Query 039144
Match_columns 208
No_of_seqs 125 out of 447
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 06:43:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039144.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039144hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.8 1.9E-19 4.1E-24 157.3 1.5 65 3-72 158-222 (261)
2 PF00046 Homeobox: Homeobox do 99.7 7.8E-19 1.7E-23 118.8 2.5 57 5-66 1-57 (57)
3 KOG0487 Transcription factor A 99.7 1.9E-18 4E-23 156.4 4.0 63 4-71 235-297 (308)
4 KOG0484 Transcription factor P 99.7 1.3E-18 2.8E-23 139.1 1.7 66 3-73 16-81 (125)
5 KOG0843 Transcription factor E 99.7 4.5E-18 9.7E-23 145.5 4.9 64 3-71 101-164 (197)
6 KOG0488 Transcription factor B 99.7 3.4E-18 7.3E-23 153.8 4.0 63 3-70 171-233 (309)
7 KOG0492 Transcription factor M 99.7 8.4E-18 1.8E-22 146.9 5.8 66 3-73 143-208 (246)
8 KOG0842 Transcription factor t 99.7 7.9E-18 1.7E-22 152.3 5.3 67 1-72 150-216 (307)
9 smart00389 HOX Homeodomain. DN 99.6 9.6E-17 2.1E-21 107.2 3.0 56 5-65 1-56 (56)
10 cd00086 homeodomain Homeodomai 99.6 1.6E-16 3.5E-21 106.3 3.1 58 5-67 1-58 (59)
11 KOG0848 Transcription factor C 99.6 7.9E-17 1.7E-21 144.9 1.9 62 6-72 201-262 (317)
12 KOG2251 Homeobox transcription 99.6 2.4E-16 5.2E-21 137.7 4.9 63 4-71 37-99 (228)
13 KOG0850 Transcription factor D 99.6 7.9E-16 1.7E-20 135.5 4.4 62 3-69 121-182 (245)
14 TIGR01565 homeo_ZF_HD homeobox 99.6 1.9E-15 4.2E-20 107.7 5.4 52 5-61 2-57 (58)
15 KOG0494 Transcription factor C 99.6 8.2E-16 1.8E-20 138.3 3.7 63 4-71 141-203 (332)
16 COG5576 Homeodomain-containing 99.5 4E-15 8.7E-20 123.2 4.7 66 2-72 49-114 (156)
17 KOG0483 Transcription factor H 99.5 3.2E-15 7E-20 128.2 3.4 99 5-108 51-152 (198)
18 KOG0493 Transcription factor E 99.5 3.6E-15 7.8E-20 134.4 3.0 64 4-72 246-309 (342)
19 KOG4577 Transcription factor L 99.5 8.6E-15 1.9E-19 133.4 4.3 64 3-71 166-229 (383)
20 KOG0485 Transcription factor N 99.5 1E-14 2.2E-19 128.6 3.2 63 5-72 105-167 (268)
21 KOG0844 Transcription factor E 99.5 2E-14 4.3E-19 131.8 2.2 61 4-69 181-241 (408)
22 KOG3802 Transcription factor O 99.4 8.5E-14 1.8E-18 129.7 5.1 62 3-69 293-354 (398)
23 KOG0486 Transcription factor P 99.4 6.1E-14 1.3E-18 128.3 3.1 66 2-72 110-175 (351)
24 KOG0490 Transcription factor, 99.4 1.3E-13 2.8E-18 113.1 3.2 62 3-69 59-120 (235)
25 KOG0491 Transcription factor B 99.4 3.4E-14 7.4E-19 121.0 -0.6 64 3-71 99-162 (194)
26 KOG0847 Transcription factor, 99.1 2E-11 4.4E-16 108.3 1.2 63 6-73 169-231 (288)
27 KOG0849 Transcription factor P 99.1 4.4E-11 9.6E-16 109.4 2.7 64 4-72 176-239 (354)
28 KOG1168 Transcription factor A 98.9 7.4E-10 1.6E-14 101.6 3.4 62 4-70 309-370 (385)
29 KOG0490 Transcription factor, 98.5 5.5E-08 1.2E-12 79.9 3.2 62 3-69 152-213 (235)
30 KOG2252 CCAAT displacement pro 98.3 4.2E-07 9.1E-12 88.3 3.3 58 2-64 418-475 (558)
31 KOG0775 Transcription factor S 98.2 1.1E-06 2.3E-11 80.1 3.8 50 11-65 183-232 (304)
32 KOG0774 Transcription factor P 98.2 4.7E-06 1E-10 76.0 6.8 61 4-68 188-250 (334)
33 PF05920 Homeobox_KN: Homeobox 97.8 2.5E-06 5.3E-11 56.7 -0.7 32 28-63 9-40 (40)
34 KOG1146 Homeobox protein [Gene 97.4 8.7E-05 1.9E-09 78.3 2.5 64 3-71 902-965 (1406)
35 KOG0773 Transcription factor M 95.1 0.017 3.6E-07 51.9 2.9 66 4-73 239-306 (342)
36 KOG3623 Homeobox transcription 95.0 0.012 2.6E-07 60.2 1.8 51 16-71 568-618 (1007)
37 PF11569 Homez: Homeodomain le 91.0 0.046 9.9E-07 39.4 -0.8 42 16-62 10-51 (56)
38 PF04218 CENP-B_N: CENP-B N-te 86.3 0.81 1.8E-05 31.5 2.9 47 5-61 1-47 (53)
39 cd06171 Sigma70_r4 Sigma70, re 83.2 0.55 1.2E-05 29.0 0.8 44 10-63 10-53 (55)
40 PF04967 HTH_10: HTH DNA bindi 77.4 2.2 4.8E-05 30.0 2.4 39 11-53 1-40 (53)
41 PRK09652 RNA polymerase sigma 68.1 4 8.8E-05 31.6 2.1 46 10-65 128-173 (182)
42 PF01527 HTH_Tnp_1: Transposas 66.1 3.4 7.3E-05 28.7 1.2 43 6-58 2-45 (76)
43 cd00569 HTH_Hin_like Helix-tur 66.0 8.2 0.00018 20.9 2.6 40 8-57 3-42 (42)
44 PF04545 Sigma70_r4: Sigma-70, 65.1 3.6 7.7E-05 27.0 1.1 37 10-56 4-40 (50)
45 PF08281 Sigma70_r4_2: Sigma-7 63.2 2.8 6E-05 27.7 0.3 40 10-59 10-49 (54)
46 TIGR02937 sigma70-ECF RNA poly 62.6 4.9 0.00011 29.3 1.6 46 10-65 110-155 (158)
47 PRK09642 RNA polymerase sigma 62.5 5.7 0.00012 30.9 2.0 47 11-67 107-153 (160)
48 PRK09644 RNA polymerase sigma 62.2 5.4 0.00012 31.4 1.8 51 10-70 108-158 (165)
49 COG3413 Predicted DNA binding 61.1 10 0.00023 32.0 3.5 41 10-54 155-196 (215)
50 KOG3623 Homeobox transcription 59.6 3.8 8.3E-05 42.8 0.7 60 3-67 625-684 (1007)
51 TIGR02948 SigW_bacill RNA poly 59.2 6.2 0.00013 31.2 1.7 46 11-66 137-182 (187)
52 PRK12519 RNA polymerase sigma 57.7 7.7 0.00017 31.2 2.1 46 11-66 142-187 (194)
53 PRK09646 RNA polymerase sigma 57.6 8.8 0.00019 31.2 2.4 39 10-58 142-180 (194)
54 TIGR02952 Sig70_famx2 RNA poly 56.8 13 0.00028 28.8 3.1 47 10-70 122-168 (170)
55 KOG3755 SATB1 matrix attachmen 55.9 3.1 6.7E-05 42.5 -0.6 23 48-70 738-760 (769)
56 PRK11924 RNA polymerase sigma 55.8 11 0.00023 29.2 2.5 45 11-65 126-170 (179)
57 PRK03975 tfx putative transcri 54.7 9.7 0.00021 31.6 2.2 46 9-65 5-50 (141)
58 PRK12526 RNA polymerase sigma 54.4 9.2 0.0002 31.6 2.1 42 11-62 154-195 (206)
59 PRK06759 RNA polymerase factor 52.9 8.5 0.00018 29.6 1.5 42 10-61 106-147 (154)
60 PRK09639 RNA polymerase sigma 52.6 12 0.00025 29.1 2.3 45 10-65 112-156 (166)
61 PF13565 HTH_32: Homeodomain-l 52.3 31 0.00068 23.9 4.2 46 4-55 26-75 (77)
62 PRK12512 RNA polymerase sigma 51.9 9.6 0.00021 30.4 1.7 49 11-69 132-180 (184)
63 PF13551 HTH_29: Winged helix- 51.8 22 0.00047 25.8 3.5 52 5-57 52-108 (112)
64 PF02796 HTH_7: Helix-turn-hel 51.8 5.9 0.00013 26.0 0.4 39 8-56 3-41 (45)
65 PRK06930 positive control sigm 51.1 12 0.00026 31.3 2.2 50 10-69 114-163 (170)
66 PRK04217 hypothetical protein; 49.9 14 0.0003 29.5 2.3 45 9-63 41-85 (110)
67 PRK12532 RNA polymerase sigma 48.6 13 0.00029 30.0 2.1 48 11-68 137-184 (195)
68 PF13936 HTH_38: Helix-turn-he 48.2 6.4 0.00014 25.9 0.2 38 9-56 3-40 (44)
69 PRK09637 RNA polymerase sigma 48.2 15 0.00033 29.8 2.4 39 10-58 106-144 (181)
70 TIGR02989 Sig-70_gvs1 RNA poly 48.0 12 0.00025 28.9 1.6 38 10-57 111-148 (159)
71 PRK09047 RNA polymerase factor 47.4 15 0.00033 28.2 2.2 48 11-72 107-154 (161)
72 smart00027 EH Eps15 homology d 46.8 18 0.0004 26.5 2.4 45 9-57 2-50 (96)
73 TIGR02939 RpoE_Sigma70 RNA pol 46.6 11 0.00024 29.8 1.3 45 11-65 139-183 (190)
74 PTZ00183 centrin; Provisional 46.2 67 0.0015 24.3 5.5 42 1-42 1-46 (158)
75 TIGR02985 Sig70_bacteroi1 RNA 46.1 15 0.00033 27.7 1.9 39 11-59 114-152 (161)
76 PRK12520 RNA polymerase sigma 45.6 17 0.00037 29.3 2.3 49 11-69 132-180 (191)
77 PRK12515 RNA polymerase sigma 45.6 18 0.0004 29.1 2.4 40 10-59 131-170 (189)
78 PRK05602 RNA polymerase sigma 45.2 16 0.00034 29.3 2.0 44 11-64 129-172 (186)
79 PRK12541 RNA polymerase sigma 44.6 12 0.00027 29.1 1.3 46 10-65 112-157 (161)
80 PRK12514 RNA polymerase sigma 44.5 17 0.00038 28.8 2.1 45 11-65 130-174 (179)
81 PF12323 HTH_OrfB_IS605: Helix 44.0 15 0.00033 24.0 1.5 27 1-27 1-27 (46)
82 TIGR02959 SigZ RNA polymerase 43.7 20 0.00043 28.6 2.4 38 10-57 100-137 (170)
83 PRK12530 RNA polymerase sigma 43.6 21 0.00046 29.0 2.6 46 11-66 135-180 (189)
84 PF00196 GerE: Bacterial regul 43.5 9.5 0.00021 25.7 0.4 43 10-63 3-45 (58)
85 PRK11923 algU RNA polymerase s 43.3 17 0.00037 29.2 1.9 45 12-66 140-184 (193)
86 TIGR02983 SigE-fam_strep RNA p 42.5 17 0.00036 28.3 1.7 45 11-65 111-155 (162)
87 smart00421 HTH_LUXR helix_turn 42.2 17 0.00037 22.7 1.5 38 10-58 3-40 (58)
88 cd02413 40S_S3_KH K homology R 41.0 21 0.00046 26.7 2.0 27 32-58 49-75 (81)
89 PRK12545 RNA polymerase sigma 40.7 24 0.00053 29.0 2.5 42 11-62 140-181 (201)
90 PRK12543 RNA polymerase sigma 40.7 27 0.00058 27.9 2.7 47 11-67 118-164 (179)
91 PRK12546 RNA polymerase sigma 40.3 17 0.00037 29.9 1.5 45 11-65 114-158 (188)
92 cd06170 LuxR_C_like C-terminal 39.6 27 0.00058 22.0 2.1 37 11-58 1-37 (57)
93 TIGR03001 Sig-70_gmx1 RNA poly 39.5 29 0.00063 30.2 2.9 55 12-76 163-217 (244)
94 PRK09413 IS2 repressor TnpA; R 39.5 28 0.00061 27.1 2.6 43 6-58 8-51 (121)
95 PRK09645 RNA polymerase sigma 39.1 26 0.00056 27.5 2.4 38 11-58 119-156 (173)
96 PRK12538 RNA polymerase sigma 38.9 21 0.00045 30.7 1.9 45 11-65 172-216 (233)
97 PRK12516 RNA polymerase sigma 38.3 26 0.00057 28.6 2.4 41 11-61 117-157 (187)
98 PRK09647 RNA polymerase sigma 38.1 28 0.00061 29.1 2.5 38 11-58 139-176 (203)
99 PRK07037 extracytoplasmic-func 38.0 23 0.00051 27.4 1.9 36 11-56 110-145 (163)
100 PF08880 QLQ: QLQ; InterPro: 37.7 27 0.00059 23.0 1.9 14 10-23 2-15 (37)
101 PRK12522 RNA polymerase sigma 37.7 29 0.00064 27.4 2.5 39 11-59 120-158 (173)
102 PRK12534 RNA polymerase sigma 37.4 54 0.0012 26.1 4.0 47 11-71 138-184 (187)
103 PRK09648 RNA polymerase sigma 37.4 24 0.00051 28.3 1.9 38 10-57 139-176 (189)
104 PF06056 Terminase_5: Putative 36.8 15 0.00033 26.0 0.6 28 20-57 7-34 (58)
105 TIGR02954 Sig70_famx3 RNA poly 36.2 24 0.00053 27.7 1.8 38 10-57 119-156 (169)
106 PRK12513 RNA polymerase sigma 36.1 13 0.00027 30.1 0.1 45 11-65 140-184 (194)
107 PRK12531 RNA polymerase sigma 35.9 29 0.00063 28.2 2.2 37 11-57 142-178 (194)
108 PF10925 DUF2680: Protein of u 35.8 46 0.001 23.9 3.0 39 11-54 1-39 (59)
109 PRK12539 RNA polymerase sigma 35.5 27 0.00059 28.0 2.0 39 10-58 131-169 (184)
110 PRK08295 RNA polymerase factor 34.5 29 0.00063 28.0 2.0 46 11-71 156-201 (208)
111 PRK13558 bacterio-opsin activa 34.4 38 0.00083 32.4 3.1 43 8-54 605-648 (665)
112 PRK00118 putative DNA-binding 34.4 27 0.00059 27.6 1.7 46 10-65 17-62 (104)
113 PRK13919 putative RNA polymera 34.2 28 0.0006 27.7 1.8 38 11-58 136-173 (186)
114 PRK12536 RNA polymerase sigma 33.5 28 0.00061 27.9 1.8 46 11-66 130-175 (181)
115 PRK09480 slmA division inhibit 33.3 31 0.00068 27.1 2.0 42 15-62 12-56 (194)
116 PRK12524 RNA polymerase sigma 33.3 33 0.00073 27.9 2.2 39 11-59 137-175 (196)
117 KOG1146 Homeobox protein [Gene 33.3 29 0.00064 38.3 2.3 58 6-68 707-764 (1406)
118 PRK06986 fliA flagellar biosyn 32.6 28 0.0006 29.4 1.7 48 11-68 185-232 (236)
119 PRK06811 RNA polymerase factor 32.5 28 0.0006 28.2 1.6 38 10-57 131-168 (189)
120 PF08279 HTH_11: HTH domain; 31.6 28 0.0006 22.9 1.2 32 15-54 2-33 (55)
121 PF08280 HTH_Mga: M protein tr 31.4 19 0.00041 24.8 0.4 33 13-54 5-37 (59)
122 PF08144 CPL: CPL (NUC119) dom 31.3 77 0.0017 26.1 4.0 38 5-43 16-55 (148)
123 PRK12547 RNA polymerase sigma 30.9 37 0.00079 26.8 2.0 42 11-62 113-154 (164)
124 PRK12544 RNA polymerase sigma 30.5 43 0.00094 28.0 2.5 45 11-65 149-193 (206)
125 PF10668 Phage_terminase: Phag 30.5 33 0.00071 24.9 1.5 16 37-56 27-42 (60)
126 PF07638 Sigma70_ECF: ECF sigm 30.5 33 0.00071 28.2 1.7 46 11-66 136-181 (185)
127 PF07750 GcrA: GcrA cell cycle 30.0 85 0.0018 26.3 4.1 35 10-53 2-36 (162)
128 PRK12518 RNA polymerase sigma 29.7 18 0.00038 28.5 -0.0 28 35-66 139-166 (175)
129 PF13873 Myb_DNA-bind_5: Myb/S 29.5 62 0.0013 22.8 2.8 58 9-67 3-75 (78)
130 PRK12511 RNA polymerase sigma 29.4 45 0.00099 27.2 2.4 38 10-57 111-148 (182)
131 PRK09641 RNA polymerase sigma 29.1 38 0.00081 26.7 1.8 44 12-65 138-181 (187)
132 PRK12523 RNA polymerase sigma 29.1 38 0.00083 26.8 1.8 39 11-59 120-158 (172)
133 smart00340 HALZ homeobox assoc 28.8 29 0.00064 24.2 1.0 26 82-107 19-44 (44)
134 KOG3039 Uncharacterized conser 28.6 3.4E+02 0.0073 25.5 7.9 29 172-200 179-208 (303)
135 PRK12533 RNA polymerase sigma 28.0 31 0.00067 29.3 1.2 49 11-73 135-183 (216)
136 PRK10100 DNA-binding transcrip 27.1 28 0.00061 29.7 0.8 51 10-71 155-205 (216)
137 TIGR02943 Sig70_famx1 RNA poly 26.7 57 0.0012 26.6 2.5 48 11-72 132-179 (188)
138 PRK12542 RNA polymerase sigma 26.2 41 0.00089 27.0 1.5 37 11-57 123-159 (185)
139 PRK15369 two component system 26.0 36 0.00078 25.6 1.1 44 10-64 149-192 (211)
140 PF13518 HTH_28: Helix-turn-he 24.9 52 0.0011 21.0 1.6 33 16-59 3-35 (52)
141 PRK09636 RNA polymerase sigma 24.5 44 0.00096 29.2 1.6 47 11-67 116-162 (293)
142 PRK12529 RNA polymerase sigma 24.2 51 0.0011 26.4 1.8 39 11-59 128-166 (178)
143 TIGR02947 SigH_actino RNA poly 24.1 36 0.00079 27.4 0.9 27 35-65 150-176 (193)
144 PRK12527 RNA polymerase sigma 23.6 58 0.0013 25.3 1.9 38 11-58 106-143 (159)
145 TIGR02957 SigX4 RNA polymerase 23.4 49 0.0011 29.0 1.6 47 11-67 109-155 (281)
146 PTZ00397 macrophage migration 23.3 51 0.0011 25.2 1.5 25 36-60 79-103 (116)
147 PRK12517 RNA polymerase sigma 23.1 82 0.0018 25.7 2.8 52 11-76 129-180 (188)
148 PF12824 MRP-L20: Mitochondria 23.0 2.8E+02 0.0062 23.5 6.0 41 7-54 82-122 (164)
149 PRK08583 RNA polymerase sigma 23.0 56 0.0012 27.9 1.9 38 11-58 206-243 (257)
150 COG4367 Uncharacterized protei 22.4 59 0.0013 26.0 1.7 39 10-53 2-40 (97)
151 PRK09651 RNA polymerase sigma 22.0 73 0.0016 25.3 2.2 38 10-57 119-156 (172)
152 PRK10360 DNA-binding transcrip 21.9 64 0.0014 24.7 1.8 43 10-63 137-179 (196)
153 PRK08301 sporulation sigma fac 21.6 67 0.0015 26.9 2.0 38 11-58 179-220 (234)
154 PRK09643 RNA polymerase sigma 21.6 1.3E+02 0.0028 24.5 3.6 34 11-54 135-168 (192)
155 PRK09640 RNA polymerase sigma 21.2 25 0.00054 28.4 -0.6 23 36-62 154-176 (188)
156 PRK06288 RNA polymerase sigma 21.1 83 0.0018 27.3 2.6 44 10-63 212-255 (268)
157 PRK09649 RNA polymerase sigma 21.1 55 0.0012 26.5 1.4 37 11-57 131-167 (185)
158 PRK09638 RNA polymerase sigma 21.0 31 0.00067 27.1 -0.1 18 36-57 146-163 (176)
159 PRK12528 RNA polymerase sigma 20.9 62 0.0014 25.1 1.6 37 11-57 114-150 (161)
