Query 007660
Match_columns 594
No_of_seqs 271 out of 994
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 13:37:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007660.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007660hhsearch_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 1.8E-37 4E-42 288.2 13.4 138 307-451 1-139 (140)
2 smart00574 POX domain associat 100.0 1.5E-35 3.2E-40 273.8 14.1 137 304-451 2-139 (140)
3 KOG0773 Transcription factor M 100.0 1E-29 2.2E-34 262.6 11.4 252 305-567 45-312 (342)
4 KOG0774 Transcription factor P 99.9 1.9E-28 4.1E-33 245.2 9.2 218 288-558 28-252 (334)
5 PF05920 Homeobox_KN: Homeobox 99.6 1.2E-15 2.6E-20 114.9 4.1 40 512-551 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.4 1.3E-12 2.8E-17 101.7 6.6 57 496-555 2-58 (59)
7 KOG0775 Transcription factor S 99.3 9.5E-13 2.1E-17 133.8 6.2 59 492-553 171-232 (304)
8 PF00046 Homeobox: Homeobox do 99.3 1.7E-12 3.7E-17 101.7 6.0 57 495-554 1-57 (57)
9 smart00389 HOX Homeodomain. DN 99.3 4.3E-12 9.4E-17 98.4 6.5 54 497-553 3-56 (56)
10 PF03792 PBC: PBC domain; Int 98.8 1E-08 2.2E-13 100.3 7.1 122 289-431 27-153 (191)
11 KOG0487 Transcription factor A 98.8 3.2E-09 7E-14 110.6 3.9 66 495-563 236-301 (308)
12 KOG0842 Transcription factor t 98.7 9.2E-09 2E-13 107.2 3.9 65 495-562 153-218 (307)
13 KOG0843 Transcription factor E 98.7 1.8E-08 3.8E-13 98.1 5.5 64 493-559 101-164 (197)
14 KOG0483 Transcription factor H 98.7 1.7E-08 3.8E-13 99.6 5.4 65 494-561 50-114 (198)
15 KOG0850 Transcription factor D 98.7 2.4E-08 5.2E-13 100.2 6.4 67 488-557 116-182 (245)
16 KOG0489 Transcription factor z 98.7 1.3E-08 2.8E-13 103.8 3.5 63 494-559 159-221 (261)
17 KOG0488 Transcription factor B 98.6 2.9E-08 6.4E-13 103.7 5.7 59 498-559 176-234 (309)
18 TIGR01565 homeo_ZF_HD homeobox 98.6 5.8E-08 1.2E-12 79.1 5.2 52 495-549 2-57 (58)
19 KOG0493 Transcription factor E 98.6 3.7E-08 8.1E-13 100.4 4.8 62 492-556 244-305 (342)
20 KOG0485 Transcription factor N 98.4 3.2E-07 7E-12 91.7 4.4 63 496-561 106-168 (268)
21 KOG3802 Transcription factor O 98.4 2.5E-07 5.5E-12 98.9 3.8 60 495-557 294-354 (398)
22 KOG0492 Transcription factor M 98.4 5E-07 1.1E-11 89.9 5.4 67 492-561 142-208 (246)
23 KOG2251 Homeobox transcription 98.3 6.4E-07 1.4E-11 89.7 6.1 62 494-558 37-98 (228)
24 KOG0484 Transcription factor P 98.3 6.3E-07 1.4E-11 81.0 5.4 64 495-561 18-81 (125)
25 COG5576 Homeodomain-containing 98.3 5.8E-07 1.3E-11 86.0 4.7 63 493-558 50-112 (156)
26 KOG0486 Transcription factor P 98.3 4.6E-07 1E-11 94.5 3.8 68 496-567 114-181 (351)
27 KOG0491 Transcription factor B 98.2 5.7E-07 1.2E-11 86.8 2.1 61 496-559 101-162 (194)
28 KOG0494 Transcription factor C 98.2 1.8E-06 4E-11 88.2 4.8 56 498-556 145-200 (332)
29 KOG0848 Transcription factor C 98.1 9.2E-07 2E-11 90.7 2.4 58 500-560 205-262 (317)
30 KOG4577 Transcription factor L 98.1 4.2E-06 9.2E-11 86.7 5.2 59 493-554 166-224 (383)
31 KOG0847 Transcription factor, 97.9 7.8E-06 1.7E-10 82.1 3.1 90 498-590 171-267 (288)
32 KOG2252 CCAAT displacement pro 97.8 1.9E-05 4.2E-10 87.5 5.6 55 495-552 421-475 (558)
33 KOG0844 Transcription factor E 97.7 1.1E-05 2.4E-10 84.1 1.4 57 498-557 185-241 (408)
34 KOG0849 Transcription factor P 97.5 7.1E-05 1.5E-09 79.9 4.0 62 494-558 176-237 (354)
35 KOG0490 Transcription factor, 97.3 0.00013 2.9E-09 70.9 2.1 60 494-556 60-119 (235)
36 KOG1168 Transcription factor A 97.2 0.00013 2.8E-09 76.0 1.1 59 493-554 308-366 (385)
37 KOG0773 Transcription factor M 97.1 0.00019 4.1E-09 75.2 1.9 61 496-557 97-157 (342)
38 PF11569 Homez: Homeodomain le 96.4 0.0024 5.3E-08 52.1 2.8 43 506-551 10-52 (56)
39 PF03791 KNOX2: KNOX2 domain ; 95.6 0.028 6E-07 45.4 5.3 43 385-446 8-50 (52)
40 KOG0490 Transcription factor, 94.6 0.027 5.9E-07 54.8 3.2 61 494-557 153-213 (235)
41 KOG1146 Homeobox protein [Gene 90.6 0.23 5E-06 60.9 4.0 59 498-559 907-965 (1406)
42 PF04218 CENP-B_N: CENP-B N-te 80.6 2.4 5.2E-05 33.8 3.8 47 495-549 1-47 (53)
43 KOG3623 Homeobox transcription 74.0 4.6 0.0001 47.7 5.0 44 506-552 568-611 (1007)
44 PF04545 Sigma70_r4: Sigma-70, 73.6 4.4 9.6E-05 31.1 3.4 47 500-554 4-50 (50)
45 cd06171 Sigma70_r4 Sigma70, re 72.6 5.9 0.00013 28.8 3.8 46 500-553 10-55 (55)
46 PRK12516 RNA polymerase sigma 71.5 53 0.0012 31.7 11.1 52 500-559 116-167 (187)
47 PF01527 HTH_Tnp_1: Transposas 71.2 6.2 0.00013 32.2 4.0 46 496-549 2-48 (76)
48 PF08281 Sigma70_r4_2: Sigma-7 69.6 6.6 0.00014 30.3 3.6 45 500-552 10-54 (54)
49 PRK09642 RNA polymerase sigma 65.2 8.2 0.00018 35.5 3.9 52 500-559 106-157 (160)
50 cd00569 HTH_Hin_like Helix-tur 64.5 13 0.00029 24.0 3.9 39 499-545 4-42 (42)
51 TIGR02980 SigBFG RNA polymeras 63.1 91 0.002 30.7 11.0 50 499-556 177-226 (227)
52 PRK11924 RNA polymerase sigma 63.1 1.2E+02 0.0027 27.7 12.5 52 500-559 125-176 (179)
53 PRK05602 RNA polymerase sigma 62.5 1.2E+02 0.0026 28.7 11.3 51 500-558 128-178 (186)
54 PRK06759 RNA polymerase factor 60.4 11 0.00023 34.4 3.7 47 500-554 106-152 (154)
55 PF13443 HTH_26: Cro/C1-type H 60.4 22 0.00048 28.0 5.1 46 509-561 2-47 (63)
56 TIGR02937 sigma70-ECF RNA poly 60.3 1.1E+02 0.0025 26.4 12.0 48 500-555 110-157 (158)
57 PRK09644 RNA polymerase sigma 59.5 13 0.00028 34.5 4.2 53 499-559 107-159 (165)
58 PRK12547 RNA polymerase sigma 59.3 1.5E+02 0.0033 27.5 11.8 50 499-556 111-160 (164)
59 PF11285 DUF3086: Protein of u 59.2 92 0.002 33.1 10.5 116 386-516 7-155 (283)
60 PRK12530 RNA polymerase sigma 59.1 15 0.00032 35.3 4.6 55 499-561 133-187 (189)
61 PRK06930 positive control sigm 57.2 12 0.00027 36.4 3.7 55 500-562 114-168 (170)
62 TIGR02985 Sig70_bacteroi1 RNA 56.4 15 0.00032 33.0 3.9 48 500-555 113-160 (161)
63 PRK12546 RNA polymerase sigma 54.8 1.5E+02 0.0032 28.7 10.8 50 500-557 113-162 (188)
64 PRK09652 RNA polymerase sigma 54.6 17 0.00036 33.5 4.0 50 500-557 128-177 (182)
65 PRK12512 RNA polymerase sigma 52.9 15 0.00033 34.6 3.5 51 500-558 131-181 (184)
66 TIGR02939 RpoE_Sigma70 RNA pol 52.2 14 0.0003 34.7 3.1 50 499-556 137-186 (190)
67 PRK09646 RNA polymerase sigma 52.0 18 0.00038 34.8 3.9 49 500-556 142-190 (194)
68 PRK00118 putative DNA-binding 51.8 19 0.00041 33.0 3.8 48 500-555 17-64 (104)
69 PRK12514 RNA polymerase sigma 51.4 19 0.00041 33.8 3.9 50 499-556 128-177 (179)
70 TIGR02999 Sig-70_X6 RNA polyme 51.0 18 0.0004 33.9 3.8 48 500-555 134-181 (183)
71 PRK12541 RNA polymerase sigma 50.3 17 0.00038 33.5 3.4 48 499-554 111-158 (161)
72 PRK12513 RNA polymerase sigma 49.9 1.5E+02 0.0033 28.2 9.9 51 499-557 138-188 (194)
73 PRK12526 RNA polymerase sigma 49.4 21 0.00045 34.9 3.9 51 499-557 152-202 (206)
74 PRK12531 RNA polymerase sigma 49.0 21 0.00045 34.3 3.8 53 499-559 140-192 (194)
75 PRK09648 RNA polymerase sigma 48.7 22 0.00048 33.7 4.0 50 499-556 138-187 (189)
76 TIGR03001 Sig-70_gmx1 RNA poly 48.7 24 0.00053 35.9 4.5 57 499-563 160-216 (244)
77 PRK09047 RNA polymerase factor 48.2 20 0.00043 32.8 3.4 52 499-558 105-156 (161)
78 TIGR02989 Sig-70_gvs1 RNA poly 47.2 24 0.00052 32.1 3.8 48 499-554 110-157 (159)
79 PRK12519 RNA polymerase sigma 47.1 22 0.00048 33.8 3.7 51 499-557 140-190 (194)
80 PRK12520 RNA polymerase sigma 47.0 28 0.0006 33.2 4.3 54 499-560 130-183 (191)
81 TIGR02943 Sig70_famx1 RNA poly 46.8 29 0.00064 33.3 4.5 55 499-561 130-184 (188)
82 PRK12532 RNA polymerase sigma 46.8 23 0.0005 33.9 3.7 52 500-559 136-187 (195)
83 PRK12523 RNA polymerase sigma 45.5 26 0.00056 32.8 3.8 50 499-556 118-167 (172)
84 PRK12536 RNA polymerase sigma 45.5 27 0.00059 33.0 4.0 50 500-557 129-178 (181)
85 PRK06811 RNA polymerase factor 45.5 23 0.0005 33.9 3.5 51 499-557 130-180 (189)
86 PRK09639 RNA polymerase sigma 45.5 26 0.00056 32.3 3.7 50 499-557 111-160 (166)
87 TIGR02983 SigE-fam_strep RNA p 45.4 25 0.00055 32.3 3.7 50 499-556 109-158 (162)
88 PRK12544 RNA polymerase sigma 45.1 34 0.00074 33.7 4.7 55 499-561 147-201 (206)
89 TIGR02954 Sig70_famx3 RNA poly 45.1 21 0.00046 33.2 3.1 49 500-556 119-167 (169)
90 PRK13919 putative RNA polymera 44.4 24 0.00053 33.2 3.5 50 499-556 134-183 (186)
91 PRK06986 fliA flagellar biosyn 44.0 22 0.00047 35.4 3.2 49 500-556 184-232 (236)
92 PRK03975 tfx putative transcri 43.7 51 0.0011 31.8 5.5 53 499-560 5-57 (141)
93 PRK12542 RNA polymerase sigma 43.6 29 0.00063 32.9 3.9 58 499-564 121-178 (185)
94 PRK12515 RNA polymerase sigma 42.2 37 0.00081 32.3 4.4 51 499-557 130-180 (189)
95 TIGR02948 SigW_bacill RNA poly 42.1 29 0.00062 32.5 3.6 50 499-556 135-184 (187)
96 TIGR02959 SigZ RNA polymerase 42.0 25 0.00054 33.1 3.2 52 499-558 99-150 (170)
97 PRK09645 RNA polymerase sigma 41.0 31 0.00067 32.1 3.6 50 500-557 118-167 (173)
98 PF10168 Nup88: Nuclear pore c 40.6 6.3E+02 0.014 30.4 14.8 17 500-516 681-697 (717)
99 smart00421 HTH_LUXR helix_turn 40.5 80 0.0017 23.2 5.2 51 500-559 3-53 (58)
100 PRK12524 RNA polymerase sigma 40.5 36 0.00077 32.8 4.0 49 500-556 136-184 (196)
101 PRK09647 RNA polymerase sigma 39.6 3.8E+02 0.0082 26.3 12.0 50 500-557 138-187 (203)
102 PRK08583 RNA polymerase sigma 39.5 33 0.00071 34.7 3.7 49 500-556 205-253 (257)
103 PRK12533 RNA polymerase sigma 39.1 27 0.00058 34.9 3.0 53 499-559 133-185 (216)
104 PRK12537 RNA polymerase sigma 39.1 38 0.00081 32.1 3.9 49 499-555 132-180 (182)
105 PRK12545 RNA polymerase sigma 38.8 40 0.00087 32.7 4.1 53 499-559 138-190 (201)
106 PRK12539 RNA polymerase sigma 37.7 37 0.0008 32.3 3.6 51 499-557 130-180 (184)
107 TIGR02947 SigH_actino RNA poly 37.6 23 0.0005 33.8 2.2 51 500-558 131-181 (193)
108 PRK15369 two component system 37.4 97 0.0021 27.9 6.1 55 499-562 148-202 (211)
109 TIGR02941 Sigma_B RNA polymera 36.9 33 0.00071 34.6 3.3 50 499-556 204-253 (255)
110 PF00196 GerE: Bacterial regul 36.8 68 0.0015 25.2 4.4 53 500-561 3-55 (58)
111 PRK12543 RNA polymerase sigma 36.7 63 0.0014 30.5 5.0 54 499-560 116-169 (179)
112 PRK09649 RNA polymerase sigma 36.2 39 0.00085 32.3 3.5 48 499-554 129-176 (185)
113 PRK04217 hypothetical protein; 35.4 54 0.0012 30.3 4.1 50 500-557 42-91 (110)
114 PRK11922 RNA polymerase sigma 35.2 3.6E+02 0.0079 26.8 10.3 53 499-559 148-200 (231)
