Query 019762
Match_columns 336
No_of_seqs 265 out of 1062
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 04:20:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019762.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019762hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0774 Transcription factor P 100.0 3.4E-32 7.3E-37 254.4 17.6 207 68-311 26-249 (334)
2 KOG0773 Transcription factor M 99.9 1.8E-27 3.9E-32 231.3 0.4 247 66-314 45-303 (342)
3 PF03791 KNOX2: KNOX2 domain ; 99.9 1.3E-22 2.7E-27 148.7 7.2 50 126-179 3-52 (52)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 5.7E-20 1.2E-24 130.7 2.8 43 71-113 1-43 (45)
5 PF05920 Homeobox_KN: Homeobox 99.6 1.2E-16 2.6E-21 111.5 4.3 40 268-307 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.5 6.1E-14 1.3E-18 102.2 6.9 57 252-311 2-58 (59)
7 smart00389 HOX Homeodomain. DN 99.5 1.3E-13 2.9E-18 99.9 6.6 55 252-309 2-56 (56)
8 PF00046 Homeobox: Homeobox do 99.5 1E-13 2.2E-18 101.5 5.7 57 251-310 1-57 (57)
9 PF03792 PBC: PBC domain; Int 99.4 1.1E-12 2.5E-17 118.8 12.9 148 68-249 24-190 (191)
10 KOG0775 Transcription factor S 99.3 6.1E-12 1.3E-16 119.4 5.8 50 257-309 183-232 (304)
11 TIGR01565 homeo_ZF_HD homeobox 98.9 1.5E-09 3.3E-14 81.7 5.1 53 250-305 1-57 (58)
12 KOG0487 Transcription factor A 98.9 5.8E-10 1.2E-14 108.3 3.1 59 251-312 236-294 (308)
13 KOG0843 Transcription factor E 98.9 1.7E-09 3.6E-14 97.7 4.4 61 249-312 101-161 (197)
14 KOG0489 Transcription factor z 98.9 1.4E-09 3.1E-14 103.5 3.9 66 250-318 159-224 (261)
15 KOG0842 Transcription factor t 98.8 3E-09 6.4E-14 103.4 3.2 60 250-312 153-212 (307)
16 KOG0493 Transcription factor E 98.8 8.8E-09 1.9E-13 97.7 5.3 59 251-312 247-305 (342)
17 KOG0488 Transcription factor B 98.7 8.1E-09 1.8E-13 100.7 4.7 60 250-312 172-231 (309)
18 KOG0850 Transcription factor D 98.7 8.2E-09 1.8E-13 96.3 4.1 60 251-313 123-182 (245)
19 KOG0483 Transcription factor H 98.7 1.5E-08 3.2E-13 93.3 4.2 59 250-311 50-108 (198)
20 COG5576 Homeodomain-containing 98.7 3E-08 6.5E-13 88.2 5.2 62 250-314 51-112 (156)
21 KOG0484 Transcription factor P 98.6 1.9E-08 4.1E-13 83.9 3.6 68 242-312 9-76 (125)
22 KOG3802 Transcription factor O 98.6 2.1E-08 4.6E-13 99.8 3.8 62 249-313 293-354 (398)
23 KOG0491 Transcription factor B 98.6 4.8E-08 1E-12 87.4 5.0 61 247-310 97-157 (194)
24 KOG0485 Transcription factor N 98.6 3E-08 6.4E-13 92.1 3.3 60 250-312 104-163 (268)
25 KOG0494 Transcription factor C 98.5 1.3E-07 2.8E-12 89.8 4.3 56 254-312 145-200 (332)
26 KOG0492 Transcription factor M 98.4 1.3E-07 2.7E-12 87.4 3.3 66 242-310 136-201 (246)
27 KOG2251 Homeobox transcription 98.4 2.4E-07 5.1E-12 86.2 4.3 59 250-311 37-95 (228)
28 KOG0848 Transcription factor C 98.4 9.1E-08 2E-12 91.2 0.5 57 254-313 203-259 (317)
29 KOG4577 Transcription factor L 98.2 4.5E-07 9.7E-12 87.3 2.0 72 243-317 160-231 (383)
30 KOG0486 Transcription factor P 98.2 6.7E-07 1.4E-11 86.9 2.7 61 251-314 113-173 (351)
31 KOG0847 Transcription factor, 98.1 1.9E-06 4E-11 80.5 3.1 61 250-313 167-227 (288)
32 KOG2252 CCAAT displacement pro 98.0 7.4E-06 1.6E-10 84.6 5.5 56 250-308 420-475 (558)
33 KOG0490 Transcription factor, 97.9 6.2E-06 1.4E-10 75.0 2.0 62 248-312 58-119 (235)
34 KOG0849 Transcription factor P 97.8 1.7E-05 3.7E-10 78.9 3.8 59 251-312 177-235 (354)
35 KOG1168 Transcription factor A 97.7 8.3E-06 1.8E-10 78.8 0.6 67 250-319 309-375 (385)
36 KOG0844 Transcription factor E 97.7 1.4E-05 3.1E-10 77.6 1.6 55 254-311 185-239 (408)
37 KOG0773 Transcription factor M 97.4 0.00011 2.3E-09 72.1 2.7 65 250-315 95-159 (342)
38 PF03789 ELK: ELK domain ; In 97.0 0.00042 9E-09 42.7 1.9 22 228-249 1-22 (22)
39 PF11569 Homez: Homeodomain le 97.0 0.00059 1.3E-08 51.2 3.0 43 262-307 10-52 (56)
40 KOG0490 Transcription factor, 95.6 0.0088 1.9E-07 54.4 2.9 60 251-313 154-213 (235)
41 KOG1146 Homeobox protein [Gene 91.5 0.21 4.5E-06 57.1 4.5 61 250-313 903-963 (1406)
42 PF04218 CENP-B_N: CENP-B N-te 86.3 1.4 3.1E-05 32.2 4.4 47 251-305 1-47 (53)
43 KOG3623 Homeobox transcription 84.7 2 4.3E-05 47.1 6.1 52 262-316 568-619 (1007)
44 PF01527 HTH_Tnp_1: Transposas 72.5 5.5 0.00012 30.0 3.7 47 252-305 2-48 (76)
45 cd06171 Sigma70_r4 Sigma70, re 70.3 7.9 0.00017 25.9 3.8 46 256-309 10-55 (55)
46 PF08281 Sigma70_r4_2: Sigma-7 63.4 6.9 0.00015 27.7 2.5 44 256-307 10-53 (54)
47 cd00569 HTH_Hin_like Helix-tur 62.7 23 0.00051 20.9 4.6 40 254-301 3-42 (42)
48 PF04545 Sigma70_r4: Sigma-70, 61.1 8.6 0.00019 27.0 2.6 47 256-310 4-50 (50)
49 PRK06759 RNA polymerase factor 57.3 14 0.00031 31.0 3.8 47 256-310 106-152 (154)
50 KOG4445 Uncharacterized conser 52.5 34 0.00074 34.2 5.9 45 132-178 134-178 (368)
51 PRK09646 RNA polymerase sigma 49.1 20 0.00043 31.9 3.5 50 256-313 142-191 (194)
52 PRK09642 RNA polymerase sigma 48.4 23 0.00049 30.1 3.6 48 256-311 106-153 (160)
53 PF13443 HTH_26: Cro/C1-type H 46.0 17 0.00036 26.4 2.1 24 282-305 12-35 (63)
54 TIGR02937 sigma70-ECF RNA poly 45.6 25 0.00055 28.3 3.4 47 256-310 110-156 (158)
55 PRK09644 RNA polymerase sigma 44.8 26 0.00057 30.0 3.5 50 255-312 107-156 (165)
56 TIGR02983 SigE-fam_strep RNA p 43.9 28 0.00062 29.5 3.6 51 256-314 110-160 (162)
57 PRK11924 RNA polymerase sigma 43.5 26 0.00056 29.8 3.3 48 256-311 125-172 (179)
58 PRK12533 RNA polymerase sigma 42.8 27 0.00058 32.2 3.4 52 256-315 134-185 (216)
59 PRK09652 RNA polymerase sigma 42.4 29 0.00064 29.5 3.4 48 256-311 128-175 (182)
60 PRK03975 tfx putative transcri 41.1 34 0.00073 30.3 3.6 48 254-310 4-51 (141)
61 PRK00118 putative DNA-binding 40.9 35 0.00077 28.6 3.5 47 256-310 17-63 (104)
62 KOG0738 AAA+-type ATPase [Post 40.8 1.2E+02 0.0027 31.7 8.0 165 67-289 218-393 (491)
63 PRK12541 RNA polymerase sigma 40.7 33 0.00071 29.2 3.5 48 255-310 111-158 (161)
64 PRK12514 RNA polymerase sigma 40.7 32 0.00069 29.9 3.4 48 256-311 129-176 (179)
65 TIGR02939 RpoE_Sigma70 RNA pol 40.5 25 0.00055 30.5 2.8 49 256-312 138-186 (190)
66 TIGR02985 Sig70_bacteroi1 RNA 39.3 42 0.00092 27.8 3.9 47 256-310 113-159 (161)
67 PF13518 HTH_28: Helix-turn-he 39.2 32 0.0007 23.7 2.7 24 283-306 15-38 (52)
68 PRK12547 RNA polymerase sigma 39.0 35 0.00077 29.3 3.4 49 256-312 112-160 (164)
69 PRK06811 RNA polymerase factor 38.9 37 0.00081 29.9 3.6 48 256-311 131-178 (189)
70 TIGR02999 Sig-70_X6 RNA polyme 37.9 40 0.00087 29.2 3.6 48 256-311 134-181 (183)
71 TIGR02989 Sig-70_gvs1 RNA poly 37.4 43 0.00093 28.2 3.6 47 256-310 111-157 (159)
72 smart00421 HTH_LUXR helix_turn 37.1 1E+02 0.0022 20.8 4.9 47 256-311 3-49 (58)
73 PRK12523 RNA polymerase sigma 36.9 43 0.00094 28.9 3.7 49 256-312 119-167 (172)
74 PRK12526 RNA polymerase sigma 35.0 45 0.00098 30.0 3.6 49 256-312 153-201 (206)
75 PRK12511 RNA polymerase sigma 34.6 48 0.001 29.4 3.6 69 256-332 111-179 (182)
76 KOG2070 Guanine nucleotide exc 34.3 46 0.00099 35.5 3.8 28 127-154 180-214 (661)
77 PF13097 CENP-U: CENP-A nucleo 34.1 1.3E+02 0.0028 27.7 6.3 46 131-179 103-149 (175)
78 PRK09648 RNA polymerase sigma 33.9 50 0.0011 29.0 3.6 48 256-311 139-186 (189)
79 PRK12512 RNA polymerase sigma 33.8 49 0.0011 28.8 3.6 50 256-313 131-180 (184)
80 PRK05602 RNA polymerase sigma 33.6 44 0.00095 29.2 3.2 49 257-313 129-177 (186)
81 PF05190 MutS_IV: MutS family 33.0 75 0.0016 24.3 4.1 26 129-154 1-26 (92)
82 PRK12516 RNA polymerase sigma 32.7 41 0.0009 29.9 2.9 51 256-314 116-166 (187)
83 PRK09649 RNA polymerase sigma 31.5 54 0.0012 28.9 3.4 48 256-311 130-177 (185)
84 PRK09047 RNA polymerase factor 31.3 64 0.0014 27.2 3.7 49 256-312 106-154 (161)
85 PRK12546 RNA polymerase sigma 31.2 51 0.0011 29.5 3.2 49 256-312 113-161 (188)
86 PRK12532 RNA polymerase sigma 31.0 56 0.0012 28.9 3.4 49 256-312 136-184 (195)
87 TIGR02948 SigW_bacill RNA poly 30.9 56 0.0012 28.3 3.4 48 256-311 136-183 (187)
88 PRK12536 RNA polymerase sigma 30.6 60 0.0013 28.3 3.6 49 256-312 129-177 (181)
89 PRK13919 putative RNA polymera 30.6 60 0.0013 28.2 3.5 49 256-312 135-183 (186)
90 PRK12519 RNA polymerase sigma 30.2 45 0.00098 29.3 2.7 47 256-310 141-187 (194)
91 PF10668 Phage_terminase: Phag 29.9 43 0.00092 25.6 2.1 19 283-301 25-43 (60)
