Query 024428
Match_columns 268
No_of_seqs 220 out of 1129
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 04:32:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024428.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024428hhsearch_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 6E-31 1.3E-35 234.5 16.2 195 8-235 26-253 (334)
2 KOG0773 Transcription factor M 99.9 8.4E-28 1.8E-32 225.7 5.1 233 10-243 49-312 (342)
3 PF03791 KNOX2: KNOX2 domain ; 99.8 2.1E-21 4.6E-26 134.8 6.2 51 61-111 2-52 (52)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 4.1E-19 8.8E-24 119.5 4.6 44 11-54 1-44 (45)
5 PF05920 Homeobox_KN: Homeobox 99.7 1.6E-17 3.4E-22 110.2 4.3 40 187-227 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.5 3.3E-14 7.2E-19 99.9 6.9 57 171-231 2-58 (59)
7 KOG0775 Transcription factor S 99.5 4.5E-14 9.7E-19 127.5 6.5 48 179-230 186-233 (304)
8 smart00389 HOX Homeodomain. DN 99.5 9.1E-14 2E-18 97.0 6.7 55 171-229 2-56 (56)
9 PF00046 Homeobox: Homeobox do 99.5 8.1E-14 1.7E-18 98.1 5.3 57 170-230 1-57 (57)
10 PF03792 PBC: PBC domain; Int 99.0 2.2E-09 4.8E-14 92.9 9.3 126 9-166 25-177 (191)
11 KOG0493 Transcription factor E 98.9 1.2E-09 2.7E-14 98.4 5.3 77 170-250 247-323 (342)
12 TIGR01565 homeo_ZF_HD homeobox 98.9 2.1E-09 4.4E-14 76.8 4.9 53 169-225 1-57 (58)
13 KOG0487 Transcription factor A 98.9 8.5E-10 1.8E-14 102.4 3.3 62 169-234 235-296 (308)
14 KOG0843 Transcription factor E 98.9 1.4E-09 3.1E-14 93.3 4.2 61 168-232 101-161 (197)
15 KOG0489 Transcription factor z 98.7 7.7E-09 1.7E-13 94.6 3.7 62 169-234 159-220 (261)
16 KOG0483 Transcription factor H 98.7 1.5E-08 3.2E-13 89.1 4.4 60 169-232 50-109 (198)
17 KOG0485 Transcription factor N 98.7 1.6E-08 3.4E-13 89.3 4.1 58 169-230 104-161 (268)
18 KOG0850 Transcription factor D 98.6 2.1E-08 4.6E-13 89.1 3.7 60 170-233 123-182 (245)
19 KOG0488 Transcription factor B 98.6 3E-08 6.5E-13 92.7 4.7 64 167-234 170-233 (309)
20 KOG0842 Transcription factor t 98.6 1.9E-08 4E-13 93.5 2.8 61 168-232 152-212 (307)
21 COG5576 Homeodomain-containing 98.6 5.1E-08 1.1E-12 82.8 4.3 60 169-232 51-110 (156)
22 KOG0484 Transcription factor P 98.5 1E-07 2.2E-12 75.3 4.1 69 161-233 9-77 (125)
23 KOG3802 Transcription factor O 98.5 1.7E-07 3.6E-12 89.2 5.7 62 168-233 293-354 (398)
24 KOG0491 Transcription factor B 98.5 6.7E-08 1.4E-12 82.1 2.0 69 168-240 99-167 (194)
25 KOG0494 Transcription factor C 98.4 2E-07 4.2E-12 84.3 4.4 57 173-233 145-201 (332)
26 KOG0492 Transcription factor M 98.4 2.9E-07 6.2E-12 80.9 3.7 68 161-232 136-203 (246)
27 KOG2251 Homeobox transcription 98.3 4.2E-07 9.2E-12 80.5 4.4 58 169-230 37-94 (228)
28 KOG0486 Transcription factor P 98.3 4E-07 8.6E-12 84.3 2.6 64 169-236 112-175 (351)
29 KOG0848 Transcription factor C 98.2 4.5E-07 9.7E-12 82.3 1.6 58 173-234 203-260 (317)
30 KOG2252 CCAAT displacement pro 98.1 3.7E-06 8.1E-11 82.9 5.6 57 168-228 419-475 (558)
31 KOG4577 Transcription factor L 98.0 3.3E-06 7E-11 77.6 2.6 64 162-229 160-223 (383)
32 KOG0847 Transcription factor, 97.8 1.3E-05 2.7E-10 71.3 2.8 62 166-231 164-225 (288)
33 KOG0844 Transcription factor E 97.8 1E-05 2.2E-10 74.8 2.2 56 172-231 184-239 (408)
34 KOG0849 Transcription factor P 97.7 4.2E-05 9.1E-10 73.0 5.6 64 169-236 176-239 (354)
35 KOG0490 Transcription factor, 97.6 2.2E-05 4.8E-10 69.1 1.9 62 167-232 58-119 (235)
36 KOG1168 Transcription factor A 97.6 1.9E-05 4.1E-10 72.7 0.6 60 167-230 307-366 (385)
37 KOG0773 Transcription factor M 97.4 5.6E-05 1.2E-09 71.3 1.7 60 169-230 95-154 (342)
38 PF11569 Homez: Homeodomain le 97.4 0.00016 3.6E-09 51.2 3.1 43 181-227 10-52 (56)
39 PF03789 ELK: ELK domain ; In 97.1 0.00024 5.3E-09 41.0 1.2 22 147-168 1-22 (22)
40 KOG0490 Transcription factor, 94.7 0.022 4.8E-07 49.9 2.6 61 169-233 153-213 (235)
41 KOG1146 Homeobox protein [Gene 90.2 0.28 6.1E-06 53.6 3.8 64 168-235 902-965 (1406)
42 PF04218 CENP-B_N: CENP-B N-te 90.1 0.54 1.2E-05 32.6 4.0 47 170-225 1-47 (53)
43 PF01527 HTH_Tnp_1: Transposas 84.6 1.9 4E-05 31.1 4.3 47 171-225 2-48 (76)
44 KOG3623 Homeobox transcription 78.7 3.5 7.5E-05 43.1 5.2 45 181-229 568-612 (1007)
45 cd06171 Sigma70_r4 Sigma70, re 76.0 5.7 0.00012 25.5 4.1 45 175-228 10-54 (55)
46 PF08281 Sigma70_r4_2: Sigma-7 71.4 9 0.00019 25.8 4.3 44 175-227 10-53 (54)
47 PF13443 HTH_26: Cro/C1-type H 70.7 5.4 0.00012 27.7 3.1 24 202-225 12-35 (63)
48 cd00569 HTH_Hin_like Helix-tur 65.3 14 0.0003 21.0 3.9 38 175-221 5-42 (42)
49 PF04545 Sigma70_r4: Sigma-70, 63.1 11 0.00024 25.0 3.4 46 175-229 4-49 (50)
50 PRK06759 RNA polymerase factor 62.3 11 0.00024 30.4 3.9 48 174-230 105-152 (154)
51 PF13518 HTH_28: Helix-turn-he 57.3 12 0.00026 24.6 2.7 24 203-226 15-38 (52)
52 PRK09642 RNA polymerase sigma 55.1 12 0.00026 30.6 2.9 50 175-233 106-155 (160)
53 PRK00118 putative DNA-binding 54.0 13 0.00028 29.6 2.8 59 175-242 17-75 (104)
54 PRK03975 tfx putative transcri 51.8 21 0.00046 29.9 3.9 57 173-239 4-60 (141)
55 PRK09413 IS2 repressor TnpA; R 49.9 30 0.00065 27.6 4.4 48 171-226 8-55 (121)
56 PF10668 Phage_terminase: Phag 48.4 15 0.00034 26.3 2.2 20 201-220 23-42 (60)
57 KOG4040 NADH:ubiquinone oxidor 46.6 12 0.00026 32.2 1.6 39 178-216 23-61 (186)
58 PRK12541 RNA polymerase sigma 46.2 24 0.00051 28.9 3.3 48 174-230 111-158 (161)
59 PRK09644 RNA polymerase sigma 45.8 24 0.00051 29.0 3.3 49 174-231 107-155 (165)
60 PF13730 HTH_36: Helix-turn-he 45.3 90 0.002 20.8 5.8 48 176-227 3-52 (55)
61 PRK09652 RNA polymerase sigma 45.1 24 0.00052 28.9 3.2 48 175-231 128-175 (182)
62 PRK11924 RNA polymerase sigma 44.9 23 0.0005 28.9 3.1 49 175-232 125-173 (179)
63 PRK12514 RNA polymerase sigma 44.2 26 0.00056 29.2 3.3 47 175-230 129-175 (179)
64 TIGR02937 sigma70-ECF RNA poly 43.6 37 0.0008 26.3 4.0 47 175-230 110-156 (158)
65 PRK06811 RNA polymerase factor 43.5 29 0.00063 29.3 3.6 51 174-233 130-180 (189)
66 PRK09646 RNA polymerase sigma 43.4 26 0.00056 29.8 3.3 48 175-231 142-189 (194)
67 PRK12547 RNA polymerase sigma 43.3 27 0.00059 28.8 3.3 48 174-230 111-158 (164)
68 TIGR02999 Sig-70_X6 RNA polyme 42.9 29 0.00064 28.8 3.5 47 175-230 134-180 (183)
69 TIGR02985 Sig70_bacteroi1 RNA 42.8 35 0.00075 27.2 3.8 47 175-230 113-159 (161)
70 TIGR02939 RpoE_Sigma70 RNA pol 42.7 21 0.00047 29.7 2.6 49 175-232 138-186 (190)
71 TIGR02989 Sig-70_gvs1 RNA poly 42.7 43 0.00093 27.0 4.3 48 174-230 110-157 (159)
72 PRK06930 positive control sigm 42.5 22 0.00047 30.5 2.6 57 174-239 113-169 (170)
73 PF01381 HTH_3: Helix-turn-hel 42.3 22 0.00048 23.7 2.1 21 203-223 12-32 (55)
74 cd00131 PAX Paired Box domain 40.8 1E+02 0.0022 25.0 6.2 46 175-224 75-127 (128)
75 PRK12523 RNA polymerase sigma 40.6 36 0.00079 28.2 3.7 47 174-229 118-164 (172)
76 PRK12526 RNA polymerase sigma 39.8 32 0.00069 29.7 3.3 49 175-232 153-201 (206)
77 PRK09648 RNA polymerase sigma 38.8 36 0.00078 28.6 3.4 49 174-231 138-186 (189)
78 smart00421 HTH_LUXR helix_turn 38.7 82 0.0018 20.2 4.6 46 175-230 3-48 (58)
79 PF00196 GerE: Bacterial regul 38.6 59 0.0013 22.2 3.9 48 175-232 3-50 (58)
80 TIGR02983 SigE-fam_strep RNA p 38.3 35 0.00075 27.8 3.1 47 175-230 110-156 (162)
81 PF13384 HTH_23: Homeodomain-l 38.1 29 0.00063 22.8 2.2 23 203-225 20-42 (50)
82 PF14978 MRP-63: Mitochondrial 37.6 1E+02 0.0022 24.0 5.4 55 169-228 8-71 (91)
83 cd01392 HTH_LacI Helix-turn-he 37.6 20 0.00044 23.6 1.3 21 205-225 2-22 (52)
84 PF13936 HTH_38: Helix-turn-he 37.6 41 0.00089 22.1 2.8 40 174-222 3-42 (44)
85 PF01726 LexA_DNA_bind: LexA D 37.4 78 0.0017 22.7 4.5 43 175-223 3-49 (65)
86 PRK09649 RNA polymerase sigma 37.1 40 0.00087 28.5 3.4 48 174-230 129-176 (185)
87 PRK09639 RNA polymerase sigma 37.1 53 0.0011 26.7 4.1 47 175-231 112-158 (166)
88 PRK10072 putative transcriptio 36.7 27 0.0006 27.2 2.1 23 203-225 49-71 (96)
89 PRK11511 DNA-binding transcrip 36.6 1.1E+02 0.0023 24.5 5.7 41 179-224 9-49 (127)
90 TIGR03070 couple_hipB transcri 36.5 28 0.0006 23.0 1.9 22 204-225 19-40 (58)
91 PRK09047 RNA polymerase factor 36.1 45 0.00099 26.9 3.5 50 174-232 105-154 (161)
92 PRK12546 RNA polymerase sigma 35.5 38 0.00082 28.9 3.0 49 175-232 113-161 (188)
93 PRK12530 RNA polymerase sigma 35.3 32 0.00069 29.2 2.5 50 175-233 134-183 (189)
94 PRK05602 RNA polymerase sigma 35.1 39 0.00085 28.3 3.0 48 176-232 129-176 (186)
95 PRK12516 RNA polymerase sigma 35.0 42 0.00092 28.5 3.3 50 175-233 116-165 (187)
96 PRK12524 RNA polymerase sigma 34.8 43 0.00093 28.5 3.3 49 175-232 136-184 (196)
97 cd00093 HTH_XRE Helix-turn-hel 34.8 35 0.00076 21.2 2.2 23 203-225 15-37 (58)
98 TIGR02954 Sig70_famx3 RNA poly 34.8 45 0.00099 27.4 3.3 48 175-231 119-166 (169)
99 TIGR02947 SigH_actino RNA poly 34.4 18 0.00039 30.6 0.9 50 175-233 131-180 (193)
100 PHA02510 X gene X product; Rev 34.3 67 0.0014 26.1 4.1 61 145-219 6-77 (116)
101 PRK12520 RNA polymerase sigma 34.3 47 0.001 28.0 3.4 49 175-232 131-179 (191)
102 COG3105 Uncharacterized protei 34.0 82 0.0018 26.2 4.5 42 68-109 37-78 (138)
103 PRK12512 RNA polymerase sigma 33.7 41 0.00089 28.1 2.9 49 175-232 131-179 (184)
104 PRK11677 hypothetical protein; 33.6 1.1E+02 0.0023 25.5 5.3 42 68-109 32-73 (134)
105 PRK12532 RNA polymerase sigma 33.2 47 0.001 28.1 3.2 50 175-233 136-185 (195)
106 PRK13919 putative RNA polymera 32.8 51 0.0011 27.5 3.4 47 175-230 135-181 (186)
107 PRK12531 RNA polymerase sigma 32.6 50 0.0011 28.0 3.3 49 174-231 140-188 (194)
108 PRK12542 RNA polymerase sigma 32.3 50 0.0011 27.6 3.3 49 175-232 122-170 (185)
109 PRK12528 RNA polymerase sigma 32.2 67 0.0015 26.1 3.9 46 174-228 112-157 (161)
110 PRK12537 RNA polymerase sigma 32.1 54 0.0012 27.4 3.4 47 175-230 133-179 (182)
111 PF13411 MerR_1: MerR HTH fami 31.3 39 0.00085 23.6 2.1 18 204-221 4-21 (69)
112 PF06295 DUF1043: Protein of u 31.3 1.2E+02 0.0027 24.6 5.3 42 68-109 28-69 (128)
113 PRK12519 RNA polymerase sigma 31.2 41 0.00089 28.3 2.5 47 175-230 141-187 (194)
114 PRK12533 RNA polymerase sigma 31.0 62 0.0013 28.5 3.7 51 175-234 134-184 (216)
115 PRK12536 RNA polymerase sigma 31.0 57 0.0012 27.2 3.4 48 175-231 129-176 (181)
116 TIGR02959 SigZ RNA polymerase 30.6 76 0.0016 26.3 4.1 50 175-233 100-149 (170)
117 PF13551 HTH_29: Winged helix- 30.4 2.3E+02 0.005 21.1 7.6 46 176-222 58-109 (112)
118 smart00530 HTH_XRE Helix-turn- 30.3 45 0.00098 20.5 2.1 22 203-224 13-34 (56)
119 PRK08583 RNA polymerase sigma 30.1 56 0.0012 29.2 3.3 47 175-230 205-251 (257)
