Query         gi|254780305|ref|YP_003064718.1| hypothetical protein CLIBASIA_00950 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 95
No_of_seqs    103 out of 449
Neff          5.6 
Searched_HMMs 39220
Date          Sun May 29 15:27:39 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780305.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10736 hypothetical protein;  99.3 3.2E-12 8.3E-17   86.2   6.2   55   36-90    300-356 (364)
  2 COG0758 Smf Predicted Rossmann  98.9 1.5E-09 3.7E-14   71.9   5.0   52   36-87    298-349 (350)
  3 COG1414 IclR Transcriptional r  97.1 0.00063 1.6E-08   41.5   4.3   54   37-90      7-63  (246)
  4 smart00346 HTH_ICLR helix_turn  97.1 0.00094 2.4E-08   40.5   4.7   52   38-89      9-63  (91)
  5 PRK11569 transcriptional repre  96.9   0.004   1E-07   37.1   6.6   57   33-89     26-86  (274)
  6 PRK09834 DNA-binding transcrip  96.5  0.0041   1E-07   37.1   4.4   55   35-89     11-69  (264)
  7 smart00420 HTH_DEOR helix_turn  96.4  0.0027 6.8E-08   38.1   3.0   51   36-86      2-53  (53)
  8 PRK10163 DNA-binding transcrip  96.2   0.013 3.2E-07   34.5   5.6   56   33-88     23-82  (271)
  9 cd00090 HTH_ARSR Arsenical Res  96.1  0.0099 2.5E-07   35.0   4.7   57   33-89      6-65  (78)
 10 pfam09339 HTH_IclR IclR helix-  96.1  0.0096 2.5E-07   35.1   4.5   44   38-81      7-52  (52)
 11 pfam08220 HTH_DeoR DeoR-like h  96.0  0.0063 1.6E-07   36.1   3.1   53   36-88      2-55  (57)
 12 pfam01978 TrmB Sugar-specific   95.9   0.017 4.5E-07   33.7   5.2   55   32-86      6-61  (68)
 13 PRK09802 DNA-binding transcrip  95.9   0.016   4E-07   33.9   4.9   54   36-89     19-73  (269)
 14 PRK10434 srlR DNA-bindng trans  95.9  0.0085 2.2E-07   35.4   3.3   53   36-88      7-60  (256)
 15 PRK10906 DNA-binding transcrip  95.8   0.011 2.7E-07   34.9   3.5   51   36-86      7-58  (252)
 16 PRK13509 transcriptional repre  95.7   0.012 3.1E-07   34.6   3.7   57   36-92      7-64  (251)
 17 pfam01726 LexA_DNA_bind LexA D  95.7   0.027 6.9E-07   32.7   5.4   53   31-83      3-62  (65)
 18 pfam01022 HTH_5 Bacterial regu  95.7   0.021 5.3E-07   33.3   4.8   46   33-78      1-46  (47)
 19 COG1349 GlpR Transcriptional r  95.6   0.012   3E-07   34.6   3.1   56   36-91      7-63  (253)
 20 COG4742 Predicted transcriptio  95.4   0.029 7.3E-07   32.5   4.7   56   33-89     12-67  (260)
 21 PRK10411 DNA-binding transcrip  95.3   0.014 3.6E-07   34.2   2.9   53   36-88      6-59  (240)
 22 COG4190 Predicted transcriptio  95.3   0.025 6.3E-07   32.9   4.0   54   32-85     62-116 (144)
 23 PRK11512 DNA-binding transcrip  94.6   0.051 1.3E-06   31.2   4.0   59   24-82     30-89  (144)
 24 pfam01047 MarR MarR family. Th  94.1   0.078   2E-06   30.2   4.1   50   33-82      2-52  (59)
 25 smart00418 HTH_ARSR helix_turn  94.0   0.054 1.4E-06   31.0   3.3   48   38-85      1-48  (66)
 26 TIGR01884 cas_HTH CRISPR locus  94.0    0.12 3.2E-06   29.1   5.0   58   25-82    160-219 (231)
 27 pfam08784 RPA_C Replication pr  93.9    0.28 7.1E-06   27.2   6.7   47   31-77     44-96  (103)
 28 COG2345 Predicted transcriptio  93.8    0.11 2.9E-06   29.3   4.6   47   34-80     11-58  (218)
 29 COG3355 Predicted transcriptio  93.8     0.1 2.6E-06   29.5   4.3   53   35-87     29-87  (126)
 30 COG1510 Predicted transcriptio  93.3    0.12   3E-06   29.2   3.9   44   37-80     29-74  (177)
 31 smart00550 Zalpha Z-DNA-bindin  93.2    0.18 4.7E-06   28.2   4.8   52   32-83      4-58  (68)
 32 PRK12423 LexA repressor; Provi  92.9    0.43 1.1E-05   26.2   6.3   59   31-89      3-68  (202)
 33 COG4189 Predicted transcriptio  92.8    0.14 3.7E-06   28.7   3.8   48   33-80     22-70  (308)
 34 smart00347 HTH_MARR helix_turn  92.5    0.19 4.8E-06   28.1   4.1   55   28-82      4-59  (101)
 35 pfam08279 HTH_11 HTH domain. T  92.3    0.27 6.9E-06   27.3   4.6   46   37-82      3-51  (55)
 36 COG1378 Predicted transcriptio  92.2     0.2   5E-06   28.0   3.9   51   33-83     15-66  (247)
 37 PRK00215 LexA repressor; Valid  92.2    0.34 8.7E-06   26.7   5.0   55   33-87      3-64  (204)
 38 COG2512 Predicted membrane-ass  92.2    0.21 5.3E-06   27.9   3.9   58   27-84    188-247 (258)
 39 PRK04172 pheS phenylalanyl-tRN  92.1    0.29 7.4E-06   27.1   4.6   48   32-79      4-52  (501)
 40 PRK03573 transcriptional regul  92.0    0.16 4.2E-06   28.4   3.3   60   24-83     21-82  (144)
 41 PRK10141 DNA-binding transcrip  91.6    0.57 1.5E-05   25.5   5.6   61   32-92     12-76  (106)
 42 TIGR02431 pcaR_pcaU beta-ketoa  90.6    0.51 1.3E-05   25.8   4.6   50   38-88     13-64  (252)
 43 PRK03902 manganese transport t  90.3    0.59 1.5E-05   25.5   4.7   53   37-89     11-64  (142)
 44 COG1777 Predicted transcriptio  90.3    0.71 1.8E-05   25.0   5.1   47   33-79     14-60  (217)
 45 COG5340 Predicted transcriptio  89.8    0.82 2.1E-05   24.7   5.1   55   34-88     17-71  (269)
 46 smart00344 HTH_ASNC helix_turn  89.6    0.68 1.7E-05   25.1   4.6   46   34-79      3-49  (108)
 47 TIGR02337 HpaR homoprotocatech  89.4    0.29 7.4E-06   27.1   2.6   50   32-81     25-76  (130)
 48 pfam01638 HxlR HxlR-like helix  88.5     0.6 1.5E-05   25.4   3.7   44   37-80      8-52  (90)
 49 COG1733 Predicted transcriptio  87.4    0.63 1.6E-05   25.3   3.2   47   37-83     26-73  (120)
 50 PRK11179 DNA-binding transcrip  87.4     1.1 2.8E-05   24.0   4.5   48   32-79      7-55  (153)
 51 COG1846 MarR Transcriptional r  87.3    0.87 2.2E-05   24.5   3.9   52   32-83     20-72  (126)
 52 PRK11639 zinc uptake transcrip  87.2     2.4 6.1E-05   22.2   6.2   57   32-88     24-88  (169)
 53 COG1522 Lrp Transcriptional re  87.1     1.2 3.1E-05   23.8   4.5   50   31-80      5-55  (154)
 54 PRK11050 manganese transport r  86.7    0.87 2.2E-05   24.5   3.6   53   37-89     43-96  (155)
 55 COG3888 Predicted transcriptio  86.6    0.87 2.2E-05   24.5   3.6   56   38-93     11-70  (321)
 56 PRK09954 hypothetical protein;  86.6     2.3 5.9E-05   22.2   5.7   52   34-88      3-55  (362)
 57 COG1959 Predicted transcriptio  86.4    0.98 2.5E-05   24.2   3.7   43   47-89     25-69  (150)
 58 pfam09012 FeoC FeoC like trans  86.3    0.94 2.4E-05   24.3   3.6   46   38-83      4-50  (68)
 59 pfam02082 Rrf2 Transcriptional  86.1    0.94 2.4E-05   24.3   3.5   53   38-90     11-69  (82)
 60 PTZ00326 phenylalanyl-tRNA syn  86.0     1.6   4E-05   23.1   4.6   47   33-79      5-52  (505)
 61 cd07153 Fur_like Ferric uptake  85.4     1.2 3.1E-05   23.8   3.8   55   35-89      2-67  (116)
 62 cd07377 WHTH_GntR Winged helix  85.3     1.1 2.7E-05   24.1   3.5   42   46-87     23-65  (66)
 63 PRK11169 leucine-responsive tr  85.1     1.4 3.7E-05   23.3   4.1   49   31-79     11-60  (164)
 64 PRK09462 fur ferric uptake reg  85.0     2.6 6.7E-05   21.9   5.4   57   32-88     15-83  (148)
 65 COG1321 TroR Mn-dependent tran  84.9     1.7 4.5E-05   22.9   4.4   53   37-89     13-66  (154)
 66 pfam04157 EAP30 EAP30/Vps36 fa  84.7     1.7 4.4E-05   22.9   4.4   48   32-79    170-218 (219)
 67 smart00529 HTH_DTXR Helix-turn  84.2    0.97 2.5E-05   24.3   2.9   40   50-89      2-41  (96)
 68 pfam05584 Sulfolobus_pRN Sulfo  84.0     2.8 7.3E-05   21.7   5.2   46   35-80      6-51  (72)
 69 cd00092 HTH_CRP helix_turn_hel  83.7     1.5 3.8E-05   23.2   3.7   43   45-87     23-65  (67)
 70 TIGR03338 phnR_burk phosphonat  83.3     2.6 6.5E-05   22.0   4.7   43   46-88     33-75  (212)
 71 PRK11534 DNA-binding transcrip  82.8       2   5E-05   22.6   4.0   44   46-89     29-72  (224)
 72 pfam01475 FUR Ferric uptake re  82.7     2.4   6E-05   22.2   4.4   53   32-84      6-67  (120)
 73 pfam04703 FaeA FaeA-like prote  82.1     1.9 4.7E-05   22.7   3.6   48   37-84      3-52  (61)
 74 pfam03444 DUF293 Domain of unk  81.6     4.3 0.00011   20.8   5.6   51   32-82      2-58  (79)
 75 TIGR00738 rrf2_super rrf2 fami  81.3     2.4   6E-05   22.2   3.9   46   44-89     21-69  (133)
 76 PRK10681 DNA-binding transcrip  81.2       1 2.6E-05   24.1   2.1   50   36-88      9-59  (252)
 77 smart00419 HTH_CRP helix_turn_  81.1     1.7 4.3E-05   23.0   3.1   41   46-87      7-47  (48)
 78 PRK10870 transcriptional repre  78.0     2.4 6.1E-05   22.2   3.1   61   24-84     45-108 (176)
 79 pfam00392 GntR Bacterial regul  77.9     1.8 4.7E-05   22.8   2.5   40   46-85     22-62  (64)
 80 PRK11414 putative DNA-binding   77.2     3.7 9.4E-05   21.1   3.9   44   46-89     33-76  (221)
 81 cd03448 HDE_HSD HDE_HSD  The R  76.2     3.9  0.0001   21.0   3.8   59   24-82      5-66  (122)
 82 PRK10857 DNA-binding transcrip  75.8     3.3 8.5E-05   21.4   3.3   46   45-90     23-70  (164)
 83 PRK11642 exoribonuclease R; Pr  75.6     3.1   8E-05   21.5   3.2   56   34-89     19-80  (813)
 84 PRK11014 transcriptional repre  75.0     3.2 8.2E-05   21.5   3.1   46   45-90     23-70  (141)
 85 pfam02295 z-alpha Adenosine de  74.7     4.8 0.00012   20.5   3.9   50   34-83      4-56  (66)
 86 PRK04214 rbn ribonuclease BN/u  74.5     6.3 0.00016   19.9   4.5   48   44-91    306-353 (411)
 87 COG1802 GntR Transcriptional r  74.4     4.1  0.0001   20.9   3.5   45   45-89     37-81  (230)
 88 smart00345 HTH_GNTR helix_turn  74.0     2.7 6.9E-05   21.9   2.5   40   46-85     18-58  (60)
 89 pfam12324 HTH_15 Helix-turn-he  73.7     7.6 0.00019   19.5   5.2   43   29-71     19-62  (77)
 90 PRK11832 putative DNA-binding   73.5       3 7.6E-05   21.6   2.6   45   48-93    161-205 (207)
 91 pfam05331 DUF742 Protein of un  72.5     2.7 6.8E-05   21.9   2.2   52   29-81     38-89  (114)
 92 PRK10225 DNA-binding transcrip  72.4     4.6 0.00012   20.6   3.4   46   43-88     27-74  (257)
 93 PRK10421 DNA-binding transcrip  71.7     6.6 0.00017   19.8   4.0   43   46-88     24-67  (253)
 94 COG1542 Uncharacterized conser  71.7     8.1 0.00021   19.3   4.5   63   27-89    418-484 (593)
 95 PRK11523 DNA-binding transcrip  71.3     4.8 0.00012   20.5   3.2   46   46-91     30-76  (258)
 96 pfam01325 Fe_dep_repress Iron   71.2     5.3 0.00014   20.3   3.5   45   37-81      9-54  (58)
 97 PRK11161 fumarate/nitrate redu  70.5     6.8 0.00017   19.7   3.9   41   47-88    184-224 (235)
 98 pfam10007 DUF2250 Uncharacteri  70.4     5.4 0.00014   20.3   3.3   55   32-86      6-61  (93)
 99 PRK03837 transcriptional regul  69.7     5.9 0.00015   20.0   3.4   45   43-87     32-78  (243)
100 TIGR03337 phnR transcriptional  68.6     4.9 0.00013   20.5   2.8   40   49-88     27-66  (231)
101 PRK09392 ftrB transcriptional   67.6      10 0.00026   18.7   4.3   42   46-89    172-213 (236)
102 COG0735 Fur Fe2+/Zn2+ uptake r  67.4     7.4 0.00019   19.5   3.6   51   32-82     19-76  (145)
103 pfam00325 Crp Bacterial regula  67.1     6.1 0.00016   20.0   3.1   31   47-77      2-32  (32)
104 PRK09863 putative frv operon r  67.0     9.5 0.00024   18.9   4.0   38   35-72      5-42  (585)
105 PRK13918 CRP/FNR family transc  66.7      10 0.00027   18.7   4.2   42   47-89    145-186 (201)
106 smart00531 TFIIE Transcription  66.4      10 0.00026   18.8   4.1   41   38-78      5-46  (147)
107 PRK09464 pdhR transcriptional   66.1       5 0.00013   20.4   2.4   52   37-88     21-75  (254)
108 pfam02002 TFIIE_alpha TFIIE al  66.0      11 0.00029   18.5   5.1   46   34-79     13-59  (105)
109 pfam05158 RNA_pol_Rpc34 RNA po  66.0     8.1 0.00021   19.3   3.5   70   24-93     73-151 (313)
110 PRK09391 fixK transcriptional   66.0     9.2 0.00023   19.0   3.8   43   46-88    172-214 (224)
111 PRK13919 putative RNA polymera  65.3      12  0.0003   18.4   4.6   40   30-69    135-174 (187)
112 TIGR02944 suf_reg_Xantho FeS a  65.2     5.2 0.00013   20.4   2.4   44   39-82     17-60  (130)
113 pfam03965 Pencillinase_R Penic  64.7      12 0.00031   18.4   5.0   54   34-87      3-61  (115)
114 PRK11753 cAMP-regulatory prote  64.2      10 0.00025   18.8   3.7   41   47-88    168-208 (211)
115 PRK09047 RNA polymerase factor  64.1      12 0.00031   18.3   4.3   39   32-70    107-145 (161)
116 PRK09526 lacI lac repressor; R  63.9     9.1 0.00023   19.0   3.5   25   44-68      2-26  (342)
117 PRK11920 rirA iron-responsive   63.2      10 0.00027   18.7   3.7   44   46-89     23-68  (153)
118 pfam04458 DUF505 Protein of un  63.0      13 0.00033   18.2   6.6   64   26-89    424-492 (591)
119 PRK12512 RNA polymerase sigma   62.4      13 0.00034   18.1   5.0   41   30-70    130-170 (184)
120 PRK11402 DNA-binding transcrip  61.8     6.9 0.00017   19.7   2.5   40   49-88     37-76  (243)
121 cd06171 Sigma70_r4 Sigma70, re  60.4      14 0.00037   17.9   4.5   40   31-70     10-49  (55)
122 PRK09990 DNA-binding transcrip  60.2      12 0.00031   18.4   3.5   42   46-87     29-71  (251)
123 pfam04545 Sigma70_r4 Sigma-70,  60.2      15 0.00037   17.9   5.0   39   31-69      4-42  (50)
124 pfam07638 Sigma70_ECF ECF sigm  59.9      15 0.00038   17.9   4.5   39   31-69    135-173 (185)
125 pfam01853 MOZ_SAS MOZ/SAS fami  59.9      13 0.00032   18.3   3.6   47   36-85    135-185 (189)
126 PRK09764 DNA-binding transcrip  59.8     7.7  0.0002   19.4   2.5   40   49-88     31-70  (239)
127 COG1725 Predicted transcriptio  59.4      12 0.00031   18.3   3.4   42   47-88     35-76  (125)
128 pfam08281 Sigma70_r4_2 Sigma-7  58.8      15 0.00039   17.8   4.2   39   31-69     10-48  (54)
129 COG2186 FadR Transcriptional r  57.6      14 0.00037   17.9   3.6   41   49-89     36-76  (241)
130 PRK12533 RNA polymerase sigma   57.4      16 0.00042   17.6   4.6   40   31-70    137-176 (217)
131 COG0640 ArsR Predicted transcr  56.9      17 0.00043   17.6   4.4   53   33-85     24-77  (110)
132 COG1654 BirA Biotin operon rep  56.1      17 0.00044   17.5   5.4   59   34-92      6-65  (79)
133 pfam04552 Sigma54_DBD Sigma-54  56.1      12 0.00029   18.5   2.9   41   46-91     48-88  (160)
134 PRK12534 RNA polymerase sigma   56.1      17 0.00044   17.5   4.5   39   32-70    138-176 (187)
135 pfam11994 DUF3489 Protein of u  56.0      17 0.00044   17.5   4.8   39   33-71      9-48  (72)
136 pfam00440 TetR_N Bacterial reg  54.5      18 0.00047   17.4   3.9   30   37-66      6-35  (47)
137 TIGR02937 sigma70-ECF RNA poly  54.4      18 0.00047   17.4   4.5   40   31-70    114-153 (162)
138 pfam10771 DUF2582 Protein of u  54.2      19 0.00047   17.3   4.3   41   36-76     10-51  (65)
139 PRK12547 RNA polymerase sigma   53.9      19 0.00048   17.3   4.5   40   31-70    112-151 (164)
140 cd00569 HTH_Hin_like Helix-tur  53.5      19 0.00049   17.3   4.1   40   29-68      3-42  (42)
141 PRK12541 RNA polymerase sigma   52.7      20  0.0005   17.2   4.6   39   32-70    113-151 (161)
142 KOG3233 consensus               51.5      21 0.00053   17.1   5.0   55   26-80     76-133 (297)
143 COG1974 LexA SOS-response tran  51.5      21 0.00053   17.1   3.9   52   36-88     15-67  (201)
144 PRK10512 selenocysteinyl-tRNA-  50.1      22 0.00056   17.0   4.7   53   36-88    495-547 (615)
145 PRK11303 DNA-binding transcrip  49.9      22 0.00056   17.0   3.5   20   49-68      2-21  (330)
146 TIGR00373 TIGR00373 conserved   49.8      22 0.00056   17.0   3.7   45   33-77     15-60  (168)
147 PRK09492 treR trehalose repres  49.6      19 0.00048   17.3   3.1   21   48-68      5-25  (315)
148 pfam00356 LacI Bacterial regul  49.4      18 0.00047   17.4   3.0   21   49-69      1-21  (46)
149 pfam04337 DUF480 Protein of un  49.2      23 0.00057   16.9   5.0   53   33-85      2-73  (148)
150 COG2188 PhnF Transcriptional r  48.7      15 0.00039   17.8   2.5   41   49-89     33-73  (236)
151 TIGR02885 spore_sigF RNA polym  48.7      23 0.00059   16.8   4.3   33   35-68    102-134 (231)
152 smart00354 HTH_LACI helix_turn  48.4      19 0.00049   17.3   3.0   21   49-69      2-22  (70)
153 pfam08221 HTH_9 RNA polymerase  48.2      23  0.0006   16.8   3.8   42   37-78     16-58  (62)
154 PRK09751 putative ATP-dependen  48.2      23  0.0006   16.8   6.1   51   33-83    974-1025(1490)
155 PRK10344 DNA-binding transcrip  47.9      24  0.0006   16.8   3.8   39   31-69      5-43  (90)
156 PRK12516 RNA polymerase sigma   47.9      24  0.0006   16.8   4.7   40   31-70    119-158 (190)
157 PRK12511 RNA polymerase sigma   47.7      24 0.00061   16.8   3.6   38   33-70    113-150 (182)
158 PRK12539 RNA polymerase sigma   47.4      24 0.00061   16.7   4.4   39   32-70    132-170 (184)
159 PRK12531 RNA polymerase sigma   47.2      24 0.00062   16.7   4.7   39   32-70    142-180 (194)
160 PRK09638 RNA polymerase sigma   46.9      25 0.00063   16.7   4.4   40   31-70    127-166 (177)
161 PRK10079 putative transcriptio  46.7      25 0.00063   16.7   3.8   40   49-88     37-76  (241)
162 PRK12532 RNA polymerase sigma   46.7      25 0.00063   16.7   4.7   38   33-70    138-175 (195)
163 PRK12518 RNA polymerase sigma   46.6      25 0.00063   16.7   4.4   39   32-70    121-159 (175)
164 PRK12546 RNA polymerase sigma   46.2      25 0.00064   16.6   4.6   40   31-70    113-152 (188)
165 PRK10014 DNA-binding transcrip  45.9      23 0.00059   16.8   3.1   22   47-68      6-27  (342)
166 PRK12537 RNA polymerase sigma   45.5      26 0.00066   16.6   4.8   38   32-69    136-173 (184)
167 PRK09649 RNA polymerase sigma   45.5      26 0.00066   16.6   4.8   40   31-70    130-169 (185)
168 PRK04984 fatty acid metabolism  45.3      19 0.00048   17.3   2.5   55   33-87     10-71  (239)
169 PRK12515 RNA polymerase sigma   45.1      26 0.00067   16.5   4.7   40   31-70    131-170 (189)
170 PRK12540 RNA polymerase sigma   44.6      27 0.00068   16.5   4.4   39   32-70    112-150 (181)
171 pfam07789 DUF1627 Protein of u  44.3      26 0.00067   16.5   3.2   45   45-89      4-49  (155)
172 PRK11041 DNA-binding transcrip  43.4      27 0.00069   16.5   3.1   21   48-68     10-30  (341)
173 pfam10975 DUF2802 Protein of u  42.9      28  0.0007   16.4   3.1   29   35-66     35-63  (70)
174 pfam03551 PadR Transcriptional  42.7      26 0.00066   16.6   2.9   43   37-79      4-54  (81)
175 PRK12535 RNA polymerase sigma   42.4      29 0.00074   16.3   4.5   40   31-70    132-171 (195)
176 KOG2747 consensus               42.3      29 0.00074   16.3   3.7   50   36-88    315-367 (396)
177 PRK08444 hypothetical protein;  42.0      17 0.00044   17.5   1.9   36   44-83    133-168 (353)
178 pfam04492 Phage_rep_O Bacterio  41.9      30 0.00076   16.3   3.7   55   32-87     30-93  (100)
179 pfam09940 DUF2172 Domain of un  41.8      30 0.00076   16.2   3.8   43   36-78    340-384 (384)
180 PRK05926 hypothetical protein;  41.7      18 0.00046   17.4   2.0   36   44-83    152-187 (371)
181 PRK12530 RNA polymerase sigma   41.6      30 0.00076   16.2   4.6   38   33-70    138-175 (191)
182 PRK12543 RNA polymerase sigma   41.5      30 0.00077   16.2   6.3   52   32-83    130-189 (190)
183 PRK13239 alkylmercury lyase; P  41.5      30 0.00077   16.2   5.5   38   34-71     22-60  (206)
184 PRK10703 DNA-binding transcrip  41.4      30 0.00077   16.2   3.1   16   52-67      6-21  (335)
185 PRK09637 RNA polymerase sigma   41.3      30 0.00077   16.2   4.7   40   31-70    106-145 (181)
186 PRK09643 RNA polymerase sigma   41.0      31 0.00078   16.2   4.6   40   31-70    131-170 (197)
187 PRK10668 DNA-binding transcrip  41.0      31 0.00078   16.2   3.7   30   37-66     21-50  (216)
188 PRK09646 RNA polymerase sigma   40.5      31  0.0008   16.1   4.1   37   33-69    144-180 (194)
189 PRK11922 RNA polymerase sigma   40.4      31  0.0008   16.1   4.6   39   32-70    150-188 (231)
190 pfam05732 RepL Firmicute plasm  40.4      31  0.0008   16.1   3.2   40   49-88     77-116 (165)
191 PTZ00064 histone acetyltransfe  40.3      31  0.0008   16.1   4.4   47   36-85    351-401 (442)
192 PRK12519 RNA polymerase sigma   40.2      32  0.0008   16.1   4.3   39   31-69    141-179 (194)
193 PRK06811 RNA polymerase factor  39.9      32 0.00081   16.1   4.6   40   31-70    128-167 (185)
194 PRK09648 RNA polymerase sigma   39.9      32 0.00081   16.1   4.6   38   32-69    138-175 (187)
195 PRK05602 RNA polymerase sigma   39.8      32 0.00082   16.1   4.7   39   32-70    129-167 (186)
196 PRK09641 RNA polymerase sigma   39.6      32 0.00082   16.0   4.4   39   32-70    137-175 (187)
197 TIGR02989 Sig-70_gvs1 RNA poly  39.1      33 0.00084   16.0   5.3   42   30-71    114-155 (163)
198 COG3423 Nlp Predicted transcri  38.9      33 0.00085   16.0   3.6   40   31-70      5-44  (82)
199 PRK09943 DNA-binding transcrip  38.4      33 0.00085   16.0   2.9   29   39-67     12-40  (185)
200 PRK12544 RNA polymerase sigma   38.3      34 0.00086   15.9   4.7   38   33-70    151-188 (207)
201 PRK08445 hypothetical protein;  37.8      22 0.00055   17.0   1.9   38   43-84    125-162 (348)
202 TIGR03433 padR_acidobact trans  37.6      35 0.00089   15.9   3.2   45   36-80      6-58  (100)
203 PRK12545 RNA polymerase sigma   37.6      35 0.00089   15.9   4.5   35   36-70    144-178 (201)
204 TIGR01714 phage_rep_org_N phag  37.6      35 0.00089   15.9   4.1   43   46-88     52-94  (121)
205 PRK05932 RNA polymerase factor  37.4      23 0.00058   16.9   2.0   37   47-88    349-385 (461)
206 COG1167 ARO8 Transcriptional r  37.3      35 0.00089   15.9   2.9   36   48-83     29-64  (459)
207 PRK11886 biotin--protein ligas  37.1      36 0.00091   15.8   4.4   52   37-88      7-60  (319)
208 PRK09640 RNA polymerase sigma   37.0      36 0.00091   15.8   4.4   39   32-70    135-173 (188)
209 KOG1206 consensus               37.0      36 0.00091   15.8   4.5   63   32-94    160-226 (272)
210 PRK12527 RNA polymerase sigma   36.2      37 0.00094   15.7   4.7   38   32-69    106-143 (159)
211 KOG2036 consensus               36.0      37 0.00095   15.7   4.7   40   31-70    849-888 (1011)
212 COG3132 Uncharacterized protei  35.6      38 0.00096   15.7   5.8   54   33-86      6-77  (215)
213 smart00342 HTH_ARAC helix_turn  35.1      38 0.00098   15.6   3.7   24   47-70      1-24  (84)
214 PRK12536 RNA polymerase sigma   34.8      39 0.00099   15.6   4.7   38   32-69    127-164 (178)
215 PRK09644 RNA polymerase sigma   34.7      39 0.00099   15.6   4.3   39   32-70    109-147 (165)
216 PRK05927 hypothetical protein;  34.7      26 0.00067   16.5   1.9   37   44-84    129-165 (350)
217 PRK12514 RNA polymerase sigma   34.4      39   0.001   15.6   4.9   39   32-70    130-168 (179)
218 TIGR03377 glycerol3P_GlpA glyc  34.3      40   0.001   15.6   3.5   46   36-81    417-463 (516)
219 COG1595 RpoE DNA-directed RNA   34.1      40   0.001   15.6   4.6   40   31-70    127-166 (182)
220 PRK12526 RNA polymerase sigma   33.3      41   0.001   15.5   4.5   38   32-69    154-191 (206)
221 cd01392 HTH_LacI Helix-turn-he  33.0      35  0.0009   15.8   2.4   18   52-69      2-19  (52)
222 PRK12538 RNA polymerase sigma   32.9      42  0.0011   15.4   4.5   39   32-70    172-210 (233)
223 COG3432 Predicted transcriptio  32.4      27 0.00069   16.4   1.7   51   38-88     22-75  (95)
224 COG1568 Predicted methyltransf  32.4      43  0.0011   15.4   3.9   49   37-88     25-74  (354)
225 PRK10339 DNA-binding transcrip  32.4      43  0.0011   15.4   3.0   16   52-67      6-21  (327)
226 pfam11800 RP-C_C Replication p  32.2      22 0.00056   17.0   1.2   46   39-86    136-181 (208)
227 PRK11239 hypothetical protein;  32.2      43  0.0011   15.4   4.8   59   33-91     96-166 (215)
228 TIGR02607 antidote_HigA addict  32.1      43  0.0011   15.4   3.8   37   31-70      7-43  (81)
229 PRK12522 RNA polymerase sigma   31.8      44  0.0011   15.3   4.7   39   32-70    120-158 (173)
230 PRK11564 stationary phase indu  31.6      44  0.0011   15.3   6.8   66   25-90      4-79  (426)
231 pfam05491 RuvB_C Holliday junc  31.4      44  0.0011   15.3   5.3   55   32-86      5-64  (75)
232 TIGR03613 RutR pyrimidine util  31.3      45  0.0011   15.3   3.8   29   37-65     18-46  (202)
233 PRK12524 RNA polymerase sigma   31.1      45  0.0011   15.3   4.6   39   32-70    137-175 (196)
234 PRK00135 scpB segregation and   30.3      46  0.0012   15.2   3.4   43   31-73     80-123 (182)
235 PRK12513 RNA polymerase sigma   29.3      48  0.0012   15.1   4.6   40   31-70    139-178 (194)
236 COG2238 RPS19A Ribosomal prote  29.1      30 0.00077   16.2   1.5   50   36-85     55-119 (147)
237 PRK11924 RNA polymerase sigma   28.9      49  0.0013   15.1   4.2   39   32-70    126-164 (180)
238 PRK12469 RNA polymerase factor  28.9      34 0.00086   16.0   1.7   38   47-89    363-400 (475)
239 pfam02796 HTH_7 Helix-turn-hel  28.8      49  0.0013   15.1   3.8   36   32-68      6-42  (45)
240 PRK09647 RNA polymerase sigma   28.8      50  0.0013   15.0   6.1   62   32-93    158-221 (222)
241 PRK09639 RNA polymerase sigma   28.7      50  0.0013   15.0   4.1   37   33-70    114-150 (166)
242 PRK11923 algU RNA polymerase s  28.5      50  0.0013   15.0   4.4   39   32-70    139-177 (193)
243 PRK12517 RNA polymerase sigma   28.3      50  0.0013   15.0   4.7   39   32-70    129-167 (188)
244 TIGR02018 his_ut_repres histid  28.2      42  0.0011   15.4   2.1   36   49-84     27-62  (234)
245 pfam08222 HTH_CodY CodY helix-  27.8      41   0.001   15.5   2.0   34   51-84      7-40  (60)
246 PRK06266 transcription initiat  27.7      52  0.0013   14.9   4.7   44   35-78     23-67  (178)
247 PRK10430 DNA-binding transcrip  27.4      52  0.0013   14.9   6.0   46   34-79    162-210 (239)
248 PRK09651 RNA polymerase sigma   27.2      53  0.0014   14.9   4.8   39   32-70    120-158 (172)
249 PRK10219 DNA-binding transcrip  27.0      53  0.0014   14.9   3.3   29   40-69     15-43  (107)
250 PRK12528 RNA polymerase sigma   26.9      54  0.0014   14.9   4.7   39   32-70    120-158 (167)
251 pfam01418 HTH_6 Helix-turn-hel  26.9      54  0.0014   14.9   3.7   46   31-76     13-63  (106)
252 PRK09975 DNA-binding transcrip  26.7      54  0.0014   14.8   3.8   30   37-66     21-50  (213)
253 PRK09642 RNA polymerase sigma   26.5      55  0.0014   14.8   4.8   38   33-70    108-145 (160)
254 COG4565 CitB Response regulato  26.5      55  0.0014   14.8   4.0   48   32-79    156-205 (224)
255 pfam04539 Sigma70_r3 Sigma-70   26.4      55  0.0014   14.8   4.7   34   35-69      9-42  (78)
256 COG4901 Ribosomal protein S25   26.2      55  0.0014   14.8   3.7   51   34-84     45-96  (107)
257 TIGR02943 Sig70_famx1 RNA poly  26.2      52  0.0013   14.9   2.3   34   37-70    143-176 (194)
258 pfam01402 RHH_1 Ribbon-helix-h  26.2      55  0.0014   14.8   2.9   22   49-70     13-34  (35)
259 PRK09334 30S ribosomal protein  25.8      45  0.0011   15.3   1.9   50   35-84     49-99  (107)
260 TIGR02684 dnstrm_HI1420 probab  25.3      58  0.0015   14.7   2.5   35   35-69     31-67  (91)
261 PRK13890 conjugal transfer pro  25.2      58  0.0015   14.7   3.3   48   37-93     51-100 (119)
262 pfam09681 Phage_rep_org_N N-te  24.6      59  0.0015   14.6   4.2   45   45-89     51-95  (121)
263 PRK09652 RNA polymerase sigma   24.5      60  0.0015   14.6   4.5   38   32-69    138-175 (192)
264 COG3697 CitX Phosphoribosyl-de  23.6      61  0.0016   14.6   2.2   21   74-94     29-49  (182)
265 pfam01399 PCI PCI domain. This  23.5      62  0.0016   14.5   2.7   35   44-78     57-91  (105)
266 pfam11569 Homez Homeodomain le  23.5      57  0.0014   14.7   2.0   22   45-66     24-45  (57)
267 KOG2578 consensus               23.5      63  0.0016   14.5   4.1   51   44-94     41-91  (388)
268 TIGR02417 fruct_sucro_rep D-fr  23.5      40   0.001   15.5   1.3   19   50-68      2-20  (335)
269 pfam04760 IF2_N Translation in  22.9      64  0.0016   14.4   3.0   26   46-71      2-27  (52)
270 smart00753 PAM PCI/PINT associ  22.8      65  0.0017   14.4   2.8   43   45-87     22-67  (88)
271 smart00088 PINT motif in prote  22.8      65  0.0017   14.4   2.8   43   45-87     22-67  (88)
272 PRK09645 RNA polymerase sigma   22.7      65  0.0017   14.4   4.5   40   31-70    116-155 (171)
273 PRK12520 RNA polymerase sigma   22.1      67  0.0017   14.3   4.4   48   33-80    133-182 (191)
274 PRK12523 RNA polymerase sigma   22.0      67  0.0017   14.3   4.4   38   32-69    120-157 (172)
275 PRK11101 glpA sn-glycerol-3-ph  21.7      68  0.0017   14.3   2.9   46   36-81    438-484 (545)
276 PRK09415 RNA polymerase factor  21.1      70  0.0018   14.2   4.6   39   32-70    128-166 (177)
277 PRK08295 RNA polymerase factor  20.8      71  0.0018   14.2   4.4   37   33-70    157-193 (209)
278 COG1609 PurR Transcriptional r  20.7      72  0.0018   14.2   3.0   20   49-68      2-21  (333)
279 PRK12525 RNA polymerase sigma   20.7      72  0.0018   14.2   4.8   38   32-69    119-156 (168)
280 pfam00196 GerE Bacterial regul  20.3      73  0.0019   14.1   5.6   41   30-71      2-42  (58)

