Query 028655
Match_columns 206
No_of_seqs 256 out of 1654
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 14:55:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028655.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028655hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.9 3.2E-22 6.9E-27 161.9 7.3 96 88-183 49-144 (198)
2 KOG0842 Transcription factor t 99.8 3.3E-19 7.1E-24 152.3 10.4 71 88-158 150-222 (307)
3 KOG0487 Transcription factor A 99.8 1.6E-18 3.5E-23 148.1 8.0 64 88-151 234-297 (308)
4 KOG0484 Transcription factor P 99.7 4E-19 8.7E-24 127.9 2.7 61 89-149 17-77 (125)
5 KOG0489 Transcription factor z 99.7 6.5E-19 1.4E-23 149.4 4.2 64 89-152 159-222 (261)
6 KOG0488 Transcription factor B 99.7 3.1E-18 6.6E-23 148.0 6.6 55 96-150 179-233 (309)
7 KOG0485 Transcription factor N 99.7 1.3E-17 2.7E-22 134.7 9.2 60 88-147 101-162 (268)
8 KOG0494 Transcription factor C 99.7 3E-17 6.4E-22 135.6 8.3 67 96-162 148-214 (332)
9 KOG0843 Transcription factor E 99.7 1.4E-17 2.9E-22 131.1 4.9 63 89-151 102-164 (197)
10 PF00046 Homeobox: Homeobox do 99.7 2.2E-17 4.9E-22 108.4 5.0 57 90-146 1-57 (57)
11 KOG0850 Transcription factor D 99.7 2.6E-16 5.6E-21 128.2 10.0 57 93-149 126-182 (245)
12 KOG2251 Homeobox transcription 99.7 4.1E-17 8.9E-22 132.2 5.0 67 85-151 33-99 (228)
13 KOG0492 Transcription factor M 99.7 1.2E-16 2.5E-21 128.3 5.1 58 90-147 145-202 (246)
14 KOG0848 Transcription factor C 99.6 1.2E-16 2.5E-21 132.6 5.0 57 96-152 206-262 (317)
15 KOG0493 Transcription factor E 99.6 6.9E-15 1.5E-19 121.8 10.5 71 90-160 247-317 (342)
16 cd00086 homeodomain Homeodomai 99.6 2.8E-15 6.1E-20 98.5 5.4 57 91-147 2-58 (59)
17 smart00389 HOX Homeodomain. DN 99.6 2.7E-15 5.9E-20 97.8 4.9 55 91-145 2-56 (56)
18 COG5576 Homeodomain-containing 99.6 3E-15 6.4E-20 117.5 5.9 71 84-154 46-116 (156)
19 KOG0844 Transcription factor E 99.6 2.7E-15 5.9E-20 126.6 4.2 62 89-150 181-242 (408)
20 TIGR01565 homeo_ZF_HD homeobox 99.5 7.9E-15 1.7E-19 96.4 5.2 52 90-141 2-57 (58)
21 KOG4577 Transcription factor L 99.5 2.7E-15 5.8E-20 125.8 3.5 78 82-159 160-244 (383)
22 KOG0486 Transcription factor P 99.5 1.5E-14 3.3E-19 122.6 6.2 65 88-152 111-175 (351)
23 KOG0491 Transcription factor B 99.5 1.6E-14 3.5E-19 112.2 4.9 59 94-152 105-163 (194)
24 KOG3802 Transcription factor O 99.4 1.2E-13 2.5E-18 120.9 4.2 61 89-149 294-354 (398)
25 KOG0847 Transcription factor, 99.4 2.6E-13 5.6E-18 110.0 2.7 52 96-147 174-225 (288)
26 KOG0490 Transcription factor, 99.3 2.2E-12 4.8E-17 106.7 3.2 61 88-148 59-119 (235)
27 KOG0849 Transcription factor P 99.1 3.9E-11 8.5E-16 105.9 5.2 63 86-148 173-235 (354)
28 KOG1168 Transcription factor A 99.0 1.5E-10 3.3E-15 97.5 2.8 62 86-147 306-367 (385)
29 KOG0775 Transcription factor S 99.0 2.9E-10 6.2E-15 95.2 4.2 52 96-147 183-234 (304)
30 PF05920 Homeobox_KN: Homeobox 98.6 2.5E-08 5.5E-13 60.8 1.9 34 110-143 7-40 (40)
31 KOG0774 Transcription factor P 98.6 3.5E-08 7.5E-13 82.3 2.7 61 87-147 186-249 (334)
32 KOG2252 CCAAT displacement pro 98.1 3.2E-06 7E-11 77.2 5.3 57 89-145 420-476 (558)
33 KOG0490 Transcription factor, 98.1 3.5E-06 7.7E-11 69.5 4.6 61 89-149 153-213 (235)
34 KOG1146 Homeobox protein [Gene 97.6 6.6E-05 1.4E-09 74.6 5.2 63 86-148 900-962 (1406)
35 PF11569 Homez: Homeodomain le 97.2 0.00017 3.7E-09 46.9 1.4 42 100-141 9-50 (56)
36 KOG0773 Transcription factor M 96.8 0.0012 2.7E-08 58.0 3.5 59 91-149 241-302 (342)
37 PF02183 HALZ: Homeobox associ 96.5 0.0056 1.2E-07 38.1 4.0 38 147-184 1-38 (45)
38 KOG3623 Homeobox transcription 95.6 0.013 2.7E-07 55.9 3.9 48 101-148 568-615 (1007)
39 PF04218 CENP-B_N: CENP-B N-te 94.0 0.12 2.6E-06 33.1 4.3 46 91-141 2-47 (53)
40 PRK09413 IS2 repressor TnpA; R 89.0 3.7 7.9E-05 30.6 8.1 43 91-138 8-51 (121)
41 KOG4196 bZIP transcription fac 88.6 3.2 6.9E-05 31.6 7.4 79 94-184 22-114 (135)
42 smart00340 HALZ homeobox assoc 86.9 1.2 2.5E-05 27.2 3.4 32 148-179 2-33 (44)
43 PF01527 HTH_Tnp_1: Transposas 78.7 1.1 2.5E-05 29.9 1.2 43 91-138 2-45 (76)
44 PF04545 Sigma70_r4: Sigma-70, 77.7 3.2 7E-05 25.6 3.0 39 96-139 5-43 (50)
45 cd00569 HTH_Hin_like Helix-tur 75.7 6.5 0.00014 21.0 3.8 39 94-137 4-42 (42)
46 PF04967 HTH_10: HTH DNA bindi 74.8 3.9 8.5E-05 26.2 2.8 39 96-134 1-41 (53)
47 cd06171 Sigma70_r4 Sigma70, re 73.3 4.7 0.0001 24.0 3.0 42 96-142 11-52 (55)
48 PF10668 Phage_terminase: Phag 67.1 3.3 7.2E-05 27.3 1.3 20 118-137 24-43 (60)
49 PF13443 HTH_26: Cro/C1-type H 65.5 4.4 9.6E-05 26.0 1.7 38 118-155 12-49 (63)
50 KOG1146 Homeobox protein [Gene 65.1 6.6 0.00014 40.5 3.4 55 93-147 448-502 (1406)
51 PF08281 Sigma70_r4_2: Sigma-7 63.7 10 0.00022 23.5 3.0 39 96-139 11-49 (54)
52 PF09607 BrkDBD: Brinker DNA-b 63.6 11 0.00025 24.6 3.2 44 93-138 3-47 (58)
53 KOG3623 Homeobox transcription 61.3 1.3 2.7E-05 42.9 -2.2 92 96-187 633-724 (1007)
54 PRK03975 tfx putative transcri 60.3 17 0.00036 28.1 4.2 48 93-146 4-51 (141)
55 PRK10072 putative transcriptio 56.6 14 0.0003 26.6 3.0 40 96-142 33-72 (96)
56 PF12824 MRP-L20: Mitochondria 55.6 80 0.0017 25.0 7.5 66 93-162 83-148 (164)
57 PF02183 HALZ: Homeobox associ 53.6 26 0.00057 21.6 3.5 34 149-182 10-43 (45)
58 PF00170 bZIP_1: bZIP transcri 52.4 49 0.0011 21.5 5.0 33 148-180 30-62 (64)
59 PF13936 HTH_38: Helix-turn-he 52.0 10 0.00022 22.9 1.5 39 94-137 3-41 (44)
60 PF00196 GerE: Bacterial regul 51.0 21 0.00046 22.5 3.0 45 95-145 3-47 (58)
61 PF02796 HTH_7: Helix-turn-hel 50.2 19 0.00041 21.8 2.5 38 95-137 5-42 (45)
62 COG2944 Predicted transcriptio 49.9 20 0.00044 26.3 3.0 39 96-141 44-82 (104)
63 COG3413 Predicted DNA binding 49.5 19 0.00041 29.3 3.2 49 95-145 155-205 (215)
64 cd04761 HTH_MerR-SF Helix-Turn 49.2 10 0.00022 22.8 1.2 23 119-141 3-25 (49)
65 PF13518 HTH_28: Helix-turn-he 48.9 11 0.00023 23.0 1.3 22 118-139 14-35 (52)
66 PF00170 bZIP_1: bZIP transcri 48.8 64 0.0014 20.9 5.1 36 148-183 23-58 (64)
67 TIGR03879 near_KaiC_dom probab 47.7 6.2 0.00013 27.0 0.0 35 105-139 21-55 (73)
68 PF00424 REV: REV protein (ant 47.7 18 0.0004 25.8 2.4 35 101-149 14-48 (91)
69 COG4367 Uncharacterized protei 47.3 24 0.00051 25.2 2.9 39 96-134 3-41 (97)
70 PF08280 HTH_Mga: M protein tr 46.3 24 0.00053 22.6 2.7 34 99-136 6-39 (59)
71 PRK09646 RNA polymerase sigma 46.0 30 0.00066 27.3 3.8 46 96-146 143-188 (194)
72 PRK06759 RNA polymerase factor 44.8 30 0.00065 25.9 3.5 45 96-145 107-151 (154)
73 KOG3755 SATB1 matrix attachmen 44.8 7.1 0.00015 37.1 -0.0 48 101-148 704-758 (769)
74 PRK12526 RNA polymerase sigma 43.8 34 0.00074 27.4 3.9 46 96-146 154-199 (206)
75 PRK04217 hypothetical protein; 43.5 36 0.00078 25.1 3.6 46 96-146 43-88 (110)
76 PRK09652 RNA polymerase sigma 43.2 32 0.0007 26.2 3.5 45 96-145 129-173 (182)
77 PF06056 Terminase_5: Putative 42.8 15 0.00033 23.8 1.3 27 118-146 15-41 (58)
78 PF13384 HTH_23: Homeodomain-l 41.8 15 0.00033 22.3 1.2 22 117-138 18-39 (50)
79 PHA02955 hypothetical protein; 40.2 42 0.00091 27.8 3.8 43 98-140 60-103 (213)
80 smart00421 HTH_LUXR helix_turn 40.1 41 0.00089 20.1 3.0 38 96-139 4-41 (58)
81 TIGR02937 sigma70-ECF RNA poly 40.0 40 0.00086 24.4 3.4 45 96-145 111-155 (158)
82 PRK00118 putative DNA-binding 39.9 45 0.00098 24.4 3.6 46 96-146 18-63 (104)
83 PRK12512 RNA polymerase sigma 39.2 44 0.00095 26.0 3.7 46 96-146 132-177 (184)
84 PRK12519 RNA polymerase sigma 39.1 33 0.00071 26.9 3.0 46 96-146 142-187 (194)
85 PRK11924 RNA polymerase sigma 39.0 41 0.00088 25.6 3.5 46 96-146 126-171 (179)
86 PRK09642 RNA polymerase sigma 39.0 48 0.0011 25.0 3.9 46 96-146 107-152 (160)
87 PF13411 MerR_1: MerR HTH fami 38.3 20 0.00044 23.2 1.4 21 119-139 3-23 (69)
88 PRK12514 RNA polymerase sigma 36.9 54 0.0012 25.3 3.9 46 96-146 130-175 (179)
89 PRK09648 RNA polymerase sigma 36.0 51 0.0011 25.7 3.7 45 96-145 140-184 (189)
90 TIGR02985 Sig70_bacteroi1 RNA 36.0 52 0.0011 24.4 3.6 45 96-145 114-158 (161)
91 PF07716 bZIP_2: Basic region 35.8 1.1E+02 0.0024 19.1 4.6 29 151-179 25-53 (54)
92 cd04762 HTH_MerR-trunc Helix-T 35.8 22 0.00048 20.7 1.2 24 119-142 3-26 (49)
93 TIGR02989 Sig-70_gvs1 RNA poly 35.1 54 0.0012 24.6 3.6 43 96-143 112-154 (159)
94 PRK05602 RNA polymerase sigma 34.6 50 0.0011 25.7 3.4 46 96-146 129-174 (186)
95 cd01392 HTH_LacI Helix-turn-he 34.4 17 0.00037 22.1 0.5 21 121-141 2-22 (52)
