Query 046396
Match_columns 314
No_of_seqs 261 out of 1219
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 11:40:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046396.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046396hhsearch_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 6.5E-37 1.4E-41 221.9 3.3 52 49-102 1-53 (53)
2 PF04770 ZF-HD_dimer: ZF-HD pr 100.0 8.4E-37 1.8E-41 228.0 3.9 57 46-104 2-59 (60)
3 TIGR01565 homeo_ZF_HD homeobox 99.8 2.2E-21 4.8E-26 145.2 6.5 58 204-261 1-58 (58)
4 KOG0484 Transcription factor P 99.7 2.9E-18 6.2E-23 142.3 0.7 69 199-271 12-80 (125)
5 KOG0843 Transcription factor E 99.7 2.2E-17 4.7E-22 147.9 2.9 65 202-270 100-164 (197)
6 KOG0494 Transcription factor C 99.7 3.5E-17 7.7E-22 153.6 4.3 66 200-269 137-202 (332)
7 KOG2251 Homeobox transcription 99.7 6.4E-17 1.4E-21 148.5 4.4 67 199-269 32-98 (228)
8 KOG0485 Transcription factor N 99.6 1.4E-16 3.1E-21 146.5 4.5 74 198-275 98-171 (268)
9 KOG0489 Transcription factor z 99.6 1.7E-16 3.7E-21 148.7 1.1 69 201-273 156-224 (261)
10 KOG0488 Transcription factor B 99.6 1.5E-15 3.3E-20 145.9 3.1 67 199-269 167-233 (309)
11 PF00046 Homeobox: Homeobox do 99.5 1.2E-15 2.6E-20 110.5 1.4 57 205-265 1-57 (57)
12 KOG0844 Transcription factor E 99.5 2.5E-15 5.4E-20 143.9 3.1 64 202-269 179-242 (408)
13 KOG0842 Transcription factor t 99.5 6.8E-15 1.5E-19 141.2 5.1 72 199-274 148-219 (307)
14 KOG0493 Transcription factor E 99.5 5.1E-15 1.1E-19 139.3 2.8 59 205-267 247-305 (342)
15 KOG0850 Transcription factor D 99.5 1.1E-14 2.4E-19 134.7 4.4 65 202-270 120-184 (245)
16 KOG4577 Transcription factor L 99.4 3.2E-14 6.9E-19 135.5 2.9 63 202-268 165-227 (383)
17 KOG0487 Transcription factor A 99.4 1.2E-13 2.5E-18 132.9 6.6 67 198-268 229-295 (308)
18 KOG0492 Transcription factor M 99.4 7E-14 1.5E-18 128.0 3.1 66 203-272 143-208 (246)
19 smart00389 HOX Homeodomain. DN 99.4 3.5E-13 7.5E-18 96.5 3.5 56 205-264 1-56 (56)
20 KOG0486 Transcription factor P 99.4 2.7E-13 5.7E-18 130.2 3.0 66 202-271 110-175 (351)
21 cd00086 homeodomain Homeodomai 99.3 4.4E-13 9.6E-18 96.4 3.1 58 205-266 1-58 (59)
22 KOG3802 Transcription factor O 99.3 2.1E-12 4.5E-17 127.2 6.1 63 202-268 292-354 (398)
23 KOG0848 Transcription factor C 99.3 3.7E-13 8E-18 127.1 0.4 67 200-270 195-261 (317)
24 KOG0490 Transcription factor, 99.3 1.2E-12 2.7E-17 116.7 2.5 64 201-268 57-120 (235)
25 COG5576 Homeodomain-containing 99.2 5.7E-12 1.2E-16 111.0 4.0 67 202-272 49-115 (156)
26 KOG0483 Transcription factor H 99.2 3.6E-12 7.8E-17 116.2 2.6 57 210-270 56-112 (198)
27 KOG0847 Transcription factor, 99.2 5.2E-12 1.1E-16 116.8 2.6 69 202-274 165-233 (288)
28 KOG0491 Transcription factor B 99.2 1.8E-12 3.9E-17 115.4 -0.9 66 202-271 98-163 (194)
29 KOG0849 Transcription factor P 99.0 8.1E-11 1.8E-15 115.2 2.7 66 199-268 171-236 (354)
30 KOG1168 Transcription factor A 98.9 5.5E-10 1.2E-14 107.0 2.2 63 201-267 306-368 (385)
31 KOG0490 Transcription factor, 98.3 3.5E-07 7.5E-12 81.7 2.0 65 200-268 149-213 (235)
32 KOG1146 Homeobox protein [Gene 98.1 2.1E-06 4.6E-11 95.0 4.4 64 201-268 900-963 (1406)
33 KOG2252 CCAAT displacement pro 98.0 4.4E-06 9.6E-11 85.8 3.9 61 203-267 419-479 (558)
34 KOG0775 Transcription factor S 97.6 7E-05 1.5E-09 71.8 4.9 51 213-267 185-235 (304)
35 KOG0774 Transcription factor P 97.2 0.00052 1.1E-08 65.8 5.5 62 205-267 189-250 (334)
36 PF05920 Homeobox_KN: Homeobox 97.2 6.4E-05 1.4E-09 52.5 -0.9 35 228-262 6-40 (40)
37 PF04218 CENP-B_N: CENP-B N-te 94.9 0.024 5.1E-07 41.5 2.8 47 205-260 1-47 (53)
38 KOG3623 Homeobox transcription 94.2 0.023 4.9E-07 61.1 1.8 54 211-269 564-617 (1007)
39 KOG0773 Transcription factor M 94.1 0.058 1.3E-06 52.2 4.2 66 202-268 237-302 (342)
40 PF11569 Homez: Homeodomain le 93.8 0.019 4.1E-07 43.3 0.2 41 216-260 10-50 (56)
41 PF01527 HTH_Tnp_1: Transposas 88.8 0.19 4.1E-06 37.7 1.0 45 206-258 2-46 (76)
42 cd00569 HTH_Hin_like Helix-tur 77.2 2.7 5.8E-05 24.9 2.5 39 209-256 4-42 (42)
43 PF04967 HTH_10: HTH DNA bindi 76.8 2 4.4E-05 31.8 2.2 41 211-253 1-41 (53)
44 KOG3623 Homeobox transcription 74.3 5 0.00011 44.0 5.1 71 202-276 624-694 (1007)
45 KOG1146 Homeobox protein [Gene 62.9 7 0.00015 45.2 3.5 67 197-267 698-764 (1406)
46 cd06171 Sigma70_r4 Sigma70, re 60.7 1.5 3.2E-05 29.2 -1.4 44 210-262 10-53 (55)
47 COG2963 Transposase and inacti 58.4 12 0.00026 30.4 3.4 42 208-257 5-47 (116)
48 PRK06424 transcription factor; 56.7 18 0.00038 31.9 4.3 53 204-261 68-123 (144)
49 PF02796 HTH_7: Helix-turn-hel 56.5 4 8.6E-05 28.5 0.2 39 209-256 4-42 (45)
50 PF08281 Sigma70_r4_2: Sigma-7 55.5 1.8 3.9E-05 30.5 -1.7 41 211-260 11-51 (54)
51 PF09607 BrkDBD: Brinker DNA-b 55.4 8 0.00017 29.5 1.7 45 208-257 3-47 (58)
52 COG3413 Predicted DNA binding 51.1 11 0.00025 34.1 2.3 49 210-262 155-203 (215)
53 PRK09413 IS2 repressor TnpA; R 49.1 18 0.0004 30.1 3.1 42 208-257 10-51 (121)
54 PRK03975 tfx putative transcri 48.8 5.7 0.00012 34.9 -0.0 49 209-267 5-53 (141)
55 PHA02893 hypothetical protein; 47.8 7.4 0.00016 31.8 0.5 9 85-93 69-77 (88)
56 TIGR03879 near_KaiC_dom probab 47.6 3.6 7.8E-05 32.5 -1.3 29 232-260 29-57 (73)
57 PRK02220 4-oxalocrotonate taut 46.8 34 0.00073 24.5 3.8 33 212-258 13-45 (61)
58 PRK09646 RNA polymerase sigma 46.7 2.8 6.1E-05 36.8 -2.3 49 210-267 142-190 (194)
59 PRK12519 RNA polymerase sigma 44.6 3.8 8.3E-05 35.6 -1.8 35 232-266 154-188 (194)
60 smart00421 HTH_LUXR helix_turn 44.3 8.9 0.00019 25.9 0.4 45 210-264 3-47 (58)
61 COG2944 Predicted transcriptio 43.4 12 0.00025 31.6 1.0 40 211-261 44-83 (104)
62 PF00196 GerE: Bacterial regul 42.8 6.6 0.00014 28.3 -0.5 47 210-266 3-49 (58)
63 PRK10072 putative transcriptio 42.7 12 0.00026 30.8 1.0 41 210-261 32-72 (96)
64 PRK12512 RNA polymerase sigma 42.0 3.4 7.4E-05 35.7 -2.5 34 236-269 148-181 (184)
65 PRK06759 RNA polymerase factor 41.9 4 8.7E-05 33.9 -2.0 30 236-265 123-152 (154)
66 PRK12526 RNA polymerase sigma 40.2 3.7 8.1E-05 36.6 -2.6 32 236-267 170-201 (206)
67 TIGR02989 Sig-70_gvs1 RNA poly 40.1 4.5 9.7E-05 33.7 -2.0 47 210-265 111-157 (159)
68 PF13936 HTH_38: Helix-turn-he 39.8 5.5 0.00012 27.8 -1.2 39 209-256 3-41 (44)
69 TIGR02939 RpoE_Sigma70 RNA pol 39.8 4.3 9.4E-05 34.8 -2.2 33 234-266 153-185 (190)
70 PF13698 DUF4156: Domain of un 39.3 13 0.00028 30.2 0.7 18 51-68 51-68 (93)
71 PF04545 Sigma70_r4: Sigma-70, 39.1 7.8 0.00017 27.0 -0.5 44 210-262 4-47 (50)
72 PRK04217 hypothetical protein; 39.1 12 0.00025 31.7 0.4 49 210-267 42-90 (110)
73 PRK09652 RNA polymerase sigma 39.1 4 8.6E-05 34.4 -2.5 48 210-266 128-175 (182)
74 PRK09644 RNA polymerase sigma 38.9 3.9 8.5E-05 34.7 -2.5 31 237-267 126-156 (165)
75 PF10668 Phage_terminase: Phag 37.5 9.2 0.0002 29.2 -0.4 20 237-256 24-43 (60)
76 PRK09648 RNA polymerase sigma 37.4 4.1 8.9E-05 35.4 -2.7 47 210-265 139-185 (189)
77 PRK02289 4-oxalocrotonate taut 36.2 69 0.0015 23.3 4.1 33 212-258 13-45 (60)
78 PRK12530 RNA polymerase sigma 36.1 4.5 9.8E-05 35.5 -2.7 31 236-266 151-181 (189)
79 PF13551 HTH_29: Winged helix- 35.8 38 0.00081 26.5 2.8 21 205-225 52-72 (112)
80 PRK12541 RNA polymerase sigma 35.8 5.2 0.00011 33.8 -2.3 31 236-266 129-159 (161)
81 PRK12546 RNA polymerase sigma 35.7 5.5 0.00012 35.3 -2.2 33 235-267 129-161 (188)
82 TIGR02950 SigM_subfam RNA poly 35.7 11 0.00024 31.2 -0.3 51 215-265 95-151 (154)
83 PRK12514 RNA polymerase sigma 35.4 5.1 0.00011 34.4 -2.4 30 237-266 147-176 (179)
84 PRK12537 RNA polymerase sigma 34.5 6.2 0.00013 34.2 -2.1 29 237-265 151-179 (182)
85 cd04761 HTH_MerR-SF Helix-Turn 34.4 11 0.00024 25.6 -0.4 23 238-260 3-25 (49)
86 PRK09642 RNA polymerase sigma 33.9 5 0.00011 33.7 -2.6 31 237-267 124-154 (160)
87 cd04762 HTH_MerR-trunc Helix-T 33.9 13 0.00029 24.5 -0.1 25 238-262 3-27 (49)
88 TIGR02948 SigW_bacill RNA poly 33.4 6.6 0.00014 33.6 -2.0 32 235-266 152-183 (187)
89 TIGR02999 Sig-70_X6 RNA polyme 33.4 5.7 0.00012 34.1 -2.4 30 236-265 151-180 (183)
90 TIGR02937 sigma70-ECF RNA poly 33.1 7.9 0.00017 30.7 -1.5 47 210-265 110-156 (158)
91 PF01381 HTH_3: Helix-turn-hel 32.9 18 0.0004 25.1 0.5 22 239-260 13-34 (55)
92 PRK12513 RNA polymerase sigma 32.7 5.9 0.00013 34.5 -2.5 36 232-267 152-187 (194)
93 PF13518 HTH_28: Helix-turn-he 32.5 14 0.0003 25.3 -0.1 25 237-261 14-38 (52)
94 PRK12540 RNA polymerase sigma 32.1 9.6 0.00021 33.4 -1.2 36 234-269 126-161 (182)