No 1  
>PRK10736 hypothetical protein; Provisional
Probab=99.32  E-value=3.2e-12  Score=86.24  Aligned_cols=55  Identities=29%  Similarity=0.401  Sum_probs=50.8

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE--ECC
Q ss_conf             9999998588988999999982999999999999999941798647986898--137
Q gi|254780305|r   36 RVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSL--TMH   90 (95)
Q Consensus        36 ~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l--~~~   90 (95)
                      ..+++..++++++++|+|+++||++++++++.|++|||+|+|+++||||+++  ++|
T Consensus       300 ~~~lL~~~g~~~~~vD~La~~tgl~v~~v~~~LleLEL~G~V~~~pGgY~RlrRa~h  356 (364)
T PRK10736        300 FPELLANVGDEVTPVDVVAERAGQPVPEVVTQLLELELAGWIAAVPGGYVRLRRAGH  356 (364)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEEECCCC
T ss_conf             799998558999899999999790999999999999948917806994799754775


No 2  
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=98.92  E-value=1.5e-09  Score=71.92  Aligned_cols=52  Identities=29%  Similarity=0.401  Sum_probs=50.7

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             9999998588988999999982999999999999999941798647986898
Q gi|254780305|r   36 RVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        36 ~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      +.++++.++++|+++|.|++.+|+++++++..|++|||.|+|.+.+||+|++
T Consensus       298 ~~~~~~~~~~~~~~~d~l~~~~~~~~~~~~~~L~elel~G~i~~~~g~~~~~  349 (350)
T COG0758         298 FLALLANLGDEPKEIDRLASCTGLTIAQVLAWLLELELEGKVKRLGGGYYRL  349 (350)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEC
T ss_conf             7999987268874699999886888999999999998469478638815854


No 3  
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=97.12  E-value=0.00063  Score=41.48  Aligned_cols=54  Identities=20%  Similarity=0.282  Sum_probs=49.1

Q ss_pred             HHHHHHHCCCCCC--HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC-CCEEEEECC
Q ss_conf             9999985889889--99999982999999999999999941798647-986898137
Q gi|254780305|r   37 VRIKQSLNNVPIH--IDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP-EGKVSLTMH   90 (95)
Q Consensus        37 ~~Il~~L~~~p~~--iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p-Gg~v~l~~~   90 (95)
                      -+||++|...|..  +-+|++++|+|.++++..|..|+=.|+|.+-+ +|+|+|...
T Consensus         7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~grY~Lg~~   63 (246)
T COG1414           7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRLGPR   63 (246)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCEEEECHH
T ss_conf             999999971888887999999879198899999999997898889799996985789


No 4  
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.07  E-value=0.00094  Score=40.54  Aligned_cols=52  Identities=13%  Similarity=0.220  Sum_probs=47.3

Q ss_pred             HHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC-CCEEEEEC
Q ss_conf             99998588--988999999982999999999999999941798647-98689813
Q gi|254780305|r   38 RIKQSLNN--VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP-EGKVSLTM   89 (95)
Q Consensus        38 ~Il~~L~~--~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p-Gg~v~l~~   89 (95)
                      +|+++++.  .|+++-+|++.+|++.++++.+|-.||-.|+|.+-+ +|.|++..
T Consensus         9 ~IL~~l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL~~~G~l~~~~~~~~Y~lG~   63 (91)
T smart00346        9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLGP   63 (91)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCEEEECH
T ss_conf             9999997289998999999998909999999999999889968849999775309


No 5  
>PRK11569 transcriptional repressor IclR; Provisional
Probab=96.87  E-value=0.004  Score=37.12  Aligned_cols=57  Identities=11%  Similarity=0.218  Sum_probs=48.9

Q ss_pred             CHHHH-HHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC-CEEEEEC
Q ss_conf             98999-99998588--9889999999829999999999999999417986479-8689813
Q gi|254780305|r   33 QCERV-RIKQSLNN--VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPE-GKVSLTM   89 (95)
Q Consensus        33 ~~~~~-~Il~~L~~--~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pG-g~v~l~~   89 (95)
                      +-++. .||++++.  .++++.+|++.+|++.++++.+|-.|+-.|+|.+.+. |+|+|..
T Consensus        26 sl~Ral~IL~~la~~~~~lsl~eia~~lglpksT~~RlL~tL~~~G~v~~~~~~~~Y~LG~   86 (274)
T PRK11569         26 SLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGELGHWAIGA   86 (274)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCEECCCH
T ss_conf             9999999999996389998999999987919999999999999769877869988022457


No 6  
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=96.51  E-value=0.0041  Score=37.09  Aligned_cols=55  Identities=20%  Similarity=0.236  Sum_probs=47.9

Q ss_pred             HHH-HHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC-CCEEEEEC
Q ss_conf             999-99998588--988999999982999999999999999941798647-98689813
Q gi|254780305|r   35 ERV-RIKQSLNN--VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP-EGKVSLTM   89 (95)
Q Consensus        35 ~~~-~Il~~L~~--~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p-Gg~v~l~~   89 (95)
                      ++. +||++++.  .+.++-+|++++|++.++++..|-.|+=.|+|.+.+ .|+|+|..
T Consensus        11 ~Ral~ILe~l~~~~~~lslsela~~lglpksTv~RlL~tL~~~G~l~~~~~~~~Y~LG~   69 (264)
T PRK09834         11 SRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFRLTL   69 (264)
T ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCEECCH
T ss_conf             99999999874179997999999997909999999999999789989967999765160


No 7  
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=96.40  E-value=0.0027  Score=38.11  Aligned_cols=51  Identities=20%  Similarity=0.264  Sum_probs=46.7

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             9999998588-98899999998299999999999999994179864798689
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVS   86 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~   86 (95)
                      +..|++.|.. .-+.+++|++..+.+..++-.-|-+||=+|.|.+..||-++
T Consensus         2 ~~~Il~~l~~~~~~~i~~La~~~~VS~~TiRRDl~~L~~~g~i~r~hGGA~s   53 (53)
T smart00420        2 QQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHGGAVS   53 (53)
T ss_pred             HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEC
T ss_conf             8999999998697979999999897999999969999988998997798839


No 8  
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=96.23  E-value=0.013  Score=34.46  Aligned_cols=56  Identities=20%  Similarity=0.184  Sum_probs=48.2

Q ss_pred             CHHHH-HHHHHHC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC-CEEEEE
Q ss_conf             98999-9999858--89889999999829999999999999999417986479-868981
Q gi|254780305|r   33 QCERV-RIKQSLN--NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPE-GKVSLT   88 (95)
Q Consensus        33 ~~~~~-~Il~~L~--~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pG-g~v~l~   88 (95)
                      +-++. .||++++  ..+..+-+|++.+|++.++++.+|-.|+-.|+|.+-+. |+|+|.
T Consensus        23 sl~Ral~IL~~la~~~~~ltl~eia~~lglpksT~~RlL~tL~~~G~v~~d~~~~~Y~lG   82 (271)
T PRK10163         23 ALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIG   82 (271)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCEECC
T ss_conf             999999999999747999799999999791999999999999968988984899917647


No 9  
>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=96.13  E-value=0.0099  Score=35.02  Aligned_cols=57  Identities=28%  Similarity=0.345  Sum_probs=51.6

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC---EEEEEC
Q ss_conf             989999999858898899999998299999999999999994179864798---689813
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG---KVSLTM   89 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg---~v~l~~   89 (95)
                      ++.+.+|+..|...+.++.+|++..|++.+.++..|-.|+=.|.|.....|   +|+++.
T Consensus         6 ~~~r~~Il~~L~~~~~~~~eia~~l~is~~~vs~hL~~L~~~Gli~~~~~~~~~~y~l~~   65 (78)
T cd00090           6 DPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD   65 (78)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCEEEEEECC
T ss_conf             999999999998489069999877784878999999999988986899988999999799


No 10 
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=96.11  E-value=0.0096  Score=35.09  Aligned_cols=44  Identities=20%  Similarity=0.285  Sum_probs=40.2

Q ss_pred             HHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99998588--988999999982999999999999999941798647
Q gi|254780305|r   38 RIKQSLNN--VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP   81 (95)
Q Consensus        38 ~Il~~L~~--~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p   81 (95)
                      +|+++++.  .|..+-+|++++|++.+.++.+|-.|+=.|+|.+-|
T Consensus         7 ~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~tL~~~G~v~~dp   52 (52)
T pfam09339         7 AILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQTLVELGYVEQDP   52 (52)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             9999986289998999999998919999999999999881911692


No 11 
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=95.97  E-value=0.0063  Score=36.07  Aligned_cols=53  Identities=21%  Similarity=0.255  Sum_probs=48.2

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999998588-9889999999829999999999999999417986479868981
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +.+|++.|.. .-+++++|++..+.+..++-.-|-+||-+|.|.|.-||-+..+
T Consensus         2 ~~~Il~~l~~~~~v~i~~La~~f~VS~~TiRRDl~~L~~~g~i~R~~GGA~~~~   55 (57)
T pfam08220         2 IQQILELLKQQGTLSVEELAELLGVSEMTIRRDLNELEEQGLLTRTHGGAVSNS   55 (57)
T ss_pred             HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEECCC
T ss_conf             899999999869797999999989599999996999998899899749577588


No 12 
>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=95.92  E-value=0.017  Score=33.69  Aligned_cols=55  Identities=20%  Similarity=0.237  Sum_probs=45.8

Q ss_pred             CCHHHHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             998999999985-8898899999998299999999999999994179864798689
Q gi|254780305|r   32 TQCERVRIKQSL-NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVS   86 (95)
Q Consensus        32 ~~~~~~~Il~~L-~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~   86 (95)
                      .+..|.+|+.+| ...+..+.+|++.+|++.+.|+.+|-.|+=+|+|.+..|....
T Consensus         6 ls~~E~~vY~~Ll~~g~~t~~eia~~~~i~r~~vY~~L~~L~~kGlv~~~~~~p~~   61 (68)
T pfam01978         6 LSEYEAKVYLALLKLGPATADEIAEESGVPRSKVYEVLRSLEKKGLVEREKGRPKK   61 (68)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCE
T ss_conf             89999999999998199889999999598898999999999988988986797447


No 13 
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=95.90  E-value=0.016  Score=33.94  Aligned_cols=54  Identities=19%  Similarity=0.194  Sum_probs=49.0

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9999998588-98899999998299999999999999994179864798689813
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      +++|++.|.. .-+++++|++..+.+..++..-|-+||=.|+|.|..||-+....
T Consensus        19 ~~~Il~~L~~~g~v~v~eLae~~~VS~~TIRRDL~~Le~~g~l~R~hGGA~~~~~   73 (269)
T PRK09802         19 REQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGALICDS   73 (269)
T ss_pred             HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEECCC
T ss_conf             9999999998698999999998796988999809999878986999687897677


No 14 
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=95.86  E-value=0.0085  Score=35.39  Aligned_cols=53  Identities=15%  Similarity=0.151  Sum_probs=48.2

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999998588-9889999999829999999999999999417986479868981
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +++|++.|.. .-+++.+|++..+.+..++..-|-+||=.|+|.|..||-+...
T Consensus         7 ~~~Il~~L~~~g~v~v~eLa~~l~VS~~TIRRDL~~Le~~G~l~R~hGGa~~~~   60 (256)
T PRK10434          7 QAAILEYLQKQGKCSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTYGGVVLNK   60 (256)
T ss_pred             HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECEEECCC
T ss_conf             999999999869799999999879699899984999987898899947386477


No 15 
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=95.76  E-value=0.011  Score=34.86  Aligned_cols=51  Identities=14%  Similarity=0.178  Sum_probs=46.7

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             9999998588-98899999998299999999999999994179864798689
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVS   86 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~   86 (95)
                      +++|++.|.. .-+++++|++..+.+..++..-|-+||=.|+|.|..||-+.
T Consensus         7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~G~l~R~hGGA~~   58 (252)
T PRK10906          7 HDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNELAEQNLILRHHGGAAL   58 (252)
T ss_pred             HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECEEEE
T ss_conf             9999999998698999999998796998998829999878988999584980


No 16 
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=95.72  E-value=0.012  Score=34.56  Aligned_cols=57  Identities=19%  Similarity=0.283  Sum_probs=50.6

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             9999998588-98899999998299999999999999994179864798689813799
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTMHLP   92 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~~~~   92 (95)
                      +++|++.|.. .-+.+.+|++..+.+..++..-|-+||=+|++.|..||-+.+....+
T Consensus         7 ~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~r~~GGA~~~~~~~~   64 (251)
T PRK13509          7 HQILLDMLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKVRNGAEAITQQRP   64 (251)
T ss_pred             HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEECCCCCC
T ss_conf             9999999998698989999999896998999839999878978999889797777776


No 17 
>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=95.71  E-value=0.027  Score=32.67  Aligned_cols=53  Identities=13%  Similarity=0.134  Sum_probs=45.4

Q ss_pred             CCCHHHHHHHHHHC------CCCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99989999999858------898899999998299-999999999999994179864798
Q gi|254780305|r   31 YTQCERVRIKQSLN------NVPIHIDDIIHHTGI-EAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        31 ~~~~~~~~Il~~L~------~~p~~iD~l~~~tgl-~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      +++.-+++||+.+.      .-|=++.||+..+|+ +.+.|...|-.||=+|+|.+.||.
T Consensus         3 ~LT~rQ~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~Le~kG~I~r~~~~   62 (65)
T pfam01726         3 PLTERQREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKALERKGYIERDPGK   62 (65)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCEECCCCC
T ss_conf             337999999999999999828898799999993899809999999999998396348999


No 18 
>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=95.70  E-value=0.021  Score=33.28  Aligned_cols=46  Identities=20%  Similarity=0.197  Sum_probs=43.1

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9899999998588988999999982999999999999999941798
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLC   78 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~   78 (95)
                      |+.+.+|+..|...|..+.+|+..++++.+.|+-.|-.|+-+|.|.
T Consensus         1 Dp~Rl~Il~~L~~~~~~v~el~~~l~~sq~~vS~HL~~L~~~GlV~   46 (47)
T pfam01022         1 DPTRLKILYLLSEGELCVCELAEILGLSQSTVSHHLKKLREAGLVE   46 (47)
T ss_pred             CHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCC
T ss_conf             9589999999980899699999998958869999999998980968


No 19 
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=95.55  E-value=0.012  Score=34.63  Aligned_cols=56  Identities=18%  Similarity=0.195  Sum_probs=50.5

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             9999998588-9889999999829999999999999999417986479868981379
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTMHL   91 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~~~   91 (95)
                      +++|++.|.. .-+++++|+++.+.+..++..-|-+||=+|.+.|..||-+......
T Consensus         7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~hGGa~~~~~~~   63 (253)
T COG1349           7 HQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVHGGAVLPDSES   63 (253)
T ss_pred             HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEECEEECCCCCC
T ss_conf             999999999859697999998859789999861999977892899606188377665


No 20 
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=95.42  E-value=0.029  Score=32.53  Aligned_cols=56  Identities=16%  Similarity=0.233  Sum_probs=52.0

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             989999999858898899999998299999999999999994179864798689813
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      +.-+..||-.|..+|..+|+|-...+.+.+.++..|-.|+=.|.|.+. |+.|+|+.
T Consensus        12 SekRk~lLllL~egPkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~~-~~~Y~LS~   67 (260)
T COG4742          12 SEKRKDLLLLLKEGPKTIEEIKNELNVSSSAILPQIKKLKDKGLVVQE-GDRYSLSS   67 (260)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEC-CCEEEECC
T ss_conf             388999999998589889999988589938889999987138987851-99987340


No 21 
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=95.32  E-value=0.014  Score=34.17  Aligned_cols=53  Identities=13%  Similarity=0.174  Sum_probs=48.1

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999998588-9889999999829999999999999999417986479868981
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +++|++.|.. .-+.+.+|++..+.+..++..-|-+||=+|+|.|..||-+.+.
T Consensus         6 ~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~G~l~R~hGGA~~~~   59 (240)
T PRK10411          6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHGRAKYIH   59 (240)
T ss_pred             HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEEEECC
T ss_conf             999999999869799999999889599899982998977898899942499756


No 22 
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=95.28  E-value=0.025  Score=32.88  Aligned_cols=54  Identities=15%  Similarity=0.217  Sum_probs=47.1

Q ss_pred             CCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             99899999998588-9889999999829999999999999999417986479868
Q gi|254780305|r   32 TQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKV   85 (95)
Q Consensus        32 ~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v   85 (95)
                      +++...++++.+.. +|.+|+|+++.+|.++..|+..|.+|+=-|+|...-+|+-
T Consensus        62 Lsp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~~gq~  116 (144)
T COG4190          62 LSPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIFFEEDGQR  116 (144)
T ss_pred             HCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEECCCCC
T ss_conf             1921899999987419513899999867546889899999986482787417731


No 23 
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=94.57  E-value=0.051  Score=31.18  Aligned_cols=59  Identities=14%  Similarity=0.076  Sum_probs=52.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             4356887999899999998588-9889999999829999999999999999417986479
Q gi|254780305|r   24 NITHYPEYTQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPE   82 (95)
Q Consensus        24 ~~~~~p~~~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pG   82 (95)
                      +....+-..+..+-.|+.+|.. +++...+|++..+++.+.+..++=.||=+|+|.|.|.
T Consensus        30 ~~~L~~~gLt~~Q~~vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ldrLe~~GlI~R~~~   89 (144)
T PRK11512         30 NEYLSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPN   89 (144)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
T ss_conf             998754599999999999999869979999999978888789999999997879663579


No 24 
>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=94.07  E-value=0.078  Score=30.19  Aligned_cols=50  Identities=18%  Similarity=0.294  Sum_probs=44.3

Q ss_pred             CHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9899999998588-9889999999829999999999999999417986479
Q gi|254780305|r   33 QCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPE   82 (95)
Q Consensus        33 ~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pG   82 (95)
                      +..|-.||..|.. .+++..+|+++.+++.+.++.++-.||=+|+|.|.+.
T Consensus         2 T~~Q~~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i~~Le~~glv~R~~~   52 (59)
T pfam01047         2 TLTQFHILRILYEHGPLTVSELAEKLGVDRSTVTRVLDRLEKKGLIERSRS   52 (59)
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCC
T ss_conf             899999999999469929999999988586549999999988979886279


No 25 
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=94.04  E-value=0.054  Score=31.04  Aligned_cols=48  Identities=23%  Similarity=0.250  Sum_probs=43.4

Q ss_pred             HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             999985889889999999829999999999999999417986479868
Q gi|254780305|r   38 RIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKV   85 (95)
Q Consensus        38 ~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v   85 (95)
                      +|+..|...+..+-+|++.++++.+.++..|-.|+=.|.|....-|+.
T Consensus         1 ~Il~~L~~~~~~~~ela~~l~is~~tvs~HL~~L~~~Glv~~~~~G~~   48 (66)
T smart00418        1 KILKLLAEGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGKR   48 (66)
T ss_pred             CHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCE
T ss_conf             958897739966999999988298888799999998892689998689


No 26 
>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=93.95  E-value=0.12  Score=29.10  Aligned_cols=58  Identities=14%  Similarity=0.149  Sum_probs=50.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             356887999899999998588--9889999999829999999999999999417986479
Q gi|254780305|r   25 ITHYPEYTQCERVRIKQSLNN--VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPE   82 (95)
Q Consensus        25 ~~~~p~~~~~~~~~Il~~L~~--~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pG   82 (95)
                      ......+.+.++-+||+.|..  .-.+++.|++..|.+.++++..|-+||=+|.|.+..+
T Consensus       160 ~~~~~~~~s~~~~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~~~~Lek~gLv~~~~~  219 (231)
T TIGR01884       160 LVPLLAGLSREELKVLEALKAEKGEKSVKNIAKKLGKSLSTISRHLAELEKKGLVESKGR  219 (231)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             224467888999999999850788052877998857888799999998874475456304


No 27 
>pfam08784 RPA_C Replication protein A C terminal. This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.
Probab=93.89  E-value=0.28  Score=27.21  Aligned_cols=47  Identities=11%  Similarity=0.147  Sum_probs=41.7

Q ss_pred             CCCHHHHHHHHHHCC-----CCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Q ss_conf             999899999998588-----988999999982-99999999999999994179
Q gi|254780305|r   31 YTQCERVRIKQSLNN-----VPIHIDDIIHHT-GIEAPVVYLVLLELDLAGRL   77 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~-----~p~~iD~l~~~t-gl~~~~v~~~LleLEL~G~i   77 (95)
                      .+++.+++||+.|..     +-+|+|+|+++. +++..+|..++=+|.=.|.|
T Consensus        44 ~ls~~~~~V~~~i~~~~~~~eG~h~~~l~~~l~~~~~~~i~~a~d~L~~eG~I   96 (103)
T pfam08784        44 GLTPLQDQVLNLIKQSCPGEEGVHVDELAAQLNGLPVNDIRQAVDFLSNEGHI   96 (103)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCEE
T ss_conf             87899999999999548898872799999998299999999999999848806


No 28 
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=93.85  E-value=0.11  Score=29.34  Aligned_cols=47  Identities=26%  Similarity=0.328  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             89999999858-898899999998299999999999999994179864
Q gi|254780305|r   34 CERVRIKQSLN-NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH   80 (95)
Q Consensus        34 ~~~~~Il~~L~-~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~   80 (95)
                      ..+++|+..|. ..|+++|+|+...|++...|-..|-.||-+|.|+..
T Consensus        11 ~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~   58 (218)
T COG2345          11 STRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE   58 (218)
T ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             589999999831698249999988599989999999999868666876


No 29 
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=93.77  E-value=0.1  Score=29.53  Aligned_cols=53  Identities=25%  Similarity=0.241  Sum_probs=41.7

Q ss_pred             HHHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC-----CCCEEEE
Q ss_conf             999999985-8898899999998299999999999999994179864-----7986898
Q gi|254780305|r   35 ERVRIKQSL-NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH-----PEGKVSL   87 (95)
Q Consensus        35 ~~~~Il~~L-~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~-----pGg~v~l   87 (95)
                      |-...+..| ...|..+|+|++..+++-++|+.+|-.|.-+|.|.|.     .||++-+
T Consensus        29 Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yi   87 (126)
T COG3355          29 DVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYL   87 (126)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCEEEE
T ss_conf             99999999864699579999999783199999999999985886666422678861488


No 30 
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=93.32  E-value=0.12  Score=29.24  Aligned_cols=44  Identities=20%  Similarity=0.206  Sum_probs=39.1

Q ss_pred             HHHHHHH--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999985--8898899999998299999999999999994179864
Q gi|254780305|r   37 VRIKQSL--NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH   80 (95)
Q Consensus        37 ~~Il~~L--~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~   80 (95)
                      .+||..|  +..|+.+|+|++.+|++-+.|+..+-+|+=.|.|+..
T Consensus        29 G~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~   74 (177)
T COG1510          29 GQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV   74 (177)
T ss_pred             HHHHHHHEECCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCHHHHH
T ss_conf             7786540006999669999999777801288999999854568853


No 31 
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=93.18  E-value=0.18  Score=28.16  Aligned_cols=52  Identities=19%  Similarity=0.266  Sum_probs=44.7

Q ss_pred             CCHHHHHHHHHHCCCC---CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9989999999858898---899999998299999999999999994179864798
Q gi|254780305|r   32 TQCERVRIKQSLNNVP---IHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p---~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      .+..+++|++.|...+   ...=.|+..+|++-.+|..+|..||=+|.|.+..|.
T Consensus         4 ~~~~eqkil~~L~~~g~~~~tA~~lak~lg~~Kk~vN~~LY~L~k~g~v~~~~~~   58 (68)
T smart00550        4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGT   58 (68)
T ss_pred             CCHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCC
T ss_conf             0079999999999748864039999999499899999999999974883106998