120 TIGR02607 antidote_HigA addict 29.9 48 0.001 23.7 2.4 20 205-224 23-42 (78)
121 TIGR02948 SigW_bacill RNA poly 29.4 54 0.0012 27.2 2.9 47 175-230 136-182 (187)
122 PRK09645 RNA polymerase sigma 29.4 63 0.0014 26.6 3.3 50 175-233 118-167 (173)
123 PRK12535 RNA polymerase sigma 29.4 63 0.0014 27.7 3.4 54 174-236 132-185 (196)
124 PRK06986 fliA flagellar biosyn 29.2 53 0.0012 28.9 3.0 47 175-230 184-230 (236)
125 TIGR03826 YvyF flagellar opero 29.1 72 0.0016 26.6 3.6 43 183-230 34-76 (137)
126 PRK12543 RNA polymerase sigma 28.9 67 0.0014 26.8 3.4 49 175-232 117-165 (179)
127 TIGR03001 Sig-70_gmx1 RNA poly 28.9 60 0.0013 29.2 3.3 51 175-234 161-211 (244)
128 PHA01976 helix-turn-helix prot 28.7 48 0.001 23.0 2.1 22 203-224 18-39 (67)
129 PRK09637 RNA polymerase sigma 28.6 76 0.0016 26.7 3.7 49 175-232 106-154 (181)
130 PRK07037 extracytoplasmic-func 27.5 71 0.0015 25.9 3.3 49 174-231 108-156 (163)
131 COG1084 Predicted GTPase [Gene 27.4 1.8E+02 0.0039 28.0 6.3 83 19-110 75-162 (346)
132 cd06170 LuxR_C_like C-terminal 27.2 1.8E+02 0.0038 18.7 4.8 30 203-232 18-47 (57)
133 PRK15369 two component system 27.1 1.1E+02 0.0023 24.6 4.3 47 175-231 149-195 (211)
134 PF04814 HNF-1_N: Hepatocyte n 27.1 1E+02 0.0022 27.0 4.2 36 178-221 117-152 (180)
135 PRK12529 RNA polymerase sigma 27.0 83 0.0018 26.3 3.7 47 175-230 127-173 (178)
136 PRK09647 RNA polymerase sigma 26.7 90 0.0019 27.0 3.9 50 175-233 138-187 (203)
137 cd04761 HTH_MerR-SF Helix-Turn 26.5 61 0.0013 20.8 2.2 19 204-222 4-22 (49)
138 PRK12545 RNA polymerase sigma 26.2 73 0.0016 27.3 3.3 50 175-233 139-188 (201)
139 PF12844 HTH_19: Helix-turn-he 26.2 52 0.0011 22.6 1.9 23 203-225 15-37 (64)
140 PRK12539 RNA polymerase sigma 26.0 74 0.0016 26.7 3.2 47 175-230 131-177 (184)
141 PRK09415 RNA polymerase factor 25.7 67 0.0015 26.8 2.9 47 175-230 127-173 (179)
142 TIGR02941 Sigma_B RNA polymera 25.7 72 0.0016 28.4 3.2 47 175-230 205-251 (255)
143 PRK07670 RNA polymerase sigma 25.5 79 0.0017 28.2 3.5 47 175-230 201-247 (251)
144 PRK12511 RNA polymerase sigma 25.1 78 0.0017 26.8 3.2 47 175-230 111-157 (182)
145 PRK12540 RNA polymerase sigma 24.8 80 0.0017 26.7 3.2 49 175-232 111-159 (182)
146 PRK06288 RNA polymerase sigma 24.7 59 0.0013 29.3 2.5 51 175-234 212-262 (268)
147 TIGR02980 SigBFG RNA polymeras 24.5 1.4E+02 0.003 25.9 4.8 47 175-230 178-224 (227)
148 COG2963 Transposase and inacti 24.5 1.6E+02 0.0034 22.9 4.7 49 173-229 5-54 (116)
149 PRK12515 RNA polymerase sigma 24.5 1.4E+02 0.003 25.0 4.6 48 175-231 131-178 (189)
150 PF07042 TrfA: TrfA protein; 24.0 1E+02 0.0022 28.9 3.9 53 171-227 206-258 (282)
151 PRK12538 RNA polymerase sigma 24.0 86 0.0019 27.8 3.4 49 175-232 171-219 (233)
152 PF07425 Pardaxin: Pardaxin; 23.9 56 0.0012 20.1 1.4 20 13-32 5-24 (33)
153 PF05190 MutS_IV: MutS family 23.6 1E+02 0.0022 22.5 3.2 23 65-87 1-23 (92)
154 TIGR02479 FliA_WhiG RNA polyme 23.4 92 0.002 27.1 3.4 47 175-230 175-221 (224)
155 PRK08301 sporulation sigma fac 23.3 77 0.0017 27.8 2.9 52 175-231 178-229 (234)
156 PRK09641 RNA polymerase sigma 23.3 88 0.0019 25.9 3.1 48 175-231 136-183 (187)
157 PF06299 DUF1045: Protein of u 23.3 1.7E+02 0.0037 25.0 4.9 44 144-187 55-98 (160)
158 PF00376 MerR: MerR family reg 23.0 70 0.0015 20.5 1.9 18 204-221 3-20 (38)
159 PRK12525 RNA polymerase sigma 22.7 1.5E+02 0.0033 24.3 4.5 47 174-229 117-163 (168)
160 PRK11923 algU RNA polymerase s 22.6 1.1E+02 0.0024 25.6 3.6 48 176-232 139-186 (193)
161 PF14229 DUF4332: Domain of un 22.4 90 0.0019 25.1 2.9 27 197-224 27-53 (122)
162 PRK12544 RNA polymerase sigma 22.4 1.3E+02 0.0027 26.1 4.1 52 174-234 147-198 (206)
163 PF06056 Terminase_5: Putative 22.2 76 0.0017 22.3 2.1 22 204-225 17-38 (58)
164 TIGR00721 tfx DNA-binding prot 21.9 1.3E+02 0.0028 25.1 3.8 54 173-236 4-57 (137)
165 TIGR02943 Sig70_famx1 RNA poly 21.8 1.1E+02 0.0024 25.8 3.5 50 175-233 131-180 (188)
166 TIGR03223 Phn_opern_protn puta 21.7 1.8E+02 0.0039 26.3 4.9 44 144-187 115-158 (228)
167 PRK12534 RNA polymerase sigma 21.6 1E+02 0.0022 25.7 3.2 47 175-230 137-183 (187)
168 PF04967 HTH_10: HTH DNA bindi 21.6 2.7E+02 0.0058 19.3 4.8 50 176-227 1-50 (53)
169 PF13097 CENP-U: CENP-A nucleo 21.6 2.4E+02 0.0052 24.6 5.5 42 68-109 104-147 (175)
170 TIGR02960 SigX5 RNA polymerase 21.5 1.1E+02 0.0024 28.0 3.7 49 175-232 142-190 (324)
171 cd04762 HTH_MerR-trunc Helix-T 21.4 92 0.002 19.4 2.3 22 204-225 4-25 (49)
172 cd04764 HTH_MlrA-like_sg1 Heli 21.4 75 0.0016 22.2 2.0 20 204-223 4-23 (67)
173 TIGR02952 Sig70_famx2 RNA poly 21.2 1.5E+02 0.0033 23.9 4.2 48 174-230 121-168 (170)
174 PRK09651 RNA polymerase sigma 20.9 83 0.0018 26.1 2.5 47 174-229 118-164 (172)
175 PRK08295 RNA polymerase factor 20.7 1.3E+02 0.0028 25.4 3.7 46 175-230 155-200 (208)
176 cd01104 HTH_MlrA-CarA Helix-Tu 20.6 77 0.0017 21.9 1.9 19 204-222 4-22 (68)
177 PRK12517 RNA polymerase sigma 20.5 1.2E+02 0.0025 25.7 3.4 49 175-232 128-176 (188)
178 PRK12527 RNA polymerase sigma 20.4 1.5E+02 0.0033 23.9 4.0 47 176-231 106-152 (159)
179 PF03672 UPF0154: Uncharacteri 20.2 2.8E+02 0.0061 20.2 4.7 36 180-219 18-55 (64)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.97 E-value=6e-31 Score=234.47 Aligned_cols=195 Identities=25% Similarity=0.392 Sum_probs=150.3
Q ss_pred CCcHHHHHHHhhCCChHHHHHHHHhc-hhcC---------CChH-HHhhHHHHHHHHhhcCCCCCCCC-----CCC----
Q 024428 8 GASSSVKAKIMAHPHYHRLLAAYANC-QKVG---------APPE-VVARLEEVCASAASMGSGGSSCI-----GQD---- 67 (268)
Q Consensus 8 ~~~~~~K~~I~~HPlyp~Ll~a~~~C-~Kvg---------ap~e-~~~~ld~~~~~~~~~~~~~~~~~-----g~d---- 67 (268)
+..++.|++|.||||||.|++++|+. +|++ .||| ++.|||+|+.+.++.+++.++.. |.|
T Consensus 26 Deaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsdY 105 (334)
T KOG0774|consen 26 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPPDPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSDY 105 (334)
T ss_pred chHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCCChHHHHHHHHHHHhcccCccccchhhhhccCCChHHH
Confidence 34558999999999999999999999 8874 3666 89999999999999988655432 222
Q ss_pred -chHhHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhhhhhccCCCCCCcchhhccCCCCccccCCCCCCCCChhHHH
Q 024428 68 -PALDQFMEAYCEMLTKYEQELSKPFKEAMSFLQKIESQFKSLSISSPNSASSEAIDRNGSSEEDFDVNIDFIDPQAEDQ 146 (268)
Q Consensus 68 -pELDqfM~~Y~~~L~ky~eeL~k~~~EA~~f~~~ie~QL~~L~~~~~~s~~~~~~~~~gsseee~d~~~~~~~~~~~~~ 146 (268)
+.|.|++..|...|++|++++.+ |++.++-+.+-.++++.++-. +-+
T Consensus 106 R~kL~qiR~iy~~ElekyeqaCne-ftthV~nlL~eQsr~RPi~~k-------------------------------e~e 153 (334)
T KOG0774|consen 106 RAKLLQIRQIYHNELEKYEQACNE-FTTHVMNLLREQSRTRPIMPK-------------------------------EIE 153 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHhcccCCCCHH-------------------------------HHH
Confidence 46999999999999999999555 444444444434444443310 112
Q ss_pred HHHHHHhhhhhcc-----------hhhhhHHhh-hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCCh
Q 024428 147 ELKGQLLRRYSGC-----------LSSLKQEFM-KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDS 214 (268)
Q Consensus 147 el~~~l~~~~~~~-----------~~~~~~~~~-k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~ 214 (268)
.+.+.+.++|+.. +-.|+.++. .+|||++|+|.++.+|.+||..|+.||||+ ++.|.+||++||++.
T Consensus 154 ~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPS-ee~K~eLAkqCnItv 232 (334)
T KOG0774|consen 154 RMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPS-EEAKEELAKQCNITV 232 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCc-HHHHHHHHHHcCcee
Confidence 3444444455444 334445553 488999999999999999999999999999 999999999999999
Q ss_pred hhhhhhhhhhhhhcCCCCcch
Q 024428 215 KQINNWFINQRKRHWKPSEDM 235 (268)
Q Consensus 215 ~QV~nWF~N~R~R~~kp~~~~ 235 (268)
+||+|||.|+|-|++|.+..+
T Consensus 233 sQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 233 SQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred hhhccccccceeehhhhhhhh
Confidence 999999999999999988543
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.94 E-value=8.4e-28 Score=225.71 Aligned_cols=233 Identities=25% Similarity=0.310 Sum_probs=171.0
Q ss_pred cHHHHHHHhhCCChHHHHHHHHhchhcCCChHHHhhHHHHHHHHhhcCCC----C---CC--CCCCCchHhHHHHHHHHH
Q 024428 10 SSSVKAKIMAHPHYHRLLAAYANCQKVGAPPEVVARLEEVCASAASMGSG----G---SS--CIGQDPALDQFMEAYCEM 80 (268)
Q Consensus 10 ~~~~K~~I~~HPlyp~Ll~a~~~C~Kvgap~e~~~~ld~~~~~~~~~~~~----~---~~--~~g~dpELDqfM~~Y~~~ 80 (268)
....|..+.+||+|..++.+|+.|.+++.+.+.+.+.+.........+.. . .. ..+.+++++.||.+|+.+
T Consensus 49 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k~~~~ 128 (342)
T KOG0773|consen 49 LASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSKLEKI 128 (342)
T ss_pred cccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchHHHHH
Confidence 44578899999999999999999999999999888866655444322110 0 11 245789999999999999
Q ss_pred HHHHHHHhcccH--HHHHHHHHHHHHhhhhhccCCCCCCcchh-----hcc------CCC-Cccc-----cCCCCCCCCC
Q 024428 81 LTKYEQELSKPF--KEAMSFLQKIESQFKSLSISSPNSASSEA-----IDR------NGS-SEED-----FDVNIDFIDP 141 (268)
Q Consensus 81 L~ky~eeL~k~~--~EA~~f~~~ie~QL~~L~~~~~~s~~~~~-----~~~------~gs-seee-----~d~~~~~~~~ 141 (268)
|..+...|.... .+++.+++++...+.......+....+.+ .+. ..+ +++. .+.......+
T Consensus 129 ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~ 208 (342)
T KOG0773|consen 129 LLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGESEQDDSEDESGP 208 (342)
T ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccccccccccccccccccCc
Confidence 999999998876 69999999999999887755432111100 000 000 1110 0000001111
Q ss_pred ---hhHHHHHHHHHhhhhhcchhhhhHHhhhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhh
Q 024428 142 ---QAEDQELKGQLLRRYSGCLSSLKQEFMKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQIN 218 (268)
Q Consensus 142 ---~~~~~el~~~l~~~~~~~~~~~~~~~~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~ 218 (268)
......++..+...++.++........++|+++.||+.++.+|+.||++|+.||||+ +.+|..||++|||+..||+
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPs-e~~K~~La~~TGLs~~Qv~ 287 (342)
T KOG0773|consen 209 SGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPS-DDEKLMLAKQTGLSRPQVS 287 (342)
T ss_pred ccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCc-chhccccchhcCCCcccCC
Confidence 122333445555555566666666677899999999999999999999999999999 9999999999999999999
Q ss_pred hhhhhhhhhcCCCCcchhhhccccC
Q 024428 219 NWFINQRKRHWKPSEDMQFMVMDAT 243 (268)
Q Consensus 219 nWF~N~R~R~~kp~~~~~~~~~~~~ 243 (268)
|||||+|+|.|+|+.+..++.++..
