Query 020252
Match_columns 328
No_of_seqs 218 out of 1330
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 08:14:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020252.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020252hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 99.9 4.7E-27 1E-31 233.7 15.1 119 209-328 57-218 (415)
2 TIGR02997 Sig70-cyanoRpoD RNA 99.9 3.2E-25 6.9E-30 209.7 14.0 116 212-328 1-117 (298)
3 PRK07406 RNA polymerase sigma 99.9 5.9E-24 1.3E-28 209.1 14.9 118 210-328 61-179 (373)
4 PRK05949 RNA polymerase sigma 99.9 1.5E-22 3.2E-27 195.5 15.3 118 210-328 16-134 (327)
5 PRK07405 RNA polymerase sigma 99.9 1.8E-22 3.8E-27 193.7 14.4 117 211-328 7-124 (317)
6 PRK05901 RNA polymerase sigma 99.8 3.8E-21 8.3E-26 195.7 9.3 107 208-328 207-314 (509)
7 COG0568 RpoD DNA-directed RNA 99.8 1.1E-19 2.4E-24 177.3 9.1 117 211-328 8-145 (342)
8 PRK07921 RNA polymerase sigma 99.7 2.3E-17 4.9E-22 159.6 11.0 106 209-328 23-129 (324)
9 PRK09210 RNA polymerase sigma 99.5 7.6E-14 1.6E-18 136.7 9.8 80 208-328 92-172 (367)
10 PRK05658 RNA polymerase sigma 99.5 4.6E-14 1E-18 146.4 8.0 45 284-328 379-423 (619)
11 PRK06596 RNA polymerase factor 99.4 2.5E-12 5.4E-17 121.7 9.9 80 209-328 11-91 (284)
12 TIGR02392 rpoH_proteo alternat 99.3 3.2E-12 6.9E-17 119.6 9.2 76 213-328 2-78 (270)
13 PRK07500 rpoH2 RNA polymerase 99.3 1.3E-11 2.8E-16 117.3 9.4 78 211-328 5-83 (289)
14 PRK07122 RNA polymerase sigma 99.2 9.1E-12 2E-16 116.8 5.1 45 284-328 39-83 (264)
15 PRK05657 RNA polymerase sigma 99.0 6.3E-10 1.4E-14 107.7 9.1 77 211-328 52-129 (325)
16 TIGR02394 rpoS_proteo RNA poly 99.0 3E-09 6.5E-14 100.3 9.6 78 210-328 11-89 (285)
17 TIGR02850 spore_sigG RNA polym 98.9 4.8E-09 1E-13 97.2 8.3 68 221-328 10-77 (254)
18 PRK07408 RNA polymerase sigma 98.9 4.6E-09 1E-13 97.9 7.5 46 283-328 23-69 (256)
19 COG1191 FliA DNA-directed RNA 98.8 5.6E-09 1.2E-13 98.7 7.2 45 283-328 22-67 (247)
20 PRK08215 sporulation sigma fac 98.8 1.1E-08 2.5E-13 94.8 8.2 67 222-328 14-80 (258)
21 PRK06288 RNA polymerase sigma 98.7 5.4E-08 1.2E-12 90.9 7.6 70 220-328 5-77 (268)
22 PRK05911 RNA polymerase sigma 98.6 7E-08 1.5E-12 90.2 5.6 46 283-328 21-69 (257)
23 PRK05803 sporulation sigma fac 98.6 2.9E-07 6.4E-12 84.1 9.2 74 213-327 17-91 (233)
24 TIGR02941 Sigma_B RNA polymera 98.5 3.2E-07 7E-12 84.7 7.9 66 224-328 7-72 (255)
25 PRK08583 RNA polymerase sigma 98.4 9.9E-07 2.1E-11 81.6 8.1 67 223-328 6-72 (257)
26 PRK05572 sporulation sigma fac 98.1 1.3E-05 2.8E-10 74.3 8.2 67 222-328 9-75 (252)
27 PF00140 Sigma70_r1_2: Sigma-7 98.0 1.9E-06 4.2E-11 59.4 1.3 33 211-244 1-34 (37)
28 PRK07670 RNA polymerase sigma 97.9 3.2E-05 7E-10 71.6 7.1 46 283-328 20-68 (251)
29 TIGR02846 spore_sigmaK RNA pol 97.8 0.00013 2.8E-09 66.7 9.3 72 216-327 19-90 (227)
30 PRK08301 sporulation sigma fac 97.7 0.00018 3.8E-09 65.6 8.3 76 212-327 19-94 (234)
31 TIGR02835 spore_sigmaE RNA pol 97.4 0.00059 1.3E-08 62.6 8.1 45 283-327 50-94 (234)
32 PF04542 Sigma70_r2: Sigma-70 97.2 0.00045 9.8E-09 50.5 4.0 38 290-327 1-38 (71)
33 PRK11922 RNA polymerase sigma 97.0 0.0017 3.7E-08 59.4 6.6 66 222-327 7-72 (231)
34 PRK05602 RNA polymerase sigma 96.8 0.0027 5.8E-08 55.5 5.7 54 274-327 8-62 (186)
35 PRK05658 RNA polymerase sigma 96.7 0.0045 9.7E-08 65.2 7.7 33 210-243 102-135 (619)
36 PRK12427 flagellar biosynthesi 96.7 0.0039 8.6E-08 57.6 6.5 21 308-328 41-61 (231)
37 PRK09641 RNA polymerase sigma 96.7 0.0033 7.1E-08 54.4 5.4 45 283-327 16-60 (187)
38 PRK08295 RNA polymerase factor 96.7 0.005 1.1E-07 54.3 6.7 45 283-327 22-66 (208)
39 TIGR02859 spore_sigH RNA polym 96.5 0.0073 1.6E-07 52.8 6.7 55 273-327 6-61 (198)
40 PF04539 Sigma70_r3: Sigma-70 96.5 0.0053 1.2E-07 47.0 5.0 40 243-282 4-43 (78)
41 PRK08311 putative RNA polymera 96.5 0.007 1.5E-07 56.9 6.5 54 275-328 7-63 (237)
42 TIGR02948 SigW_bacill RNA poly 96.4 0.0056 1.2E-07 52.9 4.9 45 283-327 16-60 (187)
43 PRK12513 RNA polymerase sigma 96.2 0.0084 1.8E-07 52.7 5.3 53 275-327 15-68 (194)
44 PRK09648 RNA polymerase sigma 96.2 0.017 3.8E-07 50.5 7.1 45 283-327 22-70 (189)
45 PRK13919 putative RNA polymera 96.1 0.013 2.9E-07 50.9 5.8 54 274-327 11-65 (186)
46 PRK09638 RNA polymerase sigma 96.0 0.017 3.8E-07 49.6 6.1 45 283-327 16-60 (176)
47 PRK11923 algU RNA polymerase s 96.0 0.02 4.2E-07 50.2 6.4 45 283-327 18-62 (193)
48 PRK09640 RNA polymerase sigma 95.9 0.019 4E-07 50.5 6.2 57 271-327 8-68 (188)
49 PRK09646 RNA polymerase sigma 95.8 0.021 4.6E-07 50.5 5.9 53 275-327 19-72 (194)
50 PRK06811 RNA polymerase factor 95.4 0.044 9.6E-07 48.3 6.6 56 272-327 4-63 (189)
51 TIGR02939 RpoE_Sigma70 RNA pol 95.4 0.036 7.8E-07 48.0 5.7 45 283-327 18-62 (190)
52 PRK12519 RNA polymerase sigma 95.2 0.042 9.2E-07 48.2 5.7 53 274-326 17-70 (194)
53 PRK12514 RNA polymerase sigma 95.2 0.038 8.2E-07 47.9 5.2 45 283-327 17-61 (179)
54 PRK12534 RNA polymerase sigma 95.0 0.044 9.5E-07 47.8 5.2 46 282-327 22-67 (187)
55 PRK12524 RNA polymerase sigma 94.9 0.063 1.4E-06 47.6 5.9 55 273-327 13-68 (196)
56 TIGR02954 Sig70_famx3 RNA poly 94.2 0.11 2.4E-06 44.5 5.7 45 283-327 14-58 (169)
57 PRK12531 RNA polymerase sigma 93.3 0.22 4.7E-06 44.1 6.1 45 283-327 25-69 (194)
58 PRK12515 RNA polymerase sigma 93.1 0.21 4.5E-06 43.8 5.7 56 272-327 8-64 (189)
59 PRK12538 RNA polymerase sigma 93.0 0.2 4.3E-06 46.5 5.6 45 283-327 61-105 (233)
60 PRK12537 RNA polymerase sigma 92.2 0.36 7.9E-06 42.1 6.0 46 282-327 20-65 (182)
61 PRK09643 RNA polymerase sigma 92.1 0.35 7.6E-06 42.9 5.7 54 274-327 15-69 (192)
62 PRK12512 RNA polymerase sigma 91.9 0.55 1.2E-05 40.8 6.7 44 283-326 20-67 (184)
63 PRK12526 RNA polymerase sigma 91.3 0.41 8.9E-06 43.0 5.4 45 283-327 36-80 (206)
64 PRK12536 RNA polymerase sigma 91.3 0.58 1.3E-05 40.8 6.2 47 281-327 17-64 (181)
65 PRK12539 RNA polymerase sigma 90.9 0.86 1.9E-05 39.8 6.9 45 283-327 19-67 (184)
66 COG1191 FliA DNA-directed RNA 84.8 1.9 4.1E-05 41.3 5.5 41 243-283 110-150 (247)
67 PRK09647 RNA polymerase sigma 84.0 1.7 3.7E-05 39.3 4.6 45 283-327 26-70 (203)
68 PRK08241 RNA polymerase factor 83.5 2.7 5.9E-05 40.3 6.1 45 283-327 17-61 (339)
69 TIGR02999 Sig-70_X6 RNA polyme 82.0 4.6 9.9E-05 34.8 6.4 43 283-325 15-62 (183)
70 PRK07408 RNA polymerase sigma 79.7 4.5 9.8E-05 37.9 6.0 37 244-280 114-150 (256)
71 TIGR02393 RpoD_Cterm RNA polym 77.6 6.2 0.00013 36.4 6.1 37 244-280 88-124 (238)
72 PRK07122 RNA polymerase sigma 77.2 6.3 0.00014 37.3 6.2 36 245-280 129-164 (264)
73 TIGR02850 spore_sigG RNA polym 77.2 6.3 0.00014 36.7 6.1 36 245-280 122-157 (254)
74 PRK12427 flagellar biosynthesi 76.2 4.7 0.0001 37.4 4.9 36 245-280 103-138 (231)
75 PRK12517 RNA polymerase sigma 75.9 4.3 9.3E-05 36.0 4.4 48 280-327 18-65 (188)
76 TIGR03001 Sig-70_gmx1 RNA poly 75.9 7.3 0.00016 36.6 6.2 55 271-325 24-79 (244)
77 PRK07921 RNA polymerase sigma 75.8 6.7 0.00014 38.7 6.1 38 243-280 173-210 (324)
78 PRK09649 RNA polymerase sigma 75.5 9.9 0.00021 33.4 6.6 44 283-327 22-65 (185)
79 PRK05911 RNA polymerase sigma 74.4 8.2 0.00018 36.3 6.1 37 245-281 112-148 (257)
80 PRK12533 RNA polymerase sigma 73.5 5.7 0.00012 36.5 4.7 45 283-327 16-60 (216)
81 PRK09210 RNA polymerase sigma 72.8 8.6 0.00019 38.3 6.1 37 244-280 217-253 (367)
82 PRK07406 RNA polymerase sigma 68.5 12 0.00026 37.8 6.1 37 243-279 223-259 (373)
83 PRK05901 RNA polymerase sigma 67.8 12 0.00026 39.5 6.1 38 243-280 358-395 (509)
84 PF01726 LexA_DNA_bind: LexA D 66.6 14 0.00031 28.3 4.9 27 254-280 20-47 (65)
85 PRK07670 RNA polymerase sigma 64.8 15 0.00033 34.1 5.6 38 244-281 110-147 (251)
86 TIGR02885 spore_sigF RNA polym 63.5 16 0.00035 33.2 5.5 36 246-281 100-135 (231)
87 PRK07598 RNA polymerase sigma 63.2 12 0.00026 38.5 5.0 38 244-281 263-300 (415)
88 TIGR02479 FliA_WhiG RNA polyme 61.7 18 0.0004 32.7 5.5 38 243-280 83-120 (224)
89 PRK05949 RNA polymerase sigma 61.1 22 0.00047 35.0 6.2 36 245-280 180-215 (327)
90 COG0568 RpoD DNA-directed RNA 60.5 21 0.00046 35.9 6.1 41 240-280 186-226 (342)
91 PRK08215 sporulation sigma fac 59.8 24 0.00053 32.8 6.1 36 245-280 125-160 (258)
92 PRK10219 DNA-binding transcrip 58.5 73 0.0016 25.4 7.9 37 246-282 8-44 (107)
93 PRK12544 RNA polymerase sigma 58.3 13 0.00029 33.6 3.9 54 269-327 7-60 (206)
94 smart00342 HTH_ARAC helix_turn 58.2 55 0.0012 23.6 6.6 56 259-318 1-59 (84)
95 PRK06288 RNA polymerase sigma 57.2 23 0.0005 33.2 5.5 37 244-280 119-155 (268)
96 PRK07405 RNA polymerase sigma 55.4 31 0.00067 33.7 6.2 37 244-280 169-205 (317)
97 TIGR02997 Sig70-cyanoRpoD RNA 54.2 35 0.00076 32.7 6.3 36 245-280 163-198 (298)
98 PRK12535 RNA polymerase sigma 50.5 42 0.0009 30.0 5.8 44 283-327 23-66 (196)
99 PRK06704 RNA polymerase factor 50.4 27 0.00058 32.8 4.7 51 275-326 8-58 (228)
100 PRK11511 DNA-binding transcrip 50.2 39 0.00085 28.4 5.3 37 245-281 11-47 (127)
101 PRK15044 transcriptional regul 48.3 78 0.0017 31.4 7.7 38 245-282 194-231 (295)
102 PF04967 HTH_10: HTH DNA bindi 47.9 43 0.00094 25.0 4.5 27 258-284 22-48 (53)
103 TIGR02980 SigBFG RNA polymeras 45.1 41 0.00088 30.4 4.9 33 248-280 95-127 (227)
104 TIGR01446 DnaD_dom DnaD and ph 41.8 47 0.001 25.0 4.1 55 253-311 6-66 (73)
105 PRK15186 AraC family transcrip 41.4 92 0.002 30.3 7.0 36 247-282 185-220 (291)
106 PRK06986 fliA flagellar biosyn 40.8 50 0.0011 30.2 4.9 36 245-280 97-132 (236)
107 PF13404 HTH_AsnC-type: AsnC-t 38.9 79 0.0017 22.2 4.5 25 258-282 16-40 (42)
108 COG4977 Transcriptional regula 37.8 76 0.0016 31.8 5.9 51 248-298 225-289 (328)
109 PRK15121 right oriC-binding tr 36.7 2.4E+02 0.0052 26.6 8.9 38 245-282 7-44 (289)
110 TIGR02941 Sigma_B RNA polymera 36.7 66 0.0014 29.8 5.0 36 245-280 118-153 (255)
111 PRK05572 sporulation sigma fac 35.8 83 0.0018 29.2 5.5 34 245-278 120-153 (252)
112 COG1476 Predicted transcriptio 35.1 79 0.0017 25.0 4.4 50 260-319 15-64 (68)
113 COG4367 Uncharacterized protei 32.3 1.9E+02 0.0041 24.4 6.4 43 250-292 13-62 (97)
114 PRK04217 hypothetical protein; 31.9 2.3E+02 0.0051 24.1 7.1 26 260-285 59-84 (110)
115 PRK05657 RNA polymerase sigma 31.8 1.1E+02 0.0023 30.2 5.8 36 245-280 175-210 (325)
