Query 006699
Match_columns 635
No_of_seqs 329 out of 1046
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 13:12:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006699.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006699hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00574 POX domain associat 100.0 3.9E-38 8.6E-43 292.8 8.6 130 200-329 2-139 (140)
2 PF07526 POX: Associated with 100.0 8.1E-38 1.8E-42 292.5 9.6 126 204-329 2-139 (140)
3 KOG0773 Transcription factor M 100.0 1.3E-32 2.9E-37 285.9 9.9 252 201-453 45-312 (342)
4 KOG0774 Transcription factor P 99.6 2.2E-15 4.8E-20 152.9 15.1 136 269-443 113-251 (334)
5 PF05920 Homeobox_KN: Homeobox 99.6 8.9E-16 1.9E-20 116.5 4.1 40 398-437 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.4 7E-13 1.5E-17 104.0 6.7 57 382-441 2-58 (59)
7 PF00046 Homeobox: Homeobox do 99.4 8.9E-13 1.9E-17 104.1 5.8 57 381-440 1-57 (57)
8 smart00389 HOX Homeodomain. DN 99.3 1.9E-12 4.1E-17 101.1 6.6 55 382-439 2-56 (56)
9 KOG0775 Transcription factor S 99.2 1.1E-11 2.3E-16 127.2 4.6 51 386-439 182-232 (304)
10 KOG0487 Transcription factor A 98.9 5.3E-10 1.2E-14 117.1 3.7 61 379-442 233-294 (308)
11 KOG0842 Transcription factor t 98.9 6.3E-10 1.4E-14 116.6 4.1 64 379-445 151-215 (307)
12 KOG0488 Transcription factor B 98.8 4.2E-09 9E-14 110.8 5.7 63 379-444 170-233 (309)
13 KOG0843 Transcription factor E 98.8 7.2E-09 1.6E-13 101.5 6.7 64 379-445 101-164 (197)
14 KOG0489 Transcription factor z 98.8 3.7E-09 8E-14 108.4 4.0 60 379-441 158-217 (261)
15 KOG0493 Transcription factor E 98.8 6.1E-09 1.3E-13 106.7 4.8 61 378-441 244-304 (342)
16 TIGR01565 homeo_ZF_HD homeobox 98.7 2E-08 4.3E-13 82.4 5.3 52 381-435 2-57 (58)
17 KOG0483 Transcription factor H 98.7 1.7E-08 3.7E-13 100.4 5.1 68 380-450 50-117 (198)
18 KOG0485 Transcription factor N 98.7 1.6E-08 3.4E-13 101.6 4.3 64 377-443 101-164 (268)
19 KOG0850 Transcription factor D 98.7 2.1E-08 4.5E-13 101.3 4.7 60 380-442 121-181 (245)
20 KOG0484 Transcription factor P 98.6 1E-07 2.2E-12 86.6 7.0 61 384-447 21-81 (125)
21 KOG3802 Transcription factor O 98.5 8.1E-08 1.8E-12 103.3 3.8 60 380-442 293-353 (398)
22 COG5576 Homeodomain-containing 98.5 1.4E-07 3.1E-12 90.8 5.1 61 379-442 50-110 (156)
23 KOG2251 Homeobox transcription 98.4 2.8E-07 6E-12 92.9 4.7 58 381-441 38-95 (228)
24 KOG0494 Transcription factor C 98.4 2.9E-07 6.3E-12 94.6 4.9 53 386-441 147-199 (332)
25 KOG0848 Transcription factor C 98.4 2.2E-07 4.7E-12 95.8 3.5 57 387-446 206-262 (317)
26 KOG0486 Transcription factor P 98.4 2.5E-07 5.4E-12 97.1 3.9 59 381-442 112-171 (351)
27 KOG0492 Transcription factor M 98.3 6.9E-07 1.5E-11 89.5 5.8 58 381-441 145-202 (246)
28 KOG0491 Transcription factor B 98.3 2.5E-07 5.4E-12 89.8 2.0 58 381-441 100-158 (194)
29 KOG0847 Transcription factor, 98.2 9.5E-07 2E-11 89.1 4.0 72 381-455 168-239 (288)
30 KOG4577 Transcription factor L 98.1 2.8E-06 6E-11 88.6 3.8 62 378-442 165-226 (383)
31 KOG2252 CCAAT displacement pro 97.9 2.8E-05 6.2E-10 86.8 9.0 57 379-438 419-475 (558)
32 KOG0844 Transcription factor E 97.8 6.6E-06 1.4E-10 86.3 1.5 57 384-443 185-241 (408)
33 KOG0849 Transcription factor P 97.5 7E-05 1.5E-09 80.5 4.3 58 382-442 178-235 (354)
34 KOG0490 Transcription factor, 97.5 4.6E-05 1E-09 74.5 2.4 60 379-441 59-118 (235)
35 KOG1168 Transcription factor A 97.3 7.5E-05 1.6E-09 78.2 1.3 59 379-440 308-366 (385)
36 KOG0773 Transcription factor M 97.3 0.00011 2.4E-09 77.5 2.1 60 382-442 97-156 (342)
37 PF11569 Homez: Homeodomain le 96.3 0.003 6.5E-08 52.1 2.8 43 392-437 10-52 (56)
38 KOG0490 Transcription factor, 95.3 0.015 3.2E-07 57.1 3.5 62 379-443 152-213 (235)
39 KOG1146 Homeobox protein [Gene 91.6 0.25 5.5E-06 60.9 5.6 57 384-443 907-963 (1406)
40 PF04218 CENP-B_N: CENP-B N-te 80.7 2.9 6.3E-05 33.6 4.3 47 381-435 1-47 (53)
41 KOG3623 Homeobox transcription 74.9 4.3 9.3E-05 48.2 5.1 45 392-439 568-612 (1007)
42 PF04545 Sigma70_r4: Sigma-70, 73.7 3.9 8.5E-05 31.6 3.2 47 386-440 4-50 (50)
43 cd06171 Sigma70_r4 Sigma70, re 72.9 4.8 0.0001 29.5 3.4 46 386-439 10-55 (55)
44 PF01527 HTH_Tnp_1: Transposas 72.2 6.1 0.00013 32.5 4.2 46 382-435 2-48 (76)
45 PF11285 DUF3086: Protein of u 69.5 47 0.001 35.5 10.7 58 261-334 5-62 (283)
46 PF08281 Sigma70_r4_2: Sigma-7 69.2 7 0.00015 30.4 3.7 45 386-438 10-54 (54)
47 cd00569 HTH_Hin_like Helix-tur 62.9 20 0.00043 23.3 4.5 39 385-431 4-42 (42)
48 PRK06759 RNA polymerase factor 53.9 15 0.00031 33.8 3.5 47 386-440 106-152 (154)
49 TIGR02937 sigma70-ECF RNA poly 53.3 21 0.00045 31.3 4.3 48 386-441 110-157 (158)
50 PRK09642 RNA polymerase sigma 52.5 18 0.0004 33.5 3.9 49 386-442 106-154 (160)
51 TIGR02985 Sig70_bacteroi1 RNA 52.4 16 0.00034 33.1 3.5 48 386-441 113-160 (161)
52 PRK12530 RNA polymerase sigma 50.9 21 0.00045 34.6 4.2 50 386-443 134-183 (189)
53 PRK09644 RNA polymerase sigma 50.9 19 0.00041 33.7 3.8 50 385-442 107-156 (165)
54 PRK00118 putative DNA-binding 49.8 19 0.0004 33.3 3.4 56 386-450 17-72 (104)
55 PRK11924 RNA polymerase sigma 48.7 21 0.00046 33.0 3.8 49 386-442 125-173 (179)
56 PRK12514 RNA polymerase sigma 48.5 28 0.0006 33.0 4.6 48 386-441 129-176 (179)
57 TIGR02939 RpoE_Sigma70 RNA pol 47.2 16 0.00034 34.6 2.7 49 386-442 138-186 (190)
58 PF00196 GerE: Bacterial regul 47.1 39 0.00085 26.8 4.6 52 386-446 3-54 (58)
59 PRK09652 RNA polymerase sigma 46.3 24 0.00052 32.8 3.7 49 386-442 128-176 (182)
60 PRK09646 RNA polymerase sigma 46.1 21 0.00046 34.5 3.4 49 386-442 142-190 (194)
61 PRK12512 RNA polymerase sigma 45.9 19 0.00042 34.2 3.1 49 386-442 131-179 (184)
62 PF13443 HTH_26: Cro/C1-type H 45.1 28 0.0006 27.7 3.4 39 395-440 2-40 (63)
63 PRK06811 RNA polymerase factor 44.6 24 0.00051 34.1 3.5 49 386-442 131-179 (189)
64 PRK09648 RNA polymerase sigma 44.1 25 0.00053 33.7 3.5 49 386-442 139-187 (189)
65 smart00421 HTH_LUXR helix_turn 43.4 66 0.0014 23.9 5.1 48 386-442 3-50 (58)
66 PRK03975 tfx putative transcri 43.4 32 0.0007 33.4 4.1 49 385-442 5-53 (141)
67 PRK12526 RNA polymerase sigma 43.1 25 0.00054 34.6 3.5 49 386-442 153-201 (206)
68 TIGR02999 Sig-70_X6 RNA polyme 42.4 28 0.00061 32.9 3.6 48 386-441 134-181 (183)
69 TIGR02989 Sig-70_gvs1 RNA poly 41.6 29 0.00063 31.9 3.4 48 385-440 110-157 (159)
70 PF03791 KNOX2: KNOX2 domain ; 41.4 97 0.0021 25.7 5.9 42 251-292 5-49 (52)
71 PRK12519 RNA polymerase sigma 40.8 27 0.00058 33.5 3.2 49 386-442 141-189 (194)
72 TIGR02948 SigW_bacill RNA poly 40.1 28 0.00062 32.8 3.2 49 386-442 136-184 (187)
73 PRK05602 RNA polymerase sigma 39.7 29 0.00062 33.2 3.2 49 386-442 128-176 (186)
74 TIGR02941 Sigma_B RNA polymera 39.5 34 0.00074 34.7 3.9 49 386-442 205-253 (255)
75 PRK12541 RNA polymerase sigma 39.3 29 0.00064 32.2 3.1 48 385-440 111-158 (161)
76 PRK12520 RNA polymerase sigma 38.9 53 0.0012 31.5 4.9 49 386-442 131-179 (191)
77 PRK12544 RNA polymerase sigma 38.0 55 0.0012 32.5 5.0 51 386-444 148-198 (206)
78 PRK08583 RNA polymerase sigma 37.9 43 0.00093 34.1 4.3 49 386-442 205-253 (257)
79 PRK12536 RNA polymerase sigma 37.8 36 0.00078 32.5 3.5 49 386-442 129-177 (181)
80 PRK12547 RNA polymerase sigma 37.4 36 0.00078 32.0 3.4 48 386-441 112-159 (164)
81 TIGR02980 SigBFG RNA polymeras 37.3 32 0.0007 34.1 3.2 49 386-442 178-226 (227)
82 PRK15369 two component system 37.2 61 0.0013 29.5 4.8 53 385-446 148-200 (211)
83 PRK12515 RNA polymerase sigma 36.8 43 0.00092 32.2 3.9 49 386-442 131-179 (189)
84 PRK09047 RNA polymerase factor 36.5 41 0.00089 31.0 3.6 50 385-442 105-154 (161)
85 PRK13919 putative RNA polymera 36.2 34 0.00073 32.6 3.1 49 386-442 135-183 (186)
86 PRK12546 RNA polymerase sigma 36.2 34 0.00074 33.4 3.1 49 386-442 113-161 (188)
87 TIGR02393 RpoD_Cterm RNA polym 36.0 51 0.0011 33.3 4.5 55 386-444 176-230 (238)
88 TIGR02983 SigE-fam_strep RNA p 35.7 42 0.00091 31.1 3.6 49 386-442 110-158 (162)
89 PRK04217 hypothetical protein; 35.4 63 0.0014 30.2 4.6 50 385-442 41-90 (110)
90 PRK09647 RNA polymerase sigma 34.9 56 0.0012 32.4 4.5 49 386-442 138-186 (203)
91 PRK12533 RNA polymerase sigma 34.9 44 0.00096 33.7 3.8 49 386-442 134-182 (216)
92 PRK12532 RNA polymerase sigma 34.8 42 0.00091 32.4 3.5 49 386-442 136-184 (195)
93 TIGR02954 Sig70_famx3 RNA poly 34.7 43 0.00093 31.4 3.5 49 386-442 119-167 (169)
94 PRK12531 RNA polymerase sigma 34.6 43 0.00094 32.4 3.6 50 385-442 140-189 (194)
95 PRK12537 RNA polymerase sigma 34.1 43 0.00093 32.0 3.4 49 385-441 132-180 (182)
96 PRK06986 fliA flagellar biosyn 33.5 36 0.00078 34.2 2.9 49 386-442 184-232 (236)
97 PRK12516 RNA polymerase sigma 33.3 49 0.0011 32.2 3.7 49 386-442 116-164 (187)
98 PRK09639 RNA polymerase sigma 32.9 47 0.001 30.8 3.4 48 386-442 112-159 (166)
99 PRK12513 RNA polymerase sigma 32.8 32 0.00069 33.1 2.3 49 386-442 139-187 (194)
100 PRK12523 RNA polymerase sigma 32.4 51 0.0011 31.1 3.6 47 386-440 119-165 (172)
101 PRK12524 RNA polymerase sigma 32.4 68 0.0015 31.1 4.5 49 386-442 136-184 (196)