92 PRK12520 RNA polymerase sigma 29.6 65 0.0014 28.3 3.6 48 256-311 131-178 (191)
93 TIGR02954 Sig70_famx3 RNA poly 29.6 64 0.0014 27.7 3.5 48 256-311 119-166 (169)
94 PRK12530 RNA polymerase sigma 29.0 63 0.0014 28.6 3.5 48 256-311 134-181 (189)
95 PRK12531 RNA polymerase sigma 29.0 65 0.0014 28.5 3.5 50 255-312 140-189 (194)
96 PRK12535 RNA polymerase sigma 28.9 73 0.0016 28.6 3.9 52 256-315 133-184 (196)
97 PF15500 Toxin_39: Putative RN 28.9 1.3E+02 0.0029 24.8 4.9 38 128-172 44-81 (96)
98 TIGR02959 SigZ RNA polymerase 28.6 70 0.0015 27.7 3.6 50 256-313 100-149 (170)
99 PRK12529 RNA polymerase sigma 28.6 79 0.0017 27.6 4.0 50 256-313 127-176 (178)
100 PRK12537 RNA polymerase sigma 28.4 67 0.0015 28.1 3.5 47 256-310 133-179 (182)
101 PF01381 HTH_3: Helix-turn-hel 28.4 44 0.00095 23.3 1.9 20 284-303 13-32 (55)
102 PRK12542 RNA polymerase sigma 28.2 67 0.0015 28.1 3.5 49 256-312 122-170 (185)
103 PRK12524 RNA polymerase sigma 28.0 67 0.0015 28.5 3.4 49 256-312 136-184 (196)
104 PRK09641 RNA polymerase sigma 27.6 76 0.0017 27.4 3.7 47 256-311 136-183 (187)
105 PRK09639 RNA polymerase sigma 27.5 73 0.0016 27.0 3.5 47 256-311 112-158 (166)
106 PRK11511 DNA-binding transcrip 27.1 1.7E+02 0.0037 24.5 5.6 42 259-304 8-49 (127)
107 PRK06986 fliA flagellar biosyn 27.0 63 0.0014 29.7 3.2 48 256-311 184-231 (236)
108 cd00131 PAX Paired Box domain 26.6 2.1E+02 0.0045 24.4 6.1 46 256-304 75-127 (128)
109 PF07425 Pardaxin: Pardaxin; 26.5 37 0.00081 22.5 1.1 22 73-94 5-26 (33)
110 TIGR03070 couple_hipB transcri 26.2 47 0.001 22.9 1.7 22 283-304 18-39 (58)
111 KOG4040 NADH:ubiquinone oxidor 26.1 41 0.00089 30.7 1.7 39 258-296 22-61 (186)
112 PRK09645 RNA polymerase sigma 25.9 81 0.0018 27.0 3.5 49 256-312 118-166 (173)
113 TIGR02859 spore_sigH RNA polym 25.1 97 0.0021 27.1 3.9 28 284-311 169-196 (198)
114 PRK15369 two component system 25.1 1.8E+02 0.0038 24.2 5.4 48 256-312 149-196 (211)
115 PRK09415 RNA polymerase factor 25.1 72 0.0016 27.8 3.1 47 256-310 127-173 (179)
116 PRK08583 RNA polymerase sigma 25.0 79 0.0017 29.5 3.5 48 256-311 205-252 (257)
117 PRK09413 IS2 repressor TnpA; R 25.0 1.1E+02 0.0024 25.6 4.0 48 252-306 8-55 (121)
118 PRK12543 RNA polymerase sigma 24.9 89 0.0019 27.2 3.6 47 256-310 117-163 (179)
119 PRK07037 extracytoplasmic-func 24.8 87 0.0019 26.5 3.4 49 256-312 109-157 (163)
120 cd01392 HTH_LacI Helix-turn-he 24.8 40 0.00088 23.3 1.1 20 285-304 2-21 (52)
121 TIGR02947 SigH_actino RNA poly 24.7 40 0.00086 29.8 1.4 49 256-312 131-179 (193)
122 PRK12515 RNA polymerase sigma 24.7 90 0.002 27.4 3.6 48 256-311 131-178 (189)
123 PRK10072 putative transcriptio 24.2 54 0.0012 27.0 1.9 23 283-305 49-71 (96)
124 PRK12539 RNA polymerase sigma 24.2 86 0.0019 27.4 3.4 48 256-311 131-178 (184)
125 PRK12528 RNA polymerase sigma 24.0 1E+02 0.0022 26.2 3.7 46 256-309 113-158 (161)
126 cd00093 HTH_XRE Helix-turn-hel 23.9 63 0.0014 20.9 2.0 21 284-304 16-36 (58)
127 PRK09636 RNA polymerase sigma 23.8 1E+02 0.0023 29.3 4.1 51 256-314 115-165 (293)
128 TIGR02941 Sigma_B RNA polymera 23.6 1E+02 0.0022 28.7 3.9 48 256-311 205-252 (255)
129 PRK12513 RNA polymerase sigma 23.5 40 0.00086 29.7 1.1 49 256-312 139-187 (194)
130 TIGR03001 Sig-70_gmx1 RNA poly 23.5 89 0.0019 29.4 3.5 48 256-311 161-208 (244)
131 TIGR02943 Sig70_famx1 RNA poly 23.2 99 0.0021 27.4 3.6 48 256-311 131-178 (188)
132 PF00196 GerE: Bacterial regul 22.9 1.3E+02 0.0027 21.6 3.5 48 256-312 3-50 (58)
133 PRK09647 RNA polymerase sigma 22.8 96 0.0021 28.1 3.5 49 256-312 138-186 (203)
134 KOG2070 Guanine nucleotide exc 22.7 57 0.0012 34.8 2.2 11 84-94 157-167 (661)
135 PRK08295 RNA polymerase factor 22.4 1.1E+02 0.0024 27.0 3.8 46 256-310 155-200 (208)
136 PRK12545 RNA polymerase sigma 22.4 98 0.0021 27.7 3.4 49 256-312 139-187 (201)
137 PF12362 DUF3646: DNA polymera 21.8 61 0.0013 27.7 1.8 27 64-90 82-108 (117)
138 PF04967 HTH_10: HTH DNA bindi 21.8 2.2E+02 0.0047 21.0 4.6 46 257-303 1-46 (53)
139 PF13411 MerR_1: MerR HTH fami 21.7 69 0.0015 23.4 1.9 17 284-300 4-20 (69)
140 TIGR02479 FliA_WhiG RNA polyme 21.5 1E+02 0.0023 28.0 3.5 47 256-310 175-221 (224)
141 PF13384 HTH_23: Homeodomain-l 21.5 79 0.0017 21.7 2.1 23 283-305 20-42 (50)
142 PRK07670 RNA polymerase sigma 21.4 1.1E+02 0.0023 28.6 3.6 47 256-310 201-247 (251)
143 PRK12538 RNA polymerase sigma 21.4 86 0.0019 29.2 2.9 49 256-312 171-219 (233)
144 PRK04217 hypothetical protein; 21.3 1.6E+02 0.0034 24.9 4.2 51 254-312 40-90 (110)
145 PRK12540 RNA polymerase sigma 21.3 1.1E+02 0.0023 27.1 3.4 51 256-314 111-161 (182)
146 PRK08241 RNA polymerase factor 21.2 1.1E+02 0.0024 29.6 3.8 50 256-313 153-202 (339)
147 TIGR02980 SigBFG RNA polymeras 21.1 1.1E+02 0.0025 27.7 3.7 47 256-310 178-224 (227)
148 PRK12534 RNA polymerase sigma 21.1 1.1E+02 0.0024 26.6 3.5 47 256-310 137-183 (187)
149 PRK06288 RNA polymerase sigma 21.0 1E+02 0.0023 29.0 3.4 48 256-311 212-259 (268)
150 PRK04053 rps13p 30S ribosomal 20.9 90 0.0019 27.9 2.8 30 250-279 49-78 (149)
151 smart00530 HTH_XRE Helix-turn- 20.8 78 0.0017 20.3 1.9 22 283-304 13-34 (56)
152 PRK12522 RNA polymerase sigma 20.6 1.5E+02 0.0032 25.6 4.1 48 256-311 119-166 (173)
153 cd06170 LuxR_C_like C-terminal 20.5 2E+02 0.0044 19.4 4.1 30 282-311 17-46 (57)
154 PRK09637 RNA polymerase sigma 20.3 1.1E+02 0.0024 26.9 3.3 51 256-314 106-156 (181)
155 PRK12544 RNA polymerase sigma 20.2 1.2E+02 0.0027 27.4 3.6 48 256-311 148-195 (206)
156 PF13730 HTH_36: Helix-turn-he 20.1 3.1E+02 0.0067 19.1 5.0 48 256-306 2-51 (55)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=100.00 E-value=3.4e-32 Score=254.40 Aligned_cols=207 Identities=23% Similarity=0.357 Sum_probs=177.4
Q ss_pred hHhHHHHHHHhhCCChHHHHHHHHhh-hhcc----CCCCchhhHHHHHhhhHHHHHHhhhccCC---------CCCCChH
Q 019762 68 WETVKCKAEIVGHPLYEQLLSAHVSC-LRIA----TPVDQLPKIDAQLSRSRDVLAKYSAVANG---------RVLDDKE 133 (336)
Q Consensus 68 ~e~~~lKa~I~sHPlYp~Ll~A~i~C-~KVG----aP~e~~~~ld~~l~~~~~~~~~~~~~~~~---------~~g~dpE 133 (336)
++.++.|.+|-+||+||.|.+++|+. .|++ ...|+-+. |.++.++++|+...+++|+. .-|+..+
T Consensus 26 Deaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~-dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsd 104 (334)
T KOG0774|consen 26 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPP-DPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSD 104 (334)
T ss_pred chHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCC-ChHHHHHHHHHHHhcccCccccchhhhhccCCChHH
Confidence 66679999999999999999999996 3333 33332222 67888899999888888762 2244566
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhCCCCCCCCCccCCCCCccCCCCCCCCCCCCCCCCC
Q 019762 134 LDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGATMSDDDEDQVDSDTNFFDGSLDGPDSMGFGPLV 213 (336)
Q Consensus 134 LDqFMe~Yc~vL~kykeEL~kp~~~~~~EA~~fc~~ie~qL~sL~~~~~s~de~~~~~s~~~~~~g~~~~~d~~~~~p~~ 213 (336)
+.+-+. ++.+.|++||++ +..+|++|++.+.+|+. +++.++||.
T Consensus 105 YR~kL~---qiR~iy~~Elek--------yeqaCneftthV~nlL~-------------------------eQsr~RPi~ 148 (334)
T KOG0774|consen 105 YRAKLL---QIRQIYHNELEK--------YEQACNEFTTHVMNLLR-------------------------EQSRTRPIM 148 (334)
T ss_pred HHHHHH---HHHHHHHHHHHH--------HHHHHHHHHHHHHHHHH-------------------------HhcccCCCC
Confidence 666554 599999999988 56789999999999996 556799999
Q ss_pred CChhhhh--hHHHHHHHHHHHHhhhhhhhHHHHHHHHhh-ccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHh
Q 019762 214 PTESERS--LMERVRHELKHELKQGYKEKIVDIREEILR-KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQET 290 (336)
Q Consensus 214 ~~~~e~s--~~~~~~~eLk~~l~~ky~~~i~~lr~e~~k-krkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~t 290 (336)
+.++++. .|++.|..++.+|++..|..+..||.+|.. +|||++|+|.++.+|..||..|..|||||++.|+.||++|
T Consensus 149 ~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqC 228 (334)
T KOG0774|consen 149 PKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQC 228 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHc
Confidence 9999985 478899999999999999999999999996 5678899999999999999999999999999999999999
Q ss_pred CCChhhhhhhhhhhhhhcccc
Q 019762 291 GLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 291 gLs~kQV~NWF~N~R~R~kk~ 311 (336)
|++..||+|||.|.|.|.||.
