Query 016972
Match_columns 379
No_of_seqs 174 out of 297
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 04:29:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016972.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016972hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01566 ZF_HD_prot_N ZF-HD h 100.0 1.1E-33 2.3E-38 212.1 3.3 50 75-126 3-53 (53)
2 PF04770 ZF-HD_dimer: ZF-HD pr 100.0 1.3E-32 2.9E-37 211.8 3.8 55 72-128 4-59 (60)
3 TIGR01565 homeo_ZF_HD homeobox 99.9 3.8E-26 8.3E-31 175.0 6.5 58 233-290 1-58 (58)
4 KOG0843 Transcription factor E 99.5 7.1E-15 1.5E-19 135.3 3.0 65 231-299 100-164 (197)
5 KOG0493 Transcription factor E 99.4 1.6E-13 3.4E-18 132.7 3.1 69 234-306 247-315 (342)
6 KOG0494 Transcription factor C 99.4 1.9E-13 4.2E-18 132.0 3.3 61 232-296 140-200 (332)
7 PF00046 Homeobox: Homeobox do 99.4 9.4E-14 2E-18 102.0 0.5 57 234-294 1-57 (57)
8 KOG2251 Homeobox transcription 99.3 6E-13 1.3E-17 125.5 3.9 67 228-298 32-98 (228)
9 KOG0484 Transcription factor P 99.3 2.8E-13 6.1E-18 116.3 -0.8 62 231-296 15-76 (125)
10 KOG4577 Transcription factor L 99.3 1.9E-12 4.2E-17 126.6 2.5 61 231-295 165-225 (383)
11 smart00389 HOX Homeodomain. DN 99.1 2.8E-11 6.1E-16 87.8 3.5 55 234-292 1-55 (56)
12 cd00086 homeodomain Homeodomai 99.1 3.7E-11 8.1E-16 87.3 2.8 58 234-295 1-58 (59)
13 KOG0488 Transcription factor B 99.0 1E-10 2.2E-15 114.7 3.5 68 229-300 168-235 (309)
14 KOG0489 Transcription factor z 99.0 1.2E-10 2.5E-15 111.2 3.4 66 231-300 157-222 (261)
15 KOG0844 Transcription factor E 99.0 1.2E-10 2.6E-15 114.9 1.7 61 232-296 180-240 (408)
16 KOG0485 Transcription factor N 98.9 2.9E-10 6.2E-15 108.0 2.0 65 229-297 100-164 (268)
17 KOG0486 Transcription factor P 98.9 6.2E-10 1.3E-14 109.9 3.1 62 232-297 111-172 (351)
18 KOG0490 Transcription factor, 98.9 6.5E-10 1.4E-14 99.8 2.3 63 230-296 57-119 (235)
19 KOG0850 Transcription factor D 98.9 7.9E-10 1.7E-14 105.3 2.1 67 229-299 118-184 (245)
20 KOG3802 Transcription factor O 98.8 1E-08 2.2E-13 103.7 6.7 63 231-297 292-354 (398)
21 KOG0842 Transcription factor t 98.7 9.2E-09 2E-13 101.3 5.0 67 229-299 149-215 (307)
22 COG5576 Homeodomain-containing 98.6 3.2E-08 6.9E-13 89.2 3.9 68 229-300 47-114 (156)
23 KOG0492 Transcription factor M 98.6 3.2E-08 7E-13 93.7 3.1 59 233-295 144-202 (246)
24 KOG0483 Transcription factor H 98.6 2.6E-08 5.7E-13 92.9 2.4 60 234-297 51-110 (198)
25 KOG0847 Transcription factor, 98.6 3.9E-08 8.5E-13 94.0 3.4 64 231-298 165-228 (288)
26 KOG0849 Transcription factor P 98.5 6.8E-08 1.5E-12 96.2 3.1 62 231-296 174-235 (354)
27 KOG0487 Transcription factor A 98.3 7.2E-07 1.6E-11 88.2 4.0 60 234-297 236-295 (308)
28 KOG0491 Transcription factor B 98.2 1.1E-07 2.3E-12 87.6 -1.7 62 231-296 98-159 (194)
29 KOG1168 Transcription factor A 98.1 1.3E-06 2.7E-11 86.5 2.0 63 230-296 306-368 (385)
30 KOG0848 Transcription factor C 98.1 5.3E-07 1.1E-11 88.2 -0.6 60 232-295 198-257 (317)
31 KOG0490 Transcription factor, 98.0 1.4E-06 3E-11 78.4 1.2 65 229-297 149-213 (235)
32 KOG1146 Homeobox protein [Gene 97.9 7.8E-06 1.7E-10 92.5 3.0 68 230-301 900-967 (1406)
33 KOG2252 CCAAT displacement pro 97.9 1.5E-05 3.2E-10 83.8 4.8 57 232-292 419-475 (558)
34 PF05920 Homeobox_KN: Homeobox 96.0 0.001 2.3E-08 47.8 -1.1 33 258-290 7-39 (40)
35 PF04218 CENP-B_N: CENP-B N-te 95.6 0.0082 1.8E-07 45.1 2.3 48 234-290 1-48 (53)
36 PF01527 HTH_Tnp_1: Transposas 95.4 0.0066 1.4E-07 46.4 1.2 47 235-289 2-48 (76)
37 KOG0774 Transcription factor P 95.1 0.021 4.4E-07 56.7 3.8 62 234-296 189-250 (334)
38 KOG0775 Transcription factor S 94.5 0.06 1.3E-06 53.6 5.2 46 244-293 187-232 (304)
39 cd00569 HTH_Hin_like Helix-tur 92.6 0.12 2.7E-06 31.4 2.6 40 237-285 3-42 (42)
40 KOG0773 Transcription factor M 91.1 0.25 5.3E-06 48.6 4.1 65 231-297 237-302 (342)
41 KOG3623 Homeobox transcription 90.9 0.12 2.5E-06 57.3 1.7 51 238-293 562-612 (1007)
42 COG2963 Transposase and inacti 88.7 0.39 8.5E-06 40.0 2.9 46 237-290 5-51 (116)
43 cd06171 Sigma70_r4 Sigma70, re 84.5 0.25 5.4E-06 33.6 -0.4 46 238-292 9-54 (55)
44 PF02796 HTH_7: Helix-turn-hel 83.5 0.25 5.5E-06 35.6 -0.7 40 238-286 4-43 (45)
45 PF11569 Homez: Homeodomain le 81.8 0.49 1.1E-05 37.0 0.2 40 246-289 11-50 (56)
46 PRK09413 IS2 repressor TnpA; R 81.2 0.87 1.9E-05 38.8 1.6 43 237-287 10-52 (121)
47 PF06163 DUF977: Bacterial pro 77.4 1.1 2.3E-05 40.3 0.9 44 239-286 4-48 (127)
48 PF13936 HTH_38: Helix-turn-he 76.9 0.59 1.3E-05 33.7 -0.6 42 237-287 2-43 (44)
49 smart00421 HTH_LUXR helix_turn 76.6 0.82 1.8E-05 31.8 0.0 45 239-293 3-47 (58)
50 KOG1146 Homeobox protein [Gene 74.9 0.54 1.2E-05 54.9 -1.9 125 230-359 441-566 (1406)
51 TIGR02989 Sig-70_gvs1 RNA poly 74.9 0.78 1.7E-05 38.9 -0.5 47 238-294 110-157 (159)
52 PRK06424 transcription factor; 74.7 1.6 3.5E-05 39.3 1.4 56 233-290 68-123 (144)
53 PF08281 Sigma70_r4_2: Sigma-7 73.8 0.77 1.7E-05 33.2 -0.7 43 239-290 10-52 (54)
54 PF04967 HTH_10: HTH DNA bindi 72.7 3.3 7.1E-05 31.7 2.4 41 240-282 1-41 (53)
55 TIGR00270 conserved hypothetic 71.8 1.2 2.5E-05 40.5 -0.2 24 266-289 84-107 (154)
56 PF13551 HTH_29: Winged helix- 71.5 4.2 9.1E-05 32.5 3.0 53 233-286 51-109 (112)
57 PF00196 GerE: Bacterial regul 70.3 0.92 2E-05 33.6 -1.0 45 239-293 3-47 (58)
58 PRK12537 RNA polymerase sigma 67.7 1.3 2.9E-05 38.9 -0.7 47 239-295 133-180 (182)
59 PRK09644 RNA polymerase sigma 66.4 1.3 2.9E-05 38.2 -0.9 49 238-296 107-156 (165)
60 PF12651 RHH_3: Ribbon-helix-h 66.4 4.5 9.8E-05 29.5 1.9 24 233-256 2-25 (44)
61 PF13022 HTH_Tnp_1_2: Helix-tu 66.3 2.6 5.6E-05 38.5 0.8 55 233-289 4-59 (142)
62 TIGR02939 RpoE_Sigma70 RNA pol 64.6 0.86 1.9E-05 39.7 -2.5 48 239-295 138-185 (190)
63 PRK09646 RNA polymerase sigma 64.4 1 2.2E-05 40.2 -2.1 48 239-296 142-190 (194)
64 KOG3755 SATB1 matrix attachmen 64.3 3.3 7.3E-05 45.5 1.3 59 232-293 646-707 (769)
65 PRK09652 RNA polymerase sigma 64.1 1 2.2E-05 38.4 -2.1 47 239-295 128-175 (182)
66 PRK12526 RNA polymerase sigma 63.9 1.5 3.2E-05 39.8 -1.2 48 239-296 153-201 (206)
67 PF13698 DUF4156: Domain of un 63.7 3.7 8E-05 34.3 1.2 22 71-92 47-68 (93)
68 PRK06759 RNA polymerase factor 63.7 1.5 3.3E-05 37.0 -1.1 47 239-295 106-153 (154)
69 PRK03975 tfx putative transcri 63.5 1.6 3.5E-05 39.4 -1.0 49 238-296 5-53 (141)
70 PRK10403 transcriptional regul 63.0 2.8 6E-05 35.4 0.4 49 238-296 152-200 (215)
71 TIGR02985 Sig70_bacteroi1 RNA 62.9 1.7 3.7E-05 36.2 -0.9 46 239-294 113-159 (161)
72 PRK09480 slmA division inhibit 62.8 5.5 0.00012 34.5 2.2 47 242-289 9-55 (194)
73 PF13384 HTH_23: Homeodomain-l 62.5 3.6 7.7E-05 29.3 0.8 22 266-287 19-40 (50)
74 PRK05602 RNA polymerase sigma 61.2 1.6 3.4E-05 38.4 -1.5 49 239-297 128-177 (186)
75 PRK12533 RNA polymerase sigma 61.2 1.4 3E-05 41.1 -2.0 58 239-306 134-191 (216)
76 PRK12512 RNA polymerase sigma 60.8 1.1 2.5E-05 39.2 -2.4 48 239-296 131-179 (184)
77 PRK09648 RNA polymerase sigma 60.3 1.2 2.6E-05 39.3 -2.4 51 235-295 135-186 (189)
78 PRK04217 hypothetical protein; 60.0 2.2 4.7E-05 37.0 -0.8 52 239-299 42-93 (110)
79 PRK02220 4-oxalocrotonate taut 59.7 17 0.00036 26.9 4.0 33 241-287 13-45 (61)
80 PRK00118 putative DNA-binding 59.3 1.4 2.9E-05 37.9 -2.1 47 239-294 17-63 (104)
81 PF04545 Sigma70_r4: Sigma-70, 59.2 1.8 3.8E-05 31.2 -1.3 44 239-291 4-47 (50)
82 cd06170 LuxR_C_like C-terminal 59.0 3.1 6.7E-05 29.1 -0.0 44 240-293 1-44 (57)
83 TIGR03070 couple_hipB transcri 58.6 7 0.00015 27.5 1.8 36 246-289 5-40 (58)
84 PF13443 HTH_26: Cro/C1-type H 58.5 5.1 0.00011 29.6 1.1 34 248-289 2-35 (63)
85 PHA02893 hypothetical protein; 58.5 3.9 8.4E-05 34.7 0.5 8 109-116 69-76 (88)
86 cd04762 HTH_MerR-trunc Helix-T 57.2 3.9 8.4E-05 27.7 0.2 24 267-290 3-26 (49)
87 PRK12514 RNA polymerase sigma 56.6 1.6 3.5E-05 38.1 -2.2 47 239-295 129-176 (179)
88 PRK12539 RNA polymerase sigma 56.6 2 4.2E-05 38.0 -1.7 49 238-296 130-179 (184)
89 PRK12530 RNA polymerase sigma 56.2 1.6 3.4E-05 39.0 -2.4 48 238-295 133-181 (189)
90 TIGR02983 SigE-fam_strep RNA p 56.0 2.5 5.5E-05 36.0 -1.0 48 239-296 110-158 (162)
91 TIGR02948 SigW_bacill RNA poly 56.0 2.2 4.8E-05 37.0 -1.4 48 238-295 135-183 (187)
92 PRK10072 putative transcriptio 55.8 7.8 0.00017 32.8 1.8 35 248-290 38-72 (96)
93 PRK09390 fixJ response regulat 55.6 3.5 7.7E-05 34.1 -0.2 47 239-295 141-187 (202)
94 TIGR02950 SigM_subfam RNA poly 55.3 2.6 5.7E-05 35.4 -1.0 50 245-294 96-151 (154)
95 PRK09726 antitoxin HipB; Provi 55.2 12 0.00026 30.1 2.8 42 239-288 7-49 (88)
96 PRK09047 RNA polymerase factor 55.1 2.9 6.2E-05 35.5 -0.8 48 238-295 105-153 (161)
97 PRK12541 RNA polymerase sigma 55.0 2 4.3E-05 36.9 -1.9 47 239-295 112-159 (161)
98 PRK09642 RNA polymerase sigma 55.0 2.8 6.1E-05 35.8 -0.9 48 239-296 106-154 (160)
99 PF01381 HTH_3: Helix-turn-hel 54.9 5.5 0.00012 28.5 0.7 22 268-289 13-34 (55)
100 PRK12515 RNA polymerase sigma 54.3 2.7 5.9E-05 37.1 -1.2 51 237-297 129-180 (189)
101 TIGR02607 antidote_HigA addict 53.5 7.2 0.00016 29.8 1.2 21 268-288 22-42 (78)
102 PRK07037 extracytoplasmic-func 53.3 2.7 5.9E-05 35.9 -1.3 48 239-296 109-157 (163)
103 smart00351 PAX Paired Box doma 52.9 8.4 0.00018 33.3 1.6 42 240-290 18-59 (125)
104 PF13518 HTH_28: Helix-turn-he 52.7 4.2 9E-05 28.7 -0.2 25 266-290 14-38 (52)
105 PRK06811 RNA polymerase factor 52.6 4 8.6E-05 36.3 -0.4 50 238-297 130-180 (189)
106 PRK12519 RNA polymerase sigma 52.4 2.1 4.5E-05 37.9 -2.2 47 239-295 141-188 (194)
107 PRK12547 RNA polymerase sigma 52.3 2.1 4.5E-05 37.1 -2.2 49 238-295 111-159 (164)
108 TIGR02937 sigma70-ECF RNA poly 52.3 2.6 5.7E-05 33.8 -1.5 47 239-294 110-156 (158)
109 cd00093 HTH_XRE Helix-turn-hel 52.1 6.2 0.00013 26.0 0.6 22 268-289 16-37 (58)
110 PF09607 BrkDBD: Brinker DNA-b 52.0 9.1 0.0002 30.3 1.5 45 237-286 3-47 (58)
111 TIGR02959 SigZ RNA polymerase 51.7 2.2 4.8E-05 37.3 -2.1 50 238-296 99-148 (170)
112 PF12844 HTH_19: Helix-turn-he 51.7 8.6 0.00019 28.4 1.3 23 267-289 15-37 (64)
113 PRK12546 RNA polymerase sigma 51.5 2.9 6.3E-05 37.7 -1.5 49 239-296 113-161 (188)
114 PRK11924 RNA polymerase sigma 50.2 2.4 5.2E-05 36.0 -2.1 48 239-295 125-172 (179)
115 PRK11891 aspartate carbamoyltr 50.2 9.6 0.00021 40.0 1.8 41 241-289 1-41 (429)
116 PRK09649 RNA polymerase sigma 49.3 2.8 6E-05 37.4 -1.9 47 238-294 129-176 (185)
117 TIGR02954 Sig70_famx3 RNA poly 49.2 4.2 9.1E-05 35.1 -0.8 47 239-295 119-166 (169)
118 PRK12513 RNA polymerase sigma 49.2 1.6 3.4E-05 38.7 -3.5 34 263-296 154-187 (194)
119 PRK12516 RNA polymerase sigma 49.2 2.7 5.9E-05 37.7 -2.0 49 239-297 116-165 (187)
120 PRK02289 4-oxalocrotonate taut 48.9 37 0.0008 25.5 4.4 34 240-287 12-45 (60)
121 PRK15369 two component system 48.6 5.7 0.00012 33.0 -0.0 46 238-293 148-193 (211)
122 PRK09975 DNA-binding transcrip 48.4 7.7 0.00017 34.4 0.7 48 242-290 10-57 (213)
123 PF13565 HTH_32: Homeodomain-l 48.3 7.1 0.00015 29.8 0.4 40 233-278 26-66 (77)
124 PRK12543 RNA polymerase sigma 48.2 4.2 9.1E-05 35.8 -1.0 48 239-296 117-165 (179)
125 PRK09645 RNA polymerase sigma 48.1 4.1 8.8E-05 35.3 -1.0 48 239-296 118-166 (173)
126 cd00491 4Oxalocrotonate_Tautom 48.0 39 0.00085 24.4 4.3 35 241-289 12-46 (58)
127 PRK12524 RNA polymerase sigma 48.0 2.9 6.3E-05 37.4 -2.0 49 238-296 135-184 (196)
128 COG3413 Predicted DNA binding 47.6 15 0.00032 34.1 2.5 43 239-283 155-197 (215)
129 PRK15008 HTH-type transcriptio 47.6 12 0.00027 33.7 2.0 59 231-290 6-64 (212)
130 PRK12536 RNA polymerase sigma 47.2 2.5 5.4E-05 37.2 -2.6 31 265-295 146-176 (181)
131 PF00249 Myb_DNA-binding: Myb- 46.7 32 0.0007 24.6 3.6 36 237-279 1-36 (48)
132 PRK12520 RNA polymerase sigma 46.7 3 6.6E-05 36.9 -2.1 50 238-296 130-179 (191)
133 PRK12522 RNA polymerase sigma 46.4 3.1 6.7E-05 36.2 -2.0 31 265-295 136-166 (173)
134 TIGR02952 Sig70_famx2 RNA poly 46.2 4.4 9.5E-05 34.6 -1.1 48 238-295 121-169 (170)
135 TIGR02999 Sig-70_X6 RNA polyme 46.1 3.2 6.9E-05 36.1 -2.0 47 240-295 135-181 (183)
136 PF06056 Terminase_5: Putative 45.9 8.2 0.00018 29.8 0.4 33 245-286 3-35 (58)
137 PRK09637 RNA polymerase sigma 45.8 4.4 9.5E-05 36.1 -1.2 48 239-296 106-154 (181)
138 PRK09639 RNA polymerase sigma 45.7 3.7 8E-05 35.1 -1.6 48 238-295 111-158 (166)
139 PRK08295 RNA polymerase factor 45.6 4.4 9.4E-05 36.0 -1.3 48 238-295 154-201 (208)
140 PRK12542 RNA polymerase sigma 45.5 4.4 9.5E-05 35.7 -1.2 49 237-295 120-169 (185)
141 PHA02535 P terminase ATPase su 45.5 13 0.00028 40.6 2.0 47 238-295 1-47 (581)
142 PF05572 Peptidase_M43: Pregna 45.5 14 0.00031 33.2 2.0 18 236-253 137-154 (154)
143 PRK12531 RNA polymerase sigma 45.1 4.8 0.00011 35.9 -1.1 49 238-296 140-189 (194)
144 PRK10651 transcriptional regul 45.1 7.3 0.00016 33.0 0.1 47 238-294 154-200 (216)
145 PF12824 MRP-L20: Mitochondria 45.1 33 0.00071 31.7 4.3 42 236-283 82-123 (164)
146 TIGR01764 excise DNA binding d 44.5 6.8 0.00015 26.7 -0.2 23 267-289 4-26 (49)
147 PRK09647 RNA polymerase sigma 44.5 4.9 0.00011 36.8 -1.2 48 239-296 138-186 (203)
148 PRK13919 putative RNA polymera 44.3 3.3 7.2E-05 36.2 -2.2 49 237-295 133-182 (186)
149 PF13309 HTH_22: HTH domain 44.3 26 0.00056 27.2 3.0 43 236-281 17-59 (64)
150 PRK12545 RNA polymerase sigma 44.2 3.7 8.1E-05 37.1 -2.0 49 239-296 139-187 (201)
151 KOG1924 RhoA GTPase effector D 44.1 40 0.00086 38.8 5.4 36 233-280 641-676 (1102)
152 TIGR00721 tfx DNA-binding prot 44.0 5.7 0.00012 35.7 -0.8 48 237-294 4-51 (137)
153 PRK10360 DNA-binding transcrip 43.4 9 0.0002 32.4 0.4 48 238-295 136-183 (196)
154 TIGR03541 reg_near_HchA LuxR f 43.1 8.6 0.00019 36.0 0.2 50 237-296 169-218 (232)
155 PF01361 Tautomerase: Tautomer 42.1 48 0.001 24.4 4.1 34 241-288 12-45 (60)
156 PRK11511 DNA-binding transcrip 42.0 14 0.00031 31.6 1.3 42 242-288 8-49 (127)
157 cd04761 HTH_MerR-SF Helix-Turn 42.0 7.2 0.00016 27.1 -0.4 23 267-289 3-25 (49)
158 PRK09935 transcriptional regul 42.0 9.1 0.0002 32.5 0.2 46 238-293 148-193 (210)
159 PHA00542 putative Cro-like pro 41.9 22 0.00048 28.6 2.4 45 234-289 12-56 (82)
160 PF13411 MerR_1: MerR HTH fami 41.9 7.6 0.00016 29.1 -0.3 23 267-289 3-25 (69)
161 PRK12538 RNA polymerase sigma 41.9 4.7 0.0001 37.9 -1.7 31 266-296 189-219 (233)
162 PRK06930 positive control sigm 41.2 5.7 0.00012 36.3 -1.3 48 238-295 113-161 (170)
163 PRK12535 RNA polymerase sigma 41.0 5 0.00011 36.4 -1.6 53 238-300 132-185 (196)
164 TIGR03879 near_KaiC_dom probab 40.9 12 0.00027 30.5 0.8 26 264-289 32-57 (73)
165 PRK09651 RNA polymerase sigma 40.9 4.3 9.3E-05 35.5 -2.0 48 237-293 117-164 (172)
166 PF02042 RWP-RK: RWP-RK domain 40.9 43 0.00093 25.8 3.7 35 239-278 4-43 (52)
167 PF08914 Myb_DNA-bind_2: Rap1 40.5 30 0.00065 27.4 2.9 47 237-284 2-49 (65)
168 PRK09641 RNA polymerase sigma 39.8 4 8.6E-05 35.5 -2.4 30 266-295 154-183 (187)
169 PHA01976 helix-turn-helix prot 39.6 21 0.00045 26.6 1.8 19 268-286 19-37 (67)
170 PRK01964 4-oxalocrotonate taut 39.6 53 0.0012 24.6 4.0 34 241-288 13-46 (64)
171 PRK12532 RNA polymerase sigma 39.5 4.2 9E-05 36.2 -2.4 48 239-296 136-184 (195)
172 PRK12511 RNA polymerase sigma 39.2 4.6 0.0001 36.2 -2.1 48 239-296 111-159 (182)
173 PRK12540 RNA polymerase sigma 39.0 4.5 9.8E-05 36.2 -2.2 50 239-297 111-160 (182)
174 TIGR03020 EpsA transcriptional 38.8 9.9 0.00022 36.8 -0.1 49 237-295 188-236 (247)
175 KOG2767 Translation initiation 38.6 9.7 0.00021 39.6 -0.2 15 109-123 118-132 (400)
176 TIGR02479 FliA_WhiG RNA polyme 38.1 5.8 0.00012 36.4 -1.7 49 238-295 174-222 (224)
177 PRK00745 4-oxalocrotonate taut 37.9 58 0.0013 24.0 3.9 34 241-288 13-46 (62)
178 TIGR02366 DHAK_reg probable di 37.8 18 0.0004 31.2 1.4 26 262-287 21-46 (176)
179 PRK12529 RNA polymerase sigma 37.7 8.2 0.00018 34.0 -0.7 47 239-295 127-174 (178)
180 TIGR02846 spore_sigmaK RNA pol 37.6 6.6 0.00014 36.3 -1.5 53 238-295 173-225 (227)
181 PF12123 Amidase02_C: N-acetyl 37.3 32 0.00068 25.9 2.4 19 240-258 24-42 (45)
182 PF12728 HTH_17: Helix-turn-he 37.2 10 0.00022 27.2 -0.2 24 267-290 4-27 (51)
183 PF05077 DUF678: Protein of un 37.2 14 0.00031 30.5 0.6 8 109-116 57-64 (74)
184 PRK10668 DNA-binding transcrip 37.2 15 0.00033 32.7 0.8 49 241-290 9-57 (215)
185 TIGR02859 spore_sigH RNA polym 37.2 8.2 0.00018 33.9 -0.9 30 266-295 167-196 (198)
186 TIGR00013 taut 4-oxalocrotonat 36.9 73 0.0016 23.5 4.4 34 241-288 13-46 (63)
187 PRK06986 fliA flagellar biosyn 36.9 6 0.00013 36.6 -1.8 32 264-295 200-231 (236)
188 PRK08301 sporulation sigma fac 36.6 7.3 0.00016 35.9 -1.3 53 238-295 177-229 (234)
189 TIGR02943 Sig70_famx1 RNA poly 36.5 5.1 0.00011 35.8 -2.3 48 239-296 131-179 (188)
190 PF06252 DUF1018: Protein of u 36.3 25 0.00054 30.0 2.0 21 238-258 20-40 (119)
191 PRK11923 algU RNA polymerase s 35.4 5.6 0.00012 35.1 -2.2 30 266-295 156-185 (193)
192 cd00029 C1 Protein kinase C co 35.2 16 0.00035 25.6 0.5 31 88-125 12-42 (50)
193 PRK12528 RNA polymerase sigma 35.2 6.5 0.00014 33.7 -1.8 45 238-292 112-157 (161)
194 PF02954 HTH_8: Bacterial regu 35.1 20 0.00043 25.4 1.0 34 244-285 6-39 (42)
195 cd08353 Glo_EDI_BRP_like_7 Thi 34.9 49 0.0011 27.2 3.5 43 243-285 12-54 (142)
196 PRK01271 4-oxalocrotonate taut 34.8 83 0.0018 25.6 4.6 34 240-287 13-46 (76)
197 TIGR02984 Sig-70_plancto1 RNA 34.4 6.9 0.00015 34.0 -1.8 47 239-294 140-186 (189)
198 PTZ00397 macrophage migration 34.0 78 0.0017 26.5 4.6 36 241-290 70-105 (116)
199 PRK12544 RNA polymerase sigma 33.7 5.9 0.00013 36.3 -2.4 48 239-296 148-196 (206)
200 PRK06704 RNA polymerase factor 33.6 8.2 0.00018 36.7 -1.5 31 266-296 134-164 (228)
201 COG4802 FtrB Ferredoxin-thiore 33.6 50 0.0011 29.2 3.3 55 241-296 2-60 (110)
202 TIGR02531 yecD_yerC TrpR-relat 33.2 17 0.00037 30.3 0.5 21 266-286 52-72 (88)
203 PRK12523 RNA polymerase sigma 33.1 7.4 0.00016 33.9 -1.8 46 238-293 118-164 (172)
204 PRK12527 RNA polymerase sigma 32.8 5 0.00011 34.3 -2.8 49 240-297 106-154 (159)
205 COG3040 Blc Bacterial lipocali 32.3 43 0.00094 31.7 3.0 26 236-261 139-165 (174)
206 PRK12525 RNA polymerase sigma 32.2 7.4 0.00016 33.9 -1.9 45 238-292 117-162 (168)
207 PRK09415 RNA polymerase factor 31.9 6.1 0.00013 34.8 -2.5 47 238-294 126-173 (179)
208 PF10668 Phage_terminase: Phag 31.5 26 0.00057 27.7 1.2 23 264-286 22-44 (60)
209 smart00109 C1 Protein kinase C 31.5 20 0.00043 24.7 0.5 29 88-124 12-40 (49)
210 PF05121 GvpK: Gas vesicle pro 31.4 91 0.002 26.6 4.5 35 238-280 40-74 (88)
211 cd02425 Peptidase_C39F A sub-f 31.2 92 0.002 25.1 4.4 46 234-285 22-67 (126)
212 PRK05657 RNA polymerase sigma 30.6 12 0.00026 37.3 -1.0 53 239-296 262-314 (325)
213 PF01710 HTH_Tnp_IS630: Transp 30.5 31 0.00068 29.4 1.6 38 240-286 3-40 (119)
214 PRK13890 conjugal transfer pro 30.5 33 0.00072 29.6 1.8 22 268-289 22-43 (120)
215 COG0289 DapB Dihydrodipicolina 30.4 40 0.00086 33.7 2.6 19 238-256 101-119 (266)
216 PF04936 DUF658: Protein of un 30.4 17 0.00036 34.4 -0.0 34 264-297 14-47 (186)
217 PRK15479 transcriptional regul 30.2 26 0.00057 29.9 1.1 49 239-293 148-201 (221)
218 PRK05803 sporulation sigma fac 30.2 11 0.00024 34.9 -1.2 52 239-295 175-226 (233)
219 PF01726 LexA_DNA_bind: LexA D 29.9 93 0.002 24.4 4.1 37 239-281 3-43 (65)
220 TIGR00290 MJ0570_dom MJ0570-re 29.7 77 0.0017 30.5 4.3 44 239-283 94-142 (223)
221 PRK13877 conjugal transfer rel 29.4 57 0.0012 28.6 3.1 26 231-256 8-33 (114)
222 PRK09643 RNA polymerase sigma 29.3 12 0.00025 33.6 -1.2 48 239-296 134-182 (192)
223 cd01104 HTH_MlrA-CarA Helix-Tu 29.2 16 0.00035 27.2 -0.3 21 267-287 3-23 (68)
224 PRK09636 RNA polymerase sigma 29.1 11 0.00025 36.0 -1.4 49 239-297 115-164 (293)
225 PRK09638 RNA polymerase sigma 28.9 5.7 0.00012 34.4 -3.2 31 265-295 143-173 (176)
226 cd02259 Peptidase_C39_like Pep 28.9 93 0.002 24.8 4.1 44 234-283 17-60 (122)
227 PRK11470 hypothetical protein; 28.7 26 0.00056 33.5 0.9 23 233-255 78-100 (200)
228 PF01710 HTH_Tnp_IS630: Transp 28.7 45 0.00097 28.4 2.3 53 234-296 51-103 (119)
229 cd04275 ZnMc_pappalysin_like Z 28.5 34 0.00073 32.8 1.6 18 235-252 207-224 (225)
230 PF05344 DUF746: Domain of Unk 28.4 25 0.00055 28.4 0.7 46 246-297 1-46 (65)
231 TIGR02957 SigX4 RNA polymerase 28.2 13 0.00028 35.6 -1.2 49 239-297 108-157 (281)
232 PRK06437 hypothetical protein; 28.2 13 0.00027 29.1 -1.0 42 250-292 3-47 (67)
233 PF13189 Cytidylate_kin2: Cyti 28.1 23 0.00049 31.8 0.4 42 246-289 14-55 (179)
234 PRK07670 RNA polymerase sigma 27.8 12 0.00026 35.2 -1.5 48 238-294 200-247 (251)
235 PF04297 UPF0122: Putative hel 27.8 34 0.00073 29.6 1.4 41 240-289 18-58 (101)
