Query 006550
Match_columns 641
No_of_seqs 304 out of 1018
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 00:55:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006550.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006550hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00574 POX domain associat 100.0 4E-40 8.7E-45 306.0 10.1 129 241-369 1-139 (140)
2 PF07526 POX: Associated with 100.0 9.6E-40 2.1E-44 304.4 10.5 126 245-370 1-140 (140)
3 KOG0773 Transcription factor M 100.0 4E-32 8.6E-37 279.7 10.3 246 243-491 45-312 (342)
4 KOG0774 Transcription factor P 99.9 1.2E-24 2.7E-29 219.5 15.0 201 299-532 99-302 (334)
5 PF05920 Homeobox_KN: Homeobox 99.6 5.4E-16 1.2E-20 117.8 3.5 40 436-475 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.4 5.5E-13 1.2E-17 103.8 6.1 57 420-479 2-58 (59)
7 PF00046 Homeobox: Homeobox do 99.4 7.5E-13 1.6E-17 103.9 5.2 57 419-478 1-57 (57)
8 smart00389 HOX Homeodomain. DN 99.4 1.4E-12 3.1E-17 101.2 6.2 55 420-477 2-56 (56)
9 KOG0775 Transcription factor S 99.2 1.3E-11 2.9E-16 126.4 4.4 50 425-477 183-232 (304)
10 KOG0842 Transcription factor t 98.9 6.5E-10 1.4E-14 116.1 4.4 64 418-484 152-216 (307)
11 KOG0487 Transcription factor A 98.9 1.4E-09 3E-14 113.7 3.8 62 417-481 234-295 (308)
12 KOG0489 Transcription factor z 98.8 4.3E-09 9.4E-14 107.3 3.5 61 417-480 158-218 (261)
13 KOG0488 Transcription factor B 98.7 1.1E-08 2.3E-13 107.2 5.2 62 418-482 172-233 (309)
14 KOG0843 Transcription factor E 98.7 1.4E-08 3E-13 99.6 4.9 64 417-483 101-164 (197)
15 KOG0483 Transcription factor H 98.7 1.7E-08 3.7E-13 100.1 5.6 72 417-491 49-120 (198)
16 KOG0493 Transcription factor E 98.7 1.1E-08 2.4E-13 104.9 4.4 59 418-479 246-304 (342)
17 KOG0850 Transcription factor D 98.7 1.6E-08 3.6E-13 102.0 4.6 63 416-481 120-182 (245)
18 TIGR01565 homeo_ZF_HD homeobox 98.7 4E-08 8.8E-13 80.6 5.7 53 418-473 1-57 (58)
19 KOG0485 Transcription factor N 98.6 3.6E-08 7.8E-13 99.2 4.1 63 416-481 102-164 (268)
20 KOG3802 Transcription factor O 98.5 1E-07 2.3E-12 102.3 4.6 61 417-480 293-353 (398)
21 COG5576 Homeodomain-containing 98.4 1.9E-07 4.1E-12 89.8 4.9 62 417-481 50-111 (156)
22 KOG0484 Transcription factor P 98.4 2.9E-07 6.3E-12 84.1 5.2 66 417-485 16-81 (125)
23 KOG0492 Transcription factor M 98.4 3.1E-07 6.7E-12 92.1 5.7 62 416-480 142-203 (246)
24 KOG2251 Homeobox transcription 98.4 3.6E-07 7.9E-12 92.0 4.6 62 416-480 35-96 (228)
25 KOG0494 Transcription factor C 98.2 8.5E-07 1.8E-11 91.3 4.4 55 422-479 145-199 (332)
26 KOG0848 Transcription factor C 98.2 7.2E-07 1.6E-11 92.1 1.9 58 423-483 204-261 (317)
27 KOG0486 Transcription factor P 98.2 9.8E-07 2.1E-11 92.7 2.7 59 419-480 113-171 (351)
28 KOG0491 Transcription factor B 98.1 1.1E-06 2.4E-11 85.7 1.4 59 419-480 101-159 (194)
29 KOG4577 Transcription factor L 98.1 2.1E-06 4.6E-11 89.5 3.6 63 416-481 165-227 (383)
30 KOG2252 CCAAT displacement pro 97.9 1.3E-05 2.8E-10 89.3 5.1 57 417-476 419-475 (558)
31 KOG0844 Transcription factor E 97.6 1.8E-05 3.8E-10 83.3 1.1 63 416-481 179-241 (408)
32 KOG0847 Transcription factor, 97.6 2.9E-05 6.4E-10 78.8 2.4 66 417-485 166-231 (288)
33 KOG0490 Transcription factor, 97.5 4.9E-05 1.1E-09 73.6 2.5 61 417-480 59-119 (235)
34 KOG0849 Transcription factor P 97.5 9.1E-05 2E-09 79.3 3.8 62 418-482 176-237 (354)
35 KOG1168 Transcription factor A 97.4 6.6E-05 1.4E-09 78.7 1.8 59 417-478 308-366 (385)
36 KOG0773 Transcription factor M 97.3 7.5E-05 1.6E-09 78.2 1.3 61 419-480 96-156 (342)
37 PF03792 PBC: PBC domain; Int 97.0 0.0053 1.1E-07 61.4 10.3 75 300-376 104-178 (191)
38 PF11569 Homez: Homeodomain le 96.1 0.0038 8.1E-08 51.6 2.2 43 430-475 10-52 (56)
39 KOG0490 Transcription factor, 95.2 0.016 3.5E-07 56.3 3.2 62 417-481 152-213 (235)
40 KOG1146 Homeobox protein [Gene 90.9 0.16 3.5E-06 62.4 3.0 60 419-481 904-963 (1406)
41 PF04218 CENP-B_N: CENP-B N-te 77.9 3.6 7.8E-05 33.1 4.0 47 419-473 1-47 (53)
42 PF03791 KNOX2: KNOX2 domain ; 73.0 2.4 5.2E-05 34.9 1.9 33 335-367 3-36 (52)
43 PF04545 Sigma70_r4: Sigma-70, 69.9 6.3 0.00014 30.5 3.5 47 424-478 4-50 (50)
44 KOG3623 Homeobox transcription 66.8 7 0.00015 46.6 4.5 44 430-476 568-611 (1007)
45 cd06171 Sigma70_r4 Sigma70, re 66.4 8 0.00017 28.1 3.4 46 424-477 10-55 (55)
46 PF01527 HTH_Tnp_1: Transposas 65.7 7.1 0.00015 32.0 3.2 46 420-473 2-48 (76)
47 cd00569 HTH_Hin_like Helix-tur 61.4 20 0.00044 23.1 4.3 39 423-469 4-42 (42)
48 PF08281 Sigma70_r4_2: Sigma-7 60.1 10 0.00022 29.5 3.0 45 424-476 10-54 (54)
49 TIGR02985 Sig70_bacteroi1 RNA 58.8 15 0.00033 33.0 4.4 48 424-479 113-160 (161)
50 TIGR02937 sigma70-ECF RNA poly 56.7 16 0.00035 31.7 4.1 48 424-479 110-157 (158)
51 PRK09642 RNA polymerase sigma 54.8 21 0.00045 32.9 4.7 51 424-482 106-156 (160)
52 PRK06759 RNA polymerase factor 54.7 12 0.00026 34.1 3.1 47 424-478 106-152 (154)
53 PRK12514 RNA polymerase sigma 52.8 21 0.00045 33.6 4.4 48 424-479 129-176 (179)
54 PRK09652 RNA polymerase sigma 50.8 25 0.00054 32.4 4.5 49 424-480 128-176 (182)
55 PRK11924 RNA polymerase sigma 49.1 27 0.00059 32.0 4.5 50 424-481 125-174 (179)
56 PF13443 HTH_26: Cro/C1-type H 48.5 15 0.00034 29.1 2.4 37 433-476 2-38 (63)
57 PRK12530 RNA polymerase sigma 48.2 32 0.00069 33.1 5.0 53 424-484 134-186 (189)
58 PRK09644 RNA polymerase sigma 46.8 32 0.00069 32.0 4.6 50 423-480 107-156 (165)
59 PRK12512 RNA polymerase sigma 46.2 26 0.00056 33.2 3.9 50 424-481 131-180 (184)
60 PRK06811 RNA polymerase factor 46.1 27 0.00059 33.4 4.1 49 424-480 131-179 (189)
61 TIGR02939 RpoE_Sigma70 RNA pol 45.3 24 0.00052 33.2 3.6 49 424-480 138-186 (190)
62 PRK09646 RNA polymerase sigma 44.9 20 0.00044 34.5 3.0 49 424-480 142-190 (194)
63 PRK00118 putative DNA-binding 43.3 37 0.00081 31.4 4.3 52 424-484 17-68 (104)
64 TIGR02989 Sig-70_gvs1 RNA poly 43.1 37 0.00079 31.0 4.3 48 423-478 110-157 (159)
65 PRK15369 two component system 42.6 64 0.0014 29.1 5.7 53 424-485 149-201 (211)
66 PRK12519 RNA polymerase sigma 41.6 35 0.00076 32.5 4.1 49 424-480 141-189 (194)
67 TIGR02999 Sig-70_X6 RNA polyme 41.5 39 0.00084 31.8 4.3 47 425-479 135-181 (183)
68 PRK12526 RNA polymerase sigma 41.3 24 0.00053 34.5 3.0 49 424-480 153-201 (206)
69 PRK03975 tfx putative transcri 41.2 41 0.00089 32.6 4.5 50 423-481 5-54 (141)
70 PRK12547 RNA polymerase sigma 40.5 26 0.00057 32.7 3.0 49 424-480 112-160 (164)
71 PRK12541 RNA polymerase sigma 40.2 40 0.00086 31.2 4.1 47 424-478 112-158 (161)
72 PRK09648 RNA polymerase sigma 39.5 44 0.00095 31.8 4.4 50 423-480 138-187 (189)
73 TIGR02948 SigW_bacill RNA poly 39.2 39 0.00085 31.7 4.0 49 424-480 136-184 (187)
74 PRK12546 RNA polymerase sigma 39.1 39 0.00084 32.9 4.0 49 424-480 113-161 (188)
75 PRK09047 RNA polymerase factor 38.9 49 0.0011 30.2 4.5 50 423-480 105-154 (161)
76 PRK09639 RNA polymerase sigma 38.7 43 0.00093 30.9 4.1 48 424-480 112-159 (166)
77 PRK05602 RNA polymerase sigma 38.4 42 0.00091 31.9 4.1 49 424-480 128-176 (186)
78 PRK12532 RNA polymerase sigma 38.3 26 0.00056 33.6 2.7 49 424-480 136-184 (195)
79 PRK12531 RNA polymerase sigma 38.3 30 0.00065 33.3 3.1 51 423-481 140-190 (194)
80 PF11285 DUF3086: Protein of u 37.5 3.7E+02 0.0079 29.2 10.9 63 303-381 7-69 (283)
