Query gi|254780805|ref|YP_003065218.1| chromosome partitioning protein B [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 300
No_of_seqs 186 out of 3259
Neff 6.5
Searched_HMMs 39220
Date Sun May 29 18:09:21 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780805.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1475 Spo0J Stage 0 sporulat 100.0 2.7E-39 6.7E-44 272.5 16.1 233 38-288 3-239 (240)
2 TIGR03454 partition_RepB plasm 100.0 2.5E-31 6.3E-36 221.3 17.7 153 32-186 57-212 (325)
3 PRK13866 plasmid partitioning 100.0 1.5E-27 3.8E-32 197.0 14.0 153 32-186 58-214 (336)
4 PRK13832 plasmid partitioning 99.9 8.4E-27 2.1E-31 192.2 13.6 174 38-212 2-181 (518)
5 TIGR00180 parB_part ParB-like 99.9 3.5E-26 8.8E-31 188.2 12.0 170 37-206 3-181 (192)
6 pfam02195 ParBc ParB-like nucl 99.9 5E-24 1.3E-28 174.3 6.0 90 40-130 1-90 (90)
7 smart00470 ParB ParB-like nucl 99.9 1.2E-22 3.1E-27 165.4 6.9 89 40-130 1-89 (89)
8 PRK13698 plasmid-partitioning 99.8 6.7E-17 1.7E-21 128.6 16.3 240 40-296 60-321 (323)
9 pfam08535 KorB KorB domain. Th 98.2 4.7E-06 1.2E-10 58.9 7.2 48 151-200 2-49 (93)
10 pfam07506 RepB RepB plasmid pa 97.7 0.00014 3.7E-09 49.4 6.4 94 131-225 1-100 (185)
11 COG5119 Uncharacterized protei 96.2 0.012 3.1E-07 37.0 5.3 79 37-118 8-105 (119)
12 PHA01976 helix-turn-helix prot 95.2 0.016 4.2E-07 36.1 2.8 35 140-174 3-37 (67)
13 KOG3388 consensus 95.2 0.018 4.6E-07 35.9 3.0 82 38-122 26-124 (136)
14 TIGR02980 SigBFG RNA polymeras 94.9 0.065 1.7E-06 32.3 5.3 67 106-174 136-218 (229)
15 TIGR02957 SigX4 RNA polymerase 94.9 0.092 2.3E-06 31.3 6.0 38 133-172 108-145 (287)
16 pfam02001 DUF134 Protein of un 94.7 0.068 1.7E-06 32.2 4.9 51 137-190 38-88 (100)
17 COG1342 Predicted DNA-binding 94.6 0.073 1.9E-06 32.0 5.0 51 137-190 35-85 (99)
18 cd00569 HTH_Hin_like Helix-tur 94.5 0.043 1.1E-06 33.4 3.5 38 134-173 5-42 (42)
19 COG2522 Predicted transcriptio 94.2 0.061 1.6E-06 32.5 3.8 43 136-179 7-49 (119)
20 PRK04217 hypothetical protein; 93.9 0.13 3.3E-06 30.4 4.9 51 137-190 44-94 (110)
21 pfam04814 HNF-1_N Hepatocyte n 93.9 0.12 2.9E-06 30.7 4.6 54 118-173 96-149 (177)
22 PRK12529 RNA polymerase sigma 93.3 0.32 8.1E-06 27.9 6.1 28 147-174 138-165 (178)
23 pfam06250 DUF1016 Protein of u 92.8 0.37 9.4E-06 27.4 5.9 66 163-230 66-137 (320)
24 pfam08857 ParBc_2 Putative Par 92.7 0.06 1.5E-06 32.5 1.7 75 39-117 2-86 (162)
25 TIGR02846 spore_sigmaK RNA pol 92.7 0.091 2.3E-06 31.4 2.6 111 59-180 71-225 (228)
26 PRK12525 RNA polymerase sigma 92.6 0.69 1.8E-05 25.7 7.0 28 147-174 129-156 (168)
27 pfam09862 DUF2089 Protein of u 92.5 0.48 1.2E-05 26.7 6.1 52 144-196 42-108 (113)
28 PRK09726 DNA-binding transcrip 92.4 0.18 4.5E-06 29.5 3.8 38 135-172 8-45 (88)
29 PRK06811 RNA polymerase factor 92.1 0.74 1.9E-05 25.5 6.7 56 134-191 128-184 (185)
30 pfam11300 DUF3102 Protein of u 92.0 0.5 1.3E-05 26.6 5.8 93 136-228 24-129 (130)
31 TIGR03070 couple_hipB transcri 91.9 0.18 4.6E-06 29.4 3.4 33 140-172 3-35 (58)
32 PRK09706 transcriptional repre 91.7 0.18 4.7E-06 29.4 3.3 39 141-179 7-45 (135)
33 smart00530 HTH_XRE Helix-turn- 91.7 0.15 3.9E-06 29.9 2.8 33 144-176 2-34 (56)
34 PRK12528 RNA polymerase sigma 91.5 0.89 2.3E-05 25.0 6.5 28 147-174 130-157 (167)
35 PRK12523 RNA polymerase sigma 91.3 0.81 2.1E-05 25.2 6.2 39 134-174 119-157 (172)
36 COG2390 DeoR Transcriptional r 91.2 0.33 8.4E-06 27.8 4.1 24 152-175 26-49 (321)
37 pfam01381 HTH_3 Helix-turn-hel 90.6 0.17 4.3E-06 29.6 2.2 33 145-177 2-34 (55)
38 pfam03235 DUF262 Protein of un 90.3 0.6 1.5E-05 26.1 4.8 54 51-104 15-68 (99)
39 COG1476 Predicted transcriptio 90.2 0.22 5.6E-06 28.9 2.5 29 143-171 5-33 (68)
40 PRK09652 RNA polymerase sigma 89.9 1.4 3.6E-05 23.7 6.3 53 133-187 136-190 (192)
41 pfam04545 Sigma70_r4 Sigma-70, 89.4 0.48 1.2E-05 26.7 3.6 39 134-174 4-42 (50)
42 pfam12116 SpoIIID Stage III sp 89.0 1.1 2.7E-05 24.5 5.2 44 139-182 6-51 (82)
43 PRK13890 conjugal transfer pro 88.9 0.34 8.7E-06 27.7 2.7 29 144-172 10-38 (119)
44 COG3355 Predicted transcriptio 88.9 0.55 1.4E-05 26.3 3.7 38 135-173 25-63 (126)
45 pfam07638 Sigma70_ECF ECF sigm 88.6 1 2.6E-05 24.6 4.9 39 137-176 137-175 (185)
46 PRK09635 sigI RNA polymerase s 88.5 0.84 2.1E-05 25.1 4.4 39 133-173 117-155 (290)
47 PRK09643 RNA polymerase sigma 88.2 2.1 5.3E-05 22.6 6.2 57 135-193 132-190 (197)
48 pfam07022 Phage_CI_repr Bacter 87.9 0.54 1.4E-05 26.4 3.1 41 143-183 2-43 (65)
49 TIGR02937 sigma70-ECF RNA poly 87.5 0.84 2.1E-05 25.1 3.9 39 134-174 114-152 (162)
50 PRK06930 positive control sigm 87.4 0.94 2.4E-05 24.8 4.1 38 135-174 115-152 (170)
51 PRK09651 RNA polymerase sigma 87.3 2.4 6.1E-05 22.2 6.3 28 147-174 130-157 (172)
52 TIGR01884 cas_HTH CRISPR locus 87.2 0.9 2.3E-05 25.0 3.9 38 140-177 171-209 (231)
53 COG3620 Predicted transcriptio 87.2 0.57 1.4E-05 26.2 2.9 31 142-172 8-38 (187)
54 pfam02796 HTH_7 Helix-turn-hel 86.9 0.75 1.9E-05 25.5 3.4 33 141-174 11-43 (45)
55 PRK13413 mpi multiple promoter 86.8 0.92 2.4E-05 24.9 3.8 33 143-176 164-196 (200)
56 PRK09943 DNA-binding transcrip 86.8 0.82 2.1E-05 25.2 3.5 35 140-174 8-42 (185)
57 cd00093 HTH_XRE Helix-turn-hel 86.8 0.56 1.4E-05 26.3 2.7 34 143-176 3-36 (58)
58 COG3283 TyrR Transcriptional r 86.7 1.3 3.4E-05 23.9 4.6 19 208-226 405-425 (511)
59 PRK08295 RNA polymerase factor 86.7 2.1 5.4E-05 22.6 5.6 54 134-192 155-208 (209)
60 PRK12515 RNA polymerase sigma 86.3 2.1 5.4E-05 22.6 5.4 58 133-194 130-187 (189)
61 PRK12527 RNA polymerase sigma 86.2 1.7 4.3E-05 23.2 4.9 28 147-174 116-143 (159)
62 TIGR02999 Sig-70_X6 RNA polyme 86.2 1.7 4.2E-05 23.3 4.8 87 90-177 96-186 (194)
63 PRK12519 RNA polymerase sigma 86.1 1.9 4.8E-05 22.9 5.1 36 151-186 156-193 (194)
64 COG2512 Predicted membrane-ass 86.0 0.96 2.4E-05 24.8 3.5 41 133-174 191-232 (258)
65 TIGR02812 fadR_gamma fatty aci 85.9 0.32 8.1E-06 27.8 1.0 56 154-220 32-104 (275)
66 cd06171 Sigma70_r4 Sigma70, re 84.9 1.4 3.6E-05 23.7 4.0 39 134-174 10-48 (55)
67 pfam01978 TrmB Sugar-specific 84.8 1.3 3.4E-05 23.8 3.8 35 140-174 10-44 (68)
68 PRK11388 DNA-binding transcrip 84.8 1.4 3.5E-05 23.7 3.9 21 210-230 529-551 (639)
69 TIGR01321 TrpR trp operon repr 84.7 2.1 5.3E-05 22.6 4.8 57 130-189 37-94 (95)
70 PRK09644 RNA polymerase sigma 84.7 2.5 6.3E-05 22.2 5.1 50 134-187 108-157 (165)
71 COG5499 Predicted transcriptio 84.5 0.98 2.5E-05 24.7 3.0 31 142-173 63-93 (120)
72 PRK04140 hypothetical protein; 84.0 1.9 4.9E-05 22.9 4.3 114 58-185 52-172 (319)
73 PRK09636 RNA polymerase sigma 83.9 2 5E-05 22.8 4.3 39 133-173 110-148 (289)
74 PHA00542 putative Cro-like pro 83.7 1.2 3.1E-05 24.1 3.2 36 136-175 19-54 (82)
75 TIGR02607 antidote_HigA addict 83.4 0.82 2.1E-05 25.2 2.2 28 146-173 14-41 (81)
76 PRK09483 response regulator; P 83.3 2.9 7.4E-05 21.7 5.0 39 133-174 147-185 (216)
77 PRK07408 RNA polymerase sigma 83.2 3.3 8.4E-05 21.3 5.2 19 154-172 131-149 (256)
78 PRK03975 tfx putative transcri 83.1 0.76 1.9E-05 25.4 2.0 26 146-172 14-39 (139)
79 PRK06759 RNA polymerase factor 83.0 2.2 5.5E-05 22.5 4.3 39 134-174 106-144 (154)
80 PRK09645 RNA polymerase sigma 82.2 4 0.0001 20.8 5.6 54 134-191 116-169 (171)
81 pfam08281 Sigma70_r4_2 Sigma-7 82.1 2.1 5.4E-05 22.6 3.9 38 135-174 11-48 (54)
82 pfam00196 GerE Bacterial regul 82.1 2 5.2E-05 22.7 3.9 38 134-174 3-40 (58)
83 PRK07500 rpoH2 RNA polymerase 82.0 3.6 9.3E-05 21.1 5.1 39 134-172 227-265 (289)
84 TIGR02985 Sig70_bacteroi1 RNA 81.8 2.2 5.5E-05 22.5 3.9 28 147-174 130-157 (167)
85 COG1813 Predicted transcriptio 81.8 1.9 4.9E-05 22.9 3.6 32 141-172 81-112 (165)
86 cd00092 HTH_CRP helix_turn_hel 81.6 2.1 5.4E-05 22.6 3.8 26 151-176 24-49 (67)
87 PRK08359 transcription factor; 81.5 2 5.2E-05 22.7 3.7 32 141-172 85-116 (175)
88 pfam01726 LexA_DNA_bind LexA D 81.2 2.8 7.2E-05 21.8 4.3 34 143-176 14-50 (65)
89 COG1318 Predicted transcriptio 81.2 4.4 0.00011 20.5 7.8 47 142-190 53-103 (182)
90 PRK12524 RNA polymerase sigma 81.0 3.8 9.6E-05 21.0 4.9 42 151-194 151-192 (196)
91 PRK10360 DNA-binding transcrip 80.9 2.4 6E-05 22.3 3.8 41 131-174 134-174 (196)
92 PRK09640 RNA polymerase sigma 80.8 4.1 0.00011 20.7 5.0 40 133-174 133-172 (188)
93 PRK05602 RNA polymerase sigma 80.7 4.5 0.00012 20.4 5.8 39 134-174 128-166 (186)
94 PRK12537 RNA polymerase sigma 80.6 2.5 6.5E-05 22.1 3.9 39 134-174 135-173 (184)
95 PRK10430 DNA-binding transcrip 80.3 2.7 6.9E-05 21.9 3.9 27 151-177 177-203 (239)
96 PRK12536 RNA polymerase sigma 80.2 4.7 0.00012 20.3 5.3 26 149-174 139-164 (178)
97 PRK11923 algU RNA polymerase s 80.2 4.7 0.00012 20.3 5.5 39 149-187 151-191 (193)
98 PRK12538 RNA polymerase sigma 80.2 4.7 0.00012 20.3 5.8 46 149-196 184-229 (233)
99 pfam02954 HTH_8 Bacterial regu 80.0 2.4 6E-05 22.3 3.6 37 137-174 4-40 (42)
100 PRK08301 sporulation sigma fac 80.0 4.3 0.00011 20.6 4.9 50 133-182 182-235 (239)
101 PRK09954 hypothetical protein; 79.9 2.5 6.4E-05 22.1 3.7 64 43-111 74-139 (362)
102 PRK09637 RNA polymerase sigma 79.9 2.9 7.3E-05 21.7 4.0 48 135-186 107-154 (181)
103 smart00421 HTH_LUXR helix_turn 79.5 2.8 7.1E-05 21.8 3.8 38 134-174 3-40 (58)
104 PRK06424 transcription factor; 79.5 2.5 6.5E-05 22.1 3.6 39 141-180 86-124 (144)
105 PRK08241 RNA polymerase factor 79.5 1.9 4.9E-05 22.8 3.0 47 123-173 147-193 (341)
106 PRK11050 manganese transport r 79.4 4.8 0.00012 20.3 5.0 73 142-226 43-116 (155)
107 cd06170 LuxR_C_like C-terminal 79.3 2.8 7E-05 21.8 3.8 37 135-174 1-37 (57)
108 PRK11924 RNA polymerase sigma 79.2 3 7.7E-05 21.6 3.9 39 134-174 125-163 (180)
109 COG3093 VapI Plasmid maintenan 79.2 1.5 3.9E-05 23.5 2.4 29 146-174 17-45 (104)
110 TIGR00721 tfx DNA-binding prot 79.1 0.99 2.5E-05 24.7 1.4 22 149-170 18-39 (142)
111 PRK10820 DNA-binding transcrip 79.0 2.7 6.9E-05 21.9 3.6 23 208-230 403-427 (513)
112 PRK09641 RNA polymerase sigma 79.0 5 0.00013 20.2 5.0 38 135-174 137-174 (187)
113 COG2197 CitB Response regulato 78.9 3 7.6E-05 21.6 3.8 38 133-173 147-184 (211)
114 pfam08279 HTH_11 HTH domain. T 78.6 2.4 6.1E-05 22.2 3.3 33 145-177 7-40 (55)
115 PRK09646 RNA polymerase sigma 78.3 3.1 7.8E-05 21.5 3.7 24 151-174 157-180 (194)
116 pfam02376 CUT CUT domain. The 78.3 3.6 9.2E-05 21.1 4.1 70 133-205 1-71 (81)
117 PRK09638 RNA polymerase sigma 78.0 3.5 9E-05 21.1 4.0 24 151-174 142-165 (177)
118 PRK06596 RNA polymerase factor 78.0 5 0.00013 20.1 4.8 20 154-173 153-172 (284)
119 cd00475 CIS_IPPS Cis (Z)-Isopr 77.9 0.53 1.4E-05 26.4 -0.2 94 90-190 6-111 (221)
120 PRK10840 transcriptional regul 77.9 3.2 8.1E-05 21.4 3.7 38 134-174 150-187 (216)
121 PRK10046 dpiA two-component re 77.7 1.9 4.7E-05 22.9 2.5 26 152-177 177-202 (225)
122 PRK12518 RNA polymerase sigma 77.5 5.7 0.00014 19.8 5.4 39 149-189 133-171 (175)
123 smart00419 HTH_CRP helix_turn_ 77.5 1.9 5E-05 22.8 2.5 24 151-174 7-30 (48)
124 PRK09047 RNA polymerase factor 77.5 5.7 0.00015 19.8 5.6 39 151-191 121-159 (161)
125 PRK07037 extracytoplasmic-func 77.4 5.7 0.00015 19.8 5.0 28 147-174 134-161 (183)
126 KOG1602 consensus 77.2 1.5 3.8E-05 23.6 1.9 94 89-189 41-149 (271)
127 PRK13919 putative RNA polymera 77.2 3.9 9.9E-05 20.9 4.0 38 135-174 137-174 (187)
128 COG3413 Predicted DNA binding 77.1 4 0.0001 20.8 4.0 42 133-174 154-200 (215)
129 COG1595 RpoE DNA-directed RNA 76.7 4 0.0001 20.8 3.9 38 135-174 128-165 (182)
130 COG3415 Transposase and inacti 76.6 5.8 0.00015 19.8 4.8 65 151-225 20-89 (138)
131 PRK12514 RNA polymerase sigma 76.6 3.8 9.8E-05 20.9 3.8 24 151-174 144-167 (179)
132 PRK11169 leucine-responsive tr 76.5 4.6 0.00012 20.4 4.2 125 133-295 10-137 (164)
133 pfam01022 HTH_5 Bacterial regu 76.5 3.5 8.9E-05 21.2 3.6 31 147-177 10-40 (47)
134 PRK09958 DNA-binding transcrip 76.5 3.8 9.8E-05 20.9 3.8 38 134-174 143-180 (204)
135 PRK12543 RNA polymerase sigma 75.9 6.3 0.00016 19.5 5.6 40 149-190 142-181 (190)
136 PRK01381 Trp operon repressor; 75.7 4.6 0.00012 20.4 4.0 54 135-189 33-93 (99)
137 COG1191 FliA DNA-directed RNA 75.4 6.5 0.00016 19.5 5.0 28 146-173 118-147 (247)
138 pfam04967 HTH_10 HTH DNA bindi 75.4 2.1 5.4E-05 22.6 2.2 25 152-176 23-47 (53)
139 COG1356 tfx Transcriptional re 75.4 1.4 3.6E-05 23.7 1.3 23 149-171 20-42 (143)
140 pfam07900 DUF1670 Protein of u 75.3 5 0.00013 20.2 4.1 64 107-175 61-128 (220)
141 PRK11179 DNA-binding transcrip 75.3 3.5 8.8E-05 21.2 3.3 48 135-192 7-54 (153)
142 pfam04218 CENP-B_N CENP-B N-te 75.2 4.8 0.00012 20.3 4.0 41 132-174 4-44 (53)
143 PRK12522 RNA polymerase sigma 75.2 5.8 0.00015 19.8 4.4 26 149-174 132-157 (173)
144 PRK10651 transcriptional regul 75.1 4.4 0.00011 20.5 3.8 38 134-174 155-192 (216)
145 cd06405 PB1_Mekk2_3 The PB1 do 74.8 6.7 0.00017 19.4 6.3 49 246-296 18-66 (79)
146 PRK12534 RNA polymerase sigma 74.8 4.7 0.00012 20.4 3.9 24 151-174 152-175 (187)
147 PRK12517 RNA polymerase sigma 74.7 5 0.00013 20.2 4.0 50 135-188 129-178 (188)
148 PRK12542 RNA polymerase sigma 74.7 4.3 0.00011 20.6 3.7 49 134-186 122-170 (185)
149 pfam10078 DUF2316 Uncharacteri 74.6 4.7 0.00012 20.4 3.8 42 135-176 3-47 (89)
150 PRK12423 LexA repressor; Provi 74.5 5.4 0.00014 20.0 4.1 48 143-199 14-66 (202)
151 pfam01255 Prenyltransf Putativ 74.4 0.97 2.5E-05 24.7 0.3 90 91-191 1-106 (222)
152 COG2944 Predicted transcriptio 74.3 3.5 8.9E-05 21.2 3.1 36 133-172 42-77 (104)
153 PRK02866 cyanate hydratase; Va 74.3 6.9 0.00018 19.3 5.0 37 149-185 15-52 (147)
154 pfam01047 MarR MarR family. Th 74.2 5.6 0.00014 19.9 4.1 36 139-174 4-39 (59)
155 COG1709 Predicted transcriptio 74.2 1.8 4.5E-05 23.1 1.6 31 143-173 31-61 (241)
156 PRK10403 transcriptional regul 74.0 4.7 0.00012 20.3 3.8 37 135-174 154-190 (215)
157 smart00418 HTH_ARSR helix_turn 73.9 3.3 8.3E-05 21.4 2.9 30 147-177 6-35 (66)
158 PRK10923 glnG nitrogen regulat 73.7 4.6 0.00012 20.4 3.6 23 207-229 343-367 (469)
159 COG2826 Tra8 Transposase and i 73.6 3.6 9.2E-05 21.1 3.0 29 144-173 16-44 (318)
160 PRK09935 transcriptional regul 73.3 4.9 0.00012 20.2 3.7 37 135-174 150-186 (210)
161 cd00090 HTH_ARSR Arsenical Res 73.3 4.6 0.00012 20.4 3.5 33 144-177 13-45 (78)
162 PRK05572 sporulation sigma fac 73.2 7.3 0.00019 19.1 5.0 17 154-170 134-150 (251)
163 PRK11608 pspF phage shock prot 73.2 4.8 0.00012 20.3 3.6 19 210-228 215-235 (325)
164 PRK09834 DNA-binding transcrip 73.1 6.2 0.00016 19.6 4.2 31 58-92 38-68 (264)
165 TIGR02960 SigX5 RNA polymerase 72.8 6.2 0.00016 19.6 4.1 52 118-173 129-180 (329)
166 PRK12512 RNA polymerase sigma 72.8 5.7 0.00015 19.8 3.9 38 134-173 131-168 (184)
167 PRK11161 fumarate/nitrate redu 72.8 5.2 0.00013 20.0 3.7 41 57-97 23-67 (235)
168 smart00344 HTH_ASNC helix_turn 72.7 4.3 0.00011 20.6 3.3 32 144-175 9-40 (108)
169 COG0020 UppS Undecaprenyl pyro 72.6 1.3 3.4E-05 23.8 0.7 135 90-231 22-181 (245)
170 COG1414 IclR Transcriptional r 72.3 6.9 0.00018 19.3 4.3 17 60-76 33-49 (246)
171 PRK08583 RNA polymerase sigma 72.2 5.4 0.00014 19.9 3.7 23 153-175 133-155 (257)
172 smart00347 HTH_MARR helix_turn 72.1 6.8 0.00017 19.3 4.2 42 132-174 5-46 (101)
173 PRK07122 RNA polymerase sigma 72.1 6 0.00015 19.7 3.9 21 153-173 143-163 (263)
174 PRK09647 RNA polymerase sigma 72.1 6 0.00015 19.7 3.9 50 135-188 158-207 (222)
175 PRK10434 srlR DNA-bindng trans 71.7 7.5 0.00019 19.0 4.3 25 152-176 100-126 (256)
176 PRK10072 putative transcriptio 71.6 7.6 0.00019 19.0 4.3 28 144-171 38-65 (96)
177 COG1522 Lrp Transcriptional re 71.3 5.7 0.00014 19.8 3.6 48 135-192 6-53 (154)
178 pfam01371 Trp_repressor Trp re 71.2 5.8 0.00015 19.7 3.7 34 143-177 41-74 (88)
179 pfam09339 HTH_IclR IclR helix- 71.2 7.5 0.00019 19.1 4.2 38 138-175 2-41 (52)
180 smart00346 HTH_ICLR helix_turn 71.0 8 0.0002 18.9 4.3 40 137-176 3-44 (91)
181 PRK13509 transcriptional repre 70.9 8.2 0.00021 18.8 4.4 19 154-172 21-39 (251)
182 PRK09415 RNA polymerase factor 70.6 7.1 0.00018 19.2 4.0 39 134-174 127-165 (177)
183 COG4565 CitB Response regulato 70.5 3.5 9E-05 21.1 2.4 28 151-178 172-199 (224)
184 PRK10906 DNA-binding transcrip 70.2 8.3 0.00021 18.7 4.3 11 152-162 100-110 (252)
185 PRK10365 transcriptional regul 70.2 5.6 0.00014 19.8 3.4 22 209-230 346-369 (441)
186 PRK08215 sporulation sigma fac 70.1 8.6 0.00022 18.7 5.0 21 153-173 140-160 (257)
187 COG2973 TrpR Trp operon repres 70.1 8.6 0.00022 18.7 4.4 47 142-189 51-98 (103)
188 PRK12513 RNA polymerase sigma 69.9 7.5 0.00019 19.0 4.0 39 134-174 139-177 (194)
189 pfam01710 Transposase_14 Trans 69.4 5.6 0.00014 19.8 3.3 26 148-174 15-40 (120)
190 PRK05911 RNA polymerase sigma 69.4 8.9 0.00023 18.6 5.3 21 154-174 128-148 (257)
191 PRK03573 transcriptional regul 69.1 9 0.00023 18.5 6.7 46 130-176 24-70 (144)
192 PRK12516 RNA polymerase sigma 69.1 7 0.00018 19.2 3.7 45 147-193 130-175 (190)
193 PRK13918 CRP/FNR family transc 69.0 4 0.0001 20.8 2.5 36 153-197 146-181 (201)
194 PRK12541 RNA polymerase sigma 68.9 7.2 0.00018 19.1 3.7 37 137-174 114-150 (161)
195 PRK12532 RNA polymerase sigma 68.6 7.3 0.00019 19.1 3.7 27 147-173 147-173 (195)
196 PRK11753 cAMP-regulatory prote 68.6 4.2 0.00011 20.7 2.5 20 154-173 170-189 (211)
197 PRK00215 LexA repressor; Valid 68.6 5.9 0.00015 19.7 3.3 48 143-199 12-64 (204)
198 PRK10339 DNA-binding transcrip 68.6 5 0.00013 20.1 2.9 10 106-115 134-143 (327)
199 TIGR02885 spore_sigF RNA polym 68.5 2.2 5.6E-05 22.5 1.0 20 153-172 200-219 (231)
200 PRK12539 RNA polymerase sigma 68.4 7.8 0.0002 18.9 3.8 27 148-174 143-169 (184)
201 PRK03902 manganese transport t 68.3 9.4 0.00024 18.4 4.3 32 143-174 12-44 (142)
202 pfam06245 DUF1015 Protein of u 68.1 4.8 0.00012 20.3 2.7 11 91-101 203-213 (411)
203 PRK09639 RNA polymerase sigma 68.1 9.5 0.00024 18.4 5.6 38 134-174 112-149 (166)
204 pfam00392 GntR Bacterial regul 68.0 9 0.00023 18.5 4.1 24 154-177 26-49 (64)
205 PRK11922 RNA polymerase sigma 68.0 8.1 0.00021 18.8 3.8 37 149-187 162-198 (231)
206 pfam03444 DUF293 Domain of unk 67.7 8.5 0.00022 18.7 3.9 34 144-177 10-48 (79)
207 PRK11512 DNA-binding transcrip 67.7 9.6 0.00025 18.3 7.3 46 128-174 31-76 (144)
208 pfam00356 LacI Bacterial regul 67.7 3.6 9.2E-05 21.1 2.0 33 154-186 1-34 (46)
209 smart00345 HTH_GNTR helix_turn 67.3 8.3 0.00021 18.7 3.8 24 154-177 22-45 (60)
210 COG1378 Predicted transcriptio 67.1 9.3 0.00024 18.4 4.0 49 125-174 4-52 (247)
211 PRK09649 RNA polymerase sigma 66.9 8.8 0.00023 18.6 3.9 24 151-174 145-168 (185)
212 TIGR02959 SigZ RNA polymerase 66.9 4.6 0.00012 20.4 2.4 35 137-172 102-136 (170)
213 TIGR00270 TIGR00270 conserved 66.7 5.7 0.00014 19.8 2.8 37 144-181 88-124 (169)
214 PRK09648 RNA polymerase sigma 66.6 9.4 0.00024 18.4 3.9 24 151-174 152-175 (187)
215 TIGR03337 phnR transcriptional 66.5 10 0.00026 18.2 4.2 21 154-174 27-47 (231)
216 PRK09391 fixK transcriptional 66.4 4.3 0.00011 20.6 2.2 22 153-174 174-195 (224)
217 PRK05803 sporulation sigma fac 66.4 8.5 0.00022 18.7 3.7 41 133-173 173-215 (228)
218 PRK11361 acetoacetate metaboli 66.3 8.9 0.00023 18.6 3.8 23 208-230 349-373 (457)
219 PRK12535 RNA polymerase sigma 66.2 10 0.00026 18.2 5.1 43 148-192 144-186 (195)
220 smart00354 HTH_LACI helix_turn 66.2 4 0.0001 20.8 2.0 33 154-186 2-35 (70)
221 PRK12526 RNA polymerase sigma 66.2 9 0.00023 18.5 3.8 24 151-174 168-191 (206)
222 PRK06288 RNA polymerase sigma 65.8 10 0.00027 18.1 5.3 22 153-174 131-152 (261)
223 PRK05412 nucleotide-binding pr 65.7 11 0.00027 18.1 4.2 38 261-300 115-152 (161)
224 pfam04461 DUF520 Protein of un 65.7 11 0.00027 18.1 4.3 38 261-300 115-152 (160)
225 PRK11886 biotin--protein ligas 65.6 11 0.00027 18.1 4.3 23 249-271 259-281 (319)
226 PRK10141 DNA-binding transcrip 65.4 7.4 0.00019 19.1 3.2 76 147-229 23-101 (106)
227 TIGR03001 Sig-70_gmx1 RNA poly 65.2 6.6 0.00017 19.4 2.9 54 121-174 142-204 (249)
228 PRK09526 lacI lac repressor; R 65.2 6.6 0.00017 19.4 2.9 17 137-153 196-212 (342)
229 PRK09642 RNA polymerase sigma 65.1 9.4 0.00024 18.4 3.7 36 151-188 121-156 (160)
230 TIGR02850 spore_sigG RNA polym 64.9 8.7 0.00022 18.6 3.5 21 152-172 222-242 (254)
231 cd07377 WHTH_GntR Winged helix 64.7 11 0.00028 18.0 4.1 24 154-177 27-50 (66)
232 PRK12427 flagellar biosynthesi 64.5 10 0.00026 18.2 3.8 39 135-175 98-138 (229)
233 PRK10163 DNA-binding transcrip 64.3 11 0.00029 17.9 4.5 18 59-76 53-70 (271)
234 PRK12547 RNA polymerase sigma 63.8 10 0.00027 18.1 3.7 28 147-174 123-150 (164)
235 pfam05732 RepL Firmicute plasm 63.7 5.9 0.00015 19.7 2.4 27 151-177 74-100 (165)
236 PRK12546 RNA polymerase sigma 63.7 10 0.00027 18.1 3.7 38 147-186 124-161 (188)
237 pfam04552 Sigma54_DBD Sigma-54 63.6 9.3 0.00024 18.4 3.5 56 125-180 13-79 (160)
238 PRK10014 DNA-binding transcrip 63.5 5.2 0.00013 20.1 2.1 26 47-75 70-95 (342)
239 COG5606 Uncharacterized conser 63.3 5.1 0.00013 20.1 2.1 33 142-174 31-63 (91)
240 pfam06322 Phage_NinH Phage Nin 63.3 5.3 0.00014 20.0 2.2 27 147-174 12-38 (64)
241 COG1349 GlpR Transcriptional r 63.3 12 0.0003 17.8 4.2 15 152-166 100-114 (253)
242 PRK12520 RNA polymerase sigma 63.1 12 0.0003 17.8 4.6 38 135-174 132-169 (191)
243 PRK09492 treR trehalose repres 62.9 5.2 0.00013 20.1 2.1 28 45-75 66-93 (315)
244 PRK10100 DNA-binding transcrip 62.7 11 0.00028 18.0 3.7 37 135-174 156-192 (216)
245 PRK11569 transcriptional repre 62.4 12 0.00031 17.7 4.3 19 58-76 55-73 (274)
246 TIGR01764 excise DNA binding d 62.2 4.1 0.00011 20.7 1.4 26 153-178 2-27 (49)
247 PRK12533 RNA polymerase sigma 62.0 12 0.00031 17.7 3.8 25 149-173 150-174 (217)
248 TIGR03020 EpsA transcriptional 61.3 8 0.0002 18.9 2.8 39 133-174 189-227 (247)
249 PRK05022 anaerobic nitric oxid 61.0 12 0.00031 17.7 3.7 22 208-229 392-415 (510)
250 PRK09764 DNA-binding transcrip 61.0 13 0.00033 17.5 4.2 21 154-174 31-51 (239)
251 KOG0257 consensus 60.9 9 0.00023 18.5 3.0 29 48-76 178-207 (420)
252 PRK12530 RNA polymerase sigma 60.9 13 0.00032 17.6 3.7 37 148-186 148-184 (191)
253 PRK07670 RNA polymerase sigma 60.7 13 0.00033 17.5 5.9 21 153-173 122-142 (250)
254 PRK09801 transcriptional activ 60.5 13 0.00033 17.5 3.9 13 250-262 289-301 (310)
255 KOG2305 consensus 60.2 9.5 0.00024 18.4 3.0 101 38-147 146-252 (313)
256 PRK09863 putative frv operon r 60.2 10 0.00026 18.1 3.2 22 79-100 124-145 (585)
257 PRK09775 hypothetical protein; 59.7 9.8 0.00025 18.3 3.0 55 70-124 74-147 (443)
258 KOG3802 consensus 59.6 12 0.0003 17.8 3.4 42 134-175 204-252 (398)
259 pfam05930 Phage_AlpA Prophage 59.6 3 7.7E-05 21.6 0.4 30 154-183 5-34 (51)
260 PRK06704 RNA polymerase factor 59.5 9.6 0.00025 18.3 2.9 50 135-186 117-171 (228)
261 PRK09390 fixJ response regulat 59.4 14 0.00035 17.4 4.9 38 134-174 141-178 (202)
262 COG1510 Predicted transcriptio 59.3 10 0.00027 18.1 3.1 52 124-176 13-65 (177)
263 TIGR03541 reg_near_HchA LuxR f 59.2 11 0.00029 17.9 3.3 37 134-174 171-208 (232)
264 PRK12540 RNA polymerase sigma 59.1 14 0.00035 17.3 3.8 43 147-191 122-164 (181)
265 pfam04539 Sigma70_r3 Sigma-70 58.9 11 0.00027 18.1 3.1 39 141-179 7-47 (78)
266 cd06811 PLPDE_III_yhfX_like Ty 58.5 4.6 0.00012 20.4 1.2 82 36-117 102-201 (382)
267 PRK11534 DNA-binding transcrip 58.4 14 0.00035 17.3 3.6 10 61-70 11-20 (224)
268 cd01392 HTH_LacI Helix-turn-he 58.2 8.8 0.00022 18.6 2.5 31 156-186 1-32 (52)
269 COG2188 PhnF Transcriptional r 57.7 15 0.00037 17.2 4.2 37 141-177 13-56 (236)
270 pfam01325 Fe_dep_repress Iron 57.5 12 0.00031 17.7 3.2 33 144-176 11-44 (58)
271 PRK09508 leuO leucine transcri 57.4 13 0.00034 17.5 3.3 17 157-173 41-57 (314)
272 PRK11303 DNA-binding transcrip 57.4 7.2 0.00018 19.1 2.0 26 47-75 67-92 (330)
273 PRK11475 DNA-binding transcrip 57.3 15 0.00038 17.2 3.8 38 133-173 133-170 (205)
274 PRK10401 DNA-binding transcrip 57.2 7.7 0.0002 19.0 2.1 19 137-155 191-209 (346)
275 PRK01905 DNA-binding protein F 56.9 15 0.00038 17.1 3.6 42 135-177 34-75 (77)
276 PRK11041 DNA-binding transcrip 56.7 7.7 0.0002 19.0 2.1 26 47-75 73-98 (341)
277 PRK10727 DNA-binding transcrip 56.7 7.7 0.0002 19.0 2.1 20 136-155 190-209 (342)
278 PRK06986 fliA flagellar biosyn 56.5 15 0.00039 17.1 5.1 22 153-174 112-133 (234)
279 PRK10703 DNA-binding transcrip 56.5 7.8 0.0002 18.9 2.0 26 47-75 65-90 (335)
280 PRK11402 DNA-binding transcrip 56.3 15 0.00039 17.0 4.2 21 154-174 37-57 (243)
281 PRK09392 ftrB transcriptional 56.2 9.8 0.00025 18.3 2.5 66 45-113 7-75 (236)
282 PRK12544 RNA polymerase sigma 55.9 16 0.0004 17.0 3.7 39 147-187 160-198 (207)
283 PRK11337 DNA-binding transcrip 55.3 15 0.00038 17.1 3.3 64 124-187 14-84 (293)
284 TIGR02941 Sigma_B RNA polymera 55.1 10 0.00026 18.2 2.4 22 152-173 222-243 (256)
285 TIGR02478 6PF1K_euk 6-phosphof 54.9 6.8 0.00017 19.3 1.5 79 96-179 295-385 (777)
286 PRK12469 RNA polymerase factor 54.2 14 0.00037 17.2 3.1 22 155-176 232-253 (475)
287 PRK11523 DNA-binding transcrip 54.1 17 0.00042 16.8 4.1 24 246-269 214-237 (258)
288 smart00529 HTH_DTXR Helix-turn 53.6 16 0.0004 17.0 3.2 59 156-227 3-62 (96)
289 PRK12511 RNA polymerase sigma 53.1 10 0.00025 18.2 2.1 38 150-189 125-162 (182)
290 COG1508 RpoN DNA-directed RNA 52.8 17 0.00044 16.7 3.8 49 126-174 295-352 (444)
291 PRK12545 RNA polymerase sigma 52.6 18 0.00045 16.7 5.0 43 147-191 150-192 (201)
292 smart00420 HTH_DEOR helix_turn 51.6 18 0.00046 16.6 3.2 30 147-176 8-38 (53)
293 pfam10654 DUF2481 Protein of u 51.2 18 0.00047 16.5 3.8 24 151-174 79-102 (126)
294 TIGR02835 spore_sigmaE RNA pol 51.1 11 0.00027 18.1 2.0 21 153-173 199-219 (234)
295 PRK12531 RNA polymerase sigma 51.0 19 0.00047 16.5 5.4 24 151-174 156-179 (194)
296 PRK04841 transcriptional regul 50.9 19 0.00048 16.5 3.6 13 284-296 872-884 (903)
297 pfam04492 Phage_rep_O Bacterio 50.8 19 0.00048 16.5 4.9 60 124-192 19-85 (100)
298 TIGR02707 butyr_kinase butyrat 50.7 19 0.00048 16.5 3.8 73 62-134 48-150 (353)
299 COG1395 Predicted transcriptio 50.1 17 0.00043 16.8 2.9 34 141-174 127-160 (313)
300 TIGR02431 pcaR_pcaU beta-ketoa 50.1 16 0.00041 16.9 2.8 22 152-173 24-45 (252)
301 COG1609 PurR Transcriptional r 50.0 11 0.00028 17.9 2.0 106 44-155 61-208 (333)
302 COG2186 FadR Transcriptional r 50.0 19 0.00049 16.4 3.8 28 61-92 49-76 (241)
303 COG4804 Predicted nuclease of 50.0 14 0.00037 17.2 2.6 34 195-228 3-39 (159)
304 pfam09048 Cro Cro. Members of 49.2 15 0.00038 17.1 2.6 28 146-175 7-34 (58)
305 TIGR02983 SigE-fam_strep RNA p 49.1 13 0.00032 17.6 2.2 22 152-173 129-150 (165)
306 PRK10225 DNA-binding transcrip 48.9 20 0.00051 16.3 4.1 35 59-97 46-80 (257)
307 smart00422 HTH_MERR helix_turn 48.3 20 0.00052 16.2 3.3 68 153-227 1-68 (70)
308 smart00352 POU Found in Pit-Oc 48.1 21 0.00053 16.2 3.6 34 141-174 13-52 (75)
309 PRK09802 DNA-binding transcrip 48.0 21 0.00053 16.2 4.0 25 152-176 115-141 (269)
310 pfam00325 Crp Bacterial regula 47.8 16 0.00042 16.8 2.6 24 153-176 3-26 (32)
311 PRK13355 bifunctional HTH-doma 47.8 21 0.00053 16.2 3.1 29 48-76 287-316 (518)
312 PRK08960 hypothetical protein; 47.7 20 0.0005 16.3 3.0 30 47-76 170-200 (387)
313 PRK00430 fis DNA-binding prote 47.7 21 0.00053 16.2 3.6 34 144-177 63-96 (98)
314 PRK10079 putative transcriptio 47.6 15 0.00039 17.0 2.4 20 154-173 37-56 (241)
315 COG2771 CsgD DNA-binding HTH d 47.5 21 0.00054 16.2 3.8 38 134-174 4-41 (65)
316 pfam01418 HTH_6 Helix-turn-hel 47.5 21 0.00054 16.2 3.8 86 131-216 10-102 (106)
317 PRK10423 transcriptional repre 47.5 12 0.00031 17.7 1.8 27 47-76 62-88 (327)
318 PRK07324 transaminase; Validat 47.1 21 0.00053 16.2 3.0 45 249-294 318-365 (373)
319 PRK06348 aspartate aminotransf 46.6 21 0.00053 16.2 2.9 43 251-295 333-381 (383)
320 COG2964 Uncharacterized protei 46.5 14 0.00035 17.3 2.0 23 154-176 193-215 (220)
321 PRK07683 aminotransferase A; V 46.2 22 0.00056 16.0 3.0 43 252-294 332-378 (387)
322 pfam01527 Transposase_8 Transp 46.1 22 0.00056 16.0 5.6 43 133-176 5-47 (75)
323 PRK13980 NAD synthetase; Provi 45.7 22 0.00057 16.0 4.4 83 136-221 138-223 (264)
324 pfam08220 HTH_DeoR DeoR-like h 45.7 22 0.00057 16.0 3.2 29 149-177 11-39 (57)
325 TIGR03537 DapC succinyldiamino 45.7 21 0.00054 16.2 2.9 43 250-295 301-349 (350)
326 TIGR02233 Myxo_sigma_rel Myxoc 45.5 21 0.00053 16.2 2.8 32 143-174 31-62 (106)
327 PRK07405 RNA polymerase sigma 45.5 23 0.00058 16.0 4.4 31 146-176 177-209 (318)
328 TIGR02997 Sig70-cyanoRpoD RNA 45.2 23 0.00058 15.9 4.3 39 152-190 64-109 (336)
329 cd04762 HTH_MerR-trunc Helix-T 45.2 13 0.00033 17.5 1.7 28 153-180 1-28 (49)
330 pfam00126 HTH_1 Bacterial regu 44.9 23 0.00059 15.9 3.7 34 142-177 5-38 (60)
331 COG3311 AlpA Predicted transcr 44.6 7.4 0.00019 19.1 0.4 31 153-183 14-44 (70)
332 COG3655 Predicted transcriptio 44.5 22 0.00057 16.0 2.8 29 143-171 6-34 (73)
333 PRK10240 undecaprenyl pyrophos 44.5 5.8 0.00015 19.7 -0.2 89 92-190 1-104 (229)
334 KOG0259 consensus 44.4 23 0.00059 15.9 2.9 29 48-76 205-234 (447)
335 pfam07750 GcrA GcrA cell cycle 43.9 19 0.00048 16.4 2.4 31 139-170 6-37 (162)
336 PRK05657 RNA polymerase sigma 43.9 24 0.00061 15.8 6.1 26 152-177 192-217 (328)
337 PRK09990 DNA-binding transcrip 43.4 24 0.00062 15.8 3.8 26 61-90 46-71 (251)
338 PRK03837 transcriptional regul 43.3 20 0.00051 16.3 2.5 15 63-77 55-69 (243)
339 COG4189 Predicted transcriptio 43.2 24 0.00062 15.7 2.9 33 144-176 29-61 (308)
340 COG3829 RocR Transcriptional r 43.1 25 0.00063 15.7 3.6 19 212-230 456-476 (560)
341 PRK05066 arginine repressor; P 42.8 25 0.00063 15.7 3.7 40 139-178 9-55 (156)
342 PRK07367 consensus 42.7 25 0.00064 15.7 3.0 43 251-294 334-379 (385)
343 PRK06207 aspartate aminotransf 42.6 24 0.00062 15.7 2.8 45 250-294 350-398 (406)
344 cd01455 vWA_F11C1-5a_type Von 42.5 11 0.00028 17.9 1.0 91 92-188 88-188 (191)
345 cd06571 Bac_DnaA_C C-terminal 42.3 25 0.00064 15.6 5.0 26 149-174 41-67 (90)
346 COG1654 BirA Biotin operon rep 42.1 25 0.00065 15.6 4.0 44 152-204 19-65 (79)
347 COG2204 AtoC Response regulato 42.0 26 0.00065 15.6 3.5 22 210-231 349-372 (464)
348 TIGR02395 rpoN_sigma RNA polym 41.9 13 0.00034 17.4 1.3 20 154-173 367-386 (477)
349 PRK07865 N-succinyldiaminopime 41.7 26 0.00066 15.6 3.0 41 251-294 317-363 (364)
350 PRK13182 racA polar chromosome 41.7 26 0.00066 15.6 4.9 24 156-179 4-27 (178)
351 pfam07037 DUF1323 Putative tra 41.7 20 0.0005 16.3 2.2 22 153-174 1-22 (122)
352 PRK08069 consensus 41.5 26 0.00066 15.6 2.8 43 251-295 341-387 (390)
353 PRK05839 hypothetical protein; 41.4 23 0.0006 15.9 2.5 43 251-295 320-370 (376)
354 pfam10302 DUF2407 Putative mem 41.4 9.8 0.00025 18.3 0.6 54 106-161 83-138 (252)
355 PRK07598 RNA polymerase sigma 41.4 26 0.00067 15.6 4.3 15 156-170 277-291 (410)
356 cd01282 HTH_MerR-like_sg3 Heli 41.2 26 0.00067 15.5 4.1 66 154-229 2-69 (112)
357 PHA00675 hypothetical protein 41.1 26 0.00067 15.5 3.6 34 140-173 27-60 (78)
358 PRK10411 DNA-binding transcrip 41.1 26 0.00067 15.5 4.2 20 154-173 20-39 (240)
359 PRK05794 consensus 40.4 25 0.00064 15.7 2.6 41 252-294 346-390 (397)
360 pfam02006 DUF137 Protein of un 40.0 27 0.0007 15.4 3.0 62 59-122 42-103 (178)
361 PRK07212 consensus 39.9 27 0.0007 15.4 2.7 43 251-295 329-375 (378)
362 TIGR02844 spore_III_D sporulat 39.7 28 0.00071 15.4 4.4 42 144-185 11-54 (80)
363 pfam10668 Phage_terminase Phag 39.6 28 0.00071 15.4 2.8 32 142-173 11-43 (60)
364 smart00342 HTH_ARAC helix_turn 39.4 23 0.00058 15.9 2.2 36 153-190 2-38 (84)
365 cd04785 HTH_CadR-PbrR-like Hel 38.9 29 0.00073 15.3 3.5 24 155-178 3-26 (126)
366 PRK08362 consensus 38.6 29 0.00073 15.3 2.9 24 271-294 356-380 (389)
367 pfam05339 DUF739 Protein of un 38.6 24 0.00061 15.8 2.2 29 146-177 11-39 (69)
368 PRK08558 adenine phosphoribosy 38.4 29 0.00074 15.3 4.3 39 142-181 14-52 (238)
369 PRK04280 arginine repressor; P 38.4 29 0.00074 15.3 4.3 129 139-295 5-147 (149)
370 PRK06375 consensus 38.4 29 0.00074 15.3 3.2 45 251-295 328-376 (381)
371 pfam07278 DUF1441 Protein of u 38.3 25 0.00063 15.7 2.3 20 133-152 62-81 (152)
372 TIGR01285 nifN nitrogenase mol 38.2 23 0.00058 16.0 2.0 112 57-169 184-315 (451)
373 PRK10227 DNA-binding transcrip 37.8 30 0.00076 15.2 4.5 13 157-169 5-17 (135)
374 PRK06855 aminotransferase; Val 37.7 30 0.00076 15.2 3.1 28 48-75 177-205 (433)
375 PRK08363 alanine aminotransfer 37.4 30 0.00077 15.2 3.1 43 252-294 343-389 (398)
376 PRK07682 hypothetical protein; 37.2 30 0.00077 15.1 3.1 41 252-294 325-371 (378)
377 pfam04645 DUF603 Protein of un 37.2 30 0.00077 15.1 2.8 33 137-172 7-39 (181)
378 PRK10188 DNA-binding transcrip 37.0 25 0.00065 15.6 2.2 38 134-174 179-216 (240)
379 TIGR02612 mob_myst_A mobile my 36.7 25 0.00064 15.7 2.1 29 143-171 28-57 (150)
380 PRK08443 consensus 36.5 31 0.00079 15.1 2.8 42 251-294 336-381 (388)
381 pfam00155 Aminotran_1_2 Aminot 36.4 31 0.00079 15.1 2.7 41 251-293 306-351 (351)
382 TIGR02787 codY_Gpos GTP-sensin 36.2 7.8 0.0002 18.9 -0.6 120 50-177 66-227 (255)
383 TIGR03542 DAPAT_plant LL-diami 36.0 32 0.0008 15.0 3.2 42 252-295 353-400 (402)
384 COG1438 ArgR Arginine represso 35.9 32 0.00081 15.0 3.8 40 140-179 7-52 (150)
385 COG2456 Uncharacterized conser 35.6 11 0.00028 18.0 0.1 10 157-166 62-71 (121)
386 TIGR01817 nifA Nif-specific re 35.0 27 0.00068 15.5 2.0 19 245-263 387-405 (574)
387 COG1168 MalY Bifunctional PLP- 34.9 33 0.00084 14.9 3.1 28 49-76 165-193 (388)
388 PRK10572 DNA-binding transcrip 34.9 33 0.00084 14.9 6.2 49 152-203 199-247 (290)
389 TIGR02087 LEUD_arch 3-isopropy 34.9 25 0.00063 15.7 1.8 75 41-125 9-92 (159)
390 PRK12414 putative aminotransfe 34.9 33 0.00084 14.9 2.8 23 273-295 360-383 (384)
391 PRK07366 succinyldiaminopimela 34.6 32 0.00081 15.0 2.3 44 251-294 338-385 (388)
392 PRK09265 aminotransferase AlaT 34.6 33 0.00084 14.9 2.4 42 253-294 351-396 (404)
393 TIGR01818 ntrC nitrogen regula 34.3 33 0.00084 14.9 2.4 15 218-232 353-367 (471)
394 PRK09276 aspartate aminotransf 34.3 33 0.00083 14.9 2.4 45 251-295 336-384 (385)
395 PRK08154 anaerobic benzoate ca 34.3 34 0.00086 14.9 3.0 18 135-152 108-125 (304)
396 PRK09464 pdhR transcriptional 34.2 30 0.00077 15.2 2.2 26 61-90 49-74 (254)
397 PRK08361 aspartate aminotransf 34.2 34 0.00086 14.8 3.1 44 251-294 337-384 (390)
398 cd04909 ACT_PDH-BS C-terminal 34.1 34 0.00086 14.8 3.0 51 249-299 14-68 (69)
399 PRK11414 putative DNA-binding 34.1 33 0.00084 14.9 2.3 15 47-61 24-38 (221)
400 COG2524 Predicted transcriptio 34.0 27 0.00068 15.5 1.9 31 59-92 38-68 (294)
401 PRK06030 hypothetical protein; 33.9 34 0.00087 14.8 4.0 37 138-174 65-103 (136)
402 pfam07453 NUMOD1 NUMOD1 domain 33.7 17 0.00044 16.7 0.9 25 148-173 13-37 (37)
403 cd01111 HTH_MerD Helix-Turn-He 33.3 35 0.00089 14.7 3.3 69 153-230 1-71 (107)
404 PRK08912 hypothetical protein; 33.0 35 0.0009 14.7 3.1 42 253-294 334-381 (387)
405 PRK05901 RNA polymerase sigma 32.9 35 0.0009 14.7 4.3 22 154-175 264-285 (398)
406 TIGR03558 oxido_grp_1 lucifera 32.9 7.4 0.00019 19.1 -1.1 63 49-112 119-182 (323)
407 PRK08175 aminotransferase; Val 32.8 35 0.0009 14.7 3.2 41 252-294 338-384 (395)
408 pfam00157 Pou Pou domain - N-t 32.8 36 0.00091 14.7 3.5 34 141-174 13-52 (75)
409 PRK06108 aspartate aminotransf 32.7 36 0.00091 14.7 2.7 44 251-294 330-377 (382)
410 TIGR01265 tyr_nico_aTase tyros 32.6 36 0.00091 14.7 3.0 77 32-115 161-256 (424)
411 PRK07568 aspartate aminotransf 32.4 36 0.00092 14.7 2.8 44 252-295 333-388 (396)
412 cd04770 HTH_HMRTR Helix-Turn-H 32.3 36 0.00092 14.6 3.9 20 155-174 3-22 (123)
413 pfam06056 Terminase_5 Putative 32.2 23 0.00058 15.9 1.3 22 151-172 12-33 (58)
414 PRK10421 DNA-binding transcrip 31.7 37 0.00094 14.6 4.1 28 59-90 39-66 (253)
415 TIGR02404 trehalos_R_Bsub treh 31.7 34 0.00088 14.8 2.1 31 154-184 26-56 (236)
416 cd00592 HTH_MerR-like Helix-Tu 31.6 37 0.00095 14.6 3.4 68 153-228 1-68 (100)
417 PRK07777 aminotransferase; Val 31.5 37 0.00095 14.6 3.1 44 251-294 331-381 (386)
418 PRK10947 global DNA-binding tr 31.5 35 0.00089 14.7 2.1 16 207-222 60-75 (135)
419 PRK07681 aspartate aminotransf 31.0 38 0.00097 14.5 3.1 47 251-297 336-386 (399)
420 COG0436 Aspartate/tyrosine/aro 30.9 38 0.00097 14.5 3.1 47 249-295 336-387 (393)
421 PRK06575 consensus 30.8 38 0.00098 14.5 3.2 43 251-295 348-394 (399)
422 TIGR03539 DapC_actino succinyl 30.6 39 0.00098 14.5 2.2 42 250-294 310-357 (357)
423 PRK07310 consensus 30.4 34 0.00085 14.9 1.9 44 250-294 341-387 (395)
424 PRK09082 putative aminotransfe 30.1 39 0.001 14.4 2.8 44 252-295 336-385 (386)
425 KOG3398 consensus 30.0 39 0.001 14.4 3.2 41 133-173 67-107 (135)
426 pfam10279 Latarcin Latarcin pr 30.0 40 0.001 14.4 2.5 19 126-144 50-69 (88)
427 TIGR02394 rpoS_proteo RNA poly 30.0 35 0.00088 14.8 1.9 29 151-179 154-182 (292)
428 PRK07309 aromatic amino acid a 29.9 40 0.001 14.4 3.2 46 251-296 336-385 (390)
429 PRK10219 DNA-binding transcrip 29.8 40 0.001 14.4 6.4 47 152-201 21-67 (107)
430 PRK11302 DNA-binding transcrip 29.7 40 0.001 14.4 3.7 44 133-176 12-58 (284)
431 TIGR03538 DapC_gpp succinyldia 29.7 40 0.001 14.4 3.0 24 272-295 368-392 (394)
432 COG4800 Predicted transcriptio 29.7 40 0.001 14.4 3.0 32 142-173 19-50 (170)
433 PRK05942 aspartate aminotransf 29.2 41 0.001 14.3 2.4 48 251-298 340-391 (394)
434 PRK07337 aminotransferase; Val 29.1 33 0.00084 14.9 1.7 42 251-294 336-384 (388)
435 PRK05658 RNA polymerase sigma 29.1 41 0.001 14.3 3.1 18 58-75 40-57 (620)
436 COG1802 GntR Transcriptional r 29.0 41 0.001 14.3 2.4 21 45-65 27-47 (230)
437 PRK01533 histidinol-phosphate 28.9 39 0.001 14.4 2.0 41 250-295 311-351 (366)
438 PRK00550 rpsE 30S ribosomal pr 28.7 42 0.0011 14.3 5.3 67 79-165 89-155 (156)
439 PRK06225 aspartate aminotransf 28.7 42 0.0011 14.3 3.2 44 249-295 317-367 (375)
440 cd04776 HTH_GnyR Helix-Turn-He 28.7 42 0.0011 14.3 3.4 27 153-179 1-27 (118)
441 cd04772 HTH_TioE_rpt1 First He 28.6 29 0.00073 15.3 1.3 29 153-181 1-29 (99)
442 pfam00440 TetR_N Bacterial reg 28.6 42 0.0011 14.2 3.6 29 146-174 7-38 (47)
443 PRK06056 consensus 28.2 43 0.0011 14.2 3.0 43 251-295 350-396 (402)
444 KOG0994 consensus 28.1 43 0.0011 14.2 10.8 12 59-70 1490-1501(1758)
445 PRK07590 L,L-diaminopimelate a 28.0 43 0.0011 14.2 3.1 45 251-295 359-407 (409)
446 pfam01316 Arg_repressor Argini 27.8 43 0.0011 14.2 3.2 35 143-177 9-49 (70)
447 TIGR01298 RNaseT ribonuclease 27.5 39 0.001 14.4 1.8 10 129-138 129-138 (201)
448 TIGR02079 THD1 threonine dehyd 27.3 44 0.0011 14.1 2.2 49 252-300 344-401 (415)
449 KOG2252 consensus 27.3 44 0.0011 14.1 3.6 62 128-193 318-381 (558)
450 TIGR02092 glgD glucose-1-phosp 27.2 17 0.00043 16.8 -0.1 36 36-71 68-114 (383)
451 TIGR01478 STEVOR variant surfa 27.0 22 0.00057 16.0 0.5 37 45-83 51-99 (315)
452 PRK05764 aspartate aminotransf 26.8 45 0.0011 14.0 3.1 43 251-295 337-383 (389)
453 PRK08068 transaminase; Reviewe 26.7 45 0.0011 14.0 2.7 45 251-295 337-385 (389)
454 TIGR01529 argR_whole arginine 26.5 45 0.0012 14.0 2.9 130 141-295 4-153 (155)
455 PRK04984 fatty acid metabolism 26.5 45 0.0012 14.0 4.3 23 63-89 48-70 (239)
456 PRK04175 rpl7ae 50S ribosomal 26.5 39 0.00099 14.5 1.6 38 133-170 55-98 (123)
457 PRK10837 putative DNA-binding 26.3 46 0.0012 14.0 3.8 12 285-296 278-289 (291)
458 cd04780 HTH_MerR-like_sg5 Heli 26.3 46 0.0012 14.0 3.4 69 154-229 2-71 (95)
459 PRK05949 RNA polymerase sigma 26.2 46 0.0012 14.0 4.4 25 153-177 195-219 (327)
460 PRK11511 DNA-binding transcrip 26.2 46 0.0012 14.0 6.9 39 152-191 25-63 (127)
461 TIGR02639 ClpA ATP-dependent C 26.0 46 0.0012 13.9 5.4 94 152-259 396-497 (774)
462 cd01821 Rhamnogalacturan_acety 26.0 38 0.00097 14.5 1.5 26 60-86 93-118 (198)
463 PRK06507 consensus 25.9 41 0.0011 14.3 1.7 43 252-295 349-394 (400)
464 smart00497 IENR1 Intron encode 25.6 31 0.00079 15.1 1.0 25 150-175 16-40 (53)
465 COG3888 Predicted transcriptio 25.5 47 0.0012 13.9 4.0 48 98-145 90-137 (321)
466 PRK11557 putative DNA-binding 25.2 48 0.0012 13.9 5.0 58 132-189 11-73 (282)
467 pfam10743 Phage_Cox Regulatory 25.2 46 0.0012 14.0 1.8 28 152-179 12-39 (87)
468 PRK03341 arginine repressor; P 25.2 48 0.0012 13.9 3.8 131 140-295 16-163 (168)
469 PRK09744 DNA-binding transcrip 25.2 48 0.0012 13.8 3.3 34 148-185 7-40 (75)
470 smart00531 TFIIE Transcription 25.0 44 0.0011 14.1 1.7 33 144-176 7-39 (147)
471 PRK09514 zntR zinc-responsive 25.0 48 0.0012 13.8 3.7 11 152-162 58-68 (140)
472 PRK10328 DNA binding protein, 24.9 49 0.0012 13.8 2.3 17 206-222 59-75 (134)
473 KOG3725 consensus 24.9 45 0.0012 14.0 1.8 84 86-174 149-235 (375)
474 PRK00423 tfb transcription ini 24.9 49 0.0012 13.8 3.4 21 154-174 184-204 (310)
475 pfam08564 CDC37_C Cdc37 C term 24.9 49 0.0012 13.8 3.0 42 175-216 11-53 (87)
476 PRK08636 aspartate aminotransf 24.9 49 0.0012 13.8 3.2 45 251-295 348-396 (403)
477 PRK07778 consensus 24.9 49 0.0012 13.8 3.0 45 250-294 332-381 (386)
478 PRK06959 putative threonine-ph 24.8 49 0.0012 13.8 2.2 46 247-295 283-329 (339)
479 pfam11353 DUF3153 Protein of u 24.7 49 0.0012 13.8 5.6 46 247-293 43-88 (210)
480 pfam00376 MerR MerR family reg 24.7 36 0.00092 14.7 1.2 27 154-180 1-27 (38)
481 PRK05957 aspartate aminotransf 24.5 49 0.0013 13.8 2.9 45 250-294 331-380 (389)
482 cd01109 HTH_YyaN Helix-Turn-He 24.5 49 0.0013 13.8 3.4 28 153-180 1-28 (113)
483 TIGR01515 branching_enzym 1,4- 24.5 11 0.00027 18.1 -1.5 22 88-109 81-104 (608)
484 PRK05201 hslU ATP-dependent pr 24.5 50 0.0013 13.8 2.3 156 133-299 2-169 (442)
485 TIGR00972 3a0107s01c2 phosphat 24.4 41 0.001 14.3 1.4 64 169-232 121-193 (248)
486 PRK09147 aminotransferase; Pro 24.4 50 0.0013 13.8 2.8 30 47-76 171-201 (397)
487 PRK07851 acetyl-CoA acetyltran 24.3 26 0.00068 15.5 0.5 128 52-195 229-360 (405)
488 pfam06970 RepA_N Replication i 24.3 50 0.0013 13.7 2.1 22 153-174 53-74 (76)
489 TIGR02094 more_P_ylases alpha- 24.1 50 0.0013 13.7 3.1 34 191-228 173-206 (618)
490 PRK05664 threonine-phosphate d 24.0 51 0.0013 13.7 3.0 27 50-76 132-159 (330)
491 TIGR02405 trehalos_R_Ecol treh 23.9 18 0.00045 16.6 -0.5 22 152-173 1-22 (311)
492 TIGR02944 suf_reg_Xantho FeS a 23.8 41 0.001 14.3 1.4 26 153-178 26-51 (130)
493 PRK08153 histidinol-phosphate 23.8 51 0.0013 13.7 2.2 27 50-76 164-191 (370)
494 PRK03321 putative aminotransfe 23.8 51 0.0013 13.7 2.0 30 47-76 150-180 (352)
495 PRK12681 cysB transcriptional 23.7 51 0.0013 13.7 4.2 39 138-177 3-41 (324)
496 PRK10402 DNA-binding transcrip 23.6 52 0.0013 13.7 4.6 51 124-174 124-178 (213)
497 PRK00118 putative DNA-binding 23.3 52 0.0013 13.6 3.6 34 140-174 22-55 (105)
498 PRK13558 bacterio-opsin activa 23.2 52 0.0013 13.6 1.9 21 154-174 641-661 (674)
499 PRK11074 putative DNA-binding 23.2 52 0.0013 13.6 3.2 34 142-177 8-41 (300)
500 COG4567 Response regulator con 23.1 53 0.0013 13.6 3.7 34 140-173 143-176 (182)
No 1
>COG1475 Spo0J Stage 0 sporulation protein J (antagonist of Soj) containing ParB-like nuclease domain [Transcription]
Probab=100.00 E-value=2.7e-39 Score=272.48 Aligned_cols=233 Identities=39% Similarity=0.634 Sum_probs=212.5
Q ss_pred CCEEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 60240389823578999876898899999998863100155046205654453335756777776421001354333464
Q gi|254780805|r 38 SQDCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVD 117 (300)
Q Consensus 38 ~~~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~ 117 (300)
....+++..|.++|++||+.|+++.+++|+.||+++|++|||+|++ +|+||+|||||+||+.+|+++|||+|++.+
T Consensus 3 ~~~~~~~~~i~~~~~~~r~~~~~~~~~~l~~SI~~~G~~~Pi~v~~----~yeiv~G~rR~~Aa~~~g~~~vp~iv~~~~ 78 (240)
T COG1475 3 RVVEIDIVLIAPNPLQPRKKFDEESLEELAASIKEFGLIQPIVVRP----RYEIVDGHRRLRAAKLLGLEEVPVIVRDLE 78 (240)
T ss_pred CCCCCCHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEECC----EEEEECCCHHHHHHHHCCCCCCCEEEECCC
T ss_conf 6442467664667666644377577999999999839816857777----248842709999999738776874883466
Q ss_pred CHHHHHHHHHHHHHCCCCCHHHHHH-HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf 1123455666543102210489999-999852101110467999974337877865656543589999876421016777
Q gi|254780805|r 118 NKSSLEIAIVENVQRKDLNPLEEAL-GYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHA 196 (300)
Q Consensus 118 d~~~~~~~l~EN~~R~dl~p~e~A~-~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~gha 196 (300)
|.++...+++||+||++++|+|++. ++..+++.++++++.++..+|+++++++|++++..+|++++.++..+.++.+|+
T Consensus 79 d~~~~~~~l~en~~r~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~~~~~~~~~~~~ 158 (240)
T COG1475 79 DEKLLELSLAENIQREDLVPIEEALGAYYELIDGFGLTRERIAKALGKSRARISNLLPLAALPEEVVEALGRIALTIRHA 158 (240)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 58899998898525566767999877699887530455999998853017654202201347888887531001368898
Q ss_pred HHHHHCCH---HHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEECCCCC
Q ss_conf 77640100---468999974222477899999976410222222345665568978999999999973987999717982
Q gi|254780805|r 197 RTLVSTSD---PLSLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLEKKISSKVGLNISIKHRNNK 273 (300)
Q Consensus 197 r~Ll~~~~---~~~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le~~L~~~lGtkV~I~~~~~k 273 (300)
++++.... +..++..++..+|+|+.++..+....... ..........+..+....|+++.++ .
