Query         gi|254780805|ref|YP_003065218.1| chromosome partitioning protein B [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 300
No_of_seqs    186 out of 3259
Neff          6.5 
Searched_HMMs 39220
Date          Sun May 29 18:09:21 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780805.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG1475 Spo0J Stage 0 sporulat 100.0 2.7E-39 6.7E-44  272.5  16.1  233   38-288     3-239 (240)
  2 TIGR03454 partition_RepB plasm 100.0 2.5E-31 6.3E-36  221.3  17.7  153   32-186    57-212 (325)
  3 PRK13866 plasmid partitioning  100.0 1.5E-27 3.8E-32  197.0  14.0  153   32-186    58-214 (336)
  4 PRK13832 plasmid partitioning   99.9 8.4E-27 2.1E-31  192.2  13.6  174   38-212     2-181 (518)
  5 TIGR00180 parB_part ParB-like   99.9 3.5E-26 8.8E-31  188.2  12.0  170   37-206     3-181 (192)
  6 pfam02195 ParBc ParB-like nucl  99.9   5E-24 1.3E-28  174.3   6.0   90   40-130     1-90  (90)
  7 smart00470 ParB ParB-like nucl  99.9 1.2E-22 3.1E-27  165.4   6.9   89   40-130     1-89  (89)
  8 PRK13698 plasmid-partitioning   99.8 6.7E-17 1.7E-21  128.6  16.3  240   40-296    60-321 (323)
  9 pfam08535 KorB KorB domain. Th  98.2 4.7E-06 1.2E-10   58.9   7.2   48  151-200     2-49  (93)
 10 pfam07506 RepB RepB plasmid pa  97.7 0.00014 3.7E-09   49.4   6.4   94  131-225     1-100 (185)
 11 COG5119 Uncharacterized protei  96.2   0.012 3.1E-07   37.0   5.3   79   37-118     8-105 (119)
 12 PHA01976 helix-turn-helix prot  95.2   0.016 4.2E-07   36.1   2.8   35  140-174     3-37  (67)
 13 KOG3388 consensus               95.2   0.018 4.6E-07   35.9   3.0   82   38-122    26-124 (136)
 14 TIGR02980 SigBFG RNA polymeras  94.9   0.065 1.7E-06   32.3   5.3   67  106-174   136-218 (229)
 15 TIGR02957 SigX4 RNA polymerase  94.9   0.092 2.3E-06   31.3   6.0   38  133-172   108-145 (287)
 16 pfam02001 DUF134 Protein of un  94.7   0.068 1.7E-06   32.2   4.9   51  137-190    38-88  (100)
 17 COG1342 Predicted DNA-binding   94.6   0.073 1.9E-06   32.0   5.0   51  137-190    35-85  (99)
 18 cd00569 HTH_Hin_like Helix-tur  94.5   0.043 1.1E-06   33.4   3.5   38  134-173     5-42  (42)
 19 COG2522 Predicted transcriptio  94.2   0.061 1.6E-06   32.5   3.8   43  136-179     7-49  (119)
 20 PRK04217 hypothetical protein;  93.9    0.13 3.3E-06   30.4   4.9   51  137-190    44-94  (110)
 21 pfam04814 HNF-1_N Hepatocyte n  93.9    0.12 2.9E-06   30.7   4.6   54  118-173    96-149 (177)
 22 PRK12529 RNA polymerase sigma   93.3    0.32 8.1E-06   27.9   6.1   28  147-174   138-165 (178)
 23 pfam06250 DUF1016 Protein of u  92.8    0.37 9.4E-06   27.4   5.9   66  163-230    66-137 (320)
 24 pfam08857 ParBc_2 Putative Par  92.7    0.06 1.5E-06   32.5   1.7   75   39-117     2-86  (162)
 25 TIGR02846 spore_sigmaK RNA pol  92.7   0.091 2.3E-06   31.4   2.6  111   59-180    71-225 (228)
 26 PRK12525 RNA polymerase sigma   92.6    0.69 1.8E-05   25.7   7.0   28  147-174   129-156 (168)
 27 pfam09862 DUF2089 Protein of u  92.5    0.48 1.2E-05   26.7   6.1   52  144-196    42-108 (113)
 28 PRK09726 DNA-binding transcrip  92.4    0.18 4.5E-06   29.5   3.8   38  135-172     8-45  (88)
 29 PRK06811 RNA polymerase factor  92.1    0.74 1.9E-05   25.5   6.7   56  134-191   128-184 (185)
 30 pfam11300 DUF3102 Protein of u  92.0     0.5 1.3E-05   26.6   5.8   93  136-228    24-129 (130)
 31 TIGR03070 couple_hipB transcri  91.9    0.18 4.6E-06   29.4   3.4   33  140-172     3-35  (58)
 32 PRK09706 transcriptional repre  91.7    0.18 4.7E-06   29.4   3.3   39  141-179     7-45  (135)
 33 smart00530 HTH_XRE Helix-turn-  91.7    0.15 3.9E-06   29.9   2.8   33  144-176     2-34  (56)
 34 PRK12528 RNA polymerase sigma   91.5    0.89 2.3E-05   25.0   6.5   28  147-174   130-157 (167)
 35 PRK12523 RNA polymerase sigma   91.3    0.81 2.1E-05   25.2   6.2   39  134-174   119-157 (172)
 36 COG2390 DeoR Transcriptional r  91.2    0.33 8.4E-06   27.8   4.1   24  152-175    26-49  (321)
 37 pfam01381 HTH_3 Helix-turn-hel  90.6    0.17 4.3E-06   29.6   2.2   33  145-177     2-34  (55)
 38 pfam03235 DUF262 Protein of un  90.3     0.6 1.5E-05   26.1   4.8   54   51-104    15-68  (99)
 39 COG1476 Predicted transcriptio  90.2    0.22 5.6E-06   28.9   2.5   29  143-171     5-33  (68)
 40 PRK09652 RNA polymerase sigma   89.9     1.4 3.6E-05   23.7   6.3   53  133-187   136-190 (192)
 41 pfam04545 Sigma70_r4 Sigma-70,  89.4    0.48 1.2E-05   26.7   3.6   39  134-174     4-42  (50)
 42 pfam12116 SpoIIID Stage III sp  89.0     1.1 2.7E-05   24.5   5.2   44  139-182     6-51  (82)
 43 PRK13890 conjugal transfer pro  88.9    0.34 8.7E-06   27.7   2.7   29  144-172    10-38  (119)
 44 COG3355 Predicted transcriptio  88.9    0.55 1.4E-05   26.3   3.7   38  135-173    25-63  (126)
 45 pfam07638 Sigma70_ECF ECF sigm  88.6       1 2.6E-05   24.6   4.9   39  137-176   137-175 (185)
 46 PRK09635 sigI RNA polymerase s  88.5    0.84 2.1E-05   25.1   4.4   39  133-173   117-155 (290)
 47 PRK09643 RNA polymerase sigma   88.2     2.1 5.3E-05   22.6   6.2   57  135-193   132-190 (197)
 48 pfam07022 Phage_CI_repr Bacter  87.9    0.54 1.4E-05   26.4   3.1   41  143-183     2-43  (65)
 49 TIGR02937 sigma70-ECF RNA poly  87.5    0.84 2.1E-05   25.1   3.9   39  134-174   114-152 (162)
 50 PRK06930 positive control sigm  87.4    0.94 2.4E-05   24.8   4.1   38  135-174   115-152 (170)
 51 PRK09651 RNA polymerase sigma   87.3     2.4 6.1E-05   22.2   6.3   28  147-174   130-157 (172)
 52 TIGR01884 cas_HTH CRISPR locus  87.2     0.9 2.3E-05   25.0   3.9   38  140-177   171-209 (231)
 53 COG3620 Predicted transcriptio  87.2    0.57 1.4E-05   26.2   2.9   31  142-172     8-38  (187)
 54 pfam02796 HTH_7 Helix-turn-hel  86.9    0.75 1.9E-05   25.5   3.4   33  141-174    11-43  (45)
 55 PRK13413 mpi multiple promoter  86.8    0.92 2.4E-05   24.9   3.8   33  143-176   164-196 (200)
 56 PRK09943 DNA-binding transcrip  86.8    0.82 2.1E-05   25.2   3.5   35  140-174     8-42  (185)
 57 cd00093 HTH_XRE Helix-turn-hel  86.8    0.56 1.4E-05   26.3   2.7   34  143-176     3-36  (58)
 58 COG3283 TyrR Transcriptional r  86.7     1.3 3.4E-05   23.9   4.6   19  208-226   405-425 (511)
 59 PRK08295 RNA polymerase factor  86.7     2.1 5.4E-05   22.6   5.6   54  134-192   155-208 (209)
 60 PRK12515 RNA polymerase sigma   86.3     2.1 5.4E-05   22.6   5.4   58  133-194   130-187 (189)
 61 PRK12527 RNA polymerase sigma   86.2     1.7 4.3E-05   23.2   4.9   28  147-174   116-143 (159)
 62 TIGR02999 Sig-70_X6 RNA polyme  86.2     1.7 4.2E-05   23.3   4.8   87   90-177    96-186 (194)
 63 PRK12519 RNA polymerase sigma   86.1     1.9 4.8E-05   22.9   5.1   36  151-186   156-193 (194)
 64 COG2512 Predicted membrane-ass  86.0    0.96 2.4E-05   24.8   3.5   41  133-174   191-232 (258)
 65 TIGR02812 fadR_gamma fatty aci  85.9    0.32 8.1E-06   27.8   1.0   56  154-220    32-104 (275)
 66 cd06171 Sigma70_r4 Sigma70, re  84.9     1.4 3.6E-05   23.7   4.0   39  134-174    10-48  (55)
 67 pfam01978 TrmB Sugar-specific   84.8     1.3 3.4E-05   23.8   3.8   35  140-174    10-44  (68)
 68 PRK11388 DNA-binding transcrip  84.8     1.4 3.5E-05   23.7   3.9   21  210-230   529-551 (639)
 69 TIGR01321 TrpR trp operon repr  84.7     2.1 5.3E-05   22.6   4.8   57  130-189    37-94  (95)
 70 PRK09644 RNA polymerase sigma   84.7     2.5 6.3E-05   22.2   5.1   50  134-187   108-157 (165)
 71 COG5499 Predicted transcriptio  84.5    0.98 2.5E-05   24.7   3.0   31  142-173    63-93  (120)
 72 PRK04140 hypothetical protein;  84.0     1.9 4.9E-05   22.9   4.3  114   58-185    52-172 (319)
 73 PRK09636 RNA polymerase sigma   83.9       2   5E-05   22.8   4.3   39  133-173   110-148 (289)
 74 PHA00542 putative Cro-like pro  83.7     1.2 3.1E-05   24.1   3.2   36  136-175    19-54  (82)
 75 TIGR02607 antidote_HigA addict  83.4    0.82 2.1E-05   25.2   2.2   28  146-173    14-41  (81)
 76 PRK09483 response regulator; P  83.3     2.9 7.4E-05   21.7   5.0   39  133-174   147-185 (216)
 77 PRK07408 RNA polymerase sigma   83.2     3.3 8.4E-05   21.3   5.2   19  154-172   131-149 (256)
 78 PRK03975 tfx putative transcri  83.1    0.76 1.9E-05   25.4   2.0   26  146-172    14-39  (139)
 79 PRK06759 RNA polymerase factor  83.0     2.2 5.5E-05   22.5   4.3   39  134-174   106-144 (154)
 80 PRK09645 RNA polymerase sigma   82.2       4  0.0001   20.8   5.6   54  134-191   116-169 (171)
 81 pfam08281 Sigma70_r4_2 Sigma-7  82.1     2.1 5.4E-05   22.6   3.9   38  135-174    11-48  (54)
 82 pfam00196 GerE Bacterial regul  82.1       2 5.2E-05   22.7   3.9   38  134-174     3-40  (58)
 83 PRK07500 rpoH2 RNA polymerase   82.0     3.6 9.3E-05   21.1   5.1   39  134-172   227-265 (289)
 84 TIGR02985 Sig70_bacteroi1 RNA   81.8     2.2 5.5E-05   22.5   3.9   28  147-174   130-157 (167)
 85 COG1813 Predicted transcriptio  81.8     1.9 4.9E-05   22.9   3.6   32  141-172    81-112 (165)
 86 cd00092 HTH_CRP helix_turn_hel  81.6     2.1 5.4E-05   22.6   3.8   26  151-176    24-49  (67)
 87 PRK08359 transcription factor;  81.5       2 5.2E-05   22.7   3.7   32  141-172    85-116 (175)
 88 pfam01726 LexA_DNA_bind LexA D  81.2     2.8 7.2E-05   21.8   4.3   34  143-176    14-50  (65)
 89 COG1318 Predicted transcriptio  81.2     4.4 0.00011   20.5   7.8   47  142-190    53-103 (182)
 90 PRK12524 RNA polymerase sigma   81.0     3.8 9.6E-05   21.0   4.9   42  151-194   151-192 (196)
 91 PRK10360 DNA-binding transcrip  80.9     2.4   6E-05   22.3   3.8   41  131-174   134-174 (196)
 92 PRK09640 RNA polymerase sigma   80.8     4.1 0.00011   20.7   5.0   40  133-174   133-172 (188)
 93 PRK05602 RNA polymerase sigma   80.7     4.5 0.00012   20.4   5.8   39  134-174   128-166 (186)
 94 PRK12537 RNA polymerase sigma   80.6     2.5 6.5E-05   22.1   3.9   39  134-174   135-173 (184)
 95 PRK10430 DNA-binding transcrip  80.3     2.7 6.9E-05   21.9   3.9   27  151-177   177-203 (239)
 96 PRK12536 RNA polymerase sigma   80.2     4.7 0.00012   20.3   5.3   26  149-174   139-164 (178)
 97 PRK11923 algU RNA polymerase s  80.2     4.7 0.00012   20.3   5.5   39  149-187   151-191 (193)
 98 PRK12538 RNA polymerase sigma   80.2     4.7 0.00012   20.3   5.8   46  149-196   184-229 (233)
 99 pfam02954 HTH_8 Bacterial regu  80.0     2.4   6E-05   22.3   3.6   37  137-174     4-40  (42)
100 PRK08301 sporulation sigma fac  80.0     4.3 0.00011   20.6   4.9   50  133-182   182-235 (239)
101 PRK09954 hypothetical protein;  79.9     2.5 6.4E-05   22.1   3.7   64   43-111    74-139 (362)
102 PRK09637 RNA polymerase sigma   79.9     2.9 7.3E-05   21.7   4.0   48  135-186   107-154 (181)
103 smart00421 HTH_LUXR helix_turn  79.5     2.8 7.1E-05   21.8   3.8   38  134-174     3-40  (58)
104 PRK06424 transcription factor;  79.5     2.5 6.5E-05   22.1   3.6   39  141-180    86-124 (144)
105 PRK08241 RNA polymerase factor  79.5     1.9 4.9E-05   22.8   3.0   47  123-173   147-193 (341)
106 PRK11050 manganese transport r  79.4     4.8 0.00012   20.3   5.0   73  142-226    43-116 (155)
107 cd06170 LuxR_C_like C-terminal  79.3     2.8   7E-05   21.8   3.8   37  135-174     1-37  (57)
108 PRK11924 RNA polymerase sigma   79.2       3 7.7E-05   21.6   3.9   39  134-174   125-163 (180)
109 COG3093 VapI Plasmid maintenan  79.2     1.5 3.9E-05   23.5   2.4   29  146-174    17-45  (104)
110 TIGR00721 tfx DNA-binding prot  79.1    0.99 2.5E-05   24.7   1.4   22  149-170    18-39  (142)
111 PRK10820 DNA-binding transcrip  79.0     2.7 6.9E-05   21.9   3.6   23  208-230   403-427 (513)
112 PRK09641 RNA polymerase sigma   79.0       5 0.00013   20.2   5.0   38  135-174   137-174 (187)
113 COG2197 CitB Response regulato  78.9       3 7.6E-05   21.6   3.8   38  133-173   147-184 (211)
114 pfam08279 HTH_11 HTH domain. T  78.6     2.4 6.1E-05   22.2   3.3   33  145-177     7-40  (55)
115 PRK09646 RNA polymerase sigma   78.3     3.1 7.8E-05   21.5   3.7   24  151-174   157-180 (194)
116 pfam02376 CUT CUT domain. The   78.3     3.6 9.2E-05   21.1   4.1   70  133-205     1-71  (81)
117 PRK09638 RNA polymerase sigma   78.0     3.5   9E-05   21.1   4.0   24  151-174   142-165 (177)
118 PRK06596 RNA polymerase factor  78.0       5 0.00013   20.1   4.8   20  154-173   153-172 (284)
119 cd00475 CIS_IPPS Cis (Z)-Isopr  77.9    0.53 1.4E-05   26.4  -0.2   94   90-190     6-111 (221)
120 PRK10840 transcriptional regul  77.9     3.2 8.1E-05   21.4   3.7   38  134-174   150-187 (216)
121 PRK10046 dpiA two-component re  77.7     1.9 4.7E-05   22.9   2.5   26  152-177   177-202 (225)
122 PRK12518 RNA polymerase sigma   77.5     5.7 0.00014   19.8   5.4   39  149-189   133-171 (175)
123 smart00419 HTH_CRP helix_turn_  77.5     1.9   5E-05   22.8   2.5   24  151-174     7-30  (48)
124 PRK09047 RNA polymerase factor  77.5     5.7 0.00015   19.8   5.6   39  151-191   121-159 (161)
125 PRK07037 extracytoplasmic-func  77.4     5.7 0.00015   19.8   5.0   28  147-174   134-161 (183)
126 KOG1602 consensus               77.2     1.5 3.8E-05   23.6   1.9   94   89-189    41-149 (271)
127 PRK13919 putative RNA polymera  77.2     3.9 9.9E-05   20.9   4.0   38  135-174   137-174 (187)
128 COG3413 Predicted DNA binding   77.1       4  0.0001   20.8   4.0   42  133-174   154-200 (215)
129 COG1595 RpoE DNA-directed RNA   76.7       4  0.0001   20.8   3.9   38  135-174   128-165 (182)
130 COG3415 Transposase and inacti  76.6     5.8 0.00015   19.8   4.8   65  151-225    20-89  (138)
131 PRK12514 RNA polymerase sigma   76.6     3.8 9.8E-05   20.9   3.8   24  151-174   144-167 (179)
132 PRK11169 leucine-responsive tr  76.5     4.6 0.00012   20.4   4.2  125  133-295    10-137 (164)
133 pfam01022 HTH_5 Bacterial regu  76.5     3.5 8.9E-05   21.2   3.6   31  147-177    10-40  (47)
134 PRK09958 DNA-binding transcrip  76.5     3.8 9.8E-05   20.9   3.8   38  134-174   143-180 (204)
135 PRK12543 RNA polymerase sigma   75.9     6.3 0.00016   19.5   5.6   40  149-190   142-181 (190)
136 PRK01381 Trp operon repressor;  75.7     4.6 0.00012   20.4   4.0   54  135-189    33-93  (99)
137 COG1191 FliA DNA-directed RNA   75.4     6.5 0.00016   19.5   5.0   28  146-173   118-147 (247)
138 pfam04967 HTH_10 HTH DNA bindi  75.4     2.1 5.4E-05   22.6   2.2   25  152-176    23-47  (53)
139 COG1356 tfx Transcriptional re  75.4     1.4 3.6E-05   23.7   1.3   23  149-171    20-42  (143)
140 pfam07900 DUF1670 Protein of u  75.3       5 0.00013   20.2   4.1   64  107-175    61-128 (220)
141 PRK11179 DNA-binding transcrip  75.3     3.5 8.8E-05   21.2   3.3   48  135-192     7-54  (153)
142 pfam04218 CENP-B_N CENP-B N-te  75.2     4.8 0.00012   20.3   4.0   41  132-174     4-44  (53)
143 PRK12522 RNA polymerase sigma   75.2     5.8 0.00015   19.8   4.4   26  149-174   132-157 (173)
144 PRK10651 transcriptional regul  75.1     4.4 0.00011   20.5   3.8   38  134-174   155-192 (216)
145 cd06405 PB1_Mekk2_3 The PB1 do  74.8     6.7 0.00017   19.4   6.3   49  246-296    18-66  (79)
146 PRK12534 RNA polymerase sigma   74.8     4.7 0.00012   20.4   3.9   24  151-174   152-175 (187)
147 PRK12517 RNA polymerase sigma   74.7       5 0.00013   20.2   4.0   50  135-188   129-178 (188)
148 PRK12542 RNA polymerase sigma   74.7     4.3 0.00011   20.6   3.7   49  134-186   122-170 (185)
149 pfam10078 DUF2316 Uncharacteri  74.6     4.7 0.00012   20.4   3.8   42  135-176     3-47  (89)
150 PRK12423 LexA repressor; Provi  74.5     5.4 0.00014   20.0   4.1   48  143-199    14-66  (202)
151 pfam01255 Prenyltransf Putativ  74.4    0.97 2.5E-05   24.7   0.3   90   91-191     1-106 (222)
152 COG2944 Predicted transcriptio  74.3     3.5 8.9E-05   21.2   3.1   36  133-172    42-77  (104)
153 PRK02866 cyanate hydratase; Va  74.3     6.9 0.00018   19.3   5.0   37  149-185    15-52  (147)
154 pfam01047 MarR MarR family. Th  74.2     5.6 0.00014   19.9   4.1   36  139-174     4-39  (59)
155 COG1709 Predicted transcriptio  74.2     1.8 4.5E-05   23.1   1.6   31  143-173    31-61  (241)
156 PRK10403 transcriptional regul  74.0     4.7 0.00012   20.3   3.8   37  135-174   154-190 (215)
157 smart00418 HTH_ARSR helix_turn  73.9     3.3 8.3E-05   21.4   2.9   30  147-177     6-35  (66)
158 PRK10923 glnG nitrogen regulat  73.7     4.6 0.00012   20.4   3.6   23  207-229   343-367 (469)
159 COG2826 Tra8 Transposase and i  73.6     3.6 9.2E-05   21.1   3.0   29  144-173    16-44  (318)
160 PRK09935 transcriptional regul  73.3     4.9 0.00012   20.2   3.7   37  135-174   150-186 (210)
161 cd00090 HTH_ARSR Arsenical Res  73.3     4.6 0.00012   20.4   3.5   33  144-177    13-45  (78)
162 PRK05572 sporulation sigma fac  73.2     7.3 0.00019   19.1   5.0   17  154-170   134-150 (251)
163 PRK11608 pspF phage shock prot  73.2     4.8 0.00012   20.3   3.6   19  210-228   215-235 (325)
164 PRK09834 DNA-binding transcrip  73.1     6.2 0.00016   19.6   4.2   31   58-92     38-68  (264)
165 TIGR02960 SigX5 RNA polymerase  72.8     6.2 0.00016   19.6   4.1   52  118-173   129-180 (329)
166 PRK12512 RNA polymerase sigma   72.8     5.7 0.00015   19.8   3.9   38  134-173   131-168 (184)
167 PRK11161 fumarate/nitrate redu  72.8     5.2 0.00013   20.0   3.7   41   57-97     23-67  (235)
168 smart00344 HTH_ASNC helix_turn  72.7     4.3 0.00011   20.6   3.3   32  144-175     9-40  (108)
169 COG0020 UppS Undecaprenyl pyro  72.6     1.3 3.4E-05   23.8   0.7  135   90-231    22-181 (245)
170 COG1414 IclR Transcriptional r  72.3     6.9 0.00018   19.3   4.3   17   60-76     33-49  (246)
171 PRK08583 RNA polymerase sigma   72.2     5.4 0.00014   19.9   3.7   23  153-175   133-155 (257)
172 smart00347 HTH_MARR helix_turn  72.1     6.8 0.00017   19.3   4.2   42  132-174     5-46  (101)
173 PRK07122 RNA polymerase sigma   72.1       6 0.00015   19.7   3.9   21  153-173   143-163 (263)
174 PRK09647 RNA polymerase sigma   72.1       6 0.00015   19.7   3.9   50  135-188   158-207 (222)
175 PRK10434 srlR DNA-bindng trans  71.7     7.5 0.00019   19.0   4.3   25  152-176   100-126 (256)
176 PRK10072 putative transcriptio  71.6     7.6 0.00019   19.0   4.3   28  144-171    38-65  (96)
177 COG1522 Lrp Transcriptional re  71.3     5.7 0.00014   19.8   3.6   48  135-192     6-53  (154)
178 pfam01371 Trp_repressor Trp re  71.2     5.8 0.00015   19.7   3.7   34  143-177    41-74  (88)
179 pfam09339 HTH_IclR IclR helix-  71.2     7.5 0.00019   19.1   4.2   38  138-175     2-41  (52)
180 smart00346 HTH_ICLR helix_turn  71.0       8  0.0002   18.9   4.3   40  137-176     3-44  (91)
181 PRK13509 transcriptional repre  70.9     8.2 0.00021   18.8   4.4   19  154-172    21-39  (251)
182 PRK09415 RNA polymerase factor  70.6     7.1 0.00018   19.2   4.0   39  134-174   127-165 (177)
183 COG4565 CitB Response regulato  70.5     3.5   9E-05   21.1   2.4   28  151-178   172-199 (224)
184 PRK10906 DNA-binding transcrip  70.2     8.3 0.00021   18.7   4.3   11  152-162   100-110 (252)
185 PRK10365 transcriptional regul  70.2     5.6 0.00014   19.8   3.4   22  209-230   346-369 (441)
186 PRK08215 sporulation sigma fac  70.1     8.6 0.00022   18.7   5.0   21  153-173   140-160 (257)
187 COG2973 TrpR Trp operon repres  70.1     8.6 0.00022   18.7   4.4   47  142-189    51-98  (103)
188 PRK12513 RNA polymerase sigma   69.9     7.5 0.00019   19.0   4.0   39  134-174   139-177 (194)
189 pfam01710 Transposase_14 Trans  69.4     5.6 0.00014   19.8   3.3   26  148-174    15-40  (120)
190 PRK05911 RNA polymerase sigma   69.4     8.9 0.00023   18.6   5.3   21  154-174   128-148 (257)
191 PRK03573 transcriptional regul  69.1       9 0.00023   18.5   6.7   46  130-176    24-70  (144)
192 PRK12516 RNA polymerase sigma   69.1       7 0.00018   19.2   3.7   45  147-193   130-175 (190)
193 PRK13918 CRP/FNR family transc  69.0       4  0.0001   20.8   2.5   36  153-197   146-181 (201)
194 PRK12541 RNA polymerase sigma   68.9     7.2 0.00018   19.1   3.7   37  137-174   114-150 (161)
195 PRK12532 RNA polymerase sigma   68.6     7.3 0.00019   19.1   3.7   27  147-173   147-173 (195)
196 PRK11753 cAMP-regulatory prote  68.6     4.2 0.00011   20.7   2.5   20  154-173   170-189 (211)
197 PRK00215 LexA repressor; Valid  68.6     5.9 0.00015   19.7   3.3   48  143-199    12-64  (204)
198 PRK10339 DNA-binding transcrip  68.6       5 0.00013   20.1   2.9   10  106-115   134-143 (327)
199 TIGR02885 spore_sigF RNA polym  68.5     2.2 5.6E-05   22.5   1.0   20  153-172   200-219 (231)
200 PRK12539 RNA polymerase sigma   68.4     7.8  0.0002   18.9   3.8   27  148-174   143-169 (184)
201 PRK03902 manganese transport t  68.3     9.4 0.00024   18.4   4.3   32  143-174    12-44  (142)
202 pfam06245 DUF1015 Protein of u  68.1     4.8 0.00012   20.3   2.7   11   91-101   203-213 (411)
203 PRK09639 RNA polymerase sigma   68.1     9.5 0.00024   18.4   5.6   38  134-174   112-149 (166)
204 pfam00392 GntR Bacterial regul  68.0       9 0.00023   18.5   4.1   24  154-177    26-49  (64)
205 PRK11922 RNA polymerase sigma   68.0     8.1 0.00021   18.8   3.8   37  149-187   162-198 (231)
206 pfam03444 DUF293 Domain of unk  67.7     8.5 0.00022   18.7   3.9   34  144-177    10-48  (79)
207 PRK11512 DNA-binding transcrip  67.7     9.6 0.00025   18.3   7.3   46  128-174    31-76  (144)
208 pfam00356 LacI Bacterial regul  67.7     3.6 9.2E-05   21.1   2.0   33  154-186     1-34  (46)
209 smart00345 HTH_GNTR helix_turn  67.3     8.3 0.00021   18.7   3.8   24  154-177    22-45  (60)
210 COG1378 Predicted transcriptio  67.1     9.3 0.00024   18.4   4.0   49  125-174     4-52  (247)
211 PRK09649 RNA polymerase sigma   66.9     8.8 0.00023   18.6   3.9   24  151-174   145-168 (185)
212 TIGR02959 SigZ RNA polymerase   66.9     4.6 0.00012   20.4   2.4   35  137-172   102-136 (170)
213 TIGR00270 TIGR00270 conserved   66.7     5.7 0.00014   19.8   2.8   37  144-181    88-124 (169)
214 PRK09648 RNA polymerase sigma   66.6     9.4 0.00024   18.4   3.9   24  151-174   152-175 (187)
215 TIGR03337 phnR transcriptional  66.5      10 0.00026   18.2   4.2   21  154-174    27-47  (231)
216 PRK09391 fixK transcriptional   66.4     4.3 0.00011   20.6   2.2   22  153-174   174-195 (224)
217 PRK05803 sporulation sigma fac  66.4     8.5 0.00022   18.7   3.7   41  133-173   173-215 (228)
218 PRK11361 acetoacetate metaboli  66.3     8.9 0.00023   18.6   3.8   23  208-230   349-373 (457)
219 PRK12535 RNA polymerase sigma   66.2      10 0.00026   18.2   5.1   43  148-192   144-186 (195)
220 smart00354 HTH_LACI helix_turn  66.2       4  0.0001   20.8   2.0   33  154-186     2-35  (70)
221 PRK12526 RNA polymerase sigma   66.2       9 0.00023   18.5   3.8   24  151-174   168-191 (206)
222 PRK06288 RNA polymerase sigma   65.8      10 0.00027   18.1   5.3   22  153-174   131-152 (261)
223 PRK05412 nucleotide-binding pr  65.7      11 0.00027   18.1   4.2   38  261-300   115-152 (161)
224 pfam04461 DUF520 Protein of un  65.7      11 0.00027   18.1   4.3   38  261-300   115-152 (160)
225 PRK11886 biotin--protein ligas  65.6      11 0.00027   18.1   4.3   23  249-271   259-281 (319)
226 PRK10141 DNA-binding transcrip  65.4     7.4 0.00019   19.1   3.2   76  147-229    23-101 (106)
227 TIGR03001 Sig-70_gmx1 RNA poly  65.2     6.6 0.00017   19.4   2.9   54  121-174   142-204 (249)
228 PRK09526 lacI lac repressor; R  65.2     6.6 0.00017   19.4   2.9   17  137-153   196-212 (342)
229 PRK09642 RNA polymerase sigma   65.1     9.4 0.00024   18.4   3.7   36  151-188   121-156 (160)
230 TIGR02850 spore_sigG RNA polym  64.9     8.7 0.00022   18.6   3.5   21  152-172   222-242 (254)
231 cd07377 WHTH_GntR Winged helix  64.7      11 0.00028   18.0   4.1   24  154-177    27-50  (66)
232 PRK12427 flagellar biosynthesi  64.5      10 0.00026   18.2   3.8   39  135-175    98-138 (229)
233 PRK10163 DNA-binding transcrip  64.3      11 0.00029   17.9   4.5   18   59-76     53-70  (271)
234 PRK12547 RNA polymerase sigma   63.8      10 0.00027   18.1   3.7   28  147-174   123-150 (164)
235 pfam05732 RepL Firmicute plasm  63.7     5.9 0.00015   19.7   2.4   27  151-177    74-100 (165)
236 PRK12546 RNA polymerase sigma   63.7      10 0.00027   18.1   3.7   38  147-186   124-161 (188)
237 pfam04552 Sigma54_DBD Sigma-54  63.6     9.3 0.00024   18.4   3.5   56  125-180    13-79  (160)
238 PRK10014 DNA-binding transcrip  63.5     5.2 0.00013   20.1   2.1   26   47-75     70-95  (342)
239 COG5606 Uncharacterized conser  63.3     5.1 0.00013   20.1   2.1   33  142-174    31-63  (91)
240 pfam06322 Phage_NinH Phage Nin  63.3     5.3 0.00014   20.0   2.2   27  147-174    12-38  (64)
241 COG1349 GlpR Transcriptional r  63.3      12  0.0003   17.8   4.2   15  152-166   100-114 (253)
242 PRK12520 RNA polymerase sigma   63.1      12  0.0003   17.8   4.6   38  135-174   132-169 (191)
243 PRK09492 treR trehalose repres  62.9     5.2 0.00013   20.1   2.1   28   45-75     66-93  (315)
244 PRK10100 DNA-binding transcrip  62.7      11 0.00028   18.0   3.7   37  135-174   156-192 (216)
245 PRK11569 transcriptional repre  62.4      12 0.00031   17.7   4.3   19   58-76     55-73  (274)
246 TIGR01764 excise DNA binding d  62.2     4.1 0.00011   20.7   1.4   26  153-178     2-27  (49)
247 PRK12533 RNA polymerase sigma   62.0      12 0.00031   17.7   3.8   25  149-173   150-174 (217)
248 TIGR03020 EpsA transcriptional  61.3       8  0.0002   18.9   2.8   39  133-174   189-227 (247)
249 PRK05022 anaerobic nitric oxid  61.0      12 0.00031   17.7   3.7   22  208-229   392-415 (510)
250 PRK09764 DNA-binding transcrip  61.0      13 0.00033   17.5   4.2   21  154-174    31-51  (239)
251 KOG0257 consensus               60.9       9 0.00023   18.5   3.0   29   48-76    178-207 (420)
252 PRK12530 RNA polymerase sigma   60.9      13 0.00032   17.6   3.7   37  148-186   148-184 (191)
253 PRK07670 RNA polymerase sigma   60.7      13 0.00033   17.5   5.9   21  153-173   122-142 (250)
254 PRK09801 transcriptional activ  60.5      13 0.00033   17.5   3.9   13  250-262   289-301 (310)
255 KOG2305 consensus               60.2     9.5 0.00024   18.4   3.0  101   38-147   146-252 (313)
256 PRK09863 putative frv operon r  60.2      10 0.00026   18.1   3.2   22   79-100   124-145 (585)
257 PRK09775 hypothetical protein;  59.7     9.8 0.00025   18.3   3.0   55   70-124    74-147 (443)
258 KOG3802 consensus               59.6      12  0.0003   17.8   3.4   42  134-175   204-252 (398)
259 pfam05930 Phage_AlpA Prophage   59.6       3 7.7E-05   21.6   0.4   30  154-183     5-34  (51)
260 PRK06704 RNA polymerase factor  59.5     9.6 0.00025   18.3   2.9   50  135-186   117-171 (228)
261 PRK09390 fixJ response regulat  59.4      14 0.00035   17.4   4.9   38  134-174   141-178 (202)
262 COG1510 Predicted transcriptio  59.3      10 0.00027   18.1   3.1   52  124-176    13-65  (177)
263 TIGR03541 reg_near_HchA LuxR f  59.2      11 0.00029   17.9   3.3   37  134-174   171-208 (232)
264 PRK12540 RNA polymerase sigma   59.1      14 0.00035   17.3   3.8   43  147-191   122-164 (181)
265 pfam04539 Sigma70_r3 Sigma-70   58.9      11 0.00027   18.1   3.1   39  141-179     7-47  (78)
266 cd06811 PLPDE_III_yhfX_like Ty  58.5     4.6 0.00012   20.4   1.2   82   36-117   102-201 (382)
267 PRK11534 DNA-binding transcrip  58.4      14 0.00035   17.3   3.6   10   61-70     11-20  (224)
268 cd01392 HTH_LacI Helix-turn-he  58.2     8.8 0.00022   18.6   2.5   31  156-186     1-32  (52)
269 COG2188 PhnF Transcriptional r  57.7      15 0.00037   17.2   4.2   37  141-177    13-56  (236)
270 pfam01325 Fe_dep_repress Iron   57.5      12 0.00031   17.7   3.2   33  144-176    11-44  (58)
271 PRK09508 leuO leucine transcri  57.4      13 0.00034   17.5   3.3   17  157-173    41-57  (314)
272 PRK11303 DNA-binding transcrip  57.4     7.2 0.00018   19.1   2.0   26   47-75     67-92  (330)
273 PRK11475 DNA-binding transcrip  57.3      15 0.00038   17.2   3.8   38  133-173   133-170 (205)
274 PRK10401 DNA-binding transcrip  57.2     7.7  0.0002   19.0   2.1   19  137-155   191-209 (346)
275 PRK01905 DNA-binding protein F  56.9      15 0.00038   17.1   3.6   42  135-177    34-75  (77)
276 PRK11041 DNA-binding transcrip  56.7     7.7  0.0002   19.0   2.1   26   47-75     73-98  (341)
277 PRK10727 DNA-binding transcrip  56.7     7.7  0.0002   19.0   2.1   20  136-155   190-209 (342)
278 PRK06986 fliA flagellar biosyn  56.5      15 0.00039   17.1   5.1   22  153-174   112-133 (234)
279 PRK10703 DNA-binding transcrip  56.5     7.8  0.0002   18.9   2.0   26   47-75     65-90  (335)
280 PRK11402 DNA-binding transcrip  56.3      15 0.00039   17.0   4.2   21  154-174    37-57  (243)
281 PRK09392 ftrB transcriptional   56.2     9.8 0.00025   18.3   2.5   66   45-113     7-75  (236)
282 PRK12544 RNA polymerase sigma   55.9      16  0.0004   17.0   3.7   39  147-187   160-198 (207)
283 PRK11337 DNA-binding transcrip  55.3      15 0.00038   17.1   3.3   64  124-187    14-84  (293)
284 TIGR02941 Sigma_B RNA polymera  55.1      10 0.00026   18.2   2.4   22  152-173   222-243 (256)
285 TIGR02478 6PF1K_euk 6-phosphof  54.9     6.8 0.00017   19.3   1.5   79   96-179   295-385 (777)
286 PRK12469 RNA polymerase factor  54.2      14 0.00037   17.2   3.1   22  155-176   232-253 (475)
287 PRK11523 DNA-binding transcrip  54.1      17 0.00042   16.8   4.1   24  246-269   214-237 (258)
288 smart00529 HTH_DTXR Helix-turn  53.6      16  0.0004   17.0   3.2   59  156-227     3-62  (96)
289 PRK12511 RNA polymerase sigma   53.1      10 0.00025   18.2   2.1   38  150-189   125-162 (182)
290 COG1508 RpoN DNA-directed RNA   52.8      17 0.00044   16.7   3.8   49  126-174   295-352 (444)
291 PRK12545 RNA polymerase sigma   52.6      18 0.00045   16.7   5.0   43  147-191   150-192 (201)
292 smart00420 HTH_DEOR helix_turn  51.6      18 0.00046   16.6   3.2   30  147-176     8-38  (53)
293 pfam10654 DUF2481 Protein of u  51.2      18 0.00047   16.5   3.8   24  151-174    79-102 (126)
294 TIGR02835 spore_sigmaE RNA pol  51.1      11 0.00027   18.1   2.0   21  153-173   199-219 (234)
295 PRK12531 RNA polymerase sigma   51.0      19 0.00047   16.5   5.4   24  151-174   156-179 (194)
296 PRK04841 transcriptional regul  50.9      19 0.00048   16.5   3.6   13  284-296   872-884 (903)
297 pfam04492 Phage_rep_O Bacterio  50.8      19 0.00048   16.5   4.9   60  124-192    19-85  (100)
298 TIGR02707 butyr_kinase butyrat  50.7      19 0.00048   16.5   3.8   73   62-134    48-150 (353)
299 COG1395 Predicted transcriptio  50.1      17 0.00043   16.8   2.9   34  141-174   127-160 (313)
300 TIGR02431 pcaR_pcaU beta-ketoa  50.1      16 0.00041   16.9   2.8   22  152-173    24-45  (252)
301 COG1609 PurR Transcriptional r  50.0      11 0.00028   17.9   2.0  106   44-155    61-208 (333)
302 COG2186 FadR Transcriptional r  50.0      19 0.00049   16.4   3.8   28   61-92     49-76  (241)
303 COG4804 Predicted nuclease of   50.0      14 0.00037   17.2   2.6   34  195-228     3-39  (159)
304 pfam09048 Cro Cro. Members of   49.2      15 0.00038   17.1   2.6   28  146-175     7-34  (58)
305 TIGR02983 SigE-fam_strep RNA p  49.1      13 0.00032   17.6   2.2   22  152-173   129-150 (165)
306 PRK10225 DNA-binding transcrip  48.9      20 0.00051   16.3   4.1   35   59-97     46-80  (257)
307 smart00422 HTH_MERR helix_turn  48.3      20 0.00052   16.2   3.3   68  153-227     1-68  (70)
308 smart00352 POU Found in Pit-Oc  48.1      21 0.00053   16.2   3.6   34  141-174    13-52  (75)
309 PRK09802 DNA-binding transcrip  48.0      21 0.00053   16.2   4.0   25  152-176   115-141 (269)
310 pfam00325 Crp Bacterial regula  47.8      16 0.00042   16.8   2.6   24  153-176     3-26  (32)
311 PRK13355 bifunctional HTH-doma  47.8      21 0.00053   16.2   3.1   29   48-76    287-316 (518)
312 PRK08960 hypothetical protein;  47.7      20  0.0005   16.3   3.0   30   47-76    170-200 (387)
313 PRK00430 fis DNA-binding prote  47.7      21 0.00053   16.2   3.6   34  144-177    63-96  (98)
314 PRK10079 putative transcriptio  47.6      15 0.00039   17.0   2.4   20  154-173    37-56  (241)
315 COG2771 CsgD DNA-binding HTH d  47.5      21 0.00054   16.2   3.8   38  134-174     4-41  (65)
316 pfam01418 HTH_6 Helix-turn-hel  47.5      21 0.00054   16.2   3.8   86  131-216    10-102 (106)
317 PRK10423 transcriptional repre  47.5      12 0.00031   17.7   1.8   27   47-76     62-88  (327)
318 PRK07324 transaminase; Validat  47.1      21 0.00053   16.2   3.0   45  249-294   318-365 (373)
319 PRK06348 aspartate aminotransf  46.6      21 0.00053   16.2   2.9   43  251-295   333-381 (383)
320 COG2964 Uncharacterized protei  46.5      14 0.00035   17.3   2.0   23  154-176   193-215 (220)
321 PRK07683 aminotransferase A; V  46.2      22 0.00056   16.0   3.0   43  252-294   332-378 (387)
322 pfam01527 Transposase_8 Transp  46.1      22 0.00056   16.0   5.6   43  133-176     5-47  (75)
323 PRK13980 NAD synthetase; Provi  45.7      22 0.00057   16.0   4.4   83  136-221   138-223 (264)
324 pfam08220 HTH_DeoR DeoR-like h  45.7      22 0.00057   16.0   3.2   29  149-177    11-39  (57)
325 TIGR03537 DapC succinyldiamino  45.7      21 0.00054   16.2   2.9   43  250-295   301-349 (350)
326 TIGR02233 Myxo_sigma_rel Myxoc  45.5      21 0.00053   16.2   2.8   32  143-174    31-62  (106)
327 PRK07405 RNA polymerase sigma   45.5      23 0.00058   16.0   4.4   31  146-176   177-209 (318)
328 TIGR02997 Sig70-cyanoRpoD RNA   45.2      23 0.00058   15.9   4.3   39  152-190    64-109 (336)
329 cd04762 HTH_MerR-trunc Helix-T  45.2      13 0.00033   17.5   1.7   28  153-180     1-28  (49)
330 pfam00126 HTH_1 Bacterial regu  44.9      23 0.00059   15.9   3.7   34  142-177     5-38  (60)
331 COG3311 AlpA Predicted transcr  44.6     7.4 0.00019   19.1   0.4   31  153-183    14-44  (70)
332 COG3655 Predicted transcriptio  44.5      22 0.00057   16.0   2.8   29  143-171     6-34  (73)
333 PRK10240 undecaprenyl pyrophos  44.5     5.8 0.00015   19.7  -0.2   89   92-190     1-104 (229)
334 KOG0259 consensus               44.4      23 0.00059   15.9   2.9   29   48-76    205-234 (447)
335 pfam07750 GcrA GcrA cell cycle  43.9      19 0.00048   16.4   2.4   31  139-170     6-37  (162)
336 PRK05657 RNA polymerase sigma   43.9      24 0.00061   15.8   6.1   26  152-177   192-217 (328)
337 PRK09990 DNA-binding transcrip  43.4      24 0.00062   15.8   3.8   26   61-90     46-71  (251)
338 PRK03837 transcriptional regul  43.3      20 0.00051   16.3   2.5   15   63-77     55-69  (243)
339 COG4189 Predicted transcriptio  43.2      24 0.00062   15.7   2.9   33  144-176    29-61  (308)
340 COG3829 RocR Transcriptional r  43.1      25 0.00063   15.7   3.6   19  212-230   456-476 (560)
341 PRK05066 arginine repressor; P  42.8      25 0.00063   15.7   3.7   40  139-178     9-55  (156)
342 PRK07367 consensus              42.7      25 0.00064   15.7   3.0   43  251-294   334-379 (385)
343 PRK06207 aspartate aminotransf  42.6      24 0.00062   15.7   2.8   45  250-294   350-398 (406)
344 cd01455 vWA_F11C1-5a_type Von   42.5      11 0.00028   17.9   1.0   91   92-188    88-188 (191)
345 cd06571 Bac_DnaA_C C-terminal   42.3      25 0.00064   15.6   5.0   26  149-174    41-67  (90)
346 COG1654 BirA Biotin operon rep  42.1      25 0.00065   15.6   4.0   44  152-204    19-65  (79)
347 COG2204 AtoC Response regulato  42.0      26 0.00065   15.6   3.5   22  210-231   349-372 (464)
348 TIGR02395 rpoN_sigma RNA polym  41.9      13 0.00034   17.4   1.3   20  154-173   367-386 (477)
349 PRK07865 N-succinyldiaminopime  41.7      26 0.00066   15.6   3.0   41  251-294   317-363 (364)
350 PRK13182 racA polar chromosome  41.7      26 0.00066   15.6   4.9   24  156-179     4-27  (178)
351 pfam07037 DUF1323 Putative tra  41.7      20  0.0005   16.3   2.2   22  153-174     1-22  (122)
352 PRK08069 consensus              41.5      26 0.00066   15.6   2.8   43  251-295   341-387 (390)
353 PRK05839 hypothetical protein;  41.4      23  0.0006   15.9   2.5   43  251-295   320-370 (376)
354 pfam10302 DUF2407 Putative mem  41.4     9.8 0.00025   18.3   0.6   54  106-161    83-138 (252)
355 PRK07598 RNA polymerase sigma   41.4      26 0.00067   15.6   4.3   15  156-170   277-291 (410)
356 cd01282 HTH_MerR-like_sg3 Heli  41.2      26 0.00067   15.5   4.1   66  154-229     2-69  (112)
357 PHA00675 hypothetical protein   41.1      26 0.00067   15.5   3.6   34  140-173    27-60  (78)
358 PRK10411 DNA-binding transcrip  41.1      26 0.00067   15.5   4.2   20  154-173    20-39  (240)
359 PRK05794 consensus              40.4      25 0.00064   15.7   2.6   41  252-294   346-390 (397)
360 pfam02006 DUF137 Protein of un  40.0      27  0.0007   15.4   3.0   62   59-122    42-103 (178)
361 PRK07212 consensus              39.9      27  0.0007   15.4   2.7   43  251-295   329-375 (378)
362 TIGR02844 spore_III_D sporulat  39.7      28 0.00071   15.4   4.4   42  144-185    11-54  (80)
363 pfam10668 Phage_terminase Phag  39.6      28 0.00071   15.4   2.8   32  142-173    11-43  (60)
364 smart00342 HTH_ARAC helix_turn  39.4      23 0.00058   15.9   2.2   36  153-190     2-38  (84)
365 cd04785 HTH_CadR-PbrR-like Hel  38.9      29 0.00073   15.3   3.5   24  155-178     3-26  (126)
366 PRK08362 consensus              38.6      29 0.00073   15.3   2.9   24  271-294   356-380 (389)
367 pfam05339 DUF739 Protein of un  38.6      24 0.00061   15.8   2.2   29  146-177    11-39  (69)
368 PRK08558 adenine phosphoribosy  38.4      29 0.00074   15.3   4.3   39  142-181    14-52  (238)
369 PRK04280 arginine repressor; P  38.4      29 0.00074   15.3   4.3  129  139-295     5-147 (149)
370 PRK06375 consensus              38.4      29 0.00074   15.3   3.2   45  251-295   328-376 (381)
371 pfam07278 DUF1441 Protein of u  38.3      25 0.00063   15.7   2.3   20  133-152    62-81  (152)
372 TIGR01285 nifN nitrogenase mol  38.2      23 0.00058   16.0   2.0  112   57-169   184-315 (451)
373 PRK10227 DNA-binding transcrip  37.8      30 0.00076   15.2   4.5   13  157-169     5-17  (135)
374 PRK06855 aminotransferase; Val  37.7      30 0.00076   15.2   3.1   28   48-75    177-205 (433)
375 PRK08363 alanine aminotransfer  37.4      30 0.00077   15.2   3.1   43  252-294   343-389 (398)
376 PRK07682 hypothetical protein;  37.2      30 0.00077   15.1   3.1   41  252-294   325-371 (378)
377 pfam04645 DUF603 Protein of un  37.2      30 0.00077   15.1   2.8   33  137-172     7-39  (181)
378 PRK10188 DNA-binding transcrip  37.0      25 0.00065   15.6   2.2   38  134-174   179-216 (240)
379 TIGR02612 mob_myst_A mobile my  36.7      25 0.00064   15.7   2.1   29  143-171    28-57  (150)
380 PRK08443 consensus              36.5      31 0.00079   15.1   2.8   42  251-294   336-381 (388)
381 pfam00155 Aminotran_1_2 Aminot  36.4      31 0.00079   15.1   2.7   41  251-293   306-351 (351)
382 TIGR02787 codY_Gpos GTP-sensin  36.2     7.8  0.0002   18.9  -0.6  120   50-177    66-227 (255)
383 TIGR03542 DAPAT_plant LL-diami  36.0      32  0.0008   15.0   3.2   42  252-295   353-400 (402)
384 COG1438 ArgR Arginine represso  35.9      32 0.00081   15.0   3.8   40  140-179     7-52  (150)
385 COG2456 Uncharacterized conser  35.6      11 0.00028   18.0   0.1   10  157-166    62-71  (121)
386 TIGR01817 nifA Nif-specific re  35.0      27 0.00068   15.5   2.0   19  245-263   387-405 (574)
387 COG1168 MalY Bifunctional PLP-  34.9      33 0.00084   14.9   3.1   28   49-76    165-193 (388)
388 PRK10572 DNA-binding transcrip  34.9      33 0.00084   14.9   6.2   49  152-203   199-247 (290)
389 TIGR02087 LEUD_arch 3-isopropy  34.9      25 0.00063   15.7   1.8   75   41-125     9-92  (159)
390 PRK12414 putative aminotransfe  34.9      33 0.00084   14.9   2.8   23  273-295   360-383 (384)
391 PRK07366 succinyldiaminopimela  34.6      32 0.00081   15.0   2.3   44  251-294   338-385 (388)
392 PRK09265 aminotransferase AlaT  34.6      33 0.00084   14.9   2.4   42  253-294   351-396 (404)
393 TIGR01818 ntrC nitrogen regula  34.3      33 0.00084   14.9   2.4   15  218-232   353-367 (471)
394 PRK09276 aspartate aminotransf  34.3      33 0.00083   14.9   2.4   45  251-295   336-384 (385)
395 PRK08154 anaerobic benzoate ca  34.3      34 0.00086   14.9   3.0   18  135-152   108-125 (304)
396 PRK09464 pdhR transcriptional   34.2      30 0.00077   15.2   2.2   26   61-90     49-74  (254)
397 PRK08361 aspartate aminotransf  34.2      34 0.00086   14.8   3.1   44  251-294   337-384 (390)
398 cd04909 ACT_PDH-BS C-terminal   34.1      34 0.00086   14.8   3.0   51  249-299    14-68  (69)
399 PRK11414 putative DNA-binding   34.1      33 0.00084   14.9   2.3   15   47-61     24-38  (221)
400 COG2524 Predicted transcriptio  34.0      27 0.00068   15.5   1.9   31   59-92     38-68  (294)
401 PRK06030 hypothetical protein;  33.9      34 0.00087   14.8   4.0   37  138-174    65-103 (136)
402 pfam07453 NUMOD1 NUMOD1 domain  33.7      17 0.00044   16.7   0.9   25  148-173    13-37  (37)
403 cd01111 HTH_MerD Helix-Turn-He  33.3      35 0.00089   14.7   3.3   69  153-230     1-71  (107)
404 PRK08912 hypothetical protein;  33.0      35  0.0009   14.7   3.1   42  253-294   334-381 (387)
405 PRK05901 RNA polymerase sigma   32.9      35  0.0009   14.7   4.3   22  154-175   264-285 (398)
406 TIGR03558 oxido_grp_1 lucifera  32.9     7.4 0.00019   19.1  -1.1   63   49-112   119-182 (323)
407 PRK08175 aminotransferase; Val  32.8      35  0.0009   14.7   3.2   41  252-294   338-384 (395)
408 pfam00157 Pou Pou domain - N-t  32.8      36 0.00091   14.7   3.5   34  141-174    13-52  (75)
409 PRK06108 aspartate aminotransf  32.7      36 0.00091   14.7   2.7   44  251-294   330-377 (382)
410 TIGR01265 tyr_nico_aTase tyros  32.6      36 0.00091   14.7   3.0   77   32-115   161-256 (424)
411 PRK07568 aspartate aminotransf  32.4      36 0.00092   14.7   2.8   44  252-295   333-388 (396)
412 cd04770 HTH_HMRTR Helix-Turn-H  32.3      36 0.00092   14.6   3.9   20  155-174     3-22  (123)
413 pfam06056 Terminase_5 Putative  32.2      23 0.00058   15.9   1.3   22  151-172    12-33  (58)
414 PRK10421 DNA-binding transcrip  31.7      37 0.00094   14.6   4.1   28   59-90     39-66  (253)
415 TIGR02404 trehalos_R_Bsub treh  31.7      34 0.00088   14.8   2.1   31  154-184    26-56  (236)
416 cd00592 HTH_MerR-like Helix-Tu  31.6      37 0.00095   14.6   3.4   68  153-228     1-68  (100)
417 PRK07777 aminotransferase; Val  31.5      37 0.00095   14.6   3.1   44  251-294   331-381 (386)
418 PRK10947 global DNA-binding tr  31.5      35 0.00089   14.7   2.1   16  207-222    60-75  (135)
419 PRK07681 aspartate aminotransf  31.0      38 0.00097   14.5   3.1   47  251-297   336-386 (399)
420 COG0436 Aspartate/tyrosine/aro  30.9      38 0.00097   14.5   3.1   47  249-295   336-387 (393)
421 PRK06575 consensus              30.8      38 0.00098   14.5   3.2   43  251-295   348-394 (399)
422 TIGR03539 DapC_actino succinyl  30.6      39 0.00098   14.5   2.2   42  250-294   310-357 (357)
423 PRK07310 consensus              30.4      34 0.00085   14.9   1.9   44  250-294   341-387 (395)
424 PRK09082 putative aminotransfe  30.1      39   0.001   14.4   2.8   44  252-295   336-385 (386)
425 KOG3398 consensus               30.0      39   0.001   14.4   3.2   41  133-173    67-107 (135)
426 pfam10279 Latarcin Latarcin pr  30.0      40   0.001   14.4   2.5   19  126-144    50-69  (88)
427 TIGR02394 rpoS_proteo RNA poly  30.0      35 0.00088   14.8   1.9   29  151-179   154-182 (292)
428 PRK07309 aromatic amino acid a  29.9      40   0.001   14.4   3.2   46  251-296   336-385 (390)
429 PRK10219 DNA-binding transcrip  29.8      40   0.001   14.4   6.4   47  152-201    21-67  (107)
430 PRK11302 DNA-binding transcrip  29.7      40   0.001   14.4   3.7   44  133-176    12-58  (284)
431 TIGR03538 DapC_gpp succinyldia  29.7      40   0.001   14.4   3.0   24  272-295   368-392 (394)
432 COG4800 Predicted transcriptio  29.7      40   0.001   14.4   3.0   32  142-173    19-50  (170)
433 PRK05942 aspartate aminotransf  29.2      41   0.001   14.3   2.4   48  251-298   340-391 (394)
434 PRK07337 aminotransferase; Val  29.1      33 0.00084   14.9   1.7   42  251-294   336-384 (388)
435 PRK05658 RNA polymerase sigma   29.1      41   0.001   14.3   3.1   18   58-75     40-57  (620)
436 COG1802 GntR Transcriptional r  29.0      41   0.001   14.3   2.4   21   45-65     27-47  (230)
437 PRK01533 histidinol-phosphate   28.9      39   0.001   14.4   2.0   41  250-295   311-351 (366)
438 PRK00550 rpsE 30S ribosomal pr  28.7      42  0.0011   14.3   5.3   67   79-165    89-155 (156)
439 PRK06225 aspartate aminotransf  28.7      42  0.0011   14.3   3.2   44  249-295   317-367 (375)
440 cd04776 HTH_GnyR Helix-Turn-He  28.7      42  0.0011   14.3   3.4   27  153-179     1-27  (118)
441 cd04772 HTH_TioE_rpt1 First He  28.6      29 0.00073   15.3   1.3   29  153-181     1-29  (99)
442 pfam00440 TetR_N Bacterial reg  28.6      42  0.0011   14.2   3.6   29  146-174     7-38  (47)
443 PRK06056 consensus              28.2      43  0.0011   14.2   3.0   43  251-295   350-396 (402)
444 KOG0994 consensus               28.1      43  0.0011   14.2  10.8   12   59-70   1490-1501(1758)
445 PRK07590 L,L-diaminopimelate a  28.0      43  0.0011   14.2   3.1   45  251-295   359-407 (409)
446 pfam01316 Arg_repressor Argini  27.8      43  0.0011   14.2   3.2   35  143-177     9-49  (70)
447 TIGR01298 RNaseT ribonuclease   27.5      39   0.001   14.4   1.8   10  129-138   129-138 (201)
448 TIGR02079 THD1 threonine dehyd  27.3      44  0.0011   14.1   2.2   49  252-300   344-401 (415)
449 KOG2252 consensus               27.3      44  0.0011   14.1   3.6   62  128-193   318-381 (558)
450 TIGR02092 glgD glucose-1-phosp  27.2      17 0.00043   16.8  -0.1   36   36-71     68-114 (383)
451 TIGR01478 STEVOR variant surfa  27.0      22 0.00057   16.0   0.5   37   45-83     51-99  (315)
452 PRK05764 aspartate aminotransf  26.8      45  0.0011   14.0   3.1   43  251-295   337-383 (389)
453 PRK08068 transaminase; Reviewe  26.7      45  0.0011   14.0   2.7   45  251-295   337-385 (389)
454 TIGR01529 argR_whole arginine   26.5      45  0.0012   14.0   2.9  130  141-295     4-153 (155)
455 PRK04984 fatty acid metabolism  26.5      45  0.0012   14.0   4.3   23   63-89     48-70  (239)
456 PRK04175 rpl7ae 50S ribosomal   26.5      39 0.00099   14.5   1.6   38  133-170    55-98  (123)
457 PRK10837 putative DNA-binding   26.3      46  0.0012   14.0   3.8   12  285-296   278-289 (291)
458 cd04780 HTH_MerR-like_sg5 Heli  26.3      46  0.0012   14.0   3.4   69  154-229     2-71  (95)
459 PRK05949 RNA polymerase sigma   26.2      46  0.0012   14.0   4.4   25  153-177   195-219 (327)
460 PRK11511 DNA-binding transcrip  26.2      46  0.0012   14.0   6.9   39  152-191    25-63  (127)
461 TIGR02639 ClpA ATP-dependent C  26.0      46  0.0012   13.9   5.4   94  152-259   396-497 (774)
462 cd01821 Rhamnogalacturan_acety  26.0      38 0.00097   14.5   1.5   26   60-86     93-118 (198)
463 PRK06507 consensus              25.9      41  0.0011   14.3   1.7   43  252-295   349-394 (400)
464 smart00497 IENR1 Intron encode  25.6      31 0.00079   15.1   1.0   25  150-175    16-40  (53)
465 COG3888 Predicted transcriptio  25.5      47  0.0012   13.9   4.0   48   98-145    90-137 (321)
466 PRK11557 putative DNA-binding   25.2      48  0.0012   13.9   5.0   58  132-189    11-73  (282)
467 pfam10743 Phage_Cox Regulatory  25.2      46  0.0012   14.0   1.8   28  152-179    12-39  (87)
468 PRK03341 arginine repressor; P  25.2      48  0.0012   13.9   3.8  131  140-295    16-163 (168)
469 PRK09744 DNA-binding transcrip  25.2      48  0.0012   13.8   3.3   34  148-185     7-40  (75)
470 smart00531 TFIIE Transcription  25.0      44  0.0011   14.1   1.7   33  144-176     7-39  (147)
471 PRK09514 zntR zinc-responsive   25.0      48  0.0012   13.8   3.7   11  152-162    58-68  (140)
472 PRK10328 DNA binding protein,   24.9      49  0.0012   13.8   2.3   17  206-222    59-75  (134)
473 KOG3725 consensus               24.9      45  0.0012   14.0   1.8   84   86-174   149-235 (375)
474 PRK00423 tfb transcription ini  24.9      49  0.0012   13.8   3.4   21  154-174   184-204 (310)
475 pfam08564 CDC37_C Cdc37 C term  24.9      49  0.0012   13.8   3.0   42  175-216    11-53  (87)
476 PRK08636 aspartate aminotransf  24.9      49  0.0012   13.8   3.2   45  251-295   348-396 (403)
477 PRK07778 consensus              24.9      49  0.0012   13.8   3.0   45  250-294   332-381 (386)
478 PRK06959 putative threonine-ph  24.8      49  0.0012   13.8   2.2   46  247-295   283-329 (339)
479 pfam11353 DUF3153 Protein of u  24.7      49  0.0012   13.8   5.6   46  247-293    43-88  (210)
480 pfam00376 MerR MerR family reg  24.7      36 0.00092   14.7   1.2   27  154-180     1-27  (38)
481 PRK05957 aspartate aminotransf  24.5      49  0.0013   13.8   2.9   45  250-294   331-380 (389)
482 cd01109 HTH_YyaN Helix-Turn-He  24.5      49  0.0013   13.8   3.4   28  153-180     1-28  (113)
483 TIGR01515 branching_enzym 1,4-  24.5      11 0.00027   18.1  -1.5   22   88-109    81-104 (608)
484 PRK05201 hslU ATP-dependent pr  24.5      50  0.0013   13.8   2.3  156  133-299     2-169 (442)
485 TIGR00972 3a0107s01c2 phosphat  24.4      41   0.001   14.3   1.4   64  169-232   121-193 (248)
486 PRK09147 aminotransferase; Pro  24.4      50  0.0013   13.8   2.8   30   47-76    171-201 (397)
487 PRK07851 acetyl-CoA acetyltran  24.3      26 0.00068   15.5   0.5  128   52-195   229-360 (405)
488 pfam06970 RepA_N Replication i  24.3      50  0.0013   13.7   2.1   22  153-174    53-74  (76)
489 TIGR02094 more_P_ylases alpha-  24.1      50  0.0013   13.7   3.1   34  191-228   173-206 (618)
490 PRK05664 threonine-phosphate d  24.0      51  0.0013   13.7   3.0   27   50-76    132-159 (330)
491 TIGR02405 trehalos_R_Ecol treh  23.9      18 0.00045   16.6  -0.5   22  152-173     1-22  (311)
492 TIGR02944 suf_reg_Xantho FeS a  23.8      41   0.001   14.3   1.4   26  153-178    26-51  (130)
493 PRK08153 histidinol-phosphate   23.8      51  0.0013   13.7   2.2   27   50-76    164-191 (370)
494 PRK03321 putative aminotransfe  23.8      51  0.0013   13.7   2.0   30   47-76    150-180 (352)
495 PRK12681 cysB transcriptional   23.7      51  0.0013   13.7   4.2   39  138-177     3-41  (324)
496 PRK10402 DNA-binding transcrip  23.6      52  0.0013   13.7   4.6   51  124-174   124-178 (213)
497 PRK00118 putative DNA-binding   23.3      52  0.0013   13.6   3.6   34  140-174    22-55  (105)
498 PRK13558 bacterio-opsin activa  23.2      52  0.0013   13.6   1.9   21  154-174   641-661 (674)
499 PRK11074 putative DNA-binding   23.2      52  0.0013   13.6   3.2   34  142-177     8-41  (300)
500 COG4567 Response regulator con  23.1      53  0.0013   13.6   3.7   34  140-173   143-176 (182)