T Consensus 229 nItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 229 NITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred Cceehhhccccccceeehhhh
Confidence 999999999999999999974
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.93 E-value=1.8e-27 Score=231.32 Aligned_cols=247 Identities=23% Similarity=0.307 Sum_probs=170.4
Q ss_pred chhHhHHHHHHHhhCCChHHHHHHHHhhhhccCCCCchhhHHHHHhhhHHHHHHhhhcc---CC--CCCCChHHHHHHHH
Q 019762 66 EDWETVKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRSRDVLAKYSAVA---NG--RVLDDKELDQFMTH 140 (336)
Q Consensus 66 ~~~e~~~lKa~I~sHPlYp~Ll~A~i~C~KVGaP~e~~~~ld~~l~~~~~~~~~~~~~~---~~--~~g~dpELDqFMe~ 140 (336)
........|..+.+||+|..++.||+.|.+++++.+.+.+.+............+...+ .+ ..+.+++++.||..
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k 124 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSK 124 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchH
Confidence 45667778999999999999999999999999999988876554332222112221111 11 34568999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhCCCCCCC-CC-cc-CCCCCc-cCCCCCC-CCCCCCCCCCCCC
Q 019762 141 YVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGATMSDD-DE-DQ-VDSDTN-FFDGSLD-GPDSMGFGPLVPT 215 (336)
Q Consensus 141 Yc~vL~kykeEL~kp~~~~~~EA~~fc~~ie~qL~sL~~~~~s~d-e~-~~-~~s~~~-~~~g~~~-~~d~~~~~p~~~~ 215 (336)
|+.+|..+...|+..+. -++++.++++++..+...++.+.... .. .. .+.+.+ ...+... ..+..++++....
T Consensus 125 ~~~~ll~~~~~~~~~~~--~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~ 202 (342)
T KOG0773|consen 125 LEKILLAVITKLTLTQV--STWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDS 202 (342)
T ss_pred HHHHHHHHHHHhhhhhH--HHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccccccccccccccc
Confidence 99999999999998763 27899999999999998875332110 00 00 000000 0000000 0011111211111
Q ss_pred hhhhhhH--HHHHHHHHHHHhhhhhhhHHHHHHHHhhccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCC
Q 019762 216 ESERSLM--ERVRHELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQ 293 (336)
Q Consensus 216 ~~e~s~~--~~~~~eLk~~l~~ky~~~i~~lr~e~~kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs 293 (336)
..+...+ ......++..+.+.+..++.....+..++|+++.||+.++.+|+.||.+|+.||||++.+|..||+.|||+
T Consensus 203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs 282 (342)
T KOG0773|consen 203 EDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLS 282 (342)
T ss_pred ccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCC
Confidence 1111100 12234555666666665666666667788889999999999999999999999999999999999999999
Q ss_pred hhhhhhhhhhhhhhccccCCC
Q 019762 294 LKQINNWFINQRKRNWHANPS 314 (336)
Q Consensus 294 ~kQV~NWF~N~R~R~kk~~~~ 314 (336)
..||+|||||+|+|.|+|+..
T Consensus 283 ~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 283 RPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred cccCCchhhhcccccCCchHH
Confidence 999999999999999999974
No 3
>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=99.87 E-value=1.3e-22 Score=148.68 Aligned_cols=50 Identities=46% Similarity=0.682 Sum_probs=47.3
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhC
Q 019762 126 GRVLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTG 179 (336)
Q Consensus 126 ~~~g~dpELDqFMe~Yc~vL~kykeEL~kp~~~~~~EA~~fc~~ie~qL~sL~~ 179 (336)
..+|+||||||||++||.||++||+||++|| .||++||++||+||++|||
T Consensus 3 ~~~~~dpELDqFMeaYc~~L~kykeeL~~p~----~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 3 SSIGADPELDQFMEAYCDMLVKYKEELQRPF----QEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhC
Confidence 4689999999999999999999999999998 5999999999999999985
No 4
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 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=99.78 E-value=5.7e-20 Score=130.67 Aligned_cols=43 Identities=35% Similarity=0.691 Sum_probs=40.0
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhhhccCCCCchhhHHHHHhhh
Q 019762 71 VKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRS 113 (336)
Q Consensus 71 ~~lKa~I~sHPlYp~Ll~A~i~C~KVGaP~e~~~~ld~~l~~~ 113 (336)
+.|||+|++||+||+||+||++|+|||||||++++|+++..+.
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~ 43 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAES 43 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 4699999999999999999999999999999999999987654
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=99.65 E-value=1.2e-16 Score=111.53 Aligned_cols=40 Identities=55% Similarity=1.074 Sum_probs=36.5
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019762 268 WWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 307 (336)
Q Consensus 268 wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R 307 (336)
||.+|..+||||.++|..||+.|||+.+||+|||+|+|+|
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 8999999999999999999999999999999999999998
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=99.49 E-value=6.1e-14 Score=102.24 Aligned_cols=57 Identities=26% Similarity=0.520 Sum_probs=54.0
Q ss_pred cCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 252 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 252 rkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
+++..+++.+..+|+.||.. +|||+..++..||..|||+..||.+||.|+|.+.++.
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 56778999999999999999 9999999999999999999999999999999998764
No 7
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.46 E-value=1.3e-13 Score=99.93 Aligned_cols=55 Identities=25% Similarity=0.497 Sum_probs=51.6
Q ss_pred cCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019762 252 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 309 (336)
Q Consensus 252 rkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~k 309 (336)
+.++.|++++..+|+.||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
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 45667999999999999999 99999999999999999999999999999999864
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.46 E-value=1e-13 Score=101.47 Aligned_cols=57 Identities=30% Similarity=0.704 Sum_probs=54.2
Q ss_pred ccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 251 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 251 krkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
||++..|+.++..+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.+.|+
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 467889999999999999999 999999999999999999999999999999999874
No 9
>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=99.45 E-value=1.1e-12 Score=118.82 Aligned_cols=148 Identities=21% Similarity=0.290 Sum_probs=118.1
Q ss_pred hHhHHHHHHHhhCCChHHHHHHHHhh-----hhccCCCCchhhHHHHHhhhHHHHHHhhhccCCCCC--------C--C-
Q 019762 68 WETVKCKAEIVGHPLYEQLLSAHVSC-----LRIATPVDQLPKIDAQLSRSRDVLAKYSAVANGRVL--------D--D- 131 (336)
Q Consensus 68 ~e~~~lKa~I~sHPlYp~Ll~A~i~C-----~KVGaP~e~~~~ld~~l~~~~~~~~~~~~~~~~~~g--------~--d- 131 (336)
+|.++.|.+|.+||+||.|.+++|+- +++..+.+..+. |+++.++++|+.+.++.|+...| . |
T Consensus 24 Deaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~-dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~ 102 (191)
T PF03792_consen 24 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPP-DPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADN 102 (191)
T ss_pred hHHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCC-chhhhhhhcchhhhcCcCCCCcccchhhhhccCccc
Confidence 56699999999999999999999986 333333332222 67888999999998888763211 1 1
Q ss_pred -hHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhCCCCCCCCCccCCCCCccCCCCCCCCCCCCCC
Q 019762 132 -KELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGATMSDDDEDQVDSDTNFFDGSLDGPDSMGFG 210 (336)
Q Consensus 132 -pELDqFMe~Yc~vL~kykeEL~kp~~~~~~EA~~fc~~ie~qL~sL~~~~~s~de~~~~~s~~~~~~g~~~~~d~~~~~ 210 (336)
-|-+.|-...-++...|+.||++ +..+|.+|...+.+|.. +++.|+
T Consensus 103 ~~d~~dYr~kL~~ir~~y~~el~k--------ye~ac~eF~~hV~~lLr-------------------------eQs~~R 149 (191)
T PF03792_consen 103 SIDHSDYRAKLSQIRQIYHSELEK--------YEQACNEFTEHVMNLLR-------------------------EQSEFR 149 (191)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHH--------HHHHhhhhHHHHHHHHH-------------------------HhcccC
Confidence 14456667777799999999987 55789999999999996 456799
Q ss_pred CCCCChhhhh--hHHHHHHHHHHHHhhhhhhhHHHHHHHHh
Q 019762 211 PLVPTESERS--LMERVRHELKHELKQGYKEKIVDIREEIL 249 (336)
Q Consensus 211 p~~~~~~e~s--~~~~~~~eLk~~l~~ky~~~i~~lr~e~~ 249 (336)
||++.++|+. .+++.+..+..+||++.|..+..||..|.
T Consensus 150 PIs~keiE~m~~~i~~Kf~~iq~qLKQstCEaVm~LRsRfl 190 (191)
T PF03792_consen 150 PISPKEIERMVNIIHRKFSKIQMQLKQSTCEAVMILRSRFL 190 (191)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999985 57899999999999999999999998875
No 10
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.25 E-value=6.1e-12 Score=119.43 Aligned_cols=50 Identities=40% Similarity=0.883 Sum_probs=47.2
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019762 257 LPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 309 (336)
Q Consensus 257 lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~k 309 (336)
|....+..|++||.. +|||++.+|+.||+.|||+..||.|||.|+|.|.+
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 345789999999998 99999999999999999999999999999999998
No 11
>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=98.92 E-value=1.5e-09 Score=81.66 Aligned_cols=53 Identities=19% Similarity=0.401 Sum_probs=50.3
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPY----PTEEDKARLVQETGLQLKQINNWFINQR 305 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PY----Ps~~eK~~LA~~tgLs~kQV~NWF~N~R 305 (336)
+||.|++|+.+|+..|+..|.. .+| |+..++..||..+||+..+|.+||+|-+
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 4778999999999999999999 999 9999999999999999999999999964
No 12
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.91 E-value=5.8e-10 Score=108.31 Aligned_cols=59 Identities=24% Similarity=0.339 Sum_probs=55.4
Q ss_pred ccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 251 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 251 krkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
+|||..++|.|+..|++-|.- |-|.|++-|.+|++.++||..||.+||||+|+|.||-+
T Consensus 236 RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred ccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 456678999999999999999 99999999999999999999999999999999999966
No 13
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.87 E-value=1.7e-09 Score=97.72 Aligned_cols=61 Identities=20% Similarity=0.277 Sum_probs=57.0
Q ss_pred hhccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 249 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 249 ~kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
..||.|+.|+.++...|+..|.. +.|-.-.||..||+.++|++.||.+||+|+|.|+|+.-
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence 34677899999999999999999 99999999999999999999999999999999999744
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.86 E-value=1.4e-09 Score=103.49 Aligned_cols=66 Identities=23% Similarity=0.264 Sum_probs=60.7
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCCcc
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSSTA 318 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~~~~~ 318 (336)
.||.|+.|+..|+..|+.-|.- |.|-|+..|.++|..+.|++.||.+||||+|+|+||.+...+..
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 5778899999999999999999 99999999999999999999999999999999999877655444
No 15
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.78 E-value=3e-09 Score=103.37 Aligned_cols=60 Identities=17% Similarity=0.293 Sum_probs=55.0
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
|||+|--|++.|+-.|++-|.+ .-|.|..||+.||..++||..||..||||+|.|.|+.-
T Consensus 153 kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 153 KRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred ccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 4555558999999999999999 99999999999999999999999999999999999744
No 16
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.76 E-value=8.8e-09 Score=97.74 Aligned_cols=59 Identities=32% Similarity=0.429 Sum_probs=56.0
Q ss_pred ccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 251 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 251 krkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
||.|+-|+.++.+.|+.-|.+ +-|.|+..|+.||.++||.+.||..||+|+|.++||..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 567889999999999999999 99999999999999999999999999999999999854
No 17
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.74 E-value=8.1e-09 Score=100.74 Aligned_cols=60 Identities=20% Similarity=0.328 Sum_probs=55.1
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
++|.|+.|+..|+..|+.-|.. --|-+..||..||...||+-.||.+||+|||.|+|+..
T Consensus 172 ~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 172 RRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred cccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 4455779999999999999999 99999999999999999999999999999999988744
No 18
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.73 E-value=8.2e-09 Score=96.32 Aligned_cols=60 Identities=18% Similarity=0.269 Sum_probs=55.8
Q ss_pred ccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 251 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 251 krkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
+|.|+.++.-+.+.|++-|++ ..|.-..||.+||..+|||+.||..||+|+|-|.||...