116 TIGR03826 YvyF flagellar opero 31.1 1E+02 0.0023 27.2 5.0 33 252-284 39-71 (137)
117 PF02796 HTH_7: Helix-turn-hel 30.7 79 0.0017 22.0 3.5 23 260-282 22-44 (45)
118 PRK13239 alkylmercury lyase; P 29.5 92 0.002 29.4 4.7 27 256-282 33-59 (206)
119 TIGR02297 HpaA 4-hydroxyphenyl 28.7 1.1E+02 0.0024 28.1 5.1 34 249-282 192-225 (287)
120 PHA01976 helix-turn-helix prot 28.6 95 0.0021 22.6 3.8 47 260-316 16-62 (67)
121 PRK15185 transcriptional regul 25.9 1.9E+02 0.0041 28.9 6.4 45 245-289 208-253 (309)
122 PF08279 HTH_11: HTH domain; 25.4 1.6E+02 0.0034 20.7 4.3 24 259-282 15-38 (55)
123 PRK12519 RNA polymerase sigma 24.8 1.3E+02 0.0028 26.2 4.5 36 259-294 157-192 (194)
124 PF07862 Nif11: Nitrogen fixat 24.5 2.1E+02 0.0045 20.2 4.8 38 277-315 10-48 (49)
125 PRK10371 DNA-binding transcrip 24.5 2.4E+02 0.0052 27.0 6.7 38 245-282 193-230 (302)
126 PF12324 HTH_15: Helix-turn-he 23.3 99 0.0021 25.1 3.2 26 257-282 36-61 (77)
127 PF00165 HTH_AraC: Bacterial r 23.2 1.2E+02 0.0025 20.5 3.1 27 255-281 4-30 (42)
128 cd04762 HTH_MerR-trunc Helix-T 22.7 96 0.0021 20.3 2.6 24 261-284 2-25 (49)
129 PRK07500 rpoH2 RNA polymerase 22.0 2.5E+02 0.0054 27.0 6.3 45 258-302 244-288 (289)
130 PF06971 Put_DNA-bind_N: Putat 21.8 2.2E+02 0.0048 21.0 4.5 23 258-280 27-49 (50)
131 TIGR02844 spore_III_D sporulat 21.8 3.7E+02 0.0081 21.6 6.2 36 245-283 8-43 (80)
132 PF08281 Sigma70_r4_2: Sigma-7 21.3 1.1E+02 0.0025 21.3 2.9 25 260-284 27-51 (54)
133 PRK06596 RNA polymerase factor 21.3 1.6E+02 0.0035 28.1 4.8 24 257-280 149-172 (284)
134 smart00345 HTH_GNTR helix_turn 21.1 1.1E+02 0.0024 21.0 2.8 24 259-282 20-43 (60)
135 PRK09393 ftrA transcriptional 20.9 1.7E+02 0.0036 28.0 4.8 35 248-282 223-257 (322)
136 PRK12523 RNA polymerase sigma 20.6 1.4E+02 0.0031 25.5 3.9 26 260-285 136-161 (172)
137 PF13936 HTH_38: Helix-turn-he 20.3 1.1E+02 0.0025 21.3 2.7 23 260-282 21-43 (44)
138 PF14711 Nitr_red_bet_C: Respi 20.1 2.6E+02 0.0057 22.8 5.1 52 213-273 31-82 (83)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=99.95 E-value=4.7e-27 Score=233.74 Aligned_cols=119 Identities=34% Similarity=0.561 Sum_probs=110.1
Q ss_pred CCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhcCCCCchHHHHH
Q 020252 209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAA 267 (328)
Q Consensus 209 ~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~--------------------Le~~r~~L~~~~GrePT~~eWA~ 267 (328)
..+|+++ ||++| |+.||||++||++|+++||+++. |++++.+|++++|++||..|||.
T Consensus 57 ~~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~ 135 (415)
T PRK07598 57 RSTDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAK 135 (415)
T ss_pred CCCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence 4479999 99999 99999999999999999999999 89999999999999999999997
Q ss_pred HhcCcHHHHHHh----------------------hhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHh
Q 020252 268 AAGVDQRELRRR----------------------LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLN 325 (328)
Q Consensus 268 a~g~d~~~L~~~----------------------L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmr 325 (328)
++|+++.+|+.+ +..|..|+++||.+|+|||++||++|.++|++++||||||+||||+
T Consensus 136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~r 215 (415)
T PRK07598 136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER 215 (415)
T ss_pred HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 777666666655 4678899999999999999999999999999999999999999999
Q ss_pred hhC
Q 020252 326 MAH 328 (328)
Q Consensus 326 Ave 328 (328)
|++
T Consensus 216 ave 218 (415)
T PRK07598 216 AVE 218 (415)
T ss_pred HHH
Confidence 984
No 2
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=99.93 E-value=3.2e-25 Score=209.70 Aligned_cols=116 Identities=44% Similarity=0.691 Sum_probs=112.9
Q ss_pred ChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHH
Q 020252 212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM 290 (328)
Q Consensus 212 d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~L 290 (328)
|++. ||+++ +++|+||++||.+|+++++.++.+++++.+|+++.|++||..+||+++|++..+|..++..|..|+++|
T Consensus 1 ~~~~~yl~~~-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L 79 (298)
T TIGR02997 1 DLVRLYLQEI-GRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM 79 (298)
T ss_pred CcHHHHHHHc-cccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence 4677 99999 999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 291 ITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 291 I~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
|.+|+|+|++||++|.|+|.+++||||||++|||+|++
T Consensus 80 v~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~ 117 (298)
T TIGR02997 80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVE 117 (298)
T ss_pred HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999974
No 3
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=99.91 E-value=5.9e-24 Score=209.05 Aligned_cols=118 Identities=41% Similarity=0.651 Sum_probs=115.0
Q ss_pred CCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHH
Q 020252 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (328)
Q Consensus 210 ~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are 288 (328)
..|++. ||++| +++|+||++||++|+++|++++.+++++.+|+++.|++|+..+||.++|++..+|++++..|..|++
T Consensus 61 ~~d~l~~Yl~~i-~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~ 139 (373)
T PRK07406 61 TEDSIRVYLQEI-GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE 139 (373)
T ss_pred CCCHHHHHHHHh-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence 468899 99999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 289 ~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
+||.+|+++|++||++|.++|++++||||||+||||+|++
T Consensus 140 ~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~ 179 (373)
T PRK07406 140 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAE 179 (373)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999974
No 4
>PRK05949 RNA polymerase sigma factor; Validated
Probab=99.89 E-value=1.5e-22 Score=195.46 Aligned_cols=118 Identities=33% Similarity=0.545 Sum_probs=115.0
Q ss_pred CCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHH
Q 020252 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (328)
Q Consensus 210 ~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are 288 (328)
.+|++. ||++| +++|+||++||++|+++||.++.+++.+..|..++|++|+..+||.+++++..+|...+..|..|++
T Consensus 16 ~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~ 94 (327)
T PRK05949 16 SADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ 94 (327)
T ss_pred CCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence 478999 99999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 289 ~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
+||.+|+++|++||++|.+.|.+++||||||++||+++++
T Consensus 95 ~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~ 134 (327)
T PRK05949 95 KMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVE 134 (327)
T ss_pred HHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999974
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=99.89 E-value=1.8e-22 Score=193.72 Aligned_cols=117 Identities=38% Similarity=0.562 Sum_probs=114.2
Q ss_pred CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHH
Q 020252 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (328)
Q Consensus 211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~ 289 (328)
+|++. ||+++ +++|+||++||++|+++|++++.+++++..|++++|++|+..+||.+++++...|...+..|..|+++
T Consensus 7 ~~~~~~yl~~i-~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~ 85 (317)
T PRK07405 7 TDLVRTYLREI-GRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85 (317)
T ss_pred CcHHHHHHHHc-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence 67899 99999 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 290 MITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
||.+|+++|+++|++|.+.|.+++||||||++||+++++
T Consensus 86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~ 124 (317)
T PRK07405 86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVE 124 (317)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999974
No 6
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=3.8e-21 Score=195.74 Aligned_cols=107 Identities=31% Similarity=0.478 Sum_probs=91.1
Q ss_pred CCCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHH
Q 020252 208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC 286 (328)
Q Consensus 208 ~~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~A 286 (328)
....|+++ ||++| +++|+||++||++|+++|+.+..++.. +.+ ..+|+.. +..+|+++++.|..|
T Consensus 207 ~~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~~---~~~-------~~~~~~~---~~~~l~~~~~~g~~A 272 (509)
T PRK05901 207 TATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEEL---LAE-------GEKLDPE---LRRDLQWIGRDGKRA 272 (509)
T ss_pred cccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhhh---hhh-------cccchhh---hhhhhhhhccchHHH
Confidence 44578999 99999 999999999999999999987544442 111 1234422 468899999999999
Q ss_pred HHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 287 re~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
+++||.+|||||++||++|.++|++++|||||||||||+||+
T Consensus 273 r~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAve 314 (509)
T PRK05901 273 KNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVE 314 (509)
T ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999984
No 7
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=99.80 E-value=1.1e-19 Score=177.30 Aligned_cols=117 Identities=32% Similarity=0.501 Sum_probs=103.5
Q ss_pred CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hcCCCCchH---------------HHHHHhcCcH
Q 020252 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVDQ 273 (328)
Q Consensus 211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~-~~GrePT~~---------------eWA~a~g~d~ 273 (328)
.|.+. |+.++ +..++++.++|..+...++....+......+.. ..+..|+.. +|+..+..+.
