Query 012938
Match_columns 453
No_of_seqs 274 out of 1029
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 07:52:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012938.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012938hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07526 POX: Associated with 100.0 3.3E-42 7.1E-47 310.2 12.1 134 173-306 1-140 (140)
2 smart00574 POX domain associat 100.0 7.9E-42 1.7E-46 306.3 11.7 135 169-306 1-140 (140)
3 KOG0773 Transcription factor M 100.0 4.3E-33 9.4E-38 278.1 10.7 254 171-428 45-312 (342)
4 KOG0775 Transcription factor S 99.9 4.8E-22 1E-26 195.1 7.8 132 245-414 101-232 (304)
5 KOG0774 Transcription factor P 99.6 3.2E-15 7E-20 146.7 13.9 149 238-419 102-252 (334)
6 PF05920 Homeobox_KN: Homeobox 99.6 2.7E-16 5.9E-21 114.8 3.9 40 373-412 1-40 (40)
7 cd00086 homeodomain Homeodomai 99.4 5.3E-13 1.1E-17 100.4 6.3 56 357-415 2-57 (59)
8 smart00389 HOX Homeodomain. DN 99.4 1.3E-12 2.7E-17 98.0 6.4 55 357-414 2-56 (56)
9 PF00046 Homeobox: Homeobox do 99.4 9.2E-13 2E-17 99.8 5.2 57 356-415 1-57 (57)
10 KOG0487 Transcription factor A 98.9 3.9E-10 8.4E-15 113.8 3.5 68 353-423 233-300 (308)
11 KOG0843 Transcription factor E 98.8 1.1E-08 2.5E-13 96.5 7.1 64 354-420 101-164 (197)
12 KOG0489 Transcription factor z 98.7 9.8E-09 2.1E-13 101.2 5.4 60 354-416 158-217 (261)
13 KOG0842 Transcription factor t 98.7 1E-08 2.2E-13 103.6 4.0 66 354-422 152-217 (307)
14 KOG0488 Transcription factor B 98.7 1.8E-08 3.9E-13 102.0 5.3 64 353-419 170-233 (309)
15 TIGR01565 homeo_ZF_HD homeobox 98.7 3.2E-08 6.9E-13 78.0 5.1 52 356-410 2-57 (58)
16 KOG0850 Transcription factor D 98.6 2.2E-08 4.7E-13 97.6 4.6 62 353-417 120-181 (245)
17 KOG0493 Transcription factor E 98.6 3.1E-08 6.8E-13 98.2 4.5 61 353-416 244-304 (342)
18 KOG0485 Transcription factor N 98.5 4.7E-08 1E-12 94.9 3.8 65 354-421 103-167 (268)
19 KOG0483 Transcription factor H 98.5 9.8E-08 2.1E-12 91.5 5.2 62 355-419 50-111 (198)
20 KOG0492 Transcription factor M 98.5 3.1E-07 6.8E-12 88.7 6.8 78 349-429 138-215 (246)
21 KOG3802 Transcription factor O 98.4 1.1E-07 2.4E-12 98.5 3.7 60 354-416 293-352 (398)
22 KOG2251 Homeobox transcription 98.4 2.3E-07 4.9E-12 90.1 4.7 63 350-415 32-94 (228)
23 COG5576 Homeodomain-containing 98.3 6.5E-07 1.4E-11 83.0 5.4 61 354-417 50-110 (156)
24 KOG0848 Transcription factor C 98.3 5.2E-07 1.1E-11 89.9 4.5 62 357-421 201-262 (317)
25 KOG0484 Transcription factor P 98.3 1.3E-06 2.8E-11 76.8 6.4 64 356-422 18-81 (125)
26 KOG0491 Transcription factor B 98.3 4.4E-07 9.6E-12 85.1 2.5 69 356-427 101-169 (194)
27 KOG0494 Transcription factor C 98.2 1.1E-06 2.5E-11 87.2 4.6 59 355-416 140-199 (332)
28 KOG0486 Transcription factor P 98.1 2.1E-06 4.6E-11 87.1 3.9 61 355-418 112-172 (351)
29 KOG4577 Transcription factor L 98.1 2.3E-06 5E-11 86.2 4.0 63 350-415 162-224 (383)
30 KOG2252 CCAAT displacement pro 98.0 1.5E-05 3.2E-10 85.8 7.5 57 354-413 419-475 (558)
31 KOG0847 Transcription factor, 97.7 2.6E-05 5.6E-10 76.3 3.9 63 357-422 169-231 (288)
32 KOG0844 Transcription factor E 97.7 1.4E-05 3E-10 81.2 1.2 62 354-418 180-241 (408)
33 KOG0849 Transcription factor P 97.6 5.7E-05 1.2E-09 77.9 4.5 61 354-417 175-235 (354)
34 KOG0490 Transcription factor, 97.5 6.9E-05 1.5E-09 70.2 2.9 60 354-416 59-118 (235)
35 KOG0773 Transcription factor M 97.3 9.2E-05 2E-09 74.9 1.8 60 357-417 97-156 (342)
36 KOG1168 Transcription factor A 97.1 0.00019 4.2E-09 72.7 1.6 58 355-415 309-366 (385)
37 PF11569 Homez: Homeodomain le 96.0 0.0038 8.3E-08 49.4 2.0 43 367-412 10-52 (56)
38 KOG0490 Transcription factor, 95.5 0.013 2.8E-07 54.9 3.7 63 353-418 151-213 (235)
39 KOG1146 Homeobox protein [Gene 91.2 0.28 6E-06 58.4 5.2 60 356-418 904-963 (1406)
40 KOG3623 Homeobox transcription 81.8 1.9 4E-05 49.3 4.7 44 367-413 568-611 (1007)
41 PF04218 CENP-B_N: CENP-B N-te 78.7 4.8 0.0001 31.0 4.8 46 357-410 2-47 (53)
42 cd06171 Sigma70_r4 Sigma70, re 73.4 5 0.00011 28.0 3.4 46 361-414 10-55 (55)
43 PF08281 Sigma70_r4_2: Sigma-7 72.6 6.6 0.00014 29.2 4.1 45 361-413 10-54 (54)
44 PF04545 Sigma70_r4: Sigma-70, 72.5 4.9 0.00011 29.7 3.3 47 361-415 4-50 (50)
45 PF01527 HTH_Tnp_1: Transposas 68.1 6.7 0.00014 30.8 3.4 45 358-410 3-48 (76)
46 cd00569 HTH_Hin_like Helix-tur 60.8 15 0.00033 22.7 3.5 39 360-406 4-42 (42)
47 PRK12530 RNA polymerase sigma 56.3 16 0.00035 33.7 4.2 55 360-422 133-187 (189)
48 TIGR02937 sigma70-ECF RNA poly 55.6 13 0.00027 31.1 3.1 48 361-416 110-157 (158)
49 PRK09652 RNA polymerase sigma 55.0 15 0.00033 32.5 3.7 50 360-417 127-176 (182)
50 PRK06930 positive control sigm 54.6 14 0.00031 34.7 3.6 55 361-423 114-168 (170)
51 PF11285 DUF3086: Protein of u 54.0 1.4E+02 0.003 30.8 10.5 60 238-313 6-65 (283)
52 PRK11924 RNA polymerase sigma 53.6 17 0.00037 32.0 3.8 52 360-419 124-175 (179)
53 PRK09642 RNA polymerase sigma 53.5 15 0.00033 32.4 3.5 51 360-418 105-155 (160)
54 PRK00118 putative DNA-binding 53.4 18 0.00038 32.0 3.7 50 360-417 16-65 (104)
55 TIGR02985 Sig70_bacteroi1 RNA 53.2 16 0.00034 31.6 3.4 48 361-416 113-160 (161)
56 PRK09644 RNA polymerase sigma 53.0 17 0.00037 32.4 3.7 51 360-418 107-157 (165)
57 PRK06759 RNA polymerase factor 52.5 16 0.00036 31.9 3.5 48 360-415 105-152 (154)
58 PRK12514 RNA polymerase sigma 51.4 17 0.00037 32.9 3.5 50 360-417 128-177 (179)
59 TIGR02939 RpoE_Sigma70 RNA pol 49.5 15 0.00032 33.2 2.8 50 360-417 137-186 (190)
60 PF13443 HTH_26: Cro/C1-type H 49.1 23 0.00049 26.9 3.3 26 388-413 13-38 (63)
61 PRK12519 RNA polymerase sigma 47.8 19 0.00042 32.9 3.3 51 360-418 140-190 (194)
62 PRK09646 RNA polymerase sigma 47.8 20 0.00044 33.0 3.5 50 360-417 141-190 (194)
63 PRK12512 RNA polymerase sigma 47.0 18 0.00039 32.8 2.9 51 360-418 130-180 (184)
64 PRK09648 RNA polymerase sigma 45.2 25 0.00054 32.1 3.6 50 360-417 138-187 (189)
65 TIGR02999 Sig-70_X6 RNA polyme 45.1 27 0.00058 31.5 3.7 48 361-416 134-181 (183)
66 PRK12532 RNA polymerase sigma 44.7 25 0.00054 32.4 3.5 55 360-422 135-189 (195)
67 TIGR02393 RpoD_Cterm RNA polym 44.1 37 0.0008 32.8 4.7 58 360-421 175-232 (238)
68 TIGR02989 Sig-70_gvs1 RNA poly 42.1 29 0.00062 30.4 3.4 48 360-415 110-157 (159)
69 PRK08583 RNA polymerase sigma 41.7 35 0.00076 33.1 4.2 50 360-417 204-253 (257)
70 PRK12526 RNA polymerase sigma 41.4 30 0.00064 32.5 3.5 50 360-417 152-201 (206)
71 PRK12520 RNA polymerase sigma 41.4 33 0.00071 31.5 3.8 54 360-421 130-183 (191)
72 TIGR02980 SigBFG RNA polymeras 40.0 28 0.0006 33.0 3.1 50 360-417 177-226 (227)
73 PRK05602 RNA polymerase sigma 39.6 30 0.00064 31.5 3.2 51 360-418 127-177 (186)
74 TIGR02941 Sigma_B RNA polymera 39.2 37 0.00079 33.0 3.9 50 360-417 204-253 (255)
75 TIGR02948 SigW_bacill RNA poly 39.2 30 0.00065 31.1 3.1 50 360-417 135-184 (187)
76 TIGR02954 Sig70_famx3 RNA poly 39.2 34 0.00073 30.6 3.4 49 361-417 119-167 (169)
77 smart00421 HTH_LUXR helix_turn 39.1 92 0.002 22.0 5.1 48 361-417 3-50 (58)
78 PRK06811 RNA polymerase factor 38.8 32 0.00069 31.6 3.3 51 360-418 130-180 (189)
79 PRK04217 hypothetical protein; 38.1 57 0.0012 29.1 4.6 51 359-417 40-90 (110)
80 PRK12541 RNA polymerase sigma 38.0 32 0.00069 30.5 3.0 48 360-415 111-158 (161)
81 PRK09047 RNA polymerase factor 37.9 32 0.0007 30.2 3.0 51 360-418 105-155 (161)
82 TIGR02943 Sig70_famx1 RNA poly 37.8 43 0.00094 31.0 4.0 54 360-421 130-183 (188)
83 PRK12544 RNA polymerase sigma 37.7 46 0.001 31.5 4.2 55 360-422 147-201 (206)
84 PRK13919 putative RNA polymera 37.5 40 0.00086 30.6 3.6 50 360-417 134-183 (186)
85 PRK12546 RNA polymerase sigma 37.4 34 0.00073 31.9 3.2 51 360-418 112-162 (188)
86 PRK12537 RNA polymerase sigma 37.4 38 0.00081 30.9 3.5 49 360-416 132-180 (182)
87 PRK12545 RNA polymerase sigma 37.3 43 0.00092 31.3 3.9 55 360-422 138-192 (201)
88 PRK12547 RNA polymerase sigma 37.2 38 0.00083 30.3 3.4 50 360-417 111-160 (164)
89 PRK03975 tfx putative transcri 37.0 47 0.001 30.8 4.0 51 360-419 5-55 (141)
90 TIGR02983 SigE-fam_strep RNA p 36.7 39 0.00085 29.8 3.4 49 360-416 109-157 (162)
91 PRK12515 RNA polymerase sigma 36.3 47 0.001 30.4 3.9 50 360-417 130-179 (189)
92 PRK06986 fliA flagellar biosyn 36.1 36 0.00078 32.6 3.3 50 360-417 183-232 (236)
93 PF00196 GerE: Bacterial regul 36.0 81 0.0018 23.9 4.6 52 361-421 3-54 (58)
94 PRK12536 RNA polymerase sigma 35.9 42 0.00092 30.5 3.6 51 360-418 128-178 (181)
95 TIGR02947 SigH_actino RNA poly 35.2 25 0.00055 32.3 2.0 51 360-418 130-180 (193)
96 PRK12523 RNA polymerase sigma 35.0 46 0.00099 30.0 3.6 48 360-415 118-165 (172)
97 PRK12531 RNA polymerase sigma 34.9 44 0.00096 30.8 3.6 51 360-418 140-190 (194)
98 cd00131 PAX Paired Box domain 34.9 1.3E+02 0.0028 27.0 6.4 46 361-409 75-127 (128)
99 TIGR03001 Sig-70_gmx1 RNA poly 34.3 55 0.0012 32.2 4.3 59 360-427 160-218 (244)
100 TIGR02479 FliA_WhiG RNA polyme 34.1 43 0.00092 31.8 3.4 49 360-416 174-222 (224)
101 PRK09639 RNA polymerase sigma 33.9 64 0.0014 28.5 4.3 49 360-417 111-159 (166)
102 PRK15369 two component system 33.9 99 0.0021 26.7 5.4 47 360-415 148-194 (211)
103 PRK12524 RNA polymerase sigma 33.4 48 0.001 30.7 3.5 50 360-417 135-184 (196)
104 PRK11511 DNA-binding transcrip 33.3 96 0.0021 27.3 5.3 43 363-409 7-49 (127)