81 PRK08583 RNA polymerase sigma 36.8 37 0.0008 34.4 3.6 49 424-480 205-253 (257)
82 PRK12513 RNA polymerase sigma 36.7 24 0.00053 33.7 2.2 49 424-480 139-187 (194)
83 PRK12516 RNA polymerase sigma 36.7 55 0.0012 31.7 4.6 50 424-481 116-165 (187)
84 PRK12520 RNA polymerase sigma 36.5 47 0.001 31.7 4.1 52 424-483 131-182 (191)
85 PRK13919 putative RNA polymera 36.3 45 0.00098 31.5 3.9 50 423-480 134-183 (186)
86 PF00196 GerE: Bacterial regul 36.1 53 0.0012 26.1 3.7 53 424-485 3-55 (58)
87 TIGR02941 Sigma_B RNA polymera 35.9 36 0.00077 34.5 3.3 49 424-480 205-253 (255)
88 PRK12523 RNA polymerase sigma 35.7 36 0.00077 32.0 3.1 49 423-479 118-166 (172)
89 TIGR02954 Sig70_famx3 RNA poly 35.6 45 0.00097 31.1 3.7 49 424-480 119-167 (169)
90 PRK12536 RNA polymerase sigma 35.1 44 0.00095 31.7 3.6 49 424-480 129-177 (181)
91 PRK06986 fliA flagellar biosyn 35.0 29 0.00063 34.7 2.5 49 424-480 184-232 (236)
92 smart00421 HTH_LUXR helix_turn 34.7 77 0.0017 23.5 4.2 47 424-479 3-49 (58)
93 PRK12515 RNA polymerase sigma 34.6 66 0.0014 30.7 4.8 50 423-480 130-179 (189)
94 TIGR03001 Sig-70_gmx1 RNA poly 34.5 43 0.00094 34.3 3.7 51 424-482 161-211 (244)
95 PRK12524 RNA polymerase sigma 34.5 55 0.0012 31.6 4.2 49 424-480 136-184 (196)
96 cd01392 HTH_LacI Helix-turn-he 34.4 38 0.00082 25.8 2.5 21 453-473 2-22 (52)
97 TIGR02983 SigE-fam_strep RNA p 34.3 56 0.0012 30.1 4.1 49 424-480 110-158 (162)
98 PRK04217 hypothetical protein; 34.2 49 0.0011 30.9 3.7 50 423-480 41-90 (110)
99 PRK12544 RNA polymerase sigma 33.5 75 0.0016 31.4 5.1 54 423-484 147-200 (206)
100 PRK12537 RNA polymerase sigma 33.3 60 0.0013 30.9 4.2 49 423-479 132-180 (182)
101 PRK12538 RNA polymerase sigma 32.9 68 0.0015 32.5 4.8 49 424-480 171-219 (233)
102 PRK09637 RNA polymerase sigma 32.2 69 0.0015 30.8 4.5 49 424-480 106-154 (181)
103 TIGR02980 SigBFG RNA polymeras 32.0 62 0.0014 31.9 4.2 49 424-480 178-226 (227)
104 PRK11511 DNA-binding transcrip 31.9 86 0.0019 28.9 4.9 44 425-472 6-49 (127)
105 PRK07037 extracytoplasmic-func 31.7 72 0.0016 29.4 4.3 49 424-480 109-157 (163)
106 PRK11923 algU RNA polymerase s 31.3 65 0.0014 30.7 4.1 49 424-480 138-186 (193)
107 PRK12545 RNA polymerase sigma 31.0 75 0.0016 31.0 4.6 50 424-481 139-188 (201)
108 TIGR02943 Sig70_famx1 RNA poly 30.3 78 0.0017 30.5 4.5 51 424-482 131-181 (188)
109 PRK12522 RNA polymerase sigma 30.3 73 0.0016 29.9 4.2 53 424-484 119-171 (173)
110 TIGR02393 RpoD_Cterm RNA polym 30.2 66 0.0014 32.3 4.2 55 424-482 176-230 (238)
111 PRK12533 RNA polymerase sigma 30.0 57 0.0012 32.8 3.6 49 424-480 134-182 (216)
112 TIGR02947 SigH_actino RNA poly 29.9 28 0.00061 33.3 1.4 50 424-481 131-180 (193)
113 PRK09641 RNA polymerase sigma 29.8 75 0.0016 29.8 4.2 49 424-480 136-184 (187)
114 PRK12543 RNA polymerase sigma 29.8 73 0.0016 30.2 4.1 50 424-481 117-166 (179)
115 PRK09649 RNA polymerase sigma 29.2 48 0.001 31.9 2.8 48 423-478 129-176 (185)
116 PRK06930 positive control sigm 29.0 83 0.0018 30.9 4.5 52 424-483 114-165 (170)
117 PRK09645 RNA polymerase sigma 28.6 80 0.0017 29.5 4.2 49 424-480 118-166 (173)
118 TIGR02479 FliA_WhiG RNA polyme 28.6 76 0.0016 31.4 4.2 48 424-479 175-222 (224)
119 TIGR02959 SigZ RNA polymerase 28.6 97 0.0021 29.3 4.7 50 423-480 99-148 (170)
120 PRK12518 RNA polymerase sigma 28.4 38 0.00081 31.6 1.9 49 424-480 120-168 (175)
121 TIGR02952 Sig70_famx2 RNA poly 28.2 87 0.0019 28.8 4.3 48 424-479 122-169 (170)
122 PRK09647 RNA polymerase sigma 28.0 82 0.0018 31.1 4.3 49 424-480 138-186 (203)
123 PRK07408 RNA polymerase sigma 27.8 74 0.0016 32.6 4.1 50 424-481 203-252 (256)
124 PF13730 HTH_36: Helix-turn-he 27.3 1.5E+02 0.0032 23.0 4.8 47 424-473 2-50 (55)
125 PRK06288 RNA polymerase sigma 26.9 62 0.0013 33.2 3.4 49 424-480 212-260 (268)
126 PRK12539 RNA polymerase sigma 26.8 56 0.0012 31.1 2.8 50 423-480 130-179 (184)
127 PF13518 HTH_28: Helix-turn-he 26.5 52 0.0011 24.9 2.1 24 451-474 15-38 (52)
128 PRK12517 RNA polymerase sigma 25.8 82 0.0018 30.5 3.8 51 423-481 127-177 (188)
129 PRK12540 RNA polymerase sigma 25.6 62 0.0014 31.2 2.9 49 424-480 111-159 (182)
130 PRK08301 sporulation sigma fac 25.5 1E+02 0.0022 30.6 4.5 53 424-480 178-230 (234)
131 PRK12528 RNA polymerase sigma 25.3 1.1E+02 0.0024 28.3 4.4 46 424-477 113-158 (161)
132 PRK12542 RNA polymerase sigma 25.1 1E+02 0.0022 29.3 4.2 50 423-480 121-170 (185)
133 PRK09415 RNA polymerase factor 25.0 90 0.002 29.7 3.9 50 423-480 126-175 (179)
134 PRK12511 RNA polymerase sigma 24.9 1.1E+02 0.0024 29.6 4.5 49 424-480 111-159 (182)
135 PRK12535 RNA polymerase sigma 24.9 65 0.0014 31.5 2.9 50 424-481 133-182 (196)
136 PRK07670 RNA polymerase sigma 24.8 98 0.0021 31.4 4.3 48 424-479 201-248 (251)
137 PRK05657 RNA polymerase sigma 24.4 1.1E+02 0.0023 32.9 4.7 53 424-480 262-314 (325)
138 PLN00064 photosystem II protei 24.2 1.9E+02 0.0041 29.2 5.9 58 309-379 94-162 (166)
139 PRK12529 RNA polymerase sigma 23.6 1.2E+02 0.0026 28.9 4.4 48 424-479 127-174 (178)
140 cd06170 LuxR_C_like C-terminal 23.4 1.2E+02 0.0027 22.6 3.6 46 425-479 1-46 (57)
141 PRK09413 IS2 repressor TnpA; R 22.9 1E+02 0.0022 28.3 3.7 47 421-474 9-55 (121)
142 PRK12534 RNA polymerase sigma 22.7 1.2E+02 0.0027 28.6 4.3 49 424-480 137-185 (187)
143 PRK08295 RNA polymerase factor 22.6 1.2E+02 0.0025 29.2 4.1 48 423-479 154-201 (208)
144 TIGR02950 SigM_subfam RNA poly 22.1 46 0.001 30.2 1.3 46 425-478 106-151 (154)
145 PF04967 HTH_10: HTH DNA bindi 21.6 1.4E+02 0.003 24.6 3.8 47 425-472 1-47 (53)
146 cd00093 HTH_XRE Helix-turn-hel 21.1 1.1E+02 0.0025 21.5 2.9 23 451-473 15-37 (58)
147 PRK12527 RNA polymerase sigma 21.0 1.7E+02 0.0036 27.1 4.7 49 424-480 105-153 (159)
148 PRK07122 RNA polymerase sigma 20.5 93 0.002 32.2 3.2 48 424-479 215-262 (264)
149 PF07638 Sigma70_ECF: ECF sigm 20.4 1.4E+02 0.0031 29.0 4.2 48 425-480 136-183 (185)
150 PRK11922 RNA polymerase sigma 20.4 84 0.0018 31.4 2.8 50 424-481 149-198 (231)
No 1
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=4e-40 Score=305.98 Aligned_cols=129 Identities=47% Similarity=0.748 Sum_probs=103.5
Q ss_pred ccccccccCCCCchHHHHHHHHHhhcCccccccccccc-CCC----CCCCcccccCCCC-----CCCCCCCchhHHHHHH
Q 006550 241 TGYASILKGSRFLKPAQQLLEEFCDVGQGVFAEKNYTV-DSS----LMDPPLVNLNASG-----IVVDDGDGSDNRRKKS 310 (641)
Q Consensus 241 tg~asvl~~SryLkpaQeLL~E~~~vg~g~~~~~~~~~-~~~----~~~~~~~~~~~~g-----~~~~~~~~~e~q~Kk~ 310 (641)
+||+++|++|||||||||||||||+|+++++..+..+. +.. ..+...+..++.+ ......+++|+|+||+
T Consensus 1 ~g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~s~~~~~~~ls~~~r~e~q~kk~ 80 (140)
T smart00574 1 TGGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQSGNDSPVSTSSNEGGGENLSGGSSSSEVPPLSTAERQELQRKKA 80 (140)
T ss_pred CchhhhccCccccccHHHHHHHHhcccHHhhcccccccccccccccccCCCcCCCCCCCCCCCCCCCchhHHHHHHHHHH
Confidence 58999999999999999999999999988764432221 111 0111222111111 1112456899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCcccchHHHHHHHHhhhcchHHHHH
Q 006550 311 RLISMLDEVYRRYKQYYQQMQAAVASFEYVAGLGNAAPFANLALKAMSKHFRSLKNAIT 369 (641)
Q Consensus 311 KLl~mLdEV~~RY~qY~~qmq~VvssFe~~aGlg~a~pYt~lAlkamSrhFr~LrdaI~ 369 (641)
||+.||||||+||+|||+|||+|+++||+++|+|+++|||+||+|+||||||||||+|.