No 32 
>PRK12423 LexA repressor; Provisional
Probab=92.88  E-value=0.43  Score=26.20  Aligned_cols=59  Identities=17%  Similarity=0.178  Sum_probs=48.9

Q ss_pred             CCCHHHHHHHHHHC------CCCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             99989999999858------898899999998299-999999999999994179864798689813
Q gi|254780305|r   31 YTQCERVRIKQSLN------NVPIHIDDIIHHTGI-EAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        31 ~~~~~~~~Il~~L~------~~p~~iD~l~~~tgl-~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      +++.-|++||+.+.      ..|=++.||++..|+ +.+.|...|-.||=+|+|.+.+|..=++..
T Consensus         3 ~LT~kQ~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~~L~~kG~i~r~~~~~R~i~l   68 (202)
T PRK12423          3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPNQARGIRL   68 (202)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCEECCCCCCEEEEE
T ss_conf             208999999999999999629898899999982999867899999999988799706999537993


No 33 
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=92.81  E-value=0.14  Score=28.74  Aligned_cols=48  Identities=23%  Similarity=0.315  Sum_probs=42.9

Q ss_pred             CHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9899999998588-98899999998299999999999999994179864
Q gi|254780305|r   33 QCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH   80 (95)
Q Consensus        33 ~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~   80 (95)
                      +.-+-+|++.|.- .|..+++|+++.|||.+.+++-+--||=+|.|+..
T Consensus        22 S~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~   70 (308)
T COG4189          22 SKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE   70 (308)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             8899999999987179878999988588656666557888864724631


No 34 
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=92.54  E-value=0.19  Score=28.11  Aligned_cols=55  Identities=18%  Similarity=0.258  Sum_probs=48.1

Q ss_pred             CCCCCCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             887999899999998588-9889999999829999999999999999417986479
Q gi|254780305|r   28 YPEYTQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPE   82 (95)
Q Consensus        28 ~p~~~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pG   82 (95)
                      .+-..+..+-.||..|.. .++..-+|++.++++.+.++.++-.||=+|+|.+.+.
T Consensus         4 ~~~glt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~glv~r~~~   59 (101)
T smart00347        4 KPLGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS   59 (101)
T ss_pred             HHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             11394999999999999769979999999989688799999999945893898218


No 35 
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=92.28  E-value=0.27  Score=27.28  Aligned_cols=46  Identities=17%  Similarity=0.300  Sum_probs=38.6

Q ss_pred             HHHHHHH--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH-HHHHCCC
Q ss_conf             9999985--88988999999982999999999999999941-7986479
Q gi|254780305|r   37 VRIKQSL--NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAG-RLCHHPE   82 (95)
Q Consensus        37 ~~Il~~L--~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G-~i~~~pG   82 (95)
                      .+|+..|  +..+++.++|++..+++..+|...+-.|+-.| .|...+|
T Consensus         3 ~~il~~L~~~~~~vt~~~La~~l~VSr~TV~rdi~~L~~~G~~I~s~~g   51 (55)
T pfam08279         3 LQILELLLQAREPISGQELAEKLGVSRRTIRRDIKALEALGVPIESEPG   51 (55)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEECCC
T ss_conf             9999999976999189999999698899999999999988997884689


No 36 
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=92.22  E-value=0.2  Score=28.00  Aligned_cols=51  Identities=20%  Similarity=0.172  Sum_probs=43.8

Q ss_pred             CHHHHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             98999999985-8898899999998299999999999999994179864798
Q gi|254780305|r   33 QCERVRIKQSL-NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        33 ~~~~~~Il~~L-~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      +.-|+++|.+| ...+....+|++.+|+|.++|+.+|=-||=+|+|...+|.
T Consensus        15 t~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~   66 (247)
T COG1378          15 TEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGR   66 (247)
T ss_pred             CHHHHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHCCCEEECCCC
T ss_conf             7889999999998188779999986599932299999999878877840799


No 37 
>PRK00215 LexA repressor; Validated
Probab=92.17  E-value=0.34  Score=26.72  Aligned_cols=55  Identities=16%  Similarity=0.221  Sum_probs=44.5

Q ss_pred             CHHHHHHHHHHC------CCCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             989999999858------898899999998299-9999999999999941798647986898
Q gi|254780305|r   33 QCERVRIKQSLN------NVPIHIDDIIHHTGI-EAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        33 ~~~~~~Il~~L~------~~p~~iD~l~~~tgl-~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      +.-|++||+.+.      .-+=++.||++..|+ +.+.|+..|-.||=+|+|.|.+|.-=++
T Consensus         3 T~kQ~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~~Le~kG~i~r~~~~~R~i   64 (204)
T PRK00215          3 TARQQEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRSRAI   64 (204)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHCCCEECCCCCCCEE
T ss_conf             98999999999999997488998999999809998189999999998797887069997338


No 38 
>COG2512 Predicted membrane-associated trancriptional regulator    [Transcription]
Probab=92.17  E-value=0.21  Score=27.91  Aligned_cols=58  Identities=14%  Similarity=0.148  Sum_probs=47.5

Q ss_pred             CCCCCCCHHHHHHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             6887999899999998588--988999999982999999999999999941798647986
Q gi|254780305|r   27 HYPEYTQCERVRIKQSLNN--VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK   84 (95)
Q Consensus        27 ~~p~~~~~~~~~Il~~L~~--~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~   84 (95)
                      ....+...+++.|++.+-.  .-+.-.||.+.+|+|-++++.+|..||=+|.|++.--|+
T Consensus       188 ~~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~  247 (258)
T COG2512         188 VNEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGR  247 (258)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             335789978999999999858978699988860997677999999998689568887088


No 39 
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=92.07  E-value=0.29  Score=27.09  Aligned_cols=48  Identities=10%  Similarity=0.110  Sum_probs=42.7

Q ss_pred             CCHHHHHHHHHHC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9989999999858-89889999999829999999999999999417986
Q gi|254780305|r   32 TQCERVRIKQSLN-NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        32 ~~~~~~~Il~~L~-~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      ++..|.+||.+|. .+....++|+..+|++...|..++-.|+-+|.|.-
T Consensus         4 L~~~E~kIL~~L~~~~~~~~eeLa~~~g~d~~~V~~ai~~L~~kglI~v   52 (501)
T PRK04172          4 LHPNEKKVLKALAELKKATAEELAEKLGLDEEAVMRAAEWLEEKGLVEV   52 (501)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             7878999999997479999999998829999999999998875899799


No 40 
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=92.01  E-value=0.16  Score=28.43  Aligned_cols=60  Identities=13%  Similarity=0.097  Sum_probs=49.4

Q ss_pred             CCCCCCCCCCHHHHHHHHHHCC-C-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             4356887999899999998588-9-8899999998299999999999999994179864798
Q gi|254780305|r   24 NITHYPEYTQCERVRIKQSLNN-V-PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        24 ~~~~~p~~~~~~~~~Il~~L~~-~-p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      +....+-.....+-.+|..|.. . .++..+|++.++++.+.+..+|-.||=+|+|.|.+..
T Consensus        21 ~~~L~~~gLt~~q~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~LE~~GlI~R~~~~   82 (144)
T PRK03573         21 DHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCA   82 (144)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             99988669982599999999973989899999999798783699999999988897862286


No 41 
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=91.58  E-value=0.57  Score=25.50  Aligned_cols=61  Identities=23%  Similarity=0.276  Sum_probs=53.1

Q ss_pred             CCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE---EEEECCCC
Q ss_conf             99899999998588-988999999982999999999999999941798647986---89813799
Q gi|254780305|r   32 TQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK---VSLTMHLP   92 (95)
Q Consensus        32 ~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~---v~l~~~~~   92 (95)
                      .|+.+-+|+..|.. ++..+-+|+...|++-+.++-.|--|.-+|.|...--|+   |+|+-+.|
T Consensus        12 aD~tRl~Il~lL~~~gelcV~eL~~~l~~sQs~vS~HL~~L~~aGlV~~rr~G~~vyY~Ln~~~~   76 (106)
T PRK10141         12 SDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIP   76 (106)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEECCEEEEEEECCCCH
T ss_conf             88999999999987499569999988699888999999999988973037414179987799885


No 42 
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794    Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=90.59  E-value=0.51  Score=25.80  Aligned_cols=50  Identities=18%  Similarity=0.228  Sum_probs=44.5

Q ss_pred             HHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99998588--9889999999829999999999999999417986479868981
Q gi|254780305|r   38 RIKQSLNN--VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        38 ~Il~~L~~--~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      .|+++.|.  ...+|=|++++|||+-+.+-.+|+.|+--|.+ ..-|++|+|+
T Consensus        13 aVi~aF~~~~~~ltl~~vA~~TGL~RAaARR~LLTL~~LGY~-~~Dg~~F~LT   64 (252)
T TIGR02431        13 AVIEAFGEERPRLTLTDVAEATGLTRAAARRFLLTLVELGYV-ESDGRLFWLT   64 (252)
T ss_pred             HHHHHHCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCE-ECCCCCEECC
T ss_conf             999973103789898999987589947988899846562304-2179833102


No 43 
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=90.35  E-value=0.59  Score=25.45  Aligned_cols=53  Identities=17%  Similarity=0.102  Sum_probs=46.1

Q ss_pred             HHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             999998588-98899999998299999999999999994179864798689813
Q gi|254780305|r   37 VRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        37 ~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      ..|+..... ..+.+-+|++..|++.+.|+.++-.|+=+|.|..-+.|.+.|+.
T Consensus        11 e~Iy~L~~~~~~vr~~dIA~~L~Vs~~SVs~mikkL~~~Glv~~~~y~~i~LT~   64 (142)
T PRK03902         11 EQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTP   64 (142)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEECCCCCEEECH
T ss_conf             999999825897129999999789953399999999987992455898756898


No 44 
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=90.27  E-value=0.71  Score=24.99  Aligned_cols=47  Identities=28%  Similarity=0.287  Sum_probs=44.1

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             98999999985889889999999829999999999999999417986
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      ...+++|+..|...|.-+-+|.+..|++...|...|-.||=+|.|.+
T Consensus        14 NetRR~Il~lLt~~p~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS   60 (217)
T COG1777          14 NETRRRILQLLTRRPCYVSEISRELGVSQKAVLKHLRILERAGLVES   60 (217)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCHH
T ss_conf             71799999998547139998776608678999999999998587121


No 45 
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=89.77  E-value=0.82  Score=24.66  Aligned_cols=55  Identities=15%  Similarity=0.125  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             8999999985889889999999829999999999999999417986479868981
Q gi|254780305|r   34 CERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        34 ~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      .++..-+.+=++.-+.|++.++-.+++.+.+..++..||-+|++.|.--|+|.+-
T Consensus        17 ~e~l~~laae~hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeRi~rG~YlI~   71 (269)
T COG5340          17 SELLSHLAAEGHKIITIRDVAETLEVAPNTLRELASRLEKKGWLERILRGRYLII   71 (269)
T ss_pred             HHHHHHHHHHHCCEEEEHHHHHHCCCCHHHHHHHHHHHHHCCHHHHHCCCCEEEE
T ss_conf             9999999987476577177566315788899999865553424666518607986


No 46 
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=89.58  E-value=0.68  Score=25.10  Aligned_cols=46  Identities=15%  Similarity=0.191  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHCCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999985889-889999999829999999999999999417986
Q gi|254780305|r   34 CERVRIKQSLNNV-PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        34 ~~~~~Il~~L~~~-p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      .--.+|+++|..+ -.++.+|++..|++.++|..-+-.||=.|.|++
T Consensus         3 ~~D~~Il~~L~~n~R~s~~~iA~~lg~S~~tv~~Ri~~L~~~GiI~~   49 (108)
T smart00344        3 EIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG   49 (108)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCE
T ss_conf             89999999999828999999999989399999999999960897320


No 47 
>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=89.41  E-value=0.29  Score=27.11  Aligned_cols=50  Identities=18%  Similarity=0.233  Sum_probs=44.4

Q ss_pred             CCHHHH-HHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             998999-99998588-988999999982999999999999999941798647
Q gi|254780305|r   32 TQCERV-RIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP   81 (95)
Q Consensus        32 ~~~~~~-~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p   81 (95)
                      +-+|++ +|+..|.. +++...+|+..|.+=...+..+|..||=+|.|.|.-
T Consensus        25 ~lTEQQWRilR~L~~~G~~e~~~LA~~A~iL~PSLTgiL~rLE~~glv~R~k   76 (130)
T TIGR02337        25 GLTEQQWRILRVLAEKGSMEFTELADRACILRPSLTGILARLEKRGLVVRLK   76 (130)
T ss_pred             CCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHCCCEECCC
T ss_conf             7964789999988338994868788664147996578999997458702258


No 48 
>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=88.48  E-value=0.6  Score=25.39  Aligned_cols=44  Identities=20%  Similarity=0.281  Sum_probs=40.2

Q ss_pred             HHHHHHHCCCCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999998588988999999982-99999999999999994179864
Q gi|254780305|r   37 VRIKQSLNNVPIHIDDIIHHT-GIEAPVVYLVLLELDLAGRLCHH   80 (95)
Q Consensus        37 ~~Il~~L~~~p~~iD~l~~~t-gl~~~~v~~~LleLEL~G~i~~~   80 (95)
                      -.|+..|...+..+++|.+.. |++...++..|-+||-.|.|.+.
T Consensus         8 ~~Il~~L~~g~~rF~el~~~l~gis~~vLs~rLk~L~~~gli~r~   52 (90)
T pfam01638         8 LLILRELLDGPKRFSELKRALPGISQKMLTQRLRELEQDGIINRE   52 (90)
T ss_pred             HHHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             999999974998899999776576989999999999988993764


No 49 
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=87.42  E-value=0.63  Score=25.29  Aligned_cols=47  Identities=19%  Similarity=0.201  Sum_probs=42.4

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999985889889999999829-9999999999999994179864798
Q gi|254780305|r   37 VRIKQSLNNVPIHIDDIIHHTG-IEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        37 ~~Il~~L~~~p~~iD~l~~~tg-l~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      --|+..|...+..+++|-+..+ ++...++..|=+||-.|+|.|....
T Consensus        26 ~lIl~~L~~g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~~~   73 (120)
T COG1733          26 LLILRDLFDGPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERVVYP   73 (120)
T ss_pred             HHHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             999999954987399998677454899999999999988998987417


No 50 
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=87.40  E-value=1.1  Score=23.98  Aligned_cols=48  Identities=10%  Similarity=0.136  Sum_probs=41.8

Q ss_pred             CCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99899999998588-9889999999829999999999999999417986
Q gi|254780305|r   32 TQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        32 ~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      .|.--.+|+++|.. .-.+.-+|+++.|++.+.|..-+-.||=+|.|+.
T Consensus         7 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~stv~~Ri~rLe~~GvI~~   55 (153)
T PRK11179          7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG   55 (153)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             7899999999999848999999999989299999999999997996589


No 51 
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=87.28  E-value=0.87  Score=24.52  Aligned_cols=52  Identities=12%  Similarity=0.116  Sum_probs=46.0

Q ss_pred             CCHHHHHHHHHHCCCCCCH-HHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9989999999858898899-999998299999999999999994179864798
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHI-DDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~i-D~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      ....+-.++..+...+-.- -+|+.+.+++.+.++.++-.||=+|+|.|.++.
T Consensus        20 l~~~q~~~L~~l~~~~~~~~~~la~~l~~~~~~vt~~l~~Le~~glv~r~~~~   72 (126)
T COG1846          20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDP   72 (126)
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             99899999999998489999999999787888899999999988993674388


No 52 
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=87.22  E-value=2.4  Score=22.17  Aligned_cols=57  Identities=18%  Similarity=0.174  Sum_probs=44.9

Q ss_pred             CCHHHHHHHHHHC--CCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHHHHC-CCCEEEEE
Q ss_conf             9989999999858--8988999999982-----99999999999999994179864-79868981
Q gi|254780305|r   32 TQCERVRIKQSLN--NVPIHIDDIIHHT-----GIEAPVVYLVLLELDLAGRLCHH-PEGKVSLT   88 (95)
Q Consensus        32 ~~~~~~~Il~~L~--~~p~~iD~l~~~t-----gl~~~~v~~~LleLEL~G~i~~~-pGg~v~l~   88 (95)
                      ..+.+..||+.|.  ..|.+.++|..+.     +++.++|+.+|=-|.=.|+|.+. .+|.|.+.
T Consensus        24 ~T~qR~~VL~~l~~~~~~lsA~eI~~~l~~~~~~is~aTVYRtL~~L~e~Glv~ri~~~n~y~~~   88 (169)
T PRK11639         24 LTPQRLEVLRLMSLQDGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNSYVLC   88 (169)
T ss_pred             CCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEECCCCEEEE
T ss_conf             89899999999995799999999999999758998827799999999978958997058855772


No 53 
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=87.13  E-value=1.2  Score=23.77  Aligned_cols=50  Identities=16%  Similarity=0.149  Sum_probs=43.6

Q ss_pred             CCCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999899999998588-98899999998299999999999999994179864
Q gi|254780305|r   31 YTQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH   80 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~   80 (95)
                      .+|.-..+||+.|.. ..++.-+|+++.|++.++|...+-.||=.|.|.+.
T Consensus         5 ~lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~   55 (154)
T COG1522           5 KLDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGY   55 (154)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             537999999999997276579999999797989999999999988976999


No 54 
>PRK11050 manganese transport regulator MntR; Provisional
Probab=86.68  E-value=0.87  Score=24.53  Aligned_cols=53  Identities=25%  Similarity=0.196  Sum_probs=46.2

Q ss_pred             HHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             999998588-98899999998299999999999999994179864798689813
Q gi|254780305|r   37 VRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        37 ~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      ..|++.... +..-.-+|+++.|++.+.|+.++-.|+=+|+|...|-+.+.|+-
T Consensus        43 E~I~~L~~~~G~aR~~DIA~~LgVs~pSVt~mlkrL~~~GlV~~~~Y~~I~LT~   96 (155)
T PRK11050         43 ELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGVFLTP   96 (155)
T ss_pred             HHHHHHHHCCCCEEHHHHHHHHCCCCHHHHHHHHHHHHCCCEEECCCCCEEECH
T ss_conf             999999982695649999989099933199999999878998871898846897


No 55 
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=86.60  E-value=0.87  Score=24.53  Aligned_cols=56  Identities=21%  Similarity=0.171  Sum_probs=40.3

Q ss_pred             HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC--CCC--EEEEECCCCC
Q ss_conf             9999858898899999998299999999999999994179864--798--6898137998
Q gi|254780305|r   38 RIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH--PEG--KVSLTMHLPS   93 (95)
Q Consensus        38 ~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~--pGg--~v~l~~~~~~   93 (95)
                      ++|..-++.-+.--+|-+.+|++-++|+.+|-+||=.|.|.|-  .|.  +|.|+-.-|-
T Consensus        11 r~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~RrkvsGKs~rVwLaey~Py   70 (321)
T COG3888          11 RELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRKVSGKSKRVWLAEYSPY   70 (321)
T ss_pred             HHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEEECCCCEEEEECCCCCC
T ss_conf             999862877765878898857456479999999885680566550575338862003787


No 56 
>PRK09954 hypothetical protein; Provisional
Probab=86.56  E-value=2.3  Score=22.24  Aligned_cols=52  Identities=21%  Similarity=0.209  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             899999998588988-9999999829999999999999999417986479868981
Q gi|254780305|r   34 CERVRIKQSLNNVPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        34 ~~~~~Il~~L~~~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      .-|++||+.+..+|. +-.+|+++.|++.+.|...+..|-=||.|.   |.-|-|.
T Consensus         3 ~re~~il~~i~~~p~i~q~ela~~lgisrs~va~hi~~l~~kg~i~---G~gyi~~   55 (362)
T PRK09954          3 NREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIK---GKGYILT   55 (362)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEC---CCEEEEC
T ss_conf             6899999999878995899999997987999999999887547652---5468877


No 57 
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=86.39  E-value=0.98  Score=24.24  Aligned_cols=43  Identities=23%  Similarity=0.308  Sum_probs=38.6

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC--CEEEEEC
Q ss_conf             889999999829999999999999999417986479--8689813
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPE--GKVSLTM   89 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pG--g~v~l~~   89 (95)
                      ++++++|+++.+++..-+..++..|.=+|.|....|  |=|+|+-
T Consensus        25 ~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar   69 (150)
T COG1959          25 PVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLAR   69 (150)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCEECCC
T ss_conf             464999999989199999999999987798785207998920238


No 58 
>pfam09012 FeoC FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor.
Probab=86.27  E-value=0.94  Score=24.34  Aligned_cols=46  Identities=17%  Similarity=0.216  Sum_probs=38.4

Q ss_pred             HHHHHHC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9999858-898899999998299999999999999994179864798
Q gi|254780305|r   38 RIKQSLN-NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        38 ~Il~~L~-~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      +|-+.+. ...++..+|+++.+++.+.|-++|-.++-+|+|++.+.+
T Consensus         4 ~lr~~l~~~g~~s~~~Ls~~f~~~~~~v~~ML~~wi~kGkv~k~~~~   50 (68)
T pfam09012         4 ELKQYLQERGRASLAELARHFKMSPDAVEAMLEVWIRKGKVRKLEDG   50 (68)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             99999999198479999989793999999999999987975872489


No 59 
>pfam02082 Rrf2 Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).
Probab=86.11  E-value=0.94  Score=24.34  Aligned_cols=53  Identities=21%  Similarity=0.245  Sum_probs=41.2

Q ss_pred             HHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC--CCCEEEEECC
Q ss_conf             9999858----898899999998299999999999999994179864--7986898137
Q gi|254780305|r   38 RIKQSLN----NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH--PEGKVSLTMH   90 (95)
Q Consensus        38 ~Il~~L~----~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~--pGg~v~l~~~   90 (95)
                      +++-.|.    ..++++++|++.+++|..-+.-++..|--+|.|...  ++|=|.|+-.
T Consensus        11 ~~l~~La~~~~~~~~s~~~iA~~~~i~~~~l~kil~~L~~~gli~s~rG~~GGy~L~k~   69 (82)
T pfam02082        11 HALLYLALHPGEGPVTSEEIAERQNISPVYLRKILAKLRKAGLVKSVRGPGGGYRLARP   69 (82)
T ss_pred             HHHHHHHHCCCCCEECHHHHHHHHCCCHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCC
T ss_conf             99999981899984959999987890999999999981027982565899988113489


No 60 
>PTZ00326 phenylalanyl-tRNA synthetase; Provisional
Probab=86.01  E-value=1.6  Score=23.14  Aligned_cols=47  Identities=11%  Similarity=0.064  Sum_probs=41.3

Q ss_pred             CHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9899999998588-9889999999829999999999999999417986
Q gi|254780305|r   33 QCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        33 ~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      ..+...||.+|.. +.+.-+++++.+|++...|..++..||-+|.|.-
T Consensus         5 ~~~~~~iL~~L~~~~~~~s~ela~~~g~~~~~Vvgai~sLeskglV~v   52 (505)
T PTZ00326          5 EEELNTLLEALESAESVTSLAVAEDLSIDHQDVVGAIKSLEALNYIKT   52 (505)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             689999999998669999999999859699999999999986899799


No 61 
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism.  A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+.  For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.  
Probab=85.41  E-value=1.2  Score=23.75  Aligned_cols=55  Identities=24%  Similarity=0.316  Sum_probs=43.4

Q ss_pred             HHHHHHHHHCC--CCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHHHHCC--CC--EEEEEC
Q ss_conf             99999998588--988999999982-----999999999999999941798647--98--689813
Q gi|254780305|r   35 ERVRIKQSLNN--VPIHIDDIIHHT-----GIEAPVVYLVLLELDLAGRLCHHP--EG--KVSLTM   89 (95)
Q Consensus        35 ~~~~Il~~L~~--~p~~iD~l~~~t-----gl~~~~v~~~LleLEL~G~i~~~p--Gg--~v~l~~   89 (95)
                      .+..|++.|-.  .+.++++|....     +++.++|+.+|-.|+=.|+|.+..  ||  +|.+..
T Consensus         2 qR~~Il~~l~~~~~h~sa~eI~~~l~~~~~~i~~~TVYR~L~~l~~~gli~~~~~~~~~~~y~~~~   67 (116)
T cd07153           2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELNT   67 (116)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCEEEEEECC
T ss_conf             589999999837989899999999997589998889999999999689569998169805998449


No 62 
>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=85.26  E-value=1.1  Score=24.05  Aligned_cols=42  Identities=17%  Similarity=0.218  Sum_probs=37.5

Q ss_pred             CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             988-999999982999999999999999941798647986898
Q gi|254780305|r   46 VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        46 ~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      +.+ +..+|++..|++...|..++-.|+-.|+|...+|.=+.+
T Consensus        23 ~~LPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G~~V   65 (66)
T cd07377          23 DRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGRGTFV   65 (66)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEE
T ss_conf             9992799999997988899999999999889589973827887


No 63 
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=85.12  E-value=1.4  Score=23.35  Aligned_cols=49  Identities=12%  Similarity=0.051  Sum_probs=42.9

Q ss_pred             CCCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             999899999998588-9889999999829999999999999999417986
Q gi|254780305|r   31 YTQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      .+|.--.+|+++|.. .-++.-+|+++.|++.+.|..-+-.||=.|.|..
T Consensus        11 ~LD~~D~~IL~~Lq~daR~s~~eLA~~vglS~stv~~RikrLe~~GiI~g   60 (164)
T PRK11169         11 DLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG   60 (164)
T ss_pred             CHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             55199999999999848999999999989299999999999997898866


No 64 
>PRK09462 fur ferric uptake regulator; Provisional
Probab=84.97  E-value=2.6  Score=21.95  Aligned_cols=57  Identities=30%  Similarity=0.427  Sum_probs=44.9

Q ss_pred             CCHHHHHHHHHHCC---CCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHHHHC--CCCE--EEEE
Q ss_conf             99899999998588---988999999982-----99999999999999994179864--7986--8981
Q gi|254780305|r   32 TQCERVRIKQSLNN---VPIHIDDIIHHT-----GIEAPVVYLVLLELDLAGRLCHH--PEGK--VSLT   88 (95)
Q Consensus        32 ~~~~~~~Il~~L~~---~p~~iD~l~~~t-----gl~~~~v~~~LleLEL~G~i~~~--pGg~--v~l~   88 (95)
                      ....+..||+.|..   .+.++|+|.++.     .++.++|+.+|-.|+=.|.|.+.  +||.  |.++
T Consensus        15 ~T~qR~~Il~~L~~~~~~hlsaeeI~~~l~~~~~~is~aTVYRtL~~L~e~Glv~~~~~~~g~~~ye~~   83 (148)
T PRK09462         15 VTLPRLKILEVLQEPDNHHVSAEDLYKKLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFELT   83 (148)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEC
T ss_conf             599999999999817999999999999999758998666299999999868967999975995799816


No 65 
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=84.90  E-value=1.7  Score=22.89  Aligned_cols=53  Identities=26%  Similarity=0.263  Sum_probs=47.0

Q ss_pred             HHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9999985-8898899999998299999999999999994179864798689813
Q gi|254780305|r   37 VRIKQSL-NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        37 ~~Il~~L-~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      ..|+... +..++..-+|+...+++.+.|..++-.|+-.|.|...+-|.|.|+-
T Consensus        13 ~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~   66 (154)
T COG1321          13 ETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTE   66 (154)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEECCCCEEECC
T ss_conf             999999843687519999998589927899999999878997884588867883


No 66 
>pfam04157 EAP30 EAP30/Vps36 family. This family includes EAP30 as well as the Vps36 protein. Vps36 is involved in Golgi to endosome trafficking. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity.
Probab=84.72  E-value=1.7  Score=22.91  Aligned_cols=48  Identities=13%  Similarity=0.130  Sum_probs=42.3

Q ss_pred             CCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99899999998588-9889999999829999999999999999417986
Q gi|254780305|r   32 TQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        32 ~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      .+.++..|++.+.. ..+++.+++...||+.......|..+|-.|.+.+
T Consensus       170 ~~~~~~~il~~~~~~~~vt~~~l~~~l~ws~~~a~e~L~~~~~~G~l~~  218 (219)
T pfam04157       170 LSTDQTKILELAEELGGVTASELAEKLGWSIGRAKEVLEKAEKEGLLWR  218 (219)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             4689999999997279948999999979889999999999997499751


No 67 
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=84.17  E-value=0.97  Score=24.27  Aligned_cols=40  Identities=23%  Similarity=0.329  Sum_probs=36.9

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             9999998299999999999999994179864798689813
Q gi|254780305|r   50 IDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        50 iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      +-+|++..|++.+.|+.++=.|+-+|.|...+.|.|.|+-
T Consensus         2 ~~diA~~L~vs~~sVs~~l~~L~~~Gli~~~~y~~i~LT~   41 (96)
T smart00529        2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPYRGITLTE   41 (96)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHCCCEEECCCCCEEECH
T ss_conf             7889988499916799999999988898874998978898


No 68 
>pfam05584 Sulfolobus_pRN Sulfolobus plasmid regulatory protein. This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=84.05  E-value=2.8  Score=21.74  Aligned_cols=46  Identities=15%  Similarity=0.168  Sum_probs=42.1

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999999858898899999998299999999999999994179864
Q gi|254780305|r   35 ERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH   80 (95)
Q Consensus        35 ~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~   80 (95)
                      ..+.|+-.|+..-.++++|.+.|+.+-+.+...|..|-=.|.|.|-
T Consensus         6 ~~~~Il~~ls~~c~tLEeL~e~T~~~k~~llV~Ltrl~k~GiI~Rk   51 (72)
T pfam05584         6 LTELILIRLSGKCATLEELQEKTGADKNELLVTLTRLYKRGIIYRK   51 (72)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHH
T ss_conf             8999999997255779999998588825799999999877750556


No 69 
>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=83.66  E-value=1.5  Score=23.24  Aligned_cols=43  Identities=23%  Similarity=0.376  Sum_probs=37.2