96 PRK09644 RNA polymerase sigma 34.2 55 0.0012 24.9 3.5 46 96-146 109-154 (165)
97 TIGR02959 SigZ RNA polymerase 34.2 57 0.0012 25.1 3.6 46 96-146 101-146 (170)
98 PRK12546 RNA polymerase sigma 34.1 38 0.00082 26.9 2.6 47 96-147 114-160 (188)
99 PF00376 MerR: MerR family reg 33.9 22 0.00048 20.9 0.9 18 120-137 3-20 (38)
100 PRK12515 RNA polymerase sigma 33.6 61 0.0013 25.4 3.7 46 96-146 132-177 (189)
101 PRK09639 RNA polymerase sigma 33.5 75 0.0016 24.0 4.2 45 96-146 113-157 (166)
102 PF01381 HTH_3: Helix-turn-hel 33.3 22 0.00048 21.8 0.9 22 119-140 12-33 (55)
103 KOG4005 Transcription factor X 33.2 2E+02 0.0044 24.4 6.7 32 150-181 103-134 (292)
104 TIGR02948 SigW_bacill RNA poly 33.0 53 0.0011 25.4 3.3 46 96-146 137-182 (187)
105 TIGR02999 Sig-70_X6 RNA polyme 32.8 62 0.0013 25.0 3.6 46 96-146 135-180 (183)
106 TIGR02939 RpoE_Sigma70 RNA pol 32.3 48 0.0011 25.7 3.0 30 117-146 155-184 (190)
107 PF10224 DUF2205: Predicted co 32.1 1.3E+02 0.0029 20.9 4.7 45 148-192 27-71 (80)
108 COG2963 Transposase and inacti 31.9 81 0.0018 22.7 3.9 42 93-138 5-47 (116)
109 cd06170 LuxR_C_like C-terminal 31.8 66 0.0014 19.2 3.0 36 97-138 2-37 (57)
110 PRK06811 RNA polymerase factor 30.8 70 0.0015 25.1 3.7 47 96-147 132-178 (189)
111 PRK12541 RNA polymerase sigma 30.7 62 0.0014 24.5 3.3 45 96-145 113-157 (161)
112 PRK06930 positive control sigm 30.6 71 0.0015 25.2 3.6 46 96-146 115-160 (170)
113 cd04763 HTH_MlrA-like Helix-Tu 30.2 29 0.00063 22.6 1.2 21 119-139 3-23 (68)
114 PRK12530 RNA polymerase sigma 29.9 70 0.0015 25.1 3.5 46 96-146 135-180 (189)
115 TIGR03070 couple_hipB transcri 29.8 28 0.00061 21.2 1.0 23 119-141 18-40 (58)
116 smart00027 EH Eps15 homology d 29.5 87 0.0019 21.8 3.6 43 96-138 4-51 (96)
117 KOG1962 B-cell receptor-associ 28.6 1E+02 0.0023 25.5 4.3 37 148-184 176-212 (216)
118 TIGR02954 Sig70_famx3 RNA poly 28.3 81 0.0018 24.0 3.6 46 96-146 120-165 (169)
119 KOG0773 Transcription factor M 28.3 46 0.00099 29.1 2.4 39 109-147 117-155 (342)
120 PRK12538 RNA polymerase sigma 27.9 72 0.0016 26.3 3.4 46 96-146 172-217 (233)
121 PRK12537 RNA polymerase sigma 27.9 91 0.002 24.2 3.8 45 96-145 134-178 (182)
122 PRK10403 transcriptional regul 27.8 53 0.0011 25.1 2.5 44 96-145 154-197 (215)
123 cd04764 HTH_MlrA-like_sg1 Heli 27.8 32 0.0007 22.2 1.0 21 119-139 3-23 (67)
124 PRK09047 RNA polymerase factor 27.7 94 0.002 23.3 3.8 45 96-145 107-151 (161)
125 PRK09637 RNA polymerase sigma 27.5 83 0.0018 24.6 3.6 46 96-146 107-152 (181)
126 PRK12547 RNA polymerase sigma 27.3 86 0.0019 23.9 3.6 45 96-145 113-157 (164)
127 TIGR02983 SigE-fam_strep RNA p 27.1 87 0.0019 23.6 3.5 46 96-146 111-156 (162)
128 PRK07037 extracytoplasmic-func 26.9 93 0.002 23.4 3.7 45 96-145 110-154 (163)
129 PF13551 HTH_29: Winged helix- 26.9 1.2E+02 0.0026 21.2 4.0 43 96-138 58-109 (112)
130 cd00093 HTH_XRE Helix-turn-hel 26.8 37 0.00081 19.6 1.1 23 119-141 15-37 (58)
131 cd02413 40S_S3_KH K homology R 26.8 38 0.00082 23.5 1.3 20 119-138 56-75 (81)
132 PRK12524 RNA polymerase sigma 26.1 90 0.0019 24.6 3.6 46 96-146 137-182 (196)
133 cd01104 HTH_MlrA-CarA Helix-Tu 25.8 42 0.00091 21.6 1.3 20 119-138 3-22 (68)
134 cd00131 PAX Paired Box domain 25.4 2.6E+02 0.0056 20.9 5.7 44 96-139 76-126 (128)
135 TIGR02952 Sig70_famx2 RNA poly 25.1 1E+02 0.0023 23.2 3.7 38 96-138 123-160 (170)
136 PF01726 LexA_DNA_bind: LexA D 24.8 1.2E+02 0.0026 19.9 3.4 37 96-134 4-44 (65)
137 COG1905 NuoE NADH:ubiquinone o 24.7 1.1E+02 0.0025 24.1 3.7 37 98-134 25-61 (160)
138 PRK12536 RNA polymerase sigma 24.5 1.1E+02 0.0023 23.7 3.7 29 118-146 147-175 (181)
139 PHA01976 helix-turn-helix prot 24.5 44 0.00095 21.4 1.2 22 119-140 18-39 (67)
140 PRK09651 RNA polymerase sigma 24.5 88 0.0019 24.1 3.2 46 96-146 120-165 (172)
141 PRK13919 putative RNA polymera 24.4 1.2E+02 0.0025 23.5 3.9 45 96-145 136-180 (186)
142 PRK12529 RNA polymerase sigma 24.4 1.1E+02 0.0024 23.7 3.7 45 96-145 128-172 (178)
143 PRK12543 RNA polymerase sigma 24.2 1.1E+02 0.0025 23.6 3.8 46 96-146 118-163 (179)
144 PRK06986 fliA flagellar biosyn 24.0 1E+02 0.0022 25.2 3.6 46 96-146 185-230 (236)
145 PRK10360 DNA-binding transcrip 24.0 71 0.0015 24.3 2.5 44 95-144 137-180 (196)
146 PRK12518 RNA polymerase sigma 23.7 54 0.0012 25.1 1.8 30 117-146 137-166 (175)
147 PRK09645 RNA polymerase sigma 23.6 1.2E+02 0.0025 23.2 3.7 46 96-146 119-164 (173)
148 PRK12532 RNA polymerase sigma 23.5 1.1E+02 0.0023 24.1 3.5 46 96-146 137-182 (195)
149 KOG3119 Basic region leucine z 23.3 1.7E+02 0.0038 24.9 4.9 25 155-179 226-250 (269)
150 cd01106 HTH_TipAL-Mta Helix-Tu 23.2 2.8E+02 0.006 19.5 6.6 35 93-140 36-70 (103)
151 PRK09649 RNA polymerase sigma 23.0 1.1E+02 0.0023 24.0 3.4 45 96-145 131-175 (185)
152 PRK09480 slmA division inhibit 22.9 82 0.0018 24.3 2.7 41 101-142 16-56 (194)
153 TIGR01764 excise DNA binding d 22.7 48 0.001 19.3 1.1 23 119-141 4-26 (49)
154 PF04936 DUF658: Protein of un 22.6 34 0.00073 27.2 0.4 31 117-147 15-45 (186)
155 PRK12539 RNA polymerase sigma 22.6 1.2E+02 0.0027 23.5 3.7 46 96-146 132-177 (184)
156 TIGR02607 antidote_HigA addict 22.3 50 0.0011 21.8 1.2 23 119-141 21-43 (78)
157 PRK12542 RNA polymerase sigma 22.2 1.8E+02 0.0039 22.5 4.6 46 96-146 123-168 (185)
158 TIGR02479 FliA_WhiG RNA polyme 21.9 1.2E+02 0.0026 24.5 3.6 45 96-145 176-220 (224)
159 TIGR02950 SigM_subfam RNA poly 21.8 61 0.0013 24.1 1.7 33 113-145 118-150 (154)
160 PRK12523 RNA polymerase sigma 21.7 1.3E+02 0.0029 23.0 3.7 46 96-146 120-165 (172)
161 TIGR02943 Sig70_famx1 RNA poly 21.7 1.3E+02 0.0029 23.5 3.8 46 96-146 132-177 (188)
162 PRK00888 ftsB cell division pr 21.7 2E+02 0.0043 20.9 4.3 47 131-178 15-61 (105)
163 PRK08583 RNA polymerase sigma 21.6 1.2E+02 0.0026 25.1 3.6 45 96-145 206-250 (257)
164 PRK09935 transcriptional regul 21.5 85 0.0018 24.0 2.5 44 95-144 149-192 (210)
165 TIGR03001 Sig-70_gmx1 RNA poly 21.4 1.2E+02 0.0025 25.4 3.5 56 96-156 162-217 (244)
166 PRK15369 two component system 21.3 1.4E+02 0.0029 22.5 3.7 45 95-145 149-193 (211)
167 PRK05988 formate dehydrogenase 21.3 1.5E+02 0.0032 23.1 3.8 35 100-134 25-59 (156)
168 TIGR00721 tfx DNA-binding prot 21.2 1.6E+02 0.0035 22.5 3.9 47 94-146 5-51 (137)
169 PRK08301 sporulation sigma fac 21.2 1.1E+02 0.0024 24.9 3.2 50 96-146 179-228 (234)
170 PRK05657 RNA polymerase sigma 21.1 1.1E+02 0.0023 26.8 3.3 50 96-146 263-312 (325)
171 PF06971 Put_DNA-bind_N: Putat 21.1 56 0.0012 20.6 1.1 16 119-134 31-46 (50)
172 PRK12545 RNA polymerase sigma 20.8 1.4E+02 0.0029 23.8 3.6 46 96-146 140-185 (201)
173 smart00422 HTH_MERR helix_turn 20.8 61 0.0013 20.8 1.3 20 119-138 3-22 (70)
174 smart00338 BRLZ basic region l 20.6 2.5E+02 0.0054 18.0 4.6 30 152-181 27-56 (65)
175 TIGR02980 SigBFG RNA polymeras 20.6 1.3E+02 0.0028 24.3 3.6 44 96-144 179-222 (227)
176 PRK10651 transcriptional regul 20.6 1.3E+02 0.0028 23.0 3.4 45 96-146 156-200 (216)
177 KOG4005 Transcription factor X 20.4 1.8E+02 0.0038 24.7 4.2 12 88-99 53-67 (292)
178 PF07638 Sigma70_ECF: ECF sigm 20.3 1.1E+02 0.0024 24.0 3.0 28 118-145 153-180 (185)
179 KOG4403 Cell surface glycoprot 20.3 1.3E+02 0.0029 27.7 3.7 33 135-167 230-265 (575)
180 PRK12516 RNA polymerase sigma 20.2 1.4E+02 0.0031 23.4 3.6 46 96-146 117-162 (187)
181 PRK09647 RNA polymerase sigma 20.1 1.4E+02 0.0031 23.8 3.7 45 96-145 139-183 (203)
182 PRK11511 DNA-binding transcrip 20.0 71 0.0015 23.7 1.7 25 115-139 24-48 (127)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.86 E-value=3.2e-22 Score=161.92 Aligned_cols=96 Identities=59% Similarity=0.882 Sum_probs=91.8
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccchHHHHHhhhhhhHHH
Q 028655 88 GQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKDYDSLKAVYDKLKDDY 167 (206)
Q Consensus 88 ~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~~~~l~~~~~~~~~~~ 167 (206)
....+++||+.+|+..||..|+.+.++.+.++..||+.|||.++||.|||||||||||.++.+.+|+.|+..++.+..++
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~ 128 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEN 128 (198)
T ss_pred ccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhh
Confidence 45677888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHHHHH
Q 028655 168 DNLLKEKQVLQNEVVI 183 (206)
Q Consensus 168 ~~~~~~~~~l~~~~~~ 183 (206)
+.+..++..|..++..
