Query 038569
Match_columns 362
No_of_seqs 234 out of 1236
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 12:22:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038569.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038569hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0773 Transcription factor M 99.9 4.1E-28 9E-33 237.9 4.4 238 116-353 50-311 (342)
2 PF03791 KNOX2: KNOX2 domain ; 99.9 2.6E-23 5.7E-28 154.2 5.6 51 169-219 2-52 (52)
3 KOG0774 Transcription factor P 99.9 2E-22 4.4E-27 191.1 11.9 199 112-346 25-253 (334)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 1.4E-19 3E-24 130.4 4.3 44 116-159 1-44 (45)
5 PF05920 Homeobox_KN: Homeobox 99.6 1.7E-16 3.6E-21 112.2 3.9 40 299-338 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.5 4.3E-14 9.3E-19 104.0 6.8 58 282-342 1-58 (59)
7 smart00389 HOX Homeodomain. DN 99.5 1E-13 2.2E-18 101.6 6.6 56 282-340 1-56 (56)
8 PF00046 Homeobox: Homeobox do 99.5 6.8E-14 1.5E-18 103.5 5.0 57 282-341 1-57 (57)
9 KOG0775 Transcription factor S 99.2 5E-12 1.1E-16 121.4 4.5 51 288-341 183-233 (304)
10 KOG0493 Transcription factor E 99.1 1.6E-10 3.5E-15 110.6 5.5 77 281-360 246-322 (342)
11 KOG0843 Transcription factor E 99.0 4.7E-10 1E-14 102.5 4.3 62 280-344 101-162 (197)
12 TIGR01565 homeo_ZF_HD homeobox 99.0 1E-09 2.2E-14 83.6 5.4 53 281-336 1-57 (58)
13 KOG0487 Transcription factor A 99.0 3.2E-10 6.8E-15 111.3 3.1 62 280-344 234-295 (308)
14 KOG0485 Transcription factor N 98.9 1.2E-09 2.7E-14 102.4 6.0 59 280-341 103-161 (268)
15 KOG0489 Transcription factor z 98.9 7.8E-10 1.7E-14 106.4 3.5 62 280-344 158-219 (261)
16 KOG0850 Transcription factor D 98.9 1.2E-09 2.7E-14 102.9 3.8 63 279-344 120-182 (245)
17 KOG3802 Transcription factor O 98.8 3.1E-09 6.7E-14 106.8 4.4 65 277-344 290-354 (398)
18 KOG0488 Transcription factor B 98.8 3.5E-09 7.6E-14 104.3 4.6 62 279-343 170-231 (309)
19 KOG0483 Transcription factor H 98.8 5.3E-09 1.1E-13 97.3 4.4 60 281-343 50-109 (198)
20 KOG0842 Transcription factor t 98.8 3.9E-09 8.5E-14 103.7 3.4 64 280-346 152-215 (307)
21 COG5576 Homeodomain-containing 98.7 7.4E-09 1.6E-13 93.1 4.3 61 281-344 51-111 (156)
22 KOG0486 Transcription factor P 98.7 7.2E-09 1.6E-13 101.5 3.1 67 280-350 111-177 (351)
23 KOG0494 Transcription factor C 98.7 1.6E-08 3.4E-13 97.1 4.3 62 281-346 140-202 (332)
24 KOG0492 Transcription factor M 98.6 2.2E-08 4.7E-13 93.5 4.1 70 270-342 133-202 (246)
25 KOG0491 Transcription factor B 98.6 1.1E-08 2.4E-13 92.5 1.2 68 278-348 97-164 (194)
26 KOG2251 Homeobox transcription 98.6 4.2E-08 9E-13 92.2 4.4 59 280-341 36-94 (228)
27 KOG0848 Transcription factor C 98.5 3.6E-08 7.8E-13 95.0 1.4 61 283-346 201-261 (317)
28 KOG0484 Transcription factor P 98.5 1.1E-07 2.3E-12 80.5 3.3 67 275-344 11-77 (125)
29 KOG4577 Transcription factor L 98.3 2.3E-07 4.9E-12 90.4 2.9 69 272-343 158-226 (383)
30 KOG2252 CCAAT displacement pro 98.1 2.8E-06 6.1E-11 88.6 5.6 58 279-339 418-475 (558)
31 KOG0844 Transcription factor E 98.1 2.5E-06 5.4E-11 83.8 3.1 59 283-344 183-241 (408)
32 KOG0849 Transcription factor P 98.0 4.9E-06 1.1E-10 83.6 4.7 64 280-346 175-238 (354)
33 KOG0490 Transcription factor, 97.9 3.8E-06 8.2E-11 77.2 2.1 62 279-343 58-119 (235)
34 KOG1168 Transcription factor A 97.9 3.5E-06 7.7E-11 82.3 0.9 67 272-341 300-366 (385)
35 KOG0847 Transcription factor, 97.9 6.1E-06 1.3E-10 78.0 2.5 63 277-342 163-225 (288)
36 KOG0773 Transcription factor M 97.3 8.8E-05 1.9E-09 73.4 1.7 62 281-343 95-156 (342)
37 PF11569 Homez: Homeodomain le 96.9 0.00091 2E-08 50.9 3.2 43 293-338 10-52 (56)
38 PF03789 ELK: ELK domain ; In 96.8 0.00059 1.3E-08 42.7 1.2 22 259-280 1-22 (22)
39 PF03792 PBC: PBC domain; Int 96.7 0.013 2.9E-07 54.5 9.5 136 114-278 25-177 (191)
40 KOG0490 Transcription factor, 96.2 0.0035 7.6E-08 57.5 2.9 60 280-342 152-211 (235)
41 KOG1146 Homeobox protein [Gene 93.2 0.064 1.4E-06 61.7 3.2 63 281-346 903-965 (1406)
42 PF04218 CENP-B_N: CENP-B N-te 88.5 0.92 2E-05 33.6 4.5 48 282-337 1-48 (53)
43 KOG3623 Homeobox transcription 81.1 2.3 4.9E-05 47.2 4.9 44 293-339 568-611 (1007)
44 cd06171 Sigma70_r4 Sigma70, re 78.3 3.6 7.9E-05 27.9 3.8 46 287-340 10-55 (55)
45 PF01527 HTH_Tnp_1: Transposas 77.6 4 8.7E-05 31.1 4.2 46 283-336 2-48 (76)
46 PF08281 Sigma70_r4_2: Sigma-7 75.6 4.4 9.5E-05 29.1 3.7 44 287-338 10-53 (54)
47 PRK00118 putative DNA-binding 75.0 1.7 3.7E-05 36.9 1.5 55 287-349 17-71 (104)
48 cd00569 HTH_Hin_like Helix-tur 73.6 10 0.00022 22.8 4.7 40 285-332 3-42 (42)
49 PF04545 Sigma70_r4: Sigma-70, 71.4 4.3 9.3E-05 29.0 2.7 46 287-340 4-49 (50)
50 PRK09642 RNA polymerase sigma 69.0 3.8 8.2E-05 35.4 2.4 54 287-348 106-159 (160)
51 PRK06759 RNA polymerase factor 64.2 8.2 0.00018 32.9 3.5 47 287-341 106-152 (154)
52 PRK03975 tfx putative transcri 63.9 6.6 0.00014 35.1 2.9 53 285-346 4-56 (141)
53 PRK09644 RNA polymerase sigma 63.1 5.3 0.00012 34.8 2.2 53 286-346 107-159 (165)
54 PRK12514 RNA polymerase sigma 59.3 7.9 0.00017 34.1 2.6 49 287-343 129-177 (179)
55 TIGR02937 sigma70-ECF RNA poly 58.0 11 0.00023 30.8 3.0 48 287-342 110-157 (158)
56 PRK12512 RNA polymerase sigma 55.8 9.7 0.00021 33.7 2.6 52 287-346 131-182 (184)
57 TIGR02989 Sig-70_gvs1 RNA poly 55.7 13 0.00027 31.8 3.2 49 286-342 110-158 (159)
58 smart00421 HTH_LUXR helix_turn 54.2 23 0.00051 24.4 3.9 45 287-340 3-47 (58)
59 TIGR02985 Sig70_bacteroi1 RNA 53.8 20 0.00043 30.2 4.1 48 287-342 113-160 (161)
60 TIGR02939 RpoE_Sigma70 RNA pol 53.7 9.4 0.0002 33.6 2.2 50 287-344 138-187 (190)
61 PF13443 HTH_26: Cro/C1-type H 52.5 12 0.00026 27.5 2.2 24 313-336 12-35 (63)
62 PRK12541 RNA polymerase sigma 52.3 14 0.00031 31.8 3.1 50 286-343 111-160 (161)
63 PRK09646 RNA polymerase sigma 52.0 12 0.00026 33.7 2.6 49 287-343 142-190 (194)
64 PRK12546 RNA polymerase sigma 51.8 12 0.00026 33.9 2.5 52 287-346 113-164 (188)
65 PRK11924 RNA polymerase sigma 51.0 14 0.0003 31.8 2.7 49 288-344 126-174 (179)
66 PRK09652 RNA polymerase sigma 49.7 15 0.00033 31.7 2.8 49 287-343 128-176 (182)
67 PRK06811 RNA polymerase factor 49.3 19 0.00042 32.2 3.5 50 287-344 131-180 (189)
68 PRK12530 RNA polymerase sigma 48.8 9.8 0.00021 34.2 1.5 52 287-346 134-185 (189)
69 PRK12526 RNA polymerase sigma 48.7 13 0.00029 33.9 2.4 50 287-344 153-202 (206)
70 PF00196 GerE: Bacterial regul 46.7 23 0.00051 25.9 3.0 45 287-340 3-47 (58)
71 TIGR02999 Sig-70_X6 RNA polyme 46.3 20 0.00043 31.5 3.1 48 287-342 134-181 (183)
72 PRK12536 RNA polymerase sigma 46.1 18 0.0004 32.0 2.8 50 287-344 129-178 (181)
73 PRK09648 RNA polymerase sigma 45.6 18 0.00039 32.1 2.7 49 287-343 139-187 (189)
74 TIGR02948 SigW_bacill RNA poly 45.5 14 0.00031 32.4 2.0 49 287-343 136-184 (187)
75 PF13518 HTH_28: Helix-turn-he 43.9 22 0.00048 24.8 2.4 25 313-337 14-38 (52)
76 PRK12547 RNA polymerase sigma 43.5 22 0.00047 31.0 2.8 48 287-342 112-159 (164)
77 PRK09047 RNA polymerase factor 43.2 17 0.00036 31.1 2.0 50 287-344 106-155 (161)
78 PRK12532 RNA polymerase sigma 43.0 14 0.0003 33.2 1.5 51 287-345 136-186 (195)
79 PRK12535 RNA polymerase sigma 42.8 25 0.00055 31.9 3.3 56 287-350 133-188 (196)
80 PRK05602 RNA polymerase sigma 42.5 21 0.00045 31.7 2.5 50 288-345 129-178 (186)
81 TIGR02983 SigE-fam_strep RNA p 41.9 22 0.00048 30.5 2.6 50 287-344 110-159 (162)
82 PRK12537 RNA polymerase sigma 41.7 25 0.00054 31.2 3.0 48 287-342 133-180 (182)
83 PRK09639 RNA polymerase sigma 41.4 25 0.00054 30.3 2.8 49 287-344 112-160 (166)
84 PRK13919 putative RNA polymera 41.2 24 0.00052 31.1 2.8 49 287-343 135-183 (186)
85 TIGR02954 Sig70_famx3 RNA poly 40.6 25 0.00055 30.5 2.8 49 287-343 119-167 (169)
86 PRK12519 RNA polymerase sigma 40.3 20 0.00043 31.9 2.1 48 287-342 141-188 (194)
87 cd06170 LuxR_C_like C-terminal 40.2 52 0.0011 22.8 3.9 46 288-342 1-46 (57)
88 TIGR02859 spore_sigH RNA polym 39.9 29 0.00062 30.8 3.1 31 313-343 167-197 (198)
89 PF13097 CENP-U: CENP-A nucleo 39.8 53 0.0011 30.6 4.8 43 176-218 104-148 (175)
90 PRK12533 RNA polymerase sigma 39.4 21 0.00046 33.3 2.2 52 287-346 134-185 (216)
91 PRK09649 RNA polymerase sigma 39.2 30 0.00066 30.9 3.1 47 287-341 130-176 (185)
92 TIGR02959 SigZ RNA polymerase 38.4 20 0.00044 31.5 1.8 52 287-346 100-151 (170)
93 PRK15369 two component system 38.3 38 0.00081 28.7 3.4 47 286-341 148-194 (211)
94 TIGR00721 tfx DNA-binding prot 38.2 26 0.00056 31.2 2.5 57 285-350 4-60 (137)
95 PRK08583 RNA polymerase sigma 38.1 30 0.00065 32.7 3.1 49 287-343 205-253 (257)
96 cd00131 PAX Paired Box domain 37.4 1.1E+02 0.0023 26.5 6.1 48 285-335 73-127 (128)
97 PRK12520 RNA polymerase sigma 37.2 33 0.00071 30.6 3.0 50 287-344 131-180 (191)
98 PRK09415 RNA polymerase factor 36.9 22 0.00048 31.5 1.9 50 287-344 127-176 (179)
99 PRK07670 RNA polymerase sigma 36.2 30 0.00066 32.6 2.8 49 287-343 201-249 (251)
100 PRK06986 fliA flagellar biosyn 35.7 25 0.00054 32.8 2.1 49 287-343 184-232 (236)
101 PF01381 HTH_3: Helix-turn-hel 35.5 32 0.00069 24.4 2.2 21 314-334 12-32 (55)
102 PRK12515 RNA polymerase sigma 35.5 36 0.00078 30.3 3.0 49 287-343 131-179 (189)
103 PRK12523 RNA polymerase sigma 35.2 42 0.0009 29.4 3.3 49 286-342 118-166 (172)
104 PRK07037 extracytoplasmic-func 35.1 36 0.00078 29.2 2.9 49 287-343 109-157 (163)
105 PRK12524 RNA polymerase sigma 35.1 54 0.0012 29.4 4.1 51 287-345 136-186 (196)
106 TIGR02943 Sig70_famx1 RNA poly 34.8 37 0.0008 30.5 3.0 50 287-344 131-180 (188)
107 PRK12542 RNA polymerase sigma 34.8 28 0.00061 30.8 2.2 50 287-344 122-171 (185)
108 PRK12543 RNA polymerase sigma 34.6 38 0.00083 29.9 3.0 52 287-346 117-168 (179)
109 TIGR02941 Sigma_B RNA polymera 34.5 36 0.00078 32.1 3.0 48 287-342 205-252 (255)
110 PRK12531 RNA polymerase sigma 34.4 37 0.0008 30.5 2.9 50 286-343 140-189 (194)
111 PRK08295 RNA polymerase factor 34.3 32 0.00069 30.8 2.5 48 287-343 155-202 (208)
112 TIGR02980 SigBFG RNA polymeras 34.3 39 0.00084 31.1 3.1 48 287-342 178-225 (227)