160 PRK12540 RNA polymerase sigma 20.8 76 0.0016 25.8 2.1 37 11-57 112-148 (182)
161 PRK12535 RNA polymerase sigma 20.7 61 0.0013 26.8 1.6 38 11-58 134-171 (196)
162 PRK10403 transcriptional regul 20.7 70 0.0015 24.3 1.8 53 9-72 152-204 (215)
163 PF11406 Tachystatin_A: Antimi 20.5 48 0.001 22.8 0.7 21 172-196 18-38 (44)
164 PRK10651 transcriptional regul 20.1 52 0.0011 25.2 1.0 46 10-66 155-200 (216)
165 TIGR02941 Sigma_B RNA polymera 20.0 69 0.0015 27.3 1.8 40 10-59 205-244 (255)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=1.9e-19 Score=157.34 Aligned_cols=65 Identities=22% Similarity=0.274 Sum_probs=60.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
..+|.||.||..||-+||+.|..|. |.++.+|.+||..|. |+|+||||||||||+|+||..+...
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN~-YLtR~RRiEiA~~L~----LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFNK-YLTRSRRIEIAHALN----LTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhcccc-ccchHHHHHHHhhcc----hhHHHHHHHHHHHHHHHHHhhcccc
Confidence 4799999999999999999999996 999999999999997 9999999999999999998776653
No 2
>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=99.74 E-value=7.8e-19 Score=118.82 Aligned_cols=57 Identities=28% Similarity=0.497 Sum_probs=54.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHH
Q 039144 5 GSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQ 66 (208)
Q Consensus 5 ~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKR 66 (208)
+|+|+.||++|+.+||++|..++ ||+.+++..||..|+ |+..+|++||||||+|+||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~-~p~~~~~~~la~~l~----l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENP-YPSKEEREELAKELG----LTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSS-SCHHHHHHHHHHHHT----SSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhc-ccccccccccccccc----ccccccccCHHHhHHHhCc
Confidence 58999999999999999999995 999999999999996 9999999999999999986
No 3
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.73 E-value=1.9e-18 Score=156.38 Aligned_cols=63 Identities=21% Similarity=0.311 Sum_probs=59.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 4 AGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
.|++|..+|+.|+.+||+.|..|. |.+.++|.+|++.|. |+|+||+|||||||+|+||.-|+.
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~-YitkeKR~ElSr~lN----LTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNM-YITKEKRLELSRTLN----LTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHH-HHhHHHHHHHHHhcc----cchhheeeeehhhhhHHhhhhhhh
Confidence 588999999999999999999997 999999999999997 999999999999999999987654
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.72 E-value=1.3e-18 Score=139.06 Aligned_cols=66 Identities=24% Similarity=0.349 Sum_probs=60.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHHh
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKLG 73 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~~ 73 (208)
.-||-||+||..||.+||.+|.+.+ ||++-.|++||-+|. |+|.+|||||||||||.+++.|-..-
T Consensus 16 KQRRIRTTFTS~QLkELErvF~ETH-YPDIYTREEiA~kid----LTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAETH-YPDIYTREEIALKID----LTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHhhc-CCcchhHHHHHHhhh----hhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 3578899999999999999999996 999999999999997 99999999999999999988776544
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.72 E-value=4.5e-18 Score=145.50 Aligned_cols=64 Identities=23% Similarity=0.396 Sum_probs=60.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
.++|.||.||++||..||.+|+.+. |....+|++||..|+ |+|.||+|||||||.|.||.+-+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~-Yvvg~eR~~LA~~L~----LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQ-YVVGAERKQLAQSLS----LSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCC-eeechHHHHHHHHcC----CChhHhhhhhhhhhHHHHHHHHHh
Confidence 5789999999999999999999996 999999999999997 999999999999999999887665
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=3.4e-18 Score=153.84 Aligned_cols=63 Identities=19% Similarity=0.290 Sum_probs=60.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRR 70 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~ 70 (208)
..|+.||.||..||..||+.|+... |.+..+|.+||+.|+ |++.||++||||||+|+||...+
T Consensus 171 K~RksRTaFT~~Ql~~LEkrF~~QK-YLS~~DR~~LA~~Lg----LTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 171 KRRKSRTAFSDHQLFELEKRFEKQK-YLSVADRIELAASLG----LTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred ccccchhhhhHHHHHHHHHHHHHhh-cccHHHHHHHHHHcC----CchhhHHHHHhhhhHHHHHHHHh
Confidence 4788999999999999999999996 999999999999996 99999999999999999998877
No 7
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.71 E-value=8.4e-18 Score=146.93 Aligned_cols=66 Identities=24% Similarity=0.379 Sum_probs=61.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHHh
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKLG 73 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~~ 73 (208)
+-|++||.||..||..||+.|.+.. |.++++|.+++..|. |+|.||+|||||||||.||.++.++.
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekq-YLSiaEraefSsSL~----LTeTqVKIWFQNRRAKaKRlQeae~E 208 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQ-YLSIAERAEFSSSLE----LTETQVKIWFQNRRAKAKRLQEAELE 208 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhh-hhhHHHHHhhhhhhh----hhhhheehhhhhhhHHHHHHHHHHHH
Confidence 3589999999999999999999995 999999999999997 99999999999999999998887754
No 8
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.71 E-value=7.9e-18 Score=152.26 Aligned_cols=67 Identities=21% Similarity=0.325 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 1 MSPAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 1 ~sp~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
|.+.||+|.-||+.|+-+||+.|...+ |.++.+|++||..|. |++.||||||||||.|.||++.++.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQR-YLSAPERE~LA~~Lr----LT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQR-YLSAPEREHLASSLR----LTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhh-ccccHhHHHHHHhcC----CCchheeeeeecchhhhhhhhhhhh
Confidence 457899999999999999999999995 999999999999997 9999999999999999998877763
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.64 E-value=9.6e-17 Score=107.22 Aligned_cols=56 Identities=30% Similarity=0.487 Sum_probs=52.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 5 GSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 5 ~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
.+.|+.||++|+.+||+.|+.++ ||+.+++.+||+.|+ |+..+|++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNP-YPSREEREELAAKLG----LSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHC----cCHHHHHHhHHHHhhccC
Confidence 36789999999999999999996 999999999999996 999999999999999864
No 10
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.63 E-value=1.6e-16 Score=106.34 Aligned_cols=58 Identities=28% Similarity=0.452 Sum_probs=54.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHH
Q 039144 5 GSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQK 67 (208)
Q Consensus 5 ~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk 67 (208)
++.|..|+++|+.+||+.|+.++ ||+.+++.+||+.|+ |++++|++||+|||++.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~~----l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNP-YPSREEREELAKELG----LTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHC----cCHHHHHHHHHHHHHHHhcc
Confidence 46899999999999999999995 999999999999996 99999999999999998864
No 11
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.63 E-value=7.9e-17 Score=144.90 Aligned_cols=62 Identities=26% Similarity=0.389 Sum_probs=56.9
Q ss_pred CCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 6 STRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 6 R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
+-|.++|..|.-+||+.|..++ |.++.++.+||..|+ |+|+||||||||||||+||..+.+.
T Consensus 201 KYRvVYTDhQRLELEKEfh~Sr-yITirRKSELA~~Lg----LsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSR-YITIRRKSELAATLG----LSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ceeEEecchhhhhhhhhhcccc-ceeeehhHHHHHhhC----ccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 4578899999999999999995 999999999999997 9999999999999999998776654
No 12
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.63 E-value=2.4e-16 Score=137.75 Aligned_cols=63 Identities=22% Similarity=0.393 Sum_probs=58.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 4 AGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
-||.||+||-.||++||.+|++.. |||...|++||.+|. |.|.+|+|||.|||||.|++++..
T Consensus 37 qRRERTtFtr~QlevLe~LF~kTq-YPDv~~rEelAlkln----LpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAKTQ-YPDVFMREELALKLN----LPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cccccceecHHHHHHHHHHHHhhc-CccHHHHHHHHHHhC----CchhhhhhhhccccchhhHhhhhh
Confidence 478999999999999999999996 999999999999997 999999999999999999766544
No 13
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.59 E-value=7.9e-16 Score=135.46 Aligned_cols=62 Identities=18% Similarity=0.255 Sum_probs=59.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLR 69 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r 69 (208)
+.|++||.++.-||+.|.+.|++.. |....+|++||+.|+ |+..||||||||||.|.||..+
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQkTQ-YLALPERAeLAAsLG----LTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQTQ-YLALPERAELAASLG----LTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhhcc-hhcCcHHHHHHHHhC----CchhHhhhhhhhhHHHHHHHHh
Confidence 4689999999999999999999995 999999999999997 9999999999999999999887
No 14
>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=99.59 E-value=1.9e-15 Score=107.67 Aligned_cols=52 Identities=15% Similarity=0.160 Sum_probs=49.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhhccCCCCCCceeeccccch
Q 039144 5 GSTRWCPTPEQLMILEEMYRSGVRT----PNASQIQHITAHLSHFGKIEGKNVFYWFQNHK 61 (208)
Q Consensus 5 ~R~Rt~FT~eQLqiLE~~F~~n~~y----P~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRR 61 (208)
+|.||.||++|++.||+.|+.+. | |+..+|.+||..|+ |++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~-y~~~~~~~~~r~~la~~lg----l~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLG-WKLKDKRREEVREFCEEIG----VTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHhC----CCHHHeeeecccCC
Confidence 79999999999999999999995 9 99999999999996 99999999999975
No 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.58 E-value=8.2e-16 Score=138.33 Aligned_cols=63 Identities=22% Similarity=0.301 Sum_probs=56.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 4 AGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
+|+-||.||..||.+||+.|.+.. |||...|+-||.++. |.|.+|+|||||||||+||++++-
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaH-YPDv~Are~la~kte----lpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAH-YPDVYAREMLADKTE----LPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhcc-CccHHHHHHHhhhcc----CchhhhhHHhhhhhHHhhhhhhhc
Confidence 344499999999999999999996 999998888888875 999999999999999999887765
No 16
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.55 E-value=4e-15 Score=123.25 Aligned_cols=66 Identities=35% Similarity=0.514 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 2 SPAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 2 sp~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
|+.++.|.+-|.+|+.+||+.|+.++ ||+...|..|+..|+ |+++.|++|||||||++|++.....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p-~Ps~~~r~~L~~~ln----m~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINP-YPSSITRIKLSLLLN----MPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCC-CCCHHHHHHHHHhcC----CChhhhhhhhchHHHHHHHhcccch
Confidence 57889999999999999999999996 999999999999996 9999999999999999998776653
No 17
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.54 E-value=3.2e-15 Score=128.21 Aligned_cols=99 Identities=20% Similarity=0.242 Sum_probs=81.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHHhHHHHHHHH---
Q 039144 5 GSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKLGKQLQLQQQ--- 81 (208)
Q Consensus 5 ~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~~k~~q~qq~--- 81 (208)
.+..-+||.+|+..||..|+.+. |...+++.+||.+|+ |.++||.|||||||||+|.++-+.....+..|=-
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~-~L~p~~K~~LAk~Lg----L~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~ 125 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEK-KLEPERKKKLAKELG----LQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLR 125 (198)
T ss_pred ccccccccHHHHHHhHHhhcccc-ccChHHHHHHHHhhC----CChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHh
Confidence 45667899999999999999996 999999999999996 9999999999999999999999998877773222
Q ss_pred HHHHhhccchhhhcCCCCCcccccccc
Q 039144 82 QQIFQHHHHLQQCCQVPNHHQQLLHCS 108 (208)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~h~~ 108 (208)
.+...|+.+++++.+.......++|++
T Consensus 126 ~~~~~Lq~e~~eL~~~~~~~~~~~~~~ 152 (198)
T KOG0483|consen 126 SENDRLQSEVQELVAELSSLKREMQKS 152 (198)
T ss_pred hhhhHHHHHHHHHHHHHhhhhhhhccC
Confidence 234557778888888766666666654
No 18
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.53 E-value=3.6e-15 Score=134.44 Aligned_cols=64 Identities=22% Similarity=0.312 Sum_probs=58.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 4 AGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
..|+||.||.|||+.|...|+.|. |.+..+|++||.+|+ |.|.||+|||||+|||.||.--.+.