115 PRK06288 RNA polymerase sigma 34.9 48 0.001 33.9 4.1 51 499-557 211-261 (268)
116 PRK12535 RNA polymerase sigma 34.7 43 0.00092 32.6 3.6 53 499-559 132-184 (196)
117 PRK12540 RNA polymerase sigma 34.4 46 0.001 31.9 3.7 53 499-559 110-162 (182)
118 PRK12517 RNA polymerase sigma 34.3 59 0.0013 31.3 4.5 53 499-559 127-179 (188)
119 PRK12538 RNA polymerase sigma 34.1 53 0.0012 33.1 4.3 51 500-558 171-221 (233)
120 TIGR02393 RpoD_Cterm RNA polym 34.1 63 0.0014 32.4 4.7 57 500-560 176-232 (238)
121 PRK07408 RNA polymerase sigma 33.9 44 0.00095 34.1 3.6 52 499-558 202-253 (256)
122 PRK09637 RNA polymerase sigma 33.6 56 0.0012 31.3 4.1 52 500-559 106-157 (181)
123 PRK07037 extracytoplasmic-func 33.5 56 0.0012 30.0 4.0 50 499-556 108-157 (163)
124 PRK08301 sporulation sigma fac 33.5 41 0.00089 33.3 3.3 54 499-556 177-230 (234)
125 TIGR02952 Sig70_famx2 RNA poly 32.7 55 0.0012 30.1 3.8 49 499-555 121-169 (170)
126 TIGR02479 FliA_WhiG RNA polyme 32.5 50 0.0011 32.6 3.7 50 499-556 174-223 (224)
127 PRK09415 RNA polymerase factor 32.5 44 0.00096 31.6 3.2 50 499-556 126-175 (179)
128 cd07597 BAR_SNX8 The Bin/Amphi 32.1 2.6E+02 0.0057 28.7 8.9 72 386-457 32-114 (246)
129 PRK12527 RNA polymerase sigma 31.5 70 0.0015 29.4 4.3 50 500-557 105-154 (159)
130 PRK09641 RNA polymerase sigma 31.3 60 0.0013 30.4 3.8 49 500-556 136-184 (187)
131 PRK12528 RNA polymerase sigma 31.3 61 0.0013 29.9 3.8 47 499-553 112-158 (161)
132 PRK12518 RNA polymerase sigma 30.7 27 0.00059 32.5 1.4 50 500-557 120-169 (175)
133 PRK12529 RNA polymerase sigma 30.7 60 0.0013 30.8 3.8 49 499-555 126-174 (178)
134 PRK12511 RNA polymerase sigma 30.7 62 0.0014 31.1 3.9 50 500-557 111-160 (182)
135 PRK12522 RNA polymerase sigma 30.5 70 0.0015 29.9 4.2 52 499-558 118-169 (173)
136 KOG4196 bZIP transcription fac 29.0 1.6E+02 0.0035 28.5 6.1 41 384-424 75-115 (135)
137 PF04967 HTH_10: HTH DNA bindi 28.8 1.1E+02 0.0023 25.0 4.3 47 501-548 1-47 (53)
138 TIGR02885 spore_sigF RNA polym 28.8 65 0.0014 31.9 3.8 49 499-555 182-230 (231)
139 PRK11923 algU RNA polymerase s 28.8 74 0.0016 30.2 4.0 50 500-557 138-187 (193)
140 cd01392 HTH_LacI Helix-turn-he 28.8 63 0.0014 24.4 2.9 21 529-549 2-22 (52)
141 PRK12534 RNA polymerase sigma 27.8 73 0.0016 30.1 3.8 49 500-556 137-185 (187)
142 TIGR02960 SigX5 RNA polymerase 26.7 72 0.0016 33.0 3.8 51 499-557 141-191 (324)
143 PF13518 HTH_28: Helix-turn-he 26.7 64 0.0014 24.2 2.6 24 527-550 15-38 (52)
144 TIGR02950 SigM_subfam RNA poly 25.8 36 0.00078 30.8 1.3 47 501-555 106-152 (154)
145 PRK08295 RNA polymerase factor 25.7 81 0.0018 30.2 3.8 49 499-556 154-202 (208)
146 cd00131 PAX Paired Box domain 25.5 1.9E+02 0.0041 27.0 6.0 47 499-548 74-127 (128)
147 PRK11511 DNA-binding transcrip 25.3 1.6E+02 0.0034 27.0 5.4 44 501-548 6-49 (127)
148 cd00093 HTH_XRE Helix-turn-hel 25.0 1.1E+02 0.0023 21.5 3.5 32 528-560 16-47 (58)
149 TIGR02859 spore_sigH RNA polym 24.8 82 0.0018 29.8 3.6 47 501-556 151-197 (198)
150 PRK09643 RNA polymerase sigma 24.4 97 0.0021 29.8 4.0 50 500-557 134-183 (192)
151 PRK09651 RNA polymerase sigma 24.2 82 0.0018 29.6 3.4 49 500-556 119-167 (172)
152 TIGR02846 spore_sigmaK RNA pol 23.9 85 0.0018 31.2 3.6 50 499-556 173-226 (227)
153 PRK05572 sporulation sigma fac 23.8 88 0.0019 31.6 3.7 50 499-556 201-250 (252)
154 PRK12525 RNA polymerase sigma 23.8 84 0.0018 29.4 3.4 49 499-555 117-165 (168)
155 PRK08215 sporulation sigma fac 23.4 91 0.002 31.6 3.8 49 500-556 209-257 (258)
156 PRK05803 sporulation sigma fac 23.2 96 0.0021 30.9 3.9 56 499-558 174-229 (233)
157 PRK06704 RNA polymerase factor 22.9 91 0.002 31.8 3.7 49 500-556 116-164 (228)
158 PF01381 HTH_3: Helix-turn-hel 22.8 1.3E+02 0.0029 22.8 3.8 20 528-547 13-32 (55)
159 COG3413 Predicted DNA binding 22.1 1.1E+02 0.0025 30.3 4.1 54 500-554 155-208 (215)
160 cd06170 LuxR_C_like C-terminal 22.0 2E+02 0.0043 21.3 4.5 47 501-556 1-47 (57)
161 PF13936 HTH_38: Helix-turn-he 21.6 80 0.0017 24.1 2.3 40 499-546 3-42 (44)
162 TIGR02394 rpoS_proteo RNA poly 20.8 1.2E+02 0.0025 31.4 4.0 52 499-558 221-276 (285)
163 PRK05911 RNA polymerase sigma 20.6 1.3E+02 0.0027 30.9 4.2 50 499-556 204-253 (257)
164 PRK07122 RNA polymerase sigma 20.3 1E+02 0.0022 31.8 3.4 50 499-556 214-263 (264)
165 PF12844 HTH_19: Helix-turn-he 20.1 1.4E+02 0.0031 23.5 3.5 33 527-560 15-47 (64)
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=1.8e-37 Score=288.20 Aligned_cols=138 Identities=28% Similarity=0.345 Sum_probs=102.4
Q ss_pred ccccCccccchhHHHHHHhhccchhhccccccccccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCChHHHH
Q 007660 307 QFISGSTYLHAVQEILAQIASYSLENLDDMSYLGVRKIGDNIPPSSSFITGKGRPPMNSDEFPNVDGCFEVQMNPSQQRQ 386 (594)
Q Consensus 307 ~~l~~SrYLk~AQELLdE~v~v~~~~v~~~~~~~g~k~g~~~~~sss~~~~~g~~~~~s~~~p~~~~~~~~~~~s~aer~ 386 (594)
++|++|||||||||||+|||+|+++........... ...... .+..... .+....+..+.....++++++|++
T Consensus 1 q~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~-~~~~~~-~~~~~~~-----~~~~~~~~~~~~~~~~~ls~~~~~ 73 (140)
T PF07526_consen 1 QVLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSG-APGGAN-SSGSSSS-----SGGSSSSSSSSDSSSPELSPAERQ 73 (140)
T ss_pred CccccchhHHHHHHHHHHHHcccchhhhcchhhccc-cccccc-cCCCCCC-----CCCCCCCccccCCCCCCCChhhHH
Confidence 579999999999999999999987422221111111 000000 0000000 010111122333446789999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCC-chhhHHHHHHHHHHhhhhhHHHHH
Q 007660 387 AVEAKKAQLLALLQMVDDRYNQCLDEIHTVVSAFHAATELD-PQVHARFALHTISFLYKNLRERIS 451 (594)
Q Consensus 387 elq~kkakLl~mL~ev~~RY~qy~~qm~~V~ssFea~~~~~-~~~yt~lAl~tmSrhFr~Lr~~Is 451 (594)
|+|+||+||+.||+||++||+|||+|||+|+++||+|||+| |++||+|||+||||||||||++|+
T Consensus 74 e~q~kK~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~ 139 (140)
T PF07526_consen 74 ELQRKKAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAIS 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999997 689999999999999999999996
No 2
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=1.5e-35 Score=273.79 Aligned_cols=137 Identities=29% Similarity=0.444 Sum_probs=103.5
Q ss_pred cccccccCccccchhHHHHHHhhccchhhccccccccccccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCChH
Q 007660 304 HFLQFISGSTYLHAVQEILAQIASYSLENLDDMSYLGVRKIGDNIPPSSSFITGKGRPPMNSDEFPNVDGCFEVQMNPSQ 383 (594)
Q Consensus 304 ~fs~~l~~SrYLk~AQELLdE~v~v~~~~v~~~~~~~g~k~g~~~~~sss~~~~~g~~~~~s~~~p~~~~~~~~~~~s~a 383 (594)
+|+.+|++|||||||||||+|||+|+++-.+.... .+.+...... ...+ ..+...+.+....+++++++
T Consensus 2 g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~-----~~~~~~~~~~--~~~~----~~~~~~g~s~~~~~~~ls~~ 70 (140)
T smart00574 2 GGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQ-----SGNDSPVSTS--SNEG----GGENLSGGSSSSEVPPLSTA 70 (140)
T ss_pred chhhhccCccccccHHHHHHHHhcccHHhhccccc-----cccccccccc--ccCC----CcCCCCCCCCCCCCCCCchh
Confidence 57889999999999999999999997543322111 1110000000 0000 00000012223357889999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCC-chhhHHHHHHHHHHhhhhhHHHHH
Q 007660 384 QRQAVEAKKAQLLALLQMVDDRYNQCLDEIHTVVSAFHAATELD-PQVHARFALHTISFLYKNLRERIS 451 (594)
Q Consensus 384 er~elq~kkakLl~mL~ev~~RY~qy~~qm~~V~ssFea~~~~~-~~~yt~lAl~tmSrhFr~Lr~~Is 451 (594)
||+|+|+||+||+.||+||++||+|||+|||+|+++|++++|+| +++||+|||+|||+||||||++|+
T Consensus 71 ~r~e~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 71 ERQELQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999997 589999999999999999999995
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.96 E-value=1e-29 Score=262.63 Aligned_cols=252 Identities=31% Similarity=0.488 Sum_probs=178.3
Q ss_pred ccccccCccccchhHHHHHHhhccchhhccccccccccccCCCCCCCCCccCCCCCCCCCCC-CCCCCCCCCCCCCCChH
Q 007660 305 FLQFISGSTYLHAVQEILAQIASYSLENLDDMSYLGVRKIGDNIPPSSSFITGKGRPPMNSD-EFPNVDGCFEVQMNPSQ 383 (594)
Q Consensus 305 fs~~l~~SrYLk~AQELLdE~v~v~~~~v~~~~~~~g~k~g~~~~~sss~~~~~g~~~~~s~-~~p~~~~~~~~~~~s~a 383 (594)
+...+..++|+++||+|++++|++.+....- +.............. ...... ...++... .+......
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~-----~~~~~~~~~~n~~~~-s~~~~~~~ 113 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKG-----KMPYDPVPRSPASLS-----PPEDKGARRGNATRE-SATLKAWL 113 (342)
T ss_pred cccccccccccccchhHHhHHhhcccccccc-----ccCcCcccccccccc-----Ccccccccccccccc-ccccccch
Confidence 5566889999999999999999876432111 000000000000000 000000 00011111 12233567
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCc-hhhHHHHHHHHHHhhhhhHH--HHHHHHHHhhcc
Q 007660 384 QRQAVEAKKAQLLALLQMVDDRYNQCLDEIHTVVSAFHAATELDP-QVHARFALHTISFLYKNLRE--RISSQILAMGAH 460 (594)
Q Consensus 384 er~elq~kkakLl~mL~ev~~RY~qy~~qm~~V~ssFea~~~~~~-~~yt~lAl~tmSrhFr~Lr~--~Is~qi~~~g~~ 460 (594)
++++++.+++||+.|+++|+++|.+|+..|+.|++.|+...+++. ..|+..++..+++||+++.+ +|..|+......
T Consensus 114 ~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~ 193 (342)
T KOG0773|consen 114 EEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEEL 193 (342)
T ss_pred hhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccc
Confidence 899999999999999999999999999999999999999999985 78999999999999999998 666776654433
Q ss_pred cCCCC--CCC---C----c--cccchhhhhhHH-HHHHhhhhhcccCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHH
Q 007660 461 FDSKS--TRG---K----D--TVMVDSFIKEQW-ALQQLKKKEHQIWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKH 528 (594)
Q Consensus 461 ~~~~~--s~~---~----e--~s~~~~~lq~q~-alqql~~k~~~~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~ 528 (594)
.+... ..+ . + .......+.++. +..+...+....||++++||+.++.+|+.|+++|+.||||++.+|.
T Consensus 194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~ 273 (342)
T KOG0773|consen 194 LGESEQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKL 273 (342)
T ss_pred cccccccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhcc
Confidence 32111 110 0 0 111111222221 2223333345789999999999999999999999999999999999
Q ss_pred HHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHhhhc
Q 007660 529 LLAMKSGLTRTQVSNWFINARVRLWKPMIEEMYREVNRR 567 (594)
Q Consensus 529 ~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~~e~~~~ 567 (594)
+||++|||++.||.|||||+|+|.|++|+++++.+..+.