T Consensus 123 RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 345778999999999999999 999999999999999999999999999999999998665
No 19
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.68 E-value=1.5e-08 Score=93.30 Aligned_cols=59 Identities=29% Similarity=0.389 Sum_probs=53.7
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.++++.+|+.+|+..|+.-|.. +-|-.+.+|..||++.||++.||.+||||+|+|.|.+
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 3556678999999999999999 7888999999999999999999999999999998753
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.65 E-value=3e-08 Score=88.19 Aligned_cols=62 Identities=18% Similarity=0.333 Sum_probs=57.4
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 314 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~ 314 (336)
.+++|.+.+..++.+|+..|.. +|||+..+|..|+..+||+++-|+.||+|+|.+.|+....
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 4667778999999999999999 9999999999999999999999999999999999986654
No 21
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.65 E-value=1.9e-08 Score=83.92 Aligned_cols=68 Identities=15% Similarity=0.272 Sum_probs=60.3
Q ss_pred HHHHHHHhhccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 242 VDIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 242 ~~lr~e~~kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
+.|.+..+.+|-|+.|+..+...|+..|.+ ..||..-.|+.||....|++..|++||+|+|.+.+|..
T Consensus 9 ~~l~ekrKQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 9 LGLTEKRKQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred CChhHHHHhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 345555556667889999999999999999 99999999999999999999999999999999998743
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.63 E-value=2.1e-08 Score=99.79 Aligned_cols=62 Identities=18% Similarity=0.438 Sum_probs=59.3
Q ss_pred hhccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 249 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 249 ~kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
.|||||+.+.-.++..|+..|.. ||-||.+|.-.||+.++|.+..|++||+|||.|.|+.++
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 56778889999999999999999 999999999999999999999999999999999999887
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.60 E-value=4.8e-08 Score=87.35 Aligned_cols=61 Identities=18% Similarity=0.303 Sum_probs=55.9
Q ss_pred HHhhccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 247 EILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 247 e~~kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
...++|.|+.|+..+...|++-|+. .-|-+-.++.+||...+|+++||..||+|+|.++||
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 3445566889999999999999998 899999999999999999999999999999999996
No 24
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.58 E-value=3e-08 Score=92.11 Aligned_cols=60 Identities=18% Similarity=0.249 Sum_probs=56.3
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
|||.|+.|+..|+..|+.-|.. --|.+-.+|..||+.+.|++.||..||||+|.+.|+.-
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 6777899999999999999999 89999999999999999999999999999999988743
No 25
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.46 E-value=1.3e-07 Score=89.82 Aligned_cols=56 Identities=20% Similarity=0.261 Sum_probs=53.2
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 254 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 254 r~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
|+.|+..+...|++-|.+ --||...-|+.||..|+|.+..|++||+|+|.+.+|..
T Consensus 145 RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred cchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 779999999999999999 99999999999999999999999999999999988744
No 26
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.43 E-value=1.3e-07 Score=87.43 Aligned_cols=66 Identities=15% Similarity=0.248 Sum_probs=59.5
Q ss_pred HHHHHHHhhccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 242 VDIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 242 ~~lr~e~~kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
..||+-...++.|+.|+..|...|++-|.+ -.|-+.+||..++..+.||..||..||||+|.|-|+
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 345555556777889999999999999999 999999999999999999999999999999999885
No 27
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.40 E-value=2.4e-07 Score=86.20 Aligned_cols=59 Identities=19% Similarity=0.345 Sum_probs=54.9
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.+|-|+.|+..+..+|+.-|.+ .-||+...+++||.+.+|.+.+|.+||.|+|++.++.
T Consensus 37 qRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred cccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 3566889999999999999999 9999999999999999999999999999999998753
No 28
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.36 E-value=9.1e-08 Score=91.16 Aligned_cols=57 Identities=23% Similarity=0.298 Sum_probs=52.4
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 254 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 254 r~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
|-.++..|+-.|++-|.. .+|.|...|.+||..+||++.||..||+|+|.|.+|-++
T Consensus 203 RvVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred eEEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 446899999999999988 999999999999999999999999999999999987553
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.23 E-value=4.5e-07 Score=87.35 Aligned_cols=72 Identities=21% Similarity=0.406 Sum_probs=64.6
Q ss_pred HHHHHHhhccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCCc
Q 019762 243 DIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSST 317 (336)
Q Consensus 243 ~lr~e~~kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~~~~ 317 (336)
.|..+-..||.|++++..+...|+.-|.. .|-|-+--|++|+.+|||+...|++||+|+|.+.|+..+..+.
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 44556678999999999999999999998 9999999999999999999999999999999999987666554
No 30
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.21 E-value=6.7e-07 Score=86.92 Aligned_cols=61 Identities=18% Similarity=0.308 Sum_probs=55.6
Q ss_pred ccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019762 251 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 314 (336)
Q Consensus 251 krkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~ 314 (336)
+|.|+-|+..+.+.|+.||.. +-||+.+.|+++|--|+|++..|.+||.|+|.+.+|....
T Consensus 113 rrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN 173 (351)
T KOG0486|consen 113 RRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN 173 (351)
T ss_pred hhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence 345678999999999999999 9999999999999999999999999999999998876543
No 31
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.10 E-value=1.9e-06 Score=80.46 Aligned_cols=61 Identities=25% Similarity=0.380 Sum_probs=55.7
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
||..+.+|+..+...|..-|.+ ..||--.++.+||...|+++.||.+||+|+|.+.+|...
T Consensus 167 rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 4556678999999999999999 999999999999999999999999999999999887654
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.00 E-value=7.4e-06 Score=84.62 Aligned_cols=56 Identities=23% Similarity=0.342 Sum_probs=52.8
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRN 308 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~ 308 (336)
.||.|-.|+..+++.|...|.+ ++||+.+.-+.|+.++||...-|.|||-|+|+|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3566779999999999999999 9999999999999999999999999999999994
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.86 E-value=6.2e-06 Score=75.04 Aligned_cols=62 Identities=13% Similarity=0.109 Sum_probs=57.0
Q ss_pred HhhccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 248 ILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 248 ~~kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
+.+++.|..|+..+...|+.-|.. .+||....++.||..+++++..|.+||+|+|+++++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 446777889999999999999999 69999999999999999999999999999999988754
No 34
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.78 E-value=1.7e-05 Score=78.87 Aligned_cols=59 Identities=24% Similarity=0.444 Sum_probs=54.6
Q ss_pred ccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 251 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 251 krkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
+|.|+.|+..+...|..+|.. .|||....|+.||.++||+...|+.||.|+|.|.++-.
T Consensus 177 rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 444678999999999999999 88999999999999999999999999999999888765
No 35
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.73 E-value=8.3e-06 Score=78.82 Aligned_cols=67 Identities=22% Similarity=0.428 Sum_probs=59.2
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCCccc
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSSTAS 319 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~~~~~~ 319 (336)
|||||+.+-..-++-|+.+|.. .|-|+-+-...+|++..|....|.+||+|+|.+.|+..-+...++
T Consensus 309 kKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa~~~m 375 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSATAVM 375 (385)
T ss_pred cccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhhceee
Confidence 6778888888888999999999 999999999999999999999999999999999998655554444
No 36
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.69 E-value=1.4e-05 Score=77.64 Aligned_cols=55 Identities=16% Similarity=0.279 Sum_probs=50.2
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 254 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 254 r~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
|+-|+.+|...|++-|+. --|-++-.|.+||..++|.+..|.+||||+|.|.|+.
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 467899999999888887 7899999999999999999999999999999999863
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.36 E-value=0.00011 Score=72.07 Aligned_cols=65 Identities=32% Similarity=0.533 Sum_probs=59.1
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCC
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSS 315 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~~ 315 (336)
..+++++++.+. ..|+.|...|..+|||++.++..|+-.++++.-||++||+|.|+|.++.+...
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~ 159 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMT 159 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCC
Confidence 345677899999 99999999999999999999999999999999999999999999999876553
No 38
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=97.03 E-value=0.00042 Score=42.72 Aligned_cols=22 Identities=41% Similarity=0.622 Sum_probs=20.5
Q ss_pred HHHHHHhhhhhhhHHHHHHHHh
Q 019762 228 ELKHELKQGYKEKIVDIREEIL 249 (336)
Q Consensus 228 eLk~~l~~ky~~~i~~lr~e~~ 249 (336)
|||++|+++|+++|++||+||+
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 5899999999999999999984
No 39
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.01 E-value=0.00059 Score=51.20 Aligned_cols=43 Identities=21% Similarity=0.477 Sum_probs=31.7
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019762 262 TSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 307 (336)
Q Consensus 262 ~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R 307 (336)
.+.|+++|.. +.++.+.+-..|+..+||+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4569999999 899999999999999999999999999877543
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=95.62 E-value=0.0088 Score=54.38 Aligned_cols=60 Identities=25% Similarity=0.480 Sum_probs=53.3
Q ss_pred ccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 251 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 251 krkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
++.+..+...+...|...|.. .+||....+..|+..+|++...|.+||+|+|.+.++...
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 154 RRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 445667888888888888888 999999999999999999999999999999999987655
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.54 E-value=0.21 Score=57.11 Aligned_cols=61 Identities=23% Similarity=0.305 Sum_probs=55.6
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
+++.|..++-.+..+++..|.. .-||+.++-+.|.+..+|....|..||+|.|.+.++.--
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4556778889999999999999 999999999999999999999999999999999998654
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=86.35 E-value=1.4 Score=32.18 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=32.7
Q ss_pred ccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019762 251 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQR 305 (336)
Q Consensus 251 krkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R 305 (336)
||+|..|+-+..-.+-..+.. .+ -...+|+..|++..+|.+|..|+.
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 456778888886666666665 33 578999999999999999999854
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=84.69 E-value=2 Score=47.07 Aligned_cols=52 Identities=31% Similarity=0.562 Sum_probs=46.5
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCC
Q 019762 262 TSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSS 316 (336)
Q Consensus 262 ~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~~~ 316 (336)
+.+|+.+|.. ++.|++++-..+|...||...-|..||.+.+.....-..+++
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 7888999998 999999999999999999999999999999998876654444
No 44
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=72.46 E-value=5.5 Score=29.98 Aligned_cols=47 Identities=17% Similarity=0.283 Sum_probs=30.6
Q ss_pred cCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019762 252 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQR 305 (336)
Q Consensus 252 rkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R 305 (336)
++++.||.+.+..+-.-... +......+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~-------~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE-------SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH-------HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH-------CCCceEeeecccccccccccHHHHHHh
Confidence 34567888886655444433 246778999999999999999987776
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=70.29 E-value=7.9 Score=25.87 Aligned_cols=46 Identities=11% Similarity=0.125 Sum_probs=34.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 309 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~k 309 (336)
.+|...+.++...+... ..-..+|..+|++...|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46777888887776442 12457899999999999999988887653
No 46
>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=63.40 E-value=6.9 Score=27.73 Aligned_cols=44 Identities=14% Similarity=0.289 Sum_probs=32.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 307 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R 307 (336)
.||+..+.++.-.+.. .+ .-.++|+.+|++...|.+|....|++
T Consensus 10 ~L~~~~r~i~~l~~~~----g~----s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQ----GM----SYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH----Cc----CHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 4788888887665554 22 23689999999999999999998876
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=62.66 E-value=23 Score=20.87 Aligned_cols=40 Identities=10% Similarity=0.155 Sum_probs=27.8
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 019762 254 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWF 301 (336)
Q Consensus 254 r~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF 301 (336)
+..++.+....+...+.. ++ ....+|+.+|++...|.+|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 344666666666665543 33 34578899999999999984
No 48
>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=61.09 E-value=8.6 Score=27.01 Aligned_cols=47 Identities=9% Similarity=0.225 Sum_probs=36.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.+|...|.. ++ .-..+|+..|++...|..+...+..+.|+
T Consensus 4 ~L~~~er~vi~~~y~~----~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----GL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----CC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 5788888999887744 22 23689999999999999999988887763
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=57.29 E-value=14 Score=31.01 Aligned_cols=47 Identities=9% Similarity=0.071 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++...|... .+ -..+|+.+|++...|.+|....|++.++
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 58888999886655442 22 3589999999999999999999998875
No 50
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=52.52 E-value=34 Score=34.18 Aligned_cols=45 Identities=11% Similarity=0.195 Sum_probs=38.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhh
Q 019762 132 KELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLT 178 (336)
Q Consensus 132 pELDqFMe~Yc~vL~kykeEL~kp~~~~~~EA~~fc~~ie~qL~sL~ 178 (336)
-+-|.||.-|| |.+|..+|.+-+|-.++++..-...+..|++.+|
T Consensus 134 T~C~Hy~H~~C--laRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavc 178 (368)
T KOG4445|consen 134 TACDHYMHFAC--LARYLTECLTGLRQEIQDAQKERQHMKEQVEAVC 178 (368)
T ss_pred ehhHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhh
Confidence 47899999999 7778888888887777888888888999999997
No 51
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=49.09 E-value=20 Score=31.86 Aligned_cols=50 Identities=8% Similarity=0.082 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
.||+..+.+|.-.+... .+| .++|+.+|++...|.+++...|++.++...
