Query 006230
Match_columns 655
No_of_seqs 322 out of 1030
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 20:16:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006230hhsearch_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 7.9E-38 1.7E-42 291.7 8.3 130 220-349 2-139 (140)
2 PF07526 POX: Associated with 100.0 1.8E-37 4E-42 290.9 9.4 126 224-349 2-139 (140)
3 KOG0773 Transcription factor M 100.0 2.1E-32 4.6E-37 284.9 9.9 252 221-473 45-312 (342)
4 KOG0774 Transcription factor P 99.6 1.3E-15 2.9E-20 155.0 13.3 137 288-463 112-251 (334)
5 PF05920 Homeobox_KN: Homeobox 99.6 1E-15 2.3E-20 116.5 4.0 40 418-457 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.4 7.9E-13 1.7E-17 103.9 6.6 57 402-461 2-58 (59)
7 PF00046 Homeobox: Homeobox do 99.4 1E-12 2.2E-17 104.0 5.7 57 401-460 1-57 (57)
8 smart00389 HOX Homeodomain. DN 99.3 2.1E-12 4.5E-17 101.1 6.6 55 402-459 2-56 (56)
9 KOG0775 Transcription factor S 99.2 1.9E-11 4.1E-16 125.7 6.9 51 406-459 182-232 (304)
10 KOG0487 Transcription factor A 98.9 6.7E-10 1.5E-14 116.7 3.7 61 399-462 233-294 (308)
11 KOG0842 Transcription factor t 98.9 1E-09 2.2E-14 115.3 4.1 65 399-466 151-216 (307)
12 KOG0488 Transcription factor B 98.8 5.6E-09 1.2E-13 110.0 5.7 63 399-464 170-233 (309)
13 KOG0489 Transcription factor z 98.8 3.7E-09 8E-14 108.7 4.0 60 399-461 158-217 (261)
14 KOG0843 Transcription factor E 98.8 1.3E-08 2.8E-13 100.0 7.0 64 399-465 101-164 (197)
15 KOG0493 Transcription factor E 98.7 8.6E-09 1.9E-13 105.9 4.8 61 398-461 244-304 (342)
16 KOG0484 Transcription factor P 98.7 2.8E-08 6.1E-13 90.6 7.1 61 404-467 21-81 (125)
17 TIGR01565 homeo_ZF_HD homeobox 98.7 2.4E-08 5.2E-13 82.2 5.4 52 401-455 2-57 (58)
18 KOG0483 Transcription factor H 98.7 1.6E-08 3.5E-13 100.8 5.1 68 400-470 50-117 (198)
19 KOG0850 Transcription factor D 98.7 1.8E-08 3.8E-13 102.2 4.7 61 399-462 120-181 (245)
20 KOG0485 Transcription factor N 98.7 1.8E-08 3.9E-13 101.5 4.3 64 397-463 101-164 (268)
21 COG5576 Homeodomain-containing 98.5 1.5E-07 3.3E-12 90.9 5.1 62 398-462 49-110 (156)
22 KOG3802 Transcription factor O 98.4 1.1E-07 2.4E-12 102.5 3.9 60 400-462 293-353 (398)
23 KOG0494 Transcription factor C 98.4 2E-07 4.4E-12 96.0 4.9 53 406-461 147-199 (332)
24 KOG2251 Homeobox transcription 98.4 2.4E-07 5.3E-12 93.6 4.7 58 401-461 38-95 (228)
25 KOG0486 Transcription factor P 98.4 1.9E-07 4.2E-12 98.2 3.9 60 400-462 111-171 (351)
26 KOG0848 Transcription factor C 98.4 2.2E-07 4.7E-12 96.1 3.5 57 407-466 206-262 (317)
27 KOG0492 Transcription factor M 98.3 1.2E-06 2.6E-11 88.1 5.7 57 402-461 146-202 (246)
28 KOG0491 Transcription factor B 98.2 3.7E-07 8.1E-12 89.0 1.9 58 401-461 100-158 (194)
29 KOG0847 Transcription factor, 98.2 9.5E-07 2.1E-11 89.4 4.0 72 401-475 168-239 (288)
30 KOG4577 Transcription factor L 98.2 1E-06 2.2E-11 92.0 3.8 62 398-462 165-226 (383)
31 KOG2252 CCAAT displacement pro 97.9 1.4E-05 3.1E-10 89.4 5.7 57 399-458 419-475 (558)
32 KOG0844 Transcription factor E 97.8 9.7E-06 2.1E-10 85.4 1.5 57 404-463 185-241 (408)
33 KOG0849 Transcription factor P 97.6 5.1E-05 1.1E-09 81.8 4.3 58 402-462 178-235 (354)
34 KOG0490 Transcription factor, 97.6 3.8E-05 8.2E-10 75.3 2.5 61 399-462 59-119 (235)
35 KOG0773 Transcription factor M 97.3 0.00011 2.3E-09 77.8 2.0 60 402-462 97-156 (342)
36 KOG1168 Transcription factor A 97.1 0.00021 4.5E-09 75.3 1.3 59 399-460 308-366 (385)
37 PF11569 Homez: Homeodomain le 96.1 0.0046 1E-07 51.2 2.8 43 412-457 10-52 (56)
38 KOG0490 Transcription factor, 95.4 0.013 2.8E-07 57.6 3.5 62 399-463 152-213 (235)
39 KOG1146 Homeobox protein [Gene 90.6 0.32 7E-06 60.2 5.2 57 404-463 907-963 (1406)
40 PF04218 CENP-B_N: CENP-B N-te 80.8 2.8 6.2E-05 33.8 4.3 47 401-455 1-47 (53)
41 KOG3623 Homeobox transcription 72.4 5.2 0.00011 47.7 5.1 45 412-459 568-612 (1007)
42 PF04545 Sigma70_r4: Sigma-70, 72.4 4.2 9.2E-05 31.6 3.1 47 406-460 4-50 (50)
43 cd06171 Sigma70_r4 Sigma70, re 71.8 5.2 0.00011 29.4 3.4 46 406-459 10-55 (55)
44 PF01527 HTH_Tnp_1: Transposas 71.2 6.6 0.00014 32.4 4.2 46 402-455 2-48 (76)
45 PF08281 Sigma70_r4_2: Sigma-7 68.3 7.5 0.00016 30.4 3.7 45 406-458 10-54 (54)
46 PF11285 DUF3086: Protein of u 67.6 51 0.0011 35.4 10.5 31 282-312 6-36 (283)
47 cd00569 HTH_Hin_like Helix-tur 63.3 19 0.00041 23.5 4.5 39 405-451 4-42 (42)
48 PRK06759 RNA polymerase factor 52.4 16 0.00034 33.7 3.4 47 406-460 106-152 (154)
49 TIGR02937 sigma70-ECF RNA poly 52.3 21 0.00046 31.3 4.2 48 406-461 110-157 (158)
50 TIGR02985 Sig70_bacteroi1 RNA 51.8 24 0.00051 32.1 4.5 48 406-461 113-160 (161)
51 PRK09642 RNA polymerase sigma 51.5 19 0.00041 33.5 3.9 49 406-462 106-154 (160)
52 PRK12530 RNA polymerase sigma 50.3 21 0.00045 34.7 4.1 51 406-464 134-184 (189)
53 PRK00118 putative DNA-binding 49.1 19 0.0004 33.4 3.3 54 405-467 16-69 (104)
54 PRK09644 RNA polymerase sigma 49.0 21 0.00045 33.6 3.8 50 405-462 107-156 (165)
55 PRK11924 RNA polymerase sigma 48.4 21 0.00045 33.2 3.6 49 406-462 125-173 (179)
56 PRK12514 RNA polymerase sigma 47.6 28 0.00061 33.0 4.5 48 406-461 129-176 (179)
57 PF13443 HTH_26: Cro/C1-type H 47.0 23 0.00051 28.2 3.3 42 415-463 2-43 (63)
58 TIGR02939 RpoE_Sigma70 RNA pol 46.2 23 0.00051 33.6 3.7 49 406-462 138-186 (190)
59 PRK09652 RNA polymerase sigma 45.7 24 0.00052 32.8 3.6 49 406-462 128-176 (182)
60 PRK12512 RNA polymerase sigma 44.8 20 0.00044 34.2 3.0 49 406-462 131-179 (184)
61 PRK09646 RNA polymerase sigma 44.6 22 0.00049 34.5 3.3 49 406-462 142-190 (194)
62 PRK03975 tfx putative transcri 44.1 36 0.00078 33.2 4.6 49 405-462 5-53 (141)
63 PRK06811 RNA polymerase factor 43.9 24 0.00052 34.1 3.4 49 406-462 131-179 (189)
64 PF00196 GerE: Bacterial regul 43.6 45 0.00098 26.6 4.4 52 406-466 3-54 (58)
65 PRK09648 RNA polymerase sigma 42.9 26 0.00056 33.7 3.4 49 406-462 139-187 (189)
66 PF03791 KNOX2: KNOX2 domain ; 42.3 90 0.002 25.9 5.9 42 271-312 5-49 (52)
67 PRK12526 RNA polymerase sigma 42.0 26 0.00057 34.5 3.4 49 406-462 153-201 (206)
68 smart00421 HTH_LUXR helix_turn 41.7 76 0.0016 23.7 5.2 48 406-462 3-50 (58)
69 TIGR02999 Sig-70_X6 RNA polyme 41.5 29 0.00062 32.9 3.5 48 406-461 134-181 (183)
70 PRK12519 RNA polymerase sigma 40.4 27 0.00058 33.6 3.1 49 406-462 141-189 (194)
71 TIGR02989 Sig-70_gvs1 RNA poly 39.7 31 0.00068 31.8 3.4 48 405-460 110-157 (159)
72 TIGR02941 Sigma_B RNA polymera 38.5 35 0.00076 34.8 3.8 49 406-462 205-253 (255)
73 TIGR02948 SigW_bacill RNA poly 38.4 30 0.00066 32.7 3.1 49 406-462 136-184 (187)
74 PRK12541 RNA polymerase sigma 38.1 31 0.00067 32.2 3.1 48 405-460 111-158 (161)
75 TIGR02393 RpoD_Cterm RNA polym 38.0 55 0.0012 33.2 5.0 56 406-465 176-231 (238)
76 PRK05602 RNA polymerase sigma 38.0 31 0.00066 33.1 3.1 49 406-462 128-176 (186)
77 PRK12520 RNA polymerase sigma 37.6 56 0.0012 31.5 4.8 49 406-462 131-179 (191)
78 PRK15369 two component system 36.9 61 0.0013 29.5 4.8 53 405-466 148-200 (211)
79 PRK12533 RNA polymerase sigma 36.9 44 0.00096 33.8 4.2 49 406-462 134-182 (216)
80 PRK09047 RNA polymerase factor 36.7 38 0.00083 31.2 3.4 50 405-462 105-154 (161)
81 PRK12547 RNA polymerase sigma 36.4 37 0.00081 32.0 3.4 49 406-462 112-160 (164)
82 PRK12536 RNA polymerase sigma 36.3 38 0.00082 32.4 3.5 49 406-462 129-177 (181)
83 PRK12546 RNA polymerase sigma 36.3 33 0.00071 33.7 3.1 49 406-462 113-161 (188)
84 PRK08583 RNA polymerase sigma 36.0 47 0.001 33.9 4.2 49 406-462 205-253 (257)
85 PRK13919 putative RNA polymera 36.0 33 0.00071 32.7 3.0 49 406-462 135-183 (186)
86 PRK12544 RNA polymerase sigma 35.9 61 0.0013 32.3 4.9 52 405-464 147-198 (206)
87 TIGR02980 SigBFG RNA polymeras 35.8 34 0.00074 34.1 3.2 49 406-462 178-226 (227)
88 PRK12515 RNA polymerase sigma 35.4 45 0.00098 32.1 3.8 49 406-462 131-179 (189)
89 PRK12532 RNA polymerase sigma 34.8 41 0.00088 32.6 3.4 49 406-462 136-184 (195)
90 TIGR02954 Sig70_famx3 RNA poly 34.8 41 0.00089 31.6 3.4 49 406-462 119-167 (169)
91 TIGR02983 SigE-fam_strep RNA p 34.3 44 0.00096 31.0 3.5 49 406-462 110-158 (162)
92 PRK04217 hypothetical protein; 34.2 65 0.0014 30.2 4.5 50 405-462 41-90 (110)
93 PRK09647 RNA polymerase sigma 33.2 60 0.0013 32.3 4.4 49 406-462 138-186 (203)
94 PRK06986 fliA flagellar biosyn 33.0 36 0.00078 34.3 2.8 49 406-462 184-232 (236)
95 PRK12537 RNA polymerase sigma 32.7 45 0.00098 32.0 3.3 49 405-461 132-180 (182)
96 PRK12531 RNA polymerase sigma 32.5 47 0.001 32.2 3.5 50 405-462 140-189 (194)
97 PRK09639 RNA polymerase sigma 32.5 46 0.001 30.9 3.3 48 406-462 112-159 (166)