T Consensus 129 ~~Lq~e~~eL~~~~~~ 144 (198)
T KOG0483|consen 129 DRLQSEVQELVAELSS 144 (198)
T ss_pred hHHHHHHHHHHHHHhh
Confidence 9999999999988764
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.79 E-value=3.3e-19 Score=152.30 Aligned_cols=71 Identities=38% Similarity=0.594 Sum_probs=63.5
Q ss_pred CCCCCCCC--CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccchHHHHH
Q 028655 88 GQSGKKRR--LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKDYDSLKA 158 (206)
Q Consensus 88 ~~~~kr~r--~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~~~~l~~ 158 (206)
.++|||+| |+..|+.+||+.|...+|++..+|+.||..|.|+++||||||||||-|.||+++++..+.+..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~ 222 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLL 222 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccC
Confidence 44444555 999999999999999999999999999999999999999999999999999998888776543
No 3
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.76 E-value=1.6e-18 Score=148.14 Aligned_cols=64 Identities=31% Similarity=0.494 Sum_probs=57.5
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhcc
Q 028655 88 GQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGK 151 (206)
Q Consensus 88 ~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~ 151 (206)
..++||..+|..|+.+||+.|-.|.|++.+.|.+|++.|+|++|||+|||||||+|.||..++.
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 4445555599999999999999999999999999999999999999999999999999976433
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.75 E-value=4e-19 Score=127.90 Aligned_cols=61 Identities=31% Similarity=0.467 Sum_probs=55.4
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhh
Q 028655 89 QSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRL 149 (206)
Q Consensus 89 ~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~ 149 (206)
+++-|+.||..||.+||++|...+||++..|++||.+++|++..|||||||||+|.||+..
T Consensus 17 QRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 17 QRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 3444445999999999999999999999999999999999999999999999999998743
No 5
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.75 E-value=6.5e-19 Score=149.41 Aligned_cols=64 Identities=31% Similarity=0.572 Sum_probs=57.1
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccc
Q 028655 89 QSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKD 152 (206)
Q Consensus 89 ~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~ 152 (206)
.+|.|+-||..|+.+||+.|..|+|+++..|.+||..|.|+++||+|||||||+||||..+...
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 3444445999999999999999999999999999999999999999999999999998655443
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=3.1e-18 Score=148.04 Aligned_cols=55 Identities=36% Similarity=0.580 Sum_probs=53.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhc
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLG 150 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~ 150 (206)
||..|+..||+.|++.+|++..+|.+||..|||+..||++||||||+||||+..+
T Consensus 179 FT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 179 FSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred hhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999997544
No 7
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.73 E-value=1.3e-17 Score=134.71 Aligned_cols=60 Identities=40% Similarity=0.587 Sum_probs=55.1
Q ss_pred CCCCCCCC--CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 88 GQSGKKRR--LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 88 ~~~~kr~r--~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
..++||+| |+..|+..||..|+..+|++..+|..||++|.|++.||+|||||||.||||+
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 33445555 9999999999999999999999999999999999999999999999999986
No 8
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=3e-17 Score=135.65 Aligned_cols=67 Identities=27% Similarity=0.384 Sum_probs=62.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccchHHHHHhhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKDYDSLKAVYDK 162 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~~~~l~~~~~~ 162 (206)
||.-|+..||+.|+..+||+...|+.||.++.|.+.+|+|||||||+||||........++..+++-
T Consensus 148 FT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeygl 214 (332)
T KOG0494|consen 148 FTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYGL 214 (332)
T ss_pred hhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhcc
Confidence 9999999999999999999999999999999999999999999999999998877777777666664
No 9
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.70 E-value=1.4e-17 Score=131.05 Aligned_cols=63 Identities=30% Similarity=0.460 Sum_probs=57.3
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhcc
Q 028655 89 QSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGK 151 (206)
Q Consensus 89 ~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~ 151 (206)
.+|.|+.|+.+|+..||..|+.++|..-.+|+.||..|+|++.||+|||||||.|.||.+.+.
T Consensus 102 ~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 102 PKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 344444599999999999999999999999999999999999999999999999999987764
No 10
>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=99.70 E-value=2.2e-17 Score=108.37 Aligned_cols=57 Identities=42% Similarity=0.658 Sum_probs=54.0
Q ss_pred CCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 90 SGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 90 ~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
++++++|+.+|+..|+.+|..++||+..+++.||..+||+..+|++||+|||+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 356777999999999999999999999999999999999999999999999999986
No 11
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.68 E-value=2.6e-16 Score=128.22 Aligned_cols=57 Identities=35% Similarity=0.578 Sum_probs=53.3
Q ss_pred CCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhh
Q 028655 93 KRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRL 149 (206)
Q Consensus 93 r~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~ 149 (206)
|+.++.-||..|.+.|+++.|+...+|.+||..|||+..||+|||||||.|.||...
T Consensus 126 RTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 126 RTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 334999999999999999999999999999999999999999999999999998644
No 12
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.67 E-value=4.1e-17 Score=132.21 Aligned_cols=67 Identities=30% Similarity=0.433 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhcc
Q 028655 85 GWLGQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGK 151 (206)
Q Consensus 85 ~~~~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~ 151 (206)
+..+++|.|++|+-.|+++||..|.++.||++..|++||.+|+|.+.+|+|||+|||+|+|++++.+
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 3445566677799999999999999999999999999999999999999999999999999987754
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.65 E-value=1.2e-16 Score=128.33 Aligned_cols=58 Identities=33% Similarity=0.544 Sum_probs=53.9
Q ss_pred CCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 90 SGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 90 ~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
++.|+.||..||..||+.|...+|+++.+|.+++..|.|++.||+|||||||+|.||-
T Consensus 145 RkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 145 RKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 3444459999999999999999999999999999999999999999999999999984
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.65 E-value=1.2e-16 Score=132.64 Aligned_cols=57 Identities=44% Similarity=0.624 Sum_probs=53.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccc
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKD 152 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~ 152 (206)
+|+-|..+||+.|..++|+++..+.+||..|||++|||+|||||||||+||..+++.
T Consensus 206 YTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999765543
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.60 E-value=6.9e-15 Score=121.82 Aligned_cols=71 Identities=34% Similarity=0.528 Sum_probs=61.6
Q ss_pred CCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccchHHHHHhh
Q 028655 90 SGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKDYDSLKAVY 160 (206)
Q Consensus 90 ~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~~~~l~~~~ 160 (206)
+|.|+-||.+||..|+..|+.++|++...|.+||.+|+|.+.||+|||||+|+|.||..-.+....+.-+-
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~lma 317 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHLMA 317 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhhhc
Confidence 34445599999999999999999999999999999999999999999999999999977666655555443
No 16
>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=99.58 E-value=2.8e-15 Score=98.51 Aligned_cols=57 Identities=47% Similarity=0.719 Sum_probs=53.2
Q ss_pred CCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 91 GKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 91 ~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
+++..|+..|+..|+.+|..++||+..++..||..+||++.+|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 345669999999999999999999999999999999999999999999999999864
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.57 E-value=2.7e-15 Score=97.80 Aligned_cols=55 Identities=40% Similarity=0.653 Sum_probs=51.2
Q ss_pred CCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 91 GKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 91 ~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+.+.+|+.+|+..|+..|..++||+..++..||..+||+..+|++||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 3455699999999999999999999999999999999999999999999998864
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.57 E-value=3e-15 Score=117.47 Aligned_cols=71 Identities=37% Similarity=0.610 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccchH
Q 028655 84 DGWLGQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKDYD 154 (206)
Q Consensus 84 ~~~~~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~~~ 154 (206)
++....+++|+|.|..|+.+|+..|+.++||+...|..|+..|+++++-|||||||||++.|+........
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~ 116 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQ 116 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhc
Confidence 34446677888899999999999999999999999999999999999999999999999999976554443
No 19
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.55 E-value=2.7e-15 Score=126.58 Aligned_cols=62 Identities=34% Similarity=0.571 Sum_probs=57.4
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhc
Q 028655 89 QSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLG 150 (206)
Q Consensus 89 ~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~ 150 (206)
-+|.|+-||.+|+..||+.|.+..|.+...|.+||..|+|++..|+|||||||+|+||+++.
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 35667779999999999999999999999999999999999999999999999999998653
No 20
>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=99.55 E-value=7.9e-15 Score=96.41 Aligned_cols=52 Identities=17% Similarity=0.332 Sum_probs=48.9
Q ss_pred CCCCCCCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHHhCCCcchhhhcccchH
Q 028655 90 SGKKRRLTATQVQFLERNFEVENK----LEPERKVQLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 90 ~~kr~r~t~~q~~~Le~~F~~~~~----p~~~~r~~La~~lgl~~~qV~vWFqNRR 141 (206)
++.|+.||.+|+..|+..|+.++| |+..++++||..+||++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 566777999999999999999999 9999999999999999999999999954
No 21
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.54 E-value=2.7e-15 Score=125.78 Aligned_cols=78 Identities=31% Similarity=0.537 Sum_probs=67.6
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh-------hhccchH
Q 028655 82 DFDGWLGQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ-------RLGKDYD 154 (206)
Q Consensus 82 ~~~~~~~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~-------~~~~~~~ 154 (206)
..++....+|.|+.+|..||+.|+..|...++|....|++|+.++||..++|||||||||||+||- +|.+.+.
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfr 239 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFR 239 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHH
Confidence 445566778888889999999999999999999999999999999999999999999999999973 5556666
Q ss_pred HHHHh
Q 028655 155 SLKAV 159 (206)
Q Consensus 155 ~l~~~ 159 (206)
.+|..
T Consensus 240 smK~s 244 (383)
T KOG4577|consen 240 SMKRS 244 (383)
T ss_pred Hhhcc
Confidence 65654
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.52 E-value=1.5e-14 Score=122.55 Aligned_cols=65 Identities=26% Similarity=0.422 Sum_probs=57.0
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccc
Q 028655 88 GQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKD 152 (206)
Q Consensus 88 ~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~ 152 (206)
++++.|+.|+..|+.+||..|++++||+...|++||..++|++.+|+|||.|||+||||+..-..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 33444445999999999999999999999999999999999999999999999999999754333
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.51 E-value=1.6e-14 Score=112.20 Aligned_cols=59 Identities=32% Similarity=0.529 Sum_probs=54.3
Q ss_pred CCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccc
Q 028655 94 RRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKD 152 (206)
Q Consensus 94 ~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~ 152 (206)
+.|+..|+..||+.|+..+|++..+|.+||..|+|++.||+.||||||+|.||.+....
T Consensus 105 tvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 105 TVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred ccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 33999999999999999999999999999999999999999999999999998754443
No 24
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.42 E-value=1.2e-13 Score=120.87 Aligned_cols=61 Identities=23% Similarity=0.391 Sum_probs=55.1
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhh
Q 028655 89 QSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRL 149 (206)
Q Consensus 89 ~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~ 149 (206)
+++||+.|.......||..|.+|++|+..++..||.+|+|...+|+|||||||.|+||...
T Consensus 294 kRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 294 KRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3444444999999999999999999999999999999999999999999999999998654
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.36 E-value=2.6e-13 Score=110.02 Aligned_cols=52 Identities=42% Similarity=0.677 Sum_probs=51.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
|+-.|+..||..|+..+|+--.+|.+||..+|+++.||+|||||||.||||+
T Consensus 174 f~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 174 FTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred ccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 9999999999999999999999999999999999999999999999999985
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.27 E-value=2.2e-12 Score=106.72 Aligned_cols=61 Identities=31% Similarity=0.382 Sum_probs=56.5
Q ss_pred CCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhh
Q 028655 88 GQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQR 148 (206)
Q Consensus 88 ~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~ 148 (206)
.+++.|+.|+..|+++||+.|+.++||+...++.||..+++++..|+|||||||++|+++.
