Query 031304
Match_columns 162
No_of_seqs 188 out of 1301
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 12:12:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031304.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031304hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484 Transcription factor P 99.8 2.2E-20 4.8E-25 132.3 4.5 66 17-87 14-79 (125)
2 KOG0488 Transcription factor B 99.8 6.9E-20 1.5E-24 153.4 6.7 82 9-95 161-242 (309)
3 KOG2251 Homeobox transcription 99.8 3.8E-19 8.3E-24 140.7 9.6 69 14-87 31-99 (228)
4 KOG0489 Transcription factor z 99.8 6.1E-20 1.3E-24 150.7 5.2 69 17-90 156-224 (261)
5 KOG0843 Transcription factor E 99.8 7E-19 1.5E-23 135.4 5.9 64 19-87 101-164 (197)
6 KOG0850 Transcription factor D 99.7 4E-18 8.7E-23 135.6 6.3 69 14-87 116-184 (245)
7 KOG0842 Transcription factor t 99.7 2.4E-18 5.3E-23 143.0 4.3 67 17-88 150-216 (307)
8 PF00046 Homeobox: Homeobox do 99.7 1.2E-17 2.7E-22 106.5 6.0 57 21-82 1-57 (57)
9 KOG0487 Transcription factor A 99.7 7.6E-18 1.7E-22 140.1 5.7 67 15-86 230-296 (308)
10 KOG0492 Transcription factor M 99.7 3.9E-17 8.5E-22 128.4 5.4 68 15-87 139-206 (246)
11 KOG0485 Transcription factor N 99.7 3.6E-17 7.8E-22 129.4 4.4 67 17-88 101-167 (268)
12 KOG0494 Transcription factor C 99.6 1.7E-16 3.6E-21 128.5 6.0 62 20-86 141-202 (332)
13 KOG0848 Transcription factor C 99.6 1.4E-16 3E-21 129.4 2.7 62 22-88 201-262 (317)
14 TIGR01565 homeo_ZF_HD homeobox 99.6 7.9E-16 1.7E-20 99.2 4.5 52 21-77 2-57 (58)
15 smart00389 HOX Homeodomain. DN 99.6 1.9E-15 4.1E-20 95.6 5.4 56 21-81 1-56 (56)
16 cd00086 homeodomain Homeodomai 99.6 2.6E-15 5.7E-20 95.6 6.1 57 22-83 2-58 (59)
17 KOG0491 Transcription factor B 99.6 1.1E-15 2.3E-20 116.5 3.4 66 19-89 99-164 (194)
18 KOG0493 Transcription factor E 99.6 3.7E-15 8.1E-20 120.8 5.8 60 20-84 246-305 (342)
19 COG5576 Homeodomain-containing 99.6 6.5E-15 1.4E-19 112.5 6.0 66 18-88 49-114 (156)
20 KOG0844 Transcription factor E 99.5 3.4E-15 7.3E-20 123.3 2.4 63 20-87 181-243 (408)
21 KOG0486 Transcription factor P 99.5 5.6E-15 1.2E-19 122.3 3.1 67 17-88 109-175 (351)
22 KOG0490 Transcription factor, 99.5 5.1E-14 1.1E-18 112.0 5.5 63 18-85 58-120 (235)
23 KOG0847 Transcription factor, 99.5 6.6E-14 1.4E-18 111.2 5.9 70 16-90 163-232 (288)
24 KOG3802 Transcription factor O 99.5 2.7E-14 5.8E-19 121.6 3.8 62 19-85 293-354 (398)
25 KOG0483 Transcription factor H 99.5 4.3E-14 9.3E-19 111.6 3.7 64 20-88 50-113 (198)
26 KOG4577 Transcription factor L 99.4 1.3E-13 2.9E-18 113.2 5.0 67 16-87 163-229 (383)
27 KOG0849 Transcription factor P 99.2 1.7E-11 3.8E-16 104.7 5.5 67 15-86 171-237 (354)
28 KOG0775 Transcription factor S 99.1 4E-10 8.6E-15 92.2 8.7 51 27-82 183-233 (304)
29 KOG1168 Transcription factor A 98.9 3.3E-10 7.2E-15 93.4 2.2 62 20-86 309-370 (385)
30 KOG0774 Transcription factor P 98.8 1.1E-08 2.4E-13 83.5 6.0 63 20-87 188-253 (334)
31 PF05920 Homeobox_KN: Homeobox 98.5 1E-07 2.2E-12 56.9 2.6 34 41-79 7-40 (40)
32 KOG2252 CCAAT displacement pro 98.4 4.6E-07 1E-11 80.4 5.2 57 19-80 419-475 (558)
33 KOG0490 Transcription factor, 98.2 1.7E-06 3.7E-11 68.6 4.5 64 17-85 150-213 (235)
34 KOG1146 Homeobox protein [Gene 97.5 0.00011 2.4E-09 71.0 5.0 62 20-86 903-964 (1406)
35 PF11569 Homez: Homeodomain le 96.4 0.0019 4.2E-08 41.2 1.9 41 32-77 10-50 (56)
36 KOG0773 Transcription factor M 95.9 0.0079 1.7E-07 51.0 3.8 58 20-82 239-299 (342)
37 PF04218 CENP-B_N: CENP-B N-te 94.6 0.12 2.5E-06 32.3 5.0 47 21-77 1-47 (53)
38 KOG3623 Homeobox transcription 93.8 0.12 2.7E-06 48.2 5.4 50 32-86 568-617 (1007)
39 PF04967 HTH_10: HTH DNA bindi 84.5 1.3 2.9E-05 27.8 3.0 41 27-72 1-43 (53)
40 PF01527 HTH_Tnp_1: Transposas 83.7 1.5 3.3E-05 28.4 3.2 45 22-76 2-47 (76)
41 PF04545 Sigma70_r4: Sigma-70, 83.6 2.9 6.3E-05 25.1 4.2 45 26-80 4-48 (50)
42 cd06171 Sigma70_r4 Sigma70, re 82.0 2.5 5.3E-05 24.5 3.4 44 26-79 10-53 (55)
43 COG3413 Predicted DNA binding 77.3 4.4 9.5E-05 32.0 4.4 50 26-82 155-206 (215)
44 PF08281 Sigma70_r4_2: Sigma-7 75.8 4.8 0.0001 24.3 3.4 42 27-78 11-52 (54)
45 PRK03975 tfx putative transcri 75.2 6.9 0.00015 29.4 4.7 49 25-84 5-53 (141)
46 cd00569 HTH_Hin_like Helix-tur 73.9 8.2 0.00018 19.8 3.8 38 26-73 5-42 (42)
47 PF13936 HTH_38: Helix-turn-he 70.1 3.5 7.6E-05 24.5 1.7 40 25-74 3-42 (44)
48 KOG3755 SATB1 matrix attachmen 68.8 4.9 0.00011 37.1 3.1 22 65-86 739-760 (769)
49 PRK04217 hypothetical protein; 67.6 24 0.00051 25.4 5.9 53 24-86 40-92 (110)
50 PRK06759 RNA polymerase factor 67.3 11 0.00023 27.4 4.2 45 27-81 107-151 (154)
51 PRK09646 RNA polymerase sigma 67.2 13 0.00028 28.4 4.8 48 27-84 143-190 (194)
52 PF00196 GerE: Bacterial regul 65.4 14 0.00031 22.7 4.0 44 26-80 3-46 (58)
53 PRK09644 RNA polymerase sigma 65.3 14 0.0003 27.3 4.6 33 50-86 126-158 (165)
54 PRK12526 RNA polymerase sigma 64.1 17 0.00037 28.2 5.0 31 50-84 171-201 (206)
55 PRK09652 RNA polymerase sigma 63.6 15 0.00032 27.1 4.5 48 26-83 128-175 (182)
56 PRK12512 RNA polymerase sigma 62.8 20 0.00044 26.9 5.2 49 27-85 132-180 (184)
57 PRK09642 RNA polymerase sigma 62.7 18 0.00039 26.5 4.7 31 50-84 124-154 (160)
58 PRK00118 putative DNA-binding 61.8 20 0.00044 25.5 4.6 47 26-82 17-63 (104)
59 PF10668 Phage_terminase: Phag 61.1 5.1 0.00011 25.8 1.3 21 49-73 23-43 (60)
60 PRK11924 RNA polymerase sigma 59.7 19 0.00041 26.4 4.4 30 50-83 143-172 (179)
61 TIGR02937 sigma70-ECF RNA poly 59.6 19 0.00042 25.1 4.3 46 27-82 111-156 (158)
62 PRK09413 IS2 repressor TnpA; R 59.5 22 0.00048 25.5 4.6 42 24-75 10-52 (121)
63 PRK12519 RNA polymerase sigma 57.8 16 0.00036 27.6 3.9 32 48-83 157-188 (194)
64 KOG1146 Homeobox protein [Gene 57.1 20 0.00043 36.1 5.0 61 19-84 704-764 (1406)
65 TIGR02989 Sig-70_gvs1 RNA poly 56.2 24 0.00051 25.6 4.4 44 27-80 112-155 (159)
66 TIGR02999 Sig-70_X6 RNA polyme 56.2 25 0.00055 26.2 4.6 46 27-82 135-180 (183)
67 PRK12514 RNA polymerase sigma 55.8 32 0.00069 25.7 5.1 30 50-83 147-176 (179)
68 TIGR02959 SigZ RNA polymerase 55.2 26 0.00056 26.2 4.5 50 26-85 100-149 (170)
69 PF02796 HTH_7: Helix-turn-hel 54.5 13 0.00028 21.9 2.2 39 25-73 4-42 (45)
70 PRK09047 RNA polymerase factor 53.9 31 0.00066 25.1 4.7 30 50-83 124-153 (161)
71 TIGR02948 SigW_bacill RNA poly 53.4 25 0.00054 26.3 4.2 31 49-83 153-183 (187)
72 PRK12533 RNA polymerase sigma 53.3 29 0.00063 27.4 4.7 34 50-87 152-185 (216)
73 PRK12537 RNA polymerase sigma 53.1 33 0.00073 25.8 4.9 29 50-82 151-179 (182)
74 PRK12541 RNA polymerase sigma 52.6 27 0.00058 25.6 4.2 46 27-82 113-158 (161)
75 PRK12516 RNA polymerase sigma 52.6 34 0.00074 26.1 4.9 33 50-86 134-166 (187)
76 smart00421 HTH_LUXR helix_turn 51.9 45 0.00097 19.2 4.5 40 26-76 3-42 (58)
77 PRK09648 RNA polymerase sigma 51.7 32 0.0007 25.9 4.6 46 27-82 140-185 (189)
78 PRK05602 RNA polymerase sigma 51.4 35 0.00075 25.7 4.8 32 50-85 146-177 (186)
79 PRK12539 RNA polymerase sigma 51.2 39 0.00085 25.4 5.0 48 27-84 132-179 (184)
80 PRK07037 extracytoplasmic-func 50.8 42 0.00091 24.5 5.0 31 50-84 127-157 (163)
81 PRK06930 positive control sigm 50.7 34 0.00074 26.2 4.6 49 26-84 114-162 (170)
82 TIGR02985 Sig70_bacteroi1 RNA 50.7 35 0.00075 24.4 4.5 28 50-81 131-158 (161)
83 PRK09639 RNA polymerase sigma 50.6 33 0.00072 25.1 4.4 47 27-84 113-159 (166)
84 PRK09637 RNA polymerase sigma 49.8 34 0.00074 25.9 4.5 32 50-85 124-155 (181)
85 PRK12536 RNA polymerase sigma 49.5 43 0.00092 25.1 5.0 31 49-83 146-176 (181)
86 TIGR02983 SigE-fam_strep RNA p 49.2 40 0.00087 24.6 4.7 46 28-83 112-157 (162)
87 PRK12515 RNA polymerase sigma 48.7 40 0.00086 25.5 4.7 31 50-84 149-179 (189)
88 PRK12530 RNA polymerase sigma 48.5 38 0.00082 25.8 4.6 30 50-83 152-181 (189)
89 TIGR02954 Sig70_famx3 RNA poly 48.5 45 0.00096 24.6 4.9 46 27-82 120-165 (169)
90 TIGR02939 RpoE_Sigma70 RNA pol 48.0 30 0.00064 25.9 3.9 33 47-83 153-185 (190)
91 PRK12529 RNA polymerase sigma 47.4 42 0.0009 25.2 4.6 46 27-82 128-173 (178)
92 cd04761 HTH_MerR-SF Helix-Turn 47.3 14 0.0003 21.4 1.6 22 51-76 3-24 (49)
93 PRK06811 RNA polymerase factor 46.6 54 0.0012 24.8 5.2 49 27-85 132-180 (189)
94 PRK13919 putative RNA polymera 46.6 51 0.0011 24.6 5.0 29 50-82 153-181 (186)
95 PRK12546 RNA polymerase sigma 46.0 50 0.0011 25.3 4.9 32 50-85 131-162 (188)
96 PRK12523 RNA polymerase sigma 45.7 61 0.0013 24.0 5.3 32 50-85 137-168 (172)
97 PRK06986 fliA flagellar biosyn 45.7 43 0.00094 26.5 4.6 31 50-84 202-232 (236)
98 TIGR02952 Sig70_famx2 RNA poly 45.6 47 0.001 24.2 4.6 28 50-81 140-167 (170)
99 PRK12543 RNA polymerase sigma 45.3 61 0.0013 24.2 5.2 32 50-85 135-166 (179)
100 PRK12538 RNA polymerase sigma 45.2 36 0.00078 27.2 4.1 31 50-84 189-219 (233)
101 PRK12547 RNA polymerase sigma 45.2 48 0.001 24.4 4.6 29 50-82 130-158 (164)
102 TIGR03879 near_KaiC_dom probab 44.7 9.4 0.0002 25.6 0.5 26 46-75 30-55 (73)
103 PF13518 HTH_28: Helix-turn-he 44.2 22 0.00048 20.8 2.1 24 50-77 14-37 (52)
104 PRK12524 RNA polymerase sigma 44.2 48 0.001 25.2 4.6 31 50-84 154-184 (196)
105 PRK05657 RNA polymerase sigma 42.9 39 0.00085 28.5 4.2 53 26-84 262-314 (325)
106 PRK12531 RNA polymerase sigma 42.8 56 0.0012 24.8 4.7 30 50-83 159-188 (194)
107 PRK09645 RNA polymerase sigma 42.3 61 0.0013 23.9 4.8 30 50-83 136-165 (173)
108 PF13384 HTH_23: Homeodomain-l 42.0 18 0.00039 21.3 1.5 22 50-75 19-40 (50)
109 PF09607 BrkDBD: Brinker DNA-b 41.9 42 0.0009 21.5 3.2 45 24-75 3-48 (58)
110 PRK10072 putative transcriptio 41.8 15 0.00032 25.8 1.2 25 50-78 48-72 (96)
111 PRK12532 RNA polymerase sigma 41.5 56 0.0012 24.8 4.5 31 50-84 154-184 (195)
112 PF06056 Terminase_5: Putative 41.0 8.2 0.00018 24.5 -0.2 21 50-74 15-35 (58)
113 smart00027 EH Eps15 homology d 40.8 67 0.0015 21.6 4.4 46 25-74 2-51 (96)
114 PF13443 HTH_26: Cro/C1-type H 40.5 18 0.0004 22.3 1.4 24 50-77 12-35 (63)