102 PRK12538 RNA polymerase sigma 31.8 55 0.0012 33.3 3.9 49 386-442 171-219 (233)
103 PF13518 HTH_28: Helix-turn-he 31.3 48 0.001 25.2 2.6 25 412-436 14-38 (52)
104 PRK07037 extracytoplasmic-func 31.1 55 0.0012 30.3 3.5 49 386-442 109-157 (163)
105 TIGR03001 Sig-70_gmx1 RNA poly 31.1 78 0.0017 32.6 4.9 50 386-443 161-210 (244)
106 PRK09641 RNA polymerase sigma 31.0 53 0.0011 31.0 3.5 49 386-442 136-184 (187)
107 TIGR02479 FliA_WhiG RNA polyme 30.9 48 0.001 33.0 3.3 48 386-441 175-222 (224)
108 PRK11923 algU RNA polymerase s 30.5 72 0.0016 30.6 4.3 49 386-442 138-186 (193)
109 PRK07408 RNA polymerase sigma 30.2 47 0.001 34.1 3.2 49 386-442 203-251 (256)
110 PRK12545 RNA polymerase sigma 30.2 61 0.0013 31.8 3.8 49 386-442 139-187 (201)
111 PRK09649 RNA polymerase sigma 29.9 53 0.0012 31.7 3.3 48 385-440 129-176 (185)
112 PF04967 HTH_10: HTH DNA bindi 29.7 1E+02 0.0022 25.3 4.3 49 387-436 1-49 (53)
113 TIGR02952 Sig70_famx2 RNA poly 29.6 58 0.0012 30.2 3.4 49 385-441 121-169 (170)
114 PRK12529 RNA polymerase sigma 29.4 79 0.0017 30.2 4.4 48 386-441 127-174 (178)
115 cd06170 LuxR_C_like C-terminal 29.3 1.4E+02 0.003 22.4 4.9 46 387-441 1-46 (57)
116 PRK09637 RNA polymerase sigma 29.3 57 0.0012 31.5 3.4 49 386-442 106-154 (181)
117 TIGR02959 SigZ RNA polymerase 29.2 60 0.0013 30.8 3.5 50 385-442 99-148 (170)
118 PRK06288 RNA polymerase sigma 29.0 62 0.0013 33.4 3.8 49 386-442 212-260 (268)
119 PRK07670 RNA polymerase sigma 28.4 56 0.0012 33.3 3.3 48 386-441 201-248 (251)
120 PRK11511 DNA-binding transcrip 28.4 1.1E+02 0.0023 28.4 4.8 44 387-434 6-49 (127)
121 TIGR02947 SigH_actino RNA poly 27.9 39 0.00084 32.6 2.0 49 386-442 131-179 (193)
122 PRK12527 RNA polymerase sigma 27.9 95 0.0021 28.8 4.5 49 386-442 105-153 (159)
123 cd00131 PAX Paired Box domain 27.9 2.8E+02 0.0061 26.1 7.6 47 385-434 74-127 (128)
124 PRK09415 RNA polymerase factor 27.9 75 0.0016 30.4 3.9 49 386-442 127-175 (179)
125 TIGR02943 Sig70_famx1 RNA poly 27.6 79 0.0017 30.6 4.1 49 386-442 131-179 (188)
126 PHA00542 putative Cro-like pro 27.6 1.7E+02 0.0036 25.4 5.7 35 412-446 33-67 (82)
127 PRK07598 RNA polymerase sigma 27.1 1.1E+02 0.0024 34.6 5.5 58 386-447 350-407 (415)
128 PRK12542 RNA polymerase sigma 27.1 68 0.0015 30.7 3.5 49 386-442 122-170 (185)
129 PRK06930 positive control sigm 27.1 70 0.0015 31.5 3.6 49 386-442 114-162 (170)
130 PRK12535 RNA polymerase sigma 26.9 67 0.0014 31.6 3.5 49 386-442 133-181 (196)
131 cd01392 HTH_LacI Helix-turn-he 26.9 56 0.0012 24.9 2.4 21 415-435 2-22 (52)
132 PRK12539 RNA polymerase sigma 26.8 72 0.0016 30.6 3.6 49 386-442 131-179 (184)
133 PRK12518 RNA polymerase sigma 26.7 54 0.0012 30.8 2.7 49 386-442 120-168 (175)
134 PF07638 Sigma70_ECF: ECF sigm 26.7 95 0.002 30.3 4.4 48 387-442 136-183 (185)
135 PRK09645 RNA polymerase sigma 26.7 66 0.0014 30.2 3.3 49 386-442 118-166 (173)
136 PRK09413 IS2 repressor TnpA; R 26.5 1.6E+02 0.0036 27.0 5.7 47 382-435 8-54 (121)
137 PRK12522 RNA polymerase sigma 26.0 84 0.0018 29.6 3.9 49 386-442 119-167 (173)
138 PRK12543 RNA polymerase sigma 26.0 95 0.0021 29.6 4.2 49 386-442 117-165 (179)
139 PRK08301 sporulation sigma fac 25.8 64 0.0014 32.2 3.2 53 386-442 178-230 (234)
140 COG1595 RpoE DNA-directed RNA 25.5 6E+02 0.013 24.3 10.7 49 386-442 127-175 (182)
141 PRK12511 RNA polymerase sigma 25.4 78 0.0017 30.7 3.6 49 386-442 111-159 (182)
142 PRK05657 RNA polymerase sigma 25.1 1.1E+02 0.0024 33.0 4.9 53 386-442 262-314 (325)
143 PF13551 HTH_29: Winged helix- 24.8 2.5E+02 0.0054 24.2 6.3 52 381-432 52-109 (112)
144 PRK08295 RNA polymerase factor 23.9 83 0.0018 30.4 3.5 47 386-441 155-201 (208)
145 TIGR02885 spore_sigF RNA polym 23.8 78 0.0017 31.6 3.3 47 386-440 183-229 (231)
146 TIGR02950 SigM_subfam RNA poly 23.8 36 0.00077 31.1 0.9 46 387-440 106-151 (154)
147 PRK12528 RNA polymerase sigma 23.8 86 0.0019 29.1 3.4 46 386-439 113-158 (161)
148 PRK12534 RNA polymerase sigma 23.7 83 0.0018 30.0 3.4 48 386-441 137-184 (187)
149 PRK12517 RNA polymerase sigma 23.6 1.5E+02 0.0032 28.8 5.2 49 386-442 128-176 (188)
150 cd00093 HTH_XRE Helix-turn-hel 22.8 1.1E+02 0.0024 21.7 3.1 23 413-435 15-37 (58)
151 PRK12540 RNA polymerase sigma 22.7 88 0.0019 30.3 3.4 49 386-442 111-159 (182)
152 PRK09651 RNA polymerase sigma 21.9 82 0.0018 29.9 2.9 49 386-442 119-167 (172)
153 COG3413 Predicted DNA binding 21.6 1.2E+02 0.0025 30.5 4.1 52 386-438 155-206 (215)
154 PF13565 HTH_32: Homeodomain-l 21.2 4.3E+02 0.0094 21.6 6.8 40 388-430 32-76 (77)
155 TIGR02960 SigX5 RNA polymerase 20.6 1.3E+02 0.0029 31.3 4.4 48 386-441 142-189 (324)
156 PRK11922 RNA polymerase sigma 20.5 85 0.0018 31.5 2.9 49 386-442 149-197 (231)
157 PRK12525 RNA polymerase sigma 20.4 96 0.0021 29.2 3.1 49 385-441 117-165 (168)
158 PRK05911 RNA polymerase sigma 20.4 1E+02 0.0022 31.8 3.5 49 386-442 205-253 (257)
159 PRK08215 sporulation sigma fac 20.4 99 0.0021 31.6 3.3 48 386-441 209-256 (258)
No 1
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=3.9e-38 Score=292.84 Aligned_cols=130 Identities=53% Similarity=0.811 Sum_probs=106.3
Q ss_pred ccceeccCCcChhHHHHHHHHHhccCCccCcchhhhh---h--h--hhccCCCCCCC-CCCccccCCchHHHHHHHHHHH
Q 006699 200 GHQFQLRNSKYLAPAQEILKEFCSLGTKQNDATKLKS---N--K--AKQQWDDENAG-SSSRKQSLCSLEFMELQKRKTK 271 (635)
Q Consensus 200 Gy~~~l~~SryL~paQeLL~E~c~v~~~~~~~~~~~s---~--~--~~~~~~~~~~~-~~s~~~elssle~~elQ~kK~k 271 (635)
||+++|++||||+||||||+|||+|+.........+. . . .....+...+. ..+..++|++++++|+|+||+|
T Consensus 2 g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~s~~~~~~~ls~~~r~e~q~kk~k 81 (140)
T smart00574 2 GGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQSGNDSPVSTSSNEGGGENLSGGSSSSEVPPLSTAERQELQRKKAK 81 (140)
T ss_pred chhhhccCccccccHHHHHHHHhcccHHhhcccccccccccccccccCCCcCCCCCCCCCCCCCCCchhHHHHHHHHHHH
Confidence 8899999999999999999999999865433221110 0 0 00111111111 2234589999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccCCCCCccCchhhhHHHhhhcccchhhhH
Q 006699 272 LLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRDGIV 329 (635)
Q Consensus 272 LL~mLEEVd~ry~qYc~qmq~v~ssFe~vaG~gaa~~Ytalal~~mSrhfr~LrdaI~ 329 (635)
||.||||||+||++||+||++|+++||+|+|.++|.|||+||+++||||||||||+|+
T Consensus 82 Ll~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 82 LLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999996
No 2
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=100.00 E-value=8.1e-38 Score=292.54 Aligned_cols=126 Identities=56% Similarity=0.808 Sum_probs=100.0
Q ss_pred eccCCcChhHHHHHHHHHhccCCccCcch-hhhhhh-------hhccC--CCCC--CCCCCccccCCchHHHHHHHHHHH
Q 006699 204 QLRNSKYLAPAQEILKEFCSLGTKQNDAT-KLKSNK-------AKQQW--DDEN--AGSSSRKQSLCSLEFMELQKRKTK 271 (635)
Q Consensus 204 ~l~~SryL~paQeLL~E~c~v~~~~~~~~-~~~s~~-------~~~~~--~~~~--~~~~s~~~elssle~~elQ~kK~k 271 (635)
+|++||||+||||||+|||+|+....... ..+... ..... .... .+.....+++++++++|+|+||+|
T Consensus 2 ~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~~~~e~q~kK~K 81 (140)
T PF07526_consen 2 VLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSGAPGGANSSGSSSSSGGSSSSSSSSDSSSPELSPAERQELQRKKAK 81 (140)
T ss_pred ccccchhHHHHHHHHHHHHcccchhhhcchhhccccccccccCCCCCCCCCCCCCccccCCCCCCCChhhHHHHHHHHHH
Confidence 69999999999999999999987311100 000000 00000 0000 112233578999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccCCCCCccCchhhhHHHhhhcccchhhhH
Q 006699 272 LLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRDGIV 329 (635)
Q Consensus 272 LL~mLEEVd~ry~qYc~qmq~v~ssFe~vaG~gaa~~Ytalal~~mSrhfr~LrdaI~ 329 (635)
||.||||||+||+|||+||++|+++||+|+|.|+|.|||+||++|||||||||||+|+
T Consensus 82 Ll~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~ 139 (140)
T PF07526_consen 82 LLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAIS 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999996
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.97 E-value=1.3e-32 Score=285.86 Aligned_cols=252 Identities=42% Similarity=0.598 Sum_probs=196.5
Q ss_pred cceeccCCcChhHHHHHHHHHhccCCccCcchh-h---hhhhhh-ccC-----CCCCCCCCCccccCCchHHHHHHHHHH
Q 006699 201 HQFQLRNSKYLAPAQEILKEFCSLGTKQNDATK-L---KSNKAK-QQW-----DDENAGSSSRKQSLCSLEFMELQKRKT 270 (635)
Q Consensus 201 y~~~l~~SryL~paQeLL~E~c~v~~~~~~~~~-~---~s~~~~-~~~-----~~~~~~~~s~~~elssle~~elQ~kK~ 270 (635)
+.+.+..++||.++|+||+|+|++......... . ....+. ... ...+.+..+ .+..+.+++.+++.+++
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~ 123 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRES-ATLKAWLEEHRLNPYPS 123 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccc-cccccchhhhhhccCch
Confidence 356789999999999999999999754321110 0 000000 000 001111112 45567889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccccCCCCCccCchhhhHHHhhhcccchh--hhHHHHHHHHhhcCCCCCCCCC
Q 006699 271 KLLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRD--GIVGQIQATKKAMGEKDPVAPG 348 (635)
