Query         gi|254780282|ref|YP_003064695.1| putative transcription regulator protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 299
No_of_seqs    183 out of 20759
Neff          10.3
Searched_HMMs 39220
Date          Sun May 29 15:56:28 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780282.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10632 putative DNA-binding  100.0       0       0  399.6  13.8  290    3-296     1-294 (309)
  2 TIGR03418 chol_sulf_TF putativ 100.0       0       0  396.5  15.0  287    3-293     1-291 (291)
  3 PRK09801 transcriptional activ 100.0       0       0  394.4  14.1  288    5-296     8-298 (310)
  4 PRK12684 transcriptional regul 100.0       0       0  392.1  14.0  288    3-294     1-295 (313)
  5 PRK11242 DNA-binding transcrip 100.0       0       0  391.0  14.5  286    3-293     1-290 (292)
  6 PRK11139 DNA-binding transcrip 100.0       0       0  387.8  15.0  286    3-296     5-294 (295)
  7 PRK11013 DNA-binding transcrip 100.0       0       0  386.8  15.0  289    1-296     1-296 (309)
  8 CHL00180 rbcR LysR transcripti 100.0       0       0  385.3  15.5  293    1-294     3-303 (307)
  9 PRK12682 transcriptional regul 100.0       0       0  385.6  14.1  289    3-295     1-296 (309)
 10 PRK10086 DNA-binding transcrip 100.0       0       0  383.1  16.3  294    1-298    11-311 (311)
 11 PRK12683 transcriptional regul 100.0       0       0  384.8  14.1  290    3-296     1-297 (308)
 12 PRK10837 putative DNA-binding  100.0       0       0  384.1  13.9  283    1-293     1-289 (291)
 13 PRK11151 DNA-binding transcrip 100.0       0       0  381.0  15.9  288    3-295     1-294 (305)
 14 PRK09791 putative DNA-binding  100.0       0       0  378.5  15.4  290    1-296     3-299 (302)
 15 PRK11233 nitrogen assimilation 100.0       0       0  374.4  15.7  288    3-298     1-302 (305)
 16 PRK12679 cbl transcriptional r 100.0       0       0  373.9  13.9  286    3-292     1-293 (316)
 17 PRK09906 DNA-binding transcrip 100.0       0       0  371.6  15.3  289    3-296     1-293 (296)
 18 TIGR03339 phn_lysR aminoethylp 100.0       0       0  369.8  15.1  275    7-289     1-278 (279)
 19 PRK12681 cysB transcriptional  100.0       0       0  368.9  13.9  286    3-292     1-293 (324)
 20 PRK11074 putative DNA-binding  100.0       0       0  367.9  13.3  286    3-297     2-295 (300)
 21 PRK10341 DNA-binding transcrip 100.0       0       0  365.7  15.0  286    4-295     8-299 (312)
 22 TIGR03298 argP transcriptional 100.0       0       0  358.9  12.1  284    3-297     1-291 (292)
 23 PRK12680 transcriptional regul 100.0       0       0  354.1  13.4  284    3-290     1-291 (327)
 24 PRK10094 DNA-binding transcrip 100.0       0       0  350.7  13.1  282    3-293     2-292 (308)
 25 PRK13348 chromosome replicatio 100.0       0       0  344.3  13.5  284    3-297     2-292 (294)
 26 PRK03635 chromosome replicatio 100.0       0       0  344.7  12.8  283    3-297     2-291 (295)
 27 PRK03601 transcriptional regul 100.0       0       0  342.6  14.3  269    3-292     1-272 (275)
 28 PRK09986 DNA-binding transcrip 100.0       0       0  345.8  11.3  273   13-291     1-277 (278)
 29 PRK10082 putative DNA-binding  100.0       0       0  341.2  14.2  285    2-293    10-298 (303)
 30 PRK09508 leuO leucine transcri 100.0       0       0  323.7  14.1  287    2-295    21-313 (314)
 31 COG0583 LysR Transcriptional r 100.0       0       0  311.9  14.4  288    3-297     1-294 (297)
 32 PRK11716 DNA-binding transcrip 100.0       0       0  311.6  11.7  261   27-292     1-268 (269)
 33 PRK11062 nhaR transcriptional  100.0       0       0  306.9  14.5  280    1-290     1-289 (296)
 34 TIGR02424 TF_pcaQ pca operon t 100.0       0       0  297.1  12.9  292    2-296     2-300 (300)
 35 TIGR02036 dsdC D-serine deamin 100.0       0       0  292.5  10.1  288    3-295     8-302 (302)
 36 PRK11482 putative DNA-binding  100.0 6.3E-39 1.6E-43  244.9   9.4  260   26-293     1-265 (266)
 37 PRK10216 DNA-binding transcrip 100.0 8.5E-33 2.2E-37  209.4  10.7  264   27-296     1-286 (288)
 38 pfam03466 LysR_substrate LysR  100.0 3.7E-31 9.3E-36  199.9   9.1  201   89-294     2-208 (209)
 39 pfam00126 HTH_1 Bacterial regu  99.8 4.3E-19 1.1E-23  130.0   7.8   60    5-64      1-60  (60)
 40 PRK10676 DNA-binding transcrip  98.4 2.9E-07 7.3E-12   61.5   4.5   74    5-78     19-97  (262)
 41 COG2005 ModE N-terminal domain  98.3 7.7E-07   2E-11   59.0   4.4   83    3-85     17-104 (130)
 42 PRK11050 manganese transport r  97.5  0.0001 2.6E-09   46.7   3.2   73    6-81     40-116 (155)
 43 smart00347 HTH_MARR helix_turn  97.3 0.00033 8.5E-09   43.7   4.6   75    2-79      7-90  (101)
 44 PRK10677 modA molybdate transp  97.3 0.00075 1.9E-08   41.7   5.9  202   88-293    22-243 (257)
 45 PRK03902 manganese transport t  97.2 0.00058 1.5E-08   42.3   4.6   73    6-81      8-84  (142)
 46 COG0725 ModA ABC-type molybdat  96.9  0.0061 1.5E-07   36.4   7.8  200   89-294    26-244 (258)
 47 smart00529 HTH_DTXR Helix-turn  96.9 0.00059 1.5E-08   42.3   2.4   61   20-83      2-63  (96)
 48 COG1846 MarR Transcriptional r  96.8  0.0017 4.4E-08   39.6   4.5   69    3-74     20-97  (126)
 49 COG1321 TroR Mn-dependent tran  96.8  0.0031 7.9E-08   38.1   5.4   78    5-84      9-89  (154)
 50 PRK03573 transcriptional regul  96.8  0.0023 5.9E-08   38.9   4.7   76    2-80     28-113 (144)
 51 TIGR00637 ModE_repress ModE mo  96.7   0.002 5.1E-08   39.2   3.9   79    3-81      2-86  (101)
 52 PRK11512 DNA-binding transcrip  96.4  0.0042 1.1E-07   37.4   4.0   70    2-74     37-115 (144)
 53 pfam09048 Cro Cro. Members of   96.3  0.0062 1.6E-07   36.4   4.4   45   14-72      9-55  (58)
 54 PRK11169 leucine-responsive tr  96.1  0.0098 2.5E-07   35.2   4.5   44    1-44     10-55  (164)
 55 TIGR01884 cas_HTH CRISPR locus  95.9   0.033 8.5E-07   32.1   6.5   61    3-63    167-231 (231)
 56 PRK10141 DNA-binding transcrip  95.9   0.025 6.3E-07   32.9   5.8   70    4-77     13-86  (106)
 57 cd00090 HTH_ARSR Arsenical Res  95.9   0.023 5.8E-07   33.1   5.6   57    4-61      6-65  (78)
 58 PRK11886 biotin--protein ligas  95.8   0.051 1.3E-06   31.1   7.1   57    7-64      6-64  (319)
 59 TIGR01256 modA molybdate ABC t  95.7   0.025 6.5E-07   32.8   5.3  185  108-293     8-215 (225)
 60 COG2998 TupB ABC-type tungstat  95.6    0.09 2.3E-06   29.6   7.9  202   89-294    26-253 (280)
 61 pfam00497 SBP_bac_3 Bacterial   95.6    0.13 3.4E-06   28.6   8.6  175  107-295    24-209 (224)
 62 pfam01022 HTH_5 Bacterial regu  95.5   0.038 9.6E-07   31.8   5.5   38    7-44      4-42  (47)
 63 PRK11179 DNA-binding transcrip  95.5   0.051 1.3E-06   31.0   6.1   44    1-44      5-50  (153)
 64 COG4742 Predicted transcriptio  95.3   0.024 6.2E-07   32.9   4.1   76    7-85     15-91  (260)
 65 smart00062 PBPb Bacterial peri  95.2    0.22 5.7E-06   27.3   9.5  170  107-295    25-206 (219)
 66 COG1522 Lrp Transcriptional re  95.1   0.078   2E-06   30.0   6.1   40    4-44     10-49  (154)
 67 TIGR03261 phnS2 putative 2-ami  94.9   0.066 1.7E-06   30.4   5.2  203   88-293    17-273 (334)
 68 pfam01047 MarR MarR family. Th  94.8   0.087 2.2E-06   29.7   5.8   42    3-44      1-44  (59)
 69 COG1654 BirA Biotin operon rep  94.8   0.098 2.5E-06   29.4   5.9   49   17-66     19-67  (79)
 70 smart00344 HTH_ASNC helix_turn  94.5    0.12 3.1E-06   28.9   5.8   42    3-44      1-44  (108)
 71 pfam01325 Fe_dep_repress Iron   94.4   0.092 2.3E-06   29.6   5.0   39    6-44      6-47  (58)
 72 PRK11260 cystine transporter s  94.2     0.4   1E-05   25.9   8.4  185   91-293    37-243 (264)
 73 smart00418 HTH_ARSR helix_turn  94.0   0.059 1.5E-06   30.7   3.4   41   15-56      8-48  (66)
 74 COG2522 Predicted transcriptio  93.8    0.11 2.8E-06   29.1   4.5   33    8-40     13-45  (119)
 75 TIGR02702 SufR_cyano iron-sulf  93.3    0.11 2.7E-06   29.2   3.7   89   11-115     7-107 (215)
 76 cd06170 LuxR_C_like C-terminal  93.3    0.34 8.6E-06   26.3   6.2   45    4-48      2-46  (57)
 77 pfam08279 HTH_11 HTH domain. T  93.0    0.31   8E-06   26.5   5.8   49    8-57      3-54  (55)
 78 pfam04967 HTH_10 HTH DNA bindi  92.9    0.43 1.1E-05   25.7   6.3   42    4-45      2-51  (53)
 79 PRK10870 transcriptional repre  92.7    0.28 7.1E-06   26.8   5.1   70    4-76     54-134 (176)
 80 pfam02954 HTH_8 Bacterial regu  92.6    0.12 3.2E-06   28.8   3.2   25   16-40     17-41  (42)
 81 COG1910 Periplasmic molybdate-  92.6    0.34 8.6E-06   26.3   5.4  152  130-292    29-199 (223)
 82 pfam00196 GerE Bacterial regul  92.5    0.52 1.3E-05   25.2   6.3   46    3-48      4-49  (58)
 83 smart00421 HTH_LUXR helix_turn  92.4    0.56 1.4E-05   25.0   6.3   46    3-48      4-49  (58)
 84 PRK10859 putative transglycosy  92.2    0.49 1.2E-05   25.4   5.9  156   91-257    41-219 (507)
 85 pfam01638 HxlR HxlR-like helix  92.0    0.23   6E-06   27.2   4.0   66    5-73      6-79  (90)
 86 TIGR02607 antidote_HigA addict  91.9     0.2 5.1E-06   27.6   3.6   29   19-47     22-61  (81)
 87 PRK10651 transcriptional regul  91.9    0.64 1.6E-05   24.7   6.2   38  107-144    17-57  (216)
 88 COG4189 Predicted transcriptio  91.8    0.38 9.6E-06   26.0   4.9   37    8-44     26-64  (308)
 89 PRK04168 hypothetical protein;  91.7    0.41   1E-05   25.8   5.0   84   88-172    28-122 (336)
 90 PRK10797 glutamate and asparta  91.4       1 2.6E-05   23.5   8.6  190   91-295    38-257 (302)
 91 PRK09495 glnH glutamine ABC tr  91.3       1 2.7E-05   23.4   6.7  170   92-278    24-216 (247)
 92 PRK04217 hypothetical protein;  91.2    0.57 1.4E-05   25.0   5.3   62    3-66     43-105 (110)
 93 PRK09775 hypothetical protein;  91.0    0.11 2.7E-06   29.2   1.4   36   13-52      6-43  (443)
 94 PRK09744 DNA-binding transcrip  90.6    0.28 7.1E-06   26.8   3.2   37   13-49      6-50  (75)
 95 COG0226 PstS ABC-type phosphat  90.2     1.3 3.4E-05   22.9   6.7  202   90-293    40-299 (318)
 96 PRK10403 transcriptional regul  90.2     1.1 2.9E-05   23.3   6.1   17  108-124    18-34  (215)
 97 COG1339 Transcriptional regula  89.6    0.18 4.6E-06   27.8   1.6   93   18-118    20-116 (214)
 98 PRK09958 DNA-binding transcrip  89.6     1.4 3.7E-05   22.7   6.2   15  110-124    62-76  (204)
 99 COG1497 Predicted transcriptio  89.5       1 2.7E-05   23.4   5.5   46   18-66     26-72  (260)
100 PRK09834 DNA-binding transcrip  89.1    0.82 2.1E-05   24.0   4.7   54    6-62     12-70  (264)
101 COG4190 Predicted transcriptio  89.1     1.6 4.1E-05   22.4   6.3   41   19-60     80-120 (144)
102 PRK10163 DNA-binding transcrip  89.0    0.51 1.3E-05   25.3   3.6   56    5-61     28-83  (271)
103 COG2345 Predicted transcriptio  89.0    0.63 1.6E-05   24.7   4.0   55   14-69     20-83  (218)
104 COG1733 Predicted transcriptio  88.8    0.71 1.8E-05   24.4   4.2   66    5-73     24-97  (120)
105 pfam01710 Transposase_14 Trans  88.7    0.85 2.2E-05   24.0   4.6   44    1-47      1-46  (120)
106 PRK09483 response regulator; P  88.1     1.9 4.8E-05   22.0   6.2   16  109-124    14-29  (216)
107 PRK09935 transcriptional regul  88.0     1.9 4.8E-05   22.0   6.1   18  109-126    16-33  (210)
108 PRK10360 DNA-binding transcrip  88.0     1.9 4.9E-05   21.9   6.0   37  108-144    13-52  (196)
109 PRK10840 transcriptional regul  87.5     2.1 5.2E-05   21.7   6.0   15  111-125    70-84  (216)
110 PRK04172 pheS phenylalanyl-tRN  87.4     1.7 4.3E-05   22.3   5.4   71    1-71      2-74  (501)
111 cd00134 PBPb Bacterial peripla  86.9     2.2 5.6E-05   21.6   9.7  168  107-293    24-203 (218)
112 pfam02001 DUF134 Protein of un  86.6     1.5 3.9E-05   22.5   4.8   49    3-51     37-86  (100)
113 PRK11477 carbohydrate diacid t  86.5     2.3 5.7E-05   21.5   5.6   20   38-57     15-34  (385)
114 pfam05043 Mga Mga helix-turn-h  86.0     1.4 3.7E-05   22.7   4.4   44    5-49     19-65  (87)
115 PRK09392 ftrB transcriptional   85.5     1.2   3E-05   23.1   3.8   16  111-126   111-126 (236)
116 PRK09390 fixJ response regulat  85.4     2.6 6.7E-05   21.1   6.2   21  109-129    63-83  (202)
117 PRK10014 DNA-binding transcrip  85.1    0.46 1.2E-05   25.5   1.5   82   19-119     8-90  (342)
118 TIGR02337 HpaR homoprotocatech  85.0    0.63 1.6E-05   24.7   2.2   78    2-82     25-112 (130)
119 pfam04545 Sigma70_r4 Sigma-70,  84.1     1.1 2.7E-05   23.4   3.1   27   16-42     19-45  (50)
120 PTZ00326 phenylalanyl-tRNA syn  84.1     1.8 4.6E-05   22.1   4.2   71    1-71      2-74  (505)
121 smart00419 HTH_CRP helix_turn_  83.7     1.8 4.6E-05   22.1   4.1   37   20-59     11-47  (48)
122 COG1342 Predicted DNA-binding   83.2       3 7.6E-05   20.8   5.0   50    2-51     33-83  (99)
123 COG4197 Uncharacterized protei  82.9     1.7 4.3E-05   22.2   3.7   34    7-40      2-35  (96)
124 COG1568 Predicted methyltransf  82.7     2.1 5.5E-05   21.7   4.1   58    9-69     26-83  (354)
125 PRK11917 bifunctional adhesin/  82.7     3.5 8.9E-05   20.4   7.1  187   91-293    36-245 (259)
126 PRK11569 transcriptional repre  80.9     1.5 3.9E-05   22.5   2.9   54    5-61     31-86  (274)
127 COG2197 CitB Response regulato  80.6     4.2 0.00011   20.0   5.6   12  111-122    15-26  (211)
128 TIGR03541 reg_near_HchA LuxR f  80.4     4.2 0.00011   19.9   6.1   23   30-52     16-38  (232)
129 COG1414 IclR Transcriptional r  80.1     2.4 6.2E-05   21.3   3.7   53    6-62      8-63  (246)
130 PRK09863 putative frv operon r  79.4     3.3 8.4E-05   20.6   4.2   52   15-66     90-141 (585)
131 PRK06424 transcription factor;  79.1     4.2 0.00011   20.0   4.6   18  225-242    82-99  (144)
132 smart00497 IENR1 Intron encode  78.9     1.1 2.8E-05   23.3   1.6   25   16-40     16-40  (53)
133 pfam09339 HTH_IclR IclR helix-  78.8     2.8 7.2E-05   20.9   3.7   39    6-44      7-45  (52)
134 COG1349 GlpR Transcriptional r  78.8     4.8 0.00012   19.6   5.8   61    1-64      1-63  (253)
135 PRK10188 DNA-binding transcrip  78.2       5 0.00013   19.5   6.3   14  278-291   179-192 (240)
136 smart00346 HTH_ICLR helix_turn  77.8     3.2 8.2E-05   20.6   3.7   60    7-67      7-69  (91)
137 PRK10434 srlR DNA-bindng trans  76.4     5.6 0.00014   19.2   5.6   56    4-62      4-61  (256)
138 COG1609 PurR Transcriptional r  76.0     1.7 4.2E-05   22.3   1.8  111   19-147     2-122 (333)
139 PRK00430 fis DNA-binding prote  75.9     3.3 8.5E-05   20.5   3.4   27   15-41     69-95  (98)
140 COG3888 Predicted transcriptio  75.2     3.9 9.8E-05   20.2   3.5  103   20-144    23-127 (321)
141 TIGR02395 rpoN_sigma RNA polym  74.7    0.72 1.8E-05   24.4  -0.3   10  289-298   319-328 (477)
142 cd06171 Sigma70_r4 Sigma70, re  74.5     6.3 0.00016   18.9   4.7   30   15-44     24-53  (55)
143 PRK00118 putative DNA-binding   73.7     5.4 0.00014   19.3   4.0   32   15-46     31-62  (105)
144 PRK09861 cytoplasmic membrane   73.3     6.7 0.00017   18.8   5.3  195   92-296    31-258 (272)
145 TIGR01529 argR_whole arginine   73.3     1.3 3.3E-05   22.9   0.7   15   27-41     31-46  (155)
146 PRK11553 alkanesulfonate trans  73.3     2.4 6.1E-05   21.4   2.1  196   91-297    25-239 (314)
147 PRK00215 LexA repressor; Valid  73.0     6.1 0.00016   19.0   4.1   45   18-65     24-72  (204)
148 pfam04297 UPF0122 Putative hel  72.6     5.9 0.00015   19.1   3.9   40    6-45     21-61  (101)
149 COG4623 Predicted soluble lyti  72.1     7.2 0.00018   18.6   5.1  150   91-249    21-187 (473)
150 pfam01726 LexA_DNA_bind LexA D  71.3     5.7 0.00015   19.2   3.6   42    3-44      4-53  (65)
151 pfam05225 HTH_psq helix-turn-h  70.9     7.7  0.0002   18.4   4.5   34    7-40      4-39  (45)
152 pfam09862 DUF2089 Protein of u  69.6     8.2 0.00021   18.3   6.1   46    3-48     34-80  (113)
153 pfam04552 Sigma54_DBD Sigma-54  69.2     4.1  0.0001   20.0   2.5   24   17-40     49-72  (160)
154 PRK11475 DNA-binding transcrip  69.0     8.4 0.00021   18.2   5.9   36  109-144    56-96  (205)
155 COG2771 CsgD DNA-binding HTH d  69.0     8.4 0.00021   18.2   6.1   47    2-48      4-50  (65)
156 pfam03180 Lipoprotein_9 NLPA l  68.8     8.5 0.00022   18.2   6.0  191   95-297     1-223 (236)
157 pfam01978 TrmB Sugar-specific   68.3     8.7 0.00022   18.1   5.7   44    2-45      5-50  (68)
158 PRK05932 RNA polymerase factor  67.8     4.8 0.00012   19.6   2.6   22   19-40     18-39  (461)
159 PRK09391 fixK transcriptional   67.6     4.8 0.00012   19.6   2.6   15  111-125   111-125 (224)
160 pfam07453 NUMOD1 NUMOD1 domain  67.4       2   5E-05   21.9   0.6   23   16-38     15-37  (37)
161 cd00092 HTH_CRP helix_turn_hel  67.2     4.7 0.00012   19.7   2.5   34   20-56     28-61  (67)
162 pfam00392 GntR Bacterial regul  66.7     6.5 0.00017   18.8   3.2   26   19-44     26-51  (64)
163 COG1510 Predicted transcriptio  66.2       6 0.00015   19.0   2.9   33   16-48     40-72  (177)
164 cd07377 WHTH_GntR Winged helix  66.0     7.6 0.00019   18.5   3.4   26   19-44     27-52  (66)
165 COG2739 Uncharacterized protei  65.4     9.9 0.00025   17.8   3.9   33   14-46     30-62  (105)
166 PRK11564 stationary phase indu  65.0      10 0.00026   17.7   5.9   47   16-62     29-79  (426)
167 PRK10906 DNA-binding transcrip  65.0      10 0.00026   17.7   6.0   60    1-63      1-62  (252)
168 COG1725 Predicted transcriptio  64.6      10 0.00026   17.7   4.4   51   17-69     35-85  (125)
169 smart00345 HTH_GNTR helix_turn  64.5     8.1 0.00021   18.3   3.3   26   19-44     22-47  (60)
170 PRK01905 DNA-binding protein F  63.9      11 0.00027   17.6   5.0   26   16-41     49-74  (77)
171 pfam07900 DUF1670 Protein of u  63.7      11 0.00028   17.6   5.2   26   24-49    112-137 (220)
172 COG0640 ArsR Predicted transcr  63.5      11 0.00028   17.6   5.4   50    6-56     26-77  (110)
173 TIGR01764 excise DNA binding d  63.1     6.5 0.00016   18.9   2.6   37   18-59      2-38  (49)
174 PRK10411 DNA-binding transcrip  62.8      11 0.00029   17.5   4.0   52    6-60      5-58  (240)
175 cd01392 HTH_LacI Helix-turn-he  62.7     5.4 0.00014   19.3   2.1   19   22-40      2-20  (52)
176 PRK12423 LexA repressor; Provi  61.9      12  0.0003   17.4   5.9   56    3-61      4-70  (202)
177 COG1508 RpoN DNA-directed RNA   61.7     7.1 0.00018   18.6   2.6   21   42-62     39-59  (444)
178 cd00283 GIY-YIG_Cterm GIYX(10-  60.6     6.1 0.00016   19.0   2.1   21   18-38     81-101 (113)
179 pfam00356 LacI Bacterial regul  60.1     9.2 0.00023   18.0   2.9   22   19-40      1-22  (46)
180 smart00354 HTH_LACI helix_turn  59.7     9.2 0.00024   18.0   2.9   22   19-40      2-23  (70)
181 PRK00082 hrcA heat-inducible t  59.6      13 0.00033   17.2   4.1   67    1-68      1-77  (339)
182 COG1458 Predicted DNA-binding   59.6     1.9 4.8E-05   22.0  -0.7  115   27-144    49-178 (221)
183 COG1737 RpiR Transcriptional r  59.5      11 0.00028   17.5   3.3   27   14-40     33-59  (281)
184 PRK11161 fumarate/nitrate redu  58.8     8.6 0.00022   18.1   2.6   17  110-126   117-133 (235)
185 COG3093 VapI Plasmid maintenan  58.8      13 0.00034   17.1   3.8   23   18-40     24-46  (104)
186 PRK12469 RNA polymerase factor  58.8     7.1 0.00018   18.6   2.2   36   15-52     14-49  (475)
187 pfam01418 HTH_6 Helix-turn-hel  58.7      13 0.00034   17.1   3.7   28   14-41     31-58  (106)
188 COG3355 Predicted transcriptio  56.5      14 0.00037   16.8   4.3   58    6-69     28-88  (126)
189 pfam04069 OpuAC Substrate bind  55.7      15 0.00038   16.8   5.5  188   94-289     2-224 (256)
190 PRK11063 metQ DL-methionine tr  55.3      15 0.00039   16.7   5.7  195   93-296    31-257 (271)
191 COG3835 CdaR Sugar diacid util  55.0      15 0.00039   16.7   4.2   16   71-86     55-70  (376)
192 PRK09726 DNA-binding transcrip  54.6      16  0.0004   16.7   4.8   47   17-63     25-82  (88)
193 PRK10727 DNA-binding transcrip  54.4      13 0.00033   17.2   2.9   22   19-40      3-24  (342)
194 PRK09526 lacI lac repressor; R  54.0      13 0.00033   17.1   2.9   22   19-40      7-28  (342)
195 PRK08898 coproporphyrinogen II  53.1      15 0.00037   16.8   3.0   10  118-127   169-178 (393)
196 PRK13870 transcriptional regul  52.3      17 0.00043   16.4   6.1   19   33-51     20-38  (234)
197 PRK11041 DNA-binding transcrip  52.3      15 0.00037   16.8   2.9  110   19-147    11-131 (341)
198 cd00569 HTH_Hin_like Helix-tur  52.1      17 0.00044   16.4   4.6   36    3-38      6-42  (42)
199 PRK05066 arginine repressor; P  51.9     7.7  0.0002   18.4   1.4   36    6-41      9-53  (156)
200 PRK10703 DNA-binding transcrip  51.8      15 0.00038   16.8   2.9  111   19-148     3-124 (335)
201 cd01104 HTH_MlrA-CarA Helix-Tu  51.5      17 0.00045   16.4   3.4   36   19-58      2-37  (68)
202 PRK10401 DNA-binding transcrip  51.2      15 0.00039   16.7   2.9   22   19-40      3-24  (346)
203 COG1777 Predicted transcriptio  51.0      18 0.00045   16.3   5.4   38   10-47     20-58  (217)
204 PRK10339 DNA-binding transcrip  50.6      16  0.0004   16.6   2.8   22   19-40      3-24  (327)
205 pfam02042 RWP-RK RWP-RK domain  50.5      18 0.00046   16.3   4.4   34    3-40      5-38  (52)
206 PRK09464 pdhR transcriptional   50.2      18 0.00047   16.2   4.4   42   19-62     36-77  (254)
207 pfam08222 HTH_CodY CodY helix-  50.2      16  0.0004   16.6   2.8   24   21-44      7-30  (60)
208 PRK11303 DNA-binding transcrip  49.1      16 0.00042   16.5   2.7   22   19-40      2-23  (330)
209 COG3415 Transposase and inacti  49.0      19 0.00049   16.1   3.7   59    3-61      7-66  (138)
210 COG2390 DeoR Transcriptional r  48.3      17 0.00042   16.5   2.7   39    6-44     13-53  (321)
211 PRK10423 transcriptional repre  47.9      13 0.00034   17.1   2.1  108   21-147     2-120 (327)
212 cd04762 HTH_MerR-trunc Helix-T  47.9      18 0.00046   16.3   2.8   22   19-40      2-23  (49)
213 PRK09492 treR trehalose repres  47.8      19 0.00048   16.2   2.9   22   19-40      6-27  (315)
214 smart00420 HTH_DEOR helix_turn  47.7      20 0.00051   16.0   4.0   39   15-56     12-50  (53)
215 PRK09333 30S ribosomal protein  47.3      14 0.00036   16.9   2.1   23  274-296   115-137 (150)
216 PRK09137 DNA topoisomerase I;   47.0     9.6 0.00025   17.9   1.3   22   50-71    506-527 (761)
217 PRK09802 DNA-binding transcrip  46.4      21 0.00054   15.9   6.4   55    6-63     18-74  (269)
218 COG2901 Fis Factor for inversi  46.3      21 0.00054   15.9   3.1   24   17-40     71-94  (98)
219 KOG1168 consensus               44.6      23 0.00057   15.7   3.7   34   45-81     38-74  (385)
220 TIGR03001 Sig-70_gmx1 RNA poly  43.9      23 0.00059   15.7   3.4   11  108-118    40-50  (249)
221 pfam01527 Transposase_8 Transp  43.9      23 0.00059   15.7   4.6   29   14-42     19-48  (75)
222 pfam07022 Phage_CI_repr Bacter  43.8      23 0.00059   15.6   3.9   32    9-40      4-35  (65)
223 PRK04280 arginine repressor; P  43.5      12 0.00032   17.2   1.4   34    8-41      7-48  (149)
224 PRK09729 hypothetical protein;  43.4      14 0.00035   16.9   1.6   40  232-272     1-41  (68)
225 pfam00325 Crp Bacterial regula  43.1      21 0.00052   16.0   2.5   23   22-44      7-29  (32)
226 PRK09954 hypothetical protein;  42.9      22 0.00057   15.7   2.6   55    4-63      2-58  (362)
227 pfam05344 DUF746 Domain of Unk  42.3      25 0.00063   15.5   4.0   33   13-45      9-41  (65)
228 pfam01316 Arg_repressor Argini  41.6      12  0.0003   17.4   1.0   16   26-41     33-48  (70)
229 COG1438 ArgR Arginine represso  41.4      20 0.00052   16.0   2.2   37    5-41      5-49  (150)
230 COG5606 Uncharacterized conser  41.3      18 0.00047   16.2   2.0   19   21-39     45-63  (91)
231 pfam05339 DUF739 Protein of un  40.6      26 0.00066   15.4   4.1   37    1-38      1-37  (69)
232 pfam01381 HTH_3 Helix-turn-hel  40.4      25 0.00064   15.4   2.6   23   17-39      9-31  (55)
233 PRK09764 DNA-binding transcrip  40.4      26 0.00065   15.4   2.6   41   19-61     31-71  (239)
234 TIGR02201 heptsyl_trn_III lipo  40.3     8.5 0.00022   18.2   0.1   38  107-144    15-52  (347)
235 COG3388 Predicted transcriptio  39.4      10 0.00026   17.7   0.5   65    5-72     14-80  (101)
236 cd00186 TOP1Ac DNA Topoisomera  39.4      12  0.0003   17.4   0.7   23   21-43     94-116 (381)
237 pfam08220 HTH_DeoR DeoR-like h  39.3      27  0.0007   15.2   4.1   47   11-60      8-54  (57)
238 TIGR03337 phnR transcriptional  39.2      27  0.0007   15.2   2.7   41   19-61     27-67  (231)
239 PRK03341 arginine repressor; P  39.0      14 0.00037   16.8   1.2   13   28-40     45-57  (168)
240 smart00530 HTH_XRE Helix-turn-  38.8      27  0.0007   15.2   2.6   23   17-39     10-32  (56)
241 cd04763 HTH_MlrA-like Helix-Tu  38.8      28 0.00071   15.2   2.7   35   19-57      2-36  (68)
242 PRK11402 DNA-binding transcrip  38.2      28 0.00073   15.1   2.6   40   19-60     37-76  (243)
243 PRK04158 transcriptional repre  37.6      25 0.00064   15.5   2.2   11   42-52     33-43  (256)
244 PRK03837 transcriptional regul  37.5      29 0.00075   15.1   2.6   38   19-59     40-78  (243)
245 cd06571 Bac_DnaA_C C-terminal   37.3      29 0.00075   15.0   5.8   42    6-47     32-75  (90)
246 TIGR02719 repress_PhaQ poly-be  37.1     7.8  0.0002   18.4  -0.4   55   29-83     55-115 (138)
247 PRK00441 argR arginine repress  36.4      16 0.00042   16.5   1.1   36    6-41      4-47  (149)
248 COG2238 RPS19A Ribosomal prote  35.9      31 0.00079   14.9   2.5   51  244-296    86-137 (147)
249 pfam08281 Sigma70_r4_2 Sigma-7  35.8      31 0.00079   14.9   4.6   31   13-43     22-52  (54)
250 PRK13182 racA polar chromosome  35.4      32 0.00081   14.9   3.0   57   20-80      3-60  (178)
251 pfam04492 Phage_rep_O Bacterio  35.3      32 0.00081   14.9   5.5   52    3-57     30-91  (100)
252 PRK11337 DNA-binding transcrip  35.2      32 0.00081   14.8   3.3   28   14-41     44-71  (293)
253 KOG2947 consensus               35.1      32 0.00081   14.8   3.9  117  134-251    76-198 (308)
254 pfam00376 MerR MerR family reg  35.1      29 0.00075   15.1   2.2   22   19-44      1-22  (38)
255 PHA01976 helix-turn-helix prot  35.0      25 0.00063   15.5   1.8   34   16-49     12-58  (67)
256 PRK11302 DNA-binding transcrip  34.8      32 0.00082   14.8   3.7   28   14-41     31-58  (284)
257 PRK13509 transcriptional repre  34.7      33 0.00083   14.8   6.2   61    1-64      1-63  (251)
258 COG2842 Uncharacterized ATPase  34.2      33 0.00084   14.8   5.2   47    1-47      1-60  (297)
259 pfam00342 PGI Phosphoglucose i  34.1      25 0.00063   15.5   1.7  111    2-127     6-131 (483)
260 PRK10225 DNA-binding transcrip  33.6      34 0.00086   14.7   3.9   40   21-62     37-76  (257)
261 smart00351 PAX Paired Box doma  33.3      32 0.00083   14.8   2.2   32   11-42     26-58  (125)
262 PHA02519 plasmid partition pro  31.6      37 0.00093   14.5   3.0   64   16-93     38-103 (387)
263 TIGR01928 menC_lowGC/arch o-su  31.4      19 0.00049   16.1   0.8   91   74-169   132-229 (326)
264 TIGR03338 phnR_burk phosphonat  31.2      37 0.00095   14.5   2.7   42   19-62     36-77  (212)
265 pfam01090 Ribosomal_S19e Ribos  31.2      34 0.00088   14.7   2.1   22  274-295   115-136 (140)
266 TIGR02195 heptsyl_trn_II lipop  31.1      21 0.00054   15.9   1.0   30  100-129     7-37  (361)
267 PRK11557 putative DNA-binding   30.9      38 0.00096   14.4   3.7   28   14-41     31-58  (282)
268 TIGR03431 PhnD phosphonate ABC  28.9      41   0.001   14.2   6.6  191   93-292    27-248 (288)
269 COG2188 PhnF Transcriptional r  28.8      41   0.001   14.2   2.6   42   19-62     33-74  (236)
270 PRK10079 putative transcriptio  27.8      43  0.0011   14.1   2.7   40   19-60     37-76  (241)
271 COG0761 lytB 4-Hydroxy-3-methy  27.7      12  0.0003   17.4  -0.9   21   34-54     16-39  (294)
272 PRK10421 DNA-binding transcrip  27.4      43  0.0011   14.1   2.6   39   21-61     30-68  (253)
273 pfam06322 Phage_NinH Phage Nin  27.4      43  0.0011   14.1   2.1   32   14-45     13-44  (64)
274 COG2826 Tra8 Transposase and i  26.6      42  0.0011   14.2   1.8   26   15-40     21-46  (318)
275 PRK11014 transcriptional repre  26.6      45  0.0011   14.0   6.0   69    7-78     10-84  (141)
276 PRK09706 transcriptional repre  26.4      45  0.0012   14.0   2.6   19   19-37     20-38  (135)
277 cd00093 HTH_XRE Helix-turn-hel  26.3      46  0.0012   13.9   2.3   23   17-39     12-34  (58)
278 cd00131 PAX Paired Box domain   25.9      46  0.0012   13.9   2.3   32   11-42     26-58  (128)
279 TIGR03453 partition_RepA plasm  25.7      47  0.0012   13.9   2.8   23   16-38     32-54  (387)
280 PRK11523 DNA-binding transcrip  25.6      47  0.0012   13.9   2.6   41   19-61     34-74  (258)
281 PRK09990 DNA-binding transcrip  25.1      48  0.0012   13.8   2.6   43   19-63     33-75  (251)
282 COG3432 Predicted transcriptio  25.1      22 0.00056   15.8   0.2   53   19-74     33-89  (95)
283 cd04765 HTH_MlrA-like_sg2 Heli  25.0      48  0.0012   13.8   3.2   35   19-57      2-36  (99)
284 COG4465 CodY Pleiotropic trans  24.8      49  0.0012   13.8   2.6   17   40-56     34-50  (261)
285 pfam08535 KorB KorB domain. Th  24.4      50  0.0013   13.7   2.4   20   21-40      7-26  (93)
286 PRK01066 porphobilinogen deami  24.3      30 0.00076   15.0   0.7   54   92-145    18-95  (234)
287 cd04764 HTH_MlrA-like_sg1 Heli  23.9      51  0.0013   13.7   3.0   34   19-57      2-35  (67)
288 PRK13507 formate--tetrahydrofo  23.7      51  0.0013   13.7   4.4   63    1-65      1-79  (587)
289 PRK03537 hypothetical protein;  23.4      52  0.0013   13.6   6.5   53  239-294   116-172 (188)
290 pfam08280 HTH_Mga M protein tr  23.4      52  0.0013   13.6   5.3   52    5-56      5-58  (59)
291 PTZ00095 40S ribosomal protein  23.3      52  0.0013   13.6   2.2   22  275-296   142-163 (169)
292 PRK13982 bifunctional SbtC-lik  23.1     4.2 0.00011   19.9  -3.8   30   94-123    73-102 (476)
293 PRK07379 coproporphyrinogen II  23.1      52  0.0013   13.6   3.3   18  274-291   378-396 (399)
294 PRK12520 RNA polymerase sigma   23.1      53  0.0013   13.6   5.2   22   64-85     13-34  (191)
295 pfam12492 DUF3705 Protein of u  22.9      40   0.001   14.3   1.1   16   49-64      2-17  (31)
296 TIGR02995 ectoine_ehuB ectoine  22.7      53  0.0014   13.5   3.3  151   90-249    31-198 (285)
297 pfam12116 SpoIIID Stage III sp  22.6      54  0.0014   13.5   2.8   28   13-40     14-42  (82)
298 pfam00292 PAX 'Paired box' dom  22.3      55  0.0014   13.5   2.3   32   11-42     26-58  (125)
299 PRK08413 consensus              21.9      45  0.0011   14.0   1.3   22   50-71    487-508 (733)
300 PRK09959 hybrid sensory histid  21.6      56  0.0014   13.4   8.3  178   94-292   303-504 (1197)
301 COG1167 ARO8 Transcriptional r  21.5      57  0.0014   13.4   3.3   29   16-44     27-55  (459)
302 PRK13777 transcriptional regul  21.4      37 0.00095   14.4   0.8   49   19-67     62-114 (190)
303 smart00437 TOP1Ac Bacterial DN  21.1      58  0.0015   13.4   2.6   40   21-61     20-59  (259)
304 PRK09057 coproporphyrinogen II  20.9      50  0.0013   13.7   1.3   18  277-294   362-379 (381)
305 TIGR02944 suf_reg_Xantho FeS a  20.7      59  0.0015   13.3   1.8   30   13-42     19-50  (130)
306 smart00422 HTH_MERR helix_turn  20.6      59  0.0015   13.3   2.2   34   19-57      2-36  (70)
307 PRK10803 hypothetical protein;  20.2      61  0.0015   13.2   2.7   73    1-91      1-77  (262)

No 1  
>PRK10632 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00  E-value=0  Score=399.59  Aligned_cols=290  Identities=28%  Similarity=0.364  Sum_probs=258.0

Q ss_pred             CC-HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH
Q ss_conf             88-89999999999827689999882899789999999999995882179769946850013433222222222210122
Q gi|254780282|r    3 FD-WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ   81 (299)
Q Consensus         3 md-~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~   81 (299)
                      || +++|++|++|+++||||+||++|++||||||++|++||++||++||+|++|++.||++|+.++++++.++++++++.
T Consensus         1 Md~L~~L~~F~~Vae~gSfs~AA~~L~~s~saVSr~I~~LE~~LG~~Lf~RttR~l~LT~~G~~~~~~~~~il~~~~~~~   80 (309)
T PRK10632          1 MERLKRMSVFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGCRRMLHEVQDVH   80 (309)
T ss_pred             CCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCCEECHHHHHHHHHHHHHHHHHHHHH
T ss_conf             97678999999999809999999997959889999999999997995689789971289899999999887767888999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             10012232222223332111000000000135667542000122222222222222222222345654321111223455
Q gi|254780282|r   82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLV  161 (299)
Q Consensus        82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~  161 (299)
                      ..+.+......|+|||+++.+++..++++.|.+|.++||+|+|++..++...|+..+++|++|+++. ..++++..++|+
T Consensus        81 ~~~~~~~~~~~G~LrI~~~~~~~~~~l~~~l~~f~~~yP~i~l~l~~~~~~~dl~~~~~Diair~g~-~~~~~l~ar~L~  159 (309)
T PRK10632         81 EQLYAFNNTPIGTLRIGCSSTMAQNVLAGLTAKMLKEYPGLSVNLVTGIPAPDLIADGLDVVIRVGA-LQDSSLFSRRLG  159 (309)
T ss_pred             HHHHHCCCCCCEEEEECCCHHHHHHHHCCHHHHHHHHCCCCCEEEECCCCCCCHHHCCCCCCEEECC-CCCCCEEEEEEE
T ss_conf             9998601787405884157177662306156788876898425776168746355505531034078-899883899914


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCE
Q ss_conf             54332112344321112222221100011235664332110002356652022343212114532420013567873842
Q gi|254780282|r  162 TIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI  241 (299)
Q Consensus       162 ~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gi  241 (299)
                      ..++++|++|+|+..++.|.+++||.+++|+.+.......   +.+....+..........+.+|+.+++++++.+|.||
T Consensus       160 ~~~~~l~Asp~yl~~~g~p~~p~dL~~~~~l~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~G~GI  236 (309)
T PRK10632        160 AMPMVVCAAKSYLAQYGTPEKPADLSSHSWLEYSVRPDNE---FELIAPEGISTRLIPQGRFVTNDPMTLVRWLTAGAGI  236 (309)
T ss_pred             ECCCEEEECHHHHHHCCCCCCHHHHHCCCCEEECCCCCCC---EEEECCCCCEEEECCCCEEEECCHHHHHHHHHHCCCC
T ss_conf             0450587278999846999999998389847633789984---3678589977998267709999899999999919991


Q ss_pred             EEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             3311777601---998466177666766008999348778888999999999999850
Q gi|254780282|r  242 ALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       242 a~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      +++|.+++++   +|+|++++|++...+.++|++|++++..++++++|+|||.+...+
T Consensus       237 a~lP~~~v~~~l~~G~Lv~llp~~~~~~~~~~~vy~~~~~~~~rvr~fidfl~e~f~~  294 (309)
T PRK10632        237 AYVPLMWVIDEINRGELEILLPRYQSDPRPVYALYTEKDKLPLKVQVVINYLTDYFVR  294 (309)
T ss_pred             HHCCHHHHHHHHHCCCCEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf             0186999999986899689599986999719999859986489999999999999988


No 2  
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=100.00  E-value=0  Score=396.52  Aligned_cols=287  Identities=25%  Similarity=0.391  Sum_probs=251.3

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      |||++|++|++|+++||||+||++|++||||||++|++||++||++||+|++|++.||++|+.|+++++.+++.++++.+
T Consensus         1 m~l~~L~~F~~Va~~gS~t~AA~~L~~sqsavS~~I~~LE~~lG~~Lf~R~~r~~~lT~aG~~l~~~a~~~l~~~~~~~~   80 (291)
T TIGR03418         1 LSLQALRVFESAARLASFTAAARELGSTQPAVSQQVKRLEEELGTPLFERGHRGIELTEDGQRLFEAVRAGLDTIDLATA   80 (291)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             97799999999998199999999988788899999999999969965897799546868899999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             00122322222233321110000000001356675420001222222222222222222223456543211112234555
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVT  162 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~  162 (299)
                      .+...  ..+|.++|+++++++..++++.+.+|++.||++++++.+++...++..+++|++|..+.+ ..++....++++
T Consensus        81 ~l~~~--~~~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~i~v~l~~~~~~~~~~~~~~Dlai~~~~~-~~~~~~~~~l~~  157 (291)
T TIGR03418        81 QLRAR--REHETLTLATDFAFATYWLMPRLHRFKRAMPDVDVSLVTSQDSLDPQRDDIDVAILFGDG-RWPGGEAHRLFS  157 (291)
T ss_pred             HHHCC--CCCCCEEEECCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHCCCCCEEEEECCC-CCCCCEEEECCC
T ss_conf             98554--667824885143887777568767899868980799995474045432787389996478-898863899105


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH-HHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCE
Q ss_conf             43321123443211122222211000112356643321100023-56652022343212114532420013567873842
Q gi|254780282|r  163 IHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFN-WLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI  241 (299)
Q Consensus       163 ~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gi  241 (299)
                      ++.+++|+|+|+..++.+.+++||.+++++.+....+..+..+. ++...+. ...+....+++|+..+++++|.+|.||
T Consensus       158 ~~~~~v~sp~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~v~~G~Gi  236 (291)
T TIGR03418       158 EEVTPVCSPALLAARATPLSAADLLRLPLLHLEPTQPARWFDWAGWFDAHGL-ERPPAPGGLTFNNYTLVIQAAIGGQGV  236 (291)
T ss_pred             CEEEEEECHHHHHHCCCCCCHHHHHCCCEEEECCCCCCCCHHHHHHHHHCCC-CCCCCCCEEEECCHHHHHHHHHHCCCE
T ss_conf             6199998859998669999999993898799538988630123556651583-015778628999899999999978987


Q ss_pred             EEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             3311777601---998466177666766008999348778888999999999999
Q gi|254780282|r  242 ALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       242 a~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      |++|.+++++   +|.|+++++++..+.+++|++|++++.++|++++|+|||++|
T Consensus       237 a~lp~~~v~~~l~~G~Lv~ll~~~~~~~~~~~lv~~~~~~~~~~~r~Fid~l~~e  291 (291)
T TIGR03418       237 ALGWAPLVDELLEAGQLVRLIDEPVVTERGYYLVRPPRKRRGPAVRRFRDWLLDE  291 (291)
T ss_pred             EEEEHHHHHHHHHCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf             9611999999987899799798556888639999839987899999999997339


No 3  
>PRK09801 transcriptional activator TtdR; Provisional
Probab=100.00  E-value=0  Score=394.44  Aligned_cols=288  Identities=24%  Similarity=0.370  Sum_probs=253.6

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHC
Q ss_conf             89999999999827689999882899789999999999995882179769946850013433222222222210122100
Q gi|254780282|r    5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIEL   84 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~   84 (299)
                      +++|++|++|+++||||+||++|++||||||++|++||++||++||+|++|++.||++|+.|+++++.++.+++++.+.+
T Consensus         8 l~dL~~F~~Va~~gSfs~AA~~L~vs~saVSr~I~~LE~~LG~~Lf~R~tR~l~LTeaG~~l~~~~~~il~~~~~~~~~~   87 (310)
T PRK09801          8 AKDLQVLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATTLLNRSARGVALTESGQRCYEHALEILTQYQRLVDDV   87 (310)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCEECCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999809999999997959889999999999986993761489984015999999999999999999999987


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             12232222223332111000000000135667542000122222222222222222222345654321111223455543
Q gi|254780282|r   85 QESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIH  164 (299)
Q Consensus        85 ~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~  164 (299)
                      .+....++|.|||+++++++..|++|.|.+|.++||+|++++..++...|+.++++|++|+++.+. ++.+..++++..+
T Consensus        88 ~~~~~~~~G~lrI~~~~~~~~~~L~p~L~~F~~~yP~I~l~l~~~~~~~dl~~~~~Dlair~~~~~-~~~~v~~~l~~~~  166 (310)
T PRK09801         88 TQIKTRPEGMIRIGCSFGFGRSHIAPAITELMRNYPELQVHFELFDRQIDLVQDNIDLDIRINDEI-PDYYIAHLLTKNK  166 (310)
T ss_pred             HHHHCCCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCEEEEECCCC-CCCCEEEECCCCC
T ss_conf             753237777459994322778889999999998789739999863765542023665568967889-9871789853563


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEE
Q ss_conf             32112344321112222221100011235664332110002356652022343212114532420013567873842331
Q gi|254780282|r  165 MHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALL  244 (299)
Q Consensus       165 ~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~l  244 (299)
                      .++||||+|+.+++.|.+++||.+++++......... ..|.+. .............+.+|+.+++++++.+|.||+++
T Consensus       167 ~~l~ASP~yl~~~~~P~~~~dL~~h~~l~~~~~~~~~-~~w~~~-~~~~~~~v~~~~~~~~n~~~~~~~aa~~G~GIa~l  244 (310)
T PRK09801        167 RILCAAPEYLQKYPQPQSLQELSRHDCLVTKERDMTH-GIWELG-NGQEKKSVKVSGHLSSNSGEIVLQWALEGKGIMLR  244 (310)
T ss_pred             EEEEECHHHHHHCCCCCCHHHHHCCCEEEECCCCCCC-CCEEEC-CCCCEEEEECCCEEEECCHHHHHHHHHHCCEEEEC
T ss_conf             6898689999857999998998469889844887776-633622-59823799616638998499999999969928999


Q ss_pred             EHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             1777601---998466177666766008999348778888999999999999850
Q gi|254780282|r  245 PDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       245 p~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      |.+++.+   +|+||+++|++. ++.++|++|++++..++++|+|+|||.+..++
T Consensus       245 p~~~v~~~l~~G~Lv~vlpd~~-~~~~~~~vy~~~~~~~~rvr~fidfl~~~~~~  298 (310)
T PRK09801        245 SEWDVLPFLESGKLVQVLPEYA-QSANIWAVYREPLYRSMKLRVCVEFLAAWCQQ  298 (310)
T ss_pred             CHHHHHHHHHCCCEEEECCCCC-CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf             7999999987899089698888-99868999968987787999999999999999


No 4  
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=100.00  E-value=0  Score=392.13  Aligned_cols=288  Identities=22%  Similarity=0.275  Sum_probs=252.6

Q ss_pred             CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEE-EEECCCCCCCCCCCCCCCCCHH
Q ss_conf             8889999999999827-6899998828997899999999999958821797699468-5001343322222222221012
Q gi|254780282|r    3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTEQGSKLHRVTSEVYHKLETT   80 (299)
Q Consensus         3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~-lT~~G~~l~~~a~~~l~~~~~~   80 (299)
                      ||++||+||++|+++| |||+||++||+||||||++|++||++||++||+|+++++. ||++|+.|+++++.++..++++
T Consensus         1 MdL~qLryf~~va~~~~sft~AA~~L~iSQpavS~~I~~LE~~LG~~Lf~R~~~r~~~LT~aG~~l~~~a~~il~~~~~~   80 (313)
T PRK12684          1 MNLHQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRVRSLTEPGRIILASVERILQEVENL   80 (313)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             94799999999998699999999997897789999999999985998899999998665988999999999999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CCC-CCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             21001223222222333211100000000013566754200012222222--222-222222222234565432111122
Q gi|254780282|r   81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KDI-DISMDYADCAIRLRKPIQSSSLIQ  157 (299)
Q Consensus        81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~~-~l~~~~~Di~i~~~~~~~~~~l~~  157 (299)
                      ...+.+.....+|+|+||++++++.+++|+.+..|+++||++++++...+  ... .+..|++|+||.......++++..
T Consensus        81 ~~~~~~~~~~~~G~l~ig~~~s~~~~~lp~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l~~  160 (313)
T PRK12684         81 KRVGKDFAAQDQGNLTIATTHTQARYALPAAIAEFKKRYPKVRLSILQGSPTQIAEMVIHDQADLAIATEAIADYKELVS  160 (313)
T ss_pred             HHHHHHHCCCCCCEEECCHHHHHHHHCCCHHHHHHHHHCCCEEEEEEECCHHHHHHHHHCCCCCEEECCCCCCCCCCEEE
T ss_conf             99999740677751411024555751594999999844898089997178899999997799665504357777787389


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH
Q ss_conf             34555433211234432111222222110001123566433211000235665202234321211453242001356787
Q gi|254780282|r  158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL  237 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~  237 (299)
                      .++++++++++++++|+...+.+++++||.++|||.+...+.....    ........+..+...+++++.+++++||.+
T Consensus       161 ~~l~~~~~~~v~~~~hpla~~~~v~l~dL~~~p~I~~~~~~~~r~~----i~~~~~~~g~~p~~~~e~~~~~~i~~~V~~  236 (313)
T PRK12684        161 LPCYQWNHAVVVPPDHPLLERKPLTLEDLAQYPLITYDDAFAGRSK----INKAFALRGLKPDIVLEAIDADVIKTYVEL  236 (313)
T ss_pred             EEEEECCEEEEECCCCCCCCCCCCCHHHHCCCCEEECCCCCCHHHH----HHHHHHHCCCCCCEEEEECCHHHHHHHHHH
T ss_conf             9803221689953898544699999999859998962899858999----999999779987479999979999999995


Q ss_pred             HCCEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             38423311777601--9984661776667660089993487788889999999999998
Q gi|254780282|r  238 GSGIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA  294 (299)
Q Consensus       238 g~Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~  294 (299)
                      |+||+++|...++.  ++.++.++.....+++.+|++|++++++|+++++|+|++.++.
T Consensus       237 GlGi~ilP~~a~~~~~~~~L~~lp~~~~~~~~~~~v~~~k~~~ls~~~r~FIe~l~e~l  295 (313)
T PRK12684        237 GLGVGIVADMAFDPERDRNLRAIPAGHLFGSNVTRVALKQGAYLRGYVYTFIELFSPTL  295 (313)
T ss_pred             CCCHHHHHHHHHCHHHCCCEEEEECCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHC
T ss_conf             98572559998467638987999784677660599999798866899999999987465


No 5  
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=100.00  E-value=0  Score=391.00  Aligned_cols=286  Identities=23%  Similarity=0.335  Sum_probs=252.1

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      ||+++|+||++|+++||||+||++||+||||||++|++||+++|++||+|++||+.||++|+.|+++++.++.+++++.+
T Consensus         1 M~L~~L~~F~~v~~~gs~t~AA~~L~isQ~avS~~i~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~a~~il~~~~~~~~   80 (292)
T PRK11242          1 MLLRHIRYFLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRYARRALQDLEAGRR   80 (292)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             93489999999998099999999988798999999999999969873898899854773699999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             001223222222333211100000000013566754200012222222--2-2222222222223456543211112234
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--K-DIDISMDYADCAIRLRKPIQSSSLIQRK  159 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~-~~~l~~~~~Di~i~~~~~~~~~~l~~~~  159 (299)
                      .+.+..+..+|.|+||++++++.+++++.+.+|++.||+++|++...+  . ...+..|++|+||.... ..++++...+
T Consensus        81 ~l~~~~~~~~G~l~ig~~~~~~~~~l~~~l~~f~~~~P~i~i~l~~~~~~~~~~~l~~~~~D~~i~~~~-~~~~~l~~~~  159 (292)
T PRK11242         81 AIHDVADLSRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMPQERIEALLADDELDVGIAFAP-VHSPEIEAQP  159 (292)
T ss_pred             HHHHHHCCCCCEEEEECHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCEEEEECC-CCCCCCEEEE
T ss_conf             998753577765863024577888738998888864889734899768899999986798557998368-8887725654


Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH
Q ss_conf             555433211234432111-2222221100011235664332110002356652022343212114532420013567873
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNC-REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG  238 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g  238 (299)
                      +++++++++++++|+... +.+++++||.++|||.+............++    ...+..+...++++++.+++++|.+|
T Consensus       160 l~~~~~~~v~~~~h~la~~~~~is~~~L~~~~~i~~~~~~~~~~~~~~~~----~~~~i~~~~~~~~~~~~~~~~~V~~g  235 (292)
T PRK11242        160 LFTETLALVVGRTHPLAARRKPLTLDELADEPLVLLSAEFATREQIDRYF----RRHGITPRVAIEANSISAVLEIVRRG  235 (292)
T ss_pred             ECCCEEEEEEECCCHHHHCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHH----HHCCCCCCEEEEECCHHHHHHHHHHC
T ss_conf             20450799990898042279999999981899899679985799999999----97699985367538899999999979


Q ss_pred             CCEEEEEHHHHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             8423311777601998466177666766008999348778888999999999999
Q gi|254780282|r  239 SGIALLPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       239 ~Gia~lp~~~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      .|++++|.+++.++++++.+..+.+.+.+++|++|++++..++++++|+|++.++
T Consensus       236 ~Gi~ilP~~~~~~~~~l~~i~l~~~~~~r~i~lv~~k~~~~s~~~~~Fid~l~e~  290 (292)
T PRK11242        236 RLATLLPAAIAREHDDLCAVALDPPLPQRTAALLRRKGAYRSAAARAFIELALER  290 (292)
T ss_pred             CEEEEEHHHHHHHCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             9699702898600899899989899870399999989398899999999999863


No 6  
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=100.00  E-value=0  Score=387.80  Aligned_cols=286  Identities=25%  Similarity=0.325  Sum_probs=251.4

Q ss_pred             C-CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH
Q ss_conf             8-889999999999827689999882899789999999999995882179769946850013433222222222210122
Q gi|254780282|r    3 F-DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ   81 (299)
Q Consensus         3 m-d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~   81 (299)
                      | +|++|++|++|+++||||+||++||+||||||++|++||+++|++||+|++|+++||++|+.|++++++++++++++.
T Consensus         5 ~~~L~~L~~F~aVa~~gS~s~AA~~L~~sqsaVS~~I~~LE~~lG~~Lf~R~~r~~~lT~~G~~l~~~a~~il~~~~~~~   84 (295)
T PRK11139          5 LPPLNALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRNRSLLLTEEGQRYFLDIREAFDQLAEAT   84 (295)
T ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCEEECHHHHHHHHHHHHHHHHHHHHH
T ss_conf             94979999999999839999999998869889999999999985984489889953680999999999999999999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             10012232222223332111000000000135667542000122222222222222222222345654321111223455
Q gi|254780282|r   82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLV  161 (299)
Q Consensus        82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~  161 (299)
                      +.+..  ....|+++|+++++++..|+++.|..|+++||++++++..++...++..+++|++|..+. ..++++...+++
T Consensus        85 ~~~~~--~~~~g~l~I~~~~~~~~~~l~p~l~~f~~~~P~i~v~l~~~~~~~~l~~~~~Diai~~~~-~~~~~l~~~~l~  161 (295)
T PRK11139         85 RKLRA--RSAKGALTVSLLPSFAIKWLVPRLSSFNEAHPDIDVRLQAVDRLEDFLRDDVDVAIRYGR-GNWPGLRVEKLL  161 (295)
T ss_pred             HHHHH--HCCCCEEEEEEECCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHCCCCEEEEEEEC-CCCCCEEEEEEE
T ss_conf             99753--077873999996322777633466666610885899999624166663347438999723-776762799940