T Consensus 8 ~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E 86 (342)
T COG0568 8 ADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE 86 (342)
T ss_pred hhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence 56788 99999 999999999999999999988777777777776 678888887 7766666655
Q ss_pred -HHHHHhhhhhHH---HHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 274 -RELRRRLNYGIL---CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 274 -~~L~~~L~~G~~---Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
..|..++..|.. |+.+||.+|||||++||++|.|+|++|.|||||||||||+||+
T Consensus 87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVe 145 (342)
T COG0568 87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVE 145 (342)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHH
Confidence 778889988865 9999999999999999999999999999999999999999985
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=99.72 E-value=2.3e-17 Score=159.58 Aligned_cols=106 Identities=32% Similarity=0.464 Sum_probs=90.4
Q ss_pred CCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHH
Q 020252 209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 287 (328)
Q Consensus 209 ~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Ar 287 (328)
..+|++. ||+++ +++|+||++||.+|+++|+.+..++.. |+..+|.... ...+|+..++.|..|+
T Consensus 23 ~~~~~~~~Yl~~i-~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~ 88 (324)
T PRK07921 23 PAADLVRVYLNGI-GKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAAR 88 (324)
T ss_pred CCCChHHHHHHHh-cccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHH
Confidence 3468899 99999 999999999999999999987665553 2223332111 4568999999999999
Q ss_pred HHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 288 e~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
++||.+|+++|+++|++|.+.|++++||||||+|||++|++
T Consensus 89 ~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~ 129 (324)
T PRK07921 89 RHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAME 129 (324)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999974
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=99.49 E-value=7.6e-14 Score=136.70 Aligned_cols=80 Identities=39% Similarity=0.642 Sum_probs=73.7
Q ss_pred CCCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHH
Q 020252 208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC 286 (328)
Q Consensus 208 ~~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~A 286 (328)
...+|+++ ||++| ++.|+||++||.+|+++++. | +..|
T Consensus 92 ~~~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~---------------G-------------------------d~~A 130 (367)
T PRK09210 92 VKINDPVRMYLKEI-GRVPLLTAEEEIELAKRIEE---------------G-------------------------DEEA 130 (367)
T ss_pred cccCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHh---------------h-------------------------HHHH
Confidence 34578999 99999 99999999999999998876 3 3679
Q ss_pred HHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 287 re~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
+++||.+|+++|++||++|.++|++++||||||+||||+|++
T Consensus 131 ~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~ 172 (367)
T PRK09210 131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVE 172 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999974
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=99.49 E-value=4.6e-14 Score=146.37 Aligned_cols=45 Identities=36% Similarity=0.580 Sum_probs=43.2
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 284 ~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
..|+++||.+|||||++||++|.++|++|+|||||||||||+||+
T Consensus 379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~ 423 (619)
T PRK05658 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 423 (619)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHH
Confidence 368999999999999999999999999999999999999999985
No 11
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=99.36 E-value=2.5e-12 Score=121.74 Aligned_cols=80 Identities=26% Similarity=0.499 Sum_probs=71.8
Q ss_pred CCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHH
Q 020252 209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK 287 (328)
Q Consensus 209 ~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Ar 287 (328)
.+.+++. |++++ ++.|+|+.++|.+|+.+++. .| +..++
T Consensus 11 ~~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~--------------~G-------------------------d~~a~ 50 (284)
T PRK06596 11 SPEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLRE--------------HG-------------------------DLEAA 50 (284)
T ss_pred CCccHHHHHHHHH-hccCCCCHHHHHHHHHHHHH--------------cC-------------------------CHHHH
Confidence 4567899 99999 99999999999999987542 14 47899
Q ss_pred HHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 288 e~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
+.||..|+++|.+||++|.+.|++++||||||++||++|++
T Consensus 51 ~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~ 91 (284)
T PRK06596 51 KQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVK 91 (284)
T ss_pred HHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999974
No 12
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=99.34 E-value=3.2e-12 Score=119.63 Aligned_cols=76 Identities=30% Similarity=0.564 Sum_probs=68.6
Q ss_pred hhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHH
Q 020252 213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291 (328)
Q Consensus 213 ~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI 291 (328)
++. ||+++ ++.|+|+.++|.+|+.+++. .| +..|+++||
T Consensus 2 ~~~~yl~~~-~~~~~l~~~~e~~l~~~~~~--------------~g-------------------------d~~a~~~Lv 41 (270)
T TIGR02392 2 SLDAYIRAV-NRIPMLTPEEEYQLAKRLRE--------------HG-------------------------DLDAAKKLV 41 (270)
T ss_pred hHHHHHHHH-hcCCCCCHHHHHHHHHHHHH--------------CC-------------------------CHHHHHHHH
Confidence 577 99999 99999999999999887532 14 478999999
Q ss_pred HHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 292 TSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 292 ~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
..|+++|.++|++|.+.|.+++||||+|++||++|++
T Consensus 42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~ 78 (270)
T TIGR02392 42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVK 78 (270)
T ss_pred HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999974
No 13
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=99.28 E-value=1.3e-11 Score=117.27 Aligned_cols=78 Identities=26% Similarity=0.364 Sum_probs=70.2
Q ss_pred CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHH
Q 020252 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (328)
Q Consensus 211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~ 289 (328)
.+.++ ||+++ .+.|+||.++|.+|+++++.. | +..|+++
T Consensus 5 ~~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~~--------------g-------------------------d~~A~~~ 44 (289)
T PRK07500 5 ASADRSMIRSA-MKAPYLEREEEHALAYRWKDH--------------R-------------------------DEDALHR 44 (289)
T ss_pred hhHHHHHHHHH-hcCCCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHH
Confidence 34566 99999 999999999999999987531 4 4789999
Q ss_pred HHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 290 MITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
||..|+++|.++|++|.+.|.+.+||+|||++||++|++
T Consensus 45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~ 83 (289)
T PRK07500 45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAA 83 (289)
T ss_pred HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999974
No 14
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=99.22 E-value=9.1e-12 Score=116.83 Aligned_cols=45 Identities=27% Similarity=0.433 Sum_probs=43.2
Q ss_pred HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 284 ~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
..++++||.+|+|||++||++|.++|++++||||+|+||||+|++
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~Aie 83 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVN 83 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Confidence 569999999999999999999999999999999999999999985
No 15
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=99.05 E-value=6.3e-10 Score=107.73 Aligned_cols=77 Identities=35% Similarity=0.531 Sum_probs=71.1
Q ss_pred CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHH
Q 020252 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK 289 (328)
Q Consensus 211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~ 289 (328)
.|.++ |+.+| +..|+||+++|..|+.+++. | +..|++.
T Consensus 52 ~~~~~~y~~~~-~~~~~l~~~ee~~li~~~~~---------------G-------------------------d~~A~~~ 90 (325)
T PRK05657 52 LDATQLYLNEI-GYSPLLTAEEEVYFARRALR---------------G-------------------------DFAARQR 90 (325)
T ss_pred ccHHHHHHHHH-hcCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHH
Confidence 56778 99999 99999999999999988876 4 4689999
Q ss_pred HHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 290 MITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
||..|.++|.++|++|.+.+.+.+||+|||++||+++++
T Consensus 91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~ 129 (325)
T PRK05657 91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVE 129 (325)
T ss_pred HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999873
No 16
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model 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 prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=98.95 E-value=3e-09 Score=100.27 Aligned_cols=78 Identities=36% Similarity=0.519 Sum_probs=72.0
Q ss_pred CCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHH
Q 020252 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288 (328)
Q Consensus 210 ~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are 288 (328)
..|.+. ||.+| +..+.|+.++|.+|+..++. | ...|++
T Consensus 11 ~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~a~~ 49 (285)
T TIGR02394 11 VADVTQLYLREI-GFKPLLTAEEEIAYARRALA---------------G-------------------------DFEARK 49 (285)
T ss_pred cchHHHHHHHHH-hccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHH
Confidence 467899 99999 99999999999999988876 4 478999
Q ss_pred HHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 289 ~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
.|+..|.++|..+|++|.+.+.+.+||+|||+|||++|++
T Consensus 50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~ 89 (285)
T TIGR02394 50 VMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVE 89 (285)
T ss_pred HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999874
No 17
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=98.89 E-value=4.8e-09 Score=97.25 Aligned_cols=68 Identities=26% Similarity=0.453 Sum_probs=61.5
Q ss_pred ccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHH
Q 020252 221 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 300 (328)
Q Consensus 221 ~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvs 300 (328)
++++|+|++++|.+|+..++. | +..++++|+..|+++|.+
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQS---------------G-------------------------DTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHHH
Confidence 468999999999999887765 4 367999999999999999
Q ss_pred HHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 301 IAKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 301 IAkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
+|++|.+.+.+.+||+|||++||+++++
T Consensus 50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~ 77 (254)
T TIGR02850 50 VIQRFNNRGEYVDDLFQVGCIGLMKSID 77 (254)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999874
No 18
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=98.87 E-value=4.6e-09 Score=97.86 Aligned_cols=46 Identities=22% Similarity=0.353 Sum_probs=42.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCC-CCChHHHHHHHHHHHHhhhC
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~-Gl~~~DLIQEG~iGLmrAve 328 (328)
...++++||.+|++||.+||++|.++ |.+++||||+|+||||+|++
T Consensus 23 d~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~ 69 (256)
T PRK07408 23 SIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIE 69 (256)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHH
Confidence 36899999999999999999999876 77899999999999999974
No 19
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=98.85 E-value=5.6e-09 Score=98.66 Aligned_cols=45 Identities=22% Similarity=0.426 Sum_probs=42.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCC-ChHHHHHHHHHHHHhhhC
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGM-NLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl-~~~DLIQEG~iGLmrAve 328 (328)
...++ +||+.|+|||.+||++|.++|. .++||||.||||||+||+
T Consensus 22 ~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aie 67 (247)
T COG1191 22 DEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIE 67 (247)
T ss_pred CHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHH
Confidence 36788 9999999999999999999998 999999999999999985
No 20
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=98.82 E-value=1.1e-08 Score=94.79 Aligned_cols=67 Identities=27% Similarity=0.475 Sum_probs=60.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHH
Q 020252 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (328)
Q Consensus 222 ~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsI 301 (328)
.++|+|+++|+..|+..++. | +..++++|+..|+++|..+
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~~~~~v~~~ 53 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQN---------------G-------------------------DKEAREKLINGNLRLVLSV 53 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHHHH
Confidence 56789999999998887764 3 4689999999999999999
Q ss_pred HhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 302 AKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 302 AkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
|++|.+.+.+.+||+|||++||++|++
T Consensus 54 a~~~~~~~~~aeDlvQe~~i~l~~a~~ 80 (258)
T PRK08215 54 IQRFNNRGENVDDLFQVGCIGLMKAID 80 (258)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999874
No 21
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=98.66 E-value=5.4e-08 Score=90.91 Aligned_cols=70 Identities=16% Similarity=0.220 Sum_probs=60.9
Q ss_pred hccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHH
Q 020252 220 TTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 299 (328)
Q Consensus 220 i~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVv 299 (328)
++|++|+||.++|.+|+..++.. | +..+++.++..|++||.