T Consensus 288 NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 288 NWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred chhhhcccccCCchHHHHHHHhhcc
Confidence 9999999999999998777777664
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=99.84 E-value=2.1e-21 Score=134.79 Aligned_cols=51 Identities=63% Similarity=1.052 Sum_probs=48.5
Q ss_pred CCCCCCCchHhHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhhhhhcc
Q 024428 61 SSCIGQDPALDQFMEAYCEMLTKYEQELSKPFKEAMSFLQKIESQFKSLSI 111 (268)
Q Consensus 61 ~~~~g~dpELDqfM~~Y~~~L~ky~eeL~k~~~EA~~f~~~ie~QL~~L~~ 111 (268)
++++|.||||||||++||.||++|+++|++|++||+.||++||+||++||+
T Consensus 2 ~~~~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 2 SSSIGADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 457899999999999999999999999999999999999999999999984
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=99.77 E-value=4.1e-19 Score=119.49 Aligned_cols=44 Identities=66% Similarity=1.064 Sum_probs=41.5
Q ss_pred HHHHHHHhhCCChHHHHHHHHhchhcCCChHHHhhHHHHHHHHh
Q 024428 11 SSVKAKIMAHPHYHRLLAAYANCQKVGAPPEVVARLEEVCASAA 54 (268)
Q Consensus 11 ~~~K~~I~~HPlyp~Ll~a~~~C~Kvgap~e~~~~ld~~~~~~~ 54 (268)
+.||++|++||+||.||.||++|+|||||||++.+||++.++++
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~~ 44 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAESQ 44 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhc
Confidence 57999999999999999999999999999999999999988764
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=99.70 E-value=1.6e-17 Score=110.17 Aligned_cols=40 Identities=55% Similarity=1.008 Sum_probs=36.5
Q ss_pred HHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 024428 187 WWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227 (268)
Q Consensus 187 w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R 227 (268)
||.+|+.||||| ++||..||..|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs-~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPS-KEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS---HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCC-HHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 999999999999 9999999999999999999999999998
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=99.52 E-value=3.3e-14 Score=99.88 Aligned_cols=57 Identities=32% Similarity=0.611 Sum_probs=53.7
Q ss_pred cCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 171 RKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 171 rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
+++..+++++..+|++||..| |||+ ..++..||..+||+..||.+||.|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~---~~P~-~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKN---PYPS-REEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhC---CCCC-HHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567889999999999999998 9999 99999999999999999999999999998764
No 7
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.48 E-value=4.5e-14 Score=127.50 Aligned_cols=48 Identities=44% Similarity=0.853 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 179 EARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 179 ~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
..+..|++||.++ |||+ ..+|.+||+.|||+..||.|||.|+|.|.+-
T Consensus 186 kSR~~LrewY~~~---~YPs-p~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 186 KSRSLLREWYLQN---PYPS-PREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHHHHHHHHhcC---CCCC-hHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 6899999999988 9999 9999999999999999999999999999983
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=9.1e-14 Score=97.01 Aligned_cols=55 Identities=33% Similarity=0.604 Sum_probs=51.5
Q ss_pred cCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 024428 171 RKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229 (268)
Q Consensus 171 rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~ 229 (268)
+.|..+++++..+|+.||..+ |||+ .+++..||..+||+..||.+||+|+|+|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~---~~P~-~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKN---PYPS-REEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhC---CCCC-HHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 456779999999999999999 9999 999999999999999999999999999864
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.46 E-value=8.1e-14 Score=98.05 Aligned_cols=57 Identities=37% Similarity=0.757 Sum_probs=53.8
Q ss_pred ccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 170 KRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 170 ~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
+|+|..|+.++..+|+.+|..+ |||+ .+++..||..+||+..||.+||.|+|.+.++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~---~~p~-~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN---PYPS-KEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS---SSCH-HHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh---cccc-ccccccccccccccccccccCHHHhHHHhCc
Confidence 5788899999999999999998 9999 9999999999999999999999999998753
No 10
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=98.99 E-value=2.2e-09 Score=92.94 Aligned_cols=126 Identities=25% Similarity=0.356 Sum_probs=89.9
Q ss_pred CcHHHHHHHhhCCChHHHHHHHHhc-hhcCC---------Ch-HHHhhHHHHHHHHhhcCCCCCCCC-----CC------
Q 024428 9 ASSSVKAKIMAHPHYHRLLAAYANC-QKVGA---------PP-EVVARLEEVCASAASMGSGGSSCI-----GQ------ 66 (268)
Q Consensus 9 ~~~~~K~~I~~HPlyp~Ll~a~~~C-~Kvga---------p~-e~~~~ld~~~~~~~~~~~~~~~~~-----g~------ 66 (268)
+..+.|.+|.+|||||.|+.++|+. +|++. || .++.|||+|+.+.++.+++.++.. +.
T Consensus 25 eaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~~~ 104 (191)
T PF03792_consen 25 EAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPPDPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADNSI 104 (191)
T ss_pred HHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCCchhhhhhhcchhhhcCcCCCCcccchhhhhccCccccc
Confidence 3488999999999999999999999 67732 44 378999999999999887544432 11
Q ss_pred C-----chHhHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhhhhhccCCCCCCcchhhccCCCCccccCCCCCCCCC
Q 024428 67 D-----PALDQFMEAYCEMLTKYEQELSKPFKEAMSFLQKIESQFKSLSISSPNSASSEAIDRNGSSEEDFDVNIDFIDP 141 (268)
Q Consensus 67 d-----pELDqfM~~Y~~~L~ky~eeL~k~~~EA~~f~~~ie~QL~~L~~~~~~s~~~~~~~~~gsseee~d~~~~~~~~ 141 (268)
| ..|.++...|...|.+|++++.. |++.+.-+-+-.+.++.++-
T Consensus 105 d~~dYr~kL~~ir~~y~~el~kye~ac~e-F~~hV~~lLreQs~~RPIs~------------------------------ 153 (191)
T PF03792_consen 105 DHSDYRAKLSQIRQIYHSELEKYEQACNE-FTEHVMNLLREQSEFRPISP------------------------------ 153 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhh-hHHHHHHHHHHhcccCCCCH------------------------------
Confidence 1 35999999999999999999555 44444333334444444331
Q ss_pred hhHHHHHHHHHhhhhhcchhhhhHH
Q 024428 142 QAEDQELKGQLLRRYSGCLSSLKQE 166 (268)
Q Consensus 142 ~~~~~el~~~l~~~~~~~~~~~~~~ 166 (268)
.+-+.+.....+||+++...+|+.
T Consensus 154 -keiE~m~~~i~~Kf~~iq~qLKQs 177 (191)
T PF03792_consen 154 -KEIERMVNIIHRKFSKIQMQLKQS 177 (191)
T ss_pred -HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 122456677788888888777754
No 11
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.92 E-value=1.2e-09 Score=98.43 Aligned_cols=77 Identities=25% Similarity=0.397 Sum_probs=66.7
Q ss_pred ccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcchhhhccccCCCcccc
Q 024428 170 KRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDMQFMVMDATQPQYYI 249 (268)
Q Consensus 170 ~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~~~~~~~~~~~~~~~ 249 (268)
||.|.-|+.++.+.|+.-|.+| .|.| +.-|..||.++||...||..||+|+|.++||......-.....+.+++|+
T Consensus 247 KRPRTAFtaeQL~RLK~EF~en---RYlT-EqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~lmaqglyN 322 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQEN---RYLT-EQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHLMAQGLYN 322 (342)
T ss_pred cCccccccHHHHHHHHHHHhhh---hhHH-HHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhhhcccccc
Confidence 6778899999999999999999 9999 99999999999999999999999999999998876554444555555564
Q ss_pred c
Q 024428 250 D 250 (268)
Q Consensus 250 ~ 250 (268)
-
T Consensus 323 H 323 (342)
T KOG0493|consen 323 H 323 (342)
T ss_pred C
Confidence 3
No 12
>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=98.90 E-value=2.1e-09 Score=76.84 Aligned_cols=53 Identities=23% Similarity=0.457 Sum_probs=50.5
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCC----CCcHHHHHHHHHHhCCChhhhhhhhhhhh
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPY----PSQESQKLALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PY----Ps~~~ek~~La~~tgL~~~QV~nWF~N~R 225 (268)
++|.|..|+.++...|+..|... +| |+ ..++..||..+||+..+|..||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~---~y~~~~~~-~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKL---GWKLKDKR-REEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHc---CCCCCCCC-HHHHHHHHHHhCCCHHHeeeecccCC
Confidence 47889999999999999999999 99 99 99999999999999999999999964
No 13
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.89 E-value=8.5e-10 Score=102.40 Aligned_cols=62 Identities=21% Similarity=0.385 Sum_probs=57.5
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcc
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSED 234 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~ 234 (268)
-+|||...+|.|+..|+.-|.-| -|.| ++-|.+|++.++||..||..||||+|.+.||-..+
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN---~Yit-keKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFN---MYIT-KEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHH---HHHh-HHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 46788899999999999999888 8999 99999999999999999999999999999987754
No 14
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.88 E-value=1.4e-09 Score=93.28 Aligned_cols=61 Identities=25% Similarity=0.384 Sum_probs=57.0
Q ss_pred hhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 168 MKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 168 ~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
+.||.|..|+.++...|+..|..+ .|-. ..||..||+.++|+..||..||+|+|.|+++-.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~---~Yvv-g~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN---QYVV-GAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC---Ceee-chHHHHHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence 357888999999999999999999 9999 999999999999999999999999999998744
No 15
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.72 E-value=7.7e-09 Score=94.57 Aligned_cols=62 Identities=23% Similarity=0.402 Sum_probs=58.3
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcc
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSED 234 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~ 234 (268)
.||.|..|+..++..|+.-|.-| .|.| ...|.++|..+.|+..||.+||+|+|.++||....
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN---~YLt-R~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~ 220 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFN---KYLT-RSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA 220 (261)
T ss_pred CCCCCcccchhhhhhhhhhhccc---cccc-hHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence 68889999999999999999999 9999 99999999999999999999999999999986654
No 16
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.69 E-value=1.5e-08 Score=89.11 Aligned_cols=60 Identities=28% Similarity=0.373 Sum_probs=54.5
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.++|+.+|+.++...|+.-|..| -|-. ..+|..||++.||++.||..||+|+|.|.+...
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~---~~L~-p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESE---KKLE-PERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccccHHHHHHhHHhhccc---cccC-hHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 35677789999999999999999 8888 999999999999999999999999999987543
No 17
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.68 E-value=1.6e-08 Score=89.26 Aligned_cols=58 Identities=26% Similarity=0.404 Sum_probs=55.5
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
|||.|.-|+..++..|+.-|... .|.+ ..+|..||.++.||..||..||+|+|.+.|+
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~k---rYLS-saeRa~LA~sLqLTETQVKIWFQNRRnKwKR 161 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFELK---RYLS-SAERAGLAASLQLTETQVKIWFQNRRNKWKR 161 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHHH---hhhh-HHHHhHHHHhhhhhhhhhhhhhhhhhHHHHH
Confidence 77889999999999999999999 9999 9999999999999999999999999999876
No 18
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.63 E-value=2.1e-08 Score=89.09 Aligned_cols=60 Identities=23% Similarity=0.369 Sum_probs=54.4
Q ss_pred ccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 170 KRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 170 ~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
+|.|..++.-+.+.|++-|.+. -|.- --||.+||..+|||..||..||+|+|-++||-+.
T Consensus 123 RKPRTIYSS~QLqaL~rRFQkT---QYLA-LPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQT---QYLA-LPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cCCcccccHHHHHHHHHHHhhc---chhc-CcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 4567788899999999999998 9999 8999999999999999999999999999987543
No 19
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.63 E-value=3e-08 Score=92.75 Aligned_cols=64 Identities=22% Similarity=0.445 Sum_probs=57.4
Q ss_pred hhhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcc
Q 024428 167 FMKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSED 234 (268)
Q Consensus 167 ~~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~ 234 (268)
.+++|.|.-|+..++..|+.-|..- -|.+ ..+|..||...|||-.||..||+|+|.+.|+..+.
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~Q---KYLS-~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQ---KYLS-VADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHh---hccc-HHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 3456677899999999999999888 8999 99999999999999999999999999998876655
No 20
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.61 E-value=1.9e-08 Score=93.53 Aligned_cols=61 Identities=21% Similarity=0.361 Sum_probs=55.5
Q ss_pred hhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 168 MKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 168 ~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.|||+|--|++.|+-.|++-|.+. .|.| .-||+.||..++||..||+.||+|+|=+.|+-.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQ---RYLS-APERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQ---RYLS-APEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred cccccccccchhHHHHHHHHHHhh---hccc-cHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 456667789999999999999999 9999 999999999999999999999999998887644
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.58 E-value=5.1e-08 Score=82.83 Aligned_cols=60 Identities=25% Similarity=0.408 Sum_probs=55.6
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.+++|.+.+..+..+|+..|..+ |||+ ...|..|+..+|++++-|..||+|+|.+.++-.
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~---p~Ps-~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEIN---PYPS-SITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred CcccceechHHHHHHHHHHhccC---CCCC-HHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 46778889999999999999999 9999 999999999999999999999999999988643
No 22
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.51 E-value=1e-07 Score=75.34 Aligned_cols=69 Identities=17% Similarity=0.333 Sum_probs=60.6
Q ss_pred hhhhHHhhhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 161 SSLKQEFMKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 161 ~~~~~~~~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
..+.+..+.+|-|..|+..+...|+..|.+. .||. --.+.+||....|+...|..||+|+|.+++|...
T Consensus 9 ~~l~ekrKQRRIRTTFTS~QLkELErvF~ET---HYPD-IYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 9 LGLTEKRKQRRIRTTFTSAQLKELERVFAET---HYPD-IYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred CChhHHHHhhhhhhhhhHHHHHHHHHHHHhh---cCCc-chhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 3444555567788999999999999999988 8999 9999999999999999999999999999987553
No 23
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.49 E-value=1.7e-07 Score=89.24 Aligned_cols=62 Identities=24% Similarity=0.458 Sum_probs=58.3
Q ss_pred hhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 168 MKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 168 ~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.|||||..+.-.++..|+..|.++ |-|| .+|.-.||++.+|...-|++||+|+|.+.|+...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~n---pKPt-~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKN---PKPT-SQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhC---CCCC-HHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 577888899999999999999999 9999 9999999999999999999999999999998665
No 24
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.46 E-value=6.7e-08 Score=82.08 Aligned_cols=69 Identities=20% Similarity=0.353 Sum_probs=59.8
Q ss_pred hhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcchhhhcc
Q 024428 168 MKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDMQFMVM 240 (268)
Q Consensus 168 ~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~~~~~~ 240 (268)
.++|.|..|+..+...|+.-|..- .|.+ -.|+.+||...+|+.+||..||+|+|.++||-....+...+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q---rYLS-~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS 167 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ---RYLS-TPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNS 167 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh---hhcc-cHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCC
Confidence 356667889999999999999988 8999 99999999999999999999999999999987766554333
No 25
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.43 E-value=2e-07 Score=84.35 Aligned_cols=57 Identities=23% Similarity=0.381 Sum_probs=53.1
Q ss_pred CCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 173 KGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 173 r~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
|..|+..+...|+.-|.+- .||. -..|+.||..|+|....|..||+|+|.+.+|...
T Consensus 145 RTiFT~~Qle~LEkaFkea---HYPD-v~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEA---HYPD-VYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred cchhhHHHHHHHHHHHhhc---cCcc-HHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 7789999999999999998 8999 9999999999999999999999999999877554
No 26
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.36 E-value=2.9e-07 Score=80.91 Aligned_cols=68 Identities=16% Similarity=0.305 Sum_probs=59.6
Q ss_pred hhhhHHhhhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 161 SSLKQEFMKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 161 ~~~~~~~~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
..|++....+|.|..|+..+...|++=|.+. .|.+ ..|+.+++....||..||..||+|+|.|-++-.
