Query 029411
Match_columns 194
No_of_seqs 219 out of 1092
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 12:29:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029411.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029411hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03791 KNOX2: KNOX2 domain ; 99.9 1.4E-25 3E-30 149.4 6.0 51 10-60 2-52 (52)
2 KOG0774 Transcription factor P 99.9 3.4E-24 7.3E-29 183.4 7.5 132 17-174 107-250 (334)
3 KOG0773 Transcription factor M 99.9 1.1E-23 2.3E-28 187.1 5.0 173 12-184 111-311 (342)
4 PF05920 Homeobox_KN: Homeobox 99.7 1.3E-18 2.8E-23 110.5 4.6 40 130-169 1-40 (40)
5 cd00086 homeodomain Homeodomai 99.6 9.2E-16 2E-20 102.5 7.1 57 114-173 2-58 (59)
6 PF00046 Homeobox: Homeobox do 99.6 1.4E-15 2.9E-20 101.9 5.6 57 113-172 1-57 (57)
7 smart00389 HOX Homeodomain. DN 99.6 2.7E-15 5.8E-20 99.7 6.9 55 114-171 2-56 (56)
8 KOG0775 Transcription factor S 99.5 3.5E-14 7.6E-19 122.6 5.8 50 122-174 186-235 (304)
9 TIGR01565 homeo_ZF_HD homeobox 99.1 7.2E-11 1.6E-15 80.7 4.9 53 112-167 1-57 (58)
10 KOG0843 Transcription factor E 99.1 7.8E-11 1.7E-15 96.7 4.3 61 111-174 101-161 (197)
11 KOG0842 Transcription factor t 99.0 1.1E-10 2.4E-15 103.1 3.4 63 111-176 152-214 (307)
12 KOG0850 Transcription factor D 99.0 1.9E-10 4.1E-15 97.5 4.3 60 113-175 123-182 (245)
13 KOG0487 Transcription factor A 99.0 2.1E-10 4.5E-15 101.4 3.4 64 112-178 235-298 (308)
14 KOG0489 Transcription factor z 98.9 7E-10 1.5E-14 96.2 3.8 61 111-174 158-218 (261)
15 KOG0493 Transcription factor E 98.9 1.8E-09 3.8E-14 93.4 5.6 60 113-175 247-306 (342)
16 KOG3802 Transcription factor O 98.9 1.1E-09 2.3E-14 99.2 3.0 63 110-175 292-354 (398)
17 COG5576 Homeodomain-containing 98.8 2.6E-09 5.6E-14 86.4 4.4 60 112-174 51-110 (156)
18 KOG0483 Transcription factor H 98.8 3.5E-09 7.5E-14 88.6 4.3 60 112-174 50-109 (198)
19 KOG0485 Transcription factor N 98.8 3.1E-09 6.7E-14 89.8 3.4 61 111-174 103-163 (268)
20 KOG0491 Transcription factor B 98.8 2.7E-09 5.9E-14 86.7 2.8 68 110-180 98-165 (194)
21 KOG0484 Transcription factor P 98.8 5.8E-09 1.3E-13 79.0 4.1 68 104-174 9-76 (125)
22 KOG0488 Transcription factor B 98.8 6.6E-09 1.4E-13 92.2 4.8 64 110-176 170-233 (309)
23 KOG0492 Transcription factor M 98.7 7E-09 1.5E-13 87.0 4.0 68 104-174 136-203 (246)
24 KOG2251 Homeobox transcription 98.6 2.3E-08 4.9E-13 84.5 4.0 60 112-174 37-96 (228)
25 KOG0494 Transcription factor C 98.5 7.8E-08 1.7E-12 83.2 4.6 54 116-172 145-198 (332)
26 KOG0486 Transcription factor P 98.5 6.4E-08 1.4E-12 85.5 2.4 64 112-178 112-175 (351)
27 KOG0848 Transcription factor C 98.5 6E-08 1.3E-12 84.1 1.6 58 114-174 201-258 (317)
28 KOG2252 CCAAT displacement pro 98.3 6.5E-07 1.4E-11 84.0 5.7 57 111-170 419-475 (558)
29 KOG4577 Transcription factor L 98.3 2.7E-07 5.8E-12 81.0 2.6 68 105-175 160-227 (383)
30 KOG1168 Transcription factor A 98.1 7E-07 1.5E-11 78.5 0.1 62 109-173 306-367 (385)
31 KOG0849 Transcription factor P 98.1 4.7E-06 1E-10 75.4 5.2 63 111-176 175-237 (354)
32 KOG0490 Transcription factor, 98.0 1.8E-06 4E-11 71.7 1.7 62 110-174 58-119 (235)
33 KOG0844 Transcription factor E 98.0 2.2E-06 4.7E-11 75.9 1.5 59 113-174 182-240 (408)
34 KOG0847 Transcription factor, 98.0 3.9E-06 8.4E-11 71.3 2.7 62 110-174 165-226 (288)
35 PF11569 Homez: Homeodomain le 97.9 1.6E-05 3.4E-10 53.9 3.4 43 124-169 10-52 (56)
36 KOG0773 Transcription factor M 97.6 3.1E-05 6.7E-10 69.0 1.9 62 112-174 95-156 (342)
37 PF03789 ELK: ELK domain ; In 97.2 0.00011 2.4E-09 40.8 0.5 22 90-111 1-22 (22)
38 KOG0490 Transcription factor, 96.2 0.0031 6.7E-08 52.2 2.5 60 112-174 153-212 (235)
39 KOG1146 Homeobox protein [Gene 94.8 0.037 8E-07 57.3 4.7 73 110-185 901-973 (1406)
40 PF03792 PBC: PBC domain; Int 94.1 0.23 5E-06 41.5 7.2 68 17-110 111-178 (191)
41 PF04218 CENP-B_N: CENP-B N-te 93.0 0.23 4.9E-06 32.9 4.5 48 113-168 1-48 (53)
42 PRK12516 RNA polymerase sigma 90.0 8.1 0.00018 31.2 11.6 140 12-176 5-166 (187)
43 PF01527 HTH_Tnp_1: Transposas 88.8 0.82 1.8E-05 31.3 4.1 46 114-167 2-48 (76)
44 PRK11924 RNA polymerase sigma 88.6 9.6 0.00021 29.4 10.8 49 118-174 125-173 (179)
45 PRK06811 RNA polymerase factor 88.3 8.5 0.00018 30.9 10.5 50 117-174 130-179 (189)
46 PF08281 Sigma70_r4_2: Sigma-7 87.7 1.3 2.8E-05 28.5 4.3 44 118-169 10-53 (54)
47 cd06171 Sigma70_r4 Sigma70, re 87.7 1.4 3E-05 26.9 4.4 46 118-171 10-55 (55)
48 PF04545 Sigma70_r4: Sigma-70, 85.5 1.3 2.7E-05 28.3 3.3 46 118-171 4-49 (50)
49 KOG3623 Homeobox transcription 84.9 1.7 3.7E-05 43.3 5.3 46 124-172 568-613 (1007)
50 cd00569 HTH_Hin_like Helix-tur 82.7 3.1 6.8E-05 22.6 4.0 39 117-163 4-42 (42)
51 PRK06759 RNA polymerase factor 80.2 3 6.5E-05 31.9 4.2 48 117-172 105-152 (154)
52 PRK09415 RNA polymerase factor 79.1 24 0.00052 27.9 9.3 50 117-174 126-175 (179)
53 TIGR02954 Sig70_famx3 RNA poly 79.0 28 0.00061 27.0 11.2 49 118-174 119-167 (169)
54 PRK09647 RNA polymerase sigma 78.2 36 0.00079 27.9 10.6 51 117-175 137-187 (203)
55 PRK09642 RNA polymerase sigma 77.9 2.6 5.5E-05 32.7 3.2 52 118-177 106-157 (160)
56 PRK00118 putative DNA-binding 77.4 2 4.4E-05 32.5 2.4 55 117-179 16-70 (104)
57 PRK03975 tfx putative transcri 73.1 5.7 0.00012 31.7 4.0 52 116-176 4-55 (141)
58 PRK09643 RNA polymerase sigma 73.0 47 0.001 26.7 10.9 51 118-176 134-184 (192)
59 TIGR02937 sigma70-ECF RNA poly 72.1 5.8 0.00012 29.2 3.7 47 118-172 110-156 (158)
60 PRK09644 RNA polymerase sigma 71.5 5.6 0.00012 31.0 3.7 51 117-175 107-157 (165)
61 PRK12541 RNA polymerase sigma 71.2 6 0.00013 30.7 3.8 50 117-174 111-160 (161)
62 PRK12533 RNA polymerase sigma 71.0 5.2 0.00011 33.4 3.6 53 117-177 133-185 (216)
63 TIGR02939 RpoE_Sigma70 RNA pol 70.7 4.3 9.3E-05 32.1 2.9 50 117-174 137-186 (190)
64 PRK12513 RNA polymerase sigma 70.5 52 0.0011 26.2 9.3 49 118-174 139-187 (194)
65 PRK12514 RNA polymerase sigma 70.4 5.7 0.00012 31.4 3.5 49 117-173 128-176 (179)
66 TIGR02989 Sig-70_gvs1 RNA poly 70.3 7.4 0.00016 29.8 4.1 48 117-172 110-157 (159)
67 PRK09652 RNA polymerase sigma 69.0 6.5 0.00014 30.5 3.5 49 118-174 128-176 (182)
68 PF07526 POX: Associated with 68.4 10 0.00022 30.2 4.5 43 18-62 81-138 (140)
69 PF13518 HTH_28: Helix-turn-he 68.2 6.7 0.00015 24.5 2.9 24 145-168 15-38 (52)
70 TIGR02985 Sig70_bacteroi1 RNA 68.1 8.2 0.00018 29.2 3.9 47 118-172 113-159 (161)
71 PRK09646 RNA polymerase sigma 68.1 6.7 0.00014 31.6 3.5 49 118-174 142-190 (194)
72 TIGR02999 Sig-70_X6 RNA polyme 65.2 9.3 0.0002 30.1 3.8 47 118-172 134-180 (183)
73 PRK12526 RNA polymerase sigma 64.9 8.4 0.00018 31.5 3.6 50 117-174 152-201 (206)
74 smart00421 HTH_LUXR helix_turn 64.9 25 0.00054 21.5 5.2 47 118-173 3-49 (58)
75 PRK12512 RNA polymerase sigma 64.0 8.2 0.00018 30.6 3.3 51 117-175 130-180 (184)
76 PRK06930 positive control sigm 63.8 6.5 0.00014 32.0 2.6 57 117-181 113-169 (170)
77 TIGR02959 SigZ RNA polymerase 63.6 7.6 0.00017 30.6 3.0 52 117-176 99-150 (170)
78 PF13443 HTH_26: Cro/C1-type H 63.1 5.9 0.00013 26.0 1.9 23 144-166 12-34 (63)
79 PRK09639 RNA polymerase sigma 63.1 10 0.00022 29.3 3.6 49 117-174 111-159 (166)
80 PRK05602 RNA polymerase sigma 63.0 8.8 0.00019 30.5 3.3 50 118-175 128-177 (186)
81 PRK09648 RNA polymerase sigma 63.0 10 0.00022 30.2 3.7 49 117-173 138-186 (189)
82 PRK12535 RNA polymerase sigma 62.6 12 0.00027 30.4 4.1 55 117-179 132-186 (196)
83 PF00196 GerE: Bacterial regul 62.4 20 0.00044 23.3 4.5 48 118-174 3-50 (58)
84 PRK04217 hypothetical protein; 62.1 13 0.00029 28.3 4.0 51 116-174 40-90 (110)
85 PRK12537 RNA polymerase sigma 61.8 11 0.00024 29.9 3.7 49 117-173 132-180 (182)
86 PRK11922 RNA polymerase sigma 60.8 47 0.001 27.6 7.5 49 118-174 149-197 (231)
87 PRK12530 RNA polymerase sigma 60.7 11 0.00024 30.2 3.6 50 117-174 133-182 (189)
88 PRK12536 RNA polymerase sigma 60.6 12 0.00027 29.6 3.8 50 117-174 128-177 (181)
89 PRK12546 RNA polymerase sigma 60.4 10 0.00023 30.7 3.3 49 118-174 113-161 (188)
90 PRK09047 RNA polymerase factor 60.1 14 0.0003 28.3 3.8 51 117-175 105-155 (161)
91 PRK13919 putative RNA polymera 59.8 13 0.00028 29.5 3.7 50 117-174 134-183 (186)
92 PF10668 Phage_terminase: Phag 59.3 8.5 0.00018 26.4 2.2 21 144-164 24-44 (60)
93 PRK09649 RNA polymerase sigma 58.6 14 0.00031 29.5 3.8 48 117-172 129-176 (185)
94 PRK12532 RNA polymerase sigma 58.5 13 0.00029 29.8 3.6 51 118-176 136-186 (195)
95 PRK12519 RNA polymerase sigma 58.4 9.8 0.00021 30.4 2.8 49 117-173 140-188 (194)
96 PF13936 HTH_38: Helix-turn-he 58.2 13 0.00027 23.4 2.7 40 117-164 3-42 (44)
97 TIGR02983 SigE-fam_strep RNA p 58.1 13 0.00029 28.6 3.5 50 117-174 109-158 (162)
98 TIGR02948 SigW_bacill RNA poly 58.0 12 0.00026 29.5 3.2 48 118-173 136-183 (187)
99 PRK12515 RNA polymerase sigma 57.9 15 0.00031 29.4 3.7 50 117-174 130-179 (189)
100 smart00574 POX domain associat 57.7 22 0.00048 28.4 4.6 44 19-62 82-138 (140)
101 PRK12523 RNA polymerase sigma 56.6 18 0.00039 28.3 4.1 49 117-173 118-166 (172)
102 PRK12524 RNA polymerase sigma 56.2 15 0.00032 29.6 3.6 50 118-175 136-185 (196)
103 cd00131 PAX Paired Box domain 56.2 47 0.001 25.6 6.2 47 117-166 74-127 (128)
104 PRK12547 RNA polymerase sigma 55.8 94 0.002 24.0 12.0 49 117-173 111-159 (164)
105 PRK08583 RNA polymerase sigma 55.8 18 0.00038 30.7 4.1 49 118-174 205-253 (257)
106 PF13730 HTH_36: Helix-turn-he 55.5 51 0.0011 20.9 5.9 48 118-168 2-51 (55)
107 cd06170 LuxR_C_like C-terminal 55.4 41 0.00089 20.7 4.9 30 144-173 17-46 (57)
108 PRK12531 RNA polymerase sigma 55.1 16 0.00036 29.3 3.6 50 117-174 140-189 (194)
109 TIGR02980 SigBFG RNA polymeras 54.6 18 0.00038 29.9 3.8 48 117-172 177-224 (227)
110 PRK12520 RNA polymerase sigma 54.3 18 0.00039 28.9 3.7 50 117-174 130-179 (191)
111 PRK07037 extracytoplasmic-func 53.9 18 0.0004 27.8 3.6 50 117-174 108-157 (163)
112 PRK06986 fliA flagellar biosyn 53.7 15 0.00032 30.7 3.3 49 118-174 184-232 (236)
113 TIGR02943 Sig70_famx1 RNA poly 53.5 19 0.0004 29.0 3.7 51 117-175 130-180 (188)
114 PRK09637 RNA polymerase sigma 53.1 17 0.00037 29.1 3.4 49 118-174 106-154 (181)
115 PF05190 MutS_IV: MutS family 52.4 21 0.00046 24.8 3.5 24 14-37 1-24 (92)
116 PRK12542 RNA polymerase sigma 52.3 19 0.00042 28.6 3.6 50 117-174 121-170 (185)
117 PRK12543 RNA polymerase sigma 51.9 21 0.00045 28.3 3.7 49 118-174 117-165 (179)
118 KOG4040 NADH:ubiquinone oxidor 51.8 9.1 0.0002 31.5 1.6 39 120-158 22-61 (186)
119 PF01381 HTH_3: Helix-turn-hel 51.8 9.5 0.00021 24.2 1.4 21 145-165 12-32 (55)
120 PRK12528 RNA polymerase sigma 51.5 25 0.00054 27.1 4.0 47 117-171 112-158 (161)
121 PF13551 HTH_29: Winged helix- 50.9 63 0.0014 23.0 5.9 46 119-164 58-109 (112)
122 PRK09645 RNA polymerase sigma 50.7 1.2E+02 0.0025 23.5 12.2 50 118-175 118-167 (173)
123 PRK09641 RNA polymerase sigma 50.6 20 0.00043 28.1 3.4 49 118-174 136-184 (187)
124 PRK09413 IS2 repressor TnpA; R 50.5 52 0.0011 24.9 5.6 48 114-168 8-55 (121)
125 PRK12544 RNA polymerase sigma 50.3 22 0.00048 29.2 3.8 51 117-175 147-197 (206)
126 PRK15369 two component system 50.2 32 0.0007 26.1 4.5 48 118-174 149-196 (211)
127 PRK12522 RNA polymerase sigma 50.0 22 0.00047 27.9 3.5 50 117-174 118-167 (173)
128 TIGR02947 SigH_actino RNA poly 49.6 9.9 0.00021 30.5 1.5 50 118-175 131-180 (193)
129 PF13411 MerR_1: MerR HTH fami 49.4 14 0.00031 24.5 2.1 19 146-164 4-22 (69)
130 PRK12539 RNA polymerase sigma 49.4 24 0.00052 28.0 3.7 50 117-174 130-179 (184)
131 PF13384 HTH_23: Homeodomain-l 49.3 16 0.00034 22.9 2.1 24 144-167 19-42 (50)
132 PRK12538 RNA polymerase sigma 49.2 18 0.00038 30.5 3.1 50 118-175 171-220 (233)
133 PF04967 HTH_10: HTH DNA bindi 49.2 57 0.0012 21.6 4.9 46 119-165 1-46 (53)
134 PRK12529 RNA polymerase sigma 49.1 30 0.00064 27.4 4.2 49 117-173 126-174 (178)
135 PRK07670 RNA polymerase sigma 49.0 23 0.0005 29.9 3.7 48 118-173 201-248 (251)
136 TIGR02479 FliA_WhiG RNA polyme 48.7 24 0.00051 29.2 3.7 48 117-172 174-221 (224)
137 TIGR02941 Sigma_B RNA polymera 48.7 21 0.00047 30.1 3.5 49 117-173 204-252 (255)
138 PF12464 Mac: Maltose acetyltr 48.4 61 0.0013 20.7 4.9 37 13-49 11-47 (55)
139 PRK12540 RNA polymerase sigma 48.1 27 0.00059 28.0 3.9 51 117-175 110-160 (182)
140 PRK12511 RNA polymerase sigma 47.7 24 0.00052 28.3 3.5 49 118-174 111-159 (182)
141 PF06295 DUF1043: Protein of u 47.5 48 0.0011 25.6 5.0 41 17-57 28-68 (128)
142 PRK12534 RNA polymerase sigma 47.2 25 0.00054 27.8 3.5 49 117-173 136-184 (187)
143 TIGR03070 couple_hipB transcri 47.1 13 0.00027 23.4 1.4 22 145-166 18-39 (58)
144 cd01392 HTH_LacI Helix-turn-he 46.8 13 0.00027 23.4 1.4 21 147-167 2-22 (52)
145 TIGR03001 Sig-70_gmx1 RNA poly 46.5 25 0.00055 29.9 3.6 50 117-174 160-209 (244)
146 PRK12545 RNA polymerase sigma 46.5 27 0.00057 28.4 3.6 51 117-175 138-188 (201)
147 PRK10072 putative transcriptio 46.4 13 0.00027 27.7 1.5 23 145-167 49-71 (96)
148 PRK08295 RNA polymerase factor 46.2 27 0.00058 28.0 3.6 49 117-174 154-202 (208)
149 PRK11677 hypothetical protein; 46.0 53 0.0011 26.0 5.0 42 16-57 31-72 (134)
150 TIGR02950 SigM_subfam RNA poly 45.9 9.9 0.00022 28.9 0.9 47 118-172 105-151 (154)
151 PRK12527 RNA polymerase sigma 45.9 30 0.00064 26.6 3.7 49 118-174 105-153 (159)
152 TIGR02952 Sig70_famx2 RNA poly 45.5 32 0.0007 26.4 3.8 48 117-172 121-168 (170)
153 PRK06288 RNA polymerase sigma 45.3 26 0.00057 29.9 3.6 52 117-176 211-262 (268)
154 TIGR02885 spore_sigF RNA polym 45.2 32 0.0007 28.4 4.0 48 117-172 182-229 (231)
155 PRK08301 sporulation sigma fac 44.6 24 0.00051 29.3 3.1 54 117-174 177-230 (234)
156 PRK11923 algU RNA polymerase s 44.4 27 0.00059 27.8 3.3 49 118-174 138-186 (193)
157 TIGR02859 spore_sigH RNA polym 44.3 38 0.00082 26.9 4.1 30 144-173 167-196 (198)
158 PF05821 NDUF_B8: NADH-ubiquin 43.9 23 0.0005 29.4 2.8 31 128-158 25-56 (179)
159 cd04761 HTH_MerR-SF Helix-Turn 43.8 23 0.00049 21.7 2.2 20 146-165 4-23 (49)
160 PRK11511 DNA-binding transcrip 43.6 83 0.0018 23.8 5.8 41 122-166 9-49 (127)
161 cd00093 HTH_XRE Helix-turn-hel 43.5 18 0.0004 21.3 1.7 21 146-166 16-36 (58)
162 PRK12518 RNA polymerase sigma 43.2 12 0.00026 29.2 1.0 50 118-175 120-169 (175)
163 PF06806 DUF1233: Putative exc 42.4 29 0.00063 24.7 2.8 41 146-190 13-53 (72)
164 PRK12525 RNA polymerase sigma 42.1 44 0.00096 26.0 4.2 47 117-171 117-163 (168)
165 TIGR03826 YvyF flagellar opero 42.0 56 0.0012 25.9 4.7 57 124-184 32-88 (137)
166 PRK05572 sporulation sigma fac 41.8 30 0.00065 29.2 3.4 50 117-174 201-250 (252)
167 TIGR00721 tfx DNA-binding prot 41.5 47 0.001 26.3 4.2 50 116-174 4-53 (137)
168 PRK09651 RNA polymerase sigma 40.7 38 0.00082 26.6 3.6 47 117-171 118-164 (172)
169 PF00376 MerR: MerR family reg 40.6 25 0.00053 21.5 1.9 19 146-164 3-21 (38)
170 PRK07408 RNA polymerase sigma 40.5 36 0.00077 29.0 3.6 50 117-174 202-251 (256)
171 PRK12517 RNA polymerase sigma 40.3 40 0.00086 27.1 3.7 49 118-174 128-176 (188)
172 KOG0738 AAA+-type ATPase [Post 39.6 72 0.0016 30.2 5.6 101 30-151 292-393 (491)
173 PF02796 HTH_7: Helix-turn-hel 39.5 69 0.0015 19.9 4.0 20 144-163 23-42 (45)
174 PF14229 DUF4332: Domain of un 39.0 33 0.00071 26.3 2.9 28 140-167 27-54 (122)
175 PRK05803 sporulation sigma fac 38.7 34 0.00074 28.5 3.2 54 117-174 174-227 (233)
176 PHA01976 helix-turn-helix prot 38.5 22 0.00047 23.5 1.6 22 145-166 18-39 (67)
177 TIGR02960 SigX5 RNA polymerase 38.4 42 0.00092 29.0 3.8 52 117-176 141-192 (324)
178 TIGR02393 RpoD_Cterm RNA polym 38.2 46 0.001 27.8 3.9 53 118-174 176-228 (238)
179 PRK07122 RNA polymerase sigma 38.0 38 0.00082 29.1 3.4 49 117-173 214-262 (264)
180 smart00530 HTH_XRE Helix-turn- 37.4 25 0.00053 20.5 1.6 22 145-166 13-34 (56)
181 cd04764 HTH_MlrA-like_sg1 Heli 37.2 28 0.00061 23.1 2.0 20 146-165 4-23 (67)
182 PRK08241 RNA polymerase factor 36.8 46 0.001 29.2 3.8 49 117-173 152-200 (339)
183 TIGR02607 antidote_HigA addict 36.7 23 0.00049 24.0 1.5 23 145-167 21-43 (78)
184 PF06299 DUF1045: Protein of u 36.1 83 0.0018 25.6 4.9 46 85-130 53-98 (160)
185 cd04762 HTH_MerR-trunc Helix-T 35.9 38 0.00082 20.1 2.3 22 146-167 4-25 (49)
186 COG3105 Uncharacterized protei 35.9 70 0.0015 25.4 4.2 41 17-57 37-77 (138)
187 cd01104 HTH_MlrA-CarA Helix-Tu 35.7 33 0.00071 22.6 2.1 19 146-164 4-22 (68)
188 PF14978 MRP-63: Mitochondrial 35.4 1.4E+02 0.003 22.1 5.6 52 114-169 10-70 (91)