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 4455666699999999999999999999999999999999999999999999999999875
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.15 E-value=3.9e-11 Score=105.91 Aligned_cols=63 Identities=33% Similarity=0.494 Sum_probs=57.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhh
Q 028655 86 WLGQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQR 148 (206)
Q Consensus 86 ~~~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~ 148 (206)
..+.++.|+.|+..|+..||+.|+.++||+...|+.||.++++++..|+|||+|||++++|..
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 334445556699999999999999999999999999999999999999999999999999965
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.01 E-value=1.5e-10 Score=97.48 Aligned_cols=62 Identities=24% Similarity=0.411 Sum_probs=56.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 86 WLGQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 86 ~~~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
...++|||+.+-..+.+.||.+|...+.|+.+.+..+|++|+|.+.+|+|||+|.|+|.||.
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 34556666668888999999999999999999999999999999999999999999999984
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.00 E-value=2.9e-10 Score=95.16 Aligned_cols=52 Identities=31% Similarity=0.484 Sum_probs=48.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
|...-...|.++|..++||++.++.+||+.+||+..||-+||.|||+|+|-.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence 5566788999999999999999999999999999999999999999999943
No 30
>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=98.58 E-value=2.5e-08 Score=60.76 Aligned_cols=34 Identities=38% Similarity=0.571 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHhCCCcchhhhcccchHHH
Q 028655 110 VENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143 (206)
Q Consensus 110 ~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak 143 (206)
.++||+.++++.||..+||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999999875
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.56 E-value=3.5e-08 Score=82.31 Aligned_cols=61 Identities=28% Similarity=0.442 Sum_probs=54.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 87 LGQSGKKRRLTATQVQFLERNFE---VENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 87 ~~~~~kr~r~t~~q~~~Le~~F~---~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
...+|||+.|+..-.++|..+|. .++||+.+.+++||++++++..||-.||.|+|-+.||.
T Consensus 186 ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 186 LDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 34567777799999999999996 57899999999999999999999999999999999974
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.13 E-value=3.2e-06 Score=77.16 Aligned_cols=57 Identities=23% Similarity=0.285 Sum_probs=51.0
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 89 QSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 89 ~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
.++.|..||..|.+.|..+|+.+++|+.+..+.|+.+|+|....|.+||-|-|.|.+
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 334444599999999999999999999999999999999999999999999887753
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.10 E-value=3.5e-06 Score=69.51 Aligned_cols=61 Identities=34% Similarity=0.601 Sum_probs=54.7
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhh
Q 028655 89 QSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRL 149 (206)
Q Consensus 89 ~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~ 149 (206)
.++.++.+...|+..|+..|..+++|+...++.|+..+|++.+.|++||||+|++.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3344445889999999999999999999999999999999999999999999999998644
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.63 E-value=6.6e-05 Score=74.63 Aligned_cols=63 Identities=22% Similarity=0.469 Sum_probs=57.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhh
Q 028655 86 WLGQSGKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQR 148 (206)
Q Consensus 86 ~~~~~~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~ 148 (206)
..+++.+|++++..||..+...|....||...+.+.|...+++..+.|++||||-|+|.|+..
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 345667788899999999999999999999999999999999999999999999999999853
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.20 E-value=0.00017 Score=46.85 Aligned_cols=42 Identities=26% Similarity=0.385 Sum_probs=31.2
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchH
Q 028655 100 QVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 100 q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRR 141 (206)
.+..|+++|...+++...+...|..+.+|+..||+.||--|+
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 356799999999999999999999999999999999997553
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.77 E-value=0.0012 Score=58.02 Aligned_cols=59 Identities=29% Similarity=0.358 Sum_probs=48.3
Q ss_pred CCCCCCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhh
Q 028655 91 GKKRRLTATQVQFLERNFEV---ENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRL 149 (206)
Q Consensus 91 ~kr~r~t~~q~~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~ 149 (206)
++++.|......+|+.+... .+||+..++..||.++||+..||.+||-|.|-|..+...
T Consensus 241 r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 241 RPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 33334888888998877433 479999999999999999999999999999887776543
No 37
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=96.46 E-value=0.0056 Score=38.10 Aligned_cols=38 Identities=50% Similarity=0.754 Sum_probs=35.1
Q ss_pred hhhccchHHHHHhhhhhhHHHHhHHHHHHHHHHHHHHh
Q 028655 147 QRLGKDYDSLKAVYDKLKDDYDNLLKEKQVLQNEVVIN 184 (206)
Q Consensus 147 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 184 (206)
++.+++|+.|+..++.+..++++|..+++.|+.+|...
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L 38 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQEL 38 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999999999999999998765
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=95.62 E-value=0.013 Score=55.91 Aligned_cols=48 Identities=19% Similarity=0.385 Sum_probs=45.0
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhh
Q 028655 101 VQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQR 148 (206)
Q Consensus 101 ~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~ 148 (206)
+..|..+|..|..|+.++...+|...||+.+.|+.||+++++......
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999999988754
No 39
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.02 E-value=0.12 Score=33.07 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=32.6
Q ss_pred CCCCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchH
Q 028655 91 GKKRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 91 ~kr~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRR 141 (206)
++|+.+|-++...+-..++... ....||.++|++..+|..|..|+.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 4566699888777777777665 578899999999999999998853
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=89.01 E-value=3.7 Score=30.58 Aligned_cols=43 Identities=23% Similarity=0.447 Sum_probs=29.1
Q ss_pred CCCCCCCHHHHH-HHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhccc
Q 028655 91 GKKRRLTATQVQ-FLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 91 ~kr~r~t~~q~~-~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFq 138 (206)
.++++|+.++.. ++...+. +.+ ...++|.++|+++.+|..|.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 335568877644 3444443 332 366789999999999999964
No 41
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=88.64 E-value=3.2 Score=31.56 Aligned_cols=79 Identities=20% Similarity=0.242 Sum_probs=53.6
Q ss_pred CCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHh----------hh----hhhccchHHHHHh
Q 028655 94 RRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARS----------RN----QRLGKDYDSLKAV 159 (206)
Q Consensus 94 ~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~----------k~----~~~~~~~~~l~~~ 159 (206)
.+|++++|..+ ..|+.--+.-|++...|-.|=|.||+-. |+ ..++++...|.++
T Consensus 22 d~lsDd~Lvsm------------SVReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qq 89 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQ 89 (135)
T ss_pred CCcCHHHHHHh------------hHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56899888776 2233323445899999999998887533 22 3456666677777
Q ss_pred hhhhhHHHHhHHHHHHHHHHHHHHh
Q 028655 160 YDKLKDDYDNLLKEKQVLQNEVVIN 184 (206)
Q Consensus 160 ~~~~~~~~~~~~~~~~~l~~~~~~~ 184 (206)
.+.+..++..+..|.+.++.-....
T Consensus 90 v~~L~~e~s~~~~E~da~k~k~e~l 114 (135)
T KOG4196|consen 90 VEKLKEENSRLRRELDAYKSKYEAL 114 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8888888888887777776544433
No 42
>smart00340 HALZ homeobox associated leucin zipper.
Probab=86.91 E-value=1.2 Score=27.17 Aligned_cols=32 Identities=28% Similarity=0.345 Sum_probs=27.4
Q ss_pred hhccchHHHHHhhhhhhHHHHhHHHHHHHHHH
Q 028655 148 RLGKDYDSLKAVYDKLKDDYDNLLKEKQVLQN 179 (206)
Q Consensus 148 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~ 179 (206)
+.+-+++.|+...+.+.+++.+|.+|.+.|+.
T Consensus 2 QTEvdCe~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 2 QTEVDCELLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56788999999999999999988888887764
No 43
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=78.68 E-value=1.1 Score=29.94 Aligned_cols=43 Identities=26% Similarity=0.436 Sum_probs=27.6
Q ss_pred CCCCCCCHHHHHHHHHhh-hhcCCCCHHHHHHHHHHhCCCcchhhhccc
Q 028655 91 GKKRRLTATQVQFLERNF-EVENKLEPERKVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 91 ~kr~r~t~~q~~~Le~~F-~~~~~p~~~~r~~La~~lgl~~~qV~vWFq 138 (206)
+++++||+++...+-..+ ... .....+|.++|+++.++..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence 345679998766655554 333 4678899999999999999964
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=77.70 E-value=3.2 Score=25.59 Aligned_cols=39 Identities=13% Similarity=0.189 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccc
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQN 139 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqN 139 (206)
+++.+..+|...|... ..-.++|..+|++...|+.+...
T Consensus 5 L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 5 LPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp S-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHH
Confidence 6788899999988322 34778999999999999877643
No 45
>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=75.71 E-value=6.5 Score=20.96 Aligned_cols=39 Identities=18% Similarity=0.330 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcc
Q 028655 94 RRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWF 137 (206)
Q Consensus 94 ~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWF 137 (206)
..++.++...+...|... + ....+|..+|++...|..|.
T Consensus 4 ~~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 346777766666666532 2 46678999999998888774
No 46
>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=74.83 E-value=3.9 Score=26.21 Aligned_cols=39 Identities=28% Similarity=0.336 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCcchhh
Q 028655 96 LTATQVQFLERNFEVENK--LEPERKVQLAKELGLQPRQVA 134 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~--p~~~~r~~La~~lgl~~~qV~ 134 (206)
+|+.|.+.|...|+..=| |-.....+||.++|++..-|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 578999999999886543 666778899999999987654
No 47
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=73.32 E-value=4.7 Score=24.04 Aligned_cols=42 Identities=14% Similarity=0.141 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHH
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRA 142 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRa 142 (206)
+++.+...+...|... ....++|..+|++...|..|...-+.
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6677777777776422 24667899999999999999865443
No 48
>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=67.12 E-value=3.3 Score=27.28 Aligned_cols=20 Identities=20% Similarity=0.511 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCCcchhhhcc
Q 028655 118 RKVQLAKELGLQPRQVAIWF 137 (206)
Q Consensus 118 ~r~~La~~lgl~~~qV~vWF 137 (206)
.-.+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 35678999999999999994
No 49
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=65.52 E-value=4.4 Score=25.99 Aligned_cols=38 Identities=13% Similarity=0.203 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCcchhhhcccchHHHhhhhhhccchHH
Q 028655 118 RKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKDYDS 155 (206)
Q Consensus 118 ~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~~~~ 155 (206)
....||+.+|++...|..|+.++.....-....+-...
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~ 49 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKA 49 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHH
Confidence 46788999999999999999877555554444333333
No 50
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=65.12 E-value=6.6 Score=40.46 Aligned_cols=55 Identities=18% Similarity=0.139 Sum_probs=48.4
Q ss_pred CCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 93 KRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 93 r~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
++|++.-|+.+|...|+...+|.-.+...++..|++..|.+-.||++++.++...
T Consensus 448 s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~ 502 (1406)
T KOG1146|consen 448 SKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQN 502 (1406)
T ss_pred hhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccc
Confidence 4457888999999999999999999999999999999999888888888777764
No 51
>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=63.73 E-value=10 Score=23.55 Aligned_cols=39 Identities=15% Similarity=0.176 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccc
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQN 139 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqN 139 (206)
+++.+..++...|-.. ..-.++|..+|+++..|+.|.+.
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHH
Confidence 4566666665554333 46788999999999999999864
No 52
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=63.58 E-value=11 Score=24.60 Aligned_cols=44 Identities=23% Similarity=0.391 Sum_probs=22.4
Q ss_pred CCCCCHH-HHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhccc
Q 028655 93 KRRLTAT-QVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 93 r~r~t~~-q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFq 138 (206)
|+.|+.. -|.+++.++..+. --...| .-|.++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNN-CKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TT-TTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccc-hhhhHH-HHHHHhCccHHHHHHHHH
Confidence 3346654 3555555544332 111233 349999999999999954
No 53
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=61.28 E-value=1.3 Score=42.89 Aligned_cols=92 Identities=13% Similarity=0.109 Sum_probs=59.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccchHHHHHhhhhhhHHHHhHHHHHH
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKDYDSLKAVYDKLKDDYDNLLKEKQ 175 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 175 (206)
...++-..|...|+.+..+.-.+-...+.+|...+.+|++||++|+..-+...+-.-...--.......+.......+.+
T Consensus 633 ~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ltss~n~~~p~ytpes~asee~Q~e 712 (1007)
T KOG3623|consen 633 IKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLFLTSSANGAAPPYTPESQASEERQDE 712 (1007)
T ss_pred CCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcccccccccCCCCCCCcchhcccccccc
Confidence 55566677888888777777666666677788889999999999999988765443333322223333333344455566
Q ss_pred HHHHHHHHhhcC
Q 028655 176 VLQNEVVINLYA 187 (206)
Q Consensus 176 ~l~~~~~~~~~~ 187 (206)
-|+-+|.+....