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfrek---qYLS-iaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFREK---QYLS-IAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhHh---hhhh-HHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 3445554556778899999999999999999 9999 999999999999999999999999999988744
No 27
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.35 E-value=4.2e-07 Score=80.47 Aligned_cols=58 Identities=21% Similarity=0.426 Sum_probs=54.7
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.+|-|..|+..+..+|+.-|.+- -||+ -..+++||...+|...+|.+||.|+|.+.++
T Consensus 37 qRRERTtFtr~QlevLe~LF~kT---qYPD-v~~rEelAlklnLpeSrVqVWFKNRRAK~r~ 94 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAKT---QYPD-VFMREELALKLNLPESRVQVWFKNRRAKCRR 94 (228)
T ss_pred cccccceecHHHHHHHHHHHHhh---cCcc-HHHHHHHHHHhCCchhhhhhhhccccchhhH
Confidence 46788999999999999999999 9999 9999999999999999999999999998764
No 28
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.28 E-value=4e-07 Score=84.28 Aligned_cols=64 Identities=23% Similarity=0.438 Sum_probs=58.0
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcchh
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDMQ 236 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~~ 236 (268)
++|-|..|+..+.+.|+.||..| -||+ .+.+.+||..|+||...|++||.|+|.+.+|-....+
T Consensus 112 qrrQrthFtSqqlqele~tF~rN---rypd-MstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQRN---RYPD-MSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhhc---cCCc-cchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 46677889999999999999998 9999 9999999999999999999999999999887665544
No 29
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.21 E-value=4.5e-07 Score=82.34 Aligned_cols=58 Identities=24% Similarity=0.400 Sum_probs=51.9
Q ss_pred CCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcc
Q 024428 173 KGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSED 234 (268)
Q Consensus 173 r~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~ 234 (268)
|-..+..+|-.|+.-|--. +|.| ..-|.+||..+||++.||..||+|+|.+.+|..+.
T Consensus 203 RvVYTDhQRLELEKEfh~S---ryIT-irRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFHTS---RYIT-IRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred eEEecchhhhhhhhhhccc---ccee-eehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 3456788999999998888 9999 99999999999999999999999999999876654
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.11 E-value=3.7e-06 Score=82.88 Aligned_cols=57 Identities=18% Similarity=0.352 Sum_probs=53.9
Q ss_pred hhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 024428 168 MKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRH 228 (268)
Q Consensus 168 ~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~ 228 (268)
..||.|-.|+..+++.|...|.++ +||+ .+.-+.|+.++||...-|.|||-|+|+|-
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~---~RPS-~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKEN---KRPS-REMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcC---CCCC-HHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 457778899999999999999999 9999 99999999999999999999999999994
No 31
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.00 E-value=3.3e-06 Score=77.57 Aligned_cols=64 Identities=23% Similarity=0.450 Sum_probs=57.7
Q ss_pred hhhHHhhhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 024428 162 SLKQEFMKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229 (268)
Q Consensus 162 ~~~~~~~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~ 229 (268)
++..+...||.|..++..+...|+.-|... |-|. .-.|++|+..|||+..-|..||+|+|.+.|
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~S---pKPA-RHVREQLsseTGLDMRVVQVWFQNRRAKEK 223 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNTS---PKPA-RHVREQLSSETGLDMRVVQVWFQNRRAKEK 223 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcCC---Cchh-HHHHHHhhhccCcceeehhhhhhhhhHHHH
Confidence 455566678999999999999999998888 9999 999999999999999999999999997665
No 32
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.80 E-value=1.3e-05 Score=71.25 Aligned_cols=62 Identities=19% Similarity=0.331 Sum_probs=54.5
Q ss_pred HhhhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 166 EFMKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 166 ~~~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
+-+|+-.|-.|+..+...|+.-|.+. .||- ..++.+||...|++..||..||+|+|.+.+|.
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqt---kyla-G~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQT---KYLA-GADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhh---hccc-chhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 33455556669999999999999999 9999 99999999999999999999999999987763
No 33
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.79 E-value=1e-05 Score=74.83 Aligned_cols=56 Identities=21% Similarity=0.370 Sum_probs=47.8
Q ss_pred CCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 172 KKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 172 kr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
=|.-|++++...|+.-|+.. -|-+ .-.|.+||..++|....|+.||+|+|.+.|+.
T Consensus 184 YRTAFTReQIaRLEKEFyrE---NYVS-RprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 184 YRTAFTREQIARLEKEFYRE---NYVS-RPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred HHhhhhHHHHHHHHHHHHHh---cccc-CchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 34669999999997655554 4899 88999999999999999999999999988753
No 34
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.75 E-value=4.2e-05 Score=72.99 Aligned_cols=64 Identities=23% Similarity=0.507 Sum_probs=56.8
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcchh
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDMQ 236 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~~ 236 (268)
.+|.|..|+..+...|+.+|... |||. -..+..||..+|++...|..||.|+|.|.++-....+
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt---~yP~-i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~~s 239 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRT---PYPD-IVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRDCS 239 (354)
T ss_pred ccccccccccchHHHHHHHhcCC---CCCc-hhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccccc
Confidence 45556789999999999999999 8999 9999999999999999999999999998887665433
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.64 E-value=2.2e-05 Score=69.05 Aligned_cols=62 Identities=23% Similarity=0.270 Sum_probs=56.5
Q ss_pred hhhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 167 FMKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 167 ~~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
+.++|.|..|+..+...|+.-|... +||. -..+..||..++++...|.+||+|+|.++.+..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~---h~Pd-~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKV---HLPC-FACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCC---CcCc-cchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 3467888889999999999999999 9999 999999999999999999999999999888644
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.58 E-value=1.9e-05 Score=72.68 Aligned_cols=60 Identities=28% Similarity=0.495 Sum_probs=54.7
Q ss_pred hhhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 167 FMKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 167 ~~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
-.|||||..+-..-++.|+++|..- |-|+ .+....+|+...|-..-|+.||+|+|.+.|+
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQ---PRPS-~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQ---PRPS-GEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred cccccccccccCcccccHHHHhccC---CCCc-hhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 3478888888888899999999999 9999 9999999999999999999999999999876
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.43 E-value=5.6e-05 Score=71.28 Aligned_cols=60 Identities=37% Similarity=0.630 Sum_probs=56.2
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
..+++++++.+. ..|+.|...|..+|||+ +.++..|+..++++.-||++||+|.|+|..+
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~-k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPS-KLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCch-HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 356778899999 99999999999999999 9999999999999999999999999999875
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.38 E-value=0.00016 Score=51.16 Aligned_cols=43 Identities=23% Similarity=0.447 Sum_probs=31.9
Q ss_pred HHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 024428 181 RQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227 (268)
Q Consensus 181 ~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R 227 (268)
.+.|+++|..| .++. +.+-..|+..+||+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~h---~~L~-E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKH---KQLQ-EEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT--------TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHc---CCcc-HhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 56699999999 9999 9999999999999999999999987544
No 39
>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=97.08 E-value=0.00024 Score=41.01 Aligned_cols=22 Identities=73% Similarity=1.050 Sum_probs=20.2
Q ss_pred HHHHHHhhhhhcchhhhhHHhh
Q 024428 147 ELKGQLLRRYSGCLSSLKQEFM 168 (268)
Q Consensus 147 el~~~l~~~~~~~~~~~~~~~~ 168 (268)
|||.+|+++|+++++++++||+
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 5899999999999999999974
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.69 E-value=0.022 Score=49.94 Aligned_cols=61 Identities=26% Similarity=0.462 Sum_probs=52.1
Q ss_pred hccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 169 KKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.++.+..+...+...+...|... +||. ...+..|+..+|++..-|.+||+|.|.+.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~---~~P~-~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRAT---PKPD-ADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccCC---CCCc-hhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 35566677777888888888877 9999 9999999999999999999999999999876433
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.16 E-value=0.28 Score=53.60 Aligned_cols=64 Identities=17% Similarity=0.246 Sum_probs=57.2
Q ss_pred hhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcch
Q 024428 168 MKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDM 235 (268)
Q Consensus 168 ~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~ 235 (268)
.+++.|..++-.+..+++..|..- -||+ +++-+.|.+..+|...-|..||+|+|.+-+|+.+..
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q---~~~~-~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQ---RTPT-MQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhc---cCCh-HHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 456667777888899999999988 9999 999999999999999999999999999999988753
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=90.15 E-value=0.54 Score=32.65 Aligned_cols=47 Identities=19% Similarity=0.323 Sum_probs=31.7
Q ss_pred ccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhh
Q 024428 170 KRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 170 ~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R 225 (268)
+|+|..|+-+..-.+-.-+... + -+..+|+.+|++..+|++|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g---~------s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG---E------SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT---T-------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC---C------CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 4677778877765555555555 2 377899999999999999999954
No 43
>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=84.58 E-value=1.9 Score=31.12 Aligned_cols=47 Identities=19% Similarity=0.307 Sum_probs=30.8
Q ss_pred cCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhh
Q 024428 171 RKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 171 rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R 225 (268)
++++.+|.+.+..+-.-.... ......+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 466778988766554443333 45778999999999999999987776
No 44
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=78.75 E-value=3.5 Score=43.13 Aligned_cols=45 Identities=20% Similarity=0.413 Sum_probs=41.7
Q ss_pred HHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 024428 181 RQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229 (268)
Q Consensus 181 ~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~ 229 (268)
+..|+++|..| +.|+ +++-..+|.+.||...-|..||.+.+....
T Consensus 568 ~sllkayyaln---~~ps-~eelskia~qvglp~~vvk~wfE~~~a~e~ 612 (1007)
T KOG3623|consen 568 TSLLKAYYALN---GLPS-EEELSKIAQQVGLPFAVVKAWFEDEEAEEM 612 (1007)
T ss_pred HHHHHHHHHhc---CCCC-HHHHHHHHHHhcccHHHHHHHHHhhhhhhh
Confidence 78899999999 9999 999999999999999999999999987654
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=75.95 E-value=5.7 Score=25.45 Aligned_cols=45 Identities=20% Similarity=0.308 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRH 228 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~ 228 (268)
.+|...+.++...+... + .-..+|..+|++..+|..|....+.+.
T Consensus 10 ~l~~~~~~~~~~~~~~~----~-----~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 10 KLPEREREVILLRFGEG----L-----SYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred hCCHHHHHHHHHHHhcC----C-----CHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 36777788887776544 2 234789999999999999999888775
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=71.44 E-value=9 Score=25.76 Aligned_cols=44 Identities=20% Similarity=0.343 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R 227 (268)
.+|+..+.++...+.+. -.-.++|+.+|++...|.+|...+|++
T Consensus 10 ~L~~~~r~i~~l~~~~g---------~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG---------MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS------------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC---------cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 47888888876655544 234579999999999999999999876
No 47
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=70.66 E-value=5.4 Score=27.65 Aligned_cols=24 Identities=17% Similarity=0.289 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhh
Q 024428 202 QKLALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 202 ek~~La~~tgL~~~QV~nWF~N~R 225 (268)
....||+.+|++..+|+.|+.+..
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 466899999999999999998763
No 48
>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=65.35 E-value=14 Score=20.98 Aligned_cols=38 Identities=16% Similarity=0.198 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhh
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWF 221 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF 221 (268)
.++.+.+..+...+.. .+ + ...+|+.+|++...|.+|.
T Consensus 5 ~~~~~~~~~i~~~~~~----~~-s----~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA----GE-S----VAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc----CC-C----HHHHHHHHCCCHHHHHHhC
Confidence 3555555555555442 33 3 3478889999999999984
No 49
>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=63.09 E-value=11 Score=25.03 Aligned_cols=46 Identities=15% Similarity=0.191 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~ 229 (268)
.||+..+.++...|.+. ..-.++|...|++...|+.+...+.++.+
T Consensus 4 ~L~~~er~vi~~~y~~~---------~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG---------LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST----------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC---------CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 47888899988777433 23457999999999999999998888764
No 50
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=62.31 E-value=11 Score=30.38 Aligned_cols=48 Identities=8% Similarity=0.043 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
..||+..+.++..-|... + .-.++|+.+|++...|.+|....|++.++
T Consensus 105 ~~L~~~~r~ii~l~~~~~----~-----s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 105 SVLDEKEKYIIFERFFVG----K-----TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred HhCCHHHHHHHHHHHhcC----C-----CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 358888999886655544 1 23479999999999999999999998764
No 51
>PF13518 HTH_28: Helix-turn-helix domain
Probab=57.29 E-value=12 Score=24.61 Aligned_cols=24 Identities=17% Similarity=0.405 Sum_probs=20.7
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhh
Q 024428 203 KLALAESTGLDSKQINNWFINQRK 226 (268)
Q Consensus 203 k~~La~~tgL~~~QV~nWF~N~R~ 226 (268)
...+|...|++..+|.+|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 346999999999999999887765
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=55.06 E-value=12 Score=30.57 Aligned_cols=50 Identities=18% Similarity=0.197 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||+..+.++.-.+.+. ++. .++|+.+|++...|.+.+..+|++.++-..
T Consensus 106 ~Lp~~~r~v~~l~~~~g----~s~-----~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE----KSY-----QEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred hCCHHHHHHHHHHHHhC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 38998899887665554 232 379999999999999999999999876443
No 53
>PRK00118 putative DNA-binding protein; Validated
Probab=54.00 E-value=13 Score=29.58 Aligned_cols=59 Identities=12% Similarity=0.097 Sum_probs=45.9
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcchhhhcccc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDMQFMVMDA 242 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~~~~~~~~ 242 (268)
.+|+.++.++..++... ++ -..+|+.+|++..-|.+|....|++.++-.+.++|..-..
T Consensus 17 ~L~ekqRevl~L~y~eg----~S-----~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~~ 75 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD----YS-----LGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFI 75 (104)
T ss_pred cCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHHH
Confidence 37888888887776655 22 3369999999999999999999999988777766654433
No 54
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=51.84 E-value=21 Score=29.87 Aligned_cols=57 Identities=14% Similarity=0.110 Sum_probs=43.2
Q ss_pred CCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcchhhhc
Q 024428 173 KGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDMQFMV 239 (268)
Q Consensus 173 r~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~~~~~ 239 (268)
...||+.++++|.. +. + .+ ...++|+.+|++...|++|..+++++.++-.....|..
T Consensus 4 ~~~Lt~rqreVL~l-r~-~---Gl-----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl~~~~ 60 (141)
T PRK03975 4 ESFLTERQIEVLRL-RE-R---GL-----TQQEIADILGTSRANVSSIEKRARENIEKARETLAFAE 60 (141)
T ss_pred ccCCCHHHHHHHHH-HH-c---CC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999876 33 2 22 23489999999999999999999999887665554443
No 55
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=49.90 E-value=30 Score=27.65 Aligned_cols=48 Identities=10% Similarity=0.155 Sum_probs=31.8
Q ss_pred cCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhh
Q 024428 171 RKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRK 226 (268)
Q Consensus 171 rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~ 226 (268)
+++++++.+.+...-.....+ .+ ....+|+..|++..+|.+|..-.+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~---g~-----sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEP---GM-----TVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcC---CC-----CHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 345667877655443333333 33 2347899999999999999776654
No 56
>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=48.36 E-value=15 Score=26.34 Aligned_cols=20 Identities=25% Similarity=0.523 Sum_probs=17.7
Q ss_pred HHHHHHHHHhCCChhhhhhh
Q 024428 201 SQKLALAESTGLDSKQINNW 220 (268)
Q Consensus 201 ~ek~~La~~tgL~~~QV~nW 220 (268)
-.-..||...|++..||..|
T Consensus 23 i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHH
Confidence 34568999999999999999
No 57
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=46.55 E-value=12 Score=32.16 Aligned_cols=39 Identities=26% Similarity=0.543 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhh
Q 024428 178 KEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQ 216 (268)
Q Consensus 178 k~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~Q 216 (268)
....+..-.|...|.-.|||+-++||.+-|++.||-+..