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             8988999999982999999999999999941798647986898
Q gi|254780305|r   45 NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        45 ~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      .-|++-.+|+..+|++..+|+..|-.|+=.|+|....-+.+.+
T Consensus        23 ~l~ltr~eiA~~lG~t~eTVsR~l~~l~~~G~I~~~gr~~~ii   65 (67)
T cd00092          23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKYRV   65 (67)
T ss_pred             ECCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCEEEEE
T ss_conf             6177999999997890999999999999899489669868983


No 70 
>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=83.32  E-value=2.6  Score=22.00  Aligned_cols=43  Identities=19%  Similarity=0.193  Sum_probs=38.6

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9889999999829999999999999999417986479868981
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +.+...+|+++.|++...|-.+|..||-.|+|...||.-+.+.
T Consensus        33 ~~L~E~~La~~~gVSRtpvREAL~~L~~eGlv~~~~~~G~~V~   75 (212)
T TIGR03338        33 AKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGVFVR   75 (212)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCHHEECCCCEEEE
T ss_conf             9818999999889694999999999998696331167761551


No 71 
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=82.79  E-value=2  Score=22.60  Aligned_cols=44  Identities=5%  Similarity=-0.050  Sum_probs=40.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             98899999998299999999999999994179864798689813
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      +.+...+|+++.|++..-|-.+|..|+-.|.|...|+.-+.++.
T Consensus        29 ~~L~e~~Lae~lgVSRtPVREAL~rL~~eGLV~~~p~rG~~V~~   72 (224)
T PRK11534         29 EKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVAS   72 (224)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEEEE
T ss_conf             95589999999798858999999999987998874797369822


No 72 
>pfam01475 FUR Ferric uptake regulator family. This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.
Probab=82.75  E-value=2.4  Score=22.18  Aligned_cols=53  Identities=23%  Similarity=0.311  Sum_probs=42.9

Q ss_pred             CCHHHHHHHHHHCC--CCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHHHHC--CCCE
Q ss_conf             99899999998588--988999999982-----99999999999999994179864--7986
Q gi|254780305|r   32 TQCERVRIKQSLNN--VPIHIDDIIHHT-----GIEAPVVYLVLLELDLAGRLCHH--PEGK   84 (95)
Q Consensus        32 ~~~~~~~Il~~L~~--~p~~iD~l~~~t-----gl~~~~v~~~LleLEL~G~i~~~--pGg~   84 (95)
                      ..+.+..|++.|-.  .|.++++|..+.     .++.++|+..|-.|+=.|+|.+.  .+|.
T Consensus         6 ~T~qR~~Il~~l~~~~~~~ta~~i~~~l~~~~~~i~~~TVYR~L~~L~~~gli~~~~~~~~~   67 (120)
T pfam01475         6 ITPQRLKILEVLEKSDEHLSAEEIYRELLEEDPNISLATVYRTLKLLEEAGIVKRLNFEGGE   67 (120)
T ss_pred             CCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCE
T ss_conf             88899999999982799989999999999658998789999999999967946999847997


No 73 
>pfam04703 FaeA FaeA-like protein. This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase.
Probab=82.15  E-value=1.9  Score=22.75  Aligned_cols=48  Identities=21%  Similarity=0.301  Sum_probs=41.9

Q ss_pred             HHHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             999998588--988999999982999999999999999941798647986
Q gi|254780305|r   37 VRIKQSLNN--VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK   84 (95)
Q Consensus        37 ~~Il~~L~~--~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~   84 (95)
                      ..|+..++.  .|..--+|+...|+++=++-.-|+.||=.|+|+|.|-++
T Consensus         3 ~~Il~~i~~i~~p~~T~eIAda~gls~YQaR~YL~~Lek~g~i~rsp~rr   52 (61)
T pfam04703         3 ESILTFINSIGAPCKTREIADALGLSAYQARYYLEQLEKEGKIERSPLRR   52 (61)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCEECCCCCC
T ss_conf             28999998748984188999985507999999999998707523055346


No 74 
>pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.).
Probab=81.64  E-value=4.3  Score=20.76  Aligned_cols=51  Identities=18%  Similarity=0.130  Sum_probs=42.7

Q ss_pred             CCHHHHHHHHHH------CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             998999999985------889889999999829999999999999999417986479
Q gi|254780305|r   32 TQCERVRIKQSL------NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPE   82 (95)
Q Consensus        32 ~~~~~~~Il~~L------~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pG   82 (95)
                      ++.-+++||.+|      ...|+.=.+|+...+++.++|--.+..||--|.|...||
T Consensus         2 LT~~Qr~IL~aLI~lY~~~~~pVks~~IAe~l~~spgTIRN~M~~L~~LGLVe~~pg   58 (79)
T pfam03444         2 LTPVQKEILQALINLYRKKGRAVKGEEIADIIGRNPGTVRNQMQSLKALGLVEGVPG   58 (79)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             778999999999999997299866799999987890889999999998588657889


No 75 
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator); InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators..
Probab=81.31  E-value=2.4  Score=22.18  Aligned_cols=46  Identities=24%  Similarity=0.313  Sum_probs=39.4

Q ss_pred             CCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC--CCEEEEEC
Q ss_conf             889-88999999982999999999999999941798647--98689813
Q gi|254780305|r   44 NNV-PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP--EGKVSLTM   89 (95)
Q Consensus        44 ~~~-p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p--Gg~v~l~~   89 (95)
                      ..+ ++++++|+++.++|.+=+.-+|-.|-=+|.|....  ||=|+|+.
T Consensus        21 ~~~~~v~~~~ia~~~~Is~~yL~K~l~~L~~~GlV~S~rG~~GGY~L~~   69 (133)
T TIGR00738        21 ADEGPVSVKEIAERQGISRSYLEKVLRTLRKAGLVESVRGPGGGYRLAR   69 (133)
T ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCC
T ss_conf             6887607899998848998799999998877076421158985631077


No 76 
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=81.16  E-value=1  Score=24.13  Aligned_cols=50  Identities=18%  Similarity=0.140  Sum_probs=41.1

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999998588-9889999999829999999999999999417986479868981
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +.+|++.|.. .-+.+.+|++..+.+..++-.-|-+++-.|++   -||++.+.
T Consensus         9 ~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRDL~~~~~~~~~---~gG~~~~~   59 (252)
T PRK10681          9 IGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAESAPVVL---LGGYIVLE   59 (252)
T ss_pred             HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHCHHHHHCCCEE---EEEEEECC
T ss_conf             9999999998697999999988797998998788865279889---63488727


No 77 
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=81.11  E-value=1.7  Score=22.99  Aligned_cols=41  Identities=20%  Similarity=0.398  Sum_probs=34.8

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             988999999982999999999999999941798647986898
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      -|++-.+|+..+|.+...|+.+|-+|+=+|+|.... +++.+
T Consensus         7 l~lt~~~iA~~lG~tretvsR~l~~l~~~GlI~~~~-~~i~i   47 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG-GRIVI   47 (48)
T ss_pred             ECCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC-CEEEE
T ss_conf             337999999997997999999999999889799789-78997


No 78 
>PRK10870 transcriptional repressor MprA; Provisional
Probab=77.96  E-value=2.4  Score=22.16  Aligned_cols=61  Identities=13%  Similarity=0.035  Sum_probs=48.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHHC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             435688799989999999858---8988999999982999999999999999941798647986
Q gi|254780305|r   24 NITHYPEYTQCERVRIKQSLN---NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK   84 (95)
Q Consensus        24 ~~~~~p~~~~~~~~~Il~~L~---~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~   84 (95)
                      +....+...+..+=.||..|.   +.+...-+|+.+.+.+.+.+..++=.||-+|+|.|.+..-
T Consensus        45 n~~L~~~GLs~~~f~vL~~L~~~~~~~l~PseLa~~l~~s~a~iTr~vD~LEkkGlV~R~~s~~  108 (176)
T PRK10870         45 NKMLKAQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDN  108 (176)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf             9899882998889999999971899985989999997787101999999999889978723712


No 79 
>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=77.95  E-value=1.8  Score=22.79  Aligned_cols=40  Identities=15%  Similarity=0.196  Sum_probs=35.7

Q ss_pred             CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             988-9999999829999999999999999417986479868
Q gi|254780305|r   46 VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKV   85 (95)
Q Consensus        46 ~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v   85 (95)
                      +.+ +..+|++..+.+.++|..++-+|+-.|+|...+|.=+
T Consensus        22 ~~LPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G~   62 (64)
T pfam00392        22 DKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRPGRGT   62 (64)
T ss_pred             CCCHHHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEE
T ss_conf             99847999999979699999999999998893899779536


No 80 
>PRK11414 putative DNA-binding transcriptional regulator; Provisional
Probab=77.24  E-value=3.7  Score=21.15  Aligned_cols=44  Identities=16%  Similarity=0.200  Sum_probs=40.7

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             98899999998299999999999999994179864798689813
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      +.+...+|+++.|++..-|-.+|..|+-.|.|...|+.-+.++.
T Consensus        33 ~~L~e~~La~~lgVSRtPVREAL~rL~~eGLv~~~p~rG~~V~~   76 (221)
T PRK11414         33 ARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPE   76 (221)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCEEEEC
T ss_conf             97189999999799906899999999988895650487337507


No 81 
>cd03448 HDE_HSD HDE_HSD  The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins.  Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit.
Probab=76.15  E-value=3.9  Score=20.98  Aligned_cols=59  Identities=14%  Similarity=0.138  Sum_probs=35.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHCC-CCCCHH-HHHHHHCCCHHHHHHHHH-HHHHHHHHHHCCC
Q ss_conf             4356887999899999998588-988999-999982999999999999-9999417986479
Q gi|254780305|r   24 NITHYPEYTQCERVRIKQSLNN-VPIHID-DIIHHTGIEAPVVYLVLL-ELDLAGRLCHHPE   82 (95)
Q Consensus        24 ~~~~~p~~~~~~~~~Il~~L~~-~p~~iD-~l~~~tgl~~~~v~~~Ll-eLEL~G~i~~~pG   82 (95)
                      ++.....+..+++.-++..-|+ .|+|+| +.++.+|++-..+..+++ -+=....+....+
T Consensus         5 pd~~~~~~t~~~~~l~yrlSGD~NPiH~D~~~A~~agf~~~I~HGm~t~g~~~~av~~~~~~   66 (122)
T cd03448           5 PDAVVEIPTSPDQALLYRLSGDYNPLHIDPAFAKAAGFPRPILHGLCTYGFAARAVLEAFAD   66 (122)
T ss_pred             CCEEEECCCCHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCEEHHHHHHHHHHHHHHHHHCC
T ss_conf             98789404876499999985799843179999997399985413667999999999986758


No 82 
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=75.83  E-value=3.3  Score=21.37  Aligned_cols=46  Identities=22%  Similarity=0.301  Sum_probs=39.4

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC--CCCEEEEECC
Q ss_conf             898899999998299999999999999994179864--7986898137
Q gi|254780305|r   45 NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH--PEGKVSLTMH   90 (95)
Q Consensus        45 ~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~--pGg~v~l~~~   90 (95)
                      ..|+++.+|+++.++|..-+.-+|..|--+|.|...  ++|=|+|+..
T Consensus        23 ~~~vsi~eIAe~~~Is~~~LekIl~~L~kaGlV~S~RG~~GGY~Lar~   70 (164)
T PRK10857         23 AGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKD   70 (164)
T ss_pred             CCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCCEECCCCCCCCCCCCC
T ss_conf             980949999988791999999999999867850632688888033699


No 83 
>PRK11642 exoribonuclease R; Provisional
Probab=75.58  E-value=3.1  Score=21.51  Aligned_cols=56  Identities=18%  Similarity=0.174  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHCC--CCCCHHHHHHHHCCC----HHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             899999998588--988999999982999----99999999999994179864798689813
Q gi|254780305|r   34 CERVRIKQSLNN--VPIHIDDIIHHTGIE----APVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        34 ~~~~~Il~~L~~--~p~~iD~l~~~tgl~----~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      +.+..||+.|..  .|++..+|++..++.    ...+...|-+||=.|.|.+.-.|.|.+..
T Consensus        19 psre~il~~l~~~~~p~~~~el~~~~~l~~~~~~~~L~~~L~~l~~~g~l~~~r~~~y~~~~   80 (813)
T PRK11642         19 PSREFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPE   80 (813)
T ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCEEECCCCCCCCCC
T ss_conf             99999999999688989999999981999889999999999999968977874897236777


No 84 
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=74.97  E-value=3.2  Score=21.45  Aligned_cols=46  Identities=15%  Similarity=0.204  Sum_probs=39.4

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC--CCCEEEEECC
Q ss_conf             898899999998299999999999999994179864--7986898137
Q gi|254780305|r   45 NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH--PEGKVSLTMH   90 (95)
Q Consensus        45 ~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~--pGg~v~l~~~   90 (95)
                      .+++++.+|+++.++|.+-+.-++-.|-=+|+|...  ++|=|+|+.-
T Consensus        23 ~~~~~~~eIae~~~Ip~~~L~KIl~~L~~aGlv~S~RG~~GGy~Lar~   70 (141)
T PRK11014         23 GRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKP   70 (141)
T ss_pred             CCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCEECCCC
T ss_conf             984749999998794999999999999887956720479988321489


No 85 
>pfam02295 z-alpha Adenosine deaminase z-alpha domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.
Probab=74.71  E-value=4.8  Score=20.51  Aligned_cols=50  Identities=22%  Similarity=0.272  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHCC-CCCCHHHHHHHHCC--CHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             899999998588-98899999998299--999999999999994179864798
Q gi|254780305|r   34 CERVRIKQSLNN-VPIHIDDIIHHTGI--EAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        34 ~~~~~Il~~L~~-~p~~iD~l~~~tgl--~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      ..+++|++.|-. .....-.++..-||  +..+|..+|..||=+|.|.+..|.
T Consensus         4 ~~eekil~~L~~~g~~ta~~~ak~~gL~~~k~evN~~Ly~L~~~g~v~~~~~~   56 (66)
T pfam02295         4 ELEEKILEFLRNSGGKTATAIALARGLSKEKKEINRILYDLERKGELCKEDGT   56 (66)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEECCCC
T ss_conf             88999999999647505999999852287588999999999977894107998


No 86 
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=74.48  E-value=6.3  Score=19.87  Aligned_cols=48  Identities=19%  Similarity=0.124  Sum_probs=42.8

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             889889999999829999999999999999417986479868981379
Q gi|254780305|r   44 NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTMHL   91 (95)
Q Consensus        44 ~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~~~   91 (95)
                      ...+.+.+++.++.+++..++..+|-.||=.|.|.|.-+|.+.|+-.+
T Consensus       306 ~g~~~~~~~l~~~~~~~~~~~~~~l~~L~~~~~v~~~~~~~~vl~rd~  353 (411)
T PRK04214        306 HGKGLDEDEIRRLEPMGYDELGELLCELARIGYLRRGERGQWVLARDA  353 (411)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEECCCCCEEEECCH
T ss_conf             589999999997728986899999999997898166688976884387


No 87 
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=74.41  E-value=4.1  Score=20.90  Aligned_cols=45  Identities=13%  Similarity=0.177  Sum_probs=40.6

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             898899999998299999999999999994179864798689813
Q gi|254780305|r   45 NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        45 ~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      .+.+..++|++..|++..-|-.+|..|+=.|.|...|+.-..++.
T Consensus        37 G~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~V~~   81 (230)
T COG1802          37 GERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAFVAP   81 (230)
T ss_pred             CCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCEEECC
T ss_conf             298179999999888907999999999889794777998326628


No 88 
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=74.04  E-value=2.7  Score=21.86  Aligned_cols=40  Identities=15%  Similarity=0.228  Sum_probs=35.4

Q ss_pred             CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             988-9999999829999999999999999417986479868
Q gi|254780305|r   46 VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKV   85 (95)
Q Consensus        46 ~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v   85 (95)
                      +.+ ++.+|++.-+.+...|..++-+|+-.|+|.+.+|.=+
T Consensus        18 ~~LPs~~~la~~~~vSr~tvr~A~~~L~~~G~i~~~~g~G~   58 (60)
T smart00345       18 DKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGSGT   58 (60)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEE
T ss_conf             98810999999989499999999999998897899668546


No 89 
>pfam12324 HTH_15 Helix-turn-helix domain of alkylmercury lyase. Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This is the N terminal helix-turn-helix domain associated with pfam03243.
Probab=73.69  E-value=7.6  Score=19.45  Aligned_cols=43  Identities=21%  Similarity=0.203  Sum_probs=34.4

Q ss_pred             CCCCCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             87999899999998588-98899999998299999999999999
Q gi|254780305|r   29 PEYTQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLEL   71 (95)
Q Consensus        29 p~~~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleL   71 (95)
                      |...-.-...+|..|.. .|+++..|+..+|++..+|..+|-.+
T Consensus        19 p~~~~~l~~~LLr~La~G~PVt~~~LA~a~g~~~e~V~~~L~~~   62 (77)
T pfam12324        19 PKSMAWLFRPLLRMLADGRPVTREDLAGATGKPVERVAKVLAQA   62 (77)
T ss_pred             CCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             64208999999999947998689999989698999999999858


No 90 
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=73.51  E-value=3  Score=21.65  Aligned_cols=45  Identities=29%  Similarity=0.273  Sum_probs=40.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             8999999982999999999999999941798647986898137998
Q gi|254780305|r   48 IHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTMHLPS   93 (95)
Q Consensus        48 ~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~~~~~   93 (95)
                      .-.|-|.++|+++.+.++.+|.+|---|.|.-.-|..+++. ++|.
T Consensus       161 ~v~~yI~~rT~lSRS~im~vls~Lk~ggyI~i~~G~L~~i~-~LP~  205 (207)
T PRK11832        161 GVMNYIHQRTRISRSVVAEVLAALRKGGYIEMNKGKLVAIN-RLPS  205 (207)
T ss_pred             CHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEEECCEEEECC-CCCC
T ss_conf             59999998744209999999999844997898637897714-5776


No 91 
>pfam05331 DUF742 Protein of unknown function (DUF742). This family consists of several uncharacterized Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=72.46  E-value=2.7  Score=21.90  Aligned_cols=52  Identities=27%  Similarity=0.305  Sum_probs=44.7

Q ss_pred             CCCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             87999899999998588988999999982999999999999999941798647
Q gi|254780305|r   29 PEYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP   81 (95)
Q Consensus        29 p~~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p   81 (95)
                      +....+|+++|++.- ..|.++=||+.+.++|.+.+-..+-.|-=.|.|...+
T Consensus        38 ~~~l~pE~~~Il~lC-~~p~SVAEiAA~L~LPl~VvrVLl~DL~~~G~v~v~~   89 (114)
T pfam05331        38 PPTLQPEHRRILRLC-RAPLSVAEIAARLDLPVGVVRVLLSDLLDAGLLTVRA   89 (114)
T ss_pred             CCCCCHHHHHHHHHH-CCCCCHHHHHHHHCCCCEEEEEEHHHHHHCCCEEECC
T ss_conf             888897999999995-5852099999731898402301587687589768508


No 92 
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=72.42  E-value=4.6  Score=20.63  Aligned_cols=46  Identities=15%  Similarity=0.165  Sum_probs=37.8

Q ss_pred             HCC-CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             588-988-9999999829999999999999999417986479868981
Q gi|254780305|r   43 LNN-VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        43 L~~-~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      |.+ +.+ .--+|+++.|++-..|-.+|-.||-.|+|...+|+-+.+.
T Consensus        27 l~PGdrLP~EreLAe~lgVSRt~VREAL~~Le~~GLV~~r~G~Gt~V~   74 (257)
T PRK10225         27 YNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYVL   74 (257)
T ss_pred             CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEEEE
T ss_conf             999793952999999979887899999999998899799648877882


No 93 
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=71.71  E-value=6.6  Score=19.78  Aligned_cols=43  Identities=14%  Similarity=0.159  Sum_probs=36.9

Q ss_pred             CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             988-9999999829999999999999999417986479868981
Q gi|254780305|r   46 VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        46 ~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +.+ +-.+|++..|++-+.|-.+|-.|+-.|+|...+|+-..+.
T Consensus        24 ~~LP~E~eLae~~GVSRt~VREAL~~L~~eGlV~~~~g~G~~V~   67 (253)
T PRK10421         24 MKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIR   67 (253)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEEEC
T ss_conf             95933999999979698999999999998898799757824873


No 94 
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=71.70  E-value=8.1  Score=19.30  Aligned_cols=63  Identities=22%  Similarity=0.206  Sum_probs=49.6

Q ss_pred             CCCCCCCHHHHHHHHHHCCC----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             68879998999999985889----8899999998299999999999999994179864798689813
Q gi|254780305|r   27 HYPEYTQCERVRIKQSLNNV----PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        27 ~~p~~~~~~~~~Il~~L~~~----p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      ...+-....+..++-.+-..    -.-|.+++.+.|..-.++.-.|-.||-+|+|.-+|.+.|.|+-
T Consensus       418 kRkP~LT~~e~kvl~kiP~~~ikrg~liedi~~~~g~~eeev~~sl~kleskgfveeL~n~gv~LTe  484 (593)
T COG1542         418 KRKPYLTKYEIKVLIKIPRKYIKRGELIEDIQGHVGGDEEEVIKSLGKLESKGFVEELPNKGVKLTE  484 (593)
T ss_pred             HCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHHCCCCEEEEH
T ss_conf             4076643047789986464333120599998754073189999988877643669885667678614


No 95 
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=71.30  E-value=4.8  Score=20.55  Aligned_cols=46  Identities=11%  Similarity=0.116  Sum_probs=38.1

Q ss_pred             CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             988-9999999829999999999999999417986479868981379
Q gi|254780305|r   46 VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTMHL   91 (95)
Q Consensus        46 ~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~~~   91 (95)
                      +-+ +--+|+...|++-..|-.+|-.||-.|+|...+|.-..+....
T Consensus        30 drLPsEreLAe~fGVSRt~VREAL~~Le~~GlVe~r~G~Gt~V~~~~   76 (258)
T PRK11523         30 DKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQ   76 (258)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEEECCCC
T ss_conf             90966999999979887999999999998899899637815874588


No 96 
>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=71.21  E-value=5.3  Score=20.29  Aligned_cols=45  Identities=16%  Similarity=0.200  Sum_probs=37.9

Q ss_pred             HHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999998588-988999999982999999999999999941798647
Q gi|254780305|r   37 VRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP   81 (95)
Q Consensus        37 ~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p   81 (95)
                      ..|+..-.. .++.+-+|+++.|.+.+.|..++-.|+=+|+|...|
T Consensus         9 k~Iy~l~~~~~~v~~~~iA~~L~Vs~~SVt~mlkkL~~~GlV~~e~   54 (58)
T pfam01325         9 ETIYTLSEEKGVVKTKDLAERLNVSPSTVSEMLKKLEKDGYVVYEP   54 (58)
T ss_pred             HHHHHHHCCCCCEEHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEEC
T ss_conf             9999988269961299999995999252999999999889978532


No 97 
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=70.51  E-value=6.8  Score=19.71  Aligned_cols=41  Identities=15%  Similarity=0.194  Sum_probs=36.3

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             889999999829999999999999999417986479868981
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      |++-.+|+...|++..+|+.+|-+|+=+|+|. .-|+++.+.
T Consensus       184 ~lt~~dLA~~lG~trEtVsR~L~~L~~~GlI~-~~~~~I~I~  224 (235)
T PRK11161        184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLA-VKGKYITIE  224 (235)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-ECCCEEEEC
T ss_conf             37899999887898999999999999789799-739999987


No 98 
>pfam10007 DUF2250 Uncharacterized protein conserved in archaea (DUF2250). Members of this family of hypothetical archaeal proteins have no known function.
Probab=70.44  E-value=5.4  Score=20.27  Aligned_cols=55  Identities=18%  Similarity=0.069  Sum_probs=45.3

Q ss_pred             CCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             99899999998588-98899999998299999999999999994179864798689
Q gi|254780305|r   32 TQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVS   86 (95)
Q Consensus        32 ~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~   86 (95)
                      .+...-.|+..+.. .+=.--.|+..+++|..+|...|-.||=.|.|++.-|..+.
T Consensus         6 ~d~~~l~IL~hl~~a~~DYak~ia~~t~ipleev~~~l~~L~~~GLlEr~~g~~iK   61 (93)
T pfam10007         6 DDPLMLTILKHLKKANVDYAKSIAKNTKIPLEEVRDLLDKLEEMGLLERVTGSTIK   61 (93)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEHHHHHHH
T ss_conf             08888999999998487499999998189899999999999987680010014776


No 99 
>PRK03837 transcriptional regulator NanR; Provisional
Probab=69.75  E-value=5.9  Score=20.04  Aligned_cols=45  Identities=13%  Similarity=0.188  Sum_probs=36.4

Q ss_pred             HCC-CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             588-988-999999982999999999999999941798647986898
Q gi|254780305|r   43 LNN-VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        43 L~~-~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      +.+ +.+ ...+|+++.|++...|-.+|..||-.|+|...+|....+
T Consensus        32 l~pG~rLp~E~eLae~lgVSRtpVREAL~~L~~~GlV~~~~g~g~~V   78 (243)
T PRK03837         32 FGPGEQLPSERELMAFFGVGRPSVREALQALKRKGLVQISHGERARV   78 (243)
T ss_pred             CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCEE
T ss_conf             99949793599999997969789999999999889989950897068


No 100
>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=68.58  E-value=4.9  Score=20.46  Aligned_cols=40  Identities=10%  Similarity=0.063  Sum_probs=35.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999999829999999999999999417986479868981
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +..+|+++-|.+..+|..+|-+|+-.|.|.+..|.=..++
T Consensus        27 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~GTfV~   66 (231)
T TIGR03337        27 SERDLGERFNTTRVTIREALQQLEAEGLIYREDRRGWFVS   66 (231)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEEC
T ss_conf             8999999979799999999999998799699668667988


No 101
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=67.61  E-value=10  Score=18.71  Aligned_cols=42  Identities=14%  Similarity=0.179  Sum_probs=35.6

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             98899999998299999999999999994179864798689813
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      -|.+-.+|+...|.+...|+.+|-+|+=+| |. .-|+++.+..
T Consensus       172 l~~t~~~lA~~lG~tretvsR~L~~L~~~G-I~-~~~~~I~I~D  213 (236)
T PRK09392        172 LPYEKRTLASYLGMTPENLSRAFAALASHG-VH-VQGSAVTITD  213 (236)
T ss_pred             ECCCHHHHHHHHCCCHHHHHHHHHHHHHCC-CE-EECCEEEECC
T ss_conf             347899999987898999999999999799-68-9699999988


No 102
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=67.42  E-value=7.4  Score=19.50  Aligned_cols=51  Identities=18%  Similarity=0.172  Sum_probs=41.4

Q ss_pred             CCHHHHHHHHHHCC--CCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99899999998588--9889999999829-----999999999999999417986479
Q gi|254780305|r   32 TQCERVRIKQSLNN--VPIHIDDIIHHTG-----IEAPVVYLVLLELDLAGRLCHHPE   82 (95)
Q Consensus        32 ~~~~~~~Il~~L~~--~p~~iD~l~~~tg-----l~~~~v~~~LleLEL~G~i~~~pG   82 (95)
                      ....|..|++.|..  ++.+.++|-....     ++.++|+.+|-.|+=.|+|.++--
T Consensus        19 ~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~   76 (145)
T COG0735          19 LTPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEF   76 (145)
T ss_pred             CCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             6888999999999668999999999999974899988799999999998898799973


No 103
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=67.11  E-value=6.1  Score=19.96  Aligned_cols=31  Identities=23%  Similarity=0.329  Sum_probs=27.6

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf             8899999998299999999999999994179
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVLLELDLAGRL   77 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i   77 (95)
                      |++--+|+.-+|+.+..|+.+|..|+=+|.|
T Consensus         2 pmsrqdIadylGlt~ETVsR~l~~L~~~glI   32 (32)
T pfam00325         2 PMSRQEIADYLGLTRETVSRLLKRLREKGLI   32 (32)
T ss_pred             CCCHHHHHHHHCCHHHHHHHHHHHHHHCCCC
T ss_conf             8658899998472599999999999985789


No 104
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=66.97  E-value=9.5  Score=18.91  Aligned_cols=38  Identities=8%  Similarity=0.158  Sum_probs=32.4

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             99999998588988999999982999999999999999
Q gi|254780305|r   35 ERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELD   72 (95)
Q Consensus        35 ~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLE   72 (95)
                      =+.+|++.|..+|++-|+|+++.|.+.-+|..-+-++.
T Consensus         5 Rq~~il~lL~~~~lt~~eLA~~L~VS~RTIR~DI~~iN   42 (585)
T PRK09863          5 RELKIVDLLEQQDRSGGELAQQLGVSRRTIVRDIAYIN   42 (585)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             99999999975999989999874997117899999999


No 105
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=66.74  E-value=10  Score=18.71  Aligned_cols=42  Identities=24%  Similarity=0.183  Sum_probs=36.6

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             8899999998299999999999999994179864798689813
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      +++-++|+..+|.+..+|+.+|-+|+=.|+|. .-+|++.+..
T Consensus       145 ~lT~~eLA~~iGttREtVsR~L~~l~~~GlI~-~~~~~I~I~D  186 (201)
T PRK13918        145 YATHDELAAAVGSVRETVTKVVGELSREGVIR-SGYGKIQLLD  186 (201)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-ECCCEEEEEC
T ss_conf             57999999885986899999999999889889-6799899928


No 106
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=66.42  E-value=10  Score=18.77  Aligned_cols=41  Identities=17%  Similarity=0.122  Sum_probs=35.2

Q ss_pred             HHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             999985-88988999999982999999999999999941798
Q gi|254780305|r   38 RIKQSL-NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLC   78 (95)
Q Consensus        38 ~Il~~L-~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~   78 (95)
                      -|+++| .+.-++-|+|+..+|+...+|..+|..|.-.+.|.
T Consensus         5 ~Vid~L~~~~~v~dedLa~~l~~~~n~vRkiL~~L~e~~lv~   46 (147)
T smart00531        5 LVLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIK   46 (147)
T ss_pred             EHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf             622988865970799999997999999999999999779646


No 107
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=66.09  E-value=5  Score=20.45  Aligned_cols=52  Identities=13%  Similarity=0.199  Sum_probs=39.9