T Consensus 5 ~~~~~~~~~~~~e~~l~~~~~~~--------------~-------------------------d~~a~~~l~~~y~~lv~ 45 (268)
T PRK06288 5 MSGKIPKYAQQDETELWREYKKT--------------G-------------------------DPKIREYLILKYSPLVK 45 (268)
T ss_pred ccCCCccccchHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHH
Confidence 35889999999999999887752 3 46789999999999999
Q ss_pred HHHhhcc-C--CCCChHHHHHHHHHHHHhhhC
Q 020252 300 SIAKNYQ-G--AGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 300 sIAkrY~-g--~Gl~~~DLIQEG~iGLmrAve 328 (328)
.+|++|. + .+.+.+||+|||++||++|++
T Consensus 46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~ 77 (268)
T PRK06288 46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIE 77 (268)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 9999986 2 578899999999999999974
No 22
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=98.57 E-value=7e-08 Score=90.17 Aligned_cols=46 Identities=17% Similarity=0.177 Sum_probs=41.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhcc---CCCCChHHHHHHHHHHHHhhhC
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~---g~Gl~~~DLIQEG~iGLmrAve 328 (328)
+..+|++||..|++||.+||++|. ..+++++||+|+|+|||++|++
T Consensus 21 ~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~ 69 (257)
T PRK05911 21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVE 69 (257)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 467999999999999999999986 2456899999999999999985
No 23
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=98.56 E-value=2.9e-07 Score=84.09 Aligned_cols=74 Identities=23% Similarity=0.432 Sum_probs=66.4
Q ss_pred hhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHH
Q 020252 213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291 (328)
Q Consensus 213 ~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI 291 (328)
.+. |+.++ ++.++||+++|..|...++. | +..+.+.|+
T Consensus 17 ~~~~~~~~~-~~~~~~~~~~e~~l~~~~~~---------------g-------------------------d~~a~~~l~ 55 (233)
T PRK05803 17 FLVSYVKNN-SFPQPLSEEEERKYLELMKE---------------G-------------------------DEEARNILI 55 (233)
T ss_pred HHHHHHHHh-cccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHH
Confidence 345 99999 99999999999988777654 3 467899999
Q ss_pred HHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 292 TSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 292 ~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
..+.++|.+++.+|.+.+.+.+||+|||.|||++++
T Consensus 56 ~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~ 91 (233)
T PRK05803 56 ERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAI 91 (233)
T ss_pred HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999986
No 24
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=98.50 E-value=3.2e-07 Score=84.74 Aligned_cols=66 Identities=29% Similarity=0.295 Sum_probs=58.1
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHHh
Q 020252 224 SRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAK 303 (328)
Q Consensus 224 ~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIAk 303 (328)
.+.||+++|.+|...++.. | +..|.++|+..|.++|..+|+
T Consensus 7 ~~~l~~~~~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~y~~~v~~~a~ 47 (255)
T TIGR02941 7 PTNLTKEDVIQWIAEFQQN--------------Q-------------------------NGEAQEKLVDHYQNLVYSIAY 47 (255)
T ss_pred CCCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHHHHHHhHHHHHHHHH
Confidence 3678999998888877752 2 367999999999999999999
Q ss_pred hccCCCCChHHHHHHHHHHHHhhhC
Q 020252 304 NYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 304 rY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
+|.+.+.+.+||+|||++||+++++
T Consensus 48 ~~~~~~~~aeDlvQe~~i~l~~a~~ 72 (255)
T TIGR02941 48 KYSKGGPMHEDLVQVGMLGLLGAIR 72 (255)
T ss_pred HHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999874
No 25
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=98.39 E-value=9.9e-07 Score=81.63 Aligned_cols=67 Identities=24% Similarity=0.237 Sum_probs=58.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHH
Q 020252 223 SSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302 (328)
Q Consensus 223 ~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIA 302 (328)
..+.|++++|.+|..+++.. | ...|.+.|+..|.++|..+|
T Consensus 6 ~~~~l~~~e~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~~~~~v~~~a 46 (257)
T PRK08583 6 QPTKLTKEEVNKWIAEYQEN--------------Q-------------------------DEEAQEKLVKHYKNLVESLA 46 (257)
T ss_pred cCCcCChHHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHHHHH
Confidence 34789999999888777641 3 36799999999999999999
Q ss_pred hhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 303 KNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 303 krY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
++|.+.+.+.+||+|||++||+++++
T Consensus 47 ~~~~~~~~~aeDlvQe~~l~l~~~~~ 72 (257)
T PRK08583 47 YKYSKGQSHHEDLVQVGMVGLLGAIR 72 (257)
T ss_pred HHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999863
No 26
>PRK05572 sporulation sigma factor SigF; Validated
Probab=98.07 E-value=1.3e-05 Score=74.28 Aligned_cols=67 Identities=25% Similarity=0.414 Sum_probs=58.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHH
Q 020252 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (328)
Q Consensus 222 ~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsI 301 (328)
...|.||.+++.+|...++. | ...+.++|+..|.++|..+
T Consensus 9 ~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~y~~~v~~~ 48 (252)
T PRK05572 9 KKKPQLKDEENKELIKKSQD---------------G-------------------------DQEARDTLVEKNLRLVWSV 48 (252)
T ss_pred cCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHHHH
Confidence 45789999998888766554 3 3678999999999999999
Q ss_pred HhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252 302 AKNYQGAGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 302 AkrY~g~Gl~~~DLIQEG~iGLmrAve 328 (328)
|++|.+.+.+.+||+|||.++|+++++
T Consensus 49 a~~~~~~~~~aeDl~Qe~~l~l~~~~~ 75 (252)
T PRK05572 49 VQRFLNRGYEPDDLFQIGCIGLLKAVD 75 (252)
T ss_pred HHHHccCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999863
No 27
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 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 recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=98.03 E-value=1.9e-06 Score=59.38 Aligned_cols=33 Identities=42% Similarity=0.554 Sum_probs=29.2
Q ss_pred CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHH
Q 020252 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK 244 (328)
Q Consensus 211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~ 244 (328)
+|+++ ||++| +++||||++||++|+++|+.+..
T Consensus 1 ~D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g~~ 34 (37)
T PF00140_consen 1 SDSLRLYLKEI-GRYPLLTAEEEIELARRIRKGDE 34 (37)
T ss_dssp HHHHHHHHHHH-HHS-EETTHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHhHH
Confidence 37899 99999 99999999999999999998754
No 28
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=97.88 E-value=3.2e-05 Score=71.61 Aligned_cols=46 Identities=17% Similarity=0.146 Sum_probs=42.0
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccC---CCCChHHHHHHHHHHHHhhhC
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g---~Gl~~~DLIQEG~iGLmrAve 328 (328)
...|.++|+..|.++|.++|.+|.+ .+.+.+||+|||++||+++++
T Consensus 20 d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~ 68 (251)
T PRK07670 20 DPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALE 68 (251)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999965 688999999999999999874
No 29
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. 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 homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also 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.
Probab=97.79 E-value=0.00013 Score=66.68 Aligned_cols=72 Identities=22% Similarity=0.446 Sum_probs=62.2
Q ss_pred HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhH
Q 020252 216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI 295 (328)
Q Consensus 216 YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNL 295 (328)
|.-.-.++.+.|++.+|.+|...++. | +..+.+.|+..|.
T Consensus 19 ~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~af~~l~~~y~ 58 (227)
T TIGR02846 19 YVTNNGSFPQPLSEEEEKKYLDRLKE---------------G-------------------------DEEARNVLIERNL 58 (227)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhH
Confidence 65443367888999999999877765 4 3678999999999
Q ss_pred HHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 296 RLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 296 RLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
++|.+++.+|.+.+.+.+||+||+.+++++++
T Consensus 59 ~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~ 90 (227)
T TIGR02846 59 RLVAHIVKKFSNTGEDVDDLISIGTIGLIKAI 90 (227)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999886
No 30
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=97.67 E-value=0.00018 Score=65.58 Aligned_cols=76 Identities=24% Similarity=0.486 Sum_probs=60.5
Q ss_pred ChhHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHH
Q 020252 212 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291 (328)
Q Consensus 212 d~l~YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI 291 (328)
|.+-|+.+...-.+.++..++.+|...++. | +..+.+.|+
T Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~---------------g-------------------------d~~af~~l~ 58 (234)
T PRK08301 19 DEIYYIGGSEALPPPLSKEEEEYLLNKLPK---------------G-------------------------DEAVRSLLI 58 (234)
T ss_pred HHHHHhccccccCCcCCHHHHHHHHHHHHc---------------c-------------------------CHHHHHHHH
Confidence 344477766334556777777777665554 3 367899999
Q ss_pred HHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 292 TSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 292 ~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
..+.++|..+|.+|.+.+.+.+||+||+.+++++++
T Consensus 59 ~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~ 94 (234)
T PRK08301 59 ERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAV 94 (234)
T ss_pred HHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999875
No 31
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=97.41 E-value=0.00059 Score=62.64 Aligned_cols=45 Identities=27% Similarity=0.572 Sum_probs=42.6
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+..+.+.++..+.+.|..++++|.+.+.+-+||+||+.+++++++
T Consensus 50 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~ 94 (234)
T TIGR02835 50 DESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAV 94 (234)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHH
Confidence 468999999999999999999999999999999999999999875
No 32
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 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 recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=97.20 E-value=0.00045 Score=50.55 Aligned_cols=38 Identities=21% Similarity=0.306 Sum_probs=36.1
Q ss_pred HHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 290 MITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
|++.+.++|..++.+|.+.+.+.+|++||+.++|++++
T Consensus 1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~ 38 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAI 38 (71)
T ss_dssp HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhh
Confidence 68899999999999999999999999999999999875
No 33
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=97.01 E-value=0.0017 Score=59.41 Aligned_cols=66 Identities=20% Similarity=0.204 Sum_probs=57.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHH
Q 020252 222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 301 (328)
Q Consensus 222 ~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsI 301 (328)
.+.|+|+...+..|...++. | +..+.+.|+..|.++|..+
T Consensus 7 ~~~~~~~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~y~~~l~~~ 46 (231)
T PRK11922 7 SRPPPLSAASDRELVARVLA---------------G-------------------------DEAAFEALMRRHNRRLYRT 46 (231)
T ss_pred CCCCCcCcccHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHHHH
Confidence 46788888888887776654 3 4678899999999999999
Q ss_pred HhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 302 AKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 302 AkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+++|.+.+-+-+||+||+.++|++.+
T Consensus 47 a~~~~~~~~~AEDlvQE~fi~l~~~~ 72 (231)
T PRK11922 47 ARAILRNDAEAEDVVQEAYLRAFRAL 72 (231)
T ss_pred HHHHhCChhhHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999875
No 34
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=96.78 E-value=0.0027 Score=55.46 Aligned_cols=54 Identities=19% Similarity=0.214 Sum_probs=46.1
Q ss_pred HHHHHhhh-hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 274 RELRRRLN-YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 274 ~~L~~~L~-~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
..|-..+. .+..+.+.|+..|.++|..+|.+|.+.+.+.+|++||+.++|++.+
T Consensus 8 ~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~ 62 (186)
T PRK05602 8 EELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQA 62 (186)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHh
Confidence 34433333 3478999999999999999999999999999999999999999875
No 35
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=96.71 E-value=0.0045 Score=65.17 Aligned_cols=33 Identities=33% Similarity=0.537 Sum_probs=31.2
Q ss_pred CCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHH
Q 020252 210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLL 243 (328)
Q Consensus 210 ~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~ 243 (328)
.+||++ ||++| |..||||+++|++++++|..+.
T Consensus 102 t~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 102 TDDPVRMYLREM-GTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred CCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHHH
Confidence 599999 99999 9999999999999999999873
No 36
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=96.70 E-value=0.0039 Score=57.64 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=18.8
Q ss_pred CCCChHHHHHHHHHHHHhhhC
Q 020252 308 AGMNLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 308 ~Gl~~~DLIQEG~iGLmrAve 328 (328)
.+++.+||||+|+|||++|++
T Consensus 41 ~~~~~eDLvQeg~igL~~a~~ 61 (231)
T PRK12427 41 SVIDREDMEQIALMGLLEALR 61 (231)
T ss_pred CCCCHHHHHHHHHHHHHHHHH
Confidence 457999999999999999974
No 37
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=96.67 E-value=0.0033 Score=54.36 Aligned_cols=45 Identities=9% Similarity=0.003 Sum_probs=42.1
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.+.++..+.++|..+|.+|.+.+.+.+|++||+.++|+++.
