Query 003323
Match_columns 830
No_of_seqs 313 out of 1022
Neff 3.1
Searched_HMMs 46136
Date Thu Mar 28 21:19:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003323.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003323hhsearch_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 1.6E-41 3.4E-46 322.0 13.5 139 387-527 1-139 (140)
2 PF07526 POX: Associated with 100.0 2.7E-40 5.8E-45 314.0 13.8 136 391-527 1-139 (140)
3 KOG0773 Transcription factor M 100.0 2E-34 4.3E-39 301.0 10.9 261 389-652 45-312 (342)
4 KOG0774 Transcription factor P 99.9 3.3E-21 7.2E-26 198.8 12.6 151 463-654 102-261 (334)
5 PF05920 Homeobox_KN: Homeobox 99.6 2.1E-15 4.5E-20 117.4 4.0 40 597-636 1-40 (40)
6 KOG0775 Transcription factor S 99.5 8.2E-14 1.8E-18 145.3 9.8 50 586-638 183-232 (304)
7 cd00086 homeodomain Homeodomai 99.4 1.1E-12 2.4E-17 104.0 6.6 57 581-640 2-58 (59)
8 PF00046 Homeobox: Homeobox do 99.3 1.9E-12 4.2E-17 103.6 5.9 57 580-639 1-57 (57)
9 smart00389 HOX Homeodomain. DN 99.3 3.8E-12 8.3E-17 100.7 6.5 55 581-638 2-56 (56)
10 KOG0487 Transcription factor A 98.8 2.7E-09 5.8E-14 113.9 3.5 64 579-645 235-298 (308)
11 KOG0842 Transcription factor t 98.8 3.4E-09 7.4E-14 113.0 3.9 65 579-646 152-217 (307)
12 KOG0488 Transcription factor B 98.6 3.1E-08 6.7E-13 105.7 5.4 58 583-643 176-233 (309)
13 KOG0843 Transcription factor E 98.6 2.8E-08 6.1E-13 99.7 4.2 63 579-644 102-164 (197)
14 KOG0483 Transcription factor H 98.6 4.4E-08 9.6E-13 99.3 5.6 71 579-652 50-120 (198)
15 KOG0489 Transcription factor z 98.6 2.5E-08 5.5E-13 103.6 3.8 61 579-642 159-219 (261)
16 KOG0493 Transcription factor E 98.6 3.8E-08 8.2E-13 103.3 4.8 63 576-641 243-305 (342)
17 TIGR01565 homeo_ZF_HD homeobox 98.5 2.2E-07 4.9E-12 78.3 5.5 52 580-634 2-57 (58)
18 KOG0850 Transcription factor D 98.4 1.6E-07 3.5E-12 97.1 4.6 60 580-642 123-182 (245)
19 KOG3802 Transcription factor O 98.4 1.6E-07 3.4E-12 103.0 3.9 60 579-641 293-353 (398)
20 KOG0484 Transcription factor P 98.4 9.6E-07 2.1E-11 82.8 7.3 63 582-647 20-82 (125)
21 COG5576 Homeodomain-containing 98.4 4E-07 8.6E-12 89.4 5.0 64 577-643 49-112 (156)
22 KOG0485 Transcription factor N 98.4 3E-07 6.5E-12 94.8 4.2 62 579-643 104-165 (268)
23 KOG2251 Homeobox transcription 98.3 8.2E-07 1.8E-11 91.5 4.5 59 580-641 38-96 (228)
24 KOG0486 Transcription factor P 98.2 7E-07 1.5E-11 95.8 3.9 58 585-645 118-175 (351)
25 KOG0492 Transcription factor M 98.2 1.3E-06 2.8E-11 89.7 5.0 60 579-641 144-203 (246)
26 KOG0848 Transcription factor C 98.1 1.3E-06 2.8E-11 92.3 2.9 58 585-645 205-262 (317)
27 KOG0494 Transcription factor C 98.1 2.3E-06 5E-11 90.2 4.7 56 583-641 145-200 (332)
28 KOG4577 Transcription factor L 98.1 2.7E-06 5.8E-11 90.7 3.6 63 576-641 164-226 (383)
29 KOG0491 Transcription factor B 98.0 2.6E-06 5.6E-11 85.1 2.2 56 583-641 104-159 (194)
30 KOG2252 CCAAT displacement pro 97.8 2E-05 4.3E-10 89.6 5.5 56 579-637 420-475 (558)
31 KOG0847 Transcription factor, 97.6 2.6E-05 5.5E-10 81.0 2.5 62 583-647 171-232 (288)
32 KOG0844 Transcription factor E 97.6 2.5E-05 5.4E-10 84.0 1.4 62 579-643 181-242 (408)
33 KOG0849 Transcription factor P 97.5 9.2E-05 2E-09 80.7 4.2 60 580-642 177-236 (354)
34 KOG0490 Transcription factor, 97.4 6.9E-05 1.5E-09 73.8 2.3 60 579-641 60-119 (235)
35 KOG0773 Transcription factor M 97.4 6.9E-05 1.5E-09 79.8 2.0 60 581-641 97-156 (342)
36 KOG1168 Transcription factor A 97.2 0.00011 2.5E-09 78.7 1.3 59 578-639 308-366 (385)
37 PF11569 Homez: Homeodomain le 96.1 0.0041 8.8E-08 52.9 2.7 43 591-636 10-52 (56)
38 KOG0490 Transcription factor, 94.7 0.027 5.9E-07 55.7 3.6 62 578-642 152-213 (235)
39 PF03791 KNOX2: KNOX2 domain ; 92.9 0.14 3E-06 43.3 4.0 40 474-534 8-51 (52)
40 KOG1146 Homeobox protein [Gene 90.9 0.17 3.7E-06 63.4 3.3 59 581-642 905-963 (1406)
41 PF03792 PBC: PBC domain; Int 88.5 6.6 0.00014 41.0 11.9 73 458-537 101-182 (191)
42 PF11285 DUF3086: Protein of u 87.0 6.7 0.00014 42.8 11.3 121 460-600 6-154 (283)
43 KOG3623 Homeobox transcription 81.8 8 0.00017 47.2 10.0 45 591-638 568-612 (1007)
44 PF04218 CENP-B_N: CENP-B N-te 79.0 3.8 8.3E-05 34.0 4.6 47 580-634 1-47 (53)
45 PRK09646 RNA polymerase sigma 74.2 34 0.00074 33.7 10.5 49 585-641 142-190 (194)
46 PF04545 Sigma70_r4: Sigma-70, 71.6 4.5 9.8E-05 32.1 3.1 47 585-639 4-50 (50)
47 cd06171 Sigma70_r4 Sigma70, re 71.4 5.4 0.00012 29.8 3.4 45 586-638 11-55 (55)
48 PRK12536 RNA polymerase sigma 71.4 1E+02 0.0023 29.9 14.0 48 586-641 130-177 (181)
49 PRK12547 RNA polymerase sigma 70.0 1.1E+02 0.0023 29.4 13.0 49 585-641 112-160 (164)
50 PF08281 Sigma70_r4_2: Sigma-7 64.8 10 0.00022 30.3 3.9 44 586-637 11-54 (54)
51 TIGR02937 sigma70-ECF RNA poly 64.0 1.1E+02 0.0023 27.2 11.3 48 585-640 110-157 (158)
52 PF01527 HTH_Tnp_1: Transposas 63.0 12 0.00026 31.4 4.2 46 581-634 2-48 (76)
53 PRK12516 RNA polymerase sigma 61.8 1.7E+02 0.0038 29.0 13.6 49 586-642 117-165 (187)
54 PRK09642 RNA polymerase sigma 61.0 9.7 0.00021 35.9 3.6 50 585-642 106-155 (160)
55 PRK12546 RNA polymerase sigma 60.3 1.9E+02 0.004 29.0 12.6 49 585-641 113-161 (188)
56 cd00569 HTH_Hin_like Helix-tur 59.3 15 0.00033 24.4 3.4 38 585-630 5-42 (42)
57 PRK12530 RNA polymerase sigma 58.2 13 0.00027 36.7 4.0 54 585-646 134-187 (189)
58 PRK11924 RNA polymerase sigma 57.2 1.7E+02 0.0037 27.5 12.8 49 586-642 126-174 (179)
59 PRK06759 RNA polymerase factor 52.8 15 0.00033 34.1 3.5 48 585-640 106-153 (154)
60 PRK12540 RNA polymerase sigma 52.7 2.4E+02 0.0053 27.9 12.9 49 586-642 112-160 (182)
61 TIGR02985 Sig70_bacteroi1 RNA 51.6 17 0.00036 33.5 3.4 48 585-640 113-160 (161)
62 PRK12532 RNA polymerase sigma 50.9 16 0.00035 35.8 3.5 52 585-644 136-187 (195)
63 PRK09644 RNA polymerase sigma 50.8 18 0.00039 34.4 3.7 49 585-641 108-156 (165)
64 PRK12514 RNA polymerase sigma 49.2 18 0.00038 34.9 3.4 49 585-641 129-177 (179)
65 PRK09652 RNA polymerase sigma 48.9 19 0.00042 33.8 3.5 50 585-642 128-177 (182)
66 PRK12512 RNA polymerase sigma 47.2 17 0.00037 35.1 3.0 50 585-642 131-180 (184)
67 TIGR02939 RpoE_Sigma70 RNA pol 46.4 16 0.00034 35.1 2.6 49 585-641 138-186 (190)
68 PRK06811 RNA polymerase factor 46.1 21 0.00046 35.0 3.4 50 585-642 131-180 (189)
69 smart00421 HTH_LUXR helix_turn 45.0 52 0.0011 25.1 4.8 51 585-644 3-53 (58)
70 PRK00118 putative DNA-binding 44.8 23 0.00049 33.7 3.2 49 585-641 17-65 (104)
71 PF13443 HTH_26: Cro/C1-type H 44.3 25 0.00055 28.7 3.1 27 611-637 12-38 (63)
72 PRK12519 RNA polymerase sigma 43.9 21 0.00045 34.8 3.0 50 585-642 141-190 (194)
73 PRK12541 RNA polymerase sigma 43.7 25 0.00054 33.3 3.4 48 585-640 112-159 (161)
74 TIGR03001 Sig-70_gmx1 RNA poly 43.2 35 0.00075 35.9 4.6 53 585-645 161-213 (244)
75 TIGR02999 Sig-70_X6 RNA polyme 41.9 28 0.0006 33.5 3.5 47 586-640 135-181 (183)
76 TIGR02989 Sig-70_gvs1 RNA poly 41.6 29 0.00063 32.4 3.5 47 585-639 111-157 (159)
77 PRK03975 tfx putative transcri 41.3 29 0.00062 34.6 3.5 50 584-642 5-54 (141)
78 PRK15369 two component system 41.3 67 0.0015 29.5 5.7 54 585-647 149-202 (211)
79 PRK12526 RNA polymerase sigma 41.0 27 0.00059 34.9 3.4 49 585-641 153-201 (206)
80 TIGR02983 SigE-fam_strep RNA p 40.9 29 0.00063 32.7 3.4 49 585-641 110-158 (162)
81 PRK09648 RNA polymerase sigma 40.4 29 0.00063 33.8 3.4 49 585-641 139-187 (189)
82 PRK12545 RNA polymerase sigma 40.2 34 0.00075 34.1 3.9 51 585-643 139-189 (201)
83 PRK09047 RNA polymerase factor 40.1 28 0.00061 32.6 3.1 50 585-642 106-155 (161)
84 PRK12531 RNA polymerase sigma 39.6 33 0.00071 33.8 3.6 50 585-642 141-190 (194)
85 TIGR02941 Sigma_B RNA polymera 39.1 34 0.00074 35.4 3.8 49 585-641 205-253 (255)
86 TIGR02393 RpoD_Cterm RNA polym 39.0 41 0.0009 34.6 4.4 57 585-645 176-232 (238)
87 PRK08583 RNA polymerase sigma 38.1 40 0.00088 34.9 4.2 49 585-641 205-253 (257)
88 PRK05602 RNA polymerase sigma 37.7 31 0.00066 33.5 3.1 48 586-641 129-176 (186)
89 PF00196 GerE: Bacterial regul 37.5 53 0.0012 26.9 4.0 53 585-646 3-55 (58)
90 PRK13919 putative RNA polymera 36.9 31 0.00067 33.3 3.0 48 586-641 136-183 (186)
91 PRK12523 RNA polymerase sigma 36.9 39 0.00085 32.5 3.6 49 585-641 119-167 (172)
92 PRK09639 RNA polymerase sigma 36.3 36 0.00078 32.1 3.2 47 586-641 113-159 (166)
93 PRK06930 positive control sigm 36.2 38 0.00082 34.2 3.5 52 586-645 115-166 (170)