95 PF01361 Tautomerase: Tautomer 31.7 81 0.0017 22.6 3.8 33 212-258 12-44 (60)
96 PRK12539 RNA polymerase sigma 31.3 8.3 0.00018 33.5 -1.8 32 235-266 147-178 (184)
97 PRK09649 RNA polymerase sigma 31.0 6.8 0.00015 34.3 -2.4 30 236-265 147-176 (185)
98 PF13443 HTH_26: Cro/C1-type H 31.0 13 0.00028 26.8 -0.6 27 237-263 12-38 (63)
99 PRK00118 putative DNA-binding 30.9 13 0.00027 31.2 -0.7 47 210-265 17-63 (104)
100 KOG1924 RhoA GTPase effector D 30.7 1.1E+02 0.0024 34.4 6.1 6 240-245 657-662 (1102)
101 PRK09047 RNA polymerase factor 30.5 5.9 0.00013 33.1 -2.8 48 210-266 106-153 (161)
102 TIGR02947 SigH_actino RNA poly 30.5 7.3 0.00016 34.0 -2.3 37 231-267 143-179 (193)
103 PRK12516 RNA polymerase sigma 30.5 7.5 0.00016 34.3 -2.2 33 236-268 133-165 (187)
104 TIGR02959 SigZ RNA polymerase 29.8 6.8 0.00015 33.7 -2.6 49 210-267 100-148 (170)
105 PRK06811 RNA polymerase factor 29.6 8 0.00017 33.8 -2.2 49 210-267 131-179 (189)
106 TIGR02985 Sig70_bacteroi1 RNA 29.4 6.6 0.00014 32.3 -2.6 29 237-265 131-159 (161)
107 PRK12547 RNA polymerase sigma 29.4 6.7 0.00015 33.4 -2.6 31 235-265 128-158 (164)
108 PRK05657 RNA polymerase sigma 29.3 17 0.00036 35.5 -0.2 53 210-267 262-314 (325)
109 PRK11924 RNA polymerase sigma 29.1 7.7 0.00017 32.5 -2.3 30 236-265 142-171 (179)
110 PRK00745 4-oxalocrotonate taut 29.0 93 0.002 22.3 3.7 33 212-258 13-45 (62)
111 TIGR02983 SigE-fam_strep RNA p 29.0 8.4 0.00018 32.3 -2.1 31 237-267 128-158 (162)
112 PRK01271 4-oxalocrotonate taut 28.6 1.1E+02 0.0023 24.2 4.2 33 212-258 14-46 (76)
113 PRK12524 RNA polymerase sigma 28.5 7.7 0.00017 34.1 -2.5 30 237-266 154-183 (196)
114 PRK01964 4-oxalocrotonate taut 28.5 99 0.0021 22.5 3.9 33 212-258 13-45 (64)
115 PRK09726 antitoxin HipB; Provi 28.0 61 0.0013 25.4 2.8 43 210-260 7-50 (88)
116 PRK05602 RNA polymerase sigma 27.9 7.3 0.00016 33.7 -2.7 31 237-267 146-176 (186)
117 PRK10403 transcriptional regul 27.9 22 0.00047 29.6 0.3 49 209-267 152-200 (215)
118 PRK12545 RNA polymerase sigma 27.9 8.6 0.00019 34.1 -2.3 33 235-267 155-187 (201)
119 PRK09651 RNA polymerase sigma 27.7 10 0.00022 32.6 -1.8 33 232-264 132-164 (172)
120 PRK09639 RNA polymerase sigma 27.6 9.2 0.0002 32.2 -2.1 47 210-266 112-158 (166)
121 TIGR00270 conserved hypothetic 27.5 16 0.00034 32.4 -0.7 25 237-261 84-108 (154)
122 cd00491 4Oxalocrotonate_Tautom 27.4 1.3E+02 0.0027 21.1 4.1 34 212-259 12-45 (58)
123 PRK12532 RNA polymerase sigma 27.4 8.6 0.00019 33.6 -2.4 32 236-267 153-184 (195)
124 PF13411 MerR_1: MerR HTH fami 27.3 17 0.00037 26.5 -0.5 22 238-259 3-24 (69)
125 KOG2767 Translation initiation 27.2 20 0.00043 36.4 -0.2 15 85-99 118-132 (400)
126 PRK12543 RNA polymerase sigma 27.1 8.8 0.00019 33.2 -2.3 32 236-267 134-165 (179)
127 PRK12529 RNA polymerase sigma 26.5 8 0.00017 33.5 -2.7 47 210-265 127-173 (178)
128 PRK12535 RNA polymerase sigma 26.3 12 0.00026 33.3 -1.7 36 236-271 150-185 (196)
129 PRK12520 RNA polymerase sigma 26.3 9 0.00019 33.4 -2.5 32 236-267 148-179 (191)
130 PRK08301 sporulation sigma fac 26.2 18 0.0004 32.7 -0.5 52 210-266 178-229 (234)
131 PRK09637 RNA polymerase sigma 26.2 11 0.00023 33.1 -2.0 31 236-266 123-153 (181)
132 PF05077 DUF678: Protein of un 26.1 24 0.00052 28.1 0.2 9 85-93 57-65 (74)
133 PRK12533 RNA polymerase sigma 26.1 9.6 0.00021 34.8 -2.4 34 234-267 149-182 (216)
134 PRK12536 RNA polymerase sigma 25.8 8.4 0.00018 33.4 -2.7 33 234-266 144-176 (181)
135 TIGR03070 couple_hipB transcri 25.6 51 0.0011 22.5 1.8 23 238-260 18-40 (58)
136 PRK12515 RNA polymerase sigma 25.6 8.6 0.00019 33.5 -2.7 49 210-267 131-179 (189)
137 PF06252 DUF1018: Protein of u 25.5 73 0.0016 26.5 3.0 26 207-232 18-43 (119)
138 PRK09645 RNA polymerase sigma 25.3 10 0.00022 32.3 -2.2 30 237-266 136-165 (173)
139 PRK12538 RNA polymerase sigma 25.3 9.3 0.0002 35.3 -2.7 33 235-267 187-219 (233)
140 PF11516 DUF3220: Protein of u 24.7 13 0.00028 30.4 -1.5 10 251-260 32-41 (106)
141 PRK13558 bacterio-opsin activa 24.5 51 0.0011 34.2 2.3 42 209-252 606-647 (665)
142 cd06170 LuxR_C_like C-terminal 24.5 29 0.00062 23.6 0.3 22 237-258 17-38 (57)
143 PRK13919 putative RNA polymera 24.5 10 0.00023 32.6 -2.4 30 237-266 153-182 (186)
144 PRK12511 RNA polymerase sigma 24.4 11 0.00024 33.1 -2.3 33 235-267 127-159 (182)
145 PRK06986 fliA flagellar biosyn 24.1 14 0.00031 33.6 -1.7 34 233-266 198-231 (236)
146 PRK12518 RNA polymerase sigma 24.0 8 0.00017 32.9 -3.1 37 231-267 132-168 (175)
147 PRK12522 RNA polymerase sigma 23.8 12 0.00026 32.0 -2.2 33 234-266 134-166 (173)
148 PTZ00397 macrophage migration 23.7 1.3E+02 0.0029 24.5 4.2 36 212-261 70-105 (116)
149 TIGR02952 Sig70_famx2 RNA poly 23.6 12 0.00025 31.5 -2.2 29 237-265 140-168 (170)
150 PF13384 HTH_23: Homeodomain-l 23.2 21 0.00045 24.6 -0.6 23 237-259 19-41 (50)
151 PF06056 Terminase_5: Putative 23.1 30 0.00065 25.8 0.2 36 220-266 7-42 (58)
152 PRK09638 RNA polymerase sigma 22.8 12 0.00026 31.8 -2.3 35 232-266 139-173 (176)
153 PRK12542 RNA polymerase sigma 22.7 11 0.00024 32.6 -2.6 30 237-266 140-169 (185)
154 TIGR00013 taut 4-oxalocrotonat 22.4 1.7E+02 0.0037 20.9 4.1 34 212-259 13-46 (63)
155 PRK11511 DNA-binding transcrip 22.4 42 0.0009 28.0 1.0 42 213-259 8-49 (127)
156 PRK07037 extracytoplasmic-func 22.3 10 0.00022 31.8 -2.7 30 237-266 127-156 (163)
157 PF04936 DUF658: Protein of un 22.2 26 0.00057 32.1 -0.3 36 236-271 15-50 (186)
158 PRK10100 DNA-binding transcrip 22.0 39 0.00084 30.9 0.7 48 210-267 155-202 (216)
159 PRK11923 algU RNA polymerase s 21.9 13 0.00028 32.3 -2.3 34 233-266 152-185 (193)
160 TIGR00721 tfx DNA-binding prot 21.8 33 0.00071 30.0 0.2 48 208-265 4-51 (137)
161 PHA02535 P terminase ATPase su 21.6 75 0.0016 34.1 2.8 46 209-265 1-46 (581)
162 PRK12523 RNA polymerase sigma 21.4 12 0.00027 31.9 -2.5 32 235-266 135-166 (172)
163 PRK06930 positive control sigm 21.1 12 0.00026 33.4 -2.8 49 210-267 114-162 (170)
164 cd04763 HTH_MlrA-like Helix-Tu 21.1 26 0.00056 25.8 -0.5 21 238-258 3-23 (68)
165 PRK09480 slmA division inhibit 20.8 65 0.0014 27.4 1.9 31 230-261 26-56 (194)
166 PRK09641 RNA polymerase sigma 20.8 13 0.00028 31.9 -2.6 33 234-266 151-183 (187)
167 PRK09643 RNA polymerase sigma 20.3 16 0.00034 32.2 -2.2 32 236-267 151-182 (192)
168 PF01873 eIF-5_eIF-2B: Domain 20.1 38 0.00083 29.1 0.3 12 84-95 113-124 (125)
169 PRK10360 DNA-binding transcrip 20.1 40 0.00086 28.1 0.4 47 210-266 137-183 (196)
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=100.00 E-value=6.5e-37 Score=221.89 Aligned_cols=52 Identities=79% Similarity=1.495 Sum_probs=47.9
Q ss_pred ehHHHhhhhhhccCCccccCcccccc-CCCCCCCCcCCccccccCCccccccCCC
Q 046396 49 SYKECLKNHAASLGGHALDGCGEFMP-SPTATSNDPASLNCAACGCHRNFHRRDP 102 (314)
Q Consensus 49 ~y~ec~~nha~~~g~~~~dgc~ef~~-~~~~g~~d~~~l~caac~chrnfhr~~~ 102 (314)
+||||||||||+|||||||||||||| ++++|+ +++|+||||||||||||||+
T Consensus 1 ~Y~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~--~~al~CaACgCHRnFHRre~ 53 (53)
T TIGR01566 1 LYKECLKNHAASIGGHALDGCGEFMPSSGEEGD--PESLTCAACGCHRNFHRKEP 53 (53)
T ss_pred CHHHHHHhhHHHhCCcccccccccccCCCCCCC--CcceeeeecCcccccccCCC
Confidence 69999999999999999999999999 666654 56999999999999999984
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=100.00 E-value=8.4e-37 Score=228.03 Aligned_cols=57 Identities=70% Similarity=1.328 Sum_probs=52.8
Q ss_pred ceeehHHHhhhhhhccCCccccCccccccC-CCCCCCCcCCccccccCCccccccCCCCC
Q 046396 46 MVVSYKECLKNHAASLGGHALDGCGEFMPS-PTATSNDPASLNCAACGCHRNFHRRDPYE 104 (314)
Q Consensus 46 ~~~~y~ec~~nha~~~g~~~~dgc~ef~~~-~~~g~~d~~~l~caac~chrnfhr~~~~~ 104 (314)
.+|+||||||||||+|||||||||+||||+ +++|+ +++|+||||||||||||||+++
T Consensus 2 ~~v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~--~~al~CaACgCHRnFHRre~~~ 59 (60)
T PF04770_consen 2 KVVRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGT--PEALKCAACGCHRNFHRREVEG 59 (60)
T ss_pred CceeHHHHHhhHhHhhCCcccccccccccCCCCCCC--cccceecccCcchhcccCCcCC
Confidence 579999999999999999999999999999 77765 6699999999999999999865
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=99.84 E-value=2.2e-21 Score=145.16 Aligned_cols=58 Identities=64% Similarity=1.130 Sum_probs=56.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccc
Q 046396 204 KKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKN 261 (314)
Q Consensus 204 kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRa 261 (314)
+||+||+||++|++.|+.+|+++|||++.|+..+|++||.+|||++.||||||||+|.