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCE
Q ss_conf             54332112344321112222221100011235664332110002356652022343212114532420013567873842
Q gi|254780282|r  162 TIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGI  241 (299)
Q Consensus       162 ~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gi  241 (299)
                      .+++++||+|+|+.+.+.+.+++||.+++++.....    ..+..|+...+ .........+.+++...++++|.+|.||
T Consensus       162 ~~~~~~vasp~~~~~~~~~~~~~dL~~~~li~~~~~----~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~v~~G~Gi  236 (295)
T PRK11139        162 DEYLFPVCSPALLNGGKPLKTPEDLARHTLLHDDSR----EDWRAWFRAAG-LNDINVQQGPIFSHSSMALQAAIHGQGV  236 (295)
T ss_pred             CCEEEEEECHHHHHHCCCCCCHHHHHCCCEEEECCC----CHHHHHHHHCC-CCCCCCCCCEEECCHHHHHHHHHHCCEE
T ss_conf             446999988799964799999999818987963696----21588998569-8654678752887899999999959929


Q ss_pred             EEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             3311777601---998466177666766008999348778888999999999999850
Q gi|254780282|r  242 ALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       242 a~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      |++|.+++.+   +|+||.++++...+++++|++|++++..+|++++|+|||.+++.+
T Consensus       237 a~lp~~~v~~~l~~G~Lv~~l~~~~~~~~~~~lv~~~~~~~~p~v~~F~~~L~~~~~~  294 (295)
T PRK11139        237 ALGRRVLAQPEIEAGRLVCPFDIVLPSKNAFYLVCPPSQAELPKVAAFRQWLLAEAAQ  294 (295)
T ss_pred             EECCHHHHHHHHHCCCEEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             9777999999987899799898666788759999808987898999999999998536


No 7  
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=100.00  E-value=0  Score=386.80  Aligned_cols=289  Identities=22%  Similarity=0.279  Sum_probs=248.6

Q ss_pred             CC-CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCH
Q ss_conf             98-88899999999998276899998828997899999999999958821797699468500134332222222222101
Q gi|254780282|r    1 MS-FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLET   79 (299)
Q Consensus         1 m~-md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~   79 (299)
                      |+ ||+++|+||++|+++||||+||++||+||||||++|++||++||++||+|++|++.||++|+.|++++++++..+++
T Consensus         1 m~~m~LrqL~~F~aVa~~gsft~AA~~L~isQpavS~~I~~LE~~LG~~Lf~R~~r~v~lT~~G~~l~~~a~~~l~~l~~   80 (309)
T PRK11013          1 MAAVSLRHIEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEQVIGLTLFERVRGRLHPTVQGLRLFEEVQRSYYGLDR   80 (309)
T ss_pred             CCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99888899999999998099999999988888899999999999979991898899611768899999999999999999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             2210012232222223332111000000000135667542000122222222--2-222222222223456543211112
Q gi|254780282|r   80 TQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--D-IDISMDYADCAIRLRKPIQSSSLI  156 (299)
Q Consensus        80 ~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~-~~l~~~~~Di~i~~~~~~~~~~l~  156 (299)
                      +...+...++..+|+++||++++++.+++|+.+.+|+++||++++++...+.  . ..+..+++|+||.... ..++++.
T Consensus        81 ~~~~~~~~~~~~~G~lri~~~~~~~~~~lp~~l~~f~~~~P~v~v~i~~~~~~~~~~~l~~~~~Dl~l~~~~-~~~~~~~  159 (309)
T PRK11013         81 IVSAAESLREFRQGQLSIACLPVFSQSLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETL-HTPAGTE  159 (309)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEEECC-CCCCCCE
T ss_conf             999999866123676565300678988665231567843898079999898599999997599778996078-8998757


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH
Q ss_conf             23455543321123443211122222211000112356643321100023566520223432121145324200135678
Q gi|254780282|r  157 QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV  236 (299)
Q Consensus       157 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~  236 (299)
                      ..+++.++.+++++++|+...+..++++||.++|||.+....+...    ++.......+..+...+++++..+++.+|.
T Consensus       160 ~~~l~~~~~~~v~~~~hpla~~~~i~~~dL~~~~~i~~~~~~~~r~----~~~~~~~~~g~~~~~~~e~~~~~~~~~lV~  235 (309)
T PRK11013        160 RTELLTLDEVCVLPDGHPLAAKKVLTPDDFQGENFISLSRTDSYRQ----LLDQLFAEHGVKRRMVVETHSAASVCAMVR  235 (309)
T ss_pred             EEEEEEEEEEEECCCCCCCCCCCCCCHHHHCCCCEEECCCCCCHHH----HHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             8886420146754789800049999999973898696389994999----999999976999776999896999999999


Q ss_pred             HHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             738423311777601---998466177666766008999348778888999999999999850
Q gi|254780282|r  237 LGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       237 ~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      +|.|++++|.+.+.+   .|-.+..+  .+..++.++++|+++++.||++++|+|||.++++.
T Consensus       236 ~G~Gvail~~~~~~~~~~~g~~~~pl--~~~~~~~~~lv~~~~r~~s~~~~aF~~~Lr~~a~a  296 (309)
T PRK11013        236 AGLGVSIVNPLTALDYAGSGLVVRPF--SISVPFTVSLIRPLHRPSSALVDAFSEHLQAQAKA  296 (309)
T ss_pred             HCCEEEEECHHHHHHHHHCCEEEEEC--CCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf             79969994699998662199099988--88996189999989997799999999999999999


No 8  
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=100.00  E-value=0  Score=385.31  Aligned_cols=293  Identities=22%  Similarity=0.184  Sum_probs=253.5

Q ss_pred             CCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHH
Q ss_conf             98888999999999982768999988289978999999999999588217976994685001343322222222221012
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETT   80 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~   80 (299)
                      |.++++||++|++|+++|||++||++||+||||||++|++||+++|++||+|++|++.||++|+.|+++++.++.+++++
T Consensus         3 ~~~tL~qL~~F~~va~~gsft~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~v~LT~aG~~l~~~a~~il~~~~~~   82 (307)
T CHL00180          3 LPFTLDQLRILKAIASEGSFKKAAESLYVSQPAVSLQIQNLEKQLNIPLFDRGGRKALLTEAGHLLLRYGERILALCEET   82 (307)
T ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHH
T ss_conf             98489999999999980999999999888878999999999998699928998991010987999999899999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCC--CCCCCCC
Q ss_conf             210012232222223332111000000000135667542000122222222---22222222222234565--4321111
Q gi|254780282|r   81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRK--PIQSSSL  155 (299)
Q Consensus        81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~--~~~~~~l  155 (299)
                      .+.+.+.+...+|+|+||++++++.+++|+.+..|.++||++++++...+.   ...+.+|++|++|....  +...+++
T Consensus        83 ~~~~~~~~~~~~g~lrI~~~~s~~~~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~l  162 (307)
T CHL00180         83 CRALEDLKNLQGGTLIIGASQTTGTYLMPRLIGLFRQKYPQIAVQLQVHSTRRIAWSVANGQIDLAIIGGEVPTELKDNL  162 (307)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCEEEEEECCCCCCCCCCCE
T ss_conf             97799875112586010104066666435889999998889972789779999999998798009997577886667854


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHH
Q ss_conf             22345554332112344321112222221100011235664332110002356652022343212114532420013567
Q gi|254780282|r  156 IQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYC  235 (299)
Q Consensus       156 ~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v  235 (299)
                      ...++++++++++|+++|+...+..++++||.+++||.+............++...+... ......+++++.++++++|
T Consensus       163 ~~~~l~~~~~~lv~~~~hpla~~~~v~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~v  241 (307)
T CHL00180        163 QVTPYAEDELALILPKSHPFAKLKKIQKEDLYRLRFIALDSQSTIRKVIDNILIQNGIDS-SRFKIEMELNSIEAIKNAV  241 (307)
T ss_pred             EEEEEECCCEEEEECCCCHHHCCCCCCHHHHHCCCEEEECCCCCHHHHHHHHHHHCCCCC-CCCEEEEEECCHHHHHHHH
T ss_conf             999943242799973898022399999999817984871799968999999999769984-5542799978099999999


Q ss_pred             HHHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             8738423311777601---9984661776667660089993487788889999999999998
Q gi|254780282|r  236 VLGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA  294 (299)
Q Consensus       236 ~~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~  294 (299)
                      .+|+||+++|...+.+   .|.++.+..+.+...++++++|++++..||++++|+|||.+..
T Consensus       242 ~~g~Gia~lP~~~v~~~~~~g~l~~~~~~~~~~~r~i~lv~~~~r~~s~a~~~F~~~l~~~f  303 (307)
T CHL00180        242 QSGLGAAFVSVSAIEKELELGTLHWAKIENITIKRTLSIITNPNRYRSKAAETFSKEILTLF  303 (307)
T ss_pred             HHCCEEEECCHHHHHHHHHCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHC
T ss_conf             93994998259999989877988999789998504999999795977999999999999854


No 9  
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=100.00  E-value=0  Score=385.58  Aligned_cols=289  Identities=21%  Similarity=0.233  Sum_probs=253.0

Q ss_pred             CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE-EEEECCCCCCCCCCCCCCCCCHH
Q ss_conf             8889999999999827-689999882899789999999999995882179769946-85001343322222222221012
Q gi|254780282|r    3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL-TLTEQGSKLHRVTSEVYHKLETT   80 (299)
Q Consensus         3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~   80 (299)
                      ||+++|+||++|+++| |||+||++|++||||||++|++||++||++||+|+++++ .||++|+.|+++++++++.++++
T Consensus         1 M~l~~L~~f~~vv~~~~Sft~AA~~L~isQ~avS~~I~~LE~~Lg~~Lf~R~~~r~~~LT~~G~~l~~~a~~il~~~~~~   80 (309)
T PRK12682          1 MNLQQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFERHGKRLKGLTEPGKAVLDVIERILREVGNI   80 (309)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             94799999999998699999999997898789999999999985998899889998570188999999999999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             210012232222223332111000000000135667542000122222222--2-2222222222234565432111122
Q gi|254780282|r   81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--D-IDISMDYADCAIRLRKPIQSSSLIQ  157 (299)
Q Consensus        81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~-~~l~~~~~Di~i~~~~~~~~~~l~~  157 (299)
                      ...+........|+|+||++++++.+++|+.+..|+++||++++++..++.  . ..+..|.+|++|.......++++..
T Consensus        81 ~~~~~~~~~~~~G~lrIg~~~~~~~~~lp~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l~~  160 (309)
T PRK12682         81 KRIGDEFSNQDSGTLTIATTHTQARYVLPRVVAKFRKRYPKVNLSLHQGSPDEIAQMVISGEADIGIATESLDDDPDLVT  160 (309)
T ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCHHHHHCCCCCCCCEEE
T ss_conf             99998752567774121243133320386253999987898379998378299999997699764565077778988089


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH
Q ss_conf             34555433211234432111222222110001123566433211000235665202234321211453242001356787
Q gi|254780282|r  158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL  237 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~  237 (299)
                      .++++++++++++++|+.....+++++||.++|||.+............++    ...+..+...++++|.++++++|.+
T Consensus       161 ~~l~~~~~~~v~~~~h~la~~~~i~~~dL~~~p~I~~~~~~~~r~~~~~~~----~~~g~~p~~~~~~~~~~~~~~~v~~  236 (309)
T PRK12682        161 LPCYDWTHAVIVPSDHPLAQKERITLEDLAEYPLITYHPGFTGRSAIDKAF----AAAGLQPDIVLEAIDSDVIKTYVRL  236 (309)
T ss_pred             EEEECCCEEEEECCCCHHHCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHH----HHCCCCCCEEEEECCHHHHHHHHHH
T ss_conf             993315236761699721149999999982899797279986799999999----9779996269999989999999995


Q ss_pred             HCCEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             38423311777601--99846617766676600899934877888899999999999985
Q gi|254780282|r  238 GSGIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR  295 (299)
Q Consensus       238 g~Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r  295 (299)
                      |+||+++|.+.+++  ++++|.++.+...+.+++|++|++++.+++++++|+||+.++..
T Consensus       237 G~Gi~~lp~~~~~~~~~~~Lv~v~~~~~~~~~~~~l~~rk~~~l~~~~~~FId~l~e~l~  296 (309)
T PRK12682        237 GLGVGIIAEMAYRPDRDGDLVALPAGHLFGPNTAWVAVKRGAYLRNYVYDFIELLAPHLS  296 (309)
T ss_pred             CCEEEHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCC
T ss_conf             994242289983376479989997988777617999996966118999999999998729


No 10 
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=100.00  E-value=0  Score=383.07  Aligned_cols=294  Identities=22%  Similarity=0.306  Sum_probs=244.2

Q ss_pred             CC-CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCH
Q ss_conf             98-88899999999998276899998828997899999999999958821797699468500134332222222222101
Q gi|254780282|r    1 MS-FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLET   79 (299)
Q Consensus         1 m~-md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~   79 (299)
                      || ++|++|++|++|+++||||+||++|++||||||++|++||++||++||+|++|++.||++|+.|+++++.+++.+++
T Consensus        11 ~~~~~L~~L~~F~aVa~~gSft~AA~~L~vsqsaVS~~I~~LE~~LG~~Lf~R~~R~l~LT~aG~~l~~~~~~~l~~l~~   90 (311)
T PRK10086         11 LNGWQLSKLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWALKSSLDTLNQ   90 (311)
T ss_pred             CCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCEEEHHHHHHHHHHHHHHHHHHHH
T ss_conf             68587788999999998299999999978698999999999999859843897599168909999999999999999999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             22100122322222233321110000000001356675420001222222222222222222223456543211112234
Q gi|254780282|r   80 TQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRK  159 (299)
Q Consensus        80 ~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~  159 (299)
                      ....+..  ...+|.|+|+++++++..|++|.+.+|.++||+|+|++..++...++..+++|++|+++.. .++++..++
T Consensus        91 ~~~~~~~--~~~~G~LrI~~~~~~~~~~L~p~L~~F~~~~P~i~l~l~~~~~~~dl~~~~~Dlai~~g~~-~~~~l~~~~  167 (311)
T PRK10086         91 EILDIKN--QELSGTLTVYSRPSIAQCWLVPRLADFTRRYPSISLTILTGNENINFQRAGIDLAIYFDDA-PSAQLTHHF  167 (311)
T ss_pred             HHHHHHC--CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHCCCCEEEEEECCC-CCCCCEEEE
T ss_conf             9999735--7867851036772799875169999999618976999996477464102675058994788-999848999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH
Q ss_conf             55543321123443211122222211000112356643---321100023566520223432121145324200135678
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDL---IPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV  236 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~  236 (299)
                      |+++++++||||+|+.+++.+.++++|.+++++.....   ......+..|....+ ....+....+++++.+.++.++.
T Consensus       168 L~~~~~~~vasP~y~~~~~~~~~p~~L~~~~ll~~~~~~~~~~~~~~w~~~~~~~~-~~~~~~~~~~~~~~~~~~~~aa~  246 (311)
T PRK10086        168 LMDESILPVCSPEYAERHALTNNPNNLRHCTLLHDRQAWSNDSGTDEWHSWAQHFG-VNLLPDSSGIGFDRSDLAVIAAM  246 (311)
T ss_pred             CCCCEEEEEECHHHHHHCCCCCCHHHHHHCHHHCCCCCCCCCCCCHHHHHHHHHCC-CCCCCCCCCEEECCHHHHHHHHH
T ss_conf             74662999998899975799999899861633134432246788226664775178-52036788259867899999999


Q ss_pred             HHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCC
Q ss_conf             738423311777601---99846617766676600899934877888899999999999985066
Q gi|254780282|r  237 LGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDWK  298 (299)
Q Consensus       237 ~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~~  298 (299)
                      +|.||+++|.+++.+   +|+||.+++++..+....|.++++++..+|++++|+|||.+++.+-|
T Consensus       247 ~G~Gia~~p~~~v~~~l~~G~LV~~l~~~~~~~~~~~~l~~~~~~~~p~vr~Fid~L~e~~~q~e  311 (311)
T PRK10086        247 NHIGVAMGRKRLVQKRLASGELVAPFGDMEVKCHQHYYVVTLPGRQWPKIEAFIDWLKEQVAQVE  311 (311)
T ss_pred             HCCCEEECCHHHHHHHHHCCCCEEECCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             78998963599999999789988889887788886699997899989899999999999857349


No 11 
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=100.00  E-value=0  Score=384.83  Aligned_cols=290  Identities=20%  Similarity=0.248  Sum_probs=251.4

Q ss_pred             CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEE-EEECCCCCCCCCCCCCCCCCHH
Q ss_conf             8889999999999827-6899998828997899999999999958821797699468-5001343322222222221012
Q gi|254780282|r    3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTEQGSKLHRVTSEVYHKLETT   80 (299)
Q Consensus         3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~-lT~~G~~l~~~a~~~l~~~~~~   80 (299)
                      ||++||+||++++++| |||+||++||+||||||++|++||+++|++||+|+++++. ||++|+.|++++++++...+++
T Consensus         1 M~lrqL~~F~~~v~~~~s~t~AA~~L~iSQpavS~~Ik~LE~eLG~~LF~R~~~r~~~LT~~G~~l~~~a~~il~~~~~~   80 (308)
T PRK12683          1 MNFQQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRRGKRLTGLTEPGKELLQIVERMLLDAENL   80 (308)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             96799999999998689999999997897779999999999996997389869987557876999999999999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             210012232222223332111000000000135667542000122222222---22222222222234565432111122
Q gi|254780282|r   81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQ  157 (299)
Q Consensus        81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~  157 (299)
                      .+.+++......|+|+||++++++.+++|+.+..|+++||+++|++...+.   ...|.+|++|+||........+++..
T Consensus        81 ~~~~~~~~~~~~G~l~Ig~~~~~~~~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l~~  160 (308)
T PRK12683         81 RRLARQFADRDSGRLTVATTHTQARYALPKVVRQFTEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDLVS  160 (308)
T ss_pred             HHHHHHHHCCCCCEEEECCCCHHHHHCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEECCCCCCCCCCCEE
T ss_conf             99998752677762420013201120168466899987899669996078699999997799778806667788877168


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH
Q ss_conf             34555433211234432111222222110001123566433211000235665202234321211453242001356787
Q gi|254780282|r  158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL  237 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~  237 (299)
                      .++++++++++++++|+.....+++++||.++|||.+...+........++    ...+..+...+++++.++++.+|.+
T Consensus       161 ~~l~~~~~~lv~~~~hpla~~~~v~l~dl~~~p~I~~~~~~~~r~~i~~~~----~~~g~~p~~~~e~~~~~~i~~~V~~  236 (308)
T PRK12683        161 FPYYSWHHVVVVPKGHPLTGRENLTLEALAEYPIITYDQGFTGRSHIDQAF----AEAGAVPDIVLTALDADVIKTYVEL  236 (308)
T ss_pred             EEECCCCEEEEECCCCCCCCCCCCCHHHHCCCCEEECCCCCCHHHHHHHHH----HHCCCCCCEEEEECCHHHHHHHHHH
T ss_conf             761245158984699953369999999985999896189982999999999----9779998579999989999999997


Q ss_pred             HCCEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             38423311777601--998466177666766008999348778888999999999999850
Q gi|254780282|r  238 GSGIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       238 g~Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      |+|++++|...++.  +++++.+..+.....+.+|++|+|++++|+++++|+|++.++..+
T Consensus       237 g~Gi~ilp~~~~~~~~~~~lv~l~~~~~~~~~~~~i~~rk~~~Ls~~a~~Fie~l~~~l~~  297 (308)
T PRK12683        237 GMGVGIVAAMAYDPQRDTGLVALDTQHLFEANTTRVALRRGAYLRGYAYRFIEMFAPHLSE  297 (308)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCH
T ss_conf             9847078999987886099799989788766179999909685799999999998886298


No 12 
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00  E-value=0  Score=384.06  Aligned_cols=283  Identities=20%  Similarity=0.222  Sum_probs=243.4

Q ss_pred             CCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHH
Q ss_conf             98888999999999982768999988289978999999999999588217976994685001343322222222221012
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETT   80 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~   80 (299)
                      |+||+++|++|++|+++||||+||++||+||||||++|++||++||++||+|++||+.||++|+.|+++++.++++..++
T Consensus         1 M~m~L~~L~~F~~va~~gsft~AA~~L~isQpavS~~I~~LE~~Lg~~Lf~R~~r~v~lT~~G~~l~~~a~~~l~~~~~~   80 (291)
T PRK10837          1 MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEI   80 (291)
T ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             98869999999999980999999999888878999999999999699228985996524685999999999999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             210012232222223332111000000000135667542000122222222---22222222222234565432111122
Q gi|254780282|r   81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQ  157 (299)
Q Consensus        81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~  157 (299)
                      .+.    ..+..|.++||++++++.+++|+.+..|+++||+++|++..++.   ...+.++++|++|.. .+...+++..
T Consensus        81 ~~~----~~~~~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~~~~D~~i~~-~~~~~~~l~~  155 (291)
T PRK10837         81 EQL----FREDNGAIRIYASSTIGNYILPAMIARYRHDYPQLPLELSVGNSQDVIQAVLDFRVDIGLIE-GPCHSTEIIS  155 (291)
T ss_pred             HHH----HCCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCEEEEC-CCCCCCCEEE
T ss_conf             997----34788629999617999999999999999648993599998888999999980884166741-7889987189


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH
Q ss_conf             34555433211234432111222222110001123566433211000235665202234321211453242001356787
Q gi|254780282|r  158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL  237 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~  237 (299)
                      .+++++++++||+|+|+...+ +++++||.++|||.+............++.    ..+......+++++.++++++|.+
T Consensus       156 ~~l~~~~~~~v~~p~~~l~~~-~i~~~~l~~~~~i~~~~~~~~r~~~~~~~~----~~~~~~~~~~~~~~~~~i~~~v~~  230 (291)
T PRK10837        156 EPWLEDELVVFAAPDSPLARG-PVTLEQLAAAPWILRERGSGTREIVDYLLL----SHLPRFEMAMELGNSEAIKHAVRH  230 (291)
T ss_pred             EEEECCCEEEEECCCCHHHCC-CCCHHHHHCCCEEEECCCCCHHHHHHHHHH----HCCCCCCEEEECCCHHHHHHHHHH
T ss_conf             994414189998788665379-999899807987994499868999999998----548865301312979999999995


Q ss_pred             HCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             38423311777601---998466177666766008999348778888999999999999
Q gi|254780282|r  238 GSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       238 g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      |+||+++|.+++++   .|.|+.+..+.+...+++|++|++++..++++++|+||+.++
T Consensus       231 G~Gia~lp~~~v~~~l~~g~L~~l~~~~~~~~~~~~lv~~k~~~ls~~~~~Fidfl~~a  289 (291)
T PRK10837        231 GLGISCLSRRVIADQLQAGTLVEVAVPLPRLMRTLWRIHHRQKHLSNALQRFLSYCQPA  289 (291)
T ss_pred             CCCEEECCHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             99189724999999987899799707888861279999989786599999999998620


No 13 
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=100.00  E-value=0  Score=380.99  Aligned_cols=288  Identities=20%  Similarity=0.236  Sum_probs=248.6

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      ||+++|+||++|+++||||+||++||+||||||++|++||++||++||+|++||+.||++|+.|+++++.++.+++++.+
T Consensus         1 M~lrqL~~F~aVae~gSfs~AA~~L~isQpavS~~I~~LE~~LG~~LF~R~~r~v~LT~aG~~l~~~a~~il~~~~~~~~   80 (305)
T PRK11151          1 MNIRDLEYLVALAEHKHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAGLLLVDQAKTVLREVKVLKE   80 (305)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCEEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             96799999999997299999999978987899999999999979865898599046888699999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             001223222222333211100000000013566754200012222222--2-2222222222223456543211112234
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--K-DIDISMDYADCAIRLRKPIQSSSLIQRK  159 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~-~~~l~~~~~Di~i~~~~~~~~~~l~~~~  159 (299)
                      .+........|.++||++++++.+++|+++.+|+++||+++|++...+  . ...+..|++|++|.. .+...+++...+
T Consensus        81 ~~~~~~~~~~G~lrig~~~~~~~~llp~~l~~f~~~~P~v~i~l~~~~~~~l~~~l~~g~~D~~i~~-~~~~~~~~~~~~  159 (305)
T PRK11151         81 MASQQGETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILA-LVKESEAFIEVP  159 (305)
T ss_pred             HHHHHCCCCCCEEEEEEHHHHHHHCCCHHHHHHHHCCCCCEEEEEECCCHHHHHHHHCCCCCEEEEE-CCCCCCCCEEEE
T ss_conf             9886317876414311022233323827799986238983799998875777878657885379984-588998726876


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC
Q ss_conf             55543321123443211122222211000112356643321100023566520223432121145324200135678738
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS  239 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~  239 (299)
                      +++++++++++++|+...+..++++||.+++||.+..+.........+..    ..+......+++++.+++.+||.+|.
T Consensus       160 l~~e~l~lv~~~~hpla~~~~i~l~~L~~~~~i~~~~~~~~r~~~~~~~~----~~g~~~~~~~~~~~~~~i~~lV~~G~  235 (305)
T PRK11151        160 LFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCF----EAGADEDTHFRATSLETLRNMVAAGS  235 (305)
T ss_pred             ECCCCEEEEEECCCCCCCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHHH----HCCCCCCEEEEEECHHHHHHHHHHCC
T ss_conf             20462799995898433699989999769988996899859999999999----77999873899944799999999299


Q ss_pred             CEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             423311777601---99846617766676600899934877888899999999999985
Q gi|254780282|r  240 GIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR  295 (299)
Q Consensus       240 Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r  295 (299)
                      |++++|.+.+.+   .+.++.++...+.+.++++++|++++++++++++|+|+|.+...
T Consensus       236 Gv~ilp~~~v~~~~~~~~l~~~pl~~~~~~r~i~lv~r~~~~ls~~~~~~~e~ir~~l~  294 (305)
T PRK11151        236 GITLLPALAVPNERKRDGVCYLPCIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMD  294 (305)
T ss_pred             CEEECCHHHHHHHCCCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHH
T ss_conf             68983599986221269889998889997369999998909878999999999999888


No 14 
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00  E-value=0  Score=378.52  Aligned_cols=290  Identities=17%  Similarity=0.234  Sum_probs=250.0

Q ss_pred             CCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHH
Q ss_conf             98888999999999982768999988289978999999999999588217976994685001343322222222221012
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETT   80 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~   80 (299)
                      |+||++||+||++|+++||||+||++||+||||||++|++||+++|++||+|++||++||++|+.|+++++.++++++.+
T Consensus         3 ~~m~l~qLr~F~av~~~gs~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~R~~r~~~LT~~G~~l~~~a~~il~~~~~~   82 (302)
T PRK09791          3 FQVKIHQIRAFVEVARQGSIRGASRMLNMSQPALSKSIQELEEGLAAQLFFRRSKGVTLTDAGESFYQHASLILEELRAA   82 (302)
T ss_pred             CCCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             88739999999999980999999999789879999999999999599689999998354779999999999999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCC-CCCCCCCCC
Q ss_conf             210012232222223332111000000000135667542000122222222---2222222222223456-543211112
Q gi|254780282|r   81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLR-KPIQSSSLI  156 (299)
Q Consensus        81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~-~~~~~~~l~  156 (299)
                      .+.+.+..+...|+++||++++++..++|+++..|+++||+|+|++...+.   ..++..|++|++|... ....++++.
T Consensus        83 ~~~~~~~~~~~~G~l~Ig~~~~~~~~~lp~~l~~f~~~~P~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~l~  162 (302)
T PRK09791         83 QEDIRQRQGQLAGQINIGMGASISRSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDHEFT  162 (302)
T ss_pred             HHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCCCEE
T ss_conf             99999850676633999862688987119999999998879779999899999999998799778996567887887647


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH
Q ss_conf             23455543321123443211122222211000112356643321100023566520223432121145324200135678
Q gi|254780282|r  157 QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV  236 (299)
Q Consensus       157 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~  236 (299)
                      ..++++++++++++++|+....  .+++|+.+++|+.........    .++.......+..+...++++++.+++++|.
T Consensus       163 ~~~l~~~~~~~v~~~~hpl~~~--~~l~~l~~~~~~~~~~~~~~~----~~~~~~~~~~g~~p~~~~~~~~~~~~~~lv~  236 (302)
T PRK09791        163 FEKLLEKQFAIFCRPGHPAIGA--RSIKQLLDYSWTMPTPHGSYY----KQLSELLDDQAQTPQVGVVCETFSACISLVA  236 (302)
T ss_pred             EEEEEEEEEEEEECCCCCCCCC--CCHHHHHCCCEEEECCCCCHH----HHHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             9997740159998389843579--899998479938757999799----9999999967999856999992999999999


Q ss_pred             HHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             738423311777601---998466177666766008999348778888999999999999850
Q gi|254780282|r  237 LGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       237 ~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      .|.||+++|..++.+   .++++.++.+.+.+.+.+|++|++++.++|++++|++++.+++..
T Consensus       237 ~g~gv~ilp~~~~~~~~~~~~lv~lpl~~~~~~~~~~lv~r~~~~~spa~~~fi~~lr~~~~~  299 (302)
T PRK09791        237 KSDFLSILPEEMGCDPLHGQGLVMLPVSEILPKAAYYLIQRRDSRQTPLTASLITQFRRECGY  299 (302)
T ss_pred             HCCEEEEECHHHHHHHHHCCCEEEEECCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf             789679631999987874899999979998860089999989098899999999999999887


No 15 
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=100.00  E-value=0  Score=374.35  Aligned_cols=288  Identities=18%  Similarity=0.238  Sum_probs=242.3

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      ||+++|+||++|+++||||+||++||+||||||++|++||+++|++||+|++||+.||++|+.|+++++.++..++++..
T Consensus         1 M~lrqLr~F~aVae~gs~s~AA~~L~isQpavS~~I~~LE~~LG~~Lf~R~~r~v~lT~~G~~l~~~a~~il~~~~~~~~   80 (305)
T PRK11233          1 MNFRRLKYFVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTKRGVTPTEAGKILYTHARAILRQCEQAQL   80 (305)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             95799999999998099999999988987899999999999969977998499177988389999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCC-CCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             0012232222223332111-000000000135667542000122222222---222222222222345654321111223
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTI-DLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQR  158 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~-~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~  158 (299)
                      .+.+.....+|+++||+.+ +.+..++++.+.+|+++||++++++...+.   ...+.+|++|+||.... ...+++...
T Consensus        81 ~~~~~~~~~~G~l~ig~~p~~~~~~l~~p~l~~f~~~~P~v~v~l~~~~~~~l~~~l~~g~~Dlai~~~~-~~~~~l~~~  159 (305)
T PRK11233         81 AVHNVGQALSGQVSIGLAPGTAASSITMPLLQAVRAEFPEIVIYLHENSGAVLNEKLINGQLDMAVIYEH-SPVAGVSSQ  159 (305)
T ss_pred             HHHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHCCCEEEEEEECC-CCCCCCEEE
T ss_conf             9997507874049999962155665369999999997894299972388799999987698479998279-898882899


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH
Q ss_conf             45554332112344321112222221100011235664332110002356652022343212114532420013567873
Q gi|254780282|r  159 KLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG  238 (299)
Q Consensus       159 ~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g  238 (299)
                      ++++++++++++++|+   +..+++.|+.+++++.........    ..........+......+++++.+++..+|.+|
T Consensus       160 ~l~~~~l~lv~~~~~p---~~~i~l~~l~~~~~i~~~~~~~~r----~~~~~~~~~~~~~~~~~~e~~~~~~i~~~V~~G  232 (305)
T PRK11233        160 ALLKEDLFLVGTQDCP---GQSVDLNAIAQMNLFLPRDYSAVR----LRVDEAFSLRRLTAKVIGEIESIATLTAAIASG  232 (305)
T ss_pred             EEEECCEEEEECCCCC---CCCCCHHHHCCCCEEECCCCCHHH----HHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHC
T ss_conf             9985358999847788---787899998089989879998499----999999997799984799999699999999979


Q ss_pred             CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH-------HCCC
Q ss_conf             8423311777601---9984661776667660089993487788889999999999998-------5066
Q gi|254780282|r  239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA-------RDWK  298 (299)
Q Consensus       239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~-------r~~~  298 (299)
                      .|++++|.+.+++   .+.++.+.+..+...++++++|++++++||++++|+|+|.+.+       |||-
T Consensus       233 ~GiailP~~~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~r~lspaa~af~d~L~~~~~~p~~e~r~~~  302 (305)
T PRK11233        233 MGVTVLPESAARSLCGAVNGWMSRITTPSMSLSLSLNLSARANLSPQAQAVKEILLSLISSPVMEKRQWQ  302 (305)
T ss_pred             CEEEEEHHHHHHHHHHCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCE
T ss_conf             9789871999998753497699925999866599999989098899999999999997747162788661


No 16 
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=100.00  E-value=0  Score=373.88  Aligned_cols=286  Identities=23%  Similarity=0.281  Sum_probs=250.1

Q ss_pred             CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC-EEEEECCCCCCCCCCCCCCCCCHH
Q ss_conf             8889999999999827-68999988289978999999999999588217976994-685001343322222222221012
Q gi|254780282|r    3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG-LTLTEQGSKLHRVTSEVYHKLETT   80 (299)
Q Consensus         3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~-~~lT~~G~~l~~~a~~~l~~~~~~   80 (299)
                      ||++||+||++|++++ |||+||++||+||||||++|++||++||++||+|.|++ +.||++|+.|++++++++...+++
T Consensus         1 M~l~QLr~f~~va~~~~s~t~AAe~L~iSQPavS~qIk~LE~eLGv~LF~R~gkr~v~LT~~G~~l~~~a~~il~~~~~~   80 (316)
T PRK12679          1 MNFQQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFVRRGKRLLGMTEPGKALLVIAERILNEASNV   80 (316)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             96799999999998689999999997897789999999999995991289808998775888999999999999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             210012232222223332111000000000135667542000122222222--22-222222222234565432111122
Q gi|254780282|r   81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--DI-DISMDYADCAIRLRKPIQSSSLIQ  157 (299)
Q Consensus        81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~~-~l~~~~~Di~i~~~~~~~~~~l~~  157 (299)
                      ...++...+..+|+++||++++++.+++|+.+.+|+++||++++++...+.  .. .+..|++|+||.......++++..
T Consensus        81 ~~~~~~~~~~~~G~l~Ig~~~t~a~~~LP~~l~~F~~~~P~v~l~l~~~~~~~i~~~l~~g~~Dl~i~~~~~~~~p~l~~  160 (316)
T PRK12679         81 RRLADLFTNDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLVA  160 (316)
T ss_pred             HHHHHHHCCCCCCEEEEEEEECCHHCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEECCCCCCCCCCCEE
T ss_conf             99999853887764999985032010381999999986899538998478799999998799885222467789976079


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH
Q ss_conf             34555433211234432111222222110001123566433211000235665202234321211453242001356787
Q gi|254780282|r  158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL  237 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~  237 (299)
                      .++++++++++++++|+...+.+++++||.++|||.+..++.....    +.......+..+..++++++.++++.+|.+
T Consensus       161 ~p~~~~~~~lvvp~~HpLa~~~~vsl~~L~~~plI~~~~g~~~R~~----id~~f~~~G~~p~i~~e~~~~~~i~~~V~~  236 (316)
T PRK12679        161 FPWFRWHHSLLVPLDHPLTQITPLTLESIAKWPLITYRQGITGRSR----IDDAFARKGLLADIVLSAQDSDVIKTYVAL  236 (316)
T ss_pred             EEEEECCEEEEECCCCCCCCCCCCCHHHHCCCCEEEECCCCHHHHH----HHHHHHHCCCCCCEEEEECCHHHHHHHHHH
T ss_conf             9805534135601899512489989999879998950899849999----999999779999779999989999999998


Q ss_pred             HCCEEEEEHHHHC--CCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             3842331177760--199846617766676600899934877888899999999999
Q gi|254780282|r  238 GSGIALLPDYIVK--DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL  292 (299)
Q Consensus       238 g~Gia~lp~~~~~--~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~  292 (299)
                      |+|||++|+..+.  ++++++.+.......+..+|+++++++.+++.+..|+++...
T Consensus       237 GlGvailp~~a~~~~~~~~l~~~~~~~~~~~~~~~~~~~r~~~l~~~~~~Fi~~~~~  293 (316)
T PRK12679        237 GLGIGLVAEQSSGEQEEKNLIRLDTRHLFDANTVWLGLKRGQLQRNYVWRFLELCNA  293 (316)
T ss_pred             CCCEEECHHHHCCCCCCCCEEEECCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHC
T ss_conf             990997014450754689889932634676653899996787556999999997520


No 17 
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=100.00  E-value=0  Score=371.65  Aligned_cols=289  Identities=20%  Similarity=0.216  Sum_probs=243.8

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      |||++|+||++|+++||||+||++|||||||||++|++||++||++||+|++||++||++|+.|+++++.++..++++..
T Consensus         1 M~l~~L~~F~~va~~gs~s~AA~~L~iSQpalS~~I~~LE~~lG~~Lf~R~~r~v~LT~aG~~l~~~a~~il~~~~~~~~   80 (296)
T PRK09906          1 MELRHLRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQDARLILEQAEKAKL   80 (296)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             95799999999998099999999988887899999999999859887998899512787089999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             0012232222223332111000000000135667542000122222222---2222222222223456543211112234
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQRK  159 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~~  159 (299)
                      ....... ..|.++||++++++..++|+++.+|.+.||++++++...+.   ...+..|++|++|.. .+..++++...+
T Consensus        81 ~~~~~~~-~~~~l~ig~~~~~~~~~lp~~l~~f~~~~P~v~v~l~~~~~~~~~~~l~~g~~D~~i~~-~~~~~~~l~~~~  158 (296)
T PRK09906         81 MARKIVQ-EDRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLINTQQEEKLRRGELDVGFMR-HPVYSDEIDYLE  158 (296)
T ss_pred             HHHHHCC-CCCEEEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHCCCCCEEEEE-CCCCCCCEEEEE
T ss_conf             9986506-77138832122569999999999987408986348997580899999986997679873-688998818998


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC
Q ss_conf             55543321123443211122222211000112356643321100023566520223432121145324200135678738
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS  239 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~  239 (299)
                      +++++++++++++|+......++++||.+++||.+.......  ............+..+...+++++..+++++|..|.
T Consensus       159 l~~~~~~~~~~~~hpla~~~~i~~~dl~~~~~i~~~~~~~~~--~~~~~~~~~~~~g~~p~~~~~~~~~~~~~~~v~~G~  236 (296)
T PRK09906        159 LLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISPDPAQSGS--LAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMGL  236 (296)
T ss_pred             EECCEEEEEEECCCCCCCCCCCCHHHHCCCCEEEECCCCCCC--HHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCC
T ss_conf             504607999828981005999899997599879636654760--999999999977999746999898999999999498


Q ss_pred             CEEEEEHHHHCC-CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             423311777601-998466177666766008999348778888999999999999850
Q gi|254780282|r  240 GIALLPDYIVKD-NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       240 Gia~lp~~~~~~-~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      ||+++|.+++.. .++++.++...+.+.+.++++|+++. .+|++++|++|+.++..+
T Consensus       237 Gi~~lP~~~~~~~~~~l~~~pl~~~~~~~~~~l~~r~~~-~spa~~~Fi~~l~e~~a~  293 (296)
T PRK09906        237 GCTIIPGYMNNFNTGQVVFRPLAGNVPSIALLMAWKKGE-MKPALRDFIAIVQERLAS  293 (296)
T ss_pred             EEEECHHHHHHHCCCCEEEEECCCCCCEEEEEEEECCCC-CCHHHHHHHHHHHHHHCC
T ss_conf             999845877310689999998899987028999987999-999999999999998544


No 18 
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=100.00  E-value=0  Score=369.77  Aligned_cols=275  Identities=24%  Similarity=0.317  Sum_probs=241.7

Q ss_pred             HHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCC
Q ss_conf             99999999982768999988289978999999999999588217976994685001343322222222221012210012
Q gi|254780282|r    7 KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQE   86 (299)
Q Consensus         7 ~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~   86 (299)
                      ||+||++|+++||||+||++|||||||||++|++||++||++||+|++|++.||++|+.|++++++++...+++...+++
T Consensus         1 qL~~F~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~v~lT~~G~~l~~~a~~il~~~~~~~~~~~~   80 (279)
T TIGR03339         1 QLKAFHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVELFHRNGRRLELTDAGHRLLPIVERLFQQEAEAEFLLRE   80 (279)
T ss_pred             CHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             97899999980999999999888889999999999998598859998982589948889999999999999999999985


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             232222223332111000000000135667542000122222222---22222222222234565432111122345554
Q gi|254780282|r   87 SSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQRKLVTI  163 (299)
Q Consensus        87 ~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~  163 (299)
                      ..+...|+++||++   +..++++.+.+|+++||++++++...+.   ...|..|++|++|.. .+..++++...+++++
T Consensus        81 ~~~~~~g~l~ig~~---~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~~~~~L~~~~~Di~i~~-~~~~~~~~~~~~l~~~  156 (279)
T TIGR03339        81 SGALREGSLRIAAT---APYYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSS-EVVDDPRLDRVVLGND  156 (279)
T ss_pred             CCCCCCCEEEECCC---HHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCEEEEEEC-CCCCCCCEEEEEEECC
T ss_conf             02787451686175---1778999999999858986057895580877754025965899972-7889998399994044


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEE
Q ss_conf             33211234432111222222110001123566433211000235665202234321211453242001356787384233
Q gi|254780282|r  164 HMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIAL  243 (299)
Q Consensus       164 ~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~  243 (299)
                      +++++++++|+......++++|+.++|||.++......    ..+.......+..+...+++++..+++++|.+|.|+|+
T Consensus       157 ~~~~~~~~~~~la~~~~i~~~~l~~~~~i~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G~Giai  232 (279)
T TIGR03339       157 PLVAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTR----QTTEEALAAAGVAPRPALEIGSREAIREAVLAGLGVSV  232 (279)
T ss_pred             CEEEEEECCCHHHCCCCCCHHHHCCCCEEEECCCCCHH----HHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCCEEEE
T ss_conf             48999918863323999999997699989828998399----99999999779987536778969999999997993897


Q ss_pred             EEHHHHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHH
Q ss_conf             1177760199846617766676600899934877888899999999
Q gi|254780282|r  244 LPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNF  289 (299)
Q Consensus       244 lp~~~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~  289 (299)
                      +|...+.++++++.++...+.+.+++|++|++++..+|++++|+|+
T Consensus       233 lP~~~v~~~~~l~~~pl~~~~~~~~~~l~~~~~r~~sp~~~aFie~  278 (279)
T TIGR03339       233 VSAAEVGRDPRLRVLPIVGAEPTMDEYLYCLKERRGARLIAAFLEL  278 (279)
T ss_pred             EEHHHHHHCCCEEEEECCCCCCCCEEEEEEECCCCCCHHHHHHHHH
T ss_conf             1489961098989998988898627999998998689999999965


No 19 
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=100.00  E-value=0  Score=368.87  Aligned_cols=286  Identities=23%  Similarity=0.250  Sum_probs=250.6

Q ss_pred             CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE-EEEECCCCCCCCCCCCCCCCCHH
Q ss_conf             8889999999999827-689999882899789999999999995882179769946-85001343322222222221012
Q gi|254780282|r    3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL-TLTEQGSKLHRVTSEVYHKLETT   80 (299)
Q Consensus         3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~-~lT~~G~~l~~~a~~~l~~~~~~   80 (299)
                      ||++||+||++|+++| |||+||++|++||||||++|++||++||++||+|+||++ .+|++|+.|++++++++..++++
T Consensus         1 M~l~QLryf~~va~~~~n~t~AA~~L~iSQPavS~qIk~LE~eLGv~LF~R~gr~l~~LT~aG~~l~~~a~~iL~~~~~i   80 (324)
T PRK12681          1 MKLQQLRYIVEVVNHNLNVSATAESLYTSQPGISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRIAREILSKVESI   80 (324)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             94699999999997699999999997897779999999999984996189889988860988999999999999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             21001223222222333211100000000013566754200012222222--22-2222222222234565432111122
Q gi|254780282|r   81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMDYADCAIRLRKPIQSSSLIQ  157 (299)
Q Consensus        81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~~~Di~i~~~~~~~~~~l~~  157 (299)
                      ...+++......|+|+||++++++.+++|+.+.+|+++||+|++++...+  .. ..+..|++|+||........+++..
T Consensus        81 ~~~~~~~~~~~~G~L~Ia~~~t~a~~~LP~~i~~F~~~~P~v~l~l~~~~~~~i~~~l~~g~~DlaI~~e~~~~~~dl~~  160 (324)
T PRK12681         81 KSVAGEHTWPDKGSLYIATTHTQARYALPPVIKGFIKRYPRVSLHMHQGSPTQIAEAAAKGEADFAIATEALHLYDDLIM  160 (324)
T ss_pred             HHHHHHHCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCEE
T ss_conf             99999752887634999853588887725999999987899844653178799999998799872312466666887468


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH
Q ss_conf             34555433211234432111222222110001123566433211000235665202234321211453242001356787
Q gi|254780282|r  158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL  237 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~  237 (299)
                      .++++++.+++++++|+......++++||.++|+|.+..+....    ..........+..+..++++++.++++.+|..
T Consensus       161 ~P~~~~~~~vvvp~~HPLa~~~~itl~dL~~~plI~~~~g~~~R----~~id~~f~~~g~~P~iv~e~~~~~~I~~~V~~  236 (324)
T PRK12681        161 LPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGR----SELDTAFNRAGLTPRIVFTATDADVIKTYVRL  236 (324)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCCCHHHHCCCCEEEECCCCCHH----HHHHHHHHHCCCCCEEEEEECCHHHHHHHHHH
T ss_conf             64000322245799996557999999998699859614998299----99999999889976079998989999999995


Q ss_pred             HCCEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             38423311777601--99846617766676600899934877888899999999999
Q gi|254780282|r  238 GSGIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL  292 (299)
Q Consensus       238 g~Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~  292 (299)
                      |+||+++|...+..  +.+|+.+.....-.....|++|+++..+++.+..|++.+..
T Consensus       237 GlGV~ilp~mA~~~~~d~~l~~~~~~~~f~~~~t~i~~r~g~~l~~~~~~Fi~~~~p  293 (324)
T PRK12681        237 GLGVGVIASMAVDPVADPDLVAIDASHLFAHSTTKIGFRRGTFLRSYMYDFIERFAP  293 (324)
T ss_pred             CCEEEECHHHHCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHC
T ss_conf             991397035551965578817843655677764799997997157999999998612


No 20 
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00  E-value=0  Score=367.89  Aligned_cols=286  Identities=21%  Similarity=0.236  Sum_probs=241.4

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      .+|++|++|++|+++||||+||++||+||||||++|++||++||++||+|++|+++||++|+.|+++++.++.+++++..
T Consensus         2 ~~~~~L~~F~aVa~~gSft~AA~~L~isqsaVS~~I~~LE~~LG~~Lf~R~~r~v~LT~aG~~ll~~a~~il~~~~~~~~   81 (300)
T PRK11074          2 WSEYSLEVVDAVARNGSFSAAAQELHKVPSAVSYTVRQLEEWLAVPLFERRHRDVELTPAGEWFLKEARSVLKKMEETRR   81 (300)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98899999999997099999999978887899999999999959963998799669996289999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCC-CCCCCCCC
Q ss_conf             00122322222233321110000000001356675420001222222--22-2222222222223456543-21111223
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILD--NK-DIDISMDYADCAIRLRKPI-QSSSLIQR  158 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~--~~-~~~l~~~~~Di~i~~~~~~-~~~~l~~~  158 (299)
                      .+.....+.+|+++|+++.+++..++++.+.+|.++||+|++++...  +. ...+.+|++|++|...... ..+++..+
T Consensus        82 ~~~~~~~~~~G~lri~~~~~~~~~~l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dlai~~~~~~p~~~~~~~~  161 (300)
T PRK11074         82 QTQRVANGWRGQLSIALDNIVRPDRTRQLIADFYRHFDDVELIIRQEVFNGVWDALADGRADIAIGATRAIPVGGRFAFR  161 (300)
T ss_pred             HHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEECCCCCCCCCCEEEE
T ss_conf             99976269842599986533578999999999999886957999976636799999769977899437677888865788


Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH
Q ss_conf             455543321123443211-1222222110001123566433211000235665202234321211453242001356787
Q gi|254780282|r  159 KLVTIHMHAYAAPHYLKN-CREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL  237 (299)
Q Consensus       159 ~l~~~~~~~v~~~~~~~~-~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~  237 (299)
                      +++..++++|++++|+.. .+.+.+.++|.++|+|.+.+..........|...        ....+.+++.++++++|.+
T Consensus       162 ~l~~~~~~~v~~~~hpLa~~~~~l~~~~l~~~p~i~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~v~~  233 (300)
T PRK11074        162 DMGMLSWAFVVSSDHPLALMDGPLSDDELRPYPSICLEDTSRTLPKRITWLLD--------NQRRLVVPDWESAINCLSA  233 (300)
T ss_pred             ECCCCEEEEEECCCCHHHCCCCCCCHHHHHHCCEEEECCCCCCCCCCCEEEEC--------CCCEEEECCHHHHHHHHHH
T ss_conf             81442056674589755408998999999619778862662223210003545--------7647998989999999996


Q ss_pred             HCCEEEEEHHHHC---CCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             3842331177760---19984661776667660089993487788889999999999998506
Q gi|254780282|r  238 GSGIALLPDYIVK---DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW  297 (299)
Q Consensus       238 g~Gia~lp~~~~~---~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~  297 (299)
                      |+||+++|.++++   ++|+|+.+..+.+.+..+++++|+++. .+|++++|+|||.+..+.|
T Consensus       234 GlGia~lP~~~~~~~l~~G~Lv~l~~~~~~~~~~~~lv~~~~~-~sPa~r~fld~L~d~~~~~  295 (300)
T PRK11074        234 GLGVGMVPTHFAKPLIESGKLVEKTLENPKPDSPCCLTWNQND-MSPALAWLLDYLGDSETLN  295 (300)
T ss_pred             CCEEEHHHHHHHHHHHHCCCEEEECCCCCCCCEEEEEEECCCC-CCHHHHHHHHHHHCCHHHH
T ss_conf             9968940699999996089999982788888538999988999-9989999999983710022


No 21 
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=100.00  E-value=0  Score=365.67  Aligned_cols=286  Identities=16%  Similarity=0.186  Sum_probs=246.4

Q ss_pred             CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             88999999999982768999988289978999999999999588217976994685001343322222222221012210
Q gi|254780282|r    4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE   83 (299)
Q Consensus         4 d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~   83 (299)
                      +++||+||++|+++||||+||++||+||||||++|++||++||++||+|++||+.||++|+.|+++++.++++++++.+.
T Consensus         8 ~~rqL~~F~aVa~~gS~t~AA~~L~iSQpavS~~I~~LE~eLG~~LF~R~~r~v~LT~~G~~l~~~a~~il~~~~~~~~~   87 (312)
T PRK10341          8 KTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTPAGQVLLSRSESITREMKNMVNE   87 (312)
T ss_pred             CHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCEECHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             67799999999981999999999888878999999999998498528988998616788999999999999999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--C-CCCCCCCCCCCCCCC-CCCCCCCCCCCCC
Q ss_conf             01223222222333211100000000013566754200012222222--2-222222222222345-6543211112234
Q gi|254780282|r   84 LQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--K-DIDISMDYADCAIRL-RKPIQSSSLIQRK  159 (299)
Q Consensus        84 ~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~-~~~l~~~~~Di~i~~-~~~~~~~~l~~~~  159 (299)
                      +........|+++||++++++..++|+.+.+|.+.||++++++...+  . ...+.+|++|++|.. ..+...+++...+
T Consensus        88 ~~~~~~~~~~~l~ig~~~~~~~~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~  167 (312)
T PRK10341         88 INGMSSEAVVDVSFGFPSLIGFTFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLHVEP  167 (312)
T ss_pred             HHHHCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCEEEEEECCCCCCCCCEEEEE
T ss_conf             98722687325743540688999999999999998889779999899999999996698619997436877778749999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC
Q ss_conf             55543321123443211122222211000112356643321100023566520223432121145324200135678738
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS  239 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~  239 (299)
                      +++++++++++++|+...  +.+++||.+++||.+............++    ...+......+++++..+++++|.+|.
T Consensus       168 l~~~~~~lv~~~~~p~~~--~~~l~~L~~~~~il~~~~~~~~~~~~~~~----~~~g~~~~~~~~~~s~~~i~~lv~~g~  241 (312)
T PRK10341        168 LFESEFVLVASKSRTCTG--TTTLESLKNEQWVLPQTNMGYYSELLTTL----QRNGISIENIVKTDSVVTIYNLVLNAD  241 (312)
T ss_pred             EECCCEEEEECCCCCCCC--CCCHHHHCCCCEEEECCCCCHHHHHHHHH----HHCCCCCCCEEEECHHHHHHHHHHHCC
T ss_conf             512428999767542348--97989980798686069985899999999----976999881699890999999999799


Q ss_pred             CEEEEEHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             423311777601--99846617766676600899934877888899999999999985
Q gi|254780282|r  240 GIALLPDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR  295 (299)
Q Consensus       240 Gia~lp~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r  295 (299)
                      |++++|.+++.+  +++++.++...+.+.+.++++|++++.++|++++|+|++.+.+.
T Consensus       242 gi~~lP~~~~~~~~~~~L~~lpl~~~~~~~~~~lv~~k~~~ls~a~~~fie~~ke~~s  299 (312)
T PRK10341        242 FLTVIPCDMTSPFGSNQFITIPIKETLPVARYAAVWSKNYRIKKAASVLVELAKEYSS  299 (312)
T ss_pred             EEEEEHHHHHHHHCCCCEEEEECCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHCC
T ss_conf             5897269999663189899998999885118999998939889999999999998706


No 22 
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PMID:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PMID: 15150242).
Probab=100.00  E-value=0  Score=358.93  Aligned_cols=284  Identities=19%  Similarity=0.206  Sum_probs=237.1

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      |||++|++|++|+++||||+||++||+||||||++|++||++||++||+| +|++.||++|+.|++++++++...+++..
T Consensus         1 mdl~~L~~F~aVa~~gSfs~AA~~L~~sqsaVS~~I~~LE~~LG~~Lf~R-tr~v~LT~aG~~l~~~a~~i~~~~~~~~~   79 (292)
T TIGR03298         1 LDYKQLAALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLA   79 (292)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHEEC-CCCCEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98899999999998199999999978887899999999999829623188-99980488999999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CCCC-CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             001223222222333211100000000013566754200012222222--2222-2222222223456543211112234
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KDID-ISMDYADCAIRLRKPIQSSSLIQRK  159 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~~~-l~~~~~Di~i~~~~~~~~~~l~~~~  159 (299)
                      .+........|+++|++++.....|+.|.+..|.+.+ ++.+++..++  ...+ +..|.+|++|.... .+.+++..++
T Consensus        80 ~~~~~~~~~~g~l~i~~~~~~~~~~l~p~l~~f~~~~-~v~l~l~~~~~~~~~d~l~~g~~~~ai~~~~-~~~~~~~~~~  157 (292)
T TIGR03298        80 ELPGLAPGAPVTLSIAVNADSLATWFLPALAPVLAQE-GVLLDLVVEDQDHTAELLRSGEVLGAVTTQA-KPVQGCRVVP  157 (292)
T ss_pred             HHHCCCCCCCEEEEEEECHHHHHHHHHHHHHHHHHCC-CCEEEEEECCCHHHHHHHHCCCEEEEEECCC-CCCCCCEEEE
T ss_conf             8752477774258887635778887899999999808-9879998545245899985697589997578-8898867999


Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH
Q ss_conf             555433211234432111-2222221100011235664332110002356652022343212114532420013567873
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNC-REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG  238 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g  238 (299)
                      |+++++++|++|+|+.++ +.+.++++|.++|++.+.......   ..+...........  +...++|.++++++|.+|
T Consensus       158 L~~~~~~~vasP~~~~~~~~~~~~~~~L~~~p~l~~~~~~~~~---~~~~~~~~~~~~~~--~~~~v~s~~~~~~~v~aG  232 (292)
T TIGR03298       158 LGAMRYLAVASPAFAARYFPDGVTAEALARAPVIVFNRKDDLQ---DRFLRRLFGLPVSP--PRHYVPSSEGFVEAARAG  232 (292)
T ss_pred             CCCEEEEEEECHHHHHHCCCCCCCHHHHHCCCEEEECCCCCHH---HHHHHHCCCCCCCC--CEEEECCHHHHHHHHHHC
T ss_conf             1140189998889998628999999999369879965996478---99998505777665--168988899999999949


Q ss_pred             CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             8423311777601---9984661776667660089993487788889999999999998506
Q gi|254780282|r  239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW  297 (299)
Q Consensus       239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~  297 (299)
                      +||+++|.+++++   +|+||+++|+++   .++.++|++++..||++++|+||+.+.+|.|
T Consensus       233 lGia~lP~~~v~~~l~~G~LV~llp~~~---~~~~l~~~~~r~~s~~~r~f~d~l~~~ar~~  291 (292)
T TIGR03298       233 LGWGMVPELQAEPHLAAGRLVDLAPGRA---LDVPLYWHHWRLESRVLERLTDAVVAAARRA  291 (292)
T ss_pred             CEEEECCHHHHHHHHHCCCEEEECCCCC---CCCCEECCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             9889696999999985898588499987---9821648066867889999999999999864


No 23 
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=100.00  E-value=0  Score=354.08  Aligned_cols=284  Identities=18%  Similarity=0.205  Sum_probs=244.4

Q ss_pred             CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEE-EEECCCCCCCCCCCCCCCCCHH
Q ss_conf             8889999999999827-6899998828997899999999999958821797699468-5001343322222222221012
Q gi|254780282|r    3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT-LTEQGSKLHRVTSEVYHKLETT   80 (299)
Q Consensus         3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~-lT~~G~~l~~~a~~~l~~~~~~   80 (299)
                      ||++||+||++|++++ |||+||++||+|||+||++|++||++||++||+|+||++. ||++|+.++++++.++..++++
T Consensus         1 M~L~QLr~f~aVa~~~~n~s~AA~~L~iSQPaVSkqIk~LE~eLGv~LF~R~gr~l~~LT~aG~~ll~~a~~iL~~~~~i   80 (327)
T PRK12680          1 MTLTQLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRKGRSLDSVTPAGVEVIERARAVLSEVNNI   80 (327)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             92899999999996589999999997897679999999999985996699879987767786999999999999999999


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             21001223222222333211100000000013566754200012222222--22-2222222222234565432111122
Q gi|254780282|r   81 QIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMDYADCAIRLRKPIQSSSLIQ  157 (299)
Q Consensus        81 ~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~~~Di~i~~~~~~~~~~l~~  157 (299)
                      .....+.....+|+++||++++.+.+++|+++.+|+++||+|++++...+  .. ..+.+|++|+||.......++++..
T Consensus        81 ~~~~~~~~~~~~G~L~Ig~~~t~a~~~LP~vi~~f~~~yP~V~l~l~~~~~~~l~e~l~~g~~Diai~~~~~~~~~~~~~  160 (327)
T PRK12680         81 RTYAANQRRESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAVVSTAGGEPSAGIA  160 (327)
T ss_pred             HHHHHHHCCCCCEEEEEEEECHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEECCCCCCCCCCEE
T ss_conf             99998625887337999984227777568999999986899679999898288999997899409994477779976547


Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH
Q ss_conf             345554332112344321-1122222211000112356643321100023566520223432121145324200135678
Q gi|254780282|r  158 RKLVTIHMHAYAAPHYLK-NCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV  236 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~~~~-~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~  236 (299)
                      .+++.++.+++++++|+. ..+.+++++||.++|||.+..+.....    .+.......+..+..++++++.++++.+|+
T Consensus       161 ~pl~~~~~~vvvP~~HpL~~~~~~i~L~~La~~plI~~~~g~~~r~----~id~af~~~Gl~P~iv~ea~~~d~Ik~~V~  236 (327)
T PRK12680        161 VPLYRWRRLVVVPRGHALDTPRTAPDMAALAEHPLISYDSSTRPGS----SLQRAFAQVGLEPSIALTALDADLIKTYVR  236 (327)
T ss_pred             EEEEECCEEEEEECCCCCCCCCCCCCHHHHHCCCEEECCCCCCHHH----HHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             6752235799997898100589999999980898896389986799----999999977997647999995999999999