Q ss_pred             HHHHHH-HCC-CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             999998-588-988-9999999829999999999999999417986479868981
Q gi|254780305|r   37 VRIKQS-LNN-VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        37 ~~Il~~-L~~-~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      ..|+.. |.+ +.+ +-.+|++..|++-..|-.+|-.||-.|+|...+|+-+.+.
T Consensus        21 ~~I~~G~l~pGd~LPsE~eLA~~lgVSR~~VREAL~~L~~~GlV~~r~g~G~~V~   75 (254)
T PRK09464         21 FLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQ   75 (254)
T ss_pred             HHHHCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEECCCCEEEC
T ss_conf             9998499999396936999999868995599999999998899897178713646


No 108
>pfam02002 TFIIE_alpha TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits.
Probab=66.05  E-value=11  Score=18.52  Aligned_cols=46  Identities=20%  Similarity=0.137  Sum_probs=39.5

Q ss_pred             HHHHHHHHHH-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999985-889889999999829999999999999999417986
Q gi|254780305|r   34 CERVRIKQSL-NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        34 ~~~~~Il~~L-~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      .+.-.|+++| ...-+.-|+|+..+|+...+|..+|..|.=.|.|..
T Consensus        13 ~e~v~vid~L~~~~~v~dedLa~~l~~~~n~vRkiL~~L~e~~lv~~   59 (105)
T pfam02002        13 DEAVLVLDALLRKGEVTEEDLAELLGIDLNELRKLLYRLYDARLVKY   59 (105)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             23899999997168838999999978988899999999987886588


No 109
>pfam05158 RNA_pol_Rpc34 RNA polymerase Rpc34 subunit. Subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of yeast RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and is therefore participates in Pol III recruitment.
Probab=65.98  E-value=8.1  Score=19.28  Aligned_cols=70  Identities=16%  Similarity=0.043  Sum_probs=52.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC-----CC-EEEEECCCCC
Q ss_conf             435688799989999999858---8988999999982999999999999999941798647-----98-6898137998
Q gi|254780305|r   24 NITHYPEYTQCERVRIKQSLN---NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP-----EG-KVSLTMHLPS   93 (95)
Q Consensus        24 ~~~~~p~~~~~~~~~Il~~L~---~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p-----Gg-~v~l~~~~~~   93 (95)
                      ..+.....++.++.-||..+.   ..-+-.-+|..+|+|+...+..+|-.||-++.|+...     .. +|.|....|+
T Consensus        73 e~a~k~~~l~~eE~lVY~~Ie~ag~~GIW~k~i~~~tnL~~~~l~K~LK~LEsk~lIKsVksV~~~~rKvYmL~~LePS  151 (313)
T pfam05158        73 EEAKKKATLSDEESLVYSIIEESGNEGIWTRTIKNRTNLHQSVLKKCLKSLESKKYIKSVKSVKAPTRKMYMLYNLEPS  151 (313)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHCCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEEECCCCC
T ss_conf             9987652898889999999986276774499999880998899999999997568615421456787059998347747


No 110
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=65.96  E-value=9.2  Score=18.99  Aligned_cols=43  Identities=21%  Similarity=0.265  Sum_probs=36.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9889999999829999999999999999417986479868981
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      -|.+-.+|+...|++...|+.+|-+|+=.|+|....+..+.+.
T Consensus       172 l~lT~~dLA~~lG~trETVsR~L~~L~~eGlI~~~g~R~I~I~  214 (224)
T PRK09391        172 LPMSRRDIADYLGLTIETVSRALSQLKDRGVIGLSGARQIELR  214 (224)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCEEEEC
T ss_conf             1579999998879979999999999998898996589769988


No 111
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=65.25  E-value=12  Score=18.43  Aligned_cols=40  Identities=10%  Similarity=-0.041  Sum_probs=33.9

Q ss_pred             CCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             7999899999998588988999999982999999999999
Q gi|254780305|r   30 EYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        30 ~~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      ..+++++++|+...-.+..+..||++..|++.++|-+.|.
T Consensus       135 ~~L~~~~r~vi~L~~~~g~s~~EIA~~L~is~~TVk~~l~  174 (187)
T PRK13919        135 KALSPEERRVIEVLYYQGYTHREAARLLGLPLGTLKTWAR  174 (187)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             8499999999999998599999999998939999999999


No 112
>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=65.24  E-value=5.2  Score=20.36  Aligned_cols=44  Identities=23%  Similarity=0.336  Sum_probs=38.1

Q ss_pred             HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99985889889999999829999999999999999417986479
Q gi|254780305|r   39 IKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPE   82 (95)
Q Consensus        39 Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pG   82 (95)
                      +++.=+.++-+.=+|++.|||.+++|+-+|=.|-.+|.|...=|
T Consensus        17 ~lA~~~~~~ySAA~lA~~tgL~~pTvsK~Lk~L~~A~lV~S~RG   60 (130)
T TIGR02944        17 VLAQADEQTYSAAELAEQTGLEAPTVSKILKALSEAGLVTSKRG   60 (130)
T ss_pred             HHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCC
T ss_conf             98528997006888786459886047899887642875324346


No 113
>pfam03965 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein.
Probab=64.65  E-value=12  Score=18.37  Aligned_cols=54  Identities=15%  Similarity=0.209  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHCC-CCCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             899999998588-988999999982----999999999999999941798647986898
Q gi|254780305|r   34 CERVRIKQSLNN-VPIHIDDIIHHT----GIEAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        34 ~~~~~Il~~L~~-~p~~iD~l~~~t----gl~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      ..|..|++.|=. +|..+.+|....    ++..++|...|-.|+=||.|.+.-.|+..+
T Consensus         3 ~~E~~IM~~lW~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~~~gr~~~   61 (115)
T pfam03965         3 DAEWEVMRILWALGPATVKEVVEELPEPRDWAYSTVKTLLTRLVKKGLLSREKDGRAYI   61 (115)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCEE
T ss_conf             89999999998079977999999851456885728999999999778626873399479


No 114
>PRK11753 cAMP-regulatory protein; Provisional
Probab=64.19  E-value=10  Score=18.81  Aligned_cols=41  Identities=20%  Similarity=0.140  Sum_probs=35.4

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             889999999829999999999999999417986479868981
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +++-.+|+...|.+...|+.+|-+|+=.|+|. .-|+.+.+-
T Consensus       168 ~lt~~eLA~~lG~sretvsR~L~~L~~~GlI~-~~~~~I~I~  208 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLIS-AHGKTIVVY  208 (211)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-ECCCEEEEE
T ss_conf             46999999886998999999999999889999-859999997


No 115
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=64.15  E-value=12  Score=18.31  Aligned_cols=39  Identities=5%  Similarity=-0.130  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+-.--.+-.+++||++.+|++.+.|.+.|..
T Consensus       107 Lp~~qR~vl~L~~~egls~~EIA~~l~is~~tVk~~l~R  145 (161)
T PRK09047        107 LPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSR  145 (161)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999998999998779999999989699999999999


No 116
>PRK09526 lacI lac repressor; Reviewed
Probab=63.91  E-value=9.1  Score=19.02  Aligned_cols=25  Identities=24%  Similarity=0.409  Sum_probs=19.5

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             8898899999998299999999999
Q gi|254780305|r   44 NNVPIHIDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        44 ~~~p~~iD~l~~~tgl~~~~v~~~L   68 (95)
                      ...++.|.+|++.+|++.++|+.+|
T Consensus         2 ~~k~~TikDIA~~agVS~sTVSrvL   26 (342)
T PRK09526          2 KSKPVTLYDVARYAGVSYQTVSRVL   26 (342)
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             9899769999999896999999997


No 117
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=63.25  E-value=10  Score=18.69  Aligned_cols=44  Identities=23%  Similarity=0.238  Sum_probs=37.7

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC--CCCEEEEEC
Q ss_conf             98899999998299999999999999994179864--798689813
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH--PEGKVSLTM   89 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~--pGg~v~l~~   89 (95)
                      ....+.+|+++.|+|.+-+..++-.|-=+|+|...  ++|=|+|+-
T Consensus        23 ~~~~~~~Ia~~~~is~~~l~kIl~~L~~~Glv~S~RG~~GGy~Lar   68 (153)
T PRK11920         23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGK   68 (153)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCEEECC
T ss_conf             9767999998889199999999999998898784588988635448


No 118
>pfam04458 DUF505 Protein of unknown function (DUF505). Family of uncharacterized prokaryotic proteins.
Probab=63.02  E-value=13  Score=18.19  Aligned_cols=64  Identities=20%  Similarity=0.230  Sum_probs=49.2

Q ss_pred             CCCCCCCCHHHHHHHHHHCC-CCCCHHHHHHH----HCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             56887999899999998588-98899999998----299999999999999994179864798689813
Q gi|254780305|r   26 THYPEYTQCERVRIKQSLNN-VPIHIDDIIHH----TGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        26 ~~~p~~~~~~~~~Il~~L~~-~p~~iD~l~~~----tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      ....+....-+..|+..+-. .-+|-|+++..    .|..-.++..+|-+||-+|+|.-+|.|+|.++-
T Consensus       424 ikR~P~lTryE~~vl~kiP~k~~~~~~~l~e~v~d~~g~eE~eI~~Al~klEakGfie~Lpng~v~lTe  492 (591)
T pfam04458       424 IKRKPFLTRYEAKVLYKIPRKSYIHRGELIELVQDRVGGEEKEIIEALGKLEAKGFVEELPNGGVKLTE  492 (591)
T ss_pred             HHCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHCCCCCEEEEH
T ss_conf             403774128899999866865554378999998875067289999999998856539873899678741


No 119
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=62.43  E-value=13  Score=18.13  Aligned_cols=41  Identities=15%  Similarity=0.089  Sum_probs=34.6

Q ss_pred             CCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             79998999999985889889999999829999999999999
Q gi|254780305|r   30 EYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        30 ~~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ..+.+.++.|+.....+..++.+|++.+|++.++|.+.|..
T Consensus       130 ~~Lp~~~R~vi~L~~~~g~s~~EIA~~lgis~~tVk~~l~R  170 (184)
T PRK12512        130 ETLPPRQRDVVQSIAVEGASIKETAAKLSMSEGAVRVALHR  170 (184)
T ss_pred             HCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             68999999999999855979999999989199999999999


No 120
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=61.76  E-value=6.9  Score=19.68  Aligned_cols=40  Identities=8%  Similarity=0.073  Sum_probs=35.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999999829999999999999999417986479868981
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +..+|+++-|.+..+|-.+|-+|+-.|.|.+..|.=..+.
T Consensus        37 sE~eLa~~y~VSR~TVR~Al~~L~~eGli~r~~G~GtfV~   76 (243)
T PRK11402         37 TENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQ   76 (243)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEEC
T ss_conf             9999999979799999999999997899999779668995


No 121
>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=60.43  E-value=14  Score=17.93  Aligned_cols=40  Identities=13%  Similarity=0.003  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+++.++.|+..--++..+..||+...|++.+.|...+..
T Consensus        10 ~L~~~~r~vl~l~y~~~~s~~EIa~~lgis~~tVk~~l~r   49 (55)
T cd06171          10 KLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHR   49 (55)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             3999998989999980999999999989599999999999


No 122
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=60.23  E-value=12  Score=18.36  Aligned_cols=42  Identities=10%  Similarity=0.004  Sum_probs=35.1

Q ss_pred             CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             988-999999982999999999999999941798647986898
Q gi|254780305|r   46 VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        46 ~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      +.+ +-.+|++..|++-+.|-.+|-.||-.|+|...+|.-+.+
T Consensus        29 ~~LP~E~eLae~~gVSR~~VREAL~~L~~~GlV~~~~g~G~~V   71 (251)
T PRK09990         29 QALPSERRLTEKLGVSRSALREGLKVLRGRGIIETAQGRGSFV   71 (251)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCEE
T ss_conf             9792399999998979599999999999889979857985067


No 123
>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=60.22  E-value=15  Score=17.91  Aligned_cols=39  Identities=10%  Similarity=-0.019  Sum_probs=33.4

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             999899999998588988999999982999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      .+++.++.|+..-=++..+..||+...|++.+.|...+-
T Consensus         4 ~L~~~~r~ii~l~y~~~~t~~EIA~~lgis~~~V~~~~~   42 (50)
T pfam04545         4 SLPPREREVLVLRFGEGLTLEEIGERLGISRERVRQIEK   42 (50)
T ss_pred             HCCHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf             689999999998706882499999998979999999999


No 124
>pfam07638 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.
Probab=59.92  E-value=15  Score=17.88  Aligned_cols=39  Identities=13%  Similarity=0.044  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             999899999998588988999999982999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      .+.++++.|+..--.+-.+..||+..+|++.++|-.-|.
T Consensus       135 ~Lpp~~r~v~~L~~~eglS~~EIAe~Lgis~~TVk~rl~  173 (185)
T pfam07638       135 SLSPRQARLVELRFFAGLSNDEIAERLGVSERTVERNWA  173 (185)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             489988889888997599999999997969989999999


No 125
>pfam01853 MOZ_SAS MOZ/SAS family. This region of these proteins has been suggested to be homologous to acetyltransferases.
Probab=59.88  E-value=13  Score=18.26  Aligned_cols=47  Identities=17%  Similarity=0.164  Sum_probs=33.3

Q ss_pred             HHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             999999858----89889999999829999999999999999417986479868
Q gi|254780305|r   36 RVRIKQSLN----NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKV   85 (95)
Q Consensus        36 ~~~Il~~L~----~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v   85 (95)
                      ...|++.|-    .+.++|++|++.||+....+..+|-.|.   .+...-|.++
T Consensus       135 ~~~il~~L~~~~~~~~isi~dis~~T~i~~~Dii~tL~~l~---~lk~~kg~~~  185 (189)
T pfam01853       135 SQTLLELLLEHRDEHKITIKELSKMTGITVEDIISTLQSLN---MIKYYKGQHI  185 (189)
T ss_pred             HHHHHHHHHHCCCCCCEEHHHHHHHHCCCHHHHHHHHHHCC---CEEEECCEEE
T ss_conf             99999999963999847599999886899999999998779---8999898599


No 126
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=59.83  E-value=7.7  Score=19.42  Aligned_cols=40  Identities=13%  Similarity=-0.008  Sum_probs=35.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999999829999999999999999417986479868981
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +-.+|+++-|.+..+|-.+|-+|+-.|.|.|..|.=..++
T Consensus        31 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~GTfV~   70 (239)
T PRK09764         31 TESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYVK   70 (239)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEEC
T ss_conf             9999999979799999999999997899999868778988


No 127
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=59.42  E-value=12  Score=18.33  Aligned_cols=42  Identities=14%  Similarity=0.154  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             889999999829999999999999999417986479868981
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      =-++-+++..+|+++++|..+.-+||=.|+|...-|--+.++
T Consensus        35 LPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G~fV~   76 (125)
T COG1725          35 LPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRGKGTFVT   76 (125)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCEEEEEC
T ss_conf             975999999819898899999999997887798667057974


No 128
>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=58.80  E-value=15  Score=17.77  Aligned_cols=39  Identities=13%  Similarity=-0.066  Sum_probs=32.6

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             999899999998588988999999982999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      .+...++.++..--.+-.+.+||++..|++.+.|...+.
T Consensus        10 ~Lp~~~r~~~~l~~~~~~s~~eIA~~lg~s~~tVk~~l~   48 (54)
T pfam08281        10 ELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLS   48 (54)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             599999989687998785999999998949999999999


No 129
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=57.57  E-value=14  Score=17.95  Aligned_cols=41  Identities=15%  Similarity=0.130  Sum_probs=36.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             99999998299999999999999994179864798689813
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      .--+|+++.|.+-+.|--+|-.||-+|+|..-+|.-+.+..
T Consensus        36 ~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~Gt~V~~   76 (241)
T COG2186          36 SERELAERFGVSRTVVREALKRLEAKGLVEIRQGSGTFVRP   76 (241)
T ss_pred             CHHHHHHHHCCCCHHHHHHHHHHHHCCCEECCCCCCEEECC
T ss_conf             89999999789956899999999987886305899827647


No 130
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=57.38  E-value=16  Score=17.64  Aligned_cols=40  Identities=10%  Similarity=-0.036  Sum_probs=32.1

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+..+++.|+-.--.+-.+.+||++.+|++.++|.+-|..
T Consensus       137 ~Lp~~~R~vl~Lr~~eglS~~EIAeiLgip~gTVKSRL~R  176 (217)
T PRK12533        137 KLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLAR  176 (217)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             0999886899999980999999999989499999999999


No 131
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=56.89  E-value=17  Score=17.59  Aligned_cols=53  Identities=21%  Similarity=0.256  Sum_probs=45.1

Q ss_pred             CHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             9899999998588-9889999999829999999999999999417986479868
Q gi|254780305|r   33 QCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKV   85 (95)
Q Consensus        33 ~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v   85 (95)
                      ++.+.+|+..|.. .+..+.+|+...+++.+.++..|..|+-+|.|...-.|..
T Consensus        24 ~~~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~~~~~~   77 (110)
T COG0640          24 DPTRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREAGLVELRREGRL   77 (110)
T ss_pred             CHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCE
T ss_conf             758999999998735137999998857678899999999987899578864645


No 132
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=56.13  E-value=17  Score=17.52  Aligned_cols=59  Identities=12%  Similarity=0.019  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-HHHCCCCEEEEECCCC
Q ss_conf             8999999985889889999999829999999999999999417-9864798689813799
Q gi|254780305|r   34 CERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGR-LCHHPEGKVSLTMHLP   92 (95)
Q Consensus        34 ~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~-i~~~pGg~v~l~~~~~   92 (95)
                      .....++..+++.+++=++|+...|++...|.-..=.|+-.|. |....+..|+|.+-+.
T Consensus         6 ~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L~~~~~   65 (79)
T COG1654           6 QMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKGYLLPQLPD   65 (79)
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCEEECCCCCEECCCCCC
T ss_conf             999999997379966689999997865999999999999809716860788636567501


No 133
>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=56.13  E-value=12  Score=18.46  Aligned_cols=41  Identities=15%  Similarity=0.340  Sum_probs=36.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             9889999999829999999999999999417986479868981379
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTMHL   91 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~~~   91 (95)
                      .|...-+|+..+|+..++|+.++     +|.-...|+|.|.|..+-
T Consensus        48 ~PLtlk~iA~~l~lh~STVSRav-----~~Kyi~tp~Gi~~lk~fF   88 (160)
T pfam04552        48 RPLTLREVAEALGMHESTVSRAT-----TNKYLATPRGLFELKYFF   88 (160)
T ss_pred             CCCCHHHHHHHCCCCCCHHHHHH-----HHHHHHCCCCEEEHHHHH
T ss_conf             57619999988099810699999-----613976799516599985


No 134
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=56.11  E-value=17  Score=17.52  Aligned_cols=39  Identities=10%  Similarity=0.008  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +.+.++.|+..--.+-.+..+|++.+|++.++|-+.|..
T Consensus       138 L~~~~r~vi~l~~~eg~s~~EIA~~l~i~~gTVksrl~r  176 (187)
T PRK12534        138 LEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRR  176 (187)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             899899999999984999999999989199999999999


No 135
>pfam11994 DUF3489 Protein of unknown function (DUF3489). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=55.97  E-value=17  Score=17.51  Aligned_cols=39  Identities=23%  Similarity=0.196  Sum_probs=33.1

Q ss_pred             CHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9899999998588-98899999998299999999999999
Q gi|254780305|r   33 QCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLEL   71 (95)
Q Consensus        33 ~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleL   71 (95)
                      ..-+.++++.|.. +-..|++|+..+||-...+-.+|.-+
T Consensus         9 ~tKqa~li~mL~~p~Gati~~i~~atGWq~HTvRgalaG~   48 (72)
T pfam11994         9 GSKQARVIAMLRRPEGATIAAISEATGWQPHTVRGALAGL   48 (72)
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             7579999999648889879999998687403589999888


No 136
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=54.54  E-value=18  Score=17.37  Aligned_cols=30  Identities=10%  Similarity=0.233  Sum_probs=27.1

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             999998588988999999982999999999
Q gi|254780305|r   37 VRIKQSLNNVPIHIDDIIHHTGIEAPVVYL   66 (95)
Q Consensus        37 ~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~   66 (95)
                      .+++..-|++-+++++|++++|++.+.++-
T Consensus         6 ~~l~~~~G~~~~s~~~Ia~~agvs~~~iy~   35 (47)
T pfam00440         6 LELFAEKGYDATTVREIAKEAGVSKGALYR   35 (47)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             999998691507799999997969889998


No 137
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This entry is found in all varieties of the sigma-70 type sigma factors, including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (IPR000394 from INTERPRO) are included within this entry. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=54.42  E-value=18  Score=17.36  Aligned_cols=40  Identities=13%  Similarity=-0.049  Sum_probs=33.9

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+++.++.|+..--....+..+|++.+|++.++|...+..
T Consensus       114 ~Lp~~~r~~~~l~~~~~~s~~eIA~~lg~s~~~v~~~~~r  153 (162)
T TIGR02937       114 KLPEREREVLVLRYLEGLSYKEIAEILGISEGTVKSRLKR  153 (162)
T ss_pred             HCCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             4799899999999971899889999868999999999999


No 138
>pfam10771 DUF2582 Protein of unknown function (DUF2582). This family is conserved in bacteria and archaea. The function is not known.
Probab=54.24  E-value=19  Score=17.35  Aligned_cols=41  Identities=15%  Similarity=0.154  Sum_probs=33.1

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             9999998588-9889999999829999999999999999417
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGR   76 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~   76 (95)
                      .-+|+..|+. ...++.+|.+.+|++...+..++==|-=.+.
T Consensus        10 AG~IW~~L~e~~~~s~~~lk~~~~l~~~~~~~AiGWLaRE~K   51 (65)
T pfam10771        10 AGKVWHLLNENGEWSLSELKRKTGLSDKDLALAIGWLAREDK   51 (65)
T ss_pred             HHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
T ss_conf             999999965688594999998859898999998758861573


No 139
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=53.93  E-value=19  Score=17.32  Aligned_cols=40  Identities=3%  Similarity=-0.017  Sum_probs=32.6

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      -+...++.|+-..-.+-.+..||+..+|++.++|-+.|..
T Consensus       112 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVksrl~r  151 (164)
T PRK12547        112 LLPADQREAIILIGASGFSYEEAAEICGCAVGTIKSRVSR  151 (164)
T ss_pred             HCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             5899999999989984999999999989399999999999


No 140
>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=53.49  E-value=19  Score=17.28  Aligned_cols=40  Identities=18%  Similarity=0.271  Sum_probs=29.5

Q ss_pred             CCCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             8799989999999858898899999998299999999999
Q gi|254780305|r   29 PEYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        29 p~~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~L   68 (95)
                      |+-.+.++.+-...+-....++-+|++..|++.++++..|
T Consensus         3 ~~~lt~~q~~~ar~l~~~G~~~~~iA~~~GVsr~Tiyr~l   42 (42)
T cd00569           3 PPKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHC
T ss_conf             9869999999999999978989999999797999998659


No 141
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=52.73  E-value=20  Score=17.21  Aligned_cols=39  Identities=18%  Similarity=0.144  Sum_probs=31.0

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +..+++.|+..--.+-.+..||++.+|++.++|-+.|..
T Consensus       113 Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~R  151 (161)
T PRK12541        113 LPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR  151 (161)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999989974999999999989399999999999


No 142
>KOG3233 consensus
Probab=51.51  E-value=21  Score=17.10  Aligned_cols=55  Identities=15%  Similarity=0.093  Sum_probs=45.9

Q ss_pred             CCCCCCCCHHHHHHHHHH---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             568879998999999985---8898899999998299999999999999994179864
Q gi|254780305|r   26 THYPEYTQCERVRIKQSL---NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH   80 (95)
Q Consensus        26 ~~~p~~~~~~~~~Il~~L---~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~   80 (95)
                      +......+.+|+.||..+   |..-+-+-+|-++++|+...|..+|-.||-+..|...
T Consensus        76 a~~~~~~e~eEk~vy~lIe~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKkLIKsV  133 (297)
T KOG3233          76 ASKGKGMENEEKLVYSLIEESGNEGIWSKEIKRKSNLPQTVVNKILKSLESKKLIKSV  133 (297)
T ss_pred             HCCCCCCCHHHHHHHHHHHHCCCCCEEEEHHHHCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             0355567748999999999738983562203211588799999999987777899999


No 143
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=51.45  E-value=21  Score=17.09  Aligned_cols=52  Identities=15%  Similarity=0.188  Sum_probs=43.3

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99999985889889999999829-999999999999999417986479868981
Q gi|254780305|r   36 RVRIKQSLNNVPIHIDDIIHHTG-IEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        36 ~~~Il~~L~~~p~~iD~l~~~tg-l~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      ...+++..|+.| ++.++.+..| .+.+.+...|-.|+-+|.+.+.++..-.+.
T Consensus        15 ~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~g~i~~~~~~~r~i~   67 (201)
T COG1974          15 IRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERKGYIRRDPTKARAIR   67 (201)
T ss_pred             HHHHHHHHCCCC-HHHHHHHHHCCCCHHHHHHHHHHHHCCCCEEECCCCCCCEE
T ss_conf             999999728993-08999875178984899999999730885874589874301


No 144
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=50.10  E-value=22  Score=16.97  Aligned_cols=53  Identities=13%  Similarity=0.203  Sum_probs=46.2

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             99999985889889999999829999999999999999417986479868981
Q gi|254780305|r   36 RVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        36 ~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      .++|...++.+|..+.++++.++++...+..+|-.|--.|.+.+..+++|.+.
T Consensus       495 ~~~i~~~~~~~p~~~~dl~~~~~~~~~~~~~~L~~l~~~G~lv~i~~d~~~~~  547 (615)
T PRK10512        495 WQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRN  547 (615)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEECH
T ss_conf             99999987419997788997848998999999999997890899669879868


No 145
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=49.91  E-value=22  Score=16.96  Aligned_cols=20  Identities=20%  Similarity=0.453  Sum_probs=9.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999998299999999999
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~L   68 (95)
                      .|.+|++++|++.++||.+|
T Consensus         2 TikDVA~~AGVS~aTVSrvL   21 (330)
T PRK11303          2 KLDEIARLAGVSRTTASYVI   21 (330)
T ss_pred             CHHHHHHHHCCCHHHHHHHH
T ss_conf             78999999797998998883


No 146
>TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241    This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. .
Probab=49.84  E-value=22  Score=16.95  Aligned_cols=45  Identities=27%  Similarity=0.268  Sum_probs=38.1

Q ss_pred             CHHHHHHHHHHC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf             989999999858-898899999998299999999999999994179
Q gi|254780305|r   33 QCERVRIKQSLN-NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRL   77 (95)
Q Consensus        33 ~~~~~~Il~~L~-~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i   77 (95)
                      |.+--.|++.|. .+-+.=|+|+..+|+..+.|-.+|..|==+|++
T Consensus        15 dEe~~~vl~~L~~kGe~Tdeeis~elg~klN~vRk~Ly~LYdagla   60 (168)
T TIGR00373        15 DEEAIEVLESLLIKGEVTDEEISKELGIKLNVVRKLLYKLYDAGLA   60 (168)
T ss_pred             CCCHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCEEE
T ss_conf             5321344422202687477888888384055788999987303010


No 147
>PRK09492 treR trehalose repressor; Provisional
Probab=49.58  E-value=19  Score=17.31  Aligned_cols=21  Identities=33%  Similarity=0.488  Sum_probs=12.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH
Q ss_conf             899999998299999999999
Q gi|254780305|r   48 IHIDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        48 ~~iD~l~~~tgl~~~~v~~~L   68 (95)
                      +.|.+|++.+|++.++|+.+|
T Consensus         5 vTikDIA~~aGVS~aTVSrvL   25 (315)
T PRK09492          5 LTIKDIARLSGVGKSTVSRVL   25 (315)
T ss_pred             CCHHHHHHHHCCCHHHHHHHH
T ss_conf             879999999897999999997


No 148
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=49.42  E-value=18  Score=17.36  Aligned_cols=21  Identities=29%  Similarity=0.382  Sum_probs=18.2

Q ss_pred             CHHHHHHHHCCCHHHHHHHHH
Q ss_conf             999999982999999999999
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      .|-+|++.+|++.++|+.+|-
T Consensus         1 Ti~DIA~~agVS~~TVSr~ln   21 (46)
T pfam00356         1 TIKDVARLAGVSKATVSRVLN   21 (46)
T ss_pred             CHHHHHHHHCCCHHHHHHHHC
T ss_conf             999999998979999999987


No 149
>pfam04337 DUF480 Protein of unknown function, DUF480. This family consists of several proteins of uncharacterized function.
Probab=49.23  E-value=23  Score=16.90  Aligned_cols=53  Identities=17%  Similarity=0.241  Sum_probs=36.7

Q ss_pred             CHHHHHHHHHH--------CCCCCCHHHHHHHHC----------CCHHHHHHHHHHHHHHHHHHH-CCCCEE
Q ss_conf             98999999985--------889889999999829----------999999999999999417986-479868
Q gi|254780305|r   33 QCERVRIKQSL--------NNVPIHIDDIIHHTG----------IEAPVVYLVLLELDLAGRLCH-HPEGKV   85 (95)
Q Consensus        33 ~~~~~~Il~~L--------~~~p~~iD~l~~~tg----------l~~~~v~~~LleLEL~G~i~~-~pGg~v   85 (95)
                      ++.+.+|+.+|        ...|.+++.+...|+          ++-++|..+|-+|.-+|.|.. ..|+++
T Consensus         2 s~~E~RVlG~LiEKe~TTPd~YPLtLNaL~~aCNQKsnR~PVm~l~e~eV~~ald~L~~~~Lv~~~~~gsRv   73 (148)
T pfam04337         2 SALEARVLGCLLEKEVTTPDQYPLSLNALTTACNQKSSREPVMNLSESEVQQALDELKAKGLVRESGFGSRV   73 (148)
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCH
T ss_conf             788887998853112358776764099999885154566864358999999999999978785554778740