105 PRK07037 extracytoplasmic-func 33.0 52 0.0011 29.1 3.6 50 360-417 108-157 (163)
106 PRK07670 RNA polymerase sigma 32.3 48 0.001 32.2 3.5 49 360-416 200-248 (251)
107 PRK12516 RNA polymerase sigma 32.0 56 0.0012 30.3 3.7 51 360-418 115-165 (187)
108 PRK06288 RNA polymerase sigma 32.0 55 0.0012 32.2 3.9 50 360-417 211-260 (268)
109 PRK07408 RNA polymerase sigma 31.3 49 0.0011 32.5 3.4 50 360-417 202-251 (256)
110 PRK09641 RNA polymerase sigma 31.2 51 0.0011 29.7 3.2 50 360-417 135-184 (187)
111 PF13518 HTH_28: Helix-turn-he 31.0 45 0.00097 24.1 2.4 24 388-411 15-38 (52)
112 KOG0809 SNARE protein TLG2/Syn 30.9 1.7E+02 0.0036 30.7 7.1 61 250-310 104-169 (305)
113 PRK12538 RNA polymerase sigma 30.3 64 0.0014 31.4 3.9 51 360-418 170-220 (233)
114 PRK12511 RNA polymerase sigma 29.6 94 0.002 28.8 4.8 49 360-416 110-158 (182)
115 PRK12513 RNA polymerase sigma 29.5 31 0.00067 31.6 1.6 50 360-417 138-187 (194)
116 TIGR02959 SigZ RNA polymerase 29.2 66 0.0014 29.1 3.7 50 360-417 99-148 (170)
117 PRK12543 RNA polymerase sigma 29.2 92 0.002 28.3 4.6 54 360-421 116-169 (179)
118 PRK09647 RNA polymerase sigma 28.8 1.1E+02 0.0023 29.0 5.1 50 360-417 137-186 (203)
119 PRK12533 RNA polymerase sigma 28.5 1.2E+02 0.0026 29.2 5.4 50 360-417 133-182 (216)
120 PRK12542 RNA polymerase sigma 28.1 66 0.0014 29.3 3.5 50 360-417 121-170 (185)
121 TIGR02885 spore_sigF RNA polym 28.1 60 0.0013 30.9 3.3 49 360-416 182-230 (231)
122 PRK05657 RNA polymerase sigma 27.7 1.1E+02 0.0024 31.5 5.3 54 360-417 261-314 (325)
123 PRK12539 RNA polymerase sigma 27.4 73 0.0016 29.1 3.6 50 360-417 130-179 (184)
124 PRK09413 IS2 repressor TnpA; R 27.4 1.6E+02 0.0036 25.8 5.7 45 359-410 10-54 (121)
125 PRK09637 RNA polymerase sigma 27.1 67 0.0014 29.6 3.3 49 361-417 106-154 (181)
126 COG1734 DksA DnaK suppressor p 26.7 4.5E+02 0.0097 23.9 8.4 72 238-310 3-74 (120)
127 PRK07598 RNA polymerase sigma 26.5 1.5E+02 0.0034 32.0 6.3 61 360-424 349-409 (415)
128 PRK09645 RNA polymerase sigma 26.2 78 0.0017 28.3 3.5 50 360-417 117-166 (173)
129 PRK11923 algU RNA polymerase s 26.2 72 0.0016 29.1 3.4 50 360-417 137-186 (193)
130 PRK12535 RNA polymerase sigma 25.9 72 0.0016 29.9 3.4 52 360-419 132-183 (196)
131 PRK12522 RNA polymerase sigma 25.8 89 0.0019 28.1 3.8 51 360-418 118-168 (173)
132 PRK08301 sporulation sigma fac 25.8 1.2E+02 0.0027 28.8 5.0 54 360-417 177-230 (234)
133 PF13551 HTH_29: Winged helix- 25.8 1.5E+02 0.0033 24.3 4.9 51 357-407 53-109 (112)
134 PRK09649 RNA polymerase sigma 25.7 72 0.0016 29.3 3.3 48 360-415 129-176 (185)
135 TIGR02952 Sig70_famx2 RNA poly 25.7 77 0.0017 27.9 3.4 49 360-416 121-169 (170)
136 cd01392 HTH_LacI Helix-turn-he 25.6 66 0.0014 23.3 2.4 21 390-410 2-22 (52)
137 PRK12527 RNA polymerase sigma 25.5 88 0.0019 27.6 3.7 50 361-418 105-154 (159)
138 PRK12518 RNA polymerase sigma 24.8 36 0.00078 30.5 1.1 49 361-417 120-168 (175)
139 PF13730 HTH_36: Helix-turn-he 24.8 2.2E+02 0.0047 21.0 5.2 46 361-410 2-50 (55)
140 PRK09415 RNA polymerase factor 24.8 72 0.0016 29.1 3.1 50 360-417 126-175 (179)
141 PRK08295 RNA polymerase factor 24.5 84 0.0018 28.9 3.5 48 360-416 154-201 (208)
142 PF04967 HTH_10: HTH DNA bindi 23.9 1.5E+02 0.0033 23.2 4.2 50 362-412 1-50 (53)
143 PRK12534 RNA polymerase sigma 23.9 91 0.002 28.3 3.5 50 360-417 136-185 (187)
144 PRK12528 RNA polymerase sigma 23.9 90 0.0019 27.6 3.4 47 360-414 112-158 (161)
145 PRK12529 RNA polymerase sigma 23.9 86 0.0019 28.6 3.4 48 360-415 126-173 (178)
146 PRK05572 sporulation sigma fac 23.8 85 0.0018 30.5 3.5 50 360-417 201-250 (252)
147 PF07765 KIP1: KIP1-like prote 23.7 1.2E+02 0.0026 25.7 3.8 31 235-265 41-72 (74)
148 PRK05803 sporulation sigma fac 23.6 1.5E+02 0.0033 28.4 5.1 56 360-419 174-229 (233)
149 TIGR02950 SigM_subfam RNA poly 23.4 39 0.00085 29.4 1.0 47 361-415 105-151 (154)
150 PRK08215 sporulation sigma fac 23.0 88 0.0019 30.5 3.5 50 360-417 208-257 (258)
151 PRK07122 RNA polymerase sigma 22.9 78 0.0017 31.4 3.1 49 360-416 214-262 (264)
152 TIGR02846 spore_sigmaK RNA pol 22.7 1.4E+02 0.0031 28.5 4.8 53 360-416 173-225 (227)
153 cd00093 HTH_XRE Helix-turn-hel 22.7 1.2E+02 0.0026 20.4 3.2 23 388-410 15-37 (58)
154 PF01381 HTH_3: Helix-turn-hel 22.2 1.2E+02 0.0026 22.2 3.3 21 388-408 12-32 (55)
155 PRK12540 RNA polymerase sigma 21.9 98 0.0021 28.6 3.4 51 360-418 110-160 (182)
156 PRK12517 RNA polymerase sigma 21.5 1.4E+02 0.003 27.7 4.3 53 360-420 127-179 (188)
157 cd06170 LuxR_C_like C-terminal 21.3 2.1E+02 0.0045 20.3 4.4 45 362-415 1-45 (57)
158 PRK05911 RNA polymerase sigma 21.1 1.1E+02 0.0023 30.3 3.6 50 360-417 204-253 (257)
159 PRK11922 RNA polymerase sigma 21.0 62 0.0014 31.0 1.9 51 360-418 148-198 (231)
160 PF10668 Phage_terminase: Phag 20.6 74 0.0016 25.7 2.0 21 387-407 24-44 (60)
161 PF13384 HTH_23: Homeodomain-l 20.6 77 0.0017 23.0 1.9 23 388-410 20-42 (50)
162 PF07638 Sigma70_ECF: ECF sigm 20.5 1.1E+02 0.0025 28.3 3.5 48 362-417 136-183 (185)
No 1
>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=3.3e-42 Score=310.20 Aligned_cols=134 Identities=46% Similarity=0.635 Sum_probs=100.1
Q ss_pred ccccCCCCchhHHHHHHHHHhcCccc-ccchhhhhhh----ccCCCCCCCcccCchhhh-hhcCCCCCchHHHHHHHHHH
Q 012938 173 YAVGNSRFLRPAQSLLEEVVNVGKNI-DMSDERYISK----LYHGSRRGGLRLSSELKA-EMCNTGTLSAEKQELHLRIA 246 (453)
Q Consensus 173 ~~l~~SryLkpAQeLL~E~~~v~~~~-~~~~~~~~~~----~~~~~~~g~~~~ss~~~~-~~~~~~~~~~er~Elq~kka 246 (453)
++|++|||||||||||||||+|++.. .....+.... ...+...+....+..... ...+.++++++|+|+|+||+
T Consensus 1 q~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~~~~e~q~kK~ 80 (140)
T PF07526_consen 1 QVLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSGAPGGANSSGSSSSSGGSSSSSSSSDSSSPELSPAERQELQRKKA 80 (140)
T ss_pred CccccchhHHHHHHHHHHHHcccchhhhcchhhccccccccccCCCCCCCCCCCCCccccCCCCCCCChhhHHHHHHHHH
Confidence 48999999999999999999999631 1111100000 000000011111111111 11234567899999999999
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHhhhhhhccCccchhhhhHHHHHHHHHhhhHHhHHH
Q 012938 247 KLISLLEEVESKYEIYYNQMEEVVSSYEVIAGLGAAKSYTSLALQAMSRHFCSLRDAIIS 306 (453)
Q Consensus 247 kLl~mL~ev~~ry~qy~~qmq~v~ssFe~~aGlgaa~~ytalal~amSrhfr~LrdaI~~ 306 (453)
|||.||||||+||+|||||||+|+++||+|||+|+|++||+|||||||||||||||+|++
T Consensus 81 KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~~ 140 (140)
T PF07526_consen 81 KLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAISD 140 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999999999999999999999963
No 2
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=7.9e-42 Score=306.35 Aligned_cols=135 Identities=41% Similarity=0.585 Sum_probs=105.0
Q ss_pred ccccccccCCCCchhHHHHHHHHHhcCcccccchhhh-h----hhccCCCCCCCcccCchhhhhhcCCCCCchHHHHHHH
Q 012938 169 ESFAYAVGNSRFLRPAQSLLEEVVNVGKNIDMSDERY-I----SKLYHGSRRGGLRLSSELKAEMCNTGTLSAEKQELHL 243 (453)
Q Consensus 169 ~~~a~~l~~SryLkpAQeLL~E~~~v~~~~~~~~~~~-~----~~~~~~~~~g~~~~ss~~~~~~~~~~~~~~er~Elq~ 243 (453)
+||+++|++|||||||||||||||+|++++...+... . ......+.++....++. .....+++++||+|+|+
T Consensus 1 ~g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~s~---~~~~~~ls~~~r~e~q~ 77 (140)
T smart00574 1 TGGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQSGNDSPVSTSSNEGGGENLSGGSS---SSEVPPLSTAERQELQR 77 (140)
T ss_pred CchhhhccCccccccHHHHHHHHhcccHHhhcccccccccccccccccCCCcCCCCCCCC---CCCCCCCchhHHHHHHH
Confidence 4789999999999999999999999996664322100 0 00000010110000111 11234577899999999
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHhhhhhhccCccchhhhhHHHHHHHHHhhhHHhHHH
Q 012938 244 RIAKLISLLEEVESKYEIYYNQMEEVVSSYEVIAGLGAAKSYTSLALQAMSRHFCSLRDAIIS 306 (453)
Q Consensus 244 kkakLl~mL~ev~~ry~qy~~qmq~v~ssFe~~aGlgaa~~ytalal~amSrhfr~LrdaI~~ 306 (453)
||+||+.||+|||+||+|||||||+|+++||+++|+|+|++||+||+||||||||||||+|.+
T Consensus 78 kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~g 140 (140)
T smart00574 78 KKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIAG 140 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999999999999999999999999963
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=100.00 E-value=4.3e-33 Score=278.15 Aligned_cols=254 Identities=36% Similarity=0.508 Sum_probs=186.2
Q ss_pred ccccccCCCCchhHHHHHHHHHhcCcccccc---hhhhhh--hccCCCCCCCcccCchhhhhhcCCCCCchHHHHHHHHH
Q 012938 171 FAYAVGNSRFLRPAQSLLEEVVNVGKNIDMS---DERYIS--KLYHGSRRGGLRLSSELKAEMCNTGTLSAEKQELHLRI 245 (453)
Q Consensus 171 ~a~~l~~SryLkpAQeLL~E~~~v~~~~~~~---~~~~~~--~~~~~~~~g~~~~ss~~~~~~~~~~~~~~er~Elq~kk 245 (453)
+...+..++||++||+||+++|++....... -+.... .........+...... ..+. .......++++++.++
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~-~~~s-~~~~~~~~~~~~~~~~ 122 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNA-TRES-ATLKAWLEEHRLNPYP 122 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccc-cccc-cccccchhhhhhccCc
Confidence 5667889999999999999999997322110 000000 0000000000000000 0011 1122457999999999
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHhhhhhhccCccchhhhhHHHHHHHHHhhhHH--hHHHHHHHHHHhhcCC----C
Q 012938 246 AKLISLLEEVESKYEIYYNQMEEVVSSYEVIAGLGAAKSYTSLALQAMSRHFCSLRD--AIISQINIASRRFYQD----L 319 (453)
Q Consensus 246 akLl~mL~ev~~ry~qy~~qmq~v~ssFe~~aGlgaa~~ytalal~amSrhfr~Lrd--aI~~qi~~~~~~l~~d----~ 319 (453)
+|++.||.+|+.+|.+|+..|+.|.++|+...|++.+.+|+.+++.++++||+++++ +|.+|+......++.. .