94 TIGR02954 Sig70_famx3 RNA poly 36.0 32 0.00069 32.8 2.8 49 585-641 119-167 (169)
95 PRK12533 RNA polymerase sigma 36.0 31 0.00066 35.5 2.9 49 585-641 134-182 (216)
96 COG1595 RpoE DNA-directed RNA 36.0 4.3E+02 0.0092 25.9 13.1 49 586-642 128-176 (182)
97 PRK06986 fliA flagellar biosyn 35.8 30 0.00065 35.4 2.8 48 586-641 185-232 (236)
98 PRK12520 RNA polymerase sigma 35.8 45 0.00097 32.7 3.9 51 585-643 131-181 (191)
99 TIGR02948 SigW_bacill RNA poly 35.6 35 0.00076 32.7 3.1 49 585-641 136-184 (187)
100 TIGR02980 SigBFG RNA polymeras 35.5 36 0.00078 34.4 3.3 49 585-641 178-226 (227)
101 PRK12544 RNA polymerase sigma 35.0 48 0.001 33.6 4.1 53 585-645 148-200 (206)
102 PRK12538 RNA polymerase sigma 34.8 43 0.00092 34.8 3.7 49 586-642 172-220 (233)
103 PRK12537 RNA polymerase sigma 34.7 36 0.00079 33.1 3.1 48 585-640 133-180 (182)
104 PRK12515 RNA polymerase sigma 34.7 46 0.001 32.5 3.8 49 585-641 131-179 (189)
105 PRK09640 RNA polymerase sigma 34.6 4.5E+02 0.0098 25.8 12.6 48 586-641 135-182 (188)
106 TIGR02943 Sig70_famx1 RNA poly 34.1 48 0.001 32.8 3.8 50 585-642 131-180 (188)
107 PRK04217 hypothetical protein; 33.9 65 0.0014 31.0 4.5 49 585-641 42-90 (110)
108 TIGR02479 FliA_WhiG RNA polyme 32.4 43 0.00093 33.9 3.2 49 585-641 175-223 (224)
109 TIGR02947 SigH_actino RNA poly 31.9 29 0.00064 33.9 1.9 50 585-642 131-180 (193)
110 PRK09415 RNA polymerase factor 31.9 4.9E+02 0.011 25.4 12.6 49 585-641 127-175 (179)
111 PRK09649 RNA polymerase sigma 31.6 49 0.0011 32.5 3.4 47 585-639 130-176 (185)
112 PRK12524 RNA polymerase sigma 30.9 50 0.0011 32.6 3.3 49 585-641 136-184 (196)
113 PRK09645 RNA polymerase sigma 30.7 47 0.001 31.7 3.1 48 586-641 119-166 (173)
114 PRK07037 extracytoplasmic-func 30.7 54 0.0012 30.9 3.4 49 585-641 109-157 (163)
115 PRK07670 RNA polymerase sigma 30.5 48 0.001 34.4 3.3 48 585-640 201-248 (251)
116 PHA00542 putative Cro-like pro 30.3 1.5E+02 0.0032 26.5 5.9 36 611-646 33-68 (82)
117 PRK07408 RNA polymerase sigma 30.1 46 0.00099 34.9 3.1 49 585-641 203-251 (256)
118 PRK12513 RNA polymerase sigma 30.1 26 0.00057 34.2 1.3 49 585-641 139-187 (194)
119 PRK12539 RNA polymerase sigma 29.1 58 0.0012 31.8 3.4 49 585-641 131-179 (184)
120 PRK09641 RNA polymerase sigma 28.8 58 0.0013 31.3 3.3 49 585-641 136-184 (187)
121 PRK12542 RNA polymerase sigma 28.6 63 0.0014 31.5 3.6 49 585-641 122-170 (185)
122 PRK06288 RNA polymerase sigma 28.6 60 0.0013 34.1 3.7 49 585-641 212-260 (268)
123 PRK12522 RNA polymerase sigma 27.9 65 0.0014 31.0 3.5 51 585-643 119-169 (173)
124 PRK09647 RNA polymerase sigma 27.6 67 0.0015 32.5 3.7 49 585-641 138-186 (203)
125 PRK12543 RNA polymerase sigma 27.6 98 0.0021 30.1 4.7 50 585-642 117-166 (179)
126 TIGR02952 Sig70_famx2 RNA poly 27.5 65 0.0014 30.4 3.4 48 585-640 122-169 (170)
127 cd06170 LuxR_C_like C-terminal 27.3 1.5E+02 0.0033 22.7 4.9 48 586-642 1-48 (57)
128 PRK12517 RNA polymerase sigma 27.3 87 0.0019 31.0 4.3 50 585-642 128-177 (188)
129 PRK09637 RNA polymerase sigma 27.3 66 0.0014 31.7 3.5 49 585-641 106-154 (181)
130 cd01392 HTH_LacI Helix-turn-he 27.3 50 0.0011 25.9 2.2 21 614-634 2-22 (52)
131 PRK12534 RNA polymerase sigma 26.6 71 0.0015 31.0 3.5 48 586-641 138-185 (187)
132 PF05722 Ustilago_mating: Usti 26.4 23 0.0005 37.8 0.2 37 690-727 32-68 (286)
133 PF07638 Sigma70_ECF: ECF sigm 26.3 6.6E+02 0.014 25.1 15.5 48 586-641 136-183 (185)
134 PRK11511 DNA-binding transcrip 25.5 1.2E+02 0.0027 28.6 4.8 43 587-633 7-49 (127)
135 PRK12529 RNA polymerase sigma 25.5 79 0.0017 30.8 3.6 48 585-640 127-174 (178)
136 TIGR02959 SigZ RNA polymerase 25.4 74 0.0016 30.8 3.4 49 585-641 100-148 (170)
137 PRK12528 RNA polymerase sigma 25.3 85 0.0018 29.7 3.7 46 585-638 113-158 (161)
138 PRK12535 RNA polymerase sigma 24.9 73 0.0016 31.9 3.3 50 585-642 133-182 (196)
139 TIGR02885 spore_sigF RNA polym 24.7 74 0.0016 32.3 3.4 48 585-640 183-230 (231)
140 PRK11923 algU RNA polymerase s 24.6 72 0.0016 31.1 3.2 48 586-641 139-186 (193)
141 PRK08295 RNA polymerase factor 24.5 76 0.0017 31.1 3.3 48 585-641 155-202 (208)
142 PRK08301 sporulation sigma fac 24.3 68 0.0015 32.6 3.1 53 585-641 178-230 (234)
143 TIGR02960 SigX5 RNA polymerase 24.0 81 0.0018 33.4 3.6 49 585-641 142-190 (324)
144 PF13945 NST1: Salt tolerance 24.0 1.1E+02 0.0023 32.3 4.3 32 471-502 152-183 (190)
145 PF13518 HTH_28: Helix-turn-he 24.0 75 0.0016 24.8 2.6 25 611-635 14-38 (52)
146 TIGR02859 spore_sigH RNA polym 23.9 98 0.0021 30.1 3.9 46 586-640 151-196 (198)
147 PRK12511 RNA polymerase sigma 23.5 84 0.0018 31.1 3.4 49 585-641 111-159 (182)
148 PRK12518 RNA polymerase sigma 23.4 36 0.00078 32.5 0.8 48 586-641 121-168 (175)
149 TIGR02950 SigM_subfam RNA poly 23.2 36 0.00078 31.6 0.8 46 586-639 106-151 (154)
150 PRK12527 RNA polymerase sigma 23.1 89 0.0019 29.5 3.4 48 586-641 106-153 (159)
151 TIGR02394 rpoS_proteo RNA poly 22.3 1E+02 0.0022 32.8 3.9 54 585-642 222-275 (285)
152 cd00093 HTH_XRE Helix-turn-hel 22.0 1.1E+02 0.0023 22.2 3.0 23 612-634 15-37 (58)
153 PRK07598 RNA polymerase sigma 21.8 1.8E+02 0.0038 33.8 5.9 60 585-648 350-409 (415)
154 cd00131 PAX Paired Box domain 21.2 4.7E+02 0.01 25.3 7.9 47 584-633 74-127 (128)
155 PRK05657 RNA polymerase sigma 21.1 1.2E+02 0.0025 33.5 4.2 54 585-642 262-315 (325)
156 PRK07122 RNA polymerase sigma 20.8 83 0.0018 33.4 3.0 48 585-640 215-262 (264)
157 PRK05572 sporulation sigma fac 20.6 82 0.0018 32.7 2.8 49 585-641 202-250 (252)
158 PRK08215 sporulation sigma fac 20.2 96 0.0021 32.3 3.2 49 585-641 209-257 (258)
159 PRK05911 RNA polymerase sigma 20.1 1.1E+02 0.0023 32.3 3.6 49 585-641 205-253 (257)
No 1
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=1.6e-41 Score=321.97 Aligned_cols=139 Identities=65% Similarity=0.938 Sum_probs=111.7
Q ss_pred ccccccccCccchhHHHHHHHHHhhcccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhhHHHHHHH
Q 003323 387 LGVVNVLRNSKYAKAAQELLEEFCSVGRGQFKKSKFGKNNTNPSSSSGGGGGGVGCGGSSSSTKDLPPLSAADRIEHQRR 466 (830)
Q Consensus 387 tG~asvL~~SRYLkpAQeLLdE~csVg~~~~~~~k~~~~~~~~~~~~~~gg~~~~~~gssss~~~~~~lS~aer~E~q~k 466 (830)
+||+++|++|||||||||||||||+|+++...+.+..+..+........++++ ..+.+++.+..++++++||+|+|+|
T Consensus 1 ~g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~g~s~~~~~~~ls~~~r~e~q~k 78 (140)
T smart00574 1 TGGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQSGNDSPVSTSSNEGGGE--NLSGGSSSSEVPPLSTAERQELQRK 78 (140)
T ss_pred CchhhhccCccccccHHHHHHHHhcccHHhhcccccccccccccccccCCCcC--CCCCCCCCCCCCCCchhHHHHHHHH
Confidence 68999999999999999999999999887654333222111111111111111 1112333455778999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCCccchHHHHHHHHHhhhhHHHHHH
Q 003323 467 KVKLLSMLDEVDRRYNHYCEQMQMVVTSFDLVMGFGAAVPYTALAQKAMSRHFRCLKDAIA 527 (830)
Q Consensus 467 KaKLL~mLdEVDrRYeqY~eQmq~VvsSFe~vaG~Gaa~pYtaLAlkamSRhFR~LkDAI~ 527 (830)
|+||+.||+|||+||+|||+|||+|+++||.|+|+|++.|||+||+|+||||||||||+|.
T Consensus 79 k~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 79 KAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999999995
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=2.7e-40 Score=313.97 Aligned_cols=136 Identities=60% Similarity=0.864 Sum_probs=103.0
Q ss_pred ccccCccchhHHHHHHHHHhhccccccccccc---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhhHHHHHHHH
Q 003323 391 NVLRNSKYAKAAQELLEEFCSVGRGQFKKSKF---GKNNTNPSSSSGGGGGGVGCGGSSSSTKDLPPLSAADRIEHQRRK 467 (830)
Q Consensus 391 svL~~SRYLkpAQeLLdE~csVg~~~~~~~k~---~~~~~~~~~~~~~gg~~~~~~gssss~~~~~~lS~aer~E~q~kK 467 (830)
+||++|||||||||||||||+|+++....... ........+....+.++ .....+++.+..+++++++++|+|+||
T Consensus 1 q~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ls~~~~~e~q~kK 79 (140)
T PF07526_consen 1 QVLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSGAPGGANSSGSSSSSGG-SSSSSSSSDSSSPELSPAERQELQRKK 79 (140)
T ss_pred CccccchhHHHHHHHHHHHHcccchhhhcchhhccccccccccCCCCCCCCC-CCCCccccCCCCCCCChhhHHHHHHHH
Confidence 47999999999999999999998842111100 00000000001111100 011122223445779999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCCccchHHHHHHHHHhhhhHHHHHH
Q 003323 468 VKLLSMLDEVDRRYNHYCEQMQMVVTSFDLVMGFGAAVPYTALAQKAMSRHFRCLKDAIA 527 (830)
Q Consensus 468 aKLL~mLdEVDrRYeqY~eQmq~VvsSFe~vaG~Gaa~pYtaLAlkamSRhFR~LkDAI~ 527 (830)
+|||.||||||+||+|||+|||+|+++||.|+|+|++.|||+||+|+||||||||||+|.