Q ss_pred             HHCCEEEEEHHHHCC-CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             738423311777601-998466177666766008999348778888999999999
Q gi|254780282|r  237 LGSGIALLPDYIVKD-NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI  290 (299)
Q Consensus       237 ~g~Gia~lp~~~~~~-~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l  290 (299)
                      .|+|||++|+..++. +.+|+.+.....-.....|++++++..+..-+=.|++..
T Consensus       237 ~GlGV~Ivp~mA~~~~d~~l~~~~~~~l~~~~~~~~~~~~~~~lr~~~~~fi~~~  291 (327)
T PRK12680        237 AGLGVGLVAEMAVNAFDEDLRAWPAPAPIAECIAWAVLPRDRVLRDYALDLVHVL  291 (327)
T ss_pred             HCCEEEECHHHHHCCCCCCEEEEECCCCCCCCEEEEEEECCCHHHHHHHHHHHHH
T ss_conf             4986188164762876898389406457775605999978846899999999986


No 24 
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=100.00  E-value=0  Score=350.68  Aligned_cols=282  Identities=22%  Similarity=0.276  Sum_probs=232.5

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      ||+++|++|++|+++||||+||++||+||||||++|++||++||++||+|++|++.||++|+.|+++|+.++..++++..
T Consensus         2 mDl~~Lr~F~aVae~gSfs~AA~~L~isqsavS~~I~~LE~~LGv~Lf~Rt~R~v~LT~aG~~l~~~a~~il~~~~~~~~   81 (308)
T PRK10094          2 FDPETLRTFIAVAETGSFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQARDWLSWLESMPS   81 (308)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89899999999998199999999978987899999999999969963997799743988999999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCCC-CCCCCCCCCC
Q ss_conf             001223222222333211100-000000013566754200012222222---22222222222223456-5432111122
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDL-GQNLLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIRLR-KPIQSSSLIQ  157 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~-~~~~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~~~-~~~~~~~l~~  157 (299)
                      .+++...+..|+++|++++.+ ...++++++..|+++||++++++....   ...++..+++|++|.+. .+...+++..
T Consensus        82 ~l~~~~~~~~g~l~i~~~~~~~~~~~l~~ll~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~dl~i~~~~~~~~~~~~~~  161 (308)
T PRK10094         82 ELQQVNDGVERQVNIVINNLLYNPQAVASLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALANTFSL  161 (308)
T ss_pred             HHHHHHCCCCCEEEEEECCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHCCCCCEEEEECCCCCCCCCEEE
T ss_conf             99864158754499995220111667999999999978998899996023347999974997299993688778887699


Q ss_pred             CCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH
Q ss_conf             3455543321123443211-122222211000112356643321100023566520223432121145324200135678
Q gi|254780282|r  158 RKLVTIHMHAYAAPHYLKN-CREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV  236 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~~~~~-~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~  236 (299)
                      .+++++++++||+++|+.. .+.+.+.+++..++++.+............|     ..   .....+.+++.++++.+|.
T Consensus       162 ~~l~~~~~~~v~~~~hpla~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~-----~~---~~~~~~~~~~~~~~~~~v~  233 (308)
T PRK10094        162 DPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAW-----RL---PGQKEIIVPDMETKIAAHL  233 (308)
T ss_pred             EECCCCHHHHHHCCCCHHHCCCCCCCHHHHHHCCEEEECCCCCCHHHHHEE-----EE---CCCCEEEECCHHHHHHHHH
T ss_conf             993130233210789844528999999999619656730651100020125-----50---7875499898999999999


Q ss_pred             HHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             738423311777601---998466177666766008999348778888999999999999
Q gi|254780282|r  237 LGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       237 ~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      +|+|||++|.+++++   +|+||.+..+...++++++++|+++. .+|+++.|+|++.+.
T Consensus       234 aGlGia~lP~~~v~~~l~~G~LV~~~l~~~~~~~~l~l~wr~~~-~~~~v~~~i~l~~~~  292 (308)
T PRK10094        234 AGVGIGFLPKSLCQSMIDNQQLVSRVIPTMRPPSPLSLAWRKFG-SGKAVEDIVTLFTQR  292 (308)
T ss_pred             HCCEEECCHHHHHHHHHHCCCEEEEECCCCCCCEEEEEEEECCC-CCHHHHHHHHHHHHC
T ss_conf             79988923499999998789889996899999808999997799-987999999999871


No 25 
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=100.00  E-value=0  Score=344.27  Aligned_cols=284  Identities=19%  Similarity=0.213  Sum_probs=228.5

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      |||++|++|++|+++||||+||++||+||||||++|++||+++|++||+| +|++.||++|+.|+++++.+....+++.+
T Consensus         2 md~~~L~~F~aVa~~Gsfs~AA~~L~~sqsavS~~I~~LE~~LG~~Lf~R-tR~~~LT~aG~~l~~~a~~i~~~~~~~~~   80 (294)
T PRK13348          2 LDYKQLEALAAVVETGSFERAARRLHVTRSAVSQRIKALEESLGQPLLVR-TRPCRPTPAGQRLLRHLRQVALLEADLLS   80 (294)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEC-CCCCEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89899999999998099999999978887899999999999839843888-99973558999999999999999999998


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--C-CCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             0012232222223332111000000000135667542000122222222--2-222222222223456543211112234
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--D-IDISMDYADCAIRLRKPIQSSSLIQRK  159 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~-~~l~~~~~Di~i~~~~~~~~~~l~~~~  159 (299)
                      .+... ....+.++++++......++.+.+..|.++ |++.+++..++.  . ..+.+|.+|++|... +...+++..++
T Consensus        81 ~~~~~-~~~~~~l~i~~~~~~~~~~l~p~l~~~~~~-p~~~l~l~~~~~~~~~~~l~~g~~d~ai~~~-~~~~~~~~~~~  157 (294)
T PRK13348         81 TLPAE-RGSPITLAIAVNADSLATWFLPALASVLAG-ERILLELIVDDQDHTFALLERGEVVGCVSTQ-SKPMRGCLAEP  157 (294)
T ss_pred             HHHHC-CCCCCEEEEEECHHHHHHHHHHHHHHHHHC-CCCEEEEEECCCHHHHHHHHCCCCEEEEECC-CCCCCCCEEEE
T ss_conf             76533-678603899975678898779999999856-7977888734513689999749412445337-88888856898


Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH
Q ss_conf             555433211234432111-2222221100011235664332110002356652022343212114532420013567873
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNC-REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG  238 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g  238 (299)
                      ++..++++|++|+|...+ ..+.+++++...|++.+........   .+.... ........+...++|.++++++|.+|
T Consensus       158 l~~~~~~~vasp~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~---~~~~~~-~~~~~~~~~~~~~~s~~~~~~~v~~G  233 (294)
T PRK13348        158 LGTMRYRCVAAPAFAARYFPQGLTRHSALKAPAVAFNRKDTLQS---SFLQRL-FGLPVGAYPRHYVPSTHAHLAAIRHG  233 (294)
T ss_pred             CCCEEEEEEECHHHHHHCCCCCCCHHHHHCCCEEEECCCCCHHH---HHHHHC-CCCCCCCCCEEEECCHHHHHHHHHHC
T ss_conf             22515999987789986078999988982598899659971668---999864-68876766468989799999999979


Q ss_pred             CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             8423311777601---9984661776667660089993487788889999999999998506
Q gi|254780282|r  239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW  297 (299)
Q Consensus       239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~  297 (299)
                      +||+++|.+++++   +|+||+++|++   +.+++++|++++..||++++|+|||.+.+|+|
T Consensus       234 ~Gi~~lP~~~v~~~l~~G~Lv~vlp~~---~~~v~l~~~~~~~~~p~~~af~d~l~~~a~~~  292 (294)
T PRK13348        234 LGYGMVPELLIGPLLAAGRLVDLAPAH---PVDVALYWHHWEVEPPTMEALSQRVVEAARRL  292 (294)
T ss_pred             CEEEECCHHHHHHHHHCCCEEECCCCC---CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             928966499999998489878917999---77147980068868979999999999999996


No 26 
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=100.00  E-value=0  Score=344.73  Aligned_cols=283  Identities=20%  Similarity=0.253  Sum_probs=224.0

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      |||++|++|++|+++|||++||++||+||||||++|++||++||++||+| +|+++||++|+.|+++++++....+++..
T Consensus         2 mdl~~Lr~F~aVa~~GSfs~AA~~L~~tqsaVS~~I~~LE~~LG~~Lf~R-tr~~~LT~aG~~ll~~a~~v~~le~~~~~   80 (295)
T PRK03635          2 LDYKQLEALAAVIREGSFERAAQALHITQSAVSQRIKALEERVGQPLLVR-TQPCRATEAGQRLLRHARQVRLLEAELLG   80 (295)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEC-CCCCEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89899999999998099999999978886699999999999949723178-99874488899999999999999999998


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CCCC-CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             001223222222333211100000000013566754200012222222--2222-2222222223456543211112234
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KDID-ISMDYADCAIRLRKPIQSSSLIQRK  159 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~~~-l~~~~~Di~i~~~~~~~~~~l~~~~  159 (299)
                      .+.....  .++++|+++......|++|.+.+|.+.|| +.+++..++  ...+ +.+|.+|++|... +.+.+++..++
T Consensus        81 ~~~~~~~--~~~l~l~~~~~~l~~~l~p~l~~f~~~~p-v~l~l~~~~~~~~~~~l~~g~~~~ai~~~-~~~~~g~~~~~  156 (295)
T PRK03635         81 ELPALDP--PLRLSIAVNADSLATWFLPALAPVLAQHG-VLLDLVVDDQDHTLELLRRGEVLGAVTTE-AQPVAGCRVDP  156 (295)
T ss_pred             HHHCCCC--CCEEEECCCHHHHHHHHHHHHHHHHHHCC-EEEEEEECCHHHHHHHHHCCCEEEEEECC-CCCCCCCEEEE
T ss_conf             7207688--82675034603788988999999998174-25777744407799999569627999658-87788867887


Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH
Q ss_conf             555433211234432111-2222221100011235664332110002356652022343212114532420013567873
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNC-REPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG  238 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g  238 (299)
                      |+..++++||+|+|..++ +.+.+++||.++|+|.++.....   .+.+..... .......+.+.++|.++++++|.+|
T Consensus       157 L~~~~~~~vAsP~~~~~~~~~~~~~~~L~~~p~l~~~~~~~~---~~~~~~~~~-~~~~~~~~~~~~~s~~a~~~av~aG  232 (295)
T PRK03635        157 LGAMRYLAVASPAFAARYFPDGVTAAALAKAPAVVFNRKDDL---QDRFLRRLF-GLPPGSVPCHYVPSSEGFVRAALAG  232 (295)
T ss_pred             CCCCEEEEEECHHHHHHHCCCCCCHHHHHCCCEEEECCCCCH---HHHHHHHCC-CCCCCCCCEEEECCHHHHHHHHHHC
T ss_conf             256369999878999972799999999943987883698737---899998646-8776767658989899999999969


Q ss_pred             CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             8423311777601---9984661776667660089993487788889999999999998506
Q gi|254780282|r  239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW  297 (299)
Q Consensus       239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~  297 (299)
                      +||+++|.+++++   +|+||+++|+++   .++.++|++.+..||++++|+|||.+.++||
T Consensus       233 lGia~lP~~~v~~~L~~G~LV~llp~~~---~~~~l~~~~~r~~s~~l~~~~~~l~~~~~~~  291 (295)
T PRK03635        233 LGWGMIPELQAEPELASGELVDLTPGRP---LDVPLYWHHWRLESRLLDRLTDALLAAAAQV  291 (295)
T ss_pred             CEEEECHHHHHHHHHHCCCEEEECCCCC---CCCCEECCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             9089881999999984898188798997---9800516244547889999999999999987


No 27 
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=100.00  E-value=0  Score=342.63  Aligned_cols=269  Identities=21%  Similarity=0.246  Sum_probs=222.1

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      |||++|++|++|+++|||++||++||+||||||++|++||++||++||+|++||+.||++|+.|+++|+.+++..+++..
T Consensus         1 Md~~~L~~F~~va~~gsft~AA~~L~isQsavS~~Ik~LE~~LG~~Lf~R~~~~~~LT~~G~~l~~~A~~il~~~~~~~~   80 (275)
T PRK03601          1 MDTELLKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTAAGEKLLPYAETLMNTWQAARK   80 (275)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98799999999998099999999978987899999999999969832998799432998899999999999999999999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             0012232222223332111000000000135667542000122222222---2222222222223456543211112234
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQRK  159 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~~  159 (299)
                      ++...  ...|.++||++++++..++++.+.+|++.||+++|++..++.   ..+|.+|++|++|....| ..+++..++
T Consensus        81 ~~~~~--~~~~~l~ig~~~~~~~~~l~~~l~~~~~~~P~v~l~l~~~~~~~~~~~L~~~~~Dl~i~~~~p-~~~~l~~~~  157 (275)
T PRK03601         81 EVAHT--SRHNEFSIGASASLWECMLNQWLGRLYQNQEELQFEARIAQRQSLVKQLHERQLDLLITTEAP-KMDEFSSQL  157 (275)
T ss_pred             HHHHC--CCCCCEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCC-CCCCEEEEE
T ss_conf             99725--677609999775778999999999999978896799998898999999977993589977799-888847999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC
Q ss_conf             55543321123443211122222211000112356643321100023566520223432121145324200135678738
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS  239 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~  239 (299)
                      ++++++++++++.+.....          .+++........    ..+...   .......+.+++++.++++++|.+|.
T Consensus       158 l~~~~l~l~~s~~~~~~~~----------~~~i~l~~~~~~----~~~~~~---~~~~~~~p~~~~~s~~~~~~~v~~g~  220 (275)
T PRK03601        158 LGHFTLALYTSAPSKNKSE----------LNYLRLEWGPDF----QQHEAG---LIGADEVPILTTSSAELARQQLATLN  220 (275)
T ss_pred             ECCEEEEEEECCCCCCCCC----------CCEEEEECCCCH----HHHHHH---HCCCCCCCEEEECHHHHHHHHHHHCC
T ss_conf             5235689997786433468----------875882067206----799975---23567798588578999999999789


Q ss_pred             CEEEEEHHHHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             42331177760199846617766676600899934877888899999999999
Q gi|254780282|r  240 GIALLPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL  292 (299)
Q Consensus       240 Gia~lp~~~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~  292 (299)
                      |++++|.+++++.|+++.+ ++.+..++++|++|+|++..++.++.|+++...
T Consensus       221 Gia~LP~~~~~~~g~L~~v-~~~~~~~rp~y~v~~k~~~~~~~ir~~l~~~~~  272 (275)
T PRK03601        221 GCAWLPVHWAKEKGGLHTV-VDSTTLSRPLYAIWLQNSDKQALIRDLLKIPVL  272 (275)
T ss_pred             CEEECCHHHHHHCCCEEEC-CCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHC
T ss_conf             0999937887118998999-999977147999996889737999999822411


No 28 
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=100.00  E-value=0  Score=345.79  Aligned_cols=273  Identities=18%  Similarity=0.235  Sum_probs=232.3

Q ss_pred             HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCC
Q ss_conf             99982768999988289978999999999999588217976994685001343322222222221012210012232222
Q gi|254780282|r   13 VVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPS   92 (299)
Q Consensus        13 ~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~   92 (299)
                      ||||+||||+||++|++||||||++|++||++||++||+|++|++.||++|+.|++++++++..++++...+........
T Consensus         1 AVae~~sft~AAe~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~v~LT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~   80 (278)
T PRK09986          1 AVAEELHFGRAAARLNMSQPPLSIHIKELEDQLGTLLFIRHSRSVALTHAGKILMEESRRLLDNANNALARVEQIGRGEA   80 (278)
T ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             92255989999999888888999999999998599869999997708988999999999999999999999998635777


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             22333211100000000013566754200012222222---222222222222234565432111122345554332112
Q gi|254780282|r   93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYA  169 (299)
Q Consensus        93 g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~~~~v~  169 (299)
                      |+|+||+.+++...++++.+.+|+++||++++++....   ....|.++++|+||........+++...+++.+++++++
T Consensus        81 g~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~v~i~~~~~~~~~~~l~~~~~D~a~~~~~~~~~~~~~~~~l~~~~~~~~~  160 (278)
T PRK09986         81 GRIELGVVGTALWGRMRPAMRHFLKENPNVEVLFREKSPSMQMALLERRELDAGIWRMALEPNPGFTSLRLHESAFAVAV  160 (278)
T ss_pred             CCEEEEECHHHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCCCEEEEEEECCCEEEE
T ss_conf             73368742168887642899999987898399999788699999997799758996377778877426887741637996


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEEEHHHH
Q ss_conf             34432111222222110001123566433211000235665202234321211453242001356787384233117776
Q gi|254780282|r  170 APHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIV  249 (299)
Q Consensus       170 ~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~lp~~~~  249 (299)
                      +++|+......++++||.+++||.+.......    .+........+..+...+++++..+++++|.+|+|++++|++++
T Consensus       161 ~~~hpla~~~~i~~~~l~~~~~i~~~~~~~~~----~~~~~~~~~~g~~~~~~~~~~~~~~~~~~V~~G~Giailp~~~~  236 (278)
T PRK09986        161 PEEHLLASKSSVPLKALRNEYFVTLPSVHSDW----GFLQRVCQQAGFSPQIIREVNEPQTVLAMVSMGIGITLVADSYA  236 (278)
T ss_pred             CCCCCCCCCCCCCHHHHCCCCEEEECCCCCHH----HHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCCEEEEEHHHHH
T ss_conf             59873336999999998599979867998669----99999999779985179999989999999997998998417774


Q ss_pred             CCC-CCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf             019-984661776667660089993487788889999999999
Q gi|254780282|r  250 KDN-PNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIF  291 (299)
Q Consensus       250 ~~~-~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~  291 (299)
                      +.. ++++.+ |-.+.+++.++++|+++. .+|++++|+++|.
T Consensus       237 ~~~~~~v~~~-Pl~~~~~~~~~lv~~~~~-~~p~~~~fi~~l~  277 (278)
T PRK09986        237 QMPWPGVVFR-PLKERIPADLYIVYHQQQ-ATPALEKLLAALT  277 (278)
T ss_pred             CCCCCCEEEE-ECCCCCCEEEEEEECCCC-CCHHHHHHHHHHC
T ss_conf             2378999999-889998038999984999-9999999999865


No 29 
>PRK10082 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00  E-value=0  Score=341.20  Aligned_cols=285  Identities=20%  Similarity=0.245  Sum_probs=222.5

Q ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH
Q ss_conf             88889999999999827689999882899789999999999995882179769946850013433222222222210122
Q gi|254780282|r    2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ   81 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~   81 (299)
                      |||+++|++|++|+++||||+||++||+||||||++|++||++||++||+|++|++.||++|+.|+++++.+++++++..
T Consensus        10 nmelr~L~~F~~Vae~gSFs~AA~~L~itQpavS~~I~~LE~~LGv~Lf~R~tr~v~LT~aG~~~~~~a~~il~~le~~~   89 (303)
T PRK10082         10 NIETKWLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQVTPLQLSEQGKIFHSQIRHLLQQLESNL   89 (303)
T ss_pred             CCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHH
T ss_conf             66299999999999809999999997898159999999999996995086799983036889999999999999999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCC
Q ss_conf             1001223222222333211100000000013566754200012222222222222222222234565-432111122345
Q gi|254780282|r   82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRK-PIQSSSLIQRKL  160 (299)
Q Consensus        82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~-~~~~~~l~~~~l  160 (299)
                      ..++.......|+++|+++++++.+++|+.++.|...+|..-..+..++....+.+|.+|+++.+.+ +.....+...++
T Consensus        90 ~~l~~~~~~~~g~l~i~a~~~~~~~~Lp~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~~l~~~~~~~~~l  169 (303)
T PRK10082         90 AELRGGSDYAQRKIKIAAAHSLSLGLLPSIISQMPPLFTWAIEAIDVDEAVDKLREGQSDCIFSFHDEDLLEAPFDHIRL  169 (303)
T ss_pred             HHHHCCCCCCCCEEEEEECHHHHHHHHHHHHHHHHHHCCEEEEEECHHHHHHHHHCCCCCEEEECCCCCCCCCCCCEEEE
T ss_conf             99860545675469998317769999999999744127767885048999999987997199983564334477632466


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCC
Q ss_conf             55433211234432111222222110001123566433211000235665202234321211453242001356787384
Q gi|254780282|r  161 VTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSG  240 (299)
Q Consensus       161 ~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~G  240 (299)
                      +.++++++|++++   ++.+....+..++|++.+.............+   .+.........+++++.++++++|.+|+|
T Consensus       170 ~~~~~~~v~~~~~---~~~~~~~~~~~~~pll~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~l~~~v~~G~G  243 (303)
T PRK10082        170 FESQLFPVCASDE---HGEALFNLAQPHFPLLNYSRNSYMGRLINRTL---TRHSELSFSTFFVSSMSELLKQVALDGCG  243 (303)
T ss_pred             ECCCEEEEECCCC---CCCCCCCCCCCCCCEEECCCCCCHHHHHHHHH---HHCCCCCCCEEEEECHHHHHHHHHHHCCE
T ss_conf             3262699986886---68878664367986796589970879998877---53566667627997589999999996999


Q ss_pred             EEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             23311777601---998466177666766008999348778888999999999999
Q gi|254780282|r  241 IALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       241 ia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      |+++|.+++++   +|+|+.+.+++...++.+| +|+++++++|++++|+++|.|.
T Consensus       244 Ia~lP~~~V~~el~~G~Lv~l~~d~~~~~~~~y-~~~~~~~lsP~a~~F~~~Lre~  298 (303)
T PRK10082        244 IAWLPEYAIQQEIRSGRLVVLNRDELVIPIQAY-AYRMNTRMNPVAERFWRELREL  298 (303)
T ss_pred             EEECCHHHHHHHHHCCCCEEECCCCCCCCEEEE-EEECCCCCCHHHHHHHHHHHHH
T ss_conf             998829999999878981895664565731799-9989898898999999999987


No 30 
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=100.00  E-value=0  Score=323.71  Aligned_cols=287  Identities=13%  Similarity=0.141  Sum_probs=235.5

Q ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH
Q ss_conf             88889999999999827689999882899789999999999995882179769946850013433222222222210122
Q gi|254780282|r    2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ   81 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~   81 (299)
                      +||+|+|++|.+|+++||||+||++||+||||||++|++||+.||++||+|+|+|++||+.|+.++++++++++.+++..
T Consensus        21 ~~DLNLL~~F~al~e~~svtrAA~~L~vSQpAvS~aL~rLr~~~gd~LFvR~grg~~pT~~a~~L~~~~~~~L~~i~~~~  100 (314)
T PRK09508         21 MVDLNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLVQNEL  100 (314)
T ss_pred             HCCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             15877899999999829999999997898669999999999981995488349935429989999999999999999762


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1001223222222333211100000000013566754200012222222--22-22222222222345654321111223
Q gi|254780282|r   82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMDYADCAIRLRKPIQSSSLIQR  158 (299)
Q Consensus        82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~~~Di~i~~~~~~~~~~l~~~  158 (299)
                      ...........+.++|+++.++...++|+++..|.+.+|+++|++....  .. ..|..|++|++|.... ..++++...
T Consensus       101 ~~~~f~p~~~~~~~~i~~~~~~~~~llp~ll~~~~~~~P~v~l~~~~~~~~~~~~~L~~g~iDl~I~~~~-~~~~~~~~~  179 (314)
T PRK09508        101 PGSGFEPESSERVFNLCICSPLDNRLASQIYNRIEQIAPNIHLVFKSSLNQNIEHQLRYQETEFVISYEE-FDRPEFTSV  179 (314)
T ss_pred             HHCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEECCC-CCCCCCEEE
T ss_conf             1213681004736999963078999999999999986899779998577064999997699529996787-799873489


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH
Q ss_conf             45554332112344321112222221100011235664332110002356652022343212114532420013567873
Q gi|254780282|r  159 KLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG  238 (299)
Q Consensus       159 ~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g  238 (299)
                      +|++++++++|+++||... .+++.+++..++++..... ...    ..........+..+...++++++.++..+|..|
T Consensus       180 ~L~~d~~v~v~~~~HP~~~-~~lt~~~~~~~~hv~~s~~-~~~----~~~~~~l~~~~~~r~i~~~~~s~~~~~~lv~~t  253 (314)
T PRK09508        180 PLFKDELVLVASKNHPRIK-GPILEEQLYNEQHAVVSLD-RFA----SFSQPWYDTVDKQASIAYQGMALSSVLNVVSQT  253 (314)
T ss_pred             EEEECCEEEEECCCCCCCC-CCCCHHHHHHCCCEEEECC-CCC----CHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHC
T ss_conf             9972464999829997678-9999999961998899639-988----589999995798631899958899999999839


Q ss_pred             CCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             8423311777601---99846617766676600899934877888899999999999985
Q gi|254780282|r  239 SGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR  295 (299)
Q Consensus       239 ~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r  295 (299)
                      .|++++|.++++.   .+.+..+.++.+.+.++++++||++...+|+.++|.+-|.+-+|
T Consensus       254 d~ia~lP~~~a~~~~~~~~l~~~~lP~~~~~~~~~l~WH~r~~~dp~~~WlR~~i~~v~~  313 (314)
T PRK09508        254 HLVAIAPRWLAEEFAESLELQILPLPLKNNSRTCYLSWHESAGRDKGHQWMEDLLVSICK  313 (314)
T ss_pred             CEEEHHHHHHHHHHHHCCCCEEECCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHC
T ss_conf             977589999999864429957978998988736999978998899899999999999975


No 31 
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=100.00  E-value=0  Score=311.87  Aligned_cols=288  Identities=30%  Similarity=0.356  Sum_probs=235.2

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      ||+++|++|++|+++|||++||++|++||||||++|++||++||++||+|+++++.||++|+.++++++.++..++++..
T Consensus         1 ~~l~~L~~F~~v~~~gs~t~AA~~L~isq~avS~~I~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   80 (297)
T COG0583           1 MDLRQLRAFVAVAEEGSFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTRRVRLTEAGERLLERARRILAELEEALA   80 (297)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98789999999984599899998839990589999999999849864886799845588899999999999999999999


Q ss_pred             HCCCCCCCCC-CCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCC-CCCCCC
Q ss_conf             0012232222-223332111000000000135667542000122222222-2222222222223456543211-112234
Q gi|254780282|r   83 ELQESSVKPS-GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK-DIDISMDYADCAIRLRKPIQSS-SLIQRK  159 (299)
Q Consensus        83 ~~~~~~~~~~-g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~-~~~l~~~~~Di~i~~~~~~~~~-~l~~~~  159 (299)
                      .+........ +.++|+++++++..++++.+.+|.+.||++.+++...+. ..++..+++|++|....+ ..+ ++...+
T Consensus        81 ~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~l~~f~~~~P~~~~~~~~~~~~~~~l~~~~~D~~i~~~~~-~~~~~~~~~~  159 (297)
T COG0583          81 EAARLARGEPGGLLRIAAPSTAASSLLPPLLARFRARYPEIELELGTSDRLLEDLVEGELDLAIRAGPP-PPPDGLVARP  159 (297)
T ss_pred             HHHHHCCCCCCCEEEEEECCHHHHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHCCCCEEEEEECCC-CCCCCEEEEE
T ss_conf             997512567775599996707679999999999999789839998256649999877993499995886-6888746889


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC
Q ss_conf             55543321123443211122222211000112356643321100023566520223432121145324200135678738
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS  239 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~  239 (299)
                      ++.++++++++++|+...+..  ++++..++++.+....................    ....+++++..+++++|.+|.
T Consensus       160 l~~~~~~~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~v~~g~  233 (297)
T COG0583         160 LFSEELVLVVPASHPLAARHG--LPDLPGEPLILLEHGCILRRLLDQALALAGWR----PRIRLEVNSAEALLQAVAAGL  233 (297)
T ss_pred             EECCCEEEEEECCCHHHHCCC--CCCCCCCHHHCCCCCCHHHHHHHHHHHHCCCC----CCCEEEECCHHHHHHHHHHCC
T ss_conf             603647999957846651478--64477241230676531577667788862466----686599990999999999699


Q ss_pred             CEEEEEHHHHCCC--CCEEEECCCCC-CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf             4233117776019--98466177666-7660089993487788889999999999998506
Q gi|254780282|r  240 GIALLPDYIVKDN--PNLVRIMEDVI-TPSFTVYFCYPEALKNTGKLKAFRNFIFLKARDW  297 (299)
Q Consensus       240 Gia~lp~~~~~~~--~~lv~i~~~~~-~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~~  297 (299)
                      |++++|..++...  +..+.+.+... .....+|++|++++..+++++.|++++.+..++.
T Consensus       234 gi~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  294 (297)
T COG0583         234 GIALLPESLARPDLAGRLVRVLPLPPPPLPRPLYLVWRKSRLLSPAVRAFIDFLREALARL  294 (297)
T ss_pred             CEEEECHHHHHHHHCCCCEEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             8386419999887548918995477788776399999588668989999999999997653


No 32 
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=100.00  E-value=0  Score=311.63  Aligned_cols=261  Identities=21%  Similarity=0.239  Sum_probs=213.6

Q ss_pred             HCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             28997899999999999958821797699468500134332222222222101221001223222222333211100000
Q gi|254780282|r   27 LHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQN  106 (299)
Q Consensus        27 L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~~~~~~~~~  106 (299)
                      |||||||||++|++||+++|++||+|++|++.||++|+.|+++|++++.+++++...+.......+|+|+||++.+.+.+
T Consensus         1 LhvSQpavS~~I~~LE~~lG~~Lf~R~~r~v~LT~~G~~l~~~a~~il~~~~~~~~~~~~~~~~~~G~lri~~~~t~~~~   80 (269)
T PRK11716          1 MHVSPSTLSRQIQRLEEELGQPLFVRDNRSVTLTEAGEELRPFAQQTLLQWQQLKHTLDQQQPSLSGELSLFCSVTAAYS   80 (269)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECHHHHHH
T ss_conf             90855899999999999969965998899875878999999999999999999999998405687662699851488777


Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCC
Q ss_conf             0000135667542000122222222---222222222222345654321111223455543321123443211-122222
Q gi|254780282|r  107 LLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKN-CREPLS  182 (299)
Q Consensus       107 ~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~~~~v~~~~~~~~-~~~~~~  182 (299)
                      ++|+.+.+|+++||+|++++...+.   ...+.+|++|+||.......++++...++++++++++++.++... .....+
T Consensus        81 ~lp~~l~~f~~~~P~v~~~l~~~~~~~~~~~l~~g~~D~ai~~~p~~~~~~l~~~~l~~~~l~~v~p~~~~~~~~~~~~~  160 (269)
T PRK11716         81 HLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPSSLAFSPIDEIPLVLIAPALPCPVRQQVSQE  160 (269)
T ss_pred             HCCHHHHHHHHHCCCCEEEEECCCHHHHHHHHHCCCCCEEEEECCCCCCCCEEEEEEEEEEEEEEEECCCCHHHCCCCCC
T ss_conf             54678999999888944898428999999999869955899937878999769999656418999978841543635688


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEEEHHHHCCC---CCEEEEC
Q ss_conf             2110001123566433211000235665202234321211453242001356787384233117776019---9846617
Q gi|254780282|r  183 IQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKDN---PNLVRIM  259 (299)
Q Consensus       183 ~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~lp~~~~~~~---~~lv~i~  259 (299)
                      ..|+.++|+|....... ......|+..    .+..+...+++++.+++++||.+|+|++++|+++++++   ++++.+.
T Consensus       161 ~~dl~~~p~il~~~~~~-r~~~~~~~~~----~~~~p~i~~e~~~~~~i~~~V~~G~GiailP~~~~~~~~~~~~l~~l~  235 (269)
T PRK11716        161 KPDWSRIPFILPEHGPA-RRRIDLWFRR----HKIKPNIYAQVSGHEAIVSMVALGCGVGILPEVVLDNSPVRDRVQRLE  235 (269)
T ss_pred             HHHHHCCCEEECCCCCH-HHHHHHHHHH----CCCCCCEEEEECCHHHHHHHHHHCCEEEEHHHHHHHCCCCCCCEEEEE
T ss_conf             44683386781589827-9999999997----699971799989799999999979941720599983275579889974


Q ss_pred             CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             766676600899934877888899999999999
Q gi|254780282|r  260 EDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL  292 (299)
Q Consensus       260 ~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~  292 (299)
                      ...+.++++++++|++++..+|++++|+|++.+
T Consensus       236 ~~~~~~~~~i~l~~~~~r~~sPa~~aF~~~l~~  268 (269)
T PRK11716        236 VPPELTPFELGVCCQKKRLHEPLIDAFWQLLEN  268 (269)
T ss_pred             CCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             899887369999997998679999999999965


No 33 
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=100.00  E-value=0  Score=306.88  Aligned_cols=280  Identities=19%  Similarity=0.196  Sum_probs=231.0

Q ss_pred             CC-CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCH
Q ss_conf             98-88899999999998276899998828997899999999999958821797699468500134332222222222101
Q gi|254780282|r    1 MS-FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLET   79 (299)
Q Consensus         1 m~-md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~   79 (299)
                      |+ ||++||+||++|+++|||++||++|++||||||++|++||+++|++||+|++|++.||++|+.+++||++++...++
T Consensus         1 m~~ln~~~L~~F~~va~~gs~~~Aa~~L~~tq~~vS~qi~~LE~~lg~~Lf~R~~r~~~lT~~G~~~~~~a~~i~~l~~e   80 (296)
T PRK11062          1 MSHLNYNHLYYFWMVYKEGSVVGAAEALFLTPQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADKMFTLSYE   80 (296)
T ss_pred             CCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEECCCCEEECHHHHHHHHHHHHHHHHHHH
T ss_conf             99888899999999998099999999968981799999999999959910998899828858999999999999999999


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCCCCCC--CCCCCC
Q ss_conf             2210012232222223332111000000000135667542000122222222---22222222222234565--432111
Q gi|254780282|r   80 TQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAIRLRK--PIQSSS  154 (299)
Q Consensus        80 ~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i~~~~--~~~~~~  154 (299)
                      +.+.++. .....+.++||+..+++..++++++..+.+.+|++++.+..++.   ..+|..+++|+++.-.+  +...++
T Consensus        81 l~~~~~~-~~~~~~~lrvGi~~tl~k~~~~~lL~~~~~~~~~v~l~~~eg~~~~LL~~L~~~~LDlvLsd~p~~~~~~~~  159 (296)
T PRK11062         81 MLDIVNY-RKESNLLFDVGVADALSKRLVSRVLLAAVPEDESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEG  159 (296)
T ss_pred             HHHHHHH-CCCCCCEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHCCCCCEEEECCCCCCCCCCC
T ss_conf             9999850-457770599985246469899999999972289779999349879999999838987576068887556886


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHH
Q ss_conf             12234555433211234432111222222110001123566433211000235665202234321211453242001356
Q gi|254780282|r  155 LIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQY  234 (299)
Q Consensus       155 l~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~  234 (299)
                      +.+.+|++.++.+++++.+...    ..+++|.+.|++.++..++.......|+...    +..+..+.++||..++..+
T Consensus       160 ~~s~~L~~~~v~~~~~~~l~~~----~fP~~L~~~plllp~~~S~lR~~ld~wf~~~----gI~P~Iv~E~dD~allk~~  231 (296)
T PRK11062        160 LFSKKLGECGVSFFCTNPLPEK----PFPACLEERRLLIPGRRTMLGRKLLNWFNSQ----GLNVEILGEFDDAALMKAF  231 (296)
T ss_pred             EEEEECCCCCEEEEECCCCCCC----CCHHHHCCCCCCCCCCCCHHHHHHHHHHHHC----CCCCEEEEEECCHHHHHHH
T ss_conf             3898746684689845744458----7957755798402799875899999999968----9984499985989999999


Q ss_pred             HHHHCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHH
Q ss_conf             78738423311777601---998466177666766008999348778888999999999
Q gi|254780282|r  235 CVLGSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFI  290 (299)
Q Consensus       235 v~~g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l  290 (299)
                      +..|.|++++|..++++   .++++.+ ...+...-.+|+++.+++...|++++..|.-
T Consensus       232 a~~G~Gva~~P~~v~~d~~~~~~l~~~-g~~~~v~e~fyAIt~~R~~~hP~v~~i~~~~  289 (296)
T PRK11062        232 GAYHDAIFVAPSIYAQDIYADHSVVEI-GRVENVKEEYHVIFAERMIQHPAVQRICNTD  289 (296)
T ss_pred             HHHCCCEEECCHHHHHHHHHCCCCEEE-CCCCCCEEEEEEEECCCCCCCHHHHHHHHHH
T ss_conf             981998898789999999857991894-4578842679998504468986999999999


No 34 
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ; InterPro: IPR012787    Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate . Members occur only in proteobacteria.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0019619 protocatechuate catabolic process, 0045941 positive regulation of transcription.
Probab=100.00  E-value=0  Score=297.14  Aligned_cols=292  Identities=18%  Similarity=0.194  Sum_probs=254.2

Q ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH
Q ss_conf             88889999999999827689999882899789999999999995882179769946850013433222222222210122
Q gi|254780282|r    2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ   81 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~   81 (299)
                      ++.+|||+.|++|++.||+++||+.|+||||||||.||+||+-+|.+||+|+++|++||++|+.|+++|..-+..+.+..
T Consensus         2 r~KfRHL~~FvEVAR~~Sv~rAae~L~~tQPAvsKTlrELE~~LG~~L~eR~~~GiRlT~~G~~Fl~hAg~Sl~ALR~Gv   81 (300)
T TIGR02424         2 RIKFRHLECFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLLERDRRGIRLTRYGEVFLRHAGASLAALRQGV   81 (300)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             63188899999999988999999862488107889999999872974511478635637221154666658999998658


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCCCCCCCCC-CCCCCCCCCCCCC
Q ss_conf             10012232222223332111000000000135667542000122222222---2222222222223-4565432111122
Q gi|254780282|r   82 IELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISMDYADCAI-RLRKPIQSSSLIQ  157 (299)
Q Consensus        82 ~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~~~~Di~i-~~~~~~~~~~l~~  157 (299)
                      +.+++......-+++||+-||.+..++|..+++|.+++|+..+.|.++..   ...|..|++|++| +.+.|..-.++.+
T Consensus        82 ~~l~~lg~~~~~~~~~GaLPTVaA~L~P~~~~~f~~~~p~~~~~i~tG~n~~Lld~LR~G~LDlVvGRL~ape~MqGl~F  161 (300)
T TIGR02424        82 ASLSQLGEGEGPTVRVGALPTVAARLMPEVVKRFLAEAPRLRLRIVTGENAYLLDQLRVGELDLVVGRLGAPETMQGLSF  161 (300)
T ss_pred             HHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHCCCCCEEEEECCCCCHHHCCCCC
T ss_conf             99998421489648972646689999999999999616895589987785787987228980277606888321158642


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHH
Q ss_conf             34555433211234432111222222110001123566433211000235665202234321211453242001356787
Q gi|254780282|r  158 RKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVL  237 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~  237 (299)
                      ++||.|++.+|+.++||+.....+..+.|.+||.+.+..+..-..-..+++..++.....   ..+++=|...-.+++.+
T Consensus       162 e~LY~E~v~~VVragHPL~~~p~~~~~~L~~yPvl~P~~g~~IR~~~erll~a~G~~~l~---~r~EtvS~~fgR~y~~~  238 (300)
T TIGR02424       162 EHLYNERVVFVVRAGHPLLAAPSLSVASLADYPVLLPPEGSIIRPLVERLLIACGIPALP---QRIETVSDSFGRRYVRE  238 (300)
T ss_pred             CCCCCCCEEEEECCCCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC---CHHHHHHHHHHHHHHHH
T ss_conf             514477337887085785578877778873388104862226799999999874765566---01344315788777645


Q ss_pred             HCCEEEEEHHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             38423311777601---998466177666766008999348778888999999999999850
Q gi|254780282|r  238 GSGIALLPDYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       238 g~Gia~lp~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      ...|=|+|...+..   +|+|+++.-+.....-+++|+.|.+...|++.+.|++.|.+.+.+
T Consensus       239 sdA~WiiS~gvv~~dl~~G~L~~Lp~~~~~t~GPVGL~~R~d~~~s~aaq~f~~alr~~~~~  300 (300)
T TIGR02424       239 SDAVWIISEGVVAKDLADGTLVELPVDTRETAGPVGLCTRPDEQLSRAAQLFVDALRSAAEA  300 (300)
T ss_pred             CCCEEECCHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             47257726678988752892776465757788770215488877898999999999998519


No 35 
>TIGR02036 dsdC D-serine deaminase transcriptional activator; InterPro: IPR011781    This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including Escherichia coli, Vibrio cholerae, and Colwellia psychrerythraea..
Probab=100.00  E-value=0  Score=292.53  Aligned_cols=288  Identities=23%  Similarity=0.327  Sum_probs=244.0

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHH
Q ss_conf             88899999999998276899998828997899999999999958821797699468500134332222222222101221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQI   82 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~   82 (299)
                      ..|-.|.+|.+.|||.||+-||++|.+||||||.||.+||+|||.+||+|+.|+++||.+|+++|-..+.-++.++|=.-
T Consensus         8 fQLSKmHTFEVAARH~SFsLAAeELSltPSAiSHRIN~LEeElGI~LF~RsHRKveLT~EG~RiY~alkssl~~LNQEIl   87 (302)
T TIGR02036         8 FQLSKMHTFEVAARHQSFSLAAEELSLTPSAISHRINKLEEELGIKLFKRSHRKVELTKEGKRIYIALKSSLDSLNQEIL   87 (302)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHCCEEE
T ss_conf             32335667888875133778887531673457775443356521442033565256446774046677876543141210


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             00122322222233321110000000001356675420001222222222222222222223456543211112234555
Q gi|254780282|r   83 ELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVT  162 (299)
Q Consensus        83 ~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~  162 (299)
                      +++  .+..+|.|+|..=|+|++-||.|.|.+|.++||.|.+++.+++..+.+...++|+||.+ +...++.|.++.|.+
T Consensus        88 diK--n~E~SG~LT~YSRPSfAQCWLVPri~~F~~~YPsIsL~~LTGNeNinfqg~GIDvAIYF-Dd~~p~kL~c~~im~  164 (302)
T TIGR02036        88 DIK--NQELSGELTVYSRPSFAQCWLVPRIADFKKRYPSISLKVLTGNENINFQGAGIDVAIYF-DDKQPAKLSCKEIMD  164 (302)
T ss_pred             HHC--CCCCCCCEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCEECCCCCCEEEEEE-CCCCCCCCCHHHHCC
T ss_conf             002--67512102002255333443323232120038712211001535320135750378870-788874212012124


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC
Q ss_conf             43321123443211122222211000112356643---321100023566520223432121145324200135678738
Q gi|254780282|r  163 IHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDL---IPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS  239 (299)
Q Consensus       163 ~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~  239 (299)
                      |.+++||+|.|..+..-.-++..|.+..++.=...   .+....|..|......+ ..+....+.+|-.+.++=++..+.
T Consensus       165 E~I~PVCsPEYAq~~~L~~~~~NL~~cTLLHDnQAW~ydS~tDEW~~WAn~~~~n-~L~~ss~IgFDRSDLAVIAA~Nna  243 (302)
T TIGR02036       165 ETIVPVCSPEYAQKYALTSKVDNLSQCTLLHDNQAWSYDSDTDEWKSWANAYAVN-NLESSSSIGFDRSDLAVIAAMNNA  243 (302)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-HHHHHCCCCCCHHHHHHHHHHHHC
T ss_conf             3313434813555553654456765211100012037888854789888632132-113222367654479999998504


Q ss_pred             CEEEEEHHHHCC---CCCEEEECCCC-CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             423311777601---99846617766-676600899934877888899999999999985
Q gi|254780282|r  240 GIALLPDYIVKD---NPNLVRIMEDV-ITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR  295 (299)
Q Consensus       240 Gia~lp~~~~~~---~~~lv~i~~~~-~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r  295 (299)
                      |||.--..+++.   .|+|++++++. ....-.||+.+.++++.+ +++.|++||.++++
T Consensus       244 GvAMGR~slv~~rl~sGEL~~Pf~d~~v~C~QrYYvaTLPn~~n~-KielFI~WL~~qVk  302 (302)
T TIGR02036       244 GVAMGRKSLVKKRLASGELVKPFIDKKVLCKQRYYVATLPNKKNT-KIELFIEWLKEQVK  302 (302)
T ss_pred             CHHCCHHHHHHHHHCCCCCCCCCCCCEEEECCCEEEECCCCCCCC-HHHHHHHHHHHHCC
T ss_conf             411023789886521675326778865562563067408888770-57888799996349


No 36 
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=100.00  E-value=6.3e-39  Score=244.90  Aligned_cols=260  Identities=17%  Similarity=0.092  Sum_probs=207.0

Q ss_pred             HHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             82899789999999999995882179769946850013433222222222210122100122322222233321110000
Q gi|254780282|r   26 QLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQ  105 (299)
Q Consensus        26 ~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~~~~~~~~  105 (299)
                      .||+||||||++|++||+.||++||+|+|+|++||+.|+.|++.+++.++.+.+..+......  .+++++|++++.+..
T Consensus         1 ~L~lSQsAvS~aL~rLR~~~~DpLFvR~g~g~~PT~~A~~L~~~i~~~l~~i~~~l~~~~~~~--~~~~~~i~~~~~~~~   78 (266)
T PRK11482          1 ILNLTPSAISQSIQKLRVIFPDPLFIRKGQGVTPTAYATHLHEYISQGLESILGALDITGSYD--KQRTITIATTPSVGA   78 (266)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CCEEEEEEECHHHHH
T ss_conf             987687999999999999869950786499726648999999999999999998741568888--652599997588999


Q ss_pred             CCCCCHHHHHHHHHHCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             00000135667542000122222-22222222222222234565432111122345554332112344321112222221
Q gi|254780282|r  106 NLLQGNLKEFLLLYPDIQIQLIL-DNKDIDISMDYADCAIRLRKPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQ  184 (299)
Q Consensus       106 ~~l~~~l~~f~~~~P~i~i~i~~-~~~~~~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~~~~v~~~~~~~~~~~~~~~~  184 (299)
                      .++|.++..+.+.+|++.++... ++....|..|++|++|.... ..++++..+.|++++++++|+++||... .+++++
T Consensus        79 ~~lp~l~~~l~~~aP~i~l~~~~~~~~~~~L~~~~~Dl~i~~~~-~~~~~~~~~~L~~d~~v~v~~~~HP~~~-~~~t~e  156 (266)
T PRK11482         79 LVLPVIYQAIKPHYPQLLLRNIPISDAENQLSQFQTDLIIDTHS-CTNRTIQHHVLFTDNMVLVCRQGHPCLS-LEDDEE  156 (266)
T ss_pred             HHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHCCCCCEEEECCC-CCCCCEEEEEEEECCEEEEEECCCCCCC-CCCCHH
T ss_conf             99999999999779986999568657889985699888985688-8987638999994288999989685569-999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEEEHHHHCC---CCCEEEEC-C
Q ss_conf             1000112356643321100023566520223432121145324200135678738423311777601---99846617-7
Q gi|254780282|r  185 ELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLPDYIVKD---NPNLVRIM-E  260 (299)
Q Consensus       185 dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~lp~~~~~~---~~~lv~i~-~  260 (299)
                      ++..++++.+........    .........+..+...++++++.++..++.....|+++|..+++.   ...++.+. |
T Consensus       157 ~~~~~~Hv~~~~~~~~~~----~~~~~l~~~~~~R~i~~~~~~~~~~~~lv~~tdli~~~P~~la~~~~~~~~L~~lp~p  232 (266)
T PRK11482        157 TLDNAAHTLLLPEGQNFS----GLRQRLQEMFPDRQISFSSYNILTIAALIASSDMLGLMPSRFYNLFSRCWPLEKLPFP  232 (266)
T ss_pred             HHHCCCCEEEECCCCCCC----HHHHHHHHCCCCCEEEEEECCHHHHHHHHHHCCEEEEHHHHHHHHHHHHCCCEEECCC
T ss_conf             996299999976999877----9999999749998599997999999999984999985899999998876798794689


Q ss_pred             CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             666766008999348778888999999999999
Q gi|254780282|r  261 DVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       261 ~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      +...+..+++++||++...+|+.++|+|.+.+.
T Consensus       233 p~~~~~~~~~l~Wh~r~~~DP~~~wlr~~i~e~  265 (266)
T PRK11482        233 SLNEEQIDFSLHYNKLSLRDPVLENVIDVIREA  265 (266)
T ss_pred             CCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf             988996469999885542676899999999986


No 37 
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=100.00  E-value=8.5e-33  Score=209.39  Aligned_cols=264  Identities=13%  Similarity=0.052  Sum_probs=194.6

Q ss_pred             HCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             28997899999999999958821797699468500134332222222222101221001223222222333211100000
Q gi|254780282|r   27 LHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIATTIDLGQN  106 (299)
Q Consensus        27 L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~~~~~~~~~  106 (299)
                      ||+||||||+.+++|++.||++||+|+|+|++||+.++.|.+.++++++.++++......... ...+++|+++..+...
T Consensus         1 L~lSQpAvS~aL~RLR~~f~DpLFvR~g~gm~PT~~A~~L~~~l~~~L~~~~~~~~~~~~~~p-~~~~F~ia~~d~~~~~   79 (288)
T PRK10216          1 MNVTPSAVSKSLAKLRAWFDDPLFVNTPLGLSPTPLMVSMEQNLADWMQMGNQLLDKPHHQTP-RGLKFELAAESPLMMI   79 (288)
T ss_pred             CCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCEEEEEECCHHHHH
T ss_conf             998778999999999998799448960992315668999999999999999997378878985-5707999963678999


Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCC---------CCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             00001356675420001222222--2222222222222234565432---------111122345554332112344321
Q gi|254780282|r  107 LLQGNLKEFLLLYPDIQIQLILD--NKDIDISMDYADCAIRLRKPIQ---------SSSLIQRKLVTIHMHAYAAPHYLK  175 (299)
Q Consensus       107 ~l~~~l~~f~~~~P~i~i~i~~~--~~~~~l~~~~~Di~i~~~~~~~---------~~~l~~~~l~~~~~~~v~~~~~~~  175 (299)
                      ++|+++..+.++.|++.+++...  +....|..|++|++|......+         +..+..+.++++.++++++++||.
T Consensus        80 llp~l~~~i~~~AP~v~l~~~~~~~~~~~~L~~g~iDl~i~~~~~~p~~~~~~~~~p~~~~~~~l~~d~~~v~~r~~HP~  159 (288)
T PRK10216         80 MLNALSQQIYQRYPQATIKLRNWDYDSLDAITRGEVDIGFTGRESHPRSRELLSLLPLAIDFEVLFSDLPCVWLRKDHPA  159 (288)
T ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHCCCCCEEEECCCCCCCCHHHHHCCCCCCCEEEEEEEEEEEEECCCCCC
T ss_conf             99999999997699977996248935599997599768983565686304555127643431799960069998089943


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC--CEEEEEHHHHC---
Q ss_conf             1122222211000112356643321100023566520223432121145324200135678738--42331177760---
Q gi|254780282|r  176 NCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS--GIALLPDYIVK---  250 (299)
Q Consensus       176 ~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~--Gia~lp~~~~~---  250 (299)
                      .. ..++++++..++.+...........    ........+..+...++++++.+...++....  .++.+|.+..+   
T Consensus       160 ~~-~~ltle~y~~~~Hv~v~~~~~~~~~----~d~~L~~~g~~R~i~~~~~~f~~~~~~~~~~~~~li~t~p~~a~~~~~  234 (288)
T PRK10216        160 LH-EEWNLDTFLRYPHISICWEQSDTWA----LDDVLQELGRERTIALSLPGFEQSLFMAAQPDHLLLATAPRYCQHYNQ  234 (288)
T ss_pred             CC-CCCCHHHHHHCCCEEEECCCCCCCH----HHHHHHHCCCCCCEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHH
T ss_conf             46-8989999975898698448888762----799999739865179994988988999956898499810999999987


Q ss_pred             C-CCCEEEECCCCCC-----CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             1-9984661776667-----66008999348778888999999999999850
Q gi|254780282|r  251 D-NPNLVRIMEDVIT-----PSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       251 ~-~~~lv~i~~~~~~-----~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      . ...++....+...     ...+++++||++...+|+.+++.+-|.+-..+
T Consensus       235 ~~~~~l~~~plP~~~~~~~~~~~~~~l~WH~r~~~dp~h~WLRe~I~~l~a~  286 (288)
T PRK10216        235 LHQLPLVARPLPFDESQQEKLEVPFTLLWHKRNSHNPKIVWLRETIKNLYAS  286 (288)
T ss_pred             HCCCCEEECCCCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             6489957608998874444566338997699887998999999999999985


No 38 
>pfam03466 LysR_substrate LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins.
Probab=99.97  E-value=3.7e-31  Score=199.92  Aligned_cols=201  Identities=24%  Similarity=0.258  Sum_probs=168.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--CC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             2222223332111000000000135667542000122222222--22-22222222223456543211112234555433
Q gi|254780282|r   89 VKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--DI-DISMDYADCAIRLRKPIQSSSLIQRKLVTIHM  165 (299)
Q Consensus        89 ~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~~-~l~~~~~Di~i~~~~~~~~~~l~~~~l~~~~~  165 (299)
                      .+.+|+||||++++++..++|+.|.+|+++||+|+|++...+.  .. .+..|++|+||.... ...+++...+|+++++
T Consensus         2 ~~~~G~i~I~~~~~~~~~~lp~~l~~f~~~~P~i~i~i~~~~~~~i~~~l~~g~~Di~i~~~~-~~~~~~~~~~l~~~~~   80 (209)
T pfam03466         2 GGPRGRLRIGAPPTFAAYLLPPLLARFRERYPDVELELREGDSEELLDLLAEGELDLAIRRGP-PDDPGLEARPLFEEPL   80 (209)
T ss_pred             CCCCEEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCC-CCCCCEEEEEEEEEEE
T ss_conf             998789999938899999999999999998889289999898488999998698148873178-9999808999762413


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEEE
Q ss_conf             21123443211122222211000112356643321100023566520223432121145324200135678738423311
Q gi|254780282|r  166 HAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALLP  245 (299)
Q Consensus       166 ~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~lp  245 (299)
                      +++|+++|+...+.+++++||.++++|.+............++    ...+......+++++..++.++|..|.|++++|
T Consensus        81 ~~~~s~~~~l~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~lv~~g~Gi~~lp  156 (209)
T pfam03466        81 VLVAPPDHPLAAGEPVSLEDLADEPLILLEPGSGLRDLVDRAL----ERAGLRPRVALEVNSLEALLAAVAAGLGIALLP  156 (209)
T ss_pred             EEEECCCCHHHCCCCCCHHHHCCCCEEEECCCCCCHHHHHHHH----HHCCCCCCEEEEECCHHHHHHHHHHCCEEEECC
T ss_conf             6553367055428975435514665798569987137998778----764876302467478799999999499999913


Q ss_pred             HHHHCC---CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             777601---9984661776667660089993487788889999999999998
Q gi|254780282|r  246 DYIVKD---NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA  294 (299)
Q Consensus       246 ~~~~~~---~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~  294 (299)
                      .+++++   +++++.+......+.+.+|++|++++.++++++.|++|+.++.
T Consensus       157 ~~~~~~~~~~~~L~~i~~~~~~~~~~~~li~~~~~~~s~~~~~f~~~l~e~~  208 (209)
T pfam03466       157 RSAVARELADGRLVVLPLPDPPLPRPIYLVYRKGRRLSPAVRAFIDFLREAL  208 (209)
T ss_pred             HHHHHHHHHCCCEEEEECCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHC
T ss_conf             9999988758998999588888744799999894978999999999999963


No 39 
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=99.78  E-value=4.3e-19  Score=129.98  Aligned_cols=60  Identities=57%  Similarity=0.801  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCC
Q ss_conf             899999999998276899998828997899999999999958821797699468500134
Q gi|254780282|r    5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGS   64 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~   64 (299)
                      +++|++|++++++|||++||+.|++|||+||++|++||+++|++||+|+++++.||++|+
T Consensus         1 l~~l~~f~~v~~~gs~~~AA~~l~isqs~vs~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~   60 (60)
T pfam00126         1 LRQLRVFVAVAEEGSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGLRLTPAGE   60 (60)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECCCCC
T ss_conf             977999999998099999999979898899999999999959970788899742893749


No 40 
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=98.42  E-value=2.9e-07  Score=61.47  Aligned_cols=74  Identities=20%  Similarity=0.205  Sum_probs=63.0

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEEC-----CCCEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             8999999999982768999988289978999999999999588217976-----9946850013433222222222210
Q gi|254780282|r    5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRH-----ARGLTLTEQGSKLHRVTSEVYHKLE   78 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~~a~~~l~~~~   78 (299)
                      -+.++.+.++.++||+++||+.+++|=-+-...|..+++.++.||+.|.     |+|-.||++|+.+++.-+.+-...+
T Consensus        19 ~~ri~LL~~I~~~gSIs~Aak~~g~SYk~AW~~i~~~n~~~~~plv~~~~GG~~Ggg~~lT~~G~~li~~y~~l~~~~~   97 (262)
T PRK10676         19 PRRISLLKQIALSGSISQGAKDAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGQRLIQLYDLLAQIQQ   97 (262)
T ss_pred             CCHHHHHHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCEECHHHHHHHHHHHHHHHHHH
T ss_conf             6789999999874999999998199699999999999754679779974599999886875789999999999999999


No 41 
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=98.30  E-value=7.7e-07  Score=59.00  Aligned_cols=83  Identities=23%  Similarity=0.266  Sum_probs=69.1

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-----CCEEEEECCCCCCCCCCCCCCCC
Q ss_conf             8889999999999827689999882899789999999999995882179769-----94685001343322222222221
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-----RGLTLTEQGSKLHRVTSEVYHKL   77 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-----~~~~lT~~G~~l~~~a~~~l~~~   77 (299)
                      ++-.-.+.+.++.++||+|+||+.+++|=-..-..|+.+|+-+|.+|+++..     .|-.||+.|+.+++.-+.+-..+
T Consensus        17 ~g~g~~~LL~~I~etGSIs~AAk~~GiSYk~AW~~i~~~n~~~~~plVe~~rGGk~gGga~LT~~g~~ll~~y~~l~~~~   96 (130)
T COG2005          17 AGPGRIELLKAIAETGSISAAAKAAGISYKSAWDYIKALNRLLGEPLVERRRGGKGGGGAVLTDFGERLLEEYRLLEKEI   96 (130)
T ss_pred             CCCHHHHHHHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             48369999999999688999999849977999999999999838870663357788885113799999999999999999


Q ss_pred             CHHHHHCC
Q ss_conf             01221001
Q gi|254780282|r   78 ETTQIELQ   85 (299)
Q Consensus        78 ~~~~~~~~   85 (299)
                      +.......
T Consensus        97 ~~~~~~~~  104 (130)
T COG2005          97 EEALRKLE  104 (130)
T ss_pred             HHHHHHHH
T ss_conf             99998874


No 42 
>PRK11050 manganese transport regulator MntR; Provisional
Probab=97.45  E-value=0.0001  Score=46.69  Aligned_cols=73  Identities=22%  Similarity=0.273  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHCCHHHH---HHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-CCEEEEECCCCCCCCCCCCCCCCCHHH
Q ss_conf             999999999982768999---9882899789999999999995882179769-946850013433222222222210122
Q gi|254780282|r    6 DKLRVFYVVARSGSFTHA---AEQLHLSQSSISRQISGLETEVGIKLFYRHA-RGLTLTEQGSKLHRVTSEVYHKLETTQ   81 (299)
Q Consensus         6 ~~L~~f~~v~~~gs~s~A---A~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~~l~~~~~~~   81 (299)
                      +-|+.++.+.+.+...+.   |++||||+|+||+.|++|++.   -|+...+ +++.||+.|+.+...+..=-..++.+.
T Consensus        40 DYlE~I~~L~~~~G~aR~~DIA~~LgVs~pSVt~mlkrL~~~---GlV~~~~Y~~I~LT~~G~~~A~~i~~RHrile~FL  116 (155)
T PRK11050         40 DYVELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARD---GLVEMRPYRGVFLTPEGEKLAQESRERHQIVENFL  116 (155)
T ss_pred             HHHHHHHHHHHCCCCEEHHHHHHHHCCCCHHHHHHHHHHHHC---CCEEECCCCCEEECHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999982695649999989099933199999999878---99887189884689779999999999999999999