T Consensus 123 ~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~ 202 (342)
T KOG0773|consen 123 SKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDS 202 (342)
T ss_pred hHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccccccccccccccc
Confidence 999999999999999999999999999999999999999999999999999999998 8888998888776521 1
Q ss_pred CCCCCC---CCCCccchHHHhhhhhhhhhccccccccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC
Q 012938 320 PKISSG---LSQLSLFDREARHHRMSLQQLGMFHSQRQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTG 396 (453)
Q Consensus 320 p~~s~~---~~~l~~~d~~~~q~r~~~qq~g~~~~~rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TG 396 (453)
...... .+.....+...++++-...+.+ ......||++++||+.++.+|++|+++|+.||||++.+|..||++||
T Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TG 280 (342)
T KOG0773|consen 203 EDESGPSGSEPPLRLAKQSLRQQRSAYDGSG--GKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTG 280 (342)
T ss_pred ccccCcccccCCccccccccccccccccccc--ccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcC
Confidence 111111 1222233333333321111122 22246899999999999999999999999999999999999999999
Q ss_pred CChhhhhhhhhhhhhhhchhhHHHHHHHhhcC
Q 012938 397 LTKNQVSNWFINARVRLWKPMIEEMYREEFAD 428 (453)
Q Consensus 397 LS~sQVsNWFiNaR~Rl~Kpmi~el~~e~~~~ 428 (453)
|+..||+|||||+|+|+|+||+++++.+.+..
T Consensus 281 Ls~~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 281 LSRPQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred CCcccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 99999999999999999999999999998875
No 4
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.86 E-value=4.8e-22 Score=195.07 Aligned_cols=132 Identities=31% Similarity=0.402 Sum_probs=122.3
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHhhhhhhccCccchhhhhHHHHHHHHHhhhHHhHHHHHHHHHHhhcCCCCCCCC
Q 012938 245 IAKLISLLEEVESKYEIYYNQMEEVVSSYEVIAGLGAAKSYTSLALQAMSRHFCSLRDAIISQINIASRRFYQDLPKISS 324 (453)
Q Consensus 245 kakLl~mL~ev~~ry~qy~~qmq~v~ssFe~~aGlgaa~~ytalal~amSrhfr~LrdaI~~qi~~~~~~l~~d~p~~s~ 324 (453)
.-|..+++.++.+.|+.+|+.|+.+.++-+.++.|++ ||++|++++.+.+|++.++.|.+||.+...++|++
T Consensus 101 vLkArA~vafH~gnf~eLY~iLE~h~Fs~~~h~~LQ~------lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrT-- 172 (304)
T KOG0775|consen 101 VLKARAVVAFHSGNFRELYHILENHKFSPHNHPKLQA------LWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRT-- 172 (304)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHhccCChhhhHHHHH------HHHHHHHHHHHHhcCCcCCccccceeeccCCCCCc--
Confidence 4566789999999999999999999999999999977 99999999999999999999999998888888887
Q ss_pred CCCCCccchHHHhhhhhhhhhccccccccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhh
Q 012938 325 GLSQLSLFDREARHHRMSLQQLGMFHSQRQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSN 404 (453)
Q Consensus 325 ~~~~l~~~d~~~~q~r~~~qq~g~~~~~rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsN 404 (453)
+||++... .||.++++.+||.||. .+|||++++|.+||+.||||..||+|
T Consensus 173 ------IWDGEet~---------------------yCFKekSR~~LrewY~---~~~YPsp~eKReLA~aTgLt~tQVsN 222 (304)
T KOG0775|consen 173 ------IWDGEETV---------------------YCFKEKSRSLLREWYL---QNPYPSPREKRELAEATGLTITQVSN 222 (304)
T ss_pred ------cccCceee---------------------eehhHhhHHHHHHHHh---cCCCCChHHHHHHHHHhCCchhhhhh
Confidence 78865442 5799999999999999 99999999999999999999999999
Q ss_pred hhhhhhhhhc
Q 012938 405 WFINARVRLW 414 (453)
Q Consensus 405 WFiNaR~Rl~ 414 (453)
||+|+|.|.+
T Consensus 223 WFKNRRQRDR 232 (304)
T KOG0775|consen 223 WFKNRRQRDR 232 (304)
T ss_pred hhhhhhhhhh
Confidence 9999999987
No 5
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.63 E-value=3.2e-15 Score=146.74 Aligned_cols=149 Identities=22% Similarity=0.352 Sum_probs=100.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhh-hhhhccCccchhhhhHHHHHHHHHhhhHHhHHHHHHHHHHhhc
Q 012938 238 KQELHLRIAKLISLLEEVESKYEIYYNQMEEVVSSY-EVIAGLGAAKSYTSLALQAMSRHFCSLRDAIISQINIASRRFY 316 (453)
Q Consensus 238 r~Elq~kkakLl~mL~ev~~ry~qy~~qmq~v~ssF-e~~aGlgaa~~ytalal~amSrhfr~LrdaI~~qi~~~~~~l~ 316 (453)
--+...|..+...++..--+.|++-|.+.-.+|-.. -....... .|-+.|.+++..|.+...+..-.+.
T Consensus 102 hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~nlL~eQsr~RP----------i~~ke~e~m~~~i~~kF~~iq~~lk 171 (334)
T KOG0774|consen 102 HSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLLREQSRTRP----------IMPKEIERMVQIISKKFSHIQMQLK 171 (334)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCC----------CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346677777777777777777777666655544432 11111111 2333444455555555554444443
Q ss_pred CCCCCCCCCCCCCccchHHH-hhhhhhhhhccccccccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHh
Q 012938 317 QDLPKISSGLSQLSLFDREA-RHHRMSLQQLGMFHSQRQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQT 395 (453)
Q Consensus 317 ~d~p~~s~~~~~l~~~d~~~-~q~r~~~qq~g~~~~~rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~T 395 (453)
+.. .+... ...| + -..+|+||+|+|.++.||..||..|+.||||++++|+.||+++
T Consensus 172 qst------------ce~vmiLr~r-------~----ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC 228 (334)
T KOG0774|consen 172 QST------------CEAVMILRSR-------F----LDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC 228 (334)
T ss_pred HHH------------HHHHHHHHHH-------H----HHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc
Confidence 210 00000 0111 1 1345788999999999999999999999999999999999999
Q ss_pred CCChhhhhhhhhhhhhhhchhhHH
Q 012938 396 GLTKNQVSNWFINARVRLWKPMIE 419 (453)
Q Consensus 396 GLS~sQVsNWFiNaR~Rl~Kpmi~ 419 (453)
+++.+||+|||.|.|.|.+|.+..
T Consensus 229 nItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 229 NITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred Cceehhhccccccceeehhhhhhh
Confidence 999999999999999999999864
No 6
>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=99.62 E-value=2.7e-16 Score=114.78 Aligned_cols=40 Identities=63% Similarity=1.159 Sum_probs=36.5
Q ss_pred HHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 012938 373 WLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVR 412 (453)
Q Consensus 373 Wf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~R 412 (453)
||.+|+.||||+++||..||++|||+.+||+|||+|+|+|
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 9999999999999999999999999999999999999997
No 7
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.40 E-value=5.3e-13 Score=100.42 Aligned_cols=56 Identities=32% Similarity=0.507 Sum_probs=52.6
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 357 R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
+++..|++.++.+|++||. .+|||+.+++..||.++||+..||.+||.|+|.+.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~---~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFE---KNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 4567899999999999999 6999999999999999999999999999999999865
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.36 E-value=1.3e-12 Score=98.02 Aligned_cols=55 Identities=29% Similarity=0.490 Sum_probs=50.9
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhc
Q 012938 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLW 414 (453)
Q Consensus 357 R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~ 414 (453)
+++..|+++++.+|+.||. .+|||+.+++..||..+||+..||.+||+|+|.|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~---~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQ---KNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHH---hCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 3456799999999999999 889999999999999999999999999999999863
No 9
>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=99.35 E-value=9.2e-13 Score=99.82 Aligned_cols=57 Identities=33% Similarity=0.567 Sum_probs=53.6
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 356 WRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 356 ~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
+|+|+.|+++++.+|+.+|. .+|||+.+++..||.++||+..||.+||+|+|.+.++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~---~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQ---ENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHH---HSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHH---HhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 36789999999999999999 6999999999999999999999999999999999764
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.95 E-value=3.9e-10 Score=113.77 Aligned_cols=68 Identities=21% Similarity=0.223 Sum_probs=59.9
Q ss_pred cccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHHH
Q 012938 353 RQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMYR 423 (453)
Q Consensus 353 rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~~ 423 (453)
++.++||..++|.|+..|+.-|+ -|-|.+++-|.+|++.++||..||+.||||||+|+||-..+...+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFl---fN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~ 300 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFL---FNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK 300 (308)
T ss_pred cccccccCCchHHHHHHHHHHHH---HHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence 55677889999999999988888 799999999999999999999999999999999998755444433
No 11
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.79 E-value=1.1e-08 Score=96.54 Aligned_cols=64 Identities=22% Similarity=0.236 Sum_probs=59.8
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHH
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEE 420 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~e 420 (453)
+.+|.|+.|+..+...|+..|. .+.|-.-.||+.||+.++|++.||+.||+|+|.|.|+.-.++
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~---~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFE---GNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHh---cCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 6778899999999999999999 899999999999999999999999999999999998866654
No 12
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.74 E-value=9.8e-09 Score=101.19 Aligned_cols=60 Identities=22% Similarity=0.281 Sum_probs=56.2
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
+.+|.|+.|+..|+..|+.-|. .|.|.+...|++||..+.||+.||++||+|+|++.||.
T Consensus 158 ~~kR~RtayT~~QllELEkEFh---fN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFH---FNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhc---cccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 3677889999999999999999 99999999999999999999999999999999998763
No 13
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.69 E-value=1e-08 Score=103.57 Aligned_cols=66 Identities=23% Similarity=0.246 Sum_probs=58.6
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHH
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMY 422 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~ 422 (453)
+++|+|--|++.||-.|++-|. ..-|.+..||+.||+.++||.+||+.||+|+|.|.|+.-++.-.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFr---qQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFR---QQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred cccccccccchhHHHHHHHHHH---hhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 4555666799999999999999 88999999999999999999999999999999999886665443
No 14
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.68 E-value=1.8e-08 Score=101.95 Aligned_cols=64 Identities=22% Similarity=0.325 Sum_probs=58.3
Q ss_pred cccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHH
Q 012938 353 RQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIE 419 (453)
Q Consensus 353 rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~ 419 (453)
+++++.|+.|+..++..|+.-|. .--|.+..||..||...|||..||..||+|||+|+|+...+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~---~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFE---KQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHH---HhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 55677889999999999999999 88999999999999999999999999999999997665554
No 15
>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=98.67 E-value=3.2e-08 Score=78.02 Aligned_cols=52 Identities=13% Similarity=0.219 Sum_probs=49.5
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 012938 356 WRPIRGLPETSVGILRSWLFEHFLHPY----PNDSEKQLLASQTGLTKNQVSNWFINAR 410 (453)
Q Consensus 356 ~R~Rr~Lpk~~~~iLraWf~eH~~nPY----PS~eeK~~LAk~TGLS~sQVsNWFiNaR 410 (453)
+|+|+.|+.+++..|+..|. .++| |+..++..||..+||++.+|..||+|.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe---~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAE---KLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHH---HcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 57889999999999999999 8999 9999999999999999999999999964
No 16
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.65 E-value=2.2e-08 Score=97.59 Aligned_cols=62 Identities=27% Similarity=0.352 Sum_probs=57.9
Q ss_pred cccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 353 RQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 353 rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
++.|++|+-++.-+...|++-|. +..|..-.||.+||..+|||..||+.||+|+|-|+||-+
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQ---kTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQ---QTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHh---hcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 56788999999999999999999 889999999999999999999999999999999987743
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.61 E-value=3.1e-08 Score=98.15 Aligned_cols=61 Identities=25% Similarity=0.430 Sum_probs=57.1
Q ss_pred cccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 353 RQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 353 rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
+..+|||+.|+.++.+.|++-|. .|.|.++.-|..||.++||.+.||..||+|+|.++||.
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~---enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQ---ENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred chhcCccccccHHHHHHHHHHHh---hhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 45678999999999999999999 78999999999999999999999999999999999873
No 18
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.55 E-value=4.7e-08 Score=94.86 Aligned_cols=65 Identities=25% Similarity=0.285 Sum_probs=59.5
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHH
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEM 421 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el 421 (453)
+++|+|+.|+..|+..|+.-|. ...|.+..||.-||+++.||+.||+.||+|+|.+.|+....++
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe---~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFE---LKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHH---HHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 5678899999999999999999 8899999999999999999999999999999999888775443
No 19
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.52 E-value=9.8e-08 Score=91.45 Aligned_cols=62 Identities=27% Similarity=0.280 Sum_probs=55.4
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHH
Q 012938 355 VWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIE 419 (453)
Q Consensus 355 ~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~ 419 (453)
.++++++|+.+++..|+.-|. .+-|..++.|..||++.||...||..||+|+|.|.+.+-.+
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~---~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFE---SEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred cccccccccHHHHHHhHHhhc---cccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 456678899999999999999 77888999999999999999999999999999998665543
No 20
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.46 E-value=3.1e-07 Score=88.72 Aligned_cols=78 Identities=19% Similarity=0.246 Sum_probs=64.9
Q ss_pred cccccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHHHHhhcC
Q 012938 349 FHSQRQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMYREEFAD 428 (453)
Q Consensus 349 ~~~~rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~~e~~~~ 428 (453)
++.++.-++||+.|+..+...|++-|. ...|.+.+|+.+++....||..||..||+|+|.|.|+---.|.-+-.++-
T Consensus 138 LrKhk~nRkPRtPFTtqQLlaLErkfr---ekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~kmaa 214 (246)
T KOG0492|consen 138 LRKHKPNRKPRTPFTTQQLLALERKFR---EKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKLKMAA 214 (246)
T ss_pred hcccCCCCCCCCCCCHHHHHHHHHHHh---HhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHhhhhh
Confidence 344556678999999999999999999 77999999999999999999999999999999998775555444444443
Q ss_pred C
Q 012938 429 S 429 (453)
Q Consensus 429 ~ 429 (453)
.