T Consensus 142 ~L~~~~r~vl~l~~~~~--~s~------~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--LTY------REVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 48899999986655542 332 589999999999999999999999987553
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=48.45 E-value=23 Score=30.14 Aligned_cols=48 Identities=17% Similarity=0.280 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++.-.+... .+| ..+|+.+|++...|.+.+.-+|++.++.
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s~------~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KSY------QEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48999988886655542 333 4899999999999999999999998764
No 53
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=45.99 E-value=17 Score=26.37 Aligned_cols=24 Identities=13% Similarity=0.279 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhh
Q 019762 282 DKARLVQETGLQLKQINNWFINQR 305 (336)
Q Consensus 282 eK~~LA~~tgLs~kQV~NWF~N~R 305 (336)
....||+.+|++..+|+.|+.+..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 356899999999999999999763
No 54
>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=45.64 E-value=25 Score=28.28 Aligned_cols=47 Identities=17% Similarity=0.285 Sum_probs=35.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++...+.. .| .-..+|+.+|+++..|.+|....+++.++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4677777777544333 33 23489999999999999999999998875
No 55
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=44.82 E-value=26 Score=30.02 Aligned_cols=50 Identities=16% Similarity=0.106 Sum_probs=40.2
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 255 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 255 ~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
..||...+.++.-++..+ .+| .++|..+|++...|.+|..-.|++.++-.
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~s~------~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--LTY------EEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358888999998765552 333 58999999999999999999999998743
No 56
>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=43.85 E-value=28 Score=29.51 Aligned_cols=51 Identities=10% Similarity=0.221 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 314 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~ 314 (336)
.||...+.++.-.+... .+ -..+|..+|++...|.++....|++.++....
T Consensus 110 ~L~~~~r~i~~l~~~~g--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 110 RLPARQRAVVVLRYYED--LS------EAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred hCCHHHHHHhhhHHHhc--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 58888888886655542 22 24789999999999999999999999875543
No 57
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=43.48 E-value=26 Score=29.77 Aligned_cols=48 Identities=8% Similarity=0.160 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++...+.. .+ .-..+|+..|++...|.+|..-.|++.++.
T Consensus 125 ~L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3777788887665544 22 226899999999999999999999998863
No 58
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=42.83 E-value=27 Score=32.23 Aligned_cols=52 Identities=15% Similarity=0.168 Sum_probs=41.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSS 315 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~~ 315 (336)
.||...+.++.-.|..+ .+| .++|+.+|++...|.++....|++.++.....
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s~------~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MSY------REIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 58888999998776662 232 57999999999999999999999999855433
No 59
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=42.39 E-value=29 Score=29.53 Aligned_cols=48 Identities=10% Similarity=0.210 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++.-.+... .+| ..+|+.+|++...|.+|....+++.++.
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s~------~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LSY------EEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888886654431 232 4799999999999999999999998864
No 60
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=41.10 E-value=34 Score=30.26 Aligned_cols=48 Identities=8% Similarity=0.022 Sum_probs=38.4
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 254 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 254 r~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
...||+.++.+|... .. .+ .-.++|+.+|++...|.+|....+++.++
T Consensus 4 ~~~Lt~rqreVL~lr-~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ER----GL----TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 457899999999773 33 22 23589999999999999999999988775
No 61
>PRK00118 putative DNA-binding protein; Validated
Probab=40.93 E-value=35 Score=28.59 Aligned_cols=47 Identities=9% Similarity=0.122 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||..++.++..++...+ .-..+|+.+|++..-|.+|....|++.++
T Consensus 17 ~L~ekqRevl~L~y~eg~--------S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY--------SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888877766622 22469999999999999999999988775
No 62
>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=40.81 E-value=1.2e+02 Score=31.66 Aligned_cols=165 Identities=14% Similarity=0.126 Sum_probs=92.5
Q ss_pred hhHhHHHHHHHhhCCChHHHHHHHHh----hhhccCCCCchhhHHHHHhhhHHHHHHhhhccCCCCCCChHHHHHHHHHH
Q 019762 67 DWETVKCKAEIVGHPLYEQLLSAHVS----CLRIATPVDQLPKIDAQLSRSRDVLAKYSAVANGRVLDDKELDQFMTHYV 142 (336)
Q Consensus 67 ~~e~~~lKa~I~sHPlYp~Ll~A~i~----C~KVGaP~e~~~~ld~~l~~~~~~~~~~~~~~~~~~g~dpELDqFMe~Yc 142 (336)
++.-..||-+++--=.||.++..... .+=||-|.---..|.-.+ + .-++.++|. ..-.
T Consensus 218 ~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAv-------A--TEc~tTFFN---------VSss 279 (491)
T KOG0738|consen 218 HEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAV-------A--TECGTTFFN---------VSSS 279 (491)
T ss_pred HHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHH-------H--HhhcCeEEE---------echh
Confidence 35567789999888889988876554 455676654333221111 1 111222221 2223
Q ss_pred HHHHHHHHHHHHHHHhhHHHH------HHHHHHHHHHHHHhhCCCCCCCCCccCCCCCccCCCCCCCCCCCCCCCCCCCh
Q 019762 143 LLLYSFKEQLQQHVRVHAMEA------VMACWDLEQSLQSLTGATMSDDDEDQVDSDTNFFDGSLDGPDSMGFGPLVPTE 216 (336)
Q Consensus 143 ~vL~kykeEL~kp~~~~~~EA------~~fc~~ie~qL~sL~~~~~s~de~~~~~s~~~~~~g~~~~~d~~~~~p~~~~~ 216 (336)
.+--||+=|=+|-+|+-|.=| ++|+++|+ +||+.- |+..+++
T Consensus 280 tltSKwRGeSEKlvRlLFemARfyAPStIFiDEID----slcs~R-----------------G~s~EHE----------- 327 (491)
T KOG0738|consen 280 TLTSKWRGESEKLVRLLFEMARFYAPSTIFIDEID----SLCSQR-----------------GGSSEHE----------- 327 (491)
T ss_pred hhhhhhccchHHHHHHHHHHHHHhCCceeehhhHH----HHHhcC-----------------CCccchh-----------
Confidence 355566666666666555444 67888776 477410 0001111
Q ss_pred hhhhhHHHHHHHHHHHHhhhhhhhHHHHHH-HHhhccCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHH
Q 019762 217 SERSLMERVRHELKHELKQGYKEKIVDIRE-EILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQE 289 (336)
Q Consensus 217 ~e~s~~~~~~~eLk~~l~~ky~~~i~~lr~-e~~kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~ 289 (336)
..+-+|.+|+..--|.-..+.. ...-.-..++||=+.-..|+.-|...+.-|-|+.+.|..|-+.
T Consensus 328 --------aSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrRRlEKRIyIPLP~~~~R~~Li~~ 393 (491)
T KOG0738|consen 328 --------ASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPWDIDEALRRRLEKRIYIPLPDAEARSALIKI 393 (491)
T ss_pred --------HHHHHHHHHHHHhhccccccccceeEEEEeccCCCcchHHHHHHHHhhheeeeCCCHHHHHHHHHH
Confidence 1234555555432221111111 0001124678999999999999999999999999999988654
No 63
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=40.68 E-value=33 Score=29.22 Aligned_cols=48 Identities=21% Similarity=0.259 Sum_probs=38.7
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 255 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 255 ~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
..||..++.++.-.+... .+| .++|..+|++...|.++....|++.++
T Consensus 111 ~~L~~~~r~v~~l~~~~~--~s~------~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG--FSY------KEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 358888988887765542 333 589999999999999999999999875
No 64
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=40.68 E-value=32 Score=29.85 Aligned_cols=48 Identities=13% Similarity=0.270 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++.-.+.. .++ -..+|+.+|++...|.+++...|++.++.
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 4788888888777655 222 35899999999999999999999998764
No 65
>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=40.48 E-value=25 Score=30.52 Aligned_cols=49 Identities=10% Similarity=0.057 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.++.-.+..+ . .-..+|+.+|++...|.++.-..|++.++..
T Consensus 138 ~L~~~~r~v~~l~~~~~--~------s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG--L------SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 36777878876554441 2 2358999999999999999999999988754
No 66
>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=39.28 E-value=42 Score=27.83 Aligned_cols=47 Identities=15% Similarity=0.202 Sum_probs=36.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||...+.++.-.+.. .++ -..+|+.+|++...|.++....|++.++
T Consensus 113 ~L~~~~r~il~l~~~~----~~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GKS----YKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4778888888765444 332 2468999999999999999999998875
No 67
>PF13518 HTH_28: Helix-turn-helix domain
Probab=39.18 E-value=32 Score=23.66 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhh
Q 019762 283 KARLVQETGLQLKQINNWFINQRK 306 (336)
Q Consensus 283 K~~LA~~tgLs~kQV~NWF~N~R~ 306 (336)
...+|+..|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 356999999999999999987765
No 68
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=39.03 E-value=35 Score=29.31 Aligned_cols=49 Identities=14% Similarity=-0.002 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.++.-.+.+.+. -..+|+.+|++...|.++..-.|++.+...
T Consensus 112 ~L~~~~r~v~~l~~~~g~s--------~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASGFS--------YEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5888899988776655332 248999999999999999999999987643
No 69
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=38.92 E-value=37 Score=29.95 Aligned_cols=48 Identities=17% Similarity=0.172 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++.-.|... .+| ..+|+.+|++...|.+...-.|++.++.
T Consensus 131 ~L~~~~r~i~~l~~~~g--~s~------~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--EKI------EEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred hCCHHHHHHHHHHHHcc--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 58999999987655441 333 5899999999999999999999998874
No 70
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=37.86 E-value=40 Score=29.19 Aligned_cols=48 Identities=4% Similarity=0.104 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+.++.++.-.+.+. .+| .++|+.+|++...|.+.+...|++.++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g--~s~------~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG--LTV------EEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC--CCH------HHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48889988887776552 222 5899999999999999999999988763
No 71
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=37.36 E-value=43 Score=28.18 Aligned_cols=47 Identities=19% Similarity=0.233 Sum_probs=37.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++.-.+.. .++ -..+|+.+|++...|.++..-.|++.+.
T Consensus 111 ~L~~~~r~v~~l~~~~----g~~----~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQR----GVS----LTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 5888888888775444 222 2579999999999999999999988765
No 72
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=37.12 E-value=1e+02 Score=20.78 Aligned_cols=47 Identities=11% Similarity=0.147 Sum_probs=34.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.|+.....++..+ .. .+ ....+|+.+|++...|..|....+.+..-.
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 4677777777543 22 22 347899999999999999999887776543
No 73
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=36.92 E-value=43 Score=28.93 Aligned_cols=49 Identities=12% Similarity=0.197 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+.++.++.-.+... .+| .++|+.+|++..-|.++...++++.+...
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s~------~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MGH------AEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 48888888887655442 343 58999999999999999999999987543
No 74
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=35.05 E-value=45 Score=30.02 Aligned_cols=49 Identities=14% Similarity=0.207 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+.++.++.-.+... .. -..+|+.+|++...|.+++...|++.++-.
T Consensus 153 ~L~~~~r~vl~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--LS------QEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887655442 22 258999999999999999999999887644
No 75
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=34.58 E-value=48 Score=29.43 Aligned_cols=69 Identities=12% Similarity=0.124 Sum_probs=47.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCCcccccccccCCCCCCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSSTASKSKRKSNAGKSSN 332 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~~~~~~~~~~k~~~~~~~~ 332 (336)
.||+.++.++.-.+... .+| ..+|+.+|++..-|.++..-.|++.++-...-.+.....-.+--|.|+.