98 PRK12516 RNA polymerase sigma 32.3 50 0.0011 32.2 3.6 49 406-462 116-164 (187)
99 PRK12524 RNA polymerase sigma 31.5 70 0.0015 31.1 4.4 49 406-462 136-184 (196)
100 PRK12523 RNA polymerase sigma 31.4 53 0.0011 31.1 3.5 47 406-460 119-165 (172)
101 PF04967 HTH_10: HTH DNA bindi 31.3 89 0.0019 25.8 4.3 50 407-457 1-50 (53)
102 PRK12538 RNA polymerase sigma 30.7 57 0.0012 33.3 3.8 49 406-462 171-219 (233)
103 PRK09641 RNA polymerase sigma 30.4 54 0.0012 31.1 3.4 49 406-462 136-184 (187)
104 PRK12545 RNA polymerase sigma 30.1 59 0.0013 31.9 3.7 50 406-463 139-188 (201)
105 TIGR02479 FliA_WhiG RNA polyme 30.1 49 0.0011 33.0 3.2 48 406-461 175-222 (224)
106 PRK07037 extracytoplasmic-func 29.9 58 0.0013 30.3 3.5 49 406-462 109-157 (163)
107 PRK11923 algU RNA polymerase s 29.6 74 0.0016 30.6 4.2 49 406-462 138-186 (193)
108 PRK07408 RNA polymerase sigma 29.3 49 0.0011 34.2 3.1 49 406-462 203-251 (256)
109 PF13518 HTH_28: Helix-turn-he 29.2 53 0.0012 25.0 2.6 25 432-456 14-38 (52)
110 PRK09649 RNA polymerase sigma 28.9 55 0.0012 31.7 3.3 48 405-460 129-176 (185)
111 TIGR02952 Sig70_famx2 RNA poly 28.9 59 0.0013 30.2 3.3 49 405-461 121-169 (170)
112 PHA00542 putative Cro-like pro 28.7 1.6E+02 0.0034 25.7 5.7 35 432-466 33-67 (82)
113 PRK12513 RNA polymerase sigma 28.6 42 0.00092 32.3 2.4 49 406-462 139-187 (194)
114 COG1595 RpoE DNA-directed RNA 28.0 5.5E+02 0.012 24.6 10.5 49 406-462 127-175 (182)
115 PRK06288 RNA polymerase sigma 28.0 64 0.0014 33.4 3.7 49 406-462 212-260 (268)
116 TIGR03001 Sig-70_gmx1 RNA poly 27.9 79 0.0017 32.7 4.3 50 406-463 161-210 (244)
117 PRK07670 RNA polymerase sigma 27.9 57 0.0012 33.3 3.3 48 406-461 201-248 (251)
118 cd00131 PAX Paired Box domain 27.9 2.7E+02 0.0059 26.2 7.6 48 404-454 73-127 (128)
119 PRK09637 RNA polymerase sigma 27.7 61 0.0013 31.4 3.3 49 406-462 106-154 (181)
120 TIGR02959 SigZ RNA polymerase 27.5 66 0.0014 30.7 3.4 50 405-462 99-148 (170)
121 cd06170 LuxR_C_like C-terminal 27.4 1.5E+02 0.0033 22.2 4.9 46 407-461 1-46 (57)
122 PRK11511 DNA-binding transcrip 27.2 1.1E+02 0.0024 28.4 4.7 44 407-454 6-49 (127)
123 TIGR02947 SigH_actino RNA poly 27.2 39 0.00085 32.6 1.9 49 406-462 131-179 (193)
124 cd01392 HTH_LacI Helix-turn-he 27.0 56 0.0012 25.0 2.4 21 435-455 2-22 (52)
125 PRK12527 RNA polymerase sigma 26.9 98 0.0021 28.8 4.4 49 406-462 105-153 (159)
126 PRK06930 positive control sigm 26.8 69 0.0015 31.6 3.6 50 406-463 114-163 (170)
127 PRK07598 RNA polymerase sigma 26.6 1.1E+02 0.0024 34.7 5.5 58 406-467 350-407 (415)
128 PF07638 Sigma70_ECF: ECF sigm 26.5 93 0.002 30.4 4.4 48 407-462 136-183 (185)
129 TIGR02943 Sig70_famx1 RNA poly 26.5 80 0.0017 30.7 3.9 49 406-462 131-179 (188)
130 PRK12535 RNA polymerase sigma 26.3 68 0.0015 31.6 3.4 49 406-462 133-181 (196)
131 PRK12542 RNA polymerase sigma 26.3 70 0.0015 30.7 3.4 50 405-462 121-170 (185)
132 PRK09645 RNA polymerase sigma 25.9 61 0.0013 30.5 2.9 49 406-462 118-166 (173)
133 PF13551 HTH_29: Winged helix- 25.8 2.2E+02 0.0047 24.6 6.2 52 401-452 52-109 (112)
134 PRK12543 RNA polymerase sigma 25.8 79 0.0017 30.2 3.7 49 406-462 117-165 (179)
135 PRK12539 RNA polymerase sigma 25.4 76 0.0016 30.5 3.5 49 406-462 131-179 (184)
136 PRK08301 sporulation sigma fac 25.1 65 0.0014 32.3 3.1 53 406-462 178-230 (234)
137 PRK12518 RNA polymerase sigma 25.0 50 0.0011 31.1 2.1 49 406-462 120-168 (175)
138 PRK05657 RNA polymerase sigma 24.5 1.1E+02 0.0024 33.1 4.8 53 406-462 262-314 (325)
139 PRK09415 RNA polymerase factor 24.2 68 0.0015 30.8 2.9 49 406-462 127-175 (179)
140 PRK09413 IS2 repressor TnpA; R 24.1 1.9E+02 0.0041 26.8 5.7 47 402-455 8-54 (121)
141 PRK12529 RNA polymerase sigma 24.0 1.2E+02 0.0025 29.2 4.5 48 406-461 127-174 (178)
142 PRK12511 RNA polymerase sigma 24.0 83 0.0018 30.6 3.5 49 406-462 111-159 (182)
143 PRK12522 RNA polymerase sigma 23.9 95 0.0021 29.4 3.8 49 406-462 119-167 (173)
144 PRK08295 RNA polymerase factor 23.4 83 0.0018 30.5 3.4 47 406-461 155-201 (208)
145 COG3413 Predicted DNA binding 23.4 99 0.0021 31.1 4.0 54 406-460 155-208 (215)
146 TIGR02885 spore_sigF RNA polym 23.4 80 0.0017 31.6 3.3 48 406-461 183-230 (231)
147 cd00093 HTH_XRE Helix-turn-hel 23.3 1.1E+02 0.0023 21.8 3.2 23 433-455 15-37 (58)
148 PRK12534 RNA polymerase sigma 23.0 85 0.0018 30.0 3.3 48 406-461 137-184 (187)
149 TIGR02950 SigM_subfam RNA poly 22.5 38 0.00083 31.0 0.8 46 407-460 106-151 (154)
150 PRK12517 RNA polymerase sigma 22.4 1.6E+02 0.0034 28.7 5.1 49 406-462 128-176 (188)
151 PRK12528 RNA polymerase sigma 22.4 93 0.002 29.0 3.4 47 406-460 113-159 (161)
152 PRK12540 RNA polymerase sigma 22.0 90 0.002 30.3 3.3 49 406-462 111-159 (182)
153 PF13565 HTH_32: Homeodomain-l 21.1 4.2E+02 0.0092 21.8 6.7 40 408-450 32-76 (77)
154 TIGR02960 SigX5 RNA polymerase 20.6 1.3E+02 0.0028 31.5 4.3 48 406-461 142-189 (324)
155 PRK09651 RNA polymerase sigma 20.6 88 0.0019 29.8 2.9 49 406-462 119-167 (172)
No 1
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=7.9e-38 Score=291.69 Aligned_cols=130 Identities=53% Similarity=0.811 Sum_probs=106.3
Q ss_pred ccceeccCCCChhHHHHHHHHHhccCCccCcchhhhh---h--h--hhccCCCCCCC-CCCccccCCchHHHHHHHHHHH
Q 006230 220 GHQFQLRNSKYLAPAQEILKEFCSLGTKQNDATKLKS---N--K--AKQQWDDENAG-SSSRKQSLCSLEFMELQKRKTK 291 (655)
Q Consensus 220 Gy~~~l~~SryL~paQeLL~E~c~v~~~~~~~~~~~s---~--~--~~~~~~~~~~~-~~s~~~elssle~~elQ~kK~k 291 (655)
||+++|++||||+||||||+|||+|+.........+. . . .....++..+. ..+..++|++++++|+|+||+|
T Consensus 2 g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~s~~~~~~~ls~~~r~e~q~kk~k 81 (140)
T smart00574 2 GGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQSGNDSPVSTSSNEGGGENLSGGSSSSEVPPLSTAERQELQRKKAK 81 (140)
T ss_pred chhhhccCccccccHHHHHHHHhcccHHhhcccccccccccccccccCCCcCCCCCCCCCCCCCCCchhHHHHHHHHHHH
Confidence 8899999999999999999999999855433221110 0 0 00111111111 2234589999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccCCCCCccCchhhhhhhhhhccccchhhH
Q 006230 292 LLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRDGIV 349 (655)
Q Consensus 292 LL~mLEEVd~ry~qYc~qmq~v~ssFe~vaG~gaA~~Ytslal~amSrhfr~Lrd~I~ 349 (655)
||.||||||+||++||+||++|+++|++++|.++|.+||+||+++||||||||||+|+
T Consensus 82 Ll~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 82 LLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999996
No 2
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=100.00 E-value=1.8e-37 Score=290.91 Aligned_cols=126 Identities=56% Similarity=0.808 Sum_probs=100.0
Q ss_pred eccCCCChhHHHHHHHHHhccCCccCcch-hhhhhh-------hhccC--CCCC--CCCCCccccCCchHHHHHHHHHHH
Q 006230 224 QLRNSKYLAPAQEILKEFCSLGTKQNDAT-KLKSNK-------AKQQW--DDEN--AGSSSRKQSLCSLEFMELQKRKTK 291 (655)
Q Consensus 224 ~l~~SryL~paQeLL~E~c~v~~~~~~~~-~~~s~~-------~~~~~--~~~~--~~~~s~~~elssle~~elQ~kK~k 291 (655)
+|++||||+||||||+|||+|+....... ..+... ..... .... .+.....+++++++++|+|+||+|
T Consensus 2 ~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~~~~e~q~kK~K 81 (140)
T PF07526_consen 2 VLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSGAPGGANSSGSSSSSGGSSSSSSSSDSSSPELSPAERQELQRKKAK 81 (140)
T ss_pred ccccchhHHHHHHHHHHHHcccchhhhcchhhccccccccccCCCCCCCCCCCCCccccCCCCCCCChhhHHHHHHHHHH
Confidence 69999999999999999999987311100 000000 00000 0000 112233578999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccCCCCCccCchhhhhhhhhhccccchhhH
Q 006230 292 LLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRDGIV 349 (655)
Q Consensus 292 LL~mLEEVd~ry~qYc~qmq~v~ssFe~vaG~gaA~~Ytslal~amSrhfr~Lrd~I~ 349 (655)
||.||||||+||+|||+||++|+++||+|+|.|+|.|||+||++|||||||||||+|+
T Consensus 82 Ll~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~ 139 (140)
T PF07526_consen 82 LLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAIS 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999996
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.97 E-value=2.1e-32 Score=284.89 Aligned_cols=252 Identities=42% Similarity=0.602 Sum_probs=196.5
Q ss_pred cceeccCCCChhHHHHHHHHHhccCCccCcchh-h---hhhhhh-ccCC-----CCCCCCCCccccCCchHHHHHHHHHH
Q 006230 221 HQFQLRNSKYLAPAQEILKEFCSLGTKQNDATK-L---KSNKAK-QQWD-----DENAGSSSRKQSLCSLEFMELQKRKT 290 (655)
Q Consensus 221 y~~~l~~SryL~paQeLL~E~c~v~~~~~~~~~-~---~s~~~~-~~~~-----~~~~~~~s~~~elssle~~elQ~kK~ 290 (655)
+.+.+..+|||.++|+||+|+|++......... . ....+. .... ..+.+..+ .+..+.+++.+++.+++
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~ 123 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRES-ATLKAWLEEHRLNPYPS 123 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccc-cccccchhhhhhccCch