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~~----~ 224 (240)
T COG1475 159 RALLSLLVEELMSEIVRELVKEGLSVRWIEKLVRALIKDA----------LEELGMDKDEKLRLKQISGLAVLIK----D 224 (240)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCC----------CCCCCCHHHHHHHHHHHHCCHHHHC----C
T ss_conf 9987501245657999999861000345688887753011----------0124002889998867416044421----6
Q ss_pred EEEEEEECCHHHHHH
Q ss_conf 289998589899999
Q gi|254780805|r 274 GQFCIKYETNEQLKI 288 (300)
Q Consensus 274 GkI~I~f~s~eeLe~ 288 (300)
|++.+.|.+.+++++
T Consensus 225 ~~~~~~~~~~~~~~~ 239 (240)
T COG1475 225 GKFSVAWESEEELER 239 (240)
T ss_pred CEEEEECCCHHHHHC
T ss_conf 702211154544512
No 2
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=100.00 E-value=2.5e-31 Score=221.28 Aligned_cols=153 Identities=23% Similarity=0.359 Sum_probs=142.0
Q ss_pred CCCCCCCCEEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECC--CCCCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf 01345660240389823578999876898899999998863100155046205--6544533357567777764210013
Q gi|254780805|r 32 TETIPESQDCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAI--DNGLYKIIAGERRFRAAKMASLSEV 109 (300)
Q Consensus 32 ~~~~~~~~~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~--~~g~y~ii~G~rR~rAa~~~g~~~i 109 (300)
.....+.+.+|+.+.|.|++.+.|-.+|++.+++|.+||+++||.+||+|||. .+|+|+|++|||||+||+.+|+ .|
T Consensus 57 ~l~~G~~VvELDp~lId~S~v~DRl~~d~~~~~~L~~sI~~~Gq~~PilVRphp~~~gry~iv~G~RR~~A~~~lg~-~v 135 (325)
T TIGR03454 57 QLAEGETVVELDPALIDTSFVSDRLDSDEEAFAELVESIRENGQQVPILVRPHPEAEGRYQVAYGHRRLRAARDLGI-PV 135 (325)
T ss_pred HHHCCCEEEECCHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCEEEEECHHHHHHHHHCCC-CC
T ss_conf 87369948976988716665656777887999999999998298477697168888884788510899999998299-72
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Q ss_conf 54333464112345566654310221048999999985210111046799997433787786565654-358999987
Q gi|254780805|r 110 PVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK-LPSSVREMI 186 (300)
Q Consensus 110 p~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~-L~~~i~~~l 186 (300)
+++|++++|.++...+..||.+|.||+.||+|..+.+|.+ .|++++.|+..+|.++++||+++.+.. +|+++..++
T Consensus 136 ~A~vr~l~D~~~v~aqg~EN~~R~dLSfIErA~fA~~l~~-~g~~r~~I~~aL~vdks~lSrml~Va~~iP~elI~aI 212 (325)
T TIGR03454 136 KAVVRELSDEELVIAQGQENSARRDLSFIERALFAQRLED-RGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAI 212 (325)
T ss_pred EEEECCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHH
T ss_conf 0334579929999998876452146779999999999998-4999999999988899999999999997899999973
No 3
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=99.95 E-value=1.5e-27 Score=197.02 Aligned_cols=153 Identities=25% Similarity=0.340 Sum_probs=139.4
Q ss_pred CCCCCCCCEEEEHHHCCCCCCCCCCCCC-HHHHHHHHHHHHHCCCCCCCEEECCCC--CCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 0134566024038982357899987689-889999999886310015504620565--4453335756777776421001
Q gi|254780805|r 32 TETIPESQDCISIHSIVPNPHNPRNYFE-SEGLEDLCQSIKSHGIIQPLIVRAIDN--GLYKIIAGERRFRAAKMASLSE 108 (300)
Q Consensus 32 ~~~~~~~~~~i~i~~i~~~p~~pR~~~~-~~~l~eLa~SI~~~G~lqPi~Vr~~~~--g~y~ii~G~rR~rAa~~~g~~~ 108 (300)
.....+.+.+|+.+.|.|++.+.|-..| ++.+++|..||+++||..||+|||.++ |+|+|+.|||||+||+.+|. .
T Consensus 58 qLa~G~~VVelDp~~Id~S~v~DRl~~d~d~~~~~L~~sI~~~GQ~vPILVRphp~~~gryqi~yG~RRl~A~~~Lg~-~ 136 (336)
T PRK13866 58 QLAAGEAVVSLDPSMIDGSPIADRLPSDVDPKFEQLEASISQDGQQVPILVRPHPEAAGRYQIVYGRRRLRAAVNLRR-E 136 (336)
T ss_pred HHHCCCEEEECCHHHCCCCCCHHCCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCCCEEEEHHHHHHHHHHHHCC-C
T ss_conf 985699489738664255310103778753799999999998398476685779888885663054899999998099-6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Q ss_conf 35433346411234556665431022104899999998521011104679999743378778656565-4358999987
Q gi|254780805|r 109 VPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL-KLPSSVREMI 186 (300)
Q Consensus 109 ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l 186 (300)
|.++|++++|.++...+-.||..|.||+.||+|..-.+|.+ .|++++.|...++.+++.+|+++.+. .+|+++..++
T Consensus 137 VkA~Vr~L~D~~~v~aQG~EN~~R~dLSfIErAlFA~~l~~-~g~~r~~i~~aL~~dk~~lS~m~~v~~~iP~~~i~aI 214 (336)
T PRK13866 137 VSAIVRNLTDRELVVAQGRENLDRADLSFIEKALFALRLED-AGFDRATIIAALSTDKADLSRYITVARGIPLNLATQI 214 (336)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHH
T ss_conf 33221148809999987645331234309999999999997-6998889999967888899999999997899999974
No 4
>PRK13832 plasmid partitioning protein; Provisional
Probab=99.95 E-value=8.4e-27 Score=192.20 Aligned_cols=174 Identities=24% Similarity=0.368 Sum_probs=152.9
Q ss_pred CCEEEEHHHCCCCCCCCCCC-CCHHHHHHHHHHHHHCCCCCCCEEECCCCC--CCCCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf 60240389823578999876-898899999998863100155046205654--453335756777776421001354333
Q gi|254780805|r 38 SQDCISIHSIVPNPHNPRNY-FESEGLEDLCQSIKSHGIIQPLIVRAIDNG--LYKIIAGERRFRAAKMASLSEVPVIIR 114 (300)
Q Consensus 38 ~~~~i~i~~i~~~p~~pR~~-~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g--~y~ii~G~rR~rAa~~~g~~~ip~iv~ 114 (300)
.++.++...+.+||+|||+. -++.+...|..||+..|++||.+|++..+| .|.|.+||||.++|..+|+++|.+.|.
T Consensus 2 ~L~~vDPraLk~nPd~~R~tks~~qadalLlatIkaVGivqPPvV~~~~dggng~~I~aGhRRv~~aIaA~L~eI~VlV~ 81 (518)
T PRK13832 2 ELRKVDPRALKDNPDNTRRTKSSPQADALLLATIKAVGIVQPPVVAPESDGGNGYIIDAGHRRVKQAIAAGLEEIQVLVT 81 (518)
T ss_pred CCCCCCHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCCEEEEEECCHHHHHHHHCCCCEEEEEEE
T ss_conf 74103804314599963568897567999998766410446864421268985268850536899988647554789972
Q ss_pred CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CH
Q ss_conf 46411234556665431022104899999998521011104679999743378778656565435899998764210-16
Q gi|254780805|r 115 NVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI-SL 193 (300)
Q Consensus 115 ~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i-s~ 193 (300)
+.++.--...+++||+.|++|||.|+++++.+|++ .|||.+.||-.|+.+..+|..+..|.++-|.+++.+..|.+ +.
T Consensus 82 e~~~d~~amrs~~EN~aRE~mnpvDqWRaierlva-lGwTeeaIa~ALal~vrqiRkLrLLAnv~PamLd~ma~GdmP~e 160 (518)
T PRK13832 82 EAANDNGAMRSMVENIAREPLNPVDQWRAIERLVA-LGWTEEAIAVALALPVRQIRKLRLLANVLPAMLDHMAKGDMPNE 160 (518)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCH
T ss_conf 16775178999998764067986999999999998-49988999999668999999999997655799999844788759
Q ss_pred HHHHHH--HHCCHHHHHHHHH
Q ss_conf 777776--4010046899997
Q gi|254780805|r 194 GHARTL--VSTSDPLSLAQVI 212 (300)
Q Consensus 194 ghar~L--l~~~~~~~la~~I 212 (300)
.+-|++ .++++|.+++++.
T Consensus 161 ~qlrtiA~asldeQ~eVWk~~ 181 (518)
T PRK13832 161 QQLRTIAAASLDEQKEVWKAH 181 (518)
T ss_pred HHHHHHHHCCHHHHHHHHHHC
T ss_conf 999998716878899999850
No 5
>TIGR00180 parB_part ParB-like partition proteins; InterPro: IPR004437 This group of chromosomal and plasmid partition proteins are related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.; GO: 0003677 DNA binding.
Probab=99.94 E-value=3.5e-26 Score=188.24 Aligned_cols=170 Identities=47% Similarity=0.794 Sum_probs=161.7
Q ss_pred CCCEEEEHHHCCCCCCCCCC---CCCHHHHHHHHHHHHHCCCCCCCEEECCCC----CCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf 66024038982357899987---689889999999886310015504620565----44533357567777764210013
Q gi|254780805|r 37 ESQDCISIHSIVPNPHNPRN---YFESEGLEDLCQSIKSHGIIQPLIVRAIDN----GLYKIIAGERRFRAAKMASLSEV 109 (300)
Q Consensus 37 ~~~~~i~i~~i~~~p~~pR~---~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~----g~y~ii~G~rR~rAa~~~g~~~i 109 (300)
.....++++.+.++|++||+ .|+++.+.++..||+.+|+++|++|++... |+|++++|+|||+|++.+|+..+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~g~~~p~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 82 (192)
T TIGR00180 3 GGLLELPLDLLDPNPYQPRKDNPGFSEESLEELLESIKEHGLLQPLLVRPAPDPHDPGRYEIIAGERRWRAAKLAGLKPV 82 (192)
T ss_pred CCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCEEEECCHHHHHHHHHHCCCCH
T ss_conf 53011112232146565655675534567899988887620102101103665445551443212256778876311100
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
Q ss_conf 5433346411234556665431022104899999998521011104679999743378778656565435899998764-
Q gi|254780805|r 110 PVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRK- 188 (300)
Q Consensus 110 p~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~- 188 (300)
|+++++.++......+++||++|++++|++++..|.++++.+..+++.+++.+|++++++++.++++++|.+++..+..
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~ 162 (192)
T TIGR00180 83 PAIVRELDDEQLLALALLENLQREDLSPLEEALAYKRLLEEFSLTQEDLAKKLGKSRAHVTNLLRLLDLPSEVQDALPEA 162 (192)
T ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHC
T ss_conf 13321001577888887643332100157888899998876301388888874232568888888750537899874201
Q ss_pred -HHCCHHHHHHHHHCCHHH
Q ss_conf -210167777764010046
Q gi|254780805|r 189 -EEISLGHARTLVSTSDPL 206 (300)
Q Consensus 189 -~~is~ghar~Ll~~~~~~ 206 (300)
+.++.+|++.+..++...
T Consensus 163 ~~~~~~~~~~~~~~~~~~~ 181 (192)
T TIGR00180 163 PGLLSSGHARLLLALKKKP 181 (192)
T ss_pred CHHHHHHHHHHHHHHCCCH
T ss_conf 1122456888887630330
No 6
>pfam02195 ParBc ParB-like nuclease domain.
Probab=99.90 E-value=5e-24 Score=174.35 Aligned_cols=90 Identities=43% Similarity=0.736 Sum_probs=85.9
Q ss_pred EEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCH
Q ss_conf 24038982357899987689889999999886310015504620565445333575677777642100135433346411
Q gi|254780805|r 40 DCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNK 119 (300)
Q Consensus 40 ~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~ 119 (300)
.+||++.|.|+|+|||+.+ ++++++|+.||+++|++||++|++.++|+|+|++|||||+||+.+|+.+|||+|.++++.
T Consensus 1 ~ei~i~~i~~~p~npR~~~-~~~i~~L~~SI~~~G~~~PiiV~~~~~~~y~ii~G~~R~~A~~~lg~~~ip~~v~d~~~~ 79 (90)
T pfam02195 1 VEVPIDKLRPNEDQPRLTS-EEELEELIASIKEHGLLQPIIVRKTPGGRYEIIDGHRRLRAAKLLGLKEVPVIVLELDDE 79 (90)
T ss_pred CEEEHHHCCCCCCCCCCCC-HHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEEEEHHHHHHHCCCCEEEEEEEECCHH
T ss_conf 9824899754988969889-899999999999859647879997488978995686199999986998610999989989
Q ss_pred HHHHHHHHHHH
Q ss_conf 23455666543
Q gi|254780805|r 120 SSLEIAIVENV 130 (300)
Q Consensus 120 ~~~~~~l~EN~ 130 (300)
++..+++.||+
T Consensus 80 ea~~~~l~eNi 90 (90)
T pfam02195 80 EAIALSLEENI 90 (90)
T ss_pred HHHHHHHHCCC
T ss_conf 99999987459
No 7
>smart00470 ParB ParB-like nuclease domain. Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5--3 exonuclease activity.
Probab=99.87 E-value=1.2e-22 Score=165.43 Aligned_cols=89 Identities=47% Similarity=0.859 Sum_probs=84.3
Q ss_pred EEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCH
Q ss_conf 24038982357899987689889999999886310015504620565445333575677777642100135433346411
Q gi|254780805|r 40 DCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNK 119 (300)
Q Consensus 40 ~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~ 119 (300)
.+||++.|.|+|+|||+. +++++++|+.||+++|++||++|++.+ |+|+|++|||||+||+.+|+++|||+|.+++|.
T Consensus 1 ~~i~i~~l~~~p~n~r~~-~~~~~~~L~~SI~~~G~~~Pi~v~~~~-~~y~ii~G~rR~~Aa~~lg~~~ip~~v~d~~~~ 78 (89)
T smart00470 1 VEVPIEKLRPNPDQPRLT-SEESLEELAESIKENGLLQPIIVRPND-GRYEIIDGERRLRAAKLLGLKEVPVIVRDLDDE 78 (89)
T ss_pred CEEEHHHCCCCCCCCCCC-CHHHHHHHHHHHHHHCCCCCEEEEECC-CCEEECCCHHHHHHHHHCCCCCCEEEEEECCHH
T ss_conf 994189965498995989-999999999999982964776998539-956986878999999986998031999979999
Q ss_pred HHHHHHHHHHH
Q ss_conf 23455666543
Q gi|254780805|r 120 SSLEIAIVENV 130 (300)
Q Consensus 120 ~~~~~~l~EN~ 130 (300)
++..+++.||+
T Consensus 79 ~a~~~~~~eN~ 89 (89)
T smart00470 79 EAIALSLIENI 89 (89)
T ss_pred HHHHHHHHCCC
T ss_conf 99999987449
No 8
>PRK13698 plasmid-partitioning protein; Provisional
Probab=99.76 E-value=6.7e-17 Score=128.55 Aligned_cols=240 Identities=19% Similarity=0.248 Sum_probs=173.2
Q ss_pred EEEEHHHCC----CCCCCCC-CC-CCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCC
Q ss_conf 240389823----5789998-76-89889999999886310015504620565445333575677777642100135433
Q gi|254780805|r 40 DCISIHSIV----PNPHNPR-NY-FESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVII 113 (300)
Q Consensus 40 ~~i~i~~i~----~~p~~pR-~~-~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv 113 (300)
..||-++|. .+-.|-| +. .++.++.+|..|++..||..|.++|... |.++|++|-||+.+|.+.+.+ ..+.|
T Consensus 60 ~~I~a~~ve~~T~Vw~~N~RdQ~lLtE~slsDli~s~~~~GQQ~PAigRr~~-g~iEVlDGSRRR~a~il~~~D-y~VlV 137 (323)
T PRK13698 60 EVIRGDSVESKTRVWSGNERDQELLTEDSLDDLIPSFLLTGQQTPAFGRRVS-GVIEIADGSRRRKAAILTESD-YRVLV 137 (323)
T ss_pred EEECHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEECC-CCEEEECCHHHHHHHHCCCCC-EEEEE
T ss_conf 9821445546667774054667764177888889999971884762103417-968980352777877606884-48997
Q ss_pred CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH-HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHC
Q ss_conf 346411234556665431022104899999998-5210111046799997433787786565654358999987-64210
Q gi|254780805|r 114 RNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQ-LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI-RKEEI 191 (300)
Q Consensus 114 ~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~-l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l-~~~~i 191 (300)
.+++|+++..++-++|-.|. ++.+|.+.-|.+ |...|+.+|.++|+.+|.|+++|++.+....||.++.++. .-++|
T Consensus 138 ~el~Deq~~~Lsdv~N~~rp-~SayErg~ry~~rL~~~~~gnqs~lAe~~~iSra~vsR~i~tA~LP~e~v~aFp~p~eL 216 (323)
T PRK13698 138 GELDDEQMAALSRLGNDYRP-TSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALFAHPGEL 216 (323)
T ss_pred EECCHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHCCHHHHHHCCCHHHH
T ss_conf 30887999999998750177-30888899999998634046699999985889999998887743879999866991232
Q ss_pred CHHHHHHHHHC----CHH-HHHHHHHHHCC--CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCE
Q ss_conf 16777776401----004-68999974222--477899999976410222222345665568978999999999973987
Q gi|254780805|r 192 SLGHARTLVST----SDP-LSLAQVIVSKK--MSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLEKKISSKVGLN 264 (300)
Q Consensus 192 s~ghar~Ll~~----~~~-~~la~~Ii~~~--LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le~~L~~~lGtk 264 (300)
|+..+.+|... +++ ...+..+.+.+ =..=++|+++..+..-...+... .+.. .....||.-
T Consensus 217 sAR~Ge~L~k~~~~~e~~~~~~a~~l~~~~~~g~~f~teeii~~l~~~~k~~~~~-----~~~~-------~~~r~f~~G 284 (323)
T PRK13698 217 SARSGEALQKAFEDKEELLKQQTHKLHKQKKAGRIFETEEVIVLLTSVLKQSSAS-----RTSL-------SSRHQFAPG 284 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCC-----CCCC-------HHHHHCCCC
T ss_conf 0330389999984369999999999999886157678999999999987266655-----6651-------255550577
Q ss_pred EEEECCCCCEEEEEEECC-------HHHHHHHHHHHCCC
Q ss_conf 999717982289998589-------89999999983756
Q gi|254780805|r 265 ISIKHRNNKGQFCIKYET-------NEQLKIICSLLGEN 296 (300)
Q Consensus 265 V~I~~~~~kGkI~I~f~s-------~eeLe~Il~kL~~~ 296 (300)
+++..+++ +++|+..+ .++++.|++.+.+.
T Consensus 285 ~~a~yk~~--~v~~~l~~~~~~~~~i~kiE~~l~~~~k~ 321 (323)
T PRK13698 285 ATALYKGD--KVVFNLDRSRVPEECIEQIEAILKELEKE 321 (323)
T ss_pred CEEEEECC--EEEEEECCCCCCHHHHHHHHHHHHHHHCC
T ss_conf 36886087--58998368889999999999999986224
No 9
>pfam08535 KorB KorB domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This domain includes the DNA-binding HTH motif.
Probab=98.23 E-value=4.7e-06 Score=58.88 Aligned_cols=48 Identities=33% Similarity=0.475 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 11104679999743378778656565435899998764210167777764
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLV 200 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll 200 (300)
.|+++.+||+++|+|.+|||.+++|+++|++|.+++.+|..+. .++|.
T Consensus 2 ~G~kk~~IAk~LGks~s~VS~hlaL~d~Pd~l~~l~~~g~~~d--v~~l~ 49 (93)
T pfam08535 2 KGVKQAEIAKKLGKSKSFVSQHLALLDMPDCIREAYDSGRCSD--IRALY 49 (93)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCC--HHHHH
T ss_conf 9877999999978898899999998348699999987477687--99999
No 10
>pfam07506 RepB RepB plasmid partitioning protein. This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens.
Probab=97.67 E-value=0.00014 Score=49.35 Aligned_cols=94 Identities=17% Similarity=0.257 Sum_probs=68.7
Q ss_pred HCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH--HHH-HHHHHHHHHHHHHHCCHHHHHHH--HHCCHH
Q ss_conf 1022104899999998521011104679999743378778656--565-43589999876421016777776--401004
Q gi|254780805|r 131 QRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL--RIL-KLPSSVREMIRKEEISLGHARTL--VSTSDP 205 (300)
Q Consensus 131 ~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L--rLl-~L~~~i~~~l~~~~is~ghar~L--l~~~~~ 205 (300)
.|.||+++|++.-..++.+. |++.+.|+..+|.+.++|++++ +++ .+|+++.+++.+.........++ ++-+-+
T Consensus 1 ar~~Ls~Ie~~~~a~rl~~~-G~~~~~I~~aL~vd~~~is~~~~~~~~~~i~~e~~~lL~d~~~~~~~ig~a~kigr~Rw 79 (185)
T pfam07506 1 ARADLSFIERARFAARLLER-GVPRAEIAAALGLDPQTVSKMVARAIPEGICPEEEALLKDVETGIAAFGLARKIGRDRW 79 (185)
T ss_pred CCCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCHHHHHHHCCCCCHHH
T ss_conf 98642299999999999986-99999999998679999999999987511688999986034564988765100582789
Q ss_pred HHHHHHHH-HCCCCHHHHHHH
Q ss_conf 68999974-222477899999
Q gi|254780805|r 206 LSLAQVIV-SKKMSVRDTEEL 225 (300)
Q Consensus 206 ~~la~~Ii-~~~LSVRe~E~l 225 (300)
.++++..+ .+.+++...+.+
T Consensus 80 ~e~aelm~a~~~~~~~~~~al 100 (185)
T pfam07506 80 VELAELLAAAKNVESAYFRAL 100 (185)
T ss_pred HHHHHHHHHHHHCCHHHHHHH
T ss_conf 999999987530158999864
No 11
>COG5119 Uncharacterized protein, contains ParB-like nuclease domain [General function prediction only]
Probab=96.17 E-value=0.012 Score=36.99 Aligned_cols=79 Identities=18% Similarity=0.248 Sum_probs=58.9
Q ss_pred CCCEEEEHHHCCCCCCCCCCCCCHHHHHHHH---------------HHHHHCCCCCCCEEE---CCCCCCCCCCCCHHHH
Q ss_conf 6602403898235789998768988999999---------------988631001550462---0565445333575677
Q gi|254780805|r 37 ESQDCISIHSIVPNPHNPRNYFESEGLEDLC---------------QSIKSHGIIQPLIVR---AIDNGLYKIIAGERRF 98 (300)
Q Consensus 37 ~~~~~i~i~~i~~~p~~pR~~~~~~~l~eLa---------------~SI~~~G~lqPi~Vr---~~~~g~y~ii~G~rR~ 98 (300)
-++++||++.|.. |.-| ..|+.+++.|. .++.+-|.+.|+-|- ..+...|.-..|.+|+
T Consensus 8 v~~~EiplseirR-Plpp--vlDp~Kv~am~~tM~g~t~~~sc~l~e~~a~aGelpPvDVL~~~v~Gq~~YyaFgGCHRl 84 (119)
T COG5119 8 VNIQEIPLSEIRR-PLPP--VLDPNKVNAMMETMTGKTPPASCGLTEEDAAAGELPPVDVLTFEVDGQPYYYAFGGCHRL 84 (119)
T ss_pred CCCEECCHHHHHC-CCCC--CCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCCCCCCEEEEEEECCCEEEEEECCCHHH
T ss_conf 6645535889546-7988--788899999999732899975455207677537899830678876593778861740776
Q ss_pred HHHHHHHCCCCCC-CCCCCCC
Q ss_conf 7776421001354-3334641
Q gi|254780805|r 99 RAAKMASLSEVPV-IIRNVDN 118 (300)
Q Consensus 99 rAa~~~g~~~ip~-iv~~~~d 118 (300)
+|+..+|.++|.| .|+-.+.
T Consensus 85 ~A~dr~gret~~a~rvr~~P~ 105 (119)
T COG5119 85 EACDRAGRETILAKRVRCAPN 105 (119)
T ss_pred HHHHHHHHHHHHHHHHCCCHH
T ss_conf 999887378888888713807
No 12
>PHA01976 helix-turn-helix protein
Probab=95.17 E-value=0.016 Score=36.13 Aligned_cols=35 Identities=9% Similarity=0.091 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999985210111046799997433787786565
Q gi|254780805|r 140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
-+.-+++|.+..||||+++|+++|.++++|+++-.
T Consensus 3 F~~RL~~lR~~~g~sQ~eLA~~lGVs~~~is~wE~ 37 (67)
T PHA01976 3 FAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 89999999998699999999994998999999987
No 13
>KOG3388 consensus
Probab=95.17 E-value=0.018 Score=35.87 Aligned_cols=82 Identities=16% Similarity=0.203 Sum_probs=57.0
Q ss_pred CCEEEEHHHCCCCCCCCCCCCCHHHH--------------HHHHHHHHHCCCCCCCEEECC---CCCCCCCCCCHHHHHH
Q ss_conf 60240389823578999876898899--------------999998863100155046205---6544533357567777
Q gi|254780805|r 38 SQDCISIHSIVPNPHNPRNYFESEGL--------------EDLCQSIKSHGIIQPLIVRAI---DNGLYKIIAGERRFRA 100 (300)
Q Consensus 38 ~~~~i~i~~i~~~p~~pR~~~~~~~l--------------~eLa~SI~~~G~lqPi~Vr~~---~~g~y~ii~G~rR~rA 100 (300)
...++|.+.|.- |.-| ..|.+++ .+.++||++-|.+-||-|-.. +...|.-..|.+|++|
T Consensus 26 ~pv~~~mSei~r-Pi~p--vLd~qKi~slm~Tmkn~~~c~les~d~~~~aGelpPiDvl~v~~~G~~~YyaFgGCHRleA 102 (136)
T KOG3388 26 PPVEGPMSEIVR-PIPP--VLDLQKIRSLMETMKNDQNCVLESEDSIRQAGELPPIDVLEVDSEGGDYYYAFGGCHRLEA 102 (136)
T ss_pred CCEECCHHHCCC-CCCC--CCCHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCEEEEEECCCCEEEEEECCCHHHHH
T ss_conf 954645120445-7886--4698999999998508976331357788743778981289995179667886176424478
Q ss_pred HHHHHCCCCCCCCCCCCCHHHH
Q ss_conf 7642100135433346411234
Q gi|254780805|r 101 AKMASLSEVPVIIRNVDNKSSL 122 (300)
Q Consensus 101 a~~~g~~~ip~iv~~~~d~~~~ 122 (300)
...+|..+|.|-+...+..+..
T Consensus 103 hdrlgrptiRcKlvk~T~~tLr 124 (136)
T KOG3388 103 HDRLGRPTIRCKLVKGTPETLR 124 (136)
T ss_pred HHHHCCCCEEEEEECCCHHHHH
T ss_conf 8861798546787349988877
No 14
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.93 E-value=0.065 Score=32.27 Aligned_cols=67 Identities=27% Similarity=0.440 Sum_probs=44.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCC--CCHHHHHHHHHHHHHH--------------CCCCHHHHHHHHHHHHHHH
Q ss_conf 00135433346411234556665431022--1048999999985210--------------1110467999974337877
Q gi|254780805|r 106 LSEVPVIIRNVDNKSSLEIAIVENVQRKD--LNPLEEALGYEQLISE--------------YGYTQNDIGSIVGKSRSHV 169 (300)
Q Consensus 106 ~~~ip~iv~~~~d~~~~~~~l~EN~~R~d--l~p~e~A~~~~~l~~~--------------~~~t~~~lA~~~G~s~s~V 169 (300)
..+|...+.+-+|.+ .++|++-+.-+| +.-++.-.+++.++.. -++||.|+|+.+|.|+-||
T Consensus 136 ~~Sld~~~~a~~dg~--~~~L~D~lG~~D~~~e~~~~~~aLk~~l~~LpeRER~il~lRFf~~~TQ~eiA~~lGiSQMhV 213 (229)
T TIGR02980 136 ALSLDATIEADDDGD--PIALLDTLGDEDDALETVEDRLALKPLLAALPERERRILLLRFFEDKTQSEIAERLGISQMHV 213 (229)
T ss_pred CCCCCCCCCCCCCCC--HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCHHHCEEEEEEEECCCCHHHHHHHCCCCHHHH
T ss_conf 611200045588884--245664440224326789999999999850790270761000106977899997818436788
Q ss_pred HHHHH
Q ss_conf 86565
Q gi|254780805|r 170 ANILR 174 (300)
Q Consensus 170 ~~~Lr 174 (300)
|+.++
T Consensus 214 SRl~~ 218 (229)
T TIGR02980 214 SRLLR 218 (229)
T ss_pred HHHHH
T ss_conf 99999
No 15
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; InterPro: IPR014303 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building and bidirectional best hits, to represent a conserved family. This entry is found in a limited number of bacterial lineages and ncludes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis str. MC2 155, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM 10152.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=94.88 E-value=0.092 Score=31.32 Aligned_cols=38 Identities=37% Similarity=0.587 Sum_probs=32.2
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 2210489999999852101110467999974337877865
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
|-|||.|.|.-+ |.+.|+|..+|||..+|||.+...+.
T Consensus 108 ErL~P~ERAVF~--LREVF~y~Y~EIA~~v~kS~ancRQl 145 (287)
T TIGR02957 108 ERLSPLERAVFL--LREVFDYDYEEIASIVGKSEANCRQL 145 (287)
T ss_pred HHCCHHHHHHHH--HHHHHCCCCHHHHHHCCCCHHHHHHH
T ss_conf 307978999999--99874588267897606895799999
No 16
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=94.70 E-value=0.068 Score=32.18 Aligned_cols=51 Identities=22% Similarity=0.339 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 489999999852101110467999974337877865656543589999876421
Q gi|254780805|r 137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE 190 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~ 190 (300)
.+|+.+++ ||+|--|++|++.|++.|.||+|+.+.|. ..=..|-++|..|+
T Consensus 38 ~~dE~EAi-RL~D~egl~QeeaA~~MgVSR~Tf~ril~--~ARkKvA~aLv~Gk 88 (100)
T pfam02001 38 TLDEFEAI-RLVDYEDYTQEEAAKLMGISRRTVWRLLT--SARKKIADALVEGR 88 (100)
T ss_pred CHHHHHHH-HHHHHCCCCHHHHHHHCCCCHHHHHHHHH--HHHHHHHHHHHCCC
T ss_conf 49999999-98736079899999884976999999999--99999999986798
No 17
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=94.65 E-value=0.073 Score=31.97 Aligned_cols=51 Identities=22% Similarity=0.280 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 489999999852101110467999974337877865656543589999876421
Q gi|254780805|r 137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE 190 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~ 190 (300)
.+|+.+|+ ||.+..+++|++.|.+.|.||.|+.+.|. ..-..|-++|..|+
T Consensus 35 t~eElEAl-RLvD~~~l~QeeAA~rMgISr~Tfwr~l~--sAR~KvA~aLveGk 85 (99)
T COG1342 35 TIEELEAL-RLVDYEGLTQEEAALRMGISRQTFWRLLT--SARKKVADALVEGK 85 (99)
T ss_pred CHHHHHHH-HHHHHHHCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHCCC
T ss_conf 29998899-98868610578999984642999999999--99999999985587
No 18
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=94.48 E-value=0.043 Score=33.44 Aligned_cols=38 Identities=29% Similarity=0.422 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 2104899999998521011104679999743378778656
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
-|++ |+....++|++. |.+..+||+.+|.||++|.++|
T Consensus 5 ~lt~-~q~~~ar~l~~~-G~~~~~iA~~~GVsr~Tiyr~l 42 (42)
T cd00569 5 KLTP-EQIEEARRLLAA-GESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCCH-HHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHC
T ss_conf 6999-999999999997-8989999999797999998659
No 19
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=94.23 E-value=0.061 Score=32.47 Aligned_cols=43 Identities=28% Similarity=0.328 Sum_probs=35.2
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 04899999998521011104679999743378778656565435
Q gi|254780805|r 136 NPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLP 179 (300)
Q Consensus 136 ~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~ 179 (300)
-|.=+|.--+.|.++ |+||.++|+.+|.|++.||+||+=-.=|
T Consensus 7 lPaiRa~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~ 49 (119)
T COG2522 7 LPAIRALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGS 49 (119)
T ss_pred HHHHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHCCCCCH
T ss_conf 798999999999995-8869999999688899999997367736
No 20
>PRK04217 hypothetical protein; Provisional
Probab=93.86 E-value=0.13 Score=30.35 Aligned_cols=51 Identities=27% Similarity=0.332 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 489999999852101110467999974337877865656543589999876421
Q gi|254780805|r 137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE 190 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~ 190 (300)
.+|+.+++ ||.|--|++|++.|++.|.||+|+.+.|. ..-..|-++|..|+
T Consensus 44 tvdE~Eai-RL~D~egl~qeeaA~~M~VSR~Tf~ril~--~AR~KvA~aLv~Gk 94 (110)
T PRK04217 44 TYEEFEAL-RLVDYEGLTQEEAGKRMGVSRGTVWRALT--SARKKVAQMLVEGR 94 (110)
T ss_pred CHHHHHHH-HHHHHCCCCHHHHHHHCCCCHHHHHHHHH--HHHHHHHHHHHCCC
T ss_conf 19999999-98736079899999884976999999999--99999999986797
No 21
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Probab=93.85 E-value=0.12 Score=30.69 Aligned_cols=54 Identities=20% Similarity=0.305 Sum_probs=46.3
Q ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 11234556665431022104899999998521011104679999743378778656
Q gi|254780805|r 118 NKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 118 d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
++.+..-+.+|.+-|+| |..-|.-++..+..+++.|.+++...|.+.|+++..|
T Consensus 96 EEaa~qra~Ve~ll~~d--~~~v~~~Ik~~m~~h~ipQ~~vv~~TGlnQS~lSq~L 149 (177)
T pfam04814 96 EEAAHQRAEVDRLLRED--PWRVAKMIKSYMQQHNIPQREVVDATGLNQSHLSQHL 149 (177)
T ss_pred HHHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHH
T ss_conf 58888899999999728--4999999999998768846678761065599999999
No 22
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=93.31 E-value=0.32 Score=27.87 Aligned_cols=28 Identities=18% Similarity=0.261 Sum_probs=24.2
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|....|+|+.|||+++|.|.++|.++|.
T Consensus 138 L~r~eGls~~EIAe~LgiS~~tV~~~l~ 165 (178)
T PRK12529 138 MATLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9988299999999998959999999999
No 23
>pfam06250 DUF1016 Protein of unknown function (DUF1016). Family of uncharacterized proteins found in viruses, archaea and bacteria.
Probab=92.85 E-value=0.37 Score=27.43 Aligned_cols=66 Identities=18% Similarity=0.231 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHHHHH---HHHHHHHHHHCCHHHHHHHHHCCHHHH---HHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf 433787786565654358---999987642101677777640100468---99997422247789999997641
Q gi|254780805|r 163 GKSRSHVANILRILKLPS---SVREMIRKEEISLGHARTLVSTSDPLS---LAQVIVSKKMSVRDTEELVQEQD 230 (300)
Q Consensus 163 G~s~s~V~~~LrLl~L~~---~i~~~l~~~~is~ghar~Ll~~~~~~~---la~~Ii~~~LSVRe~E~lVk~~~ 230 (300)
|.|++.+.++...-..=| .++..+ +.||-+|.+.|..+++.++ .++..+.++||||..+.-++...
T Consensus 66 GFS~~NL~~MrqFy~~y~d~~i~q~~~--~qLsW~H~~iL~k~k~~~~R~fY~~~a~~~~WS~r~L~~qI~s~l 137 (320)
T pfam06250 66 GFSAKNLKRMRQFYLTFPDEEIVQALL--RELTWTHVRLLEKVKDELTRDFYIKETIKEGWSTRILERQIESML 137 (320)
T ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHH--HHCCHHHHHHHHHCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999999999999779603444688--755959999987179989999999999997969999999998778
No 24
>pfam08857 ParBc_2 Putative ParB-like nuclease. This domain is probably distantly related to pfam02195. Suggesting these uncharacterized proteins have a nuclease function.
Probab=92.72 E-value=0.06 Score=32.52 Aligned_cols=75 Identities=13% Similarity=0.286 Sum_probs=46.1
Q ss_pred CEEEEHHHCCCCCCC--------CCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCC-C
Q ss_conf 024038982357899--------9876898899999998863100155046205654453335756777776421001-3
Q gi|254780805|r 39 QDCISIHSIVPNPHN--------PRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSE-V 109 (300)
Q Consensus 39 ~~~i~i~~i~~~p~~--------pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~-i 109 (300)
+.+|+|+.+.|--.- -+..|-..+-+++.+-++.+++ |+++- ++|.+-+++||++.+|.-.+|... +
T Consensus 2 l~~V~i~~LrPTQ~~vG~~eV~~K~~~~~~~~~~~~~~~l~~~~v--PvV~g--p~g~lyl~DhHH~~ral~e~~~~~~v 77 (162)
T pfam08857 2 LIEVPLDALRPTQITVGLREVEAKRKRWREDKKKKRLDFLRKHPV--PVVLG--PDGRLYLTDHHHLLRALLELGVGGTV 77 (162)
T ss_pred CEEEEHHHCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCC--CEEEC--CCCCEEEECCHHHHHHHHHCCCCCEE
T ss_conf 416258972784075789999999999986189999999971998--78988--99986787760889999956998638
Q ss_pred CCCC-CCCC
Q ss_conf 5433-3464
Q gi|254780805|r 110 PVII-RNVD 117 (300)
Q Consensus 110 p~iv-~~~~ 117 (300)
++.| .|++
T Consensus 78 ~v~v~~dls 86 (162)
T pfam08857 78 PVTVVADLS 86 (162)
T ss_pred EEEEEEECC
T ss_conf 999976567
No 25
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=92.68 E-value=0.091 Score=31.36 Aligned_cols=111 Identities=29% Similarity=0.370 Sum_probs=56.4
Q ss_pred CHHHHHHHHHHHHHCCCCCCCEEECCCCCC----C-------CCCCCHHHHHHHHHHHCCCCCCCCCC------------
Q ss_conf 988999999988631001550462056544----5-------33357567777764210013543334------------
Q gi|254780805|r 59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGL----Y-------KIIAGERRFRAAKMASLSEVPVIIRN------------ 115 (300)
Q Consensus 59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~----y-------~ii~G~rR~rAa~~~g~~~ip~iv~~------------ 115 (300)
..+++++|. ||-..|++..|--...+.|. | ||++- +||.|... =.|...|
T Consensus 71 ~G~~~dDLI-SIGTiGLIKAidsf~~~KGt~LATYAArCiENEILM~---lR~~KK~k---~eV~L~DPIG~DKEGNEIs 143 (228)
T TIGR02846 71 TGEDVDDLI-SIGTIGLIKAIDSFDPEKGTRLATYAARCIENEILMH---LRALKKTK---GEVSLQDPIGVDKEGNEIS 143 (228)
T ss_pred CCCCCCCHH-CCCCHHEECCEECCCCCCCCHHHHHHHHHHHHHHHHH---HHHCCCCC---CCEEECCCCCCCCCCCEEE
T ss_conf 874100001-0022010001102247877315667866534789999---97436747---8332107888676764230
Q ss_pred -----CCCHHHHHHHHHHHHHCC--------CCCHHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHHHHHH--HH
Q ss_conf -----641123455666543102--------21048999999985210111------0467999974337877865--65
Q gi|254780805|r 116 -----VDNKSSLEIAIVENVQRK--------DLNPLEEALGYEQLISEYGY------TQNDIGSIVGKSRSHVANI--LR 174 (300)
Q Consensus 116 -----~~d~~~~~~~l~EN~~R~--------dl~p~e~A~~~~~l~~~~~~------t~~~lA~~~G~s~s~V~~~--Lr 174 (300)
.+|.|...-.+..+++-+ -|.+-|+..-- ..||+ ||.|||+.+|.|||+||+- -+
T Consensus 144 L~DiL~~~~d~v~e~v~~~~~~~~l~~~~~~~L~~rE~~vi~----~RyGL~~~~~~tQREIA~~LgISRSYVSRIEK~A 219 (228)
T TIGR02846 144 LIDILGSDEDSVIEQVEKKLEIKKLYKKLNSVLKGREREVIE----MRYGLKDGREKTQREIAKILGISRSYVSRIEKKA 219 (228)
T ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 000016887316888886445999999999874088899998----7436688895417899877086500454888999
Q ss_pred HHHHHH
Q ss_conf 654358
Q gi|254780805|r 175 ILKLPS 180 (300)
Q Consensus 175 Ll~L~~ 180 (300)
|.+|..
T Consensus 220 l~Kl~~ 225 (228)
T TIGR02846 220 LKKLYK 225 (228)
T ss_pred HHHHHH
T ss_conf 999986
No 26
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=92.60 E-value=0.69 Score=25.68 Aligned_cols=28 Identities=25% Similarity=0.294 Sum_probs=23.9
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|....|+|+.|||+.+|.|.++|.++|.
T Consensus 129 L~~~eGlsy~EIAe~LgIS~~tV~~~l~ 156 (168)
T PRK12525 129 MSQLEGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999299999999998979999999999
No 27
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=92.50 E-value=0.48 Score=26.73 Aligned_cols=52 Identities=29% Similarity=0.359 Sum_probs=32.6
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HH-HHH-------------HHHHHHHHHHHCCHHHH
Q ss_conf 9985210111046799997433787786565-65-435-------------89999876421016777
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANILR-IL-KLP-------------SSVREMIRKEEISLGHA 196 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr-Ll-~L~-------------~~i~~~l~~~~is~gha 196 (300)
+..++...| +..++|+.+|.|..||.++|. +. +|- .+|+++|..|+||+-.|
T Consensus 42 i~~fi~~~G-nlke~~~~lgiSYpTvR~rLd~ii~~lGy~~~~~~~~~~~~~eIL~~Le~GEIs~eEA 108 (113)
T pfam09862 42 VELFIKCRG-NIKEVEKELGISYPTVRNRLDEIIAALGYEEEPEPEKRVDKKEILDKLEKGEISVEEA 108 (113)
T ss_pred HHHHHHHCC-CHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCHHHH
T ss_conf 999999168-8999999978881889999999999808987777777622999999998499799999
No 28
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=92.40 E-value=0.18 Score=29.51 Aligned_cols=38 Identities=18% Similarity=0.397 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 10489999999852101110467999974337877865
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
-+|-..|.+++......|+||.++|+++|..+++||+.
T Consensus 8 ~sp~qLa~~Lr~~Rk~~gLsQ~~lA~~vGi~Q~TiS~~ 45 (88)
T PRK09726 8 YSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNF 45 (88)
T ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 89999999999999985987999999819749999999
No 29
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=92.09 E-value=0.74 Score=25.48 Aligned_cols=56 Identities=23% Similarity=0.341 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHC
Q ss_conf 21048999999985210111046799997433787786565-65435899998764210
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR-ILKLPSSVREMIRKEEI 191 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr-Ll~L~~~i~~~l~~~~i 191 (300)
.|+|-++..-.-+.. .|+|.++||+.+|.|.++|..+|. -.+--...++.+..|+|
T Consensus 128 ~L~~~~r~v~~l~~~--~~~s~~EIA~~l~is~~tVk~rl~Rar~~Lr~~L~~~~~~e~ 184 (185)
T PRK06811 128 DLKKLDREIFIKRYL--LGESIEEIAKKLGLTRSAIDNRLSRGRKKLKNKLNILKKGEV 184 (185)
T ss_pred CCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 899999999999999--499999999998929999999999999999999889866788
No 30
>pfam11300 DUF3102 Protein of unknown function (DUF3102). This family of proteins has no known function.
Probab=92.03 E-value=0.5 Score=26.57 Aligned_cols=93 Identities=16% Similarity=0.144 Sum_probs=56.6
Q ss_pred CHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHH-HHHHHHHCCHHHHHHHHHCCH
Q ss_conf 048999999985210--111046799997433787786565654--------358999-987642101677777640100
Q gi|254780805|r 136 NPLEEALGYEQLISE--YGYTQNDIGSIVGKSRSHVANILRILK--------LPSSVR-EMIRKEEISLGHARTLVSTSD 204 (300)
Q Consensus 136 ~p~e~A~~~~~l~~~--~~~t~~~lA~~~G~s~s~V~~~LrLl~--------L~~~i~-~~l~~~~is~ghar~Ll~~~~ 204 (300)
|.+|....+....+. +|.=..=+-+.+++|+++-.|+|++.. +|++.- ..=.-+.++..+|-.|+++|+
T Consensus 24 ~aIEIGrrL~~~Ke~l~HGef~~WLke~v~~S~rtA~~~M~v~~eyG~~~~~~~~~~~~n~~~l~~L~ytqal~Ll~~Pe 103 (130)
T pfam11300 24 SAIEIGRRLKEAKALLPHGEWGKWLKESVSYSRRTAANLMRLYEEYGSKLASPSDDDSSNSQPLGNLTYTQALILLGVPE 103 (130)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCH
T ss_conf 99999999999998588662999999992826999999999999975012589865432453243121999999927987
Q ss_pred H--HHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 4--68999974222477899999976
Q gi|254780805|r 205 P--LSLAQVIVSKKMSVRDTEELVQE 228 (300)
Q Consensus 205 ~--~~la~~Ii~~~LSVRe~E~lVk~ 228 (300)
. +++....=-+++|+|++.+.|+.
T Consensus 104 eeR~efi~e~dve~Ms~RELqqavkE 129 (130)
T pfam11300 104 EEREQFIAENDVESMSTRELQQAVKE 129 (130)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHC
T ss_conf 89999999724101139999999864
No 31
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=91.92 E-value=0.18 Score=29.42 Aligned_cols=33 Identities=18% Similarity=0.216 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999852101110467999974337877865
Q gi|254780805|r 140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
-...++......|+||.++|+..|.|++||+..
T Consensus 3 lG~~Ir~~Rk~~glTQ~~LA~~aGvs~~~Is~i 35 (58)
T TIGR03070 3 IGALVRARRKALGLTQADLADLAGVGLRFIRDI 35 (58)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 889999999994998999998819989999999
No 32
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=91.74 E-value=0.18 Score=29.39 Aligned_cols=39 Identities=15% Similarity=0.105 Sum_probs=30.2
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999998521011104679999743378778656565435
Q gi|254780805|r 141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLP 179 (300)
Q Consensus 141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~ 179 (300)
+.-++.+..+.|+||.++|+++|.|+++|+++-+=...|
T Consensus 7 G~Ri~~~R~~~glTQ~eLA~~~Gvs~~tVs~wE~g~~~P 45 (135)
T PRK09706 7 GQRIRYRRKQLKLSQRALAKAVGVSHVSISQWERDETEP 45 (135)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCC
T ss_conf 999999999859999999999698899999998289888
No 33
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=91.70 E-value=0.15 Score=29.90 Aligned_cols=33 Identities=30% Similarity=0.371 Sum_probs=27.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 998521011104679999743378778656565
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
++.+....|+||.++|+.+|.|+++|+++.+=-
T Consensus 2 lr~~R~~~glsq~~lA~~~gis~~~is~~E~g~ 34 (56)
T smart00530 2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCC
T ss_conf 899997729999999999895999999999799
No 34
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=91.48 E-value=0.89 Score=24.99 Aligned_cols=28 Identities=25% Similarity=0.274 Sum_probs=24.1
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|....|+|+.|||+.+|.|.++|.++|.
T Consensus 130 L~r~~gls~~EIA~~LgiS~~tVk~~l~ 157 (167)
T PRK12528 130 LAQVDGLGYGEIATELGISLATVKRYLN 157 (167)
T ss_pred HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9998298999999997979999999999
No 35
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=91.30 E-value=0.81 Score=25.23 Aligned_cols=39 Identities=23% Similarity=0.161 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|.|-.+..-. |....|+|+.|||+.+|.|.++|.++|.
T Consensus 119 ~Lp~~~R~v~~--L~~~eGls~~EIA~~LgiS~~tVk~~l~ 157 (172)
T PRK12523 119 KLSSKARAAFL--YNRLDGMGHAEIAERLGVSVSRVRQYLA 157 (172)
T ss_pred CCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 49999999999--9999399999999998939999999999
No 36
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=91.17 E-value=0.33 Score=27.77 Aligned_cols=24 Identities=38% Similarity=0.564 Sum_probs=14.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 110467999974337877865656
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrL 175 (300)
|+||.|||+++|.||.+|+++|..
T Consensus 26 gltQ~eIA~~LgiSR~~v~rlL~~ 49 (321)
T COG2390 26 GLTQSEIAERLGISRATVSRLLAK 49 (321)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 887999998839889999999999
No 37
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=90.64 E-value=0.17 Score=29.59 Aligned_cols=33 Identities=27% Similarity=0.427 Sum_probs=26.8
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 985210111046799997433787786565654
Q gi|254780805|r 145 EQLISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 145 ~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+++....|+||.++|+.+|.|+++|+++-+=..
T Consensus 2 r~~R~~~g~tq~~lA~~~gis~~~is~~E~g~~ 34 (55)
T pfam01381 2 KELREELGLSQEELAEKLGVSRSTISKIENGKR 34 (55)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC
T ss_conf 898978299899999998969999999987999
No 38
>pfam03235 DUF262 Protein of unknown function DUF262.
Probab=90.34 E-value=0.6 Score=26.09 Aligned_cols=54 Identities=17% Similarity=0.286 Sum_probs=41.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 899987689889999999886310015504620565445333575677777642
Q gi|254780805|r 51 PHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMA 104 (300)
Q Consensus 51 p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~ 104 (300)
.+|=.-.-+++....|.+||...=-+-++++...+++.|+||+|..|+.+....
T Consensus 15 ~yQR~y~W~~~~~~~li~di~~~~~ig~i~l~~~~~~~~~viDGQQRltTl~~~ 68 (99)
T pfam03235 15 DYQRLYVWRKKEVSRLIEDLLYGYPIGSIVLAEKSDGKYEIIDGQQRLTTLKLF 68 (99)
T ss_pred CCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCCEEEEECCHHHHHHHHHH
T ss_conf 877757138899999999998192452699997799859997680899999999
No 39
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=90.18 E-value=0.22 Score=28.87 Aligned_cols=29 Identities=31% Similarity=0.539 Sum_probs=24.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99985210111046799997433787786
Q gi|254780805|r 143 GYEQLISEYGYTQNDIGSIVGKSRSHVAN 171 (300)
Q Consensus 143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~ 171 (300)
-++.+..++|+||+++|+.+|.||-+|..
T Consensus 5 k~k~~R~~~~ltQ~elA~~vgVsRQTi~~ 33 (68)
T COG1476 5 KLKELRAELGLTQEELAKLVGVSRQTIIA 33 (68)
T ss_pred HHHHHHHHHCCCHHHHHHHCCCCHHHHHH
T ss_conf 99999998285899999991957999999
No 40
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=89.86 E-value=1.4 Score=23.73 Aligned_cols=53 Identities=15% Similarity=0.164 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHH
Q ss_conf 221048999999985210111046799997433787786565--6543589999876
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR--ILKLPSSVREMIR 187 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~~i~~~l~ 187 (300)
+.|+|-+.. .+. |.--.|+|..+||+.+|.|.++|.+++. +-+|=..++++|.
T Consensus 136 ~~L~~~~r~-v~~-l~~~~~~s~~EIA~~lgis~~tVk~~l~Ra~~~Lr~~L~~~~~ 190 (192)
T PRK09652 136 ESLPEELRT-AIT-LREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQPLLD 190 (192)
T ss_pred HHCCHHHHH-HHH-HHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 839999998-888-9997299999999998939999999999999999999898771
No 41
>pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
Probab=89.38 E-value=0.48 Score=26.74 Aligned_cols=39 Identities=31% Similarity=0.375 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-+...-.-+.. .++|+.|+|+.+|.|+++|++.++
T Consensus 4 ~L~~~~r~ii~l~y~--~~~t~~EIA~~lgis~~~V~~~~~ 42 (50)
T pfam04545 4 SLPPREREVLVLRFG--EGLTLEEIGERLGISRERVRQIEK 42 (50)
T ss_pred HCCHHHHHHHHHHCC--CCCHHHHHHHHHCCCHHHHHHHHH
T ss_conf 689999999998706--882499999998979999999999
No 42
>pfam12116 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.
Probab=88.97 E-value=1.1 Score=24.51 Aligned_cols=44 Identities=25% Similarity=0.300 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHH
Q ss_conf 99999998521011104679999743378778656--565435899
Q gi|254780805|r 139 EEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL--RILKLPSSV 182 (300)
Q Consensus 139 e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L--rLl~L~~~i 182 (300)
|.+.-+...+-+.+-|..+.|+.||.|+|+|.+-+ ||..+.|.+
T Consensus 6 eR~~~i~~YIi~~~aTVR~tAk~FGvSKSTVHkDvTeRL~~inp~L 51 (82)
T pfam12116 6 ERVLEIANYIIENKATVRQAAKVFGVSKSTVHKDVTERLPKINPQL 51 (82)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHH
T ss_conf 9999999999962628999999969609889887999998739999
No 43
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=88.94 E-value=0.34 Score=27.66 Aligned_cols=29 Identities=21% Similarity=0.319 Sum_probs=25.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99852101110467999974337877865
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
+.||.++.|+|+.++|++-|.|.++++..
T Consensus 10 v~RLr~ErGmT~~eLAe~AGIS~s~LSqI 38 (119)
T PRK13890 10 VLRLLDERHMTKKELSDRSGVSISFLSDL 38 (119)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999985997999998829889999999
No 44
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.90 E-value=0.55 Score=26.34 Aligned_cols=38 Identities=29% Similarity=0.413 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 10489999999852-1011104679999743378778656
Q gi|254780805|r 135 LNPLEEALGYEQLI-SEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 135 l~p~e~A~~~~~l~-~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
|+..| ...|+.|+ .....|.++||+.+++|+|+|++.|
T Consensus 25 Ls~~D-v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl 63 (126)
T COG3355 25 LSELD-VEVYKALLEENGPLTVDELAEILNRSRSTVYRSL 63 (126)
T ss_pred CCHHH-HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 96889-9999999864699579999999783199999999
No 45
>pfam07638 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.
Probab=88.56 E-value=1 Score=24.62 Aligned_cols=39 Identities=18% Similarity=0.133 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 4899999998521011104679999743378778656565
Q gi|254780805|r 137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
|-++-..+ .|....|+|..|||+.+|.|.+||.++|...
T Consensus 137 pp~~r~v~-~L~~~eglS~~EIAe~Lgis~~TVk~rl~~A 175 (185)
T pfam07638 137 SPRQARLV-ELRFFAGLSNDEIAERLGVSERTVERNWALA 175 (185)
T ss_pred CHHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99888898-8899759999999999796998999999999
No 46
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=88.52 E-value=0.84 Score=25.14 Aligned_cols=39 Identities=21% Similarity=0.349 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 22104899999998521011104679999743378778656
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
+.|+|-|.|.-+ |.+.||++.+|||+.+|+|.+.+...+
T Consensus 117 e~L~P~eRaa~v--Lrdvfg~~~~EIA~~Lg~s~~a~Rqll 155 (290)
T PRK09635 117 ERLGPAERVVFV--LHEIFGLPYQQIATTIGSQASTCRQLA 155 (290)
T ss_pred HCCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 629986854552--698608988999999689989999999
No 47
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=88.16 E-value=2.1 Score=22.61 Aligned_cols=57 Identities=16% Similarity=0.159 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHCCH
Q ss_conf 1048999999985210111046799997433787786565--6543589999876421016
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR--ILKLPSSVREMIRKEEISL 193 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~~i~~~l~~~~is~ 193 (300)
|.|-+.. ++ .|..-.|+|.+|||+.+|.|..+|..+|. +.+|=..+..+-..|.-+.