T Consensus 274 ~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 274 MLAKQTGLSRPQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred ccchhcCCCcccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 999999999999999999999999999999999987764
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.95 E-value=1.9e-28 Score=245.20 Aligned_cols=218 Identities=20% Similarity=0.289 Sum_probs=174.7
Q ss_pred cccccccccccCCCCcccccc--ccCcc--ccchhHHHHHHhhccchhhccccccccccccCCCCCCCCCccCCCCCCCC
Q 007660 288 CSSNELSLSFGSHRPAHFLQF--ISGST--YLHAVQEILAQIASYSLENLDDMSYLGVRKIGDNIPPSSSFITGKGRPPM 363 (594)
Q Consensus 288 ~~~~~Lsln~g~~~p~~fs~~--l~~Sr--YLk~AQELLdE~v~v~~~~v~~~~~~~g~k~g~~~~~sss~~~~~g~~~~ 363 (594)
++.+++.++||+++|+.|+++ |+++. .+|..|++-++-.++. +||+|..++|+.+.+.+...
T Consensus 28 aqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~dpqlm--RLDnML~AEGVagPekgga~------------ 93 (334)
T KOG0774|consen 28 AQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPPDPQLM--RLDNMLLAEGVAGPEKGGAR------------ 93 (334)
T ss_pred HHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCCChHHH--HHHHHHHHhcccCccccchh------------
Confidence 346899999999999999998 78877 6699999998887776 89999999887665443210
Q ss_pred CCCCCCCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhhhhhcCCchhh--HHHHHHHHH
Q 007660 364 NSDEFPNVDGCFEVQMNPSQQRQAVEAKKAQLLALLQMVDDRYNQCLDEIHT-VVSAFHAATELDPQVH--ARFALHTIS 440 (594)
Q Consensus 364 ~s~~~p~~~~~~~~~~~s~aer~elq~kkakLl~mL~ev~~RY~qy~~qm~~-V~ssFea~~~~~~~~y--t~lAl~tmS 440 (594)
+.+.+..++.+|.+|+.|++.+|+...++|+|+|.++.. |+.-+..+.+.+|... ..-..+.|+
T Consensus 94 -------------~~~Asgg~hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~~ke~e~m~~~i~ 160 (334)
T KOG0774|consen 94 -------------AAAASGGDHSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIMPKEIERMVQIIS 160 (334)
T ss_pred -------------hhhccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHH
Confidence 111112236899999999999999999999999999988 8889999998888653 222334444
Q ss_pred HhhhhhHHHHHHHHHHhhcccCCCCCCCCccccchhhhhhHHHHHHhhhhhcccCCCCCCCChhHHHHHHHHHHHccCCC
Q 007660 441 FLYKNLRERISSQILAMGAHFDSKSTRGKDTVMVDSFIKEQWALQQLKKKEHQIWRPQRGLPEKSVSVLRAWMFQNFLHP 520 (594)
Q Consensus 441 rhFr~Lr~~Is~qi~~~g~~~~~~~s~~~e~s~~~~~lq~q~alqql~~k~~~~~RkRR~fpk~a~~iLr~Wf~eH~~~P 520 (594)
+-|...+.-| +. .-..++..||++...++||||+|+|.++.||.+||+.|+.||
T Consensus 161 ~kF~~iq~~l----kq----------------------stce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nP 214 (334)
T KOG0774|consen 161 KKFSHIQMQL----KQ----------------------STCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNP 214 (334)
T ss_pred HHHHHHHHHH----HH----------------------HHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCC
Confidence 4444332211 10 012567789998888999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 521 YPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 521 YPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
||++++|++||++++++.+||+|||.|+|.|+||.|..
T Consensus 215 YPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 215 YPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred CCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence 99999999999999999999999999999999999874
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.58 E-value=1.2e-15 Score=114.89 Aligned_cols=40 Identities=53% Similarity=1.055 Sum_probs=36.5
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 007660 512 WMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVR 551 (594)
Q Consensus 512 Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrR 551 (594)
||.+|+.||||+++||++||++|||+.+||++||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 9999999999999999999999999999999999999998
No 6
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.36 E-value=1.3e-12 Score=101.72 Aligned_cols=57 Identities=33% Similarity=0.535 Sum_probs=53.2
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 496 RPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 496 RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
+++..|+++++.+|++||..| |||+.+++..||.++||+..||.+||.|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~---~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKN---PYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 456679999999999999997 999999999999999999999999999999998764
No 7
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.34 E-value=9.5e-13 Score=133.85 Aligned_cols=59 Identities=53% Similarity=0.809 Sum_probs=54.5
Q ss_pred cccCCCCCC---CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 007660 492 HQIWRPQRG---LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLW 553 (594)
Q Consensus 492 ~~~~RkRR~---fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlk 553 (594)
+++|..--+ |.++.+.+|++||..+ |||++++|.+||+.|||+..||.|||+|+|.|.+
T Consensus 171 rTIWDGEet~yCFKekSR~~LrewY~~~---~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 171 RTIWDGEETVYCFKEKSRSLLREWYLQN---PYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred CccccCceeeeehhHhhHHHHHHHHhcC---CCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 567776554 8999999999999977 9999999999999999999999999999999998
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.34 E-value=1.7e-12 Score=101.73 Aligned_cols=57 Identities=37% Similarity=0.606 Sum_probs=53.8
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 007660 495 WRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554 (594)
Q Consensus 495 ~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkK 554 (594)
+|+|+.|+++++.+|+++|..+ |||+.++++.||.++||+..||.+||+|+|.+.++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~---~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN---PYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS---SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh---ccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4677889999999999999998 99999999999999999999999999999999875
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.31 E-value=4.3e-12 Score=98.39 Aligned_cols=54 Identities=31% Similarity=0.518 Sum_probs=50.4
Q ss_pred CCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 007660 497 PQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLW 553 (594)
Q Consensus 497 kRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlk 553 (594)
++..|+++++.+|++||..+ |||+.+++..||..+||+..||.+||+|+|+|.+
T Consensus 3 ~r~~~~~~~~~~L~~~f~~~---~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 3 KRTSFTPEQLEELEKEFQKN---PYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCcCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 44559999999999999999 9999999999999999999999999999999864
No 10
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=98.79 E-value=1e-08 Score=100.35 Aligned_cols=122 Identities=17% Similarity=0.178 Sum_probs=98.5
Q ss_pred ccccccccccCCCCcccccc--ccCcc--ccchhHHHHHHhhccchhhccccccccccccCCCCCCCCCccCCCCCCCCC
Q 007660 289 SSNELSLSFGSHRPAHFLQF--ISGST--YLHAVQEILAQIASYSLENLDDMSYLGVRKIGDNIPPSSSFITGKGRPPMN 364 (594)
Q Consensus 289 ~~~~Lsln~g~~~p~~fs~~--l~~Sr--YLk~AQELLdE~v~v~~~~v~~~~~~~g~k~g~~~~~sss~~~~~g~~~~~ 364 (594)
+++++++++|+|+|+.|+++ +++.. .++.+||..++..++. ++|+|+.++|+.+.+.+....+.
T Consensus 27 qa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~dpQl~--RLDNML~AEGV~gPe~~~~~~~~---------- 94 (191)
T PF03792_consen 27 QARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPPDPQLM--RLDNMLLAEGVAGPEKGGRAAAA---------- 94 (191)
T ss_pred HHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCCchhhh--hhhcchhhhcCcCCCCcccchhh----------
Confidence 78899999999999999988 67766 5688998887777765 89999999888666543211100
Q ss_pred CCCCCCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhhhhhcCCchhh
Q 007660 365 SDEFPNVDGCFEVQMNPSQQRQAVEAKKAQLLALLQMVDDRYNQCLDEIHT-VVSAFHAATELDPQVH 431 (594)
Q Consensus 365 s~~~p~~~~~~~~~~~s~aer~elq~kkakLl~mL~ev~~RY~qy~~qm~~-V~ssFea~~~~~~~~y 431 (594)
..+.+++.+.|..+|+.|+++++.+|++..++|++.|.++.. |+.-...+++++|++.
T Consensus 95 ---------~~~~~~~~~~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~lLreQs~~RPIs~ 153 (191)
T PF03792_consen 95 ---------AAGTAADNSIDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMNLLREQSEFRPISP 153 (191)
T ss_pred ---------hhccCcccccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhcccCCCCH
Confidence 011233667888999999999999999999999999999988 8899999999998775
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.79 E-value=3.2e-09 Score=110.56 Aligned_cols=66 Identities=23% Similarity=0.236 Sum_probs=57.8
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHH
Q 007660 495 WRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMYRE 563 (594)
Q Consensus 495 ~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~~e 563 (594)
++||-.++|.|+..|++-|.-| -|.+++-|.+|++.++||.+||+.||||+|+|+||-..+...++
T Consensus 236 RKKRcPYTK~QtlELEkEFlfN---~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~~ 301 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLFN---MYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLKE 301 (308)
T ss_pred ccccCCchHHHHHHHHHHHHHH---HHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhccc
Confidence 4445559999999999999999 99999999999999999999999999999999998766554433
No 12
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.70 E-value=9.2e-09 Score=107.18 Aligned_cols=65 Identities=28% Similarity=0.314 Sum_probs=58.6
Q ss_pred CCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHH
Q 007660 495 WRPQRG-LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMYR 562 (594)
Q Consensus 495 ~RkRR~-fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~~ 562 (594)
+||+|. |++.|+-.|+.-|.+. .|.+..||+.||+.++||.+||+.||+|+|.|.|+.-+++-..
T Consensus 153 kRKrRVLFSqAQV~ELERRFrqQ---RYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 153 KRKRRVLFSQAQVYELERRFRQQ---RYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred ccccccccchhHHHHHHHHHHhh---hccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 345555 9999999999999999 9999999999999999999999999999999999988876443
No 13
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.70 E-value=1.8e-08 Score=98.09 Aligned_cols=64 Identities=27% Similarity=0.299 Sum_probs=58.4
Q ss_pred ccCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 493 QIWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 493 ~~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
..+|.|..|+.+++..|+..|..+ -|-.-.||+.||+.++|++.||++||+|+|.|.|+.-.++
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~---~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN---QYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC---CeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 345666679999999999999999 9999999999999999999999999999999999877765
No 14
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.69 E-value=1.7e-08 Score=99.64 Aligned_cols=65 Identities=28% Similarity=0.306 Sum_probs=59.2
Q ss_pred cCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 007660 494 IWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMY 561 (594)
Q Consensus 494 ~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~ 561 (594)
.+++++.|+.+++..|+.-|..| -|-.+++|..||+++||.+.||.+||+|+|+|+|.+-.+..|
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~---~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~ 114 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESE---KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDY 114 (198)
T ss_pred cccccccccHHHHHHhHHhhccc---cccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhH
Confidence 46788889999999999999999 889999999999999999999999999999999877766544
No 15
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.69 E-value=2.4e-08 Score=100.21 Aligned_cols=67 Identities=28% Similarity=0.354 Sum_probs=59.8
Q ss_pred hhhhcccCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 488 KKKEHQIWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 488 ~~k~~~~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..|-+.+|++|+-++--+++.|+.-|.+- -|..-.||.+||..+|||..||+.||+|+|-|+||.+.
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkT---QYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQT---QYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhc---chhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 33444566777779999999999999998 99999999999999999999999999999999998775
No 16
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.66 E-value=1.3e-08 Score=103.76 Aligned_cols=63 Identities=21% Similarity=0.232 Sum_probs=57.8
Q ss_pred cCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 494 IWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 494 ~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
.+|.|..|+..|+..|++-|.-| .|.+...|.++|..+.|++.||++||+|+|+|+||....+
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN---~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFN---KYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCcccchhhhhhhhhhhccc---cccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 45667779999999999999999 9999999999999999999999999999999999866544
No 17
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.64 E-value=2.9e-08 Score=103.72 Aligned_cols=59 Identities=25% Similarity=0.371 Sum_probs=54.8
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 498 QRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 498 RR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
|.-|+..++..|+.-|..- .|.+..||.+||+.+|||-.||.+||+|+|.|+|+...+.
T Consensus 176 RTaFT~~Ql~~LEkrF~~Q---KYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 176 RTAFSDHQLFELEKRFEKQ---KYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred hhhhhHHHHHHHHHHHHHh---hcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence 3449999999999999999 9999999999999999999999999999999988888774
No 18
>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=98.61 E-value=5.8e-08 Score=79.07 Aligned_cols=52 Identities=15% Similarity=0.267 Sum_probs=48.9
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 007660 495 WRPQRGLPEKSVSVLRAWMFQNFLHPY----PKDAEKHLLAMKSGLTRTQVSNWFINAR 549 (594)
Q Consensus 495 ~RkRR~fpk~a~~iLr~Wf~eH~~~PY----PS~eEK~~LA~~TGLS~~QVsNWFiNaR 549 (594)
+|+|..|+.+|+..|++.|... +| |+..++..||..+||++.+|.+||+|.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~---~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKL---GWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHc---CCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4667779999999999999999 99 9999999999999999999999999964
No 19
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.60 E-value=3.7e-08 Score=100.36 Aligned_cols=62 Identities=26% Similarity=0.457 Sum_probs=58.0
Q ss_pred cccCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 492 HQIWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 492 ~~~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.+-+|+|.-|+.++++.|+.-|.++ .|.++..|+.||.++||.+.||+.||+|+|.|+||..
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~en---RYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQEN---RYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred chhcCccccccHHHHHHHHHHHhhh---hhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 4567888889999999999999999 9999999999999999999999999999999998754
No 20
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.36 E-value=3.2e-07 Score=91.70 Aligned_cols=63 Identities=25% Similarity=0.284 Sum_probs=57.4
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 007660 496 RPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMY 561 (594)
Q Consensus 496 RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~ 561 (594)
|.|..|+..|+..|+.-|... .|.+..||.-||+++.|++.||+.||+|+|.|+|+....++.
T Consensus 106 ktRTvFSraQV~qLEs~Fe~k---rYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 106 KTRTVFSRAQVFQLESTFELK---RYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred cchhhhhHHHHHHHHHHHHHH---hhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 455569999999999999999 999999999999999999999999999999999988776543
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.36 E-value=2.5e-07 Score=98.86 Aligned_cols=60 Identities=23% Similarity=0.309 Sum_probs=54.7
Q ss_pred CCCCCC-CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 495 WRPQRG-LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 495 ~RkRR~-fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
+||||+ +.-.++..|+..|.++ |-|+.+|.-.||.+++|.+..|++||+|+|.|.|+..-
T Consensus 294 kRKKRTSie~~vr~aLE~~F~~n---pKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 294 KRKKRTSIEVNVRGALEKHFLKN---PKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccceeHHHHHHHHHHHHhC---CCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 344454 9999999999999999 99999999999999999999999999999999998654
No 22
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.35 E-value=5e-07 Score=89.88 Aligned_cols=67 Identities=22% Similarity=0.274 Sum_probs=59.9
Q ss_pred cccCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 007660 492 HQIWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMY 561 (594)
Q Consensus 492 ~~~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~ 561 (594)
+.-+++|..|+..|...|++-|.+. .|.+.+||.+++..+.||..||+.||+|+|.|-|+--..|.-
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrek---qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E 208 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREK---QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE 208 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHh---hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence 3556777789999999999999999 999999999999999999999999999999998876665543
No 23
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.35 E-value=6.4e-07 Score=89.67 Aligned_cols=62 Identities=26% Similarity=0.410 Sum_probs=56.3
Q ss_pred cCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 494 IWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 494 ~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
.+|.|..|+.++..+|++-|.+- -||+...+++||.+.+|.+.+|++||.|+|.|.++.-..