T Consensus 80 ~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~ 139 (140)
T PF07526_consen 80 AKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAIS 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999999995
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=100.00 E-value=2e-34 Score=300.98 Aligned_cols=261 Identities=43% Similarity=0.628 Sum_probs=198.3
Q ss_pred ccccccCccchhHHHHHHHHHhhccccccccc-ccCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhhHHHHHHH
Q 003323 389 VVNVLRNSKYAKAAQELLEEFCSVGRGQFKKS-KFGKN-NTNPSSSSGGGGGGVGCGGSSSSTKDLPPLSAADRIEHQRR 466 (830)
Q Consensus 389 ~asvL~~SRYLkpAQeLLdE~csVg~~~~~~~-k~~~~-~~~~~~~~~~gg~~~~~~gssss~~~~~~lS~aer~E~q~k 466 (830)
+...+..+|||++||+||+|||+++....+.. .++.. ..+.........+. .-+...... .......++.+++.+
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~n~~~~s-~~~~~~~~~~~~~~~ 121 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGA--RRGNATRES-ATLKAWLEEHRLNPY 121 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCcccccc--ccccccccc-cccccchhhhhhccC
Confidence 56678899999999999999999987653211 11110 00000000000000 000111111 333467788899999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCCccchHHHHHHHHHhhhhHHH--HHHHHHHHHHHhhccCCCCC
Q 003323 467 KVKLLSMLDEVDRRYNHYCEQMQMVVTSFDLVMGFGAAVPYTALAQKAMSRHFRCLKD--AIAAQLKQSCELLGEKDVAG 544 (830)
Q Consensus 467 KaKLL~mLdEVDrRYeqY~eQmq~VvsSFe~vaG~Gaa~pYtaLAlkamSRhFR~LkD--AI~~QLk~s~k~lgedd~ag 544 (830)
++||+.|+.+|+++|.+|+..|+.|...|+...+++...+|+.++...++++|+++++ +|..|+...++.++..+...
T Consensus 122 ~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~ 201 (342)
T KOG0773|consen 122 PSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDD 201 (342)
T ss_pred chHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999998 88889999888776443222
Q ss_pred CCC--CCCCCCchhhHHHHHHHhhhh-hhcccccccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC
Q 003323 545 TSG--ITKGETPRLKLLEQSLRQQRA-FHQMGMMEQEAWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGL 621 (830)
Q Consensus 545 sSg--ltkGEt~Rlr~~Eq~LRQqRa-~~qlG~~~qe~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGL 621 (830)
... ......+..+..+..+++++. +...+..+...||++++||++++.+|+.||++|+.||||++.+|..||++|||
T Consensus 202 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGL 281 (342)
T KOG0773|consen 202 SEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGL 281 (342)
T ss_pred cccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCC
Confidence 111 111123444555566666543 33444556678999999999999999999999999999999999999999999
Q ss_pred ChhhHhhhhhhhhhhhcchhhHHHHHHHhhh
Q 003323 622 SRNQVSNWFINARVRLWKPMVEEMYQQEAKE 652 (830)
Q Consensus 622 S~kQVsNWFiNaRrRlKKpmieem~qqe~~e 652 (830)
++.||+|||||+|+|+||+|+++++..+.+.
T Consensus 282 s~~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 282 SRPQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred CcccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 9999999999999999999999999988876
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.85 E-value=3.3e-21 Score=198.79 Aligned_cols=151 Identities=32% Similarity=0.536 Sum_probs=116.1
Q ss_pred HHHHHHHHHHHH----HHHHHHHHHHHHHHHH-HHhhhhhhhcCCCCccchHHHHHHHHHhhhhHH---HHHHHHHHHH-
Q 003323 463 HQRRKVKLLSML----DEVDRRYNHYCEQMQM-VVTSFDLVMGFGAAVPYTALAQKAMSRHFRCLK---DAIAAQLKQS- 533 (830)
Q Consensus 463 ~q~kKaKLL~mL----dEVDrRYeqY~eQmq~-VvsSFe~vaG~Gaa~pYtaLAlkamSRhFR~Lk---DAI~~QLk~s- 533 (830)
+.++++||+++. .|+ ++|++.|.++.. |.+-+..- .-+.+++.|.|+|+...+. +.|..||+..
T Consensus 102 hsdYR~kL~qiR~iy~~El-ekyeqaCneftthV~nlL~eQ------sr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqst 174 (334)
T KOG0774|consen 102 HSDYRAKLLQIRQIYHNEL-EKYEQACNEFTTHVMNLLREQ------SRTRPIMPKEIERMVQIISKKFSHIQMQLKQST 174 (334)
T ss_pred hHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHh------cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677899999886 566 699999999864 44444332 2345567788888776654 6788888876
Q ss_pred HHhhccCCCCCCCCCCCCCCchhhHHHHHHHhhhhhhcccccccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHH
Q 003323 534 CELLGEKDVAGTSGITKGETPRLKLLEQSLRQQRAFHQMGMMEQEAWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKH 613 (830)
Q Consensus 534 ~k~lgedd~agsSgltkGEt~Rlr~~Eq~LRQqRa~~qlG~~~qe~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~ 613 (830)
|+.+. .-|.+++ +++||||+|+|.+++||.+||..|+.||||++++|+
T Consensus 175 ce~vm--------------iLr~r~l------------------darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~ 222 (334)
T KOG0774|consen 175 CEAVM--------------ILRSRFL------------------DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKE 222 (334)
T ss_pred HHHHH--------------HHHHHHH------------------HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHH
Confidence 55322 1111111 357899999999999999999999999999999999
Q ss_pred HHHHHhCCChhhHhhhhhhhhhhhcchhhHHHHHHHhhhch
Q 003323 614 LLARQTGLSRNQVSNWFINARVRLWKPMVEEMYQQEAKEGE 654 (830)
Q Consensus 614 ~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~qqe~~e~~ 654 (830)
+||++|+++..||+|||.|+|.|.||.+.. .+++.+-.+
T Consensus 223 eLAkqCnItvsQvsnwfgnkrIrykK~~~k--~~ee~~l~~ 261 (334)
T KOG0774|consen 223 ELAKQCNITVSQVSNWFGNKRIRYKKNMGK--NQEEANLYA 261 (334)
T ss_pred HHHHHcCceehhhccccccceeehhhhhhh--hhhhhhhHh
Confidence 999999999999999999999999999974 444444333
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=99.56 E-value=2.1e-15 Score=117.45 Aligned_cols=40 Identities=68% Similarity=1.194 Sum_probs=36.6
Q ss_pred HHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 003323 597 WLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVR 636 (830)
Q Consensus 597 WF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrR 636 (830)
||.+|+.||||+++||.+||++|||+.+||+|||+|+|+|
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
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.49 E-value=8.2e-14 Score=145.32 Aligned_cols=50 Identities=48% Similarity=0.821 Sum_probs=47.4
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLW 638 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlK 638 (830)
|.++++.+||+||.. +|||++++|++||+.|||+..||+|||+|+|.|.+
T Consensus 183 FKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 446889999999997 99999999999999999999999999999999987
No 7
>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=99.37 E-value=1.1e-12 Score=104.04 Aligned_cols=57 Identities=30% Similarity=0.553 Sum_probs=53.3
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 581 RPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 581 RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
+++..|+++++.+|++||.. +|||+.+++..||.++||+..||.+||.|+|.|.++.
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 9999999999999999999999999999999998764
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.33 E-value=1.9e-12 Score=103.65 Aligned_cols=57 Identities=33% Similarity=0.639 Sum_probs=54.1
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcc
Q 003323 580 WRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWK 639 (830)
Q Consensus 580 ~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKK 639 (830)
+|+|+.|+++++.+|+++|.. +|||+.+++..||..+||+..||.+||.|+|.|.||
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 999999999999999999999999999999999875
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.31 E-value=3.8e-12 Score=100.71 Aligned_cols=55 Identities=31% Similarity=0.529 Sum_probs=50.7
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 003323 581 RPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLW 638 (830)
Q Consensus 581 RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlK 638 (830)
++|..|+++++.+|++||.. +|||+.+++..||..+||+..||.+||.|+|+|.+
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 89999999999999999999999999999999864
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.79 E-value=2.7e-09 Score=113.87 Aligned_cols=64 Identities=20% Similarity=0.229 Sum_probs=55.1
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHH
Q 003323 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEM 645 (830)
Q Consensus 579 ~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem 645 (830)
.||||-.++|.|+..|++-|.= |-|.|++-|.+|++.++||..||+.||+|||+|+||-..|..
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 3455556999999999777766 799999999999999999999999999999999987765443
No 11
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.78 E-value=3.4e-09 Score=113.04 Aligned_cols=65 Identities=23% Similarity=0.313 Sum_probs=58.1
Q ss_pred cCCCCCC-CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHHH
Q 003323 579 AWRPQRG-LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEMY 646 (830)
Q Consensus 579 ~~RKRR~-LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~ 646 (830)
.|||||. |++.+|-.|++-|.+ ..|-+.-||+.||+.++||.+||+.||+|+|.|.||..+++.+
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred cccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 3455555 899999999999999 8999999999999999999999999999999999988775543
No 12
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.63 E-value=3.1e-08 Score=105.75 Aligned_cols=58 Identities=28% Similarity=0.405 Sum_probs=52.9
Q ss_pred CCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhH
Q 003323 583 QRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVE 643 (830)
Q Consensus 583 RR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmie 643 (830)
|.-|+..++..|+.-|.. -.|-+..||.+||...|||..||.+||+|||.|+||.+.+
T Consensus 176 RTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 176 RTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred hhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 344999999999999998 8999999999999999999999999999999998877743
No 13
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.61 E-value=2.8e-08 Score=99.73 Aligned_cols=63 Identities=24% Similarity=0.305 Sum_probs=57.1
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHH
Q 003323 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEE 644 (830)
Q Consensus 579 ~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmiee 644 (830)
.+|.|+.|+.+++..|+..|.. +-|-.-.||+.||+.++|+..||..||+|+|.|.||...++
T Consensus 102 ~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 102 PKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 3455666999999999999999 99999999999999999999999999999999998877654
No 14
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.61 E-value=4.4e-08 Score=99.28 Aligned_cols=71 Identities=25% Similarity=0.339 Sum_probs=62.4
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHHHHHHhhh
Q 003323 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEMYQQEAKE 652 (830)
Q Consensus 579 ~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~qqe~~e 652 (830)
.++|+++|+.+++..|+.-|.. +-|-.++.|..||++.||...||..||+|||+|+|.+..|..|.-..+.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~ 120 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQ 120 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHH
Confidence 4577788999999999999998 7888899999999999999999999999999999988887766544433
No 15
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.60 E-value=2.5e-08 Score=103.65 Aligned_cols=61 Identities=18% Similarity=0.244 Sum_probs=55.5
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 579 ~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.+|.|..|+..++..|+.-|.- |.|-+...|++||..+.|++.||.+||+|||+|+||...
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 4666777999999999999988 999999999999999999999999999999999886553
No 16
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.59 E-value=3.8e-08 Score=103.29 Aligned_cols=63 Identities=25% Similarity=0.490 Sum_probs=59.4
Q ss_pred ccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 576 EQEAWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 576 ~qe~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
..+.+|+|.-|+.++.+.|++-|.+ |.|.++..|+.||.+++|.+.||..||+|+|.|+||..
T Consensus 243 ~~eeKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 243 SKEEKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cchhcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 4577899999999999999999999 99999999999999999999999999999999999864
No 17
>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=98.47 E-value=2.2e-07 Score=78.26 Aligned_cols=52 Identities=12% Similarity=0.271 Sum_probs=49.2
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCC----CCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 003323 580 WRPQRGLPERSVNILRSWLFEHFLHPY----PSDADKHLLARQTGLSRNQVSNWFINAR 634 (830)
Q Consensus 580 ~RKRR~LPKeqv~ILraWF~eHl~nPY----PS~eEK~~LA~qTGLS~kQVsNWFiNaR 634 (830)
+|+|..|+.+++..|+..|.. .+| |+..++..||..+||+..+|.+||+|-+
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 577788999999999999999 999 9999999999999999999999999964
No 18
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.44 E-value=1.6e-07 Score=97.09 Aligned_cols=60 Identities=23% Similarity=0.340 Sum_probs=54.2
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 580 WRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 580 ~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
||+|+-++.-+...|++-|.+ .-|---.||.+||..+|||..||+.||+|||-|.||.|.