T Consensus 215 ~ 215 (246)
T KOG0492|consen 215 K 215 (246)
T ss_pred c
Confidence 3
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.45 E-value=1.1e-07 Score=98.52 Aligned_cols=60 Identities=22% Similarity=0.314 Sum_probs=56.5
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
++||||+.+.-.++..|+..|. .||.|+.+|.-.||.+.+|.+..|++||+|||.|+|+.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~---~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFL---KNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred cccccccceeHHHHHHHHHHHH---hCCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 5677889999999999999999 89999999999999999999999999999999999874
No 22
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.42 E-value=2.3e-07 Score=90.07 Aligned_cols=63 Identities=21% Similarity=0.357 Sum_probs=57.9
Q ss_pred ccccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 350 HSQRQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 350 ~~~rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
...|+.+|.|+.|+..+..+|++-|. ..-||....+++||.+.+|.+.+|.+||+|+|.+.++
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~---kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~ 94 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFA---KTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRR 94 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHH---hhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhH
Confidence 34566778899999999999999999 7899999999999999999999999999999999765
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.33 E-value=6.5e-07 Score=82.96 Aligned_cols=61 Identities=20% Similarity=0.278 Sum_probs=55.7
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..+++|+..+..++.+|+.-|. .+|||+..+|..|+..++++++-|+.||+|+|.+.++.-
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~---i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFE---INPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred cCcccceechHHHHHHHHHHhc---cCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 3456778889999999999999 999999999999999999999999999999999987644
No 24
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.31 E-value=5.2e-07 Score=89.88 Aligned_cols=62 Identities=23% Similarity=0.193 Sum_probs=56.1
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHH
Q 012938 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEM 421 (453)
Q Consensus 357 R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el 421 (453)
+-|-.++..++-.|+.-|. .++|.+..-|.+||..+|||+.||+.||+|+|.|.+|..-+..
T Consensus 201 KYRvVYTDhQRLELEKEfh---~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFH---TSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ceeEEecchhhhhhhhhhc---cccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 4456799999999999999 9999999999999999999999999999999999987666554
No 25
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.31 E-value=1.3e-06 Score=76.78 Aligned_cols=64 Identities=20% Similarity=0.273 Sum_probs=56.3
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHH
Q 012938 356 WRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMY 422 (453)
Q Consensus 356 ~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~ 422 (453)
+|-|+.|+..+...|+..|. ...||..=.+++||.+..||+..|+.||+|+|.+++|.-.-..+
T Consensus 18 RRIRTTFTS~QLkELErvF~---ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 18 RRIRTTFTSAQLKELERVFA---ETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hhhhhhhhHHHHHHHHHHHH---hhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 34468999999999999999 67899999999999999999999999999999999876544444
No 26
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.25 E-value=4.4e-07 Score=85.07 Aligned_cols=69 Identities=20% Similarity=0.269 Sum_probs=58.1
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHHHHhhc
Q 012938 356 WRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMYREEFA 427 (453)
Q Consensus 356 ~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~~e~~~ 427 (453)
++.|+.|+..+...|+.-|. ...|.+-.|+.+||...+|+++||..||+|+|++-||...+..-+.+.+
T Consensus 101 ~K~Rtvfs~~ql~~l~~rFe---~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~~ 169 (194)
T KOG0491|consen 101 RKARTVFSDPQLSGLEKRFE---RQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSNG 169 (194)
T ss_pred hhhcccccCccccccHHHHh---hhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCCc
Confidence 34568899999999999999 7899999999999999999999999999999999887665444333333
No 27
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.22 E-value=1.1e-06 Score=87.23 Aligned_cols=59 Identities=22% Similarity=0.330 Sum_probs=53.3
Q ss_pred cCCC-CCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 355 VWRP-IRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 355 ~~R~-Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
.+|+ |+.|+..+...|+.-|. .--||..-.|++||.+|+|.+..|.+||+|+|.+.+|.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFk---eaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFK---EAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred ccccccchhhHHHHHHHHHHHh---hccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 3344 78999999999999999 67899999999999999999999999999999997553
No 28
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.10 E-value=2.1e-06 Score=87.08 Aligned_cols=61 Identities=25% Similarity=0.305 Sum_probs=54.9
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 355 VWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 355 ~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
.+|-|+-|+..+.+.|+.||. .|-||+.+.+++||.-|+||+..|++||+|+|.+.+|.-.
T Consensus 112 qrrQrthFtSqqlqele~tF~---rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQ---RNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHh---hccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 345668899999999999999 7999999999999999999999999999999999766443
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.10 E-value=2.3e-06 Score=86.16 Aligned_cols=63 Identities=24% Similarity=0.356 Sum_probs=57.1
Q ss_pred ccccccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 350 HSQRQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 350 ~~~rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
+.....+|||+.++.++...|+.-|. ..|.|....|++|+.+|||....|+.||+|+|.+.|+
T Consensus 162 ~gd~~nKRPRTTItAKqLETLK~AYn---~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKR 224 (383)
T KOG4577|consen 162 EGDASNKRPRTTITAKQLETLKQAYN---TSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKR 224 (383)
T ss_pred ccccccCCCcceeeHHHHHHHHHHhc---CCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHh
Confidence 34445789999999999999999999 8999999999999999999999999999999987643
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.98 E-value=1.5e-05 Score=85.84 Aligned_cols=57 Identities=23% Similarity=0.289 Sum_probs=54.2
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhh
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRL 413 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl 413 (453)
+.+|+|..|+..+++.|++.|. .++||+.+.-+.|+.+++|...-|.|||-|+|+|-
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFk---e~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFK---ENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHh---cCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 4567899999999999999999 88999999999999999999999999999999995
No 31
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.72 E-value=2.6e-05 Score=76.29 Aligned_cols=63 Identities=22% Similarity=0.292 Sum_probs=56.1
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHH
Q 012938 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMY 422 (453)
Q Consensus 357 R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~ 422 (453)
..|..|...+...|+.-|. ...||--+++.+||...|++++||.+||+|+|.+.+|+-.-|+.
T Consensus 169 ~srPTf~g~qi~~le~~fe---qtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 169 QSRPTFTGHQIYQLERKFE---QTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred ccCCCccchhhhhhhhhhh---hhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchh
Confidence 3456799999999999999 77899999999999999999999999999999998887766665
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.67 E-value=1.4e-05 Score=81.16 Aligned_cols=62 Identities=18% Similarity=0.304 Sum_probs=55.0
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
+.+|-|+.|+.+|...|+.-|+ +.-|-+...|.+||..++|.+..|+.||+|+|++.|+..+
T Consensus 180 qmRRYRTAFTReQIaRLEKEFy---rENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFY---RENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHH---HhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 4566788999999999988888 6678999999999999999999999999999999877554
No 33
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.60 E-value=5.7e-05 Score=77.95 Aligned_cols=61 Identities=25% Similarity=0.418 Sum_probs=55.2
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..+|.|+.|+..+...|+.||. .+|||....++.||++++++...|..||.|+|.|.+|..
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~---rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQ---RTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccchHHHHHHHhc---CCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3445578899999999999999 888999999999999999999999999999999987654
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.48 E-value=6.9e-05 Score=70.22 Aligned_cols=60 Identities=17% Similarity=0.055 Sum_probs=54.5
Q ss_pred ccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 354 QVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 354 q~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..+|.|+.|+..+.+.|+.-|. ..+||....++.||..+++++..|.+||+|+|.+.++.
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~---~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFE---KVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhc---CCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 4567788999999999999999 66999999999999999999999999999999997654
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.32 E-value=9.2e-05 Score=74.89 Aligned_cols=60 Identities=48% Similarity=0.669 Sum_probs=54.6
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 357 R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
+++.+++.+. .+|+.|+.+|..+|||++-++..++-.++++..||++||+|+|+|+.+.+
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 3456788888 99999999999999999999999999999999999999999999986544
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.11 E-value=0.00019 Score=72.68 Aligned_cols=58 Identities=22% Similarity=0.367 Sum_probs=51.7
Q ss_pred cCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 355 VWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 355 ~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
++|+|+.+-..-++-|+++|. ..|-|+.+....+|.+..|.+..|+.||+|.|.+.|+
T Consensus 309 kKRKRTSIAAPEKRsLEayFa---vQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFA---VQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred cccccccccCcccccHHHHhc---cCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 456666666667789999999 8999999999999999999999999999999999876
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.03 E-value=0.0038 Score=49.38 Aligned_cols=43 Identities=16% Similarity=0.373 Sum_probs=30.7
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 012938 367 VGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVR 412 (453)
Q Consensus 367 ~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~R 412 (453)
.+.|+.+|. .|.++.+.+...|+.+++|+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~---~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYL---KHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHH---HT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHH---HcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 345999999 6688999999999999999999999999876543
No 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=95.50 E-value=0.013 Score=54.94 Aligned_cols=63 Identities=27% Similarity=0.510 Sum_probs=56.1
Q ss_pred cccCCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 353 RQVWRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 353 rq~~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
...++++..+...+...+..-|. ..+||....+..|+..+|++...|.+||+|.|.+.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFR---ATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhccc---CCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34567788999999999999988 8999999999999999999999999999999999876544
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.22 E-value=0.28 Score=58.41 Aligned_cols=60 Identities=22% Similarity=0.296 Sum_probs=54.5
Q ss_pred CCCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 356 WRPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 356 ~R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
++.|+.+...++.+|+..|. ..-||+.++.+.|....+|.+..|..||+|+|.+-++...
T Consensus 904 ~a~~~~~~d~qlk~i~~~~~---~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 904 RAYRTQESDLQLKIIKACYE---AQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhccchhHHHHHHHHHHHh---hccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 44567788899999999999 7899999999999999999999999999999999888666
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=81.80 E-value=1.9 Score=49.29 Aligned_cols=44 Identities=25% Similarity=0.479 Sum_probs=41.6
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhh
Q 012938 367 VGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRL 413 (453)
Q Consensus 367 ~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl 413 (453)
+.+|+++|. .|+.|+.++...+|.+.||...-|+.||.+.+...
T Consensus 568 ~sllkayya---ln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYA---LNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHH---hcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh
Confidence 789999999 99999999999999999999999999999988764
No 41
>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=78.70 E-value=4.8 Score=30.95 Aligned_cols=46 Identities=20% Similarity=0.132 Sum_probs=30.7
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 012938 357 RPIRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINAR 410 (453)
Q Consensus 357 R~Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR 410 (453)
|+|+.|+-+.+-.+=.-+. ..+ -+..+|++.|++.++|++|..|+.
T Consensus 2 rkR~~LTl~eK~~iI~~~e---~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLE---EGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSS--HHHHHHHHHHHH---CTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCccCCHHHHHHHHHHHH---cCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 5677787777554444455 333 488999999999999999999954
No 42
>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=73.36 E-value=5 Score=28.01 Aligned_cols=46 Identities=20% Similarity=0.204 Sum_probs=35.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhc
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLW 414 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~ 414 (453)
.++.....++...+.+. -.-..+|..+|++...|..|....+.+++
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46777788887777522 23577899999999999999988887753
No 43
>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=72.64 E-value=6.6 Score=29.16 Aligned_cols=45 Identities=24% Similarity=0.310 Sum_probs=33.4
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhh
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRL 413 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl 413 (453)
.||+....++...+.+ . -.-.++|..+|+|...|.+|...+|+++
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 4788888888776662 2 3367899999999999999999998874
No 44
>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=72.50 E-value=4.9 Score=29.66 Aligned_cols=47 Identities=21% Similarity=0.324 Sum_probs=37.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
.||++...+|...|+ .++ .-.++|...|+|...|+.+...+..++++
T Consensus 4 ~L~~~er~vi~~~y~----~~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYF----EGL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHT----ST-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc----CCC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 588889999988875 232 26789999999999999999999888753
No 45
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=68.07 E-value=6.7 Score=30.81 Aligned_cols=45 Identities=18% Similarity=0.246 Sum_probs=30.4
Q ss_pred CCCCCChhHH-HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 012938 358 PIRGLPETSV-GILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINAR 410 (453)
Q Consensus 358 ~Rr~Lpk~~~-~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR 410 (453)
+++.|+++.+ .++...+. .......+|++.|++..+|.+|-.-.+
T Consensus 3 ~r~~ys~e~K~~~v~~~~~--------~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLE--------SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHH--------HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHH--------CCCceEeeecccccccccccHHHHHHh
Confidence 4567888874 45555555 456789999999999999999976665
No 46
>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=60.79 E-value=15 Score=22.71 Aligned_cols=39 Identities=13% Similarity=0.181 Sum_probs=26.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWF 406 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWF 406 (453)
+.++.+....+..++. +.+ ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~----~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLA----AGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHH----cCC----CHHHHHHHHCCCHHHHHHhC
Confidence 3456655555555544 333 36688899999999999984
No 47
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=56.26 E-value=16 Score=33.75 Aligned_cols=55 Identities=9% Similarity=0.222 Sum_probs=44.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMY 422 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~ 422 (453)
..||+..+.++..-+++ -++ -.++|..+|++...|.++..-+|.++++.+.+.+|
T Consensus 133 ~~Lp~~~R~v~~L~~~~----g~s----~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 187 (189)
T PRK12530 133 NHLPAQQARVFMMREYL----ELS----SEQICQECDISTSNLHVLLYRARLQLQACLSKNWF 187 (189)
T ss_pred HhCCHHHHHHHhHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35899999998877763 222 57899999999999999999999999988766554
No 48
>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=55.56 E-value=13 Score=31.12 Aligned_cols=48 Identities=21% Similarity=0.239 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
.||+....++..-+. ..++ -..+|+.+|+++..|.+|....+.++++.