T Consensus 16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~ 60 (187)
T PRK09641 16 DQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNI 60 (187)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 377899999999999999999999999999999999999999875
No 38
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=96.66 E-value=0.005 Score=54.33 Aligned_cols=45 Identities=18% Similarity=0.177 Sum_probs=42.4
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.+.|+..+.++|..+|.+|.+.+.+.+||+||+.++|++++
T Consensus 22 d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~ 66 (208)
T PRK08295 22 DKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAI 66 (208)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence 477999999999999999999999999999999999999999875
No 39
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=96.52 E-value=0.0073 Score=52.80 Aligned_cols=55 Identities=16% Similarity=0.209 Sum_probs=46.8
Q ss_pred HHHHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 273 ~~~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...|-..+..| ..+.+.|+..+.+.|..+|.+|.+...+.+||+||+.+.+++.+
T Consensus 6 ~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~ 61 (198)
T TIGR02859 6 DEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAI 61 (198)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHH
Confidence 34444444444 67999999999999999999999999999999999999999875
No 40
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 recognised by the major sigma factors [, ]. 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 in 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 [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=96.50 E-value=0.0053 Score=46.96 Aligned_cols=40 Identities=30% Similarity=0.381 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
.++.+.+.+|..++||+||.+|.|+.+|++.+.++..+..
T Consensus 4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence 4566788999999999999999999999999988876653
No 41
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=96.45 E-value=0.007 Score=56.89 Aligned_cols=54 Identities=7% Similarity=0.214 Sum_probs=45.1
Q ss_pred HHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCCC--ChHHHHHHHHHHHHhhhC
Q 020252 275 ELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGM--NLQDLVQLQALRYLNMAH 328 (328)
Q Consensus 275 ~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~Gl--~~~DLIQEG~iGLmrAve 328 (328)
.|-..+..| ..|.+.|+..+.++|..+|.+|.++.. ..+|++|+|.++++++++
T Consensus 7 ~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~ 63 (237)
T PRK08311 7 DILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAID 63 (237)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHH
Confidence 334444444 679999999999999999999998876 489999999999999874
No 42
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=96.35 E-value=0.0056 Score=52.90 Aligned_cols=45 Identities=9% Similarity=0.017 Sum_probs=42.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+..+|+..+.++|..+|.+|.+.+.+.+|++||+.++|++..
T Consensus 16 d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~ 60 (187)
T TIGR02948 16 DENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNI 60 (187)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhH
Confidence 477899999999999999999999999999999999999999875
No 43
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=96.21 E-value=0.0084 Score=52.69 Aligned_cols=53 Identities=11% Similarity=0.026 Sum_probs=45.3
Q ss_pred HHHHhhhh-hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 275 ELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 275 ~L~~~L~~-G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
.|-..+.. ...+.+.|+..|.+.|..+|.+|.+...+.+|++||+.++|+++.
T Consensus 15 ~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~ 68 (194)
T PRK12513 15 ALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRAR 68 (194)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 33333343 478999999999999999999999999999999999999999875
No 44
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=96.18 E-value=0.017 Score=50.49 Aligned_cols=45 Identities=16% Similarity=0.199 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCC----CCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~----Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.++|+..+.+.|..+|.+|.+. +.+.+|++||+.++|++.+
T Consensus 22 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~ 70 (189)
T PRK09648 22 DRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITAL 70 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHH
Confidence 37899999999999999999988643 4689999999999999864
No 45
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=96.07 E-value=0.013 Score=50.85 Aligned_cols=54 Identities=15% Similarity=0.084 Sum_probs=45.6
Q ss_pred HHHHHhhh-hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 274 RELRRRLN-YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 274 ~~L~~~L~-~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
.+|-..+. ....+.+.++..|.+.|..++++|.+.+.+.+|++||+.+.|+++.
T Consensus 11 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~ 65 (186)
T PRK13919 11 EALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKA 65 (186)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhh
Confidence 34444443 3477999999999999999999999999999999999999999875
No 46
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=95.98 E-value=0.017 Score=49.60 Aligned_cols=45 Identities=11% Similarity=0.019 Sum_probs=42.1
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+..+.+.|+..+.+.|..++.+|.+..-+-+|++||+.+.|+++.
T Consensus 16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~ 60 (176)
T PRK09638 16 DDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENL 60 (176)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHH
Confidence 477999999999999999999999999999999999999999875
No 47
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=95.97 E-value=0.02 Score=50.24 Aligned_cols=45 Identities=9% Similarity=0.081 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.+.|+..|.+.|..++++|.+..-+.+|++||+.+.+++++
T Consensus 18 d~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~ 62 (193)
T PRK11923 18 DKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRAL 62 (193)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhH
Confidence 367899999999999999999999988899999999999999875
No 48
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=95.94 E-value=0.019 Score=50.50 Aligned_cols=57 Identities=18% Similarity=0.269 Sum_probs=48.8
Q ss_pred CcHHHHHHhhhh----hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 271 VDQRELRRRLNY----GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 271 ~d~~~L~~~L~~----G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
++.+.|...+.. +..+.+.|+..|.+.|..++.+|.+..-+.+|++||+.+.|++.+
T Consensus 8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~ 68 (188)
T PRK09640 8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGL 68 (188)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHH
Confidence 344555556653 488999999999999999999999999999999999999999865
No 49
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=95.78 E-value=0.021 Score=50.48 Aligned_cols=53 Identities=13% Similarity=0.014 Sum_probs=45.6
Q ss_pred HHHHhhhh-hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 275 ELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 275 ~L~~~L~~-G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
.|-..+.. ...+.++++..|.++|..++.+|.+..-+-+|++||+.+.+++.+
T Consensus 19 ~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~ 72 (194)
T PRK09646 19 ALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTA 72 (194)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhh
Confidence 34344443 478999999999999999999999999999999999999999875
No 50
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=95.44 E-value=0.044 Score=48.26 Aligned_cols=56 Identities=14% Similarity=0.099 Sum_probs=45.2
Q ss_pred cHHHHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCC---CChHHHHHHHHHHHHhhh
Q 020252 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAG---MNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 272 d~~~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~G---l~~~DLIQEG~iGLmrAv 327 (328)
+.+.|-..+..| ..+.+.|+..|.++|..++.+|.+.+ .+.+|++||+.++|++.+
T Consensus 4 ~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~ 63 (189)
T PRK06811 4 NEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNI 63 (189)
T ss_pred cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhH
Confidence 334455555544 67999999999999999999998764 358999999999999875
No 51
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=95.35 E-value=0.036 Score=47.99 Aligned_cols=45 Identities=11% Similarity=0.144 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+..+.+.|+..+.+.|..+|.++.+...+.+||+||+.++|++.+
T Consensus 18 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~ 62 (190)
T TIGR02939 18 EKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRAL 62 (190)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhH
Confidence 467899999999999999999999999999999999999998764
No 52
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=95.18 E-value=0.042 Score=48.15 Aligned_cols=53 Identities=21% Similarity=0.140 Sum_probs=44.3
Q ss_pred HHHHHhhhh-hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhh
Q 020252 274 RELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNM 326 (328)
Q Consensus 274 ~~L~~~L~~-G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrA 326 (328)
.+|-.++.. +..+.+.|+..+.++|..++++|.+...+-+|++|++.++|++.
T Consensus 17 ~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~ 70 (194)
T PRK12519 17 AELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK 70 (194)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh
Confidence 334444443 47799999999999999999999999999999999999999863
No 53
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=95.16 E-value=0.038 Score=47.85 Aligned_cols=45 Identities=7% Similarity=-0.039 Sum_probs=41.9
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+..+...|+..+.+.|..+|.+|.+...+-+|++||+.+++++.+
T Consensus 17 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~ 61 (179)
T PRK12514 17 DRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKA 61 (179)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhH
Confidence 467999999999999999999999999999999999999998765
No 54
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=95.00 E-value=0.044 Score=47.79 Aligned_cols=46 Identities=4% Similarity=-0.081 Sum_probs=42.4
Q ss_pred hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 282 ~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
....+.+.++..+.++|..++.+|.+...+-+|++||..+.+++..
T Consensus 22 ~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~ 67 (187)
T PRK12534 22 GDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKA 67 (187)
T ss_pred CCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcc
Confidence 3478999999999999999999999999999999999999999865
No 55
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=94.88 E-value=0.063 Score=47.56 Aligned_cols=55 Identities=16% Similarity=0.154 Sum_probs=47.0
Q ss_pred HHHHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 273 ~~~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...|-..+..| ..+.+.|+..+.++|..+|.+|.+...+-+|++||+.+.|++..
T Consensus 13 ~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~ 68 (196)
T PRK12524 13 DEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIA 68 (196)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhh
Confidence 34455555544 78999999999999999999999999999999999999998764
No 56
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=94.19 E-value=0.11 Score=44.54 Aligned_cols=45 Identities=11% Similarity=0.035 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+..+.+.++..+.+.+..++.+|.+..-+.+|++||..+-+.+..
T Consensus 14 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~ 58 (169)
T TIGR02954 14 NKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSI 58 (169)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999999999999999999999988753
No 57
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=93.26 E-value=0.22 Score=44.06 Aligned_cols=45 Identities=11% Similarity=-0.049 Sum_probs=41.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.+.|+..|.+.|..+|.+|.+..-.-+|++||.++.+++..
T Consensus 25 d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~ 69 (194)
T PRK12531 25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKA 69 (194)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhH
Confidence 467899999999999999999999988889999999999998764
No 58
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=93.14 E-value=0.21 Score=43.84 Aligned_cols=56 Identities=14% Similarity=0.038 Sum_probs=46.5
Q ss_pred cHHHHHHhhhh-hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 272 DQRELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 272 d~~~L~~~L~~-G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+...|...+.. +..+.+.|+..+.+.+..++.+|.+...+-+|++||..+.+++..
T Consensus 8 ~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~ 64 (189)
T PRK12515 8 TDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQA 64 (189)
T ss_pred CHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 34445444444 467999999999999999999999999999999999999998764
No 59
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=93.00 E-value=0.2 Score=46.48 Aligned_cols=45 Identities=18% Similarity=0.157 Sum_probs=41.3
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+..+.+.|+..+.+.|..++.+|.|..-+-+|++||..+.+++..
T Consensus 61 d~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~ 105 (233)
T PRK12538 61 DEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHR 105 (233)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
Confidence 367999999999999999999999988899999999999998754
No 60
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=92.25 E-value=0.36 Score=42.13 Aligned_cols=46 Identities=9% Similarity=0.031 Sum_probs=42.3
Q ss_pred hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 282 ~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
....+.+.|+..+.+.+..++.++.+...+-+|++||..+.+++..
T Consensus 20 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~ 65 (182)
T PRK12537 20 GDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGA 65 (182)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhcc
Confidence 3578999999999999999999999999999999999999998764
No 61
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=92.06 E-value=0.35 Score=42.86 Aligned_cols=54 Identities=17% Similarity=0.091 Sum_probs=45.6
Q ss_pred HHHHHhhh-hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 274 RELRRRLN-YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 274 ~~L~~~L~-~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+.+-..+. ....+.+.++..+.+.|.+++.++.+...+-+|++||..+-+++..
T Consensus 15 ~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~ 69 (192)
T PRK09643 15 AELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAA 69 (192)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHH
Confidence 34444443 4477999999999999999999999999999999999999999864
No 62
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=91.90 E-value=0.55 Score=40.81 Aligned_cols=44 Identities=14% Similarity=0.091 Sum_probs=38.4
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCC-C---CChHHHHHHHHHHHHhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGA-G---MNLQDLVQLQALRYLNM 326 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~-G---l~~~DLIQEG~iGLmrA 326 (328)
+..+.+.|+..+.+.|..+|.+|.+. | .+.+|++||+.+.+++.
