarity=0.183  Sum_probs=58.6

Q ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHH-HCCCCCCEEEECC
Q ss_conf             9999965899624884278889899999999986-1998658999635861328999999999999-7299987999748
Q gi|254781049|r  283 MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVK-EVKINIPLVMRLE  360 (398)
Q Consensus       283 mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~-~~~~~~pivvRl~  360 (398)
                      .+.+..+|.++..  .+-+..+.+.-+++++-++ ..+.+.+||       +..|.+|-|++++++ +.+.++|==+.+-
T Consensus       138 ~~al~~~gl~~~~--~~~~~~~~~~g~~~~~~ll~~~~~ptAi~-------~~nD~~A~g~l~~l~~~~g~~vP~disvv  208 (266)
T cd06278         138 RDALAAAGVPVVV--EEAGDYSYEGGYEAARRLLASRPRPDAIF-------CANDLLAIGVMDAARQEGGLRVPEDVSVI  208 (266)
T ss_pred             HHHHHHCCCCCEE--EECCCCCHHHHHHHHHHHHHCCCCCCCCE-------ECCHHHHHHHHHHHHHHCCCCCCCCEEEE
T ss_conf             9999986999438--98189998999999999984599988625-------07789999999999973588888866999


Q ss_pred             CCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             9858999999997699589-9499899999999985
Q gi|254781049|r  361 GANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       361 Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                      |-+-.   .+-+-..-++. ...+..+..++|+++.
T Consensus       209 gfD~~---~~~~~~~p~LTtv~~~~~~~g~~A~~~L  241 (266)
T cd06278         209 GFDDI---PMAAWPSYQLTTVRQPVDRMAEEAVDLL  241 (266)
T ss_pred             EECCH---HHHHCCCCCEEEEECCHHHHHHHHHHHH
T ss_conf             87880---8985449984899839999999999999


No 195
>KOG1663 consensus
Probab=58.41  E-value=7.8  Score=18.58  Aligned_cols=28  Identities=29%  Similarity=0.264  Sum_probs=24.9

Q ss_pred             HHHHHHHHCCCCCCEEEEECCCCHHHHH
Q ss_conf             9999998619986589996358613289
Q gi|254781049|r  309 AAAFKIITSDSSVKGILINIFGGIMRCD  336 (398)
Q Consensus       309 ~~a~~~il~~~~vk~iliNifGGI~~cd  336 (398)
                      .+..+.|..||+|..-+++|+.|++.|-
T Consensus       208 ~~~n~~l~~D~rV~~s~~~igdG~~i~~  235 (237)
T KOG1663         208 LNLNKKLARDPRVYISLLPIGDGITICR  235 (237)
T ss_pred             HHHHHHHCCCCCEEEEEEECCCCEEEEC
T ss_conf             5366675048603567630368505630


No 196
>cd01820 PAF_acetylesterase_like PAF_acetylhydrolase (PAF-AH)_like subfamily of SGNH-hydrolases. Platelet-activating factor (PAF) and PAF-AH are key players in inflammation and in atherosclerosis. PAF-AH is a calcium independent phospholipase A2 which exhibits strong substrate specificity towards PAF, hydrolyzing an acetyl ester at the sn-2 position. PAF-AH also degrades a family of oxidized PAF-like phospholipids with short sn-2 residues.  In addition,  PAF and PAF-AH are associated with neural migration and mammalian reproduction.
Probab=57.18  E-value=14  Score=16.90  Aligned_cols=19  Identities=16%  Similarity=0.513  Sum_probs=14.5

Q ss_pred             CCCCCCCCCEEEECCCCCE
Q ss_conf             5975102326799059967
Q gi|254781049|r  201 KDMSLLEINPLIIMKNGRL  219 (398)
Q Consensus       201 ~Da~liEINPLvvt~dg~v  219 (398)
                      .+.+.+++++..+.++|++
T Consensus       165 ~~v~yiD~~~~fl~~dG~l  183 (214)
T cd01820         165 PNVTFLDIDKGFVQSDGTI  183 (214)
T ss_pred             CCEEEEECCHHHCCCCCCC
T ss_conf             8858972742311999992


No 197
>PRK12412 pyridoxal kinase; Reviewed
Probab=57.08  E-value=14  Score=16.89  Aligned_cols=17  Identities=24%  Similarity=0.264  Sum_probs=8.9

Q ss_pred             CCCHHHHHHHHHHHHCC
Q ss_conf             55036899999999658
Q gi|254781049|r  274 NGAGLAMATMDIIKLYG  290 (398)
Q Consensus       274 nGaGlamatmD~i~~~G  290 (398)
                      .|.|=+.++.=+-...-
T Consensus       209 HGTGCtlSSAIAa~LA~  225 (268)
T PRK12412        209 HGAGCTYSAAITAELAK  225 (268)
T ss_pred             CCHHHHHHHHHHHHHHC
T ss_conf             30889999999999987


No 198
>TIGR01320 mal_quin_oxido malate:quinone-oxidoreductase; InterPro: IPR006231   The membrane-associated enzyme, malate:quinone-oxidoreductase, is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in E. coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase . ; GO: 0008924 malate dehydrogenase (acceptor) activity, 0006099 tricarboxylic acid cycle.
Probab=56.51  E-value=14  Score=16.83  Aligned_cols=21  Identities=19%  Similarity=0.216  Sum_probs=9.7

Q ss_pred             CEEEE-ECCHHHHHHHHHHHCC
Q ss_conf             70799-5899999999998618
Q gi|254781049|r   68 GGVRV-ESSLKSVISDIREILG   88 (398)
Q Consensus        68 GGV~l-~~s~~ea~~~a~~ilg   88 (398)
                      +|--+ |.|++=+++...+.-|
T Consensus       263 SG~fLR~~Npe~~~qH~AKVYG  284 (487)
T TIGR01320       263 SGLFLRCSNPELVEQHRAKVYG  284 (487)
T ss_pred             CCEECCCCCHHHHHHHCCCCCC
T ss_conf             5500017887999850562157


No 199
>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=52.54  E-value=17  Score=16.42  Aligned_cols=82  Identities=16%  Similarity=0.254  Sum_probs=53.5

Q ss_pred             CHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEE-E
Q ss_conf             9899999999-9861998658999635861328999999999999729998799974898589999999976995899-4
Q gi|254781049|r  304 DQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVIT-A  381 (398)
Q Consensus       304 ~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~-~  381 (398)
                      +.+..++.++ ++-..+++.+||       +.-|.+|.|+++++++.+.++|==+.+-|-+-.   .+.+-..-++.+ .
T Consensus       166 ~~~~~~~~~~~ll~~~~~~~av~-------~~~D~~A~g~~~~l~~~g~~vP~dvsIigfd~~---~~~~~~~P~LTti~  235 (273)
T cd01541         166 KEEKLFEKIKEILKRPERPTAIV-------CYNDEIALRVIDLLKELGLKIPEDISVVGFDDS---YLSVASEVKLTTVT  235 (273)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEE-------ECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCH---HHHHHCCCCEEEEE
T ss_conf             68999999999983699995698-------488899988998653148888877247612877---88974389829999


Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             99899999999985
Q gi|254781049|r  382 IDLDDAAQKIVHAV  395 (398)
Q Consensus       382 ~~~~~A~~~~v~~~  395 (398)
                      .+.++..+.|+++.
T Consensus       236 ~~~~~~g~~A~~~L  249 (273)
T cd01541         236 HPKEQMGEDAAKMI  249 (273)
T ss_pred             ECHHHHHHHHHHHH
T ss_conf             39999999999999


No 200
>TIGR02584 cas_NE0113 CRISPR-associated protein, NE0113 family; InterPro: IPR013413    Members of this minor CRISPR-associated (Cas) protein family are encoded in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum..
Probab=52.51  E-value=14  Score=17.03  Aligned_cols=67  Identities=19%  Similarity=0.302  Sum_probs=39.5

Q ss_pred             CCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCC
Q ss_conf             56777777707995899999999998618765442122222443301103455565058999998347780489984478
Q gi|254781049|r   60 KELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQG  139 (398)
Q Consensus        60 ~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~G  139 (398)
                      ...|-|-.||=   +|---..-.|=+||+++        . =++..|||.|-.+..++||    + |...++.+..-+.-
T Consensus       134 ~~lh~SlAGGR---KTMGfyLG~Al~Lfar~--------~-D~l~HVLV~eeFE~~r~Fy----Y-P~~~~~~l~~~~~d  196 (224)
T TIGR02584       134 AVLHASLAGGR---KTMGFYLGYALSLFARE--------Q-DRLSHVLVSEEFENLREFY----Y-PPRKSKILVIKTRD  196 (224)
T ss_pred             CEEEEEECCCH---HHHHHHHHHHHHHHCCC--------C-CEEEEEEECCCCCCCCCCC----C-CCCCCCEEEEECCC
T ss_conf             38998606872---57889999999973688--------8-7068886357778855874----8-44787267860888


Q ss_pred             CCCH
Q ss_conf             8402
Q gi|254781049|r  140 GMDI  143 (398)
Q Consensus       140 GvdI  143 (398)
                      |-.+
T Consensus       197 G~~~  200 (224)
T TIGR02584       197 GENL  200 (224)
T ss_pred             CCCC
T ss_conf             9756


No 201
>TIGR02049 gshA_ferroox glutamate--cysteine ligase; InterPro: IPR011718   This entry represents a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria . It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase..
Probab=52.06  E-value=17  Score=16.37  Aligned_cols=75  Identities=23%  Similarity=0.301  Sum_probs=42.1

Q ss_pred             CCEEECCHHHHHHHHHH------C-CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCC
Q ss_conf             81574799999999987------2-9986999712136876565655677777770799589999999999861876544
Q gi|254781049|r   21 KGVVISSVHAAESAIKT------L-PGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLIT   93 (398)
Q Consensus        21 ~g~~a~s~~ea~~~a~~------i-g~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t   93 (398)
                      ++.+|+..|..-+...+      | ..|=++|||.  +|-=|            =||..+.|.+|++.-=++     =.+
T Consensus       237 ~~~la~~Vd~vL~~~~~kY~eYgI~~~Pyv~vKAd--aGTYG------------MGimTa~sgeE~l~LNrK-----~R~  297 (436)
T TIGR02049       237 EDALATAVDQVLSKVQKKYEEYGIHEKPYVIVKAD--AGTYG------------MGIMTAKSGEEVLGLNRK-----ERN  297 (436)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEC--CCCCC------------CCEEEEECHHHHHCCCCC-----CCC
T ss_conf             36899999999999999887558756875899707--88745------------505884263785425300-----013


Q ss_pred             CC-CCCCCCCCCCEEECCCCCC
Q ss_conf             21-2222244330110345556
Q gi|254781049|r   94 KQ-TGPTGSRVNCVYVEDGADI  114 (398)
Q Consensus        94 ~q-t~~~G~~v~~vLVEe~v~~  114 (398)
                      +. .-.+|..|+.|+|+|.|.-
T Consensus       298 kM~k~KEGl~vs~ViiQEGV~T  319 (436)
T TIGR02049       298 KMAKVKEGLEVSEVIIQEGVYT  319 (436)
T ss_pred             CCCEEECCCCCCCEEEECCCCH
T ss_conf             4431125701055678478440


No 202
>PRK04531 acetylglutamate kinase; Provisional
Probab=51.48  E-value=17  Score=16.31  Aligned_cols=60  Identities=15%  Similarity=0.133  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHH------HHHCCCCEEEE--CCHHHHHHHHHHHH
Q ss_conf             32899999999999972999879997489858999999------99769958994--99899999999985
Q gi|254781049|r  333 MRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRL------IAESGLNVITA--IDLDDAAQKIVHAV  395 (398)
Q Consensus       333 ~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~i------l~~~g~~~~~~--~~~~~A~~~~v~~~  395 (398)
                      .+-+-++..|=+++++--++  ++=|-.-+|.--.+-.      ++..+-.++.+  +|+++ +.+.|+.+
T Consensus       345 a~g~gv~d~vw~~~~~d~~~--L~Wrsr~~n~~n~wyf~~~dG~~~~~~w~~FW~Gi~d~~~-~~~~i~~a  412 (421)
T PRK04531        345 ARGEGLGRDVWDVMREETPQ--LFWRSRHNNTINKWYMAESDGCYKQENWKVFWYGVQEFEQ-IPHIVAHL  412 (421)
T ss_pred             HHHCCHHHHHHHHHHHHCCC--EEEECCCCCCCCCHHHHCCEEEEECCCEEEEEECCCCHHH-HHHHHHHH
T ss_conf             24307699999999855885--1897489997340001035026964985999935787899-99999999


No 203
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase; InterPro: IPR005762   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD). MurD catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine. ; GO: 0005524 ATP binding, 0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=50.64  E-value=18  Score=16.23  Aligned_cols=109  Identities=22%  Similarity=0.271  Sum_probs=72.9

Q ss_pred             HHHHHHHHHHCCCCC---CEEEECCC--------CCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHH-HHHHHHHHHHHH
Q ss_conf             899999999658996---24884278--------889899999999986199865899963586132-899999999999
Q gi|254781049|r  279 AMATMDIIKLYGGAP---ANFLDVGG--------GADQDKVAAAFKIITSDSSVKGILINIFGGIMR-CDVLVKGILSAV  346 (398)
Q Consensus       279 amatmD~i~~~Gg~p---ANFlD~gG--------~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~-cd~vA~gii~a~  346 (398)
                      .-+..++|+.|-|-|   =-+.+..|        .++.+-+..|++-+ .+|+ |++|  |-||.-+ +|--+.  ..++
T Consensus       317 ~~~~~~~l~~F~~~~HRlE~~~~~~G~~f~NDSKATn~~At~~AL~~~-~~~~-~~~L--I~GG~~KG~df~~L--~~~~  390 (476)
T TIGR01087       317 LEAILEALRSFKGLPHRLEYVGQKNGVHFINDSKATNVHATLAALSAL-KNPK-RVIL--IVGGDDKGADFSPL--APAL  390 (476)
T ss_pred             HHHHHHHHHHCCCCCCCEEEEEECCCEEEEECCCCCCHHHHHHHHHHC-CCCC-EEEE--EEECCCCCCCHHHH--HHHH
T ss_conf             689999998457987626887772854798256212189999999847-9997-1899--96034689984899--9984


Q ss_pred             HHCCCCCCEEEECCCCCHHHHHHHHHHCCCCE-E----EECCHHHHHHHHHHHHHC
Q ss_conf             97299987999748985899999999769958-9----949989999999998506
Q gi|254781049|r  347 KEVKINIPLVMRLEGANVDIGNRLIAESGLNV-I----TAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       347 ~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~-~----~~~~~~~A~~~~v~~~k~  397 (398)
                      +    +..+-+=+-|--.++=.+.+++.+..+ .    .+++|++|++.+.+.++.
T Consensus       391 ~----~~~~~~~~~G~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~Av~~a~~~~~~  442 (476)
T TIGR01087       391 K----KKVKAVLAIGEDAAKIAKLLKEIGLVVKYGEETLVESLEEAVQAAREVAKE  442 (476)
T ss_pred             C----CCEEEEEEECCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             3----650799985354789999863427643546530577899999999997127


No 204
>TIGR00326 eubact_ribD riboflavin biosynthesis protein RibD; InterPro: IPR004794   This entry describes the riboflavin biosynthesis protein (ribD) as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region that is shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins that may be related to the riboflavin biosynthesis protein contain only the C-terminal domain.; GO: 0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity, 0008835 diaminohydroxyphosphoribosylaminopyrimidine deaminase activity, 0009231 riboflavin biosynthetic process.
Probab=50.47  E-value=18  Score=16.21  Aligned_cols=37  Identities=8%  Similarity=0.273  Sum_probs=23.1

Q ss_pred             HHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHH
Q ss_conf             999999986199865899963586132899999999999
Q gi|254781049|r  308 VAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAV  346 (398)
Q Consensus       308 ~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~  346 (398)
                      ..+.++. |.+.+++.|++= .|+...-..+.+|.++-+
T Consensus       305 ~~~~~~~-L~~r~~~~v~vE-gG~~l~~~f~~~G~~d~l  341 (393)
T TIGR00326       305 IEEVMEQ-LGKRGINSVLVE-GGPNLLGSFIDEGLVDEL  341 (393)
T ss_pred             HHHHHHH-HHHCCCCEEEEE-CHHHHHHHHHHCCCHHHH
T ss_conf             8999999-874475489872-158999999745843003


No 205
>PRK09585 anmK anhydro-N-acetylmuramic acid kinase; Reviewed
Probab=50.40  E-value=9.9  Score=17.91  Aligned_cols=119  Identities=20%  Similarity=0.132  Sum_probs=57.6

Q ss_pred             EEECCCHHHHHHHHHH-HHCCCCCCEEEECCC------CCCHHHHHHHHHHH-HCCCCCCEEEEECCC------------
Q ss_conf             9955503689999999-965899624884278------88989999999998-619986589996358------------
Q gi|254781049|r  271 CMVNGAGLAMATMDII-KLYGGAPANFLDVGG------GADQDKVAAAFKII-TSDSSVKGILINIFG------------  330 (398)
Q Consensus       271 ~~vnGaGlamatmD~i-~~~Gg~pANFlD~gG------~a~~e~~~~a~~~i-l~~~~vk~iliNifG------------  330 (398)
                      +++.--|-+.+-||.. ..+.+++  | |-.|      ..+.+-+.+.+..- ++.+-.|..=-+.|+            
T Consensus       181 ~~afD~GPgN~liD~~~~~~~~~~--y-D~~G~~A~~G~v~~~ll~~ll~~~yf~~~~PKS~gre~F~~~~l~~~~~~~~  257 (366)
T PRK09585        181 VIGFDTGPGNALIDAWVQRHTGGP--Y-DKDGAWAASGKVDEALLERLLAHPYFALPPPKSTGRELFNLAWLERLLAAFP  257 (366)
T ss_pred             EEEECCCCCHHHHHHHHHHHCCCC--C-CCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHCCHHHHHHHHHHHC
T ss_conf             577568852689999999851999--6-8998578289819999999851475158999887957669899998887641


Q ss_pred             CHHHHH-------HHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHC--CCCEEEEC------CHHHHHHHHH
Q ss_conf             613289-------9999999999972999-8799974898589999999976--99589949------9899999999
Q gi|254781049|r  331 GIMRCD-------VLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAES--GLNVITAI------DLDDAAQKIV  392 (398)
Q Consensus       331 GI~~cd-------~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~--g~~~~~~~------~~~~A~~~~v  392 (398)
                      +....|       ..|+.|.++++....+ .-|+|-=.|..-.-=.+.|++.  +.++.+.+      |+-||.--|.
T Consensus       258 ~ls~~D~laTlt~~ta~sI~~~~~~~~~~~~~i~v~GGG~~N~~L~~~l~~~l~~~~v~~~d~~gi~~d~~EA~~FA~  335 (366)
T PRK09585        258 GLSPEDVQATLTELTAASIARAVLLLPPGPRELLVCGGGARNPTLMERLAALLPGARVATTDALGIDPDAVEALAFAW  335 (366)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEECHHHHCCCHHHHHHHHHHH
T ss_conf             598778999999999999999998647996689997887557999999997689987844898099904999999999


No 206
>pfam07364 DUF1485 Protein of unknown function (DUF1485). This family consists of several hypothetical bacterial proteins of around 300 residues in length. Members of this family all appear to be in the Phylum Proteobacteria. The function of this family is unknown.
Probab=49.92  E-value=18  Score=16.15  Aligned_cols=75  Identities=13%  Similarity=0.194  Sum_probs=33.0

Q ss_pred             CCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHH--------
Q ss_conf             889899999999986199865899963586132899999999999972999879997489858999999997--------
Q gi|254781049|r  302 GADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAE--------  373 (398)
Q Consensus       302 ~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~--------  373 (398)
                      +|-.+-+..+-++ -++|+  ++-+++|+|..-.|.         .+.+.+  ++|-=. .+.+.+.++.++        
T Consensus       208 ~Pm~~l~~~~~~~-e~~~~--vl~~sv~~Gfp~aDv---------~~~G~s--vvv~td-~d~~~a~~~a~~la~~~w~~  272 (292)
T pfam07364       208 EPMRGLVDRLREL-EARGG--VLSASFFHGFPWADV---------PEMGPS--VLVYTD-GDPAAAEAAADELAAELWAR  272 (292)
T ss_pred             CCHHHHHHHHHHH-HHCCC--EEEEEEECCCCCCCC---------CCCCCE--EEEECC-CCHHHHHHHHHHHHHHHHHH
T ss_conf             8679999999999-71799--079988578555457---------777757--999908-98999999999999999975


Q ss_pred             -CCCCEEEECCHHHHHHHHH
Q ss_conf             -6995899499899999999
Q gi|254781049|r  374 -SGLNVITAIDLDDAAQKIV  392 (398)
Q Consensus       374 -~g~~~~~~~~~~~A~~~~v  392 (398)
                       ..+.. ...++++|+.+|.
T Consensus       273 R~~f~~-~~~~~~eAl~~A~  291 (292)
T pfam07364       273 RDDFVF-PFLPLDEAVDRAL  291 (292)
T ss_pred             HHHHCC-CCCCHHHHHHHHH
T ss_conf             550077-9999899999975


No 207
>COG0821 gcpE 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate synthase [Lipid metabolism]
Probab=49.68  E-value=18  Score=16.13  Aligned_cols=10  Identities=60%  Similarity=1.335  Sum_probs=5.3

Q ss_pred             EEEEECCCHH
Q ss_conf             7999555036
Q gi|254781049|r  269 IGCMVNGAGL  278 (398)
Q Consensus       269 Ig~~vnGaGl  278 (398)
                      +||+|||-|=
T Consensus       297 MGCVVNGPGE  306 (361)
T COG0821         297 MGCVVNGPGE  306 (361)
T ss_pred             EEEEECCCCC
T ss_conf             9757407850


No 208
>COG0069 GltB Glutamate synthase domain 2 [Amino acid transport and metabolism]
Probab=48.97  E-value=4.2  Score=20.34  Aligned_cols=117  Identities=19%  Similarity=0.147  Sum_probs=70.9

Q ss_pred             CCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCC------CCCCEEEECCCC
Q ss_conf             57355641027863100015622245775398644228817999555036899999999658------996248842788
Q gi|254781049|r  229 DDNALYRHLDIQELRDVSEEDSREIEAKQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYG------GAPANFLDVGGG  302 (398)
Q Consensus       229 DDnA~fR~~~~~~~~d~~~~~~~E~~A~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~G------g~pANFlD~gG~  302 (398)
                      |-.+-+||.|+....|..|.-..=.++.....-+|||--..+.=.-.+|.+=|.-|.|.--|      ..|-.|.|.-|-
T Consensus       274 ~~ISP~pHHDiysieDLaqlI~dLk~~~~~~~I~VKlva~~~v~~iaagvakA~AD~I~IdG~~GGTGAsP~~~~~~~Gi  353 (485)
T COG0069         274 GLISPPPHHDIYSIEDLAQLIKDLKEANPWAKISVKLVAEHGVGTIAAGVAKAGADVITIDGADGGTGASPLTSIDHAGI  353 (485)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHCCCC
T ss_conf             77589974665698899999999996188970699992565567787666404698899758998678785657636870