No 1  
>COG1475 Spo0J Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]
Probab=100.00  E-value=2.7e-39  Score=272.48  Aligned_cols=233  Identities=39%  Similarity=0.634  Sum_probs=212.5

Q ss_pred             CCEEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             60240389823578999876898899999998863100155046205654453335756777776421001354333464
Q gi|254780805|r   38 SQDCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVD  117 (300)
Q Consensus        38 ~~~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~  117 (300)
                      ....+++..|.++|++||+.|+++.+++|+.||+++|++|||+|++    +|+||+|||||+||+.+|+++|||+|++.+
T Consensus         3 ~~~~~~~~~i~~~~~~~r~~~~~~~~~~l~~SI~~~G~~~Pi~v~~----~yeiv~G~rR~~Aa~~~g~~~vp~iv~~~~   78 (240)
T COG1475           3 RVVEIDIVLIAPNPLQPRKKFDEESLEELAASIKEFGLIQPIVVRP----RYEIVDGHRRLRAAKLLGLEEVPVIVRDLE   78 (240)
T ss_pred             CCCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEECC----EEEEECCCHHHHHHHHCCCCCCCEEEECCC
T ss_conf             6442467664667666644377577999999999839816857777----248842709999999738776874883466


Q ss_pred             CHHHHHHHHHHHHHCCCCCHHHHHH-HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             1123455666543102210489999-999852101110467999974337877865656543589999876421016777
Q gi|254780805|r  118 NKSSLEIAIVENVQRKDLNPLEEAL-GYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHA  196 (300)
Q Consensus       118 d~~~~~~~l~EN~~R~dl~p~e~A~-~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~gha  196 (300)
                      |.++...+++||+||++++|+|++. ++..+++.++++++.++..+|+++++++|++++..+|++++.++..+.++.+|+
T Consensus        79 d~~~~~~~l~en~~r~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~  158 (240)
T COG1475          79 DEKLLELSLAENIQREDLVPIEEALGAYYELIDGFGLTRERIAKALGKSRARISNLLPLAALPEEVVEALGRIALTIRHA  158 (240)
T ss_pred             HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             58899998898525566767999877699887530455999998853017654202201347888887531001368898


Q ss_pred             HHHHHCCH---HHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEECCCCC
Q ss_conf             77640100---468999974222477899999976410222222345665568978999999999973987999717982
Q gi|254780805|r  197 RTLVSTSD---PLSLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLEKKISSKVGLNISIKHRNNK  273 (300)
Q Consensus       197 r~Ll~~~~---~~~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le~~L~~~lGtkV~I~~~~~k  273 (300)
                      ++++....   +..++..++..+|+|+.++..+.......          ..........+..+....|+++.++    .
T Consensus       159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~----~  224 (240)
T COG1475         159 RALLSLLVEELMSEIVRELVKEGLSVRWIEKLVRALIKDA----------LEELGMDKDEKLRLKQISGLAVLIK----D  224 (240)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCC----------CCCCCCHHHHHHHHHHHHCCHHHHC----C
T ss_conf             9987501245657999999861000345688887753011----------0124002889998867416044421----6


Q ss_pred             EEEEEEECCHHHHHH
Q ss_conf             289998589899999
Q gi|254780805|r  274 GQFCIKYETNEQLKI  288 (300)
Q Consensus       274 GkI~I~f~s~eeLe~  288 (300)
                      |++.+.|.+.+++++
T Consensus       225 ~~~~~~~~~~~~~~~  239 (240)
T COG1475         225 GKFSVAWESEEELER  239 (240)
T ss_pred             CEEEEECCCHHHHHC
T ss_conf             702211154544512


No 2  
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=100.00  E-value=2.5e-31  Score=221.28  Aligned_cols=153  Identities=23%  Similarity=0.359  Sum_probs=142.0

Q ss_pred             CCCCCCCCEEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECC--CCCCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             01345660240389823578999876898899999998863100155046205--6544533357567777764210013
Q gi|254780805|r   32 TETIPESQDCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAI--DNGLYKIIAGERRFRAAKMASLSEV  109 (300)
Q Consensus        32 ~~~~~~~~~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~--~~g~y~ii~G~rR~rAa~~~g~~~i  109 (300)
                      .....+.+.+|+.+.|.|++.+.|-.+|++.+++|.+||+++||.+||+|||.  .+|+|+|++|||||+||+.+|+ .|
T Consensus        57 ~l~~G~~VvELDp~lId~S~v~DRl~~d~~~~~~L~~sI~~~Gq~~PilVRphp~~~gry~iv~G~RR~~A~~~lg~-~v  135 (325)
T TIGR03454        57 QLAEGETVVELDPALIDTSFVSDRLDSDEEAFAELVESIRENGQQVPILVRPHPEAEGRYQVAYGHRRLRAARDLGI-PV  135 (325)
T ss_pred             HHHCCCEEEECCHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCEEEEECHHHHHHHHHCCC-CC
T ss_conf             87369948976988716665656777887999999999998298477697168888884788510899999998299-72


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Q ss_conf             54333464112345566654310221048999999985210111046799997433787786565654-358999987
Q gi|254780805|r  110 PVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK-LPSSVREMI  186 (300)
Q Consensus       110 p~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~-L~~~i~~~l  186 (300)
                      +++|++++|.++...+..||.+|.||+.||+|..+.+|.+ .|++++.|+..+|.++++||+++.+.. +|+++..++
T Consensus       136 ~A~vr~l~D~~~v~aqg~EN~~R~dLSfIErA~fA~~l~~-~g~~r~~I~~aL~vdks~lSrml~Va~~iP~elI~aI  212 (325)
T TIGR03454       136 KAVVRELSDEELVIAQGQENSARRDLSFIERALFAQRLED-RGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAI  212 (325)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHH
T ss_conf             0334579929999998876452146779999999999998-4999999999988899999999999997899999973


No 3  
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=99.95  E-value=1.5e-27  Score=197.02  Aligned_cols=153  Identities=25%  Similarity=0.340  Sum_probs=139.4

Q ss_pred             CCCCCCCCEEEEHHHCCCCCCCCCCCCC-HHHHHHHHHHHHHCCCCCCCEEECCCC--CCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             0134566024038982357899987689-889999999886310015504620565--4453335756777776421001
Q gi|254780805|r   32 TETIPESQDCISIHSIVPNPHNPRNYFE-SEGLEDLCQSIKSHGIIQPLIVRAIDN--GLYKIIAGERRFRAAKMASLSE  108 (300)
Q Consensus        32 ~~~~~~~~~~i~i~~i~~~p~~pR~~~~-~~~l~eLa~SI~~~G~lqPi~Vr~~~~--g~y~ii~G~rR~rAa~~~g~~~  108 (300)
                      .....+.+.+|+.+.|.|++.+.|-..| ++.+++|..||+++||..||+|||.++  |+|+|+.|||||+||+.+|. .
T Consensus        58 qLa~G~~VVelDp~~Id~S~v~DRl~~d~d~~~~~L~~sI~~~GQ~vPILVRphp~~~gryqi~yG~RRl~A~~~Lg~-~  136 (336)
T PRK13866         58 QLAAGEAVVSLDPSMIDGSPIADRLPSDVDPKFEQLEASISQDGQQVPILVRPHPEAAGRYQIVYGRRRLRAAVNLRR-E  136 (336)
T ss_pred             HHHCCCEEEECCHHHCCCCCCHHCCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCCCEEEEHHHHHHHHHHHHCC-C
T ss_conf             985699489738664255310103778753799999999998398476685779888885663054899999998099-6


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Q ss_conf             35433346411234556665431022104899999998521011104679999743378778656565-4358999987
Q gi|254780805|r  109 VPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL-KLPSSVREMI  186 (300)
Q Consensus       109 ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l  186 (300)
                      |.++|++++|.++...+-.||..|.||+.||+|..-.+|.+ .|++++.|...++.+++.+|+++.+. .+|+++..++
T Consensus       137 VkA~Vr~L~D~~~v~aQG~EN~~R~dLSfIErAlFA~~l~~-~g~~r~~i~~aL~~dk~~lS~m~~v~~~iP~~~i~aI  214 (336)
T PRK13866        137 VSAIVRNLTDRELVVAQGRENLDRADLSFIEKALFALRLED-AGFDRATIIAALSTDKADLSRYITVARGIPLNLATQI  214 (336)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHH
T ss_conf             33221148809999987645331234309999999999997-6998889999967888899999999997899999974


No 4  
>PRK13832 plasmid partitioning protein; Provisional
Probab=99.95  E-value=8.4e-27  Score=192.20  Aligned_cols=174  Identities=24%  Similarity=0.368  Sum_probs=152.9

Q ss_pred             CCEEEEHHHCCCCCCCCCCC-CCHHHHHHHHHHHHHCCCCCCCEEECCCCC--CCCCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             60240389823578999876-898899999998863100155046205654--453335756777776421001354333
Q gi|254780805|r   38 SQDCISIHSIVPNPHNPRNY-FESEGLEDLCQSIKSHGIIQPLIVRAIDNG--LYKIIAGERRFRAAKMASLSEVPVIIR  114 (300)
Q Consensus        38 ~~~~i~i~~i~~~p~~pR~~-~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g--~y~ii~G~rR~rAa~~~g~~~ip~iv~  114 (300)
                      .++.++...+.+||+|||+. -++.+...|..||+..|++||.+|++..+|  .|.|.+||||.++|..+|+++|.+.|.
T Consensus         2 ~L~~vDPraLk~nPd~~R~tks~~qadalLlatIkaVGivqPPvV~~~~dggng~~I~aGhRRv~~aIaA~L~eI~VlV~   81 (518)
T PRK13832          2 ELRKVDPRALKDNPDNTRRTKSSPQADALLLATIKAVGIVQPPVVAPESDGGNGYIIDAGHRRVKQAIAAGLEEIQVLVT   81 (518)
T ss_pred             CCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCCEEEEEECCHHHHHHHHCCCCEEEEEEE
T ss_conf             74103804314599963568897567999998766410446864421268985268850536899988647554789972


Q ss_pred             CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CH
Q ss_conf             46411234556665431022104899999998521011104679999743378778656565435899998764210-16
Q gi|254780805|r  115 NVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI-SL  193 (300)
Q Consensus       115 ~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i-s~  193 (300)
                      +.++.--...+++||+.|++|||.|+++++.+|++ .|||.+.||-.|+.+..+|..+..|.++-|.+++.+..|.+ +.
T Consensus        82 e~~~d~~amrs~~EN~aRE~mnpvDqWRaierlva-lGwTeeaIa~ALal~vrqiRkLrLLAnv~PamLd~ma~GdmP~e  160 (518)
T PRK13832         82 EAANDNGAMRSMVENIAREPLNPVDQWRAIERLVA-LGWTEEAIAVALALPVRQIRKLRLLANVLPAMLDHMAKGDMPNE  160 (518)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf             16775178999998764067986999999999998-49988999999668999999999997655799999844788759


Q ss_pred             HHHHHH--HHCCHHHHHHHHH
Q ss_conf             777776--4010046899997
Q gi|254780805|r  194 GHARTL--VSTSDPLSLAQVI  212 (300)
Q Consensus       194 ghar~L--l~~~~~~~la~~I  212 (300)
                      .+-|++  .++++|.+++++.
T Consensus       161 ~qlrtiA~asldeQ~eVWk~~  181 (518)
T PRK13832        161 QQLRTIAAASLDEQKEVWKAH  181 (518)
T ss_pred             HHHHHHHHCCHHHHHHHHHHC
T ss_conf             999998716878899999850


No 5  
>TIGR00180 parB_part ParB-like partition proteins; InterPro: IPR004437 This group of chromosomal and plasmid partition proteins are related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.; GO: 0003677 DNA binding.
Probab=99.94  E-value=3.5e-26  Score=188.24  Aligned_cols=170  Identities=47%  Similarity=0.794  Sum_probs=161.7

Q ss_pred             CCCEEEEHHHCCCCCCCCCC---CCCHHHHHHHHHHHHHCCCCCCCEEECCCC----CCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             66024038982357899987---689889999999886310015504620565----44533357567777764210013
Q gi|254780805|r   37 ESQDCISIHSIVPNPHNPRN---YFESEGLEDLCQSIKSHGIIQPLIVRAIDN----GLYKIIAGERRFRAAKMASLSEV  109 (300)
Q Consensus        37 ~~~~~i~i~~i~~~p~~pR~---~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~----g~y~ii~G~rR~rAa~~~g~~~i  109 (300)
                      .....++++.+.++|++||+   .|+++.+.++..||+.+|+++|++|++...    |+|++++|+|||+|++.+|+..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~p~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~   82 (192)
T TIGR00180         3 GGLLELPLDLLDPNPYQPRKDNPGFSEESLEELLESIKEHGLLQPLLVRPAPDPHDPGRYEIIAGERRWRAAKLAGLKPV   82 (192)
T ss_pred             CCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCEEEECCHHHHHHHHHHCCCCH
T ss_conf             53011112232146565655675534567899988887620102101103665445551443212256778876311100


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
Q ss_conf             5433346411234556665431022104899999998521011104679999743378778656565435899998764-
Q gi|254780805|r  110 PVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRK-  188 (300)
Q Consensus       110 p~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~-  188 (300)
                      |+++++.++......+++||++|++++|++++..|.++++.+..+++.+++.+|++++++++.++++++|.+++..+.. 
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~  162 (192)
T TIGR00180        83 PAIVRELDDEQLLALALLENLQREDLSPLEEALAYKRLLEEFSLTQEDLAKKLGKSRAHVTNLLRLLDLPSEVQDALPEA  162 (192)
T ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHC
T ss_conf             13321001577888887643332100157888899998876301388888874232568888888750537899874201


Q ss_pred             -HHCCHHHHHHHHHCCHHH
Q ss_conf             -210167777764010046
Q gi|254780805|r  189 -EEISLGHARTLVSTSDPL  206 (300)
Q Consensus       189 -~~is~ghar~Ll~~~~~~  206 (300)
                       +.++.+|++.+..++...
T Consensus       163 ~~~~~~~~~~~~~~~~~~~  181 (192)
T TIGR00180       163 PGLLSSGHARLLLALKKKP  181 (192)
T ss_pred             CHHHHHHHHHHHHHHCCCH
T ss_conf             1122456888887630330


No 6  
>pfam02195 ParBc ParB-like nuclease domain.
Probab=99.90  E-value=5e-24  Score=174.35  Aligned_cols=90  Identities=43%  Similarity=0.736  Sum_probs=85.9

Q ss_pred             EEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCH
Q ss_conf             24038982357899987689889999999886310015504620565445333575677777642100135433346411
Q gi|254780805|r   40 DCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNK  119 (300)
Q Consensus        40 ~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~  119 (300)
                      .+||++.|.|+|+|||+.+ ++++++|+.||+++|++||++|++.++|+|+|++|||||+||+.+|+.+|||+|.++++.
T Consensus         1 ~ei~i~~i~~~p~npR~~~-~~~i~~L~~SI~~~G~~~PiiV~~~~~~~y~ii~G~~R~~A~~~lg~~~ip~~v~d~~~~   79 (90)
T pfam02195         1 VEVPIDKLRPNEDQPRLTS-EEELEELIASIKEHGLLQPIIVRKTPGGRYEIIDGHRRLRAAKLLGLKEVPVIVLELDDE   79 (90)
T ss_pred             CEEEHHHCCCCCCCCCCCC-HHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEEEEHHHHHHHCCCCEEEEEEEECCHH
T ss_conf             9824899754988969889-899999999999859647879997488978995686199999986998610999989989


Q ss_pred             HHHHHHHHHHH
Q ss_conf             23455666543
Q gi|254780805|r  120 SSLEIAIVENV  130 (300)
Q Consensus       120 ~~~~~~l~EN~  130 (300)
                      ++..+++.||+
T Consensus        80 ea~~~~l~eNi   90 (90)
T pfam02195        80 EAIALSLEENI   90 (90)
T ss_pred             HHHHHHHHCCC
T ss_conf             99999987459


No 7  
>smart00470 ParB ParB-like nuclease domain. Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5--3 exonuclease activity.
Probab=99.87  E-value=1.2e-22  Score=165.43  Aligned_cols=89  Identities=47%  Similarity=0.859  Sum_probs=84.3

Q ss_pred             EEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCH
Q ss_conf             24038982357899987689889999999886310015504620565445333575677777642100135433346411
Q gi|254780805|r   40 DCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNK  119 (300)
Q Consensus        40 ~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~  119 (300)
                      .+||++.|.|+|+|||+. +++++++|+.||+++|++||++|++.+ |+|+|++|||||+||+.+|+++|||+|.+++|.
T Consensus         1 ~~i~i~~l~~~p~n~r~~-~~~~~~~L~~SI~~~G~~~Pi~v~~~~-~~y~ii~G~rR~~Aa~~lg~~~ip~~v~d~~~~   78 (89)
T smart00470        1 VEVPIEKLRPNPDQPRLT-SEESLEELAESIKENGLLQPIIVRPND-GRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDE   78 (89)
T ss_pred             CEEEHHHCCCCCCCCCCC-CHHHHHHHHHHHHHHCCCCCEEEEECC-CCEEECCCHHHHHHHHHCCCCCCEEEEEECCHH
T ss_conf             994189965498995989-999999999999982964776998539-956986878999999986998031999979999


Q ss_pred             HHHHHHHHHHH
Q ss_conf             23455666543
Q gi|254780805|r  120 SSLEIAIVENV  130 (300)
Q Consensus       120 ~~~~~~l~EN~  130 (300)
                      ++..+++.||+
T Consensus        79 ~a~~~~~~eN~   89 (89)
T smart00470       79 EAIALSLIENI   89 (89)
T ss_pred             HHHHHHHHCCC
T ss_conf             99999987449


No 8  
>PRK13698 plasmid-partitioning protein; Provisional
Probab=99.76  E-value=6.7e-17  Score=128.55  Aligned_cols=240  Identities=19%  Similarity=0.248  Sum_probs=173.2

Q ss_pred             EEEEHHHCC----CCCCCCC-CC-CCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCC
Q ss_conf             240389823----5789998-76-89889999999886310015504620565445333575677777642100135433
Q gi|254780805|r   40 DCISIHSIV----PNPHNPR-NY-FESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVII  113 (300)
Q Consensus        40 ~~i~i~~i~----~~p~~pR-~~-~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv  113 (300)
                      ..||-++|.    .+-.|-| +. .++.++.+|..|++..||..|.++|... |.++|++|-||+.+|.+.+.+ ..+.|
T Consensus        60 ~~I~a~~ve~~T~Vw~~N~RdQ~lLtE~slsDli~s~~~~GQQ~PAigRr~~-g~iEVlDGSRRR~a~il~~~D-y~VlV  137 (323)
T PRK13698         60 EVIRGDSVESKTRVWSGNERDQELLTEDSLDDLIPSFLLTGQQTPAFGRRVS-GVIEIADGSRRRKAAILTESD-YRVLV  137 (323)
T ss_pred             EEECHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEECC-CCEEEECCHHHHHHHHCCCCC-EEEEE
T ss_conf             9821445546667774054667764177888889999971884762103417-968980352777877606884-48997


Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH-HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHC
Q ss_conf             346411234556665431022104899999998-5210111046799997433787786565654358999987-64210
Q gi|254780805|r  114 RNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQ-LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI-RKEEI  191 (300)
Q Consensus       114 ~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~-l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l-~~~~i  191 (300)
                      .+++|+++..++-++|-.|. ++.+|.+.-|.+ |...|+.+|.++|+.+|.|+++|++.+....||.++.++. .-++|
T Consensus       138 ~el~Deq~~~Lsdv~N~~rp-~SayErg~ry~~rL~~~~~gnqs~lAe~~~iSra~vsR~i~tA~LP~e~v~aFp~p~eL  216 (323)
T PRK13698        138 GELDDEQMAALSRLGNDYRP-TSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGEL  216 (323)
T ss_pred             EECCHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHCCHHHHHHCCCHHHH
T ss_conf             30887999999998750177-30888899999998634046699999985889999998887743879999866991232


Q ss_pred             CHHHHHHHHHC----CHH-HHHHHHHHHCC--CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCE
Q ss_conf             16777776401----004-68999974222--477899999976410222222345665568978999999999973987
Q gi|254780805|r  192 SLGHARTLVST----SDP-LSLAQVIVSKK--MSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLEKKISSKVGLN  264 (300)
Q Consensus       192 s~ghar~Ll~~----~~~-~~la~~Ii~~~--LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le~~L~~~lGtk  264 (300)
                      |+..+.+|...    +++ ...+..+.+.+  =..=++|+++..+..-...+...     .+..       .....||.-
T Consensus       217 sAR~Ge~L~k~~~~~e~~~~~~a~~l~~~~~~g~~f~teeii~~l~~~~k~~~~~-----~~~~-------~~~r~f~~G  284 (323)
T PRK13698        217 SARSGEALQKAFEDKEELLKQQTHKLHKQKKAGRIFETEEVIVLLTSVLKQSSAS-----RTSL-------SSRHQFAPG  284 (323)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCC-----CCCC-------HHHHHCCCC
T ss_conf             0330389999984369999999999999886157678999999999987266655-----6651-------255550577


Q ss_pred             EEEECCCCCEEEEEEECC-------HHHHHHHHHHHCCC
Q ss_conf             999717982289998589-------89999999983756
Q gi|254780805|r  265 ISIKHRNNKGQFCIKYET-------NEQLKIICSLLGEN  296 (300)
Q Consensus       265 V~I~~~~~kGkI~I~f~s-------~eeLe~Il~kL~~~  296 (300)
                      +++..+++  +++|+..+       .++++.|++.+.+.
T Consensus       285 ~~a~yk~~--~v~~~l~~~~~~~~~i~kiE~~l~~~~k~  321 (323)
T PRK13698        285 ATALYKGD--KVVFNLDRSRVPEECIEQIEAILKELEKE  321 (323)
T ss_pred             CEEEEECC--EEEEEECCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             36886087--58998368889999999999999986224


No 9  
>pfam08535 KorB KorB domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This domain includes the DNA-binding HTH motif.
Probab=98.23  E-value=4.7e-06  Score=58.88  Aligned_cols=48  Identities=33%  Similarity=0.475  Sum_probs=42.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             11104679999743378778656565435899998764210167777764
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLV  200 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll  200 (300)
                      .|+++.+||+++|+|.+|||.+++|+++|++|.+++.+|..+.  .++|.
T Consensus         2 ~G~kk~~IAk~LGks~s~VS~hlaL~d~Pd~l~~l~~~g~~~d--v~~l~   49 (93)
T pfam08535         2 KGVKQAEIAKKLGKSKSFVSQHLALLDMPDCIREAYDSGRCSD--IRALY   49 (93)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCC--HHHHH
T ss_conf             9877999999978898899999998348699999987477687--99999


No 10 
>pfam07506 RepB RepB plasmid partitioning protein. This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens.
Probab=97.67  E-value=0.00014  Score=49.35  Aligned_cols=94  Identities=17%  Similarity=0.257  Sum_probs=68.7

Q ss_pred             HCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH--HHH-HHHHHHHHHHHHHHCCHHHHHHH--HHCCHH
Q ss_conf             1022104899999998521011104679999743378778656--565-43589999876421016777776--401004
Q gi|254780805|r  131 QRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL--RIL-KLPSSVREMIRKEEISLGHARTL--VSTSDP  205 (300)
Q Consensus       131 ~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L--rLl-~L~~~i~~~l~~~~is~ghar~L--l~~~~~  205 (300)
                      .|.||+++|++.-..++.+. |++.+.|+..+|.+.++|++++  +++ .+|+++.+++.+.........++  ++-+-+
T Consensus         1 ar~~Ls~Ie~~~~a~rl~~~-G~~~~~I~~aL~vd~~~is~~~~~~~~~~i~~e~~~lL~d~~~~~~~ig~a~kigr~Rw   79 (185)
T pfam07506         1 ARADLSFIERARFAARLLER-GVPRAEIAAALGLDPQTVSKMVARAIPEGICPEEEALLKDVETGIAAFGLARKIGRDRW   79 (185)
T ss_pred             CCCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHCCCCCHHH
T ss_conf             98642299999999999986-99999999998679999999999987511688999986034564988765100582789


Q ss_pred             HHHHHHHH-HCCCCHHHHHHH
Q ss_conf             68999974-222477899999
Q gi|254780805|r  206 LSLAQVIV-SKKMSVRDTEEL  225 (300)
Q Consensus       206 ~~la~~Ii-~~~LSVRe~E~l  225 (300)
                      .++++..+ .+.+++...+.+
T Consensus        80 ~e~aelm~a~~~~~~~~~~al  100 (185)
T pfam07506        80 VELAELLAAAKNVESAYFRAL  100 (185)
T ss_pred             HHHHHHHHHHHHCCHHHHHHH
T ss_conf             999999987530158999864


No 11 
>COG5119 Uncharacterized protein, contains ParB-like nuclease domain [General function prediction only]
Probab=96.17  E-value=0.012  Score=36.99  Aligned_cols=79  Identities=18%  Similarity=0.248  Sum_probs=58.9

Q ss_pred             CCCEEEEHHHCCCCCCCCCCCCCHHHHHHHH---------------HHHHHCCCCCCCEEE---CCCCCCCCCCCCHHHH
Q ss_conf             6602403898235789998768988999999---------------988631001550462---0565445333575677
Q gi|254780805|r   37 ESQDCISIHSIVPNPHNPRNYFESEGLEDLC---------------QSIKSHGIIQPLIVR---AIDNGLYKIIAGERRF   98 (300)
Q Consensus        37 ~~~~~i~i~~i~~~p~~pR~~~~~~~l~eLa---------------~SI~~~G~lqPi~Vr---~~~~g~y~ii~G~rR~   98 (300)
                      -++++||++.|.. |.-|  ..|+.+++.|.               .++.+-|.+.|+-|-   ..+...|.-..|.+|+
T Consensus         8 v~~~EiplseirR-Plpp--vlDp~Kv~am~~tM~g~t~~~sc~l~e~~a~aGelpPvDVL~~~v~Gq~~YyaFgGCHRl   84 (119)
T COG5119           8 VNIQEIPLSEIRR-PLPP--VLDPNKVNAMMETMTGKTPPASCGLTEEDAAAGELPPVDVLTFEVDGQPYYYAFGGCHRL   84 (119)
T ss_pred             CCCEECCHHHHHC-CCCC--CCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCCCCCCEEEEEEECCCEEEEEECCCHHH
T ss_conf             6645535889546-7988--788899999999732899975455207677537899830678876593778861740776


Q ss_pred             HHHHHHHCCCCCC-CCCCCCC
Q ss_conf             7776421001354-3334641
Q gi|254780805|r   99 RAAKMASLSEVPV-IIRNVDN  118 (300)
Q Consensus        99 rAa~~~g~~~ip~-iv~~~~d  118 (300)
                      +|+..+|.++|.| .|+-.+.
T Consensus        85 ~A~dr~gret~~a~rvr~~P~  105 (119)
T COG5119          85 EACDRAGRETILAKRVRCAPN  105 (119)
T ss_pred             HHHHHHHHHHHHHHHHCCCHH
T ss_conf             999887378888888713807


No 12 
>PHA01976 helix-turn-helix protein
Probab=95.17  E-value=0.016  Score=36.13  Aligned_cols=35  Identities=9%  Similarity=0.091  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999985210111046799997433787786565
Q gi|254780805|r  140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      -+.-+++|.+..||||+++|+++|.++++|+++-.
T Consensus         3 F~~RL~~lR~~~g~sQ~eLA~~lGVs~~~is~wE~   37 (67)
T PHA01976          3 FAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEA   37 (67)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf             89999999998699999999994998999999987


No 13 
>KOG3388 consensus
Probab=95.17  E-value=0.018  Score=35.87  Aligned_cols=82  Identities=16%  Similarity=0.203  Sum_probs=57.0

Q ss_pred             CCEEEEHHHCCCCCCCCCCCCCHHHH--------------HHHHHHHHHCCCCCCCEEECC---CCCCCCCCCCHHHHHH
Q ss_conf             60240389823578999876898899--------------999998863100155046205---6544533357567777
Q gi|254780805|r   38 SQDCISIHSIVPNPHNPRNYFESEGL--------------EDLCQSIKSHGIIQPLIVRAI---DNGLYKIIAGERRFRA  100 (300)
Q Consensus        38 ~~~~i~i~~i~~~p~~pR~~~~~~~l--------------~eLa~SI~~~G~lqPi~Vr~~---~~g~y~ii~G~rR~rA  100 (300)
                      ...++|.+.|.- |.-|  ..|.+++              .+.++||++-|.+-||-|-..   +...|.-..|.+|++|
T Consensus        26 ~pv~~~mSei~r-Pi~p--vLd~qKi~slm~Tmkn~~~c~les~d~~~~aGelpPiDvl~v~~~G~~~YyaFgGCHRleA  102 (136)
T KOG3388          26 PPVEGPMSEIVR-PIPP--VLDLQKIRSLMETMKNDQNCVLESEDSIRQAGELPPIDVLEVDSEGGDYYYAFGGCHRLEA  102 (136)
T ss_pred             CCEECCHHHCCC-CCCC--CCCHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEECCCHHHHH
T ss_conf             954645120445-7886--4698999999998508976331357788743778981289995179667886176424478


Q ss_pred             HHHHHCCCCCCCCCCCCCHHHH
Q ss_conf             7642100135433346411234
Q gi|254780805|r  101 AKMASLSEVPVIIRNVDNKSSL  122 (300)
Q Consensus       101 a~~~g~~~ip~iv~~~~d~~~~  122 (300)
                      ...+|..+|.|-+...+..+..
T Consensus       103 hdrlgrptiRcKlvk~T~~tLr  124 (136)
T KOG3388         103 HDRLGRPTIRCKLVKGTPETLR  124 (136)
T ss_pred             HHHHCCCCEEEEEECCCHHHHH
T ss_conf             8861798546787349988877


No 14 
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322   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 group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.93  E-value=0.065  Score=32.27  Aligned_cols=67  Identities=27%  Similarity=0.440  Sum_probs=44.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCC--CCHHHHHHHHHHHHHH--------------CCCCHHHHHHHHHHHHHHH
Q ss_conf             00135433346411234556665431022--1048999999985210--------------1110467999974337877
Q gi|254780805|r  106 LSEVPVIIRNVDNKSSLEIAIVENVQRKD--LNPLEEALGYEQLISE--------------YGYTQNDIGSIVGKSRSHV  169 (300)
Q Consensus       106 ~~~ip~iv~~~~d~~~~~~~l~EN~~R~d--l~p~e~A~~~~~l~~~--------------~~~t~~~lA~~~G~s~s~V  169 (300)
                      ..+|...+.+-+|.+  .++|++-+.-+|  +.-++.-.+++.++..              -++||.|+|+.+|.|+-||
T Consensus       136 ~~Sld~~~~a~~dg~--~~~L~D~lG~~D~~~e~~~~~~aLk~~l~~LpeRER~il~lRFf~~~TQ~eiA~~lGiSQMhV  213 (229)
T TIGR02980       136 ALSLDATIEADDDGD--PIALLDTLGDEDDALETVEDRLALKPLLAALPERERRILLLRFFEDKTQSEIAERLGISQMHV  213 (229)
T ss_pred             CCCCCCCCCCCCCCC--HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHCEEEEEEEECCCCHHHHHHHCCCCHHHH
T ss_conf             611200045588884--245664440224326789999999999850790270761000106977899997818436788


Q ss_pred             HHHHH
Q ss_conf             86565
Q gi|254780805|r  170 ANILR  174 (300)
Q Consensus       170 ~~~Lr  174 (300)
                      |+.++
T Consensus       214 SRl~~  218 (229)
T TIGR02980       214 SRLLR  218 (229)
T ss_pred             HHHHH
T ss_conf             99999


No 15 
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; InterPro: IPR014303   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 group of sigma factors appear by homology, tree building and bidirectional best hits, to represent a conserved family. This entry is found in a limited number of bacterial lineages and ncludes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis str. MC2 155, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM 10152.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.88  E-value=0.092  Score=31.32  Aligned_cols=38  Identities=37%  Similarity=0.587  Sum_probs=32.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             2210489999999852101110467999974337877865
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      |-|||.|.|.-+  |.+.|+|..+|||..+|||.+...+.
T Consensus       108 ErL~P~ERAVF~--LREVF~y~Y~EIA~~v~kS~ancRQl  145 (287)
T TIGR02957       108 ERLSPLERAVFL--LREVFDYDYEEIASIVGKSEANCRQL  145 (287)
T ss_pred             HHCCHHHHHHHH--HHHHHCCCCHHHHHHCCCCHHHHHHH
T ss_conf             307978999999--99874588267897606895799999


No 16 
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=94.70  E-value=0.068  Score=32.18  Aligned_cols=51  Identities=22%  Similarity=0.339  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             489999999852101110467999974337877865656543589999876421
Q gi|254780805|r  137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE  190 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~  190 (300)
                      .+|+.+++ ||+|--|++|++.|++.|.||+|+.+.|.  ..=..|-++|..|+
T Consensus        38 ~~dE~EAi-RL~D~egl~QeeaA~~MgVSR~Tf~ril~--~ARkKvA~aLv~Gk   88 (100)
T pfam02001        38 TLDEFEAI-RLVDYEDYTQEEAAKLMGISRRTVWRLLT--SARKKIADALVEGR   88 (100)
T ss_pred             CHHHHHHH-HHHHHCCCCHHHHHHHCCCCHHHHHHHHH--HHHHHHHHHHHCCC
T ss_conf             49999999-98736079899999884976999999999--99999999986798


No 17 
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=94.65  E-value=0.073  Score=31.97  Aligned_cols=51  Identities=22%  Similarity=0.280  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             489999999852101110467999974337877865656543589999876421
Q gi|254780805|r  137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE  190 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~  190 (300)
                      .+|+.+|+ ||.+..+++|++.|.+.|.||.|+.+.|.  ..-..|-++|..|+
T Consensus        35 t~eElEAl-RLvD~~~l~QeeAA~rMgISr~Tfwr~l~--sAR~KvA~aLveGk   85 (99)
T COG1342          35 TIEELEAL-RLVDYEGLTQEEAALRMGISRQTFWRLLT--SARKKVADALVEGK   85 (99)
T ss_pred             CHHHHHHH-HHHHHHHCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHCCC
T ss_conf             29998899-98868610578999984642999999999--99999999985587


No 18 
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=94.48  E-value=0.043  Score=33.44  Aligned_cols=38  Identities=29%  Similarity=0.422  Sum_probs=30.9

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             2104899999998521011104679999743378778656
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      -|++ |+....++|++. |.+..+||+.+|.||++|.++|
T Consensus         5 ~lt~-~q~~~ar~l~~~-G~~~~~iA~~~GVsr~Tiyr~l   42 (42)
T cd00569           5 KLTP-EQIEEARRLLAA-GESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCCH-HHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHC
T ss_conf             6999-999999999997-8989999999797999998659


No 19 
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=94.23  E-value=0.061  Score=32.47  Aligned_cols=43  Identities=28%  Similarity=0.328  Sum_probs=35.2

Q ss_pred             CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             04899999998521011104679999743378778656565435
Q gi|254780805|r  136 NPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLP  179 (300)
Q Consensus       136 ~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~  179 (300)
                      -|.=+|.--+.|.++ |+||.++|+.+|.|++.||+||+=-.=|
T Consensus         7 lPaiRa~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~   49 (119)
T COG2522           7 LPAIRALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGS   49 (119)
T ss_pred             HHHHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHCCCCCH
T ss_conf             798999999999995-8869999999688899999997367736


No 20 
>PRK04217 hypothetical protein; Provisional
Probab=93.86  E-value=0.13  Score=30.35  Aligned_cols=51  Identities=27%  Similarity=0.332  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             489999999852101110467999974337877865656543589999876421
Q gi|254780805|r  137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE  190 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~  190 (300)
                      .+|+.+++ ||.|--|++|++.|++.|.||+|+.+.|.  ..-..|-++|..|+
T Consensus        44 tvdE~Eai-RL~D~egl~qeeaA~~M~VSR~Tf~ril~--~AR~KvA~aLv~Gk   94 (110)
T PRK04217         44 TYEEFEAL-RLVDYEGLTQEEAGKRMGVSRGTVWRALT--SARKKVAQMLVEGR   94 (110)
T ss_pred             CHHHHHHH-HHHHHCCCCHHHHHHHCCCCHHHHHHHHH--HHHHHHHHHHHCCC
T ss_conf             19999999-98736079899999884976999999999--99999999986797


No 21 
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Probab=93.85  E-value=0.12  Score=30.69  Aligned_cols=54  Identities=20%  Similarity=0.305  Sum_probs=46.3

Q ss_pred             CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             11234556665431022104899999998521011104679999743378778656
Q gi|254780805|r  118 NKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       118 d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      ++.+..-+.+|.+-|+|  |..-|.-++..+..+++.|.+++...|.+.|+++..|
T Consensus        96 EEaa~qra~Ve~ll~~d--~~~v~~~Ik~~m~~h~ipQ~~vv~~TGlnQS~lSq~L  149 (177)
T pfam04814        96 EEAAHQRAEVDRLLRED--PWRVAKMIKSYMQQHNIPQREVVDATGLNQSHLSQHL  149 (177)
T ss_pred             HHHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHH
T ss_conf             58888899999999728--4999999999998768846678761065599999999


No 22 
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=93.31  E-value=0.32  Score=27.87  Aligned_cols=28  Identities=18%  Similarity=0.261  Sum_probs=24.2

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |....|+|+.|||+++|.|.++|.++|.
T Consensus       138 L~r~eGls~~EIAe~LgiS~~tV~~~l~  165 (178)
T PRK12529        138 MATLDGMKQKDIAQALDIALPTVKKYIH  165 (178)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9988299999999998959999999999


No 23 
>pfam06250 DUF1016 Protein of unknown function (DUF1016). Family of uncharacterized proteins found in viruses, archaea and bacteria.
Probab=92.85  E-value=0.37  Score=27.43  Aligned_cols=66  Identities=18%  Similarity=0.231  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHHHHHHH---HHHHHHHHHHCCHHHHHHHHHCCHHHH---HHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             433787786565654358---999987642101677777640100468---99997422247789999997641
Q gi|254780805|r  163 GKSRSHVANILRILKLPS---SVREMIRKEEISLGHARTLVSTSDPLS---LAQVIVSKKMSVRDTEELVQEQD  230 (300)
Q Consensus       163 G~s~s~V~~~LrLl~L~~---~i~~~l~~~~is~ghar~Ll~~~~~~~---la~~Ii~~~LSVRe~E~lVk~~~  230 (300)
                      |.|++.+.++...-..=|   .++..+  +.||-+|.+.|..+++.++   .++..+.++||||..+.-++...
T Consensus        66 GFS~~NL~~MrqFy~~y~d~~i~q~~~--~qLsW~H~~iL~k~k~~~~R~fY~~~a~~~~WS~r~L~~qI~s~l  137 (320)
T pfam06250        66 GFSAKNLKRMRQFYLTFPDEEIVQALL--RELTWTHVRLLEKVKDELTRDFYIKETIKEGWSTRILERQIESML  137 (320)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHH--HHCCHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             999999999999999779603444688--755959999987179989999999999997969999999998778


No 24 
>pfam08857 ParBc_2 Putative ParB-like nuclease. This domain is probably distantly related to pfam02195. Suggesting these uncharacterized proteins have a nuclease function.
Probab=92.72  E-value=0.06  Score=32.52  Aligned_cols=75  Identities=13%  Similarity=0.286  Sum_probs=46.1

Q ss_pred             CEEEEHHHCCCCCCC--------CCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCC-C
Q ss_conf             024038982357899--------9876898899999998863100155046205654453335756777776421001-3
Q gi|254780805|r   39 QDCISIHSIVPNPHN--------PRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSE-V  109 (300)
Q Consensus        39 ~~~i~i~~i~~~p~~--------pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~-i  109 (300)
                      +.+|+|+.+.|--.-        -+..|-..+-+++.+-++.+++  |+++-  ++|.+-+++||++.+|.-.+|... +
T Consensus         2 l~~V~i~~LrPTQ~~vG~~eV~~K~~~~~~~~~~~~~~~l~~~~v--PvV~g--p~g~lyl~DhHH~~ral~e~~~~~~v   77 (162)
T pfam08857         2 LIEVPLDALRPTQITVGLREVEAKRKRWREDKKKKRLDFLRKHPV--PVVLG--PDGRLYLTDHHHLLRALLELGVGGTV   77 (162)
T ss_pred             CEEEEHHHCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCC--CEEEC--CCCCEEEECCHHHHHHHHHCCCCCEE
T ss_conf             416258972784075789999999999986189999999971998--78988--99986787760889999956998638


Q ss_pred             CCCC-CCCC
Q ss_conf             5433-3464
Q gi|254780805|r  110 PVII-RNVD  117 (300)
Q Consensus       110 p~iv-~~~~  117 (300)
                      ++.| .|++
T Consensus        78 ~v~v~~dls   86 (162)
T pfam08857        78 PVTVVADLS   86 (162)
T ss_pred             EEEEEEECC
T ss_conf             999976567


No 25 
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209   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 , .    The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage.   Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=92.68  E-value=0.091  Score=31.36  Aligned_cols=111  Identities=29%  Similarity=0.370  Sum_probs=56.4

Q ss_pred             CHHHHHHHHHHHHHCCCCCCCEEECCCCCC----C-------CCCCCHHHHHHHHHHHCCCCCCCCCC------------
Q ss_conf             988999999988631001550462056544----5-------33357567777764210013543334------------
Q gi|254780805|r   59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGL----Y-------KIIAGERRFRAAKMASLSEVPVIIRN------------  115 (300)
Q Consensus        59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~----y-------~ii~G~rR~rAa~~~g~~~ip~iv~~------------  115 (300)
                      ..+++++|. ||-..|++..|--...+.|.    |       ||++-   +||.|...   =.|...|            
T Consensus        71 ~G~~~dDLI-SIGTiGLIKAidsf~~~KGt~LATYAArCiENEILM~---lR~~KK~k---~eV~L~DPIG~DKEGNEIs  143 (228)
T TIGR02846        71 TGEDVDDLI-SIGTIGLIKAIDSFDPEKGTRLATYAARCIENEILMH---LRALKKTK---GEVSLQDPIGVDKEGNEIS  143 (228)
T ss_pred             CCCCCCCHH-CCCCHHEECCEECCCCCCCCHHHHHHHHHHHHHHHHH---HHHCCCCC---CCEEECCCCCCCCCCCEEE
T ss_conf             874100001-0022010001102247877315667866534789999---97436747---8332107888676764230


Q ss_pred             -----CCCHHHHHHHHHHHHHCC--------CCCHHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHHHHHH--HH
Q ss_conf             -----641123455666543102--------21048999999985210111------0467999974337877865--65
Q gi|254780805|r  116 -----VDNKSSLEIAIVENVQRK--------DLNPLEEALGYEQLISEYGY------TQNDIGSIVGKSRSHVANI--LR  174 (300)
Q Consensus       116 -----~~d~~~~~~~l~EN~~R~--------dl~p~e~A~~~~~l~~~~~~------t~~~lA~~~G~s~s~V~~~--Lr  174 (300)
                           .+|.|...-.+..+++-+        -|.+-|+..--    ..||+      ||.|||+.+|.|||+||+-  -+
T Consensus       144 L~DiL~~~~d~v~e~v~~~~~~~~l~~~~~~~L~~rE~~vi~----~RyGL~~~~~~tQREIA~~LgISRSYVSRIEK~A  219 (228)
T TIGR02846       144 LIDILGSDEDSVIEQVEKKLEIKKLYKKLNSVLKGREREVIE----MRYGLKDGREKTQREIAKILGISRSYVSRIEKKA  219 (228)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             000016887316888886445999999999874088899998----7436688895417899877086500454888999


Q ss_pred             HHHHHH
Q ss_conf             654358
Q gi|254780805|r  175 ILKLPS  180 (300)
Q Consensus       175 Ll~L~~  180 (300)
                      |.+|..
T Consensus       220 l~Kl~~  225 (228)
T TIGR02846       220 LKKLYK  225 (228)
T ss_pred             HHHHHH
T ss_conf             999986


No 26 
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=92.60  E-value=0.69  Score=25.68  Aligned_cols=28  Identities=25%  Similarity=0.294  Sum_probs=23.9

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |....|+|+.|||+.+|.|.++|.++|.
T Consensus       129 L~~~eGlsy~EIAe~LgIS~~tV~~~l~  156 (168)
T PRK12525        129 MSQLEGLTYVEIGERLGVSLSRIHQYMV  156 (168)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999299999999998979999999999


No 27 
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=92.50  E-value=0.48  Score=26.73  Aligned_cols=52  Identities=29%  Similarity=0.359  Sum_probs=32.6

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HH-HHH-------------HHHHHHHHHHHCCHHHH
Q ss_conf             9985210111046799997433787786565-65-435-------------89999876421016777
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANILR-IL-KLP-------------SSVREMIRKEEISLGHA  196 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr-Ll-~L~-------------~~i~~~l~~~~is~gha  196 (300)
                      +..++...| +..++|+.+|.|..||.++|. +. +|-             .+|+++|..|+||+-.|
T Consensus        42 i~~fi~~~G-nlke~~~~lgiSYpTvR~rLd~ii~~lGy~~~~~~~~~~~~~eIL~~Le~GEIs~eEA  108 (113)
T pfam09862        42 VELFIKCRG-NIKEVEKELGISYPTVRNRLDEIIAALGYEEEPEPEKRVDKKEILDKLEKGEISVEEA  108 (113)
T ss_pred             HHHHHHHCC-CHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHH
T ss_conf             999999168-8999999978881889999999999808987777777622999999998499799999


No 28 
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=92.40  E-value=0.18  Score=29.51  Aligned_cols=38  Identities=18%  Similarity=0.397  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             10489999999852101110467999974337877865
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      -+|-..|.+++......|+||.++|+++|..+++||+.
T Consensus         8 ~sp~qLa~~Lr~~Rk~~gLsQ~~lA~~vGi~Q~TiS~~   45 (88)
T PRK09726          8 YSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNF   45 (88)
T ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             89999999999999985987999999819749999999


No 29 
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=92.09  E-value=0.74  Score=25.48  Aligned_cols=56  Identities=23%  Similarity=0.341  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHC
Q ss_conf             21048999999985210111046799997433787786565-65435899998764210
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR-ILKLPSSVREMIRKEEI  191 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr-Ll~L~~~i~~~l~~~~i  191 (300)
                      .|+|-++..-.-+..  .|+|.++||+.+|.|.++|..+|. -.+--...++.+..|+|
T Consensus       128 ~L~~~~r~v~~l~~~--~~~s~~EIA~~l~is~~tVk~rl~Rar~~Lr~~L~~~~~~e~  184 (185)
T PRK06811        128 DLKKLDREIFIKRYL--LGESIEEIAKKLGLTRSAIDNRLSRGRKKLKNKLNILKKGEV  184 (185)
T ss_pred             CCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             899999999999999--499999999998929999999999999999999889866788


No 30 
>pfam11300 DUF3102 Protein of unknown function (DUF3102). This family of proteins has no known function.
Probab=92.03  E-value=0.5  Score=26.57  Aligned_cols=93  Identities=16%  Similarity=0.144  Sum_probs=56.6

Q ss_pred             CHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHH-HHHHHHHCCHHHHHHHHHCCH
Q ss_conf             048999999985210--111046799997433787786565654--------358999-987642101677777640100
Q gi|254780805|r  136 NPLEEALGYEQLISE--YGYTQNDIGSIVGKSRSHVANILRILK--------LPSSVR-EMIRKEEISLGHARTLVSTSD  204 (300)
Q Consensus       136 ~p~e~A~~~~~l~~~--~~~t~~~lA~~~G~s~s~V~~~LrLl~--------L~~~i~-~~l~~~~is~ghar~Ll~~~~  204 (300)
                      |.+|....+....+.  +|.=..=+-+.+++|+++-.|+|++..        +|++.- ..=.-+.++..+|-.|+++|+
T Consensus        24 ~aIEIGrrL~~~Ke~l~HGef~~WLke~v~~S~rtA~~~M~v~~eyG~~~~~~~~~~~~n~~~l~~L~ytqal~Ll~~Pe  103 (130)
T pfam11300        24 SAIEIGRRLKEAKALLPHGEWGKWLKESVSYSRRTAANLMRLYEEYGSKLASPSDDDSSNSQPLGNLTYTQALILLGVPE  103 (130)
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCH
T ss_conf             99999999999998588662999999992826999999999999975012589865432453243121999999927987


Q ss_pred             H--HHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             4--68999974222477899999976
Q gi|254780805|r  205 P--LSLAQVIVSKKMSVRDTEELVQE  228 (300)
Q Consensus       205 ~--~~la~~Ii~~~LSVRe~E~lVk~  228 (300)
                      .  +++....=-+++|+|++.+.|+.
T Consensus       104 eeR~efi~e~dve~Ms~RELqqavkE  129 (130)
T pfam11300       104 EEREQFIAENDVESMSTRELQQAVKE  129 (130)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHC
T ss_conf             89999999724101139999999864


No 31 
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=91.92  E-value=0.18  Score=29.42  Aligned_cols=33  Identities=18%  Similarity=0.216  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             999999852101110467999974337877865
Q gi|254780805|r  140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      -...++......|+||.++|+..|.|++||+..
T Consensus         3 lG~~Ir~~Rk~~glTQ~~LA~~aGvs~~~Is~i   35 (58)
T TIGR03070         3 IGALVRARRKALGLTQADLADLAGVGLRFIRDI   35 (58)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             889999999994998999998819989999999


No 32 
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=91.74  E-value=0.18  Score=29.39  Aligned_cols=39  Identities=15%  Similarity=0.105  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999998521011104679999743378778656565435
Q gi|254780805|r  141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLP  179 (300)
Q Consensus       141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~  179 (300)
                      +.-++.+..+.|+||.++|+++|.|+++|+++-+=...|
T Consensus         7 G~Ri~~~R~~~glTQ~eLA~~~Gvs~~tVs~wE~g~~~P   45 (135)
T PRK09706          7 GQRIRYRRKQLKLSQRALAKAVGVSHVSISQWERDETEP   45 (135)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCC
T ss_conf             999999999859999999999698899999998289888


No 33 
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=91.70  E-value=0.15  Score=29.90  Aligned_cols=33  Identities=30%  Similarity=0.371  Sum_probs=27.4

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             998521011104679999743378778656565
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      ++.+....|+||.++|+.+|.|+++|+++.+=-
T Consensus         2 lr~~R~~~glsq~~lA~~~gis~~~is~~E~g~   34 (56)
T smart00530        2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGK   34 (56)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC
T ss_conf             899997729999999999895999999999799


No 34 
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=91.48  E-value=0.89  Score=24.99  Aligned_cols=28  Identities=25%  Similarity=0.274  Sum_probs=24.1

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |....|+|+.|||+.+|.|.++|.++|.
T Consensus       130 L~r~~gls~~EIA~~LgiS~~tVk~~l~  157 (167)
T PRK12528        130 LAQVDGLGYGEIATELGISLATVKRYLN  157 (167)
T ss_pred             HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9998298999999997979999999999


No 35 
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=91.30  E-value=0.81  Score=25.23  Aligned_cols=39  Identities=23%  Similarity=0.161  Sum_probs=27.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|.|-.+..-.  |....|+|+.|||+.+|.|.++|.++|.
T Consensus       119 ~Lp~~~R~v~~--L~~~eGls~~EIA~~LgiS~~tVk~~l~  157 (172)
T PRK12523        119 KLSSKARAAFL--YNRLDGMGHAEIAERLGVSVSRVRQYLA  157 (172)
T ss_pred             CCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             49999999999--9999399999999998939999999999


No 36 
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=91.17  E-value=0.33  Score=27.77  Aligned_cols=24  Identities=38%  Similarity=0.564  Sum_probs=14.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             110467999974337877865656
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      |+||.|||+++|.||.+|+++|..
T Consensus        26 gltQ~eIA~~LgiSR~~v~rlL~~   49 (321)
T COG2390          26 GLTQSEIAERLGISRATVSRLLAK   49 (321)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             887999998839889999999999


No 37 
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=90.64  E-value=0.17  Score=29.59  Aligned_cols=33  Identities=27%  Similarity=0.427  Sum_probs=26.8

Q ss_pred             HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             985210111046799997433787786565654
Q gi|254780805|r  145 EQLISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       145 ~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +++....|+||.++|+.+|.|+++|+++-+=..
T Consensus         2 r~~R~~~g~tq~~lA~~~gis~~~is~~E~g~~   34 (55)
T pfam01381         2 KELREELGLSQEELAEKLGVSRSTISKIENGKR   34 (55)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
T ss_conf             898978299899999998969999999987999


No 38 
>pfam03235 DUF262 Protein of unknown function DUF262.
Probab=90.34  E-value=0.6  Score=26.09  Aligned_cols=54  Identities=17%  Similarity=0.286  Sum_probs=41.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             899987689889999999886310015504620565445333575677777642
Q gi|254780805|r   51 PHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMA  104 (300)
Q Consensus        51 p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~  104 (300)
                      .+|=.-.-+++....|.+||...=-+-++++...+++.|+||+|..|+.+....
T Consensus        15 ~yQR~y~W~~~~~~~li~di~~~~~ig~i~l~~~~~~~~~viDGQQRltTl~~~   68 (99)
T pfam03235        15 DYQRLYVWRKKEVSRLIEDLLYGYPIGSIVLAEKSDGKYEIIDGQQRLTTLKLF   68 (99)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCCEEEEECCHHHHHHHHHH
T ss_conf             877757138899999999998192452699997799859997680899999999


No 39 
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=90.18  E-value=0.22  Score=28.87  Aligned_cols=29  Identities=31%  Similarity=0.539  Sum_probs=24.5

Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99985210111046799997433787786
Q gi|254780805|r  143 GYEQLISEYGYTQNDIGSIVGKSRSHVAN  171 (300)
Q Consensus       143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~  171 (300)
                      -++.+..++|+||+++|+.+|.||-+|..
T Consensus         5 k~k~~R~~~~ltQ~elA~~vgVsRQTi~~   33 (68)
T COG1476           5 KLKELRAELGLTQEELAKLVGVSRQTIIA   33 (68)
T ss_pred             HHHHHHHHHCCCHHHHHHHCCCCHHHHHH
T ss_conf             99999998285899999991957999999


No 40 
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=89.86  E-value=1.4  Score=23.73  Aligned_cols=53  Identities=15%  Similarity=0.164  Sum_probs=33.3

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHH
Q ss_conf             221048999999985210111046799997433787786565--6543589999876
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR--ILKLPSSVREMIR  187 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~~i~~~l~  187 (300)
                      +.|+|-+.. .+. |.--.|+|..+||+.+|.|.++|.+++.  +-+|=..++++|.
T Consensus       136 ~~L~~~~r~-v~~-l~~~~~~s~~EIA~~lgis~~tVk~~l~Ra~~~Lr~~L~~~~~  190 (192)
T PRK09652        136 ESLPEELRT-AIT-LREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQPLLD  190 (192)
T ss_pred             HHCCHHHHH-HHH-HHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             839999998-888-9997299999999998939999999999999999999898771


No 41 
>pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
Probab=89.38  E-value=0.48  Score=26.74  Aligned_cols=39  Identities=31%  Similarity=0.375  Sum_probs=28.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-+...-.-+..  .++|+.|+|+.+|.|+++|++.++
T Consensus         4 ~L~~~~r~ii~l~y~--~~~t~~EIA~~lgis~~~V~~~~~   42 (50)
T pfam04545         4 SLPPREREVLVLRFG--EGLTLEEIGERLGISRERVRQIEK   42 (50)
T ss_pred             HCCHHHHHHHHHHCC--CCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf             689999999998706--882499999998979999999999


No 42 
>pfam12116 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.
Probab=88.97  E-value=1.1  Score=24.51  Aligned_cols=44  Identities=25%  Similarity=0.300  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHH
Q ss_conf             99999998521011104679999743378778656--565435899
Q gi|254780805|r  139 EEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL--RILKLPSSV  182 (300)
Q Consensus       139 e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L--rLl~L~~~i  182 (300)
                      |.+.-+...+-+.+-|..+.|+.||.|+|+|.+-+  ||..+.|.+
T Consensus         6 eR~~~i~~YIi~~~aTVR~tAk~FGvSKSTVHkDvTeRL~~inp~L   51 (82)
T pfam12116         6 ERVLEIANYIIENKATVRQAAKVFGVSKSTVHKDVTERLPKINPQL   51 (82)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHH
T ss_conf             9999999999962628999999969609889887999998739999


No 43 
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=88.94  E-value=0.34  Score=27.66  Aligned_cols=29  Identities=21%  Similarity=0.319  Sum_probs=25.4

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99852101110467999974337877865
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      +.||.++.|+|+.++|++-|.|.++++..
T Consensus        10 v~RLr~ErGmT~~eLAe~AGIS~s~LSqI   38 (119)
T PRK13890         10 VLRLLDERHMTKKELSDRSGVSISFLSDL   38 (119)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             99999985997999998829889999999


No 44 
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.90  E-value=0.55  Score=26.34  Aligned_cols=38  Identities=29%  Similarity=0.413  Sum_probs=29.3

Q ss_pred             CCHHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             10489999999852-1011104679999743378778656
Q gi|254780805|r  135 LNPLEEALGYEQLI-SEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       135 l~p~e~A~~~~~l~-~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      |+..| ...|+.|+ .....|.++||+.+++|+|+|++.|
T Consensus        25 Ls~~D-v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl   63 (126)
T COG3355          25 LSELD-VEVYKALLEENGPLTVDELAEILNRSRSTVYRSL   63 (126)
T ss_pred             CCHHH-HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             96889-9999999864699579999999783199999999


No 45 
>pfam07638 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.
Probab=88.56  E-value=1  Score=24.62  Aligned_cols=39  Identities=18%  Similarity=0.133  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4899999998521011104679999743378778656565
Q gi|254780805|r  137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      |-++-..+ .|....|+|..|||+.+|.|.+||.++|...
T Consensus       137 pp~~r~v~-~L~~~eglS~~EIAe~Lgis~~TVk~rl~~A  175 (185)
T pfam07638       137 SPRQARLV-ELRFFAGLSNDEIAERLGVSERTVERNWALA  175 (185)
T ss_pred             CHHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             99888898-8899759999999999796998999999999


No 46 
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=88.52  E-value=0.84  Score=25.14  Aligned_cols=39  Identities=21%  Similarity=0.349  Sum_probs=32.8

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             22104899999998521011104679999743378778656
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      +.|+|-|.|.-+  |.+.||++.+|||+.+|+|.+.+...+
T Consensus       117 e~L~P~eRaa~v--Lrdvfg~~~~EIA~~Lg~s~~a~Rqll  155 (290)
T PRK09635        117 ERLGPAERVVFV--LHEIFGLPYQQIATTIGSQASTCRQLA  155 (290)
T ss_pred             HCCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             629986854552--698608988999999689989999999


No 47 
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=88.16  E-value=2.1  Score=22.61  Aligned_cols=57  Identities=16%  Similarity=0.159  Sum_probs=33.8