236 smart00529 HTH_DTXR Helix-turn 27.8 1.1E+02 0.0023 24.2 4.2 31 239-275 66-96 (96)
237 PRK09483 response regulator; P 27.7 20 0.00044 30.8 0.1 47 237-293 146-192 (217)
238 PRK13558 bacterio-opsin activa 27.7 36 0.00078 35.8 1.9 44 237-282 605-648 (665)
239 PRK10336 DNA-binding transcrip 27.7 30 0.00065 29.6 1.1 51 238-294 148-203 (219)
240 PF13551 HTH_29: Winged helix- 27.6 16 0.00035 29.1 -0.6 24 266-289 14-37 (112)
241 TIGR02980 SigBFG RNA polymeras 27.6 10 0.00023 34.6 -1.9 48 238-294 177-224 (227)
242 PRK12534 RNA polymerase sigma 27.4 11 0.00024 33.1 -1.7 49 237-294 135-183 (187)
243 KOG2146 Splicing coactivator S 27.3 30 0.00065 35.4 1.1 19 238-256 12-32 (354)
244 PRK10430 DNA-binding transcrip 27.2 42 0.0009 30.6 2.0 49 235-288 154-202 (239)
245 PRK10188 DNA-binding transcrip 27.1 26 0.00056 33.3 0.6 51 235-295 175-225 (240)
246 KOG4778 Mitochondrial ribosoma 27.0 35 0.00076 32.6 1.5 31 232-264 82-112 (186)
247 COG2197 CitB Response regulato 27.0 29 0.00062 32.2 0.9 45 238-292 147-191 (211)
248 PF11976 Rad60-SLD: Ubiquitin- 26.9 69 0.0015 24.2 2.8 28 264-291 24-52 (72)
249 PF01873 eIF-5_eIF-2B: Domain 26.8 24 0.00052 31.2 0.3 13 107-119 112-124 (125)
250 PRK11552 putative DNA-binding 26.5 29 0.00063 32.1 0.8 48 242-291 12-59 (225)
251 TIGR02960 SigX5 RNA polymerase 26.4 11 0.00023 36.2 -2.1 50 238-297 141-191 (324)
252 cd04763 HTH_MlrA-like Helix-Tu 26.1 19 0.00041 27.3 -0.4 21 267-287 3-23 (68)
253 PF14552 Tautomerase_2: Tautom 26.0 1E+02 0.0022 25.3 3.8 36 241-290 41-77 (82)
254 PRK08359 transcription factor; 25.9 21 0.00045 33.5 -0.2 53 234-290 72-124 (176)
255 PRK08241 RNA polymerase factor 25.8 15 0.00032 35.7 -1.3 31 266-296 171-201 (339)
256 PRK12461 UDP-N-acetylglucosami 25.5 84 0.0018 30.4 3.8 50 236-286 196-247 (255)
257 PF06524 NOA36: NOA36 protein; 25.5 1E+02 0.0022 31.4 4.4 18 283-300 225-242 (314)
258 cd01994 Alpha_ANH_like_IV This 25.5 1.2E+02 0.0025 28.2 4.5 45 238-283 96-145 (194)
259 PF08279 HTH_11: HTH domain; 25.4 29 0.00062 25.0 0.5 33 244-283 2-34 (55)
260 TIGR03001 Sig-70_gmx1 RNA poly 25.4 9.1 0.0002 36.4 -2.8 31 266-296 179-209 (244)
261 PRK09706 transcriptional repre 25.4 46 0.00099 28.6 1.8 36 246-289 8-43 (135)
262 PF12244 DUF3606: Protein of u 25.3 38 0.00083 26.0 1.2 44 233-281 8-51 (57)
263 PF13011 LZ_Tnp_IS481: leucine 25.3 42 0.00091 28.3 1.5 43 239-289 8-50 (85)
264 PF13730 HTH_36: Helix-turn-he 25.2 68 0.0015 23.0 2.4 44 238-286 1-47 (55)
265 KOG3623 Homeobox transcription 25.0 64 0.0014 36.9 3.2 65 229-297 622-686 (1007)
266 PRK10100 DNA-binding transcrip 25.0 24 0.00053 32.9 0.0 48 238-295 154-201 (216)
267 PF13720 Acetyltransf_11: Udp 24.5 83 0.0018 25.7 3.1 41 237-278 25-65 (83)
268 PRK10955 DNA-binding transcrip 24.5 26 0.00056 30.4 0.1 56 239-295 156-211 (232)
269 PRK09640 RNA polymerase sigma 24.2 15 0.00032 32.6 -1.5 54 242-295 122-181 (188)
270 PRK08583 RNA polymerase sigma 24.1 13 0.00029 34.9 -1.9 48 239-295 205-252 (257)
271 PF01402 RHH_1: Ribbon-helix-h 24.0 90 0.0019 21.2 2.7 18 239-256 5-22 (39)
272 PRK06680 D-amino acid aminotra 24.0 1.6E+02 0.0034 28.4 5.3 47 240-286 45-94 (286)
273 TIGR02394 rpoS_proteo RNA poly 23.9 25 0.00053 33.9 -0.2 54 238-296 221-274 (285)
274 PF00440 TetR_N: Bacterial reg 23.8 26 0.00057 24.9 -0.0 37 247-288 4-40 (47)
275 cd02417 Peptidase_C39_likeA A 23.7 1.4E+02 0.003 24.1 4.2 44 234-283 17-60 (121)
276 PRK13858 type IV secretion sys 23.4 1.1E+02 0.0024 28.2 3.9 38 234-275 25-62 (147)
277 COG1427 Predicted periplasmic 23.3 47 0.001 33.0 1.6 52 238-296 179-230 (252)
278 PF06252 DUF1018: Protein of u 23.3 2.3E+02 0.0049 24.1 5.6 41 237-277 52-95 (119)
279 cd02139 Nitroreductase_3 Nitro 23.2 1E+02 0.0023 26.5 3.6 41 234-274 12-61 (164)
280 PF01113 DapB_N: Dihydrodipico 23.2 30 0.00065 29.4 0.2 20 238-257 99-118 (124)
281 TIGR02947 SigH_actino RNA poly 23.1 11 0.00023 33.5 -2.6 37 260-296 143-179 (193)
282 cd08577 PI-PLCc_GDPD_SF_unchar 23.1 1.2E+02 0.0027 28.9 4.4 25 237-261 176-203 (228)
283 PRK11922 RNA polymerase sigma 22.9 9 0.00019 35.5 -3.2 50 238-296 148-197 (231)
284 PF04492 Phage_rep_O: Bacterio 22.7 81 0.0018 26.9 2.7 46 235-281 25-71 (100)
285 PF00376 MerR: MerR family reg 22.7 24 0.00051 25.0 -0.4 21 267-287 2-22 (38)
286 PF00130 C1_1: Phorbol esters/ 22.6 50 0.0011 23.8 1.3 28 90-124 14-41 (53)
287 PF04719 TAFII28: hTAFII28-lik 22.4 1.3E+02 0.0028 25.5 3.8 31 238-274 6-36 (90)
288 PRK12518 RNA polymerase sigma 22.2 8.2 0.00018 33.4 -3.4 34 263-296 135-168 (175)
289 smart00422 HTH_MERR helix_turn 22.1 27 0.00058 26.0 -0.2 20 267-286 3-22 (70)
290 PF12802 MarR_2: MarR family; 22.1 50 0.0011 23.9 1.2 37 240-282 3-39 (62)
291 TIGR02941 Sigma_B RNA polymera 22.0 18 0.00039 33.9 -1.5 49 238-295 204-252 (255)
292 cd01763 Sumo Small ubiquitin-r 21.9 93 0.002 25.1 2.8 27 266-292 37-63 (87)
293 PF00356 LacI: Bacterial regul 21.9 1E+02 0.0022 22.7 2.8 22 238-259 24-45 (46)
294 COG1309 AcrR Transcriptional r 21.8 82 0.0018 25.1 2.5 27 263-289 31-57 (201)
295 PF08280 HTH_Mga: M protein tr 21.8 63 0.0014 24.4 1.7 43 242-292 5-47 (59)
296 PF04539 Sigma70_r3: Sigma-70 21.6 27 0.00058 26.9 -0.3 43 243-287 1-43 (78)
297 PF01902 ATP_bind_4: ATP-bindi 21.6 89 0.0019 29.9 3.1 44 239-283 94-142 (218)
298 PF13223 DUF4031: Protein of u 21.5 50 0.0011 27.8 1.2 19 265-287 24-42 (83)
299 PRK14996 TetR family transcrip 21.4 58 0.0013 28.6 1.7 46 244-290 9-54 (192)
300 smart00857 Resolvase Resolvase 21.3 71 0.0015 26.9 2.1 18 242-259 18-35 (148)
301 PF14106 DUF4279: Domain of un 21.3 1.9E+02 0.0041 23.8 4.6 41 242-290 54-94 (118)
302 PF11516 DUF3220: Protein of u 21.2 17 0.00038 30.9 -1.5 10 280-289 32-41 (106)
303 PHA00675 hypothetical protein 21.0 1.3E+02 0.0028 25.3 3.5 43 233-283 16-58 (78)
304 TIGR02835 spore_sigmaE RNA pol 20.8 20 0.00044 33.3 -1.4 53 238-295 177-229 (234)
305 cd02419 Peptidase_C39C A sub-f 20.5 1.8E+02 0.0039 23.6 4.3 46 234-285 22-67 (127)
306 PF09832 DUF2059: Uncharacteri 20.0 86 0.0019 23.6 2.2 21 235-255 12-32 (64)
No 1
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=99.98 E-value=1.1e-33 Score=212.12 Aligned_cols=50 Identities=84% Similarity=1.519 Sum_probs=45.5
Q ss_pred HHHhhhhhhccCCccccCcccccc-CCCCCCCCCCccccccccccccccccCC
Q 016972 75 KECLKNHAASIGGHALDGCGEFMP-SPTATPSDPTSLKCAACGCHRNFHRREP 126 (379)
Q Consensus 75 RECLKNHAAsiGGHAvDGCGEFMP-SGeegt~dp~ALKCAACGCHRNFHRKE~ 126 (379)
..-||||||+|||||||||||||| +|++++ +++||||||||||||||||+
T Consensus 3 ~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~--~~al~CaACgCHRnFHRre~ 53 (53)
T TIGR01566 3 KECLKNHAASIGGHALDGCGEFMPSSGEEGD--PESLTCAACGCHRNFHRKEP 53 (53)
T ss_pred HHHHHhhHHHhCCcccccccccccCCCCCCC--CcceeeeecCcccccccCCC
Confidence 467999999999999999999999 677665 67999999999999999985
No 2
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=99.97 E-value=1.3e-32 Score=211.80 Aligned_cols=55 Identities=76% Similarity=1.414 Sum_probs=49.9
Q ss_pred eehHHHhhhhhhccCCccccCccccccC-CCCCCCCCCccccccccccccccccCCCC
Q 016972 72 VTYKECLKNHAASIGGHALDGCGEFMPS-PTATPSDPTSLKCAACGCHRNFHRREPDQ 128 (379)
Q Consensus 72 vrYRECLKNHAAsiGGHAvDGCGEFMPS-Geegt~dp~ALKCAACGCHRNFHRKE~e~ 128 (379)
.....-||||||+||||||||||||||+ |+||+ +++|+||||||||||||||++.
T Consensus 4 v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~--~~al~CaACgCHRnFHRre~~~ 59 (60)
T PF04770_consen 4 VRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGT--PEALKCAACGCHRNFHRREVEG 59 (60)
T ss_pred eeHHHHHhhHhHhhCCcccccccccccCCCCCCC--cccceecccCcchhcccCCcCC
Confidence 4567889999999999999999999999 88865 6799999999999999999865
No 3
>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=99.93 E-value=3.8e-26 Score=175.04 Aligned_cols=58 Identities=59% Similarity=1.074 Sum_probs=56.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
+||+||+||+|||++|++|||++||||+++|..+|++||.+|||+++||||||||||.
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~ 58 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK 58 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence 5999999999999999999999999999999999999999999999999999999984
No 4
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.50 E-value=7.1e-15 Score=135.30 Aligned_cols=65 Identities=20% Similarity=0.248 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCC
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNG 299 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~ 299 (379)
.+.||.||.||.||+.+|+..||..+ |---+++++||+.++|++..+||||||||.|+||..+..
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~----Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQ----YVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCC----eeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 37799999999999999999999985 888899999999999999999999999999998877654
No 5
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.38 E-value=1.6e-13 Score=132.74 Aligned_cols=69 Identities=19% Similarity=0.273 Sum_probs=64.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCCCCCCCC
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNGAGGSGSG 306 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~~~~~~~~ 306 (379)
||.||.||.|||++|++-|..+. |..|..+|+|++|+||++..||+||||.|+|+||-.-.-|.++|.-
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enR----YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~l 315 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENR----YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHL 315 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhh----hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhh
Confidence 89999999999999999999986 9999999999999999999999999999999999887777777764
No 6
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.38 E-value=1.9e-13 Score=131.97 Aligned_cols=61 Identities=20% Similarity=0.352 Sum_probs=57.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 232 ~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+||||||.||.-|+|+|++.|.... |||...++-|+..+.|.+.+|+|||||||+||+|+.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaH----YPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAH----YPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhcc----CccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 4567899999999999999888886 999999999999999999999999999999999986
No 7
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.37 E-value=9.4e-14 Score=101.97 Aligned_cols=57 Identities=25% Similarity=0.416 Sum_probs=53.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
||.||+||.+|++.|+++|+.. ++|+...+++||.++||+...|++||+|+|.+.+|
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 7899999999999999999997 49999999999999999999999999999987653
No 8
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.34 E-value=6e-13 Score=125.49 Aligned_cols=67 Identities=18% Similarity=0.324 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCC
Q 016972 228 GSSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLN 298 (379)
Q Consensus 228 ~~s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~ 298 (379)
.+..+.+|-||.||-+|+|.|+++|++. ||+|...+|++|.+|.|.+.+|||||.|+|+|++++..+
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kT----qYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKT----QYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhh----cCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 3456779999999999999999999887 799999999999999999999999999999999887643
No 9
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.29 E-value=2.8e-13 Score=116.29 Aligned_cols=62 Identities=19% Similarity=0.372 Sum_probs=56.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
++.+|.||.||.-||..|+..|-..+ |||.-.+|++|..|.|.+..+||||||+|+|++|+.
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETH----YPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETH----YPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhc----CCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 45689999999999999999554443 999999999999999999999999999999999986
No 10
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.25 E-value=1.9e-12 Score=126.60 Aligned_cols=61 Identities=23% Similarity=0.369 Sum_probs=55.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
...||.||.+|+.|||.|+..+.... ||-.-++|+|++|+||+.+|+||||||||+|.|+-
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~Sp----KPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL 225 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSP----KPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL 225 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCC----chhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence 45699999999999999999988874 99999999999999999999999999999987543
No 11
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.14 E-value=2.8e-11 Score=87.77 Aligned_cols=55 Identities=22% Similarity=0.418 Sum_probs=51.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTF 292 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~ 292 (379)
|+.||.||.+|++.|+++|++.. +|+.+++++++.++||+..+|++||+|+|.+.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~----~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNP----YPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC----CCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 57788999999999999999985 99999999999999999999999999999875
No 12
>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=99.11 E-value=3.7e-11 Score=87.32 Aligned_cols=58 Identities=22% Similarity=0.448 Sum_probs=53.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
++.|+.|+.+|++.|+++|+.. ++|+..++++||.++||+...|++||+|+|.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~----~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKN----PYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhC----CCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 5778999999999999999996 499999999999999999999999999999987654
No 13
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.04 E-value=1e-10 Score=114.66 Aligned_cols=68 Identities=19% Similarity=0.317 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCC
Q 016972 229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNGA 300 (379)
Q Consensus 229 ~s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~~ 300 (379)
...++|+.||.||..|+..|+.-||+.- |.....|.+||..+||+-..||+||||||.||||+...+.
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QK----YLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~ 235 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQK----YLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG 235 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhh----cccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence 3467788999999999999999999984 8999999999999999999999999999999999875543
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.03 E-value=1.2e-10 Score=111.15 Aligned_cols=66 Identities=18% Similarity=0.246 Sum_probs=59.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCC
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNGA 300 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~~ 300 (379)
...||.||.||.+|+..|+.-|.-+- |.....+-|++..+.|+++.|||||||||.||||......
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~----YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNK----YLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcccc----ccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 45799999999999999999999884 8999999999999999999999999999999988764443
No 15
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=98.99 E-value=1.2e-10 Score=114.93 Aligned_cols=61 Identities=20% Similarity=0.316 Sum_probs=52.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 232 ~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.-||.||.||-||+.+|+.-|-|- .|-..-.+=||+.++.|.+.+|||||||||.|-|++.
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrE----NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRE----NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHh----ccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 349999999999999998744443 3777777889999999999999999999999998886
No 16
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.94 E-value=2.9e-10 Score=108.04 Aligned_cols=65 Identities=17% Similarity=0.249 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 229 ~s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
+..+|||.||.|+.-|.-+|+..||.-. |...+++--||+.+.|.+-.||+||||+|+|||++-.
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~kr----YLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKR----YLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHh----hhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 4568999999999999999999999875 8889999999999999999999999999999998863
No 17
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.90 E-value=6.2e-10 Score=109.93 Aligned_cols=62 Identities=21% Similarity=0.339 Sum_probs=59.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 232 ~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
+++|.||-||..|++.|+..|.|+. |+|-..+||++..+.|++..+.|||.|+|+||+|+..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNr----ypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNR----YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhcc----CCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 5689999999999999999999997 9999999999999999999999999999999999974
No 18
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.89 E-value=6.5e-10 Score=99.78 Aligned_cols=63 Identities=19% Similarity=0.178 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 230 s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
..++||-||+||.+|++.|+..|++. +|+|...++.++..+.+++..|||||||+|++|+|+.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~----h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV----HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC----CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 35679999999999999999999998 5999999999999999999999999999999999876
No 19
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.86 E-value=7.9e-10 Score=105.32 Aligned_cols=67 Identities=22% Similarity=0.310 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCC
Q 016972 229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNG 299 (379)
Q Consensus 229 ~s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~ 299 (379)
...+.|..||+|+.-||+.|..-|++. ||.---+|.|||.+|||+.-.||+||||+|-|+||..-++
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkT----QYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQT----QYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhc----chhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence 445667899999999999999999997 7988889999999999999999999999999999987644
No 20
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.77 E-value=1e-08 Score=103.67 Aligned_cols=63 Identities=11% Similarity=0.258 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
.||||.||.|+--.|..|+.+|+++ +||..+++-++|+++.+.+.||+|||=|||.|.|+..+
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 4889999999999999999999999 59999999999999999999999999999999988776
No 21
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.74 E-value=9.2e-09 Score=101.34 Aligned_cols=67 Identities=13% Similarity=0.204 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCC
Q 016972 229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNG 299 (379)
Q Consensus 229 ~s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~ 299 (379)
+..+|||.|--||+-|.=.|+.=|.... |...-+||+||+.|.|+.-.||+||||+|+|.||+...-
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQR----YLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQR----YLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhh----ccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 4567888999999999999999777764 899999999999999999999999999999998887443
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.60 E-value=3.2e-08 Score=89.16 Aligned_cols=68 Identities=12% Similarity=0.067 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCC
Q 016972 229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNGA 300 (379)
Q Consensus 229 ~s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~~ 300 (379)
.+...|+.|++-|.+|+..|+..|+... +|+-..+++|+..|+|+.+.||+||||+|++.+++..-..