Q ss_pred             CCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             8989999999998619986589996358613289999999999
Q gi|254781049|r  303 ADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSA  345 (398)
Q Consensus       303 a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a  345 (398)
                      |...-+.++-..+..+--=..+.|-+=||+..-++||.++.--
T Consensus       354 P~e~glae~~q~L~~~glRd~v~l~~~Ggl~Tg~DVaka~aLG  396 (485)
T COG0069         354 PWELGLAETHQTLVLNGLRDKVKLIADGGLRTGADVAKAAALG  396 (485)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHC
T ss_conf             7998899999999975986416999428706789999999708


No 209
>COG0769 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=48.54  E-value=19  Score=16.01  Aligned_cols=100  Identities=15%  Similarity=0.158  Sum_probs=62.0

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHH
Q ss_conf             62488427888989999999998619986589996358613289999999999997299987999748985899999999
Q gi|254781049|r  293 PANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIA  372 (398)
Q Consensus       293 pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~  372 (398)
                      |--+.|+.-  |++-+.++++.+-...+-+.++||=+|| -| |.-=.-+..+..+...+ -++|-=.+++.|.-..|++
T Consensus       333 ~~v~VDyAH--nPd~le~~L~~~~~~~~g~li~VfG~gG-Dr-D~~kr~~mg~ia~~~ad-~vivt~dnpR~edp~~i~~  407 (475)
T COG0769         333 KLVIVDYAH--NPDGLEKALRAVRLHAAGRLIVVFGCGG-DR-DKSKRPDMGAIAEQLAD-IVIVTSDNPRSEDPAVILA  407 (475)
T ss_pred             CEEEEEECC--CHHHHHHHHHHHHHHCCCCEEEEECCCC-CC-CCCCCHHHHHHHHHCCC-CEEECCCCCCCCCHHHHHH
T ss_conf             769999534--8699999999987534984899977668-87-53430315999985599-3699189988768899999


Q ss_pred             HCCCC------EEEECCHHHHHHHHHHHHHC
Q ss_conf             76995------89949989999999998506
Q gi|254781049|r  373 ESGLN------VITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       373 ~~g~~------~~~~~~~~~A~~~~v~~~k~  397 (398)
                      +....      +....|-.+|.+++++.++.
T Consensus       408 ~i~~g~~~~~~~~~~~dr~~AI~~ai~~a~~  438 (475)
T COG0769         408 DILAGIEAPEKYEIIEDREEAIRKALDLAKE  438 (475)
T ss_pred             HHHHCCCCCCCEEECHHHHHHHHHHHHHHCC
T ss_conf             9983647664143011099999999986324


No 210
>TIGR00017 cmk cytidylate kinase; InterPro: IPR003136   This family consists of cytidylate kinase (2.7.4.14 from EC), which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors .; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=48.52  E-value=19  Score=16.01  Aligned_cols=76  Identities=17%  Similarity=0.236  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHCHHHHEEEECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC--CCCCC---CCCEEEE
Q ss_conf             884024555748312203321444578957888788751988899885999999998999955--97510---2326799
Q gi|254781049|r  139 GGMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKAFCDK--DMSLL---EINPLII  213 (398)
Q Consensus       139 GGvdIE~va~~~p~~I~~~~id~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~f~e~--Da~li---EINPLvv  213 (398)
                      -|.||++       .|.+..|+-       ++..++..        ..+-+.+.+..|-|.+.  +-..+   +|-- +|
T Consensus        83 nG~DV~~-------~I~t~~v~~-------~aS~~A~~--------~~vR~~~~~~Qq~~~~~sd~g~v~dGRDiGT-vV  139 (223)
T TIGR00017        83 NGEDVSE-------AIRTQEVAN-------LASKVAAF--------PKVREILLKRQQKLAKNSDDGIVADGRDIGT-VV  139 (223)
T ss_pred             CCCCHHH-------HCCCHHHHH-------HHHHHHCC--------HHHHHHHHHHHHHHHHHCCCCEEEECCCCCC-EE
T ss_conf             0777132-------206835899-------99987237--------7799999999999875158975884552374-46


Q ss_pred             CCCCC--EEEEEEEEEECCCHHHHHHHHH
Q ss_conf             05996--7994001321573556410278
Q gi|254781049|r  214 MKNGR--LRVLDSKISFDDNALYRHLDIQ  240 (398)
Q Consensus       214 t~dg~--vvAlDAKi~iDDnA~fR~~~~~  240 (398)
                      .||-+  ++ |||++.+  .|.=|-+++.
T Consensus       140 fPnA~~KiF-LdAsve~--RA~RR~~~~~  165 (223)
T TIGR00017       140 FPNAELKIF-LDASVEE--RAKRRYKDLQ  165 (223)
T ss_pred             CCCCCCCEE-ECCCHHH--HHHHHHHHHH
T ss_conf             788751324-3178789--9887699988


No 211
>PRK12483 threonine dehydratase; Reviewed
Probab=48.21  E-value=19  Score=15.98  Aligned_cols=13  Identities=8%  Similarity=0.250  Sum_probs=6.9

Q ss_pred             CCHHHHHHHHHHH
Q ss_conf             8999999999986
Q gi|254781049|r   74 SSLKSVISDIREI   86 (398)
Q Consensus        74 ~s~~ea~~~a~~i   86 (398)
                      .+.+++.+.+.++
T Consensus       139 ~~~dea~~~A~~l  151 (521)
T PRK12483        139 ESFPDALAHALKL  151 (521)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             9869999999999


No 212
>pfam11379 DUF3182 Protein of unknown function (DUF3182). This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=46.47  E-value=21  Score=15.81  Aligned_cols=54  Identities=26%  Similarity=0.417  Sum_probs=41.1

Q ss_pred             CCCCCEEECCHHHHHHHHHHC--CCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf             888815747999999999872--998699971213687656565567777777079958999999999986
Q gi|254781049|r   18 PVAKGVVISSVHAAESAIKTL--PGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREI   86 (398)
Q Consensus        18 pvp~g~~a~s~~ea~~~a~~i--g~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~i   86 (398)
                      -|.+|.-+.|.++|..++..+  ++|+ =+|.---.||||..              ++.+.+++..+-..+
T Consensus       113 ~vLpG~tvFs~~DAr~Aa~~Ll~~G~V-RlK~~~a~gG~GQ~--------------vv~d~~~Le~~L~a~  168 (355)
T pfam11379       113 AVLPGYTVFSLEDARDAAARLLKGGPV-RLKPPRACGGRGQQ--------------VVADADALDAALAAL  168 (355)
T ss_pred             HCCCCCCCCCHHHHHHHHHHHHCCCCE-EECCCCCCCCCCCE--------------EECCHHHHHHHHHCC
T ss_conf             103873222678899999998537972-55056223788855--------------743899999998727


No 213
>pfam03702 UPF0075 Uncharacterized protein family (UPF0075). The proteins is this family are about 370 amino acids long and have no known function.
Probab=46.12  E-value=11  Score=17.74  Aligned_cols=119  Identities=19%  Similarity=0.140  Sum_probs=63.7

Q ss_pred             EEECCCHHHHHHHHH-HHHCCCCCCEEEECCC------CCCHHHHHHHHHH-HHCCCCCCEEEEECCC----------CH
Q ss_conf             995550368999999-9965899624884278------8898999999999-8619986589996358----------61
Q gi|254781049|r  271 CMVNGAGLAMATMDI-IKLYGGAPANFLDVGG------GADQDKVAAAFKI-ITSDSSVKGILINIFG----------GI  332 (398)
Q Consensus       271 ~~vnGaGlamatmD~-i~~~Gg~pANFlD~gG------~a~~e~~~~a~~~-il~~~~vk~iliNifG----------GI  332 (398)
                      +++.--|-++.-||. +..+.++|  | |-.|      ..+.+-+.+.+.- -++.+-.|..=.+.|+          +.
T Consensus       180 i~afD~GPgN~liD~~~~~~~~~~--y-D~~G~~A~~G~v~~~ll~~ll~~~~f~~~~PKS~gre~F~~~~~~~~~~~~~  256 (363)
T pfam03702       180 VLGFDTGPGNALMDAWIQKHRGEP--F-DKNGAWAASGKVNHALLARLLADPYFALPAPKSTGRELFNLPWLEKKLAKFP  256 (363)
T ss_pred             EEEECCCCHHHHHHHHHHHCCCCC--C-CCCHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHCCHHHHHHHHCCCC
T ss_conf             366278824789999999713668--2-8681788389858999999974565326899877646459588766532589


Q ss_pred             -------HHHHHHHHHHHHHHHHCCCCC-CEEEECCCCCHHHHHHHHHHC--CCCEEEEC------CHHHHHHHHH
Q ss_conf             -------328999999999999729998-799974898589999999976--99589949------9899999999
Q gi|254781049|r  333 -------MRCDVLVKGILSAVKEVKINI-PLVMRLEGANVDIGNRLIAES--GLNVITAI------DLDDAAQKIV  392 (398)
Q Consensus       333 -------~~cd~vA~gii~a~~~~~~~~-pivvRl~Gtn~~~g~~il~~~--g~~~~~~~------~~~~A~~~~v  392 (398)
                             |=+...|+.|.++++....+. .|+|-=.|..-.-=.+.|++.  +.++.+.+      ++-||..-|.
T Consensus       257 ~~~D~~aTlt~~ta~sIa~~i~~~~~~~~~iiv~GGG~~N~~L~~~l~~~l~~~~v~~~d~~g~~~~~~EA~~FA~  332 (363)
T pfam03702       257 VPEDVQATLVELTAVTIVDALLQAGPDCERLLVCGGGARNPLLMARLAELLPNVDVASTDELGLDPDYMEAMAFAW  332 (363)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEECHHHCCCCHHHHHHHHHHH
T ss_conf             8778999999999999999999628997589997887568899999997779998842888399822899999999


No 214
>PRK03562 glutathione-regulated potassium-efflux system protein KefC; Provisional
Probab=45.48  E-value=21  Score=15.71  Aligned_cols=111  Identities=12%  Similarity=0.148  Sum_probs=67.0

Q ss_pred             HCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHH
Q ss_conf             53986442288179995550368999999996589962488427888989999999998619986589996358613289
Q gi|254781049|r  257 QHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCD  336 (398)
Q Consensus       257 ~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd  336 (398)
                      +.|.+|+-+|=|           -.+.+..+.+|. |.-|    |.++...+-++..+    .+.|.+.|-|     .-.
T Consensus       420 ~~gi~~vviD~d-----------~~~V~~~r~~G~-~v~y----GDat~~~vL~~AGi----~~Ar~vViai-----dd~  474 (615)
T PRK03562        420 SSGVKMVVLDHD-----------PDHIETLRKFGM-KVFY----GDATRMDLLESAGA----AKAEVLINAI-----DDP  474 (615)
T ss_pred             HCCCCEEEEECC-----------HHHHHHHHHCCC-EEEE----ECCCCHHHHHHCCC----CCCCEEEEEE-----CCH
T ss_conf             789987999799-----------999999996799-0897----68999999986791----4068899994-----989


Q ss_pred             HHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             99999999999729998799974898589999999976995899499899999999985
Q gi|254781049|r  337 VLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       337 ~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      .-+.-|++.++++.|++||++|-..-..   ..-|.+.|.+...-++++.+.+...+..
T Consensus       475 ~~~~~iv~~~r~~~P~l~IiaRard~~~---~~~L~~~Ga~~vv~Et~essL~l~~~~L  530 (615)
T PRK03562        475 QTNLQLTELVKEHFPHLQIIARARDVDH---YIRLRQAGVEKPERETFEGALKSGRLAL  530 (615)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCHHH---HHHHHHCCCCEEECCHHHHHHHHHHHHH
T ss_conf             9999999999975899869998397788---9999978999896665899999999999


No 215
>PRK04169 geranylgeranylglyceryl phosphate synthase-like protein; Reviewed
Probab=45.19  E-value=22  Score=15.68  Aligned_cols=50  Identities=32%  Similarity=0.474  Sum_probs=31.2

Q ss_pred             CCCCCEEEECCCCCCHH---HHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             89962488427888989---999999998619986589996358613289999999999
Q gi|254781049|r  290 GGAPANFLDVGGGADQD---KVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSA  345 (398)
Q Consensus       290 Gg~pANFlD~gG~a~~e---~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a  345 (398)
                      =|.|.=|||+||++..-   .+.++.+-.+++    ..|+ +.|||.+-+. |+-+.+|
T Consensus       154 ~g~~~iYLE~gsga~~pv~~e~V~~v~~~l~~----~~Li-vGGGIrs~e~-a~~~~~a  206 (229)
T PRK04169        154 LGMPIVYLEYGGGAGDPVPPEMVKAVKKALTD----TPLI-VGGGIRSPEQ-AREMAKA  206 (229)
T ss_pred             HCCCEEEEECCCCCCCCCCHHHHHHHHHHCCC----CCEE-EECCCCCHHH-HHHHHHC
T ss_conf             39808999658888997899999999973789----8789-9289699999-9999976


No 216
>pfam01990 ATP-synt_F ATP synthase (F/14-kDa) subunit. This family includes 14-kDa subunit from vATPases, which is in the peripheral catalytic part of the complex. The family also includes archaebacterial ATP synthase subunit F.
Probab=45.07  E-value=22  Score=15.67  Aligned_cols=52  Identities=13%  Similarity=0.307  Sum_probs=38.5

Q ss_pred             CCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCC
Q ss_conf             898999999999861998658999635861328999999999999729998799974898
Q gi|254781049|r  303 ADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGA  362 (398)
Q Consensus       303 a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gt  362 (398)
                      .+.+...++|+-+++++++-.|+|        |+.+|+-|-+.+.+.+...|+++.+-+.
T Consensus        24 ~~~~e~~~~l~~l~~~~d~gII~i--------te~~a~~i~~~i~~~~~~~P~Ii~IP~~   75 (92)
T pfam01990        24 VSPEEAEEAFEKLLEREDIGIILI--------TEDIAEEIRETIDRYESVLPAILEIPSK   75 (92)
T ss_pred             CCHHHHHHHHHHHHCCCCEEEEEE--------CHHHHHHHHHHHHHHCCCCCEEEEECCC
T ss_conf             998999999999854898599997--------4899998899999847688879996899


No 217
>COG2115 XylA Xylose isomerase [Carbohydrate transport and metabolism]
Probab=44.66  E-value=14  Score=17.02  Aligned_cols=128  Identities=23%  Similarity=0.382  Sum_probs=73.8

Q ss_pred             HCCC-CEEECC--CCEEEEEC-CCHHHHHHHHHHHHCCCCCCEEEECCCCCCH--------HHHHHHHHHHHC-------
Q ss_conf             5398-644228--81799955-5036899999999658996248842788898--------999999999861-------
Q gi|254781049|r  257 QHNL-SYIALD--GNIGCMVN-GAGLAMATMDIIKLYGGAPANFLDVGGGADQ--------DKVAAAFKIITS-------  317 (398)
Q Consensus       257 ~~~l-~yv~Ld--G~Ig~~vn-GaGlamatmD~i~~~Gg~pANFlD~gG~a~~--------e~~~~a~~~il~-------  317 (398)
                      ++|| ++++++  -|-++++. -=---+++.-+...+|---||=.|+-=|.+.        |......+++..       
T Consensus       257 ~~gLek~~K~NiEanHA~LaGHsFeHEl~~A~~lg~fGSiDaNrgd~~lGWDTDqFPn~v~e~tLamyeiL~~GGf~~GG  336 (438)
T COG2115         257 QFGLEKEFKLNIEANHATLAGHSFEHELATARALGIFGSIDANRGDYQLGWDTDQFPNNVEENTLAMYEILKAGGFTTGG  336 (438)
T ss_pred             HCCCHHHEEEECCCCCEECCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             80846553641204830011541798999998862004403688883347752326653388899999999808867787


Q ss_pred             ---CCCCCE------EEEECCCCHHHHHHHHHHHHHHHHHC---CCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHH
Q ss_conf             ---998658------99963586132899999999999972---999879997489858999999997699589949989
Q gi|254781049|r  318 ---DSSVKG------ILINIFGGIMRCDVLVKGILSAVKEV---KINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLD  385 (398)
Q Consensus       318 ---~~~vk~------iliNifGGI~~cd~vA~gii~a~~~~---~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~  385 (398)
                         |.+|+-      =|  ++|.|.-.|..|.|+-.|.+-.   -.+.||--|-.|-|++.|++|++..       .+++
T Consensus       337 ~NFDAKvRRqS~d~~DL--~~gHI~gMD~~A~gLK~AakmieD~~l~~~i~eRY~~~~s~~gq~il~G~-------~~le  407 (438)
T COG2115         337 LNFDAKVRRQSFDPYDL--FYGHIGGMDTFARGLKIAAKMIEDGVLSKPIAERYAGWNSELGQQILNGK-------TSLE  407 (438)
T ss_pred             CCCCHHHHHCCCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCC-------CCHH
T ss_conf             56115666335877887--88755218899999999999875215668999886003428779998276-------7799


Q ss_pred             HHHHHHHH
Q ss_conf             99999999
Q gi|254781049|r  386 DAAQKIVH  393 (398)
Q Consensus       386 ~A~~~~v~  393 (398)
                      +-++.+.+
T Consensus       408 ~la~~~~~  415 (438)
T COG2115         408 ELAAYALE  415 (438)
T ss_pred             HHHHHHHH
T ss_conf             99999985


No 218
>PRK09224 threonine dehydratase; Reviewed
Probab=44.54  E-value=22  Score=15.62  Aligned_cols=18  Identities=17%  Similarity=0.222  Sum_probs=10.7

Q ss_pred             EEEE-CCHHHHHHHHHHHC
Q ss_conf             7995-89999999999861
Q gi|254781049|r   70 VRVE-SSLKSVISDIREIL   87 (398)
Q Consensus        70 V~l~-~s~~ea~~~a~~il   87 (398)
                      |.+. .+.+++.+.|.++-
T Consensus       117 Vvl~G~~~dea~~~A~~la  135 (504)
T PRK09224        117 VVLHGDSFDEAYAHAIELA  135 (504)
T ss_pred             EEEECCCHHHHHHHHHHHH
T ss_conf             9995999899999999999


No 219
>cd00616 AHBA_syn 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary metabolites. Some well studied proteins in this CD are AHBA_synthase, protein product of pleiotropic regulatory gene degT,  Arnb aminotransferase and pilin glycosylation protein. The prototype of this family, the AHBA_synthase, is a dimeric PLP dependent enzyme. AHBA_syn is the terminal enzyme of 3-amino-5-hydroxybenzoic acid (AHBA) formation which is involved in the biosynthesis of ansamycin antibiotics, including rifamycin B. Some members of this CD are involved in 4-amino-6-deoxy-monosaccharide D-perosamine synthesis. Perosamine is an important element in the glycosylation of several cell products, such as antibiotics and lipopolysaccharides of gram-positive and gram-negative bacteria. The pilin glycosylation protein 
Probab=43.87  E-value=23  Score=15.55  Aligned_cols=14  Identities=29%  Similarity=0.439  Sum_probs=8.4

Q ss_pred             HHHHHHHHHHCCCC
Q ss_conf             99999999972999
Q gi|254781049|r  339 VKGILSAVKEVKIN  352 (398)
Q Consensus       339 A~gii~a~~~~~~~  352 (398)
                      -+.+++.+++.++.
T Consensus       282 R~~l~~~L~~~gI~  295 (352)
T cd00616         282 RDELIEALKEAGIE  295 (352)
T ss_pred             HHHHHHHHHHCCCC
T ss_conf             99999999987998


No 220
>pfam00462 Glutaredoxin Glutaredoxin.
Probab=43.66  E-value=23  Score=15.53  Aligned_cols=43  Identities=23%  Similarity=0.169  Sum_probs=23.5

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHC-CCCEEEEECCCCCC
Q ss_conf             999999998689888815747999999999872-99869997121368
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTL-PGPLYVVKSQIHAG   52 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~i-g~p~~VvKaQV~aG   52 (398)
                      ..+|++|+++|++.-.--+-.++ ++.....+. |.+- |  +||-.+
T Consensus        13 ~~ak~~L~~~~i~y~~~~v~~~~-~~~~~l~~~~g~~t-v--PqI~i~   56 (60)
T pfam00462        13 KRAKRLLKSLGVKFEEIDVDEDP-EIREELKELSGWRT-V--PQVFID   56 (60)
T ss_pred             HHHHHHHHHCCCCCEEEECCCCH-HHHHHHHHHHCCCC-C--CEEEEC
T ss_conf             99999999809975332158999-99999999829998-1--979889


No 221
>PRK09084 aspartate kinase III; Validated
Probab=43.44  E-value=23  Score=15.51  Aligned_cols=20  Identities=10%  Similarity=0.361  Sum_probs=10.8

Q ss_pred             CCC-CHHHHHHHHHHHHHHHH
Q ss_conf             358-61328999999999999
Q gi|254781049|r  328 IFG-GIMRCDVLVKGILSAVK  347 (398)
Q Consensus       328 ifG-GI~~cd~vA~gii~a~~  347 (398)
                      +-| |+...--+|--+..++.
T Consensus       389 vVG~gm~~~~gva~r~f~aL~  409 (447)
T PRK09084        389 LIGNNLSKACGVAKRVFGVLE  409 (447)
T ss_pred             EECCCCCCCHHHHHHHHHHHH
T ss_conf             989672328549999999853


No 222
>PRK03659 glutathione-regulated potassium-efflux system protein KefB; Provisional
Probab=43.02  E-value=23  Score=15.47  Aligned_cols=112  Identities=12%  Similarity=0.198  Sum_probs=71.6

Q ss_pred             HHCCCCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHH
Q ss_conf             75398644228817999555036899999999658996248842788898999999999861998658999635861328
Q gi|254781049|r  256 KQHNLSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRC  335 (398)
Q Consensus       256 ~~~~l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~c  335 (398)
                      ++.|.+|+-+|=|           ..+.+..+.+| .|.=|    |.++...+-++..+    .+.|.+.|-+     .-
T Consensus       420 ~~~gi~~vviD~d-----------~~~V~~~r~~G-~~v~y----GDat~~~vL~~AGi----~~A~~vViai-----~d  474 (602)
T PRK03659        420 MANKMRITVLERD-----------ISAVNLMRKYG-YKVYY----GDATQLELLRAAGA----EKAEAIVITC-----NE  474 (602)
T ss_pred             HHCCCCEEEEECC-----------HHHHHHHHHCC-CEEEE----ECCCCHHHHHHCCC----CCCCEEEEEE-----CC
T ss_conf             9789998999786-----------79999999789-90897----58999999986790----4058899982-----98