Confidence 366789999999999999999999754321100 0 000000 0000 01111122 45567889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccccCCCCCccCchhhhhhhhhhccccch--hhHHHHHHHHhhcCCCCCCCCC
Q 006230 291 KLLSMLEEVDRRYRHYCDQMKAVVSSFEAVAGNGAARVYSALASKAMSRHFRCLRD--GIVGQIQATKKAMGEKDPVAPG 368 (655)
Q Consensus 291 kLL~mLEEVd~ry~qYc~qmq~v~ssFe~vaG~gaA~~Ytslal~amSrhfr~Lrd--~I~~qi~a~~kamge~d~~~~g 368 (655)
||+.+|.+|+.+|.+||..|+.+.+.|+...|++.+.+|++.++..++++|+++.+ +|..++......++..+.....
T Consensus 124 k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~ 203 (342)
T KOG0773|consen 124 KLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDSE 203 (342)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999998 7888888877776644321111
Q ss_pred ---CCCCCCCccchhhhhHHhhh-hhhhhccccCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCCh
Q 006230 369 ---TSRGETPRLKIIDQTLRQQR-AFQQMSMMESHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSR 444 (655)
Q Consensus 369 ---~~~get~rlr~~dq~lrq~r-a~~q~~~~e~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~ 444 (655)
......+.....++.+++++ ++......+..+||++++||++++.+|+.|+++|+.||||++.+|.+||++|||++
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~ 283 (342)
T KOG0773|consen 204 DESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSR 283 (342)
T ss_pred cccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCc
Confidence 11122445555556666554 34444455567899999999999999999999999999999999999999999999
Q ss_pred hhHhhhhhhhhhhhchhhHHHHHHHhhhh
Q 006230 445 SQVSNWFINARVRLWKPMVEEMYLEETKE 473 (655)
Q Consensus 445 ~QVsNWFiNaRrRlkKp~iee~~~~~~~~ 473 (655)
.||+|||||+|+|+|+||++++|..+...
T Consensus 284 ~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 284 PQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred ccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 99999999999999999999999988875
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.64 E-value=1.3e-15 Score=154.97 Aligned_cols=137 Identities=24% Similarity=0.421 Sum_probs=95.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh---ccccccCCCCCccCchhhhhhhhhhccccchhhHHHHHHHHhhcCCCCC
Q 006230 288 RKTKLLSMLEEVDRRYRHYCDQMKAVVS---SFEAVAGNGAARVYSALASKAMSRHFRCLRDGIVGQIQATKKAMGEKDP 364 (655)
Q Consensus 288 kK~kLL~mLEEVd~ry~qYc~qmq~v~s---sFe~vaG~gaA~~Ytslal~amSrhfr~Lrd~I~~qi~a~~kamge~d~ 364 (655)
.|.-+-..|++-++.|+.||..+..++. .|-+++ .--..-..+.|++.| ..|--+|+.....
T Consensus 112 iR~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~-----~ke~e~m~~~i~~kF----~~iq~~lkqstce------ 176 (334)
T KOG0774|consen 112 IRQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIM-----PKEIERMVQIISKKF----SHIQMQLKQSTCE------ 176 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCC-----HHHHHHHHHHHHHHH----HHHHHHHHHHHHH------
Confidence 3444445688889999999988887763 333222 001122335666666 3344444321110
Q ss_pred CCCCCCCCCCCccchhhhhHHhhhhhhhhccccCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCCh
Q 006230 365 VAPGTSRGETPRLKIIDQTLRQQRAFQQMSMMESHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSR 444 (655)
Q Consensus 365 ~~~g~~~get~rlr~~dq~lrq~ra~~q~~~~e~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~ 444 (655)
.++ .||. .+. ..+||||+|+|.+++||..||+.|+.||||++++|++||++++++.
T Consensus 177 -------------~vm--iLr~--r~l-------darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItv 232 (334)
T KOG0774|consen 177 -------------AVM--ILRS--RFL-------DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITV 232 (334)
T ss_pred -------------HHH--HHHH--HHH-------HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCcee
Confidence 000 0111 111 2468899999999999999999999999999999999999999999
Q ss_pred hhHhhhhhhhhhhhchhhH
Q 006230 445 SQVSNWFINARVRLWKPMV 463 (655)
Q Consensus 445 ~QVsNWFiNaRrRlkKp~i 463 (655)
+||+|||-|+|.|.||.|.
T Consensus 233 sQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 233 SQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred hhhccccccceeehhhhhh
Confidence 9999999999999999885
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=99.58 E-value=1e-15 Score=116.53 Aligned_cols=40 Identities=68% Similarity=1.174 Sum_probs=36.5
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 006230 418 WLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVR 457 (655)
Q Consensus 418 Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrR 457 (655)
||.+|+.||||+++||++||++||||.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 9999999999999999999999999999999999999998
No 6
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.38 E-value=7.9e-13 Score=103.90 Aligned_cols=57 Identities=30% Similarity=0.538 Sum_probs=53.2
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 402 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
+++..|+++++.+|++||.. +|||+..++..||.+|||+..||.+||.|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 45667999999999999999 7999999999999999999999999999999998763
No 7
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.36 E-value=1e-12 Score=103.98 Aligned_cols=57 Identities=35% Similarity=0.622 Sum_probs=53.8
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 401 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 401 kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
+|+++.|+++++.+|+.+|.. +|||+.+++..||..+||+..||.+||.|+|.+.||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467788999999999999998 799999999999999999999999999999999875
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.34 E-value=2.1e-12 Score=101.14 Aligned_cols=55 Identities=31% Similarity=0.513 Sum_probs=50.6
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 006230 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 459 (655)
Q Consensus 402 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlk 459 (655)
+++..|+++++.+|+.||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 34455999999999999998 69999999999999999999999999999999864
No 9
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.20 E-value=1.9e-11 Score=125.73 Aligned_cols=51 Identities=49% Similarity=0.791 Sum_probs=48.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 459 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlk 459 (655)
.|.++.+.+||+||.. +|||++++|++||+.|||+..||.|||+|||.|.+
T Consensus 182 CFKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 182 CFKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred ehhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 3888999999999996 89999999999999999999999999999999987
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.91 E-value=6.7e-10 Score=116.69 Aligned_cols=61 Identities=23% Similarity=0.259 Sum_probs=54.3
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 399 HPWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 399 ~~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
+..||||. ++|.|+..|++-|.- |-|.+++-|.+|++.++||+.||+.||||||+|+||-.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 34455665 999999999888887 69999999999999999999999999999999999854
No 11
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.89 E-value=1e-09 Score=115.32 Aligned_cols=65 Identities=23% Similarity=0.307 Sum_probs=57.7
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 006230 399 HPWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 466 (655)
Q Consensus 399 ~~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~ 466 (655)
.+|||+|. |++.||-.|++-|.+ ..|.+-.||+.||..++||.+||+.||+|+|-|.|+.-+|+.
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred ccccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 35566665 999999999999998 699999999999999999999999999999999998765443
No 12
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.79 E-value=5.6e-09 Score=110.05 Aligned_cols=63 Identities=27% Similarity=0.396 Sum_probs=55.9
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 006230 399 HPWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVE 464 (655)
Q Consensus 399 ~~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ie 464 (655)
+|+||.|+ |+..|+..|+.-|.. =-|.+..||.+||+..|||-.||..||+|||+|+|+.+.+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 44555555 999999999999998 4999999999999999999999999999999999887643
No 13
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.78 E-value=3.7e-09 Score=108.71 Aligned_cols=60 Identities=18% Similarity=0.262 Sum_probs=55.1
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 399 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 399 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
+.+|.|..|+..|+..|+.-|.- |.|.+...|++||..+.||+.||++||+|||+|+||.