T Consensus 81 kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI~ 139 (140)
T smart00574 81 KLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAIA 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999996
No 2
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=100.00 E-value=9.6e-40 Score=304.39 Aligned_cols=126 Identities=48% Similarity=0.759 Sum_probs=95.2
Q ss_pred ccccCCCCchHHHHHHHHHhhcCcccc---cc-cccccCCCC--CCCccc-ccC--C---C--CCCCCCCCchhHHHHHH
Q 006550 245 SILKGSRFLKPAQQLLEEFCDVGQGVF---AE-KNYTVDSSL--MDPPLV-NLN--A---S--GIVVDDGDGSDNRRKKS 310 (641)
Q Consensus 245 svl~~SryLkpaQeLL~E~~~vg~g~~---~~-~~~~~~~~~--~~~~~~-~~~--~---~--g~~~~~~~~~e~q~Kk~ 310 (641)
++|++|||||||||||||||+|+.+.. .+ +........ ...+.. ..+ . . ..+....+++|+|+||+
T Consensus 1 q~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ls~~~~~e~q~kK~ 80 (140)
T PF07526_consen 1 QVLLGSRYLKPAQELLDEFCSVGGANKKKSDDSSSGAPGGANSSGSSSSSGGSSSSSSSSDSSSPELSPAERQELQRKKA 80 (140)
T ss_pred CccccchhHHHHHHHHHHHHcccchhhhcchhhccccccccccCCCCCCCCCCCCCccccCCCCCCCChhhHHHHHHHHH
Confidence 479999999999999999999995211 00 000000000 000000 000 0 0 01112467899999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCcccchHHHHHHHHhhhcchHHHHHH
Q 006550 311 RLISMLDEVYRRYKQYYQQMQAAVASFEYVAGLGNAAPFANLALKAMSKHFRSLKNAITD 370 (641)
Q Consensus 311 KLl~mLdEV~~RY~qY~~qmq~VvssFe~~aGlg~a~pYt~lAlkamSrhFr~LrdaI~~ 370 (641)
||+.||||||+||+|||+|||+|+++||+|||+|+|+|||+||+||||||||||||+|.+
T Consensus 81 KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LRdaI~~ 140 (140)
T PF07526_consen 81 KLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLRDAISD 140 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999999999999999999999963
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.97 E-value=4e-32 Score=279.71 Aligned_cols=246 Identities=39% Similarity=0.544 Sum_probs=182.6
Q ss_pred ccccccCCCCchHHHHHHHHHhhcCccccccccccc-----CCCCCCCcccc--cCCCC----CCCCCCCchhHHHHHHH
Q 006550 243 YASILKGSRFLKPAQQLLEEFCDVGQGVFAEKNYTV-----DSSLMDPPLVN--LNASG----IVVDDGDGSDNRRKKSR 311 (641)
Q Consensus 243 ~asvl~~SryLkpaQeLL~E~~~vg~g~~~~~~~~~-----~~~~~~~~~~~--~~~~g----~~~~~~~~~e~q~Kk~K 311 (641)
+...+..+|||++||+||+++|+++.+....+.... +.....+.... ....+ ..-...+..+++.+++|
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k 124 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSK 124 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchH
Confidence 566789999999999999999999843321111000 00000000000 00000 00013457889999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCcccchHHHHHHHHhhhcchHH--HHHHHHHHHHHHHhhhcc---CC
Q 006550 312 LISMLDEVYRRYKQYYQQMQAAVASFEYVAGLGNAAPFANLALKAMSKHFRSLKN--AITDQLQFTNKAQIQANR---GK 386 (641)
Q Consensus 312 Ll~mLdEV~~RY~qY~~qmq~VvssFe~~aGlg~a~pYt~lAlkamSrhFr~Lrd--aI~~Ql~~~~k~~~~~s~---~~ 386 (641)
++.||.+|+.+|.+|+..|+.|.++|+...|++.+.+|+..+...+++||+++++ +|..|+....+..+.... ..
T Consensus 125 ~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 204 (342)
T KOG0773|consen 125 LEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDSED 204 (342)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccccccccccccccccc
Confidence 9999999999999999999999999999999999999999999999999999999 888999887765543211 00
Q ss_pred C-----CCCCCCCCCCCCCCCCCC-ccccccccCCCCCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC
Q 006550 387 D-----EASTFGSTDRGPYGHRPV-LNSGFIERQSQPVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGL 460 (641)
Q Consensus 387 ~-----~spr~~~~d~s~~~qr~~-~~sg~l~~~~~~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGL 460 (641)
+ ..+.....+.++..++.. ...+.. ...+||++++||++++.+|+.|+++|+.||||++.+|.+||++|||
T Consensus 205 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGL 281 (342)
T KOG0773|consen 205 ESGPSGSEPPLRLAKQSLRQQRSAYDGSGGK---KQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGL 281 (342)
T ss_pred ccCcccccCCccccccccccccccccccccc---ccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCC
Confidence 0 022223333333333320 011111 1368899999999999999999999999999999999999999999
Q ss_pred ChhhhhccchhhhhhcchhhhHHHHHHHHhh
Q 006550 461 SRSQVSNWFINARVRLWKPMVEEIHMLETRQ 491 (641)
Q Consensus 461 S~sQVsNWFiNaRrRlkKpmiee~~~~e~~~ 491 (641)
++.||+|||||+|+|+|+||+++++..+...
T Consensus 282 s~~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 282 SRPQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred CcccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 9999999999999999999999999888765
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.92 E-value=1.2e-24 Score=219.48 Aligned_cols=201 Identities=26% Similarity=0.361 Sum_probs=152.2
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCcccchHHHHHHHHhhhcchHHHHHHHHHHHHHH
Q 006550 299 DGDGSDNRRKKSRLISMLDEVYRRYKQYYQQMQAAVASFEYVAGLGNAAPFANLALKAMSKHFRSLKNAITDQLQFTNKA 378 (641)
Q Consensus 299 ~~~~~e~q~Kk~KLl~mLdEV~~RY~qY~~qmq~VvssFe~~aGlg~a~pYt~lAlkamSrhFr~LrdaI~~Ql~~~~k~ 378 (641)
.+++.||+.|..+|..++++..++|+|.|.++.+.|.+.. .+.+.++|.+...+..|........+.|..||+...-.
T Consensus 99 gg~hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~nlL--~eQsr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce 176 (334)
T KOG0774|consen 99 GGDHSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLL--REQSRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCE 176 (334)
T ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999999999999999999999988 78888999988888777666666677899999865421
Q ss_pred HhhhccCCCCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHh
Q 006550 379 QIQANRGKDEASTFGSTDRGPYGHRPVLNSGFIERQSQPVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQT 458 (641)
Q Consensus 379 ~~~~s~~~~~spr~~~~d~s~~~qr~~~~sg~l~~~~~~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqT 458 (641)
. ...+.+.|++. +||||+|+|.+++||..||+.|+.||||++++|++||++|
T Consensus 177 ~-----------------------vmiLr~r~lda-----rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC 228 (334)
T KOG0774|consen 177 A-----------------------VMILRSRFLDA-----RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC 228 (334)
T ss_pred H-----------------------HHHHHHHHHHH-----HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc
Confidence 0 11233456665 7899999999999999999999999999999999999999
Q ss_pred CCChhhhhccchhhhhhcchhhh---HHHHHHHHhhhhhhhhhhhhhcCCCCCCCCCCCCCCCCCCCCCCCcccCCC
Q 006550 459 GLSRSQVSNWFINARVRLWKPMV---EEIHMLETRQGQKATQREEQSANRSSDHLPSSNSLPSENPSTSTQRVQETP 532 (641)
Q Consensus 459 GLS~sQVsNWFiNaRrRlkKpmi---ee~~~~e~~~~~~~~~~~~~s~~~ss~~~ps~~S~~s~~~Sss~~~~~~~p 532 (641)
+++.+||+|||.|+|.|+||.|. |+...++.+....... ......+...|++++........+++++.+.+
T Consensus 229 nItvsQvsnwfgnkrIrykK~~~k~~ee~~l~~~kk~~~~~~---~g~~~~~~s~~psgs~~~~~~p~~~~~~~g~~ 302 (334)
T KOG0774|consen 229 NITVSQVSNWFGNKRIRYKKNMGKNQEEANLYAAKKAVDATP---PGAPGNSYSTPPSGSSAGFMNPYSGDMFPGHQ 302 (334)
T ss_pred CceehhhccccccceeehhhhhhhhhhhhhhHhhcccccCCC---CCCCCCCCCCCCCcccCCCCCCCCcccccCCc
Confidence 99999999999999999999985 3444344433322222 11112233333334444444444556666555
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.59 E-value=5.4e-16 Score=117.75 Aligned_cols=40 Identities=70% Similarity=1.174 Sum_probs=36.5
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhh
Q 006550 436 WLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVR 475 (641)
Q Consensus 436 Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrR 475 (641)
||.+|+.||||+++||++||++|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 9999999999999999999999999999999999999998
No 6
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.39 E-value=5.5e-13 Score=103.83 Aligned_cols=57 Identities=32% Similarity=0.534 Sum_probs=53.3
Q ss_pred CCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 420 RPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 420 RkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
+++..|+++++.+|++||.. +|||+.+++..||.+|||+..||.+||.|+|.|.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 45678999999999999998 6999999999999999999999999999999998764
No 7
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.36 E-value=7.5e-13 Score=103.95 Aligned_cols=57 Identities=37% Similarity=0.620 Sum_probs=54.0
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcch
Q 006550 419 WRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478 (641)
Q Consensus 419 kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkK 478 (641)
||+|+.|+++++.+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.+.||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 577889999999999999998 799999999999999999999999999999999875
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.35 E-value=1.4e-12 Score=101.17 Aligned_cols=55 Identities=31% Similarity=0.507 Sum_probs=50.8
Q ss_pred CCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcc
Q 006550 420 RPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLW 477 (641)
Q Consensus 420 RkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlk 477 (641)
++|..|+++++.+|+.||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 45566999999999999998 58999999999999999999999999999999864
No 9
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.18 E-value=1.3e-11 Score=126.44 Aligned_cols=50 Identities=46% Similarity=0.812 Sum_probs=47.2
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcc
Q 006550 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLW 477 (641)
Q Consensus 425 Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlk 477 (641)
|.++.+.+||+||.. +|||++++|.+||+.|||+..||.|||.|+|.|.+
T Consensus 183 FKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 567889999999996 79999999999999999999999999999999976
No 10
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.93 E-value=6.5e-10 Score=116.15 Aligned_cols=64 Identities=23% Similarity=0.301 Sum_probs=56.6
Q ss_pred CCCCCCC-CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHH
Q 006550 418 VWRPQRG-LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEI 484 (641)
Q Consensus 418 ~kRkRr~-Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~ 484 (641)
+|||||. |++.||-.|++-|.+ ..|.+-.||+.||..++||.+||+.||||+|.|.||..+++.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 4555555 899999999999998 599999999999999999999999999999999998765543
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.86 E-value=1.4e-09 Score=113.73 Aligned_cols=62 Identities=21% Similarity=0.236 Sum_probs=55.3
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
..||||..++|.|+..|++-|+- |-|.|++-|.+|++.++||..||+.||||||+|+||-..
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 45666777999999999888776 599999999999999999999999999999999988654
No 12
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.76 E-value=4.3e-09 Score=107.30 Aligned_cols=61 Identities=20% Similarity=0.287 Sum_probs=56.2
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||.|+.|+..++..|+.-|.- |.|.+...|.+||..+.||+.||++||||+|+|+||..
T Consensus 158 ~~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 45788888999999999999987 69999999999999999999999999999999998753
No 13
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.72 E-value=1.1e-08 Score=107.25 Aligned_cols=62 Identities=21% Similarity=0.396 Sum_probs=54.1
Q ss_pred CCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhH
Q 006550 418 VWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVE 482 (641)
Q Consensus 418 ~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmie 482 (641)
.+|.|+.|+..++..|+.-|.. -.|.+..||.+||+.+|||-.||.+||+|||+|+||..-+
T Consensus 172 ~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 172 RRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 3444556999999999999987 4999999999999999999999999999999988776533
No 14
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.70 E-value=1.4e-08 Score=99.63 Aligned_cols=64 Identities=23% Similarity=0.285 Sum_probs=58.5
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHH
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEE 483 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee 483 (641)
..||.|+.|+.+++..|+..|.. +-|-.-.||+.||+.++||+.||+.||+|+|.|.||...++
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 56788888999999999999998 69999999999999999999999999999999998866543
No 15
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.70 E-value=1.7e-08 Score=100.13 Aligned_cols=72 Identities=28% Similarity=0.234 Sum_probs=62.7
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHHHHHHHhh
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEIHMLETRQ 491 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~~~~e~~~ 491 (641)
..++++++|+.+++..|+.-|..| -|-.+++|..||+++||...||..||+|+|+|.|.+..|.-|....+.
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~~---~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~ 120 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFESE---KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQ 120 (198)
T ss_pred ccccccccccHHHHHHhHHhhccc---cccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHH
Confidence 346778889999999999999884 888999999999999999999999999999999988877666554443
No 16
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.70 E-value=1.1e-08 Score=104.90 Aligned_cols=59 Identities=31% Similarity=0.496 Sum_probs=56.0
Q ss_pred CCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 418 VWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 418 ~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
-||+|+-|+.++.+.|++-|.+ |.|.++..|+.||.++||.+.||+.||+|+|.++||.
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 4788899999999999999999 6999999999999999999999999999999999875
No 17
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.67 E-value=1.6e-08 Score=102.04 Aligned_cols=63 Identities=25% Similarity=0.353 Sum_probs=57.2
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 416 QPVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 416 ~~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
++.|++|+.++.-+.+.|++-|.+ .-|..-.||.+||..+|||..||+.||+|+|-|.||-|.