189 TIGR02846 spore_sigmaK RNA pol 35.1 48 0.001 27.5 3.5 52 117-172 173-224 (227)
190 PF12844 HTH_19: Helix-turn-he 34.5 25 0.00055 22.9 1.4 23 145-167 15-37 (64)
191 PF06056 Terminase_5: Putative 34.1 37 0.00079 22.8 2.2 23 145-167 16-38 (58)
192 TIGR02394 rpoS_proteo RNA poly 34.0 50 0.0011 28.5 3.5 55 117-175 221-275 (285)
193 PF01726 LexA_DNA_bind: LexA D 34.0 1E+02 0.0023 21.0 4.5 41 119-164 4-48 (65)
194 PRK08215 sporulation sigma fac 33.1 54 0.0012 27.7 3.6 49 117-173 208-256 (258)
195 COG5661 Predicted secreted Zn- 32.4 1.2E+02 0.0026 25.7 5.3 45 13-60 108-152 (210)
196 PRK06704 RNA polymerase factor 32.2 52 0.0011 27.9 3.3 50 117-174 115-164 (228)
197 PF03672 UPF0154: Uncharacteri 32.2 1.4E+02 0.003 20.8 4.8 35 123-160 18-54 (64)
198 PRK05657 RNA polymerase sigma 31.8 76 0.0017 28.2 4.4 54 117-174 261-314 (325)
199 PRK10651 transcriptional regul 31.7 95 0.0021 23.8 4.5 48 118-174 155-202 (216)
200 PF13097 CENP-U: CENP-A nucleo 31.7 1.4E+02 0.0031 24.8 5.6 41 17-57 104-146 (175)
201 PRK09638 RNA polymerase sigma 31.5 27 0.00059 27.2 1.4 49 117-173 125-173 (176)
202 TIGR02984 Sig-70_plancto1 RNA 31.5 70 0.0015 25.0 3.8 48 118-173 140-187 (189)
203 smart00422 HTH_MERR helix_turn 31.4 42 0.00091 22.1 2.1 19 146-164 4-22 (70)
204 PF11629 Mst1_SARAH: C termina 31.3 57 0.0012 21.5 2.6 29 18-46 19-47 (49)
205 PRK05911 RNA polymerase sigma 31.2 63 0.0014 27.5 3.7 50 117-174 204-253 (257)
206 PRK04053 rps13p 30S ribosomal 31.0 46 0.001 26.8 2.6 29 112-140 49-77 (149)
207 TIGR03223 Phn_opern_protn puta 30.9 1.1E+02 0.0024 26.3 5.1 47 84-130 112-158 (228)
208 PRK09640 RNA polymerase sigma 30.6 22 0.00049 28.3 0.8 49 118-174 134-182 (188)
209 TIGR02957 SigX4 RNA polymerase 30.4 78 0.0017 27.2 4.2 50 117-174 107-156 (281)
210 PRK09480 slmA division inhibit 30.1 56 0.0012 25.5 3.0 29 138-167 27-55 (194)
211 PF13551 HTH_29: Winged helix- 29.9 58 0.0013 23.2 2.8 26 144-169 14-39 (112)
212 PF07638 Sigma70_ECF: ECF sigm 29.6 67 0.0015 25.8 3.4 47 119-173 136-182 (185)
213 TIGR02835 spore_sigmaE RNA pol 29.4 62 0.0013 27.0 3.3 54 117-174 177-230 (234)
214 cd04763 HTH_MlrA-like Helix-Tu 29.4 49 0.0011 22.0 2.2 20 146-165 4-23 (68)
215 PF08671 SinI: Anti-repressor 29.0 72 0.0016 18.8 2.6 20 145-164 8-27 (30)
216 COG2963 Transposase and inacti 28.7 2E+02 0.0043 21.1 5.6 49 116-171 5-54 (116)
217 PF02290 SRP14: Signal recogni 28.3 46 0.00099 24.5 2.0 16 17-32 73-88 (93)
218 PF06971 Put_DNA-bind_N: Putat 28.0 49 0.0011 21.7 1.9 16 146-161 32-47 (50)
219 smart00351 PAX Paired Box doma 28.0 2.1E+02 0.0046 21.7 5.8 45 116-163 73-124 (125)
220 TIGR03020 EpsA transcriptional 27.3 1.1E+02 0.0023 26.4 4.5 50 116-174 188-237 (247)
221 PF10782 DUF2602: Protein of u 26.8 39 0.00084 23.1 1.3 24 18-41 9-35 (58)
222 PRK09706 transcriptional repre 26.3 41 0.0009 25.7 1.5 22 146-167 22-43 (135)
223 PRK10403 transcriptional regul 26.2 1.3E+02 0.0028 23.0 4.4 48 118-174 153-200 (215)
224 PF11867 DUF3387: Domain of un 26.0 1.8E+02 0.0038 25.9 5.7 126 13-151 189-323 (335)
225 TIGR03629 arch_S13P archaeal r 25.9 72 0.0016 25.5 2.9 30 111-141 44-73 (144)
226 TIGR01764 excise DNA binding d 25.9 70 0.0015 19.1 2.3 21 146-166 5-25 (49)
227 PF12323 HTH_OrfB_IS605: Helix 25.6 56 0.0012 20.4 1.8 33 138-171 9-41 (46)
228 PF07042 TrfA: TrfA protein; 25.3 1E+02 0.0022 27.4 4.0 52 114-168 206-257 (282)
229 PF14549 P22_Cro: DNA-binding 25.1 69 0.0015 21.7 2.3 18 145-162 12-29 (60)
230 TIGR02392 rpoH_proteo alternat 24.7 91 0.002 26.7 3.5 51 117-173 217-267 (270)
231 PF07037 DUF1323: Putative tra 24.5 59 0.0013 25.4 2.0 26 145-173 3-28 (122)
232 TIGR03879 near_KaiC_dom probab 24.2 70 0.0015 22.7 2.2 41 118-165 15-55 (73)
233 PRK09636 RNA polymerase sigma 23.8 4.6E+02 0.01 22.4 12.3 50 118-175 115-164 (293)
234 PF09607 BrkDBD: Brinker DNA-b 23.8 2.2E+02 0.0048 19.4 4.5 44 117-164 4-47 (58)
235 COG3413 Predicted DNA binding 23.3 1.8E+02 0.0039 24.0 4.9 50 116-166 153-202 (215)
236 PRK13890 conjugal transfer pro 23.1 53 0.0011 25.0 1.6 23 145-167 21-43 (120)
237 PRK09726 antitoxin HipB; Provi 23.0 50 0.0011 23.4 1.4 22 145-166 28-49 (88)
238 PF05269 Phage_CII: Bacterioph 22.9 84 0.0018 23.3 2.6 25 143-167 24-48 (91)
239 PRK07500 rpoH2 RNA polymerase 22.4 1.2E+02 0.0025 26.5 3.8 52 117-174 226-277 (289)
240 cd01105 HTH_GlnR-like Helix-Tu 22.4 68 0.0015 22.9 2.0 17 146-162 5-21 (88)
241 PRK07598 RNA polymerase sigma 22.3 1.3E+02 0.0028 28.1 4.3 53 118-174 350-402 (415)
242 PF14410 GH-E: HNH/ENDO VII su 22.0 58 0.0013 22.7 1.5 17 149-165 36-52 (70)
243 PF01710 HTH_Tnp_IS630: Transp 21.7 1.6E+02 0.0035 22.1 4.1 37 120-164 4-40 (119)
244 cd07377 WHTH_GntR Winged helix 21.7 2.2E+02 0.0048 17.9 4.3 25 145-169 28-52 (66)
245 PF06786 UPF0253: Uncharacteri 21.6 1.5E+02 0.0032 20.7 3.3 16 23-38 1-16 (66)
246 PRK00523 hypothetical protein; 21.3 2.7E+02 0.0059 19.8 4.7 32 123-157 26-57 (72)
247 PRK12427 flagellar biosynthesi 21.2 1.5E+02 0.0033 24.8 4.2 47 117-171 182-228 (231)
248 PF13542 HTH_Tnp_ISL3: Helix-t 21.2 94 0.002 19.3 2.3 21 144-164 29-49 (52)
249 PF04936 DUF658: Protein of un 21.1 79 0.0017 26.2 2.3 32 143-174 15-46 (186)
250 PF09636 XkdW: XkdW protein; 21.1 49 0.0011 25.3 1.0 33 119-151 40-73 (108)
251 COG2938 Uncharacterized conser 21.0 1.3E+02 0.0028 22.4 3.2 44 123-168 29-72 (94)
252 TIGR02997 Sig70-cyanoRpoD RNA 20.9 1.5E+02 0.0032 25.8 4.2 50 118-171 249-298 (298)
253 smart00351 PAX Paired Box doma 20.6 2.2E+02 0.0048 21.6 4.6 44 117-168 16-59 (125)
254 PRK09935 transcriptional regul 20.6 2E+02 0.0044 21.9 4.5 46 118-172 149-194 (210)
255 PRK05988 formate dehydrogenase 20.2 4.2E+02 0.0091 21.1 6.3 60 122-184 24-83 (156)
256 TIGR02054 MerD mercuric resist 20.1 80 0.0017 24.2 2.0 20 145-164 6-25 (120)
No 1
>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=99.92 E-value=1.4e-25 Score=149.41 Aligned_cols=51 Identities=57% Similarity=0.992 Sum_probs=49.3
Q ss_pred CCCCCCChhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhhhhc
Q 029411 10 ASRVGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTV 60 (194)
Q Consensus 10 ~~~~~~dpeLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~ql~~L~~ 60 (194)
++++|+||||||||++||.||++|+++|++||+||+.||++||+||++||+
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 578999999999999999999999999999999999999999999999984
No 2
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.90 E-value=3.4e-24 Score=183.39 Aligned_cols=132 Identities=29% Similarity=0.413 Sum_probs=110.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhhhhcCCCCCCCCCCChhhhhccccCCCChhhhHHHHHHHH
Q 029411 17 PALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTVSSNISGQSGSSEEEIDVKDHCIDPLAEDRDLKDQLL 96 (194)
Q Consensus 17 peLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~ql~~L~~~~~~~~~~~sse~e~~~~~~~~~~~~~~~elk~~l~ 96 (194)
..|-|+...|..+|.||+++|.++.+++++.|+ .|.+...+... +-..+...+.
T Consensus 107 ~kL~qiR~iy~~ElekyeqaCneftthV~nlL~---eQsr~RPi~~k-----------------------e~e~m~~~i~ 160 (334)
T KOG0774|consen 107 AKLLQIRQIYHNELEKYEQACNEFTTHVMNLLR---EQSRTRPIMPK-----------------------EIERMVQIIS 160 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HhcccCCCCHH-----------------------HHHHHHHHHH
Confidence 689999999999999999999999999999998 56555444332 2234455555
Q ss_pred HhhcCCccchh-----------HHhh-hccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhH
Q 029411 97 RRYSGSLGSLK-----------QEFL-KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFI 164 (194)
Q Consensus 97 r~y~~~~~~~~-----------~e~~-kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~ 164 (194)
++|+.....++ .++. .+|||++|+|.++.+|++||..|+.||||++++|++||+++|++.+||+|||.
T Consensus 161 ~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfg 240 (334)
T KOG0774|consen 161 KKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFG 240 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccc
Confidence 66655554444 4444 47899999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCCC
Q 029411 165 NQRKRHWKPS 174 (194)
Q Consensus 165 N~R~R~kk~~ 174 (194)
|+|.|.+|.+
T Consensus 241 nkrIrykK~~ 250 (334)
T KOG0774|consen 241 NKRIRYKKNM 250 (334)
T ss_pred cceeehhhhh
Confidence 9999999988
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.88 E-value=1.1e-23 Score=187.13 Aligned_cols=173 Identities=29% Similarity=0.323 Sum_probs=132.1
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHhcCch--HHHHHHHHHHHHHhhhhhcCCCCCCCCC------------------CC
Q 029411 12 RVGDDPALDQFMEAYCEMLTKYEQELTKPF--KDASLFLSEIDAQLKTLTVSSNISGQSG------------------SS 71 (194)
Q Consensus 12 ~~~~dpeLd~fm~~Yc~~L~~y~~el~~p~--~ea~~fl~~ie~ql~~L~~~~~~~~~~~------------------ss 71 (194)
.-+.+++|+.||..|+.+|..+...++... .+++++.++|...+...+.......... ..
T Consensus 111 ~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~ 190 (342)
T KOG0773|consen 111 AWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSS 190 (342)
T ss_pred cchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccc
Confidence 467899999999999999999999999887 6999999999999988776544311100 00
Q ss_pred hh-----hhhccccCCCC---hhhhHHHHHHHHHhhcCCccchhHHhhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHH
Q 029411 72 EE-----EIDVKDHCIDP---LAEDRDLKDQLLRRYSGSLGSLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEP 143 (194)
Q Consensus 72 e~-----e~~~~~~~~~~---~~~~~elk~~l~r~y~~~~~~~~~e~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ 143 (194)
++ +.+.......+ ......++..+...++.+......+..++|+++.||+.++.+|+.|+.+|+.||||++.
T Consensus 191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~ 270 (342)
T KOG0773|consen 191 EELLGESEQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDD 270 (342)
T ss_pred ccccccccccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcch
Confidence 00 00011111111 22334455566666666666666667788999999999999999999999999999999
Q ss_pred HHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCcccccccc
Q 029411 144 QKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISI 184 (194)
Q Consensus 144 ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~~~~~~~ 184 (194)
+|..||.+|||+..||+|||||+|+|.|+|+.+..+..++.
T Consensus 271 ~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~~~~~~~ 311 (342)
T KOG0773|consen 271 EKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEEMYLLEDK 311 (342)
T ss_pred hccccchhcCCCcccCCchhhhcccccCCchHHHHHHHhhc
Confidence 99999999999999999999999999999997665555554
No 4
>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=99.75 E-value=1.3e-18 Score=110.53 Aligned_cols=40 Identities=55% Similarity=0.993 Sum_probs=36.4
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhh
Q 029411 130 WWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKR 169 (194)
Q Consensus 130 wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R 169 (194)
||..|..|||||.++|..||..|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 8999999999999999999999999999999999999997
No 5
>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=99.63 E-value=9.2e-16 Score=102.51 Aligned_cols=57 Identities=28% Similarity=0.575 Sum_probs=54.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 114 KKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 114 rkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
+++..+++.+..+|+.||..| |||+..++..||..|||+.+||.+||.|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~---~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKN---PYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567899999999999999998 999999999999999999999999999999998764
No 6
>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=99.60 E-value=1.4e-15 Score=101.95 Aligned_cols=57 Identities=35% Similarity=0.765 Sum_probs=54.2
Q ss_pred ccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 113 KKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 113 krkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
||++..|+.++..+|+.+|..+ |||+.+++..||..+||+..||.+||+|+|.+.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~---~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQEN---PYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHS---SSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHh---ccccccccccccccccccccccccCHHHhHHHhCc
Confidence 5788999999999999999998 99999999999999999999999999999998764
No 7
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.60 E-value=2.7e-15 Score=99.67 Aligned_cols=55 Identities=29% Similarity=0.567 Sum_probs=51.7
Q ss_pred cCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411 114 KKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHW 171 (194)
Q Consensus 114 rkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k 171 (194)
+.+..|++++..+|+.||..| |||+.+++..||..+||+..||.+||+|+|.+.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~---~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKN---PYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhC---CCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 456779999999999999999 9999999999999999999999999999999864
No 8
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.48 E-value=3.5e-14 Score=122.60 Aligned_cols=50 Identities=44% Similarity=0.860 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 122 EARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 122 ~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..+.+|++||..+ |||++.+|.+||+.||||..||.|||.|+|.|.|...
T Consensus 186 kSR~~LrewY~~~---~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 186 KSRSLLREWYLQN---PYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred hhHHHHHHHHhcC---CCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence 6899999999988 9999999999999999999999999999999999544
No 9
>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=99.13 E-value=7.2e-11 Score=80.68 Aligned_cols=53 Identities=19% Similarity=0.425 Sum_probs=50.5
Q ss_pred hccCCCCCCHHHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChHHHhhhhHHHH
Q 029411 112 KKKKKGKLPKEARQLLLDWWSRHHRWPY----PSEPQKLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 112 kkrkr~~l~k~~~~~L~~wf~~h~~~PY----Ps~~ek~~LA~~tgLt~~QV~nWF~N~R 167 (194)
+||.|+.|+.++...|+..|..+ +| |+..++..||..+||+..+|.+||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~---~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKL---GWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHc---CCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 47899999999999999999999 99 9999999999999999999999999954
No 10
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.09 E-value=7.8e-11 Score=96.67 Aligned_cols=61 Identities=23% Similarity=0.355 Sum_probs=57.6
Q ss_pred hhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 111 LKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 111 ~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
+-||.|+.|+.++...|+..|..+ .|-.-.||..||..++||..||.+||+|+|.|+|+.-
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~---~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGN---QYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcC---CeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence 357888999999999999999999 9999999999999999999999999999999998855
No 11
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.04 E-value=1.1e-10 Score=103.08 Aligned_cols=63 Identities=25% Similarity=0.391 Sum_probs=57.2
Q ss_pred hhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 111 LKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 111 ~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
+|||+|--|++.++-.|++-|.+. -|.|-.||+.||...+||++||.+||+|+|.+-|+.-.+
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQ---RYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQ---RYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred cccccccccchhHHHHHHHHHHhh---hccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence 455666699999999999999999 999999999999999999999999999999998886533
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.03 E-value=1.9e-10 Score=97.51 Aligned_cols=60 Identities=28% Similarity=0.420 Sum_probs=56.7
Q ss_pred ccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 113 KKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 113 krkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
||.|+.++.-+.+.|+.-|++. .|.--.||.+||..+|||..||.+||+|+|-+.||.+.