No 150
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=48.70  E-value=15  Score=17.83  Aligned_cols=41  Identities=15%  Similarity=0.105  Sum_probs=35.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             99999998299999999999999994179864798689813
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      +-.+|+++-|.+.-+|..+|-+|+-.|.|.|.-|.=..++.
T Consensus        33 sE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~GtfV~~   73 (236)
T COG2188          33 SERELAEQFGVSRMTVRKALDELVEEGLIVRRQGKGTFVAS   73 (236)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEEECC
T ss_conf             98999999798899999999999989988995166789887


No 151
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=48.65  E-value=23  Score=16.84  Aligned_cols=33  Identities=18%  Similarity=0.456  Sum_probs=28.3

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             9999999858898899999998299999999999
Q gi|254780305|r   35 ERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        35 ~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~L   68 (95)
                      .+..+..-|+-+|+ ||||++.+|++..+|-.++
T Consensus       102 ~kE~L~~~l~R~PT-i~Elae~lg~~~EEiv~A~  134 (231)
T TIGR02885       102 EKEELTKKLGREPT-INELAEALGVSPEEIVMAL  134 (231)
T ss_pred             HHHHHHHHHCCCCC-HHHHHHHHCCCHHHHHHHH
T ss_conf             79999998389988-8999887587887866442


No 152
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=48.40  E-value=19  Score=17.28  Aligned_cols=21  Identities=29%  Similarity=0.382  Sum_probs=18.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHH
Q ss_conf             999999982999999999999
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      .|.+|++.+|++.++|+.+|-
T Consensus         2 Ti~dvA~~aGVS~sTVSr~ln   22 (70)
T smart00354        2 TIKDVARLAGVSKATVSRVLN   22 (70)
T ss_pred             CHHHHHHHHCCCHHHHHHHHC
T ss_conf             899999998959999999977


No 153
>pfam08221 HTH_9 RNA polymerase III subunit RPC82 helix-turn-helix domain. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. This region is a probably DNA-binding helix-turn-helix.
Probab=48.23  E-value=23  Score=16.81  Aligned_cols=42  Identities=14%  Similarity=0.151  Sum_probs=32.6

Q ss_pred             HHHHHH-HCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             999998-588988999999982999999999999999941798
Q gi|254780305|r   37 VRIKQS-LNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLC   78 (95)
Q Consensus        37 ~~Il~~-L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~   78 (95)
                      ++|.+. ++.+...+.+|++.|+++..+|-.+|.-|==.+.|.
T Consensus        16 ~~V~~~Ll~~g~~tl~~i~~~t~L~~~~Vk~aL~vLIQhnlV~   58 (62)
T pfam08221        16 AKVVSTLLRKGRLTLREIVKLTKLSLDQVKKSLVVLIQHNCVQ   58 (62)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9999999985881699999782899999999999999997899


No 154
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=48.20  E-value=23  Score=16.81  Aligned_cols=51  Identities=14%  Similarity=0.120  Sum_probs=34.7

Q ss_pred             CHHHHHHHHHHC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             989999999858-898899999998299999999999999994179864798
Q gi|254780305|r   33 QCERVRIKQSLN-NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        33 ~~~~~~Il~~L~-~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      ++-..-|-..+. +.|...++++.+.|++.+.+..+|-.|+-.|.|.+..+.
T Consensus       974 d~l~~lv~r~art~GPft~~~~a~~~gl~~~~~~~aL~~L~~~G~v~~~~~~ 1025 (1490)
T PRK09751        974 YPLRDLFLRYLRAHALVTAEQLAHEFSLGIAIVEEQLQQLREQGLVMNLQQD 1025 (1490)
T ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCC
T ss_conf             5899999999871698669999988689889999999999966977527775


No 155
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=47.91  E-value=24  Score=16.78  Aligned_cols=39  Identities=10%  Similarity=0.135  Sum_probs=34.5

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             999899999998588988999999982999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      ..|...+.|.++|...-+++-.|++..|++.+++..+|.
T Consensus         5 ~~DWH~ADIiAAL~KrG~sLa~Lsr~aGls~sTL~nAL~   43 (90)
T PRK10344          5 FIDWHPADIIAGLRKKGTSMAAESRRNGLSSSTLANALS   43 (90)
T ss_pred             CCCCCHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHC
T ss_conf             366899999999998688699999990998688999874


No 156
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=47.88  E-value=24  Score=16.78  Aligned_cols=40  Identities=3%  Similarity=-0.067  Sum_probs=33.3

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+...++.|+..-..+-.+..+|++.+|++.++|.+.|..
T Consensus       119 ~Lp~~~R~vl~L~~~egls~~EIAe~Lgis~~TVksrl~R  158 (190)
T PRK12516        119 QLPDDQREAIILIGASGFAYEEAAEICGCAVGTIKSRVSR  158 (190)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             1999998999989982999999999989499999999999


No 157
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=47.74  E-value=24  Score=16.76  Aligned_cols=38  Identities=8%  Similarity=-0.028  Sum_probs=28.6

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             98999999985889889999999829999999999999
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ..+++.|+..--.+-.+..||++..|++.++|-+.|..
T Consensus       113 p~~~R~vl~L~~~egls~~EIAe~Lgis~gTVKsrl~R  150 (182)
T PRK12511        113 PEEQRAALHLVAIEGLSYQEAANVLGIPIGTLMSRIGR  150 (182)
T ss_pred             CHHHHHHEEEEEECCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99895011241007999999999989399999999999


No 158
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=47.42  E-value=24  Score=16.74  Aligned_cols=39  Identities=8%  Similarity=0.065  Sum_probs=31.9

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+...-.+-.++.+|+..+|++.++|.+.+..
T Consensus       132 Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~R  170 (184)
T PRK12539        132 LPEKMRLAIQAVKLDGLSVAEAATRSGMSESAVKVSVHR  170 (184)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999994999999999989199999999999


No 159
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=47.16  E-value=24  Score=16.71  Aligned_cols=39  Identities=10%  Similarity=-0.064  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+...-.+-.++.+|++..|++.++|-+.|..
T Consensus       142 Lp~~~R~vi~L~~~e~~s~~EIAe~l~is~~TVKsrl~r  180 (194)
T PRK12531        142 LPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRL  180 (194)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999886999999999989299999999999


No 160
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=46.85  E-value=25  Score=16.69  Aligned_cols=40  Identities=13%  Similarity=-0.096  Sum_probs=31.9

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+.+.++.|+..--.+-.+..+|+..+|++.++|-..|..
T Consensus       127 ~Lp~~~r~v~~L~~~eg~s~~EIA~~l~is~~tVk~~l~r  166 (177)
T PRK09638        127 KLPPELRAPFILKHYYGYTYEEIAKMLGIPEGTVKSRVHH  166 (177)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             5999898999999991999999999989399999999999


No 161
>PRK10079 putative transcriptional regulator; Provisional
Probab=46.73  E-value=25  Score=16.68  Aligned_cols=40  Identities=8%  Similarity=-0.018  Sum_probs=36.2

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999999829999999999999999417986479868981
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      +..+|++.-|.+..+|-.+|-+|+-.|.|.+..|.=..+.
T Consensus        37 sE~eLa~~y~VSR~TVR~Al~~L~~eGli~r~~G~GtfV~   76 (241)
T PRK10079         37 AEQQLAARFEVNRHTLRRAIDQLVERGWVQRRQGVGVLVL   76 (241)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCEEEE
T ss_conf             9999999979889999999999997798799769625993


No 162
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=46.69  E-value=25  Score=16.67  Aligned_cols=38  Identities=13%  Similarity=0.121  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             98999999985889889999999829999999999999
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ...++.|+-.-..+-.+..+|++.+|++.+.|.+.|..
T Consensus       138 p~~~R~vl~L~~~egls~~EIA~~lgis~~tVks~l~R  175 (195)
T PRK12532        138 PENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHR  175 (195)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99998999999981999999999989599999999999


No 163
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=46.56  E-value=25  Score=16.66  Aligned_cols=39  Identities=13%  Similarity=-0.022  Sum_probs=31.0

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +..+++.|+..--.+-.+.++|++.+|++.++|.+.|..
T Consensus       121 Lp~~~r~vi~l~~~~~~s~~EIA~~l~is~~tVk~~l~R  159 (175)
T PRK12518        121 LSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFY  159 (175)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999992999999999989599999999999


No 164
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=46.16  E-value=25  Score=16.63  Aligned_cols=40  Identities=8%  Similarity=-0.051  Sum_probs=31.9

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+...++.|+-.--.+..+..+|++.+|++.++|-+-|..
T Consensus       113 ~LP~~~R~vl~L~~~egls~~EIAe~Lgis~gTVKsRL~R  152 (188)
T PRK12546        113 QLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANR  152 (188)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             6999998895879982989999999989399999999999


No 165
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=45.86  E-value=23  Score=16.82  Aligned_cols=22  Identities=36%  Similarity=0.542  Sum_probs=11.7

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             8899999998299999999999
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~L   68 (95)
                      -+.|-+|++.+|++.++|+.+|
T Consensus         6 kvTi~dIA~~aGVS~aTVSrvL   27 (342)
T PRK10014          6 KITIHDVALAAGVSVSTVSLVL   27 (342)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHH
T ss_conf             8879999999896999999997


No 166
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=45.52  E-value=26  Score=16.57  Aligned_cols=38  Identities=11%  Similarity=-0.091  Sum_probs=28.6

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99899999998588988999999982999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      +.+.++.++-..-.+-.+..||++.+|++.++|-+.|.
T Consensus       136 L~~~~r~~i~l~~~eg~s~~EIA~~l~is~~TVk~rl~  173 (184)
T PRK12537        136 LEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIK  173 (184)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99989999999884399999999998929999999999


No 167
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=45.45  E-value=26  Score=16.56  Aligned_cols=40  Identities=5%  Similarity=-0.071  Sum_probs=32.5

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+..+++.|+-.--.+-.+..+|+..+|+|.++|-+-|..
T Consensus       130 ~Lp~~~R~vl~L~~~egls~~EIA~~lg~~~gTVKsRl~R  169 (185)
T PRK09649        130 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVAR  169 (185)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             4999999999989972999999999989399999999999


No 168
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=45.32  E-value=19  Score=17.33  Aligned_cols=55  Identities=16%  Similarity=0.125  Sum_probs=41.0

Q ss_pred             CHHHHHHHHHHCC------CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             9899999998588------988-999999982999999999999999941798647986898
Q gi|254780305|r   33 QCERVRIKQSLNN------VPI-HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        33 ~~~~~~Il~~L~~------~p~-~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      .-.+..|.+.+-.      +.+ +--+|++..|++...|-.+|-.|+-.|+|....|.-..+
T Consensus        10 ~~ae~~i~~~I~~g~~~~G~~LP~EreLa~~~gVsR~tvReal~~L~~~G~v~~~~G~gt~V   71 (239)
T PRK04984         10 GFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKV   71 (239)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCEE
T ss_conf             99999999999869999999898899999997988899999999999889888855999755


No 169
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=45.13  E-value=26  Score=16.54  Aligned_cols=40  Identities=10%  Similarity=0.032  Sum_probs=33.2

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+++.++.|+..--.+-.+.++|++..|++.+.|...|..
T Consensus       131 ~L~~~~R~vi~l~~~e~~s~~EIA~~lgis~~tV~~~l~R  170 (189)
T PRK12515        131 KLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFY  170 (189)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             5999999999999984999999999989299999999999


No 170
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=44.65  E-value=27  Score=16.49  Aligned_cols=39  Identities=5%  Similarity=-0.052  Sum_probs=31.2

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +..+++.|+..--.+-.+..||++.+|++.++|-+-|..
T Consensus       112 Lp~~~R~vl~L~~~egls~~EIA~iL~is~gTVKsRL~R  150 (181)
T PRK12540        112 LPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNR  150 (181)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999998998879980999999999989499999999999


No 171
>pfam07789 DUF1627 Protein of unknown function (DUF1627). This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=44.35  E-value=26  Score=16.54  Aligned_cols=45  Identities=22%  Similarity=0.201  Sum_probs=37.6

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC-CCCEEEEEC
Q ss_conf             898899999998299999999999999994179864-798689813
Q gi|254780305|r   45 NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHH-PEGKVSLTM   89 (95)
Q Consensus        45 ~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~-pGg~v~l~~   89 (95)
                      +.|...|+|+...|.+..++.+.|-.---+|++.|. -||+|+--|
T Consensus         4 ~GpqtadElA~~FG~tsRkvaStLAma~skGrLiRvNQ~gkfRYCi   49 (155)
T pfam07789         4 RGPQTADELATLFGTTSRKVASTLAMAISKGRLIRVNQGGKFRYCI   49 (155)
T ss_pred             CCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCEEEEECCCCCEEEEC
T ss_conf             6722199999886610677776789986257179974899477606


No 172
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=43.37  E-value=27  Score=16.47  Aligned_cols=21  Identities=19%  Similarity=0.357  Sum_probs=13.0

Q ss_pred             CCHHHHHHHHCCCHHHHHHHH
Q ss_conf             899999998299999999999
Q gi|254780305|r   48 IHIDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        48 ~~iD~l~~~tgl~~~~v~~~L   68 (95)
                      ..|-+|++.+|++.++||.+|
T Consensus        10 aTikDIA~~aGVS~sTVSrvL   30 (341)
T PRK11041         10 ATMKDVALKAGVSTATVSRAL   30 (341)
T ss_pred             CCHHHHHHHHCCCHHHHHHHH
T ss_conf             889999999797999999997


No 173
>pfam10975 DUF2802 Protein of unknown function (DUF2802). This bacterial family of proteins has no known function.
Probab=42.93  E-value=28  Score=16.42  Aligned_cols=29  Identities=17%  Similarity=0.313  Sum_probs=20.8

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             99999998588988999999982999999999
Q gi|254780305|r   35 ERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYL   66 (95)
Q Consensus        35 ~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~   66 (95)
                      .++.-+-.+|   .++|+|++.||||-++.--
T Consensus        35 ~~A~klv~~G---a~vdel~~~CgL~rAEAEL   63 (70)
T pfam10975        35 SRAAKLVELG---ADVDELMEECGLPRAEAEL   63 (70)
T ss_pred             HHHHHHHHCC---CCHHHHHHHCCCCHHHHHH
T ss_conf             9999999929---9999999882998899999


No 174
>pfam03551 PadR Transcriptional regulator PadR-like family. Members of this family are transcriptional regulators that appear to be related to the pfam01047 family. This family includes PadR, a protein that is involved in negative regulation of phenolic acid metabolism.
Probab=42.66  E-value=26  Score=16.57  Aligned_cols=43  Identities=19%  Similarity=0.184  Sum_probs=35.7

Q ss_pred             HHHHHHHCCCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             999998588988999999982--------9999999999999999417986
Q gi|254780305|r   37 VRIKQSLNNVPIHIDDIIHHT--------GIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        37 ~~Il~~L~~~p~~iD~l~~~t--------gl~~~~v~~~LleLEL~G~i~~   79 (95)
                      -.||..|+..|.|=-+|.+..        .++.+.++.+|-.||=+|+|..
T Consensus         4 ~~IL~~L~~~p~~GYei~~~i~~~~~~~~~~~~g~iY~~L~~Le~~G~i~~   54 (81)
T pfam03551         4 LLVLALLGEQPRYGYEIIKELEELSGGFYRPSEGTLYPILKRLEKEGLVES   54 (81)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCEEE
T ss_conf             999999860898899999999998599104796769999999998899589


No 175
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=42.36  E-value=29  Score=16.29  Aligned_cols=40  Identities=5%  Similarity=-0.066  Sum_probs=32.5

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+..+++.++..--.+-.+.+||++.+|++.++|-+-|..
T Consensus       132 ~Lp~~~R~~l~L~~~~g~s~~EIA~ilgi~~gTVKsRl~R  171 (195)
T PRK12535        132 ALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVAR  171 (195)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             4999887999999982998999999989399999999999


No 176
>KOG2747 consensus
Probab=42.33  E-value=29  Score=16.29  Aligned_cols=50  Identities=22%  Similarity=0.249  Sum_probs=34.3

Q ss_pred             HHHHHHHHCC---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999998588---9889999999829999999999999999417986479868981
Q gi|254780305|r   36 RVRIKQSLNN---VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        36 ~~~Il~~L~~---~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      ...|+..|..   ..++|++|+..||+....|..+|-.|.|   +....|+-+++.
T Consensus       315 ~~~ll~~L~~~~~~~isI~~iS~~Tgi~~~DIisTL~~L~m---~~y~k~~~~~~~  367 (396)
T KOG2747         315 RCVLLELLRKHRGEHISIKEISKETGIRPDDIISTLQSLNM---IKYYKGYIISIC  367 (396)
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHCC---CCCCCCEEEEEE
T ss_conf             99999999964787532999988658988879999986077---113477569985


No 177
>PRK08444 hypothetical protein; Provisional
Probab=42.01  E-value=17  Score=17.53  Aligned_cols=36  Identities=19%  Similarity=0.182  Sum_probs=28.1

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             8898899999998299999999999999994179864798
Q gi|254780305|r   44 NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        44 ~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      +++|..||.+++.+|++..++...|-+--|    .++|||
T Consensus       133 aft~~EI~~~a~~~~~s~~evL~~Lk~AGL----~slpGg  168 (353)
T PRK08444        133 AMTAAEVDFLSRKFGKSYEEVLEDMLEYGV----DSMPGG  168 (353)
T ss_pred             ECCHHHHHHHHHHCCCCHHHHHHHHHHHCC----CCCCCC
T ss_conf             177899999999809999999999998198----757898


No 178
>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=41.89  E-value=30  Score=16.25  Aligned_cols=55  Identities=11%  Similarity=0.112  Sum_probs=40.9

Q ss_pred             CCHHHHHHHHHH-----CC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             998999999985-----88----988999999982999999999999999941798647986898
Q gi|254780305|r   32 TQCERVRIKQSL-----NN----VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSL   87 (95)
Q Consensus        32 ~~~~~~~Il~~L-----~~----~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l   87 (95)
                      .+.-+.+|+.++     |+    +-++..++++.||++...|+.++-+|.=.|+|.+ -|+++..
T Consensus        30 lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs~a~~~Li~~~vi~~-~G~~iGv   93 (100)
T pfam04492        30 LSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVSEAKKSLVKRGIIIQ-DGRQIGV   93 (100)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCHH-CCCEECC
T ss_conf             878899999999998607785033622999999978885459999999997686441-4968545


No 179
>pfam09940 DUF2172 Domain of unknown function (DUF2172). This domain, found in various hypothetical prokaryotic proteins, has no known function. An aminopeptidase domain is conserved within the family, but its relevance has not been established yet.
Probab=41.85  E-value=30  Score=16.25  Aligned_cols=43  Identities=21%  Similarity=0.071  Sum_probs=35.1

Q ss_pred             HHHHHHHHC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             999999858--8988999999982999999999999999941798
Q gi|254780305|r   36 RVRIKQSLN--NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLC   78 (95)
Q Consensus        36 ~~~Il~~L~--~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~   78 (95)
                      ...+++.|.  ++-.++.+|+++++++...+..++-.|.=+|.|+
T Consensus       340 ~~~~l~iL~ysDGk~sl~dIae~~~l~~~~i~~~~~~L~~~~Lik  384 (384)
T pfam09940       340 EMAMLWVLNLSDGQNSLLDIAERIGLPFDRLKPAADALLDAGLLK  384 (384)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCC
T ss_conf             999998999735998899999997929999999999999867979


No 180
>PRK05926 hypothetical protein; Provisional
Probab=41.74  E-value=18  Score=17.41  Aligned_cols=36  Identities=17%  Similarity=0.086  Sum_probs=26.8

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             8898899999998299999999999999994179864798
Q gi|254780305|r   44 NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        44 ~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      +++|..|+.+++.+|++..++...|-+==|    ..+|||
T Consensus       152 aft~~EI~~~a~~~~~s~~EvL~~Lk~AGL----~SlPGg  187 (371)
T PRK05926        152 ALTAIEYAYLSKLDNLPVREVLQTLKIAGL----DSIPGG  187 (371)
T ss_pred             CCCHHHHHHHHHHCCCCHHHHHHHHHHHCC----CCCCCC
T ss_conf             488999999999809999999999998387----778887


No 181
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=41.63  E-value=30  Score=16.23  Aligned_cols=38  Identities=11%  Similarity=0.177  Sum_probs=29.1

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             98999999985889889999999829999999999999
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ...++.|+-.-..+-.+..+|++.+|++.+.|-+.|..
T Consensus       138 P~~~R~v~~Lr~~~~ls~~EIA~~l~is~~tVksrL~R  175 (191)
T PRK12530        138 PAQQARVFMMREFLELSSEQICQECHITTSNLHVLLYR  175 (191)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99999999999992999999999989699999999999


No 182
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=41.49  E-value=30  Score=16.22  Aligned_cols=52  Identities=4%  Similarity=-0.118  Sum_probs=37.7

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH--------HHHHHHHHHHCCCC
Q ss_conf             99899999998588988999999982999999999999--------99994179864798
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL--------ELDLAGRLCHHPEG   83 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll--------eLEL~G~i~~~pGg   83 (95)
                      +.+.++.|+..--.+-.++++|+...|++.++|-+.|.        .||+++.-.-.-||
T Consensus       130 Lp~~~R~vi~L~~~~g~s~~EIA~~l~is~~tVk~rl~rA~k~LR~kle~~e~~~~~~~~  189 (190)
T PRK12543        130 LPYKLKQVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKEQIEEIFLGEVGN  189 (190)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             999999999999985999999999989399999999999999999999999999722367


No 183
>PRK13239 alkylmercury lyase; Provisional
Probab=41.49  E-value=30  Score=16.22  Aligned_cols=38  Identities=18%  Similarity=0.148  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             899999998588-98899999998299999999999999
Q gi|254780305|r   34 CERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLEL   71 (95)
Q Consensus        34 ~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleL   71 (95)
                      .--..+|..|-. .|+++..|+..+|++..+|.++|-++
T Consensus        22 ~l~~~llr~La~G~PVs~~~LA~~~g~~~e~v~~~L~~~   60 (206)
T PRK13239         22 RLLVPLLRELAKGRPVSRETLAGALGWPVEEVAAVLEQA   60 (206)
T ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             599999999856999999999988699999999999857


No 184
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=41.38  E-value=30  Score=16.22  Aligned_cols=16  Identities=25%  Similarity=0.468  Sum_probs=5.2

Q ss_pred             HHHHHHCCCHHHHHHH
Q ss_conf             9999829999999999
Q gi|254780305|r   52 DIIHHTGIEAPVVYLV   67 (95)
Q Consensus        52 ~l~~~tgl~~~~v~~~   67 (95)
                      +|++.+|++.++|+.+
T Consensus         6 DIA~~AGVS~aTVSrv   21 (335)
T PRK10703          6 DVAKRAGVSTTTVSHV   21 (335)
T ss_pred             HHHHHHCCCHHHHHHH
T ss_conf             9999979899999999


No 185
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=41.26  E-value=30  Score=16.20  Aligned_cols=40  Identities=5%  Similarity=-0.084  Sum_probs=32.5

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+.+.++.|+..--.+-.+..||+...|++.++|-+.|..
T Consensus       106 ~Lp~~~R~v~~L~~~eg~s~~EIA~~L~is~~tVksrl~R  145 (181)
T PRK09637        106 ALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQR  145 (181)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             6999998997999885999999999989499999999999


No 186
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=41.01  E-value=31  Score=16.17  Aligned_cols=40  Identities=10%  Similarity=0.009  Sum_probs=32.9

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+..+++.|+...-.+-.++.||+..+|++.++|-+.|..
T Consensus       131 ~Lp~~~R~vl~L~~~eg~s~~EIA~~lgis~~tVKsrl~R  170 (197)
T PRK09643        131 RLPVEQRAALVAVDMQGYSVADTARMLGVAEGTVKSRCAR  170 (197)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             6999887999999981999999999989399999999999


No 187
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=40.95  E-value=31  Score=16.17  Aligned_cols=30  Identities=17%  Similarity=0.335  Sum_probs=25.6

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             999998588988999999982999999999
Q gi|254780305|r   37 VRIKQSLNNVPIHIDDIIHHTGIEAPVVYL   66 (95)
Q Consensus        37 ~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~   66 (95)
                      .+++..-|+.-+++++|++++|++-+.++-
T Consensus        21 ~~lFaekGy~~ttl~dIA~~AGVS~GaiY~   50 (216)
T PRK10668         21 LRLFSQQGVSATSLADIAKAAGVTRGAIYW   50 (216)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             999998493518899999996898579998


No 188
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=40.45  E-value=31  Score=16.13  Aligned_cols=37  Identities=3%  Similarity=-0.107  Sum_probs=28.6

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             9899999998588988999999982999999999999
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      +..++.|+..--.+-.+..||++.+|++.++|-+.|.
T Consensus       144 p~~~R~vi~L~~~~g~s~~EIA~~Lgis~~TVk~rl~  180 (194)
T PRK09646        144 TDTQREAITLAYYGGLTYREVAERLAVPLGTVKTRMR  180 (194)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             8157899999999399999999998919999999999


No 189
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=40.44  E-value=31  Score=16.12  Aligned_cols=39  Identities=8%  Similarity=-0.045  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+..--.+-.+..||+..+|++.++|-+.|..
T Consensus       150 Lp~~~R~v~~L~~~eglS~~EIA~~Lgis~~TVKsrL~R  188 (231)
T PRK11922        150 LPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHR  188 (231)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999993999999999989399999999999


No 190
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=40.35  E-value=31  Score=16.12  Aligned_cols=40  Identities=20%  Similarity=0.223  Sum_probs=35.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9999999829999999999999999417986479868981
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      ..-+|+..||.+..+|.-++=.|+=.|+|.+.-.|-|.+.
T Consensus        77 T~R~lae~~gvs~~TV~~tmK~L~e~~fIkk~t~GvymiN  116 (165)
T pfam05732        77 TQREIAEETGISLETVRQTMKALEEGNFLKKKTSGVYMIN  116 (165)
T ss_pred             EHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEEC
T ss_conf             7899999839529999999999975892686138769988


No 191
>PTZ00064 histone acetyltransferase; Provisional
Probab=40.30  E-value=31  Score=16.11  Aligned_cols=47  Identities=23%  Similarity=0.180  Sum_probs=34.9

Q ss_pred             HHHHHHHHCC---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC-CCEE
Q ss_conf             9999998588---988999999982999999999999999941798647-9868
Q gi|254780305|r   36 RVRIKQSLNN---VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP-EGKV   85 (95)
Q Consensus        36 ~~~Il~~L~~---~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p-Gg~v   85 (95)
                      ...|++.|-.   +.++|++|++.|++....|..+|-.|.   .++..- |.++
T Consensus       351 ~~~Ile~L~~~~~~~iSI~dis~~T~I~~~DIi~TLq~L~---llk~~~~Gq~v  401 (442)
T PTZ00064        351 SEVLLEILFDPFKENKTIDNLSRMTGFEPNDIIRCLEELG---ILHTLSNGQSV  401 (442)
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHC---HHHHHCCCCEE
T ss_conf             9999999985357885799999885898899999998726---13301389789


No 192
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=40.24  E-value=32  Score=16.11  Aligned_cols=39  Identities=10%  Similarity=-0.022  Sum_probs=30.9

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             999899999998588988999999982999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      .++..++.|+..--.+-.+..+|++..|++.++|-..|.
T Consensus       141 ~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVk~rl~  179 (194)
T PRK12519        141 QLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARAR  179 (194)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             199887568899998199999999998949999999999


No 193
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=39.90  E-value=32  Score=16.08  Aligned_cols=40  Identities=13%  Similarity=-0.007  Sum_probs=31.8

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+++.++.|+..--.+-.++.+|++..|++.++|.+.|..
T Consensus       128 ~L~~~~r~v~~l~~~~~~s~~EIA~~l~is~~tVk~rl~R  167 (185)
T PRK06811        128 DLKKLDREIFIKRYLLGESIEEIAKKLGLTRSAIDNRLSR  167 (185)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             8999999999999994999999999989299999999999


No 194
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=39.89  E-value=32  Score=16.08  Aligned_cols=38  Identities=11%  Similarity=-0.010  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99899999998588988999999982999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      +++.++.|+..--.+..+..+|++.+|++.+.|...+.
T Consensus       138 Lp~~~R~vl~L~~~~g~s~~EIA~~lg~s~~tVk~~l~  175 (187)
T PRK09648        138 LPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQH  175 (187)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999999998499999999998939999999999


No 195
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=39.83  E-value=32  Score=16.07  Aligned_cols=39  Identities=5%  Similarity=-0.100  Sum_probs=31.7

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+..--.+-.+..+|+...|++.++|...|..
T Consensus       129 Lp~~~R~v~~L~~~~g~s~~EIA~~l~is~~tVk~~l~R  167 (186)
T PRK05602        129 LPERQREAIVLQYYQGLSNIEAARVMGLSVDALESLLAR  167 (186)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             998788999999863899999999989399999999999


No 196
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=39.57  E-value=32  Score=16.05  Aligned_cols=39  Identities=5%  Similarity=-0.090  Sum_probs=30.6

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ++..++.|+..--.+-.+..+|++.+|++.++|.+.|..
T Consensus       137 Lp~~~r~v~~L~~~~~~s~~EIA~~l~is~~tVk~~l~R  175 (187)
T PRK09641        137 LPDKYRTVIVLKYIEELSLKEISEILDLPVGTVKTRIHR  175 (187)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             898888999999982998999999989399999999999


No 197
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; InterPro: IPR014331   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 of sigma factors are members of the sigma-70 family and are abundantly found in the species Rhodopirellula baltica, and Verrucomicrobium spinosum and to a lesser extent in Gemmata obscuriglobus.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=39.09  E-value=33  Score=16.00  Aligned_cols=42  Identities=17%  Similarity=0.172  Sum_probs=35.6

Q ss_pred             CCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             799989999999858898899999998299999999999999
Q gi|254780305|r   30 EYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLEL   71 (95)
Q Consensus        30 ~~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleL   71 (95)
                      +-+...+++++..-=..-+++.+|+.++|.+++.++..|.-+
T Consensus       114 ~~L~~~~R~Ll~~rY~~G~~~~~~A~~~g~~~~A~~~~L~R~  155 (163)
T TIGR02989       114 EKLPERQRELLQLRYQRGVSLEALAEQLGRTVNAVYKALSRL  155 (163)
T ss_pred             HHCCHHHHHHHHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHH
T ss_conf             635978899999982279787899988471389999999999