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHCCH
Q ss_conf             1048999999985210111046799997433787786565--6543589999876421016
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR--ILKLPSSVREMIRKEEISL  193 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~~i~~~l~~~~is~  193 (300)
                      |.|-+.. ++ .|..-.|+|.+|||+.+|.|..+|..+|.  +.+|=..+..+-..|.-+.
T Consensus       132 Lp~~~R~-vl-~L~~~eg~s~~EIA~~lgis~~tVKsrl~RAr~~Lr~~L~~l~~~g~~~~  190 (197)
T PRK09643        132 LPVEQRA-AL-VAVDMQGYSVADTARMLGVAEGTVKSRCARGRARLAELLGYLRAGGNASP  190 (197)
T ss_pred             CCHHHHH-HH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             9998879-99-99998199999999998939999999999999999999998845789999


No 48 
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.
Probab=87.92  E-value=0.54  Score=26.39  Aligned_cols=41  Identities=20%  Similarity=0.434  Sum_probs=32.9

Q ss_pred             HHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99985210111-046799997433787786565654358999
Q gi|254780805|r  143 GYEQLISEYGY-TQNDIGSIVGKSRSHVANILRILKLPSSVR  183 (300)
Q Consensus       143 ~~~~l~~~~~~-t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~  183 (300)
                      .+.|+++.+|. |+.|+|+.+|.++++|++..+=...|.+..
T Consensus         2 vi~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R~~~P~e~i   43 (65)
T pfam07022         2 VIERLMKAYGFKSRSELADHLGVSKSTLSTWYKRDSFPAEWV   43 (65)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCHHHH
T ss_conf             899999996888699999996988888999998699989999


No 49 
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284   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 is found in all varieties of the sigma-70 type sigma factors, including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (IPR000394 from INTERPRO) are included within this entry. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=87.47  E-value=0.84  Score=25.14  Aligned_cols=39  Identities=23%  Similarity=0.307  Sum_probs=28.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-++..-.-+..  .|+|+.|||+.+|.|.++|.+++.
T Consensus       114 ~Lp~~~r~~~~l~~~--~~~s~~eIA~~lg~s~~~v~~~~~  152 (162)
T TIGR02937       114 KLPEREREVLVLRYL--EGLSYKEIAEILGISEGTVKSRLK  152 (162)
T ss_pred             HCCHHHHHHHHHHHH--HCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             479989999999997--189988999986899999999999


No 50 
>PRK06930 positive control sigma-like factor; Validated
Probab=87.44  E-value=0.94  Score=24.84  Aligned_cols=38  Identities=18%  Similarity=0.364  Sum_probs=28.7

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |+|-|....+  |....|+|+.++|+.+|.|.++|.+++.
T Consensus       115 Lt~rErevfl--l~~~~glsy~EIA~~L~Is~~tV~~~l~  152 (170)
T PRK06930        115 LTEREKEVYL--MHRGYGLSYSEIAAYLNIKKSTVQSMIE  152 (170)
T ss_pred             CCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             6988889998--8976188899999997988999999999


No 51 
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=87.27  E-value=2.4  Score=22.23  Aligned_cols=28  Identities=29%  Similarity=0.273  Sum_probs=23.6

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |....|+|..|||+.+|.|.++|.++|.
T Consensus       130 L~~~egls~~EIA~~lgiS~~tVk~~l~  157 (172)
T PRK09651        130 LSQLDGLTYSEIAHKLGVSISSVKKYVA  157 (172)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9988399999999998939999999999


No 52 
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163   Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity..
Probab=87.20  E-value=0.9  Score=24.96  Aligned_cols=38  Identities=32%  Similarity=0.323  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999998521011-1046799997433787786565654
Q gi|254780805|r  140 EALGYEQLISEYG-YTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       140 ~A~~~~~l~~~~~-~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +-.-+..|.+.+| .+.+.||+.+|+|++|++|+++-|+
T Consensus       171 ~~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~~~~Le  209 (231)
T TIGR01884       171 ELKVLEALKAEKGEKSVKNIAKKLGKSLSTISRHLAELE  209 (231)
T ss_pred             HHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             999999985078805287799885788879999999887


No 53 
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=87.20  E-value=0.57  Score=26.24  Aligned_cols=31  Identities=26%  Similarity=0.336  Sum_probs=25.9

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9999852101110467999974337877865
Q gi|254780805|r  142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      +-+++...+.|+||+++|++.|.|+++|++.
T Consensus         8 edlrk~Rk~LGitQ~dLA~~aGVSQ~~IArl   38 (187)
T COG3620           8 EDLRKRRKELGITQKDLARRAGVSQPYIARL   38 (187)
T ss_pred             HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHH
T ss_conf             9999999875977899998708648889998


No 54 
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=86.95  E-value=0.75  Score=25.45  Aligned_cols=33  Identities=33%  Similarity=0.361  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999985210111046799997433787786565
Q gi|254780805|r  141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ..-..+|++. |.+..++|+.+|.|++||.+++.
T Consensus        11 ~~~v~~L~~~-G~~i~~IA~~~~vsrsTvYRyl~   43 (45)
T pfam02796        11 INEVITLLEE-GISIKQIAKIFGISRSTVYRYLA   43 (45)
T ss_pred             HHHHHHHHHC-CCCHHHHHHHHCCHHHHHHHHCC
T ss_conf             9999999987-99499999998600888876445


No 55 
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=86.79  E-value=0.92  Score=24.88  Aligned_cols=33  Identities=21%  Similarity=0.355  Sum_probs=25.1

Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9998521011104679999743378778656565
Q gi|254780805|r  143 GYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      .+..+... |.|..++|+.+|.|++||.++++-.
T Consensus       164 ~i~~~~~~-g~s~~~iak~~gvsrsTvyR~lK~~  196 (200)
T PRK13413        164 VITKELKK-GTTKSEIAKKLKVSRTTLARFLKTM  196 (200)
T ss_pred             HHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             99999988-8999999999892999999999744


No 56 
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=86.79  E-value=0.82  Score=25.23  Aligned_cols=35  Identities=14%  Similarity=0.262  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999985210111046799997433787786565
Q gi|254780805|r  140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ...-+++|..+.|+|++++|++.|.|++++++.=+
T Consensus         8 iG~rIr~lR~~~glTL~eLA~~sGvS~s~LSqIEr   42 (185)
T PRK09943          8 PGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQ   42 (185)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf             88999999998599899999887969999999987


No 57 
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=86.78  E-value=0.56  Score=26.27  Aligned_cols=34  Identities=29%  Similarity=0.362  Sum_probs=28.6

Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9998521011104679999743378778656565
Q gi|254780805|r  143 GYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      .++.+.+..|+|+.++|+.+|.++++++++..=-
T Consensus         3 ~l~~~r~~~~ls~~~lA~~~gis~~~l~~~e~g~   36 (58)
T cd00093           3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGK   36 (58)
T ss_pred             HHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCC
T ss_conf             9999999759999999571499999999998799


No 58 
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=86.72  E-value=1.3  Score=23.85  Aligned_cols=19  Identities=21%  Similarity=0.316  Sum_probs=9.4

Q ss_pred             HHHHHHHCCC--CHHHHHHHH
Q ss_conf             9999742224--778999999
Q gi|254780805|r  208 LAQVIVSKKM--SVRDTEELV  226 (300)
Q Consensus       208 la~~Ii~~~L--SVRe~E~lV  226 (300)
                      +....-..+|  +|||..+.+
T Consensus       405 ~~~~L~~y~WpGNVRqL~N~i  425 (511)
T COG3283         405 LLTVLTRYAWPGNVRQLKNAI  425 (511)
T ss_pred             HHHHHHHCCCCCCHHHHHHHH
T ss_conf             999998779996099999999


No 59 
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=86.69  E-value=2.1  Score=22.57  Aligned_cols=54  Identities=15%  Similarity=0.237  Sum_probs=36.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             21048999999985210111046799997433787786565654358999987642101
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS  192 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is  192 (300)
                      -|++.+...-.- .+  -|+|.+|||+.+|.|.++|.+++  -.+=..++..|..++++
T Consensus       155 ~l~~~e~~V~~~-~~--eg~s~~EIA~~l~is~~tV~~~l--~RarkkLr~~L~~~~~~  208 (209)
T PRK08295        155 LLSDLEKEVLEL-YL--DGKSYQEIAEELNRHVKSIDNAL--QRVKRKLEKYLEIREVT  208 (209)
T ss_pred             CCCHHHHHHHHH-HH--CCCCHHHHHHHHCCCHHHHHHHH--HHHHHHHHHHHHHCCCC
T ss_conf             691899999999-98--69999999999892999999999--99999999998744056


No 60 
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=86.31  E-value=2.1  Score=22.57  Aligned_cols=58  Identities=17%  Similarity=0.255  Sum_probs=37.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             22104899999998521011104679999743378778656565435899998764210167
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLG  194 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~g  194 (300)
                      ..|+|-++..-+-+..+  |+|.+|||+.+|.|.++|.++|.  ..=..+++.+....|..|
T Consensus       130 ~~L~~~~R~vi~l~~~e--~~s~~EIA~~lgis~~tV~~~l~--RAr~~Lr~~L~~~g~~~g  187 (189)
T PRK12515        130 AKLSPAHREIIDLVYYH--EKSVEEVGEIVGIPESTVKTRMF--YARKKLAELLKAAGVERG  187 (189)
T ss_pred             HCCCHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHCCCCC
T ss_conf             75999999999999984--99999999998929999999999--999999999997283358


No 61 
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=86.18  E-value=1.7  Score=23.20  Aligned_cols=28  Identities=29%  Similarity=0.310  Sum_probs=23.1

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |....|+|.+|||+.+|.|.++|.++|.
T Consensus       116 L~~~egls~~EIA~~lgis~~tVk~~l~  143 (159)
T PRK12527        116 LRKLEGLSHQQIAEHLGISRSLVEKHIV  143 (159)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             8987397999999998919999999999


No 62 
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517   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 a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=86.16  E-value=1.7  Score=23.25  Aligned_cols=87  Identities=20%  Similarity=0.147  Sum_probs=46.6

Q ss_pred             CCCCCHHHHHHHHHHHC-CCCCCCCCC--CCCHHHHHHHHHHH-HHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             33357567777764210-013543334--64112345566654-310221048999999985210111046799997433
Q gi|254780805|r   90 KIIAGERRFRAAKMASL-SEVPVIIRN--VDNKSSLEIAIVEN-VQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKS  165 (300)
Q Consensus        90 ~ii~G~rR~rAa~~~g~-~~ip~iv~~--~~d~~~~~~~l~EN-~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s  165 (300)
                      ++|+=-|+.+|.|.-|- ..+|-.-.+  .+.+....+...|- +.+=.-..=+.|..++ |.--.|+|.+|+|+.+|.|
T Consensus        96 IL~D~AR~~~~~KRGg~~~~~~l~~~~~~~~~~~~~~L~~Ld~aL~~L~~~~Pr~a~~ve-Lr~F~Gl~~~E~A~~L~~S  174 (194)
T TIGR02999        96 ILVDHARRRRAQKRGGGAVRVSLDEVLPDAEADADEELLDLDDALDKLAQVDPRQAEVVE-LRFFAGLTVEEIAELLGVS  174 (194)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHH-HHHHCCCCHHHHHHHHCCC
T ss_conf             999999999874136776335520000135777403599999999877400678899885-3110488989999986888


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             787786565654
Q gi|254780805|r  166 RSHVANILRILK  177 (300)
Q Consensus       166 ~s~V~~~LrLl~  177 (300)
                      .+||.|-++...
T Consensus       175 ~~Tv~Rdw~~AR  186 (194)
T TIGR02999       175 VRTVERDWRFAR  186 (194)
T ss_pred             HHHHHHHHHHHH
T ss_conf             878998799999


No 63 
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=86.14  E-value=1.9  Score=22.87  Aligned_cols=36  Identities=25%  Similarity=0.419  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Q ss_conf             111046799997433787786565--654358999987
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR--ILKLPSSVREMI  186 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~~i~~~l  186 (300)
                      .|+|.+|||+.+|.|.++|.+++.  +..|=..+++.+
T Consensus       156 eg~s~~EIA~~lgis~~tVk~rl~rA~~~Lr~~L~e~l  193 (194)
T PRK12519        156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDLL  193 (194)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             19999999999894999999999999999999989873


No 64 
>COG2512 Predicted membrane-associated trancriptional regulator    [Transcription]
Probab=85.96  E-value=0.96  Score=24.78  Aligned_cols=41  Identities=32%  Similarity=0.360  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             22104899999998521011-1046799997433787786565
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYG-YTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~-~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .+|+.-| -..+.-+.+..| .+|.+|.+.+|.|+++|++.|+
T Consensus       191 ~~L~~~e-~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~  232 (258)
T COG2512         191 YDLNEDE-KEILDLIRERGGRITQAELRRALGLSKTTVSRILR  232 (258)
T ss_pred             CCCCHHH-HHHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHHH
T ss_conf             7899789-99999999858978699988860997677999999


No 65 
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178   Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=85.89  E-value=0.32  Score=27.85  Aligned_cols=56  Identities=14%  Similarity=0.408  Sum_probs=37.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH-----------------HHHHCCHHHHHHHHHHHCC
Q ss_conf             04679999743378778656565435899998764210167777-----------------7640100468999974222
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHAR-----------------TLVSTSDPLSLAQVIVSKK  216 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar-----------------~Ll~~~~~~~la~~Ii~~~  216 (300)
                      .-.|||+.+|..|+|.+         +-+|.+-+||=||.-|++                 +|+.|+.+.  +-.++++-
T Consensus        32 AERELsElIGVTRTTLR---------EVLQRLARDGWLTIQHGKPTKVNnfWETSGLNILeTL~~LD~~~--~P~l~dnL  100 (275)
T TIGR02812        32 AERELSELIGVTRTTLR---------EVLQRLARDGWLTIQHGKPTKVNNFWETSGLNILETLIRLDGES--VPSLIDNL  100 (275)
T ss_pred             HHHHHHHHCCCCCCHHH---------HHHHHHHHHCCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHCCCC--CCHHHHHH
T ss_conf             46657542376630378---------99988764113436588998627624302735789998618777--70799999


Q ss_pred             CCHH
Q ss_conf             4778
Q gi|254780805|r  217 MSVR  220 (300)
Q Consensus       217 LSVR  220 (300)
                      ||+|
T Consensus       101 LSAR  104 (275)
T TIGR02812       101 LSAR  104 (275)
T ss_pred             HHHH
T ss_conf             9776


No 66 
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA.  Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=84.86  E-value=1.4  Score=23.69  Aligned_cols=39  Identities=28%  Similarity=0.302  Sum_probs=27.7

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-+...-.-+..  .|+|..|||+.+|.|.++|..++.
T Consensus        10 ~L~~~~r~vl~l~y~--~~~s~~EIa~~lgis~~tVk~~l~   48 (55)
T cd06171          10 KLPEREREVILLRFG--EGLSYEEIAEILGISRSTVRQRLH   48 (55)
T ss_pred             CCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             399999898999998--099999999998959999999999


No 67 
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=84.84  E-value=1.3  Score=23.83  Aligned_cols=35  Identities=34%  Similarity=0.350  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999985210111046799997433787786565
Q gi|254780805|r  140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ++..|..|+.....|..+||+.+|.+|++|.+.|.
T Consensus        10 E~~vY~~Ll~~g~~t~~eia~~~~i~r~~vY~~L~   44 (68)
T pfam01978        10 EAKVYLALLKLGPATADEIAEESGVPRSKVYEVLR   44 (68)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999981998899999995988989999999


No 68 
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=84.77  E-value=1.4  Score=23.74  Aligned_cols=21  Identities=10%  Similarity=0.132  Sum_probs=11.4

Q ss_pred             HHHHHCCC--CHHHHHHHHHHHH
Q ss_conf             99742224--7789999997641
Q gi|254780805|r  210 QVIVSKKM--SVRDTEELVQEQD  230 (300)
Q Consensus       210 ~~Ii~~~L--SVRe~E~lVk~~~  230 (300)
                      +......|  +|||.++.+....
T Consensus       529 ~~L~~y~WPGNvrEL~nvl~~a~  551 (639)
T PRK11388        529 ARLVSYRWPGNDFELRSVIENLA  551 (639)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             99972899979999999999999


No 69 
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335   The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.   This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent.
Probab=84.69  E-value=2.1  Score=22.59  Aligned_cols=57  Identities=19%  Similarity=0.257  Sum_probs=42.3

Q ss_pred             HHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Q ss_conf             31022104899999998521011104679999743378778656565-4358999987642
Q gi|254780805|r  130 VQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL-KLPSSVREMIRKE  189 (300)
Q Consensus       130 ~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l~~~  189 (300)
                      -.|+|  ...+..-+..|++. ..||.||+..+|.|-++|++==.-+ .+||++++.+...
T Consensus        37 ~Er~d--l~~R~~I~~~LL~~-~~~QREi~~~lG~SiA~ITRGSn~Lk~~D~~~~~fL~~~   94 (95)
T TIGR01321        37 DERED--LGSRVRIVEELLEG-EMSQREIAEKLGVSIATITRGSNALKALDPEFKQFLKKK   94 (95)
T ss_pred             HHHHH--HHHHHHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             37999--98799999999614-897478888637616678787887516987889998842


No 70 
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=84.67  E-value=2.5  Score=22.16  Aligned_cols=50  Identities=12%  Similarity=0.127  Sum_probs=30.4

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             210489999999852101110467999974337877865656543589999876
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIR  187 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~  187 (300)
                      .|+|-......  |..-.|+|.+|||+.+|.|.++|..+|.  ..-..+++.+.
T Consensus       108 ~Lp~~~r~v~~--L~~~~~~s~~EIA~~l~is~~tVk~rl~--RAr~~Lr~~L~  157 (165)
T PRK09644        108 TLPVIEAQAIL--LCDVHELTYEEAASVLDLKENTYKSHLF--RGRKRLKALLK  157 (165)
T ss_pred             CCCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHH
T ss_conf             29999999999--9999888999999998939999999999--99999999999


No 71 
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=84.52  E-value=0.98  Score=24.72  Aligned_cols=31  Identities=39%  Similarity=0.615  Sum_probs=25.9

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99998521011104679999743378778656
Q gi|254780805|r  142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .+++.+++.||+|+.++|..+| |+|.|||.|
T Consensus        63 e~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL   93 (120)
T COG5499          63 EVIRTLMDQYGLTLADLANEIG-SKSRVSNIL   93 (120)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHC-CHHHHHHHH
T ss_conf             9999999993871888899867-618899997


No 72 
>PRK04140 hypothetical protein; Provisional
Probab=83.96  E-value=1.9  Score=22.86  Aligned_cols=114  Identities=15%  Similarity=0.138  Sum_probs=64.2

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH------
Q ss_conf             89889999999886310015504620565445333575677777642100135433346411234556665431------
Q gi|254780805|r   58 FESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIVENVQ------  131 (300)
Q Consensus        58 ~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~~------  131 (300)
                      ++++...+|. -|..+-.-.|++|-....+ .++=.|-=       --..-|||+    +. +.+...++++..      
T Consensus        52 ~s~e~~~dLk-~la~~~~a~piiVg~r~r~-~~Le~gVV-------Y~R~gI~~v----s~-~T~~d~lv~g~~P~iya~  117 (319)
T PRK04140         52 LSEEQAEELK-KLAKYLKASPIIIGLRTRN-GELEDGVV-------YERHGIPAL----SP-ETFYDYFVEGEPPLIYAA  117 (319)
T ss_pred             CCHHHHHHHH-HHHHHHCCCCEEEEEECCC-CCCCCCCE-------EEECCCEEE----CH-HHHHHHHHCCCCCEEEEC
T ss_conf             7988999999-9999858862799971488-74667617-------986693462----69-999999836899569965


Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Q ss_conf             0221048999999985210111046799997433787786565-65435899998
Q gi|254780805|r  132 RKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR-ILKLPSSVREM  185 (300)
Q Consensus       132 R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr-Ll~L~~~i~~~  185 (300)
                      |-.+..-=.+.-++++.++.|||..+||..+|.||.+|++|=+ -...+-++-..
T Consensus       118 ~GG~yV~Idg~~Lr~~Re~~g~SlG~LA~~LGVSRrtv~~YE~g~~~~sievA~k  172 (319)
T PRK04140        118 RGGFYVNIDGDLLRELREKLGLSLGELASELGVSRRTISKYENGGMNASIEVAIK  172 (319)
T ss_pred             CCCEEEEECHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHH
T ss_conf             8847999847999999998198888999984986999999970688664999999


No 73 
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=83.88  E-value=2  Score=22.79  Aligned_cols=39  Identities=28%  Similarity=0.451  Sum_probs=31.8

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             22104899999998521011104679999743378778656
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      +.|+|-+.|.-.  |.+.+|++.+|||+.+|+|.++|...|
T Consensus       110 ~~L~p~qRav~v--Lrdv~g~s~~EIA~iLg~s~~avR~~l  148 (289)
T PRK09636        110 ERLSPLERAAFL--LHDVFGVPFDEIASTLGRSEAACRQLA  148 (289)
T ss_pred             HHCCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             739998962540--498609999999999817999999999


No 74 
>PHA00542 putative Cro-like protein
Probab=83.65  E-value=1.2  Score=24.08  Aligned_cols=36  Identities=25%  Similarity=0.312  Sum_probs=27.9

Q ss_pred             CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0489999999852101110467999974337877865656
Q gi|254780805|r  136 NPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       136 ~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      +|.|.-   +.|++ .||||++|+...|.+++.|++.|.=
T Consensus        19 ~P~E~V---~aLi~-~G~tQ~qI~~~tgv~QpsisRilsG   54 (82)
T PHA00542         19 RPDELV---CALIR-AGWSQEQIADATDVSQPTICRIYSG   54 (82)
T ss_pred             CHHHHH---HHHHH-CCCCHHHHHHHHCCCCHHHHHHHCC
T ss_conf             989999---99998-2256999998608770368999808


No 75 
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430    Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=83.39  E-value=0.82  Score=25.20  Aligned_cols=28  Identities=21%  Similarity=0.476  Sum_probs=24.2

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             8521011104679999743378778656
Q gi|254780805|r  146 QLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      ..++..|+|..++|+.+|.||++|++.+
T Consensus        14 EfL~PLg~s~~~LA~~LgVsr~~~sriv   41 (81)
T TIGR02607        14 EFLEPLGLSVRALAKALGVSRSTLSRIV   41 (81)
T ss_pred             HHHHCCCHHHHHHHHHCCCCHHHHHHHH
T ss_conf             7521047068999987099978888887


No 76 
>PRK09483 response regulator; Provisional
Probab=83.32  E-value=2.9  Score=21.68  Aligned_cols=39  Identities=21%  Similarity=0.184  Sum_probs=29.6

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             221048999999985210111046799997433787786565
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ..|||-|.-  .-+++.+ |+|-.+||.+++.|..||.++++
T Consensus       147 ~~LT~RE~e--Vl~ll~~-G~snkeIA~~L~iS~~TV~~h~~  185 (216)
T PRK09483        147 ASLSERELQ--IMLMITK-GQKVNEISEQLNLSPKTVNSYRY  185 (216)
T ss_pred             CCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             568999999--9999987-99999999996989999999999


No 77 
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=83.17  E-value=3.3  Score=21.35  Aligned_cols=19  Identities=21%  Similarity=0.233  Sum_probs=11.4

Q ss_pred             CHHHHHHHHHHHHHHHHHH
Q ss_conf             0467999974337877865
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~  172 (300)
                      |.++||+.+|.|...|...
T Consensus       131 t~~EiA~~l~is~~~v~~~  149 (256)
T PRK07408        131 TDQEIAQALDISLEEWQEI  149 (256)
T ss_pred             CHHHHHHHHCCCHHHHHHH
T ss_conf             8999998959699999999


No 78 
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=83.06  E-value=0.76  Score=25.41  Aligned_cols=26  Identities=38%  Similarity=0.639  Sum_probs=21.5

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             852101110467999974337877865
Q gi|254780805|r  146 QLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      +|. +.|+||.+||+.+|-||+.|+..
T Consensus        14 ~lR-~~G~tQ~eIA~~lgTSraNvs~i   39 (139)
T PRK03975         14 RLR-KRGLTQQEIADILGTSRANISII   39 (139)
T ss_pred             HHH-HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             999-82897999999977328899999


No 79 
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=83.00  E-value=2.2  Score=22.50  Aligned_cols=39  Identities=23%  Similarity=0.234  Sum_probs=28.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|++-|...-.....  .|.|+.|||+.+|.|.++|....+
T Consensus       106 ~L~~re~~ii~~~~~--~g~t~~EIA~~~gis~~~Vk~~~r  144 (154)
T PRK06759        106 VLDEKEKYIIFERFF--VGKTMGEIALETEMTYYQVRWIYR  144 (154)
T ss_pred             HCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             499999999999999--699899999998989999999999


No 80 
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=82.21  E-value=4  Score=20.77  Aligned_cols=54  Identities=17%  Similarity=0.254  Sum_probs=33.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             2104899999998521011104679999743378778656565435899998764210
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI  191 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i  191 (300)
                      .|+|-.+..-.-+..  .|+|.+|||+.+|.|.++|..++.  ..-..+++.+.+..|
T Consensus       116 ~L~~~~r~v~~l~~~--~g~s~~EIA~~l~is~~tVk~~l~--ra~~~Lr~~L~~~gi  169 (171)
T PRK09645        116 QLSPEHRAVLVRSYY--RGWSTAQIAADLGIPEGTVKSRLH--YAVRALRLTLQEMGV  169 (171)
T ss_pred             CCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHCCC
T ss_conf             599998879899998--699999999998929999999999--999999999997099


No 81 
>pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Probab=82.12  E-value=2.1  Score=22.59  Aligned_cols=38  Identities=24%  Similarity=0.282  Sum_probs=26.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |.+-+...-+  |..-.|+|.+|+|+.+|.|.++|.+++.
T Consensus        11 Lp~~~r~~~~--l~~~~~~s~~eIA~~lg~s~~tVk~~l~   48 (54)
T pfam08281        11 LPPRQREVFL--LRYLEGLSYAEIAELLGISEGTVKSRLS   48 (54)
T ss_pred             CCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999998968--7998785999999998949999999999


No 82 
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=82.12  E-value=2  Score=22.66  Aligned_cols=38  Identities=26%  Similarity=0.416  Sum_probs=28.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-|.-.  -+++.+ |+|..+||+.+|.|..+|.++++
T Consensus         3 ~LT~RE~~i--l~~l~~-G~s~~eIA~~L~is~~TV~~h~~   40 (58)
T pfam00196         3 SLSPREREV--LRLLAA-GKSNKEIADILGISEKTVKVHRS   40 (58)
T ss_pred             CCCHHHHHH--HHHHHH-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             779999999--999980-79999999997888999999999


No 83 
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=81.96  E-value=3.6  Score=21.06  Aligned_cols=39  Identities=31%  Similarity=0.332  Sum_probs=19.7

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             210489999999852101110467999974337877865
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      .|++-|...-..++..+-+.|..+||+.+|.|+..|++.
T Consensus       227 ~L~eREr~Ii~~r~~~~e~~TL~EIg~~lgvSreRVRQI  265 (289)
T PRK07500        227 TLNERELFIIRERRLREDGATLEALGEELGISKERVRQI  265 (289)
T ss_pred             CCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             499999999999766899858999999979799999999


No 84 
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327   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 group of sigma factors are members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037 (Tannerella forsythensis ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=81.77  E-value=2.2  Score=22.51  Aligned_cols=28  Identities=21%  Similarity=0.221  Sum_probs=20.2

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |-..-|+|..|||+.+|.|..||-++|.
T Consensus       130 lsr~eg~s~~EIA~~L~iS~~TVe~hi~  157 (167)
T TIGR02985       130 LSRFEGLSNKEIAEELGISVKTVEYHIT  157 (167)
T ss_pred             HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9886179867899884898889999999


No 85 
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=81.76  E-value=1.9  Score=22.85  Aligned_cols=32  Identities=16%  Similarity=0.208  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999852101110467999974337877865
Q gi|254780805|r  141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      +..+++-.+..||+|++||++++.+.+.|.+.
T Consensus        81 ~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~i  112 (165)
T COG1813          81 GERIREAREKRGLSQEDLAAKLKEKVSVIRRI  112 (165)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             99999999982888999999965469999999


No 86 
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=81.63  E-value=2.1  Score=22.59  Aligned_cols=26  Identities=27%  Similarity=0.446  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11104679999743378778656565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      ..+|+++||..+|.++-||++.|.-+
T Consensus        24 l~ltr~eiA~~lG~t~eTVsR~l~~l   49 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKEL   49 (67)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             17799999999789099999999999


No 87 
>PRK08359 transcription factor; Validated
Probab=81.52  E-value=2  Score=22.67  Aligned_cols=32  Identities=22%  Similarity=0.254  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999852101110467999974337877865
Q gi|254780805|r  141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      +.-+++-.+..||||++||.+++.+.+.|.+.
T Consensus        85 ~~~Ir~ARE~~GlSqeeLA~ki~ek~nvI~ki  116 (175)
T PRK08359         85 AERVYEAIRKSGLSYEELSHKVGLSVNDLRRI  116 (175)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHH
T ss_conf             99999999985999999999972229999999


No 88 
>pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.
Probab=81.22  E-value=2.8  Score=21.76  Aligned_cols=34  Identities=26%  Similarity=0.389  Sum_probs=25.6

Q ss_pred             HHHHHHHHCCC--CHHHHHHHHHH-HHHHHHHHHHHH
Q ss_conf             99985210111--04679999743-378778656565
Q gi|254780805|r  143 GYEQLISEYGY--TQNDIGSIVGK-SRSHVANILRIL  176 (300)
Q Consensus       143 ~~~~l~~~~~~--t~~~lA~~~G~-s~s~V~~~LrLl  176 (300)
                      .++..++++|+  |..||++.+|. |.++|..+|.-|
T Consensus        14 ~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~L   50 (65)
T pfam01726        14 FIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKAL   50 (65)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             9999999828898799999993899809999999999


No 89 
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=81.17  E-value=4.4  Score=20.54  Aligned_cols=47  Identities=19%  Similarity=0.267  Sum_probs=34.4

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Q ss_conf             999985210111046799997433787786565----6543589999876421
Q gi|254780805|r  142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILR----ILKLPSSVREMIRKEE  190 (300)
Q Consensus       142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr----Ll~L~~~i~~~l~~~~  190 (300)
                      -++.|  +..|+|.++||+.+|.++.+|.|+|+    =..|--++-+++..|.
T Consensus        53 ga~ar--ekag~Ti~EIAeelG~TeqTir~hlkgetkAG~lv~etY~~lK~G~  103 (182)
T COG1318          53 GALAR--EKAGMTISEIAEELGRTEQTVRNHLKGETKAGQLVRETYEKLKEGG  103 (182)
T ss_pred             HHHHH--HHCCCCHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHCC
T ss_conf             89999--8703749999999687799999997514033169999999998067


No 90 
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=81.02  E-value=3.8  Score=20.96  Aligned_cols=42  Identities=12%  Similarity=0.264  Sum_probs=28.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             11104679999743378778656565435899998764210167
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLG  194 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~g  194 (300)
                      .|+|..|||+.+|.|.++|..+|.  ..-..+++.|....-..|
T Consensus       151 eg~s~~EIA~~lgis~~tVk~~l~--Rark~Lr~~L~~~r~~~g  192 (196)
T PRK12524        151 EGLSNPEIAEVMQIGVEAVESLTA--RGKRALAALLAGQRAELG  192 (196)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHHHHCC
T ss_conf             089999999998929999999999--999999999871798749


No 91 
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=80.91  E-value=2.4  Score=22.26  Aligned_cols=41  Identities=17%  Similarity=0.222  Sum_probs=31.4

Q ss_pred             HCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10221048999999985210111046799997433787786565
Q gi|254780805|r  131 QRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       131 ~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ....|||-|.-  .-+++.+ |+|..+||..++.|..||.++++
T Consensus       134 ~~~~LT~RE~e--VL~lia~-G~snkeIA~~L~IS~~TVk~h~~  174 (196)
T PRK10360        134 RQDPLTKRERQ--VAEKLAQ-GMAVKEIAAELGLSPKTVHVHRA  174 (196)
T ss_pred             CCCCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             76899979999--9999987-99999999996999999999999


No 92 
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=80.81  E-value=4.1  Score=20.70  Aligned_cols=40  Identities=15%  Similarity=0.125  Sum_probs=28.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             221048999999985210111046799997433787786565
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ..|+|.+...-.  |....|+|..|||+.+|.|.++|..+|.
T Consensus       133 ~~L~~~~R~vl~--L~~~~~ls~~EIA~~l~is~~tVksrl~  172 (188)
T PRK09640        133 VHVNPIDREILV--LRFVAELEFQEIADIMHMGLSATKMRYK  172 (188)
T ss_pred             HHCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             848999999999--9999299999999998929999999999


No 93 
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=80.73  E-value=4.5  Score=20.44  Aligned_cols=39  Identities=15%  Similarity=0.151  Sum_probs=26.4

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-....-.  |....|+|.++||+.+|.|.++|.++|.
T Consensus       128 ~Lp~~~R~v~~--L~~~~g~s~~EIA~~l~is~~tVk~~l~  166 (186)
T PRK05602        128 ALPERQREAIV--LQYYQGLSNIEAARVMGLSVDALESLLA  166 (186)
T ss_pred             CCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             59987889999--9986389999999998939999999999


No 94 
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=80.61  E-value=2.5  Score=22.05  Aligned_cols=39  Identities=15%  Similarity=0.287  Sum_probs=26.7

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|.|-..-..+.+.+  .|+|.+|||+.+|.|.++|..+|.
T Consensus       135 ~L~~~~r~~i~l~~~--eg~s~~EIA~~l~is~~TVk~rl~  173 (184)
T PRK12537        135 QLEPARRNCILHAYV--DGCSHAEIAQRLGAPLGTVKAWIK  173 (184)
T ss_pred             HCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             099989999999884--399999999998929999999999


No 95 
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=80.31  E-value=2.7  Score=21.89  Aligned_cols=27  Identities=22%  Similarity=0.359  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565654
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      ..+|-+++|+.+|.||.|+.+||.-+.
T Consensus       177 ~~~sa~eva~~~giSRvTaRRYLe~L~  203 (239)
T PRK10430        177 YEFSTDELANEVNISRVSCRKYLIWLV  203 (239)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             984699999885852988999999998


No 96 
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=80.22  E-value=4.7  Score=20.33  Aligned_cols=26  Identities=19%  Similarity=0.206  Sum_probs=21.8

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10111046799997433787786565
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .-.|+|..|||+.+|.|.++|.+++.
T Consensus       139 ~~eg~s~~EIA~~lgis~~tVk~rl~  164 (178)
T PRK12536        139 KLEGLSVEETAQLTGLSESAVKVGIH  164 (178)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             88599999999998929999999999


No 97 
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=80.21  E-value=4.7  Score=20.33  Aligned_cols=39  Identities=13%  Similarity=0.174  Sum_probs=27.6

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHH
Q ss_conf             10111046799997433787786565--6543589999876
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANILR--ILKLPSSVREMIR  187 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~~i~~~l~  187 (300)
                      ...|+|..|||+.+|.|.++|..+|.  .-.|=..++.++.
T Consensus       151 ~~egls~~EIA~~l~is~~tVk~rl~RAr~~Lr~~L~~ll~  191 (193)
T PRK11923        151 EFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPLLQ  191 (193)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99499999999998929999999999999999999899873


No 98 
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=80.20  E-value=4.7  Score=20.33  Aligned_cols=46  Identities=17%  Similarity=0.413  Sum_probs=32.8

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             101110467999974337877865656543589999876421016777
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHA  196 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~gha  196 (300)
                      ...|+|.+|||+.+|.|.++|..+|.  .--..++++|...+....|+
T Consensus       184 ~~egls~~EIA~~Lgis~~TVKsrL~--RAr~~LR~~L~r~e~~~~~~  229 (233)
T PRK12538        184 YHENMSNGEIAEVMDTTVAAVESLLK--RGRQQLRDLLRRHERDIRHA  229 (233)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
T ss_conf             98499999999998929999999999--99999999999874888765


No 99 
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=80.02  E-value=2.4  Score=22.26  Aligned_cols=37  Identities=19%  Similarity=0.258  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             48999999985210111046799997433787786565
Q gi|254780805|r  137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .+|...-. ..++.+++.+.+.|+.+|.||+++.+.|+
T Consensus         4 ~~Er~~I~-~aL~~~~gn~~~aA~~LGisr~tL~~kmk   40 (42)
T pfam02954         4 EVEKELIE-AALERTGGNKSKAARLLGISRRTLYRKLK   40 (42)
T ss_pred             HHHHHHHH-HHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999-99999499799999997969999999997


No 100
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=79.95  E-value=4.3  Score=20.56  Aligned_cols=50  Identities=22%  Similarity=0.285  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHHHHH--HHHCCCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHH
Q ss_conf             221048999999985--21011104679999743378778656--565435899
Q gi|254780805|r  133 KDLNPLEEALGYEQL--ISEYGYTQNDIGSIVGKSRSHVANIL--RILKLPSSV  182 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l--~~~~~~t~~~lA~~~G~s~s~V~~~L--rLl~L~~~i  182 (300)
                      +.|++-|.-.--.|.  .+.-.+|++++|+.+|.|+.+|++.-  +|-+|=..+
T Consensus       182 ~~L~eREr~Ii~lRfGL~~~~~~Tl~EIa~~lgISrerVrQIe~~AL~KLR~~l  235 (239)
T PRK08301        182 KKLNDREKQIMELRFGLAGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEI  235 (239)
T ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             648999999999995788998406999999989789999999999999999999


No 101
>PRK09954 hypothetical protein; Provisional
Probab=79.88  E-value=2.5  Score=22.10  Aligned_cols=64  Identities=11%  Similarity=0.137  Sum_probs=30.1

Q ss_pred             EHHHCCCCCCCCCCCC-CHH-HHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             3898235789998768-988-99999998863100155046205654453335756777776421001354
Q gi|254780805|r   43 SIHSIVPNPHNPRNYF-ESE-GLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPV  111 (300)
Q Consensus        43 ~i~~i~~~p~~pR~~~-~~~-~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~  111 (300)
                      +...+.+.-.||-+.+ +.. .=.-.|..+.+-| .++-.+-..++..    .|+.=+..++..|...=.|
T Consensus        74 ~~~~l~~~~SNpg~i~~s~GGvGrNiA~nLarLG-~~v~lIs~VG~D~----~G~~ll~~l~~~GVd~~~v  139 (362)
T PRK09954         74 ADIRYPQAASHPGTIHCSAGGVGRNIAHNLALLG-RDVHLLSAIGDDF----YGETLLEETRRAGVNVSGC  139 (362)
T ss_pred             CCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHCC-CCEEEEEEECCCH----HHHHHHHHHHHCCCCCCEE
T ss_conf             4776656999996368888848999999999769-9769999963858----7999999999859973307


No 102
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=79.86  E-value=2.9  Score=21.73  Aligned_cols=48  Identities=19%  Similarity=0.170  Sum_probs=29.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565654358999987
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI  186 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l  186 (300)
                      |+|-....-.  |..-.|+|..|||+.+|.|.++|..+|.  ..=..+++.+
T Consensus       107 Lp~~~R~v~~--L~~~eg~s~~EIA~~L~is~~tVksrl~--RAr~~Lr~~L  154 (181)
T PRK09637        107 LPEKYAEALR--LTELEGLSQKEIAEKLGLSLSGAKSRVQ--RGRVKLKELL  154 (181)
T ss_pred             CCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHH
T ss_conf             9999989979--9988599999999998949999999999--9999999999


No 103
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=79.52  E-value=2.8  Score=21.80  Aligned_cols=38  Identities=32%  Similarity=0.476  Sum_probs=28.3

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-|....  .++.. |+|..+||+.+|.|..+|.++++
T Consensus         3 ~LT~rE~~il--~~l~~-G~s~~eIA~~L~is~~TV~~~~~   40 (58)
T smart00421        3 SLTPREREVL--RLLAE-GLTNKEIAERLGISEKTVKTHLS   40 (58)
T ss_pred             CCCHHHHHHH--HHHHH-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             6189999999--99981-79999999898978989999999


No 104
>PRK06424 transcription factor; Provisional
Probab=79.51  E-value=2.5  Score=22.06  Aligned_cols=39  Identities=15%  Similarity=0.071  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999985210111046799997433787786565654358
Q gi|254780805|r  141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPS  180 (300)
Q Consensus       141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~  180 (300)
                      +.-++.-.+..||||++||.+++.+.+.|.+.= --++.|
T Consensus        86 ~~~Ir~ARE~~GlsqeeLA~ki~ek~svI~kiE-~G~l~P  124 (144)
T PRK06424         86 AELVKNARERLSMSQADLAAKIFERKNVIASIE-RGDLLP  124 (144)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH-CCCCCC
T ss_conf             999999999849999999999654499999998-389899


No 105
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=79.46  E-value=1.9  Score=22.82  Aligned_cols=47  Identities=26%  Similarity=0.432  Sum_probs=34.0

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             556665431022104899999998521011104679999743378778656
Q gi|254780805|r  123 EIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       123 ~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .++++.=+|+  |.|-+.|.-+  |.+.+||+..|+|+.+|.|.+.|...|
T Consensus       147 ~lA~laaLq~--Lpp~QRavlv--LRdV~g~s~~EiAe~Lg~S~aAVks~L  193 (341)
T PRK08241        147 RLAFVAALQH--LPPRQRAVLL--LRDVLGWSAAEVAEALGTSTAAVNSAL  193 (341)
T ss_pred             HHHHHHHHHH--CCHHHHEEEE--HHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999983--9997902001--297529988999999789999999999


No 106
>PRK11050 manganese transport regulator MntR; Provisional
Probab=79.41  E-value=4.8  Score=20.28  Aligned_cols=73  Identities=26%  Similarity=0.305  Sum_probs=46.7

Q ss_pred             HHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCCCHH
Q ss_conf             999985210111-0467999974337877865656543589999876421016777776401004689999742224778
Q gi|254780805|r  142 LGYEQLISEYGY-TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVSKKMSVR  220 (300)
Q Consensus       142 ~~~~~l~~~~~~-t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~~~LSVR  220 (300)
                      +.+..|.++.|. -..+||+++|.|+++|++.+.         .+-..|-|....++.+.=.+...++|+.+....   |
T Consensus        43 E~I~~L~~~~G~aR~~DIA~~LgVs~pSVt~mlk---------rL~~~GlV~~~~Y~~I~LT~~G~~~A~~i~~RH---r  110 (155)
T PRK11050         43 ELIADLIAEVGEARQVDIAARLGVSQPTVAKMLK---------RLARDGLVEMRPYRGVFLTPEGEKLAQESRERH---Q  110 (155)
T ss_pred             HHHHHHHHCCCCEEHHHHHHHHCCCCHHHHHHHH---------HHHHCCCEEECCCCCEEECHHHHHHHHHHHHHH---H
T ss_conf             9999999826956499999890999331999999---------998789988718988468977999999999999---9


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780805|r  221 DTEELV  226 (300)
Q Consensus       221 e~E~lV  226 (300)
                      =++...
T Consensus       111 ile~FL  116 (155)
T PRK11050        111 IVENFL  116 (155)
T ss_pred             HHHHHH
T ss_conf             999999


No 107
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain.  For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization.  For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=79.35  E-value=2.8  Score=21.83  Aligned_cols=37  Identities=38%  Similarity=0.609  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |+|-|.-. + .++.. |+|..+||+.+|.|..+|.++++
T Consensus         1 LT~rE~~i-l-~~~~~-G~s~~eIA~~L~is~~TV~~~~~   37 (57)
T cd06170           1 LTPREREV-L-RLLAE-GKTNKEIADILGISEKTVKTHLR   37 (57)
T ss_pred             CCHHHHHH-H-HHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             98899999-9-99980-79999999998978999999999


No 108
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=79.24  E-value=3  Score=21.56  Aligned_cols=39  Identities=18%  Similarity=0.166  Sum_probs=27.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-+.-.-.-.  .-.|++.++||+.+|.|.++|.+++.
T Consensus       125 ~L~~~~r~il~l~--~~~g~s~~eIA~~lgis~~tv~~~l~  163 (180)
T PRK11924        125 ALPEKQREVFLLR--YVEGLSYQEIADQLGVPLGTVKSRLR  163 (180)
T ss_pred             HCCHHHHHHHHHH--HHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             5999999999999--99685999999998949999999999


No 109
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=79.19  E-value=1.5  Score=23.48  Aligned_cols=29  Identities=17%  Similarity=0.557  Sum_probs=24.9

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             85210111046799997433787786565
Q gi|254780805|r  146 QLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .+++.+|+|+.++|+.+|..+.+|++.+.
T Consensus        17 eflep~glt~~~lA~~lgV~r~~is~lin   45 (104)
T COG3093          17 EFLEPLGLTQTELAEALGVTRNTISELIN   45 (104)
T ss_pred             HHHCCCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf             98452169899999993998999999983


No 110
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding.
Probab=79.10  E-value=0.99  Score=24.68  Aligned_cols=22  Identities=32%  Similarity=0.555  Sum_probs=19.8

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHH
Q ss_conf             1011104679999743378778
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVA  170 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~  170 (300)
                      .+-||+|++||+.||-+|+.||
T Consensus        18 R~kGl~Q~eIAk~LkTtRaNvS   39 (142)
T TIGR00721        18 REKGLKQKEIAKILKTTRANVS   39 (142)
T ss_pred             HHCCCCHHHHHHHHCCCCHHHH
T ss_conf             6338887889877267201378


No 111
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=79.05  E-value=2.7  Score=21.89  Aligned_cols=23  Identities=17%  Similarity=0.198  Sum_probs=13.8

Q ss_pred             HHHHHHHCCCC--HHHHHHHHHHHH
Q ss_conf             99997422247--789999997641
Q gi|254780805|r  208 LAQVIVSKKMS--VRDTEELVQEQD  230 (300)
Q Consensus       208 la~~Ii~~~LS--VRe~E~lVk~~~  230 (300)
                      ..+......|-  |||.++.+.+..
T Consensus       403 a~~~L~~y~WPGNVREL~n~iera~  427 (513)
T PRK10820        403 LSTVLTRYGWPGNVRQLKNAIYRAL  427 (513)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             9999970899979999999999999


No 112
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=79.04  E-value=5  Score=20.16  Aligned_cols=38  Identities=13%  Similarity=0.079  Sum_probs=25.9

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |+|-+...-.-+..  .|+|.+|||+.+|.|.++|..++.
T Consensus       137 Lp~~~r~v~~L~~~--~~~s~~EIA~~l~is~~tVk~~l~  174 (187)
T PRK09641        137 LPDKYRTVIVLKYI--EELSLKEISEILDLPVGTVKTRIH  174 (187)
T ss_pred             CCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             89888899999998--299899999998939999999999


No 113
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=78.95  E-value=3  Score=21.60  Aligned_cols=38  Identities=24%  Similarity=0.325  Sum_probs=29.1

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             22104899999998521011104679999743378778656
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      ..|++-|..  .-+|+.+ |+|-.+||++++.|..||.++.
T Consensus       147 ~~LT~RE~e--Vl~lla~-G~snkeIA~~L~iS~~TVk~h~  184 (211)
T COG2197         147 ELLTPRELE--VLRLLAE-GLSNKEIAEELNLSEKTVKTHV  184 (211)
T ss_pred             CCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHH
T ss_conf             789989999--9999987-9988999999787898999999


No 114
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=78.64  E-value=2.4  Score=22.21  Aligned_cols=33  Identities=18%  Similarity=0.318  Sum_probs=25.3

Q ss_pred             HHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             985210-111046799997433787786565654
Q gi|254780805|r  145 EQLISE-YGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       145 ~~l~~~-~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      ..|.+. ..+|-++||+.+|.|+.+|.+.+..++
T Consensus         7 ~~L~~~~~~vt~~~La~~l~VSr~TV~rdi~~L~   40 (55)
T pfam08279         7 ELLLQAREPISGQELAEKLGVSRRTIRRDIKALE   40 (55)
T ss_pred             HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             9999769991899999996988999999999999


No 115
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=78.33  E-value=3.1  Score=21.53  Aligned_cols=24  Identities=17%  Similarity=0.214  Sum_probs=18.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|.+|||+.+|.|.++|.++|.
T Consensus       157 ~g~s~~EIA~~Lgis~~TVk~rl~  180 (194)
T PRK09646        157 GGLTYREVAERLAVPLGTVKTRMR  180 (194)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             399999999998919999999999


No 116
>pfam02376 CUT CUT domain. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein .
Probab=78.30  E-value=3.6  Score=21.06  Aligned_cols=70  Identities=16%  Similarity=0.312  Sum_probs=47.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHH
Q ss_conf             22104899999998521011104679999-74337877865656543589999876421016777776401004
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSI-VGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDP  205 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~-~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~  205 (300)
                      +.|+..+.|.-++..+..++++|.-.|+. +|+|+.+++..|+   =|.+--.+...|.-+.-.-+--+.+|+.
T Consensus         1 ~~ldT~~i~~~i~~eL~~~~I~Q~~Fa~~vL~rsQGtlSdLL~---~PKPW~~l~~~gr~~y~RM~~wL~~p~~   71 (81)
T pfam02376         1 EELDTAEIARRIKEELKRANISQALFAEVVLGRSQGSLSDLLR---RPKPWNKLLLKGREPFRRMQNFLSLPEA   71 (81)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHH---CCCCHHHHHHHHHHHHHHHHHHHCCCHH
T ss_conf             9888999999999999994976999999997318378999881---8997788508506989999999868598


No 117
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=78.05  E-value=3.5  Score=21.13  Aligned_cols=24  Identities=29%  Similarity=0.623  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|..|||+.+|.|.++|.++|.
T Consensus       142 eg~s~~EIA~~l~is~~tVk~~l~  165 (177)
T PRK09638        142 YGYTYEEIAKMLGIPEGTVKSRVH  165 (177)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             199999999998939999999999


No 118
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=78.01  E-value=5  Score=20.15  Aligned_cols=20  Identities=20%  Similarity=0.195  Sum_probs=13.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             04679999743378778656
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~L  173 (300)
                      +.+++|+.+|.+...|..+.
T Consensus       153 ~~~eiA~~l~~~~~~v~~~~  172 (284)
T PRK06596        153 EVEMIAEELGVSEEEVREME  172 (284)
T ss_pred             CHHHHHHHHCCCHHHHHHHH
T ss_conf             29999999791999999999


No 119
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=77.93  E-value=0.53  Score=26.41  Aligned_cols=94  Identities=27%  Similarity=0.272  Sum_probs=42.9

Q ss_pred             CCCCCHHHHHHHH--------HHHCCCCCCCCCCCCCHHHHHH---HH-HHHHHCCCCCHHHHHHHHHHHHHHCCCCHHH
Q ss_conf             3335756777776--------4210013543334641123455---66-6543102210489999999852101110467
Q gi|254780805|r   90 KIIAGERRFRAAK--------MASLSEVPVIIRNVDNKSSLEI---AI-VENVQRKDLNPLEEALGYEQLISEYGYTQND  157 (300)
Q Consensus        90 ~ii~G~rR~rAa~--------~~g~~~ip~iv~~~~d~~~~~~---~l-~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~  157 (300)
                      .|.+|.|||.-.+        .+|...+.-++.-.-+.....+   ++ .||..|    |-++-..+-.|+.++-   ++
T Consensus         6 iImDGNrRwA~~~g~~~~~Gh~~G~~~~~~i~~~~~~~gI~~lTvyafStEN~~R----~~~Ev~~Lm~L~~~~l---~~   78 (221)
T cd00475           6 FIMDGNRRWAKQRGMDRIEGHKAGAEKLRDILRWCLELGVKEVTLYAFSTENWKR----PKEEVDFLMELFRDVL---RR   78 (221)
T ss_pred             EECCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHCC----CHHHHHHHHHHHHHHH---HH
T ss_conf             9634869999877998789999999999999999998599989999811777677----6999999999999999---99


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999974337877865656543589999876421
Q gi|254780805|r  158 IGSIVGKSRSHVANILRILKLPSSVREMIRKEE  190 (300)
Q Consensus       158 lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~  190 (300)
                      ....+-...--|.=.=++-.||+.+++.+..-+
T Consensus        79 ~~~~~~~~~iri~~iG~~~~Lp~~l~~~i~~~e  111 (221)
T cd00475          79 ILKELEKLGVRIRIIGDLSLLPESLQKEIKKAE  111 (221)
T ss_pred             HHHHHHHCCEEEEEEECHHHCCHHHHHHHHHHH
T ss_conf             899999889799999472008989999999999


No 120
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=77.86  E-value=3.2  Score=21.43  Aligned_cols=38  Identities=21%  Similarity=0.388  Sum_probs=29.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|||-|.-  .-+|+.+ |+|..|||++++.|..||.++++
T Consensus       150 ~LT~RE~e--VL~lla~-G~snkeIA~~L~iS~~TV~~h~~  187 (216)
T PRK10840        150 RLSPKESE--VLRLFAE-GFLVTEIAKKLNRSIKTISSQKK  187 (216)
T ss_pred             CCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99989999--9999986-99999999896989999999999


No 121
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=77.69  E-value=1.9  Score=22.92  Aligned_cols=26  Identities=15%  Similarity=0.138  Sum_probs=21.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11046799997433787786565654
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      ++|-+++|+.+|.||.|+.+||-.+.
T Consensus       177 ~~ta~eva~~~giSrvTaRRYLe~L~  202 (225)
T PRK10046        177 QHTAETVAQALTISRTTARRYLEYCA  202 (225)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             86899999985851999999999998


No 122
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=77.53  E-value=5.7  Score=19.82  Aligned_cols=39  Identities=15%  Similarity=0.204  Sum_probs=26.5

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10111046799997433787786565654358999987642
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKE  189 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~  189 (300)
                      .-.|+|.+|||+.+|.|.++|..++.  ..-..+++.+...
T Consensus       133 ~~~~~s~~EIA~~l~is~~tVk~~l~--Ra~k~Lr~~L~~e  171 (175)
T PRK12518        133 DLEDLPQKEIAEILNIPVGTVKSRLF--YARRQLRKFLQQQ  171 (175)
T ss_pred             HHHCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHC
T ss_conf             99299999999998959999999999--9999999999986


No 123
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=77.50  E-value=1.9  Score=22.80  Aligned_cols=24  Identities=25%  Similarity=0.509  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ..+|++++|..+|.++.+|++.|+
T Consensus         7 l~lt~~~iA~~lG~tretvsR~l~   30 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTLK   30 (48)
T ss_pred             ECCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             337999999997997999999999


No 124
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=77.48  E-value=5.7  Score=19.81  Aligned_cols=39  Identities=10%  Similarity=0.155  Sum_probs=27.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             11104679999743378778656565435899998764210
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI  191 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i  191 (300)
                      .|+|.+|||+.+|.|.++|..+|.  ..-..+++.+....|
T Consensus       121 egls~~EIA~~l~is~~tVk~~l~--RAr~~Lr~~Le~~gi  159 (161)
T PRK09047        121 EDMDVAETAAAMGCSEGSVKTHCS--RATHTLAKALEAKGI  159 (161)
T ss_pred             HCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHCCC
T ss_conf             877999999998969999999999--999999999998698


No 125
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=77.44  E-value=5.7  Score=19.80  Aligned_cols=28  Identities=25%  Similarity=0.319  Sum_probs=23.4

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |....|+|+.|||+.+|.|.++|..+++
T Consensus       134 L~~~eg~s~~EIAe~LgiS~~tVk~~l~  161 (183)
T PRK07037        134 MVRLRGETLQDIARELNVSQTLVNFMIR  161 (183)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             8987398999999998929999999999


No 126
>KOG1602 consensus
Probab=77.22  E-value=1.5  Score=23.56  Aligned_cols=94  Identities=28%  Similarity=0.356  Sum_probs=41.8

Q ss_pred             CCCCCCHHHHHHHHHHHCCC----------CCCCC-----CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             53335756777776421001----------35433-----3464112345566654310221048999999985210111
Q gi|254780805|r   89 YKIIAGERRFRAAKMASLSE----------VPVII-----RNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGY  153 (300)
Q Consensus        89 y~ii~G~rR~rAa~~~g~~~----------ip~iv-----~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~  153 (300)
                      =.|.+|+|||  ||..|+..          +--++     .-+..-.++..+ +||-.|.   | |+-..+-.|..+.--
T Consensus        41 aFIMDGNRR~--AKk~~L~~~~GH~aGf~~l~~ile~C~~lGI~~vT~fAFS-ieNFkRs---~-eEVd~LM~L~~~k~~  113 (271)
T KOG1602          41 AFIMDGNRRY--AKKRGLETSEGHEAGFEALKEILELCKELGIKEVTVFAFS-IENFKRS---P-EEVDGLMDLALEKIE  113 (271)
T ss_pred             EEEECCCHHH--HHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEE-HHHHCCC---H-HHHHHHHHHHHHHHH
T ss_conf             9996285577--8765998530267789999999999997197279989875-6640798---8-999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565654358999987642
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKE  189 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~  189 (300)
                      ...+-++.+.+...-|+=+=.|..||+.+++.+.+=
T Consensus       114 ~~~~~~~~~~~~gvririiGdlslL~~~l~k~i~~i  149 (271)
T KOG1602         114 RLLEQGEKLDKYGVRIRVIGDLSLLPESLRKAIKKI  149 (271)
T ss_pred             HHHHHHHHHHHCCCEEEEECCHHHCCHHHHHHHHHH
T ss_conf             888876667662707999766332899999999999


No 127
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=77.19  E-value=3.9  Score=20.87  Aligned_cols=38  Identities=21%  Similarity=0.260  Sum_probs=26.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |+|-....-.-+  ...|+|..|||+.+|.|.++|..++.
T Consensus       137 L~~~~r~vi~L~--~~~g~s~~EIA~~L~is~~TVk~~l~  174 (187)
T PRK13919        137 LSPEERRVIEVL--YYQGYTHREAARLLGLPLGTLKTWAR  174 (187)
T ss_pred             CCHHHHHHHHHH--HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             999999999999--98599999999998939999999999


No 128
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=77.12  E-value=4  Score=20.81  Aligned_cols=42  Identities=19%  Similarity=0.214  Sum_probs=29.7

Q ss_pred             CCCCHHHHHHHHHHHH-HHC----CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2210489999999852-101----11046799997433787786565
Q gi|254780805|r  133 KDLNPLEEALGYEQLI-SEY----GYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~-~~~----~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .+||+.|....-..+. .-|    ..+-.+||+.+|.|+++++.+||
T Consensus       154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLR  200 (215)
T COG3413         154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR  200 (215)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             46999999999999985898887658999999995998889999999


No 129
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=76.68  E-value=4  Score=20.82  Aligned_cols=38  Identities=26%  Similarity=0.263  Sum_probs=26.9

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |.|-.+..-.  |..-.|+|+.|+|+.+|.|.++|..++.
T Consensus       128 Lp~~~R~~~~--l~~~~gls~~EIA~~l~i~~~tVks~l~  165 (182)
T COG1595         128 LPPRQREAFL--LRYLEGLSYEEIAEILGISVGTVKSRLH  165 (182)
T ss_pred             CCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999999--9998599999999895999999999999


No 130
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=76.65  E-value=5.8  Score=19.76  Aligned_cols=65  Identities=18%  Similarity=0.151  Sum_probs=36.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             111046799997433787786565654-----358999987642101677777640100468999974222477899999
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRILK-----LPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEEL  225 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~-----L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~l  225 (300)
                      -|+|..++|+++|.|.++|.+.++=.+     ||+..          .++.-..+..+..+.+.+.+-.+.|+..++..+
T Consensus        20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~----------~~GrP~kl~~~q~~~l~e~~~~k~wTl~~~~~~   89 (138)
T COG3415          20 EGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKP----------RKGRPRKLSEEQLEILLERLREKDWTLKELVEE   89 (138)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCC----------CCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             6854999999969229999999987333533156766----------899973258899999999975155218799999


No 131
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=76.58  E-value=3.8  Score=20.91  Aligned_cols=24  Identities=13%  Similarity=0.167  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|.+|||+.+|.|.++|..+|.
T Consensus       144 eg~s~~EIA~~l~is~~tVk~~l~  167 (179)
T PRK12514        144 EGLSYKELAERHDVPLNTMRTWLR  167 (179)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             699899999988909999999999


No 132
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=76.55  E-value=4.6  Score=20.39  Aligned_cols=125  Identities=14%  Similarity=0.156  Sum_probs=62.1

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHH
Q ss_conf             22104899999998521011104679999743378778656565435899998764210167777764010046899997
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVI  212 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~I  212 (300)
                      .+|+.+|... +..|.+..-.+..+||+++|.|+++|.++++         .+-.+|-|.--+|  .+   ++.++    
T Consensus        10 ~~LD~~D~~I-L~~Lq~daR~s~~eLA~~vglS~stv~~Rik---------rLe~~GiI~gy~a--~i---d~~~l----   70 (164)
T PRK11169         10 KDLDRIDRNI-LNELQKDGRISNVELSKRVGLSPTPCLERVR---------RLERQGFIQGYTA--LL---NPHYL----   70 (164)
T ss_pred             CCHHHHHHHH-HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH---------HHHHCCCEEEEEE--EE---CCCCC----
T ss_conf             4551999999-9999984899999999998929999999999---------9997898866899--97---60007----


Q ss_pred             HHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEE--CCCCCEEEEEEECCHHHHHHHH
Q ss_conf             42224778999999764102222223456655689789999999999739879997--1798228999858989999999
Q gi|254780805|r  213 VSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLEKKISSKVGLNISIK--HRNNKGQFCIKYETNEQLKIIC  290 (300)
Q Consensus       213 i~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le~~L~~~lGtkV~I~--~~~~kGkI~I~f~s~eeLe~Il  290 (300)
                         ++++.   .++.            ..-.......+..+.+.+...=.. +.+.  .+.----+.+.+.+.++|+.++
T Consensus        71 ---G~~~~---a~v~------------i~l~~~~~~~~~~~~~~l~~~peV-~~~~~vtG~~D~~l~v~~~d~~~l~~~i  131 (164)
T PRK11169         71 ---DASLL---VFVE------------ITLNRGAPDVFEQFNAAVQKLEEI-QECHLVSGDFDYLLKTRVPDMSAYRKLL  131 (164)
T ss_pred             ---CCCEE---EEEE------------EEECCCCHHHHHHHHHHHHCCCCE-EEEEEEECCCCEEEEEEECCHHHHHHHH
T ss_conf             ---98749---9999------------996588868999999998429978-9999830778899999989999999999