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enR-YlTEqRRQ~La~ELg----LNEsQIKIWFQNKRAKiKKsTgskn 309 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENR-YLTEQRRQELAQELG----LNESQIKIWFQNKRAKIKKSTGSKN 309 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhh-hHHHHHHHHHHHHhC----cCHHHhhHHhhhhhhhhhhccCCCC
Confidence 358999999999999999999995 999999999999997 9999999999999999997654443
No 19
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.51 E-value=8.6e-15 Score=133.42 Aligned_cols=64 Identities=25% Similarity=0.387 Sum_probs=55.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
+..|+||++|..||+.|..+|+..+ .|.+- ++++|+..+||+.++|||||||||||+||.++..
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~Sp-KPARH----VREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSP-KPARH----VREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCC-chhHH----HHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 4689999999999999999999995 99885 5555556667999999999999999999977654
No 20
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.49 E-value=1e-14 Score=128.60 Aligned_cols=63 Identities=21% Similarity=0.307 Sum_probs=58.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 5 GSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 5 ~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
.++||.|+..|+..||..|+-.. |.+..+|..||++|. |+|.||++||||||-|+||+-...+
T Consensus 105 KktRTvFSraQV~qLEs~Fe~kr-YLSsaeRa~LA~sLq----LTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 105 KKTRTVFSRAQVFQLESTFELKR-YLSSAERAGLAASLQ----LTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred ccchhhhhHHHHHHHHHHHHHHh-hhhHHHHhHHHHhhh----hhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 57899999999999999999995 999999999999997 9999999999999999998765543
No 21
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.45 E-value=2e-14 Score=131.83 Aligned_cols=61 Identities=20% Similarity=0.277 Sum_probs=56.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHH
Q 039144 4 AGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLR 69 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r 69 (208)
.||-||.||.|||..||+.|-... |.++.+|=+||+.|+ |.|..|||||||||+|+||++-
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrEN-YVSRprRcELAAaLN----LPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYREN-YVSRPRRCELAAALN----LPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhc-cccCchhhhHHHhhC----CCcceeehhhhhchhhhhhhhh
Confidence 578999999999999999998885 999999999999997 9999999999999999997653
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.44 E-value=8.5e-14 Score=129.73 Aligned_cols=62 Identities=23% Similarity=0.334 Sum_probs=58.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLR 69 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r 69 (208)
..|++||+|....+.+||+.|..|+ .|+.++|.+||++|+ |+..+|+|||+|||.|+||-..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~np-KPt~qEIt~iA~~L~----leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNP-KPTSQEITHIAESLQ----LEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCC-CCCHHHHHHHHHHhc----cccceEEEEeeccccccccCCC
Confidence 3589999999999999999999996 999999999999997 9999999999999999997655
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.42 E-value=6.1e-14 Score=128.28 Aligned_cols=66 Identities=27% Similarity=0.393 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 2 SPAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 2 sp~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
++.||.|+-||..||++||..|..| +||+.+.|++||.-.. |+|.+|.|||.|||||+|+.+|...
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwtN----lTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWTN----LTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhcc----ccchhhhhhcccchhhhhhhhhhHH
Confidence 5689999999999999999999999 5999999999999996 9999999999999999998777654
No 24
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.40 E-value=1.3e-13 Score=113.10 Aligned_cols=62 Identities=26% Similarity=0.283 Sum_probs=57.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLR 69 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r 69 (208)
..+|.|+.|+..|+++||.+|+..+ ||+...|+.+|..+. ++|.+|+|||||||||++++.+
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~~h-~Pd~~~r~~la~~~~----~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEKVH-LPCFACRECLALLLT----GDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcCCC-cCccchHHHHhhcCC----CCeeeeehhhhhhcHhhhhhhc
Confidence 4689999999999999999999995 999998888887775 9999999999999999998876
No 25
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.39 E-value=3.4e-14 Score=120.98 Aligned_cols=64 Identities=22% Similarity=0.310 Sum_probs=59.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
..++.|+.|+..||..||+.|+... |.+..+|.+||..|+ |++.+|+.||||||+|.||..|..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Qr-YLS~~e~~ELan~L~----LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQR-YLSTPERQELANALS----LSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhh-hcccHHHHHHHHHhh----hhHHHHHHHHHHHHHHHHHHHhcc
Confidence 3578899999999999999999995 999999999999997 999999999999999999887765
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.10 E-value=2e-11 Score=108.34 Aligned_cols=63 Identities=21% Similarity=0.312 Sum_probs=57.2
Q ss_pred CCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHHh
Q 039144 6 STRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKLG 73 (208)
Q Consensus 6 R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~~ 73 (208)
-.|-+|+-.||..||..|++.. ||-.++|.++|..|+ ++|.+|+|||||||.|+|||..-+..
T Consensus 169 ~srPTf~g~qi~~le~~feqtk-ylaG~~ra~lA~~lg----mteSqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 169 QSRPTFTGHQIYQLERKFEQTK-YLAGADRAQLAQELN----MTESQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred ccCCCccchhhhhhhhhhhhhh-cccchhHHHhhcccc----ccHHHHHHHHhcchhhhhhhhccchh
Confidence 3578899999999999999996 999999999999996 99999999999999999998766543
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.08 E-value=4.4e-11 Score=109.36 Aligned_cols=64 Identities=25% Similarity=0.360 Sum_probs=58.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 4 AGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
.+|.|++||++|+..||+.|+.++ ||+...|++||.+++ ++|.+|+|||+|||||.+|......
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~-yP~i~~Re~La~~i~----l~e~riqvwf~nrra~~rr~~~~~s 239 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTP-YPDIVGRETLAKETG----LPEPRVQVWFQNRRAKWRRQHRDCS 239 (354)
T ss_pred ccccccccccchHHHHHHHhcCCC-CCchhhHHHHhhhcc----CCchHHHHHHhhhhhhhhhcccccc
Confidence 467799999999999999999996 999999999998886 9999999999999999998876543
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.90 E-value=7.4e-10 Score=101.56 Aligned_cols=62 Identities=19% Similarity=0.332 Sum_probs=56.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHH
Q 039144 4 AGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRR 70 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~ 70 (208)
..|+||++-.-..+.||.+|...+ .|+.+.|..||++|. |...+|+|||+|.|.|.||.++.
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQP-RPS~EkIAaIAekLD----LKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQP-RPSGEKIAAIAEKLD----LKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred cccccccccCcccccHHHHhccCC-CCchhHHHHHHHhhh----hhhceEEEEeeccHHHHHHhhhh
Confidence 368999999999999999999996 999999999999997 88999999999999999985443
No 29
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.53 E-value=5.5e-08 Score=79.95 Aligned_cols=62 Identities=26% Similarity=0.459 Sum_probs=56.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLR 69 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r 69 (208)
+.++.|+.++..|+..|+..|..+. +|+...+.+|+..++ +++++|++||||+|++.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~~-~P~~~~~~~l~~~~~----~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRATP-KPDADDREQLAEETG----LSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcccCCC-CCchhhHHHHHHhcC----CChhhhhhhcccHHHHHHhhcc
Confidence 5788999999999999999999996 999988888888875 9999999999999999998766
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.29 E-value=4.2e-07 Score=88.29 Aligned_cols=58 Identities=21% Similarity=0.306 Sum_probs=53.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhH
Q 039144 2 SPAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARE 64 (208)
Q Consensus 2 sp~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRARe 64 (208)
-...++|.+||+.|++.|-.+|..++ +|+.+..+.|+.+|+ |+...|.+||.|-|-|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~-RPS~Emq~tIS~qL~----L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENK-RPSREMQETISQQLN----LELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCC-CCCHHHHHHHHHHhC----CcHHHHHHHHHhhhhhc
Confidence 34678999999999999999999996 999999999999996 99999999999988776
No 31
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.21 E-value=1.1e-06 Score=80.09 Aligned_cols=50 Identities=20% Similarity=0.385 Sum_probs=44.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
|-..=...|.+.|..++ ||+.+++.+||+..+ |+-.||-+||.|||.|+|
T Consensus 183 FKekSR~~LrewY~~~~-YPsp~eKReLA~aTg----Lt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNP-YPSPREKRELAEATG----LTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcCC-CCChHHHHHHHHHhC----Cchhhhhhhhhhhhhhhh
Confidence 44445678999999995 999999999999885 999999999999999998
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.16 E-value=4.7e-06 Score=75.99 Aligned_cols=61 Identities=21% Similarity=0.330 Sum_probs=53.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhc--CCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHH
Q 039144 4 AGSTRWCPTPEQLMILEEMYRS--GVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKL 68 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~--n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~ 68 (208)
+||+|-.|++.--++|.++|-. +.+||+.+..++||.+.+ |+-++|-+||-|+|.|-||-.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCn----ItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCN----ITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcC----ceehhhccccccceeehhhhh
Confidence 6899999999999999999943 226999998888888875 999999999999999988643
No 33
>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=97.85 E-value=2.5e-06 Score=56.67 Aligned_cols=32 Identities=19% Similarity=0.464 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHHHHhhccCCCCCCceeeccccchhh
Q 039144 28 RTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKAR 63 (208)
Q Consensus 28 ~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAR 63 (208)
+||+.+++.+||.+.+ |+..+|.+||-|.|.|
T Consensus 9 PYPs~~ek~~L~~~tg----ls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 9 PYPSKEEKEELAKQTG----LSRKQISNWFINARRR 40 (40)
T ss_dssp GS--HHHHHHHHHHHT----S-HHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHcC----CCHHHHHHHHHHhHcc
Confidence 5999999999999986 9999999999999976
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.38 E-value=8.7e-05 Score=78.31 Aligned_cols=64 Identities=19% Similarity=0.319 Sum_probs=55.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
..|+.|+.++..||++|..+|.... ||..++.+.+-..++ ++.++|.+||||-|+|.|+.....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~-~~~~~~~E~l~~~~~----~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQR-TPTMQECEVLEEPIG----LPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhcc-CChHHHHHhhccccc----CCcchhHHhhhhhhhhhhhhhhcc
Confidence 4688999999999999999999995 999988877666664 999999999999999999876543
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.12 E-value=0.017 Score=51.86 Aligned_cols=66 Identities=14% Similarity=0.145 Sum_probs=50.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcC--CCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHHh
Q 039144 4 AGSTRWCPTPEQLMILEEMYRSG--VRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKLG 73 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~n--~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~~ 73 (208)
..|++..+-++...+|+.-.... .+||+..+...||.+. ||+-.+|.+||-|.|-|..+-......
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~T----GLs~~Qv~NWFINaR~R~w~p~~~~~~ 306 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQT----GLSRPQVSNWFINARVRLWKPMIEEMY 306 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhc----CCCcccCCchhhhcccccCCchHHHHH
Confidence 45667788899999998765442 2599998877666665 599999999999999998866655433
No 36
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.96 E-value=0.012 Score=60.21 Aligned_cols=51 Identities=20% Similarity=0.336 Sum_probs=46.0
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 16 LMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 16 LqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
+..|..+|..|. .|+.++-..||..++ |.-++|+.||++++|.+....|.-
T Consensus 568 ~sllkayyaln~-~ps~eelskia~qvg----lp~~vvk~wfE~~~a~e~sv~rsp 618 (1007)
T KOG3623|consen 568 TSLLKAYYALNG-LPSEEELSKIAQQVG----LPFAVVKAWFEDEEAEEMSVERSP 618 (1007)
T ss_pred HHHHHHHHHhcC-CCCHHHHHHHHHHhc----ccHHHHHHHHHhhhhhhhhhccCc
Confidence 788999999995 999999999999996 999999999999999998776543
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=91.01 E-value=0.046 Score=39.39 Aligned_cols=42 Identities=14% Similarity=0.279 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchh
Q 039144 16 LMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKA 62 (208)
Q Consensus 16 LqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRA 62 (208)
++-|+++|.... .+...+...|.++-+ |+..+|+.||--|+.
T Consensus 10 ~~pL~~Yy~~h~-~L~E~DL~~L~~kS~----ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHK-QLQEEDLDELCDKSR----MSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHTT------HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcC-CccHhhHHHHHHHHC----CCHHHHHHHHHHhcc
Confidence 466999999995 999999988888875 999999999976644
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=86.32 E-value=0.81 Score=31.53 Aligned_cols=47 Identities=15% Similarity=0.157 Sum_probs=35.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccch
Q 039144 5 GSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHK 61 (208)
Q Consensus 5 ~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRR 61 (208)
+|+|..+|-+|.-.+=+.++.+. + ..+||.+++ ++..+|..|..||.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~---s---~~~ia~~fg----v~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE---S---KRDIAREFG----VSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT-------HHHHHHHHT------CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC---C---HHHHHHHhC----CCHHHHHHHHHhHH
Confidence 47899999999998888999983 3 347899996 99999999998864
No 39
>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=83.24 E-value=0.55 Score=29.01 Aligned_cols=44 Identities=11% Similarity=0.081 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhh
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKAR 63 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAR 63 (208)
.+++.+..+++..|..+ +... +||+.++ ++...|+.|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~--~~~~----~ia~~~~----~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG--LSYE----EIAEILG----ISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC--CCHH----HHHHHHC----cCHHHHHHHHHHHHHH
Confidence 46888999999999766 3333 6899986 9999998887654443
No 40
>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=77.36 E-value=2.2 Score=30.01 Aligned_cols=39 Identities=26% Similarity=0.377 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHhhccCCCCCCce
Q 039144 11 PTPEQLMILEEMYRSGV-RTPNASQIQHITAHLSHFGKIEGKNV 53 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~-~yP~~~~R~qLA~~L~~~g~LsE~qV 53 (208)
+|+.|.++|..+|+.+= .+|-.....+||++|+ |+..-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lg----is~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELG----ISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhC----CCHHHH
Confidence 58999999999999984 3477777889999996 776554
No 41
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=68.09 E-value=4 Score=31.62 Aligned_cols=46 Identities=11% Similarity=-0.060 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
.+++.+.++|.-.|-.+ ++-. +||+.|+ +++..|+.|...=|.|.|
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s~~----eIA~~lg----is~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LSYE----EIAEIMG----CPIGTVRSRIFRAREALR 173 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 46788889998888776 3444 6999996 999999877763333333
No 42
>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=66.06 E-value=3.4 Score=28.70 Aligned_cols=43 Identities=19% Similarity=0.358 Sum_probs=27.0
Q ss_pred CCCCCCCHHHHHHHHHHH-hcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 6 STRWCPTPEQLMILEEMY-RSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 6 R~Rt~FT~eQLqiLE~~F-~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
+.|..||+++...+=..+ ..+. .+.+||.+++ |+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g~------sv~~va~~~g----i~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESGE------SVSEVAREYG----ISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHHC------HHHHHHHHHT----S-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCCC------ceEeeecccc----cccccccHHHH
Confidence 567889998876665555 5553 4557999996 99999999943
No 43
>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=66.03 E-value=8.2 Score=20.92 Aligned_cols=40 Identities=18% Similarity=0.336 Sum_probs=27.8
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 8 RWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 8 Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
+..++.++...+...|..+ + + ..+||+.++ ++...|..|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~~--~-s---~~~ia~~~~----is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAAG--E-S---VAEIARRLG----VSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHcC--C-C---HHHHHHHHC----CCHHHHHHhC
Confidence 3456788888888888755 3 2 336888885 8887787773
No 44
>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=65.07 E-value=3.6 Score=27.02 Aligned_cols=37 Identities=19% Similarity=0.228 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeec
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYW 56 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvW 56 (208)
.+++.|.++|...|..+. +- .+||+.|+ ++...|+.+
T Consensus 4 ~L~~~er~vi~~~y~~~~--t~----~eIa~~lg----~s~~~V~~~ 40 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL--TL----EEIAERLG----ISRSTVRRI 40 (50)
T ss_dssp TS-HHHHHHHHHHHTST---SH----HHHHHHHT----SCHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC--CH----HHHHHHHC----CcHHHHHHH
Confidence 478999999999997763 33 37999997 898888754
No 45
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=63.23 E-value=2.8 Score=27.68 Aligned_cols=40 Identities=23% Similarity=0.157 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecccc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQN 59 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQN 59 (208)
.+++.+..++.-.|-.+. +.. +||+.++ +++..|++|.+.