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 455677778999999999999988 699999999999999999999999999999999988764
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=98.66 E-value=4e-08 Score=80.64 Aligned_cols=53 Identities=13% Similarity=0.237 Sum_probs=49.7
Q ss_pred CCCCCCCCChHHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChhhhhccchhhh
Q 006550 418 VWRPQRGLPERAVTVLRAWLFEHFLHPY----PTDTEKLMLAKQTGLSRSQVSNWFINAR 473 (641)
Q Consensus 418 ~kRkRr~Lpkeav~iLr~Wf~eH~~nPY----PS~~EK~~LAkqTGLS~sQVsNWFiNaR 473 (641)
++|+|+.|+.+++..|+..|.. ++| |+..++..||..+||++.+|..||+|.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3688899999999999999998 699 9999999999999999999999999964
No 19
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.58 E-value=3.6e-08 Score=99.18 Aligned_cols=63 Identities=21% Similarity=0.238 Sum_probs=57.9
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 416 QPVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 416 ~~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
+.+||+|+.|+..|+..|+.-|.. ..|.+..||.-||+++.||+.||+.||||+|.|+|+...
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 367788889999999999999988 499999999999999999999999999999999988763
No 20
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.48 E-value=1e-07 Score=102.27 Aligned_cols=61 Identities=20% Similarity=0.304 Sum_probs=55.7
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
++||||+.+...++..|+..|.+ ||-|+.+|.-.||.+++|.+..|+.||+|||.|.|+..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 45566677999999999999998 79999999999999999999999999999999998754
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.44 E-value=1.9e-07 Score=89.76 Aligned_cols=62 Identities=23% Similarity=0.352 Sum_probs=57.2
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
+.+++|++.+..++.+|+.-|.. +|||+..+|..|+..++++++-|+.||+|+|.+.|+...
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 56778888999999999999988 799999999999999999999999999999999887653
No 22
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.42 E-value=2.9e-07 Score=84.05 Aligned_cols=66 Identities=21% Similarity=0.291 Sum_probs=57.2
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHHH
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEIH 485 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~~ 485 (641)
+.+|-|+.|+..+...|+..|.+ .-||..=.|++||-+..||+..|+.||+|+|.+.+|.-.-..+
T Consensus 16 KQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 33455677999999999999999 5899999999999999999999999999999999886544443
No 23
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.41 E-value=3.1e-07 Score=92.06 Aligned_cols=62 Identities=21% Similarity=0.356 Sum_probs=57.2
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 416 QPVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 416 ~~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
++.+++|+.|+..+...|++-|.+. -|.+.+||.+++..+.||..||+.||||+|.|.|+-.
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrek---qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREK---QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHh---hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 4678889999999999999999994 9999999999999999999999999999999987643
No 24
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.35 E-value=3.6e-07 Score=92.00 Aligned_cols=62 Identities=24% Similarity=0.367 Sum_probs=56.6
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 416 QPVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 416 ~~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
++.+|.|+.|+.++.++|++-|.+ .-||....+++||.+.+|.+.+|++||.|+|.+.++..
T Consensus 35 RkqRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 35 RKQRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred hhcccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 355678888999999999999998 69999999999999999999999999999999987643
No 25
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.24 E-value=8.5e-07 Score=91.34 Aligned_cols=55 Identities=25% Similarity=0.374 Sum_probs=51.3
Q ss_pred CCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 422 QRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 422 Rr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
|+.|+.-+...|+.-|.+ --||.--.|++||.+|+|.+.+|+.||+|+|.|++|.
T Consensus 145 RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred cchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 556999999999999998 4899999999999999999999999999999998775
No 26
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.16 E-value=7.2e-07 Score=92.14 Aligned_cols=58 Identities=28% Similarity=0.255 Sum_probs=51.8
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHH
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEE 483 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee 483 (641)
-.++..++-.|+.-|.- .+|.|...|.+||..+|||+.||+.||+|||.|.+|....+
T Consensus 204 vVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 204 VVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred EEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 34799999999998876 69999999999999999999999999999999998865443
No 27
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.15 E-value=9.8e-07 Score=92.70 Aligned_cols=59 Identities=24% Similarity=0.354 Sum_probs=53.2
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 419 WRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 419 kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
+|.|+-|+..+.+.|+.||.. |.||+.+.|++||--|+||+..|++||.|+|.+++|.-
T Consensus 113 rrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 113 RRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 344455999999999999998 79999999999999999999999999999999988753
No 28
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.09 E-value=1.1e-06 Score=85.66 Aligned_cols=59 Identities=24% Similarity=0.360 Sum_probs=52.5
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 419 WRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 419 kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
++-|+.|+..+...|+.-|.. -.|.+-.|+.+||..++|+++||+.||+|+|++.||-.
T Consensus 101 ~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 101 RKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred hhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 344567999999999999987 48999999999999999999999999999999988754
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.08 E-value=2.1e-06 Score=89.52 Aligned_cols=63 Identities=22% Similarity=0.336 Sum_probs=57.6
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 416 QPVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 416 ~~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
...||+|+.++.++.+.|+..|.. .|-|..--|++|+.+|||....|+.||+|+|.+.|+-+.
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 478999999999999999999876 699999999999999999999999999999998776543
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.88 E-value=1.3e-05 Score=89.31 Aligned_cols=57 Identities=26% Similarity=0.331 Sum_probs=53.4
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhc
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRL 476 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRl 476 (641)
..||+|-.|+..+++.|++.|.+ ++||+.+.-+.|+.+++|.+.-|.|||-|+|+|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 34677888999999999999998 6999999999999999999999999999999995
No 31
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.62 E-value=1.8e-05 Score=83.35 Aligned_cols=63 Identities=16% Similarity=0.324 Sum_probs=56.1
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 416 QPVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 416 ~~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
++.+|=|+-|+++++..|++-|+.. -|-+...|=+||..++|.+.-|+.||||+|+|.|+..+
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrE---NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRE---NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHh---ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 4567778889999999998877763 79999999999999999999999999999999998764
No 32
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.61 E-value=2.9e-05 Score=78.77 Aligned_cols=66 Identities=20% Similarity=0.306 Sum_probs=57.0
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHHH
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEIH 485 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~~ 485 (641)
.++..|..|+-.++..|+.-|.+ ..||--+++-+||...|++++||..||+|+|.+++|...-||-
T Consensus 166 ~rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred cccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchh
Confidence 34444566999999999999988 5999999999999999999999999999999999887655554
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.51 E-value=4.9e-05 Score=73.61 Aligned_cols=61 Identities=16% Similarity=0.056 Sum_probs=55.3
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..+|.|+.|+..+.+.|+.-|... +||....++.||..+++++..|.+||+|+|+++++..
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~~---h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEKV---HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcCC---CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 556778889999999999999884 9999999999999999999999999999999987653
No 34
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.46 E-value=9.1e-05 Score=79.25 Aligned_cols=62 Identities=26% Similarity=0.445 Sum_probs=55.3
Q ss_pred CCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhH
Q 006550 418 VWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVE 482 (641)
Q Consensus 418 ~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmie 482 (641)
.+|.|+.|+..+...|+.||.. .|||....|+.||++++|+...|..||.|+|.|.+|....
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 3455667999999999999988 5799999999999999999999999999999999886644
No 35
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.39 E-value=6.6e-05 Score=78.75 Aligned_cols=59 Identities=20% Similarity=0.355 Sum_probs=53.2
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcch
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkK 478 (641)
.+||||+.+-.--++.|+++|.. .|-|+.+....+|+++.|-+..|+.||+|+|.+.|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 56788888866667889999998 599999999999999999999999999999999877
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.33 E-value=7.5e-05 Score=78.17 Aligned_cols=61 Identities=44% Similarity=0.687 Sum_probs=55.8
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 419 WRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 419 kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.+++.+++.+. .+|+.|+.+|..+|||+.-++.+|+-.++++..||++||+|+|+|+++.+
T Consensus 96 ~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 96 GARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred ccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 34556789999 99999999999999999999999999999999999999999999987754
No 37
>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=96.99 E-value=0.0053 Score=61.37 Aligned_cols=75 Identities=19% Similarity=0.205 Sum_probs=70.0
Q ss_pred CCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCcccchHHHHHHHHhhhcchHHHHHHHHHHHH
Q 006550 300 GDGSDNRRKKSRLISMLDEVYRRYKQYYQQMQAAVASFEYVAGLGNAAPFANLALKAMSKHFRSLKNAITDQLQFTN 376 (641)
Q Consensus 300 ~~~~e~q~Kk~KLl~mLdEV~~RY~qY~~qmq~VvssFe~~aGlg~a~pYt~lAlkamSrhFr~LrdaI~~Ql~~~~ 376 (641)
.+..||+.|.+++..++++..++|++.|.++.+.|.... ...+..+|.|..++..|....+...++|..||+..+
T Consensus 104 ~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~lL--reQs~~RPIs~keiE~m~~~i~~Kf~~iq~qLKQst 178 (191)
T PF03792_consen 104 IDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMNLL--REQSEFRPISPKEIERMVNIIHRKFSKIQMQLKQST 178 (191)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH--HHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999999999999999999988 588999999999999999999999999999998644
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.08 E-value=0.0038 Score=51.65 Aligned_cols=43 Identities=19% Similarity=0.371 Sum_probs=31.0
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhh
Q 006550 430 VTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVR 475 (641)
Q Consensus 430 v~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrR 475 (641)
.+.|+++|..| .+..+.+-..|..+|+|+..||.+||.-++.+
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 35599999985 99999999999999999999999999877544
No 39
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=95.16 E-value=0.016 Score=56.33 Aligned_cols=62 Identities=31% Similarity=0.486 Sum_probs=54.5
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 417 PVWRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 417 ~~kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
..++.++.+...+..++..-|.. .+||....++.|+..+|++...|.+||+|.|.+.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 45667778999999999888776 699999999999999999999999999999999877654
No 40
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.85 E-value=0.16 Score=62.40 Aligned_cols=60 Identities=22% Similarity=0.306 Sum_probs=54.0
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 419 WRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 419 kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
++.|..+...++.+|+..|.. .-||++++.+.|-+..+|.+..|..||+|+|.+.+|+..
T Consensus 904 ~a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 904 RAYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 455666889999999999988 599999999999999999999999999999999988764
No 41
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=77.87 E-value=3.6 Score=33.12 Aligned_cols=47 Identities=28% Similarity=0.233 Sum_probs=31.1
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhh
Q 006550 419 WRPQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINAR 473 (641)
Q Consensus 419 kRkRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaR 473 (641)
+|+|+.|+-+.+-.+-..+.. .+ -+..||+..|++.++|++|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 467788987775444444444 22 488999999999999999999853
No 42
>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=73.05 E-value=2.4 Score=34.93 Aligned_cols=33 Identities=15% Similarity=0.185 Sum_probs=24.8
Q ss_pred hhccccccCC-CcccchHHHHHHHHhhhcchHHH
Q 006550 335 ASFEYVAGLG-NAAPFANLALKAMSKHFRSLKNA 367 (641)
Q Consensus 335 ssFe~~aGlg-~a~pYt~lAlkamSrhFr~Lrda 367 (641)
.+..+.++|+ +|+.||.+..++....=|.+++|
T Consensus 3 ~~~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA 36 (52)
T PF03791_consen 3 SSIGADPELDQFMEAYCDMLVKYKEELQRPFQEA 36 (52)
T ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567788999 99999999999875544444454
No 43
>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=69.86 E-value=6.3 Score=30.46 Aligned_cols=47 Identities=34% Similarity=0.404 Sum_probs=37.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcch
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkK 478 (641)
.||++...+|...|++ .++ -.++|+..|+|...|+.|...+..++++
T Consensus 4 ~L~~~er~vi~~~y~~----~~t----~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----GLT----LEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-S----HHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----CCC----HHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 4889999999888754 332 5689999999999999999999888764
No 44
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=66.80 E-value=7 Score=46.61 Aligned_cols=44 Identities=25% Similarity=0.452 Sum_probs=40.5
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhc
Q 006550 430 VTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRL 476 (641)
Q Consensus 430 v~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRl 476 (641)
+.+|+++|.. |+.|+.+|-..+|.+.||...-|+.||.+.+...