115 PRK12535 RNA polymerase sigma 40.5 68 0.0015 24.6 4.9 34 50-87 151-184 (196)
116 TIGR02479 FliA_WhiG RNA polyme 39.7 59 0.0013 25.4 4.5 46 27-82 176-221 (224)
117 COG4367 Uncharacterized protei 39.6 40 0.00086 23.6 3.0 40 27-71 3-42 (97)
118 PRK08583 RNA polymerase sigma 38.5 68 0.0015 25.7 4.8 47 27-83 206-252 (257)
119 TIGR00721 tfx DNA-binding prot 38.0 77 0.0017 23.7 4.6 48 24-82 4-51 (137)
120 PRK09643 RNA polymerase sigma 37.9 86 0.0019 23.8 5.1 30 50-83 152-181 (192)
121 PRK12545 RNA polymerase sigma 37.7 72 0.0016 24.5 4.7 31 50-84 157-187 (201)
122 TIGR02980 SigBFG RNA polymeras 37.6 69 0.0015 25.0 4.6 46 26-81 178-223 (227)
123 PRK09649 RNA polymerase sigma 37.5 64 0.0014 24.4 4.3 29 50-82 148-176 (185)
124 PRK09647 RNA polymerase sigma 37.3 74 0.0016 24.7 4.7 31 50-84 156-186 (203)
125 PRK12528 RNA polymerase sigma 36.9 72 0.0016 23.2 4.4 43 27-79 114-156 (161)
126 PRK09651 RNA polymerase sigma 36.7 56 0.0012 24.3 3.8 30 49-82 136-165 (172)
127 PRK12542 RNA polymerase sigma 36.6 70 0.0015 24.0 4.4 30 50-83 140-169 (185)
128 PF01710 HTH_Tnp_IS630: Transp 36.5 58 0.0012 23.2 3.7 37 28-74 4-40 (119)
129 PRK12520 RNA polymerase sigma 36.5 77 0.0017 23.9 4.6 31 50-84 149-179 (191)
130 PRK12511 RNA polymerase sigma 36.5 74 0.0016 24.1 4.5 32 50-85 129-160 (182)
131 TIGR02943 Sig70_famx1 RNA poly 36.2 80 0.0017 24.0 4.7 31 50-84 149-179 (188)
132 cd04762 HTH_MerR-trunc Helix-T 36.0 28 0.0006 19.6 1.6 24 51-78 3-26 (49)
133 PRK09480 slmA division inhibit 35.8 38 0.00083 25.2 2.8 41 32-78 13-56 (194)
134 PRK12518 RNA polymerase sigma 35.6 31 0.00067 25.5 2.2 36 45-84 133-168 (175)
135 TIGR02947 SigH_actino RNA poly 35.5 38 0.00083 25.7 2.8 36 45-84 144-179 (193)
136 TIGR02941 Sigma_B RNA polymera 35.3 71 0.0015 25.5 4.4 47 26-82 205-251 (255)
137 PRK12527 RNA polymerase sigma 35.3 98 0.0021 22.4 4.9 30 50-83 123-152 (159)
138 PRK15008 HTH-type transcriptio 35.2 55 0.0012 25.2 3.7 45 31-81 20-67 (212)
139 PF01381 HTH_3: Helix-turn-hel 35.2 43 0.00093 19.8 2.5 23 51-77 12-34 (55)
140 PRK12522 RNA polymerase sigma 34.8 85 0.0019 23.2 4.6 29 50-82 137-165 (173)
141 PRK09641 RNA polymerase sigma 34.6 78 0.0017 23.5 4.3 29 50-82 154-182 (187)
142 PRK07408 RNA polymerase sigma 34.4 84 0.0018 25.3 4.7 48 27-84 204-251 (256)
143 PRK08301 sporulation sigma fac 34.4 75 0.0016 25.0 4.4 30 50-83 200-229 (234)
144 PRK12525 RNA polymerase sigma 34.4 99 0.0021 22.8 4.8 46 27-82 119-164 (168)
145 PRK07670 RNA polymerase sigma 34.2 87 0.0019 25.0 4.8 46 27-82 202-247 (251)
146 TIGR03001 Sig-70_gmx1 RNA poly 34.1 83 0.0018 25.3 4.6 31 50-84 179-209 (244)
147 PF00376 MerR: MerR family reg 32.8 31 0.00066 19.8 1.4 20 51-74 2-21 (38)
148 cd04763 HTH_MlrA-like Helix-Tu 32.6 31 0.00068 21.7 1.6 20 51-74 3-22 (68)
149 PRK12513 RNA polymerase sigma 32.1 40 0.00086 25.5 2.4 35 46-84 153-187 (194)
150 PRK12544 RNA polymerase sigma 32.0 98 0.0021 24.0 4.6 29 51-83 167-195 (206)
151 PRK11923 algU RNA polymerase s 31.9 93 0.002 23.4 4.4 31 50-84 156-186 (193)
152 PF13411 MerR_1: MerR HTH fami 31.7 25 0.00053 22.1 0.9 20 51-74 3-22 (69)
153 PRK08295 RNA polymerase factor 31.6 94 0.002 23.6 4.4 31 50-84 172-202 (208)
154 cd04764 HTH_MlrA-like_sg1 Heli 31.3 35 0.00076 21.4 1.6 21 51-75 3-23 (67)
155 PRK06288 RNA polymerase sigma 30.8 1E+02 0.0022 25.0 4.6 48 26-83 212-259 (268)
156 PRK11511 DNA-binding transcrip 30.4 70 0.0015 22.9 3.3 37 33-75 12-48 (127)
157 PF12824 MRP-L20: Mitochondria 30.2 1.4E+02 0.003 23.0 5.0 47 23-76 82-128 (164)
158 PRK09415 RNA polymerase factor 30.1 89 0.0019 23.4 4.0 29 50-82 145-173 (179)
159 TIGR02394 rpoS_proteo RNA poly 29.6 1E+02 0.0022 25.2 4.5 53 26-84 222-274 (285)
160 TIGR02859 spore_sigH RNA polym 29.5 1.2E+02 0.0027 22.7 4.7 30 49-82 166-195 (198)
161 PRK07122 RNA polymerase sigma 29.3 99 0.0021 25.1 4.4 46 27-82 216-261 (264)
162 KOG0494 Transcription factor C 28.8 20 0.00043 30.0 0.2 23 132-154 166-189 (332)
163 PRK12540 RNA polymerase sigma 28.8 1.2E+02 0.0026 22.9 4.5 32 50-85 129-160 (182)
164 PRK15369 two component system 28.8 97 0.0021 22.3 3.9 44 25-79 148-191 (211)
165 TIGR02957 SigX4 RNA polymerase 28.7 1E+02 0.0022 25.1 4.4 29 51-83 127-155 (281)
166 PRK09636 RNA polymerase sigma 28.6 1E+02 0.0023 25.1 4.4 30 51-84 134-163 (293)
167 cd06170 LuxR_C_like C-terminal 28.5 1.2E+02 0.0027 17.4 4.3 36 28-74 2-37 (57)
168 PF13412 HTH_24: Winged helix- 28.3 1.3E+02 0.0027 17.4 3.8 37 28-73 2-38 (48)
169 cd01392 HTH_LacI Helix-turn-he 27.9 27 0.00059 20.5 0.6 20 53-76 2-21 (52)
170 PRK10100 DNA-binding transcrip 27.9 1.1E+02 0.0024 24.1 4.3 45 26-81 155-199 (216)
171 PF08280 HTH_Mga: M protein tr 27.9 66 0.0014 20.0 2.4 36 30-74 6-41 (59)
172 PF07638 Sigma70_ECF: ECF sigm 27.2 1.3E+02 0.0028 22.8 4.5 29 50-82 153-181 (185)
173 PRK09640 RNA polymerase sigma 27.1 41 0.0009 25.4 1.7 33 47-83 149-181 (188)
174 PRK08215 sporulation sigma fac 27.1 1.3E+02 0.0028 24.1 4.7 46 26-81 209-254 (258)
175 cd01104 HTH_MlrA-CarA Helix-Tu 26.5 46 0.00099 20.7 1.6 20 51-74 3-22 (68)
176 TIGR02393 RpoD_Cterm RNA polym 26.5 1.2E+02 0.0026 24.0 4.3 51 26-82 176-226 (238)
177 PF08880 QLQ: QLQ; InterPro: 26.3 64 0.0014 18.6 2.0 13 26-38 2-14 (37)
178 PRK05803 sporulation sigma fac 26.3 1.1E+02 0.0025 24.0 4.1 31 49-83 196-226 (233)
179 TIGR02885 spore_sigF RNA polym 26.1 1.4E+02 0.003 23.4 4.6 42 26-77 183-224 (231)
180 PF10925 DUF2680: Protein of u 25.9 1.6E+02 0.0036 18.6 4.0 44 27-75 1-44 (59)
181 PF00440 TetR_N: Bacterial reg 25.4 42 0.00091 19.6 1.2 35 37-77 7-41 (47)
182 PRK05572 sporulation sigma fac 25.4 1.5E+02 0.0033 23.6 4.8 47 26-82 202-248 (252)
183 PRK12534 RNA polymerase sigma 25.2 2.5E+02 0.0054 20.9 5.7 29 50-82 155-183 (187)
184 PRK12517 RNA polymerase sigma 25.0 1.6E+02 0.0035 22.2 4.7 32 50-85 146-177 (188)
185 TIGR02960 SigX5 RNA polymerase 25.0 1.2E+02 0.0027 24.8 4.3 32 50-85 160-191 (324)
186 TIGR02950 SigM_subfam RNA poly 24.6 70 0.0015 22.9 2.5 34 45-82 118-151 (154)
187 PRK10360 DNA-binding transcrip 24.2 1.6E+02 0.0034 21.4 4.4 43 26-79 137-179 (196)
188 PRK11922 RNA polymerase sigma 23.9 80 0.0017 24.9 2.8 37 45-85 162-198 (231)
189 PRK10651 transcriptional regul 23.7 1.4E+02 0.003 21.8 4.0 44 26-80 155-198 (216)
190 PRK05911 RNA polymerase sigma 23.6 1.6E+02 0.0035 23.7 4.6 46 27-82 206-251 (257)
191 COG2963 Transposase and inacti 23.6 1.6E+02 0.0035 20.4 4.1 42 24-74 5-47 (116)
192 PF00424 REV: REV protein (ant 23.6 63 0.0014 22.6 1.9 36 33-87 15-50 (91)
193 TIGR02984 Sig-70_plancto1 RNA 23.4 1.8E+02 0.0038 21.5 4.6 28 50-81 158-185 (189)
194 TIGR03070 couple_hipB transcri 23.3 45 0.00098 19.6 1.0 23 51-77 18-40 (58)
195 PRK10403 transcriptional regul 23.2 1.4E+02 0.0031 21.6 4.0 43 26-79 153-195 (215)
196 TIGR03020 EpsA transcriptional 23.1 1.6E+02 0.0034 24.1 4.4 47 24-81 188-234 (247)
197 TIGR01764 excise DNA binding d 23.1 54 0.0012 18.5 1.3 23 51-77 4-26 (49)
198 cd00093 HTH_XRE Helix-turn-hel 22.9 51 0.0011 18.3 1.2 22 51-76 15-36 (58)
199 cd00131 PAX Paired Box domain 22.9 3E+02 0.0065 19.9 5.5 46 26-76 75-127 (128)
200 PRK13558 bacterio-opsin activa 22.3 82 0.0018 28.6 2.9 41 25-71 606-649 (665)
201 PHA02955 hypothetical protein; 22.1 1.1E+02 0.0024 24.7 3.2 44 29-76 60-103 (213)
202 COG2944 Predicted transcriptio 21.9 1.3E+02 0.0028 21.5 3.3 39 27-77 44-82 (104)
203 PRK06704 RNA polymerase factor 21.8 1.5E+02 0.0033 23.7 4.1 32 50-85 134-165 (228)
204 PRK11552 putative DNA-binding 21.5 98 0.0021 24.3 2.9 40 34-80 21-60 (225)
205 PF13730 HTH_36: Helix-turn-he 21.4 1.7E+02 0.0038 17.2 3.4 43 27-74 3-47 (55)
206 PRK09975 DNA-binding transcrip 21.4 85 0.0018 23.8 2.4 39 34-78 19-57 (213)
207 PRK09638 RNA polymerase sigma 20.6 1.2E+02 0.0025 22.3 3.0 34 45-82 139-172 (176)
208 TIGR03613 RutR pyrimidine util 20.5 87 0.0019 23.6 2.3 38 36-79 18-55 (202)
209 PRK14996 TetR family transcrip 20.1 1.4E+02 0.003 22.3 3.4 39 34-78 16-54 (192)
210 PRK15411 rcsA colanic acid cap 20.1 1.5E+02 0.0032 23.1 3.6 39 26-75 137-175 (207)
No 1
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.81 E-value=2.2e-20 Score=132.26 Aligned_cols=66 Identities=32% Similarity=0.532 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 17 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 17 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
.++.||-||+||..||.+||+.|-.. |||++-.|++||.++ .|++.+|+|||||||+|.+++.+..
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ET-HYPDIYTREEiA~ki----dLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAET-HYPDIYTREEIALKI----DLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhh-cCCcchhHHHHHHhh----hhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 45678899999999999999999999 699999999999999 9999999999999999999877653
No 2
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.80 E-value=6.9e-20 Score=153.43 Aligned_cols=82 Identities=21% Similarity=0.244 Sum_probs=71.0
Q ss_pred CCcccCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCC
Q 031304 9 DPFVASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 88 (162)
Q Consensus 9 ~p~~~~~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~ 88 (162)
.........|++|+.||+||..||..||+.|++. +|.+..+|.+||..| ||+..||++||||||+||||+.....
T Consensus 161 ~~~~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~Q-KYLS~~DR~~LA~~L----gLTdaQVKtWfQNRRtKWKrq~a~g~ 235 (309)
T KOG0488|consen 161 NHPYQRSTPKKRRKSRTAFSDHQLFELEKRFEKQ-KYLSVADRIELAASL----GLTDAQVKTWFQNRRTKWKRQTAEGG 235 (309)
T ss_pred CCCcccCCCcccccchhhhhHHHHHHHHHHHHHh-hcccHHHHHHHHHHc----CCchhhHHHHHhhhhHHHHHHHHhhh
Confidence 3445556678889999999999999999999999 699999999999999 99999999999999999999988754
Q ss_pred CCCCcch
Q 031304 89 PNNAESE 95 (162)
Q Consensus 89 ~~~~~~~ 95 (162)
+......