T Consensus 111 ~Lp~~~R~v~~L~~~eg--~s~------~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~~~~~~~~~~~~~~~~~~ 179 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG--LSY------QEAAAVLGIPIGTLMSRIGRARAALRAFEEGTGPARGRAHLRVVGGNDA 179 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCceeeeeecCCcc
Confidence 48999999987765552 332 5899999999999999999999998876554443332222333444443
No 76
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=34.29 E-value=46 Score=35.46 Aligned_cols=28 Identities=11% Similarity=0.211 Sum_probs=22.8
Q ss_pred CCCCChHHHHHHHHHHH-------HHHHHHHHHHH
Q 019762 127 RVLDDKELDQFMTHYVL-------LLYSFKEQLQQ 154 (336)
Q Consensus 127 ~~g~dpELDqFMe~Yc~-------vL~kykeEL~k 154 (336)
++..-|++.-..-+||. ||.+|.+||++
T Consensus 180 fln~ap~mkt~~~aYcanHP~AV~VL~k~~dELek 214 (661)
T KOG2070|consen 180 FLNLAPQMKTLYLAYCANHPSAVNVLTKHSDELEK 214 (661)
T ss_pred HHhhhHHHHHHHHHHHhcCchhhhHHHHhHHHHHH
Confidence 34567899888888985 89999999876
No 77
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=34.07 E-value=1.3e+02 Score=27.68 Aligned_cols=46 Identities=13% Similarity=0.210 Sum_probs=37.4
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHH-HHHHHHHHHHHHHhhC
Q 019762 131 DKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEA-VMACWDLEQSLQSLTG 179 (336)
Q Consensus 131 dpELDqFMe~Yc~vL~kykeEL~kp~~~~~~EA-~~fc~~ie~qL~sL~~ 179 (336)
=-|||-.+.++-.++..|++.++-.+= .+| ..||..|..||..+..
T Consensus 103 ItELDVvL~~FEk~~~eYkq~ieS~~c---r~AI~~F~~~~keqL~~~i~ 149 (175)
T PF13097_consen 103 ITELDVVLSAFEKTALEYKQSIESKIC---RKAINKFYSNFKEQLIEMIK 149 (175)
T ss_pred chHHHHHHHHHHHHHHHHHHhhccHHH---HHHHHHHHHHHHHHHHHHHH
Confidence 379999999999999999999976542 233 5689999999988773
No 78
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=33.92 E-value=50 Score=28.97 Aligned_cols=48 Identities=10% Similarity=0.008 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++.-.+... .+ -.++|+.+|++...|.++....|++.++.
T Consensus 139 ~L~~~~r~i~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVVG--LS------AEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887755552 22 36899999999999999999999998764
No 79
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=33.83 E-value=49 Score=28.78 Aligned_cols=50 Identities=4% Similarity=-0.091 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
.||+..+.++.-.+... .+ -.++|+.+|++...|.+++...|++.+....
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s------~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--AS------IKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 58888999988765552 22 2589999999999999999999999887544
No 80
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=33.55 E-value=44 Score=29.24 Aligned_cols=49 Identities=6% Similarity=0.081 Sum_probs=38.0
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 257 LPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 257 lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
||+..+.++.-.|... .+| ..+|+.+|++...|.++....|++.++...
T Consensus 129 L~~~~r~i~~l~~~~g--~s~------~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 129 LPERQREAIVLQYYQG--LSN------IEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CCHHHHHHhhHHHhcC--CCH------HHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 6778888885544441 222 579999999999999999999999987554
No 81
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=32.99 E-value=75 Score=24.34 Aligned_cols=26 Identities=27% Similarity=0.319 Sum_probs=19.6
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHHH
Q 019762 129 LDDKELDQFMTHYVLLLYSFKEQLQQ 154 (336)
Q Consensus 129 g~dpELDqFMe~Yc~vL~kykeEL~k 154 (336)
|-|+|||.....|..+.....+.+.+
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~~~ 26 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELLEE 26 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999998777666555543
No 82
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=32.73 E-value=41 Score=29.89 Aligned_cols=51 Identities=18% Similarity=0.169 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 314 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~ 314 (336)
.||...+.++.-.+... .+| .++|+.+|++...|.++....|++.++....
T Consensus 116 ~Lp~~~r~i~~L~~~~g--~s~------~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 116 QLPDDQREAIILVGASG--FAY------EEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 47888888886655541 333 4899999999999999999999999875543
No 83
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=31.53 E-value=54 Score=28.93 Aligned_cols=48 Identities=17% Similarity=0.047 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||..++.++.-.+... .+ -.++|+.+|+++..|.++..-.|++.++-
T Consensus 130 ~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 177 (185)
T PRK09649 130 DLTTDQREALLLTQLLG--LS------YADAAAVCGCPVGTIRSRVARARDALLAD 177 (185)
T ss_pred hCCHHHhHHhhhHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 58888988886665552 22 25899999999999999999999999873
No 84
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=31.32 E-value=64 Score=27.17 Aligned_cols=49 Identities=12% Similarity=0.062 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.++.-.+.+. .+| ..+|+.+|++...|.+...-.|++.++..
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s~------~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 106 KLPARQREAFLLRYWED--MDV------AETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred hCCHHHHHHHHHHHHhc--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888988887755541 333 68999999999999999999999988643
No 85
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=31.19 E-value=51 Score=29.46 Aligned_cols=49 Identities=16% Similarity=0.168 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.++.-.+... .+| ..+|+.+|++...|.+++.-.|++.++..
T Consensus 113 ~Lp~~~r~v~~L~~~~g--~s~------~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGASG--FSY------EEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58889999987765552 232 57899999999999999999999998744
No 86
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=30.97 E-value=56 Score=28.87 Aligned_cols=49 Identities=12% Similarity=0.167 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.++.-.+... .+ -..+|+.+|++...|.++...+|++.++..
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 48888888887654442 22 258999999999999999999999998754
No 87
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=30.89 E-value=56 Score=28.26 Aligned_cols=48 Identities=8% Similarity=0.113 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++.-.+... .+ -..+|+.+|++...|.+++...|++.++.
T Consensus 136 ~L~~~~r~v~~l~~~~g--~s------~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED--LS------LKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48888888886644331 23 26899999999999999999999988764
No 88
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.60 E-value=60 Score=28.33 Aligned_cols=49 Identities=18% Similarity=0.008 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.++.-.+.++ .+ -.++|+.+|++...|.+.+...|++.++..
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 46888888766554442 22 258999999999999999999999988743
No 89
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.56 E-value=60 Score=28.22 Aligned_cols=49 Identities=12% Similarity=0.135 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||...+.++.-.+... .. -..+|+.+|++...|.++..-.|++.++..
T Consensus 135 ~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG--YT------HREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 38888989887655442 22 258999999999999999999999987643
No 90
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=30.24 E-value=45 Score=29.30 Aligned_cols=47 Identities=11% Similarity=0.196 Sum_probs=36.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++.--+... .+ -..+|+.+|++...|.+|+..+|++.++
T Consensus 141 ~L~~~~~~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 141 QLPESQRQVLELAYYEG--LS------QSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hCCHHHhhhhhhhhhcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 47888888886554431 23 2589999999999999999999998876
No 91
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=29.94 E-value=43 Score=25.57 Aligned_cols=19 Identities=16% Similarity=0.415 Sum_probs=16.9
Q ss_pred HHHHHHHhCCChhhhhhhh
Q 019762 283 KARLVQETGLQLKQINNWF 301 (336)
Q Consensus 283 K~~LA~~tgLs~kQV~NWF 301 (336)
-..+|++.|+++.+|..|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 4679999999999999994
No 92
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=29.62 E-value=65 Score=28.34 Aligned_cols=48 Identities=15% Similarity=0.085 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+.++.++.-.+... .+| .++|+.+|++..-|.+.....|++.++-
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s~------~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LET------EEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48888888886665441 333 5899999999999999999999998864
No 93
>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=29.56 E-value=64 Score=27.67 Aligned_cols=48 Identities=4% Similarity=0.037 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||...+.++..-+... .+| ..+|+.+|++...|.++..-.|++.++.
T Consensus 119 ~L~~~~r~i~~l~~~~g--~s~------~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--LTI------KEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888886655541 232 5799999999999999999999988763
No 94
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=29.04 E-value=63 Score=28.59 Aligned_cols=48 Identities=10% Similarity=0.149 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||..++.++.-.+... .+ -.++|..+|+++..|.++..-+|++.++.
T Consensus 134 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--LS------SEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred hCCHHHHHHHhHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887765551 33 26899999999999999999999998863
No 95
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=28.98 E-value=65 Score=28.54 Aligned_cols=50 Identities=16% Similarity=0.281 Sum_probs=39.4
Q ss_pred CCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 255 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 255 ~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
..||+.++.++.-.+.+. .+| .++|+.+|++...|.+-+...|++.++..
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s~------~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LPH------QQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CCH------HHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 358888999987644441 443 58999999999999999999999888644
No 96
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=28.90 E-value=73 Score=28.57 Aligned_cols=52 Identities=12% Similarity=0.059 Sum_probs=41.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSS 315 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~~ 315 (336)
.||+..+.++.--+...+ + -..+|+.+|+++..|.++....|++.++.....
T Consensus 133 ~Lp~~~r~v~~l~~~~g~--s------~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 133 ALPPERREALILTQVLGY--T------YEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred cCCHHHHHHhhhHHHhCC--C------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 488888888866555522 2 258999999999999999999999999866543
No 97
>PF15500 Toxin_39: Putative RNase-like toxin
Probab=28.89 E-value=1.3e+02 Score=24.85 Aligned_cols=38 Identities=21% Similarity=0.162 Sum_probs=27.0
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Q 019762 128 VLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQ 172 (336)
Q Consensus 128 ~g~dpELDqFMe~Yc~vL~kykeEL~kp~~~~~~EA~~fc~~ie~ 172 (336)
+++||+|.+.|+. ++-+++.--++. ++||......+|.
T Consensus 44 l~a~p~lk~wne~-vq~~Rk~dp~~a------AdeaakLi~alE~ 81 (96)
T PF15500_consen 44 LAADPALKAWNET-VQAKRKLDPKFA------ADEAAKLIQALET 81 (96)
T ss_pred hccCHHHHHHHHH-HHHHHhhchhhh------HHHHHHHHHHHHH
Confidence 6789999999998 445666555554 4778766666655
No 98
>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=28.61 E-value=70 Score=27.75 Aligned_cols=50 Identities=16% Similarity=0.190 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
.||+..+.++.-.+... .+ -.++|+.+|++...|.++..-.|++.++-..
T Consensus 100 ~L~~~~r~v~~l~~~~g--~s------~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG--LS------QQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 58888888887766552 22 2589999999999999999999999887543
No 99
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.61 E-value=79 Score=27.62 Aligned_cols=50 Identities=10% Similarity=0.055 Sum_probs=39.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
.||+.++.++.-.+... .+| .++|+.+|++..-|.+.+..++.+.....+
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~s~------~EIA~~lgis~~tVk~~l~rAl~~~~~~~~ 176 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--MKQ------KDIAQALDIALPTVKKYIHQAYVTCLSLMP 176 (178)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence 48999999887765552 333 589999999999999999999988776543
No 100
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.41 E-value=67 Score=28.06 Aligned_cols=47 Identities=15% Similarity=0.212 Sum_probs=36.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++.--+... .+| ..+|+.+|++...|.+|...+|++.++
T Consensus 133 ~L~~~~r~i~~l~~~~~--~s~------~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 133 QLEPARRNCILHAYVDG--CSH------AEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 47888888665544431 333 689999999999999999999998875
No 101
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=28.39 E-value=44 Score=23.33 Aligned_cols=20 Identities=15% Similarity=0.174 Sum_probs=17.9
Q ss_pred HHHHHHhCCChhhhhhhhhh
Q 019762 284 ARLVQETGLQLKQINNWFIN 303 (336)
Q Consensus 284 ~~LA~~tgLs~kQV~NWF~N 303 (336)
..||+.+|+++..|..|..+
T Consensus 13 ~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHhCCCcchhHHHhcC
Confidence 68999999999999999988
No 102
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=28.23 E-value=67 Score=28.08 Aligned_cols=49 Identities=16% Similarity=0.203 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.++.-.+... .+| ..+|+.+|++...|.+.....|++.++..