T Consensus 23 ~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 23 PRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred ccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 334455678999999999999899999999999987754
No 58
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=46.20 E-value=24 Score=28.85 Aligned_cols=48 Identities=27% Similarity=0.215 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
..||..++.++.-.+.+. ++. .++|..+|++...|..+....|++.++
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 458999999887766555 333 378999999999999999999999864
No 59
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=45.81 E-value=24 Score=29.05 Aligned_cols=49 Identities=18% Similarity=0.064 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
..||...++++.-++..+ ++ -.++|..+|++...|.+|..-.|++.++-
T Consensus 107 ~~L~~~~r~v~~l~~~~g----~s-----~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE----LT-----YEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred HhCCHHHHHHHHhHHHhc----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457888999998776655 22 34799999999999999999999998753
No 60
>PF13730 HTH_36: Helix-turn-helix domain
Probab=45.33 E-value=90 Score=20.76 Aligned_cols=48 Identities=17% Similarity=0.270 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHH--HHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 024428 176 LPKEARQQLLDW--WSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227 (268)
Q Consensus 176 lpk~~~~~L~~w--~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R 227 (268)
|+..++.++-.- +.......||+ ...||+.+|++...|..++..-..+
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~~~pS----~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGGCFPS----QETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCCCCcC----HHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 455555544221 22223348888 4579999999999999998765443
No 61
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=45.09 E-value=24 Score=28.88 Aligned_cols=48 Identities=17% Similarity=0.131 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
.||+..++++...+... ++. ..+|+.+|++...|.+|....+++.++-
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 47888888887654433 333 3789999999999999999999998753
No 62
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=44.89 E-value=23 Score=28.91 Aligned_cols=49 Identities=16% Similarity=0.176 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..+.++...+... ++ -..+|+..|++...|.+|..-+|++.++-.
T Consensus 125 ~L~~~~r~i~~l~~~~~----~~-----~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 125 ALPVKQREVFLLRYVEG----LS-----YREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred hCCHHHHHHhhHHHHcC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 37888888876654433 22 347999999999999999999999987543
No 63
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=44.17 E-value=26 Score=29.18 Aligned_cols=47 Identities=13% Similarity=0.185 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.+|+..+.++...+.+. ++ -.++|+.+|++...|.+++..+|++.++
T Consensus 129 ~L~~~~r~i~~l~~~~g----~s-----~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEG----LS-----YKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred hCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 37888888887776654 22 2479999999999999999999998865
No 64
>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=43.64 E-value=37 Score=26.26 Aligned_cols=47 Identities=21% Similarity=0.313 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.+|+..+.++..-+.. .++. ..+|+..|++...|.+|....+++.++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~s~-----~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GLSY-----KEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CCCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4677778777543332 3443 489999999999999999999988764
No 65
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=43.50 E-value=29 Score=29.34 Aligned_cols=51 Identities=22% Similarity=0.206 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
..||+..+.++.-.|.+. ++ -.++|+.+|++...|.+...-.|++.++...
T Consensus 130 ~~L~~~~r~i~~l~~~~g----~s-----~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG----EK-----IEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HhCCHHHHHHHHHHHHcc----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 358999999987655544 22 2479999999999999999999999887543
No 66
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=43.43 E-value=26 Score=29.78 Aligned_cols=48 Identities=10% Similarity=0.010 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
.||+..+.++.-.+... ++ -.++|+.+|++...|.+++...|++.++-
T Consensus 142 ~L~~~~r~vl~l~~~~~----~s-----~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG----LT-----YREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHHcC----CC-----HHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 48898999887665555 22 34799999999999999999999988653
No 67
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=43.28 E-value=27 Score=28.75 Aligned_cols=48 Identities=15% Similarity=0.126 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
..||+..++++.-.+.+. +. -.++|+.+|++...|.++..-.|++.++
T Consensus 111 ~~L~~~~r~v~~l~~~~g----~s-----~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 111 NLLSADQREAIILIGASG----FS-----YEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred HhCCHHHHHHHHHHHHcC----CC-----HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 348888999887766655 22 2479999999999999999999998864
No 68
>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=42.85 E-value=29 Score=28.81 Aligned_cols=47 Identities=9% Similarity=0.006 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++.-.+.+. ++ -.++|+.+|++...|.+.+..+|++.++
T Consensus 134 ~Lp~~~r~v~~l~~~~g----~s-----~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG----LT-----VEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred cCCHHHHHHHHHHHHcC----CC-----HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 38999999887776655 22 2479999999999999999999998764
No 69
>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=42.80 E-value=35 Score=27.23 Aligned_cols=47 Identities=21% Similarity=0.230 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||...++++...+... ++- .++|+.+|++...|.++....|++.++
T Consensus 113 ~L~~~~r~il~l~~~~~----~~~-----~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG----KSY-----KEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 47888888887654433 333 358999999999999999999998764
No 70
>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=42.72 E-value=21 Score=29.73 Aligned_cols=49 Identities=10% Similarity=0.010 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..++++.-.+..+ ++ -.++|+.+|++...|.++.-..|++.++-.
T Consensus 138 ~L~~~~r~v~~l~~~~~----~s-----~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG----LS-----YEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC----CC-----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 36777888876554443 22 347999999999999999999999987543
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=42.72 E-value=43 Score=27.00 Aligned_cols=48 Identities=25% Similarity=0.254 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
..||+..++++..-+... ++. .++|+.+|++...|.++....|++.++
T Consensus 110 ~~L~~~~r~v~~l~~~~g----~~~-----~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG----VSL-----TALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcC----CCH-----HHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 348888888887755443 333 479999999999999999999988764
No 72
>PRK06930 positive control sigma-like factor; Validated
Probab=42.54 E-value=22 Score=30.45 Aligned_cols=57 Identities=9% Similarity=0.115 Sum_probs=43.4
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcchhhhc
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDMQFMV 239 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~~~~~ 239 (268)
..||+..+.++.-.+.+. ++ -..+|..+|++...|.+++..+|++.++-.....||+
T Consensus 113 ~~L~~rer~V~~L~~~eg----~s-----~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~l~~~ 169 (170)
T PRK06930 113 SVLTEREKEVYLMHRGYG----LS-----YSEIADYLNIKKSTVQSMIERAEKKIARQINESLFCM 169 (170)
T ss_pred HhCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 358888888887654433 22 3478999999999999999999999987666655654
No 73
>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=42.27 E-value=22 Score=23.66 Aligned_cols=21 Identities=24% Similarity=0.241 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 024428 203 KLALAESTGLDSKQINNWFIN 223 (268)
Q Consensus 203 k~~La~~tgL~~~QV~nWF~N 223 (268)
...||+.+|++...|+.|..+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHhCCCcchhHHHhcC
Confidence 468999999999999999998
No 74
>cd00131 PAX Paired Box domain
Probab=40.80 E-value=1e+02 Score=25.01 Aligned_cols=46 Identities=15% Similarity=0.099 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCC-------Chhhhhhhhhhh
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGL-------DSKQINNWFINQ 224 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL-------~~~QV~nWF~N~ 224 (268)
.........+..+..+| |.-|..+-+..|+ ..|+ +..+|+.||.++
T Consensus 75 ~~~~~~~~~i~~~v~~~---p~~Tl~El~~~L~-~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQEN---PGMFAWEIRDRLL-QEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHC---CCCCHHHHHHHHH-HcCCcccCCCCCHHHHHHHHHhc
Confidence 34445556566677777 9999445555556 4466 999999998764
No 75
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=40.57 E-value=36 Score=28.16 Aligned_cols=47 Identities=19% Similarity=0.319 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~ 229 (268)
..||+..+.++.-.+.+. ++. .++|+.+|++..-|.++...++++.+
T Consensus 118 ~~Lp~~~r~v~~L~~~~g----~s~-----~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDG----MGH-----AEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred HhCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 348888888887665544 222 36999999999999999999999875
No 76
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=39.75 E-value=32 Score=29.67 Aligned_cols=49 Identities=10% Similarity=0.080 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..+.++..-+... +. -.++|+.+|++...|.+++..+|++.++-.
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 48888899887655544 22 347999999999999999999999876543
No 77
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=38.80 E-value=36 Score=28.59 Aligned_cols=49 Identities=16% Similarity=0.070 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
..||+..+.++..-+... + .-.++|..+|++...|.++...+|++.++.
T Consensus 138 ~~L~~~~r~i~~l~~~~g----~-----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 138 DTLPEKQREILILRVVVG----L-----SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HhCCHHHHHHHHHHHHcC----C-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 348888888887655544 1 234799999999999999999999988753
No 78
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=38.73 E-value=82 Score=20.21 Aligned_cols=46 Identities=17% Similarity=0.198 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.++....+++..+ . . .+ ....+|+.+|++...|..|....+++..-
T Consensus 3 ~l~~~e~~i~~~~-~-~---g~-----s~~eia~~l~is~~tv~~~~~~~~~kl~~ 48 (58)
T smart00421 3 SLTPREREVLRLL-A-E---GL-----TNKEIAERLGISEKTVKTHLSNIMRKLGV 48 (58)
T ss_pred CCCHHHHHHHHHH-H-c---CC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 4677777776443 2 2 22 23578999999999999999988877653
No 79
>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=38.59 E-value=59 Score=22.16 Aligned_cols=48 Identities=15% Similarity=0.063 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.|++....+|.-+..-. .-.++|...|++++.|.++..+.++|..-..
T Consensus 3 ~LT~~E~~vl~~l~~G~----------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM----------SNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-----------HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHHhcC----------CcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 36667777776654432 3357899999999999999999999976443
No 80
>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=38.32 E-value=35 Score=27.76 Aligned_cols=47 Identities=15% Similarity=0.263 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++...+... ++. .++|..+|++...|.++....|++.++
T Consensus 110 ~L~~~~r~i~~l~~~~g----~s~-----~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 110 RLPARQRAVVVLRYYED----LSE-----AQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred hCCHHHHHHhhhHHHhc----CCH-----HHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 47888888886655444 333 378999999999999999999998875
No 81
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=38.15 E-value=29 Score=22.76 Aligned_cols=23 Identities=17% Similarity=0.404 Sum_probs=16.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 024428 203 KLALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 203 k~~La~~tgL~~~QV~nWF~N~R 225 (268)
...+|+.+|++...|.+|....+
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 35799999999999999976554
No 82
>PF14978 MRP-63: Mitochondrial ribosome protein 63
Probab=37.62 E-value=1e+02 Score=23.98 Aligned_cols=55 Identities=18% Similarity=0.460 Sum_probs=34.5
Q ss_pred hccCCCCCCHHHHHHHH---------HHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 024428 169 KKRKKGKLPKEARQQLL---------DWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRH 228 (268)
Q Consensus 169 k~rkr~~lpk~~~~~L~---------~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~ 228 (268)
|.|+-++++...++.+. ..|.. +||-| .+|=.-.|...+- .++...|+.-++.+.
T Consensus 8 KhR~~r~vt~~~k~~~~~~le~E~eN~~~Ls---~PYLT-~EQE~gh~~e~r~-~k~~~~~~~~~~~~k 71 (91)
T PF14978_consen 8 KHRRPRKVTWQMKENMIRRLEIEEENMYWLS---RPYLT-AEQEYGHAKERRK-EKAFFEWIKEKKRSK 71 (91)
T ss_pred cCCCcCCCCHHHHHHHHHHHHHHHHHHHHHc---CCccc-HHHHcchHHHHhH-HHHHHHHHHHHHHcc
Confidence 45555666665554443 33444 49999 7776666666665 667777777665443
No 83
>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=37.59 E-value=20 Score=23.61 Aligned_cols=21 Identities=10% Similarity=0.262 Sum_probs=19.0
Q ss_pred HHHHHhCCChhhhhhhhhhhh
Q 024428 205 ALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 205 ~La~~tgL~~~QV~nWF~N~R 225 (268)
.||+.+|++...|+.|+.+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 84
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=37.59 E-value=41 Score=22.07 Aligned_cols=40 Identities=15% Similarity=0.147 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhh
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFI 222 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~ 222 (268)
..|+.+.+..+..|+.+. .-...+|+..|.+..-|.+|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G---------~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG---------MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS------------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC---------CCHHHHHHHHCcCcHHHHHHHh
Confidence 457777888888886544 2344699999999999999875
No 85
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=37.41 E-value=78 Score=22.74 Aligned_cols=43 Identities=19% Similarity=0.416 Sum_probs=27.2
Q ss_pred CCCHHHHHHH---HHHHHhccCCCCCCcHHHHHHHHHHhCCC-hhhhhhhhhh
Q 024428 175 KLPKEARQQL---LDWWSKHYKWPYPSQESQKLALAESTGLD-SKQINNWFIN 223 (268)
Q Consensus 175 ~lpk~~~~~L---~~w~~~h~~~PYPs~~~ek~~La~~tgL~-~~QV~nWF~N 223 (268)
.|++.+.++| .+++.+| .||. .-.+||+.+|+. ..-|..-..-
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~---G~~P---t~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEEN---GYPP---TVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHH---SS------HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHc---CCCC---CHHHHHHHhCCCChHHHHHHHHH
Confidence 3566666666 5777777 8888 677999999997 7777655443
No 86
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=37.12 E-value=40 Score=28.48 Aligned_cols=48 Identities=17% Similarity=0.068 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
..||..++.++.-.+.+. ++ -.++|+.+|++...|.++..-+|++.++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g----~s-----~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLG----LS-----YADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 358888999887665555 22 2479999999999999999999999886
No 87
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=37.10 E-value=53 Score=26.72 Aligned_cols=47 Identities=21% Similarity=0.339 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
.||...+.+|.-.+ + .++. ..+|...|++...|.++....|++.++-
T Consensus 112 ~L~~~~r~il~l~~-~----g~s~-----~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF-S----GYSY-----KEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH-c----CCCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888886655 3 3444 4799999999999999999999988753
No 88
>PRK10072 putative transcriptional regulator; Provisional
Probab=36.72 E-value=27 Score=27.23 Aligned_cols=23 Identities=13% Similarity=0.229 Sum_probs=20.1
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 024428 203 KLALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 203 k~~La~~tgL~~~QV~nWF~N~R 225 (268)
...||+.+|++...|++|...+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45899999999999999988764
No 89
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=36.62 E-value=1.1e+02 Score=24.49 Aligned_cols=41 Identities=20% Similarity=0.373 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhh
Q 024428 179 EARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQ 224 (268)
Q Consensus 179 ~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~ 224 (268)
.....+.+|...|+..| ++ -..||+.+|+++.++..+|...
T Consensus 9 ~~i~~~~~~I~~~~~~~-~s----l~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 9 ITIHSILDWIEDNLESP-LS----LEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHhcCCC-CC----HHHHHHHHCcCHHHHHHHHHHH
Confidence 34566778999996655 44 4578899999999998888754
No 90
>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=36.52 E-value=28 Score=22.98 Aligned_cols=22 Identities=18% Similarity=0.166 Sum_probs=19.2
Q ss_pred HHHHHHhCCChhhhhhhhhhhh
Q 024428 204 LALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 204 ~~La~~tgL~~~QV~nWF~N~R 225 (268)
..||..+|++...|+.|..+.+
T Consensus 19 ~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 19 ADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHhCCCHHHHHHHHCCCC
Confidence 5799999999999999987653
No 91
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=36.10 E-value=45 Score=26.90 Aligned_cols=50 Identities=16% Similarity=0.154 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
..||+..+.++.-.+.+. ++- .++|..+|++...|.+...-.|++.++-.
T Consensus 105 ~~Lp~~~r~v~~l~~~~g----~s~-----~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWED----MDV-----AETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHhc----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 458999999887765554 222 47999999999999999999999987544
No 92
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=35.46 E-value=38 Score=28.93 Aligned_cols=49 Identities=20% Similarity=0.188 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..++++.-.+.+. ++. .++|...|++...|.+++.-.|++.++-.