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 5899999999999999999999999999999999999999999999999999999974
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.69 E-value=2.9e-18 Score=142.33 Aligned_cols=69 Identities=14% Similarity=0.332 Sum_probs=64.2
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccccccc
Q 046396 199 SSDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSI 271 (314)
Q Consensus 199 ~~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~ 271 (314)
...++.||-||.||..||..||..|.. .+|||+..|++||.+|.|++..|||||||||+|+||+++...
T Consensus 12 ~ekrKQRRIRTTFTS~QLkELErvF~E----THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~ 80 (125)
T KOG0484|consen 12 TEKRKQRRIRTTFTSAQLKELERVFAE----THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAI 80 (125)
T ss_pred hHHHHhhhhhhhhhHHHHHHHHHHHHh----hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHH
Confidence 345678999999999999999999999 999999999999999999999999999999999999986544
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.67 E-value=2.2e-17 Score=147.92 Aligned_cols=65 Identities=26% Similarity=0.303 Sum_probs=62.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccc
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRS 270 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~ 270 (314)
.+.||.||.||.+||.+||.+|+. ++|....+|++||+.|+|++.+|||||||||.|.||.++..
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~----~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEG----NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhc----CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 378999999999999999999999 99999999999999999999999999999999999988764
No 6
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.66 E-value=3.5e-17 Score=153.59 Aligned_cols=66 Identities=15% Similarity=0.270 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccccc
Q 046396 200 SDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQR 269 (314)
Q Consensus 200 ~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~ 269 (314)
...++|++||.||..|++.||..|.. .+|||...|+.|+.++.|++.+|||||||||+||||+++.
T Consensus 137 kk~kRRh~RTiFT~~Qle~LEkaFke----aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 137 KKKKRRHFRTIFTSYQLEELEKAFKE----AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cccccccccchhhHHHHHHHHHHHhh----ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 33445556999999999999999999 9999999999999999999999999999999999999854
No 7
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.65 E-value=6.4e-17 Score=148.53 Aligned_cols=67 Identities=19% Similarity=0.404 Sum_probs=63.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccccc
Q 046396 199 SSDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQR 269 (314)
Q Consensus 199 ~~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~ 269 (314)
.++++.||-||.||.+|++.||.+|.+ .+|||...|++||.+|+|++.+|||||.|||+|+|++++.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~k----TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAK----TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHh----hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 456888999999999999999999999 9999999999999999999999999999999999998865
No 8
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.63 E-value=1.4e-16 Score=146.46 Aligned_cols=74 Identities=19% Similarity=0.290 Sum_probs=67.6
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccccCCCC
Q 046396 198 NSSDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSINNKN 275 (314)
Q Consensus 198 ~~~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~~~~~ 275 (314)
+-+..+|||.||.|+..|+.+||..||. .+|.+..+|..||++|.|++.||||||||||.||||+-..+..+.+
T Consensus 98 ~~g~~RKKktRTvFSraQV~qLEs~Fe~----krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~s 171 (268)
T KOG0485|consen 98 GLGDDRKKKTRTVFSRAQVFQLESTFEL----KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAAS 171 (268)
T ss_pred cccccccccchhhhhHHHHHHHHHHHHH----HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhhh
Confidence 3456789999999999999999999999 9999999999999999999999999999999999999877665443
No 9
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.60 E-value=1.7e-16 Score=148.75 Aligned_cols=69 Identities=16% Similarity=0.235 Sum_probs=63.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccccCC
Q 046396 201 DNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSINN 273 (314)
Q Consensus 201 ~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~~~ 273 (314)
....||.||.||..|+..||..|.- ++|.....|.|||..|.|+|++|||||||||+||||..+.....
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhf----N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHF----NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhcc----ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 3457999999999999999999999 99999999999999999999999999999999999988665544
No 10
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.55 E-value=1.5e-15 Score=145.95 Aligned_cols=67 Identities=18% Similarity=0.310 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccccc
Q 046396 199 SSDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQR 269 (314)
Q Consensus 199 ~~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~ 269 (314)
..+.++|+.||.||..||..||.-|++ ..|....+|.+||+.|||+..|||+||||||+||||+...
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~----QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEK----QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHH----hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 344667778999999999999999999 9999999999999999999999999999999999998755
No 11
>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=99.54 E-value=1.2e-15 Score=110.50 Aligned_cols=57 Identities=25% Similarity=0.499 Sum_probs=55.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 205 KRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 205 KR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
||.|+.||.+|+..|+.+|+. ++||+..++++||.++||+..+|++||+|+|+++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE----NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH----SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH----hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 689999999999999999999 999999999999999999999999999999999875
No 12
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.54 E-value=2.5e-15 Score=143.86 Aligned_cols=64 Identities=22% Similarity=0.335 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccccc
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQR 269 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~ 269 (314)
..-||.||.||.|||.+||..|-| ..|.....|.|||.+|+|++.+|||||||||.|.|||...
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyr----ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYR----ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHH----hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 345899999999999999999999 9999999999999999999999999999999999998744
No 13
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.52 E-value=6.8e-15 Score=141.24 Aligned_cols=72 Identities=14% Similarity=0.255 Sum_probs=65.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccccCCC
Q 046396 199 SSDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSINNK 274 (314)
Q Consensus 199 ~~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~~~~ 274 (314)
.+.++|||.|--||+.|..+||+-|.. .+|....||++||..|.|++.||||||||||.|.||+++......
T Consensus 148 t~~~~kRKrRVLFSqAQV~ELERRFrq----QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 148 TGKRKKRKRRVLFSQAQVYELERRFRQ----QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccccccchhHHHHHHHHHHh----hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 346678888899999999999999999 999999999999999999999999999999999999987665433
No 14
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.51 E-value=5.1e-15 Score=139.34 Aligned_cols=59 Identities=25% Similarity=0.457 Sum_probs=56.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 205 KRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 205 KR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
||.||.||.|||++|+..|.. ++|..+..|++|+.||||.+.+|||||||+|+|.||..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~e----nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQE----NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhh----hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 688999999999999999999 99999999999999999999999999999999998864
No 15
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.50 E-value=1.1e-14 Score=134.69 Aligned_cols=65 Identities=11% Similarity=0.268 Sum_probs=60.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccc
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRS 270 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~ 270 (314)
.+-|+.||.|+.-||+.|.+-|++ .+|.-..+|.+||..|||+..+|||||||||.|+||..+..
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQk----TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQ----TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhh----cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence 344567999999999999999999 99999999999999999999999999999999999988733
No 16
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.44 E-value=3.2e-14 Score=135.51 Aligned_cols=63 Identities=25% Similarity=0.442 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccc
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQ 268 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~ 268 (314)
...||.||++|+.||+.|+..|.. .++|...+|++|+.++||..+||||||||||+|.||-++
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~----SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNT----SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcC----CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 457999999999999999999999 999999999999999999999999999999999988654
No 17
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.44 E-value=1.2e-13 Score=132.87 Aligned_cols=67 Identities=13% Similarity=0.231 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccc
Q 046396 198 NSSDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQ 268 (314)
Q Consensus 198 ~~~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~ 268 (314)
....++.|++|--+|..|+.+||..|-- |.|+..+.|-+|++.|+|+++||||||||||.|.||..+
T Consensus 229 ~~~~~~~RKKRcPYTK~QtlELEkEFlf----N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 229 ASSARRGRKKRCPYTKHQTLELEKEFLF----NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccccccCCchHHHHHHHHHHHHH----HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 3444566778889999999999999999 999999999999999999999999999999999999875
No 18
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.42 E-value=7e-14 Score=128.03 Aligned_cols=66 Identities=17% Similarity=0.298 Sum_probs=60.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccccC
Q 046396 203 GKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSIN 272 (314)
Q Consensus 203 ~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~~ 272 (314)
..|+.||-||..||..||+-|.. .||.++.+|.+|+..|.|++.+|||||||||+|.||-+..+..
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfre----kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E 208 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFRE----KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE 208 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhH----hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence 34678999999999999999999 9999999999999999999999999999999999998765553
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.37 E-value=3.5e-13 Score=96.54 Aligned_cols=56 Identities=27% Similarity=0.455 Sum_probs=53.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccc
Q 046396 205 KRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASG 264 (314)
Q Consensus 205 KR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~k 264 (314)
++.|+.|+.+|+..|+.+|+. ++||+..++++|+.++||+..+|+.||+|+|++.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~----~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQK----NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 467889999999999999999 99999999999999999999999999999998864
No 20
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.36 E-value=2.7e-13 Score=130.23 Aligned_cols=66 Identities=15% Similarity=0.331 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccccccc
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSI 271 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~ 271 (314)
.++||.||.||..|++.||..|.+ ++|||...|++||.-+.|++..|+|||.|||+||||+++...
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~r----NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQR----NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhh----ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 367889999999999999999999 999999999999999999999999999999999999985443
No 21
>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=99.35 E-value=4.4e-13 Score=96.36 Aligned_cols=58 Identities=28% Similarity=0.501 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 205 KRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 205 KR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
++.|+.|+.+|+..|+.+|+. ++||+..++++||.++||+..+|++||+|+|.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~----~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK----NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 467889999999999999999 9999999999999999999999999999999998864
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.31 E-value=2.1e-12 Score=127.20 Aligned_cols=63 Identities=13% Similarity=0.281 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccc
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQ 268 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~ 268 (314)
.+|||+||.|....+..||.+|.+ +++|+..++.+||.+|+|.+.||+|||.|||.|.||-..
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~----npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLK----NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 488999999999999999999999 999999999999999999999999999999999999876
No 23
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.30 E-value=3.7e-13 Score=127.09 Aligned_cols=67 Identities=15% Similarity=0.342 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccc
Q 046396 200 SDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRS 270 (314)
Q Consensus 200 ~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~ 270 (314)
..+.|-+.|-++|..|.-+||..|.- .+|+.+..+.|||.-|||+|++|||||||||+|.||..+..
T Consensus 195 KtRTkDKYRvVYTDhQRLELEKEfh~----SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 195 KTRTKDKYRVVYTDHQRLELEKEFHT----SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred eeecccceeEEecchhhhhhhhhhcc----ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 44556678889999999999999999 99999999999999999999999999999999999865443
No 24
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.28 E-value=1.2e-12 Score=116.72 Aligned_cols=64 Identities=16% Similarity=0.213 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccc
Q 046396 201 DNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQ 268 (314)
Q Consensus 201 ~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~ 268 (314)
..++||.||.|+..|++.|+..|++ .+|||...|+.|+..+.+++..|||||||+|+||+++++
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~----~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEK----VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcC----CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4578999999999999999999999 899999999999999999999999999999999999885
No 25
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.23 E-value=5.7e-12 Score=110.97 Aligned_cols=67 Identities=13% Similarity=0.175 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccccC
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSIN 272 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~~ 272 (314)
+..++.|++.|.+|+..|+..|+. ++||+...|.+|+..|+|+++.|||||||+|++.|++......