Q ss_pred             -HHHCC
Q ss_conf             -98375
Q gi|254780805|r  291 -SLLGE  295 (300)
Q Consensus       291 -~kL~~  295 (300)
                       ++|..
T Consensus       132 ~~~l~~  137 (164)
T PRK11169        132 GETLLR  137 (164)
T ss_pred             HHHHHC
T ss_conf             998635


No 133
>pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
Probab=76.54  E-value=3.5  Score=21.18  Aligned_cols=31  Identities=32%  Similarity=0.441  Sum_probs=25.5

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565654
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      ++.+.-.+..++|+.+|.++++|++.|+.|.
T Consensus        10 ~L~~~~~~v~el~~~l~~sq~~vS~HL~~L~   40 (47)
T pfam01022        10 LLSEGELCVCELAEILGLSQSTVSHHLKKLR   40 (47)
T ss_pred             HHHCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             9980899699999998958869999999998


No 134
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=76.51  E-value=3.8  Score=20.90  Aligned_cols=38  Identities=24%  Similarity=0.204  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|||-|.-  .-+++.+ |+|..+||++++.|..||.++++
T Consensus       143 ~Lt~RE~e--VL~ll~~-G~snkeIA~~L~iS~~TV~~h~~  180 (204)
T PRK09958        143 SLSKQEIS--VMRYILD-GKDNNDIAEKMFISNKTVSTYKS  180 (204)
T ss_pred             CCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             68999999--9999986-99999999897889999999999


No 135
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=75.92  E-value=6.3  Score=19.54  Aligned_cols=40  Identities=18%  Similarity=0.209  Sum_probs=26.8

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             101110467999974337877865656543589999876421
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE  190 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~  190 (300)
                      --.|+|.+|||+.+|.|.++|.++|.  ..-..+++.+....
T Consensus       142 ~~~g~s~~EIA~~l~is~~tVk~rl~--rA~k~LR~kle~~e  181 (190)
T PRK12543        142 YLHDYSQEEVAQILHIPIGTVKSRIH--AALKKLRQKEQIEE  181 (190)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHH
T ss_conf             98599999999998939999999999--99999999999999


No 136
>PRK01381 Trp operon repressor; Provisional
Probab=75.69  E-value=4.6  Score=20.43  Aligned_cols=54  Identities=20%  Similarity=0.241  Sum_probs=37.2

Q ss_pred             CCHHHHH------HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Q ss_conf             1048999------99998521011104679999743378778656565-4358999987642
Q gi|254780805|r  135 LNPLEEA------LGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL-KLPSSVREMIRKE  189 (300)
Q Consensus       135 l~p~e~A------~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l~~~  189 (300)
                      |+|-|.-      .-++.|+. ..++|.+||+.+|.|-++|++--+-+ ..|++.++.+..-
T Consensus        33 LTp~Er~al~~R~~I~~~Ll~-ge~sQReIa~~lgvsiAtITRGSn~LK~~~~~~k~~l~~~   93 (99)
T PRK01381         33 LTPDEREALGTRVRIVEELLR-GELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQL   93 (99)
T ss_pred             CCHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHCCCCEECCCCHHHHHCCCHHHHHHHHHH
T ss_conf             899999999999999999994-8764999999849740200002698853999999999998


No 137
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=75.40  E-value=6.5  Score=19.45  Aligned_cols=28  Identities=25%  Similarity=0.377  Sum_probs=16.4

Q ss_pred             HHHHHCC--CCHHHHHHHHHHHHHHHHHHH
Q ss_conf             8521011--104679999743378778656
Q gi|254780805|r  146 QLISEYG--YTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       146 ~l~~~~~--~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .|..++|  -|.++||+.+|.+..-+...+
T Consensus       118 ~l~~el~r~pt~~EIA~~L~i~~ee~~~~~  147 (247)
T COG1191         118 ELEQELGREPTDEEIAEELGIDKEEYIEAL  147 (247)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999984799868999989698999999999


No 138
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=75.40  E-value=2.1  Score=22.58  Aligned_cols=25  Identities=28%  Similarity=0.332  Sum_probs=21.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1104679999743378778656565
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      +.+..+||+.+|.|+++++.+||-.
T Consensus        23 ~~~l~elA~~lgis~sT~~~hLr~a   47 (53)
T pfam04967        23 RVTLKDLAKELGISKSTLSEHLRRA   47 (53)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             6889999999698999999999999


No 139
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=75.37  E-value=1.4  Score=23.69  Aligned_cols=23  Identities=35%  Similarity=0.559  Sum_probs=20.0

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             10111046799997433787786
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVAN  171 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~  171 (300)
                      .+-||||.++|+.+|-+|+.||-
T Consensus        20 RekG~tQ~eIA~~L~TTraNvSa   42 (143)
T COG1356          20 REKGLTQSEIARILKTTRANVSA   42 (143)
T ss_pred             HHCCCCHHHHHHHHCCCCCCHHH
T ss_conf             64056489999997545101799


No 140
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=75.34  E-value=5  Score=20.18  Aligned_cols=64  Identities=19%  Similarity=0.234  Sum_probs=35.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHH---HHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             013543334641123455666543102210489999---9998521011-10467999974337877865656
Q gi|254780805|r  107 SEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEAL---GYEQLISEYG-YTQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       107 ~~ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~---~~~~l~~~~~-~t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      .-+|+++.=.+.+|...  +.+   +..+..+.++.   -++.--++.| +|+.++|..+|.|.++|+++++=
T Consensus        61 ~lvpVvLtl~~~ED~e~--~~~---k~~~~~lr~~~i~Ri~~EA~~QgglLT~~Dla~LL~~S~~TI~~~ik~  128 (220)
T pfam07900        61 KLVPVILTLISPEDLEV--KEE---KVKKRELREKKIVRIFNEAYEQGALLTHADIAILLGVSTTTISRHVKE  128 (220)
T ss_pred             CCEEEEEEECCHHHHHH--HHH---HHHHHHHHHHHHHHHHHHHHHCCCEEEHHHHHHHHCCCHHHHHHHHHH
T ss_conf             41479998237888999--985---521899999999999999997388511766999988988899999999


No 141
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=75.27  E-value=3.5  Score=21.20  Aligned_cols=48  Identities=15%  Similarity=0.248  Sum_probs=32.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             1048999999985210111046799997433787786565654358999987642101
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS  192 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is  192 (300)
                      |+.+|... ++.|.+..-.+..+||+++|.|+++|.++++         .+-.+|-|.
T Consensus         7 lD~~D~~I-L~~Lq~d~R~s~~eiA~~lglS~stv~~Ri~---------rLe~~GvI~   54 (153)
T PRK11179          7 IDNLDRGI-LEALMENARTPYAELAKQFGVSPGTIHVRVE---------KMKQAGIIT   54 (153)
T ss_pred             CCHHHHHH-HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH---------HHHHCCCEE
T ss_conf             78999999-9999984899999999998929999999999---------999799658


No 142
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.
Probab=75.18  E-value=4.8  Score=20.28  Aligned_cols=41  Identities=22%  Similarity=0.287  Sum_probs=33.3

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0221048999999985210111046799997433787786565
Q gi|254780805|r  132 RKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       132 R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |-.|+.-|....++++ ++ |.+..++|+.+|..+|||+..+.
T Consensus         4 R~~LTl~eKi~iI~~~-e~-G~s~~~lar~~gi~~STl~~I~K   44 (53)
T pfam04218         4 RTSLTLREKIEVIQRS-EE-GESKASLARRFNVPRSTLRDILK   44 (53)
T ss_pred             CEEECHHHHHHHHHHH-HC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             4141699999999999-85-89688999996987979999998


No 143
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=75.17  E-value=5.8  Score=19.77  Aligned_cols=26  Identities=15%  Similarity=0.151  Sum_probs=22.0

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10111046799997433787786565
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ...|+|..|||+.+|.|.++|..+|.
T Consensus       132 ~~~~~s~~EIA~~l~is~~tVksrl~  157 (173)
T PRK12522        132 YYEQYSYKEMSEILNIPIGTVKYRLN  157 (173)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             98399999999998939999999999


No 144
>PRK10651 transcriptional regulator NarL; Provisional
Probab=75.14  E-value=4.4  Score=20.54  Aligned_cols=38  Identities=24%  Similarity=0.394  Sum_probs=27.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|||-|.-. + +++.+ |+|-.+||+.++.|..||.++++
T Consensus       155 ~LT~RE~eV-L-~ll~~-G~snkeIA~~L~iS~~TV~~h~~  192 (216)
T PRK10651        155 QLTPRERDI-L-KLIAQ-GLSNKMIARRLDITESTVKVHVK  192 (216)
T ss_pred             CCCHHHHHH-H-HHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             489899999-9-99985-99999999996978999999999


No 145
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5.  A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster.  Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=74.84  E-value=6.7  Score=19.36  Aligned_cols=49  Identities=22%  Similarity=0.405  Sum_probs=42.7

Q ss_pred             CCHHHHHHHHHHHHHHCCEEEEECCCCCEEEEEEECCHHHHHHHHHHHCCC
Q ss_conf             897899999999997398799971798228999858989999999983756
Q gi|254780805|r  246 KEKYLTDLEKKISSKVGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGEN  296 (300)
Q Consensus       246 k~~~i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL~~~  296 (300)
                      .+..+.+++.+....||-...+...++  .+.|...+.+||++-++.|..+
T Consensus        18 RPv~~~dlq~kv~~afGq~ldl~y~n~--eL~IPl~~Q~DLDkAiellD~s   66 (79)
T cd06405          18 RPVKFKDLQQKVTTAFGQPMDLHYTNN--ELLIPLKNQEDLDRAIELLDRS   66 (79)
T ss_pred             CCCCHHHHHHHHHHHHCCEEEEEEECC--EEEEECCCHHHHHHHHHHHCCC
T ss_conf             884399999999998598454577567--3788625677789999987059


No 146
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=74.80  E-value=4.7  Score=20.35  Aligned_cols=24  Identities=17%  Similarity=0.245  Sum_probs=21.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|.+|||+.+|.|.+||..+|.
T Consensus       152 eg~s~~EIA~~l~i~~gTVksrl~  175 (187)
T PRK12534        152 EGITYEELAARTDTPIGTVKSWIR  175 (187)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             499999999998919999999999


No 147
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=74.75  E-value=5  Score=20.17  Aligned_cols=50  Identities=20%  Similarity=0.282  Sum_probs=30.3

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             104899999998521011104679999743378778656565435899998764
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRK  188 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~  188 (300)
                      |.|-....-+  |....|+|..|||+.+|.|.++|..+|.  ..-..+++.+..
T Consensus       129 Lp~~~R~vi~--L~~~eg~s~~EIA~~Lgis~~tVksrl~--RAr~~Lr~~Le~  178 (188)
T PRK12517        129 LDPEYREPLL--LQVIGGFSGEEIAEILDLNKNTVMTRLF--RARNQLKEALEK  178 (188)
T ss_pred             CCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHCC
T ss_conf             9999999999--9998399999999998939999999999--999999999742


No 148
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=74.70  E-value=4.3  Score=20.58  Aligned_cols=49  Identities=22%  Similarity=0.350  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565654358999987
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI  186 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l  186 (300)
                      .|+|-.+..-.-+.  -.|+|.+|||+.+|.|.++|..+|.  ..-..+++++
T Consensus       122 ~Lp~~~R~v~~L~~--~~gls~~EIA~~L~is~~tVk~rl~--RArk~Lr~~L  170 (185)
T PRK12542        122 ELNESNRQVFKYKV--FYNLTYQEISSVMGITEANVRKQFE--RARKRVQNMI  170 (185)
T ss_pred             HCCHHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHH
T ss_conf             29998889976799--8399999999998929999999999--9999999987


No 149
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=74.63  E-value=4.7  Score=20.36  Aligned_cols=42  Identities=19%  Similarity=0.207  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             104899999998521---011104679999743378778656565
Q gi|254780805|r  135 LNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       135 l~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      ||+.+...--+.|.+   ..|+|.+++|..+|.|...|.+.|.|.
T Consensus         3 Ln~~Q~~~T~~ELqeNf~~~~ls~~~iA~dL~~s~~~ve~vL~m~   47 (89)
T pfam10078         3 LNIEEMQATRKELQANFELSGLTIEQVAKDLNTTPEKVEALLQLK   47 (89)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             889999999999999998838989999989499999999999734


No 150
>PRK12423 LexA repressor; Provisional
Probab=74.46  E-value=5.4  Score=19.98  Aligned_cols=48  Identities=21%  Similarity=0.246  Sum_probs=31.3

Q ss_pred             HHHHHHHHCCC--CHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCC--HHHHHHH
Q ss_conf             99985210111--0467999974-33787786565654358999987642101--6777776
Q gi|254780805|r  143 GYEQLISEYGY--TQNDIGSIVG-KSRSHVANILRILKLPSSVREMIRKEEIS--LGHARTL  199 (300)
Q Consensus       143 ~~~~l~~~~~~--t~~~lA~~~G-~s~s~V~~~LrLl~L~~~i~~~l~~~~is--~ghar~L  199 (300)
                      .++..++++|+  |..|||+.+| +|.++|..+|+         .+...|-|+  .+.+|++
T Consensus        14 fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~---------~L~~kG~i~r~~~~~R~i   66 (202)
T PRK12423         14 FIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQ---------ALAEAGLIEVVPNQARGI   66 (202)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHH---------HHHHCCCEECCCCCCEEE
T ss_conf             99999996298988999999829998678999999---------999887997069995379


No 151
>pfam01255 Prenyltransf Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase.
Probab=74.38  E-value=0.97  Score=24.74  Aligned_cols=90  Identities=21%  Similarity=0.229  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHH--------HHHCCCCCCCCCCCCC-----HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHH
Q ss_conf             335756777776--------4210013543334641-----123455666543102210489999999852101110467
Q gi|254780805|r   91 IIAGERRFRAAK--------MASLSEVPVIIRNVDN-----KSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQND  157 (300)
Q Consensus        91 ii~G~rR~rAa~--------~~g~~~ip~iv~~~~d-----~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~  157 (300)
                      |.+|+|||.-.+        ..|...+.-++.-..+     -..+..+ .||..|.    -+|-.++-.|+..+-   ++
T Consensus         1 ImDGNrRwAk~~~l~~~~Gh~~G~~~~~~i~~~c~~~gI~~lTvyaFS-tEN~~R~----~~Ev~~L~~l~~~~l---~~   72 (222)
T pfam01255         1 IMDGNRRWAKKRGLPRTEGHRAGAEALREILEWCLELGIKYLTLYAFS-TENWKRP----KEEVDFLMELLEEKL---RR   72 (222)
T ss_pred             CCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEHHHC-HHHCCCC----HHHHHHHHHHHHHHH---HH
T ss_conf             982879999887998779999999999999999998699989726417-8754999----899999999999999---99


Q ss_pred             HHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99997---43378778656565435899998764210
Q gi|254780805|r  158 IGSIV---GKSRSHVANILRILKLPSSVREMIRKEEI  191 (300)
Q Consensus       158 lA~~~---G~s~s~V~~~LrLl~L~~~i~~~l~~~~i  191 (300)
                      ....+   |..-..|-   ++..||+.+++.+..=+-
T Consensus        73 ~~~~~~~~~iki~~iG---~~~~Lp~~l~~~i~~~e~  106 (222)
T pfam01255        73 LLEDLHKNGVRVRVIG---DLSLLPEDLRKAIEDAEE  106 (222)
T ss_pred             HHHHHHHCCEEEEEEC---CCCCCCHHHHHHHHHHHH
T ss_conf             9999998693899952---655689899999999999


No 152
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=74.30  E-value=3.5  Score=21.17  Aligned_cols=36  Identities=28%  Similarity=0.356  Sum_probs=29.3

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             2210489999999852101110467999974337877865
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      ..|+|.|    ++.+.+.+++||.+.|..+|.|.++|++-
T Consensus        42 ~~ls~~e----Ik~iRe~~~lSq~vFA~~L~vs~~Tv~~W   77 (104)
T COG2944          42 KTLSPTE----IKAIREKLGLSQPVFARYLGVSVSTVRKW   77 (104)
T ss_pred             CCCCHHH----HHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf             8998899----99999982888999999988879999999


No 153
>PRK02866 cyanate hydratase; Validated
Probab=74.25  E-value=6.9  Score=19.27  Aligned_cols=37  Identities=32%  Similarity=0.399  Sum_probs=25.7

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Q ss_conf             1011104679999743378778656-565435899998
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANIL-RILKLPSSVREM  185 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~L-rLl~L~~~i~~~  185 (300)
                      .+-|+|=++||+.+|+|..|++..+ .-..++++--+.
T Consensus        15 ~~kgltw~~ia~~~G~s~v~~aaa~lGQ~~~~~e~A~~   52 (147)
T PRK02866         15 KEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEK   52 (147)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHH
T ss_conf             98499899999894989999999984677899999999


No 154
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=74.22  E-value=5.6  Score=19.87  Aligned_cols=36  Identities=19%  Similarity=0.193  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999985210111046799997433787786565
Q gi|254780805|r  139 EEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       139 e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .+...+..+-+.-+.++.+||+.++.++++|++.+.
T Consensus         4 ~Q~~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i~   39 (59)
T pfam01047         4 TQFHILRILYEHGPLTVSELAEKLGVDRSTVTRVLD   39 (59)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             999999999946992999999998858654999999


No 155
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=74.22  E-value=1.8  Score=23.09  Aligned_cols=31  Identities=13%  Similarity=0.201  Sum_probs=24.1

Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9998521011104679999743378778656
Q gi|254780805|r  143 GYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      ++++-.+.|+.+|.++|..+|.|.|.|+.|=
T Consensus        31 ~lrKWR~~F~iSQ~elA~~l~vSpSVISDYE   61 (241)
T COG1709          31 TLRKWREIFNVSQTELARELGVSPSVISDYE   61 (241)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCCCEEEHHH
T ss_conf             9999999818249999987289910031211


No 156
>PRK10403 transcriptional regulator NarP; Provisional
Probab=74.03  E-value=4.7  Score=20.31  Aligned_cols=37  Identities=22%  Similarity=0.310  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ||+-|.-.  -+++.. |+|-.+||+.+|.|..||.++++
T Consensus       154 LT~RE~eV--L~lla~-G~snkeIA~~L~iS~~TV~~h~~  190 (215)
T PRK10403        154 LTERELDV--LHELAQ-GLSNKQIASVLNISEQTVKVHIR  190 (215)
T ss_pred             CCHHHHHH--HHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             89999999--999986-99999999997982999999999


No 157
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=73.86  E-value=3.3  Score=21.36  Aligned_cols=30  Identities=30%  Similarity=0.391  Sum_probs=24.6

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565654
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      |. +...+..++|+.+|.|+++|+..|+.|.
T Consensus         6 L~-~~~~~~~ela~~l~is~~tvs~HL~~L~   35 (66)
T smart00418        6 LA-EGELCVCELAEILGLSQSTVSHHLKKLR   35 (66)
T ss_pred             HH-CCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             77-3996699999998829888879999999


No 158
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=73.71  E-value=4.6  Score=20.40  Aligned_cols=23  Identities=13%  Similarity=0.072  Sum_probs=12.8

Q ss_pred             HHHHHHHHCCCC--HHHHHHHHHHH
Q ss_conf             899997422247--78999999764
Q gi|254780805|r  207 SLAQVIVSKKMS--VRDTEELVQEQ  229 (300)
Q Consensus       207 ~la~~Ii~~~LS--VRe~E~lVk~~  229 (300)
                      ...+......|-  |||.++.+.+.
T Consensus       343 ~a~~~L~~y~WPGNvrEL~n~ier~  367 (469)
T PRK10923        343 ETEAALTRLAWPGNVRQLENTCRWL  367 (469)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf             9999997499998799999999999


No 159
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=73.56  E-value=3.6  Score=21.09  Aligned_cols=29  Identities=17%  Similarity=0.327  Sum_probs=12.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             998521011104679999743378778656
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      ++++.+. |+|..+||+.||+.+|||++=|
T Consensus        16 I~~l~~~-~~S~reIA~~LgRh~sTIsREl   44 (318)
T COG2826          16 IERLLKA-KMSIREIAKQLNRHHSTISREL   44 (318)
T ss_pred             HHHHHHC-CCCHHHHHHHHCCCCCHHHHHH
T ss_conf             9999985-9989999998576862042798


No 160
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=73.33  E-value=4.9  Score=20.22  Aligned_cols=37  Identities=14%  Similarity=0.170  Sum_probs=27.6

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |++-|.-  .-+|+.+ |+|..+||+.++.|..||.++++
T Consensus       150 Lt~RE~e--VL~ll~~-G~snkeIA~~L~iS~~TV~~h~~  186 (210)
T PRK09935        150 LSNREVT--VLRYLAN-GLSNKEIAEQLLLSNKTISAHKS  186 (210)
T ss_pred             CCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9989999--9999986-99999999894988999999999


No 161
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=73.30  E-value=4.6  Score=20.41  Aligned_cols=33  Identities=24%  Similarity=0.307  Sum_probs=25.4

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9985210111046799997433787786565654
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +..|.+ .+.+..+||+.+|.|+++|+..|+.|.
T Consensus        13 l~~L~~-~~~~~~eia~~l~is~~~vs~hL~~L~   45 (78)
T cd00090          13 LRLLLE-GPLTVSELAERLGLSQSTVSRHLKKLE   45 (78)
T ss_pred             HHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             999984-890699998777848789999999999


No 162
>PRK05572 sporulation sigma factor SigF; Validated
Probab=73.22  E-value=7.3  Score=19.11  Aligned_cols=17  Identities=18%  Similarity=0.362  Sum_probs=8.3

Q ss_pred             CHHHHHHHHHHHHHHHH
Q ss_conf             04679999743378778
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVA  170 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~  170 (300)
                      |.+++|+.+|.+...|.
T Consensus       134 s~~eia~~lg~~~~~v~  150 (251)
T PRK05572        134 TIEELAEYLGVTPEEVV  150 (251)
T ss_pred             CHHHHHHHHCCCHHHHH
T ss_conf             89999999793999999


No 163
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=73.18  E-value=4.8  Score=20.27  Aligned_cols=19  Identities=11%  Similarity=0.454  Sum_probs=8.7

Q ss_pred             HHHHHCCCC--HHHHHHHHHH
Q ss_conf             997422247--7899999976
Q gi|254780805|r  210 QVIVSKKMS--VRDTEELVQE  228 (300)
Q Consensus       210 ~~Ii~~~LS--VRe~E~lVk~  228 (300)
                      +.+....|.  |||.++.+.+
T Consensus       215 ~~L~~y~WPGNvrEL~n~ier  235 (325)
T PRK11608        215 ETLLNYRWPGNIRELKNVVER  235 (325)
T ss_pred             HHHHCCCCCCHHHHHHHHHHH
T ss_conf             999619999659999999999


No 164
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=73.13  E-value=6.2  Score=19.58  Aligned_cols=31  Identities=10%  Similarity=0.428  Sum_probs=19.8

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCC
Q ss_conf             89889999999886310015504620565445333
Q gi|254780805|r   58 FESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKII   92 (300)
Q Consensus        58 ~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii   92 (300)
                      .+...+.-|..++.+.|.+.    +...+|+|.+=
T Consensus        38 lpksTv~RlL~tL~~~G~l~----~~~~~~~Y~LG   68 (264)
T PRK09834         38 LHRTTVRRLLETLQEEGYVR----RSASDDSFRLT   68 (264)
T ss_pred             CCHHHHHHHHHHHHHCCCEE----EECCCCCEECC
T ss_conf             09999999999999789989----96799976516


No 165
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305   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 group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution and represent a conserved family.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=72.77  E-value=6.2  Score=19.58  Aligned_cols=52  Identities=25%  Similarity=0.422  Sum_probs=44.2

Q ss_pred             CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             11234556665431022104899999998521011104679999743378778656
Q gi|254780805|r  118 NKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       118 d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      -.|+.+++++-=||+  |.|-..|.-+  |.|..||.-.|+|+.||-|-+.|+-.|
T Consensus       129 ~~EsvrLAF~AAlQ~--LpPrQRAvL~--LRdvlGw~A~E~A~~L~~s~ASVnSaL  180 (329)
T TIGR02960       129 ARESVRLAFVAALQL--LPPRQRAVLL--LRDVLGWKAAEVAELLGTSVASVNSAL  180 (329)
T ss_pred             HHHHHHHHHHHHHHC--CCCHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             114689999999874--8814578999--898835555689987438326786588


No 166
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=72.77  E-value=5.7  Score=19.79  Aligned_cols=38  Identities=16%  Similarity=0.114  Sum_probs=25.9

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             2104899999998521011104679999743378778656
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .|.|-+...-.-+.  -.|+|..|||+.+|.|.++|..++
T Consensus       131 ~Lp~~~R~vi~L~~--~~g~s~~EIA~~lgis~~tVk~~l  168 (184)
T PRK12512        131 TLPPRQRDVVQSIA--VEGASIKETAAKLSMSEGAVRVAL  168 (184)
T ss_pred             CCCHHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             89999999999998--559799999999891999999999


No 167
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=72.77  E-value=5.2  Score=20.04  Aligned_cols=41  Identities=27%  Similarity=0.368  Sum_probs=22.2

Q ss_pred             CCCHHHHHHHHHHHHHCCCCCC--CEEECCC--CCCCCCCCCHHH
Q ss_conf             6898899999998863100155--0462056--544533357567
Q gi|254780805|r   57 YFESEGLEDLCQSIKSHGIIQP--LIVRAID--NGLYKIIAGERR   97 (300)
Q Consensus        57 ~~~~~~l~eLa~SI~~~G~lqP--i~Vr~~~--~g~y~ii~G~rR   97 (300)
                      .-+++.++.|+..++..=.+++  ++.++-+  ++-|.|..|.=+
T Consensus        23 ~L~~~el~~l~~~~~r~r~~~kGe~Lf~eGd~~~~ly~V~sG~Vk   67 (235)
T PRK11161         23 TLNEHELDQLDNIIERKKPIQKGQTLFKAGDELKSLYAIRSGTIK   67 (235)
T ss_pred             CCCHHHHHHHHHHHHEEEEECCCCEEECCCCCCCEEEEEEECEEE
T ss_conf             899999999998987404568999877895987708999779599


No 168
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=72.70  E-value=4.3  Score=20.57  Aligned_cols=32  Identities=25%  Similarity=0.284  Sum_probs=24.4

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99852101110467999974337877865656
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      ++.|.+....|..+||+.+|.|+++|.+++.=
T Consensus         9 l~~L~~n~R~s~~~iA~~lg~S~~tv~~Ri~~   40 (108)
T smart00344        9 LEELQKDARISLAELAKKVGLSPSTVHNRVKR   40 (108)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99999828999999999989399999999999


No 169
>COG0020 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism]
Probab=72.56  E-value=1.3  Score=23.83  Aligned_cols=135  Identities=22%  Similarity=0.249  Sum_probs=61.4

Q ss_pred             CCCCCHHHHHHHH--------HHHCCCCCCCCCCCCCHHHHHHH----HHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHH
Q ss_conf             3335756777776--------42100135433346411234556----66543102210489999999852101110467
Q gi|254780805|r   90 KIIAGERRFRAAK--------MASLSEVPVIIRNVDNKSSLEIA----IVENVQRKDLNPLEEALGYEQLISEYGYTQND  157 (300)
Q Consensus        90 ~ii~G~rR~rAa~--------~~g~~~ip~iv~~~~d~~~~~~~----l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~  157 (300)
                      .|.+|+|||...+        ..|...+.-++.-..+--...+.    -.||-.|    |-++-.++-.+...   ...+
T Consensus        22 iImDGN~RwAk~~~~~r~~Gh~~G~~~~~~i~~~~~~lgik~ltlyafSteN~~R----p~~Ev~~lm~l~~~---~l~~   94 (245)
T COG0020          22 IIMDGNRRWAKKRGLPRIEGHKAGAKALREILEWCLELGIKYLTLYAFSTENWKR----PKEEVSFLMELFEK---ALRE   94 (245)
T ss_pred             EEECCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEHHHCCC----CHHHHHHHHHHHHH---HHHH
T ss_conf             8756876799867997457788768999999999998198889999984664188----98999999999999---9999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCHHHHHHHHHC-------CH----HHHHHHHHHHCCCCHHHH-HH
Q ss_conf             999974337877865656543589999876421-016777776401-------00----468999974222477899-99
Q gi|254780805|r  158 IGSIVGKSRSHVANILRILKLPSSVREMIRKEE-ISLGHARTLVST-------SD----PLSLAQVIVSKKMSVRDT-EE  224 (300)
Q Consensus       158 lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~-is~ghar~Ll~~-------~~----~~~la~~Ii~~~LSVRe~-E~  224 (300)
                      ....+-+....|.-.=.+..||+.++..+...+ .|.++...-+.+       .+    ...+++.+.++.+|+-++ |+
T Consensus        95 ~~~~l~~~~v~v~~iG~~~~l~~~~~~~i~~~e~~t~~~~~~~l~~a~nYGGR~eI~~avr~ia~~v~~g~l~~~~I~e~  174 (245)
T COG0020          95 ELKKLHKNGVRIRIIGDLSRLPEEVREAIEKAEEKTKNNTGLTLNIAVNYGGRDEIVDAVRKIAEDVAAGKLSPEDIDEE  174 (245)
T ss_pred             HHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCHHHCCHH
T ss_conf             88888666749999713021988999998999984457896599985378988999999999999987189896876899


Q ss_pred             HHHHHHC
Q ss_conf             9976410
Q gi|254780805|r  225 LVQEQDN  231 (300)
Q Consensus       225 lVk~~~~  231 (300)
                      ++.+...
T Consensus       175 ~i~~~L~  181 (245)
T COG0020         175 LISSHLY  181 (245)
T ss_pred             HHHHHHC
T ss_conf             9997535


No 170
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=72.29  E-value=6.9  Score=19.25  Aligned_cols=17  Identities=18%  Similarity=0.319  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHHHHCCCC
Q ss_conf             88999999988631001
Q gi|254780805|r   60 SEGLEDLCQSIKSHGII   76 (300)
Q Consensus        60 ~~~l~eLa~SI~~~G~l   76 (300)
                      ......|-.++.++|.+
T Consensus        33 ksT~~RlL~tL~~~G~v   49 (246)
T COG1414          33 KSTVHRLLQTLVELGYV   49 (246)
T ss_pred             HHHHHHHHHHHHHCCCE
T ss_conf             88999999999978988


No 171
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=72.20  E-value=5.4  Score=19.93  Aligned_cols=23  Identities=17%  Similarity=0.280  Sum_probs=17.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10467999974337877865656
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      -|.+++|+.+|.+...|...+..
T Consensus       133 pt~~eiA~~l~~s~e~v~~~l~~  155 (257)
T PRK08583        133 PKISEIADRLGVSEEEVLEAMEM  155 (257)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             87999998959599999999997


No 172
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=72.13  E-value=6.8  Score=19.33  Aligned_cols=42  Identities=21%  Similarity=0.214  Sum_probs=29.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0221048999999985210111046799997433787786565
Q gi|254780805|r  132 RKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       132 R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .-+|++.+-. .+..+...-++|+.+||+.++.++++|++.+.
T Consensus         5 ~~glt~~q~~-vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~   46 (101)
T smart00347        5 PLGLTPTQFL-VLRILYEEGPLSVSELAKRLGVSPSTVTRVLD   46 (101)
T ss_pred             HCCCCHHHHH-HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             1394999999-99999976997999999998968879999999


No 173
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=72.08  E-value=6  Score=19.65  Aligned_cols=21  Identities=24%  Similarity=0.338  Sum_probs=14.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q ss_conf             104679999743378778656
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      -|.+++|+.+|.+...|.+.+
T Consensus       143 Pt~~EiA~~lg~~~~~v~~~l  163 (263)
T PRK07122        143 PTASELAAELGMDREEVVEGL  163 (263)
T ss_pred             CCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999989693999999999


No 174
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=72.07  E-value=6  Score=19.66  Aligned_cols=50  Identities=18%  Similarity=0.204  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             104899999998521011104679999743378778656565435899998764
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRK  188 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~  188 (300)
                      |.+-.+..-+  |....|+|.+|||+.+|.|.++|..+|.  ..=..+++.|..
T Consensus       158 Lp~~qR~vl~--Lr~~eglS~~EIAe~Lgis~gTVKsrl~--RAr~~LR~~Lea  207 (222)
T PRK09647        158 LPPEFRAAVV--LCDIEGLSYEEIAATLGVKLGTVRSRIH--RGRQALRAYLAA  207 (222)
T ss_pred             CCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHH
T ss_conf             9999988998--7996399999999998939999999999--999999999871


No 175
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=71.68  E-value=7.5  Score=19.02  Aligned_cols=25  Identities=20%  Similarity=0.315  Sum_probs=13.3

Q ss_pred             CCCHHHHHHHHHH--HHHHHHHHHHHH
Q ss_conf             1104679999743--378778656565
Q gi|254780805|r  152 GYTQNDIGSIVGK--SRSHVANILRIL  176 (300)
Q Consensus       152 ~~t~~~lA~~~G~--s~s~V~~~LrLl  176 (300)
                      |-|--.+|+.+..  +-..|+|-|.+.
T Consensus       100 GTT~~~la~~L~~~~~ltVvTNsl~ia  126 (256)
T PRK10434        100 GSTVLQMVPLLSRFNNITVMTNSLHIV  126 (256)
T ss_pred             CHHHHHHHHHHCCCCCCEEEECCHHHH
T ss_conf             768999999843369978998989999


No 176
>PRK10072 putative transcriptional regulator; Provisional
Probab=71.63  E-value=7.6  Score=19.00  Aligned_cols=28  Identities=29%  Similarity=0.443  Sum_probs=22.3

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9985210111046799997433787786
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVAN  171 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~  171 (300)
                      ++++....|++|.+.|+.+|.|-++|.+
T Consensus        38 vkaIR~~tgl~q~eFA~~lGvSv~tvks   65 (96)
T PRK10072         38 FEQLRKGTGLKIDDFARVLGVSVAMVKE   65 (96)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf             9999988099999999997777999999


No 177
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.28  E-value=5.7  Score=19.82  Aligned_cols=48  Identities=17%  Similarity=0.225  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             1048999999985210111046799997433787786565654358999987642101
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS  192 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is  192 (300)
                      |+.+|.. -++.|.+....++.++|+++|.|.++|.++++         .+..+|-|.
T Consensus         6 lD~~D~~-IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~---------~L~~~GiI~   53 (154)
T COG1522           6 LDDIDRR-ILRLLQEDARISNAELAERVGLSPSTVLRRIK---------RLEEEGVIK   53 (154)
T ss_pred             CCHHHHH-HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH---------HHHHCCCEE
T ss_conf             3799999-99999972765799999997979899999999---------999889769


No 178
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=71.24  E-value=5.8  Score=19.74  Aligned_cols=34  Identities=21%  Similarity=0.225  Sum_probs=25.9

Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99985210111046799997433787786565654
Q gi|254780805|r  143 GYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      .++.|+.. +.++.+||+.+|.|-+||++-=+-++
T Consensus        41 va~~LL~~-~~syreI~~~~g~S~aTItRvsr~Lk   74 (88)
T pfam01371        41 IAKELLRG-ELSQREIAQELGASIATITRGSNCLK   74 (88)
T ss_pred             HHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             99999978-99899999985985231478899987


No 179
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=71.23  E-value=7.5  Score=19.06  Aligned_cols=38  Identities=24%  Similarity=0.378  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999985210--1110467999974337877865656
Q gi|254780805|r  138 LEEALGYEQLISE--YGYTQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       138 ~e~A~~~~~l~~~--~~~t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      +++|..+-.++..  ..++..+||+.+|.+++++.++|.-
T Consensus         2 l~r~l~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~t   41 (52)
T pfam09339         2 LDRALAILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQT   41 (52)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             8999999999862899989999999989199999999999


No 180
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=71.05  E-value=8  Score=18.87  Aligned_cols=40  Identities=28%  Similarity=0.397  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             48999999985210--11104679999743378778656565
Q gi|254780805|r  137 PLEEALGYEQLISE--YGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       137 p~e~A~~~~~l~~~--~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      .+++|..+-.++..  .+++..+||+.+|.+++++.++|.-+
T Consensus         3 sl~ral~IL~~l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL   44 (91)
T smart00346        3 SLERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTL   44 (91)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             799999999999728999899999999890999999999999


No 181
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=70.85  E-value=8.2  Score=18.80  Aligned_cols=19  Identities=16%  Similarity=0.059  Sum_probs=7.0

Q ss_pred             CHHHHHHHHHHHHHHHHHH
Q ss_conf             0467999974337877865
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~  172 (300)
                      +..+||+.+|.|..||++-
T Consensus        21 ~v~eLa~~~~VS~~TIRRD   39 (251)
T PRK13509         21 TVEKVIERLGISPATARRD   39 (251)
T ss_pred             EHHHHHHHHCCCHHHHHHH
T ss_conf             8999999989699899983


No 182
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=70.63  E-value=7.1  Score=19.18  Aligned_cols=39  Identities=13%  Similarity=0.161  Sum_probs=26.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|++-.+..-.-+..  .|+|..+||+.+|.|.++|..+|.
T Consensus       127 ~L~~~~r~ii~l~~~--~~~s~~EIA~~l~is~~tV~~rl~  165 (177)
T PRK09415        127 SLPIKYREVIYLFYY--EELSIKEIATVTGVNENTIKTRLK  165 (177)
T ss_pred             CCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             699999999999998--099899999988929999999999


No 183
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=70.48  E-value=3.5  Score=21.13  Aligned_cols=28  Identities=21%  Similarity=0.252  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1110467999974337877865656543
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRILKL  178 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L  178 (300)
                      -.+|-+++|+.+|.||.++++||.-+.-
T Consensus       172 ~~~Taeela~~~giSRvTaRRYLeyl~~  199 (224)
T COG4565         172 QELTAEELAQALGISRVTARRYLEYLVS  199 (224)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             7647999998837219999999999984


No 184
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=70.25  E-value=8.3  Score=18.74  Aligned_cols=11  Identities=18%  Similarity=0.365  Sum_probs=5.2

Q ss_pred             CCCHHHHHHHH
Q ss_conf             11046799997
Q gi|254780805|r  152 GYTQNDIGSIV  162 (300)
Q Consensus       152 ~~t~~~lA~~~  162 (300)
                      |-|--++|+.+
T Consensus       100 GTT~~~la~~L  110 (252)
T PRK10906        100 GTTPEAVAHAL  110 (252)
T ss_pred             CHHHHHHHHHC
T ss_conf             63799998533


No 185
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=70.18  E-value=5.6  Score=19.84  Aligned_cols=22  Identities=14%  Similarity=0.311  Sum_probs=12.3

Q ss_pred             HHHHHHCCCC--HHHHHHHHHHHH
Q ss_conf             9997422247--789999997641
Q gi|254780805|r  209 AQVIVSKKMS--VRDTEELVQEQD  230 (300)
Q Consensus       209 a~~Ii~~~LS--VRe~E~lVk~~~  230 (300)
                      .+......|.  |||.++.+.+..
T Consensus       346 ~~~L~~y~WPGNvREL~n~iera~  369 (441)
T PRK10365        346 MDLLIHYDWPGNIRELENAVERAV  369 (441)
T ss_pred             HHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             999970999989999999999999


No 186
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=70.13  E-value=8.6  Score=18.66  Aligned_cols=21  Identities=24%  Similarity=0.192  Sum_probs=14.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q ss_conf             104679999743378778656
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .|.+++|+.+|.+...|...+
T Consensus       140 pt~~eiA~~l~i~~~~v~~~l  160 (257)
T PRK08215        140 PTVSEIAKELEVPREEVVFAL  160 (257)
T ss_pred             CCHHHHHHHHCCCHHHHHHHH
T ss_conf             999999988098999999999


No 187
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=70.12  E-value=8.6  Score=18.66  Aligned_cols=47  Identities=15%  Similarity=0.155  Sum_probs=34.5

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Q ss_conf             999985210111046799997433787786565-654358999987642
Q gi|254780805|r  142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILR-ILKLPSSVREMIRKE  189 (300)
Q Consensus       142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr-Ll~L~~~i~~~l~~~  189 (300)
                      .-+..|++ ...+|.||+..+|.|-++|++=-. |-.+||++++.+...
T Consensus        51 ~Iv~eLL~-ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~   98 (103)
T COG2973          51 RIVEELLR-GELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKV   98 (103)
T ss_pred             HHHHHHHH-CCCCHHHHHHHHCCCHHHHCCCHHHHCCCCHHHHHHHHHH
T ss_conf             99999995-6353999999858625655044444235987899999997


No 188
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=69.86  E-value=7.5  Score=19.02  Aligned_cols=39  Identities=18%  Similarity=0.180  Sum_probs=26.2

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-.+-.-.  |..-.|+|..|||+.+|.|.++|.++|.
T Consensus       139 ~Lp~~~r~il~--L~~~~g~s~~EIA~~l~is~~tVk~~l~  177 (194)
T PRK12513        139 TLPDEQREVFL--LREHGDLSLEEIAQLTGVPLETVKSRLR  177 (194)
T ss_pred             CCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             29989999999--9998499999999998949999999999


No 189
>pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
Probab=69.45  E-value=5.6  Score=19.84  Aligned_cols=26  Identities=15%  Similarity=0.279  Sum_probs=21.2

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             210111046799997433787786565
Q gi|254780805|r  148 ISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       148 ~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ++. |.|..++|++||.|+++|.+-++
T Consensus        15 ve~-G~S~~eaA~~F~Is~~Tv~rWlk   40 (120)
T pfam01710        15 IES-GGSITEASKVFQIGRATIYRWLK   40 (120)
T ss_pred             HHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             986-99999999993702999999985


No 190
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=69.37  E-value=8.9  Score=18.56  Aligned_cols=21  Identities=10%  Similarity=0.232  Sum_probs=13.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |.+++|+.+|.+...|...+.
T Consensus       128 t~~eiA~~l~i~~~~v~~~~~  148 (257)
T PRK05911        128 TDGELCEYLNISQQELSGWFS  148 (257)
T ss_pred             CHHHHHHHHCCCHHHHHHHHH
T ss_conf             999999883979999999998


No 191
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=69.09  E-value=9  Score=18.52  Aligned_cols=46  Identities=11%  Similarity=0.145  Sum_probs=31.4

Q ss_pred             HHCCCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             310221048999999985210-11104679999743378778656565
Q gi|254780805|r  130 VQRKDLNPLEEALGYEQLISE-YGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       130 ~~R~dl~p~e~A~~~~~l~~~-~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      +.--+|++.+ +..+..|.+. -|.||.+||+.+|.+++++++.+.=+
T Consensus        24 L~~~gLt~~q-~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~L   70 (144)
T PRK03573         24 LKPLELTQTH-WVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQL   70 (144)
T ss_pred             HHHCCCCHHH-HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             8866998259-9999999973989899999999798783699999999


No 192
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=69.07  E-value=7  Score=19.21  Aligned_cols=45  Identities=16%  Similarity=0.366  Sum_probs=30.2

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCH
Q ss_conf             52101110467999974337877865656543589999876-421016
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIR-KEEISL  193 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~-~~~is~  193 (300)
                      |....|+|.+|||+.+|.|.++|..+|.  ..=..+++.|. .|....
T Consensus       130 L~~~egls~~EIAe~Lgis~~TVksrl~--RAr~~Lr~~L~~~g~~~~  175 (190)
T PRK12516        130 LIGASGFAYEEAAEICGCAVGTIKSRVS--RARARLQEILQIEGEADY  175 (190)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHCCCCCC
T ss_conf             8998299999999998949999999999--999999999984599878


No 193
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=68.99  E-value=4  Score=20.76  Aligned_cols=36  Identities=25%  Similarity=0.459  Sum_probs=27.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH
Q ss_conf             104679999743378778656565435899998764210167777
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHAR  197 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar  197 (300)
                      +||++||..+|-+|.+|++.|.         ++-++|-|+.+..+
T Consensus       146 lT~~eLA~~iGttREtVsR~L~---------~l~~~GlI~~~~~~  181 (201)
T PRK13918        146 ATHDELAAAVGSVRETVTKVVG---------ELSREGVIRSGYGK  181 (201)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH---------HHHHCCCEEECCCE
T ss_conf             7999999885986899999999---------99988988967998


No 194
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=68.92  E-value=7.2  Score=19.15  Aligned_cols=37  Identities=30%  Similarity=0.405  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             48999999985210111046799997433787786565
Q gi|254780805|r  137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |-++-..+ .|..-.|+|..|||+.+|.|.++|..+|.
T Consensus       114 p~~~R~v~-~L~~~~g~s~~EIA~~lgis~~tVk~~l~  150 (161)
T PRK12541        114 PLERRNVL-LLRDYYGFSYKEIAEMTGLSLAKVKIELH  150 (161)
T ss_pred             CHHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999-98997499999999998939999999999


No 195
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=68.64  E-value=7.3  Score=19.12  Aligned_cols=27  Identities=26%  Similarity=0.479  Sum_probs=22.0

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             521011104679999743378778656
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      |....|+|.+|||+.+|.|.++|..+|
T Consensus       147 L~~~egls~~EIA~~lgis~~tVks~l  173 (195)
T PRK12532        147 LKEILGFSSDEIQQMCGISTSNYHTIM  173 (195)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             999819999999999895999999999


No 196
>PRK11753 cAMP-regulatory protein; Provisional
Probab=68.62  E-value=4.2  Score=20.67  Aligned_cols=20  Identities=50%  Similarity=0.768  Sum_probs=9.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             04679999743378778656
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~L  173 (300)
                      ||++||..+|.+|.+|++.|
T Consensus       170 t~~eLA~~lG~sretvsR~L  189 (211)
T PRK11753        170 TRQEIGRIVGCSREMVGRVL  189 (211)
T ss_pred             CHHHHHHHHCCCHHHHHHHH
T ss_conf             99999988699899999999


No 197
>PRK00215 LexA repressor; Validated
Probab=68.62  E-value=5.9  Score=19.68  Aligned_cols=48  Identities=31%  Similarity=0.441  Sum_probs=32.3

Q ss_pred             HHHHHHHHCCC--CHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHH
Q ss_conf             99985210111--04679999743-378778656565435899998764210--16777776
Q gi|254780805|r  143 GYEQLISEYGY--TQNDIGSIVGK-SRSHVANILRILKLPSSVREMIRKEEI--SLGHARTL  199 (300)
Q Consensus       143 ~~~~l~~~~~~--t~~~lA~~~G~-s~s~V~~~LrLl~L~~~i~~~l~~~~i--s~ghar~L  199 (300)
                      .++..++++|+  |..|||+.+|. |.++|.++|.         .+...|-|  ..|++|++
T Consensus        12 fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~---------~Le~kG~i~r~~~~~R~i   64 (204)
T PRK00215         12 FIKDRIEETGYPPSRREIADALGLRSPSAVHEHLK---------ALERKGFIRRDPGRSRAI   64 (204)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHH---------HHHHCCCEECCCCCCCEE
T ss_conf             99999997488998999999809998189999999---------998797887069997338


No 198
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=68.57  E-value=5  Score=20.15  Aligned_cols=10  Identities=0%  Similarity=-0.144  Sum_probs=4.8

Q ss_pred             CCCCCCCCCC
Q ss_conf             0013543334
Q gi|254780805|r  106 LSEVPVIIRN  115 (300)
Q Consensus       106 ~~~ip~iv~~  115 (300)
                      ...+|+++.+
T Consensus       134 ~~~~piV~v~  143 (327)
T PRK10339        134 ALTDNICFID  143 (327)
T ss_pred             HCCCCEEEEE
T ss_conf             5699999995


No 199
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=68.48  E-value=2.2  Score=22.45  Aligned_cols=20  Identities=25%  Similarity=0.506  Sum_probs=15.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHH
Q ss_conf             10467999974337877865
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~  172 (300)
                      .||-|+|..||.|+-+|||.
T Consensus       200 kTQ~eVA~~LGISQVQVSRl  219 (231)
T TIGR02885       200 KTQTEVAKMLGISQVQVSRL  219 (231)
T ss_pred             CHHHHHHHHCCCCCCHHHHH
T ss_conf             01799997718570012278


No 200
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=68.44  E-value=7.8  Score=18.91  Aligned_cols=27  Identities=19%  Similarity=0.187  Sum_probs=21.9

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             210111046799997433787786565
Q gi|254780805|r  148 ISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       148 ~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ..-.|+|..|||+.+|.|.++|..++.
T Consensus       143 ~~~eg~s~~EIA~~lgis~~tVks~l~  169 (184)
T PRK12539        143 VKLDGLSVAEAATRSGMSESAVKVSVH  169 (184)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             999499999999998919999999999


No 201
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=68.29  E-value=9.4  Score=18.42  Aligned_cols=32  Identities=25%  Similarity=0.292  Sum_probs=23.0

Q ss_pred             HHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9998521011-1046799997433787786565
Q gi|254780805|r  143 GYEQLISEYG-YTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       143 ~~~~l~~~~~-~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ++..|.++.| .+..+||+.+|.|+++|+..++
T Consensus        12 ~Iy~L~~~~~~vr~~dIA~~L~Vs~~SVs~mik   44 (142)
T PRK03902         12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQ   44 (142)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf             999998258971299999997899533999999


No 202
>pfam06245 DUF1015 Protein of unknown function (DUF1015). Family of proteins with unknown function found in archaea and bacteria.
Probab=68.10  E-value=4.8  Score=20.26  Aligned_cols=11  Identities=36%  Similarity=0.703  Sum_probs=4.1

Q ss_pred             CCCCHHHHHHH
Q ss_conf             33575677777
Q gi|254780805|r   91 IIAGERRFRAA  101 (300)
Q Consensus        91 ii~G~rR~rAa  101 (300)
                      |-+||+|+.|+
T Consensus       203 IADGHHR~~ta  213 (411)
T pfam06245       203 IADGHHRYASA  213 (411)
T ss_pred             EECCCCCHHHH
T ss_conf             81484113889


No 203
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=68.07  E-value=9.5  Score=18.39  Aligned_cols=38  Identities=18%  Similarity=0.302  Sum_probs=26.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-....-+-+   ..|+|..+||+.+|.|.++|.++|.
T Consensus       112 ~Lp~~~r~v~~l~---~~g~s~~EIA~~l~is~~tVk~~l~  149 (166)
T PRK09639        112 KMTERDRTVLLLR---FSGYSYKEIAQALGIDESSVGTTLH  149 (166)
T ss_pred             HCCHHHHHHHHHH---HHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             3999999999999---9389999999998919999999999


No 204
>pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Probab=68.02  E-value=9  Score=18.54  Aligned_cols=24  Identities=29%  Similarity=0.493  Sum_probs=20.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565654
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      |..++|+.+|.|+++|.+.+..|.
T Consensus        26 s~~~La~~~~vSr~tvr~Al~~L~   49 (64)
T pfam00392        26 SERELAAEFGVSRTTVREALRRLE   49 (64)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             799999997969999999999999


No 205
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=67.96  E-value=8.1  Score=18.82  Aligned_cols=37  Identities=14%  Similarity=0.168  Sum_probs=26.1

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             101110467999974337877865656543589999876
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIR  187 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~  187 (300)
                      ...|+|.+|||+.+|.|.+||..+|.  ..=..+.++|.
T Consensus       162 ~~eglS~~EIA~~Lgis~~TVKsrL~--RArk~LRe~La  198 (231)
T PRK11922        162 VVEELSVEETAQALGLPEETVKTRLH--RARRLLRESLA  198 (231)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHH
T ss_conf             99399999999998939999999999--99999999999


No 206
>pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.).
Probab=67.74  E-value=8.5  Score=18.70  Aligned_cols=34  Identities=29%  Similarity=0.510  Sum_probs=24.3

Q ss_pred             HHHHHHHCC-----CCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             998521011-----1046799997433787786565654
Q gi|254780805|r  144 YEQLISEYG-----YTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       144 ~~~l~~~~~-----~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      ++.|++.|.     ..-++||+.+++|.++|+|.|.-|+
T Consensus        10 L~aLI~lY~~~~~pVks~~IAe~l~~spgTIRN~M~~L~   48 (79)
T pfam03444        10 LQALINLYRKKGRAVKGEEIADIIGRNPGTVRNQMQSLK   48 (79)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             999999999729986679999998789088999999999


No 207
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=67.70  E-value=9.6  Score=18.34  Aligned_cols=46  Identities=9%  Similarity=0.076  Sum_probs=33.3

Q ss_pred             HHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             54310221048999999985210111046799997433787786565
Q gi|254780805|r  128 ENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       128 EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      +.+.--+|++.+-+ .+..|....++|+.++|+.+|.++++|++.+.
T Consensus        31 ~~L~~~gLt~~Q~~-vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ld   76 (144)
T PRK11512         31 EYLSPLDITAAQFK-VLCSIRCAACITPVELKKVLSVDLGALTRMLD   76 (144)
T ss_pred             HHHHHCCCCHHHHH-HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             98754599999999-99999986997999999997888878999999


No 208
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=67.67  E-value=3.6  Score=21.07  Aligned_cols=33  Identities=24%  Similarity=0.460  Sum_probs=23.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Q ss_conf             04679999743378778656565-4358999987
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRIL-KLPSSVREMI  186 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l  186 (300)
                      |-.++|+..|.|.++||+.|.=- ..+++.++.|
T Consensus         1 Ti~DIA~~agVS~~TVSr~ln~~~~vs~~tr~rI   34 (46)
T pfam00356         1 TIKDVARLAGVSKATVSRVLNNPERVSEETREKV   34 (46)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             9999999989799999999879798999999999


No 209
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=67.30  E-value=8.3  Score=18.75  Aligned_cols=24  Identities=25%  Similarity=0.459  Sum_probs=20.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565654
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      |..++|+.+|.|+++|.+.++.|.
T Consensus        22 s~~~la~~~~vSr~tvr~A~~~L~   45 (60)
T smart00345       22 SERELAAQLGVSRTTVREALSRLE   45 (60)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             099999998949999999999999


No 210
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=67.07  E-value=9.3  Score=18.44  Aligned_cols=49  Identities=31%  Similarity=0.374  Sum_probs=37.2

Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             66654310221048999999985210111046799997433787786565
Q gi|254780805|r  125 AIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       125 ~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .+.+|++--.|+.. +|.+|..|+.....|..++++..|..++.|...|+
T Consensus         4 ~~~~~L~~lGlt~y-Ea~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~   52 (247)
T COG1378           4 ELEENLQKLGLTEY-EAKVYLALLCLGEATAKEISEASGVPRPKVYDVLR   52 (247)
T ss_pred             HHHHHHHHCCCCHH-HHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHH
T ss_conf             79999998199788-99999999981887799999865999322999999


No 211
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=66.95  E-value=8.8  Score=18.58  Aligned_cols=24  Identities=13%  Similarity=0.268  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|.+|||+.+|.+.++|..+|.
T Consensus       145 egls~~EIA~~lg~~~gTVKsRl~  168 (185)
T PRK09649        145 LGLSYADAAAVCGCPVGTIRSRVA  168 (185)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             299999999998939999999999


No 212
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304   This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis . This group has a very sporadic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member Dechloromonas aromatica (strain RCB), that appears to have two of these sigma factors. A member of which appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri (strain ATCC 700601 / ES114), where a second one is chromosomally encoded..
Probab=66.86  E-value=4.6  Score=20.38  Aligned_cols=35  Identities=26%  Similarity=0.218  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             489999999852101110467999974337877865
Q gi|254780805|r  137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      |=+.+.|+ +|.+--|+||.++|++||.|-|.+.-+
T Consensus       102 P~~~r~a~-~L~el~G~sQ~e~A~kLGlSlSGaKSR  136 (170)
T TIGR02959       102 PDEYREAI-RLTELEGLSQKEIAEKLGLSLSGAKSR  136 (170)
T ss_pred             CHHHHHHH-HHHHCCCCCHHHHHHHCCCCCCCHHHH
T ss_conf             98678898-887507998279987617533515678


No 213
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=66.68  E-value=5.7  Score=19.81  Aligned_cols=37  Identities=11%  Similarity=0.230  Sum_probs=24.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99852101110467999974337877865656543589
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSS  181 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~  181 (300)
                      +.+-.+..|||+|+||+++..-.|+|.+. -=..|.|+
T Consensus        88 IR~eREKRgwS~E~LAkki~eK~S~i~ki-E~~e~eP~  124 (169)
T TIGR00270        88 IREEREKRGWSREELAKKIKEKASVIKKI-EREELEPE  124 (169)
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHHHHHHHH-HHHCCCCC
T ss_conf             22000146878789999874106788887-54037988


No 214
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=66.61  E-value=9.4  Score=18.40  Aligned_cols=24  Identities=17%  Similarity=0.263  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|..|||+.+|.|.++|..++.
T Consensus       152 ~g~s~~EIA~~lg~s~~tVk~~l~  175 (187)
T PRK09648        152 VGLSAEETAEAVGSTPGAVRVAQH  175 (187)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             499999999998939999999999


No 215
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=66.53  E-value=10  Score=18.20  Aligned_cols=21  Identities=19%  Similarity=0.461  Sum_probs=10.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |..+||+.+|.||.||.+.|.
T Consensus        27 sE~eLa~~~~VSR~TvR~Al~   47 (231)
T TIGR03337        27 SERDLGERFNTTRVTIREALQ   47 (231)
T ss_pred             CHHHHHHHHCCCHHHHHHHHH
T ss_conf             899999997979999999999


No 216
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=66.41  E-value=4.3  Score=20.58  Aligned_cols=22  Identities=23%  Similarity=0.383  Sum_probs=14.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      +|+++||..+|.++.+|++.|+
T Consensus       174 lT~~dLA~~lG~trETVsR~L~  195 (224)
T PRK09391        174 MSRRDIADYLGLTIETVSRALS  195 (224)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
T ss_conf             7999999887997999999999


No 217
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=66.37  E-value=8.5  Score=18.67  Aligned_cols=41  Identities=29%  Similarity=0.234  Sum_probs=27.6

Q ss_pred             CCCCHHHHHHHHHHH--HHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             221048999999985--21011104679999743378778656
Q gi|254780805|r  133 KDLNPLEEALGYEQL--ISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l--~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      ..|+|-|.-.--.+.  .+.-..|+.+||+.+|.|+.+|++.-
T Consensus       173 ~~L~~REr~II~~RfGL~~~~~~Tl~eIg~~lgiSrERVRQIe  215 (228)
T PRK05803        173 DILDPREKEVIEMRYGLGDGKEKTQREIAKALGISRSYVSRIE  215 (228)
T ss_pred             HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             5189889999999864789997159999999897999999999


No 218
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=66.30  E-value=8.9  Score=18.56  Aligned_cols=23  Identities=4%  Similarity=0.208  Sum_probs=13.2

Q ss_pred             HHHHHHHCCCC--HHHHHHHHHHHH
Q ss_conf             99997422247--789999997641
Q gi|254780805|r  208 LAQVIVSKKMS--VRDTEELVQEQD  230 (300)
Q Consensus       208 la~~Ii~~~LS--VRe~E~lVk~~~  230 (300)
                      ..+......|.  |||.++.+.+..
T Consensus       349 a~~~L~~y~WPGNvREL~n~ierav  373 (457)
T PRK11361        349 AMSLLTAWSWPGNIRELSNVIERAV  373 (457)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf             9999956999979999999999999


No 219
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=66.23  E-value=10  Score=18.16  Aligned_cols=43  Identities=12%  Similarity=0.168  Sum_probs=31.3

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             210111046799997433787786565654358999987642101
Q gi|254780805|r  148 ISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS  192 (300)
Q Consensus       148 ~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is  192 (300)
                      ..-.|+|.+|+|+.+|.+.+||..+|.  .-=..+.+++..|.=+
T Consensus       144 ~~~~g~s~~EIA~ilgi~~gTVKsRl~--RAr~~Lr~~L~~~~~~  186 (195)
T PRK12535        144 TQVLGYTYEEAAKIADVRVGTIRSRVA--RARADLVAATATGDSS  186 (195)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHCCCCC
T ss_conf             998299899999998939999999999--9999999997568976


No 220
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=66.21  E-value=4  Score=20.77  Aligned_cols=33  Identities=24%  Similarity=0.435  Sum_probs=22.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Q ss_conf             04679999743378778656565-4358999987
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRIL-KLPSSVREMI  186 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l  186 (300)
                      |-.++|++.|.|.++||+.|.=- ..+++..+.|
T Consensus         2 Ti~dvA~~aGVS~sTVSr~ln~~~~Vs~~tr~rV   35 (70)
T smart00354        2 TIKDVARLAGVSKATVSRVLNGNGRVSEETREKV   35 (70)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             8999999989599999999779998999999999


No 221
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=66.19  E-value=9  Score=18.53  Aligned_cols=24  Identities=17%  Similarity=0.198  Sum_probs=19.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|.+|||+.+|.|.+||..+|.
T Consensus       168 egls~~EIA~~l~is~~TVksrl~  191 (206)
T PRK12526        168 QELSQEQLAQQLNVPLGTVKSRLR  191 (206)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             599999999998939999999999


No 222
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=65.82  E-value=10  Score=18.11  Aligned_cols=22  Identities=23%  Similarity=0.298  Sum_probs=16.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|.+++|+.+|.+...|...+.
T Consensus       131 pt~~eia~~lg~~~~~v~~~~~  152 (261)
T PRK06288        131 PTDDEIAKELGISLEEYHSLLS  152 (261)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHH
T ss_conf             9878888781999999999999


No 223
>PRK05412 nucleotide-binding protein; Reviewed
Probab=65.66  E-value=11  Score=18.09  Aligned_cols=38  Identities=16%  Similarity=0.278  Sum_probs=29.3