T Consensus 236 ~~~~~~~ 242 (309)
T KOG0488|consen 236 ELLYQAG 242 (309)
T ss_pred ccccccc
Confidence 4433333
No 3
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.79 E-value=3.8e-19 Score=140.72 Aligned_cols=69 Identities=30% Similarity=0.504 Sum_probs=65.4
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 14 SGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 14 ~~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
+++.++.||.||+|+..||++||.+|.+.+ ||+...|++||.+| +|.+.+|+|||+|||+|+|++++..
T Consensus 31 ~~~pRkqRRERTtFtr~QlevLe~LF~kTq-YPDv~~rEelAlkl----nLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 31 SSGPRKQRRERTTFTRKQLEVLEALFAKTQ-YPDVFMREELALKL----NLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred CccchhcccccceecHHHHHHHHHHHHhhc-CccHHHHHHHHHHh----CCchhhhhhhhccccchhhHhhhhh
Confidence 367888999999999999999999999997 99999999999999 9999999999999999999988864
No 4
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.79 E-value=6.1e-20 Score=150.69 Aligned_cols=69 Identities=23% Similarity=0.322 Sum_probs=63.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCCCC
Q 031304 17 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPN 90 (162)
Q Consensus 17 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~~~ 90 (162)
....||.||.||..||.+||+.|+.| +|.+...|.|||..| .|+|+||+|||||||+||||..+.....
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN-~YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFN-KYLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccc-cccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 45579999999999999999999999 599999999999999 9999999999999999999987766544
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.76 E-value=7e-19 Score=135.44 Aligned_cols=64 Identities=36% Similarity=0.463 Sum_probs=61.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 19 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 19 ~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
+.||.||.|+.+||..||.+|+.|+ |....+|++||..| +|++.||+|||||||.|.||.+.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~-Yvvg~eR~~LA~~L----~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQ-YVVGAERKQLAQSL----SLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCC-eeechHHHHHHHHc----CCChhHhhhhhhhhhHHHHHHHHHh
Confidence 6889999999999999999999996 99999999999999 9999999999999999999988775
No 6
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.73 E-value=4e-18 Score=135.62 Aligned_cols=69 Identities=26% Similarity=0.405 Sum_probs=64.9
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 14 SGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 14 ~~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
.++.|+.|+.||.|+.-||..|.+.|++++ |+-..+|.+||..| ||+.+||+|||||||.|.||..+..
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQ-YLALPERAeLAAsL----GLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQ-YLALPERAELAASL----GLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcc-hhcCcHHHHHHHHh----CCchhHhhhhhhhhHHHHHHHHhcC
Confidence 467788889999999999999999999998 99999999999999 9999999999999999999988843
No 7
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.72 E-value=2.4e-18 Score=143.01 Aligned_cols=67 Identities=25% Similarity=0.372 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCC
Q 031304 17 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 88 (162)
Q Consensus 17 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~ 88 (162)
..++|+.|..||..|..+||+.|.++ +|.+..+|+.||..| +||++||||||||||-|+||++....
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQ-RYLSAPERE~LA~~L----rLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQ-RYLSAPEREHLASSL----RLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhh-hccccHhHHHHHHhc----CCCchheeeeeecchhhhhhhhhhhh
Confidence 44567788999999999999999999 699999999999999 99999999999999999999887653
No 8
>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=99.72 E-value=1.2e-17 Score=106.53 Aligned_cols=57 Identities=39% Similarity=0.640 Sum_probs=54.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 21 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 21 rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
|+.|+.||.+|+.+||.+|..++ ||+..++++||..| ||+..+|++||+|+|+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~-~p~~~~~~~la~~l----~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENP-YPSKEEREELAKEL----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSS-SCHHHHHHHHHHHH----TSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhc-cccccccccccccc----cccccccccCHHHhHHHhCc
Confidence 57899999999999999999997 99999999999999 99999999999999999986
No 9
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.71 E-value=7.6e-18 Score=140.11 Aligned_cols=67 Identities=27% Similarity=0.310 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcC
Q 031304 15 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 15 ~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~ 86 (162)
...+..|++|--+|..|+.+||+.|-.|. |++.+.|.||++.| +|+++||+|||||||+|+||..++
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~-YitkeKR~ElSr~l----NLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNM-YITKEKRLELSRTL----NLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHH-HHhHHHHHHHHHhc----ccchhheeeeehhhhhHHhhhhhh
Confidence 34567788999999999999999999996 99999999999999 999999999999999999998754
No 10
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.68 E-value=3.9e-17 Score=128.35 Aligned_cols=68 Identities=32% Similarity=0.413 Sum_probs=63.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 15 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 15 ~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
.+++..|+.||-||..||..||+.|.+.+ |.++.+|.+++..| .|+++||+|||||||+|.||.+..+
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrekq-YLSiaEraefSsSL----~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREKQ-YLSIAERAEFSSSL----ELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHhh-hhhHHHHHhhhhhh----hhhhhheehhhhhhhHHHHHHHHHH
Confidence 56777888999999999999999999997 99999999999999 9999999999999999999976544
No 11
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.67 E-value=3.6e-17 Score=129.40 Aligned_cols=67 Identities=28% Similarity=0.370 Sum_probs=61.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCC
Q 031304 17 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 88 (162)
Q Consensus 17 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~ 88 (162)
..+.|+.||+|+..|+-.||..|+.. +|.+..+|..||.+| .|+|+||+|||||||.||||+-....
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~k-rYLSsaeRa~LA~sL----qLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELK-RYLSSAERAGLAASL----QLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHH-hhhhHHHHhHHHHhh----hhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 34568899999999999999999999 699999999999999 99999999999999999999876543
No 12
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.65 E-value=1.7e-16 Score=128.49 Aligned_cols=62 Identities=26% Similarity=0.397 Sum_probs=57.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcC
Q 031304 20 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 20 ~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~ 86 (162)
+|+.||.||.-|+..||+.|+.. |||+...|+-||.++ .|.|.+|+|||||||+||||..+.
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkea-HYPDv~Are~la~kt----elpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEA-HYPDVYAREMLADKT----ELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhc-cCccHHHHHHHhhhc----cCchhhhhHHhhhhhHHhhhhhhh
Confidence 34449999999999999999999 699999999999999 999999999999999999997765
No 13
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.62 E-value=1.4e-16 Score=129.37 Aligned_cols=62 Identities=27% Similarity=0.344 Sum_probs=57.5
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCC
Q 031304 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 88 (162)
Q Consensus 22 r~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~ 88 (162)
+-|.++|..|+.+||+.|.-+ +|++++.+.|||.-| +|+|+||+|||||||+|+||..+...
T Consensus 201 KYRvVYTDhQRLELEKEfh~S-ryITirRKSELA~~L----gLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTS-RYITIRRKSELAATL----GLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ceeEEecchhhhhhhhhhccc-cceeeehhHHHHHhh----CccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 458899999999999999999 599999999999999 99999999999999999999777653
No 14
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.60 E-value=7.9e-16 Score=99.17 Aligned_cols=52 Identities=15% Similarity=0.332 Sum_probs=50.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCC----CCHHHHHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 21 ARQRWTPTPAQLQILEHVYDECKGT----PRKQKIQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 21 rr~Rt~ft~~ql~~Le~~F~~~~~y----p~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
||.||.||++|+..||.+|+.++ | |+...+++||..| ||++.+|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~-y~~~~~~~~~r~~la~~l----gl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLG-WKLKDKRREEVREFCEEI----GVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHh----CCCHHHeeeecccCC
Confidence 78999999999999999999996 9 9999999999999 999999999999965
No 15
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.59 E-value=1.9e-15 Score=95.64 Aligned_cols=56 Identities=39% Similarity=0.640 Sum_probs=52.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 21 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 21 rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
++.|+.|+.+|+.+|+.+|..++ ||+..++.+||..+ ||+..+|++||+|||.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~-~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNP-YPSREEREELAAKL----GLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH----CcCHHHHHHhHHHHhhccC
Confidence 35678899999999999999997 99999999999999 9999999999999998753
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=99.59 E-value=2.6e-15 Score=95.62 Aligned_cols=57 Identities=40% Similarity=0.678 Sum_probs=53.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 22 r~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
+.|+.|+..++.+||.+|..++ ||+..++.+||..+ ||++.+|++||+|||.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~----~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNP-YPSREEREELAKEL----GLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH----CcCHHHHHHHHHHHHHHHhcc
Confidence 5678999999999999999997 99999999999999 999999999999999998763
No 17
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.57 E-value=1.1e-15 Score=116.49 Aligned_cols=66 Identities=30% Similarity=0.422 Sum_probs=60.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCCC
Q 031304 19 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVP 89 (162)
Q Consensus 19 ~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~~ 89 (162)
++++.||+|+..|+..||+.|+.. +|.+..++.|||..| +|+++||+.||||||+|.||+.+....
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~Q-rYLS~~e~~ELan~L----~LS~~QVKTWFQNrRMK~Kk~~r~~~p 164 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQ-RYLSTPERQELANAL----SLSETQVKTWFQNRRMKHKKQQRNNQP 164 (194)
T ss_pred HhhhhcccccCccccccHHHHhhh-hhcccHHHHHHHHHh----hhhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 345679999999999999999998 699999999999999 999999999999999999998887653
No 18
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.56 E-value=3.7e-15 Score=120.84 Aligned_cols=60 Identities=33% Similarity=0.516 Sum_probs=56.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 20 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 20 ~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
-||.||.||.+||..|...|+.| +|.+...|.+||.+| +|.|.||+|||||+|+|.|+..
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~en-RYlTEqRRQ~La~EL----gLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQEN-RYLTEQRRQELAQEL----GLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhh-hhHHHHHHHHHHHHh----CcCHHHhhHHhhhhhhhhhhcc
Confidence 36789999999999999999999 699999999999999 9999999999999999998844
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.55 E-value=6.5e-15 Score=112.49 Aligned_cols=66 Identities=30% Similarity=0.441 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCC
Q 031304 18 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 88 (162)
Q Consensus 18 ~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~ 88 (162)
...+++|++.|..|+.+|++.|+.++ ||+...|..|+..| +|+++.|+|||||||++.|+......
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p-~Ps~~~r~~L~~~l----nm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINP-YPSSITRIKLSLLL----NMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCC-CCCHHHHHHHHHhc----CCChhhhhhhhchHHHHHHHhcccch
Confidence 44677888899999999999999998 89999999999999 99999999999999999999777643
No 20
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.52 E-value=3.4e-15 Score=123.34 Aligned_cols=63 Identities=29% Similarity=0.400 Sum_probs=58.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 20 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 20 ~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
-||-||.||.+|+..||+.|-+.. |.+...|.|||..| +|.|..|+|||||||+|.||++...
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrEN-YVSRprRcELAAaL----NLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYREN-YVSRPRRCELAAAL----NLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhc-cccCchhhhHHHhh----CCCcceeehhhhhchhhhhhhhhhc
Confidence 478899999999999999998885 99999999999999 9999999999999999999988663
No 21
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.51 E-value=5.6e-15 Score=122.30 Aligned_cols=67 Identities=27% Similarity=0.399 Sum_probs=61.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCC
Q 031304 17 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 88 (162)
Q Consensus 17 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~ 88 (162)
.+++||.||.|+..||.+||..|+.| +||+...|+|||..+ +|++.+|+|||+|||+||++..+...
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rN-rypdMstrEEIavwt----NlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRN-RYPDMSTREEIAVWT----NLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhc-cCCccchhhHHHhhc----cccchhhhhhcccchhhhhhhhhhHH
Confidence 44788999999999999999999999 699999999999999 99999999999999999998766543
No 22
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.47 E-value=5.1e-14 Score=111.99 Aligned_cols=63 Identities=27% Similarity=0.289 Sum_probs=59.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 18 KLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 18 ~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
.+.++.|+.|+..|+.+||++|+.. |||+...++.||..+ ++++..|++||||||++++++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~----~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLL----TGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcC----CCCeeeeehhhhhhcHhhhhhhc
Confidence 4568899999999999999999999 699999999999999 99999999999999999998775
No 23
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.47 E-value=6.6e-14 Score=111.18 Aligned_cols=70 Identities=26% Similarity=0.388 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCCCC
Q 031304 16 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVVPN 90 (162)
Q Consensus 16 ~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~~~ 90 (162)
+..+++..|.+|+-.|+..||+.|++.. |+-..++.+||..+ |+++.+|+|||||||.|||++...+...
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtk-ylaG~~ra~lA~~l----gmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTK-YLAGADRAQLAQEL----NMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhh-cccchhHHHhhccc----cccHHHHHHHHhcchhhhhhhhccchhh
Confidence 3455667899999999999999999995 99999999999999 9999999999999999999987765443
No 24
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.47 E-value=2.7e-14 Score=121.61 Aligned_cols=62 Identities=26% Similarity=0.345 Sum_probs=59.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 19 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 19 ~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
++|++||.|....+..||++|.+|++ |+..++..||.+| +|....|+|||+|||+|+||...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npK-Pt~qEIt~iA~~L----~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPK-PTSQEITHIAESL----QLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCC-CCHHHHHHHHHHh----ccccceEEEEeeccccccccCCC
Confidence 67889999999999999999999996 9999999999999 99999999999999999999766
No 25
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.45 E-value=4.3e-14 Score=111.59 Aligned_cols=64 Identities=30% Similarity=0.425 Sum_probs=57.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCCC
Q 031304 20 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGVV 88 (162)
Q Consensus 20 ~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~~ 88 (162)
..+++.+|+.+|...||+.|+.+. |.....+..||++| ||.++||.||||||||+||.++....
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~-~L~p~~K~~LAk~L----gL~pRQVavWFQNRRARwK~kqlE~d 113 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEK-KLEPERKKKLAKEL----GLQPRQVAVWFQNRRARWKTKQLEKD 113 (198)
T ss_pred cccccccccHHHHHHhHHhhcccc-ccChHHHHHHHHhh----CCChhHHHHHHhhccccccchhhhhh
Confidence 345566799999999999999995 89999999999999 99999999999999999998877653
No 26
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.43 E-value=1.3e-13 Score=113.22 Aligned_cols=67 Identities=30% Similarity=0.454 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 16 SQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 16 ~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
+....||+||++|+.||+.|..+|...++ |....|++|+.++ ||.-+.|||||||||+|+||.++-+
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpK-PARHVREQLsseT----GLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPK-PARHVREQLSSET----GLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCc-hhHHHHHHhhhcc----CcceeehhhhhhhhhHHHHhhhhhc
Confidence 34456899999999999999999999996 9999999999999 9999999999999999999876543
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.20 E-value=1.7e-11 Score=104.67 Aligned_cols=67 Identities=30% Similarity=0.477 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcC
Q 031304 15 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 15 ~~~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~ 86 (162)
...+..+|.||+|++.|+..||+.|+.++ ||+...|++||.++ ++++.+|++||+|||++++|....