T Consensus 37 qRRERTtFtr~QlevLe~LF~kT---qYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAKT---QYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred cccccceecHHHHHHHHHHHHhh---cCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 34566779999999999999999 999999999999999999999999999999998876544
No 24
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.34 E-value=6.3e-07 Score=80.98 Aligned_cols=64 Identities=22% Similarity=0.333 Sum_probs=56.6
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 007660 495 WRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMY 561 (594)
Q Consensus 495 ~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~ 561 (594)
+|-|.+|+..+.+.|+..|.+. -||..=.|++||-+..|++..|++||+|+|.+.+|.-.-..+
T Consensus 18 RRIRTTFTS~QLkELErvF~ET---HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 18 RRIRTTFTSAQLKELERVFAET---HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hhhhhhhhHHHHHHHHHHHHhh---cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 3445679999999999999998 899999999999999999999999999999999887654433
No 25
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.31 E-value=5.8e-07 Score=86.01 Aligned_cols=63 Identities=22% Similarity=0.290 Sum_probs=57.5
Q ss_pred ccCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 493 QIWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 493 ~~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
...++|+..+..++.+|+.-|..+ |||+..+|..|+..++++++-|+.||+|+|.+.++....
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~---p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEIN---PYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCcccceechHHHHHHHHHHhccC---CCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 345677779999999999999999 999999999999999999999999999999999876654
No 26
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.29 E-value=4.6e-07 Score=94.49 Aligned_cols=68 Identities=24% Similarity=0.383 Sum_probs=59.2
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHhhhc
Q 007660 496 RPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMYREVNRR 567 (594)
Q Consensus 496 RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~~e~~~~ 567 (594)
|.|..|+-.+.+.|+.||.+| .||+.+.|+++|--|.|++..|++||.|+|.+++|.-.... .|+.+.
T Consensus 114 rQrthFtSqqlqele~tF~rN---rypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~-ae~~k~ 181 (351)
T KOG0486|consen 114 RQRTHFTSQQLQELEATFQRN---RYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ-AELAKG 181 (351)
T ss_pred hhhhhhHHHHHHHHHHHHhhc---cCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH-HHhhhc
Confidence 444559999999999999998 99999999999999999999999999999999888766666 554443
No 27
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.20 E-value=5.7e-07 Score=86.81 Aligned_cols=61 Identities=28% Similarity=0.370 Sum_probs=54.4
Q ss_pred CCCC-CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 496 RPQR-GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 496 RkRR-~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
||.| .|+..+...|++-|... .|.+-.|+.+||..++|+++||.+||+|+|++.||-....
T Consensus 101 ~K~Rtvfs~~ql~~l~~rFe~Q---rYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 101 RKARTVFSDPQLSGLEKRFERQ---RYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred hhhcccccCccccccHHHHhhh---hhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 3444 49999999999999988 8999999999999999999999999999999999866543
No 28
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.16 E-value=1.8e-06 Score=88.22 Aligned_cols=56 Identities=21% Similarity=0.337 Sum_probs=52.1
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 498 QRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 498 RR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
|..|+..+...|++-|.+- -||..-.|++||..|+|.+..|++||+|+|.|++|.-
T Consensus 145 RTiFT~~Qle~LEkaFkea---HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEA---HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred cchhhHHHHHHHHHHHhhc---cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 4569999999999999998 8999999999999999999999999999999987743
No 29
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.15 E-value=9.2e-07 Score=90.69 Aligned_cols=58 Identities=24% Similarity=0.237 Sum_probs=54.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEM 560 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~ 560 (594)
.++..++-.|++-|.-. +|.+...|.+||..+||+++||+.||+|+|.|.+|...++.
T Consensus 205 VYTDhQRLELEKEfh~S---ryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHTS---RYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred Eecchhhhhhhhhhccc---cceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 38999999999999888 99999999999999999999999999999999998887775
No 30
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.06 E-value=4.2e-06 Score=86.66 Aligned_cols=59 Identities=24% Similarity=0.384 Sum_probs=54.9
Q ss_pred ccCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 007660 493 QIWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554 (594)
Q Consensus 493 ~~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkK 554 (594)
..+|+|.+++.++...|+.-|... |-|-.--|++|+.+|||.-..|++||+|+|.+.|+
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~S---pKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKR 224 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTS---PKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKR 224 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCC---CchhHHHHHHhhhccCcceeehhhhhhhhhHHHHh
Confidence 568999999999999999998888 99999999999999999999999999999987654
No 31
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.87 E-value=7.8e-06 Score=82.11 Aligned_cols=90 Identities=20% Similarity=0.275 Sum_probs=68.3
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHhhhccCCCC-----
Q 007660 498 QRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMYREVNRRKAQGS----- 572 (594)
Q Consensus 498 RR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~~e~~~~~s~~~----- 572 (594)
|.+|+..++..|+.-|.+. .||--+++.+||...|++++||.+||+|+|.+++|+-.-||.....|..+...
T Consensus 171 rPTf~g~qi~~le~~feqt---kylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasakkkqds~ae~~~gg 247 (288)
T KOG0847|consen 171 RPTFTGHQIYQLERKFEQT---KYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAKKKQDSGAERGAGG 247 (288)
T ss_pred CCCccchhhhhhhhhhhhh---hcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhccccCCCcccccccC
Confidence 3459999999999999999 99999999999999999999999999999999999887777654333322221
Q ss_pred --CCCCCCcccCCCCCCccc
Q 007660 573 --KEGIDSSRRSQISISNQR 590 (594)
Q Consensus 573 --ess~~~~~~~~~s~~~~~ 590 (594)
.++.+-++.-+..++.|.
T Consensus 248 ~~~eeeDDeYNkPLDPnSDD 267 (288)
T KOG0847|consen 248 APSEEEDDEYNKPLDPNSDD 267 (288)
T ss_pred CCccccccccCCCCCCCcch
Confidence 122344445555555543
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.83 E-value=1.9e-05 Score=87.48 Aligned_cols=55 Identities=24% Similarity=0.324 Sum_probs=52.1
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 007660 495 WRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRL 552 (594)
Q Consensus 495 ~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRl 552 (594)
+|+|-.|+..+++.|++.|.++ +||+.+.-+.|+.+++|.+..|.|||-|+|+|.
T Consensus 421 KKPRlVfTd~QkrTL~aiFke~---~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 421 KKPRLVFTDIQKRTLQAIFKEN---KRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCceeeecHHHHHHHHHHHhcC---CCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 5666679999999999999999 999999999999999999999999999999995
No 33
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.72 E-value=1.1e-05 Score=84.10 Aligned_cols=57 Identities=18% Similarity=0.353 Sum_probs=52.2
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 498 QRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 498 RR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
|.-|+++|+..|++-|++. -|-+...|.+||..++|.+..|++||+|+|+|.|+..+
T Consensus 185 RTAFTReQIaRLEKEFyrE---NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYRE---NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HhhhhHHHHHHHHHHHHHh---ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 3559999999999988888 79999999999999999999999999999999987655
No 34
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.52 E-value=7.1e-05 Score=79.90 Aligned_cols=62 Identities=23% Similarity=0.431 Sum_probs=56.2
Q ss_pred cCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 494 IWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 494 ~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
.+|.|..|+..+...|+++|... |||....|+.||++++|+...|+.||.|+|.|.+|....
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt---~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRT---PYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccchHHHHHHHhcCC---CCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 34556679999999999999999 899999999999999999999999999999999887643
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.26 E-value=0.00013 Score=70.85 Aligned_cols=60 Identities=18% Similarity=0.090 Sum_probs=54.5
Q ss_pred cCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 494 IWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 494 ~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.+|.|.+|+..+...|+.-|... +||+...++.||..+++++..|++||+|+|.++++..
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~~---h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEKV---HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcCC---CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 34556679999999999999999 9999999999999999999999999999999988654
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.18 E-value=0.00013 Score=76.05 Aligned_cols=59 Identities=22% Similarity=0.342 Sum_probs=52.7
Q ss_pred ccCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 007660 493 QIWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554 (594)
Q Consensus 493 ~~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkK 554 (594)
+.+|||..+-..-++.|+++|... |-|+.+....+|+++.|.+..|.+||+|+|.|.|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQ---PRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQ---PRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhccC---CCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 445666667777789999999999 99999999999999999999999999999999887
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.13 E-value=0.00019 Score=75.25 Aligned_cols=61 Identities=44% Similarity=0.662 Sum_probs=55.6
Q ss_pred CCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 496 RPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 496 RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
+++.+.+.+. ..|+.|+.+|..+|||++.++.+|+-.++++..||++||+|+|+|+++.+.
T Consensus 97 ~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~ 157 (342)
T KOG0773|consen 97 ARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELK 157 (342)
T ss_pred cccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccC
Confidence 3456689899 999999999999999999999999999999999999999999999876544
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.43 E-value=0.0024 Score=52.14 Aligned_cols=43 Identities=19% Similarity=0.361 Sum_probs=31.6
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhh
Q 007660 506 VSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVR 551 (594)
Q Consensus 506 ~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrR 551 (594)
.+.|+++|..| .++.+.+...|+.+++|+..||..||.-++.+
T Consensus 10 ~~pL~~Yy~~h---~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKH---KQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT-------TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHc---CCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 45599999999 99999999999999999999999999876543
No 39
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=95.59 E-value=0.028 Score=45.44 Aligned_cols=43 Identities=12% Similarity=0.061 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCchhhHHHHHHHHHHhhhhh
Q 007660 385 RQAVEAKKAQLLALLQMVDDRYNQCLDEIHTVVSAFHAATELDPQVHARFALHTISFLYKNL 446 (594)
Q Consensus 385 r~elq~kkakLl~mL~ev~~RY~qy~~qm~~V~ssFea~~~~~~~~yt~lAl~tmSrhFr~L 446 (594)
+.|||+||..|+.||.++++...+.+++ |..|++.|..++..|
T Consensus 8 dpELDqFMeaYc~~L~kykeeL~~p~~E-------------------A~~f~~~ie~qL~~L 50 (52)
T PF03791_consen 8 DPELDQFMEAYCDMLVKYKEELQRPFQE-------------------AMEFCREIEQQLSSL 50 (52)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHH
Confidence 4789999999999999999999999885 445666666666655
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.63 E-value=0.027 Score=54.82 Aligned_cols=61 Identities=28% Similarity=0.484 Sum_probs=53.8
Q ss_pred cCCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 494 IWRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 494 ~~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..+.+..+...+..++..-|... +||....++.|+..+|++...|.+||+|.|.+.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~---~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRAT---PKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccCC---CCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34556678999999999988888 99999999999999999999999999999999887554
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.62 E-value=0.23 Score=60.89 Aligned_cols=59 Identities=20% Similarity=0.321 Sum_probs=53.9
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 498 QRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 498 RR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
|..+.-.++++++..|..- -||+.++.+.|.+..+|.+..|..||+|+|.+-+|.....
T Consensus 907 ~~~~~d~qlk~i~~~~~~q---~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 907 RTQESDLQLKIIKACYEAQ---RTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred ccchhHHHHHHHHHHHhhc---cCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 3448889999999999998 9999999999999999999999999999999999887744
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=80.56 E-value=2.4 Score=33.80 Aligned_cols=47 Identities=19% Similarity=0.189 Sum_probs=32.4
Q ss_pred CCCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 007660 495 WRPQRGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINAR 549 (594)
Q Consensus 495 ~RkRR~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaR 549 (594)
+|+|+.|+-+.+-.+-.-+... + -+..+|+..|++.++|++|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-----~---s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-----E---SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-----T----HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-----C---CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 3667778888866655555655 2 578999999999999999999853
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=73.98 E-value=4.6 Score=47.68 Aligned_cols=44 Identities=27% Similarity=0.442 Sum_probs=41.4
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 007660 506 VSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRL 552 (594)
Q Consensus 506 ~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRl 552 (594)
+.+|+++|..+ +.|+.+|...+|.+.||...-|+.||.+.+...
T Consensus 568 ~sllkayyaln---~~ps~eelskia~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYALN---GLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHHhc---CCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh
Confidence 88999999999 999999999999999999999999999988754
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=73.63 E-value=4.4 Score=31.08 Aligned_cols=47 Identities=26% Similarity=0.370 Sum_probs=37.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkK 554 (594)
.||++.+.+|...|++. -.-.++|+..|+|...|..+...+..++++
T Consensus 4 ~L~~~er~vi~~~y~~~--------~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG--------LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTST---------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC--------CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 47889999998888555 334689999999999999999999888764
No 45
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=72.63 E-value=5.9 Score=28.78 Aligned_cols=46 Identities=22% Similarity=0.230 Sum_probs=36.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLW 553 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlk 553 (594)
.+++....++...+.+. -.-..+|..+|++..+|..|....+.+++
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 37778888888777655 23457899999999999999988887754
No 46
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=71.48 E-value=53 Score=31.66 Aligned_cols=52 Identities=19% Similarity=0.110 Sum_probs=43.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
.||+..+.++.-.+.+.+.+ .++|+.+|++...|.++...+|+++++.+...
T Consensus 116 ~Lp~~~r~i~~L~~~~g~s~--------~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~ 167 (187)
T PRK12516 116 QLPDDQREAIILVGASGFAY--------EEAAEICGCAVGTIKSRVNRARQRLQEILQIE 167 (187)
T ss_pred hCCHHHHHHHHHHHHcCCCH--------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 48999999998877776322 48999999999999999999999998876543
No 47
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=71.20 E-value=6.2 Score=32.21 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=30.5
Q ss_pred CCCCCCChhHHH-HHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhh
Q 007660 496 RPQRGLPEKSVS-VLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINAR 549 (594)
Q Consensus 496 RkRR~fpk~a~~-iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaR 549 (594)
++++.|+++.+. ++...+... .....+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g--------~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG--------ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH--------CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC--------CceEeeecccccccccccHHHHHHh
Confidence 456778888854 445554544 6788999999999999999977665
No 48
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=69.56 E-value=6.6 Score=30.29 Aligned_cols=45 Identities=24% Similarity=0.336 Sum_probs=34.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRL 552 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRl 552 (594)
.||+..+.++.-.+.+. -.-.++|+.+|++...|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 47888888888777766 3446899999999999999999998864
No 49
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=65.25 E-value=8.2 Score=35.51 Aligned_cols=52 Identities=23% Similarity=0.193 Sum_probs=43.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
.||+..+.++.-.+.+.+.+ .++|+.+|++...|.+++.-+|+++++.+.++
T Consensus 106 ~Lp~~~r~v~~l~~~~g~s~--------~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEKSY--------QEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred hCCHHHHHHHHHHHHhCCCH--------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 48999999998877776322 48999999999999999999999998876543
No 50
>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=64.54 E-value=13 Score=23.96 Aligned_cols=39 Identities=13% Similarity=0.207 Sum_probs=27.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWF 545 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWF 545 (594)
+.++.+....+..++.. .+ ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 34666666666555443 33 35588899999999999984
No 51
>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=63.11 E-value=91 Score=30.70 Aligned_cols=50 Identities=22% Similarity=0.386 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++...+.+. -.-.++|+.+|++...|..|...+++++++.+
T Consensus 177 ~~L~~~~r~vl~l~y~~~--------~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 177 AALPERERRILLLRFFED--------KTQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred HcCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 359999999998887655 23468999999999999999999999988654
No 52
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=63.09 E-value=1.2e+02 Score=27.70 Aligned_cols=52 Identities=19% Similarity=0.141 Sum_probs=41.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
.||+..+.++.-.+.+. -.-.++|+..|+++..|.+|..-+|.++++.+...