T Consensus 110 ~L~~~~~~ii~~~~~----~g~s----~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYL----EGLS----YKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHh----cCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 578888888755444 3443 56899999999999999999999888753
No 49
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=55.05 E-value=15 Score=32.51 Aligned_cols=50 Identities=20% Similarity=0.177 Sum_probs=39.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++...+++ -++ -..+|..+|++...|.+|...+++++++.+
T Consensus 127 ~~L~~~~r~vl~l~~~~----~~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 127 ESLPEELRTAITLREIE----GLS----YEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35888888888765542 232 468999999999999999999999988755
No 50
>PRK06930 positive control sigma-like factor; Validated
Probab=54.64 E-value=14 Score=34.66 Aligned_cols=55 Identities=13% Similarity=0.072 Sum_probs=44.9
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHHH
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMYR 423 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~~ 423 (453)
.||+....++...+.+ .++ -..+|..+|++...|.++...+|.++++.+-++++|
T Consensus 114 ~L~~rer~V~~L~~~e----g~s----~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~l~~ 168 (170)
T PRK06930 114 VLTEREKEVYLMHRGY----GLS----YSEIADYLNIKKSTVQSMIERAEKKIARQINESLFC 168 (170)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 5888888888776652 222 468999999999999999999999999888777765
No 51
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=54.00 E-value=1.4e+02 Score=30.84 Aligned_cols=60 Identities=20% Similarity=0.292 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhhhhhccCccchhhhhHHHHHHHHHhhhHHhHHHHHHHHHH
Q 012938 238 KQELHLRIAKLISLLEEVESKYEIYYNQMEEVVSSYEVIAGLGAAKSYTSLALQAMSRHFCSLRDAIISQINIASR 313 (453)
Q Consensus 238 r~Elq~kkakLl~mL~ev~~ry~qy~~qmq~v~ssFe~~aGlgaa~~ytalal~amSrhfr~LrdaI~~qi~~~~~ 313 (453)
-.||+.+|..|..=++.+++|-.+...+|.. +| .| ..+.+.+..+..+|...+.++....
T Consensus 6 L~eL~qrk~~Lq~eIe~LerR~~ri~~Emrt---sF-----aG--------~Sq~lA~RVqGFkdYLvGsLQDLa~ 65 (283)
T PF11285_consen 6 LKELEQRKQALQIEIEQLERRRERIEKEMRT---SF-----AG--------QSQDLAIRVQGFKDYLVGSLQDLAQ 65 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---cc-----cc--------chHHHHHHHhhhHHHHHHHHHHHHH
Confidence 3689999999999999999998888877764 55 22 2244445556667777777765544
No 52
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=53.64 E-value=17 Score=32.03 Aligned_cols=52 Identities=17% Similarity=0.142 Sum_probs=40.5
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIE 419 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~ 419 (453)
..||+..+.++..-+.+ .++ -..+|...|++...|.+|..-+|.++++.+..
T Consensus 124 ~~L~~~~r~i~~l~~~~----~~~----~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 124 DALPVKQREVFLLRYVE----GLS----YREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred HhCCHHHHHHhhHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34788888888666552 222 47899999999999999999999999875543
No 53
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=53.55 E-value=15 Score=32.42 Aligned_cols=51 Identities=24% Similarity=0.191 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+..+.++...+.+. ++ -.++|..+|++...|.+++.-+|.++++.+-
T Consensus 105 ~~Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 105 RELPENYRDVVLAHYLEE----KS----YQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred HhCCHHHHHHHHHHHHhC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 358999999987766632 22 4589999999999999999999999877653
No 54
>PRK00118 putative DNA-binding protein; Validated
Probab=53.36 E-value=18 Score=31.99 Aligned_cols=50 Identities=10% Similarity=0.042 Sum_probs=40.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+.+..++..++.+ - -.-..+|+.+|+|+.-|.+|...+|.++++..
T Consensus 16 ~~L~ekqRevl~L~y~e----g----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 16 SLLTEKQRNYMELYYLD----D----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred ccCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35788889999888773 2 22567999999999999999999999986643
No 55
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=53.20 E-value=16 Score=31.65 Aligned_cols=48 Identities=23% Similarity=0.203 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
.||.....++...+. ..++ -.++|+.+|++...|.++...+|+++++.
T Consensus 113 ~L~~~~r~il~l~~~----~~~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRF----EGKS----YKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHH----cCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 578888888887655 2443 45699999999999999999999988764
No 56
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=52.99 E-value=17 Score=32.44 Aligned_cols=51 Identities=18% Similarity=0.094 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+....++..++.++ ++ -.++|..+|++...|.+|..-+|.++++.+-
T Consensus 107 ~~L~~~~r~v~~l~~~~g----~s----~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE----LT----YEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred HhCCHHHHHHHHhHHHhc----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 468999999998877633 22 5789999999999999999999999876543
No 57
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=52.47 E-value=16 Score=31.85 Aligned_cols=48 Identities=21% Similarity=0.099 Sum_probs=38.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
..||+..+.++..-|.+. ++ -.++|..+|++...|.+|...+|.++++
T Consensus 105 ~~L~~~~r~ii~l~~~~~----~s----~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 105 SVLDEKEKYIIFERFFVG----KT----MGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred HhCCHHHHHHHHHHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 358899999887666532 22 5789999999999999999999999865
No 58
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=51.39 E-value=17 Score=32.86 Aligned_cols=50 Identities=16% Similarity=0.280 Sum_probs=41.0
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++...+++ .++ -.++|..+|++...|.+++..+|.++++.+
T Consensus 128 ~~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 177 (179)
T PRK12514 128 EELEKDRAAAVRRAYLE----GLS----YKELAERHDVPLNTMRTWLRRSLLKLRECL 177 (179)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence 45899999988888772 233 578999999999999999999999987643
No 59
>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=49.50 E-value=15 Score=33.20 Aligned_cols=50 Identities=16% Similarity=0.098 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++..-+++ .+ .-.++|..+|++...|.++.-.+|+++++.+
T Consensus 137 ~~L~~~~r~v~~l~~~~----~~----s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 137 EALPEDLRTAITLRELE----GL----SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred HcCCHHHhhhhhhhhhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 45788888888766552 22 2578999999999999999999999987755
No 60
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=49.08 E-value=23 Score=26.90 Aligned_cols=26 Identities=19% Similarity=0.277 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhhhh
Q 012938 388 KQLLASQTGLTKNQVSNWFINARVRL 413 (453)
Q Consensus 388 K~~LAk~TGLS~sQVsNWFiNaR~Rl 413 (453)
...||+.+|++..+|+.|+.+...+.
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT----
T ss_pred HHHHHHHHCcCHHHHHHHHhcccccc
Confidence 67899999999999999999774443
No 61
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=47.80 E-value=19 Score=32.89 Aligned_cols=51 Identities=18% Similarity=0.240 Sum_probs=40.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||++...++..-+++ .++ -.++|..+|++...|.+|+..+|.++++.+.
T Consensus 140 ~~L~~~~~~v~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 140 AQLPESQRQVLELAYYE----GLS----QSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred HhCCHHHhhhhhhhhhc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35888888888776652 222 5789999999999999999999999987654
No 62
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=47.79 E-value=20 Score=33.05 Aligned_cols=50 Identities=12% Similarity=0.124 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.+|..-+.++ + .-.++|..+|++...|.+++..+|.++++.+
T Consensus 141 ~~L~~~~r~vl~l~~~~~----~----s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 141 DALTDTQRESVTLAYYGG----L----TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 468999999997766632 2 2578999999999999999999999987654
No 63
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=46.96 E-value=18 Score=32.82 Aligned_cols=51 Identities=14% Similarity=0.084 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+..+.++...+++. + .-.++|..+|++...|.+++..+|.++++.+-
T Consensus 130 ~~L~~~~r~v~~l~~~~g----~----s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 130 ETLPPRQRDVVQSISVEG----A----SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 468999999998877632 2 25789999999999999999999999876553
No 64
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=45.18 E-value=25 Score=32.15 Aligned_cols=50 Identities=24% Similarity=0.135 Sum_probs=40.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++..-+++ .+ .-.++|..+|++...|.++...+|.++++.+
T Consensus 138 ~~L~~~~r~i~~l~~~~----g~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 138 DTLPEKQREILILRVVV----GL----SAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred HhCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 46899999999876663 22 2678999999999999999999999987653
No 65
>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=45.09 E-value=27 Score=31.50 Aligned_cols=48 Identities=15% Similarity=0.136 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
.||++++.++...+++. ++ -.++|..+|++...|.+.+..+|.++++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG----LT----VEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999998887732 22 47899999999999999999999998764
No 66
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=44.68 E-value=25 Score=32.39 Aligned_cols=55 Identities=13% Similarity=0.196 Sum_probs=43.0
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMY 422 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~ 422 (453)
..||+..+.++...+.+ .+. -.++|..+|++...|.++...+|+++++.+....+
T Consensus 135 ~~L~~~~r~i~~L~~~~----g~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 135 YNLPENTARVFTLKEIL----GFS----SDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HhCCHHHHHHhhhHHHh----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 35888888888765553 222 47899999999999999999999999887754443
No 67
>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=44.08 E-value=37 Score=32.75 Aligned_cols=58 Identities=16% Similarity=0.076 Sum_probs=44.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEM 421 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el 421 (453)
..||+....+|...|.-+-..++ .-.++|..+|+|...|+.+...++.++++.+..+.
T Consensus 175 ~~L~~~er~vl~l~ygl~~~~~~----t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~ 232 (238)
T TIGR02393 175 ETLTERERKVLRMRYGLLDGRPH----TLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKK 232 (238)
T ss_pred HhCCHHHHHHHHHHhCCCCCCCc----cHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhH
Confidence 36899999999887731111232 36789999999999999999999999998865443
No 68
>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=42.13 E-value=29 Score=30.44 Aligned_cols=48 Identities=31% Similarity=0.273 Sum_probs=38.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
..||+....++..-+++ .++ -.++|..+|+|...|.++..-+|++++.
T Consensus 110 ~~L~~~~r~v~~l~~~~----g~~----~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR----GVS----LTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 46889999999885552 333 5689999999999999999999988865
No 69
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=41.73 E-value=35 Score=33.15 Aligned_cols=50 Identities=16% Similarity=0.209 Sum_probs=40.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.+|...|++. ++ -.++|..+|++...|.+|...++.++++.+
T Consensus 204 ~~L~~~~r~vl~l~~~~g----~s----~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 204 PVLSDREKSIIQCTFIEN----LS----QKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred HhCCHHHHHHHHHHHhCC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 358999999998877632 22 478999999999999999999999987644
No 70
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=41.40 E-value=30 Score=32.51 Aligned_cols=50 Identities=22% Similarity=0.288 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++..-+++. + .-.++|..+|++...|.+++..+|.++++.+
T Consensus 152 ~~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 152 EKLPEAQQTVVKGVYFQE----L----SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358999999998766632 2 2578999999999999999999999987654
No 71
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=41.40 E-value=33 Score=31.46 Aligned_cols=54 Identities=13% Similarity=0.114 Sum_probs=43.6
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEM 421 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el 421 (453)
..||+.++.++...+++. ++ -.++|..+|++..-|.+....+|+++++.+-.+.
T Consensus 130 ~~Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 130 DRLPPRTGRVFMMREWLE----LE----TEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HhCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 458999999997776632 22 4789999999999999999999999987666544
No 72
>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=40.00 E-value=28 Score=33.02 Aligned_cols=50 Identities=26% Similarity=0.350 Sum_probs=41.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++...|.+ .+ .-.++|..+|++...|..|...++.++++.+
T Consensus 177 ~~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 177 AALPERERRILLLRFFE----DK----TQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred HcCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 46899999999887762 22 3678999999999999999999999987644
No 73
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=39.64 E-value=30 Score=31.55 Aligned_cols=51 Identities=12% Similarity=0.160 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||++.+.++..-+++ .++ -.++|+.+|++...|.++...+|.++++.+-
T Consensus 127 ~~L~~~~r~i~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 127 AALPERQREAIVLQYYQ----GLS----NIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred HhCCHHHHHHhhHHHhc----CCC----HHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45788888888766552 222 5689999999999999999999998876443
No 74
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=39.19 E-value=37 Score=32.98 Aligned_cols=50 Identities=18% Similarity=0.172 Sum_probs=41.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++...|++.+ .-.++|..+|++...|+.+...++.++++.+
T Consensus 204 ~~L~~~~r~ii~l~~~~g~--------s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 204 PILSEREKSIIHCTFEENL--------SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred HcCCHHHHHHHHHHHcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4689999999988876432 2478999999999999999999999987754
No 75
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=39.18 E-value=30 Score=31.15 Aligned_cols=50 Identities=16% Similarity=0.147 Sum_probs=39.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++..-+++ .++ -.++|..+|++...|.+++..+|+++++.+
T Consensus 135 ~~L~~~~r~v~~l~~~~----g~s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 135 QALPPKYRMVIVLKYME----DLS----LKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred HhCCHHHhHHhhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 46888998998764442 233 578999999999999999999999987643
No 76
>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=39.16 E-value=34 Score=30.60 Aligned_cols=49 Identities=12% Similarity=0.119 Sum_probs=39.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
.||+....++..-+++. ++ -..+|..+|+|...|.++..-+|.++++.+
T Consensus 119 ~L~~~~r~i~~l~~~~g----~s----~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----LT----IKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 58888989987777632 22 568999999999999999999999987643
No 77
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=39.09 E-value=92 Score=22.00 Aligned_cols=48 Identities=17% Similarity=0.183 Sum_probs=35.2
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
.|++....++..+ . ..+ ....+|+.+|++...|..|....+.++.-.-
T Consensus 3 ~l~~~e~~i~~~~-~----~g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~~ 50 (58)
T smart00421 3 SLTPREREVLRLL-A----EGL----TNKEIAERLGISEKTVKTHLSNIMRKLGVRS 50 (58)
T ss_pred CCCHHHHHHHHHH-H----cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Confidence 4677777777554 3 122 3578999999999999999998887775433
No 78
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=38.78 E-value=32 Score=31.64 Aligned_cols=51 Identities=20% Similarity=0.225 Sum_probs=41.0
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||++.+.++...|.+. ++ -.++|..+|+|...|.+...-+|.++++..+
T Consensus 130 ~~L~~~~r~i~~l~~~~g----~s----~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG----EK----IEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HhCCHHHHHHHHHHHHcc----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 468999999998766632 22 5789999999999999999999999876543
No 79
>PRK04217 hypothetical protein; Provisional
Probab=38.15 E-value=57 Score=29.09 Aligned_cols=51 Identities=14% Similarity=0.125 Sum_probs=41.1
Q ss_pred CCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 359 IRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 359 Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
-..|+++.+.++..++.+.+ .-.++|+.+|++...|.+.+..++.+++..+
T Consensus 40 ~~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34688888989988877432 3677999999999999999999998886644
No 80
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=37.97 E-value=32 Score=30.53 Aligned_cols=48 Identities=19% Similarity=0.149 Sum_probs=39.4
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
..||+.+..++.-.+.+. ++ -.++|..+|++...|.++...+|.++++
T Consensus 111 ~~L~~~~r~v~~l~~~~~----~s----~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG----FS----YKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 468999999998866532 22 4689999999999999999999999865
No 81
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=37.87 E-value=32 Score=30.17 Aligned_cols=51 Identities=18% Similarity=0.131 Sum_probs=41.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+..+.++.--+++ .++ -.++|..+|++...|.+...-+|.++++.+-
T Consensus 105 ~~Lp~~~r~v~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 105 QKLPARQREAFLLRYWE----DMD----VAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred HhCCHHHHHHHHHHHHh----cCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999776663 233 5789999999999999999999999877554
No 82
>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=37.82 E-value=43 Score=30.95 Aligned_cols=54 Identities=13% Similarity=0.165 Sum_probs=43.1
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEM 421 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el 421 (453)
..||+..+.++..-+++. + .-.++|..+|++..-|.++..-+|+++++.+-...