Q Consensus 271 kLL~mLEEVd~ry~qYc~qmq~v~ssFe~vaG~gaa~~Ytalal~~mSrhfr~Lrd--aI~~qi~~t~k~mge~d~~~~g 348 (635)
||+.+|.+|+.+|.+||..|+.+.+.|+...+++.+.+|++.++..++++|+++.+ +|..|+......++..+.....
T Consensus 124 k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~ 203 (342)
T KOG0773|consen 124 KLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDSE 203 (342)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999998 7888888877776644321111
Q ss_pred ---CCCCCCCcchhhhhHHHhhh-hhhhhccccCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCCh
Q 006699 349 ---TSRGETPRLKIIDQTLRQQR-AFQQMSMMESHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSR 424 (635)
Q Consensus 349 ---~~~get~rl~~~dq~lrq~r-a~~q~~~~e~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~ 424 (635)
......+.....++.+++++ ++......+..+||++++||++++.+|+.|+++|+.||||++.+|.+||++|||++
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~ 283 (342)
T KOG0773|consen 204 DESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSR 283 (342)
T ss_pred cccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCc
Confidence 11122445555556666554 34444455667899999999999999999999999999999999999999999999
Q ss_pred hhHhhhhhhhhhhhchhhHHHHHHHhhhh
Q 006699 425 SQVSNWFINARVRLWKPMVEEMYLEETKE 453 (635)
Q Consensus 425 ~QVsNWFiNaRrRlkKp~iee~~~~~~~~ 453 (635)
.||.|||||+|+|+|+||++++|..+...
T Consensus 284 ~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 284 PQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred ccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 99999999999999999999999988875
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.65 E-value=2.2e-15 Score=152.93 Aligned_cols=136 Identities=24% Similarity=0.439 Sum_probs=94.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh---ccccccCCCCCccCchhhhHHHhhhcccchhhhHHHHHHHHhhcCCCCCC
Q 006699 269 KTKLLSMLEEVDRRYRHYCDQMKAVVS---SFEAVAGNGAARVYSALASKAMSRHFRCLRDGIVGQIQATKKAMGEKDPV 345 (635)
Q Consensus 269 K~kLL~mLEEVd~ry~qYc~qmq~v~s---sFe~vaG~gaa~~Ytalal~~mSrhfr~LrdaI~~qi~~t~k~mge~d~~ 345 (635)
|.-+-..|++-++.|+.||..+..++. .|-+++- . -..-..+.|++.| ..|--+|+.....
T Consensus 113 R~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~~----k-e~e~m~~~i~~kF----~~iq~~lkqstce------- 176 (334)
T KOG0774|consen 113 RQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIMP----K-EIERMVQIISKKF----SHIQMQLKQSTCE------- 176 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCH----H-HHHHHHHHHHHHH----HHHHHHHHHHHHH-------
Confidence 334445688888899999988877763 3333220 0 0112235666666 3344444321110
Q ss_pred CCCCCCCCCCcchhhhhHHHhhhhhhhhccccCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChh
Q 006699 346 APGTSRGETPRLKIIDQTLRQQRAFQQMSMMESHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRS 425 (635)
Q Consensus 346 ~~g~~~get~rl~~~dq~lrq~ra~~q~~~~e~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~ 425 (635)
.++ .||. .+. ..+||||+|+|.++.||..||..|+.||||++++|++||++++++.+
T Consensus 177 ------------~vm--iLr~--r~l-------darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvs 233 (334)
T KOG0774|consen 177 ------------AVM--ILRS--RFL-------DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVS 233 (334)
T ss_pred ------------HHH--HHHH--HHH-------HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceeh
Confidence 000 0111 011 34688999999999999999999999999999999999999999999
Q ss_pred hHhhhhhhhhhhhchhhH
Q 006699 426 QVSNWFINARVRLWKPMV 443 (635)
Q Consensus 426 QVsNWFiNaRrRlkKp~i 443 (635)
||+|||.|.|.|.||.|.
T Consensus 234 QvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 234 QVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred hhccccccceeehhhhhh
Confidence 999999999999999885
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=99.59 E-value=8.9e-16 Score=116.52 Aligned_cols=40 Identities=68% Similarity=1.174 Sum_probs=36.5
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 006699 398 WLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVR 437 (635)
Q Consensus 398 Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrR 437 (635)
||.+|+.||||+++||++||++|||+.+||+|||+|+|+|
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 9999999999999999999999999999999999999998
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=99.39 E-value=7e-13 Score=103.96 Aligned_cols=57 Identities=30% Similarity=0.538 Sum_probs=53.1
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 382 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 382 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
+++..|+++++.+|++||.. +|||+..++..||.+|||+..||.+||.|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 45667999999999999999 7999999999999999999999999999999998763
No 7
>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=99.36 E-value=8.9e-13 Score=104.07 Aligned_cols=57 Identities=35% Similarity=0.622 Sum_probs=53.7
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 381 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 381 kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
+|+++.|+++++.+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.+.||
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 467788999999999999998 799999999999999999999999999999999875
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.34 E-value=1.9e-12 Score=101.10 Aligned_cols=55 Identities=31% Similarity=0.513 Sum_probs=50.5
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 006699 382 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 439 (635)
Q Consensus 382 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlk 439 (635)
+++..|+++++.+|+.||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 34455999999999999998 69999999999999999999999999999999864
No 9
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.20 E-value=1.1e-11 Score=127.19 Aligned_cols=51 Identities=49% Similarity=0.791 Sum_probs=48.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 439 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlk 439 (635)
.|.++.+.+||+||.. +|||++++|.+||+.|||+..||.|||+|||.|.+
T Consensus 182 CFKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 182 CFKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred ehhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 3888999999999996 89999999999999999999999999999999987
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.92 E-value=5.3e-10 Score=117.11 Aligned_cols=61 Identities=23% Similarity=0.259 Sum_probs=54.2
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 379 HPWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 379 ~~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
+..||||. ++|.|+..|++-|.- |-|.+++-|.+|++.++||+.||+.||||||+|+||-.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 34456665 999999999888887 69999999999999999999999999999999998744
No 11
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.92 E-value=6.3e-10 Score=116.56 Aligned_cols=64 Identities=23% Similarity=0.316 Sum_probs=57.1
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 006699 379 HPWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEE 445 (635)
Q Consensus 379 ~~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee 445 (635)
.+|||+|. |++.||-.|++.|.+ ..|.+-.||+.||..++||.+||+.||+|+|-|.||.-+|+
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred ccccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 35566666 999999999999998 69999999999999999999999999999999999866543
No 12
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.81 E-value=4.2e-09 Score=110.75 Aligned_cols=63 Identities=27% Similarity=0.396 Sum_probs=55.2
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 006699 379 HPWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVE 444 (635)
Q Consensus 379 ~~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ie 444 (635)
+|+|+.|+ |+..|+..|+.-|.. --|.+..||.+||+.+|||-.||++||+|||+|+|+...+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 44455554 999999999999998 4999999999999999999999999999999998776643
No 13
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.81 E-value=7.2e-09 Score=101.46 Aligned_cols=64 Identities=23% Similarity=0.336 Sum_probs=58.2
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 006699 379 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEE 445 (635)
Q Consensus 379 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee 445 (635)
++||.|+.|+.+|+..|+..|.. +-|-.-.||..||+.++||+.||+.||+|+|.|.||...|+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 66777777999999999999998 79999999999999999999999999999999998865443
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.78 E-value=3.7e-09 Score=108.45 Aligned_cols=60 Identities=18% Similarity=0.262 Sum_probs=55.0
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 379 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 379 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
+.+|.|..|+..|+..|+.-|.- |.|.+...|++||..+.||+.||++||+|||+|.||.