T Consensus 123 RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 344555899999999999999 899999999999999999999999999999999987663
No 19
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.41 E-value=1.6e-07 Score=103.00 Aligned_cols=60 Identities=20% Similarity=0.338 Sum_probs=54.0
Q ss_pred cCCCCC-CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 579 AWRPQR-GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 579 ~~RKRR-~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
+||||| .+.-.++..|++.|.+ ||.|+.+|.-.||++++|.+..|++||+|||.|+|+..
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 344444 4999999999999999 99999999999999999999999999999999998655
No 20
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.37 E-value=9.6e-07 Score=82.81 Aligned_cols=63 Identities=19% Similarity=0.302 Sum_probs=56.6
Q ss_pred CCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHHHH
Q 003323 582 PQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEMYQ 647 (830)
Q Consensus 582 KRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~q 647 (830)
-|..|+..+...|+.-|.+ .-||..=.|++||.+..|++..|++||+|+|.+.+|...-..+.
T Consensus 20 IRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~ 82 (125)
T KOG0484|consen 20 IRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAK 82 (125)
T ss_pred hhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 3556999999999999999 89999999999999999999999999999999999887654444
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.36 E-value=4e-07 Score=89.42 Aligned_cols=64 Identities=20% Similarity=0.278 Sum_probs=58.3
Q ss_pred cccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhH
Q 003323 577 QEAWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVE 643 (830)
Q Consensus 577 qe~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmie 643 (830)
...+++|++.+..++.+|+.-|.. +|||+..+|..|+..++|+.+-|+.||+|+|.+.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 345677788999999999999999 9999999999999999999999999999999999877653
No 22
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.36 E-value=3e-07 Score=94.77 Aligned_cols=62 Identities=24% Similarity=0.249 Sum_probs=55.5
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhH
Q 003323 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVE 643 (830)
Q Consensus 579 ~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmie 643 (830)
++|.|..|+..++..|+.-|.. ..|-+..||.-||+++.|++.||+.||+|+|.|+|+....
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 3445566999999999999998 8999999999999999999999999999999998877653
No 23
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.25 E-value=8.2e-07 Score=91.51 Aligned_cols=59 Identities=20% Similarity=0.390 Sum_probs=54.3
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 580 WRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 580 ~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
+|.|+.|+.++.++|++-|.+ .-||....+++||.+.+|.+.+|.+||.|+|+|.++..
T Consensus 38 RRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 38 RRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred ccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 455667999999999999999 99999999999999999999999999999999987554
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.24 E-value=7e-07 Score=95.79 Aligned_cols=58 Identities=21% Similarity=0.333 Sum_probs=53.6
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEM 645 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem 645 (830)
-|+-.+.+.|+.||.. |.||+.+.|++||.-|+||+..|++||.|+|.+++|.....+
T Consensus 118 hFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 118 HFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 3999999999999999 999999999999999999999999999999999887765444
No 25
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.21 E-value=1.3e-06 Score=89.71 Aligned_cols=60 Identities=22% Similarity=0.318 Sum_probs=54.7
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 579 ~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.|++|..|+..+...|++-|.+ .-|-+.+||.+++..+.||..||..||+|+|.|.|+-.
T Consensus 144 nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 3567777999999999999999 89999999999999999999999999999999976543
No 26
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.12 E-value=1.3e-06 Score=92.29 Aligned_cols=58 Identities=26% Similarity=0.243 Sum_probs=52.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEM 645 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem 645 (830)
.++.-++-.|++-|.- .+|.+...|.+||.-+||++.||+.||+|||.|++|...++.
T Consensus 205 VYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred Eecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 3788889999988887 899999999999999999999999999999999988775443
No 27
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.12 E-value=2.3e-06 Score=90.16 Aligned_cols=56 Identities=23% Similarity=0.377 Sum_probs=51.8
Q ss_pred CCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 583 QRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 583 RR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
|+.|+.-+...|++-|.| --||..-.|++||.+|+|.+.+|.+||+|||.|++|..
T Consensus 145 RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred cchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 445999999999999999 88999999999999999999999999999999987654
No 28
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.05 E-value=2.7e-06 Score=90.69 Aligned_cols=63 Identities=22% Similarity=0.384 Sum_probs=57.6
Q ss_pred ccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 576 EQEAWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 576 ~qe~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
+...+|+|..++.++.+.|+.-|.. .|.|..--|++|+..|||....|++||+|+|+|+|+-+
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 4567899999999999999999998 89999999999999999999999999999999876544
No 29
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.00 E-value=2.6e-06 Score=85.07 Aligned_cols=56 Identities=25% Similarity=0.368 Sum_probs=51.4
Q ss_pred CCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 583 QRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 583 RR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
|..|...+...|++-|.. -.|-+-.|+.+||...+|+++||..||+|+|+|.||..
T Consensus 104 Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 104 RTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred cccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 445899999999999997 78999999999999999999999999999999998765
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.82 E-value=2e-05 Score=89.65 Aligned_cols=56 Identities=25% Similarity=0.341 Sum_probs=53.0
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 003323 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRL 637 (830)
Q Consensus 579 ~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRl 637 (830)
.+|+|-.|+..+++.|++.|.+ ++||+.+.-+.|+.+++|.+.-|.|||-|+|+|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 4677777999999999999999 9999999999999999999999999999999995
No 31
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.63 E-value=2.6e-05 Score=81.01 Aligned_cols=62 Identities=24% Similarity=0.369 Sum_probs=56.0
Q ss_pred CCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHHHH
Q 003323 583 QRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEMYQ 647 (830)
Q Consensus 583 RR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~q 647 (830)
|.+|.-.++..|+.-|.+ ..||--+++.+||...|+++.||.+||+|+|.|++|+..-||-.
T Consensus 171 rPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 171 RPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred CCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence 334999999999999999 89999999999999999999999999999999999888766644
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.57 E-value=2.5e-05 Score=84.00 Aligned_cols=62 Identities=18% Similarity=0.302 Sum_probs=54.2
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhH
Q 003323 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVE 643 (830)
Q Consensus 579 ~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmie 643 (830)
.+|-|.-|+.+++..|++-|++ .-|-+.-.|.+||..++|.+.-|+.||+|+|+|.|+..+-
T Consensus 181 mRRYRTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3455566999999999877776 5788999999999999999999999999999999988764
No 33
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.47 E-value=9.2e-05 Score=80.74 Aligned_cols=60 Identities=25% Similarity=0.479 Sum_probs=54.9
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 580 WRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 580 ~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
+|.|..|+..+...|++||.. .|||....|+.||++++|+...|..||.|+|.|.+|...
T Consensus 177 rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 445566999999999999999 889999999999999999999999999999999887764
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.43 E-value=6.9e-05 Score=73.82 Aligned_cols=60 Identities=18% Similarity=0.099 Sum_probs=54.4
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 579 AWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 579 ~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.+|.|.+|+..+.+.|+.-|.. .+||....++.||..+++++..|.+||+|+|+++++..
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 4566667999999999999999 69999999999999999999999999999999987655
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.39 E-value=6.9e-05 Score=79.79 Aligned_cols=60 Identities=47% Similarity=0.682 Sum_probs=55.1
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 581 RPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 581 RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
+++.+++.+. .+|+.|+.+|..+|||++.++.+|+..++++..||++||+|+|+|+++.+
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 4445689999 99999999999999999999999999999999999999999999987744
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.22 E-value=0.00011 Score=78.71 Aligned_cols=59 Identities=24% Similarity=0.389 Sum_probs=53.3
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcc
Q 003323 578 EAWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWK 639 (830)
Q Consensus 578 e~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKK 639 (830)
+++|||.-+-..-++.|+++|.. -|-|+-|....+|+++.|-+..|++||+|.|.|.|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 56777777777778999999998 899999999999999999999999999999999886
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.13 E-value=0.0041 Score=52.94 Aligned_cols=43 Identities=21% Similarity=0.420 Sum_probs=31.4
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 003323 591 VNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVR 636 (830)
Q Consensus 591 v~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrR 636 (830)
.+.|+++|.. |.+..+.+...|+.+++|+..||.+||.-++.+
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 3559999999 789999999999999999999999999877554
No 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.75 E-value=0.027 Score=55.71 Aligned_cols=62 Identities=31% Similarity=0.542 Sum_probs=54.4
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 578 EAWRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 578 e~~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
..++.+..+...+..+|..-|.. .+||....+..|+..+|++...|.+||.|.|.+.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34455667888999999988887 999999999999999999999999999999999887664
No 39
>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=92.92 E-value=0.14 Score=43.25 Aligned_cols=40 Identities=23% Similarity=0.341 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHH----HHhhhhhhhcCCCCccchHHHHHHHHHhhhhHHHHHHHHHHHHH
Q 003323 474 LDEVDRRYNHYCEQMQM----VVTSFDLVMGFGAAVPYTALAQKAMSRHFRCLKDAIAAQLKQSC 534 (830)
Q Consensus 474 LdEVDrRYeqY~eQmq~----VvsSFe~vaG~Gaa~pYtaLAlkamSRhFR~LkDAI~~QLk~s~ 534 (830)
.+|||+++++||+.+.+ +..+|+.++- +.+.|+.||+.+|
T Consensus 8 dpELDqFMeaYc~~L~kykeeL~~p~~EA~~---------------------f~~~ie~qL~~Lt 51 (52)
T PF03791_consen 8 DPELDQFMEAYCDMLVKYKEELQRPFQEAME---------------------FCREIEQQLSSLT 51 (52)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHHHHHHHHh
Confidence 47999999999998854 3334443322 2467888888775
No 40
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.87 E-value=0.17 Score=63.44 Aligned_cols=59 Identities=19% Similarity=0.330 Sum_probs=53.1
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 581 RPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 581 RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
++|..+...++.+|+..|.+ .-||+.++.+.|.+..+|....|..||+|+|.+.+|+..
T Consensus 905 a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 905 AYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 34455788899999999998 889999999999999999999999999999999988774
No 41
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=88.51 E-value=6.6 Score=41.00 Aligned_cols=73 Identities=26% Similarity=0.460 Sum_probs=49.2
Q ss_pred hhHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH-HHhhhhhhhcCCCCccchHHHHHHHHHhhhhHH---HHHHHH
Q 003323 458 ADRIEHQRRKVKLLSML----DEVDRRYNHYCEQMQM-VVTSFDLVMGFGAAVPYTALAQKAMSRHFRCLK---DAIAAQ 529 (830)
Q Consensus 458 aer~E~q~kKaKLL~mL----dEVDrRYeqY~eQmq~-VvsSFe~vaG~Gaa~pYtaLAlkamSRhFR~Lk---DAI~~Q 529 (830)
.+.+|+.+++.||..+. .|+ ++|++-|.++.. |.+-+.. -+...|- ..++|.|+...+. ++|..|
T Consensus 101 ~~~~d~~dYr~kL~~ir~~y~~el-~kye~ac~eF~~hV~~lLre---Qs~~RPI---s~keiE~m~~~i~~Kf~~iq~q 173 (191)
T PF03792_consen 101 DNSIDHSDYRAKLSQIRQIYHSEL-EKYEQACNEFTEHVMNLLRE---QSEFRPI---SPKEIERMVNIIHRKFSKIQMQ 173 (191)
T ss_pred ccccchHHHHHHHHHHHHHHHHHH-HHHHHHhhhhHHHHHHHHHH---hcccCCC---CHHHHHHHHHHHHHHHHHHHHH
Confidence 56678889999998886 566 688888888854 4444332 2223444 4566666665553 799999
Q ss_pred HHHH-HHhh
Q 003323 530 LKQS-CELL 537 (830)
Q Consensus 530 Lk~s-~k~l 537 (830)
||++ |+.+
T Consensus 174 LKQstCEaV 182 (191)
T PF03792_consen 174 LKQSTCEAV 182 (191)
T ss_pred HHHHHHHHH
Confidence 9997 7764
No 42
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=86.95 E-value=6.7 Score=42.76 Aligned_cols=121 Identities=18% Similarity=0.315 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCCccchHHHHHHHHHhhhhHHHHHHHHHHHHHHhh--
Q 003323 460 RIEHQRRKVKLLSMLDEVDRRYNHYCEQMQMVVTSFDLVMGFGAAVPYTALAQKAMSRHFRCLKDAIAAQLKQSCELL-- 537 (830)
Q Consensus 460 r~E~q~kKaKLL~mLdEVDrRYeqY~eQmq~VvsSFe~vaG~Gaa~pYtaLAlkamSRhFR~LkDAI~~QLk~s~k~l-- 537 (830)
..|++.+|..|..-++++++|-++-.++|.. +|- |- .+++.+...-+||-...-|+......