T Consensus 713 pLdlslprq~ge 724 (1007)
T KOG3623|consen 713 PLDLSLPRQPGE 724 (1007)
T ss_pred ccchhcccccCC
Confidence 666666666554
No 54
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=60.27 E-value=17 Score=28.15 Aligned_cols=48 Identities=19% Similarity=0.144 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 93 KRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 93 r~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
...+++.|..+|...+ .. ....++|..+|++...|..|.++.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3458899999997742 22 246789999999999999999876666655
No 55
>PRK10072 putative transcriptional regulator; Provisional
Probab=56.63 E-value=14 Score=26.62 Aligned_cols=40 Identities=20% Similarity=0.285 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHH
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRA 142 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRa 142 (206)
.+...+..|...-.. ...+||+.+|++...|..|.+.+|.
T Consensus 33 ~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 466666666543322 2778999999999999999987653
No 56
>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=55.62 E-value=80 Score=24.98 Aligned_cols=66 Identities=18% Similarity=0.258 Sum_probs=45.4
Q ss_pred CCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccchHHHHHhhhh
Q 028655 93 KRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKDYDSLKAVYDK 162 (206)
Q Consensus 93 r~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~~~~l~~~~~~ 162 (206)
+-.++++++..+.+.-. .-|....+..||+++|++..-|.+=..--. .++...+...+.++..++.
T Consensus 83 ~y~Lt~e~i~Eir~LR~--~DP~~wTr~~LAkkF~~S~~fV~~v~~~~~--e~~~~~~~~le~~k~rWg~ 148 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRA--EDPEKWTRKKLAKKFNCSPLFVSMVAPAPK--EKKKEMEARLEAIKSRWGP 148 (164)
T ss_pred cccCCHHHHHHHHHHHH--cCchHhhHHHHHHHhCCCHHHHHHhcCCCH--HHHHHHHHHHHHHHHhccH
Confidence 34599999988877754 347778899999999999887776554333 4444445556666655543
No 57
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=53.56 E-value=26 Score=21.56 Aligned_cols=34 Identities=44% Similarity=0.613 Sum_probs=26.2
Q ss_pred hccchHHHHHhhhhhhHHHHhHHHHHHHHHHHHH
Q 028655 149 LGKDYDSLKAVYDKLKDDYDNLLKEKQVLQNEVV 182 (206)
Q Consensus 149 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~ 182 (206)
....++.|+..++.+..++..|..+...|...+.
T Consensus 10 LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~ 43 (45)
T PF02183_consen 10 LKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQ 43 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3466788888888888888888888887776553
No 58
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=52.38 E-value=49 Score=21.47 Aligned_cols=33 Identities=30% Similarity=0.467 Sum_probs=15.5
Q ss_pred hhccchHHHHHhhhhhhHHHHhHHHHHHHHHHH
Q 028655 148 RLGKDYDSLKAVYDKLKDDYDNLLKEKQVLQNE 180 (206)
Q Consensus 148 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~ 180 (206)
.++.....|..++..+..+...+..+...|..+
T Consensus 30 ~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e 62 (64)
T PF00170_consen 30 ELEEKVEELESENEELKKELEQLKKEIQSLKSE 62 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 334444444444444444444444444444443
No 59
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=52.01 E-value=10 Score=22.93 Aligned_cols=39 Identities=23% Similarity=0.219 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcc
Q 028655 94 RRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWF 137 (206)
Q Consensus 94 ~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWF 137 (206)
+++|.+|...++..++.. ....++|+.+|.+...|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 458888888888887644 346679999999998887665
No 60
>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=50.98 E-value=21 Score=22.54 Aligned_cols=45 Identities=18% Similarity=0.189 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 95 RLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 95 r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
.||+.++.+|.....-. ...++|..+++++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 47888888887776543 4778999999999999988766555544
No 61
>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=50.20 E-value=19 Score=21.75 Aligned_cols=38 Identities=16% Similarity=0.327 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcc
Q 028655 95 RLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWF 137 (206)
Q Consensus 95 r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWF 137 (206)
.+++++.+.+...+... ....++|+.+|++...|..++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 36776666666666655 247889999999998887665
No 62
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=49.94 E-value=20 Score=26.28 Aligned_cols=39 Identities=23% Similarity=0.468 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchH
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRR 141 (206)
+++.++..+.+.+... ...+|..||++..-|+.|=|+|+
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCc
Confidence 8888899888877654 56789999999999999999875
No 63
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=49.48 E-value=19 Score=29.34 Aligned_cols=49 Identities=27% Similarity=0.295 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHhhhhcC--CCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 95 RLTATQVQFLERNFEVEN--KLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 95 r~t~~q~~~Le~~F~~~~--~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
.+|+.|+++|...|...= +|-.-...+||+++|+++.-+ |..=|||..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~--~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL--SEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH--HHHHHHHHHH
Confidence 499999999999998654 477777889999999998754 3333444443
No 64
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=49.22 E-value=10 Score=22.75 Aligned_cols=23 Identities=22% Similarity=0.205 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCcchhhhcccchH
Q 028655 119 KVQLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqNRR 141 (206)
..++|+.+|+++..|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45789999999999999976543
No 65
>PF13518 HTH_28: Helix-turn-helix domain
Probab=48.88 E-value=11 Score=22.96 Aligned_cols=22 Identities=23% Similarity=0.540 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCCcchhhhcccc
Q 028655 118 RKVQLAKELGLQPRQVAIWFQN 139 (206)
Q Consensus 118 ~r~~La~~lgl~~~qV~vWFqN 139 (206)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3566899999999999999753
No 66
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=48.81 E-value=64 Score=20.90 Aligned_cols=36 Identities=22% Similarity=0.333 Sum_probs=28.0
Q ss_pred hhccchHHHHHhhhhhhHHHHhHHHHHHHHHHHHHH
Q 028655 148 RLGKDYDSLKAVYDKLKDDYDNLLKEKQVLQNEVVI 183 (206)
Q Consensus 148 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~ 183 (206)
........|......+..++..|..+...|..++..
T Consensus 23 RKk~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~ 58 (64)
T PF00170_consen 23 RKKQYIEELEEKVEELESENEELKKELEQLKKEIQS 58 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334667777788888889999999888888877654
No 67
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=47.71 E-value=6.2 Score=27.04 Aligned_cols=35 Identities=17% Similarity=0.222 Sum_probs=25.4
Q ss_pred HHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccc
Q 028655 105 ERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQN 139 (206)
Q Consensus 105 e~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqN 139 (206)
+..|...+|.......++|..+|+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 33444444444446788999999999999999853
No 68
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=47.66 E-value=18 Score=25.83 Aligned_cols=35 Identities=29% Similarity=0.354 Sum_probs=18.5
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhh
Q 028655 101 VQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRL 149 (206)
Q Consensus 101 ~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~ 149 (206)
+...+-.|+.|+||...--.. | =.|||.+||+.+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHH
Confidence 344555688999997431111 1 1589999998654
No 69
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.27 E-value=24 Score=25.17 Aligned_cols=39 Identities=18% Similarity=0.224 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVA 134 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~ 134 (206)
++++|...-...|+.+--.+....+++|.+|++++-.|+
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 567888887888887777777888999999999886554
No 70
>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=46.30 E-value=24 Score=22.60 Aligned_cols=34 Identities=24% Similarity=0.315 Sum_probs=25.5
Q ss_pred HHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhc
Q 028655 99 TQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIW 136 (206)
Q Consensus 99 ~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vW 136 (206)
.|+..|+-.+. ++..+.. +||..+|++++.|+.-
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHH
Confidence 47788888888 6666544 8999999999988743
No 71
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=45.98 E-value=30 Score=27.33 Aligned_cols=46 Identities=20% Similarity=0.151 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..+|...|-.. ..-.++|..||++...|+++...-|.+.|+
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 6777777776654333 346789999999999999988655555554
No 72
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=44.83 E-value=30 Score=25.92 Aligned_cols=45 Identities=18% Similarity=0.162 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..++...|-.. ....++|..+|++...|+.|...-+.+.|
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 6677777776655333 24788999999999999998764444443
No 73
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=44.80 E-value=7.1 Score=37.06 Aligned_cols=48 Identities=13% Similarity=0.146 Sum_probs=31.3
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhC-------CCcchhhhcccchHHHhhhhh
Q 028655 101 VQFLERNFEVENKLEPERKVQLAKELG-------LQPRQVAIWFQNRRARSRNQR 148 (206)
Q Consensus 101 ~~~Le~~F~~~~~p~~~~r~~La~~lg-------l~~~qV~vWFqNRRak~k~~~ 148 (206)
.++-+.+|-+++.+......+--.++. ....-|+.||.|||+++|+-+
T Consensus 704 ~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 704 YEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred eecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 333455566677666555544444333 345679999999999999754
No 74
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=43.82 E-value=34 Score=27.42 Aligned_cols=46 Identities=20% Similarity=0.158 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..+|...|-.. ....++|..+|+++..|+++...-+.+.++
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666666544222 347789999999999999888655555554
No 75
>PRK04217 hypothetical protein; Provisional
Probab=43.52 E-value=36 Score=25.13 Aligned_cols=46 Identities=13% Similarity=0.053 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
++.+|..++...|...- ...++|+.+|++...|...+..-+.+.+.
T Consensus 43 Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 43 MTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 78888888877764332 56789999999999999887655555543
No 76
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.18 E-value=32 Score=26.24 Aligned_cols=45 Identities=13% Similarity=-0.025 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..+|...|-.. ..-.++|..+|++...|+.|...-+.+.|
T Consensus 129 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 129 LPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6777777776654322 23568899999999999998874444444
No 77
>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=42.80 E-value=15 Score=23.78 Aligned_cols=27 Identities=26% Similarity=0.402 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 118 RKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 118 ~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
...++|..||++...|..|-+ |-+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 356899999999999999964 445443
No 78
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=41.80 E-value=15 Score=22.27 Aligned_cols=22 Identities=27% Similarity=0.439 Sum_probs=17.1
Q ss_pred HHHHHHHHHhCCCcchhhhccc
Q 028655 117 ERKVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 117 ~~r~~La~~lgl~~~qV~vWFq 138 (206)
....++|+.+|++...|..|.+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3477889999999999999964
No 79
>PHA02955 hypothetical protein; Provisional
Probab=40.17 E-value=42 Score=27.76 Aligned_cols=43 Identities=9% Similarity=0.162 Sum_probs=34.3
Q ss_pred HHHHHHHHHhhhhc-CCCCHHHHHHHHHHhCCCcchhhhcccch
Q 028655 98 ATQVQFLERNFEVE-NKLEPERKVQLAKELGLQPRQVAIWFQNR 140 (206)
Q Consensus 98 ~~q~~~Le~~F~~~-~~p~~~~r~~La~~lgl~~~qV~vWFqNR 140 (206)
..++..|-+.|... ..++.++|.++++++|+....|..||.+.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 34677777777665 56888999999999999998789999764
No 80
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.09 E-value=41 Score=20.11 Aligned_cols=38 Identities=24% Similarity=0.332 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccc
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQN 139 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqN 139 (206)
+++.+...+...+. .+ ...++|..+|++...|..|.+.
T Consensus 4 l~~~e~~i~~~~~~--g~----s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 4 LTPREREVLRLLAE--GL----TNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCHHHHHHHHHHHc--CC----CHHHHHHHHCCCHHHHHHHHHH
Confidence 67777777755432 22 4578899999999999888763
No 81
>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=39.96 E-value=40 Score=24.42 Aligned_cols=45 Identities=18% Similarity=0.192 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+...+...|-. .....++|..+|+++..|..|...-+.+-|
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 556666665544322 224668999999999999988765544444
No 82
>PRK00118 putative DNA-binding protein; Validated
Probab=39.89 E-value=45 Score=24.36 Aligned_cols=46 Identities=15% Similarity=0.154 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.|..++...|... ....++|..+|++...|..|...-|.+.|.