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i----~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~ 115 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEI----NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVE 115 (156)
T ss_pred CcCcccceechHHHHHHHHHHhcc----CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchh
Confidence 345666667799999999999999 9999999999999999999999999999999999998766443
No 26
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.23 E-value=3.6e-12 Score=116.15 Aligned_cols=57 Identities=21% Similarity=0.330 Sum_probs=53.6
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRS 270 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~ 270 (314)
+||.+|+..||..|+. ..+.....+..||++|||..++|+||||||||+||.++...
T Consensus 56 Rlt~eQ~~~LE~~F~~----~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 56 RLTSEQVKFLEKSFES----EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred cccHHHHHHhHHhhcc----ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence 5799999999999999 99999999999999999999999999999999999987543
No 27
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.21 E-value=5.2e-12 Score=116.84 Aligned_cols=69 Identities=19% Similarity=0.287 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccccCCC
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSINNK 274 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~~~~ 274 (314)
+++|-.|.+|+-.||..|+.-|+. .+|+-..+|.+||..+|+.+.+|||||||||+|||||...+....
T Consensus 165 G~rk~srPTf~g~qi~~le~~feq----tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasa 233 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQ----TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASA 233 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhh----hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhc
Confidence 567778999999999999999999 999999999999999999999999999999999999987766543
No 28
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.20 E-value=1.8e-12 Score=115.36 Aligned_cols=66 Identities=17% Similarity=0.300 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccccccc
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSI 271 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~ 271 (314)
.++++.||.|+..|+..|++-||+ .+|....+|.||+..|+|++.+||.||||||.|.||..+...
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~----QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFER----QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HHhhhhcccccCccccccHHHHhh----hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 345678999999999999999999 999999999999999999999999999999999999875544
No 29
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.04 E-value=8.1e-11 Score=115.18 Aligned_cols=66 Identities=21% Similarity=0.375 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccc
Q 046396 199 SSDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQ 268 (314)
Q Consensus 199 ~~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~ 268 (314)
....+.+|.||+|+++|++.|++.|++ .+||+...|++|+.+|++++..|+|||+|+|++++|...
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~r----t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQR----TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccccccchHHHHHHHhcC----CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 344566778999999999999999999 999999999999999999999999999999999999984
No 30
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.89 E-value=5.5e-10 Score=106.96 Aligned_cols=63 Identities=19% Similarity=0.378 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 201 DNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 201 ~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.+.|||+||.+-+-.++.||+||.. .++|+.+....+|.+|.|++.||+|||.|.|+|.||..
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFav----QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAV----QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhcc----CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 3468999999999999999999999 99999999999999999999999999999999998865
No 31
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.27 E-value=3.5e-07 Score=81.73 Aligned_cols=65 Identities=25% Similarity=0.473 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccc
Q 046396 200 SDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQ 268 (314)
Q Consensus 200 ~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~ 268 (314)
...+.++.||.|+..|+..|...|.. ..+|+...+++|+..+|+++.+|+|||||+|++.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRA----TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccC----CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34567889999999999999999999 999999999999999999999999999999999998765
No 32
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=98.11 E-value=2.1e-06 Score=94.96 Aligned_cols=64 Identities=19% Similarity=0.311 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccc
Q 046396 201 DNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQ 268 (314)
Q Consensus 201 ~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~ 268 (314)
...+|++||.|+..||..|+.+|+. ..++...+.+.|-.++++..++|+|||||.|+|.||...
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~----q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEA----QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhh----ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 3456889999999999999999999 888999999999999999999999999999999998876
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.00 E-value=4.4e-06 Score=85.78 Aligned_cols=61 Identities=16% Similarity=0.249 Sum_probs=55.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 203 GKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 203 ~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
..||.|.+||+.|++.|..+|+. +++|+....+.|+.+|+|...+|.-||.|-|.+.+-+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke----~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~~~ 479 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE----NKRPSREMQETISQQLNLELSTVINFFMNARRRSLDKK 479 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc----CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhccccc
Confidence 45788999999999999999999 99999999999999999999999999999888753333
No 34
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=97.61 E-value=7e-05 Score=71.77 Aligned_cols=51 Identities=6% Similarity=0.212 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 213 QEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 213 ~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
..-...|+++|.+ ++||...++.+||+.+||+..||--||.|||++.|-..
T Consensus 185 ekSR~~LrewY~~----~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 185 EKSRSLLREWYLQ----NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred HhhHHHHHHHHhc----CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence 3345689999999 99999999999999999999999999999999998443
No 35
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.22 E-value=0.00052 Score=65.78 Aligned_cols=62 Identities=11% Similarity=0.254 Sum_probs=56.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 205 KRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 205 KR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
||+|.-|+..--+.|..+|-. .-.++||++.+.++||++.+|+..+|--||-|.|-++||..
T Consensus 189 rRKRRNFsK~aTeiLneyF~~-h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYS-HLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHhhcccchhHHHHHHHHHHH-hcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 677889999999999999975 45588999999999999999999999999999999999864
No 36
>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=97.15 E-value=6.4e-05 Score=52.47 Aligned_cols=35 Identities=14% Similarity=0.371 Sum_probs=29.2
Q ss_pred CcCCCCCHHHHHHHHHHhCCCCCceeecccccccc
Q 046396 228 WKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNA 262 (314)
Q Consensus 228 Wr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK 262 (314)
+.++||+..++++||.++||+..+|..||-|.|.+
T Consensus 6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 45799999999999999999999999999998853
No 37
>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=94.92 E-value=0.024 Score=41.47 Aligned_cols=47 Identities=30% Similarity=0.412 Sum_probs=37.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccc
Q 046396 205 KRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNK 260 (314)
Q Consensus 205 KR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRR 260 (314)
||.|..+|-+|+-.+...++. .. ...++|.++||+..+|.-|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~----g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE----GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC----TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc----CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 688999999999999999998 43 577999999999999999998754
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.22 E-value=0.023 Score=61.10 Aligned_cols=54 Identities=13% Similarity=0.276 Sum_probs=47.5
Q ss_pred CCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccccc
Q 046396 211 FTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQR 269 (314)
Q Consensus 211 FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~ 269 (314)
|+.- +..|+.+|.. +..|...+...|+.++||+..+||+||+++++.....++.
T Consensus 564 ~~~p-~sllkayyal----n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rs 617 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYAL----NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERS 617 (1007)
T ss_pred cCCc-HHHHHHHHHh----cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccC
Confidence 4443 7788899999 9999999999999999999999999999999998877633
No 39
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.06 E-value=0.058 Score=52.18 Aligned_cols=66 Identities=12% Similarity=0.111 Sum_probs=53.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccc
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQ 268 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~ 268 (314)
..++|.+..|..+....|+.+... -...+||.+.+...|+.++||+..+|..||-|.|-+..+-..
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~-h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFE-HLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHH-hccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 446677779999999999876433 122578999999999999999999999999999998877554
No 40
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=93.83 E-value=0.019 Score=43.25 Aligned_cols=41 Identities=10% Similarity=0.301 Sum_probs=30.6
Q ss_pred HHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccc
Q 046396 216 KEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNK 260 (314)
Q Consensus 216 l~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRR 260 (314)
++.|+++|.+ .+...+...+.||.+.+|+..+|+.||--++
T Consensus 10 ~~pL~~Yy~~----h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLK----HKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHH----T----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHH----cCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 4669999999 8889999999999999999999999996443
No 41
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=88.84 E-value=0.19 Score=37.67 Aligned_cols=45 Identities=18% Similarity=0.300 Sum_probs=32.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccc
Q 046396 206 RSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHN 258 (314)
Q Consensus 206 R~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQN 258 (314)
+.|..||.+++..+...+.. ....+.++|.++||+..+|.-|..-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~--------~g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE--------SGESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHHH--------HHCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH--------CCCceEeeecccccccccccHHHHH
Confidence 46788999999999888744 2357889999999999999988753
No 42
>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=77.17 E-value=2.7 Score=24.94 Aligned_cols=39 Identities=26% Similarity=0.355 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecc
Q 046396 209 TKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWM 256 (314)
Q Consensus 209 T~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWF 256 (314)
..|+.+++..+...++. || ...+++.++|++..+|.-|+
T Consensus 4 ~~~~~~~~~~i~~~~~~-~~--------s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA-GE--------SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc-CC--------CHHHHHHHHCCCHHHHHHhC
Confidence 34678888877777764 22 45688999999998887774
No 43
>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=76.76 E-value=2 Score=31.78 Aligned_cols=41 Identities=20% Similarity=0.347 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCcee
Q 046396 211 FTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFK 253 (314)
Q Consensus 211 FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVK 253 (314)
+|..|.+.|...++. |+- .+|......+||.++||+..+|-
T Consensus 1 LT~~Q~e~L~~A~~~-GYf-d~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYEL-GYF-DVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHc-CCC-CCCCcCCHHHHHHHhCCCHHHHH
Confidence 588999999999997 332 12556778899999999988753
No 44
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=74.29 E-value=5 Score=43.97 Aligned_cols=71 Identities=11% Similarity=0.123 Sum_probs=52.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccccccccCCCCC
Q 046396 202 NGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSINNKNI 276 (314)
Q Consensus 202 ~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~~~~~~ 276 (314)
..+-+.|+.+-.++-..|...++. ...+.-.+....+.++...+.|+.||||+|+..-++-....++.+|+
T Consensus 624 ~~p~kv~sp~k~~dq~ql~~a~el----q~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ltss~n~ 694 (1007)
T KOG3623|consen 624 ERPVKVRSPIKEEDQQQLKQAYEL----QASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLFLTSSANG 694 (1007)
T ss_pred CCCccccCCCCccchhhhHhhhhc----ccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcccccccccC
Confidence 345566788888888888888887 55555445555566688889999999999999988877666655553
No 45
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=62.86 E-value=7 Score=45.16 Aligned_cols=67 Identities=18% Similarity=0.181 Sum_probs=57.5
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 197 ANSSDNGKKRSRTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 197 ~~~~~~~kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
+.+-.-+.|+-|+.+-.+++..|-+.|.. ...|...++.-|.-+...+.+++++||||.|.+.+|-.
T Consensus 698 ~~~~~~~~~~~~~~~~~~aa~~l~~a~~~----~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 698 GESLSPRDKLLRLTILPEAAMILGRAYMQ----DNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CCCCCcccccCcccccHHHHhhhhhcccC----CCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 44555667888999999999999988888 88888899999988888999999999999999988766
No 46
>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=60.72 E-value=1.5 Score=29.16 Aligned_cols=44 Identities=16% Similarity=0.257 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNA 262 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK 262 (314)
.++..+...+..+|.. .....++|.++|++..+|+.|.+.-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~---------~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGE---------GLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4677777777766532 1245688999999999999998765544
No 47
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=58.41 E-value=12 Score=30.44 Aligned_cols=42 Identities=21% Similarity=0.329 Sum_probs=35.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCC-CCCceeeccc
Q 046396 208 RTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGV-SRRVFKVWMH 257 (314)
Q Consensus 208 RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl-~~~vVKVWFQ 257 (314)
|.+||.|.+..+-+.+.. ..+ .+.++|+++|| ...++..|..
T Consensus 5 ~r~~s~EfK~~iv~~~~~----~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLR----GGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHh----cCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 789999999998887776 333 67899999996 9999988875
No 48
>PRK06424 transcription factor; Provisional
Probab=56.70 E-value=18 Score=31.87 Aligned_cols=53 Identities=15% Similarity=0.147 Sum_probs=32.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCcCCCCC---HHHHHHHHHHhCCCCCceeeccccccc
Q 046396 204 KKRSRTKFTQEQKEKMLSFAERLGWKMNRAE---EKLTQDFCSEVGVSRRVFKVWMHNNKN 261 (314)
Q Consensus 204 kKR~RT~FT~eQl~~Le~~FeklGWr~~~pd---~~~r~eLa~eiGl~~~vVKVWFQNRRa 261 (314)
++|+|..|. +..+.++.+.++ +.... .-..++||..+|++...|.-|..+++.