T Consensus 6 L~eL~qrk~~Lq~eIe~LerR~~ri~~Emrt---sFa---G~----------Sq~lA~RVqGFkdYLvGsLQDLa~saEq 69 (283)
T PF11285_consen 6 LKELEQRKQALQIEIEQLERRRERIEKEMRT---SFA---GQ----------SQDLAIRVQGFKDYLVGSLQDLAQSAEQ 69 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---ccc---cc----------hHHHHHHHhhhHHHHHHHHHHHHHHHHh
Confidence 4578889999999999999999999888854 332 22 34455556556665555555443221
Q ss_pred -c-------cC-----CCC-CCCC-----------CCCCCCchhhHHHHHHHhhhhh-hcccccccccCCCCCCCChhHH
Q 003323 538 -G-------EK-----DVA-GTSG-----------ITKGETPRLKLLEQSLRQQRAF-HQMGMMEQEAWRPQRGLPERSV 591 (830)
Q Consensus 538 -g-------ed-----d~a-gsSg-----------ltkGEt~Rlr~~Eq~LRQqRa~-~qlG~~~qe~~RKRR~LPKeqv 591 (830)
. .+ ... .... ...+..+..+.+.++|.+++.. ..+ ..+|+-||.|-.--.
T Consensus 70 LeLv~~~~~~~psp~~~~~~~~~~~~~~~~~~~~~~~~~F~~~~~~Ir~~l~qyr~~PDyY----g~PWqLRRtfe~~ha 145 (283)
T PF11285_consen 70 LELVPQPVVVQPSPLDEPAPPPQANAAKNPPTPQFAAQTFQPDERQIRRLLDQYRTQPDYY----GPPWQLRRTFEPIHA 145 (283)
T ss_pred hccCCCCcCCCCCcccccccCcccccccCCCCCcchhhhcchHHHHHHHHHHHHhhCCCcc----CChHHHHhcccHHHH
Confidence 0 00 000 0000 0011112233444455444431 112 367888889988888
Q ss_pred HHHHHHHHh
Q 003323 592 NILRSWLFE 600 (830)
Q Consensus 592 ~ILraWF~e 600 (830)
..+..||+.
T Consensus 146 e~v~~WFF~ 154 (283)
T PF11285_consen 146 ERVEDWFFN 154 (283)
T ss_pred HHHHHHHhc
Confidence 999999986
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=81.79 E-value=8 Score=47.18 Aligned_cols=45 Identities=22% Similarity=0.426 Sum_probs=42.1
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 003323 591 VNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLW 638 (830)
Q Consensus 591 v~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlK 638 (830)
+.+|+++|.. |+.|+.+|...+|.+.||...-|+.||.+.|....
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 7899999998 99999999999999999999999999999987654
No 44
>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=79.04 E-value=3.8 Score=33.96 Aligned_cols=47 Identities=28% Similarity=0.240 Sum_probs=31.4
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 003323 580 WRPQRGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINAR 634 (830)
Q Consensus 580 ~RKRR~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaR 634 (830)
+|+|+.|+-+.+-.+-.-+.+ .+ -+..||+..|++..+|++|..|+.
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 467777887775555444555 33 588999999999999999999954
No 45
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=74.23 E-value=34 Score=33.68 Aligned_cols=49 Identities=10% Similarity=0.106 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.+|...+.+. . .-.++|+.+|++...|.+|+..+|+++++.+
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 39999999998776663 2 3368999999999999999999999987654
No 46
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=71.60 E-value=4.5 Score=32.13 Aligned_cols=47 Identities=30% Similarity=0.397 Sum_probs=38.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcc
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWK 639 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKK 639 (830)
.|+++.+.+|...|++ . -.-.++|+..|+|...|+.+...+..++|+
T Consensus 4 ~L~~~er~vi~~~y~~----~----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----G----LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----C----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 4889999999888865 2 235689999999999999999999988864
No 47
>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=71.36 E-value=5.4 Score=29.77 Aligned_cols=45 Identities=27% Similarity=0.286 Sum_probs=36.2
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLW 638 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlK 638 (830)
|+.+...++..++.+. -.-..+|..+|++...|..|....|.++|
T Consensus 11 l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 11 LPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred CCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 7888888888877652 23567899999999999999988887764
No 48
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=71.36 E-value=1e+02 Score=29.94 Aligned_cols=48 Identities=23% Similarity=0.145 Sum_probs=39.9
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||+..+.++...+.+.+ .-.++|+.+|++...|.+.+..+|+++++.+
T Consensus 130 L~~~~r~v~~l~~~~g~--------s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 130 LPDRQRLPIVHVKLEGL--------SVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 88989888876666532 3468999999999999999999999998755
No 49
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=69.95 E-value=1.1e+02 Score=29.43 Aligned_cols=49 Identities=16% Similarity=0.036 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||+..+.++.-.+.+.+ .-.++|..+|++...|.++..-+|+++++.+
T Consensus 112 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASGF--------SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 389999999988777632 2358999999999999999999999987554
No 50
>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=64.81 E-value=10 Score=30.28 Aligned_cols=44 Identities=30% Similarity=0.380 Sum_probs=34.1
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRL 637 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRl 637 (830)
||++.+.++...|.+. -.-.++|+.+|++...|.+|...+|+++
T Consensus 11 L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp S-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 8899999988777762 3457899999999999999999998874
No 51
>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=63.99 E-value=1.1e+02 Score=27.23 Aligned_cols=48 Identities=27% Similarity=0.305 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.||+..+.++..-+.. .| ...++|+.+|+++..|.+|....+.++++.
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 3788888888655444 33 345899999999999999999999998764
No 52
>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=63.01 E-value=12 Score=31.42 Aligned_cols=46 Identities=24% Similarity=0.350 Sum_probs=30.6
Q ss_pred CCCCCCChhHH-HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 003323 581 RPQRGLPERSV-NILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINAR 634 (830)
Q Consensus 581 RKRR~LPKeqv-~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaR 634 (830)
++++.|+++.+ ++++..+.. ......+|+..||+..+|.+|-.-.+
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 45567888775 445555454 46788999999999999999977665
No 53
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=61.79 E-value=1.7e+02 Score=29.00 Aligned_cols=49 Identities=18% Similarity=0.146 Sum_probs=40.9
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
||++.+.++.-.+.+. .+| .++|+.+|++..-|.++...+|+++++.+.
T Consensus 117 Lp~~~r~i~~L~~~~g--~s~------~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 117 LPDDQREAIILVGASG--FAY------EEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 8999999998877763 222 589999999999999999999999987664
No 54
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=61.02 E-value=9.7 Score=35.88 Aligned_cols=50 Identities=20% Similarity=0.186 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.++...+.+. .+ -.++|+.+|++...|.+++.-+|.++++.+-
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 38999999998776663 22 2589999999999999999999999987664
No 55
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=60.28 E-value=1.9e+02 Score=28.96 Aligned_cols=49 Identities=20% Similarity=0.152 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++.-++.+- + .-.++|..+|++...|.+++.-+|+++++.+
T Consensus 113 ~Lp~~~r~v~~L~~~~g----~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGASG----F----SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998887762 2 2357999999999999999999999998655
No 56
>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=59.25 E-value=15 Score=24.35 Aligned_cols=38 Identities=21% Similarity=0.284 Sum_probs=27.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWF 630 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWF 630 (830)
.++.+....+..++.+ .+ ....+|+.+|++...|.+|.
T Consensus 5 ~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 4666666666666543 33 45688899999999999995
No 57
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=58.19 E-value=13 Score=36.71 Aligned_cols=54 Identities=11% Similarity=0.243 Sum_probs=44.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEMY 646 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~ 646 (830)
.||++.+.++.-.+++. . .-.++|..+|++..-|.++..-+|+++++.+..++|
T Consensus 134 ~Lp~~~R~v~~L~~~~g--~------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 187 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--L------SSEQICQECDISTSNLHVLLYRARLQLQACLSKNWF 187 (189)
T ss_pred hCCHHHHHHHhHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 38999999998877662 2 246899999999999999999999999988765544
No 58
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=57.23 E-value=1.7e+02 Score=27.47 Aligned_cols=49 Identities=18% Similarity=0.173 Sum_probs=39.9
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
||+..+.++..-+.+. -.-.++|+..|++...|.+|..-+|.|+++.+.
T Consensus 126 L~~~~r~i~~l~~~~~--------~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 126 LPVKQREVFLLRYVEG--------LSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHhhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 8888888887766552 233689999999999999999999999986553
No 59
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=52.84 E-value=15 Score=34.15 Aligned_cols=48 Identities=19% Similarity=0.149 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.||+..+.++..-|.+. . .-.++|+.+|++...|.+|...+|.++++.
T Consensus 106 ~L~~~~r~ii~l~~~~~--~------s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG--K------TMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred hCCHHHHHHHHHHHhcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 38999999987766652 2 246899999999999999999999998753
No 60
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=52.73 E-value=2.4e+02 Score=27.87 Aligned_cols=49 Identities=18% Similarity=0.094 Sum_probs=41.0
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
||++.+.++.-.+.+.+ .-.++|+.+|++..-|.....-+|+++++.+.
T Consensus 112 Lp~~~R~v~~L~~~~g~--------s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 112 LPQDQREALILVGASGF--------SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CCHHHHHHhhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 89999999988776632 23589999999999999999999999886654
No 61
>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=51.57 E-value=17 Score=33.49 Aligned_cols=48 Identities=27% Similarity=0.248 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.||.+...+|...+.+ .+ .-.++|+.+|++...|.++...+|+++++.
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 4889999999876655 33 235699999999999999999999998764
No 62
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=50.86 E-value=16 Score=35.77 Aligned_cols=52 Identities=17% Similarity=0.224 Sum_probs=42.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEE 644 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmiee 644 (830)
.||++.+.++.-.+.+.+ .-.++|+.+|++..-|.++...+|+++++.+...
T Consensus 136 ~L~~~~r~i~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 187 (195)
T PRK12532 136 NLPENTARVFTLKEILGF--------SSDEIQQMCGISTSNYHTIMHRARESLRQCLQIK 187 (195)
T ss_pred hCCHHHHHHhhhHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 389999999987666522 2368999999999999999999999998876433
No 63
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=50.84 E-value=18 Score=34.42 Aligned_cols=49 Identities=16% Similarity=0.068 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++..++.++ . .-.++|..+|++...|.+|..-+|+++++..
T Consensus 108 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE--L------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhHHHhc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999999887763 2 3368999999999999999999999987654
No 64
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=49.19 E-value=18 Score=34.87 Aligned_cols=49 Identities=16% Similarity=0.274 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++...|++. + .-.++|+.+|++...|.+++..+|+++++.+
T Consensus 129 ~L~~~~r~i~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 177 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEG----L----SYKELAERHDVPLNTMRTWLRRSLLKLRECL 177 (179)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence 38999999998888762 2 2468999999999999999999999997643
No 65
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=48.89 E-value=19 Score=33.81 Aligned_cols=50 Identities=20% Similarity=0.159 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.|+++.+.+|...+++. .+ -.++|+.+|++...|.+|...+|+++++.+.
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LS------YEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 38999999997665542 22 3589999999999999999999999987663
No 66
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=47.22 E-value=17 Score=35.10 Aligned_cols=50 Identities=18% Similarity=0.125 Sum_probs=41.8
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.++...+.+. . .-.++|..+|++...|.+++..+|+++++.+.
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--A------SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 38999999998877662 2 34689999999999999999999999986653
No 67
>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=46.37 E-value=16 Score=35.14 Aligned_cols=49 Identities=18% Similarity=0.147 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++.-.|.+++ .-.++|..+|++...|.++.-.+|+++++.+
T Consensus 138 ~L~~~~r~v~~l~~~~~~--------s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEGL--------SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 388999999987666521 3468999999999999999999999998765
No 68
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=46.05 E-value=21 Score=34.98 Aligned_cols=50 Identities=20% Similarity=0.262 Sum_probs=41.6
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.++.-.|.+. .+ -.++|+.+|++...|.+...-+|+++++...