Q ss_pred             HHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             999999999999729998799974898589999999976995899499899999999985
Q gi|254781049|r  336 DVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       336 d~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      ..-+.-|++..+++.|++||++|-.--..   ..-|.+.|.+...-++++.+.+..-+..
T Consensus       475 ~~~~~~iv~~~r~~~P~l~I~aRar~~~~---~~~L~~~Ga~~vv~Et~essL~l~~~~L  531 (602)
T PRK03659        475 PEDTMKLVELCQQHFPHLHILARARGRVE---AHELLQAGVTQFSRETFSSALELGRKTL  531 (602)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEECCHHH---HHHHHHCCCCEEECCHHHHHHHHHHHHH
T ss_conf             99999999999987869969998697899---9999978999786627899999999999


No 223
>PRK10638 glutaredoxin 3; Provisional
Probab=42.99  E-value=23  Score=15.46  Aligned_cols=46  Identities=26%  Similarity=0.198  Sum_probs=30.4

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             9999999986898888157479999999998729986999712136876
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGR   54 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgR   54 (398)
                      ..||++|+..||+...-.+-..++......+.-|..- |  +||-.+|.
T Consensus        16 ~~Ak~lL~~~gi~y~ei~v~~~~~~~~~l~~~tg~~T-V--PqIfI~g~   61 (83)
T PRK10638         16 HRAKALLNSKGVSFQEIPIDGDAAKREEMIKRSGRTT-V--PQIFIDAQ   61 (83)
T ss_pred             HHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHCCCCC-C--CEEEECCE
T ss_conf             9999999975998769986799999999997369996-1--96999999


No 224
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=42.61  E-value=24  Score=15.43  Aligned_cols=47  Identities=21%  Similarity=0.248  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHHCCCC-CCEEEEC--------CCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf             9999999999972999-8799974--------898589999999976995899499
Q gi|254781049|r  337 VLVKGILSAVKEVKIN-IPLVMRL--------EGANVDIGNRLIAESGLNVITAID  383 (398)
Q Consensus       337 ~vA~gii~a~~~~~~~-~pivvRl--------~Gtn~~~g~~il~~~g~~~~~~~~  383 (398)
                      ..|+-+.+.+++++++ +.|.+|=        .|+-.|-+.|-|..+|+++....|
T Consensus        50 ~aae~~a~~~~~~Gi~~v~V~ikG~G~n~~~~pGpGresAiral~~~Gl~I~~I~D  105 (114)
T TIGR03628        50 QAAGRAAEKAKERGITGLHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIED  105 (114)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf             99999999999869849999999478787778986289999999868979999898


No 225
>cd07016 S14_ClpP_1 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which a
Probab=42.52  E-value=24  Score=15.42  Aligned_cols=14  Identities=14%  Similarity=0.223  Sum_probs=6.5

Q ss_pred             CCHHHHHHHHHHCC
Q ss_conf             79999999998729
Q gi|254781049|r   26 SSVHAAESAIKTLP   39 (398)
Q Consensus        26 ~s~~ea~~~a~~ig   39 (398)
                      .++++.....+.++
T Consensus        15 ~~~~~~~~~L~~~~   28 (160)
T cd07016          15 VTAKEFKDALDALG   28 (160)
T ss_pred             CCHHHHHHHHHHCC
T ss_conf             39999999998279


No 226
>cd02066 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which 
Probab=42.36  E-value=24  Score=15.40  Aligned_cols=45  Identities=22%  Similarity=0.204  Sum_probs=24.8

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCC
Q ss_conf             999999998689888815747999999999872998699971213687
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGG   53 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGg   53 (398)
                      -.+|++|++.||+.-.--+..+++......+..|.+. |  +||-.||
T Consensus        14 ~~ak~~L~~~~i~y~e~di~~~~~~~~~l~~~~g~~t-v--PqIfi~g   58 (72)
T cd02066          14 KRAKRLLESLGIEFEEIDILEDGELREELKELSGWPT-V--PQIFING   58 (72)
T ss_pred             HHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHCCCC-C--CEEEECC
T ss_conf             9999999956997789980598889999999849988-9--9599999


No 227
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=42.33  E-value=24  Score=15.40  Aligned_cols=91  Identities=12%  Similarity=0.096  Sum_probs=51.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHC
Q ss_conf             48842788898999999999861998658999635861328999999999999729998799974898589999999976
Q gi|254781049|r  295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAES  374 (398)
Q Consensus       295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~  374 (398)
                      .|.|=+=+++.+.+..|++-+-.+.  +.+|  |.||..+-.+..+ +.+.+++.   + +.+=+-|.+.+.=.++..+.
T Consensus       314 ~fiNDSKaTN~~a~~~Al~s~~~~~--~i~l--I~GG~~K~~d~~~-l~~~~~~~---~-~~~~~~G~~~~~~~~~~~~~  384 (438)
T PRK03806        314 RWINDSKATNVGSTEAALNGLHVDG--TLHL--LLGGDGKSADFSP-LARYLNGD---N-IRLYCFGRDGAQLAALRPEV  384 (438)
T ss_pred             EEEECCCCCCHHHHHHHHHHCCCCC--CEEE--EECCCCCCCCHHH-HHHHHHCC---C-EEEEEECCCHHHHHHHCCCC
T ss_conf             9998972158999999998262039--7799--9547755578799-99986126---5-69999777889999641220


Q ss_pred             CCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             99589949989999999998506
Q gi|254781049|r  375 GLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       375 g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                         ...+++|++|++.|.+.++.
T Consensus       385 ---~~~~~~l~~Av~~a~~~a~~  404 (438)
T PRK03806        385 ---AQLTETMEQAMRLLAPRVQP  404 (438)
T ss_pred             ---CHHHHHHHHHHHHHHHHCCC
T ss_conf             ---41540099999999986689


No 228
>COG0771 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]
Probab=42.16  E-value=24  Score=15.38  Aligned_cols=106  Identities=17%  Similarity=0.187  Sum_probs=66.9

Q ss_pred             HHHHHHHHCCCCC---CEEEECC--------CCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999658996---2488427--------8889899999999986199865899963586132899999999999972
Q gi|254781049|r  281 ATMDIIKLYGGAP---ANFLDVG--------GGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEV  349 (398)
Q Consensus       281 atmD~i~~~Gg~p---ANFlD~g--------G~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~  349 (398)
                      +..+.++.|.|-|   =-+.+.+        =.++...+..|++-.   + -+++|  |.||.-+--+ -..+...++  
T Consensus       297 ~i~~~L~~F~gl~HR~e~v~~~~gv~f~NDSKATN~~At~~AL~~~---~-~~v~l--I~GG~~Kg~d-f~~L~~~~~--  367 (448)
T COG0771         297 AILEALSSFTGLPHRLEFVGEKDGVLFINDSKATNVDATLAALSGF---D-GPVIL--IAGGDDKGAD-FSPLAEILA--  367 (448)
T ss_pred             HHHHHHHHCCCCCCCEEEEEECCCEEEECCCCCCCHHHHHHHHHCC---C-CCEEE--EECCCCCCCC-HHHHHHHHH--
T ss_conf             9999997389998622798861988996078788888999999718---9-97799--9777788888-168899774--


Q ss_pred             CCCCCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             999879997489858999999997699589949989999999998506
Q gi|254781049|r  350 KINIPLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       350 ~~~~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                        +.+..+-+-|-..+.=.+.|++.+.+++.+++|++|++.+-+.++.
T Consensus       368 --~~~~~~~~~G~~~~~i~~~l~~~~~~~~~~~~le~Av~~a~~~a~~  413 (448)
T COG0771         368 --KVIKKLVLIGEDAEKIAAALKEAGPSLVICETLEEAVQLARELAQP  413 (448)
T ss_pred             --HCCEEEEEECCCHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHHCC
T ss_conf             --1555999947888999999875278536147699999999987258


No 229
>KOG2519 consensus
Probab=42.13  E-value=22  Score=15.59  Aligned_cols=27  Identities=15%  Similarity=0.210  Sum_probs=17.1

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCCC
Q ss_conf             248842788898999999999861998
Q gi|254781049|r  294 ANFLDVGGGADQDKVAAAFKIITSDSS  320 (398)
Q Consensus       294 ANFlD~gG~a~~e~~~~a~~~il~~~~  320 (398)
                      -||++.==+.+.+++..+++-+.+..+
T Consensus       305 i~fl~~~~~f~~~rv~~~~~kl~~~~~  331 (449)
T KOG2519         305 IQFLVGEKQFNEERVRKGIRKLKSSLK  331 (449)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHC
T ss_conf             999976642597887500677765521


No 230
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=41.84  E-value=24  Score=15.35  Aligned_cols=17  Identities=12%  Similarity=0.114  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHHHHHCC
Q ss_conf             28999999999999729
Q gi|254781049|r  334 RCDVLVKGILSAVKEVK  350 (398)
Q Consensus       334 ~cd~vA~gii~a~~~~~  350 (398)
                      -...+|++|+..+...+
T Consensus       368 eg~~~a~~ii~~~~~~~  384 (527)
T PRK06253        368 EGKDLAREIVETCVKHA  384 (527)
T ss_pred             HHHHHHHHHHHHHHHHC
T ss_conf             89999999999999818


No 231
>cd03419 GRX_GRXh_1_2_like Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes
Probab=41.50  E-value=23  Score=15.55  Aligned_cols=47  Identities=23%  Similarity=0.308  Sum_probs=25.0

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCH--HHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             99999999868988881574799--99999998729986999712136876
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSV--HAAESAIKTLPGPLYVVKSQIHAGGR   54 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~--~ea~~~a~~ig~p~~VvKaQV~aGgR   54 (398)
                      -.||++|.++||+-..-.+-..+  .+......++++...|  +||..+|+
T Consensus        14 ~~ak~lL~~~~i~~~~~~~d~~~~~~~~~~~l~~~~g~~Tv--PqIfi~g~   62 (82)
T cd03419          14 KRAKSLLKELGVKPAVVELDQHEDGSEIQDYLQELTGQRTV--PNVFIGGK   62 (82)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCC--CEEEECCE
T ss_conf             99999999849980699646564399999999984399988--86999998


No 232
>TIGR00612 ispG_gcpE 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; InterPro: IPR004588   This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0016114 terpenoid biosynthetic process.
Probab=41.08  E-value=13  Score=17.17  Aligned_cols=52  Identities=27%  Similarity=0.307  Sum_probs=35.8

Q ss_pred             CHHHHHH-HHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf             0368999-9999965899624884278889899999999986199865899963
Q gi|254781049|r  276 AGLAMAT-MDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINI  328 (398)
Q Consensus       276 aGlamat-mD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNi  328 (398)
                      |..+.|| .-.+-.-|.--|-.||+---|-.+.++-||+||-+ -.++...++|
T Consensus       479 aaisiatefGallldGlGeavvldlPnlPlqdvlkia~eiL~~-~G~R~~~v~~  531 (633)
T TIGR00612       479 AAISIATEFGALLLDGLGEAVVLDLPNLPLQDVLKIAYEILQS-LGLRKRGVEI  531 (633)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHH-CCCCCCCCEE
T ss_conf             4434566666787630453356416787777899999999996-4877567378


No 233
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=41.07  E-value=25  Score=15.27  Aligned_cols=106  Identities=6%  Similarity=-0.001  Sum_probs=63.9

Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEE--
Q ss_conf             9999999965899624884278889899999999986-1998658999635861328999999999999729998799--
Q gi|254781049|r  280 MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLV--  356 (398)
Q Consensus       280 matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~piv--  356 (398)
                      ....+.++.+|.+...-.=+.+..+.+..++++.-++ .+|.+.++|.       -.|.+|-|.+.++.+.+..+|--  
T Consensus       202 ~gf~~al~~~~l~~~~~~i~~~~~~~~~~~~~~~~ll~~~~~~tAi~c-------~~D~~A~g~~~~l~~~g~~v~~d~~  274 (342)
T PRK10014        202 GGYCATLLKFGLPFHSEWVLECTSSQKQAAEAITALLRHNPTISAVVC-------YNETIAMGAWFGLLRAGRQSGESGV  274 (342)
T ss_pred             HHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHCCCCCCEEEE-------ECHHHHHHHHHHHHHHCHHCCCCCC
T ss_conf             999999997699988334896689789999999999836999718999-------6789999999999995822175533


Q ss_pred             -------EECCCCCHHHHHHHHHHCCCCEE-EECCHHHHHHHHHHHH
Q ss_conf             -------97489858999999997699589-9499899999999985
Q gi|254781049|r  357 -------MRLEGANVDIGNRLIAESGLNVI-TAIDLDDAAQKIVHAV  395 (398)
Q Consensus       357 -------vRl~Gtn~~~g~~il~~~g~~~~-~~~~~~~A~~~~v~~~  395 (398)
                             +.+-|-+--.   +.....-++. ...+.++-.++|++..
T Consensus       275 ~~~ip~~vsIigfdd~~---~~~~~~P~LTtv~~~~~~ig~~a~~~L  318 (342)
T PRK10014        275 DRYFEQQVALAAFTDVP---EAELDDPPLTWASTPAREIGRTLADRM  318 (342)
T ss_pred             CCCCCCCEEEEEECCHH---HHHCCCCCCEEEECCHHHHHHHHHHHH
T ss_conf             34789858999988848---886258985699839999999999999


No 234
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions.  GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=40.70  E-value=25  Score=15.23  Aligned_cols=46  Identities=13%  Similarity=0.091  Sum_probs=29.5

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             9999999986898888157479999999998729986999712136876
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGGR   54 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGgR   54 (398)
                      ..||+||.+.|||.-.-.+-..++......+.-|... |  +||-.++.
T Consensus        15 ~~AK~lL~~kgi~y~ei~l~~~~~~~~~l~~~tg~~T-V--PQIFi~~~   60 (73)
T cd03027          15 TAVRLFLREKGLPYVEINIDIFPERKAELEERTGSSV-V--PQIFFNEK   60 (73)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHCCCC-C--CEEEECCE
T ss_conf             9999999987996499988899899999999719997-5--97999999


No 235
>PRK06382 threonine dehydratase; Provisional
Probab=39.92  E-value=26  Score=15.16  Aligned_cols=25  Identities=16%  Similarity=0.202  Sum_probs=16.9

Q ss_pred             CCCEEEEECCCHHHHHHHHHHHHCC
Q ss_conf             8817999555036899999999658
Q gi|254781049|r  266 DGNIGCMVNGAGLAMATMDIIKLYG  290 (398)
Q Consensus       266 dG~Ig~~vnGaGlamatmD~i~~~G  290 (398)
                      +.+|+|+..|+-.-+.++.-|...|
T Consensus       293 gk~Vv~vlsGGNiD~~~l~~ii~r~  317 (400)
T PRK06382        293 GKKVAIVVSGGNINPLLMSKIIYKE  317 (400)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             9849999637887978999999998


No 236
>PRK10936 periplasmic sensory protein associated with the TorRS two-component regulatory system; Provisional
Probab=39.85  E-value=26  Score=15.15  Aligned_cols=117  Identities=15%  Similarity=0.215  Sum_probs=71.0

Q ss_pred             CEEEEEC--CCHHHHHH----HHHHHHCCCCCCEEEECCCC-CCHHHHHHHHHHHH-CCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             1799955--50368999----99999658996248842788-89899999999986-19986589996358613289999
Q gi|254781049|r  268 NIGCMVN--GAGLAMAT----MDIIKLYGGAPANFLDVGGG-ADQDKVAAAFKIIT-SDSSVKGILINIFGGIMRCDVLV  339 (398)
Q Consensus       268 ~Ig~~vn--GaGlamat----mD~i~~~Gg~pANFlD~gG~-a~~e~~~~a~~~il-~~~~vk~iliNifGGI~~cd~vA  339 (398)
                      +|+++-.  |+|-+..-    .|.++   +.+-...+.--+ .+.+.-.+.++-+| ++|++++||    |    ++..|
T Consensus       171 ~Va~l~G~~~~~~~~~r~~GF~~al~---~~~ikIv~~q~ad~~r~~a~~~~e~iL~~~pdid~I~----g----~~~~a  239 (340)
T PRK10936        171 NVALLPGPEGAGGSKAVEQGFRAAIK---GSDVRIVDIAHGDNDKELQRNLLQELLERHPEIDYIA----G----SAVAA  239 (340)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHC---CCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEE----E----CCHHH
T ss_conf             99995287665147689887999970---7996799884377749999999999998499967998----0----75669


Q ss_pred             HHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECCHHH----HHHHHHHHHHC
Q ss_conf             9999999972999-8799974898589999999976995899499899----99999998506
Q gi|254781049|r  340 KGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAIDLDD----AAQKIVHAVKG  397 (398)
Q Consensus       340 ~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~----A~~~~v~~~k~  397 (398)
                      ++-+.++++.+.. ...+|-.-++..  ..+-|++-.+.....++.-.    |++.+|.+.+|
T Consensus       240 ~~Ai~al~~~g~~~~v~ivg~D~s~~--~~~~Ik~G~i~atv~Q~p~~~G~~AV~~av~~l~G  300 (340)
T PRK10936        240 EAAIGELRGRNLTDPVKLVSFYLSHQ--VYRGLKRGKVLAAPSDQMVLQGRLAIDQAVRQLEG  300 (340)
T ss_pred             HHHHHHHHHCCCCCCEEEEEECCCHH--HHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHHCC
T ss_conf             99999999608888749999269999--99999849779995378899999999999999779


No 237
>cd01844 SGNH_hydrolase_like_6 SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=39.79  E-value=26  Score=15.14  Aligned_cols=28  Identities=18%  Similarity=0.224  Sum_probs=13.9

Q ss_pred             CCCCCCCCEEECCHHHH--HHHHHHCCCCE
Q ss_conf             68988881574799999--99998729986
Q gi|254781049|r   15 YNVPVAKGVVISSVHAA--ESAIKTLPGPL   42 (398)
Q Consensus        15 ~GIpvp~g~~a~s~~ea--~~~a~~ig~p~   42 (398)
                      ||=.+..|.-++.|..+  .-++..+|+++
T Consensus         5 yG~SITqG~~AsrP~~a~~~~l~r~lg~~v   34 (177)
T cd01844           5 YGTSISQGACASRPGMAWTAILARRLGLEV   34 (177)
T ss_pred             EECHHHCCCCCCCCCCCHHHHHHHHCCCCE
T ss_conf             828376488889864416999998549977


No 238
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=39.55  E-value=26  Score=15.12  Aligned_cols=34  Identities=29%  Similarity=0.131  Sum_probs=22.9

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCC
Q ss_conf             9999999986898888157479999999998729
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTLP   39 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig   39 (398)
                      ..||++|+++||+...--+-.+++......+..+
T Consensus        14 ~~aK~lL~~~~i~y~ei~v~~~~~~~~~~~~~~~   47 (75)
T cd03418          14 VRAKALLDKKGVDYEEIDVDGDPALREEMINRSG   47 (75)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHCC
T ss_conf             9999999981998689862799999999999808


No 239
>pfam03411 Peptidase_M74 Penicillin-insensitive murein endopeptidase.
Probab=39.41  E-value=26  Score=15.11  Aligned_cols=52  Identities=19%  Similarity=0.277  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHCCCCCCEEEEECCCCHH--HHHHHHHHHHHHHHHCC----CCCCEEEECC
Q ss_conf             9999999998619986589996358613--28999999999999729----9987999748
Q gi|254781049|r  306 DKVAAAFKIITSDSSVKGILINIFGGIM--RCDVLVKGILSAVKEVK----INIPLVMRLE  360 (398)
Q Consensus       306 e~~~~a~~~il~~~~vk~iliNifGGI~--~cd~vA~gii~a~~~~~----~~~pivvRl~  360 (398)
                      ..-.+.+++-.+||+|.-||||  -+|-  -|+. |.|=-.-+..+.    -.--+-|||.
T Consensus       124 ~~h~~lik~AA~dp~V~RIFVn--p~IK~~lC~~-~~~DR~WL~KvRPw~GH~~HfHVRL~  181 (240)
T pfam03411       124 PEIFSLIKLAAQDPDVTRIFVN--PAIKQQLCLT-AGTDRDWLRKVRPWFGHRAHFHVRLT  181 (240)
T ss_pred             HHHHHHHHHHHCCCCEEEEEEC--HHHHHHHHHC-CCCCHHHHHHCCCCCCCCCEEEEEEC
T ss_conf             8999999998358771488658--9999999865-16657789742853466542478720


No 240
>TIGR00273 TIGR00273 iron-sulfur cluster binding protein; InterPro: IPR004452 Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulphur clusters..
Probab=39.38  E-value=26  Score=15.10  Aligned_cols=122  Identities=16%  Similarity=0.219  Sum_probs=59.0

Q ss_pred             EEEECCHHHHHHHHHHHCCCC---CCCCC--CCCCCCCCCCEEECCCCCCCE----EEEEEEE-EECCCCCEEEEEECCC
Q ss_conf             799589999999999861876---54421--222224433011034555650----5899999-8347780489984478
Q gi|254781049|r   70 VRVESSLKSVISDIREILGST---LITKQ--TGPTGSRVNCVYVEDGADILR----ELYLSLL-VDRTSGMVAFIASTQG  139 (398)
Q Consensus        70 V~l~~s~~ea~~~a~~ilg~~---l~t~q--t~~~G~~v~~vLVEe~v~~~~----E~ylgi~-~Dr~~~~~vii~S~~G  139 (398)
                      |..++|.|||.+.+.++.+.+   .+.+|  .-..-.-++.+|=++.+....    ||+|=+. .|+    |+=|.-   
T Consensus        67 vYyA~~~eeA~~ii~~v~~~KN~k~vvK~KSMvsEEI~Ln~~L~~~G~~v~ETDLGElI~Q~~d~d~----P~H~Vv---  139 (450)
T TIGR00273        67 VYYAKTAEEARKIILKVAQEKNGKKVVKSKSMVSEEIGLNEVLEKKGIEVVETDLGELILQLDDNDP----PSHIVV---  139 (450)
T ss_pred             EEEECCHHHHHHHHHHHHHHHCCCEEECCCCCCEEECCHHHHHHHCCCEEEEECCCEEEEEEECCCC----CEEEEE---
T ss_conf             9872787899999999886413344211346400032214888765977998004307887745888----427885---


Q ss_pred             CCCHHHHHHHCHHHHEEEECCCCCCCCHHHHHHHHH-HCCCCH-HHHHHHHHHHHHHHH-HHHHCCCCCCCCCEEEECCC
Q ss_conf             840245557483122033214445789578887887-519888-998859999999989-99955975102326799059
Q gi|254781049|r  140 GMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVASLCD-MLELQG-QARIDGGDLFPNLYK-AFCDKDMSLLEINPLIIMKN  216 (398)
Q Consensus       140 GvdIE~va~~~p~~I~~~~id~~~gl~~~~~~~l~~-~lg~~~-~~~~~~~~ii~~L~~-~f~e~Da~liEINPLvvt~d  216 (398)
                                           |..--...|+++++. +||..+ +..+.+...+.+..| =|.+.|.=.-=.| +++-..
T Consensus       140 ---------------------PAlHk~~~qig~il~Erl~~~~~E~pE~L~~~~R~~~R~~Fl~a~~GisGcN-fa~A~t  197 (450)
T TIGR00273       140 ---------------------PALHKNRKQIGEILKERLGYEGEEEPEKLALIARKFMRKKFLSADIGISGCN-FAIAET  197 (450)
T ss_pred             ---------------------CCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEECC-EEEECC
T ss_conf             ---------------------5722786898889987458998888789999999986266511345300002-046557