T Consensus 68 ~~~~~d~~~-~~~~~~~~~g~~----Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 68 KKYKKKASD-EDLDIVEDYAEL----VKNARERLSMSQADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred CCccCcccH-HHHHHHHHHHHH----HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 345555544 444555555444 21110 113569999999999999999987764
No 49
>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=56.48 E-value=4 Score=28.48 Aligned_cols=39 Identities=21% Similarity=0.309 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecc
Q 046396 209 TKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWM 256 (314)
Q Consensus 209 T~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWF 256 (314)
.+++.+|++.+..+++. - ..+.++|+++||++.+|.=|+
T Consensus 4 ~~~~~~~~~~i~~l~~~----G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAE----G-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHT----T-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHC----C-----CCHHHHHHHHCcCHHHHHHHH
Confidence 35788788888877776 1 357899999999999886554
No 50
>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=55.47 E-value=1.8 Score=30.54 Aligned_cols=41 Identities=15% Similarity=0.225 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccc
Q 046396 211 FTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNK 260 (314)
Q Consensus 211 FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRR 260 (314)
+++.|.+.+.. .|.......++|..+|++...|++|++.-|
T Consensus 11 L~~~~r~i~~l---------~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLL---------RYFQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHH---------HHTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHH---------HHHHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45555555553 344455778999999999999999997444
No 51
>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=55.41 E-value=8 Score=29.47 Aligned_cols=45 Identities=29% Similarity=0.477 Sum_probs=29.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccc
Q 046396 208 RTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMH 257 (314)
Q Consensus 208 RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQ 257 (314)
|-.|+.+.+....++|++ ...-....|.. +++.||.++.|+-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~----~~nc~~~~RAa-arkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK----DNNCKGNQRAA-ARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-----TTTTT-HHHH-HHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHH----ccchhhhHHHH-HHHhCccHHHHHHHHH
Confidence 557899999998899988 44444444544 9999999999999975
No 52
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=51.09 E-value=11 Score=34.12 Aligned_cols=49 Identities=18% Similarity=0.254 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNA 262 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK 262 (314)
.+|..|++.|...|+. |+= -+|......+||+++||++.++ |.+=||+.
T Consensus 155 ~LTdrQ~~vL~~A~~~-GYF-d~PR~~~l~dLA~~lGISkst~--~ehLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKM-GYF-DYPRRVSLKDLAKELGISKSTL--SEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHc-CCC-CCCccCCHHHHHHHhCCCHHHH--HHHHHHHH
Confidence 7999999999999997 432 2366677789999999999874 44444443
No 53
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=49.05 E-value=18 Score=30.09 Aligned_cols=42 Identities=14% Similarity=0.179 Sum_probs=30.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccc
Q 046396 208 RTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMH 257 (314)
Q Consensus 208 RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQ 257 (314)
|.+||.+++..+-...-. . ...+.++|.++||+..+|.-|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~----~----g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE----P----GMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHc----C----CCCHHHHHHHHCcCHHHHHHHHH
Confidence 456899988766554443 1 22467889999999999999954
No 54
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=48.83 E-value=5.7 Score=34.92 Aligned_cols=49 Identities=20% Similarity=0.233 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 209 TKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 209 T~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
+.+|+.|++.|.. +.+ || ..+++|..+|+++.+|+.|.+..+.|.++..
T Consensus 5 ~~Lt~rqreVL~l-r~~-Gl--------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRL-RER-GL--------TQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHH-HHc-CC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4689999999876 332 33 3568999999999999999998777776643
No 55
>PHA02893 hypothetical protein; Provisional
Probab=47.79 E-value=7.4 Score=31.80 Aligned_cols=9 Identities=44% Similarity=1.324 Sum_probs=7.9
Q ss_pred CccccccCC
Q 046396 85 SLNCAACGC 93 (314)
Q Consensus 85 ~l~caac~c 93 (314)
.|.|+|||-
T Consensus 69 tL~CaACGS 77 (88)
T PHA02893 69 NIKCIACGS 77 (88)
T ss_pred ceeehhhch
Confidence 799999983
No 56
>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=47.61 E-value=3.6 Score=32.49 Aligned_cols=29 Identities=10% Similarity=0.286 Sum_probs=23.1
Q ss_pred CCCHHHHHHHHHHhCCCCCceeecccccc
Q 046396 232 RAEEKLTQDFCSEVGVSRRVFKVWMHNNK 260 (314)
Q Consensus 232 ~pd~~~r~eLa~eiGl~~~vVKVWFQNRR 260 (314)
+.......++|..+|+++.+|++|+.+..
T Consensus 29 ~~eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 29 EEAGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 33444677999999999999999997543
No 57
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=46.83 E-value=34 Score=24.55 Aligned_cols=33 Identities=15% Similarity=0.228 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccc
Q 046396 212 TQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHN 258 (314)
Q Consensus 212 T~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQN 258 (314)
|.+||++|...+.. .|+..+|+++.-|.|+|..
T Consensus 13 s~eqk~~l~~~it~--------------~l~~~~~~p~~~v~V~i~e 45 (61)
T PRK02220 13 TEEQLKALVKDVTA--------------AVSKNTGAPAEHIHVIINE 45 (61)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcChhhEEEEEEE
Confidence 79999999766555 8899999988888877653
No 58
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=46.74 E-value=2.8 Score=36.81 Aligned_cols=49 Identities=12% Similarity=0.005 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.++..|...|...| ......+++|..+|++..+|++|++.-|.+.|+.-
T Consensus 142 ~L~~~~r~vl~l~~---------~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAY---------YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHH---------HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 45666666664322 22235679999999999999999987777666543
No 59
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=44.65 E-value=3.8 Score=35.65 Aligned_cols=35 Identities=9% Similarity=0.009 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 232 RAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 232 ~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
|.......++|..+|++..+|++|++.-|.+.|+.
T Consensus 154 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 154 YYEGLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 33445667999999999999999998777666653
No 60
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=44.33 E-value=8.9 Score=25.93 Aligned_cols=45 Identities=22% Similarity=0.408 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASG 264 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~k 264 (314)
.++..|++.+..+++ |+ ...++|..+||++.+|+.|.+.-+.|.+
T Consensus 3 ~l~~~e~~i~~~~~~--g~--------s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLAE--GL--------TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHHc--CC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 468888886654332 21 4578999999999999999875444443
No 61
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=43.39 E-value=12 Score=31.60 Aligned_cols=40 Identities=15% Similarity=0.227 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccc
Q 046396 211 FTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKN 261 (314)
Q Consensus 211 FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRa 261 (314)
++..++..|.+-+.- ....||+-+|++..+|+-|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~l-----------SQ~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGL-----------SQPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCC-----------CHHHHHHHHCCCHHHHHHHHcCCcC
Confidence 899999999877766 6789999999999999999998874
No 62
>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=42.84 E-value=6.6 Score=28.29 Aligned_cols=47 Identities=21% Similarity=0.309 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.||+.+++.|..++.- . ...++|.+++|+..+|+.+..+=+.|++-+
T Consensus 3 ~LT~~E~~vl~~l~~G----~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG----M------SNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp SS-HHHHHHHHHHHTT----S-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred ccCHHHHHHHHHHHhc----C------CcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 5788999988766655 2 567899999999999999988777666543
No 63
>PRK10072 putative transcriptional regulator; Provisional
Probab=42.71 E-value=12 Score=30.79 Aligned_cols=41 Identities=24% Similarity=0.370 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKN 261 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRa 261 (314)
..+...+..|. +++||. ..+||..+||+..+|.-|.+.+|.
T Consensus 32 ~~~~~eik~LR---~~~glT--------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLR---KGTGLK--------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHH---HHcCCC--------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 44666666654 455554 679999999999999999987764
No 64
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=42.05 E-value=3.4 Score=35.66 Aligned_cols=34 Identities=15% Similarity=0.170 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQR 269 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~ 269 (314)
...+++|..+|++..+|+++++.-|.+.|++-..
T Consensus 148 ~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 148 ASIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 3567999999999999999999888887766543
No 65
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=41.88 E-value=4 Score=33.92 Aligned_cols=30 Identities=7% Similarity=-0.012 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
....++|..+|++..+|++|.+.-|.+.|+
T Consensus 123 ~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 123 KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 356799999999999999999876666654
No 66
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=40.24 E-value=3.7 Score=36.61 Aligned_cols=32 Identities=6% Similarity=-0.030 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
...+++|.++|++..+|+++++.-|.+.++.-
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35679999999999999999987777766654
No 67
>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=40.11 E-value=4.5 Score=33.74 Aligned_cols=47 Identities=9% Similarity=0.015 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
.+++.|...+...| .......++|..+|++..+|+++++--|.+.++
T Consensus 111 ~L~~~~r~v~~l~~---------~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRY---------QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHH---------hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 45666666665422 223356789999999999999998866666554
No 68
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=39.83 E-value=5.5 Score=27.80 Aligned_cols=39 Identities=15% Similarity=0.285 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecc
Q 046396 209 TKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWM 256 (314)
Q Consensus 209 T~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWF 256 (314)
..||.+|...++.+++. .....++|+.||+++.+|.-|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~---------G~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ---------GMSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS------------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHc---------CCCHHHHHHHHCcCcHHHHHHH
Confidence 56889999998877653 2345689999999998886554
No 69
>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=39.79 E-value=4.3 Score=34.85 Aligned_cols=33 Identities=9% Similarity=0.087 Sum_probs=26.5
Q ss_pred CHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 234 EEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 234 d~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.....+++|..+|++..+|+++++.-|.+.|+.
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 334567999999999999999998777666654
No 70
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=39.30 E-value=13 Score=30.20 Aligned_cols=18 Identities=39% Similarity=0.551 Sum_probs=14.6
Q ss_pred HHHhhhhhhccCCccccC
Q 046396 51 KECLKNHAASLGGHALDG 68 (314)
Q Consensus 51 ~ec~~nha~~~g~~~~dg 68 (314)
.-=|||.||.|||.+|-.
T Consensus 51 ~NdlrNeAa~lGgntV~~ 68 (93)
T PF13698_consen 51 RNDLRNEAAKLGGNTVVL 68 (93)
T ss_pred HHHHHHHHHHhCCCEEEE
Confidence 345899999999988753
No 71
>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=39.13 E-value=7.8 Score=27.04 Aligned_cols=44 Identities=9% Similarity=0.148 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNA 262 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK 262 (314)
.+++.|.+.|...|.. .....++|..+|+++.+|+.+...-..|
T Consensus 4 ~L~~~er~vi~~~y~~---------~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE---------GLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHTS---------T-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC---------CCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 4678888888877732 2346789999999999998876544333
No 72
>PRK04217 hypothetical protein; Provisional
Probab=39.10 E-value=12 Score=31.69 Aligned_cols=49 Identities=14% Similarity=0.050 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.++.+|++.+...|.. ....+++|+.+||++.+|+..++.-+.+.+..-
T Consensus 42 ~Lt~eereai~l~~~e---------GlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 42 FMTYEEFEALRLVDYE---------GLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4688888777655533 126778999999999999999987766665543
No 73
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=39.10 E-value=4 Score=34.39 Aligned_cols=48 Identities=10% Similarity=0.104 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.+++.|++.+...|- ......++|..+|+++.+|+.|++.-|.+.++.
T Consensus 128 ~L~~~~r~vl~l~~~---------~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREI---------EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456666666654332 222456899999999999999999666666553
No 74
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=38.95 E-value=3.9 Score=34.71 Aligned_cols=31 Identities=6% Similarity=0.051 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
..+++|.++|++..+|++|++--|.+.|+.-
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5679999999999999999997777766643
No 75
>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=37.52 E-value=9.2 Score=29.19 Aligned_cols=20 Identities=25% Similarity=0.579 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCCCceeecc
Q 046396 237 LTQDFCSEVGVSRRVFKVWM 256 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWF 256 (314)
...+||.+|||++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45688999999999999995
No 76
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=37.40 E-value=4.1 Score=35.40 Aligned_cols=47 Identities=13% Similarity=0.135 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
.++..|.+.+...| ......+++|.++|++..+|+++.+.-|.+.|+
T Consensus 139 ~L~~~~r~i~~l~~---------~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRV---------VVGLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHH---------HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45666666655432 223356799999999999999999766666554
No 77
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=36.21 E-value=69 Score=23.32 Aligned_cols=33 Identities=15% Similarity=0.241 Sum_probs=27.4
Q ss_pred CHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccc
Q 046396 212 TQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHN 258 (314)
Q Consensus 212 T~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQN 258 (314)
|.||+++|-+..-. .+++.+|+++..|.|.|..