T Consensus 20 d~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~ 67 (184)
T PRK12512 20 DAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLK 67 (184)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHh
Confidence 57899999999999999999988753 3 57999999999998764
No 63
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=91.28 E-value=0.41 Score=42.97 Aligned_cols=45 Identities=11% Similarity=-0.012 Sum_probs=41.4
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.++|+..+.++|..++.+|.+..-+-+|++||+.+.+++.+
T Consensus 36 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~ 80 (206)
T PRK12526 36 DKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKA 80 (206)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhH
Confidence 477889999999999999999999888899999999999999865
No 64
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=91.26 E-value=0.58 Score=40.80 Aligned_cols=47 Identities=13% Similarity=0.015 Sum_probs=40.4
Q ss_pred hhhHHHHHHHHHHhHHHHHHHHhhcc-CCCCChHHHHHHHHHHHHhhh
Q 020252 281 NYGILCKDKMITSNIRLVISIAKNYQ-GAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 281 ~~G~~Are~LI~sNLRLVvsIAkrY~-g~Gl~~~DLIQEG~iGLmrAv 327 (328)
..+..+.++++..+.+.|..++.++. +.+.+.+||+||+.+.|++..
T Consensus 17 ~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~ 64 (181)
T PRK12536 17 AGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNAR 64 (181)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhH
Confidence 34577899999999999999998865 457899999999999998764
No 65
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=90.86 E-value=0.86 Score=39.84 Aligned_cols=45 Identities=11% Similarity=0.027 Sum_probs=39.1
Q ss_pred hHHHHHHHHHHhHHHHHHHHh----hccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAK----NYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAk----rY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+..+.+.|+..+.+.|..+++ +|.+...+-+|++||..+.|++..
T Consensus 19 d~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~ 67 (184)
T PRK12539 19 DAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRR 67 (184)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHH
Confidence 367999999999999999876 566778899999999999998764
No 66
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=84.84 E-value=1.9 Score=41.34 Aligned_cols=41 Identities=24% Similarity=0.263 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhh
Q 020252 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG 283 (328)
Q Consensus 243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G 283 (328)
.++..+..+|..++|++||..|.|+.+|++.+++...+..+
T Consensus 110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~ 150 (247)
T COG1191 110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI 150 (247)
T ss_pred HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence 34455778899999999999999999999998887766554
No 67
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=83.95 E-value=1.7 Score=39.27 Aligned_cols=45 Identities=16% Similarity=0.214 Sum_probs=41.4
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.++|+..|.+.+..++.+|.+....-+|++||..+.+++..
T Consensus 26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~ 70 (203)
T PRK09647 26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSL 70 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhH
Confidence 367889999999999999999999999999999999999998764
No 68
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=83.52 E-value=2.7 Score=40.34 Aligned_cols=45 Identities=16% Similarity=0.071 Sum_probs=41.0
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.++|+..|.+.|..++.+|.+...+-+|++||-.+-+++..
T Consensus 17 d~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~ 61 (339)
T PRK08241 17 DRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGY 61 (339)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhh
Confidence 467899999999999999999999988899999999999988754
No 69
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=81.98 E-value=4.6 Score=34.84 Aligned_cols=43 Identities=16% Similarity=0.150 Sum_probs=38.7
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCC-----ChHHHHHHHHHHHHh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGM-----NLQDLVQLQALRYLN 325 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl-----~~~DLIQEG~iGLmr 325 (328)
+..+.+.|+..+.+.+..++.+|.+... +-+|++||..+.+++
T Consensus 15 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~ 62 (183)
T TIGR02999 15 DAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSD 62 (183)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhh
Confidence 3678999999999999999999987766 789999999999986
No 70
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=79.67 E-value=4.5 Score=37.91 Aligned_cols=37 Identities=22% Similarity=0.258 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 244 ~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
++.+.+.+|...+|++||.+|.|+.+|++.++++..+
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~ 150 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK 150 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 3455677888899999999999999999998877653
No 71
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=77.61 E-value=6.2 Score=36.35 Aligned_cols=37 Identities=24% Similarity=0.293 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 244 ~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
++.+...+|...+|++||.+|.|+.+|++.+.++..+
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~ 124 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREIK 124 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 3445567788889999999999999999998887654
No 72
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=77.22 E-value=6.3 Score=37.31 Aligned_cols=36 Identities=36% Similarity=0.481 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+.+...+|...+|++||.+|.|+.+|++.+.+...+
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~ 164 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVEGL 164 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 444567788889999999999999999998887654
No 73
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=77.16 E-value=6.3 Score=36.73 Aligned_cols=36 Identities=25% Similarity=0.218 Sum_probs=29.5
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+.+...++...+|++||.+|.|+.+|++.+.+...+
T Consensus 122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 444566777888999999999999999988876654
No 74
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=76.21 E-value=4.7 Score=37.38 Aligned_cols=36 Identities=19% Similarity=0.332 Sum_probs=30.0
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+.....++..++|++||.+|.|+.+|++.+++...+
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 445567788889999999999999999998876654
No 75
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=75.91 E-value=4.3 Score=35.98 Aligned_cols=48 Identities=15% Similarity=-0.060 Sum_probs=42.8
Q ss_pred hhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 280 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 280 L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+.....+.+.++..+.+.|..+|.++.+..-+-+|++|+..+-+++..
T Consensus 18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~ 65 (188)
T PRK12517 18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSL 65 (188)
T ss_pred hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhH
Confidence 344678999999999999999999999998999999999999988753
No 76
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=75.88 E-value=7.3 Score=36.57 Aligned_cols=55 Identities=11% Similarity=-0.014 Sum_probs=46.4
Q ss_pred CcHHHHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHh
Q 020252 271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLN 325 (328)
Q Consensus 271 ~d~~~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmr 325 (328)
.+...|...+..| ..+...|+..+.+.|..++.++.+...+-+|++||-.+-++.
T Consensus 24 ~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~ 79 (244)
T TIGR03001 24 AADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLV 79 (244)
T ss_pred ccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 3455566666666 579999999999999999999989999999999999998873
No 77
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=75.81 E-value=6.7 Score=38.65 Aligned_cols=38 Identities=21% Similarity=0.329 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
.++.+.+.+|...+|++||.+|.|+.+|++.+.+...+
T Consensus 173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~ 210 (324)
T PRK07921 173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLL 210 (324)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34556677888899999999999999999988877654
No 78
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=75.54 E-value=9.9 Score=33.43 Aligned_cols=44 Identities=18% Similarity=0.108 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.+.|+..+.+.+..+++ |.+...+-+|++||..+.+++..
T Consensus 22 d~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~ 65 (185)
T PRK09649 22 NGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAI 65 (185)
T ss_pred CHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhc
Confidence 367899999999999999995 66767889999999999998754
No 79
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=74.42 E-value=8.2 Score=36.27 Aligned_cols=37 Identities=22% Similarity=0.294 Sum_probs=29.6
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~ 281 (328)
+......|...+|++||.+|.|+.+|++.+.+...+.
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~ 148 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFS 148 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3344566777889999999999999999988876543
No 80
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=73.54 E-value=5.7 Score=36.51 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=40.5
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+...|+..+.+.+..++.+|.+..-+-+|++||..+-+++..
T Consensus 16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~ 60 (216)
T PRK12533 16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFF 60 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhH
Confidence 467888999999999999999999998999999999999988753
No 81
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=72.80 E-value=8.6 Score=38.30 Aligned_cols=37 Identities=24% Similarity=0.297 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 244 ~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
++.+...+|...+|++||.+|.|+.+|++.+.++..+
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~ 253 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREIL 253 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 3556677888899999999999999999998887654
No 82
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=68.49 E-value=12 Score=37.77 Aligned_cols=37 Identities=24% Similarity=0.293 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHh
Q 020252 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR 279 (328)
Q Consensus 243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~ 279 (328)
.++.+....|...+|++||.+|.|+.+|++.+.++..
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~ 259 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI 259 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 3455567788888999999999999999999888755
No 83
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=67.77 E-value=12 Score=39.45 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
.++.+.+.+|...+|++||.+|.|+.+|++.+.+...+
T Consensus 358 ~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~ 395 (509)
T PRK05901 358 NKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQ 395 (509)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34556778888999999999999999999988877654
No 84
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=66.62 E-value=14 Score=28.26 Aligned_cols=27 Identities=33% Similarity=0.489 Sum_probs=18.3
Q ss_pred hhcCCCCchHHHHHHhcCc-HHHHHHhh
Q 020252 254 ERCGGSPTFAQWAAAAGVD-QRELRRRL 280 (328)
Q Consensus 254 ~~~GrePT~~eWA~a~g~d-~~~L~~~L 280 (328)
...|.+||..|.|+++|+. .......|
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHH
Confidence 4569999999999999995 66555444
No 85
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=64.83 E-value=15 Score=34.07 Aligned_cols=38 Identities=29% Similarity=0.309 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhh
Q 020252 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (328)
Q Consensus 244 ~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~ 281 (328)
++.+...++...+|++|+..++|+.+|++.+.++..+.
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~ 147 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN 147 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 34455667778889999999999999999988776653
No 86
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=63.54 E-value=16 Score=33.15 Aligned_cols=36 Identities=33% Similarity=0.453 Sum_probs=28.9
Q ss_pred HHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhh
Q 020252 246 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (328)
Q Consensus 246 e~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~ 281 (328)
.+....|...+|+.||..|.|+.+|++.+.+...+.
T Consensus 100 ~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~ 135 (231)
T TIGR02885 100 RYMKEELSKELGREPTINELAEALGVSPEEIVMALE 135 (231)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334567777889999999999999999888765543
No 87
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=63.19 E-value=12 Score=38.49 Aligned_cols=38 Identities=21% Similarity=0.315 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhh
Q 020252 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (328)
Q Consensus 244 ~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~ 281 (328)
++.+.+.+|...+|+.||..|.|+.+|++.+.++..+.
T Consensus 263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~ 300 (415)
T PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL 300 (415)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45566778888999999999999999999999887654
No 88
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=61.74 E-value=18 Score=32.73 Aligned_cols=38 Identities=37% Similarity=0.441 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
.++.+...+|...+|++|+.+|.|+.+|++...++..+
T Consensus 83 ~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 83 RKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 34556677788889999999999999999988877655
No 89
>PRK05949 RNA polymerase sigma factor; Validated
Probab=61.10 E-value=22 Score=35.05 Aligned_cols=36 Identities=25% Similarity=0.332 Sum_probs=29.4
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+.+.+.++...+|++||..|.|+.+|++.+.+...+
T Consensus 180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~ 215 (327)
T PRK05949 180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIREYL 215 (327)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 444566777788999999999999999988877653
No 90
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=60.46 E-value=21 Score=35.94 Aligned_cols=41 Identities=27% Similarity=0.353 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 240 QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 240 q~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
...-++.+++.+|...+|++|+.++.|+..|++...++..+
T Consensus 186 e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~ 226 (342)
T COG0568 186 ELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREML 226 (342)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHH
Confidence 34445667788888889999999999999999887666543
No 91
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=59.78 E-value=24 Score=32.83 Aligned_cols=36 Identities=25% Similarity=0.214 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+.+...++..++|++||..|.|+.+|++.+.+...+
T Consensus 125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~ 160 (258)
T PRK08215 125 ALQVREKLINENSKEPTVEEIAKELEVPREEVVFAL 160 (258)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 444566777888999999999999999988876643
No 92
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=58.51 E-value=73 Score=25.44 Aligned_cols=37 Identities=16% Similarity=0.138 Sum_probs=28.9
Q ss_pred HHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 246 EGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 246 e~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
+++..-+......+++.+++|+.+|++...|.+....
T Consensus 8 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 8 QTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444556666778899999999999999999877653
No 93
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=58.30 E-value=13 Score=33.62 Aligned_cols=54 Identities=19% Similarity=0.098 Sum_probs=42.3
Q ss_pred hcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 269 AGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 269 ~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
+.||...|-..|.. ..++..|-+.+..++.+|.+..-.-+|++||..+.+++..