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~-yP~i~~Re~La~~i----~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTP-YPDIVGRETLAKET----GLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCC-CCchhhHHHHhhhc----cCCchHHHHHHhhhhhhhhhcccc
Confidence 34455678899999999999999999997 99999999999999 999999999999999999998843
No 28
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.10 E-value=4e-10 Score=92.18 Aligned_cols=51 Identities=24% Similarity=0.400 Sum_probs=46.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
|...-..+|..+|..++ ||+..++.+||+.+ ||+..||-+||+|||+++|-
T Consensus 183 FKekSR~~LrewY~~~~-YPsp~eKReLA~aT----gLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNP-YPSPREKRELAEAT----GLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCC-CCChHHHHHHHHHh----CCchhhhhhhhhhhhhhhhh
Confidence 44444679999999998 99999999999999 99999999999999999983
No 29
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.94 E-value=3.3e-10 Score=93.43 Aligned_cols=62 Identities=24% Similarity=0.403 Sum_probs=57.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcC
Q 031304 20 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 20 ~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~ 86 (162)
.||+||.+.+.+...||.+|...|+ |+...+..||.+| +|....|+|||+|.|+|-||....
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQPR-PS~EkIAaIAekL----DLKKNVVRVWFCNQRQKQKRm~~S 370 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQPR-PSGEKIAAIAEKL----DLKKNVVRVWFCNQRQKQKRMKRS 370 (385)
T ss_pred cccccccccCcccccHHHHhccCCC-CchhHHHHHHHhh----hhhhceEEEEeeccHHHHHHhhhh
Confidence 4788999999999999999999997 9999999999999 999999999999999999985543
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.79 E-value=1.1e-08 Score=83.47 Aligned_cols=63 Identities=22% Similarity=0.417 Sum_probs=56.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh---cCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 20 TARQRWTPTPAQLQILEHVYDE---CKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 20 ~rr~Rt~ft~~ql~~Le~~F~~---~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
.+|+|..|+..-..+|..+|.. +| ||+...+++||+++ ||+..||.+||.|+|.+.|+.....
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nP-YPSee~K~eLAkqC----nItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNP-YPSEEAKEELAKQC----NITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCC-CCcHHHHHHHHHHc----Cceehhhccccccceeehhhhhhhh
Confidence 4788899999999999999964 57 99999999999999 9999999999999999998865443
No 31
>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=98.48 E-value=1e-07 Score=56.93 Aligned_cols=34 Identities=26% Similarity=0.558 Sum_probs=28.3
Q ss_pred hcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHH
Q 031304 41 ECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79 (162)
Q Consensus 41 ~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k 79 (162)
.+| ||+..++.+||.++ ||+..||..||-|.|.+
T Consensus 7 ~nP-YPs~~ek~~L~~~t----gls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNP-YPSKEEKEELAKQT----GLSRKQISNWFINARRR 40 (40)
T ss_dssp TSG-S--HHHHHHHHHHH----TS-HHHHHHHHHHHHHH
T ss_pred CCC-CCCHHHHHHHHHHc----CCCHHHHHHHHHHhHcc
Confidence 357 99999999999999 99999999999998864
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.37 E-value=4.6e-07 Score=80.37 Aligned_cols=57 Identities=26% Similarity=0.426 Sum_probs=53.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHH
Q 031304 19 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 80 (162)
Q Consensus 19 ~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~ 80 (162)
..|+.|.+||..|+..|..+|+.++ +|+....+.|+.+| +|....|.+||.|-|.+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~-RPS~Emq~tIS~qL----~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENK-RPSREMQETISQQL----NLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCC-CCCHHHHHHHHHHh----CCcHHHHHHHHHhhhhhc
Confidence 3567899999999999999999997 79999999999999 999999999999988775
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.20 E-value=1.7e-06 Score=68.64 Aligned_cols=64 Identities=34% Similarity=0.550 Sum_probs=59.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 17 QKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 17 ~~~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
..+.++.|+.++..|+..|+..|..++ +|+...+.+|+..+ |+++..|++||+|+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~P~~~~~~~l~~~~----~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATP-KPDADDREQLAEET----GLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCC-CCchhhHHHHHHhc----CCChhhhhhhcccHHHHHHhhcc
Confidence 345678899999999999999999997 89999999999999 99999999999999999998766
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.53 E-value=0.00011 Score=71.04 Aligned_cols=62 Identities=24% Similarity=0.405 Sum_probs=56.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcC
Q 031304 20 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 20 ~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~ 86 (162)
+++.|+.++..||.+|..+|... .||..++.+.|-..+ ++..+.|++||||-|+|.++....
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q-~~~~~~~~E~l~~~~----~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQ-RTPTMQECEVLEEPI----GLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhc-cCChHHHHHhhcccc----cCCcchhHHhhhhhhhhhhhhhhc
Confidence 46789999999999999999998 599999999999999 999999999999999999987763
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.44 E-value=0.0019 Score=41.18 Aligned_cols=41 Identities=24% Similarity=0.486 Sum_probs=30.7
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 32 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 32 l~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
+..|+.+|.... ++......+|..+. +|+..+|+.||-.+.
T Consensus 10 ~~pL~~Yy~~h~-~L~E~DL~~L~~kS----~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHK-QLQEEDLDELCDKS----RMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT-----TTHHHHHHHHT----T--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcC-CccHhhHHHHHHHH----CCCHHHHHHHHHHhc
Confidence 456999999985 79999999999999 999999999997654
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.95 E-value=0.0079 Score=50.97 Aligned_cols=58 Identities=24% Similarity=0.298 Sum_probs=48.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh---cCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 20 TARQRWTPTPAQLQILEHVYDE---CKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 20 ~rr~Rt~ft~~ql~~Le~~F~~---~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
..|.+..+......+|+.+... .| ||+..++..||.++ ||+..||.+||-|.|.+..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~P-YPse~~K~~La~~T----GLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHP-YPSDDEKLMLAKQT----GLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCC-CCcchhccccchhc----CCCcccCCchhhhcccccCC
Confidence 4455668999999999988444 35 99999999999999 99999999999998876554
No 37
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.56 E-value=0.12 Score=32.35 Aligned_cols=47 Identities=19% Similarity=0.249 Sum_probs=35.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 21 ARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 21 rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
+|+|..+|-++...+-..++.++ ...+||..+ |++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~------s~~~ia~~f----gv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE------SKRDIAREF----GVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT-------HHHHHHHH----T--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC------CHHHHHHHh----CCCHHHHHHHHHhHH
Confidence 57889999998888878887763 577899999 999999999999854
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.77 E-value=0.12 Score=48.19 Aligned_cols=50 Identities=14% Similarity=0.329 Sum_probs=45.3
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcC
Q 031304 32 LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 32 l~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~ 86 (162)
+.+|..+|..|+ .|+..+...+|.++ ||....|+.||+++++......+.
T Consensus 568 ~sllkayyaln~-~ps~eelskia~qv----glp~~vvk~wfE~~~a~e~sv~rs 617 (1007)
T KOG3623|consen 568 TSLLKAYYALNG-LPSEEELSKIAQQV----GLPFAVVKAWFEDEEAEEMSVERS 617 (1007)
T ss_pred HHHHHHHHHhcC-CCCHHHHHHHHHHh----cccHHHHHHHHHhhhhhhhhhccC
Confidence 778999999997 89999999999999 999999999999999998876643
No 39
>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=84.53 E-value=1.3 Score=27.76 Aligned_cols=41 Identities=29% Similarity=0.466 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHhcCCCccchhhh
Q 031304 27 PTPAQLQILEHVYDEC--KGTPRKQKIQDMTAELAKHGQISETNVYNW 72 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~--~~yp~~~~r~~LA~~l~~~~~ls~~~V~iW 72 (162)
+|+.|+.+|..+|+.. . +|-.....+||..| |++...|..-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd-~PR~~tl~elA~~l----gis~st~~~~ 43 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFD-VPRRITLEELAEEL----GISKSTVSEH 43 (53)
T ss_pred CCHHHHHHHHHHHHcCCCC-CCCcCCHHHHHHHh----CCCHHHHHHH
Confidence 5789999999999886 1 26667778999999 9998876543
No 40
>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=83.72 E-value=1.5 Score=28.39 Aligned_cols=45 Identities=22% Similarity=0.414 Sum_probs=29.5
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhh
Q 031304 22 RQRWTPTPAQLQILEHVY-DECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNR 76 (162)
Q Consensus 22 r~Rt~ft~~ql~~Le~~F-~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNR 76 (162)
+.|..||+++...+-..+ ... ....++|..+ ||++..+..|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g------~sv~~va~~~----gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG------ESVSEVAREY----GISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH------CHHHHHHHHH----TS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC------CceEeeeccc----ccccccccHHHHHH
Confidence 456789998877666665 443 3678899999 99999999998543
No 41
>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=83.65 E-value=2.9 Score=25.07 Aligned_cols=45 Identities=18% Similarity=0.288 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 80 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~ 80 (162)
.+++.+..+|...|-.+ . .-.++|..+ |++...|+.+...=..+-
T Consensus 4 ~L~~~er~vi~~~y~~~-~-----t~~eIa~~l----g~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-L-----TLEEIAERL----GISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHHTST-------SHHHHHHHH----TSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-C-----CHHHHHHHH----CCcHHHHHHHHHHHHHHh
Confidence 46788999999999554 2 467889999 999999998876544443
No 42
>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=82.01 E-value=2.5 Score=24.49 Aligned_cols=44 Identities=11% Similarity=0.164 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k 79 (162)
.+++.+..+++..|..+. ...++|..+ |++...|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~~------~~~~ia~~~----~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEGL------SYEEIAEIL----GISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcCC------CHHHHHHHH----CcCHHHHHHHHHHHHHH
Confidence 457778888888775441 356788899 99999999998765443
No 43
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=77.26 E-value=4.4 Score=32.01 Aligned_cols=50 Identities=32% Similarity=0.378 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 26 TPTPAQLQILEHVYDEC--KGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~--~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.+|+.|+.+|..+|+.. . ||-.....+||++| |++... ++.+=||+..|-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd-~PR~~~l~dLA~~l----GISkst--~~ehLRrAe~Kl 206 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFD-YPRRVSLKDLAKEL----GISKST--LSEHLRRAERKL 206 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCC-CCccCCHHHHHHHh----CCCHHH--HHHHHHHHHHHH
Confidence 69999999999999886 2 36666678899999 998875 455556666543
No 44
>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=75.82 E-value=4.8 Score=24.35 Aligned_cols=42 Identities=21% Similarity=0.199 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 78 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~ 78 (162)
+++.+..++...|-.+ ..-.++|..+ |+++..|+.|.+.=|.
T Consensus 11 L~~~~r~i~~l~~~~g------~s~~eIa~~l----~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG------MSYAEIAEIL----GISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS---------HHHHHHHC----TS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC------cCHHHHHHHH----CcCHHHHHHHHHHHHh
Confidence 5566777777666554 3577889899 9999999999975443
No 45
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=75.25 E-value=6.9 Score=29.44 Aligned_cols=49 Identities=18% Similarity=0.173 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 25 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 25 t~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
..+++.|+.+|.. +..+ . ...++|..| |++...|..|-++-+.+.++..
T Consensus 5 ~~Lt~rqreVL~l-r~~G-l-----Tq~EIAe~L----GiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG-L-----TQQEIADIL----GTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHH-HHcC-C-----CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 5688999999988 4343 2 467899999 9999999999998777766543
No 46
>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=73.91 E-value=8.2 Score=19.76 Aligned_cols=38 Identities=16% Similarity=0.413 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhh
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 73 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWF 73 (162)
.++.++...+...|... + ...++|..+ |++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~--~----s~~~ia~~~----~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG--E----SVAEIARRL----GVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC--C----CHHHHHHHH----CCCHHHHHHhC
Confidence 45677666666667543 2 456778888 99999888874
No 47
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=70.05 E-value=3.5 Score=24.45 Aligned_cols=40 Identities=18% Similarity=0.220 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhh
Q 031304 25 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 25 t~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
..+|.++...++.+++.. . ...+||+.| |++...|..+.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-~-----s~~~IA~~l----g~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-M-----SIREIAKRL----GRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS---------HHHHHHHT----T--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-C-----CHHHHHHHH----CcCcHHHHHHHh
Confidence 468889999999888765 2 466799999 999999988764
No 48
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=68.82 E-value=4.9 Score=37.14 Aligned_cols=22 Identities=36% Similarity=0.557 Sum_probs=18.0
Q ss_pred CccchhhhhhhhHHHHHHhhcC
Q 031304 65 SETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 65 s~~~V~iWFqNRR~k~kr~~~~ 86 (162)
..+.|+.||+|||.++++.+..
T Consensus 739 ~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 739 ESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhcchHHHHHHHHHHHhhhhcc
Confidence 5668999999999999886654
No 49
>PRK04217 hypothetical protein; Provisional
Probab=67.61 E-value=24 Score=25.42 Aligned_cols=53 Identities=13% Similarity=0.102 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcC
Q 031304 24 RWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 24 Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~ 86 (162)
=..++.+++.++...|...- ...+||+.+ |++...|+..+..-+.+.+.....
T Consensus 40 ~~~Lt~eereai~l~~~eGl------S~~EIAk~L----GIS~sTV~r~L~RArkkLre~L~~ 92 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL------TQEEAGKRM----GVSRGTVWRALTSARKKVAQMLVE 92 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC------CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHHh
Confidence 34688999888887776552 467799999 999999999998777776665443
No 50
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=67.34 E-value=11 Score=27.43 Aligned_cols=45 Identities=7% Similarity=0.101 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
+++.+..++...|-.+ ....+||..+ |+++..|+.|...=+.+.|
T Consensus 107 L~~~~r~ii~l~~~~~------~s~~EIA~~l----~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 107 LDEKEKYIIFERFFVG------KTMGEIALET----EMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCHHHHHHHHHHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHh
Confidence 4455555555544433 2467888899 9999999999876555544
No 51
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=67.19 E-value=13 Score=28.45 Aligned_cols=48 Identities=15% Similarity=0.136 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
+++.+..+|...|-.+ ..-.++|..| |++...|+.+...-|.+.|...
T Consensus 143 L~~~~r~vl~l~~~~~------~s~~EIA~~L----gis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 143 LTDTQRESVTLAYYGG------LTYREVAERL----AVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCChHhHHHHHHHHHHHHHHHh
Confidence 4444444554443332 2467788888 9999999999987776666543
No 52
>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=65.41 E-value=14 Score=22.68 Aligned_cols=44 Identities=23% Similarity=0.276 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 80 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~ 80 (162)
.||+.++.+|.-+..-. ...++|..+ ++++..|..+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~-------~~~eIA~~l----~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM-------SNKEIAEEL----GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS--------HHHHHHHH----TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC-------CcchhHHhc----CcchhhHHHHHHHHHHHh
Confidence 57888999998776543 467899999 999999999887655553
No 53
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=65.27 E-value=14 Score=27.30 Aligned_cols=33 Identities=15% Similarity=0.161 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcC
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~ 86 (162)
...+||..| |+++..|+.|.+.=|.+.|+.-..
T Consensus 126 s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 126 TYEEAASVL----DLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHh
Confidence 356677788 999999999998777777665443
No 54
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=64.12 E-value=17 Score=28.19 Aligned_cols=31 Identities=16% Similarity=0.213 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
...+||..+ |+++..|+.+...-+.+.++..