T Consensus 158 ~~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 35666677999999999999987 7999999999999999999999999999999998873
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.76 E-value=6.1e-09 Score=106.69 Aligned_cols=61 Identities=28% Similarity=0.488 Sum_probs=56.9
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 378 SHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 378 ~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
...||+|.-|+.++++.|++-|.+ |.|.++..|++||.+++|.+.||+.||+|+|.|+||.
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred chhcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 345788888999999999999999 7999999999999999999999999999999999874
No 16
>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=98.71 E-value=2e-08 Score=82.37 Aligned_cols=52 Identities=12% Similarity=0.248 Sum_probs=48.9
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 006699 381 WRPQRGLPERSVSVLRAWLFEHFLHPY----PSDVDKHILARQTGLSRSQVSNWFINAR 435 (635)
Q Consensus 381 kR~rR~fpk~qv~iLr~Wf~eH~~nPY----PS~~EK~~LA~qTGLS~~QVsNWFiNaR 435 (635)
+|+|+.|+.+|+..|+..|.. ++| |+..++.+||..+||++.+|.+||+|.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 677778999999999999999 799 9999999999999999999999999964
No 17
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.68 E-value=1.7e-08 Score=100.39 Aligned_cols=68 Identities=26% Similarity=0.281 Sum_probs=60.4
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHh
Q 006699 380 PWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMYLEE 450 (635)
Q Consensus 380 ~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~~~~ 450 (635)
.++++++|+.+|+..|+.-|.. +-|..+.+|..||+++||.+.||..||+|||+|.|.+-.|.-|..-
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~L 117 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESL 117 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHH
Confidence 5678899999999999999998 5889999999999999999999999999999999887776555433
No 18
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.67 E-value=1.6e-08 Score=101.56 Aligned_cols=64 Identities=20% Similarity=0.251 Sum_probs=58.3
Q ss_pred cCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006699 377 ESHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 443 (635)
Q Consensus 377 e~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 443 (635)
+++|||+|..|+..|+..|+.-|.. ..|.+..||.-||+++-||+.||+.||+|+|.|.|+...
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 4577778888999999999999998 599999999999999999999999999999999887653
No 19
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.65 E-value=2.1e-08 Score=101.31 Aligned_cols=60 Identities=25% Similarity=0.338 Sum_probs=53.5
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 380 PWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 380 ~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
|.||-|+ ++--++..|++.|.+ .-|.--.||.+||..+|||..||+.||+|||-|.||-|
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 3344444 999999999999998 69999999999999999999999999999999998854
No 20
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.59 E-value=1e-07 Score=86.60 Aligned_cols=61 Identities=20% Similarity=0.330 Sum_probs=54.5
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 006699 384 QRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMY 447 (635)
Q Consensus 384 rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~ 447 (635)
|.+|+..++..|+..|.+ ..||..-.|++||-+..||+..|++||+|+|.+.+|...-..+
T Consensus 21 RTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 21 RTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 445999999999999999 6999999999999999999999999999999999887543333
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.48 E-value=8.1e-08 Score=103.26 Aligned_cols=60 Identities=20% Similarity=0.317 Sum_probs=54.1
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 380 PWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 380 ~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
+|||||+ +.-.++..|+..|.+ ||-|+.+|.-.||.+++|.+..|++||+|||.|+|+..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 3444454 999999999999999 79999999999999999999999999999999998743
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.48 E-value=1.4e-07 Score=90.79 Aligned_cols=61 Identities=25% Similarity=0.358 Sum_probs=56.3
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 379 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 379 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
..+++|++.+..++.+|+..|.. +|||+..+|..|+..++++++-|+.||+|+|.+.|+..
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 45677888999999999999998 79999999999999999999999999999999988743
No 23
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.39 E-value=2.8e-07 Score=92.86 Aligned_cols=58 Identities=26% Similarity=0.429 Sum_probs=53.4
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 381 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 381 kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
+|.|+.|+.++..+|++-|.+ .-||+...+++||.+++|.+.+|++||.|+|+|.++.
T Consensus 38 RRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 38 RRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 355667999999999999999 6999999999999999999999999999999998764
No 24
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.39 E-value=2.9e-07 Score=94.58 Aligned_cols=53 Identities=25% Similarity=0.394 Sum_probs=50.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.|+..+...|++-|.+ -.||+.-.|++||.+|+|.+.+|++||+|||.|++|.
T Consensus 147 iFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred hhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 4999999999999999 5999999999999999999999999999999998764
No 25
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.37 E-value=2.2e-07 Score=95.83 Aligned_cols=57 Identities=26% Similarity=0.263 Sum_probs=52.4
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 006699 387 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 446 (635)
Q Consensus 387 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~ 446 (635)
++..|+-.|++-|.. .+|.|...|.+||..+|||+.||+.||+|||.|++|...+..
T Consensus 206 YTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 899999999999987 799999999999999999999999999999999988665443
No 26
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.36 E-value=2.5e-07 Score=97.05 Aligned_cols=59 Identities=27% Similarity=0.385 Sum_probs=53.4
Q ss_pred CCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 381 WRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 381 kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
+|++|+ |+-.+.+.|+.||.. |.||+.+.|++||--|+||+..|++||.|+|.+.+|..
T Consensus 112 qrrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 344455 999999999999999 79999999999999999999999999999999987743
No 27
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.32 E-value=6.9e-07 Score=89.50 Aligned_cols=58 Identities=21% Similarity=0.337 Sum_probs=52.9
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 381 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 381 kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
+++|..|+..|+..|++-|.+ .-|.+.+||.+++..+.||+.||+.||+|||.|.|+-
T Consensus 145 RkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 145 RKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 344555999999999999999 5999999999999999999999999999999998874
No 28
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.30 E-value=2.5e-07 Score=89.84 Aligned_cols=58 Identities=29% Similarity=0.412 Sum_probs=52.1
Q ss_pred CCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 381 WRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 381 kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
+||.|. |+..+...|++.|.. -.|.+-.|+.+||..++|+++||+.||+|+|+|.||-
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred hhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 344444 999999999999997 4899999999999999999999999999999999874
No 29
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.22 E-value=9.5e-07 Score=89.15 Aligned_cols=72 Identities=22% Similarity=0.327 Sum_probs=62.9
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHhhhhhc
Q 006699 381 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMYLEETKEQD 455 (635)
Q Consensus 381 kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~~~~~~~~~ 455 (635)
+..+.+|+-.++..|+.-|.+ .-||--.++.+||...|+++.||.+||+|||.|++|.-.-||.....+.+.
T Consensus 168 k~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasakkkqds 239 (288)
T KOG0847|consen 168 KQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAKKKQDS 239 (288)
T ss_pred cccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhccccCCC
Confidence 334556999999999999998 599999999999999999999999999999999999888888877666543
No 30
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.06 E-value=2.8e-06 Score=88.59 Aligned_cols=62 Identities=23% Similarity=0.364 Sum_probs=56.6
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 378 SHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 378 ~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
...||||++++.++++.|+.-|.. .|-|-.--|++|+.+|||....|++||+|+|+|.|+-.
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 356899999999999999999887 69999999999999999999999999999999877644
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.93 E-value=2.8e-05 Score=86.79 Aligned_cols=57 Identities=28% Similarity=0.348 Sum_probs=53.4
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 006699 379 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 438 (635)
Q Consensus 379 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRl 438 (635)
..||+|-.|+..|++.|+..|.+ ++||+.+.-+.|+.+++|.+.-|.|||-|+|+|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 45677777999999999999999 7999999999999999999999999999999995
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.82 E-value=6.6e-06 Score=86.35 Aligned_cols=57 Identities=18% Similarity=0.334 Sum_probs=51.8
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006699 384 QRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 443 (635)
Q Consensus 384 rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 443 (635)
|+-|+++|+..|++-|++ --|-+.-.|.+||..++|.+.-|++||+|+|+|.|+..+
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 456999999999888887 479999999999999999999999999999999998775
No 33
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.54 E-value=7e-05 Score=80.52 Aligned_cols=58 Identities=28% Similarity=0.547 Sum_probs=53.0
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 382 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 382 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
|.|+.|+..+...|+++|.. .|||....|+.||++|+|++..|..||.|+|.|.+|..
T Consensus 178 r~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 178 RNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 33456999999999999998 68999999999999999999999999999999988754
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.52 E-value=4.6e-05 Score=74.53 Aligned_cols=60 Identities=17% Similarity=0.092 Sum_probs=53.9
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 379 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 379 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
..+|.|.+|+..+++.|+.-|.. .+||....++.||..+++++..|.+||+|+|++.++.
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 34555667999999999999998 4999999999999999999999999999999998764
No 35
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.33 E-value=7.5e-05 Score=78.24 Aligned_cols=59 Identities=22% Similarity=0.354 Sum_probs=53.0
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 379 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 379 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
.+||||+.+-..-++.|+++|.. -|-|+.+....+|+++.|-+..|++||+|.|.|.|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 56777777777778899999998 599999999999999999999999999999999887
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.29 E-value=0.00011 Score=77.52 Aligned_cols=60 Identities=47% Similarity=0.716 Sum_probs=55.0
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 382 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 382 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
+++.+++.+. .+|+.|+.+|..+|||++-++.+|+..|+++..||++||+|+|+|+++.+
T Consensus 97 ~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 97 ARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred cccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 3455689999 99999999999999999999999999999999999999999999987744
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.32 E-value=0.003 Score=52.06 Aligned_cols=43 Identities=21% Similarity=0.398 Sum_probs=31.1
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 006699 392 VSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVR 437 (635)
Q Consensus 392 v~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrR 437 (635)
.+.|+++|.. |.++.+.+...|+.+++||..||.+||.-++.+
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 4559999999 599999999999999999999999999876544
No 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=95.31 E-value=0.015 Score=57.07 Aligned_cols=62 Identities=34% Similarity=0.552 Sum_probs=54.4
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006699 379 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 443 (635)
Q Consensus 379 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 443 (635)
..++++..+...+..+|..-|.. .+||....+..|+..+|++...|.+||+|.|.+.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 44556667999999999988887 799999999999999999999999999999999887543
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.62 E-value=0.25 Score=60.93 Aligned_cols=57 Identities=19% Similarity=0.358 Sum_probs=52.0
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006699 384 QRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 443 (635)
Q Consensus 384 rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 443 (635)
|..+...++++|+..|.+ .-||+.++.+.|.+..+|....|..||+|+|.+.+|+..
T Consensus 907 ~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 907 RTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred ccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 344899999999999998 699999999999999999999999999999999998753
No 40
>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=80.70 E-value=2.9 Score=33.64 Aligned_cols=47 Identities=30% Similarity=0.259 Sum_probs=31.5
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 006699 381 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 435 (635)
Q Consensus 381 kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaR 435 (635)
+|+|+.|+-+..-.+-..+.+ .+ -+..||+..|++.++|.+|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 466777988885555444554 23 588999999999999999999854
No 41
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=74.86 E-value=4.3 Score=48.24 Aligned_cols=45 Identities=27% Similarity=0.434 Sum_probs=41.3
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 006699 392 VSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 439 (635)
Q Consensus 392 v~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlk 439 (635)
+.+|+++|.. |+.|+.+|...+|.+.||...-|+.||.+.+....