No 43 
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=97.32  E-value=0.00033  Score=43.70  Aligned_cols=75  Identities=25%  Similarity=0.328  Sum_probs=60.7

Q ss_pred             CCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCCC
Q ss_conf             88889999999999827--689999882899789999999999995882179769-------946850013433222222
Q gi|254780282|r    2 SFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTSE   72 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~~   72 (299)
                      +++..++.++..+++.+  +.+.=|+.+++++|+||+.|++||+.   -|+.|..       ..+.||+.|+.+++.+..
T Consensus         7 glt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~---glv~r~~~~~D~R~~~i~LT~~G~~~~~~~~~   83 (101)
T smart00347        7 GLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK---GLIRRLPSPEDRRSVLVSLTEEGRELIEELLE   83 (101)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCC---CCEEEEECCCCCCEEEEEECHHHHHHHHHHHH
T ss_conf             949999999999997699799999999896887999999999458---93898218999885898999899999999999


Q ss_pred             CCCCCCH
Q ss_conf             2222101
Q gi|254780282|r   73 VYHKLET   79 (299)
Q Consensus        73 ~l~~~~~   79 (299)
                      ......+
T Consensus        84 ~~~~~~~   90 (101)
T smart00347       84 ARHETLA   90 (101)
T ss_pred             HHHHHHH
T ss_conf             9999999


No 44 
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=97.27  E-value=0.00075  Score=41.67  Aligned_cols=202  Identities=10%  Similarity=0.050  Sum_probs=100.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCC-CCCCCCCCCCCCC----CCCCC---
Q ss_conf             3222222333211100000000013566754200012222222--22-222222-2222234565432----11112---
Q gi|254780282|r   88 SVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMD-YADCAIRLRKPIQ----SSSLI---  156 (299)
Q Consensus        88 ~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~-~~Di~i~~~~~~~----~~~l~---  156 (299)
                      .....++|+|.+..++. .-+.++...|.+++ ++++++..+.  .+ ..+..| .+|+-+.......    ..++.   
T Consensus        22 ~~a~~~~l~V~aAAsL~-~~~~ei~~~Fek~~-g~~v~~~fgsSg~L~~QI~~GAp~DvF~sAd~~~~~~l~~~~~i~~~   99 (257)
T PRK10677         22 ALADEGKITVFAAASLT-NAMQDIATQYKKEK-GVDVVSSFASSSTLARQIEAGAPADLFISADQKWMDYAVDKKAIDTA   99 (257)
T ss_pred             CCCCCCEEEEEEECCCH-HHHHHHHHHHHHHH-CCEEEEEECCHHHHHHHHHCCCCCCEEEECCHHHHHHHHHCCCCCCC
T ss_conf             32568859999925768-99999999998841-98499996648999999982899658997875778999867785677


Q ss_pred             -CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCC-CCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCH
Q ss_conf             -23455543321123443211122222211000----1123566-43321100023566520223432121145324200
Q gi|254780282|r  157 -QRKLVTIHMHAYAAPHYLKNCREPLSIQELDK----HNLITFG-DLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLS  230 (299)
Q Consensus       157 -~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~----~~~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~  230 (299)
                       ...+....++++++++............|+..    ..+..-+ ...|.+..-...+...+.-..... .....++...
T Consensus       100 ~~~~~a~n~lvli~pk~~~~~~~~i~~~~d~~~ll~~~riaia~P~~aP~G~ya~~~L~~~gl~~~l~~-klv~~~nV~~  178 (257)
T PRK10677        100 TRQTLLGNSLVVVAPKASEQKDFTIDKKTDWTSLLNGGRLAVGDPDHVPAGIYAKEALQKLGAWDTLSP-KLAPAEDVRG  178 (257)
T ss_pred             CEEEEECCEEEEEEECCCCCCCCCCCCCCCHHHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCHHHHCC-CEEECCCHHH
T ss_conf             645621474999984687778644343323777425880898588888657999999997676655065-4132576999


Q ss_pred             HHHHHHHHC-CEEEEEHH--HHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             135678738-42331177--7601998466177666766008999348778888999999999999
Q gi|254780282|r  231 IMQYCVLGS-GIALLPDY--IVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       231 ~~~~v~~g~-Gia~lp~~--~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      .+..|..|. -+|++-.+  ...+..+.+.+.|.....+..+.++-.++ ...+.++.|++||.+.
T Consensus       179 ~l~~v~~G~adaG~Vy~Sda~~~~~~~~~~~~p~~~~~pi~y~~ai~~~-~~~~~a~~F~~fl~S~  243 (257)
T PRK10677        179 ALALVERNEAPLGIVYGSDAVASKGVKVVATFPEDSHKKVEYPMAIVEG-HNNATVSAFYDYLKGP  243 (257)
T ss_pred             HHHHHHCCCCCEEEEECCHHHCCCCCEEEEECCHHHCCCCEEEEEEECC-CCCHHHHHHHHHHCCH
T ss_conf             9999982998789997000222688649998774538961455899759-9999999999997799


No 45 
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=97.19  E-value=0.00058  Score=42.31  Aligned_cols=73  Identities=23%  Similarity=0.358  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHHHC---CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-CCEEEEECCCCCCCCCCCCCCCCCHHH
Q ss_conf             9999999999827---689999882899789999999999995882179769-946850013433222222222210122
Q gi|254780282|r    6 DKLRVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-RGLTLTEQGSKLHRVTSEVYHKLETTQ   81 (299)
Q Consensus         6 ~~L~~f~~v~~~g---s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~~l~~~~~~~   81 (299)
                      +-|+..+.+.+.+   +.+.=|+.|+||+|+||..|++|++.   -|+...+ +++.||+.|+.+...+..=-..++.+.
T Consensus         8 dYLe~Iy~L~~~~~~vr~~dIA~~L~Vs~~SVs~mikkL~~~---Glv~~~~y~~i~LT~~G~~~A~~i~~rHrlle~FL   84 (142)
T PRK03902          8 DYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD---EYLIYEKYRGLVLTPKGKKIGKRLVYRHELLEQFL   84 (142)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHC---CCCEECCCCCEEECHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999825897129999999789953399999999987---99245589875689879999999999999999999


No 46 
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=96.92  E-value=0.0061  Score=36.41  Aligned_cols=200  Identities=12%  Similarity=0.123  Sum_probs=112.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC--CC-CCCCCC-CCCCCCCCCCCC----CCCCC----C
Q ss_conf             222222333211100000000013566754200012222222--22-222222-222223456543----21111----2
Q gi|254780282|r   89 VKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN--KD-IDISMD-YADCAIRLRKPI----QSSSL----I  156 (299)
Q Consensus        89 ~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~--~~-~~l~~~-~~Di~i~~~~~~----~~~~l----~  156 (299)
                      ......++|.+..++.. -+..+...|.+++ ++++.+..+.  .. ..+..| ..|+.|......    ...++    .
T Consensus        26 ~~~~~~i~VfAAaSL~~-~l~~i~~~F~~~~-~~~V~~~f~gS~~l~~qIe~Ga~~D~fiSa~~~~~~~l~~~g~~~~~~  103 (258)
T COG0725          26 AQEAATITVFAAASLTD-ALEEIAKQFEKET-GVKVEVEFGGSGALARQIEQGAPADLFISADDAYMDKLEDKGLIYADS  103 (258)
T ss_pred             CCCCCEEEEEEEHHHHH-HHHHHHHHHHHHH-CCEEEEEECCHHHHHHHHHCCCCCCEEEECCHHHHHHHHHCCCCCCCC
T ss_conf             45674099998156689-9999999999987-987999961389999999759986879988888899998668856671


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCC--CCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHH
Q ss_conf             23455543321123443211122222211000112--356--64332110002356652022343212114532420013
Q gi|254780282|r  157 QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNL--ITF--GDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIM  232 (299)
Q Consensus       157 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~--i~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~  232 (299)
                      ...+....++++.+++-....   ..++++...+-  +..  ....|.+..-...+...+....... ......+.....
T Consensus       104 ~~~fa~n~lvl~~~~~~~~~~---~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~-k~v~~~~v~~~l  179 (258)
T COG0725         104 RIVFAGNRLVLAVPKGSKKKI---ESLEDLLERPDVRLAIGDPKTVPAGKYAKEALELLGLWYTLKD-KLVLATNVRQAL  179 (258)
T ss_pred             EEEEECCEEEEEEECCCCCCC---CHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHCHHHHCCC-CEEECCCHHHHH
T ss_conf             577425748999868874565---1298873087857996488769714999999997051453367-546536579899


Q ss_pred             HHHHHHC---CEEEEEHHHHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             5678738---4233117776019984661776667660089993487788889999999999998
Q gi|254780282|r  233 QYCVLGS---GIALLPDYIVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA  294 (299)
Q Consensus       233 ~~v~~g~---Gia~lp~~~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~  294 (299)
                      ..|..|.   |+...++.........+..++.....+..+.+.-.++..+++.++.|++||.+..
T Consensus       180 ~~V~~G~ad~g~vy~sd~~~~~~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s~~  244 (258)
T COG0725         180 AYVETGEADAGFVYVSDALLSKKVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLSPE  244 (258)
T ss_pred             HHHHCCCCCEEEEEEEHHHHCCCCEEEEECCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHCHH
T ss_conf             99863787779999763340677608997356668971678999738898599999999971877


No 47 
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=96.90  E-value=0.00059  Score=42.29  Aligned_cols=61  Identities=30%  Similarity=0.427  Sum_probs=47.1

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-CCEEEEECCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             89999882899789999999999995882179769-94685001343322222222221012210
Q gi|254780282|r   20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-RGLTLTEQGSKLHRVTSEVYHKLETTQIE   83 (299)
Q Consensus        20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~~l~~~~~~~~~   83 (299)
                      .+.=|+.|+||+|+||+.|++|++.   -|+...+ +++.||+.|+.....+..--..++.+..+
T Consensus         2 ~~diA~~L~vs~~sVs~~l~~L~~~---Gli~~~~y~~i~LT~~G~~~A~~i~~rHr~le~fL~~   63 (96)
T smart00529        2 TSEIAERLNVSPPTVTQMLKKLEKD---GLVEYEPYRGITLTEKGRRLARRLLRKHRLLERFLVD   63 (96)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHC---CCEEECCCCCEEECHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7889988499916799999999988---8988749989788987999999999999999999999


No 48 
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=96.84  E-value=0.0017  Score=39.58  Aligned_cols=69  Identities=25%  Similarity=0.312  Sum_probs=58.5

Q ss_pred             CCHHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCCCC
Q ss_conf             888999999999982768--9999882899789999999999995882179769-------9468500134332222222
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTSEV   73 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~~~   73 (299)
                      ++..++.++..+.+.+..  +.-|+.+++++|+||+.|++||+.   -|+.|..       .-+.+|+.|+.+++.....
T Consensus        20 l~~~q~~~L~~l~~~~~~~~~~la~~l~~~~~~vt~~l~~Le~~---glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~~   96 (126)
T COG1846          20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDK---GLIERLRDPEDRRAVLVRLTEKGRELLEQLLPA   96 (126)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEECCCCCCCEEEEEECHHHHHHHHHHHHH
T ss_conf             99899999999998489999999999787888899999999988---993674388886312435562159999997888


Q ss_pred             C
Q ss_conf             2
Q gi|254780282|r   74 Y   74 (299)
Q Consensus        74 l   74 (299)
                      .
T Consensus        97 ~   97 (126)
T COG1846          97 A   97 (126)
T ss_pred             H
T ss_conf             9


No 49 
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=96.78  E-value=0.0031  Score=38.09  Aligned_cols=78  Identities=24%  Similarity=0.323  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHHCC---HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHH
Q ss_conf             899999999998276---89999882899789999999999995882179769946850013433222222222210122
Q gi|254780282|r    5 WDKLRVFYVVARSGS---FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQ   81 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs---~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~   81 (299)
                      .+-|++.+.+-+.+.   .+.=|+.|+|++|+||+.+++|++ .|.--+++ .+|+.||+.|+............++.+.
T Consensus         9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~-~GlV~~~~-y~gi~LT~~G~~~a~~~~r~hrlle~fL   86 (154)
T COG1321           9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLER-LGLVEYEP-YGGVTLTEKGREKAKELLRKHRLLERFL   86 (154)
T ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHH-CCCEEEEC-CCCEEECCCHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999984368751999999858992789999999987-89978845-8886788354899999999999999999


Q ss_pred             HHC
Q ss_conf             100
Q gi|254780282|r   82 IEL   84 (299)
Q Consensus        82 ~~~   84 (299)
                      ...
T Consensus        87 ~~~   89 (154)
T COG1321          87 VDV   89 (154)
T ss_pred             HHH
T ss_conf             998


No 50 
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=96.78  E-value=0.0023  Score=38.85  Aligned_cols=76  Identities=20%  Similarity=0.245  Sum_probs=59.7

Q ss_pred             CCCHHHHHHHHHHHHHC---CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCC
Q ss_conf             88889999999999827---689999882899789999999999995882179769-------94685001343322222
Q gi|254780282|r    2 SFDWDKLRVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTS   71 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~g---s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~   71 (299)
                      .++.-|..++..+.+.+   +-+.=|+.++|++|+|++.|++||+.   -|+.|..       +.+.||+.|+.+++.+.
T Consensus        28 gLt~~q~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~LE~~---GlI~R~~~~~DrR~~~i~LT~~G~~l~~~~~  104 (144)
T PRK03573         28 ELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEK---GLISRQTCASDRRAKRIKLTEKAEPLISEME  104 (144)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEECCCCCCCEEEEEECHHHHHHHHHHH
T ss_conf             9982599999999973989899999999798783699999999988---8978622867675467678887999999999


Q ss_pred             CCCCCCCHH
Q ss_conf             222221012
Q gi|254780282|r   72 EVYHKLETT   80 (299)
Q Consensus        72 ~~l~~~~~~   80 (299)
                      .+....++-
T Consensus       105 ~~~~~~~~~  113 (144)
T PRK03573        105 AVINKTRAE  113 (144)
T ss_pred             HHHHHHHHH
T ss_conf             999999999


No 51 
>TIGR00637 ModE_repress ModE molybdate transport repressor domain; InterPro: IPR003725 Molybdenum-dependent repression of transcription of the Escherichia coli modABCD operon, which encodes the high-affinity molybdate transporter, is mediated by the ModE protein. When molybdate or tungstate bind to ModE there is little change in its alpha-helical content, but a major change in the environment of tryptophan and tyrosine residues occurs . This is the N-terminal domain of molybdenum-binding proteins ModE, ModA, MopA and MopB. These proteins are involved in molybdenum transport. ModE acts both as a repressor and activator of the mod and moa operons, respectively, depending on the properties of the binding site .; GO: 0015098 molybdate ion transmembrane transporter activity, 0015689 molybdate ion transport.
Probab=96.70  E-value=0.002  Score=39.22  Aligned_cols=79  Identities=25%  Similarity=0.283  Sum_probs=65.2

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEEC-----CCC-EEEEECCCCCCCCCCCCCCC
Q ss_conf             888999999999982768999988289978999999999999588217976-----994-68500134332222222222
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRH-----ARG-LTLTEQGSKLHRVTSEVYHK   76 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~-----~~~-~~lT~~G~~l~~~a~~~l~~   76 (299)
                      ++-+.++.+..+.++||++.||+..+++--+..-.|+.+++-++.+++++.     +.+ ..+|+.|+.++..-..+-..
T Consensus         2 ~~~~~~~ll~~i~~~G~i~~~~~~~g~~y~~~w~~~~~~~~~~~~~~~e~~~GG~~GGgg~~lt~~g~~~~~~y~~~~~~   81 (101)
T TIGR00637         2 VGPRRVALLKAIAREGSISAAAKDAGLSYKSAWDYIKAMNNLLGEPLVEAAPGGKGGGGGAVLTEAGERLIALYGLLERA   81 (101)
T ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             75477899999876120445556405616789899988887642110002578777776421217899999999999999


Q ss_pred             CCHHH
Q ss_conf             10122
Q gi|254780282|r   77 LETTQ   81 (299)
Q Consensus        77 ~~~~~   81 (299)
                      .+...
T Consensus        82 ~~~~~   86 (101)
T TIGR00637        82 LEKAL   86 (101)
T ss_pred             HHHHH
T ss_conf             99875


No 52 
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=96.40  E-value=0.0042  Score=37.35  Aligned_cols=70  Identities=11%  Similarity=0.196  Sum_probs=56.9

Q ss_pred             CCCHHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCC-------CEEEEECCCCCCCCCCC
Q ss_conf             8888999999999982768--99998828997899999999999958821797699-------46850013433222222
Q gi|254780282|r    2 SFDWDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEVGIKLFYRHAR-------GLTLTEQGSKLHRVTSE   72 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~-------~~~lT~~G~~l~~~a~~   72 (299)
                      +++.-|..++.++.+.|.+  +.=|+.+++++++||+.|.+||+.   -++.|.+.       -+.+|+.|+.+++.+.+
T Consensus        37 gLt~~Q~~vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ldrLe~~---GlI~R~~~p~DrR~~~v~LT~~G~~l~~~~~~  113 (144)
T PRK11512         37 DITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK---GWVERLPNPNDKRGVLVKLTTSGAAICEQCHQ  113 (144)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEECCCCCCCCEEEEEECHHHHHHHHHHHH
T ss_conf             999999999999998699799999999788887899999999978---79663579877624787889779999999999


Q ss_pred             CC
Q ss_conf             22
Q gi|254780282|r   73 VY   74 (299)
Q Consensus        73 ~l   74 (299)
                      ..
T Consensus       114 ~~  115 (144)
T PRK11512        114 LV  115 (144)
T ss_pred             HH
T ss_conf             99


No 53 
>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=96.31  E-value=0.0062  Score=36.35  Aligned_cols=45  Identities=31%  Similarity=0.425  Sum_probs=35.3

Q ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE--ECCCCCCCCCCC
Q ss_conf             99827689999882899789999999999995882179769946850--013433222222
Q gi|254780282|r   14 VARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT--EQGSKLHRVTSE   72 (299)
Q Consensus        14 v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT--~~G~~l~~~a~~   72 (299)
                      |.++| -.+||+.|||+|+|+|+.|+.             +|.+..|  +.|..-.+.++.
T Consensus         9 v~~~G-Q~kaA~~lGV~Q~AISKAlra-------------gR~I~v~~~~DG~v~AeEvrp   55 (58)
T pfam09048         9 VEEHG-QAKAAKDLGVNQSAISKALRA-------------GRNIEVTVYEDGSVEAEEVRP   55 (58)
T ss_pred             HHHHC-HHHHHHHCCCCHHHHHHHHHC-------------CCEEEEEECCCCCEEEEEEEC
T ss_conf             99976-598999829758999999964-------------881799986899688888615


No 54 
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=96.08  E-value=0.0098  Score=35.21  Aligned_cols=44  Identities=14%  Similarity=0.286  Sum_probs=38.2

Q ss_pred             CCCCHHHHHHHHHHHHHCCHHHH--HHHHCCCHHHHHHHHHHHHHH
Q ss_conf             98888999999999982768999--988289978999999999999
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSGSFTHA--AEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~gs~s~A--A~~L~itq~avS~~i~~LE~~   44 (299)
                      ++||--+.+.+..+-+-|..|-+  |+++|+|++||.++|++||+.
T Consensus        10 ~~LD~~D~~IL~~Lq~daR~s~~eLA~~vglS~stv~~RikrLe~~   55 (164)
T PRK11169         10 KDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ   55 (164)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             4551999999999998489999999999892999999999999978


No 55 
>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=95.90  E-value=0.033  Score=32.13  Aligned_cols=61  Identities=26%  Similarity=0.359  Sum_probs=48.2

Q ss_pred             CCHHHHHHHHHHHHH-C--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEE-CCCCEEEEECC
Q ss_conf             888999999999982-7--6899998828997899999999999958821797-69946850013
Q gi|254780282|r    3 FDWDKLRVFYVVARS-G--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYR-HARGLTLTEQG   63 (299)
Q Consensus         3 md~~~L~~f~~v~~~-g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R-~~~~~~lT~~G   63 (299)
                      ++-+.++.+.+|... |  +++.=|+.|++|.++++++|++||+.==+.=-.| .++++.+|+.|
T Consensus       167 ~s~~~~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~~~~Lek~gLv~~~~~~k~~~~~~t~Lg  231 (231)
T TIGR01884       167 LSREELKVLEALKAEKGEKSVKNIAKKLGKSLSTISRHLAELEKKGLVESKGRGKGKRYSVTKLG  231 (231)
T ss_pred             CCHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCEECCCC
T ss_conf             88999999999850788052877998857888799999998874475456304678720001369


No 56 
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=95.88  E-value=0.025  Score=32.89  Aligned_cols=70  Identities=19%  Similarity=0.243  Sum_probs=50.4

Q ss_pred             CHHHHHHHHHHHHH--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC--EEEEECCCCCCCCCCCCCCCC
Q ss_conf             88999999999982--768999988289978999999999999588217976994--685001343322222222221
Q gi|254780282|r    4 DWDKLRVFYVVARS--GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG--LTLTEQGSKLHRVTSEVYHKL   77 (299)
Q Consensus         4 d~~~L~~f~~v~~~--gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~--~~lT~~G~~l~~~a~~~l~~~   77 (299)
                      |-..++.+..+.+.  -+++.=++.+++|||+||+|++.|++ -|.---.|.|+.  +.+.|   ....+++++++..
T Consensus        13 D~tRl~Il~lL~~~gelcV~eL~~~l~~sQs~vS~HL~~L~~-aGlV~~rr~G~~vyY~Ln~---~~~~~~~~~l~~~   86 (106)
T PRK10141         13 DETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE-SGLLLDRKQGKWVHYRLSP---HIPAWAAKIIEQA   86 (106)
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-CCCCEEEECCEEEEEEECC---CCHHHHHHHHHHH
T ss_conf             899999999998749956999998869988899999999998-8973037414179987799---8859999999999


No 57 
>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=95.87  E-value=0.023  Score=33.09  Aligned_cols=57  Identities=32%  Similarity=0.406  Sum_probs=41.1

Q ss_pred             CHHHHHHHHHHHHH-CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC--CCEEEEE
Q ss_conf             88999999999982-7689999882899789999999999995882179769--9468500
Q gi|254780282|r    4 DWDKLRVFYVVARS-GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA--RGLTLTE   61 (299)
Q Consensus         4 d~~~L~~f~~v~~~-gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~--~~~~lT~   61 (299)
                      |-..++.+..+.+. .+++.-|+.+++|+|+||+|++.|++. |.---.+.+  +.+.+|+
T Consensus         6 ~~~r~~Il~~L~~~~~~~~eia~~l~is~~~vs~hL~~L~~~-Gli~~~~~~~~~~y~l~~   65 (78)
T cd00090           6 DPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEA-GLVESRREGRRVYYSLTD   65 (78)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEEEECCEEEEEECC
T ss_conf             999999999998489069999877784878999999999988-986899988999999799


No 58 
>PRK11886 biotin--protein ligase; Provisional
Probab=95.79  E-value=0.051  Score=31.06  Aligned_cols=57  Identities=28%  Similarity=0.376  Sum_probs=44.9

Q ss_pred             HHHHHHHHHH--HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCC
Q ss_conf             9999999998--276899998828997899999999999958821797699468500134
Q gi|254780282|r    7 KLRVFYVVAR--SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGS   64 (299)
Q Consensus         7 ~L~~f~~v~~--~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~   64 (299)
                      -|+.+..+++  .-|=..=|++|+||..||.|+|++|++ .|.++--..++|++|...-.
T Consensus         6 ~~~lL~~L~~g~~~SGe~la~~LgvSR~aVwK~i~~L~~-~G~~I~s~~~~GYrL~~~~~   64 (319)
T PRK11886          6 MLQLLSLLADGDFHSGEQLAEELGISRAAIWKHIQTLEE-WGLDIFSVKGKGYRLATPLS   64 (319)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH-CCCEEEEECCCCEEECCCCC
T ss_conf             999999973799296999999879889999999999997-79739997898738787756


No 59 
>TIGR01256 modA molybdate ABC transporter, periplasmic molybdate-binding protein; InterPro: IPR005950   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represents a hydrophylioc periplasmic-binding protein in Gram-negative organisms and its counterpart in Gram-positive organisms is a lipoprotein. The other components of the system include ModB, an integral membrane protein and ModC, the ATP-binding subunit. Almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.; GO: 0015412 molybdate transmembrane-transporting ATPase activity, 0015689 molybdate ion transport, 0030288 outer membrane-bounded periplasmic space.
Probab=95.70  E-value=0.025  Score=32.80  Aligned_cols=185  Identities=12%  Similarity=0.037  Sum_probs=104.0

Q ss_pred             CCCHHHHHHHHHHCCCCCCC--CCCCC-CCCCCC-CCCCCCCCCCCCC----CCCCC----CCCCCCCCCCCCCCCC-CC
Q ss_conf             00013566754200012222--22222-222222-2222234565432----11112----2345554332112344-32
Q gi|254780282|r  108 LQGNLKEFLLLYPDIQIQLI--LDNKD-IDISMD-YADCAIRLRKPIQ----SSSLI----QRKLVTIHMHAYAAPH-YL  174 (299)
Q Consensus       108 l~~~l~~f~~~~P~i~i~i~--~~~~~-~~l~~~-~~Di~i~~~~~~~----~~~l~----~~~l~~~~~~~v~~~~-~~  174 (299)
                      |-++...|.+++|+.++-+.  .|..+ ..+..| .+|+-|.......    +.++.    ...+....++++.+.. +.
T Consensus         8 l~~i~~~F~k~~g~~~Vv~sFgsSg~L~~QI~~GAP~D~F~SA~~~~~~~L~~~g~~v~~~~~~~~~n~LVL~~~~~~~~   87 (225)
T TIGR01256         8 LKEIAKQFEKRTGKNKVVFSFGSSGTLYTQIENGAPADVFISADEKRPKKLVDKGLVVKGSEFVYAGNKLVLISPKNSRV   87 (225)
T ss_pred             HHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCCCCCCHHHHHCCCEECCCCEEEEEEEEEEEECCCCCC
T ss_conf             99999886200899569998768178999997179788766146345404663787302544589862189985355420


Q ss_pred             CCCCCCCCCC---CCCCCCCCCC--CCCCCCCCCHHHHHHHHCCCCCCCCCCEEEEC-CCCHHHHHHHHHC-CEEEEEHH
Q ss_conf             1112222221---1000112356--64332110002356652022343212114532-4200135678738-42331177
Q gi|254780282|r  175 KNCREPLSIQ---ELDKHNLITF--GDLIPKCMEDFNWLATVDRPIGEPRISCLQVN-SYLSIMQYCVLGS-GIALLPDY  247 (299)
Q Consensus       175 ~~~~~~~~~~---dL~~~~~i~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-s~~~~~~~v~~g~-Gia~lp~~  247 (299)
                      .......+-.   .+.+...|..  +..-|.+..-..++...+.-...... ...-. |......+|..|. =+||+=.+
T Consensus        88 ~~~~~~l~~p~~~~~l~~~~vaigdP~~~P~G~~A~E~L~~lgl~~~l~~k-LV~g~P~vrQA~~~V~~~nA~~GiVa~S  166 (225)
T TIGR01256        88 VDSLDILKKPGWVIVLKDKTVAIGDPKHAPYGAAAKEVLQKLGLWEKLKKK-LVYGEPDVRQALQFVETGNAPIGIVALS  166 (225)
T ss_pred             CCCHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHCC-EEECCCCHHHHHHHHHHCCCCEEEEEHH
T ss_conf             130221138974899863702346824443579999999707976256448-6524888999988877258866687311


Q ss_pred             HH--CC-CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             76--01-998466177666766008999348778888999999999999
Q gi|254780282|r  248 IV--KD-NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       248 ~~--~~-~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      .+  .. ....+.++|.....+..+-++--++..+.+.+++|+|||...
T Consensus       167 dv~~~~K~~~~v~~~p~~ly~Pi~yp~~i~~~g~n~~~a~~f~dyL~sp  215 (225)
T TIGR01256       167 DVIPSGKKVGSVAVIPEDLYKPIKYPAVIVKGGKNNAAAKAFIDYLKSP  215 (225)
T ss_pred             EEEECCCCCCEEEEECHHHCCCEEEEEEEEECCCCHHHHHHHHHHHCCH
T ss_conf             0220003662799963312796021178871687608999999870796


No 60 
>COG2998 TupB ABC-type tungstate transport system, permease component [Coenzyme metabolism]
Probab=95.64  E-value=0.09  Score=29.62  Aligned_cols=202  Identities=13%  Similarity=0.131  Sum_probs=103.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCC-------CCC
Q ss_conf             22222233321110000000001356675420001222222222222---22222222345654321111-------223
Q gi|254780282|r   89 VKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKDIDI---SMDYADCAIRLRKPIQSSSL-------IQR  158 (299)
Q Consensus        89 ~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~~~l---~~~~~Di~i~~~~~~~~~~l-------~~~  158 (299)
                      ....+.+|++.+.+.-..=|.+.+-.--+.+++.++++.....-..|   .+|++|+.|... |.....+       .-+
T Consensus        26 sa~~~~LrmATTTSt~dtGLLd~l~p~fE~~~g~~v~~vAvGTG~ALkmge~gdvDvv~vHa-pk~E~~fv~~G~gv~r~  104 (280)
T COG2998          26 SADAAELRMATTTSTEDTGLLDVLLPKFEKYTGYDVQVVAVGTGKALKMGERGDVDVVIVHA-PKAEKEFVKDGFGVDRR  104 (280)
T ss_pred             CCCCCEEEEEEECCCCCCCCHHHHHHHHHHCCCCEEEEEEECCHHHHHHHCCCCCCEEEEEC-CHHHHHHHHCCCCCCCC
T ss_conf             75420378854302455631888777664336965899981235877511268867899837-07789998727886676


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC----CCC--CCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEE---CCCC
Q ss_conf             4555433211234432111222222----110--001123566433211000235665202234321211453---2420
Q gi|254780282|r  159 KLVTIHMHAYAAPHYLKNCREPLSI----QEL--DKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQV---NSYL  229 (299)
Q Consensus       159 ~l~~~~~~~v~~~~~~~~~~~~~~~----~dL--~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~s~~  229 (299)
                      ++.-..+++|.+.+.|...+...+.    +-+  .+.+||+-.+.+.............   ...|....+-.   ..+.
T Consensus       105 ~vmYNdFiiVgp~~dpA~~k~~kn~~e~fe~Ia~~ka~FvSRGD~SGT~~~E~~lWk~~---g~~p~~~~wY~s~G~GMg  181 (280)
T COG2998         105 PVMYNDFIIVGPADDPAGIKDAKNGKEAFEKIAEEKAKFVSRGDNSGTDSKELSLWKVT---GIEPTVKGWYISAGQGMG  181 (280)
T ss_pred             CEEEEEEEEECCCCCCHHCCCCHHHHHHHHHHHHCCCEEEECCCCCCCCHHHHHHHHHC---CCCCCCCCCEEECCCCHH
T ss_conf             10131179987766611112200089999999972890574278778427788899870---878898860365274457


Q ss_pred             HHHHHHHHHCCEEEEEH--HHHC-CCCCEEEECCCCCCCCCEEEE--EECCC--CCCCHHHHHHHHHHHHHH
Q ss_conf             01356787384233117--7760-199846617766676600899--93487--788889999999999998
Q gi|254780282|r  230 SIMQYCVLGSGIALLPD--YIVK-DNPNLVRIMEDVITPSFTVYF--CYPEA--LKNTGKLKAFRNFIFLKA  294 (299)
Q Consensus       230 ~~~~~v~~g~Gia~lp~--~~~~-~~~~lv~i~~~~~~~~~~~~l--v~~~~--~~~~~~~~~f~d~l~~~~  294 (299)
                      ..+.|+.+-.+.++-.+  |++- .-+.|+.++...+..-..|.+  +-+++  ..+-.++..|++|+.+..
T Consensus       182 ~tL~~A~Ek~aytLtDrgTylaYr~r~~L~iv~~gd~~L~N~Ysvi~vNP~r~~~vny~~A~kfi~w~~s~~  253 (280)
T COG2998         182 DTLNMANEKKAYTLTDRGTYLAYRNRPTLVIVLEGDPSLFNPYSVIAVNPKRVKGVNYTAATKFIEWLMSEK  253 (280)
T ss_pred             HHHHHHHHHCEEEEECCCEEEEECCCCCEEEEECCCCCCCCCEEEEEECHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf             787776551216861363056762766528996178111671258987610078857118999999996477


No 61 
>pfam00497 SBP_bac_3 Bacterial extracellular solute-binding proteins, family 3.
Probab=95.59  E-value=0.13  Score=28.65  Aligned_cols=175  Identities=9%  Similarity=0.017  Sum_probs=85.8

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCC-CC-CCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             000013566754200012222222---222222222222234-56-54321111-2234555433211234432111222
Q gi|254780282|r  107 LLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIR-LR-KPIQSSSL-IQRKLVTIHMHAYAAPHYLKNCREP  180 (299)
Q Consensus       107 ~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~-~~-~~~~~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~  180 (299)
                      +..+++..+.+.- ++++++...+   ....+.+|++|+.+. +. .+.....+ ...+++..+.+++++++........
T Consensus        24 ~~~dil~~i~~~l-g~~~~~~~~p~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~~s~p~~~~~~~~~~~~~~~~~~~~~  102 (224)
T pfam00497        24 FDVDLAKAIAKRL-GVKVEFVPVSWDGLIPALQSGKIDVIIAGMTITPERKKKVDFSDPYYYSGQVLVVRKDSPPKIKSI  102 (224)
T ss_pred             EHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEECCCCCCHHHHHHHCCCCCEEECCEEEEEECCCCCCCCCC
T ss_conf             2999999999997-996799985889999999769987661367788555102125753440471799998987654565


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEE-EEHH----HHCCCCCE
Q ss_conf             222110001123566433211000235665202234321211453242001356787384233-1177----76019984
Q gi|254780282|r  181 LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIAL-LPDY----IVKDNPNL  255 (299)
Q Consensus       181 ~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~-lp~~----~~~~~~~l  255 (299)
                      .+++||.+....... +..    ....+....    .......++++....+.++..|.-=++ .+..    .+++.+..
T Consensus       103 ~~~~dL~~~~I~v~~-g~~----~~~~l~~~~----~~~~~i~~~~~~~~~l~~L~~gr~D~~i~~~~~~~~~~~~~~~~  173 (224)
T pfam00497       103 KDLADLKGKKVGVQK-GTT----QEDLLKELA----PKGAEIVLYDDQAEALQALAAGRVDAVVADSPVAAYLIKKNPGL  173 (224)
T ss_pred             CCHHHHCCCEEEEEC-CCH----HHHHHHHHC----CCCCEEEEECCHHHHHHHHHCCCEEEEEECHHHHHHHHHHCCCC
T ss_conf             898997797799968-977----999998606----24451699542788888987497689995799999999868997


Q ss_pred             EEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             6617766676600899934877888899999999999985
Q gi|254780282|r  256 VRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR  295 (299)
Q Consensus       256 v~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r  295 (299)
                      ..+... +....+++++.+++   ++.....++--+++.+
T Consensus       174 ~~~~~~-~~~~~~~~~~~~k~---~~~l~~~~n~~l~~l~  209 (224)
T pfam00497       174 NLVVGE-PLSGEPYGIAVRKG---DPELLAAVNKALAELK  209 (224)
T ss_pred             EEEECC-CCCCCEEEEEEECC---CHHHHHHHHHHHHHHH
T ss_conf             299436-77761499999799---9999999999999999


No 62 
>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=95.50  E-value=0.038  Score=31.81  Aligned_cols=38  Identities=29%  Similarity=0.468  Sum_probs=29.9

Q ss_pred             HHHHHHHHH-HHCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             999999999-82768999988289978999999999999
Q gi|254780282|r    7 KLRVFYVVA-RSGSFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         7 ~L~~f~~v~-~~gs~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      .++.+..++ +..+++.=|+.+++|||+||+|++.|++.
T Consensus         4 Rl~Il~~L~~~~~~v~el~~~l~~sq~~vS~HL~~L~~~   42 (47)
T pfam01022         4 RLKILYLLSEGELCVCELAEILGLSQSTVSHHLKKLREA   42 (47)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             999999998089969999999895886999999999898


No 63 
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=95.47  E-value=0.051  Score=31.04  Aligned_cols=44  Identities=11%  Similarity=0.215  Sum_probs=37.4

Q ss_pred             CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             988889999999999827--68999988289978999999999999
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      |.||=-+.+.+..+.+-|  |++.=|+++|+|.|||.++|++||+.
T Consensus         5 ~klD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~stv~~Ri~rLe~~   50 (153)
T PRK11179          5 YQIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA   50 (153)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             7678999999999998489999999999892999999999999979


No 64 
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=95.32  E-value=0.024  Score=32.93  Aligned_cols=76  Identities=16%  Similarity=0.239  Sum_probs=64.0

Q ss_pred             HHHHHHHHHH-HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCC
Q ss_conf             9999999998-276899998828997899999999999958821797699468500134332222222222101221001
Q gi|254780282|r    7 KLRVFYVVAR-SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQ   85 (299)
Q Consensus         7 ~L~~f~~v~~-~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~   85 (299)
                      ..+.+..+.+ -+|+..=-..|++|.+++..|||+|++   ..|+++.++...||+.|+.+.+..+.+++.++-......
T Consensus        15 Rk~lLllL~egPkti~EI~~~l~vs~~ai~pqiKkL~~---~~LV~~~~~~Y~LS~~G~iiv~km~~ll~tl~v~e~n~d   91 (260)
T COG4742          15 RKDLLLLLKEGPKTIEEIKNELNVSSSAILPQIKKLKD---KGLVVQEGDRYSLSSLGKIIVEKMEPLLDTLEVFEENYD   91 (260)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHH---CCCEEECCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999858988999998858993888999998713---898785199987340089999999999999999973146


No 65 
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=95.18  E-value=0.22  Score=27.33  Aligned_cols=170  Identities=9%  Similarity=0.011  Sum_probs=86.0

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCC-CC-CCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             000013566754200012222222---2222222222222345-65-4321111-2234555433211234432111222
Q gi|254780282|r  107 LLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIRL-RK-PIQSSSL-IQRKLVTIHMHAYAAPHYLKNCREP  180 (299)
Q Consensus       107 ~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~~-~~-~~~~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~  180 (299)
                      +..+++..+.+.- ++++++..-+   ....+..|++|+.+.. .. +.....+ ...++.....++++.++.     .+
T Consensus        25 ~~~Dil~~~~~~l-g~~i~~~~~~~~r~~~~l~~g~~D~~~~~~~~~~~r~~~~~~s~p~~~~~~~~~~~~~~-----~~   98 (219)
T smart00062       25 FDVDLAKAIAKEL-GLKVEFVEVSFDNLLTALKSGKIDVVAAGMTITPERAKQVDFSDPYYKSGQVILVRKDS-----PI   98 (219)
T ss_pred             EHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCHHHHHCCCCCCCEECCCEEEEEECCC-----CC
T ss_conf             2999999999997-99679998478999999975897705311357867750022245500244479996589-----97


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCC-EEEEEHHHH----CCCCC-
Q ss_conf             222110001123566433211000235665202234321211453242001356787384-233117776----01998-
Q gi|254780282|r  181 LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSG-IALLPDYIV----KDNPN-  254 (299)
Q Consensus       181 ~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~G-ia~lp~~~~----~~~~~-  254 (299)
                      .+++||.+....... +..    ....+.....     .....++++...++.++..|.- +.+.+...+    ++.+. 
T Consensus        99 ~~~~dL~g~~i~~~~-g~~----~~~~l~~~~~-----~~~~~~~~~~~~~~~~l~~g~vD~~i~~~~~~~~~~~~~~~~  168 (219)
T smart00062       99 KSLEDLKGKKVAVVA-GTT----GEELLKKLYP-----EAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLP  168 (219)
T ss_pred             CCHHHHCCCEEEEEC-CCH----HHHHHHHHCC-----CCEEEEECCHHHHHHHHHCCCEEEEEECHHHHHHHHHHCCCC
T ss_conf             997996797799957-987----9999997287-----852898599999999998398799997799999999848999


Q ss_pred             EEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             46617766676600899934877888899999999999985
Q gi|254780282|r  255 LVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR  295 (299)
Q Consensus       255 lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r  295 (299)
                      -..+.........++++..+++   ++.....++--+++.+
T Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~---~~~l~~~~n~~l~~l~  206 (219)
T smart00062      169 ELKIVGDPLDTPEGYAFAVRKG---DPELLDKINKALKELK  206 (219)
T ss_pred             CEEEECCCCCCCCEEEEEEECC---CHHHHHHHHHHHHHHH
T ss_conf             8378346777764199999599---9999999999999999


No 66 
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=95.09  E-value=0.078  Score=29.99  Aligned_cols=40  Identities=40%  Similarity=0.395  Sum_probs=33.2

Q ss_pred             CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             88999999999982768999988289978999999999999
Q gi|254780282|r    4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         4 d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      |.+-|+.+..=++ .|++.-|+++|+|+|+|+++|++||+.
T Consensus        10 D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~~~   49 (154)
T COG1522          10 DRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLEEE   49 (154)
T ss_pred             HHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             9999999997276-579999999797989999999999988


No 67 
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transport system, 1-aminoethylphosphonate-binding protein component. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=94.86  E-value=0.066  Score=30.40  Aligned_cols=203  Identities=16%  Similarity=0.135  Sum_probs=92.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC---CCCCCC----CCCCCCCCCCC------------
Q ss_conf             32222223332111000000000135667542000122222222---222222----22222234565------------
Q gi|254780282|r   88 SVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK---DIDISM----DYADCAIRLRK------------  148 (299)
Q Consensus        88 ~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~---~~~l~~----~~~Di~i~~~~------------  148 (299)
                      .....++|.|-++  ....++-+++..|.++||+|++++...+.   ...|..    ..+|+.+....            
T Consensus        17 aa~~~~~l~VYss--~~~~~~~~i~~~Fek~~tgIkV~~v~~~tgel~~rl~aEk~~p~aDV~~g~~~~~~~~~~~~gll   94 (334)
T TIGR03261        17 NSKANTELTVYTA--IEDELIAKYKDAFEKVNPDIKINWVRDSTGIITAKLLAEKNNPQADVVWGLAASSLALLDKEGML   94 (334)
T ss_pred             HHCCCCEEEEEEC--CCHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHCCCC
T ss_conf             0302995999969--98889999999999777994899998972999999996457998659984565789998860431


Q ss_pred             -CCCCCCCCCC-CCCCC-------------CCCCCCCCCCCCCC--CCCCCCCCCCCCCC---CCCCC-CCCCCC-C-HH
Q ss_conf             -4321111223-45554-------------33211234432111--22222211000112---35664-332110-0-02
Q gi|254780282|r  149 -PIQSSSLIQR-KLVTI-------------HMHAYAAPHYLKNC--REPLSIQELDKHNL---ITFGD-LIPKCM-E-DF  205 (299)
Q Consensus       149 -~~~~~~l~~~-~l~~~-------------~~~~v~~~~~~~~~--~~~~~~~dL~~~~~---i~~~~-~~~~~~-~-~~  205 (299)
                       +..++.+... +-+.+             ..+++-.++.+...  ..|.+.+||.+-.|   |.+.. ..+... . ..
T Consensus        95 ~~y~~~~~~~l~~~~~d~~~~~~~~g~~~~~~~i~yN~~~~~~~~~p~P~sw~DL~dp~ykg~i~~~~p~~sg~~~~~l~  174 (334)
T TIGR03261        95 KPYKPKGLDALNPKFRDAKNPPHWVGMDAWMAAICFNTVEAKKKGLPKPTSWEDLTKPEYKGHIVMPNPASSGTGFLDVS  174 (334)
T ss_pred             CCCCCCCHHHCCHHHCCCCCCCEEEEEEEEEEEEEEEHHHCCCCCCCCCCCHHHHCCHHHCCEEECCCCCCCHHHHHHHH
T ss_conf             57775305447886529788851688752467899744440425899999999970947489587348886338999999


Q ss_pred             HHHHHHCCCCC-------CCCCCEEEECCCCHHHHHHHHHC-CEEEEEHHHH---CCCCCEEE-ECCCCCCCCCEEEEEE
Q ss_conf             35665202234-------32121145324200135678738-4233117776---01998466-1776667660089993
Q gi|254780282|r  206 NWLATVDRPIG-------EPRISCLQVNSYLSIMQYCVLGS-GIALLPDYIV---KDNPNLVR-IMEDVITPSFTVYFCY  273 (299)
Q Consensus       206 ~~~~~~~~~~~-------~~~~~~~~~~s~~~~~~~v~~g~-Gia~lp~~~~---~~~~~lv~-i~~~~~~~~~~~~lv~  273 (299)
                      .+....+...+       .... ...+.+......++..|. .+++...+.+   ..+|.-+. +.|........-.+.-
T Consensus       175 ~~~~~~G~d~g~~~l~~l~~N~-~~~~~~~~~~~~~v~~Ge~~ig~~~~~~~~~~~~~g~pv~~v~P~eG~~~~~~~~~I  253 (334)
T TIGR03261       175 AWLQMMGEDKGWDYMDKLHKNI-AVYTHSGSKPCKLAGMGEFPIGISMAYRALKEKKKGAPIDVVFPKEGLGWDIEATAI  253 (334)
T ss_pred             HHHHHHCHHHHHHHHHHHHHHH-CCCCCCCCHHHHHHHCCCEEEEEEECCHHHHHHHCCCCEEEEECCCCCEEEEEEEEE
T ss_conf             9999735288999999998632-416777638889986598579997354578876438973389458984787735888


Q ss_pred             CCCCCCCHHHHHHHHHHHHH
Q ss_conf             48778888999999999999
Q gi|254780282|r  274 PEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       274 ~~~~~~~~~~~~f~d~l~~~  293 (299)
                      .++..+...++.|+||+++.
T Consensus       254 vk~a~n~~~Ak~FidfllS~  273 (334)
T TIGR03261       254 IKGSKNNDAAKKLVDWSISD  273 (334)
T ss_pred             ECCCCCHHHHHHHHHHHCCH
T ss_conf             87998989999999997699


No 68 
>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=94.83  E-value=0.087  Score=29.71  Aligned_cols=42  Identities=19%  Similarity=0.445  Sum_probs=36.0

Q ss_pred             CCHHHHHHHHHHHHHCC--HHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             88899999999998276--8999988289978999999999999
Q gi|254780282|r    3 FDWDKLRVFYVVARSGS--FTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs--~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      +++.|+.++..+.+.+.  .+.-|+.++++++++|+.|++||+.
T Consensus         1 lT~~Q~~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i~~Le~~   44 (59)
T pfam01047         1 LTLTQFHILRILYEHGPLTVSELAEKLGVDRSTVTRVLDRLEKK   44 (59)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             98999999999994699299999999885865499999999889


No 69 
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=94.78  E-value=0.098  Score=29.42  Aligned_cols=49  Identities=24%  Similarity=0.287  Sum_probs=41.3

Q ss_pred             HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCC
Q ss_conf             27689999882899789999999999995882179769946850013433
Q gi|254780282|r   17 SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL   66 (299)
Q Consensus        17 ~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l   66 (299)
                      .-|=-+=|++|++|..||.++|++|+ +.|.+.+.+.++|..+...=..+
T Consensus        19 ~~SGe~La~~LgiSRtaVwK~Iq~Lr-~~G~~I~s~~~kGY~L~~~~~ll   67 (79)
T COG1654          19 FVSGEKLAEELGISRTAVWKHIQQLR-EEGVDIESVRGKGYLLPQLPDLL   67 (79)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHH-HHCCCEEECCCCCEECCCCCCCC
T ss_conf             66689999997865999999999999-80971686078863656750107


No 70 
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=94.47  E-value=0.12  Score=28.86  Aligned_cols=42  Identities=21%  Similarity=0.300  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHHHH--CCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             888999999999982--768999988289978999999999999
Q gi|254780282|r    3 FDWDKLRVFYVVARS--GSFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         3 md~~~L~~f~~v~~~--gs~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      ||=-+.+.+..+-+-  -|++.=|+++|+|+++|.++|++||+.
T Consensus         1 lD~~D~~Il~~L~~n~R~s~~~iA~~lg~S~~tv~~Ri~~L~~~   44 (108)
T smart00344        1 LDEIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEE   44 (108)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             98899999999998289999999999893999999999999608


No 71 
>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=94.39  E-value=0.092  Score=29.57  Aligned_cols=39  Identities=28%  Similarity=0.452  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHCC---HHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             99999999998276---8999988289978999999999999
Q gi|254780282|r    6 DKLRVFYVVARSGS---FTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         6 ~~L~~f~~v~~~gs---~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      +-|+.++.+.+.+.   .+.=|++|+||+|+||..|++|++.
T Consensus         6 dYLk~Iy~l~~~~~~v~~~~iA~~L~Vs~~SVt~mlkkL~~~   47 (58)
T pfam01325         6 DYLETIYTLSEEKGVVKTKDLAERLNVSPSTVSEMLKKLEKD   47 (58)
T ss_pred             HHHHHHHHHHCCCCCEEHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf             999999998826996129999999599925299999999988


No 72 
>PRK11260 cystine transporter subunit; Provisional
Probab=94.19  E-value=0.4  Score=25.87  Aligned_cols=185  Identities=10%  Similarity=0.005  Sum_probs=86.8

Q ss_pred             CCCCCCCCCCCCCCCC-----------CCCCHHHHHHHHHHCCCCCCCCC---CCCCCCCCCCCCCCCCCCC--CCCCCC
Q ss_conf             2222333211100000-----------00001356675420001222222---2222222222222234565--432111
Q gi|254780282|r   91 PSGKLRIATTIDLGQN-----------LLQGNLKEFLLLYPDIQIQLILD---NKDIDISMDYADCAIRLRK--PIQSSS  154 (299)
Q Consensus        91 ~~g~i~I~~~~~~~~~-----------~l~~~l~~f~~~~P~i~i~i~~~---~~~~~l~~~~~Di~i~~~~--~~~~~~  154 (299)
                      .+|+|+||+.+.+.++           +=.+++..+.++- ++++++...   +....|..|++|+++..-.  +.....
T Consensus        37 ~~G~L~Vg~~~~~pPf~~~d~~G~~~GfdvDl~~~ia~~l-g~~~e~~~~~~~~~i~~L~~g~~Di~~~~~t~T~eR~~~  115 (264)
T PRK11260         37 ERGTLLVGLEGTYPPFSFQGEDGKLTGFEVEFAEALAKHL-GVKASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKK  115 (264)
T ss_pred             HCCEEEEEECCCCCCCEEECCCCCEEEEEHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEECCCCCCHHHHHH
T ss_conf             6998999977898893689999998887199999999984-995699978889999998669946672575358888851


Q ss_pred             CC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHH
Q ss_conf             12-23455543321123443211122222211000112356643321100023566520223432121145324200135
Q gi|254780282|r  155 LI-QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQ  233 (299)
Q Consensus       155 l~-~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~  233 (299)
                      +. ..+.+.....+++.++..   ....+++||.+... ....+.    ....++...     .+......+++....+.
T Consensus       116 ~~Fs~PY~~~~~~~~v~~~~~---~~i~~~~dL~Gk~V-~v~~gs----~~~~~l~~~-----~~~~~i~~~~~~~~~~~  182 (264)
T PRK11260        116 YDFSTPYTVSGIQALVKKGNE---GTIKTAADLKGKKV-GVGLGT----NYEEWLRQN-----VQGVDVRTYDDDPTKYQ  182 (264)
T ss_pred             CCCCCCEEEEEEEEEEECCCC---CCCCCHHHHCCCEE-EEECCC----HHHHHHHHH-----CCCCCEEEECCHHHHHH
T ss_conf             776774377445999987897---66689789668716-885697----899999860-----88981686366189999


Q ss_pred             HHHHHCCEEEEEHH-----HHCCCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             67873842331177-----7601998466177666766008999348778888999999999999
Q gi|254780282|r  234 YCVLGSGIALLPDY-----IVKDNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       234 ~v~~g~Gia~lp~~-----~~~~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      .+.+|..=+++-+.     .+++.+....+... +....++++..+++   ++.....++.-+.+
T Consensus       183 ~l~~G~vDa~i~d~~~~~~~~~~~~~~~~~~~~-~~~~~~~~iav~k~---~~~L~~~in~~L~~  243 (264)
T PRK11260        183 DLRVGRIDAILVDRLAALDLVKKTNDTLAVTGE-AFSRQESGVALRKG---NPDLLKAVNNAIAE  243 (264)
T ss_pred             HHHCCCCCEEEECHHHHHHHHHHCCCCEEECCC-CCCCCEEEEEEECC---CHHHHHHHHHHHHH
T ss_conf             987598679994599999999868997898068-76665089999899---99999999999999


No 73 
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=94.00  E-value=0.059  Score=30.70  Aligned_cols=41  Identities=27%  Similarity=0.276  Sum_probs=32.5

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC
Q ss_conf             982768999988289978999999999999588217976994
Q gi|254780282|r   15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG   56 (299)
Q Consensus        15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~   56 (299)
                      -...|++.=|+.+++|||+||+|++.|++. |.-=..|.|+.
T Consensus         8 ~~~~~~~ela~~l~is~~tvs~HL~~L~~~-Glv~~~~~G~~   48 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLREA-GLVESRREGKR   48 (66)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEEEECCE
T ss_conf             399669999999882988887999999988-92689998689


No 74 
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=93.80  E-value=0.11  Score=29.11  Aligned_cols=33  Identities=27%  Similarity=0.268  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             999999998276899998828997899999999
Q gi|254780282|r    8 LRVFYVVARSGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus         8 L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      +-.-.-+-+--|-.+.|+-||+||||||+-|+.
T Consensus        13 ~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~   45 (119)
T COG2522          13 LLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSG   45 (119)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf             999999995886999999968889999999736


No 75 
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075   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 members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus..
Probab=93.29  E-value=0.11  Score=29.19  Aligned_cols=89  Identities=20%  Similarity=0.287  Sum_probs=51.1

Q ss_pred             HHHHHHHCCHHHH--HHHHCCCHHHHHHHHHHHHHHHCCEEEEEC-------CC---CEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             9999982768999--988289978999999999999588217976-------99---46850013433222222222210
Q gi|254780282|r   11 FYVVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFYRH-------AR---GLTLTEQGSKLHRVTSEVYHKLE   78 (299)
Q Consensus        11 f~~v~~~gs~s~A--A~~L~itq~avS~~i~~LE~~lg~~Lf~R~-------~~---~~~lT~~G~~l~~~a~~~l~~~~   78 (299)
                      +..+-+.|.-|++  |+.|.||+.||-||+|.||.+   .|++-.       ||   .++|...|+.=++.         
T Consensus         7 L~~LL~~Gq~sA~~lA~~L~iSpQAvRrHLKDLe~e---~Lv~~~~~~~g~~GRPQy~Y~LS~qGRe~l~~---------   74 (215)
T TIGR02702         7 LEYLLKEGQASALALAEELAISPQAVRRHLKDLETE---GLVEYKAVLQGTMGRPQYLYQLSRQGREQLPQ---------   74 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC---CHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH---------
T ss_conf             999886004889999997278867887654332101---03567777650478822542121776776366---------


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             1221001223222222333211100000000013566
Q gi|254780282|r   79 TTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEF  115 (299)
Q Consensus        79 ~~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f  115 (299)
                       ...  + ......|.+-|....|++..+-++-+.+.
T Consensus        75 -~~~--r-qqa~~~~~FAl~LLdSl~etlG~~q~~~v  107 (215)
T TIGR02702        75 -LVL--R-QQADRHGEFALSLLDSLAETLGPEQFEAV  107 (215)
T ss_pred             -HHH--H-HHCCCCCHHHHHHHHHHHHHCCHHHHHHH
T ss_conf             -554--5-41037531678899988963787789999


No 76 
>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=93.28  E-value=0.34  Score=26.29  Aligned_cols=45  Identities=16%  Similarity=0.293  Sum_probs=41.6

Q ss_pred             CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE
Q ss_conf             889999999999827689999882899789999999999995882
Q gi|254780282|r    4 DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK   48 (299)
Q Consensus         4 d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~   48 (299)
                      +-++.+.+..+++-.|...-|+.|++|..+|+.+++++-+.||+.
T Consensus         2 T~rE~~il~~~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~~~   46 (57)
T cd06170           2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVK   46 (57)
T ss_pred             CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
T ss_conf             889999999998079999999998978999999999999986899


No 77 
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=93.02  E-value=0.31  Score=26.48  Aligned_cols=49  Identities=29%  Similarity=0.447  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHC---CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE
Q ss_conf             99999999827---689999882899789999999999995882179769946
Q gi|254780282|r    8 LRVFYVVARSG---SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL   57 (299)
Q Consensus         8 L~~f~~v~~~g---s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~   57 (299)
                      ++.+..+.+..   |-..=|++|+||..||.+.|+.|+ +.|.++....|+|+
T Consensus         3 ~~il~~L~~~~~~vt~~~La~~l~VSr~TV~rdi~~L~-~~G~~I~s~~g~GY   54 (55)
T pfam08279         3 LQILELLLQAREPISGQELAEKLGVSRRTIRRDIKALE-ALGVPIESEPGRGY   54 (55)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH-HCCCCEEECCCCCC
T ss_conf             99999999769991899999996988999999999999-88997884689999


No 78 
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=92.88  E-value=0.43  Score=25.71  Aligned_cols=42  Identities=17%  Similarity=0.328  Sum_probs=35.1

Q ss_pred             CHHHHHHHHHHHHHC--------CHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             889999999999827--------689999882899789999999999995
Q gi|254780282|r    4 DWDKLRVFYVVARSG--------SFTHAAEQLHLSQSSISRQISGLETEV   45 (299)
Q Consensus         4 d~~~L~~f~~v~~~g--------s~s~AA~~L~itq~avS~~i~~LE~~l   45 (299)
                      +-+|.+++....+.|        |++.=|+.|+||+||+|.++++-|..+
T Consensus         2 T~rQ~evl~~A~~~GYfd~PR~~~l~elA~~lgis~sT~~~hLr~ae~ki   51 (53)
T pfam04967         2 TDRQREILRLAYKMGYFDYPRRVTLKDLAKELGISKSTLSEHLRRAESKL   51 (53)
T ss_pred             CHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             88999999999986897788768899999996989999999999999987


No 79 
>PRK10870 transcriptional repressor MprA; Provisional
Probab=92.66  E-value=0.28  Score=26.80  Aligned_cols=70  Identities=19%  Similarity=0.154  Sum_probs=50.9

Q ss_pred             CHHHHHHHHHHHHH----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCCC
Q ss_conf             88999999999982----7689999882899789999999999995882179769-------946850013433222222
Q gi|254780282|r    4 DWDKLRVFYVVARS----GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTSE   72 (299)
Q Consensus         4 d~~~L~~f~~v~~~----gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~~   72 (299)
                      +-.++.++..+...    -+-|.=|+.+++|.+++++.+.+||+.   -|+.|..       ..+.+|++|+.+++.+.+
T Consensus        54 s~~~f~vL~~L~~~~~~~l~PseLa~~l~~s~a~iTr~vD~LEkk---GlV~R~~s~~DRR~~~V~LT~~G~~ll~~~lP  130 (176)
T PRK10870         54 NETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKR---GWIERRESDNDRRCLHLQLTEKGHEFLREVLP  130 (176)
T ss_pred             CHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEECCCCCCCEEEEEECHHHHHHHHHHHH
T ss_conf             888999999997189998598999999778710199999999988---99787237123534788989889999999849


Q ss_pred             CCCC
Q ss_conf             2222
Q gi|254780282|r   73 VYHK   76 (299)
Q Consensus        73 ~l~~   76 (299)
                      ...+
T Consensus       131 ~~~~  134 (176)
T PRK10870        131 PQHN  134 (176)
T ss_pred             HHHH
T ss_conf             9999