T Consensus 158 ~~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 35666667999999999999998 7999999999999999999999999999999999874
No 14
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.76 E-value=1.3e-08 Score=100.03 Aligned_cols=64 Identities=23% Similarity=0.336 Sum_probs=58.2
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 006230 399 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEE 465 (655)
Q Consensus 399 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee 465 (655)
++||.|+.|+.+++..|+..|.. +-|-.-.||..||+.++||+.||+.||+|+|.|.||...|+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 66777777999999999999998 79999999999999999999999999999999998865443
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.73 E-value=8.6e-09 Score=105.93 Aligned_cols=61 Identities=28% Similarity=0.488 Sum_probs=56.9
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 398 SHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 398 ~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
...||+|.-|+.++++.|++-|.+ |.|.++..|++||.+++|.+.||+.||+|+|.|+||.
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred chhcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 345788888999999999999999 7999999999999999999999999999999999874
No 16
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.72 E-value=2.8e-08 Score=90.56 Aligned_cols=61 Identities=20% Similarity=0.330 Sum_probs=54.5
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 006230 404 QRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMY 467 (655)
Q Consensus 404 rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~ 467 (655)
|.+|+..+++.|+..|.+ ..||+.-.|++||-+..||+..|++||+|+|.+.+|...-..+
T Consensus 21 RTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 21 RTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 445999999999999999 6999999999999999999999999999999999987543333
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=98.69 E-value=2.4e-08 Score=82.20 Aligned_cols=52 Identities=12% Similarity=0.248 Sum_probs=48.9
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 006230 401 WRPQRGLPERSVSVLRAWLFEHFLHPY----PSDVDKHILARQTGLSRSQVSNWFINAR 455 (655)
Q Consensus 401 kR~rR~fpk~qv~iLr~Wf~eH~~nPY----PS~~EK~~LA~qTGLS~~QVsNWFiNaR 455 (655)
+|+|+.|+.+|+..|+..|.. ++| |+..++.+||..+||++.+|.+||+|.+
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 677778999999999999998 799 9999999999999999999999999964
No 18
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.69 E-value=1.6e-08 Score=100.83 Aligned_cols=68 Identities=26% Similarity=0.281 Sum_probs=60.5
Q ss_pred CCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHh
Q 006230 400 PWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMYLEE 470 (655)
Q Consensus 400 ~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~~~~ 470 (655)
.++++++|+.+|+..|+.-|.. +-|..+.+|..||++.||.+.||..||+|||+|+|.+-.|.-|..-
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~L 117 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESL 117 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHH
Confidence 5678889999999999999998 5888999999999999999999999999999999988776555433
No 19
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.67 E-value=1.8e-08 Score=102.16 Aligned_cols=61 Identities=25% Similarity=0.335 Sum_probs=54.4
Q ss_pred CCCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 399 HPWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 399 ~~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
+|.||-|+ ++.-++..|++.|.+ .-|.--.||.+||..+|||.+||+.||+|||-|.||.|
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 34455454 899999999999998 79999999999999999999999999999999999854
No 20
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.65 E-value=1.8e-08 Score=101.50 Aligned_cols=64 Identities=20% Similarity=0.251 Sum_probs=58.6
Q ss_pred cCCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006230 397 ESHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 463 (655)
Q Consensus 397 e~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 463 (655)
+++|||+|..|++.|+..|+.-|.. ..|.+..||.-||+++-||+.||+.||+|+|.|+|+...
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 4577777878999999999999998 599999999999999999999999999999999988654
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.47 E-value=1.5e-07 Score=90.90 Aligned_cols=62 Identities=26% Similarity=0.364 Sum_probs=56.8
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 398 SHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 398 ~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
...+++|++.+..++.+|+..|.. +|||+..+|..|+..++++++-|+.||+|+|.+.|+..
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred CcCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 346677888999999999999998 79999999999999999999999999999999998743
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.45 E-value=1.1e-07 Score=102.47 Aligned_cols=60 Identities=20% Similarity=0.317 Sum_probs=54.1
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 400 PWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 400 ~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
+|||||+ +.-.++..|+..|.+ ||.|+.+|--.||.+++|.+..|++||+|||.|.|+..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 3444454 999999999999999 79999999999999999999999999999999999843
No 23
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.43 E-value=2e-07 Score=96.03 Aligned_cols=53 Identities=25% Similarity=0.394 Sum_probs=50.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.|+..+...|++-|.+ -.||+.-.|++||.+|+|.+.+|++||+|||.|++|.
T Consensus 147 iFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred hhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 3999999999999999 6999999999999999999999999999999999875
No 24
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.40 E-value=2.4e-07 Score=93.55 Aligned_cols=58 Identities=26% Similarity=0.429 Sum_probs=53.6
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 401 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 401 kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
+|.|++|+.+++++|++-|.+ .-||+...+++||.+++|.+.+|++||.|+|+|.++.
T Consensus 38 RRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 38 RRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 355667999999999999999 7999999999999999999999999999999999874
No 25
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.39 E-value=1.9e-07 Score=98.16 Aligned_cols=60 Identities=27% Similarity=0.375 Sum_probs=54.0
Q ss_pred CCCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 400 PWRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 400 ~kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
|+|++|+ |+..+.+.|+.||.. |.||+.+.|++||--|+||+..|++||.|+|.+++|..
T Consensus 111 KqrrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 3344455 999999999999999 79999999999999999999999999999999998853
No 26
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.37 E-value=2.2e-07 Score=96.13 Aligned_cols=57 Identities=26% Similarity=0.263 Sum_probs=52.6
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 006230 407 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 466 (655)
Q Consensus 407 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~ 466 (655)
++..|+-.|++-|.. ++|.|...|.+||..+|||++||+.||+|||.|.+|...++.
T Consensus 206 YTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 899999999999987 799999999999999999999999999999999998765544
No 27
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.25 E-value=1.2e-06 Score=88.10 Aligned_cols=57 Identities=21% Similarity=0.352 Sum_probs=52.3
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 402 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
++|..|+..|+..|++-|.+ .-|.+.+||.+++..+.||+.||+.||+|||.|.|+-
T Consensus 146 kPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 146 KPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 34455999999999999999 5999999999999999999999999999999998873
No 28
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.25 E-value=3.7e-07 Score=88.97 Aligned_cols=58 Identities=29% Similarity=0.412 Sum_probs=52.2
Q ss_pred CCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 401 WRPQRG-LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 401 kR~rR~-fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
+||.|+ |+..+...|++.|.. -.|.+-.|+.+||..++|+++||+.||+|+|+|.||.
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred hhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 345454 999999999999997 4899999999999999999999999999999999874
No 29
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.21 E-value=9.5e-07 Score=89.42 Aligned_cols=72 Identities=22% Similarity=0.327 Sum_probs=63.3
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHhhhhhc
Q 006230 401 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMYLEETKEQD 475 (655)
Q Consensus 401 kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~~~~~~~~~ 475 (655)
+..|.+|+-.++..|+.-|.+ .-||--.++.+||...|++++||.+||+|||.|++|.-.-||.....+.+.
T Consensus 168 k~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasakkkqds 239 (288)
T KOG0847|consen 168 KQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAKKKQDS 239 (288)
T ss_pred cccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhccccCCC
Confidence 334556999999999999998 699999999999999999999999999999999999888888877766543
No 30
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.19 E-value=1e-06 Score=91.96 Aligned_cols=62 Identities=23% Similarity=0.364 Sum_probs=56.8
Q ss_pred CCCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 398 SHPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 398 ~~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
...||||.+++.++++.|+.-|.. .|.|..--|++|+.+|||....|++||+|+|+|.|+-.
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 356899999999999999999887 79999999999999999999999999999999877644
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.89 E-value=1.4e-05 Score=89.36 Aligned_cols=57 Identities=28% Similarity=0.348 Sum_probs=53.5
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 006230 399 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 458 (655)
Q Consensus 399 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRl 458 (655)
..||+|-.|+..|++.|+..|.+ ++||+.+.-+.|+.+++|.+.-|.|||-|+|+|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 45677777999999999999999 7999999999999999999999999999999996
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.75 E-value=9.7e-06 Score=85.41 Aligned_cols=57 Identities=18% Similarity=0.334 Sum_probs=51.6
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006230 404 QRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 463 (655)
Q Consensus 404 rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 463 (655)
|+-|+++|+..|++-|++ --|-+...|.+||..++|.+..|++||+|+|+|.|+..+
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 455999999999888876 479999999999999999999999999999999998775
No 33
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.60 E-value=5.1e-05 Score=81.78 Aligned_cols=58 Identities=28% Similarity=0.547 Sum_probs=53.1
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 402 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
|.|+.|+..+...|+++|.. .|||....|+.||++|+|++..|..||.|+|.|.+|..
T Consensus 178 r~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 178 RNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 33456999999999999998 68999999999999999999999999999999998755
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.56 E-value=3.8e-05 Score=75.29 Aligned_cols=61 Identities=16% Similarity=0.079 Sum_probs=54.5
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 399 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 399 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.++|.|.+|+..+++.|+.-|.. .+||....|+.||..+++++..|.+||+|+|+++++..
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 34555667999999999999998 59999999999999999999999999999999988743
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.29 E-value=0.00011 Score=77.82 Aligned_cols=60 Identities=47% Similarity=0.716 Sum_probs=55.0
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 402 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
+++.+++.+. .+|+.|+.+|..+|||++-++.+|+..|+++..||++||+|+|+|+++.+
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 3445689999 99999999999999999999999999999999999999999999987744
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.06 E-value=0.00021 Score=75.26 Aligned_cols=59 Identities=22% Similarity=0.354 Sum_probs=52.8
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 399 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 399 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
.+||||+.+-..-++.|+++|.. -|-|+.+....+|+++.|-+..|++||+|.|.|.|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 56777777777778899999998 599999999999999999999999999999999887
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.08 E-value=0.0046 Score=51.17 Aligned_cols=43 Identities=21% Similarity=0.398 Sum_probs=31.0
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 006230 412 VSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVR 457 (655)
Q Consensus 412 v~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrR 457 (655)
.+.|+++|.. |.++.+.+...|+.+++||..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4559999999 599999999999999999999999999876544
No 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=95.42 E-value=0.013 Score=57.63 Aligned_cols=62 Identities=34% Similarity=0.552 Sum_probs=54.5
Q ss_pred CCCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006230 399 HPWRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 463 (655)
Q Consensus 399 ~~kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 463 (655)
..++.+..+...+..+|..-|.. .+||....+..|+..+|++...|.+||+|.|.+.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 44556667999999999988887 799999999999999999999999999999999987543
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.62 E-value=0.32 Score=60.24 Aligned_cols=57 Identities=19% Similarity=0.358 Sum_probs=51.8
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006230 404 QRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 463 (655)
Q Consensus 404 rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 463 (655)
|..++..++++|+..|.+ --||+.++-+.|.+..+|....|..||+|+|.+.+|+..
T Consensus 907 ~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 907 RTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred ccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 334889999999999998 689999999999999999999999999999999998653
No 40
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=80.85 E-value=2.8 Score=33.83 Aligned_cols=47 Identities=30% Similarity=0.259 Sum_probs=31.6
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 006230 401 WRPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 455 (655)
Q Consensus 401 kR~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaR 455 (655)
+|+|+.|+-+.+-.+-.-+.+ .+ -+..||+..|++.++|++|..|+.