T Consensus 132 Lp~~~R~-vl-~L~~~eg~s~~EIA~~lgis~~tVKsrl~RAr~~Lr~~L~~l~~~g~~~~ 190 (197)
T PRK09643 132 LPVEQRA-AL-VAVDMQGYSVADTARMLGVAEGTVKSRCARGRARLAELLGYLRAGGNASP 190 (197)
T ss_pred CCHHHHH-HH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 9998879-99-99998199999999998939999999999999999999998845789999
No 48
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.
Probab=87.92 E-value=0.54 Score=26.39 Aligned_cols=41 Identities=20% Similarity=0.434 Sum_probs=32.9
Q ss_pred HHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99985210111-046799997433787786565654358999
Q gi|254780805|r 143 GYEQLISEYGY-TQNDIGSIVGKSRSHVANILRILKLPSSVR 183 (300)
Q Consensus 143 ~~~~l~~~~~~-t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~ 183 (300)
.+.|+++.+|. |+.|+|+.+|.++++|++..+=...|.+..
T Consensus 2 vi~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R~~~P~e~i 43 (65)
T pfam07022 2 VIERLMKAYGFKSRSELADHLGVSKSTLSTWYKRDSFPAEWV 43 (65)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCHHHH
T ss_conf 899999996888699999996988888999998699989999
No 49
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry is found in all varieties of the sigma-70 type sigma factors, including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (IPR000394 from INTERPRO) are included within this entry. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=87.47 E-value=0.84 Score=25.14 Aligned_cols=39 Identities=23% Similarity=0.307 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-++..-.-+.. .|+|+.|||+.+|.|.++|.+++.
T Consensus 114 ~Lp~~~r~~~~l~~~--~~~s~~eIA~~lg~s~~~v~~~~~ 152 (162)
T TIGR02937 114 KLPEREREVLVLRYL--EGLSYKEIAEILGISEGTVKSRLK 152 (162)
T ss_pred HCCHHHHHHHHHHHH--HCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 479989999999997--189988999986899999999999
No 50
>PRK06930 positive control sigma-like factor; Validated
Probab=87.44 E-value=0.94 Score=24.84 Aligned_cols=38 Identities=18% Similarity=0.364 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|+|-|....+ |....|+|+.++|+.+|.|.++|.+++.
T Consensus 115 Lt~rErevfl--l~~~~glsy~EIA~~L~Is~~tV~~~l~ 152 (170)
T PRK06930 115 LTEREKEVYL--MHRGYGLSYSEIAAYLNIKKSTVQSMIE 152 (170)
T ss_pred CCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 6988889998--8976188899999997988999999999
No 51
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=87.27 E-value=2.4 Score=22.23 Aligned_cols=28 Identities=29% Similarity=0.273 Sum_probs=23.6
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|....|+|..|||+.+|.|.++|.++|.
T Consensus 130 L~~~egls~~EIA~~lgiS~~tVk~~l~ 157 (172)
T PRK09651 130 LSQLDGLTYSEIAHKLGVSISSVKKYVA 157 (172)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9988399999999998939999999999
No 52
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity..
Probab=87.20 E-value=0.9 Score=24.96 Aligned_cols=38 Identities=32% Similarity=0.323 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999998521011-1046799997433787786565654
Q gi|254780805|r 140 EALGYEQLISEYG-YTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 140 ~A~~~~~l~~~~~-~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+-.-+..|.+.+| .+.+.||+.+|+|++|++|+++-|+
T Consensus 171 ~~~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~~~~Le 209 (231)
T TIGR01884 171 ELKVLEALKAEKGEKSVKNIAKKLGKSLSTISRHLAELE 209 (231)
T ss_pred HHHHHHHHHCCCCEECHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999985078805287799885788879999999887
No 53
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=87.20 E-value=0.57 Score=26.24 Aligned_cols=31 Identities=26% Similarity=0.336 Sum_probs=25.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999852101110467999974337877865
Q gi|254780805|r 142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
+-+++...+.|+||+++|++.|.|+++|++.
T Consensus 8 edlrk~Rk~LGitQ~dLA~~aGVSQ~~IArl 38 (187)
T COG3620 8 EDLRKRRKELGITQKDLARRAGVSQPYIARL 38 (187)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHH
T ss_conf 9999999875977899998708648889998
No 54
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=86.95 E-value=0.75 Score=25.45 Aligned_cols=33 Identities=33% Similarity=0.361 Sum_probs=27.2
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999985210111046799997433787786565
Q gi|254780805|r 141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
..-..+|++. |.+..++|+.+|.|++||.+++.
T Consensus 11 ~~~v~~L~~~-G~~i~~IA~~~~vsrsTvYRyl~ 43 (45)
T pfam02796 11 INEVITLLEE-GISIKQIAKIFGISRSTVYRYLA 43 (45)
T ss_pred HHHHHHHHHC-CCCHHHHHHHHCCHHHHHHHHCC
T ss_conf 9999999987-99499999998600888876445
No 55
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=86.79 E-value=0.92 Score=24.88 Aligned_cols=33 Identities=21% Similarity=0.355 Sum_probs=25.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9998521011104679999743378778656565
Q gi|254780805|r 143 GYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
.+..+... |.|..++|+.+|.|++||.++++-.
T Consensus 164 ~i~~~~~~-g~s~~~iak~~gvsrsTvyR~lK~~ 196 (200)
T PRK13413 164 VITKELKK-GTTKSEIAKKLKVSRTTLARFLKTM 196 (200)
T ss_pred HHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999988-8999999999892999999999744
No 56
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=86.79 E-value=0.82 Score=25.23 Aligned_cols=35 Identities=14% Similarity=0.262 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999985210111046799997433787786565
Q gi|254780805|r 140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
...-+++|..+.|+|++++|++.|.|++++++.=+
T Consensus 8 iG~rIr~lR~~~glTL~eLA~~sGvS~s~LSqIEr 42 (185)
T PRK09943 8 PGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQ 42 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 88999999998599899999887969999999987
No 57
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=86.78 E-value=0.56 Score=26.27 Aligned_cols=34 Identities=29% Similarity=0.362 Sum_probs=28.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9998521011104679999743378778656565
Q gi|254780805|r 143 GYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
.++.+.+..|+|+.++|+.+|.++++++++..=-
T Consensus 3 ~l~~~r~~~~ls~~~lA~~~gis~~~l~~~e~g~ 36 (58)
T cd00093 3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCC
T ss_conf 9999999759999999571499999999998799
No 58
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=86.72 E-value=1.3 Score=23.85 Aligned_cols=19 Identities=21% Similarity=0.316 Sum_probs=9.4
Q ss_pred HHHHHHHCCC--CHHHHHHHH
Q ss_conf 9999742224--778999999
Q gi|254780805|r 208 LAQVIVSKKM--SVRDTEELV 226 (300)
Q Consensus 208 la~~Ii~~~L--SVRe~E~lV 226 (300)
+....-..+| +|||..+.+
T Consensus 405 ~~~~L~~y~WpGNVRqL~N~i 425 (511)
T COG3283 405 LLTVLTRYAWPGNVRQLKNAI 425 (511)
T ss_pred HHHHHHHCCCCCCHHHHHHHH
T ss_conf 999998779996099999999
No 59
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=86.69 E-value=2.1 Score=22.57 Aligned_cols=54 Identities=15% Similarity=0.237 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 21048999999985210111046799997433787786565654358999987642101
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS 192 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is 192 (300)
-|++.+...-.- .+ -|+|.+|||+.+|.|.++|.+++ -.+=..++..|..++++
T Consensus 155 ~l~~~e~~V~~~-~~--eg~s~~EIA~~l~is~~tV~~~l--~RarkkLr~~L~~~~~~ 208 (209)
T PRK08295 155 LLSDLEKEVLEL-YL--DGKSYQEIAEELNRHVKSIDNAL--QRVKRKLEKYLEIREVT 208 (209)
T ss_pred CCCHHHHHHHHH-HH--CCCCHHHHHHHHCCCHHHHHHHH--HHHHHHHHHHHHHCCCC
T ss_conf 691899999999-98--69999999999892999999999--99999999998744056
No 60
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=86.31 E-value=2.1 Score=22.57 Aligned_cols=58 Identities=17% Similarity=0.255 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf 22104899999998521011104679999743378778656565435899998764210167
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLG 194 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~g 194 (300)
..|+|-++..-+-+..+ |+|.+|||+.+|.|.++|.++|. ..=..+++.+....|..|
T Consensus 130 ~~L~~~~R~vi~l~~~e--~~s~~EIA~~lgis~~tV~~~l~--RAr~~Lr~~L~~~g~~~g 187 (189)
T PRK12515 130 AKLSPAHREIIDLVYYH--EKSVEEVGEIVGIPESTVKTRMF--YARKKLAELLKAAGVERG 187 (189)
T ss_pred HCCCHHHHHHHHHHHHC--CCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHCCCCC
T ss_conf 75999999999999984--99999999998929999999999--999999999997283358
No 61
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=86.18 E-value=1.7 Score=23.20 Aligned_cols=28 Identities=29% Similarity=0.310 Sum_probs=23.1
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|....|+|.+|||+.+|.|.++|.++|.
T Consensus 116 L~~~egls~~EIA~~lgis~~tVk~~l~ 143 (159)
T PRK12527 116 LRKLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8987397999999998919999999999
No 62
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=86.16 E-value=1.7 Score=23.25 Aligned_cols=87 Identities=20% Similarity=0.147 Sum_probs=46.6
Q ss_pred CCCCCHHHHHHHHHHHC-CCCCCCCCC--CCCHHHHHHHHHHH-HHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 33357567777764210-013543334--64112345566654-310221048999999985210111046799997433
Q gi|254780805|r 90 KIIAGERRFRAAKMASL-SEVPVIIRN--VDNKSSLEIAIVEN-VQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKS 165 (300)
Q Consensus 90 ~ii~G~rR~rAa~~~g~-~~ip~iv~~--~~d~~~~~~~l~EN-~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s 165 (300)
++|+=-|+.+|.|.-|- ..+|-.-.+ .+.+....+...|- +.+=.-..=+.|..++ |.--.|+|.+|+|+.+|.|
T Consensus 96 IL~D~AR~~~~~KRGg~~~~~~l~~~~~~~~~~~~~~L~~Ld~aL~~L~~~~Pr~a~~ve-Lr~F~Gl~~~E~A~~L~~S 174 (194)
T TIGR02999 96 ILVDHARRRRAQKRGGGAVRVSLDEVLPDAEADADEELLDLDDALDKLAQVDPRQAEVVE-LRFFAGLTVEEIAELLGVS 174 (194)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHH-HHHHCCCCHHHHHHHHCCC
T ss_conf 999999999874136776335520000135777403599999999877400678899885-3110488989999986888
Q ss_pred HHHHHHHHHHHH
Q ss_conf 787786565654
Q gi|254780805|r 166 RSHVANILRILK 177 (300)
Q Consensus 166 ~s~V~~~LrLl~ 177 (300)
.+||.|-++...
T Consensus 175 ~~Tv~Rdw~~AR 186 (194)
T TIGR02999 175 VRTVERDWRFAR 186 (194)
T ss_pred HHHHHHHHHHHH
T ss_conf 878998799999
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=86.14 E-value=1.9 Score=22.87 Aligned_cols=36 Identities=25% Similarity=0.419 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Q ss_conf 111046799997433787786565--654358999987
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR--ILKLPSSVREMI 186 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~~i~~~l 186 (300)
.|+|.+|||+.+|.|.++|.+++. +..|=..+++.+
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~rA~~~Lr~~L~e~l 193 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDLL 193 (194)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 19999999999894999999999999999999989873
No 64
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=85.96 E-value=0.96 Score=24.78 Aligned_cols=41 Identities=32% Similarity=0.360 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 22104899999998521011-1046799997433787786565
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYG-YTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~-~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.+|+.-| -..+.-+.+..| .+|.+|.+.+|.|+++|++.|+
T Consensus 191 ~~L~~~e-~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~ 232 (258)
T COG2512 191 YDLNEDE-KEILDLIRERGGRITQAELRRALGLSKTTVSRILR 232 (258)
T ss_pred CCCCHHH-HHHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHHH
T ss_conf 7899789-99999999858978699988860997677999999
No 65
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178 Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=85.89 E-value=0.32 Score=27.85 Aligned_cols=56 Identities=14% Similarity=0.408 Sum_probs=37.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH-----------------HHHHCCHHHHHHHHHHHCC
Q ss_conf 04679999743378778656565435899998764210167777-----------------7640100468999974222
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHAR-----------------TLVSTSDPLSLAQVIVSKK 216 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar-----------------~Ll~~~~~~~la~~Ii~~~ 216 (300)
.-.|||+.+|..|+|.+ +-+|.+-+||=||.-|++ +|+.|+.+. +-.++++-
T Consensus 32 AERELsElIGVTRTTLR---------EVLQRLARDGWLTIQHGKPTKVNnfWETSGLNILeTL~~LD~~~--~P~l~dnL 100 (275)
T TIGR02812 32 AERELSELIGVTRTTLR---------EVLQRLARDGWLTIQHGKPTKVNNFWETSGLNILETLIRLDGES--VPSLIDNL 100 (275)
T ss_pred HHHHHHHHCCCCCCHHH---------HHHHHHHHHCCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHCCCC--CCHHHHHH
T ss_conf 46657542376630378---------99988764113436588998627624302735789998618777--70799999
Q ss_pred CCHH
Q ss_conf 4778
Q gi|254780805|r 217 MSVR 220 (300)
Q Consensus 217 LSVR 220 (300)
||+|
T Consensus 101 LSAR 104 (275)
T TIGR02812 101 LSAR 104 (275)
T ss_pred HHHH
T ss_conf 9776
No 66
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=84.86 E-value=1.4 Score=23.69 Aligned_cols=39 Identities=28% Similarity=0.302 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-+...-.-+.. .|+|..|||+.+|.|.++|..++.
T Consensus 10 ~L~~~~r~vl~l~y~--~~~s~~EIa~~lgis~~tVk~~l~ 48 (55)
T cd06171 10 KLPEREREVILLRFG--EGLSYEEIAEILGISRSTVRQRLH 48 (55)
T ss_pred CCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 399999898999998--099999999998959999999999
No 67
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=84.84 E-value=1.3 Score=23.83 Aligned_cols=35 Identities=34% Similarity=0.350 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999985210111046799997433787786565
Q gi|254780805|r 140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
++..|..|+.....|..+||+.+|.+|++|.+.|.
T Consensus 10 E~~vY~~Ll~~g~~t~~eia~~~~i~r~~vY~~L~ 44 (68)
T pfam01978 10 EAKVYLALLKLGPATADEIAEESGVPRSKVYEVLR 44 (68)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999981998899999995988989999999
No 68
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=84.77 E-value=1.4 Score=23.74 Aligned_cols=21 Identities=10% Similarity=0.132 Sum_probs=11.4
Q ss_pred HHHHHCCC--CHHHHHHHHHHHH
Q ss_conf 99742224--7789999997641
Q gi|254780805|r 210 QVIVSKKM--SVRDTEELVQEQD 230 (300)
Q Consensus 210 ~~Ii~~~L--SVRe~E~lVk~~~ 230 (300)
+......| +|||.++.+....
T Consensus 529 ~~L~~y~WPGNvrEL~nvl~~a~ 551 (639)
T PRK11388 529 ARLVSYRWPGNDFELRSVIENLA 551 (639)
T ss_pred HHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 99972899979999999999999
No 69
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent.
Probab=84.69 E-value=2.1 Score=22.59 Aligned_cols=57 Identities=19% Similarity=0.257 Sum_probs=42.3
Q ss_pred HHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Q ss_conf 31022104899999998521011104679999743378778656565-4358999987642
Q gi|254780805|r 130 VQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL-KLPSSVREMIRKE 189 (300)
Q Consensus 130 ~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l~~~ 189 (300)
-.|+| ...+..-+..|++. ..||.||+..+|.|-++|++==.-+ .+||++++.+...
T Consensus 37 ~Er~d--l~~R~~I~~~LL~~-~~~QREi~~~lG~SiA~ITRGSn~Lk~~D~~~~~fL~~~ 94 (95)
T TIGR01321 37 DERED--LGSRVRIVEELLEG-EMSQREIAEKLGVSIATITRGSNALKALDPEFKQFLKKK 94 (95)
T ss_pred HHHHH--HHHHHHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 37999--98799999999614-897478888637616678787887516987889998842
No 70
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=84.67 E-value=2.5 Score=22.16 Aligned_cols=50 Identities=12% Similarity=0.127 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 210489999999852101110467999974337877865656543589999876
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIR 187 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~ 187 (300)
.|+|-...... |..-.|+|.+|||+.+|.|.++|..+|. ..-..+++.+.
T Consensus 108 ~Lp~~~r~v~~--L~~~~~~s~~EIA~~l~is~~tVk~rl~--RAr~~Lr~~L~ 157 (165)
T PRK09644 108 TLPVIEAQAIL--LCDVHELTYEEAASVLDLKENTYKSHLF--RGRKRLKALLK 157 (165)
T ss_pred CCCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHH
T ss_conf 29999999999--9999888999999998939999999999--99999999999
No 71
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=84.52 E-value=0.98 Score=24.72 Aligned_cols=31 Identities=39% Similarity=0.615 Sum_probs=25.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99998521011104679999743378778656
Q gi|254780805|r 142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
.+++.+++.||+|+.++|..+| |+|.|||.|
T Consensus 63 e~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL 93 (120)
T COG5499 63 EVIRTLMDQYGLTLADLANEIG-SKSRVSNIL 93 (120)
T ss_pred HHHHHHHHHHCCCHHHHHHHHC-CHHHHHHHH
T ss_conf 9999999993871888899867-618899997
No 72
>PRK04140 hypothetical protein; Provisional
Probab=83.96 E-value=1.9 Score=22.86 Aligned_cols=114 Identities=15% Similarity=0.138 Sum_probs=64.2
Q ss_pred CCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH------
Q ss_conf 89889999999886310015504620565445333575677777642100135433346411234556665431------
Q gi|254780805|r 58 FESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIVENVQ------ 131 (300)
Q Consensus 58 ~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~~------ 131 (300)
++++...+|. -|..+-.-.|++|-....+ .++=.|-= --..-|||+ +. +.+...++++..
T Consensus 52 ~s~e~~~dLk-~la~~~~a~piiVg~r~r~-~~Le~gVV-------Y~R~gI~~v----s~-~T~~d~lv~g~~P~iya~ 117 (319)
T PRK04140 52 LSEEQAEELK-KLAKYLKASPIIIGLRTRN-GELEDGVV-------YERHGIPAL----SP-ETFYDYFVEGEPPLIYAA 117 (319)
T ss_pred CCHHHHHHHH-HHHHHHCCCCEEEEEECCC-CCCCCCCE-------EEECCCEEE----CH-HHHHHHHHCCCCCEEEEC
T ss_conf 7988999999-9999858862799971488-74667617-------986693462----69-999999836899569965
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Q ss_conf 0221048999999985210111046799997433787786565-65435899998
Q gi|254780805|r 132 RKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR-ILKLPSSVREM 185 (300)
Q Consensus 132 R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr-Ll~L~~~i~~~ 185 (300)
|-.+..-=.+.-++++.++.|||..+||..+|.||.+|++|=+ -...+-++-..
T Consensus 118 ~GG~yV~Idg~~Lr~~Re~~g~SlG~LA~~LGVSRrtv~~YE~g~~~~sievA~k 172 (319)
T PRK04140 118 RGGFYVNIDGDLLRELREKLGLSLGELASELGVSRRTISKYENGGMNASIEVAIK 172 (319)
T ss_pred CCCEEEEECHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHH
T ss_conf 8847999847999999998198888999984986999999970688664999999
No 73
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=83.88 E-value=2 Score=22.79 Aligned_cols=39 Identities=28% Similarity=0.451 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 22104899999998521011104679999743378778656
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
+.|+|-+.|.-. |.+.+|++.+|||+.+|+|.++|...|
T Consensus 110 ~~L~p~qRav~v--Lrdv~g~s~~EIA~iLg~s~~avR~~l 148 (289)
T PRK09636 110 ERLSPLERAAFL--LHDVFGVPFDEIASTLGRSEAACRQLA 148 (289)
T ss_pred HHCCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 739998962540--498609999999999817999999999
No 74
>PHA00542 putative Cro-like protein
Probab=83.65 E-value=1.2 Score=24.08 Aligned_cols=36 Identities=25% Similarity=0.312 Sum_probs=27.9
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0489999999852101110467999974337877865656
Q gi|254780805|r 136 NPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 136 ~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrL 175 (300)
+|.|.- +.|++ .||||++|+...|.+++.|++.|.=
T Consensus 19 ~P~E~V---~aLi~-~G~tQ~qI~~~tgv~QpsisRilsG 54 (82)
T PHA00542 19 RPDELV---CALIR-AGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred CHHHHH---HHHHH-CCCCHHHHHHHHCCCCHHHHHHHCC
T ss_conf 989999---99998-2256999998608770368999808
No 75
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=83.39 E-value=0.82 Score=25.20 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=24.2
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 8521011104679999743378778656
Q gi|254780805|r 146 QLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
..++..|+|..++|+.+|.||++|++.+
T Consensus 14 EfL~PLg~s~~~LA~~LgVsr~~~sriv 41 (81)
T TIGR02607 14 EFLEPLGLSVRALAKALGVSRSTLSRIV 41 (81)
T ss_pred HHHHCCCHHHHHHHHHCCCCHHHHHHHH
T ss_conf 7521047068999987099978888887
No 76
>PRK09483 response regulator; Provisional
Probab=83.32 E-value=2.9 Score=21.68 Aligned_cols=39 Identities=21% Similarity=0.184 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 221048999999985210111046799997433787786565
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
..|||-|.- .-+++.+ |+|-.+||.+++.|..||.++++
T Consensus 147 ~~LT~RE~e--Vl~ll~~-G~snkeIA~~L~iS~~TV~~h~~ 185 (216)
T PRK09483 147 ASLSERELQ--IMLMITK-GQKVNEISEQLNLSPKTVNSYRY 185 (216)
T ss_pred CCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 568999999--9999987-99999999996989999999999
No 77
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=83.17 E-value=3.3 Score=21.35 Aligned_cols=19 Identities=21% Similarity=0.233 Sum_probs=11.4
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q ss_conf 0467999974337877865
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~ 172 (300)
|.++||+.+|.|...|...
T Consensus 131 t~~EiA~~l~is~~~v~~~ 149 (256)
T PRK07408 131 TDQEIAQALDISLEEWQEI 149 (256)
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 8999998959699999999
No 78
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=83.06 E-value=0.76 Score=25.41 Aligned_cols=26 Identities=38% Similarity=0.639 Sum_probs=21.5
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 852101110467999974337877865
Q gi|254780805|r 146 QLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
+|. +.|+||.+||+.+|-||+.|+..
T Consensus 14 ~lR-~~G~tQ~eIA~~lgTSraNvs~i 39 (139)
T PRK03975 14 RLR-KRGLTQQEIADILGTSRANISII 39 (139)
T ss_pred HHH-HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999-82897999999977328899999
No 79
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=83.00 E-value=2.2 Score=22.50 Aligned_cols=39 Identities=23% Similarity=0.234 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|++-|...-..... .|.|+.|||+.+|.|.++|....+
T Consensus 106 ~L~~re~~ii~~~~~--~g~t~~EIA~~~gis~~~Vk~~~r 144 (154)
T PRK06759 106 VLDEKEKYIIFERFF--VGKTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred HCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 499999999999999--699899999998989999999999
No 80
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=82.21 E-value=4 Score=20.77 Aligned_cols=54 Identities=17% Similarity=0.254 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 2104899999998521011104679999743378778656565435899998764210
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI 191 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i 191 (300)
.|+|-.+..-.-+.. .|+|.+|||+.+|.|.++|..++. ..-..+++.+.+..|
T Consensus 116 ~L~~~~r~v~~l~~~--~g~s~~EIA~~l~is~~tVk~~l~--ra~~~Lr~~L~~~gi 169 (171)
T PRK09645 116 QLSPEHRAVLVRSYY--RGWSTAQIAADLGIPEGTVKSRLH--YAVRALRLTLQEMGV 169 (171)
T ss_pred CCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHCCC
T ss_conf 599998879899998--699999999998929999999999--999999999997099
No 81
>pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Probab=82.12 E-value=2.1 Score=22.59 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|.+-+...-+ |..-.|+|.+|+|+.+|.|.++|.+++.
T Consensus 11 Lp~~~r~~~~--l~~~~~~s~~eIA~~lg~s~~tVk~~l~ 48 (54)
T pfam08281 11 LPPRQREVFL--LRYLEGLSYAEIAELLGISEGTVKSRLS 48 (54)
T ss_pred CCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999998968--7998785999999998949999999999
No 82
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=82.12 E-value=2 Score=22.66 Aligned_cols=38 Identities=26% Similarity=0.416 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-|.-. -+++.+ |+|..+||+.+|.|..+|.++++
T Consensus 3 ~LT~RE~~i--l~~l~~-G~s~~eIA~~L~is~~TV~~h~~ 40 (58)
T pfam00196 3 SLSPREREV--LRLLAA-GKSNKEIADILGISEKTVKVHRS 40 (58)
T ss_pred CCCHHHHHH--HHHHHH-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 779999999--999980-79999999997888999999999
No 83
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=81.96 E-value=3.6 Score=21.06 Aligned_cols=39 Identities=31% Similarity=0.332 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 210489999999852101110467999974337877865
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
.|++-|...-..++..+-+.|..+||+.+|.|+..|++.
T Consensus 227 ~L~eREr~Ii~~r~~~~e~~TL~EIg~~lgvSreRVRQI 265 (289)
T PRK07500 227 TLNERELFIIRERRLREDGATLEALGEELGISKERVRQI 265 (289)
T ss_pred CCCHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 499999999999766899858999999979799999999
No 84
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037 (Tannerella forsythensis ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=81.77 E-value=2.2 Score=22.51 Aligned_cols=28 Identities=21% Similarity=0.221 Sum_probs=20.2
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|-..-|+|..|||+.+|.|..||-++|.
T Consensus 130 lsr~eg~s~~EIA~~L~iS~~TVe~hi~ 157 (167)
T TIGR02985 130 LSRFEGLSNKEIAEELGISVKTVEYHIT 157 (167)
T ss_pred HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9886179867899884898889999999
No 85
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=81.76 E-value=1.9 Score=22.85 Aligned_cols=32 Identities=16% Similarity=0.208 Sum_probs=24.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999852101110467999974337877865
Q gi|254780805|r 141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
+..+++-.+..||+|++||++++.+.+.|.+.
T Consensus 81 ~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~i 112 (165)
T COG1813 81 GERIREAREKRGLSQEDLAAKLKEKVSVIRRI 112 (165)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999982888999999965469999999
No 86
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=81.63 E-value=2.1 Score=22.59 Aligned_cols=26 Identities=27% Similarity=0.446 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 11104679999743378778656565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
..+|+++||..+|.++-||++.|.-+
T Consensus 24 l~ltr~eiA~~lG~t~eTVsR~l~~l 49 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKEL 49 (67)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 17799999999789099999999999
No 87
>PRK08359 transcription factor; Validated
Probab=81.52 E-value=2 Score=22.67 Aligned_cols=32 Identities=22% Similarity=0.254 Sum_probs=23.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999852101110467999974337877865
Q gi|254780805|r 141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
+.-+++-.+..||||++||.+++.+.+.|.+.
T Consensus 85 ~~~Ir~ARE~~GlSqeeLA~ki~ek~nvI~ki 116 (175)
T PRK08359 85 AERVYEAIRKSGLSYEELSHKVGLSVNDLRRI 116 (175)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHH
T ss_conf 99999999985999999999972229999999
No 88
>pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.
Probab=81.22 E-value=2.8 Score=21.76 Aligned_cols=34 Identities=26% Similarity=0.389 Sum_probs=25.6
Q ss_pred HHHHHHHHCCC--CHHHHHHHHHH-HHHHHHHHHHHH
Q ss_conf 99985210111--04679999743-378778656565
Q gi|254780805|r 143 GYEQLISEYGY--TQNDIGSIVGK-SRSHVANILRIL 176 (300)
Q Consensus 143 ~~~~l~~~~~~--t~~~lA~~~G~-s~s~V~~~LrLl 176 (300)
.++..++++|+ |..||++.+|. |.++|..+|.-|
T Consensus 14 ~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~L 50 (65)
T pfam01726 14 FIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKAL 50 (65)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 9999999828898799999993899809999999999
No 89
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=81.17 E-value=4.4 Score=20.54 Aligned_cols=47 Identities=19% Similarity=0.267 Sum_probs=34.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Q ss_conf 999985210111046799997433787786565----6543589999876421
Q gi|254780805|r 142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILR----ILKLPSSVREMIRKEE 190 (300)
Q Consensus 142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr----Ll~L~~~i~~~l~~~~ 190 (300)
-++.| +..|+|.++||+.+|.++.+|.|+|+ =..|--++-+++..|.
T Consensus 53 ga~ar--ekag~Ti~EIAeelG~TeqTir~hlkgetkAG~lv~etY~~lK~G~ 103 (182)
T COG1318 53 GALAR--EKAGMTISEIAEELGRTEQTVRNHLKGETKAGQLVRETYEKLKEGG 103 (182)
T ss_pred HHHHH--HHCCCCHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHCC
T ss_conf 89999--8703749999999687799999997514033169999999998067
No 90
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=81.02 E-value=3.8 Score=20.96 Aligned_cols=42 Identities=12% Similarity=0.264 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf 11104679999743378778656565435899998764210167
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLG 194 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~g 194 (300)
.|+|..|||+.+|.|.++|..+|. ..-..+++.|....-..|
T Consensus 151 eg~s~~EIA~~lgis~~tVk~~l~--Rark~Lr~~L~~~r~~~g 192 (196)
T PRK12524 151 EGLSNPEIAEVMQIGVEAVESLTA--RGKRALAALLAGQRAELG 192 (196)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHHHHCC
T ss_conf 089999999998929999999999--999999999871798749
No 91
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=80.91 E-value=2.4 Score=22.26 Aligned_cols=41 Identities=17% Similarity=0.222 Sum_probs=31.4
Q ss_pred HCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10221048999999985210111046799997433787786565
Q gi|254780805|r 131 QRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 131 ~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
....|||-|.- .-+++.+ |+|..+||..++.|..||.++++
T Consensus 134 ~~~~LT~RE~e--VL~lia~-G~snkeIA~~L~IS~~TVk~h~~ 174 (196)
T PRK10360 134 RQDPLTKRERQ--VAEKLAQ-GMAVKEIAAELGLSPKTVHVHRA 174 (196)
T ss_pred CCCCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 76899979999--9999987-99999999996999999999999
No 92
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=80.81 E-value=4.1 Score=20.70 Aligned_cols=40 Identities=15% Similarity=0.125 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 221048999999985210111046799997433787786565
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
..|+|.+...-. |....|+|..|||+.+|.|.++|..+|.
T Consensus 133 ~~L~~~~R~vl~--L~~~~~ls~~EIA~~l~is~~tVksrl~ 172 (188)
T PRK09640 133 VHVNPIDREILV--LRFVAELEFQEIADIMHMGLSATKMRYK 172 (188)
T ss_pred HHCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 848999999999--9999299999999998929999999999
No 93
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=80.73 E-value=4.5 Score=20.44 Aligned_cols=39 Identities=15% Similarity=0.151 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-....-. |....|+|.++||+.+|.|.++|.++|.
T Consensus 128 ~Lp~~~R~v~~--L~~~~g~s~~EIA~~l~is~~tVk~~l~ 166 (186)
T PRK05602 128 ALPERQREAIV--LQYYQGLSNIEAARVMGLSVDALESLLA 166 (186)
T ss_pred CCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 59987889999--9986389999999998939999999999
No 94
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=80.61 E-value=2.5 Score=22.05 Aligned_cols=39 Identities=15% Similarity=0.287 Sum_probs=26.7
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|.|-..-..+.+.+ .|+|.+|||+.+|.|.++|..+|.
T Consensus 135 ~L~~~~r~~i~l~~~--eg~s~~EIA~~l~is~~TVk~rl~ 173 (184)
T PRK12537 135 QLEPARRNCILHAYV--DGCSHAEIAQRLGAPLGTVKAWIK 173 (184)
T ss_pred HCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 099989999999884--399999999998929999999999
No 95
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=80.31 E-value=2.7 Score=21.89 Aligned_cols=27 Identities=22% Similarity=0.359 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565654
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
..+|-+++|+.+|.||.|+.+||.-+.
T Consensus 177 ~~~sa~eva~~~giSRvTaRRYLe~L~ 203 (239)
T PRK10430 177 YEFSTDELANEVNISRVSCRKYLIWLV 203 (239)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 984699999885852988999999998
No 96
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=80.22 E-value=4.7 Score=20.33 Aligned_cols=26 Identities=19% Similarity=0.206 Sum_probs=21.8
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10111046799997433787786565
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.-.|+|..|||+.+|.|.++|.+++.
T Consensus 139 ~~eg~s~~EIA~~lgis~~tVk~rl~ 164 (178)
T PRK12536 139 KLEGLSVEETAQLTGLSESAVKVGIH 164 (178)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 88599999999998929999999999
No 97
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=80.21 E-value=4.7 Score=20.33 Aligned_cols=39 Identities=13% Similarity=0.174 Sum_probs=27.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHH
Q ss_conf 10111046799997433787786565--6543589999876
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANILR--ILKLPSSVREMIR 187 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~~i~~~l~ 187 (300)
...|+|..|||+.+|.|.++|..+|. .-.|=..++.++.
T Consensus 151 ~~egls~~EIA~~l~is~~tVk~rl~RAr~~Lr~~L~~ll~ 191 (193)
T PRK11923 151 EFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPLLQ 191 (193)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99499999999998929999999999999999999899873
No 98
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=80.20 E-value=4.7 Score=20.33 Aligned_cols=46 Identities=17% Similarity=0.413 Sum_probs=32.8
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf 101110467999974337877865656543589999876421016777
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHA 196 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~gha 196 (300)
...|+|.+|||+.+|.|.++|..+|. .--..++++|...+....|+
T Consensus 184 ~~egls~~EIA~~Lgis~~TVKsrL~--RAr~~LR~~L~r~e~~~~~~ 229 (233)
T PRK12538 184 YHENMSNGEIAEVMDTTVAAVESLLK--RGRQQLRDLLRRHERDIRHA 229 (233)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
T ss_conf 98499999999998929999999999--99999999999874888765
No 99
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=80.02 E-value=2.4 Score=22.26 Aligned_cols=37 Identities=19% Similarity=0.258 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 48999999985210111046799997433787786565
Q gi|254780805|r 137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.+|...-. ..++.+++.+.+.|+.+|.||+++.+.|+
T Consensus 4 ~~Er~~I~-~aL~~~~gn~~~aA~~LGisr~tL~~kmk 40 (42)
T pfam02954 4 EVEKELIE-AALERTGGNKSKAARLLGISRRTLYRKLK 40 (42)
T ss_pred HHHHHHHH-HHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999-99999499799999997969999999997
No 100
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=79.95 E-value=4.3 Score=20.56 Aligned_cols=50 Identities=22% Similarity=0.285 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHHH--HHHCCCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHH
Q ss_conf 221048999999985--21011104679999743378778656--565435899
Q gi|254780805|r 133 KDLNPLEEALGYEQL--ISEYGYTQNDIGSIVGKSRSHVANIL--RILKLPSSV 182 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l--~~~~~~t~~~lA~~~G~s~s~V~~~L--rLl~L~~~i 182 (300)
+.|++-|.-.--.|. .+.-.+|++++|+.+|.|+.+|++.- +|-+|=..+
T Consensus 182 ~~L~eREr~Ii~lRfGL~~~~~~Tl~EIa~~lgISrerVrQIe~~AL~KLR~~l 235 (239)
T PRK08301 182 KKLNDREKQIMELRFGLAGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEI 235 (239)
T ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 648999999999995788998406999999989789999999999999999999
No 101
>PRK09954 hypothetical protein; Provisional
Probab=79.88 E-value=2.5 Score=22.10 Aligned_cols=64 Identities=11% Similarity=0.137 Sum_probs=30.1
Q ss_pred EHHHCCCCCCCCCCCC-CHH-HHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 3898235789998768-988-99999998863100155046205654453335756777776421001354
Q gi|254780805|r 43 SIHSIVPNPHNPRNYF-ESE-GLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPV 111 (300)
Q Consensus 43 ~i~~i~~~p~~pR~~~-~~~-~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~ 111 (300)
+...+.+.-.||-+.+ +.. .=.-.|..+.+-| .++-.+-..++.. .|+.=+..++..|...=.|
T Consensus 74 ~~~~l~~~~SNpg~i~~s~GGvGrNiA~nLarLG-~~v~lIs~VG~D~----~G~~ll~~l~~~GVd~~~v 139 (362)
T PRK09954 74 ADIRYPQAASHPGTIHCSAGGVGRNIAHNLALLG-RDVHLLSAIGDDF----YGETLLEETRRAGVNVSGC 139 (362)
T ss_pred CCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHCC-CCEEEEEEECCCH----HHHHHHHHHHHCCCCCCEE
T ss_conf 4776656999996368888848999999999769-9769999963858----7999999999859973307
No 102
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=79.86 E-value=2.9 Score=21.73 Aligned_cols=48 Identities=19% Similarity=0.170 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565654358999987
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI 186 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l 186 (300)
|+|-....-. |..-.|+|..|||+.+|.|.++|..+|. ..=..+++.+
T Consensus 107 Lp~~~R~v~~--L~~~eg~s~~EIA~~L~is~~tVksrl~--RAr~~Lr~~L 154 (181)
T PRK09637 107 LPEKYAEALR--LTELEGLSQKEIAEKLGLSLSGAKSRVQ--RGRVKLKELL 154 (181)
T ss_pred CCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHH
T ss_conf 9999989979--9988599999999998949999999999--9999999999
No 103
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=79.52 E-value=2.8 Score=21.80 Aligned_cols=38 Identities=32% Similarity=0.476 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-|.... .++.. |+|..+||+.+|.|..+|.++++
T Consensus 3 ~LT~rE~~il--~~l~~-G~s~~eIA~~L~is~~TV~~~~~ 40 (58)
T smart00421 3 SLTPREREVL--RLLAE-GLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHH--HHHHH-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 6189999999--99981-79999999898978989999999
No 104
>PRK06424 transcription factor; Provisional
Probab=79.51 E-value=2.5 Score=22.06 Aligned_cols=39 Identities=15% Similarity=0.071 Sum_probs=26.7
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999985210111046799997433787786565654358
Q gi|254780805|r 141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPS 180 (300)
Q Consensus 141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~ 180 (300)
+.-++.-.+..||||++||.+++.+.+.|.+.= --++.|
T Consensus 86 ~~~Ir~ARE~~GlsqeeLA~ki~ek~svI~kiE-~G~l~P 124 (144)
T PRK06424 86 AELVKNARERLSMSQADLAAKIFERKNVIASIE-RGDLLP 124 (144)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH-CCCCCC
T ss_conf 999999999849999999999654499999998-389899
No 105
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=79.46 E-value=1.9 Score=22.82 Aligned_cols=47 Identities=26% Similarity=0.432 Sum_probs=34.0
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 556665431022104899999998521011104679999743378778656
Q gi|254780805|r 123 EIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 123 ~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
.++++.=+|+ |.|-+.|.-+ |.+.+||+..|+|+.+|.|.+.|...|
T Consensus 147 ~lA~laaLq~--Lpp~QRavlv--LRdV~g~s~~EiAe~Lg~S~aAVks~L 193 (341)
T PRK08241 147 RLAFVAALQH--LPPRQRAVLL--LRDVLGWSAAEVAEALGTSTAAVNSAL 193 (341)
T ss_pred HHHHHHHHHH--CCHHHHEEEE--HHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999983--9997902001--297529988999999789999999999
No 106
>PRK11050 manganese transport regulator MntR; Provisional
Probab=79.41 E-value=4.8 Score=20.28 Aligned_cols=73 Identities=26% Similarity=0.305 Sum_probs=46.7
Q ss_pred HHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCCCHH
Q ss_conf 999985210111-0467999974337877865656543589999876421016777776401004689999742224778
Q gi|254780805|r 142 LGYEQLISEYGY-TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVSKKMSVR 220 (300)
Q Consensus 142 ~~~~~l~~~~~~-t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~~~LSVR 220 (300)
+.+..|.++.|. -..+||+++|.|+++|++.+. .+-..|-|....++.+.=.+...++|+.+.... |
T Consensus 43 E~I~~L~~~~G~aR~~DIA~~LgVs~pSVt~mlk---------rL~~~GlV~~~~Y~~I~LT~~G~~~A~~i~~RH---r 110 (155)
T PRK11050 43 ELIADLIAEVGEARQVDIAARLGVSQPTVAKMLK---------RLARDGLVEMRPYRGVFLTPEGEKLAQESRERH---Q 110 (155)
T ss_pred HHHHHHHHCCCCEEHHHHHHHHCCCCHHHHHHHH---------HHHHCCCEEECCCCCEEECHHHHHHHHHHHHHH---H
T ss_conf 9999999826956499999890999331999999---------998789988718988468977999999999999---9
Q ss_pred HHHHHH
Q ss_conf 999999
Q gi|254780805|r 221 DTEELV 226 (300)
Q Consensus 221 e~E~lV 226 (300)
=++...
T Consensus 111 ile~FL 116 (155)
T PRK11050 111 IVENFL 116 (155)
T ss_pred HHHHHH
T ss_conf 999999
No 107
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=79.35 E-value=2.8 Score=21.83 Aligned_cols=37 Identities=38% Similarity=0.609 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|+|-|.-. + .++.. |+|..+||+.+|.|..+|.++++
T Consensus 1 LT~rE~~i-l-~~~~~-G~s~~eIA~~L~is~~TV~~~~~ 37 (57)
T cd06170 1 LTPREREV-L-RLLAE-GKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHH-H-HHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98899999-9-99980-79999999998978999999999
No 108
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=79.24 E-value=3 Score=21.56 Aligned_cols=39 Identities=18% Similarity=0.166 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-+.-.-.-. .-.|++.++||+.+|.|.++|.+++.
T Consensus 125 ~L~~~~r~il~l~--~~~g~s~~eIA~~lgis~~tv~~~l~ 163 (180)
T PRK11924 125 ALPEKQREVFLLR--YVEGLSYQEIADQLGVPLGTVKSRLR 163 (180)
T ss_pred HCCHHHHHHHHHH--HHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 5999999999999--99685999999998949999999999
No 109
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=79.19 E-value=1.5 Score=23.48 Aligned_cols=29 Identities=17% Similarity=0.557 Sum_probs=24.9
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 85210111046799997433787786565
Q gi|254780805|r 146 QLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.+++.+|+|+.++|+.+|..+.+|++.+.
T Consensus 17 eflep~glt~~~lA~~lgV~r~~is~lin 45 (104)
T COG3093 17 EFLEPLGLTQTELAEALGVTRNTISELIN 45 (104)
T ss_pred HHHCCCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 98452169899999993998999999983
No 110
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding.
Probab=79.10 E-value=0.99 Score=24.68 Aligned_cols=22 Identities=32% Similarity=0.555 Sum_probs=19.8
Q ss_pred HHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 1011104679999743378778
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVA 170 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~ 170 (300)
.+-||+|++||+.||-+|+.||
T Consensus 18 R~kGl~Q~eIAk~LkTtRaNvS 39 (142)
T TIGR00721 18 REKGLKQKEIAKILKTTRANVS 39 (142)
T ss_pred HHCCCCHHHHHHHHCCCCHHHH
T ss_conf 6338887889877267201378
No 111
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=79.05 E-value=2.7 Score=21.89 Aligned_cols=23 Identities=17% Similarity=0.198 Sum_probs=13.8
Q ss_pred HHHHHHHCCCC--HHHHHHHHHHHH
Q ss_conf 99997422247--789999997641
Q gi|254780805|r 208 LAQVIVSKKMS--VRDTEELVQEQD 230 (300)
Q Consensus 208 la~~Ii~~~LS--VRe~E~lVk~~~ 230 (300)
..+......|- |||.++.+.+..
T Consensus 403 a~~~L~~y~WPGNVREL~n~iera~ 427 (513)
T PRK10820 403 LSTVLTRYGWPGNVRQLKNAIYRAL 427 (513)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf 9999970899979999999999999
No 112
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=79.04 E-value=5 Score=20.16 Aligned_cols=38 Identities=13% Similarity=0.079 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|+|-+...-.-+.. .|+|.+|||+.+|.|.++|..++.
T Consensus 137 Lp~~~r~v~~L~~~--~~~s~~EIA~~l~is~~tVk~~l~ 174 (187)
T PRK09641 137 LPDKYRTVIVLKYI--EELSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred CCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 89888899999998--299899999998939999999999
No 113
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=78.95 E-value=3 Score=21.60 Aligned_cols=38 Identities=24% Similarity=0.325 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 22104899999998521011104679999743378778656
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
..|++-|.. .-+|+.+ |+|-.+||++++.|..||.++.
T Consensus 147 ~~LT~RE~e--Vl~lla~-G~snkeIA~~L~iS~~TVk~h~ 184 (211)
T COG2197 147 ELLTPRELE--VLRLLAE-GLSNKEIAEELNLSEKTVKTHV 184 (211)
T ss_pred CCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHH
T ss_conf 789989999--9999987-9988999999787898999999
No 114
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=78.64 E-value=2.4 Score=22.21 Aligned_cols=33 Identities=18% Similarity=0.318 Sum_probs=25.3
Q ss_pred HHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 985210-111046799997433787786565654
Q gi|254780805|r 145 EQLISE-YGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 145 ~~l~~~-~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
..|.+. ..+|-++||+.+|.|+.+|.+.+..++
T Consensus 7 ~~L~~~~~~vt~~~La~~l~VSr~TV~rdi~~L~ 40 (55)
T pfam08279 7 ELLLQAREPISGQELAEKLGVSRRTIRRDIKALE 40 (55)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9999769991899999996988999999999999
No 115
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=78.33 E-value=3.1 Score=21.53 Aligned_cols=24 Identities=17% Similarity=0.214 Sum_probs=18.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|.+|||+.+|.|.++|.++|.
T Consensus 157 ~g~s~~EIA~~Lgis~~TVk~rl~ 180 (194)
T PRK09646 157 GGLTYREVAERLAVPLGTVKTRMR 180 (194)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 399999999998919999999999
No 116
>pfam02376 CUT CUT domain. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein .
Probab=78.30 E-value=3.6 Score=21.06 Aligned_cols=70 Identities=16% Similarity=0.312 Sum_probs=47.2
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHH
Q ss_conf 22104899999998521011104679999-74337877865656543589999876421016777776401004
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSI-VGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDP 205 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~-~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~ 205 (300)
+.|+..+.|.-++..+..++++|.-.|+. +|+|+.+++..|+ =|.+--.+...|.-+.-.-+--+.+|+.
T Consensus 1 ~~ldT~~i~~~i~~eL~~~~I~Q~~Fa~~vL~rsQGtlSdLL~---~PKPW~~l~~~gr~~y~RM~~wL~~p~~ 71 (81)
T pfam02376 1 EELDTAEIARRIKEELKRANISQALFAEVVLGRSQGSLSDLLR---RPKPWNKLLLKGREPFRRMQNFLSLPEA 71 (81)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHH---CCCCHHHHHHHHHHHHHHHHHHHCCCHH
T ss_conf 9888999999999999994976999999997318378999881---8997788508506989999999868598
No 117
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=78.05 E-value=3.5 Score=21.13 Aligned_cols=24 Identities=29% Similarity=0.623 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|..|||+.+|.|.++|.++|.
T Consensus 142 eg~s~~EIA~~l~is~~tVk~~l~ 165 (177)
T PRK09638 142 YGYTYEEIAKMLGIPEGTVKSRVH 165 (177)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 199999999998939999999999
No 118
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=78.01 E-value=5 Score=20.15 Aligned_cols=20 Identities=20% Similarity=0.195 Sum_probs=13.7
Q ss_pred CHHHHHHHHHHHHHHHHHHH
Q ss_conf 04679999743378778656
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~L 173 (300)
+.+++|+.+|.+...|..+.
T Consensus 153 ~~~eiA~~l~~~~~~v~~~~ 172 (284)
T PRK06596 153 EVEMIAEELGVSEEEVREME 172 (284)
T ss_pred CHHHHHHHHCCCHHHHHHHH
T ss_conf 29999999791999999999
No 119
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=77.93 E-value=0.53 Score=26.41 Aligned_cols=94 Identities=27% Similarity=0.272 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHH--------HHHCCCCCCCCCCCCCHHHHHH---HH-HHHHHCCCCCHHHHHHHHHHHHHHCCCCHHH
Q ss_conf 3335756777776--------4210013543334641123455---66-6543102210489999999852101110467
Q gi|254780805|r 90 KIIAGERRFRAAK--------MASLSEVPVIIRNVDNKSSLEI---AI-VENVQRKDLNPLEEALGYEQLISEYGYTQND 157 (300)
Q Consensus 90 ~ii~G~rR~rAa~--------~~g~~~ip~iv~~~~d~~~~~~---~l-~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~ 157 (300)
.|.+|.|||.-.+ .+|...+.-++.-.-+.....+ ++ .||..| |-++-..+-.|+.++- ++
T Consensus 6 iImDGNrRwA~~~g~~~~~Gh~~G~~~~~~i~~~~~~~gI~~lTvyafStEN~~R----~~~Ev~~Lm~L~~~~l---~~ 78 (221)
T cd00475 6 FIMDGNRRWAKQRGMDRIEGHKAGAEKLRDILRWCLELGVKEVTLYAFSTENWKR----PKEEVDFLMELFRDVL---RR 78 (221)
T ss_pred EECCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHCC----CHHHHHHHHHHHHHHH---HH
T ss_conf 9634869999877998789999999999999999998599989999811777677----6999999999999999---99
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999974337877865656543589999876421
Q gi|254780805|r 158 IGSIVGKSRSHVANILRILKLPSSVREMIRKEE 190 (300)
Q Consensus 158 lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~ 190 (300)
....+-...--|.=.=++-.||+.+++.+..-+
T Consensus 79 ~~~~~~~~~iri~~iG~~~~Lp~~l~~~i~~~e 111 (221)
T cd00475 79 ILKELEKLGVRIRIIGDLSLLPESLQKEIKKAE 111 (221)
T ss_pred HHHHHHHCCEEEEEEECHHHCCHHHHHHHHHHH
T ss_conf 899999889799999472008989999999999
No 120
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=77.86 E-value=3.2 Score=21.43 Aligned_cols=38 Identities=21% Similarity=0.388 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|||-|.- .-+|+.+ |+|..|||++++.|..||.++++
T Consensus 150 ~LT~RE~e--VL~lla~-G~snkeIA~~L~iS~~TV~~h~~ 187 (216)
T PRK10840 150 RLSPKESE--VLRLFAE-GFLVTEIAKKLNRSIKTISSQKK 187 (216)
T ss_pred CCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99989999--9999986-99999999896989999999999
No 121
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=77.69 E-value=1.9 Score=22.92 Aligned_cols=26 Identities=15% Similarity=0.138 Sum_probs=21.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 11046799997433787786565654
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
++|-+++|+.+|.||.|+.+||-.+.
T Consensus 177 ~~ta~eva~~~giSrvTaRRYLe~L~ 202 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLEYCA 202 (225)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 86899999985851999999999998
No 122
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=77.53 E-value=5.7 Score=19.82 Aligned_cols=39 Identities=15% Similarity=0.204 Sum_probs=26.5
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10111046799997433787786565654358999987642
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKE 189 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~ 189 (300)
.-.|+|.+|||+.+|.|.++|..++. ..-..+++.+...
T Consensus 133 ~~~~~s~~EIA~~l~is~~tVk~~l~--Ra~k~Lr~~L~~e 171 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLF--YARRQLRKFLQQQ 171 (175)
T ss_pred HHHCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHC
T ss_conf 99299999999998959999999999--9999999999986
No 123
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=77.50 E-value=1.9 Score=22.80 Aligned_cols=24 Identities=25% Similarity=0.509 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
..+|++++|..+|.++.+|++.|+
T Consensus 7 l~lt~~~iA~~lG~tretvsR~l~ 30 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLK 30 (48)
T ss_pred ECCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 337999999997997999999999
No 124
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=77.48 E-value=5.7 Score=19.81 Aligned_cols=39 Identities=10% Similarity=0.155 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 11104679999743378778656565435899998764210
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI 191 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i 191 (300)
.|+|.+|||+.+|.|.++|..+|. ..-..+++.+....|
T Consensus 121 egls~~EIA~~l~is~~tVk~~l~--RAr~~Lr~~Le~~gi 159 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCS--RATHTLAKALEAKGI 159 (161)
T ss_pred HCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHCCC
T ss_conf 877999999998969999999999--999999999998698
No 125
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=77.44 E-value=5.7 Score=19.80 Aligned_cols=28 Identities=25% Similarity=0.319 Sum_probs=23.4
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|....|+|+.|||+.+|.|.++|..+++
T Consensus 134 L~~~eg~s~~EIAe~LgiS~~tVk~~l~ 161 (183)
T PRK07037 134 MVRLRGETLQDIARELNVSQTLVNFMIR 161 (183)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8987398999999998929999999999
No 126
>KOG1602 consensus
Probab=77.22 E-value=1.5 Score=23.56 Aligned_cols=94 Identities=28% Similarity=0.356 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHCCC----------CCCCC-----CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf 53335756777776421001----------35433-----3464112345566654310221048999999985210111
Q gi|254780805|r 89 YKIIAGERRFRAAKMASLSE----------VPVII-----RNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGY 153 (300)
Q Consensus 89 y~ii~G~rR~rAa~~~g~~~----------ip~iv-----~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~ 153 (300)
=.|.+|+||| ||..|+.. +--++ .-+..-.++..+ +||-.|. | |+-..+-.|..+.--
T Consensus 41 aFIMDGNRR~--AKk~~L~~~~GH~aGf~~l~~ile~C~~lGI~~vT~fAFS-ieNFkRs---~-eEVd~LM~L~~~k~~ 113 (271)
T KOG1602 41 AFIMDGNRRY--AKKRGLETSEGHEAGFEALKEILELCKELGIKEVTVFAFS-IENFKRS---P-EEVDGLMDLALEKIE 113 (271)
T ss_pred EEEECCCHHH--HHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEE-HHHHCCC---H-HHHHHHHHHHHHHHH
T ss_conf 9996285577--8765998530267789999999999997197279989875-6640798---8-999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565654358999987642
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKE 189 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~ 189 (300)
...+-++.+.+...-|+=+=.|..||+.+++.+.+=
T Consensus 114 ~~~~~~~~~~~~gvririiGdlslL~~~l~k~i~~i 149 (271)
T KOG1602 114 RLLEQGEKLDKYGVRIRVIGDLSLLPESLRKAIKKI 149 (271)
T ss_pred HHHHHHHHHHHCCCEEEEECCHHHCCHHHHHHHHHH
T ss_conf 888876667662707999766332899999999999
No 127
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=77.19 E-value=3.9 Score=20.87 Aligned_cols=38 Identities=21% Similarity=0.260 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|+|-....-.-+ ...|+|..|||+.+|.|.++|..++.
T Consensus 137 L~~~~r~vi~L~--~~~g~s~~EIA~~L~is~~TVk~~l~ 174 (187)
T PRK13919 137 LSPEERRVIEVL--YYQGYTHREAARLLGLPLGTLKTWAR 174 (187)
T ss_pred CCHHHHHHHHHH--HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999999999--98599999999998939999999999
No 128
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=77.12 E-value=4 Score=20.81 Aligned_cols=42 Identities=19% Similarity=0.214 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHHHH-HHC----CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2210489999999852-101----11046799997433787786565
Q gi|254780805|r 133 KDLNPLEEALGYEQLI-SEY----GYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~-~~~----~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.+||+.|....-..+. .-| ..+-.+||+.+|.|+++++.+||
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred CCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 46999999999999985898887658999999995998889999999
No 129
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=76.68 E-value=4 Score=20.82 Aligned_cols=38 Identities=26% Similarity=0.263 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|.|-.+..-. |..-.|+|+.|+|+.+|.|.++|..++.
T Consensus 128 Lp~~~R~~~~--l~~~~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 128 LPPRQREAFL--LRYLEGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred CCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999999--9998599999999895999999999999
No 130
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=76.65 E-value=5.8 Score=19.76 Aligned_cols=65 Identities=18% Similarity=0.151 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 111046799997433787786565654-----358999987642101677777640100468999974222477899999
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRILK-----LPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEEL 225 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~-----L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~l 225 (300)
-|+|..++|+++|.|.++|.+.++=.+ ||+.. .++.-..+..+..+.+.+.+-.+.|+..++..+
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~----------~~GrP~kl~~~q~~~l~e~~~~k~wTl~~~~~~ 89 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKP----------RKGRPRKLSEEQLEILLERLREKDWTLKELVEE 89 (138)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCC----------CCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 6854999999969229999999987333533156766----------899973258899999999975155218799999
No 131
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=76.58 E-value=3.8 Score=20.91 Aligned_cols=24 Identities=13% Similarity=0.167 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|.+|||+.+|.|.++|..+|.
T Consensus 144 eg~s~~EIA~~l~is~~tVk~~l~ 167 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 699899999988909999999999
No 132
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=76.55 E-value=4.6 Score=20.39 Aligned_cols=125 Identities=14% Similarity=0.156 Sum_probs=62.1
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHH
Q ss_conf 22104899999998521011104679999743378778656565435899998764210167777764010046899997
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVI 212 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~I 212 (300)
.+|+.+|... +..|.+..-.+..+||+++|.|+++|.++++ .+-.+|-|.--+| .+ ++.++
T Consensus 10 ~~LD~~D~~I-L~~Lq~daR~s~~eLA~~vglS~stv~~Rik---------rLe~~GiI~gy~a--~i---d~~~l---- 70 (164)
T PRK11169 10 KDLDRIDRNI-LNELQKDGRISNVELSKRVGLSPTPCLERVR---------RLERQGFIQGYTA--LL---NPHYL---- 70 (164)
T ss_pred CCHHHHHHHH-HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH---------HHHHCCCEEEEEE--EE---CCCCC----
T ss_conf 4551999999-9999984899999999998929999999999---------9997898866899--97---60007----
Q ss_pred HHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEE--CCCCCEEEEEEECCHHHHHHHH
Q ss_conf 42224778999999764102222223456655689789999999999739879997--1798228999858989999999
Q gi|254780805|r 213 VSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLEKKISSKVGLNISIK--HRNNKGQFCIKYETNEQLKIIC 290 (300)
Q Consensus 213 i~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le~~L~~~lGtkV~I~--~~~~kGkI~I~f~s~eeLe~Il 290 (300)
++++. .++. ..-.......+..+.+.+...=.. +.+. .+.----+.+.+.+.++|+.++
T Consensus 71 ---G~~~~---a~v~------------i~l~~~~~~~~~~~~~~l~~~peV-~~~~~vtG~~D~~l~v~~~d~~~l~~~i 131 (164)
T PRK11169 71 ---DASLL---VFVE------------ITLNRGAPDVFEQFNAAVQKLEEI-QECHLVSGDFDYLLKTRVPDMSAYRKLL 131 (164)
T ss_pred ---CCCEE---EEEE------------EEECCCCHHHHHHHHHHHHCCCCE-EEEEEEECCCCEEEEEEECCHHHHHHHH
T ss_conf ---98749---9999------------996588868999999998429978-9999830778899999989999999999
Q ss_pred -HHHCC
Q ss_conf -98375
Q gi|254780805|r 291 -SLLGE 295 (300)
Q Consensus 291 -~kL~~ 295 (300)
++|..
T Consensus 132 ~~~l~~ 137 (164)
T PRK11169 132 GETLLR 137 (164)
T ss_pred HHHHHC
T ss_conf 998635
No 133
>pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
Probab=76.54 E-value=3.5 Score=21.18 Aligned_cols=31 Identities=32% Similarity=0.441 Sum_probs=25.5
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565654
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
++.+.-.+..++|+.+|.++++|++.|+.|.
T Consensus 10 ~L~~~~~~v~el~~~l~~sq~~vS~HL~~L~ 40 (47)
T pfam01022 10 LLSEGELCVCELAEILGLSQSTVSHHLKKLR 40 (47)
T ss_pred HHHCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 9980899699999998958869999999998
No 134
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=76.51 E-value=3.8 Score=20.90 Aligned_cols=38 Identities=24% Similarity=0.204 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|||-|.- .-+++.+ |+|..+||++++.|..||.++++
T Consensus 143 ~Lt~RE~e--VL~ll~~-G~snkeIA~~L~iS~~TV~~h~~ 180 (204)
T PRK09958 143 SLSKQEIS--VMRYILD-GKDNNDIAEKMFISNKTVSTYKS 180 (204)
T ss_pred CCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 68999999--9999986-99999999897889999999999
No 135
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=75.92 E-value=6.3 Score=19.54 Aligned_cols=40 Identities=18% Similarity=0.209 Sum_probs=26.8
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 101110467999974337877865656543589999876421
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE 190 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~ 190 (300)
--.|+|.+|||+.+|.|.++|.++|. ..-..+++.+....