No 198
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=38.89  E-value=33  Score=15.99  Aligned_cols=40  Identities=10%  Similarity=0.182  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ..|...+.|+++|-..-+++-.|.+..|++.+++..+|..
T Consensus         5 ~~dWh~adI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~r   44 (82)
T COG3423           5 FQDWHPADIIAALKKKGTSLAALSREAGLSSSTLANALDR   44 (82)
T ss_pred             CCCCCHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCC
T ss_conf             0237999999999985642999998808787899998747


No 199
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=38.36  E-value=33  Score=15.97  Aligned_cols=29  Identities=3%  Similarity=0.110  Sum_probs=20.8

Q ss_pred             HHHHHCCCCCCHHHHHHHHCCCHHHHHHH
Q ss_conf             99985889889999999829999999999
Q gi|254780305|r   39 IKQSLNNVPIHIDDIIHHTGIEAPVVYLV   67 (95)
Q Consensus        39 Il~~L~~~p~~iD~l~~~tgl~~~~v~~~   67 (95)
                      |-+.=...-+++++|+++||++.+.++.+
T Consensus        12 Ir~lR~~~glTL~eLA~~sGvS~s~LSqI   40 (185)
T PRK09943         12 LSEIRQQQGLSQRRAAELSGLTHSAISTI   40 (185)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf             99999985998999998879699999999


No 200
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=38.31  E-value=34  Score=15.94  Aligned_cols=38  Identities=11%  Similarity=0.212  Sum_probs=29.3

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             98999999985889889999999829999999999999
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ...++.|+-.--.+-.+.++|++..|++.+.|-+.|..
T Consensus       151 p~~~R~vl~Lr~~eglS~~EIAe~Lgis~~tVks~L~R  188 (207)
T PRK12544        151 PAKYARVFMMREFIELETPEICHNEDLTVSNLNVMLYR  188 (207)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99999999999981999999999979799999999999


No 201
>PRK08445 hypothetical protein; Provisional
Probab=37.83  E-value=22  Score=16.99  Aligned_cols=38  Identities=21%  Similarity=0.138  Sum_probs=29.3

Q ss_pred             HCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             588988999999982999999999999999941798647986
Q gi|254780305|r   43 LNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK   84 (95)
Q Consensus        43 L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~   84 (95)
                      -+++|..|+.+++.+|++..++...|-+   +|. ..+|||-
T Consensus       125 haft~~EI~~~a~~~~~s~~EvL~~Lk~---AGL-~slPGgg  162 (348)
T PRK08445        125 HGFSAVEIDYIAKISKISLKEVLERLQA---KGL-SSIPGAG  162 (348)
T ss_pred             CCCCHHHHHHHHHHHCCCHHHHHHHHHH---HCC-CCCCCCC
T ss_conf             2799999999999819899999999998---198-8788866


No 202
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=37.63  E-value=35  Score=15.87  Aligned_cols=45  Identities=22%  Similarity=0.299  Sum_probs=37.1

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9999998588988999999982--------99999999999999994179864
Q gi|254780305|r   36 RVRIKQSLNNVPIHIDDIIHHT--------GIEAPVVYLVLLELDLAGRLCHH   80 (95)
Q Consensus        36 ~~~Il~~L~~~p~~iD~l~~~t--------gl~~~~v~~~LleLEL~G~i~~~   80 (95)
                      +-.||..|+..|.|==+|.+..        .++.+.++.+|-.||=+|.|...
T Consensus         6 ~l~iL~~L~~~~~hGYei~k~i~~~~~~~~~~~~gtlYp~L~rLe~~glI~~~   58 (100)
T TIGR03433         6 DLLILRTLALGPLHGYGIAQRIQQRSEDVLQVEEGSLYPALHRLEKRGWIAAE   58 (100)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCEEEE
T ss_conf             99999998249977999999999974997067877289999999988984888


No 203
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=37.56  E-value=35  Score=15.87  Aligned_cols=35  Identities=20%  Similarity=0.162  Sum_probs=28.1

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99999985889889999999829999999999999
Q gi|254780305|r   36 RVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        36 ~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ++.|+-.=..+-.+.++|+...|++.+.|.+.|..
T Consensus       144 ~R~v~~Lr~~egls~~EIA~~L~is~~tVksrL~R  178 (201)
T PRK12545        144 IGRVFMMREFLDFEIDDICTELTLTANHCSVLLYR  178 (201)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             98898999992898999999989699999999999


No 204
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region; InterPro: IPR010056   This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region..
Probab=37.56  E-value=35  Score=15.87  Aligned_cols=43  Identities=14%  Similarity=0.221  Sum_probs=39.8

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             9889999999829999999999999999417986479868981
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      -|=.-|.||..+.-+++.|-.+|.-||-.|.|++.-.|.|.+.
T Consensus        52 ~py~~~mlA~~~~~~v~~i~~al~~l~~~gli~~~~ng~i~~~   94 (121)
T TIGR01714        52 IPYNAEMLATLFNRNVGDIRIALQTLESLGLIEKLNNGAIKLE   94 (121)
T ss_pred             CCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHEEECCCEEEEE
T ss_conf             9813799999850671388999999853100101027605775


No 205
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=37.44  E-value=23  Score=16.85  Aligned_cols=37  Identities=19%  Similarity=0.399  Sum_probs=17.0

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             889999999829999999999999999417986479868981
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      |...-+|+..+|+..|+|+.+.     +|+-..+|.|.|.|.
T Consensus       349 PL~lkdiA~~lglheSTVSRav-----~~Kyi~tp~G~~~lk  385 (461)
T PRK05932        349 PLVLKDIAEALGMHESTISRAT-----TNKYMATPRGIFELK  385 (461)
T ss_pred             CCCHHHHHHHCCCCHHHHHHHH-----HCCEECCCCCEEEHH
T ss_conf             7639999987399812588987-----166114897446699


No 206
>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=37.34  E-value=35  Score=15.86  Aligned_cols=36  Identities=19%  Similarity=0.290  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             899999998299999999999999994179864798
Q gi|254780305|r   48 IHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG   83 (95)
Q Consensus        48 ~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg   83 (95)
                      -++-+++...+++.++|..+.-+||..|.|..-+|.
T Consensus        29 Ps~R~la~~l~vs~~Tv~~ay~~L~~~G~i~~~~gs   64 (459)
T COG1167          29 PSIRQLAQDLGVSRSTVSRAYEELEARGYIESRPGS   64 (459)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
T ss_conf             766999999487488999999999976785512566


No 207
>PRK11886 biotin--protein ligase; Provisional
Probab=37.10  E-value=36  Score=15.83  Aligned_cols=52  Identities=12%  Similarity=0.077  Sum_probs=43.6

Q ss_pred             HHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH-HHCCCCEEEEE
Q ss_conf             999998588-98899999998299999999999999994179-86479868981
Q gi|254780305|r   37 VRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRL-CHHPEGKVSLT   88 (95)
Q Consensus        37 ~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i-~~~pGg~v~l~   88 (95)
                      .+||+.|.. +.++=++|+++.|++...|.-.+=.|+=.|.. ...++.=|+|.
T Consensus         7 ~~lL~~L~~g~~~SGe~la~~LgvSR~aVwK~i~~L~~~G~~I~s~~~~GYrL~   60 (319)
T PRK11886          7 LQLLSLLADGDFHSGEQLAEELGISRAAIWKHIQTLEEWGLDIFSVKGKGYRLA   60 (319)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCEEEC
T ss_conf             999999737992969999998798899999999999977973999789873878


No 208
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=37.04  E-value=36  Score=15.82  Aligned_cols=39  Identities=5%  Similarity=-0.095  Sum_probs=30.5

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +++.++.|+..--.+-.++.||+..+|++.++|-+.|..
T Consensus       135 L~~~~R~vl~L~~~~~ls~~EIA~~l~is~~tVksrl~R  173 (188)
T PRK09640        135 VNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKR  173 (188)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             899999999999992999999999989299999999999


No 209
>KOG1206 consensus
Probab=36.96  E-value=36  Score=15.81  Aligned_cols=63  Identities=17%  Similarity=0.174  Sum_probs=40.3

Q ss_pred             CCHHHHHHHHHHCC-CCCCHH-HHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC--EEEEECCCCCC
Q ss_conf             99899999998588-988999-99998299999999999999994179864798--68981379989
Q gi|254780305|r   32 TQCERVRIKQSLNN-VPIHID-DIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG--KVSLTMHLPSP   94 (95)
Q Consensus        32 ~~~~~~~Il~~L~~-~p~~iD-~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg--~v~l~~~~~~~   94 (95)
                      .+.++++.++.=|+ .|+|+| +.++.+|.....|...++-==-.+.|-.+-++  |.+++.|--.|
T Consensus       160 ts~DqaAlyrlsgD~NPLHiDPe~A~~agFetpilHGlc~lg~~~riv~a~~~~a~y~~~kvrF~sp  226 (272)
T KOG1206         160 TSEDQAALYRLSGDHNPLHIDPESALEAGFETPILHGLCTLGFSARIVGAQFPPAVYKAQKVRFSSP  226 (272)
T ss_pred             CHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHEEEEEECCC
T ss_conf             5464999998538988533587788754897712466777543488998756702200025541378


No 210
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=36.22  E-value=37  Score=15.75  Aligned_cols=38  Identities=13%  Similarity=-0.030  Sum_probs=30.3

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99899999998588988999999982999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      +.+.++.|+..--.+-.+..+|++..|++.++|-..|.
T Consensus       106 Lp~~~R~v~~L~~~egls~~EIA~~lgis~~tVk~~l~  143 (159)
T PRK12527        106 LPPICRESFLLRKLEGLSHQQIAEHLGISRSLVEKHIV  143 (159)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999899988987397999999998919999999999


No 211
>KOG2036 consensus
Probab=35.97  E-value=37  Score=15.72  Aligned_cols=40  Identities=13%  Similarity=0.080  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .++.-++.||-++|-.-.++|.|.+...|+.+++.+.|+.
T Consensus       849 ~Ls~vq~siLL~lGlQ~k~vd~i~kel~Lp~~Q~~all~k  888 (1011)
T KOG2036         849 KLSVVQSSILLALGLQHKSVDAIEKELNLPSNQLLALLTK  888 (1011)
T ss_pred             CHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             1589999899986035577889998846980359999999


No 212
>COG3132 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.60  E-value=38  Score=15.69  Aligned_cols=54  Identities=13%  Similarity=0.178  Sum_probs=43.5

Q ss_pred             CHHHHHHHHHHC--------CCCCCHHHHHHHH----------CCCHHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             989999999858--------8988999999982----------99999999999999994179864798689
Q gi|254780305|r   33 QCERVRIKQSLN--------NVPIHIDDIIHHT----------GIEAPVVYLVLLELDLAGRLCHHPEGKVS   86 (95)
Q Consensus        33 ~~~~~~Il~~L~--------~~p~~iD~l~~~t----------gl~~~~v~~~LleLEL~G~i~~~pGg~v~   86 (95)
                      .+-+++|+.+|=        ..|.+++-+...|          +|+-++|...|-.|+-+|.|+...|+++.
T Consensus         6 ~a~eARViGcLlEKqvtTPe~YPLtlN~l~~AcNQKT~RdPVmnLse~eVq~~l~~L~~r~lvr~~sgsRv~   77 (215)
T COG3132           6 TALEARVIGCLLEKQVTTPEQYPLTLNGLVTACNQKTNRDPVMNLSESEVQEQLDNLEKRHLVRTVSGSRVT   77 (215)
T ss_pred             CHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHCCCHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             648889987764202478564662198999997044444620017888999999999971469986233389


No 213
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=35.08  E-value=38  Score=15.64  Aligned_cols=24  Identities=13%  Similarity=0.391  Sum_probs=12.2

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             889999999829999999999999
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      |+++++|++..+++...+....-+
T Consensus         1 plsl~~lA~~~~~S~~~l~~~f~~   24 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFKK   24 (84)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             989999999889099999999999


No 214
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=34.79  E-value=39  Score=15.62  Aligned_cols=38  Identities=8%  Similarity=0.046  Sum_probs=29.7

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99899999998588988999999982999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      +...++.++-....+-.++.||++.+|++.+.|-+.|.
T Consensus       127 Lp~~~R~~~~l~~~eg~s~~EIA~~lgis~~tVk~rl~  164 (178)
T PRK12536        127 LPDRQRLPIVHVKLEGLSVEETAQLTGLSESAVKVGIH  164 (178)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99989999999988599999999998929999999999


No 215
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=34.69  E-value=39  Score=15.61  Aligned_cols=39  Identities=3%  Similarity=-0.069  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +.+.++.|+..--.+-.+..+|++.+|++.+.|-+.|..
T Consensus       109 Lp~~~r~v~~L~~~~~~s~~EIA~~l~is~~tVk~rl~R  147 (165)
T PRK09644        109 LPVIEAQAILLCDVHELTYEEAASVLDLKENTYKSHLFR  147 (165)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999998889999999989399999999999


No 216
>PRK05927 hypothetical protein; Provisional
Probab=34.66  E-value=26  Score=16.52  Aligned_cols=37  Identities=22%  Similarity=0.242  Sum_probs=28.8

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             88988999999982999999999999999941798647986
Q gi|254780305|r   44 NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK   84 (95)
Q Consensus        44 ~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~   84 (95)
                      +++|+.|+.+++.+|++..+++..|-+   +| +..+|||-
T Consensus       129 afs~~Ei~~~a~~~g~s~~e~L~~Lk~---AG-L~slPGgG  165 (350)
T PRK05927        129 FFSAVEIAHAAQVSGISTEQALQRLWD---AG-QRTIPGGG  165 (350)
T ss_pred             CCCHHHHHHHHHHCCCCHHHHHHHHHH---CC-CCCCCCCC
T ss_conf             699999999998859999999999997---37-67689987


No 217
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=34.38  E-value=39  Score=15.58  Aligned_cols=39  Identities=5%  Similarity=0.008  Sum_probs=29.6

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+...-.+-.+..+|++..|++.++|-..|..
T Consensus       130 Lp~~~r~~~~l~~~eg~s~~EIA~~l~is~~tVk~~l~r  168 (179)
T PRK12514        130 LEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRR  168 (179)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             559999999999606998999999889099999999999


No 218
>TIGR03377 glycerol3P_GlpA glycerol-3-phosphate dehydrogenase, anaerobic, A subunit. Members of this protein family are the A subunit, product of the glpA gene, of a three-subunit, membrane-anchored, FAD-dependent anaerobic glycerol-3-phosphate dehydrogenase.
Probab=34.34  E-value=40  Score=15.58  Aligned_cols=46  Identities=11%  Similarity=0.050  Sum_probs=39.4

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999998588-988999999982999999999999999941798647
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP   81 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p   81 (95)
                      +..|..++.. ...++|+|.+||.+-.+.+..-.......+.+.+.-
T Consensus       417 eaEI~~Ai~~~~a~tlddl~RRTR~GmG~CQG~fC~~r~~~il~~e~  463 (516)
T TIGR03377       417 AGEVEYAIRELDVNNLVDLRRRTRLGMGTCQGEFCAYRAAGLLSREG  463 (516)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             99999998667999889988987506776334465999999999863


No 219
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=34.11  E-value=40  Score=15.56  Aligned_cols=40  Identities=13%  Similarity=-0.061  Sum_probs=33.0

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+.+.++.++-..-.+-.+..||++..|++.++|.+.+..
T Consensus       127 ~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~r  166 (182)
T COG1595         127 RLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHR  166 (182)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             3999999999999985999999998959999999999999


No 220
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=33.31  E-value=41  Score=15.48  Aligned_cols=38  Identities=5%  Similarity=0.007  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99899999998588988999999982999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      +...++.|+..--.+-.+.++|++..|++.++|-+-|.
T Consensus       154 LP~~~R~vi~L~~~egls~~EIA~~l~is~~TVksrl~  191 (206)
T PRK12526        154 LPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLR  191 (206)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             89998889899998599999999998939999999999


No 221
>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=33.01  E-value=35  Score=15.85  Aligned_cols=18  Identities=33%  Similarity=0.414  Sum_probs=14.0

Q ss_pred             HHHHHHCCCHHHHHHHHH
Q ss_conf             999982999999999999
Q gi|254780305|r   52 DIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        52 ~l~~~tgl~~~~v~~~Ll   69 (95)
                      +|++++|++.++|+.+|-
T Consensus         2 diA~~~gvS~~TVSr~ln   19 (52)
T cd01392           2 DIARAAGVSVATVSRVLN   19 (52)
T ss_pred             HHHHHHCCCHHHHHHHHC
T ss_conf             288887859999999987


No 222
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=32.88  E-value=42  Score=15.44  Aligned_cols=39  Identities=8%  Similarity=-0.095  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.++..--.+-.+..||++.+|++.++|-+.|..
T Consensus       172 Lp~~~R~vl~L~~~egls~~EIA~~Lgis~~TVKsrL~R  210 (233)
T PRK12538        172 LPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKR  210 (233)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999984999999999989299999999999


No 223
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=32.45  E-value=27  Score=16.45  Aligned_cols=51  Identities=20%  Similarity=0.160  Sum_probs=43.3

Q ss_pred             HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCC---EEEEE
Q ss_conf             9999858898899999998299999999999999994179864798---68981
Q gi|254780305|r   38 RIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEG---KVSLT   88 (95)
Q Consensus        38 ~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg---~v~l~   88 (95)
                      .||.+.+...+.+--|+-.|+++-......+=+|.=+|.|...-||   .|.++
T Consensus        22 dIL~~~~~~~~~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT   75 (95)
T COG3432          22 DILKAISEGGIGITRIIYGANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELT   75 (95)
T ss_pred             HHHHHHCCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCEEECCCCCCCEEEEC
T ss_conf             999984179998624664327677999999999986787786148864458988


No 224
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=32.44  E-value=43  Score=15.40  Aligned_cols=49  Identities=22%  Similarity=0.253  Sum_probs=40.6

Q ss_pred             HHHHHH-HCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             999998-5889889999999829999999999999999417986479868981
Q gi|254780305|r   37 VRIKQS-LNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLT   88 (95)
Q Consensus        37 ~~Il~~-L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~   88 (95)
                      ..|+.+ |..+  ++=.|+..+.+|...+..++--||=.|.|..--|| +.++
T Consensus        25 e~vl~ail~~~--d~wkIvd~s~~plp~v~~i~~~l~~egiv~~~~g~-v~~T   74 (354)
T COG1568          25 ENVLSAILATN--DFWKIVDYSDLPLPLVASILEILEDEGIVKIEEGG-VELT   74 (354)
T ss_pred             HHHHHHHHCCC--CHHHHHHHCCCCCHHHHHHHHHHHHCCCEEEECCC-EEEH
T ss_conf             99999997475--27757653158726899999999866818985484-7642


No 225
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=32.35  E-value=43  Score=15.39  Aligned_cols=16  Identities=31%  Similarity=0.385  Sum_probs=5.3

Q ss_pred             HHHHHHCCCHHHHHHH
Q ss_conf             9999829999999999
Q gi|254780305|r   52 DIIHHTGIEAPVVYLV   67 (95)
Q Consensus        52 ~l~~~tgl~~~~v~~~   67 (95)
                      +|++++|++.++||.+
T Consensus         6 DVA~~AGVS~sTVSrv   21 (327)
T PRK10339          6 DIAIEAGVSLATVSRV   21 (327)
T ss_pred             HHHHHHCCCHHHHHHH
T ss_conf             9999978889999999


No 226
>pfam11800 RP-C_C Replication protein C C-terminal region. Replication protein C is involved in the early stages of viral DNA replication.
Probab=32.16  E-value=22  Score=16.96  Aligned_cols=46  Identities=22%  Similarity=0.304  Sum_probs=25.0

Q ss_pred             HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             999858898899999998299999999999999994179864798689
Q gi|254780305|r   39 IKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVS   86 (95)
Q Consensus        39 Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~   86 (95)
                      |--.||-.|-..++-++..|-..+. .++...||-.|.| +-||||++
T Consensus       136 lr~mlGIs~~a~~~A~~~mG~~~Aa-~~va~iler~~~I-~spGgYlR  181 (208)
T pfam11800       136 VRPMLGISPSAWQEACEVMGPENAA-VAVACILERAGHI-NSPGGYLR  181 (208)
T ss_pred             HHHHCCCCHHHHHHHHHHHCHHHHH-HHHHHHHHHHHHC-CCCCHHHH
T ss_conf             9887187899999999987959999-9999999765316-79647999


No 227
>PRK11239 hypothetical protein; Provisional
Probab=32.15  E-value=43  Score=15.37  Aligned_cols=59  Identities=20%  Similarity=0.184  Sum_probs=31.6

Q ss_pred             CHHHHHHHHH-HCCCCCCHHHHHHHHCC-----CHHHHHHHHHHHHHHH------HHHHCCCCEEEEECCC
Q ss_conf             9899999998-58898899999998299-----9999999999999941------7986479868981379
Q gi|254780305|r   33 QCERVRIKQS-LNNVPIHIDDIIHHTGI-----EAPVVYLVLLELDLAG------RLCHHPEGKVSLTMHL   91 (95)
Q Consensus        33 ~~~~~~Il~~-L~~~p~~iD~l~~~tgl-----~~~~v~~~LleLEL~G------~i~~~pGg~v~l~~~~   91 (95)
                      +..+..|+.. |=-+|...-||-.+++.     +++.|-..|-+|--++      ++-|.||.+=+.-||+
T Consensus        96 ~~~~~All~~LlLRGpQT~GELRtRs~Rm~~F~d~~~Ve~~L~~L~~r~~~plv~~LpR~pG~RE~Ry~hL  166 (215)
T PRK11239         96 SAAEVALITTLLLRGAQTPGELRSRAARMYEFSDMAEVESTLEQLANREDGPFVVRLAREPGKRESRYMHL  166 (215)
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCEEECCCCCCCCCCEEEEC
T ss_conf             88999999999972888747888767506667999999999999972689851346588898763200000


No 228
>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=32.09  E-value=43  Score=15.37  Aligned_cols=37  Identities=5%  Similarity=0.087  Sum_probs=27.6

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      |.+--....|+-||   +++-++++..|++.++++.++-+
T Consensus         7 PGE~L~eEfL~PLg---~s~~~LA~~LgVsr~~~sriv~~   43 (81)
T TIGR02607         7 PGEILLEEFLEPLG---LSVRALAKALGVSRSTLSRIVNG   43 (81)
T ss_pred             CCCHHHHHHHHCCC---HHHHHHHHHCCCCHHHHHHHHHC
T ss_conf             84132877521047---06899998709997888888744


No 229
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=31.83  E-value=44  Score=15.34  Aligned_cols=39  Identities=8%  Similarity=-0.128  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+-.--.+-.+..+|++.+|++.++|-+.|..
T Consensus       120 L~~~~R~vi~L~~~~~~s~~EIA~~l~is~~tVksrl~r  158 (173)
T PRK12522        120 LNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNY  158 (173)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999983999999999989399999999999


No 230
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=31.60  E-value=44  Score=15.32  Aligned_cols=66  Identities=11%  Similarity=0.185  Sum_probs=44.7

Q ss_pred             CCCCCCCCCHHHHHH---HHHHC-CCCCCHHHHHHHHCCCHHHHHHHHHHH--HHHHH----HHHCCCCEEEEECC
Q ss_conf             356887999899999---99858-898899999998299999999999999--99417----98647986898137
Q gi|254780305|r   25 ITHYPEYTQCERVRI---KQSLN-NVPIHIDDIIHHTGIEAPVVYLVLLEL--DLAGR----LCHHPEGKVSLTMH   90 (95)
Q Consensus        25 ~~~~p~~~~~~~~~I---l~~L~-~~p~~iD~l~~~tgl~~~~v~~~LleL--EL~G~----i~~~pGg~v~l~~~   90 (95)
                      ....+++.|+++++.   +..+. .+|+.++.++...+++.++++.-|-++  +|++.    +.+-+|+-|.+.+.
T Consensus         4 ~~~~~~~lS~~ER~~~ill~Ll~~~e~vtl~~L~~~l~VSr~Ti~~DLk~l~~~L~~y~~L~L~~~r~~Gy~I~G~   79 (426)
T PRK11564          4 TLAPPSVLSAPQRRCQILLMLFQPGLTVTLETISQLNGVDDDIARQDIAETAREIQRYHHLTLTTGQDGSYRIEGT   79 (426)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCEEEEEECCCEEEEECC
T ss_conf             7899988999999999999997799973499999996998889999999999998300886999817973899736


No 231
>pfam05491 RuvB_C Holliday junction DNA helicase ruvB C-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family consists of the C-terminal region of the RuvB protein which is thought to be helicase DNA-binding domain.
Probab=31.43  E-value=44  Score=15.31  Aligned_cols=55  Identities=22%  Similarity=0.255  Sum_probs=40.3

Q ss_pred             CCHHHHHHHHHH----CCCCCCHHHHHHHHCCCHHHHHHHHH-HHHHHHHHHHCCCCEEE
Q ss_conf             998999999985----88988999999982999999999999-99994179864798689
Q gi|254780305|r   32 TQCERVRIKQSL----NNVPIHIDDIIHHTGIEAPVVYLVLL-ELDLAGRLCHHPEGKVS   86 (95)
Q Consensus        32 ~~~~~~~Il~~L----~~~p~~iD~l~~~tgl~~~~v~~~Ll-eLEL~G~i~~~pGg~v~   86 (95)
                      .|...+++|..|    +..|+.+|.|+...|.+..++--..= -|=-.|+|.|.|-|++.
T Consensus         5 Ld~~D~~yL~~l~~~f~ggPvGl~tla~~l~e~~~TiE~viEPyLi~~G~i~RTprGR~~   64 (75)
T pfam05491         5 LDEMDRRYLETLIEKFGGGPVGLDTLAAALGEERDTIEDVIEPYLIQIGFIQRTPRGRVA   64 (75)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHCCCCHHHH
T ss_conf             789999999999997089971299999998687408999843999995443208854886


No 232
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=31.34  E-value=45  Score=15.30  Aligned_cols=29  Identities=7%  Similarity=0.122  Sum_probs=25.3

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHH
Q ss_conf             99999858898899999998299999999
Q gi|254780305|r   37 VRIKQSLNNVPIHIDDIIHHTGIEAPVVY   65 (95)
Q Consensus        37 ~~Il~~L~~~p~~iD~l~~~tgl~~~~v~   65 (95)
                      ..++...|+.-.++|+|++++|++-+.++
T Consensus        18 ~~~f~~~G~~g~~~~~Ia~~ag~~k~~i~   46 (202)
T TIGR03613        18 LDTFSRFGFHGTSLEQIAELAGVSKTNLL   46 (202)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHH
T ss_conf             99999849564889999998599888999


No 233
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=31.06  E-value=45  Score=15.27  Aligned_cols=39  Identities=8%  Similarity=-0.112  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +.+.++.|+..--.+-.+..+|+..+|++.++|-+.|..
T Consensus       137 Lp~~~R~vi~L~~~eg~s~~EIA~~lgis~~tVk~~l~R  175 (196)
T PRK12524        137 LPERQRQAVVLRHIEGLSNPEIAEVMQIGVEAVESLTAR  175 (196)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999998999980899999999989299999999999


No 234
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=30.31  E-value=46  Score=15.20  Aligned_cols=43  Identities=16%  Similarity=0.134  Sum_probs=25.6

Q ss_pred             CCCHHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             999899999998588-9889999999829999999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDL   73 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL   73 (95)
                      .++...-.+|+.+-+ .|+.--+|-.--|.+...+...|++.+|
T Consensus        80 ~LS~aaLETLAIIAY~QPiTr~eIe~IRGV~s~~~i~~LlergL  123 (182)
T PRK00135         80 SLSQAALEVLAIIAYKQPITRIEIDEIRGVNSDGALQTLLAKGL  123 (182)
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHCCC
T ss_conf             56999999999999739847999999809787999999998699


No 235
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=29.31  E-value=48  Score=15.10  Aligned_cols=40  Identities=15%  Similarity=0.073  Sum_probs=30.7

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+...++.|+..--.+-.+..+|++.+|++.+.|...|..
T Consensus       139 ~Lp~~~r~il~L~~~~g~s~~EIA~~l~is~~tVk~~l~r  178 (194)
T PRK12513        139 TLPDEQREVFLLREHGDLSLEEIAQLTGVPLETVKSRLRY  178 (194)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             2998999999999984999999999989499999999999


No 236
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=29.08  E-value=30  Score=16.22  Aligned_cols=50  Identities=24%  Similarity=0.409  Sum_probs=40.5

Q ss_pred             HHHHHHHHC-CCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             999999858-89889999999829--------------999999999999999417986479868
Q gi|254780305|r   36 RVRIKQSLN-NVPIHIDDIIHHTG--------------IEAPVVYLVLLELDLAGRLCHHPEGKV   85 (95)
Q Consensus        36 ~~~Il~~L~-~~p~~iD~l~~~tg--------------l~~~~v~~~LleLEL~G~i~~~pGg~v   85 (95)
                      -+.|+..+. ..|+.|.-|...-|              -+-+.+-.+|-+||-.|+|+..|+|++
T Consensus        55 aASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~~GR~  119 (147)
T COG2238          55 AASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTPKGRV  119 (147)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHCCCEEECCCCCE
T ss_conf             99999999853760199999987866668889434423773699999999997785652689865


No 237
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=28.93  E-value=49  Score=15.06  Aligned_cols=39  Identities=10%  Similarity=-0.013  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +.+.++.|+...-.+-.+..+|++..|++.+.|...|..
T Consensus       126 L~~~~r~il~l~~~~g~s~~eIA~~lgis~~tv~~~l~R  164 (180)
T PRK11924        126 LPEKQREVFLLRYVEGLSYQEIADQLGVPLGTVKSRLRR  164 (180)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999996859999999989499999999999