T Consensus 10 ~L~~~~r~i~~l~~~~g~--s~~----eIa~~l~----~s~~~v~~~l~r 49 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQGM--SYA----EIAEILG----ISESTVKRRLRR 49 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----HH----HHHHHCT----S-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCc--CHH----HHHHHHC----cCHHHHHHHHHH
Confidence 357888999999998884 544 6999996 999999988754
No 46
>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=62.64 E-value=4.9 Score=29.29 Aligned_cols=46 Identities=17% Similarity=0.125 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
.+++.|.+++...|-.+ ++.. +||+.|+ +++..|..+...=+.|.|
T Consensus 110 ~L~~~~~~ii~~~~~~g--~s~~----eIA~~l~----~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG--LSYK----EIAEILG----ISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhcC--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 46788888988877665 4444 6999996 999999876655444433
No 47
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=62.54 E-value=5.7 Score=30.89 Aligned_cols=47 Identities=13% Similarity=0.023 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQK 67 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk 67 (208)
+++.|.+++.-.|-.+. +-. +||+.|+ +++..|++....=|.+.|+.
T Consensus 107 Lp~~~r~v~~l~~~~g~--s~~----EIA~~lg----is~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK--SYQ----EIALQEK----IEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhCC--CHH----HHHHHHC----CCHHHHHHHHHHHHHHHHHH
Confidence 45666777777776663 333 6899996 99999997766444444443
No 48
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=62.20 E-value=5.4 Score=31.37 Aligned_cols=51 Identities=6% Similarity=-0.082 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRR 70 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~ 70 (208)
.+++.|.++|.-.|-.+ ++-. +||+.|+ +++..|++|.+-=|.+.|+..++
T Consensus 108 ~L~~~~r~v~~l~~~~g--~s~~----eIA~~lg----is~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE--LTYE----EAASVLD----LKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred hCCHHHHHHHHhHHHhc--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHHHHHHh
Confidence 35677778887766555 3433 6999996 99999987766555555544433
No 49
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=61.09 E-value=10 Score=31.99 Aligned_cols=41 Identities=22% Similarity=0.323 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHhhccCCCCCCcee
Q 039144 10 CPTPEQLMILEEMYRSGV-RTPNASQIQHITAHLSHFGKIEGKNVF 54 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~-~yP~~~~R~qLA~~L~~~g~LsE~qVq 54 (208)
.+|+.|+++|..+|..|= -||-....++||++|| |+...+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lG----ISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELG----ISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhC----CCHHHHH
Confidence 699999999999999984 4577777888999996 8776553
No 50
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=59.65 E-value=3.8 Score=42.78 Aligned_cols=60 Identities=15% Similarity=0.161 Sum_probs=46.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHH
Q 039144 3 PAGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQK 67 (208)
Q Consensus 3 p~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk 67 (208)
++.+.|+....++-..|-.+|+-+. -|+..+-.-++.+|. ..+.+|.+||++|+.+.+.-
T Consensus 625 ~p~kv~sp~k~~dq~ql~~a~elq~-s~~n~~~pl~~t~~~----n~~pv~ev~dhsrsstpsp~ 684 (1007)
T KOG3623|consen 625 RPVKVRSPIKEEDQQQLKQAYELQA-SPSNDEFPLIATRLQ----NDPPVVEVWDHSRSSTPSPM 684 (1007)
T ss_pred CCccccCCCCccchhhhHhhhhccc-CccCcccchhhhhcc----CCCcchhhcccCCCCCCCCC
Confidence 4667788888888899999998875 555554445666665 67888999999999988753
No 51
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=59.18 E-value=6.2 Score=31.22 Aligned_cols=46 Identities=15% Similarity=0.151 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQ 66 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKR 66 (208)
+++.+.++|+-.|-.+ ++. ++||+.|+ +++..|+++.+.=|.+.|.
T Consensus 137 L~~~~r~v~~l~~~~g--~s~----~eIA~~lg----is~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 137 LPPKYRMVIVLKYMED--LSL----KEISEILD----LPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHhHHhhhHHhcC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 4556666666655555 233 36999996 9999999877554444443
No 52
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=57.68 E-value=7.7 Score=31.20 Aligned_cols=46 Identities=22% Similarity=0.190 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQ 66 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKR 66 (208)
+++.+.++|+-.|-.+. +- ++||+.|+ +++..|++|...=|.+.|+
T Consensus 142 L~~~~~~v~~l~~~~g~--s~----~EIA~~lg----is~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAYYEGL--SQ----SEIAKRLG----IPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhhhcCC--CH----HHHHHHhC----CCHHHHHHHHHHHHHHHHH
Confidence 46677777777766663 33 37999996 9999999888544444443
No 53
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=57.58 E-value=8.8 Score=31.23 Aligned_cols=39 Identities=15% Similarity=0.147 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
.+++.|.++|.-.|-.+. .- ++||+.|+ +++..|+++..
T Consensus 142 ~L~~~~r~vl~l~~~~~~--s~----~EIA~~Lg----is~~tVk~~l~ 180 (194)
T PRK09646 142 ALTDTQRESVTLAYYGGL--TY----REVAERLA----VPLGTVKTRMR 180 (194)
T ss_pred hCCHHHHHHHHHHHHcCC--CH----HHHHHHhC----CChHhHHHHHH
Confidence 367788888888777763 33 37999996 99999976653
No 54
>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=56.83 E-value=13 Score=28.85 Aligned_cols=47 Identities=23% Similarity=0.243 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRR 70 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~ 70 (208)
.+++.|.++|.-.|-.+ ++.. +||+.|+ +++..|++. ..|.+++.++
T Consensus 122 ~L~~~~r~vl~l~~~~g--~s~~----eIA~~l~----is~~tv~~~----l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQN--LPIA----EVARILG----KTEGAVKIL----QFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhcC--CCHH----HHHHHHC----CCHHHHHHH----HHHHHHHHHH
Confidence 35677778888877666 3443 6999996 999999843 4444444443
No 55
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=55.86 E-value=3.1 Score=42.48 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=19.5
Q ss_pred CCCCceeeccccchhhHHHHHHH
Q 039144 48 IEGKNVFYWFQNHKARERQKLRR 70 (208)
Q Consensus 48 LsE~qVqvWFQNRRAReKRk~r~ 70 (208)
.++++|+.||.|||+++|+.+..
T Consensus 738 ~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 738 FESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhhcchHHHHHHHHHHHhhhhcc
Confidence 35788999999999999987654
No 56
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=55.79 E-value=11 Score=29.18 Aligned_cols=45 Identities=16% Similarity=0.106 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
+++.+.++|.-.|..+. +.. +||+.|+ +++..|+.|..-=|.|.|
T Consensus 126 L~~~~r~i~~l~~~~~~--~~~----eIA~~lg----is~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYVEGL--SYR----EIAEILG----VPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHHcCC--CHH----HHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 56677777777776663 333 6899996 999999977654444443
No 57
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=54.69 E-value=9.7 Score=31.58 Aligned_cols=46 Identities=17% Similarity=0.090 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 9 WCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 9 t~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
..+|+.|.++|+- +..+ +... +||+.|+ ++...|..|-.+.+.+.+
T Consensus 5 ~~Lt~rqreVL~l-r~~G--lTq~----EIAe~LG----iS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG--LTQQ----EIADILG----TSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHH-HHcC--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 4689999999988 5555 3333 7999997 999999999885444444
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=54.42 E-value=9.2 Score=31.64 Aligned_cols=42 Identities=12% Similarity=0.145 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchh
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKA 62 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRA 62 (208)
+++.|.++|.-.|-.+. .. ++||+.|+ +++..|+++...=|.
T Consensus 154 L~~~~r~vl~l~~~~g~--s~----~EIA~~lg----is~~tV~~~l~Ra~~ 195 (206)
T PRK12526 154 LPEAQQTVVKGVYFQEL--SQ----EQLAQQLN----VPLGTVKSRLRLALA 195 (206)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHHC----CCHHHHHHHHHHHHH
Confidence 56677777776666663 33 37999996 999999766543333
No 59
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=52.89 E-value=8.5 Score=29.55 Aligned_cols=42 Identities=12% Similarity=0.137 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccch
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHK 61 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRR 61 (208)
.+++.|.+++.-.|-.+. . .++||+.|+ +++..|++|...=|
T Consensus 106 ~L~~~~r~ii~l~~~~~~--s----~~EIA~~l~----is~~tV~~~~~ra~ 147 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK--T----MGEIALETE----MTYYQVRWIYRQAL 147 (154)
T ss_pred hCCHHHHHHHHHHHhcCC--C----HHHHHHHHC----CCHHHHHHHHHHHH
Confidence 357788888888887774 3 347999996 99999997754433
No 60
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=52.57 E-value=12 Score=29.13 Aligned_cols=45 Identities=22% Similarity=0.151 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
.+++.|..+|.-.| .+ ++.. +||+.|+ +++..|+++...=|.+.|
T Consensus 112 ~L~~~~r~il~l~~-~g--~s~~----eIA~~lg----is~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG--YSYK----EIAEALG----IKESSVGTTLARAKKKFR 156 (166)
T ss_pred cCCHHHHHHHHHHH-cC--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 36778888888888 66 4544 6999996 999999977643333333
No 61
>PF13565 HTH_32: Homeodomain-like domain
Probab=52.30 E-value=31 Score=23.89 Aligned_cols=46 Identities=20% Similarity=0.133 Sum_probs=30.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCC----CCCceee
Q 039144 4 AGSTRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKI----EGKNVFY 55 (208)
Q Consensus 4 ~~R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~L----sE~qVqv 55 (208)
+.|+|. ++++.+.|.+++..++ .-+.. +|++.|...+|+ +.+.|..
T Consensus 26 ~Grp~~--~~e~~~~i~~~~~~~p-~wt~~---~i~~~L~~~~g~~~~~S~~tv~R 75 (77)
T PF13565_consen 26 PGRPRK--DPEQRERIIALIEEHP-RWTPR---EIAEYLEEEFGISVRVSRSTVYR 75 (77)
T ss_pred CCCCCC--cHHHHHHHHHHHHhCC-CCCHH---HHHHHHHHHhCCCCCccHhHHHH
Confidence 445555 7888899999999884 44544 677777766554 4444543
No 62
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=51.94 E-value=9.6 Score=30.40 Aligned_cols=49 Identities=20% Similarity=0.195 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLR 69 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r 69 (208)
+++.+.++|.-.|-.+. .- ++||+.|+ |+...|+++...=|.+.|.+.+
T Consensus 132 L~~~~r~v~~l~~~~g~--s~----~eIA~~l~----is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 132 LPPRQRDVVQSISVEGA--SI----KETAAKLS----MSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHhC----CCHHHHHHHHHHHHHHHHHHhh
Confidence 56778888888776663 33 36999996 9999999877666666555443
No 63
>PF13551 HTH_29: Winged helix-turn helix
Probab=51.81 E-value=22 Score=25.77 Aligned_cols=52 Identities=15% Similarity=0.098 Sum_probs=32.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhcCCCCCC--HHHHHHHHHHh-hccCC--CCCCceeecc
Q 039144 5 GSTRWCPTPEQLMILEEMYRSGVRTPN--ASQIQHITAHL-SHFGK--IEGKNVFYWF 57 (208)
Q Consensus 5 ~R~Rt~FT~eQLqiLE~~F~~n~~yP~--~~~R~qLA~~L-~~~g~--LsE~qVqvWF 57 (208)
.+++..+++++.+.|.+++..++.. + .-....|++.| ...++ ++...|..|+
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~-g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPE-GRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCC-CCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 4555569999999999999987411 1 12234566655 33333 4555566554
No 64
>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=51.79 E-value=5.9 Score=26.03 Aligned_cols=39 Identities=21% Similarity=0.398 Sum_probs=28.6
Q ss_pred CCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeec
Q 039144 8 RWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYW 56 (208)
Q Consensus 8 Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvW 56 (208)
+..++++|++.+-+++..+. + +.+||+.++ |+...|+.+
T Consensus 3 p~~~~~~~~~~i~~l~~~G~--s----i~~IA~~~g----vsr~TvyR~ 41 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAEGM--S----IAEIAKQFG----VSRSTVYRY 41 (45)
T ss_dssp SSSSSHCCHHHHHHHHHTT--------HHHHHHHTT----S-HHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHCCC--C----HHHHHHHHC----cCHHHHHHH
Confidence 34588889999999999984 3 447999996 888777644
No 65
>PRK06930 positive control sigma-like factor; Validated
Probab=51.13 E-value=12 Score=31.27 Aligned_cols=50 Identities=12% Similarity=0.115 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLR 69 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r 69 (208)
.+++.+.++|.-.|..+. +.. +||+.|+ ++...|+++...=|.|.++...
T Consensus 114 ~L~~rer~V~~L~~~eg~--s~~----EIA~~lg----iS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL--SYS----EIADYLN----IKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--CHH----HHHHHHC----cCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888777773 443 6999996 9999999887655555554443
No 66
>PRK04217 hypothetical protein; Provisional
Probab=49.93 E-value=14 Score=29.48 Aligned_cols=45 Identities=11% Similarity=0.141 Sum_probs=33.7
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhh
Q 039144 9 WCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKAR 63 (208)
Q Consensus 9 t~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAR 63 (208)
-.++++|.++++..|..+. + .++||+.|+ |+...|+..+..-|.+
T Consensus 41 ~~Lt~eereai~l~~~eGl---S---~~EIAk~LG----IS~sTV~r~L~RArkk 85 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL---T---QEEAGKRMG----VSRGTVWRALTSARKK 85 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC---C---HHHHHHHHC----cCHHHHHHHHHHHHHH
Confidence 4578999999999988773 2 347999996 9999998666543333
No 67
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=48.62 E-value=13 Score=30.05 Aligned_cols=48 Identities=15% Similarity=0.088 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKL 68 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~ 68 (208)
+++.|.++++-.|-.+. .- ++||+.|+ ++...|++....=|.+.|+..
T Consensus 137 L~~~~r~i~~L~~~~g~--s~----~EIA~~lg----is~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 137 LPENTARVFTLKEILGF--SS----DEIQQMCG----ISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CCHHHHHHhhhHHHhCC--CH----HHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 45666677776665553 33 37899996 999999976654444444433
No 68
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=48.23 E-value=6.4 Score=25.94 Aligned_cols=38 Identities=24% Similarity=0.242 Sum_probs=18.0
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeec
Q 039144 9 WCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYW 56 (208)
Q Consensus 9 t~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvW 56 (208)
..+|.+|...++..++.+. . ..+||+.|+ .+...|..+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~--s----~~~IA~~lg----~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM--S----IREIAKRLG----RSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHTT------HHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC--C----HHHHHHHHC----cCcHHHHHH
Confidence 4689999999999998874 2 236999997 666656543
No 69
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=48.21 E-value=15 Score=29.79 Aligned_cols=39 Identities=13% Similarity=0.009 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
.+++.|.++|.-.|-.+ ++-. +||..|+ +++..|+..+.
T Consensus 106 ~L~~~~r~i~~l~~~~g--~~~~----EIA~~lg----is~~tV~~~l~ 144 (181)
T PRK09637 106 ALPEKYAEALRLTELEG--LSQK----EIAEKLG----LSLSGAKSRVQ 144 (181)
T ss_pred hCCHHHHHHHHHHHhcC--CCHH----HHHHHhC----CCHHHHHHHHH
Confidence 46778888888887777 3444 6999996 99998987664
No 70
>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=47.99 E-value=12 Score=28.87 Aligned_cols=38 Identities=16% Similarity=0.167 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
.+++.|.+++.-.|-.+ ++.. +||+.|+ |+...|+++.