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh
Confidence 7889999887 7999999999999999999999999999988754
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=66.39 E-value=8 Score=28.13 Aligned_cols=46 Identities=30% Similarity=0.276 Sum_probs=36.1
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcc
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLW 477 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlk 477 (641)
.|+++...++..++.+. + .-..+|+.+|++...|..|....+.+++
T Consensus 10 ~l~~~~~~~~~~~~~~~----~----~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG----L----SYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 37788888888776542 2 2567899999999999999988887764
No 46
>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=65.69 E-value=7.1 Score=32.01 Aligned_cols=46 Identities=24% Similarity=0.338 Sum_probs=30.3
Q ss_pred CCCCCCChHHH-HHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhh
Q 006550 420 RPQRGLPERAV-TVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINAR 473 (641)
Q Consensus 420 RkRr~Lpkeav-~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaR 473 (641)
++++.|+++.+ +++...+.. ......+|++.|++..+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 45677988885 455555443 35688999999999999999977665
No 47
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=61.35 E-value=20 Score=23.13 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=27.7
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccc
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWF 469 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWF 469 (641)
+.++.+....+..++.+ .+ ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 34666666666555543 33 36688999999999999994
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=60.07 E-value=10 Score=29.48 Aligned_cols=45 Identities=29% Similarity=0.374 Sum_probs=33.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhc
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRL 476 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRl 476 (641)
.||+....++...+.+. + .-.++|+.+|+|...|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~g----~----s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG----M----SYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC----c----CHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 47888888887766652 2 367899999999999999999998864
No 49
>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=58.84 E-value=15 Score=32.97 Aligned_cols=48 Identities=25% Similarity=0.232 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
.||++...++...+.+ .++ -.++|+.+|+++..|.++...+|+++++-
T Consensus 113 ~L~~~~r~il~l~~~~----~~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GKS----YKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4788888888876554 443 45799999999999999999999998764
No 50
>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=56.68 E-value=16 Score=31.69 Aligned_cols=48 Identities=29% Similarity=0.297 Sum_probs=37.7
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
.||+....++...+.. .++ -.++|+.+|+++..|.+|...++.++++-
T Consensus 110 ~L~~~~~~ii~~~~~~----g~s----~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GLS----YKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4788888887554443 443 56899999999999999999999988753
No 51
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=54.85 E-value=21 Score=32.91 Aligned_cols=51 Identities=25% Similarity=0.166 Sum_probs=41.2
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVE 482 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmie 482 (641)
.||+..+.++...+.+. ++ -.++|+.+|++...|.+++.-+|.++++.+.+
T Consensus 106 ~Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE----KS----YQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred hCCHHHHHHHHHHHHhC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 48999888887766653 22 45899999999999999999999998876643
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=54.73 E-value=12 Score=34.08 Aligned_cols=47 Identities=17% Similarity=0.099 Sum_probs=38.7
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcch
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkK 478 (641)
.||+..+.++..-+.+. ++ -.++|+.+|++...|.+|...+|.++++
T Consensus 106 ~L~~~~r~ii~l~~~~~----~s----~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG----KT----MGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 58999999887665553 22 5689999999999999999999999875
No 53
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=52.76 E-value=21 Score=33.63 Aligned_cols=48 Identities=15% Similarity=0.238 Sum_probs=40.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
.||++...++...+++ .++ -.++|+.+|++...|.+++..+|+++++-
T Consensus 129 ~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE----GLS----YKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 4898999988888776 333 56899999999999999999999998764
No 54
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=50.77 E-value=25 Score=32.42 Aligned_cols=49 Identities=22% Similarity=0.205 Sum_probs=39.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.|+++.+.++...+.. -++ -.++|+.+|++...|.+|...+|+++++-+
T Consensus 128 ~L~~~~r~vl~l~~~~----~~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIE----GLS----YEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888765544 232 458999999999999999999999988765
No 55
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=49.07 E-value=27 Score=32.04 Aligned_cols=50 Identities=20% Similarity=0.169 Sum_probs=39.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
.||+..+.++...+.+ .++ -.++|+..|++...|.+|..-+|.++++.+.
T Consensus 125 ~L~~~~r~i~~l~~~~----~~~----~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----GLS----YREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred hCCHHHHHHhhHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3788888888765554 222 4689999999999999999999999987553
No 56
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=48.48 E-value=15 Score=29.09 Aligned_cols=37 Identities=27% Similarity=0.309 Sum_probs=23.3
Q ss_pred HHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhc
Q 006550 433 LRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRL 476 (641)
Q Consensus 433 Lr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRl 476 (641)
|+.++.++ -+ ....||+.+|+++.+|+.|+.+...+.
T Consensus 2 L~~~m~~~---~i----t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 2 LKELMAER---GI----TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp HHHHHHHT---T------HHHHHHHHT--HHHHHHHHTTT----
T ss_pred HHHHHHHc---CC----CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 45566663 22 367899999999999999999874443
No 57
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=48.23 E-value=32 Score=33.13 Aligned_cols=53 Identities=15% Similarity=0.214 Sum_probs=42.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEI 484 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~ 484 (641)
.||++.+.++.-.+.+. ++ -.++|..+|++...|.+|..-+|+++++-+..++
T Consensus 134 ~Lp~~~R~v~~L~~~~g----~s----~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 186 (189)
T PRK12530 134 HLPAQQARVFMMREYLE----LS----SEQICQECDISTSNLHVLLYRARLQLQACLSKNW 186 (189)
T ss_pred hCCHHHHHHHhHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887776652 22 5689999999999999999999999988765443
No 58
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=46.78 E-value=32 Score=32.05 Aligned_cols=50 Identities=14% Similarity=0.056 Sum_probs=41.5
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||++.+.++..++.++ ++ -.++|..+|++...|.+|..-+|+++++-.
T Consensus 107 ~~L~~~~r~v~~l~~~~g----~s----~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE----LT----YEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 458999999998887764 22 568999999999999999999999987654
No 59
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=46.23 E-value=26 Score=33.16 Aligned_cols=50 Identities=18% Similarity=0.080 Sum_probs=41.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
.||++.+.++...+.+. + .-.++|..+|++...|.+++..+|+++++.+.
T Consensus 131 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG----A----SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 58999999998876653 2 25689999999999999999999999986653
No 60
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=46.09 E-value=27 Score=33.45 Aligned_cols=49 Identities=22% Similarity=0.209 Sum_probs=41.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++.-.|.+. ++ -.++|+.+|+|...|.++..-+|.++++..
T Consensus 131 ~L~~~~r~i~~l~~~~g----~s----~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG----EK----IEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 58999999998766652 22 568999999999999999999999988765
No 61
>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=45.29 E-value=24 Score=33.18 Aligned_cols=49 Identities=18% Similarity=0.136 Sum_probs=39.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++.-.+.++ ++ -.++|+.+|++...|.+|.-.+|+++++-+
T Consensus 138 ~L~~~~r~v~~l~~~~~----~s----~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG----LS----YEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 47888888887655542 22 568999999999999999999999988765
No 62
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=44.88 E-value=20 Score=34.49 Aligned_cols=49 Identities=10% Similarity=0.112 Sum_probs=40.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.+|...+.+. + .-.++|+.+|++...|.+|...+|+++++.+
T Consensus 142 ~L~~~~r~vl~l~~~~~----~----s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG----L----TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 48999999887766653 2 2568999999999999999999999987654
No 63
>PRK00118 putative DNA-binding protein; Validated
Probab=43.35 E-value=37 Score=31.37 Aligned_cols=52 Identities=17% Similarity=0.183 Sum_probs=41.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEI 484 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~ 484 (641)
.||+.++.++..++.+. ++ -.++|+.+|+|+.-|.+|...+|.++++- .+++
T Consensus 17 ~L~ekqRevl~L~y~eg----~S----~~EIAe~lGIS~~TV~r~L~RArkkLr~~-~~~~ 68 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD----YS----LGEIAEEFNVSRQAVYDNIKRTEKLLEDY-EEKL 68 (104)
T ss_pred cCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHH-HHHH
Confidence 47889999998887763 22 45799999999999999999999998764 3444
No 64
>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=43.06 E-value=37 Score=31.02 Aligned_cols=48 Identities=29% Similarity=0.280 Sum_probs=38.9
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcch
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkK 478 (641)
..||++...++..-+.+ .++ -.++|+.+|++...|.++..-+|+++++
T Consensus 110 ~~L~~~~r~v~~l~~~~----g~~----~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR----GVS----LTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 34899999988875555 333 5689999999999999999999988865
No 65
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=42.61 E-value=64 Score=29.07 Aligned_cols=53 Identities=25% Similarity=0.194 Sum_probs=41.7
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHHH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEIH 485 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~~ 485 (641)
.|++...++|+-| .++ |. ..++|+..+++.+.|.+|..+.|+|+.-.-..+..
T Consensus 149 ~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~ 201 (211)
T PRK15369 149 LLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201 (211)
T ss_pred CCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHH
Confidence 4899999999875 442 32 57899999999999999999999998755544443
No 66
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=41.56 E-value=35 Score=32.53 Aligned_cols=49 Identities=22% Similarity=0.281 Sum_probs=39.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++...++..-+++. ++ -.++|..+|++...|.+|+..+|+++++-+
T Consensus 141 ~L~~~~~~v~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 141 QLPESQRQVLELAYYEG----LS----QSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred hCCHHHhhhhhhhhhcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888887665542 22 568999999999999999999999998755
No 67
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=41.50 E-value=39 Score=31.76 Aligned_cols=47 Identities=21% Similarity=0.171 Sum_probs=40.0
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 425 Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
||++++.++.-.+.+. ++ -.++|..+|++...|.+....+|.++++-
T Consensus 135 Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG----LT----VEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 9999999998887763 22 46899999999999999999999998764
No 68
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=41.33 E-value=24 Score=34.48 Aligned_cols=49 Identities=27% Similarity=0.291 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++...++..-+++. + .-.++|..+|++...|.+++..+|+++++-+
T Consensus 153 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE----L----SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48899999888666553 2 2568999999999999999999999987655
No 69
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=41.21 E-value=41 Score=32.63 Aligned_cols=50 Identities=30% Similarity=0.207 Sum_probs=40.4
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
..|++.++.+|+. +.+ .+. -.++|+.+|++...|++|...+|.++++-..