T Consensus 171 s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQL----NVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 467788888 9999999999877666666544
No 55
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=63.60 E-value=15 Score=27.07 Aligned_cols=48 Identities=10% Similarity=0.009 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.+++.+..+|...|-.+ ....++|..| |+++..|+.|...=+.+.++.
T Consensus 128 ~L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG------LSYEEIAEIM----GCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 35556666666554333 1356788888 999999999998655555543
No 56
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=62.79 E-value=20 Score=26.86 Aligned_cols=49 Identities=24% Similarity=0.251 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
+++.+..+|...|-.+ ..-.+||..| |++...|+.++..=|.+.|....
T Consensus 132 L~~~~r~v~~l~~~~g------~s~~eIA~~l----~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 132 LPPRQRDVVQSISVEG------ASIKETAAKL----SMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHhh
Confidence 3444444554444333 2466788888 99999999999877777766543
No 57
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=62.69 E-value=18 Score=26.45 Aligned_cols=31 Identities=16% Similarity=0.156 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.++|..| |+++..|++....-|.+.|...
T Consensus 124 s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQE----KIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 356778888 9999999999987777666544
No 58
>PRK00118 putative DNA-binding protein; Validated
Probab=61.82 E-value=20 Score=25.49 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.+++.|..++...|..+. ...+||..+ |++...|..|...-|.+.+.
T Consensus 17 ~L~ekqRevl~L~y~eg~------S~~EIAe~l----GIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY------SLGEIAEEF----NVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcCC------CHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 356777777777666652 467789999 99999999999876666655
No 59
>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=61.09 E-value=5.1 Score=25.84 Aligned_cols=21 Identities=29% Similarity=0.659 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHhcCCCccchhhhh
Q 031304 49 QKIQDMTAELAKHGQISETNVYNWF 73 (162)
Q Consensus 49 ~~r~~LA~~l~~~~~ls~~~V~iWF 73 (162)
..-.+||.+| |+++.+|..|=
T Consensus 23 i~lkdIA~~L----gvs~~tIr~WK 43 (60)
T PF10668_consen 23 IKLKDIAEKL----GVSESTIRKWK 43 (60)
T ss_pred ccHHHHHHHH----CCCHHHHHHHh
Confidence 3566789999 99999999995
No 60
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=59.71 E-value=19 Score=26.40 Aligned_cols=30 Identities=13% Similarity=0.206 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.-.+||..+ |+++..|..|...=|.+.|+.
T Consensus 143 ~~~eIA~~l----gis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEIL----GVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 456788888 999999999998766666653
No 61
>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=59.55 E-value=19 Score=25.08 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.+..++...|-.. ....+||..+ |+++..|..+...-+.+.|+
T Consensus 111 L~~~~~~ii~~~~~~g------~s~~eIA~~l----~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLEG------LSYKEIAEIL----GISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 4556666665544332 2456788889 99999999998866655543
No 62
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=59.48 E-value=22 Score=25.50 Aligned_cols=42 Identities=10% Similarity=0.279 Sum_probs=28.9
Q ss_pred CCCCCHHHHH-HHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhh
Q 031304 24 RWTPTPAQLQ-ILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 75 (162)
Q Consensus 24 Rt~ft~~ql~-~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqN 75 (162)
|..|+.++.. ++...+..+ . ...++|..+ ||+...|..|.+-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g-~-----sv~evA~e~----gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG-M-----TVSLVARQH----GVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC-C-----CHHHHHHHH----CcCHHHHHHHHHH
Confidence 4567887654 444444433 2 456789999 9999999999653
No 63
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=57.82 E-value=16 Score=27.64 Aligned_cols=32 Identities=13% Similarity=0.087 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 48 KQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 48 ~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.....+||..+ |+++..|+.|+..-|.+.++.
T Consensus 157 g~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 157 GLSQSEIAKRL----GIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 34567788888 999999999998766666553
No 64
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=57.09 E-value=20 Score=36.13 Aligned_cols=61 Identities=21% Similarity=0.317 Sum_probs=53.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 19 LTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 19 ~~rr~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
+.++-|+..-.+++..|-++|-.+. .|+...+..|.-.. ..+.+.+.+||+|-+.+.++..
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~~-sps~k~~~civcd~----~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQDN-SPSLKVFDCIVCDV----FSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCCC-CHHHHHHHHhhhhh----hhhhhHHHHhhcchhhhhhhhc
Confidence 3466788888899999999999996 69999999998888 8999999999999999988755
No 65
>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=56.24 E-value=24 Score=25.62 Aligned_cols=44 Identities=20% Similarity=0.300 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 80 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~ 80 (162)
+++.+..++...|-.. ....+||..+ |++...|+++...=|.+.
T Consensus 112 L~~~~r~v~~l~~~~g------~~~~eIA~~l----~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 112 LPERQRELLQLRYQRG------VSLTALAEQL----GRTVNAVYKALSRLRVRL 155 (159)
T ss_pred CCHHHHHHHHHHHhcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHH
Confidence 4444445554433332 2467788888 999999998876544443
No 66
>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=56.17 E-value=25 Score=26.23 Aligned_cols=46 Identities=20% Similarity=0.224 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.+..++...|-.+ ..-.++|..| |+++..|++....=|.+.++
T Consensus 135 Lp~~~r~v~~l~~~~g------~s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG------LTVEEIAELL----GVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 4444444444444333 2456778888 99999999998866666554
No 67
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=55.77 E-value=32 Score=25.66 Aligned_cols=30 Identities=7% Similarity=0.333 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
..++||..| |+++..|+++.+.=|.+.|..
T Consensus 147 s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERH----DVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHH----CCChHHHHHHHHHHHHHHHHH
Confidence 366788888 999999999988666666553
No 68
>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=55.23 E-value=26 Score=26.15 Aligned_cols=50 Identities=16% Similarity=0.096 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
.+++.+..+|.-.|-.+ ...++||..| |+++..|+.+.+.=|.+.+....
T Consensus 100 ~L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG------LSQQEIAEKL----GLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555544443 2466788888 99999999998776666666443
No 69
>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=54.46 E-value=13 Score=21.95 Aligned_cols=39 Identities=18% Similarity=0.405 Sum_probs=27.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhh
Q 031304 25 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 73 (162)
Q Consensus 25 t~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWF 73 (162)
..++.++...+...+... . ...+||+.+ |++...|.-++
T Consensus 4 ~~~~~~~~~~i~~l~~~G-~-----si~~IA~~~----gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-M-----SIAEIAKQF----GVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--------HHHHHHHT----TS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC-C-----CHHHHHHHH----CcCHHHHHHHH
Confidence 346676777777777776 3 577889999 99999888766
No 70
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=53.88 E-value=31 Score=25.06 Aligned_cols=30 Identities=17% Similarity=0.215 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.-.++|..| |+++..|++....-|.+.|..
T Consensus 124 s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 124 DVAETAAAM----GCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 356788888 999999999887666665553
No 71
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=53.43 E-value=25 Score=26.27 Aligned_cols=31 Identities=13% Similarity=0.314 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 49 QKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 49 ~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
..-+++|..| |+++..|+++.+.-|.+.+..
T Consensus 153 ~s~~eIA~~l----gis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 153 LSLKEISEIL----DLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3467788888 999999999998666665543
No 72
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=53.28 E-value=29 Score=27.43 Aligned_cols=34 Identities=18% Similarity=0.260 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
.-++||..| |+++..|+.+...=|.+.+......
T Consensus 152 s~~EIAe~L----giS~~tVk~~L~RAr~~Lr~~l~~~ 185 (216)
T PRK12533 152 SYREIAAIA----DVPVGTVMSRLARARRRLAALLGGA 185 (216)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHccc
Confidence 456788888 9999999999987777766655443
No 73
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=53.09 E-value=33 Score=25.76 Aligned_cols=29 Identities=14% Similarity=0.284 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
..+++|..+ |+++..|+++...=+.+.|.
T Consensus 151 s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRL----GAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHH----CCChhhHHHHHHHHHHHHHH
Confidence 466788888 99999999998765555543
No 74
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=52.65 E-value=27 Score=25.57 Aligned_cols=46 Identities=11% Similarity=-0.054 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.|..+|.-.|-.+ ..-.++|..+ |++...|+.+...=|.+.++
T Consensus 113 L~~~~r~v~~l~~~~~------~s~~eIA~~l----gis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYYG------FSYKEIAEMT----GLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 4444444444443333 2356778888 99999999988765555544
No 75
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=52.62 E-value=34 Score=26.08 Aligned_cols=33 Identities=9% Similarity=0.037 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcC
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSG 86 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~ 86 (162)
.-.+||..| |+++..|+.....=|.+.++....
T Consensus 134 s~~EIA~~L----gis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 134 AYEEAAEIC----GCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHHh
Confidence 356778888 999999999998777776665443
No 76
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=51.86 E-value=45 Score=19.25 Aligned_cols=40 Identities=25% Similarity=0.296 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhh
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNR 76 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNR 76 (162)
.+++.+..++..++ .. . ...++|..+ |++...|..|.+.-
T Consensus 3 ~l~~~e~~i~~~~~-~g-~-----s~~eia~~l----~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLA-EG-L-----TNKEIAERL----GISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHH-cC-C-----CHHHHHHHH----CCCHHHHHHHHHHH
Confidence 46778888876643 22 1 457788899 99999999988743
No 77
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=51.72 E-value=32 Score=25.93 Aligned_cols=46 Identities=15% Similarity=-0.009 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.+..++...|-.+ ...++||..| |++...|+.+...=+.+.|+
T Consensus 140 L~~~~r~i~~l~~~~g------~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 140 LPEKQREILILRVVVG------LSAEETAEAV----GSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4444445555443333 2467788888 99999999988655555444
No 78
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=51.45 E-value=35 Score=25.67 Aligned_cols=32 Identities=16% Similarity=0.181 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
.-.+||..| |++...|+.+...=|.+.|+...
T Consensus 146 s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVM----DISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHh----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 356788888 99999999999877766666444
No 79
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=51.21 E-value=39 Score=25.43 Aligned_cols=48 Identities=13% Similarity=-0.015 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
+++.+..+++-.|-.+ ..-.++|..| |++...|+.+...-|.+.|+..
T Consensus 132 L~~~~r~v~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 132 LPEKMRLAIQAVKLEG------LSVAEAATRS----GMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred CCHHHHHHHHHHHHcC------CcHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 4444444554433322 2467788888 9999999999987676666543
No 80
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=50.75 E-value=42 Score=24.48 Aligned_cols=31 Identities=19% Similarity=0.193 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
...++|..+ |++...|+.....-+.+.++.-
T Consensus 127 s~~EIA~~l----gis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 127 TQKDIAREL----GVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 366788888 9999999998776666655543
No 81
>PRK06930 positive control sigma-like factor; Validated
Probab=50.70 E-value=34 Score=26.22 Aligned_cols=49 Identities=10% Similarity=0.100 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.+++.+..+|...|-.+ . .-.++|..+ |++...|+.+...-+.+.++.-
T Consensus 114 ~L~~rer~V~~L~~~eg-~-----s~~EIA~~l----giS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-L-----SYSEIADYL----NIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHHcC-C-----CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 46666666666655444 1 356788888 9999999999987777766543
No 82
>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=50.67 E-value=35 Score=24.43 Aligned_cols=28 Identities=21% Similarity=0.271 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
...+||..+ |+++..|+.+...=+.+.|
T Consensus 131 ~~~eIA~~l----gis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEEL----GISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 456788888 9999999998875555544
No 83
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=50.64 E-value=33 Score=25.06 Aligned_cols=47 Identities=13% Similarity=0.186 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
+++.+..+|.-.| .+ ..-.+||..+ |+++..|+.+...=|.+.|..-
T Consensus 113 L~~~~r~il~l~~-~g------~s~~eIA~~l----gis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF-SG------YSYKEIAEAL----GIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH-cC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 4444555555545 32 2466788888 9999999999976666666543
No 84
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=49.76 E-value=34 Score=25.92 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
...++|..+ |+++..|+..+..=|.+.++.-.
T Consensus 124 ~~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 124 SQKEIAEKL----GLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 466788888 99999999999866666665443
No 85
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=49.50 E-value=43 Score=25.15 Aligned_cols=31 Identities=16% Similarity=0.090 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 49 QKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 49 ~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
....++|..| |+++..|++....-|.+.|+.
T Consensus 146 ~s~~EIA~~l----~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 146 LSVAETAQLT----GLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 3467788888 999999999998777776664
No 86
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=49.22 E-value=40 Score=24.56 Aligned_cols=46 Identities=22% Similarity=0.164 Sum_probs=30.5
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 28 t~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
++.+..+|...|-.+ ..-.++|..+ |+++..|+.+-..-|.+.++.
T Consensus 112 ~~~~r~i~~l~~~~g------~s~~eIA~~l----gis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 112 PARQRAVVVLRYYED------LSEAQVAEAL----GISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHhhhHHHhc------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 344445554444332 2456778888 999999999988777666654
No 87
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=48.68 E-value=40 Score=25.47 Aligned_cols=31 Identities=16% Similarity=0.224 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.++|..+ |+++..|++-...=|.+.+...
T Consensus 149 s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 149 SVEEVGEIV----GIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 356677888 9999999998877666666543
No 88
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=48.54 E-value=38 Score=25.75 Aligned_cols=30 Identities=20% Similarity=0.234 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.-.+||..| |+++..|+.+...=|.+.|..
T Consensus 152 s~~EIA~~l----gis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 152 SSEQICQEC----DISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 467788888 999999999987666655543
No 89
>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=48.48 E-value=45 Score=24.59 Aligned_cols=46 Identities=13% Similarity=0.168 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.+..++...|-.+ ....++|..| |+++..|+++...=|.+.++
T Consensus 120 L~~~~r~i~~l~~~~g------~s~~eiA~~l----gis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD------LTIKEIAEVM----NKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 3444444554444333 2467788889 99999999988765655554
No 90
>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=48.04 E-value=30 Score=25.91 Aligned_cols=33 Identities=9% Similarity=0.099 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 47 RKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 47 ~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
....-.+||..| |+++..|+++...=|.+.|..
T Consensus 153 ~~~s~~EIA~~l----gis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 153 EGLSYEDIARIM----DCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred cCCCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 334467788888 999999999987666665554
No 91
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=47.42 E-value=42 Score=25.21 Aligned_cols=46 Identities=15% Similarity=0.115 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.|..++.-.|-.+ ..-++||..| |+++..|+.....-+.+++.
T Consensus 128 Lp~~~R~v~~L~~~~g------~s~~EIA~~l----gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 128 LRPRVKQAFLMATLDG------MKQKDIAQAL----DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4455555555544333 2466788888 99999999999876666644
No 92
>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=47.35 E-value=14 Score=21.45 Aligned_cols=22 Identities=9% Similarity=0.107 Sum_probs=17.8
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhhh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQNR 76 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqNR 76 (162)
..++|+.+ |++...|+.|.++-
T Consensus 3 ~~e~a~~~----gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLT----GVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHH----CcCHHHHHHHHHCC
Confidence 45678888 99999999997543
No 93
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=46.64 E-value=54 Score=24.79 Aligned_cols=49 Identities=16% Similarity=0.291 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
+++.+..++.-.|-.. ...++||..+ |++...|+...+.=|.+.|++..