T Consensus 142 ~~~g~s~~EIA~~l~is~~tVk~rl~--rA~k~LR~kle~~e 181 (190)
T PRK12543 142 YLHDYSQEEVAQILHIPIGTVKSRIH--AALKKLRQKEQIEE 181 (190)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHH
T ss_conf 98599999999998939999999999--99999999999999
No 136
>PRK01381 Trp operon repressor; Provisional
Probab=75.69 E-value=4.6 Score=20.43 Aligned_cols=54 Identities=20% Similarity=0.241 Sum_probs=37.2
Q ss_pred CCHHHHH------HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Q ss_conf 1048999------99998521011104679999743378778656565-4358999987642
Q gi|254780805|r 135 LNPLEEA------LGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL-KLPSSVREMIRKE 189 (300)
Q Consensus 135 l~p~e~A------~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l~~~ 189 (300)
|+|-|.- .-++.|+. ..++|.+||+.+|.|-++|++--+-+ ..|++.++.+..-
T Consensus 33 LTp~Er~al~~R~~I~~~Ll~-ge~sQReIa~~lgvsiAtITRGSn~LK~~~~~~k~~l~~~ 93 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLR-GELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQL 93 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHCCCCEECCCCHHHHHCCCHHHHHHHHHH
T ss_conf 899999999999999999994-8764999999849740200002698853999999999998
No 137
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=75.40 E-value=6.5 Score=19.45 Aligned_cols=28 Identities=25% Similarity=0.377 Sum_probs=16.4
Q ss_pred HHHHHCC--CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 8521011--104679999743378778656
Q gi|254780805|r 146 QLISEYG--YTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 146 ~l~~~~~--~t~~~lA~~~G~s~s~V~~~L 173 (300)
.|..++| -|.++||+.+|.+..-+...+
T Consensus 118 ~l~~el~r~pt~~EIA~~L~i~~ee~~~~~ 147 (247)
T COG1191 118 ELEQELGREPTDEEIAEELGIDKEEYIEAL 147 (247)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999984799868999989698999999999
No 138
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=75.40 E-value=2.1 Score=22.58 Aligned_cols=25 Identities=28% Similarity=0.332 Sum_probs=21.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1104679999743378778656565
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
+.+..+||+.+|.|+++++.+||-.
T Consensus 23 ~~~l~elA~~lgis~sT~~~hLr~a 47 (53)
T pfam04967 23 RVTLKDLAKELGISKSTLSEHLRRA 47 (53)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 6889999999698999999999999
No 139
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=75.37 E-value=1.4 Score=23.69 Aligned_cols=23 Identities=35% Similarity=0.559 Sum_probs=20.0
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 10111046799997433787786
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVAN 171 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~ 171 (300)
.+-||||.++|+.+|-+|+.||-
T Consensus 20 RekG~tQ~eIA~~L~TTraNvSa 42 (143)
T COG1356 20 REKGLTQSEIARILKTTRANVSA 42 (143)
T ss_pred HHCCCCHHHHHHHHCCCCCCHHH
T ss_conf 64056489999997545101799
No 140
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=75.34 E-value=5 Score=20.18 Aligned_cols=64 Identities=19% Similarity=0.234 Sum_probs=35.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHH---HHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 013543334641123455666543102210489999---9998521011-10467999974337877865656
Q gi|254780805|r 107 SEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEAL---GYEQLISEYG-YTQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 107 ~~ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~---~~~~l~~~~~-~t~~~lA~~~G~s~s~V~~~LrL 175 (300)
.-+|+++.=.+.+|... +.+ +..+..+.++. -++.--++.| +|+.++|..+|.|.++|+++++=
T Consensus 61 ~lvpVvLtl~~~ED~e~--~~~---k~~~~~lr~~~i~Ri~~EA~~QgglLT~~Dla~LL~~S~~TI~~~ik~ 128 (220)
T pfam07900 61 KLVPVILTLISPEDLEV--KEE---KVKKRELREKKIVRIFNEAYEQGALLTHADIAILLGVSTTTISRHVKE 128 (220)
T ss_pred CCEEEEEEECCHHHHHH--HHH---HHHHHHHHHHHHHHHHHHHHHCCCEEEHHHHHHHHCCCHHHHHHHHHH
T ss_conf 41479998237888999--985---521899999999999999997388511766999988988899999999
No 141
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=75.27 E-value=3.5 Score=21.20 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 1048999999985210111046799997433787786565654358999987642101
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS 192 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is 192 (300)
|+.+|... ++.|.+..-.+..+||+++|.|+++|.++++ .+-.+|-|.
T Consensus 7 lD~~D~~I-L~~Lq~d~R~s~~eiA~~lglS~stv~~Ri~---------rLe~~GvI~ 54 (153)
T PRK11179 7 IDNLDRGI-LEALMENARTPYAELAKQFGVSPGTIHVRVE---------KMKQAGIIT 54 (153)
T ss_pred CCHHHHHH-HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH---------HHHHCCCEE
T ss_conf 78999999-9999984899999999998929999999999---------999799658
No 142
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.
Probab=75.18 E-value=4.8 Score=20.28 Aligned_cols=41 Identities=22% Similarity=0.287 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0221048999999985210111046799997433787786565
Q gi|254780805|r 132 RKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 132 R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|-.|+.-|....++++ ++ |.+..++|+.+|..+|||+..+.
T Consensus 4 R~~LTl~eKi~iI~~~-e~-G~s~~~lar~~gi~~STl~~I~K 44 (53)
T pfam04218 4 RTSLTLREKIEVIQRS-EE-GESKASLARRFNVPRSTLRDILK 44 (53)
T ss_pred CEEECHHHHHHHHHHH-HC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 4141699999999999-85-89688999996987979999998
No 143
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=75.17 E-value=5.8 Score=19.77 Aligned_cols=26 Identities=15% Similarity=0.151 Sum_probs=22.0
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10111046799997433787786565
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
...|+|..|||+.+|.|.++|..+|.
T Consensus 132 ~~~~~s~~EIA~~l~is~~tVksrl~ 157 (173)
T PRK12522 132 YYEQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98399999999998939999999999
No 144
>PRK10651 transcriptional regulator NarL; Provisional
Probab=75.14 E-value=4.4 Score=20.54 Aligned_cols=38 Identities=24% Similarity=0.394 Sum_probs=27.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|||-|.-. + +++.+ |+|-.+||+.++.|..||.++++
T Consensus 155 ~LT~RE~eV-L-~ll~~-G~snkeIA~~L~iS~~TV~~h~~ 192 (216)
T PRK10651 155 QLTPRERDI-L-KLIAQ-GLSNKMIARRLDITESTVKVHVK 192 (216)
T ss_pred CCCHHHHHH-H-HHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 489899999-9-99985-99999999996978999999999
No 145
>cd06405 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, f
Probab=74.84 E-value=6.7 Score=19.36 Aligned_cols=49 Identities=22% Similarity=0.405 Sum_probs=42.7
Q ss_pred CCHHHHHHHHHHHHHHCCEEEEECCCCCEEEEEEECCHHHHHHHHHHHCCC
Q ss_conf 897899999999997398799971798228999858989999999983756
Q gi|254780805|r 246 KEKYLTDLEKKISSKVGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGEN 296 (300)
Q Consensus 246 k~~~i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL~~~ 296 (300)
.+..+.+++.+....||-...+...++ .+.|...+.+||++-++.|..+
T Consensus 18 RPv~~~dlq~kv~~afGq~ldl~y~n~--eL~IPl~~Q~DLDkAiellD~s 66 (79)
T cd06405 18 RPVKFKDLQQKVTTAFGQPMDLHYTNN--ELLIPLKNQEDLDRAIELLDRS 66 (79)
T ss_pred CCCCHHHHHHHHHHHHCCEEEEEEECC--EEEEECCCHHHHHHHHHHHCCC
T ss_conf 884399999999998598454577567--3788625677789999987059
No 146
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=74.80 E-value=4.7 Score=20.35 Aligned_cols=24 Identities=17% Similarity=0.245 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|.+|||+.+|.|.+||..+|.
T Consensus 152 eg~s~~EIA~~l~i~~gTVksrl~ 175 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIR 175 (187)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 499999999998919999999999
No 147
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=74.75 E-value=5 Score=20.17 Aligned_cols=50 Identities=20% Similarity=0.282 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 104899999998521011104679999743378778656565435899998764
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRK 188 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~ 188 (300)
|.|-....-+ |....|+|..|||+.+|.|.++|..+|. ..-..+++.+..
T Consensus 129 Lp~~~R~vi~--L~~~eg~s~~EIA~~Lgis~~tVksrl~--RAr~~Lr~~Le~ 178 (188)
T PRK12517 129 LDPEYREPLL--LQVIGGFSGEEIAEILDLNKNTVMTRLF--RARNQLKEALEK 178 (188)
T ss_pred CCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHCC
T ss_conf 9999999999--9998399999999998939999999999--999999999742
No 148
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=74.70 E-value=4.3 Score=20.58 Aligned_cols=49 Identities=22% Similarity=0.350 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565654358999987
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI 186 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l 186 (300)
.|+|-.+..-.-+. -.|+|.+|||+.+|.|.++|..+|. ..-..+++++
T Consensus 122 ~Lp~~~R~v~~L~~--~~gls~~EIA~~L~is~~tVk~rl~--RArk~Lr~~L 170 (185)
T PRK12542 122 ELNESNRQVFKYKV--FYNLTYQEISSVMGITEANVRKQFE--RARKRVQNMI 170 (185)
T ss_pred HCCHHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHH
T ss_conf 29998889976799--8399999999998929999999999--9999999987
No 149
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=74.63 E-value=4.7 Score=20.36 Aligned_cols=42 Identities=19% Similarity=0.207 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 104899999998521---011104679999743378778656565
Q gi|254780805|r 135 LNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 135 l~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
||+.+...--+.|.+ ..|+|.+++|..+|.|...|.+.|.|.
T Consensus 3 Ln~~Q~~~T~~ELqeNf~~~~ls~~~iA~dL~~s~~~ve~vL~m~ 47 (89)
T pfam10078 3 LNIEEMQATRKELQANFELSGLTIEQVAKDLNTTPEKVEALLQLK 47 (89)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 889999999999999998838989999989499999999999734
No 150
>PRK12423 LexA repressor; Provisional
Probab=74.46 E-value=5.4 Score=19.98 Aligned_cols=48 Identities=21% Similarity=0.246 Sum_probs=31.3
Q ss_pred HHHHHHHHCCC--CHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCC--HHHHHHH
Q ss_conf 99985210111--0467999974-33787786565654358999987642101--6777776
Q gi|254780805|r 143 GYEQLISEYGY--TQNDIGSIVG-KSRSHVANILRILKLPSSVREMIRKEEIS--LGHARTL 199 (300)
Q Consensus 143 ~~~~l~~~~~~--t~~~lA~~~G-~s~s~V~~~LrLl~L~~~i~~~l~~~~is--~ghar~L 199 (300)
.++..++++|+ |..|||+.+| +|.++|..+|+ .+...|-|+ .+.+|++
T Consensus 14 fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~---------~L~~kG~i~r~~~~~R~i 66 (202)
T PRK12423 14 FIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQ---------ALAEAGLIEVVPNQARGI 66 (202)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHH---------HHHHCCCEECCCCCCEEE
T ss_conf 99999996298988999999829998678999999---------999887997069995379
No 151
>pfam01255 Prenyltransf Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase.
Probab=74.38 E-value=0.97 Score=24.74 Aligned_cols=90 Identities=21% Similarity=0.229 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHH--------HHHCCCCCCCCCCCCC-----HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHH
Q ss_conf 335756777776--------4210013543334641-----123455666543102210489999999852101110467
Q gi|254780805|r 91 IIAGERRFRAAK--------MASLSEVPVIIRNVDN-----KSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQND 157 (300)
Q Consensus 91 ii~G~rR~rAa~--------~~g~~~ip~iv~~~~d-----~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~ 157 (300)
|.+|+|||.-.+ ..|...+.-++.-..+ -..+..+ .||..|. -+|-.++-.|+..+- ++
T Consensus 1 ImDGNrRwAk~~~l~~~~Gh~~G~~~~~~i~~~c~~~gI~~lTvyaFS-tEN~~R~----~~Ev~~L~~l~~~~l---~~ 72 (222)
T pfam01255 1 IMDGNRRWAKKRGLPRTEGHRAGAEALREILEWCLELGIKYLTLYAFS-TENWKRP----KEEVDFLMELLEEKL---RR 72 (222)
T ss_pred CCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEHHHC-HHHCCCC----HHHHHHHHHHHHHHH---HH
T ss_conf 982879999887998779999999999999999998699989726417-8754999----899999999999999---99
Q ss_pred HHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99997---43378778656565435899998764210
Q gi|254780805|r 158 IGSIV---GKSRSHVANILRILKLPSSVREMIRKEEI 191 (300)
Q Consensus 158 lA~~~---G~s~s~V~~~LrLl~L~~~i~~~l~~~~i 191 (300)
....+ |..-..|- ++..||+.+++.+..=+-
T Consensus 73 ~~~~~~~~~iki~~iG---~~~~Lp~~l~~~i~~~e~ 106 (222)
T pfam01255 73 LLEDLHKNGVRVRVIG---DLSLLPEDLRKAIEDAEE 106 (222)
T ss_pred HHHHHHHCCEEEEEEC---CCCCCCHHHHHHHHHHHH
T ss_conf 9999998693899952---655689899999999999
No 152
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=74.30 E-value=3.5 Score=21.17 Aligned_cols=36 Identities=28% Similarity=0.356 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 2210489999999852101110467999974337877865
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
..|+|.| ++.+.+.+++||.+.|..+|.|.++|++-
T Consensus 42 ~~ls~~e----Ik~iRe~~~lSq~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 42 KTLSPTE----IKAIREKLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred CCCCHHH----HHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8998899----99999982888999999988879999999
No 153
>PRK02866 cyanate hydratase; Validated
Probab=74.25 E-value=6.9 Score=19.27 Aligned_cols=37 Identities=32% Similarity=0.399 Sum_probs=25.7
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Q ss_conf 1011104679999743378778656-565435899998
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANIL-RILKLPSSVREM 185 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~L-rLl~L~~~i~~~ 185 (300)
.+-|+|=++||+.+|+|..|++..+ .-..++++--+.
T Consensus 15 ~~kgltw~~ia~~~G~s~v~~aaa~lGQ~~~~~e~A~~ 52 (147)
T PRK02866 15 KEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEK 52 (147)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHH
T ss_conf 98499899999894989999999984677899999999
No 154
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=74.22 E-value=5.6 Score=19.87 Aligned_cols=36 Identities=19% Similarity=0.193 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999985210111046799997433787786565
Q gi|254780805|r 139 EEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 139 e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.+...+..+-+.-+.++.+||+.++.++++|++.+.
T Consensus 4 ~Q~~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~i~ 39 (59)
T pfam01047 4 TQFHILRILYEHGPLTVSELAEKLGVDRSTVTRVLD 39 (59)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999999946992999999998858654999999
No 155
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=74.22 E-value=1.8 Score=23.09 Aligned_cols=31 Identities=13% Similarity=0.201 Sum_probs=24.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9998521011104679999743378778656
Q gi|254780805|r 143 GYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
++++-.+.|+.+|.++|..+|.|.|.|+.|=
T Consensus 31 ~lrKWR~~F~iSQ~elA~~l~vSpSVISDYE 61 (241)
T COG1709 31 TLRKWREIFNVSQTELARELGVSPSVISDYE 61 (241)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCCCEEEHHH
T ss_conf 9999999818249999987289910031211
No 156
>PRK10403 transcriptional regulator NarP; Provisional
Probab=74.03 E-value=4.7 Score=20.31 Aligned_cols=37 Identities=22% Similarity=0.310 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
||+-|.-. -+++.. |+|-.+||+.+|.|..||.++++
T Consensus 154 LT~RE~eV--L~lla~-G~snkeIA~~L~iS~~TV~~h~~ 190 (215)
T PRK10403 154 LTERELDV--LHELAQ-GLSNKQIASVLNISEQTVKVHIR 190 (215)
T ss_pred CCHHHHHH--HHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 89999999--999986-99999999997982999999999
No 157
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=73.86 E-value=3.3 Score=21.36 Aligned_cols=30 Identities=30% Similarity=0.391 Sum_probs=24.6
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565654
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
|. +...+..++|+.+|.|+++|+..|+.|.
T Consensus 6 L~-~~~~~~~ela~~l~is~~tvs~HL~~L~ 35 (66)
T smart00418 6 LA-EGELCVCELAEILGLSQSTVSHHLKKLR 35 (66)
T ss_pred HH-CCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 77-3996699999998829888879999999
No 158
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=73.71 E-value=4.6 Score=20.40 Aligned_cols=23 Identities=13% Similarity=0.072 Sum_probs=12.8
Q ss_pred HHHHHHHHCCCC--HHHHHHHHHHH
Q ss_conf 899997422247--78999999764
Q gi|254780805|r 207 SLAQVIVSKKMS--VRDTEELVQEQ 229 (300)
Q Consensus 207 ~la~~Ii~~~LS--VRe~E~lVk~~ 229 (300)
...+......|- |||.++.+.+.
T Consensus 343 ~a~~~L~~y~WPGNvrEL~n~ier~ 367 (469)
T PRK10923 343 ETEAALTRLAWPGNVRQLENTCRWL 367 (469)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf 9999997499998799999999999
No 159
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=73.56 E-value=3.6 Score=21.09 Aligned_cols=29 Identities=17% Similarity=0.327 Sum_probs=12.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 998521011104679999743378778656
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
++++.+. |+|..+||+.||+.+|||++=|
T Consensus 16 I~~l~~~-~~S~reIA~~LgRh~sTIsREl 44 (318)
T COG2826 16 IERLLKA-KMSIREIAKQLNRHHSTISREL 44 (318)
T ss_pred HHHHHHC-CCCHHHHHHHHCCCCCHHHHHH
T ss_conf 9999985-9989999998576862042798
No 160
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=73.33 E-value=4.9 Score=20.22 Aligned_cols=37 Identities=14% Similarity=0.170 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|++-|.- .-+|+.+ |+|..+||+.++.|..||.++++
T Consensus 150 Lt~RE~e--VL~ll~~-G~snkeIA~~L~iS~~TV~~h~~ 186 (210)
T PRK09935 150 LSNREVT--VLRYLAN-GLSNKEIAEQLLLSNKTISAHKS 186 (210)
T ss_pred CCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9989999--9999986-99999999894988999999999
No 161
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=73.30 E-value=4.6 Score=20.41 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=25.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9985210111046799997433787786565654
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+..|.+ .+.+..+||+.+|.|+++|+..|+.|.
T Consensus 13 l~~L~~-~~~~~~eia~~l~is~~~vs~hL~~L~ 45 (78)
T cd00090 13 LRLLLE-GPLTVSELAERLGLSQSTVSRHLKKLE 45 (78)
T ss_pred HHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999984-890699998777848789999999999
No 162
>PRK05572 sporulation sigma factor SigF; Validated
Probab=73.22 E-value=7.3 Score=19.11 Aligned_cols=17 Identities=18% Similarity=0.362 Sum_probs=8.3
Q ss_pred CHHHHHHHHHHHHHHHH
Q ss_conf 04679999743378778
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVA 170 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~ 170 (300)
|.+++|+.+|.+...|.
T Consensus 134 s~~eia~~lg~~~~~v~ 150 (251)
T PRK05572 134 TIEELAEYLGVTPEEVV 150 (251)
T ss_pred CHHHHHHHHCCCHHHHH
T ss_conf 89999999793999999
No 163
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=73.18 E-value=4.8 Score=20.27 Aligned_cols=19 Identities=11% Similarity=0.454 Sum_probs=8.7
Q ss_pred HHHHHCCCC--HHHHHHHHHH
Q ss_conf 997422247--7899999976
Q gi|254780805|r 210 QVIVSKKMS--VRDTEELVQE 228 (300)
Q Consensus 210 ~~Ii~~~LS--VRe~E~lVk~ 228 (300)
+.+....|. |||.++.+.+
T Consensus 215 ~~L~~y~WPGNvrEL~n~ier 235 (325)
T PRK11608 215 ETLLNYRWPGNIRELKNVVER 235 (325)
T ss_pred HHHHCCCCCCHHHHHHHHHHH
T ss_conf 999619999659999999999
No 164
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=73.13 E-value=6.2 Score=19.58 Aligned_cols=31 Identities=10% Similarity=0.428 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCC
Q ss_conf 89889999999886310015504620565445333
Q gi|254780805|r 58 FESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKII 92 (300)
Q Consensus 58 ~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii 92 (300)
.+...+.-|..++.+.|.+. +...+|+|.+=
T Consensus 38 lpksTv~RlL~tL~~~G~l~----~~~~~~~Y~LG 68 (264)
T PRK09834 38 LHRTTVRRLLETLQEEGYVR----RSASDDSFRLT 68 (264)
T ss_pred CCHHHHHHHHHHHHHCCCEE----EECCCCCEECC
T ss_conf 09999999999999789989----96799976516
No 165
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution and represent a conserved family.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=72.77 E-value=6.2 Score=19.58 Aligned_cols=52 Identities=25% Similarity=0.422 Sum_probs=44.2
Q ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 11234556665431022104899999998521011104679999743378778656
Q gi|254780805|r 118 NKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 118 d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
-.|+.+++++-=||+ |.|-..|.-+ |.|..||.-.|+|+.||-|-+.|+-.|
T Consensus 129 ~~EsvrLAF~AAlQ~--LpPrQRAvL~--LRdvlGw~A~E~A~~L~~s~ASVnSaL 180 (329)
T TIGR02960 129 ARESVRLAFVAALQL--LPPRQRAVLL--LRDVLGWKAAEVAELLGTSVASVNSAL 180 (329)
T ss_pred HHHHHHHHHHHHHHC--CCCHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 114689999999874--8814578999--898835555689987438326786588
No 166
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=72.77 E-value=5.7 Score=19.79 Aligned_cols=38 Identities=16% Similarity=0.114 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 2104899999998521011104679999743378778656
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
.|.|-+...-.-+. -.|+|..|||+.+|.|.++|..++
T Consensus 131 ~Lp~~~R~vi~L~~--~~g~s~~EIA~~lgis~~tVk~~l 168 (184)
T PRK12512 131 TLPPRQRDVVQSIA--VEGASIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred CCCHHHHHHHHHHH--HCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 89999999999998--559799999999891999999999
No 167
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=72.77 E-value=5.2 Score=20.04 Aligned_cols=41 Identities=27% Similarity=0.368 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHHHHHCCCCCC--CEEECCC--CCCCCCCCCHHH
Q ss_conf 6898899999998863100155--0462056--544533357567
Q gi|254780805|r 57 YFESEGLEDLCQSIKSHGIIQP--LIVRAID--NGLYKIIAGERR 97 (300)
Q Consensus 57 ~~~~~~l~eLa~SI~~~G~lqP--i~Vr~~~--~g~y~ii~G~rR 97 (300)
.-+++.++.|+..++..=.+++ ++.++-+ ++-|.|..|.=+
T Consensus 23 ~L~~~el~~l~~~~~r~r~~~kGe~Lf~eGd~~~~ly~V~sG~Vk 67 (235)
T PRK11161 23 TLNEHELDQLDNIIERKKPIQKGQTLFKAGDELKSLYAIRSGTIK 67 (235)
T ss_pred CCCHHHHHHHHHHHHEEEEECCCCEEECCCCCCCEEEEEEECEEE
T ss_conf 899999999998987404568999877895987708999779599
No 168
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=72.70 E-value=4.3 Score=20.57 Aligned_cols=32 Identities=25% Similarity=0.284 Sum_probs=24.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99852101110467999974337877865656
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrL 175 (300)
++.|.+....|..+||+.+|.|+++|.+++.=
T Consensus 9 l~~L~~n~R~s~~~iA~~lg~S~~tv~~Ri~~ 40 (108)
T smart00344 9 LEELQKDARISLAELAKKVGLSPSTVHNRVKR 40 (108)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99999828999999999989399999999999
No 169
>COG0020 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism]
Probab=72.56 E-value=1.3 Score=23.83 Aligned_cols=135 Identities=22% Similarity=0.249 Sum_probs=61.4
Q ss_pred CCCCCHHHHHHHH--------HHHCCCCCCCCCCCCCHHHHHHH----HHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHH
Q ss_conf 3335756777776--------42100135433346411234556----66543102210489999999852101110467
Q gi|254780805|r 90 KIIAGERRFRAAK--------MASLSEVPVIIRNVDNKSSLEIA----IVENVQRKDLNPLEEALGYEQLISEYGYTQND 157 (300)
Q Consensus 90 ~ii~G~rR~rAa~--------~~g~~~ip~iv~~~~d~~~~~~~----l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~ 157 (300)
.|.+|+|||...+ ..|...+.-++.-..+--...+. -.||-.| |-++-.++-.+... ...+
T Consensus 22 iImDGN~RwAk~~~~~r~~Gh~~G~~~~~~i~~~~~~lgik~ltlyafSteN~~R----p~~Ev~~lm~l~~~---~l~~ 94 (245)
T COG0020 22 IIMDGNRRWAKKRGLPRIEGHKAGAKALREILEWCLELGIKYLTLYAFSTENWKR----PKEEVSFLMELFEK---ALRE 94 (245)
T ss_pred EEECCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEHHHCCC----CHHHHHHHHHHHHH---HHHH
T ss_conf 8756876799867997457788768999999999998198889999984664188----98999999999999---9999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCHHHHHHHHHC-------CH----HHHHHHHHHHCCCCHHHH-HH
Q ss_conf 999974337877865656543589999876421-016777776401-------00----468999974222477899-99
Q gi|254780805|r 158 IGSIVGKSRSHVANILRILKLPSSVREMIRKEE-ISLGHARTLVST-------SD----PLSLAQVIVSKKMSVRDT-EE 224 (300)
Q Consensus 158 lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~-is~ghar~Ll~~-------~~----~~~la~~Ii~~~LSVRe~-E~ 224 (300)
....+-+....|.-.=.+..||+.++..+...+ .|.++...-+.+ .+ ...+++.+.++.+|+-++ |+
T Consensus 95 ~~~~l~~~~v~v~~iG~~~~l~~~~~~~i~~~e~~t~~~~~~~l~~a~nYGGR~eI~~avr~ia~~v~~g~l~~~~I~e~ 174 (245)
T COG0020 95 ELKKLHKNGVRIRIIGDLSRLPEEVREAIEKAEEKTKNNTGLTLNIAVNYGGRDEIVDAVRKIAEDVAAGKLSPEDIDEE 174 (245)
T ss_pred HHHHHHHCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCHHHCCHH
T ss_conf 88888666749999713021988999998999984457896599985378988999999999999987189896876899
Q ss_pred HHHHHHC
Q ss_conf 9976410
Q gi|254780805|r 225 LVQEQDN 231 (300)
Q Consensus 225 lVk~~~~ 231 (300)
++.+...
T Consensus 175 ~i~~~L~ 181 (245)
T COG0020 175 LISSHLY 181 (245)
T ss_pred HHHHHHC
T ss_conf 9997535
No 170
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=72.29 E-value=6.9 Score=19.25 Aligned_cols=17 Identities=18% Similarity=0.319 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHCCCC
Q ss_conf 88999999988631001
Q gi|254780805|r 60 SEGLEDLCQSIKSHGII 76 (300)
Q Consensus 60 ~~~l~eLa~SI~~~G~l 76 (300)
......|-.++.++|.+
T Consensus 33 ksT~~RlL~tL~~~G~v 49 (246)
T COG1414 33 KSTVHRLLQTLVELGYV 49 (246)
T ss_pred HHHHHHHHHHHHHCCCE
T ss_conf 88999999999978988
No 171
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=72.20 E-value=5.4 Score=19.93 Aligned_cols=23 Identities=17% Similarity=0.280 Sum_probs=17.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10467999974337877865656
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrL 175 (300)
-|.+++|+.+|.+...|...+..
T Consensus 133 pt~~eiA~~l~~s~e~v~~~l~~ 155 (257)
T PRK08583 133 PKISEIADRLGVSEEEVLEAMEM 155 (257)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 87999998959599999999997
No 172
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=72.13 E-value=6.8 Score=19.33 Aligned_cols=42 Identities=21% Similarity=0.214 Sum_probs=29.4
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0221048999999985210111046799997433787786565
Q gi|254780805|r 132 RKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 132 R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.-+|++.+-. .+..+...-++|+.+||+.++.++++|++.+.
T Consensus 5 ~~glt~~q~~-vL~~l~~~~~~t~~~la~~l~~~~~~vs~~v~ 46 (101)
T smart00347 5 PLGLTPTQFL-VLRILYEEGPLSVSELAKRLGVSPSTVTRVLD 46 (101)
T ss_pred HCCCCHHHHH-HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 1394999999-99999976997999999998968879999999
No 173
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=72.08 E-value=6 Score=19.65 Aligned_cols=21 Identities=24% Similarity=0.338 Sum_probs=14.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 104679999743378778656
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~L 173 (300)
-|.+++|+.+|.+...|.+.+
T Consensus 143 Pt~~EiA~~lg~~~~~v~~~l 163 (263)
T PRK07122 143 PTASELAAELGMDREEVVEGL 163 (263)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999989693999999999
No 174
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=72.07 E-value=6 Score=19.66 Aligned_cols=50 Identities=18% Similarity=0.204 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 104899999998521011104679999743378778656565435899998764
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRK 188 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~ 188 (300)
|.+-.+..-+ |....|+|.+|||+.+|.|.++|..+|. ..=..+++.|..
T Consensus 158 Lp~~qR~vl~--Lr~~eglS~~EIAe~Lgis~gTVKsrl~--RAr~~LR~~Lea 207 (222)
T PRK09647 158 LPPEFRAAVV--LCDIEGLSYEEIAATLGVKLGTVRSRIH--RGRQALRAYLAA 207 (222)
T ss_pred CCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHH
T ss_conf 9999988998--7996399999999998939999999999--999999999871
No 175
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=71.68 E-value=7.5 Score=19.02 Aligned_cols=25 Identities=20% Similarity=0.315 Sum_probs=13.3
Q ss_pred CCCHHHHHHHHHH--HHHHHHHHHHHH
Q ss_conf 1104679999743--378778656565
Q gi|254780805|r 152 GYTQNDIGSIVGK--SRSHVANILRIL 176 (300)
Q Consensus 152 ~~t~~~lA~~~G~--s~s~V~~~LrLl 176 (300)
|-|--.+|+.+.. +-..|+|-|.+.
T Consensus 100 GTT~~~la~~L~~~~~ltVvTNsl~ia 126 (256)
T PRK10434 100 GSTVLQMVPLLSRFNNITVMTNSLHIV 126 (256)
T ss_pred CHHHHHHHHHHCCCCCCEEEECCHHHH
T ss_conf 768999999843369978998989999
No 176
>PRK10072 putative transcriptional regulator; Provisional
Probab=71.63 E-value=7.6 Score=19.00 Aligned_cols=28 Identities=29% Similarity=0.443 Sum_probs=22.3
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9985210111046799997433787786
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVAN 171 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~ 171 (300)
++++....|++|.+.|+.+|.|-++|.+
T Consensus 38 vkaIR~~tgl~q~eFA~~lGvSv~tvks 65 (96)
T PRK10072 38 FEQLRKGTGLKIDDFARVLGVSVAMVKE 65 (96)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999988099999999997777999999
No 177
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=71.28 E-value=5.7 Score=19.82 Aligned_cols=48 Identities=17% Similarity=0.225 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 1048999999985210111046799997433787786565654358999987642101
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS 192 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is 192 (300)
|+.+|.. -++.|.+....++.++|+++|.|.++|.++++ .+..+|-|.
T Consensus 6 lD~~D~~-IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~---------~L~~~GiI~ 53 (154)
T COG1522 6 LDDIDRR-ILRLLQEDARISNAELAERVGLSPSTVLRRIK---------RLEEEGVIK 53 (154)
T ss_pred CCHHHHH-HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH---------HHHHCCCEE
T ss_conf 3799999-99999972765799999997979899999999---------999889769
No 178
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=71.24 E-value=5.8 Score=19.74 Aligned_cols=34 Identities=21% Similarity=0.225 Sum_probs=25.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99985210111046799997433787786565654
Q gi|254780805|r 143 GYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
.++.|+.. +.++.+||+.+|.|-+||++-=+-++
T Consensus 41 va~~LL~~-~~syreI~~~~g~S~aTItRvsr~Lk 74 (88)
T pfam01371 41 IAKELLRG-ELSQREIAQELGASIATITRGSNCLK 74 (88)
T ss_pred HHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 99999978-99899999985985231478899987
No 179
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=71.23 E-value=7.5 Score=19.06 Aligned_cols=38 Identities=24% Similarity=0.378 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8999999985210--1110467999974337877865656
Q gi|254780805|r 138 LEEALGYEQLISE--YGYTQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 138 ~e~A~~~~~l~~~--~~~t~~~lA~~~G~s~s~V~~~LrL 175 (300)
+++|..+-.++.. ..++..+||+.+|.+++++.++|.-
T Consensus 2 l~r~l~iL~~~~~~~~~~~l~eia~~~gl~kstv~RlL~t 41 (52)
T pfam09339 2 LDRALAILEALAEAPGGLSLTEIARRTGLPKSTAHRLLQT 41 (52)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 8999999999862899989999999989199999999999
No 180
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=71.05 E-value=8 Score=18.87 Aligned_cols=40 Identities=28% Similarity=0.397 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 48999999985210--11104679999743378778656565
Q gi|254780805|r 137 PLEEALGYEQLISE--YGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 137 p~e~A~~~~~l~~~--~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
.+++|..+-.++.. .+++..+||+.+|.+++++.++|.-+
T Consensus 3 sl~ral~IL~~l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL 44 (91)
T smart00346 3 SLERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 799999999999728999899999999890999999999999
No 181
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=70.85 E-value=8.2 Score=18.80 Aligned_cols=19 Identities=16% Similarity=0.059 Sum_probs=7.0
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q ss_conf 0467999974337877865
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~ 172 (300)
+..+||+.+|.|..||++-
T Consensus 21 ~v~eLa~~~~VS~~TIRRD 39 (251)
T PRK13509 21 TVEKVIERLGISPATARRD 39 (251)
T ss_pred EHHHHHHHHCCCHHHHHHH
T ss_conf 8999999989699899983
No 182
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=70.63 E-value=7.1 Score=19.18 Aligned_cols=39 Identities=13% Similarity=0.161 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|++-.+..-.-+.. .|+|..+||+.+|.|.++|..+|.
T Consensus 127 ~L~~~~r~ii~l~~~--~~~s~~EIA~~l~is~~tV~~rl~ 165 (177)
T PRK09415 127 SLPIKYREVIYLFYY--EELSIKEIATVTGVNENTIKTRLK 165 (177)
T ss_pred CCCHHHHHHHHHHHH--CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 699999999999998--099899999988929999999999
No 183
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=70.48 E-value=3.5 Score=21.13 Aligned_cols=28 Identities=21% Similarity=0.252 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1110467999974337877865656543
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRILKL 178 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L 178 (300)
-.+|-+++|+.+|.||.++++||.-+.-
T Consensus 172 ~~~Taeela~~~giSRvTaRRYLeyl~~ 199 (224)
T COG4565 172 QELTAEELAQALGISRVTARRYLEYLVS 199 (224)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 7647999998837219999999999984
No 184
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=70.25 E-value=8.3 Score=18.74 Aligned_cols=11 Identities=18% Similarity=0.365 Sum_probs=5.2
Q ss_pred CCCHHHHHHHH
Q ss_conf 11046799997
Q gi|254780805|r 152 GYTQNDIGSIV 162 (300)
Q Consensus 152 ~~t~~~lA~~~ 162 (300)
|-|--++|+.+
T Consensus 100 GTT~~~la~~L 110 (252)
T PRK10906 100 GTTPEAVAHAL 110 (252)
T ss_pred CHHHHHHHHHC
T ss_conf 63799998533
No 185
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=70.18 E-value=5.6 Score=19.84 Aligned_cols=22 Identities=14% Similarity=0.311 Sum_probs=12.3
Q ss_pred HHHHHHCCCC--HHHHHHHHHHHH
Q ss_conf 9997422247--789999997641
Q gi|254780805|r 209 AQVIVSKKMS--VRDTEELVQEQD 230 (300)
Q Consensus 209 a~~Ii~~~LS--VRe~E~lVk~~~ 230 (300)
.+......|. |||.++.+.+..
T Consensus 346 ~~~L~~y~WPGNvREL~n~iera~ 369 (441)
T PRK10365 346 MDLLIHYDWPGNIRELENAVERAV 369 (441)
T ss_pred HHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 999970999989999999999999
No 186
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=70.13 E-value=8.6 Score=18.66 Aligned_cols=21 Identities=24% Similarity=0.192 Sum_probs=14.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 104679999743378778656
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~L 173 (300)
.|.+++|+.+|.+...|...+
T Consensus 140 pt~~eiA~~l~i~~~~v~~~l 160 (257)
T PRK08215 140 PTVSEIAKELEVPREEVVFAL 160 (257)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999988098999999999
No 187
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=70.12 E-value=8.6 Score=18.66 Aligned_cols=47 Identities=15% Similarity=0.155 Sum_probs=34.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Q ss_conf 999985210111046799997433787786565-654358999987642
Q gi|254780805|r 142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILR-ILKLPSSVREMIRKE 189 (300)
Q Consensus 142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr-Ll~L~~~i~~~l~~~ 189 (300)
.-+..|++ ...+|.||+..+|.|-++|++=-. |-.+||++++.+...
T Consensus 51 ~Iv~eLL~-ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~ 98 (103)
T COG2973 51 RIVEELLR-GELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKV 98 (103)
T ss_pred HHHHHHHH-CCCCHHHHHHHHCCCHHHHCCCHHHHCCCCHHHHHHHHHH
T ss_conf 99999995-6353999999858625655044444235987899999997
No 188
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=69.86 E-value=7.5 Score=19.02 Aligned_cols=39 Identities=18% Similarity=0.180 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-.+-.-. |..-.|+|..|||+.+|.|.++|.++|.
T Consensus 139 ~Lp~~~r~il~--L~~~~g~s~~EIA~~l~is~~tVk~~l~ 177 (194)
T PRK12513 139 TLPDEQREVFL--LREHGDLSLEEIAQLTGVPLETVKSRLR 177 (194)
T ss_pred CCCHHHHHHHH--HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 29989999999--9998499999999998949999999999
No 189
>pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
Probab=69.45 E-value=5.6 Score=19.84 Aligned_cols=26 Identities=15% Similarity=0.279 Sum_probs=21.2
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 210111046799997433787786565
Q gi|254780805|r 148 ISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 148 ~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
++. |.|..++|++||.|+++|.+-++
T Consensus 15 ve~-G~S~~eaA~~F~Is~~Tv~rWlk 40 (120)
T pfam01710 15 IES-GGSITEASKVFQIGRATIYRWLK 40 (120)
T ss_pred HHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 986-99999999993702999999985
No 190
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=69.37 E-value=8.9 Score=18.56 Aligned_cols=21 Identities=10% Similarity=0.232 Sum_probs=13.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|.+++|+.+|.+...|...+.
T Consensus 128 t~~eiA~~l~i~~~~v~~~~~ 148 (257)
T PRK05911 128 TDGELCEYLNISQQELSGWFS 148 (257)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999883979999999998
No 191
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=69.09 E-value=9 Score=18.52 Aligned_cols=46 Identities=11% Similarity=0.145 Sum_probs=31.4
Q ss_pred HHCCCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 310221048999999985210-11104679999743378778656565
Q gi|254780805|r 130 VQRKDLNPLEEALGYEQLISE-YGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 130 ~~R~dl~p~e~A~~~~~l~~~-~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
+.--+|++.+ +..+..|.+. -|.||.+||+.+|.+++++++.+.=+
T Consensus 24 L~~~gLt~~q-~~~L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ld~L 70 (144)
T PRK03573 24 LKPLELTQTH-WVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQL 70 (144)
T ss_pred HHHCCCCHHH-HHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 8866998259-9999999973989899999999798783699999999
No 192
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=69.07 E-value=7 Score=19.21 Aligned_cols=45 Identities=16% Similarity=0.366 Sum_probs=30.2
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCH
Q ss_conf 52101110467999974337877865656543589999876-421016
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIR-KEEISL 193 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~-~~~is~ 193 (300)
|....|+|.+|||+.+|.|.++|..+|. ..=..+++.|. .|....
T Consensus 130 L~~~egls~~EIAe~Lgis~~TVksrl~--RAr~~Lr~~L~~~g~~~~ 175 (190)
T PRK12516 130 LIGASGFAYEEAAEICGCAVGTIKSRVS--RARARLQEILQIEGEADY 175 (190)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHCCCCCC
T ss_conf 8998299999999998949999999999--999999999984599878
No 193
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=68.99 E-value=4 Score=20.76 Aligned_cols=36 Identities=25% Similarity=0.459 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH
Q ss_conf 104679999743378778656565435899998764210167777
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHAR 197 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar 197 (300)
+||++||..+|-+|.+|++.|. ++-++|-|+.+..+
T Consensus 146 lT~~eLA~~iGttREtVsR~L~---------~l~~~GlI~~~~~~ 181 (201)
T PRK13918 146 ATHDELAAAVGSVRETVTKVVG---------ELSREGVIRSGYGK 181 (201)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH---------HHHHCCCEEECCCE
T ss_conf 7999999885986899999999---------99988988967998
No 194
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=68.92 E-value=7.2 Score=19.15 Aligned_cols=37 Identities=30% Similarity=0.405 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 48999999985210111046799997433787786565
Q gi|254780805|r 137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|-++-..+ .|..-.|+|..|||+.+|.|.++|..+|.
T Consensus 114 p~~~R~v~-~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 150 (161)
T PRK12541 114 PLERRNVL-LLRDYYGFSYKEIAEMTGLSLAKVKIELH 150 (161)
T ss_pred CHHHHHHH-HHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999-98997499999999998939999999999
No 195
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=68.64 E-value=7.3 Score=19.12 Aligned_cols=27 Identities=26% Similarity=0.479 Sum_probs=22.0
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 521011104679999743378778656
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
|....|+|.+|||+.+|.|.++|..+|
T Consensus 147 L~~~egls~~EIA~~lgis~~tVks~l 173 (195)
T PRK12532 147 LKEILGFSSDEIQQMCGISTSNYHTIM 173 (195)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999819999999999895999999999
No 196
>PRK11753 cAMP-regulatory protein; Provisional
Probab=68.62 E-value=4.2 Score=20.67 Aligned_cols=20 Identities=50% Similarity=0.768 Sum_probs=9.4
Q ss_pred CHHHHHHHHHHHHHHHHHHH
Q ss_conf 04679999743378778656
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~L 173 (300)
||++||..+|.+|.+|++.|
T Consensus 170 t~~eLA~~lG~sretvsR~L 189 (211)
T PRK11753 170 TRQEIGRIVGCSREMVGRVL 189 (211)
T ss_pred CHHHHHHHHCCCHHHHHHHH
T ss_conf 99999988699899999999
No 197
>PRK00215 LexA repressor; Validated
Probab=68.62 E-value=5.9 Score=19.68 Aligned_cols=48 Identities=31% Similarity=0.441 Sum_probs=32.3
Q ss_pred HHHHHHHHCCC--CHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHH
Q ss_conf 99985210111--04679999743-378778656565435899998764210--16777776
Q gi|254780805|r 143 GYEQLISEYGY--TQNDIGSIVGK-SRSHVANILRILKLPSSVREMIRKEEI--SLGHARTL 199 (300)
Q Consensus 143 ~~~~l~~~~~~--t~~~lA~~~G~-s~s~V~~~LrLl~L~~~i~~~l~~~~i--s~ghar~L 199 (300)
.++..++++|+ |..|||+.+|. |.++|.++|. .+...|-| ..|++|++
T Consensus 12 fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~---------~Le~kG~i~r~~~~~R~i 64 (204)
T PRK00215 12 FIKDRIEETGYPPSRREIADALGLRSPSAVHEHLK---------ALERKGFIRRDPGRSRAI 64 (204)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHH---------HHHHCCCEECCCCCCCEE
T ss_conf 99999997488998999999809998189999999---------998797887069997338
No 198
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=68.57 E-value=5 Score=20.15 Aligned_cols=10 Identities=0% Similarity=-0.144 Sum_probs=4.8
Q ss_pred CCCCCCCCCC
Q ss_conf 0013543334
Q gi|254780805|r 106 LSEVPVIIRN 115 (300)
Q Consensus 106 ~~~ip~iv~~ 115 (300)
...+|+++.+
T Consensus 134 ~~~~piV~v~ 143 (327)
T PRK10339 134 ALTDNICFID 143 (327)
T ss_pred HCCCCEEEEE
T ss_conf 5699999995
No 199
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=68.48 E-value=2.2 Score=22.45 Aligned_cols=20 Identities=25% Similarity=0.506 Sum_probs=15.7
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q ss_conf 10467999974337877865
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~ 172 (300)
.||-|+|..||.|+-+|||.
T Consensus 200 kTQ~eVA~~LGISQVQVSRl 219 (231)
T TIGR02885 200 KTQTEVAKMLGISQVQVSRL 219 (231)
T ss_pred CHHHHHHHHCCCCCCHHHHH
T ss_conf 01799997718570012278
No 200
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=68.44 E-value=7.8 Score=18.91 Aligned_cols=27 Identities=19% Similarity=0.187 Sum_probs=21.9
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 210111046799997433787786565
Q gi|254780805|r 148 ISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 148 ~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
..-.|+|..|||+.+|.|.++|..++.
T Consensus 143 ~~~eg~s~~EIA~~lgis~~tVks~l~ 169 (184)
T PRK12539 143 VKLDGLSVAEAATRSGMSESAVKVSVH 169 (184)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 999499999999998919999999999
No 201
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=68.29 E-value=9.4 Score=18.42 Aligned_cols=32 Identities=25% Similarity=0.292 Sum_probs=23.0
Q ss_pred HHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9998521011-1046799997433787786565
Q gi|254780805|r 143 GYEQLISEYG-YTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 143 ~~~~l~~~~~-~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
++..|.++.| .+..+||+.+|.|+++|+..++
T Consensus 12 ~Iy~L~~~~~~vr~~dIA~~L~Vs~~SVs~mik 44 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQ 44 (142)
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 999998258971299999997899533999999
No 202
>pfam06245 DUF1015 Protein of unknown function (DUF1015). Family of proteins with unknown function found in archaea and bacteria.
Probab=68.10 E-value=4.8 Score=20.26 Aligned_cols=11 Identities=36% Similarity=0.703 Sum_probs=4.1
Q ss_pred CCCCHHHHHHH
Q ss_conf 33575677777
Q gi|254780805|r 91 IIAGERRFRAA 101 (300)
Q Consensus 91 ii~G~rR~rAa 101 (300)
|-+||+|+.|+
T Consensus 203 IADGHHR~~ta 213 (411)
T pfam06245 203 IADGHHRYASA 213 (411)
T ss_pred EECCCCCHHHH
T ss_conf 81484113889
No 203
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=68.07 E-value=9.5 Score=18.39 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-....-+-+ ..|+|..+||+.+|.|.++|.++|.
T Consensus 112 ~Lp~~~r~v~~l~---~~g~s~~EIA~~l~is~~tVk~~l~ 149 (166)
T PRK09639 112 KMTERDRTVLLLR---FSGYSYKEIAQALGIDESSVGTTLH 149 (166)
T ss_pred HCCHHHHHHHHHH---HHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 3999999999999---9389999999998919999999999
No 204
>pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Probab=68.02 E-value=9 Score=18.54 Aligned_cols=24 Identities=29% Similarity=0.493 Sum_probs=20.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565654
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
|..++|+.+|.|+++|.+.+..|.
T Consensus 26 s~~~La~~~~vSr~tvr~Al~~L~ 49 (64)
T pfam00392 26 SERELAAEFGVSRTTVREALRRLE 49 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 799999997969999999999999
No 205
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=67.96 E-value=8.1 Score=18.82 Aligned_cols=37 Identities=14% Similarity=0.168 Sum_probs=26.1
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 101110467999974337877865656543589999876
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIR 187 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~ 187 (300)
...|+|.+|||+.+|.|.+||..+|. ..=..+.++|.
T Consensus 162 ~~eglS~~EIA~~Lgis~~TVKsrL~--RArk~LRe~La 198 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLH--RARRLLRESLA 198 (231)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHH
T ss_conf 99399999999998939999999999--99999999999
No 206
>pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.).
Probab=67.74 E-value=8.5 Score=18.70 Aligned_cols=34 Identities=29% Similarity=0.510 Sum_probs=24.3
Q ss_pred HHHHHHHCC-----CCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 998521011-----1046799997433787786565654
Q gi|254780805|r 144 YEQLISEYG-----YTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 144 ~~~l~~~~~-----~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
++.|++.|. ..-++||+.+++|.++|+|.|.-|+
T Consensus 10 L~aLI~lY~~~~~pVks~~IAe~l~~spgTIRN~M~~L~ 48 (79)
T pfam03444 10 LQALINLYRKKGRAVKGEEIADIIGRNPGTVRNQMQSLK 48 (79)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999999729986679999998789088999999999
No 207
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=67.70 E-value=9.6 Score=18.34 Aligned_cols=46 Identities=9% Similarity=0.076 Sum_probs=33.3
Q ss_pred HHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 54310221048999999985210111046799997433787786565
Q gi|254780805|r 128 ENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 128 EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
+.+.--+|++.+-+ .+..|....++|+.++|+.+|.++++|++.+.
T Consensus 31 ~~L~~~gLt~~Q~~-vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ld 76 (144)
T PRK11512 31 EYLSPLDITAAQFK-VLCSIRCAACITPVELKKVLSVDLGALTRMLD 76 (144)
T ss_pred HHHHHCCCCHHHHH-HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98754599999999-99999986997999999997888878999999
No 208
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=67.67 E-value=3.6 Score=21.07 Aligned_cols=33 Identities=24% Similarity=0.460 Sum_probs=23.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Q ss_conf 04679999743378778656565-4358999987
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRIL-KLPSSVREMI 186 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l 186 (300)
|-.++|+..|.|.++||+.|.=- ..+++.++.|
T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~~~~vs~~tr~rI 34 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVLNNPERVSEETREKV 34 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 9999999989799999999879798999999999
No 209
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=67.30 E-value=8.3 Score=18.75 Aligned_cols=24 Identities=25% Similarity=0.459 Sum_probs=20.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565654
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
|..++|+.+|.|+++|.+.++.|.
T Consensus 22 s~~~la~~~~vSr~tvr~A~~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 099999998949999999999999
No 210
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=67.07 E-value=9.3 Score=18.44 Aligned_cols=49 Identities=31% Similarity=0.374 Sum_probs=37.2
Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 66654310221048999999985210111046799997433787786565
Q gi|254780805|r 125 AIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 125 ~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.+.+|++--.|+.. +|.+|..|+.....|..++++..|..++.|...|+
T Consensus 4 ~~~~~L~~lGlt~y-Ea~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~ 52 (247)
T COG1378 4 ELEENLQKLGLTEY-EAKVYLALLCLGEATAKEISEASGVPRPKVYDVLR 52 (247)
T ss_pred HHHHHHHHCCCCHH-HHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHH
T ss_conf 79999998199788-99999999981887799999865999322999999
No 211
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=66.95 E-value=8.8 Score=18.58 Aligned_cols=24 Identities=13% Similarity=0.268 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|.+|||+.+|.+.++|..+|.
T Consensus 145 egls~~EIA~~lg~~~gTVKsRl~ 168 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 299999999998939999999999
No 212
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304 This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis . This group has a very sporadic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member Dechloromonas aromatica (strain RCB), that appears to have two of these sigma factors. A member of which appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri (strain ATCC 700601 / ES114), where a second one is chromosomally encoded..
Probab=66.86 E-value=4.6 Score=20.38 Aligned_cols=35 Identities=26% Similarity=0.218 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 489999999852101110467999974337877865
Q gi|254780805|r 137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
|=+.+.|+ +|.+--|+||.++|++||.|-|.+.-+
T Consensus 102 P~~~r~a~-~L~el~G~sQ~e~A~kLGlSlSGaKSR 136 (170)
T TIGR02959 102 PDEYREAI-RLTELEGLSQKEIAEKLGLSLSGAKSR 136 (170)
T ss_pred CHHHHHHH-HHHHCCCCCHHHHHHHCCCCCCCHHHH
T ss_conf 98678898-887507998279987617533515678
No 213
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=66.68 E-value=5.7 Score=19.81 Aligned_cols=37 Identities=11% Similarity=0.230 Sum_probs=24.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99852101110467999974337877865656543589
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSS 181 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~ 181 (300)
+.+-.+..|||+|+||+++..-.|+|.+. -=..|.|+
T Consensus 88 IR~eREKRgwS~E~LAkki~eK~S~i~ki-E~~e~eP~ 124 (169)
T TIGR00270 88 IREEREKRGWSREELAKKIKEKASVIKKI-EREELEPE 124 (169)
T ss_pred HHHHCCCCCCCHHHHHHHHHHHHHHHHHH-HHHCCCCC
T ss_conf 22000146878789999874106788887-54037988
No 214
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=66.61 E-value=9.4 Score=18.40 Aligned_cols=24 Identities=17% Similarity=0.263 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|..|||+.+|.|.++|..++.
T Consensus 152 ~g~s~~EIA~~lg~s~~tVk~~l~ 175 (187)
T PRK09648 152 VGLSAEETAEAVGSTPGAVRVAQH 175 (187)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 499999999998939999999999
No 215
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=66.53 E-value=10 Score=18.20 Aligned_cols=21 Identities=19% Similarity=0.461 Sum_probs=10.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|..+||+.+|.||.||.+.|.
T Consensus 27 sE~eLa~~~~VSR~TvR~Al~ 47 (231)
T TIGR03337 27 SERDLGERFNTTRVTIREALQ 47 (231)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 899999997979999999999
No 216
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=66.41 E-value=4.3 Score=20.58 Aligned_cols=22 Identities=23% Similarity=0.383 Sum_probs=14.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
+|+++||..+|.++.+|++.|+
T Consensus 174 lT~~dLA~~lG~trETVsR~L~ 195 (224)
T PRK09391 174 MSRRDIADYLGLTIETVSRALS 195 (224)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 7999999887997999999999
No 217
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=66.37 E-value=8.5 Score=18.67 Aligned_cols=41 Identities=29% Similarity=0.234 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHHHHH--HHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 221048999999985--21011104679999743378778656
Q gi|254780805|r 133 KDLNPLEEALGYEQL--ISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l--~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
..|+|-|.-.--.+. .+.-..|+.+||+.+|.|+.+|++.-
T Consensus 173 ~~L~~REr~II~~RfGL~~~~~~Tl~eIg~~lgiSrERVRQIe 215 (228)
T PRK05803 173 DILDPREKEVIEMRYGLGDGKEKTQREIAKALGISRSYVSRIE 215 (228)
T ss_pred HCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 5189889999999864789997159999999897999999999
No 218
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=66.30 E-value=8.9 Score=18.56 Aligned_cols=23 Identities=4% Similarity=0.208 Sum_probs=13.2
Q ss_pred HHHHHHHCCCC--HHHHHHHHHHHH
Q ss_conf 99997422247--789999997641
Q gi|254780805|r 208 LAQVIVSKKMS--VRDTEELVQEQD 230 (300)
Q Consensus 208 la~~Ii~~~LS--VRe~E~lVk~~~ 230 (300)
..+......|. |||.++.+.+..
T Consensus 349 a~~~L~~y~WPGNvREL~n~ierav 373 (457)
T PRK11361 349 AMSLLTAWSWPGNIRELSNVIERAV 373 (457)
T ss_pred HHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 9999956999979999999999999
No 219
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=66.23 E-value=10 Score=18.16 Aligned_cols=43 Identities=12% Similarity=0.168 Sum_probs=31.3
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 210111046799997433787786565654358999987642101
Q gi|254780805|r 148 ISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS 192 (300)
Q Consensus 148 ~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is 192 (300)
..-.|+|.+|+|+.+|.+.+||..+|. .-=..+.+++..|.=+
T Consensus 144 ~~~~g~s~~EIA~ilgi~~gTVKsRl~--RAr~~Lr~~L~~~~~~ 186 (195)
T PRK12535 144 TQVLGYTYEEAAKIADVRVGTIRSRVA--RARADLVAATATGDSS 186 (195)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHCCCCC
T ss_conf 998299899999998939999999999--9999999997568976
No 220
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=66.21 E-value=4 Score=20.77 Aligned_cols=33 Identities=24% Similarity=0.435 Sum_probs=22.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Q ss_conf 04679999743378778656565-4358999987
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRIL-KLPSSVREMI 186 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l 186 (300)
|-.++|++.|.|.++||+.|.=- ..+++..+.|
T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln~~~~Vs~~tr~rV 35 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNGNGRVSEETREKV 35 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 8999999989599999999779998999999999
No 221
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=66.19 E-value=9 Score=18.53 Aligned_cols=24 Identities=17% Similarity=0.198 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|.+|||+.+|.|.+||..+|.
T Consensus 168 egls~~EIA~~l~is~~TVksrl~ 191 (206)
T PRK12526 168 QELSQEQLAQQLNVPLGTVKSRLR 191 (206)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 599999999998939999999999
No 222
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=65.82 E-value=10 Score=18.11 Aligned_cols=22 Identities=23% Similarity=0.298 Sum_probs=16.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|.+++|+.+|.+...|...+.
T Consensus 131 pt~~eia~~lg~~~~~v~~~~~ 152 (261)
T PRK06288 131 PTDDEIAKELGISLEEYHSLLS 152 (261)
T ss_pred CCHHHHHHHCCCCHHHHHHHHH
T ss_conf 9878888781999999999999
No 223
>PRK05412 nucleotide-binding protein; Reviewed
Probab=65.66 E-value=11 Score=18.09 Aligned_cols=38 Identities=16% Similarity=0.278 Sum_probs=29.3
Q ss_pred HCCEEEEECCCCCEEEEEEECCHHHHHHHHHHHCCCCCCC
Q ss_conf 3987999717982289998589899999999837564569
Q gi|254780805|r 261 VGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGENDFEY 300 (300)
Q Consensus 261 lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL~~~~~~~ 300 (300)
.+.||+..-.+. .|.+.-+..|+|..++..|++.+|++
T Consensus 115 ~klKVqa~IQGd--~vRVtgKkrDDLQ~vi~llk~~d~~~ 152 (161)
T PRK05412 115 SKLKVQAQIQGD--QVRVTGKKRDDLQAVIALLRGADLGQ 152 (161)
T ss_pred CCCCEEEEECCC--EEEEECCCHHHHHHHHHHHHHCCCCC
T ss_conf 488136886485--78861598889999999998327799
No 224
>pfam04461 DUF520 Protein of unknown function (DUF520). Family of uncharacterized proteins.
Probab=65.65 E-value=11 Score=18.09 Aligned_cols=38 Identities=18% Similarity=0.345 Sum_probs=29.4
Q ss_pred HCCEEEEECCCCCEEEEEEECCHHHHHHHHHHHCCCCCCC
Q ss_conf 3987999717982289998589899999999837564569
Q gi|254780805|r 261 VGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGENDFEY 300 (300)
Q Consensus 261 lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL~~~~~~~ 300 (300)
.+.||+..-.+. .|.+.-+..|+|...+..|+..+|++
T Consensus 115 ~klKVqa~IQGd--~vRVsgKkrDDLQ~vi~~lK~~d~~~ 152 (160)
T pfam04461 115 SKLKVQAAIQGD--QVRVTGKKRDDLQAVIALLREADLDL 152 (160)
T ss_pred CCCCEEEEECCC--EEEEECCCHHHHHHHHHHHHHCCCCC
T ss_conf 488036886485--78861598889999999998327799
No 225
>PRK11886 biotin--protein ligase; Provisional
Probab=65.63 E-value=11 Score=18.09 Aligned_cols=23 Identities=13% Similarity=0.098 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHCCEEEEECCC
Q ss_conf 89999999999739879997179
Q gi|254780805|r 249 YLTDLEKKISSKVGLNISIKHRN 271 (300)
Q Consensus 249 ~i~~le~~L~~~lGtkV~I~~~~ 271 (300)
.+.+..++....+|..|.+...+
T Consensus 259 ~~~~~w~~~~~~~Gk~V~v~~~~ 281 (319)
T PRK11886 259 PFLERWKKLDLFLGREVKLIIGQ 281 (319)
T ss_pred HHHHHHHHHHCCCCCEEEEEECC
T ss_conf 99999998507169879999899
No 226
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=65.43 E-value=7.4 Score=19.09 Aligned_cols=76 Identities=12% Similarity=0.125 Sum_probs=41.3
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHC-CHHHHHHHHHHHCCCCHH--HHH
Q ss_conf 52101110467999974337877865656543589999876421016777776401-004689999742224778--999
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVST-SDPLSLAQVIVSKKMSVR--DTE 223 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~-~~~~~la~~Ii~~~LSVR--e~E 223 (300)
|.+...++.-++++.+|.|+++||+.|+.+.-. .+...=++|.- ....+ ++....+..++.+.|+-. +++
T Consensus 23 L~~~gelcV~eL~~~l~~sQs~vS~HL~~L~~a-GlV~~rr~G~~------vyY~Ln~~~~~~~~~~l~~~~~~~~~~~~ 95 (106)
T PRK10141 23 LRESGELCVCDLCTALDQSQPKISRHLALLRES-GLLLDRKQGKW------VHYRLSPHIPAWAAKIIEQAWLCQQEDVQ 95 (106)
T ss_pred HHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCCEEEECCEE------EEEEECCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 987499569999988699888999999999988-97303741417------99877998859999999999983599999
Q ss_pred HHHHHH
Q ss_conf 999764
Q gi|254780805|r 224 ELVQEQ 229 (300)
Q Consensus 224 ~lVk~~ 229 (300)
++++++
T Consensus 96 ~~~~kl 101 (106)
T PRK10141 96 AIVRKL 101 (106)
T ss_pred HHHHHH
T ss_conf 999988
No 227
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=65.22 E-value=6.6 Score=19.39 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHCCCCC-HHHHH--------HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3455666543102210-48999--------999985210111046799997433787786565
Q gi|254780805|r 121 SLEIAIVENVQRKDLN-PLEEA--------LGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 121 ~~~~~l~EN~~R~dl~-p~e~A--------~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
-.++.++-.-.|.++. .+.+| +.+-||.=-.++|-++||..+|.++||||+.+.