T Consensus 131 ~L~~~~r~i~~l~~~~g--~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--EK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred hCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 49999999998766652 22 3689999999999999999999999988764
No 69
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=44.99 E-value=52 Score=25.10 Aligned_cols=51 Identities=22% Similarity=0.229 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEE 644 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmiee 644 (830)
.|+++...++..+ .+ .+ ...++|+.+|++...|..|....+.++.-....+
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~~~ 53 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQ 53 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHH
Confidence 3777778887554 33 22 4478999999999999999998888876555433
No 70
>PRK00118 putative DNA-binding protein; Validated
Probab=44.80 E-value=23 Score=33.71 Aligned_cols=49 Identities=16% Similarity=0.110 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||+.++.++..++.+. -.-.++|+.+|+++.-|.+|...+|.++++-.
T Consensus 17 ~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 38999999998888872 23457999999999999999999999988744
No 71
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=44.35 E-value=25 Score=28.65 Aligned_cols=27 Identities=30% Similarity=0.350 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhhhh
Q 003323 611 DKHLLARQTGLSRNQVSNWFINARVRL 637 (830)
Q Consensus 611 EK~~LA~qTGLS~kQVsNWFiNaRrRl 637 (830)
....||+.+|+++..|+.|+.+...+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 466899999999999999999874443
No 72
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=43.87 E-value=21 Score=34.82 Aligned_cols=50 Identities=18% Similarity=0.256 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.++..-+++. . .-.++|..+|++..-|.+|+..+|+++++.+.
T Consensus 141 ~L~~~~~~v~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 141 QLPESQRQVLELAYYEG--L------SQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred hCCHHHhhhhhhhhhcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999997766652 2 33689999999999999999999999987653
No 73
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=43.75 E-value=25 Score=33.30 Aligned_cols=48 Identities=23% Similarity=0.124 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.||++++.++.-.+.+. . .-.++|..+|++...|.++...+|+|+++.
T Consensus 112 ~L~~~~r~v~~l~~~~~--~------s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG--F------SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhHHhcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 48999999998877663 2 235899999999999999999999998764
No 74
>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=43.23 E-value=35 Score=35.87 Aligned_cols=53 Identities=25% Similarity=0.391 Sum_probs=43.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEM 645 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem 645 (830)
.||++.+.++.-.+++.+. -.++|..+|++..-|.++...+|+++++.+....
T Consensus 161 ~Lp~~~R~v~~L~~~eg~S--------~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~ 213 (244)
T TIGR03001 161 ALSERERHLLRLHFVDGLS--------MDRIGAMYQVHRSTVSRWVAQARERLLERTRRRL 213 (244)
T ss_pred hCCHHHHHHHHHHHHcCCC--------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3899999999888877432 3589999999999999999999999988775433
No 75
>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=41.90 E-value=28 Score=33.49 Aligned_cols=47 Identities=19% Similarity=0.201 Sum_probs=40.2
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
||++.+.++.-.+.+.+ .-.++|..+|++..-|.+.+..+|.++++.
T Consensus 135 Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGL--------TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 89999999988877632 236899999999999999999999998764
No 76
>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=41.64 E-value=29 Score=32.41 Aligned_cols=47 Identities=32% Similarity=0.314 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcc
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWK 639 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKK 639 (830)
.||++.+.++..-+.+. + .-.++|+.+|++...|.++...+|+++++
T Consensus 111 ~L~~~~r~v~~l~~~~g----~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG----V----SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 38999999998866652 2 33689999999999999999999998875
No 77
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=41.31 E-value=29 Score=34.64 Aligned_cols=50 Identities=28% Similarity=0.207 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 584 RGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 584 R~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
..|++.++.+|+. +.+ .+ ...++|+.+|++...|++|..++|.++++-..
T Consensus 5 ~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3589999999977 333 22 34689999999999999999999998876553
No 78
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=41.30 E-value=67 Score=29.54 Aligned_cols=54 Identities=26% Similarity=0.222 Sum_probs=42.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHHHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEMYQ 647 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~q 647 (830)
.|++...++|+-+ .++ | ..+++|+..+++.+-|.+|..|.|+|+.-....+++.
T Consensus 149 ~lt~~e~~vl~l~-~~g----~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~~ 202 (211)
T PRK15369 149 LLTPRERQILKLI-TEG----Y----TNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLN 202 (211)
T ss_pred CCCHHHHHHHHHH-HCC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHH
Confidence 4899999999875 442 2 2478999999999999999999999987665554443
No 79
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=41.03 E-value=27 Score=34.93 Aligned_cols=49 Identities=22% Similarity=0.310 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.+|..-+++.+ .-.++|..+|++...|.+++..+|+++++.+
T Consensus 153 ~L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQEL--------SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 389999999987666532 3468999999999999999999999987655
No 80
>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=40.94 E-value=29 Score=32.68 Aligned_cols=49 Identities=22% Similarity=0.317 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++..-|.+. + .-.++|..+|++...|.++...+|.++++.+
T Consensus 110 ~L~~~~r~i~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYED----L----SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHhc----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 38999999997766652 2 2357999999999999999999999988644
No 81
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=40.35 E-value=29 Score=33.77 Aligned_cols=49 Identities=22% Similarity=0.148 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++..-|++. -.-.++|..+|++..-|.++...+|.++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 139 TLPEKQREILILRVVVG--------LSAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 38999999998876662 23468999999999999999999999988654
No 82
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=40.18 E-value=34 Score=34.10 Aligned_cols=51 Identities=24% Similarity=0.238 Sum_probs=41.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVE 643 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmie 643 (830)
.||+..+.++.--+++. .+ -.++|..+|++..-|.+....+|+++++.+.+
T Consensus 139 ~Lp~~~r~v~~L~~~eg--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~ 189 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD--FE------IDDICTELTLTANHCSVLLYRARTRLRTCLSE 189 (201)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 38999999998777663 22 36899999999999999999999999876643
No 83
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=40.09 E-value=28 Score=32.58 Aligned_cols=50 Identities=22% Similarity=0.157 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.++.-.+++. .+ -.++|..+|++...|.+...-+|+++++.+.
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 106 KLPARQREAFLLRYWED--MD------VAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hCCHHHHHHHHHHHHhc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 49999999998866662 22 3689999999999999999999999886553
No 84
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=39.60 E-value=33 Score=33.80 Aligned_cols=50 Identities=20% Similarity=0.261 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.++.-.+.+. .+ -.++|..+|++...|.+.+..+|+++++.+-
T Consensus 141 ~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 48999999998766653 23 3689999999999999999999999886553
No 85
>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=39.13 E-value=34 Score=35.36 Aligned_cols=49 Identities=22% Similarity=0.220 Sum_probs=41.4
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++...|++.+ .-.++|+.+|++...|+.+...++.++++.+
T Consensus 205 ~L~~~~r~ii~l~~~~g~--------s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL--------SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 489999999988877632 2368999999999999999999999998755
No 86
>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=39.04 E-value=41 Score=34.57 Aligned_cols=57 Identities=18% Similarity=0.131 Sum_probs=44.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEM 645 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem 645 (830)
.||+..+.+|...|.-.-..++ .-.++|..+|++...|+.+...+++|+|+.+.++.
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~----t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~ 232 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPH----TLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKK 232 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCc----cHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhH
Confidence 3899999999887721001232 46789999999999999999999999998865443
No 87
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=38.06 E-value=40 Score=34.88 Aligned_cols=49 Identities=20% Similarity=0.270 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.+|...|++.+ .-.++|+.+|++...|.+|...+|+++++.+
T Consensus 205 ~L~~~~r~vl~l~~~~g~--------s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIENL--------SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 389999999988777632 2378999999999999999999999987654
No 88
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=37.65 E-value=31 Score=33.55 Aligned_cols=48 Identities=17% Similarity=0.200 Sum_probs=39.1
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||++.+.++..-|++. . .-.++|+.+|++...|.++...+|+++++.+
T Consensus 129 L~~~~r~i~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 129 LPERQREAIVLQYYQG--L------SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHhhHHHhcC--C------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 8899999887766652 2 2368999999999999999999999987655
No 89
>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=37.47 E-value=53 Score=26.86 Aligned_cols=53 Identities=21% Similarity=0.211 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEMY 646 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~ 646 (830)
.|++...++|+.+..- ....++|...+++.+-|.++..+.++|+.-....+++
T Consensus 3 ~LT~~E~~vl~~l~~G---------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l~ 55 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG---------MSNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAELI 55 (58)
T ss_dssp SS-HHHHHHHHHHHTT---------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHHH
T ss_pred ccCHHHHHHHHHHHhc---------CCcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHHH
Confidence 3788888998776554 2457899999999999999999999998877665554
No 90
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=36.94 E-value=31 Score=33.33 Aligned_cols=48 Identities=15% Similarity=0.148 Sum_probs=40.0
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||+..+.+|.-.+.+. . .-.++|..+|++...|.++...+|.++++.+
T Consensus 136 L~~~~r~vl~l~~~~~--~------s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 136 LSPEERRVIEVLYYQG--Y------THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred CCHHHHHHHHHHHHcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 8999999998776652 2 3368999999999999999999999987654
No 91
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=36.93 E-value=39 Score=32.47 Aligned_cols=49 Identities=10% Similarity=0.150 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++.-.+.+. .+ -.++|+.+|++..-|.++...+|+|++..+
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 38999999998776663 23 358999999999999999999999986443
No 92
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=36.30 E-value=36 Score=32.11 Aligned_cols=47 Identities=19% Similarity=0.289 Sum_probs=39.3
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||++.+.+|.-.+ +. + .-.++|..+|++...|.++...+|.++|+-+
T Consensus 113 L~~~~r~il~l~~-~g----~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF-SG----Y----SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH-cC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 8999988887776 52 2 3468999999999999999999999988755
No 93
>PRK06930 positive control sigma-like factor; Validated
Probab=36.16 E-value=38 Score=34.16 Aligned_cols=52 Identities=13% Similarity=0.103 Sum_probs=42.2
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHH
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEM 645 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem 645 (830)
||+..+.++...|.+- . .-.++|..+|++...|.++...+|.++++.+-+++
T Consensus 115 L~~rer~V~~L~~~eg--~------s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~l 166 (170)
T PRK06930 115 LTEREKEVYLMHRGYG--L------SYSEIADYLNIKKSTVQSMIERAEKKIARQINESL 166 (170)
T ss_pred CCHHHHHHHHHHHHcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 8999999998766652 2 23689999999999999999999999987765443
No 94
>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=36.01 E-value=32 Score=32.83 Aligned_cols=49 Identities=12% Similarity=0.125 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++..-+++. . .-.++|..+|++...|.++..-+|+++++.+
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 38999999998777662 2 3368999999999999999999999988654
No 95
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=36.01 E-value=31 Score=35.49 Aligned_cols=49 Identities=22% Similarity=0.222 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++..+|.++ .+| .++|+.+|++..-|.++...+|+++++.+
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s~------~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MSY------REIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999999888774 222 58999999999999999999999987665
No 96
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=35.98 E-value=4.3e+02 Score=25.86 Aligned_cols=49 Identities=24% Similarity=0.314 Sum_probs=38.7
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
||++.+.++.--+.+- .+| .++|+.+|++..-|..|..-+|.++++.+-
T Consensus 128 Lp~~~R~~~~l~~~~g--ls~------~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 128 LPPRQREAFLLRYLEG--LSY------EEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CCHHHhHHhhhHhhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 8888888776555542 232 578999999999999999999999987664
No 97
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=35.81 E-value=30 Score=35.35 Aligned_cols=48 Identities=27% Similarity=0.344 Sum_probs=40.6
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||+..+.++..-|++.+ .-.++|+.+|++..-|.++...+|+++++.+
T Consensus 185 L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 185 LPEREQLVLSLYYQEEL--------NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHhHhccCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 89999999988776522 3468999999999999999999999998754
No 98
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=35.80 E-value=45 Score=32.66 Aligned_cols=51 Identities=14% Similarity=0.152 Sum_probs=42.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVE 643 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmie 643 (830)
.||++.+.++.-.+++. .+ -.++|..+|++..-|.+....+|+++++.+-.