113 PF10668 Phage_terminase: Phag 34.2 32 0.0007 26.6 2.1 20 313-332 24-43 (60)
114 PRK12516 RNA polymerase sigma 34.1 36 0.00079 30.6 2.8 52 287-346 116-167 (187)
115 PRK09645 RNA polymerase sigma 34.0 34 0.00074 29.8 2.6 51 287-345 118-168 (173)
116 PRK09647 RNA polymerase sigma 33.9 37 0.00081 31.1 2.9 51 287-345 138-188 (203)
117 PRK06930 positive control sigm 33.7 25 0.00055 32.0 1.7 54 287-348 114-167 (170)
118 PRK12539 RNA polymerase sigma 33.4 36 0.00077 30.2 2.6 50 287-344 131-180 (184)
119 PF13936 HTH_38: Helix-turn-he 33.4 39 0.00085 23.8 2.3 40 286-333 3-42 (44)
120 PRK12538 RNA polymerase sigma 33.0 32 0.00069 32.5 2.3 50 287-344 171-220 (233)
121 PRK12513 RNA polymerase sigma 32.5 19 0.00041 32.2 0.7 50 287-344 139-188 (194)
122 PRK06288 RNA polymerase sigma 32.2 23 0.00051 33.8 1.3 51 287-345 212-262 (268)
123 PRK12534 RNA polymerase sigma 32.0 38 0.00081 30.0 2.5 49 287-343 137-185 (187)
124 PRK04217 hypothetical protein; 31.9 59 0.0013 27.9 3.5 54 283-344 38-91 (110)
125 TIGR02479 FliA_WhiG RNA polyme 31.6 41 0.00089 31.0 2.8 48 287-342 175-222 (224)
126 TIGR02947 SigH_actino RNA poly 31.6 21 0.00046 31.9 0.8 50 287-344 131-180 (193)
127 PRK09641 RNA polymerase sigma 31.0 37 0.0008 29.7 2.3 49 287-343 136-184 (187)
128 PRK09637 RNA polymerase sigma 30.9 42 0.00092 30.0 2.7 49 287-343 106-154 (181)
129 PRK12544 RNA polymerase sigma 30.8 47 0.001 30.6 3.0 51 287-345 148-198 (206)
130 PRK12522 RNA polymerase sigma 30.7 45 0.00098 29.1 2.8 49 287-343 119-167 (173)
131 PF13551 HTH_29: Winged helix- 30.4 2.4E+02 0.0053 22.3 6.9 74 260-333 28-109 (112)
132 PRK09413 IS2 repressor TnpA; R 30.2 1.1E+02 0.0023 26.0 4.9 48 283-337 8-55 (121)
133 PRK12511 RNA polymerase sigma 30.0 46 0.001 29.9 2.7 50 287-344 111-160 (182)
134 PF13384 HTH_23: Homeodomain-l 29.8 44 0.00096 23.4 2.1 26 312-337 18-43 (50)
135 PRK12528 RNA polymerase sigma 29.4 60 0.0013 27.9 3.3 45 287-339 113-157 (161)
136 TIGR03001 Sig-70_gmx1 RNA poly 29.2 48 0.001 31.6 2.9 51 287-345 161-211 (244)
137 PRK12545 RNA polymerase sigma 29.1 50 0.0011 30.0 2.9 52 287-346 139-190 (201)
138 PRK12527 RNA polymerase sigma 29.0 53 0.0012 28.2 2.9 49 288-344 106-154 (159)
139 PRK11923 algU RNA polymerase s 29.0 42 0.0009 29.8 2.3 49 288-344 139-187 (193)
140 TIGR03070 couple_hipB transcri 29.0 43 0.00093 23.4 1.9 23 314-336 18-40 (58)
141 PRK12529 RNA polymerase sigma 29.0 64 0.0014 28.6 3.5 48 287-342 127-174 (178)
142 TIGR02952 Sig70_famx2 RNA poly 28.9 59 0.0013 27.9 3.1 49 286-342 121-169 (170)
143 cd01392 HTH_LacI Helix-turn-he 28.8 34 0.00074 24.0 1.4 21 316-336 2-22 (52)
144 TIGR02960 SigX5 RNA polymerase 28.7 57 0.0012 31.5 3.3 51 287-345 142-192 (324)
145 PRK10072 putative transcriptio 28.7 43 0.00093 28.0 2.1 24 313-336 48-71 (96)
146 PRK08301 sporulation sigma fac 28.2 34 0.00074 31.7 1.6 53 287-343 178-230 (234)
147 cd00093 HTH_XRE Helix-turn-hel 28.2 52 0.0011 21.6 2.2 23 314-336 15-37 (58)
148 PF13730 HTH_36: Helix-turn-he 27.8 1.7E+02 0.0036 20.8 4.9 49 287-338 2-52 (55)
149 PF02796 HTH_7: Helix-turn-hel 27.6 1.1E+02 0.0023 21.6 3.7 40 285-332 3-42 (45)
150 KOG3755 SATB1 matrix attachmen 26.2 55 0.0012 36.0 2.9 58 281-340 647-707 (769)
151 PF04967 HTH_10: HTH DNA bindi 26.1 1.4E+02 0.0029 22.5 4.2 47 288-335 1-47 (53)
152 PRK11511 DNA-binding transcrip 26.0 1.2E+02 0.0025 25.9 4.4 42 290-335 8-49 (127)
153 PF13411 MerR_1: MerR HTH fami 26.0 54 0.0012 24.3 2.1 18 315-332 4-21 (69)
154 TIGR02885 spore_sigF RNA polym 25.3 73 0.0016 29.4 3.3 47 287-341 183-229 (231)
155 TIGR02984 Sig-70_plancto1 RNA 25.2 62 0.0013 28.3 2.7 49 287-343 140-188 (189)
156 PRK12540 RNA polymerase sigma 25.2 63 0.0014 28.9 2.8 51 287-345 111-161 (182)
157 PRK10651 transcriptional regul 25.1 86 0.0019 26.9 3.5 45 287-340 155-199 (216)
158 PRK07408 RNA polymerase sigma 24.9 58 0.0013 31.1 2.6 50 287-344 203-252 (256)
159 PRK12517 RNA polymerase sigma 24.8 70 0.0015 28.7 3.0 50 287-344 128-177 (188)
160 smart00530 HTH_XRE Helix-turn- 24.7 65 0.0014 20.9 2.1 22 314-335 13-34 (56)
161 TIGR02950 SigM_subfam RNA poly 24.6 45 0.00097 28.2 1.6 47 288-342 106-152 (154)
162 PRK08241 RNA polymerase factor 24.2 73 0.0016 31.2 3.2 48 287-342 153-200 (339)
163 PRK09651 RNA polymerase sigma 24.0 54 0.0012 28.8 2.1 46 287-340 119-164 (172)
164 PF14904 FAM86: Family of unkn 23.9 1.2E+02 0.0027 25.8 4.0 56 110-189 42-100 (100)
165 PF11348 DUF3150: Protein of u 23.5 1E+02 0.0022 30.0 4.0 47 133-195 60-118 (257)
166 PRK07122 RNA polymerase sigma 23.2 67 0.0015 30.9 2.7 49 287-343 215-263 (264)
167 PF11288 DUF3089: Protein of u 23.2 28 0.00061 33.0 0.1 29 115-147 110-138 (207)
168 PRK05572 sporulation sigma fac 23.0 67 0.0014 30.3 2.6 49 287-343 202-250 (252)
169 TIGR01601 PYST-C1 Plasmodium y 23.0 44 0.00096 27.4 1.2 14 43-56 61-74 (82)
170 PRK12518 RNA polymerase sigma 22.8 38 0.00082 29.5 0.8 51 287-345 120-170 (175)
171 PF14229 DUF4332: Domain of un 22.7 79 0.0017 27.2 2.8 29 308-336 26-54 (122)
172 KOG4040 NADH:ubiquinone oxidor 22.5 48 0.001 30.7 1.4 38 290-327 23-61 (186)
173 TIGR02835 spore_sigmaE RNA pol 22.3 63 0.0014 30.2 2.2 54 287-344 178-231 (234)
174 PRK12525 RNA polymerase sigma 22.2 1E+02 0.0022 26.9 3.4 47 286-340 117-163 (168)
175 cd04761 HTH_MerR-SF Helix-Turn 22.2 75 0.0016 21.8 2.1 20 315-334 4-23 (49)
176 PHA01976 helix-turn-helix prot 22.1 73 0.0016 23.5 2.2 23 314-336 18-40 (67)
177 TIGR02607 antidote_HigA addict 21.9 72 0.0016 24.2 2.1 23 314-336 21-43 (78)
178 PRK09636 RNA polymerase sigma 21.6 1.1E+02 0.0023 29.6 3.7 49 288-344 116-164 (293)
179 PRK05803 sporulation sigma fac 21.6 73 0.0016 29.6 2.5 53 287-343 175-227 (233)
180 PRK09643 RNA polymerase sigma 21.2 60 0.0013 29.2 1.8 49 288-344 135-183 (192)
181 TIGR02846 spore_sigmaK RNA pol 21.2 82 0.0018 29.2 2.8 51 287-341 174-224 (227)
182 TIGR02393 RpoD_Cterm RNA polym 21.0 1E+02 0.0022 28.8 3.3 53 287-343 176-228 (238)
183 PRK11922 RNA polymerase sigma 20.9 47 0.001 30.9 1.1 49 288-344 150-198 (231)
184 PRK05657 RNA polymerase sigma 20.8 90 0.002 31.1 3.1 54 287-344 262-315 (325)
No 1
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.94 E-value=4.1e-28 Score=237.92 Aligned_cols=238 Identities=24% Similarity=0.282 Sum_probs=175.1
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhHhccCchhhhhhHHHHHhhcccc-Cccccc-----CCCCCCCCCcccHHHHHHHHHH
Q 038569 116 SAIRAQIASHPLYPKLLQAYIDCQKVGASPEIANVLDDIRREGDVS-NRNWVV-----SSCCWGADPELDEFMETYCDIL 189 (362)
Q Consensus 116 ~~~Ka~I~sHPLYp~Ll~Ayi~C~KVgaPpd~~~~Ldei~~~~~~~-~~~~~~-----~~~~~g~dpELDqFMe~Yc~~L 189 (362)
...|..+.+||||+.++.||+.|.+++++.+.+.+++...+..... .+...+ .....+.+++++.||..|+.+|
T Consensus 50 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k~~~~l 129 (342)
T KOG0773|consen 50 ASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSKLEKIL 129 (342)
T ss_pred ccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchHHHHHH
Confidence 4678999999999999999999999999999887766544443321 111111 1123567899999999999999
Q ss_pred HHHHHHhcCch--HHHHHHHHHHHHHhhhhcCCCCCCCCC------CCCC-----CCCCC-cccCCCCCc---cccccCC
Q 038569 190 VKYKSDLSKPY--DEASSFLNNMETQLSNLCNVVSRSHGS------DEAD-----PGGSW-EEDLSGGET---EVSECFR 252 (362)
Q Consensus 190 ~kykeEL~kp~--~EA~~Fc~~iE~QL~~L~~gss~s~~s------de~~-----~~~SS-eee~sgGe~---d~~e~d~ 252 (362)
..+...|+..+ .++++++++++..+..++..+...... +... +..+. ++...-++. .......
T Consensus 130 l~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~ 209 (342)
T KOG0773|consen 130 LAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDSEDESGPS 209 (342)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccccccccccccccCcc
Confidence 99999999988 699999999999999987654432110 0000 01111 111110111 1100110
Q ss_pred -CCcccHHHHHHHHHhhccchhhhhhhhccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhh
Q 038569 253 -MPPVDRETKDNLIRKYGGYISTLKHEFSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNW 331 (362)
Q Consensus 253 -~~~ed~eLk~~L~rkys~~i~~lk~e~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nW 331 (362)
.......++..+.+.+..++.....+..++|+++.||+.++.+|+.||.+|+.||||++.+|..||++|||+..||+||
T Consensus 210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NW 289 (342)
T KOG0773|consen 210 GSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNW 289 (342)
T ss_pred cccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCch
Confidence 0134455666666666667777777777889999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhcCCCCCCchhhhccc
Q 038569 332 FINQRKRHWKPSESVQFNLMDS 353 (362)
Q Consensus 332 F~N~RrR~kkp~e~~~~~~~d~ 353 (362)
|||+|+|+|+|+....+..++.
T Consensus 290 FINaR~R~w~p~~~~~~~~~~~ 311 (342)
T KOG0773|consen 290 FINARVRLWKPMIEEMYLLEDK 311 (342)
T ss_pred hhhcccccCCchHHHHHHHhhc
Confidence 9999999999998776666654
No 2
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.88 E-value=2.6e-23 Score=154.16 Aligned_cols=51 Identities=57% Similarity=1.007 Sum_probs=48.9
Q ss_pred CCCCCCCCcccHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhhhcC
Q 038569 169 SCCWGADPELDEFMETYCDILVKYKSDLSKPYDEASSFLNNMETQLSNLCN 219 (362)
Q Consensus 169 ~~~~g~dpELDqFMe~Yc~~L~kykeEL~kp~~EA~~Fc~~iE~QL~~L~~ 219 (362)
+.++|+||||||||++||.||++||+||+|||+||+.|||+||+||++||+
T Consensus 2 ~~~~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 2 SSSIGADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 467899999999999999999999999999999999999999999999985
No 3
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.88 E-value=2e-22 Score=191.09 Aligned_cols=199 Identities=24% Similarity=0.348 Sum_probs=145.4
Q ss_pred hhHHHHHHHHHhhCCChHHHHHHHHhhHh-cc---------Cchh-hhhhHHHHH-hhccccCccccc--CCCCCCC---
Q 038569 112 EQVSSAIRAQIASHPLYPKLLQAYIDCQK-VG---------ASPE-IANVLDDIR-REGDVSNRNWVV--SSCCWGA--- 174 (362)
Q Consensus 112 ~~~~~~~Ka~I~sHPLYp~Ll~Ayi~C~K-Vg---------aPpd-~~~~Ldei~-~~~~~~~~~~~~--~~~~~g~--- 174 (362)
-|+.++.|.+|-+||+||.|....++... ++ .|+| .+.+||.+. ++..+....+++ ....-|.