T Consensus 142 DpEl~llr~~~r~~f~~Al~~Al~~L~~rER~LLRLHfv~~Ls~~r~g~my~~~~STvsR~~~ 204 (249)
T TIGR03001 142 DPELDLLRERYRQEFRAALREALAALSERERTLLRLHFVEGLSMDRLGAMYQVHRSTVSRWVA 204 (249)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 178999999999999999999873289868765556882033299998774577507899999
No 228
>PRK09526 lacI lac repressor; Reviewed
Probab=65.21 E-value=6.6 Score=19.39 Aligned_cols=17 Identities=6% Similarity=0.104 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHCCC
Q ss_conf 48999999985210111
Q gi|254780805|r 137 PLEEALGYEQLISEYGY 153 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~ 153 (300)
..++..+|++.+.++|.
T Consensus 196 ~~~R~~Gf~~~~~~~~l 212 (342)
T PRK09526 196 ARLRLAGWLEYLTRNQL 212 (342)
T ss_pred HHHHHHHHHHHHHHCCC
T ss_conf 99999999999997798
No 229
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=65.13 E-value=9.4 Score=18.41 Aligned_cols=36 Identities=8% Similarity=-0.007 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 11104679999743378778656565435899998764
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRK 188 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~ 188 (300)
.|+|.+|||..+|.|.++|..+|. ..-..+++.+.+
T Consensus 121 e~~s~~EIA~~l~is~~tVk~~l~--RArk~Lkk~lke 156 (160)
T PRK09642 121 EEKSYQEIALQENIEVKTVEMKLY--RARKWIKKHWKE 156 (160)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHH
T ss_conf 299999999998919999999999--999999999987
No 230
>TIGR02850 spore_sigG RNA polymerase sigma-G factor; InterPro: IPR014212 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=64.93 E-value=8.7 Score=18.63 Aligned_cols=21 Identities=29% Similarity=0.517 Sum_probs=13.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 110467999974337877865
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~ 172 (300)
|-||-++|+.+|.|+++|+++
T Consensus 222 G~tqmeva~eiGisqaqvsrl 242 (254)
T TIGR02850 222 GKTQMEVAEEIGISQAQVSRL 242 (254)
T ss_pred CCHHHHHHHHHCCHHHHHHHH
T ss_conf 631334565403016888888
No 231
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=64.65 E-value=11 Score=17.97 Aligned_cols=24 Identities=29% Similarity=0.500 Sum_probs=20.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565654
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+..++|+.+|.|+++|.+.+..|.
T Consensus 27 s~~~La~~~~vSr~tvr~Al~~L~ 50 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 799999997988899999999999
No 232
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=64.50 E-value=10 Score=18.23 Aligned_cols=39 Identities=15% Similarity=0.198 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 104899999998521011--10467999974337877865656
Q gi|254780805|r 135 LNPLEEALGYEQLISEYG--YTQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~--~t~~~lA~~~G~s~s~V~~~LrL 175 (300)
.+-++.| ...|..+.| -|.++||+.+|.+...|...+..
T Consensus 98 ~~ki~~a--~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~ 138 (229)
T PRK12427 98 THKTNEA--IRQIAKRLGHEPNFEEISAELNLTADEYQEYLLL 138 (229)
T ss_pred HHHHHHH--HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999--9999998588999999998919999999999998
No 233
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=64.28 E-value=11 Score=17.92 Aligned_cols=18 Identities=6% Similarity=0.054 Sum_probs=9.8
Q ss_pred CHHHHHHHHHHHHHCCCC
Q ss_conf 988999999988631001
Q gi|254780805|r 59 ESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 59 ~~~~l~eLa~SI~~~G~l 76 (300)
+...+.-|..++.+.|.+
T Consensus 53 pksT~~RlL~tL~~~G~v 70 (271)
T PRK10163 53 PLSTTFRLLKVLQAADFV 70 (271)
T ss_pred CHHHHHHHHHHHHHCCCE
T ss_conf 999999999999968988
No 234
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=63.81 E-value=10 Score=18.12 Aligned_cols=28 Identities=18% Similarity=0.374 Sum_probs=22.8
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|....|+|..|||+.+|.|.++|..+|.
T Consensus 123 L~~~~g~s~~EIA~~lgis~~tVksrl~ 150 (164)
T PRK12547 123 LIGASGFSYEEAAEICGCAVGTIKSRVS 150 (164)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8998499999999998939999999999
No 235
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=63.68 E-value=5.9 Score=19.73 Aligned_cols=27 Identities=26% Similarity=0.282 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565654
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+-+|+.++|+..|.|+.+|.+.|.+|.
T Consensus 74 lI~T~R~lae~~gvs~~TV~~tmK~L~ 100 (165)
T pfam05732 74 LIMTQREIAEETGISLETVRQTMKALE 100 (165)
T ss_pred EEEEHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 998789999983952999999999997
No 236
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=63.66 E-value=10 Score=18.12 Aligned_cols=38 Identities=13% Similarity=0.350 Sum_probs=26.2
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565654358999987
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI 186 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l 186 (300)
|..-.|+|..|||+.+|.|.++|..+|. ..=..+++++
T Consensus 124 L~~~egls~~EIAe~Lgis~gTVKsRL~--RAR~~Lr~~L 161 (188)
T PRK12546 124 LVGASGFSYEEAAEMCGVAVGTVKSRAN--RARARLAELL 161 (188)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHH
T ss_conf 7998298999999998939999999999--9999999987
No 237
>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
Probab=63.60 E-value=9.3 Score=18.43 Aligned_cols=56 Identities=14% Similarity=0.227 Sum_probs=34.2
Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHC---------CCCHHHHHHHHHHHHHHHHHHHH--HHHHHH
Q ss_conf 666543102210489999999852101---------11046799997433787786565--654358
Q gi|254780805|r 125 AIVENVQRKDLNPLEEALGYEQLISEY---------GYTQNDIGSIVGKSRSHVANILR--ILKLPS 180 (300)
Q Consensus 125 ~l~EN~~R~dl~p~e~A~~~~~l~~~~---------~~t~~~lA~~~G~s~s~V~~~Lr--Ll~L~~ 180 (300)
.++.++++..-+-+.-+..+-....+| -+|..++|+.+|.+.||||+.++ .+..|-
T Consensus 13 ~li~~i~~R~~Tl~~V~~~Iv~~Q~~Ff~~g~~~l~PLtlk~iA~~l~lh~STVSRav~~Kyi~tp~ 79 (160)
T pfam04552 13 WLIRSLEQRAETLLKVAREIVRRQEDFLEKGPEALRPLTLREVAEALGMHESTVSRATTNKYLATPR 79 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCC
T ss_conf 9999999999999999999999979998478535757619999988099810699999613976799
No 238
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=63.50 E-value=5.2 Score=20.06 Aligned_cols=26 Identities=27% Similarity=0.433 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf 23578999876898899999998863100
Q gi|254780805|r 47 IVPNPHNPRNYFESEGLEDLCQSIKSHGI 75 (300)
Q Consensus 47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~ 75 (300)
+.|+..+| |-.+-+..+.+...++|.
T Consensus 70 v~~~~~~~---f~~~~i~gi~~~~~~~g~ 95 (342)
T PRK10014 70 IVRDLSAP---FYAELTAGLTEALEAQGR 95 (342)
T ss_pred ECCCCCCH---HHHHHHHHHHHHHHHCCC
T ss_conf 05445776---779999999999998198
No 239
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=63.35 E-value=5.1 Score=20.11 Aligned_cols=33 Identities=21% Similarity=0.466 Sum_probs=27.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999985210111046799997433787786565
Q gi|254780805|r 142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
..+..+++..+++|.++|+.+|.+++-|+...+
T Consensus 31 ~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~ 63 (91)
T COG5606 31 MAIKQWIEQAALSQAQIAELLGVTQPRVSDLAR 63 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf 999999999787799999983888731889983
No 240
>pfam06322 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=63.34 E-value=5.3 Score=19.98 Aligned_cols=27 Identities=30% Similarity=0.481 Sum_probs=23.1
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210111046799997433787786565
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|++.+| .|.++|+.++.+|.+|.+|.+
T Consensus 12 Li~~~G-N~teVaR~L~c~R~TVrkY~~ 38 (64)
T pfam06322 12 LIETYG-NQTEVARRLNCSRNTVRKYAE 38 (64)
T ss_pred HHHHHC-CHHHHHHHHCCHHHHHHHHHC
T ss_conf 999707-799997885110888998723
No 241
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=63.26 E-value=12 Score=17.80 Aligned_cols=15 Identities=13% Similarity=0.173 Sum_probs=7.0
Q ss_pred CCCHHHHHHHHHHHH
Q ss_conf 110467999974337
Q gi|254780805|r 152 GYTQNDIGSIVGKSR 166 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~ 166 (300)
|-|-..+|+.+....
T Consensus 100 GTT~~~la~~L~~~~ 114 (253)
T COG1349 100 GTTTLALARALPDDN 114 (253)
T ss_pred CCHHHHHHHHCCCCC
T ss_conf 624999999717688
No 242
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=63.07 E-value=12 Score=17.78 Aligned_cols=38 Identities=8% Similarity=-0.019 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|.|-.+...+ |....|+|..|||+.+|.|.++|..+|.
T Consensus 132 Lp~~~R~v~~--Lr~~~~ls~~EIA~~l~~s~~tVk~~l~ 169 (191)
T PRK12520 132 LPARTGRVFM--MREWLELETEEICKELQITATNLWVMLY 169 (191)
T ss_pred CCHHHHHHHH--HHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 7499999999--9999389999999998949999999999
No 243
>PRK09492 treR trehalose repressor; Provisional
Probab=62.91 E-value=5.2 Score=20.06 Aligned_cols=28 Identities=18% Similarity=0.273 Sum_probs=12.9
Q ss_pred HHCCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf 9823578999876898899999998863100
Q gi|254780805|r 45 HSIVPNPHNPRNYFESEGLEDLCQSIKSHGI 75 (300)
Q Consensus 45 ~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~ 75 (300)
.-|.|+..+| |..+-+..+...+.++|.
T Consensus 66 g~i~~~~~~~---~~~~~~~~i~~~~~~~gy 93 (315)
T PRK09492 66 GIIVSRLDSP---SENLAVQTMLPAFYQQGY 93 (315)
T ss_pred EEECCCCCCH---HHHHHHHHHHHHHHHCCC
T ss_conf 6622677883---678999999999997498
No 244
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=62.73 E-value=11 Score=17.99 Aligned_cols=37 Identities=22% Similarity=0.162 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
||+-|.- +-+++.+ |+|-.|||+.++.|..||.+++.
T Consensus 156 LT~RE~e--IL~lla~-G~sNkEIA~~L~iSe~TVk~H~~ 192 (216)
T PRK10100 156 LTHREKE--ILNKLRI-GASNNEIARSLFISENTVKTHLY 192 (216)
T ss_pred CCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9989999--9999987-99999999894988989999999
No 245
>PRK11569 transcriptional repressor IclR; Provisional
Probab=62.41 E-value=12 Score=17.71 Aligned_cols=19 Identities=11% Similarity=0.359 Sum_probs=10.2
Q ss_pred CCHHHHHHHHHHHHHCCCC
Q ss_conf 8988999999988631001
Q gi|254780805|r 58 FESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 58 ~~~~~l~eLa~SI~~~G~l 76 (300)
++...+.-|..++.+.|.+
T Consensus 55 lpksT~~RlL~tL~~~G~v 73 (274)
T PRK11569 55 LPNSTTHRLLTTMQQQGFV 73 (274)
T ss_pred CCHHHHHHHHHHHHHCCCE
T ss_conf 1999999999999976987
No 246
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=62.16 E-value=4.1 Score=20.70 Aligned_cols=26 Identities=23% Similarity=0.295 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10467999974337877865656543
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKL 178 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L 178 (300)
+|.+|+|+.+|.|++||.+.+.=..|
T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~~g~l 27 (49)
T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIEEGEL 27 (49)
T ss_pred CCHHHHHHHCCCCHHHHHHHHHCCCC
T ss_conf 87788997719990578999971898
No 247
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=62.04 E-value=12 Score=17.73 Aligned_cols=25 Identities=16% Similarity=0.125 Sum_probs=21.0
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 1011104679999743378778656
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
.-.|+|.+|||+.+|.+.+||..+|
T Consensus 150 ~~eglS~~EIAeiLgip~gTVKSRL 174 (217)
T PRK12533 150 ELEDMSYREIAAIADVPVGTVMSRL 174 (217)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9809999999999894999999999
No 248
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=61.25 E-value=8 Score=18.85 Aligned_cols=39 Identities=26% Similarity=0.326 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 221048999999985210111046799997433787786565
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.-|++-|.- +-+++.+ |.|-.|||..+|.|..||.++++
T Consensus 189 glLT~RE~E--VL~~va~-G~sn~eIA~~L~iS~~TVk~H~~ 227 (247)
T TIGR03020 189 GLITAREAE--ILAWVRD-GKTNEEIAAILGISSLTVKNHLQ 227 (247)
T ss_pred CCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 899989999--9999987-99999999994979999999999
No 249
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=61.04 E-value=12 Score=17.70 Aligned_cols=22 Identities=14% Similarity=0.303 Sum_probs=13.7
Q ss_pred HHHHHHHCCCC--HHHHHHHHHHH
Q ss_conf 99997422247--78999999764
Q gi|254780805|r 208 LAQVIVSKKMS--VRDTEELVQEQ 229 (300)
Q Consensus 208 la~~Ii~~~LS--VRe~E~lVk~~ 229 (300)
..+......|- |||.|..+.+.
T Consensus 392 Al~~L~~Y~WPGNVRELenvIeRA 415 (510)
T PRK05022 392 AQAALLQYDWPGNVRELEHVISRA 415 (510)
T ss_pred HHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf 999997099997899999999999
No 250
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=61.01 E-value=13 Score=17.55 Aligned_cols=21 Identities=33% Similarity=0.436 Sum_probs=10.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|..+||+.+|.||.||.+.|.
T Consensus 31 sE~eLa~~~~VSR~TvR~Al~ 51 (239)
T PRK09764 31 TESALQTEFGVSRVTVRQALR 51 (239)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999997979999999999
No 251
>KOG0257 consensus
Probab=60.91 E-value=9 Score=18.51 Aligned_cols=29 Identities=38% Similarity=0.762 Sum_probs=25.3
Q ss_pred CCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf 35789998-768988999999988631001
Q gi|254780805|r 48 VPNPHNPR-NYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 48 ~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l 76 (300)
--+|+||- +.|+.+.|+++|+=.+.||++
T Consensus 178 ~ntPhNPtGkvfsReeLe~ia~l~~k~~~l 207 (420)
T KOG0257 178 LNTPHNPTGKVFSREELERIAELCKKHGLL 207 (420)
T ss_pred EECCCCCCCCCCCHHHHHHHHHHHHHCCEE
T ss_conf 948999867305799999999999878979
No 252
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=60.87 E-value=13 Score=17.59 Aligned_cols=37 Identities=8% Similarity=0.047 Sum_probs=25.2
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 210111046799997433787786565654358999987
Q gi|254780805|r 148 ISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMI 186 (300)
Q Consensus 148 ~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l 186 (300)
..-.|+|.+|||+.+|.|.++|..+|. ..=..+++.|
T Consensus 148 r~~~~ls~~EIA~~l~is~~tVksrL~--RAR~~Lr~~L 184 (191)
T PRK12530 148 REFLELSSEQICQECHITTSNLHVLLY--RARLQLQACL 184 (191)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHH
T ss_conf 999299999999998969999999999--9999999999
No 253
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=60.75 E-value=13 Score=17.52 Aligned_cols=21 Identities=19% Similarity=0.370 Sum_probs=13.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 104679999743378778656
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~L 173 (300)
.|.+++|+.+|.+...|...+
T Consensus 122 ps~~eia~~lg~s~~~v~~~~ 142 (250)
T PRK07670 122 VTPSEVAAELGMSEEEVVTTM 142 (250)
T ss_pred CCHHHHHHHCCCCHHHHHHHH
T ss_conf 988899877199999999999
No 254
>PRK09801 transcriptional activator TtdR; Provisional
Probab=60.55 E-value=13 Score=17.50 Aligned_cols=13 Identities=15% Similarity=0.199 Sum_probs=5.3
Q ss_pred HHHHHHHHHHHHC
Q ss_conf 9999999999739
Q gi|254780805|r 250 LTDLEKKISSKVG 262 (300)
Q Consensus 250 i~~le~~L~~~lG 262 (300)
+.-+...+++.+|
T Consensus 289 idfl~~~~~~~~~ 301 (310)
T PRK09801 289 VEFLAAWCQQRLG 301 (310)
T ss_pred HHHHHHHHHHHHC
T ss_conf 9999999999858
No 255
>KOG2305 consensus
Probab=60.23 E-value=9.5 Score=18.38 Aligned_cols=101 Identities=18% Similarity=0.260 Sum_probs=54.7
Q ss_pred CCEEEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEE-ECCCC-----CCCCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 60240389823578999876898899999998863100155046-20565-----4453335756777776421001354
Q gi|254780805|r 38 SQDCISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIV-RAIDN-----GLYKIIAGERRFRAAKMASLSEVPV 111 (300)
Q Consensus 38 ~~~~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~V-r~~~~-----g~y~ii~G~rR~rAa~~~g~~~ip~ 111 (300)
....||+-.|.|.||- +++.++.-.+-++..||- |+.. |+..+ -.|-|.+--+|+-|+-.++..+++.
T Consensus 146 PPyfiPLvElVPaPwT-----sp~tVdrt~~lM~sigq~-pV~l~rei~Gf~lnriq~Ailne~wrLvasGil~v~dvD~ 219 (313)
T KOG2305 146 PPYFIPLVELVPAPWT-----SPDTVDRTRALMRSIGQE-PVTLKREILGFALNRIQYAILNETWRLVASGILNVNDVDA 219 (313)
T ss_pred CCCCCCHHEECCCCCC-----CHHHHHHHHHHHHHHCCC-CCCCCCCCCCCEECCCCHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf 9741201101368878-----802789999999983777-7544340114242133188999999998706765222999
Q ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 333464112345566654310221048999999985
Q gi|254780805|r 112 IIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQL 147 (300)
Q Consensus 112 iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l 147 (300)
+.-.. --.+-+++--+.-.-||+.-.|.-|+|.
T Consensus 220 VmS~G---LG~RYAflG~lET~HLNA~Gv~dYf~Ry 252 (313)
T KOG2305 220 VMSAG---LGPRYAFLGPLETAHLNAEGVADYFKRY 252 (313)
T ss_pred HHHCC---CCCCHHCCCCHHHHHCCCHHHHHHHHHH
T ss_conf 98667---7721100261354315867789999986
No 256
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=60.23 E-value=10 Score=18.13 Aligned_cols=22 Identities=9% Similarity=-0.241 Sum_probs=9.0
Q ss_pred CEEECCCCCCCCCCCCHHHHHH
Q ss_conf 0462056544533357567777
Q gi|254780805|r 79 LIVRAIDNGLYKIIAGERRFRA 100 (300)
Q Consensus 79 i~Vr~~~~g~y~ii~G~rR~rA 100 (300)
+.+...+.-++.+...|-|.|.
T Consensus 124 l~i~~k~~~gi~i~g~E~~~r~ 145 (585)
T PRK09863 124 CCIASRPGLGHFIDETEEKRID 145 (585)
T ss_pred CEEEECCCCCEEEECCHHHHHH
T ss_conf 5891048985798351799999
No 257
>PRK09775 hypothetical protein; Provisional
Probab=59.73 E-value=9.8 Score=18.28 Aligned_cols=55 Identities=24% Similarity=0.287 Sum_probs=30.5
Q ss_pred HHHCCCCCCCE------EECCCCCCCCCCCC-------------HHHHHHHHHHHCCCCCCCCCCCCCHHHHHH
Q ss_conf 86310015504------62056544533357-------------567777764210013543334641123455
Q gi|254780805|r 70 IKSHGIIQPLI------VRAIDNGLYKIIAG-------------ERRFRAAKMASLSEVPVIIRNVDNKSSLEI 124 (300)
Q Consensus 70 I~~~G~lqPi~------Vr~~~~g~y~ii~G-------------~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~ 124 (300)
+...|.+-|+. |....+|.+..-+| =-|..|...+....+|--+++++|++++..
T Consensus 74 a~~~g~L~pv~P~g~~~v~~~~d~~~~~~dgLPw~L~DMRPQGfLGR~~a~~~a~~L~Lp~d~~~W~ed~~L~A 147 (443)
T PRK09775 74 AHKFGQLYPLWPAGSCLVTLAEDGDWGWFDGLPWYLDDMRPQGFLGRAWGRRHAALLQLPEDIRLWQEDDVLYA 147 (443)
T ss_pred CCCCEEEEEEECCCCEEEEECCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHCCHHHHHHH
T ss_conf 20143689972598469972478853223899805551584204668999987886389997032787899999
No 258
>KOG3802 consensus
Probab=59.63 E-value=12 Score=17.80 Aligned_cols=42 Identities=31% Similarity=0.530 Sum_probs=28.3
Q ss_pred CCCHHHH-HHHHHHHHHHCCCCHHHHHHHHHH------HHHHHHHHHHH
Q ss_conf 2104899-999998521011104679999743------37877865656
Q gi|254780805|r 134 DLNPLEE-ALGYEQLISEYGYTQNDIGSIVGK------SRSHVANILRI 175 (300)
Q Consensus 134 dl~p~e~-A~~~~~l~~~~~~t~~~lA~~~G~------s~s~V~~~LrL 175 (300)
|+.-+|+ |..||+=.=.+|+||.+++..+|+ |+++|.|+=+|
T Consensus 204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEAL 252 (398)
T KOG3802 204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEAL 252 (398)
T ss_pred CHHHHHHHHHHHHHHEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf 9999999999987650003644267888987650764430266676762
No 259
>pfam05930 Phage_AlpA Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.
Probab=59.62 E-value=3 Score=21.56 Aligned_cols=30 Identities=17% Similarity=0.431 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565654358999
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILKLPSSVR 183 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~ 183 (300)
...++.+.+|.|+++|.++++--+.|.+++
T Consensus 5 r~~eV~~~~glsrstiyr~i~~G~FP~pik 34 (51)
T pfam05930 5 RLKEVEQLTGLSRSTIYRLIKDGEFPKPIK 34 (51)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCEE
T ss_conf 799999998989999999998799999876
No 260
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=59.50 E-value=9.6 Score=18.34 Aligned_cols=50 Identities=24% Similarity=0.302 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHH
Q ss_conf 104899999998521011104679999743378778656-----5654358999987
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL-----RILKLPSSVREMI 186 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L-----rLl~L~~~i~~~l 186 (300)
|||-.-. +--|.+.|+++..++|+.+++|.+.|.-.| ||-.++++..+.+
T Consensus 117 L~p~Q~v--IfLLkDVF~ys~~eiAe~~s~sEGaVKasLfRsR~RLK~~~ee~~~~~ 171 (228)
T PRK06704 117 LNVQQSA--ILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIV 171 (228)
T ss_pred CCHHHHH--HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCHHHCCCC
T ss_conf 5888899--999999987559999999556634999999999999873385312456
No 261
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=59.43 E-value=14 Score=17.38 Aligned_cols=38 Identities=16% Similarity=0.107 Sum_probs=25.0
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-|.-. + +++.+ |+|-.+||..++.|..||.++.+
T Consensus 141 ~LT~RE~eV-L-~ll~~-G~snkeIA~~L~iS~~TV~~h~~ 178 (202)
T PRK09390 141 SLSERERQV-M-DGLVA-GLSNKVIARDLDISPRTVEVYRA 178 (202)
T ss_pred CCCHHHHHH-H-HHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 699899999-9-99983-89689999997987889999999
No 262
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=59.30 E-value=10 Score=18.12 Aligned_cols=52 Identities=27% Similarity=0.283 Sum_probs=30.5
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHH-HHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 566654310221048999999985-21011104679999743378778656565
Q gi|254780805|r 124 IAIVENVQRKDLNPLEEALGYEQL-ISEYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 124 ~~l~EN~~R~dl~p~e~A~~~~~l-~~~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
..+.||..|-.+|-. -...|.-| +..--+|.+++++.+|.|++.||.-++=+
T Consensus 13 e~fae~m~r~G~nrt-VG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL 65 (177)
T COG1510 13 EHFAETMSRWGINRT-VGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKL 65 (177)
T ss_pred HHHHHHHHHHCCCCH-HHHHHHHHEECCCCCCHHHHHHHHCCCCCHHHHHHHHH
T ss_conf 999999998487642-77786540006999669999999777801288999999
No 263
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=59.24 E-value=11 Score=17.85 Aligned_cols=37 Identities=38% Similarity=0.479 Sum_probs=28.0
Q ss_pred CCCHHHH-HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2104899-9999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEE-ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~-A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-|. ...| ..+ |.|..|||..+|.|..||..+|+
T Consensus 171 ~LT~RE~E~L~w---~A~-Gkt~~eIa~iL~iSe~TV~~hl~ 208 (232)
T TIGR03541 171 VLSEREREVLAW---TAL-GRRQADIAAILGISERTVENHLR 208 (232)
T ss_pred CCCHHHHHHHHH---HHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 989899999999---987-99999999996989999999999
No 264
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=59.11 E-value=14 Score=17.34 Aligned_cols=43 Identities=14% Similarity=0.323 Sum_probs=29.7
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 521011104679999743378778656565435899998764210
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI 191 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i 191 (300)
|....|+|.+|||+.+|.|.++|..+|. ..=..++++|....+
T Consensus 122 L~~~egls~~EIA~iL~is~gTVKsRL~--RAr~kLr~~L~~~g~ 164 (181)
T PRK12540 122 LVGASGFSYEDAAAICGCAVGTIKSRVN--RARSKLSALLYVDGA 164 (181)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHCCC
T ss_conf 7998099999999998949999999999--999999999874655
No 265
>pfam04539 Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Probab=58.86 E-value=11 Score=18.06 Aligned_cols=39 Identities=26% Similarity=0.365 Sum_probs=29.2
Q ss_pred HHHHHHHHHHCCC--CHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999985210111--04679999743378778656565435
Q gi|254780805|r 141 ALGYEQLISEYGY--TQNDIGSIVGKSRSHVANILRILKLP 179 (300)
Q Consensus 141 A~~~~~l~~~~~~--t~~~lA~~~G~s~s~V~~~LrLl~L~ 179 (300)
.++.++|..++|- |.+|||..+|.|...|...+.+..-+
T Consensus 7 ~ka~~~L~q~lgR~Pt~eEiA~~l~~s~~~v~~~~~~~~~~ 47 (78)
T pfam04539 7 KRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREP 47 (78)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf 99999999998889999999999694999999999875898
No 266
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX. This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=58.53 E-value=4.6 Score=20.38 Aligned_cols=82 Identities=13% Similarity=0.282 Sum_probs=53.1
Q ss_pred CCCCEEEEHHHCCC-CCCCCC--CCCCHHHHHHHHHHHHHCCCCCCCEEECCCCC---------CCC------CCCCHHH
Q ss_conf 56602403898235-789998--76898899999998863100155046205654---------453------3357567
Q gi|254780805|r 36 PESQDCISIHSIVP-NPHNPR--NYFESEGLEDLCQSIKSHGIIQPLIVRAIDNG---------LYK------IIAGERR 97 (300)
Q Consensus 36 ~~~~~~i~i~~i~~-~p~~pR--~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g---------~y~------ii~G~rR 97 (300)
.+-...||-..+.. =.++|- +.|+-|+..++.+--++.|..|++++|-.+++ .|. +++-=.+
T Consensus 102 vGHLVQiP~~~v~~iv~~~PeviTVfS~ekA~eis~aA~~~g~~Q~illrV~~~~D~~Y~GQegGf~l~eL~~v~~~i~~ 181 (382)
T cd06811 102 VGHLVQIPRHQVPAVLAMRPEVITVYSLEKAREISDAAVELGRVQDVLLRVYGDEDTLYPGQEGGFPLEELPAVLAAIKA 181 (382)
T ss_pred CCCCCCCCHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCEEHHHHHHHHHHHHH
T ss_conf 15713685768999997499789992099999999999981973326999964898463775377548999999999972
Q ss_pred HHHHHHHHCCCCCCCCCCCC
Q ss_conf 77776421001354333464
Q gi|254780805|r 98 FRAAKMASLSEVPVIIRNVD 117 (300)
Q Consensus 98 ~rAa~~~g~~~ip~iv~~~~ 117 (300)
+-..+.+|+++-||+..|..
T Consensus 182 l~gi~i~GvT~FPc~L~d~~ 201 (382)
T cd06811 182 LPGIRIAGLTSFPCFLYDEE 201 (382)
T ss_pred CCCCEEEEEECEEEEEECCC
T ss_conf 89967966432006877477
No 267
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=58.43 E-value=14 Score=17.35 Aligned_cols=10 Identities=30% Similarity=0.365 Sum_probs=3.2
Q ss_pred HHHHHHHHHH
Q ss_conf 8999999988
Q gi|254780805|r 61 EGLEDLCQSI 70 (300)
Q Consensus 61 ~~l~eLa~SI 70 (300)
+..+.|.+.|
T Consensus 11 ~AY~~Lr~~I 20 (224)
T PRK11534 11 DGYRWLKNDI 20 (224)
T ss_pred HHHHHHHHHH
T ss_conf 9999999999
No 268
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=58.22 E-value=8.8 Score=18.60 Aligned_cols=31 Identities=26% Similarity=0.384 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHH
Q ss_conf 679999743378778656565-4358999987
Q gi|254780805|r 156 NDIGSIVGKSRSHVANILRIL-KLPSSVREMI 186 (300)
Q Consensus 156 ~~lA~~~G~s~s~V~~~LrLl-~L~~~i~~~l 186 (300)
.+||++.|.|.++|++.|.=- ..+++..+.|
T Consensus 1 ~diA~~~gvS~~TVSr~ln~~~~Vs~~tr~~I 32 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGKPRVSEETRERV 32 (52)
T ss_pred CHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHH
T ss_conf 92888878599999999879898999999999
No 269
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=57.72 E-value=15 Score=17.19 Aligned_cols=37 Identities=24% Similarity=0.214 Sum_probs=24.5
Q ss_pred HHHHHHHHHHCCC-------CHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999985210111-------046799997433787786565654
Q gi|254780805|r 141 ALGYEQLISEYGY-------TQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 141 A~~~~~l~~~~~~-------t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+..++..+....| +..+||+.+|.||-||.+.|.+|.
T Consensus 13 ~~~i~~~I~~G~~~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~ 56 (236)
T COG2188 13 AEDIRQRIESGELPPGDKLPSERELAEQFGVSRMTVRKALDELV 56 (236)
T ss_pred HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 99999999829999989595989999997988999999999999
No 270
>pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Probab=57.47 E-value=12 Score=17.68 Aligned_cols=33 Identities=24% Similarity=0.234 Sum_probs=23.7
Q ss_pred HHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99852101-1104679999743378778656565
Q gi|254780805|r 144 YEQLISEY-GYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 144 ~~~l~~~~-~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
+-.|.++. ..+..+||+++|.++++|++.++-|
T Consensus 11 Iy~l~~~~~~v~~~~iA~~L~Vs~~SVt~mlkkL 44 (58)
T pfam01325 11 IYTLSEEKGVVKTKDLAERLNVSPSTVSEMLKKL 44 (58)
T ss_pred HHHHHCCCCCEEHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 9998826996129999999599925299999999
No 271
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=57.44 E-value=13 Score=17.46 Aligned_cols=17 Identities=24% Similarity=0.315 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 79999743378778656
Q gi|254780805|r 157 DIGSIVGKSRSHVANIL 173 (300)
Q Consensus 157 ~lA~~~G~s~s~V~~~L 173 (300)
..|+++|.|++.||+.|
T Consensus 41 rAA~~L~vSQpAvS~aL 57 (314)
T PRK09508 41 RAAHNLGMSQPAVSNAV 57 (314)
T ss_pred HHHHHHCCCHHHHHHHH
T ss_conf 99999789866999999
No 272
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=57.35 E-value=7.2 Score=19.13 Aligned_cols=26 Identities=23% Similarity=0.377 Sum_probs=13.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf 23578999876898899999998863100
Q gi|254780805|r 47 IVPNPHNPRNYFESEGLEDLCQSIKSHGI 75 (300)
Q Consensus 47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~ 75 (300)
|.|+-.||. | .+-+..+.....++|.
T Consensus 67 vvp~~~n~~--~-~~l~~~i~~~~~~~gy 92 (330)
T PRK11303 67 IIPDLENTS--Y-ARIAKLLEQQARQRGY 92 (330)
T ss_pred ECCCCCCCH--H-HHHHHHHHHHHHHCCC
T ss_conf 545444315--6-7888999999996698
No 273
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=57.35 E-value=15 Score=17.15 Aligned_cols=38 Identities=18% Similarity=0.331 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 22104899999998521011104679999743378778656
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
+.|+|-|.- +-+++.+ |+|-.+||.+++.|..||+.+-
T Consensus 133 ~~Lt~rE~e--Vl~l~a~-G~s~~eIA~~L~~S~kTv~thr 170 (205)
T PRK11475 133 RMLSPTERE--ILRFMSR-GYSMPQIAEQLERNIKTIRAHK 170 (205)
T ss_pred CCCCHHHHH--HHHHHHC-CCCHHHHHHHHCCCHHHHHHHH
T ss_conf 889858999--9999976-9999999999788888999999
No 274
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=57.17 E-value=7.7 Score=18.98 Aligned_cols=19 Identities=16% Similarity=0.207 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHCCCCH
Q ss_conf 4899999998521011104
Q gi|254780805|r 137 PLEEALGYEQLISEYGYTQ 155 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~t~ 155 (300)
..++..+|++-+.++|+..
T Consensus 191 ~~~R~~G~~~al~~~gl~~ 209 (346)
T PRK10401 191 DAMRKAGWLSALKEQGIIP 209 (346)
T ss_pred HHHHHHHHHHHHHHCCCCC
T ss_conf 8999999999999849998
No 275
>PRK01905 DNA-binding protein Fis; Provisional
Probab=56.92 E-value=15 Score=17.11 Aligned_cols=42 Identities=21% Similarity=0.269 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1048999999985210111046799997433787786565654
Q gi|254780805|r 135 LNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+.-+|... +...++..+..|...|+.+|.+|.|.+..|+-..
T Consensus 34 l~evE~pL-i~~vl~~~~gNQ~kAA~~LGinR~TLRkKlk~yg 75 (77)
T PRK01905 34 LSCVEKPL-LEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQHG 75 (77)
T ss_pred HHHHHHHH-HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf 99989999-9999998459499999997865888999999808
No 276
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=56.73 E-value=7.7 Score=18.96 Aligned_cols=26 Identities=35% Similarity=0.533 Sum_probs=14.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf 23578999876898899999998863100
Q gi|254780805|r 47 IVPNPHNPRNYFESEGLEDLCQSIKSHGI 75 (300)
Q Consensus 47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~ 75 (300)
|.|+-.|| |-.+-+..+.....++|.
T Consensus 73 i~p~~~~~---~~~~~~~gi~~~~~~~gy 98 (341)
T PRK11041 73 IVPDICDP---FFSEIIRGIEVTAAEHGY 98 (341)
T ss_pred EECCCCCC---HHHHHHHHHHHHHHHCCC
T ss_conf 96776541---356766339999997699
No 277
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=56.71 E-value=7.7 Score=18.96 Aligned_cols=20 Identities=20% Similarity=0.381 Sum_probs=13.4
Q ss_pred CHHHHHHHHHHHHHHCCCCH
Q ss_conf 04899999998521011104
Q gi|254780805|r 136 NPLEEALGYEQLISEYGYTQ 155 (300)
Q Consensus 136 ~p~e~A~~~~~l~~~~~~t~ 155 (300)
+..++..+|.+-+.++|+..
T Consensus 190 ~~~~R~~g~~~al~~~gl~~ 209 (342)
T PRK10727 190 DAEDRLQGYYDALAESGIPA 209 (342)
T ss_pred HHHHHHHHHHHHHHHCCCCC
T ss_conf 59999999999999769999
No 278
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=56.50 E-value=15 Score=17.06 Aligned_cols=22 Identities=18% Similarity=0.238 Sum_probs=15.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
-|.+++|+.+|.+...|...+.
T Consensus 112 pt~~eia~~l~~s~e~v~~~~~ 133 (234)
T PRK06986 112 PTDTEVAEKLGLSLEEYREMLL 133 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9899999895949999999999
No 279
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=56.48 E-value=7.8 Score=18.94 Aligned_cols=26 Identities=15% Similarity=0.312 Sum_probs=15.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf 23578999876898899999998863100
Q gi|254780805|r 47 IVPNPHNPRNYFESEGLEDLCQSIKSHGI 75 (300)
Q Consensus 47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~ 75 (300)
|.|+..+| |-.+-+..+.....++|.
T Consensus 65 iv~~~~~~---~~~~~~~~i~~~~~~~gy 90 (335)
T PRK10703 65 LATSSEAP---YFAEIIEAVEKNCYQKGY 90 (335)
T ss_pred EECCCCCC---EEHHHHHHHHHHHHHCCC
T ss_conf 95478886---506543369999997399
No 280
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=56.29 E-value=15 Score=17.04 Aligned_cols=21 Identities=19% Similarity=0.297 Sum_probs=14.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|..+||+.+|.||.||.+.|.
T Consensus 37 sE~eLa~~y~VSR~TVR~Al~ 57 (243)
T PRK11402 37 TENELCTQYNVSRITIRKAIS 57 (243)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999997979999999999
No 281
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=56.19 E-value=9.8 Score=18.29 Aligned_cols=66 Identities=11% Similarity=0.102 Sum_probs=33.0
Q ss_pred HHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC-CEEECC--CCCCCCCCCCHHHHHHHHHHHCCCCCCCC
Q ss_conf 9823578999876898899999998863100155-046205--65445333575677777642100135433
Q gi|254780805|r 45 HSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQP-LIVRAI--DNGLYKIIAGERRFRAAKMASLSEVPVII 113 (300)
Q Consensus 45 ~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqP-i~Vr~~--~~g~y~ii~G~rR~rAa~~~g~~~ip~iv 113 (300)
+.+.--|. ....+++.+++|.......-.-.- +++++- .++-|.|+.|.=|..... -|-+.+-.++
T Consensus 7 e~L~~~pl--F~~Ls~~~l~~L~~~~~~~~~~~ge~lf~~Gd~~~~ly~i~~G~Vkv~~~~-~g~e~~l~~~ 75 (236)
T PRK09392 7 EALRNLPL--FADMADATFERLMRGAFLQRFPPGTTLITEGEPADFLFVVLDGLVELSASS-QDRETTLAIL 75 (236)
T ss_pred HHHHCCCC--CCCCCHHHHHHHHHCCEEEEECCCCEEECCCCCCCEEEEEEEEEEEEEECC-CCCCEEEEEE
T ss_conf 99846931--038999999999842879998999999899998665899963589998707-8884999998
No 282
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=55.90 E-value=16 Score=17.00 Aligned_cols=39 Identities=13% Similarity=0.077 Sum_probs=25.8
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 52101110467999974337877865656543589999876
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIR 187 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~ 187 (300)
|..-.|++.+|||+.+|.|.++|..+|. ..=..+++.|.
T Consensus 160 Lr~~eglS~~EIAe~Lgis~~tVks~L~--RAR~~Lr~~Le 198 (207)
T PRK12544 160 MREFIELETPEICHNEDLTVSNLNVMLY--RSRLRLRECLE 198 (207)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHH
T ss_conf 9998199999999997979999999999--99999999999
No 283
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=55.34 E-value=15 Score=17.14 Aligned_cols=64 Identities=11% Similarity=0.228 Sum_probs=40.7
Q ss_pred HHHHHHH--HCCCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHH
Q ss_conf 5666543--1022104899999998521---011104679999743378778656565435--89999876
Q gi|254780805|r 124 IAIVENV--QRKDLNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRILKLP--SSVREMIR 187 (300)
Q Consensus 124 ~~l~EN~--~R~dl~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~--~~i~~~l~ 187 (300)
+.+++.| ..++|+|.|+..+=.-|-. ...+|-.+||+..|.|.++|.|.-+=+-.. ++.+..+.
T Consensus 14 ~~l~~~Ir~~~~~Lt~sEk~IA~yIL~~~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~ 84 (293)
T PRK11337 14 IGLAPYIRMKQEGMTENESRVVDWLLKPGNLSCATALKDVAEALAVSEAMIVKVAKLLGFSGFRNLRSALE 84 (293)
T ss_pred CCHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 78999999977644999999999998298999766699999895998889999999957897899999999
No 284
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes and Bacillus cereus (strain ATCC 14579 / DSM 31) ..
Probab=55.14 E-value=10 Score=18.19 Aligned_cols=22 Identities=27% Similarity=0.493 Sum_probs=10.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 1104679999743378778656
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~L 173 (300)
+++|.+-+++||.|+=||||.-
T Consensus 222 nlsQKeTGErlGiSQMHVSRl~ 243 (256)
T TIGR02941 222 NLSQKETGERLGISQMHVSRLQ 243 (256)
T ss_pred CCCCCHHHHHCCHHHHHHHHHH
T ss_conf 7873002322240355677888
No 285
>TIGR02478 6PF1K_euk 6-phosphofructokinase; InterPro: IPR009161 Members of this family are eukaryotic (with one exception) ATP-dependent 6-phosphofructokinases (2.7.1.11 from EC) in which two tandem copies of the phosphofructokinase are found . Members are found, often including several isozymes, in animals and fungi and in the bacterium Propionibacterium acnes KPA171202 (a human skin commensal). Phosphofructokinase (PFK) catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate, which then enters the Embden-Meyerhof pathway. PFK is a key regulatory enzyme in glycolysis. For additional information please see , , .; GO: 0003872 6-phosphofructokinase activity, 0006096 glycolysis, 0005737 cytoplasm.
Probab=54.90 E-value=6.8 Score=19.32 Aligned_cols=79 Identities=23% Similarity=0.375 Sum_probs=45.0
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCH----------HHHHHHHHHH-HHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHH-
Q ss_conf 677777642100135433346411----------2345566654-3102210489999999852101110467999974-
Q gi|254780805|r 96 RRFRAAKMASLSEVPVIIRNVDNK----------SSLEIAIVEN-VQRKDLNPLEEALGYEQLISEYGYTQNDIGSIVG- 163 (300)
Q Consensus 96 rR~rAa~~~g~~~ip~iv~~~~d~----------~~~~~~l~EN-~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G- 163 (300)
=||.|+ +.|.+-|.+|..-.+|. -+..+++-|| ++|. |+-+|..-.+-+.+ .+.+.+-++.+.
T Consensus 295 DR~Lat-~~GvEAV~avL~~tpe~~GavvtGqk~ps~VI~l~gNkI~R~---PL~~~V~~T~~V~~-~i~~~~f~~A~~L 369 (777)
T TIGR02478 295 DRILAT-LQGVEAVLAVLESTPETEGAVVTGQKTPSPVISLRGNKIVRK---PLVEAVRQTKTVAK-AIKERRFDEAVRL 369 (777)
T ss_pred HHHHHH-HHHHHHHHHHHCCCCCCCCCEEECCCCCCEEEEECCCEEEEC---HHHHHHHHHHHHHH-HHHCCCCHHHHHC
T ss_conf 999998-644999999972687768747615435551475068702213---18899998999899-8731775458723
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 3378778656565435
Q gi|254780805|r 164 KSRSHVANILRILKLP 179 (300)
Q Consensus 164 ~s~s~V~~~LrLl~L~ 179 (300)
+.++++.++--++.++
T Consensus 370 Rg~eF~~~~~~~~~~s 385 (777)
T TIGR02478 370 RGREFVENLATFLELS 385 (777)
T ss_pred CCHHHHHHHHHHHHHC
T ss_conf 5723577544477620
No 286
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=54.17 E-value=14 Score=17.20 Aligned_cols=22 Identities=9% Similarity=0.235 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 4679999743378778656565
Q gi|254780805|r 155 QNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 155 ~~~lA~~~G~s~s~V~~~LrLl 176 (300)
...|++.+|.+...|...+.+.
T Consensus 232 ~~~i~k~l~~~~~~l~~a~~~I 253 (475)
T PRK12469 232 TAEIQRRIGCDQETLREACALV 253 (475)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999999594999999999999
No 287
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=54.13 E-value=17 Score=16.82 Aligned_cols=24 Identities=4% Similarity=-0.011 Sum_probs=13.6
Q ss_pred CCHHHHHHHHHHHHHHCCEEEEEC
Q ss_conf 897899999999997398799971
Q gi|254780805|r 246 KEKYLTDLEKKISSKVGLNISIKH 269 (300)
Q Consensus 246 k~~~i~~le~~L~~~lGtkV~I~~ 269 (300)
...|+.+..+.|-+.++....|+.
T Consensus 214 M~~HLensr~~L~~~~~~~~~~~~ 237 (258)
T PRK11523 214 MWQHLENTKIMLFNETSDDFEFNA 237 (258)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 999999999999886188767554
No 288
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=53.59 E-value=16 Score=16.97 Aligned_cols=59 Identities=17% Similarity=0.257 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHC-CHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 67999974337877865656543589999876421016777776401-0046899997422247789999997
Q gi|254780805|r 156 NDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVST-SDPLSLAQVIVSKKMSVRDTEELVQ 227 (300)
Q Consensus 156 ~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~-~~~~~la~~Ii~~~LSVRe~E~lVk 227 (300)
.+||+.+|.|+++|+..++ .+-..|-|...+.+. +.+ +...++|+.|+... |-.|.+..
T Consensus 3 ~diA~~L~vs~~sVs~~l~---------~L~~~Gli~~~~y~~-i~LT~~G~~~A~~i~~rH---r~le~fL~ 62 (96)
T smart00529 3 SEIAERLNVSPPTVTQMLK---------KLEKDGLVEYEPYRG-ITLTEKGRRLARRLLRKH---RLLERFLV 62 (96)
T ss_pred HHHHHHHCCCCHHHHHHHH---------HHHHCCCEEECCCCC-EEECHHHHHHHHHHHHHH---HHHHHHHH
T ss_conf 8899884999167999999---------999888988749989-788987999999999999---99999999
No 289
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=53.06 E-value=10 Score=18.24 Aligned_cols=38 Identities=8% Similarity=0.189 Sum_probs=25.8
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0111046799997433787786565654358999987642
Q gi|254780805|r 150 EYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKE 189 (300)
Q Consensus 150 ~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~ 189 (300)
-.|+|..|||+.+|.|.++|..+|. ..=..+.+++...
T Consensus 125 ~egls~~EIAe~Lgis~gTVKsrl~--RAr~~LR~~le~~ 162 (182)
T PRK12511 125 IEGLSYQEAANVLGIPIGTLMSRIG--RARAALRAFEEGT 162 (182)
T ss_pred ECCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHC
T ss_conf 0799999999998939999999999--9999999986312
No 290
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=52.81 E-value=17 Score=16.68 Aligned_cols=49 Identities=12% Similarity=0.255 Sum_probs=28.5
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHH---CC------CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6654310221048999999985210---11------1046799997433787786565
Q gi|254780805|r 126 IVENVQRKDLNPLEEALGYEQLISE---YG------YTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 126 l~EN~~R~dl~p~e~A~~~~~l~~~---~~------~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|+.|++...-|-+.-|..+-+.... +| ++..++|..+|.+.|||++..+
T Consensus 295 LiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 295 LIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999999999999999999999983785457763199999883712888999982
No 291
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=52.61 E-value=18 Score=16.66 Aligned_cols=43 Identities=12% Similarity=0.266 Sum_probs=30.0
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 521011104679999743378778656565435899998764210
Q gi|254780805|r 147 LISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI 191 (300)
Q Consensus 147 l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i 191 (300)
|.+-.|++.+|||+.+|.|.++|..+| -..=..+++.|.+..+
T Consensus 150 Lr~~egls~~EIA~~L~is~~tVksrL--~RAR~~LR~~L~ek~~ 192 (201)
T PRK12545 150 MREFLDFEIDDICTELTLTANHCSVLL--YRARTRLRTCLSEKGL 192 (201)
T ss_pred HHHHHCCCHHHHHHHHCCCHHHHHHHH--HHHHHHHHHHHHHCCC
T ss_conf 999928989999999896999999999--9999999999998187
No 292
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=51.56 E-value=18 Score=16.61 Aligned_cols=30 Identities=17% Similarity=0.292 Sum_probs=22.8
Q ss_pred HHHH-CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5210-11104679999743378778656565
Q gi|254780805|r 147 LISE-YGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 147 l~~~-~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
++.+ ...+..++|+.||.|..||.+-|.-|
T Consensus 8 ~l~~~~~~~i~~La~~~~VS~~TiRRDl~~L 38 (53)
T smart00420 8 LLAQQGKVSVEELAELLGVSEMTIRRDLNKL 38 (53)
T ss_pred HHHHCCCEEHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9998697979999999897999999969999
No 293
>pfam10654 DUF2481 Protein of unknown function (DUF2481). This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems.
Probab=51.16 E-value=18 Score=16.52 Aligned_cols=24 Identities=33% Similarity=0.261 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
-|+|...||+.++.|+|+|-|+-+
T Consensus 79 AGlt~~aIAD~F~iS~s~~~nft~ 102 (126)
T pfam10654 79 AGLTGYAIADHFKVSKSVVFNFTR 102 (126)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 588607999997477999999999
No 294
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=51.12 E-value=11 Score=18.06 Aligned_cols=21 Identities=24% Similarity=0.445 Sum_probs=18.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 104679999743378778656
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~L 173 (300)
-||.++|..+|.|+|+|++.=
T Consensus 199 ~tqk~vad~lGisqsyisrle 219 (234)
T TIGR02835 199 KTQKEVADLLGISQSYISRLE 219 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
T ss_conf 467888988624689999999
No 295
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=51.04 E-value=19 Score=16.51 Aligned_cols=24 Identities=13% Similarity=0.173 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 111046799997433787786565
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|..|||+.+|.|.+||..+|.
T Consensus 156 e~~s~~EIAe~l~is~~TVKsrl~ 179 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLR 179 (194)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 699999999998929999999999
No 296
>PRK04841 transcriptional regulator MalT; Provisional
Probab=50.91 E-value=19 Score=16.49 Aligned_cols=13 Identities=15% Similarity=0.304 Sum_probs=8.0
Q ss_pred HHHHHHHHHHCCC
Q ss_conf 9999999983756
Q gi|254780805|r 284 EQLKIICSLLGEN 296 (300)
Q Consensus 284 eeLe~Il~kL~~~ 296 (300)
-.+.+|+.||+-.
T Consensus 872 ~HlrnIy~KLgV~ 884 (903)
T PRK04841 872 THIRNLYQKLGIA 884 (903)
T ss_pred HHHHHHHHHCCCC
T ss_conf 9999998565999
No 297
>pfam04492 Phage_rep_O Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction.
Probab=50.78 E-value=19 Score=16.48 Aligned_cols=60 Identities=25% Similarity=0.423 Sum_probs=38.8
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 566654310221048999999985210111-------046799997433787786565654358999987642101
Q gi|254780805|r 124 IAIVENVQRKDLNPLEEALGYEQLISEYGY-------TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEIS 192 (300)
Q Consensus 124 ~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~-------t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is 192 (300)
-.|.+.+-+.+|+.-+--..+.-....||| +..++|+..|.++.+|++.+ .+++..+-|.
T Consensus 19 NeLldal~~~~lt~rq~kv~~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs~a~---------~~Li~~~vi~ 85 (100)
T pfam04492 19 NEILEALCRADLSGRQLKVLLAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVSEAK---------KSLVKRGIII 85 (100)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHH---------HHHHHCCCCH
T ss_conf 999999980888788999999999986077850336229999999788854599999---------9999768644
No 298
>TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245 This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm.
Probab=50.70 E-value=19 Score=16.47 Aligned_cols=73 Identities=23% Similarity=0.439 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHCCC----CCCCEEE-----CCCCCCCCCCC--------CHHHHHH--------HHHHHCCC-CCCCCCC
Q ss_conf 99999998863100----1550462-----05654453335--------7567777--------76421001-3543334
Q gi|254780805|r 62 GLEDLCQSIKSHGI----IQPLIVR-----AIDNGLYKIIA--------GERRFRA--------AKMASLSE-VPVIIRN 115 (300)
Q Consensus 62 ~l~eLa~SI~~~G~----lqPi~Vr-----~~~~g~y~ii~--------G~rR~rA--------a~~~g~~~-ip~iv~~ 115 (300)
+-+-+.+-++++|. ++.++.| |.+.|.|.+-. |.|=-+| ...|.-.. ||++|.|
T Consensus 48 R~~~i~~~L~e~Gi~~~~l~AvVgRGGLLkPi~GGTY~Vn~~MleDLk~~~~GeHASNLGaIIA~~lA~~~~diPafIVD 127 (353)
T TIGR02707 48 RKQVILEVLEEKGINISKLDAVVGRGGLLKPIEGGTYLVNEKMLEDLKEGKRGEHASNLGAIIARELADELNDIPAFIVD 127 (353)
T ss_pred HHHHHHHHHHHCCCCHHHEEEEEECCCCCCCCCCCEEEECHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEC
T ss_conf 99999999874088712431579727702333896047765568888510588784336899999987651894358826
Q ss_pred ---CCC-HHHHHHHHHHHHHCCC
Q ss_conf ---641-1234556665431022
Q gi|254780805|r 116 ---VDN-KSSLEIAIVENVQRKD 134 (300)
Q Consensus 116 ---~~d-~~~~~~~l~EN~~R~d 134 (300)
+|+ ++.++++=.-+++|..
T Consensus 128 PVVVDEledvARISG~P~i~RkS 150 (353)
T TIGR02707 128 PVVVDELEDVARISGLPEIERKS 150 (353)
T ss_pred CCEECCCCCHHHHCCCCCCCCEE
T ss_conf 83350551013213889864110
No 299
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=50.10 E-value=17 Score=16.75 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=27.9
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999985210111046799997433787786565
Q gi|254780805|r 141 ALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 141 A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
+..++.+.++.|+|...+|..+|.||.+|+.|=+
T Consensus 127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~ 160 (313)
T COG1395 127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEK 160 (313)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 2999999998086787889883846888987624
No 300
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794 Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=50.06 E-value=16 Score=16.93 Aligned_cols=22 Identities=23% Similarity=0.363 Sum_probs=19.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 1104679999743378778656
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~L 173 (300)
.+|-.|+|++.|.+|+++.+.|
T Consensus 24 ~ltl~~vA~~TGL~RAaARR~L 45 (252)
T TIGR02431 24 RLTLTDVAEATGLTRAAARRFL 45 (252)
T ss_pred CCCHHHHHHHHCCCCHHHHHHH
T ss_conf 9898999987589947988899
No 301
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=50.05 E-value=11 Score=17.93 Aligned_cols=106 Identities=23% Similarity=0.305 Sum_probs=49.1
Q ss_pred HHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEC----------------CCCCCCCCCCC--HHHHHHHHHHH
Q ss_conf 8982357899987689889999999886310015504620----------------56544533357--56777776421
Q gi|254780805|r 44 IHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRA----------------IDNGLYKIIAG--ERRFRAAKMAS 105 (300)
Q Consensus 44 i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~----------------~~~g~y~ii~G--~rR~rAa~~~g 105 (300)
|..|.|+-.|| |-.+-+..+.....++|..-=+.... .-|| .|+.| ..... ...+.
T Consensus 61 Ig~i~p~~~~~---~~~~i~~gi~~~~~~~gy~~~l~~~~~~~~~e~~~~~~l~~~~vdG--iIi~~~~~~~~~-~~~l~ 134 (333)
T COG1609 61 IGLVVPDITNP---FFAEILKGIEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRVDG--LILLGERPNDSL-LELLA 134 (333)
T ss_pred EEEEECCCCCH---HHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCE--EEEECCCCCHHH-HHHHH
T ss_conf 99994687775---8999999999999983998999837898699999999998769898--999358788088-99998
Q ss_pred CCCCCCCCCCC------------CCHHHH---HHHHHHHHHC---------CCCCHHHHHHHHHHHHHHCCCCH
Q ss_conf 00135433346------------411234---5566654310---------22104899999998521011104
Q gi|254780805|r 106 LSEVPVIIRNV------------DNKSSL---EIAIVENVQR---------KDLNPLEEALGYEQLISEYGYTQ 155 (300)
Q Consensus 106 ~~~ip~iv~~~------------~d~~~~---~~~l~EN~~R---------~dl~p~e~A~~~~~l~~~~~~t~ 155 (300)
...+|+|+.+. |+..+. .-.|++.-+| ...+..++..+|.+-+.++|+..
T Consensus 135 ~~~~P~V~i~~~~~~~~~~~V~~Dn~~~~~~a~~~L~~~G~~~i~~i~~~~~~~~~~~R~~Gf~~al~~~~~~~ 208 (333)
T COG1609 135 AAGIPVVVIDRSPPGLGVPSVGIDNFAGAYLATEHLIELGHRRIAFIGGPLDSSASRERLEGYRAALREAGLPI 208 (333)
T ss_pred HCCCCEEEEECCCCCCCCCEEECCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 65999899937677778977970989999999999998799859999679877218999999999999759997
No 302
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=50.01 E-value=19 Score=16.40 Aligned_cols=28 Identities=7% Similarity=0.235 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHCCCCCCCEEECCCCCCCCCC
Q ss_conf 89999999886310015504620565445333
Q gi|254780805|r 61 EGLEDLCQSIKSHGIIQPLIVRAIDNGLYKII 92 (300)
Q Consensus 61 ~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii 92 (300)
..+.|=-..+...|++.+ ..+.|.|..-
T Consensus 49 ~~vREAl~~L~a~Glve~----r~G~Gt~V~~ 76 (241)
T COG2186 49 TVVREALKRLEAKGLVEI----RQGSGTFVRP 76 (241)
T ss_pred HHHHHHHHHHHHCCCEEC----CCCCCEEECC
T ss_conf 689999999998788630----5899827647
No 303
>COG4804 Predicted nuclease of restriction endonuclease-like fold [General function prediction only]
Probab=50.00 E-value=14 Score=17.20 Aligned_cols=34 Identities=24% Similarity=0.304 Sum_probs=20.1
Q ss_pred HHHHHHHCCH---HHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 7777640100---468999974222477899999976
Q gi|254780805|r 195 HARTLVSTSD---PLSLAQVIVSKKMSVRDTEELVQE 228 (300)
Q Consensus 195 har~Ll~~~~---~~~la~~Ii~~~LSVRe~E~lVk~ 228 (300)
|.+.++++++ ....+...+..+||||+.+..+..
T Consensus 3 h~~~l~s~kn~~~r~~Y~~~~~r~rws~r~l~~~I~s 39 (159)
T COG4804 3 HYKLLLSVKNLDKRLFYEIETLRNRWSVRQLERQIAS 39 (159)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf 5102100258356778999999831019999999999
No 304
>pfam09048 Cro Cro. Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands.
Probab=49.22 E-value=15 Score=17.09 Aligned_cols=28 Identities=25% Similarity=0.402 Sum_probs=21.6
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 852101110467999974337877865656
Q gi|254780805|r 146 QLISEYGYTQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~LrL 175 (300)
...+++| |...|+.+|..++.|+..||-
T Consensus 7 dyv~~~G--Q~kaA~~lGV~Q~AISKAlra 34 (58)
T pfam09048 7 DYVEEHG--QAKAAKDLGVNQSAISKALRA 34 (58)
T ss_pred HHHHHHC--HHHHHHHCCCCHHHHHHHHHC
T ss_conf 9999976--598999829758999999964
No 305
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives..
Probab=49.08 E-value=13 Score=17.56 Aligned_cols=22 Identities=18% Similarity=0.376 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 1104679999743378778656
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~L 173 (300)
++|.+|+|..+|.|.+||.-++
T Consensus 129 DlSe~~~A~~LG~SvGTVKS~~ 150 (165)
T TIGR02983 129 DLSEAEVAEVLGISVGTVKSRL 150 (165)
T ss_pred CCCHHHHHHHHCCCCHHHHHHH
T ss_conf 8986899988199932289989
No 306
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=48.87 E-value=20 Score=16.29 Aligned_cols=35 Identities=11% Similarity=0.286 Sum_probs=19.4
Q ss_pred CHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHH
Q ss_conf 988999999988631001550462056544533357567
Q gi|254780805|r 59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERR 97 (300)
Q Consensus 59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR 97 (300)
+-..+.|=-..+...|+++. ++ +.|.|..-.....
T Consensus 46 SRt~VREAL~~Le~~GLV~~---r~-G~Gt~V~~~~~~~ 80 (257)
T PRK10225 46 TRTVVREALIMLEIKGLVEV---RR-GAGIYVLDSSGSH 80 (257)
T ss_pred CHHHHHHHHHHHHHCCCEEE---EE-CCEEEEECCCHHH
T ss_conf 87899999999998899799---64-8877882687042
No 307
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=48.30 E-value=20 Score=16.23 Aligned_cols=68 Identities=21% Similarity=0.236 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 104679999743378778656565435899998764210167777764010046899997422247789999997
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEELVQ 227 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~lVk 227 (300)
+|-.|+|+.+|.+.++|.-+-+.--++|.....=.-...+..|.. ........-+.++|+.++-+++.