T Consensus 123 RKPRTIYSS~QLqaL~rRFQkT---QYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQT---QYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cCCcccccHHHHHHHHHHHhhc---chhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 5677899999999999999999 99999999999999999999999999999999999774
No 13
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.00 E-value=2.1e-10 Score=101.38 Aligned_cols=64 Identities=22% Similarity=0.353 Sum_probs=58.8
Q ss_pred hccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCcc
Q 029411 112 KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQ 178 (194)
Q Consensus 112 kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~ 178 (194)
-+|||-.++|.|+..|+.-|.-| =|.|.+-|.+|++.++||..||.+||||+|.+.||-..+..
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN---~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFN---MYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHH---HHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 46777899999999999999999 99999999999999999999999999999999999885433
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.92 E-value=7e-10 Score=96.16 Aligned_cols=61 Identities=20% Similarity=0.356 Sum_probs=57.7
Q ss_pred hhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 111 LKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 111 ~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||.|+.|+..++..|+.=|.-| .|.|...|.++|..+.||..||.+||+|+|.+.||-.
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN---~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFN---KYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhccc---cccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 368899999999999999999999 9999999999999999999999999999999998765
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.91 E-value=1.8e-09 Score=93.36 Aligned_cols=60 Identities=28% Similarity=0.452 Sum_probs=57.4
Q ss_pred ccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 113 KKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 113 krkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
||.|+-|+.++.+-|+.-|.+| -|.|+.-|..||.++||...||..||+|+|.+.||...
T Consensus 247 KRPRTAFtaeQL~RLK~EF~en---RYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQEN---RYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred cCccccccHHHHHHHHHHHhhh---hhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 6788899999999999999999 99999999999999999999999999999999999874
No 16
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.87 E-value=1.1e-09 Score=99.16 Aligned_cols=63 Identities=24% Similarity=0.433 Sum_probs=59.8
Q ss_pred hhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 110 FLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 110 ~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
.+|||||+.+.-.++..|+..|..| |-||.+|.-.||.+++|.+.-|++||||+|.+.|+...
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~n---pKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKN---PKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhC---CCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3678889999999999999999999 99999999999999999999999999999999999875
No 17
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.85 E-value=2.6e-09 Score=86.38 Aligned_cols=60 Identities=25% Similarity=0.419 Sum_probs=56.7
Q ss_pred hccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 112 KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 112 kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.+++|.+.+..+..+|+..|..+ |||+..+|..|+..+||+++-|..||+|+|.+.|+..
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~---p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEIN---PYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred CcccceechHHHHHHHHHHhccC---CCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 46778889999999999999999 9999999999999999999999999999999998876
No 18
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.82 E-value=3.5e-09 Score=88.62 Aligned_cols=60 Identities=28% Similarity=0.389 Sum_probs=54.7
Q ss_pred hccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 112 KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 112 kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.+.|+.+|+.++...|+.-|..| -|..+..|..||+++||++.||.+||+|+|.|-|..-
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~---~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESE---KKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccccHHHHHHhHHhhccc---cccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 45777889999999999999999 9999999999999999999999999999999965443
No 19
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.80 E-value=3.1e-09 Score=89.77 Aligned_cols=61 Identities=25% Similarity=0.343 Sum_probs=57.4
Q ss_pred hhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 111 LKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 111 ~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.|||.|+.|+..++..|+.-|... -|.+..+|..||.++.||..||..||+|+|.+-|+..
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~k---rYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELK---RYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHH---hhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 478889999999999999999999 9999999999999999999999999999999977755
No 20
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.80 E-value=2.7e-09 Score=86.69 Aligned_cols=68 Identities=25% Similarity=0.418 Sum_probs=60.9
Q ss_pred hhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCcccc
Q 029411 110 FLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFN 180 (194)
Q Consensus 110 ~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~~~ 180 (194)
..++|-|..|+..+...|+.-|+.. -|.+-.++.+||..++|+.+||..||+|+|.++||.-+.-+..
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~Q---rYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~ 165 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFERQ---RYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPK 165 (194)
T ss_pred HHhhhhcccccCccccccHHHHhhh---hhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 3456777899999999999999999 9999999999999999999999999999999999987665543
No 21
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.78 E-value=5.8e-09 Score=79.04 Aligned_cols=68 Identities=16% Similarity=0.287 Sum_probs=61.0
Q ss_pred cchhHHhhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 104 GSLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 104 ~~~~~e~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.++.+..+.+|-|+.|+..+...|+..|.+. -||..-.+++||....||...|.+||+|+|.+.+|.-
T Consensus 9 ~~l~ekrKQRRIRTTFTS~QLkELErvF~ET---HYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 9 LGLTEKRKQRRIRTTFTSAQLKELERVFAET---HYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred CChhHHHHhhhhhhhhhHHHHHHHHHHHHhh---cCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 4455555667888999999999999999999 9999999999999999999999999999999998864
No 22
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.77 E-value=6.6e-09 Score=92.24 Aligned_cols=64 Identities=22% Similarity=0.416 Sum_probs=56.8
Q ss_pred hhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 110 FLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 110 ~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
.+++|.|+-|+..++..|+.-|..- =|.+..+|..||..+|||-.||.+||+|+|.+-|+..+.
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~Q---KYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQ---KYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHh---hcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 3446677899999999999999999 999999999999999999999999999998886665533
No 23
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.75 E-value=7e-09 Score=87.05 Aligned_cols=68 Identities=18% Similarity=0.292 Sum_probs=60.3
Q ss_pred cchhHHhhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 104 GSLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 104 ~~~~~e~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..|++-...++.|+.|+..+...|++=|.+. .|.+.+|+.+++..+.||..||..||+|+|.|.|+--
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfrek---qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFREK---QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhHh---hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 3444444457788999999999999999999 9999999999999999999999999999999988754
No 24
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.65 E-value=2.3e-08 Score=84.49 Aligned_cols=60 Identities=17% Similarity=0.419 Sum_probs=55.8
Q ss_pred hccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 112 KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 112 kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.+|-|+.|+..+..+|+.-|.+- .||+...+++||.+.+|...+|.+||.|+|.+.++.-
T Consensus 37 qRRERTtFtr~QlevLe~LF~kT---qYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAKT---QYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred cccccceecHHHHHHHHHHHHhh---cCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 46888999999999999999999 9999999999999999999999999999998876543
No 25
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.54 E-value=7.8e-08 Score=83.21 Aligned_cols=54 Identities=24% Similarity=0.362 Sum_probs=51.0
Q ss_pred CCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 116 KGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 116 r~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
|+.|+..+...|+.-|.+. -||+...|+.||..|+|....|.+||+|+|.+-+|
T Consensus 145 RTiFT~~Qle~LEkaFkea---HYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk 198 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEA---HYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRK 198 (332)
T ss_pred cchhhHHHHHHHHHHHhhc---cCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhh
Confidence 7799999999999999999 99999999999999999999999999999987544
No 26
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.48 E-value=6.4e-08 Score=85.50 Aligned_cols=64 Identities=22% Similarity=0.413 Sum_probs=56.1
Q ss_pred hccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCcc
Q 029411 112 KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQ 178 (194)
Q Consensus 112 kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~ 178 (194)
++|-|..|+..+.+.|+.||..| -||+.+.++++|.-|+||...|++||.|+|.+-+|.-..++
T Consensus 112 qrrQrthFtSqqlqele~tF~rN---rypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQRN---RYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhhc---cCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 45667799999999999999998 99999999999999999999999999999988555443333
No 27
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.45 E-value=6e-08 Score=84.13 Aligned_cols=58 Identities=26% Similarity=0.374 Sum_probs=52.8
Q ss_pred cCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 114 KKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 114 rkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
|-|-.++..++-.|+.-|-.. +|.|..-|.+||..+||++.||..||+|+|.+.||..
T Consensus 201 KYRvVYTDhQRLELEKEfh~S---ryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTS---RYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ceeEEecchhhhhhhhhhccc---cceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 345578889999999999888 9999999999999999999999999999999988765
No 28
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.34 E-value=6.5e-07 Score=84.03 Aligned_cols=57 Identities=19% Similarity=0.338 Sum_probs=54.2
Q ss_pred hhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhc
Q 029411 111 LKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRH 170 (194)
Q Consensus 111 ~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~ 170 (194)
..||.|-.|+..+++.|...|.++ +||+.+.-+.|+.++||....|.|||-|+|+|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~---~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKEN---KRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcC---CCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 357788899999999999999999 999999999999999999999999999999994
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.33 E-value=2.7e-07 Score=80.98 Aligned_cols=68 Identities=21% Similarity=0.408 Sum_probs=60.9
Q ss_pred chhHHhhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 105 SLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 105 ~~~~e~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
+|..+...||.|+.++..+...|+.-|... |-|..--|++|+..|||+..-|++||+|+|.+.|+-..
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~S---pKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNTS---PKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcCC---CchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 555566789999999999999999999988 99999999999999999999999999999987766553
No 30
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.09 E-value=7e-07 Score=78.46 Aligned_cols=62 Identities=26% Similarity=0.437 Sum_probs=56.8
Q ss_pred HhhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 109 EFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 109 e~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
...|||||+.+-..-++-|++||... |-|+.+-...+|+++.|...-|++||+|+|.+.|+-
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQ---PRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQ---PRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred ccccccccccccCcccccHHHHhccC---CCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 34578899888888899999999999 999999999999999999999999999999998873
No 31
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.08 E-value=4.7e-06 Score=75.36 Aligned_cols=63 Identities=24% Similarity=0.493 Sum_probs=56.7
Q ss_pred hhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 111 LKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 111 ~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
..+|.|..|+..+...|..+|... |||....++.||.++||+...|..||.|+|.+.++....
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~rt---~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQRT---PYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccchHHHHHHHhcCC---CCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 345567789999999999999999 899999999999999999999999999999988776643
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.04 E-value=1.8e-06 Score=71.67 Aligned_cols=62 Identities=21% Similarity=0.240 Sum_probs=57.1
Q ss_pred hhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 110 FLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 110 ~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
+++++.|..|+..+.+.|+.-|... +||....++.||..+++++..|.+||+|+|.+.++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~---h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKV---HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCC---CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 3467888899999999999999999 9999999999999999999999999999999887654
No 33
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=98.00 E-value=2.2e-06 Score=75.88 Aligned_cols=59 Identities=24% Similarity=0.420 Sum_probs=53.2
Q ss_pred ccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 113 KKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 113 krkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
+|-|+-|+.+++.-|+.-|+.. -|-+...|.+||..++|....|.+||+|+|.+.|++-
T Consensus 182 RRYRTAFTReQIaRLEKEFyrE---NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEFYRE---NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred HHHHhhhhHHHHHHHHHHHHHh---ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 3556889999999998888877 7999999999999999999999999999999998765
No 34
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.98 E-value=3.9e-06 Score=71.33 Aligned_cols=62 Identities=18% Similarity=0.303 Sum_probs=54.6
Q ss_pred hhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 110 FLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 110 ~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
-++|..+..|+..++..|..-|.+. .||--.++.+||...|++..||.+||+|+|.+-+|..
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqt---kylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQT---KYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhh---hcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 3455556679999999999999999 9999999999999999999999999999998866544
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.86 E-value=1.6e-05 Score=53.94 Aligned_cols=43 Identities=21% Similarity=0.423 Sum_probs=32.0
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhh
Q 029411 124 RQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKR 169 (194)
Q Consensus 124 ~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R 169 (194)
.+.|..+|..| .++.+.+-..|+.++||+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~h---~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKH---KQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT-------TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHc---CCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 46699999999 99999999999999999999999999877543
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.57 E-value=3.1e-05 Score=69.02 Aligned_cols=62 Identities=35% Similarity=0.600 Sum_probs=57.1
Q ss_pred hccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 112 KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 112 kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
...++++++.+. ..|..|...|..+|||+..++..|+..++++..||.+||+|.|+|.++-.
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 456778889998 99999999999999999999999999999999999999999999987754
No 37
>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=97.20 E-value=0.00011 Score=40.81 Aligned_cols=22 Identities=64% Similarity=1.005 Sum_probs=20.3
Q ss_pred HHHHHHHHhhcCCccchhHHhh
Q 029411 90 DLKDQLLRRYSGSLGSLKQEFL 111 (194)
Q Consensus 90 elk~~l~r~y~~~~~~~~~e~~ 111 (194)
|||.+|+++|+++++++++||+
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 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.22 E-value=0.0031 Score=52.24 Aligned_cols=60 Identities=25% Similarity=0.475 Sum_probs=53.2
Q ss_pred hccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 112 KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 112 kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.++.+..+...+...|..-|... +||....+..|+..+|++..-|.+||+|.|.+.++..
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~---~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRAT---PKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cCCCccccccchhHhhhhcccCC---CCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 35566788888889998888888 9999999999999999999999999999999998643
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=94.79 E-value=0.037 Score=57.31 Aligned_cols=73 Identities=15% Similarity=0.197 Sum_probs=63.0
Q ss_pred hhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCccccccccc
Q 029411 110 FLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISIM 185 (194)
Q Consensus 110 ~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~~~~~~~~ 185 (194)
..+++.+..++..+..+++..|..- -||+.++-+.|.+..+|.+.-|..||+|.|.+-+|+.+...-...++.
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q---~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~~~~ss~~~ 973 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQ---RTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNGTAASSTGG 973 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhc---cCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcccccccccc
Confidence 3456778888999999999999999 999999999999999999999999999999999999985544444443
No 40
>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=94.13 E-value=0.23 Score=41.50 Aligned_cols=68 Identities=25% Similarity=0.248 Sum_probs=53.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhhhhcCCCCCCCCCCChhhhhccccCCCChhhhHHHHHHHH
Q 029411 17 PALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTVSSNISGQSGSSEEEIDVKDHCIDPLAEDRDLKDQLL 96 (194)
Q Consensus 17 peLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~ql~~L~~~~~~~~~~~sse~e~~~~~~~~~~~~~~~elk~~l~ 96 (194)
.+|-++...|..+|.+|++.+..+..+.++.|+ .|-+...++. .+-+.+...+.
T Consensus 111 ~kL~~ir~~y~~el~kye~ac~eF~~hV~~lLr---eQs~~RPIs~-----------------------keiE~m~~~i~ 164 (191)
T PF03792_consen 111 AKLSQIRQIYHSELEKYEQACNEFTEHVMNLLR---EQSEFRPISP-----------------------KEIERMVNIIH 164 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHH---HhcccCCCCH-----------------------HHHHHHHHHHH
Confidence 489999999999999999999999999999998 5555544433 23445667788
Q ss_pred HhhcCCccchhHHh
Q 029411 97 RRYSGSLGSLKQEF 110 (194)
Q Consensus 97 r~y~~~~~~~~~e~ 110 (194)
+||+++...|++..
T Consensus 165 ~Kf~~iq~qLKQst 178 (191)
T PF03792_consen 165 RKFSKIQMQLKQST 178 (191)
T ss_pred HHHHHHHHHHHHHH
Confidence 99998888888753
No 41
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.04 E-value=0.23 Score=32.92 Aligned_cols=48 Identities=19% Similarity=0.300 Sum_probs=33.5
Q ss_pred ccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHh
Q 029411 113 KKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRK 168 (194)
Q Consensus 113 krkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~ 168 (194)
||+|..|+-+..-.+-..+... | -...||+.+|++..+|++|..|+.+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g-----~---s~~~ia~~fgv~~sTv~~I~K~k~~ 48 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEG-----E---SKRDIAREFGVSRSTVSTILKNKDK 48 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCT-----T----HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHcC-----C---CHHHHHHHhCCCHHHHHHHHHhHHH
Confidence 4677788888766555556666 3 5789999999999999999999643
No 42
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=90.04 E-value=8.1 Score=31.20 Aligned_cols=140 Identities=14% Similarity=0.131 Sum_probs=79.7
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHH----HhhhhhcCCCC------------------CCCCC
Q 029411 12 RVGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDA----QLKTLTVSSNI------------------SGQSG 69 (194)
Q Consensus 12 ~~~~dpeLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~----ql~~L~~~~~~------------------~~~~~ 69 (194)
..+++..+.++++.|...|..|---+....++|..+++.+=- .+..+...... .....
T Consensus 5 ~~~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~~~~awL~~Ia~n~~~d~~R~~~~~~ 84 (187)
T PRK12516 5 SVEGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREV 84 (187)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcccHHHHHHHHHHHHHHHHHHhhcCCc
Confidence 456678999999999999999999998877777777663211 11222111110 00000
Q ss_pred CChhhhhccccCCCChhhhHHHHHHHHHhhcCCccchhHHhhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHH
Q 029411 70 SSEEEIDVKDHCIDPLAEDRDLKDQLLRRYSGSLGSLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALA 149 (194)
Q Consensus 70 sse~e~~~~~~~~~~~~~~~elk~~l~r~y~~~~~~~~~e~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA 149 (194)
...++.........+.....+.... +..- =..||...+.++.-.+.+.+ + -.++|
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~-----------l~~~------L~~Lp~~~r~i~~L~~~~g~--s------~~EIA 139 (187)
T PRK12516 85 QDTDGMFTEQLAVHPSQYGTLDLQD-----------FRAA------LDQLPDDQREAIILVGASGF--A------YEEAA 139 (187)
T ss_pred cccccccccccCCCcchhhHHHHHH-----------HHHH------HHhCCHHHHHHHHHHHHcCC--C------HHHHH
Confidence 0000000000000111111110011 1111 13578889988877666551 2 34789
Q ss_pred HHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 150 ESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 150 ~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
..+|++...|.++....|++.++..+.
T Consensus 140 ~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 140 EICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999887643
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=88.78 E-value=0.82 Score=31.31 Aligned_cols=46 Identities=15% Similarity=0.306 Sum_probs=30.9
Q ss_pred cCCCCCCHHHHH-HHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHH
Q 029411 114 KKKGKLPKEARQ-LLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 114 rkr~~l~k~~~~-~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R 167 (194)
+++..||++.+. ++...+... .....+|...|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g--------~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG--------ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH--------CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC--------CceEeeecccccccccccHHHHHHh
Confidence 456788888864 445554444 5788999999999999999988777
No 44
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=88.64 E-value=9.6 Score=29.44 Aligned_cols=49 Identities=16% Similarity=0.172 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.++...+... -.-..+|..+|++...|.+|..-.|++.++..
T Consensus 125 ~L~~~~r~i~~l~~~~~--------~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 125 ALPVKQREVFLLRYVEG--------LSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred hCCHHHHHHhhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888887655544 23368999999999999999999999987644
No 45
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=88.32 E-value=8.5 Score=30.87 Aligned_cols=50 Identities=22% Similarity=0.299 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.|... -.-.++|+.+|++...|.+...-.|++.+++.
T Consensus 130 ~~L~~~~r~i~~l~~~~g--------~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG--------EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred HhCCHHHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 478999999998766555 13458999999999999999999999998876
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=87.74 E-value=1.3 Score=28.53 Aligned_cols=44 Identities=20% Similarity=0.382 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhh
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKR 169 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R 169 (194)
.+|+..+.++.-.|... -.-.++|..+|+|+..|.+|....|++
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 57888888887766665 345689999999999999999998876
No 47
>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=87.70 E-value=1.4 Score=26.91 Aligned_cols=46 Identities=20% Similarity=0.303 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHW 171 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k 171 (194)
.+|...+.++...+... -.-..+|..+|++..+|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46777888887776555 13457799999999999999988887653
No 48
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=85.48 E-value=1.3 Score=28.31 Aligned_cols=46 Identities=15% Similarity=0.220 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHW 171 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k 171 (194)
.||+..+.+|...|... -.-.++|..+|++...|+.+......+.|
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 57888999998887444 23568899999999999999998887765
No 49
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=84.91 E-value=1.7 Score=43.30 Aligned_cols=46 Identities=22% Similarity=0.441 Sum_probs=42.1
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 124 RQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 124 ~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
..+|+.+|..| +.|++++-..+|.+-||...-|..||.+.+.....