No 80 
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=92.58  E-value=0.12  Score=28.81  Aligned_cols=25  Identities=24%  Similarity=0.393  Sum_probs=22.7

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             8276899998828997899999999
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      -.||.++||+.||||.+++.+.|++
T Consensus        17 ~~gn~~~aA~~LGisr~tL~~kmkk   41 (42)
T pfam02954        17 TGGNKSKAARLLGISRRTLYRKLKK   41 (42)
T ss_pred             HCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             4997999999979699999999973


No 81 
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=92.55  E-value=0.34  Score=26.29  Aligned_cols=152  Identities=11%  Similarity=-0.005  Sum_probs=83.0

Q ss_pred             CCCCCCCCCCCCCC-CCCCCCC------------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCC
Q ss_conf             22222222222222-3456543------------211112234555433211234432111222222110001--12356
Q gi|254780282|r  130 NKDIDISMDYADCA-IRLRKPI------------QSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKH--NLITF  194 (299)
Q Consensus       130 ~~~~~l~~~~~Di~-i~~~~~~------------~~~~l~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~--~~i~~  194 (299)
                      .....+.+|++|++ +.+.+..            -.+.......+.-+..+++++..|..   ..+++||.+.  .+|.-
T Consensus        29 gG~~~i~~G~adiag~hlld~~~g~ynip~v~~~~~~~~~LI~g~~Re~Gl~v~~gnpk~---i~~~edl~~~d~~fVNR  105 (223)
T COG1910          29 GGLLAIKRGEADIAGIHLLDNESGTYNIPYVKKYLPGEAVLIRGYLREQGLMVQKGNPKN---ISSLEDLLRKDLRFVNR  105 (223)
T ss_pred             CCHHHHHHCCCCEEEEEECCCCCCCEEHHHHHHCCCCCEEEEEEEEEEEEEEEECCCCCC---CCCHHHHHHCCCEEEEC
T ss_conf             554766625451444213257787442300423078846998536651036886489776---62499885267578715


Q ss_pred             CCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHC---CEEEEEHHHHCCC-CCEEEECCCCCCCCCEEE
Q ss_conf             643321100023566520223432121145324200135678738---4233117776019-984661776667660089
Q gi|254780282|r  195 GDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGS---GIALLPDYIVKDN-PNLVRIMEDVITPSFTVY  270 (299)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~---Gia~lp~~~~~~~-~~lv~i~~~~~~~~~~~~  270 (299)
                      ...+.........+...+......+-...++.+.....+.|.+|-   |++  -++.++.. ..-+++      ..-+|.
T Consensus       106 ~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~AD~GvG--lr~~A~~~gL~Fipl------~~E~YD  177 (223)
T COG1910         106 NRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGRADAGVG--LRHAAEKYGLDFIPL------GDEEYD  177 (223)
T ss_pred             CCCCCHHHHHHHHHHHCCCCCHHCCCCCCCCCCCHHHHHHHHCCCCCCCCC--HHHHHHHCCCCEEEC------CCCEEE
T ss_conf             899658999999998737670105784323212089999997589872501--799999849851774------562578


Q ss_pred             EEECCCCCCCHHHHHHHHHHHH
Q ss_conf             9934877888899999999999
Q gi|254780282|r  271 FCYPEALKNTGKLKAFRNFIFL  292 (299)
Q Consensus       271 lv~~~~~~~~~~~~~f~d~l~~  292 (299)
                      ++.+|+....|.++.|++.|.+
T Consensus       178 ~virke~~~~~~vr~fi~~L~s  199 (223)
T COG1910         178 FVIRKERLDKPVVRAFIKALKS  199 (223)
T ss_pred             EEEEHHHCCCHHHHHHHHHHCC
T ss_conf             9984567058889999998612


No 82 
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=92.54  E-value=0.52  Score=25.22  Aligned_cols=46  Identities=15%  Similarity=0.205  Sum_probs=42.5

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE
Q ss_conf             8889999999999827689999882899789999999999995882
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK   48 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~   48 (299)
                      ++-++.+++.-+++-.+-..-|+.|++|..+|+.+++++-+.||+.
T Consensus         4 LT~RE~~il~~l~~G~s~~eIA~~L~is~~TV~~h~~~i~~Kl~v~   49 (58)
T pfam00196         4 LSPREREVLRLLAAGKSNKEIADILGISEKTVKVHRSNIMRKLNVH   49 (58)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
T ss_conf             7999999999998079999999997888999999999999980999


No 83 
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=92.36  E-value=0.56  Score=25.03  Aligned_cols=46  Identities=17%  Similarity=0.322  Sum_probs=42.5

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE
Q ss_conf             8889999999999827689999882899789999999999995882
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK   48 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~   48 (299)
                      ++=++.+++..+++-.|...-|+.|++|..+|..+++++=+.||+.
T Consensus         4 LT~rE~~il~~l~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~   49 (58)
T smart00421        4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVR   49 (58)
T ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
T ss_conf             1899999999998179999999898978989999999999984899


No 84 
>PRK10859 putative transglycosylase; Provisional
Probab=92.19  E-value=0.49  Score=25.36  Aligned_cols=156  Identities=13%  Similarity=0.102  Sum_probs=77.8

Q ss_pred             CCCCCCCCCCCCCCCCCCC---------CHHHHHHHHHHCCCCCCCCCCC----CCCCCCCCCCCCCC-CC-CCCCCCCC
Q ss_conf             2222333211100000000---------0135667542000122222222----22222222222234-56-54321111
Q gi|254780282|r   91 PSGKLRIATTIDLGQNLLQ---------GNLKEFLLLYPDIQIQLILDNK----DIDISMDYADCAIR-LR-KPIQSSSL  155 (299)
Q Consensus        91 ~~g~i~I~~~~~~~~~~l~---------~~l~~f~~~~P~i~i~i~~~~~----~~~l~~~~~Di~i~-~~-~~~~~~~l  155 (299)
                      .+|.|+|++..+-..++..         +++.+|.+.. +|++++...+.    ...|..|.+|++-. .. .+.....+
T Consensus        41 ~rG~LrV~T~~spttYy~~~~~~~GFEYELak~FA~~L-GV~L~i~~~~~~~el~~~L~~G~~DiaAAgLt~t~~R~~~~  119 (507)
T PRK10859         41 ARGELRVSTIHSPLTYSTINGKPFGLDYELAKQFADYL-GVKLKVTVRQNISQLFDDLDNGNADLLAAGLVYNSERVKNY  119 (507)
T ss_pred             HCCEEEEEEECCCCEEEECCCCCCCHHHHHHHHHHHHC-CCEEEEEECCCHHHHHHHHHCCCCCEEECCCCCCHHHHHCC
T ss_conf             78968999975896599419964779999999999980-99179997499999999986799888955787785367404


Q ss_pred             CCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEE--ECCCCHHH
Q ss_conf             223-455543321123443211122222211000112356643321100023566520223432121145--32420013
Q gi|254780282|r  156 IQR-KLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQ--VNSYLSIM  232 (299)
Q Consensus       156 ~~~-~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~s~~~~~  232 (299)
                      ... +.....-.+|+.++    ...|.+++||.+..+.... +++    ....+...... ..|.....+  .-+.+.++
T Consensus       120 ~~~p~Y~~v~q~LVyr~g----~~rP~~l~DL~G~~I~V~~-gSs----y~e~L~~Lk~~-~~P~L~w~~~~~~~teeLL  189 (507)
T PRK10859        120 QPGPTYYSVSQQLVYRVG----QYRPRTLGDLTGEQLTVAP-GHV----VVNDLQTLKET-KFPELSWKVDDKKGSAELL  189 (507)
T ss_pred             CCCCCCCCEEEEEEEECC----CCCCCCHHHCCCCEEEECC-CCH----HHHHHHHHHHC-CCCCEEEEECCCCCHHHHH
T ss_conf             356865030039999589----9898897783798699817-975----99999998853-4897159955899999999


Q ss_pred             HHHHHHC-CEEEEEHHHHCC----CCCEEE
Q ss_conf             5678738-423311777601----998466
Q gi|254780282|r  233 QYCVLGS-GIALLPDYIVKD----NPNLVR  257 (299)
Q Consensus       233 ~~v~~g~-Gia~lp~~~~~~----~~~lv~  257 (299)
                      ++|..|. -.+++....+.-    .+++..
T Consensus       190 ~~V~~g~IdyTVaDS~~~~l~qr~~P~L~v  219 (507)
T PRK10859        190 EQVIEGKLDYTIADSVAISLFQRVHPELAV  219 (507)
T ss_pred             HHHHCCCCCEEEECCHHHHHHHHHCCCHHC
T ss_conf             999759877688554889987764844012


No 85 
>pfam01638 HxlR HxlR-like helix-turn-helix. HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.
Probab=92.01  E-value=0.23  Score=27.21  Aligned_cols=66  Identities=21%  Similarity=0.394  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHH-CCCHHHHHHHHHHHHHHHCCEEEEECC-------CCEEEEECCCCCCCCCCCC
Q ss_conf             89999999999827689999882-899789999999999995882179769-------9468500134332222222
Q gi|254780282|r    5 WDKLRVFYVVARSGSFTHAAEQL-HLSQSSISRQISGLETEVGIKLFYRHA-------RGLTLTEQGSKLHRVTSEV   73 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~s~AA~~L-~itq~avS~~i~~LE~~lg~~Lf~R~~-------~~~~lT~~G~~l~~~a~~~   73 (299)
                      |..+-..........|+.=.+.+ ++|+..+|+++++||+.   -|+.|..       -.+.||+.|+.|.+-...+
T Consensus         6 Wt~~Il~~L~~g~~rF~el~~~l~gis~~vLs~rLk~L~~~---gli~r~~~~~~p~~~eY~LT~~G~~l~pvl~~l   79 (90)
T pfam01638         6 WKLLILRELLDGPKRFSELKRALPGISQKMLTQRLRELEQD---GIINREVYPEVPPKVEYSLTEKGRSLEPILQAM   79 (90)
T ss_pred             CHHHHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHC---CCEEEEECCCCCCCEEEEECCCHHHHHHHHHHH
T ss_conf             79999999974998899999776576989999999999988---993764569999936874390787899999999


No 86 
>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=91.95  E-value=0.2  Score=27.60  Aligned_cols=29  Identities=31%  Similarity=0.438  Sum_probs=25.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHH-----------HHHHHHCC
Q ss_conf             689999882899789999999-----------99999588
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQIS-----------GLETEVGI   47 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~-----------~LE~~lg~   47 (299)
                      |+++.|+.|+||+++||+-+.           +|++.||.
T Consensus        22 s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~   61 (81)
T TIGR02607        22 SVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGT   61 (81)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf             6899998709997888888744899888899999997389


No 87 
>PRK10651 transcriptional regulator NarL; Provisional
Probab=91.93  E-value=0.64  Score=24.70  Aligned_cols=38  Identities=21%  Similarity=0.299  Sum_probs=19.1

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCC--CCC-CCCCCCCCCC
Q ss_conf             0000135667542000122222222--222-2222222223
Q gi|254780282|r  107 LLQGNLKEFLLLYPDIQIQLILDNK--DID-ISMDYADCAI  144 (299)
Q Consensus       107 ~l~~~l~~f~~~~P~i~i~i~~~~~--~~~-l~~~~~Di~i  144 (299)
                      .+-..+..+.+..|++++--..++.  ..+ +.....|+.|
T Consensus        17 l~r~gl~~~L~~~~~~~vv~~a~~~~ea~~~~~~~~pDlvl   57 (216)
T PRK10651         17 MLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLIL   57 (216)
T ss_pred             HHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHCCCCEEE
T ss_conf             99999999997589938999989999999998707999999


No 88 
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=91.81  E-value=0.38  Score=26.02  Aligned_cols=37  Identities=32%  Similarity=0.473  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             99999999827--68999988289978999999999999
Q gi|254780282|r    8 LRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         8 L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      ++.+..+-+.|  |+..-|++|+++||++|..|+.||+.
T Consensus        26 v~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~a   64 (308)
T COG4189          26 VAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKA   64 (308)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             999999987179878999988588656666557888864


No 89 
>PRK04168 hypothetical protein; Provisional
Probab=91.73  E-value=0.41  Score=25.83  Aligned_cols=84  Identities=19%  Similarity=0.198  Sum_probs=48.3

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCC--CCC-CCC-C-CCCCCCCCCCCCCC----CCC--C
Q ss_conf             32222223332111000000000135667542000122222222--222-222-2-22222345654321----111--2
Q gi|254780282|r   88 SVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNK--DID-ISM-D-YADCAIRLRKPIQS----SSL--I  156 (299)
Q Consensus        88 ~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~--~~~-l~~-~-~~Di~i~~~~~~~~----~~l--~  156 (299)
                      ...+.|+|.|....|+... +-.+-..|.++||++++....+.+  ... +.+ | .+|+.+......-+    +++  .
T Consensus        28 ~~~~~~~l~Vf~AGSL~~p-f~ei~~~Fe~~~p~v~v~~e~~GS~~~ar~Ite~g~~aDVfaSAD~~~i~~ll~p~~adw  106 (336)
T PRK04168         28 EAEPPGKLKIFHAGSLSVP-FEEYEKEFEAYYPNVDVQREAGGSVACVRKITELGKPADILASADYTLIPKMMIPEYADW  106 (336)
T ss_pred             CCCCCEEEEEEECCCCHHH-HHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCCCEEEECCHHHHHHHHCCCCCCC
T ss_conf             7788615999975525899-999999999878996599984738999999995799988899898578788746443341


Q ss_pred             CCCCCCCCCCCCCCCC
Q ss_conf             2345554332112344
Q gi|254780282|r  157 QRKLVTIHMHAYAAPH  172 (299)
Q Consensus       157 ~~~l~~~~~~~v~~~~  172 (299)
                      ...+.+.+++++-+++
T Consensus       107 ~v~FA~N~lViayt~~  122 (336)
T PRK04168        107 YVMFATNEIVLAYTDK  122 (336)
T ss_pred             EEEECCCEEEEEECCC
T ss_conf             0121155389997688


No 90 
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=91.36  E-value=1  Score=23.50  Aligned_cols=190  Identities=10%  Similarity=0.059  Sum_probs=92.7

Q ss_pred             CCCCCCCCCCCCCCCCCC-----------CCH---HH-HHHH--HHHCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             222233321110000000-----------001---35-6675--42000122222---2222222222222223456543
Q gi|254780282|r   91 PSGKLRIATTIDLGQNLL-----------QGN---LK-EFLL--LYPDIQIQLIL---DNKDIDISMDYADCAIRLRKPI  150 (299)
Q Consensus        91 ~~g~i~I~~~~~~~~~~l-----------~~~---l~-~f~~--~~P~i~i~i~~---~~~~~~l~~~~~Di~i~~~~~~  150 (299)
                      .+|+|+||+..++.+.-.           .++   +. .+.+  ..|++++++..   .++...|..|.+|+.+.--...
T Consensus        38 ~~G~l~vG~~~~~pPf~~~d~~g~~vGfdvDla~~ia~~l~~~l~~~~~~v~~v~~~~~~rip~L~~gk~Di~~~~~t~T  117 (302)
T PRK10797         38 KNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNN  117 (302)
T ss_pred             HCCEEEEEECCCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCCC
T ss_conf             69989999899989971689999851541799999999998774467734999975788877999789808897357569


Q ss_pred             C--CCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECC
Q ss_conf             2--1111-223455543321123443211122222211000112356643321100023566520223432121145324
Q gi|254780282|r  151 Q--SSSL-IQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNS  227 (299)
Q Consensus       151 ~--~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s  227 (299)
                      +  ...+ ...+.+.....+++.++     ....+++||.+-....- .+..    ...++...... .........+++
T Consensus       118 ~eR~k~vdFS~pY~~~~~~llv~k~-----s~Iks~~DL~GK~V~V~-~GTt----~e~~~~~~~~~-~~~~~~iv~~~~  186 (302)
T PRK10797        118 LERQKQAAFSDTIFVVGTRLLTKKG-----GDIKDFADLKGKAVVVT-SGTT----SEVLLNKLNEE-QKMNMRIISAKD  186 (302)
T ss_pred             HHHHCCEEECCCCEECCEEEEEECC-----CCCCCHHHHCCCEEEEE-CCCH----HHHHHHHHHHH-HCCCCEEEECCC
T ss_conf             7774124214662771468999778-----86667566089979996-7873----99999986675-067723785088


Q ss_pred             CCHHHHHHHHHCCEEEEEHH-H-----HC-CCCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             20013567873842331177-7-----60-199846617766676600899934877888899999999999985
Q gi|254780282|r  228 YLSIMQYCVLGSGIALLPDY-I-----VK-DNPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKAR  295 (299)
Q Consensus       228 ~~~~~~~v~~g~Gia~lp~~-~-----~~-~~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r  295 (299)
                      ...+...+.+|..-+++-+. .     +. ..+....+... +....++++..+|+   .+..+.+++--+++.+
T Consensus       187 ~~~a~~~L~~GrvDA~~~D~~~l~~~~~~~~~~~~~~iv~~-~~~~e~ygia~rKg---d~~L~~~Vn~aL~~l~  257 (302)
T PRK10797        187 HGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGK-PQSQEAYGCMLRKD---DPQFKKLMDDTIAQAQ  257 (302)
T ss_pred             HHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCEEEECC-CCCCCCEEEEEECC---CHHHHHHHHHHHHHHH
T ss_conf             89999999859950998122988899986369975499378-67776079999689---9999999999999999


No 91 
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=91.28  E-value=1  Score=23.45  Aligned_cols=170  Identities=10%  Similarity=0.028  Sum_probs=82.9

Q ss_pred             CCCCCCCCCCCCCCCC----------CCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCC-CCC-CCCCCCC-
Q ss_conf             2223332111000000----------00013566754200012222222---222222222222234-565-4321111-
Q gi|254780282|r   92 SGKLRIATTIDLGQNL----------LQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIR-LRK-PIQSSSL-  155 (299)
Q Consensus        92 ~g~i~I~~~~~~~~~~----------l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~-~~~-~~~~~~l-  155 (299)
                      .++|+||+.+.+.++-          -.+++..+.++- ++++++...+   ....|..|++|+++. +.. +.....+ 
T Consensus        24 ~~~l~Vg~~~~~pPf~f~~~g~~~GfdvDl~~~ia~~l-g~~~e~~~~~~~~~i~~l~~g~~D~~~~~~~~T~eR~~~~~  102 (247)
T PRK09495         24 DKELVVATDTAFVPFEFKQGDKYVGFDVDLWAAIAKEL-KLDYTLKPMDFSGIIPALQTKNIDLALAGITITDERKKAID  102 (247)
T ss_pred             CCEEEEEECCCCCCEEECCCCEEEEEHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEECCCCCCHHHHHHCC
T ss_conf             99499998998798057679927882999999999996-99469997788999999976995636466014789984333


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHH
Q ss_conf             22345554332112344321112222221100011235664332110002356652022343212114532420013567
Q gi|254780282|r  156 IQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYC  235 (299)
Q Consensus       156 ~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v  235 (299)
                      ...+.+.....+++..+.    ....+++||.+... ....++.    ...++...     .+......+++...+..++
T Consensus       103 FS~py~~~~~~i~v~~~~----~~i~~~~dL~Gk~v-~v~~Gs~----~~~~~~~~-----~~~~~i~~~~~~~~~~~aL  168 (247)
T PRK09495        103 FSDGYYKSGLLVMVKANN----NDIKSVKDLDGKVV-AVKSGTG----SVDYAKAN-----IKTKDLRQFPNIDNAYLEL  168 (247)
T ss_pred             CCCCCEEEEEEEEEECCC----CCCCCHHHCCCCEE-EEECCCH----HHHHHHHH-----CCCCCEEECCCHHHHHHHH
T ss_conf             477707724699998999----77798245489889-9846958----99999963-----8898669659889999987


Q ss_pred             HHHCCEEEEEHH-----HHCCC--CCEEEECCCCCCCCCEEEEEECCCCC
Q ss_conf             873842331177-----76019--98466177666766008999348778
Q gi|254780282|r  236 VLGSGIALLPDY-----IVKDN--PNLVRIMEDVITPSFTVYFCYPEALK  278 (299)
Q Consensus       236 ~~g~Gia~lp~~-----~~~~~--~~lv~i~~~~~~~~~~~~lv~~~~~~  278 (299)
                      .+|..=+++-+.     .++..  +.+ ++... +.....+++..+++..
T Consensus       169 ~~GrvDa~v~d~~~~~~~~~~~~~~~~-~~~~~-~~~~~~~~ia~~k~~~  216 (247)
T PRK09495        169 GTGRADAVLHDTPNILYFIKTAGNGQF-KAVGD-SLEAQQYGIAFPKGSD  216 (247)
T ss_pred             HCCCEEEEEECHHHHHHHHHHCCCCCE-EEECC-CCCCCEEEEEEECCHH
T ss_conf             658734999568999999984899978-99467-7776459999928829


No 92 
>PRK04217 hypothetical protein; Provisional
Probab=91.21  E-value=0.57  Score=24.98  Aligned_cols=62  Identities=16%  Similarity=0.318  Sum_probs=45.1

Q ss_pred             CCHHHHHHHHHH-HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCC
Q ss_conf             888999999999-9827689999882899789999999999995882179769946850013433
Q gi|254780282|r    3 FDWDKLRVFYVV-ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL   66 (299)
Q Consensus         3 md~~~L~~f~~v-~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l   66 (299)
                      |+++.|+.+.-+ .+--+-..||++++||++|+.+-+.+-...+...|+.  |+.+..-+.|..+
T Consensus        43 LtvdE~EaiRL~D~egl~qeeaA~~M~VSR~Tf~ril~~AR~KvA~aLv~--Gkal~I~~~g~~~  105 (110)
T PRK04217         43 MTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVE--GRELIILPQGNEV  105 (110)
T ss_pred             ECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC--CCEEEEECCCCCE
T ss_conf             11999999998736079899999884976999999999999999999867--9748997489960


No 93 
>PRK09775 hypothetical protein; Provisional
Probab=91.01  E-value=0.11  Score=29.22  Aligned_cols=36  Identities=25%  Similarity=0.428  Sum_probs=25.3

Q ss_pred             HHHHHCCHHHH--HHHHCCCHHHHHHHHHHHHHHHCCEEEEE
Q ss_conf             99982768999--98828997899999999999958821797
Q gi|254780282|r   13 VVARSGSFTHA--AEQLHLSQSSISRQISGLETEVGIKLFYR   52 (299)
Q Consensus        13 ~v~~~gs~s~A--A~~L~itq~avS~~i~~LE~~lg~~Lf~R   52 (299)
                      ++-+-|-.+.+  |++|+|||||||++|+.    +|.+....
T Consensus         6 ~Ll~~Gp~~a~eLa~~lgvSqpTlSR~l~~----l~~~Vv~~   43 (443)
T PRK09775          6 TLLLQGPLSAAELAQRLGISQATLSRLLAA----AGPQVLRF   43 (443)
T ss_pred             HHHHCCCCCHHHHHHHHCCCHHHHHHHHHH----CCCCEEEE
T ss_conf             999739935999999868888889999986----25727885


No 94 
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=90.55  E-value=0.28  Score=26.79  Aligned_cols=37  Identities=24%  Similarity=0.153  Sum_probs=26.9

Q ss_pred             HHHHHCCHHHHHHHHCCCHHHHHHHH--------HHHHHHHCCEE
Q ss_conf             99982768999988289978999999--------99999958821
Q gi|254780282|r   13 VVARSGSFTHAAEQLHLSQSSISRQI--------SGLETEVGIKL   49 (299)
Q Consensus        13 ~v~~~gs~s~AA~~L~itq~avS~~i--------~~LE~~lg~~L   49 (299)
                      ++.-.||.++.|+.||||+|+||+-=        -+||+.-|-.|
T Consensus         6 vi~~FGsk~klA~aLgIs~~aVsqWge~IPE~rAy~le~iT~G~L   50 (75)
T PRK09744          6 AIAFFGSKTKLANAAGVRLASVAAWGELVPEGRAMRLQEASGGEL   50 (75)
T ss_pred             HHHHHCCHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHCCCE
T ss_conf             999961299999994998799988740160688999999858851


No 95 
>COG0226 PstS ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=90.18  E-value=1.3  Score=22.86  Aligned_cols=202  Identities=12%  Similarity=0.102  Sum_probs=99.6

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCC---CC-------CCC
Q ss_conf             22222333211100000000013566754200012222222---222222222222234565432---11-------112
Q gi|254780282|r   90 KPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIRLRKPIQ---SS-------SLI  156 (299)
Q Consensus        90 ~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~~~~~~~---~~-------~l~  156 (299)
                      ...+.|+++-+.+. ..+.-.....|.+.||++.+++....   .......+++|++- ...|..   ..       .+.
T Consensus        40 ~~~~~l~~~GSttv-~p~~~~~a~~~~~~~~~~~v~~q~~GSg~G~~~~~~~~vDig~-ss~p~~~~e~~~~~~~~~~l~  117 (318)
T COG0226          40 GASGSLTIAGSTTV-APLMEAWAEEFQKAYPNVKVNVQAGGSGAGIKQALAGGVDIGA-SSRPLKDSEKEADAKAGKKLV  117 (318)
T ss_pred             CCCCEEEEECCCCH-HHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCCCCCCC-CCCCCCCCHHHHHHHCCCCCE
T ss_conf             55435998365738-9999999999998789947876368661889987526770313-576666326799874079866


Q ss_pred             CCCCCCCCCCCCCCCCCCC-CC-----------CCCCCCCCCC----CCCC--CCCCCCCCCCCCHHHHHHHHCC--CCC
Q ss_conf             2345554332112344321-11-----------2222221100----0112--3566433211000235665202--234
Q gi|254780282|r  157 QRKLVTIHMHAYAAPHYLK-NC-----------REPLSIQELD----KHNL--ITFGDLIPKCMEDFNWLATVDR--PIG  216 (299)
Q Consensus       157 ~~~l~~~~~~~v~~~~~~~-~~-----------~~~~~~~dL~----~~~~--i~~~~~~~~~~~~~~~~~~~~~--~~~  216 (299)
                      ..++.-+.++++..+.-+. ..           +....+.|+.    +.+.  +.-.+.......+..++.....  ..+
T Consensus       118 ~~pva~d~i~vi~N~~~~~~~~Lt~~~l~~If~G~it~W~d~~~~~~n~~I~vv~R~~~SGT~~~F~~~l~~~~~~~~~g  197 (318)
T COG0226         118 EFPVAIDAIVVIVNLPNPDVLNLTKDQLADIFSGKITNWNDVGGQLLNPGITVVGRSDGSGTTETFTEYLLGWKKKVGAG  197 (318)
T ss_pred             EEEEEEEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             97788777999975898541347999999997088875556686558998568847877776999999987653203456


Q ss_pred             --CCCCCEEEECCCCHHHHHHHHH-CCEEEEEHHHHCCC-----------CC---EEE-----ECCCCC-CCCCEEEEEE
Q ss_conf             --3212114532420013567873-84233117776019-----------98---466-----177666-7660089993
Q gi|254780282|r  217 --EPRISCLQVNSYLSIMQYCVLG-SGIALLPDYIVKDN-----------PN---LVR-----IMEDVI-TPSFTVYFCY  273 (299)
Q Consensus       217 --~~~~~~~~~~s~~~~~~~v~~g-~Gia~lp~~~~~~~-----------~~---lv~-----i~~~~~-~~~~~~~lv~  273 (299)
                        ..........+...+...|... .+|+++--..+.++           +.   -+.     +..... +..+..|+++
T Consensus       198 ~~~~~~~~~~~~~n~~v~~~v~~tp~aIGYv~~~y~~~n~~~~~~~~~~~~~~~~~v~p~~~~i~~~~y~Pi~~~~~~~v  277 (318)
T COG0226         198 KTVDWPAAVGGKGNEGVVAAVSQTPGAIGYVGYAYAVQNNLKLAALANKAGGVGPTVEPTAENIANGKYSPIVRPLFIYV  277 (318)
T ss_pred             CCCCCCCEECCCCCHHHHHHHHCCCCCEEEEEEHHHHHCCCHHHHHHHCCCCCCCCCCCHHHHHHCCCCCCCEEEEEEEE
T ss_conf             65445640036885788988853998459998679652430566642015776666564577753377355125789998


Q ss_pred             CCCCC--CCHHHHHHHHHHHHH
Q ss_conf             48778--888999999999999
Q gi|254780282|r  274 PEALK--NTGKLKAFRNFIFLK  293 (299)
Q Consensus       274 ~~~~~--~~~~~~~f~d~l~~~  293 (299)
                      .+...  ..+.++.|++|.+..
T Consensus       278 ~~~~~~~~~~~~~~Fi~~~~~~  299 (318)
T COG0226         278 NKNPKDTKAPAVKAFLDWALSP  299 (318)
T ss_pred             ECCCCCCCCHHHHHHHHHHHCC
T ss_conf             2776666588999999999678


No 96 
>PRK10403 transcriptional regulator NarP; Provisional
Probab=90.17  E-value=1.1  Score=23.26  Aligned_cols=17  Identities=18%  Similarity=0.546  Sum_probs=8.2

Q ss_pred             CCCHHHHHHHHHHCCCC
Q ss_conf             00013566754200012
Q gi|254780282|r  108 LQGNLKEFLLLYPDIQI  124 (299)
Q Consensus       108 l~~~l~~f~~~~P~i~i  124 (299)
                      +-..+..+.+..|++++
T Consensus        18 ~r~gl~~~L~~~~~~~v   34 (215)
T PRK10403         18 MRRGVRQLLELDPGFEV   34 (215)
T ss_pred             HHHHHHHHHHHCCCEEE
T ss_conf             99999999975899289


No 97 
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=89.59  E-value=0.18  Score=27.85  Aligned_cols=93  Identities=18%  Similarity=0.214  Sum_probs=55.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHH-CCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCC-CCCCCCC
Q ss_conf             7689999882899789999999999995-8821797699468500134332222222222101221001223-2222223
Q gi|254780282|r   18 GSFTHAAEQLHLSQSSISRQISGLETEV-GIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESS-VKPSGKL   95 (299)
Q Consensus        18 gs~s~AA~~L~itq~avS~~i~~LE~~l-g~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~-~~~~g~i   95 (299)
                      -+.+..|++|++|+++.|+.|++||+.= =.+-..+.|.-+..|+.|..++...      +++....+.... -...|.+
T Consensus        20 ~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~------~~d~~r~~~~~~~i~i~G~V   93 (214)
T COG1339          20 VTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKE------YEDLSRIFDSGGNIVIEGEV   93 (214)
T ss_pred             CCHHHHHHHHCCCCHHHHHHHHHHCCCCCEEEEECCCCCEEEEHHHHHHHHHHH------HHHHHHHHCCCCCEEEEEEE
T ss_conf             208999988574707788998864117847888337984898167689999999------99999996688736999889


Q ss_pred             CCCCCCCCCCCCC--CCHHHHHHHH
Q ss_conf             3321110000000--0013566754
Q gi|254780282|r   96 RIATTIDLGQNLL--QGNLKEFLLL  118 (299)
Q Consensus        96 ~I~~~~~~~~~~l--~~~l~~f~~~  118 (299)
                      .=|+..  +.+++  +..-..|++.
T Consensus        94 ~SGlGE--G~yyvS~~~Y~~qf~ek  116 (214)
T COG1339          94 VSGLGE--GRYYVSLPGYRRQFREK  116 (214)
T ss_pred             ECCCCC--CEEEEECHHHHHHHHHH
T ss_conf             525556--43797268889999998


No 98 
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=89.56  E-value=1.4  Score=22.66  Aligned_cols=15  Identities=13%  Similarity=-0.204  Sum_probs=5.9

Q ss_pred             CHHHHHHHHHHCCCC
Q ss_conf             013566754200012
Q gi|254780282|r  110 GNLKEFLLLYPDIQI  124 (299)
Q Consensus       110 ~~l~~f~~~~P~i~i  124 (299)
                      ..+..+++.+|+..+
T Consensus        62 ~~~~~ir~~~~~~~v   76 (204)
T PRK09958         62 QVLETLRKRQYSGII   76 (204)
T ss_pred             HHHHHHHHHCCCEEE
T ss_conf             678889872798059


No 99 
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=89.51  E-value=1  Score=23.45  Aligned_cols=46  Identities=22%  Similarity=0.338  Sum_probs=37.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCC-CEEEEECCCCC
Q ss_conf             76899998828997899999999999958821797699-46850013433
Q gi|254780282|r   18 GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHAR-GLTLTEQGSKL   66 (299)
Q Consensus        18 gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~-~~~lT~~G~~l   66 (299)
                      -+-+.=|+.|+||..|||.+||+|-++   -|++..|| ....|..|...
T Consensus        26 v~q~eIA~~lgiT~QaVsehiK~Lv~e---G~i~~~gR~~Y~iTkkG~e~   72 (260)
T COG1497          26 VKQKEIAKKLGITLQAVSEHIKELVKE---GLIEKEGRGEYEITKKGAEW   72 (260)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHHHC---CCEEECCCEEEEEEHHHHHH
T ss_conf             788899987098799999999999866---46661487258972668999


No 100
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=89.13  E-value=0.82  Score=24.05  Aligned_cols=54  Identities=24%  Similarity=0.325  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHH---HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEE--CCCCEEEEEC
Q ss_conf             99999999998---276899998828997899999999999958821797--6994685001
Q gi|254780282|r    6 DKLRVFYVVAR---SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYR--HARGLTLTEQ   62 (299)
Q Consensus         6 ~~L~~f~~v~~---~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R--~~~~~~lT~~   62 (299)
                      |-|..+.++++   --|++.-|++++++.|++.+.++.|++. |  ++.|  ..+++.|++.
T Consensus        12 Ral~ILe~l~~~~~~lslsela~~lglpksTv~RlL~tL~~~-G--~l~~~~~~~~Y~LG~~   70 (264)
T PRK09834         12 RGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE-G--YVRRSASDDSFRLTLK   70 (264)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEEECCCCCEECCHH
T ss_conf             999999987417999799999999790999999999999978-9--9899679997651607


No 101
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=89.08  E-value=1.6  Score=22.36  Aligned_cols=41  Identities=20%  Similarity=0.276  Sum_probs=17.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE
Q ss_conf             689999882899789999999999995882179769946850
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT   60 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT   60 (299)
                      |++.+|+.-+--.+.||+.++.||. +|.--|+++|+..+|+
T Consensus        80 Si~ElAe~vgRdv~nvhr~Ls~l~~-~GlI~fe~~gq~k~P~  120 (144)
T COG4190          80 SINELAELVGRDVKNVHRTLSTLAD-LGLIFFEEDGQRKQPV  120 (144)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH-CCEEEEECCCCCCCCE
T ss_conf             3899999867546889899999986-4827874177313752


No 102
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=89.01  E-value=0.51  Score=25.25  Aligned_cols=56  Identities=14%  Similarity=0.029  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE
Q ss_conf             899999999998276899998828997899999999999958821797699468500
Q gi|254780282|r    5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE   61 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~   61 (299)
                      ++-|++|-.--..-+++.-|+.++++.|++.+-++.|+++ |.--.+..++.+.|..
T Consensus        28 l~IL~~la~~~~~ltl~eia~~lglpksT~~RlL~tL~~~-G~v~~d~~~~~Y~lG~   83 (271)
T PRK10163         28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA-DFVYQDSQLGWWHIGL   83 (271)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEECCCCCEECCH
T ss_conf             9999999747999799999999791999999999999968-9889848999176478


No 103
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=88.97  E-value=0.63  Score=24.73  Aligned_cols=55  Identities=29%  Similarity=0.375  Sum_probs=39.1

Q ss_pred             HHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHH--CCEEEEECCC-----CEEEEECCCCCCCC
Q ss_conf             99827--689999882899789999999999995--8821797699-----46850013433222
Q gi|254780282|r   14 VARSG--SFTHAAEQLHLSQSSISRQISGLETEV--GIKLFYRHAR-----GLTLTEQGSKLHRV   69 (299)
Q Consensus        14 v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~l--g~~Lf~R~~~-----~~~lT~~G~~l~~~   69 (299)
                      +-+.|  |....|++|+||..||-+|+..||++=  ... +.+.++     .+++|+.|..-+++
T Consensus        20 L~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~-~~~~g~GRP~~~y~Lt~~g~~~f~~   83 (218)
T COG2345          20 LKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE-RQQGGRGRPAKLYRLTEKGREQFPK   83 (218)
T ss_pred             HHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE-ECCCCCCCCCEEEEECCCCHHHCCH
T ss_conf             831698249999988599989999999999868666876-4257899973332200262654453


No 104
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=88.84  E-value=0.71  Score=24.42  Aligned_cols=66  Identities=24%  Similarity=0.335  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCCEEEEECCC-------CEEEEECCCCCCCCCCCC
Q ss_conf             899999999998276899998828-997899999999999958821797699-------468500134332222222
Q gi|254780282|r    5 WDKLRVFYVVARSGSFTHAAEQLH-LSQSSISRQISGLETEVGIKLFYRHAR-------GLTLTEQGSKLHRVTSEV   73 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~s~AA~~L~-itq~avS~~i~~LE~~lg~~Lf~R~~~-------~~~lT~~G~~l~~~a~~~   73 (299)
                      |.-+-..........|+.=-+.+. |||-.+|++++.||+.   -|+.|.-.       ...||+.|+.|.+....+
T Consensus        24 W~~lIl~~L~~g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~---Glv~R~~~~~~PprveY~LT~~G~~L~~vl~~l   97 (120)
T COG1733          24 WTLLILRDLFDGPKRFNELRRSIGGISPKMLSRRLKELEED---GLVERVVYPEEPPRVEYRLTEKGRDLLPVLLAL   97 (120)
T ss_pred             CHHHHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHC---CCEEEEECCCCCCEEEEEEHHHHHHHHHHHHHH
T ss_conf             49999999954987399998677454899999999999988---998987417899534777634327699999999


No 105
>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=88.74  E-value=0.85  Score=23.98  Aligned_cols=44  Identities=25%  Similarity=0.493  Sum_probs=32.1

Q ss_pred             CCC--CHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             988--88999999999982768999988289978999999999999588
Q gi|254780282|r    1 MSF--DWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGI   47 (299)
Q Consensus         1 m~m--d~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~   47 (299)
                      |..  ||++ +++-.+-+.+|.+.||+..+||.++|-+=+++  .+.|.
T Consensus         1 MaYS~DlR~-rVl~~ve~G~S~~eaA~~F~Is~~Tv~rWlkr--~~~~~   46 (120)
T pfam01710         1 MAYSLDLRK-KVIDYIESGGSITEASKVFQIGRATIYRWLKR--EKLGA   46 (120)
T ss_pred             CCCCHHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC--HHCCC
T ss_conf             987689999-99999986999999999937029999999855--00147


No 106
>PRK09483 response regulator; Provisional
Probab=88.11  E-value=1.9  Score=21.98  Aligned_cols=16  Identities=13%  Similarity=0.291  Sum_probs=7.1

Q ss_pred             CCHHHHHHHHHHCCCC
Q ss_conf             0013566754200012
Q gi|254780282|r  109 QGNLKEFLLLYPDIQI  124 (299)
Q Consensus       109 ~~~l~~f~~~~P~i~i  124 (299)
                      -.-+..+.+..|++++
T Consensus        14 r~gl~~~L~~~~~~~v   29 (216)
T PRK09483         14 RAGIRRILEDIKGIKV   29 (216)
T ss_pred             HHHHHHHHHHCCCCEE
T ss_conf             9999999974899589


No 107
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=88.04  E-value=1.9  Score=21.95  Aligned_cols=18  Identities=22%  Similarity=0.313  Sum_probs=8.4

Q ss_pred             CCHHHHHHHHHHCCCCCC
Q ss_conf             001356675420001222
Q gi|254780282|r  109 QGNLKEFLLLYPDIQIQL  126 (299)
Q Consensus       109 ~~~l~~f~~~~P~i~i~i  126 (299)
                      -.-+..+.+..|++++-.
T Consensus        16 r~gl~~~l~~~~~~~vv~   33 (210)
T PRK09935         16 RMSIEVLLQKNSNIQVVL   33 (210)
T ss_pred             HHHHHHHHHCCCCEEEEE
T ss_conf             999999996298928999


No 108
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=87.96  E-value=1.9  Score=21.92  Aligned_cols=37  Identities=16%  Similarity=0.250  Sum_probs=16.3

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCCCC---CCCCCCCCCCCC
Q ss_conf             0001356675420001222222222---222222222223
Q gi|254780282|r  108 LQGNLKEFLLLYPDIQIQLILDNKD---IDISMDYADCAI  144 (299)
Q Consensus       108 l~~~l~~f~~~~P~i~i~i~~~~~~---~~l~~~~~Di~i  144 (299)
                      +-.-+..+.+.+|++++--..++..   ..+.....|+.|
T Consensus        13 ~r~gl~~~l~~~~~~~vv~~~~~~~~~l~~~~~~~~dvvl   52 (196)
T PRK10360         13 VRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCI   52 (196)
T ss_pred             HHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHCCCCEEE
T ss_conf             9999999981299959999989999999988744999999


No 109
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=87.46  E-value=2.1  Score=21.75  Aligned_cols=15  Identities=20%  Similarity=0.299  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHCCCCC
Q ss_conf             135667542000122
Q gi|254780282|r  111 NLKEFLLLYPDIQIQ  125 (299)
Q Consensus       111 ~l~~f~~~~P~i~i~  125 (299)
                      .+..+++.+|++.|-
T Consensus        70 ~~~~i~~~~p~~~vi   84 (216)
T PRK10840         70 LIKYIKRHFPSLSII   84 (216)
T ss_pred             HHHHHHHHCCCCEEE
T ss_conf             999999858998089


No 110
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=87.39  E-value=1.7  Score=22.27  Aligned_cols=71  Identities=21%  Similarity=0.198  Sum_probs=54.5

Q ss_pred             CCCCHHHHHHHHHHHHH--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCC
Q ss_conf             98888999999999982--768999988289978999999999999588217976994685001343322222
Q gi|254780282|r    1 MSFDWDKLRVFYVVARS--GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTS   71 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~--gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~   71 (299)
                      |.+..++.+.+.++.+.  .+....|+.+++.+..|-+.++.|++.==+..-.+....+.||++|+..++.--
T Consensus         2 ~~L~~~E~kIL~~L~~~~~~~~eeLa~~~g~d~~~V~~ai~~L~~kglI~vee~~~~~~~LTeEG~~yle~Gl   74 (501)
T PRK04172          2 MELHPNEKKVLKALAELKKATAEELAEKLGLDEEAVMRAAEWLEEKGLVEVEEKVTEFYELTEEGKKYLEEGL   74 (501)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEEEEEEEEECHHHHHHHHCCC
T ss_conf             7478789999999974799999999988299999999999988758997999888889998888999997699


No 111
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=86.92  E-value=2.2  Score=21.57  Aligned_cols=168  Identities=8%  Similarity=0.037  Sum_probs=79.4

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCC-CC-CCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             000013566754200012222222---222222222222234-56-54321111-2234555433211234432111222
Q gi|254780282|r  107 LLQGNLKEFLLLYPDIQIQLILDN---KDIDISMDYADCAIR-LR-KPIQSSSL-IQRKLVTIHMHAYAAPHYLKNCREP  180 (299)
Q Consensus       107 ~l~~~l~~f~~~~P~i~i~i~~~~---~~~~l~~~~~Di~i~-~~-~~~~~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~  180 (299)
                      +..+++..+.+.- ++++++...+   ....+..|++|+++. +. .+.....+ ...++.....++++.++.     ..
T Consensus        24 ~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~fs~p~~~~~~~~~~~~~~-----~~   97 (218)
T cd00134          24 FDVDLAKAIAKEL-GVKVKFVEVDWDGLITALKSGKVDLIAAGMTITPERAKQVDFSDPYYKSGQVILVKKGS-----PI   97 (218)
T ss_pred             EHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHCCCCCEEEEEECCCHHHHCCCCCCCCEECCCEEEEEECCC-----CC
T ss_conf             3999999999996-99669997588999999857997768885025856614145576444157079998689-----99


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHCCEEEE-EHHH----HCCCC-C
Q ss_conf             2221100011235664332110002356652022343212114532420013567873842331-1777----60199-8
Q gi|254780282|r  181 LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLGSGIALL-PDYI----VKDNP-N  254 (299)
Q Consensus       181 ~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g~Gia~l-p~~~----~~~~~-~  254 (299)
                      .+++||.+...... .+..    ....+....     +......+++...++.++..|..=+++ +...    .++.+ .
T Consensus        98 ~~~~dl~g~~i~v~-~g~~----~~~~l~~~~-----~~~~~~~~~~~~~~~~~l~~G~vD~~v~~~~~~~~~~~~~~~~  167 (218)
T cd00134          98 KSVKDLKGKKVAVQ-KGST----AEKYLKKAL-----PEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHPPE  167 (218)
T ss_pred             CCHHHHCCCEEEEE-CCCH----HHHHHHHHH-----CCCEEEEECCHHHHHHHHHCCCCEEEEECHHHHHHHHHHCCCC
T ss_conf             99899779626795-8988----999999731-----5754999699999999998599469997699999999867998


Q ss_pred             EEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             466177666766008999348778888999999999999
Q gi|254780282|r  255 LVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       255 lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      +..+.+.....+..+++..+++   ++.....++-.+++
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~---~~~l~~~~n~~l~~  203 (218)
T cd00134         168 LKIVGPSIDLEPLGFGVAVGKD---NKELLDAVNKALKE  203 (218)
T ss_pred             CEEECCCCCCCCEEEEEEECCC---CHHHHHHHHHHHHH
T ss_conf             1996356676734899997499---99999999999999


No 112
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=86.62  E-value=1.5  Score=22.51  Aligned_cols=49  Identities=14%  Similarity=0.215  Sum_probs=36.0

Q ss_pred             CCHHHHHHHHHHH-HHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEE
Q ss_conf             8889999999999-827689999882899789999999999995882179
Q gi|254780282|r    3 FDWDKLRVFYVVA-RSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFY   51 (299)
Q Consensus         3 md~~~L~~f~~v~-~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~   51 (299)
                      |..+.|+.+.-+. +--+-..||++++||++|+++-+.+-...+...|+.
T Consensus        37 L~~dE~EAiRL~D~egl~QeeaA~~MgVSR~Tf~ril~~ARkKvA~aLv~   86 (100)
T pfam02001        37 ITLDEFEAIRLVDYEDYTQEEAAKLMGISRRTVWRLLTSARKKIADALVE   86 (100)
T ss_pred             ECHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             34999999998736079899999884976999999999999999999867


No 113
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=86.47  E-value=2.3  Score=21.52  Aligned_cols=20  Identities=15%  Similarity=0.155  Sum_probs=7.7

Q ss_pred             HHHHHHHHCCEEEEECCCCE
Q ss_conf             99999995882179769946
Q gi|254780282|r   38 ISGLETEVGIKLFYRHARGL   57 (299)
Q Consensus        38 i~~LE~~lg~~Lf~R~~~~~   57 (299)
                      +.++-+.+|...-+=+.+|+
T Consensus        15 V~~~~~ii~~nINimD~~G~   34 (385)
T PRK11477         15 VARTMRIIDTNINVMDARGR   34 (385)
T ss_pred             HHHHHHHCCCCEEEECCCCE
T ss_conf             99999756998699999947


No 114
>pfam05043 Mga Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.
Probab=86.02  E-value=1.4  Score=22.65  Aligned_cols=44  Identities=23%  Similarity=0.380  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH---CCEE
Q ss_conf             89999999999827689999882899789999999999995---8821
Q gi|254780282|r    5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEV---GIKL   49 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~l---g~~L   49 (299)
                      ++-|+.+. -.+.-|+..-|++++||.|++.+.|+++...|   |..+
T Consensus        19 f~il~~lf-~~~~~s~~~~a~~l~iS~sTl~R~ik~l~~~L~~~~l~i   65 (87)
T pfam05043        19 FQLLKFLF-FHEFFSLTSLAQKLFISESTLYRLIKKLNKLLKEFDLSI   65 (87)
T ss_pred             HHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCEEE
T ss_conf             99999998-189998999999978899999999999999999859688


No 115
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=85.52  E-value=1.2  Score=23.12  Aligned_cols=16  Identities=13%  Similarity=0.110  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHCCCCCC
Q ss_conf             1356675420001222
Q gi|254780282|r  111 NLKEFLLLYPDIQIQL  126 (299)
Q Consensus       111 ~l~~f~~~~P~i~i~i  126 (299)
                      .+..+.+++|++...+
T Consensus       111 ~f~~ll~~~p~l~~~l  126 (236)
T PRK09392        111 LVREAMSEDPAFARAV  126 (236)
T ss_pred             HHHHHHHHCHHHHHHH
T ss_conf             9999998799999999


No 116
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=85.43  E-value=2.6  Score=21.12  Aligned_cols=21  Identities=5%  Similarity=0.010  Sum_probs=14.0

Q ss_pred             CCHHHHHHHHHHCCCCCCCCC
Q ss_conf             001356675420001222222
Q gi|254780282|r  109 QGNLKEFLLLYPDIQIQLILD  129 (299)
Q Consensus       109 ~~~l~~f~~~~P~i~i~i~~~  129 (299)
                      ...+.++++.+|++.|=+.+.
T Consensus        63 ~e~l~~l~~~~p~~~vivlT~   83 (202)
T PRK09390         63 IELLRRLKARGSPLPVIVMTG   83 (202)
T ss_pred             HHHHHHHHHCCCCCCEEEEEE
T ss_conf             079999872289986799974


No 117
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=85.10  E-value=0.46  Score=25.53  Aligned_cols=82  Identities=13%  Similarity=0.086  Sum_probs=41.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH-CCCCCCCCCCCCCC
Q ss_conf             68999988289978999999999999588217976994685001343322222222221012210-01223222222333
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE-LQESSVKPSGKLRI   97 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~-~~~~~~~~~g~i~I   97 (299)
                      +++--|+..|||++|||+.|..             ..++.  +   .--+++.++..++.-.-+. .+..+.+.++.|-+
T Consensus         8 Ti~dIA~~aGVS~aTVSrvLn~-------------~~~Vs--~---eTr~rV~~aa~elgY~pn~~A~~l~~~~t~~Ig~   69 (342)
T PRK10014          8 TIHDVALAAGVSVSTVSLVLSG-------------KGRIS--T---ATGERVNQAIEELGFVRNRQASALRGGQSGVIGL   69 (342)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC-------------CCCCC--H---HHHHHHHHHHHHHCCCCCHHHHHHCCCCCCEEEE
T ss_conf             7999999989699999999779-------------89999--9---9999999999994899786788641387736886


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             2111000000000135667542
Q gi|254780282|r   98 ATTIDLGQNLLQGNLKEFLLLY  119 (299)
Q Consensus        98 ~~~~~~~~~~l~~~l~~f~~~~  119 (299)
                      -+ +.+...+...++..+.+..
T Consensus        70 v~-~~~~~~f~~~~i~gi~~~~   90 (342)
T PRK10014         70 IV-RDLSAPFYAELTAGLTEAL   90 (342)
T ss_pred             EC-CCCCCHHHHHHHHHHHHHH
T ss_conf             05-4457767799999999999


No 118
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR; InterPro: IPR012712    This Helix-Turn-Helix transcriptional regulator is a member of the MarR family and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0010124 phenylacetate catabolic process, 0016481 negative regulation of transcription.
Probab=85.00  E-value=0.63  Score=24.73  Aligned_cols=78  Identities=23%  Similarity=0.323  Sum_probs=61.3

Q ss_pred             CCCHHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-----CC--EEEEECCCCCCCCCCC
Q ss_conf             8888999999999982768--9999882899789999999999995882179769-----94--6850013433222222
Q gi|254780282|r    2 SFDWDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-----RG--LTLTEQGSKLHRVTSE   72 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-----~~--~~lT~~G~~l~~~a~~   72 (299)
                      |++=.|.|++..+++.|++  +.=|...+|=.|++|+-|++||+   ..|+.|..     |+  +.+|++|..|++.+.+
T Consensus        25 ~lTEQQWRilR~L~~~G~~e~~~LA~~A~iL~PSLTgiL~rLE~---~glv~R~k~~~DQRR~~~~lT~~G~~L~~~~~p  101 (130)
T TIGR02337        25 GLTEQQWRILRVLAEKGSMEFTELADRACILRPSLTGILARLEK---RGLVVRLKASNDQRRVYISLTKKGQALYESVSP  101 (130)
T ss_pred             CCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHHH---CCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             79647899999883389948687886641479965789999974---587022588877441242223789999998515


Q ss_pred             CCCC-CCHHHH
Q ss_conf             2222-101221
Q gi|254780282|r   73 VYHK-LETTQI   82 (299)
Q Consensus        73 ~l~~-~~~~~~   82 (299)
                      -.+. +++++.
T Consensus       102 ~~e~~Y~~I~~  112 (130)
T TIGR02337       102 QVEEIYAAIEE  112 (130)
T ss_pred             HHHHHHHHHHH
T ss_conf             69999999998


No 119
>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=84.14  E-value=1.1  Score=23.40  Aligned_cols=27  Identities=11%  Similarity=0.113  Sum_probs=23.7

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             827689999882899789999999999
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQISGLE   42 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i~~LE   42 (299)
                      +..++...|+.||+|+++||+.+++-=
T Consensus        19 ~~~t~~EIA~~lgis~~~V~~~~~ral   45 (50)
T pfam04545        19 EGLTLEEIGERLGISRERVRQIEKRAL   45 (50)
T ss_pred             CCCHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             882499999998979999999999999


No 120
>PTZ00326 phenylalanyl-tRNA synthetase; Provisional
Probab=84.06  E-value=1.8  Score=22.06  Aligned_cols=71  Identities=21%  Similarity=0.180  Sum_probs=50.0

Q ss_pred             CCCCHHHHHHHHHHHHHCC--HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCC
Q ss_conf             9888899999999998276--8999988289978999999999999588217976994685001343322222
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSGS--FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTS   71 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~gs--~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~   71 (299)
                      |++.-..-..+.++...++  --..|+.+++.+..|-+.++.||+.==+..=.+....+.||++|+..++.--
T Consensus         2 ~~~~~~~~~iL~~L~~~~~~~s~ela~~~g~~~~~Vvgai~sLeskglV~vee~~~~~~~LTeEG~~yle~Gl   74 (505)
T PTZ00326          2 MQKEEELNTLLEALESAESVTSLAVAEDLSIDHQDVVGAIKSLEALNYIKTEEIKSNTLKLTKEGKDILESGS   74 (505)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEEEEEEECHHHHHHHHCCC
T ss_conf             6416899999999986699999999998596999999999999868997999998889998988999998599


No 121
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=83.65  E-value=1.8  Score=22.07  Aligned_cols=37  Identities=30%  Similarity=0.420  Sum_probs=28.6

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEE
Q ss_conf             8999988289978999999999999588217976994685
Q gi|254780282|r   20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTL   59 (299)
Q Consensus        20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~l   59 (299)
                      -..=|+.+|+|..+||+.+++|+++   -++.+.++.+.+
T Consensus        11 ~~~iA~~lG~tretvsR~l~~l~~~---GlI~~~~~~i~i   47 (48)
T smart00419       11 RQEIAELLGLTRETVSRTLKRLEKE---GLISREGGRIVI   47 (48)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHC---CCEEECCCEEEE
T ss_conf             9999999799799999999999988---979978978997


No 122
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=83.16  E-value=3  Score=20.80  Aligned_cols=50  Identities=16%  Similarity=0.174  Sum_probs=39.7

Q ss_pred             CCCHHHHHHHHHH-HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEE
Q ss_conf             8888999999999-9827689999882899789999999999995882179
Q gi|254780282|r    2 SFDWDKLRVFYVV-ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFY   51 (299)
Q Consensus         2 ~md~~~L~~f~~v-~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~   51 (299)
                      .|+++.|+.+.-+ ++.-+...||.+++||++|+.+.+++-....-..|+.
T Consensus        33 ~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLve   83 (99)
T COG1342          33 ILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTSARKKVADALVE   83 (99)
T ss_pred             EECHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             522999889998868610578999984642999999999999999999855


No 123
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=82.92  E-value=1.7  Score=22.23  Aligned_cols=34  Identities=29%  Similarity=0.387  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9999999998276899998828997899999999
Q gi|254780282|r    7 KLRVFYVVARSGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus         7 ~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      .|..|++...-|.=+++|..|+|++|.|+|-++-
T Consensus         2 ~ls~~va~~vvg~q~a~a~LLgvsp~~vnQw~~g   35 (96)
T COG4197           2 NLSIFVACAVVGGQKALARLLGVSPPSVNQWIKG   35 (96)
T ss_pred             CHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf             6018899999703899999972681478877652


No 124
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=82.68  E-value=2.1  Score=21.65  Aligned_cols=58  Identities=21%  Similarity=0.286  Sum_probs=51.0

Q ss_pred             HHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCC
Q ss_conf             9999999827689999882899789999999999995882179769946850013433222
Q gi|254780282|r    9 RVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRV   69 (299)
Q Consensus         9 ~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~   69 (299)
                      +.+.++..+++|-+-+..-..+-|.|+.-++.||++   .++.+..+++.+|+.|+.|.+.
T Consensus        26 ~vl~ail~~~d~wkIvd~s~~plp~v~~i~~~l~~e---giv~~~~g~v~~TekG~E~~e~   83 (354)
T COG1568          26 NVLSAILATNDFWKIVDYSDLPLPLVASILEILEDE---GIVKIEEGGVELTEKGEELAEE   83 (354)
T ss_pred             HHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHC---CCEEEECCCEEEHHHHHHHHHH
T ss_conf             999999747527757653158726899999999866---8189854847642626999998


No 125
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=82.67  E-value=3.5  Score=20.42  Aligned_cols=187  Identities=11%  Similarity=0.061  Sum_probs=84.8

Q ss_pred             CCCCCCCCCCCCCCCCCC------------CCHHHHHHHHH--HCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCC--
Q ss_conf             222233321110000000------------00135667542--000122222---22222222222222234565432--
Q gi|254780282|r   91 PSGKLRIATTIDLGQNLL------------QGNLKEFLLLY--PDIQIQLIL---DNKDIDISMDYADCAIRLRKPIQ--  151 (299)
Q Consensus        91 ~~g~i~I~~~~~~~~~~l------------~~~l~~f~~~~--P~i~i~i~~---~~~~~~l~~~~~Di~i~~~~~~~--  151 (299)
                      .+|+|+||+...+.+.-+            .++...+.+..  .++.+++..   .+....|..|.+|+.+.--...+  
T Consensus        36 ~~G~L~vg~~~~~pPf~~~d~~~g~~~GfDvDla~~iAk~llg~~~~v~~v~~~~~~~~p~L~~gkvD~i~~~~tiT~eR  115 (259)
T PRK11917         36 SKGQLIVGVKNDVPHYALLDQATGEIKGFEIDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTITPER  115 (259)
T ss_pred             HCCEEEEEECCCCCCCCEEECCCCCEEEEEHHHHHHHHHHHCCCCCEEEEEEECHHHHHHHHHCCCEEEEEECCCCCCCH
T ss_conf             59989999878978862056799967888799999999996599856999970678776898779855998664767654


Q ss_pred             CCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCH
Q ss_conf             1111-223455543321123443211122222211000112356643321100023566520223432121145324200
Q gi|254780282|r  152 SSSL-IQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLS  230 (299)
Q Consensus       152 ~~~l-~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~  230 (299)
                      ...+ ...+.+.....+++.++     ....+++||.+-.. +......    ...+........+.. ....++++...
T Consensus       116 ~k~vdFS~PY~~~~~~ilv~k~-----~~i~~~~DL~gk~V-gv~~gst----~~~~~~~~~~~~~~~-~~~~~~~~~~~  184 (259)
T PRK11917        116 KRIYNFSEPYYQDAIGLLVLKE-----KNYKSLADMKGANI-GVAQAAT----TKKAIGEAAKKIGID-VKFSEFPDYPS  184 (259)
T ss_pred             HCCEEECCCEEEEEEEEEEECC-----CCCCCHHHHCCCCE-EEEECCC----HHHHHHHHHHHCCCC-EEEEECCCHHH
T ss_conf             3057622476996559999899-----99999899589817-9992784----699999988860885-16996499999