Q ss_pred             HCCEEEEECCCCCEEEEEEECCHHHHHHHHHHHCCCCCCC
Q ss_conf             3987999717982289998589899999999837564569
Q gi|254780805|r  261 VGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGENDFEY  300 (300)
Q Consensus       261 lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL~~~~~~~  300 (300)
                      .+.||+..-.+.  .|.+.-+..|+|..++..|++.+|++
T Consensus       115 ~klKVqa~IQGd--~vRVtgKkrDDLQ~vi~llk~~d~~~  152 (161)
T PRK05412        115 SKLKVQAQIQGD--QVRVTGKKRDDLQAVIALLRGADLGQ  152 (161)
T ss_pred             CCCCEEEEECCC--EEEEECCCHHHHHHHHHHHHHCCCCC
T ss_conf             488136886485--78861598889999999998327799


No 224
>pfam04461 DUF520 Protein of unknown function (DUF520). Family of uncharacterized proteins.
Probab=65.65  E-value=11  Score=18.09  Aligned_cols=38  Identities=18%  Similarity=0.345  Sum_probs=29.4

Q ss_pred             HCCEEEEECCCCCEEEEEEECCHHHHHHHHHHHCCCCCCC
Q ss_conf             3987999717982289998589899999999837564569
Q gi|254780805|r  261 VGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGENDFEY  300 (300)
Q Consensus       261 lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL~~~~~~~  300 (300)
                      .+.||+..-.+.  .|.+.-+..|+|...+..|+..+|++
T Consensus       115 ~klKVqa~IQGd--~vRVsgKkrDDLQ~vi~~lK~~d~~~  152 (160)
T pfam04461       115 SKLKVQAAIQGD--QVRVTGKKRDDLQAVIALLREADLDL  152 (160)
T ss_pred             CCCCEEEEECCC--EEEEECCCHHHHHHHHHHHHHCCCCC
T ss_conf             488036886485--78861598889999999998327799


No 225
>PRK11886 biotin--protein ligase; Provisional
Probab=65.63  E-value=11  Score=18.09  Aligned_cols=23  Identities=13%  Similarity=0.098  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHCCEEEEECCC
Q ss_conf             89999999999739879997179
Q gi|254780805|r  249 YLTDLEKKISSKVGLNISIKHRN  271 (300)
Q Consensus       249 ~i~~le~~L~~~lGtkV~I~~~~  271 (300)
                      .+.+..++....+|..|.+...+
T Consensus       259 ~~~~~w~~~~~~~Gk~V~v~~~~  281 (319)
T PRK11886        259 PFLERWKKLDLFLGREVKLIIGQ  281 (319)
T ss_pred             HHHHHHHHHHCCCCCEEEEEECC
T ss_conf             99999998507169879999899


No 226
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=65.43  E-value=7.4  Score=19.09  Aligned_cols=76  Identities=12%  Similarity=0.125  Sum_probs=41.3

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHC-CHHHHHHHHHHHCCCCHH--HHH
Q ss_conf             52101110467999974337877865656543589999876421016777776401-004689999742224778--999
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVST-SDPLSLAQVIVSKKMSVR--DTE  223 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~-~~~~~la~~Ii~~~LSVR--e~E  223 (300)
                      |.+...++.-++++.+|.|+++||+.|+.+.-. .+...=++|.-      ....+ ++....+..++.+.|+-.  +++
T Consensus        23 L~~~gelcV~eL~~~l~~sQs~vS~HL~~L~~a-GlV~~rr~G~~------vyY~Ln~~~~~~~~~~l~~~~~~~~~~~~   95 (106)
T PRK10141         23 LRESGELCVCDLCTALDQSQPKISRHLALLRES-GLLLDRKQGKW------VHYRLSPHIPAWAAKIIEQAWLCQQEDVQ   95 (106)
T ss_pred             HHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCCEEEECCEE------EEEEECCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             987499569999988699888999999999988-97303741417------99877998859999999999983599999


Q ss_pred             HHHHHH
Q ss_conf             999764
Q gi|254780805|r  224 ELVQEQ  229 (300)
Q Consensus       224 ~lVk~~  229 (300)
                      ++++++
T Consensus        96 ~~~~kl  101 (106)
T PRK10141         96 AIVRKL  101 (106)
T ss_pred             HHHHHH
T ss_conf             999988


No 227
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745   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 describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=65.22  E-value=6.6  Score=19.39  Aligned_cols=54  Identities=20%  Similarity=0.292  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHCCCCC-HHHHH--------HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3455666543102210-48999--------999985210111046799997433787786565
Q gi|254780805|r  121 SLEIAIVENVQRKDLN-PLEEA--------LGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       121 ~~~~~l~EN~~R~dl~-p~e~A--------~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      -.++.++-.-.|.++. .+.+|        +.+-||.=-.++|-++||..+|.++||||+.+.
T Consensus       142 DpEl~llr~~~r~~f~~Al~~Al~~L~~rER~LLRLHfv~~Ls~~r~g~my~~~~STvsR~~~  204 (249)
T TIGR03001       142 DPELDLLRERYRQEFRAALREALAALSERERTLLRLHFVEGLSMDRLGAMYQVHRSTVSRWVA  204 (249)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf             178999999999999999999873289868765556882033299998774577507899999


No 228
>PRK09526 lacI lac repressor; Reviewed
Probab=65.21  E-value=6.6  Score=19.39  Aligned_cols=17  Identities=6%  Similarity=0.104  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHHHHHCCC
Q ss_conf             48999999985210111
Q gi|254780805|r  137 PLEEALGYEQLISEYGY  153 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~  153 (300)
                      ..++..+|++.+.++|.
T Consensus       196 ~~~R~~Gf~~~~~~~~l  212 (342)
T PRK09526        196 ARLRLAGWLEYLTRNQL  212 (342)
T ss_pred             HHHHHHHHHHHHHHCCC
T ss_conf             99999999999997798


No 229
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=65.13  E-value=9.4  Score=18.41  Aligned_cols=36  Identities=8%  Similarity=-0.007  Sum_probs=24.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11104679999743378778656565435899998764
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRK  188 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~  188 (300)
                      .|+|.+|||..+|.|.++|..+|.  ..-..+++.+.+
T Consensus       121 e~~s~~EIA~~l~is~~tVk~~l~--RArk~Lkk~lke  156 (160)
T PRK09642        121 EEKSYQEIALQENIEVKTVEMKLY--RARKWIKKHWKE  156 (160)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHH
T ss_conf             299999999998919999999999--999999999987


No 230
>TIGR02850 spore_sigG RNA polymerase sigma-G factor; InterPro: IPR014212   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Members of this entry comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=64.93  E-value=8.7  Score=18.63  Aligned_cols=21  Identities=29%  Similarity=0.517  Sum_probs=13.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHH
Q ss_conf             110467999974337877865
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      |-||-++|+.+|.|+++|+++
T Consensus       222 G~tqmeva~eiGisqaqvsrl  242 (254)
T TIGR02850       222 GKTQMEVAEEIGISQAQVSRL  242 (254)
T ss_pred             CCHHHHHHHHHCCHHHHHHHH
T ss_conf             631334565403016888888


No 231
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications.  Binding of the effector to GntR-like transcriptional regulators is 
Probab=64.65  E-value=11  Score=17.97  Aligned_cols=24  Identities=29%  Similarity=0.500  Sum_probs=20.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565654
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +..++|+.+|.|+++|.+.+..|.
T Consensus        27 s~~~La~~~~vSr~tvr~Al~~L~   50 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELE   50 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             799999997988899999999999


No 232
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=64.50  E-value=10  Score=18.23  Aligned_cols=39  Identities=15%  Similarity=0.198  Sum_probs=24.5

Q ss_pred             CCHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             104899999998521011--10467999974337877865656
Q gi|254780805|r  135 LNPLEEALGYEQLISEYG--YTQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~--~t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      .+-++.|  ...|..+.|  -|.++||+.+|.+...|...+..
T Consensus        98 ~~ki~~a--~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~  138 (229)
T PRK12427         98 THKTNEA--IRQIAKRLGHEPNFEEISAELNLTADEYQEYLLL  138 (229)
T ss_pred             HHHHHHH--HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999999--9999998588999999998919999999999998


No 233
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=64.28  E-value=11  Score=17.92  Aligned_cols=18  Identities=6%  Similarity=0.054  Sum_probs=9.8

Q ss_pred             CHHHHHHHHHHHHHCCCC
Q ss_conf             988999999988631001
Q gi|254780805|r   59 ESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        59 ~~~~l~eLa~SI~~~G~l   76 (300)
                      +...+.-|..++.+.|.+
T Consensus        53 pksT~~RlL~tL~~~G~v   70 (271)
T PRK10163         53 PLSTTFRLLKVLQAADFV   70 (271)
T ss_pred             CHHHHHHHHHHHHHCCCE
T ss_conf             999999999999968988


No 234
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=63.81  E-value=10  Score=18.12  Aligned_cols=28  Identities=18%  Similarity=0.374  Sum_probs=22.8

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |....|+|..|||+.+|.|.++|..+|.
T Consensus       123 L~~~~g~s~~EIA~~lgis~~tVksrl~  150 (164)
T PRK12547        123 LIGASGFSYEEAAEICGCAVGTIKSRVS  150 (164)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             8998499999999998939999999999


No 235
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=63.68  E-value=5.9  Score=19.73  Aligned_cols=27  Identities=26%  Similarity=0.282  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565654
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +-+|+.++|+..|.|+.+|.+.|.+|.
T Consensus        74 lI~T~R~lae~~gvs~~TV~~tmK~L~  100 (165)
T pfam05732        74 LIMTQREIAEETGISLETVRQTMKALE  100 (165)
T ss_pred             EEEEHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             998789999983952999999999997


No 236
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=63.66  E-value=10  Score=18.12  Aligned_cols=38  Identities=13%  Similarity=0.350  Sum_probs=26.2

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565654358999987
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI  186 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l  186 (300)
                      |..-.|+|..|||+.+|.|.++|..+|.  ..=..+++++
T Consensus       124 L~~~egls~~EIAe~Lgis~gTVKsRL~--RAR~~Lr~~L  161 (188)
T PRK12546        124 LVGASGFSYEEAAEMCGVAVGTVKSRAN--RARARLAELL  161 (188)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHH
T ss_conf             7998298999999998939999999999--9999999987


No 237
>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
Probab=63.60  E-value=9.3  Score=18.43  Aligned_cols=56  Identities=14%  Similarity=0.227  Sum_probs=34.2

Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHC---------CCCHHHHHHHHHHHHHHHHHHHH--HHHHHH
Q ss_conf             666543102210489999999852101---------11046799997433787786565--654358
Q gi|254780805|r  125 AIVENVQRKDLNPLEEALGYEQLISEY---------GYTQNDIGSIVGKSRSHVANILR--ILKLPS  180 (300)
Q Consensus       125 ~l~EN~~R~dl~p~e~A~~~~~l~~~~---------~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~  180 (300)
                      .++.++++..-+-+.-+..+-....+|         -+|..++|+.+|.+.||||+.++  .+..|-
T Consensus        13 ~li~~i~~R~~Tl~~V~~~Iv~~Q~~Ff~~g~~~l~PLtlk~iA~~l~lh~STVSRav~~Kyi~tp~   79 (160)
T pfam04552        13 WLIRSLEQRAETLLKVAREIVRRQEDFLEKGPEALRPLTLREVAEALGMHESTVSRATTNKYLATPR   79 (160)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCC
T ss_conf             9999999999999999999999979998478535757619999988099810699999613976799


No 238
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=63.50  E-value=5.2  Score=20.06  Aligned_cols=26  Identities=27%  Similarity=0.433  Sum_probs=14.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             23578999876898899999998863100
Q gi|254780805|r   47 IVPNPHNPRNYFESEGLEDLCQSIKSHGI   75 (300)
Q Consensus        47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~   75 (300)
                      +.|+..+|   |-.+-+..+.+...++|.
T Consensus        70 v~~~~~~~---f~~~~i~gi~~~~~~~g~   95 (342)
T PRK10014         70 IVRDLSAP---FYAELTAGLTEALEAQGR   95 (342)
T ss_pred             ECCCCCCH---HHHHHHHHHHHHHHHCCC
T ss_conf             05445776---779999999999998198


No 239
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=63.35  E-value=5.1  Score=20.11  Aligned_cols=33  Identities=21%  Similarity=0.466  Sum_probs=27.9

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999985210111046799997433787786565
Q gi|254780805|r  142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ..+..+++..+++|.++|+.+|.+++-|+...+
T Consensus        31 ~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~   63 (91)
T COG5606          31 MAIKQWIEQAALSQAQIAELLGVTQPRVSDLAR   63 (91)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf             999999999787799999983888731889983


No 240
>pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=63.34  E-value=5.3  Score=19.98  Aligned_cols=27  Identities=30%  Similarity=0.481  Sum_probs=23.1

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210111046799997433787786565
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |++.+| .|.++|+.++.+|.+|.+|.+
T Consensus        12 Li~~~G-N~teVaR~L~c~R~TVrkY~~   38 (64)
T pfam06322        12 LIETYG-NQTEVARRLNCSRNTVRKYAE   38 (64)
T ss_pred             HHHHHC-CHHHHHHHHCCHHHHHHHHHC
T ss_conf             999707-799997885110888998723


No 241
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=63.26  E-value=12  Score=17.80  Aligned_cols=15  Identities=13%  Similarity=0.173  Sum_probs=7.0

Q ss_pred             CCCHHHHHHHHHHHH
Q ss_conf             110467999974337
Q gi|254780805|r  152 GYTQNDIGSIVGKSR  166 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~  166 (300)
                      |-|-..+|+.+....
T Consensus       100 GTT~~~la~~L~~~~  114 (253)
T COG1349         100 GTTTLALARALPDDN  114 (253)
T ss_pred             CCHHHHHHHHCCCCC
T ss_conf             624999999717688


No 242
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=63.07  E-value=12  Score=17.78  Aligned_cols=38  Identities=8%  Similarity=-0.019  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |.|-.+...+  |....|+|..|||+.+|.|.++|..+|.
T Consensus       132 Lp~~~R~v~~--Lr~~~~ls~~EIA~~l~~s~~tVk~~l~  169 (191)
T PRK12520        132 LPARTGRVFM--MREWLELETEEICKELQITATNLWVMLY  169 (191)
T ss_pred             CCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             7499999999--9999389999999998949999999999


No 243
>PRK09492 treR trehalose repressor; Provisional
Probab=62.91  E-value=5.2  Score=20.06  Aligned_cols=28  Identities=18%  Similarity=0.273  Sum_probs=12.9

Q ss_pred             HHCCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             9823578999876898899999998863100
Q gi|254780805|r   45 HSIVPNPHNPRNYFESEGLEDLCQSIKSHGI   75 (300)
Q Consensus        45 ~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~   75 (300)
                      .-|.|+..+|   |..+-+..+...+.++|.
T Consensus        66 g~i~~~~~~~---~~~~~~~~i~~~~~~~gy   93 (315)
T PRK09492         66 GIIVSRLDSP---SENLAVQTMLPAFYQQGY   93 (315)
T ss_pred             EEECCCCCCH---HHHHHHHHHHHHHHHCCC
T ss_conf             6622677883---678999999999997498


No 244
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=62.73  E-value=11  Score=17.99  Aligned_cols=37  Identities=22%  Similarity=0.162  Sum_probs=26.6

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ||+-|.-  +-+++.+ |+|-.|||+.++.|..||.+++.
T Consensus       156 LT~RE~e--IL~lla~-G~sNkEIA~~L~iSe~TVk~H~~  192 (216)
T PRK10100        156 LTHREKE--ILNKLRI-GASNNEIARSLFISENTVKTHLY  192 (216)
T ss_pred             CCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9989999--9999987-99999999894988989999999


No 245
>PRK11569 transcriptional repressor IclR; Provisional
Probab=62.41  E-value=12  Score=17.71  Aligned_cols=19  Identities=11%  Similarity=0.359  Sum_probs=10.2

Q ss_pred             CCHHHHHHHHHHHHHCCCC
Q ss_conf             8988999999988631001
Q gi|254780805|r   58 FESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        58 ~~~~~l~eLa~SI~~~G~l   76 (300)
                      ++...+.-|..++.+.|.+
T Consensus        55 lpksT~~RlL~tL~~~G~v   73 (274)
T PRK11569         55 LPNSTTHRLLTTMQQQGFV   73 (274)
T ss_pred             CCHHHHHHHHHHHHHCCCE
T ss_conf             1999999999999976987


No 246
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093   An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=62.16  E-value=4.1  Score=20.70  Aligned_cols=26  Identities=23%  Similarity=0.295  Sum_probs=19.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10467999974337877865656543
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKL  178 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L  178 (300)
                      +|.+|+|+.+|.|++||.+.+.=..|
T Consensus         2 lTv~EaA~yLgv~~~t~~~l~~~g~l   27 (49)
T TIGR01764         2 LTVEEAAEYLGVSKSTVYRLIEEGEL   27 (49)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHHCCCC
T ss_conf             87788997719990578999971898


No 247
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=62.04  E-value=12  Score=17.73  Aligned_cols=25  Identities=16%  Similarity=0.125  Sum_probs=21.0

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             1011104679999743378778656
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .-.|+|.+|||+.+|.+.+||..+|
T Consensus       150 ~~eglS~~EIAeiLgip~gTVKSRL  174 (217)
T PRK12533        150 ELEDMSYREIAAIADVPVGTVMSRL  174 (217)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9809999999999894999999999


No 248
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=61.25  E-value=8  Score=18.85  Aligned_cols=39  Identities=26%  Similarity=0.326  Sum_probs=27.0

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             221048999999985210111046799997433787786565
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .-|++-|.-  +-+++.+ |.|-.|||..+|.|..||.++++
T Consensus       189 glLT~RE~E--VL~~va~-G~sn~eIA~~L~iS~~TVk~H~~  227 (247)
T TIGR03020       189 GLITAREAE--ILAWVRD-GKTNEEIAAILGISSLTVKNHLQ  227 (247)
T ss_pred             CCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             899989999--9999987-99999999994979999999999


No 249
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=61.04  E-value=12  Score=17.70  Aligned_cols=22  Identities=14%  Similarity=0.303  Sum_probs=13.7

Q ss_pred             HHHHHHHCCCC--HHHHHHHHHHH
Q ss_conf             99997422247--78999999764
Q gi|254780805|r  208 LAQVIVSKKMS--VRDTEELVQEQ  229 (300)
Q Consensus       208 la~~Ii~~~LS--VRe~E~lVk~~  229 (300)
                      ..+......|-  |||.|..+.+.
T Consensus       392 Al~~L~~Y~WPGNVRELenvIeRA  415 (510)
T PRK05022        392 AQAALLQYDWPGNVRELEHVISRA  415 (510)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf             999997099997899999999999


No 250
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=61.01  E-value=13  Score=17.55  Aligned_cols=21  Identities=33%  Similarity=0.436  Sum_probs=10.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |..+||+.+|.||.||.+.|.
T Consensus        31 sE~eLa~~~~VSR~TvR~Al~   51 (239)
T PRK09764         31 TESALQTEFGVSRVTVRQALR   51 (239)
T ss_pred             CHHHHHHHHCCCHHHHHHHHH
T ss_conf             999999997979999999999


No 251
>KOG0257 consensus
Probab=60.91  E-value=9  Score=18.51  Aligned_cols=29  Identities=38%  Similarity=0.762  Sum_probs=25.3

Q ss_pred             CCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf             35789998-768988999999988631001
Q gi|254780805|r   48 VPNPHNPR-NYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        48 ~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      --+|+||- +.|+.+.|+++|+=.+.||++
T Consensus       178 ~ntPhNPtGkvfsReeLe~ia~l~~k~~~l  207 (420)
T KOG0257         178 LNTPHNPTGKVFSREELERIAELCKKHGLL  207 (420)
T ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHCCEE
T ss_conf             948999867305799999999999878979


No 252
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=60.87  E-value=13  Score=17.59  Aligned_cols=37  Identities=8%  Similarity=0.047  Sum_probs=25.2

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             210111046799997433787786565654358999987
Q gi|254780805|r  148 ISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI  186 (300)
Q Consensus       148 ~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l  186 (300)
                      ..-.|+|.+|||+.+|.|.++|..+|.  ..=..+++.|
T Consensus       148 r~~~~ls~~EIA~~l~is~~tVksrL~--RAR~~Lr~~L  184 (191)
T PRK12530        148 REFLELSSEQICQECHITTSNLHVLLY--RARLQLQACL  184 (191)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHH
T ss_conf             999299999999998969999999999--9999999999


No 253
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=60.75  E-value=13  Score=17.52  Aligned_cols=21  Identities=19%  Similarity=0.370  Sum_probs=13.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q ss_conf             104679999743378778656
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .|.+++|+.+|.+...|...+
T Consensus       122 ps~~eia~~lg~s~~~v~~~~  142 (250)
T PRK07670        122 VTPSEVAAELGMSEEEVVTTM  142 (250)
T ss_pred             CCHHHHHHHCCCCHHHHHHHH
T ss_conf             988899877199999999999


No 254
>PRK09801 transcriptional activator TtdR; Provisional
Probab=60.55  E-value=13  Score=17.50  Aligned_cols=13  Identities=15%  Similarity=0.199  Sum_probs=5.3

Q ss_pred             HHHHHHHHHHHHC
Q ss_conf             9999999999739
Q gi|254780805|r  250 LTDLEKKISSKVG  262 (300)
Q Consensus       250 i~~le~~L~~~lG  262 (300)
                      +.-+...+++.+|
T Consensus       289 idfl~~~~~~~~~  301 (310)
T PRK09801        289 VEFLAAWCQQRLG  301 (310)
T ss_pred             HHHHHHHHHHHHC
T ss_conf             9999999999858


No 255
>KOG2305 consensus
Probab=60.23  E-value=9.5  Score=18.38  Aligned_cols=101  Identities=18%  Similarity=0.260  Sum_probs=54.7

Q ss_pred             CCEEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEE-ECCCC-----CCCCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             60240389823578999876898899999998863100155046-20565-----4453335756777776421001354
Q gi|254780805|r   38 SQDCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIV-RAIDN-----GLYKIIAGERRFRAAKMASLSEVPV  111 (300)
Q Consensus        38 ~~~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~V-r~~~~-----g~y~ii~G~rR~rAa~~~g~~~ip~  111 (300)
                      ....||+-.|.|.||-     +++.++.-.+-++..||- |+.. |+..+     -.|-|.+--+|+-|+-.++..+++.
T Consensus       146 PPyfiPLvElVPaPwT-----sp~tVdrt~~lM~sigq~-pV~l~rei~Gf~lnriq~Ailne~wrLvasGil~v~dvD~  219 (313)
T KOG2305         146 PPYFIPLVELVPAPWT-----SPDTVDRTRALMRSIGQE-PVTLKREILGFALNRIQYAILNETWRLVASGILNVNDVDA  219 (313)
T ss_pred             CCCCCCHHEECCCCCC-----CHHHHHHHHHHHHHHCCC-CCCCCCCCCCCEECCCCHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             9741201101368878-----802789999999983777-7544340114242133188999999998706765222999


Q ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             333464112345566654310221048999999985
Q gi|254780805|r  112 IIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQL  147 (300)
Q Consensus       112 iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l  147 (300)
                      +.-..   --.+-+++--+.-.-||+.-.|.-|+|.
T Consensus       220 VmS~G---LG~RYAflG~lET~HLNA~Gv~dYf~Ry  252 (313)
T KOG2305         220 VMSAG---LGPRYAFLGPLETAHLNAEGVADYFKRY  252 (313)
T ss_pred             HHHCC---CCCCHHCCCCHHHHHCCCHHHHHHHHHH
T ss_conf             98667---7721100261354315867789999986


No 256
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=60.23  E-value=10  Score=18.13  Aligned_cols=22  Identities=9%  Similarity=-0.241  Sum_probs=9.0

Q ss_pred             CEEECCCCCCCCCCCCHHHHHH
Q ss_conf             0462056544533357567777
Q gi|254780805|r   79 LIVRAIDNGLYKIIAGERRFRA  100 (300)
Q Consensus        79 i~Vr~~~~g~y~ii~G~rR~rA  100 (300)
                      +.+...+.-++.+...|-|.|.
T Consensus       124 l~i~~k~~~gi~i~g~E~~~r~  145 (585)
T PRK09863        124 CCIASRPGLGHFIDETEEKRID  145 (585)
T ss_pred             CEEEECCCCCEEEECCHHHHHH
T ss_conf             5891048985798351799999


No 257
>PRK09775 hypothetical protein; Provisional
Probab=59.73  E-value=9.8  Score=18.28  Aligned_cols=55  Identities=24%  Similarity=0.287  Sum_probs=30.5

Q ss_pred             HHHCCCCCCCE------EECCCCCCCCCCCC-------------HHHHHHHHHHHCCCCCCCCCCCCCHHHHHH
Q ss_conf             86310015504------62056544533357-------------567777764210013543334641123455
Q gi|254780805|r   70 IKSHGIIQPLI------VRAIDNGLYKIIAG-------------ERRFRAAKMASLSEVPVIIRNVDNKSSLEI  124 (300)
Q Consensus        70 I~~~G~lqPi~------Vr~~~~g~y~ii~G-------------~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~  124 (300)
                      +...|.+-|+.      |....+|.+..-+|             =-|..|...+....+|--+++++|++++..
T Consensus        74 a~~~g~L~pv~P~g~~~v~~~~d~~~~~~dgLPw~L~DMRPQGfLGR~~a~~~a~~L~Lp~d~~~W~ed~~L~A  147 (443)
T PRK09775         74 AHKFGQLYPLWPAGSCLVTLAEDGDWGWFDGLPWYLDDMRPQGFLGRAWGRRHAALLQLPEDIRLWQEDDVLYA  147 (443)
T ss_pred             CCCCEEEEEEECCCCEEEEECCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHCCHHHHHHH
T ss_conf             20143689972598469972478853223899805551584204668999987886389997032787899999


No 258
>KOG3802 consensus
Probab=59.63  E-value=12  Score=17.80  Aligned_cols=42  Identities=31%  Similarity=0.530  Sum_probs=28.3

Q ss_pred             CCCHHHH-HHHHHHHHHHCCCCHHHHHHHHHH------HHHHHHHHHHH
Q ss_conf             2104899-999998521011104679999743------37877865656
Q gi|254780805|r  134 DLNPLEE-ALGYEQLISEYGYTQNDIGSIVGK------SRSHVANILRI  175 (300)
Q Consensus       134 dl~p~e~-A~~~~~l~~~~~~t~~~lA~~~G~------s~s~V~~~LrL  175 (300)
                      |+.-+|+ |..||+=.=.+|+||.+++..+|+      |+++|.|+=+|
T Consensus       204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEAL  252 (398)
T KOG3802         204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEAL  252 (398)
T ss_pred             CHHHHHHHHHHHHHHEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             9999999999987650003644267888987650764430266676762


No 259
>pfam05930 Phage_AlpA Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.
Probab=59.62  E-value=3  Score=21.56  Aligned_cols=30  Identities=17%  Similarity=0.431  Sum_probs=25.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565654358999
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILKLPSSVR  183 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~  183 (300)
                      ...++.+.+|.|+++|.++++--+.|.+++
T Consensus         5 r~~eV~~~~glsrstiyr~i~~G~FP~pik   34 (51)
T pfam05930         5 RLKEVEQLTGLSRSTIYRLIKDGEFPKPIK   34 (51)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCCCCCEE
T ss_conf             799999998989999999998799999876


No 260
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=59.50  E-value=9.6  Score=18.34  Aligned_cols=50  Identities=24%  Similarity=0.302  Sum_probs=34.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHH
Q ss_conf             104899999998521011104679999743378778656-----5654358999987
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL-----RILKLPSSVREMI  186 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L-----rLl~L~~~i~~~l  186 (300)
                      |||-.-.  +--|.+.|+++..++|+.+++|.+.|.-.|     ||-.++++..+.+
T Consensus       117 L~p~Q~v--IfLLkDVF~ys~~eiAe~~s~sEGaVKasLfRsR~RLK~~~ee~~~~~  171 (228)
T PRK06704        117 LNVQQSA--ILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIV  171 (228)
T ss_pred             CCHHHHH--HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHCCCC
T ss_conf             5888899--999999987559999999556634999999999999873385312456


No 261
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=59.43  E-value=14  Score=17.38  Aligned_cols=38  Identities=16%  Similarity=0.107  Sum_probs=25.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-|.-. + +++.+ |+|-.+||..++.|..||.++.+
T Consensus       141 ~LT~RE~eV-L-~ll~~-G~snkeIA~~L~iS~~TV~~h~~  178 (202)
T PRK09390        141 SLSERERQV-M-DGLVA-GLSNKVIARDLDISPRTVEVYRA  178 (202)
T ss_pred             CCCHHHHHH-H-HHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             699899999-9-99983-89689999997987889999999


No 262
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=59.30  E-value=10  Score=18.12  Aligned_cols=52  Identities=27%  Similarity=0.283  Sum_probs=30.5

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHHH-HHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             566654310221048999999985-21011104679999743378778656565
Q gi|254780805|r  124 IAIVENVQRKDLNPLEEALGYEQL-ISEYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       124 ~~l~EN~~R~dl~p~e~A~~~~~l-~~~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      ..+.||..|-.+|-. -...|.-| +..--+|.+++++.+|.|++.||.-++=+
T Consensus        13 e~fae~m~r~G~nrt-VG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL   65 (177)
T COG1510          13 EHFAETMSRWGINRT-VGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKL   65 (177)
T ss_pred             HHHHHHHHHHCCCCH-HHHHHHHHEECCCCCCHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             999999998487642-77786540006999669999999777801288999999


No 263
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=59.24  E-value=11  Score=17.85  Aligned_cols=37  Identities=38%  Similarity=0.479  Sum_probs=28.0

Q ss_pred             CCCHHHH-HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2104899-9999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEE-ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~-A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-|. ...|   ..+ |.|..|||..+|.|..||..+|+
T Consensus       171 ~LT~RE~E~L~w---~A~-Gkt~~eIa~iL~iSe~TV~~hl~  208 (232)
T TIGR03541       171 VLSEREREVLAW---TAL-GRRQADIAAILGISERTVENHLR  208 (232)
T ss_pred             CCCHHHHHHHHH---HHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             989899999999---987-99999999996989999999999


No 264
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=59.11  E-value=14  Score=17.34  Aligned_cols=43  Identities=14%  Similarity=0.323  Sum_probs=29.7

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             521011104679999743378778656565435899998764210
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI  191 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i  191 (300)
                      |....|+|.+|||+.+|.|.++|..+|.  ..=..++++|....+
T Consensus       122 L~~~egls~~EIA~iL~is~gTVKsRL~--RAr~kLr~~L~~~g~  164 (181)
T PRK12540        122 LVGASGFSYEDAAAICGCAVGTIKSRVN--RARSKLSALLYVDGA  164 (181)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHCCC
T ss_conf             7998099999999998949999999999--999999999874655


No 265
>pfam04539 Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Probab=58.86  E-value=11  Score=18.06  Aligned_cols=39  Identities=26%  Similarity=0.365  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHCCC--CHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999985210111--04679999743378778656565435
Q gi|254780805|r  141 ALGYEQLISEYGY--TQNDIGSIVGKSRSHVANILRILKLP  179 (300)
Q Consensus       141 A~~~~~l~~~~~~--t~~~lA~~~G~s~s~V~~~LrLl~L~  179 (300)
                      .++.++|..++|-  |.+|||..+|.|...|...+.+..-+
T Consensus         7 ~ka~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~~~~   47 (78)
T pfam04539         7 KRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREP   47 (78)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf             99999999998889999999999694999999999875898


No 266
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX. This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=58.53  E-value=4.6  Score=20.38  Aligned_cols=82  Identities=13%  Similarity=0.282  Sum_probs=53.1

Q ss_pred             CCCCEEEEHHHCCC-CCCCCC--CCCCHHHHHHHHHHHHHCCCCCCCEEECCCCC---------CCC------CCCCHHH
Q ss_conf             56602403898235-789998--76898899999998863100155046205654---------453------3357567
Q gi|254780805|r   36 PESQDCISIHSIVP-NPHNPR--NYFESEGLEDLCQSIKSHGIIQPLIVRAIDNG---------LYK------IIAGERR   97 (300)
Q Consensus        36 ~~~~~~i~i~~i~~-~p~~pR--~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g---------~y~------ii~G~rR   97 (300)
                      .+-...||-..+.. =.++|-  +.|+-|+..++.+--++.|..|++++|-.+++         .|.      +++-=.+
T Consensus       102 vGHLVQiP~~~v~~iv~~~PeviTVfS~ekA~eis~aA~~~g~~Q~illrV~~~~D~~Y~GQegGf~l~eL~~v~~~i~~  181 (382)
T cd06811         102 VGHLVQIPRHQVPAVLAMRPEVITVYSLEKAREISDAAVELGRVQDVLLRVYGDEDTLYPGQEGGFPLEELPAVLAAIKA  181 (382)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCEEHHHHHHHHHHHHH
T ss_conf             15713685768999997499789992099999999999981973326999964898463775377548999999999972


Q ss_pred             HHHHHHHHCCCCCCCCCCCC
Q ss_conf             77776421001354333464
Q gi|254780805|r   98 FRAAKMASLSEVPVIIRNVD  117 (300)
Q Consensus        98 ~rAa~~~g~~~ip~iv~~~~  117 (300)
                      +-..+.+|+++-||+..|..
T Consensus       182 l~gi~i~GvT~FPc~L~d~~  201 (382)
T cd06811         182 LPGIRIAGLTSFPCFLYDEE  201 (382)
T ss_pred             CCCCEEEEEECEEEEEECCC
T ss_conf             89967966432006877477


No 267
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=58.43  E-value=14  Score=17.35  Aligned_cols=10  Identities=30%  Similarity=0.365  Sum_probs=3.2

Q ss_pred             HHHHHHHHHH
Q ss_conf             8999999988
Q gi|254780805|r   61 EGLEDLCQSI   70 (300)
Q Consensus        61 ~~l~eLa~SI   70 (300)
                      +..+.|.+.|
T Consensus        11 ~AY~~Lr~~I   20 (224)
T PRK11534         11 DGYRWLKNDI   20 (224)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 268
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=58.22  E-value=8.8  Score=18.60  Aligned_cols=31  Identities=26%  Similarity=0.384  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Q ss_conf             679999743378778656565-4358999987
Q gi|254780805|r  156 NDIGSIVGKSRSHVANILRIL-KLPSSVREMI  186 (300)
Q Consensus       156 ~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l  186 (300)
                      .+||++.|.|.++|++.|.=- ..+++..+.|
T Consensus         1 ~diA~~~gvS~~TVSr~ln~~~~Vs~~tr~~I   32 (52)
T cd01392           1 KDIARAAGVSVATVSRVLNGKPRVSEETRERV   32 (52)
T ss_pred             CHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             92888878599999999879898999999999


No 269
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=57.72  E-value=15  Score=17.19  Aligned_cols=37  Identities=24%  Similarity=0.214  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHCCC-------CHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999985210111-------046799997433787786565654
Q gi|254780805|r  141 ALGYEQLISEYGY-------TQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       141 A~~~~~l~~~~~~-------t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +..++..+....|       +..+||+.+|.||-||.+.|.+|.
T Consensus        13 ~~~i~~~I~~G~~~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~   56 (236)
T COG2188          13 AEDIRQRIESGELPPGDKLPSERELAEQFGVSRMTVRKALDELV   56 (236)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             99999999829999989595989999997988999999999999


No 270
>pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Probab=57.47  E-value=12  Score=17.68  Aligned_cols=33  Identities=24%  Similarity=0.234  Sum_probs=23.7

Q ss_pred             HHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99852101-1104679999743378778656565
Q gi|254780805|r  144 YEQLISEY-GYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       144 ~~~l~~~~-~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      +-.|.++. ..+..+||+++|.++++|++.++-|
T Consensus        11 Iy~l~~~~~~v~~~~iA~~L~Vs~~SVt~mlkkL   44 (58)
T pfam01325        11 IYTLSEEKGVVKTKDLAERLNVSPSTVSEMLKKL   44 (58)
T ss_pred             HHHHHCCCCCEEHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             9998826996129999999599925299999999


No 271
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=57.44  E-value=13  Score=17.46  Aligned_cols=17  Identities=24%  Similarity=0.315  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             79999743378778656
Q gi|254780805|r  157 DIGSIVGKSRSHVANIL  173 (300)
Q Consensus       157 ~lA~~~G~s~s~V~~~L  173 (300)
                      ..|+++|.|++.||+.|
T Consensus        41 rAA~~L~vSQpAvS~aL   57 (314)
T PRK09508         41 RAAHNLGMSQPAVSNAV   57 (314)
T ss_pred             HHHHHHCCCHHHHHHHH
T ss_conf             99999789866999999


No 272
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=57.35  E-value=7.2  Score=19.13  Aligned_cols=26  Identities=23%  Similarity=0.377  Sum_probs=13.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             23578999876898899999998863100
Q gi|254780805|r   47 IVPNPHNPRNYFESEGLEDLCQSIKSHGI   75 (300)
Q Consensus        47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~   75 (300)
                      |.|+-.||.  | .+-+..+.....++|.
T Consensus        67 vvp~~~n~~--~-~~l~~~i~~~~~~~gy   92 (330)
T PRK11303         67 IIPDLENTS--Y-ARIAKLLEQQARQRGY   92 (330)
T ss_pred             ECCCCCCCH--H-HHHHHHHHHHHHHCCC
T ss_conf             545444315--6-7888999999996698


No 273
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=57.35  E-value=15  Score=17.15  Aligned_cols=38  Identities=18%  Similarity=0.331  Sum_probs=29.3

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             22104899999998521011104679999743378778656
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      +.|+|-|.-  +-+++.+ |+|-.+||.+++.|..||+.+-
T Consensus       133 ~~Lt~rE~e--Vl~l~a~-G~s~~eIA~~L~~S~kTv~thr  170 (205)
T PRK11475        133 RMLSPTERE--ILRFMSR-GYSMPQIAEQLERNIKTIRAHK  170 (205)
T ss_pred             CCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHH
T ss_conf             889858999--9999976-9999999999788888999999


No 274
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=57.17  E-value=7.7  Score=18.98  Aligned_cols=19  Identities=16%  Similarity=0.207  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHCCCCH
Q ss_conf             4899999998521011104
Q gi|254780805|r  137 PLEEALGYEQLISEYGYTQ  155 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~t~  155 (300)
                      ..++..+|++-+.++|+..
T Consensus       191 ~~~R~~G~~~al~~~gl~~  209 (346)
T PRK10401        191 DAMRKAGWLSALKEQGIIP  209 (346)
T ss_pred             HHHHHHHHHHHHHHCCCCC
T ss_conf             8999999999999849998


No 275
>PRK01905 DNA-binding protein Fis; Provisional
Probab=56.92  E-value=15  Score=17.11  Aligned_cols=42  Identities=21%  Similarity=0.269  Sum_probs=29.1

Q ss_pred             CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1048999999985210111046799997433787786565654
Q gi|254780805|r  135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +.-+|... +...++..+..|...|+.+|.+|.|.+..|+-..
T Consensus        34 l~evE~pL-i~~vl~~~~gNQ~kAA~~LGinR~TLRkKlk~yg   75 (77)
T PRK01905         34 LSCVEKPL-LEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQHG   75 (77)
T ss_pred             HHHHHHHH-HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf             99989999-9999998459499999997865888999999808


No 276
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=56.73  E-value=7.7  Score=18.96  Aligned_cols=26  Identities=35%  Similarity=0.533  Sum_probs=14.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             23578999876898899999998863100
Q gi|254780805|r   47 IVPNPHNPRNYFESEGLEDLCQSIKSHGI   75 (300)
Q Consensus        47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~   75 (300)
                      |.|+-.||   |-.+-+..+.....++|.
T Consensus        73 i~p~~~~~---~~~~~~~gi~~~~~~~gy   98 (341)
T PRK11041         73 IVPDICDP---FFSEIIRGIEVTAAEHGY   98 (341)
T ss_pred             EECCCCCC---HHHHHHHHHHHHHHHCCC
T ss_conf             96776541---356766339999997699


No 277
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=56.71  E-value=7.7  Score=18.96  Aligned_cols=20  Identities=20%  Similarity=0.381  Sum_probs=13.4

Q ss_pred             CHHHHHHHHHHHHHHCCCCH
Q ss_conf             04899999998521011104
Q gi|254780805|r  136 NPLEEALGYEQLISEYGYTQ  155 (300)
Q Consensus       136 ~p~e~A~~~~~l~~~~~~t~  155 (300)
                      +..++..+|.+-+.++|+..
T Consensus       190 ~~~~R~~g~~~al~~~gl~~  209 (342)
T PRK10727        190 DAEDRLQGYYDALAESGIPA  209 (342)
T ss_pred             HHHHHHHHHHHHHHHCCCCC
T ss_conf             59999999999999769999


No 278
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=56.50  E-value=15  Score=17.06  Aligned_cols=22  Identities=18%  Similarity=0.238  Sum_probs=15.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      -|.+++|+.+|.+...|...+.
T Consensus       112 pt~~eia~~l~~s~e~v~~~~~  133 (234)
T PRK06986        112 PTDTEVAEKLGLSLEEYREMLL  133 (234)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9899999895949999999999


No 279
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=56.48  E-value=7.8  Score=18.94  Aligned_cols=26  Identities=15%  Similarity=0.312  Sum_probs=15.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             23578999876898899999998863100
Q gi|254780805|r   47 IVPNPHNPRNYFESEGLEDLCQSIKSHGI   75 (300)
Q Consensus        47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~   75 (300)
                      |.|+..+|   |-.+-+..+.....++|.
T Consensus        65 iv~~~~~~---~~~~~~~~i~~~~~~~gy   90 (335)
T PRK10703         65 LATSSEAP---YFAEIIEAVEKNCYQKGY   90 (335)
T ss_pred             EECCCCCC---EEHHHHHHHHHHHHHCCC
T ss_conf             95478886---506543369999997399


No 280
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=56.29  E-value=15  Score=17.04  Aligned_cols=21  Identities=19%  Similarity=0.297  Sum_probs=14.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |..+||+.+|.||.||.+.|.
T Consensus        37 sE~eLa~~y~VSR~TVR~Al~   57 (243)
T PRK11402         37 TENELCTQYNVSRITIRKAIS   57 (243)
T ss_pred             CHHHHHHHHCCCHHHHHHHHH
T ss_conf             999999997979999999999


No 281
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=56.19  E-value=9.8  Score=18.29  Aligned_cols=66  Identities=11%  Similarity=0.102  Sum_probs=33.0

Q ss_pred             HHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC-CEEECC--CCCCCCCCCCHHHHHHHHHHHCCCCCCCC
Q ss_conf             9823578999876898899999998863100155-046205--65445333575677777642100135433
Q gi|254780805|r   45 HSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQP-LIVRAI--DNGLYKIIAGERRFRAAKMASLSEVPVII  113 (300)
Q Consensus        45 ~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqP-i~Vr~~--~~g~y~ii~G~rR~rAa~~~g~~~ip~iv  113 (300)
                      +.+.--|.  ....+++.+++|.......-.-.- +++++-  .++-|.|+.|.=|..... -|-+.+-.++
T Consensus         7 e~L~~~pl--F~~Ls~~~l~~L~~~~~~~~~~~ge~lf~~Gd~~~~ly~i~~G~Vkv~~~~-~g~e~~l~~~   75 (236)
T PRK09392          7 EALRNLPL--FADMADATFERLMRGAFLQRFPPGTTLITEGEPADFLFVVLDGLVELSASS-QDRETTLAIL   75 (236)
T ss_pred             HHHHCCCC--CCCCCHHHHHHHHHCCEEEEECCCCEEECCCCCCCEEEEEEEEEEEEEECC-CCCCEEEEEE
T ss_conf             99846931--038999999999842879998999999899998665899963589998707-8884999998


No 282
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=55.90  E-value=16  Score=17.00  Aligned_cols=39  Identities=13%  Similarity=0.077  Sum_probs=25.8

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             52101110467999974337877865656543589999876
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIR  187 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~  187 (300)
                      |..-.|++.+|||+.+|.|.++|..+|.  ..=..+++.|.
T Consensus       160 Lr~~eglS~~EIAe~Lgis~~tVks~L~--RAR~~Lr~~Le  198 (207)
T PRK12544        160 MREFIELETPEICHNEDLTVSNLNVMLY--RSRLRLRECLE  198 (207)
T ss_pred             HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHH
T ss_conf             9998199999999997979999999999--99999999999


No 283
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=55.34  E-value=15  Score=17.14  Aligned_cols=64  Identities=11%  Similarity=0.228  Sum_probs=40.7

Q ss_pred             HHHHHHH--HCCCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHH
Q ss_conf             5666543--1022104899999998521---011104679999743378778656565435--89999876
Q gi|254780805|r  124 IAIVENV--QRKDLNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRILKLP--SSVREMIR  187 (300)
Q Consensus       124 ~~l~EN~--~R~dl~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~--~~i~~~l~  187 (300)
                      +.+++.|  ..++|+|.|+..+=.-|-.   ...+|-.+||+..|.|.++|.|.-+=+-..  ++.+..+.
T Consensus        14 ~~l~~~Ir~~~~~Lt~sEk~IA~yIL~~~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~   84 (293)
T PRK11337         14 IGLAPYIRMKQEGMTENESRVVDWLLKPGNLSCATALKDVAEALAVSEAMIVKVAKLLGFSGFRNLRSALE   84 (293)
T ss_pred             CCHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             78999999977644999999999998298999766699999895998889999999957897899999999


No 284
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288   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 sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes  and Bacillus cereus (strain ATCC 14579 / DSM 31) ..
Probab=55.14  E-value=10  Score=18.19  Aligned_cols=22  Identities=27%  Similarity=0.493  Sum_probs=10.4

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             1104679999743378778656
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      +++|.+-+++||.|+=||||.-
T Consensus       222 nlsQKeTGErlGiSQMHVSRl~  243 (256)
T TIGR02941       222 NLSQKETGERLGISQMHVSRLQ  243 (256)
T ss_pred             CCCCCHHHHHCCHHHHHHHHHH
T ss_conf             7873002322240355677888


No 285
>TIGR02478 6PF1K_euk 6-phosphofructokinase; InterPro: IPR009161    Members of this family are eukaryotic (with one exception) ATP-dependent 6-phosphofructokinases (2.7.1.11 from EC) in which two tandem copies of the phosphofructokinase are found . Members are found, often including several isozymes, in animals and fungi and in the bacterium Propionibacterium acnes KPA171202 (a human skin commensal).   Phosphofructokinase (PFK) catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate, which then enters the Embden-Meyerhof pathway. PFK is a key regulatory enzyme in glycolysis.   For additional information please see , , .; GO: 0003872 6-phosphofructokinase activity, 0006096 glycolysis, 0005737 cytoplasm.
Probab=54.90  E-value=6.8  Score=19.32  Aligned_cols=79  Identities=23%  Similarity=0.375  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCH----------HHHHHHHHHH-HHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHH-
Q ss_conf             677777642100135433346411----------2345566654-3102210489999999852101110467999974-
Q gi|254780805|r   96 RRFRAAKMASLSEVPVIIRNVDNK----------SSLEIAIVEN-VQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVG-  163 (300)
Q Consensus        96 rR~rAa~~~g~~~ip~iv~~~~d~----------~~~~~~l~EN-~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G-  163 (300)
                      =||.|+ +.|.+-|.+|..-.+|.          -+..+++-|| ++|.   |+-+|..-.+-+.+ .+.+.+-++.+. 
T Consensus       295 DR~Lat-~~GvEAV~avL~~tpe~~GavvtGqk~ps~VI~l~gNkI~R~---PL~~~V~~T~~V~~-~i~~~~f~~A~~L  369 (777)
T TIGR02478       295 DRILAT-LQGVEAVLAVLESTPETEGAVVTGQKTPSPVISLRGNKIVRK---PLVEAVRQTKTVAK-AIKERRFDEAVRL  369 (777)
T ss_pred             HHHHHH-HHHHHHHHHHHCCCCCCCCCEEECCCCCCEEEEECCCEEEEC---HHHHHHHHHHHHHH-HHHCCCCHHHHHC
T ss_conf             999998-644999999972687768747615435551475068702213---18899998999899-8731775458723


Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             3378778656565435
Q gi|254780805|r  164 KSRSHVANILRILKLP  179 (300)
Q Consensus       164 ~s~s~V~~~LrLl~L~  179 (300)
                      +.++++.++--++.++
T Consensus       370 Rg~eF~~~~~~~~~~s  385 (777)
T TIGR02478       370 RGREFVENLATFLELS  385 (777)
T ss_pred             CCHHHHHHHHHHHHHC
T ss_conf             5723577544477620


No 286
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=54.17  E-value=14  Score=17.20  Aligned_cols=22  Identities=9%  Similarity=0.235  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4679999743378778656565
Q gi|254780805|r  155 QNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       155 ~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      ...|++.+|.+...|...+.+.
T Consensus       232 ~~~i~k~l~~~~~~l~~a~~~I  253 (475)
T PRK12469        232 TAEIQRRIGCDQETLREACALV  253 (475)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9999999594999999999999


No 287
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=54.13  E-value=17  Score=16.82  Aligned_cols=24  Identities=4%  Similarity=-0.011  Sum_probs=13.6

Q ss_pred             CCHHHHHHHHHHHHHHCCEEEEEC
Q ss_conf             897899999999997398799971
Q gi|254780805|r  246 KEKYLTDLEKKISSKVGLNISIKH  269 (300)
Q Consensus       246 k~~~i~~le~~L~~~lGtkV~I~~  269 (300)
                      ...|+.+..+.|-+.++....|+.
T Consensus       214 M~~HLensr~~L~~~~~~~~~~~~  237 (258)
T PRK11523        214 MWQHLENTKIMLFNETSDDFEFNA  237 (258)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             999999999999886188767554


No 288
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=53.59  E-value=16  Score=16.97  Aligned_cols=59  Identities=17%  Similarity=0.257  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHC-CHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             67999974337877865656543589999876421016777776401-0046899997422247789999997
Q gi|254780805|r  156 NDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVST-SDPLSLAQVIVSKKMSVRDTEELVQ  227 (300)
Q Consensus       156 ~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~-~~~~~la~~Ii~~~LSVRe~E~lVk  227 (300)
                      .+||+.+|.|+++|+..++         .+-..|-|...+.+. +.+ +...++|+.|+...   |-.|.+..
T Consensus         3 ~diA~~L~vs~~sVs~~l~---------~L~~~Gli~~~~y~~-i~LT~~G~~~A~~i~~rH---r~le~fL~   62 (96)
T smart00529        3 SEIAERLNVSPPTVTQMLK---------KLEKDGLVEYEPYRG-ITLTEKGRRLARRLLRKH---RLLERFLV   62 (96)
T ss_pred             HHHHHHHCCCCHHHHHHHH---------HHHHCCCEEECCCCC-EEECHHHHHHHHHHHHHH---HHHHHHHH
T ss_conf             8899884999167999999---------999888988749989-788987999999999999---99999999


No 289
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=53.06  E-value=10  Score=18.24  Aligned_cols=38  Identities=8%  Similarity=0.189  Sum_probs=25.8

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0111046799997433787786565654358999987642
Q gi|254780805|r  150 EYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKE  189 (300)
Q Consensus       150 ~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~  189 (300)
                      -.|+|..|||+.+|.|.++|..+|.  ..=..+.+++...
T Consensus       125 ~egls~~EIAe~Lgis~gTVKsrl~--RAr~~LR~~le~~  162 (182)
T PRK12511        125 IEGLSYQEAANVLGIPIGTLMSRIG--RARAALRAFEEGT  162 (182)
T ss_pred             ECCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHC
T ss_conf             0799999999998939999999999--9999999986312


No 290
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=52.81  E-value=17  Score=16.68  Aligned_cols=49  Identities=12%  Similarity=0.255  Sum_probs=28.5

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHH---CC------CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6654310221048999999985210---11------1046799997433787786565
Q gi|254780805|r  126 IVENVQRKDLNPLEEALGYEQLISE---YG------YTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       126 l~EN~~R~dl~p~e~A~~~~~l~~~---~~------~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |+.|++...-|-+.-|..+-+....   +|      ++..++|..+|.+.|||++..+
T Consensus       295 LiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~  352 (444)
T COG1508         295 LIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT  352 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999999999999999999999983785457763199999883712888999982


No 291
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=52.61  E-value=18  Score=16.66  Aligned_cols=43  Identities=12%  Similarity=0.266  Sum_probs=30.0

Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             521011104679999743378778656565435899998764210
Q gi|254780805|r  147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI  191 (300)
Q Consensus       147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i  191 (300)
                      |.+-.|++.+|||+.+|.|.++|..+|  -..=..+++.|.+..+
T Consensus       150 Lr~~egls~~EIA~~L~is~~tVksrL--~RAR~~LR~~L~ek~~  192 (201)
T PRK12545        150 MREFLDFEIDDICTELTLTANHCSVLL--YRARTRLRTCLSEKGL  192 (201)
T ss_pred             HHHHHCCCHHHHHHHHCCCHHHHHHHH--HHHHHHHHHHHHHCCC
T ss_conf             999928989999999896999999999--9999999999998187


No 292
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=51.56  E-value=18  Score=16.61  Aligned_cols=30  Identities=17%  Similarity=0.292  Sum_probs=22.8

Q ss_pred             HHHH-CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5210-11104679999743378778656565
Q gi|254780805|r  147 LISE-YGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       147 l~~~-~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      ++.+ ...+..++|+.||.|..||.+-|.-|
T Consensus         8 ~l~~~~~~~i~~La~~~~VS~~TiRRDl~~L   38 (53)
T smart00420        8 LLAQQGKVSVEELAELLGVSEMTIRRDLNKL   38 (53)
T ss_pred             HHHHCCCEEHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9998697979999999897999999969999


No 293
>pfam10654 DUF2481 Protein of unknown function (DUF2481). This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems.
Probab=51.16  E-value=18  Score=16.52  Aligned_cols=24  Identities=33%  Similarity=0.261  Sum_probs=21.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      -|+|...||+.++.|+|+|-|+-+
T Consensus        79 AGlt~~aIAD~F~iS~s~~~nft~  102 (126)
T pfam10654        79 AGLTGYAIADHFKVSKSVVFNFTR  102 (126)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             588607999997477999999999


No 294
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=51.12  E-value=11  Score=18.06  Aligned_cols=21  Identities=24%  Similarity=0.445  Sum_probs=18.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHH
Q ss_conf             104679999743378778656
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      -||.++|..+|.|+|+|++.=
T Consensus       199 ~tqk~vad~lGisqsyisrle  219 (234)
T TIGR02835       199 KTQKEVADLLGISQSYISRLE  219 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             467888988624689999999


No 295
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=51.04  E-value=19  Score=16.51  Aligned_cols=24  Identities=13%  Similarity=0.173  Sum_probs=19.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             111046799997433787786565
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|..|||+.+|.|.+||..+|.
T Consensus       156 e~~s~~EIAe~l~is~~TVKsrl~  179 (194)
T PRK12531        156 EELPHQQVAEMFDIPLGTVKSRLR  179 (194)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             699999999998929999999999


No 296
>PRK04841 transcriptional regulator MalT; Provisional
Probab=50.91  E-value=19  Score=16.49  Aligned_cols=13  Identities=15%  Similarity=0.304  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHCCC
Q ss_conf             9999999983756
Q gi|254780805|r  284 EQLKIICSLLGEN  296 (300)
Q Consensus       284 eeLe~Il~kL~~~  296 (300)
                      -.+.+|+.||+-.
T Consensus       872 ~HlrnIy~KLgV~  884 (903)
T PRK04841        872 THIRNLYQKLGIA  884 (903)
T ss_pred             HHHHHHHHHCCCC
T ss_conf             9999998565999


No 297
>pfam04492 Phage_rep_O Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction.
Probab=50.78  E-value=19  Score=16.48  Aligned_cols=60  Identities=25%  Similarity=0.423  Sum_probs=38.8

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             566654310221048999999985210111-------046799997433787786565654358999987642101
Q gi|254780805|r  124 IAIVENVQRKDLNPLEEALGYEQLISEYGY-------TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS  192 (300)
Q Consensus       124 ~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~-------t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is  192 (300)
                      -.|.+.+-+.+|+.-+--..+.-....|||       +..++|+..|.++.+|++.+         .+++..+-|.
T Consensus        19 NeLldal~~~~lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs~a~---------~~Li~~~vi~   85 (100)
T pfam04492        19 NEILEALCRADLSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVSEAK---------KSLVKRGIII   85 (100)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHH---------HHHHHCCCCH
T ss_conf             999999980888788999999999986077850336229999999788854599999---------9999768644


No 298
>TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245   This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm.
Probab=50.70  E-value=19  Score=16.47  Aligned_cols=73  Identities=23%  Similarity=0.439  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHCCC----CCCCEEE-----CCCCCCCCCCC--------CHHHHHH--------HHHHHCCC-CCCCCCC
Q ss_conf             99999998863100----1550462-----05654453335--------7567777--------76421001-3543334
Q gi|254780805|r   62 GLEDLCQSIKSHGI----IQPLIVR-----AIDNGLYKIIA--------GERRFRA--------AKMASLSE-VPVIIRN  115 (300)
Q Consensus        62 ~l~eLa~SI~~~G~----lqPi~Vr-----~~~~g~y~ii~--------G~rR~rA--------a~~~g~~~-ip~iv~~  115 (300)
                      +-+-+.+-++++|.    ++.++.|     |.+.|.|.+-.        |.|=-+|        ...|.-.. ||++|.|
T Consensus        48 R~~~i~~~L~e~Gi~~~~l~AvVgRGGLLkPi~GGTY~Vn~~MleDLk~~~~GeHASNLGaIIA~~lA~~~~diPafIVD  127 (353)
T TIGR02707        48 RKQVILEVLEEKGINISKLDAVVGRGGLLKPIEGGTYLVNEKMLEDLKEGKRGEHASNLGAIIARELADELNDIPAFIVD  127 (353)
T ss_pred             HHHHHHHHHHHCCCCHHHEEEEEECCCCCCCCCCCEEEECHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             99999999874088712431579727702333896047765568888510588784336899999987651894358826


Q ss_pred             ---CCC-HHHHHHHHHHHHHCCC
Q ss_conf             ---641-1234556665431022
Q gi|254780805|r  116 ---VDN-KSSLEIAIVENVQRKD  134 (300)
Q Consensus       116 ---~~d-~~~~~~~l~EN~~R~d  134 (300)
                         +|+ ++.++++=.-+++|..
T Consensus       128 PVVVDEledvARISG~P~i~RkS  150 (353)
T TIGR02707       128 PVVVDELEDVARISGLPEIERKS  150 (353)
T ss_pred             CCEECCCCCHHHHCCCCCCCCEE
T ss_conf             83350551013213889864110


No 299
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=50.10  E-value=17  Score=16.75  Aligned_cols=34  Identities=21%  Similarity=0.308  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999985210111046799997433787786565
Q gi|254780805|r  141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      +..++.+.++.|+|...+|..+|.||.+|+.|=+
T Consensus       127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~  160 (313)
T COG1395         127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEK  160 (313)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf             2999999998086787889883846888987624


No 300
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794    Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=50.06  E-value=16  Score=16.93  Aligned_cols=22  Identities=23%  Similarity=0.363  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             1104679999743378778656
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .+|-.|+|++.|.+|+++.+.|
T Consensus        24 ~ltl~~vA~~TGL~RAaARR~L   45 (252)
T TIGR02431        24 RLTLTDVAEATGLTRAAARRFL   45 (252)
T ss_pred             CCCHHHHHHHHCCCCHHHHHHH
T ss_conf             9898999987589947988899


No 301
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=50.05  E-value=11  Score=17.93  Aligned_cols=106  Identities=23%  Similarity=0.305  Sum_probs=49.1

Q ss_pred             HHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEC----------------CCCCCCCCCCC--HHHHHHHHHHH
Q ss_conf             8982357899987689889999999886310015504620----------------56544533357--56777776421
Q gi|254780805|r   44 IHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRA----------------IDNGLYKIIAG--ERRFRAAKMAS  105 (300)
Q Consensus        44 i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~----------------~~~g~y~ii~G--~rR~rAa~~~g  105 (300)
                      |..|.|+-.||   |-.+-+..+.....++|..-=+....                .-||  .|+.|  ..... ...+.
T Consensus        61 Ig~i~p~~~~~---~~~~i~~gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdG--iIi~~~~~~~~~-~~~l~  134 (333)
T COG1609          61 IGLVVPDITNP---FFAEILKGIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDG--LILLGERPNDSL-LELLA  134 (333)
T ss_pred             EEEEECCCCCH---HHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCE--EEEECCCCCHHH-HHHHH
T ss_conf             99994687775---8999999999999983998999837898699999999998769898--999358788088-99998


Q ss_pred             CCCCCCCCCCC------------CCHHHH---HHHHHHHHHC---------CCCCHHHHHHHHHHHHHHCCCCH
Q ss_conf             00135433346------------411234---5566654310---------22104899999998521011104
Q gi|254780805|r  106 LSEVPVIIRNV------------DNKSSL---EIAIVENVQR---------KDLNPLEEALGYEQLISEYGYTQ  155 (300)
Q Consensus       106 ~~~ip~iv~~~------------~d~~~~---~~~l~EN~~R---------~dl~p~e~A~~~~~l~~~~~~t~  155 (300)
                      ...+|+|+.+.            |+..+.   .-.|++.-+|         ...+..++..+|.+-+.++|+..
T Consensus       135 ~~~~P~V~i~~~~~~~~~~~V~~Dn~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~  208 (333)
T COG1609         135 AAGIPVVVIDRSPPGLGVPSVGIDNFAGAYLATEHLIELGHRRIAFIGGPLDSSASRERLEGYRAALREAGLPI  208 (333)
T ss_pred             HCCCCEEEEECCCCCCCCCEEECCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             65999899937677778977970989999999999998799859999679877218999999999999759997


No 302
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=50.01  E-value=19  Score=16.40  Aligned_cols=28  Identities=7%  Similarity=0.235  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHCCCCCCCEEECCCCCCCCCC
Q ss_conf             89999999886310015504620565445333
Q gi|254780805|r   61 EGLEDLCQSIKSHGIIQPLIVRAIDNGLYKII   92 (300)
Q Consensus        61 ~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii   92 (300)
                      ..+.|=-..+...|++.+    ..+.|.|..-
T Consensus        49 ~~vREAl~~L~a~Glve~----r~G~Gt~V~~   76 (241)
T COG2186          49 TVVREALKRLEAKGLVEI----RQGSGTFVRP   76 (241)
T ss_pred             HHHHHHHHHHHHCCCEEC----CCCCCEEECC
T ss_conf             689999999998788630----5899827647