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~ 612 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEM 612 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhh
Confidence 7888999887 79999999999999999999999999999987643
No 42
>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=73.75 E-value=3.9 Score=31.65 Aligned_cols=47 Identities=34% Similarity=0.419 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
.||++...+|...|.+ ++ .-.++|+..|+|...|+.+...+..++++
T Consensus 4 ~L~~~er~vi~~~y~~----~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----GL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----CC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 4889999999888865 32 45789999999999999999999888764
No 43
>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=72.88 E-value=4.8 Score=29.48 Aligned_cols=46 Identities=30% Similarity=0.307 Sum_probs=36.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 439 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlk 439 (635)
.|+.+...++...+.+. -.-.++|..+|++...|..|....+.+++
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 36788888888777542 24567899999999999999988887764
No 44
>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=72.21 E-value=6.1 Score=32.52 Aligned_cols=46 Identities=26% Similarity=0.331 Sum_probs=30.6
Q ss_pred CCCCCCChhHHH-HHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 006699 382 RPQRGLPERSVS-VLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 435 (635)
Q Consensus 382 R~rR~fpk~qv~-iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaR 435 (635)
++++.||++.+. ++...+.. ......+|+..|+++.+|.+|-.-.+
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 345679888854 45555454 46889999999999999999977665
No 45
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=69.53 E-value=47 Score=35.50 Aligned_cols=58 Identities=28% Similarity=0.508 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccCCCCCccCchhhhHHHhhhcccchhhhHHHHHH
Q 006699 261 EFMELQKRKTKLLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRDGIVGQIQA 334 (635)
Q Consensus 261 e~~elQ~kK~kLL~mLEEVd~ry~qYc~qmq~v~ssFe~vaG~gaa~~Ytalal~~mSrhfr~LrdaI~~qi~~ 334 (635)
-..+|+.+|..|..-++++++|-.+...+|.+ +|. |-+ +.+.+.-+..+|=.++.++.
T Consensus 5 ~L~eL~qrk~~Lq~eIe~LerR~~ri~~Emrt---sFa---G~S----------q~lA~RVqGFkdYLvGsLQD 62 (283)
T PF11285_consen 5 ALKELEQRKQALQIEIEQLERRRERIEKEMRT---SFA---GQS----------QDLAIRVQGFKDYLVGSLQD 62 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---ccc---cch----------HHHHHHHhhhHHHHHHHHHH
Confidence 35789999999999999999999988888876 454 322 34444455556666666554
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=69.22 E-value=7 Score=30.43 Aligned_cols=45 Identities=29% Similarity=0.386 Sum_probs=34.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 438 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRl 438 (635)
.||+....++...+.+. -.-.++|+.+|+|...|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 47888888887776652 3557899999999999999999998874
No 47
>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=62.89 E-value=20 Score=23.31 Aligned_cols=39 Identities=23% Similarity=0.278 Sum_probs=27.6
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWF 431 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF 431 (635)
+.++.+....+..++.. .+ ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 34666666666555543 33 45688899999999999984
No 48
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=53.92 E-value=15 Score=33.76 Aligned_cols=47 Identities=17% Similarity=0.116 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
.||+..+.++...+.+. + .-.++|..+|++...|.+|...+|.++++
T Consensus 106 ~L~~~~r~ii~l~~~~~----~----s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG----K----TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 58999999987666652 2 35789999999999999999999999875
No 49
>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=53.28 E-value=21 Score=31.29 Aligned_cols=48 Identities=29% Similarity=0.309 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||+....++...+.. .| .-.++|+.+|+++..|.+|....+.++++-
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 4788888887655443 44 446899999999999999999999988753
No 50
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=52.49 E-value=18 Score=33.49 Aligned_cols=49 Identities=24% Similarity=0.197 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++.-.+.+. .+ -.++|+.+|++...|.+++.-+|.++++.+
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999997776652 22 358999999999999999999999988755
No 51
>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=52.43 E-value=16 Score=33.13 Aligned_cols=48 Identities=25% Similarity=0.239 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||++...++...+.+ .+ .-.++|+.+|+|+..|.++...+|+++++-
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 5888999999876655 33 345699999999999999999999998763
No 52
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=50.88 E-value=21 Score=34.62 Aligned_cols=50 Identities=16% Similarity=0.238 Sum_probs=41.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 443 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 443 (635)
.||+.++.++.-.+.+ -+ .-.++|..+|+|+..|.++..-+|+++++-+.
T Consensus 134 ~Lp~~~R~v~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 134 HLPAQQARVFMMREYL----EL----SSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred hCCHHHHHHHhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4899999998877765 22 35789999999999999999999999988664
No 53
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=50.86 E-value=19 Score=33.71 Aligned_cols=50 Identities=14% Similarity=0.060 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
..||++.+.++..++.++ . .-.++|..+|++...|.+|..-+|+++++-+
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--L------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 458999999998887763 2 3478999999999999999999999987643
No 54
>PRK00118 putative DNA-binding protein; Validated
Probab=49.76 E-value=19 Score=33.28 Aligned_cols=56 Identities=20% Similarity=0.201 Sum_probs=43.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMYLEE 450 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~~~~ 450 (635)
.||+.++.++..++.+. + .-.++|+.+|+|+.-|.+|...+|.++++- ++.+..-+
T Consensus 17 ~L~ekqRevl~L~y~eg----~----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~-~~~~~~~~ 72 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD----Y----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY-EEKLHLYE 72 (104)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH-HHHHChHH
Confidence 47899999998887762 2 346799999999999999999999998873 45554433
No 55
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=48.74 E-value=21 Score=32.99 Aligned_cols=49 Identities=20% Similarity=0.200 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++...+.+ -+ .-.++|+.+|+|+..|.+|..-+|.++++.+
T Consensus 125 ~L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred hCCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3888888888766554 22 3478999999999999999999999998754
No 56
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=48.46 E-value=28 Score=32.98 Aligned_cols=48 Identities=15% Similarity=0.253 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||++...++...+.+ .+ .-.++|..+|++...|.+++..+|+++++-
T Consensus 129 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE----GL----SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 4899999998888876 33 357899999999999999999999998764
No 57
>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=47.19 E-value=16 Score=34.64 Aligned_cols=49 Identities=18% Similarity=0.154 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.-.+.+. + .-.++|..+|++...|.++.-.+|+++++.+
T Consensus 138 ~L~~~~r~v~~l~~~~~----~----s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG----L----SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 47888888887766652 2 4478999999999999999999999988754
No 58
>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=47.07 E-value=39 Score=26.85 Aligned_cols=52 Identities=23% Similarity=0.222 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 446 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~ 446 (635)
.|++....+|+.+..- + ...++|...+++++-|..+..+.++|+.-+...+.
T Consensus 3 ~LT~~E~~vl~~l~~G-----~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l 54 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG-----M----SNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAEL 54 (58)
T ss_dssp SS-HHHHHHHHHHHTT-----S-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHH
T ss_pred ccCHHHHHHHHHHHhc-----C----CcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHH
Confidence 4788889998777554 2 56789999999999999999999999865554443
No 59
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=46.30 E-value=24 Score=32.77 Aligned_cols=49 Identities=20% Similarity=0.205 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++...+.. -+ .-.++|+.+|++...|.+|...+|+++++.+
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 4889999998766554 22 2358999999999999999999999998755
No 60
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=46.10 E-value=21 Score=34.53 Aligned_cols=49 Identities=10% Similarity=0.126 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.+|...+.+. + .-.++|+.+|++...|.++...+|+++++.+
T Consensus 142 ~L~~~~r~vl~l~~~~~----~----s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG----L----TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 48999999998776663 2 4478999999999999999999999987644
No 61
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=45.91 E-value=19 Score=34.18 Aligned_cols=49 Identities=18% Similarity=0.125 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++...+.+. . .-.++|..+|++...|.+++..+|+++++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--A------SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998876662 2 4578999999999999999999999998654
No 62
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=45.08 E-value=28 Score=27.71 Aligned_cols=39 Identities=28% Similarity=0.281 Sum_probs=23.5
Q ss_pred HHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 395 LRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 395 Lr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
|+.++.++ -+ ....||+.+|+++..|+.|+.+...+..-
T Consensus 2 L~~~m~~~---~i----t~~~La~~~gis~~tl~~~~~~~~~~~~~ 40 (63)
T PF13443_consen 2 LKELMAER---GI----TQKDLARKTGISRSTLSRILNGKPSNPSL 40 (63)
T ss_dssp HHHHHHHT---T------HHHHHHHHT--HHHHHHHHTTT-----H
T ss_pred HHHHHHHc---CC----CHHHHHHHHCcCHHHHHHHHhcccccccH
Confidence 45566653 22 56789999999999999999987544433
No 63
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=44.61 E-value=24 Score=34.05 Aligned_cols=49 Identities=20% Similarity=0.258 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.-.+.+. . .-.++|+.+|+|...|.+...-+|+++++..
T Consensus 131 ~L~~~~r~i~~l~~~~g--~------s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--E------KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 58999999998766652 2 3478999999999999999999999988754
No 64
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=44.11 E-value=25 Score=33.71 Aligned_cols=49 Identities=20% Similarity=0.152 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+.++.++...+.+. + .-.++|..+|++...|.++...+|.++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 139 TLPEKQREILILRVVVG----L----SAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998776662 2 3578999999999999999999999988643
No 65
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=43.43 E-value=66 Score=23.92 Aligned_cols=48 Identities=25% Similarity=0.245 Sum_probs=35.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.|+++...++..+ .. .+ ...++|+.+|++...|..|....+.++.-..
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~~ 50 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVRS 50 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Confidence 4778888887554 32 22 4578999999999999999998877775433
No 66
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=43.37 E-value=32 Score=33.35 Aligned_cols=49 Identities=31% Similarity=0.237 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
..|++.++.+|+. +.+ .+ .-.++|+.+|+|...|++|...+|.++++-.
T Consensus 5 ~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4589999999977 333 33 4568999999999999999999999987654
No 67
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=43.14 E-value=25 Score=34.58 Aligned_cols=49 Identities=24% Similarity=0.304 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+++..++...+++. + .-.++|..+|++...|.+++..+|+++++.+
T Consensus 153 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE----L----SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998766652 2 4578999999999999999999999987654
No 68
>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=42.40 E-value=28 Score=32.92 Aligned_cols=48 Identities=21% Similarity=0.176 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||++++.++.-.+.+. + .-.++|..+|++...|.+.+..+|.++++-
T Consensus 134 ~Lp~~~r~v~~l~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG----L----TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999998887762 2 347899999999999999999999998763
No 69
>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=41.58 E-value=29 Score=31.89 Aligned_cols=48 Identities=29% Similarity=0.286 Sum_probs=39.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
..||++...++...+.+ .+ .-.++|+.+|+|...|.++..-+|+++++
T Consensus 110 ~~L~~~~r~v~~l~~~~----g~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR----GV----SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 35899999999886665 33 34679999999999999999999988865
No 70
>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=41.39 E-value=97 Score=25.66 Aligned_cols=42 Identities=19% Similarity=0.090 Sum_probs=30.8
Q ss_pred CCccccCCchHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 006699 251 SSRKQSLCSLEFM---ELQKRKTKLLSMLEEVDRRYRHYCDQMKA 292 (635)
Q Consensus 251 ~s~~~elssle~~---elQ~kK~kLL~mLEEVd~ry~qYc~qmq~ 292 (635)
...+||||--|.. -|.++|..|...++|....|+.-..|+..