T Consensus 122 ~L~~~~r~i~~l~~~~g--~s~------~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN--LTY------QEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887644441 332 57999999999999999999999988743
No 103
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.05 E-value=67 Score=28.49 Aligned_cols=49 Identities=4% Similarity=0.043 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+.++.++.-.+.. ..+| ..+|+.+|++...|.+++.-+|++.++..
T Consensus 136 ~L~~~~r~i~~L~~~~--g~s~------~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE--GLSN------PEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc--CCCH------HHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5888888887665443 1333 57999999999999999999999998744
No 104
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=27.60 E-value=76 Score=27.39 Aligned_cols=47 Identities=9% Similarity=0.142 Sum_probs=36.1
Q ss_pred CCChhHHHHHHH-HHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKA-WWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~-wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||...+.+|.- +|.. .+| ..+|+.+|++...|.+.....|++.++.
T Consensus 136 ~L~~~~r~il~l~~~~~---~s~------~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 136 QLPEKYRTVIVLKYIED---LSL------KEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHHHHhhhHHhhC---CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 367777777744 3333 333 6899999999999999999999998764
No 105
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=27.52 E-value=73 Score=27.02 Aligned_cols=47 Identities=13% Similarity=0.249 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||..++.+|.-.+ . .+ .-..+|..+|++...|.++....|++.++-
T Consensus 112 ~L~~~~r~il~l~~-~----g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----GY----SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH-c----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888886666 4 22 236899999999999999999999988763
No 106
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=27.07 E-value=1.7e+02 Score=24.53 Aligned_cols=42 Identities=12% Similarity=0.227 Sum_probs=31.3
Q ss_pred hhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 019762 259 GDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQ 304 (336)
Q Consensus 259 k~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~ 304 (336)
......+..|...|+..| ++. ..||+.+|+++.++..+|...
T Consensus 8 ~~~i~~~~~~I~~~~~~~-~sl---~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNLESP-LSL---EKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhcCCC-CCH---HHHHHHHCcCHHHHHHHHHHH
Confidence 344567788889987766 454 568888999999988887654
No 107
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=26.99 E-value=63 Score=29.74 Aligned_cols=48 Identities=13% Similarity=0.167 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||...+.++..-|...+ .-..+|+.+|++...|.++....|++.++.
T Consensus 184 ~L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQEEL--------NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhccCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 378888888877655422 246899999999999999999999998864
No 108
>cd00131 PAX Paired Box domain
Probab=26.55 E-value=2.1e+02 Score=24.42 Aligned_cols=46 Identities=11% Similarity=0.082 Sum_probs=32.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------Chhhhhhhhhhh
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGL-------QLKQINNWFINQ 304 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgL-------s~kQV~NWF~N~ 304 (336)
++.......+..+..+ +|.-|..|-..+-...|+ +..+|+.||.++
T Consensus 75 ~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 4455555666667777 898888777665335576 999999998764
No 109
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=26.48 E-value=37 Score=22.46 Aligned_cols=22 Identities=41% Similarity=0.563 Sum_probs=17.5
Q ss_pred HHHHHhhCCChHHHHHHHHhhh
Q 019762 73 CKAEIVGHPLYEQLLSAHVSCL 94 (336)
Q Consensus 73 lKa~I~sHPlYp~Ll~A~i~C~ 94 (336)
+-.+|++.|||.-||+|--..+
T Consensus 5 lipkiissplfktllsavgsal 26 (33)
T PF07425_consen 5 LIPKIISSPLFKTLLSAVGSAL 26 (33)
T ss_dssp CHHHHCCTTTCHHHHHHHHHHC
T ss_pred hhhHHHccHHHHHHHHHHHHHH
Confidence 3468999999999998865544
No 110
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=26.18 E-value=47 Score=22.94 Aligned_cols=22 Identities=23% Similarity=0.259 Sum_probs=19.0
Q ss_pred HHHHHHHhCCChhhhhhhhhhh
Q 019762 283 KARLVQETGLQLKQINNWFINQ 304 (336)
Q Consensus 283 K~~LA~~tgLs~kQV~NWF~N~ 304 (336)
-..||+.+|+++..|+.|....
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 3579999999999999998664
No 111
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=26.08 E-value=41 Score=30.70 Aligned_cols=39 Identities=26% Similarity=0.534 Sum_probs=30.4
Q ss_pred ChhHHHHHHHHHHHccCCCCCC-HHHHHHHHHHhCCChhh
Q 019762 258 PGDTTSLLKAWWLSHAKWPYPT-EEDKARLVQETGLQLKQ 296 (336)
Q Consensus 258 pk~a~~~L~~wf~~H~~~PYPs-~~eK~~LA~~tgLs~kQ 296 (336)
........-.|...|.-.|||+ ++||..-|++.||-+..
T Consensus 22 ~~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 22 MPRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred cccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 3444556678999999999995 77888999999987654
No 112
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.94 E-value=81 Score=27.05 Aligned_cols=49 Identities=12% Similarity=0.223 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.+|.--+... .+ -.++|+.+|++...|.+..--.|++.++..
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 48888988887665542 33 258999999999999999999999988744
No 113
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=25.15 E-value=97 Score=27.06 Aligned_cols=28 Identities=11% Similarity=0.136 Sum_probs=25.1
Q ss_pred HHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 284 ARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 284 ~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
..+|+.+|++...|.+++.-.|++.++.
T Consensus 169 ~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 169 QEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 5899999999999999999999988763
No 114
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=25.12 E-value=1.8e+02 Score=24.22 Aligned_cols=48 Identities=13% Similarity=0.185 Sum_probs=38.3
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.|++..+++|.-+ .++ |. ...+|+..+++.+.|.++..+.|++..-.+
T Consensus 149 ~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~ 196 (211)
T PRK15369 149 LLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHK 196 (211)
T ss_pred CCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 4888888998774 442 22 468899999999999999999999987543
No 115
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=25.11 E-value=72 Score=27.85 Aligned_cols=47 Identities=9% Similarity=0.185 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
+||+.++.++.-.+... .+| ..+|+.+|++...|.++..-.|++.++
T Consensus 127 ~L~~~~r~v~~l~~~~g--~s~------~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE--LSI------KEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 58888988876655442 332 589999999999999999999998875
No 116
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=25.03 E-value=79 Score=29.46 Aligned_cols=48 Identities=10% Similarity=0.159 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.+|.-.|... .+ -..+|+.+|++...|.+|....+++.++.
T Consensus 205 ~L~~~~r~vl~l~~~~g--~s------~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN--LS------QKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48888999997766552 22 26899999999999999999999988764
No 117
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=25.03 E-value=1.1e+02 Score=25.59 Aligned_cols=48 Identities=6% Similarity=0.060 Sum_probs=31.6
Q ss_pred cCCCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhh
Q 019762 252 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 306 (336)
Q Consensus 252 rkr~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~ 306 (336)
+++++++.+-+...-..... ..+ ....+|++.|++..+|.+|..-.+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~---~g~----sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE---PGM----TVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc---CCC----CHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 34566777775544333333 232 2357899999999999999766554
No 118
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=24.92 E-value=89 Score=27.20 Aligned_cols=47 Identities=13% Similarity=0.177 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++.--+..++ + -.++|+.+|++...|.+.....|++.++
T Consensus 117 ~Lp~~~r~i~~l~~~e~~--s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 117 KLPYKLRQVIILRYLHDY--S------QEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred hCCHHHHHHHHHHHHccC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 488888888877554422 2 2589999999999999999999999876
No 119
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=24.84 E-value=87 Score=26.52 Aligned_cols=49 Identities=14% Similarity=0.155 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.++.-.|... .+ -..+|+.+|++...|.....-.|++.++..
T Consensus 109 ~L~~~~r~v~~l~~~~~--~s------~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG--ET------QKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888888886554441 33 357999999999999999998888887643
No 120
>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=24.80 E-value=40 Score=23.28 Aligned_cols=20 Identities=5% Similarity=0.293 Sum_probs=18.4
Q ss_pred HHHHHhCCChhhhhhhhhhh
Q 019762 285 RLVQETGLQLKQINNWFINQ 304 (336)
Q Consensus 285 ~LA~~tgLs~kQV~NWF~N~ 304 (336)
.||+.+|++...|+.|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 58999999999999999876
No 121
>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=24.75 E-value=40 Score=29.76 Aligned_cols=49 Identities=10% Similarity=0.075 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||...+.++.-.+... .+ -..+|+.+|++...|.++..-.|++.++..
T Consensus 131 ~Lp~~~r~i~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEG--FA------YKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47777777775444331 22 258999999999999999999999988743
No 122
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.73 E-value=90 Score=27.37 Aligned_cols=48 Identities=10% Similarity=0.131 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.+|.--+... .+ -..+|+.+|++...|.+-+...|++.++.
T Consensus 131 ~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE--KS------VEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 47888888886554441 23 25899999999999999999999998874
No 123
>PRK10072 putative transcriptional regulator; Provisional
Probab=24.21 E-value=54 Score=27.04 Aligned_cols=23 Identities=9% Similarity=0.289 Sum_probs=20.3
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 019762 283 KARLVQETGLQLKQINNWFINQR 305 (336)
Q Consensus 283 K~~LA~~tgLs~kQV~NWF~N~R 305 (336)
...||+.+|++...|++|...+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999998765
No 124
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=24.17 E-value=86 Score=27.44 Aligned_cols=48 Identities=15% Similarity=0.069 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+.++.++.-.+... .+| ..+|+.+|++...|.++.-..|++.++.
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s~------~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--LSV------AEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred hCCHHHHHHHHHHHHcC--CcH------HHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 48999999997655442 332 5899999999999999999999998864
No 125
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=24.00 E-value=1e+02 Score=26.18 Aligned_cols=46 Identities=15% Similarity=0.254 Sum_probs=35.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 309 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~k 309 (336)
.||+.++.++.-.+... .+| ..+|+.+|++...|.++....+++..
T Consensus 113 ~L~~~~r~v~~L~~~~g--~s~------~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG--LGY------GEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 48888888886655441 343 57999999999999999998887754
No 126
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=23.94 E-value=63 Score=20.89 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=18.6
Q ss_pred HHHHHHhCCChhhhhhhhhhh
Q 019762 284 ARLVQETGLQLKQINNWFINQ 304 (336)
Q Consensus 284 ~~LA~~tgLs~kQV~NWF~N~ 304 (336)
..+|+.+|++...|+.|..+.
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCC
Confidence 488999999999999998765
No 127
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=23.81 E-value=1e+02 Score=29.32 Aligned_cols=51 Identities=14% Similarity=0.095 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 314 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~ 314 (336)
.||+.++.++.-.+... .+| .++|+.+|++..-|.+.+..+|++.++..+.
T Consensus 115 ~L~~~~R~v~~L~~~~g--~s~------~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~ 165 (293)
T PRK09636 115 RLSPLERAAFLLHDVFG--VPF------DEIASTLGRSPAACRQLASRARKHVRAARPR 165 (293)
T ss_pred hCCHHHHHHHHHHHHhC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 38888888875544331 444 5899999999999999999999999987653
No 128
>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=23.64 E-value=1e+02 Score=28.73 Aligned_cols=48 Identities=8% Similarity=0.067 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||...+.++.-.|...+ . -..+|+.+|++...|..+...++++.++.
T Consensus 205 ~L~~~~r~ii~l~~~~g~--s------~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL--S------QKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCCC--C------HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 588889888877765522 2 26899999999999999999999988763
No 129
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=23.50 E-value=40 Score=29.71 Aligned_cols=49 Identities=8% Similarity=0.090 Sum_probs=36.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||+..+.++.-.+... .+| ..+|+.+|++...|.++....|++.++..
T Consensus 139 ~L~~~~r~i~~l~~~~g--~s~------~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHGD--LEL------EEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehccC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777777776543331 232 57899999999999999999999988744
No 130
>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=23.45 E-value=89 Score=29.42 Aligned_cols=48 Identities=15% Similarity=0.273 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||...+.++.-.+...+. | ..+|..+|++...|.++....|++.++.