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p----~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINP----YPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCC----CCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence 3445678888889999999999999995 9999999999999999999999999999999988775433
No 23
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.57 E-value=3.2e-08 Score=93.71 Aligned_cols=59 Identities=19% Similarity=0.247 Sum_probs=52.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.|..||-||..||.-|+.-|... ||...+++.+|+.-+-|++-.+|+||||||+|-|+-
T Consensus 144 nRkPRtPFTtqQLlaLErkfrek----qYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREK----QYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHh----hhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 47799999999999999855443 699999999999999999999999999999987543
No 24
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.56 E-value=2.6e-08 Score=92.90 Aligned_cols=60 Identities=17% Similarity=0.344 Sum_probs=52.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
++.+-+||.||...|+.-|+-.- |..-....+||+++||..+.|+|||||||++||.+..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~----~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEK----KLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred ccccccccHHHHHHhHHhhcccc----ccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 44445699999999999888874 7778889999999999999999999999999988763
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.56 E-value=3.9e-08 Score=93.97 Aligned_cols=64 Identities=20% Similarity=0.349 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCC
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLN 298 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~ 298 (379)
.+||..|-.|+-.|+..++..||.. +|.--..+-+++..+|..+..+||||||||.||+||.-.
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqt----kylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQT----KYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhh----hcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 5688999999999999999999987 588888999999999999999999999999999999743
No 26
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.48 E-value=6.8e-08 Score=96.24 Aligned_cols=62 Identities=27% Similarity=0.414 Sum_probs=58.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.+.+|-||+||++|++.|++.|++.. |+|...+++++++||+.+..|+|||+|+|++++|..
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~rt~----yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQRTP----YPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccchHHHHHHHhcCCC----CCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 44577799999999999999999985 999999999999999999999999999999999887
No 27
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.25 E-value=7.2e-07 Score=88.19 Aligned_cols=60 Identities=12% Similarity=0.159 Sum_probs=49.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
|+.|--.|..|+.+|+.-|-=+ .|...+-|-||++.|.|+++.||+||||||.|.||...
T Consensus 236 RKKRcPYTK~QtlELEkEFlfN----~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLFN----MYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccCCchHHHHHHHHHHHHHH----HHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 4445567889999988744333 28888999999999999999999999999999987763
No 28
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.25 E-value=1.1e-07 Score=87.62 Aligned_cols=62 Identities=24% Similarity=0.331 Sum_probs=56.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.++++.||.|+.-|+.-|++-||+.. |..-.+++||++.++|+...+|.||||+|.|.||..
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~Qr----YLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFERQR----YLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred HHhhhhcccccCccccccHHHHhhhh----hcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999999999875 888899999999999999999999999999987764
No 29
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.09 E-value=1.3e-06 Score=86.52 Aligned_cols=63 Identities=16% Similarity=0.389 Sum_probs=57.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 230 s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
..-|||.||.+-+-+|..|++||.... +|.-+-+..+|.++.|++.|++|||=|.|+|.|+..
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQP----RPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQP----RPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCC----CCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 456899999999999999999988774 788899999999999999999999999999987754
No 30
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.09 E-value=5.3e-07 Score=88.16 Aligned_cols=60 Identities=13% Similarity=0.279 Sum_probs=51.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 232 ~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
-|-+.|-..|..|+-+|+.-|--.. |......-||+.-+||++|.||+||||||+|.+|.
T Consensus 198 TkDKYRvVYTDhQRLELEKEfh~Sr----yITirRKSELA~~LgLsERQVKIWFQNRRAKERK~ 257 (317)
T KOG0848|consen 198 TKDKYRVVYTDHQRLELEKEFHTSR----YITIRRKSELAATLGLSERQVKIWFQNRRAKERKD 257 (317)
T ss_pred cccceeEEecchhhhhhhhhhcccc----ceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHH
Confidence 3556778899999999999887765 66666778999999999999999999999998664
No 31
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.05 E-value=1.4e-06 Score=78.43 Aligned_cols=65 Identities=26% Similarity=0.424 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 229 ~s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
...+.+|.||.|+..|++.+...|.... +++...+++++..+|+..+||+|||+|+|.+.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATP----KPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCC----CCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3456799999999999999999888764 9999999999999999999999999999999987654
No 32
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.86 E-value=7.8e-06 Score=92.48 Aligned_cols=68 Identities=24% Similarity=0.364 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCCC
Q 016972 230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNGAG 301 (379)
Q Consensus 230 s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~~~ 301 (379)
...+++.||.|+.+|+..|+.|+++.- ++-++..|.+-..|++..+||+|||||+|.+-+|...+++.
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~----~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~~~ 967 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQR----TPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNGTA 967 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhcc----CChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcccc
Confidence 345799999999999999999999974 67777888999999999999999999999999888765543
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.85 E-value=1.5e-05 Score=83.83 Aligned_cols=57 Identities=11% Similarity=0.216 Sum_probs=53.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 016972 232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTF 292 (379)
Q Consensus 232 ~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~ 292 (379)
.-||.|+.||..||+.|.++|+.. ++|..++.+.|+++++|.+.+|..||+|-|.+.
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 458999999999999999999998 599999999999999999999999999999874
No 34
>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=96.01 E-value=0.001 Score=47.81 Aligned_cols=33 Identities=15% Similarity=0.364 Sum_probs=27.6
Q ss_pred cCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 258 KMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 258 RIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
.-.||.+++.++||+++|+++..|..||-|.|.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 347999999999999999999999999999885
No 35
>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=95.64 E-value=0.0082 Score=45.09 Aligned_cols=48 Identities=21% Similarity=0.318 Sum_probs=38.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
||.|..+|-+||-++...+|.-. -+.++|.++||.+.+|.-|+.|...
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~---------s~~~ia~~fgv~~sTv~~I~K~k~~ 48 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE---------SKRDIAREFGVSRSTVSTILKNKDK 48 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT----------HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC---------CHHHHHHHhCCCHHHHHHHHHhHHH
Confidence 78999999999999999988742 6789999999999999999988643
No 36
>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=95.43 E-value=0.0066 Score=46.42 Aligned_cols=47 Identities=23% Similarity=0.345 Sum_probs=34.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 235 RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 235 R~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
|.|..||+|+|..+...+..-| ..|.++|.+.||++.+|-.|..--+
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 5678999999999999885443 5889999999999999999987654
No 37
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=95.12 E-value=0.021 Score=56.69 Aligned_cols=62 Identities=16% Similarity=0.297 Sum_probs=55.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+|.|--|+..-.|+|.++|-.. ---.||.+++.++||++-+|+...+-.||-|.|-+++|..
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h-~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSH-LSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHh-cCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 6788899999999999988764 3447899999999999999999999999999999998876
No 38
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=94.47 E-value=0.06 Score=53.58 Aligned_cols=46 Identities=13% Similarity=0.192 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 244 QKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 244 QkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
-+-.|++++-+. +||......+|++.+||+.-.|-.||.|||++-+
T Consensus 187 SR~~LrewY~~~----~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 187 SRSLLREWYLQN----PYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hHHHHHHHHhcC----CCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 345677777766 5999999999999999999999999999999886
No 39
>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=92.58 E-value=0.12 Score=31.45 Aligned_cols=40 Identities=25% Similarity=0.356 Sum_probs=30.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeec
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWM 285 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWf 285 (379)
+.+|+.+++..+.+.++ .|| .+.++|.++||.+.+|..|+
T Consensus 3 ~~~~~~~~~~~i~~~~~-~~~--------s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLA-AGE--------SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHH-cCC--------CHHHHHHHHCCCHHHHHHhC
Confidence 34478888888887764 332 56799999999999998885
No 40
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=91.11 E-value=0.25 Score=48.58 Aligned_cols=65 Identities=14% Similarity=0.178 Sum_probs=54.4
Q ss_pred CCCCCCCCCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 231 GGRKRFRTKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
..++|.+..|-.+...+|++ +|+-+-| .||.+.....|+.++||++..|..||-|.|-+..|-+.
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~~--PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFEHLLH--PYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhccC--CCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 45788899999999999998 5554433 57888788899999999999999999999998876653
No 41
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=90.87 E-value=0.12 Score=57.31 Aligned_cols=51 Identities=14% Similarity=0.358 Sum_probs=44.4
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
-.|++- ++.|++++..++ .+.++++.+|+.+|||+..|+|+||++.|+...
T Consensus 562 k~~~~p-~sllkayyaln~----~ps~eelskia~qvglp~~vvk~wfE~~~a~e~ 612 (1007)
T KOG3623|consen 562 KQFNHP-TSLLKAYYALNG----LPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEM 612 (1007)
T ss_pred cccCCc-HHHHHHHHHhcC----CCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhh
Confidence 345555 888999999987 899999999999999999999999999998654
No 42
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=88.75 E-value=0.39 Score=39.97 Aligned_cols=46 Identities=30% Similarity=0.392 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCC-CCceeeeecccccc
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGV-DRTVLKVWMHNNKS 290 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv-~r~V~KVWfhNnK~ 290 (379)
|.+||.|-|..+-+++..-| ..|.++|+++|| ....|..|+..-+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g--------~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGG--------DTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcC--------ccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 99999999999999887765 278999999996 99999999875544
No 43
>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=84.49 E-value=0.25 Score=33.56 Aligned_cols=46 Identities=13% Similarity=0.250 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTF 292 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~ 292 (379)
..++++|++.+..++.. ....+++|.++|+++.+|+.|.+.-|.++
T Consensus 9 ~~l~~~~~~~~~~~~~~---------~~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 9 DKLPEREREVILLRFGE---------GLSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred HhCCHHHHHHHHHHHhc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 35788888888776531 22457889999999999999998776654
No 44
>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=83.50 E-value=0.25 Score=35.57 Aligned_cols=40 Identities=23% Similarity=0.377 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecc
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfh 286 (379)
.+++.+|.+.+.+..+. ...+.++|+++||++.+|.-|+.
T Consensus 4 ~~~~~~~~~~i~~l~~~---------G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAE---------GMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSHCCHHHHHHHHHT---------T--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHC---------CCCHHHHHHHHCcCHHHHHHHHh
Confidence 46788888888776543 25689999999999999876654
No 45
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=81.76 E-value=0.49 Score=36.97 Aligned_cols=40 Identities=8% Similarity=0.334 Sum_probs=29.4
Q ss_pred HHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 246 EKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 246 ekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
+-|++|+.+.+ ...+..+++||.+.|++-..|+.||--+.
T Consensus 11 ~pL~~Yy~~h~----~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 11 QPLEDYYLKHK----QLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp HHHHHHHHHT--------TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred HHHHHHHHHcC----CccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 34889988875 67778999999999999999999997554
No 46
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=81.19 E-value=0.87 Score=38.85 Aligned_cols=43 Identities=19% Similarity=0.263 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhN 287 (379)
|.+||.|+|..+....-..| ..|.++|.++||+..+|--|..-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g--------~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG--------MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC--------CCHHHHHHHHCcCHHHHHHHHHH
Confidence 56699999988777655444 35679999999999999999543
No 47
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=77.36 E-value=1.1 Score=40.27 Aligned_cols=44 Identities=16% Similarity=0.385 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecc
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfh 286 (379)
.||+||+++|++ .-|-+ ......++.+++.++|+++.++++-|.
T Consensus 4 ~~T~eer~eLk~rIvElV----Re~GRiTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 4 VFTPEEREELKARIVELV----REHGRITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred cCCHHHHHHHHHHHHHHH----HHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 599999999887 33332 234466889999999999999986554
No 48
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=76.95 E-value=0.59 Score=33.69 Aligned_cols=42 Identities=10% Similarity=0.244 Sum_probs=21.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhN 287 (379)
...||.+|+.+++.+-+ .-.-+.++|.++|+++.+|--|+..
T Consensus 2 ~~~Lt~~eR~~I~~l~~---------~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLE---------QGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHHHC---------S---HHHHHHHTT--HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHH---------cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 35799999999888732 2245678999999999998877654
No 49
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=76.63 E-value=0.82 Score=31.76 Aligned_cols=45 Identities=16% Similarity=0.294 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
.++.+|++.+..++ .|+ ..+++|+++||++.+|+.|++.-+.+++
T Consensus 3 ~l~~~e~~i~~~~~--~g~--------s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLA--EGL--------TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 57889988765543 332 4589999999999999999987666554
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=74.91 E-value=0.54 Score=54.88 Aligned_cols=125 Identities=13% Similarity=0.017 Sum_probs=80.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCCCCCCCCCCC
Q 016972 230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNGAGGSGSGSAG 309 (379)
Q Consensus 230 s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~~~~~~~~~~~ 309 (379)
....+-.||+|+.-|...|..|++.+ .++--.+++++++-+||-.++.-+|+++.+.++++.-.+... ...+..+
T Consensus 441 ~~e~~~~s~r~~~~~t~~L~S~~kt~----~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~ar-g~~~~~~ 515 (1406)
T KOG1146|consen 441 KAEPLLESKRSLEGQTVVLHSFFKTL----KCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLAR-GEVYRCP 515 (1406)
T ss_pred chhhhhhhhcccccceeeeecccccc----cCCccchhhhhHHHhhhcccccccccchhHhHhccccccccc-cccccCC
Confidence 34457789999999999999999554 467788999999999999999999999977777665544432 2223333
Q ss_pred CCccc-cccCCCCCCCCCCcCCCCCCCCCchhhhcccCCcccccccccccc
Q 016972 310 GGIGR-INLDDDNTGNDNINNSKSGDGDDQDEEEGINNNNNGVRNLNHQFG 359 (379)
Q Consensus 310 ~~~g~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 359 (379)
+.-++ ..-+..-|.+++.-+----|.+++.+++.+.++...|+-+-|-..
T Consensus 516 ~~p~~C~~C~~stttng~LsihlqS~~h~~~lee~~~~~g~~v~~~~~~v~ 566 (1406)
T KOG1146|consen 516 GKPYPCRACNYSTTTNGNLSIHLQSDLHRNELEEAEENAGEQVRLLPASVT 566 (1406)
T ss_pred CCcccceeeeeeeecchHHHHHHHHHhhHHHHHHHHhccccchhhhhhhhc
Confidence 33333 222222233232222122345555566666677777777666533
No 51
>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=74.89 E-value=0.78 Score=38.85 Aligned_cols=47 Identities=11% Similarity=0.188 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
.+++++|++.+.- |++.. ..+++|..+||++.+++++++.-|.++++
T Consensus 110 ~~L~~~~r~v~~l~~~~g~----------~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRGV----------SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 5678888888877 44432 45799999999999999999999988765
No 52
>PRK06424 transcription factor; Provisional
Probab=74.70 E-value=1.6 Score=39.33 Aligned_cols=56 Identities=11% Similarity=0.074 Sum_probs=37.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
++|.|.. ..+..+.|..|++++-+....... ..++||..+||++..|.-|..+.+.
T Consensus 68 ~~~~~d~-~~~~~~~~~~~g~~Ir~lRe~~GL-SQ~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 68 KKYKKKA-SDEDLDIVEDYAELVKNARERLSM-SQADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred CCccCcc-cHHHHHHHHHHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 3444554 455568888888776422222221 3679999999999999999987753
No 53
>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=73.78 E-value=0.77 Score=33.22 Aligned_cols=43 Identities=12% Similarity=0.183 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
+++++|++.+.-+ +-+.-..+++|..+|++...+++|++.-|.
T Consensus 10 ~L~~~~r~i~~l~---------~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLR---------YFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHH---------HTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHH---------HHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 4567777777664 233446789999999999999999987654
No 54
>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=72.69 E-value=3.3 Score=31.73 Aligned_cols=41 Identities=17% Similarity=0.303 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceee
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLK 282 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~K 282 (379)
+|..|++.|+...+. | =...|.+..++++|+++||++.+|-
T Consensus 1 LT~~Q~e~L~~A~~~-G-Yfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYEL-G-YFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHc-C-CCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 689999998876554 4 1223667899999999999988764
No 55
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=71.77 E-value=1.2 Score=40.48 Aligned_cols=24 Identities=4% Similarity=0.108 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCCceeeeeccccc
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
..++||+.+||++.+|.-|-.+.+
T Consensus 84 SqeeLA~~lgvs~s~IsriE~G~~ 107 (154)
T TIGR00270 84 SQEQLAKKIQEKESLIKKIENAEI 107 (154)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 468999999999999999997754
No 56
>PF13551 HTH_29: Winged helix-turn helix
Probab=71.46 E-value=4.2 Score=32.46 Aligned_cols=53 Identities=15% Similarity=0.238 Sum_probs=32.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCccCCC--CCHHHHHH-H-HHH--hCCCCceeeeecc
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQK--RDDDLVHE-F-CNE--VGVDRTVLKVWMH 286 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~GWRIqk--~d~~~vq~-f-c~e--iGv~r~V~KVWfh 286 (379)
.+|.++++|+||++.+.+++...... .+ .....+.+ + -++ +.|+..+|.-|++
T Consensus 51 ~g~~~~~l~~~~~~~l~~~~~~~p~~-g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 51 GGRPRKRLSEEQRAQLIELLRENPPE-GRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHCCCC-CCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 46667779999999999999986422 11 12233333 2 222 3566666666654
No 57
>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=70.29 E-value=0.92 Score=33.61 Aligned_cols=45 Identities=13% Similarity=0.220 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
.||+.|++.|.-+++-. ..+++|.++||+..+|+.+..+=+.|++
T Consensus 3 ~LT~~E~~vl~~l~~G~----------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM----------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-----------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC----------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 58999999998887654 4679999999999999999988777764
No 58
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=67.71 E-value=1.3 Score=38.94 Aligned_cols=47 Identities=9% Similarity=0.335 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+++++|++.+.- |++.. ..+++|+++||++.++++|++.-|.++++.
T Consensus 133 ~L~~~~r~i~~l~~~~~~----------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYVDGC----------SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHHcCC----------CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 566777775444 44433 467999999999999999999988877653
No 59
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=66.44 E-value=1.3 Score=38.16 Aligned_cols=49 Identities=4% Similarity=0.037 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
-+++++|++.+.- +++.. ..+++|.++|++..++++|++--|.++++.-
T Consensus 107 ~~L~~~~r~v~~l~~~~g~----------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHEL----------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhcC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567778777764 44443 4579999999999999999999999887653
No 60
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=66.36 E-value=4.5 Score=29.54 Aligned_cols=24 Identities=38% Similarity=0.576 Sum_probs=22.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERVG 256 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~G 256 (379)
||||-+.+..|+.++|.+++++.|
T Consensus 2 r~r~t~~l~~el~~~L~~ls~~t~ 25 (44)
T PF12651_consen 2 RKRFTFSLDKELYEKLKELSEETG 25 (44)
T ss_pred ceEEEEecCHHHHHHHHHHHHHHC
Confidence 789999999999999999999998
No 61
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=66.28 E-value=2.6 Score=38.50 Aligned_cols=55 Identities=25% Similarity=0.391 Sum_probs=35.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCccCCCC-CHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKR-DDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~GWRIqk~-d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
.|+.--++|.+|+..-+-.++.-= +... +....+++|.++||++.+|--|.+-+|
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~--~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENEL--MPENGERRTQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHH--S------S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHH--hhhccccchHHHHHHHhCCCHHHHHHHHhcCH
Confidence 345557899999996665555420 1111 445789999999999999999998666
No 62
>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=64.63 E-value=0.86 Score=39.71 Aligned_cols=48 Identities=4% Similarity=0.055 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+++++|++.+.-+ +-..-..+++|+.+||++.++++|++.-|.++++.
T Consensus 138 ~L~~~~r~v~~l~---------~~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 138 ALPEDLRTAITLR---------ELEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred cCCHHHhhhhhhh---------hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3455666655432 22223568999999999999999999999888765
No 63
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=64.41 E-value=1 Score=40.19 Aligned_cols=48 Identities=13% Similarity=0.115 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.- +++. -..+++|+++||++.+||+|++.-|.++++.-
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 577888887754 3333 24679999999999999999999998887653
No 64
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=64.27 E-value=3.3 Score=45.50 Aligned_cols=59 Identities=17% Similarity=0.291 Sum_probs=54.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHH---HHHHHHHhCCCCceeeeecccccccCC
Q 016972 232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDL---VHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 232 ~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~---vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
-++||||+++-|-+..+.+|+...| -|+|+.. ..-|...+.+.++.+-..|+|.|.-.+
T Consensus 646 ~~p~~~~~isge~~~~~qs~i~~~g---l~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~ 707 (769)
T KOG3755|consen 646 HKPRKRTKISGEALGILQSFITDVG---LYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVK 707 (769)
T ss_pred cCccccceecccchHHHHHHHHHhc---cCchhhcccccchhhhhhcccHHHHHHhhhcceeecc
Confidence 3799999999999999999999998 6889888 999999999999999999999998654
No 65
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=64.05 E-value=1 Score=38.41 Aligned_cols=47 Identities=6% Similarity=0.095 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHH-HHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFEF-AERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~f-aEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.++++|++.+.-+ ++. -..+++|+.+||++.+|+.|++.-|.++++.
T Consensus 128 ~L~~~~r~vl~l~~~~~----------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG----------LSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5778888887654 322 2457999999999999999999888887664
No 66
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=63.91 E-value=1.5 Score=39.84 Aligned_cols=48 Identities=8% Similarity=0.141 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.- +++.+ ..+++|.++||+..+|+++++.-|.++++..
T Consensus 153 ~L~~~~r~vl~l~~~~g~----------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQEL----------SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 466778887765 43333 5689999999999999999999998887654
No 67
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=63.74 E-value=3.7 Score=34.26 Aligned_cols=22 Identities=27% Similarity=0.377 Sum_probs=18.4
Q ss_pred eeehHHHhhhhhhccCCccccC
Q 016972 71 VVTYKECLKNHAASIGGHALDG 92 (379)
Q Consensus 71 ~vrYRECLKNHAAsiGGHAvDG 92 (379)
.......|||.||.|||.+|-.
T Consensus 47 ~~ga~NdlrNeAa~lGgntV~~ 68 (93)
T PF13698_consen 47 MRGARNDLRNEAAKLGGNTVVL 68 (93)
T ss_pred HHHHHHHHHHHHHHhCCCEEEE
Confidence 4557889999999999988853
No 68
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=63.69 E-value=1.5 Score=37.01 Aligned_cols=47 Identities=13% Similarity=0.137 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
++++.|++.+.. |++. -..+++|+.+||+..++++|++.-|.++++.
T Consensus 106 ~L~~~~r~ii~l~~~~~----------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG----------KTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred hCCHHHHHHHHHHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 556666666544 3332 3468999999999999999999988887653
No 69
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=63.51 E-value=1.6 Score=39.35 Aligned_cols=49 Identities=14% Similarity=0.156 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+.+|+.|++.|+.++ .|| ..+++|.++||++..++.|.+.-+.++++..
T Consensus 5 ~~Lt~rqreVL~lr~--~Gl--------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRLRE--RGL--------TQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 568899999987753 343 3479999999999999999999888876654
No 70
>PRK10403 transcriptional regulator NarP; Provisional
Probab=62.98 E-value=2.8 Score=35.38 Aligned_cols=49 Identities=12% Similarity=0.259 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
..||..+++.|..+++.. ..+++++.+++++++++++++|=+.|++-+.
T Consensus 152 ~~Lt~~e~~vl~~~~~g~----------s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 152 SVLTERELDVLHELAQGL----------SNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred ccCCHHHHHHHHHHHCCC----------CHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 469999999988776542 3468899999999999999999888876543
No 71
>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=62.87 E-value=1.7 Score=36.20 Aligned_cols=46 Identities=13% Similarity=0.187 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
+++.+|++.+.- +.+.+ .++++|+.+||++..|+++++.-|.++++
T Consensus 113 ~L~~~~r~il~l~~~~~~----------~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEGK----------SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 556777777665 33322 46789999999999999999998888765
No 72
>PRK09480 slmA division inhibitor protein; Provisional
Probab=62.79 E-value=5.5 Score=34.54 Aligned_cols=47 Identities=11% Similarity=0.131 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 242 QSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 242 ~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
.+.++++.+.|.++=+.-.. +...++++|++.||++.+|=.+|.|..
T Consensus 9 ~~~r~~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 9 GERREQILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred hhHHHHHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 66677777776666222224 788999999999999999999999965
No 73
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=62.55 E-value=3.6 Score=29.25 Aligned_cols=22 Identities=23% Similarity=0.632 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCCCceeeeeccc
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhN 287 (379)
.+.++|+.+||++.+|.-|+..
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4679999999999999999865
No 74
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=61.20 E-value=1.6 Score=38.42 Aligned_cols=49 Identities=8% Similarity=0.141 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
+++++|++.+.- |++.. ..+++|+.+||++.+|+++++.-|.++++.-.
T Consensus 128 ~L~~~~r~i~~l~~~~g~----------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 128 ALPERQREAIVLQYYQGL----------SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred hCCHHHHHHhhHHHhcCC----------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 456777776644 44443 45799999999999999999999999877653
No 75
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=61.18 E-value=1.4 Score=41.07 Aligned_cols=58 Identities=14% Similarity=0.103 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCCCCCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNGAGGSGSG 306 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~~~~~~~~ 306 (379)
++++.|++.+.-++ -+.-..+++|..+||+..+|+++++.-|.++++.- .+++.++..