T Consensus 5 ~~Lt~rqreVL~l-r~~----GlT----q~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRL-RER----GLT----QQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHH-HHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5689999999977 333 332 5689999999999999999999999877653
No 70
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=40.55 E-value=26 Score=32.71 Aligned_cols=49 Identities=14% Similarity=0.011 Sum_probs=40.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||+..+.++.-.+.+. +. -.++|+.+|++...|.++..-+|+++++-+
T Consensus 112 ~L~~~~r~v~~l~~~~g----~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASG----FS----YEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999888877663 22 468999999999999999999999987543
No 71
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=40.16 E-value=40 Score=31.20 Aligned_cols=47 Identities=23% Similarity=0.165 Sum_probs=39.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcch
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkK 478 (641)
.||++++.++.-.+.+. ++ -.++|..+|++...|..+...+|.++++
T Consensus 112 ~L~~~~r~v~~l~~~~~----~s----~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG----FS----YKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 58999999888776653 22 4689999999999999999999999875
No 72
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=39.54 E-value=44 Score=31.82 Aligned_cols=50 Identities=20% Similarity=0.130 Sum_probs=40.8
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||++.+.++..-+.+. ++ -.++|..+|++...|.++...+|.++++.+
T Consensus 138 ~~L~~~~r~i~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 138 DTLPEKQREILILRVVVG----LS----AEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred HhCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 358999999988766652 22 568999999999999999999999988653
No 73
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=39.16 E-value=39 Score=31.68 Aligned_cols=49 Identities=18% Similarity=0.172 Sum_probs=38.9
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||+..+.++..-+.+ .++ -.++|+.+|++...|.+++..+|+++++-+
T Consensus 136 ~L~~~~r~v~~l~~~~----g~s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DLS----LKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 5888888888764444 232 568999999999999999999999987643
No 74
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=39.07 E-value=39 Score=32.88 Aligned_cols=49 Identities=20% Similarity=0.142 Sum_probs=41.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++.-++.+ -++ -.++|..+|+|...|.+++.-+|+++++-+
T Consensus 113 ~Lp~~~r~v~~L~~~~----g~s----~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGAS----GFS----YEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999888776 333 468999999999999999999999988755
No 75
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=38.94 E-value=49 Score=30.24 Aligned_cols=50 Identities=22% Similarity=0.186 Sum_probs=41.1
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||++.+.++.-.+++ -++ -.++|..+|++...|.++..-+|+++++.+
T Consensus 105 ~~Lp~~~r~v~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWE----DMD----VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHh----cCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45899999998876666 333 568999999999999999999999987655
No 76
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=38.66 E-value=43 Score=30.88 Aligned_cols=48 Identities=25% Similarity=0.291 Sum_probs=39.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++...+|...+ + -++ -.++|..+|++...|.++...+|.++++-+
T Consensus 112 ~L~~~~r~il~l~~-~----g~s----~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----GYS----YKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-c----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887666 4 333 568999999999999999999999988755
No 77
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=38.42 E-value=42 Score=31.87 Aligned_cols=49 Identities=16% Similarity=0.243 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++..-+++. ++ -.++|+.+|++...|.++...+|+++++.+
T Consensus 128 ~L~~~~r~i~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQG----LS----NIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhcC----CC----HHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 37888888886655542 22 568999999999999999999999987754
No 78
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=38.31 E-value=26 Score=33.61 Aligned_cols=49 Identities=20% Similarity=0.227 Sum_probs=40.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++.-.+.+. +. -.++|+.+|++...|.++...+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILG----FS----SDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887655552 22 468999999999999999999999998765
No 79
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=38.28 E-value=30 Score=33.31 Aligned_cols=51 Identities=24% Similarity=0.238 Sum_probs=40.5
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
..||++...++...+.+. -+ -.++|..+|++...|.+....+|+++++-+-
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 458999999998766553 12 4589999999999999999999998876553
No 80
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=37.51 E-value=3.7e+02 Score=29.21 Aligned_cols=63 Identities=19% Similarity=0.318 Sum_probs=46.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCcccchHHHHHHHHhhhcchHHHHHHHHHHHHHHHhh
Q 006550 303 SDNRRKKSRLISMLDEVYRRYKQYYQQMQAAVASFEYVAGLGNAAPFANLALKAMSKHFRSLKNAITDQLQFTNKAQIQ 381 (641)
Q Consensus 303 ~e~q~Kk~KLl~mLdEV~~RY~qY~~qmq~VvssFe~~aGlg~a~pYt~lAlkamSrhFr~LrdaI~~Ql~~~~k~~~~ 381 (641)
.|++.+|..|..=++++++|-++-..+|.+ +|. |.+ +.+.+.-+..||-+...|+-+..+.-+
T Consensus 7 ~eL~qrk~~Lq~eIe~LerR~~ri~~Emrt---sFa---G~S----------q~lA~RVqGFkdYLvGsLQDLa~saEq 69 (283)
T PF11285_consen 7 KELEQRKQALQIEIEQLERRRERIEKEMRT---SFA---GQS----------QDLAIRVQGFKDYLVGSLQDLAQSAEQ 69 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---ccc---cch----------HHHHHHHhhhHHHHHHHHHHHHHHHHh
Confidence 588999999999999999999999988764 553 332 334445567788888888876654333
No 81
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=36.82 E-value=37 Score=34.39 Aligned_cols=49 Identities=18% Similarity=0.253 Sum_probs=40.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.+|...|++. ++ -.++|+.+|++...|..|...+|+++++.+
T Consensus 205 ~L~~~~r~vl~l~~~~g----~s----~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----LS----QKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48999999998877653 22 478999999999999999999999987643
No 82
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=36.69 E-value=24 Score=33.67 Aligned_cols=49 Identities=18% Similarity=0.159 Sum_probs=38.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++.-.+.+ .++ -.++|+.+|++...|.++...+|+++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHG----DLE----LEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehcc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4777777777655544 333 568999999999999999999999988754
No 83
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=36.66 E-value=55 Score=31.72 Aligned_cols=50 Identities=16% Similarity=0.096 Sum_probs=41.1
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
.||++.+.++.-.+.+ -++ -.++|+.+|++...|.++...+|+++++-+.
T Consensus 116 ~Lp~~~r~i~~L~~~~----g~s----~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGAS----GFA----YEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4899999988877766 333 4589999999999999999999999887653
No 84
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=36.46 E-value=47 Score=31.73 Aligned_cols=52 Identities=15% Similarity=0.153 Sum_probs=42.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEE 483 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee 483 (641)
.||++++.++.-.+.+. ++ -.++|..+|++..-|.++...+|+++++-+..+
T Consensus 131 ~Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 182 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE----LE----TEEICQELQITATNAWVLLYRARMRLRECLDLH 182 (191)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999988887776663 22 468999999999999999999999998765443
No 85
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=36.30 E-value=45 Score=31.48 Aligned_cols=50 Identities=18% Similarity=0.222 Sum_probs=40.3
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||+..+.++.-.+.+. +. -.++|+.+|++...|.++..-+|.++++.+
T Consensus 134 ~~L~~~~r~vl~l~~~~~----~s----~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 134 KALSPEERRVIEVLYYQG----YT----HREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred HhCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 348999999888766553 22 568999999999999999999999987654
No 86
>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=36.06 E-value=53 Score=26.09 Aligned_cols=53 Identities=23% Similarity=0.192 Sum_probs=40.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHHH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEIH 485 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~~ 485 (641)
.|++...++|+.+..- + ...++|...+++.+-|..+..+.++|+.=+...++.
T Consensus 3 ~LT~~E~~vl~~l~~G-----~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~l~ 55 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG-----M----SNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAELI 55 (58)
T ss_dssp SS-HHHHHHHHHHHTT-----S-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHHHH
T ss_pred ccCHHHHHHHHHHHhc-----C----CcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHHHH
Confidence 5888899998777543 3 267899999999999999999999998755544443
No 87
>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=35.88 E-value=36 Score=34.45 Aligned_cols=49 Identities=20% Similarity=0.202 Sum_probs=40.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++...|.+. + .-.++|+.+|++...|+.|...++.++++.+
T Consensus 205 ~L~~~~r~ii~l~~~~g----~----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN----L----SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48899998888777653 2 1468999999999999999999999988754
No 88
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=35.68 E-value=36 Score=32.02 Aligned_cols=49 Identities=14% Similarity=0.160 Sum_probs=39.7
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
..||++++.++.-.+.+. .+ -.++|+.+|++..-|.++...+|+|++..
T Consensus 118 ~~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDG--MG------HAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 348999999988776653 22 45899999999999999999999998643
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=35.61 E-value=45 Score=31.10 Aligned_cols=49 Identities=14% Similarity=0.155 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++..-+++. ++ -.++|+.+|+|...|.++..-+|.++++-+
T Consensus 119 ~L~~~~r~i~~l~~~~g----~s----~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----LT----IKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48888888887776653 22 568999999999999999999999988754
No 90
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=35.12 E-value=44 Score=31.75 Aligned_cols=49 Identities=24% Similarity=0.143 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||+....++...+.+. ++ -.++|+.+|+++..|.++...+|+++++.+
T Consensus 129 ~L~~~~r~v~~l~~~~g----~s----~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG----LS----VAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 37888888776655553 22 568999999999999999999999998755
No 91
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=34.96 E-value=29 Score=34.67 Aligned_cols=49 Identities=31% Similarity=0.333 Sum_probs=40.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||+..+.++..-|.+. + .-.++|+.+|++..-|.+|...+|+++++.+
T Consensus 184 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE----L----NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhccC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888887766552 2 2568999999999999999999999998754
No 92
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=34.67 E-value=77 Score=23.46 Aligned_cols=47 Identities=26% Similarity=0.247 Sum_probs=35.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
.|+++...++..+ .+ .+ ...++|+.+|++...|..|....+.++.-.
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 4788888877554 32 22 357899999999999999999887776543
No 93
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=34.58 E-value=66 Score=30.68 Aligned_cols=50 Identities=14% Similarity=0.169 Sum_probs=40.2
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||++.+.+|..-+.+ .++ -.++|+.+|++...|.+.+..+|+++++-.
T Consensus 130 ~~L~~~~r~vl~l~~~~----~~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 130 AKLSPAHREIIDLVYYH----EKS----VEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35899999998776655 232 568999999999999999999999887643
No 94
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=34.53 E-value=43 Score=34.33 Aligned_cols=51 Identities=27% Similarity=0.361 Sum_probs=42.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVE 482 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmie 482 (641)
.||++.+.++.-.+.+. ++ -.++|..+|++..-|.++...+|+++++.+..
T Consensus 161 ~Lp~~~R~v~~L~~~eg----~S----~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~ 211 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG----LS----MDRIGAMYQVHRSTVSRWVAQARERLLERTRR 211 (244)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 48999988888777764 22 46899999999999999999999999876633
No 95
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=34.49 E-value=55 Score=31.58 Aligned_cols=49 Identities=16% Similarity=0.140 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++++.++.-.+++ -|+ -.++|+.+|++...|.+++.-+|+++++-+
T Consensus 136 ~L~~~~r~i~~L~~~~----g~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GLS----NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4899998888776554 333 568999999999999999999999988644
No 96
>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=34.36 E-value=38 Score=25.81 Aligned_cols=21 Identities=24% Similarity=0.265 Sum_probs=19.0
Q ss_pred HHHHHhCCChhhhhccchhhh
Q 006550 453 MLAKQTGLSRSQVSNWFINAR 473 (641)
Q Consensus 453 ~LAkqTGLS~sQVsNWFiNaR 473 (641)
+||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999875
No 97
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=34.32 E-value=56 Score=30.07 Aligned_cols=49 Identities=24% Similarity=0.327 Sum_probs=39.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++..-+.+ .++ -.++|..+|++...|.+|...+|.++++.+
T Consensus 110 ~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE----DLS----EAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHh----cCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4788888888766655 332 468999999999999999999999987644
No 98
>PRK04217 hypothetical protein; Provisional
Probab=34.22 E-value=49 Score=30.88 Aligned_cols=50 Identities=20% Similarity=0.164 Sum_probs=40.6
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..|+++.+.++..++.+. + .-.++|+.+|++...|.+.+..+|.+++.-+
T Consensus 41 ~~Lt~eereai~l~~~eG----l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG----L----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 348899999998887663 2 3567999999999999999999888886543
No 99
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=33.53 E-value=75 Score=31.43 Aligned_cols=54 Identities=22% Similarity=0.272 Sum_probs=43.1
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHH
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEI 484 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~ 484 (641)
..||++.+.++.--+++. ++ -.++|+.+|++..-|.++..-+|+++++.+....