Q ss_pred             CCEE
Q ss_conf             9679
Q gi|254781049|r  217 GRLR  220 (398)
Q Consensus       217 g~vv  220 (398)
                      |++.
T Consensus       198 G~i~  201 (450)
T TIGR00273       198 GSIF  201 (450)
T ss_pred             CEEE
T ss_conf             5189


No 241
>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=38.76  E-value=27  Score=15.04  Aligned_cols=84  Identities=6%  Similarity=0.070  Sum_probs=57.3

Q ss_pred             CCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCE
Q ss_conf             8889899999999-986199865899963586132899999999999972999-87999748985899999999769958
Q gi|254781049|r  301 GGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNV  378 (398)
Q Consensus       301 G~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~  378 (398)
                      |..+.+..++.++ ++.++|++++|+    |    ++..+.|.++++++.+.. ...++=..++  .+..+.+++-.+..
T Consensus       164 ~~~~~~~a~~~~~~~L~~~pdi~~i~----~----~~~~a~~a~~a~~~~g~~~~v~vvg~d~~--~~~~~~i~~G~i~a  233 (268)
T cd06306         164 GDTGKEVQRKLVEEALEAHPDIDYIV----G----SAVAAEAAVGILRQRGLTDQIKIVSTYLS--HAVYRGLKRGKILA  233 (268)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCEEE----E----CCHHHHHHHHHHHHCCCCCCEEEEEECCC--HHHHHHHHCCCEEE
T ss_conf             78749999999999986299988999----5----74679999999986077997599993699--89999998598379


Q ss_pred             EEECCHHHHHHHHHHH
Q ss_conf             9949989999999998
Q gi|254781049|r  379 ITAIDLDDAAQKIVHA  394 (398)
Q Consensus       379 ~~~~~~~~A~~~~v~~  394 (398)
                      ....+....-..+|+.
T Consensus       234 tv~Q~p~~~G~~av~~  249 (268)
T cd06306         234 APTDSMVLQGRLAIDQ  249 (268)
T ss_pred             EEECCHHHHHHHHHHH
T ss_conf             9956999999999999


No 242
>KOG3857 consensus
Probab=38.39  E-value=13  Score=17.05  Aligned_cols=37  Identities=22%  Similarity=0.074  Sum_probs=24.0

Q ss_pred             HHHHHHHHCCCCCCCC------EEECCHHHHHHHHHHCCCCEE
Q ss_conf             9999999868988881------574799999999987299869
Q gi|254781049|r    7 QAKALLRKYNVPVAKG------VVISSVHAAESAIKTLPGPLY   43 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g------~~a~s~~ea~~~a~~ig~p~~   43 (398)
                      -+++.|.+-||++--+      --+.|..++.+.+++=.+..+
T Consensus        89 ~a~~~L~~~~I~~~vyD~v~~ePtv~s~~~alefak~~~fDs~  131 (465)
T KOG3857          89 VAQDSLEENGINVEVYDKVQPEPTVGSVTAALEFAKKKNFDSF  131 (465)
T ss_pred             HHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCEE
T ss_conf             9999999759816972476479862349999999873366558


No 243
>PRK01077 cobyrinic acid a,c-diamide synthase; Validated
Probab=38.30  E-value=27  Score=14.99  Aligned_cols=15  Identities=27%  Similarity=0.184  Sum_probs=8.8

Q ss_pred             HHHHHCCCCCCCCEE
Q ss_conf             999986898888157
Q gi|254781049|r   10 ALLRKYNVPVAKGVV   24 (398)
Q Consensus        10 ~lL~~~GIpvp~g~~   24 (398)
                      ++|++-|+.|.++.+
T Consensus        26 r~l~~rG~~VapFK~   40 (451)
T PRK01077         26 RALRRRGLRVQPFKV   40 (451)
T ss_pred             HHHHHCCCCCCCCCC
T ss_conf             999968794575357


No 244
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=38.25  E-value=28  Score=14.99  Aligned_cols=49  Identities=18%  Similarity=0.207  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHCCCC-CCEEEECC--------CCCHHHHHHHHHHCCCCEEEECCH
Q ss_conf             99999999999972999-87999748--------985899999999769958994998
Q gi|254781049|r  336 DVLVKGILSAVKEVKIN-IPLVMRLE--------GANVDIGNRLIAESGLNVITAIDL  384 (398)
Q Consensus       336 d~vA~gii~a~~~~~~~-~pivvRl~--------Gtn~~~g~~il~~~g~~~~~~~~~  384 (398)
                      -..|+-+.+.+++++++ +.|.||=.        |+..|-+.+-|..+|+++....|.
T Consensus        53 q~aae~~~~~a~~~Gi~~v~V~vkG~G~~~~k~pGpGr~~air~l~~~Gl~I~~I~Dv  110 (129)
T PRK09607         53 MQAAFRAAELAKDKGITGVHIKVRAPGGNGSKTPGPGAQAAIRALARAGLRIGRIEDV  110 (129)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEE
T ss_conf             9999999999997698589999983787776788842899999998689789898870


No 245
>cd00394 Clp_protease_like Caseinolytic protease (ClpP) is an ATP-dependent protease. Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradec
Probab=38.08  E-value=28  Score=14.97  Aligned_cols=11  Identities=9%  Similarity=0.184  Sum_probs=4.3

Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999989999
Q gi|254781049|r  189 DLFPNLYKAFC  199 (398)
Q Consensus       189 ~ii~~L~~~f~  199 (398)
                      +.+.++++.|.
T Consensus       113 ~~~~~~~~~~~  123 (161)
T cd00394         113 RIILYFIARFI  123 (161)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 246
>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=37.77  E-value=28  Score=14.94  Aligned_cols=90  Identities=14%  Similarity=0.175  Sum_probs=52.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHC
Q ss_conf             48842788898999999999861998658999635861328999999999999729998799974898589999999976
Q gi|254781049|r  295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAES  374 (398)
Q Consensus       295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~  374 (398)
                      .|-|=+=+++.+.+..|++-+- .|+ +.+|  |.||..+-.+..+ +.+.+++.    ..-+-+-|.+.++   +... 
T Consensus       315 ~~iNDSKaTN~~a~~~Al~~~~-~~~-~i~l--I~GG~~Kg~d~~~-l~~~~~~~----~~~~~~~G~~~~~---~~~~-  381 (438)
T PRK04663        315 KWVNDSKATNVASTLAALSGLN-LEG-KLYL--LVGGVGKGADFSE-LKPVLATL----NLQLCCFGEDGDQ---FMPL-  381 (438)
T ss_pred             EEECCCCCCCHHHHHHHHHHCC-CCC-CEEE--EECCCCCCCCHHH-HHHHHHHC----CEEEEEECCCHHH---HHHH-
T ss_conf             9974787788789999998367-778-4799--9657666668799-99998523----7699998888999---9743-


Q ss_pred             CCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             99589949989999999998506
Q gi|254781049|r  375 GLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       375 g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      .-+...+++|++|++.|-+.++.
T Consensus       382 ~~~~~~~~~l~~Av~~a~~~a~~  404 (438)
T PRK04663        382 HPSARRFETMEDAIESISPQLKS  404 (438)
T ss_pred             CCCCEECCCHHHHHHHHHHHCCC
T ss_conf             24534406799999999986779


No 247
>PRK08190 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated
Probab=37.69  E-value=18  Score=16.23  Aligned_cols=72  Identities=19%  Similarity=0.231  Sum_probs=32.8

Q ss_pred             EECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCC----------CCHHHHHHHHHHCC-CC-EEE--ECCHHHHHHHH
Q ss_conf             963586132899999999999972999879997489----------85899999999769-95-899--49989999999
Q gi|254781049|r  326 INIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEG----------ANVDIGNRLIAESG-LN-VIT--AIDLDDAAQKI  391 (398)
Q Consensus       326 iNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~G----------tn~~~g~~il~~~g-~~-~~~--~~~~~~A~~~~  391 (398)
                      +||+=..-.--++-+--|+..+.+++..|=|.=|+-          |-....+..+.+.| ++ .+.  --.||.|+.+-
T Consensus       303 ini~P~l~~K~~Ii~Nai~~a~~lG~~~PKVAiLsAvE~vnp~mpsTlDAa~L~kma~rGqi~g~ivdGPLa~DnAis~e  382 (465)
T PRK08190        303 INIAPTLEQKRDIVQNAIDLAHALGVEEPKVAILSAVETVNPKIPSTLDAAALCKMADRGQITGGIVDGPLAFDNAISAE  382 (465)
T ss_pred             EEECCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCEEECCCHHHHHCCHH
T ss_conf             33488989999999999999998199998299996001448889645889999999974896884887784277537998


Q ss_pred             HHHHHC
Q ss_conf             998506
Q gi|254781049|r  392 VHAVKG  397 (398)
Q Consensus       392 v~~~k~  397 (398)
                      -...||
T Consensus       383 AA~~Kg  388 (465)
T PRK08190        383 AAKTKG  388 (465)
T ss_pred             HHHHCC
T ss_conf             996469


No 248
>PRK06464 phosphoenolpyruvate synthase; Validated
Probab=37.57  E-value=16  Score=16.47  Aligned_cols=55  Identities=13%  Similarity=0.111  Sum_probs=29.1

Q ss_pred             CCHHHHHHHHHHH----CCCCCCCCCCCCCCC----CCCCEEECCCCCCCE-EEEEEEEEECCCC
Q ss_conf             8999999999986----187654421222224----433011034555650-5899999834778
Q gi|254781049|r   74 SSLKSVISDIREI----LGSTLITKQTGPTGS----RVNCVYVEDGADILR-ELYLSLLVDRTSG  129 (398)
Q Consensus        74 ~s~~ea~~~a~~i----lg~~l~t~qt~~~G~----~v~~vLVEe~v~~~~-E~ylgi~~Dr~~~  129 (398)
                      ...+++..+.+..    ++.+-++.... .|.    .-..|.|++||.... --=+.+++||.++
T Consensus       148 ~g~e~L~~Aik~v~aS~~s~RAi~YR~~-~gi~~~~~~~AV~VQ~MV~~d~~asGV~FTrdP~tG  211 (794)
T PRK06464        148 RGIDDVLDAVKHCFASLFTDRAISYRVH-QGFDHFKVALSAGVQKMVRSDLAASGVMFTLDTESG  211 (794)
T ss_pred             CCHHHHHHHHHHHHHHHCCHHHHHHHHH-CCCCHHHHCCEEEEEEEECCCCCCCEEEEEECCCCC
T ss_conf             8999999999999986026899999998-499826637068999863266645425784067789


No 249
>PRK08198 threonine dehydratase; Provisional
Probab=37.46  E-value=28  Score=14.91  Aligned_cols=25  Identities=8%  Similarity=0.234  Sum_probs=14.5

Q ss_pred             CCCEEEEECCCHHHHHHHHHHHHCC
Q ss_conf             8817999555036899999999658
Q gi|254781049|r  266 DGNIGCMVNGAGLAMATMDIIKLYG  290 (398)
Q Consensus       266 dG~Ig~~vnGaGlamatmD~i~~~G  290 (398)
                      +.+|+|+..|+-.-+.++.-|...|
T Consensus       298 gk~Vv~ilsGGNiD~~~l~~i~er~  322 (406)
T PRK08198        298 GKKVVAVLSGGNIDVLLLSRVIERG  322 (406)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             9849999725787989999999998


No 250
>COG4789 EscV Type III secretory pathway, component EscV [Intracellular trafficking and secretion]
Probab=36.75  E-value=15  Score=16.71  Aligned_cols=14  Identities=14%  Similarity=0.332  Sum_probs=8.0

Q ss_pred             CCHHHHHHHHHHCC
Q ss_conf             65799999999868
Q gi|254781049|r    3 IHEYQAKALLRKYN   16 (398)
Q Consensus         3 L~EyqaK~lL~~~G   16 (398)
                      |.|++|-++...||
T Consensus        90 LL~adAG~II~sFG  103 (689)
T COG4789          90 LLEADAGEIIYSFG  103 (689)
T ss_pred             HHHCCCCHHHHHHC
T ss_conf             87523251888727


No 251
>COG1646 Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]
Probab=36.36  E-value=29  Score=14.80  Aligned_cols=51  Identities=27%  Similarity=0.413  Sum_probs=34.0

Q ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf             996248842788898999999999861998658999635861328999999999999
Q gi|254781049|r  291 GAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVK  347 (398)
Q Consensus       291 g~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~  347 (398)
                      |-|.-||++||++..-.-.+..+.++++-    .|  |+||-.|.-+.|.-+..|.-
T Consensus       164 g~~~~YlEagsga~~Pv~~e~v~~v~~~~----~L--ivGGGIrs~E~A~~~a~agA  214 (240)
T COG1646         164 GMPVVYLEAGSGAGDPVPVEMVSRVLSDT----PL--IVGGGIRSPEQAREMAEAGA  214 (240)
T ss_pred             CCEEEEEEECCCCCCCCCHHHHHHHHCCC----EE--EECCCCCCHHHHHHHHHCCC
T ss_conf             98589998068889986889999861455----08--98588498999999997179


No 252
>pfam08981 consensus
Probab=36.23  E-value=30  Score=14.78  Aligned_cols=17  Identities=29%  Similarity=0.100  Sum_probs=7.4

Q ss_pred             HHHHHHHHHCCCCEEEE
Q ss_conf             99999998729986999
Q gi|254781049|r   29 HAAESAIKTLPGPLYVV   45 (398)
Q Consensus        29 ~ea~~~a~~ig~p~~Vv   45 (398)
                      +-|.+-++++|-..+||
T Consensus        15 ~~a~~ra~e~gI~~iVv   31 (181)
T pfam08981        15 ELAAERAKELGIKHIVV   31 (181)
T ss_pred             HHHHHHHHHCCCCEEEE
T ss_conf             99999999769976999


No 253
>PRK08526 threonine dehydratase; Provisional
Probab=35.76  E-value=30  Score=14.74  Aligned_cols=24  Identities=21%  Similarity=0.538  Sum_probs=16.6

Q ss_pred             CCEEEEECCCHHHHHHHHHHHHCC
Q ss_conf             817999555036899999999658
Q gi|254781049|r  267 GNIGCMVNGAGLAMATMDIIKLYG  290 (398)
Q Consensus       267 G~Ig~~vnGaGlamatmD~i~~~G  290 (398)
                      .+|+|+..|+-.-+.++.-|...|
T Consensus       296 k~Vv~ilsGGNiD~~~l~~ii~r~  319 (403)
T PRK08526        296 AKIGVVLSGGNIDVQMLNVIIEKG  319 (403)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             979999715888988999999998


No 254
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=35.62  E-value=30  Score=14.72  Aligned_cols=63  Identities=16%  Similarity=0.127  Sum_probs=33.8

Q ss_pred             HHHHHCCCCCCCCEEE-CCHHHHHHHHHHC--CCCEEEEECCCCCCCCCCCCCCCCCCC--CCCEEEEECCHH
Q ss_conf             9999868988881574-7999999999872--998699971213687656565567777--777079958999
Q gi|254781049|r   10 ALLRKYNVPVAKGVVI-SSVHAAESAIKTL--PGPLYVVKSQIHAGGRGKGRFKELPAD--SKGGVRVESSLK   77 (398)
Q Consensus        10 ~lL~~~GIpvp~g~~a-~s~~ea~~~a~~i--g~p~~VvKaQV~aGgRGKa~~~~~hk~--~~GGV~l~~s~~   77 (398)
                      +.|..+|+++-+..++ +++++...+....  .+. +|    |.+||=|--+.|++.-.  ..=|+.++.+++
T Consensus        28 ~~L~~~G~~v~~~~~VgD~~~~I~~~l~~a~~r~D-~v----I~tGGLGPT~DDiT~e~vAka~g~~lv~~~~   95 (255)
T COG1058          28 DELTELGVDLARITTVGDNPDRIVEALREASERAD-VV----ITTGGLGPTHDDLTAEAVAKALGRPLVLDEE   95 (255)
T ss_pred             HHHHHCCCEEEEEEECCCCHHHHHHHHHHHHHCCC-EE----EECCCCCCCCCHHHHHHHHHHHCCCCCCCHH
T ss_conf             99996496189999639999999999999971899-89----9879858996276899999982998566999


No 255
>pfam02195 ParBc ParB-like nuclease domain.
Probab=35.44  E-value=30  Score=14.70  Aligned_cols=55  Identities=20%  Similarity=0.374  Sum_probs=22.4

Q ss_pred             HHHHHHHCCCCCCEEEEC---------CCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             999999729998799974---------89858999999997699589949989999999998506
Q gi|254781049|r  342 ILSAVKEVKINIPLVMRL---------EGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       342 ii~a~~~~~~~~pivvRl---------~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      +...+++.+...|++||-         .|..--.+.+.+....+++.. .++++.-.++..++++
T Consensus        26 L~~SI~~~G~~~PiiV~~~~~~~y~ii~G~~R~~A~~~lg~~~ip~~v-~d~~~~ea~~~~l~eN   89 (90)
T pfam02195        26 LIASIKEHGLLQPIIVRKTPGGRYEIIDGHRRLRAAKLLGLKEVPVIV-LELDDEEAIALSLEEN   89 (90)
T ss_pred             HHHHHHHHCCCCCEEEEECCCCCEEEEEEEEHHHHHHHCCCCEEEEEE-EECCHHHHHHHHHHCC
T ss_conf             999999859647879997488978995686199999986998610999-9899899999998745


No 256
>PRK03995 hypothetical protein; Provisional
Probab=34.77  E-value=31  Score=14.63  Aligned_cols=40  Identities=20%  Similarity=0.213  Sum_probs=21.2

Q ss_pred             HHHHHHHHHCCCCCC-EEEECC---CCCHHHHHHHHHHCCCCEE
Q ss_conf             999999997299987-999748---9858999999997699589
Q gi|254781049|r  340 KGILSAVKEVKINIP-LVMRLE---GANVDIGNRLIAESGLNVI  379 (398)
Q Consensus       340 ~gii~a~~~~~~~~p-ivvRl~---Gtn~~~g~~il~~~g~~~~  379 (398)
                      +-+.+++.+.....+ +++-..   |..-+.-.++|++.|+++.
T Consensus       219 e~~~~~~~~~~~~~~~a~iD~K~~kg~~R~~i~~~l~~~gi~v~  262 (264)
T PRK03995        219 EVILRAIIKHTEPVDAAYIDRKGLKSEDRREIEEFLDELGLEVI  262 (264)
T ss_pred             HHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             99999999731689889995577987899999999998699461


No 257
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=34.43  E-value=32  Score=14.60  Aligned_cols=91  Identities=20%  Similarity=0.164  Sum_probs=54.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHH--
Q ss_conf             488427888989999999998619986589996358613289999999999997299987999748985899999999--
Q gi|254781049|r  295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIA--  372 (398)
Q Consensus       295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~--  372 (398)
                      .|.+=+=+++.+.+..|++-. .++  +.+|  |.||..+-.+... +...+   ..++++.+=+-|-+.++=.+.++  
T Consensus       324 ~fiNDSKATN~~a~~~AL~~f-~~~--~iil--I~GG~~Kg~d~~~-l~~~~---~~~~~~~vi~~G~~~~~i~~~~~~~  394 (468)
T PRK04690        324 TYVNDSISTTPHASLAALDCF-AGR--RVAL--LVGGHDRGLDWTD-FAAHM---AQQAPLEIVTMGANGPRIHALLAPL  394 (468)
T ss_pred             EEECCCCCCCHHHHHHHHHHC-CCC--CEEE--EECCCCCCCCHHH-HHHHH---HHCCCEEEEEECCCHHHHHHHHHHC
T ss_conf             997378778989999999727-668--5799--9736766778799-99998---6337689999747889999997523


Q ss_pred             --HCCCCEEEECCHHHHHHHHHHH
Q ss_conf             --7699589949989999999998
Q gi|254781049|r  373 --ESGLNVITAIDLDDAAQKIVHA  394 (398)
Q Consensus       373 --~~g~~~~~~~~~~~A~~~~v~~  394 (398)
                        ...++++.+++|++|++.+.+.
T Consensus       395 ~~~~~~~~~~~~~l~~Av~~a~~~  418 (468)
T PRK04690        395 ADAGRFGLHAADDLPHAMALARTA  418 (468)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHH
T ss_conf             445631025406799999999996


No 258
>PTZ00317 malic enzyme; Provisional
Probab=34.11  E-value=32  Score=14.57  Aligned_cols=22  Identities=14%  Similarity=0.300  Sum_probs=10.7

Q ss_pred             HHHHHHHHHCCCCCCEEEECCCC
Q ss_conf             99999999729998799974898
Q gi|254781049|r  340 KGILSAVKEVKINIPLVMRLEGA  362 (398)
Q Consensus       340 ~gii~a~~~~~~~~pivvRl~Gt  362 (398)
                      +-+++++... ...|||.-|+-+
T Consensus       396 eevv~~Ma~~-~erPIIFaLSNP  417 (570)
T PTZ00317        396 EEIVKFMASN-CERPIIFPLSNP  417 (570)
T ss_pred             HHHHHHHHHC-CCCCEEEECCCC
T ss_conf             9999999855-998879977898


No 259
>PRK05878 pyruvate phosphate dikinase; Provisional
Probab=33.84  E-value=22  Score=15.69  Aligned_cols=32  Identities=9%  Similarity=-0.146  Sum_probs=20.7

Q ss_pred             CCEEECCCCCCCE----EEEEEEEEECCCCCEEEEE
Q ss_conf             3011034555650----5899999834778048998
Q gi|254781049|r  104 NCVYVEDGADILR----ELYLSLLVDRTSGMVAFIA  135 (398)
Q Consensus       104 ~~vLVEe~v~~~~----E~ylgi~~Dr~~~~~vii~  135 (398)
                      ..|-|+.||-..+    --=+.+++||.+|.+-+++
T Consensus       192 ~AV~VQ~MVfgn~~d~sgsGV~FTrdP~TG~~~~~g  227 (529)
T PRK05878        192 TAVVVQAMVFGNLDANSGAGVLFSRNPITGANEPFG  227 (529)
T ss_pred             CEEEEEEEEECCCCCCCCCEEEEEECCCCCCCEEEE
T ss_conf             316899835527899876137897068889960799


No 260
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.  E. coli DnaG is a single subunit enzyme.
Probab=33.74  E-value=32  Score=14.53  Aligned_cols=54  Identities=24%  Similarity=0.260  Sum_probs=31.4

Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCCHH-HHHHHHHHCCCCEEEECCHHHHHHHHHH
Q ss_conf             99999999729998799974898589-9999999769958994998999999999
Q gi|254781049|r  340 KGILSAVKEVKINIPLVMRLEGANVD-IGNRLIAESGLNVITAIDLDDAAQKIVH  393 (398)
Q Consensus       340 ~gii~a~~~~~~~~pivvRl~Gtn~~-~g~~il~~~g~~~~~~~~~~~A~~~~v~  393 (398)
                      ||..+++.-....++-+|-+.||+-. +-.++|++..-+++.+-|-|+|-++|..
T Consensus         7 EG~~D~i~~~~~G~~n~VA~~Gt~~t~~q~~~L~~~~~~vil~~D~D~AG~~Aa~   61 (79)
T cd03364           7 EGYMDVIALHQAGIKNVVASLGTALTEEQAELLKRLAKEVILAFDGDEAGQKAAL   61 (79)
T ss_pred             ECHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHCCCCCEEEEECCCHHHHHHHH
T ss_conf             6779999999859962562566547199999772315867999789889999999