T Consensus 568 ~sllkayyaln---~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~s 613 (1007)
T KOG3623|consen 568 TSLLKAYYALN---GLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMS 613 (1007)
T ss_pred HHHHHHHHHhc---CCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhh
Confidence 78899999999 99999999999999999999999999998876543
No 50
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=82.70 E-value=3.1 Score=22.62 Aligned_cols=39 Identities=13% Similarity=0.137 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhh
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWF 163 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF 163 (194)
..++.+....+...+.. .+ ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 34566666666555543 33 35578899999999999984
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=80.19 E-value=3 Score=31.94 Aligned_cols=48 Identities=8% Similarity=0.085 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
..||+..+.++...|... -.-.++|..+|++...|.+|....|++.++
T Consensus 105 ~~L~~~~r~ii~l~~~~~--------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 105 SVLDEKEKYIIFERFFVG--------KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred HhCCHHHHHHHHHHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 468898999887665555 135689999999999999999999998875
No 52
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=79.07 E-value=24 Score=27.94 Aligned_cols=50 Identities=16% Similarity=0.234 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.+||+..+.++.-.+..+ -.-.++|..+|++...|.++..-.|++.++-.
T Consensus 126 ~~L~~~~r~v~~l~~~~g--------~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 126 MSLPIKYREVIYLFYYEE--------LSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred HhCCHHHhhHhHhHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 368999999987665555 13458999999999999999999999887643
No 53
>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=78.99 E-value=28 Score=27.04 Aligned_cols=49 Identities=10% Similarity=0.084 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||...+.++..-+... -.-..+|..+|+|...|.++..-.|++.++-.
T Consensus 119 ~L~~~~r~i~~l~~~~g--------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 57888888887666555 13357899999999999999999999887643
No 54
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=78.16 E-value=36 Score=27.86 Aligned_cols=51 Identities=14% Similarity=0.108 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
..||+..+.++.-.+..+ + .-.++|..+|++...|.++..-.|++.++-.+
T Consensus 137 ~~L~~~~r~v~~L~~~~g----~----s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 137 DSLPPEFRAAVVLCDIEG----L----SYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 367888888775555444 1 23578999999999999999999999987553
No 55
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=77.94 E-value=2.6 Score=32.68 Aligned_cols=52 Identities=17% Similarity=0.222 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCc
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDM 177 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~ 177 (194)
.||+..+.++.-.+.+.+ .-.++|..+|++...|.+.+...|++.++.....
T Consensus 106 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEK--------SYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred hCCHHHHHHHHHHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 589999999877666551 2348999999999999999999999988765443
No 56
>PRK00118 putative DNA-binding protein; Validated
Probab=77.41 E-value=2 Score=32.53 Aligned_cols=55 Identities=11% Similarity=0.108 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCccc
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQF 179 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~~ 179 (194)
..+|..++.++..++... -.-..+|+.+|+++..|.+|+...|++.++-.+.+.+
T Consensus 16 ~~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~ 70 (104)
T PRK00118 16 SLLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL 70 (104)
T ss_pred ccCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence 356788888887777766 2345699999999999999999999998876655443
No 57
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=73.06 E-value=5.7 Score=31.69 Aligned_cols=52 Identities=15% Similarity=0.135 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 116 KGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 116 r~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
...||+.++.+|... .+. + .-.++|..+|++...|++|..+.+++.++-.+.
T Consensus 4 ~~~Lt~rqreVL~lr-~~G----l----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERG----L----TQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred ccCCCHHHHHHHHHH-HcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999773 333 2 345899999999999999999999988776544
No 58
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=73.04 E-value=47 Score=26.66 Aligned_cols=51 Identities=18% Similarity=0.099 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
.||+..+.+|.-.+... -.-.++|..+|++...|.+=+...|++.++..+.
T Consensus 134 ~Lp~~~r~i~~l~~~~g--------~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~ 184 (192)
T PRK09643 134 RLPVEQRAALVAVDMQG--------YSVADAARMLGVAEGTVKSRCARGRARLAELLGY 184 (192)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 48888899887655555 1335789999999999999888888888876543
No 59
>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=72.14 E-value=5.8 Score=29.18 Aligned_cols=47 Identities=21% Similarity=0.326 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
.||+..+.++...+... + .-..+|..+|+++..|.++....+.+.++
T Consensus 110 ~L~~~~~~ii~~~~~~g----~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG----L----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 56777888875544433 2 34489999999999999999999988765
No 60
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=71.54 E-value=5.6 Score=31.04 Aligned_cols=51 Identities=18% Similarity=0.036 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
..||+..+.++.-++..+ -.-.++|..+|++...|.+|..-.|++.++-.+
T Consensus 107 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--------LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 568899999998777666 234689999999999999999999999877543
No 61
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=71.16 E-value=6 Score=30.65 Aligned_cols=50 Identities=26% Similarity=0.180 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+.++.++.-.+..++ .-.++|..+|++...|.++....|++.++..
T Consensus 111 ~~L~~~~r~v~~l~~~~~~--------s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYGF--------SYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HHCCHHHHHHhhhHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 4689999999987766661 2357899999999999999999999987643
No 62
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=71.02 E-value=5.2 Score=33.45 Aligned_cols=53 Identities=17% Similarity=0.109 Sum_probs=43.7
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCc
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDM 177 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~ 177 (194)
..||...+.++.-.|..++ .-.++|..+|++...|.++....|++.++..+..
T Consensus 133 ~~Lp~~~R~v~~L~y~eg~--------s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 133 AKLPVEYREVLVLRELEDM--------SYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred HcCCHHHHhHhhhHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 3688889999988777761 2347899999999999999999999999877443
No 63
>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=70.70 E-value=4.3 Score=32.12 Aligned_cols=50 Identities=10% Similarity=-0.027 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.|..+ -.-.++|..+|++...|.++....|++.++..
T Consensus 137 ~~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 137 EALPEDLRTAITLRELEG--------LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred HcCCHHHhhhhhhhhhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 356788888887655554 23458899999999999999999999988654
No 64
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=70.49 E-value=52 Score=26.18 Aligned_cols=49 Identities=18% Similarity=0.205 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.++.-.+... -.-.++|..+|++...|.++....|++.++..
T Consensus 139 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHGD--------LELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehccC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57777788776654444 13457899999999999999999999988644
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=70.38 E-value=5.7 Score=31.35 Aligned_cols=49 Identities=12% Similarity=0.141 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+..+.++...|... + .-.++|..+|++...|.+++...|++.++.
T Consensus 128 ~~L~~~~r~i~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 128 EELEKDRAAAVRRAYLEG----L----SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred HhCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 357888888888777655 1 245789999999999999999999998764
No 66
>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=70.26 E-value=7.4 Score=29.82 Aligned_cols=48 Identities=29% Similarity=0.297 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
..||+..+.++...+... -.-.++|..+|++...|.++....|++.++
T Consensus 110 ~~L~~~~r~v~~l~~~~g--------~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG--------VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 468888999988755554 134578999999999999999999988765
No 67
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=69.04 E-value=6.5 Score=30.52 Aligned_cols=49 Identities=16% Similarity=0.099 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.++...+... + .-..+|..+|++...|.+|....+++.++..
T Consensus 128 ~L~~~~r~vl~l~~~~~----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIEG----L----SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888888887655444 1 2347899999999999999999999987644
No 68
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=68.39 E-value=10 Score=30.19 Aligned_cols=43 Identities=14% Similarity=0.319 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhc---------------CchHHHHHHHHHHHHHhhhhhcCC
Q 029411 18 ALDQFMEAYCEMLTKYEQELT---------------KPFKDASLFLSEIDAQLKTLTVSS 62 (194)
Q Consensus 18 eLd~fm~~Yc~~L~~y~~el~---------------~p~~ea~~fl~~ie~ql~~L~~~~ 62 (194)
+|-..++..+.-...|.++++ +|| +..+|++|++||+||...+
T Consensus 81 KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~Y--talAlqamSrhFR~LRdaI 138 (140)
T PF07526_consen 81 KLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPY--TALALQAMSRHFRCLRDAI 138 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhh--HHHHHHHHHHHHHHHHHHh
Confidence 344556666666677777764 355 4789999999999998754
No 69
>PF13518 HTH_28: Helix-turn-helix domain
Probab=68.18 E-value=6.7 Score=24.54 Aligned_cols=24 Identities=17% Similarity=0.429 Sum_probs=20.7
Q ss_pred HHHHHHHhCCChHHHhhhhHHHHh
Q 029411 145 KLALAESTGLDQKQINNWFINQRK 168 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~R~ 168 (194)
...+|..+|++..+|.+|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456999999999999999987765
No 70
>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=68.09 E-value=8.2 Score=29.19 Aligned_cols=47 Identities=21% Similarity=0.251 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
.||...+.++.-.+... + .-.++|..+|+++..|.++....|++.++
T Consensus 113 ~L~~~~r~il~l~~~~~----~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG----K----SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 57888888887655443 2 23468999999999999999999988775
No 71
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=68.06 E-value=6.7 Score=31.61 Aligned_cols=49 Identities=10% Similarity=-0.032 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.+|.-.+..+ -.-.++|+.+|++...|.+++...|++.++..
T Consensus 142 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 58999999997766666 23457899999999999999999999887643
No 72
>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=65.21 E-value=9.3 Score=30.10 Aligned_cols=47 Identities=9% Similarity=0.010 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
.||+.++.++.-.+.+.+ .-.++|..+|+++..|.+.+...|++.++
T Consensus 134 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAGL--------TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred cCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 489999999887766651 34588999999999999999999998765
No 73
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=64.94 E-value=8.4 Score=31.50 Aligned_cols=50 Identities=10% Similarity=0.082 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++...+... -.-.++|..+|++...|.+++...+++.++..
T Consensus 152 ~~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 152 EKLPEAQQTVVKGVYFQE--------LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358888999988665555 23458999999999999999999999887654
No 74
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=64.88 E-value=25 Score=21.55 Aligned_cols=47 Identities=17% Similarity=0.222 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
.|+.....++..+ ... + ....+|..+|++...|..|....+.+..-.
T Consensus 3 ~l~~~e~~i~~~~-~~g----~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLL-AEG----L----TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHH-HcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 4677777777543 322 2 346889999999999999999888776533
No 75
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=64.04 E-value=8.2 Score=30.56 Aligned_cols=51 Identities=8% Similarity=-0.021 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
..||+..+.++...+... -.-.++|..+|++...|.+++...|++.+....
T Consensus 130 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 130 ETLPPRQRDVVQSISVEG--------ASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 368888999998876555 234689999999999999999999999876553
No 76
>PRK06930 positive control sigma-like factor; Validated
Probab=63.76 E-value=6.5 Score=31.98 Aligned_cols=57 Identities=9% Similarity=0.097 Sum_probs=45.1
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCccccc
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFND 181 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~~~~ 181 (194)
..||+..+.++.-.+... -.-..+|..+|++...|.+++...+++.++....-.||.
T Consensus 113 ~~L~~rer~V~~L~~~eg--------~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~l~~~ 169 (170)
T PRK06930 113 SVLTEREKEVYLMHRGYG--------LSYSEIADYLNIKKSTVQSMIERAEKKIARQINESLFCM 169 (170)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 468888999887755444 134578999999999999999999999988776666654
No 77
>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=63.57 E-value=7.6 Score=30.64 Aligned_cols=52 Identities=21% Similarity=0.136 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
..||+..+.+|.-.+.+. -.-.++|..+|++...|.++..-.|++.++-...
T Consensus 99 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 99 KELPDEYREAIRLTELEG--------LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 368888999988776666 2345899999999999999999999998886643
No 78
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=63.12 E-value=5.9 Score=25.99 Aligned_cols=23 Identities=17% Similarity=0.339 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChHHHhhhhHHH
Q 029411 144 QKLALAESTGLDQKQINNWFINQ 166 (194)
Q Consensus 144 ek~~LA~~tgLt~~QV~nWF~N~ 166 (194)
....||+.+|++..+|+.|+.+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 45689999999999999999976
No 79
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=63.10 E-value=10 Score=29.33 Aligned_cols=49 Identities=20% Similarity=0.345 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.+|.-.+ .. + .-..+|..+|++...|.++....|++.++..
T Consensus 111 ~~L~~~~r~il~l~~-~g----~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 111 AKMTERDRTVLLLRF-SG----Y----SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred HcCCHHHHHHHHHHH-cC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 357888888887776 44 2 3457899999999999999999999987754
No 80
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=62.98 E-value=8.8 Score=30.51 Aligned_cols=50 Identities=10% Similarity=0.177 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
.||+..+.++...|... -.-.++|+.+|++...|.++....|++.++-..
T Consensus 128 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 128 ALPERQREAIVLQYYQG--------LSNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred hCCHHHHHHhhHHHhcC--------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 47888888886655544 134578999999999999999999999887543
No 81
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=62.98 E-value=10 Score=30.17 Aligned_cols=49 Identities=16% Similarity=0.081 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+..+.++...|... ..-.++|..+|++...|.++....|++.++.
T Consensus 138 ~~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 138 DTLPEKQREILILRVVVG--------LSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 468888888888765555 2356899999999999999999999988764
No 82
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=62.64 E-value=12 Score=30.43 Aligned_cols=55 Identities=16% Similarity=0.031 Sum_probs=44.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCccc
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQF 179 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~~ 179 (194)
.+||+..+.++.--+..+ -.-.++|..+|+++..|.++....|++.++.....+.
T Consensus 132 ~~Lp~~~r~v~~l~~~~g--------~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 186 (196)
T PRK12535 132 DALPPERREALILTQVLG--------YTYEEAAKIADVRVGTIRSRVARARADLIAATATGQA 186 (196)
T ss_pred HcCCHHHHHHhhhHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccc
Confidence 458898999887776666 2345899999999999999999999999988765553
No 83
>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=62.36 E-value=20 Score=23.27 Aligned_cols=48 Identities=15% Similarity=0.097 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.|++....+|.-+..-. .-.++|...|++++.|.++..+.+++..-+.
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 46777788887665444 5568899999999999999999999876543
No 84
>PRK04217 hypothetical protein; Provisional
Probab=62.13 E-value=13 Score=28.33 Aligned_cols=51 Identities=10% Similarity=-0.085 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 116 KGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 116 r~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
-..++.+.+.++..++.+.+ .-.++|+.+|++...|.+.+...++..+...
T Consensus 40 ~~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45788888888877776652 4557999999999999999999999987766
No 85
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=61.82 E-value=11 Score=29.89 Aligned_cols=49 Identities=14% Similarity=0.192 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+..+.++..-+... -.-..+|..+|++...|.+|....|++.++-
T Consensus 132 ~~L~~~~r~i~~l~~~~~--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHAYVDG--------CSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 367888888776665555 2345899999999999999999999887653
No 86
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=60.84 E-value=47 Score=27.59 Aligned_cols=49 Identities=14% Similarity=0.164 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||...+.++...+... -.-.++|..+|++...|.+.....|.+.++..
T Consensus 149 ~L~~~~r~i~~l~~~~g--------~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 149 ALPDAFRAVFVLRVVEE--------LSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hCCHHHhhhheeehhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 47888888876544433 24568999999999999999999999988865
No 87
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=60.75 E-value=11 Score=30.24 Aligned_cols=50 Identities=6% Similarity=0.062 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.+... -.-.++|..+|+++..|.++..-.|++.++..
T Consensus 133 ~~Lp~~~R~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 133 NHLPAQQARVFMMREYLE--------LSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred HhCCHHHHHHHhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 368888999887776655 13458999999999999999999999988754
No 88
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=60.59 E-value=12 Score=29.62 Aligned_cols=50 Identities=16% Similarity=0.058 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.+.++ -.-.++|+.+|++...|.+.+...|++.++..
T Consensus 128 ~~L~~~~r~v~~l~~~~g--------~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 128 EQLPDRQRLPIVHVKLEG--------LSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HHCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 357888888876665555 23458999999999999999999999988754
No 89
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=60.36 E-value=10 Score=30.67 Aligned_cols=49 Identities=20% Similarity=0.138 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.++.-.+...+ .-.++|..+|++...|.+++.-.|++.++..
T Consensus 113 ~Lp~~~r~v~~L~~~~g~--------s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGASGF--------SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 689999999987766551 2347899999999999999999999988765
No 90
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=60.09 E-value=14 Score=28.33 Aligned_cols=51 Identities=18% Similarity=0.171 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
..||+..+.++.-.+.+.+ .-.++|..+|++...|.+...-.|++.++...
T Consensus 105 ~~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 105 QKLPARQREAFLLRYWEDM--------DVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred HhCCHHHHHHHHHHHHhcC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999877665551 24588999999999999999999999876543
No 91
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=59.82 E-value=13 Score=29.45 Aligned_cols=50 Identities=14% Similarity=0.049 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.+... -.-.++|..+|++...|.++....|++.++..
T Consensus 134 ~~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 134 KALSPEERRVIEVLYYQG--------YTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 358899999998665555 13457899999999999999999999887643
No 92
>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=59.25 E-value=8.5 Score=26.41 Aligned_cols=21 Identities=24% Similarity=0.469 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCChHHHhhhhH
Q 029411 144 QKLALAESTGLDQKQINNWFI 164 (194)
Q Consensus 144 ek~~LA~~tgLt~~QV~nWF~ 164 (194)
.-..+|.++|++..||..|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456789999999999999943
No 93
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=58.55 E-value=14 Score=29.50 Aligned_cols=48 Identities=17% Similarity=0.043 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
..||+.++.++.-.+...+ .-.++|..+|+++..|.++..-.|++.++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLGL--------SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4688899998877666661 24589999999999999999999999987
No 94
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=58.51 E-value=13 Score=29.78 Aligned_cols=51 Identities=8% Similarity=0.016 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
.||+..+.++.-.+.+. -.-.++|..+|++...|.+.....|++.++..+.
T Consensus 136 ~L~~~~r~i~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 186 (195)
T PRK12532 136 NLPENTARVFTLKEILG--------FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186 (195)
T ss_pred hCCHHHHHHhhhHHHhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 58888888887655554 1345899999999999999999999998876543
No 95
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=58.41 E-value=9.8 Score=30.39 Aligned_cols=49 Identities=14% Similarity=0.123 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+..+.++.-.+... -.-.++|..+|++...|.+|+...|++.++-
T Consensus 140 ~~L~~~~~~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 140 AQLPESQRQVLELAYYEG--------LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred HhCCHHHhhhhhhhhhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 367888888886655444 2345789999999999999999999988753
No 96
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=58.19 E-value=13 Score=23.39 Aligned_cols=40 Identities=13% Similarity=0.117 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhH
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFI 164 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~ 164 (194)
..|+.+.+..+..++.+. .-...+|+..|.++.-|.++..
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 457778888888887655 3455799999999999999864
No 97
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=58.11 E-value=13 Score=28.57 Aligned_cols=50 Identities=14% Similarity=0.230 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++...+... + .-.++|..+|++...|.++....|++.++..
T Consensus 109 ~~L~~~~r~i~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 109 RRLPARQRAVVVLRYYED----L----SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred HhCCHHHHHHhhhHHHhc----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 357888888887666554 1 2347889999999999999999999887644
No 98
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=57.97 E-value=12 Score=29.47 Aligned_cols=48 Identities=15% Similarity=0.143 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
.||+..+.++.-.+... -.-.++|..+|++...|.+++...|++.++-
T Consensus 136 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED--------LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888886644433 1345789999999999999999999988754
No 99
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=57.88 E-value=15 Score=29.37 Aligned_cols=50 Identities=14% Similarity=0.180 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.+|.-.+.+. -.-.++|..+|+++..|.+-+...|++.++..
T Consensus 130 ~~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHE--------KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 368899999997666555 13457899999999999999999999987754
No 100
>smart00574 POX domain associated with HOX domains.
Probab=57.71 E-value=22 Score=28.43 Aligned_cols=44 Identities=16% Similarity=0.195 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHHhcC-------------chHHHHHHHHHHHHHhhhhhcCC
Q 029411 19 LDQFMEAYCEMLTKYEQELTK-------------PFKDASLFLSEIDAQLKTLTVSS 62 (194)
Q Consensus 19 Ld~fm~~Yc~~L~~y~~el~~-------------p~~ea~~fl~~ie~ql~~L~~~~ 62 (194)
|-..++..+.-...|.++++. +-.-+..+|+.|++||+||...+
T Consensus 82 Ll~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~LrdaI 138 (140)
T smart00574 82 LLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRCLKDAI 138 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHh
Confidence 444556666666666666642 12234789999999999998754
No 101
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=56.62 E-value=18 Score=28.34 Aligned_cols=49 Identities=18% Similarity=0.280 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+.++.++.-.+.+.+ .-.++|..+|++..-|.++....+++.+.-
T Consensus 118 ~~Lp~~~r~v~~L~~~~g~--------s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDGM--------GHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4688889988876655551 235789999999999999999999987543
No 102
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=56.22 E-value=15 Score=29.61 Aligned_cols=50 Identities=12% Similarity=0.107 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
.||+..+.++.-.+... | .-.++|+.+|++...|.+++.-.|++.++-..