T Consensus 7 ~~~~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~ 60 (206)
T PRK12544 7 VAMDSSDLGNLLQD-----PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNA 60 (206)
T ss_pred hhcchhhHHHHhhh-----HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHH
Confidence 34555555444433 3677889999999999999999999999999999998754
No 94
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=58.24 E-value=55 Score=23.63 Aligned_cols=56 Identities=18% Similarity=0.229 Sum_probs=33.5
Q ss_pred CCchHHHHHHhcCcHHHHHHhhhhh--HHHHHHHHHHhHHHHHHHHhhccCC-CCChHHHHHH
Q 020252 259 SPTFAQWAAAAGVDQRELRRRLNYG--ILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQL 318 (328)
Q Consensus 259 ePT~~eWA~a~g~d~~~L~~~L~~G--~~Are~LI~sNLRLVvsIAkrY~g~-Gl~~~DLIQE 318 (328)
++|..++|+.+|++...|.+.+..- ...++.+-. .| +.-|..|... .+++.|+-++
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~--~r--~~~a~~~l~~~~~~~~~ia~~ 59 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRD--RR--LERARRLLRDTDLSVTEIALR 59 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHH--HH--HHHHHHHHHcCCCCHHHHHHH
Confidence 3688999999999999998877632 223332221 22 2223333222 5788887654
No 95
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=57.23 E-value=23 Score=33.22 Aligned_cols=37 Identities=24% Similarity=0.355 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 244 ~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
++.+.+..|+..+|++||.++.|+..|++...+...+
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~ 155 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLL 155 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 4556677888899999999999999999987776654
No 96
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=55.39 E-value=31 Score=33.68 Aligned_cols=37 Identities=22% Similarity=0.368 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 244 ~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
++.+.+.++...+|+.||..|.|+.+|++.+.+...+
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~ 205 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYL 205 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 3455667777888999999999999999887777654
No 97
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=54.20 E-value=35 Score=32.70 Aligned_cols=36 Identities=25% Similarity=0.430 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+.+.+.++...+|+.||..+.|..+|++.+.+...+
T Consensus 163 ~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~ 198 (298)
T TIGR02997 163 IKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELL 198 (298)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 444556777788999999999999999988776554
No 98
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=50.51 E-value=42 Score=30.02 Aligned_cols=44 Identities=18% Similarity=0.080 Sum_probs=37.2
Q ss_pred hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA 327 (328)
Q Consensus 283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv 327 (328)
...+.+.++..+...+..+++ |.+...+-+|++||-.+.|++..
T Consensus 23 d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~ 66 (196)
T PRK12535 23 DRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSAL 66 (196)
T ss_pred CHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHh
Confidence 467888999999999999975 56777789999999999998753
No 99
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=50.44 E-value=27 Score=32.78 Aligned_cols=51 Identities=12% Similarity=0.048 Sum_probs=38.7
Q ss_pred HHHHhhhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhh
Q 020252 275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNM 326 (328)
Q Consensus 275 ~L~~~L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrA 326 (328)
.|++.+.-.....+.+++.+ +.+...+.++.+..-+-+||+||..+-+++.
T Consensus 8 ~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~ 58 (228)
T PRK06704 8 ILKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK 58 (228)
T ss_pred HHhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 34444444455666666666 7889999999988889999999999998865
No 100
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=50.21 E-value=39 Score=28.35 Aligned_cols=37 Identities=8% Similarity=0.255 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~ 281 (328)
+.++..-+.......++.+++|+.+|++...|.+...
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3444555666777889999999999999999987765
No 101
>PRK15044 transcriptional regulator SirC; Provisional
Probab=48.33 E-value=78 Score=31.43 Aligned_cols=38 Identities=16% Similarity=0.086 Sum_probs=31.8
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
.+++..-+.+..+++++.++||+.+|++...|.++...
T Consensus 194 ~~kV~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~ 231 (295)
T PRK15044 194 KEKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAA 231 (295)
T ss_pred HHHHHHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 44566667778889999999999999999999987753
No 102
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=47.91 E-value=43 Score=24.98 Aligned_cols=27 Identities=15% Similarity=0.214 Sum_probs=23.5
Q ss_pred CCCchHHHHHHhcCcHHHHHHhhhhhH
Q 020252 258 GSPTFAQWAAAAGVDQRELRRRLNYGI 284 (328)
Q Consensus 258 rePT~~eWA~a~g~d~~~L~~~L~~G~ 284 (328)
|..|..+.|+.+|++...+-..|+.+.
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 567899999999999999998888764
No 103
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=45.06 E-value=41 Score=30.41 Aligned_cols=33 Identities=39% Similarity=0.535 Sum_probs=26.8
Q ss_pred HHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 248 LREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 248 ~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
....+....|+.||..|.|+.+|++...+...+
T Consensus 95 ~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~ 127 (227)
T TIGR02980 95 ATEELTQRLGRSPTIAEIAEELGVSEEEVVEAL 127 (227)
T ss_pred HHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 455677777999999999999999988876543
No 104
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=41.84 E-value=47 Score=24.99 Aligned_cols=55 Identities=16% Similarity=0.344 Sum_probs=37.4
Q ss_pred HhhcCCCCc------hHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHHhhccCCCCC
Q 020252 253 SERCGGSPT------FAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMN 311 (328)
Q Consensus 253 ~~~~GrePT------~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~ 311 (328)
+...||.|| +.+|....|++.+.+...++.... + -..|++.|-.|++++...|+.
T Consensus 6 e~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~---~-~~~~~~Yi~~Il~~W~~~gi~ 66 (73)
T TIGR01446 6 EENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEAVS---N-NKANYKYIDAILNNWKNNGIK 66 (73)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH---c-CCCCHHHHHHHHHHHHHcCCC
Confidence 334466666 456777778777766666655322 1 246789999999999999865
No 105
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=41.37 E-value=92 Score=30.28 Aligned_cols=36 Identities=8% Similarity=0.135 Sum_probs=29.9
Q ss_pred HHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 247 GLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 247 ~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
++..-+........|.++||+.+||+...|.+.+..
T Consensus 185 ~i~~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~ 220 (291)
T PRK15186 185 NIYNIIISDISRKWALKDISDSLYMSCSTLKRKLKQ 220 (291)
T ss_pred HHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344556667788999999999999999999998765
No 106
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=40.85 E-value=50 Score=30.21 Aligned_cols=36 Identities=25% Similarity=0.293 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+.+....+...+|++||..++|+.+|++...+...+
T Consensus 97 ~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~ 132 (236)
T PRK06986 97 VAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREML 132 (236)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence 334556667778999999999999999988865544
No 107
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=38.86 E-value=79 Score=22.17 Aligned_cols=25 Identities=28% Similarity=0.590 Sum_probs=19.3
Q ss_pred CCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 258 GSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 258 rePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
..-++.+.|+.+|++...+.++++.
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 3467999999999999999888764
No 108
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=37.78 E-value=76 Score=31.83 Aligned_cols=51 Identities=14% Similarity=0.229 Sum_probs=37.4
Q ss_pred HHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhh--------------HHHHHHHHHHhHHHH
Q 020252 248 LREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG--------------ILCKDKMITSNIRLV 298 (328)
Q Consensus 248 ~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G--------------~~Are~LI~sNLRLV 298 (328)
+...++..++.+-+.++.|..+|||...|.+.-+.. ..||+-|..+|+.+.
T Consensus 225 ~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~~lG~sP~~yy~~lRL~~Ar~LL~~t~~si~ 289 (328)
T COG4977 225 AIELMEANLEEPLSLEELADRAGLSRRQLERLFRAELGVSPARYYLRLRLERARRLLEQTRLSIA 289 (328)
T ss_pred HHHHHHHhhcCCcCHHHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhCCCcHH
Confidence 344455667788889999999999999988764321 567777888887754
No 109
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=36.71 E-value=2.4e+02 Score=26.56 Aligned_cols=38 Identities=21% Similarity=0.198 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
+.++..-++..+...++.++||..+|+|...|.+....
T Consensus 7 i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 7 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34445556667788899999999999999999887653
No 110
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=36.66 E-value=66 Score=29.78 Aligned_cols=36 Identities=17% Similarity=0.284 Sum_probs=28.4
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+......+...+|+.||..+.|..+|++.+.+...+
T Consensus 118 ~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~ 153 (255)
T TIGR02941 118 IKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIM 153 (255)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 334566777788999999999999999988876543
No 111
>PRK05572 sporulation sigma factor SigF; Validated
Probab=35.76 E-value=83 Score=29.19 Aligned_cols=34 Identities=26% Similarity=0.356 Sum_probs=26.6
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHH
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR 278 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~ 278 (328)
+.+.+.++....|+.|+..+.|+..|++.+.+..
T Consensus 120 ~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~ 153 (252)
T PRK05572 120 IRKDKDELSKELGREPTIEELAEYLGVTPEEVVL 153 (252)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence 4445566777789999999999999998876643
No 112
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=35.14 E-value=79 Score=25.00 Aligned_cols=50 Identities=22% Similarity=0.366 Sum_probs=37.3
Q ss_pred CchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHH
Q 020252 260 PTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQ 319 (328)
Q Consensus 260 PT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG 319 (328)
-|-++.|..+|++...+-..-. |. -...+.|...||+-|. .+++|+++.+
T Consensus 15 ltQ~elA~~vgVsRQTi~~iEk-gk------y~Psl~La~kia~~f~---~~iedIF~~~ 64 (68)
T COG1476 15 LTQEELAKLVGVSRQTIIAIEK-GK------YNPSLELALKIARVFG---KTIEDIFQLE 64 (68)
T ss_pred cCHHHHHHHcCcCHHHHHHHHc-CC------CCchHHHHHHHHHHhC---CCHHHHHhhh
Confidence 4677888899988776654332 21 3567899999999986 8999999854
No 113
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.32 E-value=1.9e+02 Score=24.40 Aligned_cols=43 Identities=14% Similarity=0.044 Sum_probs=30.4
Q ss_pred HHHHhhcC-CCCchHHHHHHhcCcHHHHHHhh------hhhHHHHHHHHH
Q 020252 250 EVLSERCG-GSPTFAQWAAAAGVDQRELRRRL------NYGILCKDKMIT 292 (328)
Q Consensus 250 ~~L~~~~G-rePT~~eWA~a~g~d~~~L~~~L------~~G~~Are~LI~ 292 (328)
.+|++.+. ..-|.++.|.+++.+...|++.| +.++..|+-|++
T Consensus 13 ~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~~dvW~lRd~l~~ 62 (97)
T COG4367 13 QELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRPADVWRLRDFLVQ 62 (97)
T ss_pred HHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhccchhHHHHHHHHH
Confidence 34444333 45679999999999999999888 455666765544
No 114
>PRK04217 hypothetical protein; Provisional
Probab=31.87 E-value=2.3e+02 Score=24.07 Aligned_cols=26 Identities=19% Similarity=0.109 Sum_probs=22.5
Q ss_pred CchHHHHHHhcCcHHHHHHhhhhhHH
Q 020252 260 PTFAQWAAAAGVDQRELRRRLNYGIL 285 (328)
Q Consensus 260 PT~~eWA~a~g~d~~~L~~~L~~G~~ 285 (328)
-|..|+|+.+|++...+.+.++.+..
T Consensus 59 lS~~EIAk~LGIS~sTV~r~L~RArk 84 (110)
T PRK04217 59 LTQEEAGKRMGVSRGTVWRALTSARK 84 (110)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 38999999999999999999987544
No 115
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=31.76 E-value=1.1e+02 Score=30.16 Aligned_cols=36 Identities=14% Similarity=0.109 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+.+....|...+|++||..+.|..+|++.+++++.+
T Consensus 175 ~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l 210 (325)
T PRK05657 175 YLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRML 210 (325)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 334456677788999999999999999988876654
No 116
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=31.14 E-value=1e+02 Score=27.22 Aligned_cols=33 Identities=15% Similarity=0.240 Sum_probs=27.3
Q ss_pred HHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhH
Q 020252 252 LSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 284 (328)
Q Consensus 252 L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~ 284 (328)
|.+.-++..|..+.+++.|++.+.+.+.+++|+
T Consensus 39 Lr~~p~~~ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 39 LRKHENRQATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred HHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 334446667899999999999999999998884
No 117
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=30.73 E-value=79 Score=22.04 Aligned_cols=23 Identities=30% Similarity=0.323 Sum_probs=17.0
Q ss_pred CchHHHHHHhcCcHHHHHHhhhh
Q 020252 260 PTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 260 PT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
-|..+.|..+|++...+.+.+..