T Consensus 132 L~~~~r~i~~l~~~~g------~s~~EIAe~l----gis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 132 LEKLDREIFIRRYLLG------EKIEEIAKKL----GLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred CCHHHHHHHHHHHHcc------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHccc
Confidence 4444555554433222 2356788888 99999999988766666555443
No 94
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=46.55 E-value=51 Score=24.63 Aligned_cols=29 Identities=14% Similarity=0.123 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.-.+||..+ |+++..|+.+.+.=|.+.+.
T Consensus 153 s~~eIA~~l----gis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 153 THREAAQLL----GLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 356677788 99999999988755555444
No 95
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=46.04 E-value=50 Score=25.28 Aligned_cols=32 Identities=16% Similarity=0.126 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
...++|..| |+++..|+++...=|.+.|+...
T Consensus 131 s~~EIA~~L----giS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMC----GVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHh
Confidence 356778888 99999999999877777766544
No 96
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=45.73 E-value=61 Score=24.01 Aligned_cols=32 Identities=9% Similarity=0.081 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
.-.+||..| |+++..|+++...-+.+.+....
T Consensus 137 s~~EIA~~l----gis~~tV~~~l~ra~~~~~~~l~ 168 (172)
T PRK12523 137 GHAEIAERL----GVSVSRVRQYLAQGLRQCYIALY 168 (172)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHhc
Confidence 356778888 99999999999877777665443
No 97
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=45.71 E-value=43 Score=26.46 Aligned_cols=31 Identities=23% Similarity=0.357 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.++|..+ |++...|+.+...-+.+.|+.-
T Consensus 202 s~~EIA~~l----gis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 202 NLKEIGAVL----GVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 567788888 9999999999987777776643
No 98
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=45.64 E-value=47 Score=24.25 Aligned_cols=28 Identities=18% Similarity=0.064 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
.-.+||..| |+++..|+....-=|.+.|
T Consensus 140 s~~eIA~~l----~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 140 PIAEVARIL----GKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHH
Confidence 456777888 9999999988765444444
No 99
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=45.26 E-value=61 Score=24.24 Aligned_cols=32 Identities=19% Similarity=0.270 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
...+||..| |+++..|++....-+.+.|+.-.
T Consensus 135 s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 135 SQEEIAQLL----QIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 456777888 99999999999887777776443
No 100
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=45.18 E-value=36 Score=27.17 Aligned_cols=31 Identities=10% Similarity=0.170 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.+||..| |+++..|++..+.-|.+.|+..
T Consensus 189 s~~EIA~~L----gis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 189 SNGEIAEVM----DTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 456778888 9999999999987777766544
No 101
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=45.15 E-value=48 Score=24.45 Aligned_cols=29 Identities=17% Similarity=0.182 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.-+++|..| |+++..|+.+...=|.+.|.
T Consensus 130 s~~eIA~~l----gis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 130 SYEDAAAIC----GCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 467788888 99999999998766655554
No 102
>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=44.65 E-value=9.4 Score=25.56 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=21.3
Q ss_pred CCHHHHHHHHHHHHHhcCCCccchhhhhhh
Q 031304 46 PRKQKIQDMTAELAKHGQISETNVYNWFQN 75 (162)
Q Consensus 46 p~~~~r~~LA~~l~~~~~ls~~~V~iWFqN 75 (162)
-......+||..| |+++..|+.|+.+
T Consensus 30 ~eGlS~kEIAe~L----GIS~~TVk~~l~~ 55 (73)
T TIGR03879 30 EAGKTASEIAEEL----GRTEQTVRNHLKG 55 (73)
T ss_pred HcCCCHHHHHHHH----CcCHHHHHHHHhc
Confidence 3334678899999 9999999999864
No 103
>PF13518 HTH_28: Helix-turn-helix domain
Probab=44.16 E-value=22 Score=20.85 Aligned_cols=24 Identities=29% Similarity=0.757 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
...++|..+ ||+..+|..|.+.-+
T Consensus 14 s~~~~a~~~----gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREF----GISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHH----CCCHhHHHHHHHHHH
Confidence 355688899 999999999997544
No 104
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=44.16 E-value=48 Score=25.23 Aligned_cols=31 Identities=10% Similarity=0.069 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-++||..| |++...|+.+...=|.+.|+.-
T Consensus 154 s~~eIA~~l----gis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 154 SNPEIAEVM----EIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 356778888 9999999999987666666543
No 105
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=42.89 E-value=39 Score=28.54 Aligned_cols=53 Identities=13% Similarity=0.157 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.+++.+..+|+..|--. |-.....++||..| |++...|+.+.+.=+.+.|+.-
T Consensus 262 ~L~~~~R~vl~lrygL~--~~e~~s~~EIA~~L----gis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLL--GYEAATLEDVAREI----GLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccC--CCCCcCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 56667777777666332 24445678899999 9999999999987777776644
No 106
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=42.80 E-value=56 Score=24.83 Aligned_cols=30 Identities=13% Similarity=0.152 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.-+++|..| |++...|++-...-|.+.|+.
T Consensus 159 s~~EIA~~l----gis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 159 PHQQVAEMF----DIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CHHHHHHHh----CcCHHHHHHHHHHHHHHHHHH
Confidence 456788888 999999998887666555543
No 107
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=42.26 E-value=61 Score=23.90 Aligned_cols=30 Identities=20% Similarity=0.238 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.-++||..| |+++..|+.....-|.+.|+.
T Consensus 136 s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 136 STAQIAADL----GIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 356778888 999999999887655555543
No 108
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=42.00 E-value=18 Score=21.30 Aligned_cols=22 Identities=27% Similarity=0.767 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQN 75 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqN 75 (162)
...++|..| |++...|..|.+.
T Consensus 19 s~~~ia~~l----gvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRL----GVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHH----TS-HHHHHHHHT-
T ss_pred CHHHHHHHH----CcCHHHHHHHHHH
Confidence 467789999 9999999999864
No 109
>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=41.93 E-value=42 Score=21.50 Aligned_cols=45 Identities=16% Similarity=0.267 Sum_probs=23.3
Q ss_pred CCCCCHHH-HHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhh
Q 031304 24 RWTPTPAQ-LQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 75 (162)
Q Consensus 24 Rt~ft~~q-l~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqN 75 (162)
|-.|+... |.+++.+...+ . --...|. -|.+. |+++++|+-|-+-
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~-n-c~~~~RA-aarkf----~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDN-N-CKGNQRA-AARKF----NVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH-T-T-TTT-HHH-HHHHT----TS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHHcc-c-hhhhHHH-HHHHh----CccHHHHHHHHHH
Confidence 44566644 45555555443 1 2223343 47888 9999999999853
No 110
>PRK10072 putative transcriptional regulator; Provisional
Probab=41.77 E-value=15 Score=25.81 Aligned_cols=25 Identities=32% Similarity=0.436 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRA 78 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~ 78 (162)
...+||..+ |++...|..|.+.+|.
T Consensus 48 TQ~elA~~l----GvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 48 KIDDFARVL----GVSVAMVKEWESRRVK 72 (96)
T ss_pred CHHHHHHHh----CCCHHHHHHHHcCCCC
Confidence 367788888 9999999999987663
No 111
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=41.47 E-value=56 Score=24.77 Aligned_cols=31 Identities=16% Similarity=0.188 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.+||..| |+++..|+.....-|.+.|+..
T Consensus 154 s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 154 SSDEIQQMC----GISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 456788888 9999999999987666666544
No 112
>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=41.00 E-value=8.2 Score=24.48 Aligned_cols=21 Identities=29% Similarity=0.759 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
...+||..| |++...|+.|-+
T Consensus 15 ~~~eIA~~L----g~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEEL----GVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHH----CCChHHHHHHHH
Confidence 467789999 999999999975
No 113
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=40.79 E-value=67 Score=21.64 Aligned_cols=46 Identities=13% Similarity=0.309 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHHHHHhhc----CCCCCHHHHHHHHHHHHHhcCCCccchhhhhh
Q 031304 25 WTPTPAQLQILEHVYDEC----KGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 25 t~ft~~ql~~Le~~F~~~----~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
+.++.+|+..|...|... ..+.+..+...+...+ |+++..|..+|.
T Consensus 2 ~~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~----~~~~~ev~~i~~ 51 (96)
T smart00027 2 WAISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKS----GLPQTLLAKIWN 51 (96)
T ss_pred CCCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHc----CCCHHHHHHHHH
Confidence 457889999999998763 1246666666655555 777777776663
No 114
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=40.55 E-value=18 Score=22.27 Aligned_cols=24 Identities=13% Similarity=0.252 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
...+||+.+ |++...|..|+.++.
T Consensus 12 t~~~La~~~----gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKT----GISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHH----T--HHHHHHHHTTT-
T ss_pred CHHHHHHHH----CcCHHHHHHHHhccc
Confidence 567789899 999999999998874
No 115
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=40.47 E-value=68 Score=24.64 Aligned_cols=34 Identities=9% Similarity=0.054 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
.-.+||..| |+++..|+++...=|.+.|+.....
T Consensus 151 s~~EIAe~l----gis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 151 TYEEAAKIA----DVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHhccc
Confidence 356777888 9999999999887777766655443
No 116
>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=39.69 E-value=59 Score=25.41 Aligned_cols=46 Identities=15% Similarity=0.231 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.+..+|...|-.. ....++|..+ |++...|+.+.+.-+.+.|+
T Consensus 176 L~~~~r~il~l~y~~~------~s~~eIA~~l----gis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE------LNLKEIGEVL----GLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHhCC------CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 4555555665555333 2457788888 99999999988765555544
No 117
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.61 E-value=40 Score=23.57 Aligned_cols=40 Identities=13% Similarity=0.069 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhh
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYN 71 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~i 71 (162)
++++|...-...|+.+- -.+....+++|..| ++++..|.-
T Consensus 3 Ln~eq~~~Tk~elqan~-el~~LS~~~iA~~L----n~t~~~lek 42 (97)
T COG4367 3 LNPEQKQRTKQELQANF-ELCPLSDEEIATAL----NWTEVKLEK 42 (97)
T ss_pred CCHHHHHHHHHHHHHhh-hhccccHHHHHHHh----CCCHHHHHH
Confidence 56777776655555552 35556778899999 988876543
No 118
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=38.51 E-value=68 Score=25.68 Aligned_cols=47 Identities=15% Similarity=0.184 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
+++.+..+|...|-.. ..-.+||..| |++...|+.|...=+.+.|..
T Consensus 206 L~~~~r~vl~l~~~~g------~s~~eIA~~l----~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 206 LSDREKSIIQCTFIEN------LSQKETGERL----GISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CCHHHHHHHHHHHhCC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 4555566666555333 1357788888 999999999987666665543
No 119
>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=37.99 E-value=77 Score=23.68 Aligned_cols=48 Identities=17% Similarity=0.205 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 24 RWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 24 Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.+.+++.|+.+|+-. ..+ . ...++|..| |++...|..+-+.-+.+-++
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G-l-----Tq~EIAe~L----giS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG-L-----SQKEIAKEL----KTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC-C-----CHHHHHHHH----CcCHHHHHHHHHhHHHHHHH
Confidence 357889999999884 333 2 567899999 99999999988766655554
No 120
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=37.92 E-value=86 Score=23.83 Aligned_cols=30 Identities=27% Similarity=0.310 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.-.+||..+ |++...|++=...=|.+.|+.
T Consensus 152 s~~EIA~~l----g~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 152 SVADAARML----GVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 456778888 999999987554444444443
No 121
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=37.67 E-value=72 Score=24.49 Aligned_cols=31 Identities=23% Similarity=0.370 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.+||..| |+++..|++....-|.+.|+.-
T Consensus 157 s~~EIA~~l----gis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTEL----TLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 466788888 9999999999876666665543
No 122
>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=37.62 E-value=69 Score=24.97 Aligned_cols=46 Identities=17% Similarity=0.214 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
.+++.+..+|...|-.. ....+||..+ |++...|+.|...=+.+.|
T Consensus 178 ~L~~~~r~vl~l~y~~~------~s~~eIA~~l----gis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 178 ALPERERRILLLRFFED------KTQSEIAERL----GISQMHVSRLLRRALKKLR 223 (227)
T ss_pred cCCHHHHHHHHHHHhcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHH
Confidence 45666666666655433 2467788888 9999999999875555544
No 123
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=37.48 E-value=64 Score=24.40 Aligned_cols=29 Identities=14% Similarity=0.047 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.-.+||..| |+++..|+.+...=|.+.|+
T Consensus 148 s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVC----GCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHh
Confidence 356777788 99999999988655555444
No 124
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=37.31 E-value=74 Score=24.67 Aligned_cols=31 Identities=16% Similarity=0.265 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.++|..| |+++..|+.+...=|.+.++..
T Consensus 156 s~~EIA~~L----gis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 156 SYEEIAATL----GVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 356677788 9999999999986666665533
No 125
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=36.93 E-value=72 Score=23.22 Aligned_cols=43 Identities=16% Similarity=0.156 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k 79 (162)
+++.|..++.-.|-.+ ..-.+||..+ |++...|+.+...=+.+
T Consensus 114 L~~~~r~v~~L~~~~g------~s~~EIA~~l----~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 114 LPPLVKRAFLLAQVDG------LGYGEIATEL----GISLATVKRYLNKAAMR 156 (161)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHH
Confidence 3344444554444333 2356778888 99999999987654443
No 126
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=36.67 E-value=56 Score=24.31 Aligned_cols=30 Identities=10% Similarity=0.156 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 49 QKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 49 ~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
....+||..| |++...|+++...=+.+++.
T Consensus 136 ~s~~EIA~~l----gis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 136 LTYSEIAHKL----GVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CCHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 3467788888 99999999998765555543
No 127
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=36.58 E-value=70 Score=24.01 Aligned_cols=30 Identities=27% Similarity=0.474 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.-++||..+ |+++..|+.....-|.+.+..
T Consensus 140 s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 140 TYQEISSVM----GITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 456778888 999999999887666665553
No 128
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=36.52 E-value=58 Score=23.23 Aligned_cols=37 Identities=16% Similarity=0.341 Sum_probs=26.0
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhh
Q 031304 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 28 t~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
+-+-....-.+++.. + ...++|..+ +++...|..||+
T Consensus 4 S~DlR~rVl~~~~~g-~-----s~~eaa~~F----~VS~~Tv~~W~k 40 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKG-K-----SIREAAKRF----GVSRNTVYRWLK 40 (119)
T ss_pred CHHHHHHHHHHHHcc-c-----hHHHHHHHh----CcHHHHHHHHHH
Confidence 334444444566665 3 456678888 999999999998
No 129
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=36.50 E-value=77 Score=23.89 Aligned_cols=31 Identities=29% Similarity=0.448 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.+||..| |+++..|++....=|.+.|...