T Consensus 25 lDeaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsd 104 (334)
T KOG0774|consen 25 LDEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPPDPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSD 104 (334)
T ss_pred cchHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCCChHHHHHHHHHHHhcccCccccchhhhhccCCChHH
Confidence 34556999999999999999999988765 22 1777 899999864 555554443221 1111111
Q ss_pred -CCcccHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCcccCCCCCccccccCCC
Q 038569 175 -DPELDEFMETYCDILVKYKSDLSKPYDEASSFLNNMETQLSNLCNVVSRSHGSDEADPGGSWEEDLSGGETEVSECFRM 253 (362)
Q Consensus 175 -dpELDqFMe~Yc~~L~kykeEL~kp~~EA~~Fc~~iE~QL~~L~~gss~s~~sde~~~~~SSeee~sgGe~d~~e~d~~ 253 (362)
...|-|.-..|...|.||.+ .|+++.+.+.+|....+.. -+..
T Consensus 105 YR~kL~qiR~iy~~Elekyeq-----------aCneftthV~nlL~eQsr~-------------------------RPi~ 148 (334)
T KOG0774|consen 105 YRAKLLQIRQIYHNELEKYEQ-----------ACNEFTTHVMNLLREQSRT-------------------------RPIM 148 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhccc-------------------------CCCC
Confidence 24566777777777777766 6666666666665422111 0011
Q ss_pred CcccHHHHHHHHHhhccchhhhhhh-----------h-ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHh
Q 038569 254 PPVDRETKDNLIRKYGGYISTLKHE-----------F-SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAEST 321 (362)
Q Consensus 254 ~~ed~eLk~~L~rkys~~i~~lk~e-----------~-~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~T 321 (362)
+.+-+.+.+.+.+||+..-..+|++ + ..+|||++|+|.++.+|..||..|+.||||++++|++||++|
T Consensus 149 ~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC 228 (334)
T KOG0774|consen 149 PKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC 228 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc
Confidence 2345567778888888766666654 3 247889999999999999999999999999999999999999
Q ss_pred CCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 322 GLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 322 gLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
|++..||+|||-|.|.|.||.+.+.
T Consensus 229 nItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 229 NITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred Cceehhhccccccceeehhhhhhhh
Confidence 9999999999999999999987544
No 4
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.78 E-value=1.4e-19 Score=130.37 Aligned_cols=44 Identities=66% Similarity=1.090 Sum_probs=41.3
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhHhccCchhhhhhHHHHHhhcc
Q 038569 116 SAIRAQIASHPLYPKLLQAYIDCQKVGASPEIANVLDDIRREGD 159 (362)
Q Consensus 116 ~~~Ka~I~sHPLYp~Ll~Ayi~C~KVgaPpd~~~~Ldei~~~~~ 159 (362)
+.|||+|++|||||+||.||++|+|||||||++++||++.++.+
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~~ 44 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAESQ 44 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhc
Confidence 47999999999999999999999999999999999999987754
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.63 E-value=1.7e-16 Score=112.16 Aligned_cols=40 Identities=50% Similarity=0.990 Sum_probs=36.5
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 038569 299 WWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKR 338 (362)
Q Consensus 299 wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR 338 (362)
||.+|+.||||+++||..||++|||+.+||++||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 8999999999999999999999999999999999999998
No 6
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.50 E-value=4.3e-14 Score=104.04 Aligned_cols=58 Identities=28% Similarity=0.545 Sum_probs=54.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 282 KKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 282 krkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
++++..+++++..+|++||.. +|||+..++..||..|||+.+||.+||+|+|++.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 356788999999999999999 8999999999999999999999999999999997764
No 7
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.47 E-value=1e-13 Score=101.59 Aligned_cols=56 Identities=29% Similarity=0.535 Sum_probs=52.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcC
Q 038569 282 KKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHW 340 (362)
Q Consensus 282 krkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~k 340 (362)
++.+..|+.++..+|+.||.. +|||+.+++..||..+||+.+||.+||+|+|+|.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 355677999999999999999 89999999999999999999999999999999854
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.46 E-value=6.8e-14 Score=103.49 Aligned_cols=57 Identities=35% Similarity=0.744 Sum_probs=54.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 282 KKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 282 krkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
||+|..|+.++..+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.+.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578899999999999999999 999999999999999999999999999999999763
No 9
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.24 E-value=5e-12 Score=121.39 Aligned_cols=51 Identities=39% Similarity=0.783 Sum_probs=47.3
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
|....|.+|++||.+ +|||++.+|.+||+.|||+..||.|||.|+|.|.|-
T Consensus 183 FKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 455689999999998 999999999999999999999999999999999763
No 10
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.06 E-value=1.6e-10 Score=110.61 Aligned_cols=77 Identities=25% Similarity=0.287 Sum_probs=70.6
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCchhhhcccCCCCCcc
Q 038569 281 KKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESVQFNLMDSVCGPIVI 360 (362)
Q Consensus 281 kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~~~~~~d~~~~~~~~ 360 (362)
.||.|+-|+.++.+.|+.-|.+ |.|.|+.-|+.||.++||.+.||.+||+|+|.++||.........+..+..++|.
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~lmaqglyN 322 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHLMAQGLYN 322 (342)
T ss_pred hcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhhhcccccc
Confidence 4688999999999999999999 8999999999999999999999999999999999999888877777777777664
No 11
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.96 E-value=4.7e-10 Score=102.48 Aligned_cols=62 Identities=24% Similarity=0.346 Sum_probs=58.0
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 280 SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 280 ~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
+.||.|+.|+.++...|+..|.. +.|-.-.||..||+.++|+..||.+||||+|.|+|+.-.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 56888999999999999999999 999999999999999999999999999999999887543
No 12
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=98.96 E-value=1e-09 Score=83.58 Aligned_cols=53 Identities=17% Similarity=0.408 Sum_probs=50.6
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 038569 281 KKKKKGKLPKEARQILFDWWNLHYNWPY----PTEADKVALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 281 kkrkr~~lpke~~~iL~~wf~~H~~nPY----Ps~~eK~~LA~~TgLs~kQI~nWF~N~R 336 (362)
+||.|++|+.+|+..|+..|.. ++| |+..++..||..+||+..+|.+||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999 899 9999999999999999999999999964
No 13
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.96 E-value=3.2e-10 Score=111.32 Aligned_cols=62 Identities=24% Similarity=0.347 Sum_probs=57.8
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 280 SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 280 ~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
+.||||-.++|.|+..|++-|.- |-|.|++-|.+|++.++||.+||.+||||||.|.||...
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 45777888999999999999999 899999999999999999999999999999999998774
No 14
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.93 E-value=1.2e-09 Score=102.35 Aligned_cols=59 Identities=27% Similarity=0.405 Sum_probs=55.5
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 280 SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 280 ~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
+|||.|+.|+..|+..|+.-|.. ..|.+.++|..||.++.|++.||.+||||+|.+-|+
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKR 161 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKR 161 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHH
Confidence 58899999999999999999999 799999999999999999999999999999999443
No 15
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.90 E-value=7.8e-10 Score=106.35 Aligned_cols=62 Identities=23% Similarity=0.385 Sum_probs=57.4
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 280 SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 280 ~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
+.||.|+.|+..|+..|++-|.- |.|.+...|.+||..+.|+++||.+||||+|.+.||...
T Consensus 158 ~~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 47889999999999999999999 899999999999999999999999999999999665443
No 16
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.87 E-value=1.2e-09 Score=102.91 Aligned_cols=63 Identities=25% Similarity=0.314 Sum_probs=58.4
Q ss_pred hccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 279 FSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 279 ~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
+|.||.|+.++.-+.+.|+.-|++ ..|.--.||.+||..+||++.||.+||+|+|-+.||.+.
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 356788999999999999999999 899999999999999999999999999999999888665
No 17
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.81 E-value=3.1e-09 Score=106.84 Aligned_cols=65 Identities=25% Similarity=0.390 Sum_probs=60.9
Q ss_pred hhhccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 277 HEFSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 277 ~e~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
...+|||||+.+...++..|+..|.+ ||-|+.+|.-.||++++|....|++||+|||.|.|+...
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 34478999999999999999999999 999999999999999999999999999999999988766
No 18
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.81 E-value=3.5e-09 Score=104.34 Aligned_cols=62 Identities=24% Similarity=0.407 Sum_probs=56.4
Q ss_pred hccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 279 FSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 279 ~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
+++||.|+.|+..|+..|++-|.. -.|.+..+|..||...||+-.||.+||||||.|-|+..
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 567888999999999999999999 79999999999999999999999999999999944433
No 19
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.78 E-value=5.3e-09 Score=97.28 Aligned_cols=60 Identities=30% Similarity=0.349 Sum_probs=53.1
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 281 KKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 281 kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.++++.+|+.++...|+.-|.. +-|-.+..|..||++.||.+.||.+||||+|.|-|.+-
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 4566778999999999999999 68888899999999999999999999999999944433
No 20
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.76 E-value=3.9e-09 Score=103.66 Aligned_cols=64 Identities=20% Similarity=0.294 Sum_probs=57.7
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 280 SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 280 ~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
+|||+|--|++-|+-.|+.-|.+ ..|.+..||+.||...+||..||.+||||+|-|-|+...+.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 47777888999999999999999 89999999999999999999999999999999877755433
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.75 E-value=7.4e-09 Score=93.06 Aligned_cols=61 Identities=21% Similarity=0.425 Sum_probs=56.5
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 281 KKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 281 kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.+++|.+.+..++.+|+..|.. +|||+..+|..|+..++|+++-|+.||||+|.+.|+...
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred CcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 5677888999999999999999 999999999999999999999999999999999877543
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.70 E-value=7.2e-09 Score=101.50 Aligned_cols=67 Identities=21% Similarity=0.388 Sum_probs=60.6
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCchhhh
Q 038569 280 SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESVQFNL 350 (362)
Q Consensus 280 ~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~~~~~ 350 (362)
|++|.|+.|+..+.+.|+.||.+ |.||+.+.|++||..|+|+.+.|++||.|+|.+ |++-|+.+-+.
T Consensus 111 KqrrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrak-wrkrErN~~ae 177 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK-WRKRERNQQAE 177 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhh-hhhhhhhHHHH
Confidence 46788899999999999999999 999999999999999999999999999999999 66666665544
No 23
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.67 E-value=1.6e-08 Score=97.08 Aligned_cols=62 Identities=24% Similarity=0.434 Sum_probs=55.1
Q ss_pred cCCC-CCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 281 KKKK-KGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 281 kkrk-r~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
|||+ |+.|+..+...|++-|.+ --||+--.|+.||..|+|.+.+|++||+|+|.+ |++.|+.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAK-WRk~Ek~ 202 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAK-WRKTEKR 202 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHH-hhhhhhh
Confidence 3444 899999999999999999 899999999999999999999999999999998 5555443
No 24
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.64 E-value=2.2e-08 Score=93.51 Aligned_cols=70 Identities=19% Similarity=0.267 Sum_probs=63.7
Q ss_pred cchhhhhhhhccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 270 GYISTLKHEFSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 270 ~~i~~lk~e~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
-.+..|++....||.|+.|+..|...|++-|.+ ..|.+.+||.+++..+.|+..||.+||||+|.|.|+-
T Consensus 133 p~~C~LrKhk~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 133 PTTCTLRKHKPNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred cccchhcccCCCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 344677777788999999999999999999999 7999999999999999999999999999999997763
No 25
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.61 E-value=1.1e-08 Score=92.47 Aligned_cols=68 Identities=21% Similarity=0.329 Sum_probs=62.4
Q ss_pred hhccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCchh
Q 038569 278 EFSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESVQF 348 (362)
Q Consensus 278 e~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~~~ 348 (362)
..+++|.|+.|+..+...|++-|+. -.|.+-.++.+||...+|+.+||..||+|+|.++||..++.+.
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p 164 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQP 164 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 4567888999999999999999998 6899999999999999999999999999999999998877763
No 26
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.58 E-value=4.2e-08 Score=92.21 Aligned_cols=59 Identities=17% Similarity=0.373 Sum_probs=55.3
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 280 SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 280 ~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
+.+|.|+.|+..+..+|+..|.+ ..||+...+++||.+.+|...+|++||.|+|++-|+
T Consensus 36 kqRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~ 94 (228)
T KOG2251|consen 36 KQRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRR 94 (228)
T ss_pred hcccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhH
Confidence 46889999999999999999999 899999999999999999999999999999998443
No 27
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.50 E-value=3.6e-08 Score=94.96 Aligned_cols=61 Identities=28% Similarity=0.347 Sum_probs=55.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 283 KKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 283 rkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
|-|-.++..||-.|++-|-. ++|.|..-|.+||..+||+++||.+||||||.+.||...+.
T Consensus 201 KYRvVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 44667899999999999998 89999999999999999999999999999999988766555
No 28
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.46 E-value=1.1e-07 Score=80.50 Aligned_cols=67 Identities=16% Similarity=0.279 Sum_probs=59.9
Q ss_pred hhhhhccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 275 LKHEFSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 275 lk~e~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
+.+..+.+|-|+.|+.-+...|+..|.+ .-||+.-.|++||....|+...|++||+|+|.+.+|...
T Consensus 11 l~ekrKQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 11 LTEKRKQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hhHHHHhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 3444456778899999999999999999 799999999999999999999999999999999888654
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.35 E-value=2.3e-07 Score=90.39 Aligned_cols=69 Identities=25% Similarity=0.410 Sum_probs=61.9
Q ss_pred hhhhhhhhccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 272 ISTLKHEFSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 272 i~~lk~e~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
...|.-+...||.|+.++-.+...|+.-|.. .|-|-.-.|++|+.+|||+.+.|++||||+|.+.|+-.