No 261
>PRK08928 consensus
Probab=33.73  E-value=32  Score=14.53  Aligned_cols=25  Identities=16%  Similarity=0.167  Sum_probs=16.2

Q ss_pred             CHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf             9899999999986199865899963
Q gi|254781049|r  304 DQDKVAAAFKIITSDSSVKGILINI  328 (398)
Q Consensus       304 ~~e~~~~a~~~il~~~~vk~iliNi  328 (398)
                      ..+.....++-++.|++++.|.=|+
T Consensus       358 ~~~~~~~~l~~lLed~~i~KIghNl  382 (861)
T PRK08928        358 ITDAFSDIIFNLLTDKSILKITYDL  382 (861)
T ss_pred             CHHHHHHHHHHHHCCCCCCEEECCH
T ss_conf             2478999999984399975445457


No 262
>pfam00411 Ribosomal_S11 Ribosomal protein S11.
Probab=33.59  E-value=33  Score=14.51  Aligned_cols=49  Identities=20%  Similarity=0.252  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf             899999999999972999-8799974898589999999976995899499
Q gi|254781049|r  335 CDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAID  383 (398)
Q Consensus       335 cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~  383 (398)
                      ...+|+-+.+.+++++++ +.|++|=-|+..+-..+-|..+|+++....|
T Consensus        45 a~~aa~~~~~~~~~~gi~~v~v~ikG~G~Gr~~air~l~~~gl~I~~I~D   94 (109)
T pfam00411        45 AQTAAENAAKIAKEQGIKALEVKIKGPGPGRESALRALARSGLRIGRIRD   94 (109)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf             99999999999998198599999988998789999999877998999998


No 263
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=33.41  E-value=33  Score=14.49  Aligned_cols=49  Identities=18%  Similarity=0.298  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf             899999999999972999-8799974898589999999976995899499
Q gi|254781049|r  335 CDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAID  383 (398)
Q Consensus       335 cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~  383 (398)
                      ...+|+-+.+.+++++++ +-|++|=-|+..+-..+-|..+|+.+....|
T Consensus        45 a~~aa~~~~~~~~~~gi~~v~V~ikG~G~Gr~~air~l~~~glkI~~I~D   94 (108)
T TIGR03632        45 AQLAAEDAAKKAKEFGMKTVDVYVKGPGAGRESAIRALQAAGLEVTSIKD   94 (108)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf             99999999999997096199999968997479999999988988999998


No 264
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=33.37  E-value=33  Score=14.49  Aligned_cols=120  Identities=17%  Similarity=0.207  Sum_probs=74.9

Q ss_pred             CCEEEEECCCHHH------HHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHH-HHHCCCCCCEEEEECCCCHHHHHHHH
Q ss_conf             8179995550368------9999999965899624884278889899999999-98619986589996358613289999
Q gi|254781049|r  267 GNIGCMVNGAGLA------MATMDIIKLYGGAPANFLDVGGGADQDKVAAAFK-IITSDSSVKGILINIFGGIMRCDVLV  339 (398)
Q Consensus       267 G~Ig~~vnGaGla------matmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~-~il~~~~vk~iliNifGGI~~cd~vA  339 (398)
                      |++.++..-.|..      ....+.+..+++..---....+..+.++.++..+ ++.++|++++|+-       .-|.+|
T Consensus       159 g~v~~~~g~~~~~~~~~R~~G~~~~l~~~~~~~~v~~~~~~~~~~~~a~~~~~~~L~~~pdi~~i~~-------~~d~~a  231 (322)
T COG1879         159 GKVVVLVGSPGNSSAEERVKGFRDALKEHPPDIEVVDVQTGDWDRDKALEVMEDLLAANPDIDGIYA-------ANDGMA  231 (322)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEE-------CCCCHH
T ss_conf             8489997888995199999999999975599559975436887688999999999975899449998-------997069


Q ss_pred             HHHHHHHHHCCCCC-CEEEECCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             99999999729998-799974898589999999976995899499899999999985
Q gi|254781049|r  340 KGILSAVKEVKINI-PLVMRLEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       340 ~gii~a~~~~~~~~-pivvRl~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      .|.++|+++.+..- ..|+=..|+.  +.++.+++-.+......+.......+++++
T Consensus       232 ~ga~~a~~~ag~~~~v~v~g~D~~~--~~~~~i~~G~~~~~v~q~p~~~g~~~~~~~  286 (322)
T COG1879         232 LGAIQALKAAGRKGDVVVVGFDGTP--DALKALKDGKLDATVLQDPAAQGAAAVELA  286 (322)
T ss_pred             HHHHHHHHHCCCCCCEEEEEECCCH--HHHHHHHCCCEEEEECCCHHHHHHHHHHHH
T ss_conf             9999999976998806999947979--999999669736996379888899999999


No 265
>PRK00536 speE spermidine synthase; Provisional
Probab=33.22  E-value=27  Score=15.00  Aligned_cols=39  Identities=5%  Similarity=-0.072  Sum_probs=25.2

Q ss_pred             EEEEEECCCCCEEEEEECCCCCCHHHHHHHCHHHHEEEECC
Q ss_conf             99998347780489984478840245557483122033214
Q gi|254781049|r  120 LSLLVDRTSGMVAFIASTQGGMDIEEVAKDYPQKIFKLLID  160 (398)
Q Consensus       120 lgi~~Dr~~~~~vii~S~~GGvdIE~va~~~p~~I~~~~id  160 (398)
                      +.+..-|+-.++++++++-||+-=|-+..  |..+.-+.||
T Consensus        65 vpl~~Hp~Pk~VLIIGGGDGG~~REvlKH--~~~v~~VEID  103 (262)
T PRK00536         65 MGGCTKKELKEVLIVDGFDLELAHQLFKY--DTHVDFVQAD  103 (262)
T ss_pred             HHHHCCCCCCEEEEECCCCHHHHHHHHCC--CCEEEEEEEC
T ss_conf             02321899787999868755999998728--9766999967


No 266
>CHL00041 rps11 ribosomal protein S11
Probab=32.30  E-value=34  Score=14.37  Aligned_cols=49  Identities=18%  Similarity=0.278  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf             899999999999972999-8799974898589999999976995899499
Q gi|254781049|r  335 CDVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAID  383 (398)
Q Consensus       335 cd~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~  383 (398)
                      +..+|+-+.+..++++++ +-|++|=-|...+-..+-|+.+|+++....|
T Consensus        58 a~~aa~~~~~~a~~~Gi~~v~v~vkG~G~GR~~aik~l~~~glkI~~I~D  107 (116)
T CHL00041         58 AQTAAENAIRTVIDQGMKRAEVMIKGPGLGRDTALRAIRRSGLKLSSIRD  107 (116)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf             99999999999997398499999978884589999999878988999998


No 267
>COG0281 SfcA Malic enzyme [Energy production and conversion]
Probab=32.22  E-value=34  Score=14.37  Aligned_cols=28  Identities=32%  Similarity=0.444  Sum_probs=11.1

Q ss_pred             EEEEECCCHHH-HHHHHHHHHCCCCCCEE
Q ss_conf             79995550368-99999999658996248
Q gi|254781049|r  269 IGCMVNGAGLA-MATMDIIKLYGGAPANF  296 (398)
Q Consensus       269 Ig~~vnGaGla-matmD~i~~~Gg~pANF  296 (398)
                      +=+++||||.| .+.++++..+|-++.|+
T Consensus       200 ~kiv~~GAGAAgiaia~~l~~~g~~~~~i  228 (432)
T COG0281         200 QKIVINGAGAAGIAIADLLVAAGVKEENI  228 (432)
T ss_pred             EEEEEECCCHHHHHHHHHHHHHCCCCCCE
T ss_conf             38999677588999999999828984458


No 268
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family; InterPro: IPR014252   This entry shows some relation to the widely distributed ATP-dependent protease La, also called Lon or LonA (IPR004815 from INTERPRO), but is more closely related to LonB (IPR014251 from INTERPRO), a LonA paralog found only in endospore-forming bacteria. Proteins in this entry are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ). They are restricted to a subset of endospore-forming species, and probably participate in the program of endospore formation. We propose the designation LonC..
Probab=31.72  E-value=3.3  Score=21.10  Aligned_cols=58  Identities=28%  Similarity=0.405  Sum_probs=39.8

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHH--CCCCCC--EEEEECCCCHH----H-HHHHHHHHHHHHHHCCC
Q ss_conf             24884278889899999999986--199865--89996358613----2-89999999999997299
Q gi|254781049|r  294 ANFLDVGGGADQDKVAAAFKIIT--SDSSVK--GILINIFGGIM----R-CDVLVKGILSAVKEVKI  351 (398)
Q Consensus       294 ANFlD~gG~a~~e~~~~a~~~il--~~~~vk--~iliNifGGI~----~-cd~vA~gii~a~~~~~~  351 (398)
                      --|=|.-|+=+.+.+-+|+..|=  .+..++  =|-||+-||--    + -.-+--.|+.|+.+..+
T Consensus       480 ~RfNdTAGSMaKDSvFNAasviRk~T~~D~~~yD~HVNViGGG~IDGPSAG~Ai~~~~~SA~~~~p~  546 (616)
T TIGR02903       480 VRFNDTAGSMAKDSVFNAASVIRKITGKDLKDYDIHVNVIGGGRIDGPSAGAAITLCIISAILDKPI  546 (616)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             8861565530357789889998653046834165178885277017532579999999998708983


No 269
>PRK11660 putative sulfate transporter YchM; Provisional
Probab=31.67  E-value=35  Score=14.31  Aligned_cols=84  Identities=10%  Similarity=0.133  Sum_probs=56.8

Q ss_pred             CHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHH-HHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHCCCC-----
Q ss_conf             989999999998619986589996358613289999-99999999729998799974898589999999976995-----
Q gi|254781049|r  304 DQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLV-KGILSAVKEVKINIPLVMRLEGANVDIGNRLIAESGLN-----  377 (398)
Q Consensus       304 ~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA-~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~g~~-----  377 (398)
                      +.+++.+.++-  ..+++|.+.+ -+.+++..|.-| +.+-+-.++.+-  -+.+.+.+-+.+. ++.|+.+|+-     
T Consensus       476 na~~~~~~l~~--~~~~~~~vVl-d~~~v~~iD~Tg~~~L~~l~~~l~~--gi~l~~a~~~~~v-~~~l~r~gl~~~ig~  549 (567)
T PRK11660        476 AAERLFTELES--RTEGKRIVVL-KWDAVPVLDAGGLDAFQRFVERLPE--GCELRICNLQFQP-LRTLARAGIQPIPGR  549 (567)
T ss_pred             HHHHHHHHHHH--HCCCCCEEEE-ECCCCCCCCHHHHHHHHHHHHHHHC--CCEEEEECCCHHH-HHHHHHCCCHHHCCC
T ss_conf             39999999986--2689988999-7489996168999999999999977--9989996698689-999998799312596


Q ss_pred             EEEECCHHHHHHHHHH
Q ss_conf             8994998999999999
Q gi|254781049|r  378 VITAIDLDDAAQKIVH  393 (398)
Q Consensus       378 ~~~~~~~~~A~~~~v~  393 (398)
                      -+.+.+.+||++.+++
T Consensus       550 ~~~f~t~~~Av~~~~~  565 (567)
T PRK11660        550 LAFYPTLREALADLLS  565 (567)
T ss_pred             CCEECCHHHHHHHHHH
T ss_conf             5426989999999984


No 270
>PRK07334 threonine dehydratase; Provisional
Probab=31.64  E-value=35  Score=14.30  Aligned_cols=23  Identities=17%  Similarity=0.401  Sum_probs=13.4

Q ss_pred             CEEEEECCCHHHHHHHHHHHHCC
Q ss_conf             17999555036899999999658
Q gi|254781049|r  268 NIGCMVNGAGLAMATMDIIKLYG  290 (398)
Q Consensus       268 ~Ig~~vnGaGlamatmD~i~~~G  290 (398)
                      +|+|+..|+-.-+.++.-|...|
T Consensus       294 ~Vv~vlsGGNiD~~~l~~ii~r~  316 (399)
T PRK07334        294 KVGLVLCGGNIDTRLLANVLLRG  316 (399)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             19999686886988999999998


No 271
>PRK09492 treR trehalose repressor; Provisional
Probab=31.52  E-value=35  Score=14.29  Aligned_cols=98  Identities=13%  Similarity=0.140  Sum_probs=62.2

Q ss_pred             HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCE-EEEC
Q ss_conf             999999965899624884278889899999999986199865899963586132899999999999972999879-9974
Q gi|254781049|r  281 ATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPL-VMRL  359 (398)
Q Consensus       281 atmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pi-vvRl  359 (398)
                      ...+..+.+|..|.-+.   +..+.+.-++..+-+++ +++.+||.       -.|.+|-|+++++++.+++ ++ |+=+
T Consensus       197 g~~~~~~~~~l~~~~~~---~~~~~~~~~~~~~~~l~-~~~~ai~~-------~~D~~A~g~~~~l~~~gi~-disi~g~  264 (315)
T PRK09492        197 AYLAFCKQHKLHPVAAL---GGLSMKSGYELVAKVLT-PETTALVC-------ATDTLALGASKYLQEQGRE-TLQVAGV  264 (315)
T ss_pred             HHHHHHHHCCCCCEEEE---CCCCHHHHHHHHHHHHC-CCCCEEEE-------ECHHHHHHHHHHHHHCCCC-CEEEEEE
T ss_conf             99999997799960665---68887889999999606-79985999-------5679999999999971999-8589998


Q ss_pred             CCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHH
Q ss_conf             898589999999976995899499899999999985
Q gi|254781049|r  360 EGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAV  395 (398)
Q Consensus       360 ~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~  395 (398)
                      .++.  .. +++ ...+.- ...+.++..++|+++.
T Consensus       265 d~~~--~~-~~~-~P~LTT-i~~~~~~~g~~A~~~L  295 (315)
T PRK09492        265 GNTP--LL-KFL-FPNIVS-VDPGYAEAGRQAACQL  295 (315)
T ss_pred             CCHH--HH-HHC-CCCCEE-EEECHHHHHHHHHHHH
T ss_conf             8818--89-845-899749-9859999999999999


No 272
>pfam09840 DUF2067 Uncharacterized protein conserved in archaea (DUF2067). This domain, found in various archaeal proteins, has no known function.
Probab=31.51  E-value=35  Score=14.29  Aligned_cols=20  Identities=5%  Similarity=-0.017  Sum_probs=12.3

Q ss_pred             HHHHHHHHHHHHHHHHHHCC
Q ss_conf             98859999999989999559
Q gi|254781049|r  183 ARIDGGDLFPNLYKAFCDKD  202 (398)
Q Consensus       183 ~~~~~~~ii~~L~~~f~e~D  202 (398)
                      .++.+.+++.+|+.++.+..
T Consensus       114 p~eev~e~~~~L~eiy~ei~  133 (190)
T pfam09840       114 PLEEVVEVARELSEIYKELR  133 (190)
T ss_pred             CHHHHHHHHHHHHHHHHHHH
T ss_conf             79999999999999999985


No 273
>PRK13529 malate dehydrogenase; Provisional
Probab=31.32  E-value=35  Score=14.27  Aligned_cols=14  Identities=7%  Similarity=0.000  Sum_probs=5.7

Q ss_pred             ECCHHHHHHHHHHH
Q ss_conf             58999999999986
Q gi|254781049|r   73 ESSLKSVISDIREI   86 (398)
Q Consensus        73 ~~s~~ea~~~a~~i   86 (398)
                      ..+...+.+..++|
T Consensus       129 ~~d~g~i~~il~nw  142 (563)
T PRK13529        129 YPDRDRIDDILRNA  142 (563)
T ss_pred             CCCHHHHHHHHHHC
T ss_conf             26666899999708


No 274
>pfam01341 Glyco_hydro_6 Glycosyl hydrolases family 6.
Probab=31.04  E-value=36  Score=14.24  Aligned_cols=67  Identities=19%  Similarity=0.207  Sum_probs=47.9

Q ss_pred             CCCEEEECCCC--------CCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHH--HHHHHHHHHCCCCCCEEEE
Q ss_conf             96248842788--------8989999999998619986589996358613289999--9999999972999879997
Q gi|254781049|r  292 APANFLDVGGG--------ADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLV--KGILSAVKEVKINIPLVMR  358 (398)
Q Consensus       292 ~pANFlD~gG~--------a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA--~gii~a~~~~~~~~pivvR  358 (398)
                      ....|||.|.+        ++.+.+.+.++-.-.-.+++++..|+-.=-.-+|+++  +.+..++...+.....||-
T Consensus       154 nv~vYlDaGh~~Wlgw~~n~~a~~~a~~l~~ag~~~~~rGfatNvSNy~~t~~e~~y~~~l~~~l~~~G~~~~fVID  230 (295)
T pfam01341       154 NVAVYLDAGHSGWLGWDANPAAQLFAERLKNAGSGASARGFATNVSNYNPTADEKAYAEALSPALGAAGFGAHFVID  230 (295)
T ss_pred             CEEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEE
T ss_conf             84899968773224887653899999999965885402478850456777178999999999998505898886886


No 275
>COG0646 MetH Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]
Probab=30.96  E-value=36  Score=14.23  Aligned_cols=159  Identities=17%  Similarity=0.298  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCEEEEEEEEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHHCC---
Q ss_conf             98859999999989999559751023267990599679940013215735564102786310001562224577539---
Q gi|254781049|r  183 ARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRLRVLDSKISFDDNALYRHLDIQELRDVSEEDSREIEAKQHN---  259 (398)
Q Consensus       183 ~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~vvAlDAKi~iDDnA~fR~~~~~~~~d~~~~~~~E~~A~~~~---  259 (398)
                      ....--+.|.++-+.|.+-.|..+|-|-+--|    -+++ ++-.+.|....-+.+-.++       .++ -|.+.+   
T Consensus        47 LnlT~Pd~I~~IH~aY~eAGADiIeTNTFgat----~i~l-ady~led~v~~in~~aa~i-------AR~-aA~~~~~~k  113 (311)
T COG0646          47 LNLTKPDVIEAIHRAYIEAGADIIETNTFGAT----TIKL-ADYGLEDKVYEINQKAARI-------ARR-AADEAGDPK  113 (311)
T ss_pred             HHCCCCHHHHHHHHHHHHCCCCEEEECCCCCC----HHHH-HHHCHHHHHHHHHHHHHHH-------HHH-HHHHCCCCC
T ss_conf             75479499999999999646767873477865----3657-5507388999999999999-------999-986447887


Q ss_pred             CCEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCE-EEECCC--CCCHHHHHHHHHH---HHCCCCCCEEEEECCCCHH
Q ss_conf             864422881799955503689999999965899624-884278--8898999999999---8619986589996358613
Q gi|254781049|r  260 LSYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPAN-FLDVGG--GADQDKVAAAFKI---ITSDSSVKGILINIFGGIM  333 (398)
Q Consensus       260 l~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pAN-FlD~gG--~a~~e~~~~a~~~---il~~~~vk~iliNifGGI~  333 (398)
                      =.||-  |.||                      |-| ++.+.|  ..+-+.++.+++-   .|-+-.+..+||--+=-+-
T Consensus       114 ~rfVa--GsiG----------------------Pt~k~~~~~~~~~v~fd~l~~ay~eq~~~Li~gG~D~iLiET~~D~l  169 (311)
T COG0646         114 PRFVA--GSIG----------------------PTNKTLSISPDFAVTFDELVEAYREQVEGLIDGGADLILIETIFDTL  169 (311)
T ss_pred             CEEEE--EECC----------------------CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEHHCCHH
T ss_conf             53898--7326----------------------86776776876663599999999999999983787589975221689


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEE---------CCCCCHHHHHHHHHHCCCCE
Q ss_conf             2899999999999972999879997---------48985899999999769958
Q gi|254781049|r  334 RCDVLVKGILSAVKEVKINIPLVMR---------LEGANVDIGNRLIAESGLNV  378 (398)
Q Consensus       334 ~cd~vA~gii~a~~~~~~~~pivvR---------l~Gtn~~~g~~il~~~g~~~  378 (398)
                      ++.....++-+..++.+..+|+++.         |.|..-+..+.-|+..+...
T Consensus       170 ~~KaA~~a~~~~~~~~~~~LPv~~s~Ti~~sG~tl~Gq~~~a~~~~l~~~~~~~  223 (311)
T COG0646         170 NAKAAVFAAREVFEELGVRLPVMISGTITDSGRTLSGQTIEAFLNSLEHLGPDA  223 (311)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCEECCCCCHHHHHHHHHCCCCCE
T ss_conf             899999999999873277654799999803761237986899999866359747


No 276
>TIGR00962 atpA ATP synthase F1, alpha subunit; InterPro: IPR005294   ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , .  F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.   F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient.   This entry represents the alpha subunit found in the F1 complex of F-ATPases. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha-subunit contains a highly conserved adenine-specific non-catalytic nucleotide-binding domain, with a conserved amino acid sequence of Gly-X-X-X-X-Gly-Lys. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself is driven by the movement of protons through the F0 complex C subunit .   More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0016820 hydrolase activity acting on acid anhydrides catalyzing transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0016469 proton-transporting two-sector ATPase complex.
Probab=30.90  E-value=22  Score=15.64  Aligned_cols=49  Identities=22%  Similarity=0.315  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHHCCCCCCCC--CCCCCCCCCCCEEECCCCCCCE---EEEEEEEEECCCCCEEE
Q ss_conf             99999999998618765442--1222224433011034555650---58999998347780489
Q gi|254781049|r   75 SLKSVISDIREILGSTLITK--QTGPTGSRVNCVYVEDGADILR---ELYLSLLVDRTSGMVAF  133 (398)
Q Consensus        75 s~~ea~~~a~~ilg~~l~t~--qt~~~G~~v~~vLVEe~v~~~~---E~ylgi~~Dr~~~~~vi  133 (398)
                      ....+...|--++.++-+..  |||-+       =|-.|+||+|   ||++|   ||++|+-.+
T Consensus       124 ~~~~~E~~APGv~~RkSV~ePlQTGIk-------AIDAliPIGRGQRELIIG---DRqTGKTav  177 (520)
T TIGR00962       124 EFRPIEKIAPGVIERKSVHEPLQTGIK-------AIDALIPIGRGQRELIIG---DRQTGKTAV  177 (520)
T ss_pred             CCCCCCCCCCCEEECCCCCCCCHHHHH-------HHHCCCCCCCCCEEEEEC---CCCCCCCHH
T ss_conf             634321458855214667873000055-------764146898762223423---266673056


No 277
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=30.24  E-value=37  Score=14.15  Aligned_cols=35  Identities=11%  Similarity=0.181  Sum_probs=28.7