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 38999999998877763 23 36899999999999999999999999876643
No 99
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=35.63 E-value=35 Score=32.73 Aligned_cols=49 Identities=16% Similarity=0.157 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++..-+.+. . .-.++|+.+|++...|.+++..+|+++++.+
T Consensus 136 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED--L------SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 38999999987755541 2 3368999999999999999999999987644
No 100
>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=35.49 E-value=36 Score=34.37 Aligned_cols=49 Identities=31% Similarity=0.426 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||+..+.+|...|.+. -.-.++|+.+|++...|..|...+++++++.+
T Consensus 178 ~L~~~~r~vl~l~y~~~--------~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 178 ALPERERRILLLRFFED--------KTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred cCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 38999999998877651 24578999999999999999999999987643
No 101
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=35.02 E-value=48 Score=33.57 Aligned_cols=53 Identities=19% Similarity=0.284 Sum_probs=43.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEM 645 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem 645 (830)
.||++.+.++.--|++. .+ -.++|..+|++..-|.++..-+|+++++.+....
T Consensus 148 ~L~~~~r~v~~L~~~~g--~s------~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 148 GLPAKYARVFMMREFIE--LE------TNEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 38999999888777663 22 3689999999999999999999999998775433
No 102
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=34.76 E-value=43 Score=34.78 Aligned_cols=49 Identities=16% Similarity=0.123 Sum_probs=40.1
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
||++.+.++.-.+++. . .-.++|+.+|++...|.++...+|+++++.+.
T Consensus 172 Lp~~~R~v~~L~~~eg--~------s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 172 LPEQQRIAVILSYHEN--M------SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CCHHHHHHhhhHHhcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 8999999887666652 2 23689999999999999999999999987653
No 103
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=34.68 E-value=36 Score=33.08 Aligned_cols=48 Identities=15% Similarity=0.147 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.||++.+.++..-|.+. . .-.++|+.+|++...|.+|...+|+++++.
T Consensus 133 ~L~~~~r~i~~l~~~~~--~------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYVDG--C------SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 48999999877766652 2 336899999999999999999999998754
No 104
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=34.67 E-value=46 Score=32.51 Aligned_cols=49 Identities=14% Similarity=0.208 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.+|.--+++. -.-.++|..+|++...|.+.+..+|+++++..
T Consensus 131 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE--------KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 38999999997766652 23468999999999999999999999987654
No 105
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=34.59 E-value=4.5e+02 Score=25.75 Aligned_cols=48 Identities=10% Similarity=0.015 Sum_probs=37.7
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||++.+.++.-.+.+. .+ -.++|..+|++..-|.+|...+|.++++.+
T Consensus 135 L~~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 135 VNPIDREILVLRFVAE--LE------FQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred cChhheeeeeeHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 7777777776544442 22 378999999999999999999999988754
No 106
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=34.14 E-value=48 Score=32.77 Aligned_cols=50 Identities=14% Similarity=0.200 Sum_probs=42.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.++..-|++. . .-.++|..+|++..-|.++..-+|+++++.+.
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--F------ESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999998877763 2 34789999999999999999999999987664
No 107
>PRK04217 hypothetical protein; Provisional
Probab=33.92 E-value=65 Score=31.00 Aligned_cols=49 Identities=18% Similarity=0.207 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.|+++.+.++..++.+.+ .-.++|+.+|++..-|.+.+..+|.+++..+
T Consensus 42 ~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 488889999988887632 4567999999999999999999999887554
No 108
>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=32.37 E-value=43 Score=33.93 Aligned_cols=49 Identities=22% Similarity=0.350 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||+..+.+|...|.+.+ .-.++|+.+|++...|..+...+++++++.+
T Consensus 175 ~L~~~~r~il~l~y~~~~--------s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEEL--------NLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred hCCHHHHHHHHHHHhCCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 389999999998887622 3478999999999999999999999987643
No 109
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=31.95 E-value=29 Score=33.94 Aligned_cols=50 Identities=26% Similarity=0.249 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.++.-.+.+.+ .-.++|+.+|++...|.++..-+|+++++.+.
T Consensus 131 ~Lp~~~r~i~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEGF--------AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehhhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 388888888876665522 23689999999999999999999999987663
No 110
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=31.88 E-value=4.9e+02 Score=25.36 Aligned_cols=49 Identities=22% Similarity=0.321 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++..-+.+. .+ -.++|..+|++...|.++..-+|.++++-+
T Consensus 127 ~L~~~~r~v~~l~~~~g--~s------~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE--LS------IKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 49999999987766663 22 368999999999999999999999987644
No 111
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=31.59 E-value=49 Score=32.52 Aligned_cols=47 Identities=15% Similarity=0.009 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcc
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWK 639 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKK 639 (830)
.||++++.++.-.+++.+ .-.++|..+|++..-|.++..-+|+++++
T Consensus 130 ~Lp~~~r~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLLGL--------SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 389999999987777632 23689999999999999999999999876
No 112
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=30.85 E-value=50 Score=32.63 Aligned_cols=49 Identities=16% Similarity=0.138 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++.-.+++ -| .-.++|+.+|++...|.+++.-+|+++++.+
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 3899999888776665 22 2368999999999999999999999998654
No 113
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=30.75 E-value=47 Score=31.72 Aligned_cols=48 Identities=15% Similarity=0.153 Sum_probs=40.4
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||++.+.+|..-+++. .+ -.++|+.+|++..-|.++..-+|+++++.+
T Consensus 119 L~~~~r~vl~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG--WS------TAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred CCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 8999999998877663 22 368999999999999999999999988655
No 114
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=30.67 E-value=54 Score=30.94 Aligned_cols=49 Identities=22% Similarity=0.268 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.+|..-|++. . ...++|+.+|++...|..+..-+|+++++.+
T Consensus 109 ~L~~~~r~v~~l~~~~~--~------s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG--E------TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 38999999998766652 2 2468999999999999999999999888665
No 115
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=30.47 E-value=48 Score=34.35 Aligned_cols=48 Identities=19% Similarity=0.199 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.||+..+.++...|++.+ .-.++|..+|+|...|.+++..+|+++|+.
T Consensus 201 ~L~~~~r~vl~l~~~~~~--------s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYKEEL--------TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHhcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 389999999988776522 347899999999999999999999999753
No 116
>PHA00542 putative Cro-like protein
Probab=30.29 E-value=1.5e+02 Score=26.48 Aligned_cols=36 Identities=14% Similarity=0.199 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHHH
Q 003323 611 DKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEMY 646 (830)
Q Consensus 611 EK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~ 646 (830)
...+||+.+|++...|+.|......+.....++++.
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~ 68 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLR 68 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHH
Confidence 455799999999999999998886555544444443
No 117
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=30.14 E-value=46 Score=34.91 Aligned_cols=49 Identities=22% Similarity=0.211 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.+|...|.+ .+ .-.++|..+|++...|+.+..-++.|+++.+
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 3899999999887775 22 3478999999999999999999999988655
No 118
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=30.10 E-value=26 Score=34.22 Aligned_cols=49 Identities=16% Similarity=0.192 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++.-.+.+. . .-.++|+.+|++...|.++...+|+++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHGD--L------ELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehccC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 38888888887765542 2 2367999999999999999999999998655
No 119
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=29.07 E-value=58 Score=31.78 Aligned_cols=49 Identities=18% Similarity=0.144 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++.-.+++.+ .-.++|+.+|++..-|.++.-.+|+++++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEGL--------SVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHcCC--------cHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 389999999987666532 3468999999999999999999999987654
No 120
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=28.83 E-value=58 Score=31.26 Aligned_cols=49 Identities=18% Similarity=0.189 Sum_probs=37.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||.+...+|.--+.+. . .-.++|..+|++...|.++...+|+++++.+
T Consensus 136 ~L~~~~r~il~l~~~~~--~------s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYIED--L------SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHhhC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 38888888885543331 2 3468999999999999999999999988654
No 121
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=28.61 E-value=63 Score=31.47 Aligned_cols=49 Identities=18% Similarity=0.265 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++.-.+++. . .-.++|..+|++..-|.+....+|+++++.+
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 38999999998766652 2 2368999999999999999999999987654
No 122
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=28.56 E-value=60 Score=34.05 Aligned_cols=49 Identities=20% Similarity=0.393 Sum_probs=41.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.+|...|++. -.-.++|..+|++...|..+...+++++++.+
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 38999999998887762 23578999999999999999999999998765
No 123
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=27.93 E-value=65 Score=30.97 Aligned_cols=51 Identities=12% Similarity=0.134 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVE 643 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmie 643 (830)
.||++...++.-.|.+. .+ -.++|..+|++...|.++...+|+++++.+.+
T Consensus 119 ~L~~~~r~i~~l~~~~~--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQ--YS------YKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 38888888887665552 23 36899999999999999999999999876643
No 124
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=27.63 E-value=67 Score=32.49 Aligned_cols=49 Identities=18% Similarity=0.190 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++..-+++. .+| .++|+.+|++..-|.++..-+|+++++.+
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s~------~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LSY------EEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 38888888876666653 333 68999999999999999999999988654
No 125
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=27.56 E-value=98 Score=30.07 Aligned_cols=50 Identities=12% Similarity=0.140 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||+..+.++.--+.+++ .-.++|..+|++..-|.+....+|.++++.+-
T Consensus 117 ~Lp~~~r~i~~l~~~e~~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 117 KLPYKLRQVIILRYLHDY--------SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred hCCHHHHHHHHHHHHccC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 389999999888766632 23689999999999999999999999986653
No 126
>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=27.55 E-value=65 Score=30.35 Aligned_cols=48 Identities=15% Similarity=0.069 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.||+..+.+|.-.|++. . .-.++|+.+|++...|.+...-+|+++|+.
T Consensus 122 ~L~~~~r~vl~l~~~~g--~------s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQN--L------PIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred hCCHHHHHHHHHHHhcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 38999999998866652 2 236899999999999999999888888764
No 127
>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=27.29 E-value=1.5e+02 Score=22.72 Aligned_cols=48 Identities=23% Similarity=0.184 Sum_probs=33.6
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
|++....++..+ .+ .+ ...++|+.++++...|..|..-.+.++.....
T Consensus 1 l~~~e~~i~~~~-~~----~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~~ 48 (57)
T cd06170 1 LTPREREVLRLL-AE----GK----TNKEIADILGISEKTVKTHLRNIMRKLGVKSR 48 (57)
T ss_pred CCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCH
Confidence 355566666543 32 22 45788999999999999999877777665443
No 128
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=27.28 E-value=87 Score=31.03 Aligned_cols=50 Identities=20% Similarity=0.172 Sum_probs=41.8
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.++...+.+++ .-.++|..+|++..-|.++..-+|.++++.+-
T Consensus 128 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 128 KLDPEYREPLLLQVIGGF--------SGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred hCCHHHHHHHHHHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 389999999988877742 23689999999999999999999999887664
No 129
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.27 E-value=66 Score=31.70 Aligned_cols=49 Identities=27% Similarity=0.332 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++..-+.+ -| .-.++|...|++..-|.+.+..+|+++++.+
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 3899999999776655 22 3468999999999999999999999987654
No 130
>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=27.25 E-value=50 Score=25.88 Aligned_cols=21 Identities=29% Similarity=0.259 Sum_probs=19.0
Q ss_pred HHHHHhCCChhhHhhhhhhhh
Q 003323 614 LLARQTGLSRNQVSNWFINAR 634 (830)
Q Consensus 614 ~LA~qTGLS~kQVsNWFiNaR 634 (830)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999875
No 131
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=26.65 E-value=71 Score=31.00 Aligned_cols=48 Identities=21% Similarity=0.301 Sum_probs=39.5
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||+....++..-|.+.+ .-.++|..+|++...|.+....+|+++++.+
T Consensus 138 L~~~~r~i~~l~~~~g~--------s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 138 LEPPRSELIRTAFFEGI--------TYEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 89999999887776532 3368999999999999999999999987643
No 132
>PF05722 Ustilago_mating: Ustilago B locus mating-type protein; InterPro: IPR008888 This domain consists of several Ustilago mating-type proteins. The b locus of the phytopathogenic fungus Ustilago maydis encodes a multiallelic recognition function that controls the ability of the fungus to form a dikaryon and complete the sexual stage of the life cycle. The b locus has at least 25 alleles and any combination of two different alleles, brought together by mating between haploid cells, allows the fungus to cause disease and undergo sexual development within the plant [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=26.40 E-value=23 Score=37.78 Aligned_cols=37 Identities=11% Similarity=0.161 Sum_probs=29.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCcchhcccccccccccccc
Q 003323 690 STTITPTGKRSEINEPESSPSLIAINRQCFSETHAKQS 727 (830)
Q Consensus 690 ~t~~~~s~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 727 (830)
++..++..+.++|...+... |.++|+++|.|+|.+|-
T Consensus 32 ~t~~sl~~~lDdvL~dNLgr-LT~aDK~eFEddW~SMi 68 (286)
T PF05722_consen 32 STSSSLSNNLDDVLSDNLGR-LTPADKKEFEDDWNSMI 68 (286)
T ss_pred CCCccccccHHHHHHhhhcc-CChhhhhHHHHHHHHHH
Confidence 34455677888887666666 99999999999998763
No 133
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=26.35 E-value=6.6e+02 Score=25.06 Aligned_cols=48 Identities=23% Similarity=0.334 Sum_probs=38.3
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
++++..+++.-.|++ .| ...++|+.+|+|..-|.+.+..+|.++.+.+
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 677777888777665 44 4567899999999999999999998876543
No 134
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=25.49 E-value=1.2e+02 Score=28.57 Aligned_cols=43 Identities=14% Similarity=0.343 Sum_probs=34.2
Q ss_pred ChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhh
Q 003323 587 PERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINA 633 (830)
Q Consensus 587 PKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNa 633 (830)
....+..+.+|+.+|+..+ ++ -..||+.+|+++..+..||...