T Consensus 158 ~~~l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 158 CNELEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred ccccccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 3356667788999999999999999999998 89999999999999999999999999999998765544
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.13 E-value=2.8e-06 Score=88.64 Aligned_cols=58 Identities=17% Similarity=0.301 Sum_probs=55.1
Q ss_pred hccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhc
Q 038569 279 FSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRH 339 (362)
Q Consensus 279 ~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~ 339 (362)
...||.|-.|+..+++.|...|.+ +++|+.+..+.|+.++||....|.|||-|+|||.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 456888999999999999999999 9999999999999999999999999999999994
No 31
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=98.05 E-value=2.5e-06 Score=83.81 Aligned_cols=59 Identities=19% Similarity=0.271 Sum_probs=52.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 283 KKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 283 rkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
|-|+-|+++|+..|++-|++ .-|-+...|.+||..++|.+..|.+||||+|.+.|+...
T Consensus 183 RYRTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 183 RYRTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 44788999999999988888 689999999999999999999999999999999766543
No 32
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.02 E-value=4.9e-06 Score=83.56 Aligned_cols=64 Identities=20% Similarity=0.452 Sum_probs=57.8
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 280 SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 280 ~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
+.+|.|+.|+..+...|+++|.. +|||.-..|+.||.+|+|+...|+.||.|+|.|.+|....+
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~~ 238 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRDC 238 (354)
T ss_pred cccccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccccc
Confidence 45666889999999999999999 89999999999999999999999999999999877766543
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.94 E-value=3.8e-06 Score=77.15 Aligned_cols=62 Identities=24% Similarity=0.242 Sum_probs=57.1
Q ss_pred hccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 279 FSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 279 ~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
+++++.|..|+..+...|+.-|.. .+||+...++.||..+++++..|.+||+|+|++.++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 457888999999999999999999 69999999999999999999999999999999976543
No 34
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.89 E-value=3.5e-06 Score=82.26 Aligned_cols=67 Identities=25% Similarity=0.445 Sum_probs=58.1
Q ss_pred hhhhhhhhccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 272 ISTLKHEFSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 272 i~~lk~e~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
|..+-....|||||+.+--.-++-|+++|.. -|-|+.+-...||++..|....|++||+|+|.+.|+
T Consensus 300 ~~~l~~~~ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 300 INELLPGGEKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred hhhccCccccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 3344444557888888888888999999999 899999999999999999999999999999999776
No 35
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.89 E-value=6.1e-06 Score=77.97 Aligned_cols=63 Identities=21% Similarity=0.300 Sum_probs=55.6
Q ss_pred hhhccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 277 HEFSKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 277 ~e~~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
+.-+||..|..|+..++..|+.-|.+ ..||--.++.+||...|+++.||.+||||+|.+-+|+
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 33456667778999999999999999 7999999999999999999999999999999985444
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.32 E-value=8.8e-05 Score=73.36 Aligned_cols=62 Identities=34% Similarity=0.574 Sum_probs=56.7
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 281 KKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 281 kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
..++++.++.+. ..|+.|...|..+|||++.++..|+..|+++..||++||+|.|+|+++..
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 456678899999 99999999999999999999999999999999999999999999976643
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.90 E-value=0.00091 Score=50.88 Aligned_cols=43 Identities=21% Similarity=0.356 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 038569 293 RQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKR 338 (362)
Q Consensus 293 ~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR 338 (362)
++.|+++|.. +.++.+.+-..|+.+|+|+..||..||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 5669999999 599999999999999999999999999877654
No 38
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=96.80 E-value=0.00059 Score=42.70 Aligned_cols=22 Identities=64% Similarity=1.094 Sum_probs=20.3
Q ss_pred HHHHHHHHhhccchhhhhhhhc
Q 038569 259 ETKDNLIRKYGGYISTLKHEFS 280 (362)
Q Consensus 259 eLk~~L~rkys~~i~~lk~e~~ 280 (362)
|||.+|+|+|+++|+++++||.
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 5899999999999999999974
No 39
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=96.65 E-value=0.013 Score=54.52 Aligned_cols=136 Identities=18% Similarity=0.224 Sum_probs=78.7
Q ss_pred HHHHHHHHHhhCCChHHHHHHHHhhHh-ccC---------chh-hhhhHHHHH-hhccccCcccccCCCC---CCCCCcc
Q 038569 114 VSSAIRAQIASHPLYPKLLQAYIDCQK-VGA---------SPE-IANVLDDIR-REGDVSNRNWVVSSCC---WGADPEL 178 (362)
Q Consensus 114 ~~~~~Ka~I~sHPLYp~Ll~Ayi~C~K-Vga---------Ppd-~~~~Ldei~-~~~~~~~~~~~~~~~~---~g~dpEL 178 (362)
+..+.|.+|.+||+||.|..+.++-.. ++. |+| .+.+||.+. ++...+...++..... .+++..+
T Consensus 25 eaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~~~ 104 (191)
T PF03792_consen 25 EAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPPDPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADNSI 104 (191)
T ss_pred HHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCCchhhhhhhcchhhhcCcCCCCcccchhhhhccCccccc
Confidence 349999999999999999999988774 221 444 778999865 4555444332111111 1123333
Q ss_pred cH--HHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCCCCCcccCCCCCccccccCCCCcc
Q 038569 179 DE--FMETYCDILVKYKSDLSKPYDEASSFLNNMETQLSNLCNVVSRSHGSDEADPGGSWEEDLSGGETEVSECFRMPPV 256 (362)
Q Consensus 179 Dq--FMe~Yc~~L~kykeEL~kp~~EA~~Fc~~iE~QL~~L~~gss~s~~sde~~~~~SSeee~sgGe~d~~e~d~~~~e 256 (362)
|+ +-..--++=..|..||++-..-|.+||..+..=|+.=.. .+ +..+.+
T Consensus 105 d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~lLreQs~--~R---------------------------PIs~ke 155 (191)
T PF03792_consen 105 DHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMNLLREQSE--FR---------------------------PISPKE 155 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhcc--cC---------------------------CCCHHH
Confidence 32 222222233344555554445566666665554443111 00 011245
Q ss_pred cHHHHHHHHHhhccchhhhhhh
Q 038569 257 DRETKDNLIRKYGGYISTLKHE 278 (362)
Q Consensus 257 d~eLk~~L~rkys~~i~~lk~e 278 (362)
-+.+...+.+||+++...||+.
T Consensus 156 iE~m~~~i~~Kf~~iq~qLKQs 177 (191)
T PF03792_consen 156 IERMVNIIHRKFSKIQMQLKQS 177 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5667888889999999998775
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.18 E-value=0.0035 Score=57.53 Aligned_cols=60 Identities=28% Similarity=0.494 Sum_probs=54.7
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 280 SKKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 280 ~kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
+.++.+..+...+...|..-|.. .+||+...+..|+..+|++...|.+||+|+|.+.++.
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred ccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 45677888999999999999988 8999999999999999999999999999999998754
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=93.20 E-value=0.064 Score=61.70 Aligned_cols=63 Identities=22% Similarity=0.298 Sum_probs=58.1
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 281 KKKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 281 kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
+++.|..++..+..+++..|.. --||++++-+.|.+..+|....|..||+|.|.+.+|+-++-
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 5677888999999999999999 89999999999999999999999999999999999988743
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=88.49 E-value=0.92 Score=33.64 Aligned_cols=48 Identities=19% Similarity=0.255 Sum_probs=33.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhh
Q 038569 282 KKKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRK 337 (362)
Q Consensus 282 krkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~Rr 337 (362)
||+|..|+-+..-.+-..+.. .+ -+..||+..|++..+|..|..|+.+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~~ 48 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKDK 48 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHHH
Confidence 467788998886666566666 23 6889999999999999999999643
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=81.05 E-value=2.3 Score=47.16 Aligned_cols=44 Identities=20% Similarity=0.462 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhc
Q 038569 293 RQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRH 339 (362)
Q Consensus 293 ~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~ 339 (362)
..+|+.+|.. |+.|++++-..+|.+-||...-|..||.+.+...
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh
Confidence 7888999999 9999999999999999999999999999998764
No 44
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=78.30 E-value=3.6 Score=27.92 Aligned_cols=46 Identities=17% Similarity=0.289 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHW 340 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~k 340 (362)
.++...+.++...+... ..-..+|+.+|++..+|..|....+++.|
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46788888887776542 24567899999999999999998888754
No 45
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=77.61 E-value=4 Score=31.10 Aligned_cols=46 Identities=15% Similarity=0.279 Sum_probs=30.8
Q ss_pred CCCCCCCHHHHHHH-HHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 038569 283 KKKGKLPKEARQIL-FDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 283 rkr~~lpke~~~iL-~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~R 336 (362)
++++.||.+.+..+ ...+.. ......+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 45677999985544 444344 26788999999999999999988776
No 46
>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=75.57 E-value=4.4 Score=29.12 Aligned_cols=44 Identities=20% Similarity=0.373 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKR 338 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR 338 (362)
.||+..+.++.-.+... -.-.++|+.+|++...|.+|....|++
T Consensus 10 ~L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 47888888887665552 456789999999999999999999886
No 47
>PRK00118 putative DNA-binding protein; Validated
Probab=74.97 E-value=1.7 Score=36.95 Aligned_cols=55 Identities=11% Similarity=0.064 Sum_probs=45.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCchhh
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESVQFN 349 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~~~~ 349 (362)
.+|..++.++..++... ..-..+|+.+|+++..|.+|....|++.++..++++|-
T Consensus 17 ~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~ 71 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLY 71 (104)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChH
Confidence 47888899987776662 34567999999999999999999999999887777653
No 48
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=73.55 E-value=10 Score=22.83 Aligned_cols=40 Identities=13% Similarity=0.115 Sum_probs=28.1
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhh
Q 038569 285 KGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWF 332 (362)
Q Consensus 285 r~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF 332 (362)
+..++.+.+..+..++.. .+ ....+|+.+|++...|.+|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 334666666666565543 33 45688999999999999984
No 49
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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 is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; 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: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=71.39 E-value=4.3 Score=28.96 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHW 340 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~k 340 (362)
.||+..+.+|...|.. . ..-.++|+..|++...|..+...+.+++|
T Consensus 4 ~L~~~er~vi~~~y~~----~----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----G----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----C----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 5888999999888754 2 34578999999999999999998888865
No 50
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=68.98 E-value=3.8 Score=35.37 Aligned_cols=54 Identities=15% Similarity=0.216 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCchh
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESVQF 348 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~~~ 348 (362)
+||+..+.++.-.+.+. -.-.++|+.+|++...|.+++.-+|+++++...+..|
T Consensus 106 ~Lp~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 159 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--------KSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEEF 159 (160)
T ss_pred hCCHHHHHHHHHHHHhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 38999999987765552 2345899999999999999999999998887665544
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=64.15 E-value=8.2 Score=32.89 Aligned_cols=47 Identities=13% Similarity=0.164 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
.||+..+.++...|... -.-.++|+.+|++...|.+|....|+++++
T Consensus 106 ~L~~~~r~ii~l~~~~~--------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG--------KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 58999999886655442 236789999999999999999999999875
No 52
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=63.88 E-value=6.6 Score=35.13 Aligned_cols=53 Identities=13% Similarity=0.107 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 285 KGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 285 r~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
...|++.++++|... .+ . -...++|+.+|++...|.+|...+|+++++-....
T Consensus 4 ~~~Lt~rqreVL~lr-~~----G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ER----G----LTQQEIADILGTSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred ccCCCHHHHHHHHHH-Hc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999773 33 2 24568999999999999999999999877655443
No 53
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=63.11 E-value=5.3 Score=34.76 Aligned_cols=53 Identities=15% Similarity=0.001 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 286 GKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 286 ~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
..||..++.++.-++..+ ..-.++|..+|++...|.+|..-.|+++++..+..
T Consensus 107 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 159 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--------LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 357999999998776553 34578999999999999999999999988765443
No 54
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=59.25 E-value=7.9 Score=34.06 Aligned_cols=49 Identities=12% Similarity=0.100 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.++...+.. .+ .-.++|+.+|++...|.+++..+|+++|+..
T Consensus 129 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 177 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE----GL----SYKELAERHDVPLNTMRTWLRRSLLKLRECL 177 (179)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence 3788888888777765 22 3568999999999999999999999988754
No 55
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=58.04 E-value=11 Score=30.84 Aligned_cols=48 Identities=21% Similarity=0.276 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
.||+..+.++...+.. .+ .-..+|+.+|+++..|.+|....++++++.
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4677888887554433 33 345899999999999999999999987753
No 56
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=55.75 E-value=9.7 Score=33.66 Aligned_cols=52 Identities=12% Similarity=-0.021 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
.||+..+.++.-.+... -.-.++|+.+|++...|.+++..+|+++++..++.
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~~ 182 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--------ASIKETAAKLSMSEGAVRVALHRGLAALAAKFRSE 182 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Confidence 58999999998865552 34578999999999999999999999988776553
No 57
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=55.65 E-value=13 Score=31.83 Aligned_cols=49 Identities=24% Similarity=0.230 Sum_probs=39.2
Q ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 286 GKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 286 ~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
..||...+.++...+.. . -.-.++|+.+|++...|.++..-.|+++++.
T Consensus 110 ~~L~~~~r~v~~l~~~~----g----~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~ 158 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR----G----VSLTALAEQLGRTVNAVYKALSRLRVRLRDC 158 (159)
T ss_pred HHCCHHHHHHHHHHHhc----C----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence 35899999998875544 2 2346899999999999999999999988763
No 58
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=54.19 E-value=23 Score=24.36 Aligned_cols=45 Identities=16% Similarity=0.184 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHW 340 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~k 340 (362)
.|+...+.++..++ . . ....++|+.+|++...|..|....+++..
T Consensus 3 ~l~~~e~~i~~~~~-~----g----~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLA-E----G----LTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHH-c----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 47777777775542 2 2 24578999999999999999998877754
No 59
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=53.78 E-value=20 Score=30.16 Aligned_cols=48 Identities=21% Similarity=0.214 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
.||...+.++...+.. .+ .-.++|+.+|++...|.++....|+++++.
T Consensus 113 ~L~~~~r~il~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5788888888775544 33 345699999999999999999999998753
No 60
>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=53.69 E-value=9.4 Score=33.61 Aligned_cols=50 Identities=10% Similarity=-0.034 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||+..++++.-.+..+ ..-.++|+.+|++...|.++....|+++++...