No 303
>COG4804 Predicted nuclease of restriction endonuclease-like fold [General    function prediction only]
Probab=50.00  E-value=14  Score=17.20  Aligned_cols=34  Identities=24%  Similarity=0.304  Sum_probs=20.1

Q ss_pred             HHHHHHHCCH---HHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             7777640100---468999974222477899999976
Q gi|254780805|r  195 HARTLVSTSD---PLSLAQVIVSKKMSVRDTEELVQE  228 (300)
Q Consensus       195 har~Ll~~~~---~~~la~~Ii~~~LSVRe~E~lVk~  228 (300)
                      |.+.++++++   ....+...+..+||||+.+..+..
T Consensus         3 h~~~l~s~kn~~~r~~Y~~~~~r~rws~r~l~~~I~s   39 (159)
T COG4804           3 HYKLLLSVKNLDKRLFYEIETLRNRWSVRQLERQIAS   39 (159)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             5102100258356778999999831019999999999


No 304
>pfam09048 Cro Cro. Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands.
Probab=49.22  E-value=15  Score=17.09  Aligned_cols=28  Identities=25%  Similarity=0.402  Sum_probs=21.6

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             852101110467999974337877865656
Q gi|254780805|r  146 QLISEYGYTQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      ...+++|  |...|+.+|..++.|+..||-
T Consensus         7 dyv~~~G--Q~kaA~~lGV~Q~AISKAlra   34 (58)
T pfam09048         7 DYVEEHG--QAKAAKDLGVNQSAISKALRA   34 (58)
T ss_pred             HHHHHHC--HHHHHHHCCCCHHHHHHHHHC
T ss_conf             9999976--598999829758999999964


No 305
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325   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 group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives..
Probab=49.08  E-value=13  Score=17.56  Aligned_cols=22  Identities=18%  Similarity=0.376  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             1104679999743378778656
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      ++|.+|+|..+|.|.+||.-++
T Consensus       129 DlSe~~~A~~LG~SvGTVKS~~  150 (165)
T TIGR02983       129 DLSEAEVAEVLGISVGTVKSRL  150 (165)
T ss_pred             CCCHHHHHHHHCCCCHHHHHHH
T ss_conf             8986899988199932289989


No 306
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=48.87  E-value=20  Score=16.29  Aligned_cols=35  Identities=11%  Similarity=0.286  Sum_probs=19.4

Q ss_pred             CHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHH
Q ss_conf             988999999988631001550462056544533357567
Q gi|254780805|r   59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERR   97 (300)
Q Consensus        59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR   97 (300)
                      +-..+.|=-..+...|+++.   ++ +.|.|..-.....
T Consensus        46 SRt~VREAL~~Le~~GLV~~---r~-G~Gt~V~~~~~~~   80 (257)
T PRK10225         46 TRTVVREALIMLEIKGLVEV---RR-GAGIYVLDSSGSH   80 (257)
T ss_pred             CHHHHHHHHHHHHHCCCEEE---EE-CCEEEEECCCHHH
T ss_conf             87899999999998899799---64-8877882687042


No 307
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=48.30  E-value=20  Score=16.23  Aligned_cols=68  Identities=21%  Similarity=0.236  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             104679999743378778656565435899998764210167777764010046899997422247789999997
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEELVQ  227 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~lVk  227 (300)
                      +|-.|+|+.+|.+.++|.-+-+.--++|.....=.-...+..|..       ........-+.++|+.++-+++.
T Consensus         1 ytI~e~a~~~gvs~~tlR~ye~~Gll~p~~r~~~g~R~Y~~~di~-------~l~~I~~lr~~G~~l~~Ik~~l~   68 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLE-------RLRFIKRLKELGFSLEEIKELLE   68 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHH-------HHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             978899999896999999999858989984489997443999999-------99999999997899999999996


No 308
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=48.07  E-value=21  Score=16.21  Aligned_cols=34  Identities=26%  Similarity=0.447  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHH------HHHHHHHHHH
Q ss_conf             999998521011104679999743------3787786565
Q gi|254780805|r  141 ALGYEQLISEYGYTQNDIGSIVGK------SRSHVANILR  174 (300)
Q Consensus       141 A~~~~~l~~~~~~t~~~lA~~~G~------s~s~V~~~Lr  174 (300)
                      |..|+.-.=..|+||.+++..+|.      |+++|++.=+
T Consensus        13 a~~fk~rRi~LG~TQ~dVG~aL~~l~g~~~SQttIcRFE~   52 (75)
T smart00352       13 AKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA   52 (75)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             9999998987377599999999986186431468889886


No 309
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=47.97  E-value=21  Score=16.20  Aligned_cols=25  Identities=20%  Similarity=0.270  Sum_probs=13.7

Q ss_pred             CCCHHHHHHHHHH--HHHHHHHHHHHH
Q ss_conf             1104679999743--378778656565
Q gi|254780805|r  152 GYTQNDIGSIVGK--SRSHVANILRIL  176 (300)
Q Consensus       152 ~~t~~~lA~~~G~--s~s~V~~~LrLl  176 (300)
                      |-|..++|+.+..  +-..|+|-|.+.
T Consensus       115 GTT~~~la~~L~~~~~ltVvTNsl~ia  141 (269)
T PRK09802        115 GTTTFEIARLMRKHTDVIAMTNGMNVA  141 (269)
T ss_pred             CHHHHHHHHHHHCCCCEEEEECCHHHH
T ss_conf             679999997323269859997879999


No 310
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=47.81  E-value=16  Score=16.84  Aligned_cols=24  Identities=25%  Similarity=0.540  Sum_probs=20.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             104679999743378778656565
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      +|..+||+.+|.++.+|++.|.-+
T Consensus         3 msrqdIadylGlt~ETVsR~l~~L   26 (32)
T pfam00325         3 MSRQEIADYLGLTRETVSRLLKRL   26 (32)
T ss_pred             CCHHHHHHHHCCHHHHHHHHHHHH
T ss_conf             658899998472599999999999


No 311
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=47.75  E-value=21  Score=16.18  Aligned_cols=29  Identities=28%  Similarity=0.591  Sum_probs=24.1

Q ss_pred             CCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf             35789998-768988999999988631001
Q gi|254780805|r   48 VPNPHNPR-NYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        48 ~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      .-||+||- ..|+.+.++++++=.++|+++
T Consensus       287 InNPNNPTGAVyS~E~LeeIaeiArehdLi  316 (518)
T PRK13355        287 IINPNNPTGALYPKEVLQQIVDIAREHQLI  316 (518)
T ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHCCEE
T ss_conf             968989888788999999999999985969


No 312
>PRK08960 hypothetical protein; Provisional
Probab=47.72  E-value=20  Score=16.33  Aligned_cols=30  Identities=30%  Similarity=0.545  Sum_probs=17.4

Q ss_pred             CCCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf             235789998-768988999999988631001
Q gi|254780805|r   47 IVPNPHNPR-NYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        47 i~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      +..||+||- ..++.+.+++|++-.++||++
T Consensus       170 il~nP~NPTG~v~s~~~l~~l~~~a~~~~~~  200 (387)
T PRK08960        170 LVASPANPTGTLLSRDELAALSQALKARGGH  200 (387)
T ss_pred             EECCCCCCCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf             9768989886314689999999987623977


No 313
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=47.69  E-value=21  Score=16.17  Aligned_cols=34  Identities=12%  Similarity=0.154  Sum_probs=25.6

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9985210111046799997433787786565654
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +...++..+.-|...|+.+|.+|.++.+.|+-..
T Consensus        63 l~~vL~~t~gNqskAA~~LGInR~TLRkKlk~yg   96 (98)
T PRK00430         63 LDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYG   96 (98)
T ss_pred             HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf             9999999669599999997877889999999848


No 314
>PRK10079 putative transcriptional regulator; Provisional
Probab=47.59  E-value=15  Score=17.02  Aligned_cols=20  Identities=5%  Similarity=0.204  Sum_probs=9.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             04679999743378778656
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~L  173 (300)
                      |..+||+.+|.||.||.+.|
T Consensus        37 sE~eLa~~y~VSR~TVR~Al   56 (241)
T PRK10079         37 AEQQLAARFEVNRHTLRRAI   56 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHH
T ss_conf             99999999798899999999


No 315
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=47.54  E-value=21  Score=16.16  Aligned_cols=38  Identities=34%  Similarity=0.591  Sum_probs=27.5

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|+|-|...  .++... |.+..++|..+|.|..+|..+++
T Consensus         4 ~Lt~rE~~~--~~l~~~-G~s~~eia~~l~is~~tV~~h~~   41 (65)
T COG2771           4 DLTPREREI--LRLVAQ-GKSNKEIARILGISEETVKTHLR   41 (65)
T ss_pred             CCCHHHHHH--HHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             138889999--999986-99899999998779999999999


No 316
>pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene.
Probab=47.54  E-value=21  Score=16.16  Aligned_cols=86  Identities=15%  Similarity=0.166  Sum_probs=47.8

Q ss_pred             HCCCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHCCHHH-H-HHHHHCC
Q ss_conf             1022104899999998521---011104679999743378778656565435--8999987642101677-7-7764010
Q gi|254780805|r  131 QRKDLNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRILKLP--SSVREMIRKEEISLGH-A-RTLVSTS  203 (300)
Q Consensus       131 ~R~dl~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~--~~i~~~l~~~~is~gh-a-r~Ll~~~  203 (300)
                      +.+.|+|.|+..+=.-+-.   -..+|..++|++.|.|.++|.|.-+-+...  ++.+-.|....-.... . +.+-.-+
T Consensus        10 ~~~~lt~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kklG~~Gf~efk~~La~~~~~~~~~~~~~I~~~D   89 (106)
T pfam01418        10 LYSKLTKSEKKIADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRKLGFSGFSDLKVALAGELAQSESILHSEIAPDD   89 (106)
T ss_pred             HHHHCCHHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             89764999999999999299999883399999896998999999999958998999999999986536664447789999


Q ss_pred             HHHHHHHHHHHCC
Q ss_conf             0468999974222
Q gi|254780805|r  204 DPLSLAQVIVSKK  216 (300)
Q Consensus       204 ~~~~la~~Ii~~~  216 (300)
                      +...+.+++....
T Consensus        90 s~~~i~~Kv~~~~  102 (106)
T pfam01418        90 DLEAIANKLFTNT  102 (106)
T ss_pred             CHHHHHHHHHHHH
T ss_conf             9999999999998


No 317
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=47.46  E-value=12  Score=17.72  Aligned_cols=27  Identities=26%  Similarity=0.349  Sum_probs=16.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             235789998768988999999988631001
Q gi|254780805|r   47 IVPNPHNPRNYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      |.|+..||   |-.+-+..+.....++|..
T Consensus        62 iv~~~~~~---f~~~i~~~i~~~~~~~gy~   88 (327)
T PRK10423         62 LITASTNP---FYSELVRGVERSCFERGYS   88 (327)
T ss_pred             EECCCCCC---HHHHHHHHHHHHHHHCCCE
T ss_conf             97366551---2678899999999985998


No 318
>PRK07324 transaminase; Validated
Probab=47.15  E-value=21  Score=16.20  Aligned_cols=45  Identities=18%  Similarity=0.191  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHCCEEEEECC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             8999999999973987999717--98228999858-9899999999837
Q gi|254780805|r  249 YLTDLEKKISSKVGLNISIKHR--NNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       249 ~i~~le~~L~~~lGtkV~I~~~--~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      +-.++-.+|-+.-|.-|. -..  +..|-+.|.|. +.++|+.=+++|.
T Consensus       318 ~~~~~~~~ll~~~gV~v~-PG~~F~~~g~~Ri~fa~~~~~l~egl~RL~  365 (373)
T PRK07324        318 DSEEFCEKLLKETGVLLV-PGNRFDLEGHVRIGYCCDTKTLKKGLKKLS  365 (373)
T ss_pred             CHHHHHHHHHHHCCEEEE-CCCCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf             999999999996899997-488658999499998198999999999999


No 319
>PRK06348 aspartate aminotransferase; Provisional
Probab=46.61  E-value=21  Score=16.19  Aligned_cols=43  Identities=7%  Similarity=0.132  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHCCEEEEE-----CCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             999999999739879997-----1798228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK-----HRNNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++...|-+.-|  |-+.     ...+.|-|.|.|. +.++|+.-+++|++
T Consensus       333 ~~~~~~ll~~~g--V~v~PG~~Fg~~g~~~iRls~~~~~~~l~ea~~Rl~k  381 (383)
T PRK06348        333 VEFCEYLLKEAH--VLVIPGKAFGKSGEGYIRLACTVGLEELEEAFNRIEK  381 (383)
T ss_pred             HHHHHHHHHHCC--EEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             999999998689--9997854548899997999984899999999999974


No 320
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.51  E-value=14  Score=17.34  Aligned_cols=23  Identities=30%  Similarity=0.327  Sum_probs=19.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             04679999743378778656565
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      ....+|+.+|.||++|.+||+=.
T Consensus       193 Ai~~VA~~L~iSr~TVY~YL~~~  215 (220)
T COG2964         193 AINIVADRLGISRHTVYRYLRKF  215 (220)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             89999999688758999999986


No 321
>PRK07683 aminotransferase A; Validated
Probab=46.15  E-value=22  Score=16.02  Aligned_cols=43  Identities=21%  Similarity=0.243  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             9999999973987999---71798228999858-9899999999837
Q gi|254780805|r  252 DLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       252 ~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      ++...|-+..|.-|.=   ....+.|-+.|.|. +.++++.=+++|.
T Consensus       332 ~~~~~ll~~~gV~v~PG~~Fg~~g~g~~Rlsfa~~~e~l~eal~Rl~  378 (387)
T PRK07683        332 DFALDLVEEAGLAVVPGSAFSEYGEGYVRLSYAYSIETLKEGLDRLE  378 (387)
T ss_pred             HHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf             99999998399999878422889988699997199999999999999


No 322
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=46.11  E-value=22  Score=16.02  Aligned_cols=43  Identities=9%  Similarity=0.064  Sum_probs=31.5

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             22104899999998521011104679999743378778656565
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      ...++=....+.+..++ -|.+..++|+.+|.+.+++.+-.+..
T Consensus         5 rrys~efK~~~V~~~~~-~g~sv~~var~~gi~~~~l~~W~k~~   47 (75)
T pfam01527         5 RRYSEEFKARAVKESLE-PGASVSELAREHGVSPATLYKWRKKY   47 (75)
T ss_pred             CCCCHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             88999999999999980-99849999999895999999999998


No 323
>PRK13980 NAD synthetase; Provisional
Probab=45.70  E-value=22  Score=15.98  Aligned_cols=83  Identities=20%  Similarity=0.249  Sum_probs=40.6

Q ss_pred             CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH-HHHHHC--CHHHHHHHHH
Q ss_conf             0489999999852101110467999974337877865656543589999876421016777-776401--0046899997
Q gi|254780805|r  136 NPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHA-RTLVST--SDPLSLAQVI  212 (300)
Q Consensus       136 ~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~gha-r~Ll~~--~~~~~la~~I  212 (300)
                      |-.|.+.+|-.+-.+   .--.++-.-+..++.|..+-+.+..|+.|.+.--+-.+-.||- .-=+|.  +..+.+....
T Consensus       138 NksE~~~Gy~TkyGD---~~~d~~Pi~dL~Kt~V~~La~~l~vP~~Ii~k~PSa~L~~~Q~DE~~LG~~Y~~lD~iL~~~  214 (264)
T PRK13980        138 NKSELLLGYFTKYGD---GAVDINPIGDLYKTQVRELARHLGVPEDIIEKPPSADLWEGQTDEDELGFSYEEIDEILYAL  214 (264)
T ss_pred             CHHHHHHHHCCCCCC---CCCCHHHHCCCCHHHHHHHHHHHCCCHHHEECCCCCCCCCCCCCHHHCCCCHHHHHHHHHHH
T ss_conf             674798721001687---66562452587399999999993996644036999776799998777199999999999999


Q ss_pred             HHCCCCHHH
Q ss_conf             422247789
Q gi|254780805|r  213 VSKKMSVRD  221 (300)
Q Consensus       213 i~~~LSVRe  221 (300)
                      +.+++|..+
T Consensus       215 ie~~~~~~~  223 (264)
T PRK13980        215 FDKKMPREE  223 (264)
T ss_pred             HHCCCCHHH
T ss_conf             976999999


No 324
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=45.69  E-value=22  Score=15.98  Aligned_cols=29  Identities=14%  Similarity=0.233  Sum_probs=22.5

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10111046799997433787786565654
Q gi|254780805|r  149 SEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      .....+..++|+.|+.|..||.+-|.-|.
T Consensus        11 ~~~~v~i~~La~~f~VS~~TiRRDl~~L~   39 (57)
T pfam08220        11 QQGTLSVEELAELLGVSEMTIRRDLNELE   39 (57)
T ss_pred             HCCCEEHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             86979799999998959999999699999


No 325
>TIGR03537 DapC succinyldiaminopimelate transaminase. Note: the detailed information included in the EC:2.6.1.17 record includes the assertions that the enzyme uses the pyridoxal pyrophosphate cofactor, which is consistent with the pfam00155 family, and the assertion that the amino group donor is L-glutamate, which is undetermined for the sequences in this clade.
Probab=45.67  E-value=21  Score=16.15  Aligned_cols=43  Identities=14%  Similarity=0.177  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHCCEEEEE-----CCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             9999999999739879997-----1798228999858-98999999998375
Q gi|254780805|r  250 LTDLEKKISSKVGLNISIK-----HRNNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       250 i~~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      -.++..+|.+. |  |-+.     ...+.|-+.|.|. +.|+++.=+.+|.+
T Consensus       301 ~~~~~~~ll~~-g--V~v~pG~~Fg~~~~~~~Rl~~~~~~e~l~ealrrl~~  349 (350)
T TIGR03537       301 SKDYALRLLEN-G--IVVAPGENFGSGEEGYVRVALVPTLEECEEALRIWES  349 (350)
T ss_pred             HHHHHHHHHHC-C--EEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHC
T ss_conf             99999999979-9--8997673118999986999972899999999999861


No 326
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=45.50  E-value=21  Score=16.20  Aligned_cols=32  Identities=25%  Similarity=0.339  Sum_probs=26.7

Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99985210111046799997433787786565
Q gi|254780805|r  143 GYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ..-||.--.|+|-+.||..+|.++|+|++.+.
T Consensus        31 ~lLRLH~~~gLsldR~~~lY~~hrStvaR~v~   62 (106)
T TIGR02233        31 TLLRLHHVEGLSLDRLGTLYGVHRSTVARWVA   62 (106)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf             56667762365589999884788616999999


No 327
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=45.48  E-value=23  Score=15.96  Aligned_cols=31  Identities=19%  Similarity=0.220  Sum_probs=22.0

Q ss_pred             HHHHHCC--CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8521011--104679999743378778656565
Q gi|254780805|r  146 QLISEYG--YTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       146 ~l~~~~~--~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      +|..++|  -|.++||+.+|.+...|..++...
T Consensus       177 ~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~~  209 (318)
T PRK07405        177 QLSQQLGRAATIGELAEELELTPKQVREYLERA  209 (318)
T ss_pred             HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             999871898648999988599999999999980


No 328
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=45.20  E-value=23  Score=15.93  Aligned_cols=39  Identities=15%  Similarity=0.297  Sum_probs=29.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
Q ss_conf             11046799997433787786565-------6543589999876421
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILR-------ILKLPSSVREMIRKEE  190 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~Lr-------Ll~L~~~i~~~l~~~~  190 (300)
                      ..|.+++|+.+|.|...+.+.|+       -.+|.-+++...+.|.
T Consensus        64 ~ps~~ewA~~~~~~~~~l~~~l~G~~aWA~~a~l~leLk~~~r~G~  109 (336)
T TIGR02997        64 EPSKEEWAAALGLSEAELRQRLRGLQAWAEAAQLELELKLVLRQGQ  109 (336)
T ss_pred             CCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9987899987189988999998765788998422589999999789


No 329
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=45.18  E-value=13  Score=17.54  Aligned_cols=28  Identities=21%  Similarity=0.280  Sum_probs=21.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565654358
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKLPS  180 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~  180 (300)
                      +|..|+|+.+|.|..+|.+.-+--.+++
T Consensus         1 lt~~e~A~~lgVs~~TlrrW~~~G~i~~   28 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGKLKA   28 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCE
T ss_conf             9889999997989999999998799431


No 330
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=44.89  E-value=23  Score=15.90  Aligned_cols=34  Identities=15%  Similarity=0.198  Sum_probs=24.6

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999985210111046799997433787786565654
Q gi|254780805|r  142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      ..|..+.+ .| +-...|+.+|.|+++|++.++-++
T Consensus         5 ~~f~~v~~-~g-s~~~AA~~l~isqs~vs~~i~~LE   38 (60)
T pfam00126         5 RVFVAVAE-EG-SFTAAAERLGLSQPAVSRQIKRLE   38 (60)
T ss_pred             HHHHHHHH-CC-CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             99999998-09-999999997989889999999999


No 331
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=44.60  E-value=7.4  Score=19.08  Aligned_cols=31  Identities=19%  Similarity=0.404  Sum_probs=25.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565654358999
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKLPSSVR  183 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~  183 (300)
                      +.-.|++..+|.|++||.+++.=...|.+++
T Consensus        14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvk   44 (70)
T COG3311          14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVK   44 (70)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCCCCCCEE
T ss_conf             2089999997766899999980477999862


No 332
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=44.51  E-value=22  Score=15.99  Aligned_cols=29  Identities=7%  Similarity=0.327  Sum_probs=22.7

Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99985210111046799997433787786
Q gi|254780805|r  143 GYEQLISEYGYTQNDIGSIVGKSRSHVAN  171 (300)
Q Consensus       143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~  171 (300)
                      -+..++.+.+++..++|+.+|.|.++++.
T Consensus         6 ~l~~~l~~r~~~~~eLa~~igis~~~ls~   34 (73)
T COG3655           6 RLDVMLADRKISLKELAEAIGISEANLSK   34 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             67999999750177899998436989999


No 333
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=44.46  E-value=5.8  Score=19.73  Aligned_cols=89  Identities=19%  Similarity=0.188  Sum_probs=39.1

Q ss_pred             CCCHHHHHHHH--------HHHCCCCCCCCCCCCC-----HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf             35756777776--------4210013543334641-----1234556665431022104899999998521011104679
Q gi|254780805|r   92 IAGERRFRAAK--------MASLSEVPVIIRNVDN-----KSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDI  158 (300)
Q Consensus        92 i~G~rR~rAa~--------~~g~~~ip~iv~~~~d-----~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~l  158 (300)
                      .+|.|||...+        .+|...+.-+|.-..+     -..+..+ .||-.|.    -++-..+-.|+..+-  .+++
T Consensus         1 MDGNrRWAk~~gl~~~~GH~~G~~~l~~iv~~~~~~gI~~lTlyaFS-tENw~R~----~~EV~~Lm~L~~~~l--~~~~   73 (229)
T PRK10240          1 MDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFS-SENWNRP----AQEVSALMELFVWAL--DSEV   73 (229)
T ss_pred             CCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECC-HHHCCCC----HHHHHHHHHHHHHHH--HHHH
T ss_conf             98638999887998789999999999999999998699989999608-7664999----799999999999999--9999


Q ss_pred             HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99--974337877865656543589999876421
Q gi|254780805|r  159 GS--IVGKSRSHVANILRILKLPSSVREMIRKEE  190 (300)
Q Consensus       159 A~--~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~  190 (300)
                      ..  .-|..-.+|-   .+..||+++++.+..-.
T Consensus        74 ~~l~~~~iri~~iG---d~~~Lp~~l~~~i~~~e  104 (229)
T PRK10240         74 KSLHRHNVRLRIIG---DTSRFNSRLQERIRKSE  104 (229)
T ss_pred             HHHHHCCEEEEEEE---CCCCCCHHHHHHHHHHH
T ss_conf             99998794899964---41006758999999999


No 334
>KOG0259 consensus
Probab=44.39  E-value=23  Score=15.90  Aligned_cols=29  Identities=34%  Similarity=0.667  Sum_probs=19.6

Q ss_pred             CCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf             35789998-768988999999988631001
Q gi|254780805|r   48 VPNPHNPR-NYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        48 ~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      .-||.||- -.|+.+.|+++++.-+++|++
T Consensus       205 viNP~NPcGnVys~~HL~kiae~A~klgi~  234 (447)
T KOG0259         205 VINPNNPCGNVYSEDHLKKIAETAKKLGIM  234 (447)
T ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHHCCE
T ss_conf             967999986515199999999999984976


No 335
>pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.
Probab=43.95  E-value=19  Score=16.45  Aligned_cols=31  Identities=29%  Similarity=0.356  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHH-HHHHHHH
Q ss_conf             9999999852101110467999974-3378778
Q gi|254780805|r  139 EEALGYEQLISEYGYTQNDIGSIVG-KSRSHVA  170 (300)
Q Consensus       139 e~A~~~~~l~~~~~~t~~~lA~~~G-~s~s~V~  170 (300)
                      |.-..+++|=.+ |+|..+||+.|| .||..|-
T Consensus         6 Erve~LkkLW~e-GlSaSqIA~~LGgvTRNAVI   37 (162)
T pfam07750         6 ERVELLKKLWLE-GLSASQIAAQLGGVSRNAVI   37 (162)
T ss_pred             HHHHHHHHHHHC-CCCHHHHHHHHCCCCCCCEE
T ss_conf             999999999985-36599999997655400000


No 336
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=43.91  E-value=24  Score=15.80  Aligned_cols=26  Identities=15%  Similarity=0.317  Sum_probs=21.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11046799997433787786565654
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      ..|.++||+.+|.+...|...+.+..
T Consensus       192 ~pt~eEIA~~lg~~~~~v~~~l~~~~  217 (328)
T PRK05657        192 EPSAEEIAELLDKPVDDVSRMLALNE  217 (328)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             99899999996959999999997458


No 337
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=43.41  E-value=24  Score=15.76  Aligned_cols=26  Identities=19%  Similarity=0.420  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHCCCCCCCEEECCCCCCCC
Q ss_conf             899999998863100155046205654453
Q gi|254780805|r   61 EGLEDLCQSIKSHGIIQPLIVRAIDNGLYK   90 (300)
Q Consensus        61 ~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~   90 (300)
                      ..+.|=-..+...|++.   +++ +.|.|.
T Consensus        46 ~~VREAL~~L~~~GlV~---~~~-g~G~~V   71 (251)
T PRK09990         46 SALREGLKVLRGRGIIE---TAQ-GRGSFV   71 (251)
T ss_pred             HHHHHHHHHHHHCCCEE---EEC-CCCCEE
T ss_conf             99999999999889979---857-985067


No 338
>PRK03837 transcriptional regulator NanR; Provisional
Probab=43.33  E-value=20  Score=16.28  Aligned_cols=15  Identities=27%  Similarity=0.614  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHCCCCC
Q ss_conf             999999886310015
Q gi|254780805|r   63 LEDLCQSIKSHGIIQ   77 (300)
Q Consensus        63 l~eLa~SI~~~G~lq   77 (300)
                      +.|=-..+...|++.
T Consensus        55 VREAL~~L~~~GlV~   69 (243)
T PRK03837         55 VREALQALKRKGLVQ   69 (243)
T ss_pred             HHHHHHHHHHCCCEE
T ss_conf             999999999889989


No 339
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=43.22  E-value=24  Score=15.74  Aligned_cols=33  Identities=18%  Similarity=0.294  Sum_probs=22.6

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             998521011104679999743378778656565
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      ++.|....++...|+|+++|.++|+++--+..|
T Consensus        29 l~lL~~k~plNvneiAe~lgLpqst~s~~ik~L   61 (308)
T COG4189          29 LQLLHRKGPLNVNEIAEALGLPQSTMSANIKVL   61 (308)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             999987179878999988588656666557888


No 340
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=43.15  E-value=25  Score=15.73  Aligned_cols=19  Identities=16%  Similarity=0.363  Sum_probs=9.7

Q ss_pred             HHHCCC--CHHHHHHHHHHHH
Q ss_conf             742224--7789999997641
Q gi|254780805|r  212 IVSKKM--SVRDTEELVQEQD  230 (300)
Q Consensus       212 Ii~~~L--SVRe~E~lVk~~~  230 (300)
                      .....|  +||+.|+++.+..
T Consensus       456 L~~y~WPGNVRELeNviER~v  476 (560)
T COG3829         456 LLRYDWPGNVRELENVIERAV  476 (560)
T ss_pred             HHHCCCCCHHHHHHHHHHHHH
T ss_conf             986899960999999999998


No 341
>PRK05066 arginine repressor; Provisional
Probab=42.79  E-value=25  Score=15.70  Aligned_cols=40  Identities=23%  Similarity=0.375  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHCCC-CHHHHHHHH---HH---HHHHHHHHHHHHHH
Q ss_conf             999999985210111-046799997---43---37877865656543
Q gi|254780805|r  139 EEALGYEQLISEYGY-TQNDIGSIV---GK---SRSHVANILRILKL  178 (300)
Q Consensus       139 e~A~~~~~l~~~~~~-t~~~lA~~~---G~---s~s~V~~~LrLl~L  178 (300)
                      +.-.++++|+..+.. ||++|.+.+   |.   +++|||+-|+-+.+
T Consensus         9 ~~~~aIk~lI~~~~I~tQeeL~~~L~~~G~~~VTQATvSRDlkeLg~   55 (156)
T PRK05066          9 ELVKAFKALLKEEKFGSQGEIVTALQEQGFDNINQSKVSRMLTKFGA   55 (156)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHCCC
T ss_conf             99999999985189667999999999739861208888878998299


No 342
>PRK07367 consensus
Probab=42.69  E-value=25  Score=15.68  Aligned_cols=43  Identities=5%  Similarity=0.038  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHCCEEEE--ECCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             99999999973987999--71798228999858-9899999999837
Q gi|254780805|r  251 TDLEKKISSKVGLNISI--KHRNNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I--~~~~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      .++.++|-+..|.-|.=  .+ +..|-|.|.|. +.++++.=+++|.
T Consensus       334 ~~~~~~ll~~~gV~v~PG~~F-g~~~~~Rl~~a~~~~~l~ea~~RL~  379 (385)
T PRK07367        334 LEFCRQLLEEHHVAAIPGIAF-GADDHIRLSYATDLATIEKGLERLE  379 (385)
T ss_pred             HHHHHHHHHHCCEEEECCCCC-CCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf             999999999699999758746-9999399997098999999999999


No 343
>PRK06207 aspartate aminotransferase; Provisional
Probab=42.64  E-value=24  Score=15.75  Aligned_cols=45  Identities=9%  Similarity=0.224  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHCCEEE--EE-CCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             99999999997398799--97-1798228999858-9899999999837
Q gi|254780805|r  250 LTDLEKKISSKVGLNIS--IK-HRNNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       250 i~~le~~L~~~lGtkV~--I~-~~~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      ..++...|.+.-|.-+.  .- .....|-|.|.|. +.+.+..=+++|.
T Consensus       350 ~~~f~~~Ll~e~gVav~PG~~FG~~~~~~vRlsfa~~~e~l~eal~RL~  398 (406)
T PRK06207        350 LADFVKILRLQAGVVVTPGTEFSPHTADSIRLNFSQDHAAAVAAVERIA  398 (406)
T ss_pred             HHHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             9999999998589999886565899989799997398999999999999


No 344
>cd01455 vWA_F11C1-5a_type Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A 
Probab=42.51  E-value=11  Score=17.93  Aligned_cols=91  Identities=15%  Similarity=0.301  Sum_probs=47.8

Q ss_pred             CCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH-HHHHCCCCCHHHHHHHHHH---------HHHHCCCCHHHHHHH
Q ss_conf             357567777764210013543334641123455666-5431022104899999998---------521011104679999
Q gi|254780805|r   92 IAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIV-ENVQRKDLNPLEEALGYEQ---------LISEYGYTQNDIGSI  161 (300)
Q Consensus        92 i~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~-EN~~R~dl~p~e~A~~~~~---------l~~~~~~t~~~lA~~  161 (300)
                      .+|-.-+.|.+.+-- ++  .-.+ +.++...+.+. .|+.|-..+|-+-|.++++         ++..+|--.+.|++.
T Consensus        88 ~sGD~Tlea~~~Ai~-~l--~a~~-d~De~fVivlSDANL~RYgI~p~~l~~~l~~~p~V~a~~IfIgslg~eA~~l~~~  163 (191)
T cd01455          88 WSGDHTVEATEFAIK-EL--AAKE-DFDEAIVIVLSDANLERYGIQPKKLADALAREPNVNAFVIFIGSLSDEADQLQRE  163 (191)
T ss_pred             ECCCCHHHHHHHHHH-HH--HHCC-CCCCCEEEEECCCCHHHCCCCHHHHHHHHHCCCCCCEEEEEEECHHHHHHHHHHH
T ss_conf             258844899999999-87--5302-6776089998147644318898999999733877668999973516799999974


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             743378778656565435899998764
Q gi|254780805|r  162 VGKSRSHVANILRILKLPSSVREMIRK  188 (300)
Q Consensus       162 ~G~s~s~V~~~LrLl~L~~~i~~~l~~  188 (300)
                      +-..+++|-  +..-+||.-+|+.+.+
T Consensus       164 lP~G~~fVc--~dt~~lP~il~qIfts  188 (191)
T cd01455         164 LPAGKAFVC--MDTSELPHIMQQIFTS  188 (191)
T ss_pred             CCCCCEEEE--CCHHHHHHHHHHHHHH
T ss_conf             899741785--3653678999999887


No 345
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=42.31  E-value=25  Score=15.65  Aligned_cols=26  Identities=27%  Similarity=0.448  Sum_probs=21.7

Q ss_pred             HHCCCCHHHHHHHHH-HHHHHHHHHHH
Q ss_conf             101110467999974-33787786565
Q gi|254780805|r  149 SEYGYTQNDIGSIVG-KSRSHVANILR  174 (300)
Q Consensus       149 ~~~~~t~~~lA~~~G-~s~s~V~~~Lr  174 (300)
                      +..++|..+||+.|| ++.++|....+
T Consensus        41 ~~~~~s~~~Ig~~fg~rdHsTV~~a~~   67 (90)
T cd06571          41 ELTGLSLPEIGRAFGGRDHSTVLHAVR   67 (90)
T ss_pred             HHHCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf             997889999999958997149999999


No 346
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=42.06  E-value=25  Score=15.62  Aligned_cols=44  Identities=20%  Similarity=0.255  Sum_probs=27.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HC-C-HHHHHHHHHCCH
Q ss_conf             11046799997433787786565654358999987642-10-1-677777640100
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKE-EI-S-LGHARTLVSTSD  204 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~-~i-s-~ghar~Ll~~~~  204 (300)
                      -.+.++||+.+|.||+.|...+.         .+=..| .| + .++.+.|.+.++
T Consensus        19 ~~SGe~La~~LgiSRtaVwK~Iq---------~Lr~~G~~I~s~~~kGY~L~~~~~   65 (79)
T COG1654          19 FVSGEKLAEELGISRTAVWKHIQ---------QLREEGVDIESVRGKGYLLPQLPD   65 (79)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH---------HHHHHCCCEEECCCCCEECCCCCC
T ss_conf             66689999997865999999999---------999809716860788636567501


No 347
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=42.01  E-value=26  Score=15.62  Aligned_cols=22  Identities=18%  Similarity=0.294  Sum_probs=12.9

Q ss_pred             HHHHHCCC--CHHHHHHHHHHHHC
Q ss_conf             99742224--77899999976410
Q gi|254780805|r  210 QVIVSKKM--SVRDTEELVQEQDN  231 (300)
Q Consensus       210 ~~Ii~~~L--SVRe~E~lVk~~~~  231 (300)
                      +......|  +|||.++.+.+..-
T Consensus       349 ~~L~~y~WPGNVREL~N~ver~~i  372 (464)
T COG2204         349 AALLAYDWPGNVRELENVVERAVI  372 (464)
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             999738998189999999999985


No 348
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor; InterPro: IPR000394 Sigma factors  are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. 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. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor ,  required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions:  A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=41.95  E-value=13  Score=17.45  Aligned_cols=20  Identities=15%  Similarity=0.333  Sum_probs=9.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             04679999743378778656
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~L  173 (300)
                      +-.+||..+|.+.|||||..
T Consensus       367 ~L~~vA~el~~heSTiSRai  386 (477)
T TIGR02395       367 TLREVAEELGLHESTISRAI  386 (477)
T ss_pred             CHHHHHHHHCCCCCCEEEEE
T ss_conf             38999988588987246331


No 349
>PRK07865 N-succinyldiaminopimelate aminotransferase; Reviewed
Probab=41.71  E-value=26  Score=15.59  Aligned_cols=41  Identities=15%  Similarity=0.179  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHCCEEEEE-----CCCCCEEEEEEE-CCHHHHHHHHHHHC
Q ss_conf             999999999739879997-----179822899985-89899999999837
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK-----HRNNKGQFCIKY-ETNEQLKIICSLLG  294 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f-~s~eeLe~Il~kL~  294 (300)
                      .+..+.|.+. |  |-+.     ...+.|-|.|.| .+.|+|+.=+++|.
T Consensus       317 ~~~~~~l~e~-g--V~v~PG~~Fg~~g~~~vRls~~~~~e~l~ea~~RLa  363 (364)
T PRK07865        317 WDTVAWLAER-G--ILVAPGDFYGPAGAQHVRVALTATDERIAAAVERLT  363 (364)
T ss_pred             HHHHHHHHHC-C--EEEECCCCCCCCCCCEEEEEECCCHHHHHHHHHHHC
T ss_conf             9999999979-9--899188743689998699996598999999999868


No 350
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=41.71  E-value=26  Score=15.59  Aligned_cols=24  Identities=25%  Similarity=0.344  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             679999743378778656565435
Q gi|254780805|r  156 NDIGSIVGKSRSHVANILRILKLP  179 (300)
Q Consensus       156 ~~lA~~~G~s~s~V~~~LrLl~L~  179 (300)
                      .++|+++|.|..+|.+-.+-++||
T Consensus         4 ~~vAk~LGVspkTVQRWvKq~ni~   27 (178)
T PRK13182          4 PFVAKKLGVSPKTVQRWVKQLNLP   27 (178)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf             788999399929999999995899


No 351
>pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.
Probab=41.70  E-value=20  Score=16.34  Aligned_cols=22  Identities=23%  Similarity=0.472  Sum_probs=14.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      +|.+|+|..+|.|+-+|++..|
T Consensus         1 mT~eELa~~~G~srQtINkwaR   22 (122)
T pfam07037         1 MTPEELAELTGYSRQTINRWVR   22 (122)
T ss_pred             CCHHHHHHHHCCHHHHHHHHHH
T ss_conf             9878998874712999999999


No 352
>PRK08069 consensus
Probab=41.46  E-value=26  Score=15.58  Aligned_cols=43  Identities=9%  Similarity=0.143  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             999999999739879997-17--98228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++...|-+.-|  |-+. ..  +..|-+.|.|. +.++++.=+++|+.
T Consensus       341 ~~~~~~ll~~~g--V~v~PG~~Fg~~~~~Rl~fa~~~~~l~eal~RL~~  387 (390)
T PRK08069        341 DEFVKALLEEEK--VALVPGSGFGAPDNVRLSYATSLELLEEAIERIHR  387 (390)
T ss_pred             HHHHHHHHHHCC--EEEECCCCCCCCCCEEEEEECCHHHHHHHHHHHHH
T ss_conf             999999998599--99981876799983899984999999999999999


No 353
>PRK05839 hypothetical protein; Provisional
Probab=41.45  E-value=23  Score=15.86  Aligned_cols=43  Identities=16%  Similarity=0.166  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHCCEEEEE----CC-C--CCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             999999999739879997----17-9--8228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK----HR-N--NKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~----~~-~--~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++.+.|-+.-  .|-+.    .. .  ++|-|.|.|. +.+.|+.=+++|++
T Consensus       320 ~~f~~~Ll~~~--gV~v~PG~~FG~~~~g~~~vRls~~~~~e~L~eal~Rl~~  370 (376)
T PRK05839        320 ENFTKKLYQNE--GIKVLPGSYLGRNGIGKDYVRLALVYDTPKLKKALERIKT  370 (376)
T ss_pred             HHHHHHHHHCC--CEEEECCCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             99999999809--9999774001799998996999970889999999999999


No 354
>pfam10302 DUF2407 Putative membrane protein (DUF2407). This is a family of proteins found in fungi. The function is not known. There is a characteristic GFDRL sequence motif.
Probab=41.36  E-value=9.8  Score=18.28  Aligned_cols=54  Identities=13%  Similarity=0.294  Sum_probs=33.3

Q ss_pred             CCCCCCCCCC-CCCHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             0013543334-641123-4556665431022104899999998521011104679999
Q gi|254780805|r  106 LSEVPVIIRN-VDNKSS-LEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSI  161 (300)
Q Consensus       106 ~~~ip~iv~~-~~d~~~-~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~  161 (300)
                      .-.|.|+|-| +++++. .+.++..+-+. .-+....+++|-||+.. |+|++|++..
T Consensus        83 r~YIHCsIGd~Lt~eeLa~E~~~~~~~~~-~~sTtp~~rGFDRLlsa-GFs~~EV~~L  138 (252)
T pfam10302        83 RIYIHCSIGDELTAEELAAEAALDDDGPQ-ASSTTPQPRGFDRLLSA-GFSPAEVSLL  138 (252)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHCCCCCCC-CCCCCCCCCCHHHHHHC-CCCHHHHHHH
T ss_conf             27999632762698887424401567888-77788887448789875-8999999999


No 355
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=41.35  E-value=26  Score=15.55  Aligned_cols=15  Identities=20%  Similarity=0.297  Sum_probs=5.5

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             679999743378778
Q gi|254780805|r  156 NDIGSIVGKSRSHVA  170 (300)
Q Consensus       156 ~~lA~~~G~s~s~V~  170 (300)
                      ++||+.+|.+...|.
T Consensus       277 eEIA~~lg~s~e~V~  291 (410)
T PRK07598        277 EDIAQELEMTPTQVR  291 (410)
T ss_pred             HHHHHHCCCCHHHHH
T ss_conf             999988099999999


No 356
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.23  E-value=26  Score=15.54  Aligned_cols=66  Identities=8%  Similarity=0.045  Sum_probs=31.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             0467999974337877865656543589999876421--016777776401004689999742224778999999764
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE--ISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEELVQEQ  229 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~--is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~lVk~~  229 (300)
                      +-.++|+.+|.|..++.-|-+..=|||. .  -..|-  .+..+..       ...+....-.-|+|+.++-.++...
T Consensus         2 ~Ige~a~~~gvs~~tlRyYe~~GLl~p~-r--~~~gyR~Y~~~~~~-------~l~~I~~lr~~G~sl~eI~~~l~~~   69 (112)
T cd01282           2 RIGELAARTGVSVRSLRYYEEQGLLVPE-R--SANGYRDYDEAAVD-------RVRQIRRLLAAGLTLEEIREFLPCL   69 (112)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCCCCC-C--CCCCCEECCHHHHH-------HHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             6899999989799999999984899998-0--89987005999999-------9999999999699999999999877


No 357
>PHA00675 hypothetical protein
Probab=41.12  E-value=26  Score=15.53  Aligned_cols=34  Identities=18%  Similarity=0.171  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999998521011104679999743378778656
Q gi|254780805|r  140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .-..+..|.+.+|++-..||..+..++++|+..-
T Consensus        27 ~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkIC   60 (78)
T PHA00675         27 EVERIRELHEVEGMSYAVLAEKFEQSKGAIAKIC   60 (78)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999998728438999999727568999998


No 358
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=41.07  E-value=26  Score=15.53  Aligned_cols=20  Identities=15%  Similarity=0.219  Sum_probs=8.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             04679999743378778656
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~L  173 (300)
                      +..+||+.+|.|..||++-|
T Consensus        20 ~v~eLa~~~~VS~~TIRRDL   39 (240)
T PRK10411         20 TTEALAEQLNVSKETIRRDL   39 (240)
T ss_pred             EHHHHHHHHCCCHHHHHHHH
T ss_conf             99999998895998999829


No 359
>PRK05794 consensus
Probab=40.36  E-value=25  Score=15.67  Aligned_cols=41  Identities=10%  Similarity=0.148  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             99999999739879997-17--98228999858-9899999999837
Q gi|254780805|r  252 DLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       252 ~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      ++...|-+.-  .|-+. ..  +..|-|.|.|. +.++++.-+++|.
T Consensus       346 ~f~~~ll~~~--gV~v~PG~~Fg~~~~vRl~f~~~~e~l~eal~RL~  390 (397)
T PRK05794        346 DFANLLLEEE--NVAVVPGIAFGMDNYIRLSYATSMENIEKGLDRIE  390 (397)
T ss_pred             HHHHHHHHHC--CEEEEECCCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf             9999999849--99998185358998399998299999999999999


No 360
>pfam02006 DUF137 Protein of unknown function DUF137. This family of archaeal proteins has no known function.
Probab=40.03  E-value=27  Score=15.42  Aligned_cols=62  Identities=15%  Similarity=0.177  Sum_probs=34.1

Q ss_pred             CHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHH
Q ss_conf             9889999999886310015504620565445333575677777642100135433346411234
Q gi|254780805|r   59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSL  122 (300)
Q Consensus        59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~  122 (300)
                      .++.++.++.-++++|.-.-+-+-+...++..=+.|.|++  |-.-|.-.-++++..+.|-|-.
T Consensus        42 T~eR~~~I~~~L~~~g~~~vlG~~~d~~~~ipgL~~~R~~--~~~~GI~~ADvVLVPLEDGDR~  103 (178)
T pfam02006        42 TEERVEKIAEVLREHGAKEVLGVGPDASERIPGLDHERGK--VSPDGIYSADVVLVPLEDGDRT  103 (178)
T ss_pred             CHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCE--ECCCCCCCCCEEEEECCCCCHH
T ss_conf             9899999999999759755544687645527898785340--4604541033799845778589


No 361
>PRK07212 consensus
Probab=39.91  E-value=27  Score=15.41  Aligned_cols=43  Identities=21%  Similarity=0.315  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEECC-HHHHHHHHHHHCC
Q ss_conf             999999999739879997-17--982289998589-8999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYET-NEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~s-~eeLe~Il~kL~~  295 (300)
                      .++...+-+.-  +|-+. ..  +..|-+.|.|.. .++|+.-+++|.+
T Consensus       329 ~~~~~~ll~~~--gV~v~pG~~Fg~~g~iRl~~a~~~e~l~eal~RL~~  375 (378)
T PRK07212        329 TAVAERLLKDA--HVAVTPGSAFGAPGWIRISYATSMERLKEALERLEK  375 (378)
T ss_pred             HHHHHHHHHHC--CEEEEECCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             99999999709--899981744599993999980899999999999999


No 362
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID; InterPro: IPR014208   Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation ..
Probab=39.71  E-value=28  Score=15.39  Aligned_cols=42  Identities=21%  Similarity=0.273  Sum_probs=27.1

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Q ss_conf             998521011104679999743378778656--565435899998
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANIL--RILKLPSSVREM  185 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L--rLl~L~~~i~~~  185 (300)
                      +...+-+..-|..+.|..+|.|+|+|..-+  ||-...+++...
T Consensus        11 ~~~~i~~~~~t~r~~a~~fGvskst~hkd~terlP~in~~~~~~   54 (80)
T TIGR02844        11 IAKYIVETKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEE   54 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             99999976899999998834325677666876300026899999


No 363
>pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.
Probab=39.61  E-value=28  Score=15.38  Aligned_cols=32  Identities=16%  Similarity=0.048  Sum_probs=22.9

Q ss_pred             HHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999852101-1104679999743378778656
Q gi|254780805|r  142 LGYEQLISEY-GYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       142 ~~~~~l~~~~-~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .||+-.++.. ..+..+||+.||.|.++|++--
T Consensus        11 kA~eiy~~s~G~~~l~~IA~~L~vs~~~IrkWK   43 (60)
T pfam10668        11 KAKEMWKESGGTMKLKDIANKLNVSESQIRKWK   43 (60)
T ss_pred             HHHHHHHHCCCCEEHHHHHHHHCCCHHHHHHCC
T ss_conf             999999982896449999999687988876031


No 364
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=39.41  E-value=23  Score=15.93  Aligned_cols=36  Identities=17%  Similarity=0.350  Sum_probs=24.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565-6543589999876421
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILR-ILKLPSSVREMIRKEE  190 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~Lr-Ll~L~~~i~~~l~~~~  190 (300)
                      +|.+++|+.+|.|++++++.++ ....+  ..+.+..-.
T Consensus         2 lsl~~lA~~~~~S~~~l~~~f~~~~g~s--~~~~i~~~R   38 (84)
T smart00342        2 LTLEDLAEALGMSPRHLQRLFKKETGTT--PKQYLRDRR   38 (84)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHCCC--HHHHHHHHH
T ss_conf             8999999988909999999999988939--999999999


No 365
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.88  E-value=29  Score=15.31  Aligned_cols=24  Identities=13%  Similarity=0.065  Sum_probs=10.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             467999974337877865656543
Q gi|254780805|r  155 QNDIGSIVGKSRSHVANILRILKL  178 (300)
Q Consensus       155 ~~~lA~~~G~s~s~V~~~LrLl~L  178 (300)
                      -.++|+.+|.|..+|.-|=+.-=|
T Consensus         3 IgelA~~~gvs~~tlRyYE~~GLl   26 (126)
T cd04785           3 IGELARRTGVNVETIRYYESIGLL   26 (126)
T ss_pred             HHHHHHHHCCCHHHHHHHHHCCCC
T ss_conf             899999989499999999984998


No 366
>PRK08362 consensus
Probab=38.60  E-value=29  Score=15.28  Aligned_cols=24  Identities=25%  Similarity=0.337  Sum_probs=13.9

Q ss_pred             CCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf             982289998589-899999999837
Q gi|254780805|r  271 NNKGQFCIKYET-NEQLKIICSLLG  294 (300)
Q Consensus       271 ~~kGkI~I~f~s-~eeLe~Il~kL~  294 (300)
                      .+.|-+.|.|.. .++++.-+++|.
T Consensus       356 ~~~~~~Rl~~a~~~e~l~ea~~RL~  380 (389)
T PRK08362        356 AGEGYIRISYATAYEKLEEAMDRME  380 (389)
T ss_pred             CCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             9989799997199999999999999


No 367
>pfam05339 DUF739 Protein of unknown function (DUF739). This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins.
Probab=38.59  E-value=24  Score=15.82  Aligned_cols=29  Identities=28%  Similarity=0.592  Sum_probs=22.2

Q ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             85210111046799997433787786565654
Q gi|254780805|r  146 QLISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      ++++.|| ||..-|..+|.|..+++  ++|.+
T Consensus        11 rI~Ek~g-tq~~Fa~~lg~se~tls--lkln~   39 (69)
T pfam05339        11 RILEKYG-TQYNFASAIGLSERSLS--LKLND   39 (69)
T ss_pred             HHHHHHC-CHHHHHHHHCCCHHHHH--HHHCC
T ss_conf             2889956-79899999581176888--98768


No 368
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=38.43  E-value=29  Score=15.27  Aligned_cols=39  Identities=26%  Similarity=0.398  Sum_probs=29.9

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999852101110467999974337877865656543589
Q gi|254780805|r  142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSS  181 (300)
Q Consensus       142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~  181 (300)
                      ..+-|++.. -+|-+|+++.+|.+.+.+++|.+.--||..
T Consensus        14 v~~LR~lK~-~~tykELs~~~gip~s~L~RYv~g~vlPs~   52 (238)
T PRK08558         14 VRYLRSLKK-TYTYEELSSILGLPESVLSRYVNGHVLPSV   52 (238)
T ss_pred             HHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHCCCCCCCH
T ss_conf             999999850-268999998879799998505348878758


No 369
>PRK04280 arginine repressor; Provisional
Probab=38.40  E-value=29  Score=15.26  Aligned_cols=129  Identities=11%  Similarity=0.130  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHHHCC-CCHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCH------HH
Q ss_conf             99999998521011-10467999974-----33787786565654358999987642101677777640100------46
Q gi|254780805|r  139 EEALGYEQLISEYG-YTQNDIGSIVG-----KSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSD------PL  206 (300)
Q Consensus       139 e~A~~~~~l~~~~~-~t~~~lA~~~G-----~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~------~~  206 (300)
                      ++=..+++++.+.. .||+||.+.+.     .+++|||+-|+=+.+-.   -.-.+|.     .+  ..++.      ..
T Consensus         5 ~R~~~I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATlSRDlkeL~~vK---v~~~~G~-----~~--Y~lp~~~~~~~~~   74 (149)
T PRK04280          5 QRHIKIREIITNEEIETQDELVDRLREYGFNVTQATVSRDIKELHLVK---VPLPDGR-----YK--YSLPADQRFNPLQ   74 (149)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHHCCEE---EECCCCC-----EE--EEECCCCCCCHHH
T ss_conf             999999999974897789999999998597553898898799818888---6669997-----89--9846766658689


Q ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHH-H-HHHHHHHCCEEEEECCCCCEEEEEEECCHH
Q ss_conf             89999742224778999999764102222223456655689789999-9-999997398799971798228999858989
Q gi|254780805|r  207 SLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDL-E-KKISSKVGLNISIKHRNNKGQFCIKYETNE  284 (300)
Q Consensus       207 ~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~l-e-~~L~~~lGtkV~I~~~~~kGkI~I~f~s~e  284 (300)
                      .+...+...=+||...+.++=            ....+..-..+... . ..+.+.+||      =.+-..|-|-+.|.+
T Consensus        75 ~l~~~~~~~v~~i~~~~~lvV------------ikT~pG~A~~va~~iD~~~~~~I~GT------iAGdDTilVi~~s~~  136 (149)
T PRK04280         75 KLKRYLMDSFVKIDGAGNLLV------------LKTLPGNAQSIGALLDNLDWEEILGT------ICGDDTCLIICRTPE  136 (149)
T ss_pred             HHHHHHHHHEEEEEECCCEEE------------EEECCCCHHHHHHHHHHCCCCCCEEE------EECCCEEEEEECCHH
T ss_conf             999999988468853176999------------99289958999999984799871898------604998999989999


Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999998375
Q gi|254780805|r  285 QLKIICSLLGE  295 (300)
Q Consensus       285 eLe~Il~kL~~  295 (300)
                      +-+.+.++|.+
T Consensus       137 ~a~~l~~~l~~  147 (149)
T PRK04280        137 DTEVVKDRFLN  147 (149)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999997


No 370
>PRK06375 consensus
Probab=38.37  E-value=29  Score=15.26  Aligned_cols=45  Identities=11%  Similarity=0.202  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             99999999973987999---71798228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++...|-+.-|.-|.=   -...+.|-+.|.|. +.+.++.-+++|++
T Consensus       328 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~~Ri~~a~~~e~l~ea~~RL~~  376 (381)
T PRK06375        328 YKAAENLLENKNVVVTPGSAFGRQGEHHFRISFATSEDIIKEGIERIGK  376 (381)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             9999999985999997873548899997999981999999999999999


No 371
>pfam07278 DUF1441 Protein of unknown function (DUF1441). This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown. However, it appears to be distantly related to other HTH families so may act as a transcriptional regulator.
Probab=38.27  E-value=25  Score=15.70  Aligned_cols=20  Identities=10%  Similarity=0.155  Sum_probs=12.1

Q ss_pred             CCCCHHHHHHHHHHHHHHCC
Q ss_conf             22104899999998521011
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYG  152 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~  152 (300)
                      .+|+|.|+-.-|+...+...
T Consensus        62 ~~M~P~dRKaw~QsE~eRlk   81 (152)
T pfam07278        62 HKMTPKERKAWFQSENERLK   81 (152)
T ss_pred             CCCCHHHHHHHHHHHHHHHH
T ss_conf             54985889999998889998


No 372
>TIGR01285 nifN nitrogenase molybdenum-iron cofactor biosynthesis protein NifN; InterPro: IPR005975    The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene. Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I.; GO: 0005515 protein binding, 0006461 protein complex assembly, 0009399 nitrogen fixation.
Probab=38.15  E-value=23  Score=15.96  Aligned_cols=112  Identities=15%  Similarity=0.248  Sum_probs=64.3

Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCCEEECC--------CCCCCC-CCCCHHHHHHHHHHHCCCCCCCCCC-CC-CHHHHH-H
Q ss_conf             6898899999998863100155046205--------654453-3357567777764210013543334-64-112345-5
Q gi|254780805|r   57 YFESEGLEDLCQSIKSHGIIQPLIVRAI--------DNGLYK-IIAGERRFRAAKMASLSEVPVIIRN-VD-NKSSLE-I  124 (300)
Q Consensus        57 ~~~~~~l~eLa~SI~~~G~lqPi~Vr~~--------~~g~y~-ii~G~rR~rAa~~~g~~~ip~iv~~-~~-d~~~~~-~  124 (300)
                      .+++.+|++|.+-|+++| |+||+.-..        .++.|. +-.|..+++-.+.+|..-.--+|-+ +. ..+... .
T Consensus       184 ~ltpgDie~l~~~vEaFG-L~P~~LPDLS~SLDGHLa~dd~s~~T~GGT~l~~i~~~g~s~~tlaIGe~mr~aA~~l~~R  262 (451)
T TIGR01285       184 LLTPGDIEELRDMVEAFG-LKPVVLPDLSRSLDGHLADDDFSPITLGGTTLEDIRELGQSAVTLAIGESMRAAAELLKDR  262 (451)
T ss_pred             CCCHHHHHHHHHHHHHCC-CCCEECCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             888867999999998608-9722402110024650087870056789973599987368874688777654446752212


Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHC-CC-------CHHHHHHHHHHHHHHH
Q ss_conf             666543102210489999999852101-11-------0467999974337877
Q gi|254780805|r  125 AIVENVQRKDLNPLEEALGYEQLISEY-GY-------TQNDIGSIVGKSRSHV  169 (300)
Q Consensus       125 ~l~EN~~R~dl~p~e~A~~~~~l~~~~-~~-------t~~~lA~~~G~s~s~V  169 (300)
                      ...+-.--..|+-+|...+|-..+-+. |.       -.-.+=+++++.|.+.
T Consensus       263 ~g~~y~vF~~L~GLeavD~F~~~L~~~SG~~CdhhfPfvP~vP~~~~RqR~QL  315 (451)
T TIGR01285       263 CGVPYEVFPSLMGLEAVDAFVSVLSKISGSRCDHHFPFVPAVPERFERQRAQL  315 (451)
T ss_pred             CCCCCHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             17740010122446899999999999844321567898898863345207889


No 373
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=37.79  E-value=30  Score=15.20  Aligned_cols=13  Identities=23%  Similarity=0.529  Sum_probs=4.7

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             7999974337877
Q gi|254780805|r  157 DIGSIVGKSRSHV  169 (300)
Q Consensus       157 ~lA~~~G~s~s~V  169 (300)
                      ++|++.|.+..+|
T Consensus         5 elAk~tGv~~~TI   17 (135)
T PRK10227          5 DVAKITGLTSKAI   17 (135)
T ss_pred             HHHHHHCCCHHHH
T ss_conf             9999989699999


No 374
>PRK06855 aminotransferase; Validated
Probab=37.71  E-value=30  Score=15.19  Aligned_cols=28  Identities=21%  Similarity=0.434  Sum_probs=18.6

Q ss_pred             CCCCCCCC-CCCCHHHHHHHHHHHHHCCC
Q ss_conf             35789998-76898899999998863100
Q gi|254780805|r   48 VPNPHNPR-NYFESEGLEDLCQSIKSHGI   75 (300)
Q Consensus        48 ~~~p~~pR-~~~~~~~l~eLa~SI~~~G~   75 (300)
                      .-||.||- ..++.+.+++|++-.++|++
T Consensus       177 i~nP~NPTG~v~s~e~l~~i~~~a~~~~i  205 (433)
T PRK06855        177 LINPDNPTGAVYPKEILREIVDIAREYDL  205 (433)
T ss_pred             EECCCCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             83899998866799999999999997598


No 375
>PRK08363 alanine aminotransferase; Validated
Probab=37.38  E-value=30  Score=15.16  Aligned_cols=43  Identities=9%  Similarity=0.087  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHCCEEE--EE-CCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             999999997398799--97-1798228999858-9899999999837
Q gi|254780805|r  252 DLEKKISSKVGLNIS--IK-HRNNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       252 ~le~~L~~~lGtkV~--I~-~~~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      ++..+|-+.-|.-|.  .. ...+.|-+.|.|. +.++++.-+++|+
T Consensus       343 ef~~~ll~e~gV~v~PG~~Fg~~g~g~vRlsf~~~~e~l~eal~Rl~  389 (398)
T PRK08363        343 EFVLDLLHEAHVLFVHGSGFGEYGAGHFRLVFLPPVEILEEAMDRFE  389 (398)
T ss_pred             HHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf             99999998599999896432889998699998389999999999999


No 376
>PRK07682 hypothetical protein; Validated
Probab=37.24  E-value=30  Score=15.15  Aligned_cols=41  Identities=15%  Similarity=0.233  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHCCEEEEE-----CCCCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf             99999999739879997-----17982289998589-899999999837
Q gi|254780805|r  252 DLEKKISSKVGLNISIK-----HRNNKGQFCIKYET-NEQLKIICSLLG  294 (300)
Q Consensus       252 ~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~s-~eeLe~Il~kL~  294 (300)
                      ++..+|-..  .+|-+.     ...+.|-+.|.|.. .++|+.=+++|+
T Consensus       325 ~~~~~ll~~--~~V~v~PG~~Fg~~g~~~iRl~~a~~~e~l~eal~Rl~  371 (378)
T PRK07682        325 EFAEQLLLE--EKVAVVPGSVFGESGEGFIRCSYATSLEQLQEAMKRMK  371 (378)
T ss_pred             HHHHHHHHH--CCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             999999996--99999886222899989799996199999999999999