T Consensus 147 ~~L~~~~r~v~~L~~~~g----~s----~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 147 DGLPAKYARVFMMREFIE----LE----TNEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred HhCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 348888888887766653 22 4689999999999999999999999988775443
No 100
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=33.32 E-value=60 Score=30.86 Aligned_cols=49 Identities=12% Similarity=0.131 Sum_probs=38.9
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
..||++.+.++..-+.+ -++ -.++|+.+|+|...|.+|...+|+++++-
T Consensus 132 ~~L~~~~r~i~~l~~~~----~~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHAYVD----GCS----HAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 35888888877666655 222 56899999999999999999999988753
No 101
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=32.91 E-value=68 Score=32.54 Aligned_cols=49 Identities=16% Similarity=0.161 Sum_probs=39.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||+.++.++.-.+.+. ++ -.++|+.+|++...|.++...+|+++++.+
T Consensus 171 ~Lp~~~R~v~~L~~~eg----~s----~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN----MS----NGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHhcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 47888888876665552 22 568999999999999999999999998755
No 102
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=32.23 E-value=69 Score=30.79 Aligned_cols=49 Identities=29% Similarity=0.336 Sum_probs=39.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++..-+.+ .++ -.++|..+|++...|.+++..+|+++++-+
T Consensus 106 ~L~~~~r~i~~l~~~~----g~~----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELE----GLS----QKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888766555 343 568999999999999999999999887654
No 103
>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=32.02 E-value=62 Score=31.94 Aligned_cols=49 Identities=29% Similarity=0.405 Sum_probs=40.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||+..+.++...+.+ .+ .-.++|+.+|++...|..|...+++++++-+
T Consensus 178 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l 226 (227)
T TIGR02980 178 ALPERERRILLLRFFE----DK----TQSEIAERLGISQMHVSRLLRRALKKLREQL 226 (227)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 5899999999887665 22 2678999999999999999999999987643
No 104
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=31.90 E-value=86 Score=28.87 Aligned_cols=44 Identities=11% Similarity=0.292 Sum_probs=35.3
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhh
Q 006550 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINA 472 (641)
Q Consensus 425 Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNa 472 (641)
-....+..+.+|+.+|+..+ ++ -..||+.+|+++..+..||...
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 34455677889999987766 44 6789999999999999999876
No 105
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=31.66 E-value=72 Score=29.41 Aligned_cols=49 Identities=20% Similarity=0.229 Sum_probs=39.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++..-+++ .++ ..++|+.+|++...|..+..-+|+++++-+
T Consensus 109 ~L~~~~r~v~~l~~~~----~~s----~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLH----GET----QKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4889999988776665 222 568999999999999999988888887654
No 106
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=31.27 E-value=65 Score=30.68 Aligned_cols=49 Identities=22% Similarity=0.171 Sum_probs=38.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++.--+.+ .|+ -.++|+.+|++...|.++..-+|+++++-+
T Consensus 138 ~L~~~~r~v~~l~~~~----g~s----~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 138 QLPEDLRTALTLREFD----GLS----YEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred hCCHHHhHHHhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3777777776654444 443 568999999999999999999999988765
No 107
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=30.99 E-value=75 Score=30.98 Aligned_cols=50 Identities=22% Similarity=0.224 Sum_probs=40.9
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
.||+..+.++.--+++. ++ -.++|..+|++..-|.+....+|+++++-+.
T Consensus 139 ~Lp~~~r~v~~L~~~eg----~s----~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD----FE----IDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887766653 32 4689999999999999999999999987663
No 108
>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=30.27 E-value=78 Score=30.53 Aligned_cols=51 Identities=20% Similarity=0.201 Sum_probs=41.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVE 482 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmie 482 (641)
.||++.+.++..-+++. + .-.++|+.+|++..-|.++..-+|+++++-+..
T Consensus 131 ~L~~~~r~v~~l~~~~g----~----s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG----F----ESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred hCCHHHHHHHHHHHHhC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 58888888887776653 2 257899999999999999999999999886643
No 109
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=30.26 E-value=73 Score=29.89 Aligned_cols=53 Identities=17% Similarity=0.198 Sum_probs=40.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHHH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEEI 484 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee~ 484 (641)
.||++...++.-.+.+. ++ -.++|..+|++...|..+...+|+++++-+.+..
T Consensus 119 ~L~~~~r~i~~l~~~~~----~s----~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQ----YS----YKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47887877776555542 22 4689999999999999999999999987765443
No 110
>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=30.23 E-value=66 Score=32.33 Aligned_cols=55 Identities=22% Similarity=0.122 Sum_probs=42.1
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVE 482 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmie 482 (641)
.||+..+.+|...|.-.-..++ .-.++|+.+|+|...|+.+...+++++|+.+..
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~----t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~ 230 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPH----TLEEVGKEFNVTRERIRQIESKALRKLRHPSRS 230 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCc----cHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHH
Confidence 4888888888877621101233 267899999999999999999999999987533
No 111
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=30.02 E-value=57 Score=32.76 Aligned_cols=49 Identities=22% Similarity=0.150 Sum_probs=41.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++..++.++ |+ -.++|+.+|++..-|.++...+|+++++.+
T Consensus 134 ~Lp~~~R~v~~L~y~eg----~s----~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELED----MS----YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999998877764 32 468999999999999999999999988765
No 112
>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=29.86 E-value=28 Score=33.32 Aligned_cols=50 Identities=24% Similarity=0.244 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
.||++.+.++.-.+.+. ++ -.++|+.+|++...|.++..-+|+++++-+.
T Consensus 131 ~Lp~~~r~i~~L~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEG----FA----YKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehhhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47777777776555442 22 5689999999999999999999999987653
No 113
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=29.78 E-value=75 Score=29.80 Aligned_cols=49 Identities=22% Similarity=0.206 Sum_probs=37.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++...++.--+.+ .++ -.++|..+|++...|.++...+|+++++-+
T Consensus 136 ~L~~~~r~il~l~~~~----~~s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYIE----DLS----LKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHhh----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4788787777543333 222 568999999999999999999999988644
No 114
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=29.76 E-value=73 Score=30.21 Aligned_cols=50 Identities=16% Similarity=0.158 Sum_probs=40.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
.||+..+.++..-+.+. + + -.++|+.+|++..-|.+....+|.++++-+-
T Consensus 117 ~Lp~~~r~i~~l~~~e~----~-s---~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD----Y-S---QEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred hCCHHHHHHHHHHHHcc----C-C---HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48999988887766654 1 2 5689999999999999999999999987653
No 115
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=29.22 E-value=48 Score=31.85 Aligned_cols=48 Identities=15% Similarity=-0.002 Sum_probs=39.5
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcch
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkK 478 (641)
..||++++.++.-.+.+. ++ -.++|+.+|++...|.++..-+|+++++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLG----LS----YADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 358999999887776653 22 4689999999999999999999999876
No 116
>PRK06930 positive control sigma-like factor; Validated
Probab=29.01 E-value=83 Score=30.93 Aligned_cols=52 Identities=17% Similarity=0.080 Sum_probs=41.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhhHH
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMVEE 483 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmiee 483 (641)
.||+..+.++...+.+ .++ -.++|..+|++...|.+|...+|.++++.+.++
T Consensus 114 ~L~~rer~V~~L~~~e----g~s----~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~ 165 (170)
T PRK06930 114 VLTEREKEVYLMHRGY----GLS----YSEIADYLNIKKSTVQSMIERAEKKIARQINES 165 (170)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4888888888776654 222 468999999999999999999999998766444
No 117
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=28.63 E-value=80 Score=29.47 Aligned_cols=49 Identities=16% Similarity=0.181 Sum_probs=40.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++...+|..-+.+. ++ -.++|+.+|++..-|.++.--+|.++++-+
T Consensus 118 ~L~~~~r~vl~L~~~~g----~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRG----WS----TAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48999999888766653 33 568999999999999999999999988755
No 118
>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=28.60 E-value=76 Score=31.42 Aligned_cols=48 Identities=27% Similarity=0.335 Sum_probs=40.2
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
.||+..+.+|...|.+. + .-.++|+.+|++...|..|...+++++++.
T Consensus 175 ~L~~~~r~il~l~y~~~----~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE----L----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999998877653 2 257899999999999999999999998764
No 119
>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=28.57 E-value=97 Score=29.28 Aligned_cols=50 Identities=22% Similarity=0.265 Sum_probs=40.7
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||++.+.++..-+.+ -|+ -.++|+.+|++...|.++..-+|+++++-+
T Consensus 99 ~~L~~~~r~v~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 99 KELPDEYREAIRLTELE----GLS----QQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred HhCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35899999988877665 333 568999999999999999999998887754
No 120
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=28.43 E-value=38 Score=31.63 Aligned_cols=49 Identities=22% Similarity=0.198 Sum_probs=38.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||+..+.+|...+.+ .++ -.++|+.+|++...|.+++..+|+++++-+
T Consensus 120 ~L~~~~r~vl~l~~~~----g~s----~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 120 TLSLEHRAVLVLHDLE----DLP----QKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hCCHHHeeeeeehHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3777777777665554 333 578999999999999999999999988754
No 121
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=28.22 E-value=87 Score=28.83 Aligned_cols=48 Identities=17% Similarity=0.109 Sum_probs=38.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
.||+..+.++...+++ -++ -.++|+.+|++...|.+...-+|.++++.
T Consensus 122 ~L~~~~r~vl~l~~~~----g~s----~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQ----NLP----IAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred hCCHHHHHHHHHHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 4888888888776554 332 56899999999999999999888888764
No 122
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=27.96 E-value=82 Score=31.09 Aligned_cols=49 Identities=16% Similarity=0.143 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++..-+.+. ++ -.++|+.+|++..-|.++..-+|+++++-+
T Consensus 138 ~L~~~~r~v~~L~~~~g----~s----~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG----LS----YEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888776655553 32 468999999999999999999999988654
No 123
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=27.83 E-value=74 Score=32.61 Aligned_cols=50 Identities=24% Similarity=0.190 Sum_probs=40.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
.||++.+.+|...|.+ .+ .-.++|..+|++...|+.+..-++.++++-+.
T Consensus 203 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 203 QLEERTREVLEFVFLH----DL----TQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred cCCHHHHHHHHHHHHC----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 4788888888776654 22 25689999999999999999999999887653
No 124
>PF13730 HTH_36: Helix-turn-helix domain
Probab=27.29 E-value=1.5e+02 Score=23.04 Aligned_cols=47 Identities=23% Similarity=0.178 Sum_probs=30.9
Q ss_pred CCChHHHHHHHHH--HHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhh
Q 006550 424 GLPERAVTVLRAW--LFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINAR 473 (641)
Q Consensus 424 ~Lpkeav~iLr~W--f~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaR 473 (641)
+|+..++.++-.- +......-||+ ...||+.+|+++..|..+...-+
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHH
Confidence 4666666655322 11122347887 77899999999999998875443
No 125
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=26.90 E-value=62 Score=33.18 Aligned_cols=49 Identities=27% Similarity=0.402 Sum_probs=40.7
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++...|.+. + .-.++|..+|++...|..+...+++++++.+
T Consensus 212 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED----L----TLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48888888888877653 2 2578999999999999999999999988765
No 126
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=26.80 E-value=56 Score=31.11 Aligned_cols=50 Identities=22% Similarity=0.166 Sum_probs=40.6
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||+..+.++.-.+.+. + .-.++|+.+|++..-|.++.-.+|+++++-+
T Consensus 130 ~~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLEG----L----SVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred HhCCHHHHHHHHHHHHcC----C----cHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 348999999998766653 2 2568999999999999999999999987654
No 127
>PF13518 HTH_28: Helix-turn-helix domain
Probab=26.54 E-value=52 Score=24.89 Aligned_cols=24 Identities=33% Similarity=0.498 Sum_probs=20.6
Q ss_pred HHHHHHHhCCChhhhhccchhhhh
Q 006550 451 KLMLAKQTGLSRSQVSNWFINARV 474 (641)
Q Consensus 451 K~~LAkqTGLS~sQVsNWFiNaRr 474 (641)
..++|++.|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 567999999999999999876654
No 128
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=25.79 E-value=82 Score=30.46 Aligned_cols=51 Identities=16% Similarity=0.125 Sum_probs=41.9
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
..||++.+.++...+.++ ++ -.++|..+|++..-|.++..-+|.++++-+.