T Consensus 138 ~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG--------LSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred cCCHHHhhhhhhhhhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 36788888886654442 345789999999999999999999999887653
No 61
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=52.53 E-value=12 Score=27.49 Aligned_cols=24 Identities=17% Similarity=0.314 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhh
Q 038569 313 DKVALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 313 eK~~LA~~TgLs~kQI~nWF~N~R 336 (362)
....||+.+|++..+|+.|+.+..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 567899999999999999999773
No 62
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=52.33 E-value=14 Score=31.81 Aligned_cols=50 Identities=24% Similarity=0.179 Sum_probs=40.3
Q ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 286 GKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 286 ~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
..||..++.++.-.+... -.-.++|+.+|++...|..+....|+++++..
T Consensus 111 ~~L~~~~r~v~~l~~~~~--------~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG--------FSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HHCCHHHHHHhhhHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 358999999987765552 23468999999999999999999999987643
No 63
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=51.98 E-value=12 Score=33.67 Aligned_cols=49 Identities=10% Similarity=-0.046 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.+|.-.+... -.-.++|+.+|++...|.+++...|+++++..
T Consensus 142 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 48999999997665552 34578999999999999999999999987654
No 64
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=51.81 E-value=12 Score=33.95 Aligned_cols=52 Identities=19% Similarity=0.126 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
.||..++.++.-.+.. .+ .-.++|+.+|++...|.+++.-.|+++++..+..
T Consensus 113 ~Lp~~~r~v~~L~~~~----g~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~~ 164 (188)
T PRK12546 113 QLPDEQREALILVGAS----GF----SYEEAAEMCGVAVGTVKSRANRARARLAELLQLE 164 (188)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 5899999999777555 22 3467999999999999999999999988766543
No 65
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=51.02 E-value=14 Score=31.82 Aligned_cols=49 Identities=16% Similarity=0.175 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
||+..+.++...+.. . -.-.++|+..|++...|.+|..-+|+++++..+
T Consensus 126 L~~~~r~i~~l~~~~----~----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 126 LPVKQREVFLLRYVE----G----LSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHhhHHHHc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 788888888665544 2 234789999999999999999999999876544
No 66
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=49.68 E-value=15 Score=31.65 Aligned_cols=49 Identities=16% Similarity=0.075 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.|++..+.++...+.. -+ .-..+|+.+|++...|.+|....|+++++..
T Consensus 128 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIE----GL----SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888765444 22 3458999999999999999999999987644
No 67
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=49.26 E-value=19 Score=32.16 Aligned_cols=50 Identities=26% Similarity=0.310 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
+||+..+.++.-.|... -.-.++|+.+|++...|.+...-.|+++++...
T Consensus 131 ~L~~~~r~i~~l~~~~g--------~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--------EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred hCCHHHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 58999999998655542 235689999999999999999999999887654
No 68
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=48.76 E-value=9.8 Score=34.19 Aligned_cols=52 Identities=8% Similarity=0.101 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
.||..++.++.-.+..- -.-.++|+.+|+++..|.++..-+|+++++.....
T Consensus 134 ~Lp~~~R~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 185 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--------LSSEQICQECDISTSNLHVLLYRARLQLQACLSKN 185 (189)
T ss_pred hCCHHHHHHHhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899988887766552 23578999999999999999999999988765443
No 69
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=48.71 E-value=13 Score=33.87 Aligned_cols=50 Identities=10% Similarity=0.076 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||+.++.++...+... -.-.++|+.+|++...|.+++..+|+++++..+
T Consensus 153 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--------LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 47899999987655442 345789999999999999999999999876553
No 70
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=46.71 E-value=23 Score=25.89 Aligned_cols=45 Identities=13% Similarity=0.100 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHW 340 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~k 340 (362)
.|++....+|..+..- ....++|+..|++++.|..+..+.++|..
T Consensus 3 ~LT~~E~~vl~~l~~G---------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG---------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT---------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc---------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 4778888888776655 35678999999999999999999999854
No 71
>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=46.32 E-value=20 Score=31.47 Aligned_cols=48 Identities=10% Similarity=0.027 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
.||+.++.++.-.+.+. -.-.++|+.+|++...|.+.+..+|+++++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG--------LTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999998776652 2346899999999999999999999997653
No 72
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=46.06 E-value=18 Score=31.99 Aligned_cols=50 Identities=16% Similarity=0.042 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||+..+.++.-.+.+. -.-.++|+.+|++...|.+.+..+|+++++...
T Consensus 129 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~ 178 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG--------LSVAETAQLTGLSESAVKVGIHRGLKALAAKIR 178 (181)
T ss_pred HCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 36888888776555442 245789999999999999999999999887554
No 73
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=45.60 E-value=18 Score=32.12 Aligned_cols=49 Identities=18% Similarity=0.098 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+.++.++..-+... ..-.++|+.+|++...|..+...+|+++++..
T Consensus 139 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 139 TLPEKQREILILRVVVG--------LSAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888887755542 34678999999999999999999999987653
No 74
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=45.51 E-value=14 Score=32.40 Aligned_cols=49 Identities=14% Similarity=0.102 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.++...+.. . ..-.++|+.+|++...|.+++...|+++++..
T Consensus 136 ~L~~~~r~v~~l~~~~----g----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----D----LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4888898888664433 1 24568999999999999999999999987644
No 75
>PF13518 HTH_28: Helix-turn-helix domain
Probab=43.86 E-value=22 Score=24.83 Aligned_cols=25 Identities=16% Similarity=0.417 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhh
Q 038569 313 DKVALAESTGLDQRQINNWFINQRK 337 (362)
Q Consensus 313 eK~~LA~~TgLs~kQI~nWF~N~Rr 337 (362)
....+|++.|++..+|..|....+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3556999999999999999887765
No 76
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=43.46 E-value=22 Score=31.01 Aligned_cols=48 Identities=15% Similarity=0.019 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
.||+..++++.-.+... -.-.++|+.+|++...|.++..-.|+++++.
T Consensus 112 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGASG--------FSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 47999999887766552 2356899999999999999999999997754
No 77
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=43.23 E-value=17 Score=31.10 Aligned_cols=50 Identities=18% Similarity=0.182 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
+||+.++.++.-.+.+ .+ .-.++|+.+|++...|.+...-.|+++++...
T Consensus 106 ~Lp~~~r~v~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 106 KLPARQREAFLLRYWE----DM----DVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hCCHHHHHHHHHHHHh----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999775555 22 24689999999999999999999999876554
No 78
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=43.05 E-value=14 Score=33.16 Aligned_cols=51 Identities=10% Similarity=0.082 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
.||+.++.++.-.+.+. -.-.++|+.+|++...|.++...+|+++++..+.
T Consensus 136 ~L~~~~r~i~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 186 (195)
T PRK12532 136 NLPENTARVFTLKEILG--------FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186 (195)
T ss_pred hCCHHHHHHhhhHHHhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 48899988887654442 2457899999999999999999999998886643
No 79
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=42.80 E-value=25 Score=31.94 Aligned_cols=56 Identities=18% Similarity=0.071 Sum_probs=44.4
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCchhhh
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESVQFNL 350 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~~~~~ 350 (362)
+||+..+.++.--+... ..-.++|+.+|++...|.++...+|+++++.....+-..
T Consensus 133 ~Lp~~~r~v~~l~~~~g--------~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~ 188 (196)
T PRK12535 133 ALPPERREALILTQVLG--------YTYEEAAKIADVRVGTIRSRVARARADLIAATATGQASA 188 (196)
T ss_pred cCCHHHHHHhhhHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccchh
Confidence 48898888886665553 245789999999999999999999999988776655433
No 80
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=42.47 E-value=21 Score=31.69 Aligned_cols=50 Identities=10% Similarity=0.163 Sum_probs=39.3
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
||+..+.++..-|... ..-.++|+.+|++...|.++...+|+++++...+
T Consensus 129 L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 129 LPERQREAIVLQYYQG--------LSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred CCHHHHHHhhHHHhcC--------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 6888888886644442 2456899999999999999999999998876543
No 81
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=41.94 E-value=22 Score=30.51 Aligned_cols=50 Identities=16% Similarity=0.236 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||...+.++...+.. . -.-.++|+.+|++...|.++....|+++++..+
T Consensus 110 ~L~~~~r~i~~l~~~~----g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE----D----LSEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred hCCHHHHHHhhhHHHh----c----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 4788888888666554 2 234679999999999999999999999877543
No 82
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=41.67 E-value=25 Score=31.18 Aligned_cols=48 Identities=13% Similarity=0.194 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
+||+.++.++..-+... ..-.++|+.+|++...|.+|...+|+++++.
T Consensus 133 ~L~~~~r~i~~l~~~~~--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYVDG--------CSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 47888888776655442 2457899999999999999999999998764
No 83
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=41.36 E-value=25 Score=30.28 Aligned_cols=49 Identities=18% Similarity=0.282 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||..++.+|.-.+ . . -.-.++|+.+|++...|.++....|+++|+...
T Consensus 112 ~L~~~~r~il~l~~-~----g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----G----YSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred cCCHHHHHHHHHHH-c----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 37888888887766 5 2 245789999999999999999999999876543
No 84
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=41.19 E-value=24 Score=31.11 Aligned_cols=49 Identities=14% Similarity=0.049 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.+|.-.+... -.-.++|+.+|++...|.++...+|+++++..
T Consensus 135 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG--------YTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 38999999997655442 24578999999999999999999999987643
No 85
>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=40.59 E-value=25 Score=30.53 Aligned_cols=49 Identities=10% Similarity=0.072 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||...+.++..-+... ..-.++|+.+|++...|.++..-.|+++++..
T Consensus 119 ~L~~~~r~i~~l~~~~g--------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888886665552 24468999999999999999999999987644
No 86
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=40.26 E-value=20 Score=31.94 Aligned_cols=48 Identities=15% Similarity=0.123 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
.||++.+.++.--+... -.-.++|+.+|++...|.+|+..+|+++++.
T Consensus 141 ~L~~~~~~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 141 QLPESQRQVLELAYYEG--------LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hCCHHHhhhhhhhhhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888886654441 3457899999999999999999999998764
No 87
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=40.22 E-value=52 Score=22.77 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
|+.....++..++ . . ....++|+.+|++...|..|..-.+++..-+
T Consensus 1 l~~~e~~i~~~~~-~----~----~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 1 LTPREREVLRLLA-E----G----KTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCHHHHHHHHHHH-c----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 3455566664432 2 2 2557899999999999999998777765443
No 88
>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=39.91 E-value=29 Score=30.79 Aligned_cols=31 Identities=13% Similarity=0.040 Sum_probs=27.3
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 313 DKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 313 eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.-..+|+.+|++...|.+++.-.|+++++..
T Consensus 167 s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l 197 (198)
T TIGR02859 167 SYQEIACDLNRHVKSIDNALQRVKRKLEKYL 197 (198)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 4578999999999999999999999987654
No 89
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=39.83 E-value=53 Score=30.61 Aligned_cols=43 Identities=23% Similarity=0.427 Sum_probs=37.2
Q ss_pred CcccHHHHHHHHHHHHHHHHhcCch-HHHH-HHHHHHHHHhhhhc
Q 038569 176 PELDEFMETYCDILVKYKSDLSKPY-DEAS-SFLNNMETQLSNLC 218 (362)
Q Consensus 176 pELDqFMe~Yc~~L~kykeEL~kp~-~EA~-~Fc~~iE~QL~~L~ 218 (362)
-|||-...++-.++..|++.++-.+ .+|+ .|+..+..||-.+.
T Consensus 104 tELDVvL~~FEk~~~eYkq~ieS~~cr~AI~~F~~~~keqL~~~i 148 (175)
T PF13097_consen 104 TELDVVLSAFEKTALEYKQSIESKICRKAINKFYSNFKEQLIEMI 148 (175)
T ss_pred hHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHH
Confidence 5999999999999999999997765 6665 79999999988765
No 90
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=39.39 E-value=21 Score=33.31 Aligned_cols=52 Identities=17% Similarity=0.097 Sum_probs=42.7
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
.||..++.++.-.+..+ | .-.++|+.+|++...|.++....|+++++..+..
T Consensus 134 ~Lp~~~R~v~~L~y~eg----~----s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 134 KLPVEYREVLVLRELED----M----SYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred cCCHHHHhHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 57888999998877663 2 3467999999999999999999999998876543
No 91
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=39.17 E-value=30 Score=30.89 Aligned_cols=47 Identities=17% Similarity=0.083 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
.||..++.++.-.+... -.-.++|+.+|+++..|.++..-+|+++++
T Consensus 130 ~Lp~~~r~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLLG--------LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 58999999887665552 234689999999999999999999999887
No 92
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=38.36 E-value=20 Score=31.54 Aligned_cols=52 Identities=21% Similarity=0.130 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
+||+..+.+|.-.+.+. -.-.++|+.+|++...|.++..-.|+++++.....
T Consensus 100 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 151 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG--------LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETC 151 (170)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 48888889887766552 23568999999999999999999999988765543
No 93
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=38.27 E-value=38 Score=28.67 Aligned_cols=47 Identities=19% Similarity=0.161 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 286 GKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 286 ~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
..|++..+++|+-+ .++ |. ..++|+..+++.+.|.+|..+.|++..-
T Consensus 148 ~~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 35899999999874 442 22 5789999999999999999999999653
No 94
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=38.18 E-value=26 Score=31.21 Aligned_cols=57 Identities=11% Similarity=0.015 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCchhhh
Q 038569 285 KGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESVQFNL 350 (362)
Q Consensus 285 r~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~~~~~ 350 (362)
.+.|+..++.+|.-. .+ . -...++|+.+|++...|..|-...|+++++......+..
T Consensus 4 ~~~Lte~qr~VL~Lr-~~----G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~ 60 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EK----G----LSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVK 60 (137)
T ss_pred cCCCCHHHHHHHHHH-Hc----C----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHH
Confidence 567899999999763 23 2 256789999999999999999999999887655554443
No 95
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=38.14 E-value=30 Score=32.68 Aligned_cols=49 Identities=12% Similarity=0.129 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.+|.-.|... + .-.++|+.+|++...|..|....|+++++..