T Consensus 5 ~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~ 49 (52)
T PF03791_consen 5 IGADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLSS 49 (52)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457999987754 37788999999999996666655555554
No 71
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=40.83 E-value=27 Score=33.51 Aligned_cols=49 Identities=20% Similarity=0.290 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++...++..-+.+. + .-.++|..+|++...|.+|+..+|+++++-+
T Consensus 141 ~L~~~~~~v~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYYEG----L----SQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhhcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58889988887766552 2 3478999999999999999999999998754
No 72
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=40.06 E-value=28 Score=32.83 Aligned_cols=49 Identities=18% Similarity=0.177 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++...+.+ .+ .-.++|+.+|++...|.+++..+|+++++-+
T Consensus 136 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 5899999998775554 22 3478999999999999999999999987643
No 73
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=39.70 E-value=29 Score=33.19 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++...+++. + .-.++|+.+|++...|.++...+|+++++.+
T Consensus 128 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQG----L----SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhcC----C----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 47888999887766552 2 3468999999999999999999999988744
No 74
>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=39.48 E-value=34 Score=34.75 Aligned_cols=49 Identities=22% Similarity=0.218 Sum_probs=41.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++...|.+. + .-.++|..+|++...|+.+...++.++++.+
T Consensus 205 ~L~~~~r~ii~l~~~~g----~----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN----L----SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998887763 2 2378999999999999999999999998754
No 75
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=39.35 E-value=29 Score=32.23 Aligned_cols=48 Identities=23% Similarity=0.175 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
..||++++.++.-.+.+. + .-.++|..+|+|...|..+...+|+++++
T Consensus 111 ~~L~~~~r~v~~l~~~~~----~----s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG----F----SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 358999999998876653 2 34689999999999999999999999875
No 76
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=38.88 E-value=53 Score=31.54 Aligned_cols=49 Identities=16% Similarity=0.208 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++++.++.-.+.+. .+ -.++|..+|+|..-|.+....+|+++++-+
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999988777662 23 378999999999999999999999998754
No 77
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=38.01 E-value=55 Score=32.51 Aligned_cols=51 Identities=24% Similarity=0.327 Sum_probs=42.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVE 444 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ie 444 (635)
.||++++.++.--+++. . .-.++|..+|+|...|.++..-+|+++++.+.+
T Consensus 148 ~L~~~~r~v~~L~~~~g--~------s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~ 198 (206)
T PRK12544 148 GLPAKYARVFMMREFIE--L------ETNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198 (206)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 58999999887777663 2 237899999999999999999999999886643
No 78
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=37.85 E-value=43 Score=34.09 Aligned_cols=49 Identities=20% Similarity=0.268 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.+|...+.+. + .-.++|+.+|++...|.+|...+|+++++.+
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 48999999998877652 2 2478999999999999999999999987643
No 79
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=37.81 E-value=36 Score=32.52 Aligned_cols=49 Identities=24% Similarity=0.139 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+....++.-.+.+. + .-.++|+.+|+++..|.+.+..+|+++++.+
T Consensus 129 ~L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG----L----SVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888876666652 2 4578999999999999999999999998754
No 80
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=37.39 E-value=36 Score=31.97 Aligned_cols=48 Identities=15% Similarity=0.013 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.++..-+|+++++-
T Consensus 112 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGASG----F----SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999988877663 2 346899999999999999999999998764
No 81
>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=37.32 E-value=32 Score=34.13 Aligned_cols=49 Identities=29% Similarity=0.410 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++...+.+ .+ .-.++|+.+|++...|..|...+++++++.+
T Consensus 178 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 178 ALPERERRILLLRFFE----DK----TQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 5899999999887765 22 4678999999999999999999999987643
No 82
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=37.18 E-value=61 Score=29.46 Aligned_cols=53 Identities=25% Similarity=0.209 Sum_probs=41.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 446 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~ 446 (635)
..|++...++|+-+ .+ .|. ..++|+..+++.+.|.+|..+.|+|+.-....+.
T Consensus 148 ~~lt~~e~~vl~l~-~~----g~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l 200 (211)
T PRK15369 148 PLLTPRERQILKLI-TE----GYT----NRDIAEQLSISIKTVETHRLNMMRKLDVHKVAEL 200 (211)
T ss_pred cCCCHHHHHHHHHH-HC----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 34999999999885 44 232 5789999999999999999999999864443333
No 83
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=36.83 E-value=43 Score=32.16 Aligned_cols=49 Identities=14% Similarity=0.195 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.+|.-.+.+ .+ .-.++|..+|+|...|.+.+..+|+++++..
T Consensus 131 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYH----EK----SVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999776665 22 4578999999999999999999999887643
No 84
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=36.52 E-value=41 Score=30.96 Aligned_cols=50 Identities=24% Similarity=0.223 Sum_probs=41.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
..||+.++.++.-.+.+ -+ .-.++|..+|++...|.+...-+|+++++.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWE----DM----DVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHh----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35899999999886666 23 2478999999999999999999999987654
No 85
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=36.21 E-value=34 Score=32.56 Aligned_cols=49 Identities=18% Similarity=0.223 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++.-.+.+. + .-.++|..+|+|...|.++...+|.++++.+
T Consensus 135 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG----Y----THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998766652 2 3478999999999999999999999987643
No 86
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=36.16 E-value=34 Score=33.43 Aligned_cols=49 Identities=20% Similarity=0.159 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+.++.++.-.+.+ -+ .-.++|..+|+|...|.+++.-+|+++++-+
T Consensus 113 ~Lp~~~r~v~~L~~~~----g~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGAS----GF----SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999888776 33 3467899999999999999999999988654
No 87
>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=35.98 E-value=51 Score=33.30 Aligned_cols=55 Identities=20% Similarity=0.135 Sum_probs=43.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVE 444 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ie 444 (635)
.||+..+.+|...|.-.-..++ .-.++|..+|+|...|+.+...+++|++..+.+
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~----t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~ 230 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPH----TLEEVGKEFNVTRERIRQIESKALRKLRHPSRS 230 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCc----cHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHH
Confidence 4899999999887721101233 467899999999999999999999999987643
No 88
>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=35.67 E-value=42 Score=31.07 Aligned_cols=49 Identities=24% Similarity=0.325 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++...+.+ .+ .-.++|..+|++...|.++...+|.++++.+
T Consensus 110 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE----DL----SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHh----cC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 5889999998776665 23 3467899999999999999999999987643
No 89
>PRK04217 hypothetical protein; Provisional
Probab=35.37 E-value=63 Score=30.17 Aligned_cols=50 Identities=18% Similarity=0.181 Sum_probs=40.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
..|+++.+.++..++.+. + .-.++|+.+|++...|.+.+..+|.+++..+
T Consensus 41 ~~Lt~eereai~l~~~eG----l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG----L----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 358999999998887763 2 5677999999999999999999988886543
No 90
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=34.94 E-value=56 Score=32.38 Aligned_cols=49 Identities=16% Similarity=0.146 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++..-+.+. .+ -.++|+.+|++..-|.++..-+|+++++-+
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LS------YEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888876666653 33 378999999999999999999999988644
No 91
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=34.92 E-value=44 Score=33.65 Aligned_cols=49 Identities=22% Similarity=0.159 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++.-.+.+. -+ -.++|+.+|+|..-|.++...+|+++++.+
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MS------YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998887773 23 367999999999999999999999988754
No 92
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=34.79 E-value=42 Score=32.37 Aligned_cols=49 Identities=20% Similarity=0.259 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++.-.+.+. + .-.++|+.+|++...|.++...+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILG----F----SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999987665552 2 3478999999999999999999999998755
No 93
>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=34.74 E-value=43 Score=31.41 Aligned_cols=49 Identities=12% Similarity=0.158 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++..-+++. + .-.++|+.+|+|...|.++..-+|+++++-+
T Consensus 119 ~L~~~~r~i~~l~~~~g----~----s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----L----TIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48889999987777662 2 3467999999999999999999999987643
No 94
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=34.56 E-value=43 Score=32.40 Aligned_cols=50 Identities=22% Similarity=0.221 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
..||+++..++.-.+.+. . .-.++|..+|++...|.+.+..+|+++++-+
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~------s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--L------PHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--C------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 458999999998766652 2 3368999999999999999999999988754
No 95
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=34.13 E-value=43 Score=32.02 Aligned_cols=49 Identities=12% Similarity=0.137 Sum_probs=39.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
..||++.+.++..-+.+. + .-.++|+.+|+|...|.+|...+|+++++-
T Consensus 132 ~~L~~~~r~i~~l~~~~~----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHAYVDG----C----SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 358899988877666652 2 347899999999999999999999988753
No 96
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=33.51 E-value=36 Score=34.19 Aligned_cols=49 Identities=31% Similarity=0.344 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++..-+.+ .+ .-.++|+.+|++...|.++...+|+++++.+
T Consensus 184 ~L~~~~r~vl~l~~~~----g~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQE----EL----NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999998877665 22 4578999999999999999999999998744
No 97
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=33.34 E-value=49 Score=32.18 Aligned_cols=49 Identities=16% Similarity=0.120 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.-.+.+ -| .-.++|+.+|++...|.++...+|+++++-+
T Consensus 116 ~Lp~~~r~i~~L~~~~----g~----s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGAS----GF----AYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999998887766 23 2357999999999999999999999988755
No 98
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=32.95 E-value=47 Score=30.84 Aligned_cols=48 Identities=23% Similarity=0.299 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+++..+|.-.+ + -+ .-.++|..+|++...|.++...+|.++++-+
T Consensus 112 ~L~~~~r~il~l~~-~----g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----GY----SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887776 5 23 4478999999999999999999999988744
No 99
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=32.78 E-value=32 Score=33.09 Aligned_cols=49 Identities=18% Similarity=0.197 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.-.+.+ .| .-.++|+.+|++...|.++...+|+++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHG----DL----ELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888766554 22 3467999999999999999999999998754
No 100
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=32.44 E-value=51 Score=31.12 Aligned_cols=47 Identities=13% Similarity=0.159 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
.||++++.++.-.+.+. .+ -.++|+.+|++..-|.++...+|+|++.
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 48999999988776652 23 3689999999999999999999999864
No 101
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=32.40 E-value=68 Score=31.11 Aligned_cols=49 Identities=16% Similarity=0.142 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++++.++.-.+.+ -| .-.++|+.+|++...|.+++.-+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~----g~----s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GL----SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4899999888776655 33 2478999999999999999999999988644
No 102
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=31.76 E-value=55 Score=33.30 Aligned_cols=49 Identities=16% Similarity=0.166 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+.++.++.-.+.+. + .-.++|+.+|++...|.++...+|+++++-+
T Consensus 171 ~Lp~~~R~v~~L~~~eg----~----s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN----M----SNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 47889999877666552 2 3478999999999999999999999998755
No 103
>PF13518 HTH_28: Helix-turn-helix domain
Probab=31.26 E-value=48 Score=25.16 Aligned_cols=25 Identities=36% Similarity=0.539 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhh
Q 006699 412 DKHILARQTGLSRSQVSNWFINARV 436 (635)
Q Consensus 412 EK~~LA~qTGLS~~QVsNWFiNaRr 436 (635)
...++|++.|++..+|..|....+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3466999999999999999877665
No 104
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=31.12 E-value=55 Score=30.32 Aligned_cols=49 Identities=22% Similarity=0.261 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.-.+.+ .+ ...++|+.+|++...|..+..-+|+++++-+
T Consensus 109 ~L~~~~r~v~~l~~~~----~~----s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH----GE----TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999999776665 22 3578999999999999999988888887654
No 105
>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=31.07 E-value=78 Score=32.60 Aligned_cols=50 Identities=28% Similarity=0.391 Sum_probs=41.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 443 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 443 (635)
.||++.+.++.-.+.+. + .-.++|..+|++..-|.++...+|+++++.+.