T Consensus 149 s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 149 ETEEICQEL----QITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 356788888 9999999999876666665543
No 130
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=36.49 E-value=74 Score=24.14 Aligned_cols=32 Identities=22% Similarity=0.222 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
.-.+||..| |+++..|+++...=|.+.++...
T Consensus 129 s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 129 SYQEAAAVL----GIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CHHHHHHHh----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 356778888 99999999998766666555443
No 131
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=36.23 E-value=80 Score=23.97 Aligned_cols=31 Identities=23% Similarity=0.275 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
...+||..| |++...|+.....=|.+.|+.-
T Consensus 149 s~~EIA~~l----gis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 149 ESDEICQEL----EISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHHH
Confidence 467788888 9999999998876665555543
No 132
>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=35.99 E-value=28 Score=19.64 Aligned_cols=24 Identities=13% Similarity=0.390 Sum_probs=19.2
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhhhHH
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQNRRA 78 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqNRR~ 78 (162)
..++|..| |++.+.|..|.++...
T Consensus 3 ~~e~a~~l----gvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELL----GVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHH----CcCHHHHHHHHHcCCC
Confidence 45778888 9999999999876443
No 133
>PRK09480 slmA division inhibitor protein; Provisional
Probab=35.84 E-value=38 Score=25.21 Aligned_cols=41 Identities=20% Similarity=0.359 Sum_probs=31.2
Q ss_pred HHHHHH---HHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHH
Q 031304 32 LQILEH---VYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 78 (162)
Q Consensus 32 l~~Le~---~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~ 78 (162)
..+|+. .|...+ . ......+||+.. |++...+..+|.|+-.
T Consensus 13 ~~Il~aa~~l~~~~~-G-~~~ti~~Ia~~a----gvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 13 EQILQALAQMLESPP-G-ERITTAKLAARV----GVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHHHHhcC-C-CccCHHHHHHHh----CCCHhHHHHHCCCHHH
Confidence 344444 354443 5 777889999999 9999999999999773
No 134
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=35.61 E-value=31 Score=25.51 Aligned_cols=36 Identities=14% Similarity=0.130 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 45 TPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 45 yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
|.....-+++|..+ |+++..|++.+..-|.+.++..
T Consensus 133 ~~~g~s~~eIA~~l----g~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 133 DLEDLPQKEIAEIL----NIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HhcCCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 34444567888899 9999999999987777766644
No 135
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=35.49 E-value=38 Score=25.66 Aligned_cols=36 Identities=8% Similarity=0.158 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 45 TPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 45 yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
|.....-.+||..| |+++..|+++...=|.+.|+.-
T Consensus 144 ~~~g~s~~EIA~~l----gis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 144 DVEGFAYKEIAEIM----GTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hhcCCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 34445577888999 9999999999987777776644
No 136
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=35.34 E-value=71 Score=25.51 Aligned_cols=47 Identities=17% Similarity=0.235 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.+++.+..+|...|-.+ ....+||..+ |+++..|+.+...=+.+.|.
T Consensus 205 ~L~~~~r~ii~l~~~~g------~s~~eIA~~l----gis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN------LSQKETGERL----GISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 34555566666555443 1356788888 99999999988765655544
No 137
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=35.33 E-value=98 Score=22.44 Aligned_cols=30 Identities=20% Similarity=0.190 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
...++|..| |+++..|+.....-+.+.+..
T Consensus 123 s~~eIA~~l----gis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 123 SHQQIAEHL----GISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHHH
Confidence 456677788 999999999887655555544
No 138
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=35.23 E-value=55 Score=25.21 Aligned_cols=45 Identities=16% Similarity=0.299 Sum_probs=32.7
Q ss_pred HHHHHHH---HHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 31 QLQILEH---VYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 31 ql~~Le~---~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
.-.+|+. .|.... .......+||+.. |++...|...|.|+..=..
T Consensus 20 r~~IL~AA~~lf~e~G--y~~~s~~dIA~~a----Gvs~gtiY~hF~sKe~L~~ 67 (212)
T PRK15008 20 KKAILSAALDTFSQFG--FHGTRLEQIAELA----GVSKTNLLYYFPSKEALYI 67 (212)
T ss_pred HHHHHHHHHHHHHHhC--cccCCHHHHHHHh----CcCHHHHHHHCCCHHHHHH
Confidence 3344444 477774 4455677789999 9999999999999876443
No 139
>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=35.18 E-value=43 Score=19.84 Aligned_cols=23 Identities=17% Similarity=0.332 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
..+||..+ |++...|..|..+++
T Consensus 12 ~~~la~~~----gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKL----GISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHH----TS-HHHHHHHHTTSS
T ss_pred HHHHHHHh----CCCcchhHHHhcCCC
Confidence 46677788 888888888887643
No 140
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=34.84 E-value=85 Score=23.18 Aligned_cols=29 Identities=14% Similarity=0.245 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.-+++|..| |+++..|+.....=|.+.++
T Consensus 137 s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 137 SYKEMSEIL----NIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred CHHHHHHHh----CCCHHHHHHHHHHHHHHHHH
Confidence 456778888 99999999998765655554
No 141
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=34.57 E-value=78 Score=23.50 Aligned_cols=29 Identities=14% Similarity=0.337 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.-+++|..| |++...|+.....=|.+.++
T Consensus 154 s~~eIA~~l----gis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 154 SLKEISEIL----DLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 456778888 99999999988766666554
No 142
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=34.42 E-value=84 Score=25.34 Aligned_cols=48 Identities=19% Similarity=0.178 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
+++.+..+|...|-.. ....+||..+ |++...|+.+...=+.+.|...
T Consensus 204 L~~~~r~vl~l~y~~~------~s~~eIA~~l----gvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 204 LEERTREVLEFVFLHD------LTQKEAAERL----GISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred CCHHHHHHHHHHHHCC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHh
Confidence 3444445555544333 2467788888 9999999999876666655543
No 143
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=34.41 E-value=75 Score=24.95 Aligned_cols=30 Identities=20% Similarity=0.253 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.-.++|..| |+++..|+.+...=+.+-|+.
T Consensus 200 s~~EIA~~l----gis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 200 TQKEVADML----GISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 467788889 999999999987666665553
No 144
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=34.39 E-value=99 Score=22.79 Aligned_cols=46 Identities=7% Similarity=-0.049 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.+..++.-.|-.+ ..-+++|..| |+++..|+.+..+-+..++.
T Consensus 119 L~~~~r~v~~L~~~eg------~s~~EIA~~l----~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 119 LSGKARAAFLMSQLEG------LTYVEIGERL----GVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred CCHHHHHHHHHHHHcC------CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 4444444444443333 1356778888 99999999988766655543
No 145
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=34.20 E-value=87 Score=25.02 Aligned_cols=46 Identities=13% Similarity=0.242 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.+..++...|-.. ..-.+||..| |+++..|+.++..-+.+.|.
T Consensus 202 L~~~~r~vl~l~~~~~------~s~~EIA~~l----gis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYKEE------LTLTEIGQVL----NLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHhcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 3444555555444332 2467788888 99999999998766665554
No 146
>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=34.14 E-value=83 Score=25.35 Aligned_cols=31 Identities=23% Similarity=0.468 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
...+||..| |+++..|+.+...=|.+.|+.-
T Consensus 179 S~~EIA~~L----gis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 179 SMDRIGAMY----QVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHH
Confidence 467788888 9999999999987777666543
No 147
>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=32.84 E-value=31 Score=19.81 Aligned_cols=20 Identities=15% Similarity=0.220 Sum_probs=15.3
Q ss_pred HHHHHHHHHHhcCCCccchhhhhh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
+.++|+.+ |++.+.|+.|=+
T Consensus 2 i~e~A~~~----gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLL----GVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHH----TS-HHHHHHHHH
T ss_pred HHHHHHHH----CCCHHHHHHHHH
Confidence 35678888 999999999964
No 148
>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=32.58 E-value=31 Score=21.75 Aligned_cols=20 Identities=15% Similarity=0.238 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhcCCCccchhhhhh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
..++|+.+ |++...++.|.+
T Consensus 3 i~e~A~~~----gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLT----GIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHH----CcCHHHHHHHHH
Confidence 45788888 999999999975
No 149
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=32.13 E-value=40 Score=25.54 Aligned_cols=35 Identities=9% Similarity=0.159 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 46 PRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 46 p~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.....-.++|..| |++...|+.+...=|.+.|...
T Consensus 153 ~~g~s~~EIA~~l----gis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 153 HGDLELEEIAELT----GVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred ccCCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 3444567888899 9999999998876666666543
No 150
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=32.05 E-value=98 Score=24.02 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=22.9
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
..+||..+ |++...|+...+.=|.+.|+.
T Consensus 167 ~~EIAe~l----gis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 167 TNEICHAV----DLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred HHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 56778888 999999999988666666654
No 151
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=31.86 E-value=93 Score=23.39 Aligned_cols=31 Identities=13% Similarity=0.190 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.++|..| |+++..|++....=|.+-|+.-
T Consensus 156 s~~eIA~~l----gis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 156 SYEDIASVM----QCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 456777888 9999999998887666666543
No 152
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=31.69 E-value=25 Score=22.06 Aligned_cols=20 Identities=15% Similarity=0.290 Sum_probs=16.6
Q ss_pred HHHHHHHHHHhcCCCccchhhhhh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
..++|+.+ |++...|+.|=+
T Consensus 3 i~eva~~~----gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLL----GVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHT----TTTHHHHHHHHH
T ss_pred HHHHHHHH----CcCHHHHHHHHH
Confidence 35678888 999999999964
No 153
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=31.56 E-value=94 Score=23.56 Aligned_cols=31 Identities=19% Similarity=0.273 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.-.+||..| |+++..|++....-|.+.++.-
T Consensus 172 s~~EIA~~l----gis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 172 SYQEIAEEL----NRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 356677888 9999999998887776666543
No 154
>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=31.26 E-value=35 Score=21.40 Aligned_cols=21 Identities=5% Similarity=0.232 Sum_probs=17.7
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQN 75 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqN 75 (162)
..++|+.+ |++.+.++.|-+.
T Consensus 3 i~evA~~~----gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEII----GVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHH----CcCHHHHHHHHHh
Confidence 45788888 9999999999764
No 155
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=30.81 E-value=1e+02 Score=24.98 Aligned_cols=48 Identities=17% Similarity=0.235 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
.+++.+..+|...|... ....+||..+ |++...|+.....-+.+.|+.
T Consensus 212 ~L~~~~r~vl~l~~~~~------~s~~eIA~~l----gis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYYED------LTLKEIGKVL----GVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 34555555565555443 2467788888 999999998887666665554
No 156
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=30.45 E-value=70 Score=22.93 Aligned_cols=37 Identities=5% Similarity=0.097 Sum_probs=25.4
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhh
Q 031304 33 QILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 75 (162)
Q Consensus 33 ~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqN 75 (162)
..+..+...+ +-.....++||..+ |++++.+.-+|+.
T Consensus 12 ~~~~~~I~~~--~~~~~sl~~lA~~~----g~S~~~l~r~Fk~ 48 (127)
T PRK11511 12 HSILDWIEDN--LESPLSLEKVSERS----GYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHh--cCCCCCHHHHHHHH----CcCHHHHHHHHHH
Confidence 3344444443 33445678899999 9999999888875
No 157
>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=30.19 E-value=1.4e+02 Score=22.98 Aligned_cols=47 Identities=17% Similarity=0.198 Sum_probs=38.7
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhh
Q 031304 23 QRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNR 76 (162)
Q Consensus 23 ~Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNR 76 (162)
+...+|++++.++.++-.++ |..-.+..||+++ |++..-|.+-..--
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D---P~~wTr~~LAkkF----~~S~~fV~~v~~~~ 128 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED---PEKWTRKKLAKKF----NCSPLFVSMVAPAP 128 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC---chHhhHHHHHHHh----CCCHHHHHHhcCCC
Confidence 44689999999999988776 6788899999999 99988877765443
No 158
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=30.12 E-value=89 Score=23.35 Aligned_cols=29 Identities=17% Similarity=0.347 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.-.++|..| |++...|+.+...-|.+.+.
T Consensus 145 s~~EIA~~l----~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 145 SIKEIAEVT----GVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 356778888 99999999988766655554
No 159
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=29.57 E-value=1e+02 Score=25.21 Aligned_cols=53 Identities=13% Similarity=0.171 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
.+++.+..+|...|.-. |-....-.+||..| |+++..|+.+...-+.+.|+.-
T Consensus 222 ~Lp~~~R~Vl~l~ygL~--~~e~~s~~EIA~~L----gis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 222 ELNERQREVLARRFGLL--GYEPATLEEVAAEV----GLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred cCCHHHHHHHHHHhCCC--CCCCccHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHH
Confidence 34555555666555111 12233567788899 9999999999877666666543
No 160
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=29.48 E-value=1.2e+02 Score=22.66 Aligned_cols=30 Identities=17% Similarity=0.335 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 49 QKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 49 ~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
....+||..| |+++..|++.+..-|.+.|.
T Consensus 166 ~s~~eIA~~l----~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 166 KSYQEIACDL----NRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 3456788888 99999999988755555443
No 161
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=29.35 E-value=99 Score=25.15 Aligned_cols=46 Identities=17% Similarity=0.201 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.+..+|...|-.. ....+||..| |++...|+.+...-+.+.|.
T Consensus 216 L~~rer~vl~l~y~~~------~t~~EIA~~l----gis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 216 LPERERTVLVLRFFES------MTQTQIAERV----GISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHHHhcCC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 4455555665555333 2457888889 99999999998766655554
No 162
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=28.84 E-value=20 Score=29.96 Aligned_cols=23 Identities=26% Similarity=0.433 Sum_probs=17.7
Q ss_pred CCCC-hhHhhcCcCCCCCCccccc
Q 031304 132 PDLG-IDQMIGKMEIPGSFSFHWQ 154 (162)
Q Consensus 132 p~~~-~~~l~~~~~~p~s~~~~~~ 154 (162)
||.- .|-|+.++++|+.||++|=
T Consensus 166 PDv~Are~la~ktelpEDRIqVWf 189 (332)
T KOG0494|consen 166 PDVYAREMLADKTELPEDRIQVWF 189 (332)
T ss_pred ccHHHHHHHhhhccCchhhhhHHh
Confidence 4443 3667789999999999993
No 163
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=28.82 E-value=1.2e+02 Score=22.92 Aligned_cols=32 Identities=13% Similarity=0.081 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
.-.+||..| |+++..|+.....=|.+.++...
T Consensus 129 s~~EIA~~L----gis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAIC----GCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 456778888 99999999988765555555433
No 164
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=28.81 E-value=97 Score=22.33 Aligned_cols=44 Identities=27% Similarity=0.185 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHH
Q 031304 25 WTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79 (162)
Q Consensus 25 t~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k 79 (162)
..+|+.+..+|.- +..+ +. ..++|..+ +++++.|+.+.++=+.|
T Consensus 148 ~~lt~~e~~vl~l-~~~g--~~----~~~Ia~~l----~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG--YT----NRDIAEQL----SISIKTVETHRLNMMRK 191 (211)
T ss_pred cCCCHHHHHHHHH-HHCC--CC----HHHHHHHh----CCCHHHHHHHHHHHHHH
Confidence 3488888888876 4444 22 56788899 99999999998874444
No 165
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=28.72 E-value=1e+02 Score=25.12 Aligned_cols=29 Identities=17% Similarity=0.273 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
-.+||..| |+++..|+..++.=|.+.+..