T Consensus 205 ~L~~~~r~vl~l~~~~g----~----s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----L----SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998766552 1 3478999999999999999999999987654
No 96
>cd00131 PAX Paired Box domain
Probab=37.41 E-value=1.1e+02 Score=26.53 Aligned_cols=48 Identities=13% Similarity=-0.051 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCC-------ChhhHhhhhhhh
Q 038569 285 KGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGL-------DQRQINNWFINQ 335 (362)
Q Consensus 285 r~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgL-------s~kQI~nWF~N~ 335 (362)
++++.......+..+..+ +|.-|..|-..+-...|+ +..+|+.||.++
T Consensus 73 pr~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 73 PRVATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCcCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 344555666666677777 798888877666335576 999999998764
No 97
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=37.15 E-value=33 Score=30.60 Aligned_cols=50 Identities=10% Similarity=0.122 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||+.++.++.-.+... + .-.++|+.+|++...|.+.....|+++++...
T Consensus 131 ~Lp~~~r~v~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE----L----ETEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47888888887665552 2 34689999999999999999999999877543
No 98
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=36.88 E-value=22 Score=31.47 Aligned_cols=50 Identities=18% Similarity=0.315 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
+||+.++.++.-.+... -.-.++|+.+|++...|.++..-+|+++++...
T Consensus 127 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~ 176 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE--------LSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176 (179)
T ss_pred hCCHHHhhHhHhHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 58999999986655552 234689999999999999999999999876443
No 99
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=36.20 E-value=30 Score=32.64 Aligned_cols=49 Identities=8% Similarity=0.085 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.++...|... -.-.++|..+|++...|.+++..+|+++|+..
T Consensus 201 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 249 (251)
T PRK07670 201 QLSEKEQLVISLFYKEE--------LTLTEIGQVLNLSTSRISQIHSKALFKLKKLL 249 (251)
T ss_pred cCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 37898999987766542 24578999999999999999999999987654
No 100
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=35.66 E-value=25 Score=32.76 Aligned_cols=49 Identities=12% Similarity=0.207 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||...+.++..-|... ..-.++|+.+|++...|.++...+|+++++..
T Consensus 184 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE--------LNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhccC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 37888888887765542 24578999999999999999999999987654
No 101
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=35.49 E-value=32 Score=24.40 Aligned_cols=21 Identities=24% Similarity=0.270 Sum_probs=18.6
Q ss_pred HHHHHHHhCCChhhHhhhhhh
Q 038569 314 KVALAESTGLDQRQINNWFIN 334 (362)
Q Consensus 314 K~~LA~~TgLs~kQI~nWF~N 334 (362)
...||+.+|+++..|..|..+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHhCCCcchhHHHhcC
Confidence 478999999999999999998
No 102
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=35.47 E-value=36 Score=30.27 Aligned_cols=49 Identities=16% Similarity=0.173 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.+|.--+.+ . -.-.++|+.+|++...|.+-+..+|+++++..
T Consensus 131 ~L~~~~r~vl~l~~~~----~----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYH----E----KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4799999999665544 1 24578999999999999999999999977643
No 103
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=35.20 E-value=42 Score=29.39 Aligned_cols=49 Identities=16% Similarity=0.256 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 286 GKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 286 ~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
..||+.++.++.-.+... -.-.++|+.+|++...|.++...+|+|.+..
T Consensus 118 ~~Lp~~~r~v~~L~~~~g--------~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDG--------MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 347899999887665552 2346899999999999999999999987543
No 104
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=35.15 E-value=36 Score=29.22 Aligned_cols=49 Identities=14% Similarity=0.089 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.++.-.|.. . -.-.++|+.+|++...|..+..-+|++.++..
T Consensus 109 ~L~~~~r~v~~l~~~~----~----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH----G----ETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999998765544 1 23578999999999999999998988877654
No 105
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=35.06 E-value=54 Score=29.45 Aligned_cols=51 Identities=12% Similarity=0.070 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
.||+.++.++.-.+.. .+ .-.++|+.+|++...|.+++.-+|+++++....
T Consensus 136 ~L~~~~r~i~~L~~~~----g~----s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 186 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GL----SNPEIAEVMEIGVEAVESLTARGKRALAALLAG 186 (196)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 5899998888765444 22 346899999999999999999999998876543
No 106
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 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.
Probab=34.83 E-value=37 Score=30.48 Aligned_cols=50 Identities=8% Similarity=0.078 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
+||..++.++...+... ..-.++|+.+|++..-|.++..-.|+++++...
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--------FESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred hCCHHHHHHHHHHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 57888888887765553 345789999999999999999999999887554
No 107
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=34.78 E-value=28 Score=30.85 Aligned_cols=50 Identities=16% Similarity=0.151 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||+..+.++.-.+... -.-.++|+.+|++...|.+....+|+++++...
T Consensus 122 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 171 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN--------LTYQEISSVMGITEANVRKQFERARKRVQNMIG 171 (185)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 48889999987644441 234689999999999999999999999877553
No 108
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=34.55 E-value=38 Score=29.88 Aligned_cols=52 Identities=13% Similarity=0.139 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
.||+..+.++.--+..+ -.-.++|+.+|++...|.+.....|+++++...+.
T Consensus 117 ~Lp~~~r~i~~l~~~e~--------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--------YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred hCCHHHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 48899988887755442 24578999999999999999999999988765443
No 109
>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=34.54 E-value=36 Score=32.09 Aligned_cols=48 Identities=10% Similarity=0.134 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
.||...+.++...|... + .-.++|+.+|++...|..+...+++++++.
T Consensus 205 ~L~~~~r~ii~l~~~~g----~----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN----L----SQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 58999999998776653 1 337899999999999999999999987763
No 110
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=34.38 E-value=37 Score=30.47 Aligned_cols=50 Identities=14% Similarity=0.147 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 286 GKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 286 ~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
..||+.++.++.-.+.+. -.-.++|+.+|++...|.+.+..+|+++++..
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--------~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--------LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 458899999997644442 23468999999999999999999999887654
No 111
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=34.32 E-value=32 Score=30.84 Aligned_cols=48 Identities=15% Similarity=0.106 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||...+.++..+|.. -.-.++|..+|+++..|.+.+...|+++++..
T Consensus 155 ~L~~~~r~vl~l~~e~---------~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 155 LLSELEKEVLELYLDG---------KSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred hCCHHHHHHHHHHHcc---------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4688888888774333 24568999999999999999999999987654
No 112
>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=34.29 E-value=39 Score=31.11 Aligned_cols=48 Identities=21% Similarity=0.310 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
.||+..+.++...+.. . ..-.++|+.+|++...|..|....++++++.
T Consensus 178 ~L~~~~r~vl~l~y~~----~----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 178 ALPERERRILLLRFFE----D----KTQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred cCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5899999999887654 1 2467899999999999999999999987653
No 113
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=34.17 E-value=32 Score=26.60 Aligned_cols=20 Identities=25% Similarity=0.508 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCChhhHhhhh
Q 038569 313 DKVALAESTGLDQRQINNWF 332 (362)
Q Consensus 313 eK~~LA~~TgLs~kQI~nWF 332 (362)
.-..||++.|++..||..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45679999999999999993
No 114
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=34.12 E-value=36 Score=30.62 Aligned_cols=52 Identities=17% Similarity=0.123 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
.||..++.++.-.+.. .+ .-.++|+.+|++...|.++....|+++++...+.
T Consensus 116 ~Lp~~~r~i~~L~~~~----g~----s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~ 167 (187)
T PRK12516 116 QLPDDQREAIILVGAS----GF----AYEEAAEICGCAVGTIKSRVNRARQRLQEILQIE 167 (187)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 3789998888776555 22 2358999999999999999999999988766543
No 115
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=33.97 E-value=34 Score=29.76 Aligned_cols=51 Identities=12% Similarity=0.195 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
.||+..+.+|.--+... + .-.++|+.+|++...|.....-+|+++++..+.
T Consensus 118 ~L~~~~r~vl~L~~~~g----~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 168 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRG----W----STAQIAADLGIPEGTVKSRLHYALRALRLALQE 168 (173)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhc
Confidence 38999999987765552 2 346899999999999999999999998876543
No 116
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=33.86 E-value=37 Score=31.15 Aligned_cols=51 Identities=14% Similarity=0.087 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
.||+..+.++.--+... + .-.++|+.+|++...|.++..-+|+++++..+.
T Consensus 138 ~L~~~~r~v~~L~~~~g----~----s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG----L----SYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 47888888775554442 2 346899999999999999999999998876543
No 117
>PRK06930 positive control sigma-like factor; Validated
Probab=33.74 E-value=25 Score=31.95 Aligned_cols=54 Identities=7% Similarity=0.135 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCchh
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESVQF 348 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~~~ 348 (362)
.||+..+.++.-.+.. . ..-.++|+.+|++...|..++...|+++++......|
T Consensus 114 ~L~~rer~V~~L~~~e----g----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~l~ 167 (170)
T PRK06930 114 VLTEREKEVYLMHRGY----G----LSYSEIADYLNIKKSTVQSMIERAEKKIARQINESLF 167 (170)
T ss_pred hCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4888888888775544 1 2456899999999999999999999998876655444
No 118
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=33.42 E-value=36 Score=30.22 Aligned_cols=50 Identities=12% Similarity=0.012 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||+.++.++.-.+... -.-.++|+.+|++...|.++....|+++++...
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--------LSVAEAATRSGMSESAVKVSVHRGLKALAALIG 180 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHh
Confidence 48999999998655442 345789999999999999999999999887553
No 119
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=33.42 E-value=39 Score=23.85 Aligned_cols=40 Identities=13% Similarity=0.101 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhh
Q 038569 286 GKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFI 333 (362)
Q Consensus 286 ~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~ 333 (362)
..|+.+.+..+..|+.+. ....+||+..|.+...|.+|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G--------~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG--------MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS-----------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC--------CCHHHHHHHHCcCcHHHHHHHh
Confidence 458888888888887662 3456799999999999999864
No 120
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=32.96 E-value=32 Score=32.46 Aligned_cols=50 Identities=12% Similarity=0.157 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||..++.++.-.+.+. -.-.++|+.+|++...|.++....|+++|+..+
T Consensus 171 ~Lp~~~R~v~~L~~~eg--------~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN--------MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred hCCHHHHHHhhhHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46888888876555441 245789999999999999999999999887554
No 121
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=32.46 E-value=19 Score=32.18 Aligned_cols=50 Identities=16% Similarity=0.191 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||+..+.++.-.+.. . ..-.++|+.+|++...|.++...+|+++++...
T Consensus 139 ~L~~~~r~i~~l~~~~----g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 139 TLPDEQREVFLLREHG----D----LELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred hCCHhHhhheeeehcc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3677777777654433 2 234679999999999999999999999876543
No 122
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=32.24 E-value=23 Score=33.79 Aligned_cols=51 Identities=10% Similarity=0.201 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
.||+..+.+|...|... ..-.++|+.+|++...|......+++++++...+
T Consensus 212 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 212 TLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 48888999887776552 3467899999999999999999999998776543
No 123
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=32.02 E-value=38 Score=29.97 Aligned_cols=49 Identities=10% Similarity=0.034 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.++...|.+. -.-.++|+.+|++...|.+....+|+++++..
T Consensus 137 ~L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 137 ELEPPRSELIRTAFFEG--------ITYEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 47888888887766542 23468999999999999999999999987643
No 124
>PRK04217 hypothetical protein; Provisional
Probab=31.92 E-value=59 Score=27.94 Aligned_cols=54 Identities=11% Similarity=-0.079 Sum_probs=42.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 283 KKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 283 rkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
..-..++.+.+.++..++.+. + .-.++|+.+|++...|.+.+...|+++++...
T Consensus 38 ~p~~~Lt~eereai~l~~~eG----l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 38 KPPIFMTYEEFEALRLVDYEG----L----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred CCcccCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 345568899998888777652 1 56779999999999999999999998866543
No 125
>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=31.64 E-value=41 Score=30.99 Aligned_cols=48 Identities=13% Similarity=0.188 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
.||...+.+|...|... ..-.++|+.+|++...|..+...+++++++.
T Consensus 175 ~L~~~~r~il~l~y~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE--------LNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhCC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999998877652 2457899999999999999999999987754
No 126
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 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 (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=31.55 E-value=21 Score=31.88 Aligned_cols=50 Identities=22% Similarity=0.089 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||...+.++.-.+.. . -.-.++|+.+|++...|.++..-+|+++++...
T Consensus 131 ~Lp~~~r~i~~L~~~~----g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLADVE----G----FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehhhc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4777787777554433 1 245689999999999999999999999887664
No 127
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=30.96 E-value=37 Score=29.72 Aligned_cols=49 Identities=14% Similarity=0.129 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||...+.+|.-.+.. . ..-.++|+.+|++...|.++....|+++++..
T Consensus 136 ~L~~~~r~il~l~~~~----~----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYIE----D----LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHhh----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3688888888543333 1 34578999999999999999999999987643
No 128
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=30.92 E-value=42 Score=29.97 Aligned_cols=49 Identities=16% Similarity=0.018 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+.++.++.-.+.+ . -.-.++|..+|++...|.+.+..+|+++++..
T Consensus 106 ~L~~~~r~i~~l~~~~----g----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELE----G----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhc----C----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888665544 2 24568999999999999999999999877644
No 129
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=30.82 E-value=47 Score=30.55 Aligned_cols=51 Identities=14% Similarity=0.166 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
.||+.++.++.--+... -.-.++|+.+|++...|.++..-.|+++++..+.
T Consensus 148 ~L~~~~r~v~~L~~~~g--------~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~ 198 (206)
T PRK12544 148 GLPAKYARVFMMREFIE--------LETNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198 (206)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 47888888887666552 2347899999999999999999999998886653
No 130
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=30.71 E-value=45 Score=29.12 Aligned_cols=49 Identities=8% Similarity=0.083 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||..++.++.-.+... ..-.++|+.+|++...|..+....|+++++..