T Consensus 7 ~~~~i~~~~~~I~~~~~~~-~s---l~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 7 DAITIHSILDWIEDNLESP-LS---LEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cHHHHHHHHHHHHHhcCCC-CC---HHHHHHHHCcCHHHHHHHHHHH
Confidence 3445677788999988776 33 4678999999999999999866
No 135
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=25.46 E-value=79 Score=30.84 Aligned_cols=48 Identities=13% Similarity=0.070 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.||++++.++.-.+.+. .+ -.++|..+|++..-|.+....+++++.+.
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--MK------QKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 39999999998877763 22 36899999999999999999998887543
No 136
>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=25.40 E-value=74 Score=30.80 Aligned_cols=49 Identities=20% Similarity=0.250 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.+|.--+.+. | .-.++|..+|++...|.++..-+|+++++-+
T Consensus 100 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG----L----SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998776662 2 3468999999999999999999998887644
No 137
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=25.27 E-value=85 Score=29.74 Aligned_cols=46 Identities=20% Similarity=0.216 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLW 638 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlK 638 (830)
.||++++.++...+.+. .+ -.++|..+|++...|.++...+++++.
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 38999999998777663 22 358999999999999999999988864
No 138
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.93 E-value=73 Score=31.94 Aligned_cols=50 Identities=14% Similarity=0.094 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||+..+.++..-+++.+ .-.++|..+|++..-|.++...+|+++++.+.
T Consensus 133 ~Lp~~~r~v~~l~~~~g~--------s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 133 ALPPERREALILTQVLGY--------TYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred cCCHHHHHHhhhHHHhCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 389999999977776632 24689999999999999999999999886554
No 139
>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=24.70 E-value=74 Score=32.34 Aligned_cols=48 Identities=23% Similarity=0.216 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.|+++.+.++...|.+ . ..-.++|+.+|+|...|..+-..+..|+++.
T Consensus 183 ~L~~~e~~i~~~~~~~----~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~ 230 (231)
T TIGR02885 183 KLDERERQIIMLRYFK----D----KTQTEVANMLGISQVQVSRLEKKVLKKMKEK 230 (231)
T ss_pred cCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 4899999999877664 2 2467899999999999999999988888753
No 140
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=24.59 E-value=72 Score=31.12 Aligned_cols=48 Identities=21% Similarity=0.163 Sum_probs=39.0
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||++.+.++.--+.+ .| .-.++|..+|++...|.+....+|+++++.+
T Consensus 139 L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 139 LPEDLRTALTLREFD----GL----SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CCHHHhHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 888888887665554 33 3468999999999999999999999998766
No 141
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.49 E-value=76 Score=31.15 Aligned_cols=48 Identities=15% Similarity=0.124 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||+..+.+|.. +.+. | .-.++|..+|++...|.+.+..+|+++++.+
T Consensus 155 ~L~~~~r~vl~l-~~e~----~----s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 155 LLSELEKEVLEL-YLDG----K----SYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred hCCHHHHHHHHH-HHcc----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 488999999987 5552 2 3368999999999999998888888877643
No 142
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=24.33 E-value=68 Score=32.63 Aligned_cols=53 Identities=19% Similarity=0.095 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++.-.|+-+...-+ .-.++|..+|++...|.++...+|+++|+.+
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 3899999998776521000111 3468999999999999999999999998764
No 143
>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=24.04 E-value=81 Score=33.39 Aligned_cols=49 Identities=22% Similarity=0.035 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.++.-.+.+. .+| .++|+.+|++..-|.+.+.-+|+++++.+
T Consensus 142 ~Lp~~~R~v~~L~~~~g--~s~------~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLG--WRA------AETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred hCCHHHhhHhhhHHHhC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 38999999987766653 233 68999999999999999999999998655
No 144
>PF13945 NST1: Salt tolerance down-regulator
Probab=24.04 E-value=1.1e+02 Score=32.32 Aligned_cols=32 Identities=22% Similarity=0.391 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCC
Q 003323 471 LSMLDEVDRRYNHYCEQMQMVVTSFDLVMGFG 502 (830)
Q Consensus 471 L~mLdEVDrRYeqY~eQmq~VvsSFe~vaG~G 502 (830)
..|-+|||+-|..||++|...+.--..+...+
T Consensus 152 ~~ie~ele~ly~~~y~~l~~~~~~~~~~~~~~ 183 (190)
T PF13945_consen 152 TAIEEELERLYDAYYEELEQYANHQQSVSNGG 183 (190)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhchhhcCC
Confidence 45668999999999999977665433344433
No 145
>PF13518 HTH_28: Helix-turn-helix domain
Probab=23.98 E-value=75 Score=24.76 Aligned_cols=25 Identities=32% Similarity=0.521 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhh
Q 003323 611 DKHLLARQTGLSRNQVSNWFINARV 635 (830)
Q Consensus 611 EK~~LA~qTGLS~kQVsNWFiNaRr 635 (830)
...++|++.|++..+|.+|....+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3456999999999999999876654
No 146
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=23.91 E-value=98 Score=30.10 Aligned_cols=46 Identities=15% Similarity=0.161 Sum_probs=33.6
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
+++..+.++.. +++. . .-.++|..+|++...|.+++.-+|+++++.
T Consensus 151 l~~~~~~i~~~-~~~~--~------s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 151 LSDLEWKVLQS-YLDG--K------SYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred cCHHHHHHHHH-HHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 34555556654 4442 2 346899999999999999999999988764
No 147
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=23.52 E-value=84 Score=31.13 Aligned_cols=49 Identities=20% Similarity=0.101 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||+..+.++.-.+++. . .-.++|..+|++..-|.++..-+|.++++-+
T Consensus 111 ~Lp~~~R~v~~L~~~eg--~------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG--L------SYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 38999999998877762 2 2368999999999999999999999887544
No 148
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=23.37 E-value=36 Score=32.49 Aligned_cols=48 Identities=19% Similarity=0.149 Sum_probs=39.5
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||+..+.+|..-+.+ .+ .-.++|..+|++..-|.+.+..+|+++++.+
T Consensus 121 L~~~~r~vl~l~~~~----g~----s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 121 LSLEHRAVLVLHDLE----DL----PQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CCHHHeeeeeehHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 888888888776655 22 2468999999999999999999999988654
No 149
>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=23.17 E-value=36 Score=31.61 Aligned_cols=46 Identities=28% Similarity=0.269 Sum_probs=36.7
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcc
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWK 639 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKK 639 (830)
||+..+.++...+.+. . .-.++|..+|++...|.++..-+|+++++
T Consensus 106 L~~~~r~i~~l~~~~g--~------s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 106 LPENYRTVLILREFKE--F------SYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred CCHhheeeeeehhhcc--C------cHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 7888878776554442 2 34689999999999999999999999875
No 150
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.11 E-value=89 Score=29.54 Aligned_cols=48 Identities=23% Similarity=0.257 Sum_probs=40.5
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 586 LPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 586 LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
||++...++.-.+.+. .+ -.++|..+|++..-|.+....+|+++++.+
T Consensus 106 L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 106 LPPACRDSFLLRKLEG--LS------HQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred CCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 8999999998887763 22 368999999999999999999999987664
No 151
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=22.35 E-value=1e+02 Score=32.82 Aligned_cols=54 Identities=24% Similarity=0.247 Sum_probs=41.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||+..+.+|.-.|.-+.... -.-.++|..+|++...|+.+...+|+++|+.+-
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~----~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEP----ATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCC----ccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 389999999987761100112 235789999999999999999999999988664
No 152
>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=21.96 E-value=1.1e+02 Score=22.21 Aligned_cols=23 Identities=30% Similarity=0.351 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChhhHhhhhhhhh
Q 003323 612 KHLLARQTGLSRNQVSNWFINAR 634 (830)
Q Consensus 612 K~~LA~qTGLS~kQVsNWFiNaR 634 (830)
...+|+.+|++...|++|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35788888888888888887753
No 153
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=21.80 E-value=1.8e+02 Score=33.78 Aligned_cols=60 Identities=22% Similarity=0.213 Sum_probs=47.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhhHHHHHH
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMVEEMYQQ 648 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmieem~qq 648 (830)
.|++..+.+|+-.|.-.-..+| .-.++|+.+|+|...|+.+...+++++++|.....+++
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~----Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~ 409 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTY----SLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRD 409 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHH
Confidence 3899999999887762111244 35789999999999999999999999999887655543
No 154
>cd00131 PAX Paired Box domain
Probab=21.24 E-value=4.7e+02 Score=25.27 Aligned_cols=47 Identities=17% Similarity=0.079 Sum_probs=32.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC-------ChhhHhhhhhhh
Q 003323 584 RGLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGL-------SRNQVSNWFINA 633 (830)
Q Consensus 584 R~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGL-------S~kQVsNWFiNa 633 (830)
+.+..+....+..+..+ +|.-+-.|-..+-...|+ +...|+.||.++
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 34555666666667777 898888776665335566 999999997664
No 155
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.10 E-value=1.2e+02 Score=33.48 Aligned_cols=54 Identities=20% Similarity=0.182 Sum_probs=41.8
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchhh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPMV 642 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpmi 642 (830)
.||++.+.+|..-|.-+....+ .-.++|..+|++...|+.+...+|+++|+.+.
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~----s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAA----TLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCc----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3899999999865522212233 45789999999999999999999999987663
No 156
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=20.83 E-value=83 Score=33.37 Aligned_cols=48 Identities=29% Similarity=0.454 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcch
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKP 640 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKp 640 (830)
.||+..+.+|...|++ .+ .-.++|..+|++...|..|...++.++++.
T Consensus 215 ~L~~rer~vl~l~y~~----~~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 215 ALPERERTVLVLRFFE----SM----TQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred cCCHHHHHHHHHHhcC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4899999999888765 22 247899999999999999999999998764
No 157
>PRK05572 sporulation sigma factor SigF; Validated
Probab=20.62 E-value=82 Score=32.74 Aligned_cols=49 Identities=24% Similarity=0.257 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++...++...|.+ .-.-.++|+.+|++...|..|-..+..|+++.+
T Consensus 202 ~L~~~~~~v~~l~~~~--------~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 202 ELDERERLIVYLRYFK--------DKTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred cCCHHHHHHHHHHHhC--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3889999998877765 134578999999999999999999999988654
No 158
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=20.23 E-value=96 Score=32.34 Aligned_cols=49 Identities=27% Similarity=0.253 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.|+++.+.+|..-|++ .+ .-.++|+.+|++...|+.+-.+++.|+++.+
T Consensus 209 ~L~~~er~vi~~~~~~----~~----t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 209 KLNDREKLILNLRFFQ----GK----TQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3899999998887765 22 3568999999999999999999999987653
No 159
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=20.11 E-value=1.1e+02 Score=32.28 Aligned_cols=49 Identities=18% Similarity=0.320 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhcchh
Q 003323 585 GLPERSVNILRSWLFEHFLHPYPSDADKHLLARQTGLSRNQVSNWFINARVRLWKPM 641 (830)
Q Consensus 585 ~LPKeqv~ILraWF~eHl~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlKKpm 641 (830)
.||++.+.+|...|++ .+ .-.++|..+|++...|+.+..-++.++++.+
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 4899999999888765 22 3478999999999999999999999998765
Done!