T Consensus 13 s~EqK~~L~~~it~--------------a~~~~~~~p~~~v~V~i~e 45 (60)
T PRK02289 13 SQEQKNALAREVTE--------------VVSRIAKAPKEAIHVFIND 45 (60)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcCcceEEEEEEE
Confidence 89999999755555 7888999999999998863
No 78
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=36.08 E-value=4.5 Score=35.50 Aligned_cols=31 Identities=13% Similarity=0.194 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
...+++|..+|+++.+|+++++--|.+.|+.
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 151 LSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999999998666666553
No 79
>PF13551 HTH_29: Winged helix-turn helix
Probab=35.79 E-value=38 Score=26.46 Aligned_cols=21 Identities=19% Similarity=0.550 Sum_probs=17.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHh
Q 046396 205 KRSRTKFTQEQKEKMLSFAER 225 (314)
Q Consensus 205 KR~RT~FT~eQl~~Le~~Fek 225 (314)
.|.+..++++|.+.|.+++..
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHH
Confidence 444445999999999999998
No 80
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=35.76 E-value=5.2 Score=33.76 Aligned_cols=31 Identities=13% Similarity=0.173 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
...+++|..+|++..+|+++.+.-|.+.++.
T Consensus 129 ~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 129 FSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 3567999999999999999998777776654
No 81
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=35.74 E-value=5.5 Score=35.29 Aligned_cols=33 Identities=9% Similarity=-0.033 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 235 EKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 235 ~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
....+++|..+|++..+|+++++--|.+.|+.-
T Consensus 129 g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 129 GFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345679999999999999999998887777654
No 82
>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=35.67 E-value=11 Score=31.22 Aligned_cols=51 Identities=12% Similarity=0.133 Sum_probs=34.5
Q ss_pred HHHHHHHHHHhcC------CcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 215 QKEKMLSFAERLG------WKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 215 Ql~~Le~~FeklG------Wr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
+...|..+.++|. ....|......+++|..+|++..+|+++++--|.+.++
T Consensus 95 ~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 95 EQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred HHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444555555543 11234556677899999999999999999866655544
No 83
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=35.42 E-value=5.1 Score=34.38 Aligned_cols=30 Identities=7% Similarity=0.173 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCCCceeecccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
..+++|..+|++...|+++++.-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 467999999999999999998777766654
No 84
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=34.47 E-value=6.2 Score=34.21 Aligned_cols=29 Identities=14% Similarity=0.326 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCCCceeeccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
..+++|..+|++..+|++|.+.-|.+.|+
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 56799999999999999999866665554
No 85
>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=34.36 E-value=11 Score=25.56 Aligned_cols=23 Identities=13% Similarity=0.202 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCCCceeecccccc
Q 046396 238 TQDFCSEVGVSRRVFKVWMHNNK 260 (314)
Q Consensus 238 r~eLa~eiGl~~~vVKVWFQNRR 260 (314)
..++|+.+||+..+|+.|.+...
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 46889999999999999976544
No 86
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=33.90 E-value=5 Score=33.71 Aligned_cols=31 Identities=3% Similarity=-0.012 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
..+++|..+|++..+|+++++--|.+.|+.-
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4569999999999999999987777666543
No 87
>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=33.88 E-value=13 Score=24.47 Aligned_cols=25 Identities=24% Similarity=0.473 Sum_probs=21.0
Q ss_pred HHHHHHHhCCCCCceeecccccccc
Q 046396 238 TQDFCSEVGVSRRVFKVWMHNNKNA 262 (314)
Q Consensus 238 r~eLa~eiGl~~~vVKVWFQNRRaK 262 (314)
..++|..+||++++|.-|.++.+-.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 4688999999999999999876543
No 88
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=33.40 E-value=6.6 Score=33.64 Aligned_cols=32 Identities=9% Similarity=0.201 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 235 EKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 235 ~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
....+++|..+|+++.+|+++++.-|.+.++.
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34667999999999999999998766666553
No 89
>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=33.36 E-value=5.7 Score=34.07 Aligned_cols=30 Identities=13% Similarity=0.045 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
...+++|..+|++..+|++.++.-|.+.++
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 151 LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 355699999999999999999877766654
No 90
>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=33.11 E-value=7.9 Score=30.73 Aligned_cols=47 Identities=11% Similarity=0.136 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
.++..|...+...|-. .....++|.++|+++.+|+.|.+.-+.|.|+
T Consensus 110 ~L~~~~~~ii~~~~~~---------g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE---------GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4556666665443322 2245699999999999999998866666554
No 91
>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=32.87 E-value=18 Score=25.12 Aligned_cols=22 Identities=14% Similarity=0.406 Sum_probs=16.7
Q ss_pred HHHHHHhCCCCCceeecccccc
Q 046396 239 QDFCSEVGVSRRVFKVWMHNNK 260 (314)
Q Consensus 239 ~eLa~eiGl~~~vVKVWFQNRR 260 (314)
.+||+.+|+++.+|.=|+.+++
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 92
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=32.67 E-value=5.9 Score=34.53 Aligned_cols=36 Identities=8% Similarity=0.017 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 232 RAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 232 ~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
|......+++|.++|++..+|+++++.-|.+.|+.-
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 445556789999999999999999987777777654
No 93
>PF13518 HTH_28: Helix-turn-helix domain
Probab=32.47 E-value=14 Score=25.34 Aligned_cols=25 Identities=20% Similarity=0.525 Sum_probs=20.7
Q ss_pred HHHHHHHHhCCCCCceeeccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKN 261 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRa 261 (314)
...++|.++||+..+|.-|.+.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 4667999999999999999975443
No 94
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=32.14 E-value=9.6 Score=33.43 Aligned_cols=36 Identities=8% Similarity=-0.041 Sum_probs=27.9
Q ss_pred CHHHHHHHHHHhCCCCCceeeccccccccccccccc
Q 046396 234 EEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQR 269 (314)
Q Consensus 234 d~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~ 269 (314)
.....+++|..+|++..+|++.++--|.+.|+.-..
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 334567999999999999999998777766665543
No 95
>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=31.70 E-value=81 Score=22.57 Aligned_cols=33 Identities=18% Similarity=0.253 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccc
Q 046396 212 TQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHN 258 (314)
Q Consensus 212 T~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQN 258 (314)
|.+|+++|-+..-. .+.+.+|+++..|.|.|+.
T Consensus 12 ~~e~K~~l~~~it~--------------~~~~~lg~~~~~i~V~i~E 44 (60)
T PF01361_consen 12 TAEQKRELAEAITD--------------AVVEVLGIPPERISVVIEE 44 (60)
T ss_dssp -HHHHHHHHHHHHH--------------HHHHHHTS-GGGEEEEEEE
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcCCCeEEEEEEE
Confidence 78998888655544 6788899999999999864
No 96
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=31.31 E-value=8.3 Score=33.49 Aligned_cols=32 Identities=19% Similarity=0.167 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 235 EKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 235 ~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
....+++|..+|++..+|+.+++.-|.+.|+.
T Consensus 147 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 147 GLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34567999999999999999998777666654
No 97
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=31.02 E-value=6.8 Score=34.29 Aligned_cols=30 Identities=10% Similarity=0.024 Sum_probs=24.6
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
...+++|..+|++..+|+++++--|.+.|+
T Consensus 147 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 147 LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 356799999999999999999866666655
No 98
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=30.96 E-value=13 Score=26.76 Aligned_cols=27 Identities=15% Similarity=0.356 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCCCCceeeccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNAS 263 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~ 263 (314)
.+.+||+.+||++.+|.-|+.++..+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 567899999999999999999774443
No 99
>PRK00118 putative DNA-binding protein; Validated
Probab=30.93 E-value=13 Score=31.15 Aligned_cols=47 Identities=15% Similarity=0.132 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
.++..|.+.+...|.. .....++|..+|+++.+|+.|++.-|.+.++
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 3466666666544433 2356789999999999999999866666554
No 100
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=30.66 E-value=1.1e+02 Score=34.42 Aligned_cols=6 Identities=17% Similarity=0.556 Sum_probs=2.3
Q ss_pred HHHHHh
Q 046396 240 DFCSEV 245 (314)
Q Consensus 240 eLa~ei 245 (314)
.|-.+|
T Consensus 657 dlfakL 662 (1102)
T KOG1924|consen 657 DLFAKL 662 (1102)
T ss_pred HHHHHH
Confidence 333333
No 101
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=30.54 E-value=5.9 Score=33.09 Aligned_cols=48 Identities=19% Similarity=0.178 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
+++..|.+.+.-.|- ......++|..+|++..+|+++++--|.+.|+.
T Consensus 106 ~Lp~~~r~v~~l~~~---------~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYW---------EDMDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHH---------hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 445555555544222 223457999999999999999988666665543
No 102
>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=30.49 E-value=7.3 Score=34.01 Aligned_cols=37 Identities=8% Similarity=0.095 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 231 NRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 231 ~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.|.......++|..+|++..+|+++++--|.+.|+.-
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 3445556789999999999999999997777776654
No 103
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=30.46 E-value=7.5 Score=34.29 Aligned_cols=33 Identities=9% Similarity=-0.002 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCCCCceeecccccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQ 268 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~ 268 (314)
....++|..+|++..+|+++++.-|.+.++.-.
T Consensus 133 ~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 133 FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 355699999999999999999977777776543
No 104
>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=29.82 E-value=6.8 Score=33.72 Aligned_cols=49 Identities=12% Similarity=0.081 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.+++.|...+.-.|-. ....+++|.++|++..+|+++.+--|.++++.-
T Consensus 100 ~L~~~~r~v~~l~~~~---------g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELE---------GLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4556665555543322 234579999999999999999987666666644
No 105
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=29.59 E-value=8 Score=33.80 Aligned_cols=49 Identities=6% Similarity=0.187 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.+++.|...+.-.| ......+++|..+|++..+|++..+--|.+.|++.
T Consensus 131 ~L~~~~r~i~~l~~---------~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRY---------LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHH---------HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 45555555554322 12235679999999999999999987777777766
No 106
>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=29.41 E-value=6.6 Score=32.27 Aligned_cols=29 Identities=10% Similarity=0.236 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCCCceeeccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
...++|..+|+++.+|+.+.+.-|.+.|+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 55689999999999999998866666554
No 107
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=29.37 E-value=6.7 Score=33.40 Aligned_cols=31 Identities=13% Similarity=0.065 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 235 EKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 235 ~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
....+++|..+|++..+|+++.+--|.+.|+
T Consensus 128 g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 128 GFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3456799999999999999999865555544
No 108
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=29.25 E-value=17 Score=35.50 Aligned_cols=53 Identities=13% Similarity=0.083 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.+++.|...|...|-. .+......+++|..+||+..+|+++.+.-+.|.|+.-
T Consensus 262 ~L~~~~R~vl~lrygL-----~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGL-----LGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhcc-----CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5667777777655532 3345567789999999999999999997777776644
No 109
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=29.07 E-value=7.7 Score=32.53 Aligned_cols=30 Identities=10% Similarity=0.112 Sum_probs=24.6
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
....++|..+|+++.+|+.|++--|.+.|+
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345799999999999999999866666654
No 110
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=29.00 E-value=93 Score=22.28 Aligned_cols=33 Identities=21% Similarity=0.278 Sum_probs=27.0
Q ss_pred CHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccc
Q 046396 212 TQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHN 258 (314)
Q Consensus 212 T~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQN 258 (314)
|.+|++.|-+..-. .+++.+|++..-|.|.|..