T Consensus 125 ~L~~~~r~i~~l~~~~~--------~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~ 176 (179)
T PRK11924 125 ALPVKQREVFLLRYVEG--------LSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ 176 (179)
T ss_pred hCCHHHHHHhhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 38888888887666554 22368999999999999999999999998766543
No 53
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=62.53 E-value=1.2e+02 Score=28.74 Aligned_cols=51 Identities=14% Similarity=0.212 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
.||++.+.++.--+++.+ .-.++|+.+|++...|.++...+|+++++.+..
T Consensus 128 ~L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 128 ALPERQREAIVLQYYQGL--------SNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred hCCHHHHHHhhHHHhcCC--------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 488999999877666662 235899999999999999999999998876543
No 54
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=60.45 E-value=11 Score=34.38 Aligned_cols=47 Identities=19% Similarity=0.145 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkK 554 (594)
.||+..+.++..-+.+.+. -.++|+.+|++...|.+|...+|+++++
T Consensus 106 ~L~~~~r~ii~l~~~~~~s--------~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGKT--------MGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 5899999998777666622 4589999999999999999999999875
No 55
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=60.39 E-value=22 Score=28.03 Aligned_cols=46 Identities=20% Similarity=0.228 Sum_probs=26.9
Q ss_pred HHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 007660 509 LRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMY 561 (594)
Q Consensus 509 Lr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~ 561 (594)
|+.++.++ -+ ....||+.+|+++.+|..|+.+...+..-..+.++-
T Consensus 2 L~~~m~~~---~i----t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia 47 (63)
T PF13443_consen 2 LKELMAER---GI----TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIA 47 (63)
T ss_dssp HHHHHHHT---T------HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHH
T ss_pred HHHHHHHc---CC----CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHH
Confidence 45556665 22 456899999999999999999885555544454443
No 56
>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=60.28 E-value=1.1e+02 Score=26.38 Aligned_cols=48 Identities=23% Similarity=0.253 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
.||+..+.++...+... | ...++|+.+|+++..|.+|....+.++++.
T Consensus 110 ~L~~~~~~ii~~~~~~g----~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG----L----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 47888888876554443 2 345899999999999999999999988764
No 57
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=59.48 E-value=13 Score=34.51 Aligned_cols=53 Identities=17% Similarity=0.112 Sum_probs=44.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
..||+..+.++.-++.+++ .-.++|..+|++...|.+|..-+|+++++-+.++
T Consensus 107 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 159 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHEL--------TYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159 (165)
T ss_pred HhCCHHHHHHHHhHHHhcC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 4589999999998888873 3358999999999999999999999998765443
No 58
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=59.25 E-value=1.5e+02 Score=27.53 Aligned_cols=50 Identities=16% Similarity=0.039 Sum_probs=42.1
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..++++.-.+.+.+. -.++|+.+|+++..|.++..-+|+++++.+
T Consensus 111 ~~L~~~~r~v~~l~~~~g~s--------~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 111 NLLSADQREAIILIGASGFS--------YEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred HhCCHHHHHHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 35899999999888777733 348999999999999999999999988654
No 59
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=59.21 E-value=92 Score=33.15 Aligned_cols=116 Identities=12% Similarity=0.305 Sum_probs=67.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCchhhHHHHHHHHHHhhhhhHHHHHHHHHHhhc---ccC
Q 007660 386 QAVEAKKAQLLALLQMVDDRYNQCLDEIHTVVSAFHAATELDPQVHARFALHTISFLYKNLRERISSQILAMGA---HFD 462 (594)
Q Consensus 386 ~elq~kkakLl~mL~ev~~RY~qy~~qm~~V~ssFea~~~~~~~~yt~lAl~tmSrhFr~Lr~~Is~qi~~~g~---~~~ 462 (594)
.+|+++|..|..-++++++|-++--.+|.+ +|--+. +.+.+--+-.++-+.+.++.+.. .++
T Consensus 7 ~eL~qrk~~Lq~eIe~LerR~~ri~~Emrt---sFaG~S------------q~lA~RVqGFkdYLvGsLQDLa~saEqLe 71 (283)
T PF11285_consen 7 KELEQRKQALQIEIEQLERRRERIEKEMRT---SFAGQS------------QDLAIRVQGFKDYLVGSLQDLAQSAEQLE 71 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---ccccch------------HHHHHHHhhhHHHHHHHHHHHHHHHHhhc
Confidence 688999999999999999999999998887 554221 22223333334444454443221 110
Q ss_pred --C------CCCCC-------------C-ccccchhhhhhH-----HHHHHhhhh---hcccCCCCCCCChhHHHHHHHH
Q 007660 463 --S------KSTRG-------------K-DTVMVDSFIKEQ-----WALQQLKKK---EHQIWRPQRGLPEKSVSVLRAW 512 (594)
Q Consensus 463 --~------~~s~~-------------~-e~s~~~~~lq~q-----~alqql~~k---~~~~~RkRR~fpk~a~~iLr~W 512 (594)
+ ..+.+ . ...+..+..+.+ ..+.|++.+ +-..|+-||+|.+--...+.+|
T Consensus 72 Lv~~~~~~~psp~~~~~~~~~~~~~~~~~~~~~~~~~F~~~~~~Ir~~l~qyr~~PDyYg~PWqLRRtfe~~hae~v~~W 151 (283)
T PF11285_consen 72 LVPQPVVVQPSPLDEPAPPPQANAAKNPPTPQFAAQTFQPDERQIRRLLDQYRTQPDYYGPPWQLRRTFEPIHAERVEDW 151 (283)
T ss_pred cCCCCcCCCCCcccccccCcccccccCCCCCcchhhhcchHHHHHHHHHHHHhhCCCccCChHHHHhcccHHHHHHHHHH
Confidence 0 00000 0 001112222222 334455544 3467999999999999999999
Q ss_pred HHHc
Q 007660 513 MFQN 516 (594)
Q Consensus 513 f~eH 516 (594)
|+.-
T Consensus 152 FF~q 155 (283)
T PF11285_consen 152 FFNQ 155 (283)
T ss_pred Hhcc
Confidence 9974
No 60
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=59.07 E-value=15 Score=35.31 Aligned_cols=55 Identities=11% Similarity=0.260 Sum_probs=45.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMY 561 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~ 561 (594)
..||+..+.++.-.+.+.+ .-.++|..+|+++..|.++..-+|+++++.+.++++
T Consensus 133 ~~Lp~~~R~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~ 187 (189)
T PRK12530 133 NHLPAQQARVFMMREYLEL--------SSEQICQECDISTSNLHVLLYRARLQLQACLSKNWF 187 (189)
T ss_pred HhCCHHHHHHHhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3489999999988777762 235899999999999999999999999998876654
No 61
>PRK06930 positive control sigma-like factor; Validated
Probab=57.24 E-value=12 Score=36.41 Aligned_cols=55 Identities=13% Similarity=0.103 Sum_probs=46.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMYR 562 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~~ 562 (594)
.||+..+.++.-.+.+.+ .-.++|..+|++...|.++...+|.++++.+.++++|
T Consensus 114 ~L~~rer~V~~L~~~eg~--------s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~l~~ 168 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL--------SYSEIADYLNIKKSTVQSMIERAEKKIARQINESLFC 168 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 488999999887666652 2358999999999999999999999999988877765
No 62
>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=56.40 E-value=15 Score=33.03 Aligned_cols=48 Identities=21% Similarity=0.210 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
.||++...++.-.+.+. + ...++|+.+|+++..|.++...+|+++++.
T Consensus 113 ~L~~~~r~il~l~~~~~----~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG----K----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 58888899988766554 2 234699999999999999999999998864
No 63
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=54.83 E-value=1.5e+02 Score=28.74 Aligned_cols=50 Identities=22% Similarity=0.135 Sum_probs=42.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.||+..+.++.-.+.+.+. -.++|+.+|++...|.+++.-+|+++++.+.
T Consensus 113 ~Lp~~~r~v~~L~~~~g~s--------~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 113 QLPDEQREALILVGASGFS--------YEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred hCCHHHhHHhhhHHhcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 5899999999888777632 2489999999999999999999999987664
No 64
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=54.56 E-value=17 Score=33.51 Aligned_cols=50 Identities=18% Similarity=0.177 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.|++..+.++.-.+...+ + -.++|+.+|+++..|.+|...+|+++++.+.
T Consensus 128 ~L~~~~r~vl~l~~~~~~--s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 128 SLPEELRTAITLREIEGL--S------YEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred hCCHHHHHHHHHHHHcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 488999999976655542 2 2489999999999999999999999987663
No 65
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=52.90 E-value=15 Score=34.64 Aligned_cols=51 Identities=14% Similarity=0.075 Sum_probs=42.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
.||+..+.++.-.+.+.+ .-.++|+.+|++...|.+++..+|+++++.+..
T Consensus 131 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA--------SIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 589999999988777762 235899999999999999999999999876643
No 66
>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=52.16 E-value=14 Score=34.75 Aligned_cols=50 Identities=14% Similarity=0.091 Sum_probs=41.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++.-.+.++ -.-.++|+.+|++...|.++...+|+++++.+
T Consensus 137 ~~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 137 EALPEDLRTAITLRELEG--------LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred HcCCHHHhhhhhhhhhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 348888899987766666 23358999999999999999999999998765
No 67
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=52.02 E-value=18 Score=34.79 Aligned_cols=49 Identities=10% Similarity=0.124 Sum_probs=41.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.||+..+.+|.-.+.+.+ .-.++|+.+|++...|.++...+|+++++.+
T Consensus 142 ~L~~~~r~vl~l~~~~~~--------s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGGL--------TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 499999999988777772 2358999999999999999999999988765
No 68
>PRK00118 putative DNA-binding protein; Validated
Probab=51.78 E-value=19 Score=32.97 Aligned_cols=48 Identities=15% Similarity=0.075 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
.+|+.++.++..++.+. -.-..+|+.+|+++..|.+|...+|+++++-
T Consensus 17 ~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 47888999998888776 2234799999999999999999999988763
No 69
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=51.44 E-value=19 Score=33.83 Aligned_cols=50 Identities=12% Similarity=0.268 Sum_probs=41.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||++.+.++.-.+.+.+ .-.++|+.+|++...|.++...+|+++++-+
T Consensus 128 ~~L~~~~r~i~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 177 (179)
T PRK12514 128 EELEKDRAAAVRRAYLEGL--------SYKELAERHDVPLNTMRTWLRRSLLKLRECL 177 (179)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence 3489999999988887662 2358999999999999999999999998754
No 70
>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=51.05 E-value=18 Score=33.87 Aligned_cols=48 Identities=17% Similarity=0.145 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
.||++.+.++.-.+.+.+. -.++|..+|+++..|.+....+|.++++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g~s--------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAGLT--------VEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4999999999888877632 35899999999999999999999998874
No 71
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=50.35 E-value=17 Score=33.46 Aligned_cols=48 Identities=21% Similarity=0.167 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkK 554 (594)
..||++++.++.-.+.+.+. -.++|..+|++...|..+...+|+++++
T Consensus 111 ~~L~~~~r~v~~l~~~~~~s--------~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYGFS--------YKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45999999999887777732 3489999999999999999999999875
No 72
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=49.93 E-value=1.5e+02 Score=28.21 Aligned_cols=51 Identities=18% Similarity=0.204 Sum_probs=40.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..||+..+.++.-.+.+.+ .-.++|+.+|++...|.++...+|+++++.+.
T Consensus 138 ~~L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 138 ETLPDEQREVFLLREHGDL--------ELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred HhCCHhHhhheeeehccCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3488888888876655552 23589999999999999999999999988664
No 73
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=49.38 E-value=21 Score=34.88 Aligned_cols=51 Identities=24% Similarity=0.247 Sum_probs=42.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..||++.+.++.--+++.+ .-.++|..+|++...|.++...+|+++++.+.
T Consensus 152 ~~L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 152 EKLPEAQQTVVKGVYFQEL--------SQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3489999999987777663 23589999999999999999999999887664
No 74
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=48.96 E-value=21 Score=34.29 Aligned_cols=53 Identities=21% Similarity=0.182 Sum_probs=42.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
..||++.+.++.-.+.+.+. -.++|..+|++...|.+....+|+++++.+.++
T Consensus 140 ~~Lp~~~r~v~~l~~~eg~s--------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~~ 192 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEELP--------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDAE 192 (194)
T ss_pred HhCCHHHHHHHHHHHHcCCC--------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhhc
Confidence 45899999999877766632 348999999999999999999999888766543
No 75
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=48.74 E-value=22 Score=33.72 Aligned_cols=50 Identities=24% Similarity=0.147 Sum_probs=41.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++.--+.+.+ .-.++|..+|++...|.++...+|+++++.+
T Consensus 138 ~~L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 138 DTLPEKQREILILRVVVGL--------SAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4589999999988777662 2458999999999999999999999988754
No 76
>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=48.71 E-value=24 Score=35.95 Aligned_cols=57 Identities=21% Similarity=0.327 Sum_probs=47.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMYRE 563 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~~e 563 (594)
..||++.+.++.-.+.+.+. -.++|..+|++...|.++...+|+++++.+.++....