T Consensus 134 ~Lp~~~R~v~~L~y---------~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l-~~~~~~~~~ 191 (216)
T PRK12533 134 KLPVEYREVLVLRE---------LEDMSYREIAAIADVPVGTVMSRLARARRRLAALL-GGASAAQAA 191 (216)
T ss_pred cCCHHHHhHhhhHH---------hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH-cccchhhcC
Confidence 45566666665532 12235689999999999999999999999998775 555544443
No 76
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=60.82 E-value=1.1 Score=39.17 Aligned_cols=48 Identities=13% Similarity=0.243 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHH-HHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFEF-AERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~f-aEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.-+ ++. -..+++|.++||++.+|+++++.-|.+++++.
T Consensus 131 ~L~~~~r~v~~l~~~~g----------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG----------ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 5667788777774 332 24689999999999999999999999887654
No 77
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=60.34 E-value=1.2 Score=39.30 Aligned_cols=51 Identities=14% Similarity=0.156 Sum_probs=39.6
Q ss_pred CCCCCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 235 RFRTKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 235 R~RTkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+.-.++++.|++.+.- |++- ...+++|+++||++.+|+++++.-|.++++.
T Consensus 135 ~~l~~L~~~~r~i~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 135 ELLDTLPEKQREILILRVVVG----------LSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HHHHhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3445677888888776 4443 2468999999999999999999988887654
No 78
>PRK04217 hypothetical protein; Provisional
Probab=59.97 E-value=2.2 Score=37.05 Aligned_cols=52 Identities=13% Similarity=0.069 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNG 299 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~ 299 (379)
++|.+|++.+...+.. +-.++++|+.+||++.+|++.++.-+.+++......
T Consensus 42 ~Lt~eereai~l~~~e---------GlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~ 93 (110)
T PRK04217 42 FMTYEEFEALRLVDYE---------GLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEG 93 (110)
T ss_pred cCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 4678998776554321 126789999999999999999999998887665433
No 79
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=59.66 E-value=17 Score=26.86 Aligned_cols=33 Identities=9% Similarity=0.206 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhN 287 (379)
|.|||++|.+. +-+.++..+|+++.-+.|+|..
T Consensus 13 s~eqk~~l~~~--------------it~~l~~~~~~p~~~v~V~i~e 45 (61)
T PRK02220 13 TEEQLKALVKD--------------VTAAVSKNTGAPAEHIHVIINE 45 (61)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcChhhEEEEEEE
Confidence 79999998764 4467899999977666666654
No 80
>PRK00118 putative DNA-binding protein; Validated
Probab=59.31 E-value=1.4 Score=37.95 Aligned_cols=47 Identities=15% Similarity=0.168 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
++++.|++.+..++.. +..+.++|+++||++.+|+.|++.-|.++++
T Consensus 17 ~L~ekqRevl~L~y~e---------g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLD---------DYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3567788887664332 3356899999999999999999987766654
No 81
>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=59.21 E-value=1.8 Score=31.18 Aligned_cols=44 Identities=9% Similarity=0.185 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccccc
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKST 291 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k 291 (379)
.++++|++.+...+ -.....++++..+||++..++.|...-..+
T Consensus 4 ~L~~~er~vi~~~y---------~~~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRY---------FEGLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHH---------TST-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh---------cCCCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 47889999998875 223357899999999999998887654443
No 82
>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=59.00 E-value=3.1 Score=29.09 Aligned_cols=44 Identities=16% Similarity=0.271 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
++..|++.+..++ .|| ..+++|+.++|++.+|+.|++--+.++.
T Consensus 1 l~~~e~~i~~~~~--~~~--------s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 1 LTPREREVLRLLA--EGK--------TNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred CCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 4667777654443 232 4589999999999999999986554443
No 83
>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=58.65 E-value=7 Score=27.55 Aligned_cols=36 Identities=8% Similarity=0.085 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 246 EKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 246 ekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
++|+++-++.||. .++||..+||++.+|.-|....+
T Consensus 5 ~~l~~~r~~~glt--------q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 5 MLVRARRKALGLT--------QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHCCCC
Confidence 4566666677653 46899999999999999986653
No 84
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=58.55 E-value=5.1 Score=29.55 Aligned_cols=34 Identities=15% Similarity=0.329 Sum_probs=22.5
Q ss_pred HHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 248 MFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 248 M~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
|+.+.++.|+ .+.+||+++||++.+|.-|++++.
T Consensus 2 L~~~m~~~~i--------t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 2 LKELMAERGI--------TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp HHHHHHHTT----------HHHHHHHHT--HHHHHHHHTTT-
T ss_pred HHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHhccc
Confidence 4555555542 457899999999999999998774
No 85
>PHA02893 hypothetical protein; Provisional
Probab=58.51 E-value=3.9 Score=34.66 Aligned_cols=8 Identities=63% Similarity=1.585 Sum_probs=7.5
Q ss_pred cccccccc
Q 016972 109 SLKCAACG 116 (379)
Q Consensus 109 ALKCAACG 116 (379)
.|+|+|||
T Consensus 69 tL~CaACG 76 (88)
T PHA02893 69 NIKCIACG 76 (88)
T ss_pred ceeehhhc
Confidence 79999998
No 86
>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=57.17 E-value=3.9 Score=27.68 Aligned_cols=24 Identities=25% Similarity=0.513 Sum_probs=21.1
Q ss_pred HHHHHHHhCCCCceeeeecccccc
Q 016972 267 VHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
++++|+.+||++.+|..|..+.+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 578999999999999999987653
No 87
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=56.62 E-value=1.6 Score=38.08 Aligned_cols=47 Identities=9% Similarity=0.169 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHH-HHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFEFA-ERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~fa-Ek~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+++++|++.+.-.+ +. -..+++|+++||+...+|++++.-|.++++.
T Consensus 129 ~L~~~~r~i~~l~~~~g----------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEG----------LSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 45677777655532 22 2468999999999999999999988888664
No 88
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=56.61 E-value=2 Score=37.99 Aligned_cols=49 Identities=16% Similarity=0.165 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.+++++|++.+.- +++ .-.++++|+++||++.+++.+++.-|.++++.-
T Consensus 130 ~~L~~~~r~v~~l~~~~----------g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLE----------GLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred HhCCHHHHHHHHHHHHc----------CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4566777776664 333 235689999999999999999999998887643
No 89
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=56.20 E-value=1.6 Score=39.00 Aligned_cols=48 Identities=10% Similarity=0.142 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHH-HHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEF-AERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~f-aEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.+++++|++.+.-+ ++. -.++++|..+||+..++|+|++.-|.++++.
T Consensus 133 ~~Lp~~~R~v~~L~~~~g----------~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 133 NHLPAQQARVFMMREYLE----------LSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred HhCCHHHHHHHhHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35667777777664 232 2468999999999999999999998888764
No 90
>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=56.04 E-value=2.5 Score=36.03 Aligned_cols=48 Identities=8% Similarity=0.160 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.- |++.. ..+++|..+||++.++++|.+.-|.++++.-
T Consensus 110 ~L~~~~r~i~~l~~~~g~----------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYEDL----------SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHhcC----------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 455677776644 33322 3579999999999999999999998887653
No 91
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=56.01 E-value=2.2 Score=37.03 Aligned_cols=48 Identities=10% Similarity=0.196 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.+++++|++.+.- +++. ...+++|+.+||++.+++++++.-|.++++.
T Consensus 135 ~~L~~~~r~v~~l~~~~g----------~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 135 QALPPKYRMVIVLKYMED----------LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HhCCHHHhHHhhhHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3577788887655 4443 3568999999999999999999988887654
No 92
>PRK10072 putative transcriptional regulator; Provisional
Probab=55.76 E-value=7.8 Score=32.79 Aligned_cols=35 Identities=20% Similarity=0.466 Sum_probs=28.1
Q ss_pred HHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 248 MFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 248 M~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
++++-+++||. .++||..+||+..+|.-|.+.+|.
T Consensus 38 ik~LR~~~glT--------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 38 FEQLRKGTGLK--------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 45556777765 579999999999999999987763
No 93
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=55.58 E-value=3.5 Score=34.14 Aligned_cols=47 Identities=9% Similarity=0.181 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+|++.|++.|..+++.. ..+++++++|++..++++++++-|.|+++.
T Consensus 141 ~l~~~e~~vl~~~~~~~----------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 141 SLSERERQVMDGLVAGL----------SNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred hhhhhHHHHHHHHHccC----------chHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 46777777776555432 246788999999999999999999888654
No 94
>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=55.28 E-value=2.6 Score=35.43 Aligned_cols=50 Identities=10% Similarity=0.145 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhC------ccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 245 KEKMFEFAERVG------WKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 245 kekM~~faEk~G------WRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
.+.+..+.+++. ..+.+-+.-..+++|+.+||+..+|+++++--|.++++
T Consensus 96 ~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 96 QEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred HHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344555555554 22233444578999999999999999999988877754
No 95
>PRK09726 antitoxin HipB; Provisional
Probab=55.23 E-value=12 Score=30.11 Aligned_cols=42 Identities=19% Similarity=0.441 Sum_probs=32.1
Q ss_pred CCCHHHH-HHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 016972 239 KFSQSQK-EKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNN 288 (379)
Q Consensus 239 kFT~EQk-ekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNn 288 (379)
.++++++ ++|+.+-++.||. .++||+.+||++..|.-|..+.
T Consensus 7 ~~~~~~l~~~lk~~R~~~glt--------q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 7 IYSPTQLANAMKLVRQQNGWT--------QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred ccCHHHHHHHHHHHHHHcCCC--------HHHHHHHHCcCHHHHHHHHCCC
Confidence 3455666 5677777777753 5799999999999999998864
No 96
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=55.14 E-value=2.9 Score=35.47 Aligned_cols=48 Identities=21% Similarity=0.271 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
-+++++|++.+.- +++.. ..+++|+.+||+..++|++++--|.++++.
T Consensus 105 ~~Lp~~~r~v~~l~~~~g~----------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 105 QKLPARQREAFLLRYWEDM----------DVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HhCCHHHHHHHHHHHHhcC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4566778777766 44433 368999999999999999999888887654
No 97
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=55.04 E-value=2 Score=36.87 Aligned_cols=47 Identities=9% Similarity=0.113 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHH-HHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFEF-AERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~f-aEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.++++|++.+.-. .+.+ ..+++|..+||++.+++++++.-|.++++.
T Consensus 112 ~L~~~~r~v~~l~~~~~~----------s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLRDYYGF----------SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhHHhcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5667777776653 2332 468999999999999999999999988764
No 98
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=55.01 E-value=2.8 Score=35.80 Aligned_cols=48 Identities=6% Similarity=0.147 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.- +++.. ..+++|..+||+..++|++++.-|.++++.-
T Consensus 106 ~Lp~~~r~v~~l~~~~g~----------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEK----------SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHHhCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 466777776644 33433 4579999999999999999999988876643
No 99
>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=54.93 E-value=5.5 Score=28.48 Aligned_cols=22 Identities=14% Similarity=0.444 Sum_probs=17.1
Q ss_pred HHHHHHhCCCCceeeeeccccc
Q 016972 268 HEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 268 q~fc~eiGv~r~V~KVWfhNnK 289 (379)
++||..+||++.+|.-|+.+.+
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHhCCCcchhHHHhcCCC
Confidence 6888888888888888887744
No 100
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=54.27 E-value=2.7 Score=37.14 Aligned_cols=51 Identities=20% Similarity=0.206 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 237 RTKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 237 RTkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
-..++++|++.+.- +++.. ..+++|..+||+..++++.++.-|.++++.-.
T Consensus 129 l~~L~~~~r~vl~l~~~~~~----------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 129 LAKLSPAHREIIDLVYYHEK----------SVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred HHhCCHHHHHHHHHHHHcCC----------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34677888888754 55444 46899999999999999999999998877643
No 101
>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=53.50 E-value=7.2 Score=29.79 Aligned_cols=21 Identities=19% Similarity=0.417 Sum_probs=13.0
Q ss_pred HHHHHHhCCCCceeeeecccc
Q 016972 268 HEFCNEVGVDRTVLKVWMHNN 288 (379)
Q Consensus 268 q~fc~eiGv~r~V~KVWfhNn 288 (379)
++||+.+||++..|-.|+.++
T Consensus 22 ~~lA~~~gis~~tis~~~~g~ 42 (78)
T TIGR02607 22 RALAKALGVSRSTLSRIVNGR 42 (78)
T ss_pred HHHHHHhCCCHHHHHHHHcCC
Confidence 466666666666666666544
No 102
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=53.31 E-value=2.7 Score=35.88 Aligned_cols=48 Identities=10% Similarity=0.086 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.|.- |++-. ..+++|+++||++.+|+++++--+.++++.-
T Consensus 109 ~L~~~~r~v~~l~~~~~~----------s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLHGE----------TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 556677776654 33322 3579999999999999999988887776653
No 103
>smart00351 PAX Paired Box domain.
Probab=52.92 E-value=8.4 Score=33.26 Aligned_cols=42 Identities=10% Similarity=0.215 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
++.|+++++..+++ .|+ ...++|+++||++.++..|++--+.
T Consensus 18 ~s~~~R~riv~~~~-~G~--------s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELAQ-NGV--------RPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHHH-cCC--------CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 88999999999886 452 3468999999999999999986543
No 104
>PF13518 HTH_28: Helix-turn-helix domain
Probab=52.75 E-value=4.2 Score=28.72 Aligned_cols=25 Identities=24% Similarity=0.590 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCCceeeeecccccc
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
.+.++|+++||++.+|..|++.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 6788999999999999999976543
No 105
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=52.62 E-value=4 Score=36.30 Aligned_cols=50 Identities=12% Similarity=0.331 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
-+++++|++.+.- |.+-+ -.+++|+.+||++.+++++++--|.+++|+..
T Consensus 130 ~~L~~~~r~i~~l~~~~g~----------s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLGE----------KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HhCCHHHHHHHHHHHHccC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 4677888888765 44432 46799999999999999999999999988764
No 106
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=52.40 E-value=2.1 Score=37.85 Aligned_cols=47 Identities=13% Similarity=0.155 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+++++|++.+.- +++- -..+++|..+||++.+|++|++.-|.++++.
T Consensus 141 ~L~~~~~~v~~l~~~~g----------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 141 QLPESQRQVLELAYYEG----------LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hCCHHHhhhhhhhhhcC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 455666666544 3332 3568999999999999999999888877653
No 107
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=52.35 E-value=2.1 Score=37.13 Aligned_cols=49 Identities=10% Similarity=0.114 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
-+++++|++.+.-+. -+.-..+++|.++||++.+++++++--|.++++.
T Consensus 111 ~~L~~~~r~v~~l~~---------~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 111 NLLSADQREAIILIG---------ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred HhCCHHHHHHHHHHH---------HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 355666666554431 1223578999999999999999999888877643
No 108
>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=52.33 E-value=2.6 Score=33.84 Aligned_cols=47 Identities=13% Similarity=0.186 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
+++..|++.+...+- .| ...+++|+++||++.+|+.|++.-+.++++
T Consensus 110 ~L~~~~~~ii~~~~~-~g--------~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EG--------LSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh-cC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 667888888655422 12 245699999999999999999888777654
No 109
>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=52.06 E-value=6.2 Score=26.01 Aligned_cols=22 Identities=18% Similarity=0.445 Sum_probs=15.6
Q ss_pred HHHHHHhCCCCceeeeeccccc
Q 016972 268 HEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 268 q~fc~eiGv~r~V~KVWfhNnK 289 (379)
.+||..+|+++..|..|+.+.+
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCCC
Confidence 4777777777777777776653
No 110
>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=52.01 E-value=9.1 Score=30.25 Aligned_cols=45 Identities=20% Similarity=0.339 Sum_probs=30.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecc
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfh 286 (379)
|-.||.+=|-+..++|++.+ ........-+.+.||+|+.|+-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~-----nc~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDN-----NCKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-T-----TTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHcc-----chhhhHHHHHHHhCccHHHHHHHHH
Confidence 56799999999999999874 2222345678999999999999976
No 111
>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=51.75 E-value=2.2 Score=37.34 Aligned_cols=50 Identities=8% Similarity=0.075 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.+|+++|++.+.-++-. .-..+++|.++||+..+++++++--|.++++.-
T Consensus 99 ~~L~~~~r~v~~l~~~~---------g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 99 KELPDEYREAIRLTELE---------GLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred HhCCHHHHHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777777776654221 124679999999999999999999999887764
No 112
>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=51.69 E-value=8.6 Score=28.43 Aligned_cols=23 Identities=9% Similarity=0.394 Sum_probs=15.1
Q ss_pred HHHHHHHhCCCCceeeeeccccc
Q 016972 267 VHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
.++||..+||++..|.-|..+.+
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 45677777777777777776654
No 113
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=51.48 E-value=2.9 Score=37.72 Aligned_cols=49 Identities=14% Similarity=0.135 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.-. +-+.-..+++|..+||+..+++++++--|.++++.-
T Consensus 113 ~Lp~~~r~v~~L~---------~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILV---------GASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhH---------HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4556666665442 112234689999999999999999999999988765
No 114
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=50.22 E-value=2.4 Score=36.05 Aligned_cols=48 Identities=13% Similarity=0.117 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
++++.+++.+.-++ -+.-..+++|.++||++.+|+.|++--|.++++.
T Consensus 125 ~L~~~~r~i~~l~~---------~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRY---------VEGLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35556666654432 1223468999999999999999999888877653
No 115
>PRK11891 aspartate carbamoyltransferase; Provisional
Probab=50.20 E-value=9.6 Score=40.03 Aligned_cols=41 Identities=22% Similarity=0.434 Sum_probs=33.3
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
|..|-+-|...-.++| -.+++||++|||+++.|..|+-=+-
T Consensus 1 ~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~l~~wl~p~~ 41 (429)
T PRK11891 1 TVPQQAFLRDAMRRLN--------MTREAFANRIGVSRRALDTWLLPDD 41 (429)
T ss_pred ChhHHHHHHHHHHHhC--------CCHHHHHHHhCCcHHhHHhhcCCCC
Confidence 4578888888888886 2568999999999999999986443
No 116
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=49.34 E-value=2.8 Score=37.35 Aligned_cols=47 Identities=6% Similarity=0.070 Sum_probs=35.8
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
.+++++|++.+.- +++. -..+++|..+||+..++|++++--|.++++
T Consensus 129 ~~Lp~~~r~v~~L~~~~g----------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLLG----------LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3455666666544 2233 246899999999999999999999999877
No 117
>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=49.22 E-value=4.2 Score=35.14 Aligned_cols=47 Identities=11% Similarity=0.283 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+++.+|++.+.. |++.. ..+++|+.+||+..+++++++--|.++++.
T Consensus 119 ~L~~~~r~i~~l~~~~g~----------s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHDL----------TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 566777777744 44432 357999999999999999999888877654
No 118
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=49.22 E-value=1.6 Score=38.71 Aligned_cols=34 Identities=15% Similarity=0.117 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 263 DDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 263 d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+.-..+++|.++||++.+|+++++.-|.++++.-
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3446789999999999999999999999887653
No 119
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=49.17 E-value=2.7 Score=37.69 Aligned_cols=49 Identities=12% Similarity=0.082 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
+++++|++.+.- +++. -..+++|..+||++.++|++++.-|.++++...
T Consensus 116 ~Lp~~~r~i~~L~~~~g----------~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGASG----------FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 455666666554 3333 245799999999999999999999999877653
No 120
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=48.88 E-value=37 Score=25.53 Aligned_cols=34 Identities=15% Similarity=0.206 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhN 287 (379)
.|.|||++|-+- +-+.+++.+|+++..|.|.|..
T Consensus 12 rs~EqK~~L~~~--------------it~a~~~~~~~p~~~v~V~i~e 45 (60)
T PRK02289 12 RSQEQKNALARE--------------VTEVVSRIAKAPKEAIHVFIND 45 (60)
T ss_pred CCHHHHHHHHHH--------------HHHHHHHHhCcCcceEEEEEEE
Confidence 379999998654 4467889999999999998864
No 121
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=48.63 E-value=5.7 Score=33.03 Aligned_cols=46 Identities=4% Similarity=0.094 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
..||+.|++.|.-+++-. ..++++++++++.+++++|++|=+.|+.
T Consensus 148 ~~lt~~e~~vl~l~~~g~----------~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLITEGY----------TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHHHCCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 459999999987765432 2578999999999999999999887765
No 122
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=48.35 E-value=7.7 Score=34.42 Aligned_cols=48 Identities=10% Similarity=0.237 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 242 QSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 242 ~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
.+-++++.+.|.++ +.=+--+...++++|++.||++.+|-.+|.|...
T Consensus 10 ~~~r~~Il~aa~~l-f~~~G~~~~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 10 LKTRQELIETAIAQ-FALRGVSNTTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHHHHHH-HHHcCcccCCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 34455666655554 2222346679999999999999999999987665
No 123
>PF13565 HTH_32: Homeodomain-like domain
Probab=48.35 E-value=7.1 Score=29.85 Aligned_cols=40 Identities=20% Similarity=0.418 Sum_probs=27.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHh-CccCCCCCHHHHHHHHHHhCCCC
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERV-GWKMQKRDDDLVHEFCNEVGVDR 278 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~-GWRIqk~d~~~vq~fc~eiGv~r 278 (379)
.-|.|+ +.||.+.|.++++.. .|. -..+.+.|..+.|+..
T Consensus 26 ~Grp~~--~~e~~~~i~~~~~~~p~wt----~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 26 PGRPRK--DPEQRERIIALIEEHPRWT----PREIAEYLEEEFGISV 66 (77)
T ss_pred CCCCCC--cHHHHHHHHHHHHhCCCCC----HHHHHHHHHHHhCCCC
Confidence 344555 899989999987775 333 3456777888777543
No 124
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=48.24 E-value=4.2 Score=35.75 Aligned_cols=48 Identities=8% Similarity=0.175 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
++++.|++.+.- +++-+ ..+++|..+||+..++++.++.-|.++++.-
T Consensus 117 ~Lp~~~r~i~~l~~~e~~----------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 117 KLPYKLRQVIILRYLHDY----------SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred hCCHHHHHHHHHHHHccC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 455666666555 33433 4689999999999999999999999887654
No 125
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=48.14 E-value=4.1 Score=35.26 Aligned_cols=48 Identities=8% Similarity=0.184 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.|.- ++|.. ..+++|..+||++.+++++++.-|.++++.-
T Consensus 118 ~L~~~~r~vl~L~~~~g~----------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRGW----------STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHcCC----------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 466778777766 34433 4689999999999999999999998887653
No 126
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=48.02 E-value=39 Score=24.37 Aligned_cols=35 Identities=14% Similarity=0.263 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
|.|||++|.+. +.+.+++.+|+++..+-|.|+...
T Consensus 12 t~eqk~~l~~~--------------i~~~l~~~~g~~~~~v~V~i~e~~ 46 (58)
T cd00491 12 TDEQKRELIER--------------VTEAVSEILGAPEATIVVIIDEMP 46 (58)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcCcccEEEEEEEeC
Confidence 58999987654 456788899999999999887543
No 127
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=47.99 E-value=2.9 Score=37.38 Aligned_cols=49 Identities=10% Similarity=0.110 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
-+++++|++.+.- +++.. ..+++|+.+||+..+|+++++--|.++++.-
T Consensus 135 ~~L~~~~r~i~~L~~~~g~----------s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 135 AALPERQRQAVVLRHIEGL----------SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred HhCCHHHHHHHHHHHHcCC----------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3677788877666 33332 3579999999999999999999999987754
No 128
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=47.58 E-value=15 Score=34.06 Aligned_cols=43 Identities=14% Similarity=0.243 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeee
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKV 283 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KV 283 (379)
.||..|++.|+..++ .| =.-+|.....++||+++||++.+|.-
T Consensus 155 ~LTdrQ~~vL~~A~~-~G-YFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYK-MG-YFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHH-cC-CCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 899999999877654 35 12236678999999999999988753
No 129
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=47.57 E-value=12 Score=33.67 Aligned_cols=59 Identities=12% Similarity=0.117 Sum_probs=40.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
..+++.|+.=-.+.++++++.|.++=|+-.+ +...+.++|++.||++..|-.-|.|...
T Consensus 6 ~~~~~~~~~~~~~~r~~IL~AA~~lf~e~Gy-~~~s~~dIA~~aGvs~gtiY~hF~sKe~ 64 (212)
T PRK15008 6 VKTTGKRSRAVSAKKKAILSAALDTFSQFGF-HGTRLEQIAELAGVSKTNLLYYFPSKEA 64 (212)
T ss_pred CCCCCCcchhhHHHHHHHHHHHHHHHHHhCc-ccCCHHHHHHHhCcCHHHHHHHCCCHHH
Confidence 3445555544456677777766655333334 4458899999999999999999987665
No 130
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=47.16 E-value=2.5 Score=37.25 Aligned_cols=31 Identities=23% Similarity=0.282 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 265 DLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 265 ~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
-..+++|.++||++.+||++++.-|.++++.
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999999999888764
No 131
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=46.74 E-value=32 Score=24.56 Aligned_cols=36 Identities=19% Similarity=0.314 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCc
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRT 279 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~ 279 (379)
|-.||+|+-++|+++..+.|- . .-..++..++..|.