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 466777988885555455554 23 588999999999999999999853
No 41
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=72.44 E-value=5.2 Score=47.73 Aligned_cols=45 Identities=27% Similarity=0.434 Sum_probs=41.2
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 006230 412 VSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 459 (655)
Q Consensus 412 v~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlk 459 (655)
+.+|+++|.. |+.|+.+|...+|.+.||...-|+.||.+.|....
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~ 612 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEM 612 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhh
Confidence 7888999887 79999999999999999999999999999887643
No 42
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=72.36 E-value=4.2 Score=31.58 Aligned_cols=47 Identities=34% Similarity=0.419 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
.||++...+|...|.+ ++ .-.++|+..|+|...|+.+...+..++++
T Consensus 4 ~L~~~er~vi~~~y~~----~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----GL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----CC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 4889999999888865 32 45789999999999999999999988864
No 43
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=71.82 E-value=5.2 Score=29.41 Aligned_cols=46 Identities=30% Similarity=0.307 Sum_probs=36.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLW 459 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlk 459 (655)
.++.+...++...+.+. -.-.++|..+|++...|..|....+.+++
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 36788888888777542 24567899999999999999998887764
No 44
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=71.22 E-value=6.6 Score=32.45 Aligned_cols=46 Identities=26% Similarity=0.331 Sum_probs=30.5
Q ss_pred CCCCCCChhHHH-HHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 006230 402 RPQRGLPERSVS-VLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 455 (655)
Q Consensus 402 R~rR~fpk~qv~-iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaR 455 (655)
++++.||++.+. ++...+.. ......+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 345679888854 45555454 46889999999999999999976665
No 45
>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=68.27 E-value=7.5 Score=30.37 Aligned_cols=45 Identities=29% Similarity=0.385 Sum_probs=34.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRL 458 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRl 458 (655)
.||+....++.-.+.+ - -.-.++|+.+|+|...|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~----g----~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQ----G----MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH----C----cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 4788888888777666 2 3557899999999999999999999874
No 46
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=67.63 E-value=51 Score=35.42 Aligned_cols=31 Identities=29% Similarity=0.483 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 006230 282 FMELQKRKTKLLSMLEEVDRRYRHYCDQMKA 312 (655)
Q Consensus 282 ~~elQ~kK~kLL~mLEEVd~ry~qYc~qmq~ 312 (655)
..+|+.+|..|..-++++++|-.+...+|.+
T Consensus 6 L~eL~qrk~~Lq~eIe~LerR~~ri~~Emrt 36 (283)
T PF11285_consen 6 LKELEQRKQALQIEIEQLERRRERIEKEMRT 36 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 5689999999999999999999988888876
No 47
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=63.35 E-value=19 Score=23.48 Aligned_cols=39 Identities=23% Similarity=0.278 Sum_probs=27.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWF 451 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWF 451 (655)
+.++.+....+..++.. .+ ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 34666666666555543 33 45688899999999999994
No 48
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=52.38 E-value=16 Score=33.67 Aligned_cols=47 Identities=17% Similarity=0.116 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
.||+..+.++..-+.+. + .-.++|..+|++...|.+|...+|.++++
T Consensus 106 ~L~~~~r~ii~l~~~~~----~----s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG----K----TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 58999999987666652 2 35789999999999999999999999875
No 49
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=52.31 E-value=21 Score=31.29 Aligned_cols=48 Identities=29% Similarity=0.309 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||+....++..-+.. .| .-.++|+.+|+++..|.+|...++.++++.
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 4788888887655444 44 446899999999999999999999998763
No 50
>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=51.77 E-value=24 Score=32.11 Aligned_cols=48 Identities=25% Similarity=0.239 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||++...++...+.+ .+ .-.++|+.+|+|+..|.++...+|+++++.
T Consensus 113 ~L~~~~r~il~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5888999999876655 33 345699999999999999999999998763
No 51
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=51.48 E-value=19 Score=33.52 Aligned_cols=49 Identities=24% Similarity=0.197 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++.-.+.+. .+ -.++|+.+|++...|.+++.-+|.++++.+
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999997776662 22 368999999999999999999999998755
No 52
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=50.26 E-value=21 Score=34.71 Aligned_cols=51 Identities=16% Similarity=0.241 Sum_probs=42.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVE 464 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ie 464 (655)
.||++++.++.-.+.+ -+ .-.++|..+|+++..|.++..-+|+++++-+.+
T Consensus 134 ~Lp~~~R~v~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~ 184 (189)
T PRK12530 134 HLPAQQARVFMMREYL----EL----SSEQICQECDISTSNLHVLLYRARLQLQACLSK 184 (189)
T ss_pred hCCHHHHHHHhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4899999998887766 22 357899999999999999999999999886643
No 53
>PRK00118 putative DNA-binding protein; Validated
Probab=49.13 E-value=19 Score=33.41 Aligned_cols=54 Identities=17% Similarity=0.177 Sum_probs=43.1
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMY 467 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~ 467 (655)
..||+.++.++..++.+. + .-.++|+.+|+|+.-|.+|...+|.++++- ++.+.
T Consensus 16 ~~L~ekqRevl~L~y~eg----~----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~-~~~~~ 69 (104)
T PRK00118 16 SLLTEKQRNYMELYYLDD----Y----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY-EEKLH 69 (104)
T ss_pred ccCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH-HHHHC
Confidence 357999999998887762 2 346799999999999999999999998874 34443
No 54
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=49.01 E-value=21 Score=33.57 Aligned_cols=50 Identities=14% Similarity=0.060 Sum_probs=41.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
..||++.++++.-++.++ . .-.++|..+|++...|.+|..-+|+++++-+
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--L------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 458999999998887763 2 3478999999999999999999999997743
No 55
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=48.35 E-value=21 Score=33.17 Aligned_cols=49 Identities=20% Similarity=0.200 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++..-+.+ -+ .-.++|+..|+|+..|.+|..-+|.++++.+
T Consensus 125 ~L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred hCCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888766554 22 3478999999999999999999999998754
No 56
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=47.62 E-value=28 Score=33.03 Aligned_cols=48 Identities=15% Similarity=0.253 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||++...++...+.+ .+ .-.++|+.+|++...|.+++..+|+++++-
T Consensus 129 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE----GL----SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 4899999999888876 33 347899999999999999999999999864
No 57
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=47.02 E-value=23 Score=28.23 Aligned_cols=42 Identities=26% Similarity=0.265 Sum_probs=24.6
Q ss_pred HHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006230 415 LRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 463 (655)
Q Consensus 415 Lr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 463 (655)
|+.++.++ -+ ....||+.+|+++..|+.|+.+...+..-..+
T Consensus 2 L~~~m~~~---~i----t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l 43 (63)
T PF13443_consen 2 LKELMAER---GI----TQKDLARKTGISRSTLSRILNGKPSNPSLDTL 43 (63)
T ss_dssp HHHHHHHT---T------HHHHHHHHT--HHHHHHHHTTT-----HHHH
T ss_pred HHHHHHHc---CC----CHHHHHHHHCcCHHHHHHHHhcccccccHHHH
Confidence 45566653 22 56789999999999999999987544443333
No 58
>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=46.23 E-value=23 Score=33.59 Aligned_cols=49 Identities=18% Similarity=0.154 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.-.+.++ + .-.++|..+|++...|.++.-.+|+++++.+
T Consensus 138 ~L~~~~r~v~~l~~~~~----~----s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG----L----SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 47888888887766552 2 4478999999999999999999999998754
No 59
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=45.68 E-value=24 Score=32.85 Aligned_cols=49 Identities=20% Similarity=0.205 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++...+.. -+ .-.++|+.+|++...|.+|...+|+++++.+
T Consensus 128 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIE----GL----SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4889999998766554 22 2358999999999999999999999998755
No 60
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=44.80 E-value=20 Score=34.18 Aligned_cols=49 Identities=18% Similarity=0.125 Sum_probs=41.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++...+.+. . .-.++|..+|++...|.+++..+|+++++.+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--A------SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998876662 2 4578999999999999999999999998755
No 61
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=44.60 E-value=22 Score=34.47 Aligned_cols=49 Identities=10% Similarity=0.126 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.+|.-.+.+. + .-.++|+.+|++...|.++...+|+++++.+
T Consensus 142 ~L~~~~r~vl~l~~~~~----~----s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG----L----TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 48999999998776663 2 3478999999999999999999999988754
No 62
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=44.06 E-value=36 Score=33.16 Aligned_cols=49 Identities=31% Similarity=0.237 Sum_probs=40.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
..|++.++++|+. +.+ .+ .-.++|+.+|+|...|++|...+|.++++..
T Consensus 5 ~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4589999999977 333 33 4568999999999999999999999988755
No 63
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=43.91 E-value=24 Score=34.13 Aligned_cols=49 Identities=20% Similarity=0.258 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.-.|.+. . .-.++|+.+|+|...|.+...-+|+++++..
T Consensus 131 ~L~~~~r~i~~l~~~~g--~------s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--E------KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 58999999998766652 2 3478999999999999999999999998764
No 64
>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=43.61 E-value=45 Score=26.62 Aligned_cols=52 Identities=23% Similarity=0.222 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 466 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~ 466 (655)
.|++...++|+.+..- + ...++|...+++++-|..+..+.++|+.-+...++
T Consensus 3 ~LT~~E~~vl~~l~~G-----~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l 54 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG-----M----SNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAEL 54 (58)
T ss_dssp SS-HHHHHHHHHHHTT-----S-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHH
T ss_pred ccCHHHHHHHHHHHhc-----C----CcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHH
Confidence 4788889998777554 2 56789999999999999999999999876554444
No 65
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=42.90 E-value=26 Score=33.69 Aligned_cols=49 Identities=20% Similarity=0.150 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..++++..-+.+ .+ .-.++|..+|++...|.++...+|.++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 139 TLPEKQREILILRVVV----GL----SAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 5899999999887666 22 3578999999999999999999999998753
No 66
>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=42.28 E-value=90 Score=25.95 Aligned_cols=42 Identities=19% Similarity=0.090 Sum_probs=31.1
Q ss_pred CCccccCCchHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 006230 271 SSRKQSLCSLEFM---ELQKRKTKLLSMLEEVDRRYRHYCDQMKA 312 (655)
Q Consensus 271 ~s~~~elssle~~---elQ~kK~kLL~mLEEVd~ry~qYc~qmq~ 312 (655)
...+||||--|.. -|.++|..|...++|....|+.-..|+..
T Consensus 5 ~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~ 49 (52)
T PF03791_consen 5 IGADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLSS 49 (52)
T ss_pred CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457999987754 37788999999999996666665555554
No 67
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=41.96 E-value=26 Score=34.52 Aligned_cols=49 Identities=24% Similarity=0.304 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++++.++..-+++. + .-.++|..+|++...|.+++..+|+++++.+
T Consensus 153 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE----L----SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998766652 2 4578999999999999999999999987754
No 68
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=41.66 E-value=76 Score=23.68 Aligned_cols=48 Identities=25% Similarity=0.245 Sum_probs=36.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.|+++...++..+ .. .+ ...++|+.+|+++..|..|....+.++.-..