Q ss_pred             CHHHHHHHHHHCCCCCCC-CEEECCHHHHHHHHHHC
Q ss_conf             579999999986898888-15747999999999872
Q gi|254781049|r    4 HEYQAKALLRKYNVPVAK-GVVISSVHAAESAIKTL   38 (398)
Q Consensus         4 ~EyqaK~lL~~~GIpvp~-g~~a~s~~ea~~~a~~i   38 (398)
                      +.||.-+.|++.|+||.+ ..+|.+.+|..+..+.+
T Consensus       237 t~~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~  272 (667)
T COG0272         237 TQSERLAFLKAWGFPVNPYTRLCKNADEVLAFYEEW  272 (667)
T ss_pred             CHHHHHHHHHHCCCCCCCHHHHCCCHHHHHHHHHHH
T ss_conf             799999999975999880766608999999999999


No 278
>COG2759 MIS1 Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism]
Probab=30.16  E-value=37  Score=14.14  Aligned_cols=14  Identities=43%  Similarity=0.821  Sum_probs=7.3

Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99999999658996
Q gi|254781049|r  280 MATMDIIKLYGGAP  293 (398)
Q Consensus       280 matmD~i~~~Gg~p  293 (398)
                      .||.-.++.+||-|
T Consensus       326 VATvRALK~hGG~~  339 (554)
T COG2759         326 VATVRALKMHGGVP  339 (554)
T ss_pred             EEEHHHHHHCCCCC
T ss_conf             61368998728988


No 279
>TIGR01418 PEP_synth phosphoenolpyruvate synthase; InterPro: IPR006319   This family represents phosphoenolpyruvate synthase; also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes. ; GO: 0008986 pyruvate water dikinase activity, 0006094 gluconeogenesis.
Probab=29.77  E-value=17  Score=16.35  Aligned_cols=95  Identities=21%  Similarity=0.233  Sum_probs=47.9

Q ss_pred             CCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEE----------CCCCH----HH-HHHHH
Q ss_conf             50368999999996589962488427888989999999998619986589996----------35861----32-89999
Q gi|254781049|r  275 GAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILIN----------IFGGI----MR-CDVLV  339 (398)
Q Consensus       275 GaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliN----------ifGGI----~~-cd~vA  339 (398)
                      |=||+=.=+=+...-+-.|=-|+|+---.+.+ =.+--+++-..--|+.-||-          ++-|-    .. -|.+|
T Consensus       564 GVGLaR~EfII~~~i~~HP~aLi~~~d~~~~~-K~EI~el~dekGfvqfkliyhyanGrlanKL~aGY~~~~~~fv~kLa  642 (877)
T TIGR01418       564 GVGLARIEFIILNWIKIHPLALIDDDDLKEVE-KAEIEELMDEKGFVQFKLIYHYANGRLANKLAAGYANPRDFFVDKLA  642 (877)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH-HHHHHHHHCCCCEEEEEEEEEECCCHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             62278899999857765468745776877588-89998632057605667765420432667765045881257889999


Q ss_pred             HHHHHHHHHCCCCCCEEEECCCCCHHHHHHHH
Q ss_conf             99999999729998799974898589999999
Q gi|254781049|r  340 KGILSAVKEVKINIPLVMRLEGANVDIGNRLI  371 (398)
Q Consensus       340 ~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il  371 (398)
                      +||..-.... ...||+||++=--..|=++|+
T Consensus       643 eGia~vA~AF-YPkPV~VR~SDFKsNEY~~L~  673 (877)
T TIGR01418       643 EGIAKVAAAF-YPKPVIVRTSDFKSNEYRNLI  673 (877)
T ss_pred             HHHHHHHHHH-CCCCCEEEECCCCCHHHHHHC
T ss_conf             9999998753-889718981369836998716


No 280
>pfam01949 DUF99 Protein of unknown function DUF99. The function of this archaebacterial protein family is unknown.
Probab=29.00  E-value=39  Score=14.01  Aligned_cols=20  Identities=20%  Similarity=0.458  Sum_probs=9.0

Q ss_pred             CEEEECCCCCHHHHHHHHHH
Q ss_conf             79997489858999999997
Q gi|254781049|r  354 PLVMRLEGANVDIGNRLIAE  373 (398)
Q Consensus       354 pivvRl~Gtn~~~g~~il~~  373 (398)
                      |+++|..|-+.+++.++++.
T Consensus       139 ~iyvq~~Gi~~~~A~~ii~~  158 (185)
T pfam01949       139 PVYIQAAGIDPEEAKELIER  158 (185)
T ss_pred             CEEEEECCCCHHHHHHHHHH
T ss_conf             69999869999999999999


No 281
>TIGR00644 recJ single-stranded-DNA-specific exonuclease RecJ; InterPro: IPR004610 All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair. RecJ is a single-stranded DNA-specific endonuclease which is required for many types of recombination events, although the stringency of the requirement for RecJ appears to vary with the type of recombinational event monitored, and the other recombination gene products which are available.; GO: 0008409 5'-3' exonuclease activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=28.88  E-value=39  Score=14.00  Aligned_cols=14  Identities=14%  Similarity=0.048  Sum_probs=8.1

Q ss_pred             ECCHHHHHHHHHHH
Q ss_conf             58999999999986
Q gi|254781049|r   73 ESSLKSVISDIREI   86 (398)
Q Consensus        73 ~~s~~ea~~~a~~i   86 (398)
                      .+++.++.+-++++
T Consensus       422 ~~d~~~a~~la~~l  435 (705)
T TIGR00644       422 TDDPKQARELAEEL  435 (705)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             30389999999999


No 282
>COG2379 GckA Putative glycerate kinase [Carbohydrate transport and metabolism]
Probab=28.85  E-value=17  Score=16.40  Aligned_cols=54  Identities=22%  Similarity=0.290  Sum_probs=25.9

Q ss_pred             CCEEEEEECCCCCCHHHHHHHCHHHHEEEECCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             804899844788402455574831220332144457895788878875198889988599999999899
Q gi|254781049|r  129 GMVAFIASTQGGMDIEEVAKDYPQKIFKLLIDPLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYKA  197 (398)
Q Consensus       129 ~~~vii~S~~GGvdIE~va~~~p~~I~~~~id~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~~  197 (398)
                      ...+++.|+ ||-           .+.  + -|..|++-.+...+-+.|=-+|..+..+..+=+.|+++
T Consensus       113 D~Vi~LISG-GGS-----------aL~--e-~P~eGitL~d~~avn~~LL~sGA~I~emNtVRkhLS~V  166 (422)
T COG2379         113 DLVIVLISG-GGS-----------ALL--E-LPAEGITLEDLIAVNRALLKSGAPISEMNTVRKHLSRV  166 (422)
T ss_pred             CEEEEEEEC-CCH-----------HHC--C-CCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf             679999817-831-----------400--3-89667878999999999997599869999999988561


No 283
>TIGR01746 Thioester-redct thioester reductase domain; InterPro: IPR010080   This domain includes the C-terminal domain from the fungal alpha aminoadipate reductase enzyme (also known as aminoadipate semialdehyde dehydrogenase) which is involved in the biosynthesis of lysine , as well as the reductase-containing component of the myxochelin biosynthetic gene cluster, MxcG . The mechanism of reduction involves activation of the substrate by adenylation and transfer to a covalently-linked pantetheine cofactor as a thioester. This thioester is then reduced to give an aldehyde (thus releasing the product) and a regenerated pantetheine thiol ; in myxochelin biosynthesis this aldehyde is further reduced to an alcohol or converted to an amine by an aminotransferase. This is a fundamentally different reaction than beta-ketoreductase domains of polyketide synthases which act at a carbonyl two carbons removed from the thioester and forms an alcohol as a product. The majority of bacterial sequences containing this domain are non-ribosomal peptide synthetases in which this domain is similarly located proximal to a thiolation domain (IPR006163 from INTERPRO). In some cases this domain is found at the end of a polyketide synthetase enzyme, but is unlike ketoreductase domains which are found before the thiolase domains. Exceptions to this observed relationship with the thiolase domain include three proteins which consist of stand-alone reductase domains (from Mycobacterium leprae, Anabaena and from Streptomyces coelicolor) and one protein (from Nostoc) which contains N-terminal homology with a small group of hypothetical proteins but no evidence of a thiolation domain next to the putative reductase domain.; GO: 0004043 L-aminoadipate-semialdehyde dehydrogenase activity.
Probab=28.81  E-value=39  Score=13.99  Aligned_cols=62  Identities=13%  Similarity=0.210  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCC---CEEEECCC-----CCHHHHHHHHHH-CCCCEEEECCHHHHHHHHHH
Q ss_conf             1328999999999999729998---79997489-----858999999997-69958994998999999999
Q gi|254781049|r  332 IMRCDVLVKGILSAVKEVKINI---PLVMRLEG-----ANVDIGNRLIAE-SGLNVITAIDLDDAAQKIVH  393 (398)
Q Consensus       332 I~~cd~vA~gii~a~~~~~~~~---pivvRl~G-----tn~~~g~~il~~-~g~~~~~~~~~~~A~~~~v~  393 (398)
                      .+.-|.+|+.|..-......+.   -.+.-+.+     =..++=...+++ .|.++....+++|.-++.=+
T Consensus       257 ~~pVd~~a~ai~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~f~~~~~~~~G~~~~~~~~~~eW~~~l~~  327 (405)
T TIGR01746       257 LTPVDYVARAIVALSSQPAAEAQAGGAVFHLVNPEPEPVSLDEFLEWLKRSAGYELKLLVSFDEWLQRLED  327 (405)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf             31099999999999987646432772178722899856578999999988618865342898999999986


No 284
>PRK02255 putrescine carbamoyltransferase; Provisional
Probab=28.77  E-value=39  Score=13.99  Aligned_cols=15  Identities=27%  Similarity=0.301  Sum_probs=7.6

Q ss_pred             HHHHHHHCCCCEEEE
Q ss_conf             999998729986999
Q gi|254781049|r   31 AESAIKTLPGPLYVV   45 (398)
Q Consensus        31 a~~~a~~ig~p~~Vv   45 (398)
                      -..++.++|+.+..+
T Consensus        61 FE~A~~~LGg~~i~l   75 (341)
T PRK02255         61 FETAMTQLGGHAQYL   75 (341)
T ss_pred             HHHHHHHCCCCEEEC
T ss_conf             999999859979982


No 285
>COG0616 SppA Periplasmic serine proteases (ClpP class) [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=28.75  E-value=39  Score=13.99  Aligned_cols=24  Identities=25%  Similarity=0.252  Sum_probs=15.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             988899885999999998999955
Q gi|254781049|r  178 ELQGQARIDGGDLFPNLYKAFCDK  201 (398)
Q Consensus       178 g~~~~~~~~~~~ii~~L~~~f~e~  201 (398)
                      .+..+....+...+...|+.|.+.
T Consensus       201 ~~t~e~~~~~q~~~~e~y~~F~~~  224 (317)
T COG0616         201 PLTEEEREILQKEIDETYDEFVDK  224 (317)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             369899999999999999999999


No 286
>TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase; InterPro: IPR010121   Pyruvate phosphate dikinase (PPDK, or pyruvate orthophosphate dikinase) is found in plants, bacteria and archaea. The amino acid sequence identity between bacterial and plant enzymes is high, and they are similar in sequence to other PEP-utilizing enzymes. PPDK catalyses the reversible conversion of ATP and pyruvate to AMP and PEP (phosphoenolpyruvate). In bacteria such as Clostridium symbiosum, PPDK uses Mg2+ and NH4+ ions as cofactors . The enzyme has three domains: the N- and C-terminal domains each have an active site centre that catalyses a different step in the reaction, and the middle domain has a carrier histidine residue that moves between the two active centres.   In plants, PPDK is localised predominantly in chloroplast stroma where it catalyses the rate-limiting step in the C4 photosynthetic pathway, namely the synthesis of PEP, which acts as the primary CO2 acceptor in C4 photosynthesis . PPDK activity in C4 plants is strictly regulated by light, its activity decreasing in darkness. This response is regulated by phosphorylation and dephosphorylation of the enzyme using ADP; such regulation is not seen in the bacterial form of the enzyme. PPDK is also found in C3 plants, but it is not known to have a photosynthetic role .; GO: 0050242 pyruvate phosphate dikinase activity.
Probab=28.73  E-value=27  Score=15.07  Aligned_cols=46  Identities=26%  Similarity=0.302  Sum_probs=29.2

Q ss_pred             CEEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHC
Q ss_conf             644228817999555036899999999658996248842788898999999999861
Q gi|254781049|r  261 SYIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITS  317 (398)
Q Consensus       261 ~yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~  317 (398)
                      .||.+||.-|++-+|.=..           -+|.+=-|+-|.|..+.+.+|.+.||+
T Consensus       519 D~isiDGsTG~iYlGe~~~-----------~~p~~~~~f~G~Paedelvravd~im~  564 (920)
T TIGR01828       519 DIISIDGSTGEIYLGEVPL-----------IEPEVSGDFEGEPAEDELVRAVDTIMS  564 (920)
T ss_pred             EEEEEECCCCCEECCCCCC-----------CCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             3799708606235375442-----------166778766787505789999999999


No 287
>PRK05309 30S ribosomal protein S11; Validated
Probab=28.52  E-value=39  Score=13.96  Aligned_cols=48  Identities=19%  Similarity=0.298  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHCCCC-CCEEEECCCCCHHHHHHHHHHCCCCEEEECC
Q ss_conf             99999999999972999-8799974898589999999976995899499
Q gi|254781049|r  336 DVLVKGILSAVKEVKIN-IPLVMRLEGANVDIGNRLIAESGLNVITAID  383 (398)
Q Consensus       336 d~vA~gii~a~~~~~~~-~pivvRl~Gtn~~~g~~il~~~g~~~~~~~~  383 (398)
                      ...|+-+.+-+++++++ +-|.+|=-|+..+-+.+-|..+|+.+....|
T Consensus        62 ~~aa~~~~~~~~~~Gi~~v~V~ikG~G~GR~~air~L~~~gikI~~I~D  110 (126)
T PRK05309         62 QVAAEDAAKKAKEHGMKTVEVFVKGPGSGRESAIRALQAAGLEVTSIKD  110 (126)
T ss_pred             HHHHHHHHHHHHHCCCEEEEEEEECCCCCHHHHHHHHHHCCCEEEEEEE
T ss_conf             9999999999997297199999977883389999999878988999998


No 288
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=28.42  E-value=25  Score=15.29  Aligned_cols=17  Identities=18%  Similarity=0.260  Sum_probs=7.5

Q ss_pred             HHHHHHHCCCCHHHHHH
Q ss_conf             88788751988899885
Q gi|254781049|r  170 VASLCDMLELQGQARID  186 (398)
Q Consensus       170 ~~~l~~~lg~~~~~~~~  186 (398)
                      +..++..|+++....+.
T Consensus       104 l~~~~~~l~LP~~v~e~  120 (285)
T COG1405         104 LERIASALGLPESVRET  120 (285)
T ss_pred             HHHHHHHHCCCCHHHHH
T ss_conf             99999871898037999


No 289
>pfam02571 CbiJ Precorrin-6x reductase CbiJ/CobK. This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyses the reaction: precorrin-6Y + NADP(+) <= precorrin-6X + NADPH. CbiJ and CobK both catalyse the reduction of macocycle in the colbalmin biosynthesis pathway.
Probab=28.39  E-value=40  Score=13.95  Aligned_cols=62  Identities=13%  Similarity=0.209  Sum_probs=38.5

Q ss_pred             HCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEC
Q ss_conf             658996248842788898999999999861998658999635861328999999999999729998799974
Q gi|254781049|r  288 LYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRL  359 (398)
Q Consensus       288 ~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl  359 (398)
                      ..|..+.|+.-.-|--+.|.=.    -++..-++.+++--==||- -..    .=++|.+++++.+ |++++
T Consensus       162 ~~g~~~~~iIa~~gPfs~e~n~----al~~~~~i~~lVtK~SG~~-g~~----~Ki~AA~~lgi~v-ivI~R  223 (246)
T pfam02571       162 ALGFPNAEIIAARGPFSLELER----ALLRRHGIDVLVTKNSGGA-GTY----AKLAAARELGLPV-IMIKR  223 (246)
T ss_pred             CCCCCHHCEEEECCCCCHHHHH----HHHHHCCCCEEEEECCCCH-HHH----HHHHHHHHCCCEE-EEEEC
T ss_conf             4799800189904999989999----9999709999999288865-069----9999999849929-99958


No 290
>pfam04223 CitF Citrate lyase, alpha subunit (CitF). In citrate-utilising prokaryotes, citrate lyase EC:4.1.3.6 cleaves intracellular citrate into acetate and oxaloacetate, and is organized as a functional complex consisting of alpha, beta, and gamma subunits. The gamma subunit serves as an acyl carrier protein (ACP), and has a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group. The citrate lyase is active only if this prosthetic group is acetylated; this acetylation is catalysed by an acetate:SH-citrate lyase ligase. The alpha subunit substitutes citryl for the acetyl group to form citryl-S-ACP. The beta subunit completes the reaction by cleaving the citryl to yield oxaloacetate and (regenerated) acetyl-S-ACP. This family represents the alpha subunit EC:2.8.3.10.
Probab=28.06  E-value=40  Score=13.91  Aligned_cols=66  Identities=20%  Similarity=0.278  Sum_probs=48.0

Q ss_pred             HHHHHHHCCC-CCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHH--HHHHHHHHHHHHHHC
Q ss_conf             9999996589-9624884278889899999999986199865899963586132--899999999999972
Q gi|254781049|r  282 TMDIIKLYGG-APANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMR--CDVLVKGILSAVKEV  349 (398)
Q Consensus       282 tmD~i~~~Gg-~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~--cd~vA~gii~a~~~~  349 (398)
                      ..+.|...|. +..=-+-.|-|-.+-.+.+.++-.+...++|+=|.  .||||.  ||..-+|+++++-+.
T Consensus       216 aa~vI~~sg~~kdGFSfQTGaGGaSLAv~~~l~~~M~~~~Ik~sFa--~GGIT~~~vdmleeGL~~~l~Dv  284 (466)
T pfam04223       216 AADVIVNSPYFKEGFSFQTGTGGASLAVTRFLREKMIRENIKASFA--LGGITATMVDLLEEGLVDKLLDV  284 (466)
T ss_pred             HHHHHHHCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEE--CCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             9999985776537636665888699999999999999759769988--77740999999871334634113


No 291
>PRK09466 metL bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional
Probab=27.56  E-value=41  Score=13.85  Aligned_cols=23  Identities=17%  Similarity=0.205  Sum_probs=10.5

Q ss_pred             CCEEEECCCC-------CCHHHHHHHHHHH
Q ss_conf             6248842788-------8989999999998
Q gi|254781049|r  293 PANFLDVGGG-------ADQDKVAAAFKII  315 (398)
Q Consensus       293 pANFlD~gG~-------a~~e~~~~a~~~i  315 (398)
                      .-|..-+|-+       -....+.+|++.+
T Consensus       419 nI~iiaqg~SEinIS~VI~~~d~~kAv~aL  448 (810)
T PRK09466        419 PVEFLWQSEDGLSLVAVLRQGPTESLIQGL  448 (810)
T ss_pred             CCEEEEECCCCCEEEEEECHHHHHHHHHHH
T ss_conf             940899817885699997476699999999


No 292
>TIGR01091 upp uracil phosphoribosyltransferase; InterPro: IPR005765    The enzyme uracil phosphoribosyltransferase (UPRT, 2.4.2.9 from EC) catalyzes conversion of uracil to uridine 5'-monophosphate utilizing 5'-phosphoribosyl--1-pyrophosphate (PRPP).  UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate  ; GO: 0004845 uracil phosphoribosyltransferase activity, 0006223 uracil salvage.
Probab=27.25  E-value=41  Score=13.82  Aligned_cols=33  Identities=24%  Similarity=0.382  Sum_probs=18.2

Q ss_pred             CCEEECC----CCEEE----EECCCHHHHHHHHHHHHCCCC
Q ss_conf             8644228----81799----955503689999999965899
Q gi|254781049|r  260 LSYIALD----GNIGC----MVNGAGLAMATMDIIKLYGGA  292 (398)
Q Consensus       260 l~yv~Ld----G~Ig~----~vnGaGlamatmD~i~~~Gg~  292 (398)
                      .-|.||-    ++.-+    |-.=+|..++|.|.++.+|-+
T Consensus       117 ~Yy~KLP~~~~~~~v~v~DPMLATGgt~~~a~~~lk~~g~~  157 (213)
T TIGR01091       117 VYYSKLPEDIDERTVIVLDPMLATGGTMIAALDLLKKRGAK  157 (213)
T ss_pred             ECCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCC
T ss_conf             32200543468886999728734305899999999853999


No 293
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein 
Probab=27.12  E-value=42  Score=13.80  Aligned_cols=45  Identities=13%  Similarity=0.200  Sum_probs=23.2

Q ss_pred             HHHHHHHHHCCCCCCCCEEECCHHHHHHHHHHC-CCCEEEEECCCCCCCC
Q ss_conf             999999998689888815747999999999872-9986999712136876
Q gi|254781049|r    6 YQAKALLRKYNVPVAKGVVISSVHAAESAIKTL-PGPLYVVKSQIHAGGR   54 (398)
Q Consensus         6 yqaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~i-g~p~~VvKaQV~aGgR   54 (398)
                      ..||+||.++|++.-..-+-.++ +......++ +.|- |  +||-.+|.
T Consensus        27 ~~a~~lL~~~~v~~~~~dv~~d~-~~r~~l~~~s~~~T-v--Pqifi~g~   72 (90)
T cd03028          27 RKVVQILNQLGVDFGTFDILEDE-EVRQGLKEYSNWPT-F--PQLYVNGE   72 (90)
T ss_pred             HHHHHHHHHHCCCCEECCHHCCH-HHHHHHHHHCCCCC-C--CCEEECCE
T ss_conf             99999999968997413300589-99999999716898-8--83779998


No 294
>PRK09429 mepA penicillin-insensitive murein endopeptidase; Reviewed
Probab=26.94  E-value=42  Score=13.78  Aligned_cols=54  Identities=24%  Similarity=0.346  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHCCCCCCEEEEECCCCHH--HHHHHHHHHHHHHHHCC----CCCCEEEECCC
Q ss_conf             89999999998619986589996358613--28999999999999729----99879997489
Q gi|254781049|r  305 QDKVAAAFKIITSDSSVKGILINIFGGIM--RCDVLVKGILSAVKEVK----INIPLVMRLEG  361 (398)
Q Consensus       305 ~e~~~~a~~~il~~~~vk~iliNifGGI~--~cd~vA~gii~a~~~~~----~~~pivvRl~G  361 (398)
                      ..+-.+.+++-.+||+|.-||||  -+|-  -|++ |.|=-.-+..+.    -+--+-|||.=
T Consensus       153 t~~h~~li~~AA~dp~V~RIFVn--p~IK~~lC~~-~~~DR~WL~KvRPw~GH~~HfHVRL~C  212 (270)
T PRK09429        153 TPQHASLIKLAAQDPRVTRIFVN--PAIKKQLCRT-AGGDRSWLRKVRPWWGHDYHFHVRLRC  212 (270)
T ss_pred             CHHHHHHHHHHHCCCCEEEEEEC--HHHHHHHHHH-CCCCHHHHHCCCCCCCCCCEEEEEEEC
T ss_conf             68999999998448652477646--8988999870-024177886568535766414788527