T Consensus 130 ~~L~~~~r~v~~l~~~~g----~----s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~ 183 (188)
T TIGR02943 130 YHLPEQTARVFMMREVLG----F----ESDEICQELEISTSNCHVLLYRARLSLRACLSINW 183 (188)
T ss_pred HhCCHHHHHHHHHHHHhC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 368888988887776632 2 25789999999999999999999999988665443
No 83
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=37.74 E-value=46 Score=31.55 Aligned_cols=55 Identities=16% Similarity=0.276 Sum_probs=44.4
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMY 422 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~ 422 (453)
..||++.+.++..-+++. ++ -.++|..+|++...|.++..-+|+++++.+....+
T Consensus 147 ~~L~~~~r~v~~L~~~~g----~s----~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 201 (206)
T PRK12544 147 DGLPAKYARVFMMREFIE----LE----TNEICHAVDLSVSNLNVLLYRARLRLRECLENKWF 201 (206)
T ss_pred HhCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 468888888887776632 22 47899999999999999999999999988765554
No 84
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=37.45 E-value=40 Score=30.58 Aligned_cols=50 Identities=16% Similarity=0.213 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++...+.+ .+. -.++|..+|++...|.++...+|.++++.+
T Consensus 134 ~~L~~~~r~vl~l~~~~----~~s----~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 134 KALSPEERRVIEVLYYQ----GYT----HREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 45899999999876663 222 578999999999999999999999987643
No 85
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=37.37 E-value=34 Score=31.93 Aligned_cols=51 Identities=20% Similarity=0.120 Sum_probs=41.6
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+....++...+++ .++ -.++|...|+|...|.+++.-+|.++++.+-
T Consensus 112 ~~Lp~~~r~v~~L~~~~----g~s----~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 112 AQLPDEQREALILVGAS----GFS----YEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred HhCCHHHhHHhhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 36899999999888763 233 4689999999999999999999999876553
No 86
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=37.35 E-value=38 Score=30.91 Aligned_cols=49 Identities=12% Similarity=0.129 Sum_probs=38.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||++.+.++..-+++ .++ -.++|..+|+|...|.+|...+|.++++.
T Consensus 132 ~~L~~~~r~i~~l~~~~----~~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHAYVD----GCS----HAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 45888888877666652 222 57899999999999999999999988754
No 87
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=37.33 E-value=43 Score=31.33 Aligned_cols=55 Identities=24% Similarity=0.229 Sum_probs=43.1
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMY 422 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~ 422 (453)
..||+..+.++..-+++ -++ -.++|..+|++...|.+....+|.++++.+-+..+
T Consensus 138 ~~Lp~~~r~v~~L~~~e----g~s----~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 138 DHLPEQIGRVFMMREFL----DFE----IDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35899999998776663 222 46899999999999999999999999887654433
No 88
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=37.17 E-value=38 Score=30.31 Aligned_cols=50 Identities=16% Similarity=0.046 Sum_probs=40.6
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++.-.+.+.+ . -.++|..+|++...|.++..-+|+++++.+
T Consensus 111 ~~L~~~~r~v~~l~~~~g~----s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 111 NLLSADQREAIILIGASGF----S----YEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred HhCCHHHHHHHHHHHHcCC----C----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999988776332 2 468999999999999999999999987543
No 89
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=36.99 E-value=47 Score=30.81 Aligned_cols=51 Identities=24% Similarity=0.153 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIE 419 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~ 419 (453)
..|++.++.+|+. +. ..+. -.++|..+|++...|++|..+++.++++-...
T Consensus 5 ~~Lt~rqreVL~l-r~----~GlT----q~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 5 SFLTERQIEVLRL-RE----RGLT----QQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred cCCCHHHHHHHHH-HH----cCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999977 33 2332 56899999999999999999999998765543
No 90
>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=36.74 E-value=39 Score=29.82 Aligned_cols=49 Identities=20% Similarity=0.294 Sum_probs=39.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||+..+.++..-+++ .++ -.++|..+|++...|.++...+|.++++.
T Consensus 109 ~~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 109 RRLPARQRAVVVLRYYE----DLS----EAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred HhCCHHHHHHhhhHHHh----cCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 35888888888776663 332 46789999999999999999999998764
No 91
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=36.33 E-value=47 Score=30.41 Aligned_cols=50 Identities=14% Similarity=0.189 Sum_probs=40.1
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....+|..-+++ .++ -.++|...|++...|.+-+..+|.++++.+
T Consensus 130 ~~L~~~~r~vl~l~~~~----~~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 130 AKLSPAHREIIDLVYYH----EKS----VEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46899999999776662 222 578999999999999999999998887643
No 92
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=36.11 E-value=36 Score=32.64 Aligned_cols=50 Identities=22% Similarity=0.290 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++..-|++. + .-.++|..+|++...|.++...+|+++++.+
T Consensus 183 ~~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 183 ESLPEREQLVLSLYYQEE----L----NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred HhCCHHHHHHHHhHhccC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358999999997776632 2 3578999999999999999999999997744
No 93
>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=36.01 E-value=81 Score=23.85 Aligned_cols=52 Identities=17% Similarity=0.178 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHH
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEM 421 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el 421 (453)
.|++....+|+.+.. .+. ..++|...|++++.|.++..+.+.|+.-+-..++
T Consensus 3 ~LT~~E~~vl~~l~~-----G~~----~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l 54 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ-----GMS----NKEIAEELGISEKTVKSHRRRIMKKLGVKNRAEL 54 (58)
T ss_dssp SS-HHHHHHHHHHHT-----TS-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHH
T ss_pred ccCHHHHHHHHHHHh-----cCC----cchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHH
Confidence 478888889976644 443 5789999999999999999999999865444443
No 94
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=35.88 E-value=42 Score=30.54 Aligned_cols=51 Identities=18% Similarity=0.059 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+....++...+.++ ++ -.++|..+|++...|.+.+..+|.++++.+.
T Consensus 128 ~~L~~~~r~v~~l~~~~g----~s----~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~ 178 (181)
T PRK12536 128 EQLPDRQRLPIVHVKLEG----LS----VAETAQLTGLSESAVKVGIHRGLKALAAKIR 178 (181)
T ss_pred HHCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 357888888876665532 22 5789999999999999999999999887553
No 95
>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=35.18 E-value=25 Score=32.28 Aligned_cols=51 Identities=22% Similarity=0.233 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+....++...+.+ -++ -.++|..+|++...|.++..-+|.++++.+-
T Consensus 130 ~~Lp~~~r~i~~L~~~~----g~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 130 QGLPEEFRQAVYLADVE----GFA----YKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred HhCCHHHhhheeehhhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35788888777655552 222 5689999999999999999999999987664
No 96
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=34.98 E-value=46 Score=30.01 Aligned_cols=48 Identities=8% Similarity=0.113 Sum_probs=39.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
..||++.+.++...+++. .+ -.++|..+|++..-|.++...++++++.
T Consensus 118 ~~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 468999999998776632 22 4689999999999999999999999854
No 97
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=34.94 E-value=44 Score=30.85 Aligned_cols=51 Identities=22% Similarity=0.249 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+....++...+.+. .+ -.++|..+|++...|.+.+..+|+++++.+-
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 568999999998766532 22 4689999999999999999999988876543
No 98
>cd00131 PAX Paired Box domain
Probab=34.89 E-value=1.3e+02 Score=27.00 Aligned_cols=46 Identities=13% Similarity=-0.006 Sum_probs=31.5
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC-------Chhhhhhhhhhh
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGL-------TKNQVSNWFINA 409 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGL-------S~sQVsNWFiNa 409 (453)
.+.......+..+.. .||.-+..|-..+-...|+ +.+.|+.||.++
T Consensus 75 ~~~~~~~~~i~~~v~---~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQ---ENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHH---HCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 344455555666666 7888888777665335576 899999998764
No 99
>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=34.32 E-value=55 Score=32.17 Aligned_cols=59 Identities=20% Similarity=0.332 Sum_probs=45.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHHHHhhc
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMYREEFA 427 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~~e~~~ 427 (453)
..||+..+.++.-.+++.+. -.++|..+|++..-|.++...+|.++++.+.++. .+..+
T Consensus 160 ~~Lp~~~R~v~~L~~~eg~S--------~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~-~~~~~ 218 (244)
T TIGR03001 160 AALSERERHLLRLHFVDGLS--------MDRIGAMYQVHRSTVSRWVAQARERLLERTRRRL-AERLK 218 (244)
T ss_pred HhCCHHHHHHHHHHHHcCCC--------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH-HHhcC
Confidence 46899999999888774322 4689999999999999999999999988665443 34443
No 100
>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=34.12 E-value=43 Score=31.82 Aligned_cols=49 Identities=22% Similarity=0.285 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||+....+|...|++. + .-.++|..+|++...|..+...++.++++.
T Consensus 174 ~~L~~~~r~il~l~y~~~----~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 174 ESLSEREQLVLSLYYYEE----L----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred HhCCHHHHHHHHHHHhCC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 458999999998887632 2 257899999999999999999999998764
No 101
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=33.93 E-value=64 Score=28.51 Aligned_cols=49 Identities=16% Similarity=0.230 Sum_probs=38.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....+|..-+ + .++ -.++|..+|++...|.++...+|.++++.+
T Consensus 111 ~~L~~~~r~il~l~~-~----g~s----~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 111 AKMTERDRTVLLLRF-S----GYS----YKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred HcCCHHHHHHHHHHH-c----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 357888888876655 3 333 578999999999999999999999987754
No 102
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=33.93 E-value=99 Score=26.72 Aligned_cols=47 Identities=19% Similarity=0.100 Sum_probs=37.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
..|++...++|+-+.. .|. ..++|+..+++.+.|.+|..|.|+++.-
T Consensus 148 ~~lt~~e~~vl~l~~~-----g~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKLITE-----GYT----NRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHHHHC-----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3488889999987532 232 5789999999999999999999999843
No 103
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=33.36 E-value=48 Score=30.66 Aligned_cols=50 Identities=14% Similarity=0.083 Sum_probs=40.6
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++..-+++ .|+ -.++|..+|++...|.+++.-+|+++++.+
T Consensus 135 ~~L~~~~r~i~~L~~~~----g~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 135 AALPERQRQAVVLRHIE----GLS----NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 36899999888776652 333 568999999999999999999999987654
No 104
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=33.34 E-value=96 Score=27.28 Aligned_cols=43 Identities=12% Similarity=0.334 Sum_probs=33.8
Q ss_pred ChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 012938 363 PETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINA 409 (453)
Q Consensus 363 pk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNa 409 (453)
....+..+.+|+.+|+..| ++ -..||+.+|+++..+..+|...
T Consensus 7 ~~~~i~~~~~~I~~~~~~~-~s---l~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 7 DAITIHSILDWIEDNLESP-LS---LEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cHHHHHHHHHHHHHhcCCC-CC---HHHHHHHHCcCHHHHHHHHHHH
Confidence 3444567779999998777 45 5778899999999999998855
No 105
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=32.99 E-value=52 Score=29.06 Aligned_cols=50 Identities=16% Similarity=0.161 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++..-|++ .++ -.++|..+|++...|.....-+|+++++.+
T Consensus 108 ~~L~~~~r~v~~l~~~~----~~s----~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 108 SELPARTRYAFEMYRLH----GET----QKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35899999999776662 222 578999999999999999988988887654
No 106
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=32.32 E-value=48 Score=32.19 Aligned_cols=49 Identities=16% Similarity=0.156 Sum_probs=40.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||+..+.++...|++ .+ .-..+|..+|+|...|.+++..+|.++++.
T Consensus 200 ~~L~~~~r~vl~l~~~~----~~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 200 KQLSEKEQLVISLFYKE----EL----TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred hcCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45899999999877762 22 257899999999999999999999998763
No 107
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=32.02 E-value=56 Score=30.34 Aligned_cols=51 Identities=16% Similarity=0.094 Sum_probs=41.1
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+....++...+++ -|+ -.++|..+|++...|.++...+|.++++.+.