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~----~---~W~~Ia~~~~~~Rt 36 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGK----D---NWKKIAKRMPGGRT 36 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTT----T---HHHHHHHHHSSSST
T ss_pred CCCCCHHHHHHHHHHHHHhCC----c---HHHHHHHHcCCCCC
Confidence 568999999999999999872 2 45677777774443
No 132
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=46.72 E-value=3 Score=36.91 Aligned_cols=50 Identities=10% Similarity=0.076 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.+++++|++.+.-.+ -+.-..+++|+.+||++.+|+++++.-|.++++.-
T Consensus 130 ~~Lp~~~r~v~~l~~---------~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 130 DRLPPRTGRVFMMRE---------WLELETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred HhCCHHHHHHHHHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 346666776665431 12235689999999999999999999998887654
No 133
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=46.35 E-value=3.1 Score=36.18 Aligned_cols=31 Identities=10% Similarity=0.109 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 265 DLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 265 ~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
--.+++|+++||+..+++++++.-|.++++.
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 136 YSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999999999988887653
No 134
>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=46.23 E-value=4.4 Score=34.57 Aligned_cols=48 Identities=13% Similarity=0.197 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.++++.|++.+.- |++. -..+++|..+||++.++++.++--|.+++++
T Consensus 121 ~~L~~~~r~vl~l~~~~g----------~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQN----------LPIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred HhCCHHHHHHHHHHHhcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 3566777777766 3332 2467999999999999999998888777653
No 135
>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=46.10 E-value=3.2 Score=36.14 Aligned_cols=47 Identities=15% Similarity=-0.004 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+.+.|++.+.-.+. +.-..+++|..+||+..++|+.++.-|.++++.
T Consensus 135 Lp~~~r~v~~l~~~---------~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFF---------AGLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHH---------cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 56666666655322 222467999999999999999999988877653
No 136
>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=45.89 E-value=8.2 Score=29.80 Aligned_cols=33 Identities=30% Similarity=0.666 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecc
Q 016972 245 KEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 245 kekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfh 286 (379)
|++-+.++.+ ||++ .++|+++||++.+|.-|-.
T Consensus 3 k~~A~~LY~~-G~~~--------~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 3 KEQARSLYLQ-GWSI--------KEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHHc-CCCH--------HHHHHHHCCChHHHHHHHH
Confidence 3444555553 7664 5999999999999999975
No 137
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=45.79 E-value=4.4 Score=36.12 Aligned_cols=48 Identities=10% Similarity=0.094 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.- +++.. ..+++|..+||++.+++++++.-|.++++.-
T Consensus 106 ~L~~~~r~i~~l~~~~g~----------~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTELEGL----------SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHhcCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 566677776644 33332 4679999999999999999999998887654
No 138
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=45.73 E-value=3.7 Score=35.08 Aligned_cols=48 Identities=15% Similarity=0.297 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.+++.+|++.|.-.+ .|| ..+++|+.+||+..+++++++.-|.++++.
T Consensus 111 ~~L~~~~r~il~l~~--~g~--------s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 111 AKMTERDRTVLLLRF--SGY--------SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred HcCCHHHHHHHHHHH--cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 346777777766654 342 457999999999999999999888887654
No 139
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=45.63 E-value=4.4 Score=36.04 Aligned_cols=48 Identities=15% Similarity=0.140 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.++++.+++.+.-+++.+ ..+++|+.+||++.++++.++.-|.++++.
T Consensus 154 ~~L~~~~r~vl~l~~e~~----------s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 154 ELLSELEKEVLELYLDGK----------SYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred HhCCHHHHHHHHHHHccC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456677777776565543 457999999999999999999988887664
No 140
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=45.52 E-value=4.4 Score=35.71 Aligned_cols=49 Identities=6% Similarity=0.127 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 237 RTKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 237 RTkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
=.+++++|++.+.- +++.. ..+++|+.+||+..++++.++.-|.++++.
T Consensus 120 l~~L~~~~r~i~~l~~~~g~----------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 120 LKELNESNRQVFKYKVFYNL----------TYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred HHhCCHHHHHHHHHHHHcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567777777765 44443 468999999999999999999999888764
No 141
>PHA02535 P terminase ATPase subunit; Provisional
Probab=45.48 E-value=13 Score=40.62 Aligned_cols=47 Identities=15% Similarity=0.408 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
++||.|-|+.....+.+ ||+| .++|+++||++++|.-|.. |.+|..-
T Consensus 1 ~~yt~EfK~~Av~Ly~~-G~sv--------~eIA~~LGv~~~Tl~~W~k--r~~w~~~ 47 (581)
T PHA02535 1 TAYDDDVRRAAKFLYWQ-GWTV--------AEIAEELGLKSRTIYSWKE--RDGWRDL 47 (581)
T ss_pred CCCCHHHHHHHHHHHHc-CCCH--------HHHHHHhCCChhHHHHHhc--ccccccc
Confidence 46999999888887777 8764 5999999999999999954 4445444
No 142
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=45.46 E-value=14 Score=33.17 Aligned_cols=18 Identities=22% Similarity=0.235 Sum_probs=13.3
Q ss_pred CCCCCCHHHHHHHHHHHH
Q 016972 236 FRTKFSQSQKEKMFEFAE 253 (379)
Q Consensus 236 ~RTkFT~EQkekM~~faE 253 (379)
.++.||+.|+++|+.+-|
T Consensus 137 c~~~FT~gQ~~RM~~~l~ 154 (154)
T PF05572_consen 137 CMNMFTPGQVARMRAVLE 154 (154)
T ss_dssp G--B-BHHHHHHHHHHHH
T ss_pred cccccCHHHHHHHHHHhC
Confidence 789999999999998754
No 143
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=45.13 E-value=4.8 Score=35.90 Aligned_cols=49 Identities=6% Similarity=0.147 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
-+++++|++.|.- +++.. ..+++|+++||+..++|+.++.-|.++++.-
T Consensus 140 ~~Lp~~~r~v~~l~~~eg~----------s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEEL----------PHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcCC----------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 4566778887765 44443 4679999999999999999999988887654
No 144
>PRK10651 transcriptional regulator NarL; Provisional
Probab=45.07 E-value=7.3 Score=32.97 Aligned_cols=47 Identities=6% Similarity=0.157 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
..||+.|++.|.-+++-. ..++++++++|+.+++++...|=+.|++=
T Consensus 154 ~~Lt~rE~~vl~~l~~g~----------~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 154 NQLTPRERDILKLIAQGL----------PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred ccCCHHHHHHHHHHHcCC----------CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 359999999998776532 24688999999999999999998877753
No 145
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=45.06 E-value=33 Score=31.73 Aligned_cols=42 Identities=0% Similarity=0.075 Sum_probs=33.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeee
Q 016972 236 FRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKV 283 (379)
Q Consensus 236 ~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KV 283 (379)
....+|+||.++|+.+=. +-|..-.|.+||++.||++.-|.+
T Consensus 82 k~y~Lt~e~i~Eir~LR~------~DP~~wTr~~LAkkF~~S~~fV~~ 123 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRA------EDPEKWTRKKLAKKFNCSPLFVSM 123 (164)
T ss_pred ccccCCHHHHHHHHHHHH------cCchHhhHHHHHHHhCCCHHHHHH
Confidence 447899999999999833 356678999999999999865543
No 146
>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=44.48 E-value=6.8 Score=26.74 Aligned_cols=23 Identities=22% Similarity=0.390 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCCceeeeeccccc
Q 016972 267 VHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
+++.|+.+||++..|.-|+.+.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 67899999999999999987654
No 147
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=44.45 E-value=4.9 Score=36.79 Aligned_cols=48 Identities=10% Similarity=0.151 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++.+|++.+.- |++-. -.+++|+.+||++.+|+++++--|.++++..
T Consensus 138 ~L~~~~r~v~~L~~~~g~----------s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEGL----------SYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHHcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 455667665433 33332 4579999999999999999999999987754
No 148
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=44.30 E-value=3.3 Score=36.22 Aligned_cols=49 Identities=12% Similarity=0.093 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 237 RTKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 237 RTkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
-.+++..|++.+.- +.+.. ..+++|+++||++.+++++++.-|.++++.
T Consensus 133 l~~L~~~~r~vl~l~~~~~~----------s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 133 LKALSPEERRVIEVLYYQGY----------THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred HHhCCHHHHHHHHHHHHcCC----------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34577777777764 33332 457999999999999999999988887654
No 149
>PF13309 HTH_22: HTH domain
Probab=44.26 E-value=26 Score=27.23 Aligned_cols=43 Identities=14% Similarity=0.199 Sum_probs=34.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCcee
Q 016972 236 FRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVL 281 (379)
Q Consensus 236 ~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~ 281 (379)
....++.++|..+-..-.+.| -..=...|+..|+.+||++.++
T Consensus 17 ~~~~l~~~~k~~iV~~L~~~G---~F~lKgav~~vA~~L~iS~~TV 59 (64)
T PF13309_consen 17 PPSRLSKEEKKEIVRQLYEKG---IFLLKGAVEYVAEKLGISRATV 59 (64)
T ss_pred ChhhCCHHHHHHHHHHHHHCC---CcccCcHHHHHHHHHCCCHHHH
Confidence 335678899988888888888 3444568999999999999875
No 150
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=44.21 E-value=3.7 Score=37.09 Aligned_cols=49 Identities=8% Similarity=0.100 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.-. +-+.-..+++|..+||++.++|+.++.-|.++++.-
T Consensus 139 ~Lp~~~r~v~~L~---------~~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMR---------EFLDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4556666665543 222235689999999999999999999999887754
No 151
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=44.14 E-value=40 Score=38.75 Aligned_cols=36 Identities=14% Similarity=0.263 Sum_probs=19.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCce
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTV 280 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V 280 (379)
.+-|.+|-..+|++- -++|.|+ .-.||.++-+++..
T Consensus 641 ~~cFWvkv~Edk~en-~dlfakL-----------~~~Fatq~k~~k~~ 676 (1102)
T KOG1924|consen 641 ENCFWVKVNEDKLEN-DDLFAKL-----------ALKFATQPKVKKEQ 676 (1102)
T ss_pred ccceeeecchhhccc-hHHHHHH-----------HHHhhccccccccc
Confidence 355666766666665 3344443 23566666555544
No 152
>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=44.01 E-value=5.7 Score=35.70 Aligned_cols=48 Identities=15% Similarity=0.118 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
.+.+|..|++.+.-++ .|| ..+++|.++|+++..++.|.+.-+.++++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~Gl--------Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KGL--------SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cCC--------CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678999999987753 443 45799999999999999999999988875
No 153
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=43.41 E-value=9 Score=32.43 Aligned_cols=48 Identities=15% Similarity=0.250 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
..||..+++.|.-+++-. ..++++++++++.++|++.+.+=|.|+.-+
T Consensus 136 ~~Lt~~E~~il~~l~~g~----------~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~ 183 (196)
T PRK10360 136 DPLTKRERQVAEKLAQGM----------AVKEIAAELGLSPKTVHVHRANLMEKLGVS 183 (196)
T ss_pred cCCCHHHHHHHHHHHCCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 369999999999888642 467889999999999999999988877533
No 154
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=43.07 E-value=8.6 Score=36.00 Aligned_cols=50 Identities=10% Similarity=0.214 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
..+||+.|+|.|.-++ .| | ..++++..+||++++++.++.|-+.|++-+.
T Consensus 169 ~~~Lt~re~evl~~~a--~G----~----t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~ 218 (232)
T TIGR03541 169 AGVLSEREREVLAWTA--LG----R----RQADIAAILGISERTVENHLRSARRKLGVAT 218 (232)
T ss_pred hccCCHHHHHHHHHHH--CC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHCCCC
Confidence 4589999999988765 33 2 3468999999999999999999998886543
No 155
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=42.09 E-value=48 Score=24.42 Aligned_cols=34 Identities=15% Similarity=0.259 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNN 288 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNn 288 (379)
|+|||++|.+- +-+.+++-+|+++..+-|.|+--
T Consensus 12 ~~e~K~~l~~~--------------it~~~~~~lg~~~~~i~V~i~E~ 45 (60)
T PF01361_consen 12 TAEQKRELAEA--------------ITDAVVEVLGIPPERISVVIEEV 45 (60)
T ss_dssp -HHHHHHHHHH--------------HHHHHHHHHTS-GGGEEEEEEEE
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcCCCeEEEEEEEE
Confidence 78998887654 34568889999999999988753
No 156
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=42.04 E-value=14 Score=31.55 Aligned_cols=42 Identities=7% Similarity=0.105 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 016972 242 QSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNN 288 (379)
Q Consensus 242 ~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNn 288 (379)
..-.+++.+|-+.. ..+.-.++++|+++||+++.|.-||+..
T Consensus 8 ~~~i~~~~~~I~~~-----~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDN-----LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHh-----cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34456777777775 3445678999999999999998777654
No 157
>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=42.03 E-value=7.2 Score=27.14 Aligned_cols=23 Identities=17% Similarity=0.302 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCCceeeeeccccc
Q 016972 267 VHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
+.++|+.+||++.+|+.|.....
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 57899999999999999976655
No 158
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=41.97 E-value=9.1 Score=32.48 Aligned_cols=46 Identities=9% Similarity=0.076 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
-.+|..+.+.|.-+++-. ..++++.+++++.+++++++.+=|.|+.
T Consensus 148 ~~lt~re~~vl~~l~~g~----------s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVSGL----------SNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHcCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 358999999988776653 4679999999999999999999988875
No 159
>PHA00542 putative Cro-like protein
Probab=41.93 E-value=22 Score=28.63 Aligned_cols=45 Identities=9% Similarity=0.068 Sum_probs=31.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
+..+.+|.+.++. .+.+..|| ...++|+.+||++.+|.-|.....
T Consensus 12 Rp~~~~~~~~~l~---~~l~~~gl--------Tq~elA~~lgIs~~tIsr~e~g~~ 56 (82)
T PHA00542 12 IPAAYTQRPDELV---CALIRAGW--------SQEQIADATDVSQPTICRIYSGRH 56 (82)
T ss_pred CCcccCcCHHHHH---HHHHHCCC--------CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 3344566655443 34456665 446899999999999999997763
No 160
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=41.93 E-value=7.6 Score=29.06 Aligned_cols=23 Identities=17% Similarity=0.382 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCCceeeeeccccc
Q 016972 267 VHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
+.++|+.+||++++|+.|-..--
T Consensus 3 i~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTTS
T ss_pred HHHHHHHHCcCHHHHHHHHHhcC
Confidence 57899999999999999976544
No 161
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=41.87 E-value=4.7 Score=37.89 Aligned_cols=31 Identities=3% Similarity=0.033 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
..+++|+++||+..++|++++.-|.++++.-
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999999887653
No 162
>PRK06930 positive control sigma-like factor; Validated
Probab=41.16 E-value=5.7 Score=36.26 Aligned_cols=48 Identities=8% Similarity=0.218 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.+|++.+++.+.- |++-. ..+++|..+||++.++++|++.-|.++++.
T Consensus 113 ~~L~~rer~V~~L~~~eg~----------s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 113 SVLTEREKEVYLMHRGYGL----------SYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred HhCCHHHHHHHHHHHHcCC----------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4577777777665 44433 467999999999999999999988887654
No 163
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=41.03 E-value=5 Score=36.36 Aligned_cols=53 Identities=8% Similarity=0.083 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDLNGA 300 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~~~~ 300 (379)
.++++.|++.+.- +++- -.++++|..+||+..+++++++.-|.++++.-.++-
T Consensus 132 ~~Lp~~~r~v~~l~~~~g----------~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 132 DALPPERREALILTQVLG----------YTYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred HcCCHHHHHHhhhHHHhC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 4566666666643 3333 257899999999999999999999999988765553
No 164
>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=40.91 E-value=12 Score=30.48 Aligned_cols=26 Identities=12% Similarity=0.282 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhCCCCceeeeeccccc
Q 016972 264 DDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 264 ~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
.-.++++|+++||++..+++|+++..
T Consensus 32 GlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 32 GKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 34678999999999999999998644
No 165
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=40.90 E-value=4.3 Score=35.55 Aligned_cols=48 Identities=13% Similarity=0.176 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
-.+++++|++.+.-. +-+....+++|+.+||+..+++++++.-+.++.
T Consensus 117 l~~L~~~~r~i~~l~---------~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 117 LDGLNGKTREAFLLS---------QLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred HHhCCHHHhHHhhhh---------hccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 345666666664432 222334689999999999999999987766543
No 166
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=40.87 E-value=43 Score=25.81 Aligned_cols=35 Identities=17% Similarity=0.356 Sum_probs=26.3
Q ss_pred CCCHHHHHH-----HHHHHHHhCccCCCCCHHHHHHHHHHhCCCC
Q 016972 239 KFSQSQKEK-----MFEFAERVGWKMQKRDDDLVHEFCNEVGVDR 278 (379)
Q Consensus 239 kFT~EQkek-----M~~faEk~GWRIqk~d~~~vq~fc~eiGv~r 278 (379)
.||-|+++. +.+.|.++| -...++.+.|++.||.|
T Consensus 4 ~lt~~~L~~~fhlp~~eAA~~Lg-----v~~T~LKr~CR~~GI~R 43 (52)
T PF02042_consen 4 SLTLEDLSQYFHLPIKEAAKELG-----VSVTTLKRRCRRLGIPR 43 (52)
T ss_pred ccCHHHHHHHhCCCHHHHHHHhC-----CCHHHHHHHHHHcCCCC
Confidence 456666665 456788885 56789999999999875
No 167
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=40.53 E-value=30 Score=27.41 Aligned_cols=47 Identities=13% Similarity=0.338 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCcc-CCCCCHHHHHHHHHHhCCCCceeeee
Q 016972 237 RTKFSQSQKEKMFEFAERVGWK-MQKRDDDLVHEFCNEVGVDRTVLKVW 284 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWR-Iqk~d~~~vq~fc~eiGv~r~V~KVW 284 (379)
||.||.|.=+.|..|..+..+. .......+-++|+.+ .+.+++.|-|
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~-~~t~HtwQSw 49 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEK-HPTRHTWQSW 49 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS--SSS--SHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH-cCCCCCHHHH
Confidence 8999999999999998654332 334455677777655 4667777666
No 168
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=39.76 E-value=4 Score=35.49 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
..+++|+++||+..+++++++.-|.++++.
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999999999887653
No 169
>PHA01976 helix-turn-helix protein
Probab=39.59 E-value=21 Score=26.61 Aligned_cols=19 Identities=16% Similarity=0.310 Sum_probs=9.3
Q ss_pred HHHHHHhCCCCceeeeecc
Q 016972 268 HEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 268 q~fc~eiGv~r~V~KVWfh 286 (379)
++||+.+||++..|.-|..
T Consensus 19 ~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 19 PELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHHHHhCCCHHHHHHHHc
Confidence 3455555555555554443
No 170
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=39.57 E-value=53 Score=24.65 Aligned_cols=34 Identities=6% Similarity=0.195 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNN 288 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNn 288 (379)
|.|||++|.+. +-+.++..+|+++..+-|.+...
T Consensus 13 t~eqk~~l~~~--------------it~~l~~~lg~p~~~v~V~i~e~ 46 (64)
T PRK01964 13 PEEKIKNLIRE--------------VTEAISATLDVPKERVRVIVNEV 46 (64)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcChhhEEEEEEEc
Confidence 78999987664 34578899999999888877654
No 171
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=39.46 E-value=4.2 Score=36.16 Aligned_cols=48 Identities=8% Similarity=0.040 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.- +++. -..+++|..+||+..+++++++.-|.++++.-
T Consensus 136 ~L~~~~r~i~~L~~~~g----------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILG----------FSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456667766653 3332 24689999999999999999999888887653
No 172
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=39.17 E-value=4.6 Score=36.18 Aligned_cols=48 Identities=10% Similarity=0.114 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
++++.|++.+.- +++. -..+++|..+||+..+++++++--|.++++..
T Consensus 111 ~Lp~~~R~v~~L~~~eg----------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG----------LSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 567777777665 3332 24689999999999999999999999887654
No 173
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=39.02 E-value=4.5 Score=36.16 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
+++++|++.+.-.+ -+.-..+++|+++||++.++++.++--|.++++.-.
T Consensus 111 ~Lp~~~R~v~~L~~---------~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 111 KLPQDQREALILVG---------ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred hCCHHHHHHhhHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45566666654421 122356899999999999999999999999987753
No 174
>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=38.79 E-value=9.9 Score=36.82 Aligned_cols=49 Identities=14% Similarity=0.208 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
..++|+.|+|.|.-.++ | |.. +++++.+||+++++|+++.|-+.|++-.
T Consensus 188 ~~~LT~RE~evl~l~a~--G----~s~----~eIA~~L~IS~~TVk~hl~~i~~KL~v~ 236 (247)
T TIGR03020 188 AGLITAREAEILAWVRD--G----KTN----EEIAAILGISSLTVKNHLQHIFKKLDVR 236 (247)
T ss_pred ccCCCHHHHHHHHHHHC--C----CCH----HHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence 45799999999997653 3 333 6899999999999999999988887644
No 175
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=38.62 E-value=9.7 Score=39.63 Aligned_cols=15 Identities=47% Similarity=0.946 Sum_probs=11.9
Q ss_pred ccccccccccccccc
Q 016972 109 SLKCAACGCHRNFHR 123 (379)
Q Consensus 109 ALKCAACGCHRNFHR 123 (379)
+++|+||||+-+---
T Consensus 118 ~~~CkACG~r~~~d~ 132 (400)
T KOG2767|consen 118 SLKCKACGFRSDMDL 132 (400)
T ss_pred hhHHHHcCCcccccc
Confidence 699999999866533
No 176
>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=38.07 E-value=5.8 Score=36.39 Aligned_cols=49 Identities=6% Similarity=0.095 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.++++.|++.+..++. +....+++|..+||+..++++|++.-+.++++.
T Consensus 174 ~~L~~~~r~il~l~y~---------~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 174 ESLSEREQLVLSLYYY---------EELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred HhCCHHHHHHHHHHHh---------CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4567777777766431 222568999999999999999999888777653
No 177
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=37.88 E-value=58 Score=24.02 Aligned_cols=34 Identities=15% Similarity=0.236 Sum_probs=27.1
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNN 288 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNn 288 (379)
|.|||+.|-+. +.+.+++.+|+++..+-|.|...
T Consensus 13 s~eqk~~l~~~--------------it~~l~~~~~~p~~~v~V~i~e~ 46 (62)
T PRK00745 13 TVEQKRKLVEE--------------ITRVTVETLGCPPESVDIIITDV 46 (62)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHcCCChhHEEEEEEEc
Confidence 79999887654 44678899999999999888653
No 178
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=37.82 E-value=18 Score=31.23 Aligned_cols=26 Identities=8% Similarity=0.095 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHHhCCCCceeeeeccc
Q 016972 262 RDDDLVHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 262 ~d~~~vq~fc~eiGv~r~V~KVWfhN 287 (379)
-+.-.|+++|++.||+|.+|=.-|.+
T Consensus 21 ~~~ITV~~I~~~AgvsR~TFY~hF~d 46 (176)
T TIGR02366 21 FSKISVSDIMSTAQIRRQTFYNHFQD 46 (176)
T ss_pred CccCCHHHHHHHhCCCHHHHHHHCCC
Confidence 45568999999999999999765555
No 179
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=37.74 E-value=8.2 Score=34.04 Aligned_cols=47 Identities=9% Similarity=0.159 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+++++|++.+.- +++.. ..+++|..+||+..++|++++.-+.+....
T Consensus 127 ~Lp~~~R~v~~L~~~~g~----------s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDGM----------KQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 466777776555 33332 468999999999999999999766655433
No 180
>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=37.59 E-value=6.6 Score=36.34 Aligned_cols=53 Identities=9% Similarity=0.058 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.++++.|++.|.-.+-- ..-++-..+++|+++||++.+++++++.-+.+++++
T Consensus 173 ~~L~~~~r~il~l~y~~-----~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 173 SVLDGREREVIEMRYGL-----GDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred HhCCHHHHHHHHHHHcC-----CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56778888887775310 001233578999999999999999988877776553
No 181
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=37.28 E-value=32 Score=25.91 Aligned_cols=19 Identities=21% Similarity=0.561 Sum_probs=14.5
Q ss_pred CCHHHHHHHHHHHHHhCcc
Q 016972 240 FSQSQKEKMFEFAERVGWK 258 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWR 258 (379)
++..|+++|+++.++-||-
T Consensus 24 ~s~~~L~k~~~wld~rgWw 42 (45)
T PF12123_consen 24 LSDAELDKFTAWLDERGWW 42 (45)
T ss_dssp --HHHHHHHHHHHHHTT--
T ss_pred CCHHHHHHHHHHHHhcCcE
Confidence 4589999999999999994
No 182
>PF12728 HTH_17: Helix-turn-helix domain
Probab=37.22 E-value=10 Score=27.17 Aligned_cols=24 Identities=25% Similarity=0.551 Sum_probs=20.3
Q ss_pred HHHHHHHhCCCCceeeeecccccc
Q 016972 267 VHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
++|+|+.+||++.+|.-|.+..+-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 678999999999999999976543
No 183
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=37.20 E-value=14 Score=30.50 Aligned_cols=8 Identities=63% Similarity=1.609 Sum_probs=7.5
Q ss_pred cccccccc
Q 016972 109 SLKCAACG 116 (379)
Q Consensus 109 ALKCAACG 116 (379)
.|.|||||
T Consensus 57 tLsCsACG 64 (74)
T PF05077_consen 57 TLSCSACG 64 (74)
T ss_pred eEeehhcc
Confidence 69999998
No 184
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=37.19 E-value=15 Score=32.69 Aligned_cols=49 Identities=14% Similarity=0.216 Sum_probs=36.2
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
.++-++++.+.|.++=|+- .-+...++++|++.||++..|-.+|-|...