T Consensus 160 ~~Lp~~~R~v~~L~~~eg~S--------~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~ 216 (244)
T TIGR03001 160 AALSERERHLLRLHFVDGLS--------MDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAER 216 (244)
T ss_pred HhCCHHHHHHHHHHHHcCCC--------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45899999999888887733 3489999999999999999999999999887765543
No 77
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=48.23 E-value=20 Score=32.75 Aligned_cols=52 Identities=15% Similarity=0.124 Sum_probs=43.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
..||+..+.++.-.+.+.+. -.++|..+|++...|.+...-+|+++++.+.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~g~s--------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 156 (161)
T PRK09047 105 QKLPARQREAFLLRYWEDMD--------VAETAAAMGCSEGSVKTHCSRATHALAKALEA 156 (161)
T ss_pred HhCCHHHHHHHHHHHHhcCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 45999999999887777632 35899999999999999999999999876643
No 78
>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=47.20 E-value=24 Score=32.15 Aligned_cols=48 Identities=27% Similarity=0.270 Sum_probs=39.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkK 554 (594)
..||+..+.++.-.+.+.+ .-.++|+.+|++...|.++..-+|+++++
T Consensus 110 ~~L~~~~r~v~~l~~~~g~--------~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRGV--------SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3489999999988666652 23589999999999999999999988875
No 79
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=47.09 E-value=22 Score=33.80 Aligned_cols=51 Identities=18% Similarity=0.237 Sum_probs=41.6
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..||++.+.++.--+.+.+ .-.++|..+|++...|.+|+..+|+++++.+.
T Consensus 140 ~~L~~~~~~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 140 AQLPESQRQVLELAYYEGL--------SQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred HhCCHHHhhhhhhhhhcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3588889999877766652 23589999999999999999999999988654
No 80
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=47.03 E-value=28 Score=33.21 Aligned_cols=54 Identities=17% Similarity=0.158 Sum_probs=44.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEM 560 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~ 560 (594)
..||++++.++.-.+.+.+ + -.++|..+|++...|.+....+|+++++-+..+.
T Consensus 130 ~~Lp~~~r~v~~l~~~~g~--s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 130 DRLPPRTGRVFMMREWLEL--E------TEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HhCCHHHHHHHHHHHHcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3489999999988777662 2 3589999999999999999999999988776654
No 81
>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=46.82 E-value=29 Score=33.31 Aligned_cols=55 Identities=16% Similarity=0.231 Sum_probs=45.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMY 561 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~ 561 (594)
..||++.+.++.-.+.+.+ .-.++|+.+|++..-|.+...-+|+++++-+.....
T Consensus 130 ~~L~~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~~ 184 (188)
T TIGR02943 130 YHLPEQTARVFMMREVLGF--------ESDEICQELEISTSNCHVLLYRARLSLRACLSINWF 184 (188)
T ss_pred HhCCHHHHHHHHHHHHhCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3589999999988877772 346899999999999999999999999987765543
No 82
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=46.78 E-value=23 Score=33.89 Aligned_cols=52 Identities=17% Similarity=0.236 Sum_probs=43.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
.||+..+.++.-.+.+.+ .-.++|+.+|++...|.++...+|+++++.+..+
T Consensus 136 ~L~~~~r~i~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 187 (195)
T PRK12532 136 NLPENTARVFTLKEILGF--------SSDEIQQMCGISTSNYHTIMHRARESLRQCLQIK 187 (195)
T ss_pred hCCHHHHHHhhhHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 589999999987666662 2358999999999999999999999999877544
No 83
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=45.53 E-value=26 Score=32.85 Aligned_cols=50 Identities=12% Similarity=0.183 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||++++.++.-.+.+.+.+ .++|+.+|++...|.++...+|++++..+
T Consensus 118 ~~Lp~~~r~v~~L~~~~g~s~--------~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDGMGH--------AEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred HhCCHHHHHHHHHHHHcCCCH--------HHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 348999999998877766322 48999999999999999999999986543
No 84
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=45.52 E-value=27 Score=33.04 Aligned_cols=50 Identities=14% Similarity=0.086 Sum_probs=41.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.||+..+.++.-.+.+++ .-.++|+.+|+++..|.+....+|+++++.+.
T Consensus 129 ~L~~~~r~v~~l~~~~g~--------s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~ 178 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEGL--------SVAETAQLTGLSESAVKVGIHRGLKALAAKIR 178 (181)
T ss_pred HCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 488888888877777662 23589999999999999999999999988654
No 85
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=45.50 E-value=23 Score=33.85 Aligned_cols=51 Identities=22% Similarity=0.232 Sum_probs=41.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..||++.+.++.-.|.+.+ + -.++|+.+|++...|.+...-+|+++++..+
T Consensus 130 ~~L~~~~r~i~~l~~~~g~--s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLGE--K------IEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HhCCHHHHHHHHHHHHccC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 4599999999987766662 2 3589999999999999999999999887543
No 86
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=45.48 E-value=26 Score=32.27 Aligned_cols=50 Identities=18% Similarity=0.233 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..||++.+.+|.-.+ +. + .-.++|+.+|++...|.++...+|.++++-+.
T Consensus 111 ~~L~~~~r~il~l~~-~g----~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 111 AKMTERDRTVLLLRF-SG----Y----SYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred HcCCHHHHHHHHHHH-cC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 348888888887776 55 2 34589999999999999999999999887654
No 87
>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=45.44 E-value=25 Score=32.29 Aligned_cols=50 Identities=20% Similarity=0.302 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++.--+.+.+. -.++|..+|++...|.++...+|.++++.+
T Consensus 109 ~~L~~~~r~i~~l~~~~g~s--------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 109 RRLPARQRAVVVLRYYEDLS--------EAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred HhCCHHHHHHhhhHHHhcCC--------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 35889999999777766632 248999999999999999999999988754
No 88
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=45.14 E-value=34 Score=33.70 Aligned_cols=55 Identities=22% Similarity=0.346 Sum_probs=45.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMY 561 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~ 561 (594)
..||++.+.++.--+++.+ .-.++|..+|++...|.++..-+|+++++.+....+
T Consensus 147 ~~L~~~~r~v~~L~~~~g~--------s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 201 (206)
T PRK12544 147 DGLPAKYARVFMMREFIEL--------ETNEICHAVDLSVSNLNVLLYRARLRLRECLENKWF 201 (206)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3589999999988777772 235899999999999999999999999998875543
No 89
>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=45.08 E-value=21 Score=33.18 Aligned_cols=49 Identities=14% Similarity=0.146 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.||++.+.++..-+++.+. -.++|+.+|++...|.++..-+|+++++.+
T Consensus 119 ~L~~~~r~i~~l~~~~g~s--------~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHDLT--------IKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4888999999877776622 348999999999999999999999988754
No 90
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=44.43 E-value=24 Score=33.23 Aligned_cols=50 Identities=18% Similarity=0.203 Sum_probs=41.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++.-.+.+.+ .-.++|+.+|++...|.++...+|.++++.+
T Consensus 134 ~~L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 134 KALSPEERRVIEVLYYQGY--------THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3499999999987776662 2358999999999999999999999988755
No 91
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=43.96 E-value=22 Score=35.43 Aligned_cols=49 Identities=22% Similarity=0.312 Sum_probs=41.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.||+..+.++...|.+.+ .-.++|+.+|++...|.++...+|+++++.+
T Consensus 184 ~L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQEEL--------NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhccCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 489999999988776652 3458999999999999999999999998755
No 92
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=43.73 E-value=51 Score=31.76 Aligned_cols=53 Identities=25% Similarity=0.150 Sum_probs=41.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEM 560 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~ 560 (594)
..|++.++++|+. +.+. -.-.++|+.+|++...|++|-..+|.++++-...=.
T Consensus 5 ~~Lt~rqreVL~l-r~~G--------lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl~ 57 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG--------LTQQEIADILGTSRANVSSIEKRARENIEKARETLA 57 (141)
T ss_pred cCCCHHHHHHHHH-HHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999977 3333 233589999999999999999999999877665433
No 93
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=43.58 E-value=29 Score=32.88 Aligned_cols=58 Identities=22% Similarity=0.226 Sum_probs=45.6
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHHHh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMYREV 564 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~~e~ 564 (594)
..||+..+.++.-.+.+.+. -.++|+.+|++...|.+....+|+++++.+......++
T Consensus 121 ~~L~~~~r~i~~l~~~~g~s--------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~ 178 (185)
T PRK12542 121 KELNESNRQVFKYKVFYNLT--------YQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDEF 178 (185)
T ss_pred HhCCHHHHHHHHHHHHcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHHH
Confidence 45899999999876666632 24899999999999999999999999887655444443
No 94
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=42.22 E-value=37 Score=32.30 Aligned_cols=51 Identities=12% Similarity=0.144 Sum_probs=42.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..||++.+.+|.--+.+.+ .-.++|+.+|+++..|.+-+..+|+++++.+.
T Consensus 130 ~~L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHEK--------SVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3589999999977776662 23589999999999999999999999887654
No 95
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=42.11 E-value=29 Score=32.52 Aligned_cols=50 Identities=18% Similarity=0.147 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++.--+.+. -.-.++|+.+|++...|.+++..+|+++++.+
T Consensus 135 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 135 QALPPKYRMVIVLKYMED--------LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred HhCCHHHhHHhhhHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 358999999987755544 22358999999999999999999999988754
No 96
>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=42.02 E-value=25 Score=33.10 Aligned_cols=52 Identities=17% Similarity=0.252 Sum_probs=42.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
..||++.+.++.-.+.+.+ .-.++|+.+|++...|.++..-+|+++++-+..
T Consensus 99 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 99 KELPDEYREAIRLTELEGL--------SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999988777763 235899999999999999999999998886543
No 97
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=41.01 E-value=31 Score=32.13 Aligned_cols=50 Identities=16% Similarity=0.152 Sum_probs=42.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.||+..+.+|.--+.+.+. -.++|+.+|++...|.+...-+|+++++.+.
T Consensus 118 ~L~~~~r~vl~L~~~~g~s--------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRGWS--------TAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred hCCHHHHHHHHHHHHcCCC--------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 4899999999887777632 3589999999999999999999999987664
No 98
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=40.56 E-value=6.3e+02 Score=30.42 Aligned_cols=17 Identities=18% Similarity=0.192 Sum_probs=14.8
Q ss_pred CCChhHHHHHHHHHHHc
Q 007660 500 GLPEKSVSVLRAWMFQN 516 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH 516 (594)
.|++.|.+.+++-+.++
T Consensus 681 ~L~~~Q~~~I~~iL~~~ 697 (717)
T PF10168_consen 681 VLSESQKRTIKEILKQQ 697 (717)
T ss_pred cCCHHHHHHHHHHHHHH
Confidence 59999999998888877
No 99
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.54 E-value=80 Score=23.25 Aligned_cols=51 Identities=18% Similarity=0.194 Sum_probs=36.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
.|+++...++..+ .+. + ...++|+.+|+++..|..|....+.++.-....+
T Consensus 3 ~l~~~e~~i~~~~-~~g----~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~~~ 53 (58)
T smart00421 3 SLTPREREVLRLL-AEG----L----TNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQ 53 (58)
T ss_pred CCCHHHHHHHHHH-HcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHH
Confidence 4777778877543 322 2 3468999999999999999998887776554443
No 100
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=40.46 E-value=36 Score=32.75 Aligned_cols=49 Identities=12% Similarity=0.110 Sum_probs=40.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.||++.+.++.-.+.+.+ + -.++|+.+|++...|.+++.-+|+++++.+
T Consensus 136 ~L~~~~r~i~~L~~~~g~--s------~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIEGL--S------NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHcCC--C------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 589999998877666552 2 358999999999999999999999998755
No 101
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=39.64 E-value=3.8e+02 Score=26.33 Aligned_cols=50 Identities=14% Similarity=0.159 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.||+..+.++.--+.+.+ + -.++|+.+|++...|.++..-+|+++++.+.
T Consensus 138 ~L~~~~r~v~~L~~~~g~--s------~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEGL--S------YEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred hCCHHHHHHHHHHHHcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 488888888766666662 2 2589999999999999999999999987664
No 102
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=39.54 E-value=33 Score=34.66 Aligned_cols=49 Identities=16% Similarity=0.239 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.||+..+.+|.-.|.+.+. -.++|+.+|++...|..|...+|+++++.+
T Consensus 205 ~L~~~~r~vl~l~~~~g~s--------~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIENLS--------QKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4899999999887776532 268999999999999999999999988654
No 103
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=39.06 E-value=27 Score=34.90 Aligned_cols=53 Identities=19% Similarity=0.112 Sum_probs=44.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
..||+..+.++.-.+.+++. -.++|+.+|++...|.++...+|+++++.+.++
T Consensus 133 ~~Lp~~~R~v~~L~y~eg~s--------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 133 AKLPVEYREVLVLRELEDMS--------YREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred HcCCHHHHhHhhhHHhcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 45899999999988888732 248999999999999999999999999877544
No 104
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=39.06 E-value=38 Score=32.14 Aligned_cols=49 Identities=12% Similarity=0.106 Sum_probs=40.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
..||++.+.++.--+.+.+ .-.++|+.+|++...|.+|...+|+++++.
T Consensus 132 ~~L~~~~r~i~~l~~~~~~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHAYVDGC--------SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 4589999998877776662 235899999999999999999999988764
No 105
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=38.79 E-value=40 Score=32.73 Aligned_cols=53 Identities=26% Similarity=0.262 Sum_probs=43.6
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
..||+..+.++.--+++.+. -.++|..+|++...|.+....+|+++++.+.+.
T Consensus 138 ~~Lp~~~r~v~~L~~~eg~s--------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 190 (201)
T PRK12545 138 DHLPEQIGRVFMMREFLDFE--------IDDICTELTLTANHCSVLLYRARTRLRTCLSEK 190 (201)
T ss_pred HhCCHHHHHHHHHHHHcCCC--------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34899999999887777632 248999999999999999999999999877543
No 106
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=37.70 E-value=37 Score=32.26 Aligned_cols=51 Identities=20% Similarity=0.140 Sum_probs=42.1
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..||+..+.++.-.+.+.+ .-.++|+.+|++...|.++...+|+++++-+.
T Consensus 130 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLEGL--------SVAEAATRSGMSESAVKVSVHRGLKALAALIG 180 (184)
T ss_pred HhCCHHHHHHHHHHHHcCC--------cHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHh
Confidence 3489999999988777663 23589999999999999999999999887553
No 107
>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=37.62 E-value=23 Score=33.80 Aligned_cols=51 Identities=22% Similarity=0.240 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
.||++.+.++.-.+.+.+. -.++|+.+|++...|.++..-+|+++++.+..
T Consensus 131 ~Lp~~~r~i~~L~~~~g~s--------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEGFA--------YKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred hCCHHHhhheeehhhcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4888888888666666522 35899999999999999999999999887653
No 108
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=37.45 E-value=97 Score=27.91 Aligned_cols=55 Identities=15% Similarity=0.158 Sum_probs=43.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMYR 562 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~~ 562 (594)
..|++...++|+-+ .++ |. ..++|+..+++.+.|.+|..+.|+|+.-....++..