T Consensus 119 ~L~~~~r~i~~l~~~~~--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQ--------YSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 47887877776554442 23468999999999999999999999987654
No 131
>PF13551 HTH_29: Winged helix-turn helix
Probab=30.44 E-value=2.4e+02 Score=22.30 Aligned_cols=74 Identities=18% Similarity=0.139 Sum_probs=39.4
Q ss_pred HHHHHHHhhc-cchhhhhhh-hccCCCCCCCCHHHHHHHHHHHHHhcCCC--CCCHHHHHH-H-HHHh--CCChhhHhhh
Q 038569 260 TKDNLIRKYG-GYISTLKHE-FSKKKKKGKLPKEARQILFDWWNLHYNWP--YPTEADKVA-L-AEST--GLDQRQINNW 331 (362)
Q Consensus 260 Lk~~L~rkys-~~i~~lk~e-~~kkrkr~~lpke~~~iL~~wf~~H~~nP--YPs~~eK~~-L-A~~T--gLs~kQI~nW 331 (362)
.-...+++|. +-+..+... ....+.+..++.+....|.+++.++.... ..+...-.. | .+.+ .++...|..|
T Consensus 28 Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~ 107 (112)
T PF13551_consen 28 TVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRI 107 (112)
T ss_pred HHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHH
Confidence 3444455553 223344442 22233333399999999999999942111 223333332 3 2333 3778888887
Q ss_pred hh
Q 038569 332 FI 333 (362)
Q Consensus 332 F~ 333 (362)
+.
T Consensus 108 L~ 109 (112)
T PF13551_consen 108 LK 109 (112)
T ss_pred HH
Confidence 64
No 132
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=30.24 E-value=1.1e+02 Score=26.00 Aligned_cols=48 Identities=10% Similarity=0.081 Sum_probs=32.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhh
Q 038569 283 KKKGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRK 337 (362)
Q Consensus 283 rkr~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~Rr 337 (362)
+++++++.+.+...-..... +. .....+|+..|++..+|.+|..-.|.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~---~g----~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE---PG----MTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc---CC----CCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 44566888875544333333 23 24567899999999999999776654
No 133
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=29.97 E-value=46 Score=29.88 Aligned_cols=50 Identities=18% Similarity=0.036 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||+.++.++.-.+... + .-.++|+.+|++...|.++..-.|+++++...
T Consensus 111 ~Lp~~~R~v~~L~~~eg----~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG----L----SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999998766552 2 34689999999999999999999999876443
No 134
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=29.76 E-value=44 Score=23.37 Aligned_cols=26 Identities=15% Similarity=0.354 Sum_probs=17.5
Q ss_pred HHHHHHHHHhCCChhhHhhhhhhhhh
Q 038569 312 ADKVALAESTGLDQRQINNWFINQRK 337 (362)
Q Consensus 312 ~eK~~LA~~TgLs~kQI~nWF~N~Rr 337 (362)
....++|+.+|++...|.+|....+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT----
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 35678999999999999999766543
No 135
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=29.41 E-value=60 Score=27.90 Aligned_cols=45 Identities=11% Similarity=0.087 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhc
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRH 339 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~ 339 (362)
.||+.++.++.-.+... -.-.++|+.+|++...|.++...++++.
T Consensus 113 ~L~~~~r~v~~L~~~~g--------~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG--------LGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 47999999887665552 2346899999999999999999888774
No 136
>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=29.16 E-value=48 Score=31.59 Aligned_cols=51 Identities=12% Similarity=0.208 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
.||..++.++.-.+... -.-.++|..+|++...|.++...+|+++++..++
T Consensus 161 ~Lp~~~R~v~~L~~~eg--------~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~ 211 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG--------LSMDRIGAMYQVHRSTVSRWVAQARERLLERTRR 211 (244)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 47999988887776663 2356899999999999999999999998876543
No 137
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=29.13 E-value=50 Score=29.96 Aligned_cols=52 Identities=12% Similarity=0.134 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCCc
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSESV 346 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~~ 346 (362)
.||..++.++.-.+.+. + .-.++|+.+|++...|.+....+|+++++.....
T Consensus 139 ~Lp~~~r~v~~L~~~eg----~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 190 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD----F----EIDDICTELTLTANHCSVLLYRARTRLRTCLSEK 190 (201)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999988887765552 2 3468999999999999999999999988866433
No 138
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=29.05 E-value=53 Score=28.18 Aligned_cols=49 Identities=16% Similarity=0.175 Sum_probs=40.2
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
||+..+.++.-.+... -.-.++|+.+|++..-|.+....+|+++++...
T Consensus 106 L~~~~r~v~~l~~~~~--------~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 106 LPPACRDSFLLRKLEG--------LSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred CCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 8999999997776653 235789999999999999999999998776543
No 139
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=29.04 E-value=42 Score=29.84 Aligned_cols=49 Identities=14% Similarity=0.013 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
||...+.++.--+.. .| .-.++|+.+|++...|.+...-.|+++++...
T Consensus 139 L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 139 LPEDLRTALTLREFD----GL----SYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CCHHHhHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 677777777553333 33 34689999999999999999999999877543
No 140
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=29.03 E-value=43 Score=23.43 Aligned_cols=23 Identities=22% Similarity=0.235 Sum_probs=19.9
Q ss_pred HHHHHHHhCCChhhHhhhhhhhh
Q 038569 314 KVALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 314 K~~LA~~TgLs~kQI~nWF~N~R 336 (362)
...||+.+|+++..|..|....+
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46899999999999999987653
No 141
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=29.01 E-value=64 Score=28.56 Aligned_cols=48 Identities=6% Similarity=-0.001 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
+||++++.++.-.+.+. -.-.++|+.+|++...|...+..++++....
T Consensus 127 ~Lp~~~R~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--------MKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 48999999887766552 2346899999999999999999888886543
No 142
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 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 a limited number of Gram-positive bacterial lineages.
Probab=28.90 E-value=59 Score=27.91 Aligned_cols=49 Identities=8% Similarity=0.040 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 286 GKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 286 ~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
..||+..+.+|.-.+.. . ..-.++|+.+|++...|.+...-.|+++|+.
T Consensus 121 ~~L~~~~r~vl~l~~~~----g----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQ----N----LPIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred HhCCHHHHHHHHHHHhc----C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 35899999999875554 2 2346899999999999999998888887753
No 143
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=28.82 E-value=34 Score=23.99 Aligned_cols=21 Identities=10% Similarity=0.251 Sum_probs=19.1
Q ss_pred HHHHHhCCChhhHhhhhhhhh
Q 038569 316 ALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 316 ~LA~~TgLs~kQI~nWF~N~R 336 (362)
.||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999874
No 144
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 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.
Probab=28.71 E-value=57 Score=31.54 Aligned_cols=51 Identities=22% Similarity=0.168 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
+||+.++.++.-.+... + .-.++|+.+|++...|.+.+.-.|+++++....
T Consensus 142 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLG----W----RAAETAELLGTSTASVNSALQRARATLDEVGPS 192 (324)
T ss_pred hCCHHHhhHhhhHHHhC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence 47888888886655442 1 346899999999999999999999998887653
No 145
>PRK10072 putative transcriptional regulator; Provisional
Probab=28.69 E-value=43 Score=27.98 Aligned_cols=24 Identities=13% Similarity=0.232 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhh
Q 038569 313 DKVALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 313 eK~~LA~~TgLs~kQI~nWF~N~R 336 (362)
....||+.+|++...|++|...+|
T Consensus 48 TQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 48 KIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 367899999999999999998765
No 146
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=28.23 E-value=34 Score=31.71 Aligned_cols=53 Identities=25% Similarity=0.194 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.++.-.|.-+. -..-.-.++|+.+|++...|.++...+|+++|+..
T Consensus 178 ~Lp~~~R~v~~L~y~l~~----~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNG----GEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 488889888876552100 01124578999999999999999999999987654
No 147
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=28.17 E-value=52 Score=21.59 Aligned_cols=23 Identities=26% Similarity=0.319 Sum_probs=19.8
Q ss_pred HHHHHHHhCCChhhHhhhhhhhh
Q 038569 314 KVALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 314 K~~LA~~TgLs~kQI~nWF~N~R 336 (362)
...+|+.+|++...|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45899999999999999988753
No 148
>PF13730 HTH_36: Helix-turn-helix domain
Probab=27.84 E-value=1.7e+02 Score=20.82 Aligned_cols=49 Identities=14% Similarity=0.255 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHHh--cCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 038569 287 KLPKEARQILFDWWNLH--YNWPYPTEADKVALAESTGLDQRQINNWFINQRKR 338 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H--~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR 338 (362)
.|+..++.++-.-+... ....||+ ...||+.+|++.+.|..++..-+.+
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 35566655553322221 2247786 6789999999999999887655443
No 149
>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=27.65 E-value=1.1e+02 Score=21.58 Aligned_cols=40 Identities=15% Similarity=0.252 Sum_probs=26.2
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhh
Q 038569 285 KGKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWF 332 (362)
Q Consensus 285 r~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF 332 (362)
+.+++++....+..-+.. . .....+|+.+|++...|..++
T Consensus 3 p~~~~~~~~~~i~~l~~~----G----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAE----G----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSSHCCHHHHHHHHHT----T------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHC----C----CCHHHHHHHHCcCHHHHHHHH
Confidence 345666555555555544 2 357899999999999998776
No 150
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=26.23 E-value=55 Score=36.03 Aligned_cols=58 Identities=28% Similarity=0.309 Sum_probs=50.4
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHH---HHHHHHHhCCChhhHhhhhhhhhhhcC
Q 038569 281 KKKKKGKLPKEARQILFDWWNLHYNWPYPTEAD---KVALAESTGLDQRQINNWFINQRKRHW 340 (362)
Q Consensus 281 kkrkr~~lpke~~~iL~~wf~~H~~nPYPs~~e---K~~LA~~TgLs~kQI~nWF~N~RrR~k 340 (362)
+++++.+...+...+|..+...- --||+... -..|+.++.+..+.|...|+|.|.-.+
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~--gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~ 707 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDV--GLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVK 707 (769)
T ss_pred CccccceecccchHHHHHHHHHh--ccCchhhcccccchhhhhhcccHHHHHHhhhcceeecc
Confidence 67788889999999998887664 78999888 889999999999999999999987643
No 151
>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=26.06 E-value=1.4e+02 Score=22.48 Aligned_cols=47 Identities=23% Similarity=0.352 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhh
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQ 335 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~ 335 (362)
|+..++.+|+.-+..=+. -+|-...-..||+..|++..-+..-+.+.
T Consensus 1 LT~~Q~e~L~~A~~~GYf-d~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF-DVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHHHHHHcCCC-CCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 577888888877766432 34888889999999999999987654443
No 152
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.00 E-value=1.2e+02 Score=25.87 Aligned_cols=42 Identities=14% Similarity=0.324 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhh
Q 038569 290 KEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQ 335 (362)
Q Consensus 290 ke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~ 335 (362)
......+..|...|+..+ ++ -..||+.+|+++.++..+|...
T Consensus 8 ~~~i~~~~~~I~~~~~~~-~s---l~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNLESP-LS---LEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhcCCC-CC---HHHHHHHHCcCHHHHHHHHHHH
Confidence 344667788999987665 44 4678899999999999888754
No 153
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.98 E-value=54 Score=24.32 Aligned_cols=18 Identities=11% Similarity=0.200 Sum_probs=16.3
Q ss_pred HHHHHHhCCChhhHhhhh
Q 038569 315 VALAESTGLDQRQINNWF 332 (362)
Q Consensus 315 ~~LA~~TgLs~kQI~nWF 332 (362)
.++|+.+|++..+|..|-
T Consensus 4 ~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 578999999999999993
No 154
>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=25.29 E-value=73 Score=29.43 Aligned_cols=47 Identities=21% Similarity=0.217 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
.||...+.++...|.. . ..-.++|+.+|+++..|..+-....+|+++
T Consensus 183 ~L~~~e~~i~~~~~~~----~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYFK----D----KTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5899999998776654 2 357889999999999999999888888765
No 155
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=25.17 E-value=62 Score=28.28 Aligned_cols=49 Identities=14% Similarity=0.148 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.++...+.. . ..-.++|..+|++...|.+=....|+++++..
T Consensus 140 ~L~~~~r~vi~l~~~~----g----~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l 188 (189)
T TIGR02984 140 KLPEDYREVILLRHLE----G----LSFAEVAERMDRSEGAVSMLWVRGLARLRQIL 188 (189)
T ss_pred cCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3788888888664433 2 34578999999999999999999998887643
No 156
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=25.16 E-value=63 Score=28.93 Aligned_cols=51 Identities=18% Similarity=0.038 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
+||+.++.++.-.+... -.-.++|+.+|++...|.....-+|+++++....
T Consensus 111 ~Lp~~~R~v~~L~~~~g--------~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 111 KLPQDQREALILVGASG--------FSYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred hCCHHHHHHhhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 37899999887765552 2356899999999999999999999998876653
No 157
>PRK10651 transcriptional regulator NarL; Provisional
Probab=25.07 E-value=86 Score=26.89 Aligned_cols=45 Identities=13% Similarity=0.053 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHW 340 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~k 340 (362)
.|++...++|+-+... + .-..+|+.++++.+.|.+...+.|+|..
T Consensus 155 ~Lt~rE~~vl~~l~~g-----~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQG-----L----PNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHcC-----C----CHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 4999999999765432 2 3467789999999999999999999964
No 158
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=24.93 E-value=58 Score=31.05 Aligned_cols=50 Identities=14% Similarity=0.087 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||...+.+|...|.. . ..-.++|+.+|++...|..+..-.++++++...
T Consensus 203 ~L~~~~r~vl~l~y~~----~----~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 203 QLEERTREVLEFVFLH----D----LTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred cCCHHHHHHHHHHHHC----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 4788888888777655 2 345789999999999999999999999876543
No 159
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=24.82 E-value=70 Score=28.74 Aligned_cols=50 Identities=20% Similarity=0.107 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||..++.++.-.+..+ ..-.++|..+|++...|.++..-.|+++++...
T Consensus 128 ~Lp~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 128 KLDPEYREPLLLQVIGG--------FSGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred hCCHHHHHHHHHHHHhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 58999999887766663 234689999999999999999999999876553
No 160
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=24.73 E-value=65 Score=20.92 Aligned_cols=22 Identities=18% Similarity=0.244 Sum_probs=19.0
Q ss_pred HHHHHHHhCCChhhHhhhhhhh
Q 038569 314 KVALAESTGLDQRQINNWFINQ 335 (362)
Q Consensus 314 K~~LA~~TgLs~kQI~nWF~N~ 335 (362)
...||+.+|++..+|..|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4589999999999999997654
No 161
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=24.57 E-value=45 Score=28.20 Aligned_cols=47 Identities=21% Similarity=0.156 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
||+..+.++...+... -.-.++|+.+|++...|.++..-+|+++++.