T Consensus 161 ~Lp~~~R~v~~L~~~eg----~----S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG----L----SMDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999988887763 2 24689999999999999999999999987653
No 106
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.01 E-value=53 Score=31.00 Aligned_cols=49 Identities=20% Similarity=0.222 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||.....+|.--+.+ . ..-.++|..+|+|...|.++...+|+++++-+
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 4788888888554433 2 23478999999999999999999999988643
No 107
>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=30.92 E-value=48 Score=32.99 Aligned_cols=48 Identities=27% Similarity=0.342 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||+..+.+|...|.+ .+ .-.++|+.+|++...|..+...+++++++.
T Consensus 175 ~L~~~~r~il~l~y~~----~~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYE----EL----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhC----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4899999999888776 22 347899999999999999999999998764
No 108
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=30.51 E-value=72 Score=30.56 Aligned_cols=49 Identities=20% Similarity=0.173 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.--+.+ .| .-.++|..+|++...|.+...-+|+++++-+
T Consensus 138 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 138 QLPEDLRTALTLREFD----GL----SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred hCCHHHhHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888877665554 44 3478999999999999999999999998765
No 109
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=30.22 E-value=47 Score=34.14 Aligned_cols=49 Identities=24% Similarity=0.221 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.+|...|.+ .+ .-.++|..+|++...|..+..-++.++++.+
T Consensus 203 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFLH----DL----TQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 5889999998887765 22 4578999999999999999999999988754
No 110
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=30.17 E-value=61 Score=31.76 Aligned_cols=49 Identities=22% Similarity=0.272 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+.++.++.--+++. + .-.++|..+|++..-|.+....+|+++++-+
T Consensus 139 ~Lp~~~r~v~~L~~~eg----~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD----F----EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48999999988776662 2 2367999999999999999999999998755
No 111
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=29.91 E-value=53 Score=31.67 Aligned_cols=48 Identities=15% Similarity=-0.000 Sum_probs=39.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
..||++++.++.-.+.+. + .-.++|..+|+|...|.++..-+|+++++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLG----L----SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 358999999987777662 2 34689999999999999999999999876
No 112
>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=29.66 E-value=1e+02 Score=25.34 Aligned_cols=49 Identities=27% Similarity=0.338 Sum_probs=37.0
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhh
Q 006699 387 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARV 436 (635)
Q Consensus 387 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRr 436 (635)
|++.+.++|+.-+..=+ .-+|-...-.+||+..|+++.-|..-+.++=+
T Consensus 1 LT~~Q~e~L~~A~~~GY-fd~PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 1 LTDRQREILKAAYELGY-FDVPRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCHHHHHHHHHHHHcCC-CCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 57888899987776532 23488889999999999999988765544433
No 113
>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=29.61 E-value=58 Score=30.19 Aligned_cols=49 Identities=16% Similarity=0.084 Sum_probs=39.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
..||+..+.++...+.+ -+ .-.++|+.+|++...|.+...-+|+++++.
T Consensus 121 ~~L~~~~r~vl~l~~~~----g~----s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQ----NL----PIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred HhCCHHHHHHHHHHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 35899999999887665 22 347899999999999999998888888763
No 114
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=29.37 E-value=79 Score=30.23 Aligned_cols=48 Identities=13% Similarity=0.104 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||++++.++.-.+.+. | .-.++|..+|++..-|.+....+++++...
T Consensus 127 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG----M----KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 48999999998877763 2 347899999999999999999999887653
No 115
>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=29.27 E-value=1.4e+02 Score=22.38 Aligned_cols=46 Identities=26% Similarity=0.216 Sum_probs=32.5
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 387 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 387 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
|++....++..+ .. .+ ...++|+.++++...|..|..-.+.++..+
T Consensus 1 l~~~e~~i~~~~-~~----~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 1 LTPREREVLRLL-AE----GK----TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 455666666543 22 22 557899999999999999998777766543
No 116
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=29.27 E-value=57 Score=31.50 Aligned_cols=49 Identities=29% Similarity=0.349 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++++.++.-.+.+ -+ .-.++|..+|+|...|.+.+..+|+++++-+
T Consensus 106 ~L~~~~r~i~~l~~~~----g~----~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELE----GL----SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5899999998776665 33 3478999999999999999999998887644
No 117
>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=29.22 E-value=60 Score=30.80 Aligned_cols=50 Identities=22% Similarity=0.278 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
..||++.+.++.-.+.+ -| .-.++|+.+|++...|.++..-+|+++++-+
T Consensus 99 ~~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 99 KELPDEYREAIRLTELE----GL----SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred HhCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35899999999887765 33 3478999999999999999999998887643
No 118
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=29.04 E-value=62 Score=33.37 Aligned_cols=49 Identities=24% Similarity=0.426 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.+|...|.+. -.-.++|..+|++...|......+++++++.+
T Consensus 212 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998887762 23578999999999999999999999988754
No 119
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=28.44 E-value=56 Score=33.29 Aligned_cols=48 Identities=23% Similarity=0.203 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||+..+.++...+.+ .+ .-.++|..+|+|...|.+++..+|+++++-
T Consensus 201 ~L~~~~r~vl~l~~~~----~~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYKE----EL----TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4899999999877765 22 357899999999999999999999998763
No 120
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.39 E-value=1.1e+02 Score=28.35 Aligned_cols=44 Identities=11% Similarity=0.304 Sum_probs=34.8
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhh
Q 006699 387 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINA 434 (635)
Q Consensus 387 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNa 434 (635)
-....+..+.+|+.+|+..| + ...+||+.+|+++..+..+|...
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~-~---sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESP-L---SLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCC-C---CHHHHHHHHCcCHHHHHHHHHHH
Confidence 34555677889999987665 3 45788999999999999999866
No 121
>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=27.88 E-value=39 Score=32.55 Aligned_cols=49 Identities=22% Similarity=0.226 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.-.+.+ -+ .-.++|+.+|+|...|.++..-+|+++++.+
T Consensus 131 ~Lp~~~r~i~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADVE----GF----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888887665554 22 3478999999999999999999999998755
No 122
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=27.88 E-value=95 Score=28.78 Aligned_cols=49 Identities=24% Similarity=0.253 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++...++.-.+.+. .+ -.++|..+|++..-|.+....+|+++++-+
T Consensus 105 ~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLRKLEG--LS------HQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998877763 23 478999999999999999999999887654
No 123
>cd00131 PAX Paired Box domain
Probab=27.87 E-value=2.8e+02 Score=26.07 Aligned_cols=47 Identities=19% Similarity=0.101 Sum_probs=33.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------ChhhHhhhhhhh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGL-------SRSQVSNWFINA 434 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGL-------S~~QVsNWFiNa 434 (635)
+.+..+....+..+..+ ||..+..|-.++-...|+ +...|..||.++
T Consensus 74 r~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 74 RVATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CcCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 34566666666667676 698888777666335566 999999997763
No 124
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=27.85 E-value=75 Score=30.36 Aligned_cols=49 Identities=22% Similarity=0.319 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+.++.++...+.+. + .-.++|+.+|++...|.++..-+|.++++-+
T Consensus 127 ~L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE----L----SIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999987776663 2 3478999999999999999999999987643
No 125
>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=27.57 E-value=79 Score=30.63 Aligned_cols=49 Identities=18% Similarity=0.224 Sum_probs=41.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++++.++...+.+. . .-.++|..+|++..-|.++..-+|+++++-+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--F------ESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999988877663 2 4578999999999999999999999998755
No 126
>PHA00542 putative Cro-like protein
Probab=27.56 E-value=1.7e+02 Score=25.38 Aligned_cols=35 Identities=14% Similarity=0.231 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 006699 412 DKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 446 (635)
Q Consensus 412 EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~ 446 (635)
...+||+.+|++...|..|.....++.....++++
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki 67 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKL 67 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHH
Confidence 45679999999999999999887655554444444
No 127
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=27.14 E-value=1.1e+02 Score=34.60 Aligned_cols=58 Identities=24% Similarity=0.199 Sum_probs=45.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMY 447 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~ 447 (635)
.||+..+.+|+-.|.-.-..|+ .-.++|+.+|+|+..|+.+...+++++++|.....+
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~----Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l 407 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTY----SLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRI 407 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHH
Confidence 4899999999888762111244 468899999999999999999999999988754433
No 128
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=27.14 E-value=68 Score=30.68 Aligned_cols=49 Identities=20% Similarity=0.285 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++.-.+.+. | .-.++|..+|++..-|.+....+|+++++-+
T Consensus 122 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN----L----TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998766552 2 3468999999999999999999999987644
No 129
>PRK06930 positive control sigma-like factor; Validated
Probab=27.13 E-value=70 Score=31.50 Aligned_cols=49 Identities=16% Similarity=0.080 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++.-.+.+ .+ .-.++|..+|++...|.++...+|.++++.+
T Consensus 114 ~L~~rer~V~~L~~~e----g~----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRGY----GL----SYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4889999988876655 22 3468999999999999999999999988754
No 130
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=26.94 E-value=67 Score=31.55 Aligned_cols=49 Identities=14% Similarity=0.062 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+....++..-+.+. -.-.++|..+|++...|.++...+|+++++-+
T Consensus 133 ~Lp~~~r~v~~l~~~~g--------~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 133 ALPPERREALILTQVLG--------YTYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred cCCHHHHHHhhhHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999987777663 23578999999999999999999999988654
No 131
>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=26.94 E-value=56 Score=24.93 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=19.1
Q ss_pred HHHHHhCCChhhHhhhhhhhh
Q 006699 415 ILARQTGLSRSQVSNWFINAR 435 (635)
Q Consensus 415 ~LA~qTGLS~~QVsNWFiNaR 435 (635)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999875
No 132
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=26.76 E-value=72 Score=30.56 Aligned_cols=49 Identities=22% Similarity=0.173 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+.++.++.-.+.+. -.-.++|+.+|++...|.++.-.+|+++++-+
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--------LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998766652 24578999999999999999999999987643
No 133
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=26.72 E-value=54 Score=30.78 Aligned_cols=49 Identities=20% Similarity=0.157 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.+|...+.+ .+ .-.++|..+|+|...|.+.+..+|+++++-+
T Consensus 120 ~L~~~~r~vl~l~~~~----g~----s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 120 TLSLEHRAVLVLHDLE----DL----PQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hCCHHHeeeeeehHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888776665 33 2578999999999999999999999988754