T Consensus 111 ~L~~~~r~v~~l~~~~g--~~~~----eIA~~l~----is~~tv~~~l 148 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG--VSLT----ALAEQLG----RTVNAVYKAL 148 (159)
T ss_pred HCCHHHHHHHHHHHhcC--CCHH----HHHHHhC----CCHHHHHHHH
Confidence 36778888888877666 3443 6999996 9999999653
No 71
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=47.39 E-value=15 Score=28.24 Aligned_cols=48 Identities=17% Similarity=0.088 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
+++.|.+++.-.|-.+ ++.. +||+.|+ +++..|++.. .|.+++.+..+
T Consensus 107 Lp~~~r~v~~l~~~~g--~s~~----EIA~~lg----is~~tV~~~l----~ra~~~Lr~~l 154 (161)
T PRK09047 107 LPARQREAFLLRYWED--MDVA----ETAAAMG----CSEGSVKTHC----SRATHALAKAL 154 (161)
T ss_pred CCHHHHHHHHHHHHhc--CCHH----HHHHHHC----CCHHHHHHHH----HHHHHHHHHHH
Confidence 4567777777777666 3433 7999996 9999998544 44444444443
No 72
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=46.83 E-value=18 Score=26.54 Aligned_cols=45 Identities=20% Similarity=0.253 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHHHHHhcC----CCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 9 WCPTPEQLMILEEMYRSG----VRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 9 t~FT~eQLqiLE~~F~~n----~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
|.+|++|+..|.++|..- ..+.+..+..++-..+ ++++..|...|
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~----~~~~~ev~~i~ 50 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKS----GLPQTLLAKIW 50 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHc----CCCHHHHHHHH
Confidence 788999999999999762 2456665444443332 36655555444
No 73
>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=46.58 E-value=11 Score=29.80 Aligned_cols=45 Identities=7% Similarity=-0.088 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
+++.+.+++.-.|-.+ ++- ++||+.|+ |++..|+++...=|.+.|
T Consensus 139 L~~~~r~v~~l~~~~~--~s~----~EIA~~lg----is~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 139 LPEDLRTAITLRELEG--LSY----EDIARIMD----CPVGTVRSRIFRAREAIA 183 (190)
T ss_pred CCHHHhhhhhhhhhcC--CCH----HHHHHHHC----cCHHHHHHHHHHHHHHHH
Confidence 3445555555555444 232 37899996 999999877644443333
No 74
>PTZ00183 centrin; Provisional
Probab=46.20 E-value=67 Score=24.26 Aligned_cols=42 Identities=21% Similarity=0.179 Sum_probs=31.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhc----CCCCCCHHHHHHHHHHh
Q 039144 1 MSPAGSTRWCPTPEQLMILEEMYRS----GVRTPNASQIQHITAHL 42 (208)
Q Consensus 1 ~sp~~R~Rt~FT~eQLqiLE~~F~~----n~~yP~~~~R~qLA~~L 42 (208)
|-..+..|..++++|+..|+.+|.. +..+.+..+...+...+
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~ 46 (158)
T PTZ00183 1 MRKRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSL 46 (158)
T ss_pred CCccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHh
Confidence 5567788999999999999999974 22467777655555554
No 75
>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=46.11 E-value=15 Score=27.73 Aligned_cols=39 Identities=21% Similarity=0.135 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQN 59 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQN 59 (208)
+++.+.++|.-.|-.+ ++.. +||+.|+ +++..|+.+...
T Consensus 114 L~~~~r~il~l~~~~~--~~~~----eIA~~lg----is~~tv~~~~~r 152 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG--KSYK----EIAEELG----ISVKTVEYHISK 152 (161)
T ss_pred CCHHHHHHHHHHHHcC--CCHH----HHHHHHC----CCHHHHHHHHHH
Confidence 4677777888766665 3444 6899986 999999865443
No 76
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=45.62 E-value=17 Score=29.31 Aligned_cols=49 Identities=16% Similarity=0.150 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLR 69 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r 69 (208)
+++.|.+++.-.|-.+ ++- ++||+.|+ +++..|++....=|.+.|+...
T Consensus 132 Lp~~~r~v~~l~~~~g--~s~----~EIA~~lg----is~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 132 LPPRTGRVFMMREWLE--LET----EEICQELQ----ITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred CCHHHHHHHHHHHHcC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHHHHHH
Confidence 4566667777666665 343 37999996 9999999765544444444333
No 77
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=45.56 E-value=18 Score=29.07 Aligned_cols=40 Identities=13% Similarity=0.091 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecccc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQN 59 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQN 59 (208)
.+++.|.++|+-.|-.+. +-. +||+.|+ +++..|++-...
T Consensus 131 ~L~~~~r~vl~l~~~~~~--s~~----eIA~~lg----is~~tV~~~l~R 170 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEK--SVE----EVGEIVG----IPESTVKTRMFY 170 (189)
T ss_pred hCCHHHHHHHHHHHHcCC--CHH----HHHHHHC----cCHHHHHHHHHH
Confidence 467788888888777763 333 6999996 999999865543
No 78
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=45.22 E-value=16 Score=29.30 Aligned_cols=44 Identities=14% Similarity=0.080 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARE 64 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRARe 64 (208)
+++.+.++|.-.|-.+. +-. +||+.|+ ++...|+++...=|.+.
T Consensus 129 L~~~~r~i~~l~~~~g~--s~~----EIA~~lg----is~~tV~~~l~Rar~~L 172 (186)
T PRK05602 129 LPERQREAIVLQYYQGL--SNI----EAAAVMD----ISVDALESLLARGRRAL 172 (186)
T ss_pred CCHHHHHHhhHHHhcCC--CHH----HHHHHhC----cCHHHHHHHHHHHHHHH
Confidence 56777888887776663 333 6899996 99999997664333333
No 79
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=44.55 E-value=12 Score=29.11 Aligned_cols=46 Identities=11% Similarity=-0.020 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
.+++.|..+|+-.|-.+ ++.. +||+.|+ +++..|+++...=|.|.|
T Consensus 112 ~L~~~~r~v~~l~~~~~--~s~~----eIA~~lg----is~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG--FSYK----EIAEMTG----LSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCHHHHHHhhhHHhcC--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 36777888888877776 3444 6999996 999888876654444444
No 80
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=44.54 E-value=17 Score=28.78 Aligned_cols=45 Identities=9% Similarity=0.253 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
+++.+-++|.-.|-.+. + .++||+.|+ +++..|+++.+.=|.+.|
T Consensus 130 L~~~~r~i~~l~~~~g~--s----~~eIA~~lg----is~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 130 LEKDRAAAVRRAYLEGL--S----YKELAERHD----VPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CChHHHHHHHHHHHHHHH
Confidence 45566667776766652 3 337999996 999999766554444333
No 81
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=44.00 E-value=15 Score=24.01 Aligned_cols=27 Identities=33% Similarity=0.234 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcCC
Q 039144 1 MSPAGSTRWCPTPEQLMILEEMYRSGV 27 (208)
Q Consensus 1 ~sp~~R~Rt~FT~eQLqiLE~~F~~n~ 27 (208)
|-.+-+-|..||++|.+.|+..|....
T Consensus 1 M~~~~k~rl~Pt~~Q~~~L~~~~~~~R 27 (46)
T PF12323_consen 1 MLKAYKYRLYPTKEQEEKLERWFGACR 27 (46)
T ss_pred CCcceEEEEecCHHHHHHHHHHHHHHH
Confidence 444556678888999999888887763
No 82
>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=43.74 E-value=20 Score=28.61 Aligned_cols=38 Identities=11% Similarity=-0.043 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
.+++.+..+|+-.|-.+ ++-. +||+.|+ +++..|+++-
T Consensus 100 ~L~~~~r~v~~l~~~~g--~s~~----eIA~~lg----is~~tV~~~l 137 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG--LSQQ----EIAEKLG----LSLSGAKSRV 137 (170)
T ss_pred hCCHHHHHHHHHHHHcC--CCHH----HHHHHHC----CCHHHHHHHH
Confidence 56788888888888777 3444 6999996 9999998654
No 83
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=43.61 E-value=21 Score=29.01 Aligned_cols=46 Identities=9% Similarity=0.064 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQ 66 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKR 66 (208)
+++.|.+++.-.|-.+. .- ++||+.|+ +++..|+++...=|.+.|.
T Consensus 135 Lp~~~R~v~~L~~~~g~--s~----~EIA~~lg----is~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYLEL--SS----EQICQECD----ISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHcCC--CH----HHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 34556666666666653 33 37999996 9999999876544444443
No 84
>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=43.48 E-value=9.5 Score=25.73 Aligned_cols=43 Identities=21% Similarity=0.184 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhh
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKAR 63 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAR 63 (208)
.||+.++++|+-+..... . .+||+.|+ ++++.|+++..|=+.|
T Consensus 3 ~LT~~E~~vl~~l~~G~~---~----~eIA~~l~----is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS---N----KEIAEELG----ISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTTS----H----HHHHHHHT----SHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcCC---c----chhHHhcC----cchhhHHHHHHHHHHH
Confidence 589999999998877653 3 37999997 9999998765544443
No 85
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=43.30 E-value=17 Score=29.18 Aligned_cols=45 Identities=9% Similarity=-0.042 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHH
Q 039144 12 TPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQ 66 (208)
Q Consensus 12 T~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKR 66 (208)
++++.+++.-.|-.+ ++- ++||+.|+ +++..|++..+.=|.+.|+
T Consensus 140 ~~~~r~v~~l~~~~g--~s~----~eIA~~lg----is~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 140 PEDLRTALTLREFDG--LSY----EDIASVMQ----CPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred CHHHhHHHhhHHhcC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 344444444444333 233 36899996 9999997655444444433
No 86
>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=42.51 E-value=17 Score=28.26 Aligned_cols=45 Identities=20% Similarity=0.147 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
+++.+..+|+-.|-.+ ++.. +||+.|+ +++..|+++-..=|.+.|
T Consensus 111 L~~~~r~i~~l~~~~g--~s~~----eIA~~lg----is~~tV~~~l~ra~~~Lr 155 (162)
T TIGR02983 111 LPARQRAVVVLRYYED--LSEA----QVAEALG----ISVGTVKSRLSRALARLR 155 (162)
T ss_pred CCHHHHHHhhhHHHhc--CCHH----HHHHHhC----CCHHHHHHHHHHHHHHHH
Confidence 4677888888877666 3444 6999996 999999966544444333
No 87
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.24 E-value=17 Score=22.71 Aligned_cols=38 Identities=26% Similarity=0.330 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
.+++.+.++++. +..+ +.. .+||+.|+ ++...|+.|.+
T Consensus 3 ~l~~~e~~i~~~-~~~g--~s~----~eia~~l~----is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRL-LAEG--LTN----KEIAERLG----ISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHH-HHcC--CCH----HHHHHHHC----CCHHHHHHHHH
Confidence 478899999876 4444 222 47899996 99999987655
No 88
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=40.96 E-value=21 Score=26.66 Aligned_cols=27 Identities=11% Similarity=0.122 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 32 ASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 32 ~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
...+.+|++.|....+|++.+|.+|+.
T Consensus 49 G~~i~~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 49 GRRIRELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred chhHHHHHHHHHHHhCCCCCeEEEEEE
Confidence 356788999999999999999999985
No 89
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=40.71 E-value=24 Score=29.02 Aligned_cols=42 Identities=5% Similarity=-0.061 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchh
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKA 62 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRA 62 (208)
+++.|.+++.-.|-.+ ++- ++||+.|+ +++..|++....=|.
T Consensus 140 Lp~~~r~v~~L~~~eg--~s~----~EIA~~lg----is~~tVk~~l~RAr~ 181 (201)
T PRK12545 140 LPEQIGRVFMMREFLD--FEI----DDICTELT----LTANHCSVLLYRART 181 (201)
T ss_pred CCHHHHHHHHHHHHcC--CCH----HHHHHHHC----cCHHHHHHHHHHHHH
Confidence 3455566666666555 333 37999996 999999876543333
No 90
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=40.68 E-value=27 Score=27.93 Aligned_cols=47 Identities=17% Similarity=0.042 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQK 67 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk 67 (208)
+++.+.+++.-.|-.+. . .++||+.|+ |++..|++....=|.+.|+.
T Consensus 118 Lp~~~r~i~~l~~~e~~--s----~~EIA~~lg----is~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 118 LPYKLRQVIILRYLHDY--S----QEEIAQLLQ----IPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred CCHHHHHHHHHHHHccC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHH
Confidence 55667777777666653 2 237999996 99999986655554444443
No 91
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=40.26 E-value=17 Score=29.93 Aligned_cols=45 Identities=18% Similarity=-0.017 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
+++.|.++|.-.|-.+ ++.. +||+.|+ |++..|+++.+-=|.+.|
T Consensus 114 Lp~~~r~v~~L~~~~g--~s~~----EIA~~Lg----iS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 114 LPDEQREALILVGASG--FSYE----EAAEMCG----VAVGTVKSRANRARARLA 158 (188)
T ss_pred CCHHHhHHhhhHHhcC--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 5677777777776665 3444 6899996 999999977654444333
No 92
>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=39.61 E-value=27 Score=22.03 Aligned_cols=37 Identities=24% Similarity=0.286 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
+++.|.++++.++ .+ +. .++||+.++ ++...|+.|..
T Consensus 1 l~~~e~~i~~~~~-~~--~s----~~eia~~l~----~s~~tv~~~~~ 37 (57)
T cd06170 1 LTPREREVLRLLA-EG--KT----NKEIADILG----ISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHHHH-cC--CC----HHHHHHHHC----CCHHHHHHHHH
Confidence 3677888887644 43 32 247888886 89998987764
No 93
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=39.49 E-value=29 Score=30.20 Aligned_cols=55 Identities=20% Similarity=0.413 Sum_probs=36.8
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHHhHHH
Q 039144 12 TPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKLGKQL 76 (208)
Q Consensus 12 T~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~~k~~ 76 (208)
.+.|.+++.-.|-.+. . .++||+.|+ |++..|+++...=|.+.|+..++.....+
T Consensus 163 p~~~R~v~~L~~~eg~--S----~~EIA~~Lg----is~~TVk~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 163 SERERHLLRLHFVDGL--S----MDRIGAMYQ----VHRSTVSRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred CHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4455555555565552 3 347999996 99999999887777777666655554433
No 94
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=39.46 E-value=28 Score=27.11 Aligned_cols=43 Identities=14% Similarity=0.434 Sum_probs=30.5
Q ss_pred CCCCCCCHHH-HHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 6 STRWCPTPEQ-LMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 6 R~Rt~FT~eQ-LqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
.+|-.||.+. ++++..++..+. +-. +||.+++ |+...|+.|-.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~--sv~----evA~e~g----Is~~tl~~W~r 51 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM--TVS----LVARQHG----VAASQLFLWRK 51 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC--CHH----HHHHHHC----cCHHHHHHHHH
Confidence 4455577776 556677777663 333 6899996 99999999954
No 95
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=39.15 E-value=26 Score=27.55 Aligned_cols=38 Identities=29% Similarity=0.352 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
+++.+.++|.-.|-.+ ++.. +||+.|+ +++..|+....