T Consensus 106 L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 106 LPENYRTVLILREFKE--------FSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred CCHhheeeeeehhhcc--------CcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 6777767665433331 3457899999999999999999999998763
No 162
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=24.17 E-value=73 Score=31.21 Aligned_cols=48 Identities=19% Similarity=0.109 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKP 342 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp 342 (362)
+||...+.++.-.+.+. -.-.++|+.+|++...|.+....+|+++++.
T Consensus 153 ~Lp~~~R~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 200 (339)
T PRK08241 153 HLPPRQRAVLILRDVLG--------WSAAEVAELLDTSVAAVNSALQRARATLAER 200 (339)
T ss_pred hCCHHHhhhhhhHHhhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence 37888888886665552 2346899999999999999999999999883
No 163
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=24.00 E-value=54 Score=28.77 Aligned_cols=46 Identities=9% Similarity=0.073 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHW 340 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~k 340 (362)
.||++++.++.-.+... ..-.++|+.+|++...|.++...++++.+
T Consensus 119 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 119 GLNGKTREAFLLSQLDG--------LTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred hCCHHHhHHhhhhhccC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 47888888876554442 24578999999999999999988887643
No 164
>PF14904 FAM86: Family of unknown function
Probab=23.91 E-value=1.2e+02 Score=25.81 Aligned_cols=56 Identities=23% Similarity=0.421 Sum_probs=33.7
Q ss_pred chhhHHHHHHHHHhhCCChHHHHHHHHhhHhccCchh---hhhhHHHHHhhccccCcccccCCCCCCCCCcccHHHHHHH
Q 038569 110 SEEQVSSAIRAQIASHPLYPKLLQAYIDCQKVGASPE---IANVLDDIRREGDVSNRNWVVSSCCWGADPELDEFMETYC 186 (362)
Q Consensus 110 ~~~~~~~~~Ka~I~sHPLYp~Ll~Ayi~C~KVgaPpd---~~~~Ldei~~~~~~~~~~~~~~~~~~g~dpELDqFMe~Yc 186 (362)
++.+....|=++-+-||++-+ -||- ..+.|.++-++.+.... + -||+..++|+
T Consensus 42 ~~sel~~~IL~~Tv~HPlc~k------------~Pps~kY~~~FLk~lI~k~Ea~~~-----------E-plDeLYeala 97 (100)
T PF14904_consen 42 SDSELQLDILQKTVKHPLCVK------------YPPSVKYRRCFLKELIKKHEAVHC-----------E-PLDELYEALA 97 (100)
T ss_pred CcHHHHHHHHHHHhcCcchhh------------CCCchhHHHHHHHHHHHHHHHhcC-----------C-cHHHHHHHHH
Confidence 455566666677789998632 3433 33355555445443221 2 3789999998
Q ss_pred HHH
Q 038569 187 DIL 189 (362)
Q Consensus 187 ~~L 189 (362)
++|
T Consensus 98 e~l 100 (100)
T PF14904_consen 98 EVL 100 (100)
T ss_pred hhC
Confidence 875
No 165
>PF11348 DUF3150: Protein of unknown function (DUF3150); InterPro: IPR021496 This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=23.47 E-value=1e+02 Score=30.00 Aligned_cols=47 Identities=28% Similarity=0.479 Sum_probs=28.4
Q ss_pred HHHHhhHhccCc--------hh----hhhhHHHHHhhccccCcccccCCCCCCCCCcccHHHHHHHHHHHHHHHH
Q 038569 133 QAYIDCQKVGAS--------PE----IANVLDDIRREGDVSNRNWVVSSCCWGADPELDEFMETYCDILVKYKSD 195 (362)
Q Consensus 133 ~Ayi~C~KVgaP--------pd----~~~~Ldei~~~~~~~~~~~~~~~~~~g~dpELDqFMe~Yc~~L~kykeE 195 (362)
+|.--|+|+|.| .+ +...|++|..+.. .+.++|+..|-+.+..+..+
T Consensus 60 ~A~r~~~~~G~rFlgG~aVP~~~~~~l~~~L~~i~~eF~----------------~~k~~Fl~~Yd~~i~~w~~~ 118 (257)
T PF11348_consen 60 RAERLCLKVGVRFLGGYAVPEDKAEELAEELEDIKTEFE----------------QEKQDFLANYDQAIEEWIDR 118 (257)
T ss_pred HHHHHHHHcCCcccceeEcCHHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHHHHH
Confidence 456678888884 33 3334444444433 24567887777777777665
No 166
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=23.23 E-value=67 Score=30.90 Aligned_cols=49 Identities=18% Similarity=0.283 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||...+.+|...|.. .+ .-.++|+.+|++...|..+...+++++++..
T Consensus 215 ~L~~rer~vl~l~y~~----~~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 215 ALPERERTVLVLRFFE----SM----TQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred cCCHHHHHHHHHHhcC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 4899999999887754 22 3478999999999999999999999887653
No 167
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=23.16 E-value=28 Score=33.02 Aligned_cols=29 Identities=28% Similarity=0.581 Sum_probs=25.7
Q ss_pred HHHHHHHHhhCCChHHHHHHHHhhHhccCchhh
Q 038569 115 SSAIRAQIASHPLYPKLLQAYIDCQKVGASPEI 147 (362)
Q Consensus 115 ~~~~Ka~I~sHPLYp~Ll~Ayi~C~KVgaPpd~ 147 (362)
...||..|..+||..+||+||+ ||.|.-.
T Consensus 110 ~~LL~e~~~~~pl~~rLVAAYl----iG~~v~~ 138 (207)
T PF11288_consen 110 LRLLKEEIAGDPLRKRLVAAYL----IGYPVTV 138 (207)
T ss_pred HHHHHHHhcCchHHhhhheeee----cCccccH
Confidence 5789999999999999999998 8887554
No 168
>PRK05572 sporulation sigma factor SigF; Validated
Probab=23.01 E-value=67 Score=30.33 Aligned_cols=49 Identities=16% Similarity=0.164 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||...+.++...|... ..-.++|+.+|+++..|..+-....+++++..
T Consensus 202 ~L~~~~~~v~~l~~~~~--------~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 202 ELDERERLIVYLRYFKD--------KTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred cCCHHHHHHHHHHHhCC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998776541 35678999999999999999999998887643
No 169
>TIGR01601 PYST-C1 Plasmodium yoelii subtelomeric domain PYST-C1. The C-terminal portions of the genes which contain this domain are divergent and some contain other yoelii-specific paralogous domains such as PYST-C2 (TIGR01604).
Probab=23.00 E-value=44 Score=27.40 Aligned_cols=14 Identities=64% Similarity=0.779 Sum_probs=7.4
Q ss_pred CCCCCCCCCCCccc
Q 038569 43 NNNNNDDDDDDDNI 56 (362)
Q Consensus 43 ~~~~~~~~~~~~~~ 56 (362)
|||+.||.||-|+|
T Consensus 61 NnN~kdd~ddk~ni 74 (82)
T TIGR01601 61 NNNPKDDIDDKDNP 74 (82)
T ss_pred CCCCCCccccccCc
Confidence 44455565555543
No 170
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=22.84 E-value=38 Score=29.47 Aligned_cols=51 Identities=16% Similarity=0.096 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSES 345 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e~ 345 (362)
.||...+.+|.-.+.. .+ .-.++|+.+|++...|.+.+...|++.++..++
T Consensus 120 ~L~~~~r~vl~l~~~~----g~----s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~ 170 (175)
T PRK12518 120 TLSLEHRAVLVLHDLE----DL----PQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170 (175)
T ss_pred hCCHHHeeeeeehHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3788888887664444 22 357899999999999999999999998876543
No 171
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=22.74 E-value=79 Score=27.18 Aligned_cols=29 Identities=24% Similarity=0.407 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 038569 308 YPTEADKVALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 308 YPs~~eK~~LA~~TgLs~kQI~nWF~N~R 336 (362)
-+++..|..||..+|++.+.|..|-.-++
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~~Ad 54 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVNQAD 54 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHhHHH
Confidence 47888999999999999999999954443
No 172
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=22.47 E-value=48 Score=30.71 Aligned_cols=38 Identities=29% Similarity=0.517 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHhcCCCCCC-HHHHHHHHHHhCCChhh
Q 038569 290 KEARQILFDWWNLHYNWPYPT-EADKVALAESTGLDQRQ 327 (362)
Q Consensus 290 ke~~~iL~~wf~~H~~nPYPs-~~eK~~LA~~TgLs~kQ 327 (362)
.......-.|...|+-.|||+ ++||..-|++.||-+..
T Consensus 23 ~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 23 PRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred ccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 444555678999999999995 77889999999987654
No 173
>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=22.31 E-value=63 Score=30.17 Aligned_cols=54 Identities=20% Similarity=0.128 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||+..+.++.-.+....... -.-.++|+.+|++...|.++..-+|+++|+-..
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg----~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~ 231 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTE----KTQKEVADMLGISQSYISRLEKRILKRLKKEIN 231 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence 488888888876552000001 245689999999999999999999999877544
No 174
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=22.22 E-value=1e+02 Score=26.89 Aligned_cols=47 Identities=17% Similarity=0.197 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcC
Q 038569 286 GKLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHW 340 (362)
Q Consensus 286 ~~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~k 340 (362)
..||+..+.++.-.+.+. -.-.++|+.+|++...|.++..++|+..+
T Consensus 117 ~~L~~~~r~v~~L~~~eg--------~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEG--------LTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 358888888887765552 23468999999999999999988887754
No 175
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.16 E-value=75 Score=21.77 Aligned_cols=20 Identities=20% Similarity=0.167 Sum_probs=17.1
Q ss_pred HHHHHHhCCChhhHhhhhhh
Q 038569 315 VALAESTGLDQRQINNWFIN 334 (362)
Q Consensus 315 ~~LA~~TgLs~kQI~nWF~N 334 (362)
.++|+.+|++...|..|...
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999543
No 176
>PHA01976 helix-turn-helix protein
Probab=22.15 E-value=73 Score=23.53 Aligned_cols=23 Identities=17% Similarity=0.339 Sum_probs=19.5
Q ss_pred HHHHHHHhCCChhhHhhhhhhhh
Q 038569 314 KVALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 314 K~~LA~~TgLs~kQI~nWF~N~R 336 (362)
..+||+.+|++...|.+|....+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46799999999999999986543
No 177
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=21.85 E-value=72 Score=24.18 Aligned_cols=23 Identities=22% Similarity=0.320 Sum_probs=19.9
Q ss_pred HHHHHHHhCCChhhHhhhhhhhh
Q 038569 314 KVALAESTGLDQRQINNWFINQR 336 (362)
Q Consensus 314 K~~LA~~TgLs~kQI~nWF~N~R 336 (362)
...||+.+|++...|..|..+.|
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999997653
No 178
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=21.60 E-value=1.1e+02 Score=29.62 Aligned_cols=49 Identities=12% Similarity=-0.003 Sum_probs=38.9
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
||+.++.++.--+... -.-.++|+.+|++...|.+.+..+|+++++...
T Consensus 116 L~~~~R~v~~L~~~~g--------~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 116 LSPLERAAFLLHDVFG--------VPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred CCHHHHHHHHHHHHhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 7888888875544332 234689999999999999999999999887554
No 179
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=21.58 E-value=73 Score=29.64 Aligned_cols=53 Identities=13% Similarity=0.177 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.++...|..+ -+ ....-.++|+.+|++...|.+|...+|+++++..
T Consensus 175 ~Lp~~~R~i~~l~y~~~---~~-e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l 227 (233)
T PRK05803 175 ILDEREKEVIEMRYGLG---NG-KEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227 (233)
T ss_pred hCCHHHHHHHHHHhCCC---CC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58999999987755211 00 0124578999999999999999888888876643
No 180
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=21.25 E-value=60 Score=29.17 Aligned_cols=49 Identities=18% Similarity=0.086 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
||+..+.+|.--+... ..-.++|..+|++...|.+=+-.+|+++++..+
T Consensus 135 Lp~~~r~i~~l~~~~g--------~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~ 183 (192)
T PRK09643 135 LPVEQRAALVAVDMQG--------YSVADAARMLGVAEGTVKSRCARGRARLAELLG 183 (192)
T ss_pred CCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 7888988886644441 245689999999999999988888888776554
No 181
>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=21.22 E-value=82 Score=29.24 Aligned_cols=51 Identities=12% Similarity=0.132 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWK 341 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kk 341 (362)
.||+..+.++.-.|....... -.-.++|+.+|+++..|..+...+|+++++
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~----~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRR----KTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCC----cCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 589999999988764100011 245789999999999999988888888765
No 182
>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=20.95 E-value=1e+02 Score=28.84 Aligned_cols=53 Identities=13% Similarity=0.147 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPS 343 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~ 343 (362)
.||+..+.+|...|.-+ -+ ....-.++|+.+|++...|..+...+++++|+..
T Consensus 176 ~L~~~er~vl~l~ygl~---~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRYGLL---DG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHhCCC---CC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 47888889998776321 01 1135678999999999999999999999998764
No 183
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=20.95 E-value=47 Score=30.91 Aligned_cols=49 Identities=14% Similarity=0.138 Sum_probs=38.6
Q ss_pred CCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 288 LPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 288 lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
||...+.++.-.+.. . ..-.++|+.+|++...|.+...-.|+++|+...
T Consensus 150 L~~~~r~i~~l~~~~----g----~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 150 LPDAFRAVFVLRVVE----E----LSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred CCHHHhhhheeehhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 688888887554433 2 355789999999999999999999999887654
No 184
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.77 E-value=90 Score=31.13 Aligned_cols=54 Identities=17% Similarity=0.197 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhcCCCCC
Q 038569 287 KLPKEARQILFDWWNLHYNWPYPTEADKVALAESTGLDQRQINNWFINQRKRHWKPSE 344 (362)
Q Consensus 287 ~lpke~~~iL~~wf~~H~~nPYPs~~eK~~LA~~TgLs~kQI~nWF~N~RrR~kkp~e 344 (362)
.||...+.+|..-|..+.... -.-.++|+.+|++...|..+...+|+++|+...
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~----~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEA----ATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCC----cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 489999999986553321122 355789999999999999999999999887553
Done!