T Consensus 148 ~~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~~ 202 (211)
T PRK15369 148 PLLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLN 202 (211)
T ss_pred cCCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHH
Confidence 34999999999874 444 22 468899999999999999999999987666655544
No 109
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=36.92 E-value=33 Score=34.60 Aligned_cols=50 Identities=18% Similarity=0.179 Sum_probs=42.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++.-.|.+.+. -.++|+.+|++...|..+...++.++++.+
T Consensus 204 ~~L~~~~r~ii~l~~~~g~s--------~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 204 PILSEREKSIIHCTFEENLS--------QKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred HcCCHHHHHHHHHHHcCCCC--------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 35899999999888776632 368999999999999999999999988755
No 110
>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=36.80 E-value=68 Score=25.25 Aligned_cols=53 Identities=19% Similarity=0.158 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEMY 561 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~~ 561 (594)
.|++....+|+-+..-. ...++|+..|++++.|..+..+.++|+.-+...++.
T Consensus 3 ~LT~~E~~vl~~l~~G~---------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l~ 55 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM---------SNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAELI 55 (58)
T ss_dssp SS-HHHHHHHHHHHTTS----------HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHHH
T ss_pred ccCHHHHHHHHHHHhcC---------CcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHHH
Confidence 47778888887665444 346899999999999999999999998776666554
No 111
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=36.71 E-value=63 Score=30.53 Aligned_cols=54 Identities=17% Similarity=0.110 Sum_probs=44.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEM 560 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~ 560 (594)
..||+..+.++.--+.+++ .-.++|+.+|++...|.+....+|.++++-+....
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 3589999999988777772 23589999999999999999999999998776553
No 112
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=36.22 E-value=39 Score=32.31 Aligned_cols=48 Identities=15% Similarity=0.014 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkK 554 (594)
..||++++.++.-.+.+.+. -.++|+.+|+++..|.++..-+|+++++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g~s--------~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLGLS--------YADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45899999999887777732 3489999999999999999999999887
No 113
>PRK04217 hypothetical protein; Provisional
Probab=35.44 E-value=54 Score=30.32 Aligned_cols=50 Identities=14% Similarity=0.202 Sum_probs=41.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.++++.+.++..++.+.+ .-.++|+.+|++...|.+.+..+|.+++..+.
T Consensus 42 ~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred cCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 388888988888877663 45679999999999999999999988876554
No 114
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=35.22 E-value=3.6e+02 Score=26.79 Aligned_cols=53 Identities=21% Similarity=0.217 Sum_probs=41.5
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
..||++.+.++.-.+.+. -.-.++|+.+|++...|.+...-+|.++++.+.+.
T Consensus 148 ~~L~~~~r~i~~l~~~~g--------~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~~ 200 (231)
T PRK11922 148 DALPDAFRAVFVLRVVEE--------LSVEETAQALGLPEETVKTRLHRARRLLRESLARE 200 (231)
T ss_pred HhCCHHHhhhheeehhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 348888888886655544 33458999999999999999999999988876543
No 115
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=34.94 E-value=48 Score=33.88 Aligned_cols=51 Identities=20% Similarity=0.376 Sum_probs=43.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..||+..+.++...|.+.+ .-.++|..+|++...|......+++++++.+.
T Consensus 211 ~~L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 261 (268)
T PRK06288 211 KTLPEREKKVLILYYYEDL--------TLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261 (268)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3589999999988877663 24589999999999999999999999988764
No 116
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=34.74 E-value=43 Score=32.63 Aligned_cols=53 Identities=13% Similarity=0.077 Sum_probs=43.9
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
..||+..+.++.--+.+.+ .-.++|+.+|+++..|.++...+|+++++-+-+-
T Consensus 132 ~~Lp~~~r~v~~l~~~~g~--------s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 132 DALPPERREALILTQVLGY--------TYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred HcCCHHHHHHhhhHHHhCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 3489999999988877773 2458999999999999999999999998766543
No 117
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=34.41 E-value=46 Score=31.93 Aligned_cols=53 Identities=17% Similarity=0.087 Sum_probs=43.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
..||+..+.++.-.+.+.+.+ .++|+.+|++...|.....-+|+++++.+...
T Consensus 110 ~~Lp~~~R~v~~L~~~~g~s~--------~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~ 162 (182)
T PRK12540 110 DKLPQDQREALILVGASGFSY--------EDAAAICGCAVGTIKSRVNRARSKLSALLYVD 162 (182)
T ss_pred HhCCHHHHHHhhHHHHcCCCH--------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 348999999998877777333 48999999999999999999999998776543
No 118
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=34.33 E-value=59 Score=31.29 Aligned_cols=53 Identities=17% Similarity=0.117 Sum_probs=44.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
..||+..+.++.-.+.+++. -.++|..+|++...|.++..-+|+++++.+.+.
T Consensus 127 ~~Lp~~~r~v~~l~~~~g~s--------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 127 AKLDPEYREPLLLQVIGGFS--------GEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred HhCCHHHHHHHHHHHHhCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35899999999888888732 358999999999999999999999998877654
No 119
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=34.13 E-value=53 Score=33.12 Aligned_cols=51 Identities=18% Similarity=0.140 Sum_probs=41.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
.||+..+.++.-.+.+.+ .-.++|+.+|++...|.++...+|+++++.+.+
T Consensus 171 ~Lp~~~R~v~~L~~~eg~--------s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~ 221 (233)
T PRK12538 171 RLPEQQRIAVILSYHENM--------SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRR 221 (233)
T ss_pred hCCHHHHHHhhhHHhcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 488889998877666652 235899999999999999999999999886643
No 120
>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=34.08 E-value=63 Score=32.36 Aligned_cols=57 Identities=19% Similarity=0.096 Sum_probs=44.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEM 560 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~ 560 (594)
.||+..+.+|...|.-+-..+ -.-.++|+.+|++...|+.+...+++|+++.+..+.
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~----~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~ 232 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRP----HTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKK 232 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCC----ccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhH
Confidence 589999999988763210112 235689999999999999999999999998865543
No 121
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=33.88 E-value=44 Score=34.10 Aligned_cols=52 Identities=19% Similarity=0.178 Sum_probs=42.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
..||+..+.+|...|.+. -.-.++|..+|++...|..+..-++.++++.+..
T Consensus 202 ~~L~~~~r~vl~l~y~~~--------~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~ 253 (256)
T PRK07408 202 AQLEERTREVLEFVFLHD--------LTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQP 253 (256)
T ss_pred HcCCHHHHHHHHHHHHCC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhc
Confidence 358999999998877665 2346899999999999999999999999876644
No 122
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=33.56 E-value=56 Score=31.28 Aligned_cols=52 Identities=25% Similarity=0.268 Sum_probs=42.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHHH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIEE 559 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee 559 (594)
.||++.+.++.-.+.+. -.-.++|..+|++...|.+.+..+|+++++-+...
T Consensus 106 ~L~~~~r~i~~l~~~~g--------~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (181)
T PRK09637 106 ALPEKYAEALRLTELEG--------LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGC 157 (181)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence 48899999997776665 22458999999999999999999999988766553
No 123
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=33.47 E-value=56 Score=30.02 Aligned_cols=50 Identities=18% Similarity=0.204 Sum_probs=40.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||++.+.++.--+.+.+ ...++|+.+|++...|.....-+|+++++.+
T Consensus 108 ~~L~~~~r~v~~l~~~~~~--------s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 108 SELPARTRYAFEMYRLHGE--------TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3489999999987776662 2358999999999999999988888888765
No 124
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=33.46 E-value=41 Score=33.32 Aligned_cols=54 Identities=15% Similarity=0.100 Sum_probs=39.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||++.+.++.-.+.-+.... -.-.++|..+|++...|.++...+|+++++.+
T Consensus 177 ~~Lp~~~R~v~~L~y~l~~~eg----~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 177 KKLSDREKQIMELRFGLNGGEE----KTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred HhCCHHHHHHHHHHhccCCCCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3589999999877652110011 12358999999999999999999999998764
No 125
>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=32.67 E-value=55 Score=30.05 Aligned_cols=49 Identities=22% Similarity=0.084 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
..||+..+.++.-.+.+.+ .-.++|+.+|++...|.+...-+|+++++.
T Consensus 121 ~~L~~~~r~vl~l~~~~g~--------s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQNL--------PIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred HhCCHHHHHHHHHHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 4589999999988766652 235899999999999999998888888764
No 126
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=32.54 E-value=50 Score=32.56 Aligned_cols=50 Identities=22% Similarity=0.315 Sum_probs=41.8
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.+|...|.+.+ .-.++|+.+|++...|..+...+++++++.+
T Consensus 174 ~~L~~~~r~il~l~y~~~~--------s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 223 (224)
T TIGR02479 174 ESLSEREQLVLSLYYYEEL--------NLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223 (224)
T ss_pred HhCCHHHHHHHHHHHhCCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence 3589999999998877662 2368999999999999999999999987643
No 127
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=32.53 E-value=44 Score=31.63 Aligned_cols=50 Identities=20% Similarity=0.260 Sum_probs=41.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++.-.+.+.+. -.++|+.+|++...|.++..-+|+++++-+
T Consensus 126 ~~L~~~~r~v~~l~~~~g~s--------~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 126 MSLPIKYREVIYLFYYEELS--------IKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred HhCCHHHhhHhHhHHhcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35999999998877777632 358999999999999999999999988754
No 128
>cd07597 BAR_SNX8 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 8. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX8 and the yeast counterpart Mvp1p are involved in sorting and delivery of late-Golgi proteins, such as carboxypeptidase Y, to vacuoles. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=32.10 E-value=2.6e+02 Score=28.72 Aligned_cols=72 Identities=14% Similarity=0.110 Sum_probs=55.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCchhhHH-----------HHHHHHHHhhhhhHHHHHHHH
Q 007660 386 QAVEAKKAQLLALLQMVDDRYNQCLDEIHTVVSAFHAATELDPQVHAR-----------FALHTISFLYKNLRERISSQI 454 (594)
Q Consensus 386 ~elq~kkakLl~mL~ev~~RY~qy~~qm~~V~ssFea~~~~~~~~yt~-----------lAl~tmSrhFr~Lr~~Is~qi 454 (594)
..+.....+|+.+.+.+..|-++.-..+..+...+...+...+.+|+. -++..|+.||..+.+-...+.
T Consensus 32 ~~l~~~~~~l~~l~er~~kR~~~~A~d~~~f~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~s~~~~~~s~~~~~~a 111 (246)
T cd07597 32 RRLLESWTKLRVLAERYEKRSQQQAADRAEFARLLNSLGELTARLYPWAGDSDTWGDINEGLSSLSKHFQLLSDLSEDEA 111 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCccCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556778888888888888888888888888888887777655553 377899999999888776665
Q ss_pred HHh
Q 007660 455 LAM 457 (594)
Q Consensus 455 ~~~ 457 (594)
...
T Consensus 112 ~~~ 114 (246)
T cd07597 112 RAE 114 (246)
T ss_pred HHH
Confidence 544
No 129
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=31.55 E-value=70 Score=29.40 Aligned_cols=50 Identities=18% Similarity=0.229 Sum_probs=42.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.||++...++.-.+.+.+ .-.++|..+|++..-|.+....+|+++++.+.
T Consensus 105 ~L~~~~r~v~~l~~~~~~--------s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 105 ELPPACRDSFLLRKLEGL--------SHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 489999999988877772 23589999999999999999999999887654
No 130
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.30 E-value=60 Score=30.39 Aligned_cols=49 Identities=20% Similarity=0.173 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.||+....+|.--+.+. ..-.++|..+|++...|.++...+|+++++.+
T Consensus 136 ~L~~~~r~il~l~~~~~--------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYIED--------LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHhhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888885544433 22368999999999999999999999998754
No 131
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=31.26 E-value=61 Score=29.87 Aligned_cols=47 Identities=17% Similarity=0.220 Sum_probs=38.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhc
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLW 553 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlk 553 (594)
..||++++.++.-.+.+.+. -.++|+.+|++...|.++...+++++.
T Consensus 112 ~~L~~~~r~v~~L~~~~g~s--------~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVDGLG--------YGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HHCCHHHHHHHHHHHHcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34899999999887777632 248999999999999999999988764
No 132
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=30.72 E-value=27 Score=32.49 Aligned_cols=50 Identities=18% Similarity=0.139 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.||+..+.+|.-.+.+.+ .-.++|+.+|++...|.+.+..+|+++++.+.
T Consensus 120 ~L~~~~r~vl~l~~~~g~--------s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 120 TLSLEHRAVLVLHDLEDL--------PQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred hCCHHHeeeeeehHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 488888888877655551 24689999999999999999999999988654
No 133
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=30.71 E-value=60 Score=30.81 Aligned_cols=49 Identities=10% Similarity=0.055 Sum_probs=40.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
..||++++.++.-.+.+.+. -.++|..+|+++..|......+++++...
T Consensus 126 ~~Lp~~~R~v~~L~~~~g~s--------~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 126 DTLRPRVKQAFLMATLDGMK--------QKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HhCCHHHHHHHHHHHHcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 35999999999887777632 35899999999999999999998887544
No 134
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=30.66 E-value=62 Score=31.11 Aligned_cols=50 Identities=18% Similarity=0.100 Sum_probs=41.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.||+..+.++.-.+.+.+. -.++|..+|++...|.++..-+|+++++-+.
T Consensus 111 ~Lp~~~R~v~~L~~~eg~s--------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 111 DLPEEQRAALHLVAIEGLS--------YQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hCCHHHHHHHHHHHHcCCC--------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 5999999999888777622 3589999999999999999999998886544
No 135
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=30.48 E-value=70 Score=29.89 Aligned_cols=52 Identities=13% Similarity=0.148 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
..||++..+++.-.+.+.+ .-.++|..+|++...|..+...+|+++++.+.+
T Consensus 118 ~~L~~~~r~i~~l~~~~~~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 169 (173)
T PRK12522 118 QLLNEKYKTVLVLYYYEQY--------SYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3588888888876666662 235899999999999999999999999876644
No 136
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=28.97 E-value=1.6e+02 Score=28.45 Aligned_cols=41 Identities=20% Similarity=0.313 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 007660 384 QRQAVEAKKAQLLALLQMVDDRYNQCLDEIHTVVSAFHAAT 424 (594)
Q Consensus 384 er~elq~kkakLl~mL~ev~~RY~qy~~qm~~V~ssFea~~ 424 (594)
++++|+..++.|..=++.+.+.+.+.+.+.++....|++..
T Consensus 75 Qk~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~ 115 (135)
T KOG4196|consen 75 QKHELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQ 115 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999999999988888777777653
No 137
>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=28.83 E-value=1.1e+02 Score=24.96 Aligned_cols=47 Identities=21% Similarity=0.325 Sum_probs=36.4
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhh
Q 007660 501 LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINA 548 (594)
Q Consensus 501 fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNa 548 (594)
|++.+..+|+.-+..=+ .-+|-...-..||++.|+++.-+..-.-++
T Consensus 1 LT~~Q~e~L~~A~~~GY-fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 1 LTDRQREILKAAYELGY-FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHHHHHHcCC-CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 57788888887766553 345889999999999999999887655444
No 138
>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=28.82 E-value=65 Score=31.86 Aligned_cols=49 Identities=16% Similarity=0.199 Sum_probs=40.1
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
..||+..+.++...|.+. ..-.++|+.+|+++..|..+-..+..|+++.