Q ss_pred             HHHHHHHHCCEEEE-EHHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf             13567873842331-1777601--998466177666766008999348778888999999999999
Q gi|254780282|r  231 IMQYCVLGSGIALL-PDYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK  293 (299)
Q Consensus       231 ~~~~v~~g~Gia~l-p~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~  293 (299)
                      +...+.+|..-+++ ....+..  +... .+.++ +-.+.++++..+++   ++..+.+++-.+.+
T Consensus       185 ~~~~l~~grvDa~~~d~~~~~~~~~~~~-~~~~~-~~~~~~~giavrKg---d~~l~~~vn~~i~~  245 (259)
T PRK11917        185 IKAALDAKRVDAFSVDKSILLGYVDDKS-EILPD-SFEPQSYGIVTKKD---DPAFAKYVDDFVKE  245 (259)
T ss_pred             HHHHHHCCCEEEEECCHHHHHHHHHCCC-CCCCC-CCCCCEEEEEEECC---CHHHHHHHHHHHHH
T ss_conf             9999984980299826999999986198-01688-88752589999489---98999999999999


No 126
>PRK11569 transcriptional repressor IclR; Provisional
Probab=80.92  E-value=1.5  Score=22.50  Aligned_cols=54  Identities=17%  Similarity=0.179  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC--CCEEEEE
Q ss_conf             89999999999827689999882899789999999999995882179769--9468500
Q gi|254780282|r    5 WDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA--RGLTLTE   61 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~--~~~~lT~   61 (299)
                      ++-|++|-.--..-+++.-|++++++.|++.+-++.||+. |  ++.|.+  +.+.|.+
T Consensus        31 l~IL~~la~~~~~lsl~eia~~lglpksT~~RlL~tL~~~-G--~v~~~~~~~~Y~LG~   86 (274)
T PRK11569         31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ-G--FVRQVGELGHWAIGA   86 (274)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEECCCCCEECCCH
T ss_conf             9999999638999899999998791999999999999976-9--877869988022457


No 127
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=80.55  E-value=4.2  Score=19.97  Aligned_cols=12  Identities=42%  Similarity=0.789  Sum_probs=4.6

Q ss_pred             HHHHHHHHHHCC
Q ss_conf             135667542000
Q gi|254780282|r  111 NLKEFLLLYPDI  122 (299)
Q Consensus       111 ~l~~f~~~~P~i  122 (299)
                      -+..+...++++
T Consensus        15 gl~~~L~~~~~~   26 (211)
T COG2197          15 GLRQLLELEPDL   26 (211)
T ss_pred             HHHHHHHHCCCC
T ss_conf             999999868996


No 128
>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=80.36  E-value=4.2  Score=19.93  Aligned_cols=23  Identities=13%  Similarity=0.286  Sum_probs=15.6

Q ss_pred             CHHHHHHHHHHHHHHHCCEEEEE
Q ss_conf             97899999999999958821797
Q gi|254780282|r   30 SQSSISRQISGLETEVGIKLFYR   52 (299)
Q Consensus        30 tq~avS~~i~~LE~~lg~~Lf~R   52 (299)
                      |...|-..+.++-..+|..-|.=
T Consensus        16 t~~~l~~~l~~~~~~~Gfd~~~y   38 (232)
T TIGR03541        16 TLEAIQDAVREFAQNLGYDRFVL   38 (232)
T ss_pred             CHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             99999999999999849988999


No 129
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=80.07  E-value=2.4  Score=21.32  Aligned_cols=53  Identities=21%  Similarity=0.244  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC--CCEEEEEC
Q ss_conf             9999999999827-689999882899789999999999995882179769--94685001
Q gi|254780282|r    6 DKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA--RGLTLTEQ   62 (299)
Q Consensus         6 ~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~--~~~~lT~~   62 (299)
                      +-|.+|-. ...+ +++.-|++++++.|++++.+..|++.   -+..+.+  +.+.|++.
T Consensus         8 ~iL~~l~~-~~~~l~l~ela~~~glpksT~~RlL~tL~~~---G~v~~d~~~grY~Lg~~   63 (246)
T COG1414           8 AILDLLAE-GPGGLSLAELAERLGLPKSTVHRLLQTLVEL---GYVEQDPEDGRYRLGPR   63 (246)
T ss_pred             HHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEECCCCCEEEECHH
T ss_conf             99999971-8888879999998791988999999999978---98889799996985789


No 130
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=79.42  E-value=3.3  Score=20.56  Aligned_cols=52  Identities=13%  Similarity=0.102  Sum_probs=39.4

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCC
Q ss_conf             9827689999882899789999999999995882179769946850013433
Q gi|254780282|r   15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKL   66 (299)
Q Consensus        15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l   66 (299)
                      .+.=++..=|+.++||.+++.+-++++++++...|-.+...|....-.|...
T Consensus        90 ~~~i~l~dLAd~lfVSrsTi~~dl~~vre~l~~~l~i~~k~~~gi~i~g~E~  141 (585)
T PRK09863         90 NTFTPMGQLASALFLSRTWVAERLPRLNQRYERTCCIASRPGLGHFIDETEE  141 (585)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEECCCCCEEEECCHH
T ss_conf             6898899999985839999999999999987314589104898579835179


No 131
>PRK06424 transcription factor; Provisional
Probab=79.14  E-value=4.2  Score=19.97  Aligned_cols=18  Identities=11%  Similarity=0.237  Sum_probs=9.9

Q ss_pred             ECCCCHHHHHHHHHCCEE
Q ss_conf             324200135678738423
Q gi|254780282|r  225 VNSYLSIMQYCVLGSGIA  242 (299)
Q Consensus       225 ~~s~~~~~~~v~~g~Gia  242 (299)
                      ++||...+.=++...|++
T Consensus        82 veDy~~~Ir~ARE~~Gls   99 (144)
T PRK06424         82 VEDYAELVKNARERLSMS   99 (144)
T ss_pred             HHHHHHHHHHHHHHCCCC
T ss_conf             877999999999984999


No 132
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=78.89  E-value=1.1  Score=23.30  Aligned_cols=25  Identities=36%  Similarity=0.384  Sum_probs=23.1

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             8276899998828997899999999
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      ...|++.||+.|++++++||+.++.
T Consensus        16 ~f~Si~~aak~l~~~~~~I~~~l~~   40 (53)
T smart00497       16 EFSSIREAAKYLGISHSSISKYLNT   40 (53)
T ss_pred             HHHHHHHHHHHHCCCCCCHHHHHCC
T ss_conf             7787999999858883238887067


No 133
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=78.84  E-value=2.8  Score=20.94  Aligned_cols=39  Identities=21%  Similarity=0.140  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             999999999982768999988289978999999999999
Q gi|254780282|r    6 DKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         6 ~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      +-|++|-.--+.-+++.-|+.++++.|++.+.+..||++
T Consensus         7 ~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~tL~~~   45 (52)
T pfam09339         7 AILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQTLVEL   45 (52)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             999998628999899999999891999999999999988


No 134
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=78.75  E-value=4.8  Score=19.63  Aligned_cols=61  Identities=25%  Similarity=0.355  Sum_probs=49.6

Q ss_pred             CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCC
Q ss_conf             988889999999999827--6899998828997899999999999958821797699468500134
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGS   64 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~   64 (299)
                      |...-|+-+.+-.|.+.|  ++...|+.++||..||-|=|.+||+.   -++.|..+|..++..-.
T Consensus         1 m~~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---g~l~R~hGGa~~~~~~~   63 (253)
T COG1349           1 MLKEERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQ---GLLLRVHGGAVLPDSES   63 (253)
T ss_pred             CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CEEEEEECEEECCCCCC
T ss_conf             9777899999999998596979999988597899998619999778---92899606188377665


No 135
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=78.21  E-value=5  Score=19.54  Aligned_cols=14  Identities=7%  Similarity=0.038  Sum_probs=6.0

Q ss_pred             CCCHHHHHHHHHHH
Q ss_conf             88889999999999
Q gi|254780282|r  278 KNTGKLKAFRNFIF  291 (299)
Q Consensus       278 ~~~~~~~~f~d~l~  291 (299)
                      .++++.+-.+.|..
T Consensus       179 ~LT~RE~E~L~W~A  192 (240)
T PRK10188        179 NFSKREKEILKWTA  192 (240)
T ss_pred             CCCHHHHHHHHHHH
T ss_conf             89989999999997


No 136
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=77.79  E-value=3.2  Score=20.64  Aligned_cols=60  Identities=23%  Similarity=0.195  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHH---CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCC
Q ss_conf             99999999982---76899998828997899999999999958821797699468500134332
Q gi|254780282|r    7 KLRVFYVVARS---GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLH   67 (299)
Q Consensus         7 ~L~~f~~v~~~---gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~   67 (299)
                      -+..+..+++.   -+++.-|+.++++.|++.+-++.||+. |.--.+..++++.|++.--.+-
T Consensus         7 al~IL~~l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL~~~-G~l~~~~~~~~Y~lG~~~~~lg   69 (91)
T smart00346        7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL-GYVEQDGQNGRYRLGPKVLELG   69 (91)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEECCCCEEEECHHHHHHH
T ss_conf             99999999728999899999999890999999999999988-9968849999775309999999


No 137
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=76.39  E-value=5.6  Score=19.23  Aligned_cols=56  Identities=16%  Similarity=0.259  Sum_probs=43.1

Q ss_pred             CHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC
Q ss_conf             889999999999827--68999988289978999999999999588217976994685001
Q gi|254780282|r    4 DWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ   62 (299)
Q Consensus         4 d~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~   62 (299)
                      .-|+-+..-.+-+.|  ++..-|+.++||..||-|=++.||++   .++.|..+|..++..
T Consensus         4 ~eR~~~Il~~L~~~g~v~v~eLa~~l~VS~~TIRRDL~~Le~~---G~l~R~hGGa~~~~~   61 (256)
T PRK10434          4 RQRQAAILEYLQKQGKCSVEELAQYFDTTGTTIRKDLVILEHA---GTVIRTYGGVVLNKE   61 (256)
T ss_pred             HHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECEEECCCC
T ss_conf             9999999999998697999999998796998999849999878---988999473864777


No 138
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=76.04  E-value=1.7  Score=22.28  Aligned_cols=111  Identities=14%  Similarity=0.138  Sum_probs=54.2

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf             68999988289978999999999999588217976994685001343322222222221012210012232222223332
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIA   98 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~   98 (299)
                      ++.--|+..|||.+|||+.+..             +..+. -+--+++.+.++++=-.-+..   .+.++.+..+.|-+-
T Consensus         2 TikDVA~~AGVS~sTVSrvln~-------------~~~Vs-~eTr~rV~~a~~elgY~pn~~---Ar~L~~~~s~~Ig~i   64 (333)
T COG1609           2 TIKDVAKLAGVSKATVSRVLNG-------------SPYVS-EETREKVLAAIKELGYRPNAV---ARSLRTGRTKTIGLV   64 (333)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC-------------CCCCC-HHHHHHHHHHHHHHCCCCCHH---HHHHHHCCCCEEEEE
T ss_conf             6899999968999898898779-------------99879-999999999999978998989---999874778889999


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCCCCCC--CCCC--------CCCCCCCCCCCCCCCC
Q ss_conf             11100000000013566754200012222--2222--------2222222222223456
Q gi|254780282|r   99 TTIDLGQNLLQGNLKEFLLLYPDIQIQLI--LDNK--------DIDISMDYADCAIRLR  147 (299)
Q Consensus        99 ~~~~~~~~~l~~~l~~f~~~~P~i~i~i~--~~~~--------~~~l~~~~~Di~i~~~  147 (299)
                      .+ .+...+...++..+.+..-+-..++.  .++.        ...+...++|-.|..+
T Consensus        65 ~p-~~~~~~~~~i~~gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdGiIi~~  122 (333)
T COG1609          65 VP-DITNPFFAEILKGIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDGLILLG  122 (333)
T ss_pred             EC-CCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             46-87775899999999999998399899983789869999999999876989899935


No 139
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=75.88  E-value=3.3  Score=20.53  Aligned_cols=27  Identities=19%  Similarity=0.306  Sum_probs=22.6

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             982768999988289978999999999
Q gi|254780282|r   15 ARSGSFTHAAEQLHLSQSSISRQISGL   41 (299)
Q Consensus        15 ~~~gs~s~AA~~L~itq~avS~~i~~L   41 (299)
                      .-.||-++||+.|||+..++-+.|++.
T Consensus        69 ~t~gNqskAA~~LGInR~TLRkKlk~y   95 (98)
T PRK00430         69 YTRGNQTRAALMLGINRGTLRKKLKKY   95 (98)
T ss_pred             HHCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             966959999999787788999999984


No 140
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=75.17  E-value=3.9  Score=20.17  Aligned_cols=103  Identities=20%  Similarity=0.135  Sum_probs=57.8

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             89999882899789999999999995882179769946850013433222222222210122100122322222233321
Q gi|254780282|r   20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGKLRIAT   99 (299)
Q Consensus        20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~i~I~~   99 (299)
                      =+.-.+..|.|.|+||..++.||++=   .+.|..      -.|+..    +-.|.         +..+-...+-+|||+
T Consensus        23 Q~eIeel~GlSKStvSEaLs~LE~~g---iv~Rrk------vsGKs~----rVwLa---------ey~Py~d~~~lRiGi   80 (321)
T COG3888          23 QTEIEELMGLSKSTVSEALSELEKQG---IVKRRK------VSGKSK----RVWLA---------EYSPYPDSRFLRIGI   80 (321)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHCC---EEEEEE------ECCCCE----EEEEC---------CCCCCCCCCCEEEEE
T ss_conf             87889885745647999999988568---056655------057533----88620---------037877756078856


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHCCCCCCCCC--CCCCCCCCCCCCCCC
Q ss_conf             110000000001356675420001222222--222222222222223
Q gi|254780282|r  100 TIDLGQNLLQGNLKEFLLLYPDIQIQLILD--NKDIDISMDYADCAI  144 (299)
Q Consensus       100 ~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~--~~~~~l~~~~~Di~i  144 (299)
                      .-+.-...+.+....+.+.-=++.|++.-+  +-.-||..|.+|+|+
T Consensus        81 LRatEYp~~i~aaKnl~e~ki~a~iR~Yddaisit~DLv~g~ld~~l  127 (321)
T COG3888          81 LRATEYPFFISAAKNLEERKISATIRFYDDAISITRDLVEGKLDFGL  127 (321)
T ss_pred             EECCCCHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHHHCC
T ss_conf             41233125758987664436408999963577899988764446201


No 141
>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=74.65  E-value=0.72  Score=24.40  Aligned_cols=10  Identities=10%  Similarity=0.238  Sum_probs=4.6

Q ss_pred             HHHHHHHCCC
Q ss_conf             9999985066
Q gi|254780282|r  289 FIFLKARDWK  298 (299)
Q Consensus       289 ~l~~~~r~~~  298 (299)
                      ||.++.+||+
T Consensus       319 yl~~k~~eA~  328 (477)
T TIGR02395       319 YLKEKLQEAR  328 (477)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 142
>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=74.46  E-value=6.3  Score=18.93  Aligned_cols=30  Identities=20%  Similarity=0.284  Sum_probs=25.8

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             982768999988289978999999999999
Q gi|254780282|r   15 ARSGSFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus        15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      .+.-|+...|+.||+|.++|+.++.+--+.
T Consensus        24 ~~~~s~~EIa~~lgis~~tVk~~l~rA~~~   53 (55)
T cd06171          24 GEGLSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             809999999999895999999999999987


No 143
>PRK00118 putative DNA-binding protein; Validated
Probab=73.67  E-value=5.4  Score=19.31  Aligned_cols=32  Identities=19%  Similarity=0.217  Sum_probs=26.6

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             98276899998828997899999999999958
Q gi|254780282|r   15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVG   46 (299)
Q Consensus        15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg   46 (299)
                      .+--|++.-|+.++||.+||+-.|++-|..|.
T Consensus        31 ~~DlSl~EIAe~~~iSRQaV~D~ikr~~~~L~   62 (105)
T PRK00118         31 LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLE   62 (105)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             85499999989969859999999999999999


No 144
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=73.32  E-value=6.7  Score=18.77  Aligned_cols=195  Identities=9%  Similarity=0.079  Sum_probs=86.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCC-CCCC---CCCCCCCCCCCCCCCCCCC-----CCCCCCCCC---
Q ss_conf             222333211100000000013566754200012222-2222---2222222222223456543-----211112234---
Q gi|254780282|r   92 SGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI-LDNK---DIDISMDYADCAIRLRKPI-----QSSSLIQRK---  159 (299)
Q Consensus        92 ~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~-~~~~---~~~l~~~~~Di~i~~~~~~-----~~~~l~~~~---  159 (299)
                      .-+|+||++++....++ .......++.-++++++. .++-   ...|..|++|.-+.-..|.     ...+..-..   
T Consensus        31 ~k~ikVG~~~~p~~~i~-e~~~~~~~ek~G~~leiv~FsDy~~PN~AL~~G~iDaN~fQH~pyL~~~n~~~g~~L~~v~~  109 (272)
T PRK09861         31 AKHIKVGVINGAEQDVA-EVAKKVAKEKYGLDVELVGFSGSLLPNDATNHGELDANVFQHRPFLEQDNQAHGYKLVAVGN  109 (272)
T ss_pred             CCEEEEEECCCCHHHHH-HHHHHHHHHHCCCEEEEEEECCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             97389996789869999-99998887617976899994686226289767983602455799999999986995799731


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC---------------CCC-CEE
Q ss_conf             5554332112344321112222221100011235664332110002356652022343---------------212-114
Q gi|254780282|r  160 LVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGE---------------PRI-SCL  223 (299)
Q Consensus       160 l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~-~~~  223 (299)
                      ...+++.++..        ...+++||.+-.-|..+.......+-...++..+.-...               |.. ...
T Consensus       110 ~~~~P~glYS~--------K~ksl~dlp~Ga~IaIPnDpsN~~RAL~lL~~aGLI~Lk~~~~~~~t~~DI~~NPk~lk~~  181 (272)
T PRK09861        110 TFVFPMAGYSK--------KIKTVAQIKEGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLPTALDITDNPRHLQIM  181 (272)
T ss_pred             EEEEEEEECCC--------CCCCHHHCCCCCEEEECCCHHHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHCCCCCCEEE
T ss_conf             67830140344--------6598758479998980478126999999999889789779999777744576088776799


Q ss_pred             EECCCCHHHHHHHH-HCCEEEEEHHHHCCCC-CE--EEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH-HHC
Q ss_conf             53242001356787-3842331177760199-84--66177666766008999348778888999999999999-850
Q gi|254780282|r  224 QVNSYLSIMQYCVL-GSGIALLPDYIVKDNP-NL--VRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK-ARD  296 (299)
Q Consensus       224 ~~~s~~~~~~~v~~-g~Gia~lp~~~~~~~~-~l--v~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~-~r~  296 (299)
                      +++.... -+.... ..-.++++...+.+.| .-  -.++.+....++-..++.+++...+|.++.|++.+.+. +++
T Consensus       182 e~~aaql-~rsl~Dp~vD~avin~n~a~~agl~p~~dal~~E~~~~py~niiavr~~~~d~~~ik~lv~a~~S~evk~  258 (272)
T PRK09861        182 ELEGAQL-PRVLDDPKVDVAIISTTYIQQTGLSPVHDSVFIEDKNSPYVNILVAREDNKNAENVKEFLQSYQSPEVAK  258 (272)
T ss_pred             ECCHHHH-HHHHCCCCCCEEEECHHHHHHCCCCCCCCCEEECCCCCCEEEEEEECCCCCCCHHHHHHHHHHCCHHHHH
T ss_conf             8267774-6750577616899760579887779440020366899983799998276769989999999977999999


No 145
>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=73.29  E-value=1.3  Score=22.91  Aligned_cols=15  Identities=27%  Similarity=0.616  Sum_probs=10.3

Q ss_pred             HC-CCHHHHHHHHHHH
Q ss_conf             28-9978999999999
Q gi|254780282|r   27 LH-LSQSSISRQISGL   41 (299)
Q Consensus        27 L~-itq~avS~~i~~L   41 (299)
                      -. ||||+|||=|++|
T Consensus        31 ~~nvTQaTvSRDL~el   46 (155)
T TIGR01529        31 VKNVTQATVSRDLREL   46 (155)
T ss_pred             CCEECCCCHHHHHHHH
T ss_conf             7511234067878752


No 146
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=73.28  E-value=2.4  Score=21.35  Aligned_cols=196  Identities=11%  Similarity=0.012  Sum_probs=85.2

Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC---CC-CCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCC--
Q ss_conf             22223332111000000000135667542000122222---22-2222222222222345654321---111223455--
Q gi|254780282|r   91 PSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLIL---DN-KDIDISMDYADCAIRLRKPIQS---SSLIQRKLV--  161 (299)
Q Consensus        91 ~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~---~~-~~~~l~~~~~Di~i~~~~~~~~---~~l~~~~l~--  161 (299)
                      ...+||||-..+-....+...-.-|.+.+|+++|+...   +. ....|..|.+|++..-..|.--   .+.....+.  
T Consensus        25 ~~~~lrIgyq~~~~~~~~~~~~~~~ek~~~~~kV~w~~F~~G~~~~eAl~aG~iD~~~~g~~p~i~a~a~G~~~~~va~~  104 (314)
T PRK11553         25 SPEALRIGYQKGSIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGSTGDIPPIFAQAAGADLVYVGVE  104 (314)
T ss_pred             CCCEEEEEECCCCHHHHHHHHCCHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCEEEECCHHHHHHHHCCCCEEEEEEE
T ss_conf             89759999617741589998528676617898358997897489999997699754511585899998669986999986


Q ss_pred             ---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHH
Q ss_conf             ---54332112344321112222221100011235664332110002356652022343212114532420013567873
Q gi|254780282|r  162 ---TIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCVLG  238 (299)
Q Consensus       162 ---~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g  238 (299)
                         .....++++++     ....+++||.+-.. .+..+...+......+...+.....  ...+..+ ......+...|
T Consensus       105 ~~~~~~~~i~V~~~-----S~I~s~aDLkGKkV-a~~~Gs~~~~~l~~aL~~aGL~~~D--V~~v~l~-p~d~~aAl~~G  175 (314)
T PRK11553        105 PPKPKAEVILVAEN-----SPIKTVADLKGHKV-AFQKGSSSHNLLLRALRQAGLKFTD--IQPTYLT-PADARAAFQQG  175 (314)
T ss_pred             CCCCCCEEEEEECC-----CCCCCHHHHCCCEE-EEECCCHHHHHHHHHHHHCCCCHHH--EEEEECC-CHHHHHHHHCC
T ss_conf             37886418998489-----87788889389989-7417973799999999986998899--1898459-38899999669


Q ss_pred             --CCEEEEEHHHH--CCCCCEEEECCCC--CCCCCEEEEEECCCCCC-CHHHHHHHHHHHHHHHCC
Q ss_conf             --84233117776--0199846617766--67660089993487788-889999999999998506
Q gi|254780282|r  239 --SGIALLPDYIV--KDNPNLVRIMEDV--ITPSFTVYFCYPEALKN-TGKLKAFRNFIFLKARDW  297 (299)
Q Consensus       239 --~Gia~lp~~~~--~~~~~lv~i~~~~--~~~~~~~~lv~~~~~~~-~~~~~~f~d~l~~~~r~~  297 (299)
                        .+++.-..+..  ...+.. +++.+.  ......++++.++-... +..++.|++.+.+ +.+|
T Consensus       176 ~VDA~~~w~P~~~~a~~~~ga-Rvl~dg~~~~~~~~~~~~~~~fa~~~p~~v~~~l~~l~~-a~~w  239 (314)
T PRK11553        176 NVDAWAIWDPYYSAALLQGGV-RVLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLSE-ADAL  239 (314)
T ss_pred             CCCEEEECCHHHHHHHHCCCC-EEEECCCCCCCCCCEEEECHHHHHHCHHHHHHHHHHHHH-HHHH
T ss_conf             978899756789999862895-898537666777616886189888799999999999999-9999


No 147
>PRK00215 LexA repressor; Validated
Probab=72.99  E-value=6.1  Score=19.00  Aligned_cols=45  Identities=22%  Similarity=0.329  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHCC-CHHHHHHHHHHHHHHHCCEEEEE---CCCCEEEEECCCC
Q ss_conf             768999988289-97899999999999958821797---6994685001343
Q gi|254780282|r   18 GSFTHAAEQLHL-SQSSISRQISGLETEVGIKLFYR---HARGLTLTEQGSK   65 (299)
Q Consensus        18 gs~s~AA~~L~i-tq~avS~~i~~LE~~lg~~Lf~R---~~~~~~lT~~G~~   65 (299)
                      =|+..=|+.+++ |.++|.++|++||+.   -.+.|   ..|++++|+.+..
T Consensus        24 Ps~rEI~~~~g~~S~~tV~~~l~~Le~k---G~i~r~~~~~R~i~i~~~~~~   72 (204)
T PRK00215         24 PSRREIADALGLRSPSAVHEHLKALERK---GFIRRDPGRSRAIEVLPAEAA   72 (204)
T ss_pred             CCHHHHHHHHCCCCCHHHHHHHHHHHHC---CCEECCCCCCCEEEEECCCCC
T ss_conf             9899999980999818999999999879---788706999733897157665


No 148
>pfam04297 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway.
Probab=72.56  E-value=5.9  Score=19.10  Aligned_cols=40  Identities=18%  Similarity=0.240  Sum_probs=29.2

Q ss_pred             HHHHHHHH-HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             99999999-99827689999882899789999999999995
Q gi|254780282|r    6 DKLRVFYV-VARSGSFTHAAEQLHLSQSSISRQISGLETEV   45 (299)
Q Consensus         6 ~~L~~f~~-v~~~gs~s~AA~~L~itq~avS~~i~~LE~~l   45 (299)
                      +|-.+|-. ..+--|++.-|+.++||.+||+-.|++-|..|
T Consensus        21 KQ~~~~~lyy~eDlSL~EIAe~~~iSRQaV~D~ikR~~~~L   61 (101)
T pfam04297        21 KQKNYFELYYLDDLSLSEIAEEFNVSRQAVYDNIKRTEKML   61 (101)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             99999999987639899999881985999999999999999


No 149
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=72.06  E-value=7.2  Score=18.59  Aligned_cols=150  Identities=14%  Similarity=0.067  Sum_probs=69.8

Q ss_pred             CCCCCCCCCCCCCCCCCCC---------CHHHHHHHHHHCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             2222333211100000000---------0135667542000122222222----22222222222234565432111122
Q gi|254780282|r   91 PSGKLRIATTIDLGQNLLQ---------GNLKEFLLLYPDIQIQLILDNK----DIDISMDYADCAIRLRKPIQSSSLIQ  157 (299)
Q Consensus        91 ~~g~i~I~~~~~~~~~~l~---------~~l~~f~~~~P~i~i~i~~~~~----~~~l~~~~~Di~i~~~~~~~~~~l~~  157 (299)
                      .+|.+++++..+-..++..         .+.++|. +|=+|++++...+.    ..+|..|+.|++- .+--....++..
T Consensus        21 ~rGvLrV~tinsp~sy~~~~~~p~G~eYelak~Fa-~yLgV~Lki~~~~n~dqLf~aL~ng~~DL~A-agl~~~~~~l~~   98 (473)
T COG4623          21 ARGVLRVSTINSPLSYFEDKGGPTGLEYELAKAFA-DYLGVKLKIIPADNIDQLFDALDNGNADLAA-AGLLYNSERLKN   98 (473)
T ss_pred             HCCEEEEEEECCCCCEECCCCCCCCHHHHHHHHHH-HHHCCEEEEEECCCHHHHHHHHHCCCCCEEC-CCCCCCHHHHCC
T ss_conf             66807998405865000037986535599999999-9859768998667788899998579933242-656679667404


Q ss_pred             CCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCC-CCCCCCCCEEEECCCCHHHHH
Q ss_conf             345554332112344--32111222222110001123566433211000235665202-234321211453242001356
Q gi|254780282|r  158 RKLVTIHMHAYAAPH--YLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDR-PIGEPRISCLQVNSYLSIMQY  234 (299)
Q Consensus       158 ~~l~~~~~~~v~~~~--~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~s~~~~~~~  234 (299)
                      -+  ..+...-+|..  |.....+|.++++|.+.... ...+.+    ....+....+ ..+...-..-..-+.+-++++
T Consensus        99 ~~--~gP~y~svs~qlVyRkG~~Rp~~l~~L~g~~i~-v~~gs~----~~~~l~~lk~~kyP~l~~k~d~~~~~~dLle~  171 (473)
T COG4623          99 FQ--PGPTYYSVSQQLVYRKGQYRPRSLGQLKGRQIT-VAKGSA----HVEDLKLLKETKYPELIWKVDDKLGVEDLLEM  171 (473)
T ss_pred             CC--CCCCEECCCHHHHHHCCCCCCCCHHHCCCCEEE-CCCCCH----HHHHHHHHHHHHCCHHHHHHCCCCCHHHHHHH
T ss_conf             67--887200225888765288787888873675564-069968----88999999873163443020221269999999


Q ss_pred             HHHH-CCEEEEEHHHH
Q ss_conf             7873-84233117776
Q gi|254780282|r  235 CVLG-SGIALLPDYIV  249 (299)
Q Consensus       235 v~~g-~Gia~lp~~~~  249 (299)
                      |..| ++.++.....+
T Consensus       172 v~~Gkldytiads~~i  187 (473)
T COG4623         172 VAEGKLDYTIADSVEI  187 (473)
T ss_pred             HHCCCCCEEEECCHHH
T ss_conf             9647766155161888


No 150
>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=71.27  E-value=5.7  Score=19.19  Aligned_cols=42  Identities=21%  Similarity=0.227  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHHHH-------CCHHHHHHHHCC-CHHHHHHHHHHHHHH
Q ss_conf             888999999999982-------768999988289-978999999999999
Q gi|254780282|r    3 FDWDKLRVFYVVARS-------GSFTHAAEQLHL-SQSSISRQISGLETE   44 (299)
Q Consensus         3 md~~~L~~f~~v~~~-------gs~s~AA~~L~i-tq~avS~~i~~LE~~   44 (299)
                      |+-+|-++|..+.++       =|+..-|+.+++ |.++|.++|+.||+.
T Consensus         4 LT~rQ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~Le~k   53 (65)
T pfam01726         4 LTERQREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKALERK   53 (65)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf             37999999999999999828898799999993899809999999999998


No 151
>pfam05225 HTH_psq helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence.
Probab=70.88  E-value=7.7  Score=18.44  Aligned_cols=34  Identities=26%  Similarity=0.426  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             999999999827--6899998828997899999999
Q gi|254780282|r    7 KLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus         7 ~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~   40 (299)
                      +|.--+.-++.|  |+.+||...+|..|++.++++.
T Consensus         4 ~l~~Al~av~~g~~S~~kAa~~ygIP~sTL~~r~~g   39 (45)
T pfam05225         4 DLAEALEAVRNGKMSLRKAARKYGIPRSTLWRRLRG   39 (45)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf             999999999919967999999978985899999756


No 152
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=69.58  E-value=8.2  Score=18.27  Aligned_cols=46  Identities=11%  Similarity=0.283  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHHH-HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE
Q ss_conf             888999999999-9827689999882899789999999999995882
Q gi|254780282|r    3 FDWDKLRVFYVV-ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK   48 (299)
Q Consensus         3 md~~~L~~f~~v-~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~   48 (299)
                      ++-+++...... --.||+..-|+.|+||=|||-.++.++=+.+|-.
T Consensus        34 L~~E~l~Fi~~fi~~~Gnlke~~~~lgiSYpTvR~rLd~ii~~lGy~   80 (113)
T pfam09862        34 LTPEQLEFVELFIKCRGNIKEVEKELGISYPTVRNRLDEIIAALGYE   80 (113)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCC
T ss_conf             89999999999999168899999997888188999999999980898


No 153
>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=69.21  E-value=4.1  Score=20.04  Aligned_cols=24  Identities=25%  Similarity=0.380  Sum_probs=18.8

Q ss_pred             HCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             276899998828997899999999
Q gi|254780282|r   17 SGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        17 ~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      --++...|+.|+++.||||+.++.
T Consensus        49 PLtlk~iA~~l~lh~STVSRav~~   72 (160)
T pfam04552        49 PLTLREVAEALGMHESTVSRATTN   72 (160)
T ss_pred             CCCHHHHHHHCCCCCCHHHHHHHH
T ss_conf             761999998809981069999961


No 154
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=69.04  E-value=8.4  Score=18.20  Aligned_cols=36  Identities=19%  Similarity=0.298  Sum_probs=20.6

Q ss_pred             CCHHHHHHHHHHCCCCCCC-CCCCCC----CCCCCCCCCCC
Q ss_conf             0013566754200012222-222222----22222222223
Q gi|254780282|r  109 QGNLKEFLLLYPDIQIQLI-LDNKDI----DISMDYADCAI  144 (299)
Q Consensus       109 ~~~l~~f~~~~P~i~i~i~-~~~~~~----~l~~~~~Di~i  144 (299)
                      ...+..+.+.||++++=+. +.+...    .|..++++..+
T Consensus        56 L~~~~~L~r~~P~vriLVLTm~d~e~~v~~aL~~aga~Gyl   96 (205)
T PRK11475         56 LSCLTELAIKFPRMRRLVIADDDIEARLIGSLSPSPLDGVL   96 (205)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHCCEEE
T ss_conf             99999999978997189997476879999999984166888


No 155
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=69.02  E-value=8.4  Score=18.20  Aligned_cols=47  Identities=17%  Similarity=0.299  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE
Q ss_conf             88889999999999827689999882899789999999999995882
Q gi|254780282|r    2 SFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIK   48 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~   48 (299)
                      .++-++.+....+++-.+...-|..|++|..+|..+++++...+|+.
T Consensus         4 ~Lt~rE~~~~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~   50 (65)
T COG2771           4 DLTPREREILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVK   50 (65)
T ss_pred             CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
T ss_conf             13888999999998699899999998779999999999999997758


No 156
>pfam03180 Lipoprotein_9 NLPA lipoprotein. This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to pfam00497 which are solute binding proteins.
Probab=68.78  E-value=8.5  Score=18.17  Aligned_cols=191  Identities=10%  Similarity=0.047  Sum_probs=85.5

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC-CCC---CCCCCCCCCCCCCCCCCCCC-----CCCCCC---CCCCC
Q ss_conf             3332111000000000135667542000122222-222---22222222222234565432-----111122---34555
Q gi|254780282|r   95 LRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLIL-DNK---DIDISMDYADCAIRLRKPIQ-----SSSLIQ---RKLVT  162 (299)
Q Consensus        95 i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~-~~~---~~~l~~~~~Di~i~~~~~~~-----~~~l~~---~~l~~  162 (299)
                      |+||++++-...++ ..+....++. ++++++.. ++-   ...|..|++|+-+.-..+.-     ..+..-   -+.+.
T Consensus         1 lkvG~~~~p~~~i~-~~v~~~~~~~-Gi~veiv~F~Dy~~pN~AL~~GeIDaN~fQH~~yl~~~n~~~g~~L~~v~~~~~   78 (236)
T pfam03180         1 LKVGATPGPHAEVL-EVAKPLAKKK-GLDLEIVEFTDYVQPNTALADGEIDANAFQHLPYLDQFNKEGGLDLVAVGNTHV   78 (236)
T ss_pred             CEEEECCCCHHHHH-HHHHHHHHHC-CCEEEEEEECCCCCHHHHHHCCCCCHHHHCCHHHHHHHHHHCCCCEEEEEEEEE
T ss_conf             98964389769999-9999999964-987999981686455079778995524443899999999977996799630467


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC---------------CC-CCEEEEC
Q ss_conf             4332112344321112222221100011235664332110002356652022343---------------21-2114532
Q gi|254780282|r  163 IHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGE---------------PR-ISCLQVN  226 (299)
Q Consensus       163 ~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~-~~~~~~~  226 (299)
                      .++.++..        ...+++||.+-.-|..+.......+-...++..+.-...               |. ....+++
T Consensus        79 ~p~glYS~--------k~ksl~~lp~Ga~IaIpnD~sN~~RAL~lL~~aGLI~Lk~~~~~~~t~~DI~~Npk~l~~~ev~  150 (236)
T pfam03180        79 EPIGLYSK--------KYKSLSELPDGATIAVPNDPSNEGRALLLLEKAGLIKLKDGAGLLATVKDITENPKNLKIKELE  150 (236)
T ss_pred             CCEEEEEC--------CCCCHHHCCCCCEEEECCCCCHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHHCCCCCEEEEEC
T ss_conf             23795433--------7688758579998981588442999999999889889768999878988897286776699916


Q ss_pred             CCCHHHHHHHHHCCEEEEEHHHHCCCC-CEE--EECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH-HHCC
Q ss_conf             420013567873842331177760199-846--6177666766008999348778888999999999999-8506
Q gi|254780282|r  227 SYLSIMQYCVLGSGIALLPDYIVKDNP-NLV--RIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK-ARDW  297 (299)
Q Consensus       227 s~~~~~~~v~~g~Gia~lp~~~~~~~~-~lv--~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~-~r~~  297 (299)
                      ...... . ....-.++++...+.+.| ...  .+..+....+....++.+++...++.++.|++.+.+. +|+|
T Consensus       151 a~ql~~-~-l~dvD~avin~n~a~~agl~p~~~~l~~e~~~~~y~n~ivvr~~~~d~~~ik~l~e~~~s~~vk~~  223 (236)
T pfam03180       151 AAQLPR-A-LDDVDAAVINTNYALQAGLDPKKDALFEEDKDSPYVNIIVVREDDKDDPAVKKLVKAYQSEEVKAF  223 (236)
T ss_pred             HHHHHH-H-CCCCCEEEECHHHHHHCCCCHHHHHHHCCCCCCCEEEEEEEECCCCCCHHHHHHHHHHCCHHHHHH
T ss_conf             777554-2-166578998656798879492121331478899837999981777699999999999879999999


No 157
>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=68.33  E-value=8.7  Score=18.12  Aligned_cols=44  Identities=16%  Similarity=0.240  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             8888999999999982768--9999882899789999999999995
Q gi|254780282|r    2 SFDWDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEV   45 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~l   45 (299)
                      .++=++-+.+.++.+.|..  +.-|+.++++.|.|-..+++|++.=
T Consensus         5 Gls~~E~~vY~~Ll~~g~~t~~eia~~~~i~r~~vY~~L~~L~~kG   50 (68)
T pfam01978         5 GLSEYEAKVYLALLKLGPATADEIAEESGVPRSKVYEVLRSLEKKG   50 (68)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf             9899999999999981998899999995988989999999999889


No 158
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=67.82  E-value=4.8  Score=19.64  Aligned_cols=22  Identities=23%  Similarity=0.345  Sum_probs=10.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      .+-.|=+-|.++.--+...|++
T Consensus        18 ql~QsikLLql~~~EL~~~I~~   39 (461)
T PRK05932         18 QLQQAIRLLQLSTLELQQEIEQ   39 (461)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHH
T ss_conf             9999999988699999999999


No 159
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=67.59  E-value=4.8  Score=19.62  Aligned_cols=15  Identities=13%  Similarity=0.051  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHCCCCC
Q ss_conf             135667542000122
Q gi|254780282|r  111 NLKEFLLLYPDIQIQ  125 (299)
Q Consensus       111 ~l~~f~~~~P~i~i~  125 (299)
                      .+..+..++|++...
T Consensus       111 ~~~~ll~~~p~la~~  125 (224)
T PRK09391        111 SLEQAAATDVDVARA  125 (224)
T ss_pred             HHHHHHHHCHHHHHH
T ss_conf             999998769899999


No 160
>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=67.44  E-value=2  Score=21.86  Aligned_cols=23  Identities=30%  Similarity=0.434  Sum_probs=19.9

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             82768999988289978999999
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQI   38 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i   38 (299)
                      ...|++.||+.|+++.+++++.+
T Consensus        15 ~f~Si~~aa~~L~i~~~tI~~~~   37 (37)
T pfam07453        15 KFSSIREAARALGISHSTINKYL   37 (37)
T ss_pred             HHHHHHHHHHHHCCCHHHHHCCC
T ss_conf             24679999998476465665029


No 161
>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=67.22  E-value=4.7  Score=19.68  Aligned_cols=34  Identities=35%  Similarity=0.524  Sum_probs=25.9

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC
Q ss_conf             8999988289978999999999999588217976994
Q gi|254780282|r   20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG   56 (299)
Q Consensus        20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~   56 (299)
                      -..=|+.+|+|.-+||+.+++|+++   -++.+.+++
T Consensus        28 r~eiA~~lG~t~eTVsR~l~~l~~~---G~I~~~gr~   61 (67)
T cd00092          28 RQEIADYLGLTRETVSRTLKELEEE---GLISRRGRG   61 (67)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHC---CCEEECCCE
T ss_conf             9999999789099999999999989---948966986


No 162
>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=66.74  E-value=6.5  Score=18.84  Aligned_cols=26  Identities=23%  Similarity=0.347  Sum_probs=22.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             68999988289978999999999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      |...=|+.+++|.++|.+.++.|+++
T Consensus        26 s~~~La~~~~vSr~tvr~Al~~L~~~   51 (64)
T pfam00392        26 SERELAAEFGVSRTTVREALRRLEAE   51 (64)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             79999999796999999999999988


No 163
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=66.23  E-value=6  Score=19.03  Aligned_cols=33  Identities=24%  Similarity=0.257  Sum_probs=25.7

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCE
Q ss_conf             827689999882899789999999999995882
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQISGLETEVGIK   48 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~   48 (299)
                      +--+.+.=++.|++|-|.||..+++|++.-=+.
T Consensus        40 ~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~   72 (177)
T COG1510          40 KPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVK   72 (177)
T ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHHHCCHHH
T ss_conf             996699999997778012889999998545688


No 164
>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=65.97  E-value=7.6  Score=18.47  Aligned_cols=26  Identities=31%  Similarity=0.422  Sum_probs=23.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             68999988289978999999999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      |...-|+.+++|.++|.+.++.|+++
T Consensus        27 s~~~La~~~~vSr~tvr~Al~~L~~~   52 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELEAE   52 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             79999999798889999999999988


No 165
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.42  E-value=9.9  Score=17.80  Aligned_cols=33  Identities=21%  Similarity=0.232  Sum_probs=27.6

Q ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf             998276899998828997899999999999958
Q gi|254780282|r   14 VARSGSFTHAAEQLHLSQSSISRQISGLETEVG   46 (299)
Q Consensus        14 v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg   46 (299)
                      ..+--|++.-|+..+||.+||...|++-|..|.
T Consensus        30 y~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~   62 (105)
T COG2739          30 YLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILE   62 (105)
T ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             981166999999957509999999999999999


No 166
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=65.04  E-value=10  Score=17.73  Aligned_cols=47  Identities=6%  Similarity=0.075  Sum_probs=36.4

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHHHHHHH----CCEEEEECCCCEEEEEC
Q ss_conf             827689999882899789999999999995----88217976994685001
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQISGLETEV----GIKLFYRHARGLTLTEQ   62 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i~~LE~~l----g~~Lf~R~~~~~~lT~~   62 (299)
                      +.=++-.=|+.++||.+||++=|+++++++    +..|..+.++|+.+.-.
T Consensus        29 e~vtl~~L~~~l~VSr~Ti~~DLk~l~~~L~~y~~L~L~~~r~~Gy~I~G~   79 (426)
T PRK11564         29 LTVTLETISQLNGVDDDIARQDIAETAREIQRYHHLTLTTGQDGSYRIEGT   79 (426)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEECC
T ss_conf             973499999996998889999999999998300886999817973899736


No 167
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=65.03  E-value=10  Score=17.73  Aligned_cols=60  Identities=23%  Similarity=0.357  Sum_probs=44.0

Q ss_pred             CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECC
Q ss_conf             988889999999999827--689999882899789999999999995882179769946850013
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG   63 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G   63 (299)
                      |.=+=|+-+..-.+-+.|  ++..-|+.++||..||-|=+..||++   -++.|..+|..+....
T Consensus         1 M~~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---G~l~R~hGGA~~~~~~   62 (252)
T PRK10906          1 MKQTQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNELAEQ---NLILRHHGGAALPSSS   62 (252)
T ss_pred             CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECEEEECCCC
T ss_conf             9879999999999998698999999998796998998829999878---9889995849806877


No 168
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=64.60  E-value=10  Score=17.68  Aligned_cols=51  Identities=20%  Similarity=0.236  Sum_probs=41.0

Q ss_pred             HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCC
Q ss_conf             27689999882899789999999999995882179769946850013433222
Q gi|254780282|r   17 SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRV   69 (299)
Q Consensus        17 ~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~   69 (299)
                      .=|+..=|..++|++-||+|.-+.||++  -=++.+.|.|.-.|+.|....+.
T Consensus        35 LPSvRelA~~~~VNpnTv~raY~eLE~e--G~i~t~rg~G~fV~~~~~~~~~~   85 (125)
T COG1725          35 LPSVRELAKDLGVNPNTVQRAYQELERE--GIVETKRGKGTFVTEDAKEILDQ   85 (125)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCEEEEECCCCHHHHHH
T ss_conf             9759999998198988999999999978--87798667057974771455788


No 169
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=64.54  E-value=8.1  Score=18.31  Aligned_cols=26  Identities=35%  Similarity=0.417  Sum_probs=23.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             68999988289978999999999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      |...-|+.++||.++|.+.++.|+++
T Consensus        22 s~~~la~~~~vSr~tvr~A~~~L~~~   47 (60)
T smart00345       22 SERELAAQLGVSRTTVREALSRLEAE   47 (60)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             09999999894999999999999988


No 170
>PRK01905 DNA-binding protein Fis; Provisional
Probab=63.89  E-value=11  Score=17.60  Aligned_cols=26  Identities=19%  Similarity=0.362  Sum_probs=23.2

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             82768999988289978999999999
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQISGL   41 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i~~L   41 (299)
                      -.||-++||+.|||+..|+.+.|++.
T Consensus        49 ~~gNQ~kAA~~LGinR~TLRkKlk~y   74 (77)
T PRK01905         49 AGGNQSLAAEYLGINRNTLRKKLQQH   74 (77)
T ss_pred             HCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             45949999999786588899999980


No 171
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=63.66  E-value=11  Score=17.58  Aligned_cols=26  Identities=31%  Similarity=0.387  Sum_probs=10.5

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCEE
Q ss_conf             98828997899999999999958821
Q gi|254780282|r   24 AEQLHLSQSSISRQISGLETEVGIKL   49 (299)
Q Consensus        24 A~~L~itq~avS~~i~~LE~~lg~~L   49 (299)
                      |--|++|.++||+.|+.+|++.|.-|
T Consensus       112 a~LL~~S~~TI~~~ik~ye~~~g~vv  137 (220)
T pfam07900       112 AILLGVSTTTISRHVKEYEERTGEVV  137 (220)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             99988988899999999999709663


No 172
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=63.46  E-value=11  Score=17.56  Aligned_cols=50  Identities=28%  Similarity=0.327  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHH--HCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC
Q ss_conf             99999999998--2768999988289978999999999999588217976994
Q gi|254780282|r    6 DKLRVFYVVAR--SGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG   56 (299)
Q Consensus         6 ~~L~~f~~v~~--~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~   56 (299)
                      ..++.+..+.+  .-++..-++.+++++++||++++.|++.--+.. .+.++.
T Consensus        26 ~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~-~~~~~~   77 (110)
T COG0640          26 TRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREAGLVEL-RREGRL   77 (110)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-EEECCE
T ss_conf             8999999998735137999998857678899999999987899578-864645


No 173
>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=63.09  E-value=6.5  Score=18.87  Aligned_cols=37  Identities=32%  Similarity=0.342  Sum_probs=26.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEE
Q ss_conf             768999988289978999999999999588217976994685
Q gi|254780282|r   18 GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTL   59 (299)
Q Consensus        18 gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~l   59 (299)
                      -|+..||+.||||-++|-+-|++     |.==|.|.|+.+..
T Consensus         2 lTv~EaA~yLgv~~~t~~~l~~~-----g~l~~~~~G~~~ri   38 (49)
T TIGR01764         2 LTVEEAAEYLGVSKSTVYRLIEE-----GELPAYRVGRHYRI   38 (49)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHHC-----CCCCEEECCCCEEC
T ss_conf             87788997719990578999971-----89850006860202


No 174
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=62.83  E-value=11  Score=17.49  Aligned_cols=52  Identities=19%  Similarity=0.261  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE
Q ss_conf             9999999999827--689999882899789999999999995882179769946850
Q gi|254780282|r    6 DKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT   60 (299)
Q Consensus         6 ~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT   60 (299)
                      |+-+..-.+-+.|  ++..-|+.++||..||-|=+..||++   -++.|..+|..+.
T Consensus         5 R~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---G~l~R~hGGA~~~   58 (240)
T PRK10411          5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQ---GKILRNHGRAKYI   58 (240)
T ss_pred             HHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEEEEEEEC
T ss_conf             99999999998697999999998895998999829989778---9889994249975


No 175
>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=62.65  E-value=5.4  Score=19.34  Aligned_cols=19  Identities=26%  Similarity=0.413  Sum_probs=16.3

Q ss_pred             HHHHHHCCCHHHHHHHHHH
Q ss_conf             9998828997899999999
Q gi|254780282|r   22 HAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        22 ~AA~~L~itq~avS~~i~~   40 (299)
                      .-|+++|+|.++||+.+..
T Consensus         2 diA~~~gvS~~TVSr~ln~   20 (52)
T cd01392           2 DIARAAGVSVATVSRVLNG   20 (52)
T ss_pred             HHHHHHCCCHHHHHHHHCC
T ss_conf             2888878599999999879


No 176
>PRK12423 LexA repressor; Provisional
Probab=61.94  E-value=12  Score=17.39  Aligned_cols=56  Identities=18%  Similarity=0.293  Sum_probs=38.4

Q ss_pred             CCHHHHHHHHHHHHH-------CCHHHHHHHHCC-CHHHHHHHHHHHHHHHCCEEEEE---CCCCEEEEE
Q ss_conf             888999999999982-------768999988289-97899999999999958821797---699468500
Q gi|254780282|r    3 FDWDKLRVFYVVARS-------GSFTHAAEQLHL-SQSSISRQISGLETEVGIKLFYR---HARGLTLTE   61 (299)
Q Consensus         3 md~~~L~~f~~v~~~-------gs~s~AA~~L~i-tq~avS~~i~~LE~~lg~~Lf~R---~~~~~~lT~   61 (299)
                      |+-+|-+.+-.+.++       =|++.-|+.+++ |.++|.++|++||+.   -.+.|   ..|+++++.
T Consensus         4 LT~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~~L~~k---G~i~r~~~~~R~i~l~~   70 (202)
T PRK12423          4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEA---GLIEVVPNQARGIRLPG   70 (202)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHC---CCEECCCCCCEEEEECC
T ss_conf             08999999999999999629898899999982999867899999999988---79970699953799368


No 177
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=61.73  E-value=7.1  Score=18.62  Aligned_cols=21  Identities=10%  Similarity=-0.092  Sum_probs=12.5

Q ss_pred             HHHHCCEEEEECCCCEEEEEC
Q ss_conf             999588217976994685001
Q gi|254780282|r   42 ETEVGIKLFYRHARGLTLTEQ   62 (299)
Q Consensus        42 E~~lg~~Lf~R~~~~~~lT~~   62 (299)
                      |+-..-||+++...+-..+-+
T Consensus        39 ~~~e~NPlLe~~~~~~~~~s~   59 (444)
T COG1508          39 QELEDNPLLERKDTDDKEFSD   59 (444)
T ss_pred             HHHHHCCCCCCCCCCCCCCCC
T ss_conf             998629771366677643341


No 178
>cd00283 GIY-YIG_Cterm GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix.  Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing sit
Probab=60.58  E-value=6.1  Score=19.00  Aligned_cols=21  Identities=38%  Similarity=0.438  Sum_probs=9.3

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH
Q ss_conf             768999988289978999999
Q gi|254780282|r   18 GSFTHAAEQLHLSQSSISRQI   38 (299)
Q Consensus        18 gs~s~AA~~L~itq~avS~~i   38 (299)
                      +|...||+.|+++.++||+.|
T Consensus        81 ~S~~eAAr~l~~s~~tIs~~~  101 (113)
T cd00283          81 DSTTEAARFLKVHSGTISKNI  101 (113)
T ss_pred             HHHHHHHHHHCCCCHHHHHHH
T ss_conf             349999999689840488996


No 179
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=60.09  E-value=9.2  Score=17.99  Aligned_cols=22  Identities=18%  Similarity=0.341  Sum_probs=18.2

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      ++.--|+..|||.++||+.+..
T Consensus         1 Ti~DIA~~agVS~~TVSr~ln~   22 (46)
T pfam00356         1 TIKDVARLAGVSKATVSRVLNN   22 (46)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC
T ss_conf             9999999989799999999879


No 180
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=59.71  E-value=9.2  Score=17.97  Aligned_cols=22  Identities=23%  Similarity=0.434  Sum_probs=19.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      ++..-|+..|||+++||+.+..
T Consensus         2 Ti~dvA~~aGVS~sTVSr~ln~   23 (70)
T smart00354        2 TIKDVARLAGVSKATVSRVLNG   23 (70)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC
T ss_conf             8999999989599999999779


No 181
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=59.61  E-value=13  Score=17.15  Aligned_cols=67  Identities=22%  Similarity=0.288  Sum_probs=49.4

Q ss_pred             CCC-CHHHHHHHHHHHHH--------CCHHHHHH-HHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCC
Q ss_conf             988-88999999999982--------76899998-8289978999999999999588217976994685001343322
Q gi|254780282|r    1 MSF-DWDKLRVFYVVARS--------GSFTHAAE-QLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHR   68 (299)
Q Consensus         1 m~m-d~~~L~~f~~v~~~--------gs~s~AA~-~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~   68 (299)
                      |+| |=|+.+.|.+++++        ||=+-+-+ .|++|++||-.-++.||+. |.=-=-.+.-|=.||+.|-++|-
T Consensus         1 m~mLt~R~~~IL~aiVe~Yi~tg~PVGSk~L~~~~~l~~SsATIRNeMa~LE~~-G~L~qpHTSAGRIPT~kGYR~YV   77 (339)
T PRK00082          1 MSMLDERQREILRAIVEDYIATGEPVGSKTLSERYGLGVSSATIRNDMADLEEL-GLLEKPHTSSGRIPTDKGYRYFV   77 (339)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHC-CCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             986579999999999999851498556799997649997817899999999978-78367989998785678999999


No 182
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=59.60  E-value=1.9  Score=21.97  Aligned_cols=115  Identities=9%  Similarity=0.157  Sum_probs=70.7

Q ss_pred             HCCCHHHHHHHHHHHHHHHCCE----------EEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCC-C
Q ss_conf             2899789999999999995882----------1797699468500134332222222222101221001223222222-3
Q gi|254780282|r   27 LHLSQSSISRQISGLETEVGIK----------LFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIELQESSVKPSGK-L   95 (299)
Q Consensus        27 L~itq~avS~~i~~LE~~lg~~----------Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g~-i   95 (299)
                      ++|. |+|-+-+...=+..|++          +..+.++..+++--++.|++++..+-..++....-....--...+. .
T Consensus        49 cyiP-PsVY~El~~fm~r~gc~~e~~~ki~twivkKtPnryevkiPa~ifyeyV~diR~RinkGlRvAE~~i~eA~~~~~  127 (221)
T COG1458          49 CYIP-PSVYRELMGFMERNGCPEEVIAKIETWIVKKTPNRYEVKIPAAIFYEYVEDIRERINKGLRVAEEAIREASIECY  127 (221)
T ss_pred             EEEC-HHHHHHHHHHHHHCCCCHHHHHHHHEEEEECCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9728-189999999997479968888866603675599822321709999999999999987126468999999988888


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC--CC--CCCCCCCCCC
Q ss_conf             3321110000000001356675420001222222222--22--2222222223
Q gi|254780282|r   96 RIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--ID--ISMDYADCAI  144 (299)
Q Consensus        96 ~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~--~~--l~~~~~Di~i  144 (299)
                      .+- ...+....+...++.|++.|-.. ++--.-|+.  .|  |++-++|.++
T Consensus       128 ~~~-~~~i~~e~igk~I~~lR~KYR~a-lR~GiLDSapDlDvLLLAkELdaav  178 (221)
T COG1458         128 ELE-KEEIIREVVGKIIRKLREKYREA-LRKGILDSAPDLDVLLLAKELDAAV  178 (221)
T ss_pred             HHH-HHHHHHHHHHHHHHHHHHHHHHH-HHHCCCCCCCHHHHHHHHHHHCCEE
T ss_conf             751-44677888999999999999999-9834446654068999999838637


No 183
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=59.52  E-value=11  Score=17.49  Aligned_cols=27  Identities=19%  Similarity=0.095  Sum_probs=24.1

Q ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998276899998828997899999999
Q gi|254780282|r   14 VARSGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        14 v~~~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      -+-..|+..=|++.|||+|||.|-.++
T Consensus        33 ~~~~~si~elA~~a~VS~aTv~Rf~~k   59 (281)
T COG1737          33 EVALLSIAELAERAGVSPATVVRFARK   59 (281)
T ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             885614999998819988899999998


No 184
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=58.82  E-value=8.6  Score=18.14  Aligned_cols=17  Identities=18%  Similarity=0.317  Sum_probs=10.6

Q ss_pred             CHHHHHHHHHHCCCCCC
Q ss_conf             01356675420001222
Q gi|254780282|r  110 GNLKEFLLLYPDIQIQL  126 (299)
Q Consensus       110 ~~l~~f~~~~P~i~i~i  126 (299)
                      ..+..+..+||++...+
T Consensus       117 ~~~~~l~~~~p~l~~~l  133 (235)
T PRK11161        117 ETLDDLSGKMPKLRQQI  133 (235)
T ss_pred             HHHHHHHHHCHHHHHHH
T ss_conf             99999997798999999


No 185
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=58.82  E-value=13  Score=17.07  Aligned_cols=23  Identities=35%  Similarity=0.411  Sum_probs=17.6

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             76899998828997899999999
Q gi|254780282|r   18 GSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        18 gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      -|.+..|+.|+|+..+||.-|..
T Consensus        24 lt~~~lA~~lgV~r~~is~ling   46 (104)
T COG3093          24 LTQTELAEALGVTRNTISELING   46 (104)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCC
T ss_conf             98999999939989999999837


No 186
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=58.79  E-value=7.1  Score=18.61  Aligned_cols=36  Identities=11%  Similarity=0.086  Sum_probs=23.4

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEE
Q ss_conf             98276899998828997899999999999958821797
Q gi|254780282|r   15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYR   52 (299)
Q Consensus        15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R   52 (299)
                      +=+-.+-.|-+-|.++.--+...|++  +-..-|+++.
T Consensus        14 ~LTpql~QsikLLQls~~EL~~~I~~--el~eNPlLE~   49 (475)
T PRK12469         14 ALTPRLQQSLRLLQLSSLEFQQELRE--ALDTNPFLED   49 (475)
T ss_pred             HHCHHHHHHHHHHCCCHHHHHHHHHH--HHHHCCCCCC
T ss_conf             41699999999988498999999999--9982876467


No 187
>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=58.70  E-value=13  Score=17.06  Aligned_cols=28  Identities=25%  Similarity=0.143  Sum_probs=23.0

Q ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9982768999988289978999999999
Q gi|254780282|r   14 VARSGSFTHAAEQLHLSQSSISRQISGL   41 (299)
Q Consensus        14 v~~~gs~s~AA~~L~itq~avS~~i~~L   41 (299)
                      -+...|++.-|++.++|+++|.|-.++|
T Consensus        31 ~~~~~si~~lA~~~~vS~atv~Rf~kkl   58 (106)
T pfam01418        31 NAIHLSIAELAKAAGVSEASVVRFCRKL   58 (106)
T ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9988339999989699899999999995