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5666667766555443 246679999999999999998755555554
No 83
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=39.22 E-value=44 Score=25.98 Aligned_cols=46 Identities=13% Similarity=0.044 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-.. ..-.++|..+|++...|+.++..-|.+.|.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6777777776654432 346789999999999999998766666554
No 84
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=39.07 E-value=33 Score=26.94 Aligned_cols=46 Identities=26% Similarity=0.283 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|- ......++|..+|++...|++|+..-|.+.|+
T Consensus 142 L~~~~~~v~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAYY-----EGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhhh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 55555555555432 22346789999999999999998755555554
No 85
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=39.03 E-value=41 Score=25.58 Aligned_cols=46 Identities=17% Similarity=0.148 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-. ...-.++|..+|++...|..|...-|.+.|+
T Consensus 126 L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 555555555544432 2345789999999999999998755555553
No 86
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=38.97 E-value=48 Score=25.01 Aligned_cols=46 Identities=11% Similarity=0.130 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-.. ..-.++|..+|+++..|+++...-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5566666665544322 235688999999999999988755555554
No 87
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=38.33 E-value=20 Score=23.19 Aligned_cols=21 Identities=24% Similarity=0.407 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCcchhhhcccc
Q 028655 119 KVQLAKELGLQPRQVAIWFQN 139 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqN 139 (206)
..++|+.+|++...|+.|=+.
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999543
No 88
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=36.94 E-value=54 Score=25.32 Aligned_cols=46 Identities=13% Similarity=0.223 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-.. ...+++|..+|+++..|+++...-|.+.|+
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 5566666555554221 237789999999999999988755555544
No 89
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=36.04 E-value=51 Score=25.73 Aligned_cols=45 Identities=24% Similarity=0.204 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.|..++...|-.. ....++|..+|++...|+.+...-|.+.|
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6677777776654432 34788999999999999988754444444
No 90
>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=36.04 E-value=52 Score=24.43 Aligned_cols=45 Identities=16% Similarity=0.141 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..+|...|-. . ....++|..+|+++..|+.+...-|.+.|
T Consensus 114 L~~~~r~il~l~~~~-~----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFE-G----KSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHc-C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 556666666554422 2 23667899999999999988765444444
No 91
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=35.82 E-value=1.1e+02 Score=19.08 Aligned_cols=29 Identities=17% Similarity=0.314 Sum_probs=15.3
Q ss_pred cchHHHHHhhhhhhHHHHhHHHHHHHHHH
Q 028655 151 KDYDSLKAVYDKLKDDYDNLLKEKQVLQN 179 (206)
Q Consensus 151 ~~~~~l~~~~~~~~~~~~~~~~~~~~l~~ 179 (206)
.....+......+..++..|..+...|..
T Consensus 25 ~~~~~le~~~~~L~~en~~L~~~i~~L~~ 53 (54)
T PF07716_consen 25 QREEELEQEVQELEEENEQLRQEIAQLER 53 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 44444555555555555555555555543
No 92
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=35.75 E-value=22 Score=20.73 Aligned_cols=24 Identities=21% Similarity=0.497 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCcchhhhcccchHH
Q 028655 119 KVQLAKELGLQPRQVAIWFQNRRA 142 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqNRRa 142 (206)
..++|+.+|++...|..|.++..-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999876543
No 93
>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=35.14 E-value=54 Score=24.60 Aligned_cols=43 Identities=23% Similarity=0.251 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHH
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRAR 143 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak 143 (206)
+++.+..++...|-. ...-.++|..+|++...|.++...-|.+
T Consensus 112 L~~~~r~v~~l~~~~-----g~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 112 LPERQRELLQLRYQR-----GVSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 667776666664432 2346789999999999999876544433
No 94
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=34.64 E-value=50 Score=25.72 Aligned_cols=46 Identities=11% Similarity=0.109 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-.. ..-.++|..+|++...|+.+...-|.+.|+
T Consensus 129 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 129 LPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred CCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 5666666665544222 246788999999999999988655555554
No 95
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=34.44 E-value=17 Score=22.10 Aligned_cols=21 Identities=14% Similarity=0.290 Sum_probs=19.0
Q ss_pred HHHHHhCCCcchhhhcccchH
Q 028655 121 QLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 121 ~La~~lgl~~~qV~vWFqNRR 141 (206)
+||+.+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 96
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=34.17 E-value=55 Score=24.92 Aligned_cols=46 Identities=15% Similarity=-0.008 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-. .....++|..+|+++..|++|.+.-|.+.|+
T Consensus 109 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 109 LPVIEAQAILLCDVH-----ELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CCHHHHHHHHhHHHh-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 556666665543322 1346789999999999999998755555544
No 97
>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=34.17 E-value=57 Score=25.14 Aligned_cols=46 Identities=15% Similarity=0.118 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..+|...|-.. ....++|..+|+++..|+++...-|.+.+.
T Consensus 101 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 101 LPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6677777776655333 246789999999999999887644444443
No 98
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=34.13 E-value=38 Score=26.89 Aligned_cols=47 Identities=19% Similarity=-0.014 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
+++.+..+|.-.|-.. ....++|..+|++...|+++...-|.+.|+.
T Consensus 114 Lp~~~r~v~~L~~~~g-----~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 114 LPDEQREALILVGASG-----FSYEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred CCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 6666666665543321 2467889999999999999988666666653
No 99
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=33.92 E-value=22 Score=20.88 Aligned_cols=18 Identities=33% Similarity=0.530 Sum_probs=14.8
Q ss_pred HHHHHHhCCCcchhhhcc
Q 028655 120 VQLAKELGLQPRQVAIWF 137 (206)
Q Consensus 120 ~~La~~lgl~~~qV~vWF 137 (206)
-++|+.+|++.+.|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 478999999999999884
No 100
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=33.59 E-value=61 Score=25.36 Aligned_cols=46 Identities=11% Similarity=0.195 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..+|...|-.. ..-.++|..+|+++..|++-...-|.+.|+
T Consensus 132 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6677777776654322 246788999999999999877655555554
No 101
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=33.52 E-value=75 Score=24.01 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..+|.-.| ..+ .-.++|..+|++...|+.+...-|.+.|+
T Consensus 113 L~~~~r~il~l~~--~g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 113 MTERDRTVLLLRF--SGY----SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666777776666 222 46788999999999999888654544443
No 102
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=33.26 E-value=22 Score=21.84 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=18.5
Q ss_pred HHHHHHHhCCCcchhhhcccch
Q 028655 119 KVQLAKELGLQPRQVAIWFQNR 140 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqNR 140 (206)
..+||+.+|++...|..|..++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHHHHhCCCcchhHHHhcCC
Confidence 4789999999999999999873
No 103
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=33.17 E-value=2e+02 Score=24.37 Aligned_cols=32 Identities=22% Similarity=0.355 Sum_probs=15.7
Q ss_pred ccchHHHHHhhhhhhHHHHhHHHHHHHHHHHH
Q 028655 150 GKDYDSLKAVYDKLKDDYDNLLKEKQVLQNEV 181 (206)
Q Consensus 150 ~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~ 181 (206)
..+++.|..+++.+..-+..|+.++..|+.++
T Consensus 103 ~een~~L~~en~~Lr~~n~~L~~~n~el~~~l 134 (292)
T KOG4005|consen 103 TEENEILQNENDSLRAINESLLAKNHELDSEL 134 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 33444455555555555555555555554433
No 104
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=32.97 E-value=53 Score=25.38 Aligned_cols=46 Identities=13% Similarity=0.090 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-. ...-.++|..+|+++..|+++++.-|.+.|.
T Consensus 137 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 137 LPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 666666666554322 2346788999999999999998755555543
No 105
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=32.81 E-value=62 Score=25.00 Aligned_cols=46 Identities=22% Similarity=0.211 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-.. ..-.++|..+|+++..|++....-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5555655555554322 246788999999999999988755554443
No 106
>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=32.27 E-value=48 Score=25.68 Aligned_cols=30 Identities=10% Similarity=-0.065 Sum_probs=23.1
Q ss_pred HHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 117 ERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 117 ~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
..-.++|..+|+++..|+++...-|.+.|+
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999988655555443
No 107
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=32.13 E-value=1.3e+02 Score=20.88 Aligned_cols=45 Identities=18% Similarity=0.262 Sum_probs=31.6
Q ss_pred hhccchHHHHHhhhhhhHHHHhHHHHHHHHHHHHHHhhcCCCCCC
Q 028655 148 RLGKDYDSLKAVYDKLKDDYDNLLKEKQVLQNEVVINLYATSLSS 192 (206)
Q Consensus 148 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ss 192 (206)
..+.....|....+.+..+++.|..+++-|..=+.+.+.+.....
T Consensus 27 ~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~~s~v~~ 71 (80)
T PF10224_consen 27 ELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMSSSSVFQ 71 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 445566667777788888888888889888877766655444333
No 108
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.93 E-value=81 Score=22.73 Aligned_cols=42 Identities=12% Similarity=0.192 Sum_probs=30.9
Q ss_pred CCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCC-Ccchhhhccc
Q 028655 93 KRRLTATQVQFLERNFEVENKLEPERKVQLAKELGL-QPRQVAIWFQ 138 (206)
Q Consensus 93 r~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl-~~~qV~vWFq 138 (206)
+++|+.+....+-..+....+ ....+|+++|+ ...++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 566998876665555544443 57889999996 9999998864
No 109
>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=31.77 E-value=66 Score=19.24 Aligned_cols=36 Identities=19% Similarity=0.286 Sum_probs=25.0
Q ss_pred CHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhccc
Q 028655 97 TATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 97 t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFq 138 (206)
++.+...+...+ .. ....++|+.++++...|..|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 455566665433 22 2467889999999999998875
No 110
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=30.78 E-value=70 Score=25.06 Aligned_cols=47 Identities=19% Similarity=0.328 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
+++.+..++.-.|-.. ....++|..+|++...|++..+.-|.+.|++
T Consensus 132 L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 132 LEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 6677777766544322 2467899999999999998876555555543
No 111
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=30.71 E-value=62 Score=24.47 Aligned_cols=45 Identities=18% Similarity=0.104 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.|..+|.-.|-.. ..-.++|..+|++...|+.+...-|.+.|
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6666666665544322 24678899999999999988765554444
No 112
>PRK06930 positive control sigma-like factor; Validated
Probab=30.62 E-value=71 Score=25.22 Aligned_cols=46 Identities=11% Similarity=0.066 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|... ..-.++|..+|++...|+.+...-+.+.++
T Consensus 115 L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 115 LTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6777777776654322 246788999999999999998766555554
No 113
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=30.21 E-value=29 Score=22.57 Aligned_cols=21 Identities=19% Similarity=0.398 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCcchhhhcccc
Q 028655 119 KVQLAKELGLQPRQVAIWFQN 139 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqN 139 (206)
..++|+.+|+++..++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999753
No 114
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=29.86 E-value=70 Score=25.15 Aligned_cols=46 Identities=15% Similarity=0.178 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.|-.. ....++|..+|+++..|+++...-|.+.|+
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666665554322 236789999999999999997654544443
No 115
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=29.79 E-value=28 Score=21.22 Aligned_cols=23 Identities=17% Similarity=0.114 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCcchhhhcccchH
Q 028655 119 KVQLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqNRR 141 (206)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999987654
No 116
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=29.55 E-value=87 Score=21.77 Aligned_cols=43 Identities=12% Similarity=0.180 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHhhhh-----cCCCCHHHHHHHHHHhCCCcchhhhccc
Q 028655 96 LTATQVQFLERNFEV-----ENKLEPERKVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~-----~~~p~~~~r~~La~~lgl~~~qV~vWFq 138 (206)
++.+|+..|...|.. +.+.+..+...+-..+|+++..|..+|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 678899999999875 2367778777777778888877777764
No 117
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=28.65 E-value=1e+02 Score=25.55 Aligned_cols=37 Identities=35% Similarity=0.522 Sum_probs=28.8
Q ss_pred hhccchHHHHHhhhhhhHHHHhHHHHHHHHHHHHHHh
Q 028655 148 RLGKDYDSLKAVYDKLKDDYDNLLKEKQVLQNEVVIN 184 (206)
Q Consensus 148 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 184 (206)
..++..+.++...+.+..+++++.++.++|++++...
T Consensus 176 ~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~~~ 212 (216)
T KOG1962|consen 176 KAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIESG 212 (216)
T ss_pred HHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHhcc
Confidence 3456667777777888888999999999998888654
No 118
>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=28.35 E-value=81 Score=24.03 Aligned_cols=46 Identities=7% Similarity=0.073 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-.. ....++|..+|+++..|+++...-|.+.|+
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666666554333 246788999999999999877544444443
No 119
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=28.34 E-value=46 Score=29.11 Aligned_cols=39 Identities=28% Similarity=0.373 Sum_probs=34.5
Q ss_pred hhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 109 EVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 109 ~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
..++||+..+...|+....++..+|.+||-|-|.+.+..