No 295
>cd04258 AAK_AKiii-LysC-EC AAK_AKiii-LysC-EC: Amino Acid Kinase Superfamily (AAK), AKiii-LysC-EC: this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKIII. AKIII is a monofunctional class enzyme (LysC) found in some bacteria such as E. coli. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. In E. coli, LysC is reported to be a homodimer of 50 kD subunits.
Probab=26.74  E-value=42  Score=13.76  Aligned_cols=41  Identities=17%  Similarity=0.035  Sum_probs=25.5

Q ss_pred             EEECCCCEEEEECCCHHHHHHHHHHHHCCCCCCEEEECCCC
Q ss_conf             44228817999555036899999999658996248842788
Q gi|254781049|r  262 YIALDGNIGCMVNGAGLAMATMDIIKLYGGAPANFLDVGGG  302 (398)
Q Consensus       262 yv~LdG~Ig~~vnGaGlamatmD~i~~~Gg~pANFlD~gG~  302 (398)
                      -..-+|.+-++.-|+-=--||+=.....--+.-++-|+-|=
T Consensus       188 g~~~~G~~ttLGRGGSDyTA~~la~~l~A~~v~iwtDV~Gi  228 (292)
T cd04258         188 GSTEKGRTTTLGRGGSDYSAALLAEALHAEELQIWTDVAGI  228 (292)
T ss_pred             EECCCCCEEECCCCCCHHHHHHHHHHCCCCEEEEEECCCCC
T ss_conf             43799977753789616899999997699889999678878


No 296
>PRK12861 malic enzyme; Reviewed
Probab=26.51  E-value=43  Score=13.73  Aligned_cols=38  Identities=18%  Similarity=0.274  Sum_probs=14.4

Q ss_pred             HHHHHHHHHHCCCCC-CEEEECC-----CCCCHHHHHHHHHHHH
Q ss_conf             899999999658996-2488427-----8889899999999986
Q gi|254781049|r  279 AMATMDIIKLYGGAP-ANFLDVG-----GGADQDKVAAAFKIIT  316 (398)
Q Consensus       279 amatmD~i~~~Gg~p-ANFlD~g-----G~a~~e~~~~a~~~il  316 (398)
                      |..|-+.++.+|-+| .-||-++     -+++.++|.+|.+++-
T Consensus       617 Ai~aA~~ar~fGiePRVAmLSfSnFGS~~~~~~~KVreAveil~  660 (762)
T PRK12861        617 TIAAARQMEWLNLTPKVALLSRSNFGSGSAASGVKMRRALEIVR  660 (762)
T ss_pred             HHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             99999999983999738998057899999971579999999999


No 297
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679   DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC).   This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=25.94  E-value=44  Score=13.66  Aligned_cols=36  Identities=22%  Similarity=0.350  Sum_probs=29.9

Q ss_pred             CCHHHHHHHHHHCCCC-CCCCE-EEC--CHHHHHHHHHHC
Q ss_conf             6579999999986898-88815-747--999999999872
Q gi|254781049|r    3 IHEYQAKALLRKYNVP-VAKGV-VIS--SVHAAESAIKTL   38 (398)
Q Consensus         3 L~EyqaK~lL~~~GIp-vp~g~-~a~--s~~ea~~~a~~i   38 (398)
                      -+.||+-++|++.|+| |-+.. .|.  +.+|..+..+++
T Consensus       240 ~t~~~~L~~L~~~GF~TV~~~~~~~~ln~~~eV~~~~~~~  279 (706)
T TIGR00575       240 RTQYEALAWLKKLGFPTVNPHIRLCKLNSIEEVLEYYEEI  279 (706)
T ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             7789999999863884201257763038988999999999


No 298
>TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504   RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ).   RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=25.81  E-value=44  Score=13.65  Aligned_cols=163  Identities=17%  Similarity=0.353  Sum_probs=78.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCE-------EEEEEEEEECCCHHHHHHHHHHHHCCCCCCHHHH--
Q ss_conf             9885999999998999955975102326799059967-------9940013215735564102786310001562224--
Q gi|254781049|r  183 ARIDGGDLFPNLYKAFCDKDMSLLEINPLIIMKNGRL-------RVLDSKISFDDNALYRHLDIQELRDVSEEDSREI--  253 (398)
Q Consensus       183 ~~~~~~~ii~~L~~~f~e~Da~liEINPLvvt~dg~v-------vAlDAKi~iDDnA~fR~~~~~~~~d~~~~~~~E~--  253 (398)
                      -..|+-++-.-|-|+-...+..++=|=  =||+||.+       .++|+.+-||-++.-+|.=|-..+. +--...|+  
T Consensus       219 SVsQVRE~t~~Lmr~AKt~~iaifiVG--HVTKeGsiAGPkvLEH~vD~vLyfeGd~~~~~R~LRS~KN-RFGat~E~G~  295 (481)
T TIGR00416       219 SVSQVRECTAELMRLAKTRGIAIFIVG--HVTKEGSIAGPKVLEHMVDTVLYFEGDRDSRFRILRSVKN-RFGATNEIGI  295 (481)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCEEEEE--EECCCCCCCCCHHHHHHHHHHEECCCCCCCCCCHHHCCCC-CCCCCCCCCC
T ss_conf             423888999999876521686579970--0435675434046663433110115887534440100015-6787342101


Q ss_pred             -HHHHCCCCEEE-------------CCCC-EEEEECCCHHHHHHHHHHHHCC--CCC---CEEEECCCCCCHHHHHHHHH
Q ss_conf             -57753986442-------------2881-7999555036899999999658--996---24884278889899999999
Q gi|254781049|r  254 -EAKQHNLSYIA-------------LDGN-IGCMVNGAGLAMATMDIIKLYG--GAP---ANFLDVGGGADQDKVAAAFK  313 (398)
Q Consensus       254 -~A~~~~l~yv~-------------LdG~-Ig~~vnGaGlamatmD~i~~~G--g~p---ANFlD~gG~a~~e~~~~a~~  313 (398)
                       +.++.||.=|+             ..|. |-+..-|.=-=+.=+-++..+-  ++|   ||=+      +.-|+.--+=
T Consensus       296 FeM~e~GL~ev~nPS~iFL~~~~e~~~GSsitv~~EGtRPLlvEiQALVs~~s~anPrR~A~G~------d~NRL~~LlA  369 (481)
T TIGR00416       296 FEMTEQGLREVLNPSAIFLSRREEVMSGSSITVALEGTRPLLVEIQALVSPTSFANPRRVATGL------DQNRLALLLA  369 (481)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCHHHHHHHHHHCCCCCCCCCCCEECCH------HHHHHHHHHH
T ss_conf             0000233564531456641576456667301234237348888887522614368863100442------2568999999


Q ss_pred             HH-------HCCCCCCEEEEECCCCH----HHHHH-HHHHHHHHHHHCCCCCCEEE
Q ss_conf             98-------61998658999635861----32899-99999999997299987999
Q gi|254781049|r  314 II-------TSDSSVKGILINIFGGI----MRCDV-LVKGILSAVKEVKINIPLVM  357 (398)
Q Consensus       314 ~i-------l~~~~vk~iliNifGGI----~~cd~-vA~gii~a~~~~~~~~pivv  357 (398)
                      ++       |++..   +|||+-||+    +.||. ++-.|+-.+++..++-..++
T Consensus       370 vLek~~Gl~l~~~D---vf~~V~GGvkv~Epa~DLA~~~a~~SSFrdr~~~~~~~~  422 (481)
T TIGR00416       370 VLEKRLGLPLADQD---VFLNVAGGVKVSEPAVDLALLIALVSSFRDRPLDPDLVI  422 (481)
T ss_pred             HHHHHCCCCHHHCC---EEEEEECCEEECCHHHHHHHHHHHHHHHCCCCCCCCEEE
T ss_conf             98764066111173---479862350541057889999999987517887856388


No 299
>PRK09902 hypothetical protein; Provisional
Probab=25.72  E-value=40  Score=13.91  Aligned_cols=17  Identities=6%  Similarity=-0.087  Sum_probs=5.8

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             99999999899995597
Q gi|254781049|r  187 GGDLFPNLYKAFCDKDM  203 (398)
Q Consensus       187 ~~~ii~~L~~~f~e~Da  203 (398)
                      ++.++.+|-..=....|
T Consensus       137 ~a~~l~rlH~~~~qHgc  153 (216)
T PRK09902        137 VALAFKKMHSVNRQHGC  153 (216)
T ss_pred             HHHHHHHHHHCCCCCCC
T ss_conf             99999999867833467


No 300
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Probab=25.71  E-value=42  Score=13.75  Aligned_cols=35  Identities=20%  Similarity=0.243  Sum_probs=24.9

Q ss_pred             HHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCE
Q ss_conf             99999986898888157479999999998729986
Q gi|254781049|r    8 AKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPL   42 (398)
Q Consensus         8 aK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~   42 (398)
                      .++|++.||-|.|+.....++++..++.+.+|++.
T Consensus        18 ~~rl~~~~~~pt~~~l~~~~~~~l~~~i~~~G~~~   52 (144)
T pfam00730        18 TKRLFERYGFPTPEDLAEADEEELRELIKGLGFYR   52 (144)
T ss_pred             HHHHHHHHCCCCHHHHHCCCHHHHHHHHHCCCCHH
T ss_conf             99999982898999998599999999987089769


No 301
>pfam06714 Gp5_OB Gp5 N-terminal OB domain. This domain is found at the N terminus of the Gp5 baseplate protein of bacteriophage T4. This domain binds to the Gp27 protein. This domain has the common OB fold.
Probab=24.64  E-value=46  Score=13.51  Aligned_cols=28  Identities=11%  Similarity=0.124  Sum_probs=23.0

Q ss_pred             EEEEEEEEECCCCCEEEEEECCCCCCHHH
Q ss_conf             58999998347780489984478840245
Q gi|254781049|r  117 ELYLSLLVDRTSGMVAFIASTQGGMDIEE  145 (398)
Q Consensus       117 E~ylgi~~Dr~~~~~vii~S~~GGvdIE~  145 (398)
                      -+.+|+.+|.....|++|+| .+|+-.|.
T Consensus        48 swV~GFF~D~~~Q~PvImGt-lpG~P~e~   75 (144)
T pfam06714        48 THVYGFFLDKWYQNGVILGT-YPGIYKEK   75 (144)
T ss_pred             CEEEEEEECCCCCCCEEEEC-CCCCCCCC
T ss_conf             88999887821367768860-79975667


No 302
>TIGR02181 GRX_bact glutaredoxin 3; InterPro: IPR011900   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 family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulphides .; GO: 0006118 electron transport, 0045454 cell redox homeostasis.
Probab=24.46  E-value=47  Score=13.48  Aligned_cols=44  Identities=27%  Similarity=0.240  Sum_probs=31.2

Q ss_pred             HHHHHHHHCCC-CCCCCEEECCH-HHHHHHHHHCCCCEEEEECCCCCC
Q ss_conf             99999998689-88881574799-999999987299869997121368
Q gi|254781049|r    7 QAKALLRKYNV-PVAKGVVISSV-HAAESAIKTLPGPLYVVKSQIHAG   52 (398)
Q Consensus         7 qaK~lL~~~GI-pvp~g~~a~s~-~ea~~~a~~ig~p~~VvKaQV~aG   52 (398)
                      .||.||++-|| ..-+-.+-.++ ..-.+-.+.=++-.-|  +||=.|
T Consensus        14 rAK~LL~~kGv~~~~Ei~vd~dpD~~r~eM~~Rs~Gr~TV--PQIFIg   59 (82)
T TIGR02181        14 RAKALLESKGVGTFTEIRVDGDPDALRDEMMQRSGGRRTV--PQIFIG   59 (82)
T ss_pred             HHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHCCCCCC--CEEEEC
T ss_conf             8899998569886303445798106889999982899404--337629


No 303
>PRK00766 hypothetical protein; Provisional
Probab=24.36  E-value=47  Score=13.47  Aligned_cols=21  Identities=14%  Similarity=0.275  Sum_probs=10.4

Q ss_pred             CEEEECCCCCHHHHHHHHHHC
Q ss_conf             799974898589999999976
Q gi|254781049|r  354 PLVMRLEGANVDIGNRLIAES  374 (398)
Q Consensus       354 pivvRl~Gtn~~~g~~il~~~  374 (398)
                      ++++|..|-+.+++.++++..
T Consensus       146 ~iyvq~~Gi~~~~A~~ii~~~  166 (194)
T PRK00766        146 NLYIQAAGIEPETAAEVIRVT  166 (194)
T ss_pred             CEEEEECCCCHHHHHHHHHHH
T ss_conf             279998599999999999997


No 304
>cd05147 RIO1_euk RIO kinase family; eukaryotic RIO1, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. RIO1 is present in archaea, bacteria and eukaryotes. This subfamily is composed of RIO1 proteins from eukaryotes. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle progression and c
Probab=24.14  E-value=47  Score=13.45  Aligned_cols=36  Identities=22%  Similarity=0.264  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHHHHC---CCCCCCCCEEEECCCCCEEEEEE
Q ss_conf             999999998999955---97510232679905996799400
Q gi|254781049|r  187 GGDLFPNLYKAFCDK---DMSLLEINPLIIMKNGRLRVLDS  224 (398)
Q Consensus       187 ~~~ii~~L~~~f~e~---Da~liEINPLvvt~dg~vvAlDA  224 (398)
                      +.+++..+.++|.+.   ..+|=|-|=|+  .+++++..|-
T Consensus       123 ~~~il~~~~~ly~~~~lVHGDLSEyNIl~--~~~~~~iID~  161 (190)
T cd05147         123 YLQVIQIMRILYQDCRLVHADLSEYNLLY--HDGKLYIIDV  161 (190)
T ss_pred             HHHHHHHHHHHHHHCCCEECCCCHHHEEE--CCCCEEEEEC
T ss_conf             99999999999997493224531542052--4899899966


No 305
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298   DNA carries the biological information that instructs cells how to exist in an ordered fashion. Accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=23.52  E-value=48  Score=13.37  Aligned_cols=39  Identities=15%  Similarity=0.243  Sum_probs=20.3

Q ss_pred             HHHHHHHCCCCCCC--CEEECCH-HHHHHHHHHCCCCEEEEE
Q ss_conf             99999986898888--1574799-999999987299869997
Q gi|254781049|r    8 AKALLRKYNVPVAK--GVVISSV-HAAESAIKTLPGPLYVVK   46 (398)
Q Consensus         8 aK~lL~~~GIpvp~--g~~a~s~-~ea~~~a~~ig~p~~VvK   46 (398)
                      .|++|.++|||+-+  |+=|++. --..+.+..-||.+.+|-
T Consensus        92 i~e~l~algi~~~e~~GYEADD~IaTLA~~a~~~G~~V~I~s  133 (1005)
T TIGR00593        92 IKELLEALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIIS  133 (1005)
T ss_pred             HHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             999999719818822887101289998887754685489983


No 306
>pfam04414 tRNA_deacylase D-aminoacyl-tRNA deacylase. Several aminoacyl-tRNA synthetases have the ability to transfer the D-isomer of their amino acid onto their cognate tRNA. D-aminoacyl-tRNA deacylases hydrolyse the ester bond between the polynucleotide and the D-amino acid, thereby preventing the accumulation of such mis-acylated and metabolically inactive tRNA molecules.
Probab=22.94  E-value=50  Score=13.30  Aligned_cols=38  Identities=18%  Similarity=0.229  Sum_probs=16.8

Q ss_pred             HHHHHHHHCCCCCCEEEECCCCC---HHHHHHHHHHCCCCEE
Q ss_conf             99999997299987999748985---8999999997699589
Q gi|254781049|r  341 GILSAVKEVKINIPLVMRLEGAN---VDIGNRLIAESGLNVI  379 (398)
Q Consensus       341 gii~a~~~~~~~~pivvRl~Gtn---~~~g~~il~~~g~~~~  379 (398)
                      -|.+|++...... +++-..|.+   -+.-.++|++.|+++.
T Consensus       172 ~l~~a~~~s~~~~-a~iD~Ks~kg~~r~~i~~~l~~~gi~v~  212 (214)
T pfam04414       172 VIRQAIEKSGADA-AIIDRKSLKSEDRSRITEFLEELGLEVI  212 (214)
T ss_pred             HHHHHHHHCCCCE-EEEECCCCCHHHHHHHHHHHHHCCCCEE
T ss_conf             9999998389968-9997577977899999999998699210


No 307
>TIGR02665 molyb_mobA molybdopterin-guanine dinucleotide biosynthesis protein A; InterPro: IPR013482    In many molybdopterin-containing enzymes, including nitrate reductase and dimethylsulphoxide reductase, the cofactor is molybdopterin-guanine dinucleotide. This entry describes proteobacterial MobA (molybdopterin-guanine dinucleotide biosynthesis protein A). MobA synthesises molybdopterin-guanine dinucleotide from molybdopterin and GTP. ; GO: 0003824 catalytic activity, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=22.85  E-value=45  Score=13.61  Aligned_cols=120  Identities=21%  Similarity=0.278  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCCE--EEEE--EEE
Q ss_conf             213687656565567777777079958999999999986187654421222224433011034555650--5899--999
Q gi|254781049|r   48 QIHAGGRGKGRFKELPADSKGGVRVESSLKSVISDIREILGSTLITKQTGPTGSRVNCVYVEDGADILR--ELYL--SLL  123 (398)
Q Consensus        48 QV~aGgRGKa~~~~~hk~~~GGV~l~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~~--E~yl--gi~  123 (398)
                      =|||||||-    =|...|+|.|-+..  .-+.+..-+.+     ++|       |..|+|.-=-+.++  .+.+  -++
T Consensus         4 viLAGG~ar----RMGG~DKGL~~L~g--~PL~~hv~~rL-----~PQ-------v~~~~IsANRn~~~Y~~~g~Gl~V~   65 (202)
T TIGR02665         4 VILAGGRAR----RMGGRDKGLVELGG--KPLIEHVLARL-----RPQ-------VSDLAISANRNPERYAQAGFGLPVV   65 (202)
T ss_pred             EEECCCCCC----CCCCCCCCCEECCC--CCHHHHHHHHH-----CCC-------HHHHHHHCCCCHHHHHHHCCCCEEC
T ss_conf             676587400----26888866101286--52899999984-----350-------7666741388977898860897312


Q ss_pred             EEC---CCCCEEEEEECCCCCCHHHHHH---HCHHHHEEEECC-CCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf             834---7780489984478840245557---483122033214-445789578887887519888998859999999989
Q gi|254781049|r  124 VDR---TSGMVAFIASTQGGMDIEEVAK---DYPQKIFKLLID-PLIGVTSEDVASLCDMLELQGQARIDGGDLFPNLYK  196 (398)
Q Consensus       124 ~Dr---~~~~~vii~S~~GGvdIE~va~---~~p~~I~~~~id-~~~gl~~~~~~~l~~~lg~~~~~~~~~~~ii~~L~~  196 (398)
                      -|.   ..+.+    .+..||.-=-.+-   ..-+-+...|-| |+                ++       .+++.+|+.
T Consensus        66 ~D~~DA~~~F~----GPLAGilagL~~a~~~~~~~~vl~~PCD~P~----------------lP-------~dLv~RL~~  118 (202)
T TIGR02665        66 PDDVDALADFP----GPLAGILAGLRWAVAGTGTDWVLTVPCDTPF----------------LP-------EDLVARLAA  118 (202)
T ss_pred             CCCCCCCCCCC----CCHHHHHHHHHHHHHCCCCCEEEEECCCCCC----------------CC-------HHHHHHHHH
T ss_conf             78534357888----8768999999999844699828882288899----------------88-------789999999


Q ss_pred             HHHHCCCCCCCCCEEEE--CCCCC
Q ss_conf             99955975102326799--05996
Q gi|254781049|r  197 AFCDKDMSLLEINPLII--MKNGR  218 (398)
Q Consensus       197 ~f~e~Da~liEINPLvv--t~dg~  218 (398)
                      .....+      +++++  -.||.
T Consensus       119 a~~~~~------a~iavATA~~G~  136 (202)
T TIGR02665       119 ALEAQD------ADIAVATAHDGG  136 (202)
T ss_pred             HHHCCC------CCEEEEECCCCC
T ss_conf             975289------978998704488


No 308
>TIGR02291 rimK_rel_E_lig alpha-L-glutamate ligase homolog; InterPro: IPR011758   Members of this protein family contain a region of homology to the RimK family of alpha-L-glutamate ligases (IPR004666 from INTERPRO), various members of which modify the Glu-Glu C-terminus of ribosomal protein S6, or tetrahydromethanopterin, or a form of coenzyme F420 derivative. Members of this family are found so far in various Vibrio and Pseudomonas species and some other gamma and beta Proteobacteria. The function is unknown..
Probab=22.78  E-value=50  Score=13.28  Aligned_cols=99  Identities=18%  Similarity=0.145  Sum_probs=59.6

Q ss_pred             HHHHHHHHCCCCCCCCE-EECCHHHHHHHHHHC-CCCEEEEECCCCCCCCCCCCCCCCCCCC-----CCEEEEECCHHHH
Q ss_conf             99999998689888815-747999999999872-9986999712136876565655677777-----7707995899999
Q gi|254781049|r    7 QAKALLRKYNVPVAKGV-VISSVHAAESAIKTL-PGPLYVVKSQIHAGGRGKGRFKELPADS-----KGGVRVESSLKSV   79 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~-~a~s~~ea~~~a~~i-g~p~~VvKaQV~aGgRGKa~~~~~hk~~-----~GGV~l~~s~~ea   79 (398)
                      ..|.+=.+.||.||.=. ++++-.|....-+=+ +.|-+|+|+--=|||.|-.  .++.+-+     .-|-  .-|.+|+
T Consensus        40 ~TK~~A~AaGi~VPelyGVI~~q~ev~~~~~ivkdh~dFVIKPAqGsGG~GIl--Vit~r~~~ryr~~sG~--~i~~eei  115 (320)
T TIGR02291        40 KTKILAIAAGIAVPELYGVIEIQKEVKSLDDIVKDHEDFVIKPAQGSGGDGIL--VITDRLDERYRKSSGA--LISKEEI  115 (320)
T ss_pred             HHHHHHHHCCCCCCHHCCCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCCEEE--EECCCCCCCEECCCCC--CCCHHHH
T ss_conf             78899873367110130100234665434666278898367266067987279--9703668840354101--0154567


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCEEECCCCCCC
Q ss_conf             999998618765442122222443301103455565
Q gi|254781049|r   80 ISDIREILGSTLITKQTGPTGSRVNCVYVEDGADIL  115 (398)
Q Consensus        80 ~~~a~~ilg~~l~t~qt~~~G~~v~~vLVEe~v~~~  115 (398)
                      +....++|.=-     -.--|++ ..=|||-.+..+
T Consensus       116 E~hvSniL~GL-----ySLGG~~-D~AliEyrvkfD  145 (320)
T TIGR02291       116 ERHVSNILAGL-----YSLGGKR-DRALIEYRVKFD  145 (320)
T ss_pred             HHHHHHHHHHH-----HHCCCCC-CEEEEEEECCCC
T ss_conf             78888888777-----6507997-736885320105