T Consensus 13 s~eqk~~l~~~it~--------------~l~~~~~~p~~~v~V~i~e 45 (62)
T PRK00745 13 TVEQKRKLVEEITR--------------VTVETLGCPPESVDIIITD 45 (62)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHcCCChhHEEEEEEE
Confidence 78999888655544 7899999999999998864
No 111
>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=28.96 E-value=8.4 Score=32.35 Aligned_cols=31 Identities=10% Similarity=0.019 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
..+++|..+|++..+|+++...-|.+.++.-
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4568999999999999999987777776643
No 112
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=28.65 E-value=1.1e+02 Score=24.18 Aligned_cols=33 Identities=9% Similarity=0.104 Sum_probs=28.2
Q ss_pred CHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccc
Q 046396 212 TQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHN 258 (314)
Q Consensus 212 T~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQN 258 (314)
|.||++.|-+.+-+ .+++.+|.++..|.|.|+-
T Consensus 14 s~EqK~~La~~iT~--------------a~~~~lg~~~e~v~V~I~e 46 (76)
T PRK01271 14 DEEQKAALAADITD--------------VIIRHLNSKDSSISIALQQ 46 (76)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcCcceEEEEEEE
Confidence 89999999766655 7799999999999999964
No 113
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.54 E-value=7.7 Score=34.10 Aligned_cols=30 Identities=7% Similarity=0.047 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCCCceeecccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
..+++|..+||+..+|+++++--|.+.|+.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456999999999999999998766666654
No 114
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=28.48 E-value=99 Score=22.52 Aligned_cols=33 Identities=9% Similarity=0.258 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccc
Q 046396 212 TQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHN 258 (314)
Q Consensus 212 T~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQN 258 (314)
|.+|+++|-+..-. .++..+|+++..|.|.|..
T Consensus 13 t~eqk~~l~~~it~--------------~l~~~lg~p~~~v~V~i~e 45 (64)
T PRK01964 13 PEEKIKNLIREVTE--------------AISATLDVPKERVRVIVNE 45 (64)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcChhhEEEEEEE
Confidence 78999888655544 7899999999999987754
No 115
>PRK09726 antitoxin HipB; Provisional
Probab=27.95 E-value=61 Score=25.38 Aligned_cols=43 Identities=14% Similarity=0.401 Sum_probs=28.5
Q ss_pred CCCHHHH-HHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccc
Q 046396 210 KFTQEQK-EKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNK 260 (314)
Q Consensus 210 ~FT~eQl-~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRR 260 (314)
.+++.++ ..|+.+-++.||. ..+||..+||+..+|.-|..+++
T Consensus 7 ~~~~~~l~~~lk~~R~~~glt--------q~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 7 IYSPTQLANAMKLVRQQNGWT--------QSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred ccCHHHHHHHHHHHHHHcCCC--------HHHHHHHHCcCHHHHHHHHCCCC
Confidence 3455555 3555555554443 56888889999888888887543
No 116
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=27.95 E-value=7.3 Score=33.74 Aligned_cols=31 Identities=6% Similarity=0.054 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
..+++|..+|++..+|+++.+.-|.+.|+.-
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4569999999999999999987777766654
No 117
>PRK10403 transcriptional regulator NarP; Provisional
Probab=27.94 E-value=22 Score=29.64 Aligned_cols=49 Identities=14% Similarity=0.207 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 209 TKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 209 T~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
..+|..+++.|..+++. ..+.+++..+++++++|+++.+|=|.|...+.
T Consensus 152 ~~Lt~~e~~vl~~~~~g----------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 152 SVLTERELDVLHELAQG----------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred ccCCHHHHHHHHHHHCC----------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 36899999888755432 34678899999999999999988777765543
No 118
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=27.87 E-value=8.6 Score=34.14 Aligned_cols=33 Identities=12% Similarity=0.164 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 235 EKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 235 ~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.....++|..+|++..+||+.++.-|.+.|+.-
T Consensus 155 g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 155 DFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 345679999999999999999987776666543
No 119
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.74 E-value=10 Score=32.58 Aligned_cols=33 Identities=12% Similarity=0.164 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHHhCCCCCceeecccccccccc
Q 046396 232 RAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASG 264 (314)
Q Consensus 232 ~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~k 264 (314)
|.......++|..+|++..+|++++..-+.+++
T Consensus 132 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 132 QLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred hccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 334445679999999999999999975555443
No 120
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=27.63 E-value=9.2 Score=32.17 Aligned_cols=47 Identities=11% Similarity=0.132 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.++..|...|.-.| ......++|..+|++..+|+.+.+.-|.+.|+.
T Consensus 112 ~L~~~~r~il~l~~----------~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF----------SGYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH----------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35566666555444 233567999999999999999998766666553
No 121
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=27.48 E-value=16 Score=32.40 Aligned_cols=25 Identities=4% Similarity=0.081 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCCCCceeeccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKN 261 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRa 261 (314)
.+++||..+|++..+|.-|-.+.+.
T Consensus 84 SqeeLA~~lgvs~s~IsriE~G~~~ 108 (154)
T TIGR00270 84 SQEQLAKKIQEKESLIKKIENAEIE 108 (154)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCCC
Confidence 4679999999999999999977654
No 122
>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=27.44 E-value=1.3e+02 Score=21.09 Aligned_cols=34 Identities=18% Similarity=0.258 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccc
Q 046396 212 TQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNN 259 (314)
Q Consensus 212 T~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNR 259 (314)
+.+|+++|-+..-. .++..+|+++..|-|.|+..
T Consensus 12 t~eqk~~l~~~i~~--------------~l~~~~g~~~~~v~V~i~e~ 45 (58)
T cd00491 12 TDEQKRELIERVTE--------------AVSEILGAPEATIVVIIDEM 45 (58)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcCcccEEEEEEEe
Confidence 58899888654444 77888999999999988643
No 123
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=27.43 E-value=8.6 Score=33.61 Aligned_cols=32 Identities=13% Similarity=0.172 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
...+++|..+|++..+|+++++.-|.+.|+.-
T Consensus 153 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 153 FSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35679999999999999999987777766643
No 124
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=27.31 E-value=17 Score=26.53 Aligned_cols=22 Identities=14% Similarity=0.335 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCCCceeeccccc
Q 046396 238 TQDFCSEVGVSRRVFKVWMHNN 259 (314)
Q Consensus 238 r~eLa~eiGl~~~vVKVWFQNR 259 (314)
..++|+.+||+.++|+.|-..-
T Consensus 3 i~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHHhc
Confidence 4689999999999999996533
No 125
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=27.21 E-value=20 Score=36.38 Aligned_cols=15 Identities=40% Similarity=0.893 Sum_probs=11.9
Q ss_pred CccccccCCcccccc
Q 046396 85 SLNCAACGCHRNFHR 99 (314)
Q Consensus 85 ~l~caac~chrnfhr 99 (314)
+++|+||||+-.---
T Consensus 118 ~~~CkACG~r~~~d~ 132 (400)
T KOG2767|consen 118 SLKCKACGFRSDMDL 132 (400)
T ss_pred hhHHHHcCCcccccc
Confidence 689999999866543
No 126
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=27.10 E-value=8.8 Score=33.16 Aligned_cols=32 Identities=9% Similarity=0.119 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
....++|..+|++..+|++.++.-|.+.|+.-
T Consensus 134 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 134 YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35669999999999999999998888777643
No 127
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=26.52 E-value=8 Score=33.52 Aligned_cols=47 Identities=11% Similarity=0.153 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
.++++|...+.-. +.+....+++|..+|+++.+|++.++.-+.+.+.
T Consensus 127 ~Lp~~~R~v~~L~---------~~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMA---------TLDGMKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHH---------HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3555555555432 2223356799999999999999999866655543
No 128
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=26.34 E-value=12 Score=33.28 Aligned_cols=36 Identities=3% Similarity=-0.093 Sum_probs=28.5
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSI 271 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~ 271 (314)
...+++|..+|++..+|+++.+.-|.+.|+.-....
T Consensus 150 ~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 150 YTYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 356799999999999999999877777766554444
No 129
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=26.29 E-value=9 Score=33.40 Aligned_cols=32 Identities=13% Similarity=0.092 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
...+++|..+|++..+|++.++.-|.+.|+.-
T Consensus 148 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 148 LETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35679999999999999999987777666543
No 130
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=26.22 E-value=18 Score=32.70 Aligned_cols=52 Identities=17% Similarity=0.171 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.+++.|.+.+.-.|.. .+......+++|..+||+..+|+.+.+.-|.+.|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l-----~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGL-----NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhcc-----CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4556666666544411 113344577999999999999999998777776654
No 131
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=26.16 E-value=11 Score=33.08 Aligned_cols=31 Identities=10% Similarity=0.073 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
...+++|..+|++..+|+.+++.-|.+.++.
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999999998666666553
No 132
>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=26.15 E-value=24 Score=28.14 Aligned_cols=9 Identities=56% Similarity=1.464 Sum_probs=7.9
Q ss_pred CccccccCC
Q 046396 85 SLNCAACGC 93 (314)
Q Consensus 85 ~l~caac~c 93 (314)
.|.|+|||-
T Consensus 57 tLsCsACGS 65 (74)
T PF05077_consen 57 TLSCSACGS 65 (74)
T ss_pred eEeehhccc
Confidence 699999983
No 133
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=26.09 E-value=9.6 Score=34.79 Aligned_cols=34 Identities=6% Similarity=-0.015 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 234 EEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 234 d~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.....+++|..+||+..+|+++.+.-|.+.++.-
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345679999999999999999997777777654
No 134
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=25.79 E-value=8.4 Score=33.36 Aligned_cols=33 Identities=24% Similarity=0.221 Sum_probs=27.1
Q ss_pred CHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 234 EEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 234 d~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.....+++|..+|+++.+|++.++.-|.+.|+.
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 334567999999999999999998877777664
No 135
>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=25.63 E-value=51 Score=22.51 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCCCceeecccccc
Q 046396 238 TQDFCSEVGVSRRVFKVWMHNNK 260 (314)
Q Consensus 238 r~eLa~eiGl~~~vVKVWFQNRR 260 (314)
..+||..+|++..+|.-|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56889999999999888886654
No 136
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=25.63 E-value=8.6 Score=33.46 Aligned_cols=49 Identities=16% Similarity=0.157 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.++++|.+.|...| ......+++|..+|++..+|++.++.-|.++++.-
T Consensus 131 ~L~~~~r~vl~l~~---------~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVY---------YHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHH---------HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 56666666664322 12235568999999999999999987777776653
No 137
>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=25.54 E-value=73 Score=26.46 Aligned_cols=26 Identities=35% Similarity=0.500 Sum_probs=21.6
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCcCCC
Q 046396 207 SRTKFTQEQKEKMLSFAERLGWKMNR 232 (314)
Q Consensus 207 ~RT~FT~eQl~~Le~~FeklGWr~~~ 232 (314)
.=+.+|..|+..+...|+++||+.++
T Consensus 18 S~k~lt~~el~~vl~~l~~~G~k~~~ 43 (119)
T PF06252_consen 18 SSKDLTEAELEKVLDELKRLGFKPPK 43 (119)
T ss_pred hHHHCCHHHHHHHHHHHHHccCcCcc
Confidence 33468999999999999999997544
No 138
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.34 E-value=10 Score=32.27 Aligned_cols=30 Identities=17% Similarity=0.229 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCCCceeecccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
..+++|..+|+++.+|+++++--|.+.|+.
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467999999999999999988666665553
No 139
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=25.26 E-value=9.3 Score=35.26 Aligned_cols=33 Identities=0% Similarity=-0.023 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 235 EKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 235 ~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
....+++|..+|++..+|+++++.-|.+.|+.-
T Consensus 187 g~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 187 NMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 345579999999999999999987777776643
No 140
>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=24.73 E-value=13 Score=30.39 Aligned_cols=10 Identities=50% Similarity=0.850 Sum_probs=7.8
Q ss_pred ceeecccccc
Q 046396 251 VFKVWMHNNK 260 (314)
Q Consensus 251 vVKVWFQNRR 260 (314)
-|||||||--
T Consensus 32 dvkvwmqnle 41 (106)
T PF11516_consen 32 DVKVWMQNLE 41 (106)
T ss_dssp HHHHHHHHHH
T ss_pred cHHHHHHHHH
Confidence 4799999853
No 141
>PRK13558 bacterio-opsin activator; Provisional
Probab=24.53 E-value=51 Score=34.23 Aligned_cols=42 Identities=17% Similarity=0.288 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCce
Q 046396 209 TKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVF 252 (314)
Q Consensus 209 T~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vV 252 (314)
..+|..|.+.|+..|+. |+- ..|....-++||.+|||+..+|
T Consensus 606 ~~lt~~q~e~l~~a~~~-gyf-~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 606 NDLTDRQLTALQKAYVS-GYF-EWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhCCHHHHHHHHHHHHc-CCC-CCCccCCHHHHHHHhCCCHHHH
Confidence 47999999999999997 321 1266778899999999999875
No 142
>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=24.52 E-value=29 Score=23.57 Aligned_cols=22 Identities=18% Similarity=0.444 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCCCCceeecccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHN 258 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQN 258 (314)
...++|..+++++.+|+.|.+-
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4578899999999999999863
No 143
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=24.51 E-value=10 Score=32.62 Aligned_cols=30 Identities=7% Similarity=0.034 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCCCCceeecccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
..+++|..+|++..+|+++.+.-|.+.|+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999998666665543
No 144
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=24.38 E-value=11 Score=33.14 Aligned_cols=33 Identities=9% Similarity=0.043 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 235 EKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 235 ~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
....+++|..+|++..+|+++.+--|.+.++..