T Consensus 161 ~Lp~~~R~v~~L~~~eg~S--~------~EIA~~Lgis~~TVk~rl~RAr~~Lr~~ 208 (244)
T TIGR03001 161 ALSERERHLLRLHFVDGLS--M------DRIGAMYQVHRSTVSRWVAQARERLLER 208 (244)
T ss_pred hCCHHHHHHHHHHHHcCCC--H------HHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5888888888776665322 2 5899999999999999999999988864
No 131
>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=23.25 E-value=99 Score=27.38 Aligned_cols=48 Identities=13% Similarity=0.129 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++.-.+... .+ -..+|+.+|++..-|.+...-.|++.++.
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--FE------SDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887765552 33 26899999999999999999999998864
No 132
>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=22.94 E-value=1.3e+02 Score=21.64 Aligned_cols=48 Identities=15% Similarity=0.121 Sum_probs=34.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.|++....+|.-+..- + .-..+|...|++++.|..+..+.++|..-++
T Consensus 3 ~LT~~E~~vl~~l~~G-----~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG-----M----SNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHHTT-----S-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHHhc-----C----CcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 4667777777655443 2 3468899999999999999999999876543
No 133
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.83 E-value=96 Score=28.07 Aligned_cols=49 Identities=14% Similarity=0.200 Sum_probs=37.2
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||...+.++.-.+... .+| .++|+.+|++...|.++..-.|++.++..
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s~------~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LSY------EEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47777777664444331 443 58999999999999999999999998643
No 134
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=22.71 E-value=57 Score=34.76 Aligned_cols=11 Identities=18% Similarity=0.456 Sum_probs=6.6
Q ss_pred HHHHHHHHhhh
Q 019762 84 EQLLSAHVSCL 94 (336)
Q Consensus 84 p~Ll~A~i~C~ 94 (336)
..|+.+..+|.
T Consensus 157 qdL~~qlEec~ 167 (661)
T KOG2070|consen 157 QDLVQQLEECT 167 (661)
T ss_pred HHHHHHHHHhh
Confidence 34556666676
No 135
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.44 E-value=1.1e+02 Score=26.99 Aligned_cols=46 Identities=13% Similarity=0.122 Sum_probs=35.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++.-+|.. .. -..+|..+|+++..|.+.+...|++.++
T Consensus 155 ~L~~~~r~vl~l~~e~---~s------~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 155 LLSELEKEVLELYLDG---KS------YQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred hCCHHHHHHHHHHHcc---CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4677788888663332 22 2589999999999999999999998876
No 136
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=22.40 E-value=98 Score=27.72 Aligned_cols=49 Identities=12% Similarity=0.121 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||...+.++.-.+... .+| ..+|..+|++...|.+....+|++.++..
T Consensus 139 ~Lp~~~r~v~~L~~~eg--~s~------~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD--FEI------DDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887655542 233 57999999999999999999999998744
No 137
>PF12362 DUF3646: DNA polymerase III gamma and tau subunits C terminal; InterPro: IPR022107 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00004 from PFAM. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=21.81 E-value=61 Score=27.71 Aligned_cols=27 Identities=26% Similarity=0.310 Sum_probs=22.3
Q ss_pred ccchhHhHHHHHHHhhCCChHHHHHHH
Q 019762 64 RAEDWETVKCKAEIVGHPLYEQLLSAH 90 (336)
Q Consensus 64 ~~~~~e~~~lKa~I~sHPlYp~Ll~A~ 90 (336)
+....+.+..++.+..||++-..|.+|
T Consensus 82 E~~~~~~~~~~~~a~~~P~V~avL~~F 108 (117)
T PF12362_consen 82 EQEAAAKEARRAAARAHPLVKAVLAAF 108 (117)
T ss_pred HHHHHHHHHHHHHHHhCcHHHHHHHHC
Confidence 444566678899999999999999887
No 138
>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=21.78 E-value=2.2e+02 Score=21.02 Aligned_cols=46 Identities=17% Similarity=0.160 Sum_probs=35.1
Q ss_pred CChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhh
Q 019762 257 LPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFIN 303 (336)
Q Consensus 257 lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N 303 (336)
|+..++.+|..-+..=+.. +|-...-..||++.|++..-+..=+-+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd-~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFD-VPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCHHHHHHHHHHHHcCCCC-CCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5677888888877764433 488888999999999999888754433
No 139
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=21.65 E-value=69 Score=23.44 Aligned_cols=17 Identities=6% Similarity=0.227 Sum_probs=15.8
Q ss_pred HHHHHHhCCChhhhhhh
Q 019762 284 ARLVQETGLQLKQINNW 300 (336)
Q Consensus 284 ~~LA~~tgLs~kQV~NW 300 (336)
..+|+.+|++..+|..|
T Consensus 4 ~eva~~~gvs~~tlr~y 20 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYY 20 (69)
T ss_dssp HHHHHHTTTTHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHH
Confidence 47899999999999999
No 140
>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=21.53 E-value=1e+02 Score=27.96 Aligned_cols=47 Identities=11% Similarity=0.158 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||...+.+|...|... + .-..+|+.+|++...|..+....+++.++
T Consensus 175 ~L~~~~r~il~l~y~~~----~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE----L----NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 48999999998877552 2 23689999999999999999999988875
No 141
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=21.51 E-value=79 Score=21.75 Aligned_cols=23 Identities=13% Similarity=0.379 Sum_probs=16.9
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 019762 283 KARLVQETGLQLKQINNWFINQR 305 (336)
Q Consensus 283 K~~LA~~tgLs~kQV~NWF~N~R 305 (336)
...+|+.+|++...|.+|...-+
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHHCcCHHHHHHHHHHcc
Confidence 46899999999999999976543
No 142
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=21.42 E-value=1.1e+02 Score=28.63 Aligned_cols=47 Identities=9% Similarity=0.065 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++.-.|.. .+ .-..+|..+|++...|.+++...|++.++
T Consensus 201 ~L~~~~r~vl~l~~~~----~~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLFYKE----EL----TLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4788888888776554 21 23689999999999999999999998875
No 143
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=21.37 E-value=86 Score=29.17 Aligned_cols=49 Identities=6% Similarity=0.095 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
.||..++.++.-.+... .+| .++|+.+|++...|.+.....|++.++..
T Consensus 171 ~Lp~~~R~v~~L~~~eg--~s~------~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN--MSN------GEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHhcC--CCH------HHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 47888888765544431 333 58999999999999999999999988643
No 144
>PRK04217 hypothetical protein; Provisional
Probab=21.30 E-value=1.6e+02 Score=24.95 Aligned_cols=51 Identities=8% Similarity=-0.058 Sum_probs=40.0
Q ss_pred CCCCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019762 254 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 312 (336)
Q Consensus 254 r~~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~ 312 (336)
-..++.+.+.++..++.+.+ .-..+|+.+|++...|.+.+...|++.+...
T Consensus 40 ~~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34678888888877765522 3457999999999999999999999887643
No 145
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.29 E-value=1.1e+02 Score=27.14 Aligned_cols=51 Identities=18% Similarity=0.010 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 314 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~ 314 (336)
.||+..+.++.-.+...+. -.++|+.+|++...|.....-+|++.++....
T Consensus 111 ~Lp~~~R~v~~L~~~~g~s--------~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 111 KLPQDQREALILVGASGFS--------YEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred hCCHHHHHHhhHHHHcCCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 4788888888776555222 25899999999999999999999999876654
No 146
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=21.19 E-value=1.1e+02 Score=29.56 Aligned_cols=50 Identities=16% Similarity=0.201 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 313 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~ 313 (336)
.||...+.++.-.+... .+| .++|+.+|++...|.+...-.|++.++..+
T Consensus 153 ~Lp~~~R~v~~L~~~~g--~s~------~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~ 202 (339)
T PRK08241 153 HLPPRQRAVLILRDVLG--WSA------AEVAELLDTSVAAVNSALQRARATLAERGP 202 (339)
T ss_pred hCCHHHhhhhhhHHhhC--CCH------HHHHHHhCCCHHHHHHHHHHHHHHHhhcCC
Confidence 47888888886655442 232 589999999999999999999999998544
No 147
>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=21.12 E-value=1.1e+02 Score=27.66 Aligned_cols=47 Identities=11% Similarity=0.227 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++...|.. .+ .-..+|+.+|++...|..|....+++.++
T Consensus 178 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFE----DK----TQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5889999998877654 21 24689999999999999999999988775
No 148
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=21.10 E-value=1.1e+02 Score=26.59 Aligned_cols=47 Identities=11% Similarity=0.202 Sum_probs=36.9
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 310 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk 310 (336)
.||+..+.++...|... .+ -.++|..+|++...|.+-...+|++.+.
T Consensus 137 ~L~~~~r~i~~l~~~~g--~s------~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 137 ELEPPRSELIRTAFFEG--IT------YEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 47888888886665441 22 2589999999999999999999998875
No 149
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=20.99 E-value=1e+02 Score=29.02 Aligned_cols=48 Identities=10% Similarity=0.142 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++...|...+ .-..+|..+|++...|.......+++.++.
T Consensus 212 ~L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYYEDL--------TLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 488888888877765522 246899999999999999999999988764
No 150
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=20.92 E-value=90 Score=27.86 Aligned_cols=30 Identities=13% Similarity=0.139 Sum_probs=25.0
Q ss_pred hccCCCCCChhHHHHHHHHHHHccCCCCCC
Q 019762 250 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPT 279 (336)
Q Consensus 250 kkrkr~~lpk~a~~~L~~wf~~H~~~PYPs 279 (336)
...+-+.|+.++...|..++...+..++|+
T Consensus 49 ~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~ 78 (149)
T PRK04053 49 PNAKLGYLSDEEIEKIEEALEDPAEEGIPS 78 (149)
T ss_pred CCCccCcCCHHHHHHHHHHHHhhccccCch
Confidence 455678899999999999998877777774
No 151
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=20.81 E-value=78 Score=20.26 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChhhhhhhhhhh
Q 019762 283 KARLVQETGLQLKQINNWFINQ 304 (336)
Q Consensus 283 K~~LA~~tgLs~kQV~NWF~N~ 304 (336)
...+|+.+|++...|..|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4588999999999999997554
No 152
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=20.56 E-value=1.5e+02 Score=25.56 Aligned_cols=48 Identities=8% Similarity=0.218 Sum_probs=36.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+..+.++.-.+... .+| ..+|+.+|++...|.......|++.++.
T Consensus 119 ~L~~~~r~i~~l~~~~~--~s~------~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQ--YSY------KEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 47777777775544331 333 6899999999999999999999988763
No 153
>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=20.47 E-value=2e+02 Score=19.38 Aligned_cols=30 Identities=10% Similarity=0.113 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 282 DKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 282 eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.-..+|+.+|++...|..|..-.+++..-.
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 446889999999999999998776665543
No 154
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=20.30 E-value=1.1e+02 Score=26.92 Aligned_cols=51 Identities=16% Similarity=0.141 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 314 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~~~~ 314 (336)
.||+.++.++.-.+.+ .+| -..+|..+|++...|.+.+...|++.++....
T Consensus 106 ~L~~~~r~i~~l~~~~----g~~----~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 106 ALPEKYAEALRLTELE----GLS----QKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred hCCHHHHHHHHHHHhc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 5788888888665444 222 25799999999999999999999998875443
No 155
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=20.21 E-value=1.2e+02 Score=27.44 Aligned_cols=48 Identities=13% Similarity=0.162 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019762 256 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 311 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~R~kk~ 311 (336)
.||+.++.++.-.+... .+| .++|+.+|++...|.+...-.|++.++.
T Consensus 148 ~L~~~~r~v~~L~~~~g--~s~------~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 148 GLPAKYARVFMMREFIE--LET------NEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 57888888886655552 333 6899999999999999999999998874
No 156
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.08 E-value=3.1e+02 Score=19.08 Aligned_cols=48 Identities=8% Similarity=0.109 Sum_probs=30.9
Q ss_pred CCChhHHHHHHHHHHH--ccCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhh
Q 019762 256 KLPGDTTSLLKAWWLS--HAKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 306 (336)
Q Consensus 256 ~lpk~a~~~L~~wf~~--H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R~ 306 (336)
.|+..+..++-.-+.. .....||| ...||+.+|++...|..+...-..
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3555555555332222 23347886 667999999999999988765443
Done!