No 377
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=37.19  E-value=30  Score=15.14  Aligned_cols=33  Identities=21%  Similarity=0.355  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             489999999852101110467999974337877865
Q gi|254780805|r  137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      ++|...+|-   .+..++-.+||..+|.||+.|.+.
T Consensus         7 sfddYv~yF---~eG~L~D~eIA~~LGVsr~nV~km   39 (181)
T pfam04645         7 SFDDYVAYF---KEGSLSDAEIAKELGVSRVNVWRM   39 (181)
T ss_pred             HHHHHHHHH---HCCCCCHHHHHHHHCCHHHHHHHH
T ss_conf             289999999---617875799999978309999999


No 378
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=37.00  E-value=25  Score=15.63  Aligned_cols=38  Identities=21%  Similarity=0.233  Sum_probs=26.3

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21048999999985210111046799997433787786565
Q gi|254780805|r  134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      .|++-|.- .+ +...+ |.|-.|||..+|.|..||.-+|+
T Consensus       179 ~LT~RE~E-~L-~W~A~-GKTs~EIa~IL~ISe~TV~fHl~  216 (240)
T PRK10188        179 NFSKREKE-IL-KWTAE-GKTSAEIAMILSISENTVNFHQK  216 (240)
T ss_pred             CCCHHHHH-HH-HHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             89989999-99-99977-99999999883999999999999


No 379
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435    Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain..
Probab=36.66  E-value=25  Score=15.65  Aligned_cols=29  Identities=14%  Similarity=0.363  Sum_probs=22.4

Q ss_pred             HHHH-HHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9998-5210111046799997433787786
Q gi|254780805|r  143 GYEQ-LISEYGYTQNDIGSIVGKSRSHVAN  171 (300)
Q Consensus       143 ~~~~-l~~~~~~t~~~lA~~~G~s~s~V~~  171 (300)
                      ||=| +.+-.|+|-.++|.++|..++.|..
T Consensus        28 GWvR~~R~ALGms~~QLA~RlGV~p~Rv~~   57 (150)
T TIGR02612        28 GWVRAIRKALGMSGAQLAARLGVTPQRVEA   57 (150)
T ss_pred             CCHHHHHHHHCCCHHHHHHHCCCCHHHHHH
T ss_conf             616889877251578876652897377999


No 380
>PRK08443 consensus
Probab=36.52  E-value=31  Score=15.07  Aligned_cols=42  Identities=17%  Similarity=0.267  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             999999999739879997-17--98228999858-9899999999837
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      ..+..+|-+.-|  |-+. ..  +..|-+.|.|. +.+.++.=+++|.
T Consensus       336 ~~f~~~ll~~~g--V~v~PG~~Fg~~g~vRl~~~~~~e~l~ea~~RL~  381 (388)
T PRK08443        336 MKFCKKLLEQEG--VAVVPGIGFGMEGYFRLSFATSIESIKKGIERIA  381 (388)
T ss_pred             HHHHHHHHHHCC--EEEECCCCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf             999999998199--9997274358898599998288999999999999


No 381
>pfam00155 Aminotran_1_2 Aminotransferase class I and II.
Probab=36.44  E-value=31  Score=15.07  Aligned_cols=41  Identities=20%  Similarity=0.324  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHCCEEEEEC---CCCCEEEEEEEC--CHHHHHHHHHHH
Q ss_conf             9999999997398799971---798228999858--989999999983
Q gi|254780805|r  251 TDLEKKISSKVGLNISIKH---RNNKGQFCIKYE--TNEQLKIICSLL  293 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~~---~~~kGkI~I~f~--s~eeLe~Il~kL  293 (300)
                      ..+...|-+.-|  |-+.-   =+..|.|.|.|.  +.|+++..++.|
T Consensus       306 ~~~~~~Ll~~~g--V~v~pG~~fg~~~~iRis~a~~s~e~i~~~~~rl  351 (351)
T pfam00155       306 KELAQVLLEEVG--VYVTPGSSPGVPGWLRITVAGGTEEELEELLEAI  351 (351)
T ss_pred             HHHHHHHHHCCC--EEEECCCCCCCCCEEEEEECCCCHHHHHHHHHHC
T ss_conf             999999997598--9997788889999089981789999999999419


No 382
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY; InterPro: IPR014154   This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. All have a C-terminal helix-turn-helix DNA-binding region..
Probab=36.17  E-value=7.8  Score=18.91  Aligned_cols=120  Identities=18%  Similarity=0.225  Sum_probs=60.6

Q ss_pred             CCCCCCCCCCHHH---HHHHHHHHHHCCCCCCCEEECCCC-CCCC--------CCCCHHHHHHHHHHHCCCCCCCC-CCC
Q ss_conf             7899987689889---999999886310015504620565-4453--------33575677777642100135433-346
Q gi|254780805|r   50 NPHNPRNYFESEG---LEDLCQSIKSHGIIQPLIVRAIDN-GLYK--------IIAGERRFRAAKMASLSEVPVII-RNV  116 (300)
Q Consensus        50 ~p~~pR~~~~~~~---l~eLa~SI~~~G~lqPi~Vr~~~~-g~y~--------ii~G~rR~rAa~~~g~~~ip~iv-~~~  116 (300)
                      +-++-|+ |.++-   +.-+.++.....+-.|+.|.|.+. ..|.        |+-|..|+      | +=|-+.. .+.
T Consensus        66 ~~~~~r~-FPeeY~~~~~~i~~T~AN~p~~~~lt~Fp~e~~~~~~~G~tTIvPi~G~G~RL------G-TliL~R~~~~F  137 (255)
T TIGR02787        66 KMFQDRK-FPEEYTKALVNIYDTEANIPVDSELTVFPEESRDLFPKGLTTIVPIYGSGERL------G-TLILARLDKEF  137 (255)
T ss_pred             HHHHCCC-CCHHHHHHHHCCCCCCCCCCCCCCEEECCCCCHHHHCCCCEEEEEEEECCCHH------H-HHHEECCCCCC
T ss_conf             8874386-86577730002135504688998803514643433127966989731277102------0-21000027873


Q ss_pred             CCHHHHHHHHH--------HHHHCCC-------CCHHHHH---------HHHHHHHHH-----CCCCHHHHHHHHHHHHH
Q ss_conf             41123455666--------5431022-------1048999---------999985210-----11104679999743378
Q gi|254780805|r  117 DNKSSLEIAIV--------ENVQRKD-------LNPLEEA---------LGYEQLISE-----YGYTQNDIGSIVGKSRS  167 (300)
Q Consensus       117 ~d~~~~~~~l~--------EN~~R~d-------l~p~e~A---------~~~~~l~~~-----~~~t~~~lA~~~G~s~s  167 (300)
                      +|+|....=+.        -|.|++.       -+....|         +|.+..+++     ..++-..||+++|..||
T Consensus       138 ~DdDLvLaE~aaTVvG~elL~~~~~e~Eee~R~~a~VqmAi~TLSYSEL~AV~aIf~ELdG~EG~LvAS~IAD~vGITRS  217 (255)
T TIGR02787       138 NDDDLVLAEYAATVVGMELLRAKAEEIEEEARKKAAVQMAINTLSYSELEAVEAIFEELDGNEGLLVASKIADRVGITRS  217 (255)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCHH
T ss_conf             61377788899899999998866555699999999999998720288999999998422899662775302071266033


Q ss_pred             HHHHHHHHHH
Q ss_conf             7786565654
Q gi|254780805|r  168 HVANILRILK  177 (300)
Q Consensus       168 ~V~~~LrLl~  177 (300)
                      .|=|.||=++
T Consensus       218 VIVNALRKlE  227 (255)
T TIGR02787       218 VIVNALRKLE  227 (255)
T ss_pred             HHHHHHHHHH
T ss_conf             5545434442


No 383
>TIGR03542 DAPAT_plant LL-diaminopimelate aminotransferase. This clade of the pfam00155 superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). This clade includes characterized species in plants and Chlamydia. Every member of this clade is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known succinylases, desuccinylases, acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct, NADPH-dependent enzyme (ddh).
Probab=36.04  E-value=32  Score=15.03  Aligned_cols=42  Identities=12%  Similarity=0.082  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHCCEEEEE-----CCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             99999999739879997-----1798228999858-98999999998375
Q gi|254780805|r  252 DLEKKISSKVGLNISIK-----HRNNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       252 ~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      ++...|-+.-|  |-+-     ...+.|-|.|.|. +.|+|+.=+++|++
T Consensus       353 ~~~~~ll~e~~--V~vvPG~~FG~~g~g~vRls~a~~~e~l~ea~~Rl~~  400 (402)
T TIGR03542       353 DFFDFLLYQYH--IVGTPGSGFGSSGEGFVRFSAFGKRENIVAACERIKH  400 (402)
T ss_pred             HHHHHHHHHCC--EEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             99999998599--9997644768999896999972999999999999997


No 384
>COG1438 ArgR Arginine repressor [Transcription]
Probab=35.90  E-value=32  Score=15.01  Aligned_cols=40  Identities=20%  Similarity=0.208  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHCC-CCHHHHHHHHH-----HHHHHHHHHHHHHHHH
Q ss_conf             9999998521011-10467999974-----3378778656565435
Q gi|254780805|r  140 EALGYEQLISEYG-YTQNDIGSIVG-----KSRSHVANILRILKLP  179 (300)
Q Consensus       140 ~A~~~~~l~~~~~-~t~~~lA~~~G-----~s~s~V~~~LrLl~L~  179 (300)
                      +-..+++++.+.. .||+||.+.+-     .++++||+-|+-+.+-
T Consensus         7 R~~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~vTQaTvSRDlkelglv   52 (150)
T COG1438           7 RLELIKEIITEEKISTQEELVELLQEEGIEVTQATVSRDLKELGLV   52 (150)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHCCCEEEHHHHHHHHHHCCCE
T ss_conf             9999999998677778999999999829758639878779985988


No 385
>COG2456 Uncharacterized conserved protein [Function unknown]
Probab=35.56  E-value=11  Score=18.00  Aligned_cols=10  Identities=40%  Similarity=0.760  Sum_probs=3.9

Q ss_pred             HHHHHHHHHH
Q ss_conf             7999974337
Q gi|254780805|r  157 DIGSIVGKSR  166 (300)
Q Consensus       157 ~lA~~~G~s~  166 (300)
                      ++|+.+|..|
T Consensus        62 ~Ia~ilGlGR   71 (121)
T COG2456          62 EIAEILGLGR   71 (121)
T ss_pred             HHHHHHCCCC
T ss_conf             9999956365


No 386
>TIGR01817 nifA Nif-specific regulatory protein; InterPro: IPR010113   This entry represents NifA, a DNA-binding regulatory protein for nitrogen fixation. Not included in this group are: the homologue in Aquifex aeolicus (which lacks nitrogenase), transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.   In diazotrophic proteobacteria, the sigma54-dependent activator NifA activates transcription of the nif (nitrogen fixation) genes by a conserved mechanism common to members of the enhancer binding protein family. Although NifA proteins have similar domain structures, both transcriptional regulation of nifA expression and posttranslational regulation of NifA activity by oxygen and fixed nitrogen vary significantly from one organism to another. In Klebsiella pneumoniae and Azotobacter vinelandii, nifA is co-ordinately transcribed with a second gene, nifL, whose product inhibits NifA activity in response to oxygen and fixed nitrogen .; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0009399 nitrogen fixation.
Probab=35.00  E-value=27  Score=15.50  Aligned_cols=19  Identities=16%  Similarity=0.167  Sum_probs=9.1

Q ss_pred             CCCHHHHHHHHHHHHHHCC
Q ss_conf             6897899999999997398
Q gi|254780805|r  245 EKEKYLTDLEKKISSKVGL  263 (300)
Q Consensus       245 ~k~~~i~~le~~L~~~lGt  263 (300)
                      +...||-.|.+.|-++|+.
T Consensus       387 ER~~DIP~LA~~fL~kf~~  405 (574)
T TIGR01817       387 ERREDIPLLAEAFLEKFNR  405 (574)
T ss_pred             CCCCHHHHHHHHHHHHHHH
T ss_conf             8731168999999998766


No 387
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=34.91  E-value=33  Score=14.91  Aligned_cols=28  Identities=32%  Similarity=0.581  Sum_probs=24.6

Q ss_pred             CCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf             5789998-768988999999988631001
Q gi|254780805|r   49 PNPHNPR-NYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        49 ~~p~~pR-~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      -||.||- +.++.+.|..|++--++||++
T Consensus       165 CnPHNP~Grvwt~eeL~~i~elc~kh~v~  193 (388)
T COG1168         165 CNPHNPTGRVWTKEELRKIAELCLRHGVR  193 (388)
T ss_pred             ECCCCCCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf             37999998643699999999999983998


No 388
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=34.90  E-value=33  Score=14.91  Aligned_cols=49  Identities=27%  Similarity=0.331  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCC
Q ss_conf             1104679999743378778656565435899998764210167777764010
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTS  203 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~  203 (300)
                      .+|.++||+.+|.|+++.++..+= .+--.+.+.+..-.|.  +|+.||...
T Consensus       199 ~isl~~lA~~~~lS~s~l~rlFk~-~~G~sp~~yl~~~Ri~--~A~~lL~~t  247 (290)
T PRK10572        199 EFDIESVAQHVCLSPSRLSHLFRQ-QLGISVLSWREDQRIS--RAKLLLSTT  247 (290)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH-HHCCCHHHHHHHHHHH--HHHHHHHCC
T ss_conf             999999998969799999999998-6498999999999999--999998738


No 389
>TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827   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 is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis.    The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=34.87  E-value=25  Score=15.72  Aligned_cols=75  Identities=25%  Similarity=0.321  Sum_probs=40.7

Q ss_pred             EEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCC---------HHHHHHHHHHHCCCCCC
Q ss_conf             403898235789998768988999999988631001550462056544533357---------56777776421001354
Q gi|254780805|r   41 CISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAG---------ERRFRAAKMASLSEVPV  111 (300)
Q Consensus        41 ~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G---------~rR~rAa~~~g~~~ip~  111 (300)
                      .|+.|.|.|.+|+ |+ +|  ++++|| ++.=.|+ .|=--++...| =.||||         |+=--|.|+||   |-|
T Consensus         9 dvDTD~IIPGrYL-R~-~~--D~~eLA-~haM~g~-~PeF~~kvr~G-DviVAGkNFGcGSSREQA~~ALK~aG---v~a   78 (159)
T TIGR02087         9 DVDTDVIIPGRYL-RT-TD--DPDELA-SHAMEGI-DPEFAKKVREG-DVIVAGKNFGCGSSREQAALALKAAG---VAA   78 (159)
T ss_pred             CCCCCEECCCCCC-CC-CC--CHHHHH-HHCCCCC-CCCHHHHCCCC-CEEEECCCCCCCCCHHHHHHHHHHCC---EEE
T ss_conf             6467704585225-75-47--778899-8705589-96313407899-78871416477887788999997479---048


Q ss_pred             CCCCCCCHHHHHHH
Q ss_conf             33346411234556
Q gi|254780805|r  112 IIRNVDNKSSLEIA  125 (300)
Q Consensus       112 iv~~~~d~~~~~~~  125 (300)
                      ||-+---.=.++-|
T Consensus        79 viA~SFARIFYRNA   92 (159)
T TIGR02087        79 VIAESFARIFYRNA   92 (159)
T ss_pred             EEEEECCCHHHHHH
T ss_conf             98520166010323


No 390
>PRK12414 putative aminotransferase; Provisional
Probab=34.87  E-value=33  Score=14.91  Aligned_cols=23  Identities=13%  Similarity=0.144  Sum_probs=15.9

Q ss_pred             CEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             228999858-98999999998375
Q gi|254780805|r  273 KGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       273 kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .|-|.|.|. +.++|+.=+++|++
T Consensus       360 ~g~iRlsfa~~~e~l~eg~~RL~~  383 (384)
T PRK12414        360 TGVIRLSFSKDDATLVEGARRLCS  383 (384)
T ss_pred             CCEEEEEECCCHHHHHHHHHHHHC
T ss_conf             998999967999999999999703


No 391
>PRK07366 succinyldiaminopimelate transaminase; Validated
Probab=34.63  E-value=32  Score=15.02  Aligned_cols=44  Identities=9%  Similarity=0.172  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHCCEEE--EE-CCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             9999999997398799--97-1798228999858-9899999999837
Q gi|254780805|r  251 TDLEKKISSKVGLNIS--IK-HRNNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~--I~-~~~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      .++..+|-+.-|.-|.  .. ...+.|-|.|.|. +.+.|+.=+++|.
T Consensus       338 ~ef~~~Ll~~~gV~v~PG~~Fg~~g~g~iRl~~a~~~~~l~eal~Rl~  385 (388)
T PRK07366        338 VEFCTQLVAQTGVAASPGSGFGKSGEGYVRFALVHDPDILEEAVERIA  385 (388)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             999999998399999766465889998699996299999999999999


No 392
>PRK09265 aminotransferase AlaT; Validated
Probab=34.55  E-value=33  Score=14.91  Aligned_cols=42  Identities=10%  Similarity=0.038  Sum_probs=21.4

Q ss_pred             HHHHHHHHHCCEEE--EEC-CCCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf             99999997398799--971-7982289998589-899999999837
Q gi|254780805|r  253 LEKKISSKVGLNIS--IKH-RNNKGQFCIKYET-NEQLKIICSLLG  294 (300)
Q Consensus       253 le~~L~~~lGtkV~--I~~-~~~kGkI~I~f~s-~eeLe~Il~kL~  294 (300)
                      +..+|-+.-|.-|.  .-. ....|-+.|.|.. .+.|+.=+++|.
T Consensus       351 f~~~Ll~e~gV~v~PG~~Fg~~~~~~vRlsf~~~~e~l~eal~Rl~  396 (404)
T PRK09265        351 FVLDLLLQEKVLLVQGTGFNWPEPDHFRIVTLPRVDDLEDAIGRIG  396 (404)
T ss_pred             HHHHHHHHCCEEEECCCCCCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             9999998699999778502889999899997999999999999999


No 393
>TIGR01818 ntrC nitrogen regulation protein NR(I); InterPro: IPR010114   This entry represents Nitrogen regulatory protein C (NtrC), which is a bacterial enhancer-binding protein that activates the transcription of genes encoding enzymes required for nitrogen metabolism. It is phosphorylated by NtrB and interacts with sigma-54. One of the best studied examples is its activation of the gene glnA, which encodes the enzyme glutamine synthetase.. NtrC is composed of three domains , . The 124 residue N-terminal domain is homologous to receiver domains of other response regulator proteins in two-component signal transduction systems , . The 240 residue central domain of NtrC is homologous to a domain found in all activators of the sigma-54 RNA polymerase holoenzyme , . The C-terminal domain has been indicated to contain the determinants necessary for both DNA-binding and dimerization of full-length NtrC.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0009399 nitrogen fixation, 0050906 detection of stimulus during sensory perception.
Probab=34.34  E-value=33  Score=14.91  Aligned_cols=15  Identities=20%  Similarity=0.284  Sum_probs=10.1

Q ss_pred             CHHHHHHHHHHHHCC
Q ss_conf             778999999764102
Q gi|254780805|r  218 SVRDTEELVQEQDNK  232 (300)
Q Consensus       218 SVRe~E~lVk~~~~~  232 (300)
                      +||+.|++++.+..-
T Consensus       353 NVR~LEN~cR~l~~l  367 (471)
T TIGR01818       353 NVRELENVCRRLTVL  367 (471)
T ss_pred             CHHHHHHHHHHHHHH
T ss_conf             524577899999873


No 394
>PRK09276 aspartate aminotransferase; Provisional
Probab=34.33  E-value=33  Score=14.94  Aligned_cols=45  Identities=13%  Similarity=0.264  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             99999999973987999---71798228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++...|-+.-|.-|.=   ....+.|-+.|.|. +.++++.=+++|++
T Consensus       336 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~iRl~~a~~~e~l~eal~Rl~k  384 (385)
T PRK09276        336 AEFATLLLDKAGIVVTPGNGFGTAGEGYFRIALTVPDERIEEAVERIKK  384 (385)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHC
T ss_conf             9999999981999998874218899886999975999999999999842


No 395
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=34.33  E-value=34  Score=14.85  Aligned_cols=18  Identities=22%  Similarity=0.246  Sum_probs=9.2

Q ss_pred             CCHHHHHHHHHHHHHHCC
Q ss_conf             104899999998521011
Q gi|254780805|r  135 LNPLEEALGYEQLISEYG  152 (300)
Q Consensus       135 l~p~e~A~~~~~l~~~~~  152 (300)
                      .+|-+.+.+...|...++
T Consensus       108 ~~~~~~~~~~~~l~~~~~  125 (304)
T PRK08154        108 ATPAQLARARDALSGMLG  125 (304)
T ss_pred             CCHHHHHHHHHHHHHHHC
T ss_conf             899999999999876302


No 396
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=34.18  E-value=30  Score=15.16  Aligned_cols=26  Identities=19%  Similarity=0.509  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHCCCCCCCEEECCCCCCCC
Q ss_conf             899999998863100155046205654453
Q gi|254780805|r   61 EGLEDLCQSIKSHGIIQPLIVRAIDNGLYK   90 (300)
Q Consensus        61 ~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~   90 (300)
                      ..+.|=-..+...|++   .+++ +.|.|.
T Consensus        49 ~~VREAL~~L~~~GlV---~~r~-g~G~~V   74 (254)
T PRK09464         49 PSLREAIQRLEAKGLL---LRRQ-GGGTFV   74 (254)
T ss_pred             HHHHHHHHHHHHCCCE---EEEC-CCCEEE
T ss_conf             5999999999988998---9717-871364


No 397
>PRK08361 aspartate aminotransferase; Provisional
Probab=34.16  E-value=34  Score=14.84  Aligned_cols=44  Identities=18%  Similarity=0.184  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf             99999999973987999---717982289998589-899999999837
Q gi|254780805|r  251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYET-NEQLKIICSLLG  294 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~s-~eeLe~Il~kL~  294 (300)
                      .++.+.|-+.-|.-|.=   -...+.|-+.|.|.. .+++..=+++|.
T Consensus       337 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~iRl~f~~~~e~l~eal~Rl~  384 (390)
T PRK08361        337 EDFSEWLLEKARVVVIPGTAFGKMGEGYVRISYATSKEKLIEAMERME  384 (390)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             999999997199999887322889999799997299999999999999


No 398
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional  chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli  do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=34.15  E-value=34  Score=14.83  Aligned_cols=51  Identities=20%  Similarity=0.324  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHH-HC-CEEEEECC-C-CCEEEEEEECCHHHHHHHHHHHCCCCCC
Q ss_conf             899999999997-39-87999717-9-8228999858989999999983756456
Q gi|254780805|r  249 YLTDLEKKISSK-VG-LNISIKHR-N-NKGQFCIKYETNEQLKIICSLLGENDFE  299 (300)
Q Consensus       249 ~i~~le~~L~~~-lG-tkV~I~~~-~-~kGkI~I~f~s~eeLe~Il~kL~~~~~~  299 (300)
                      -+..+..-|.+. +. +.+.|.+. . -.|.+.|.|++.+++++=.+.|.+.+++
T Consensus        14 ~Ia~vt~~L~~~~IsI~nI~Il~~RE~~~GvLri~F~~~~d~~~A~~~L~~~~Y~   68 (69)
T cd04909          14 VIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEILKEAGYE   68 (69)
T ss_pred             HHHHHHHHHHHCCCCEEEEEEEEEECCCCCEEEEEECCHHHHHHHHHHHHHCCCC
T ss_conf             6999999999879874724876851478847999968989999999999984951


No 399
>PRK11414 putative DNA-binding transcriptional regulator; Provisional
Probab=34.10  E-value=33  Score=14.92  Aligned_cols=15  Identities=7%  Similarity=0.120  Sum_probs=4.8

Q ss_pred             CCCCCCCCCCCCCHH
Q ss_conf             235789998768988
Q gi|254780805|r   47 IVPNPHNPRNYFESE   61 (300)
Q Consensus        47 i~~~p~~pR~~~~~~   61 (300)
                      |.-.-+.|=....+.
T Consensus        24 I~~G~l~PG~~L~e~   38 (221)
T PRK11414         24 LSIGALKPGARLITK   38 (221)
T ss_pred             HHCCCCCCCCCCCHH
T ss_conf             983998995971899


No 400
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=34.02  E-value=27  Score=15.51  Aligned_cols=31  Identities=23%  Similarity=0.302  Sum_probs=18.5

Q ss_pred             CHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCC
Q ss_conf             9889999999886310015504620565445333
Q gi|254780805|r   59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKII   92 (300)
Q Consensus        59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii   92 (300)
                      ++..+.-...|++..|+..-   +|-+.|+|.--
T Consensus        38 npGTVRNqmq~LkaLgLVeg---vpGPkGGY~PT   68 (294)
T COG2524          38 NPGTVRNQMQSLKALGLVEG---VPGPKGGYKPT   68 (294)
T ss_pred             CCCHHHHHHHHHHHCCCCCC---CCCCCCCCCCC
T ss_conf             96169999999885275225---66898896533


No 401
>PRK06030 hypothetical protein; Provisional
Probab=33.93  E-value=34  Score=14.81  Aligned_cols=37  Identities=11%  Similarity=0.214  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHH--HHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999852--10111046799997433787786565
Q gi|254780805|r  138 LEEALGYEQLI--SEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       138 ~e~A~~~~~l~--~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      +-.++-+..++  ..+|++..++|..+|++++||..-.+
T Consensus        65 var~RQIAMYLahv~~~~sl~~Ig~~FgRDrTTv~HAc~  103 (136)
T PRK06030         65 VSRIRQIAMYVAHTSLGMPMNEVALGFARDRTTVGHACH  103 (136)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             638999999999998678899999997643159999999


No 402
>pfam07453 NUMOD1 NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs).
Probab=33.70  E-value=17  Score=16.71  Aligned_cols=25  Identities=20%  Similarity=0.405  Sum_probs=19.1

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             21011104679999743378778656
Q gi|254780805|r  148 ISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       148 ~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      +..|. |..++|+.+|.++++|++++
T Consensus        13 i~~f~-Si~~aa~~L~i~~~tI~~~~   37 (37)
T pfam07453        13 IGKFS-SIREAARALGISHSTINKYL   37 (37)
T ss_pred             EEHHH-HHHHHHHHHCCCHHHHHCCC
T ss_conf             62246-79999998476465665029


No 403
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, 
Probab=33.31  E-value=35  Score=14.75  Aligned_cols=69  Identities=16%  Similarity=0.148  Sum_probs=33.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCH--HHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             1046799997433787786565654358999987642101677777640100--46899997422247789999997641
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSD--PLSLAQVIVSKKMSVRDTEELVQEQD  230 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~--~~~la~~Ii~~~LSVRe~E~lVk~~~  230 (300)
                      ||-.++|+..|.|..+|..|-+..=|||.-...  .|      .| +.+-.+  ...+....-.-++|+.++..++....
T Consensus         1 ytIgelA~~~Gvs~~TiRyYe~~GLl~~~~Rt~--~G------yR-~Y~~~~l~rL~fI~~~r~~G~sl~eI~~lL~~~d   71 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARTE--GG------YG-LFDDCALQRLRFVRAAFEAGIGLDELARLCRALD   71 (107)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC--CC------CC-CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf             958899999788948998999878989988899--98------81-3599999999999999987999999999996053


No 404
>PRK08912 hypothetical protein; Provisional
Probab=33.00  E-value=35  Score=14.71  Aligned_cols=42  Identities=7%  Similarity=0.075  Sum_probs=21.2

Q ss_pred             HHHHHHHHHCCEEE---EEC--CCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             99999997398799---971--798228999858-9899999999837
Q gi|254780805|r  253 LEKKISSKVGLNIS---IKH--RNNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       253 le~~L~~~lGtkV~---I~~--~~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      ...+|-+.-|.-|.   ...  ...+|-|.|.|. +.|+++.=+++|.
T Consensus       334 f~~~ll~e~gV~~vPG~~F~~~~~~~~~iRlsfa~~~e~l~ea~~RL~  381 (387)
T PRK08912        334 FCRRLVEEAGVAAIPVSAFYEEDPVTSVVRFCFAKRDATLDEAVERLA  381 (387)
T ss_pred             HHHHHHHHCCEEEECCCCCCCCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             999999968999981501289999998599997999999999999999


No 405
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=32.93  E-value=35  Score=14.71  Aligned_cols=22  Identities=14%  Similarity=0.223  Sum_probs=11.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0467999974337877865656
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      |.++||+.+|.+...|...+++
T Consensus       264 t~eEiA~~lg~~~~~v~~~~~~  285 (398)
T PRK05901        264 TPEELAEEMDFTPEKVREIQKY  285 (398)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999998819999999999997


No 406
>TIGR03558 oxido_grp_1 luciferase family oxidoreductase, group 1. The Pfam domain family pfam00296 is named for luciferase-like monooxygenases, but the family also contains several coenzyme F420-dependent enzymes. This protein family represents a well-resolved clade within family pfam00296 and shows no restriction to coenzyme F420-positive species, unlike some other clades within pfam00296.
Probab=32.85  E-value=7.4  Score=19.07  Aligned_cols=63  Identities=13%  Similarity=0.051  Sum_probs=24.7

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCC-CCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCC
Q ss_conf             57899987689889999999886310-01550462056544533357567777764210013543
Q gi|254780805|r   49 PNPHNPRNYFESEGLEDLCQSIKSHG-IIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVI  112 (300)
Q Consensus        49 ~~p~~pR~~~~~~~l~eLa~SI~~~G-~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~i  112 (300)
                      .++...+..|+ +.+++|..-+...+ -.+++.++|.....-.+..+..--..+..++..-++.+
T Consensus       119 ~~~~~~~~~f~-e~~~~l~~~~~~~~~~~~~v~~~P~~~~~ppiw~~~~s~~s~~~Aa~~G~~~~  182 (323)
T TIGR03558       119 RGLDARADDFP-EQVAELQAYLGPEGHPYQGVRAVPGPGTNPPLWLLGSSLYSAQLAAELGLPFA  182 (323)
T ss_pred             CCHHHHHHHHH-HHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEECCCHHHHHHHHHCCCCEE
T ss_conf             45020576689-99999999856788788862123899999986897088489999998499620


No 407
>PRK08175 aminotransferase; Validated
Probab=32.85  E-value=35  Score=14.70  Aligned_cols=41  Identities=7%  Similarity=0.186  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHCCEEEEE-----CCCCCEEEEEEECCH-HHHHHHHHHHC
Q ss_conf             99999999739879997-----179822899985898-99999999837
Q gi|254780805|r  252 DLEKKISSKVGLNISIK-----HRNNKGQFCIKYETN-EQLKIICSLLG  294 (300)
Q Consensus       252 ~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~s~-eeLe~Il~kL~  294 (300)
                      ++..+|-+.-  +|-+.     ...+.|-|.|.|... +.++.=+++|+
T Consensus       338 ef~~~ll~e~--~V~v~PG~~Fg~~g~~~vRl~~~~~~~~l~eal~Ri~  384 (395)
T PRK08175        338 EFAKKLLNEA--KVCVSPGIGFGDYGDTHVRFALIENRDRIRQAVRGIK  384 (395)
T ss_pred             HHHHHHHHHC--CEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             9999999849--8999777332779998699997289999999999999


No 408
>pfam00157 Pou Pou domain - N-terminal to homeobox domain.
Probab=32.82  E-value=36  Score=14.70  Aligned_cols=34  Identities=29%  Similarity=0.476  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHH------HHHHHHHHHH
Q ss_conf             999998521011104679999743------3787786565
Q gi|254780805|r  141 ALGYEQLISEYGYTQNDIGSIVGK------SRSHVANILR  174 (300)
Q Consensus       141 A~~~~~l~~~~~~t~~~lA~~~G~------s~s~V~~~Lr  174 (300)
                      |..|+.-.=..|+||.+++..+|.      |+++|++.=+
T Consensus        13 a~~fk~rRi~LG~TQ~dVg~al~~l~G~~~SQttIcRFE~   52 (75)
T pfam00157        13 AKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEA   52 (75)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             9999998987377599999999987086542358888885


No 409
>PRK06108 aspartate aminotransferase; Provisional
Probab=32.66  E-value=36  Score=14.68  Aligned_cols=44  Identities=16%  Similarity=0.196  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHCCEEE---EECCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             9999999997398799---971798228999858-9899999999837
Q gi|254780805|r  251 TDLEKKISSKVGLNIS---IKHRNNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~---I~~~~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      .++...|-+..|.-|.   .-...+.|-|.|.|. +.++|+.=+++|+
T Consensus       330 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~iRl~~a~~~~~l~eal~RL~  377 (382)
T PRK06108        330 LALAKRLVDEAGLGLAPGTAFGPGGEGFLRWCFARDPARLDEGVERLR  377 (382)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             999999999699999878411889999799996299999999999999


No 410
>TIGR01265 tyr_nico_aTase tyrosine/nicotianamine aminotransferases; InterPro: IPR005958   This entry describes tyrosine aminotransferase (2.6.1.5 from EC) as found in animals and Trypanosoma cruzi (Euglenozoa). It is the first enzyme of a pathway of tyrosine degradation via homogentisate.  L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase, an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway are included in this family. ; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding, 0006519 amino acid and derivative metabolic process.
Probab=32.63  E-value=36  Score=14.68  Aligned_cols=77  Identities=27%  Similarity=0.487  Sum_probs=47.5

Q ss_pred             CCC-CCCCCEEEEHHHC------------CCCCCCCC-CCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCC-CCCCCH-
Q ss_conf             013-4566024038982------------35789998-7689889999999886310015504620565445-333575-
Q gi|254780805|r   32 TET-IPESQDCISIHSI------------VPNPHNPR-NYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLY-KIIAGE-   95 (300)
Q Consensus        32 ~~~-~~~~~~~i~i~~i------------~~~p~~pR-~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y-~ii~G~-   95 (300)
                      ... .+++-=+|+|+.|            .-||.||= -.|+.+.|+++++.=+++|++  |+-    |.=| -+|.|. 
T Consensus       161 ydLdlPe~~WeiDL~~le~l~DekT~A~vv~NP~NPCGsVF~~~HL~k~~~~A~kl~i~--iIA----DEiY~~~Vf~dk  234 (424)
T TIGR01265       161 YDLDLPEKDWEIDLDGLESLADEKTVAIVVINPSNPCGSVFSRDHLEKIAEVARKLGIP--IIA----DEIYGHLVFGDK  234 (424)
T ss_pred             CCCCCCCCCCEECHHHHHHHHCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCC--EEE----EEECCCCCCCCC
T ss_conf             24678887523647899876326876999847566788887888899999999870982--687----763164144889


Q ss_pred             ---HHHHHHHHHHCCCCCCCCCC
Q ss_conf             ---67777764210013543334
Q gi|254780805|r   96 ---RRFRAAKMASLSEVPVIIRN  115 (300)
Q Consensus        96 ---rR~rAa~~~g~~~ip~iv~~  115 (300)
                         --+-+.-.+. ..||+++..
T Consensus       235 DPn~~F~p~a~f~-~~VPvl~lG  256 (424)
T TIGR01265       235 DPNAPFVPMASFA-SIVPVLSLG  256 (424)
T ss_pred             CCCCCCCCCCCCC-CCCCEEEEC
T ss_conf             7888622300357-868868863


No 411
>PRK07568 aspartate aminotransferase; Provisional
Probab=32.44  E-value=36  Score=14.66  Aligned_cols=44  Identities=20%  Similarity=0.336  Sum_probs=23.0

Q ss_pred             HHHHHHHHHH---CCEEEEE----C--CC--CCEEEEEEE-CCHHHHHHHHHHHCC
Q ss_conf             9999999973---9879997----1--79--822899985-898999999998375
Q gi|254780805|r  252 DLEKKISSKV---GLNISIK----H--RN--NKGQFCIKY-ETNEQLKIICSLLGE  295 (300)
Q Consensus       252 ~le~~L~~~l---GtkV~I~----~--~~--~kGkI~I~f-~s~eeLe~Il~kL~~  295 (300)
                      +....|-+.+   +..|-+-    .  ..  ++|-|.|.| .+.|+++.=+++|++
T Consensus       333 ~f~~~ll~~~~~~~~~V~v~PG~~F~~~~g~g~~~iRls~~~~~e~l~ea~~Rl~~  388 (396)
T PRK07568        333 DFAKWMLTDFEYNGETVMVAPASGFYATPGLGKDEIRIAYVLEKEDLRRAMEILKK  388 (396)
T ss_pred             HHHHHHHHHHHHCCCEEEEECCHHHCCCCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             99999999621248869997763416899899996999971999999999999999


No 412
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper),  CadR (cadmium),  PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=32.27  E-value=36  Score=14.64  Aligned_cols=20  Identities=15%  Similarity=0.212  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             46799997433787786565
Q gi|254780805|r  155 QNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       155 ~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      -.++|+.+|.|..++.-|=+
T Consensus         3 Ige~A~~~gvs~~tlR~Ye~   22 (123)
T cd04770           3 IGELAKAAGVSPDTIRYYER   22 (123)
T ss_pred             HHHHHHHHCCCHHHHHHHHH
T ss_conf             89999998959999999998


No 413
>pfam06056 Terminase_5 Putative ATPase subunit of terminase (gpP-like). This family of proteins are annotated as ATPase subunits of phage terminase after. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.
Probab=32.16  E-value=23  Score=15.92  Aligned_cols=22  Identities=23%  Similarity=0.339  Sum_probs=18.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             1110467999974337877865
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANI  172 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~  172 (300)
                      -||+..+||+.+|.+.++|..-
T Consensus        12 qg~~~~eIA~~Lg~~~~tVysW   33 (58)
T pfam06056        12 QGYRPAEIAQELGLKARTVYSW   33 (58)
T ss_pred             CCCCHHHHHHHHCCCCCHHHHH
T ss_conf             6898999999978993145658


No 414
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=31.74  E-value=37  Score=14.58  Aligned_cols=28  Identities=18%  Similarity=0.436  Sum_probs=14.9

Q ss_pred             CHHHHHHHHHHHHHCCCCCCCEEECCCCCCCC
Q ss_conf             98899999998863100155046205654453
Q gi|254780805|r   59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYK   90 (300)
Q Consensus        59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~   90 (300)
                      +-..+.|=-..+...|++   .+++ +.|.|.
T Consensus        39 SRt~VREAL~~L~~eGlV---~~~~-g~G~~V   66 (253)
T PRK10421         39 SRNSLREALAKLVSEGVL---LSRR-GGGTFI   66 (253)
T ss_pred             CHHHHHHHHHHHHHCCCE---EEEE-CCEEEE
T ss_conf             989999999999988987---9975-782487


No 415
>TIGR02404 trehalos_R_Bsub trehalose operon repressor; InterPro: IPR012770    This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from Escherichia coli..
Probab=31.69  E-value=34  Score=14.79  Aligned_cols=31  Identities=19%  Similarity=0.350  Sum_probs=21.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0467999974337877865656543589999
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILKLPSSVRE  184 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~  184 (300)
                      |-.+|.+..|-||.||++.|.+|.=.=.||.
T Consensus        26 SE~~L~~~Y~~SReTvRKAL~~L~~~GyIQK   56 (236)
T TIGR02404        26 SEHELMEQYGASRETVRKALNLLTEAGYIQK   56 (236)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             8789998606874588999999985787167


No 416
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements.  A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=31.58  E-value=37  Score=14.57  Aligned_cols=68  Identities=19%  Similarity=0.206  Sum_probs=36.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             1046799997433787786565654358999987642101677777640100468999974222477899999976
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEELVQE  228 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~lVk~  228 (300)
                      +|-.++|+.+|.+.+++.-|=+.-=|||+--+. .-...+..+..       ..........-++|..++..++..
T Consensus         1 ysI~eva~~~gvs~~tlR~Ye~~GLl~p~r~~~-g~R~Y~~~~i~-------~l~~I~~lr~~G~sl~~I~~~l~~   68 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSEN-GYRLYSEEDLE-------RLRLIRRLRELGLSLKEIRELLDA   68 (100)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC-CCCCCCHHHHH-------HHHHHHHHHHCCCCHHHHHHHHHC
T ss_conf             978899999895999999998769999883589-97425699999-------999999999979999999999835


No 417
>PRK07777 aminotransferase; Validated
Probab=31.52  E-value=37  Score=14.56  Aligned_cols=44  Identities=11%  Similarity=0.101  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHHCCEEE---EE---CCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             9999999997398799---97---1798228999858-9899999999837
Q gi|254780805|r  251 TDLEKKISSKVGLNIS---IK---HRNNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~---I~---~~~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      ..+...|.+..|.-|.   ..   .....+-|.|.|. +.|+|+.=+++|+
T Consensus       331 ~~f~~~L~~~~gV~v~PG~~F~~~~~~g~~~vRlsf~~~~e~l~ea~~RL~  381 (386)
T PRK07777        331 TAFCRALPERVGVAAIPMSAFCDPADAWNHLVRFAFCKRDDTLDEAIRRLR  381 (386)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             999999998689999887442889877899799996899999999999999


No 418
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=31.45  E-value=35  Score=14.74  Aligned_cols=16  Identities=0%  Similarity=0.256  Sum_probs=8.8

Q ss_pred             HHHHHHHHCCCCHHHH
Q ss_conf             8999974222477899
Q gi|254780805|r  207 SLAQVIVSKKMSVRDT  222 (300)
Q Consensus       207 ~la~~Ii~~~LSVRe~  222 (300)
                      ++.+.+...|++.-++
T Consensus        60 ~~~e~l~~~Gid~~eL   75 (135)
T PRK10947         60 QYREMLIADGIDPNEL   75 (135)
T ss_pred             HHHHHHHHCCCCHHHH
T ss_conf             9999999859999999


No 419
>PRK07681 aspartate aminotransferase; Provisional
Probab=30.99  E-value=38  Score=14.50  Aligned_cols=47  Identities=11%  Similarity=0.196  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHCCEEEE--E-CCCCCEEEEEEE-CCHHHHHHHHHHHCCCC
Q ss_conf             99999999973987999--7-179822899985-89899999999837564
Q gi|254780805|r  251 TDLEKKISSKVGLNISI--K-HRNNKGQFCIKY-ETNEQLKIICSLLGEND  297 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I--~-~~~~kGkI~I~f-~s~eeLe~Il~kL~~~~  297 (300)
                      .++...|-+..|.-|.=  . ...+.|-|.|.| .+.++|+.-+++|++.+
T Consensus       336 ~~f~~~Ll~~~gV~v~PG~~Fg~~g~g~iRl~f~~~~e~l~eal~RLk~a~  386 (399)
T PRK07681        336 LDFAYALMDRANVVVTPGHAFGPHGEGFVRIALVQDKEVLQQVVENIRNSG  386 (399)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHCC
T ss_conf             999999998299999886465899988699997188999999999998888


No 420
>COG0436 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=30.94  E-value=38  Score=14.50  Aligned_cols=47  Identities=15%  Similarity=0.216  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHCCEEEE--EC-C-CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             8999999999973987999--71-7-98228999858-98999999998375
Q gi|254780805|r  249 YLTDLEKKISSKVGLNISI--KH-R-NNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       249 ~i~~le~~L~~~lGtkV~I--~~-~-~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      +-.++..+|-+..|.-|.=  -. . .+.|-|.|.|. +.++++..++.|..
T Consensus       336 d~~~f~~~Ll~~~gV~v~PG~~Fg~~~g~~~vRis~~~~~~~l~~a~~rl~~  387 (393)
T COG0436         336 DSEEFAKKLLEEAGVAVVPGSGFGEPPGEGYVRLSLATSEETLEEALRRLAR  387 (393)
T ss_pred             CHHHHHHHHHHHCCEEEECHHHHCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             9899999999867999957257497877987999973689999999999999


No 421
>PRK06575 consensus
Probab=30.84  E-value=38  Score=14.49  Aligned_cols=43  Identities=19%  Similarity=0.369  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             999999999739879997-17--98228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++.+.|-+.-  +|-+. ..  +..|-+.|.|. +.++|+.-+++|++
T Consensus       348 ~~f~~~Ll~e~--~V~v~PG~~FG~~g~~Rl~~a~~~e~l~ea~~Rl~~  394 (399)
T PRK06575        348 NDFAEYLLEEA--KVAVVPGIAFGLEGYFRISYATSMEELEEACIRIER  394 (399)
T ss_pred             HHHHHHHHHHC--CEEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             99999999729--999984855589983999973989999999999999


No 422
>TIGR03539 DapC_actino succinyldiaminopimelate transaminase. This family of actinobacterial succinyldiaminopimelate transaminase enzymes (DapC) are members of the pfam00155 superfamily. Many of these genes appear adjacent to other genes encoding enzymes of the lysine biosynthesis via diaminopimelate pathway (GenProp0125).
Probab=30.62  E-value=39  Score=14.46  Aligned_cols=42  Identities=14%  Similarity=0.195  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHCCEEEEE-----CCCCCEEEEEEE-CCHHHHHHHHHHHC
Q ss_conf             9999999999739879997-----179822899985-89899999999837
Q gi|254780805|r  250 LTDLEKKISSKVGLNISIK-----HRNNKGQFCIKY-ETNEQLKIICSLLG  294 (300)
Q Consensus       250 i~~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f-~s~eeLe~Il~kL~  294 (300)
                      .....+.|.+. |  |-+.     ...+.|-|.|.| .+.|+|+.=+++|.
T Consensus       310 ~~~~~~~l~e~-g--V~v~PG~~Fg~~g~~~vRis~~~~~e~l~eal~Rls  357 (357)
T TIGR03539       310 AWDTVDRLAEL-G--ILVAPGDFYGPAGSQHVRVALTATDERIAAAVARLT  357 (357)
T ss_pred             HHHHHHHHHHC-C--EEEECCCCCCCCCCCEEEEEECCCHHHHHHHHHHCC
T ss_conf             99999999969-9--899478744789999799997299999999998575


No 423
>PRK07310 consensus
Probab=30.35  E-value=34  Score=14.86  Aligned_cols=44  Identities=25%  Similarity=0.307  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHCCEEEEECC--CCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf             999999999973987999717--982289998589-899999999837
Q gi|254780805|r  250 LTDLEKKISSKVGLNISIKHR--NNKGQFCIKYET-NEQLKIICSLLG  294 (300)
Q Consensus       250 i~~le~~L~~~lGtkV~I~~~--~~kGkI~I~f~s-~eeLe~Il~kL~  294 (300)
                      ..++...|-+..|.-|. ...  +..|.|.|.|.. .+.|+.-+++|+
T Consensus       341 ~~~~~~~ll~~~gV~v~-PG~~FG~~~~vRl~~a~~~~~l~eal~RL~  387 (395)
T PRK07310        341 VTDFTTAILEEVGVALV-TGAGFGAPENVRLSYATDLETLKEAVRRLH  387 (395)
T ss_pred             HHHHHHHHHHHCCEEEE-CCCCCCCCCCEEEEECCCHHHHHHHHHHHH
T ss_conf             99999999984999998-897669999889998099999999999999


No 424
>PRK09082 putative aminotransferase; Validated
Probab=30.14  E-value=39  Score=14.41  Aligned_cols=44  Identities=9%  Similarity=0.081  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHCCEEE---EECC--CCCEEEEEEECC-HHHHHHHHHHHCC
Q ss_conf             999999997398799---9717--982289998589-8999999998375
Q gi|254780805|r  252 DLEKKISSKVGLNIS---IKHR--NNKGQFCIKYET-NEQLKIICSLLGE  295 (300)
Q Consensus       252 ~le~~L~~~lGtkV~---I~~~--~~kGkI~I~f~s-~eeLe~Il~kL~~  295 (300)
                      ++...|.+.-|.-|.   ....  .+.|-|.|.|.. .++++.=+++|.+
T Consensus       336 ~f~~~l~~e~gV~v~PG~~F~~~~~~~~~iRl~fa~~~e~l~ea~~RLak  385 (386)
T PRK09082        336 EFCQWLTREHGVAAIPLSVFYADPFPHRLVRFCFAKQEETLDAAAERLCQ  385 (386)
T ss_pred             HHHHHHHHHCCEEEECCHHHCCCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             99999998589999827110579999997999968999999999999842


No 425
>KOG3398 consensus
Probab=30.05  E-value=39  Score=14.40  Aligned_cols=41  Identities=20%  Similarity=0.287  Sum_probs=31.5

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             22104899999998521011104679999743378778656
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      -+-.+.+-..++++-..+-||||.+||.++......|..|=
T Consensus        67 ~~~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyE  107 (135)
T KOG3398          67 HDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYE  107 (135)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf             23014789999999888637548899999602861365575


No 426
>pfam10279 Latarcin Latarcin precursor. This family represents the precursor proteins for a number of short antimicrobial peptides called Latarcins. Latarcins were discovered in the venom of the spider Lachesana tarabaevi. Latarcins are likely to adopt amphipathic alpha-helical structure in the plasma membrane.
Probab=29.99  E-value=40  Score=14.40  Aligned_cols=19  Identities=37%  Similarity=0.604  Sum_probs=15.3

Q ss_pred             HHHHHH-CCCCCHHHHHHHH
Q ss_conf             665431-0221048999999
Q gi|254780805|r  126 IVENVQ-RKDLNPLEEALGY  144 (300)
Q Consensus       126 l~EN~~-R~dl~p~e~A~~~  144 (300)
                      +.||++ ++|+...|+|+++
T Consensus        50 ~~e~l~kled~~~~EEARg~   69 (88)
T pfam10279        50 IAEALEKLEDFENTEEARGF   69 (88)
T ss_pred             HHHHHHHHCCCCCHHHHHHH
T ss_conf             99998863263217999988


No 427
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761   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 clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=29.96  E-value=35  Score=14.76  Aligned_cols=29  Identities=14%  Similarity=0.203  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11104679999743378778656565435
Q gi|254780805|r  151 YGYTQNDIGSIVGKSRSHVANILRILKLP  179 (300)
Q Consensus       151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~  179 (300)
                      .--|.++||..+||+---|+..|.|..=+
T Consensus       154 ~EpS~eeiA~~~~kpvedv~~~L~Lne~~  182 (292)
T TIGR02394       154 REPSVEEIAELLDKPVEDVSKVLALNERI  182 (292)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf             77887899988389888999998417995


No 428
>PRK07309 aromatic amino acid aminotransferase; Validated
Probab=29.93  E-value=40  Score=14.39  Aligned_cols=46  Identities=15%  Similarity=0.156  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHCCEEEE--E-CCCCCEEEEEEEC-CHHHHHHHHHHHCCC
Q ss_conf             99999999973987999--7-1798228999858-989999999983756
Q gi|254780805|r  251 TDLEKKISSKVGLNISI--K-HRNNKGQFCIKYE-TNEQLKIICSLLGEN  296 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I--~-~~~~kGkI~I~f~-s~eeLe~Il~kL~~~  296 (300)
                      .++...|.+.-|.-|.=  . ...+.|-+.|.|. +.++|+.=+++|++-
T Consensus       336 ~~~~~~l~~~~gV~v~PG~~Fg~~g~g~iRl~~a~~~e~l~eal~Rl~~~  385 (390)
T PRK07309        336 FKFLQDFAKEKAVAIIPGVAFGPYGEGYVRLSYAASMETIKEAMKRLKEY  385 (390)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHH
T ss_conf             99999999969999977732288999879999828999999999999999


No 429
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=29.84  E-value=40  Score=14.38  Aligned_cols=47  Identities=13%  Similarity=0.162  Sum_probs=30.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             11046799997433787786565654358999987642101677777640
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVS  201 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~  201 (300)
                      .+|.+++|+.+|.|+++.++..+- .....+.+.+..-.+.  +|+.||.
T Consensus        21 ~i~l~~lA~~~~~S~~~l~r~Fk~-~~g~t~~~yi~~~Rl~--~A~~lL~   67 (107)
T PRK10219         21 PLNIDVVAKKSGYSKWYLQRMFRT-VTHQTLGDYIRQRRLL--LAAVELR   67 (107)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH-HHCCCHHHHHHHHHHH--HHHHHHH
T ss_conf             999999998989399999999999-9890999999999999--9999988


No 430
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=29.69  E-value=40  Score=14.36  Aligned_cols=44  Identities=18%  Similarity=0.162  Sum_probs=24.2

Q ss_pred             CCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             22104899999998521---011104679999743378778656565
Q gi|254780805|r  133 KDLNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      .+|+|-|+-.+=.-|-.   ...+|-.++|+..|.|.++|.|.-+=+
T Consensus        12 ~~Lt~~Ek~iA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkL   58 (284)
T PRK11302         12 EHLSKSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSL   58 (284)
T ss_pred             HHCCHHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             64599999999999809899976669999989699888999999995


No 431
>TIGR03538 DapC_gpp succinyldiaminopimelate transaminase. This family of succinyldiaminopimelate transaminases (DapC) includes the experimentally characterized enzyme from Bordatella pertussis. The majority of genes in this family are proximal to genes encoding components of the lysine biosynthesis via diaminopimelate pathway (GenProp0125).
Probab=29.68  E-value=40  Score=14.36  Aligned_cols=24  Identities=13%  Similarity=0.059  Sum_probs=16.5

Q ss_pred             CCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             8228999858-98999999998375
Q gi|254780805|r  272 NKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       272 ~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      +.|-|.|.|. +.++|+.=+++|.+
T Consensus       368 G~g~iR~s~~~~~e~l~ea~~Rl~~  392 (394)
T TIGR03538       368 GAGRVRIALVAPLEECVEAAERIRR  392 (394)
T ss_pred             CCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             9998999975989999999999998


No 432
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=29.66  E-value=40  Score=14.36  Aligned_cols=32  Identities=22%  Similarity=0.299  Sum_probs=27.3

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99998521011104679999743378778656
Q gi|254780805|r  142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      ..+++++++.|+|..+.|++-|...|+....|
T Consensus        19 ~~l~~~l~Elglt~~eFak~anIP~StLYKil   50 (170)
T COG4800          19 SCLQKLLDELGLTPSEFAKRANIPLSTLYKIL   50 (170)
T ss_pred             HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHH
T ss_conf             99999999819998999887099899999998


No 433
>PRK05942 aspartate aminotransferase; Provisional
Probab=29.15  E-value=41  Score=14.30  Aligned_cols=48  Identities=15%  Similarity=0.172  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHCCCCC
Q ss_conf             99999999973987999---71798228999858-98999999998375645
Q gi|254780805|r  251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLGENDF  298 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~~~~~  298 (300)
                      .++...|-+.-|.-|.=   ....+.|-|.|.|. +.++++.=+++|.+.-.
T Consensus       340 ~~f~~~ll~~~gV~v~PG~~Fg~~g~~~iRlsf~~~~~~l~ea~~Rl~~a~~  391 (394)
T PRK05942        340 TDFALNVLQKTGVVVTPGNAFGEGGEGYVRISLIADCDRLGEALHRIKQAGI  391 (394)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHHHH
T ss_conf             9999999984999998873117899987999971889999999999999998


No 434
>PRK07337 aminotransferase; Validated
Probab=29.12  E-value=33  Score=14.91  Aligned_cols=42  Identities=14%  Similarity=0.259  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHCCEEEEE----CC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             999999999739879997----17--98228999858-9899999999837
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK----HR--NNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~----~~--~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      .++...|-+.-|  |-+.    +.  .+.|-+.|.|. +.++|+.=+++|+
T Consensus       336 ~~~~~~ll~e~g--V~v~PG~~Fg~~~~~~~iRl~~a~~~~~l~eal~RL~  384 (388)
T PRK07337        336 AALTFAMLHDAG--VVLVPGMDFGPHAPRDYIRLSYATSYSRLEEAVARLG  384 (388)
T ss_pred             HHHHHHHHHHCC--EEEECCHHHCCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf             999999998599--9997762218999999799997199999999999999


No 435
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=29.06  E-value=41  Score=14.29  Aligned_cols=18  Identities=39%  Similarity=0.626  Sum_probs=8.8

Q ss_pred             CCHHHHHHHHHHHHHCCC
Q ss_conf             898899999998863100
Q gi|254780805|r   58 FESEGLEDLCQSIKSHGI   75 (300)
Q Consensus        58 ~~~~~l~eLa~SI~~~G~   75 (300)
                      ++++.|+++...+...|+
T Consensus        40 ~~~eqId~ii~~L~~~GI   57 (620)
T PRK05658         40 VDSEQIEDIISMINDMGI   57 (620)
T ss_pred             CCHHHHHHHHHHHHHCCC
T ss_conf             998999999999997797


No 436
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=28.98  E-value=41  Score=14.29  Aligned_cols=21  Identities=19%  Similarity=0.366  Sum_probs=9.8

Q ss_pred             HHCCCCCCCCCCCCCHHHHHH
Q ss_conf             982357899987689889999
Q gi|254780805|r   45 HSIVPNPHNPRNYFESEGLED   65 (300)
Q Consensus        45 ~~i~~~p~~pR~~~~~~~l~e   65 (300)
                      +.|.-..+.|-..+++..|.+
T Consensus        27 ~~Il~g~l~pG~~l~e~~La~   47 (230)
T COG1802          27 EAILSGELAPGERLSEEELAE   47 (230)
T ss_pred             HHHHHCCCCCCCEECHHHHHH
T ss_conf             999829989829817999999


No 437
>PRK01533 histidinol-phosphate aminotransferase; Validated
Probab=28.87  E-value=39  Score=14.43  Aligned_cols=41  Identities=20%  Similarity=0.149  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHCCEEEEECCCCCEEEEEEECCHHHHHHHHHHHCC
Q ss_conf             9999999999739879997179822899985898999999998375
Q gi|254780805|r  250 LTDLEKKISSKVGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGE  295 (300)
Q Consensus       250 i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL~~  295 (300)
                      -..+.+.|.+. |  +-|..-  .+-|.|.-.+.+|-+++++.|++
T Consensus       311 ~~~l~~~L~~~-G--IlVR~~--~~~iRIsvgt~eeN~~ll~aLke  351 (366)
T PRK01533        311 GGEIYEACAHA-G--FIIRPF--PNGVRITVGTREQNEGVISVLQQ  351 (366)
T ss_pred             HHHHHHHHHHC-C--EEEEEC--CCCEEEECCCHHHHHHHHHHHHH
T ss_conf             99999999968-9--899899--59878827999999999999999


No 438
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=28.72  E-value=42  Score=14.26  Aligned_cols=67  Identities=18%  Similarity=0.239  Sum_probs=44.0

Q ss_pred             CEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf             04620565445333575677777642100135433346411234556665431022104899999998521011104679
Q gi|254780805|r   79 LIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDI  158 (300)
Q Consensus        79 i~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~l  158 (300)
                      +.++|.+.| +-|++|..=..-+..+|++.+-+-+.- +                 =||+--+.|+-.-+.. ..|.+++
T Consensus        89 V~l~Pap~G-~Gl~a~~~~r~vl~laGI~d~~~K~~G-s-----------------~n~~NvvkA~~~aL~~-~~t~~~i  148 (156)
T PRK00550         89 VLLKPASEG-TGVIAGGAMRAVLELAGVHDVLAKSLG-S-----------------NNPINVVRATFDALKK-LRTPEEV  148 (156)
T ss_pred             EEEEECCCC-CCEECCHHHHHHHHHCCCCCEEEECCC-C-----------------CCHHHHHHHHHHHHHH-CCCHHHH
T ss_conf             999967999-557838799999997591605767168-9-----------------9788999999999981-8999999


Q ss_pred             HHHHHHH
Q ss_conf             9997433
Q gi|254780805|r  159 GSIVGKS  165 (300)
Q Consensus       159 A~~~G~s  165 (300)
                      |+.-|++
T Consensus       149 A~~rG~~  155 (156)
T PRK00550        149 AAKRGKS  155 (156)
T ss_pred             HHHHCCC
T ss_conf             9984898


No 439
>PRK06225 aspartate aminotransferase; Provisional
Probab=28.72  E-value=42  Score=14.26  Aligned_cols=44  Identities=11%  Similarity=0.235  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHCCEEEEEC-----C-CCCEEEEEEECC-HHHHHHHHHHHCC
Q ss_conf             899999999997398799971-----7-982289998589-8999999998375
Q gi|254780805|r  249 YLTDLEKKISSKVGLNISIKH-----R-NNKGQFCIKYET-NEQLKIICSLLGE  295 (300)
Q Consensus       249 ~i~~le~~L~~~lGtkV~I~~-----~-~~kGkI~I~f~s-~eeLe~Il~kL~~  295 (300)
                      +-..+.+.|.+. |  |-|..     . .+.|-|.|.|.. .|+++..++.|++
T Consensus       317 ~~~~~~~~l~e~-g--V~v~pG~~~~~~~g~~~iRis~~~~~e~l~~a~~rl~~  367 (375)
T PRK06225        317 RPEDLVEYLLER-K--IFVRQGTYTSKRFGDRFIRVSFSIPREWVERFCEEFPD  367 (375)
T ss_pred             CHHHHHHHHHHC-C--EEEECCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             999999999978-9--09968986788789992999970489999999999999


No 440
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.68  E-value=42  Score=14.25  Aligned_cols=27  Identities=11%  Similarity=0.016  Sum_probs=13.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             104679999743378778656565435
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKLP  179 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~  179 (300)
                      ||-.++|+.+|.|..+|.-|=+..=|+
T Consensus         1 ytIge~A~~~gvs~~tlRyYe~~GLl~   27 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYEDKGLLS   27 (118)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCC
T ss_conf             958899999897999999999869987


No 441
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=28.59  E-value=29  Score=15.28  Aligned_cols=29  Identities=24%  Similarity=0.372  Sum_probs=21.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10467999974337877865656543589
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKLPSS  181 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~  181 (300)
                      ++..|+|+.+|.|..+|..|-+.-=|||.
T Consensus         1 Yri~ElA~~~Gvs~~tiR~YE~~GLlpp~   29 (99)
T cd04772           1 YRTVDLARAIGLSPQTVRNYESLGLIPPA   29 (99)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf             97899999989699999999996999997


No 442
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=28.58  E-value=42  Score=14.24  Aligned_cols=29  Identities=21%  Similarity=0.256  Sum_probs=22.0