T Consensus 127 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 127 GLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 345679999999999999999986666665543
No 145
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=24.07 E-value=14 Score=33.62 Aligned_cols=34 Identities=15% Similarity=0.082 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 233 AEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 233 pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.......++|..+||+..+|+.+++.-+.+.|+.
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3444567999999999999999999888777664
No 146
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=24.03 E-value=8 Score=32.92 Aligned_cols=37 Identities=5% Similarity=0.041 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 231 NRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 231 ~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.|......+++|..+|++..+|++.++.-|.+.++.-
T Consensus 132 ~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 132 HDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3445556789999999999999999987777766643
No 147
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=23.79 E-value=12 Score=32.04 Aligned_cols=33 Identities=9% Similarity=0.105 Sum_probs=25.7
Q ss_pred CHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 234 EEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 234 d~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
+....+++|..+|++..+|+++++.-|.+.++.
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 334556999999999999999998666666543
No 148
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=23.68 E-value=1.3e+02 Score=24.48 Aligned_cols=36 Identities=6% Similarity=0.082 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccc
Q 046396 212 TQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKN 261 (314)
Q Consensus 212 T~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRa 261 (314)
+.+|+++|-+..- +.|.+.+|++...|-|.|++...
T Consensus 70 ~~e~k~~l~~~i~--------------~~l~~~lgi~~~rv~I~f~~~~~ 105 (116)
T PTZ00397 70 SRSNNSSIAAAIT--------------KILASHLKVKSERVYIEFKDCSA 105 (116)
T ss_pred CHHHHHHHHHHHH--------------HHHHHHhCcCcccEEEEEEECCh
Confidence 5788888754433 47899999999999999987643
No 149
>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=23.59 E-value=12 Score=31.48 Aligned_cols=29 Identities=10% Similarity=0.129 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCCCCceeeccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
...++|..+|++..+|++...--|.+.|+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45699999999999999988655555443
No 150
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.24 E-value=21 Score=24.62 Aligned_cols=23 Identities=22% Similarity=0.497 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCCCceeeccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNN 259 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNR 259 (314)
...++|+.+||++.+|.-|.+.-
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT--
T ss_pred CHHHHHHHHCcCHHHHHHHHHHc
Confidence 46789999999999999998643
No 151
>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=23.06 E-value=30 Score=25.84 Aligned_cols=36 Identities=22% Similarity=0.504 Sum_probs=26.3
Q ss_pred HHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 220 LSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 220 e~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
..+|.+ ||+. .++|.+|||+..+|.-|-+ |.+|...
T Consensus 7 ~~LY~~-G~~~--------~eIA~~Lg~~~~TV~~W~~--r~~W~~~ 42 (58)
T PF06056_consen 7 RSLYLQ-GWSI--------KEIAEELGVPRSTVYSWKD--RYKWDEL 42 (58)
T ss_pred HHHHHc-CCCH--------HHHHHHHCCChHHHHHHHH--hhCcccc
Confidence 444554 6654 6899999999999999975 5555443
No 152
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=22.83 E-value=12 Score=31.82 Aligned_cols=35 Identities=6% Similarity=0.078 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 232 RAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 232 ~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
|......+++|..+|++...|+++...-|.+.+++
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 34445677999999999999999997666666553
No 153
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.70 E-value=11 Score=32.64 Aligned_cols=30 Identities=10% Similarity=0.160 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCCCceeecccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
..+++|..+|++..+|++..+.-|.+.++.
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 557999999999999999988666666553
No 154
>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=22.44 E-value=1.7e+02 Score=20.87 Aligned_cols=34 Identities=18% Similarity=0.264 Sum_probs=26.5
Q ss_pred CHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccc
Q 046396 212 TQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNN 259 (314)
Q Consensus 212 T~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNR 259 (314)
|.+|++.|-...-. .|+..+|+++..|-|.|...
T Consensus 13 t~eqK~~l~~~it~--------------~l~~~lg~~~~~v~V~i~e~ 46 (63)
T TIGR00013 13 TDEQKRQLIEGVTE--------------AMAETLGANLESIVVIIDEM 46 (63)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCCCcccEEEEEEEc
Confidence 78999888654444 78999999999988877543
No 155
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=22.43 E-value=42 Score=28.01 Aligned_cols=42 Identities=12% Similarity=0.142 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccc
Q 046396 213 QEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNN 259 (314)
Q Consensus 213 ~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNR 259 (314)
..-+.++..+.+. ++.+...+++||..+||+++.++-||+..
T Consensus 8 ~~~i~~~~~~I~~-----~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIED-----NLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHH-----hcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4445666666665 44445678899999999999998888754
No 156
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=22.35 E-value=10 Score=31.83 Aligned_cols=30 Identities=17% Similarity=0.262 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCCCceeecccccccccccc
Q 046396 237 LTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 237 ~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
..+++|.++|++..+|+++++--|.+.++.
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456999999999999999987666666554
No 157
>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=22.18 E-value=26 Score=32.08 Aligned_cols=36 Identities=22% Similarity=0.368 Sum_probs=30.9
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRKDQRSI 271 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~~~~~ 271 (314)
-..++|+..++|++.+|-+|+.|-+...+++....+
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~yKh 50 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKYKH 50 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccchhhH
Confidence 367899999999999999999999999888765443
No 158
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.01 E-value=39 Score=30.90 Aligned_cols=48 Identities=17% Similarity=0.163 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.+|+.|++.|+-.++ ||. ..++|.++++++++||.+..+=..|..-+.
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s--------~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~n 202 (216)
T PRK10100 155 LLTHREKEILNKLRI--GAS--------NNEIARSLFISENTVKTHLYNLFKKIAVKN 202 (216)
T ss_pred CCCHHHHHHHHHHHc--CCC--------HHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 489999999987666 443 458899999999999999988777766544
No 159
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=21.90 E-value=13 Score=32.31 Aligned_cols=34 Identities=9% Similarity=0.090 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 233 AEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 233 pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
......+++|..+|++..+|+++++--|.+.|+.
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3444567999999999999999998777776654
No 160
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=21.77 E-value=33 Score=30.04 Aligned_cols=48 Identities=13% Similarity=0.139 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 208 RTKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 208 RT~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
.+.+|..|++.|.-.+ . || ..+++|..+|+++..|+.|.+.-+.|.++
T Consensus 4 ~~~Lte~qr~VL~Lr~-~-Gl--------Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-K-GL--------SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-c-CC--------CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678999999987642 2 33 56799999999999999999887777775
No 161
>PHA02535 P terminase ATPase subunit; Provisional
Probab=21.56 E-value=75 Score=34.09 Aligned_cols=46 Identities=15% Similarity=0.439 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccc
Q 046396 209 TKFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGR 265 (314)
Q Consensus 209 T~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kK 265 (314)
+.||.|.+..-...|.+ ||+. .++|++|||++++|.-|-. |.+|..
T Consensus 1 ~~yt~EfK~~Av~Ly~~-G~sv--------~eIA~~LGv~~~Tl~~W~k--r~~w~~ 46 (581)
T PHA02535 1 TAYDDDVRRAAKFLYWQ-GWTV--------AEIAEELGLKSRTIYSWKE--RDGWRD 46 (581)
T ss_pred CCCCHHHHHHHHHHHHc-CCCH--------HHHHHHhCCChhHHHHHhc--cccccc
Confidence 35889988888888877 7764 5889999999999999954 566654
No 162
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=21.37 E-value=12 Score=31.95 Aligned_cols=32 Identities=9% Similarity=0.078 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 235 EKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 235 ~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.....++|..+|++..+|+++++.-+.+.+..
T Consensus 135 g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 135 GMGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567999999999999999998666665443
No 163
>PRK06930 positive control sigma-like factor; Validated
Probab=21.09 E-value=12 Score=33.43 Aligned_cols=49 Identities=10% Similarity=0.127 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
.+++.+++.+.-.|. ......++|..+|++..+|++++..-|.|.++.-
T Consensus 114 ~L~~rer~V~~L~~~---------eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRG---------YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 466666666654221 2234568999999999999999998777776643
No 164
>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=21.07 E-value=26 Score=25.84 Aligned_cols=21 Identities=14% Similarity=0.449 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCCCceeecccc
Q 046396 238 TQDFCSEVGVSRRVFKVWMHN 258 (314)
Q Consensus 238 r~eLa~eiGl~~~vVKVWFQN 258 (314)
..++|+.+||+.++|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 468899999999999999753
No 165
>PRK09480 slmA division inhibitor protein; Provisional
Probab=20.83 E-value=65 Score=27.40 Aligned_cols=31 Identities=19% Similarity=0.193 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHHHHhCCCCCceeeccccccc
Q 046396 230 MNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKN 261 (314)
Q Consensus 230 ~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRa 261 (314)
... ......++|++.||++.+|=-+|.|+..
T Consensus 26 ~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 26 PPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred cCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 346 7788999999999999999999999764
No 166
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=20.80 E-value=13 Score=31.86 Aligned_cols=33 Identities=12% Similarity=0.231 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 234 EEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 234 d~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.....+++|..+|++..+|+++.+.-|.+.|+.
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 334567999999999999999988777776653
No 167
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=20.29 E-value=16 Score=32.21 Aligned_cols=32 Identities=13% Similarity=0.032 Sum_probs=23.9
Q ss_pred HHHHHHHHHhCCCCCceeeccccccccccccc
Q 046396 236 KLTQDFCSEVGVSRRVFKVWMHNNKNASGRKD 267 (314)
Q Consensus 236 ~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk~ 267 (314)
...+++|..+||+..+|++=+..-|.+.|+.-
T Consensus 151 ~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 151 YSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35569999999999999886665555555544
No 168
>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=20.13 E-value=38 Score=29.10 Aligned_cols=12 Identities=50% Similarity=1.049 Sum_probs=10.0
Q ss_pred CCccccccCCcc
Q 046396 84 ASLNCAACGCHR 95 (314)
Q Consensus 84 ~~l~caac~chr 95 (314)
-.|+|.|||..|
T Consensus 113 ~~l~C~aCGa~~ 124 (125)
T PF01873_consen 113 IFLKCKACGASR 124 (125)
T ss_dssp CEEEETTTSCEE
T ss_pred EEEEecccCCcC
Confidence 368999999876
No 169
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=20.07 E-value=40 Score=28.14 Aligned_cols=47 Identities=17% Similarity=0.266 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcCCCCCHHHHHHHHHHhCCCCCceeecccccccccccc
Q 046396 210 KFTQEQKEKMLSFAERLGWKMNRAEEKLTQDFCSEVGVSRRVFKVWMHNNKNASGRK 266 (314)
Q Consensus 210 ~FT~eQl~~Le~~FeklGWr~~~pd~~~r~eLa~eiGl~~~vVKVWFQNRRaK~kKk 266 (314)
.+|..+.+.|.-+++- ..+++++.+++++.++|++..++=|.|...+
T Consensus 137 ~Lt~~E~~il~~l~~g----------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~ 183 (196)
T PRK10360 137 PLTKRERQVAEKLAQG----------MAVKEIAAELGLSPKTVHVHRANLMEKLGVS 183 (196)
T ss_pred CCCHHHHHHHHHHHCC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 5888888888776653 1577999999999999999888777776543
Done!