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~~ 50 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVRS 50 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Confidence 4778888877554 32 22 4578999999999999999998888775443
No 69
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=41.48 E-value=29 Score=32.95 Aligned_cols=48 Identities=21% Similarity=0.176 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||++++.++.-.+.+. + .-.++|..+|++...|.+....+|.++++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG----L----TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999998887762 2 347899999999999999999999998764
No 70
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=40.43 E-value=27 Score=33.63 Aligned_cols=49 Identities=20% Similarity=0.290 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++...++..-+.+. + .-.++|..+|++...|.+|+..+|+++++.+
T Consensus 141 ~L~~~~~~v~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYYEG----L----SQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhhcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58889999987766552 2 3478999999999999999999999998754
No 71
>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=39.75 E-value=31 Score=31.76 Aligned_cols=48 Identities=29% Similarity=0.286 Sum_probs=39.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
..||++.+.++..-+.+ .+ .-.++|+.+|+|...|.++..-+|+++++
T Consensus 110 ~~L~~~~r~v~~l~~~~----g~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR----GV----SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 35899999999886665 33 34679999999999999999999988875
No 72
>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=38.52 E-value=35 Score=34.77 Aligned_cols=49 Identities=22% Similarity=0.218 Sum_probs=41.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++...|.+. + .-.++|+.+|++...|+.+...++.++++.+
T Consensus 205 ~L~~~~r~ii~l~~~~g----~----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN----L----SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 58999999998887763 2 3378999999999999999999999998755
No 73
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=38.42 E-value=30 Score=32.73 Aligned_cols=49 Identities=18% Similarity=0.177 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++..-+.+ .+ .-.++|+.+|++...|.+++..+|+++++-+
T Consensus 136 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 5899999998775554 22 3478999999999999999999999987643
No 74
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=38.08 E-value=31 Score=32.19 Aligned_cols=48 Identities=23% Similarity=0.175 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
..||++++.++.-.+.+. + .-.++|..+|+|...|..+...+|+++++
T Consensus 111 ~~L~~~~r~v~~l~~~~~----~----s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG----F----SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 358999999998876662 2 34689999999999999999999999876
No 75
>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=38.00 E-value=55 Score=33.19 Aligned_cols=56 Identities=20% Similarity=0.140 Sum_probs=43.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEE 465 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee 465 (655)
.||+..+.+|...|.-.-..++ .-.++|..+|+|...|+.+...+++|+|+.+.++
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~----t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~ 231 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPH----TLEEVGKEFNVTRERIRQIESKALRKLRHPSRSK 231 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCc----cHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHh
Confidence 4899999999887721101233 4688999999999999999999999999876443
No 76
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=37.98 E-value=31 Score=33.08 Aligned_cols=49 Identities=16% Similarity=0.207 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++..-+++ .+ .-.++|+.+|++...|.++...+|+++++.+
T Consensus 128 ~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQ----GL----SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhc----CC----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788999988776655 22 3468999999999999999999999988754
No 77
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=37.56 E-value=56 Score=31.51 Aligned_cols=49 Identities=16% Similarity=0.208 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++++.++.-.+.+. .+ -.++|..+|+|..-|.+....+|+++++-+
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999988777662 23 378999999999999999999999998755
No 78
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=36.93 E-value=61 Score=29.54 Aligned_cols=53 Identities=25% Similarity=0.209 Sum_probs=41.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 466 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~ 466 (655)
..|++...++|+-+ .+ .| ...++|+..+++.+.|.+|..+.|+|+.-.-..+.
T Consensus 148 ~~lt~~e~~vl~l~-~~----g~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l 200 (211)
T PRK15369 148 PLLTPRERQILKLI-TE----GY----TNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAEL 200 (211)
T ss_pred cCCCHHHHHHHHHH-HC----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 34999999999885 44 23 25789999999999999999999999865444343
No 79
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=36.87 E-value=44 Score=33.76 Aligned_cols=49 Identities=22% Similarity=0.159 Sum_probs=41.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+.++.++.-.+.++ -+ -.++|..+|+|...|.++...+|+++++.+
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MS------YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998887773 23 367999999999999999999999998765
No 80
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=36.70 E-value=38 Score=31.24 Aligned_cols=50 Identities=24% Similarity=0.223 Sum_probs=41.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
..||+.++.++.-.+.+ -+ .-.++|..+|++...|.+...-+|+++++.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWE----DM----DVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHh----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35899999999886666 23 2478999999999999999999999998754
No 81
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=36.36 E-value=37 Score=31.98 Aligned_cols=49 Identities=14% Similarity=0.032 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..++++.-.+.+. + .-.++|+.+|++...|.++..-+|+++++-+
T Consensus 112 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASG----F----SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999988877663 2 3468999999999999999999999988643
No 82
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=36.32 E-value=38 Score=32.45 Aligned_cols=49 Identities=24% Similarity=0.139 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+....++.-.+.+. + .-.++|+.+|+++..|.+....+|+++++.+
T Consensus 129 ~L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG----L----SVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888876666652 2 4578999999999999999999999998754
No 83
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=36.32 E-value=33 Score=33.65 Aligned_cols=49 Identities=20% Similarity=0.159 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+++++++.-.+.+ -+ .-.++|..+|+|...|.+++.-+|+++++-+
T Consensus 113 ~Lp~~~r~v~~L~~~~----g~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGAS----GF----SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999888776 33 3467899999999999999999999998754
No 84
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=36.00 E-value=47 Score=33.95 Aligned_cols=49 Identities=20% Similarity=0.268 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.+|...|.+. + .-.++|+.+|++...|.+|...+|+++++.+
T Consensus 205 ~L~~~~r~vl~l~~~~g----~----s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----L----SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998877652 2 3478999999999999999999999998644
No 85
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=35.99 E-value=33 Score=32.71 Aligned_cols=49 Identities=18% Similarity=0.223 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.+|.-.+.+. + .-.++|..+|+|...|.++...+|.++++.+
T Consensus 135 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG----Y----THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998776652 2 3478999999999999999999999988654
No 86
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=35.87 E-value=61 Score=32.32 Aligned_cols=52 Identities=23% Similarity=0.298 Sum_probs=42.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVE 464 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ie 464 (655)
..||++++.++.--+.+. .+ -.++|..+|+|...|.++..-+|+++++.+.+
T Consensus 147 ~~L~~~~r~v~~L~~~~g--~s------~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~ 198 (206)
T PRK12544 147 DGLPAKYARVFMMREFIE--LE------TNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198 (206)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 358999999987777663 22 37899999999999999999999999987643
No 87
>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=35.82 E-value=34 Score=34.05 Aligned_cols=49 Identities=29% Similarity=0.410 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++...+.+ .+ .-.++|+.+|++...|..|...+++++++.+
T Consensus 178 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 178 ALPERERRILLLRFFE----DK----TQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 5899999999887765 22 4678999999999999999999999988643
No 88
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=35.37 E-value=45 Score=32.09 Aligned_cols=49 Identities=14% Similarity=0.195 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.+|.--+.+ .+ .-.++|..+|+|...|.+.+..+|+++++.+
T Consensus 131 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYH----EK----SVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999776665 22 4578999999999999999999999988743
No 89
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=34.78 E-value=41 Score=32.55 Aligned_cols=49 Identities=20% Similarity=0.258 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++.-.+.+ -+ .-.++|+.+|++...|.++...+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEIL----GF----SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHh----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5899999998766555 22 3478999999999999999999999998865
No 90
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=34.75 E-value=41 Score=31.64 Aligned_cols=49 Identities=12% Similarity=0.158 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.++++..-+++. + .-.++|..+|+|...|.++..-+|+++++-+
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 48889999997777662 2 3467999999999999999999999988744
No 91
>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=34.28 E-value=44 Score=31.01 Aligned_cols=49 Identities=24% Similarity=0.325 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++..-+.+ .+ .-.++|..+|++...|.++...+|.++++.+
T Consensus 110 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE----DL----SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHh----cC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 5889999998776665 23 3467899999999999999999999988643
No 92
>PRK04217 hypothetical protein; Provisional
Probab=34.23 E-value=65 Score=30.19 Aligned_cols=50 Identities=18% Similarity=0.181 Sum_probs=41.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
..|+++.+.++..++.+. + .-.++|+.+|++...|.+.+..+|.+++..+
T Consensus 41 ~~Lt~eereai~l~~~eG----l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG----L----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 358999999998888763 2 5677999999999999999999998887643
No 93
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=33.22 E-value=60 Score=32.26 Aligned_cols=49 Identities=16% Similarity=0.146 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++..-+.+. .+ -.++|+.+|++..-|.++..-+|+++++.+
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LS------YEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888876666652 33 378999999999999999999999998754
No 94
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=33.02 E-value=36 Score=34.29 Aligned_cols=49 Identities=31% Similarity=0.344 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++..-|.+ .+ .-.++|+.+|++...|.++...+|+++++.+
T Consensus 184 ~L~~~~r~vl~l~~~~----g~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQE----EL----NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999999877665 22 4578999999999999999999999998754
No 95
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=32.70 E-value=45 Score=31.95 Aligned_cols=49 Identities=12% Similarity=0.137 Sum_probs=39.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
..||++++.++..-+.+. + .-.++|+.+|+|...|.+|...+|+++++-
T Consensus 132 ~~L~~~~r~i~~l~~~~~----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHAYVDG----C----SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 358999998877766652 2 347899999999999999999999988763
No 96
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=32.55 E-value=47 Score=32.23 Aligned_cols=50 Identities=24% Similarity=0.276 Sum_probs=40.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
..||++++.++.-.+.+. .+ -.++|..+|+|...|.+.+..+|+++++.+
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 458999999998766652 23 368999999999999999999999988755
No 97
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=32.51 E-value=46 Score=30.94 Aligned_cols=48 Identities=23% Similarity=0.299 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+++..+|.-.+ + -+ .-.++|..+|++...|.++...+|.++++-+
T Consensus 112 ~L~~~~r~il~l~~-~----g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----GY----SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888988887776 5 23 4478999999999999999999999988754
No 98
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=32.34 E-value=50 Score=32.20 Aligned_cols=49 Identities=16% Similarity=0.120 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.-.+.+ -| .-.++|+.+|++...|.++...+|+++++.+
T Consensus 116 ~Lp~~~r~i~~L~~~~----g~----s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGAS----GF----AYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4899999999887766 23 2357999999999999999999999998755
No 99
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=31.46 E-value=70 Score=31.12 Aligned_cols=49 Identities=16% Similarity=0.142 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++++.++.-.+.+ -| .-.++|+.+|++...|.+++.-+|+++++-+
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 5899999888776665 33 2478999999999999999999999998744
No 100
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=31.42 E-value=53 Score=31.13 Aligned_cols=47 Identities=13% Similarity=0.159 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
.||++++.++.-.+.+. .+ -.++|+.+|++..-|.++...+|+|++.