No 188
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=56.52  E-value=14  Score=16.84  Aligned_cols=58  Identities=21%  Similarity=0.202  Sum_probs=42.5

Q ss_pred             HHHHHHHHHH-HH--CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCC
Q ss_conf             9999999999-82--7689999882899789999999999995882179769946850013433222
Q gi|254780282|r    6 DKLRVFYVVA-RS--GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRV   69 (299)
Q Consensus         6 ~~L~~f~~v~-~~--gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~   69 (299)
                      .+..+|.++. ..  .++-.=|+.|+.+-|+|++.+++|.+   .-|+.|.....   +.|...|-|
T Consensus        28 ~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~---~GlV~Rek~~~---~~Ggy~yiY   88 (126)
T COG3355          28 LDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLE---AGLVEREKVNL---KGGGYYYLY   88 (126)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH---CCCEEEEEECC---CCCCEEEEE
T ss_conf             89999999986469957999999978319999999999998---58866664226---788614887


No 189
>pfam04069 OpuAC Substrate binding domain of ABC-type glycine betaine transport system. Part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. Family members are often integral membrane proteins or predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis. The family member OpuBC is closely related, and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine. L-carnitine is important for osmoregulation in Listeria monocytogenes. Family also contains proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA).
Probab=55.70  E-value=15  Score=16.76  Aligned_cols=188  Identities=15%  Similarity=0.061  Sum_probs=89.6

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC-CCC---CCCCCCCCCCCCCCCCCCCCC--------CCCCC---C
Q ss_conf             23332111000000000135667542000122222-222---222222222222345654321--------11122---3
Q gi|254780282|r   94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLIL-DNK---DIDISMDYADCAIRLRKPIQS--------SSLIQ---R  158 (299)
Q Consensus        94 ~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~-~~~---~~~l~~~~~Di~i~~~~~~~~--------~~l~~---~  158 (299)
                      +|+||.........+..+.....++. +.+++... +..   ...|..|++|+......|...        .+...   .
T Consensus         2 tI~ig~~~w~e~~i~a~i~~~~Le~~-G~~V~~~~~~~~~~~~~al~~G~iDi~~~~w~~~~~~~~~~~~~~~~~~~~~~   80 (256)
T pfam04069         2 TIVIGSKNWTEQEILANIAAQLLEAL-GYVVELVGLGSTAVLFAALASGDIDLYPEEWTGTTYEAYKKAVEEKLGLLVLG   80 (256)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHC-CCCEEEEECCCCHHHHHHHHCCCCCEEEHHCCCCHHHHHHHHHHCCCCEEECC
T ss_conf             29992688628999999999999976-98169854787089999997699758633306625799998751468738613


Q ss_pred             C-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCC
Q ss_conf             4-55543321123443211122222211000112---------3566433211000235665202234321211453242
Q gi|254780282|r  159 K-LVTIHMHAYAAPHYLKNCREPLSIQELDKHNL---------ITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSY  228 (299)
Q Consensus       159 ~-l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~---------i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~  228 (299)
                      + .......+++ |.+........+++||.+.+-         +...++.+........+...+...    .. +...|.
T Consensus        81 ~~~~~~~~g~~V-p~~~a~~~~i~si~dL~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~yGl~~----~~-~~~~s~  154 (256)
T pfam04069        81 PLGAGNTYGLAV-PKYVAEKPGIKSISDLAKPADDELGFKGEFIGRPDGWGCTRSTEGLLKAYGLDK----YE-LVEGSE  154 (256)
T ss_pred             CCCCCCEEEEEE-CHHHHHHCCCCCHHHHHCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHCCCCC----EE-ECCCCH
T ss_conf             577787589998-588883569987999727421024888655327888540067899998639764----01-235855


Q ss_pred             C----HHHHHHHHHCCEE---EEEHHHHCCCCCEEEECCCC-C-CCCCEEEEEECCC-CCCCHHHHHHHHH
Q ss_conf             0----0135678738423---31177760199846617766-6-7660089993487-7888899999999
Q gi|254780282|r  229 L----SIMQYCVLGSGIA---LLPDYIVKDNPNLVRIMEDV-I-TPSFTVYFCYPEA-LKNTGKLKAFRNF  289 (299)
Q Consensus       229 ~----~~~~~v~~g~Gia---~lp~~~~~~~~~lv~i~~~~-~-~~~~~~~lv~~~~-~~~~~~~~~f~d~  289 (299)
                      .    .+..++.+|..+.   .-|.++.... +++.+-.+. . .+...++.+.+++ ....|.+..|++-
T Consensus       155 ~~~~a~~~~A~~~g~~~v~~~w~p~~~~~~~-dl~~L~Dp~~~~~~~~~v~~v~~~~~~~~~P~~~~~l~~  224 (256)
T pfam04069       155 AAMDALLYAAIKRGEPDVVYAWTPDWMIKKY-DLVVLEDPKGLFPPAYNVVPVVRKGFAEKHPEVAAFLNK  224 (256)
T ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCHHHHHC-CEEECCCCCCCCCCCCEEEEEECHHHHHHCHHHHHHHHH
T ss_conf             5459999999984998899963761655427-969936886457976558752104677779899999986


No 190
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=55.28  E-value=15  Score=16.72  Aligned_cols=195  Identities=9%  Similarity=0.073  Sum_probs=82.9

Q ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCC-CCCC---CCCCCCCCCCCCCCCCCCCC-----CCCCCCCCC---
Q ss_conf             22333211100000000013566754200012222-2222---22222222222234565432-----111122345---
Q gi|254780282|r   93 GKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLI-LDNK---DIDISMDYADCAIRLRKPIQ-----SSSLIQRKL---  160 (299)
Q Consensus        93 g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~-~~~~---~~~l~~~~~Di~i~~~~~~~-----~~~l~~~~l---  160 (299)
                      .+|+||++++....++- ......++--++++++. .++-   ...|..|++|+-+.-..|.-     ..+.....+   
T Consensus        31 ~~ikVG~~~gp~~ei~e-~~~~~~~ek~G~~veiv~FsDy~~pN~AL~~G~iDaN~fQH~~yL~~~nk~~g~~L~~v~~~  109 (271)
T PRK11063         31 NHIKVGVIVGAEQQVAE-VAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQIKDRGYKLVAVGNT  109 (271)
T ss_pred             CEEEEEECCCCHHHHHH-HHHHHHHHHCCCEEEEEEECCCHHHHHHHHCCCCCHHHHHCHHHHHHHHHHCCCCEEEEEEE
T ss_conf             81899846898799999-98888886079768999936832155898679844234557999999999779957998667


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC---------------C-CCEEE
Q ss_conf             5543321123443211122222211000112356643321100023566520223432---------------1-21145
Q gi|254780282|r  161 VTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEP---------------R-ISCLQ  224 (299)
Q Consensus       161 ~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~-~~~~~  224 (299)
                      +..++.+|..        ...+++||.+-.-|..+.......+-...++..+.-...+               . ....+
T Consensus       110 ~~~P~glYS~--------K~ksl~elp~Ga~IaIPND~sN~~RAL~lL~~aGLIkLk~~~~~~~T~~DI~~Npk~l~~~e  181 (271)
T PRK11063        110 FVYPIAGYSK--------KIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVE  181 (271)
T ss_pred             EEEEEEEEEC--------CCCCHHHCCCCCEEEECCCCCHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHCCCCCCEEEE
T ss_conf             7841586423--------65886475699999804885609999999998898897799998789668854887748999


Q ss_pred             ECCCCHHHHHHHHHCCEEEEEHHHHCCCC-CEE--EECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH-HHC
Q ss_conf             32420013567873842331177760199-846--6177666766008999348778888999999999999-850
Q gi|254780282|r  225 VNSYLSIMQYCVLGSGIALLPDYIVKDNP-NLV--RIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLK-ARD  296 (299)
Q Consensus       225 ~~s~~~~~~~v~~g~Gia~lp~~~~~~~~-~lv--~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~-~r~  296 (299)
                      ++.......+-......+++....+.+.| ...  .++.+....++-..++.+++...+|.++.|++.+.++ +++
T Consensus       182 ~daaql~rsl~D~dv~~aviN~~~a~~agl~p~kdal~~E~~~~py~Nvivvr~~~kd~~~ik~lv~~~~S~evk~  257 (271)
T PRK11063        182 LEAPQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKDSPYVNLIVAREDNKDAENVKKFVQAYQSDEVYE  257 (271)
T ss_pred             CCHHHHHHHCCCCCEEEEEECHHHHHHCCCCCCCCCEEECCCCCCEEEEEEECCCCCCCHHHHHHHHHHCCHHHHH
T ss_conf             0377644313576510898147789777989342504777899983899998277779989999999977999999


No 191
>COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]
Probab=54.98  E-value=15  Score=16.69  Aligned_cols=16  Identities=13%  Similarity=0.052  Sum_probs=6.0

Q ss_pred             CCCCCCCCHHHHHCCC
Q ss_conf             2222221012210012
Q gi|254780282|r   71 SEVYHKLETTQIELQE   86 (299)
Q Consensus        71 ~~~l~~~~~~~~~~~~   86 (299)
                      ++++...++....++.
T Consensus        55 ~R~V~Id~~~a~~l~g   70 (376)
T COG3835          55 RRVVEIDQAVARKLKG   70 (376)
T ss_pred             CCEEEEEHHHHHHHCC
T ss_conf             8679964888887558


No 192
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=54.56  E-value=16  Score=16.65  Aligned_cols=47  Identities=11%  Similarity=0.126  Sum_probs=33.8

Q ss_pred             HCCHHHHHHHHCCCHHHHHHH-----------HHHHHHHHCCEEEEECCCCEEEEECC
Q ss_conf             276899998828997899999-----------99999995882179769946850013
Q gi|254780282|r   17 SGSFTHAAEQLHLSQSSISRQ-----------ISGLETEVGIKLFYRHARGLTLTEQG   63 (299)
Q Consensus        17 ~gs~s~AA~~L~itq~avS~~-----------i~~LE~~lg~~Lf~R~~~~~~lT~~G   63 (299)
                      --|=+.+|++.|+.|++||+-           +=++=..||..|-++..+.-.|+..+
T Consensus        25 gLsQ~~lA~~vGi~Q~TiS~~E~~p~~~~leTLFkiL~aL~Lel~i~~~~~~~p~~~~   82 (88)
T PRK09726         25 GWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAKNASPESTE   82 (88)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCC
T ss_conf             9879999998197499999997599878699999999967876887138999988876


No 193
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=54.37  E-value=13  Score=17.15  Aligned_cols=22  Identities=23%  Similarity=0.314  Sum_probs=19.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      ++.--|+..|||++|||+.+..
T Consensus         3 TIkDIA~~AGVS~sTVSrvLN~   24 (342)
T PRK10727          3 TIKDVARLAGVSVATVSRVINN   24 (342)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC
T ss_conf             8899999979699999999779


No 194
>PRK09526 lacI lac repressor; Reviewed
Probab=54.04  E-value=13  Score=17.10  Aligned_cols=22  Identities=18%  Similarity=0.241  Sum_probs=19.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      ++.--|+.+|||.+|||+.+..
T Consensus         7 TikDIA~~agVS~sTVSrvLn~   28 (342)
T PRK09526          7 TLYDVARYAGVSYQTVSRVLNQ   28 (342)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC
T ss_conf             6999999989699999999789


No 195
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=53.14  E-value=15  Score=16.80  Aligned_cols=10  Identities=10%  Similarity=0.554  Sum_probs=4.4

Q ss_pred             HHHCCCCCCC
Q ss_conf             4200012222
Q gi|254780282|r  118 LYPDIQIQLI  127 (299)
Q Consensus       118 ~~P~i~i~i~  127 (299)
                      .+.+|++++.
T Consensus       169 ~f~~iniDLi  178 (393)
T PRK08898        169 HFDNFNLDLM  178 (393)
T ss_pred             HCCCCCCHHH
T ss_conf             3746672898


No 196
>PRK13870 transcriptional regulator TraR; Provisional
Probab=52.34  E-value=17  Score=16.44  Aligned_cols=19  Identities=5%  Similarity=0.235  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHCCEEEE
Q ss_conf             9999999999995882179
Q gi|254780282|r   33 SISRQISGLETEVGIKLFY   51 (299)
Q Consensus        33 avS~~i~~LE~~lg~~Lf~   51 (299)
                      .+=..++++-+.+|...|-
T Consensus        20 ~~~~~l~~~a~~~gf~~~a   38 (234)
T PRK13870         20 ILKTGLADIAEHFGFTGYA   38 (234)
T ss_pred             HHHHHHHHHHHHCCCCCEE
T ss_conf             9999999999983998579


No 197
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=52.26  E-value=15  Score=16.81  Aligned_cols=110  Identities=8%  Similarity=0.109  Sum_probs=51.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH-CCCCCCCCCCCCCC
Q ss_conf             68999988289978999999999999588217976994685001343322222222221012210-01223222222333
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE-LQESSVKPSGKLRI   97 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~-~~~~~~~~~g~i~I   97 (299)
                      ++.--|+..|||.+|||+.|..             +.++.  ++   --+++.+..+++.-.-+. .+..+.+.++.|-+
T Consensus        11 TikDIA~~aGVS~sTVSrvLn~-------------~~~Vs--~~---Tr~rV~~aa~eLgY~pn~~Ar~L~~~~s~~Igv   72 (341)
T PRK11041         11 TMKDVALKAGVSTATVSRALMN-------------PEKVS--QS---TRNRVEQAVLEVGYSPQSLGRNLKRNESRTILV   72 (341)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC-------------CCCCC--HH---HHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEE
T ss_conf             8999999979799999999789-------------89999--99---999999999981998388888775388888999


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHCCCCCCCC--C-CC------CCC-CCCCCCCCCCCCC
Q ss_conf             2111000000000135667542000122222--2-22------222-2222222223456
Q gi|254780282|r   98 ATTIDLGQNLLQGNLKEFLLLYPDIQIQLIL--D-NK------DID-ISMDYADCAIRLR  147 (299)
Q Consensus        98 ~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~--~-~~------~~~-l~~~~~Di~i~~~  147 (299)
                      -+ +.+...++..++..+.+..-+-...+..  + +.      ..+ +....+|-.|.++
T Consensus        73 i~-p~~~~~~~~~~~~gi~~~~~~~gy~~li~~~~~~~~~e~~~~~~l~~~~vdGiIi~~  131 (341)
T PRK11041         73 IV-PDICDPFFSEIIRGIEVTAAEHGYLVLIGDCAHQNQQEKTFVNLIITKQIDGMLLLG  131 (341)
T ss_pred             EE-CCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             96-776541356766339999997699899982688658899999988754877699956


No 198
>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=52.09  E-value=17  Score=16.42  Aligned_cols=36  Identities=19%  Similarity=0.274  Sum_probs=26.3

Q ss_pred             CCHHHHHHHHHHHHHC-CHHHHHHHHCCCHHHHHHHH
Q ss_conf             8889999999999827-68999988289978999999
Q gi|254780282|r    3 FDWDKLRVFYVVARSG-SFTHAAEQLHLSQSSISRQI   38 (299)
Q Consensus         3 md~~~L~~f~~v~~~g-s~s~AA~~L~itq~avS~~i   38 (299)
                      |+-++++-.....+.| +.+..|+.++||.++|.+.+
T Consensus         6 lt~~q~~~ar~l~~~G~~~~~iA~~~GVsr~Tiyr~l   42 (42)
T cd00569           6 LTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             9999999999999978989999999797999998659


No 199
>PRK05066 arginine repressor; Provisional
Probab=51.86  E-value=7.7  Score=18.42  Aligned_cols=36  Identities=19%  Similarity=0.410  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHCCHHHHHH------HHC---CCHHHHHHHHHHH
Q ss_conf             99999999998276899998------828---9978999999999
Q gi|254780282|r    6 DKLRVFYVVARSGSFTHAAE------QLH---LSQSSISRQISGL   41 (299)
Q Consensus         6 ~~L~~f~~v~~~gs~s~AA~------~L~---itq~avS~~i~~L   41 (299)
                      +.++.+..+.+...++.=.+      ..|   |||++|||-|++|
T Consensus         9 ~~~~aIk~lI~~~~I~tQeeL~~~L~~~G~~~VTQATvSRDlkeL   53 (156)
T PRK05066          9 ELVKAFKALLKEEKFGSQGEIVTALQEQGFDNINQSKVSRMLTKF   53 (156)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHC
T ss_conf             999999999851896679999999997398612088888789982


No 200
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=51.82  E-value=15  Score=16.77  Aligned_cols=111  Identities=9%  Similarity=0.029  Sum_probs=51.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH-CCCCCCCCCCCCCC
Q ss_conf             68999988289978999999999999588217976994685001343322222222221012210-01223222222333
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE-LQESSVKPSGKLRI   97 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~-~~~~~~~~~g~i~I   97 (299)
                      ++.--|+..|||.+|||+.+.+             .+++..     .--+++.++.+++.-.-+. .+.++.+.++.|-+
T Consensus         3 TikDIA~~AGVS~aTVSrvLn~-------------~~~Vs~-----~Tr~rV~~aa~eLgY~pn~~Ar~L~~~~s~~Igv   64 (335)
T PRK10703          3 TIKDVAKRAGVSTTTVSHVINK-------------TRFVAE-----ETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGL   64 (335)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC-------------CCCCCH-----HHHHHHHHHHHHHCCCCCHHHHHHCCCCCCEEEE
T ss_conf             8899999979899999999689-------------699899-----9999999999982999787787541177745999


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHCCCCCCC--CCCC--------CCCCCCCCCCCCCCCCC
Q ss_conf             211100000000013566754200012222--2222--------22222222222234565
Q gi|254780282|r   98 ATTIDLGQNLLQGNLKEFLLLYPDIQIQLI--LDNK--------DIDISMDYADCAIRLRK  148 (299)
Q Consensus        98 ~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~--~~~~--------~~~l~~~~~Di~i~~~~  148 (299)
                      -+ +.+...++..++..+.+..-+-...+.  .++.        ...+....+|-.|.+..
T Consensus        65 iv-~~~~~~~~~~~~~~i~~~~~~~gy~~~l~~~~~~~~~~~~~l~~l~~~~vdGiIi~~~  124 (335)
T PRK10703         65 LA-TSSEAPYFAEIIEAVEKNCYQKGYTLILCNAWNNLEKQRAYLSMLAQKRVDGLLVMCS  124 (335)
T ss_pred             EE-CCCCCCEEHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             95-4788865065433699999973997999927898699999999999558877999768


No 201
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium.  Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=51.55  E-value=17  Score=16.36  Aligned_cols=36  Identities=17%  Similarity=0.164  Sum_probs=27.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEE
Q ss_conf             6899998828997899999999999958821797699468
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLT   58 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~   58 (299)
                      +++.+|+.+|||+    +.|+--|+++|..--.|+.+|.+
T Consensus         2 tI~eva~~~gv~~----~tLR~wE~~~~l~~p~R~~~g~R   37 (68)
T cd01104           2 TIGAVARLTGVSP----DTLRAWERRYGLPAPQRTDGGHR   37 (68)
T ss_pred             CHHHHHHHHCCCH----HHHHHHHHHCCCCCCCCCCCCCE
T ss_conf             7899999988298----99999998579999974999985


No 202
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=51.23  E-value=15  Score=16.68  Aligned_cols=22  Identities=23%  Similarity=0.356  Sum_probs=18.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      ++.--|+..|||++|||+.+..
T Consensus         3 Ti~DVA~~AGVS~aTVSrvLn~   24 (346)
T PRK10401          3 TIRDVARQAGVSVATVSRVLNN   24 (346)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC
T ss_conf             7899999989799999999779


No 203
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=51.03  E-value=18  Score=16.32  Aligned_cols=38  Identities=16%  Similarity=0.307  Sum_probs=26.2

Q ss_pred             HHHHHHHHCCHH-HHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             999999827689-99988289978999999999999588
Q gi|254780282|r   10 VFYVVARSGSFT-HAAEQLHLSQSSISRQISGLETEVGI   47 (299)
Q Consensus        10 ~f~~v~~~gs~s-~AA~~L~itq~avS~~i~~LE~~lg~   47 (299)
                      .+.-+++.-+|. .-++.++|+|-||-+|++.||+.==+
T Consensus        20 Il~lLt~~p~yvsEiS~~lgvsqkAVl~HL~~LE~AGlv   58 (217)
T COG1777          20 ILQLLTRRPCYVSEISRELGVSQKAVLKHLRILERAGLV   58 (217)
T ss_pred             HHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHCCCC
T ss_conf             999985471399987766086789999999999985871


No 204
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=50.63  E-value=16  Score=16.65  Aligned_cols=22  Identities=18%  Similarity=0.294  Sum_probs=19.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      ++.--|+..|||.+|||+.|..
T Consensus         3 TikDVA~~AGVS~sTVSrvLn~   24 (327)
T PRK10339          3 TLKDIAIEAGVSLATVSRVLND   24 (327)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC
T ss_conf             6899999978889999999589


No 205
>pfam02042 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development.
Probab=50.49  E-value=18  Score=16.27  Aligned_cols=34  Identities=12%  Similarity=0.181  Sum_probs=24.6

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             88899999999998276899998828997899999999
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      +++++|+-.    =+.++..||+.|||+.+++-+.-++
T Consensus         5 lt~~dl~~~----F~lpi~~AA~~Lgv~~T~LKk~CR~   38 (52)
T pfam02042         5 LTLEDLSKY----FHLPIKEAAKELGVCLTVLKKICRQ   38 (52)
T ss_pred             CCHHHHHHH----HCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             569999998----1875999999968779999999998


No 206
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=50.21  E-value=18  Score=16.24  Aligned_cols=42  Identities=26%  Similarity=0.386  Sum_probs=31.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC
Q ss_conf             68999988289978999999999999588217976994685001
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ   62 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~   62 (299)
                      |=..=|+.++||.++|-..|+.|| ..|. +-.|.|+|...+..
T Consensus        36 sE~eLA~~lgVSR~~VREAL~~L~-~~Gl-V~~r~g~G~~V~~~   77 (254)
T PRK09464         36 PERELAKQFDVSRPSLREAIQRLE-AKGL-LLRRQGGGTFVQSS   77 (254)
T ss_pred             CHHHHHHHHCCCCHHHHHHHHHHH-HCCC-EEEECCCCEEECCC
T ss_conf             699999986899559999999999-8899-89717871364677


No 207
>pfam08222 HTH_CodY CodY helix-turn-helix domain. This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk.
Probab=50.16  E-value=16  Score=16.61  Aligned_cols=24  Identities=21%  Similarity=0.418  Sum_probs=21.6

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             999988289978999999999999
Q gi|254780282|r   21 THAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus        21 s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      |+-|++.+||.|-+-..+++||..
T Consensus         7 SkiAd~~giTRSVIVNAlRKlESA   30 (60)
T pfam08222         7 SKIADRIGITRSVIVNALRKLESA   30 (60)
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHC
T ss_conf             566676296189999999876434


No 208
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=49.05  E-value=16  Score=16.51  Aligned_cols=22  Identities=23%  Similarity=0.280  Sum_probs=18.4

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      ++.--|+..|||.+|||+.|..
T Consensus         2 TikDVA~~AGVS~aTVSrvLNg   23 (330)
T PRK11303          2 KLDEIARLAGVSRTTASYVING   23 (330)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC
T ss_conf             7899999979799899888389


No 209
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.01  E-value=19  Score=16.13  Aligned_cols=59  Identities=24%  Similarity=0.081  Sum_probs=41.4

Q ss_pred             CCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC-EEEEECCCCEEEEE
Q ss_conf             888999999999982768999988289978999999999999588-21797699468500
Q gi|254780282|r    3 FDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGI-KLFYRHARGLTLTE   61 (299)
Q Consensus         3 md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~-~Lf~R~~~~~~lT~   61 (299)
                      .|++.+..-..+++--|...||++++||-++|-+=+++.++.=.. +--.+.|+.=.+++
T Consensus         7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~   66 (138)
T COG3415           7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSE   66 (138)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH
T ss_conf             899999999999768549999999692299999999873335331567668999732588


No 210
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=48.33  E-value=17  Score=16.50  Aligned_cols=39  Identities=21%  Similarity=0.181  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             9999999999827--68999988289978999999999999
Q gi|254780282|r    6 DKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus         6 ~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      +++.-...++=..  +=+.=|++||||.+.||+-+++..++
T Consensus        13 ~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~   53 (321)
T COG2390          13 RLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREE   53 (321)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             99999999998468879999988398899999999999987


No 211
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=47.91  E-value=13  Score=17.08  Aligned_cols=108  Identities=10%  Similarity=0.028  Sum_probs=48.6

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCCCCHHHHH-CCCCCCCCCCCCCCCC
Q ss_conf             999988289978999999999999588217976994685001343322222222221012210-0122322222233321
Q gi|254780282|r   21 THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHKLETTQIE-LQESSVKPSGKLRIAT   99 (299)
Q Consensus        21 s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~-~~~~~~~~~g~i~I~~   99 (299)
                      .--|+..|||.+|||+.+..             .+++.+     ..-+++.++.+++.-.-+. .+.++.+.++.|-+-+
T Consensus         2 kDIA~~AGVS~sTVSrvLn~-------------~~~Vs~-----~tr~rV~~aa~elgY~pn~~Ar~L~~~~s~~Igviv   63 (327)
T PRK10423          2 KDVARLAGVSTSTVSHVINK-------------DRFVSE-----AITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLI   63 (327)
T ss_pred             HHHHHHHCCCHHHHHHHHCC-------------CCCCCH-----HHHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEE
T ss_conf             68987869899999999789-------------599999-----999999999998299868888877537876799997


Q ss_pred             CCCCCCCCCCCHHHHHHHHHH--CCCCCCCCCCC--------CCCCCCCCCCCCCCCC
Q ss_conf             110000000001356675420--00122222222--------2222222222223456
Q gi|254780282|r  100 TIDLGQNLLQGNLKEFLLLYP--DIQIQLILDNK--------DIDISMDYADCAIRLR  147 (299)
Q Consensus       100 ~~~~~~~~l~~~l~~f~~~~P--~i~i~i~~~~~--------~~~l~~~~~Di~i~~~  147 (299)
                      + .....+...++..+.+..-  +..+-+...+.        ...+....+|-.|.+.
T Consensus        64 ~-~~~~~f~~~i~~~i~~~~~~~gy~~~l~~~~~~~~~~~~~l~~l~~~~vdGiIi~~  120 (327)
T PRK10423         64 T-ASTNPFYSELVRGVERSCFERGYSLVLCNTEGDEQRMNRNLETLMQKRVDGLLLLC  120 (327)
T ss_pred             C-CCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             3-66551267889999999998599899982689879999999999955987699974


No 212
>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=47.85  E-value=18  Score=16.30  Aligned_cols=22  Identities=32%  Similarity=0.360  Sum_probs=18.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      +.+.||+.|+||+++|-+=.++
T Consensus         2 t~~e~A~~lgVs~~TlrrW~~~   23 (49)
T cd04762           2 TTKEAAELLGVSPSTLRRWVKE   23 (49)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHC
T ss_conf             8899999979899999999987


No 213
>PRK09492 treR trehalose repressor; Provisional
Probab=47.83  E-value=19  Score=16.17  Aligned_cols=22  Identities=18%  Similarity=0.303  Sum_probs=18.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             6899998828997899999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~   40 (299)
                      ++.--|+..|||.+|||+.+..
T Consensus         6 TikDIA~~aGVS~aTVSrvLn~   27 (315)
T PRK09492          6 TIKDIARLSGVGKSTVSRVLNN   27 (315)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC
T ss_conf             7999999989799999999789


No 214
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=47.71  E-value=20  Score=16.01  Aligned_cols=39  Identities=31%  Similarity=0.356  Sum_probs=29.8

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC
Q ss_conf             982768999988289978999999999999588217976994
Q gi|254780282|r   15 ARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG   56 (299)
Q Consensus        15 ~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~   56 (299)
                      -..-++..-|+.++||..||-+=|..||++   .++.|..+|
T Consensus        12 ~~~~~i~~La~~~~VS~~TiRRDl~~L~~~---g~i~r~hGG   50 (53)
T smart00420       12 QGKVSVEELAELLGVSEMTIRRDLNKLEEQ---GLLTRVHGG   50 (53)
T ss_pred             CCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECC
T ss_conf             697979999999897999999969999988---998997798


No 215
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=47.30  E-value=14  Score=16.93  Aligned_cols=23  Identities=9%  Similarity=0.007  Sum_probs=18.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             48778888999999999999850
Q gi|254780282|r  274 PEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       274 ~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      .+++..+|.-+.++|-+..++.+
T Consensus       115 ~~GR~iT~~G~~~LD~iA~~v~~  137 (150)
T PRK09333        115 KKGRVITPKGRSLLDKLATEVKK  137 (150)
T ss_pred             CCCCEECHHHHHHHHHHHHHHHH
T ss_conf             99867798689999999999999


No 216
>PRK09137 DNA topoisomerase I; Validated
Probab=46.95  E-value=9.6  Score=17.87  Aligned_cols=22  Identities=9%  Similarity=0.167  Sum_probs=8.5

Q ss_pred             EEECCCCEEEEECCCCCCCCCC
Q ss_conf             7976994685001343322222
Q gi|254780282|r   50 FYRHARGLTLTEQGSKLHRVTS   71 (299)
Q Consensus        50 f~R~~~~~~lT~~G~~l~~~a~   71 (299)
                      +.+.++.+.||+.|..+.+...
T Consensus       506 v~~~~k~l~pT~lG~~v~~~L~  527 (761)
T PRK09137        506 VRLDKKRFIPTDVGRIVNKFLT  527 (761)
T ss_pred             EEEECCEEEECHHHHHHHHHHH
T ss_conf             9965998856467999999998


No 217
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=46.39  E-value=21  Score=15.89  Aligned_cols=55  Identities=13%  Similarity=0.207  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECC
Q ss_conf             9999999999827--689999882899789999999999995882179769946850013
Q gi|254780282|r    6 DKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG   63 (299)
Q Consensus         6 ~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G   63 (299)
                      |+-+..-.+-+.|  ++..-|+.++||..||-|=++.||++   .+..|..+|..+.+..
T Consensus        18 R~~~Il~~L~~~g~v~v~eLae~~~VS~~TIRRDL~~Le~~---g~l~R~hGGA~~~~~~   74 (269)
T PRK09802         18 RREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQ---GIAVRAYGGALICDST   74 (269)
T ss_pred             HHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECCEEECCCC
T ss_conf             99999999998698999999998796988999809999878---9869996878976778


No 218
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=46.30  E-value=21  Score=15.88  Aligned_cols=24  Identities=21%  Similarity=0.378  Sum_probs=14.6

Q ss_pred             HCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             276899998828997899999999
Q gi|254780282|r   17 SGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        17 ~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      .||=|+||..|||...++-+.+++
T Consensus        71 ~gNQtrAa~mLGinR~TLRKKLkq   94 (98)
T COG2901          71 RGNQTRAALMLGINRGTLRKKLKK   94 (98)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             264889999974328899999998


No 219
>KOG1168 consensus
Probab=44.60  E-value=23  Score=15.72  Aligned_cols=34  Identities=12%  Similarity=0.109  Sum_probs=14.1

Q ss_pred             HCCEEEEECCCCEEEEE---CCCCCCCCCCCCCCCCCHHH
Q ss_conf             58821797699468500---13433222222222210122
Q gi|254780282|r   45 VGIKLFYRHARGLTLTE---QGSKLHRVTSEVYHKLETTQ   81 (299)
Q Consensus        45 lg~~Lf~R~~~~~~lT~---~G~~l~~~a~~~l~~~~~~~   81 (299)
                      ++.+||.|.   ..||+   -|..+.-.-..++...+.+.
T Consensus        38 ~~S~~~~~a---~lp~~~~~~snifa~~deslLaRaeala   74 (385)
T KOG1168          38 FPSELFRRA---CLPSPISRGSNIFAGTDESLLARAEALA   74 (385)
T ss_pred             CCHHHHHHH---HCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             750766676---4479656677642334488999887666


No 220
>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=43.93  E-value=23  Score=15.66  Aligned_cols=11  Identities=9%  Similarity=-0.121  Sum_probs=4.8

Q ss_pred             CCCHHHHHHHH
Q ss_conf             00013566754
Q gi|254780282|r  108 LQGNLKEFLLL  118 (299)
Q Consensus       108 l~~~l~~f~~~  118 (299)
                      .|..+..|-++
T Consensus        40 ~p~Al~~lErh   50 (249)
T TIGR03001        40 EPAALAALERH   50 (249)
T ss_pred             CHHHHHHHHHH
T ss_conf             28999999999


No 221
>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=43.93  E-value=23  Score=15.66  Aligned_cols=29  Identities=14%  Similarity=0.159  Sum_probs=24.7

Q ss_pred             HHHHC-CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             99827-689999882899789999999999
Q gi|254780282|r   14 VARSG-SFTHAAEQLHLSQSSISRQISGLE   42 (299)
Q Consensus        14 v~~~g-s~s~AA~~L~itq~avS~~i~~LE   42 (299)
                      +.+.| |++..|+.++|+++++.+=+++..
T Consensus        19 ~~~~g~sv~~var~~gi~~~~l~~W~k~~~   48 (75)
T pfam01527        19 SLEPGASVSELAREHGVSPATLYKWRKKYR   48 (75)
T ss_pred             HHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             980998499999998959999999999984


No 222
>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=43.80  E-value=23  Score=15.65  Aligned_cols=32  Identities=19%  Similarity=0.104  Sum_probs=25.1

Q ss_pred             HHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99999998276899998828997899999999
Q gi|254780282|r    9 RVFYVVARSGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus         9 ~~f~~v~~~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      +=+..+.-..+-+.=|+.|+|++++||...++
T Consensus         4 ~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R   35 (65)
T pfam07022         4 ERLMKAYGFKSRSELADHLGVSKSTLSTWYKR   35 (65)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf             99999968886999999969888889999986


No 223
>PRK04280 arginine repressor; Provisional
Probab=43.54  E-value=12  Score=17.22  Aligned_cols=34  Identities=15%  Similarity=0.198  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHCCHHH--------HHHHHCCCHHHHHHHHHHH
Q ss_conf             999999998276899--------9988289978999999999
Q gi|254780282|r    8 LRVFYVVARSGSFTH--------AAEQLHLSQSSISRQISGL   41 (299)
Q Consensus         8 L~~f~~v~~~gs~s~--------AA~~L~itq~avS~~i~~L   41 (299)
                      .+....+..++.++.        +++-..+||+||||-|++|
T Consensus         7 ~~~I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATlSRDlkeL   48 (149)
T PRK04280          7 HIKIREIITNEEIETQDELVDRLREYGFNVTQATVSRDIKEL   48 (149)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHH
T ss_conf             999999997489778999999999859755389889879981


No 224
>PRK09729 hypothetical protein; Provisional
Probab=43.37  E-value=14  Score=16.94  Aligned_cols=40  Identities=25%  Similarity=0.268  Sum_probs=25.2

Q ss_pred             HHHHHHHCCEEEEEHHHHCC-CCCEEEECCCCCCCCCEEEEE
Q ss_conf             35678738423311777601-998466177666766008999
Q gi|254780282|r  232 MQYCVLGSGIALLPDYIVKD-NPNLVRIMEDVITPSFTVYFC  272 (299)
Q Consensus       232 ~~~v~~g~Gia~lp~~~~~~-~~~lv~i~~~~~~~~~~~~lv  272 (299)
                      ++.++.|+||+++|+...+. .|++..+.. .+..-+.+.+.
T Consensus         1 ~~firqglgiallpeltlk~~~g~lcsv~l-eptfyrqisll   41 (68)
T PRK09729          1 MNFIRQGLGIALQPELTLKSIAGELCSVPL-EPTFYRQISLL   41 (68)
T ss_pred             CCHHHHCCCEEECCHHHHHHHCCCEECCCC-CHHHHHHHHHH
T ss_conf             926760665222204438874174012346-63799999998


No 225
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=43.14  E-value=21  Score=15.96  Aligned_cols=23  Identities=26%  Similarity=0.437  Sum_probs=20.1

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             99988289978999999999999
Q gi|254780282|r   22 HAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus        22 ~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      .-|+-|+.|.-+||+.+++|+++
T Consensus         7 dIadylGlt~ETVsR~l~~L~~~   29 (32)
T pfam00325         7 EIADYLGLTRETVSRLLKRLREK   29 (32)
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHC
T ss_conf             99998472599999999999985


No 226
>PRK09954 hypothetical protein; Provisional
Probab=42.93  E-value=22  Score=15.75  Aligned_cols=55  Identities=22%  Similarity=0.308  Sum_probs=35.6

Q ss_pred             CHHHHHHHHHHHHHCCHH--HHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECC
Q ss_conf             889999999999827689--999882899789999999999995882179769946850013
Q gi|254780282|r    4 DWDKLRVFYVVARSGSFT--HAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG   63 (299)
Q Consensus         4 d~~~L~~f~~v~~~gs~s--~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G   63 (299)
                      +=|.-+.+-.+=+.--++  .=|+.|++|.|+|.-||.+|=+.    =+.+ |||+.+++.-
T Consensus         2 t~re~~il~~i~~~p~i~q~ela~~lgisrs~va~hi~~l~~k----g~i~-G~gyi~~~~~   58 (362)
T PRK09954          2 NNREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRK----GRIK-GKGYILTEQE   58 (362)
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC----CEEC-CCEEEECCCC
T ss_conf             8689999999987899589999999798799999999988754----7652-5468877997


No 227
>pfam05344 DUF746 Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons.
Probab=42.28  E-value=25  Score=15.51  Aligned_cols=33  Identities=18%  Similarity=0.209  Sum_probs=28.4

Q ss_pred             HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             999827689999882899789999999999995
Q gi|254780282|r   13 VVARSGSFTHAAEQLHLSQSSISRQISGLETEV   45 (299)
Q Consensus        13 ~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~l   45 (299)
                      -+..--|+..||+.+++++-+|.+-++...+++
T Consensus         9 lLs~p~s~~qaa~~lg~~~~~i~~wv~~fr~~l   41 (65)
T pfam05344         9 LLSQPISCAQAADQLGTDEGIIRKWVRMFRRWL   41 (65)
T ss_pred             HHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             826666599999997878889999999999999


No 228
>pfam01316 Arg_repressor Arginine repressor, DNA binding domain.
Probab=41.65  E-value=12  Score=17.37  Aligned_cols=16  Identities=25%  Similarity=0.596  Sum_probs=11.7

Q ss_pred             HHCCCHHHHHHHHHHH
Q ss_conf             8289978999999999
Q gi|254780282|r   26 QLHLSQSSISRQISGL   41 (299)
Q Consensus        26 ~L~itq~avS~~i~~L   41 (299)
                      -..+||++|||-|++|
T Consensus        33 G~~vTQATlSRDl~eL   48 (70)
T pfam01316        33 GINVTQATVSRDLKEL   48 (70)
T ss_pred             CCCEEEHHHHHHHHHH
T ss_conf             9856417888779993


No 229
>COG1438 ArgR Arginine repressor [Transcription]
Probab=41.41  E-value=20  Score=15.97  Aligned_cols=37  Identities=16%  Similarity=0.355  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHCCHHH--------HHHHHCCCHHHHHHHHHHH
Q ss_conf             899999999998276899--------9988289978999999999
Q gi|254780282|r    5 WDKLRVFYVVARSGSFTH--------AAEQLHLSQSSISRQISGL   41 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~s~--------AA~~L~itq~avS~~i~~L   41 (299)
                      =+.++.+..+.....++.        +.+-..+||++|||-|++|
T Consensus         5 ~~R~~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~vTQaTvSRDlkel   49 (150)
T COG1438           5 EERLELIKEIITEEKISTQEELVELLQEEGIEVTQATVSRDLKEL   49 (150)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCEEEHHHHHHHHHHC
T ss_conf             899999999998677778999999999829758639878779985


No 230
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=41.28  E-value=18  Score=16.24  Aligned_cols=19  Identities=26%  Similarity=0.293  Sum_probs=12.8

Q ss_pred             HHHHHHHCCCHHHHHHHHH
Q ss_conf             9999882899789999999
Q gi|254780282|r   21 THAAEQLHLSQSSISRQIS   39 (299)
Q Consensus        21 s~AA~~L~itq~avS~~i~   39 (299)
                      +++|+.|+||||.||--.+
T Consensus        45 ~qiae~lgV~qprvS~l~~   63 (91)
T COG5606          45 AQIAELLGVTQPRVSDLAR   63 (91)
T ss_pred             HHHHHHHCCCCCHHHHHHH
T ss_conf             9999983888731889983


No 231
>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=40.63  E-value=26  Score=15.36  Aligned_cols=37  Identities=27%  Similarity=0.428  Sum_probs=32.2

Q ss_pred             CCCCHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             98888999999999982768999988289978999999
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSGSFTHAAEQLHLSQSSISRQI   38 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~gs~s~AA~~L~itq~avS~~i   38 (299)
                      |..|+..|+-.. +-++|+.-.=|..+++|.-++|-.+
T Consensus         1 m~~dY~kLrgrI-~Ek~gtq~~Fa~~lg~se~tlslkl   37 (69)
T pfam05339         1 MKYDYSKLKGRI-LEKYGTQYNFASAIGLSERSLSLKL   37 (69)
T ss_pred             CCCCHHHHCCHH-HHHHCCHHHHHHHHCCCHHHHHHHH
T ss_conf             976678860328-8995679899999581176888987


No 232
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=40.38  E-value=25  Score=15.45  Aligned_cols=23  Identities=35%  Similarity=0.280  Sum_probs=17.1

Q ss_pred             HCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             27689999882899789999999
Q gi|254780282|r   17 SGSFTHAAEQLHLSQSSISRQIS   39 (299)
Q Consensus        17 ~gs~s~AA~~L~itq~avS~~i~   39 (299)
                      --|-...|+.+++|+++||+--+
T Consensus         9 g~tq~~lA~~~gis~~~is~~E~   31 (55)
T pfam01381         9 GLSQEELAEKLGVSRSTISKIEN   31 (55)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHC
T ss_conf             99899999998969999999987


No 233
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=40.37  E-value=26  Score=15.40  Aligned_cols=41  Identities=12%  Similarity=0.139  Sum_probs=30.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE
Q ss_conf             6899998828997899999999999958821797699468500
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE   61 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~   61 (299)
                      |=..=|+..+||..||-++|+.||++  --+..+.|+|.-.++
T Consensus        31 sE~eLa~~~~VSR~TvR~Al~~L~~e--Gli~r~~G~GTfV~~   71 (239)
T PRK09764         31 TESALQTEFGVSRVTVRQALRQLVEQ--QILESIQGSGTYVKE   71 (239)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCCEEEECC
T ss_conf             99999999797999999999999978--999998687789888


No 234
>TIGR02201 heptsyl_trn_III lipopolysaccharide heptosyltransferase III, putative; InterPro: IPR011916    This family consists of examples of the putative ADP-heptose:LPS heptosyltransferase III, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. This enzyme may be less widely distributed than heptosyltransferases I and II..
Probab=40.29  E-value=8.5  Score=18.18  Aligned_cols=38  Identities=21%  Similarity=0.351  Sum_probs=28.2

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             00001356675420001222222222222222222223
Q gi|254780282|r  107 LLQGNLKEFLLLYPDIQIQLILDNKDIDISMDYADCAI  144 (299)
Q Consensus       107 ~l~~~l~~f~~~~P~i~i~i~~~~~~~~l~~~~~Di~i  144 (299)
                      +..|++..+.++||+.+|++..-....+++...=|+.=
T Consensus        15 L~TPvi~~LK~~yP~a~iDvLlY~eT~p~L~~NPdI~~   52 (347)
T TIGR02201        15 LTTPVIRALKKRYPDAKIDVLLYRETVPLLSENPDIAR   52 (347)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHCCCCHHH
T ss_conf             88799999851188850430210315888762883355


No 235
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=39.40  E-value=10  Score=17.70  Aligned_cols=65  Identities=15%  Similarity=0.195  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHHHCCH--HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCC
Q ss_conf             8999999999982768--9999882899789999999999995882179769946850013433222222
Q gi|254780282|r    5 WDKLRVFYVVARSGSF--THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSE   72 (299)
Q Consensus         5 ~~~L~~f~~v~~~gs~--s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~   72 (299)
                      .++|.++-.|++++-+  -+-++..|+..--|-..++-||++   .++.-+..|-.+|+.+-.+.+....
T Consensus        14 ~RHl~Vl~~v~eeqPiGI~klS~~TGmp~HKVRYSLRVLEq~---~iI~PS~~GAi~td~~~e~ie~i~~   80 (101)
T COG3388          14 KRHLSVLKVVLEEQPIGIIKLSDETGMPEHKVRYSLRVLEQE---NIISPSRQGAILTDDFPEFIEEIIG   80 (101)
T ss_pred             HHHHHHHHHHHHHCCCEEEEECHHCCCCHHHHHHHHHHHHHC---CCCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             999999999998388316850010188403345666545235---7567353677138507899999997


No 236
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=39.38  E-value=12  Score=17.37  Aligned_cols=23  Identities=17%  Similarity=0.140  Sum_probs=14.2

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99998828997899999999999
Q gi|254780282|r   21 THAAEQLHLSQSSISRQISGLET   43 (299)
Q Consensus        21 s~AA~~L~itq~avS~~i~~LE~   43 (299)
                      ..|++++++|+.-+-+..++|=+
T Consensus        94 ~~a~~~~g~s~~~tl~iaQ~LYE  116 (381)
T cd00186          94 QEASSKLGFSAKKTMQIAQKLYE  116 (381)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             99986069599999999999986


No 237
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=39.34  E-value=27  Score=15.24  Aligned_cols=47  Identities=26%  Similarity=0.284  Sum_probs=35.4

Q ss_pred             HHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE
Q ss_conf             99999827689999882899789999999999995882179769946850
Q gi|254780282|r   11 FYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT   60 (299)
Q Consensus        11 f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT   60 (299)
                      ++.-...-++..-|+.++||..||-+-|..||+.   .++.|..+|..+.
T Consensus         8 ~l~~~~~v~i~~La~~f~VS~~TiRRDl~~L~~~---g~i~R~~GGA~~~   54 (57)
T pfam08220         8 LLKQQGTLSVEELAELLGVSEMTIRRDLNELEEQ---GLLTRTHGGAVSN   54 (57)
T ss_pred             HHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECCEECC
T ss_conf             9998697979999999895999999969999988---9989974957758


No 238
>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=39.24  E-value=27  Score=15.23  Aligned_cols=41  Identities=20%  Similarity=0.302  Sum_probs=29.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE
Q ss_conf             6899998828997899999999999958821797699468500
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE   61 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~   61 (299)
                      |-..=|++.+||..||.++|+.|+++  --+..+.|+|.-.++
T Consensus        27 sE~eLa~~~~VSR~TvR~Al~~L~~e--Gli~r~~G~GTfV~~   67 (231)
T TIGR03337        27 SERDLGERFNTTRVTIREALQQLEAE--GLIYREDRRGWFVSP   67 (231)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCCEEEECC
T ss_conf             89999999797999999999999987--996996686679888


No 239
>PRK03341 arginine repressor; Provisional
Probab=38.99  E-value=14  Score=16.84  Aligned_cols=13  Identities=23%  Similarity=0.560  Sum_probs=6.5

Q ss_pred             CCCHHHHHHHHHH
Q ss_conf             8997899999999
Q gi|254780282|r   28 HLSQSSISRQISG   40 (299)
Q Consensus        28 ~itq~avS~~i~~   40 (299)
                      .+||+||||-|++
T Consensus        45 ~vTQATiSRDikE   57 (168)
T PRK03341         45 DVTQATLSRDLEE   57 (168)
T ss_pred             CEEHHHHHHHHHH
T ss_conf             6542787752998


No 240
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=38.84  E-value=27  Score=15.23  Aligned_cols=23  Identities=30%  Similarity=0.281  Sum_probs=18.0

Q ss_pred             HCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             27689999882899789999999
Q gi|254780282|r   17 SGSFTHAAEQLHLSQSSISRQIS   39 (299)
Q Consensus        17 ~gs~s~AA~~L~itq~avS~~i~   39 (299)
                      --|....|+.+|+|+++||+-.+
T Consensus        10 glsq~~lA~~~gis~~~is~~E~   32 (56)
T smart00530       10 GLTQEELAEKLGVSRSTLSRIEN   32 (56)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHC
T ss_conf             99999999998959999999997


No 241
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=38.79  E-value=28  Score=15.19  Aligned_cols=35  Identities=17%  Similarity=0.155  Sum_probs=25.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE
Q ss_conf             689999882899789999999999995882179769946
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL   57 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~   57 (299)
                      +++.+|+.++|++    ..|+--|+++|..=-.|+.+|.
T Consensus         2 sI~eva~~~Gv~~----~tLR~wE~~~~l~~p~R~~~g~   36 (68)
T cd04763           2 TIGEVALLTGIKP----HVLRAWEREFGLLKPQRSDGGH   36 (68)
T ss_pred             CHHHHHHHHCCCH----HHHHHHHHCCCCCCCCCCCCCC
T ss_conf             7889999988794----5758988705899986799999


No 242
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=38.23  E-value=28  Score=15.14  Aligned_cols=40  Identities=20%  Similarity=0.248  Sum_probs=29.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE
Q ss_conf             689999882899789999999999995882179769946850
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT   60 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT   60 (299)
                      |-..=|++.+||..||-++|+.|+++  --+..+.|+|.-..
T Consensus        37 sE~eLa~~y~VSR~TVR~Al~~L~~e--Gli~r~~G~GtfV~   76 (243)
T PRK11402         37 TENELCTQYNVSRITIRKAISDLVAD--GVLIRWQGKGTFVQ   76 (243)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCCEEEEC
T ss_conf             99999999797999999999999978--99999779668995


No 243
>PRK04158 transcriptional repressor CodY; Validated
Probab=37.60  E-value=25  Score=15.45  Aligned_cols=11  Identities=0%  Similarity=0.126  Sum_probs=3.7

Q ss_pred             HHHHCCEEEEE
Q ss_conf             99958821797
Q gi|254780282|r   42 ETEVGIKLFYR   52 (299)
Q Consensus        42 E~~lg~~Lf~R   52 (299)
                      -+-+.+..++=
T Consensus        33 ~~vl~~NvyIi   43 (256)
T PRK04158         33 SDVIECNVYII   43 (256)
T ss_pred             HHHHCCEEEEE
T ss_conf             86540739999


No 244
>PRK03837 transcriptional regulator NanR; Provisional
Probab=37.49  E-value=29  Score=15.07  Aligned_cols=38  Identities=16%  Similarity=0.263  Sum_probs=26.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEE-EECCCCEEE
Q ss_conf             68999988289978999999999999588217-976994685
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLF-YRHARGLTL   59 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf-~R~~~~~~l   59 (299)
                      +-..=|+.++||.++|-..++.||.+ |  |+ .|.|+|...
T Consensus        40 ~E~eLae~lgVSRtpVREAL~~L~~~-G--lV~~~~g~g~~V   78 (243)
T PRK03837         40 SERELMAFFGVGRPSVREALQALKRK-G--LVQISHGERARV   78 (243)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC-C--CEEEEECCCCEE
T ss_conf             59999999796978999999999988-9--989950897068


No 245
>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=37.28  E-value=29  Score=15.05  Aligned_cols=42  Identities=7%  Similarity=0.140  Sum_probs=32.2

Q ss_pred             HHHHHHHHHH-HHCCHHHHHHHHC-CCHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999-8276899998828-9978999999999999588
Q gi|254780282|r    6 DKLRVFYVVA-RSGSFTHAAEQLH-LSQSSISRQISGLETEVGI   47 (299)
Q Consensus         6 ~~L~~f~~v~-~~gs~s~AA~~L~-itq~avS~~i~~LE~~lg~   47 (299)
                      +++-++++-- -.-|++.=|+.+| ..++||+..+++.|+++..
T Consensus        32 R~ia~yL~r~~~~~s~~~Ig~~fg~rdHsTV~~a~~kv~~~~~~   75 (90)
T cd06571          32 RQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE   75 (90)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999999999788999999995899714999999999999983


No 246
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor; InterPro: IPR014091   Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family..
Probab=37.12  E-value=7.8  Score=18.39  Aligned_cols=55  Identities=15%  Similarity=0.175  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHHHHHH-CCEEEEE-----CCCCEEEEECCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             99789999999999995-8821797-----6994685001343322222222221012210
Q gi|254780282|r   29 LSQSSISRQISGLETEV-GIKLFYR-----HARGLTLTEQGSKLHRVTSEVYHKLETTQIE   83 (299)
Q Consensus        29 itq~avS~~i~~LE~~l-g~~Lf~R-----~~~~~~lT~~G~~l~~~a~~~l~~~~~~~~~   83 (299)
                      |-|--|=|.+++||++= =..=-+-     ..|=..||++|+..+.-+..-+++++++.+.
T Consensus        55 VDQGNVYRTLR~LEK~NLI~S~WDTS~~GPA~RIYSLT~~GEQYL~~~A~SlE~YQNML~~  115 (138)
T TIGR02719        55 VDQGNVYRTLRKLEKDNLISSTWDTSDEGPAKRIYSLTDAGEQYLSTCATSLEQYQNMLDS  115 (138)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             2310377898887665135566646887863000001311057899998789999889999


No 247
>PRK00441 argR arginine repressor; Provisional
Probab=36.35  E-value=16  Score=16.52  Aligned_cols=36  Identities=17%  Similarity=0.263  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHCCHHHH--------HHHHCCCHHHHHHHHHHH
Q ss_conf             999999999982768999--------988289978999999999
Q gi|254780282|r    6 DKLRVFYVVARSGSFTHA--------AEQLHLSQSSISRQISGL   41 (299)
Q Consensus         6 ~~L~~f~~v~~~gs~s~A--------A~~L~itq~avS~~i~~L   41 (299)
                      ...+....+.....++.=        .+-..+||+||||-|++|
T Consensus         4 ~Rq~~I~~lI~~~~I~tQ~eL~~~L~~~Gi~vTQATlSRDl~eL   47 (149)
T PRK00441          4 SRHAKILEIINSKEIETQEELAEELKKMGFDVTQATVSRDIKEL   47 (149)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHC
T ss_conf             99999999997289678999999999869976658988869981


No 248
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=35.91  E-value=31  Score=14.92  Aligned_cols=51  Identities=14%  Similarity=0.189  Sum_probs=27.0

Q ss_pred             EEHHHHCCCCCEEE-ECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             11777601998466-177666766008999348778888999999999999850
Q gi|254780282|r  244 LPDYIVKDNPNLVR-IMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       244 lp~~~~~~~~~lv~-i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      -|......+|..++ ++...  ....+---.++++..+|.-+.|+|-+..++.+
T Consensus        86 rP~~~~~gsgsI~RkilqqL--E~~G~V~k~~~GR~ltp~GrsllD~~a~ei~e  137 (147)
T COG2238          86 RPEKFRKGSGSIIRKVLQQL--EKAGLVEKTPKGRVLTPKGRSLLDRIATEIKE  137 (147)
T ss_pred             CCHHHHCCCCHHHHHHHHHH--HHCCCEEECCCCCEECCCCHHHHHHHHHHHHH
T ss_conf             94344237736999999999--97785652689865081306589999999999


No 249
>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=35.79  E-value=31  Score=14.91  Aligned_cols=31  Identities=19%  Similarity=0.249  Sum_probs=26.2

Q ss_pred             HHHHHCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             9998276899998828997899999999999
Q gi|254780282|r   13 VVARSGSFTHAAEQLHLSQSSISRQISGLET   43 (299)
Q Consensus        13 ~v~~~gs~s~AA~~L~itq~avS~~i~~LE~   43 (299)
                      ...+.-|+...|+.||+|.++|..++.+-.+
T Consensus        22 ~~~~~~s~~eIA~~lg~s~~tVk~~l~RA~~   52 (54)
T pfam08281        22 RYLEGLSYAEIAELLGISEGTVKSRLSRARK   52 (54)
T ss_pred             HHHHCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             9987859999999989499999999999997


No 250
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=35.39  E-value=32  Score=14.87  Aligned_cols=57  Identities=12%  Similarity=0.138  Sum_probs=35.0

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCC-CCCCCCCCCCCCCHH
Q ss_conf             8999988289978999999999999588217976994685001343-322222222221012
Q gi|254780282|r   20 FTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSK-LHRVTSEVYHKLETT   80 (299)
Q Consensus        20 ~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~-l~~~a~~~l~~~~~~   80 (299)
                      -+.+|++||||+.||-|=+++    |+.+.=.-.-+.+..|+.--. ++.+.+.-+.+-..+
T Consensus         3 T~~vAk~LGVspkTVQRWvKq----~ni~~~rNE~GHy~Ft~e~l~~lLk~~~~q~~qg~~~   60 (178)
T PRK13182          3 TPFVAKKLGVSPKTVQRWVKQ----LNLPIERNEYGHYIFTEDDLDQLLKYHRSQIEQGQNM   60 (178)
T ss_pred             HHHHHHHHCCCHHHHHHHHHH----HCCCCCCCCCCCEEECHHHHHHHHHHHHHHHHCCCCC
T ss_conf             178899939992999999999----5899553655443324989999999999986057545


No 251
>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=35.27  E-value=32  Score=14.86  Aligned_cols=52  Identities=21%  Similarity=0.276  Sum_probs=32.9

Q ss_pred             CCHHHHHHHHHHHHH----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE
Q ss_conf             888999999999982----------7689999882899789999999999995882179769946
Q gi|254780282|r    3 FDWDKLRVFYVVARS----------GSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL   57 (299)
Q Consensus         3 md~~~L~~f~~v~~~----------gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~   57 (299)
                      |.-+++++|.+|++.          =+-+.=|+.-+++...||+.+++|.++   .++.+.|+.+
T Consensus        30 lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs~a~~~Li~~---~vi~~~G~~i   91 (100)
T pfam04492        30 LSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVSEAKKSLVKR---GIIIQDGRQI   91 (100)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC---CCCHHCCCEE
T ss_conf             8788999999999986077850336229999999788854599999999976---8644149685


No 252
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=35.16  E-value=32  Score=14.85  Aligned_cols=28  Identities=21%  Similarity=0.262  Sum_probs=24.2

Q ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9982768999988289978999999999
Q gi|254780282|r   14 VARSGSFTHAAEQLHLSQSSISRQISGL   41 (299)
Q Consensus        14 v~~~gs~s~AA~~L~itq~avS~~i~~L   41 (299)
                      .+-.-|++.-|+..++|+++|.|-.++|
T Consensus        44 ~v~~~si~eLA~~~~vS~aTVvRf~kkL   71 (293)
T PRK11337         44 LSCATALKDVAEALAVSEAMIVKVAKLL   71 (293)
T ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9976669999989599888999999995


No 253
>KOG2947 consensus
Probab=35.15  E-value=32  Score=14.85  Aligned_cols=117  Identities=13%  Similarity=0.095  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCHHHHHHH
Q ss_conf             22222222223456--5432111122345554332112344321112222221100011235664332-11000235665
Q gi|254780282|r  134 DISMDYADCAIRLR--KPIQSSSLIQRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIP-KCMEDFNWLAT  210 (299)
Q Consensus       134 ~l~~~~~Di~i~~~--~~~~~~~l~~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~-~~~~~~~~~~~  210 (299)
                      ++...++|+-=+..  ..++.+.+....=-....++.|.++++.-.-.--.--||..+.||.+....+ ...........
T Consensus        76 d~~~rgIdishcp~td~~pp~ssiI~~r~~~trTiv~~dks~p~vT~~dF~kvdl~qy~WihfE~Rnp~etlkM~~~I~~  155 (308)
T KOG2947          76 DLRRRGIDISHCPFTDHSPPFSSIIINRNSGTRTILYCDKSLPDVTATDFEKVDLTQYGWIHFEARNPSETLKMLQRIDA  155 (308)
T ss_pred             HHHHCCCCCCCCCCCCCCCCCCEEEEECCCCCEEEEEECCCCCCCCHHHHHHCCCCEEEEEEEECCCHHHHHHHHHHHHH
T ss_conf             79864877555766578998305888416883489993477852348777542600002699964790999999999998