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 48888999987766544 333 37899999999999999999999987533
No 93
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=35.29 E-value=32 Score=29.20 Aligned_cols=50 Identities=6% Similarity=0.066 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||...+.++.-.+.+. ++ -.++|..+|++...|.++..-+|++.++-..
T Consensus 134 ~Lp~~~R~v~~L~~~~g----~s-----~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 134 HLPAQQARVFMMREYLE----LS-----SEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred hCCHHHHHHHhHHHHcC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887765554 22 3479999999999999999999999876544
No 94
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=35.06 E-value=39 Score=28.30 Aligned_cols=48 Identities=10% Similarity=0.216 Sum_probs=37.1
Q ss_pred CCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 176 LPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 176 lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
||+..+.++..-+... ++. .++|+.+|++...|.++...+|++.++-.
T Consensus 129 L~~~~r~i~~l~~~~g----~s~-----~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 129 LPERQREAIVLQYYQG----LSN-----IEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHhhHHHhcC----CCH-----HHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 6788888886654444 222 37999999999999999999999987633
No 95
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=35.05 E-value=42 Score=28.52 Aligned_cols=50 Identities=18% Similarity=0.195 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||...+.++.-.+.+. ++. .++|+.+|++...|.++....|++.++-..
T Consensus 116 ~Lp~~~r~i~~L~~~~g----~s~-----~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGASG----FAY-----EEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47888888887665544 333 378999999999999999999999876443
No 96
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=34.84 E-value=43 Score=28.48 Aligned_cols=49 Identities=12% Similarity=0.127 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..+.++.-.+.+. |+- .++|+.+|++...|.+++.-+|++.++-.
T Consensus 136 ~L~~~~r~i~~L~~~~g----~s~-----~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIEG----LSN-----PEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58888888886654433 333 37999999999999999999999987543
No 97
>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=34.81 E-value=35 Score=21.22 Aligned_cols=23 Identities=26% Similarity=0.286 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 024428 203 KLALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 203 k~~La~~tgL~~~QV~nWF~N~R 225 (268)
...+|+.+|++...|++|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35899999999999999988763
No 98
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=34.81 E-value=45 Score=27.37 Aligned_cols=48 Identities=10% Similarity=0.113 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
.+|...++++..-+... ++ -..+|+.+|++...|.++..-.|++.++-
T Consensus 119 ~L~~~~r~i~~l~~~~g----~s-----~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----LT-----IKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888886665544 22 23789999999999999999999987653
No 99
>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=34.44 E-value=18 Score=30.62 Aligned_cols=50 Identities=22% Similarity=0.146 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||+..+.++.-.+.+. ++ -.++|+.+|++...|.++..-+|++.++-..
T Consensus 131 ~Lp~~~r~i~~L~~~~g----~s-----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEG----FA-----YKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehhhcC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47777777775544433 22 3479999999999999999999999987554
No 100
>PHA02510 X gene X product; Reviewed
Probab=34.35 E-value=67 Score=26.14 Aligned_cols=61 Identities=15% Similarity=0.339 Sum_probs=42.0
Q ss_pred HHHHHHHHhhhhhcchhhhhHHhhhccCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHH-----------HHhCCC
Q 024428 145 DQELKGQLLRRYSGCLSSLKQEFMKKRKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALA-----------ESTGLD 213 (268)
Q Consensus 145 ~~el~~~l~~~~~~~~~~~~~~~~k~rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La-----------~~tgL~ 213 (268)
|.++...|..+|..+ .++|++|..-...|..|+...-...|-. -|..+. ...|++
T Consensus 6 d~~v~~~l~~~~~t~-----------t~~G~~s~aka~~~f~~y~~l~~~g~~~---vk~~l~k~tFyrhr~~L~~iGId 71 (116)
T PHA02510 6 DSQVIDAIINKFFSI-----------TKSGNLSSAKAMRYFGFYRRLVNEGYDN---VADTMSRATFWRHRKVLKEFGID 71 (116)
T ss_pred HHHHHHHHHhhheee-----------CCCCCcCHHHHHHHHHHHHhhhhhhHHH---HHHHccHHHHHHHHHHHHHcCCC
Confidence 566777777777766 6789999988999999998775444422 222222 245888
Q ss_pred hhhhhh
Q 024428 214 SKQINN 219 (268)
Q Consensus 214 ~~QV~n 219 (268)
..|+.|
T Consensus 72 ia~l~n 77 (116)
T PHA02510 72 KAQLMN 77 (116)
T ss_pred hhhccc
Confidence 888777
No 101
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=34.32 E-value=47 Score=27.99 Aligned_cols=49 Identities=8% Similarity=0.037 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+.++.++.-.+.+. ++- .++|..+|++..-|.+.....|++.++-.
T Consensus 131 ~Lp~~~r~v~~l~~~~g----~s~-----~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE----LET-----EEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887665554 232 37999999999999999999999987643
No 102
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.02 E-value=82 Score=26.23 Aligned_cols=42 Identities=26% Similarity=0.433 Sum_probs=35.2
Q ss_pred chHhHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhhhhh
Q 024428 68 PALDQFMEAYCEMLTKYEQELSKPFKEAMSFLQKIESQFKSL 109 (268)
Q Consensus 68 pELDqfM~~Y~~~L~ky~eeL~k~~~EA~~f~~~ie~QL~~L 109 (268)
..|..=|+..-.-|..|++||.++|.+.++.++++-+-...|
T Consensus 37 ~~~q~ELe~~K~~ld~~rqel~~HFa~sAeLlktl~~dYqkl 78 (138)
T COG3105 37 QKLQYELEKVKAQLDEYRQELVKHFARSAELLKTLAQDYQKL 78 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667788888999999999999999999999987766554
No 103
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=33.69 E-value=41 Score=28.07 Aligned_cols=49 Identities=8% Similarity=-0.063 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..+.++...+.+. + .-.++|+.+|++...|.+++..+|++.++-.
T Consensus 131 ~L~~~~r~v~~l~~~~g----~-----s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG----A-----SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC----C-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58888999988765554 1 2347999999999999999999999987543
No 104
>PRK11677 hypothetical protein; Provisional
Probab=33.59 E-value=1.1e+02 Score=25.50 Aligned_cols=42 Identities=26% Similarity=0.422 Sum_probs=34.8
Q ss_pred chHhHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhhhhh
Q 024428 68 PALDQFMEAYCEMLTKYEQELSKPFKEAMSFLQKIESQFKSL 109 (268)
Q Consensus 68 pELDqfM~~Y~~~L~ky~eeL~k~~~EA~~f~~~ie~QL~~L 109 (268)
.+|.+=.++.-..|..|++++..+|.+....+.+|....+.|
T Consensus 32 ~~le~eLe~~k~ele~YkqeV~~HFa~TA~Ll~~L~~~Y~~L 73 (134)
T PRK11677 32 QALQYELEKNKAELEEYRQELVSHFARSAELLDTMAKDYRQL 73 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457777777888899999999999999999888887766654
No 105
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=33.16 E-value=47 Score=28.11 Aligned_cols=50 Identities=8% Similarity=0.090 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||+..+.++.-.+.+. +. -.++|+.+|++...|.++...+|++.++-..
T Consensus 136 ~L~~~~r~i~~L~~~~g----~s-----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEILG----FS-----SDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHHhC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887654444 22 3479999999999999999999999887554
No 106
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=32.77 E-value=51 Score=27.46 Aligned_cols=47 Identities=17% Similarity=0.138 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++.-.+... +. -.++|+..|++...|.++...+|++.++
T Consensus 135 ~L~~~~r~vl~l~~~~~----~s-----~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG----YT-----HREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred hCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 38888999887665544 22 2479999999999999999999998764
No 107
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=32.64 E-value=50 Score=27.99 Aligned_cols=49 Identities=16% Similarity=0.228 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
..||+..+.++.-.+.+. ++ -.++|+.+|++...|.+.+..+|++.++-
T Consensus 140 ~~Lp~~~r~v~~l~~~eg----~s-----~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE----LP-----HQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred HhCCHHHHHHHHHHHHcC----CC-----HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 458888999987655544 22 23799999999999999999999988753
No 108
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=32.28 E-value=50 Score=27.64 Aligned_cols=49 Identities=16% Similarity=0.123 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..+.++.-.+... ++ -.++|+.+|++...|.+....+|++.++-.
T Consensus 122 ~L~~~~r~i~~l~~~~g----~s-----~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN----LT-----YQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888999887654444 22 237999999999999999999999887543
No 109
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=32.20 E-value=67 Score=26.11 Aligned_cols=46 Identities=13% Similarity=0.133 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRH 228 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~ 228 (268)
..||+.++.++.-.+.+. ++- .++|..+|++...|.++...++++.
T Consensus 112 ~~L~~~~r~v~~L~~~~g----~s~-----~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVDG----LGY-----GEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HHCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 348888999887665544 233 3799999999999999999998875
No 110
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=32.06 E-value=54 Score=27.44 Aligned_cols=47 Identities=15% Similarity=0.244 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++..-+.+. ++ -.++|+.+|++...|.+|...+|++.++
T Consensus 133 ~L~~~~r~i~~l~~~~~----~s-----~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 133 QLEPARRNCILHAYVDG----CS-----HAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 47888888776555444 22 3479999999999999999999988764
No 111
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=31.34 E-value=39 Score=23.57 Aligned_cols=18 Identities=11% Similarity=0.209 Sum_probs=16.2
Q ss_pred HHHHHHhCCChhhhhhhh
Q 024428 204 LALAESTGLDSKQINNWF 221 (268)
Q Consensus 204 ~~La~~tgL~~~QV~nWF 221 (268)
.++|+.+|++..+|..|-
T Consensus 4 ~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 478999999999999993
No 112
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=31.32 E-value=1.2e+02 Score=24.60 Aligned_cols=42 Identities=24% Similarity=0.475 Sum_probs=34.1
Q ss_pred chHhHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhhhhh
Q 024428 68 PALDQFMEAYCEMLTKYEQELSKPFKEAMSFLQKIESQFKSL 109 (268)
Q Consensus 68 pELDqfM~~Y~~~L~ky~eeL~k~~~EA~~f~~~ie~QL~~L 109 (268)
.+|.+=.++--..|..|++++..+|..+...+..|....+.|
T Consensus 28 ~~l~~eL~~~k~el~~yk~~V~~HF~~ta~Ll~~l~~~Y~~l 69 (128)
T PF06295_consen 28 AKLEQELEQAKQELEQYKQEVNDHFAQTAELLDNLTQDYQKL 69 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355666667778899999999999999999999888766654
No 113
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=31.18 E-value=41 Score=28.32 Aligned_cols=47 Identities=15% Similarity=0.138 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++.--+... ++ -.++|+.+|++...|.+|+..+|++.++
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 47888888876554443 22 3479999999999999999999998865
No 114
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=31.02 E-value=62 Score=28.47 Aligned_cols=51 Identities=18% Similarity=0.111 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSED 234 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~ 234 (268)
.||...+.++.-.+.++ |+. .++|+.+|++...|.++....|++.++-.++
T Consensus 134 ~Lp~~~R~v~~L~y~eg----~s~-----~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~ 184 (216)
T PRK12533 134 KLPVEYREVLVLRELED----MSY-----REIAAIADVPVGTVMSRLARARRRLAALLGG 184 (216)
T ss_pred cCCHHHHhHhhhHHhcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 58888999998877766 343 3789999999999999999999999875544
No 115
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.96 E-value=57 Score=27.24 Aligned_cols=48 Identities=17% Similarity=0.106 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
.||+..+.++.-.+.+. ++ -.++|+.+|++...|.+.+..+|++.++-
T Consensus 129 ~L~~~~r~v~~l~~~~g----~s-----~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG----LS-----VAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 37888888776655544 22 34799999999999999999999998763
No 116
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=30.63 E-value=76 Score=26.29 Aligned_cols=50 Identities=22% Similarity=0.166 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||+..+.++.-.+.+. ++. .++|+.+|++...|.++..-.|++.++-..
T Consensus 100 ~L~~~~r~v~~l~~~~g----~s~-----~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG----LSQ-----QEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887766555 333 479999999999999999999999876443
No 117
>PF13551 HTH_29: Winged helix-turn helix
Probab=30.44 E-value=2.3e+02 Score=21.11 Aligned_cols=46 Identities=17% Similarity=0.137 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHHhccCCC--CCCcHHHHHH-H-HHHh--CCChhhhhhhhh
Q 024428 176 LPKEARQQLLDWWSKHYKWP--YPSQESQKLA-L-AEST--GLDSKQINNWFI 222 (268)
Q Consensus 176 lpk~~~~~L~~w~~~h~~~P--YPs~~~ek~~-L-a~~t--gL~~~QV~nWF~ 222 (268)
++.+..+.|.+++.++.... ..+ ...-.. | .+.+ .++...|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t-~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWT-LEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCccc-HHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 89999999999999982211 233 222222 4 3333 478888888874
No 118
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=30.26 E-value=45 Score=20.50 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=18.6
Q ss_pred HHHHHHHhCCChhhhhhhhhhh
Q 024428 203 KLALAESTGLDSKQINNWFINQ 224 (268)
Q Consensus 203 k~~La~~tgL~~~QV~nWF~N~ 224 (268)
...+|+.+|++..+|+.|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4489999999999999997654
No 119
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=30.07 E-value=56 Score=29.17 Aligned_cols=47 Identities=9% Similarity=0.104 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.+|...|... + .-.++|+.+|++...|.+|....+++.++
T Consensus 205 ~L~~~~r~vl~l~~~~g----~-----s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----L-----SQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred hCCHHHHHHHHHHHhCC----C-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 48888999988766544 1 23579999999999999999999998764
No 120
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=29.86 E-value=48 Score=23.67 Aligned_cols=20 Identities=20% Similarity=0.335 Sum_probs=11.7
Q ss_pred HHHHHhCCChhhhhhhhhhh
Q 024428 205 ALAESTGLDSKQINNWFINQ 224 (268)
Q Consensus 205 ~La~~tgL~~~QV~nWF~N~ 224 (268)
.||+.+|++...|+.|..+.
T Consensus 23 ~lA~~~gis~~tis~~~~g~ 42 (78)
T TIGR02607 23 ALAKALGVSRSTLSRIVNGR 42 (78)
T ss_pred HHHHHhCCCHHHHHHHHcCC
Confidence 46666666666666665443
No 121
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=29.45 E-value=54 Score=27.20 Aligned_cols=47 Identities=15% Similarity=0.151 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++..-+.+. ++. .++|+.+|++...|.+++...|++.++
T Consensus 136 ~L~~~~r~v~~l~~~~g----~s~-----~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED----LSL-----KEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHhHHhhhHHhcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47888888886644433 333 478999999999999999999998764
No 122
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=29.37 E-value=63 Score=26.55 Aligned_cols=50 Identities=12% Similarity=0.197 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||+..+.++.--+.+. ++. .++|+.+|++...|.+...-+|++.++-.+
T Consensus 118 ~L~~~~r~vl~L~~~~g----~s~-----~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRG----WST-----AQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 48888999887765554 333 379999999999999999999999876443
No 123
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=29.36 E-value=63 Score=27.70 Aligned_cols=54 Identities=19% Similarity=0.123 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcchh
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDMQ 236 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~~ 236 (268)
..||+..+.++.--+.+. + .-.++|+.+|++...|.++...+|++.++-....+
T Consensus 132 ~~Lp~~~r~v~~l~~~~g----~-----s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 132 DALPPERREALILTQVLG----Y-----TYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred HcCCHHHHHHhhhHHHhC----C-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 348888888886666555 2 23479999999999999999999999987665533
No 124
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=29.19 E-value=53 Score=28.92 Aligned_cols=47 Identities=13% Similarity=0.206 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++..-|... -.-.++|+.+|++...|.++...+|++.++
T Consensus 184 ~L~~~~r~vl~l~~~~g---------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE---------LNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred hCCHHHHHHHHhHhccC---------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 37888888887665443 123589999999999999999999999865
No 125
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=29.14 E-value=72 Score=26.60 Aligned_cols=43 Identities=19% Similarity=0.261 Sum_probs=31.7
Q ss_pred HHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 183 QLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 183 ~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
..++++..| |-+. ..-.++++.||.+.++|..|..--|--.+.