T Consensus 1 ytI~e~a~~~gvs~~tlR~ye~~Gll~p~~r~~~g~R~Y~~~di~-------~l~~I~~lr~~G~~l~~Ik~~l~ 68 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLE-------RLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHH-------HHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 978899999896999999999858989984489997443999999-------99999999997899999999996
No 308
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=48.07 E-value=21 Score=16.21 Aligned_cols=34 Identities=26% Similarity=0.447 Sum_probs=23.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHH------HHHHHHHHHH
Q ss_conf 999998521011104679999743------3787786565
Q gi|254780805|r 141 ALGYEQLISEYGYTQNDIGSIVGK------SRSHVANILR 174 (300)
Q Consensus 141 A~~~~~l~~~~~~t~~~lA~~~G~------s~s~V~~~Lr 174 (300)
|..|+.-.=..|+||.+++..+|. |+++|++.=+
T Consensus 13 a~~fk~rRi~LG~TQ~dVG~aL~~l~g~~~SQttIcRFE~ 52 (75)
T smart00352 13 AKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 9999998987377599999999986186431468889886
No 309
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=47.97 E-value=21 Score=16.20 Aligned_cols=25 Identities=20% Similarity=0.270 Sum_probs=13.7
Q ss_pred CCCHHHHHHHHHH--HHHHHHHHHHHH
Q ss_conf 1104679999743--378778656565
Q gi|254780805|r 152 GYTQNDIGSIVGK--SRSHVANILRIL 176 (300)
Q Consensus 152 ~~t~~~lA~~~G~--s~s~V~~~LrLl 176 (300)
|-|..++|+.+.. +-..|+|-|.+.
T Consensus 115 GTT~~~la~~L~~~~~ltVvTNsl~ia 141 (269)
T PRK09802 115 GTTTFEIARLMRKHTDVIAMTNGMNVA 141 (269)
T ss_pred CHHHHHHHHHHHCCCCEEEEECCHHHH
T ss_conf 679999997323269859997879999
No 310
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=47.81 E-value=16 Score=16.84 Aligned_cols=24 Identities=25% Similarity=0.540 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 104679999743378778656565
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
+|..+||+.+|.++.+|++.|.-+
T Consensus 3 msrqdIadylGlt~ETVsR~l~~L 26 (32)
T pfam00325 3 MSRQEIADYLGLTRETVSRLLKRL 26 (32)
T ss_pred CCHHHHHHHHCCHHHHHHHHHHHH
T ss_conf 658899998472599999999999
No 311
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=47.75 E-value=21 Score=16.18 Aligned_cols=29 Identities=28% Similarity=0.591 Sum_probs=24.1
Q ss_pred CCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf 35789998-768988999999988631001
Q gi|254780805|r 48 VPNPHNPR-NYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 48 ~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l 76 (300)
.-||+||- ..|+.+.++++++=.++|+++
T Consensus 287 InNPNNPTGAVyS~E~LeeIaeiArehdLi 316 (518)
T PRK13355 287 IINPNNPTGALYPKEVLQQIVDIAREHQLI 316 (518)
T ss_pred EECCCCCCCCCCCHHHHHHHHHHHHHCCEE
T ss_conf 968989888788999999999999985969
No 312
>PRK08960 hypothetical protein; Provisional
Probab=47.72 E-value=20 Score=16.33 Aligned_cols=30 Identities=30% Similarity=0.545 Sum_probs=17.4
Q ss_pred CCCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf 235789998-768988999999988631001
Q gi|254780805|r 47 IVPNPHNPR-NYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 47 i~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l 76 (300)
+..||+||- ..++.+.+++|++-.++||++
T Consensus 170 il~nP~NPTG~v~s~~~l~~l~~~a~~~~~~ 200 (387)
T PRK08960 170 LVASPANPTGTLLSRDELAALSQALKARGGH 200 (387)
T ss_pred EECCCCCCCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf 9768989886314689999999987623977
No 313
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=47.69 E-value=21 Score=16.17 Aligned_cols=34 Identities=12% Similarity=0.154 Sum_probs=25.6
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9985210111046799997433787786565654
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+...++..+.-|...|+.+|.+|.++.+.|+-..
T Consensus 63 l~~vL~~t~gNqskAA~~LGInR~TLRkKlk~yg 96 (98)
T PRK00430 63 LDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYG 96 (98)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf 9999999669599999997877889999999848
No 314
>PRK10079 putative transcriptional regulator; Provisional
Probab=47.59 E-value=15 Score=17.02 Aligned_cols=20 Identities=5% Similarity=0.204 Sum_probs=9.2
Q ss_pred CHHHHHHHHHHHHHHHHHHH
Q ss_conf 04679999743378778656
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~L 173 (300)
|..+||+.+|.||.||.+.|
T Consensus 37 sE~eLa~~y~VSR~TVR~Al 56 (241)
T PRK10079 37 AEQQLAARFEVNRHTLRRAI 56 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999798899999999
No 315
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=47.54 E-value=21 Score=16.16 Aligned_cols=38 Identities=34% Similarity=0.591 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|+|-|... .++... |.+..++|..+|.|..+|..+++
T Consensus 4 ~Lt~rE~~~--~~l~~~-G~s~~eia~~l~is~~tV~~h~~ 41 (65)
T COG2771 4 DLTPREREI--LRLVAQ-GKSNKEIARILGISEETVKTHLR 41 (65)
T ss_pred CCCHHHHHH--HHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 138889999--999986-99899999998779999999999
No 316
>pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene.
Probab=47.54 E-value=21 Score=16.16 Aligned_cols=86 Identities=15% Similarity=0.166 Sum_probs=47.8
Q ss_pred HCCCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHCCHHH-H-HHHHHCC
Q ss_conf 1022104899999998521---011104679999743378778656565435--8999987642101677-7-7764010
Q gi|254780805|r 131 QRKDLNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRILKLP--SSVREMIRKEEISLGH-A-RTLVSTS 203 (300)
Q Consensus 131 ~R~dl~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~--~~i~~~l~~~~is~gh-a-r~Ll~~~ 203 (300)
+.+.|+|.|+..+=.-+-. -..+|..++|++.|.|.++|.|.-+-+... ++.+-.|....-.... . +.+-.-+
T Consensus 10 ~~~~lt~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kklG~~Gf~efk~~La~~~~~~~~~~~~~I~~~D 89 (106)
T pfam01418 10 LYSKLTKSEKKIADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRKLGFSGFSDLKVALAGELAQSESILHSEIAPDD 89 (106)
T ss_pred HHHHCCHHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf 89764999999999999299999883399999896998999999999958998999999999986536664447789999
Q ss_pred HHHHHHHHHHHCC
Q ss_conf 0468999974222
Q gi|254780805|r 204 DPLSLAQVIVSKK 216 (300)
Q Consensus 204 ~~~~la~~Ii~~~ 216 (300)
+...+.+++....
T Consensus 90 s~~~i~~Kv~~~~ 102 (106)
T pfam01418 90 DLEAIANKLFTNT 102 (106)
T ss_pred CHHHHHHHHHHHH
T ss_conf 9999999999998
No 317
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=47.46 E-value=12 Score=17.72 Aligned_cols=27 Identities=26% Similarity=0.349 Sum_probs=16.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf 235789998768988999999988631001
Q gi|254780805|r 47 IVPNPHNPRNYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 47 i~~~p~~pR~~~~~~~l~eLa~SI~~~G~l 76 (300)
|.|+..|| |-.+-+..+.....++|..
T Consensus 62 iv~~~~~~---f~~~i~~~i~~~~~~~gy~ 88 (327)
T PRK10423 62 LITASTNP---FYSELVRGVERSCFERGYS 88 (327)
T ss_pred EECCCCCC---HHHHHHHHHHHHHHHCCCE
T ss_conf 97366551---2678899999999985998
No 318
>PRK07324 transaminase; Validated
Probab=47.15 E-value=21 Score=16.20 Aligned_cols=45 Identities=18% Similarity=0.191 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHCCEEEEECC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 8999999999973987999717--98228999858-9899999999837
Q gi|254780805|r 249 YLTDLEKKISSKVGLNISIKHR--NNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 249 ~i~~le~~L~~~lGtkV~I~~~--~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
+-.++-.+|-+.-|.-|. -.. +..|-+.|.|. +.++|+.=+++|.
T Consensus 318 ~~~~~~~~ll~~~gV~v~-PG~~F~~~g~~Ri~fa~~~~~l~egl~RL~ 365 (373)
T PRK07324 318 DSEEFCEKLLKETGVLLV-PGNRFDLEGHVRIGYCCDTKTLKKGLKKLS 365 (373)
T ss_pred CHHHHHHHHHHHCCEEEE-CCCCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf 999999999996899997-488658999499998198999999999999
No 319
>PRK06348 aspartate aminotransferase; Provisional
Probab=46.61 E-value=21 Score=16.19 Aligned_cols=43 Identities=7% Similarity=0.132 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHCCEEEEE-----CCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 999999999739879997-----1798228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK-----HRNNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++...|-+.-| |-+. ...+.|-|.|.|. +.++|+.-+++|++
T Consensus 333 ~~~~~~ll~~~g--V~v~PG~~Fg~~g~~~iRls~~~~~~~l~ea~~Rl~k 381 (383)
T PRK06348 333 VEFCEYLLKEAH--VLVIPGKAFGKSGEGYIRLACTVGLEELEEAFNRIEK 381 (383)
T ss_pred HHHHHHHHHHCC--EEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 999999998689--9997854548899997999984899999999999974
No 320
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.51 E-value=14 Score=17.34 Aligned_cols=23 Identities=30% Similarity=0.327 Sum_probs=19.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 04679999743378778656565
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
....+|+.+|.||++|.+||+=.
T Consensus 193 Ai~~VA~~L~iSr~TVY~YL~~~ 215 (220)
T COG2964 193 AINIVADRLGISRHTVYRYLRKF 215 (220)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 89999999688758999999986
No 321
>PRK07683 aminotransferase A; Validated
Probab=46.15 E-value=22 Score=16.02 Aligned_cols=43 Identities=21% Similarity=0.243 Sum_probs=22.3
Q ss_pred HHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 9999999973987999---71798228999858-9899999999837
Q gi|254780805|r 252 DLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 252 ~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
++...|-+..|.-|.= ....+.|-+.|.|. +.++++.=+++|.
T Consensus 332 ~~~~~ll~~~gV~v~PG~~Fg~~g~g~~Rlsfa~~~e~l~eal~Rl~ 378 (387)
T PRK07683 332 DFALDLVEEAGLAVVPGSAFSEYGEGYVRLSYAYSIETLKEGLDRLE 378 (387)
T ss_pred HHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf 99999998399999878422889988699997199999999999999
No 322
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=46.11 E-value=22 Score=16.02 Aligned_cols=43 Identities=9% Similarity=0.064 Sum_probs=31.5
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 22104899999998521011104679999743378778656565
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
...++=....+.+..++ -|.+..++|+.+|.+.+++.+-.+..
T Consensus 5 rrys~efK~~~V~~~~~-~g~sv~~var~~gi~~~~l~~W~k~~ 47 (75)
T pfam01527 5 RRYSEEFKARAVKESLE-PGASVSELAREHGVSPATLYKWRKKY 47 (75)
T ss_pred CCCCHHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 88999999999999980-99849999999895999999999998
No 323
>PRK13980 NAD synthetase; Provisional
Probab=45.70 E-value=22 Score=15.98 Aligned_cols=83 Identities=20% Similarity=0.249 Sum_probs=40.6
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH-HHHHHC--CHHHHHHHHH
Q ss_conf 0489999999852101110467999974337877865656543589999876421016777-776401--0046899997
Q gi|254780805|r 136 NPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHA-RTLVST--SDPLSLAQVI 212 (300)
Q Consensus 136 ~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~gha-r~Ll~~--~~~~~la~~I 212 (300)
|-.|.+.+|-.+-.+ .--.++-.-+..++.|..+-+.+..|+.|.+.--+-.+-.||- .-=+|. +..+.+....
T Consensus 138 NksE~~~Gy~TkyGD---~~~d~~Pi~dL~Kt~V~~La~~l~vP~~Ii~k~PSa~L~~~Q~DE~~LG~~Y~~lD~iL~~~ 214 (264)
T PRK13980 138 NKSELLLGYFTKYGD---GAVDINPIGDLYKTQVRELARHLGVPEDIIEKPPSADLWEGQTDEDELGFSYEEIDEILYAL 214 (264)
T ss_pred CHHHHHHHHCCCCCC---CCCCHHHHCCCCHHHHHHHHHHHCCCHHHEECCCCCCCCCCCCCHHHCCCCHHHHHHHHHHH
T ss_conf 674798721001687---66562452587399999999993996644036999776799998777199999999999999
Q ss_pred HHCCCCHHH
Q ss_conf 422247789
Q gi|254780805|r 213 VSKKMSVRD 221 (300)
Q Consensus 213 i~~~LSVRe 221 (300)
+.+++|..+
T Consensus 215 ie~~~~~~~ 223 (264)
T PRK13980 215 FDKKMPREE 223 (264)
T ss_pred HHCCCCHHH
T ss_conf 976999999
No 324
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=45.69 E-value=22 Score=15.98 Aligned_cols=29 Identities=14% Similarity=0.233 Sum_probs=22.5
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10111046799997433787786565654
Q gi|254780805|r 149 SEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
.....+..++|+.|+.|..||.+-|.-|.
T Consensus 11 ~~~~v~i~~La~~f~VS~~TiRRDl~~L~ 39 (57)
T pfam08220 11 QQGTLSVEELAELLGVSEMTIRRDLNELE 39 (57)
T ss_pred HCCCEEHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 86979799999998959999999699999
No 325
>TIGR03537 DapC succinyldiaminopimelate transaminase. Note: the detailed information included in the EC:2.6.1.17 record includes the assertions that the enzyme uses the pyridoxal pyrophosphate cofactor, which is consistent with the pfam00155 family, and the assertion that the amino group donor is L-glutamate, which is undetermined for the sequences in this clade.
Probab=45.67 E-value=21 Score=16.15 Aligned_cols=43 Identities=14% Similarity=0.177 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHCCEEEEE-----CCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 9999999999739879997-----1798228999858-98999999998375
Q gi|254780805|r 250 LTDLEKKISSKVGLNISIK-----HRNNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 250 i~~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
-.++..+|.+. | |-+. ...+.|-+.|.|. +.|+++.=+.+|.+
T Consensus 301 ~~~~~~~ll~~-g--V~v~pG~~Fg~~~~~~~Rl~~~~~~e~l~ealrrl~~ 349 (350)
T TIGR03537 301 SKDYALRLLEN-G--IVVAPGENFGSGEEGYVRVALVPTLEECEEALRIWES 349 (350)
T ss_pred HHHHHHHHHHC-C--EEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHC
T ss_conf 99999999979-9--8997673118999986999972899999999999861
No 326
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=45.50 E-value=21 Score=16.20 Aligned_cols=32 Identities=25% Similarity=0.339 Sum_probs=26.7
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99985210111046799997433787786565
Q gi|254780805|r 143 GYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
..-||.--.|+|-+.||..+|.++|+|++.+.
T Consensus 31 ~lLRLH~~~gLsldR~~~lY~~hrStvaR~v~ 62 (106)
T TIGR02233 31 TLLRLHHVEGLSLDRLGTLYGVHRSTVARWVA 62 (106)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHH
T ss_conf 56667762365589999884788616999999
No 327
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=45.48 E-value=23 Score=15.96 Aligned_cols=31 Identities=19% Similarity=0.220 Sum_probs=22.0
Q ss_pred HHHHHCC--CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8521011--104679999743378778656565
Q gi|254780805|r 146 QLISEYG--YTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 146 ~l~~~~~--~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
+|..++| -|.++||+.+|.+...|..++...
T Consensus 177 ~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~~ 209 (318)
T PRK07405 177 QLSQQLGRAATIGELAEELELTPKQVREYLERA 209 (318)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999871898648999988599999999999980
No 328
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=45.20 E-value=23 Score=15.93 Aligned_cols=39 Identities=15% Similarity=0.297 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
Q ss_conf 11046799997433787786565-------6543589999876421
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILR-------ILKLPSSVREMIRKEE 190 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~Lr-------Ll~L~~~i~~~l~~~~ 190 (300)
..|.+++|+.+|.|...+.+.|+ -.+|.-+++...+.|.
T Consensus 64 ~ps~~ewA~~~~~~~~~l~~~l~G~~aWA~~a~l~leLk~~~r~G~ 109 (336)
T TIGR02997 64 EPSKEEWAAALGLSEAELRQRLRGLQAWAEAAQLELELKLVLRQGQ 109 (336)
T ss_pred CCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9987899987189988999998765788998422589999999789
No 329
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=45.18 E-value=13 Score=17.54 Aligned_cols=28 Identities=21% Similarity=0.280 Sum_probs=21.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565654358
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKLPS 180 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~ 180 (300)
+|..|+|+.+|.|..+|.+.-+--.+++
T Consensus 1 lt~~e~A~~lgVs~~TlrrW~~~G~i~~ 28 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGKLKA 28 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCE
T ss_conf 9889999997989999999998799431
No 330
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=44.89 E-value=23 Score=15.90 Aligned_cols=34 Identities=15% Similarity=0.198 Sum_probs=24.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999985210111046799997433787786565654
Q gi|254780805|r 142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
..|..+.+ .| +-...|+.+|.|+++|++.++-++
T Consensus 5 ~~f~~v~~-~g-s~~~AA~~l~isqs~vs~~i~~LE 38 (60)
T pfam00126 5 RVFVAVAE-EG-SFTAAAERLGLSQPAVSRQIKRLE 38 (60)
T ss_pred HHHHHHHH-CC-CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 99999998-09-999999997989889999999999
No 331
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=44.60 E-value=7.4 Score=19.08 Aligned_cols=31 Identities=19% Similarity=0.404 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565654358999
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKLPSSVR 183 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~ 183 (300)
+.-.|++..+|.|++||.+++.=...|.+++
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvk 44 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVK 44 (70)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCCCCCCEE
T ss_conf 2089999997766899999980477999862
No 332
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=44.51 E-value=22 Score=15.99 Aligned_cols=29 Identities=7% Similarity=0.327 Sum_probs=22.7
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99985210111046799997433787786
Q gi|254780805|r 143 GYEQLISEYGYTQNDIGSIVGKSRSHVAN 171 (300)
Q Consensus 143 ~~~~l~~~~~~t~~~lA~~~G~s~s~V~~ 171 (300)
-+..++.+.+++..++|+.+|.|.++++.
T Consensus 6 ~l~~~l~~r~~~~~eLa~~igis~~~ls~ 34 (73)
T COG3655 6 RLDVMLADRKISLKELAEAIGISEANLSK 34 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf 67999999750177899998436989999
No 333
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=44.46 E-value=5.8 Score=19.73 Aligned_cols=89 Identities=19% Similarity=0.188 Sum_probs=39.1
Q ss_pred CCCHHHHHHHH--------HHHCCCCCCCCCCCCC-----HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 35756777776--------4210013543334641-----1234556665431022104899999998521011104679
Q gi|254780805|r 92 IAGERRFRAAK--------MASLSEVPVIIRNVDN-----KSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDI 158 (300)
Q Consensus 92 i~G~rR~rAa~--------~~g~~~ip~iv~~~~d-----~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~l 158 (300)
.+|.|||...+ .+|...+.-+|.-..+ -..+..+ .||-.|. -++-..+-.|+..+- .+++
T Consensus 1 MDGNrRWAk~~gl~~~~GH~~G~~~l~~iv~~~~~~gI~~lTlyaFS-tENw~R~----~~EV~~Lm~L~~~~l--~~~~ 73 (229)
T PRK10240 1 MDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFS-SENWNRP----AQEVSALMELFVWAL--DSEV 73 (229)
T ss_pred CCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECC-HHHCCCC----HHHHHHHHHHHHHHH--HHHH
T ss_conf 98638999887998789999999999999999998699989999608-7664999----799999999999999--9999
Q ss_pred HH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99--974337877865656543589999876421
Q gi|254780805|r 159 GS--IVGKSRSHVANILRILKLPSSVREMIRKEE 190 (300)
Q Consensus 159 A~--~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~ 190 (300)
.. .-|..-.+|- .+..||+++++.+..-.
T Consensus 74 ~~l~~~~iri~~iG---d~~~Lp~~l~~~i~~~e 104 (229)
T PRK10240 74 KSLHRHNVRLRIIG---DTSRFNSRLQERIRKSE 104 (229)
T ss_pred HHHHHCCEEEEEEE---CCCCCCHHHHHHHHHHH
T ss_conf 99998794899964---41006758999999999
No 334
>KOG0259 consensus
Probab=44.39 E-value=23 Score=15.90 Aligned_cols=29 Identities=34% Similarity=0.667 Sum_probs=19.6
Q ss_pred CCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf 35789998-768988999999988631001
Q gi|254780805|r 48 VPNPHNPR-NYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 48 ~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l 76 (300)
.-||.||- -.|+.+.|+++++.-+++|++
T Consensus 205 viNP~NPcGnVys~~HL~kiae~A~klgi~ 234 (447)
T KOG0259 205 VINPNNPCGNVYSEDHLKKIAETAKKLGIM 234 (447)
T ss_pred EECCCCCCCCCCCHHHHHHHHHHHHHHCCE
T ss_conf 967999986515199999999999984976
No 335
>pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.
Probab=43.95 E-value=19 Score=16.45 Aligned_cols=31 Identities=29% Similarity=0.356 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHH-HHHHHHH
Q ss_conf 9999999852101110467999974-3378778
Q gi|254780805|r 139 EEALGYEQLISEYGYTQNDIGSIVG-KSRSHVA 170 (300)
Q Consensus 139 e~A~~~~~l~~~~~~t~~~lA~~~G-~s~s~V~ 170 (300)
|.-..+++|=.+ |+|..+||+.|| .||..|-
T Consensus 6 Erve~LkkLW~e-GlSaSqIA~~LGgvTRNAVI 37 (162)
T pfam07750 6 ERVELLKKLWLE-GLSASQIAAQLGGVSRNAVI 37 (162)
T ss_pred HHHHHHHHHHHC-CCCHHHHHHHHCCCCCCCEE
T ss_conf 999999999985-36599999997655400000
No 336
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=43.91 E-value=24 Score=15.80 Aligned_cols=26 Identities=15% Similarity=0.317 Sum_probs=21.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 11046799997433787786565654
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
..|.++||+.+|.+...|...+.+..
T Consensus 192 ~pt~eEIA~~lg~~~~~v~~~l~~~~ 217 (328)
T PRK05657 192 EPSAEEIAELLDKPVDDVSRMLALNE 217 (328)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 99899999996959999999997458
No 337
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=43.41 E-value=24 Score=15.76 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHCCCCCCCEEECCCCCCCC
Q ss_conf 899999998863100155046205654453
Q gi|254780805|r 61 EGLEDLCQSIKSHGIIQPLIVRAIDNGLYK 90 (300)
Q Consensus 61 ~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ 90 (300)
..+.|=-..+...|++. +++ +.|.|.
T Consensus 46 ~~VREAL~~L~~~GlV~---~~~-g~G~~V 71 (251)
T PRK09990 46 SALREGLKVLRGRGIIE---TAQ-GRGSFV 71 (251)
T ss_pred HHHHHHHHHHHHCCCEE---EEC-CCCCEE
T ss_conf 99999999999889979---857-985067
No 338
>PRK03837 transcriptional regulator NanR; Provisional
Probab=43.33 E-value=20 Score=16.28 Aligned_cols=15 Identities=27% Similarity=0.614 Sum_probs=7.9
Q ss_pred HHHHHHHHHHCCCCC
Q ss_conf 999999886310015
Q gi|254780805|r 63 LEDLCQSIKSHGIIQ 77 (300)
Q Consensus 63 l~eLa~SI~~~G~lq 77 (300)
+.|=-..+...|++.
T Consensus 55 VREAL~~L~~~GlV~ 69 (243)
T PRK03837 55 VREALQALKRKGLVQ 69 (243)
T ss_pred HHHHHHHHHHCCCEE
T ss_conf 999999999889989
No 339
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=43.22 E-value=24 Score=15.74 Aligned_cols=33 Identities=18% Similarity=0.294 Sum_probs=22.6
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 998521011104679999743378778656565
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
++.|....++...|+|+++|.++|+++--+..|
T Consensus 29 l~lL~~k~plNvneiAe~lgLpqst~s~~ik~L 61 (308)
T COG4189 29 LQLLHRKGPLNVNEIAEALGLPQSTMSANIKVL 61 (308)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999987179878999988588656666557888
No 340
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=43.15 E-value=25 Score=15.73 Aligned_cols=19 Identities=16% Similarity=0.363 Sum_probs=9.7
Q ss_pred HHHCCC--CHHHHHHHHHHHH
Q ss_conf 742224--7789999997641
Q gi|254780805|r 212 IVSKKM--SVRDTEELVQEQD 230 (300)
Q Consensus 212 Ii~~~L--SVRe~E~lVk~~~ 230 (300)
.....| +||+.|+++.+..
T Consensus 456 L~~y~WPGNVRELeNviER~v 476 (560)
T COG3829 456 LLRYDWPGNVRELENVIERAV 476 (560)
T ss_pred HHHCCCCCHHHHHHHHHHHHH
T ss_conf 986899960999999999998
No 341
>PRK05066 arginine repressor; Provisional
Probab=42.79 E-value=25 Score=15.70 Aligned_cols=40 Identities=23% Similarity=0.375 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHCCC-CHHHHHHHH---HH---HHHHHHHHHHHHHH
Q ss_conf 999999985210111-046799997---43---37877865656543
Q gi|254780805|r 139 EEALGYEQLISEYGY-TQNDIGSIV---GK---SRSHVANILRILKL 178 (300)
Q Consensus 139 e~A~~~~~l~~~~~~-t~~~lA~~~---G~---s~s~V~~~LrLl~L 178 (300)
+.-.++++|+..+.. ||++|.+.+ |. +++|||+-|+-+.+
T Consensus 9 ~~~~aIk~lI~~~~I~tQeeL~~~L~~~G~~~VTQATvSRDlkeLg~ 55 (156)
T PRK05066 9 ELVKAFKALLKEEKFGSQGEIVTALQEQGFDNINQSKVSRMLTKFGA 55 (156)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHCCC
T ss_conf 99999999985189667999999999739861208888878998299
No 342
>PRK07367 consensus
Probab=42.69 E-value=25 Score=15.68 Aligned_cols=43 Identities=5% Similarity=0.038 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHCCEEEE--ECCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 99999999973987999--71798228999858-9899999999837
Q gi|254780805|r 251 TDLEKKISSKVGLNISI--KHRNNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I--~~~~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
.++.++|-+..|.-|.= .+ +..|-|.|.|. +.++++.=+++|.
T Consensus 334 ~~~~~~ll~~~gV~v~PG~~F-g~~~~~Rl~~a~~~~~l~ea~~RL~ 379 (385)
T PRK07367 334 LEFCRQLLEEHHVAAIPGIAF-GADDHIRLSYATDLATIEKGLERLE 379 (385)
T ss_pred HHHHHHHHHHCCEEEECCCCC-CCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf 999999999699999758746-9999399997098999999999999
No 343
>PRK06207 aspartate aminotransferase; Provisional
Probab=42.64 E-value=24 Score=15.75 Aligned_cols=45 Identities=9% Similarity=0.224 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHCCEEE--EE-CCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 99999999997398799--97-1798228999858-9899999999837
Q gi|254780805|r 250 LTDLEKKISSKVGLNIS--IK-HRNNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 250 i~~le~~L~~~lGtkV~--I~-~~~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
..++...|.+.-|.-+. .- .....|-|.|.|. +.+.+..=+++|.
T Consensus 350 ~~~f~~~Ll~e~gVav~PG~~FG~~~~~~vRlsfa~~~e~l~eal~RL~ 398 (406)
T PRK06207 350 LADFVKILRLQAGVVVTPGTEFSPHTADSIRLNFSQDHAAAVAAVERIA 398 (406)
T ss_pred HHHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 9999999998589999886565899989799997398999999999999
No 344
>cd01455 vWA_F11C1-5a_type Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=42.51 E-value=11 Score=17.93 Aligned_cols=91 Identities=15% Similarity=0.301 Sum_probs=47.8
Q ss_pred CCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHH-HHHHCCCCCHHHHHHHHHH---------HHHHCCCCHHHHHHH
Q ss_conf 357567777764210013543334641123455666-5431022104899999998---------521011104679999
Q gi|254780805|r 92 IAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIV-ENVQRKDLNPLEEALGYEQ---------LISEYGYTQNDIGSI 161 (300)
Q Consensus 92 i~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~-EN~~R~dl~p~e~A~~~~~---------l~~~~~~t~~~lA~~ 161 (300)
.+|-.-+.|.+.+-- ++ .-.+ +.++...+.+. .|+.|-..+|-+-|.++++ ++..+|--.+.|++.
T Consensus 88 ~sGD~Tlea~~~Ai~-~l--~a~~-d~De~fVivlSDANL~RYgI~p~~l~~~l~~~p~V~a~~IfIgslg~eA~~l~~~ 163 (191)
T cd01455 88 WSGDHTVEATEFAIK-EL--AAKE-DFDEAIVIVLSDANLERYGIQPKKLADALAREPNVNAFVIFIGSLSDEADQLQRE 163 (191)
T ss_pred ECCCCHHHHHHHHHH-HH--HHCC-CCCCCEEEEECCCCHHHCCCCHHHHHHHHHCCCCCCEEEEEEECHHHHHHHHHHH
T ss_conf 258844899999999-87--5302-6776089998147644318898999999733877668999973516799999974
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 743378778656565435899998764
Q gi|254780805|r 162 VGKSRSHVANILRILKLPSSVREMIRK 188 (300)
Q Consensus 162 ~G~s~s~V~~~LrLl~L~~~i~~~l~~ 188 (300)
+-..+++|- +..-+||.-+|+.+.+
T Consensus 164 lP~G~~fVc--~dt~~lP~il~qIfts 188 (191)
T cd01455 164 LPAGKAFVC--MDTSELPHIMQQIFTS 188 (191)
T ss_pred CCCCCEEEE--CCHHHHHHHHHHHHHH
T ss_conf 899741785--3653678999999887
No 345
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=42.31 E-value=25 Score=15.65 Aligned_cols=26 Identities=27% Similarity=0.448 Sum_probs=21.7
Q ss_pred HHCCCCHHHHHHHHH-HHHHHHHHHHH
Q ss_conf 101110467999974-33787786565
Q gi|254780805|r 149 SEYGYTQNDIGSIVG-KSRSHVANILR 174 (300)
Q Consensus 149 ~~~~~t~~~lA~~~G-~s~s~V~~~Lr 174 (300)
+..++|..+||+.|| ++.++|....+
T Consensus 41 ~~~~~s~~~Ig~~fg~rdHsTV~~a~~ 67 (90)
T cd06571 41 ELTGLSLPEIGRAFGGRDHSTVLHAVR 67 (90)
T ss_pred HHHCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf 997889999999958997149999999
No 346
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=42.06 E-value=25 Score=15.62 Aligned_cols=44 Identities=20% Similarity=0.255 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HC-C-HHHHHHHHHCCH
Q ss_conf 11046799997433787786565654358999987642-10-1-677777640100
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKE-EI-S-LGHARTLVSTSD 204 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~-~i-s-~ghar~Ll~~~~ 204 (300)
-.+.++||+.+|.||+.|...+. .+=..| .| + .++.+.|.+.++
T Consensus 19 ~~SGe~La~~LgiSRtaVwK~Iq---------~Lr~~G~~I~s~~~kGY~L~~~~~ 65 (79)
T COG1654 19 FVSGEKLAEELGISRTAVWKHIQ---------QLREEGVDIESVRGKGYLLPQLPD 65 (79)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH---------HHHHHCCCEEECCCCCEECCCCCC
T ss_conf 66689999997865999999999---------999809716860788636567501
No 347
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=42.01 E-value=26 Score=15.62 Aligned_cols=22 Identities=18% Similarity=0.294 Sum_probs=12.9
Q ss_pred HHHHHCCC--CHHHHHHHHHHHHC
Q ss_conf 99742224--77899999976410
Q gi|254780805|r 210 QVIVSKKM--SVRDTEELVQEQDN 231 (300)
Q Consensus 210 ~~Ii~~~L--SVRe~E~lVk~~~~ 231 (300)
+......| +|||.++.+.+..-
T Consensus 349 ~~L~~y~WPGNVREL~N~ver~~i 372 (464)
T COG2204 349 AALLAYDWPGNVRELENVVERAVI 372 (464)
T ss_pred HHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 999738998189999999999985
No 348
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor; InterPro: IPR000394 Sigma factors are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma- 70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes: the sigma-54 and sigma-70 families. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor , required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=41.95 E-value=13 Score=17.45 Aligned_cols=20 Identities=15% Similarity=0.333 Sum_probs=9.6
Q ss_pred CHHHHHHHHHHHHHHHHHHH
Q ss_conf 04679999743378778656
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~L 173 (300)
+-.+||..+|.+.|||||..
T Consensus 367 ~L~~vA~el~~heSTiSRai 386 (477)
T TIGR02395 367 TLREVAEELGLHESTISRAI 386 (477)
T ss_pred CHHHHHHHHCCCCCCEEEEE
T ss_conf 38999988588987246331
No 349
>PRK07865 N-succinyldiaminopimelate aminotransferase; Reviewed
Probab=41.71 E-value=26 Score=15.59 Aligned_cols=41 Identities=15% Similarity=0.179 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHCCEEEEE-----CCCCCEEEEEEE-CCHHHHHHHHHHHC
Q ss_conf 999999999739879997-----179822899985-89899999999837
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK-----HRNNKGQFCIKY-ETNEQLKIICSLLG 294 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f-~s~eeLe~Il~kL~ 294 (300)
.+..+.|.+. | |-+. ...+.|-|.|.| .+.|+|+.=+++|.
T Consensus 317 ~~~~~~l~e~-g--V~v~PG~~Fg~~g~~~vRls~~~~~e~l~ea~~RLa 363 (364)
T PRK07865 317 WDTVAWLAER-G--ILVAPGDFYGPAGAQHVRVALTATDERIAAAVERLT 363 (364)
T ss_pred HHHHHHHHHC-C--EEEECCCCCCCCCCCEEEEEECCCHHHHHHHHHHHC
T ss_conf 9999999979-9--899188743689998699996598999999999868
No 350
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=41.71 E-value=26 Score=15.59 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 679999743378778656565435
Q gi|254780805|r 156 NDIGSIVGKSRSHVANILRILKLP 179 (300)
Q Consensus 156 ~~lA~~~G~s~s~V~~~LrLl~L~ 179 (300)
.++|+++|.|..+|.+-.+-++||
T Consensus 4 ~~vAk~LGVspkTVQRWvKq~ni~ 27 (178)
T PRK13182 4 PFVAKKLGVSPKTVQRWVKQLNLP 27 (178)
T ss_pred HHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf 788999399929999999995899
No 351
>pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.
Probab=41.70 E-value=20 Score=16.34 Aligned_cols=22 Identities=23% Similarity=0.472 Sum_probs=14.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
+|.+|+|..+|.|+-+|++..|
T Consensus 1 mT~eELa~~~G~srQtINkwaR 22 (122)
T pfam07037 1 MTPEELAELTGYSRQTINRWVR 22 (122)
T ss_pred CCHHHHHHHHCCHHHHHHHHHH
T ss_conf 9878998874712999999999
No 352
>PRK08069 consensus
Probab=41.46 E-value=26 Score=15.58 Aligned_cols=43 Identities=9% Similarity=0.143 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 999999999739879997-17--98228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++...|-+.-| |-+. .. +..|-+.|.|. +.++++.=+++|+.
T Consensus 341 ~~~~~~ll~~~g--V~v~PG~~Fg~~~~~Rl~fa~~~~~l~eal~RL~~ 387 (390)
T PRK08069 341 DEFVKALLEEEK--VALVPGSGFGAPDNVRLSYATSLELLEEAIERIHR 387 (390)
T ss_pred HHHHHHHHHHCC--EEEECCCCCCCCCCEEEEEECCHHHHHHHHHHHHH
T ss_conf 999999998599--99981876799983899984999999999999999
No 353
>PRK05839 hypothetical protein; Provisional
Probab=41.45 E-value=23 Score=15.86 Aligned_cols=43 Identities=16% Similarity=0.166 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHCCEEEEE----CC-C--CCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 999999999739879997----17-9--8228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK----HR-N--NKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~----~~-~--~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++.+.|-+.- .|-+. .. . ++|-|.|.|. +.+.|+.=+++|++
T Consensus 320 ~~f~~~Ll~~~--gV~v~PG~~FG~~~~g~~~vRls~~~~~e~L~eal~Rl~~ 370 (376)
T PRK05839 320 ENFTKKLYQNE--GIKVLPGSYLGRNGIGKDYVRLALVYDTPKLKKALERIKT 370 (376)
T ss_pred HHHHHHHHHCC--CEEEECCCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 99999999809--9999774001799998996999970889999999999999
No 354
>pfam10302 DUF2407 Putative membrane protein (DUF2407). This is a family of proteins found in fungi. The function is not known. There is a characteristic GFDRL sequence motif.
Probab=41.36 E-value=9.8 Score=18.28 Aligned_cols=54 Identities=13% Similarity=0.294 Sum_probs=33.3
Q ss_pred CCCCCCCCCC-CCCHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 0013543334-641123-4556665431022104899999998521011104679999
Q gi|254780805|r 106 LSEVPVIIRN-VDNKSS-LEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDIGSI 161 (300)
Q Consensus 106 ~~~ip~iv~~-~~d~~~-~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~ 161 (300)
.-.|.|+|-| +++++. .+.++..+-+. .-+....+++|-||+.. |+|++|++..
T Consensus 83 r~YIHCsIGd~Lt~eeLa~E~~~~~~~~~-~~sTtp~~rGFDRLlsa-GFs~~EV~~L 138 (252)
T pfam10302 83 RIYIHCSIGDELTAEELAAEAALDDDGPQ-ASSTTPQPRGFDRLLSA-GFSPAEVSLL 138 (252)
T ss_pred CEEEEEECCCCCCHHHHHHHHHCCCCCCC-CCCCCCCCCCHHHHHHC-CCCHHHHHHH
T ss_conf 27999632762698887424401567888-77788887448789875-8999999999
No 355
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=41.35 E-value=26 Score=15.55 Aligned_cols=15 Identities=20% Similarity=0.297 Sum_probs=5.5
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 679999743378778
Q gi|254780805|r 156 NDIGSIVGKSRSHVA 170 (300)
Q Consensus 156 ~~lA~~~G~s~s~V~ 170 (300)
++||+.+|.+...|.
T Consensus 277 eEIA~~lg~s~e~V~ 291 (410)
T PRK07598 277 EDIAQELEMTPTQVR 291 (410)
T ss_pred HHHHHHCCCCHHHHH
T ss_conf 999988099999999
No 356
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.23 E-value=26 Score=15.54 Aligned_cols=66 Identities=8% Similarity=0.045 Sum_probs=31.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf 0467999974337877865656543589999876421--016777776401004689999742224778999999764
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEE--ISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEELVQEQ 229 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~--is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~lVk~~ 229 (300)
+-.++|+.+|.|..++.-|-+..=|||. . -..|- .+..+.. ...+....-.-|+|+.++-.++...
T Consensus 2 ~Ige~a~~~gvs~~tlRyYe~~GLl~p~-r--~~~gyR~Y~~~~~~-------~l~~I~~lr~~G~sl~eI~~~l~~~ 69 (112)
T cd01282 2 RIGELAARTGVSVRSLRYYEEQGLLVPE-R--SANGYRDYDEAAVD-------RVRQIRRLLAAGLTLEEIREFLPCL 69 (112)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCC-C--CCCCCEECCHHHHH-------HHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 6899999989799999999984899998-0--89987005999999-------9999999999699999999999877
No 357
>PHA00675 hypothetical protein
Probab=41.12 E-value=26 Score=15.53 Aligned_cols=34 Identities=18% Similarity=0.171 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999998521011104679999743378778656
Q gi|254780805|r 140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
.-..+..|.+.+|++-..||..+..++++|+..-
T Consensus 27 ~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkIC 60 (78)
T PHA00675 27 EVERIRELHEVEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999998728438999999727568999998
No 358
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=41.07 E-value=26 Score=15.53 Aligned_cols=20 Identities=15% Similarity=0.219 Sum_probs=8.4
Q ss_pred CHHHHHHHHHHHHHHHHHHH
Q ss_conf 04679999743378778656
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~L 173 (300)
+..+||+.+|.|..||++-|
T Consensus 20 ~v~eLa~~~~VS~~TIRRDL 39 (240)
T PRK10411 20 TTEALAEQLNVSKETIRRDL 39 (240)
T ss_pred EHHHHHHHHCCCHHHHHHHH
T ss_conf 99999998895998999829
No 359
>PRK05794 consensus
Probab=40.36 E-value=25 Score=15.67 Aligned_cols=41 Identities=10% Similarity=0.148 Sum_probs=20.7
Q ss_pred HHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 99999999739879997-17--98228999858-9899999999837
Q gi|254780805|r 252 DLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 252 ~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
++...|-+.- .|-+. .. +..|-|.|.|. +.++++.-+++|.
T Consensus 346 ~f~~~ll~~~--gV~v~PG~~Fg~~~~vRl~f~~~~e~l~eal~RL~ 390 (397)
T PRK05794 346 DFANLLLEEE--NVAVVPGIAFGMDNYIRLSYATSMENIEKGLDRIE 390 (397)
T ss_pred HHHHHHHHHC--CEEEEECCCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf 9999999849--99998185358998399998299999999999999
No 360
>pfam02006 DUF137 Protein of unknown function DUF137. This family of archaeal proteins has no known function.
Probab=40.03 E-value=27 Score=15.42 Aligned_cols=62 Identities=15% Similarity=0.177 Sum_probs=34.1
Q ss_pred CHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHH
Q ss_conf 9889999999886310015504620565445333575677777642100135433346411234
Q gi|254780805|r 59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSL 122 (300)
Q Consensus 59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~ 122 (300)
.++.++.++.-++++|.-.-+-+-+...++..=+.|.|++ |-.-|.-.-++++..+.|-|-.
T Consensus 42 T~eR~~~I~~~L~~~g~~~vlG~~~d~~~~ipgL~~~R~~--~~~~GI~~ADvVLVPLEDGDR~ 103 (178)
T pfam02006 42 TEERVEKIAEVLREHGAKEVLGVGPDASERIPGLDHERGK--VSPDGIYSADVVLVPLEDGDRT 103 (178)
T ss_pred CHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCE--ECCCCCCCCCEEEEECCCCCHH
T ss_conf 9899999999999759755544687645527898785340--4604541033799845778589
No 361
>PRK07212 consensus
Probab=39.91 E-value=27 Score=15.41 Aligned_cols=43 Identities=21% Similarity=0.315 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEECC-HHHHHHHHHHHCC
Q ss_conf 999999999739879997-17--982289998589-8999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYET-NEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~s-~eeLe~Il~kL~~ 295 (300)
.++...+-+.- +|-+. .. +..|-+.|.|.. .++|+.-+++|.+
T Consensus 329 ~~~~~~ll~~~--gV~v~pG~~Fg~~g~iRl~~a~~~e~l~eal~RL~~ 375 (378)
T PRK07212 329 TAVAERLLKDA--HVAVTPGSAFGAPGWIRISYATSMERLKEALERLEK 375 (378)
T ss_pred HHHHHHHHHHC--CEEEEECCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 99999999709--899981744599993999980899999999999999
No 362
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation ..
Probab=39.71 E-value=28 Score=15.39 Aligned_cols=42 Identities=21% Similarity=0.273 Sum_probs=27.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHH
Q ss_conf 998521011104679999743378778656--565435899998
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANIL--RILKLPSSVREM 185 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L--rLl~L~~~i~~~ 185 (300)
+...+-+..-|..+.|..+|.|+|+|..-+ ||-...+++...
T Consensus 11 ~~~~i~~~~~t~r~~a~~fGvskst~hkd~terlP~in~~~~~~ 54 (80)
T TIGR02844 11 IAKYIVETKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEE 54 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf 99999976899999998834325677666876300026899999
No 363
>pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.
Probab=39.61 E-value=28 Score=15.38 Aligned_cols=32 Identities=16% Similarity=0.048 Sum_probs=22.9
Q ss_pred HHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999852101-1104679999743378778656
Q gi|254780805|r 142 LGYEQLISEY-GYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 142 ~~~~~l~~~~-~~t~~~lA~~~G~s~s~V~~~L 173 (300)
.||+-.++.. ..+..+||+.||.|.++|++--
T Consensus 11 kA~eiy~~s~G~~~l~~IA~~L~vs~~~IrkWK 43 (60)
T pfam10668 11 KAKEMWKESGGTMKLKDIANKLNVSESQIRKWK 43 (60)
T ss_pred HHHHHHHHCCCCEEHHHHHHHHCCCHHHHHHCC
T ss_conf 999999982896449999999687988876031
No 364
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=39.41 E-value=23 Score=15.93 Aligned_cols=36 Identities=17% Similarity=0.350 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565-6543589999876421
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILR-ILKLPSSVREMIRKEE 190 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~Lr-Ll~L~~~i~~~l~~~~ 190 (300)
+|.+++|+.+|.|++++++.++ ....+ ..+.+..-.
T Consensus 2 lsl~~lA~~~~~S~~~l~~~f~~~~g~s--~~~~i~~~R 38 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTT--PKQYLRDRR 38 (84)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCCC--HHHHHHHHH
T ss_conf 8999999988909999999999988939--999999999
No 365
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.88 E-value=29 Score=15.31 Aligned_cols=24 Identities=13% Similarity=0.065 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 467999974337877865656543
Q gi|254780805|r 155 QNDIGSIVGKSRSHVANILRILKL 178 (300)
Q Consensus 155 ~~~lA~~~G~s~s~V~~~LrLl~L 178 (300)
-.++|+.+|.|..+|.-|=+.-=|
T Consensus 3 IgelA~~~gvs~~tlRyYE~~GLl 26 (126)
T cd04785 3 IGELARRTGVNVETIRYYESIGLL 26 (126)
T ss_pred HHHHHHHHCCCHHHHHHHHHCCCC
T ss_conf 899999989499999999984998
No 366
>PRK08362 consensus
Probab=38.60 E-value=29 Score=15.28 Aligned_cols=24 Identities=25% Similarity=0.337 Sum_probs=13.9
Q ss_pred CCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf 982289998589-899999999837
Q gi|254780805|r 271 NNKGQFCIKYET-NEQLKIICSLLG 294 (300)
Q Consensus 271 ~~kGkI~I~f~s-~eeLe~Il~kL~ 294 (300)
.+.|-+.|.|.. .++++.-+++|.
T Consensus 356 ~~~~~~Rl~~a~~~e~l~ea~~RL~ 380 (389)
T PRK08362 356 AGEGYIRISYATAYEKLEEAMDRME 380 (389)
T ss_pred CCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 9989799997199999999999999
No 367
>pfam05339 DUF739 Protein of unknown function (DUF739). This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins.
Probab=38.59 E-value=24 Score=15.82 Aligned_cols=29 Identities=28% Similarity=0.592 Sum_probs=22.2
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 85210111046799997433787786565654
Q gi|254780805|r 146 QLISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 146 ~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
++++.|| ||..-|..+|.|..+++ ++|.+
T Consensus 11 rI~Ek~g-tq~~Fa~~lg~se~tls--lkln~ 39 (69)
T pfam05339 11 RILEKYG-TQYNFASAIGLSERSLS--LKLND 39 (69)
T ss_pred HHHHHHC-CHHHHHHHHCCCHHHHH--HHHCC
T ss_conf 2889956-79899999581176888--98768
No 368
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=38.43 E-value=29 Score=15.27 Aligned_cols=39 Identities=26% Similarity=0.398 Sum_probs=29.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999852101110467999974337877865656543589
Q gi|254780805|r 142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSS 181 (300)
Q Consensus 142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~ 181 (300)
..+-|++.. -+|-+|+++.+|.+.+.+++|.+.--||..
T Consensus 14 v~~LR~lK~-~~tykELs~~~gip~s~L~RYv~g~vlPs~ 52 (238)
T PRK08558 14 VRYLRSLKK-TYTYEELSSILGLPESVLSRYVNGHVLPSV 52 (238)
T ss_pred HHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHCCCCCCCH
T ss_conf 999999850-268999998879799998505348878758
No 369
>PRK04280 arginine repressor; Provisional
Probab=38.40 E-value=29 Score=15.26 Aligned_cols=129 Identities=11% Similarity=0.130 Sum_probs=62.1
Q ss_pred HHHHHHHHHHHHCC-CCHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCH------HH
Q ss_conf 99999998521011-10467999974-----33787786565654358999987642101677777640100------46
Q gi|254780805|r 139 EEALGYEQLISEYG-YTQNDIGSIVG-----KSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSD------PL 206 (300)
Q Consensus 139 e~A~~~~~l~~~~~-~t~~~lA~~~G-----~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~------~~ 206 (300)
++=..+++++.+.. .||+||.+.+. .+++|||+-|+=+.+-. -.-.+|. .+ ..++. ..
T Consensus 5 ~R~~~I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATlSRDlkeL~~vK---v~~~~G~-----~~--Y~lp~~~~~~~~~ 74 (149)
T PRK04280 5 QRHIKIREIITNEEIETQDELVDRLREYGFNVTQATVSRDIKELHLVK---VPLPDGR-----YK--YSLPADQRFNPLQ 74 (149)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHHCCEE---EECCCCC-----EE--EEECCCCCCCHHH
T ss_conf 999999999974897789999999998597553898898799818888---6669997-----89--9846766658689
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHH-H-HHHHHHHCCEEEEECCCCCEEEEEEECCHH
Q ss_conf 89999742224778999999764102222223456655689789999-9-999997398799971798228999858989
Q gi|254780805|r 207 SLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDL-E-KKISSKVGLNISIKHRNNKGQFCIKYETNE 284 (300)
Q Consensus 207 ~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~l-e-~~L~~~lGtkV~I~~~~~kGkI~I~f~s~e 284 (300)
.+...+...=+||...+.++= ....+..-..+... . ..+.+.+|| =.+-..|-|-+.|.+
T Consensus 75 ~l~~~~~~~v~~i~~~~~lvV------------ikT~pG~A~~va~~iD~~~~~~I~GT------iAGdDTilVi~~s~~ 136 (149)
T PRK04280 75 KLKRYLMDSFVKIDGAGNLLV------------LKTLPGNAQSIGALLDNLDWEEILGT------ICGDDTCLIICRTPE 136 (149)
T ss_pred HHHHHHHHHEEEEEECCCEEE------------EEECCCCHHHHHHHHHHCCCCCCEEE------EECCCEEEEEECCHH
T ss_conf 999999988468853176999------------99289958999999984799871898------604998999989999
Q ss_pred HHHHHHHHHCC
Q ss_conf 99999998375
Q gi|254780805|r 285 QLKIICSLLGE 295 (300)
Q Consensus 285 eLe~Il~kL~~ 295 (300)
+-+.+.++|.+
T Consensus 137 ~a~~l~~~l~~ 147 (149)
T PRK04280 137 DTEVVKDRFLN 147 (149)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999997
No 370
>PRK06375 consensus
Probab=38.37 E-value=29 Score=15.26 Aligned_cols=45 Identities=11% Similarity=0.202 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 99999999973987999---71798228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++...|-+.-|.-|.= -...+.|-+.|.|. +.+.++.-+++|++
T Consensus 328 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~~Ri~~a~~~e~l~ea~~RL~~ 376 (381)
T PRK06375 328 YKAAENLLENKNVVVTPGSAFGRQGEHHFRISFATSEDIIKEGIERIGK 376 (381)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 9999999985999997873548899997999981999999999999999
No 371
>pfam07278 DUF1441 Protein of unknown function (DUF1441). This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown. However, it appears to be distantly related to other HTH families so may act as a transcriptional regulator.
Probab=38.27 E-value=25 Score=15.70 Aligned_cols=20 Identities=10% Similarity=0.155 Sum_probs=12.1
Q ss_pred CCCCHHHHHHHHHHHHHHCC
Q ss_conf 22104899999998521011
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYG 152 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~ 152 (300)
.+|+|.|+-.-|+...+...
T Consensus 62 ~~M~P~dRKaw~QsE~eRlk 81 (152)
T pfam07278 62 HKMTPKERKAWFQSENERLK 81 (152)
T ss_pred CCCCHHHHHHHHHHHHHHHH
T ss_conf 54985889999998889998
No 372
>TIGR01285 nifN nitrogenase molybdenum-iron cofactor biosynthesis protein NifN; InterPro: IPR005975 The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene. Two operons, nifDK and nifEN, encode a tetrameric (alpha2beta2 and N2E2) enzymatic complex. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE and of some other nif genes. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I.; GO: 0005515 protein binding, 0006461 protein complex assembly, 0009399 nitrogen fixation.
Probab=38.15 E-value=23 Score=15.96 Aligned_cols=112 Identities=15% Similarity=0.248 Sum_probs=64.3
Q ss_pred CCCHHHHHHHHHHHHHCCCCCCCEEECC--------CCCCCC-CCCCHHHHHHHHHHHCCCCCCCCCC-CC-CHHHHH-H
Q ss_conf 6898899999998863100155046205--------654453-3357567777764210013543334-64-112345-5
Q gi|254780805|r 57 YFESEGLEDLCQSIKSHGIIQPLIVRAI--------DNGLYK-IIAGERRFRAAKMASLSEVPVIIRN-VD-NKSSLE-I 124 (300)
Q Consensus 57 ~~~~~~l~eLa~SI~~~G~lqPi~Vr~~--------~~g~y~-ii~G~rR~rAa~~~g~~~ip~iv~~-~~-d~~~~~-~ 124 (300)
.+++.+|++|.+-|+++| |+||+.-.. .++.|. +-.|..+++-.+.+|..-.--+|-+ +. ..+... .
T Consensus 184 ~ltpgDie~l~~~vEaFG-L~P~~LPDLS~SLDGHLa~dd~s~~T~GGT~l~~i~~~g~s~~tlaIGe~mr~aA~~l~~R 262 (451)
T TIGR01285 184 LLTPGDIEELRDMVEAFG-LKPVVLPDLSRSLDGHLADDDFSPITLGGTTLEDIRELGQSAVTLAIGESMRAAAELLKDR 262 (451)
T ss_pred CCCHHHHHHHHHHHHHCC-CCCEECCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 888867999999998608-9722402110024650087870056789973599987368874688777654446752212
Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHC-CC-------CHHHHHHHHHHHHHHH
Q ss_conf 666543102210489999999852101-11-------0467999974337877
Q gi|254780805|r 125 AIVENVQRKDLNPLEEALGYEQLISEY-GY-------TQNDIGSIVGKSRSHV 169 (300)
Q Consensus 125 ~l~EN~~R~dl~p~e~A~~~~~l~~~~-~~-------t~~~lA~~~G~s~s~V 169 (300)
...+-.--..|+-+|...+|-..+-+. |. -.-.+=+++++.|.+.
T Consensus 263 ~g~~y~vF~~L~GLeavD~F~~~L~~~SG~~CdhhfPfvP~vP~~~~RqR~QL 315 (451)
T TIGR01285 263 CGVPYEVFPSLMGLEAVDAFVSVLSKISGSRCDHHFPFVPAVPERFERQRAQL 315 (451)
T ss_pred CCCCCHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 17740010122446899999999999844321567898898863345207889
No 373
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=37.79 E-value=30 Score=15.20 Aligned_cols=13 Identities=23% Similarity=0.529 Sum_probs=4.7
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 7999974337877
Q gi|254780805|r 157 DIGSIVGKSRSHV 169 (300)
Q Consensus 157 ~lA~~~G~s~s~V 169 (300)
++|++.|.+..+|
T Consensus 5 elAk~tGv~~~TI 17 (135)
T PRK10227 5 DVAKITGLTSKAI 17 (135)
T ss_pred HHHHHHCCCHHHH
T ss_conf 9999989699999
No 374
>PRK06855 aminotransferase; Validated
Probab=37.71 E-value=30 Score=15.19 Aligned_cols=28 Identities=21% Similarity=0.434 Sum_probs=18.6
Q ss_pred CCCCCCCC-CCCCHHHHHHHHHHHHHCCC
Q ss_conf 35789998-76898899999998863100
Q gi|254780805|r 48 VPNPHNPR-NYFESEGLEDLCQSIKSHGI 75 (300)
Q Consensus 48 ~~~p~~pR-~~~~~~~l~eLa~SI~~~G~ 75 (300)
.-||.||- ..++.+.+++|++-.++|++
T Consensus 177 i~nP~NPTG~v~s~e~l~~i~~~a~~~~i 205 (433)
T PRK06855 177 LINPDNPTGAVYPKEILREIVDIAREYDL 205 (433)
T ss_pred EECCCCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf 83899998866799999999999997598
No 375
>PRK08363 alanine aminotransferase; Validated
Probab=37.38 E-value=30 Score=15.16 Aligned_cols=43 Identities=9% Similarity=0.087 Sum_probs=21.6
Q ss_pred HHHHHHHHHHCCEEE--EE-CCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 999999997398799--97-1798228999858-9899999999837
Q gi|254780805|r 252 DLEKKISSKVGLNIS--IK-HRNNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 252 ~le~~L~~~lGtkV~--I~-~~~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
++..+|-+.-|.-|. .. ...+.|-+.|.|. +.++++.-+++|+
T Consensus 343 ef~~~ll~e~gV~v~PG~~Fg~~g~g~vRlsf~~~~e~l~eal~Rl~ 389 (398)
T PRK08363 343 EFVLDLLHEAHVLFVHGSGFGEYGAGHFRLVFLPPVEILEEAMDRFE 389 (398)
T ss_pred HHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf 99999998599999896432889998699998389999999999999
No 376
>PRK07682 hypothetical protein; Validated
Probab=37.24 E-value=30 Score=15.15 Aligned_cols=41 Identities=15% Similarity=0.233 Sum_probs=20.7
Q ss_pred HHHHHHHHHHCCEEEEE-----CCCCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf 99999999739879997-----17982289998589-899999999837
Q gi|254780805|r 252 DLEKKISSKVGLNISIK-----HRNNKGQFCIKYET-NEQLKIICSLLG 294 (300)
Q Consensus 252 ~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~s-~eeLe~Il~kL~ 294 (300)
++..+|-.. .+|-+. ...+.|-+.|.|.. .++|+.=+++|+
T Consensus 325 ~~~~~ll~~--~~V~v~PG~~Fg~~g~~~iRl~~a~~~e~l~eal~Rl~ 371 (378)
T PRK07682 325 EFAEQLLLE--EKVAVVPGSVFGESGEGFIRCSYATSLEQLQEAMKRMK 371 (378)
T ss_pred HHHHHHHHH--CCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 999999996--99999886222899989799996199999999999999
No 377
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=37.19 E-value=30 Score=15.14 Aligned_cols=33 Identities=21% Similarity=0.355 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 489999999852101110467999974337877865
Q gi|254780805|r 137 PLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 137 p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
++|...+|- .+..++-.+||..+|.||+.|.+.
T Consensus 7 sfddYv~yF---~eG~L~D~eIA~~LGVsr~nV~km 39 (181)
T pfam04645 7 SFDDYVAYF---KEGSLSDAEIAKELGVSRVNVWRM 39 (181)
T ss_pred HHHHHHHHH---HCCCCCHHHHHHHHCCHHHHHHHH
T ss_conf 289999999---617875799999978309999999
No 378
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=37.00 E-value=25 Score=15.63 Aligned_cols=38 Identities=21% Similarity=0.233 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21048999999985210111046799997433787786565
Q gi|254780805|r 134 DLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 134 dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
.|++-|.- .+ +...+ |.|-.|||..+|.|..||.-+|+
T Consensus 179 ~LT~RE~E-~L-~W~A~-GKTs~EIa~IL~ISe~TV~fHl~ 216 (240)
T PRK10188 179 NFSKREKE-IL-KWTAE-GKTSAEIAMILSISENTVNFHQK 216 (240)
T ss_pred CCCHHHHH-HH-HHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 89989999-99-99977-99999999883999999999999
No 379
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435 Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain..
Probab=36.66 E-value=25 Score=15.65 Aligned_cols=29 Identities=14% Similarity=0.363 Sum_probs=22.4
Q ss_pred HHHH-HHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9998-5210111046799997433787786
Q gi|254780805|r 143 GYEQ-LISEYGYTQNDIGSIVGKSRSHVAN 171 (300)
Q Consensus 143 ~~~~-l~~~~~~t~~~lA~~~G~s~s~V~~ 171 (300)
||=| +.+-.|+|-.++|.++|..++.|..
T Consensus 28 GWvR~~R~ALGms~~QLA~RlGV~p~Rv~~ 57 (150)
T TIGR02612 28 GWVRAIRKALGMSGAQLAARLGVTPQRVEA 57 (150)
T ss_pred CCHHHHHHHHCCCHHHHHHHCCCCHHHHHH
T ss_conf 616889877251578876652897377999
No 380
>PRK08443 consensus
Probab=36.52 E-value=31 Score=15.07 Aligned_cols=42 Identities=17% Similarity=0.267 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 999999999739879997-17--98228999858-9899999999837
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
..+..+|-+.-| |-+. .. +..|-+.|.|. +.+.++.=+++|.
T Consensus 336 ~~f~~~ll~~~g--V~v~PG~~Fg~~g~vRl~~~~~~e~l~ea~~RL~ 381 (388)
T PRK08443 336 MKFCKKLLEQEG--VAVVPGIGFGMEGYFRLSFATSIESIKKGIERIA 381 (388)
T ss_pred HHHHHHHHHHCC--EEEECCCCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf 999999998199--9997274358898599998288999999999999
No 381
>pfam00155 Aminotran_1_2 Aminotransferase class I and II.