No 309
>pfam01163 RIO1 RIO1 family. This is a family of atypical serine kinases which are found in archaea, bacteria and eukaryotes. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined.
Probab=22.73  E-value=50  Score=13.27  Aligned_cols=38  Identities=13%  Similarity=0.227  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHHHHHC---CCCCCCCCEEEECCCCCEEEEEE
Q ss_conf             85999999998999955---97510232679905996799400
Q gi|254781049|r  185 IDGGDLFPNLYKAFCDK---DMSLLEINPLIIMKNGRLRVLDS  224 (398)
Q Consensus       185 ~~~~~ii~~L~~~f~e~---Da~liEINPLvvt~dg~vvAlDA  224 (398)
                      .-+.+++..+.++|...   .+.|=|-|=|+  .+++++..|-
T Consensus       107 ~~~~~ii~~~~~~y~~~glVHgDLSEyNIL~--~~~~~~iID~  147 (186)
T pfam01163       107 EIYDEIIREMRRLYQEAGLVHGDLSEYNVLV--DDDKPVIIDV  147 (186)
T ss_pred             HHHHHHHHHHHHHHHHCCCEECCCHHHHEEE--ECCCEEEEEC
T ss_conf             9999999999999996693213620655064--3896799956


No 310
>PRK06740 histidinol-phosphatase; Validated
Probab=22.35  E-value=51  Score=13.22  Aligned_cols=89  Identities=15%  Similarity=0.209  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHH--HHHH--HHHHHHHHHHCCCCCC
Q ss_conf             89999999965899624884278889899999999986199865899963586132--8999--9999999997299987
Q gi|254781049|r  279 AMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMR--CDVL--VKGILSAVKEVKINIP  354 (398)
Q Consensus       279 amatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~--cd~v--A~gii~a~~~~~~~~p  354 (398)
                      .++-+|+||.+|.+|-      ...-.+-..++++.+ .+.+ -+|=|| -|.--|  |-++  ..-+.+.+.+  .++|
T Consensus       218 IiGHlDlIK~Fg~rp~------~~~~~~~~e~~a~ai-k~~~-~avEIN-AGLg~RkPV~EiYPs~~~Le~~~~--~gIP  286 (338)
T PRK06740        218 IIAHLDNIKVFNYRLD------ENEQLSYYKEIARAL-VETN-TATEIN-AGLYYRYPVREMCPSPLYLQVLAK--HGVP  286 (338)
T ss_pred             EECCHHHHHHCCCCCC------CHHHHHHHHHHHHHH-HHCC-CEEEEE-CCCCCCCCCCCCCCCHHHHHHHHH--CCCC
T ss_conf             6236216766188899------125899999999999-9749-379982-675346874456887999999997--6998


Q ss_pred             EEEEC-------CCCCHHHHHHHHHHCCCCE
Q ss_conf             99974-------8985899999999769958
Q gi|254781049|r  355 LVMRL-------EGANVDIGNRLIAESGLNV  378 (398)
Q Consensus       355 ivvRl-------~Gtn~~~g~~il~~~g~~~  378 (398)
                      |++--       -|...+++.+++++.|+.-
T Consensus       287 ItlgSDAH~Pe~VG~~~~ea~~llk~~Gyte  317 (338)
T PRK06740        287 ITLSSDAHYPNDLGKYVEENVKTLRNHGISH  317 (338)
T ss_pred             EEEECCCCCHHHHCCCHHHHHHHHHHCCCCE
T ss_conf             7851688996785665999999999749825


No 311
>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=22.27  E-value=51  Score=13.21  Aligned_cols=84  Identities=12%  Similarity=-0.001  Sum_probs=53.9

Q ss_pred             CCHHHHHH-HHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCC-CCCEEEECCCCCHHHHHHHHHHCCCCEEE
Q ss_conf             89899999-99998619986589996358613289999999999997299-98799974898589999999976995899
Q gi|254781049|r  303 ADQDKVAA-AFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKI-NIPLVMRLEGANVDIGNRLIAESGLNVIT  380 (398)
Q Consensus       303 a~~e~~~~-a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~-~~pivvRl~Gtn~~~g~~il~~~g~~~~~  380 (398)
                      .+.+..+. .-.++.++|++++|+-       ..|..+.|.++|+++.+. ..-.|+=..|+.  ++.+.+++--+....
T Consensus       161 ~~~~~a~~~~~~~L~~~pdi~~i~~-------~~~~~a~ga~~Al~~~g~~~~i~vvg~D~~~--~~~~~i~~G~i~~tv  231 (271)
T cd06314         161 EDFAKAKSNAEDALNAHPDLKCMFG-------LYAYNGPAIAEAVKAAGKLGKVKIVGFDEDP--DTLQGVKEGTIQGTV  231 (271)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEE-------ECCCCHHHHHHHHHHHCCCCCCEEEEECCCH--HHHHHHHCCCCEEEE
T ss_conf             6388999999999975899878998-------0885169999999984758996799878989--999999829985998


Q ss_pred             ECCHHHHHHHHHHHH
Q ss_conf             499899999999985
Q gi|254781049|r  381 AIDLDDAAQKIVHAV  395 (398)
Q Consensus       381 ~~~~~~A~~~~v~~~  395 (398)
                      ..+..+--..+|+.+
T Consensus       232 ~Q~p~~~G~~av~~~  246 (271)
T cd06314         232 VQRPYQMGYLSVTVL  246 (271)
T ss_pred             ECCHHHHHHHHHHHH
T ss_conf             389999999999999


No 312
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=22.23  E-value=51  Score=13.20  Aligned_cols=71  Identities=20%  Similarity=0.231  Sum_probs=41.9

Q ss_pred             CCHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEE-ECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             79999999998729986999712136876565655677777770799-58999999999986187654421222224433
Q gi|254781049|r   26 SSVHAAESAIKTLPGPLYVVKSQIHAGGRGKGRFKELPADSKGGVRV-ESSLKSVISDIREILGSTLITKQTGPTGSRVN  104 (398)
Q Consensus        26 ~s~~ea~~~a~~ig~p~~VvKaQV~aGgRGKa~~~~~hk~~~GGV~l-~~s~~ea~~~a~~ilg~~l~t~qt~~~G~~v~  104 (398)
                      -|++|...++++.|.|+ |.    .+                ||==+ -.+..|..+.+.+. ++.+ +-.|       +
T Consensus        59 Ls~ee~~~~~~e~Gap~-V~----it----------------GGEPLLr~dl~eIv~~a~~~-g~~v-~l~T-------N  108 (318)
T TIGR03470        59 LSVEECLRAVDECGAPV-VS----IP----------------GGEPLLHPEIDEIVRGLVAR-KKFV-YLCT-------N  108 (318)
T ss_pred             CCHHHHHHHHHHCCCCE-EE----EC----------------CCCCCCCCCHHHHHHHHHHC-CCEE-EEEC-------C
T ss_conf             89999999999849978-99----51----------------88745564799999999975-9979-9977-------5


Q ss_pred             CEEECCCCCC---CEEEEEEEEEEC
Q ss_conf             0110345556---505899999834
Q gi|254781049|r  105 CVYVEDGADI---LRELYLSLLVDR  126 (398)
Q Consensus       105 ~vLVEe~v~~---~~E~ylgi~~Dr  126 (398)
                      +.|+++.++-   ..=+|++|.+|.
T Consensus       109 G~Ll~k~i~~~~~~~~~~~~VsLDG  133 (318)
T TIGR03470       109 ALLLEKKLDKFEPSPYLTFSVHLDG  133 (318)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             5200999999851888369998017


No 313
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=22.15  E-value=51  Score=13.19  Aligned_cols=90  Identities=19%  Similarity=0.352  Sum_probs=58.1

Q ss_pred             CCCCEEEEECCCHHHHHHHHHHHHCCCC-C-CEEEE----CCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHH
Q ss_conf             2881799955503689999999965899-6-24884----2788898999999999861998658999635861328999
Q gi|254781049|r  265 LDGNIGCMVNGAGLAMATMDIIKLYGGA-P-ANFLD----VGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVL  338 (398)
Q Consensus       265 LdG~Ig~~vnGaGlamatmD~i~~~Gg~-p-ANFlD----~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~v  338 (398)
                      +-=+||++..-.|.+..  |+++-..-+ | .+|.=    +=|.-.+..+.+|++.+-.++.+.+|.| +=||--.-|..
T Consensus       134 ~P~~IgvITS~tgAa~~--Di~~~~~~R~p~~~i~l~p~~VQG~~A~~~I~~ai~~~~~~~~~DvIIi-~RGGGS~eDL~  210 (443)
T PRK00286        134 FPKRIGVITSPTGAAIR--DILTVLSRRFPSVEVIIYPTLVQGEGAAASIVEAIERANARGEVDVLIV-ARGGGSLEDLW  210 (443)
T ss_pred             CCCEEEEEECCCHHHHH--HHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCEEEE-ECCCCCHHHHH
T ss_conf             85579998368438999--9999985049965999981456265479999999999852248888999-36878888976


Q ss_pred             H---HHHHHHHHHCCCCCCEEEEC
Q ss_conf             9---99999999729998799974
Q gi|254781049|r  339 V---KGILSAVKEVKINIPLVMRL  359 (398)
Q Consensus       339 A---~gii~a~~~~~~~~pivvRl  359 (398)
                      +   |.+++|+-+  .++|||.=.
T Consensus       211 ~FNdE~varaI~~--s~iPVISaI  232 (443)
T PRK00286        211 AFNDEAVARAIAA--SKIPVISAV  232 (443)
T ss_pred             HCCCHHHHHHHHH--CCCCEEECC
T ss_conf             5187999999984--899789514


No 314
>COG1486 CelF Alpha-galactosidases/6-phospho-beta-glucosidases, family 4 of glycosyl hydrolases [Carbohydrate transport and metabolism]
Probab=21.79  E-value=52  Score=13.15  Aligned_cols=39  Identities=28%  Similarity=0.419  Sum_probs=24.2

Q ss_pred             HHHHHHHHCCCCCCCCEEECCHHHHHHHHHHCCCCEEEEECCCCCCC
Q ss_conf             99999998689888815747999999999872998699971213687
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVISSVHAAESAIKTLPGPLYVVKSQIHAGG   53 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~s~~ea~~~a~~ig~p~~VvKaQV~aGg   53 (398)
                      -+|.++++.|.| -+-...++.++|..-     .. +|+ .|+..||
T Consensus        51 ~~~~~v~~~g~~-~kv~~ttd~~eAl~g-----Ad-fVi-~~~rvG~   89 (442)
T COG1486          51 LAKKLVEEAGAP-VKVEATTDRREALEG-----AD-FVI-TQIRVGG   89 (442)
T ss_pred             HHHHHHHHHCCC-EEEEEECCHHHHHCC-----CC-EEE-EEEEECC
T ss_conf             999999963998-589994589998447-----98-899-9875068


No 315
>pfam11094 UL11 Membrane-associated tegument protein. The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment. UL11 is acylated which is crucial for lipid raft association.
Probab=21.63  E-value=53  Score=13.13  Aligned_cols=16  Identities=25%  Similarity=0.509  Sum_probs=12.6

Q ss_pred             CEEEECCCCCEEEEEEE
Q ss_conf             26799059967994001
Q gi|254781049|r  209 NPLIIMKNGRLRVLDSK  225 (398)
Q Consensus       209 NPLvvt~dg~vvAlDAK  225 (398)
                      |- ++|.+|++++|||-
T Consensus        16 N~-LvT~~GevvsL~a~   31 (39)
T pfam11094        16 NV-LVTSSGEVVSLDAD   31 (39)
T ss_pred             CE-EECCCCCEEEECHH
T ss_conf             88-98058868987234


No 316
>TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This entry represents the proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat.
Probab=21.46  E-value=17  Score=16.40  Aligned_cols=22  Identities=14%  Similarity=0.200  Sum_probs=12.9

Q ss_pred             CCCCHHHHHHHHHHCCCCHHHH
Q ss_conf             5789578887887519888998
Q gi|254781049|r  163 IGVTSEDVASLCDMLELQGQAR  184 (398)
Q Consensus       163 ~gl~~~~~~~l~~~lg~~~~~~  184 (398)
                      ..+++.++..+|..||++....
T Consensus       139 gw~~~~e~~~~A~~L~V~~~eV  160 (279)
T TIGR02392       139 GWLNPEEVEAIAEELGVSEEEV  160 (279)
T ss_pred             CCCCHHHHHHHHHHCCCCHHHH
T ss_conf             7989899999997638988899


No 317
>cd08025 RNR_PFL_like_DUF711 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase. This subfamily contains Streptococcus pneumoniae Sp0239 and similar uncharacterized proteins. Sp0239 is structurally similar to ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL), which are believed to have diverged from a common ancestor. RNR and PFL possess a ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. PFL is an essential enzyme in anaerobic bacteria that catalyzes the conversion of pyruvate and CoA to acteylCoA and formate.
Probab=21.35  E-value=53  Score=13.09  Aligned_cols=23  Identities=9%  Similarity=0.177  Sum_probs=17.6

Q ss_pred             HHHHHHHHCCCCCCCCEEECCHH
Q ss_conf             99999998689888815747999
Q gi|254781049|r    7 QAKALLRKYNVPVAKGVVISSVH   29 (398)
Q Consensus         7 qaK~lL~~~GIpvp~g~~a~s~~   29 (398)
                      .++++.++|||||-.-++..||=
T Consensus        55 ~~~~i~~~~GipIvnkRisvtPi   77 (400)
T cd08025          55 TVEEVSSELGVPIVNKRISVTPI   77 (400)
T ss_pred             HHHHHHHHHCCCEEEEEEEECHH
T ss_conf             99999998599447657750439


No 318
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=21.34  E-value=53  Score=13.09  Aligned_cols=89  Identities=12%  Similarity=0.146  Sum_probs=53.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHC
Q ss_conf             48842788898999999999861998658999635861328999999999999729998799974898589999999976
Q gi|254781049|r  295 NFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSAVKEVKINIPLVMRLEGANVDIGNRLIAES  374 (398)
Q Consensus       295 NFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a~~~~~~~~pivvRl~Gtn~~~g~~il~~~  374 (398)
                      .|-|=+=+++.+.+..|++-.   ++  .+|  |.||..+-....+ +...+++    +.-++ +-|...+.=.+.++. 
T Consensus       321 ~~iNDSKaTN~~a~~~Al~~~---~~--i~l--I~GG~~K~~d~~~-l~~~~~~----v~~~~-l~G~~~~~~~~~~~~-  386 (450)
T PRK01368        321 SFYNDSKATNAISAVQSIKAL---DN--IYW--LAGGIPKEGGIEE-IKPYFSK----IKKAY-FYGQAKEMFANTAKN-  386 (450)
T ss_pred             EEECCCCCCCHHHHHHHHHCC---CC--EEE--EEECCCCCCCHHH-HHHHHHC----CCEEE-EECCCHHHHHHHCCC-
T ss_conf             997178878999999998568---97--399--9941577788799-9988743----87999-989789999986058-


Q ss_pred             CCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             99589949989999999998506
Q gi|254781049|r  375 GLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       375 g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      ..++..+++|++|+..|+..++.
T Consensus       387 ~~~~~~~~~l~~av~~a~~~a~~  409 (450)
T PRK01368        387 IVDFVICDNLEQAFDLAYKDAVG  409 (450)
T ss_pred             CCCEEECCCHHHHHHHHHHHHHC
T ss_conf             98769649999999999999755


No 319
>PRK09271 flavodoxin; Provisional
Probab=21.00  E-value=54  Score=13.04  Aligned_cols=13  Identities=15%  Similarity=0.038  Sum_probs=7.4

Q ss_pred             CHHHHHHHHHHHC
Q ss_conf             9999999999861
Q gi|254781049|r   75 SLKSVISDIREIL   87 (398)
Q Consensus        75 s~~ea~~~a~~il   87 (398)
                      |.+++.+...+-|
T Consensus        13 NTE~vA~~I~~~l   25 (160)
T PRK09271         13 NTREVARMIAARC   25 (160)
T ss_pred             CHHHHHHHHHHHH
T ss_conf             6899999999999


No 320
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=20.99  E-value=54  Score=13.04  Aligned_cols=49  Identities=18%  Similarity=0.218  Sum_probs=29.5

Q ss_pred             CEEEEEECCCCCCHH--------HHHHHCHHHHEEEECCCCCCCC---------HHHHHHHHHHCC
Q ss_conf             048998447884024--------5557483122033214445789---------578887887519
Q gi|254781049|r  130 MVAFIASTQGGMDIE--------EVAKDYPQKIFKLLIDPLIGVT---------SEDVASLCDMLE  178 (398)
Q Consensus       130 ~~vii~S~~GGvdIE--------~va~~~p~~I~~~~id~~~gl~---------~~~~~~l~~~lg  178 (398)
                      .|-+-++.-||.+-.        +..-++|+...+..+.|-.|+-         ...++.++...+
T Consensus       126 ~P~v~~~dIGGl~~~k~el~E~velPl~~pe~f~~~Gi~pPkGvLLyGPPGtGKTllAkAvA~e~~  191 (390)
T PRK03992        126 SPDVTYEDIGGLDEQIREVREAVELPLKNPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN  191 (390)
T ss_pred             CCCCCHHHHCCHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             999984661498999999999999986598999976999997278689899978999999998748


No 321
>PRK07679 pyrroline-5-carboxylate reductase; Reviewed
Probab=20.71  E-value=28  Score=14.94  Aligned_cols=38  Identities=16%  Similarity=0.158  Sum_probs=25.4

Q ss_pred             CCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHC
Q ss_conf             489858999999997699589949989999999998506
Q gi|254781049|r  359 LEGANVDIGNRLIAESGLNVITAIDLDDAAQKIVHAVKG  397 (398)
Q Consensus       359 l~Gtn~~~g~~il~~~g~~~~~~~~~~~A~~~~v~~~k~  397 (398)
                      =.||. ++|.+.|++.+++-...+.++.|.+|+-|++|.
T Consensus       234 pgGtT-~~gl~~Le~~~~~~~i~~Av~aA~~Rs~el~k~  271 (279)
T PRK07679        234 PGGTT-EAGIEVLQEHKFQQALISCITQATQRSHNLGKT  271 (279)
T ss_pred             CCHHH-HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             94659-999999998881999999999999999999999


No 322
>cd05119 RIO RIO kinase family, catalytic domain. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). RIO kinases are atypical protein serine kinases present in archaea, bacteria and eukaryotes. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. RIO kinases contain a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. Most organisms contain at least two RIO kinases, RIO1 and RIO2. A third protein, RIO3, is present in multicellular eukaryotes. In yeast, RIO1 and RIO2 are essential for survival. They funct
Probab=20.43  E-value=56  Score=12.97  Aligned_cols=37  Identities=19%  Similarity=0.344  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHHHHC---CCCCCCCCEEEECCCCCEEEEEEE
Q ss_conf             999999998999955---975102326799059967994001
Q gi|254781049|r  187 GGDLFPNLYKAFCDK---DMSLLEINPLIIMKNGRLRVLDSK  225 (398)
Q Consensus       187 ~~~ii~~L~~~f~e~---Da~liEINPLvvt~dg~vvAlDAK  225 (398)
                      +.+++..+.+++.+.   .++|=|-|=|+  .+++++..|-=
T Consensus       120 ~~~il~~~~~~~~~~glVHgDLSeyNilv--~~~~~~iID~p  159 (187)
T cd05119         120 YDQILELMRKLYREAGLVHGDLSEYNILV--DDGKVYIIDVP  159 (187)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHHEEE--ECCEEEEEECC
T ss_conf             99999999999997493103655554589--89908999557


No 323
>cd02812 PcrB_like PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either prenyltransferases or are involved in lipoteichoic acid biosynthesis although the exact function is still unknown.
Probab=20.37  E-value=56  Score=12.96  Aligned_cols=60  Identities=28%  Similarity=0.337  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             8999999996589962488427888989999999998619986589996358613289999999999
Q gi|254781049|r  279 AMATMDIIKLYGGAPANFLDVGGGADQDKVAAAFKIITSDSSVKGILINIFGGIMRCDVLVKGILSA  345 (398)
Q Consensus       279 amatmD~i~~~Gg~pANFlD~gG~a~~e~~~~a~~~il~~~~vk~iliNifGGI~~cd~vA~gii~a  345 (398)
                      +.+|.=+-.++| -|-=|||.+|.+-...+.++.+-.+++    ..|+ +.|||-+-+ -|+-+.+|
T Consensus       137 ~~ayAlaae~lg-~~~iYLEgSGa~v~~e~V~~vk~~l~~----~~Li-vGGGIrs~e-~a~~~~~A  196 (219)
T cd02812         137 AAAYALAAEYLG-MPIVYLEYSGAYGPPEVVRAVKKVLGD----TPLI-VGGGIRSGE-QAKEMAEA  196 (219)
T ss_pred             HHHHHHHHHHHC-CCEEEEECCCCCCCHHHHHHHHHHCCC----CEEE-EECCCCCHH-HHHHHHHC
T ss_conf             999999999829-938999568997999999999984679----7099-928979999-99999986


No 324
>PRK11706 TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional
Probab=20.30  E-value=56  Score=12.95  Aligned_cols=14  Identities=21%  Similarity=0.321  Sum_probs=8.9

Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             99999999729998
Q gi|254781049|r  340 KGILSAVKEVKINI  353 (398)
Q Consensus       340 ~gii~a~~~~~~~~  353 (398)
                      ..+++.+++.++..
T Consensus       303 d~l~~~L~~~gI~t  316 (375)
T PRK11706        303 SALINFLKEAGIMA  316 (375)
T ss_pred             HHHHHHHHHCCCCE
T ss_conf             99999999879983


No 325
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=20.04  E-value=57  Score=12.91  Aligned_cols=37  Identities=22%  Similarity=0.407  Sum_probs=19.3

Q ss_pred             CCCCCCEEECCCCCCCEEEEEEEEEECCCCCEEEEEECCCCC
Q ss_conf             244330110345556505899999834778048998447884
Q gi|254781049|r  100 GSRVNCVYVEDGADILRELYLSLLVDRTSGMVAFIASTQGGM  141 (398)
Q Consensus       100 G~~v~~vLVEe~v~~~~E~ylgi~~Dr~~~~~vii~S~~GGv  141 (398)
                      |+-++++-..+.-|+-..+|++-|.|     .+++||..|=+
T Consensus       550 GkG~~g~~~~~G~D~i~~~lvasTHD-----~~Lfftn~G~v  586 (864)
T TIGR01063       550 GKGVSGADLKDGDDFIEQLLVASTHD-----YLLFFTNRGKV  586 (864)
T ss_pred             CCCCCCCCCCCCCCEEEEEEEEECCC-----EEEEEECCCCE
T ss_conf             64643253123685056778830776-----07888188826


Done!