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 48999999998776652 23 3689999999999999999999999864
No 101
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=31.25 E-value=89 Score=25.77 Aligned_cols=50 Identities=26% Similarity=0.349 Sum_probs=38.0
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 006230 407 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVR 457 (655)
Q Consensus 407 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrR 457 (655)
|++.+.++|+.-+..=+ .-+|-...-.+||+..|+++.-|..-+.++=++
T Consensus 1 LT~~Q~e~L~~A~~~GY-fd~PR~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 1 LTDRQREILKAAYELGY-FDVPRRITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHHHHHHHcCC-CCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 57888999988777532 234888999999999999999887655544433
No 102
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=30.69 E-value=57 Score=33.31 Aligned_cols=49 Identities=16% Similarity=0.152 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+.++.++.-.+.+ -+ .-.++|+.+|++...|.++...+|+++++.+
T Consensus 171 ~Lp~~~R~v~~L~~~e----g~----s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYHE----NM----SNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4789999987766655 22 3478999999999999999999999998755
No 103
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=30.37 E-value=54 Score=31.07 Aligned_cols=49 Identities=20% Similarity=0.210 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+....+|.--+.+ .+ .-.++|..+|+|...|.++...+|+++++-+
T Consensus 136 ~L~~~~r~il~l~~~~----~~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYIE----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHhh----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888554433 22 3478999999999999999999999998743
No 104
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=30.12 E-value=59 Score=31.94 Aligned_cols=50 Identities=22% Similarity=0.260 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 463 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 463 (655)
.||+.++.++.--+.+. + .-.++|..+|++..-|.+....+|+++++-+-
T Consensus 139 ~Lp~~~r~v~~L~~~eg----~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD----F----EIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999988776662 2 23679999999999999999999999987653
No 105
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=30.12 E-value=49 Score=33.02 Aligned_cols=48 Identities=27% Similarity=0.342 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||+..+.+|...|.+ .+ .-.++|+.+|++...|..+...+++++++.
T Consensus 175 ~L~~~~r~il~l~y~~----~~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYE----EL----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhC----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4899999999888776 22 347899999999999999999999998764
No 106
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=29.91 E-value=58 Score=30.29 Aligned_cols=49 Identities=22% Similarity=0.261 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.--+.+ .+ ...++|+.+|++...|..+..-+|+++++-+
T Consensus 109 ~L~~~~r~v~~l~~~~----~~----s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH----GE----TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999776665 22 3478999999999999999999998888654
No 107
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=29.61 E-value=74 Score=30.58 Aligned_cols=49 Identities=20% Similarity=0.173 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.--+.+ .| .-.++|..+|+++..|.+...-+|+++++.+
T Consensus 138 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 138 QLPEDLRTALTLREFD----GL----SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred hCCHHHhHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888887665554 44 3478999999999999999999999998865
No 108
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=29.30 E-value=49 Score=34.16 Aligned_cols=49 Identities=24% Similarity=0.221 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.+|...|.+ .+ .-.++|..+|++...|..+..-++.++++.+
T Consensus 203 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFLH----DL----TQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 5889999998887765 22 4578999999999999999999999998755
No 109
>PF13518 HTH_28: Helix-turn-helix domain
Probab=29.17 E-value=53 Score=25.00 Aligned_cols=25 Identities=36% Similarity=0.539 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhh
Q 006230 432 DKHILARQTGLSRSQVSNWFINARV 456 (655)
Q Consensus 432 EK~~LA~qTGLS~~QVsNWFiNaRr 456 (655)
...++|++.|++..+|..|....+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3466999999999999999877665
No 110
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=28.93 E-value=55 Score=31.66 Aligned_cols=48 Identities=15% Similarity=-0.000 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
..||++++.++.-.+.+. + .-.++|..+|++...|.++..-+|+++++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLG----L----SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 358999999998777662 2 34789999999999999999999999876
No 111
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=28.85 E-value=59 Score=30.23 Aligned_cols=49 Identities=16% Similarity=0.084 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
..||+..+.++.-.+.+ -+ .-.++|+.+|++...|.+...-+|+++++.
T Consensus 121 ~~L~~~~r~vl~l~~~~----g~----s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQ----NL----PIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred HhCCHHHHHHHHHHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 35899999999887665 22 347899999999999999999888888763
No 112
>PHA00542 putative Cro-like protein
Probab=28.67 E-value=1.6e+02 Score=25.65 Aligned_cols=35 Identities=14% Similarity=0.231 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 006230 432 DKHILARQTGLSRSQVSNWFINARVRLWKPMVEEM 466 (655)
Q Consensus 432 EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~ 466 (655)
...+||+.+|++...|..|.....++.....++++
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki 67 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKL 67 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHH
Confidence 45679999999999999999888655554444444
No 113
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=28.56 E-value=42 Score=32.35 Aligned_cols=49 Identities=18% Similarity=0.197 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.-.+.+ .| .-.++|+.+|++...|.++...+|+++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHG----DL----ELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehcc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888766554 22 3467899999999999999999999998754
No 114
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=28.01 E-value=5.5e+02 Score=24.64 Aligned_cols=49 Identities=22% Similarity=0.273 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.--+.+ -|+ -.++|..+|++..-|..|..-+|.++++.+
T Consensus 127 ~Lp~~~R~~~~l~~~~----gls----~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 127 RLPPRQREAFLLRYLE----GLS----YEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred hCCHHHhHHhhhHhhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888877655554 332 367888899999999999999999998765
No 115
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=28.00 E-value=64 Score=33.35 Aligned_cols=49 Identities=24% Similarity=0.426 Sum_probs=41.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.+|...|.+. -.-.++|..+|++...|......+++++++.+
T Consensus 212 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998887762 23578999999999999999999999998754
No 116
>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=27.93 E-value=79 Score=32.69 Aligned_cols=50 Identities=28% Similarity=0.391 Sum_probs=42.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 463 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 463 (655)
.||++.+.++.-.+.+. + .-.++|..+|++..-|.++...+|+++++.+.
T Consensus 161 ~Lp~~~R~v~~L~~~eg----~----S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG----L----SMDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 58999999988887763 2 24689999999999999999999999988653
No 117
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=27.89 E-value=57 Score=33.30 Aligned_cols=48 Identities=23% Similarity=0.203 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||+..+.++...+.+ .+ .-.++|..+|+|...|.+++..+|+++++-
T Consensus 201 ~L~~~~r~vl~l~~~~----~~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYKE----EL----TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4899999999887765 22 357899999999999999999999999763
No 118
>cd00131 PAX Paired Box domain
Probab=27.86 E-value=2.7e+02 Score=26.23 Aligned_cols=48 Identities=19% Similarity=0.098 Sum_probs=33.7
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------ChhhHhhhhhhh
Q 006230 404 QRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGL-------SRSQVSNWFINA 454 (655)
Q Consensus 404 rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGL-------S~~QVsNWFiNa 454 (655)
++.+..+....+..+..+ ||..+..|-.++-...|+ +...|+.||.++
T Consensus 73 pr~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 73 PRVATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCcCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 334566666667777776 688887777666335566 999999998764
No 119
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.68 E-value=61 Score=31.38 Aligned_cols=49 Identities=29% Similarity=0.349 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++++.++.-.+.+ -+ .-.++|..+|+|...|.+.+..+|+++++-+
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 5899999999776665 33 3478999999999999999999999987644
No 120
>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=27.46 E-value=66 Score=30.65 Aligned_cols=50 Identities=22% Similarity=0.278 Sum_probs=40.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
..||++.+.+|.-.+.+ -| .-.++|+.+|++...|.++..-+|+++++-+
T Consensus 99 ~~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 99 KELPDEYREAIRLTELE----GL----SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred HhCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35899999999877766 33 3478999999999999999999999888744
No 121
>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=27.41 E-value=1.5e+02 Score=22.23 Aligned_cols=46 Identities=26% Similarity=0.216 Sum_probs=32.8
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 407 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 407 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
|++....++..+ .. .+ ...++|+.++++...|..|..-.+.++..+
T Consensus 1 l~~~e~~i~~~~-~~----~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 1 LTPREREVLRLL-AE----GK----TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 455666666543 22 22 557899999999999999998777766543
No 122
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=27.21 E-value=1.1e+02 Score=28.35 Aligned_cols=44 Identities=11% Similarity=0.304 Sum_probs=34.8
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhh
Q 006230 407 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINA 454 (655)
Q Consensus 407 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNa 454 (655)
-....+..+.+|+.+|+..| + ...+||+.+|+++..+..+|...
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~-~---sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESP-L---SLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCC-C---CHHHHHHHHCcCHHHHHHHHHHH
Confidence 34455677889999987665 3 45788999999999999999866
No 123
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=27.19 E-value=39 Score=32.60 Aligned_cols=49 Identities=22% Similarity=0.226 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.-.+.+ -+ .-.++|+.+|+|...|.++..-+|+++++.+
T Consensus 131 ~Lp~~~r~i~~L~~~~----g~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADVE----GF----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788888887665554 22 3478999999999999999999999998765
No 124
>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=27.05 E-value=56 Score=25.00 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=19.1
Q ss_pred HHHHHhCCChhhHhhhhhhhh
Q 006230 435 ILARQTGLSRSQVSNWFINAR 455 (655)
Q Consensus 435 ~LA~qTGLS~~QVsNWFiNaR 455 (655)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999875
No 125
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=26.88 E-value=98 Score=28.78 Aligned_cols=49 Identities=24% Similarity=0.253 Sum_probs=41.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++..+++.-.+.+. .+ -.++|..+|++..-|.+....+|+++++.+
T Consensus 105 ~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLRKLEG--LS------HQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998887763 23 478999999999999999999999988754
No 126
>PRK06930 positive control sigma-like factor; Validated
Probab=26.84 E-value=69 Score=31.65 Aligned_cols=50 Identities=16% Similarity=0.064 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMV 463 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~i 463 (655)
.||+..+.++.-.+.+ .+ .-.++|..+|++...|.++...+|.++++.+-
T Consensus 114 ~L~~rer~V~~L~~~e----g~----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGY----GL----SYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4899999998876655 22 34689999999999999999999999987553
No 127
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=26.61 E-value=1.1e+02 Score=34.67 Aligned_cols=58 Identities=24% Similarity=0.199 Sum_probs=45.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPMVEEMY 467 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~iee~~ 467 (655)
.||+..+.+|+-.|.-.-..|+ .-.++|+.+|+|+..|+.+..-+++++++|.....+
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~----Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l 407 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTY----SLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRI 407 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHH
Confidence 4899999999888762111244 468899999999999999999999999988754443
No 128
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=26.53 E-value=93 Score=30.44 Aligned_cols=48 Identities=25% Similarity=0.336 Sum_probs=39.1
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 407 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 407 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
++++..+++.-.++. .| ...++|+.+|+|+..|.+.+..+|.++.+.+
T Consensus 136 l~~~~~~~v~l~~~~----Gl----s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l 183 (185)
T PF07638_consen 136 LDPRQRRVVELRFFE----GL----SVEEIAERLGISERTVRRRLRRARAWLRREL 183 (185)
T ss_pred cCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 677788888777665 55 5678999999999999999999998876643
No 129
>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=26.46 E-value=80 Score=30.69 Aligned_cols=49 Identities=18% Similarity=0.224 Sum_probs=41.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++++.++..-+.+. . .-.++|..+|++..-|.++..-+|+++++-+
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--F------ESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998877663 2 4578999999999999999999999998755
No 130
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=26.31 E-value=68 Score=31.62 Aligned_cols=49 Identities=16% Similarity=0.122 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++..-+.+. + .-.++|..+|+++..|.++...+|+++++-+
T Consensus 133 ~Lp~~~r~v~~l~~~~g----~----s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 133 ALPPERREALILTQVLG----Y----TYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred cCCHHHHHHhhhHHHhC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999987777663 2 3578999999999999999999999998755
No 131
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=26.27 E-value=70 Score=30.69 Aligned_cols=50 Identities=20% Similarity=0.297 Sum_probs=40.6
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 405 RGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 405 R~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
..||++.+.++.-.+.+. | .-.++|..+|++...|.+....+|+++++-+
T Consensus 121 ~~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 121 KELNESNRQVFKYKVFYN----L----TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358999999998766552 2 3468999999999999999999999997754
No 132
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.92 E-value=61 Score=30.53 Aligned_cols=49 Identities=16% Similarity=0.183 Sum_probs=40.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.+|.--+.+ -+ .-.++|+.+|++..-|.++..-+|+++++.+
T Consensus 118 ~L~~~~r~vl~L~~~~----g~----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYR----GW----STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4899999999887766 23 2468999999999999999999999998754
No 133
>PF13551 HTH_29: Winged helix-turn helix
Probab=25.83 E-value=2.2e+02 Score=24.62 Aligned_cols=52 Identities=19% Similarity=0.088 Sum_probs=31.3
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCC--CCCHHHHHH-H-HHHh--CCChhhHhhhhh
Q 006230 401 WRPQRGLPERSVSVLRAWLFEHFLHP--YPSDVDKHI-L-ARQT--GLSRSQVSNWFI 452 (655)
Q Consensus 401 kR~rR~fpk~qv~iLr~Wf~eH~~nP--YPS~~EK~~-L-A~qT--GLS~~QVsNWFi 452 (655)
.|+++.++++....|.+++.++.... ..+..+-.. | .+.+ .++...|..|+.