T Consensus 9 ~~~~R~~Il~AA~~lf~e~-G~~~~t~~~Ia~~agvs~~tlY~~F~sKe~ 57 (215)
T PRK10668 9 AQETRQHILDAALRLFSQQ-GVSATSLADIAKAAGVTRGAIYWHFKNKSD 57 (215)
T ss_pred HHHHHHHHHHHHHHHHHHc-CcccCCHHHHHHHhCCChHHHHHHCCCHHH
Confidence 3666777777666653332 344568999999999999999999976654
No 185
>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=37.17 E-value=8.2 Score=33.94 Aligned_cols=30 Identities=10% Similarity=0.089 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
..+++|+++||+..+|+++++--|.++++.
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 467999999999999999999888877653
No 186
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=36.90 E-value=73 Score=23.48 Aligned_cols=34 Identities=15% Similarity=0.290 Sum_probs=27.2
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNN 288 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNn 288 (379)
|.|||++|.+. +-+.++..+|+++..+-|.+...
T Consensus 13 t~eqK~~l~~~--------------it~~l~~~lg~~~~~v~V~i~e~ 46 (63)
T TIGR00013 13 TDEQKRQLIEG--------------VTEAMAETLGANLESIVVIIDEM 46 (63)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCCCcccEEEEEEEc
Confidence 79999987654 45678899999999888887654
No 187
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=36.88 E-value=6 Score=36.65 Aligned_cols=32 Identities=13% Similarity=0.124 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 264 DDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 264 ~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.-..+++|..+||++.+|++|++.-+.++++.
T Consensus 200 g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 200 ELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999999988887654
No 188
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=36.57 E-value=7.3 Score=35.88 Aligned_cols=53 Identities=13% Similarity=0.170 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.+++++|++.+.-.+. +.+-++-..+++|+.+||+..+++++++.-+.++++.
T Consensus 177 ~~Lp~~~R~v~~L~y~-----l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 177 KKLSDREKQIMELRFG-----LNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred HhCCHHHHHHHHHHhc-----cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3566777777766431 0012333578999999999999999999988887654
No 189
>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=36.52 E-value=5.1 Score=35.84 Aligned_cols=48 Identities=8% Similarity=0.119 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.- |++.. ..+++|+++||+...+|++++.-|.++++.-
T Consensus 131 ~L~~~~r~v~~l~~~~g~----------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVLGF----------ESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHhCC----------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 566777776655 33332 4689999999999999999999998887654
No 190
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=36.31 E-value=25 Score=29.98 Aligned_cols=21 Identities=24% Similarity=0.566 Sum_probs=10.8
Q ss_pred CCCCHHHHHHHHHHHHHhCcc
Q 016972 238 TKFSQSQKEKMFEFAERVGWK 258 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWR 258 (379)
+.+|..|+++|.+.++++||+
T Consensus 20 k~lt~~el~~vl~~l~~~G~k 40 (119)
T PF06252_consen 20 KDLTEAELEKVLDELKRLGFK 40 (119)
T ss_pred HHCCHHHHHHHHHHHHHccCc
Confidence 344555555555555555554
No 191
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=35.39 E-value=5.6 Score=35.10 Aligned_cols=30 Identities=3% Similarity=0.095 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.++++|+.+||+..+++++++.-|.++++.
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999999999888664
No 192
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=35.20 E-value=16 Score=25.56 Aligned_cols=31 Identities=19% Similarity=0.338 Sum_probs=21.9
Q ss_pred ccccCccccccCCCCCCCCCCccccccccccccccccC
Q 016972 88 HALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRRE 125 (379)
Q Consensus 88 HAvDGCGEFMPSGeegt~dp~ALKCAACGCHRNFHRKE 125 (379)
..=+-|+++|.+. ...+|+|..| ..+.|+|=
T Consensus 12 ~~C~~C~~~i~~~-----~~~~~~C~~C--~~~~H~~C 42 (50)
T cd00029 12 TFCDVCRKSIWGL-----FKQGLRCSWC--KVKCHKKC 42 (50)
T ss_pred CChhhcchhhhcc-----ccceeEcCCC--CCchhhhh
Confidence 3457799999874 1358999987 56666653
No 193
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=35.19 E-value=6.5 Score=33.70 Aligned_cols=45 Identities=11% Similarity=0.180 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTF 292 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~ 292 (379)
.+++++|++.+.- +++-. ..+++|..+||+..+++++++.-+.++
T Consensus 112 ~~L~~~~r~v~~L~~~~g~----------s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVDGL----------GYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HHCCHHHHHHHHHHHHcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4566777777644 33433 457999999999999999998765443
No 194
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=35.05 E-value=20 Score=25.44 Aligned_cols=34 Identities=21% Similarity=0.273 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeec
Q 016972 244 QKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWM 285 (379)
Q Consensus 244 QkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWf 285 (379)
+++.+.+..++.+|.+ .+-|+.+||++.+|.--|
T Consensus 6 E~~~i~~aL~~~~gn~--------~~aA~~Lgisr~tL~~kl 39 (42)
T PF02954_consen 6 EKQLIRQALERCGGNV--------SKAARLLGISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHTTT-H--------HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCCH--------HHHHHHHCCCHHHHHHHH
Confidence 5666777888887654 689999999999875433
No 195
>cd08353 Glo_EDI_BRP_like_7 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=34.91 E-value=49 Score=27.19 Aligned_cols=43 Identities=16% Similarity=0.156 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeec
Q 016972 243 SQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWM 285 (379)
Q Consensus 243 EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWf 285 (379)
..++++.+|++++||++.......-..+...+|+....+.+||
T Consensus 12 ~Dl~~s~~FY~~LG~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 54 (142)
T cd08353 12 RDLEAAIAFFLELGLELEGRAEIEGEWADRVTGLDGVRVEIAM 54 (142)
T ss_pred CCHHHHHHHHHHcCCEEccccccChHHHHHhcCCCCceEEEEE
Confidence 4689999999999998865432111234446787766666665
No 196
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=34.80 E-value=83 Score=25.63 Aligned_cols=34 Identities=6% Similarity=0.167 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhN 287 (379)
.|.|||++|-+- +-+.+++-+|+++.++.|.|.-
T Consensus 13 ~s~EqK~~La~~--------------iT~a~~~~lg~~~e~v~V~I~e 46 (76)
T PRK01271 13 LDEEQKAALAAD--------------ITDVIIRHLNSKDSSISIALQQ 46 (76)
T ss_pred CCHHHHHHHHHH--------------HHHHHHHHhCcCcceEEEEEEE
Confidence 479999887553 3356888999999999998864
No 197
>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=34.37 E-value=6.9 Score=33.97 Aligned_cols=47 Identities=6% Similarity=0.070 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
++++.|++.+.... -+....+++|..+||++.+|++=++.-|.++++
T Consensus 140 ~L~~~~r~vi~l~~---------~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRH---------LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHH---------hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57788888776632 123356899999999999999988888877765
No 198
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=34.01 E-value=78 Score=26.54 Aligned_cols=36 Identities=8% Similarity=0.138 Sum_probs=28.6
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
+.|||++|-+. +-+.|.+++||+...|-|.|++...
T Consensus 70 ~~e~k~~l~~~--------------i~~~l~~~lgi~~~rv~I~f~~~~~ 105 (116)
T PTZ00397 70 SRSNNSSIAAA--------------ITKILASHLKVKSERVYIEFKDCSA 105 (116)
T ss_pred CHHHHHHHHHH--------------HHHHHHHHhCcCcccEEEEEEECCh
Confidence 57999887553 3456888999999999999998754
No 199
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=33.75 E-value=5.9 Score=36.33 Aligned_cols=48 Identities=10% Similarity=0.113 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+++++|++.+.- |++.. ..+++|..+||+..+++++++--|.++++..
T Consensus 148 ~L~~~~r~v~~L~~~~g~----------s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 148 GLPAKYARVFMMREFIEL----------ETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred hCCHHHHHHHHHHHHcCC----------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 556777776655 33332 4589999999999999999999999887754
No 200
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=33.64 E-value=8.2 Score=36.74 Aligned_cols=31 Identities=6% Similarity=0.177 Sum_probs=27.9
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
..+++|+.+||++.++|++++--|.++++.-
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999999999999997664
No 201
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=33.58 E-value=50 Score=29.17 Aligned_cols=55 Identities=16% Similarity=0.319 Sum_probs=42.7
Q ss_pred CHHHHHHHHH----HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 241 SQSQKEKMFE----FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 241 T~EQkekM~~----faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+.|.|++|.. +|||.|||+ .+|.+.+..|..-+-..+..+-.|.=-.|.--.|+.
T Consensus 2 ~~e~l~~my~~~eq~AeksG~~l-npD~e~~~~v~~gL~~~ke~yG~~~CPCRl~~g~ee 60 (110)
T COG4802 2 SDEELNKMYRFTEQYAEKSGYRL-NPDREFTAEVLRGLASNKERYGYPSCPCRLVTGKEE 60 (110)
T ss_pred cHHHHHHHHHHHHHHHHhcCcee-CCCHHHHHHHHHHHHHhHHHhCCCCCCeecccCCHH
Confidence 3567777765 678999998 478888888988888888888888887777665543
No 202
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=33.20 E-value=17 Score=30.32 Aligned_cols=21 Identities=10% Similarity=0.105 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCCCceeeeecc
Q 016972 266 LVHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfh 286 (379)
.+.++|+++||++.+|..|..
T Consensus 52 S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 52 TYSDIEAETGASTATISRVKR 72 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999999775
No 203
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=33.12 E-value=7.4 Score=33.89 Aligned_cols=46 Identities=11% Similarity=0.132 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHHHH-HHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 238 TKFSQSQKEKMFEF-AERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 238 TkFT~EQkekM~~f-aEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
.+++++|++.+.-. ++- -..+++|+.+||+..+|+++++.-+.+++
T Consensus 118 ~~Lp~~~r~v~~L~~~~g----------~s~~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDG----------MGHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45666666665543 232 25689999999999999999988776653
No 204
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=32.81 E-value=5 Score=34.31 Aligned_cols=49 Identities=10% Similarity=0.170 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
++.+|++.+.-. +-+.-..+++|.++|+++.++++.+..-+.++++.-.
T Consensus 106 L~~~~r~v~~l~---------~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 106 LPPACRDSFLLR---------KLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred CCHHHHHHHHHH---------HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 556666655442 1122346899999999999999999988887766543
No 205
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=32.29 E-value=43 Score=31.70 Aligned_cols=26 Identities=38% Similarity=0.585 Sum_probs=22.7
Q ss_pred CCCC-CCHHHHHHHHHHHHHhCccCCC
Q 016972 236 FRTK-FSQSQKEKMFEFAERVGWKMQK 261 (379)
Q Consensus 236 ~RTk-FT~EQkekM~~faEk~GWRIqk 261 (379)
-||- .++|++++|++.|+++||-+.+
T Consensus 139 sRtP~~s~~~~~~ml~~ak~~Gfdv~~ 165 (174)
T COG3040 139 SRTPTLSQETLKRMLEIAKRRGFDVSK 165 (174)
T ss_pred ecCCCCCHHHHHHHHHHHHHcCCCcce
Confidence 4788 9999999999999999987654
No 206
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=32.15 E-value=7.4 Score=33.85 Aligned_cols=45 Identities=13% Similarity=0.106 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHHH-HHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 016972 238 TKFSQSQKEKMFEF-AERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTF 292 (379)
Q Consensus 238 TkFT~EQkekM~~f-aEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~ 292 (379)
.+|+++|++.+.-+ +|- -..+++|..+|+++.++|.++.+.+...
T Consensus 117 ~~L~~~~r~v~~L~~~eg----------~s~~EIA~~l~is~~tV~~~l~ra~~~~ 162 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEG----------LTYVEIGERLGVSLSRIHQYMVEAFKCC 162 (168)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45667777766553 332 2568999999999999999998766543
No 207
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=31.93 E-value=6.1 Score=34.83 Aligned_cols=47 Identities=17% Similarity=0.352 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
.+++++|++.+.- +++.. ..+++|..+||++.+++.+++--|.++++
T Consensus 126 ~~L~~~~r~v~~l~~~~g~----------s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 126 MSLPIKYREVIYLFYYEEL----------SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred HhCCHHHhhHhHhHHhcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3567777777644 44443 46899999999999999999988887764
No 208
>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=31.49 E-value=26 Score=27.68 Aligned_cols=23 Identities=13% Similarity=0.492 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhCCCCceeeeecc
Q 016972 264 DDLVHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 264 ~~~vq~fc~eiGv~r~V~KVWfh 286 (379)
.-...++|.++||+..+|..|=.
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhh
Confidence 34567899999999999999954
No 209
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=31.47 E-value=20 Score=24.73 Aligned_cols=29 Identities=17% Similarity=0.391 Sum_probs=20.2
Q ss_pred ccccCccccccCCCCCCCCCCcccccccccccccccc
Q 016972 88 HALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRR 124 (379)
Q Consensus 88 HAvDGCGEFMPSGeegt~dp~ALKCAACGCHRNFHRK 124 (379)
..=+-|+++|.... .+|+|+.| ....|+|
T Consensus 12 ~~C~~C~~~i~~~~------~~~~C~~C--~~~~H~~ 40 (49)
T smart00109 12 TKCCVCRKSIWGSF------QGLRCSWC--KVKCHKK 40 (49)
T ss_pred CCccccccccCcCC------CCcCCCCC--CchHHHH
Confidence 34588999998742 37999987 4555544
No 210
>PF05121 GvpK: Gas vesicle protein K ; InterPro: IPR007805 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. Proteins containing this domain are involved in the formation of gas vesicles [].; GO: 0031412 gas vesicle organization
Probab=31.37 E-value=91 Score=26.63 Aligned_cols=35 Identities=20% Similarity=0.396 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCce
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTV 280 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V 280 (379)
-.+|.+|.|++-....++ ++.++++|...||+..=
T Consensus 40 G~Lse~qiErlG~tLm~L--------e~~~~~l~~~~gl~~~d 74 (88)
T PF05121_consen 40 GSLSEEQIERLGETLMKL--------EEAMEELCERFGLTPED 74 (88)
T ss_pred CCCCHHHHHHHHHHHHHH--------HHHHHHHHHHcCCCHHH
Confidence 358899999999888887 67899999999998753
No 211
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=31.24 E-value=92 Score=25.10 Aligned_cols=46 Identities=15% Similarity=0.162 Sum_probs=36.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeec
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWM 285 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWf 285 (379)
+++...++.+++.. ..+|.-+..+...+.++++++|++-+++++=+
T Consensus 22 ~~~~~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~~~ 67 (126)
T cd02425 22 NYFGYKVSLNELRE------KYELGRDGLSLSYLKQLLEEYGFKCKVYKISF 67 (126)
T ss_pred HHhCCCCCHHHHHH------hccCCCCCcCHHHHHHHHHHCCCcceEEEEch
Confidence 56777788888653 34677677889999999999999999988733
No 212
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=30.56 E-value=12 Score=37.26 Aligned_cols=53 Identities=11% Similarity=0.187 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
++++.|++.+...| | +.+-+.-..+++|..+||++.+|+++++.-+.++++.-
T Consensus 262 ~L~~~~R~vl~lry---g--L~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRF---G--LLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHh---c--cCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 56666666665443 1 12334557799999999999999999999999997654
No 213
>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=30.49 E-value=31 Score=29.38 Aligned_cols=38 Identities=21% Similarity=0.603 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecc
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfh 286 (379)
.|.+=++++.+++++ | ..+.+.|...+|++.+|..||.
T Consensus 3 YS~DlR~rVl~~~~~-g--------~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEK-G--------KSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCHHHHHHHHHHHHc-c--------chHHHHHHHhCcHHHHHHHHHH
Confidence 456778899998877 3 1556889999999999999999
No 214
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=30.48 E-value=33 Score=29.63 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=12.9
Q ss_pred HHHHHHhCCCCceeeeeccccc
Q 016972 268 HEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 268 q~fc~eiGv~r~V~KVWfhNnK 289 (379)
++||+.+||++..|--|.++++
T Consensus 22 ~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 22 KELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHCcCHHHHHHHHcCCC
Confidence 4566666666666665555543
No 215
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=30.42 E-value=40 Score=33.71 Aligned_cols=19 Identities=47% Similarity=0.538 Sum_probs=17.9
Q ss_pred CCCCHHHHHHHHHHHHHhC
Q 016972 238 TKFSQSQKEKMFEFAERVG 256 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~G 256 (379)
|=||.||+++|++|+|+.+
T Consensus 101 TGf~~e~~~~l~~~a~~v~ 119 (266)
T COG0289 101 TGFTEEQLEKLREAAEKVP 119 (266)
T ss_pred CCCCHHHHHHHHHHHhhCC
Confidence 8899999999999999975
No 216
>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=30.41 E-value=17 Score=34.44 Aligned_cols=34 Identities=24% Similarity=0.436 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 264 DDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 264 ~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
-..+++++..++|++..+-+||.|-|...++++.
T Consensus 14 tgt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 14 TGTIDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred cccHHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 3578999999999999999999999998888774
No 217
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=30.20 E-value=26 Score=29.92 Aligned_cols=49 Identities=8% Similarity=0.151 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhC-----CCCceeeeecccccccCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVG-----VDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiG-----v~r~V~KVWfhNnK~k~~ 293 (379)
++|+-|.+.|.-++...| ....++++++++. ++.+++++++.+=|.|+.
T Consensus 148 ~Lt~~E~~il~~l~~~~~------~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~ 201 (221)
T PRK15479 148 ALTPREQALLTVLMYRRT------RPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ 201 (221)
T ss_pred ecCHHHHHHHHHHHhCCC------CcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence 599999999999988765 2234678888875 999999999999888885
No 218
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=30.17 E-value=11 Score=34.91 Aligned_cols=52 Identities=12% Similarity=0.151 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
+++++|++.+.-++- +..-+....+++|.++||++.+|++|++..+.++++.
T Consensus 175 ~Lp~~~R~i~~l~y~-----~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYG-----LGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhC-----CCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 566777777766430 1112334578999999999999999988887776554
No 219
>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=29.94 E-value=93 Score=24.37 Aligned_cols=37 Identities=22% Similarity=0.366 Sum_probs=23.2
Q ss_pred CCCHHHHHHHHH---HHHHhCccCCCCCHHHHHHHHHHhCCC-Ccee
Q 016972 239 KFSQSQKEKMFE---FAERVGWKMQKRDDDLVHEFCNEVGVD-RTVL 281 (379)
Q Consensus 239 kFT~EQkekM~~---faEk~GWRIqk~d~~~vq~fc~eiGv~-r~V~ 281 (379)
.+|+-|++.|.- |-++.| ++- .+.|+|+.+||+ ..++
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G----~~P--t~rEIa~~~g~~S~~tv 43 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENG----YPP--TVREIAEALGLKSTSTV 43 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHS----S-----HHHHHHHHTSSSHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcC----CCC--CHHHHHHHhCCCChHHH
Confidence 578888887654 556666 543 789999999997 4444
No 220
>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.
Probab=29.69 E-value=77 Score=30.55 Aligned_cols=44 Identities=23% Similarity=0.437 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHHhCccC-----CCCCHHHHHHHHHHhCCCCceeee
Q 016972 239 KFSQSQKEKMFEFAERVGWKM-----QKRDDDLVHEFCNEVGVDRTVLKV 283 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRI-----qk~d~~~vq~fc~eiGv~r~V~KV 283 (379)
.|+.+|+..++..++++|++. ++..++.+++|. +.|++-.+++|
T Consensus 94 I~s~~qr~~~e~v~~~lgl~~~~PLW~~~~~~ll~e~i-~~G~~aiIv~v 142 (223)
T TIGR00290 94 IYSEYQKTRIERVCRELGLKSFAPLWHRDPEKLMEEFV-EEKFEARIIAV 142 (223)
T ss_pred cccHHHHHHHHHHHHhcCCEEeccccCCCHHHHHHHHH-HcCCeEEEEEE
Confidence 477899999999999999765 345567788887 77888888877
No 221
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=29.43 E-value=57 Score=28.56 Aligned_cols=26 Identities=15% Similarity=0.190 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhC
Q 016972 231 GGRKRFRTKFSQSQKEKMFEFAERVG 256 (379)
Q Consensus 231 ~~kKR~RTkFT~EQkekM~~faEk~G 256 (379)
.+.++.++++|+|+++.+++-|+..|
T Consensus 8 KR~~~I~vrvt~eE~~~I~~kA~~AG 33 (114)
T PRK13877 8 KRGRHLRVPVLPDEKAEIEANAAAAG 33 (114)
T ss_pred ccCceeEEEeCHHHHHHHHHHHHHhC
Confidence 34566889999999999999999887
No 222
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=29.32 E-value=12 Score=33.61 Aligned_cols=48 Identities=13% Similarity=0.148 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
++.++|++.|.- +++.. ..+++|+++||+..++|+=++.-|.++++.-
T Consensus 134 ~Lp~~~r~i~~l~~~~g~----------s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 134 RLPVEQRAALVAVDMQGY----------SVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred hCCHHHHHHHHHHHHcCC----------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 356777776654 33332 4679999999999999999999888887764
No 223
>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=29.19 E-value=16 Score=27.15 Aligned_cols=21 Identities=19% Similarity=0.466 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCCceeeeeccc
Q 016972 267 VHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfhN 287 (379)
+.++|+.+||+..+|..|.+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568999999999999999853
No 224
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=29.10 E-value=11 Score=36.04 Aligned_cols=49 Identities=8% Similarity=0.076 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
+++++|++.+.- +++.. ..+++|+.+|++..++|+.++.-|.++++..+
T Consensus 115 ~L~~~~R~v~~L~~~~g~----------s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 115 RLSPLERAAFLLHDVFGV----------PFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred hCCHHHHHHHHHHHHhCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 467778777554 23322 45799999999999999999999999988654
No 225
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=28.90 E-value=5.7 Score=34.35 Aligned_cols=31 Identities=13% Similarity=0.191 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 265 DLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 265 ~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
-..+++|+.+||+...++++++.-|.+++++
T Consensus 143 ~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 143 YTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred CCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 4568999999999999999999998887764
No 226
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=28.90 E-value=93 Score=24.77 Aligned_cols=44 Identities=11% Similarity=0.088 Sum_probs=33.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeee
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKV 283 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KV 283 (379)
+.++..++.+|+. +..+|.-...+...+.++|+.+|++-+.+++
T Consensus 17 ~~~g~~~~~~~l~------~~~~~~~~~~~~~~l~~~a~~~gl~~~~~~~ 60 (122)
T cd02259 17 RYFGIPVRRDVLL------NAQQRRQQGLSLADLVSLANKLGLTAQGVKL 60 (122)
T ss_pred HHcCCCCCHHHHH------HHHhhccCCCCHHHHHHHHHHcCCeeeEEEc
Confidence 5567778888873 3344554568888999999999999998875
No 227
>PRK11470 hypothetical protein; Provisional
Probab=28.74 E-value=26 Score=33.46 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=20.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHh
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERV 255 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~ 255 (379)
-+|.++.+|.+|+++|.++|++.
T Consensus 78 v~Rl~~~l~~~~~~~~~~~A~~~ 100 (200)
T PRK11470 78 IKRLDAGLTEQQKQRIVEQVPSR 100 (200)
T ss_pred EEEecCCCCHHHHHHHHHHHHHH
Confidence 48889999999999999999874
No 228
>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=28.71 E-value=45 Score=28.43 Aligned_cols=53 Identities=19% Similarity=0.270 Sum_probs=38.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.|.|.|+. .+.|+++.+. ++|. .+.|+|.++||+..+|-..++--.-+++|+.
T Consensus 51 ~r~~~Kid---~~~L~~~v~~------~pd~-tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK~~ 103 (119)
T PF01710_consen 51 PRGRKKID---RDELKALVEE------NPDA-TLRELAERLGVSPSTIWRALKRLGITRKKKT 103 (119)
T ss_pred cccccccc---HHHHHHHHHH------CCCc-CHHHHHHHcCCCHHHHHHHHHHcCchhccCc
Confidence 33333664 4556666666 5665 4568999999999999888888887777766
No 229
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=28.49 E-value=34 Score=32.80 Aligned_cols=18 Identities=17% Similarity=0.307 Sum_probs=15.4
Q ss_pred CCCCCCCHHHHHHHHHHH
Q 016972 235 RFRTKFSQSQKEKMFEFA 252 (379)
Q Consensus 235 R~RTkFT~EQkekM~~fa 252 (379)
..+..||+.|+++|++..