T Consensus 34 kV~~yLr~~---p~~~--ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 34 KVYKFLRKH---ENRQ--ATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred HHHHHHHHC---CCCC--CCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 445666666 6533 456789999999999999998776665543
No 126
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=28.94 E-value=67 Score=26.78 Aligned_cols=49 Identities=16% Similarity=0.165 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..+.++.--+.++ -+ -.++|+.+|++...|.+.....|++.++-.
T Consensus 117 ~Lp~~~r~i~~l~~~e~-----~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD-----YS----QEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHHHHcc-----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888888887765555 12 347999999999999999999999987644
No 127
>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=28.92 E-value=60 Score=29.18 Aligned_cols=51 Identities=12% Similarity=0.213 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSED 234 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~ 234 (268)
.||...+.++.-.+.+. ++ -.++|..+|++...|.++...+|++.++-...
T Consensus 161 ~Lp~~~R~v~~L~~~eg----~S-----~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~ 211 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG----LS-----MDRIGAMYQVHRSTVSRWVAQARERLLERTRR 211 (244)
T ss_pred hCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887766655 22 34799999999999999999999999876544
No 128
>PHA01976 helix-turn-helix protein
Probab=28.74 E-value=48 Score=23.00 Aligned_cols=22 Identities=14% Similarity=0.259 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChhhhhhhhhhh
Q 024428 203 KLALAESTGLDSKQINNWFINQ 224 (268)
Q Consensus 203 k~~La~~tgL~~~QV~nWF~N~ 224 (268)
..+||+.+|++...|++|....
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 3579999999999999998654
No 129
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=28.55 E-value=76 Score=26.74 Aligned_cols=49 Identities=16% Similarity=0.058 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..+.++.-.+.+. +|- .++|...|++...|.+.+..+|++.++-.
T Consensus 106 ~L~~~~r~i~~l~~~~g----~~~-----~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELEG----LSQ-----KEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhcC----CCH-----HHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888886655444 343 47899999999999999999999987644
No 130
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=27.47 E-value=71 Score=25.90 Aligned_cols=49 Identities=14% Similarity=0.128 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
..||+..+.++.--+.+. ++ -.++|+.+|++...|.....-+|++.++-
T Consensus 108 ~~L~~~~r~v~~l~~~~~----~s-----~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 108 SELPARTRYAFEMYRLHG----ET-----QKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred HhCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 348888899887655544 22 34799999999999999999888887653
No 131
>COG1084 Predicted GTPase [General function prediction only]
Probab=27.36 E-value=1.8e+02 Score=28.00 Aligned_cols=83 Identities=16% Similarity=0.310 Sum_probs=40.5
Q ss_pred hCCChHHHHHHHHhchhcCCCh---HHH-hhHHHHHHHHhhcCCCCCCCCCCCc-hHhHHHHHHHHHHHHHHHHhcccHH
Q 024428 19 AHPHYHRLLAAYANCQKVGAPP---EVV-ARLEEVCASAASMGSGGSSCIGQDP-ALDQFMEAYCEMLTKYEQELSKPFK 93 (268)
Q Consensus 19 ~HPlyp~Ll~a~~~C~Kvgap~---e~~-~~ld~~~~~~~~~~~~~~~~~g~dp-ELDqfM~~Y~~~L~ky~eeL~k~~~ 93 (268)
-||+|..|+++.++..+.-..- +-+ ..++++....-.. ...+.|| +..++|.+|-.-+..-...+.
T Consensus 75 LhpFY~eLidvl~d~d~~k~sLs~v~~A~~~i~~l~~eYi~~-----lk~a~~~~~~~~lrR~a~GR~aSiik~i~---- 145 (346)
T COG1084 75 LHPFYRELIDVLVDIDHLKISLSAVSWASKIIEKLAREYIRL-----LKAAKDPKEANQLRRQAFGRVASIIKKID---- 145 (346)
T ss_pred cChHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HhcCCChhHHHHHHHHHHHHHHHHHHHhh----
Confidence 4999999999999873321111 111 1111221111110 1122333 588888887754444433432
Q ss_pred HHHHHHHHHHHhhhhhc
Q 024428 94 EAMSFLQKIESQFKSLS 110 (268)
Q Consensus 94 EA~~f~~~ie~QL~~L~ 110 (268)
....|++..-..|+.|.
T Consensus 146 ~~L~fL~~~r~~l~~LP 162 (346)
T COG1084 146 DDLEFLRKARDHLKKLP 162 (346)
T ss_pred HHHHHHHHHHHHHhcCC
Confidence 23345555555555554
No 132
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=27.25 E-value=1.8e+02 Score=18.70 Aligned_cols=30 Identities=17% Similarity=0.220 Sum_probs=24.4
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 203 KLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 203 k~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
-..+|+.+|++...|..|....+++..-+.
T Consensus 18 ~~eia~~l~~s~~tv~~~~~~~~~~l~~~~ 47 (57)
T cd06170 18 NKEIADILGISEKTVKTHLRNIMRKLGVKS 47 (57)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHhCCCC
Confidence 357889999999999999988777765443
No 133
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=27.09 E-value=1.1e+02 Score=24.60 Aligned_cols=47 Identities=19% Similarity=0.169 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
.||+..+++|.-+ .++ |. ...+|+..+++.+.|.++..|.|++..-.
T Consensus 149 ~lt~~e~~vl~l~-~~g----~~-----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~ 195 (211)
T PRK15369 149 LLTPRERQILKLI-TEG----YT-----NRDIAEQLSISIKTVETHRLNMMRKLDVH 195 (211)
T ss_pred CCCHHHHHHHHHH-HCC----CC-----HHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 4888888998774 443 32 24788899999999999999999997643
No 134
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=27.07 E-value=1e+02 Score=27.04 Aligned_cols=36 Identities=8% Similarity=0.307 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhh
Q 024428 178 KEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWF 221 (268)
Q Consensus 178 k~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF 221 (268)
-.+....+.|+.+| --|- ..++..|||+.+.|+-|+
T Consensus 117 ~~VkeeIK~fl~~h---~IsQ-----~~V~q~TGisQS~lSq~L 152 (180)
T PF04814_consen 117 WRVKEEIKAFLQQH---NISQ-----REVVQVTGISQSHLSQHL 152 (180)
T ss_dssp HHHHHHHHHHHHHC---T--C-----HHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHHHHHHHc---CCcH-----HHHHHHhhhhHHHHHHHH
Confidence 34677888898888 4333 468899999999999997
No 135
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=26.96 E-value=83 Score=26.29 Aligned_cols=47 Identities=9% Similarity=0.054 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+.++.++.-.+.+. ++- .++|..+|++..-|.+.+..++++...
T Consensus 127 ~Lp~~~R~v~~L~~~~g----~s~-----~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG----MKQ-----KDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 48999999887766554 232 479999999999999999998887654
No 136
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=26.69 E-value=90 Score=26.98 Aligned_cols=50 Identities=14% Similarity=0.120 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||+..+.++.--+.+. ++- .++|+.+|++...|.++..-+|++.++-..
T Consensus 138 ~L~~~~r~v~~L~~~~g----~s~-----~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG----LSY-----EEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47777888765544443 333 378999999999999999999999875443
No 137
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.50 E-value=61 Score=20.79 Aligned_cols=19 Identities=21% Similarity=0.221 Sum_probs=16.6
Q ss_pred HHHHHHhCCChhhhhhhhh
Q 024428 204 LALAESTGLDSKQINNWFI 222 (268)
Q Consensus 204 ~~La~~tgL~~~QV~nWF~ 222 (268)
.++|+.+|++...|..|..
T Consensus 4 ~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 4 GELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999953
No 138
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=26.22 E-value=73 Score=27.30 Aligned_cols=50 Identities=10% Similarity=0.074 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||...+.++.--+.+. ++- .++|..+|++...|.+....+|++.++-..
T Consensus 139 ~Lp~~~r~v~~L~~~eg----~s~-----~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD----FEI-----DDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887665554 222 378999999999999999999999876443
No 139
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=26.16 E-value=52 Score=22.58 Aligned_cols=23 Identities=26% Similarity=0.313 Sum_probs=19.4
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 024428 203 KLALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 203 k~~La~~tgL~~~QV~nWF~N~R 225 (268)
...+|+.+|++..+|+.|-.+.|
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHHCcCHHHHHHHHCCCc
Confidence 45799999999999999999855
No 140
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=25.97 E-value=74 Score=26.65 Aligned_cols=47 Identities=13% Similarity=0.082 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++.-.+... + .-.++|+.+|++...|.++....|++.++
T Consensus 131 ~L~~~~r~v~~l~~~~g----~-----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG----L-----SVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHcC----C-----cHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 48999999988655544 2 23479999999999999999999998875
No 141
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=25.71 E-value=67 Score=26.83 Aligned_cols=47 Identities=17% Similarity=0.292 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
+||+..+.++.-.+... ++- .++|..+|++...|.++..-+|++.++
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 48888988876655544 332 479999999999999999999998875
No 142
>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=25.66 E-value=72 Score=28.41 Aligned_cols=47 Identities=9% Similarity=0.097 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||...+.++...|... + | -.++|+.+|++...|+.+...++++.++
T Consensus 205 ~L~~~~r~ii~l~~~~g----~-s----~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN----L-S----QKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC----C-C----HHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 58888999887776544 2 2 2489999999999999999999988764
No 143
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=25.52 E-value=79 Score=28.18 Aligned_cols=47 Identities=9% Similarity=0.112 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++...+.+. -.-..+|..+|++...|.+++..+|++.++
T Consensus 201 ~L~~~~r~vl~l~~~~~---------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLFYKEE---------LTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHHHhcC---------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 37888899887765533 223589999999999999999999998764
No 144
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=25.13 E-value=78 Score=26.79 Aligned_cols=47 Identities=17% Similarity=0.065 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++.-.+.+. ++. .++|..+|++..-|.++..-+|++.++
T Consensus 111 ~Lp~~~R~v~~L~~~eg----~s~-----~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG----LSY-----QEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 48999999998766654 333 478999999999999999999999875
No 145
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=24.76 E-value=80 Score=26.66 Aligned_cols=49 Identities=18% Similarity=0.151 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..+.++.-.+.+. +. -.++|+.+|++...|.....-+|++.++-.
T Consensus 111 ~Lp~~~R~v~~L~~~~g----~s-----~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 111 KLPQDQREALILVGASG----FS-----YEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred hCCHHHHHHhhHHHHcC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888899887765554 22 347999999999999999999999987643
No 146
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=24.69 E-value=59 Score=29.35 Aligned_cols=51 Identities=10% Similarity=0.205 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSED 234 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~ 234 (268)
.||+..+.++...|.+. ..-.++|..+|++...|......++++.++-..+
T Consensus 212 ~L~~~~r~vl~l~~~~~---------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 212 TLPEREKKVLILYYYED---------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred hCCHHHHHHHHHHHHcC---------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 48888899887776544 2245899999999999999999999988765443
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=24.54 E-value=1.4e+02 Score=25.95 Aligned_cols=47 Identities=19% Similarity=0.309 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++...+... ..-.++|+.+|++...|..|....+++.++
T Consensus 178 ~L~~~~r~vl~l~y~~~---------~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFED---------KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhcC---------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 58898999987766543 134579999999999999999999988764
No 148
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.50 E-value=1.6e+02 Score=22.88 Aligned_cols=49 Identities=16% Similarity=0.264 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCC-ChhhhhhhhhhhhhhcC
Q 024428 173 KGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGL-DSKQINNWFINQRKRHW 229 (268)
Q Consensus 173 r~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL-~~~QV~nWF~N~R~R~~ 229 (268)
++++|.+-+..+-+-..+. ......+|+..|+ +..++..|.+..+....
T Consensus 5 ~r~~s~EfK~~iv~~~~~~--------g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~ 54 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRG--------GDTVSEVAREFGIVSATQLYKWRIQLQKGGG 54 (116)
T ss_pred cccCCHHHHHHHHHHHHhc--------CccHHHHHHHhCCCChHHHHHHHHHHHHccc
Confidence 6778888766554444433 2346789999996 99999999998888763
No 149
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.48 E-value=1.4e+02 Score=25.01 Aligned_cols=48 Identities=15% Similarity=0.147 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
.||+..+.+|.--+.+. ++ -.++|+..|++...|.+-+..+|++.++-
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 48888999986655544 22 34799999999999999999999988753
No 150
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=24.00 E-value=1e+02 Score=28.88 Aligned_cols=53 Identities=25% Similarity=0.446 Sum_probs=38.6
Q ss_pred cCCCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 024428 171 RKKGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227 (268)
Q Consensus 171 rkr~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R 227 (268)
.+|+.|+....+-|-.+|..| ..|||- .-++ |-..||-..+++.+|=++-++-
T Consensus 206 e~R~~L~~~lA~wLh~yyaSH-~~P~P~-kvet--l~~lcGS~~~~l~~FR~~Lk~A 258 (282)
T PF07042_consen 206 EQRRKLSPRLAKWLHGYYASH-KKPYPI-KVET--LRELCGSESSRLRKFRQQLKKA 258 (282)
T ss_pred HHHhhcCcHHHHHHHHHHhcC-CCCCCc-cHHH--HHHHcCCCccCHHHHHHHHHHH
Confidence 344556555567788999999 579999 6664 4556899888999997765543
No 151
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=23.96 E-value=86 Score=27.85 Aligned_cols=49 Identities=12% Similarity=0.192 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||...+.++.-.+.+. ++ -.++|+.+|++...|.++....|++.++-.
T Consensus 171 ~Lp~~~R~v~~L~~~eg----~s-----~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN----MS-----NGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHhcC----CC-----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 47888888876555444 22 247999999999999999999999987643
No 152
>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=23.91 E-value=56 Score=20.11 Aligned_cols=20 Identities=30% Similarity=0.561 Sum_probs=15.9
Q ss_pred HHHHHhhCCChHHHHHHHHh
Q 024428 13 VKAKIMAHPHYHRLLAAYAN 32 (268)
Q Consensus 13 ~K~~I~~HPlyp~Ll~a~~~ 32 (268)
+-.+|.+.|||..|+.|.-.
T Consensus 5 lipkiissplfktllsavgs 24 (33)
T PF07425_consen 5 LIPKIISSPLFKTLLSAVGS 24 (33)
T ss_dssp CHHHHCCTTTCHHHHHHHHH
T ss_pred hhhHHHccHHHHHHHHHHHH
Confidence 44689999999999987543
No 153
>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=23.56 E-value=1e+02 Score=22.51 Aligned_cols=23 Identities=35% Similarity=0.497 Sum_probs=17.4
Q ss_pred CCCchHhHHHHHHHHHHHHHHHH
Q 024428 65 GQDPALDQFMEAYCEMLTKYEQE 87 (268)
Q Consensus 65 g~dpELDqfM~~Y~~~L~ky~ee 87 (268)
|-|++||..+..|..+.....+.