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 34444499999999999999852211 223333333 3 3332 477777877764
No 134
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=25.77 E-value=79 Score=30.21 Aligned_cols=49 Identities=14% Similarity=0.109 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.++.--+.+. - .-.++|..+|++..-|.+....+|.++++-+
T Consensus 117 ~Lp~~~r~i~~l~~~e~--~------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--Y------SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999988766663 1 3478999999999999999999999998755
No 135
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=25.43 E-value=76 Score=30.48 Aligned_cols=49 Identities=22% Similarity=0.173 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+.++.++.-.+.+. -.-.++|+.+|++...|.++...+|+++++-+
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--------LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998766652 24478999999999999999999999988643
No 136
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=25.15 E-value=65 Score=32.29 Aligned_cols=53 Identities=19% Similarity=0.100 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.-.|.-+....+ .-.++|..+|++...|.++...+|+++++.+
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 5899999998776521000122 3578999999999999999999999998754
No 137
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=25.00 E-value=50 Score=31.10 Aligned_cols=49 Identities=20% Similarity=0.157 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+..+.+|...+.+ .+ .-.++|..+|+|...|.+.+..+|+++++-+
T Consensus 120 ~L~~~~r~vl~l~~~~----g~----s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 120 TLSLEHRAVLVLHDLE----DL----PQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hCCHHHeeeeeehHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888776655 33 2578999999999999999999999998754
No 138
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=24.47 E-value=1.1e+02 Score=33.07 Aligned_cols=53 Identities=23% Similarity=0.186 Sum_probs=41.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.+|...|.-+....+ .-.++|..+|++...|+.+...+|+++|+.+
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~----s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAA----TLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCc----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999866522112233 5688999999999999999999999998755
No 139
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=24.21 E-value=68 Score=30.75 Aligned_cols=49 Identities=22% Similarity=0.319 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
+||+.++.++...+.+. + .-.++|+.+|++...|.++..-+|.++++-+
T Consensus 127 ~L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE----L----SIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999987776663 2 3478999999999999999999999988644
No 140
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=24.13 E-value=1.9e+02 Score=26.76 Aligned_cols=47 Identities=21% Similarity=0.253 Sum_probs=31.0
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 006230 402 RPQRGLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINAR 455 (655)
Q Consensus 402 R~rR~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaR 455 (655)
+++++++.+.+...-....+ +.+ ...++|+..|++..+|.+|..-.|
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~---~g~----sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE---PGM----TVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc---CCC----CHHHHHHHHCcCHHHHHHHHHHHh
Confidence 34566877775544333333 232 456789999999999999955443
No 141
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.04 E-value=1.2e+02 Score=29.16 Aligned_cols=48 Identities=13% Similarity=0.104 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||++++.++.-.+.+. | .-.++|..+|++..-|.+....+++++...
T Consensus 127 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG----M----KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 48999999998877763 2 347899999999999999999999988653
No 142
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=24.04 E-value=83 Score=30.62 Aligned_cols=49 Identities=20% Similarity=0.135 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||+.++.++.-.+.+ -+ .-.++|..+|++..-|.++..-+|.++++-+
T Consensus 111 ~Lp~~~R~v~~L~~~e----g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIE----GL----SYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999887776 23 3478999999999999999999999988643
No 143
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=23.91 E-value=95 Score=29.37 Aligned_cols=49 Identities=14% Similarity=0.173 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++..+++.-.+.+. . .-.++|..+|++...|..+...+|+++++-+
T Consensus 119 ~L~~~~r~i~~l~~~~~--~------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQ--Y------SYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888888886655552 2 3478999999999999999999999998765
No 144
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=23.44 E-value=83 Score=30.45 Aligned_cols=47 Identities=17% Similarity=0.104 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||+..+.++.. +.+ .| .-.++|..+|++...|.+.+..+|+++++-
T Consensus 155 ~L~~~~r~vl~l-~~e----~~----s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 155 LLSELEKEVLEL-YLD----GK----SYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred hCCHHHHHHHHH-HHc----cC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 578889999877 555 23 347899999999999999888888887764
No 145
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=23.40 E-value=99 Score=31.10 Aligned_cols=54 Identities=30% Similarity=0.428 Sum_probs=42.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
.|+++++++|+.-|..=+ .=||-...-.+||++.|+++.-+..=..++=+|+-.
T Consensus 155 ~LTdrQ~~vL~~A~~~GY-Fd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGY-FDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHHHHHHcCC-CCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 599999999988877532 345899999999999999999887766655555433
No 146
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=23.36 E-value=80 Score=31.61 Aligned_cols=48 Identities=21% Similarity=0.213 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||++...++...|.+ . ..-.++|+.+|+|+..|..+-..+..|+++.
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 5899999999877654 2 2578899999999999999999988888753
No 147
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=23.29 E-value=1.1e+02 Score=21.82 Aligned_cols=23 Identities=35% Similarity=0.371 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChhhHhhhhhhhh
Q 006230 433 KHILARQTGLSRSQVSNWFINAR 455 (655)
Q Consensus 433 K~~LA~qTGLS~~QVsNWFiNaR 455 (655)
...+|+.+|+++..|.+|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45888999999999999988764
No 148
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=22.98 E-value=85 Score=30.01 Aligned_cols=48 Identities=21% Similarity=0.245 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||+....++..-+.+ .+ .-.++|..+|++...|.+....+|+++++-
T Consensus 137 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 137 ELEPPRSELIRTAFFE----GI----TYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 4889999998877765 22 347899999999999999999999998764
No 149
>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=22.50 E-value=38 Score=31.02 Aligned_cols=46 Identities=30% Similarity=0.297 Sum_probs=36.1
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 407 LPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 407 fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
||+....++...+.+. -.-.++|..+|++...|.++..-+|+++++
T Consensus 106 L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 106 LPENYRTVLILREFKE--------FSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred CCHhheeeeeehhhcc--------CcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6777777766544441 245789999999999999999999999876
No 150
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=22.45 E-value=1.6e+02 Score=28.75 Aligned_cols=49 Identities=16% Similarity=0.128 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++++.++.-.+.++ . .-.++|..+|++..-|.++..-+|+++++-+
T Consensus 128 ~Lp~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQVIGG--F------SGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999988877773 2 3468999999999999999999999988765
No 151
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.39 E-value=93 Score=29.01 Aligned_cols=47 Identities=19% Similarity=0.207 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWK 460 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkK 460 (655)
.||++++.++.-.+.+. .+ -.++|..+|++...|.++...+++++..
T Consensus 113 ~L~~~~r~v~~L~~~~g--~s------~~EIA~~l~is~~tV~~~l~ra~~~~~~ 159 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG--LG------YGEIATELGISLATVKRYLNKAAMRCYF 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 48999999997777662 23 3679999999999999999999888753
No 152
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.95 E-value=90 Score=30.32 Aligned_cols=49 Identities=16% Similarity=0.090 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.-.+.+. + .-.++|+.+|+|...|.....-+|+++++.+
T Consensus 111 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 111 KLPQDQREALILVGASG----F----SYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred hCCHHHHHHhhHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999988776662 2 3468999999999999999999999998755
No 153
>PF13565 HTH_32: Homeodomain-like domain
Probab=21.14 E-value=4.2e+02 Score=21.76 Aligned_cols=40 Identities=25% Similarity=0.200 Sum_probs=26.4
Q ss_pred ChhHHHHHHHHHHHccCCCCCCH-HHHHHHHHHhCC----ChhhHhhh
Q 006230 408 PERSVSVLRAWLFEHFLHPYPSD-VDKHILARQTGL----SRSQVSNW 450 (655)
Q Consensus 408 pk~qv~iLr~Wf~eH~~nPYPS~-~EK~~LA~qTGL----S~~QVsNW 450 (655)
+.++.+.|.+++.+| |.-+. .-...|+.++|+ +...|..|
T Consensus 32 ~~e~~~~i~~~~~~~---p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEH---PRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 677778889998884 54343 445556666663 66666655
No 154
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=20.59 E-value=1.3e+02 Score=31.46 Aligned_cols=48 Identities=25% Similarity=0.101 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKP 461 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp 461 (655)
.||++++.++.-.+.+. .+ -.++|+.+|+|..-|.+.+.-+|+++++.
T Consensus 142 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLG--WR------AAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred hCCHHHhhHhhhHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 58999999887766652 23 36899999999999999999999998764
No 155
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.57 E-value=88 Score=29.77 Aligned_cols=49 Identities=16% Similarity=0.125 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 006230 406 GLPERSVSVLRAWLFEHFLHPYPSDVDKHILARQTGLSRSQVSNWFINARVRLWKPM 462 (655)
Q Consensus 406 ~fpk~qv~iLr~Wf~eH~~nPYPS~~EK~~LA~qTGLS~~QVsNWFiNaRrRlkKp~ 462 (655)
.||++.+.++.--+.+. . .-.++|+.+|++...|.++...++.++++-.
T Consensus 119 ~L~~~~r~i~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~ 167 (172)
T PRK09651 119 GLNGKTREAFLLSQLDG--L------TYSEIAHKLGVSVSSVKKYVAKATEHCLLFR 167 (172)
T ss_pred hCCHHHhHHhhhhhccC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887766553 2 3478999999999999999998888876543
Done!