No 134
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=26.71 E-value=95 Score=30.28 Aligned_cols=48 Identities=25% Similarity=0.336 Sum_probs=38.9
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 387 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 387 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
++++..+++.-.++. .| ...++|+.+|+|+..|.+.+..+|.++.+.+
T Consensus 136 l~~~~~~~v~l~~~~----Gl----s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l 183 (185)
T PF07638_consen 136 LDPRQRRVVELRFFE----GL----SVEEIAERLGISERTVRRRLRRARAWLRREL 183 (185)
T ss_pred cCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 677788888777665 55 5678999999999999999999998876543
No 135
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=26.66 E-value=66 Score=30.20 Aligned_cols=49 Identities=16% Similarity=0.183 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.+|.--+.+ -+ .-.++|+.+|++..-|.++..-+|.++++-+
T Consensus 118 ~L~~~~r~vl~L~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYR----GW----STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4899999999887766 23 2468999999999999999999999988754
No 136
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=26.45 E-value=1.6e+02 Score=27.03 Aligned_cols=47 Identities=21% Similarity=0.253 Sum_probs=31.1
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 006699 382 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 435 (635)
Q Consensus 382 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaR 435 (635)
+++++++.+.+...-....+ +.+ ...++|+..|++..+|.+|..-.|
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~---~g~----sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE---PGM----TVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc---CCC----CHHHHHHHHCcCHHHHHHHHHHHh
Confidence 34566877775544333333 232 457789999999999999955443
No 137
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=26.04 E-value=84 Score=29.62 Aligned_cols=49 Identities=14% Similarity=0.173 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++...++.-.+.+. . .-.++|..+|++...|..+...+|+++++-+
T Consensus 119 ~L~~~~r~i~~l~~~~~--~------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQ--Y------SYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888886655552 2 3478999999999999999999999998755
No 138
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=25.98 E-value=95 Score=29.59 Aligned_cols=49 Identities=14% Similarity=0.109 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.++.--+.+. - .-.++|..+|+|..-|.+....+|.++++-+
T Consensus 117 ~Lp~~~r~i~~l~~~e~--~------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--Y------SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999998888766663 1 3468999999999999999999999988755
No 139
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=25.79 E-value=64 Score=32.23 Aligned_cols=53 Identities=19% Similarity=0.100 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.-.+.-+....+ .-.++|..+|++...|.++...+|+++++.+
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~----s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEK----TQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5899999998776521001122 3578999999999999999999999998754
No 140
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=25.46 E-value=6e+02 Score=24.27 Aligned_cols=49 Identities=22% Similarity=0.273 Sum_probs=38.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++++.++.--+.+ -|+ -.++|..+|++..-|..|..-+|.++++.+
T Consensus 127 ~Lp~~~R~~~~l~~~~----gls----~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 127 RLPPRQREAFLLRYLE----GLS----YEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred hCCHHHhHHhhhHhhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788887777555554 332 367888899999999999999999988765
No 141
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=25.36 E-value=78 Score=30.71 Aligned_cols=49 Identities=20% Similarity=0.135 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+.++.++.-.+.+ -+ .-.++|..+|++..-|.++..-+|.++++-+
T Consensus 111 ~Lp~~~R~v~~L~~~e----g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIE----GL----SYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4899999999887776 23 3478999999999999999999999887643
No 142
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=25.11 E-value=1.1e+02 Score=33.01 Aligned_cols=53 Identities=23% Similarity=0.186 Sum_probs=41.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.+|...|.-+....+ .-.++|..+|++...|+.+...+|+++|+.+
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~----s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAA----TLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCc----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999866522112233 5688999999999999999999999998755
No 143
>PF13551 HTH_29: Winged helix-turn helix
Probab=24.84 E-value=2.5e+02 Score=24.19 Aligned_cols=52 Identities=19% Similarity=0.088 Sum_probs=31.4
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCC--CCCHHHHHH-H-HHHh--CCChhhHhhhhh
Q 006699 381 WRPQRGLPERSVSVLRAWLFEHFLHP--YPSDVDKHI-L-ARQT--GLSRSQVSNWFI 432 (635)
Q Consensus 381 kR~rR~fpk~qv~iLr~Wf~eH~~nP--YPS~~EK~~-L-A~qT--GLS~~QVsNWFi 432 (635)
.|+++.++++....|.+++.++.... ..+..+-.. | .+.+ .++...|..|+.
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 34444499999999999999852111 233333333 3 2232 477777877764
No 144
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=23.87 E-value=83 Score=30.36 Aligned_cols=47 Identities=17% Similarity=0.104 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||+..+.++.. +.+ .| .-.++|..+|++...|.+.+..+|+++++-
T Consensus 155 ~L~~~~r~vl~l-~~e----~~----s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 155 LLSELEKEVLEL-YLD----GK----SYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred hCCHHHHHHHHH-HHc----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 578888898877 555 23 347899999999999999888888887763
No 145
>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=23.84 E-value=78 Score=31.59 Aligned_cols=47 Identities=21% Similarity=0.222 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
.||+....++...|.+ . ..-.++|+.+|+|+..|..+-..+..|+++
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 5899999998877654 2 257889999999999999998888888775
No 146
>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=23.81 E-value=36 Score=31.11 Aligned_cols=46 Identities=30% Similarity=0.297 Sum_probs=35.8
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006699 387 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 440 (635)
Q Consensus 387 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 440 (635)
||+....++...+.+. -.-.++|..+|++...|.++..-+|+++++
T Consensus 106 L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 106 LPENYRTVLILREFKE--------FSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred CCHhheeeeeehhhcc--------CcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6777777766544441 245789999999999999999999999875
No 147
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=23.76 E-value=86 Score=29.13 Aligned_cols=46 Identities=20% Similarity=0.236 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 439 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlk 439 (635)
.||++++.++.-.+.+. .+ -.++|..+|++...|.++...+++++.
T Consensus 113 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG--LG------YGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 48999999997777662 23 367999999999999999999988764
No 148
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=23.74 E-value=83 Score=29.99 Aligned_cols=48 Identities=21% Similarity=0.245 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||+....++...+.+ .+ .-.++|..+|++...|.+....+|+++++-
T Consensus 137 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 137 ELEPPRSELIRTAFFE----GI----TYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 4889999998877765 22 347899999999999999999999998764
No 149
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=23.64 E-value=1.5e+02 Score=28.82 Aligned_cols=49 Identities=16% Similarity=0.128 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+.++.++.-.+.++ . .-.++|..+|++..-|.++..-+|.++++-+
T Consensus 128 ~Lp~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQVIGG--F------SGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999988877773 2 3468999999999999999999999987755
No 150
>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=22.75 E-value=1.1e+02 Score=21.70 Aligned_cols=23 Identities=35% Similarity=0.371 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChhhHhhhhhhhh
Q 006699 413 KHILARQTGLSRSQVSNWFINAR 435 (635)
Q Consensus 413 K~~LA~qTGLS~~QVsNWFiNaR 435 (635)
...+|+.+|++...|.+|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45888999999999999988764
No 151
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=22.73 E-value=88 Score=30.30 Aligned_cols=49 Identities=16% Similarity=0.090 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.-.+.+. + .-.++|+.+|+|...|.....-+|+++++.+
T Consensus 111 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 111 KLPQDQREALILVGASG----F----SYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred hCCHHHHHHhhHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47999999988776662 2 3468999999999999999999999988754
No 152
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=21.91 E-value=82 Score=29.89 Aligned_cols=49 Identities=16% Similarity=0.125 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++.--+.+. . .-.++|+.+|++...|.++...++.++++-.
T Consensus 119 ~L~~~~r~i~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~ 167 (172)
T PRK09651 119 GLNGKTREAFLLSQLDG--L------TYSEIAHKLGVSVSSVKKYVAKATEHCLLFR 167 (172)
T ss_pred hCCHHHhHHhhhhhccC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887766653 2 3478999999999999999988888876543
No 153
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=21.56 E-value=1.2e+02 Score=30.49 Aligned_cols=52 Identities=31% Similarity=0.448 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 438 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRl 438 (635)
.|++.++++|+.-|..=+ -=||-...-.+||+++|+++.-+..=..++=+|+
T Consensus 155 ~LTdrQ~~vL~~A~~~GY-Fd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGY-FDYPRRVSLKDLAKELGISKSTLSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHHcCC-CCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 599999999988877532 3458899999999999999998866555554444
No 154
>PF13565 HTH_32: Homeodomain-like domain
Probab=21.20 E-value=4.3e+02 Score=21.63 Aligned_cols=40 Identities=25% Similarity=0.199 Sum_probs=26.2
Q ss_pred ChhHHHHHHHHHHHccCCCCCCHH-HHHHHHHHhCC----ChhhHhhh
Q 006699 388 PERSVSVLRAWLFEHFLHPYPSDV-DKHILARQTGL----SRSQVSNW 430 (635)
Q Consensus 388 pk~qv~iLr~Wf~eH~~nPYPS~~-EK~~LA~qTGL----S~~QVsNW 430 (635)
+.++.+.+.+++.+| |.-+.. -...|+.++|+ +...|..|
T Consensus 32 ~~e~~~~i~~~~~~~---p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEH---PRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 677778889998884 644443 44556666663 66666655
No 155
>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=20.62 E-value=1.3e+02 Score=31.27 Aligned_cols=48 Identities=25% Similarity=0.101 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||++++.++.-.+.+. .+ -.++|+.+|+|..-|.+.+.-+|+++++.
T Consensus 142 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLG--WR------AAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred hCCHHHhhHhhhHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 58899988887766652 23 36899999999999999999999998764
No 156
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=20.53 E-value=85 Score=31.52 Aligned_cols=49 Identities=22% Similarity=0.257 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||++.+.++...+.+ .+ .-.++|..+|+|...|.+...-+|.++++-+
T Consensus 149 ~L~~~~r~i~~l~~~~----g~----s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 149 ALPDAFRAVFVLRVVE----EL----SVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hCCHHHhhhheeehhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888665554 33 4578999999999999999999998888754
No 157
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=20.41 E-value=96 Score=29.23 Aligned_cols=49 Identities=14% Similarity=0.217 Sum_probs=39.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 385 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 385 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
..||++.+.++.-.+.+. + .-.++|..+|++..-|.++..++|+.++..
T Consensus 117 ~~L~~~~r~v~~L~~~eg----~----s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEG----L----TYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 358999999987766662 2 346899999999999999998888887643
No 158
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=20.40 E-value=1e+02 Score=31.79 Aligned_cols=49 Identities=22% Similarity=0.333 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 442 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 442 (635)
.||+..+.+|...|.+ .+ .-.++|..+|+|...|+.+..-++.++++.+
T Consensus 205 ~L~~~er~vi~l~y~e----~~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 205 ALEEKERKVMALYYYE----EL----VLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999888765 32 4578999999999999999999999988754
No 159
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=20.36 E-value=99 Score=31.65 Aligned_cols=48 Identities=25% Similarity=0.257 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006699 386 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 441 (635)
Q Consensus 386 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 441 (635)
.||+..+.++...|.+ .+ .-.++|+.+|+|...|..+-.+++.|+++.
T Consensus 209 ~L~~~er~vi~~~~~~----~~----t~~eIA~~lgis~~~V~~~~~~al~kLr~~ 256 (258)
T PRK08215 209 KLNDREKLILNLRFFQ----GK----TQMEVAEEIGISQAQVSRLEKAALKHMRKY 256 (258)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4899999998887765 32 357899999999999999999999888764
Done!