T Consensus 119 L~~~~r~vl~L~~~~g--~s~~----EIA~~lg----is~~tV~~~l~ 156 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG--WSTA----QIAADLG----IPEGTVKSRLH 156 (173)
T ss_pred CCHHHHHHHHHHHHcC--CCHH----HHHHHHC----cCHHHHHHHHH
Confidence 5677778888877776 3444 6999996 99999986543
No 96
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=38.92 E-value=21 Score=30.68 Aligned_cols=45 Identities=13% Similarity=0.126 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
+++.|.++|.-.|-.+. +- ++||+.|+ +++..|++..+.=|.+.|
T Consensus 172 Lp~~~R~v~~L~~~eg~--s~----~EIA~~Lg----is~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 172 LPEQQRIAVILSYHENM--SN----GEIAEVMD----TTVAAVESLLKRGRQQLR 216 (233)
T ss_pred CCHHHHHHhhhHHhcCC--CH----HHHHHHHC----cCHHHHHHHHHHHHHHHH
Confidence 45666777777666663 33 37999996 999999866544333333
No 97
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=38.30 E-value=26 Score=28.63 Aligned_cols=41 Identities=7% Similarity=-0.091 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccch
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHK 61 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRR 61 (208)
+++.|.+++.-.|-.+ ++.. +||+.|+ |++..|++....=|
T Consensus 117 Lp~~~r~i~~L~~~~g--~s~~----EIA~~Lg----is~~tVk~~l~Rar 157 (187)
T PRK12516 117 LPDDQREAIILVGASG--FAYE----EAAEICG----CAVGTIKSRVNRAR 157 (187)
T ss_pred CCHHHHHHHHHHHHcC--CCHH----HHHHHHC----CCHHHHHHHHHHHH
Confidence 4566777777777666 3544 6999996 99999986554333
No 98
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=38.10 E-value=28 Score=29.07 Aligned_cols=38 Identities=18% Similarity=0.072 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
+++.+.+++.-.|-.+ ++-. +||+.|+ +++..|+++..
T Consensus 139 L~~~~r~v~~L~~~~g--~s~~----EIA~~Lg----is~~tV~~~l~ 176 (203)
T PRK09647 139 LPPEFRAAVVLCDIEG--LSYE----EIAATLG----VKLGTVRSRIH 176 (203)
T ss_pred CCHHHHHHHHHHHHcC--CCHH----HHHHHHC----CCHHHHHHHHH
Confidence 4566666666666665 3444 6999996 99999986654
No 99
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=37.96 E-value=23 Score=27.43 Aligned_cols=36 Identities=14% Similarity=0.131 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeec
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYW 56 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvW 56 (208)
+++.+.++|+-.|-.+. +. ++||+.|+ ++...|+..
T Consensus 110 L~~~~r~v~~l~~~~~~--s~----~EIA~~lg----is~~tV~~~ 145 (163)
T PRK07037 110 LPARTRYAFEMYRLHGE--TQ----KDIARELG----VSPTLVNFM 145 (163)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHHC----CCHHHHHHH
Confidence 46667777777776663 33 37999996 999999964
No 100
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=37.69 E-value=27 Score=23.01 Aligned_cols=14 Identities=36% Similarity=0.213 Sum_probs=11.9
Q ss_pred CCCHHHHHHHHHHH
Q 039144 10 CPTPEQLMILEEMY 23 (208)
Q Consensus 10 ~FT~eQLqiLE~~F 23 (208)
.||++|+.+||.--
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 59999999999743
No 101
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=37.65 E-value=29 Score=27.40 Aligned_cols=39 Identities=15% Similarity=0.109 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQN 59 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQN 59 (208)
+++.+.+++.-.|-.+. +.. +||+.|+ +++..|++....
T Consensus 120 L~~~~r~i~~l~~~~~~--s~~----EIA~~lg----is~~tV~~~l~R 158 (173)
T PRK12522 120 LNEKYKTVLVLYYYEQY--SYK----EMSEILN----IPIGTVKYRLNY 158 (173)
T ss_pred CCHHHHHHHHHHHHcCC--CHH----HHHHHhC----CCHHHHHHHHHH
Confidence 34555566665565552 333 7899996 999999865443
No 102
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=37.37 E-value=54 Score=26.13 Aligned_cols=47 Identities=15% Similarity=0.152 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
+++.+.+++.-.|-.+ ++- ++||+.|+ |++..|+ +|..|.+++.+..
T Consensus 138 L~~~~r~i~~l~~~~g--~s~----~eIA~~lg----is~~~v~----~~l~Rar~~Lr~~ 184 (187)
T PRK12534 138 LEPPRSELIRTAFFEG--ITY----EELAARTD----TPIGTVK----SWIRRGLAKLKAC 184 (187)
T ss_pred CCHHHHHHHHHHHHcC--CCH----HHHHHHhC----CChhHHH----HHHHHHHHHHHHH
Confidence 4556666666666655 233 36899996 9998887 4556666555544
No 103
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=37.35 E-value=24 Score=28.34 Aligned_cols=38 Identities=13% Similarity=-0.061 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
.+++.|.++++-.|-.+. . .++||+.|+ ++...|+++.
T Consensus 139 ~L~~~~r~i~~l~~~~g~--s----~~EIA~~lg----is~~tV~~~l 176 (189)
T PRK09648 139 TLPEKQREILILRVVVGL--S----AEETAEAVG----STPGAVRVAQ 176 (189)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----CCHHHHHHHH
Confidence 356778888888777763 3 347999996 9999998665
No 104
>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=36.81 E-value=15 Score=25.96 Aligned_cols=28 Identities=21% Similarity=0.465 Sum_probs=21.2
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 20 EEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 20 E~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
..+|-++ |+-. +||+.|+ ++.+.|+.|-
T Consensus 7 ~~LY~~G--~~~~----eIA~~Lg----~~~~TV~~W~ 34 (58)
T PF06056_consen 7 RSLYLQG--WSIK----EIAEELG----VPRSTVYSWK 34 (58)
T ss_pred HHHHHcC--CCHH----HHHHHHC----CChHHHHHHH
Confidence 4567666 4544 6999997 9999999994
No 105
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=36.19 E-value=24 Score=27.68 Aligned_cols=38 Identities=8% Similarity=0.009 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
.+++.+.+++.-.|-.+. +.. +||+.|+ |++..|+++.
T Consensus 119 ~L~~~~r~i~~l~~~~g~--s~~----eiA~~lg----is~~tv~~~l 156 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHDL--TIK----EIAEVMN----KPEGTVKTYL 156 (169)
T ss_pred hCCHHHhHHHHHHHHcCC--CHH----HHHHHHC----CCHHHHHHHH
Confidence 356778888888887773 333 6999996 9999998543
No 106
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=36.11 E-value=13 Score=30.06 Aligned_cols=45 Identities=11% Similarity=0.032 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
+++.+..++.-.|-.+ ++ .++||+.|+ |+...|+++...=|.+.|
T Consensus 140 L~~~~r~i~~l~~~~g--~s----~~EIA~~lg----is~~tV~~~l~ra~~~Lr 184 (194)
T PRK12513 140 LPDEQREVFLLREHGD--LE----LEEIAELTG----VPEETVKSRLRYALQKLR 184 (194)
T ss_pred CCHhHhhheeeehccC--CC----HHHHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 3444555555555444 23 337999996 999999855444333333
No 107
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=35.94 E-value=29 Score=28.19 Aligned_cols=37 Identities=19% Similarity=0.241 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
+++.|.++|.-.|-.+. +- ++||+.|+ ++...|++-.
T Consensus 142 Lp~~~r~v~~l~~~eg~--s~----~EIA~~lg----is~~tVk~rl 178 (194)
T PRK12531 142 LPKAQRDVLQAVYLEEL--PH----QQVAEMFD----IPLGTVKSRL 178 (194)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHhC----cCHHHHHHHH
Confidence 45566667776666653 33 37999996 9999996443
No 108
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=35.76 E-value=46 Score=23.86 Aligned_cols=39 Identities=18% Similarity=0.147 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCcee
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVF 54 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVq 54 (208)
+|++|+..|+++|..= .+.++++-.+.-..|-|+..+=.
T Consensus 1 lT~~Qk~el~~l~~qm-----~e~kK~~idk~Ve~G~iTqeqAd 39 (59)
T PF10925_consen 1 LTDQQKKELKALYKQM-----LELKKQIIDKYVEAGVITQEQAD 39 (59)
T ss_pred CCHHHHHHHHHHHHHH-----HHHHHHHHHHHHHcCCCCHHHHH
Confidence 5899999999999875 46678888888889989876643
No 109
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=35.49 E-value=27 Score=28.04 Aligned_cols=39 Identities=5% Similarity=0.019 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
.+++.|.++|+-.|-.+. +- ++||+.|+ ++...|+.+..
T Consensus 131 ~L~~~~r~v~~l~~~~g~--s~----~eIA~~lg----is~~tV~~~l~ 169 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEGL--SV----AEAATRSG----MSESAVKVSVH 169 (184)
T ss_pred hCCHHHHHHHHHHHHcCC--cH----HHHHHHHC----cCHHHHHHHHH
Confidence 467778888887666663 33 37999996 99999996653
No 110
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=34.53 E-value=29 Score=28.02 Aligned_cols=46 Identities=24% Similarity=0.250 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
+++.+.++|.- |-.+ +.. ++||+.|+ ++...|++ |..|.|++.+..
T Consensus 156 L~~~~r~vl~l-~~e~--~s~----~EIA~~lg----is~~tV~~----~l~rar~~Lr~~ 201 (208)
T PRK08295 156 LSELEKEVLEL-YLDG--KSY----QEIAEELN----RHVKSIDN----ALQRVKRKLEKY 201 (208)
T ss_pred CCHHHHHHHHH-HHcc--CCH----HHHHHHHC----CCHHHHHH----HHHHHHHHHHHH
Confidence 34555555555 4443 233 36899996 99999974 555555555544
No 111
>PRK13558 bacterio-opsin activator; Provisional
Probab=34.42 E-value=38 Score=32.44 Aligned_cols=43 Identities=21% Similarity=0.244 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHhcCC-CCCCHHHHHHHHHHhhccCCCCCCcee
Q 039144 8 RWCPTPEQLMILEEMYRSGV-RTPNASQIQHITAHLSHFGKIEGKNVF 54 (208)
Q Consensus 8 Rt~FT~eQLqiLE~~F~~n~-~yP~~~~R~qLA~~L~~~g~LsE~qVq 54 (208)
+..+|+.|.++|+.+|+.+= -.|-...-.+||+.|+ |+..-+.
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~----is~~t~~ 648 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMG----ISRSTFH 648 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhC----CCHHHHH
Confidence 35799999999999999982 1276667778999996 7765553
No 112
>PRK00118 putative DNA-binding protein; Validated
Probab=34.40 E-value=27 Score=27.59 Aligned_cols=46 Identities=13% Similarity=0.118 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
.+++.|.+++.-.|..+. .-. +||+.++ ++...|+.|...-|.+.|
T Consensus 17 ~L~ekqRevl~L~y~eg~--S~~----EIAe~lG----IS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY--SLG----EIAEEFN----VSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred cCCHHHHHHHHHHHHcCC--CHH----HHHHHHC----cCHHHHHHHHHHHHHHHH
Confidence 357888999988888874 333 6999996 999999888765444444
No 113
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=34.23 E-value=28 Score=27.70 Aligned_cols=38 Identities=16% Similarity=0.239 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
+++.+.++|.-.|-.+. .- ++||+.|+ +++..|+++-.
T Consensus 136 L~~~~r~vl~l~~~~~~--s~----~eIA~~lg----is~~~V~~~l~ 173 (186)
T PRK13919 136 LSPEERRVIEVLYYQGY--TH----REAAQLLG----LPLGTLKTRAR 173 (186)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHHC----cCHHHHHHHHH
Confidence 46666777776665552 22 36899996 99988886543
No 114
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=33.46 E-value=28 Score=27.87 Aligned_cols=46 Identities=7% Similarity=-0.054 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQ 66 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKR 66 (208)
+++.|..++.-.|-.+. +- ++||+.|+ +++..|++....-|.+.|+
T Consensus 130 L~~~~r~v~~l~~~~g~--s~----~EIA~~l~----is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 130 LPDRQRLPIVHVKLEGL--SV----AETAQLTG----LSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 34555566666665552 33 37999996 9999999777554444443
No 115
>PRK09480 slmA division inhibitor protein; Provisional
Probab=33.35 E-value=31 Score=27.09 Aligned_cols=42 Identities=14% Similarity=0.241 Sum_probs=30.9
Q ss_pred HHHHHHH---HHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchh
Q 039144 15 QLMILEE---MYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKA 62 (208)
Q Consensus 15 QLqiLE~---~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRA 62 (208)
..++|+. +|.... . +...+.+||++.+ ++...++.+|.|+-.
T Consensus 12 r~~Il~aa~~l~~~~~-G-~~~ti~~Ia~~ag----vs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 12 REQILQALAQMLESPP-G-ERITTAKLAARVG----VSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHHHHHhcC-C-CccCHHHHHHHhC----CCHhHHHHHCCCHHH
Confidence 3344444 455442 5 6777889999996 999999999999764
No 116
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=33.33 E-value=33 Score=27.87 Aligned_cols=39 Identities=15% Similarity=-0.008 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQN 59 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQN 59 (208)
+++.|.++|.-.|-.+ ++-. +||+.|+ ++...|+++..-
T Consensus 137 L~~~~r~i~~L~~~~g--~s~~----eIA~~lg----is~~tV~~~l~R 175 (196)
T PRK12524 137 LPERQRQAVVLRHIEG--LSNP----EIAEVME----IGVEAVESLTAR 175 (196)
T ss_pred CCHHHHHHHHHHHHcC--CCHH----HHHHHHC----cCHHHHHHHHHH
Confidence 5666777777776665 3433 6899996 999999976643
No 117
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=33.25 E-value=29 Score=38.30 Aligned_cols=58 Identities=24% Similarity=0.372 Sum_probs=47.2
Q ss_pred CCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHH
Q 039144 6 STRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKL 68 (208)
Q Consensus 6 R~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~ 68 (208)
+.|...=++++.+|=..|..+. .|+...+.-|...- ..+.+.+++||+|=|.|.++..
T Consensus 707 ~~~~~~~~~aa~~l~~a~~~~~-sps~k~~~civcd~----~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 707 LLRLTILPEAAMILGRAYMQDN-SPSLKVFDCIVCDV----FSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cCcccccHHHHhhhhhcccCCC-CHHHHHHHHhhhhh----hhhhhHHHHhhcchhhhhhhhc
Confidence 4566666799999999999996 89997666555544 4788889999999999999776
No 118
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=32.57 E-value=28 Score=29.42 Aligned_cols=48 Identities=19% Similarity=0.262 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKL 68 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~ 68 (208)
+.+.|.++|.-.|..+. . .++||+.|+ ++...|+++...=+.+.|+..
T Consensus 185 L~~~~r~vl~l~~~~g~--s----~~EIA~~lg----is~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 185 LPEREQLVLSLYYQEEL--N----LKEIGAVLG----VSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHhHhccCC--C----HHHHHHHHC----CCHHHHHHHHHHHHHHHHHHH
Confidence 45667777777776663 2 347999996 999999988766666665543
No 119
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=32.50 E-value=28 Score=28.18 Aligned_cols=38 Identities=13% Similarity=0.046 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
.+++.|..++.-.|-.+ ++-. +||+.|+ ++...|++.-
T Consensus 131 ~L~~~~r~i~~l~~~~g--~s~~----EIAe~lg----is~~~V~~~l 168 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--EKIE----EIAKKLG----LTRSAIDNRL 168 (189)
T ss_pred hCCHHHHHHHHHHHHcc--CCHH----HHHHHHC----CCHHHHHHHH
Confidence 35778888888777665 3433 6999996 8998887543
No 120
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=31.64 E-value=28 Score=22.88 Aligned_cols=32 Identities=19% Similarity=0.255 Sum_probs=22.6
Q ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCcee
Q 039144 15 QLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVF 54 (208)
Q Consensus 15 QLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVq 54 (208)
|.++|+.+++... +.+. ++||++|+ ++.+.|+
T Consensus 2 ~~~il~~L~~~~~-~it~---~eLa~~l~----vS~rTi~ 33 (55)
T PF08279_consen 2 QKQILKLLLESKE-PITA---KELAEELG----VSRRTIR 33 (55)
T ss_dssp HHHHHHHHHHTTT-SBEH---HHHHHHCT----S-HHHHH
T ss_pred HHHHHHHHHHcCC-CcCH---HHHHHHhC----CCHHHHH
Confidence 5778888878774 4555 47889886 8877765
No 121
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=31.39 E-value=19 Score=24.84 Aligned_cols=33 Identities=18% Similarity=0.270 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCcee
Q 039144 13 PEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVF 54 (208)
Q Consensus 13 ~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVq 54 (208)
..|+++|+-+|..+ ..+.. +||+.|+ ++++.|+
T Consensus 5 ~rq~~Ll~~L~~~~--~~~~~---ela~~l~----~S~rti~ 37 (59)
T PF08280_consen 5 KRQLKLLELLLKNK--WITLK---ELAKKLN----ISERTIK 37 (59)
T ss_dssp HHHHHHHHHHHHHT--SBBHH---HHHHHCT----S-HHHHH
T ss_pred HHHHHHHHHHHcCC--CCcHH---HHHHHHC----CCHHHHH
Confidence 46899999999943 56664 7888886 8887775
No 122
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [].; GO: 0003723 RNA binding
Probab=31.30 E-value=77 Score=26.11 Aligned_cols=38 Identities=13% Similarity=0.152 Sum_probs=30.6
Q ss_pred CCCCCCCCHHHHHHHHHHH--hcCCCCCCHHHHHHHHHHhh
Q 039144 5 GSTRWCPTPEQLMILEEMY--RSGVRTPNASQIQHITAHLS 43 (208)
Q Consensus 5 ~R~Rt~FT~eQLqiLE~~F--~~n~~yP~~~~R~qLA~~L~ 43 (208)
+|-+..|+++++++|++.- ..+ ..+...+|++|.+.++
T Consensus 16 ~~d~~~f~p~~i~~L~~~d~~~tS-KKd~~~Rr~ELl~~~s 55 (148)
T PF08144_consen 16 PRDPRYFSPEIIKLLKEGDRNATS-KKDPEVRRKELLEAIS 55 (148)
T ss_pred CCCcccCCHHHHHHHhhhcccccc-cCCHHHHHHHHHHHhh
Confidence 5678889999999999987 334 4788888888888775
No 123
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=30.86 E-value=37 Score=26.77 Aligned_cols=42 Identities=10% Similarity=-0.017 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchh
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKA 62 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRA 62 (208)
+++.+.++|.-.|-.+. .. ++||+.|+ +++..|+++..-=|.