T Consensus 136 ~L~~~~r~i~~L~~~~g----~----s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 136 ALPERQRQAVVLRHIEG----L----SNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 68888888887655544 2 24578999999999999999999999987553
No 103
>cd00131 PAX Paired Box domain
Probab=56.18 E-value=47 Score=25.61 Aligned_cols=47 Identities=13% Similarity=-0.007 Sum_probs=33.6
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------ChHHHhhhhHHH
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGL-------DQKQINNWFINQ 166 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgL-------t~~QV~nWF~N~ 166 (194)
..+.......+..+..+| |.-|..|-..+-...|+ +..+|+.||.++
T Consensus 74 r~~~~~~~~~i~~~v~~~---p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 74 RVATPEVVKKIEIYKQEN---PGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CcCCHHHHHHHHHHHHHC---CCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 344555666667778888 88887777665335576 999999998764
No 104
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=55.85 E-value=94 Score=24.04 Aligned_cols=49 Identities=14% Similarity=0.059 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+..++++.-.+.+.+ .-.++|..+|+++..|.++..-.|++.++.
T Consensus 111 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 111 NLLSADQREAIILIGASGF--------SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4689999998887766661 345789999999999999999999988754
No 105
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=55.76 E-value=18 Score=30.66 Aligned_cols=49 Identities=10% Similarity=0.140 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.+|...|...+ .-.++|..+|++...|.+|....+++.++..
T Consensus 205 ~L~~~~r~vl~l~~~~g~--------s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIENL--------SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 689999999987765552 2368999999999999999999999887543
No 106
>PF13730 HTH_36: Helix-turn-helix domain
Probab=55.51 E-value=51 Score=20.86 Aligned_cols=48 Identities=19% Similarity=0.246 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHHH--ccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHh
Q 029411 118 KLPKEARQLLLDWWSR--HHRWPYPSEPQKLALAESTGLDQKQINNWFINQRK 168 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~--h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~ 168 (194)
+|+..++.++-.-... +..+.||| ...||+.+|++...|..++..-..
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3555555555332222 23348886 557899999999999998765544
No 107
>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=55.39 E-value=41 Score=20.68 Aligned_cols=30 Identities=13% Similarity=0.212 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 144 QKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 144 ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
.-..+|+.+|++...|..|....+++...+
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 446788999999999999998777766554
No 108
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=55.06 E-value=16 Score=29.31 Aligned_cols=50 Identities=14% Similarity=0.167 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.+.+. -.-.++|..+|++...|.+-+...|++.++..
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--------~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--------LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 568899999998755555 12357899999999999999999999887644
No 109
>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=54.61 E-value=18 Score=29.87 Aligned_cols=48 Identities=21% Similarity=0.345 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
..||+..+.++...|... -.-.++|+.+|++...|..|....+++.++
T Consensus 177 ~~L~~~~r~vl~l~y~~~--------~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 177 AALPERERRILLLRFFED--------KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred HcCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 468999999998776544 235689999999999999999999888764
No 110
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=54.31 E-value=18 Score=28.88 Aligned_cols=50 Identities=8% Similarity=0.042 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+.++.++.-.+...+ .-.++|..+|++..-|.+.....|++.++..
T Consensus 130 ~~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 130 DRLPPRTGRVFMMREWLEL--------ETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3588888888877665551 2357899999999999999999999987754
No 111
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=53.87 E-value=18 Score=27.80 Aligned_cols=50 Identities=14% Similarity=0.115 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.|... -.-.++|+.+|++...|.....-.|++.++..
T Consensus 108 ~~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 108 SELPARTRYAFEMYRLHG--------ETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 468888999987665555 12457899999999999999988888887643
No 112
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=53.72 E-value=15 Score=30.68 Aligned_cols=49 Identities=12% Similarity=0.203 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.++...|... -.-.++|..+|++...|.++....+++.++..
T Consensus 184 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE--------LNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhccC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57888888887766554 13468999999999999999999999987643
No 113
>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=53.52 E-value=19 Score=28.98 Aligned_cols=51 Identities=6% Similarity=-0.004 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
..||+..+.++.-.|..+ -.-.++|..+|++..-|.+...-.|++.++...
T Consensus 130 ~~L~~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 130 YHLPEQTARVFMMREVLG--------FESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred HhCCHHHHHHHHHHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 368888888887776666 245689999999999999999999999887553
No 114
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=53.07 E-value=17 Score=29.07 Aligned_cols=49 Identities=16% Similarity=0.041 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.++.-.+.+. -.-.++|..+|++...|.+.+...|++.++..
T Consensus 106 ~L~~~~r~i~~l~~~~g--------~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELEG--------LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 67888999887665555 23458899999999999999999999988755
No 115
>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=52.42 E-value=21 Score=24.81 Aligned_cols=24 Identities=38% Similarity=0.505 Sum_probs=18.9
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHh
Q 029411 14 GDDPALDQFMEAYCEMLTKYEQEL 37 (194)
Q Consensus 14 ~~dpeLd~fm~~Yc~~L~~y~~el 37 (194)
|-||+||..++.|..+.....+.+
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~ 24 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELL 24 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH
Confidence 569999999999988876655444
No 116
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=52.27 E-value=19 Score=28.56 Aligned_cols=50 Identities=16% Similarity=0.134 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.+...+ .-.++|..+|++...|.+.....|++.++-.
T Consensus 121 ~~L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 121 KELNESNRQVFKYKVFYNL--------TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4688889999877555541 2357899999999999999999999988755
No 117
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=51.89 E-value=21 Score=28.25 Aligned_cols=49 Identities=14% Similarity=0.173 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.++.--+..+ . .-.++|..+|++...|.+.....|++.++-.
T Consensus 117 ~Lp~~~r~i~~l~~~e~-----~---s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD-----Y---SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHHHHcc-----C---CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888998887766666 1 3457899999999999999999999988755
No 118
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=51.84 E-value=9.1 Score=31.46 Aligned_cols=39 Identities=26% Similarity=0.514 Sum_probs=31.0
Q ss_pred CHHHHHHHHHHHHHccCCCCC-CHHHHHHHHHHhCCChHH
Q 029411 120 PKEARQLLLDWWSRHHRWPYP-SEPQKLALAESTGLDQKQ 158 (194)
Q Consensus 120 ~k~~~~~L~~wf~~h~~~PYP-s~~ek~~LA~~tgLt~~Q 158 (194)
........-.|...|.-.||| |++||..-|++.||-+..
T Consensus 22 ~~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 22 MPRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred cccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 344455667899899999999 688899999999997764
No 119
>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=51.83 E-value=9.5 Score=24.18 Aligned_cols=21 Identities=24% Similarity=0.268 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChHHHhhhhHH
Q 029411 145 KLALAESTGLDQKQINNWFIN 165 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N 165 (194)
...||+.+|+++..|+.|..+
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 368999999999999999998
No 120
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=51.49 E-value=25 Score=27.12 Aligned_cols=47 Identities=13% Similarity=0.140 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHW 171 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k 171 (194)
..||+.++.++.-.+...+ .-.++|..+|++...|.++....+++..
T Consensus 112 ~~L~~~~r~v~~L~~~~g~--------s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVDGL--------GYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HHCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4688989998876665551 2357899999999999999998887653
No 121
>PF13551 HTH_29: Winged helix-turn helix
Probab=50.86 E-value=63 Score=22.96 Aligned_cols=46 Identities=15% Similarity=0.103 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHHHccCCC--CCCHHHHHH-H-HHHh--CCChHHHhhhhH
Q 029411 119 LPKEARQLLLDWWSRHHRWP--YPSEPQKLA-L-AEST--GLDQKQINNWFI 164 (194)
Q Consensus 119 l~k~~~~~L~~wf~~h~~~P--YPs~~ek~~-L-A~~t--gLt~~QV~nWF~ 164 (194)
++.+....|.+++.++.... ..+...-.. | ...+ .++...|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 89999999999999992111 233343333 4 3333 478888888874
No 122
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=50.70 E-value=1.2e+02 Score=23.54 Aligned_cols=50 Identities=14% Similarity=0.199 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
.||+..+.+|.--+.+.+ .-.++|..+|++...|.+.....|++.++..+
T Consensus 118 ~L~~~~r~vl~L~~~~g~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRGW--------STAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 589999999887665551 24588999999999999999999999887553
No 123
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=50.63 E-value=20 Score=28.14 Aligned_cols=49 Identities=14% Similarity=0.155 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||...+.+|.-.+... ..-.++|..+|++...|.+.....|++.++..
T Consensus 136 ~L~~~~r~il~l~~~~~--------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 136 QLPEKYRTVIVLKYIED--------LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHHHHhhhHHhhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57777888885443333 13457899999999999999999999887643
No 124
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=50.54 E-value=52 Score=24.87 Aligned_cols=48 Identities=10% Similarity=0.140 Sum_probs=32.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHh
Q 029411 114 KKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRK 168 (194)
Q Consensus 114 rkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~ 168 (194)
+++++++.+.+...-.....+ .+ ....+|...|++..+|.+|..-.+.
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 345668888754433333333 32 3457899999999999999776654
No 125
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=50.31 E-value=22 Score=29.20 Aligned_cols=51 Identities=14% Similarity=0.111 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
..||+..+.++.--|..+ -.-.++|..+|++...|.+...-.|++.++..+
T Consensus 147 ~~L~~~~r~v~~L~~~~g--------~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 147 DGLPAKYARVFMMREFIE--------LETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 468888888887766666 134689999999999999999999999887654
No 126
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=50.15 E-value=32 Score=26.11 Aligned_cols=48 Identities=19% Similarity=0.193 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.|++..+++|.-+ .++ |. ...+|+..+++.+.|.++..|.+++..-..
T Consensus 149 ~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~ 196 (211)
T PRK15369 149 LLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHK 196 (211)
T ss_pred CCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 4888889998764 444 22 468889999999999999999999976443
No 127
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=50.03 E-value=22 Score=27.87 Aligned_cols=50 Identities=8% Similarity=0.084 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.|... -.-.++|..+|++...|.+.....|++.++..
T Consensus 118 ~~L~~~~r~i~~l~~~~~--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 118 QLLNEKYKTVLVLYYYEQ--------YSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 467888888876655555 12357899999999999999999999887643
No 128
>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=49.63 E-value=9.9 Score=30.46 Aligned_cols=50 Identities=22% Similarity=0.070 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
.||+..+.++.-.+... -.-.++|..+|++...|.++..-.|++.++...
T Consensus 131 ~Lp~~~r~i~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEG--------FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehhhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 57888887776554444 134579999999999999999999999988764
No 129
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=49.44 E-value=14 Score=24.51 Aligned_cols=19 Identities=11% Similarity=0.146 Sum_probs=16.7
Q ss_pred HHHHHHhCCChHHHhhhhH
Q 029411 146 LALAESTGLDQKQINNWFI 164 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~ 164 (194)
.++|+.+|+++.+|..|-.
T Consensus 4 ~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4789999999999999943
No 130
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=49.42 E-value=24 Score=28.01 Aligned_cols=50 Identities=12% Similarity=0.036 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.+..+ -.-.++|..+|++...|.++....|++.++..
T Consensus 130 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLEG--------LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred HhCCHHHHHHHHHHHHcC--------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 468999999998766555 23458999999999999999999999987654
No 131
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=49.28 E-value=16 Score=22.87 Aligned_cols=24 Identities=17% Similarity=0.414 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCChHHHhhhhHHHH
Q 029411 144 QKLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 144 ek~~LA~~tgLt~~QV~nWF~N~R 167 (194)
....+|+.+|++...|.+|....+
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT---
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcc
Confidence 456899999999999999976544
No 132
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=49.23 E-value=18 Score=30.53 Aligned_cols=50 Identities=12% Similarity=0.159 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
.||...+.++.-.+.+. -.-.++|..+|++...|.+.....|++.++..+
T Consensus 171 ~Lp~~~R~v~~L~~~eg--------~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN--------MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred hCCHHHHHHhhhHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 57888888876655554 134578999999999999999999999987654
No 133
>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=49.17 E-value=57 Score=21.61 Aligned_cols=46 Identities=17% Similarity=0.221 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHH
Q 029411 119 LPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFIN 165 (194)
Q Consensus 119 l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N 165 (194)
|+..++.+|..-+..-|- -+|-...-..||...|++..-+..=+.+
T Consensus 1 LT~~Q~e~L~~A~~~GYf-d~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF-DVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCHHHHHHHHHHHHcCCC-CCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 567788889887776633 3377888899999999999998874443
No 134
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=49.13 E-value=30 Score=27.44 Aligned_cols=49 Identities=8% Similarity=0.036 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+.++.++.-.+.+. -.-.++|..+|++...|.+.+...+.+...-
T Consensus 126 ~~Lp~~~R~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 126 DTLRPRVKQAFLMATLDG--------MKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 468999999888766665 1345789999999999999999888876443
No 135
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=49.02 E-value=23 Score=29.90 Aligned_cols=48 Identities=8% Similarity=0.099 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
.||+..+.++.-.|... -.-.++|..+|+|...|.+++...|++.++-
T Consensus 201 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 201 QLSEKEQLVISLFYKEE--------LTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred cCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 57888898888766544 1346899999999999999999999988753
No 136
>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=48.73 E-value=24 Score=29.16 Aligned_cols=48 Identities=13% Similarity=0.185 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
..||...+.+|...|...+ .-.++|..+|++...|..+....+++.++
T Consensus 174 ~~L~~~~r~il~l~y~~~~--------s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 174 ESLSEREQLVLSLYYYEEL--------NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred HhCCHHHHHHHHHHHhCCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3589999999988776551 34689999999999999999999988765
No 137
>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=48.71 E-value=21 Score=30.08 Aligned_cols=49 Identities=8% Similarity=0.102 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+..+.++...|...+ .-.++|..+|++...|..+....+++.++.
T Consensus 204 ~~L~~~~r~ii~l~~~~g~--------s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 204 PILSEREKSIIHCTFEENL--------SQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred HcCCHHHHHHHHHHHcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3688999999887776552 236899999999999999999999887753
No 138
>PF12464 Mac: Maltose acetyltransferase ; InterPro: IPR024688 Maltose acetyltransferase uses acetyl-CoA as acetyl donor to acetylate cytoplasmic maltose [], while galactoside acetyltransferase act on galactosides. ; GO: 0016407 acetyltransferase activity; PDB: 3V4E_A 4EGG_E 4DCL_A 3FTT_A 1KRR_B 1KRU_A 1KRV_C 1KQA_A 3NZ2_J 3ECT_A ....
Probab=48.39 E-value=61 Score=20.72 Aligned_cols=37 Identities=19% Similarity=0.301 Sum_probs=29.3
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHH
Q 029411 13 VGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLS 49 (194)
Q Consensus 13 ~~~dpeLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~ 49 (194)
...||||......-...+.+|-+--.....+....|+
T Consensus 11 ~~~d~el~~~r~~a~~l~~~~N~~~~~d~~~r~~llk 47 (55)
T PF12464_consen 11 DASDPELQEIRARAKRLLQRYNQTPPEDPEERQELLK 47 (55)
T ss_dssp ETTSHHHHHHHHHHHHHHHHHHHSHTTTHHHHHHHHH
T ss_pred CCCChHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 4579999999999999999999777565655555555
No 139
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=48.09 E-value=27 Score=27.96 Aligned_cols=51 Identities=18% Similarity=0.081 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
..||+..+.++.-.+.+.+ .-.++|..+|++...|.+...-.|++.++...
T Consensus 110 ~~Lp~~~R~v~~L~~~~g~--------s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 110 DKLPQDQREALILVGASGF--------SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred HhCCHHHHHHhhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3578889999877666652 24589999999999999999999999988663
No 140
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=47.65 E-value=24 Score=28.32 Aligned_cols=49 Identities=16% Similarity=0.022 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.++.-.+... + .-.++|..+|++...|.++..-.|++.++-.
T Consensus 111 ~Lp~~~R~v~~L~~~eg----~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG----L----SYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 68999999998766655 1 2457899999999999999999999887654
No 141
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=47.53 E-value=48 Score=25.62 Aligned_cols=41 Identities=22% Similarity=0.388 Sum_probs=33.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhh
Q 029411 17 PALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKT 57 (194)
Q Consensus 17 peLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~ql~~ 57 (194)
-+|.+=.+.--..|..|+++|..+|...+..+..|...-+.
T Consensus 28 ~~l~~eL~~~k~el~~yk~~V~~HF~~ta~Ll~~l~~~Y~~ 68 (128)
T PF06295_consen 28 AKLEQELEQAKQELEQYKQEVNDHFAQTAELLDNLTQDYQK 68 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666778899999999999999999999888775544
No 142
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=47.16 E-value=25 Score=27.81 Aligned_cols=49 Identities=12% Similarity=0.072 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+..+.++...|.++ -.-.++|..+|++...|.+-....|++.++-
T Consensus 136 ~~L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 136 AELEPPRSELIRTAFFEG--------ITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 367888888887776655 1345789999999999999999999887653
No 143
>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=47.09 E-value=13 Score=23.38 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChHHHhhhhHHH
Q 029411 145 KLALAESTGLDQKQINNWFINQ 166 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~ 166 (194)
-..||..+|+++..|+.|..+.
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 3689999999999999998665
No 144
>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=46.84 E-value=13 Score=23.36 Aligned_cols=21 Identities=10% Similarity=0.254 Sum_probs=18.9
Q ss_pred HHHHHhCCChHHHhhhhHHHH
Q 029411 147 ALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 147 ~LA~~tgLt~~QV~nWF~N~R 167 (194)
.||+.+|++...|+.|+.|..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998873
No 145
>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=46.53 E-value=25 Score=29.92 Aligned_cols=50 Identities=14% Similarity=0.249 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||...+.++.-.+.+++ .-.++|..+|++...|.+++...|++.++-.
T Consensus 160 ~~Lp~~~R~v~~L~~~eg~--------S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 160 AALSERERHLLRLHFVDGL--------SMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3688888888877776661 2457899999999999999999999988765
No 146
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=46.49 E-value=27 Score=28.40 Aligned_cols=51 Identities=10% Similarity=0.064 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
..||+..+.++.-.+.+.+ .-.++|..+|++...|.+.....|++.++-..
T Consensus 138 ~~Lp~~~r~v~~L~~~eg~--------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 138 DHLPEQIGRVFMMREFLDF--------EIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4588889988877665551 23578999999999999999999999988653
No 147
>PRK10072 putative transcriptional regulator; Provisional
Probab=46.38 E-value=13 Score=27.70 Aligned_cols=23 Identities=13% Similarity=0.222 Sum_probs=20.2
Q ss_pred HHHHHHHhCCChHHHhhhhHHHH
Q 029411 145 KLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~R 167 (194)
...||+.+|++...|++|....|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999998664
No 148
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=46.17 E-value=27 Score=28.04 Aligned_cols=49 Identities=16% Similarity=0.080 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.. +.+. | .-.++|..+|+++..|.+-+...|++.++..
T Consensus 154 ~~L~~~~r~vl~l-~~e~----~----s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 154 ELLSELEKEVLEL-YLDG----K----SYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred HhCCHHHHHHHHH-HHcc----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578888888877 4443 1 3457899999999999999999999887643
No 149
>PRK11677 hypothetical protein; Provisional
Probab=45.96 E-value=53 Score=25.99 Aligned_cols=42 Identities=24% Similarity=0.337 Sum_probs=33.5
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhh
Q 029411 16 DPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKT 57 (194)
Q Consensus 16 dpeLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~ql~~ 57 (194)
.-+|.+=.+.--..|..|+++|..+|.+.+..+..|-..-+.
T Consensus 31 q~~le~eLe~~k~ele~YkqeV~~HFa~TA~Ll~~L~~~Y~~ 72 (134)
T PRK11677 31 QQALQYELEKNKAELEEYRQELVSHFARSAELLDTMAKDYRQ 72 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666777778899999999999999999998877664443
No 150
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=45.89 E-value=9.9 Score=28.92 Aligned_cols=47 Identities=21% Similarity=0.217 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
.||+..+.++.-.+... -.-.++|..+|+++..|.++..-.|++.++
T Consensus 105 ~L~~~~r~i~~l~~~~g--------~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 105 RLPENYRTVLILREFKE--------FSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hCCHhheeeeeehhhcc--------CcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36777777765443333 235689999999999999999999988765
No 151
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=45.88 E-value=30 Score=26.61 Aligned_cols=49 Identities=18% Similarity=0.212 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
+||+..+.++.-.+..+ -.-.++|..+|++..-|.+.....|++.++-.
T Consensus 105 ~L~~~~r~v~~l~~~~~--------~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLRKLEG--------LSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 48999999998776666 13458899999999999999999998887654
No 152
>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=45.53 E-value=32 Score=26.41 Aligned_cols=48 Identities=8% Similarity=0.063 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
..||+..+.+|.-.|... -.-.++|+.+|++...|.+...-.|++.++
T Consensus 121 ~~L~~~~r~vl~l~~~~g--------~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQN--------LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HhCCHHHHHHHHHHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 468888999988765555 134578999999999999999888888765
No 153
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=45.27 E-value=26 Score=29.90 Aligned_cols=52 Identities=10% Similarity=0.219 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
..||+..+.+|...|... -.-.++|..+|++...|.......+++.++....