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 457899999999999999999999999999988887763
No 120
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=27.88 E-value=72 Score=26.31 Aligned_cols=46 Identities=13% Similarity=0.132 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.|..++.-.|-.. ..-.++|..+|++...|+++...-|.+.|+
T Consensus 172 Lp~~~R~v~~L~~~eg-----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 172 LPEQQRIAVILSYHEN-----MSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4555555544443222 246789999999999999888755555554
No 121
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=27.85 E-value=91 Score=24.20 Aligned_cols=45 Identities=16% Similarity=0.258 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..++...|-.. ....++|..+|++...|++|...-|.+.|
T Consensus 134 L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 134 LEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 5666666555544222 24678999999999999988764444433
No 122
>PRK10403 transcriptional regulator NarP; Provisional
Probab=27.81 E-value=53 Score=25.12 Aligned_cols=44 Identities=18% Similarity=0.205 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+|..+..+|+..... ....++|+.++++++.|++..+|=+.|-.
T Consensus 154 Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 154 LTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred CCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 788888888765442 34678899999999999988876655543
No 123
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=27.77 E-value=32 Score=22.23 Aligned_cols=21 Identities=10% Similarity=0.371 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCcchhhhcccc
Q 028655 119 KVQLAKELGLQPRQVAIWFQN 139 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqN 139 (206)
..++|+.+|+++..|+.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 124
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=27.72 E-value=94 Score=23.28 Aligned_cols=45 Identities=13% Similarity=0.054 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..++.-.|-.. ..-.++|..+|++...|++....-|.+.|
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 107 LPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALA 151 (161)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6666666666644322 23678899999999999987764444444
No 125
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.51 E-value=83 Score=24.61 Aligned_cols=46 Identities=17% Similarity=0.148 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..+|...|-.. ....++|..+|++...|+..+..-|.+.|+
T Consensus 107 L~~~~r~i~~l~~~~g-----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 107 LPEKYAEALRLTELEG-----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5666666665543222 246789999999999999888654544443
No 126
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=27.33 E-value=86 Score=23.87 Aligned_cols=45 Identities=16% Similarity=-0.031 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..++.-.|-.. ..-.++|..+|+++..|+++...-|.+.|
T Consensus 113 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 113 LSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 6677777666654322 24678999999999999998765554444
No 127
>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=27.05 E-value=87 Score=23.57 Aligned_cols=46 Identities=24% Similarity=0.253 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..+|...|-. . ..-.++|..+|++...|+.+-..-|.+-|+
T Consensus 111 L~~~~r~i~~l~~~~-g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRYYE-D----LSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHHHh-c----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 566666666655522 2 236788999999999999887765555554
No 128
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=26.89 E-value=93 Score=23.44 Aligned_cols=45 Identities=24% Similarity=0.287 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..++...|-.. ....++|..+|++...|+.....-+.+.|
T Consensus 110 L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~~lr 154 (163)
T PRK07037 110 LPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALVHCR 154 (163)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5566666665544222 23678999999999999987654444444
No 129
>PF13551 HTH_29: Winged helix-turn helix
Probab=26.87 E-value=1.2e+02 Score=21.15 Aligned_cols=43 Identities=16% Similarity=0.193 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHhhhhcCC-----CCHHHHHH-H-HHHh--CCCcchhhhccc
Q 028655 96 LTATQVQFLERNFEVENK-----LEPERKVQ-L-AKEL--GLQPRQVAIWFQ 138 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~-----p~~~~r~~-L-a~~l--gl~~~qV~vWFq 138 (206)
+++++...|.+.+..++. .+.....+ | .... .++...|..|++
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 899999999999987762 33333333 3 2333 456677777663
No 130
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=26.83 E-value=37 Score=19.59 Aligned_cols=23 Identities=22% Similarity=0.381 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCcchhhhcccchH
Q 028655 119 KVQLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqNRR 141 (206)
...+|+.+|+++..|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999987653
No 131
>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=26.82 E-value=38 Score=23.45 Aligned_cols=20 Identities=10% Similarity=0.257 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCcchhhhccc
Q 028655 119 KVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFq 138 (206)
+..|.+.++|...||.+|+.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 56688889999999999985
No 132
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.15 E-value=90 Score=24.60 Aligned_cols=46 Identities=11% Similarity=-0.016 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.|-. ...-.++|..+|++...|++++..-|.+.|+
T Consensus 137 L~~~~r~i~~L~~~~-----g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 137 LPERQRQAVVLRHIE-----GLSNPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 555555555444332 1236788999999999999998755555544
No 133
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=25.83 E-value=42 Score=21.55 Aligned_cols=20 Identities=20% Similarity=0.423 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCcchhhhccc
Q 028655 119 KVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFq 138 (206)
..++|+.+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 134
>cd00131 PAX Paired Box domain
Probab=25.39 E-value=2.6e+02 Score=20.87 Aligned_cols=44 Identities=11% Similarity=-0.014 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCC-------Ccchhhhcccc
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGL-------QPRQVAIWFQN 139 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl-------~~~qV~vWFqN 139 (206)
.+..+...++.....++..+..+..++...-|+ +...|-.||++
T Consensus 76 ~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 76 ATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 566776777776777777766665554224465 67777777654
No 135
>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=25.08 E-value=1e+02 Score=23.21 Aligned_cols=38 Identities=24% Similarity=0.212 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhccc
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFq 138 (206)
+++.+..+|...|-.. ..-.++|..+|++...|+....
T Consensus 123 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 123 LTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 6666666666644322 3467889999999999987664
No 136
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=24.75 E-value=1.2e+02 Score=19.92 Aligned_cols=37 Identities=30% Similarity=0.313 Sum_probs=23.2
Q ss_pred CCHHHHHHHHH---hhhhcCCCCHHHHHHHHHHhCCC-cchhh
Q 028655 96 LTATQVQFLER---NFEVENKLEPERKVQLAKELGLQ-PRQVA 134 (206)
Q Consensus 96 ~t~~q~~~Le~---~F~~~~~p~~~~r~~La~~lgl~-~~qV~ 134 (206)
+|+.|.++|+- +...+.||. ...+||+.+|+. ...|+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~ 44 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQ 44 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHH
Confidence 57777666654 456677863 677889999997 65554
No 137
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=24.70 E-value=1.1e+02 Score=24.10 Aligned_cols=37 Identities=24% Similarity=0.264 Sum_probs=32.4
Q ss_pred HHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhh
Q 028655 98 ATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVA 134 (206)
Q Consensus 98 ~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~ 134 (206)
..-+..|...++...|......+.+|..||++...|.
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 4567888999999999999999999999999987765
No 138
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=24.52 E-value=1.1e+02 Score=23.74 Aligned_cols=29 Identities=14% Similarity=0.068 Sum_probs=23.5
Q ss_pred HHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 118 RKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 118 ~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
...++|..+|++...|++....-|.+.|+
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999988766665554
No 139
>PHA01976 helix-turn-helix protein
Probab=24.51 E-value=44 Score=21.42 Aligned_cols=22 Identities=9% Similarity=0.229 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCcchhhhcccch
Q 028655 119 KVQLAKELGLQPRQVAIWFQNR 140 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqNR 140 (206)
..+||..+|++...|..|...+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 5679999999999999998654
No 140
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=24.48 E-value=88 Score=24.08 Aligned_cols=46 Identities=13% Similarity=0.123 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.| .......++|..+|++...|+++...-+.+.+.
T Consensus 120 L~~~~r~i~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 120 LNGKTREAFLLSQ-----LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CCHHHhHHhhhhh-----ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5555555544432 222347789999999999999887544444443
No 141
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=24.42 E-value=1.2e+02 Score=23.51 Aligned_cols=45 Identities=16% Similarity=0.144 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..+|...|-.. ..-.++|..+|++...|+.+...-|.+.|
T Consensus 136 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 136 LSPEERRVIEVLYYQG-----YTHREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 6666666666544222 24678899999999999987764444444
No 142
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.41 E-value=1.1e+02 Score=23.69 Aligned_cols=45 Identities=11% Similarity=0.036 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.|..++.-.|-.. ..-.++|..||+++..|+.....-+.+.+
T Consensus 128 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 128 LRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6777777766654332 24678999999999999988775555544
No 143
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=24.16 E-value=1.1e+02 Score=23.56 Aligned_cols=46 Identities=13% Similarity=0.082 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-.. ..-.++|..+|++...|++....-|.+.|+
T Consensus 118 Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 118 LPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5555555555543222 246788999999999999887766666664
No 144
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=24.01 E-value=1e+02 Score=25.16 Aligned_cols=46 Identities=17% Similarity=0.195 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|... ..-.++|..+|++...|+.+...-+.+.|+
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5566666666655322 346789999999999999998766666654
No 145
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=24.00 E-value=71 Score=24.29 Aligned_cols=44 Identities=27% Similarity=0.286 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHh
Q 028655 95 RLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARS 144 (206)
Q Consensus 95 r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~ 144 (206)
.+|+.+.+.|+-..+- + .+.++|..++++++.|++..++=|.|-
T Consensus 137 ~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4788888777766542 2 578889999999999988776655543
No 146
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=23.71 E-value=54 Score=25.12 Aligned_cols=30 Identities=17% Similarity=0.132 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 117 ERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 117 ~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
..-+++|..+|+++..|++.+..-|.+.|+
T Consensus 137 ~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 137 LPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 347889999999999999988766666554
No 147
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=23.57 E-value=1.2e+02 Score=23.18 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..+|.-.|-.. ..-.++|..+|+++..|+.....-|.+.|+
T Consensus 119 L~~~~r~vl~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG-----WSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6677777776654322 236789999999999999877544444443
No 148
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=23.53 E-value=1.1e+02 Score=24.06 Aligned_cols=46 Identities=9% Similarity=0.095 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.|-.. ..-.++|..+|++...|+.+...-|.+.|+
T Consensus 137 L~~~~r~i~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 137 LPENTARVFTLKEILG-----FSSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5555655555433222 236789999999999999988755555554
No 149
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=23.31 E-value=1.7e+02 Score=24.90 Aligned_cols=25 Identities=24% Similarity=0.349 Sum_probs=10.5
Q ss_pred HHHHhhhhhhHHHHhHHHHHHHHHH
Q 028655 155 SLKAVYDKLKDDYDNLLKEKQVLQN 179 (206)
Q Consensus 155 ~l~~~~~~~~~~~~~~~~~~~~l~~ 179 (206)
.|..++..+....+.|..+...++.
T Consensus 226 ~leken~~lr~~v~~l~~el~~~~~ 250 (269)
T KOG3119|consen 226 ELEKENEALRTQVEQLKKELATLRR 250 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444444444444443
No 150
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=23.17 E-value=2.8e+02 Score=19.55 Aligned_cols=35 Identities=20% Similarity=0.298 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccch
Q 028655 93 KRRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNR 140 (206)
Q Consensus 93 r~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNR 140 (206)
.+.|+..++..|..... .+.+|++..+|+.++...
T Consensus 36 ~R~y~~~di~~l~~i~~-------------lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 36 YRLYTEEDLERLQQILF-------------LKELGFSLKEIKELLKDP 70 (103)
T ss_pred ceeeCHHHHHHHHHHHH-------------HHHcCCCHHHHHHHHHcC
Confidence 34499999998865532 345688888888877654
No 151
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=22.97 E-value=1.1e+02 Score=23.99 Aligned_cols=45 Identities=16% Similarity=-0.028 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.|..++.-.|-.. ..-.++|..+|+++..|+++...-|.+.|
T Consensus 131 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 131 LTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALL 175 (185)
T ss_pred CCHHHhHHhhhHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5666666655543222 24678999999999999988764444444
No 152
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.92 E-value=82 Score=24.31 Aligned_cols=41 Identities=20% Similarity=0.247 Sum_probs=31.9
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHH
Q 028655 101 VQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRA 142 (206)
Q Consensus 101 ~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRa 142 (206)
+......|...+. .......||++.|++...+-.+|.|+-.
T Consensus 16 l~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 16 LQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 3344445655556 7778999999999999999999999763
No 153
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=22.71 E-value=48 Score=19.34 Aligned_cols=23 Identities=17% Similarity=0.148 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCcchhhhcccchH
Q 028655 119 KVQLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqNRR 141 (206)
..++|+.+|++...|..|.+..+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 46789999999999999986554
No 154
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=22.60 E-value=34 Score=27.23 Aligned_cols=31 Identities=19% Similarity=0.407 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCCcchhhhcccchHHHhhhh
Q 028655 117 ERKVQLAKELGLQPRQVAIWFQNRRARSRNQ 147 (206)
Q Consensus 117 ~~r~~La~~lgl~~~qV~vWFqNRRak~k~~ 147 (206)
....+|+.-++++..+|-+|..|-+...+..