Q ss_pred             HCCCCCCCCCCEEEE---CCCCHHHHHHHHHCCEEEEEHHHHCC
Q ss_conf             202234321211453---24200135678738423311777601
Q gi|254780282|r  211 VDRPIGEPRISCLQV---NSYLSIMQYCVLGSGIALLPDYIVKD  251 (299)
Q Consensus       211 ~~~~~~~~~~~~~~~---~s~~~~~~~v~~g~Gia~lp~~~~~~  251 (299)
                      ++...+....+.+++   +..+....+..-+. +.++...+++.
T Consensus       156 ~N~r~pe~qrI~vSvd~en~req~~~l~am~D-yVfvsK~~a~~  198 (308)
T KOG2947         156 HNTRQPEEQRIRVSVDVENPREQLFQLFAMCD-YVFVSKDVAKH  198 (308)
T ss_pred             HHCCCCCCCEEEEEEEECCCHHHHHHHHHHCC-EEEEEHHHHHH
T ss_conf             62589830207999980681799998761134-89987898765


No 254
>pfam00376 MerR MerR family regulatory protein.
Probab=35.11  E-value=29  Score=15.06  Aligned_cols=22  Identities=18%  Similarity=0.172  Sum_probs=16.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             68999988289978999999999999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      +++.+|+.++||..+|    +..|++
T Consensus         1 ti~e~A~~~gvs~~tl----R~ye~~   22 (38)
T pfam00376         1 TIGEVAKLLGVSPRTL----RYYEKI   22 (38)
T ss_pred             CHHHHHHHHCCCHHHH----HHHHHC
T ss_conf             9899999988799999----999986


No 255
>PHA01976 helix-turn-helix protein
Probab=35.05  E-value=25  Score=15.50  Aligned_cols=34  Identities=15%  Similarity=0.284  Sum_probs=21.8

Q ss_pred             HHCCH--HHHHHHHCCCHHHHHH-----------HHHHHHHHHCCEE
Q ss_conf             82768--9999882899789999-----------9999999958821
Q gi|254780282|r   16 RSGSF--THAAEQLHLSQSSISR-----------QISGLETEVGIKL   49 (299)
Q Consensus        16 ~~gs~--s~AA~~L~itq~avS~-----------~i~~LE~~lg~~L   49 (299)
                      +..++  ..-|+++|||+++||+           .+.+|-+-||+.+
T Consensus        12 ~~~g~sQ~eLA~~lGVs~~~is~wE~g~~~P~~d~L~~la~~~~VS~   58 (67)
T PHA01976         12 NARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTL   58 (67)
T ss_pred             HHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
T ss_conf             98699999999994998999999987898999899999999979789


No 256
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=34.84  E-value=32  Score=14.82  Aligned_cols=28  Identities=21%  Similarity=0.262  Sum_probs=24.5

Q ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9982768999988289978999999999
Q gi|254780282|r   14 VARSGSFTHAAEQLHLSQSSISRQISGL   41 (299)
Q Consensus        14 v~~~gs~s~AA~~L~itq~avS~~i~~L   41 (299)
                      -+-..|++.=|++.++|+|||+|-.++|
T Consensus        31 ~v~~~si~eLA~~~~vS~aTV~Rf~kkL   58 (284)
T PRK11302         31 TAIHSSIATLAKMANVSEPTVNRFCRSL   58 (284)
T ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9976669999989699888999999995


No 257
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=34.65  E-value=33  Score=14.80  Aligned_cols=61  Identities=18%  Similarity=0.226  Sum_probs=42.0

Q ss_pred             CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCC
Q ss_conf             988889999999999827--6899998828997899999999999958821797699468500134
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGS   64 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~   64 (299)
                      |.-+=|+=+.+..+-+.|  ++...|+.++||..||-|=++.||++   -++.|..+|..+.+.+.
T Consensus         1 M~~~eR~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~---g~l~r~~GGA~~~~~~~   63 (251)
T PRK13509          1 MNEAQRHQILLDMLAQLGFVTVEKVIERLGISPATARRDINKLDES---GKLKKVRNGAEAITQQR   63 (251)
T ss_pred             CCHHHHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHC---CCEEEEECCEEECCCCC
T ss_conf             9889999999999998698989999999896998999839999878---97899988979777777


No 258
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=34.24  E-value=33  Score=14.76  Aligned_cols=47  Identities=9%  Similarity=0.087  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHH-----------HHHHHHCC
Q ss_conf             988889999999999827--689999882899789999999-----------99999588
Q gi|254780282|r    1 MSFDWDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQIS-----------GLETEVGI   47 (299)
Q Consensus         1 m~md~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~-----------~LE~~lg~   47 (299)
                      |+.|+...+-+...++..  +....|...++++|+||+.+.           ++|..++.
T Consensus         1 ~~~n~~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g~~g~~~~~~a~ia~~le~   60 (297)
T COG2842           1 KQINFIEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNGYKGDYATNEAKIAAFLEK   60 (297)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHHCC
T ss_conf             940389999999999861666999998736684457878437674177789999999727


No 259
>pfam00342 PGI Phosphoglucose isomerase. Phosphoglucose isomerase catalyses the interconversion of glucose-6-phosphate and fructose-6-phosphate.
Probab=34.12  E-value=25  Score=15.51  Aligned_cols=111  Identities=12%  Similarity=0.192  Sum_probs=63.0

Q ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHHCC------C--HHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCC
Q ss_conf             8888999999999982768999988289------9--7899999999999958821797699468500134332222222
Q gi|254780282|r    2 SFDWDKLRVFYVVARSGSFTHAAEQLHL------S--QSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEV   73 (299)
Q Consensus         2 ~md~~~L~~f~~v~~~gs~s~AA~~L~i------t--q~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~   73 (299)
                      .+|=+.|..|..++++-.+..+-+.|.-      |  +|+..-.++             .+.+-.....|+.+.+.+...
T Consensus         6 ~i~~~~l~~l~~la~~~~l~~~~~~lf~G~~vN~tE~r~vlH~~lR-------------~~~~~~~~~~~~~~~~~v~~~   72 (483)
T pfam00342         6 HINDETLSALLKLAEEAGLDAKREAMFLGEKINTTENRAVLHVALR-------------NRSNRPIYVDGKDVMPEVDNV   72 (483)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCHHHH-------------CCCCCCCCCCCHHHHHHHHHH
T ss_conf             5899999999999997885999999967998688999422679995-------------999898547850558999999


Q ss_pred             CCCCCHHHHHCCCCC------CCCCCCCCCCCCC-CCCCCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf             222101221001223------2222223332111-00000000013566754200012222
Q gi|254780282|r   74 YHKLETTQIELQESS------VKPSGKLRIATTI-DLGQNLLQGNLKEFLLLYPDIQIQLI  127 (299)
Q Consensus        74 l~~~~~~~~~~~~~~------~~~~g~i~I~~~~-~~~~~~l~~~l~~f~~~~P~i~i~i~  127 (299)
                      ++.+.++.+.++...      ...+-.|.||..- .+++..+...|..+....  +++.+.
T Consensus        73 ~~~~~~~~~~i~~g~~~g~~g~~~~~vV~IGIGGS~LGp~~~~~AL~~~~~~~--~~~~Fv  131 (483)
T pfam00342        73 LDKMKDFFERIRSGAWKGYTGKAITDVVNIGIGGSDLGPRMVIEALKHYSENA--LIVFFV  131 (483)
T ss_pred             HHHHHHHHHHHHCCCEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCC--CEEEEE
T ss_conf             99999999999729710678982343899565650076999999986533698--228995


No 260
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=33.60  E-value=34  Score=14.70  Aligned_cols=40  Identities=20%  Similarity=0.349  Sum_probs=29.1

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC
Q ss_conf             999988289978999999999999588217976994685001
Q gi|254780282|r   21 THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ   62 (299)
Q Consensus        21 s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~   62 (299)
                      ..=|+.+|||.++|-..|+.||.+ |.- -.|.|+|...++.
T Consensus        37 reLAe~lgVSRt~VREAL~~Le~~-GLV-~~r~G~Gt~V~~~   76 (257)
T PRK10225         37 REIAEMLDVTRTVVREALIMLEIK-GLV-EVRRGAGIYVLDS   76 (257)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHC-CCE-EEEECCEEEEECC
T ss_conf             999999798878999999999988-997-9964887788268


No 261
>smart00351 PAX Paired Box domain.
Probab=33.31  E-value=32  Score=14.81  Aligned_cols=32  Identities=19%  Similarity=0.257  Sum_probs=22.3

Q ss_pred             HHHHHHHC-CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             99999827-689999882899789999999999
Q gi|254780282|r   11 FYVVARSG-SFTHAAEQLHLSQSSISRQISGLE   42 (299)
Q Consensus        11 f~~v~~~g-s~s~AA~~L~itq~avS~~i~~LE   42 (299)
                      ++.++..| .-..=++.|.||+..|||-+.++.
T Consensus        26 IveLa~~G~rpcdISr~L~VShGCVSKIL~Ry~   58 (125)
T smart00351       26 IVELAQNGVRPCDISRQLCVSHGCVSKILGRYY   58 (125)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             999998599899987564577106999999997


No 262
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=31.61  E-value=37  Score=14.50  Aligned_cols=64  Identities=14%  Similarity=0.189  Sum_probs=34.1

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEE--EECCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCC
Q ss_conf             82768999988289978999999999999588217976994685--0013433222222222210122100122322222
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTL--TEQGSKLHRVTSEVYHKLETTQIELQESSVKPSG   93 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~l--T~~G~~l~~~a~~~l~~~~~~~~~~~~~~~~~~g   93 (299)
                      +.=|.+.||+-++||++++-+.    +.+         |++..|  ++.|+.= .+..-.+++++.+...+......+.|
T Consensus        38 R~Fs~~E~A~l~gvs~~~lR~~----~~~---------g~~P~p~~~~~gr~~-~rr~ytl~~i~~lR~~l~~~~~rp~~  103 (387)
T PHA02519         38 RRWGITEVADLIGVTPQAIRDA----EKS---------GRLPPPDFETRGRVE-RRAGYTIDQISHMRDHFGNPNQRPDD  103 (387)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHH----HHC---------CCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHCCCCCCCCC
T ss_conf             7788899999959998999878----756---------899999768888755-33435799999999986456679898


No 263
>TIGR01928 menC_lowGC/arch o-succinylbenzoic acid (OSB) synthetase; InterPro: IPR010197   This entry describes the enzyme o-succinylbenzoic acid synthetase (menC) that is involved in one of the steps of the menaquinone biosynthesis pathway. It takes SHCHC and makes it into 2-succinylbenzoate. Also included are enzymes with the common name of N-acylamino acid racemase (or the more general term, racemase / racemase family), which refers to the enzyme's industrial application as racemases, and not to its biological function as o-succinylbenzoic acid synthetase . Members are restricted to the are low GC Gram-positive bacteria and archaea. .
Probab=31.42  E-value=19  Score=16.10  Aligned_cols=91  Identities=16%  Similarity=0.214  Sum_probs=53.5

Q ss_pred             CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC--CC---CCC-CCCCCCCCCC
Q ss_conf             22210122100122322222233321110000000001356675420001222222222--22---222-2222223456
Q gi|254780282|r   74 YHKLETTQIELQESSVKPSGKLRIATTIDLGQNLLQGNLKEFLLLYPDIQIQLILDNKD--ID---ISM-DYADCAIRLR  147 (299)
Q Consensus        74 l~~~~~~~~~~~~~~~~~~g~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~i~i~~~~~~--~~---l~~-~~~Di~i~~~  147 (299)
                      +...+++..++.+.....-.+|.|-..|..    -..++...+.+||++.+.+-.+.+.  .|   |.. ++.++. ++.
T Consensus       132 l~~~e~~lk~ie~~~~~g~~RIKlKi~Pq~----~~~L~~~~~~~FP~i~L~~DAN~sy~~~D~~~Lk~Ld~~~l~-~IE  206 (326)
T TIGR01928       132 LAKLEEMLKEIESLKKEGYKRIKLKISPQI----EVDLVKKVRKRFPDIPLVVDANESYELKDIPRLKELDRYDLL-YIE  206 (326)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEEEEECCCC----CHHHHHHHHHHCCCCEEEEECCCCCCCCCCHHHHHHHHCCCE-EEE
T ss_conf             476578999999998569807887516887----534767767637972389733778885656576554440620-332


Q ss_pred             CCCCCCCCCCCC-CCCCCCCCCC
Q ss_conf             543211112234-5554332112
Q gi|254780282|r  148 KPIQSSSLIQRK-LVTIHMHAYA  169 (299)
Q Consensus       148 ~~~~~~~l~~~~-l~~~~~~~v~  169 (299)
                      .|.+..++.... |.+.-.-++|
T Consensus       207 ~Pf~~dDl~~l~~l~~~~~tpic  229 (326)
T TIGR01928       207 EPFKADDLSELKELKKELLTPIC  229 (326)
T ss_pred             CCCCCCHHHHHHHHHHCCCCCEE
T ss_conf             78984226668777521788631


No 264
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. 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 Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=31.24  E-value=37  Score=14.46  Aligned_cols=42  Identities=21%  Similarity=0.325  Sum_probs=30.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC
Q ss_conf             68999988289978999999999999588217976994685001
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ   62 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~   62 (299)
                      +-..=|++++||.+.|-..++.||.+ |.- -.+.++|+..++.
T Consensus        36 ~E~~La~~~gVSRtpvREAL~~L~~e-Glv-~~~~~~G~~V~~~   77 (212)
T TIGR03338        36 NESDIAARLGVSRGPVREAFRALEEA-GLV-RNEKNRGVFVREI   77 (212)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC-CCH-HEECCCCEEEECC
T ss_conf             89999998896949999999999986-963-3116776155117


No 265
>pfam01090 Ribosomal_S19e Ribosomal protein S19e.
Probab=31.21  E-value=34  Score=14.66  Aligned_cols=22  Identities=9%  Similarity=-0.144  Sum_probs=17.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             4877888899999999999985
Q gi|254780282|r  274 PEALKNTGKLKAFRNFIFLKAR  295 (299)
Q Consensus       274 ~~~~~~~~~~~~f~d~l~~~~r  295 (299)
                      ..++..+|.-+.++|-+..++-
T Consensus       115 ~~GR~iT~~G~~~LD~iA~~v~  136 (140)
T pfam01090       115 KGGRRLTPQGRSDLDRIAAEVL  136 (140)
T ss_pred             CCCCEECHHHHHHHHHHHHHHH
T ss_conf             9993789868999999999999


No 266
>TIGR02195 heptsyl_trn_II lipopolysaccharide heptosyltransferase II; InterPro: IPR011910    This family consists of examples of ADP-heptose:LPS heptosyltransferase II, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.; GO: 0016757 transferase activity transferring glycosyl groups, 0009103 lipopolysaccharide biosynthetic process.
Probab=31.15  E-value=21  Score=15.88  Aligned_cols=30  Identities=17%  Similarity=0.263  Sum_probs=18.5

Q ss_pred             CCCCCCCCCCC-HHHHHHHHHHCCCCCCCCC
Q ss_conf             11000000000-1356675420001222222
Q gi|254780282|r  100 TIDLGQNLLQG-NLKEFLLLYPDIQIQLILD  129 (299)
Q Consensus       100 ~~~~~~~~l~~-~l~~f~~~~P~i~i~i~~~  129 (299)
                      |..++..++.. +.+.+.++||++.|++.+.
T Consensus         7 PsWVGDmvMaQ~Lf~~Lk~~yP~~~IDV~AP   37 (361)
T TIGR02195         7 PSWVGDMVMAQSLFRLLKKRYPDAVIDVLAP   37 (361)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             8736555676899999998589838972075


No 267
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=30.90  E-value=38  Score=14.43  Aligned_cols=28  Identities=32%  Similarity=0.239  Sum_probs=24.7

Q ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9982768999988289978999999999
Q gi|254780282|r   14 VARSGSFTHAAEQLHLSQSSISRQISGL   41 (299)
Q Consensus        14 v~~~gs~s~AA~~L~itq~avS~~i~~L   41 (299)
                      .+...|++.=|++.++|++||+|-.++|
T Consensus        31 ~v~~~si~eLA~~~~vS~aTVvRf~kkL   58 (282)
T PRK11557         31 TARHLSSQQLANEAGVSQSSVVKFAQKL   58 (282)
T ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             9976569999989699988999999993


No 268
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=28.90  E-value=41  Score=14.23  Aligned_cols=191  Identities=9%  Similarity=-0.037  Sum_probs=86.7

Q ss_pred             CCCCCCCCCCCCCCCCCCHH---HHHHHHHHCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCC-
Q ss_conf             22333211100000000013---5667542000122222222----22222222222234565432--11112234555-
Q gi|254780282|r   93 GKLRIATTIDLGQNLLQGNL---KEFLLLYPDIQIQLILDNK----DIDISMDYADCAIRLRKPIQ--SSSLIQRKLVT-  162 (299)
Q Consensus        93 g~i~I~~~~~~~~~~l~~~l---~~f~~~~P~i~i~i~~~~~----~~~l~~~~~Di~i~~~~~~~--~~~l~~~~l~~-  162 (299)
                      -++++|+.|.....-+-...   .++..+.=+..|++.....    ...+..|++|+++.......  ......+++.. 
T Consensus        27 ~~l~~gv~P~~~~~~~~~~~~Pl~~yL~~~lg~~Ve~~~~~~y~~~~eal~~g~~Dia~~~p~~yv~a~~~~~~~~la~~  106 (288)
T TIGR03431        27 KELNFGIIPTENASDLKQRWEPLADYLSKKLGVKVKLFFATDYAGVIEGMRFGKVDIAWYGPSSYAEAYQKANAEAFAIE  106 (288)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEEECCHHHHHHHHCCCCEEEEEE
T ss_conf             36899980699999999999999999999878978999689999999999859830999884788998652597488998


Q ss_pred             --------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH--HH-HHHCCCCCCCCCCEEEECCCCHH
Q ss_conf             --------43321123443211122222211000112356643321100023--56-65202234321211453242001
Q gi|254780282|r  163 --------IHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFN--WL-ATVDRPIGEPRISCLQVNSYLSI  231 (299)
Q Consensus       163 --------~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~s~~~~  231 (299)
                              ..-++++.++     ....+++||.+..+..-+.. +.+.....  .+ ...+............+.+.+..
T Consensus       107 ~~~~g~~~y~s~iivr~D-----s~i~sl~DLkGk~iaf~~~~-StSG~l~P~~~L~~~~g~~~~~~f~~v~~~gshd~~  180 (288)
T TIGR03431       107 VNADGSTGYYSVLIVKKD-----SPIKSLEDLKGKTFGFVDPN-STSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAA  180 (288)
T ss_pred             ECCCCCCCEEEEEEEECC-----CCCCCHHHHCCCEEEECCCC-CCHHHHHHHHHHHHHCCCCHHHHHHHEEECCCHHHH
T ss_conf             515888645799999899-----98887789579876602874-111139999999986599725455313315787899


Q ss_pred             HHHHHHHCC-EEEEEHHHHC----C-CCC---EEEECCCCCCCCCEEEEEECCCCCCCHH-HHHHHHHHHH
Q ss_conf             356787384-2331177760----1-998---4661776667660089993487788889-9999999999
Q gi|254780282|r  232 MQYCVLGSG-IALLPDYIVK----D-NPN---LVRIMEDVITPSFTVYFCYPEALKNTGK-LKAFRNFIFL  292 (299)
Q Consensus       232 ~~~v~~g~G-ia~lp~~~~~----~-~~~---lv~i~~~~~~~~~~~~lv~~~~~~~~~~-~~~f~d~l~~  292 (299)
                      +..|..|.. +|.+.....+    . .++   -+++.-..+..+...+++ +++  .++. .+.+.+.|++
T Consensus       181 ~~aV~~G~~Dag~~~~~~~~~~~~~~~~~~~~~lrvi~~S~~iP~~~~~v-~~~--l~~~~~~~i~~all~  248 (288)
T TIGR03431       181 ILAVANGTVDAATTNDENLDRMIRKGQPDAMEDLRIIWKSPLIPNGPIVY-RKD--LPADLKAKIRKAFLN  248 (288)
T ss_pred             HHHHHCCCCCEEEECHHHHHHHHHCCCCCHHHCEEEEEECCCCCCCCEEE-ECC--CCHHHHHHHHHHHHH
T ss_conf             99998599329983388899999747963031369998678888771899-699--999999999999980


No 269
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=28.83  E-value=41  Score=14.22  Aligned_cols=42  Identities=21%  Similarity=0.278  Sum_probs=30.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEEC
Q ss_conf             68999988289978999999999999588217976994685001
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQ   62 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~   62 (299)
                      |=..=|+.++||.-||-++|+.|+++  --|..+.|+|.-..+.
T Consensus        33 sE~eLa~~f~VSR~TvRkAL~~L~~e--Gli~r~~G~GtfV~~~   74 (236)
T COG2188          33 SERELAEQFGVSRMTVRKALDELVEE--GLIVRRQGKGTFVASP   74 (236)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEEECCEEEECCC
T ss_conf             98999999798899999999999989--9889951667898877


No 270
>PRK10079 putative transcriptional regulator; Provisional
Probab=27.76  E-value=43  Score=14.11  Aligned_cols=40  Identities=15%  Similarity=0.197  Sum_probs=30.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEE
Q ss_conf             689999882899789999999999995882179769946850
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLT   60 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT   60 (299)
                      |=..=|+..+||..||-++|+.|+++  --|..+.|+|.-.+
T Consensus        37 sE~eLa~~y~VSR~TVR~Al~~L~~e--Gli~r~~G~GtfV~   76 (241)
T PRK10079         37 AEQQLAARFEVNRHTLRRAIDQLVER--GWVQRRQGVGVLVL   76 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC--CCEEEECCCCEEEE
T ss_conf             99999999798899999999999977--98799769625993


No 271
>COG0761 lytB 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]
Probab=27.66  E-value=12  Score=17.39  Aligned_cols=21  Identities=29%  Similarity=0.515  Sum_probs=11.6

Q ss_pred             HHHHHH---HHHHHHCCEEEEECC
Q ss_conf             999999---999995882179769
Q gi|254780282|r   34 ISRQIS---GLETEVGIKLFYRHA   54 (299)
Q Consensus        34 vS~~i~---~LE~~lg~~Lf~R~~   54 (299)
                      |-++|+   +.-+++|.+..+|..
T Consensus        16 V~RAI~ive~al~~~g~pIyv~~e   39 (294)
T COG0761          16 VDRAIQIVERALEEYGAPIYVRHE   39 (294)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             899999999999971998589700


No 272
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=27.42  E-value=43  Score=14.07  Aligned_cols=39  Identities=28%  Similarity=0.402  Sum_probs=28.7

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE
Q ss_conf             99998828997899999999999958821797699468500
Q gi|254780282|r   21 THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE   61 (299)
Q Consensus        21 s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~   61 (299)
                      ..=|+.++||.++|-..|+.||.+ |. +-.|.|+|...+.
T Consensus        30 ~eLae~~GVSRt~VREAL~~L~~e-Gl-V~~~~g~G~~V~~   68 (253)
T PRK10421         30 RQLAMQLGVSRNSLREALAKLVSE-GV-LLSRRGGGTFIRW   68 (253)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHC-CC-EEEEECCEEEECC
T ss_conf             999999796989999999999988-98-7997578248734


No 273
>pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=27.40  E-value=43  Score=14.07  Aligned_cols=32  Identities=19%  Similarity=0.259  Sum_probs=26.3

Q ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             99827689999882899789999999999995
Q gi|254780282|r   14 VARSGSFTHAAEQLHLSQSSISRQISGLETEV   45 (299)
Q Consensus        14 v~~~gs~s~AA~~L~itq~avS~~i~~LE~~l   45 (299)
                      +--.||.+..|+.|+.+..+|-+-....|.+.
T Consensus        13 i~~~GN~teVaR~L~c~R~TVrkY~~D~~~k~   44 (64)
T pfam06322        13 IETYGNQTEVARRLNCSRNTVRKYAEDKEGKG   44 (64)
T ss_pred             HHHHCCHHHHHHHHCCHHHHHHHHHCCCCCCE
T ss_conf             99707799997885110888998723555623


No 274
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=26.64  E-value=42  Score=14.17  Aligned_cols=26  Identities=31%  Similarity=0.344  Sum_probs=23.3

Q ss_pred             HHHCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             98276899998828997899999999
Q gi|254780282|r   15 ARSGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        15 ~~~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      .+--|+..=|+.||..+||||+-|++
T Consensus        21 ~~~~S~reIA~~LgRh~sTIsRElkR   46 (318)
T COG2826          21 KAKMSIREIAKQLNRHHSTISRELKR   46 (318)
T ss_pred             HCCCCHHHHHHHHCCCCCHHHHHHHC
T ss_conf             85998999999857686204279866


No 275
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=26.63  E-value=45  Score=13.99  Aligned_cols=69  Identities=25%  Similarity=0.359  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHH--C---CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECC-CCEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             99999999982--7---689999882899789999999999995882179769-946850013433222222222210
Q gi|254780282|r    7 KLRVFYVVARS--G---SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHA-RGLTLTEQGSKLHRVTSEVYHKLE   78 (299)
Q Consensus         7 ~L~~f~~v~~~--g---s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~~l~~~~   78 (299)
                      -|+.+..+++.  |   ++..-|++.+|+++.+.|-+++|.+. |.--=.|+. +|+.|+...+.+-  ..++++.++
T Consensus        10 AlraL~~LA~~~~~~~~~~~eIae~~~Ip~~~L~KIl~~L~~a-Glv~S~RG~~GGy~Lar~p~~It--l~dVi~aiE   84 (141)
T PRK11014         10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA-GYVTAVRGKNGGIRLGKPASTIR--IGDVVRELE   84 (141)
T ss_pred             HHHHHHHHHHCCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEECCCCCCCEECCCCHHHCC--HHHHHHHHC
T ss_conf             9999999983999984749999998794999999999999887-95672047998832148988797--999999946


No 276
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=26.38  E-value=45  Score=13.96  Aligned_cols=19  Identities=32%  Similarity=0.223  Sum_probs=11.0

Q ss_pred             CHHHHHHHHCCCHHHHHHH
Q ss_conf             6899998828997899999
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQ   37 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~   37 (299)
                      |-+.-|+.+|||+++||+=
T Consensus        20 TQ~eLA~~~Gvs~~tVs~w   38 (135)
T PRK09706         20 SQRALAKAVGVSHVSISQW   38 (135)
T ss_pred             CHHHHHHHHCCCHHHHHHH
T ss_conf             9999999969889999999


No 277
>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=26.26  E-value=46  Score=13.95  Aligned_cols=23  Identities=35%  Similarity=0.299  Sum_probs=18.8

Q ss_pred             HCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             27689999882899789999999
Q gi|254780282|r   17 SGSFTHAAEQLHLSQSSISRQIS   39 (299)
Q Consensus        17 ~gs~s~AA~~L~itq~avS~~i~   39 (299)
                      ..|...-|+.+|+|++++|+-.+
T Consensus        12 ~ls~~~lA~~~gis~~~l~~~e~   34 (58)
T cd00093          12 GLTQEELAEKLGVSRSTISRIEN   34 (58)
T ss_pred             CCCHHHHHHHCCCCHHHHHHHHC
T ss_conf             99999995714999999999987


No 278
>cd00131 PAX Paired Box domain
Probab=25.88  E-value=46  Score=13.91  Aligned_cols=32  Identities=22%  Similarity=0.279  Sum_probs=18.6

Q ss_pred             HHHHHHHCC-HHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             999998276-89999882899789999999999
Q gi|254780282|r   11 FYVVARSGS-FTHAAEQLHLSQSSISRQISGLE   42 (299)
Q Consensus        11 f~~v~~~gs-~s~AA~~L~itq~avS~~i~~LE   42 (299)
                      ++.++..|. -..=++.|.||+..|||-+.+..
T Consensus        26 IVeLa~~G~RpcdISR~L~VShGCVSKIL~Ry~   58 (128)
T cd00131          26 IVELAQSGIRPCDISRQLRVSHGCVSKILNRYY   58 (128)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             999998599788888763777216899999887


No 279
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=25.66  E-value=47  Score=13.88  Aligned_cols=23  Identities=22%  Similarity=0.140  Sum_probs=17.3

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             82768999988289978999999
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQI   38 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i   38 (299)
                      +.=|.+.||+-|+|+++++.+.-
T Consensus        32 r~f~~~e~a~l~gv~~~~lr~~~   54 (387)
T TIGR03453        32 RRFTSGEAAKLLGVTDSYLRQLS   54 (387)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             88888999988496999999998


No 280
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=25.58  E-value=47  Score=13.87  Aligned_cols=41  Identities=22%  Similarity=0.301  Sum_probs=29.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE
Q ss_conf             6899998828997899999999999958821797699468500
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE   61 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~   61 (299)
                      |=..=|+.++||.++|-..|+.||.. |.- -.|.|+|...+.
T Consensus        34 sEreLAe~fGVSRt~VREAL~~Le~~-GlV-e~r~G~Gt~V~~   74 (258)
T PRK11523         34 AERFIADEKNVSRTVVREAIIMLEVE-GYV-EVRKGSGIHVVS   74 (258)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC-CCE-EEEECCEEEECC
T ss_conf             69999999798879999999999988-998-996378158745


No 281
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=25.13  E-value=48  Score=13.82  Aligned_cols=43  Identities=23%  Similarity=0.290  Sum_probs=30.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECC
Q ss_conf             689999882899789999999999995882179769946850013
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQG   63 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G   63 (299)
                      +-..-|+.+|||.++|-..++.||.+ |. +-.|.|+|...++..
T Consensus        33 ~E~eLae~~gVSR~~VREAL~~L~~~-Gl-V~~~~g~G~~V~~~~   75 (251)
T PRK09990         33 SERRLTEKLGVSRSALREGLKVLRGR-GI-IETAQGRGSFVARLN   75 (251)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC-CC-EEEECCCCCEEECCC
T ss_conf             39999999897959999999999988-99-798579850671587


No 282
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=25.12  E-value=22  Score=15.81  Aligned_cols=53  Identities=25%  Similarity=0.334  Sum_probs=31.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC----EEEEECCCCCCCCCCCCC
Q ss_conf             68999988289978999999999999588217976994----685001343322222222
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG----LTLTEQGSKLHRVTSEVY   74 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~----~~lT~~G~~l~~~a~~~l   74 (299)
                      .+|+=.-..|++-....+-|..|++. |  |+.+...|    +.+|+.|+.|++....+-
T Consensus        33 ~~Tri~y~aNlny~~~~~yi~~L~~~-G--li~~~~~~~~~~y~lT~KG~~fle~y~~i~   89 (95)
T COG3432          33 GITRIIYGANLNYKRAQKYIEMLVEK-G--LIIKQDNGRRKVYELTEKGKRFLEKYSEIR   89 (95)
T ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHC-C--CEEECCCCCCCEEEECHHHHHHHHHHHHHH
T ss_conf             86246643276779999999999867-8--778614886445898856899999999999


No 283
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=25.04  E-value=48  Score=13.81  Aligned_cols=35  Identities=29%  Similarity=0.159  Sum_probs=26.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE
Q ss_conf             689999882899789999999999995882179769946
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL   57 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~   57 (299)
                      |++.+|+.+++++++    |+--|+++|..--.|+.+|.
T Consensus         2 sIgEva~~~gv~~~t----LRywE~~~~~~~P~r~~~g~   36 (99)
T cd04765           2 SIGEVAEILGLPPHV----LRYWETEFPQLKPVKRAGGR   36 (99)
T ss_pred             CHHHHHHHHCCCHHH----HHHHHHHCCCCCCCCCCCCC
T ss_conf             788999998949999----99999874774887589988


No 284
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=24.79  E-value=49  Score=13.79  Aligned_cols=17  Identities=18%  Similarity=0.280  Sum_probs=9.2

Q ss_pred             HHHHHHCCEEEEECCCC
Q ss_conf             99999588217976994
Q gi|254780282|r   40 GLETEVGIKLFYRHARG   56 (299)
Q Consensus        40 ~LE~~lg~~Lf~R~~~~   56 (299)
                      .|-+-+.+..|+=+++|
T Consensus        34 ~ladVi~~N~~iis~kG   50 (261)
T COG4465          34 TLADVIECNAFIISRKG   50 (261)
T ss_pred             HHHHHHHCCEEEEECCC
T ss_conf             99877603259992797


No 285
>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=24.39  E-value=50  Score=13.74  Aligned_cols=20  Identities=25%  Similarity=0.275  Sum_probs=13.4

Q ss_pred             HHHHHHHCCCHHHHHHHHHH
Q ss_conf             99998828997899999999
Q gi|254780282|r   21 THAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        21 s~AA~~L~itq~avS~~i~~   40 (299)
                      +.=|++||.+.+-||++++-
T Consensus         7 ~~IAk~LGks~s~VS~hlaL   26 (93)
T pfam08535         7 AEIAKKLGKSKSFVSQHLAL   26 (93)
T ss_pred             HHHHHHHCCCHHHHHHHHHH
T ss_conf             99999978898899999998


No 286
>PRK01066 porphobilinogen deaminase; Provisional
Probab=24.30  E-value=30  Score=15.02  Aligned_cols=54  Identities=20%  Similarity=0.186  Sum_probs=31.5

Q ss_pred             CCCCCCCCCCCCCCCCCCC-HHHHHHHHHHCCCCCCC----CCCCC-------------------CCCCCCCCCCCCC
Q ss_conf             2223332111000000000-13566754200012222----22222-------------------2222222222234
Q gi|254780282|r   92 SGKLRIATTIDLGQNLLQG-NLKEFLLLYPDIQIQLI----LDNKD-------------------IDISMDYADCAIR  145 (299)
Q Consensus        92 ~g~i~I~~~~~~~~~~l~~-~l~~f~~~~P~i~i~i~----~~~~~-------------------~~l~~~~~Di~i~  145 (299)
                      +..|+||.=.|-.+.+-.. +...+.+.||++++++.    .+|..                   ..|..|++|+++-
T Consensus        18 kk~IrIGTR~S~LAl~Qa~~V~~~L~~~~p~~~~ei~~i~T~GD~~~~~~L~~iggkG~Ftkele~aLl~g~iDiAVH   95 (234)
T PRK01066         18 KRPLRIASRKSPLAKAQVHECLRLLRSFFPKLWFQISTTTTQGDLDQKTPLHLVENTGFFTDDVDFLVLSGKCDLAIH   95 (234)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCHHHCCCCCEEHHHHHHHHHCCCCCEEEE
T ss_conf             884699958879999999999999997689973999999633731457768774897454899999997698778987


No 287
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=23.90  E-value=51  Score=13.69  Aligned_cols=34  Identities=15%  Similarity=0.241  Sum_probs=22.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCE
Q ss_conf             689999882899789999999999995882179769946
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGL   57 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~   57 (299)
                      +++.+|+.+|||..+    |+--|++++.. ..|+.+|.
T Consensus         2 tI~eva~~~Gv~~~t----LRyyEk~~~l~-~~R~~~G~   35 (67)
T cd04764           2 TIKEVSEIIGVKPHT----LRYYEKEFNLY-IPRTENGR   35 (67)
T ss_pred             CHHHHHHHHCCCHHH----HHHHHHCCCCC-CCCCCCCC
T ss_conf             789999998868789----99998737999-99699989


No 288
>PRK13507 formate--tetrahydrofolate ligase; Provisional
Probab=23.69  E-value=51  Score=13.66  Aligned_cols=63  Identities=22%  Similarity=0.211  Sum_probs=39.9

Q ss_pred             CCCC---HHHHHHHHHHHH-HCCHHHHHHHHCCCHHHHH------------HHHHHHHHHHCCEEEEECCCCEEEEECCC
Q ss_conf             9888---899999999998-2768999988289978999------------99999999958821797699468500134
Q gi|254780282|r    1 MSFD---WDKLRVFYVVAR-SGSFTHAAEQLHLSQSSIS------------RQISGLETEVGIKLFYRHARGLTLTEQGS   64 (299)
Q Consensus         1 m~md---~~~L~~f~~v~~-~gs~s~AA~~L~itq~avS------------~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~   64 (299)
                      |+|+   +.+++.-.+.-. ...++.-|++|++++..+.            .-++++++.=.-+|+.=+  ++.|||+|+
T Consensus         1 ~~~~~~~~sDieIaq~a~~~l~pI~~iA~~lgl~~~~le~YG~~kAKi~~~~~~~~~~~~~~gklILVT--aitPTP~GE   78 (587)
T PRK13507          1 MALDPVLMKDWEIAEEAEKFMKSPKQLAEELGLTKEEIIPYGRYIAKVDFAKILSRLKDRPDGKYIDVT--AITPTPLGE   78 (587)
T ss_pred             CCCCCCCCCHHHHHHHCHHCCCCHHHHHHHCCCCHHHHHHCCCCCEEECHHHHHHHHCCCCCCEEEEEE--ECCCCCCCC
T ss_conf             997843347999998543137899999988398979976247754660588988874048996399998--468888889


Q ss_pred             C
Q ss_conf             3
Q gi|254780282|r   65 K   65 (299)
Q Consensus        65 ~   65 (299)
                      =
T Consensus        79 G   79 (587)
T PRK13507         79 G   79 (587)
T ss_pred             C
T ss_conf             8


No 289
>PRK03537 hypothetical protein; Provisional
Probab=23.40  E-value=52  Score=13.63  Aligned_cols=53  Identities=9%  Similarity=0.130  Sum_probs=29.8

Q ss_pred             CCEEEEEHHHHC-C-CCC--EEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             842331177760-1-998--4661776667660089993487788889999999999998
Q gi|254780282|r  239 SGIALLPDYIVK-D-NPN--LVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFLKA  294 (299)
Q Consensus       239 ~Gia~lp~~~~~-~-~~~--lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~~~  294 (299)
                      .|++...+.... . ..+  .+.+ |+.......|.+...++.  ++.+++|++||++..
T Consensus       116 a~ivY~TdA~~a~~~~~~l~~v~i-P~~~~~~~~Y~iav~~~a--~~~A~~f~~flls~~  172 (188)
T PRK03537        116 IFIGYCTSAALALKEVPDLQIVDL-PEPLAVGANYGLAVLKDA--SEAARPLAEFILSPK  172 (188)
T ss_pred             EEEEEECCHHHHHHCCCCCEEEEC-CCCCCCCCCEEEEECCCC--CHHHHHHHHHHCCHH
T ss_conf             799985147878515898549958-800066632357873688--099999999973999


No 290
>pfam08280 HTH_Mga M protein trans-acting positive regulator (MGA) HTH domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions.
Probab=23.35  E-value=52  Score=13.62  Aligned_cols=52  Identities=21%  Similarity=0.243  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCC
Q ss_conf             89999999999827--68999988289978999999999999588217976994
Q gi|254780282|r    5 WDKLRVFYVVARSG--SFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARG   56 (299)
Q Consensus         5 ~~~L~~f~~v~~~g--s~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~   56 (299)
                      +++++....+.+.+  ++...|+.||.|.-++-.-|.+|-+.|+..++.-..++
T Consensus         5 ~rk~~Ll~lL~~~~~~~l~el~~~l~ls~~tl~~~i~~L~~~f~~~l~i~~~k~   58 (59)
T pfam08280         5 KRKLKLLELLTENKSITLDELAKQLGLSELTLKSYIHELNELFPDELSIVIKKG   58 (59)
T ss_pred             HHHHHHHHHHHCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEEEEECC
T ss_conf             899999999980883649999988099799999999999987376469984058


No 291
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=23.34  E-value=52  Score=13.62  Aligned_cols=22  Identities=18%  Similarity=-0.037  Sum_probs=18.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHC
Q ss_conf             8778888999999999999850
Q gi|254780282|r  275 EALKNTGKLKAFRNFIFLKARD  296 (299)
Q Consensus       275 ~~~~~~~~~~~f~d~l~~~~r~  296 (299)
                      +++..++.-+.++|-+..|+..
T Consensus       142 ~GR~iT~~G~~~LD~iA~qI~~  163 (169)
T PTZ00095        142 SGRRLTRKGCNFANAFARQVTI  163 (169)
T ss_pred             CCCEECHHHHHHHHHHHHHHHH
T ss_conf             9888787478999999999998


No 292
>PRK13982 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional
Probab=23.12  E-value=4.2  Score=19.94  Aligned_cols=30  Identities=0%  Similarity=-0.003  Sum_probs=14.5

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             233321110000000001356675420001
Q gi|254780282|r   94 KLRIATTIDLGQNLLQGNLKEFLLLYPDIQ  123 (299)
Q Consensus        94 ~i~I~~~~~~~~~~l~~~l~~f~~~~P~i~  123 (299)
                      +|-+|++-+++.+--+.+++.+++.--+|+
T Consensus        73 kIlLgVtGsIAAYKa~~LvR~L~k~Ga~V~  102 (476)
T PRK13982         73 RITLIIGGGIAAYKALDLIRRLKERGAEVR  102 (476)
T ss_pred             EEEEEECCHHHHHHHHHHHHHHHHCCCEEE
T ss_conf             799996748999999999999997899899


No 293
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=23.12  E-value=52  Score=13.59  Aligned_cols=18  Identities=11%  Similarity=0.174  Sum_probs=9.7

Q ss_pred             CCCCCCCHHH-HHHHHHHH
Q ss_conf             4877888899-99999999
Q gi|254780282|r  274 PEALKNTGKL-KAFRNFIF  291 (299)
Q Consensus       274 ~~~~~~~~~~-~~f~d~l~  291 (299)
                      +++...+-.+ ..|+|++-
T Consensus       378 p~G~l~~n~I~~~l~d~~~  396 (399)
T PRK07379        378 PEGFLFSNTVLASLFEALE  396 (399)
T ss_pred             CCCEEEHHHHHHHHHHHHH
T ss_conf             7835429899999999875


No 294
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=23.11  E-value=53  Score=13.59  Aligned_cols=22  Identities=9%  Similarity=-0.049  Sum_probs=11.1

Q ss_pred             CCCCCCCCCCCCCCCHHHHHCC
Q ss_conf             4332222222222101221001
Q gi|254780282|r   64 SKLHRVTSEVYHKLETTQIELQ   85 (299)
Q Consensus        64 ~~l~~~a~~~l~~~~~~~~~~~   85 (299)
                      ..|+.+|..++..-+.++.-++
T Consensus        13 ~~L~r~A~~~v~d~~~AEDvvQ   34 (191)
T PRK12520         13 PYLLRFARLQLRDEAWAEDAVS   34 (191)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999999499999999999


No 295
>pfam12492 DUF3705 Protein of unknown function (DUF3705). This domain family is found in bacteria, and is approximately 30 amino acids in length.
Probab=22.92  E-value=40  Score=14.31  Aligned_cols=16  Identities=25%  Similarity=0.420  Sum_probs=12.3

Q ss_pred             EEEECCCCEEEEECCC
Q ss_conf             1797699468500134
Q gi|254780282|r   49 LFYRHARGLTLTEQGS   64 (299)
Q Consensus        49 Lf~R~~~~~~lT~~G~   64 (299)
                      -|.|.++++.||+.++
T Consensus         2 fF~r~gd~f~Pt~~A~   17 (31)
T pfam12492         2 FFVRDGDGFVPTRFAR   17 (31)
T ss_pred             CEEECCCCCCCCEECC
T ss_conf             1685388623243021


No 296
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein; InterPro: IPR014337   Members of this entry are the extracellular solute-binding proteins of ABC transporters and they closely resemble amino acid transporters. The member from Sinorhizobium meliloti (Rhizobium meliloti) is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes..
Probab=22.71  E-value=53  Score=13.55  Aligned_cols=151  Identities=14%  Similarity=0.069  Sum_probs=82.0

Q ss_pred             CCCCCCCCCCCCCCC----------CCCCCCHHHHHHHHH--HCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             222223332111000----------000000135667542--000122222-2222222222222223456543211112
Q gi|254780282|r   90 KPSGKLRIATTIDLG----------QNLLQGNLKEFLLLY--PDIQIQLIL-DNKDIDISMDYADCAIRLRKPIQSSSLI  156 (299)
Q Consensus        90 ~~~g~i~I~~~~~~~----------~~~l~~~l~~f~~~~--P~i~i~i~~-~~~~~~l~~~~~Di~i~~~~~~~~~~l~  156 (299)
                      +.+|-+|||...-.-          .-.-|++=..+.++-  -+|.-.++. +...--|..|+.|. |..+.-+.+.++.
T Consensus        31 KeQG~~Ria~ANE~Pf~y~g~DGkv~G~~PdvA~aifK~lGi~dVn~~~te~G~lIPGL~AgRfDa-iaAg~~i~PeRCk  109 (285)
T TIGR02995        31 KEQGFVRIAIANEVPFAYVGADGKVAGAAPDVARAIFKRLGIKDVNASVTEYGALIPGLKAGRFDA-IAAGLFIKPERCK  109 (285)
T ss_pred             HCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCHHHH-HHHCCCCCHHHHH
T ss_conf             235304774006786400268853136855789999985481100000356403145410102568-8611578856664


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHH
Q ss_conf             234555433211234432111222---22211000112356643321100023566520223432121145324200135
Q gi|254780282|r  157 QRKLVTIHMHAYAAPHYLKNCREP---LSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQ  233 (299)
Q Consensus       157 ~~~l~~~~~~~v~~~~~~~~~~~~---~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~  233 (299)
                      . -+|++|.... +...+...|.|   .+.+|+++-|=+...-.  .....    ..+.+..|++...++.+.+....+.
T Consensus       110 q-Vaft~P~~~~-~eallvkKGNPk~L~sY~DiAknP~~K~a~~--~G~~e----~~~ar~~GVk~eqi~~vPd~~~~l~  181 (285)
T TIGR02995       110 Q-VAFTEPILSL-AEALLVKKGNPKELKSYKDIAKNPEVKVAVV--AGAVE----VKYAREAGVKEEQIVVVPDTASALK  181 (285)
T ss_pred             H-HHHCCCCCCC-CCCCCCCCCCCCCCCCCCCHHCCCCCEEEEC--CCCHH----HHHHHHCCCCCCEEEEECCCHHHHH
T ss_conf             6-4406886447-5521125878888775202006823127612--47237----8999865898660788248716788


Q ss_pred             HHHHHCC-EEEEEHHHH
Q ss_conf             6787384-233117776
Q gi|254780282|r  234 YCVLGSG-IALLPDYIV  249 (299)
Q Consensus       234 ~v~~g~G-ia~lp~~~~  249 (299)
                      +|++|-. +...|...+
T Consensus       182 ~vq~~RaDay~~t~Lt~  198 (285)
T TIGR02995       182 AVQDKRADAYAATELTV  198 (285)
T ss_pred             HHHHHCCCEECCCCCCH
T ss_conf             87740342200332347


No 297
>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=22.59  E-value=54  Score=13.53  Aligned_cols=28  Identities=14%  Similarity=0.351  Sum_probs=21.5

Q ss_pred             HHHH-HCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998-276899998828997899999999
Q gi|254780282|r   13 VVAR-SGSFTHAAEQLHLSQSSISRQISG   40 (299)
Q Consensus        13 ~v~~-~gs~s~AA~~L~itq~avS~~i~~   40 (299)
                      -+.+ .-.+..||+..|||-|+|.+-+..
T Consensus        14 YIi~~~aTVR~tAk~FGvSKSTVHkDvTe   42 (82)
T pfam12116        14 YIIENKATVRQAAKVFGVSKSTVHKDVTE   42 (82)
T ss_pred             HHHHCCHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99962628999999969609889887999


No 298
>pfam00292 PAX 'Paired box' domain.
Probab=22.29  E-value=55  Score=13.50  Aligned_cols=32  Identities=22%  Similarity=0.318  Sum_probs=19.7

Q ss_pred             HHHHHHHCC-HHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             999998276-89999882899789999999999
Q gi|254780282|r   11 FYVVARSGS-FTHAAEQLHLSQSSISRQISGLE   42 (299)
Q Consensus        11 f~~v~~~gs-~s~AA~~L~itq~avS~~i~~LE   42 (299)
                      .+.+|..|. -..=++.|.||+..|||-+.+..
T Consensus        26 IVeLa~~G~RpCdISR~L~VShGCVSKIL~Ry~   58 (125)
T pfam00292        26 IVELAHSGVRPCDISRQLRVSHGCVSKILGRYQ   58 (125)
T ss_pred             HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             999998499788887762676216899999887


No 299
>PRK08413 consensus
Probab=21.94  E-value=45  Score=13.99  Aligned_cols=22  Identities=18%  Similarity=0.104  Sum_probs=8.6

Q ss_pred             EEECCCCEEEEECCCCCCCCCC
Q ss_conf             7976994685001343322222
Q gi|254780282|r   50 FYRHARGLTLTEQGSKLHRVTS   71 (299)
Q Consensus        50 f~R~~~~~~lT~~G~~l~~~a~   71 (299)
                      +.+.++.+.||+.|..+.+...
T Consensus       487 v~~~~k~l~pT~~G~~v~~~L~  508 (733)
T PRK08413        487 VKIEKKQIIPTESAFKVIEVLE  508 (733)
T ss_pred             EEECCCEEEECHHHHHHHHHHH
T ss_conf             9941977877469999999998


No 300
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=21.59  E-value=56  Score=13.41  Aligned_cols=178  Identities=15%  Similarity=0.133  Sum_probs=83.9

Q ss_pred             CCCCCCCCCCCCC-----------CCCCHHHHHHHHHHCCCCCCCC-CCC---CCCCCCCCCCCCCCCC-CCCC-CCCCC
Q ss_conf             2333211100000-----------0000135667542000122222-222---2222222222223456-5432-11112
Q gi|254780282|r   94 KLRIATTIDLGQN-----------LLQGNLKEFLLLYPDIQIQLIL-DNK---DIDISMDYADCAIRLR-KPIQ-SSSLI  156 (299)
Q Consensus        94 ~i~I~~~~~~~~~-----------~l~~~l~~f~~~~P~i~i~i~~-~~~---~~~l~~~~~Di~i~~~-~~~~-~~~l~  156 (299)
                      .|++++.+.+++.           +..+.|..+.. .-+++|+... ++.   ...+..|++|+.-... .+.. ..-..
T Consensus       303 ~irv~~~~~~aP~sf~D~~G~~~Gi~aD~L~lIs~-rtGL~Fe~v~~~~~~~~~~~l~~g~~D~l~~~~~s~~r~~~l~f  381 (1197)
T PRK09959        303 DLKVLENPYSPPYSMTDENGSVRGVMGDILNIITL-QTGLNFSPITVSHNIHAGTQLNPGGWDILPGAIYSEDRENNVLF  381 (1197)
T ss_pred             CEEEEECCCCCCEEEECCCCCCCCCHHHHHHHHHH-HHCCEEEEEECCCHHHHHHHHHCCCCHHCCCCCCCCCCCCCCEE
T ss_conf             75997179989945788899764327999999999-87966899836987999999876981220323578544346554


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCHHHHHHH
Q ss_conf             23455543321123443211122222211000112356643321100023566520223432121145324200135678
Q gi|254780282|r  157 QRKLVTIHMHAYAAPHYLKNCREPLSIQELDKHNLITFGDLIPKCMEDFNWLATVDRPIGEPRISCLQVNSYLSIMQYCV  236 (299)
Q Consensus       157 ~~~l~~~~~~~v~~~~~~~~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~  236 (299)
                      .+++...++++|..++..       ....+..-.-|..    +.......++..     ..|......+++....+++|.
T Consensus       382 T~py~~~p~ViV~r~~~~-------~~~~l~~gkrvai----~~~~~~~~~l~~-----~yP~i~~v~v~s~~~al~~v~  445 (1197)
T PRK09959        382 AEAFITTPYVFVMQKAPD-------SEQTLKKGMKVAI----PYYYELHSQLKE-----MYPEVEWIKVDNASAAFHKVK  445 (1197)
T ss_pred             CCCCCCCCEEEEEECCCC-------CCCCHHCCCEEEE----CCCCCHHHHHHH-----HCCCCEEEEECCHHHHHHHHH
T ss_conf             132356875999963786-------3011421988999----178506899998-----689834998099999999997


Q ss_pred             HHCCEEEEE-----HHHHCC--CCCEEEECCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             738423311-----777601--99846617766676600899934877888899999999999
Q gi|254780282|r  237 LGSGIALLP-----DYIVKD--NPNLVRIMEDVITPSFTVYFCYPEALKNTGKLKAFRNFIFL  292 (299)
Q Consensus       237 ~g~Gia~lp-----~~~~~~--~~~lv~i~~~~~~~~~~~~lv~~~~~~~~~~~~~f~d~l~~  292 (299)
                      .|..=+.+-     .+++++  .++++.+.... .++..+.+..++   ..|..+..+|=.+.
T Consensus       446 ~G~aDa~v~~l~~a~y~i~~~~~~~L~~~~~~~-~~~~~lafaV~~---d~peL~sILnKaL~  504 (1197)
T PRK09959        446 EGELDALVATQLNSRYMIDHYYPNELYHFLIPG-VPNASLSFAFPR---GEPELKDIINKALN  504 (1197)
T ss_pred             CCCCCEEEEHHHHHHHHHHHHCCCCCEEEECCC-CCCCCEEEEECC---CCHHHHHHHHHHHH
T ss_conf             788766742447789999874566504874158-776326999879---98899999999998


No 301
>COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]
Probab=21.54  E-value=57  Score=13.41  Aligned_cols=29  Identities=34%  Similarity=0.437  Sum_probs=26.0

Q ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             82768999988289978999999999999
Q gi|254780282|r   16 RSGSFTHAAEQLHLSQSSISRQISGLETE   44 (299)
Q Consensus        16 ~~gs~s~AA~~L~itq~avS~~i~~LE~~   44 (299)
                      +.-|...-|+.+++|.++|++..++||.+
T Consensus        27 rLPs~R~la~~l~vs~~Tv~~ay~~L~~~   55 (459)
T COG1167          27 RLPSIRQLAQDLGVSRSTVSRAYEELEAR   55 (459)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             18766999999487488999999999976


No 302
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=21.44  E-value=37  Score=14.45  Aligned_cols=49  Identities=20%  Similarity=0.116  Sum_probs=19.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHH----HCCEEEEECCCCEEEEECCCCCC
Q ss_conf             68999988289978999999999999----58821797699468500134332
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETE----VGIKLFYRHARGLTLTEQGSKLH   67 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~----lg~~Lf~R~~~~~~lT~~G~~l~   67 (299)
                      |+|.-|+-=-+.-|+.=.-=++||++    +-.+..++.+.-++||+.|+.++
T Consensus        62 sISdiAkfGVMHVSTaFNFSKkLEeRG~L~fsKk~~DKRNTYi~LT~~G~e~~  114 (190)
T PRK13777         62 SISEIAKFGVMHVSTAFNFSKKLEERGYLVFSKKEDDKRNTYIELTDKGEELL  114 (190)
T ss_pred             CHHHHHHHCCEEEEEHHHHHHHHHHCCCEECCCCCCCCCCCEEEECCCHHHHH
T ss_conf             39999870724630032055777755345334002465553588650168999


No 303
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=21.10  E-value=58  Score=13.35  Aligned_cols=40  Identities=18%  Similarity=0.141  Sum_probs=24.9

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEE
Q ss_conf             99998828997899999999999958821797699468500
Q gi|254780282|r   21 THAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTE   61 (299)
Q Consensus        21 s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~   61 (299)
                      ..|+.++++|..-+-...++|=+ =|.-=.-|+-...-+.+
T Consensus        20 ~~as~~~g~sa~~tl~iaQ~LYe-~g~ITYpRTds~~l~~~   59 (259)
T smart00437       20 QEASRKLGFSAKKTMQIAQKLYE-KGLITYPRTDSTRLSEE   59 (259)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHH-CCCEEECCCCCCCCCHH
T ss_conf             99998669999999999999986-78553347687463999


No 304
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=20.91  E-value=50  Score=13.71  Aligned_cols=18  Identities=11%  Similarity=0.060  Sum_probs=11.5

Q ss_pred             CCCCHHHHHHHHHHHHHH
Q ss_conf             788889999999999998
Q gi|254780282|r  277 LKNTGKLKAFRNFIFLKA  294 (299)
Q Consensus       277 ~~~~~~~~~f~d~l~~~~  294 (299)
                      -..++.-+.|.|.+..+.
T Consensus       362 l~lT~~G~~l~d~v~~eL  379 (381)
T PRK09057        362 LRATPAGRLVLDAVVADL  379 (381)
T ss_pred             EEECHHHHHHHHHHHHHH
T ss_conf             999978879999999997


No 305
>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=20.72  E-value=59  Score=13.31  Aligned_cols=30  Identities=27%  Similarity=0.392  Sum_probs=18.0

Q ss_pred             HHHHHCCHHHH--HHHHCCCHHHHHHHHHHHH
Q ss_conf             99982768999--9882899789999999999
Q gi|254780282|r   13 VVARSGSFTHA--AEQLHLSQSSISRQISGLE   42 (299)
Q Consensus        13 ~v~~~gs~s~A--A~~L~itq~avS~~i~~LE   42 (299)
                      +-..+..||+|  |+.=+++-|||||-+|.|-
T Consensus        19 A~~~~~~ySAA~lA~~tgL~~pTvsK~Lk~L~   50 (130)
T TIGR02944        19 AQADEQTYSAAELAEQTGLEAPTVSKILKALS   50 (130)
T ss_pred             HCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf             52899700688878645988604789988764


No 306
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=20.60  E-value=59  Score=13.29  Aligned_cols=34  Identities=18%  Similarity=0.148  Sum_probs=19.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCEE-EEECCCCE
Q ss_conf             6899998828997899999999999958821-79769946
Q gi|254780282|r   19 SFTHAAEQLHLSQSSISRQISGLETEVGIKL-FYRHARGL   57 (299)
Q Consensus        19 s~s~AA~~L~itq~avS~~i~~LE~~lg~~L-f~R~~~~~   57 (299)
                      |++.+|+.++||++++    +--|++ |.-- -.|+.+|.
T Consensus         2 tI~e~a~~~gvs~~tl----R~ye~~-Gll~p~~r~~~g~   36 (70)
T smart00422        2 TIGEVAKLAGVSVRTL----RYYERI-GLLPPPIRTEGGY   36 (70)
T ss_pred             CHHHHHHHHCCCHHHH----HHHHHC-CCCCCCCCCCCCC
T ss_conf             7889999989699999----999985-8989984489997


No 307
>PRK10803 hypothetical protein; Provisional
Probab=20.16  E-value=61  Score=13.24  Aligned_cols=73  Identities=12%  Similarity=0.114  Sum_probs=44.3

Q ss_pred             CCCCHHHHHH----HHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCCCCCCCCCC
Q ss_conf             9888899999----999998276899998828997899999999999958821797699468500134332222222222
Q gi|254780282|r    1 MSFDWDKLRV----FYVVARSGSFTHAAEQLHLSQSSISRQISGLETEVGIKLFYRHARGLTLTEQGSKLHRVTSEVYHK   76 (299)
Q Consensus         1 m~md~~~L~~----f~~v~~~gs~s~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~a~~~l~~   76 (299)
                      ||-|++++-.    |+.++--.--.+.|=.-++...++..+|.+||..+...       +-.           ..++-.+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~a~a~apv~~~~~gs~e~Rl~~LEr~~~~~-------~~~-----------~~qlq~Q   62 (262)
T PRK10803          1 MSSNFRHHLLSLSLLVGIAAPWAAFAQAPISSVGSGSVEDRVTQLERISNAH-------SQL-----------LTQLQQQ   62 (262)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCHHHHHHHHHHHHHHH-------HHH-----------HHHHHHH
T ss_conf             9741999999999999986078770344376603786999999999999974-------279-----------9999999


Q ss_pred             CCHHHHHCCCCCCCC
Q ss_conf             101221001223222
Q gi|254780282|r   77 LETTQIELQESSVKP   91 (299)
Q Consensus        77 ~~~~~~~~~~~~~~~   91 (299)
                      ++++..+++.+++..
T Consensus        63 l~~LQ~EV~~LRGqi   77 (262)
T PRK10803         63 LSDNQSDIDSLRGQI   77 (262)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999999998799


Done!