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~ 23 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEEL 23 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHH
Confidence 45899999999988776655444
No 154
>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=23.44 E-value=92 Score=27.09 Aligned_cols=47 Identities=13% Similarity=0.180 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||...+.++...|.+. + .-.++|..+|++...|..+...++++.++
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 48899999998876544 1 23589999999999999999999988764
No 155
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=23.31 E-value=77 Score=27.76 Aligned_cols=52 Identities=19% Similarity=0.128 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
.||+..+.++.--+.-+. -. .-.-.++|..+|++...|.++...+|++.++-
T Consensus 178 ~Lp~~~R~v~~L~y~l~~----~e-g~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGLNG----GE-EKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhccCC----CC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 488888888866542110 01 22345799999999999999999999988753
No 156
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=23.28 E-value=88 Score=25.88 Aligned_cols=48 Identities=15% Similarity=0.176 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
.||...+.++.--+... ++ -.++|+.+|++...|.+.....|++.++-
T Consensus 136 ~L~~~~r~il~l~~~~~----~s-----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 136 QLPEKYRTVIVLKYIED----LS-----LKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHHHHhhhHHhhC----CC-----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 36777788775433322 23 34799999999999999999999988653
No 157
>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=23.26 E-value=1.7e+02 Score=25.03 Aligned_cols=44 Identities=20% Similarity=0.357 Sum_probs=29.4
Q ss_pred HHHHHHHHHhhhhhcchhhhhHHhhhccCCCCCCHHHHHHHHHH
Q 024428 144 EDQELKGQLLRRYSGCLSSLKQEFMKKRKKGKLPKEARQQLLDW 187 (268)
Q Consensus 144 ~~~el~~~l~~~~~~~~~~~~~~~~k~rkr~~lpk~~~~~L~~w 187 (268)
.-+.|-....+.+..+-.-+...-.-+|++..++..+...|.+|
T Consensus 55 ~L~~LAa~cV~~~d~fRAPls~aelaRR~~~~Ls~~Q~~~L~rW 98 (160)
T PF06299_consen 55 ALQALAAACVRAFDPFRAPLSEAELARRRPAGLSPRQRANLERW 98 (160)
T ss_pred HHHHHHHHHHHhhhhccCCCChHHHhhcCcccCCHHHHHHHHHh
Confidence 33455555556555544434344446777888999999999999
No 158
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=23.04 E-value=70 Score=20.47 Aligned_cols=18 Identities=11% Similarity=0.215 Sum_probs=14.8
Q ss_pred HHHHHHhCCChhhhhhhh
Q 024428 204 LALAESTGLDSKQINNWF 221 (268)
Q Consensus 204 ~~La~~tgL~~~QV~nWF 221 (268)
-++|+.+|++.+.|..|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 368999999999999994
No 159
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=22.71 E-value=1.5e+02 Score=24.29 Aligned_cols=47 Identities=17% Similarity=0.248 Sum_probs=36.8
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~ 229 (268)
..||+..+.++.-.+.+. ++. .++|+.+|++...|.++..++++..+
T Consensus 117 ~~L~~~~r~v~~L~~~eg----~s~-----~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEG----LTY-----VEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HhCCHHHHHHHHHHHHcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 458888888887665555 333 37899999999999999998888754
No 160
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=22.60 E-value=1.1e+02 Score=25.64 Aligned_cols=48 Identities=15% Similarity=0.042 Sum_probs=36.2
Q ss_pred CCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 176 LPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 176 lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
||...+.++.--+.+ .|+. .++|+.+|++...|.+.....|++.++-.
T Consensus 139 L~~~~r~v~~l~~~~----g~s~-----~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 139 LPEDLRTALTLREFD----GLSY-----EDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CCHHHhHHHhhHHhc----CCCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 677777776553333 3444 47999999999999999999999987543
No 161
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=22.44 E-value=90 Score=25.15 Aligned_cols=27 Identities=19% Similarity=0.405 Sum_probs=23.2
Q ss_pred CCcHHHHHHHHHHhCCChhhhhhhhhhh
Q 024428 197 PSQESQKLALAESTGLDSKQINNWFINQ 224 (268)
Q Consensus 197 Ps~~~ek~~La~~tgL~~~QV~nWF~N~ 224 (268)
++ +..+..||..+|++.+.|..|-.-+
T Consensus 27 ~~-~~~r~~La~~~~i~~~~l~~w~~~A 53 (122)
T PF14229_consen 27 DT-PLGRKALAKKLGISERNLLKWVNQA 53 (122)
T ss_pred CC-HHHHHHHHHhcCCCHHHHHHHHhHH
Confidence 67 7789999999999999999995433
No 162
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.39 E-value=1.3e+02 Score=26.10 Aligned_cols=52 Identities=13% Similarity=0.108 Sum_probs=40.6
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcc
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSED 234 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~ 234 (268)
..||+..+.++.--+.+. ++ -.++|+.+|++...|.+...-+|++.++-...
T Consensus 147 ~~L~~~~r~v~~L~~~~g----~s-----~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~ 198 (206)
T PRK12544 147 DGLPAKYARVFMMREFIE----LE-----TNEICHAVDLSVSNLNVLLYRARLRLRECLEN 198 (206)
T ss_pred HhCCHHHHHHHHHHHHcC----CC-----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 358888888887666555 22 24799999999999999999999998875543
No 163
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=22.17 E-value=76 Score=22.33 Aligned_cols=22 Identities=18% Similarity=0.368 Sum_probs=18.0
Q ss_pred HHHHHHhCCChhhhhhhhhhhh
Q 024428 204 LALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 204 ~~La~~tgL~~~QV~nWF~N~R 225 (268)
..+|+.+|++...|.+|-.--.
T Consensus 17 ~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 17 KEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred HHHHHHHCCChHHHHHHHHhhC
Confidence 3799999999999999954433
No 164
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=21.93 E-value=1.3e+02 Score=25.09 Aligned_cols=54 Identities=9% Similarity=-0.019 Sum_probs=41.1
Q ss_pred CCCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCcchh
Q 024428 173 KGKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSEDMQ 236 (268)
Q Consensus 173 r~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~~~~ 236 (268)
.+.||..++.+|.- +. . .+ ...++|+..|+|...|.+|-...|++.++......
T Consensus 4 ~~~Lte~qr~VL~L-r~-~---Gl-----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~ 57 (137)
T TIGR00721 4 KTFLTERQIKVLEL-RE-K---GL-----SQKEIAKELKTTRANVSAIEKRAMENIEKARNTLD 57 (137)
T ss_pred cCCCCHHHHHHHHH-HH-c---CC-----CHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHH
Confidence 46788888998866 32 2 22 34579999999999999999999999987554433
No 165
>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=21.80 E-value=1.1e+02 Score=25.84 Aligned_cols=50 Identities=6% Similarity=0.070 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCCc
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPSE 233 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~~ 233 (268)
.||...+.++.-.+.+. + .-.++|+.+|++..-|.+...-.|++.++-..
T Consensus 131 ~L~~~~r~v~~l~~~~g----~-----s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG----F-----ESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred hCCHHHHHHHHHHHHhC----C-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 58888888887765555 2 23479999999999999999999999876443
No 166
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=21.73 E-value=1.8e+02 Score=26.35 Aligned_cols=44 Identities=20% Similarity=0.323 Sum_probs=30.5
Q ss_pred HHHHHHHHHhhhhhcchhhhhHHhhhccCCCCCCHHHHHHHHHH
Q 024428 144 EDQELKGQLLRRYSGCLSSLKQEFMKKRKKGKLPKEARQQLLDW 187 (268)
Q Consensus 144 ~~~el~~~l~~~~~~~~~~~~~~~~k~rkr~~lpk~~~~~L~~w 187 (268)
.-..|-..+.+.+..+-.-+...-.-+|++..|+..+...|.+|
T Consensus 115 ~L~~LAa~~V~~~d~fRAPls~aelaRRr~~~Ls~~Q~~~L~~W 158 (228)
T TIGR03223 115 ALQALAAACVRELDPFRAPLTEAELARRRPDQLTPRQRALLERW 158 (228)
T ss_pred HHHHHHHHHHHhhhhccCCCCHHHHhhcCccCCCHHHHHHHHHc
Confidence 34555566666665554444444456778888999999999999
No 167
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=21.63 E-value=1e+02 Score=25.69 Aligned_cols=47 Identities=11% Similarity=0.075 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++...+.+. ++- .++|..+|++...|.+-...+|++.++
T Consensus 137 ~L~~~~r~i~~l~~~~g----~s~-----~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 137 ELEPPRSELIRTAFFEG----ITY-----EELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred hCCHHHHHHHHHHHHcC----CCH-----HHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 47888888887666544 333 479999999999999999999998764
No 168
>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=21.61 E-value=2.7e+02 Score=19.31 Aligned_cols=50 Identities=18% Similarity=0.317 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 024428 176 LPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKR 227 (268)
Q Consensus 176 lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R 227 (268)
|+..++.+|..-+..-+ .=+|- +..-..||+..|++..-++.-+.+.=++
T Consensus 1 LT~~Q~e~L~~A~~~GY-fd~PR-~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 1 LTDRQREILKAAYELGY-FDVPR-RITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHHHHHHHcCC-CCCCC-cCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 46677788876554432 23466 6788899999999999888766554433
No 169
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=21.59 E-value=2.4e+02 Score=24.57 Aligned_cols=42 Identities=19% Similarity=0.353 Sum_probs=32.0
Q ss_pred chHhHHHHHHHHHHHHHHHHhcccHH-HH-HHHHHHHHHhhhhh
Q 024428 68 PALDQFMEAYCEMLTKYEQELSKPFK-EA-MSFLQKIESQFKSL 109 (268)
Q Consensus 68 pELDqfM~~Y~~~L~ky~eeL~k~~~-EA-~~f~~~ie~QL~~L 109 (268)
-|||-+..++-..+..|++.++..++ +| ..|+..+..||-.+
T Consensus 104 tELDVvL~~FEk~~~eYkq~ieS~~cr~AI~~F~~~~keqL~~~ 147 (175)
T PF13097_consen 104 TELDVVLSAFEKTALEYKQSIESKICRKAINKFYSNFKEQLIEM 147 (175)
T ss_pred hHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHH
Confidence 58999999999999999999987663 33 45666666666443
No 170
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.53 E-value=1.1e+02 Score=28.04 Aligned_cols=49 Identities=20% Similarity=0.121 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||+..+.++.-.+... ++- .++|+.+|++...|.+.+.-.|++.++-.
T Consensus 142 ~Lp~~~R~v~~L~~~~g----~s~-----~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLG----WRA-----AETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred hCCHHHhhHhhhHHHhC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 58888888886655544 222 37999999999999999999999987643
No 171
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=21.45 E-value=92 Score=19.39 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=18.8
Q ss_pred HHHHHHhCCChhhhhhhhhhhh
Q 024428 204 LALAESTGLDSKQINNWFINQR 225 (268)
Q Consensus 204 ~~La~~tgL~~~QV~nWF~N~R 225 (268)
.++|+.+|++...|..|..+-+
T Consensus 4 ~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 4 KEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHcCC
Confidence 5789999999999999987643
No 172
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=21.38 E-value=75 Score=22.18 Aligned_cols=20 Identities=10% Similarity=0.212 Sum_probs=17.3
Q ss_pred HHHHHHhCCChhhhhhhhhh
Q 024428 204 LALAESTGLDSKQINNWFIN 223 (268)
Q Consensus 204 ~~La~~tgL~~~QV~nWF~N 223 (268)
.++|+.+|++...|..|-..
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46899999999999999654
No 173
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=21.24 E-value=1.5e+02 Score=23.90 Aligned_cols=48 Identities=10% Similarity=0.102 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
..||+..+.++.-.+... ++. .++|+.+|++...|.+...-.|++.++
T Consensus 121 ~~L~~~~r~vl~l~~~~g----~s~-----~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQN----LPI-----AEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HhCCHHHHHHHHHHHhcC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 358888888887755544 343 478999999999999999888888764
No 174
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.92 E-value=83 Score=26.07 Aligned_cols=47 Identities=11% Similarity=0.135 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcC
Q 024428 174 GKLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHW 229 (268)
Q Consensus 174 ~~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~ 229 (268)
..||+..+.++.--+.+. + .-.++|+.+|++...|.++...++++..
T Consensus 118 ~~L~~~~r~i~~l~~~~g----~-----s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 118 DGLNGKTREAFLLSQLDG----L-----TYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred HhCCHHHhHHhhhhhccC----C-----CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 347888888876554444 2 2347999999999999999988887754
No 175
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=20.72 E-value=1.3e+02 Score=25.45 Aligned_cols=46 Identities=17% Similarity=0.117 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWK 230 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~k 230 (268)
.||+..+.++.. +.+. |.. .++|..+|++...|.+.+...|++.++
T Consensus 155 ~L~~~~r~vl~l-~~e~----~s~-----~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 155 LLSELEKEVLEL-YLDG----KSY-----QEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred hCCHHHHHHHHH-HHcc----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888877 4443 333 478999999999999999999998765
No 176
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=20.64 E-value=77 Score=21.92 Aligned_cols=19 Identities=26% Similarity=0.413 Sum_probs=17.1
Q ss_pred HHHHHHhCCChhhhhhhhh
Q 024428 204 LALAESTGLDSKQINNWFI 222 (268)
Q Consensus 204 ~~La~~tgL~~~QV~nWF~ 222 (268)
.++|+.+|++...|.+|-.
T Consensus 4 ~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 4 GAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999975
No 177
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=20.45 E-value=1.2e+02 Score=25.73 Aligned_cols=49 Identities=20% Similarity=0.191 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCCC
Q 024428 175 KLPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKPS 232 (268)
Q Consensus 175 ~lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp~ 232 (268)
.||...+.++.-.+.++ ++. .++|..+|++..-|.++..-.|++.++-.
T Consensus 128 ~Lp~~~r~v~~l~~~~g----~s~-----~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQVIGG----FSG-----EEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHHHHhC----CCH-----HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888899887766655 333 47899999999999999999999887644
No 178
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=20.36 E-value=1.5e+02 Score=23.88 Aligned_cols=47 Identities=19% Similarity=0.249 Sum_probs=38.2
Q ss_pred CCHHHHHHHHHHHHhccCCCCCCcHHHHHHHHHHhCCChhhhhhhhhhhhhhcCCC
Q 024428 176 LPKEARQQLLDWWSKHYKWPYPSQESQKLALAESTGLDSKQINNWFINQRKRHWKP 231 (268)
Q Consensus 176 lpk~~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tgL~~~QV~nWF~N~R~R~~kp 231 (268)
||+..+.++.-.+... ++ -.++|..+|++..-|.+....+|++.++-
T Consensus 106 L~~~~r~v~~l~~~~~----~s-----~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 106 LPPACRDSFLLRKLEG----LS-----HQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CCHHHHHHHHHHHHcC----CC-----HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 8898999887776655 22 24799999999999999999999987653
No 179
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=20.23 E-value=2.8e+02 Score=20.20 Aligned_cols=36 Identities=25% Similarity=0.244 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhccCCCCCCcHHHHHHHHHHhC--CChhhhhh
Q 024428 180 ARQQLLDWWSKHYKWPYPSQESQKLALAESTG--LDSKQINN 219 (268)
Q Consensus 180 ~~~~L~~w~~~h~~~PYPs~~~ek~~La~~tg--L~~~QV~n 219 (268)
++..++..+.+| |=.+ ++.-..+..+-| .|.+||+.
T Consensus 18 ar~~~~k~l~~N---Ppin-e~mir~M~~QMG~kpSekqi~Q 55 (64)
T PF03672_consen 18 ARKYMEKQLKEN---PPIN-EKMIRAMMMQMGRKPSEKQIKQ 55 (64)
T ss_pred HHHHHHHHHHHC---CCCC-HHHHHHHHHHhCCCccHHHHHH
Confidence 355666666666 8778 888888888888 45555543
Done!