T Consensus 211 ~~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~ 262 (268)
T PRK06288 211 KTLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262 (268)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 368888899988776655 2356899999999999999999999988776543
No 154
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=45.23 E-value=32 Score=28.42 Aligned_cols=48 Identities=19% Similarity=0.250 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
..||+..+.++...|... ..-.++|..+|+++..|..+-....++.+.
T Consensus 182 ~~L~~~e~~i~~~~~~~~--------~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 182 SKLDERERQIIMLRYFKD--------KTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred HcCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888887766443 246789999999999999999888888764
No 155
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=44.55 E-value=24 Score=29.30 Aligned_cols=54 Identities=19% Similarity=0.112 Sum_probs=39.0
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.|.-+.... -.-.++|..+|++...|.++....|++.++..
T Consensus 177 ~~Lp~~~R~v~~L~y~l~~~eg----~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 177 KKLSDREKQIMELRFGLNGGEE----KTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred HhCCHHHHHHHHHHhccCCCCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3688888888876552110001 13457899999999999999999999987654
No 156
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=44.44 E-value=27 Score=27.76 Aligned_cols=49 Identities=14% Similarity=0.035 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||...+.++.--+... | .-.++|..+|+++..|.+.....|++.++..
T Consensus 138 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 138 QLPEDLRTALTLREFDG----L----SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred hCCHHHhHHHhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777777775543333 2 3457899999999999999999999987654
No 157
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=44.32 E-value=38 Score=26.87 Aligned_cols=30 Identities=17% Similarity=0.066 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 144 QKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 144 ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
.-..+|..+|++...|.+.+.-.|++.++-
T Consensus 167 s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 167 SYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 345799999999999999999999988764
No 158
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=43.88 E-value=23 Score=29.36 Aligned_cols=31 Identities=26% Similarity=0.487 Sum_probs=23.2
Q ss_pred HHHHHHccCCCCC-CHHHHHHHHHHhCCChHH
Q 029411 128 LDWWSRHHRWPYP-SEPQKLALAESTGLDQKQ 158 (194)
Q Consensus 128 ~~wf~~h~~~PYP-s~~ek~~LA~~tgLt~~Q 158 (194)
-.|=..+.-.||| |++||...|++.||.++.
T Consensus 25 ~~~~kd~~PgpyP~t~eer~aaAkKY~l~ped 56 (179)
T PF05821_consen 25 SGWNKDWKPGPYPKTPEERAAAAKKYGLRPED 56 (179)
T ss_pred ccCCccCCCCCCCCCHHHHHHHHHHcCCCHHH
Confidence 3442233345999 899999999999998875
No 159
>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=43.76 E-value=23 Score=21.72 Aligned_cols=20 Identities=20% Similarity=0.154 Sum_probs=17.1
Q ss_pred HHHHHHhCCChHHHhhhhHH
Q 029411 146 LALAESTGLDQKQINNWFIN 165 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~N 165 (194)
.++|+.+|+++..|..|..+
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 47899999999999999543
No 160
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=43.62 E-value=83 Score=23.81 Aligned_cols=41 Identities=20% Similarity=0.337 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHH
Q 029411 122 EARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQ 166 (194)
Q Consensus 122 ~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~ 166 (194)
.....+.+|...|+..| ++ -..||..+|+++.++..+|...
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 34566778888996555 44 4578889999999998888754
No 161
>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=43.47 E-value=18 Score=21.32 Aligned_cols=21 Identities=24% Similarity=0.241 Sum_probs=18.8
Q ss_pred HHHHHHhCCChHHHhhhhHHH
Q 029411 146 LALAESTGLDQKQINNWFINQ 166 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~N~ 166 (194)
..+|+.+|+++..|++|..+.
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCC
Confidence 488999999999999998875
No 162
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=43.17 E-value=12 Score=29.22 Aligned_cols=50 Identities=16% Similarity=0.134 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
.||...+.+|...+... + .-.++|..+|++...|.+.+...|++.++..+
T Consensus 120 ~L~~~~r~vl~l~~~~g----~----s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 120 TLSLEHRAVLVLHDLED----L----PQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred hCCHHHeeeeeehHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47888888886644443 1 24689999999999999999999999887553
No 163
>PF06806 DUF1233: Putative excisionase (DUF1233); InterPro: IPR009634 This family consists of several putative phage and prophage excisionase proteins of around 80 residues in length.; PDB: 2KVV_A.
Probab=42.41 E-value=29 Score=24.70 Aligned_cols=41 Identities=22% Similarity=0.262 Sum_probs=23.6
Q ss_pred HHHHHHhCCChHHHhhhhHHHHhhcCCCCCCcccccccccCCCCC
Q 029411 146 LALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISIMNGPEG 190 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~~~~~~~~~~~~~ 190 (194)
..|...|||++.+|. ..|.+.|-...+......||.+.+.+
T Consensus 13 ~~L~a~tGls~~~I~----~yR~~~WieG~hyk~vs~dg~p~~~~ 53 (72)
T PF06806_consen 13 ELLMAITGLSPGTIK----RYRKKSWIEGRHYKKVSPDGQPKPNS 53 (72)
T ss_dssp HHHHHHH---HHHHH----HHHTTT--TTTSEEEE-SSSS--TT-
T ss_pred HHHHHHHCCCHHHHH----HHHHHHhhccceeEecCCCCCcCCCc
Confidence 367779999999996 46777777777777776777665543
No 164
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=42.09 E-value=44 Score=26.05 Aligned_cols=47 Identities=17% Similarity=0.220 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHW 171 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k 171 (194)
..||+..+.++.-.+.++ -.-.++|..+|++...|.++..+.++..+
T Consensus 117 ~~L~~~~r~v~~L~~~eg--------~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEG--------LTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 468888988887766665 12357899999999999999988887654
No 165
>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=42.05 E-value=56 Score=25.93 Aligned_cols=57 Identities=12% Similarity=0.045 Sum_probs=40.1
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCcccccccc
Q 029411 124 RQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISI 184 (194)
Q Consensus 124 ~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~~~~~~~ 184 (194)
-...++++..| |-+. ..-..++..||.+.++|..|..--|--.+..+...-+++.=|
T Consensus 32 f~kV~~yLr~~---p~~~-ati~eV~e~tgVs~~~I~~~IreGRL~~~~~~nl~~~CE~CG 88 (137)
T TIGR03826 32 FEKVYKFLRKH---ENRQ-ATVSEIVEETGVSEKLILKFIREGRLQLKHFPNLGYPCERCG 88 (137)
T ss_pred HHHHHHHHHHC---CCCC-CCHHHHHHHHCcCHHHHHHHHHcCCeeccCCCCCcCcccccC
Confidence 34556666777 5422 345678999999999999999888877776555555555443
No 166
>PRK05572 sporulation sigma factor SigF; Validated
Probab=41.81 E-value=30 Score=29.22 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++...|... -.-..+|..+|+++..|..+-....++.++..
T Consensus 201 ~~L~~~~~~v~~l~~~~~--------~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 201 RELDERERLIVYLRYFKD--------KTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred HcCCHHHHHHHHHHHhCC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 468999999987776544 34568999999999999999999988877543
No 167
>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=41.50 E-value=47 Score=26.31 Aligned_cols=50 Identities=10% Similarity=-0.003 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 116 KGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 116 r~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.+.||..++.+|.-. .+. + .-.++|..+|+|...|.++-...+++.++..
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G----l----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~a~ 53 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG----L----SQKEIAKELKTTRANVSAIEKRAMENIEKAR 53 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC----C----CHHHHHHHHCcCHHHHHHHHHhHHHHHHHHh
Confidence 467889999998763 332 2 4568999999999999999999999998644
No 168
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=40.70 E-value=38 Score=26.59 Aligned_cols=47 Identities=11% Similarity=0.102 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHW 171 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k 171 (194)
..||+..+.++.-.+..+ -.-.++|..+|++...|.++....+.+.+
T Consensus 118 ~~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 118 DGLNGKTREAFLLSQLDG--------LTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred HhCCHHHhHHhhhhhccC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 467888888877655555 23468999999999999999988777643
No 169
>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=40.56 E-value=25 Score=21.55 Aligned_cols=19 Identities=11% Similarity=0.151 Sum_probs=15.3
Q ss_pred HHHHHHhCCChHHHhhhhH
Q 029411 146 LALAESTGLDQKQINNWFI 164 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~ 164 (194)
-++|+.+|++.+.|..|=.
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4689999999999999943
No 170
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=40.54 E-value=36 Score=29.02 Aligned_cols=50 Identities=14% Similarity=0.100 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||...+.+|...|... -.-..+|..+|++...|..+..-.+++.++..
T Consensus 202 ~~L~~~~r~vl~l~y~~~--------~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 202 AQLEERTREVLEFVFLHD--------LTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred HcCCHHHHHHHHHHHHCC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 367888888887777654 23468999999999999999999999887654
No 171
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=40.33 E-value=40 Score=27.08 Aligned_cols=49 Identities=20% Similarity=0.115 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||...+.++.-.+..+ -.-.++|..+|++..-|.++..-.|++.++..
T Consensus 128 ~Lp~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQVIGG--------FSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHHHHhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 68888999887776666 23457899999999999999999999887755
No 172
>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=39.60 E-value=72 Score=30.19 Aligned_cols=101 Identities=25% Similarity=0.393 Sum_probs=65.4
Q ss_pred HHHHHHHhcCchHHHHHHHHHHHHHhhhhhcCCCCCCCCCCChhhhhccccCCCChhhhHHHHHHHHHhhcCCccchhHH
Q 029411 30 LTKYEQELTKPFKDASLFLSEIDAQLKTLTVSSNISGQSGSSEEEIDVKDHCIDPLAEDRDLKDQLLRRYSGSLGSLKQE 109 (194)
Q Consensus 30 L~~y~~el~~p~~ea~~fl~~ie~ql~~L~~~~~~~~~~~sse~e~~~~~~~~~~~~~~~elk~~l~r~y~~~~~~~~~e 109 (194)
|++..=||.+++-=.+-|+.+|+ +||. -+++++|-| ..+.+|..|+-..-|..+++...
T Consensus 292 lvRlLFemARfyAPStIFiDEID----slcs-----~RG~s~EHE------------aSRRvKsELLvQmDG~~~t~e~~ 350 (491)
T KOG0738|consen 292 LVRLLFEMARFYAPSTIFIDEID----SLCS-----QRGGSSEHE------------ASRRVKSELLVQMDGVQGTLENS 350 (491)
T ss_pred HHHHHHHHHHHhCCceeehhhHH----HHHh-----cCCCccchh------------HHHHHHHHHHHHhhccccccccc
Confidence 44455566666655566776554 4442 133333333 23567777776666666555441
Q ss_pred hh-hccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHH
Q 029411 110 FL-KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAES 151 (194)
Q Consensus 110 ~~-kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~ 151 (194)
.. =-=-.++||-+.=..|++-|.....-|-|+.+.|..|-+.
T Consensus 351 k~VmVLAATN~PWdiDEAlrRRlEKRIyIPLP~~~~R~~Li~~ 393 (491)
T KOG0738|consen 351 KVVMVLAATNFPWDIDEALRRRLEKRIYIPLPDAEARSALIKI 393 (491)
T ss_pred eeEEEEeccCCCcchHHHHHHHHhhheeeeCCCHHHHHHHHHH
Confidence 00 0124579999999999999999999999999999988653
No 173
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=39.53 E-value=69 Score=19.90 Aligned_cols=20 Identities=10% Similarity=0.333 Sum_probs=15.8
Q ss_pred HHHHHHHHhCCChHHHhhhh
Q 029411 144 QKLALAESTGLDQKQINNWF 163 (194)
Q Consensus 144 ek~~LA~~tgLt~~QV~nWF 163 (194)
....+|+.+|++...|-.++
T Consensus 23 si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 23 SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp -HHHHHHHTTS-HHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998775
No 174
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=39.03 E-value=33 Score=26.27 Aligned_cols=28 Identities=18% Similarity=0.402 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHHhCCChHHHhhhhHHHH
Q 029411 140 PSEPQKLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 140 Ps~~ek~~LA~~tgLt~~QV~nWF~N~R 167 (194)
+++..+..||..+|++.+.|..|-.-..
T Consensus 27 ~~~~~r~~La~~~~i~~~~l~~w~~~Ad 54 (122)
T PF14229_consen 27 DTPLGRKALAKKLGISERNLLKWVNQAD 54 (122)
T ss_pred CCHHHHHHHHHhcCCCHHHHHHHHhHHH
Confidence 8889999999999999999999955443
No 175
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=38.72 E-value=34 Score=28.48 Aligned_cols=54 Identities=11% Similarity=0.135 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++...|.-+ -+ ....-.++|..+|+|...|.++...++++.++..
T Consensus 174 ~~Lp~~~R~i~~l~y~~~---~~-e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l 227 (233)
T PRK05803 174 DILDEREKEVIEMRYGLG---NG-KEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227 (233)
T ss_pred HhCCHHHHHHHHHHhCCC---CC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 468888999887755211 00 0123457899999999999999888888776654
No 176
>PHA01976 helix-turn-helix protein
Probab=38.55 E-value=22 Score=23.51 Aligned_cols=22 Identities=14% Similarity=0.280 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChHHHhhhhHHH
Q 029411 145 KLALAESTGLDQKQINNWFINQ 166 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~ 166 (194)
...||..+|++...|.+|....
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 3579999999999999998654
No 177
>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=38.38 E-value=42 Score=29.03 Aligned_cols=52 Identities=19% Similarity=0.093 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~ 176 (194)
..||+..+.++.-.+...+ .-.++|..+|++...|.+.+.-.|++.++....
T Consensus 141 ~~Lp~~~R~v~~L~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 141 QYLPPRQRAVLLLRDVLGW--------RAAETAELLGTSTASVNSALQRARATLDEVGPS 192 (324)
T ss_pred HhCCHHHhhHhhhHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence 4688888888876655551 235789999999999999999999999887653
No 178
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=38.23 E-value=46 Score=27.81 Aligned_cols=53 Identities=13% Similarity=0.171 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.+|...|.-+-..+ -.-.++|..+|++...|+.+....+++.|...
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~----~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRP----HTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCC----ccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 688888999987763220112 24568999999999999999999999998765
No 179
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=37.96 E-value=38 Score=29.14 Aligned_cols=49 Identities=18% Similarity=0.317 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||...+.+|...|... + .-.++|..+|++...|..+....+.+.++.
T Consensus 214 ~~L~~rer~vl~l~y~~~----~----t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 214 AALPERERTVLVLRFFES----M----TQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred HcCCHHHHHHHHHHhcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 368888999998877544 2 247899999999999999999999887754
No 180
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=37.39 E-value=25 Score=20.54 Aligned_cols=22 Identities=18% Similarity=0.235 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChHHHhhhhHHH
Q 029411 145 KLALAESTGLDQKQINNWFINQ 166 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~ 166 (194)
...+|+.+|++..+|..|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4588999999999999997654
No 181
>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=37.19 E-value=28 Score=23.14 Aligned_cols=20 Identities=10% Similarity=0.202 Sum_probs=17.4
Q ss_pred HHHHHHhCCChHHHhhhhHH
Q 029411 146 LALAESTGLDQKQINNWFIN 165 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~N 165 (194)
.++|+.+|+++..|..|-..
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46899999999999999654
No 182
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=36.84 E-value=46 Score=29.15 Aligned_cols=49 Identities=16% Similarity=0.079 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||...+.++.-.+.+.+ .-.++|..+|++...|.+.....|++.++.
T Consensus 152 ~~Lp~~~R~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 200 (339)
T PRK08241 152 QHLPPRQRAVLILRDVLGW--------SAAEVAELLDTSVAAVNSALQRARATLAER 200 (339)
T ss_pred HhCCHHHhhhhhhHHhhCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence 3578888888876665552 235789999999999999999999999984
No 183
>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=36.70 E-value=23 Score=24.05 Aligned_cols=23 Identities=22% Similarity=0.322 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChHHHhhhhHHHH
Q 029411 145 KLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~R 167 (194)
...||+.+|++...|+.|..+.+
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 35799999999999999997653
No 184
>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=36.11 E-value=83 Score=25.63 Aligned_cols=46 Identities=17% Similarity=0.265 Sum_probs=34.5
Q ss_pred hhhhHHHHHHHHHhhcCCccchhHHhhhccCCCCCCHHHHHHHHHH
Q 029411 85 LAEDRDLKDQLLRRYSGSLGSLKQEFLKKKKKGKLPKEARQLLLDW 130 (194)
Q Consensus 85 ~~~~~elk~~l~r~y~~~~~~~~~e~~kkrkr~~l~k~~~~~L~~w 130 (194)
...-+.|-....+.+-.+-.-+...-.-+|+...|+..+...|..|
T Consensus 53 ~~~L~~LAa~cV~~~d~fRAPls~aelaRR~~~~Ls~~Q~~~L~rW 98 (160)
T PF06299_consen 53 CPALQALAAACVRAFDPFRAPLSEAELARRRPAGLSPRQRANLERW 98 (160)
T ss_pred CHHHHHHHHHHHHhhhhccCCCChHHHhhcCcccCCHHHHHHHHHh
Confidence 3445666777777776666666555556788889999999999999
No 185
>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=35.91 E-value=38 Score=20.13 Aligned_cols=22 Identities=18% Similarity=0.400 Sum_probs=18.9
Q ss_pred HHHHHHhCCChHHHhhhhHHHH
Q 029411 146 LALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~N~R 167 (194)
.++|+.+|++...|..|..+-.
T Consensus 4 ~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 4 KEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHcCC
Confidence 5789999999999999987644
No 186
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.87 E-value=70 Score=25.43 Aligned_cols=41 Identities=24% Similarity=0.344 Sum_probs=33.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhh
Q 029411 17 PALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKT 57 (194)
Q Consensus 17 peLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~ql~~ 57 (194)
..|-.=|+..-.-|..|++||.++|.+.+..|.+|-+--+.
T Consensus 37 ~~~q~ELe~~K~~ld~~rqel~~HFa~sAeLlktl~~dYqk 77 (138)
T COG3105 37 QKLQYELEKVKAQLDEYRQELVKHFARSAELLKTLAQDYQK 77 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555678888999999999999999999999988764443
No 187
>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=35.67 E-value=33 Score=22.63 Aligned_cols=19 Identities=26% Similarity=0.403 Sum_probs=17.2
Q ss_pred HHHHHHhCCChHHHhhhhH
Q 029411 146 LALAESTGLDQKQINNWFI 164 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~ 164 (194)
.++|+.+|++...|.+|-.
T Consensus 4 ~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 4 GAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999975
No 188
>PF14978 MRP-63: Mitochondrial ribosome protein 63
Probab=35.38 E-value=1.4e+02 Score=22.06 Aligned_cols=52 Identities=15% Similarity=0.402 Sum_probs=34.0
Q ss_pred cCCCCCCHHHHHHH---------HHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhh
Q 029411 114 KKKGKLPKEARQLL---------LDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKR 169 (194)
Q Consensus 114 rkr~~l~k~~~~~L---------~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R 169 (194)
|+-.+++....+.+ +.+|..| ||-|.++-.-.|...+- .++...|+.-++.+
T Consensus 10 R~~r~vt~~~k~~~~~~le~E~eN~~~Ls~---PYLT~EQE~gh~~e~r~-~k~~~~~~~~~~~~ 70 (91)
T PF14978_consen 10 RRPRKVTWQMKENMIRRLEIEEENMYWLSR---PYLTAEQEYGHAKERRK-EKAFFEWIKEKKRS 70 (91)
T ss_pred CCcCCCCHHHHHHHHHHHHHHHHHHHHHcC---CcccHHHHcchHHHHhH-HHHHHHHHHHHHHc
Confidence 44445555544444 4555666 99999998888887776 56666666665433
No 189
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=35.07 E-value=48 Score=27.51 Aligned_cols=52 Identities=10% Similarity=0.093 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
..||+..+.++.-.|.......+ .-.++|+.+|+++..|..+....+++.++
T Consensus 173 ~~L~~~~r~il~l~y~~~~~e~~----S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDGRRK----TQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCCCCc----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46888899999877641100011 34578999999999999998888887765
No 190
>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=34.48 E-value=25 Score=22.92 Aligned_cols=23 Identities=26% Similarity=0.338 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChHHHhhhhHHHH
Q 029411 145 KLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~R 167 (194)
-..+|..+|++..+|+.|-.+.+
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 45789999999999999998854
No 191
>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=34.13 E-value=37 Score=22.81 Aligned_cols=23 Identities=17% Similarity=0.346 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChHHHhhhhHHHH
Q 029411 145 KLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~R 167 (194)
-..+|+.+|++...|.+|-.--.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred HHHHHHHHCCChHHHHHHHHhhC
Confidence 34789999999999999965433
No 192
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=33.98 E-value=50 Score=28.51 Aligned_cols=55 Identities=16% Similarity=0.215 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
..||+..+.+|.-.|.-++... -.-.++|..+|++...|..+...++++.++...