No 238
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=28.89  E-value=34  Score=15.96  Aligned_cols=38  Identities=16%  Similarity=0.379  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             8899999998299999999999999994179864798689813
Q gi|254780305|r   47 PIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        47 p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      |...-+|+...|+..++|+.+.     +|+-..+|.|.|.|..
T Consensus       363 PL~lkdiA~~lglheSTVSRav-----~~Kyi~tp~Gi~~lk~  400 (475)
T PRK12469        363 PLVLRDVAEELGLHESTVSRAT-----GNKYMATPRGTFEFKH  400 (475)
T ss_pred             CCCHHHHHHHHCCCCCHHHHHH-----CCCEECCCCCEEEHHH
T ss_conf             7349999998199820376886-----2750237985466998


No 239
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=28.80  E-value=49  Score=15.05  Aligned_cols=36  Identities=25%  Similarity=0.255  Sum_probs=28.0

Q ss_pred             CCH-HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             998-9999999858898899999998299999999999
Q gi|254780305|r   32 TQC-ERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        32 ~~~-~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~L   68 (95)
                      .+. +...|...+... .+|-+|+...+++.++|+..|
T Consensus         6 l~~~~~~~v~~L~~~G-~~i~~IA~~~~vsrsTvYRyl   42 (45)
T pfam02796         6 LNEEDINEVITLLEEG-ISIKQIAKIFGISRSTVYRYL   42 (45)
T ss_pred             CCHHHHHHHHHHHHCC-CCHHHHHHHHCCHHHHHHHHC
T ss_conf             3899999999999879-949999999860088887644


No 240
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=28.76  E-value=50  Score=15.05  Aligned_cols=62  Identities=16%  Similarity=0.054  Sum_probs=44.9

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH--HHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             998999999985889889999999829999999999999--99941798647986898137998
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE--LDLAGRLCHHPEGKVSLTMHLPS   93 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle--LEL~G~i~~~pGg~v~l~~~~~~   93 (95)
                      +...++.|+-.--.+-.+..+|++.+|++.++|.+.|..  -.|+..+..+.+-.=.|++-.|+
T Consensus       158 Lp~~qR~vl~Lr~~eglS~~EIAe~Lgis~gTVKsrl~RAr~~LR~~Lea~~~~~e~~~~~~~~  221 (222)
T PRK09647        158 LPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQALRAYLAAHAPHGEELAGVAPS  221 (222)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCC
T ss_conf             9999988998799639999999999893999999999999999999987109972176436789


No 241
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=28.68  E-value=50  Score=15.04  Aligned_cols=37  Identities=16%  Similarity=0.089  Sum_probs=27.5

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             98999999985889889999999829999999999999
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ...++.|+ .|.+.-.+..+|+...|++.++|-..|..
T Consensus       114 p~~~r~v~-~l~~~g~s~~EIA~~l~is~~tVk~~l~R  150 (166)
T PRK09639        114 TERDRTVL-LLRFSGYSYKEIAQALGIDESSVGTTLHR  150 (166)
T ss_pred             CHHHHHHH-HHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99999999-99993899999999989199999999999


No 242
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=28.51  E-value=50  Score=15.02  Aligned_cols=39  Identities=8%  Similarity=-0.098  Sum_probs=29.9

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+..--.+-.+..+|+...|++.++|-+.|..
T Consensus       139 Lp~~~R~v~~L~~~egls~~EIA~~l~is~~tVk~rl~R  177 (193)
T PRK11923        139 LPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFR  177 (193)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             789899999999994999999999989299999999999


No 243
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=28.33  E-value=50  Score=15.00  Aligned_cols=39  Identities=10%  Similarity=-0.105  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+..--.+-.+..+|+...|++.++|-+.|..
T Consensus       129 Lp~~~R~vi~L~~~eg~s~~EIA~~Lgis~~tVksrl~R  167 (188)
T PRK12517        129 LDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFR  167 (188)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999983999999999989399999999999


No 244
>TIGR02018 his_ut_repres histidine utilization repressor; InterPro: IPR010248   This entry represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0006547 histidine metabolic process, 0045892 negative regulation of transcription DNA-dependent.
Probab=28.18  E-value=42  Score=15.44  Aligned_cols=36  Identities=22%  Similarity=0.205  Sum_probs=32.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             999999982999999999999999941798647986
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK   84 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~   84 (95)
                      +-.||+..-|.+-=+|+.+|-||-=+|+|.|..|-=
T Consensus        27 sE~EL~~~~G~SRMTvnrALreLt~~G~l~R~qg~G   62 (234)
T TIGR02018        27 SENELVAQFGVSRMTVNRALRELTDAGLLERRQGVG   62 (234)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCE
T ss_conf             779999774872335789999887568188127850


No 245
>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=27.77  E-value=41  Score=15.48  Aligned_cols=34  Identities=26%  Similarity=0.341  Sum_probs=29.3

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             9999982999999999999999941798647986
Q gi|254780305|r   51 DDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK   84 (95)
Q Consensus        51 D~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~   84 (95)
                      -.|+-+.|+..+.+.-+|-.||-+|.|+.-.-||
T Consensus         7 SkiAd~~giTRSVIVNAlRKlESAGvIesrSlGm   40 (60)
T pfam08222         7 SKIADRIGITRSVIVNALRKLESAGIIESRSLGM   40 (60)
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHCCCEEECCCCC
T ss_conf             5666762961899999998764347255214677


No 246
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=27.68  E-value=52  Score=14.94  Aligned_cols=44  Identities=25%  Similarity=0.257  Sum_probs=37.3

Q ss_pred             HHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99999998588-988999999982999999999999999941798
Q gi|254780305|r   35 ERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLC   78 (95)
Q Consensus        35 ~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~   78 (95)
                      +--.|+++|-. +-++=++|++.+|+.++.|-.+|..|-=.|.+.
T Consensus        23 eg~~v~~~l~~~~evTDEeiAe~~gi~lN~VRk~LY~Lye~~La~   67 (178)
T PRK06266         23 EGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDAGLAD   67 (178)
T ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCE
T ss_conf             076999972654657899999996997899999999998576413


No 247
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=27.44  E-value=52  Score=14.91  Aligned_cols=46  Identities=13%  Similarity=0.026  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHCC---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             899999998588---9889999999829999999999999999417986
Q gi|254780305|r   34 CERVRIKQSLNN---VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        34 ~~~~~Il~~L~~---~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      ..-++|+++|..   .+.+.+++++.+|++-.++..=|--|+-.|.+..
T Consensus       162 ~TL~~i~~~l~~~~~~~~sa~eva~~~giSRvTaRRYLe~L~~~g~~~~  210 (239)
T PRK10430        162 QTLRTLCQWIDAHQDYEFSTDELANEVNISRVSCRKYLIWLVNCHILFT  210 (239)
T ss_pred             HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEE
T ss_conf             9999999999827999846999998858529889999999986895899


No 248
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.18  E-value=53  Score=14.89  Aligned_cols=39  Identities=10%  Similarity=0.020  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +...++.|+-.=-.+-.+..||+...|++.++|-..+..
T Consensus       120 Lp~~~R~v~~L~~~egls~~EIA~~lgiS~~tVk~~l~r  158 (172)
T PRK09651        120 LNGKTREAFLLSQLDGLTYSEIAHKLGVSISSVKKYVAK  158 (172)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999883999999999989399999999999


No 249
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=26.99  E-value=53  Score=14.87  Aligned_cols=29  Identities=14%  Similarity=0.309  Sum_probs=22.3

Q ss_pred             HHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             998588988999999982999999999999
Q gi|254780305|r   40 KQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        40 l~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      -+.+ .+|+.+++|+..+|++...+....-
T Consensus        15 ~~h~-~~~i~l~~lA~~~~~S~~~l~r~Fk   43 (107)
T PRK10219         15 DEHI-DQPLNIDVVAKKSGYSKWYLQRMFR   43 (107)
T ss_pred             HHHC-CCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             9866-9999999999898939999999999


No 250
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=26.90  E-value=54  Score=14.86  Aligned_cols=39  Identities=15%  Similarity=-0.047  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +.+.+++|+..--.+-.+..||++..|++.++|-..+..
T Consensus       120 LP~~~R~vf~L~r~~gls~~EIA~~LgiS~~tVk~~l~r  158 (167)
T PRK12528        120 LPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNK  158 (167)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999982989999999979799999999999


No 251
>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=26.89  E-value=54  Score=14.86  Aligned_cols=46  Identities=15%  Similarity=0.241  Sum_probs=35.3

Q ss_pred             CCCHHHHHHHHHHCCCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             99989999999858898-----89999999829999999999999999417
Q gi|254780305|r   31 YTQCERVRIKQSLNNVP-----IHIDDIIHHTGIEAPVVYLVLLELDLAGR   76 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p-----~~iD~l~~~tgl~~~~v~~~LleLEL~G~   76 (95)
                      ..+..+++|.+.+-..|     .++.+|++++|.+.+.|....=.|-.+|+
T Consensus        13 ~lt~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kklG~~Gf   63 (106)
T pfam01418        13 KLTKSEKKIADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRKLGFSGF   63 (106)
T ss_pred             HCCHHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCH
T ss_conf             649999999999992999998833999998969989999999999589989


No 252
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=26.72  E-value=54  Score=14.84  Aligned_cols=30  Identities=10%  Similarity=0.156  Sum_probs=24.2

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             999998588988999999982999999999
Q gi|254780305|r   37 VRIKQSLNNVPIHIDDIIHHTGIEAPVVYL   66 (95)
Q Consensus        37 ~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~   66 (95)
                      .+++..=|+.-+++++|++..|++-+.++-
T Consensus        21 ~~lFae~G~~~tTl~~IA~~AGVt~GaiY~   50 (213)
T PRK09975         21 IAQFALRGVANTTLNDIADAANVTRGAIYW   50 (213)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHH
T ss_conf             999998594558899999996898489998


No 253
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.51  E-value=55  Score=14.82  Aligned_cols=38  Identities=13%  Similarity=0.024  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             98999999985889889999999829999999999999
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ...++.|+..--.+-.+..+|+..+|++.++|-+.|..
T Consensus       108 p~~~R~v~~L~~~e~~s~~EIA~~l~is~~tVk~~l~R  145 (160)
T PRK09642        108 PENYRDVVLAHYLEEKSYQEIALQENIEVKTVEMKLYR  145 (160)
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             99999997999982999999999989199999999999


No 254
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=26.47  E-value=55  Score=14.82  Aligned_cols=48  Identities=15%  Similarity=0.182  Sum_probs=40.2

Q ss_pred             CCHHHHHHHHHHC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9989999999858--89889999999829999999999999999417986
Q gi|254780305|r   32 TQCERVRIKQSLN--NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH   79 (95)
Q Consensus        32 ~~~~~~~Il~~L~--~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~   79 (95)
                      +....+.|.+.+.  ..+.+.|++++.+|++-.++..-|--|+-.|.+..
T Consensus       156 ~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a  205 (224)
T COG4565         156 DELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEA  205 (224)
T ss_pred             CHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEE
T ss_conf             79999999999867577647999998837219999999999984682357


No 255
>pfam04539 Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Probab=26.39  E-value=55  Score=14.81  Aligned_cols=34  Identities=26%  Similarity=0.339  Sum_probs=27.9

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99999998588988999999982999999999999
Q gi|254780305|r   35 ERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        35 ~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      ..+++.+.+|-+| +.++|+..+|++..+|..++.
T Consensus         9 a~~~L~q~lgR~P-t~eEiA~~l~~s~~~v~~~~~   42 (78)
T pfam04539         9 AQRELEQELGREP-TPEEIAEELGISEEKVREVLE   42 (78)
T ss_pred             HHHHHHHHHCCCC-CHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999988899-999999996949999999998


No 256
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=26.22  E-value=55  Score=14.79  Aligned_cols=51  Identities=16%  Similarity=0.158  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             899999998588-988999999982999999999999999941798647986
Q gi|254780305|r   34 CERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK   84 (95)
Q Consensus        34 ~~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~   84 (95)
                      .-..+|..-+.. .-++.-.|+.+.|+..+-.--+|=+||-.|.|....+|+
T Consensus        45 e~~~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvsknr   96 (107)
T COG4901          45 ELLDKIRKEVPRERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVSKNR   96 (107)
T ss_pred             HHHHHHHHHCCCCEEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf             9999999862545155499988885552589999999987677444001676


No 257
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family; InterPro: IPR014289   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This group of sigma factors are part of the larger sigma-70 family. From homology, tree building, bidirectional best hits and their one-to-a-genome distribution, they appear to represent a conserved family..
Probab=26.20  E-value=52  Score=14.93  Aligned_cols=34  Identities=15%  Similarity=0.168  Sum_probs=25.1

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9999985889889999999829999999999999
Q gi|254780305|r   37 VRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        37 ~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ++|+-.=-.=...+|+||..++++++-++.+|-.
T Consensus       143 ARVF~MRE~L~~~~~eIC~~l~is~~N~~VlLyR  176 (194)
T TIGR02943       143 ARVFMMREVLGFESEEICQELEISASNCHVLLYR  176 (194)
T ss_pred             CCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHH
T ss_conf             0135556542486688753003137679999999


No 258
>pfam01402 RHH_1 Ribbon-helix-helix protein, copG family. The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement. The helix-turn-helix-like structure is involved in dimerization and not DNA binding as might have been expected.
Probab=26.19  E-value=55  Score=14.79  Aligned_cols=22  Identities=14%  Similarity=0.327  Sum_probs=18.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9999999829999999999999
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      -+|++++++|++.+.+....+.
T Consensus        13 ~L~ela~~~g~S~S~~ir~al~   34 (35)
T pfam01402        13 RLDELAKKRGLSRSELIREALR   34 (35)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHH
T ss_conf             9999999748868999999871


No 259
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=25.76  E-value=45  Score=15.29  Aligned_cols=50  Identities=24%  Similarity=0.263  Sum_probs=41.7

Q ss_pred             HHHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf             99999998588-988999999982999999999999999941798647986
Q gi|254780305|r   35 ERVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGK   84 (95)
Q Consensus        35 ~~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~   84 (95)
                      -..+|...+.. .-+.--.|+.+.++..+..-.+|=+|+-.|.|....+|+
T Consensus        49 ~~~ki~kEV~k~k~VTPy~La~K~~I~~SvArkvLr~L~~rG~l~lvsk~r   99 (107)
T PRK09334         49 LLKRIAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKGR   99 (107)
T ss_pred             HHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCC
T ss_conf             999999985048367589999885710899999999999789789981897


No 260
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057   Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=25.32  E-value=58  Score=14.70  Aligned_cols=35  Identities=17%  Similarity=0.259  Sum_probs=29.8

Q ss_pred             HHHHHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99999998588--988999999982999999999999
Q gi|254780305|r   35 ERVRIKQSLNN--VPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        35 ~~~~Il~~L~~--~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      |-.-|..+||.  -...+=+|++.|||+...++..|-
T Consensus        31 Dp~~~~~ALG~iArArGMtqlA~~tGlsREsLYkALs   67 (91)
T TIGR02684        31 DPALIAAALGVIARARGMTQLAKKTGLSRESLYKALS   67 (91)
T ss_pred             CHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHC
T ss_conf             9889999988998651657899982876788788735


No 261
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=25.21  E-value=58  Score=14.68  Aligned_cols=48  Identities=23%  Similarity=0.299  Sum_probs=27.5

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH--HHCCCCEEEEECCCCC
Q ss_conf             99999858898899999998299999999999999994179--8647986898137998
Q gi|254780305|r   37 VRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRL--CHHPEGKVSLTMHLPS   93 (95)
Q Consensus        37 ~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i--~~~pGg~v~l~~~~~~   93 (95)
                      .+|-++|+   +.+..|.+.++++...+.+      |+|.-  ..+|-|+++++.-+|-
T Consensus        51 e~IA~AL~---VPL~~Lle~~dld~~~l~~------l~g~~~~~slp~g~~rv~avl~e  100 (119)
T PRK13890         51 EDIAQALE---TPLPLLLESTDLDKEALDA------LAGGKAPRSLPPGFERVAAVLPE  100 (119)
T ss_pred             HHHHHHHC---CCHHHHHHHCCCCHHHHHH------HCCCCCCCCCCCCCEEEEEECHH
T ss_conf             99999987---9779987623589899988------73897877789761201124405


No 262
>pfam09681 Phage_rep_org_N N-terminal phage replisome organiser (Phage_rep_org_N). This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region.
Probab=24.64  E-value=59  Score=14.62  Aligned_cols=45  Identities=16%  Similarity=0.174  Sum_probs=40.8

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             898899999998299999999999999994179864798689813
Q gi|254780305|r   45 NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTM   89 (95)
Q Consensus        45 ~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~   89 (95)
                      ..|-..++|+..++-+++.|-.+|--++=.|.|+..-.|.+.+..
T Consensus        51 ~ipy~~e~LA~~~~~~~~~V~~Al~~f~~~glIe~~e~g~i~i~~   95 (121)
T pfam09681        51 NIPYTAEMLATIFDRPLNTVRLALKVFEKLGMIEITENGVIKIPN   95 (121)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEEEC
T ss_conf             889879999999888878999999999988978980299388653


No 263
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=24.47  E-value=60  Score=14.60  Aligned_cols=38  Identities=11%  Similarity=-0.040  Sum_probs=29.1

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99899999998588988999999982999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      +++.++.|+..--.+-.+..+|+...|++.+.|...+.
T Consensus       138 L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tVk~~l~  175 (192)
T PRK09652        138 LPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIF  175 (192)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999988889997299999999998939999999999


No 264
>COG3697 CitX Phosphoribosyl-dephospho-CoA transferase (holo-ACP synthetase) [Coenzyme metabolism / Lipid metabolism]
Probab=23.59  E-value=61  Score=14.56  Aligned_cols=21  Identities=33%  Similarity=0.398  Sum_probs=15.8

Q ss_pred             HHHHHHCCCCEEEEECCCCCC
Q ss_conf             417986479868981379989
Q gi|254780305|r   74 AGRLCHHPEGKVSLTMHLPSP   94 (95)
Q Consensus        74 ~G~i~~~pGg~v~l~~~~~~~   94 (95)
                      .-++.+++++.+|++|..|-|
T Consensus        29 ~~~L~~~~~pLvSfT~~aPGp   49 (182)
T COG3697          29 REWLKRYPLPLVSFTVNAPGP   49 (182)
T ss_pred             HHHHHHCCCCEEEEEEECCCC
T ss_conf             999985788737999835775


No 265
>pfam01399 PCI PCI domain. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Probab=23.53  E-value=62  Score=14.50  Aligned_cols=35  Identities=23%  Similarity=0.285  Sum_probs=31.1

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             88988999999982999999999999999941798
Q gi|254780305|r   44 NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLC   78 (95)
Q Consensus        44 ~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~   78 (95)
                      .+..++++++++.+|++...|-..+..|=..|+|.
T Consensus        57 ~y~~i~~~~ia~~l~i~~~~vE~~l~~~I~~g~i~   91 (105)
T pfam01399        57 PYSSISLSDLAKLLGLSVDEVEKILSKLIRDGRIR   91 (105)
T ss_pred             HHHHCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf             57541198899882999999999999999779889


No 266
>pfam11569 Homez Homeodomain leucine-zipper encoding, Homez. Homez contains two leucine zipper-like motifs and an acidic domain and belongs to the superfamily of homeobox-containing proteins. The presence of leucine zippers suggests that Homez can function as a homo or heterodimer in the nucleus. It is thought that the first leucine zipper and homeodomain 1 (HD1)of Homez is responsible for dimerization and HD2 has a specific DNA-binding activity. Homez is also thought to function as a transcriptional repressor due to the acidic region in its C-terminal domain. Homez is involved in a complex regulatory network.
Probab=23.53  E-value=57  Score=14.73  Aligned_cols=22  Identities=14%  Similarity=0.120  Sum_probs=18.5

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             8988999999982999999999
Q gi|254780305|r   45 NVPIHIDDIIHHTGIEAPVVYL   66 (95)
Q Consensus        45 ~~p~~iD~l~~~tgl~~~~v~~   66 (95)
                      -..-.+|.|+.+|+++..+|..
T Consensus        24 l~E~DL~~Lc~ks~ms~qQVk~   45 (57)
T pfam11569        24 LQEKDLDGLCEKSGMSYEQVRD   45 (57)
T ss_pred             CHHHHHHHHHHHHCCCHHHHHH
T ss_conf             4187799999982898999999


No 267
>KOG2578 consensus
Probab=23.48  E-value=63  Score=14.50  Aligned_cols=51  Identities=18%  Similarity=0.244  Sum_probs=44.6

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC
Q ss_conf             889889999999829999999999999999417986479868981379989
Q gi|254780305|r   44 NNVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHPEGKVSLTMHLPSP   94 (95)
Q Consensus        44 ~~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~pGg~v~l~~~~~~~   94 (95)
                      +.+-+++|+.+++.|..--+++-+.--||--|.+.|-.-++|+-..+.-.|
T Consensus        41 dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkGf~aiP   91 (388)
T KOG2578          41 DVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKGFGAIP   91 (388)
T ss_pred             CCCEECHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHH
T ss_conf             744314066787607047778889999998789986056720113411325


No 268
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor; InterPro: IPR012781    Members of this family belong the lacI helix-turn-helix family of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterised members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.; GO: 0003677 DNA binding, 0006355 regulation of transcription DNA-dependent, 0009750 response to fructose stimulus, 0045449 regulation of transcription.
Probab=23.47  E-value=40  Score=15.54  Aligned_cols=19  Identities=26%  Similarity=0.504  Sum_probs=11.7

Q ss_pred             HHHHHHHHCCCHHHHHHHH
Q ss_conf             9999998299999999999
Q gi|254780305|r   50 IDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        50 iD~l~~~tgl~~~~v~~~L   68 (95)
                      +|||++.+|++..++|-+|
T Consensus         2 L~dIA~LAGVS~TTASyVi   20 (335)
T TIGR02417         2 LDDIAKLAGVSKTTASYVI   20 (335)
T ss_pred             CHHHHHHCCCCHHHHHHHH
T ss_conf             0057666082323221200


No 269
>pfam04760 IF2_N Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.
Probab=22.94  E-value=64  Score=14.44  Aligned_cols=26  Identities=15%  Similarity=0.307  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             98899999998299999999999999
Q gi|254780305|r   46 VPIHIDDIIHHTGIEAPVVYLVLLEL   71 (95)
Q Consensus        46 ~p~~iD~l~~~tgl~~~~v~~~LleL   71 (95)
                      +.+.|-+|+...|++...|...|+.+
T Consensus         2 ~~itV~elA~~l~~~~~~vi~~L~~~   27 (52)
T pfam04760         2 EKIRVYELAKELGVSSKELIKKLFKL   27 (52)
T ss_pred             CCEEHHHHHHHHCCCHHHHHHHHHHC
T ss_conf             81739999999888899999999987


No 270
>smart00753 PAM PCI/PINT associated module.
Probab=22.75  E-value=65  Score=14.42  Aligned_cols=43  Identities=19%  Similarity=0.295  Sum_probs=33.5

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH---CCCCEEEE
Q ss_conf             89889999999829999999999999999417986---47986898
Q gi|254780305|r   45 NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH---HPEGKVSL   87 (95)
Q Consensus        45 ~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~---~pGg~v~l   87 (95)
                      +..++++.|+...+++...+-..+.+|=..|.|..   +..|.+..
T Consensus        22 Y~~is~~~la~~l~l~~~~vE~~l~~~I~~~~l~akIDq~~g~v~f   67 (88)
T smart00753       22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEF   67 (88)
T ss_pred             HCEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEEE
T ss_conf             2425699999894929999999999999679779998089998986


No 271
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=22.75  E-value=65  Score=14.42  Aligned_cols=43  Identities=19%  Similarity=0.295  Sum_probs=33.5

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH---CCCCEEEE
Q ss_conf             89889999999829999999999999999417986---47986898
Q gi|254780305|r   45 NVPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCH---HPEGKVSL   87 (95)
Q Consensus        45 ~~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~---~pGg~v~l   87 (95)
                      +..++++.|+...+++...+-..+.+|=..|.|..   +..|.+..
T Consensus        22 Y~~is~~~la~~l~l~~~~vE~~l~~~I~~~~l~akIDq~~g~v~f   67 (88)
T smart00088       22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEF   67 (88)
T ss_pred             HCEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEEE
T ss_conf             2425699999894929999999999999679779998089998986


No 272
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=22.70  E-value=65  Score=14.41  Aligned_cols=40  Identities=15%  Similarity=-0.071  Sum_probs=30.8

Q ss_pred             CCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9998999999985889889999999829999999999999
Q gi|254780305|r   31 YTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        31 ~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      .+.+.++.|+..--.+-.+..||+..+|++.++|.+.+..
T Consensus       116 ~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tVk~~l~r  155 (171)
T PRK09645        116 QLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHY  155 (171)
T ss_pred             CCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             5999988798999986999999999989299999999999


No 273
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=22.06  E-value=67  Score=14.34  Aligned_cols=48  Identities=19%  Similarity=0.227  Sum_probs=31.9

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH--HHHHHHHHHC
Q ss_conf             98999999985889889999999829999999999999--9994179864
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE--LDLAGRLCHH   80 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle--LEL~G~i~~~   80 (95)
                      .+.++.|+-.--..-.+.++|++..|++.+.|...|..  --|+..++.+
T Consensus       133 p~~~R~v~~Lr~~~~ls~~EIA~~l~~s~~tVk~~l~RAR~~Lr~~Le~~  182 (191)
T PRK12520        133 PARTGRVFMMREWLELETEEICKELQITATNLWVMLYRARLRLRECLELH  182 (191)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             49999999999993899999999989499999999999999999999886


No 274
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=21.96  E-value=67  Score=14.32  Aligned_cols=38  Identities=11%  Similarity=-0.054  Sum_probs=29.8

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99899999998588988999999982999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      +.+.++.|+-.--.+-.+..||++..|++.++|-..|.
T Consensus       120 Lp~~~R~v~~L~~~eGls~~EIA~~LgiS~~tVk~~l~  157 (172)
T PRK12523        120 LSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLA  157 (172)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999999999399999999998939999999999


No 275
>PRK11101 glpA sn-glycerol-3-phosphate dehydrogenase subunit A; Provisional
Probab=21.68  E-value=68  Score=14.29  Aligned_cols=46  Identities=15%  Similarity=0.057  Sum_probs=38.0

Q ss_pred             HHHHHHHHCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999998588-988999999982999999999999999941798647
Q gi|254780305|r   36 RVRIKQSLNN-VPIHIDDIIHHTGIEAPVVYLVLLELDLAGRLCHHP   81 (95)
Q Consensus        36 ~~~Il~~L~~-~p~~iD~l~~~tgl~~~~v~~~LleLEL~G~i~~~p   81 (95)
                      +..|.+++.. .+.++|+|-+||.+-.+++..-....-..+.+.|.-
T Consensus       438 e~EI~~Ai~~~~a~tlddlkRRTR~GmGrCQGgfC~~Rv~~il~r~~  484 (545)
T PRK11101        438 AGEVQYAVENLNVNNLLDLRRRTRVGMGTCQGELCACRAAGLLQRFN  484 (545)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHC
T ss_conf             99999998657999889988986078767762344899999999855


No 276
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=21.08  E-value=70  Score=14.22  Aligned_cols=39  Identities=13%  Similarity=0.112  Sum_probs=31.1

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             998999999985889889999999829999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      ++..++.|+..--.+-.+..+|+...|++.+.|...|..
T Consensus       128 L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~rl~R  166 (177)
T PRK09415        128 LPIKYREVIYLFYYEELSIKEIATVTGVNENTIKTRLKK  166 (177)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             999999999999980998999999889299999999999


No 277
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=20.84  E-value=71  Score=14.19  Aligned_cols=37  Identities=5%  Similarity=-0.129  Sum_probs=28.8

Q ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             98999999985889889999999829999999999999
Q gi|254780305|r   33 QCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLE   70 (95)
Q Consensus        33 ~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Lle   70 (95)
                      +..+..|+.. ..+-.+..+|+...|++.++|...|..
T Consensus       157 ~~~e~~V~~~-~~eg~s~~EIA~~l~is~~tV~~~l~R  193 (209)
T PRK08295        157 SDLEKEVLEL-YLDGKSYQEIAEELNRHVKSIDNALQR  193 (209)
T ss_pred             CHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             1899999999-986999999999989299999999999


No 278
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=20.73  E-value=72  Score=14.18  Aligned_cols=20  Identities=30%  Similarity=0.451  Sum_probs=10.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHH
Q ss_conf             99999998299999999999
Q gi|254780305|r   49 HIDDIIHHTGIEAPVVYLVL   68 (95)
Q Consensus        49 ~iD~l~~~tgl~~~~v~~~L   68 (95)
                      .|.++++..|++.++|+.+|
T Consensus         2 TikDVA~~AGVS~sTVSrvl   21 (333)
T COG1609           2 TIKDVAKLAGVSKATVSRVL   21 (333)
T ss_pred             CHHHHHHHHCCCHHHHHHHH
T ss_conf             68999999689998988987


No 279
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=20.73  E-value=72  Score=14.18  Aligned_cols=38  Identities=5%  Similarity=-0.080  Sum_probs=28.6

Q ss_pred             CCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             99899999998588988999999982999999999999
Q gi|254780305|r   32 TQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLL   69 (95)
Q Consensus        32 ~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~Ll   69 (95)
                      +.+..+.|+-.-..+-.+..||+++.|++.++|-..+.
T Consensus       119 LP~~~R~vflL~~~eGlsy~EIAe~LgIS~~tV~~~l~  156 (168)
T PRK12525        119 LSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMV  156 (168)
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             99999999999999299999999998979999999999


No 280
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=20.31  E-value=73  Score=14.13  Aligned_cols=41  Identities=12%  Similarity=0.062  Sum_probs=33.6

Q ss_pred             CCCCHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             799989999999858898899999998299999999999999
Q gi|254780305|r   30 EYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVYLVLLEL   71 (95)
Q Consensus        30 ~~~~~~~~~Il~~L~~~p~~iD~l~~~tgl~~~~v~~~LleL   71 (95)
                      +++++-|.+|+..+. +..+..+|+...+++..+|...+-.+
T Consensus         2 ~~LT~RE~~il~~l~-~G~s~~eIA~~L~is~~TV~~h~~~i   42 (58)
T pfam00196         2 DSLSPREREVLRLLA-AGKSNKEIADILGISEKTVKVHRSNI   42 (58)
T ss_pred             CCCCHHHHHHHHHHH-HCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             977999999999998-07999999999788899999999999


Done!