T Consensus 113 L~~~~r~v~~l~~~~g~--s~----~eIA~~lg----is~~tV~~~l~Rar~ 154 (164)
T PRK12547 113 LSADQREAIILIGASGF--SY----EDAAAICG----CAVGTIKSRVSRARN 154 (164)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHhC----CCHHHHHHHHHHHHH
Confidence 46677777777766663 33 37899996 999999876543333
No 124
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=30.53 E-value=43 Score=28.00 Aligned_cols=45 Identities=9% Similarity=0.011 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
+++.|.+++.-.|-.+. +- ++||+.|+ ++...|++..+-=|.+.|
T Consensus 149 L~~~~r~v~~L~~~~g~--s~----~EIAe~lg----is~~tV~~~l~RAr~~Lr 193 (206)
T PRK12544 149 LPAKYARVFMMREFIEL--ET----NEICHAVD----LSVSNLNVLLYRARLRLR 193 (206)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHHC----cCHHHHHHHHHHHHHHHH
Confidence 44555566666665552 33 36899996 999999865543333333
No 125
>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=30.52 E-value=33 Score=24.94 Aligned_cols=16 Identities=19% Similarity=0.524 Sum_probs=14.8
Q ss_pred HHHHHhhccCCCCCCceeec
Q 039144 37 HITAHLSHFGKIEGKNVFYW 56 (208)
Q Consensus 37 qLA~~L~~~g~LsE~qVqvW 56 (208)
+||++|+ +++.+|..|
T Consensus 27 dIA~~Lg----vs~~tIr~W 42 (60)
T PF10668_consen 27 DIAEKLG----VSESTIRKW 42 (60)
T ss_pred HHHHHHC----CCHHHHHHH
Confidence 7999997 999999988
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=30.47 E-value=33 Score=28.18 Aligned_cols=46 Identities=22% Similarity=0.323 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQ 66 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKR 66 (208)
..+++.+++|-.|-.| |- .++||+.|+ |+++.|+..++.=|++.++
T Consensus 136 l~~~~~~~v~l~~~~G--ls----~~EIA~~lg----iS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 136 LDPRQRRVVELRFFEG--LS----VEEIAERLG----ISERTVRRRLRRARAWLRR 181 (185)
T ss_pred cCHHHHHHHHHHHHCC--CC----HHHHHHHHC----cCHHHHHHHHHHHHHHHHH
Confidence 3456677777776666 32 237889996 9999998666555544443
No 127
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=29.99 E-value=85 Score=26.33 Aligned_cols=35 Identities=26% Similarity=0.395 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCce
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNV 53 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qV 53 (208)
..|+|.++.|.+++..+. +.. +||++|+ +++-.-|
T Consensus 2 ~Wtde~~~~L~~lw~~G~---Sas---qIA~~lg---~vsRnAV 36 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL---SAS---QIARQLG---GVSRNAV 36 (162)
T ss_pred CCCHHHHHHHHHHHHcCC---CHH---HHHHHhC---Ccchhhh
Confidence 479999999999999994 443 7999997 4555434
No 128
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=29.71 E-value=18 Score=28.48 Aligned_cols=28 Identities=18% Similarity=0.094 Sum_probs=19.3
Q ss_pred HHHHHHHhhccCCCCCCceeeccccchhhHHH
Q 039144 35 IQHITAHLSHFGKIEGKNVFYWFQNHKARERQ 66 (208)
Q Consensus 35 R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKR 66 (208)
.++||+.|+ +++..|++.+..=|.+.|+
T Consensus 139 ~~eIA~~lg----~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 139 QKEIAEILN----IPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHHH
Confidence 347899996 9999999776444444433
No 129
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=29.47 E-value=62 Score=22.78 Aligned_cols=58 Identities=17% Similarity=0.189 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHhcCC-----CCCCHHHH-------HHHHHHhhccCCCCCCc---eeeccccchhhHHHH
Q 039144 9 WCPTPEQLMILEEMYRSGV-----RTPNASQI-------QHITAHLSHFGKIEGKN---VFYWFQNHKARERQK 67 (208)
Q Consensus 9 t~FT~eQLqiLE~~F~~n~-----~yP~~~~R-------~qLA~~L~~~g~LsE~q---VqvWFQNRRAReKRk 67 (208)
-.||.+|+.+|-++++... ...+.... .+||..|...++. .+. |+..+.|=+++.|++
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~-~Rs~~~lkkkW~nlk~~~Kk~ 75 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPG-KRSWKQLKKKWKNLKSKAKKK 75 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHHHHHHH
Confidence 4699999999999887642 11222111 4688999877764 333 556667766666654
No 130
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=29.43 E-value=45 Score=27.20 Aligned_cols=38 Identities=18% Similarity=0.037 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
.+++.|.++|+-.|-.+ ++.. +||+.|+ |++..|+++.
T Consensus 111 ~Lp~~~R~v~~L~~~eg--~s~~----EIA~~lg----is~~tV~~~l 148 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG--LSYQ----EAAAVLG----IPIGTLMSRI 148 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CCHH----HHHHHhC----cCHHHHHHHH
Confidence 35677777888777666 3544 6999996 9999998765
No 131
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=29.14 E-value=38 Score=26.74 Aligned_cols=44 Identities=11% Similarity=0.061 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 12 TPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 12 T~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
++.+.++|.-.|-.+ ++- ++||+.|+ ++...|++....=|.+.|
T Consensus 138 ~~~~r~il~l~~~~~--~s~----~eIA~~lg----is~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 138 PEKYRTVIVLKYIED--LSL----KEISEILD----LPVGTVKTRIHRGREALR 181 (187)
T ss_pred CHHHHHHhhhHHhhC--CCH----HHHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 444555555544444 233 37899996 998888765544443333
No 132
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=29.13 E-value=38 Score=26.80 Aligned_cols=39 Identities=13% Similarity=0.098 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQN 59 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQN 59 (208)
+++.|.+++.-.|-.+ ++-. +||+.|+ +++..|+++...
T Consensus 120 Lp~~~r~v~~L~~~~g--~s~~----EIA~~lg----is~~tV~~~l~r 158 (172)
T PRK12523 120 LSSKARAAFLYNRLDG--MGHA----EIAERLG----VSVSRVRQYLAQ 158 (172)
T ss_pred CCHHHHHHHHHHHHcC--CCHH----HHHHHHC----CCHHHHHHHHHH
Confidence 4566777777776666 3444 6899996 999999877643
No 133
>smart00340 HALZ homeobox associated leucin zipper.
Probab=28.79 E-value=29 Score=24.16 Aligned_cols=26 Identities=4% Similarity=-0.006 Sum_probs=20.7
Q ss_pred HHHHhhccchhhhcCCCCCccccccc
Q 039144 82 QQIFQHHHHLQQCCQVPNHHQQLLHC 107 (208)
Q Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~h~ 107 (208)
+++.+|+++++++++.+..+..|+|+
T Consensus 19 eeNrRL~ke~~eLralk~~~~~~m~~ 44 (44)
T smart00340 19 EENRRLQKEVQELRALKLSPPLYMQH 44 (44)
T ss_pred HHHHHHHHHHHHHHhcccCCcccccC
Confidence 67788889999999988777766653
No 134
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.55 E-value=3.4e+02 Score=25.55 Aligned_cols=29 Identities=31% Similarity=0.520 Sum_probs=23.9
Q ss_pred CCCCCCCCC-CCCCccccccccccccchhh
Q 039144 172 APRSLQPCC-SKPPLRTLELFPITATNLKE 200 (208)
Q Consensus 172 ~p~~~~~cc-~~~plktl~lfp~t~t~~k~ 200 (208)
.|++-+-|= ++.|||-=|||++.-|-++.
T Consensus 179 kP~~~v~CP~s~kplklkdL~~VkFT~l~s 208 (303)
T KOG3039|consen 179 KPSTTVVCPVSGKPLKLKDLFAVKFTPLNS 208 (303)
T ss_pred CCCceeeccCCCCccchhhcceeeeeecCC
Confidence 566666676 89999999999999886664
No 135
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=28.03 E-value=31 Score=29.35 Aligned_cols=49 Identities=20% Similarity=0.131 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHHh
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKLG 73 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~~ 73 (208)
+++.|.++|.-.|-.+ ++-. +||+.|+ |++..|+++-. |.|++.+..+.
T Consensus 135 Lp~~~R~v~~L~y~eg--~s~~----EIAe~Lg----iS~~tVk~~L~----RAr~~Lr~~l~ 183 (216)
T PRK12533 135 LPVEYREVLVLRELED--MSYR----EIAAIAD----VPVGTVMSRLA----RARRRLAALLG 183 (216)
T ss_pred CCHHHHhHhhhHHhcC--CCHH----HHHHHHC----CCHHHHHHHHH----HHHHHHHHHHc
Confidence 4556677777766665 3444 6999996 99999975543 44444444443
No 136
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=27.09 E-value=28 Score=29.67 Aligned_cols=51 Identities=24% Similarity=0.169 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRK 71 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~ 71 (208)
.+|+-|+++|+-+.+ + +.+. +||+.|+ ++++.|+.+..|=..|..-+.|-.
T Consensus 155 ~Lt~rE~~Vl~l~~~-G--~s~~----eIA~~L~----iS~~TVk~~~~~i~~Kl~v~nr~e 205 (216)
T PRK10100 155 LLTHREKEILNKLRI-G--ASNN----EIARSLF----ISENTVKTHLYNLFKKIAVKNRTQ 205 (216)
T ss_pred CCCHHHHHHHHHHHc-C--CCHH----HHHHHhC----CCHHHHHHHHHHHHHHhCCCCHHH
Confidence 489999999999988 4 3454 7999996 999999988877666655444433
No 137
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=26.67 E-value=57 Score=26.57 Aligned_cols=48 Identities=21% Similarity=0.171 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
+.+.|.++|.-.|-.+. + .++||+.|+ ++...|++.. +|.+++.+..+
T Consensus 132 L~~~~r~v~~l~~~~g~--s----~~EIA~~lg----is~~tvk~rl----~Rar~~Lr~~l 179 (188)
T TIGR02943 132 LPEQTARVFMMREVLGF--E----SDEICQELE----ISTSNCHVLL----YRARLSLRACL 179 (188)
T ss_pred CCHHHHHHHHHHHHhCC--C----HHHHHHHhC----CCHHHHHHHH----HHHHHHHHHHH
Confidence 34556666666666653 3 347999996 9999997543 44444444443
No 138
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=26.19 E-value=41 Score=26.95 Aligned_cols=37 Identities=16% Similarity=0.111 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
+++.|.+++.-.|-.+. .- ++||+.|+ +++..|++..
T Consensus 123 L~~~~r~i~~l~~~~g~--s~----~EIA~~lg----is~~tVk~~l 159 (185)
T PRK12542 123 LNESNRQVFKYKVFYNL--TY----QEISSVMG----ITEANVRKQF 159 (185)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHHC----CCHHHHHHHH
Confidence 45667777776666652 33 36899996 9999999754
No 139
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=26.02 E-value=36 Score=25.60 Aligned_cols=44 Identities=30% Similarity=0.223 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARE 64 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRARe 64 (208)
.+|+.+.++|+- +..+ +.. ++||+.|+ ++++.|+++.+|=|.|.
T Consensus 149 ~lt~~e~~vl~l-~~~g--~~~----~~Ia~~l~----~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 149 LLTPRERQILKL-ITEG--YTN----RDIAEQLS----ISIKTVETHRLNMMRKL 192 (211)
T ss_pred CCCHHHHHHHHH-HHCC--CCH----HHHHHHhC----CCHHHHHHHHHHHHHHh
Confidence 489999999987 5666 443 47999985 99999998776644333
No 140
>PF13518 HTH_28: Helix-turn-helix domain
Probab=24.86 E-value=52 Score=20.95 Aligned_cols=33 Identities=24% Similarity=0.539 Sum_probs=22.5
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecccc
Q 039144 16 LMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQN 59 (208)
Q Consensus 16 LqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQN 59 (208)
+++++.+. .+ . +. .++|.+++ |+...|..|.+.
T Consensus 3 ~~iv~~~~-~g--~-s~---~~~a~~~g----is~~tv~~w~~~ 35 (52)
T PF13518_consen 3 LQIVELYL-EG--E-SV---REIAREFG----ISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHH-cC--C-CH---HHHHHHHC----CCHhHHHHHHHH
Confidence 34566655 44 2 32 36888886 999999999754
No 141
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=24.53 E-value=44 Score=29.21 Aligned_cols=47 Identities=13% Similarity=0.023 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQK 67 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk 67 (208)
+++.|.+++.-.|-.+ ++-. +||+.|+ +++..|+...+.=|.+.|+.
T Consensus 116 L~~~~R~v~~L~~~~g--~s~~----EIA~~lg----~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 116 LSPLERAAFLLHDVFG--VPFD----EIASTLG----RSPAACRQLASRARKHVRAA 162 (293)
T ss_pred CCHHHHHHHHHHHHhC--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHHhh
Confidence 4556666666655555 3333 6899996 99999998887555555543
No 142
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.23 E-value=51 Score=26.43 Aligned_cols=39 Identities=15% Similarity=0.121 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQN 59 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQN 59 (208)
+++.|..++.-.|-.+. .-. +||+.|+ +++..|++....
T Consensus 128 Lp~~~R~v~~L~~~~g~--s~~----EIA~~lg----is~~tVk~~l~r 166 (178)
T PRK12529 128 LRPRVKQAFLMATLDGM--KQK----DIAQALD----IALPTVKKYIHQ 166 (178)
T ss_pred CCHHHHHHHHHHHHcCC--CHH----HHHHHHC----CCHHHHHHHHHH
Confidence 56777777777777663 333 7999996 999999876653
No 143
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=24.07 E-value=36 Score=27.43 Aligned_cols=27 Identities=11% Similarity=0.124 Sum_probs=19.1
Q ss_pred HHHHHHHhhccCCCCCCceeeccccchhhHH
Q 039144 35 IQHITAHLSHFGKIEGKNVFYWFQNHKARER 65 (208)
Q Consensus 35 R~qLA~~L~~~g~LsE~qVqvWFQNRRAReK 65 (208)
.++||+.|+ |++..|+++..-=|.+.|
T Consensus 150 ~~EIA~~lg----is~~tVk~~l~Rar~~Lr 176 (193)
T TIGR02947 150 YKEIAEIMG----TPIGTVMSRLHRGRKQLR 176 (193)
T ss_pred HHHHHHHHC----CCHHHHHHHHHHHHHHHH
Confidence 347999996 999999977654444433
No 144
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.63 E-value=58 Score=25.28 Aligned_cols=38 Identities=18% Similarity=0.081 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
+++.+.+++.-.|-.+. +.. +||+.|+ +++..|++.-.