T Consensus 221 ~~Lp~~~R~Vl~l~ygL~~~e~----~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 221 AELNERQREVLARRFGLLGYEP----ATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred HcCCHHHHHHHHHHhCCCCCCC----ccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999987762111112 245689999999999999999999999988654
No 193
>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=33.95 E-value=1e+02 Score=20.97 Aligned_cols=41 Identities=20% Similarity=0.437 Sum_probs=26.0
Q ss_pred CCHHHHHHH---HHHHHHccCCCCCCHHHHHHHHHHhCCC-hHHHhhhhH
Q 029411 119 LPKEARQLL---LDWWSRHHRWPYPSEPQKLALAESTGLD-QKQINNWFI 164 (194)
Q Consensus 119 l~k~~~~~L---~~wf~~h~~~PYPs~~ek~~LA~~tgLt-~~QV~nWF~ 164 (194)
|++.+.++| .+++.+| .||. .-.+||+.+|+. ..-|..-..
T Consensus 4 LT~rQ~~vL~~I~~~~~~~---G~~P--t~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEEN---GYPP--TVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp --HHHHHHHHHHHHHHHHH---SS-----HHHHHHHHTSSSHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHc---CCCC--CHHHHHHHhCCCChHHHHHHHH
Confidence 555555555 6777788 8886 566899999997 777766443
No 194
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=33.14 E-value=54 Score=27.74 Aligned_cols=49 Identities=20% Similarity=0.194 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||...+.++...|... ..-.++|..+|++...|...-.+..++.++.
T Consensus 208 ~~L~~~er~vi~~~~~~~--------~t~~eIA~~lgis~~~V~~~~~~al~kLr~~ 256 (258)
T PRK08215 208 KKLNDREKLILNLRFFQG--------KTQMEVAEEIGISQAQVSRLEKAALKHMRKY 256 (258)
T ss_pred HcCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 368888888887776443 1346899999999999999999888887653
No 195
>COG5661 Predicted secreted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=32.40 E-value=1.2e+02 Score=25.66 Aligned_cols=45 Identities=18% Similarity=0.197 Sum_probs=37.2
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhhhhc
Q 029411 13 VGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTV 60 (194)
Q Consensus 13 ~~~dpeLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~ql~~L~~ 60 (194)
-++||||.-|-++|-.-+.++++- +..=|-..-+.||.+|.+|..
T Consensus 108 r~a~pElalvwdtlladikrHEEr---H~eiar~har~mEkaL~sl~p 152 (210)
T COG5661 108 RKADPELALVWDTLLADIKRHEER---HAEIARYHAREMEKALLSLRP 152 (210)
T ss_pred CCCCHhHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHhcCC
Confidence 478999999999999999888763 445566777899999999874
No 196
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=32.18 E-value=52 Score=27.90 Aligned_cols=50 Identities=14% Similarity=0.060 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.+||..++.++.-.+.+. -.-.++|+.+|++..-|.++..-.|++.++-.
T Consensus 115 ~~Lp~~~R~v~lL~~~eg--------~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 115 SSLNVQQSAILLLKDVFQ--------YSIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred HhCCHHHhhHhhhHHhhC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 368888888877655554 12357899999999999999999999998765
No 197
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=32.16 E-value=1.4e+02 Score=20.76 Aligned_cols=35 Identities=26% Similarity=0.262 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC--ChHHHh
Q 029411 123 ARQLLLDWWSRHHRWPYPSEPQKLALAESTGL--DQKQIN 160 (194)
Q Consensus 123 ~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgL--t~~QV~ 160 (194)
++..++..+.+| |=-+++.-..+..+-|- |.+||+
T Consensus 18 ar~~~~k~l~~N---Ppine~mir~M~~QMG~kpSekqi~ 54 (64)
T PF03672_consen 18 ARKYMEKQLKEN---PPINEKMIRAMMMQMGRKPSEKQIK 54 (64)
T ss_pred HHHHHHHHHHHC---CCCCHHHHHHHHHHhCCCccHHHHH
Confidence 345566677777 87799999999999884 455554
No 198
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=31.84 E-value=76 Score=28.24 Aligned_cols=54 Identities=13% Similarity=0.115 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||...+.+|...|.-++..+ -.-.++|..+|++...|..+....+++.|+..
T Consensus 261 ~~L~~~~R~vl~lrygL~~~e~----~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 261 FELNDKQREVLARRFGLLGYEA----ATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred HcCCHHHHHHHHHHhccCCCCC----cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4688889999986653332223 34568999999999999999999999998765
No 199
>PRK10651 transcriptional regulator NarL; Provisional
Probab=31.71 E-value=95 Score=23.82 Aligned_cols=48 Identities=13% Similarity=0.075 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.|++...++|.-+. +. + .-..+|+.++++...|.+...|.|++..-..
T Consensus 155 ~Lt~rE~~vl~~l~-~g----~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~~ 202 (216)
T PRK10651 155 QLTPRERDILKLIA-QG----L----PNKMIARRLDITESTVKVHVKHMLKKMKLKS 202 (216)
T ss_pred cCCHHHHHHHHHHH-cC----C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 48999999987553 32 2 2346788899999999999999999975433
No 200
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=31.70 E-value=1.4e+02 Score=24.75 Aligned_cols=41 Identities=24% Similarity=0.406 Sum_probs=32.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCch-HHH-HHHHHHHHHHhhh
Q 029411 17 PALDQFMEAYCEMLTKYEQELTKPF-KDA-SLFLSEIDAQLKT 57 (194)
Q Consensus 17 peLd~fm~~Yc~~L~~y~~el~~p~-~ea-~~fl~~ie~ql~~ 57 (194)
-|||=+..++-.++..|+|.+.-.+ ..| ..|+..|..||..
T Consensus 104 tELDVvL~~FEk~~~eYkq~ieS~~cr~AI~~F~~~~keqL~~ 146 (175)
T PF13097_consen 104 TELDVVLSAFEKTALEYKQSIESKICRKAINKFYSNFKEQLIE 146 (175)
T ss_pred hHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHH
Confidence 4999999999999999999996543 444 3577777777654
No 201
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=31.55 E-value=27 Score=27.19 Aligned_cols=49 Identities=14% Similarity=0.020 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||+..+.++.-.+... -.-..+|..+|++.+.|.++....|.+.++.
T Consensus 125 ~~L~~~~r~v~~l~~~~g--------~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 125 SKLDPEFRAPVILKHYYG--------YTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred HcCCHHHhheeeehhhcC--------CCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 357888888765432222 2345789999999999999999999987763
No 202
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=31.53 E-value=70 Score=24.97 Aligned_cols=48 Identities=17% Similarity=0.197 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
.||+..+.++...+... + .-.++|..+|++...|.+=....|++.++-
T Consensus 140 ~L~~~~r~vi~l~~~~g----~----s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 140 KLPEDYREVILLRHLEG----L----SFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cCCHHHHHHHHHHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 57888888887644333 2 345789999999999999998888887754
No 203
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=31.42 E-value=42 Score=22.09 Aligned_cols=19 Identities=11% Similarity=0.162 Sum_probs=16.7
Q ss_pred HHHHHHhCCChHHHhhhhH
Q 029411 146 LALAESTGLDQKQINNWFI 164 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~ 164 (194)
.++|+.+|+++..|..|-.
T Consensus 4 ~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999954
No 204
>PF11629 Mst1_SARAH: C terminal SARAH domain of Mst1; InterPro: IPR024205 The SARAH (Sav/Rassf/Hpo) domain is found at the C terminus in three classes of eukaryotic tumour suppressors that give the domain its name. In the Sav (Salvador) and Hpo (Hippo) families, the SARAH domain mediates signal transduction from Hpo via the Sav scaffolding protein to the downstream component Wts (Warts); the phosphorylation of Wts by Hpo triggers cell cycle arrest and apoptosis by down-regulating cyclin E, Diap 1 and other targets []. The SARAH domain is also involved in dimerisation, as in the human Hpo orthologue, Mst1, which homodimerises via its C-terminal SARAH domain. The SARAH domain is found associated with other domains, such as protein kinase domains, WW/rsp5/WWP domain (IPR001202 from INTERPRO), C1 domain (IPR002219 from INTERPRO), LIM domain (IPR001781 from INTERPRO), or the Ras-associating (RA) domain (IPR000159 from INTERPRO).; GO: 0004674 protein serine/threonine kinase activity; PDB: 2JO8_A.
Probab=31.28 E-value=57 Score=21.53 Aligned_cols=29 Identities=34% Similarity=0.265 Sum_probs=24.5
Q ss_pred hHHHHHHHHHHHHHHHHHHhcCchHHHHH
Q 029411 18 ALDQFMEAYCEMLTKYEQELTKPFKDASL 46 (194)
Q Consensus 18 eLd~fm~~Yc~~L~~y~~el~~p~~ea~~ 46 (194)
-||..||.=+..|.+=.+.=.+|+-.|+.
T Consensus 19 ~LD~~ME~Eieelr~RY~~KRqPIldAie 47 (49)
T PF11629_consen 19 SLDPEMEQEIEELRQRYQAKRQPILDAIE 47 (49)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred hCCHHHHHHHHHHHHHHHHhhccHHHHHh
Confidence 47889999999998888888889987764
No 205
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=31.18 E-value=63 Score=27.54 Aligned_cols=50 Identities=6% Similarity=0.092 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++...|... -.-.++|..+|++...|..+..-.+++.++..
T Consensus 204 ~~L~~~er~vi~l~y~e~--------~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 204 LALEEKERKVMALYYYEE--------LVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred HcCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 368888888888776544 23468999999999999999999888877643
No 206
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=30.96 E-value=46 Score=26.76 Aligned_cols=29 Identities=17% Similarity=0.105 Sum_probs=24.9
Q ss_pred hccCCCCCCHHHHHHHHHHHHHccCCCCC
Q 029411 112 KKKKKGKLPKEARQLLLDWWSRHHRWPYP 140 (194)
Q Consensus 112 kkrkr~~l~k~~~~~L~~wf~~h~~~PYP 140 (194)
...+-+.|+.++...|..+...++..++|
T Consensus 49 ~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP 77 (149)
T PRK04053 49 PNAKLGYLSDEEIEKIEEALEDPAEEGIP 77 (149)
T ss_pred CCCccCcCCHHHHHHHHHHHHhhccccCc
Confidence 45677899999999999999888777888
No 207
>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=30.90 E-value=1.1e+02 Score=26.27 Aligned_cols=47 Identities=21% Similarity=0.347 Sum_probs=35.3
Q ss_pred ChhhhHHHHHHHHHhhcCCccchhHHhhhccCCCCCCHHHHHHHHHH
Q 029411 84 PLAEDRDLKDQLLRRYSGSLGSLKQEFLKKKKKGKLPKEARQLLLDW 130 (194)
Q Consensus 84 ~~~~~~elk~~l~r~y~~~~~~~~~e~~kkrkr~~l~k~~~~~L~~w 130 (194)
+...-..|-..+.+.+-.+-.-+...-.-+|++..|+..+...|..|
T Consensus 112 ~~~~L~~LAa~~V~~~d~fRAPls~aelaRRr~~~Ls~~Q~~~L~~W 158 (228)
T TIGR03223 112 PCPALQALAAACVRELDPFRAPLTEAELARRRPDQLTPRQRALLERW 158 (228)
T ss_pred CCHHHHHHHHHHHHhhhhccCCCCHHHHhhcCccCCCHHHHHHHHHc
Confidence 33445667777777777666666655566788889999999999999
No 208
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=30.55 E-value=22 Score=28.29 Aligned_cols=49 Identities=6% Similarity=0.032 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.++.-.+... -.-.++|..+|++...|.++....|.+.++..
T Consensus 134 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 134 HVNPIDREILVLRFVAE--------LEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred hcChhheeeeeeHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 56666777775444433 12368999999999999999999999887643
No 209
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=30.38 E-value=78 Score=27.21 Aligned_cols=50 Identities=10% Similarity=0.042 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+.++.++.-.+... . .-.++|..+|++...|.+.+...|++.+...
T Consensus 107 ~~L~~~~R~v~~L~~~~g--~------s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 107 ERLSPLERAVFVLREVFD--Y------PYEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred hhCCHHHHHHHHHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 457888888876544443 1 2357899999999999999999999988754
No 210
>PRK09480 slmA division inhibitor protein; Provisional
Probab=30.07 E-value=56 Score=25.53 Aligned_cols=29 Identities=17% Similarity=0.271 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHHHHhCCChHHHhhhhHHHH
Q 029411 138 PYPSEPQKLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 138 PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R 167 (194)
++ ....-..+|+..|+++..|-.+|.|+-
T Consensus 27 ~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 27 PG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred CC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 67 888889999999999999999999976
No 211
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.91 E-value=58 Score=23.18 Aligned_cols=26 Identities=15% Similarity=0.443 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChHHHhhhhHHHHhh
Q 029411 144 QKLALAESTGLDQKQINNWFINQRKR 169 (194)
Q Consensus 144 ek~~LA~~tgLt~~QV~nWF~N~R~R 169 (194)
....+|+.+|++...|.+|....+..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~ 39 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREG 39 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcc
Confidence 46789999999999999999886643
No 212
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=29.64 E-value=67 Score=25.82 Aligned_cols=47 Identities=13% Similarity=0.177 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 119 LPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 119 l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
+++....++.-.|..- | .-.++|..+|+++..|.+.+...|.+..+.
T Consensus 136 l~~~~~~~v~l~~~~G----l----s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 136 LDPRQRRVVELRFFEG----L----SVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred cCHHHHHHHHHHHHCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5666666666555444 2 445789999999999999999999876543
No 213
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=29.44 E-value=62 Score=26.98 Aligned_cols=54 Identities=17% Similarity=0.083 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||+..+.++.-.|....-..+ .-.++|+.+|+++..|.++..-.|++.++-.
T Consensus 177 ~~Lp~~~R~ii~L~~~l~~~eg~----s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 177 AKLNDREKKIMELRFGLVGGTEK----TQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred HhCCHHHHHHHHHHHccCCCCCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 35888888888765531000011 3457899999999999999999999887654
No 214
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, 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-like proteins in this group appear to lack the long dimerization helix seen
Probab=29.39 E-value=49 Score=22.04 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=17.3
Q ss_pred HHHHHHhCCChHHHhhhhHH
Q 029411 146 LALAESTGLDQKQINNWFIN 165 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~N 165 (194)
.++|+.+|+++..|..|...
T Consensus 4 ~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 4 GEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999653
No 215
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=29.02 E-value=72 Score=18.82 Aligned_cols=20 Identities=20% Similarity=0.441 Sum_probs=14.5
Q ss_pred HHHHHHHhCCChHHHhhhhH
Q 029411 145 KLALAESTGLDQKQINNWFI 164 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~ 164 (194)
-..-|+..|||..+|..++.
T Consensus 8 Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34568899999999999875
No 216
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.68 E-value=2e+02 Score=21.10 Aligned_cols=49 Identities=18% Similarity=0.210 Sum_probs=36.4
Q ss_pred CCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-ChHHHhhhhHHHHhhcC
Q 029411 116 KGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGL-DQKQINNWFINQRKRHW 171 (194)
Q Consensus 116 r~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgL-t~~QV~nWF~N~R~R~k 171 (194)
+.+||.+-+.-+-+-..+. .+ ....+|+..|+ +..++..|-+..+...-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~---g~----sv~~vAr~~gv~~~~~l~~W~~~~~~~~~ 54 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRG---GD----TVSEVAREFGIVSATQLYKWRIQLQKGGG 54 (116)
T ss_pred cccCCHHHHHHHHHHHHhc---Cc----cHHHHHHHhCCCChHHHHHHHHHHHHccc
Confidence 6788888775554443433 22 57789999996 99999999998887653
No 217
>PF02290 SRP14: Signal recognition particle 14kD protein; InterPro: IPR003210 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 14 kDa SRP14 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0030942 endoplasmic reticulum signal peptide binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0005786 signal recognition particle, endoplasmic reticulum targeting; PDB: 1914_A 1RY1_D 1E8O_B 2W9J_B.
Probab=28.34 E-value=46 Score=24.46 Aligned_cols=16 Identities=31% Similarity=0.677 Sum_probs=14.2
Q ss_pred hhHHHHHHHHHHHHHH
Q 029411 17 PALDQFMEAYCEMLTK 32 (194)
Q Consensus 17 peLd~fm~~Yc~~L~~ 32 (194)
-+|+.|...|+.+|..
T Consensus 73 ~~l~~F~~~Y~~v~K~ 88 (93)
T PF02290_consen 73 DDLDKFWQSYANVLKA 88 (93)
T ss_dssp TCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHh
Confidence 4899999999999864
No 218
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=28.01 E-value=49 Score=21.71 Aligned_cols=16 Identities=31% Similarity=0.499 Sum_probs=12.9
Q ss_pred HHHHHHhCCChHHHhh
Q 029411 146 LALAESTGLDQKQINN 161 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~n 161 (194)
..||+.+|+++.||+-
T Consensus 32 ~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 32 QELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHTS-HHHHHH
T ss_pred HHHHHHHCCCHHHhcc
Confidence 4799999999999974
No 219
>smart00351 PAX Paired Box domain.
Probab=27.98 E-value=2.1e+02 Score=21.68 Aligned_cols=45 Identities=13% Similarity=0.036 Sum_probs=30.6
Q ss_pred CCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------ChHHHhhhh
Q 029411 116 KGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGL-------DQKQINNWF 163 (194)
Q Consensus 116 r~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgL-------t~~QV~nWF 163 (194)
....+......+.....+| |.-+..+-...-...|+ +.+.|+.||
T Consensus 73 p~~~~~~~~~~I~~~~~~~---p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 73 PKVATPKVVKKIADYKQEN---PGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred CCccCHHHHHHHHHHHHHC---CCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 3445555566666677788 88888777544446766 678888887
No 220
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=27.32 E-value=1.1e+02 Score=26.43 Aligned_cols=50 Identities=14% Similarity=0.199 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 116 KGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 116 r~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
...||+..+++|. |..+. + .-.++|..+|++...|++...|.+++..-..
T Consensus 188 ~~~LT~RE~evl~-l~a~G----~----s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILA-WVRDG----K----TNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHH-HHHCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 4479999999998 54433 2 3457888999999999999999999876544
No 221
>PF10782 DUF2602: Protein of unknown function (DUF2602); InterPro: IPR019718 This bacterial family of proteins that has no known function.
Probab=26.77 E-value=39 Score=23.10 Aligned_cols=24 Identities=21% Similarity=0.621 Sum_probs=17.6
Q ss_pred hHHHHHHHHHHHH---HHHHHHhcCch
Q 029411 18 ALDQFMEAYCEML---TKYEQELTKPF 41 (194)
Q Consensus 18 eLd~fm~~Yc~~L---~~y~~el~~p~ 41 (194)
++|++|++||.== ..++.+..+.+
T Consensus 9 ~I~~L~dtyC~gC~lk~~~rk~~gk~~ 35 (58)
T PF10782_consen 9 EIDDLQDTYCKGCFLKKHFRKEKGKTY 35 (58)
T ss_pred HHHHHHHHHhcCCchHHHhHHHhcccc
Confidence 7899999999743 55566666655
No 222
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=26.26 E-value=41 Score=25.70 Aligned_cols=22 Identities=18% Similarity=0.391 Sum_probs=19.8
Q ss_pred HHHHHHhCCChHHHhhhhHHHH
Q 029411 146 LALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~N~R 167 (194)
..||..+|+++..|++|..+.+
T Consensus 22 ~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 22 RSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHhCCCHHHHHHHHcCCC
Confidence 5899999999999999998864
No 223
>PRK10403 transcriptional regulator NarP; Provisional
Probab=26.17 E-value=1.3e+02 Score=22.97 Aligned_cols=48 Identities=10% Similarity=0.075 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.|+.....+|. ++..+ | ....+|+..+++...|.+...|.|++..-..
T Consensus 153 ~Lt~~e~~vl~-~~~~g----~----s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 153 VLTERELDVLH-ELAQG----L----SNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred cCCHHHHHHHH-HHHCC----C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 57888888876 33433 2 2457889999999999999999999975544
No 224
>PF11867 DUF3387: Domain of unknown function (DUF3387); InterPro: IPR021810 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with PF04851 from PFAM, PF04313 from PFAM.
Probab=26.01 E-value=1.8e+02 Score=25.93 Aligned_cols=126 Identities=21% Similarity=0.291 Sum_probs=59.3
Q ss_pred CCCChhH-HHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhhhhcCCCCCCCCCCChhhhhccccC-----CCChh
Q 029411 13 VGDDPAL-DQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTVSSNISGQSGSSEEEIDVKDHC-----IDPLA 86 (194)
Q Consensus 13 ~~~dpeL-d~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~ql~~L~~~~~~~~~~~sse~e~~~~~~~-----~~~~~ 86 (194)
+..||-- ..|.+-+..+|.+|...-- ....++..+-.-...+..........|.+++|....... .....