Probab=36.44 E-value=31 Score=15.07 Aligned_cols=41 Identities=20% Similarity=0.324 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHCCEEEEEC---CCCCEEEEEEEC--CHHHHHHHHHHH
Q ss_conf 9999999997398799971---798228999858--989999999983
Q gi|254780805|r 251 TDLEKKISSKVGLNISIKH---RNNKGQFCIKYE--TNEQLKIICSLL 293 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~~---~~~kGkI~I~f~--s~eeLe~Il~kL 293 (300)
..+...|-+.-| |-+.- =+..|.|.|.|. +.|+++..++.|
T Consensus 306 ~~~~~~Ll~~~g--V~v~pG~~fg~~~~iRis~a~~s~e~i~~~~~rl 351 (351)
T pfam00155 306 KELAQVLLEEVG--VYVTPGSSPGVPGWLRITVAGGTEEELEELLEAI 351 (351)
T ss_pred HHHHHHHHHCCC--EEEECCCCCCCCCEEEEEECCCCHHHHHHHHHHC
T ss_conf 999999997598--9997788889999089981789999999999419
No 382
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY; InterPro: IPR014154 This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. All have a C-terminal helix-turn-helix DNA-binding region..
Probab=36.17 E-value=7.8 Score=18.91 Aligned_cols=120 Identities=18% Similarity=0.225 Sum_probs=60.6
Q ss_pred CCCCCCCCCCHHH---HHHHHHHHHHCCCCCCCEEECCCC-CCCC--------CCCCHHHHHHHHHHHCCCCCCCC-CCC
Q ss_conf 7899987689889---999999886310015504620565-4453--------33575677777642100135433-346
Q gi|254780805|r 50 NPHNPRNYFESEG---LEDLCQSIKSHGIIQPLIVRAIDN-GLYK--------IIAGERRFRAAKMASLSEVPVII-RNV 116 (300)
Q Consensus 50 ~p~~pR~~~~~~~---l~eLa~SI~~~G~lqPi~Vr~~~~-g~y~--------ii~G~rR~rAa~~~g~~~ip~iv-~~~ 116 (300)
+-++-|+ |.++- +.-+.++.....+-.|+.|.|.+. ..|. |+-|..|+ | +=|-+.. .+.
T Consensus 66 ~~~~~r~-FPeeY~~~~~~i~~T~AN~p~~~~lt~Fp~e~~~~~~~G~tTIvPi~G~G~RL------G-TliL~R~~~~F 137 (255)
T TIGR02787 66 KMFQDRK-FPEEYTKALVNIYDTEANIPVDSELTVFPEESRDLFPKGLTTIVPIYGSGERL------G-TLILARLDKEF 137 (255)
T ss_pred HHHHCCC-CCHHHHHHHHCCCCCCCCCCCCCCEEECCCCCHHHHCCCCEEEEEEEECCCHH------H-HHHEECCCCCC
T ss_conf 8874386-86577730002135504688998803514643433127966989731277102------0-21000027873
Q ss_pred CCHHHHHHHHH--------HHHHCCC-------CCHHHHH---------HHHHHHHHH-----CCCCHHHHHHHHHHHHH
Q ss_conf 41123455666--------5431022-------1048999---------999985210-----11104679999743378
Q gi|254780805|r 117 DNKSSLEIAIV--------ENVQRKD-------LNPLEEA---------LGYEQLISE-----YGYTQNDIGSIVGKSRS 167 (300)
Q Consensus 117 ~d~~~~~~~l~--------EN~~R~d-------l~p~e~A---------~~~~~l~~~-----~~~t~~~lA~~~G~s~s 167 (300)
+|+|....=+. -|.|++. -+....| +|.+..+++ ..++-..||+++|..||
T Consensus 138 ~DdDLvLaE~aaTVvG~elL~~~~~e~Eee~R~~a~VqmAi~TLSYSEL~AV~aIf~ELdG~EG~LvAS~IAD~vGITRS 217 (255)
T TIGR02787 138 NDDDLVLAEYAATVVGMELLRAKAEEIEEEARKKAAVQMAINTLSYSELEAVEAIFEELDGNEGLLVASKIADRVGITRS 217 (255)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCHH
T ss_conf 61377788899899999998866555699999999999998720288999999998422899662775302071266033
Q ss_pred HHHHHHHHHH
Q ss_conf 7786565654
Q gi|254780805|r 168 HVANILRILK 177 (300)
Q Consensus 168 ~V~~~LrLl~ 177 (300)
.|=|.||=++
T Consensus 218 VIVNALRKlE 227 (255)
T TIGR02787 218 VIVNALRKLE 227 (255)
T ss_pred HHHHHHHHHH
T ss_conf 5545434442
No 383
>TIGR03542 DAPAT_plant LL-diaminopimelate aminotransferase. This clade of the pfam00155 superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). This clade includes characterized species in plants and Chlamydia. Every member of this clade is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known succinylases, desuccinylases, acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct, NADPH-dependent enzyme (ddh).
Probab=36.04 E-value=32 Score=15.03 Aligned_cols=42 Identities=12% Similarity=0.082 Sum_probs=23.7
Q ss_pred HHHHHHHHHHCCEEEEE-----CCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 99999999739879997-----1798228999858-98999999998375
Q gi|254780805|r 252 DLEKKISSKVGLNISIK-----HRNNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 252 ~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
++...|-+.-| |-+- ...+.|-|.|.|. +.|+|+.=+++|++
T Consensus 353 ~~~~~ll~e~~--V~vvPG~~FG~~g~g~vRls~a~~~e~l~ea~~Rl~~ 400 (402)
T TIGR03542 353 DFFDFLLYQYH--IVGTPGSGFGSSGEGFVRFSAFGKRENIVAACERIKH 400 (402)
T ss_pred HHHHHHHHHCC--EEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 99999998599--9997644768999896999972999999999999997
No 384
>COG1438 ArgR Arginine repressor [Transcription]
Probab=35.90 E-value=32 Score=15.01 Aligned_cols=40 Identities=20% Similarity=0.208 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHCC-CCHHHHHHHHH-----HHHHHHHHHHHHHHHH
Q ss_conf 9999998521011-10467999974-----3378778656565435
Q gi|254780805|r 140 EALGYEQLISEYG-YTQNDIGSIVG-----KSRSHVANILRILKLP 179 (300)
Q Consensus 140 ~A~~~~~l~~~~~-~t~~~lA~~~G-----~s~s~V~~~LrLl~L~ 179 (300)
+-..+++++.+.. .||+||.+.+- .++++||+-|+-+.+-
T Consensus 7 R~~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~vTQaTvSRDlkelglv 52 (150)
T COG1438 7 RLELIKEIITEEKISTQEELVELLQEEGIEVTQATVSRDLKELGLV 52 (150)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHCCCEEEHHHHHHHHHHCCCE
T ss_conf 9999999998677778999999999829758639878779985988
No 385
>COG2456 Uncharacterized conserved protein [Function unknown]
Probab=35.56 E-value=11 Score=18.00 Aligned_cols=10 Identities=40% Similarity=0.760 Sum_probs=3.9
Q ss_pred HHHHHHHHHH
Q ss_conf 7999974337
Q gi|254780805|r 157 DIGSIVGKSR 166 (300)
Q Consensus 157 ~lA~~~G~s~ 166 (300)
++|+.+|..|
T Consensus 62 ~Ia~ilGlGR 71 (121)
T COG2456 62 EIAEILGLGR 71 (121)
T ss_pred HHHHHHCCCC
T ss_conf 9999956365
No 386
>TIGR01817 nifA Nif-specific regulatory protein; InterPro: IPR010113 This entry represents NifA, a DNA-binding regulatory protein for nitrogen fixation. Not included in this group are: the homologue in Aquifex aeolicus (which lacks nitrogenase), transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms. In diazotrophic proteobacteria, the sigma54-dependent activator NifA activates transcription of the nif (nitrogen fixation) genes by a conserved mechanism common to members of the enhancer binding protein family. Although NifA proteins have similar domain structures, both transcriptional regulation of nifA expression and posttranslational regulation of NifA activity by oxygen and fixed nitrogen vary significantly from one organism to another. In Klebsiella pneumoniae and Azotobacter vinelandii, nifA is co-ordinately transcribed with a second gene, nifL, whose product inhibits NifA activity in response to oxygen and fixed nitrogen .; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0009399 nitrogen fixation.
Probab=35.00 E-value=27 Score=15.50 Aligned_cols=19 Identities=16% Similarity=0.167 Sum_probs=9.1
Q ss_pred CCCHHHHHHHHHHHHHHCC
Q ss_conf 6897899999999997398
Q gi|254780805|r 245 EKEKYLTDLEKKISSKVGL 263 (300)
Q Consensus 245 ~k~~~i~~le~~L~~~lGt 263 (300)
+...||-.|.+.|-++|+.
T Consensus 387 ER~~DIP~LA~~fL~kf~~ 405 (574)
T TIGR01817 387 ERREDIPLLAEAFLEKFNR 405 (574)
T ss_pred CCCCHHHHHHHHHHHHHHH
T ss_conf 8731168999999998766
No 387
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=34.91 E-value=33 Score=14.91 Aligned_cols=28 Identities=32% Similarity=0.581 Sum_probs=24.6
Q ss_pred CCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf 5789998-768988999999988631001
Q gi|254780805|r 49 PNPHNPR-NYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 49 ~~p~~pR-~~~~~~~l~eLa~SI~~~G~l 76 (300)
-||.||- +.++.+.|..|++--++||++
T Consensus 165 CnPHNP~Grvwt~eeL~~i~elc~kh~v~ 193 (388)
T COG1168 165 CNPHNPTGRVWTKEELRKIAELCLRHGVR 193 (388)
T ss_pred ECCCCCCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf 37999998643699999999999983998
No 388
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=34.90 E-value=33 Score=14.91 Aligned_cols=49 Identities=27% Similarity=0.331 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCC
Q ss_conf 1104679999743378778656565435899998764210167777764010
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTS 203 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~ 203 (300)
.+|.++||+.+|.|+++.++..+= .+--.+.+.+..-.|. +|+.||...
T Consensus 199 ~isl~~lA~~~~lS~s~l~rlFk~-~~G~sp~~yl~~~Ri~--~A~~lL~~t 247 (290)
T PRK10572 199 EFDIESVAQHVCLSPSRLSHLFRQ-QLGISVLSWREDQRIS--RAKLLLSTT 247 (290)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH-HHCCCHHHHHHHHHHH--HHHHHHHCC
T ss_conf 999999998969799999999998-6498999999999999--999998738
No 389
>TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827 3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus . This entry is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis. The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=34.87 E-value=25 Score=15.72 Aligned_cols=75 Identities=25% Similarity=0.321 Sum_probs=40.7
Q ss_pred EEEHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCC---------HHHHHHHHHHHCCCCCC
Q ss_conf 403898235789998768988999999988631001550462056544533357---------56777776421001354
Q gi|254780805|r 41 CISIHSIVPNPHNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKIIAG---------ERRFRAAKMASLSEVPV 111 (300)
Q Consensus 41 ~i~i~~i~~~p~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii~G---------~rR~rAa~~~g~~~ip~ 111 (300)
.|+.|.|.|.+|+ |+ +| ++++|| ++.=.|+ .|=--++...| =.|||| |+=--|.|+|| |-|
T Consensus 9 dvDTD~IIPGrYL-R~-~~--D~~eLA-~haM~g~-~PeF~~kvr~G-DviVAGkNFGcGSSREQA~~ALK~aG---v~a 78 (159)
T TIGR02087 9 DVDTDVIIPGRYL-RT-TD--DPDELA-SHAMEGI-DPEFAKKVREG-DVIVAGKNFGCGSSREQAALALKAAG---VAA 78 (159)
T ss_pred CCCCCEECCCCCC-CC-CC--CHHHHH-HHCCCCC-CCCHHHHCCCC-CEEEECCCCCCCCCHHHHHHHHHHCC---EEE
T ss_conf 6467704585225-75-47--778899-8705589-96313407899-78871416477887788999997479---048
Q ss_pred CCCCCCCHHHHHHH
Q ss_conf 33346411234556
Q gi|254780805|r 112 IIRNVDNKSSLEIA 125 (300)
Q Consensus 112 iv~~~~d~~~~~~~ 125 (300)
||-+---.=.++-|
T Consensus 79 viA~SFARIFYRNA 92 (159)
T TIGR02087 79 VIAESFARIFYRNA 92 (159)
T ss_pred EEEEECCCHHHHHH
T ss_conf 98520166010323
No 390
>PRK12414 putative aminotransferase; Provisional
Probab=34.87 E-value=33 Score=14.91 Aligned_cols=23 Identities=13% Similarity=0.144 Sum_probs=15.9
Q ss_pred CEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 228999858-98999999998375
Q gi|254780805|r 273 KGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 273 kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.|-|.|.|. +.++|+.=+++|++
T Consensus 360 ~g~iRlsfa~~~e~l~eg~~RL~~ 383 (384)
T PRK12414 360 TGVIRLSFSKDDATLVEGARRLCS 383 (384)
T ss_pred CCEEEEEECCCHHHHHHHHHHHHC
T ss_conf 998999967999999999999703
No 391
>PRK07366 succinyldiaminopimelate transaminase; Validated
Probab=34.63 E-value=32 Score=15.02 Aligned_cols=44 Identities=9% Similarity=0.172 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHCCEEE--EE-CCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 9999999997398799--97-1798228999858-9899999999837
Q gi|254780805|r 251 TDLEKKISSKVGLNIS--IK-HRNNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~--I~-~~~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
.++..+|-+.-|.-|. .. ...+.|-|.|.|. +.+.|+.=+++|.
T Consensus 338 ~ef~~~Ll~~~gV~v~PG~~Fg~~g~g~iRl~~a~~~~~l~eal~Rl~ 385 (388)
T PRK07366 338 VEFCTQLVAQTGVAASPGSGFGKSGEGYVRFALVHDPDILEEAVERIA 385 (388)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 999999998399999766465889998699996299999999999999
No 392
>PRK09265 aminotransferase AlaT; Validated
Probab=34.55 E-value=33 Score=14.91 Aligned_cols=42 Identities=10% Similarity=0.038 Sum_probs=21.4
Q ss_pred HHHHHHHHHCCEEE--EEC-CCCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf 99999997398799--971-7982289998589-899999999837
Q gi|254780805|r 253 LEKKISSKVGLNIS--IKH-RNNKGQFCIKYET-NEQLKIICSLLG 294 (300)
Q Consensus 253 le~~L~~~lGtkV~--I~~-~~~kGkI~I~f~s-~eeLe~Il~kL~ 294 (300)
+..+|-+.-|.-|. .-. ....|-+.|.|.. .+.|+.=+++|.
T Consensus 351 f~~~Ll~e~gV~v~PG~~Fg~~~~~~vRlsf~~~~e~l~eal~Rl~ 396 (404)
T PRK09265 351 FVLDLLLQEKVLLVQGTGFNWPEPDHFRIVTLPRVDDLEDAIGRIG 396 (404)
T ss_pred HHHHHHHHCCEEEECCCCCCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 9999998699999778502889999899997999999999999999
No 393
>TIGR01818 ntrC nitrogen regulation protein NR(I); InterPro: IPR010114 This entry represents Nitrogen regulatory protein C (NtrC), which is a bacterial enhancer-binding protein that activates the transcription of genes encoding enzymes required for nitrogen metabolism. It is phosphorylated by NtrB and interacts with sigma-54. One of the best studied examples is its activation of the gene glnA, which encodes the enzyme glutamine synthetase.. NtrC is composed of three domains , . The 124 residue N-terminal domain is homologous to receiver domains of other response regulator proteins in two-component signal transduction systems , . The 240 residue central domain of NtrC is homologous to a domain found in all activators of the sigma-54 RNA polymerase holoenzyme , . The C-terminal domain has been indicated to contain the determinants necessary for both DNA-binding and dimerization of full-length NtrC.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0009399 nitrogen fixation, 0050906 detection of stimulus during sensory perception.
Probab=34.34 E-value=33 Score=14.91 Aligned_cols=15 Identities=20% Similarity=0.284 Sum_probs=10.1
Q ss_pred CHHHHHHHHHHHHCC
Q ss_conf 778999999764102
Q gi|254780805|r 218 SVRDTEELVQEQDNK 232 (300)
Q Consensus 218 SVRe~E~lVk~~~~~ 232 (300)
+||+.|++++.+..-
T Consensus 353 NVR~LEN~cR~l~~l 367 (471)
T TIGR01818 353 NVRELENVCRRLTVL 367 (471)
T ss_pred CHHHHHHHHHHHHHH
T ss_conf 524577899999873
No 394
>PRK09276 aspartate aminotransferase; Provisional
Probab=34.33 E-value=33 Score=14.94 Aligned_cols=45 Identities=13% Similarity=0.264 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 99999999973987999---71798228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++...|-+.-|.-|.= ....+.|-+.|.|. +.++++.=+++|++
T Consensus 336 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~iRl~~a~~~e~l~eal~Rl~k 384 (385)
T PRK09276 336 AEFATLLLDKAGIVVTPGNGFGTAGEGYFRIALTVPDERIEEAVERIKK 384 (385)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHC
T ss_conf 9999999981999998874218899886999975999999999999842
No 395
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=34.33 E-value=34 Score=14.85 Aligned_cols=18 Identities=22% Similarity=0.246 Sum_probs=9.2
Q ss_pred CCHHHHHHHHHHHHHHCC
Q ss_conf 104899999998521011
Q gi|254780805|r 135 LNPLEEALGYEQLISEYG 152 (300)
Q Consensus 135 l~p~e~A~~~~~l~~~~~ 152 (300)
.+|-+.+.+...|...++
T Consensus 108 ~~~~~~~~~~~~l~~~~~ 125 (304)
T PRK08154 108 ATPAQLARARDALSGMLG 125 (304)
T ss_pred CCHHHHHHHHHHHHHHHC
T ss_conf 899999999999876302
No 396
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=34.18 E-value=30 Score=15.16 Aligned_cols=26 Identities=19% Similarity=0.509 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHCCCCCCCEEECCCCCCCC
Q ss_conf 899999998863100155046205654453
Q gi|254780805|r 61 EGLEDLCQSIKSHGIIQPLIVRAIDNGLYK 90 (300)
Q Consensus 61 ~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ 90 (300)
..+.|=-..+...|++ .+++ +.|.|.
T Consensus 49 ~~VREAL~~L~~~GlV---~~r~-g~G~~V 74 (254)
T PRK09464 49 PSLREAIQRLEAKGLL---LRRQ-GGGTFV 74 (254)
T ss_pred HHHHHHHHHHHHCCCE---EEEC-CCCEEE
T ss_conf 5999999999988998---9717-871364
No 397
>PRK08361 aspartate aminotransferase; Provisional
Probab=34.16 E-value=34 Score=14.84 Aligned_cols=44 Identities=18% Similarity=0.184 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf 99999999973987999---717982289998589-899999999837
Q gi|254780805|r 251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYET-NEQLKIICSLLG 294 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~s-~eeLe~Il~kL~ 294 (300)
.++.+.|-+.-|.-|.= -...+.|-+.|.|.. .+++..=+++|.
T Consensus 337 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~iRl~f~~~~e~l~eal~Rl~ 384 (390)
T PRK08361 337 EDFSEWLLEKARVVVIPGTAFGKMGEGYVRISYATSKEKLIEAMERME 384 (390)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 999999997199999887322889999799997299999999999999
No 398
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=34.15 E-value=34 Score=14.83 Aligned_cols=51 Identities=20% Similarity=0.324 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHH-HC-CEEEEECC-C-CCEEEEEEECCHHHHHHHHHHHCCCCCC
Q ss_conf 899999999997-39-87999717-9-8228999858989999999983756456
Q gi|254780805|r 249 YLTDLEKKISSK-VG-LNISIKHR-N-NKGQFCIKYETNEQLKIICSLLGENDFE 299 (300)
Q Consensus 249 ~i~~le~~L~~~-lG-tkV~I~~~-~-~kGkI~I~f~s~eeLe~Il~kL~~~~~~ 299 (300)
-+..+..-|.+. +. +.+.|.+. . -.|.+.|.|++.+++++=.+.|.+.+++
T Consensus 14 ~Ia~vt~~L~~~~IsI~nI~Il~~RE~~~GvLri~F~~~~d~~~A~~~L~~~~Y~ 68 (69)
T cd04909 14 VIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQEDRERAKEILKEAGYE 68 (69)
T ss_pred HHHHHHHHHHHCCCCEEEEEEEEEECCCCCEEEEEECCHHHHHHHHHHHHHCCCC
T ss_conf 6999999999879874724876851478847999968989999999999984951
No 399
>PRK11414 putative DNA-binding transcriptional regulator; Provisional
Probab=34.10 E-value=33 Score=14.92 Aligned_cols=15 Identities=7% Similarity=0.120 Sum_probs=4.8
Q ss_pred CCCCCCCCCCCCCHH
Q ss_conf 235789998768988
Q gi|254780805|r 47 IVPNPHNPRNYFESE 61 (300)
Q Consensus 47 i~~~p~~pR~~~~~~ 61 (300)
|.-.-+.|=....+.
T Consensus 24 I~~G~l~PG~~L~e~ 38 (221)
T PRK11414 24 LSIGALKPGARLITK 38 (221)
T ss_pred HHCCCCCCCCCCCHH
T ss_conf 983998995971899
No 400
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=34.02 E-value=27 Score=15.51 Aligned_cols=31 Identities=23% Similarity=0.302 Sum_probs=18.5
Q ss_pred CHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCC
Q ss_conf 9889999999886310015504620565445333
Q gi|254780805|r 59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYKII 92 (300)
Q Consensus 59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ii 92 (300)
++..+.-...|++..|+..- +|-+.|+|.--
T Consensus 38 npGTVRNqmq~LkaLgLVeg---vpGPkGGY~PT 68 (294)
T COG2524 38 NPGTVRNQMQSLKALGLVEG---VPGPKGGYKPT 68 (294)
T ss_pred CCCHHHHHHHHHHHCCCCCC---CCCCCCCCCCC
T ss_conf 96169999999885275225---66898896533
No 401
>PRK06030 hypothetical protein; Provisional
Probab=33.93 E-value=34 Score=14.81 Aligned_cols=37 Identities=11% Similarity=0.214 Sum_probs=25.6
Q ss_pred HHHHHHHHHHH--HHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999852--10111046799997433787786565
Q gi|254780805|r 138 LEEALGYEQLI--SEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 138 ~e~A~~~~~l~--~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
+-.++-+..++ ..+|++..++|..+|++++||..-.+
T Consensus 65 var~RQIAMYLahv~~~~sl~~Ig~~FgRDrTTv~HAc~ 103 (136)
T PRK06030 65 VSRIRQIAMYVAHTSLGMPMNEVALGFARDRTTVGHACH 103 (136)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 638999999999998678899999997643159999999
No 402
>pfam07453 NUMOD1 NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs).
Probab=33.70 E-value=17 Score=16.71 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=19.1
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 21011104679999743378778656
Q gi|254780805|r 148 ISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 148 ~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
+..|. |..++|+.+|.++++|++++
T Consensus 13 i~~f~-Si~~aa~~L~i~~~tI~~~~ 37 (37)
T pfam07453 13 IGKFS-SIREAARALGISHSTINKYL 37 (37)
T ss_pred EEHHH-HHHHHHHHHCCCHHHHHCCC
T ss_conf 62246-79999998476465665029
No 403
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=33.31 E-value=35 Score=14.75 Aligned_cols=69 Identities=16% Similarity=0.148 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCH--HHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf 1046799997433787786565654358999987642101677777640100--46899997422247789999997641
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSD--PLSLAQVIVSKKMSVRDTEELVQEQD 230 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~--~~~la~~Ii~~~LSVRe~E~lVk~~~ 230 (300)
||-.++|+..|.|..+|..|-+..=|||.-... .| .| +.+-.+ ...+....-.-++|+.++..++....
T Consensus 1 ytIgelA~~~Gvs~~TiRyYe~~GLl~~~~Rt~--~G------yR-~Y~~~~l~rL~fI~~~r~~G~sl~eI~~lL~~~d 71 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARTE--GG------YG-LFDDCALQRLRFVRAAFEAGIGLDELARLCRALD 71 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC--CC------CC-CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf 958899999788948998999878989988899--98------81-3599999999999999987999999999996053
No 404
>PRK08912 hypothetical protein; Provisional
Probab=33.00 E-value=35 Score=14.71 Aligned_cols=42 Identities=7% Similarity=0.075 Sum_probs=21.2
Q ss_pred HHHHHHHHHCCEEE---EEC--CCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 99999997398799---971--798228999858-9899999999837
Q gi|254780805|r 253 LEKKISSKVGLNIS---IKH--RNNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 253 le~~L~~~lGtkV~---I~~--~~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
...+|-+.-|.-|. ... ...+|-|.|.|. +.|+++.=+++|.
T Consensus 334 f~~~ll~e~gV~~vPG~~F~~~~~~~~~iRlsfa~~~e~l~ea~~RL~ 381 (387)
T PRK08912 334 FCRRLVEEAGVAAIPVSAFYEEDPVTSVVRFCFAKRDATLDEAVERLA 381 (387)
T ss_pred HHHHHHHHCCEEEECCCCCCCCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 999999968999981501289999998599997999999999999999
No 405
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=32.93 E-value=35 Score=14.71 Aligned_cols=22 Identities=14% Similarity=0.223 Sum_probs=11.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0467999974337877865656
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrL 175 (300)
|.++||+.+|.+...|...+++
T Consensus 264 t~eEiA~~lg~~~~~v~~~~~~ 285 (398)
T PRK05901 264 TPEELAEEMDFTPEKVREIQKY 285 (398)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999998819999999999997
No 406
>TIGR03558 oxido_grp_1 luciferase family oxidoreductase, group 1. The Pfam domain family pfam00296 is named for luciferase-like monooxygenases, but the family also contains several coenzyme F420-dependent enzymes. This protein family represents a well-resolved clade within family pfam00296 and shows no restriction to coenzyme F420-positive species, unlike some other clades within pfam00296.
Probab=32.85 E-value=7.4 Score=19.07 Aligned_cols=63 Identities=13% Similarity=0.051 Sum_probs=24.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCC-CCCCCEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCC
Q ss_conf 57899987689889999999886310-01550462056544533357567777764210013543
Q gi|254780805|r 49 PNPHNPRNYFESEGLEDLCQSIKSHG-IIQPLIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVI 112 (300)
Q Consensus 49 ~~p~~pR~~~~~~~l~eLa~SI~~~G-~lqPi~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~i 112 (300)
.++...+..|+ +.+++|..-+...+ -.+++.++|.....-.+..+..--..+..++..-++.+
T Consensus 119 ~~~~~~~~~f~-e~~~~l~~~~~~~~~~~~~v~~~P~~~~~ppiw~~~~s~~s~~~Aa~~G~~~~ 182 (323)
T TIGR03558 119 RGLDARADDFP-EQVAELQAYLGPEGHPYQGVRAVPGPGTNPPLWLLGSSLYSAQLAAELGLPFA 182 (323)
T ss_pred CCHHHHHHHHH-HHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEECCCHHHHHHHHHCCCCEE
T ss_conf 45020576689-99999999856788788862123899999986897088489999998499620
No 407
>PRK08175 aminotransferase; Validated
Probab=32.85 E-value=35 Score=14.70 Aligned_cols=41 Identities=7% Similarity=0.186 Sum_probs=21.0
Q ss_pred HHHHHHHHHHCCEEEEE-----CCCCCEEEEEEECCH-HHHHHHHHHHC
Q ss_conf 99999999739879997-----179822899985898-99999999837
Q gi|254780805|r 252 DLEKKISSKVGLNISIK-----HRNNKGQFCIKYETN-EQLKIICSLLG 294 (300)
Q Consensus 252 ~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f~s~-eeLe~Il~kL~ 294 (300)
++..+|-+.- +|-+. ...+.|-|.|.|... +.++.=+++|+
T Consensus 338 ef~~~ll~e~--~V~v~PG~~Fg~~g~~~vRl~~~~~~~~l~eal~Ri~ 384 (395)
T PRK08175 338 EFAKKLLNEA--KVCVSPGIGFGDYGDTHVRFALIENRDRIRQAVRGIK 384 (395)
T ss_pred HHHHHHHHHC--CEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 9999999849--8999777332779998699997289999999999999
No 408
>pfam00157 Pou Pou domain - N-terminal to homeobox domain.
Probab=32.82 E-value=36 Score=14.70 Aligned_cols=34 Identities=29% Similarity=0.476 Sum_probs=23.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHH------HHHHHHHHHH
Q ss_conf 999998521011104679999743------3787786565
Q gi|254780805|r 141 ALGYEQLISEYGYTQNDIGSIVGK------SRSHVANILR 174 (300)
Q Consensus 141 A~~~~~l~~~~~~t~~~lA~~~G~------s~s~V~~~Lr 174 (300)
|..|+.-.=..|+||.+++..+|. |+++|++.=+
T Consensus 13 a~~fk~rRi~LG~TQ~dVg~al~~l~G~~~SQttIcRFE~ 52 (75)
T pfam00157 13 AKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEA 52 (75)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 9999998987377599999999987086542358888885
No 409
>PRK06108 aspartate aminotransferase; Provisional
Probab=32.66 E-value=36 Score=14.68 Aligned_cols=44 Identities=16% Similarity=0.196 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHCCEEE---EECCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 9999999997398799---971798228999858-9899999999837
Q gi|254780805|r 251 TDLEKKISSKVGLNIS---IKHRNNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~---I~~~~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
.++...|-+..|.-|. .-...+.|-|.|.|. +.++|+.=+++|+
T Consensus 330 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~iRl~~a~~~~~l~eal~RL~ 377 (382)
T PRK06108 330 LALAKRLVDEAGLGLAPGTAFGPGGEGFLRWCFARDPARLDEGVERLR 377 (382)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 999999999699999878411889999799996299999999999999
No 410
>TIGR01265 tyr_nico_aTase tyrosine/nicotianamine aminotransferases; InterPro: IPR005958 This entry describes tyrosine aminotransferase (2.6.1.5 from EC) as found in animals and Trypanosoma cruzi (Euglenozoa). It is the first enzyme of a pathway of tyrosine degradation via homogentisate. L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase, an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway are included in this family. ; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding, 0006519 amino acid and derivative metabolic process.
Probab=32.63 E-value=36 Score=14.68 Aligned_cols=77 Identities=27% Similarity=0.487 Sum_probs=47.5
Q ss_pred CCC-CCCCCEEEEHHHC------------CCCCCCCC-CCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCCC-CCCCCH-
Q ss_conf 013-4566024038982------------35789998-7689889999999886310015504620565445-333575-
Q gi|254780805|r 32 TET-IPESQDCISIHSI------------VPNPHNPR-NYFESEGLEDLCQSIKSHGIIQPLIVRAIDNGLY-KIIAGE- 95 (300)
Q Consensus 32 ~~~-~~~~~~~i~i~~i------------~~~p~~pR-~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y-~ii~G~- 95 (300)
... .+++-=+|+|+.| .-||.||= -.|+.+.|+++++.=+++|++ |+- |.=| -+|.|.
T Consensus 161 ydLdlPe~~WeiDL~~le~l~DekT~A~vv~NP~NPCGsVF~~~HL~k~~~~A~kl~i~--iIA----DEiY~~~Vf~dk 234 (424)
T TIGR01265 161 YDLDLPEKDWEIDLDGLESLADEKTVAIVVINPSNPCGSVFSRDHLEKIAEVARKLGIP--IIA----DEIYGHLVFGDK 234 (424)
T ss_pred CCCCCCCCCCEECHHHHHHHHCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCC--EEE----EEECCCCCCCCC
T ss_conf 24678887523647899876326876999847566788887888899999999870982--687----763164144889
Q ss_pred ---HHHHHHHHHHCCCCCCCCCC
Q ss_conf ---67777764210013543334
Q gi|254780805|r 96 ---RRFRAAKMASLSEVPVIIRN 115 (300)
Q Consensus 96 ---rR~rAa~~~g~~~ip~iv~~ 115 (300)
--+-+.-.+. ..||+++..
T Consensus 235 DPn~~F~p~a~f~-~~VPvl~lG 256 (424)
T TIGR01265 235 DPNAPFVPMASFA-SIVPVLSLG 256 (424)
T ss_pred CCCCCCCCCCCCC-CCCCEEEEC
T ss_conf 7888622300357-868868863
No 411
>PRK07568 aspartate aminotransferase; Provisional
Probab=32.44 E-value=36 Score=14.66 Aligned_cols=44 Identities=20% Similarity=0.336 Sum_probs=23.0
Q ss_pred HHHHHHHHHH---CCEEEEE----C--CC--CCEEEEEEE-CCHHHHHHHHHHHCC
Q ss_conf 9999999973---9879997----1--79--822899985-898999999998375
Q gi|254780805|r 252 DLEKKISSKV---GLNISIK----H--RN--NKGQFCIKY-ETNEQLKIICSLLGE 295 (300)
Q Consensus 252 ~le~~L~~~l---GtkV~I~----~--~~--~kGkI~I~f-~s~eeLe~Il~kL~~ 295 (300)
+....|-+.+ +..|-+- . .. ++|-|.|.| .+.|+++.=+++|++
T Consensus 333 ~f~~~ll~~~~~~~~~V~v~PG~~F~~~~g~g~~~iRls~~~~~e~l~ea~~Rl~~ 388 (396)
T PRK07568 333 DFAKWMLTDFEYNGETVMVAPASGFYATPGLGKDEIRIAYVLEKEDLRRAMEILKK 388 (396)
T ss_pred HHHHHHHHHHHHCCCEEEEECCHHHCCCCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf 99999999621248869997763416899899996999971999999999999999
No 412
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=32.27 E-value=36 Score=14.64 Aligned_cols=20 Identities=15% Similarity=0.212 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q ss_conf 46799997433787786565
Q gi|254780805|r 155 QNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 155 ~~~lA~~~G~s~s~V~~~Lr 174 (300)
-.++|+.+|.|..++.-|=+
T Consensus 3 Ige~A~~~gvs~~tlR~Ye~ 22 (123)
T cd04770 3 IGELAKAAGVSPDTIRYYER 22 (123)
T ss_pred HHHHHHHHCCCHHHHHHHHH
T ss_conf 89999998959999999998
No 413
>pfam06056 Terminase_5 Putative ATPase subunit of terminase (gpP-like). This family of proteins are annotated as ATPase subunits of phage terminase after. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.
Probab=32.16 E-value=23 Score=15.92 Aligned_cols=22 Identities=23% Similarity=0.339 Sum_probs=18.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 1110467999974337877865
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANI 172 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~ 172 (300)
-||+..+||+.+|.+.++|..-
T Consensus 12 qg~~~~eIA~~Lg~~~~tVysW 33 (58)
T pfam06056 12 QGYRPAEIAQELGLKARTVYSW 33 (58)
T ss_pred CCCCHHHHHHHHCCCCCHHHHH
T ss_conf 6898999999978993145658
No 414
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=31.74 E-value=37 Score=14.58 Aligned_cols=28 Identities=18% Similarity=0.436 Sum_probs=14.9
Q ss_pred CHHHHHHHHHHHHHCCCCCCCEEECCCCCCCC
Q ss_conf 98899999998863100155046205654453
Q gi|254780805|r 59 ESEGLEDLCQSIKSHGIIQPLIVRAIDNGLYK 90 (300)
Q Consensus 59 ~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g~y~ 90 (300)
+-..+.|=-..+...|++ .+++ +.|.|.
T Consensus 39 SRt~VREAL~~L~~eGlV---~~~~-g~G~~V 66 (253)
T PRK10421 39 SRNSLREALAKLVSEGVL---LSRR-GGGTFI 66 (253)
T ss_pred CHHHHHHHHHHHHHCCCE---EEEE-CCEEEE
T ss_conf 989999999999988987---9975-782487
No 415
>TIGR02404 trehalos_R_Bsub trehalose operon repressor; InterPro: IPR012770 This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from Escherichia coli..
Probab=31.69 E-value=34 Score=14.79 Aligned_cols=31 Identities=19% Similarity=0.350 Sum_probs=21.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 0467999974337877865656543589999
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILKLPSSVRE 184 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~ 184 (300)
|-.+|.+..|-||.||++.|.+|.=.=.||.
T Consensus 26 SE~~L~~~Y~~SReTvRKAL~~L~~~GyIQK 56 (236)
T TIGR02404 26 SEHELMEQYGASRETVRKALNLLTEAGYIQK 56 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf 8789998606874588999999985787167
No 416
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=31.58 E-value=37 Score=14.57 Aligned_cols=68 Identities=19% Similarity=0.206 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 1046799997433787786565654358999987642101677777640100468999974222477899999976
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEELVQE 228 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~lVk~ 228 (300)
+|-.++|+.+|.+.+++.-|=+.-=|||+--+. .-...+..+.. ..........-++|..++..++..
T Consensus 1 ysI~eva~~~gvs~~tlR~Ye~~GLl~p~r~~~-g~R~Y~~~~i~-------~l~~I~~lr~~G~sl~~I~~~l~~ 68 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSEN-GYRLYSEEDLE-------RLRLIRRLRELGLSLKEIRELLDA 68 (100)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC-CCCCCCHHHHH-------HHHHHHHHHHCCCCHHHHHHHHHC
T ss_conf 978899999895999999998769999883589-97425699999-------999999999979999999999835
No 417
>PRK07777 aminotransferase; Validated
Probab=31.52 E-value=37 Score=14.56 Aligned_cols=44 Identities=11% Similarity=0.101 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHCCEEE---EE---CCCCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 9999999997398799---97---1798228999858-9899999999837
Q gi|254780805|r 251 TDLEKKISSKVGLNIS---IK---HRNNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~---I~---~~~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
..+...|.+..|.-|. .. .....+-|.|.|. +.|+|+.=+++|+
T Consensus 331 ~~f~~~L~~~~gV~v~PG~~F~~~~~~g~~~vRlsf~~~~e~l~ea~~RL~ 381 (386)
T PRK07777 331 TAFCRALPERVGVAAIPMSAFCDPADAWNHLVRFAFCKRDDTLDEAIRRLR 381 (386)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 999999998689999887442889877899799996899999999999999
No 418
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=31.45 E-value=35 Score=14.74 Aligned_cols=16 Identities=0% Similarity=0.256 Sum_probs=8.8
Q ss_pred HHHHHHHHCCCCHHHH
Q ss_conf 8999974222477899
Q gi|254780805|r 207 SLAQVIVSKKMSVRDT 222 (300)
Q Consensus 207 ~la~~Ii~~~LSVRe~ 222 (300)
++.+.+...|++.-++
T Consensus 60 ~~~e~l~~~Gid~~eL 75 (135)
T PRK10947 60 QYREMLIADGIDPNEL 75 (135)
T ss_pred HHHHHHHHCCCCHHHH
T ss_conf 9999999859999999
No 419
>PRK07681 aspartate aminotransferase; Provisional
Probab=30.99 E-value=38 Score=14.50 Aligned_cols=47 Identities=11% Similarity=0.196 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHCCEEEE--E-CCCCCEEEEEEE-CCHHHHHHHHHHHCCCC
Q ss_conf 99999999973987999--7-179822899985-89899999999837564
Q gi|254780805|r 251 TDLEKKISSKVGLNISI--K-HRNNKGQFCIKY-ETNEQLKIICSLLGEND 297 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I--~-~~~~kGkI~I~f-~s~eeLe~Il~kL~~~~ 297 (300)
.++...|-+..|.-|.= . ...+.|-|.|.| .+.++|+.-+++|++.+
T Consensus 336 ~~f~~~Ll~~~gV~v~PG~~Fg~~g~g~iRl~f~~~~e~l~eal~RLk~a~ 386 (399)
T PRK07681 336 LDFAYALMDRANVVVTPGHAFGPHGEGFVRIALVQDKEVLQQVVENIRNSG 386 (399)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHCC
T ss_conf 999999998299999886465899988699997188999999999998888
No 420
>COG0436 Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=30.94 E-value=38 Score=14.50 Aligned_cols=47 Identities=15% Similarity=0.216 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHCCEEEE--EC-C-CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 8999999999973987999--71-7-98228999858-98999999998375
Q gi|254780805|r 249 YLTDLEKKISSKVGLNISI--KH-R-NNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 249 ~i~~le~~L~~~lGtkV~I--~~-~-~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
+-.++..+|-+..|.-|.= -. . .+.|-|.|.|. +.++++..++.|..
T Consensus 336 d~~~f~~~Ll~~~gV~v~PG~~Fg~~~g~~~vRis~~~~~~~l~~a~~rl~~ 387 (393)
T COG0436 336 DSEEFAKKLLEEAGVAVVPGSGFGEPPGEGYVRLSLATSEETLEEALRRLAR 387 (393)
T ss_pred CHHHHHHHHHHHCCEEEECHHHHCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 9899999999867999957257497877987999973689999999999999
No 421
>PRK06575 consensus
Probab=30.84 E-value=38 Score=14.49 Aligned_cols=43 Identities=19% Similarity=0.369 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 999999999739879997-17--98228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++.+.|-+.- +|-+. .. +..|-+.|.|. +.++|+.-+++|++
T Consensus 348 ~~f~~~Ll~e~--~V~v~PG~~FG~~g~~Rl~~a~~~e~l~ea~~Rl~~ 394 (399)
T PRK06575 348 NDFAEYLLEEA--KVAVVPGIAFGLEGYFRISYATSMEELEEACIRIER 394 (399)
T ss_pred HHHHHHHHHHC--CEEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf 99999999729--999984855589983999973989999999999999
No 422
>TIGR03539 DapC_actino succinyldiaminopimelate transaminase. This family of actinobacterial succinyldiaminopimelate transaminase enzymes (DapC) are members of the pfam00155 superfamily. Many of these genes appear adjacent to other genes encoding enzymes of the lysine biosynthesis via diaminopimelate pathway (GenProp0125).
Probab=30.62 E-value=39 Score=14.46 Aligned_cols=42 Identities=14% Similarity=0.195 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHCCEEEEE-----CCCCCEEEEEEE-CCHHHHHHHHHHHC
Q ss_conf 9999999999739879997-----179822899985-89899999999837
Q gi|254780805|r 250 LTDLEKKISSKVGLNISIK-----HRNNKGQFCIKY-ETNEQLKIICSLLG 294 (300)
Q Consensus 250 i~~le~~L~~~lGtkV~I~-----~~~~kGkI~I~f-~s~eeLe~Il~kL~ 294 (300)
.....+.|.+. | |-+. ...+.|-|.|.| .+.|+|+.=+++|.
T Consensus 310 ~~~~~~~l~e~-g--V~v~PG~~Fg~~g~~~vRis~~~~~e~l~eal~Rls 357 (357)
T TIGR03539 310 AWDTVDRLAEL-G--ILVAPGDFYGPAGSQHVRVALTATDERIAAAVARLT 357 (357)
T ss_pred HHHHHHHHHHC-C--EEEECCCCCCCCCCCEEEEEECCCHHHHHHHHHHCC
T ss_conf 99999999969-9--899478744789999799997299999999998575
No 423
>PRK07310 consensus
Probab=30.35 E-value=34 Score=14.86 Aligned_cols=44 Identities=25% Similarity=0.307 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHCCEEEEECC--CCCEEEEEEECC-HHHHHHHHHHHC
Q ss_conf 999999999973987999717--982289998589-899999999837
Q gi|254780805|r 250 LTDLEKKISSKVGLNISIKHR--NNKGQFCIKYET-NEQLKIICSLLG 294 (300)
Q Consensus 250 i~~le~~L~~~lGtkV~I~~~--~~kGkI~I~f~s-~eeLe~Il~kL~ 294 (300)
..++...|-+..|.-|. ... +..|.|.|.|.. .+.|+.-+++|+
T Consensus 341 ~~~~~~~ll~~~gV~v~-PG~~FG~~~~vRl~~a~~~~~l~eal~RL~ 387 (395)
T PRK07310 341 VTDFTTAILEEVGVALV-TGAGFGAPENVRLSYATDLETLKEAVRRLH 387 (395)
T ss_pred HHHHHHHHHHHCCEEEE-CCCCCCCCCCEEEEECCCHHHHHHHHHHHH
T ss_conf 99999999984999998-897669999889998099999999999999
No 424
>PRK09082 putative aminotransferase; Validated
Probab=30.14 E-value=39 Score=14.41 Aligned_cols=44 Identities=9% Similarity=0.081 Sum_probs=22.6
Q ss_pred HHHHHHHHHHCCEEE---EECC--CCCEEEEEEECC-HHHHHHHHHHHCC
Q ss_conf 999999997398799---9717--982289998589-8999999998375
Q gi|254780805|r 252 DLEKKISSKVGLNIS---IKHR--NNKGQFCIKYET-NEQLKIICSLLGE 295 (300)
Q Consensus 252 ~le~~L~~~lGtkV~---I~~~--~~kGkI~I~f~s-~eeLe~Il~kL~~ 295 (300)
++...|.+.-|.-|. .... .+.|-|.|.|.. .++++.=+++|.+
T Consensus 336 ~f~~~l~~e~gV~v~PG~~F~~~~~~~~~iRl~fa~~~e~l~ea~~RLak 385 (386)
T PRK09082 336 EFCQWLTREHGVAAIPLSVFYADPFPHRLVRFCFAKQEETLDAAAERLCQ 385 (386)
T ss_pred HHHHHHHHHCCEEEECCHHHCCCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf 99999998589999827110579999997999968999999999999842
No 425
>KOG3398 consensus
Probab=30.05 E-value=39 Score=14.40 Aligned_cols=41 Identities=20% Similarity=0.287 Sum_probs=31.5
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 22104899999998521011104679999743378778656
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
-+-.+.+-..++++-..+-||||.+||.++......|..|=
T Consensus 67 ~~~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyE 107 (135)
T KOG3398 67 HDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYE 107 (135)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 23014789999999888637548899999602861365575
No 426
>pfam10279 Latarcin Latarcin precursor. This family represents the precursor proteins for a number of short antimicrobial peptides called Latarcins. Latarcins were discovered in the venom of the spider Lachesana tarabaevi. Latarcins are likely to adopt amphipathic alpha-helical structure in the plasma membrane.
Probab=29.99 E-value=40 Score=14.40 Aligned_cols=19 Identities=37% Similarity=0.604 Sum_probs=15.3
Q ss_pred HHHHHH-CCCCCHHHHHHHH
Q ss_conf 665431-0221048999999
Q gi|254780805|r 126 IVENVQ-RKDLNPLEEALGY 144 (300)
Q Consensus 126 l~EN~~-R~dl~p~e~A~~~ 144 (300)
+.||++ ++|+...|+|+++
T Consensus 50 ~~e~l~kled~~~~EEARg~ 69 (88)
T pfam10279 50 IAEALEKLEDFENTEEARGF 69 (88)
T ss_pred HHHHHHHHCCCCCHHHHHHH
T ss_conf 99998863263217999988
No 427
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=29.96 E-value=35 Score=14.76 Aligned_cols=29 Identities=14% Similarity=0.203 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 11104679999743378778656565435
Q gi|254780805|r 151 YGYTQNDIGSIVGKSRSHVANILRILKLP 179 (300)
Q Consensus 151 ~~~t~~~lA~~~G~s~s~V~~~LrLl~L~ 179 (300)
.--|.++||..+||+---|+..|.|..=+
T Consensus 154 ~EpS~eeiA~~~~kpvedv~~~L~Lne~~ 182 (292)
T TIGR02394 154 REPSVEEIAELLDKPVEDVSKVLALNERI 182 (292)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHCCCC
T ss_conf 77887899988389888999998417995
No 428
>PRK07309 aromatic amino acid aminotransferase; Validated
Probab=29.93 E-value=40 Score=14.39 Aligned_cols=46 Identities=15% Similarity=0.156 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHCCEEEE--E-CCCCCEEEEEEEC-CHHHHHHHHHHHCCC
Q ss_conf 99999999973987999--7-1798228999858-989999999983756
Q gi|254780805|r 251 TDLEKKISSKVGLNISI--K-HRNNKGQFCIKYE-TNEQLKIICSLLGEN 296 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I--~-~~~~kGkI~I~f~-s~eeLe~Il~kL~~~ 296 (300)
.++...|.+.-|.-|.= . ...+.|-+.|.|. +.++|+.=+++|++-
T Consensus 336 ~~~~~~l~~~~gV~v~PG~~Fg~~g~g~iRl~~a~~~e~l~eal~Rl~~~ 385 (390)
T PRK07309 336 FKFLQDFAKEKAVAIIPGVAFGPYGEGYVRLSYAASMETIKEAMKRLKEY 385 (390)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHH
T ss_conf 99999999969999977732288999879999828999999999999999
No 429
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=29.84 E-value=40 Score=14.38 Aligned_cols=47 Identities=13% Similarity=0.162 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf 11046799997433787786565654358999987642101677777640
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVS 201 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~ 201 (300)
.+|.+++|+.+|.|+++.++..+- .....+.+.+..-.+. +|+.||.
T Consensus 21 ~i~l~~lA~~~~~S~~~l~r~Fk~-~~g~t~~~yi~~~Rl~--~A~~lL~ 67 (107)
T PRK10219 21 PLNIDVVAKKSGYSKWYLQRMFRT-VTHQTLGDYIRQRRLL--LAAVELR 67 (107)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH-HHCCCHHHHHHHHHHH--HHHHHHH
T ss_conf 999999998989399999999999-9890999999999999--9999988
No 430
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=29.69 E-value=40 Score=14.36 Aligned_cols=44 Identities=18% Similarity=0.162 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 22104899999998521---011104679999743378778656565
Q gi|254780805|r 133 KDLNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
.+|+|-|+-.+=.-|-. ...+|-.++|+..|.|.++|.|.-+=+
T Consensus 12 ~~Lt~~Ek~iA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkL 58 (284)
T PRK11302 12 EHLSKSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSL 58 (284)
T ss_pred HHCCHHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 64599999999999809899976669999989699888999999995
No 431
>TIGR03538 DapC_gpp succinyldiaminopimelate transaminase. This family of succinyldiaminopimelate transaminases (DapC) includes the experimentally characterized enzyme from Bordatella pertussis. The majority of genes in this family are proximal to genes encoding components of the lysine biosynthesis via diaminopimelate pathway (GenProp0125).
Probab=29.68 E-value=40 Score=14.36 Aligned_cols=24 Identities=13% Similarity=0.059 Sum_probs=16.5
Q ss_pred CCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 8228999858-98999999998375
Q gi|254780805|r 272 NKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 272 ~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
+.|-|.|.|. +.++|+.=+++|.+
T Consensus 368 G~g~iR~s~~~~~e~l~ea~~Rl~~ 392 (394)
T TIGR03538 368 GAGRVRIALVAPLEECVEAAERIRR 392 (394)
T ss_pred CCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf 9998999975989999999999998
No 432
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=29.66 E-value=40 Score=14.36 Aligned_cols=32 Identities=22% Similarity=0.299 Sum_probs=27.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99998521011104679999743378778656
Q gi|254780805|r 142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
..+++++++.|+|..+.|++-|...|+....|
T Consensus 19 ~~l~~~l~Elglt~~eFak~anIP~StLYKil 50 (170)
T COG4800 19 SCLQKLLDELGLTPSEFAKRANIPLSTLYKIL 50 (170)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHH
T ss_conf 99999999819998999887099899999998
No 433
>PRK05942 aspartate aminotransferase; Provisional
Probab=29.15 E-value=41 Score=14.30 Aligned_cols=48 Identities=15% Similarity=0.172 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHCCCCC
Q ss_conf 99999999973987999---71798228999858-98999999998375645
Q gi|254780805|r 251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLGENDF 298 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~~~~~ 298 (300)
.++...|-+.-|.-|.= ....+.|-|.|.|. +.++++.=+++|.+.-.
T Consensus 340 ~~f~~~ll~~~gV~v~PG~~Fg~~g~~~iRlsf~~~~~~l~ea~~Rl~~a~~ 391 (394)
T PRK05942 340 TDFALNVLQKTGVVVTPGNAFGEGGEGYVRISLIADCDRLGEALHRIKQAGI 391 (394)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHHHHH
T ss_conf 9999999984999998873117899987999971889999999999999998
No 434
>PRK07337 aminotransferase; Validated
Probab=29.12 E-value=33 Score=14.91 Aligned_cols=42 Identities=14% Similarity=0.259 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHCCEEEEE----CC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 999999999739879997----17--98228999858-9899999999837
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK----HR--NNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~----~~--~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
.++...|-+.-| |-+. +. .+.|-+.|.|. +.++|+.=+++|+
T Consensus 336 ~~~~~~ll~e~g--V~v~PG~~Fg~~~~~~~iRl~~a~~~~~l~eal~RL~ 384 (388)
T PRK07337 336 AALTFAMLHDAG--VVLVPGMDFGPHAPRDYIRLSYATSYSRLEEAVARLG 384 (388)
T ss_pred HHHHHHHHHHCC--EEEECCHHHCCCCCCCEEEEEECCCHHHHHHHHHHHH
T ss_conf 999999998599--9997762218999999799997199999999999999
No 435
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=29.06 E-value=41 Score=14.29 Aligned_cols=18 Identities=39% Similarity=0.626 Sum_probs=8.8
Q ss_pred CCHHHHHHHHHHHHHCCC
Q ss_conf 898899999998863100
Q gi|254780805|r 58 FESEGLEDLCQSIKSHGI 75 (300)
Q Consensus 58 ~~~~~l~eLa~SI~~~G~ 75 (300)
++++.|+++...+...|+
T Consensus 40 ~~~eqId~ii~~L~~~GI 57 (620)
T PRK05658 40 VDSEQIEDIISMINDMGI 57 (620)
T ss_pred CCHHHHHHHHHHHHHCCC
T ss_conf 998999999999997797
No 436
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=28.98 E-value=41 Score=14.29 Aligned_cols=21 Identities=19% Similarity=0.366 Sum_probs=9.8
Q ss_pred HHCCCCCCCCCCCCCHHHHHH
Q ss_conf 982357899987689889999
Q gi|254780805|r 45 HSIVPNPHNPRNYFESEGLED 65 (300)
Q Consensus 45 ~~i~~~p~~pR~~~~~~~l~e 65 (300)
+.|.-..+.|-..+++..|.+
T Consensus 27 ~~Il~g~l~pG~~l~e~~La~ 47 (230)
T COG1802 27 EAILSGELAPGERLSEEELAE 47 (230)
T ss_pred HHHHHCCCCCCCEECHHHHHH
T ss_conf 999829989829817999999
No 437
>PRK01533 histidinol-phosphate aminotransferase; Validated
Probab=28.87 E-value=39 Score=14.43 Aligned_cols=41 Identities=20% Similarity=0.149 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHCCEEEEECCCCCEEEEEEECCHHHHHHHHHHHCC
Q ss_conf 9999999999739879997179822899985898999999998375
Q gi|254780805|r 250 LTDLEKKISSKVGLNISIKHRNNKGQFCIKYETNEQLKIICSLLGE 295 (300)
Q Consensus 250 i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL~~ 295 (300)
-..+.+.|.+. | +-|..- .+-|.|.-.+.+|-+++++.|++
T Consensus 311 ~~~l~~~L~~~-G--IlVR~~--~~~iRIsvgt~eeN~~ll~aLke 351 (366)
T PRK01533 311 GGEIYEACAHA-G--FIIRPF--PNGVRITVGTREQNEGVISVLQQ 351 (366)
T ss_pred HHHHHHHHHHC-C--EEEEEC--CCCEEEECCCHHHHHHHHHHHHH
T ss_conf 99999999968-9--899899--59878827999999999999999
No 438
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=28.72 E-value=42 Score=14.26 Aligned_cols=67 Identities=18% Similarity=0.239 Sum_probs=44.0
Q ss_pred CEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHH
Q ss_conf 04620565445333575677777642100135433346411234556665431022104899999998521011104679
Q gi|254780805|r 79 LIVRAIDNGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLISEYGYTQNDI 158 (300)
Q Consensus 79 i~Vr~~~~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~~~~~t~~~l 158 (300)
+.++|.+.| +-|++|..=..-+..+|++.+-+-+.- + =||+--+.|+-.-+.. ..|.+++
T Consensus 89 V~l~Pap~G-~Gl~a~~~~r~vl~laGI~d~~~K~~G-s-----------------~n~~NvvkA~~~aL~~-~~t~~~i 148 (156)
T PRK00550 89 VLLKPASEG-TGVIAGGAMRAVLELAGVHDVLAKSLG-S-----------------NNPINVVRATFDALKK-LRTPEEV 148 (156)
T ss_pred EEEEECCCC-CCEECCHHHHHHHHHCCCCCEEEECCC-C-----------------CCHHHHHHHHHHHHHH-CCCHHHH
T ss_conf 999967999-557838799999997591605767168-9-----------------9788999999999981-8999999
Q ss_pred HHHHHHH
Q ss_conf 9997433
Q gi|254780805|r 159 GSIVGKS 165 (300)
Q Consensus 159 A~~~G~s 165 (300)
|+.-|++
T Consensus 149 A~~rG~~ 155 (156)
T PRK00550 149 AAKRGKS 155 (156)
T ss_pred HHHHCCC
T ss_conf 9984898
No 439
>PRK06225 aspartate aminotransferase; Provisional
Probab=28.72 E-value=42 Score=14.26 Aligned_cols=44 Identities=11% Similarity=0.235 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHCCEEEEEC-----C-CCCEEEEEEECC-HHHHHHHHHHHCC
Q ss_conf 899999999997398799971-----7-982289998589-8999999998375
Q gi|254780805|r 249 YLTDLEKKISSKVGLNISIKH-----R-NNKGQFCIKYET-NEQLKIICSLLGE 295 (300)
Q Consensus 249 ~i~~le~~L~~~lGtkV~I~~-----~-~~kGkI~I~f~s-~eeLe~Il~kL~~ 295 (300)
+-..+.+.|.+. | |-|.. . .+.|-|.|.|.. .|+++..++.|++
T Consensus 317 ~~~~~~~~l~e~-g--V~v~pG~~~~~~~g~~~iRis~~~~~e~l~~a~~rl~~ 367 (375)
T PRK06225 317 RPEDLVEYLLER-K--IFVRQGTYTSKRFGDRFIRVSFSIPREWVERFCEEFPD 367 (375)
T ss_pred CHHHHHHHHHHC-C--EEEECCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 999999999978-9--09968986788789992999970489999999999999
No 440
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.68 E-value=42 Score=14.25 Aligned_cols=27 Identities=11% Similarity=0.016 Sum_probs=13.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 104679999743378778656565435
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKLP 179 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~ 179 (300)
||-.++|+.+|.|..+|.-|=+..=|+
T Consensus 1 ytIge~A~~~gvs~~tlRyYe~~GLl~ 27 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDKGLLS 27 (118)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCC
T ss_conf 958899999897999999999869987
No 441
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=28.59 E-value=29 Score=15.28 Aligned_cols=29 Identities=24% Similarity=0.372 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10467999974337877865656543589
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKLPSS 181 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~~ 181 (300)
++..|+|+.+|.|..+|..|-+.-=|||.
T Consensus 1 Yri~ElA~~~Gvs~~tiR~YE~~GLlpp~ 29 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGLIPPA 29 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCC
T ss_conf 97899999989699999999996999997
No 442
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=28.58 E-value=42 Score=14.24 Aligned_cols=29 Identities=21% Similarity=0.256 Sum_probs=22.0
Q ss_pred HHHHHC---CCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 852101---11046799997433787786565
Q gi|254780805|r 146 QLISEY---GYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 146 ~l~~~~---~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
+++.+. +.|-.+||++.|.|++++.++..
T Consensus 7 ~l~~~~G~~~~s~~~Ia~~agvs~~~iy~~F~ 38 (47)
T pfam00440 7 ELFAEKGYDATTVREIAKEAGVSKGALYRHFP 38 (47)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 99998691507799999997969889998876
No 443
>PRK06056 consensus
Probab=28.15 E-value=43 Score=14.19 Aligned_cols=43 Identities=16% Similarity=0.247 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 999999999739879997-17--98228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++...|-+.-| |-+- .. +..|-+.|.|. +.|+++.=+++|.+
T Consensus 350 ~~~~~~ll~e~g--V~v~PG~~Fg~~g~~Risfa~~~e~l~eal~RL~~ 396 (402)
T PRK06056 350 AELAALILEEAE--VAVVPGEAFGTPGYLRLSYALGDDDLVEGVRRLQE 396 (402)
T ss_pred HHHHHHHHHHCC--EEEECCCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 999999997098--99974844489983999970899999999999999
No 444
>KOG0994 consensus
Probab=28.07 E-value=43 Score=14.19 Aligned_cols=12 Identities=8% Similarity=0.628 Sum_probs=6.0
Q ss_pred CHHHHHHHHHHH
Q ss_conf 988999999988
Q gi|254780805|r 59 ESEGLEDLCQSI 70 (300)
Q Consensus 59 ~~~~l~eLa~SI 70 (300)
|+++|+++|.-.
T Consensus 1490 dp~si~~vA~~v 1501 (1758)
T KOG0994 1490 DPDSIEEVAEEV 1501 (1758)
T ss_pred CHHHHHHHHHHH
T ss_conf 979999999999
No 445
>PRK07590 L,L-diaminopimelate aminotransferase; Validated
Probab=27.97 E-value=43 Score=14.17 Aligned_cols=45 Identities=11% Similarity=0.033 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 99999999973987999---71798228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++..+|-+.-|.-|.= -...+.|-+.|.|. +.++|+.=+++|++
T Consensus 359 ~ef~~~Ll~e~~Vav~PG~~FG~~g~g~vRls~a~~~e~l~ea~~Ri~~ 407 (409)
T PRK07590 359 WDFFDKLLQEANVVGTPGSGFGPAGEGYFRLSAFGSRENVLEAMERIKK 407 (409)
T ss_pred HHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf 9999999986999996864658999896999972899999999999998
No 446
>pfam01316 Arg_repressor Arginine repressor, DNA binding domain.