T Consensus 207 ~C~~~FT~~Q~~RM~~~~ 224 (225)
T cd04275 207 SCMNEFTPGQVTRMRSYL 224 (225)
T ss_pred chhcccCHHHHHHHHHHh
Confidence 457899999999999864
No 230
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=28.42 E-value=25 Score=28.39 Aligned_cols=46 Identities=17% Similarity=0.311 Sum_probs=35.3
Q ss_pred HHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 246 EKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 246 ekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
|||.+|.--++|.|. +.+.+.++|++..++.-|.--=|.-+-+-++
T Consensus 1 ~~~~~fIrlLs~~~s------~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDP 46 (65)
T PF05344_consen 1 EKARAFIRLLSQQIS------VAQAADRLGTDPGTVRRWVRMFRQWLLQLDP 46 (65)
T ss_pred CcHHHHHHHhccccc------HHHHHHHHCcCHHHHHHHHHHHHHHHHHcCC
Confidence 578899999998775 5678999999999999998665554443333
No 231
>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=28.24 E-value=13 Score=35.64 Aligned_cols=49 Identities=10% Similarity=0.077 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 239 KFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 239 kFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
++++.|++.+.- +++.. ..+++|+.+|+++.++|++++.-|.++++..+
T Consensus 108 ~L~~~~R~v~~L~~~~g~----------s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 108 RLSPLERAVFVLREVFDY----------PYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred hCCHHHHHHHHHHHHcCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 566777776544 23322 35799999999999999999999999987644
No 232
>PRK06437 hypothetical protein; Provisional
Probab=28.23 E-value=13 Score=29.10 Aligned_cols=42 Identities=14% Similarity=0.231 Sum_probs=32.1
Q ss_pred HHHHHhC---ccCCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 016972 250 EFAERVG---WKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTF 292 (379)
Q Consensus 250 ~faEk~G---WRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~ 292 (379)
+|++-+| |.++.++...+.+|.+++|++...+.|+ .|.+.-.
T Consensus 3 ~~~~v~g~~~~~~~i~~~~tv~dLL~~Lgi~~~~vaV~-vNg~iv~ 47 (67)
T PRK06437 3 AMIRVKGHINKTIEIDHELTVNDIIKDLGLDEEEYVVI-VNGSPVL 47 (67)
T ss_pred ceEEecCCcceEEEcCCCCcHHHHHHHcCCCCccEEEE-ECCEECC
Confidence 3444456 6677777788999999999999999888 6766543
No 233
>PF13189 Cytidylate_kin2: Cytidylate kinase-like family; PDB: 3FDI_A.
Probab=28.08 E-value=23 Score=31.83 Aligned_cols=42 Identities=19% Similarity=0.385 Sum_probs=20.8
Q ss_pred HHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 246 EKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 246 ekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
+.=+..||++|+++ -|.+.+++.+++.||++..|..|.....
T Consensus 14 ~Ia~~LA~~Lg~~~--~d~~ii~~~a~~~~~~~~~~~~~~e~~~ 55 (179)
T PF13189_consen 14 EIAERLAEKLGYPY--YDREIIEEAAKESGISEEEFEEFDEKKP 55 (179)
T ss_dssp HHHHHHHHHCT--E--E-HHHHHHCT------------SS-HHH
T ss_pred HHHHHHHHHcCCcc--CCHHHHHHHHHHccCCHHHHHHHhcccc
Confidence 34467899999554 7779999999999999999998887665
No 234
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=27.85 E-value=12 Score=35.15 Aligned_cols=48 Identities=8% Similarity=0.114 Sum_probs=35.8
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
.++.+.|++.|.-.+ -++-..+++|..+||++..++++++.-+.++++
T Consensus 200 ~~L~~~~r~vl~l~~---------~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 200 KQLSEKEQLVISLFY---------KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred hcCCHHHHHHHHHHH---------hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345666776666532 233356899999999999999999988887754
No 235
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=27.82 E-value=34 Score=29.57 Aligned_cols=41 Identities=17% Similarity=0.317 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
+|..|++.|.-+ +.++--+.++|.++||+|+.+.-|++--+
T Consensus 18 LT~kQ~~~l~ly---------y~eDlSlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 18 LTEKQREILELY---------YEEDLSLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp S-HHHHHHHHHH---------CTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHH---------HccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 788999998877 66677899999999999998877776544
No 236
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=27.77 E-value=1.1e+02 Score=24.18 Aligned_cols=31 Identities=19% Similarity=0.192 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVG 275 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiG 275 (379)
.|+.|+++++...++++ -.++..+.||+.+|
T Consensus 66 ~~~~~e~~~l~~~l~~~------~~~~~~~~~~~~~~ 96 (96)
T smart00529 66 GVDEEEVHEEAERLEHV------LSDELEDRLDRFLG 96 (96)
T ss_pred CCCHHHHHHHHHHHHcc------CCHHHHHHHHHHhC
Confidence 68888888888877763 57778888888775
No 237
>PRK09483 response regulator; Provisional
Probab=27.75 E-value=20 Score=30.79 Aligned_cols=47 Identities=13% Similarity=0.227 Sum_probs=36.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCC
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFA 293 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~ 293 (379)
...||+-++|.|.-+++ | + ..+++|++++|+.+++|.-.+|=+.|+.
T Consensus 146 ~~~Lt~rE~~vl~~~~~--G----~----~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 146 FASLSERELQIMLMITK--G----Q----KVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred ccccCHHHHHHHHHHHC--C----C----CHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 35699999999976643 2 2 3459999999999999998888777774
No 238
>PRK13558 bacterio-opsin activator; Provisional
Probab=27.74 E-value=36 Score=35.82 Aligned_cols=44 Identities=11% Similarity=0.173 Sum_probs=34.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceee
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLK 282 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~K 282 (379)
+..+|..|+|.|+..++. | =...|.+...+++|.++||++.+|-
T Consensus 605 ~~~lt~~q~e~l~~a~~~-g-yf~~pr~~~~~e~a~~l~is~~t~~ 648 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVS-G-YFEWPRRVEGEELAESMGISRSTFH 648 (665)
T ss_pred hhhCCHHHHHHHHHHHHc-C-CCCCCccCCHHHHHHHhCCCHHHHH
Confidence 358999999998877665 4 1122778899999999999998764
No 239
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=27.69 E-value=30 Score=29.60 Aligned_cols=51 Identities=8% Similarity=0.045 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhC-----CCCceeeeecccccccCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVG-----VDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiG-----v~r~V~KVWfhNnK~k~~k 294 (379)
.+||..|.+.|.-+++..| ..-.+++++.++. +..++|++.+.+=|.|+..
T Consensus 148 ~~Lt~~E~~il~~l~~~~~------~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~ 203 (219)
T PRK10336 148 LTLKPKEFALLELLMRNAG------RVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS 203 (219)
T ss_pred EecCHHHHHHHHHHHhCCC------ccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCC
Confidence 4699999999999988754 1224568888886 9999999999999888864
No 240
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.64 E-value=16 Score=29.10 Aligned_cols=24 Identities=17% Similarity=0.559 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCCceeeeeccccc
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
.+.++|+.+||++++|.-|.+.=+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 588999999999999999998744
No 241
>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=27.61 E-value=10 Score=34.62 Aligned_cols=48 Identities=6% Similarity=0.175 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
.+|++.|++.+...+. +...++++|.++||++..|++|++.-+.++++
T Consensus 177 ~~L~~~~r~vl~l~y~---------~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 177 AALPERERRILLLRFF---------EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred HcCCHHHHHHHHHHHh---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5677888887776532 22357899999999999999999887776654
No 242
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=27.41 E-value=11 Score=33.08 Aligned_cols=49 Identities=8% Similarity=0.119 Sum_probs=36.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCC
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAK 294 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k 294 (379)
-..|++.|++.+...+. +.-..+++|..+||++.++++.++.-|.++++
T Consensus 135 l~~L~~~~r~i~~l~~~---------~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 135 LAELEPPRSELIRTAFF---------EGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred HHhCCHHHHHHHHHHHH---------cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 35566777777665431 22356899999999999999999988887754
No 243
>KOG2146 consensus Splicing coactivator SRm160/300, subunit SRm160 (contains PWI domain) [RNA processing and modification; General function prediction only]
Probab=27.28 E-value=30 Score=35.43 Aligned_cols=19 Identities=32% Similarity=0.496 Sum_probs=14.7
Q ss_pred CCCCHHHHHHHHH--HHHHhC
Q 016972 238 TKFSQSQKEKMFE--FAERVG 256 (379)
Q Consensus 238 TkFT~EQkekM~~--faEk~G 256 (379)
|.||..||..|+. |.+-|-
T Consensus 12 trFSdkeKKLmkqmKF~~~le 32 (354)
T KOG2146|consen 12 TRFSDKEKKLMKQMKFPACLE 32 (354)
T ss_pred cccchHHHHHHHhcccHHHHh
Confidence 6799999999987 666553
No 244
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=27.20 E-value=42 Score=30.57 Aligned_cols=49 Identities=10% Similarity=0.184 Sum_probs=37.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 016972 235 RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNN 288 (379)
Q Consensus 235 R~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNn 288 (379)
+.+..+|+.+++.+..+.+.. ....-..+++|++++|++.++|.-+.+=
T Consensus 154 ~~~~~Lt~re~~~l~~~i~~~-----~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 154 RLPKGLTPQTLRTLCQWIDAH-----QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred cCCCCCCHHHHHHHHHHHHhC-----CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 345569999999988887653 2233467899999999999999877754
No 245
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=27.06 E-value=26 Score=33.25 Aligned_cols=51 Identities=20% Similarity=0.197 Sum_probs=41.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 235 RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 235 R~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
..+.+||+-|+|.|+-.|+- |- -.++|..+||++++++.-+.|-+.|+.-.
T Consensus 175 ~~~~~LT~rE~evl~~~a~G------~t----~~eIa~~l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 175 TPEMNFSKREKEILKWTAEG------KT----SAEIAMILSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred CCCCCCCHHHHHHHHHHHcC------CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 34568999999999888654 33 36999999999999999999988887643
No 246
>KOG4778 consensus Mitochondrial ribosomal protein L28 [Translation, ribosomal structure and biogenesis]
Probab=27.05 E-value=35 Score=32.57 Aligned_cols=31 Identities=26% Similarity=0.381 Sum_probs=26.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCH
Q 016972 232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDD 264 (379)
Q Consensus 232 ~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~ 264 (379)
.+.|.++++|.||+++ .+.+++. |+|.+.++
T Consensus 82 ~rqrp~~klt~e~~e~-rav~~k~-W~~y~~~~ 112 (186)
T KOG4778|consen 82 KRQRPLLKLTDEQLEK-RAVILKT-WSIYKQQQ 112 (186)
T ss_pred cccCCcccCCHHHHHH-HHHHHHH-HHHHHHHH
Confidence 3459999999999999 7888887 99977665
No 247
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=27.03 E-value=29 Score=32.18 Aligned_cols=45 Identities=16% Similarity=0.189 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTF 292 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~ 292 (379)
..||+.|++.|+-+++=+ ..+++|.+++|+++++|+-.+|==.|+
T Consensus 147 ~~LT~RE~eVL~lla~G~----------snkeIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAEGL----------SNKEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHCCC----------CHHHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 579999999999987653 346999999999999999887755544
No 248
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=26.94 E-value=69 Score=24.18 Aligned_cols=28 Identities=11% Similarity=0.513 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhCCCC-ceeeeeccccccc
Q 016972 264 DDLVHEFCNEVGVDR-TVLKVWMHNNKST 291 (379)
Q Consensus 264 ~~~vq~fc~eiGv~r-~V~KVWfhNnK~k 291 (379)
..+.+.||++.|++. ..++.+|...+-.
T Consensus 24 ~~l~~~~~~~~~i~~~~~~~l~fdG~~L~ 52 (72)
T PF11976_consen 24 SKLIEKYCEKKGIPPEESIRLIFDGKRLD 52 (72)
T ss_dssp HHHHHHHHHHHTTTT-TTEEEEETTEEE-
T ss_pred HHHHHHHHHhhCCCccceEEEEECCEEcC
Confidence 467889999999999 9999999887753
No 249
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=26.83 E-value=24 Score=31.22 Aligned_cols=13 Identities=54% Similarity=0.976 Sum_probs=10.7
Q ss_pred CCccccccccccc
Q 016972 107 PTSLKCAACGCHR 119 (379)
Q Consensus 107 p~ALKCAACGCHR 119 (379)
.-.|+|.|||..|
T Consensus 112 ~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 112 LIFLKCKACGASR 124 (125)
T ss_dssp CCEEEETTTSCEE
T ss_pred EEEEEecccCCcC
Confidence 3479999999876
No 250
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=26.45 E-value=29 Score=32.05 Aligned_cols=48 Identities=6% Similarity=0.106 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccccc
Q 016972 242 QSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKST 291 (379)
Q Consensus 242 ~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k 291 (379)
.+-++++.+.|.++=+.-.|. ..++++|++.||++..|-.+|.|...-
T Consensus 12 ~~~r~~Il~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L 59 (225)
T PRK11552 12 EQAKQQLIAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDL 59 (225)
T ss_pred HHHHHHHHHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHH
Confidence 355556655444331121244 789999999999999999999886653
No 251
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=26.43 E-value=11 Score=36.22 Aligned_cols=50 Identities=8% Similarity=0.050 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHH-HHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 238 TKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 238 TkFT~EQkekM~~-faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
.+++++|++.+.- +++.+ ..+++|+.+||+..++|+.++--|.++++.-.
T Consensus 141 ~~Lp~~~R~v~~L~~~~g~----------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 141 QYLPPRQRAVLLLRDVLGW----------RAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HhCCHHHhhHhhhHHHhCC----------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 4566667666544 33332 46799999999999999999999998877653
No 252
>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=26.11 E-value=19 Score=27.30 Aligned_cols=21 Identities=24% Similarity=0.525 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCceeeeeccc
Q 016972 267 VHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfhN 287 (379)
+.++|+.+||+..+|+.|...
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568999999999999999654
No 253
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=25.96 E-value=1e+02 Score=25.31 Aligned_cols=36 Identities=17% Similarity=0.388 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeec-ccccc
Q 016972 241 SQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWM-HNNKS 290 (379)
Q Consensus 241 T~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWf-hNnK~ 290 (379)
|.|||++|-+. ++++|++++||...=|-|=+ .|.+.
T Consensus 41 s~e~K~~ly~~--------------l~~~L~~~~gi~p~Dv~I~l~e~~~e 77 (82)
T PF14552_consen 41 STEQKKALYRA--------------LAERLAEKLGIRPEDVMIVLVENPRE 77 (82)
T ss_dssp -HHHHHHHHHH--------------HHHHHHHHH---GGGEEEEEEEE-GG
T ss_pred CHHHHHHHHHH--------------HHHHHHHHcCCCHHHEEEEEEECCcc
Confidence 48999987654 66788999999987655443 34443
No 254
>PRK08359 transcription factor; Validated
Probab=25.93 E-value=21 Score=33.48 Aligned_cols=53 Identities=23% Similarity=0.324 Sum_probs=32.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
+|.|-.| -.+.+.+|++++- .+...-.-..++||..+||++.+|.-|=.+.+.
T Consensus 72 ~~~~d~~---~~elv~dy~~rIk-eaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~ 124 (176)
T PRK08359 72 RRERPLY---TEDIVEDYAERVY-EAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYE 124 (176)
T ss_pred CCcccch---HHHHHHHHHHHHH-HHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcC
Confidence 3445667 2255566665541 000000013579999999999999988777663
No 255
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=25.81 E-value=15 Score=35.70 Aligned_cols=31 Identities=13% Similarity=0.209 Sum_probs=27.9
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
..+++|..+||+..++|+.++.-|.++++..
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~ 201 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAERG 201 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhhcC
Confidence 5689999999999999999999999998843
No 256
>PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=25.53 E-value=84 Score=30.40 Aligned_cols=50 Identities=14% Similarity=0.056 Sum_probs=37.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCce--eeeecc
Q 016972 236 FRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTV--LKVWMH 286 (379)
Q Consensus 236 ~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V--~KVWfh 286 (379)
.|--|+.|+.+.|++.+..+ ||-...-++.++++.+++.-.+.+ |--|+.
T Consensus 196 ~r~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~ 247 (255)
T PRK12461 196 RRRGFSSRAIRALKRAYKII-YRSGLSVQQAVAELELQQFESPEVEELIDFIK 247 (255)
T ss_pred hhcCCCHHHHHHHHHHHHHH-HhcCCCHHHHHHHHHHhccCCHHHHHHHHHHH
Confidence 56679999999999999887 777777778888888887655443 444553
No 257
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=25.50 E-value=1e+02 Score=31.41 Aligned_cols=18 Identities=6% Similarity=0.215 Sum_probs=12.7
Q ss_pred eecccccccCCCCCCCCC
Q 016972 283 VWMHNNKSTFAKRDLNGA 300 (379)
Q Consensus 283 VWfhNnK~k~~k~~~~~~ 300 (379)
.=|.-++++++++.....
T Consensus 225 LSmStR~hkyGRQ~~~~~ 242 (314)
T PF06524_consen 225 LSMSTRSHKYGRQGQADE 242 (314)
T ss_pred ceeeeecchhccccCCCc
Confidence 456778888988875544
No 258
>cd01994 Alpha_ANH_like_IV This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=25.50 E-value=1.2e+02 Score=28.22 Aligned_cols=45 Identities=24% Similarity=0.478 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHHHHHHHhCccC-----CCCCHHHHHHHHHHhCCCCceeee
Q 016972 238 TKFSQSQKEKMFEFAERVGWKM-----QKRDDDLVHEFCNEVGVDRTVLKV 283 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRI-----qk~d~~~vq~fc~eiGv~r~V~KV 283 (379)
+.++..|+..++..++++|.+. ++..++.+++|. +.|+.-.+++|
T Consensus 96 ~i~sd~~~~~~e~~~~~~gl~~~~PLW~~~~~~ll~e~~-~~g~~~~iv~v 145 (194)
T cd01994 96 AILSEYQRTRVERVCERLGLEPLAPLWGRDQEELLREMI-EAGFKAIIIKV 145 (194)
T ss_pred ccccHHHHHHHHHHHHHcCCEEEecccCCCHHHHHHHHH-HcCCeEEEEEe
Confidence 3456788888888888888443 334456777777 66777777666
No 259
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=25.42 E-value=29 Score=25.05 Aligned_cols=33 Identities=24% Similarity=0.302 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeee
Q 016972 244 QKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKV 283 (379)
Q Consensus 244 QkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KV 283 (379)
|++.|.-+.+..+ .-..++||+++||++++|+-
T Consensus 2 ~~~il~~L~~~~~-------~it~~eLa~~l~vS~rTi~~ 34 (55)
T PF08279_consen 2 QKQILKLLLESKE-------PITAKELAEELGVSRRTIRR 34 (55)
T ss_dssp HHHHHHHHHHTTT-------SBEHHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHcCC-------CcCHHHHHHHhCCCHHHHHH
Confidence 3445555545432 14678999999999998864
No 260
>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=25.42 E-value=9.1 Score=36.45 Aligned_cols=31 Identities=13% Similarity=0.320 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
..+++|..+||+..++|++++.-|.++++..
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999998887654
No 261
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=25.40 E-value=46 Score=28.60 Aligned_cols=36 Identities=8% Similarity=0.241 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 246 EKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 246 ekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
++|+.+-++.||. .++||..+||++..|.-|..+.+
T Consensus 8 ~rlk~~R~~~glt--------q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 8 QRIRYRRKQLKLS--------QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHcCCC
Confidence 4556666666543 36888888888888888887764
No 262
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=25.31 E-value=38 Score=26.02 Aligned_cols=44 Identities=20% Similarity=0.305 Sum_probs=24.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCcee
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVL 281 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~ 281 (379)
..+-|..+.-.|.-.+.-+++++| -.++.+++.-.++|-.+.-|
T Consensus 8 ~~~D~~~I~~~e~~ev~ywa~~~g-----vt~~~L~~AV~~vG~~~~~V 51 (57)
T PF12244_consen 8 GPQDRDRIDLSEPYEVRYWAKRFG-----VTEEQLREAVRAVGNSRAAV 51 (57)
T ss_pred CCCChHhcCCCCHHHHHHHHHHHC-----cCHHHHHHHHHHHCcCHHHH
Confidence 345555666555566666666664 44455555556666554433
No 263
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=25.26 E-value=42 Score=28.27 Aligned_cols=43 Identities=19% Similarity=0.444 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
.+|+..++.|-.---.-||. +.+.|++.||++.+...|+.--|
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~~--------~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGWP--------VAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCHHHHHHHHHHHHHcCCc--------HHHHHHHhCCCHHHHHHHHHHHH
Confidence 47888888887765555554 46999999999999999986444
No 264
>PF13730 HTH_36: Helix-turn-helix domain
Probab=25.18 E-value=68 Score=23.05 Aligned_cols=44 Identities=16% Similarity=0.160 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHHHHHHH---hCccCCCCCHHHHHHHHHHhCCCCceeeeecc
Q 016972 238 TKFSQSQKEKMFEFAER---VGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 238 TkFT~EQkekM~~faEk---~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfh 286 (379)
+.+++.++-.+..++.. .+| -+| -++.+|.++|+++++|+-++.
T Consensus 1 ~~Ls~~~~~v~~~l~~~~~~~~~--~~p---S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 1 KNLSPTAKLVYLYLASYANKNGG--CFP---SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCCHHHHHHHHHHHHhcCCCCC--CCc---CHHHHHHHHCcCHHHHHHHHH
Confidence 35667777766654444 332 334 468999999999999987764
No 265
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=25.02 E-value=64 Score=36.89 Aligned_cols=65 Identities=18% Similarity=0.250 Sum_probs=44.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCCC
Q 016972 229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRDL 297 (379)
Q Consensus 229 ~s~~kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~~ 297 (379)
.+.++-|.|+-...++-..+...+|-.- + +.....--.+.++-....|+.||+|+|+.+-++.+.
T Consensus 622 sg~~p~kv~sp~k~~dq~ql~~a~elq~-s---~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 622 SGERPVKVRSPIKEEDQQQLKQAYELQA-S---PSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred CCCCCccccCCCCccchhhhHhhhhccc-C---ccCcccchhhhhccCCCcchhhcccCCCCCCCCCcc
Confidence 3445677888888888888887755431 2 222222233455788899999999999998777764
No 266
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=25.00 E-value=24 Score=32.90 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
..||+-|+|.|.-.++ || ..+++|++++|+++++|.++.+-..|++-+
T Consensus 154 ~~Lt~rE~~Vl~l~~~--G~--------s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 154 ALLTHREKEILNKLRI--GA--------SNNEIARSLFISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred CCCCHHHHHHHHHHHc--CC--------CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 3599999999998877 52 246899999999999999999887776543
No 267
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=24.53 E-value=83 Score=25.68 Aligned_cols=41 Identities=12% Similarity=0.117 Sum_probs=29.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCC
Q 016972 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDR 278 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r 278 (379)
|--||.||...|+.++..+ |+-...-++.++++-++..-..
T Consensus 25 R~Gfs~~~i~~l~~ayr~l-~~~~~~~~~a~~~l~~~~~~~~ 65 (83)
T PF13720_consen 25 RRGFSKEEISALRRAYRIL-FRSGLTLEEALEELEEEYPDSP 65 (83)
T ss_dssp HTTS-HHHHHHHHHHHHHH-HTSSS-HHHHHHHHHHHTTSCH
T ss_pred HcCCCHHHHHHHHHHHHHH-HhCCCCHHHHHHHHHHhccCCH
Confidence 5679999999999999888 6655566677777777655443
No 268
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=24.50 E-value=26 Score=30.39 Aligned_cols=56 Identities=9% Similarity=0.182 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.+|..+.+.|.-+++..|--+. .++-..+.++.++.+..+++++++.+=|.|+..+
T Consensus 156 ~Lt~~E~~~l~~l~~~~~~v~s-r~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~~ 211 (232)
T PRK10955 156 ELTGTEFTLLYLLAQHLGQVVS-REHLSQEVLGKRLTPFDRAIDMHISNLRRKLPDR 211 (232)
T ss_pred cCCHHHHHHHHHHHhCCCceEc-HHHHHHHHhCCCCCCCCcCHHHHHHHHHHhcccC
Confidence 6999999999999998772221 2222335577788889999999999999988643
No 269
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=24.20 E-value=15 Score=32.58 Aligned_cols=54 Identities=6% Similarity=0.045 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHhCcc------CCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 242 QSQKEKMFEFAERVGWK------MQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 242 ~EQkekM~~faEk~GWR------Iqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.|+.+.|.+..+++.=+ +-+-..-..+++|..+||++.++++|++.-|.++++.
T Consensus 122 ~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 122 PEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred HHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35556666666665411 0122234568999999999999999999998887654
No 270
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=24.07 E-value=13 Score=34.85 Aligned_cols=48 Identities=8% Similarity=0.035 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
++++.|++.+.-.+- +.-..+++|..+||++.+|++|++.-+.++++.
T Consensus 205 ~L~~~~r~vl~l~~~---------~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFI---------ENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHh---------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466677766655321 122468999999999999999999888777543
No 271
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=24.01 E-value=90 Score=21.15 Aligned_cols=18 Identities=22% Similarity=0.466 Sum_probs=15.9
Q ss_pred CCCHHHHHHHHHHHHHhC
Q 016972 239 KFSQSQKEKMFEFAERVG 256 (379)
Q Consensus 239 kFT~EQkekM~~faEk~G 256 (379)
+|+.|++++|.+.|++.|
T Consensus 5 ~l~~~~~~~l~~~a~~~g 22 (39)
T PF01402_consen 5 RLPDELYERLDELAKELG 22 (39)
T ss_dssp EEEHHHHHHHHHHHHHHT
T ss_pred EeCHHHHHHHHHHHHHHC
Confidence 567899999999999997
No 272
>PRK06680 D-amino acid aminotransferase; Reviewed
Probab=24.00 E-value=1.6e+02 Score=28.40 Aligned_cols=47 Identities=6% Similarity=0.073 Sum_probs=37.0
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCH---HHHHHHHHHhCCCCceeeeecc
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDD---DLVHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~---~~vq~fc~eiGv~r~V~KVWfh 286 (379)
|=.+-+++|+.-|+.+|+.+....+ +.++++++.-++....|++|+-
T Consensus 45 ~l~~Hl~RL~~Sa~~L~i~~~~~~~~l~~~i~~~~~~~~~~~~~lr~~vt 94 (286)
T PRK06680 45 DLDRHLARLFRSLGEIRIAPPMTRAELVEVLRELIRRNRVREGLVYLQVT 94 (286)
T ss_pred chHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHcCCCceEEEEEEE
Confidence 5589999999999999987765443 4566666666888888998875
No 273
>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=23.86 E-value=25 Score=33.85 Aligned_cols=54 Identities=15% Similarity=0.205 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.++++.|++.|.-++ | +.+...-..+++|..+||+...||.+++.-+.++++..