T Consensus 189 ~~~N~~~~~~fsErLe~iI~~Y~~~~i----~~~e~~~eLi~la~el~~~~~r~~~~gLseeE~AFyd~L~~~~~~~~~~ 264 (335)
T PF11867_consen 189 MKENPVRYKKFSERLEEIIEKYNNRSI----SSEEVIEELIKLAKELREEEERAEELGLSEEELAFYDALAKNESAVEEM 264 (335)
T ss_pred HhcCHHHHHHHHHHHHHHHHHHHcccc----hHHHHHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHccccccccc
Confidence 4457764 7888999999999987652 122333222222222222211123345666664322111 11112
Q ss_pred hhHHHHH---HHHHhhcCCccchhHHhhhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHH
Q 029411 87 EDRDLKD---QLLRRYSGSLGSLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAES 151 (194)
Q Consensus 87 ~~~elk~---~l~r~y~~~~~~~~~e~~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~ 151 (194)
+++.++. .|.....+.+.- -+.++...-...+..++..+..+ .||...........
T Consensus 265 ~~e~l~~la~el~~~lk~~~~v------DW~~ke~~ra~~r~~Ik~~L~k~---~ypp~~~~~~~~~v 323 (335)
T PF11867_consen 265 GDEELKELAKELTETLKENVTV------DWTKKEDVRAKMRRAIKRLLRKY---GYPPDKQEEAVDEV 323 (335)
T ss_pred cHHHHHHHHHHHHHHhccccCc------CceeCccHHHHHHHHHHHHHHHc---CCChHHHHHHHHHH
Confidence 2233322 222221111110 24444444455666667777777 99986665554433
No 225
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=25.93 E-value=72 Score=25.46 Aligned_cols=30 Identities=23% Similarity=0.158 Sum_probs=22.5
Q ss_pred hhccCCCCCCHHHHHHHHHHHHHccCCCCCC
Q 029411 111 LKKKKKGKLPKEARQLLLDWWSRHHRWPYPS 141 (194)
Q Consensus 111 ~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs 141 (194)
....+-+-|+.++...|..+... ...++|.
T Consensus 44 ~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~ 73 (144)
T TIGR03629 44 DPNAKLGYLDDEEIEKLEEAVEN-YEYGIPS 73 (144)
T ss_pred CCCCCcccCCHHHHHHHHHHHHh-ccccCCH
Confidence 34567788999999999999876 5555554
No 226
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=25.87 E-value=70 Score=19.05 Aligned_cols=21 Identities=14% Similarity=0.156 Sum_probs=17.6
Q ss_pred HHHHHHhCCChHHHhhhhHHH
Q 029411 146 LALAESTGLDQKQINNWFINQ 166 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nWF~N~ 166 (194)
.++|+.+|++...|.+|..+-
T Consensus 5 ~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 5 EEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred HHHHHHHCCCHHHHHHHHHcC
Confidence 567889999999999997543
No 227
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=25.62 E-value=56 Score=20.36 Aligned_cols=33 Identities=27% Similarity=0.510 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411 138 PYPSEPQKLALAESTGLDQKQINNWFINQRKRHW 171 (194)
Q Consensus 138 PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k 171 (194)
=|||.+++..|.+..|.. ..|=||.-..|...+
T Consensus 9 l~Pt~~Q~~~L~~~~~~~-R~vyN~~L~~~~~~y 41 (46)
T PF12323_consen 9 LYPTKEQEEKLERWFGAC-RFVYNWALAERKEAY 41 (46)
T ss_pred EecCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
Confidence 378888888888777653 556777777766544
No 228
>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=25.32 E-value=1e+02 Score=27.39 Aligned_cols=52 Identities=21% Similarity=0.453 Sum_probs=37.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHh
Q 029411 114 KKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRK 168 (194)
Q Consensus 114 rkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~ 168 (194)
.++..|++....-|-.+|..| ..|||-.-++.. ..+|-..+++.+|=++-++
T Consensus 206 e~R~~L~~~lA~wLh~yyaSH-~~P~P~kvetl~--~lcGS~~~~l~~FR~~Lk~ 257 (282)
T PF07042_consen 206 EQRRKLSPRLAKWLHGYYASH-KKPYPIKVETLR--ELCGSESSRLRKFRQQLKK 257 (282)
T ss_pred HHHhhcCcHHHHHHHHHHhcC-CCCCCccHHHHH--HHcCCCccCHHHHHHHHHH
Confidence 344556555456788898888 579998777544 4688888889888766554
No 229
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=25.10 E-value=69 Score=21.72 Aligned_cols=18 Identities=22% Similarity=0.654 Sum_probs=15.5
Q ss_pred HHHHHHHhCCChHHHhhh
Q 029411 145 KLALAESTGLDQKQINNW 162 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nW 162 (194)
...||+.+|+++.-|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357999999999999999
No 230
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. 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 RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=24.74 E-value=91 Score=26.69 Aligned_cols=51 Identities=20% Similarity=0.225 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
..||...+.+|...|... .+ -.-.++|..+|+|...|+....+...+.|+.
T Consensus 217 ~~L~~rer~vl~l~y~~~--~~----~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 217 GSLDARSRRIIEARWLDD--DK----LTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred HcCCHHHHHHHHHHhcCC--CC----cCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 368888999998776421 02 2346899999999999999999999888753
No 231
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=24.45 E-value=59 Score=25.44 Aligned_cols=26 Identities=46% Similarity=0.819 Sum_probs=20.6
Q ss_pred HHHHHHHhCCChHHHhhhhHHHHhhcCCC
Q 029411 145 KLALAESTGLDQKQINNWFINQRKRHWKP 173 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~R~R~kk~ 173 (194)
.++||..||++...|+-|. |+-.|+-
T Consensus 3 ~eELA~~tG~srQTINrWv---RkegW~T 28 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWV---RKEGWKT 28 (122)
T ss_pred HHHHHHHhCccHHHHHHHH---HhcCcee
Confidence 3689999999999999996 4445543
No 232
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=24.24 E-value=70 Score=22.71 Aligned_cols=41 Identities=12% Similarity=0.005 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHH
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFIN 165 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N 165 (194)
.+|...+++..-....+ -+ .-.++|..+|+|+..|.+|+.+
T Consensus 15 ~l~~~~r~af~L~R~~e---Gl----S~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 15 WVDSLAEAAAALAREEA---GK----TASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCHHHHHHHHHHHHHc---CC----CHHHHHHHHCcCHHHHHHHHhc
Confidence 45665555544332212 22 4568999999999999999864
No 233
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=23.79 E-value=4.6e+02 Score=22.40 Aligned_cols=50 Identities=14% Similarity=-0.017 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSE 175 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~ 175 (194)
.||+.++.++.-.+... -.-.++|+.+|++..-|.+.+...|++.++..+
T Consensus 115 ~L~~~~R~v~~L~~~~g--------~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 115 RLSPLERAAFLLHDVFG--------VPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred hCCHHHHHHHHHHHHhC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 58888888876554444 123578999999999999999999999988543
No 234
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=23.78 E-value=2.2e+02 Score=19.38 Aligned_cols=44 Identities=11% Similarity=0.258 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhH
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFI 164 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~ 164 (194)
..|+-.-.-..-.++..+-.+ ...-..-|++.|++.++|.-|..
T Consensus 4 rsy~~~FKL~Vv~~a~~~~nc----~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 4 RSYTAEFKLKVVEYAEKDNNC----KGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ----HHHHHHHHHHHHH-TTT----TT-HHHHHHHTTS-HHHHHHHHT
T ss_pred cccChHHHHHHHHHHHHccch----hhhHHHHHHHhCccHHHHHHHHH
Confidence 445555554455566655211 11234678999999999999965
No 235
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=23.26 E-value=1.8e+02 Score=23.98 Aligned_cols=50 Identities=16% Similarity=0.205 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHH
Q 029411 116 KGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQ 166 (194)
Q Consensus 116 r~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~ 166 (194)
...|+..++.+|+.-|..-|- =||-...-..||+..|+++.-+..=..++
T Consensus 153 ~~~LTdrQ~~vL~~A~~~GYF-d~PR~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 153 KNDLTDRQLEVLRLAYKMGYF-DYPRRVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred cccCCHHHHHHHHHHHHcCCC-CCCccCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 347999999999998887743 34788899999999999999887744443
No 236
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=23.14 E-value=53 Score=25.05 Aligned_cols=23 Identities=17% Similarity=0.281 Sum_probs=20.2
Q ss_pred HHHHHHHhCCChHHHhhhhHHHH
Q 029411 145 KLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~R 167 (194)
...||..+|++...|+.|..+.+
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 45799999999999999998774
No 237
>PRK09726 antitoxin HipB; Provisional
Probab=22.97 E-value=50 Score=23.43 Aligned_cols=22 Identities=32% Similarity=0.424 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChHHHhhhhHHH
Q 029411 145 KLALAESTGLDQKQINNWFINQ 166 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~ 166 (194)
...||+.+|+++..|++|..+.
T Consensus 28 q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCC
Confidence 4589999999999999998864
No 238
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=22.93 E-value=84 Score=23.26 Aligned_cols=25 Identities=24% Similarity=0.400 Sum_probs=20.6
Q ss_pred HHHHHHHHHhCCChHHHhhhhHHHH
Q 029411 143 PQKLALAESTGLDQKQINNWFINQR 167 (194)
Q Consensus 143 ~ek~~LA~~tgLt~~QV~nWF~N~R 167 (194)
-.-..+|+..|++.+||+.|..+.+
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~ 48 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFI 48 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHH
Confidence 3556899999999999999976644
No 239
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=22.45 E-value=1.2e+02 Score=26.50 Aligned_cols=52 Identities=12% Similarity=0.117 Sum_probs=40.3
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..||...+.+|...|.. ..+ -.-.++|...|+|...|..+....+++.+...
T Consensus 226 ~~L~~rer~vl~lr~~~--~~~----~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 226 QTLNERELRIIRERRLR--EDG----ATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred hcCCHHHHHHHHHHhcC--CCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 36888889998876531 012 24578999999999999999999999988654
No 240
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription 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 conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.38 E-value=68 Score=22.85 Aligned_cols=17 Identities=24% Similarity=0.591 Sum_probs=15.7
Q ss_pred HHHHHHhCCChHHHhhh
Q 029411 146 LALAESTGLDQKQINNW 162 (194)
Q Consensus 146 ~~LA~~tgLt~~QV~nW 162 (194)
.++|+.+|++..+|..|
T Consensus 5 ~evA~~~gvs~~tLR~y 21 (88)
T cd01105 5 GEVSKLTGVSPRQLRYW 21 (88)
T ss_pred HHHHHHHCcCHHHHHHH
Confidence 47899999999999999
No 241
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=22.26 E-value=1.3e+02 Score=28.10 Aligned_cols=53 Identities=9% Similarity=0.191 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
.||+..+.+|.-.|.-+-..|+ .-..+|..+|++...|..+...++++.++|.
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~----Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~ 402 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTY----SLAEIGRALDLSRERVRQIESKALQKLRQPK 402 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHhchh
Confidence 5888899999877753211133 3568999999999999999999999999886
No 242
>PF14410 GH-E: HNH/ENDO VII superfamily nuclease with conserved GHE residues
Probab=22.03 E-value=58 Score=22.74 Aligned_cols=17 Identities=29% Similarity=0.780 Sum_probs=14.1
Q ss_pred HHHhCCChHHHhhhhHH
Q 029411 149 AESTGLDQKQINNWFIN 165 (194)
Q Consensus 149 A~~tgLt~~QV~nWF~N 165 (194)
|...|+|.+||..|+.|
T Consensus 36 ~~~~~~t~ke~~d~~n~ 52 (70)
T PF14410_consen 36 AEEGGITRKEFLDWYND 52 (70)
T ss_pred HHhcCCCHHHHHHHHhC
Confidence 34589999999999974
No 243
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.75 E-value=1.6e+02 Score=22.06 Aligned_cols=37 Identities=16% Similarity=0.334 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhH
Q 029411 120 PKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFI 164 (194)
Q Consensus 120 ~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~ 164 (194)
+-+-++.+-+.+... .-....|...+++...|.+||.
T Consensus 4 S~DlR~rVl~~~~~g--------~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKG--------KSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CHHHHHHHHHHHHcc--------chHHHHHHHhCcHHHHHHHHHH
Confidence 445555555565554 2456788899999999999998
No 244
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=21.65 E-value=2.2e+02 Score=17.85 Aligned_cols=25 Identities=16% Similarity=0.247 Sum_probs=20.4
Q ss_pred HHHHHHHhCCChHHHhhhhHHHHhh
Q 029411 145 KLALAESTGLDQKQINNWFINQRKR 169 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~N~R~R 169 (194)
...||..+|++...|...+..-...
T Consensus 28 ~~~la~~~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 28 ERELAEELGVSRTTVREALRELEAE 52 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4569999999999999888776654
No 245
>PF06786 UPF0253: Uncharacterised protein family (UPF0253); InterPro: IPR009624 This is a group of proteins of unknown function.
Probab=21.59 E-value=1.5e+02 Score=20.67 Aligned_cols=16 Identities=25% Similarity=0.752 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHhc
Q 029411 23 MEAYCEMLTKYEQELT 38 (194)
Q Consensus 23 m~~Yc~~L~~y~~el~ 38 (194)
|..||+..++...+.-
T Consensus 1 M~~YCeliR~~ya~Ig 16 (66)
T PF06786_consen 1 MQVYCELIRELYAQIG 16 (66)
T ss_pred CcHHHHHHHHHHHHhc
Confidence 7789999998888874
No 246
>PRK00523 hypothetical protein; Provisional
Probab=21.25 E-value=2.7e+02 Score=19.80 Aligned_cols=32 Identities=13% Similarity=0.123 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChH
Q 029411 123 ARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQK 157 (194)
Q Consensus 123 ~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~ 157 (194)
++..++..+.+| |=-+++.-.....+-|-.++
T Consensus 26 ark~~~k~l~~N---Ppine~mir~M~~QMGqKPS 57 (72)
T PRK00523 26 SKKMFKKQIREN---PPITENMIRAMYMQMGRKPS 57 (72)
T ss_pred HHHHHHHHHHHC---cCCCHHHHHHHHHHhCCCcc
Confidence 345567777777 87888888888888885444
No 247
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=21.21 E-value=1.5e+02 Score=24.79 Aligned_cols=47 Identities=11% Similarity=0.083 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHW 171 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k 171 (194)
..||...+.++...|... ..-..+|..+|++..+|+.--...+.+.+
T Consensus 182 ~~L~~~er~vi~l~~~~~--------~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 182 SQLDEREQLILHLYYQHE--------MSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred HcCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 468888889998887554 22568999999999999998888877765
No 248
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=21.19 E-value=94 Score=19.31 Aligned_cols=21 Identities=14% Similarity=0.151 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCChHHHhhhhH
Q 029411 144 QKLALAESTGLDQKQINNWFI 164 (194)
Q Consensus 144 ek~~LA~~tgLt~~QV~nWF~ 164 (194)
....+|+.+|++...|.++|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 345789999999999999884
No 249
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=21.13 E-value=79 Score=26.17 Aligned_cols=32 Identities=13% Similarity=0.209 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCChHHHhhhhHHHHhhcCCCC
Q 029411 143 PQKLALAESTGLDQKQINNWFINQRKRHWKPS 174 (194)
Q Consensus 143 ~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~ 174 (194)
..+.+||...++++.+|..|..|=+--.++.+
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~ 46 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKP 46 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccc
Confidence 35678999999999999999999877666554
No 250
>PF09636 XkdW: XkdW protein; InterPro: IPR019094 This entry includes the phage SPbeta protein YorD, the function of which is not known, It also contains the protein XkdW (P54342 from SWISSPROT) from the Phage-like element PBSX in Bacillus subtilis. XkdW is approximately 100 residues long and contains two alpha helices and two beta strands, and is probably monomeric. XkdW is expressed in bacteria but is probably viral in origin. Its function is unknown. PBSX, a defective prophage of B. subtilis, is a chromosomally based element which encodes a non-infectious phage-like particle with bactericidal activity. PBSX is induced by agents which elicit the SOS response [].; PDB: 2HG7_A.
Probab=21.09 E-value=49 Score=25.33 Aligned_cols=33 Identities=21% Similarity=0.353 Sum_probs=13.6
Q ss_pred CCHHHHHHHHHHHHHccCCC-CCCHHHHHHHHHH
Q 029411 119 LPKEARQLLLDWWSRHHRWP-YPSEPQKLALAES 151 (194)
Q Consensus 119 l~k~~~~~L~~wf~~h~~~P-YPs~~ek~~LA~~ 151 (194)
.|..+..-|..||.++..|| |+.+.+...|+..
T Consensus 40 ~p~Pt~~El~~a~ee~~~~p~~~~P~qle~L~qe 73 (108)
T PF09636_consen 40 APQPTEAELQSAWEELQKNPDYEPPNQLELLGQE 73 (108)
T ss_dssp S----HHHHHHHHHHHHHS---------------
T ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchhhhHHHHH
Confidence 67778889999999998888 7777777777643
No 251
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=20.96 E-value=1.3e+02 Score=22.40 Aligned_cols=44 Identities=9% Similarity=0.196 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHh
Q 029411 123 ARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRK 168 (194)
Q Consensus 123 ~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~ 168 (194)
.=-+|..++..+ .+--|++++..+-.-...+-.++-+||-|...
T Consensus 29 lDlil~~Fae~~--~~~lsd~el~~f~~LLe~~D~dL~~Wi~g~~~ 72 (94)
T COG2938 29 LDLILGPFAEKE--FDSLSDEELDEFERLLECEDNDLFNWIMGHGE 72 (94)
T ss_pred HHHHHHHHHHHH--HhhCCHHHHHHHHHHHcCCcHHHHHHHhCCCC
Confidence 335667777776 55579999999999999999999999999765
No 252
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=20.85 E-value=1.5e+02 Score=25.79 Aligned_cols=50 Identities=12% Similarity=0.132 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHW 171 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k 171 (194)
.||+..+.+|...|.-+-..|+ .-.++|+.+|+|...|......++++.+
T Consensus 249 ~L~~rer~Vi~lr~gl~~~~~~----Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGGEPL----TLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred cCCHHHHHHHHHHhccCCCCCc----CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 5889999999887742211132 4668999999999999999988888764
No 253
>smart00351 PAX Paired Box domain.
Probab=20.63 E-value=2.2e+02 Score=21.60 Aligned_cols=44 Identities=11% Similarity=0.141 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHh
Q 029411 117 GKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRK 168 (194)
Q Consensus 117 ~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~ 168 (194)
..++.+.+..+-..+... .-...+|+.+|++...|..|..-.+.
T Consensus 16 ~~~s~~~R~riv~~~~~G--------~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 16 RPLPDEERQRIVELAQNG--------VRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 347777776665555543 13458899999999999999887653
No 254
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=20.56 E-value=2e+02 Score=21.93 Aligned_cols=46 Identities=13% Similarity=-0.003 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCC
Q 029411 118 KLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172 (194)
Q Consensus 118 ~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk 172 (194)
.+++....+|.- +.++ -...++|...+++..-|.++..+.|++..-
T Consensus 149 ~lt~re~~vl~~-l~~g--------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 149 VLSNREVTILRY-LVSG--------LSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCHHHHHHHHH-HHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 577777777764 3333 246688899999999999999999998753
No 255
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=20.21 E-value=4.2e+02 Score=21.13 Aligned_cols=60 Identities=12% Similarity=0.065 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCcccccccc
Q 029411 122 EARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISI 184 (194)
Q Consensus 122 ~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~~~~~~~ 184 (194)
....+|...=... .|.+++.-..+|+.+|+++.+|..=....-.=+.+|.......+.++
T Consensus 24 ~li~~L~~vQ~~~---G~Ip~e~~~~iA~~l~v~~~~V~~vatFY~~f~~~p~Gk~~I~VC~~ 83 (156)
T PRK05988 24 ALLPILHAIQDEF---GYVPEDAVPVIAEALNLSRAEVHGVITFYHDFRTHPPGRHVLKLCRA 83 (156)
T ss_pred HHHHHHHHHHHHc---CCCCHHHHHHHHHHhCCCHHHHHHHHHHhhccCCCCCCCEEEEEeCC
Confidence 3566675554444 79999999999999999999987654433333344554444444333
No 256
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=20.09 E-value=80 Score=24.25 Aligned_cols=20 Identities=20% Similarity=0.456 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChHHHhhhhH
Q 029411 145 KLALAESTGLDQKQINNWFI 164 (194)
Q Consensus 145 k~~LA~~tgLt~~QV~nWF~ 164 (194)
...||+.||+|...|..|-.
T Consensus 6 I~elA~~~gvs~~tlR~Ye~ 25 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLL 25 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46799999999999999954
Done!