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~ 45 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAK 45 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCccccc
Confidence 4578899999999999999999998777653
No 155
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=22.58 E-value=1.2e+02 Score=23.50 Aligned_cols=46 Identities=9% Similarity=-0.050 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.|-.. ..-.++|..+|++...|+.+...-|.+.|+
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 132 LPEKMRLAIQAVKLEG-----LSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6667766666544322 346789999999999999887655554443
No 156
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=22.26 E-value=50 Score=21.77 Aligned_cols=23 Identities=30% Similarity=0.380 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCcchhhhcccchH
Q 028655 119 KVQLAKELGLQPRQVAIWFQNRR 141 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFqNRR 141 (206)
..+||+.+|++...|..|...++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999997654
No 157
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.15 E-value=1.8e+02 Score=22.52 Aligned_cols=46 Identities=17% Similarity=0.251 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.|-.. ..-.++|..+|+++..|++....-|.+.|+
T Consensus 123 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 123 LNESNRQVFKYKVFYN-----LTYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666665543222 246789999999999999977655555444
No 158
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=21.93 E-value=1.2e+02 Score=24.50 Aligned_cols=45 Identities=18% Similarity=0.193 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..+|...|-.. ....++|..+|++...|+.+...-+.+.|
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 6777777777766332 24688999999999999888764444443
No 159
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=21.79 E-value=61 Score=24.13 Aligned_cols=33 Identities=15% Similarity=0.108 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 113 KLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 113 ~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
|.....-.++|..+|+++..|+++...-|.+.|
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELK 150 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 344456788999999999999988764444443
No 160
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=21.75 E-value=1.3e+02 Score=22.98 Aligned_cols=46 Identities=13% Similarity=0.093 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.|-.. ..-.++|..+|++...|+++...-+.+.+.
T Consensus 120 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 120 LSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5566666665543222 246788999999999999988665555543
No 161
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.73 E-value=1.3e+02 Score=23.50 Aligned_cols=46 Identities=11% Similarity=0.128 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++...|-.. ....++|..+|++...|++....-|.+.|+
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 132 LPEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5666666666554332 246789999999999998877654444444
No 162
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=21.67 E-value=2e+02 Score=20.86 Aligned_cols=47 Identities=23% Similarity=0.333 Sum_probs=21.3
Q ss_pred chhhhcccchHHHhhhhhhccchHHHHHhhhhhhHHHHhHHHHHHHHH
Q 028655 131 RQVAIWFQNRRARSRNQRLGKDYDSLKAVYDKLKDDYDNLLKEKQVLQ 178 (206)
Q Consensus 131 ~qV~vWFqNRRak~k~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~ 178 (206)
-++..||.+.=- .+-....++...++.++..+.+++..|..+...|+
T Consensus 15 l~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~ 61 (105)
T PRK00888 15 LQYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK 61 (105)
T ss_pred HHHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 455678855410 01112223444444445555555555555544443
No 163
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=21.58 E-value=1.2e+02 Score=25.13 Aligned_cols=45 Identities=13% Similarity=0.205 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..+|...|-.. ..-.++|..+|++...|+.|...=+.+.|
T Consensus 206 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 206 LSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6777777777765322 23578999999999999988765444444
No 164
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=21.49 E-value=85 Score=24.00 Aligned_cols=44 Identities=18% Similarity=0.131 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHh
Q 028655 95 RLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARS 144 (206)
Q Consensus 95 r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~ 144 (206)
.++..+..+|....+. ..++++|.+++++.+.|+++..+=|.|-
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 3788888888654433 4588899999999999999876655544
No 165
>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=21.42 E-value=1.2e+02 Score=25.36 Aligned_cols=56 Identities=14% Similarity=0.195 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhhhhhccchHHH
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRNQRLGKDYDSL 156 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~~~~~~~~~~l 156 (206)
+++.+..++.-.|-.. ..-.++|..+|++...|+++...-|.+.|+.-..+....+
T Consensus 162 Lp~~~R~v~~L~~~eg-----~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 162 LSERERHLLRLHFVDG-----LSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4555555554443322 2467899999999999999998777777765444444333
No 166
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=21.35 E-value=1.4e+02 Score=22.48 Aligned_cols=45 Identities=18% Similarity=0.145 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 95 RLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 95 r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
.+|+.+..+|.- +..+ + ...++|+.++++++.|+.|.++=+.|-.
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 388888888876 3332 2 2578899999999999999876554443
No 167
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=21.27 E-value=1.5e+02 Score=23.13 Aligned_cols=35 Identities=14% Similarity=0.100 Sum_probs=28.2
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhh
Q 028655 100 QVQFLERNFEVENKLEPERKVQLAKELGLQPRQVA 134 (206)
Q Consensus 100 q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~ 134 (206)
-+..|...=+...|.+.+....+|..||+++.+|.
T Consensus 25 li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 25 LLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 35556555566679999999999999999998875
No 168
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=21.21 E-value=1.6e+02 Score=22.53 Aligned_cols=47 Identities=21% Similarity=0.159 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 94 RRLTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 94 ~r~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
.-+++.|..+|.-.+ .. ....++|..+|++...|..|-..-+.+-++
T Consensus 5 ~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 347888988887742 22 247789999999999999887655555553
No 169
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=21.16 E-value=1.1e+02 Score=24.89 Aligned_cols=50 Identities=18% Similarity=0.244 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.|... +.....-.++|..+|++...|+.+...-|.+-|+
T Consensus 179 Lp~~~R~v~~L~y~l~-~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 179 LSDREKQIMELRFGLN-GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6677777776665211 0222346788999999999999887655555444
No 170
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.14 E-value=1.1e+02 Score=26.82 Aligned_cols=50 Identities=26% Similarity=0.319 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.|..+|...|.... .......++|..+|++...|+.+...-+.+.|+
T Consensus 263 L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 263 LNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred CCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 78888888887763322 233457889999999999999988755555554
No 171
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=21.12 E-value=56 Score=20.55 Aligned_cols=16 Identities=44% Similarity=0.704 Sum_probs=13.0
Q ss_pred HHHHHHHhCCCcchhh
Q 028655 119 KVQLAKELGLQPRQVA 134 (206)
Q Consensus 119 r~~La~~lgl~~~qV~ 134 (206)
-.+||+.+|++..||+
T Consensus 31 S~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 31 SQELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCCCHHHhc
Confidence 5678999999999986
No 172
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=20.79 E-value=1.4e+02 Score=23.77 Aligned_cols=46 Identities=15% Similarity=0.151 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.|-.. ..-.++|..+|+++..|++....-|.+.|+
T Consensus 140 Lp~~~r~v~~L~~~eg-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 140 LPEQIGRVFMMREFLD-----FEIDDICTELTLTANHCSVLLYRARTRLRT 185 (201)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5555555555543222 236788999999999999887655555444
No 173
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=20.77 E-value=61 Score=20.79 Aligned_cols=20 Identities=20% Similarity=0.225 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCcchhhhccc
Q 028655 119 KVQLAKELGLQPRQVAIWFQ 138 (206)
Q Consensus 119 r~~La~~lgl~~~qV~vWFq 138 (206)
..++|+.+|+++..|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999964
No 174
>smart00338 BRLZ basic region leucin zipper.
Probab=20.61 E-value=2.5e+02 Score=18.04 Aligned_cols=30 Identities=23% Similarity=0.419 Sum_probs=15.4
Q ss_pred chHHHHHhhhhhhHHHHhHHHHHHHHHHHH
Q 028655 152 DYDSLKAVYDKLKDDYDNLLKEKQVLQNEV 181 (206)
Q Consensus 152 ~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~ 181 (206)
....|......+..++..|..+...|..++
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~ 56 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRREL 56 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444445555555555555555555444
No 175
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=20.58 E-value=1.3e+02 Score=24.28 Aligned_cols=44 Identities=16% Similarity=0.265 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARS 144 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~ 144 (206)
+++.+..++...|-.. ....++|..+|++...|..|...=+.+.
T Consensus 179 L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~L 222 (227)
T TIGR02980 179 LPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKL 222 (227)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 7777777777766422 2477899999999999998875433333
No 176
>PRK10651 transcriptional regulator NarL; Provisional
Probab=20.57 E-value=1.3e+02 Score=22.96 Aligned_cols=45 Identities=13% Similarity=0.142 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+|+.+.++|+-..+. + .-.++|++++++.+.|++..++=|.|-.-
T Consensus 156 Lt~rE~~vl~~l~~g--~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 156 LTPRERDILKLIAQG--L----PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred CCHHHHHHHHHHHcC--C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 899999888775532 1 35677999999999999988876666543
No 177
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=20.42 E-value=1.8e+02 Score=24.73 Aligned_cols=12 Identities=33% Similarity=0.418 Sum_probs=6.4
Q ss_pred CCCCCCCC---CCHH
Q 028655 88 GQSGKKRR---LTAT 99 (206)
Q Consensus 88 ~~~~kr~r---~t~~ 99 (206)
..++||+| ++.+
T Consensus 53 ~~~rKr~RL~HLS~E 67 (292)
T KOG4005|consen 53 QPKRKRRRLDHLSWE 67 (292)
T ss_pred chHHHHHhhcccCHH
Confidence 44556666 5544
No 178
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.30 E-value=1.1e+02 Score=24.04 Aligned_cols=28 Identities=29% Similarity=0.389 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 118 RKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 118 ~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
..+++|..+|++++.|+..++.=|++.+
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5778999999999999887766554444
No 179
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=20.29 E-value=1.3e+02 Score=27.69 Aligned_cols=33 Identities=30% Similarity=0.575 Sum_probs=23.2
Q ss_pred hcc---cchHHHhhhhhhccchHHHHHhhhhhhHHH
Q 028655 135 IWF---QNRRARSRNQRLGKDYDSLKAVYDKLKDDY 167 (206)
Q Consensus 135 vWF---qNRRak~k~~~~~~~~~~l~~~~~~~~~~~ 167 (206)
+|| ||+.+|.+-.+.-++.+.|+..-..+.+-.
T Consensus 230 cw~ay~Qnk~akehv~km~kdle~Lq~aEqsl~dlQ 265 (575)
T KOG4403|consen 230 CWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSLEDLQ 265 (575)
T ss_pred hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 788 899999887777777777766555544433
No 180
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=20.19 E-value=1.4e+02 Score=23.42 Aligned_cols=46 Identities=13% Similarity=-0.031 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSRN 146 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k~ 146 (206)
+++.+..++.-.|-.. ..-.++|..||+++..|+++...-|.+.|+
T Consensus 117 Lp~~~r~i~~L~~~~g-----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~ 162 (187)
T PRK12516 117 LPDDQREAIILVGASG-----FAYEEAAEICGCAVGTIKSRVNRARQRLQE 162 (187)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666665543322 235688999999999999887655544443
No 181
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=20.09 E-value=1.4e+02 Score=23.83 Aligned_cols=45 Identities=16% Similarity=0.023 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcchhhhcccchHHHhh
Q 028655 96 LTATQVQFLERNFEVENKLEPERKVQLAKELGLQPRQVAIWFQNRRARSR 145 (206)
Q Consensus 96 ~t~~q~~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~vWFqNRRak~k 145 (206)
+++.+..++...|-.. ..-.++|..+|+++..|+++...-|.+.|
T Consensus 139 L~~~~r~v~~L~~~~g-----~s~~EIA~~Lgis~~tV~~~l~RArk~Lr 183 (203)
T PRK09647 139 LPPEFRAAVVLCDIEG-----LSYEEIAATLGVKLGTVRSRIHRGRQQLR 183 (203)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555555444443211 23678899999999999998864444444
No 182
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=20.04 E-value=71 Score=23.66 Aligned_cols=25 Identities=12% Similarity=0.242 Sum_probs=20.9
Q ss_pred CHHHHHHHHHHhCCCcchhhhcccc
Q 028655 115 EPERKVQLAKELGLQPRQVAIWFQN 139 (206)
Q Consensus 115 ~~~~r~~La~~lgl~~~qV~vWFqN 139 (206)
......+||..+|++++.+..+|+.
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3356788999999999999999964
Done!