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHHCC
T ss_pred CCHHHHHHHHCcCHHHHHHHHhc
Confidence 56889999999999998887653
No 118
>PRK13239 alkylmercury lyase; Provisional
Probab=29.49 E-value=92 Score=29.36 Aligned_cols=27 Identities=26% Similarity=0.212 Sum_probs=24.9
Q ss_pred cCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 256 CGGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 256 ~GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
.|++||..+.|++.|.+.+++++.|+.
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~ 59 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEA 59 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 499999999999999999999988876
No 119
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=28.71 E-value=1.1e+02 Score=28.12 Aligned_cols=34 Identities=12% Similarity=0.187 Sum_probs=26.6
Q ss_pred HHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 249 REVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 249 r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
..-+.+......|.++||+.+|+|...|.+..+.
T Consensus 192 ~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 192 NFLIEENYKQHLRLPEYADRLGISESRLNDICRR 225 (287)
T ss_pred HHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3345556677889999999999999999876653
No 120
>PHA01976 helix-turn-helix protein
Probab=28.65 E-value=95 Score=22.56 Aligned_cols=47 Identities=17% Similarity=0.166 Sum_probs=32.4
Q ss_pred CchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHH
Q 020252 260 PTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLV 316 (328)
Q Consensus 260 PT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLI 316 (328)
-|..++|+.+|++...+.+..+... .-+...+..||+-| |+++++|+
T Consensus 16 lt~~~lA~~~gvs~~~v~~~e~g~~-------~p~~~~l~~ia~~l---~v~~~~l~ 62 (67)
T PHA01976 16 WSAPELSRRAGVRHSLIYDFEADKR-------LPNLKTLLRLADAL---GVTLDWLC 62 (67)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC-------CCCHHHHHHHHHHH---CcCHHHHh
Confidence 5778899999998877776444321 34566677888766 57777764
No 121
>PRK15185 transcriptional regulator HilD; Provisional
Probab=25.88 E-value=1.9e+02 Score=28.86 Aligned_cols=45 Identities=18% Similarity=0.150 Sum_probs=33.3
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhh-hhHHHHHH
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN-YGILCKDK 289 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~-~G~~Are~ 289 (328)
.++++.-+....+...|.++||+.+|++...|.+.+. .|....+.
T Consensus 208 ~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~~G~S~~~y 253 (309)
T PRK15185 208 KERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSFSDI 253 (309)
T ss_pred HHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHH
Confidence 3445556667788899999999999999999988764 24334433
No 122
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=25.37 E-value=1.6e+02 Score=20.71 Aligned_cols=24 Identities=29% Similarity=0.407 Sum_probs=19.8
Q ss_pred CCchHHHHHHhcCcHHHHHHhhhh
Q 020252 259 SPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 259 ePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
..|..+.|+.+|+|...+++.+..
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHH
Confidence 489999999999999998877764
No 123
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=24.85 E-value=1.3e+02 Score=26.22 Aligned_cols=36 Identities=14% Similarity=0.215 Sum_probs=27.8
Q ss_pred CCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHh
Q 020252 259 SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSN 294 (328)
Q Consensus 259 ePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sN 294 (328)
.-+..|.|+..|++...++.+++.+...-.+.+..|
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~ 192 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDL 192 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999988755444444443
No 124
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=24.51 E-value=2.1e+02 Score=20.18 Aligned_cols=38 Identities=13% Similarity=0.250 Sum_probs=26.0
Q ss_pred HHhhhhhHHHHHHHHHH-hHHHHHHHHhhccCCCCChHHH
Q 020252 277 RRRLNYGILCKDKMITS-NIRLVISIAKNYQGAGMNLQDL 315 (328)
Q Consensus 277 ~~~L~~G~~Are~LI~s-NLRLVvsIAkrY~g~Gl~~~DL 315 (328)
-..+......|++|-.+ |..=++.||+.+ |+-.+-+||
T Consensus 10 l~~~~~d~~l~~~l~~~~~~~e~~~lA~~~-Gy~ft~~el 48 (49)
T PF07862_consen 10 LEKVKSDPELREQLKACQNPEEVVALAREA-GYDFTEEEL 48 (49)
T ss_pred HHHHhcCHHHHHHHHhcCCHHHHHHHHHHc-CCCCCHHHh
Confidence 33444556666666665 888889999876 776666665
No 125
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=24.51 E-value=2.4e+02 Score=26.97 Aligned_cols=38 Identities=8% Similarity=0.039 Sum_probs=29.0
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
++++..-+.......+|.++||..+|++...|.+..+.
T Consensus 193 i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44445555666677899999999999999988776654
No 126
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=23.29 E-value=99 Score=25.08 Aligned_cols=26 Identities=38% Similarity=0.353 Sum_probs=19.9
Q ss_pred CCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 257 GGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 257 GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
|++.|..+.|.++|.+.++++..|..
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 99999999999999999999888754
No 127
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=23.22 E-value=1.2e+02 Score=20.50 Aligned_cols=27 Identities=19% Similarity=0.175 Sum_probs=17.9
Q ss_pred hcCCCCchHHHHHHhcCcHHHHHHhhh
Q 020252 255 RCGGSPTFAQWAAAAGVDQRELRRRLN 281 (328)
Q Consensus 255 ~~GrePT~~eWA~a~g~d~~~L~~~L~ 281 (328)
.+....+..+.|..+|+|..-|.+..+
T Consensus 4 ~~~~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 4 NLQQKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp TT-SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred cccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345567899999999998888876654
No 128
>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=22.66 E-value=96 Score=20.31 Aligned_cols=24 Identities=33% Similarity=0.338 Sum_probs=18.5
Q ss_pred chHHHHHHhcCcHHHHHHhhhhhH
Q 020252 261 TFAQWAAAAGVDQRELRRRLNYGI 284 (328)
Q Consensus 261 T~~eWA~a~g~d~~~L~~~L~~G~ 284 (328)
|..|.|+.+|++...+.+.+..|.
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCC
Confidence 456788888998888887777663
No 129
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=22.04 E-value=2.5e+02 Score=27.01 Aligned_cols=45 Identities=13% Similarity=0.130 Sum_probs=34.7
Q ss_pred CCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHH
Q 020252 258 GSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302 (328)
Q Consensus 258 rePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIA 302 (328)
..-|..|.|+..|++...+++.++.+..--...+..+.+-|.+.|
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~~~~~~~~~ 288 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEARALEKLRRALLSQSPEVAYFA 288 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcCchhhhhc
Confidence 567899999999999999999999886544455566666665543
No 130
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=21.84 E-value=2.2e+02 Score=21.01 Aligned_cols=23 Identities=22% Similarity=0.346 Sum_probs=17.9
Q ss_pred CCCchHHHHHHhcCcHHHHHHhh
Q 020252 258 GSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 258 rePT~~eWA~a~g~d~~~L~~~L 280 (328)
.-.+..+.|+.+|++..++|+.+
T Consensus 27 ~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 27 ERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred eeECHHHHHHHHCCCHHHhcccC
Confidence 45778999999999999998765
No 131
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are 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 as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=21.76 E-value=3.7e+02 Score=21.62 Aligned_cols=36 Identities=14% Similarity=0.186 Sum_probs=27.6
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhh
Q 020252 245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG 283 (328)
Q Consensus 245 Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G 283 (328)
++.+.+-|.. ..+|..+.|+.+|++.....+.|+.+
T Consensus 8 ~~~I~e~l~~---~~~ti~dvA~~~gvS~~TVsr~L~~~ 43 (80)
T TIGR02844 8 VLEIGKYIVE---TKATVRETAKVFGVSKSTVHKDVTER 43 (80)
T ss_pred HHHHHHHHHH---CCCCHHHHHHHhCCCHHHHHHHhcCC
Confidence 3344444544 46789999999999999999999764
No 132
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=21.34 E-value=1.1e+02 Score=21.34 Aligned_cols=25 Identities=24% Similarity=0.441 Sum_probs=19.4
Q ss_pred CchHHHHHHhcCcHHHHHHhhhhhH
Q 020252 260 PTFAQWAAAAGVDQRELRRRLNYGI 284 (328)
Q Consensus 260 PT~~eWA~a~g~d~~~L~~~L~~G~ 284 (328)
=|..|.|+..|++...++..++.+.
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4688999999999999998888764
No 133
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=21.33 E-value=1.6e+02 Score=28.14 Aligned_cols=24 Identities=21% Similarity=0.170 Sum_probs=21.1
Q ss_pred CCCCchHHHHHHhcCcHHHHHHhh
Q 020252 257 GGSPTFAQWAAAAGVDQRELRRRL 280 (328)
Q Consensus 257 GrePT~~eWA~a~g~d~~~L~~~L 280 (328)
+++||.+|.|+.+|++.+.+...+
T Consensus 149 ~~~~t~~eiA~~l~~~~~~v~~~~ 172 (284)
T PRK06596 149 LNPEEVEMVAEELGVSEEEVREME 172 (284)
T ss_pred CCCCCHHHHHHHhCcCHHHHHHHH
Confidence 589999999999999998887654
No 134
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=21.07 E-value=1.1e+02 Score=20.98 Aligned_cols=24 Identities=29% Similarity=0.390 Sum_probs=19.8
Q ss_pred CCchHHHHHHhcCcHHHHHHhhhh
Q 020252 259 SPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 259 ePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
-||..++|+.+|++...+++.+..
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 458999999999999888876653
No 135
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=20.85 E-value=1.7e+02 Score=27.97 Aligned_cols=35 Identities=26% Similarity=0.291 Sum_probs=27.6
Q ss_pred HHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252 248 LREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 248 ~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
+..-+.......+|.+++|+.+|++...|.+..+.
T Consensus 223 ~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~ 257 (322)
T PRK09393 223 LIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEA 257 (322)
T ss_pred HHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33445556677899999999999999999887764
No 136
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.58 E-value=1.4e+02 Score=25.54 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=22.8
Q ss_pred CchHHHHHHhcCcHHHHHHhhhhhHH
Q 020252 260 PTFAQWAAAAGVDQRELRRRLNYGIL 285 (328)
Q Consensus 260 PT~~eWA~a~g~d~~~L~~~L~~G~~ 285 (328)
-+..|.|+.+|++...++.+|+.+..
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 136 MGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 57899999999999999999988743
No 137
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=20.33 E-value=1.1e+02 Score=21.28 Aligned_cols=23 Identities=17% Similarity=0.228 Sum_probs=14.8
Q ss_pred CchHHHHHHhcCcHHHHHHhhhh
Q 020252 260 PTFAQWAAAAGVDQRELRRRLNY 282 (328)
Q Consensus 260 PT~~eWA~a~g~d~~~L~~~L~~ 282 (328)
.|..+.|..+|.+...+.+.|..
T Consensus 21 ~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 21 MSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp --HHHHHHHTT--HHHHHHHHHH
T ss_pred CCHHHHHHHHCcCcHHHHHHHhc
Confidence 57788888888888887766654
No 138
>PF14711 Nitr_red_bet_C: Respiratory nitrate reductase beta C-terminal; PDB: 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B 1Y4Z_B 1Y5L_B 3IR6_B 3IR5_B ....
Probab=20.06 E-value=2.6e+02 Score=22.78 Aligned_cols=52 Identities=23% Similarity=0.413 Sum_probs=28.4
Q ss_pred hhHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcH
Q 020252 213 PLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 273 (328)
Q Consensus 213 ~l~YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~ 273 (328)
|++||.++ ||+-+|.-.-..++.++.+..-.+.. ..|. +...++.+++|++.
T Consensus 31 Pi~YLAnL------ftAGd~~~V~~~L~rL~AmR~ymR~~--~v~~-~~~~~~l~~~glt~ 82 (83)
T PF14711_consen 31 PIEYLANL------FTAGDEEPVRRALKRLLAMRSYMRAK--NVGG-EPDEEVLEAVGLTE 82 (83)
T ss_dssp -HHHHHHH------HSTT-HHHHHHHHHHHHHHHHHHHHH--HTT--S---HHHHHTT--H
T ss_pred cHHHHHHH------HccCChHHHHHHHHHHHHHHHHHHHH--HhCC-CCcHHHHHHcCCCC
Confidence 77788875 77777777766666655444333322 3454 44578888998864
Done!