T Consensus 106 L~~~~r~v~~l~~~~~~--s~~----eIA~~lg----is~~tv~~~l~ 143 (159)
T PRK12527 106 LPPACRDSFLLRKLEGL--SHQ----QIAEHLG----ISRSLVEKHIV 143 (159)
T ss_pred CCHHHHHHHHHHHHcCC--CHH----HHHHHhC----CCHHHHHHHHH
Confidence 56667777777776663 433 6899996 99988885443
No 145
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=23.39 E-value=49 Score=28.96 Aligned_cols=47 Identities=9% Similarity=0.013 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQK 67 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk 67 (208)
+++.|..+|.-.|-.+ ++-. +||+.|+ +++..|+..++.=|.+.|..
T Consensus 109 L~~~~R~v~~L~~~~g--~s~~----EIA~~lg----~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 109 LSPLERAVFVLREVFD--YPYE----EIASIVG----KSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred CCHHHHHHHHHHHHcC--CCHH----HHHHHHC----CCHHHHHHHHHHHHHHHHhh
Confidence 4566666666665555 2333 6899996 99999998887666666553
No 146
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=23.30 E-value=51 Score=25.20 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=20.2
Q ss_pred HHHHHHhhccCCCCCCceeeccccc
Q 039144 36 QHITAHLSHFGKIEGKNVFYWFQNH 60 (208)
Q Consensus 36 ~qLA~~L~~~g~LsE~qVqvWFQNR 60 (208)
+.|++.|.+.+|++..+|++-|++=
T Consensus 79 ~~i~~~l~~~lgi~~~rv~I~f~~~ 103 (116)
T PTZ00397 79 AAITKILASHLKVKSERVYIEFKDC 103 (116)
T ss_pred HHHHHHHHHHhCcCcccEEEEEEEC
Confidence 3567777888889999999998763
No 147
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=23.08 E-value=82 Score=25.70 Aligned_cols=52 Identities=23% Similarity=0.186 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHHhHHH
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKLGKQL 76 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~~k~~ 76 (208)
+.+.|..++.-.|-.+ ++.. +||+.|+ |++..|+++ -.|.+++.+..+.+..
T Consensus 129 Lp~~~r~v~~l~~~~g--~s~~----EIA~~lg----is~~tV~~~----l~Rar~~Lr~~l~~~~ 180 (188)
T PRK12517 129 LDPEYREPLLLQVIGG--FSGE----EIAEILD----LNKNTVMTR----LFRARNQLKEALEKPD 180 (188)
T ss_pred CCHHHHHHHHHHHHhC--CCHH----HHHHHHC----CCHHHHHHH----HHHHHHHHHHHHHHHH
Confidence 4556666666666666 3544 6999996 999999854 4455555565555444
No 148
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=22.97 E-value=2.8e+02 Score=23.46 Aligned_cols=41 Identities=12% Similarity=0.207 Sum_probs=33.4
Q ss_pred CCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCcee
Q 039144 7 TRWCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVF 54 (208)
Q Consensus 7 ~Rt~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVq 54 (208)
+...+|+++++++-++=.++ |..=.|..||++.+ ++.--|.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D---P~~wTr~~LAkkF~----~S~~fV~ 122 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED---PEKWTRKKLAKKFN----CSPLFVS 122 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC---chHhhHHHHHHHhC----CCHHHHH
Confidence 44689999999999999988 67778889999986 6665554
No 149
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=22.96 E-value=56 Score=27.95 Aligned_cols=38 Identities=11% Similarity=0.120 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
+++.|.++|.-.|-.+. .- ++||+.|+ |+...|+.|..
T Consensus 206 L~~~~r~vl~l~~~~g~--s~----~eIA~~l~----is~~tV~~~~~ 243 (257)
T PRK08583 206 LSDREKSIIQCTFIENL--SQ----KETGERLG----ISQMHVSRLQR 243 (257)
T ss_pred CCHHHHHHHHHHHhCCC--CH----HHHHHHHC----CCHHHHHHHHH
Confidence 57778888888887663 33 37999996 99999976543
No 150
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.39 E-value=59 Score=25.97 Aligned_cols=39 Identities=13% Similarity=0.083 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCce
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNV 53 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qV 53 (208)
+++++|+++-.+.|+.|- -...-.+++||..|+ +++..|
T Consensus 2 SLn~eq~~~Tk~elqan~-el~~LS~~~iA~~Ln----~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQANF-ELCPLSDEEIATALN----WTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHhh-hhccccHHHHHHHhC----CCHHHH
Confidence 578999988777776663 444444568999996 665433
No 151
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=22.03 E-value=73 Score=25.33 Aligned_cols=38 Identities=11% Similarity=0.021 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
.+++.|.+++.-.|-.+. +- ++||+.|+ ++...|+++.
T Consensus 119 ~L~~~~r~i~~l~~~~g~--s~----~EIA~~lg----is~~tV~~~l 156 (172)
T PRK09651 119 GLNGKTREAFLLSQLDGL--TY----SEIAHKLG----VSVSSVKKYV 156 (172)
T ss_pred hCCHHHhHHhhhhhccCC--CH----HHHHHHhC----CCHHHHHHHH
Confidence 356667777777666653 33 37899996 9999998765
No 152
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=21.88 E-value=64 Score=24.73 Aligned_cols=43 Identities=21% Similarity=0.258 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhh
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKAR 63 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAR 63 (208)
.+|+.+.++|+-+.+ + + .+++||++|+ ++++.|++..++=|.|
T Consensus 137 ~Lt~~E~~il~~l~~-g--~----~~~~Ia~~l~----~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQ-G--M----AVKEIAAELG----LSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHC-C--C----CHHHHHHHhC----CCHHHHHHHHHHHHHH
Confidence 588888888887664 3 3 3457999985 8999997665554444
No 153
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=21.61 E-value=67 Score=26.93 Aligned_cols=38 Identities=11% Similarity=0.082 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHH----hcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 11 PTPEQLMILEEMY----RSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 11 FT~eQLqiLE~~F----~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
+++.|..++.-.| ..+. . .++||+.|+ +++..|+++..
T Consensus 179 Lp~~~R~v~~L~y~l~~~eg~--s----~~EIA~~lg----is~~tVk~~~~ 220 (234)
T PRK08301 179 LSDREKQIMELRFGLNGGEEK--T----QKEVADMLG----ISQSYISRLEK 220 (234)
T ss_pred CCHHHHHHHHHHhccCCCCCC--C----HHHHHHHHC----CCHHHHHHHHH
Confidence 4455666666666 2332 2 347889986 99999975443
No 154
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=21.61 E-value=1.3e+02 Score=24.53 Aligned_cols=34 Identities=18% Similarity=0.061 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCcee
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVF 54 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVq 54 (208)
+.+.|.++|+-.|-.+. +- ++||+.|+ ++...|+
T Consensus 135 Lp~~~r~i~~l~~~~g~--s~----~EIA~~lg----~s~~tV~ 168 (192)
T PRK09643 135 LPVEQRAALVAVDMQGY--SV----ADAARMLG----VAEGTVK 168 (192)
T ss_pred CCHHHHHHHHHHHHcCC--CH----HHHHHHHC----cCHHHHH
Confidence 56778888887777763 33 36899996 8998885
No 155
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=21.16 E-value=25 Score=28.37 Aligned_cols=23 Identities=9% Similarity=0.053 Sum_probs=15.9
Q ss_pred HHHHHHhhccCCCCCCceeeccccchh
Q 039144 36 QHITAHLSHFGKIEGKNVFYWFQNHKA 62 (208)
Q Consensus 36 ~qLA~~L~~~g~LsE~qVqvWFQNRRA 62 (208)
++||+.|+ +++..|+++...=|.
T Consensus 154 ~EIA~~lg----is~~tV~~~l~Ra~~ 176 (188)
T PRK09640 154 QEIADIMH----MGLSATKMRYKRALD 176 (188)
T ss_pred HHHHHHHC----CCHHHHHHHHHHHHH
Confidence 47888886 888888876543333
No 156
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=21.13 E-value=83 Score=27.27 Aligned_cols=44 Identities=9% Similarity=0.105 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhh
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKAR 63 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAR 63 (208)
.+++.+.++|.-.|..+. . .++||+.|+ ++...|+.....=+.+
T Consensus 212 ~L~~~~r~vl~l~~~~~~--s----~~eIA~~lg----is~~tV~~~~~ra~~~ 255 (268)
T PRK06288 212 TLPEREKKVLILYYYEDL--T----LKEIGKVLG----VTESRISQLHTKAVLQ 255 (268)
T ss_pred hCCHHHHHHHHHHHHcCC--C----HHHHHHHHC----cCHHHHHHHHHHHHHH
Confidence 356777888888887764 2 347899996 9999997544433333
No 157
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.13 E-value=55 Score=26.49 Aligned_cols=37 Identities=14% Similarity=-0.085 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
+++.|.+++.-.|-.+. +- ++||+.|+ +++..|+++-
T Consensus 131 Lp~~~r~v~~L~~~~g~--s~----~EIA~~lg----is~~tVk~~l 167 (185)
T PRK09649 131 LTTDQREALLLTQLLGL--SY----ADAAAVCG----CPVGTIRSRV 167 (185)
T ss_pred CCHHHhHHhhhHHHcCC--CH----HHHHHHHC----CCHHHHHHHH
Confidence 45566666666666652 33 36888986 9999998665
No 158
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=21.03 E-value=31 Score=27.11 Aligned_cols=18 Identities=22% Similarity=0.163 Sum_probs=14.5
Q ss_pred HHHHHHhhccCCCCCCceeecc
Q 039144 36 QHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 36 ~qLA~~L~~~g~LsE~qVqvWF 57 (208)
++||+.|+ ++.+.|+++.
T Consensus 146 ~eIA~~l~----is~~~V~~~l 163 (176)
T PRK09638 146 EEIAKMLN----IPEGTVKSRV 163 (176)
T ss_pred HHHHHHHC----CChhHHHHHH
Confidence 47899996 9999997665
No 159
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=20.86 E-value=62 Score=25.15 Aligned_cols=37 Identities=16% Similarity=0.089 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
+++.|.++++-.|-.+. +.. +||+.|+ ++...|+++-
T Consensus 114 L~~~~r~v~~L~~~~g~--s~~----EIA~~l~----is~~tV~~~l 150 (161)
T PRK12528 114 LPPLVKRAFLLAQVDGL--GYG----EIATELG----ISLATVKRYL 150 (161)
T ss_pred CCHHHHHHHHHHHHcCC--CHH----HHHHHHC----CCHHHHHHHH
Confidence 56778888888887773 444 6899996 8998888543
No 160
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=20.84 E-value=76 Score=25.83 Aligned_cols=37 Identities=14% Similarity=-0.053 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWF 57 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWF 57 (208)
+++.+.+++.-.|..+. .. ++||+.|+ +++..|++..
T Consensus 112 Lp~~~R~v~~L~~~~g~--s~----~EIA~~Lg----is~~tV~~~l 148 (182)
T PRK12540 112 LPQDQREALILVGASGF--SY----EDAAAICG----CAVGTIKSRV 148 (182)
T ss_pred CCHHHHHHhhHHHHcCC--CH----HHHHHHHC----CCHHHHHHHH
Confidence 45667777777776663 33 36899996 9998888543
No 161
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=20.69 E-value=61 Score=26.76 Aligned_cols=38 Identities=11% Similarity=-0.024 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccc
Q 039144 11 PTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQ 58 (208)
Q Consensus 11 FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQ 58 (208)
+++.|.+++.-.|-.+. . .++||+.|+ +++..|+++..
T Consensus 134 Lp~~~r~v~~l~~~~g~--s----~~EIAe~lg----is~~tV~~~l~ 171 (196)
T PRK12535 134 LPPERREALILTQVLGY--T----YEEAAKIAD----VRVGTIRSRVA 171 (196)
T ss_pred CCHHHHHHhhhHHHhCC--C----HHHHHHHhC----CCHHHHHHHHH
Confidence 45666677776766663 3 237899996 99999987663
No 162
>PRK10403 transcriptional regulator NarP; Provisional
Probab=20.68 E-value=70 Score=24.35 Aligned_cols=53 Identities=23% Similarity=0.248 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHHHHHHHH
Q 039144 9 WCPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQKLRRKL 72 (208)
Q Consensus 9 t~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKRk~r~~~ 72 (208)
..+|+.+.++|+.+.. + +.. ++||+.|+ ++++.|++...|=|.|..-..+..+
T Consensus 152 ~~Lt~~e~~vl~~~~~-g--~s~----~~ia~~l~----~s~~tv~~~~~~i~~kl~~~~~~~~ 204 (215)
T PRK10403 152 SVLTERELDVLHELAQ-G--LSN----KQIASVLN----ISEQTVKVHIRNLLRKLNVRSRVAA 204 (215)
T ss_pred ccCCHHHHHHHHHHHC-C--CCH----HHHHHHcC----CCHHHHHHHHHHHHHHcCCCCHHHH
Confidence 3589999999986543 3 333 47899995 8999998777666665544444443
No 163
>PF11406 Tachystatin_A: Antimicrobial peptide tachystatin A; InterPro: IPR022717 Tachystatin A contains a cysteine-stabilised triple-stranded beta-sheet and shows features common to membrane-interactive peptides. Tachystatin A is thought to have an antimicrobial activity similar to defensins.Tachystatin A is also a chitin-binding peptide []. ; PDB: 1CIX_A.
Probab=20.52 E-value=48 Score=22.76 Aligned_cols=21 Identities=33% Similarity=0.698 Sum_probs=10.4
Q ss_pred CCCCCCCCCCCCCcccccccccccc
Q 039144 172 APRSLQPCCSKPPLRTLELFPITAT 196 (208)
Q Consensus 172 ~p~~~~~cc~~~plktl~lfp~t~t 196 (208)
+|. +||| |-|.--..||-++-
T Consensus 18 lpt--ipcc--rgltcrsyfpgsty 38 (44)
T PF11406_consen 18 LPT--IPCC--RGLTCRSYFPGSTY 38 (44)
T ss_dssp S-S--------TT-EEEESSTT-S-
T ss_pred CCC--cccc--CCceeeeecCCccc
Confidence 566 9999 88888889997654
No 164
>PRK10651 transcriptional regulator NarL; Provisional
Probab=20.07 E-value=52 Score=25.19 Aligned_cols=46 Identities=24% Similarity=0.262 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeeccccchhhHHH
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQNHKARERQ 66 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQNRRAReKR 66 (208)
.+|+.+.++|+-+. .+ +++. +||.+|+ ++++.|++..+|=|.|..-
T Consensus 155 ~Lt~rE~~vl~~l~-~g--~~~~----~ia~~l~----is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIA-QG--LPNK----MIARRLD----ITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHH-cC--CCHH----HHHHHcC----CCHHHHHHHHHHHHHHcCC
Confidence 49999999998755 43 3554 6899986 9999998777666655543
No 165
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=20.02 E-value=69 Score=27.35 Aligned_cols=40 Identities=10% Similarity=0.125 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhccCCCCCCceeecccc
Q 039144 10 CPTPEQLMILEEMYRSGVRTPNASQIQHITAHLSHFGKIEGKNVFYWFQN 59 (208)
Q Consensus 10 ~FT~eQLqiLE~~F~~n~~yP~~~~R~qLA~~L~~~g~LsE~qVqvWFQN 59 (208)
.+++.|.++|.-.|..+. .- .+||+.|+ ++...|+.+...
T Consensus 205 ~L~~~~r~ii~l~~~~g~--s~----~eIA~~lg----is~~~V~~~~~r 244 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL--SQ----KETGERLG----ISQMHVSRLQRQ 244 (255)
T ss_pred cCCHHHHHHHHHHHcCCC--CH----HHHHHHHC----cCHHHHHHHHHH
Confidence 357788888888887763 22 47899996 999999765543
Done!