T Consensus 115 ~~Lp~~~r~i~~L~~~~----g~s----~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 115 DQLPDDQREAIILVGAS----GFA----YEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35899999998777663 333 4589999999999999999999999877554
No 108
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=31.98 E-value=55 Score=32.20 Aligned_cols=50 Identities=20% Similarity=0.352 Sum_probs=41.6
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.+|...|++. -.-.++|..+|++...|......++.++++.+
T Consensus 211 ~~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 211 KTLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 468999999998887732 22678999999999999999999999987765
No 109
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=31.29 E-value=49 Score=32.52 Aligned_cols=50 Identities=18% Similarity=0.161 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.+|...|.+ .+ .-..+|..+|++...|+.+..-++.++++.+
T Consensus 202 ~~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 202 AQLEERTREVLEFVFLH----DL----TQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred HcCCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 46888888898877763 22 3578999999999999999999999987654
No 110
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.19 E-value=51 Score=29.67 Aligned_cols=50 Identities=16% Similarity=0.131 Sum_probs=38.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||.....+|..-+. ..++ -.++|..+|++...|.++...+|+++++.+
T Consensus 135 ~~L~~~~r~il~l~~~----~~~s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 135 LQLPEKYRTVIVLKYI----EDLS----LKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred HhCCHHHHHHhhhHHh----hCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578888888854433 1332 578999999999999999999999987644
No 111
>PF13518 HTH_28: Helix-turn-helix domain
Probab=30.98 E-value=45 Score=24.09 Aligned_cols=24 Identities=21% Similarity=0.443 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhh
Q 012938 388 KQLLASQTGLTKNQVSNWFINARV 411 (453)
Q Consensus 388 K~~LAk~TGLS~sQVsNWFiNaR~ 411 (453)
...+|++.|++..+|.+|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 567999999999999999887665
No 112
>KOG0809 consensus SNARE protein TLG2/Syntaxin 16 [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.92 E-value=1.7e+02 Score=30.71 Aligned_cols=61 Identities=20% Similarity=0.274 Sum_probs=47.8
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHhhh-----hhhccCccchhhhhHHHHHHHHHhhhHHhHHHHHHH
Q 012938 250 SLLEEVESKYEIYYNQMEEVVSSYE-----VIAGLGAAKSYTSLALQAMSRHFCSLRDAIISQINI 310 (453)
Q Consensus 250 ~mL~ev~~ry~qy~~qmq~v~ssFe-----~~aGlgaa~~ytalal~amSrhfr~LrdaI~~qi~~ 310 (453)
.+=.++..-+.+|+..|+.+.++.. -.-..-++..|-++.||+.|..||.+....+..|+.
T Consensus 104 ~ltq~Itqll~~cqk~iq~~~a~~n~~~~~e~~~~~n~~~~la~~LQ~~s~~fR~~Qs~YLK~l~~ 169 (305)
T KOG0809|consen 104 ELTQEITQLLQKCQKLIQRLSASLNQLSPSERLLRKNAQGYLALQLQTLSREFRGLQSKYLKRLRN 169 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3346777777899999999999874 222333678899999999999999998888877773
No 113
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=30.29 E-value=64 Score=31.37 Aligned_cols=51 Identities=18% Similarity=0.100 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+..+.++...+++ .++ -.++|..+|++...|.++...+|.++++.+-
T Consensus 170 ~~Lp~~~R~v~~L~~~e----g~s----~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 170 QRLPEQQRIAVILSYHE----NMS----NGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred HhCCHHHHHHhhhHHhc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35788888887666552 222 5789999999999999999999999987654
No 114
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=29.64 E-value=94 Score=28.76 Aligned_cols=49 Identities=22% Similarity=0.127 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||+....++...+++ -++ -.++|..+|++..-|.++..-+|.++++.
T Consensus 110 ~~Lp~~~R~v~~L~~~e----g~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 110 FDLPEEQRAALHLVAIE----GLS----YQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 35899999999887763 333 56899999999999999999999888753
No 115
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=29.54 E-value=31 Score=31.64 Aligned_cols=50 Identities=16% Similarity=0.167 Sum_probs=39.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++...++ ..++ -.++|..+|++...|.++...+|+++++.+
T Consensus 138 ~~L~~~~r~i~~l~~~----~g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 138 ETLPDEQREVFLLREH----GDLE----LEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred HhCCHhHhhheeeehc----cCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578888888866544 2333 568999999999999999999999987754
No 116
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=29.22 E-value=66 Score=29.09 Aligned_cols=50 Identities=20% Similarity=0.251 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++..-+.+ -|+ -.++|..+|++...|.++..-+|.++++.+
T Consensus 99 ~~L~~~~r~v~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 99 KELPDEYREAIRLTELE----GLS----QQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46899999998776652 333 578999999999999999999998887644
No 117
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=29.20 E-value=92 Score=28.29 Aligned_cols=54 Identities=13% Similarity=0.096 Sum_probs=43.0
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEM 421 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el 421 (453)
..||+..+.++..-+++++ .-.++|..+|++...|.+....+|.++++.+-...
T Consensus 116 ~~Lp~~~r~i~~l~~~e~~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 169 (179)
T PRK12543 116 HKLPYKLRQVIILRYLHDY--------SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE 169 (179)
T ss_pred HhCCHHHHHHHHHHHHccC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3589999988887666332 25789999999999999999999999987665443
No 118
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=28.78 E-value=1.1e+02 Score=29.02 Aligned_cols=50 Identities=16% Similarity=0.153 Sum_probs=39.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++..-+++ .++ -.++|..+|++..-|.++..-+|+++++.+
T Consensus 137 ~~L~~~~r~v~~L~~~~----g~s----~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 137 DSLPPEFRAAVVLCDIE----GLS----YEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35888888877665552 333 478999999999999999999999987654
No 119
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=28.50 E-value=1.2e+02 Score=29.21 Aligned_cols=50 Identities=20% Similarity=0.158 Sum_probs=41.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++...+.++ |+ -.++|..+|++...|.++...+|+++++.+
T Consensus 133 ~~Lp~~~R~v~~L~y~eg----~s----~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 133 AKLPVEYREVLVLRELED----MS----YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred HcCCHHHHhHhhhHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 468999999998877733 33 468999999999999999999999987755
No 120
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=28.15 E-value=66 Score=29.33 Aligned_cols=50 Identities=24% Similarity=0.329 Sum_probs=40.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++...+++. |+ -.++|..+|++...|.+....+|.++++.+
T Consensus 121 ~~L~~~~r~i~~l~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 121 KELNESNRQVFKYKVFYN----LT----YQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HhCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 458999999998765522 22 468999999999999999999999987654
No 121
>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=28.12 E-value=60 Score=30.87 Aligned_cols=49 Identities=18% Similarity=0.170 Sum_probs=39.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||+....++...|.+ + ..-.++|..+|+|...|..+-..+..|+++.
T Consensus 182 ~~L~~~e~~i~~~~~~~----~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~ 230 (231)
T TIGR02885 182 SKLDERERQIIMLRYFK----D----KTQTEVANMLGISQVQVSRLEKKVLKKMKEK 230 (231)
T ss_pred HcCCHHHHHHHHHHHHc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 46899999998877652 2 2378899999999999999998888887653
No 122
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=27.69 E-value=1.1e+02 Score=31.47 Aligned_cols=54 Identities=19% Similarity=0.116 Sum_probs=42.2
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.+|..-|.-+...++ .-.++|..+|++...|+.+...++.++++.+
T Consensus 261 ~~L~~~~R~vl~lrygL~~~e~~----s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 261 FELNDKQREVLARRFGLLGYEAA----TLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred HcCCHHHHHHHHHHhccCCCCCc----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46899999999766522223333 3688999999999999999999999998755
No 123
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=27.44 E-value=73 Score=29.07 Aligned_cols=50 Identities=16% Similarity=0.111 Sum_probs=40.5
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++..-+++. + .-.++|..+|++...|.++.-.+|+++++.+
T Consensus 130 ~~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLEG----L----SVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred HhCCHHHHHHHHHHHHcC----C----cHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 468999999998766632 2 2568999999999999999999999987644
No 124
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=27.43 E-value=1.6e+02 Score=25.76 Aligned_cols=45 Identities=18% Similarity=0.120 Sum_probs=30.4
Q ss_pred CCCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 012938 359 IRGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINAR 410 (453)
Q Consensus 359 Rr~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR 410 (453)
++.++.+.+...-.... .+.++ ...+|++.|++..+|.+|..-.+
T Consensus 10 rr~ys~EfK~~aV~~~~---~~g~s----v~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSF---EPGMT----VSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCHHHHHHHHHHHH---cCCCC----HHHHHHHHCcCHHHHHHHHHHHh
Confidence 45677776543333333 34443 67889999999999999966544
No 125
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.09 E-value=67 Score=29.59 Aligned_cols=49 Identities=22% Similarity=0.281 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
.||+..+.++..-++ ..+| -.++|...|++...|.+.+..+|.++++.+
T Consensus 106 ~L~~~~r~i~~l~~~----~g~~----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTEL----EGLS----QKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHh----cCCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 588888888866655 2333 578999999999999999999998887644
No 126
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=26.71 E-value=4.5e+02 Score=23.89 Aligned_cols=72 Identities=14% Similarity=0.039 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhhhhhhccCccchhhhhHHHHHHHHHhhhHHhHHHHHHH
Q 012938 238 KQELHLRIAKLISLLEEVESKYEIYYNQMEEVVSSYEVIAGLGAAKSYTSLALQAMSRHFCSLRDAIISQINI 310 (453)
Q Consensus 238 r~Elq~kkakLl~mL~ev~~ry~qy~~qmq~v~ssFe~~aGlgaa~~ytalal~amSrhfr~LrdaI~~qi~~ 310 (453)
+..++..|.+|+.+-.+...+.++..+.++.....|.-.+-. +...+..-...+...+.+.+-..|-..+..
T Consensus 3 ~~~~~~fk~~L~~~k~~l~~~~~~~~~~~~~~~~~~~d~aD~-a~~~~~~~~~~~~~~r~r~~l~~i~~al~r 74 (120)
T COG1734 3 KEQLEHFKNKLLEWKKDLLEELEQTEEHLQDENEASPDPADR-ATQEEERELELRLRDRERKLLRKIESALDR 74 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCchhhh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788899999999999999999999988744444222211 112233333333333444444444444443
No 127
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=26.49 E-value=1.5e+02 Score=31.99 Aligned_cols=61 Identities=16% Similarity=0.155 Sum_probs=47.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHHHHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEEMYRE 424 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~el~~e 424 (453)
..||+..+.+|+..|.-+-..|+. -..+|..+|+|...|+.+...++.++++|......++
T Consensus 349 ~~L~~reR~VI~LRygl~d~~~~T----l~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~ 409 (415)
T PRK07598 349 ADLTSRERDVIRMRFGLADGHTYS----LAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRD 409 (415)
T ss_pred HhCCHHHHHHHHHHHhcCCCCCCC----HHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHH
Confidence 458999999998877522123442 6789999999999999999999999998876655544
No 128
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=26.20 E-value=78 Score=28.30 Aligned_cols=50 Identities=14% Similarity=0.189 Sum_probs=40.6
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....+|..-+++ .++ -.++|..+|++..-|.+...-+|.++++.+
T Consensus 117 ~~L~~~~r~vl~L~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 117 AQLSPEHRAVLVRSYYR----GWS----TAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 35899999999877663 233 568999999999999999999999987654
No 129
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=26.19 E-value=72 Score=29.13 Aligned_cols=50 Identities=22% Similarity=0.160 Sum_probs=38.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++..-+. ..|+ -.++|..+|++...|.+....+|+++++.+
T Consensus 137 ~~L~~~~r~v~~l~~~----~g~s----~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 137 QQLPEDLRTALTLREF----DGLS----YEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred HhCCHHHhHHHhhHHh----cCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3478887777765444 3444 578999999999999999999999987654
No 130
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=25.90 E-value=72 Score=29.87 Aligned_cols=52 Identities=13% Similarity=0.061 Sum_probs=41.4
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIE 419 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~ 419 (453)
..||+....++..-+++++ .-.++|..+|++...|.++...+|+++++.+-.
T Consensus 132 ~~Lp~~~r~v~~l~~~~g~--------s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 132 DALPPERREALILTQVLGY--------TYEEAAKIADVRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred HcCCHHHHHHhhhHHHhCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 4589999888877766332 256899999999999999999999998765543
No 131
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=25.80 E-value=89 Score=28.09 Aligned_cols=51 Identities=14% Similarity=0.177 Sum_probs=39.6
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+....++..-+.+ .++ -.++|..+|++...|.++...+|+++++.+-
T Consensus 118 ~~L~~~~r~i~~l~~~~----~~s----~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 168 (173)
T PRK12522 118 QLLNEKYKTVLVLYYYE----QYS----YKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168 (173)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45788888887655542 222 4789999999999999999999999987654
No 132
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=25.80 E-value=1.2e+02 Score=28.83 Aligned_cols=54 Identities=15% Similarity=0.075 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++..-|+-+....+ .-.++|..+|++...|.++...+|.++++.+
T Consensus 177 ~~Lp~~~R~v~~L~y~l~~~eg~----s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 177 KKLSDREKQIMELRFGLNGGEEK----TQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred HhCCHHHHHHHHHHhccCCCCCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46899998888776521111222 2578999999999999999999999987753
No 133
>PF13551 HTH_29: Winged helix-turn helix
Probab=25.77 E-value=1.5e+02 Score=24.32 Aligned_cols=51 Identities=18% Similarity=0.086 Sum_probs=30.8
Q ss_pred CCCCCCChhHHHHHHHHHHhhcCCC--CCCHHHHHH-H-HHHh--CCChhhhhhhhh
Q 012938 357 RPIRGLPETSVGILRSWLFEHFLHP--YPNDSEKQL-L-ASQT--GLTKNQVSNWFI 407 (453)
Q Consensus 357 R~Rr~Lpk~~~~iLraWf~eH~~nP--YPS~eeK~~-L-Ak~T--GLS~sQVsNWFi 407 (453)
+++..++++....|.+++.++.... ..+...-.. | .+.+ .++...|..|+.
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 4444499999999999999553222 233333333 3 3333 467777777764
No 134
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=25.73 E-value=72 Score=29.33 Aligned_cols=48 Identities=15% Similarity=-0.004 Sum_probs=39.4
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
..||++++.++.-.+++. ++ -.++|..+|++...|.++..-+|.++++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLG----LS----YADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 468999999997776632 22 4689999999999999999999999876
No 135
>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=25.66 E-value=77 Score=27.95 Aligned_cols=49 Identities=16% Similarity=0.089 Sum_probs=38.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||+..+.++...+++ .++ -.++|+.+|++...|.+...-+|.++++.