Probab=27.77 E-value=43 Score=14.15 Aligned_cols=35 Identities=20% Similarity=0.270 Sum_probs=18.5
Q ss_pred HHHHHHHHCC-CCHHHHHHHHHH-----HHHHHHHHHHHHH
Q ss_conf 9998521011-104679999743-----3787786565654
Q gi|254780805|r 143 GYEQLISEYG-YTQNDIGSIVGK-----SRSHVANILRILK 177 (300)
Q Consensus 143 ~~~~l~~~~~-~t~~~lA~~~G~-----s~s~V~~~LrLl~ 177 (300)
.+++++.... -||++|...|.. +++|||+-|+=+.
T Consensus 9 ~I~~li~~~~i~tQ~eL~~~L~~~G~~vTQATlSRDl~eLg 49 (70)
T pfam01316 9 LIKEIITEEKISTQEELVALLKAEGINVTQATVSRDLKELG 49 (70)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHCCCCEEEHHHHHHHHHHC
T ss_conf 99999970897899999999997698564178887799939
No 447
>TIGR01298 RNaseT ribonuclease T; InterPro: IPR005987 Ribonuclease T (3.1.13 from EC) is an enzyme found so far only in gamma-subdivision proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a UV-repair defect caused by deletion of three other single-stranded DNA exonucleases.; GO: 0004540 ribonuclease activity, 0006396 RNA processing.
Probab=27.48 E-value=39 Score=14.42 Aligned_cols=10 Identities=20% Similarity=0.687 Sum_probs=3.6
Q ss_pred HHHCCCCCHH
Q ss_conf 4310221048
Q gi|254780805|r 129 NVQRKDLNPL 138 (300)
Q Consensus 129 N~~R~dl~p~ 138 (300)
++.|...+|+
T Consensus 129 ~~KRnPFH~F 138 (201)
T TIGR01298 129 ALKRNPFHPF 138 (201)
T ss_pred HCCCCCCCCC
T ss_conf 1157898765
No 448
>TIGR02079 THD1 threonine dehydratase; InterPro: IPR011820 This entry represents threonine dehydratase, the first step in the pathway converting threonine into isoleucine. At least two other clades of biosynthetic threonine dehydratases are described by IPR005787 from INTERPRO and IPR005789 from INTERPRO. The sequences described by this entry are exclusively found in species containing the rest of the isoleucine pathway and which are generally lacking in members of the other two clades of threonine dehydratases. The sequences associated with this entry are often cluster with other elements of the isoleucine pathway.; GO: 0004794 L-threonine ammonia-lyase activity, 0030170 pyridoxal phosphate binding, 0009097 isoleucine biosynthetic process.
Probab=27.30 E-value=44 Score=14.10 Aligned_cols=49 Identities=20% Similarity=0.327 Sum_probs=35.4
Q ss_pred HHHHHHHHHHCCEEEE------E-CCCCCEEEE--EEECCHHHHHHHHHHHCCCCCCC
Q ss_conf 9999999973987999------7-179822899--98589899999999837564569
Q gi|254780805|r 252 DLEKKISSKVGLNISI------K-HRNNKGQFC--IKYETNEQLKIICSLLGENDFEY 300 (300)
Q Consensus 252 ~le~~L~~~lGtkV~I------~-~~~~kGkI~--I~f~s~eeLe~Il~kL~~~~~~~ 300 (300)
.|.+=|.+.||-.=.| + ++++.|.+. |...+.+||+++++++.-.|-+|
T Consensus 344 ALreFln~vLGP~DDIT~FEY~KK~nRe~GpaliGiel~~~~D~~GLL~Rm~A~~i~Y 401 (415)
T TIGR02079 344 ALREFLNDVLGPNDDITKFEYTKKSNRETGPALIGIELSDKEDFEGLLERMAAADIHY 401 (415)
T ss_pred HHHHHHHHHCCCCCCCCCCEEEECCCCCCCCEEEEEECCCCCHHHHHHHHHHHCCCCE
T ss_conf 3688765406788752331000201478787799875036100677999998559941
No 449
>KOG2252 consensus
Probab=27.27 E-value=44 Score=14.09 Aligned_cols=62 Identities=15% Similarity=0.223 Sum_probs=43.1
Q ss_pred HHH-HCCCCCHHHHHHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
Q ss_conf 543-1022104899999998521011104679999-74337877865656543589999876421016
Q gi|254780805|r 128 ENV-QRKDLNPLEEALGYEQLISEYGYTQNDIGSI-VGKSRSHVANILRILKLPSSVREMIRKEEISL 193 (300)
Q Consensus 128 EN~-~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~-~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ 193 (300)
||+ +-+-|+-.|.|.-++.-+.+|++.|.-.|++ |++|+++++.+||= |+=-..+..|.-++
T Consensus 318 ~~~~d~eeldTkeia~rI~~eLk~~sIpQaiFAervLcRSQGTLSDLLrn----PKPW~klKsGRetF 381 (558)
T KOG2252 318 EESGDDEELDTKEIAQRIKAELKRYSIPQAIFAERVLCRSQGTLSDLLRN----PKPWSKLKSGRETF 381 (558)
T ss_pred HHCCCCCEECHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHC----CCCHHHHCCCCHHH
T ss_conf 11277521018999999999986457737888888861252229999638----99525440320999
No 450
>TIGR02092 glgD glucose-1-phosphate adenylyltransferase, GlgD subunit; InterPro: IPR011832 This family is GlgD, an apparent regulatory protein that appears in an alpha2/beta2 heterotetramer with GlgC (glucose-1-phosphate adenylyltransferase, IPR011831 from INTERPRO) in a subset of bacteria that use GlgC for glycogen biosynthesis.; GO: 0005978 glycogen biosynthetic process.
Probab=27.19 E-value=17 Score=16.77 Aligned_cols=36 Identities=14% Similarity=0.094 Sum_probs=18.5
Q ss_pred CCCCEEEEHHHCC----CCC--CCCCCCCCHHH-----HHHHHHHHH
Q ss_conf 5660240389823----578--99987689889-----999999886
Q gi|254780805|r 36 PESQDCISIHSIV----PNP--HNPRNYFESEG-----LEDLCQSIK 71 (300)
Q Consensus 36 ~~~~~~i~i~~i~----~~p--~~pR~~~~~~~-----l~eLa~SI~ 71 (300)
-+.-.+++|+.+. ..| +|-+..+.++. .+.+.+++.
T Consensus 68 Lg~G~eWdL~r~~~glF~~pP~~~~~~~~~~~~kaall~~~~~~~l~ 114 (383)
T TIGR02092 68 LGSGREWDLNRKRDGLFLFPPKYNDRDDVSEGGKAALLKRYFSNNLE 114 (383)
T ss_pred CCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 34868836110257527706876864323456337788999988767
No 451
>TIGR01478 STEVOR variant surface antigen, stevor family; InterPro: IPR006374 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see . This entry represents the stevor (short for "subtelomeric variable open reading frame") family of predicted variant surface antigens. This is the third largest variant surface antigen family in P. falciparum, with 33 genes identified in the genome of this parasite . The function of these proteins is not known, but they are expressed during several stages of the parasite life-cycle and may play a variety of roles in parasite survival and infection ..
Probab=26.97 E-value=22 Score=16.00 Aligned_cols=37 Identities=24% Similarity=0.496 Sum_probs=19.8
Q ss_pred HHCCCCCCCCCCCCCHHHHHHHHH-----HHHH-------CCCCCCCEEEC
Q ss_conf 982357899987689889999999-----8863-------10015504620
Q gi|254780805|r 45 HSIVPNPHNPRNYFESEGLEDLCQ-----SIKS-------HGIIQPLIVRA 83 (300)
Q Consensus 45 ~~i~~~p~~pR~~~~~~~l~eLa~-----SI~~-------~G~lqPi~Vr~ 83 (300)
.+|.. |.|| +++++..|.|..| -|+. +-|||-+++..
T Consensus 51 Aeiq~-P~NP-HYhNDPELKeIIDKLNeEAIKKYq~THdPYEqL~elVeKn 99 (315)
T TIGR01478 51 AEIQR-PKNP-HYHNDPELKEIIDKLNEEAIKKYQKTHDPYEQLKELVEKN 99 (315)
T ss_pred HHHCC-CCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
T ss_conf 75357-6322-9898734666862402677866530588157774455420
No 452
>PRK05764 aspartate aminotransferase; Provisional
Probab=26.83 E-value=45 Score=14.04 Aligned_cols=43 Identities=12% Similarity=0.261 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHCCEEEEE-CC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 999999999739879997-17--98228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISIK-HR--NNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I~-~~--~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++...|-+..| |.+. .. +..|-+.|.|. +.++++.-+++|++
T Consensus 337 ~~~~~~ll~~~g--V~~~PG~~Fg~~g~~Rl~fa~~~e~l~ea~~RL~~ 383 (389)
T PRK05764 337 EDFAEALLEEAG--VAVVPGIAFGAPGYVRLSYATSLEDIEEALERIER 383 (389)
T ss_pred HHHHHHHHHHCC--EEEEECCCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 999999998199--99980732489984999983889999999999999
No 453
>PRK08068 transaminase; Reviewed
Probab=26.71 E-value=45 Score=14.03 Aligned_cols=45 Identities=9% Similarity=0.143 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHCCEEEE---ECCCCCEEEEEEE-CCHHHHHHHHHHHCC
Q ss_conf 99999999973987999---7179822899985-898999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNISI---KHRNNKGQFCIKY-ETNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~I---~~~~~kGkI~I~f-~s~eeLe~Il~kL~~ 295 (300)
.++...|-+.-|.-|.= ....+.|-|.|.| .+.++++.=+++|++
T Consensus 337 ~~~~~~ll~~~gV~v~PG~~Fg~~g~~~vRl~fa~~~e~l~ea~~RL~~ 385 (389)
T PRK08068 337 EQFADLLLEKAHVAVAPGNGFGEHGEGYVRVGLLIDEERLREAINRIAK 385 (389)
T ss_pred HHHHHHHHHCCCEEEECCHHHCCCCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf 9999999970999998785437899696999983899999999999972
No 454
>TIGR01529 argR_whole arginine repressor; InterPro: IPR001669 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia . The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 100f total cell protein . Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR . This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine . The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography . The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription DNA-dependent.
Probab=26.52 E-value=45 Score=14.01 Aligned_cols=130 Identities=18% Similarity=0.215 Sum_probs=63.0
Q ss_pred HHHHHHHHHHCC-CCHHHHHHHH-----H-HHHHHHHHHHHHHHHHHHHHHHHHHH-HCCHHHHHHHHH-------CCH-
Q ss_conf 999998521011-1046799997-----4-33787786565654358999987642-101677777640-------100-
Q gi|254780805|r 141 ALGYEQLISEYG-YTQNDIGSIV-----G-KSRSHVANILRILKLPSSVREMIRKE-EISLGHARTLVS-------TSD- 204 (300)
Q Consensus 141 A~~~~~l~~~~~-~t~~~lA~~~-----G-~s~s~V~~~LrLl~L~~~i~~~l~~~-~is~ghar~Ll~-------~~~- 204 (300)
-..+++++.+-+ -||+||...| - ..+++|||-|+=+.|- +-.-.+| . +..+|.. ..+
T Consensus 4 ~~~Ik~Ii~~e~~~tQ~El~~~L~~~G~~nvTQaTvSRDL~el~lv---K~~~~~gG~----~~Y~L~~~~sPvrg~~~~ 76 (155)
T TIGR01529 4 QEAIKEIITEEKISTQEELVALLKKEGVKNVTQATVSRDLRELGLV---KVRDEKGGS----YVYSLPAEGSPVRGVSDP 76 (155)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHCCCCEECCCCHHHHHHHHCCE---ECCCCCCCE----EEEEECCCCCCCCCCCCC
T ss_conf 9999999874376798899999986597511234067878752204---223699744----899860687853899875
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHH--HHH--HHHHCCEEEEECCCCCEEEEEEE
Q ss_conf 46899997422247789999997641022222234566556897899999--999--99739879997179822899985
Q gi|254780805|r 205 PLSLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLE--KKI--SSKVGLNISIKHRNNKGQFCIKY 280 (300)
Q Consensus 205 ~~~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le--~~L--~~~lGtkV~I~~~~~kGkI~I~f 280 (300)
..++.+..-.-=+||+..+.++ +....+..-..+.++= ... .+.+|| | .+--.|-+-|
T Consensus 77 ~~~l~r~l~~~v~~id~~~~l~------------VirT~pG~A~~iA~llD~~~~~r~~IlGT---i---AGdDTilV~~ 138 (155)
T TIGR01529 77 TEKLKRLLKSFVLSIDRAGNLI------------VIRTKPGEASVIANLLDRLKKARDEILGT---I---AGDDTILVIC 138 (155)
T ss_pred CHHHHHHHHHHHEEEEECCCEE------------EEECCCCCHHHHHHHHHCCCCCCCCCEEE---E---ECCCEEEEEE
T ss_conf 1125787897500001046178------------88559984756887540013467330145---4---2567178874
Q ss_pred CCHHHHHHHHHHHCC
Q ss_conf 898999999998375
Q gi|254780805|r 281 ETNEQLKIICSLLGE 295 (300)
Q Consensus 281 ~s~eeLe~Il~kL~~ 295 (300)
-+.+..+.|.+.|.+
T Consensus 139 r~~~~~~~l~~~l~~ 153 (155)
T TIGR01529 139 RDEETAELLEEELLE 153 (155)
T ss_pred CCCHHHHHHHHHHHH
T ss_conf 580307999999985
No 455
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=26.50 E-value=45 Score=14.01 Aligned_cols=23 Identities=13% Similarity=0.164 Sum_probs=9.8
Q ss_pred HHHHHHHHHHCCCCCCCEEECCCCCCC
Q ss_conf 999999886310015504620565445
Q gi|254780805|r 63 LEDLCQSIKSHGIIQPLIVRAIDNGLY 89 (300)
Q Consensus 63 l~eLa~SI~~~G~lqPi~Vr~~~~g~y 89 (300)
+.|--..+...|++ ....+.|.|
T Consensus 48 vReal~~L~~~G~v----~~~~G~gt~ 70 (239)
T PRK04984 48 LREVLQRLARDGWL----TIQHGKPTK 70 (239)
T ss_pred HHHHHHHHHHCCCE----EEECCCCCE
T ss_conf 99999999988988----885599975
No 456
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=26.49 E-value=39 Score=14.46 Aligned_cols=38 Identities=21% Similarity=0.300 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHHHH
Q ss_conf 221048999999985210111------04679999743378778
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGY------TQNDIGSIVGKSRSHVA 170 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~------t~~~lA~~~G~s~s~V~ 170 (300)
.|.+|+|.-..+-.|.++.+. |.++|++..|.++++.+
T Consensus 55 ~Dv~P~eiv~hlP~LCeek~IPy~~V~sk~~LG~A~G~~r~t~a 98 (123)
T PRK04175 55 EDVDPEEIVAHLPLLCEEKKIPYVYVPSKEELGKAAGLEVGAAA 98 (123)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCEEEECCHHHHHHHHCCCCCEEE
T ss_conf 89990999998899998549998997899999999689977799
No 457
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=26.35 E-value=46 Score=13.99 Aligned_cols=12 Identities=17% Similarity=0.038 Sum_probs=4.9
Q ss_pred HHHHHHHHHCCC
Q ss_conf 999999983756
Q gi|254780805|r 285 QLKIICSLLGEN 296 (300)
Q Consensus 285 eLe~Il~kL~~~ 296 (300)
-+..+++.|...
T Consensus 278 ~~~~Fidfl~~a 289 (291)
T PRK10837 278 ALQRFLSYCQPA 289 (291)
T ss_pred HHHHHHHHHHHC
T ss_conf 999999998620
No 458
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.34 E-value=46 Score=13.99 Aligned_cols=69 Identities=19% Similarity=0.238 Sum_probs=36.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHH-CCCCHHHHHHHHHHH
Q ss_conf 0467999974337877865656543589999876421016777776401004689999742-224778999999764
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPLSLAQVIVS-KKMSVRDTEELVQEQ 229 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~~la~~Ii~-~~LSVRe~E~lVk~~ 229 (300)
+-.|+|++.|.|..+|.=|-+.-=|||.-...=.-...+..|.+ ...+.+..-. -++|..++.++....
T Consensus 2 ~IgelA~~tGvs~~TIRyYe~~GLL~p~~R~~~g~r~Y~~~~v~-------rL~~Ir~l~~~lG~sL~eIr~lL~~~ 71 (95)
T cd04780 2 RMSELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVE-------RLRLIRALQQEGGLPISQIKEVLDAI 71 (95)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHH-------HHHHHHHHHHHCCCCHHHHHHHHHCC
T ss_conf 78999999897899999999978999877699987154999999-------99999999993699999999998436
No 459
>PRK05949 RNA polymerase sigma factor; Validated
Probab=26.25 E-value=46 Score=13.98 Aligned_cols=25 Identities=16% Similarity=0.247 Sum_probs=19.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565654
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
-|.+++|+.+|.+...|..++.+..
T Consensus 195 pt~~EiA~~l~i~~~~v~~~l~~~~ 219 (327)
T PRK05949 195 ATPAEIAKALELEPSQIREYLSMAR 219 (327)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 9889999894999999999998418
No 460
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.23 E-value=46 Score=13.98 Aligned_cols=39 Identities=15% Similarity=0.297 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 1104679999743378778656565435899998764210
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI 191 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i 191 (300)
.+|.++||+.+|.|+++.++..+= ..--.+.+.+..-.|
T Consensus 25 ~lsl~~lA~~~~~S~~~l~r~Fk~-~~G~s~~~Yi~~~Rl 63 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKK-ETGHSLGQYIRSRKM 63 (127)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH-HHCCCHHHHHHHHHH
T ss_conf 999999999989599999999999-989199999999999
No 461
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461 Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=25.99 E-value=46 Score=13.95 Aligned_cols=94 Identities=19% Similarity=0.241 Sum_probs=51.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHHH-------HHHHHHHHCCCCHHHHHH
Q ss_conf 1104679999743378778656565435899998764210167777764010046-------899997422247789999
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSDPL-------SLAQVIVSKKMSVRDTEE 224 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~~~-------~la~~Ii~~~LSVRe~E~ 224 (300)
.||.+.|-..+-+|.-||+-+ -||++..+++++=- |..=+....+. +=.+.-.--..+|+++|+
T Consensus 396 ~Y~~eal~~Av~LS~ryI~DR----fLPDKAIDviDEaG-----A~~~l~~~~~~~~~eadekGleetalPev~~~diE~ 466 (774)
T TIGR02639 396 KYSDEALEAAVELSARYINDR----FLPDKAIDVIDEAG-----AAFRLRAKAKKKANEADEKGLEETALPEVNVKDIEE 466 (774)
T ss_pred ECCHHHHHHHHHHHHHHCCCC----CCCCHHHHHHHHHH-----HHHHHHHHCCCCCCCHHHCCCCCCCCCCCCHHHHHH
T ss_conf 138699999999988860257----89854322889999-----999971202776432011253000478785444999
Q ss_pred HHHHHHCCCCCCCCCCCCCCCC-CHHHHHHHHHHHH
Q ss_conf 9976410222222345665568-9789999999999
Q gi|254780805|r 225 LVQEQDNKKEKRKKIFEGSREK-EKYLTDLEKKISS 259 (300)
Q Consensus 225 lVk~~~~~~~~~kk~~~~~~~k-~~~i~~le~~L~~ 259 (300)
.|.+...-+...- +..- ...+++|+.+|+.
T Consensus 467 vvak~a~iP~~~~-----s~ddD~~~L~~L~~~L~~ 497 (774)
T TIGR02639 467 VVAKMAKIPVKTV-----SSDDDREKLKNLEKELKA 497 (774)
T ss_pred HHHHHHCCCCEEE-----CCCHHHHHHHHHHHHHHC
T ss_conf 9988718994154-----264479887204476301
No 462
>cd01821 Rhamnogalacturan_acetylesterase_like Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are highly branched regions in pectic polysaccharides, consisting of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide units, with many rhamnose residues substituted by neutral oligosaccharides such as arabinans, galactans and arabinogalactans. Extracellular enzymes participating in the degradation of plant cell wall polymers, such as Rhamnogalacturonan acetylesterase, would typically be found in saprophytic and plant pathogenic fungi and bacteria.
Probab=25.99 E-value=38 Score=14.51 Aligned_cols=26 Identities=19% Similarity=0.414 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHCCCCCCCEEECCCC
Q ss_conf 889999999886310015504620565
Q gi|254780805|r 60 SEGLEDLCQSIKSHGIIQPLIVRAIDN 86 (300)
Q Consensus 60 ~~~l~eLa~SI~~~G~lqPi~Vr~~~~ 86 (300)
.+.|..+..-+++.| ..||+|.|.+.
T Consensus 93 ~~nL~~~i~~~r~~g-a~pIL~Tp~~R 118 (198)
T cd01821 93 KEYLRRYIAEARAKG-ATPILVTPVTR 118 (198)
T ss_pred HHHHHHHHHHHHHCC-CEEEEECCCCC
T ss_conf 999999999999759-98999758877
No 463
>PRK06507 consensus
Probab=25.90 E-value=41 Score=14.27 Aligned_cols=43 Identities=14% Similarity=0.194 Sum_probs=22.5
Q ss_pred HHHHHHHHHHCCEEEEECC--CCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 9999999973987999717--98228999858-98999999998375
Q gi|254780805|r 252 DLEKKISSKVGLNISIKHR--NNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 252 ~le~~L~~~lGtkV~I~~~--~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
+....|-+.-|.-|. -.. +..|-|.|.|. +.++|+.-+++|.+
T Consensus 349 ~f~~~Ll~e~gV~v~-PG~~FG~~~~vRis~a~~~~~l~eal~Rl~~ 394 (400)
T PRK06507 349 DFVMALLEEQHVATV-QGAAYGMSPYFRLSYATDMESLGEGCARIAQ 394 (400)
T ss_pred HHHHHHHHHCCEEEE-CCCCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf 999999985899997-7874489983999964999999999999999
No 464
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=25.58 E-value=31 Score=15.08 Aligned_cols=25 Identities=20% Similarity=0.400 Sum_probs=19.9
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 01110467999974337877865656
Q gi|254780805|r 150 EYGYTQNDIGSIVGKSRSHVANILRI 175 (300)
Q Consensus 150 ~~~~t~~~lA~~~G~s~s~V~~~LrL 175 (300)
.|. +..+.|+.+|.++++|++++.-
T Consensus 16 ~f~-Si~~aak~l~~~~~~I~~~l~~ 40 (53)
T smart00497 16 EFS-SIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred HHH-HHHHHHHHHCCCCCCHHHHHCC
T ss_conf 778-7999999858883238887067
No 465
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=25.54 E-value=47 Score=13.89 Aligned_cols=48 Identities=23% Similarity=0.262 Sum_probs=30.2
Q ss_pred HHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf 777764210013543334641123455666543102210489999999
Q gi|254780805|r 98 FRAAKMASLSEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYE 145 (300)
Q Consensus 98 ~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~ 145 (300)
..|+|.+.-..+.++|+=++|.-....-|++-.---.|+|+=.-.-|.
T Consensus 90 i~aaKnl~e~ki~a~iR~Yddaisit~DLv~g~ld~~lSPiiTq~ifs 137 (321)
T COG3888 90 ISAAKNLEERKISATIRFYDDAISITRDLVEGKLDFGLSPIITQIIFS 137 (321)
T ss_pred HHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 589876644364089999635778999887644462012789999999
No 466
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=25.23 E-value=48 Score=13.86 Aligned_cols=58 Identities=14% Similarity=0.178 Sum_probs=35.3
Q ss_pred CCCCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHH
Q ss_conf 022104899999998521---011104679999743378778656565435--8999987642
Q gi|254780805|r 132 RKDLNPLEEALGYEQLIS---EYGYTQNDIGSIVGKSRSHVANILRILKLP--SSVREMIRKE 189 (300)
Q Consensus 132 R~dl~p~e~A~~~~~l~~---~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~--~~i~~~l~~~ 189 (300)
..+|+|.|+-.+-.-+-. -..+|-.+||+..|.|.++|.|.-+-+-.. ++.+..+.+.
T Consensus 11 ~~~Lt~~Ek~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~ 73 (282)
T PRK11557 11 YPGLAQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALSEA 73 (282)
T ss_pred HHHCCHHHHHHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 854499999999999809899976569999989699988999999993899899999999999
No 467
>pfam10743 Phage_Cox Regulatory phage protein cox. This family of phage Cox proteins is expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes.
Probab=25.23 E-value=46 Score=13.97 Aligned_cols=28 Identities=21% Similarity=0.487 Sum_probs=21.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1104679999743378778656565435
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANILRILKLP 179 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~LrLl~L~ 179 (300)
..+.+.-|+.+|++.+.|+.+..=.+||
T Consensus 12 av~~ekFA~~IGKt~~AVr~Mi~~gKLP 39 (87)
T pfam10743 12 ALSVEEFALLIGKTPTAVREMVKAGKLP 39 (87)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCCCC
T ss_conf 0169999999689899999999849997
No 468
>PRK03341 arginine repressor; Provisional
Probab=25.19 E-value=48 Score=13.85 Aligned_cols=131 Identities=11% Similarity=0.106 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHCC-CCHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCH---------
Q ss_conf 9999998521011-104679999743-----3787786565654358999987642101677777640100---------
Q gi|254780805|r 140 EALGYEQLISEYG-YTQNDIGSIVGK-----SRSHVANILRILKLPSSVREMIRKEEISLGHARTLVSTSD--------- 204 (300)
Q Consensus 140 ~A~~~~~l~~~~~-~t~~~lA~~~G~-----s~s~V~~~LrLl~L~~~i~~~l~~~~is~ghar~Ll~~~~--------- 204 (300)
+=..+++|+.+.. .||++|.+.|.. +++|||+-|+=+.+-. -.-.+|.. ....+..+.
T Consensus 16 Rq~~I~~lI~~~~I~tQeeL~~~L~~~Gi~vTQATiSRDikEL~lvK---v~~~~G~~----~yy~lp~~~~~~~~~~~~ 88 (168)
T PRK03341 16 RQARIVAILSSQSVRSQSELAALLADEGIDVTQATLSRDLEELGAVK---LRGADGGL----GVYVVPEDGSPRRGVAGG 88 (168)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHCCCCEEHHHHHHHHHHHCCEE---EECCCCCE----EEEEECCCCCCCCCCCCH
T ss_conf 99999999960897889999999997698654278775299838767---32589988----999945766644455557
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHH--HHHHHHHCCEEEEECCCCCEEEEEEECC
Q ss_conf 46899997422247789999997641022222234566556897899999--9999973987999717982289998589
Q gi|254780805|r 205 PLSLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLE--KKISSKVGLNISIKHRNNKGQFCIKYET 282 (300)
Q Consensus 205 ~~~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le--~~L~~~lGtkV~I~~~~~kGkI~I~f~s 282 (300)
..++...+-..=+||...+.++= .+..+..-..+..+= ..+.+.+|| | .+-..|-|-+.+
T Consensus 89 ~~~l~~~~~~~v~~v~~~~nlvV------------ikT~pG~A~~va~~iD~~~~~eI~GT---I---AGdDTIlVi~~~ 150 (168)
T PRK03341 89 TERLRRLLGELLVSTDASGNLAV------------LRTPPGAAQYLASAIDRAALPYVVGT---I---AGDDTVLVVARE 150 (168)
T ss_pred HHHHHHHHHHHEEEEEECCCEEE------------EEECCCCHHHHHHHHHHCCCCCCEEE---E---ECCCEEEEEECC
T ss_conf 89999999987567751076899------------98189948999999984799873798---6---049989999788
Q ss_pred HHHHHHHHHHHCC
Q ss_conf 8999999998375
Q gi|254780805|r 283 NEQLKIICSLLGE 295 (300)
Q Consensus 283 ~eeLe~Il~kL~~ 295 (300)
.++-+.+.++|.+
T Consensus 151 ~~~a~~l~~~L~~ 163 (168)
T PRK03341 151 PMTGAELAARLEN 163 (168)
T ss_pred HHHHHHHHHHHHH
T ss_conf 8899999999999
No 469
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=25.15 E-value=48 Score=13.85 Aligned_cols=34 Identities=24% Similarity=0.323 Sum_probs=24.8
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 21011104679999743378778656565435899998
Q gi|254780805|r 148 ISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREM 185 (300)
Q Consensus 148 ~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~ 185 (300)
+.-|| +...+|+.+|.|.+.|++- -+..|+.+.+
T Consensus 7 i~~FG-sk~klA~aLgIs~~aVsqW---ge~IPE~rAy 40 (75)
T PRK09744 7 IAFFG-SKTKLANAAGVRLASVAAW---GELVPEGRAM 40 (75)
T ss_pred HHHHC-CHHHHHHHHCCCHHHHHHH---HHHCCHHHHH
T ss_conf 99961-2999999949987999887---4016068899
No 470
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=25.04 E-value=44 Score=14.10 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=24.8
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 998521011104679999743378778656565
Q gi|254780805|r 144 YEQLISEYGYTQNDIGSIVGKSRSHVANILRIL 176 (300)
Q Consensus 144 ~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl 176 (300)
+..|+...-.|-++||+.+|.+...|++.|.-|
T Consensus 7 id~L~~~~~v~dedLa~~l~~~~n~vRkiL~~L 39 (147)
T smart00531 7 LDALMRNGCVTEEDLAELLGIKQKQLRKILYLL 39 (147)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 298886597079999999799999999999999
No 471
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=24.99 E-value=48 Score=13.83 Aligned_cols=11 Identities=27% Similarity=0.727 Sum_probs=3.9
Q ss_pred CCCHHHHHHHH
Q ss_conf 11046799997
Q gi|254780805|r 152 GYTQNDIGSIV 162 (300)
Q Consensus 152 ~~t~~~lA~~~ 162 (300)
|+|.++|.+.+
T Consensus 58 GfsL~eI~~ll 68 (140)
T PRK09514 58 GFTLEEIRELL 68 (140)
T ss_pred CCCHHHHHHHH
T ss_conf 99999999998
No 472
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=24.94 E-value=49 Score=13.82 Aligned_cols=17 Identities=0% Similarity=0.096 Sum_probs=9.6
Q ss_pred HHHHHHHHHCCCCHHHH
Q ss_conf 68999974222477899
Q gi|254780805|r 206 LSLAQVIVSKKMSVRDT 222 (300)
Q Consensus 206 ~~la~~Ii~~~LSVRe~ 222 (300)
.++.+.+...|+|.-++
T Consensus 59 ~~~~~~l~~~Gi~peeL 75 (134)
T PRK10328 59 NTWLELMKADGINPEEL 75 (134)
T ss_pred HHHHHHHHHCCCCHHHH
T ss_conf 99999999869999999
No 473
>KOG3725 consensus
Probab=24.92 E-value=45 Score=14.02 Aligned_cols=84 Identities=25% Similarity=0.317 Sum_probs=37.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH-HCCCCHHHHHHHH--
Q ss_conf 5445333575677777642100135433346411234556665431022104899999998521-0111046799997--
Q gi|254780805|r 86 NGLYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIVENVQRKDLNPLEEALGYEQLIS-EYGYTQNDIGSIV-- 162 (300)
Q Consensus 86 ~g~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~~R~dl~p~e~A~~~~~l~~-~~~~t~~~lA~~~-- 162 (300)
+|.|-.|.-||++.-.+.+.+..-...++. ..+.+..-.-|-.-..-..+|.|+.--|... +|. .|.+|-+.+
T Consensus 149 EGD~KTI~KERklLqnkRLDLDAcKsRLKK---AKaae~q~~rN~~~s~~~~ie~aEqelRvaQ~EFD-rQaEiTrLLLE 224 (375)
T KOG3725 149 EGDMKTIQKERKLLQNKRLDLDACKSRLKK---AKAAELQTVRNSKTSGGFTIEQAEQELRVAQAEFD-RQAEITRLLLE 224 (375)
T ss_pred HCCHHHHHHHHHHHHHCCCCHHHHHHHHHH---HHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
T ss_conf 110788999999986145676889998877---65554414334324676417678888888887775-78899999997
Q ss_pred HHHHHHHHHHHH
Q ss_conf 433787786565
Q gi|254780805|r 163 GKSRSHVANILR 174 (300)
Q Consensus 163 G~s~s~V~~~Lr 174 (300)
|.|-.|+ |.||
T Consensus 225 GIsstH~-nhLr 235 (375)
T KOG3725 225 GISSTHN-NHLR 235 (375)
T ss_pred HHHHHHH-HHHH
T ss_conf 6636536-6889
No 474
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=24.92 E-value=49 Score=13.82 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=13.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|..|+|..++.++..+.+..+
T Consensus 184 tl~Eia~~~~i~~k~i~r~~~ 204 (310)
T PRK00423 184 TLDEIAEVSRVSRKEIGRTYR 204 (310)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 499999995988999999999
No 475
>pfam08564 CDC37_C Cdc37 C terminal domain. Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the C terminal domain whose function is unclear. It is found C terminal to the Hsp90 chaperone (Heat shocked protein 90) binding domain pfam08565 and the N terminal kinase binding domain of Cdc37 pfam03234.
Probab=24.90 E-value=49 Score=13.82 Aligned_cols=42 Identities=5% Similarity=0.141 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHCCHHH-HHHHHHCCHHHHHHHHHHHCC
Q ss_conf 654358999987642101677-777640100468999974222
Q gi|254780805|r 175 ILKLPSSVREMIRKEEISLGH-ARTLVSTSDPLSLAQVIVSKK 216 (300)
Q Consensus 175 Ll~L~~~i~~~l~~~~is~gh-ar~Ll~~~~~~~la~~Ii~~~ 216 (300)
+-.||+++|.++.++.|..=. +-+=+..++++.+.++++.-+
T Consensus 11 FeslP~emq~a~es~dld~ln~vl~~M~~eeAe~~~~~~~dsG 53 (87)
T pfam08564 11 FESLPPELQKAFETKDLDEVNKVLAKMPVEEAEYHMERLIDSG 53 (87)
T ss_pred HHHCCHHHHHHHHHCCHHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf 9868999999998578999999998099999999999987258
No 476
>PRK08636 aspartate aminotransferase; Provisional
Probab=24.90 E-value=49 Score=13.82 Aligned_cols=45 Identities=7% Similarity=0.086 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHCCEEE---EECCCCCEEEEEEEC-CHHHHHHHHHHHCC
Q ss_conf 9999999997398799---971798228999858-98999999998375
Q gi|254780805|r 251 TDLEKKISSKVGLNIS---IKHRNNKGQFCIKYE-TNEQLKIICSLLGE 295 (300)
Q Consensus 251 ~~le~~L~~~lGtkV~---I~~~~~kGkI~I~f~-s~eeLe~Il~kL~~ 295 (300)
.++...|-+.-|.-|. .-...+.|-+.|.|. +.++++.=+++|.+
T Consensus 348 ~ef~~~ll~~~gV~v~PG~~Fg~~g~~~vRisf~~~~e~l~ea~~Rl~~ 396 (403)
T PRK08636 348 LEFSKQLLTEAKVAVSPGIGFGEYGDEYVRIALIENENRIRQAARNIKK 396 (403)
T ss_pred HHHHHHHHHCCCEEEECCHHHCCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf 9999999974979998875328899987999971899999999999999
No 477
>PRK07778 consensus
Probab=24.88 E-value=49 Score=13.82 Aligned_cols=45 Identities=11% Similarity=0.231 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHCCEEE--EECC--CCCEEEEEEEC-CHHHHHHHHHHHC
Q ss_conf 99999999997398799--9717--98228999858-9899999999837
Q gi|254780805|r 250 LTDLEKKISSKVGLNIS--IKHR--NNKGQFCIKYE-TNEQLKIICSLLG 294 (300)
Q Consensus 250 i~~le~~L~~~lGtkV~--I~~~--~~kGkI~I~f~-s~eeLe~Il~kL~ 294 (300)
-.++...|-+.-|.-|. ..+. .+.|-|.|.|. +.++|+.=+++|.
T Consensus 332 ~~~f~~~Ll~~~gV~v~PG~~Fg~~~g~~~vRlsf~~~~~~l~eal~RL~ 381 (386)
T PRK07778 332 SLAFCSKLLADTGVAIAPGIDFDTVRGNSFVRLSFAGPTADIEEALRRIG 381 (386)
T ss_pred HHHHHHHHHHHCCEEEECCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf 99999999983999997585668899999699998398999999999999
No 478
>PRK06959 putative threonine-phosphate decarboxylase; Provisional
Probab=24.78 E-value=49 Score=13.81 Aligned_cols=46 Identities=11% Similarity=0.123 Sum_probs=27.9
Q ss_pred CHHHHHHHHHHHHHHCCEEEEECCCCCEEEEEEE-CCHHHHHHHHHHHCC
Q ss_conf 9789999999999739879997179822899985-898999999998375
Q gi|254780805|r 247 EKYLTDLEKKISSKVGLNISIKHRNNKGQFCIKY-ETNEQLKIICSLLGE 295 (300)
Q Consensus 247 ~~~i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f-~s~eeLe~Il~kL~~ 295 (300)
..+-..+.+.|.++ |.-|- .-...+.+.|.- .+.+|.+|+++-|.+
T Consensus 283 ~~~a~~~~~~L~~~-GIlVR--~f~~p~~LRi~vp~~e~e~~RL~~AL~e 329 (339)
T PRK06959 283 DPRAAALHAALAAR-GIWTR--YFAAPPSVRIGLPADEAEWQRLEDALAE 329 (339)
T ss_pred CCCHHHHHHHHHHC-CEEEE--ECCCCCCEEEECCCCHHHHHHHHHHHHH
T ss_conf 88999999999849-92995--8899998898678999999999999999
No 479
>pfam11353 DUF3153 Protein of unknown function (DUF3153). This family of proteins with unknown function appear to be restricted to Cyanobacteria. Some members are annotated as membrane proteins however this cannot be confirmed.
Probab=24.75 E-value=49 Score=13.80 Aligned_cols=46 Identities=9% Similarity=0.261 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHHHHHCCEEEEECCCCCEEEEEEECCHHHHHHHHHHH
Q ss_conf 97899999999997398799971798228999858989999999983
Q gi|254780805|r 247 EKYLTDLEKKISSKVGLNISIKHRNNKGQFCIKYETNEQLKIICSLL 293 (300)
Q Consensus 247 ~~~i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f~s~eeLe~Il~kL 293 (300)
-|+...+|+++++..| +++|....+.-.+++.|.+.+|++..++..
T Consensus 43 ~pWq~~fe~~~k~l~~-~~~~~~~~~~~~l~~p~ln~~dl~~~l~~~ 88 (210)
T pfam11353 43 LPWQEQFEQRLKDLGP-DVEIRSSEGEQRLTIPFLNSQELAELLNRF 88 (210)
T ss_pred CCHHHHHHHHHHHHCC-CCEEECCCCEEEEECCCCCHHHHHHHHHHH
T ss_conf 7439999999987489-752753887389976889999999999999
No 480
>pfam00376 MerR MerR family regulatory protein.
Probab=24.67 E-value=36 Score=14.66 Aligned_cols=27 Identities=22% Similarity=0.325 Sum_probs=20.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565654358
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILRILKLPS 180 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~LrLl~L~~ 180 (300)
|-.++|+.+|.|..+|..+-+.-.+|+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gli~~ 27 (38)
T pfam00376 1 TIGEVAKLLGVSPRTLRYYEKIGLLPP 27 (38)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 989999998879999999998689899
No 481
>PRK05957 aspartate aminotransferase; Provisional
Probab=24.54 E-value=49 Score=13.78 Aligned_cols=45 Identities=16% Similarity=0.037 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHCCEEE--EE-CCCCCEEEEEEE-C-CHHHHHHHHHHHC
Q ss_conf 99999999997398799--97-179822899985-8-9899999999837
Q gi|254780805|r 250 LTDLEKKISSKVGLNIS--IK-HRNNKGQFCIKY-E-TNEQLKIICSLLG 294 (300)
Q Consensus 250 i~~le~~L~~~lGtkV~--I~-~~~~kGkI~I~f-~-s~eeLe~Il~kL~ 294 (300)
-.++..+|-+.-|.-|. .. ...+.|-+.|.| . +.|+++.=+++|.
T Consensus 331 ~~~~~~~ll~e~gV~v~PG~~Fg~~~~~~~Rlsf~~~~~e~l~eg~~RL~ 380 (389)
T PRK05957 331 DFELVKQLIRDYRVAVIPGSTFGMKNGCYLRIAYGALQKATAKEGIERLV 380 (389)
T ss_pred HHHHHHHHHHHCCEEEECCHHHCCCCCCEEEEEECCCCHHHHHHHHHHHH
T ss_conf 99999999997999997873108899998999854299999999999999
No 482
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.50 E-value=49 Score=13.77 Aligned_cols=28 Identities=21% Similarity=0.260 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565654358
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKLPS 180 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L~~ 180 (300)
+|-.++|+.+|.|..+|.-|=++.=++|
T Consensus 1 ytIgelA~~~gvs~~tlRyYe~~GLl~~ 28 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLLPP 28 (113)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 9788999998959999999998389799
No 483
>TIGR01515 branching_enzym 1,4-alpha-glucan branching enzyme; InterPro: IPR006407 This entry represents the core region of the glycogen branching enzymes, which are responsible for the transfer of chains of approximately seven alpha(1,4)-linked glucosyl residues to other similar chains (in new alpha-(1,6) linkages) in the biosynthesis of glycogen . The branching enzyme is responsible for the degree of alpha(1,6) branch linkages found in polysaccharides .; GO: 0003844 14-alpha-glucan branching enzyme activity, 0005978 glycogen biosynthetic process.
Probab=24.49 E-value=11 Score=18.05 Aligned_cols=22 Identities=41% Similarity=0.605 Sum_probs=9.4
Q ss_pred CCCCCC--CHHHHHHHHHHHCCCC
Q ss_conf 453335--7567777764210013
Q gi|254780805|r 88 LYKIIA--GERRFRAAKMASLSEV 109 (300)
Q Consensus 88 ~y~ii~--G~rR~rAa~~~g~~~i 109 (300)
+|||+. |++|++|=-.|-..+|
T Consensus 81 KYEi~~~~G~~~lkaDPyA~y~ev 104 (608)
T TIGR01515 81 KYEIVDANGEIRLKADPYAFYAEV 104 (608)
T ss_pred EEEEECCCCCEEECCCCCCCCCCC
T ss_conf 046676898756436753012468
No 484
>PRK05201 hslU ATP-dependent protease ATP-binding subunit; Provisional
Probab=24.46 E-value=50 Score=13.77 Aligned_cols=156 Identities=19% Similarity=0.200 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC----CHHHHHHHH--------
Q ss_conf 22104899999998521011104679999743378778656565435899998764210----167777764--------
Q gi|254780805|r 133 KDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILKLPSSVREMIRKEEI----SLGHARTLV-------- 200 (300)
Q Consensus 133 ~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~L~~~i~~~l~~~~i----s~ghar~Ll-------- 200 (300)
.+|+|-|.- ..+++|-..|++.-+.+... +.|+.|=..||+++++-+.-..| ..|-+++++
T Consensus 2 ~~ltP~eIv----~~LD~yIIGQ~~AKkavAVA---lrNr~RR~~l~~~lr~Ei~pkNILmIGPTGvGKTeIARrLAkl~ 74 (442)
T PRK05201 2 SELTPREIV----SELDKYIIGQDDAKRAVAIA---LRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLA 74 (442)
T ss_pred CCCCHHHHH----HHHCCCCCCCHHHHHHHHHH---HHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHH
T ss_conf 989989999----98536010827766787778---87778753166221233464316887888866789999999984
Q ss_pred HCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEECCCCCEEEEEEE
Q ss_conf 01004689999742224778999999764102222223456655689789999999999739879997179822899985
Q gi|254780805|r 201 STSDPLSLAQVIVSKKMSVRDTEELVQEQDNKKEKRKKIFEGSREKEKYLTDLEKKISSKVGLNISIKHRNNKGQFCIKY 280 (300)
Q Consensus 201 ~~~~~~~la~~Ii~~~LSVRe~E~lVk~~~~~~~~~kk~~~~~~~k~~~i~~le~~L~~~lGtkV~I~~~~~kGkI~I~f 280 (300)
+.|-...=|.+.-.-|.-=|++|.+|+.+......-.+......-+...-...++++-+.|--.. ++..+.-.-.-
T Consensus 75 ~aPFvkveATk~TEvGYvGrDVEsiIrdLv~~a~~~~k~~~~~~v~~~A~~~a~~ril~~L~~~~----~~~~~~~~~~~ 150 (442)
T PRK05201 75 NAPFIKVEATKFTEVGYVGRDVESIIRDLVEIAVKMVREEKREKVREKAEEAAEERILDALLPPA----KNNWGEEEEEE 150 (442)
T ss_pred CCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC----CCCCCCCCCCC
T ss_conf 89858752131000343564378899999999999999999999999999999999999855865----55555545420
Q ss_pred CCHHHHHHHHHHHCCCCCC
Q ss_conf 8989999999983756456
Q gi|254780805|r 281 ETNEQLKIICSLLGENDFE 299 (300)
Q Consensus 281 ~s~eeLe~Il~kL~~~~~~ 299 (300)
.+....+.+.++|.++..|
T Consensus 151 ~~~~tre~~r~~Lr~G~Ld 169 (442)
T PRK05201 151 ESSATRQKFRKKLREGELD 169 (442)
T ss_pred HHHHHHHHHHHHHHCCCCC
T ss_conf 2367899999998658866
No 485
>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein; InterPro: IPR005670 This is a family of phosphate transport system permease proteins.; GO: 0005315 inorganic phosphate transmembrane transporter activity, 0015114 phosphate transmembrane transporter activity, 0006817 phosphate transport, 0016020 membrane.
Probab=24.43 E-value=41 Score=14.32 Aligned_cols=64 Identities=27% Similarity=0.342 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH--HCCHHH------HHHHHHCCHHHHHHH-HHHHCCCCHHHHHHHHHHHHCC
Q ss_conf 786565654358999987642--101677------777640100468999-9742224778999999764102
Q gi|254780805|r 169 VANILRILKLPSSVREMIRKE--EISLGH------ARTLVSTSDPLSLAQ-VIVSKKMSVRDTEELVQEQDNK 232 (300)
Q Consensus 169 V~~~LrLl~L~~~i~~~l~~~--~is~gh------ar~Ll~~~~~~~la~-~Ii~~~LSVRe~E~lVk~~~~~ 232 (300)
|...|+=..|.++|++-|.+. -||-|| ||+|.--||-.=+-| --.=+.-|+.++|+++.+++..
T Consensus 121 Ve~sL~~AALWDEVKD~L~~sa~~LSGGQQQRLCIARalA~ePeVlLlDEPTSALDPIaT~~IEeLi~eLk~~ 193 (248)
T TIGR00972 121 VEESLKKAALWDEVKDRLHDSALGLSGGQQQRLCIARALAVEPEVLLLDEPTSALDPIATGKIEELIQELKKK 193 (248)
T ss_pred HHHHHHHCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHC
T ss_conf 9999861687135524213588978726889999998752488521057888757877899999999987652
No 486
>PRK09147 aminotransferase; Provisional
Probab=24.37 E-value=50 Score=13.76 Aligned_cols=30 Identities=20% Similarity=0.327 Sum_probs=0.0
Q ss_pred CCCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf 235789998-768988999999988631001
Q gi|254780805|r 47 IVPNPHNPR-NYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 47 i~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l 76 (300)
+..||+||- +.++.+.+++|++=-++||++
T Consensus 171 il~sP~NPTG~v~s~e~l~~l~~la~~~~i~ 201 (397)
T PRK09147 171 FVCSPGNPTGAVLPLDDWKKLFALSDRYGFV 201 (397)
T ss_pred EECCCCCCCCCCCCHHHHHHHHHHHCCCEEE
T ss_conf 8689989889988889999999963247289
No 487
>PRK07851 acetyl-CoA acetyltransferase; Provisional
Probab=24.33 E-value=26 Score=15.52 Aligned_cols=128 Identities=18% Similarity=0.275 Sum_probs=0.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCC-CCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 999876898899999998863100155046205654-4533357567777764210013543334641123455666543
Q gi|254780805|r 52 HNPRNYFESEGLEDLCQSIKSHGIIQPLIVRAIDNG-LYKIIAGERRFRAAKMASLSEVPVIIRNVDNKSSLEIAIVENV 130 (300)
Q Consensus 52 ~~pR~~~~~~~l~eLa~SI~~~G~lqPi~Vr~~~~g-~y~ii~G~rR~rAa~~~g~~~ip~iv~~~~d~~~~~~~l~EN~ 130 (300)
..||...+.|.+..|.--.+..|.++.----+..|| -..|++.+...+..-+--+-.|-..-.-..|-+..-++-+.
T Consensus 229 e~~R~~tt~e~La~L~P~F~~~GtvTAgNaS~~~DGAAavll~se~~a~~~gl~Plari~~~~~~g~dP~~m~~~Pv~-- 306 (405)
T PRK07851 229 DGPRAGTTYEAVSQLKPVFRPDGTVTAGNACPLNDGAAAVVIMSDTKARELGLTPLARIVSTGVSGLSPEIMGLGPIE-- 306 (405)
T ss_pred CCCCCCCCHHHHHHCCCCCCCCCCEECCCCCCCCCHHHHHHHCCHHHHHHCCCCCEEEEEECCCCCCCHHHHCCCHHH--
T ss_conf 772268886668507864156886755437865434699887279999977998159999540056487884618899--
Q ss_pred HCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHCCHHH
Q ss_conf 1022104899999998521011104679999743378778656---5654358999987642101677
Q gi|254780805|r 131 QRKDLNPLEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL---RILKLPSSVREMIRKEEISLGH 195 (300)
Q Consensus 131 ~R~dl~p~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L---rLl~L~~~i~~~l~~~~is~gh 195 (300)
+.+++++..|++.+++ ..+-...++-+..| +-+.++++ +=-+.-|-|+.||
T Consensus 307 ------------A~~~~L~~agl~~~Di-d~~EinEAFA~q~l~~~~~lgid~~-kvNv~GGaiAlGH 360 (405)
T PRK07851 307 ------------ASKQALARAGMTIDDI-DLVEINEAFAVQVLGSARELGIDED-KLNVSGGAIALGH 360 (405)
T ss_pred ------------HHHHHHHHCCCCCCCC-CEEEEEHHHHHHHHHHHHHHCCCHH-HCCCCCCHHHHCC
T ss_conf ------------9999999769980248-7556406678889999998489888-8199855887388
No 488
>pfam06970 RepA_N Replication initiator protein A (RepA) N-terminus. This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included.
Probab=24.30 E-value=50 Score=13.75 Aligned_cols=22 Identities=18% Similarity=0.415 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1046799997433787786565
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
+|.+++++.+|.|+.+|.+.++
T Consensus 53 ft~~el~~~L~~s~~~v~k~~k 74 (76)
T pfam06970 53 FTNEELMELLNCSKQKVIKIKK 74 (76)
T ss_pred EEHHHHHHHHCCCHHHHHHHHH
T ss_conf 6499999997878889999996
No 489
>TIGR02094 more_P_ylases alpha-glucan phosphorylases; InterPro: IPR011834 This family consists of known phosphorylases, and homologues believed to share the function of using inorganic phosphate to cleave an alpha 1,4 linkage between the terminal glucose residue and the rest of the polymer (maltodextrin, glycogen, etc.). The name of the glucose storage polymer substrate, and therefore the name of this enzyme, depends on the chain lengths and branching patterns. A number of the members of this family have been shown to operate on small maltodextrins, as may be obtained by utilization of exogenous sources. This family represents a distinct clade from the related families: Glycogen/starch/alpha-glucan phosphorylase and Glycosyl transferase, family 35.; GO: 0004645 phosphorylase activity, 0030170 pyridoxal phosphate binding, 0005975 carbohydrate metabolic process.
Probab=24.07 E-value=50 Score=13.72 Aligned_cols=34 Identities=24% Similarity=0.422 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 01677777640100468999974222477899999976
Q gi|254780805|r 191 ISLGHARTLVSTSDPLSLAQVIVSKKMSVRDTEELVQE 228 (300)
Q Consensus 191 is~ghar~Ll~~~~~~~la~~Ii~~~LSVRe~E~lVk~ 228 (300)
+..||| |++.+ +.+.+.|-++|+|..++.+.|+.
T Consensus 173 ~NEGHA-AF~~L---Erir~~~~~~G~~F~~A~e~Vr~ 206 (618)
T TIGR02094 173 LNEGHA-AFVTL---ERIRELIEAQGLSFEEALEAVRK 206 (618)
T ss_pred CCCCHH-HHHHH---HHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 177668-99999---99999999728889899999852
No 490
>PRK05664 threonine-phosphate decarboxylase; Reviewed
Probab=23.97 E-value=51 Score=13.71 Aligned_cols=27 Identities=26% Similarity=0.425 Sum_probs=0.0
Q ss_pred CCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf 789998-768988999999988631001
Q gi|254780805|r 50 NPHNPR-NYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 50 ~p~~pR-~~~~~~~l~eLa~SI~~~G~l 76 (300)
||+||- +.++.+.+.++++.+..+|.+
T Consensus 132 nPNNPTG~~~~~~~l~~~~~~~~~~~~~ 159 (330)
T PRK05664 132 NPNNPTGRRFDPARLLAWHARLAARGGW 159 (330)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf 7928866898999999999986531988
No 491
>TIGR02405 trehalos_R_Ecol trehalose operon repressor; InterPro: IPR012771 Trehalose is a non-reducing disaccharide which can be used as both a carbon source and an osmoprotectant in bacteria. Trehalose uptake into the cytoplasm occurs via a trehalose-specific phosphotransferase system which phosphorylates trehalase to trehalose-6-phosphate (Tre6P) during transport into the cytoplasm, and a hydrolase which hydrolyses Tre6P to glucose and glucose-6-phophate. This entry represents LacI-type TreR, a transcriptional repressor of trehalose uptake found mainly within the gamma-proteobacteria. It does not include the GntR-type TreR's such as those found in Bacillus species. It is capable of binding both the inducer Tre6P and trehalose. Binding of trehalose does not affect the repressor's affinity for its DNA binding site, while binding Tre6P substantially reduces its affinity. The repression activity of TreR is therefore regulated by the ratio of trehalose to Tre6P within the cell . The protein is composed of two domains, an N-terminal DNA-binding helix-turn-helix domain, and a C-terminal effector-binding domain which is homologous to that of LacI. The effector-binding domain is composed of two subdomains, both of which form an alpha-beta-alpha sandwhich, with the effector binding site located at the interface of these subdomains . Tre6P and trehalose bind competitively to this site, with the affinty for trehalose substantially lower than that for Tre6P.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0005991 trehalose metabolic process, 0016481 negative regulation of transcription.
Probab=23.88 E-value=18 Score=16.64 Aligned_cols=22 Identities=32% Similarity=0.516 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 1104679999743378778656
Q gi|254780805|r 152 GYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 152 ~~t~~~lA~~~G~s~s~V~~~L 173 (300)
.+|-.+||+.-|.++|||||.|
T Consensus 1 kLTIkDIArLagVgKSTVSRVL 22 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVL 22 (311)
T ss_pred CCHHHHHHHHHCCCCEEEEEEE
T ss_conf 9617776977088620233156
No 492
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role..
Probab=23.82 E-value=41 Score=14.29 Aligned_cols=26 Identities=23% Similarity=0.434 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10467999974337877865656543
Q gi|254780805|r 153 YTQNDIGSIVGKSRSHVANILRILKL 178 (300)
Q Consensus 153 ~t~~~lA~~~G~s~s~V~~~LrLl~L 178 (300)
|+-.+||+..|.+-+||++.|+.|..
T Consensus 26 ySAA~lA~~tgL~~pTvsK~Lk~L~~ 51 (130)
T TIGR02944 26 YSAAELAEQTGLEAPTVSKILKALSE 51 (130)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHC
T ss_conf 06888786459886047899887642
No 493
>PRK08153 histidinol-phosphate aminotransferase; Provisional
Probab=23.82 E-value=51 Score=13.69 Aligned_cols=27 Identities=15% Similarity=0.470 Sum_probs=0.0
Q ss_pred CCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf 789998-768988999999988631001
Q gi|254780805|r 50 NPHNPR-NYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 50 ~p~~pR-~~~~~~~l~eLa~SI~~~G~l 76 (300)
||+||- ..++.+.+.++++.+..++++
T Consensus 164 nPNNPTG~~~~~~~l~~l~~~~~~~~lv 191 (370)
T PRK08153 164 NPDNPMGSWHPAADIVAFIEALPETTLL 191 (370)
T ss_pred CCCCCCCCCCCHHHHHHHHHHCCCCCEE
T ss_conf 8959857767868899999847777389
No 494
>PRK03321 putative aminotransferase; Provisional
Probab=23.75 E-value=51 Score=13.68 Aligned_cols=30 Identities=20% Similarity=0.430 Sum_probs=0.0
Q ss_pred CCCCCCCCC-CCCCHHHHHHHHHHHHHCCCC
Q ss_conf 235789998-768988999999988631001
Q gi|254780805|r 47 IVPNPHNPR-NYFESEGLEDLCQSIKSHGII 76 (300)
Q Consensus 47 i~~~p~~pR-~~~~~~~l~eLa~SI~~~G~l 76 (300)
+..||+||- ..++.+.++++++.+..+.++
T Consensus 150 ~l~nPnNPTG~~~~~~~l~~l~~~~~~~~~v 180 (352)
T PRK03321 150 FVCNPNNPTGTVVTPAALARFVAAVPADVLV 180 (352)
T ss_pred EECCCCCCCCCCCCCHHHHHHHHHCCCCCEE
T ss_conf 9849999730136837589999755478479
No 495
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=23.67 E-value=51 Score=13.67 Aligned_cols=39 Identities=10% Similarity=0.186 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8999999985210111046799997433787786565654
Q gi|254780805|r 138 LEEALGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 138 ~e~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+.+=+.|....+. |++-.+.|++++.|++.||+.++.|+
T Consensus 3 l~QLryf~~va~~-~~n~t~AA~~L~iSQPavS~qIk~LE 41 (324)
T PRK12681 3 LQQLRYIVEVVNH-NLNVSATAESLYTSQPGISKQVRMLE 41 (324)
T ss_pred HHHHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 6999999999976-99999999997897779999999999
No 496
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=23.55 E-value=52 Score=13.66 Aligned_cols=51 Identities=20% Similarity=0.270 Sum_probs=0.0
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHH----CCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 566654310221048999999985210----111046799997433787786565
Q gi|254780805|r 124 IAIVENVQRKDLNPLEEALGYEQLISE----YGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 124 ~~l~EN~~R~dl~p~e~A~~~~~l~~~----~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
....+++......+.+.-.+..-|... +..++.++|..+|.|+.+|++.|.
T Consensus 124 ~~~~~~~~~~~~~~~~~RlA~~LL~~~~~~~~~~~~~elA~~lG~Sretl~R~L~ 178 (213)
T PRK10402 124 YRNIVSYTQNQSFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLA 178 (213)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999987537889999999998610786666799999997988999999999
No 497
>PRK00118 putative DNA-binding protein; Validated
Probab=23.32 E-value=52 Score=13.63 Aligned_cols=34 Identities=18% Similarity=0.197 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999985210111046799997433787786565
Q gi|254780805|r 140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~Lr 174 (300)
+-..+.-...+ .+|-.|||+.+|.||..|...++
T Consensus 22 Q~~~~~lyy~~-DlSl~EIAe~~~iSRQaV~D~ik 55 (105)
T PRK00118 22 QRNYMELYYLD-DYSLGEIAEEFNVSRQAVYDNIK 55 (105)
T ss_pred HHHHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99999999885-49999998996985999999999
No 498
>PRK13558 bacterio-opsin activator; Provisional
Probab=23.21 E-value=52 Score=13.61 Aligned_cols=21 Identities=10% Similarity=0.066 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHH
Q ss_conf 046799997433787786565
Q gi|254780805|r 154 TQNDIGSIVGKSRSHVANILR 174 (300)
Q Consensus 154 t~~~lA~~~G~s~s~V~~~Lr 174 (300)
|-++||+.+|.|+++..++||
T Consensus 641 TGeElAesLgIS~pTfhqHLR 661 (674)
T PRK13558 641 EGKQLAESMDIVPSTYHQHLQ 661 (674)
T ss_pred CHHHHHHHCCCCHHHHHHHHH
T ss_conf 789999870988388999999
No 499
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=23.16 E-value=52 Score=13.61 Aligned_cols=34 Identities=15% Similarity=0.123 Sum_probs=0.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999985210111046799997433787786565654
Q gi|254780805|r 142 LGYEQLISEYGYTQNDIGSIVGKSRSHVANILRILK 177 (300)
Q Consensus 142 ~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~LrLl~ 177 (300)
+.|....+..++| ..|+++|.|++.||+.++-|+
T Consensus 8 ~~F~aVa~~gSft--~AA~~L~isqsaVS~~I~~LE 41 (300)
T PRK11074 8 EVVDAVARNGSFS--AAAQELHKVPSAVSYTVRQLE 41 (300)
T ss_pred HHHHHHHHCCCHH--HHHHHHCCCHHHHHHHHHHHH
T ss_conf 9999999709999--999997888789999999999
No 500
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=23.11 E-value=53 Score=13.60 Aligned_cols=34 Identities=9% Similarity=0.064 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999998521011104679999743378778656
Q gi|254780805|r 140 EALGYEQLISEYGYTQNDIGSIVGKSRSHVANIL 173 (300)
Q Consensus 140 ~A~~~~~l~~~~~~t~~~lA~~~G~s~s~V~~~L 173 (300)
+++.+|+...+++....+-|+++|.-|.+..+.|
T Consensus 143 ~WEhIqrvl~e~~~NiSeTARrL~MHRRTLqRkL 176 (182)
T COG4567 143 RWEHIQRVLEECEGNISETARRLNMHRRTLQRKL 176 (182)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 6999999999937777899999621399999997
Done!