T Consensus 127 ~~Lp~~~r~v~~l~~~~g----~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 127 AKLDPEYREPLLLQVIGG----FS----GEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred HhCCHHHHHHHHHHHHhC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 358999999988777764 22 4689999999999999999999999877663
No 129
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=25.64 E-value=62 Score=31.18 Aligned_cols=49 Identities=16% Similarity=0.070 Sum_probs=40.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++.-.+.+. +. -.++|+.+|++...|.....-+|+++++.+
T Consensus 111 ~Lp~~~R~v~~L~~~~g----~s----~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 111 KLPQDQREALILVGASG----FS----YEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred hCCHHHHHHhhHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999887776653 22 468999999999999999999999988665
No 130
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=25.47 E-value=1e+02 Score=30.62 Aligned_cols=53 Identities=19% Similarity=0.090 Sum_probs=39.1
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.++.-.+.-+....+ .-.++|+.+|++...|.++...+|+++++.+
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~----s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEK----TQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4888888888765521101122 2568999999999999999999999998754
No 131
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=25.30 E-value=1.1e+02 Score=28.31 Aligned_cols=46 Identities=20% Similarity=0.243 Sum_probs=37.7
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcc
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLW 477 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlk 477 (641)
.||++++.++...+.+. ++ -.++|+.+|++...|.++...+++++.
T Consensus 113 ~L~~~~r~v~~L~~~~g----~s----~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG----LG----YGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 48999999997776653 22 468999999999999999999988764
No 132
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=25.12 E-value=1e+02 Score=29.32 Aligned_cols=50 Identities=20% Similarity=0.276 Sum_probs=40.3
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||++.+.++...+.+. ++ -.++|+.+|++..-|.+....+|.++++-+
T Consensus 121 ~~L~~~~r~i~~l~~~~g----~s----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 121 KELNESNRQVFKYKVFYN----LT----YQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HhCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 348999999988765552 22 468999999999999999999999987654
No 133
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=24.96 E-value=90 Score=29.66 Aligned_cols=50 Identities=22% Similarity=0.289 Sum_probs=40.3
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
..||++.+.++...+.+. ++ -.++|+.+|++...|.++..-+|.++++-+
T Consensus 126 ~~L~~~~r~v~~l~~~~g----~s----~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 126 MSLPIKYREVIYLFYYEE----LS----IKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred HhCCHHHhhHhHhHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358999988887766653 22 468999999999999999999999987644
No 134
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=24.93 E-value=1.1e+02 Score=29.59 Aligned_cols=49 Identities=20% Similarity=0.115 Sum_probs=40.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||+..+.++.-.+++ -++ -.++|..+|++..-|.++..-+|.++++-+
T Consensus 111 ~Lp~~~R~v~~L~~~e----g~s----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIE----GLS----YQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 5899999999887776 333 568999999999999999999999887643
No 135
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.88 E-value=65 Score=31.50 Aligned_cols=50 Identities=18% Similarity=0.102 Sum_probs=40.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
.||+....++..-+++. + .-.++|+.+|++...|.++...+|+++++-+.
T Consensus 133 ~Lp~~~r~v~~l~~~~g----~----s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 133 ALPPERREALILTQVLG----Y----TYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred cCCHHHHHHhhhHHHhC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 48888888887666663 2 15689999999999999999999999886653
No 136
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=24.82 E-value=98 Score=31.39 Aligned_cols=48 Identities=23% Similarity=0.212 Sum_probs=39.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
.||+..+.++...+.+. +. -.++|..+|+|...|.+++..+|+++++-
T Consensus 201 ~L~~~~r~vl~l~~~~~----~s----~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYKEE----LT----LTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHhcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 48888888888776652 22 57899999999999999999999998753
No 137
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=24.36 E-value=1.1e+02 Score=32.94 Aligned_cols=53 Identities=21% Similarity=0.154 Sum_probs=39.9
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++.+.+|..-|.-+....+ .-.++|+.+|++...|+.+...+|+++|+-+
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~----s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAA----TLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCc----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788888887755422212233 2678999999999999999999999998765
No 138
>PLN00064 photosystem II protein Psb27; Provisional
Probab=24.25 E-value=1.9e+02 Score=29.23 Aligned_cols=58 Identities=21% Similarity=0.262 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCC-CcccchHHHHHHHHhhhc----------chHHHHHHHHHHHHH
Q 006550 309 KSRLISMLDEVYRRYKQYYQQMQAAVASFEYVAGLG-NAAPFANLALKAMSKHFR----------SLKNAITDQLQFTNK 377 (641)
Q Consensus 309 k~KLl~mLdEV~~RY~qY~~qmq~VvssFe~~aGlg-~a~pYt~lAlkamSrhFr----------~LrdaI~~Ql~~~~k 377 (641)
.+++..+.-+.-.||+. ...+.|+. +..-|| ||.+++-||- .||++|+.++..+.+
T Consensus 94 ~aeaR~~iNdyvSrYRr-----------~~~v~Gl~SFttMyT--ALNaLAGHY~SfgpnrPlPeKlK~RL~qE~~~AEk 160 (166)
T PLN00064 94 VAELRETSNSWVAKYRR-----------EKALLGRPSFRDMYS--ALNAVSGHYISFGPTAPIPAKRKARILEEMDTAEK 160 (166)
T ss_pred HHHHHHHHHHHHHHhcC-----------CCcccCcccHHHHHH--HHHHHHHHhhccCCCCCCcHHHHHHHHHHHHHHHH
Confidence 44455555566667776 45667776 566676 7889999993 468999999988776
Q ss_pred HH
Q 006550 378 AQ 379 (641)
Q Consensus 378 ~~ 379 (641)
++
T Consensus 161 al 162 (166)
T PLN00064 161 AL 162 (166)
T ss_pred HH
Confidence 64
No 139
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=23.56 E-value=1.2e+02 Score=28.90 Aligned_cols=48 Identities=13% Similarity=0.089 Sum_probs=39.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
.||++++.++.-.+.+. |+ -.++|..+|++..-|.++...+++++..-
T Consensus 127 ~Lp~~~R~v~~L~~~~g----~s----~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG----MK----QKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 48999999998877763 22 46899999999999999999999887543
No 140
>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=23.38 E-value=1.2e+02 Score=22.60 Aligned_cols=46 Identities=26% Similarity=0.203 Sum_probs=32.6
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 425 Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
|++....++..+ .. .+ ...++|+.++++...|..|..-.+.++.-+
T Consensus 1 l~~~e~~i~~~~-~~----~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 1 LTPREREVLRLL-AE----GK----TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 455666666544 32 22 367899999999999999998777766544
No 141
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=22.88 E-value=1e+02 Score=28.30 Aligned_cols=47 Identities=19% Similarity=0.217 Sum_probs=31.4
Q ss_pred CCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhh
Q 006550 421 PQRGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARV 474 (641)
Q Consensus 421 kRr~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRr 474 (641)
++++++.+.+...-....+ +.++ ...+|+..|++..+|.+|..-.|.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~---~g~s----v~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFE---PGMT----VSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCHHHHHHHHHHHHc---CCCC----HHHHHHHHCcCHHHHHHHHHHHhh
Confidence 3456877775433333333 2332 668899999999999999766553
No 142
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=22.69 E-value=1.2e+02 Score=28.65 Aligned_cols=49 Identities=20% Similarity=0.240 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||+....++..-+.+ .++ -.++|..+|++...|.+....+|+++++-+
T Consensus 137 ~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 137 ELEPPRSELIRTAFFE----GIT----YEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 4788888888776665 332 568999999999999999999999987643
No 143
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.63 E-value=1.2e+02 Score=29.20 Aligned_cols=48 Identities=17% Similarity=0.092 Sum_probs=37.1
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 423 RGLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 423 r~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
..||+..+.++.. +.+ .|. -.++|..+|++...|.+.+..+|+++++-
T Consensus 154 ~~L~~~~r~vl~l-~~e----~~s----~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 154 ELLSELEKEVLEL-YLD----GKS----YQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred HhCCHHHHHHHHH-HHc----cCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3578888888877 554 332 56899999999999998888888887663
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=22.15 E-value=46 Score=30.19 Aligned_cols=46 Identities=33% Similarity=0.275 Sum_probs=34.9
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcch
Q 006550 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWK 478 (641)
Q Consensus 425 Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkK 478 (641)
||+....++...+.+. -.-.++|+.+|++...|.++..-+|+++++
T Consensus 106 L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 106 LPENYRTVLILREFKE--------FSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred CCHhheeeeeehhhcc--------CcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666665443332 226789999999999999999999999875
No 145
>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=21.64 E-value=1.4e+02 Score=24.64 Aligned_cols=47 Identities=28% Similarity=0.320 Sum_probs=35.4
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhh
Q 006550 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINA 472 (641)
Q Consensus 425 Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNa 472 (641)
|++.+.++|+.-+..=+ .-+|-...-..||+..|+++.-+..-+-++
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 57888999987766532 234788888999999999998887654443
No 146
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=21.11 E-value=1.1e+02 Score=21.49 Aligned_cols=23 Identities=35% Similarity=0.346 Sum_probs=19.6
Q ss_pred HHHHHHHhCCChhhhhccchhhh
Q 006550 451 KLMLAKQTGLSRSQVSNWFINAR 473 (641)
Q Consensus 451 K~~LAkqTGLS~sQVsNWFiNaR 473 (641)
...+|+.+|++...|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45899999999999999988764
No 147
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=21.01 E-value=1.7e+02 Score=27.06 Aligned_cols=49 Identities=24% Similarity=0.245 Sum_probs=40.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
.||++...++...+.+. .+ -.++|..+|++..-|.+....+|+++++-+
T Consensus 105 ~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLRKLEG--LS------HQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 38999999998877764 22 568999999999999999999998887654
No 148
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=20.52 E-value=93 Score=32.20 Aligned_cols=48 Identities=33% Similarity=0.484 Sum_probs=39.2
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKP 479 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKp 479 (641)
.||+..+.+|...|.+ .+. -.++|+.+|++...|..|...++.++++.
T Consensus 215 ~L~~rer~vl~l~y~~----~~t----~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 215 ALPERERTVLVLRFFE----SMT----QTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred cCCHHHHHHHHHHhcC----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4788888888877754 332 47899999999999999999999998764
No 149
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.41 E-value=1.4e+02 Score=28.97 Aligned_cols=48 Identities=25% Similarity=0.329 Sum_probs=38.1
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhh
Q 006550 425 LPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPM 480 (641)
Q Consensus 425 Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpm 480 (641)
++++..+++.-.++. .| | ..++|+.+|+|+..|...+..+|.++.+.+
T Consensus 136 l~~~~~~~v~l~~~~----Gl-s---~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l 183 (185)
T PF07638_consen 136 LDPRQRRVVELRFFE----GL-S---VEEIAERLGISERTVRRRLRRARAWLRREL 183 (185)
T ss_pred cCHHHHHHHHHHHHC----CC-C---HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 677777777776665 55 3 668999999999999999999998876543
No 150
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=20.37 E-value=84 Score=31.39 Aligned_cols=50 Identities=22% Similarity=0.234 Sum_probs=38.9
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhccchhhhhhcchhhh
Q 006550 424 GLPERAVTVLRAWLFEHFLHPYPTDTEKLMLAKQTGLSRSQVSNWFINARVRLWKPMV 481 (641)
Q Consensus 424 ~Lpkeav~iLr~Wf~eH~~nPYPS~~EK~~LAkqTGLS~sQVsNWFiNaRrRlkKpmi 481 (641)
.||++.+.++...+.+ .+ .-.++|+.+|++...|.+...-+|.++++-+.
T Consensus 149 ~L~~~~r~i~~l~~~~----g~----s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 149 ALPDAFRAVFVLRVVE----EL----SVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hCCHHHhhhheeehhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3788887777655443 33 26789999999999999999999999887653
Done!