T Consensus 182 ~~L~~~e~~i~~~~~~~~--------~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~ 230 (231)
T TIGR02885 182 SKLDERERQIIMLRYFKD--------KTQTEVANMLGISQVQVSRLEKKVLKKMKEK 230 (231)
T ss_pred HcCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 358999999998776544 3467899999999999999998888888764
No 139
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=28.77 E-value=74 Score=30.23 Aligned_cols=50 Identities=20% Similarity=0.140 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.||+..+.++.--+.+. | .-.++|+.+|+++..|.+...-+|+++++.+.
T Consensus 138 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 138 QLPEDLRTALTLREFDG----L----SYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred hCCHHHhHHHhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47888888876655554 2 23589999999999999999999999987664
No 140
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=28.76 E-value=63 Score=24.41 Aligned_cols=21 Identities=19% Similarity=0.166 Sum_probs=19.1
Q ss_pred HHHHHhCCChhhHhhhhhhhh
Q 007660 529 LLAMKSGLTRTQVSNWFINAR 549 (594)
Q Consensus 529 ~LA~~TGLS~~QVsNWFiNaR 549 (594)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999875
No 141
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=27.80 E-value=73 Score=30.10 Aligned_cols=49 Identities=16% Similarity=0.258 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.||+....++...+.+.+ .-.++|..+|+++..|.+....+|+++++-+
T Consensus 137 ~L~~~~r~i~~l~~~~g~--------s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 137 ELEPPRSELIRTAFFEGI--------TYEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 488999999888777662 2358999999999999999999999988654
No 142
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=26.72 E-value=72 Score=32.97 Aligned_cols=51 Identities=20% Similarity=0.066 Sum_probs=41.6
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
..||++.+.++.-.+.+.+. -.++|+.+|++...|.+...-+|+++++.+.
T Consensus 141 ~~Lp~~~R~v~~L~~~~g~s--------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 141 QYLPPRQRAVLLLRDVLGWR--------AAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HhCCHHHhhHhhhHHHhCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 35899999999777766632 2489999999999999999999999887553
No 143
>PF13518 HTH_28: Helix-turn-helix domain
Probab=26.72 E-value=64 Score=24.23 Aligned_cols=24 Identities=25% Similarity=0.430 Sum_probs=20.6
Q ss_pred HHHHHHHhCCChhhHhhhhhhhhh
Q 007660 527 KHLLAMKSGLTRTQVSNWFINARV 550 (594)
Q Consensus 527 K~~LA~~TGLS~~QVsNWFiNaRr 550 (594)
..++|++.|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456999999999999999877665
No 144
>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=25.76 E-value=36 Score=30.83 Aligned_cols=47 Identities=28% Similarity=0.235 Sum_probs=36.8
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 501 LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 501 fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
||+..+.++.-.+.+. -.-.++|+.+|+++..|.++..-+|+++++-
T Consensus 106 L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 106 LPENYRTVLILREFKE--------FSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred CCHhheeeeeehhhcc--------CcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 7777777776554444 2346899999999999999999999998763
No 145
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=25.69 E-value=81 Score=30.18 Aligned_cols=49 Identities=16% Similarity=0.086 Sum_probs=38.3
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++.- +.+.+ .-.++|..+|+++..|.+.+..+|+++++-+
T Consensus 154 ~~L~~~~r~vl~l-~~e~~--------s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 154 ELLSELEKEVLEL-YLDGK--------SYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred HhCCHHHHHHHHH-HHccC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3588889999977 55541 2358999999999999998888888877644
No 146
>cd00131 PAX Paired Box domain
Probab=25.50 E-value=1.9e+02 Score=26.97 Aligned_cols=47 Identities=15% Similarity=0.130 Sum_probs=33.1
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------ChhhHhhhhhhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGL-------TRTQVSNWFINA 548 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGL-------S~~QVsNWFiNa 548 (594)
+....+....+..+..+| |.-+..|..++-...|+ +.++|..||.++
T Consensus 74 r~~~~~~~~~i~~~v~~~---p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 74 RVATPEVVKKIEIYKQEN---PGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CcCCHHHHHHHHHHHHHC---CCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 345556666667777777 88887776655335577 999999998764
No 147
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=25.33 E-value=1.6e+02 Score=26.99 Aligned_cols=44 Identities=14% Similarity=0.297 Sum_probs=34.4
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhh
Q 007660 501 LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINA 548 (594)
Q Consensus 501 fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNa 548 (594)
-....+..+.+|+.+|+..| ++ ...||+.+|+++.++..+|...
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~-~s---l~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESP-LS---LEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCC-CC---HHHHHHHHCcCHHHHHHHHHHH
Confidence 34455677889999996665 34 4678999999999999999876
No 148
>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=25.00 E-value=1.1e+02 Score=21.51 Aligned_cols=32 Identities=25% Similarity=0.240 Sum_probs=22.3
Q ss_pred HHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 007660 528 HLLAMKSGLTRTQVSNWFINARVRLWKPMIEEM 560 (594)
Q Consensus 528 ~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~ 560 (594)
..+|+.+|+++..|..|..+.+ ......+.++
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~~-~~~~~~~~~i 47 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGKR-NPSLETLEKL 47 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCCC-CCCHHHHHHH
Confidence 4788889999999999988764 3433333333
No 149
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=24.78 E-value=82 Score=29.83 Aligned_cols=47 Identities=15% Similarity=0.152 Sum_probs=33.9
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 501 LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 501 fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
+++..+.++.. +.+. -.-.++|+.+|++...|.+++.-+|+++++.+
T Consensus 151 l~~~~~~i~~~-~~~~--------~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l 197 (198)
T TIGR02859 151 LSDLEWKVLQS-YLDG--------KSYQEIACDLNRHVKSIDNALQRVKRKLEKYL 197 (198)
T ss_pred cCHHHHHHHHH-HHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 34445555554 4454 23358999999999999999999998887643
No 150
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=24.45 E-value=97 Score=29.82 Aligned_cols=50 Identities=22% Similarity=0.169 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhH
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMI 557 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmi 557 (594)
.||++.+.+|.--+.+.+ .-.++|..+|++...|.+=.-.+|+++++.+.
T Consensus 134 ~Lp~~~r~i~~l~~~~g~--------s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~ 183 (192)
T PRK09643 134 RLPVEQRAALVAVDMQGY--------SVADAARMLGVAEGTVKSRCARGRARLAELLG 183 (192)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 489999999977666662 23489999999999998888778877776554
No 151
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=24.15 E-value=82 Score=29.61 Aligned_cols=49 Identities=16% Similarity=0.141 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.||++.+.++.--+.+.+ .-.++|+.+|++...|.++...++.++++-.
T Consensus 119 ~L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~ 167 (172)
T PRK09651 119 GLNGKTREAFLLSQLDGL--------TYSEIAHKLGVSVSSVKKYVAKATEHCLLFR 167 (172)
T ss_pred hCCHHHhHHhhhhhccCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 488888899877766662 2358999999999999999988888876543
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=23.85 E-value=85 Score=31.22 Aligned_cols=50 Identities=20% Similarity=0.209 Sum_probs=39.6
Q ss_pred CCCChhHHHHHHHHHH----HccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMF----QNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~----eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||++.+.++.-.+. ++ -.-+++|+.+|+++..|..+...+|+++++.+
T Consensus 173 ~~L~~~~r~il~l~y~~~~~e~--------~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~ 226 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDGRR--------KTQREIAKILGISRSYVSRIEKRALMKLYKEL 226 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCCCC--------cCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4599999999988774 33 12358999999999999999888888887653
No 153
>PRK05572 sporulation sigma factor SigF; Validated
Probab=23.81 E-value=88 Score=31.63 Aligned_cols=50 Identities=18% Similarity=0.244 Sum_probs=41.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++...|.+. -...++|+.+|++...|..+-..+..++++.+
T Consensus 201 ~~L~~~~~~v~~l~~~~~--------~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 201 RELDERERLIVYLRYFKD--------KTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred HcCCHHHHHHHHHHHhCC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 358999999998877654 33468999999999999999999999888654
No 154
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=23.76 E-value=84 Score=29.38 Aligned_cols=49 Identities=10% Similarity=0.204 Sum_probs=39.6
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKP 555 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKp 555 (594)
..||++.+.++.-.+.+.+. -.++|..+|++...|.++..++++.++..
T Consensus 117 ~~L~~~~r~v~~L~~~eg~s--------~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEGLT--------YVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred HhCCHHHHHHHHHHHHcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 45899999999877777732 35899999999999999998888877643
No 155
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=23.37 E-value=91 Score=31.61 Aligned_cols=49 Identities=22% Similarity=0.247 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.|++..+.++...|.+. ..-.++|+.+|++...|..+-..++.|+++.|
T Consensus 209 ~L~~~er~vi~~~~~~~--------~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 209 KLNDREKLILNLRFFQG--------KTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred cCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 58999999988877544 22468999999999999999999998888654
No 156
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=23.22 E-value=96 Score=30.90 Aligned_cols=56 Identities=20% Similarity=0.131 Sum_probs=40.6
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
..||+..+.++.-.+.-+.... ..-+++|..+|++...|.++-.-+|+++++.+..
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 4589999999977552110001 2345899999999999999988888888877654
No 157
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=22.87 E-value=91 Score=31.80 Aligned_cols=49 Identities=14% Similarity=0.062 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
.||++++.++.-.+.+.+. -.++|+.+|++...|.++..-+|.++++.+
T Consensus 116 ~Lp~~~R~v~lL~~~eg~S--------~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 116 SLNVQQSAILLLKDVFQYS--------IADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred hCCHHHhhHhhhHHhhCCC--------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5888888888777666522 358999999999999999999999998654
No 158
>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=22.77 E-value=1.3e+02 Score=22.82 Aligned_cols=20 Identities=30% Similarity=0.300 Sum_probs=17.1
Q ss_pred HHHHHHhCCChhhHhhhhhh
Q 007660 528 HLLAMKSGLTRTQVSNWFIN 547 (594)
Q Consensus 528 ~~LA~~TGLS~~QVsNWFiN 547 (594)
.+||+.+|+++..|..|..+
T Consensus 13 ~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHhCCCcchhHHHhcC
Confidence 68899999999999999988
No 159
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=22.06 E-value=1.1e+02 Score=30.29 Aligned_cols=54 Identities=22% Similarity=0.353 Sum_probs=42.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhch
Q 007660 500 GLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWK 554 (594)
Q Consensus 500 ~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkK 554 (594)
.|++.++++|+.-|..= ..=||-...-..||++.|+++.-+..=..++=+|+-.
T Consensus 155 ~LTdrQ~~vL~~A~~~G-YFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 155 DLTDRQLEVLRLAYKMG-YFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHHHHHHcC-CCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 59999999999887665 3356999999999999999999988766555444433
No 160
>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=22.04 E-value=2e+02 Score=21.31 Aligned_cols=47 Identities=19% Similarity=0.155 Sum_probs=32.6
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 501 LPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 501 fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
|++....++.-+ ... + ...++|+.++++...|..|..-.++++..+.
T Consensus 1 l~~~e~~i~~~~-~~~----~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~ 47 (57)
T cd06170 1 LTPREREVLRLL-AEG----K----TNKEIADILGISEKTVKTHLRNIMRKLGVKS 47 (57)
T ss_pred CCHHHHHHHHHH-HcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHhCCCC
Confidence 355666666443 322 2 4468899999999999999987777665543
No 161
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=21.56 E-value=80 Score=24.13 Aligned_cols=40 Identities=20% Similarity=0.200 Sum_probs=21.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFI 546 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFi 546 (594)
+.|+.+.+..+..|+.+. .-..++|+..|.+++.|.+|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G--------~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG--------MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS-----------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC--------CCHHHHHHHHCcCcHHHHHHHh
Confidence 457778888888886655 3455799999999999998864
No 162
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=20.82 E-value=1.2e+02 Score=31.43 Aligned_cols=52 Identities=25% Similarity=0.302 Sum_probs=42.6
Q ss_pred CCCChhHHHHHHHHH----HHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhhHH
Q 007660 499 RGLPEKSVSVLRAWM----FQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPMIE 558 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf----~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpmie 558 (594)
..||+..+.+|.-.| +++ -.-.++|..+|++...|..+...+|+++++.+.+
T Consensus 221 ~~Lp~~~R~Vl~l~ygL~~~e~--------~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~ 276 (285)
T TIGR02394 221 AELNERQREVLARRFGLLGYEP--------ATLEEVAAEVGLTRERVRQIQVEALKKLRRILER 276 (285)
T ss_pred HcCCHHHHHHHHHHhCCCCCCC--------ccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 459999999998776 333 2356899999999999999999999999987653
No 163
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=20.62 E-value=1.3e+02 Score=30.86 Aligned_cols=50 Identities=18% Similarity=0.265 Sum_probs=41.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.++.-.|.+. -.-.++|..+|++...|..+..-+++++++.+
T Consensus 204 ~~L~~~er~vi~l~y~e~--------~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 204 LALEEKERKVMALYYYEE--------LVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred HcCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 358999999998887654 23468999999999999999999999988765
No 164
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=20.26 E-value=1e+02 Score=31.77 Aligned_cols=50 Identities=24% Similarity=0.442 Sum_probs=41.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhhhhhhhhhhchhh
Q 007660 499 RGLPEKSVSVLRAWMFQNFLHPYPKDAEKHLLAMKSGLTRTQVSNWFINARVRLWKPM 556 (594)
Q Consensus 499 R~fpk~a~~iLr~Wf~eH~~~PYPS~eEK~~LA~~TGLS~~QVsNWFiNaRrRlkKpm 556 (594)
..||+..+.+|...|.+.+ .-.++|+.+|++...|..+...++.++++.+
T Consensus 214 ~~L~~rer~vl~l~y~~~~--------t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 263 (264)
T PRK07122 214 AALPERERTVLVLRFFESM--------TQTQIAERVGISQMHVSRLLAKTLARLRDQL 263 (264)
T ss_pred HcCCHHHHHHHHHHhcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence 3589999999988876542 2368999999999999999999999988653
No 165
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=20.05 E-value=1.4e+02 Score=23.47 Aligned_cols=33 Identities=21% Similarity=0.263 Sum_probs=19.6
Q ss_pred HHHHHHHhCCChhhHhhhhhhhhhhhchhhHHHH
Q 007660 527 KHLLAMKSGLTRTQVSNWFINARVRLWKPMIEEM 560 (594)
Q Consensus 527 K~~LA~~TGLS~~QVsNWFiNaRrRlkKpmiee~ 560 (594)
...+|+.+|+++.+|..|-.+.| ......+.++
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~-~~~~~~l~~i 47 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKR-KPSVSTLKKI 47 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS---BHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHCCCc-CCCHHHHHHH
Confidence 34677777888888888877765 4444444443
Done!