Q ss_pred             HHHHHC---CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             852101---11046799997433787786565
Q gi|254780805|r  146 QLISEY---GYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       146 ~l~~~~---~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      +++.+.   +.|-.+||++.|.|++++.++..
T Consensus         7 ~l~~~~G~~~~s~~~Ia~~agvs~~~iy~~F~   38 (47)
T pfam00440         7 ELFAEKGYDATTVREIAKEAGVSKGALYRHFP   38 (47)
T ss_pred             HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf             99998691507799999997969889998876


No 443
>PRK06056 consensus
Probab=28.15  E-value=43  Score=14.19  Aligned_cols=43  Identities=16%  Similarity=0.247  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             999999999739879997-17--98228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++...|-+.-|  |-+- ..  +..|-+.|.|. +.|+++.=+++|.+
T Consensus       350 ~~~~~~ll~e~g--V~v~PG~~Fg~~g~~Risfa~~~e~l~eal~RL~~  396 (402)
T PRK06056        350 AELAALILEEAE--VAVVPGEAFGTPGYLRLSYALGDDDLVEGVRRLQE  396 (402)
T ss_pred             HHHHHHHHHHCC--EEEECCCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             999999997098--99974844489983999970899999999999999


No 444
>KOG0994 consensus
Probab=28.07  E-value=43  Score=14.19  Aligned_cols=12  Identities=8%  Similarity=0.628  Sum_probs=6.0

Q ss_pred             CHHHHHHHHHHH
Q ss_conf             988999999988
Q gi|254780805|r   59 ESEGLEDLCQSI   70 (300)
Q Consensus        59 ~~~~l~eLa~SI   70 (300)
                      |+++|+++|.-.
T Consensus      1490 dp~si~~vA~~v 1501 (1758)
T KOG0994        1490 DPDSIEEVAEEV 1501 (1758)
T ss_pred             CHHHHHHHHHHH
T ss_conf             979999999999


No 445
>PRK07590 L,L-diaminopimelate aminotransferase; Validated
Probab=27.97  E-value=43  Score=14.17  Aligned_cols=45  Identities=11%  Similarity=0.033  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             99999999973987999---71798228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++..+|-+.-|.-|.=   -...+.|-+.|.|. +.++|+.=+++|++
T Consensus       359 ~ef~~~Ll~e~~Vav~PG~~FG~~g~g~vRls~a~~~e~l~ea~~Ri~~  407 (409)
T PRK07590        359 WDFFDKLLQEANVVGTPGSGFGPAGEGYFRLSAFGSRENVLEAMERIKK  407 (409)
T ss_pred             HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             9999999986999996864658999896999972899999999999998


No 446
>pfam01316 Arg_repressor Arginine repressor, DNA binding domain.
Probab=27.77  E-value=43  Score=14.15  Aligned_cols=35  Identities=20%  Similarity=0.270  Sum_probs=18.5

Q ss_pred             HHHHHHHHCC-CCHHHHHHHHHH-----HHHHHHHHHHHHH
Q ss_conf             9998521011-104679999743-----3787786565654
Q gi|254780805|r  143 GYEQLISEYG-YTQNDIGSIVGK-----SRSHVANILRILK  177 (300)
Q Consensus       143 ~~~~l~~~~~-~t~~~lA~~~G~-----s~s~V~~~LrLl~  177 (300)
                      .+++++.... -||++|...|..     +++|||+-|+=+.
T Consensus         9 ~I~~li~~~~i~tQ~eL~~~L~~~G~~vTQATlSRDl~eLg   49 (70)
T pfam01316         9 LIKEIITEEKISTQEELVALLKAEGINVTQATVSRDLKELG   49 (70)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHCCCCEEEHHHHHHHHHHC
T ss_conf             99999970897899999999997698564178887799939


No 447
>TIGR01298 RNaseT ribonuclease T; InterPro: IPR005987    Ribonuclease T (3.1.13 from EC) is an enzyme found so far only in gamma-subdivision proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a UV-repair defect caused by deletion of three other single-stranded DNA exonucleases.; GO: 0004540 ribonuclease activity, 0006396 RNA processing.
Probab=27.48  E-value=39  Score=14.42  Aligned_cols=10  Identities=20%  Similarity=0.687  Sum_probs=3.6

Q ss_pred             HHHCCCCCHH
Q ss_conf             4310221048
Q gi|254780805|r  129 NVQRKDLNPL  138 (300)
Q Consensus       129 N~~R~dl~p~  138 (300)
                      ++.|...+|+
T Consensus       129 ~~KRnPFH~F  138 (201)
T TIGR01298       129 ALKRNPFHPF  138 (201)
T ss_pred             HCCCCCCCCC
T ss_conf             1157898765


No 448
>TIGR02079 THD1 threonine dehydratase; InterPro: IPR011820    This entry represents threonine dehydratase, the first step in the pathway converting threonine into isoleucine. At least two other clades of biosynthetic threonine dehydratases are described by IPR005787 from INTERPRO and IPR005789 from INTERPRO. The sequences described by this entry are exclusively found in species containing the rest of the isoleucine pathway and which are generally lacking in members of the other two clades of threonine dehydratases. The sequences associated with this entry are often cluster with other elements of the isoleucine pathway.; GO: 0004794 L-threonine ammonia-lyase activity, 0030170 pyridoxal phosphate binding, 0009097 isoleucine biosynthetic process.
Probab=27.30  E-value=44  Score=14.10  Aligned_cols=49  Identities=20%  Similarity=0.327  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHCCEEEE------E-CCCCCEEEE--EEECCHHHHHHHHHHHCCCCCCC
Q ss_conf             9999999973987999------7-179822899--98589899999999837564569
Q gi|254780805|r  252 DLEKKISSKVGLNISI------K-HRNNKGQFC--IKYETNEQLKIICSLLGENDFEY  300 (300)
Q Consensus       252 ~le~~L~~~lGtkV~I------~-~~~~kGkI~--I~f~s~eeLe~Il~kL~~~~~~~  300 (300)
                      .|.+=|.+.||-.=.|      + ++++.|.+.  |...+.+||+++++++.-.|-+|
T Consensus       344 ALreFln~vLGP~DDIT~FEY~KK~nRe~GpaliGiel~~~~D~~GLL~Rm~A~~i~Y  401 (415)
T TIGR02079       344 ALREFLNDVLGPNDDITKFEYTKKSNRETGPALIGIELSDKEDFEGLLERMAAADIHY  401 (415)
T ss_pred             HHHHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCE
T ss_conf             3688765406788752331000201478787799875036100677999998559941


No 449
>KOG2252 consensus
Probab=27.27  E-value=44  Score=14.09  Aligned_cols=62  Identities=15%  Similarity=0.223  Sum_probs=43.1

Q ss_pred             HHH-HCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf             543-1022104899999998521011104679999-74337877865656543589999876421016
Q gi|254780805|r  128 ENV-QRKDLNPLEEALGYEQLISEYGYTQNDIGSI-VGKSRSHVANILRILKLPSSVREMIRKEEISL  193 (300)
Q Consensus       128 EN~-~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~-~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~  193 (300)
                      ||+ +-+-|+-.|.|.-++.-+.+|++.|.-.|++ |++|+++++.+||=    |+=-..+..|.-++
T Consensus       318 ~~~~d~eeldTkeia~rI~~eLk~~sIpQaiFAervLcRSQGTLSDLLrn----PKPW~klKsGRetF  381 (558)
T KOG2252         318 EESGDDEELDTKEIAQRIKAELKRYSIPQAIFAERVLCRSQGTLSDLLRN----PKPWSKLKSGRETF  381 (558)
T ss_pred             HHCCCCCEECHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHC----CCCHHHHCCCCHHH
T ss_conf             11277521018999999999986457737888888861252229999638----99525440320999


No 450
>TIGR02092 glgD glucose-1-phosphate adenylyltransferase, GlgD subunit; InterPro: IPR011832    This family is GlgD, an apparent regulatory protein that appears in an alpha2/beta2 heterotetramer with GlgC (glucose-1-phosphate adenylyltransferase, IPR011831 from INTERPRO) in a subset of bacteria that use GlgC for glycogen biosynthesis.; GO: 0005978 glycogen biosynthetic process.
Probab=27.19  E-value=17  Score=16.77  Aligned_cols=36  Identities=14%  Similarity=0.094  Sum_probs=18.5

Q ss_pred             CCCCEEEEHHHCC----CCC--CCCCCCCCHHH-----HHHHHHHHH
Q ss_conf             5660240389823----578--99987689889-----999999886
Q gi|254780805|r   36 PESQDCISIHSIV----PNP--HNPRNYFESEG-----LEDLCQSIK   71 (300)
Q Consensus        36 ~~~~~~i~i~~i~----~~p--~~pR~~~~~~~-----l~eLa~SI~   71 (300)
                      -+.-.+++|+.+.    ..|  +|-+..+.++.     .+.+.+++.
T Consensus        68 Lg~G~eWdL~r~~~glF~~pP~~~~~~~~~~~~kaall~~~~~~~l~  114 (383)
T TIGR02092        68 LGSGREWDLNRKRDGLFLFPPKYNDRDDVSEGGKAALLKRYFSNNLE  114 (383)
T ss_pred             CCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             34868836110257527706876864323456337788999988767


No 451
>TIGR01478 STEVOR variant surface antigen, stevor family; InterPro: IPR006374   Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see .   This entry represents the stevor (short for "subtelomeric variable open reading frame") family of predicted variant surface antigens. This is the third largest variant surface antigen family in P. falciparum, with 33 genes identified in the genome of this parasite . The function of these proteins is not known, but they are expressed during several stages of the parasite life-cycle and may play a variety of roles in parasite survival and infection ..
Probab=26.97  E-value=22  Score=16.00  Aligned_cols=37  Identities=24%  Similarity=0.496  Sum_probs=19.8

Q ss_pred             HHCCCCCCCCCCCCCHHHHHHHHH-----HHHH-------CCCCCCCEEEC
Q ss_conf             982357899987689889999999-----8863-------10015504620
Q gi|254780805|r   45 HSIVPNPHNPRNYFESEGLEDLCQ-----SIKS-------HGIIQPLIVRA   83 (300)
Q Consensus        45 ~~i~~~p~~pR~~~~~~~l~eLa~-----SI~~-------~G~lqPi~Vr~   83 (300)
                      .+|.. |.|| +++++..|.|..|     -|+.       +-|||-+++..
T Consensus        51 Aeiq~-P~NP-HYhNDPELKeIIDKLNeEAIKKYq~THdPYEqL~elVeKn   99 (315)
T TIGR01478        51 AEIQR-PKNP-HYHNDPELKEIIDKLNEEAIKKYQKTHDPYEQLKELVEKN   99 (315)
T ss_pred             HHHCC-CCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
T ss_conf             75357-6322-9898734666862402677866530588157774455420


No 452
>PRK05764 aspartate aminotransferase; Provisional
Probab=26.83  E-value=45  Score=14.04  Aligned_cols=43  Identities=12%  Similarity=0.261  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             999999999739879997-17--98228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++...|-+..|  |.+. ..  +..|-+.|.|. +.++++.-+++|++
T Consensus       337 ~~~~~~ll~~~g--V~~~PG~~Fg~~g~~Rl~fa~~~e~l~ea~~RL~~  383 (389)
T PRK05764        337 EDFAEALLEEAG--VAVVPGIAFGAPGYVRLSYATSLEDIEEALERIER  383 (389)
T ss_pred             HHHHHHHHHHCC--EEEEECCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             999999998199--99980732489984999983889999999999999


No 453
>PRK08068 transaminase; Reviewed
Probab=26.71  E-value=45  Score=14.03  Aligned_cols=45  Identities=9%  Similarity=0.143  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEE-CCHHHHHHHHHHHCC
Q ss_conf             99999999973987999---7179822899985-898999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKY-ETNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f-~s~eeLe~Il~kL~~  295 (300)
                      .++...|-+.-|.-|.=   ....+.|-|.|.| .+.++++.=+++|++
T Consensus       337 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~vRl~fa~~~e~l~ea~~RL~~  385 (389)
T PRK08068        337 EQFADLLLEKAHVAVAPGNGFGEHGEGYVRVGLLIDEERLREAINRIAK  385 (389)
T ss_pred             HHHHHHHHHCCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             9999999970999998785437899696999983899999999999972


No 454
>TIGR01529 argR_whole arginine repressor; InterPro: IPR001669   The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia . The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 100f total cell protein .   Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR . This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine . The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography . The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription DNA-dependent.
Probab=26.52  E-value=45  Score=14.01  Aligned_cols=130  Identities=18%  Similarity=0.215  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHCC-CCHHHHHHHH-----H-HHHHHHHHHHHHHHHHHHHHHHHHHH-HCCHHHHHHHHH-------CCH-
Q ss_conf             999998521011-1046799997-----4-33787786565654358999987642-101677777640-------100-
Q gi|254780805|r  141 ALGYEQLISEYG-YTQNDIGSIV-----G-KSRSHVANILRILKLPSSVREMIRKE-EISLGHARTLVS-------TSD-  204 (300)
Q Consensus       141 A~~~~~l~~~~~-~t~~~lA~~~-----G-~s~s~V~~~LrLl~L~~~i~~~l~~~-~is~ghar~Ll~-------~~~-  204 (300)
                      -..+++++.+-+ -||+||...|     - ..+++|||-|+=+.|-   +-.-.+| .    +..+|..       ..+ 
T Consensus         4 ~~~Ik~Ii~~e~~~tQ~El~~~L~~~G~~nvTQaTvSRDL~el~lv---K~~~~~gG~----~~Y~L~~~~sPvrg~~~~   76 (155)
T TIGR01529         4 QEAIKEIITEEKISTQEELVALLKKEGVKNVTQATVSRDLRELGLV---KVRDEKGGS----YVYSLPAEGSPVRGVSDP   76 (155)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHCCCCEECCCCHHHHHHHHCCE---ECCCCCCCE----EEEEECCCCCCCCCCCCC
T ss_conf             9999999874376798899999986597511234067878752204---223699744----899860687853899875


Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHH--HHH--HHHHCCEEEEECCCCCEEEEEEE
Q ss_conf             46899997422247789999997641022222234566556897899999--999--99739879997179822899985
Q gi|254780805|r  205 PLSLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLE--KKI--SSKVGLNISIKHRNNKGQFCIKY  280 (300)
Q Consensus       205 ~~~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le--~~L--~~~lGtkV~I~~~~~kGkI~I~f  280 (300)
                      ..++.+..-.-=+||+..+.++            +....+..-..+.++=  ...  .+.+||   |   .+--.|-+-|
T Consensus        77 ~~~l~r~l~~~v~~id~~~~l~------------VirT~pG~A~~iA~llD~~~~~r~~IlGT---i---AGdDTilV~~  138 (155)
T TIGR01529        77 TEKLKRLLKSFVLSIDRAGNLI------------VIRTKPGEASVIANLLDRLKKARDEILGT---I---AGDDTILVIC  138 (155)
T ss_pred             CHHHHHHHHHHHEEEEECCCEE------------EEECCCCCHHHHHHHHHCCCCCCCCCEEE---E---ECCCEEEEEE
T ss_conf             1125787897500001046178------------88559984756887540013467330145---4---2567178874


Q ss_pred             CCHHHHHHHHHHHCC
Q ss_conf             898999999998375
Q gi|254780805|r  281 ETNEQLKIICSLLGE  295 (300)
Q Consensus       281 ~s~eeLe~Il~kL~~  295 (300)
                      -+.+..+.|.+.|.+
T Consensus       139 r~~~~~~~l~~~l~~  153 (155)
T TIGR01529       139 RDEETAELLEEELLE  153 (155)
T ss_pred             CCCHHHHHHHHHHHH
T ss_conf             580307999999985


No 455
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=26.50  E-value=45  Score=14.01  Aligned_cols=23  Identities=13%  Similarity=0.164  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHCCCCCCCEEECCCCCCC
Q ss_conf             999999886310015504620565445
Q gi|254780805|r   63 LEDLCQSIKSHGIIQPLIVRAIDNGLY   89 (300)
Q Consensus        63 l~eLa~SI~~~G~lqPi~Vr~~~~g~y   89 (300)
                      +.|--..+...|++    ....+.|.|
T Consensus        48 vReal~~L~~~G~v----~~~~G~gt~   70 (239)
T PRK04984         48 LREVLQRLARDGWL----TIQHGKPTK   70 (239)
T ss_pred             HHHHHHHHHHCCCE----EEECCCCCE
T ss_conf             99999999988988----885599975


No 456
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=26.49  E-value=39  Score=14.46  Aligned_cols=38  Identities=21%  Similarity=0.300  Sum_probs=28.4

Q ss_pred             CCCCHHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHHHH
Q ss_conf             221048999999985210111------04679999743378778
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGY------TQNDIGSIVGKSRSHVA  170 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~------t~~~lA~~~G~s~s~V~  170 (300)
                      .|.+|+|.-..+-.|.++.+.      |.++|++..|.++++.+
T Consensus        55 ~Dv~P~eiv~hlP~LCeek~IPy~~V~sk~~LG~A~G~~r~t~a   98 (123)
T PRK04175         55 EDVDPEEIVAHLPLLCEEKKIPYVYVPSKEELGKAAGLEVGAAA   98 (123)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEECCHHHHHHHHCCCCCEEE
T ss_conf             89990999998899998549998997899999999689977799


No 457
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=26.35  E-value=46  Score=13.99  Aligned_cols=12  Identities=17%  Similarity=0.038  Sum_probs=4.9

Q ss_pred             HHHHHHHHHCCC
Q ss_conf             999999983756
Q gi|254780805|r  285 QLKIICSLLGEN  296 (300)
Q Consensus       285 eLe~Il~kL~~~  296 (300)
                      -+..+++.|...
T Consensus       278 ~~~~Fidfl~~a  289 (291)
T PRK10837        278 ALQRFLSYCQPA  289 (291)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999999998620


No 458
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.34  E-value=46  Score=13.99  Aligned_cols=69  Identities=19%  Similarity=0.238  Sum_probs=36.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHH-CCCCHHHHHHHHHHH
Q ss_conf             0467999974337877865656543589999876421016777776401004689999742-224778999999764
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVS-KKMSVRDTEELVQEQ  229 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~-~~LSVRe~E~lVk~~  229 (300)
                      +-.|+|++.|.|..+|.=|-+.-=|||.-...=.-...+..|.+       ...+.+..-. -++|..++.++....
T Consensus         2 ~IgelA~~tGvs~~TIRyYe~~GLL~p~~R~~~g~r~Y~~~~v~-------rL~~Ir~l~~~lG~sL~eIr~lL~~~   71 (95)
T cd04780           2 RMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVE-------RLRLIRALQQEGGLPISQIKEVLDAI   71 (95)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHH-------HHHHHHHHHHHCCCCHHHHHHHHHCC
T ss_conf             78999999897899999999978999877699987154999999-------99999999993699999999998436


No 459
>PRK05949 RNA polymerase sigma factor; Validated
Probab=26.25  E-value=46  Score=13.98  Aligned_cols=25  Identities=16%  Similarity=0.247  Sum_probs=19.6

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565654
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      -|.+++|+.+|.+...|..++.+..
T Consensus       195 pt~~EiA~~l~i~~~~v~~~l~~~~  219 (327)
T PRK05949        195 ATPAEIAKALELEPSQIREYLSMAR  219 (327)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             9889999894999999999998418


No 460
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.23  E-value=46  Score=13.98  Aligned_cols=39  Identities=15%  Similarity=0.297  Sum_probs=25.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             1104679999743378778656565435899998764210
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI  191 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i  191 (300)
                      .+|.++||+.+|.|+++.++..+= ..--.+.+.+..-.|
T Consensus        25 ~lsl~~lA~~~~~S~~~l~r~Fk~-~~G~s~~~Yi~~~Rl   63 (127)
T PRK11511         25 PLSLEKVSERSGYSKWHLQRMFKK-ETGHSLGQYIRSRKM   63 (127)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH-HHCCCHHHHHHHHHH
T ss_conf             999999999989599999999999-989199999999999


No 461
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461    Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=25.99  E-value=46  Score=13.95  Aligned_cols=94  Identities=19%  Similarity=0.241  Sum_probs=51.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHH-------HHHHHHHHCCCCHHHHHH
Q ss_conf             1104679999743378778656565435899998764210167777764010046-------899997422247789999
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPL-------SLAQVIVSKKMSVRDTEE  224 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~-------~la~~Ii~~~LSVRe~E~  224 (300)
                      .||.+.|-..+-+|.-||+-+    -||++..+++++=-     |..=+....+.       +=.+.-.--..+|+++|+
T Consensus       396 ~Y~~eal~~Av~LS~ryI~DR----fLPDKAIDviDEaG-----A~~~l~~~~~~~~~eadekGleetalPev~~~diE~  466 (774)
T TIGR02639       396 KYSDEALEAAVELSARYINDR----FLPDKAIDVIDEAG-----AAFRLRAKAKKKANEADEKGLEETALPEVNVKDIEE  466 (774)
T ss_pred             ECCHHHHHHHHHHHHHHCCCC----CCCCHHHHHHHHHH-----HHHHHHHHCCCCCCCHHHCCCCCCCCCCCCHHHHHH
T ss_conf             138699999999988860257----89854322889999-----999971202776432011253000478785444999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCC-CHHHHHHHHHHHH
Q ss_conf             9976410222222345665568-9789999999999
Q gi|254780805|r  225 LVQEQDNKKEKRKKIFEGSREK-EKYLTDLEKKISS  259 (300)
Q Consensus       225 lVk~~~~~~~~~kk~~~~~~~k-~~~i~~le~~L~~  259 (300)
                      .|.+...-+...-     +..- ...+++|+.+|+.
T Consensus       467 vvak~a~iP~~~~-----s~ddD~~~L~~L~~~L~~  497 (774)
T TIGR02639       467 VVAKMAKIPVKTV-----SSDDDREKLKNLEKELKA  497 (774)
T ss_pred             HHHHHHCCCCEEE-----CCCHHHHHHHHHHHHHHC
T ss_conf             9988718994154-----264479887204476301


No 462
>cd01821 Rhamnogalacturan_acetylesterase_like Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are highly branched regions in pectic polysaccharides, consisting of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide units, with many rhamnose residues substituted by neutral oligosaccharides such as arabinans, galactans and arabinogalactans. Extracellular enzymes participating in the degradation of plant cell wall polymers, such as Rhamnogalacturonan acetylesterase, would typically be found in saprophytic and plant pathogenic fungi and bacteria.
Probab=25.99  E-value=38  Score=14.51  Aligned_cols=26  Identities=19%  Similarity=0.414  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHCCCCCCCEEECCCC
Q ss_conf             889999999886310015504620565
Q gi|254780805|r   60 SEGLEDLCQSIKSHGIIQPLIVRAIDN   86 (300)
Q Consensus        60 ~~~l~eLa~SI~~~G~lqPi~Vr~~~~   86 (300)
                      .+.|..+..-+++.| ..||+|.|.+.
T Consensus        93 ~~nL~~~i~~~r~~g-a~pIL~Tp~~R  118 (198)
T cd01821          93 KEYLRRYIAEARAKG-ATPILVTPVTR  118 (198)
T ss_pred             HHHHHHHHHHHHHCC-CEEEEECCCCC
T ss_conf             999999999999759-98999758877


No 463
>PRK06507 consensus
Probab=25.90  E-value=41  Score=14.27  Aligned_cols=43  Identities=14%  Similarity=0.194  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHCCEEEEECC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             9999999973987999717--98228999858-98999999998375
Q gi|254780805|r  252 DLEKKISSKVGLNISIKHR--NNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       252 ~le~~L~~~lGtkV~I~~~--~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      +....|-+.-|.-|. -..  +..|-|.|.|. +.++|+.-+++|.+
T Consensus       349 ~f~~~Ll~e~gV~v~-PG~~FG~~~~vRis~a~~~~~l~eal~Rl~~  394 (400)
T PRK06507        349 DFVMALLEEQHVATV-QGAAYGMSPYFRLSYATDMESLGEGCARIAQ  394 (400)
T ss_pred             HHHHHHHHHCCEEEE-CCCCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             999999985899997-7874489983999964999999999999999


No 464
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=25.58  E-value=31  Score=15.08  Aligned_cols=25  Identities=20%  Similarity=0.400  Sum_probs=19.9

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             01110467999974337877865656
Q gi|254780805|r  150 EYGYTQNDIGSIVGKSRSHVANILRI  175 (300)
Q Consensus       150 ~~~~t~~~lA~~~G~s~s~V~~~LrL  175 (300)
                      .|. +..+.|+.+|.++++|++++.-
T Consensus        16 ~f~-Si~~aak~l~~~~~~I~~~l~~   40 (53)
T smart00497       16 EFS-SIREAAKYLGISHSSISKYLNT   40 (53)
T ss_pred             HHH-HHHHHHHHHCCCCCCHHHHHCC
T ss_conf             778-7999999858883238887067


No 465
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=25.54  E-value=47  Score=13.89  Aligned_cols=48  Identities=23%  Similarity=0.262  Sum_probs=30.2

Q ss_pred             HHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             777764210013543334641123455666543102210489999999
Q gi|254780805|r   98 FRAAKMASLSEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYE  145 (300)
Q Consensus        98 ~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~  145 (300)
                      ..|+|.+.-..+.++|+=++|.-....-|++-.---.|+|+=.-.-|.
T Consensus        90 i~aaKnl~e~ki~a~iR~Yddaisit~DLv~g~ld~~lSPiiTq~ifs  137 (321)
T COG3888          90 ISAAKNLEERKISATIRFYDDAISITRDLVEGKLDFGLSPIITQIIFS  137 (321)
T ss_pred             HHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             589876644364089999635778999887644462012789999999


No 466
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=25.23  E-value=48  Score=13.86  Aligned_cols=58  Identities=14%  Similarity=0.178  Sum_probs=35.3

Q ss_pred             CCCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHH
Q ss_conf             022104899999998521---011104679999743378778656565435--8999987642
Q gi|254780805|r  132 RKDLNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRILKLP--SSVREMIRKE  189 (300)
Q Consensus       132 R~dl~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~--~~i~~~l~~~  189 (300)
                      ..+|+|.|+-.+-.-+-.   -..+|-.+||+..|.|.++|.|.-+-+-..  ++.+..+.+.
T Consensus        11 ~~~Lt~~Ek~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~   73 (282)
T PRK11557         11 YPGLAQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALSEA   73 (282)
T ss_pred             HHHCCHHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             854499999999999809899976569999989699988999999993899899999999999


No 467
>pfam10743 Phage_Cox Regulatory phage protein cox. This family of phage Cox proteins is expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes.
Probab=25.23  E-value=46  Score=13.97  Aligned_cols=28  Identities=21%  Similarity=0.487  Sum_probs=21.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1104679999743378778656565435
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANILRILKLP  179 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~  179 (300)
                      ..+.+.-|+.+|++.+.|+.+..=.+||
T Consensus        12 av~~ekFA~~IGKt~~AVr~Mi~~gKLP   39 (87)
T pfam10743        12 ALSVEEFALLIGKTPTAVREMVKAGKLP   39 (87)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHCCCCC
T ss_conf             0169999999689899999999849997


No 468
>PRK03341 arginine repressor; Provisional
Probab=25.19  E-value=48  Score=13.85  Aligned_cols=131  Identities=11%  Similarity=0.106  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHCC-CCHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCH---------
Q ss_conf             9999998521011-104679999743-----3787786565654358999987642101677777640100---------
Q gi|254780805|r  140 EALGYEQLISEYG-YTQNDIGSIVGK-----SRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSD---------  204 (300)
Q Consensus       140 ~A~~~~~l~~~~~-~t~~~lA~~~G~-----s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~---------  204 (300)
                      +=..+++|+.+.. .||++|.+.|..     +++|||+-|+=+.+-.   -.-.+|..    ....+..+.         
T Consensus        16 Rq~~I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATiSRDikEL~lvK---v~~~~G~~----~yy~lp~~~~~~~~~~~~   88 (168)
T PRK03341         16 RQARIVAILSSQSVRSQSELAALLADEGIDVTQATLSRDLEELGAVK---LRGADGGL----GVYVVPEDGSPRRGVAGG   88 (168)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHHCCEE---EECCCCCE----EEEEECCCCCCCCCCCCH
T ss_conf             99999999960897889999999997698654278775299838767---32589988----999945766644455557


Q ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHH--HHHHHHHCCEEEEECCCCCEEEEEEECC
Q ss_conf             46899997422247789999997641022222234566556897899999--9999973987999717982289998589
Q gi|254780805|r  205 PLSLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLE--KKISSKVGLNISIKHRNNKGQFCIKYET  282 (300)
Q Consensus       205 ~~~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le--~~L~~~lGtkV~I~~~~~kGkI~I~f~s  282 (300)
                      ..++...+-..=+||...+.++=            .+..+..-..+..+=  ..+.+.+||   |   .+-..|-|-+.+
T Consensus        89 ~~~l~~~~~~~v~~v~~~~nlvV------------ikT~pG~A~~va~~iD~~~~~eI~GT---I---AGdDTIlVi~~~  150 (168)
T PRK03341         89 TERLRRLLGELLVSTDASGNLAV------------LRTPPGAAQYLASAIDRAALPYVVGT---I---AGDDTVLVVARE  150 (168)
T ss_pred             HHHHHHHHHHHEEEEEECCCEEE------------EEECCCCHHHHHHHHHHCCCCCCEEE---E---ECCCEEEEEECC
T ss_conf             89999999987567751076899------------98189948999999984799873798---6---049989999788


Q ss_pred             HHHHHHHHHHHCC
Q ss_conf             8999999998375
Q gi|254780805|r  283 NEQLKIICSLLGE  295 (300)
Q Consensus       283 ~eeLe~Il~kL~~  295 (300)
                      .++-+.+.++|.+
T Consensus       151 ~~~a~~l~~~L~~  163 (168)
T PRK03341        151 PMTGAELAARLEN  163 (168)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8899999999999


No 469
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=25.15  E-value=48  Score=13.85  Aligned_cols=34  Identities=24%  Similarity=0.323  Sum_probs=24.8

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             21011104679999743378778656565435899998
Q gi|254780805|r  148 ISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREM  185 (300)
Q Consensus       148 ~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~  185 (300)
                      +.-|| +...+|+.+|.|.+.|++-   -+..|+.+.+
T Consensus         7 i~~FG-sk~klA~aLgIs~~aVsqW---ge~IPE~rAy   40 (75)
T PRK09744          7 IAFFG-SKTKLANAAGVRLASVAAW---GELVPEGRAM   40 (75)
T ss_pred             HHHHC-CHHHHHHHHCCCHHHHHHH---HHHCCHHHHH
T ss_conf             99961-2999999949987999887---4016068899


No 470
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=25.04  E-value=44  Score=14.10  Aligned_cols=33  Identities=21%  Similarity=0.434  Sum_probs=24.8

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             998521011104679999743378778656565
Q gi|254780805|r  144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRIL  176 (300)
Q Consensus       144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl  176 (300)
                      +..|+...-.|-++||+.+|.+...|++.|.-|
T Consensus         7 id~L~~~~~v~dedLa~~l~~~~n~vRkiL~~L   39 (147)
T smart00531        7 LDALMRNGCVTEEDLAELLGIKQKQLRKILYLL   39 (147)
T ss_pred             HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             298886597079999999799999999999999


No 471
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=24.99  E-value=48  Score=13.83  Aligned_cols=11  Identities=27%  Similarity=0.727  Sum_probs=3.9

Q ss_pred             CCCHHHHHHHH
Q ss_conf             11046799997
Q gi|254780805|r  152 GYTQNDIGSIV  162 (300)
Q Consensus       152 ~~t~~~lA~~~  162 (300)
                      |+|.++|.+.+
T Consensus        58 GfsL~eI~~ll   68 (140)
T PRK09514         58 GFTLEEIRELL   68 (140)
T ss_pred             CCCHHHHHHHH
T ss_conf             99999999998


No 472
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=24.94  E-value=49  Score=13.82  Aligned_cols=17  Identities=0%  Similarity=0.096  Sum_probs=9.6

Q ss_pred             HHHHHHHHHCCCCHHHH
Q ss_conf             68999974222477899
Q gi|254780805|r  206 LSLAQVIVSKKMSVRDT  222 (300)
Q Consensus       206 ~~la~~Ii~~~LSVRe~  222 (300)
                      .++.+.+...|+|.-++
T Consensus        59 ~~~~~~l~~~Gi~peeL   75 (134)
T PRK10328         59 NTWLELMKADGINPEEL   75 (134)
T ss_pred             HHHHHHHHHCCCCHHHH
T ss_conf             99999999869999999


No 473
>KOG3725 consensus
Probab=24.92  E-value=45  Score=14.02  Aligned_cols=84  Identities=25%  Similarity=0.317  Sum_probs=37.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH-HCCCCHHHHHHHH--
Q ss_conf             5445333575677777642100135433346411234556665431022104899999998521-0111046799997--
Q gi|254780805|r   86 NGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLIS-EYGYTQNDIGSIV--  162 (300)
Q Consensus        86 ~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~-~~~~t~~~lA~~~--  162 (300)
                      +|.|-.|.-||++.-.+.+.+..-...++.   ..+.+..-.-|-.-..-..+|.|+.--|... +|. .|.+|-+.+  
T Consensus       149 EGD~KTI~KERklLqnkRLDLDAcKsRLKK---AKaae~q~~rN~~~s~~~~ie~aEqelRvaQ~EFD-rQaEiTrLLLE  224 (375)
T KOG3725         149 EGDMKTIQKERKLLQNKRLDLDACKSRLKK---AKAAELQTVRNSKTSGGFTIEQAEQELRVAQAEFD-RQAEITRLLLE  224 (375)
T ss_pred             HCCHHHHHHHHHHHHHCCCCHHHHHHHHHH---HHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
T ss_conf             110788999999986145676889998877---65554414334324676417678888888887775-78899999997


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             433787786565
Q gi|254780805|r  163 GKSRSHVANILR  174 (300)
Q Consensus       163 G~s~s~V~~~Lr  174 (300)
                      |.|-.|+ |.||
T Consensus       225 GIsstH~-nhLr  235 (375)
T KOG3725         225 GISSTHN-NHLR  235 (375)
T ss_pred             HHHHHHH-HHHH
T ss_conf             6636536-6889


No 474
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=24.92  E-value=49  Score=13.82  Aligned_cols=21  Identities=24%  Similarity=0.403  Sum_probs=13.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |..|+|..++.++..+.+..+
T Consensus       184 tl~Eia~~~~i~~k~i~r~~~  204 (310)
T PRK00423        184 TLDEIAEVSRVSRKEIGRTYR  204 (310)
T ss_pred             CHHHHHHHHCCCHHHHHHHHH
T ss_conf             499999995988999999999


No 475
>pfam08564 CDC37_C Cdc37 C terminal domain. Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the C terminal domain whose function is unclear. It is found C terminal to the Hsp90 chaperone (Heat shocked protein 90) binding domain pfam08565 and the N terminal kinase binding domain of Cdc37 pfam03234.
Probab=24.90  E-value=49  Score=13.82  Aligned_cols=42  Identities=5%  Similarity=0.141  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHHHCCHHH-HHHHHHCCHHHHHHHHHHHCC
Q ss_conf             654358999987642101677-777640100468999974222
Q gi|254780805|r  175 ILKLPSSVREMIRKEEISLGH-ARTLVSTSDPLSLAQVIVSKK  216 (300)
Q Consensus       175 Ll~L~~~i~~~l~~~~is~gh-ar~Ll~~~~~~~la~~Ii~~~  216 (300)
                      +-.||+++|.++.++.|..=. +-+=+..++++.+.++++.-+
T Consensus        11 FeslP~emq~a~es~dld~ln~vl~~M~~eeAe~~~~~~~dsG   53 (87)
T pfam08564        11 FESLPPELQKAFETKDLDEVNKVLAKMPVEEAEYHMERLIDSG   53 (87)
T ss_pred             HHHCCHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf             9868999999998578999999998099999999999987258


No 476
>PRK08636 aspartate aminotransferase; Provisional
Probab=24.90  E-value=49  Score=13.82  Aligned_cols=45  Identities=7%  Similarity=0.086  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHCCEEE---EECCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf             9999999997398799---971798228999858-98999999998375
Q gi|254780805|r  251 TDLEKKISSKVGLNIS---IKHRNNKGQFCIKYE-TNEQLKIICSLLGE  295 (300)
Q Consensus       251 ~~le~~L~~~lGtkV~---I~~~~~kGkI~I~f~-s~eeLe~Il~kL~~  295 (300)
                      .++...|-+.-|.-|.   .-...+.|-+.|.|. +.++++.=+++|.+
T Consensus       348 ~ef~~~ll~~~gV~v~PG~~Fg~~g~~~vRisf~~~~e~l~ea~~Rl~~  396 (403)
T PRK08636        348 LEFSKQLLTEAKVAVSPGIGFGEYGDEYVRIALIENENRIRQAARNIKK  396 (403)
T ss_pred             HHHHHHHHHCCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             9999999974979998875328899987999971899999999999999


No 477
>PRK07778 consensus
Probab=24.88  E-value=49  Score=13.82  Aligned_cols=45  Identities=11%  Similarity=0.231  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHCCEEE--EECC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf             99999999997398799--9717--98228999858-9899999999837
Q gi|254780805|r  250 LTDLEKKISSKVGLNIS--IKHR--NNKGQFCIKYE-TNEQLKIICSLLG  294 (300)
Q Consensus       250 i~~le~~L~~~lGtkV~--I~~~--~~kGkI~I~f~-s~eeLe~Il~kL~  294 (300)
                      -.++...|-+.-|.-|.  ..+.  .+.|-|.|.|. +.++|+.=+++|.
T Consensus       332 ~~~f~~~Ll~~~gV~v~PG~~Fg~~~g~~~vRlsf~~~~~~l~eal~RL~  381 (386)
T PRK07778        332 SLAFCSKLLADTGVAIAPGIDFDTVRGNSFVRLSFAGPTADIEEALRRIG  381 (386)
T ss_pred             HHHHHHHHHHHCCEEEECCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf             99999999983999997585668899999699998398999999999999


No 478
>PRK06959 putative threonine-phosphate decarboxylase; Provisional
Probab=24.78  E-value=49  Score=13.81  Aligned_cols=46  Identities=11%  Similarity=0.123  Sum_probs=27.9

Q ss_pred             CHHHHHHHHHHHHHHCCEEEEECCCCCEEEEEEE-CCHHHHHHHHHHHCC
Q ss_conf             9789999999999739879997179822899985-898999999998375
Q gi|254780805|r  247 EKYLTDLEKKISSKVGLNISIKHRNNKGQFCIKY-ETNEQLKIICSLLGE  295 (300)
Q Consensus       247 ~~~i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f-~s~eeLe~Il~kL~~  295 (300)
                      ..+-..+.+.|.++ |.-|-  .-...+.+.|.- .+.+|.+|+++-|.+
T Consensus       283 ~~~a~~~~~~L~~~-GIlVR--~f~~p~~LRi~vp~~e~e~~RL~~AL~e  329 (339)
T PRK06959        283 DPRAAALHAALAAR-GIWTR--YFAAPPSVRIGLPADEAEWQRLEDALAE  329 (339)
T ss_pred             CCCHHHHHHHHHHC-CEEEE--ECCCCCCEEEECCCCHHHHHHHHHHHHH
T ss_conf             88999999999849-92995--8899998898678999999999999999


No 479
>pfam11353 DUF3153 Protein of unknown function (DUF3153). This family of proteins with unknown function appear to be restricted to Cyanobacteria. Some members are annotated as membrane proteins however this cannot be confirmed.
Probab=24.75  E-value=49  Score=13.80  Aligned_cols=46  Identities=9%  Similarity=0.261  Sum_probs=24.6

Q ss_pred             CHHHHHHHHHHHHHHCCEEEEECCCCCEEEEEEECCHHHHHHHHHHH
Q ss_conf             97899999999997398799971798228999858989999999983
Q gi|254780805|r  247 EKYLTDLEKKISSKVGLNISIKHRNNKGQFCIKYETNEQLKIICSLL  293 (300)
Q Consensus       247 ~~~i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL  293 (300)
                      -|+...+|+++++..| +++|....+.-.+++.|.+.+|++..++..
T Consensus        43 ~pWq~~fe~~~k~l~~-~~~~~~~~~~~~l~~p~ln~~dl~~~l~~~   88 (210)
T pfam11353        43 LPWQEQFEQRLKDLGP-DVEIRSSEGEQRLTIPFLNSQELAELLNRF   88 (210)
T ss_pred             CCHHHHHHHHHHHHCC-CCEEECCCCEEEEECCCCCHHHHHHHHHHH
T ss_conf             7439999999987489-752753887389976889999999999999


No 480
>pfam00376 MerR MerR family regulatory protein.
Probab=24.67  E-value=36  Score=14.66  Aligned_cols=27  Identities=22%  Similarity=0.325  Sum_probs=20.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565654358
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILRILKLPS  180 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~LrLl~L~~  180 (300)
                      |-.++|+.+|.|..+|..+-+.-.+|+
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~~Gli~~   27 (38)
T pfam00376         1 TIGEVAKLLGVSPRTLRYYEKIGLLPP   27 (38)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             989999998879999999998689899


No 481
>PRK05957 aspartate aminotransferase; Provisional
Probab=24.54  E-value=49  Score=13.78  Aligned_cols=45  Identities=16%  Similarity=0.037  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHCCEEE--EE-CCCCCEEEEEEE-C-CHHHHHHHHHHHC
Q ss_conf             99999999997398799--97-179822899985-8-9899999999837
Q gi|254780805|r  250 LTDLEKKISSKVGLNIS--IK-HRNNKGQFCIKY-E-TNEQLKIICSLLG  294 (300)
Q Consensus       250 i~~le~~L~~~lGtkV~--I~-~~~~kGkI~I~f-~-s~eeLe~Il~kL~  294 (300)
                      -.++..+|-+.-|.-|.  .. ...+.|-+.|.| . +.|+++.=+++|.
T Consensus       331 ~~~~~~~ll~e~gV~v~PG~~Fg~~~~~~~Rlsf~~~~~e~l~eg~~RL~  380 (389)
T PRK05957        331 DFELVKQLIRDYRVAVIPGSTFGMKNGCYLRIAYGALQKATAKEGIERLV  380 (389)
T ss_pred             HHHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCCHHHHHHHHHHHH
T ss_conf             99999999997999997873108899998999854299999999999999


No 482
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.50  E-value=49  Score=13.77  Aligned_cols=28  Identities=21%  Similarity=0.260  Sum_probs=18.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565654358
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKLPS  180 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~  180 (300)
                      +|-.++|+.+|.|..+|.-|=++.=++|
T Consensus         1 ytIgelA~~~gvs~~tlRyYe~~GLl~~   28 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEKEGLLPP   28 (113)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf             9788999998959999999998389799


No 483
>TIGR01515 branching_enzym 1,4-alpha-glucan branching enzyme; InterPro: IPR006407   This entry represents the core region of the glycogen branching enzymes, which are responsible for the transfer of chains of approximately seven alpha(1,4)-linked glucosyl residues to other similar chains (in new alpha-(1,6) linkages) in the biosynthesis of glycogen . The branching enzyme is responsible for the degree of alpha(1,6) branch linkages found in polysaccharides .; GO: 0003844 14-alpha-glucan branching enzyme activity, 0005978 glycogen biosynthetic process.
Probab=24.49  E-value=11  Score=18.05  Aligned_cols=22  Identities=41%  Similarity=0.605  Sum_probs=9.4

Q ss_pred             CCCCCC--CHHHHHHHHHHHCCCC
Q ss_conf             453335--7567777764210013
Q gi|254780805|r   88 LYKIIA--GERRFRAAKMASLSEV  109 (300)
Q Consensus        88 ~y~ii~--G~rR~rAa~~~g~~~i  109 (300)
                      +|||+.  |++|++|=-.|-..+|
T Consensus        81 KYEi~~~~G~~~lkaDPyA~y~ev  104 (608)
T TIGR01515        81 KYEIVDANGEIRLKADPYAFYAEV  104 (608)
T ss_pred             EEEEECCCCCEEECCCCCCCCCCC
T ss_conf             046676898756436753012468


No 484
>PRK05201 hslU ATP-dependent protease ATP-binding subunit; Provisional
Probab=24.46  E-value=50  Score=13.77  Aligned_cols=156  Identities=19%  Similarity=0.200  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CHHHHHHHH--------
Q ss_conf             22104899999998521011104679999743378778656565435899998764210----167777764--------
Q gi|254780805|r  133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI----SLGHARTLV--------  200 (300)
Q Consensus       133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i----s~ghar~Ll--------  200 (300)
                      .+|+|-|.-    ..+++|-..|++.-+.+...   +.|+.|=..||+++++-+.-..|    ..|-+++++        
T Consensus         2 ~~ltP~eIv----~~LD~yIIGQ~~AKkavAVA---lrNr~RR~~l~~~lr~Ei~pkNILmIGPTGvGKTeIARrLAkl~   74 (442)
T PRK05201          2 SELTPREIV----SELDKYIIGQDDAKRAVAIA---LRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLA   74 (442)
T ss_pred             CCCCHHHHH----HHHCCCCCCCHHHHHHHHHH---HHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHH
T ss_conf             989989999----98536010827766787778---87778753166221233464316887888866789999999984


Q ss_pred             HCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEECCCCCEEEEEEE
Q ss_conf             01004689999742224778999999764102222223456655689789999999999739879997179822899985
Q gi|254780805|r  201 STSDPLSLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLEKKISSKVGLNISIKHRNNKGQFCIKY  280 (300)
Q Consensus       201 ~~~~~~~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f  280 (300)
                      +.|-...=|.+.-.-|.-=|++|.+|+.+......-.+......-+...-...++++-+.|--..    ++..+.-.-.-
T Consensus        75 ~aPFvkveATk~TEvGYvGrDVEsiIrdLv~~a~~~~k~~~~~~v~~~A~~~a~~ril~~L~~~~----~~~~~~~~~~~  150 (442)
T PRK05201         75 NAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKMVREEKREKVREKAEEAAEERILDALLPPA----KNNWGEEEEEE  150 (442)
T ss_pred             CCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCCCCCCCCCC
T ss_conf             89858752131000343564378899999999999999999999999999999999999855865----55555545420


Q ss_pred             CCHHHHHHHHHHHCCCCCC
Q ss_conf             8989999999983756456
Q gi|254780805|r  281 ETNEQLKIICSLLGENDFE  299 (300)
Q Consensus       281 ~s~eeLe~Il~kL~~~~~~  299 (300)
                      .+....+.+.++|.++..|
T Consensus       151 ~~~~tre~~r~~Lr~G~Ld  169 (442)
T PRK05201        151 ESSATRQKFRKKLREGELD  169 (442)
T ss_pred             HHHHHHHHHHHHHHCCCCC
T ss_conf             2367899999998658866


No 485
>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein; InterPro: IPR005670   This is a family of phosphate transport system permease proteins.; GO: 0005315 inorganic phosphate transmembrane transporter activity, 0015114 phosphate transmembrane transporter activity, 0006817 phosphate transport, 0016020 membrane.
Probab=24.43  E-value=41  Score=14.32  Aligned_cols=64  Identities=27%  Similarity=0.342  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH--HCCHHH------HHHHHHCCHHHHHHH-HHHHCCCCHHHHHHHHHHHHCC
Q ss_conf             786565654358999987642--101677------777640100468999-9742224778999999764102
Q gi|254780805|r  169 VANILRILKLPSSVREMIRKE--EISLGH------ARTLVSTSDPLSLAQ-VIVSKKMSVRDTEELVQEQDNK  232 (300)
Q Consensus       169 V~~~LrLl~L~~~i~~~l~~~--~is~gh------ar~Ll~~~~~~~la~-~Ii~~~LSVRe~E~lVk~~~~~  232 (300)
                      |...|+=..|.++|++-|.+.  -||-||      ||+|.--||-.=+-| --.=+.-|+.++|+++.+++..
T Consensus       121 Ve~sL~~AALWDEVKD~L~~sa~~LSGGQQQRLCIARalA~ePeVlLlDEPTSALDPIaT~~IEeLi~eLk~~  193 (248)
T TIGR00972       121 VEESLKKAALWDEVKDRLHDSALGLSGGQQQRLCIARALAVEPEVLLLDEPTSALDPIATGKIEELIQELKKK  193 (248)
T ss_pred             HHHHHHHCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             9999861687135524213588978726889999998752488521057888757877899999999987652


No 486
>PRK09147 aminotransferase; Provisional
Probab=24.37  E-value=50  Score=13.76  Aligned_cols=30  Identities=20%  Similarity=0.327  Sum_probs=0.0

Q ss_pred             CCCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf             235789998-768988999999988631001
Q gi|254780805|r   47 IVPNPHNPR-NYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        47 i~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      +..||+||- +.++.+.+++|++=-++||++
T Consensus       171 il~sP~NPTG~v~s~e~l~~l~~la~~~~i~  201 (397)
T PRK09147        171 FVCSPGNPTGAVLPLDDWKKLFALSDRYGFV  201 (397)
T ss_pred             EECCCCCCCCCCCCHHHHHHHHHHHCCCEEE
T ss_conf             8689989889988889999999963247289


No 487
>PRK07851 acetyl-CoA acetyltransferase; Provisional
Probab=24.33  E-value=26  Score=15.52  Aligned_cols=128  Identities=18%  Similarity=0.275  Sum_probs=0.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCC-CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             999876898899999998863100155046205654-4533357567777764210013543334641123455666543
Q gi|254780805|r   52 HNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNG-LYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIVENV  130 (300)
Q Consensus        52 ~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g-~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~  130 (300)
                      ..||...+.|.+..|.--.+..|.++.----+..|| -..|++.+...+..-+--+-.|-..-.-..|-+..-++-+.  
T Consensus       229 e~~R~~tt~e~La~L~P~F~~~GtvTAgNaS~~~DGAAavll~se~~a~~~gl~Plari~~~~~~g~dP~~m~~~Pv~--  306 (405)
T PRK07851        229 DGPRAGTTYEAVSQLKPVFRPDGTVTAGNACPLNDGAAAVVIMSDTKARELGLTPLARIVSTGVSGLSPEIMGLGPIE--  306 (405)
T ss_pred             CCCCCCCCHHHHHHCCCCCCCCCCEECCCCCCCCCHHHHHHHCCHHHHHHCCCCCEEEEEECCCCCCCHHHHCCCHHH--
T ss_conf             772268886668507864156886755437865434699887279999977998159999540056487884618899--


Q ss_pred             HCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHCCHHH
Q ss_conf             1022104899999998521011104679999743378778656---5654358999987642101677
Q gi|254780805|r  131 QRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL---RILKLPSSVREMIRKEEISLGH  195 (300)
Q Consensus       131 ~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L---rLl~L~~~i~~~l~~~~is~gh  195 (300)
                                  +.+++++..|++.+++ ..+-...++-+..|   +-+.++++ +=-+.-|-|+.||
T Consensus       307 ------------A~~~~L~~agl~~~Di-d~~EinEAFA~q~l~~~~~lgid~~-kvNv~GGaiAlGH  360 (405)
T PRK07851        307 ------------ASKQALARAGMTIDDI-DLVEINEAFAVQVLGSARELGIDED-KLNVSGGAIALGH  360 (405)
T ss_pred             ------------HHHHHHHHCCCCCCCC-CEEEEEHHHHHHHHHHHHHHCCCHH-HCCCCCCHHHHCC
T ss_conf             ------------9999999769980248-7556406678889999998489888-8199855887388


No 488
>pfam06970 RepA_N Replication initiator protein A (RepA) N-terminus. This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included.
Probab=24.30  E-value=50  Score=13.75  Aligned_cols=22  Identities=18%  Similarity=0.415  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1046799997433787786565
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      +|.+++++.+|.|+.+|.+.++
T Consensus        53 ft~~el~~~L~~s~~~v~k~~k   74 (76)
T pfam06970        53 FTNEELMELLNCSKQKVIKIKK   74 (76)
T ss_pred             EEHHHHHHHHCCCHHHHHHHHH
T ss_conf             6499999997878889999996


No 489
>TIGR02094 more_P_ylases alpha-glucan phosphorylases; InterPro: IPR011834    This family consists of known phosphorylases, and homologues believed to share the function of using inorganic phosphate to cleave an alpha 1,4 linkage between the terminal glucose residue and the rest of the polymer (maltodextrin, glycogen, etc.). The name of the glucose storage polymer substrate, and therefore the name of this enzyme, depends on the chain lengths and branching patterns. A number of the members of this family have been shown to operate on small maltodextrins, as may be obtained by utilization of exogenous sources. This family represents a distinct clade from the related families: Glycogen/starch/alpha-glucan phosphorylase and Glycosyl transferase, family 35.; GO: 0004645 phosphorylase activity, 0030170 pyridoxal phosphate binding, 0005975 carbohydrate metabolic process.
Probab=24.07  E-value=50  Score=13.72  Aligned_cols=34  Identities=24%  Similarity=0.422  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             01677777640100468999974222477899999976
Q gi|254780805|r  191 ISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEELVQE  228 (300)
Q Consensus       191 is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~lVk~  228 (300)
                      +..||| |++.+   +.+.+.|-++|+|..++.+.|+.
T Consensus       173 ~NEGHA-AF~~L---Erir~~~~~~G~~F~~A~e~Vr~  206 (618)
T TIGR02094       173 LNEGHA-AFVTL---ERIRELIEAQGLSFEEALEAVRK  206 (618)
T ss_pred             CCCCHH-HHHHH---HHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             177668-99999---99999999728889899999852


No 490
>PRK05664 threonine-phosphate decarboxylase; Reviewed
Probab=23.97  E-value=51  Score=13.71  Aligned_cols=27  Identities=26%  Similarity=0.425  Sum_probs=0.0

Q ss_pred             CCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf             789998-768988999999988631001
Q gi|254780805|r   50 NPHNPR-NYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        50 ~p~~pR-~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      ||+||- +.++.+.+.++++.+..+|.+
T Consensus       132 nPNNPTG~~~~~~~l~~~~~~~~~~~~~  159 (330)
T PRK05664        132 NPNNPTGRRFDPARLLAWHARLAARGGW  159 (330)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf             7928866898999999999986531988


No 491
>TIGR02405 trehalos_R_Ecol trehalose operon repressor; InterPro: IPR012771   Trehalose is a non-reducing disaccharide which can be used as both a carbon source and an osmoprotectant in bacteria. Trehalose uptake into the cytoplasm occurs via a trehalose-specific phosphotransferase system which phosphorylates trehalase to trehalose-6-phosphate (Tre6P) during transport into the cytoplasm, and a hydrolase which hydrolyses Tre6P to glucose and glucose-6-phophate.   This entry represents LacI-type TreR, a transcriptional repressor of trehalose uptake found mainly within the gamma-proteobacteria. It does not include the GntR-type TreR's such as those found in Bacillus species. It is capable of binding both the inducer Tre6P and trehalose. Binding of trehalose does not affect the repressor's affinity for its DNA binding site, while binding Tre6P substantially reduces its affinity. The repression activity of TreR is therefore regulated by the ratio of trehalose to Tre6P within the cell . The protein is composed of two domains, an N-terminal DNA-binding helix-turn-helix domain, and a C-terminal effector-binding domain which is homologous to that of LacI. The effector-binding domain is composed of two subdomains, both of which form an alpha-beta-alpha sandwhich, with the effector binding site located at the interface of these subdomains . Tre6P and trehalose bind competitively to this site, with the affinty for trehalose substantially lower than that for Tre6P.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0005991 trehalose metabolic process, 0016481 negative regulation of transcription.
Probab=23.88  E-value=18  Score=16.64  Aligned_cols=22  Identities=32%  Similarity=0.516  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             1104679999743378778656
Q gi|254780805|r  152 GYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       152 ~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      .+|-.+||+.-|.++|||||.|
T Consensus         1 kLTIkDIArLagVgKSTVSRVL   22 (311)
T TIGR02405         1 KLTIKDIARLAGVGKSTVSRVL   22 (311)
T ss_pred             CCHHHHHHHHHCCCCEEEEEEE
T ss_conf             9617776977088620233156


No 492
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role..
Probab=23.82  E-value=41  Score=14.29  Aligned_cols=26  Identities=23%  Similarity=0.434  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10467999974337877865656543
Q gi|254780805|r  153 YTQNDIGSIVGKSRSHVANILRILKL  178 (300)
Q Consensus       153 ~t~~~lA~~~G~s~s~V~~~LrLl~L  178 (300)
                      |+-.+||+..|.+-+||++.|+.|..
T Consensus        26 ySAA~lA~~tgL~~pTvsK~Lk~L~~   51 (130)
T TIGR02944        26 YSAAELAEQTGLEAPTVSKILKALSE   51 (130)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHC
T ss_conf             06888786459886047899887642


No 493
>PRK08153 histidinol-phosphate aminotransferase; Provisional
Probab=23.82  E-value=51  Score=13.69  Aligned_cols=27  Identities=15%  Similarity=0.470  Sum_probs=0.0

Q ss_pred             CCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf             789998-768988999999988631001
Q gi|254780805|r   50 NPHNPR-NYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        50 ~p~~pR-~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      ||+||- ..++.+.+.++++.+..++++
T Consensus       164 nPNNPTG~~~~~~~l~~l~~~~~~~~lv  191 (370)
T PRK08153        164 NPDNPMGSWHPAADIVAFIEALPETTLL  191 (370)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHCCCCCEE
T ss_conf             8959857767868899999847777389


No 494
>PRK03321 putative aminotransferase; Provisional
Probab=23.75  E-value=51  Score=13.68  Aligned_cols=30  Identities=20%  Similarity=0.430  Sum_probs=0.0

Q ss_pred             CCCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf             235789998-768988999999988631001
Q gi|254780805|r   47 IVPNPHNPR-NYFESEGLEDLCQSIKSHGII   76 (300)
Q Consensus        47 i~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l   76 (300)
                      +..||+||- ..++.+.++++++.+..+.++
T Consensus       150 ~l~nPnNPTG~~~~~~~l~~l~~~~~~~~~v  180 (352)
T PRK03321        150 FVCNPNNPTGTVVTPAALARFVAAVPADVLV  180 (352)
T ss_pred             EECCCCCCCCCCCCCHHHHHHHHHCCCCCEE
T ss_conf             9849999730136837589999755478479


No 495
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=23.67  E-value=51  Score=13.67  Aligned_cols=39  Identities=10%  Similarity=0.186  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999985210111046799997433787786565654
Q gi|254780805|r  138 LEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       138 ~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +.+=+.|....+. |++-.+.|++++.|++.||+.++.|+
T Consensus         3 l~QLryf~~va~~-~~n~t~AA~~L~iSQPavS~qIk~LE   41 (324)
T PRK12681          3 LQQLRYIVEVVNH-NLNVSATAESLYTSQPGISKQVRMLE   41 (324)
T ss_pred             HHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             6999999999976-99999999997897779999999999


No 496
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=23.55  E-value=52  Score=13.66  Aligned_cols=51  Identities=20%  Similarity=0.270  Sum_probs=0.0

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHH----CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             566654310221048999999985210----111046799997433787786565
Q gi|254780805|r  124 IAIVENVQRKDLNPLEEALGYEQLISE----YGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       124 ~~l~EN~~R~dl~p~e~A~~~~~l~~~----~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      ....+++......+.+.-.+..-|...    +..++.++|..+|.|+.+|++.|.
T Consensus       124 ~~~~~~~~~~~~~~~~~RlA~~LL~~~~~~~~~~~~~elA~~lG~Sretl~R~L~  178 (213)
T PRK10402        124 YRNIVSYTQNQSFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLA  178 (213)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999987537889999999998610786666799999997988999999999


No 497
>PRK00118 putative DNA-binding protein; Validated
Probab=23.32  E-value=52  Score=13.63  Aligned_cols=34  Identities=18%  Similarity=0.197  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999985210111046799997433787786565
Q gi|254780805|r  140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      +-..+.-...+ .+|-.|||+.+|.||..|...++
T Consensus        22 Q~~~~~lyy~~-DlSl~EIAe~~~iSRQaV~D~ik   55 (105)
T PRK00118         22 QRNYMELYYLD-DYSLGEIAEEFNVSRQAVYDNIK   55 (105)
T ss_pred             HHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999885-49999998996985999999999


No 498
>PRK13558 bacterio-opsin activator; Provisional
Probab=23.21  E-value=52  Score=13.61  Aligned_cols=21  Identities=10%  Similarity=0.066  Sum_probs=0.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             046799997433787786565
Q gi|254780805|r  154 TQNDIGSIVGKSRSHVANILR  174 (300)
Q Consensus       154 t~~~lA~~~G~s~s~V~~~Lr  174 (300)
                      |-++||+.+|.|+++..++||
T Consensus       641 TGeElAesLgIS~pTfhqHLR  661 (674)
T PRK13558        641 EGKQLAESMDIVPSTYHQHLQ  661 (674)
T ss_pred             CHHHHHHHCCCCHHHHHHHHH
T ss_conf             789999870988388999999


No 499
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=23.16  E-value=52  Score=13.61  Aligned_cols=34  Identities=15%  Similarity=0.123  Sum_probs=0.0

Q ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999985210111046799997433787786565654
Q gi|254780805|r  142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK  177 (300)
Q Consensus       142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~  177 (300)
                      +.|....+..++|  ..|+++|.|++.||+.++-|+
T Consensus         8 ~~F~aVa~~gSft--~AA~~L~isqsaVS~~I~~LE   41 (300)
T PRK11074          8 EVVDAVARNGSFS--AAAQELHKVPSAVSYTVRQLE   41 (300)
T ss_pred             HHHHHHHHCCCHH--HHHHHHCCCHHHHHHHHHHHH
T ss_conf             9999999709999--999997888789999999999


No 500
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=23.11  E-value=53  Score=13.60  Aligned_cols=34  Identities=9%  Similarity=0.064  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999998521011104679999743378778656
Q gi|254780805|r  140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL  173 (300)
Q Consensus       140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L  173 (300)
                      +++.+|+...+++....+-|+++|.-|.+..+.|
T Consensus       143 ~WEhIqrvl~e~~~NiSeTARrL~MHRRTLqRkL  176 (182)
T COG4567         143 RWEHIQRVLEECEGNISETARRLNMHRRTLQRKL  176 (182)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             6999999999937777899999621399999997


Done!