T Consensus 121 ~~L~~~~r~vl~l~~~~----g~s----~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQ----NLP----IAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred HhCCHHHHHHHHHHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 46889999999876652 333 57899999999999999998888887753
No 136
>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=25.58 E-value=66 Score=23.33 Aligned_cols=21 Identities=19% Similarity=0.175 Sum_probs=18.3
Q ss_pred HHHHHhCCChhhhhhhhhhhh
Q 012938 390 LLASQTGLTKNQVSNWFINAR 410 (453)
Q Consensus 390 ~LAk~TGLS~sQVsNWFiNaR 410 (453)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 588999999999999998874
No 137
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=25.54 E-value=88 Score=27.65 Aligned_cols=50 Identities=20% Similarity=0.223 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
.||+....++...+.++ ++ -.++|..+|++..-|.+....+|.++++.+.
T Consensus 105 ~L~~~~r~v~~l~~~~~----~s----~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 105 ELPPACRDSFLLRKLEG----LS----HQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48999999998877733 22 5789999999999999999999988876543
No 138
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=24.81 E-value=36 Score=30.45 Aligned_cols=49 Identities=18% Similarity=0.180 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
.||+....+|..-++ ..++ -.++|..+|++...|.+.+..+|+++++.+
T Consensus 120 ~L~~~~r~vl~l~~~----~g~s----~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 120 TLSLEHRAVLVLHDL----EDLP----QKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hCCHHHeeeeeehHh----cCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888876554 2333 578999999999999999999999987754
No 139
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.78 E-value=2.2e+02 Score=20.98 Aligned_cols=46 Identities=17% Similarity=0.208 Sum_probs=30.2
Q ss_pred CCChhHHHHHHHHHHhh---cCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 012938 361 GLPETSVGILRSWLFEH---FLHPYPNDSEKQLLASQTGLTKNQVSNWFINAR 410 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH---~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR 410 (453)
+|+..++.++ .++..+ -...||+ ...||+.+|+++..|..+...-.
T Consensus 2 ~Ls~~~~~v~-~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 2 NLSPTAKLVY-LYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CCCHHHHHHH-HHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHH
Confidence 3555555555 223322 2337887 77899999999999988876443
No 140
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=24.76 E-value=72 Score=29.06 Aligned_cols=50 Identities=22% Similarity=0.289 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+..+.++..-+.+ .++ -.++|..+|++...|.++..-+|.++++.+
T Consensus 126 ~~L~~~~r~v~~l~~~~----g~s----~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 126 MSLPIKYREVIYLFYYE----ELS----IKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred HhCCHHHhhHhHhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46899999998776653 222 468999999999999999999999987644
No 141
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.48 E-value=84 Score=28.92 Aligned_cols=48 Identities=17% Similarity=0.110 Sum_probs=37.5
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||+..+.++.. +++ .|. -.++|..+|++...|.+.+..+|+++++.
T Consensus 154 ~~L~~~~r~vl~l-~~e----~~s----~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 154 ELLSELEKEVLEL-YLD----GKS----YQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred HhCCHHHHHHHHH-HHc----cCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4688888888877 552 232 57899999999999998888888887664
No 142
>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=23.90 E-value=1.5e+02 Score=23.19 Aligned_cols=50 Identities=22% Similarity=0.274 Sum_probs=35.8
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 012938 362 LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVR 412 (453)
Q Consensus 362 Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~R 412 (453)
|++.+..+|+.-+..=+ .-+|-...-..||.+.|+++.-++.-+.++=++
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 56777888877665332 234788889999999999999887655544333
No 143
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=23.86 E-value=91 Score=28.33 Aligned_cols=50 Identities=20% Similarity=0.283 Sum_probs=39.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++..-|.+ .++ -.++|..+|++...|.+....+|+++++.+
T Consensus 136 ~~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 136 AELEPPRSELIRTAFFE----GIT----YEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 45889888888777662 232 578999999999999999999999887643
No 144
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=23.86 E-value=90 Score=27.64 Aligned_cols=47 Identities=17% Similarity=0.230 Sum_probs=38.1
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhc
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLW 414 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~ 414 (453)
..||+.++.++...+++. ++ -.++|..+|++...|.++...+++++.
T Consensus 112 ~~L~~~~r~v~~L~~~~g----~s----~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVDG----LG----YGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HHCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 458999999997777632 22 468999999999999999999988864
No 145
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=23.85 E-value=86 Score=28.58 Aligned_cols=48 Identities=10% Similarity=0.041 Sum_probs=39.1
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
..||++++.++.-.+.+. |+ -.++|..+|++..-|.+.+..++.++..
T Consensus 126 ~~Lp~~~R~v~~L~~~~g----~s----~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 126 DTLRPRVKQAFLMATLDG----MK----QKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HhCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 458999999998877733 22 4789999999999999999998888754
No 146
>PRK05572 sporulation sigma factor SigF; Validated
Probab=23.82 E-value=85 Score=30.54 Aligned_cols=50 Identities=20% Similarity=0.189 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++...|++ . -.-..+|..+|++...|..+-..+..++++.+
T Consensus 201 ~~L~~~~~~v~~l~~~~----~----~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 201 RELDERERLIVYLRYFK----D----KTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred HcCCHHHHHHHHHHHhC----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 46899999998777652 1 23678999999999999999999999887654
No 147
>PF07765 KIP1: KIP1-like protein; InterPro: IPR011684 This is a group of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase []. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions []. It has also been suggested that the coiled-coils of the protein allow it to dimerise in vivo [].
Probab=23.68 E-value=1.2e+02 Score=25.69 Aligned_cols=31 Identities=29% Similarity=0.370 Sum_probs=22.8
Q ss_pred chHHHHH-HHHHHHHHHHHHHHHhHHHHHHHH
Q 012938 235 SAEKQEL-HLRIAKLISLLEEVESKYEIYYNQ 265 (453)
Q Consensus 235 ~~er~El-q~kkakLl~mL~ev~~ry~qy~~q 265 (453)
.++|.|. -+|+..|++||+++.+.|+-+.++
T Consensus 41 fakrAEmyy~kRp~Li~~vee~yr~YrsLAer 72 (74)
T PF07765_consen 41 FAKRAEMYYKKRPELISLVEEFYRSYRSLAER 72 (74)
T ss_pred HHHhhHHHhcccHHHHHHHHHHHHHHHHHHHh
Confidence 3456663 455679999999999999876653
No 148
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=23.56 E-value=1.5e+02 Score=28.40 Aligned_cols=56 Identities=16% Similarity=0.093 Sum_probs=41.1
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIE 419 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~ 419 (453)
..||+..+.++...++-+.... ..-+.+|..+|+|...|.+|...+++++++.+..
T Consensus 174 ~~Lp~~~R~i~~l~y~~~~~e~----~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~ 229 (233)
T PRK05803 174 DILDEREKEVIEMRYGLGNGKE----KTQREIAKALGISRSYVSRIEKRALKKLFKELYR 229 (233)
T ss_pred HhCCHHHHHHHHHHhCCCCCCC----cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999977553110112 2257899999999999999988899888776654
No 149
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=23.38 E-value=39 Score=29.40 Aligned_cols=47 Identities=26% Similarity=0.242 Sum_probs=35.6
Q ss_pred CCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 361 GLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 361 ~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
.||+....++...+.+ .-.-.++|..+|++...|.++..-+|.++++
T Consensus 105 ~L~~~~r~i~~l~~~~--------g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 105 RLPENYRTVLILREFK--------EFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hCCHhheeeeeehhhc--------cCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3677776766554441 2226789999999999999999999998865
No 150
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=23.04 E-value=88 Score=30.55 Aligned_cols=50 Identities=22% Similarity=0.219 Sum_probs=39.9
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++..-|++ ++ .-..+|..+|++...|+.+-.++..++++.|
T Consensus 208 ~~L~~~er~vi~~~~~~----~~----t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 208 KKLNDREKLILNLRFFQ----GK----TQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred HcCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 36888898888877652 22 2578999999999999999999998887643
No 151
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=22.86 E-value=78 Score=31.40 Aligned_cols=49 Identities=24% Similarity=0.393 Sum_probs=40.1
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||+....+|...|++ +++ -..+|..+|++...|..+...++.++++.
T Consensus 214 ~~L~~rer~vl~l~y~~----~~t----~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 214 AALPERERTVLVLRFFE----SMT----QTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred HcCCHHHHHHHHHHhcC----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46888888899887762 332 57899999999999999999999998764
No 152
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=22.67 E-value=1.4e+02 Score=28.51 Aligned_cols=53 Identities=15% Similarity=0.051 Sum_probs=39.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKP 416 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kp 416 (453)
..||+..+.++...|+......++ -.++|..+|+++..|..+...+++++++.
T Consensus 173 ~~L~~~~r~il~l~y~~~~~e~~S----~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDGRRKT----QREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCCCCcC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 468999999998877411012222 57899999999999999888888887654
No 153
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=22.65 E-value=1.2e+02 Score=20.37 Aligned_cols=23 Identities=22% Similarity=0.328 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 012938 388 KQLLASQTGLTKNQVSNWFINAR 410 (453)
Q Consensus 388 K~~LAk~TGLS~sQVsNWFiNaR 410 (453)
...+|+.+|++...|.+|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45788888999999999887763
No 154
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=22.23 E-value=1.2e+02 Score=22.15 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 012938 388 KQLLASQTGLTKNQVSNWFIN 408 (453)
Q Consensus 388 K~~LAk~TGLS~sQVsNWFiN 408 (453)
...||+.+|+++..|+.|..+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHhCCCcchhHHHhcC
Confidence 467888889999999999888
No 155
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.92 E-value=98 Score=28.59 Aligned_cols=51 Identities=16% Similarity=0.080 Sum_probs=41.0
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+....++...+.+. +. -.++|..+|++...|.....-+|+++++.+.
T Consensus 110 ~~Lp~~~R~v~~L~~~~g----~s----~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 110 DKLPQDQREALILVGASG----FS----YEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred HhCCHHHHHHhhHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 458999999987776633 22 4689999999999999999999999877554
No 156
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=21.50 E-value=1.4e+02 Score=27.70 Aligned_cols=53 Identities=19% Similarity=0.139 Sum_probs=42.7
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhHHH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMIEE 420 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi~e 420 (453)
..||+....++...+.++ ++ -.++|..+|++..-|.++..-+|.++++.+-..
T Consensus 127 ~~Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 127 AKLDPEYREPLLLQVIGG----FS----GEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred HhCCHHHHHHHHHHHHhC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999988777743 22 468999999999999999999999987766533
No 157
>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=21.26 E-value=2.1e+02 Score=20.30 Aligned_cols=45 Identities=18% Similarity=0.166 Sum_probs=31.3
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhch
Q 012938 362 LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWK 415 (453)
Q Consensus 362 Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~K 415 (453)
|++....++..+ . ..+ ...++|+.++++...|..|..-.+.++.-
T Consensus 1 l~~~e~~i~~~~-~----~~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 1 LTPREREVLRLL-A----EGK----TNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CCHHHHHHHHHH-H----cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 345556666443 3 122 36788999999999999998877776644
No 158
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=21.13 E-value=1.1e+02 Score=30.26 Aligned_cols=50 Identities=16% Similarity=0.265 Sum_probs=41.1
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
..||+....++...|++ .+ .-.++|..+|++...|+.+..-++.++++.+
T Consensus 204 ~~L~~~er~vi~l~y~e----~~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 204 LALEEKERKVMALYYYE----EL----VLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred HcCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46899999999887762 22 2578999999999999999999999987755
No 159
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=20.96 E-value=62 Score=30.97 Aligned_cols=51 Identities=18% Similarity=0.222 Sum_probs=39.8
Q ss_pred CCCChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhhH
Q 012938 360 RGLPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPMI 418 (453)
Q Consensus 360 r~Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpmi 418 (453)
..||+....++...++ ..++ -.++|..+|++...|.+....+|.++++.+-
T Consensus 148 ~~L~~~~r~i~~l~~~----~g~s----~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 148 DALPDAFRAVFVLRVV----EELS----VEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred HhCCHHHhhhheeehh----cCCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4588888888866554 2333 6789999999999999999999988877554
No 160
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=20.63 E-value=74 Score=25.72 Aligned_cols=21 Identities=14% Similarity=0.430 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCChhhhhhhhh
Q 012938 387 EKQLLASQTGLTKNQVSNWFI 407 (453)
Q Consensus 387 eK~~LAk~TGLS~sQVsNWFi 407 (453)
.-..||.+.|++..+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 367899999999999999943
No 161
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.55 E-value=77 Score=22.98 Aligned_cols=23 Identities=22% Similarity=0.483 Sum_probs=17.4
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 012938 388 KQLLASQTGLTKNQVSNWFINAR 410 (453)
Q Consensus 388 K~~LAk~TGLS~sQVsNWFiNaR 410 (453)
...+|+.+|++...|.+|....+
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHHCcCHHHHHHHHHHcc
Confidence 67899999999999999976544
No 162
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.45 E-value=1.1e+02 Score=28.33 Aligned_cols=48 Identities=17% Similarity=0.275 Sum_probs=37.6
Q ss_pred CChhHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhhchhh
Q 012938 362 LPETSVGILRSWLFEHFLHPYPNDSEKQLLASQTGLTKNQVSNWFINARVRLWKPM 417 (453)
Q Consensus 362 Lpk~~~~iLraWf~eH~~nPYPS~eeK~~LAk~TGLS~sQVsNWFiNaR~Rl~Kpm 417 (453)
+++....++.-.++ ..| ...++|..+|+|+..|.+.+..+|.++.+.+
T Consensus 136 l~~~~~~~v~l~~~----~Gl----s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l 183 (185)
T PF07638_consen 136 LDPRQRRVVELRFF----EGL----SVEEIAERLGISERTVRRRLRRARAWLRREL 183 (185)
T ss_pred cCHHHHHHHHHHHH----CCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 67777777777666 344 3678899999999999999999998776543
Done!