T Consensus 221 ~~Lp~~~R~Vl~l~y---g--L~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 221 AELNERQREVLARRF---G--LLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred HcCCHHHHHHHHHHh---C--CCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456666666665543 1 22344456789999999999999999999998887654
No 274
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=23.78 E-value=26 Score=24.94 Aligned_cols=37 Identities=11% Similarity=0.317 Sum_probs=26.8
Q ss_pred HHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccc
Q 016972 247 KMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNN 288 (379)
Q Consensus 247 kM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNn 288 (379)
.-.+.+.+.|| +...++++|+++||++..|---|.|.
T Consensus 4 aa~~l~~~~G~-----~~~s~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 4 AALELFAEKGY-----EAVSIRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp HHHHHHHHHHT-----TTSSHHHHHHHHTSCHHHHHHHCSSH
T ss_pred HHHHHHHHhCH-----HhCCHHHHHHHHccchhhHHHHcCCH
Confidence 33455556652 34578899999999999998777764
No 275
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=23.66 E-value=1.4e+02 Score=24.06 Aligned_cols=44 Identities=7% Similarity=0.049 Sum_probs=34.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeee
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKV 283 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KV 283 (379)
+.+.-.++.+++... ++|.-+..+...+.+.++++|++-+.+++
T Consensus 17 ~~~g~~~~~~~l~~~------~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~ 60 (121)
T cd02417 17 RYHGIAADPEQLRHE------FGLAGEPFNSTELLLAAKSLGLKAKAVRQ 60 (121)
T ss_pred HHcCCCCCHHHHHHH------hcCCCCCCCHHHHHHHHHHcCCeeEEEec
Confidence 456667788888754 34555568889999999999999999876
No 276
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=23.41 E-value=1.1e+02 Score=28.22 Aligned_cols=38 Identities=18% Similarity=0.246 Sum_probs=31.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhC
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVG 275 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiG 275 (379)
|.+.++||.++++.+.+-|+..|+ ..-+.+.+.+..++
T Consensus 25 kvVsvRLTe~Ey~~L~~rA~~aGl----S~SEfIRqAi~~~~ 62 (147)
T PRK13858 25 KVVSTRLRSAEYESFSAQARLLGL----SDSMAIRVAVRRIG 62 (147)
T ss_pred eEEEEecCHHHHHHHHHHHHHcCC----CHHHHHHHHHHhcC
Confidence 788999999999999999999993 44456666666666
No 277
>COG1427 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=23.34 E-value=47 Score=32.96 Aligned_cols=52 Identities=12% Similarity=0.256 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+.|-+-+.++|+....+. + +.++++.|+.+||++++++-.|.|-|..+..+.
T Consensus 179 ~~~~~~~~~~~~~~~~~~------~-~ei~~~~a~~lglp~~~~~eYy~~~~Y~l~~e~ 230 (252)
T COG1427 179 KPFYKRALLEFEETKAKF------P-AEILKEAAKRLGLPRSDVEEYYTNIRYSLGTEE 230 (252)
T ss_pred CCchhhhHHHHHHHHHhh------h-HHHHHHHHHHcCCCHHHHHHHHHHheeecCHHH
Confidence 455555666666554442 2 789999999999999999999999999886653
No 278
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=23.32 E-value=2.3e+02 Score=24.14 Aligned_cols=41 Identities=17% Similarity=0.280 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCc--cCCCCCHHHHHHHHHHh-CCC
Q 016972 237 RTKFSQSQKEKMFEFAERVGW--KMQKRDDDLVHEFCNEV-GVD 277 (379)
Q Consensus 237 RTkFT~EQkekM~~faEk~GW--RIqk~d~~~vq~fc~ei-Gv~ 277 (379)
+...+..|+.|+.+....+|| -|..+.+.....|+..+ ||.
T Consensus 52 ~~~~~~~q~~KI~aLw~~~~~~~~v~~~s~~aL~~fvkr~~gv~ 95 (119)
T PF06252_consen 52 PGMATSAQLRKIRALWKQLGKPGAVRDPSEAALDAFVKRQFGVD 95 (119)
T ss_pred CCCcchHHHHHHHHHHHHhhccCCccchHHHHHHHHHHHHHCCC
Confidence 344599999999999999984 45667777888888654 444
No 279
>cd02139 Nitroreductase_3 Nitroreductase-like family 3. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=23.22 E-value=1e+02 Score=26.51 Aligned_cols=41 Identities=10% Similarity=0.379 Sum_probs=31.8
Q ss_pred CCCCCC-CCHHHHHHHHHHHHH-------hCccCCC-CCHHHHHHHHHHh
Q 016972 234 KRFRTK-FSQSQKEKMFEFAER-------VGWKMQK-RDDDLVHEFCNEV 274 (379)
Q Consensus 234 KR~RTk-FT~EQkekM~~faEk-------~GWRIqk-~d~~~vq~fc~ei 274 (379)
|+|..+ ++.|++++|++.+.. ..||+.. .+.+.+++|...+
T Consensus 12 R~f~~~~v~~e~l~~ll~aa~~aPs~~n~qp~~~~vv~~~~~~~~l~~~~ 61 (164)
T cd02139 12 RKYKDDPVEEEKLERILEAARLAPSAKNLQPWRFIVVESEEGLKKLAAAY 61 (164)
T ss_pred eccCCCCCCHHHHHHHHHHHhhCCCCCCCCCeEEEEEeCHHHHHHHHHHh
Confidence 556664 999999999999887 6799876 5567777777654
No 280
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [, , ]. In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH []. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms. This entry represents the N-terminal domain of dihydrodipicolinate reductase which binds the dinucleotide NAD(P)H.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0055114 oxidation-reduction process; PDB: 3QY9_D 1VM6_C 1ARZ_A 1DIH_A 1DRW_A 1DRV_A 1DRU_A 2DAP_A 1DAP_B 3DAP_A ....
Probab=23.20 E-value=30 Score=29.44 Aligned_cols=20 Identities=30% Similarity=0.433 Sum_probs=17.3
Q ss_pred CCCCHHHHHHHHHHHHHhCc
Q 016972 238 TKFSQSQKEKMFEFAERVGW 257 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GW 257 (379)
|-|+.||+++|++++++.+|
T Consensus 99 TG~~~~~~~~l~~~a~~~~v 118 (124)
T PF01113_consen 99 TGFSDEQIDELEELAKKIPV 118 (124)
T ss_dssp SSSHHHHHHHHHHHTTTSEE
T ss_pred CCCCHHHHHHHHHHhccCCE
Confidence 56899999999999998765
No 281
>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=23.08 E-value=11 Score=33.48 Aligned_cols=37 Identities=11% Similarity=0.132 Sum_probs=31.3
Q ss_pred CCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 260 QKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 260 qk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.+-+.-..+++|..+||+..++|++++--|.++++.-
T Consensus 143 ~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 143 ADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3444556789999999999999999999999987764
No 282
>cd08577 PI-PLCc_GDPD_SF_unchar3 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=23.07 E-value=1.2e+02 Score=28.93 Aligned_cols=25 Identities=24% Similarity=0.284 Sum_probs=17.4
Q ss_pred CCCCCHHHHHHHHHH---HHHhCccCCC
Q 016972 237 RTKFSQSQKEKMFEF---AERVGWKMQK 261 (379)
Q Consensus 237 RTkFT~EQkekM~~f---aEk~GWRIqk 261 (379)
|-.|+.+|+++|+++ |.+.|+++..
T Consensus 176 ~g~~~~~q~~~l~~~v~~a~~~Gl~vr~ 203 (228)
T cd08577 176 KGDTPEDEKEKLKSIIDKAHARGKKVRF 203 (228)
T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCEEEE
Confidence 345999999999997 4444554433
No 283
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=22.95 E-value=9 Score=35.46 Aligned_cols=50 Identities=10% Similarity=0.178 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
.+++.+|++.+.- .+-..-..+++|+.+||+..++++.++.-|.++++.-
T Consensus 148 ~~L~~~~r~i~~l---------~~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 148 DALPDAFRAVFVL---------RVVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred HhCCHHHhhhhee---------ehhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3455666666533 1223346789999999999999999999999988764
No 284
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=22.72 E-value=81 Score=26.90 Aligned_cols=46 Identities=20% Similarity=0.374 Sum_probs=35.5
Q ss_pred CCCCCCCHHHHHHHHHHHHH-hCccCCCCCHHHHHHHHHHhCCCCcee
Q 016972 235 RFRTKFSQSQKEKMFEFAER-VGWKMQKRDDDLVHEFCNEVGVDRTVL 281 (379)
Q Consensus 235 R~RTkFT~EQkekM~~faEk-~GWRIqk~d~~~vq~fc~eiGv~r~V~ 281 (379)
=.|..||.-|+..|++..-+ .||. ++-|.=...+||..+|+++..+
T Consensus 25 l~~~dls~rq~ki~~ai~RkTyG~n-Kk~d~Is~sq~~e~tg~~~~~V 71 (100)
T PF04492_consen 25 LLRADLSGRQLKILLAIIRKTYGWN-KKMDRISNSQIAEMTGLSRDHV 71 (100)
T ss_pred HHhccccHHHHHHHHHHHHHccCCC-CccceeeHHHHHHHHCcCHHHH
Confidence 34678999999888886655 5776 5566678889999999887654
No 285
>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=22.66 E-value=24 Score=25.02 Aligned_cols=21 Identities=19% Similarity=0.387 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCCceeeeeccc
Q 016972 267 VHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfhN 287 (379)
+.++|+.+||+.++|..|-.-
T Consensus 2 i~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHHT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 468999999999999999754
No 286
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=22.61 E-value=50 Score=23.78 Aligned_cols=28 Identities=29% Similarity=0.687 Sum_probs=18.2
Q ss_pred ccCccccccCCCCCCCCCCcccccccccccccccc
Q 016972 90 LDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRR 124 (379)
Q Consensus 90 vDGCGEFMPSGeegt~dp~ALKCAACGCHRNFHRK 124 (379)
=|=|+++|.+. -..+++|..|+ ...|++
T Consensus 14 C~~C~~~i~g~-----~~~g~~C~~C~--~~~H~~ 41 (53)
T PF00130_consen 14 CDVCGKFIWGL-----GKQGYRCSWCG--LVCHKK 41 (53)
T ss_dssp -TTSSSBECSS-----SSCEEEETTTT---EEETT
T ss_pred CcccCcccCCC-----CCCeEEECCCC--ChHhhh
Confidence 36799999541 14589999765 555555
No 287
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=22.39 E-value=1.3e+02 Score=25.53 Aligned_cols=31 Identities=19% Similarity=0.404 Sum_probs=17.0
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHh
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV 274 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~ei 274 (379)
..||+||+++-+.| -+. .-....|.++++++
T Consensus 6 ~~f~~eQ~~Rye~f-RRs-----~~~k~~ikkli~~~ 36 (90)
T PF04719_consen 6 SNFDEEQLDRYEAF-RRS-----SFNKAAIKKLINQV 36 (90)
T ss_dssp ----HHHHHHHHHH-HH---------HHHHHHHHHHH
T ss_pred HcCCHHHHHHHHHH-HHc-----cCCHHHHHHHHHHH
Confidence 46999999996554 443 45566788888774
No 288
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=22.24 E-value=8.2 Score=33.36 Aligned_cols=34 Identities=12% Similarity=0.084 Sum_probs=29.1
Q ss_pred CHHHHHHHHHHhCCCCceeeeecccccccCCCCC
Q 016972 263 DDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKRD 296 (379)
Q Consensus 263 d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~~ 296 (379)
+.-..+++|+.+|++..+++++++.-|.++++.-
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345789999999999999999999999887654
No 289
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=22.10 E-value=27 Score=25.97 Aligned_cols=20 Identities=20% Similarity=0.345 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCCceeeeecc
Q 016972 267 VHEFCNEVGVDRTVLKVWMH 286 (379)
Q Consensus 267 vq~fc~eiGv~r~V~KVWfh 286 (379)
+.++|+.+||+..+|+.|..
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 57899999999999999975
No 290
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=22.08 E-value=50 Score=23.92 Aligned_cols=37 Identities=16% Similarity=0.381 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceee
Q 016972 240 FSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLK 282 (379)
Q Consensus 240 FT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~K 282 (379)
||..|...|..+++.-+ +.-.+.++|+.+++++..+.
T Consensus 3 lt~~q~~vL~~l~~~~~------~~~t~~~la~~l~~~~~~vs 39 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPG------EELTQSELAERLGISKSTVS 39 (62)
T ss_dssp STHHHHHHHHHHHHSTT------SGEEHHHHHHHHTS-HHHHH
T ss_pred cCHHHHHHHHHHHHCCC------CCcCHHHHHHHHCcCHHHHH
Confidence 78899999888877643 23478899999999987653
No 291
>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=22.04 E-value=18 Score=33.94 Aligned_cols=49 Identities=12% Similarity=0.113 Sum_probs=35.8
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
.++++.|++.+...+. +....+++|..+||++.+++.|++.-+.++++.
T Consensus 204 ~~L~~~~r~ii~l~~~---------~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 204 PILSEREKSIIHCTFE---------ENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred HcCCHHHHHHHHHHHc---------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3566777776665432 222458999999999999999998887776653
No 292
>cd01763 Sumo Small ubiquitin-related modifier (SUMO). Small ubiquitin-related modifier (SUMO) proteins are conjugated to numerous intracellular targets and serve to modulate protein interaction, localization, activity or stability. SUMO (also known as "Smt3" and "sentrin" in other organisms) is linked to several different pathways, including nucleocytoplasmic transport. Attachment of SUMO to targets proteins is stimulated by PIAS (Protein inhibitor of activated STATs) proteins which serve as E3-like ligases.
Probab=21.90 E-value=93 Score=25.06 Aligned_cols=27 Identities=11% Similarity=0.398 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCCceeeeecccccccC
Q 016972 266 LVHEFCNEVGVDRTVLKVWMHNNKSTF 292 (379)
Q Consensus 266 ~vq~fc~eiGv~r~V~KVWfhNnK~k~ 292 (379)
+.+.||...||+...++-||..+|-..
T Consensus 37 l~~~y~~~~gi~~~~~rf~f~G~~L~~ 63 (87)
T cd01763 37 LMEAYCQRQGLSMNSVRFLFDGQRIRD 63 (87)
T ss_pred HHHHHHHHhCCCccceEEEECCeECCC
Confidence 345677788899999999998877554
No 293
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. 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, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=21.87 E-value=1e+02 Score=22.74 Aligned_cols=22 Identities=27% Similarity=0.622 Sum_probs=18.6
Q ss_pred CCCCHHHHHHHHHHHHHhCccC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKM 259 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRI 259 (379)
-.+++|=+++.++.++++||+-
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-S
T ss_pred CCCCHHHHHHHHHHHHHHCCCC
Confidence 3688999999999999999763
No 294
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=21.85 E-value=82 Score=25.11 Aligned_cols=27 Identities=19% Similarity=0.280 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHhCCCCceeeeeccccc
Q 016972 263 DDDLVHEFCNEVGVDRTVLKVWMHNNK 289 (379)
Q Consensus 263 d~~~vq~fc~eiGv~r~V~KVWfhNnK 289 (379)
+...++++|++.||++..|-.+|.|..
T Consensus 31 ~~~t~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 31 AATTVDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred CCCCHHHHHHHhCCCcchhHHHcCCHH
Confidence 445789999999999999999999875
No 295
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=21.76 E-value=63 Score=24.38 Aligned_cols=43 Identities=12% Similarity=0.227 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccC
Q 016972 242 QSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTF 292 (379)
Q Consensus 242 ~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~ 292 (379)
..|++.|.-+.+ .+|- .++++|.++||++++|+.-+.+=+..+
T Consensus 5 ~rq~~Ll~~L~~-~~~~-------~~~ela~~l~~S~rti~~~i~~L~~~f 47 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWI-------TLKELAKKLNISERTIKNDINELNEFF 47 (59)
T ss_dssp HHHHHHHHHHHH-HTSB-------BHHHHHHHCTS-HHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHc-CCCC-------cHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 357777777777 6654 456999999999999987665544433
No 296
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=21.62 E-value=27 Score=26.86 Aligned_cols=43 Identities=9% Similarity=0.200 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 016972 243 SQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 243 EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhN 287 (379)
|.+.+|....+++-.+.++ .-..+++|..+||+..-|+-.|+=
T Consensus 1 E~l~~i~~a~~~L~~~lgr--~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGR--EPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS----BHHHHHHHHTS-HHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHhCC--CCCHHHHHHHHcccHHHHHHHHHh
Confidence 3445555554444333323 456799999999999999877753
No 297
>PF01902 ATP_bind_4: ATP-binding region; InterPro: IPR002761 This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N-terminal. The structure of Q8U2K6 from SWISSPROT from Pyrococcus furiosus has been resolved to 2.7A and is suggested to be a putative N-type pytophosphatase. In some members of the family e.g. Q12429 from SWISSPROT, this domain is associated with IPR006175 from INTERPRO, another domain of unknown function. Proteins with this uncharacterised domain include two apparent ortholog families in the archaea, one of which is universal among the first four completed archaeal genomes. The domain comprises the full length of the archaeal proteins and the first third of fungal proteins.; PDB: 3RK0_A 3RK1_A 3RJZ_A 2D13_D.
Probab=21.61 E-value=89 Score=29.88 Aligned_cols=44 Identities=25% Similarity=0.381 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHHhCccCCC-----CCHHHHHHHHHHhCCCCceeee
Q 016972 239 KFSQSQKEKMFEFAERVGWKMQK-----RDDDLVHEFCNEVGVDRTVLKV 283 (379)
Q Consensus 239 kFT~EQkekM~~faEk~GWRIqk-----~d~~~vq~fc~eiGv~r~V~KV 283 (379)
.|+.+|+..++..++++|++.-. ..++.+++|... |+.-.+++|
T Consensus 94 I~~~~~r~~~e~vc~~lGl~~~~PLW~~d~~~ll~e~i~~-Gf~aiIv~V 142 (218)
T PF01902_consen 94 IDSEYQRNWVERVCERLGLEAVFPLWGRDREELLREFIES-GFEAIIVKV 142 (218)
T ss_dssp TS-HHHHHHHHHHHHHCT-EEE-TTTT--HHHHHHHHHHT-T-EEEEEEE
T ss_pred CCcHHHHHHHHHHHHHcCCEEEecccCCCHHHHHHHHHHC-CCeEEEEEE
Confidence 47899999999999999988643 334677787754 988888887
No 298
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=21.48 E-value=50 Score=27.77 Aligned_cols=19 Identities=37% Similarity=0.903 Sum_probs=11.9
Q ss_pred HHHHHHHHHhCCCCceeeeeccc
Q 016972 265 DLVHEFCNEVGVDRTVLKVWMHN 287 (379)
Q Consensus 265 ~~vq~fc~eiGv~r~V~KVWfhN 287 (379)
+++.+||..|||+|+ |||.
T Consensus 24 ~ELHafA~riGv~rr----~fq~ 42 (83)
T PF13223_consen 24 DELHAFAARIGVPRR----WFQR 42 (83)
T ss_pred HHHHHHHHHcCCCHH----HHcC
Confidence 444555666677774 7776
No 299
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=21.37 E-value=58 Score=28.62 Aligned_cols=46 Identities=15% Similarity=0.124 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 244 QKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 244 QkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
.++++.+.|.++=|.-.+ ....++++|++.||++..|--+|.|...
T Consensus 9 ~R~~Il~aA~~lf~e~G~-~~tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 9 RREVILQAAMRVALAEGF-AAMTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHHHHHHHHhcCh-hhccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 356666655554344335 4568999999999999999999976544
No 300
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=21.26 E-value=71 Score=26.85 Aligned_cols=18 Identities=28% Similarity=0.637 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHhCccC
Q 016972 242 QSQKEKMFEFAERVGWKM 259 (379)
Q Consensus 242 ~EQkekM~~faEk~GWRI 259 (379)
..|++.+++||++.||.|
T Consensus 18 ~~Q~~~~~~~a~~~g~~i 35 (148)
T smart00857 18 ERQLEALRAYAKANGWEV 35 (148)
T ss_pred HHHHHHHHHHHHHCCCEE
Confidence 689999999999999986
No 301
>PF14106 DUF4279: Domain of unknown function (DUF4279)
Probab=21.25 E-value=1.9e+02 Score=23.78 Aligned_cols=41 Identities=7% Similarity=0.250 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccc
Q 016972 242 QSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKS 290 (379)
Q Consensus 242 ~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~ 290 (379)
.+|+++| .+++ .+....+.+|+++.++...++-+|+.....
T Consensus 54 ~~~l~~l---l~~L-----~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~ 94 (118)
T PF14106_consen 54 EDHLEEL---LDRL-----EPKREIIKELKEKYNLEIQFFCYFSSISGG 94 (118)
T ss_pred HHHHHHH---HHHH-----cccHHHHHHHHHhcCcceEEEEEEEecCCC
Confidence 4555554 4555 578889999999999998889899876554
No 302
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=21.21 E-value=17 Score=30.92 Aligned_cols=10 Identities=50% Similarity=0.906 Sum_probs=7.6
Q ss_pred eeeeeccccc
Q 016972 280 VLKVWMHNNK 289 (379)
Q Consensus 280 V~KVWfhNnK 289 (379)
-+||||||-.
T Consensus 32 dvkvwmqnle 41 (106)
T PF11516_consen 32 DVKVWMQNLE 41 (106)
T ss_dssp HHHHHHHHHH
T ss_pred cHHHHHHHHH
Confidence 4689999854
No 303
>PHA00675 hypothetical protein
Probab=21.02 E-value=1.3e+02 Score=25.27 Aligned_cols=43 Identities=12% Similarity=0.160 Sum_probs=35.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeee
Q 016972 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKV 283 (379)
Q Consensus 233 kKR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KV 283 (379)
.+-...|+|..|-+.++..-|+.| .-..++|.++||++..|..
T Consensus 16 e~h~~AKLt~~qV~~IR~l~~r~G--------~s~~~IA~~fGVsrstV~~ 58 (78)
T PHA00675 16 EDHPNAKLTDAEVERIRELHEVEG--------MSYAVLAEKFEQSKGAIAK 58 (78)
T ss_pred CCCCCcccCHHHHHHHHHHHHhcC--------ccHHHHHHHhCCCHHHHHH
Confidence 356778999999999999988776 1456899999999988753
No 304
>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=20.83 E-value=20 Score=33.28 Aligned_cols=53 Identities=11% Similarity=0.131 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 016972 238 TKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWMHNNKSTFAKR 295 (379)
Q Consensus 238 TkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWfhNnK~k~~k~ 295 (379)
..+++.|++.+.-.+- +..-++-..+++|+.+||++.+|+++++--|.++++.
T Consensus 177 ~~Lp~~~R~ii~L~~~-----l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 177 AKLNDREKKIMELRFG-----LVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred HhCCHHHHHHHHHHHc-----cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567778877775431 0011223568999999999999999998877777654
No 305
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=20.46 E-value=1.8e+02 Score=23.56 Aligned_cols=46 Identities=7% Similarity=0.113 Sum_probs=35.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCccCCCCCHHHHHHHHHHhCCCCceeeeec
Q 016972 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEVGVDRTVLKVWM 285 (379)
Q Consensus 234 KR~RTkFT~EQkekM~~faEk~GWRIqk~d~~~vq~fc~eiGv~r~V~KVWf 285 (379)
+.++..++.+++.. .++|.-...+...+.++|+++|++-+++++=+
T Consensus 22 ~~~g~~~~~~~l~~------~~~~~~~~~~~~~l~~~a~~~Gl~~~~~~~~~ 67 (127)
T cd02419 22 SYHGHHVDLASLRQ------RFPVSLKGATLADLIDIAQQLGLSTRALRLDL 67 (127)
T ss_pred HHcCCCCCHHHHHH------HcCCCCCCcCHHHHHHHHHHCCCceeEEEccH
Confidence 56777888888764 34566566888999999999999999988643
No 306
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=20.03 E-value=86 Score=23.57 Aligned_cols=21 Identities=14% Similarity=0.411 Sum_probs=16.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHh
Q 016972 235 RFRTKFSQSQKEKMFEFAERV 255 (379)
Q Consensus 235 R~RTkFT~EQkekM~~faEk~ 255 (379)
.+...||.++++.|.+|++.-
T Consensus 12 ~y~~~ft~~El~~i~~FY~Sp 32 (64)
T PF09832_consen 12 IYAEHFTEEELDAILAFYESP 32 (64)
T ss_dssp HHHHHS-HHHHHHHHHHHHSH
T ss_pred HHHHHCCHHHHHHHHHHHCCH
Confidence 456789999999999998863
Done!