T Consensus 127 ~~EIA~~l----g~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIV----GKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHhh
Confidence 45667777 999999999998766666553
No 166
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=28.65 E-value=1e+02 Score=25.14 Aligned_cols=30 Identities=10% Similarity=0.191 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~ 84 (162)
-.+||..| |+++..|+...+.-|.+.+...
T Consensus 134 ~~EIA~~l----g~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 134 FDEIASTL----GRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred HHHHHHHH----CCCHHHHHHHHHHHHHHHHhhC
Confidence 45677777 9999999999986666665543
No 167
>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=28.51 E-value=1.2e+02 Score=17.36 Aligned_cols=36 Identities=25% Similarity=0.358 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhh
Q 031304 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 28 t~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
++.+..++..++ .. ....++|..+ +++...|+.|..
T Consensus 2 ~~~e~~i~~~~~-~~------~s~~eia~~l----~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA-EG------KTNKEIADIL----GISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH-cC------CCHHHHHHHH----CCCHHHHHHHHH
Confidence 455666665543 22 1457788889 999999999886
No 168
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=28.35 E-value=1.3e+02 Score=17.40 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhh
Q 031304 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 73 (162)
Q Consensus 28 t~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWF 73 (162)
+..+..+|...++.. . ....+||..+ |++...|..-+
T Consensus 2 ~~~~~~Il~~l~~~~-~----~t~~ela~~~----~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRENP-R----ITQKELAEKL----GISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHHCT-T----S-HHHHHHHH----TS-HHHHHHHH
T ss_pred CHHHHHHHHHHHHcC-C----CCHHHHHHHh----CCCHHHHHHHH
Confidence 456777887766633 2 4677889999 99998887654
No 169
>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=27.90 E-value=27 Score=20.54 Aligned_cols=20 Identities=15% Similarity=0.243 Sum_probs=17.9
Q ss_pred HHHHHHHHhcCCCccchhhhhhhh
Q 031304 53 DMTAELAKHGQISETNVYNWFQNR 76 (162)
Q Consensus 53 ~LA~~l~~~~~ls~~~V~iWFqNR 76 (162)
+||..+ |++...|..|+.++
T Consensus 2 ~lA~~~----gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAA----GVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHH----CcCHHHHHHHHcCC
Confidence 578888 99999999999887
No 170
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=27.86 E-value=1.1e+02 Score=24.11 Aligned_cols=45 Identities=20% Similarity=0.179 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
.+|+.++.+|+-..+-. .-.++|..| ++++..|+.+..+=..|..
T Consensus 155 ~Lt~rE~~Vl~l~~~G~-------s~~eIA~~L----~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEILNKLRIGA-------SNNEIARSL----FISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHHHHHHcCC-------CHHHHHHHh----CCCHHHHHHHHHHHHHHhC
Confidence 58999999998887632 357789999 9999999999987655543
No 171
>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=27.86 E-value=66 Score=19.95 Aligned_cols=36 Identities=28% Similarity=0.374 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhh
Q 031304 30 AQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 30 ~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
.|+..|+-.+. +.+ .+ ..+||..+ |++++.|+.-..
T Consensus 6 rq~~Ll~~L~~-~~~-~~---~~ela~~l----~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKW-IT---LKELAKKL----NISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTS-BB---HHHHHHHC----TS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCC-Cc---HHHHHHHH----CCCHHHHHHHHH
Confidence 57888999998 533 44 34788899 999999887654
No 172
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=27.18 E-value=1.3e+02 Score=22.84 Aligned_cols=29 Identities=31% Similarity=0.514 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
..+|||..| |++++.|+..++.=|.+.++
T Consensus 153 s~~EIA~~l----giS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 153 SVEEIAERL----GISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 456777888 99999999988766655443
No 173
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=27.12 E-value=41 Score=25.39 Aligned_cols=33 Identities=9% Similarity=0.233 Sum_probs=25.2
Q ss_pred CHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 47 RKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 47 ~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
....-++||..| |++...|+++...-+.+.|..
T Consensus 149 ~g~s~~EIA~~l----gis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 149 AELEFQEIADIM----HMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred cCCCHHHHHHHH----CCCHHHHHHHHHHHHHHHHHH
Confidence 334567888888 999999999998666666553
No 174
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=27.09 E-value=1.3e+02 Score=24.13 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
.+++.+..+|+..|-.+ ....++|..+ |++...|...-.+=..+.|
T Consensus 209 ~L~~~er~vi~~~~~~~------~t~~eIA~~l----gis~~~V~~~~~~al~kLr 254 (258)
T PRK08215 209 KLNDREKLILNLRFFQG------KTQMEVAEEI----GISQAQVSRLEKAALKHMR 254 (258)
T ss_pred cCCHHHHHHHHHHHhcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHH
Confidence 56777777777777443 2467889999 9999999887665444443
No 175
>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=26.52 E-value=46 Score=20.68 Aligned_cols=20 Identities=15% Similarity=0.268 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhcCCCccchhhhhh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
..++|+.+ |++...++.|-+
T Consensus 3 ~~eva~~~----gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLT----GVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHH----CcCHHHHHHHHH
Confidence 45788888 999999999985
No 176
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=26.52 E-value=1.2e+02 Score=24.02 Aligned_cols=51 Identities=14% Similarity=0.246 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.+++.+..+|...|.... -......+||..| |++...|+.....=..|.|.
T Consensus 176 ~L~~~er~vl~l~ygl~~--~~~~t~~EIA~~l----gis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLD--GRPHTLEEVGKEF----NVTRERIRQIESKALRKLRH 226 (238)
T ss_pred hCCHHHHHHHHHHhCCCC--CCCccHHHHHHHH----CCCHHHHHHHHHHHHHHHhh
Confidence 456666777777663221 1223578889999 99999999988766666554
No 177
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=26.31 E-value=64 Score=18.57 Aligned_cols=13 Identities=54% Similarity=0.452 Sum_probs=11.1
Q ss_pred CCCHHHHHHHHHH
Q 031304 26 TPTPAQLQILEHV 38 (162)
Q Consensus 26 ~ft~~ql~~Le~~ 38 (162)
.||+.|+..|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5899999999864
No 178
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=26.26 E-value=1.1e+02 Score=24.01 Aligned_cols=31 Identities=16% Similarity=0.199 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHh
Q 031304 49 QKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83 (162)
Q Consensus 49 ~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~ 83 (162)
..-++||..+ |++...|+.+-..-+.+.|+.
T Consensus 196 ~S~~EIA~~l----gis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 196 KTQREIAKAL----GISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred cCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHH
Confidence 3567788899 999999988854444444443
No 179
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=26.15 E-value=1.4e+02 Score=23.35 Aligned_cols=42 Identities=17% Similarity=0.084 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
.+++.+..++...|..+ ....++|..+ |++...|..+-..=.
T Consensus 183 ~L~~~e~~i~~~~~~~~------~t~~eIA~~l----gis~~~V~~~~~~al 224 (231)
T TIGR02885 183 KLDERERQIIMLRYFKD------KTQTEVANML----GISQVQVSRLEKKVL 224 (231)
T ss_pred cCCHHHHHHHHHHHHcC------CCHHHHHHHH----CcCHHHHHHHHHHHH
Confidence 45555666666655433 2577889999 999999987765433
No 180
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=25.90 E-value=1.6e+02 Score=18.62 Aligned_cols=44 Identities=14% Similarity=0.173 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhh
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 75 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqN 75 (162)
+|.+|+..|+.+|..- ...+..+..+.-++|-|+..+-..|-.+
T Consensus 1 lT~~Qk~el~~l~~qm-----~e~kK~~idk~Ve~G~iTqeqAd~ik~~ 44 (59)
T PF10925_consen 1 LTDQQKKELKALYKQM-----LELKKQIIDKYVEAGVITQEQADAIKKH 44 (59)
T ss_pred CCHHHHHHHHHHHHHH-----HHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 5889999999999775 2456666667778888998877776654
No 181
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=25.43 E-value=42 Score=19.62 Aligned_cols=35 Identities=17% Similarity=0.399 Sum_probs=25.5
Q ss_pred HHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 37 HVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 37 ~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
..|.... ........||+.+ |++...+...|.|+-
T Consensus 7 ~l~~~~G--~~~~s~~~Ia~~~----gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 7 ELFAEKG--YEAVSIRDIARRA----GVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHH--TTTSSHHHHHHHH----TSCHHHHHHHCSSHH
T ss_pred HHHHHhC--HHhCCHHHHHHHH----ccchhhHHHHcCCHH
Confidence 3444442 4445567789999 999999999998864
No 182
>PRK05572 sporulation sigma factor SigF; Validated
Probab=25.39 E-value=1.5e+02 Score=23.60 Aligned_cols=47 Identities=15% Similarity=0.099 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.+++.+..+|...|..+ ....+||..+ |++...|..+-..=..+.|+
T Consensus 202 ~L~~~~~~v~~l~~~~~------~s~~eIA~~l----gis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 202 ELDERERLIVYLRYFKD------KTQSEVAKRL----GISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred cCCHHHHHHHHHHHhCC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 56666777777666443 2467889999 99999998877655555443
No 183
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=25.17 E-value=2.5e+02 Score=20.86 Aligned_cols=29 Identities=21% Similarity=0.390 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
.-+++|..| |+++..|+.-...=|.+.|.
T Consensus 155 s~~eIA~~l----gis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 155 TYEELAART----DTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CHHHHHHHh----CCChhHHHHHHHHHHHHHHH
Confidence 456778888 99999998877655544443
No 184
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=25.01 E-value=1.6e+02 Score=22.24 Aligned_cols=32 Identities=16% Similarity=0.253 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
.-.++|..| |+++..|+++..-=|.+.++...
T Consensus 146 s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 146 SGEEIAEIL----DLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHHHH
Confidence 456778888 99999999998766666655443
No 185
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=24.98 E-value=1.2e+02 Score=24.80 Aligned_cols=32 Identities=22% Similarity=0.218 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
.-.+||..| |+++..|+.....=|.+.|+...
T Consensus 160 s~~EIA~~l----gis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 160 RAAETAELL----GTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred CHHHHHHHH----CCCHHHHHHHHHHHHHHHHHhcc
Confidence 356778888 99999999998866666655444
No 186
>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=24.62 E-value=70 Score=22.90 Aligned_cols=34 Identities=18% Similarity=0.217 Sum_probs=25.1
Q ss_pred CCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 45 TPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 45 yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
|.....-+++|..+ |+++..|+++...-|.+.++
T Consensus 118 ~~~g~s~~eIA~~l----gis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELL----NLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHH----CCCHHHHHHHHHHHHHHHHH
Confidence 44455667788888 99999999988765555543
No 187
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=24.23 E-value=1.6e+02 Score=21.40 Aligned_cols=43 Identities=21% Similarity=0.219 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k 79 (162)
.+|+.+..+|+-+.+. | .+++||..+ +++++.|++..++=+.|
T Consensus 137 ~Lt~~E~~il~~l~~g---~----~~~~Ia~~l----~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQG---M----AVKEIAAEL----GLSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHCC---C----CHHHHHHHh----CCCHHHHHHHHHHHHHH
Confidence 5888888888776642 2 477889999 99999998887765544
No 188
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.88 E-value=80 Score=24.86 Aligned_cols=37 Identities=14% Similarity=0.250 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 45 TPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 45 yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
|.......+||..| |++...|++....-|.+.|+...
T Consensus 162 ~~~g~s~~EIAe~l----gis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 162 VVEELSVEETAQAL----GLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hhcCCCHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 44455678889999 99999999988777777776554
No 189
>PRK10651 transcriptional regulator NarL; Provisional
Probab=23.65 E-value=1.4e+02 Score=21.80 Aligned_cols=44 Identities=18% Similarity=0.234 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 80 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~ 80 (162)
.+|+.+..+|+-+.+.- ...++|..+ ++++..|++..++=+.|.
T Consensus 155 ~Lt~rE~~vl~~l~~g~-------~~~~ia~~l----~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRERDILKLIAQGL-------PNKMIARRL----DITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHHHHHHHHHcCC-------CHHHHHHHc----CCCHHHHHHHHHHHHHHc
Confidence 48999999998755321 256678889 999999999887755554
No 190
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=23.62 E-value=1.6e+02 Score=23.70 Aligned_cols=46 Identities=15% Similarity=0.205 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
+++.+..+|...|... ..-.+||..| |++...|+.+...=+.+.|+
T Consensus 206 L~~~er~vi~l~y~e~------~t~~EIA~~l----gis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 206 LEEKERKVMALYYYEE------LVLKEIGKIL----GVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred CCHHHHHHHHHHHhcC------CCHHHHHHHH----CcCHHHHHHHHHHHHHHHHH
Confidence 4455555555555433 2467888899 99999999987655555444
No 191
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.61 E-value=1.6e+02 Score=20.42 Aligned_cols=42 Identities=21% Similarity=0.307 Sum_probs=31.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCC-Cccchhhhhh
Q 031304 24 RWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQI-SETNVYNWFQ 74 (162)
Q Consensus 24 Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~l-s~~~V~iWFq 74 (162)
|..|+.+....+-..+.... + ...++|+.+ |+ ...++..|-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g-~----sv~~vAr~~----gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGG-D----TVSEVAREF----GIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcC-c----cHHHHHHHh----CCCChHHHHHHHH
Confidence 67899988776666665543 2 577889999 96 9999998875
No 192
>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=23.56 E-value=63 Score=22.56 Aligned_cols=36 Identities=22% Similarity=0.422 Sum_probs=19.6
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhcCC
Q 031304 33 QILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQSGV 87 (162)
Q Consensus 33 ~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~~~ 87 (162)
.+..-.|+.|| ||...-- +..- .|||.+|++.+.+.
T Consensus 15 RiIk~LyqsnP-yP~~~GT---r~aR---------------RnRRRRWR~rq~QI 50 (91)
T PF00424_consen 15 RIIKILYQSNP-YPSPEGT---RQAR---------------RNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHTS--S--S-S----HHHH---------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHcccc-CCCCCCc---cccc---------------cchhhhHHHHHHHH
Confidence 34455689998 8973311 1111 48899998877664
No 193
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=23.44 E-value=1.8e+02 Score=21.50 Aligned_cols=28 Identities=21% Similarity=0.281 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
.-.+||..| |++...|+.=...=|.+.|
T Consensus 158 s~~eIA~~l----gis~~~v~~~l~Ra~~~Lr 185 (189)
T TIGR02984 158 SFAEVAERM----DRSEGAVSMLWVRGLARLR 185 (189)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHH
Confidence 466778888 9999999886655454444
No 194
>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=23.27 E-value=45 Score=19.56 Aligned_cols=23 Identities=4% Similarity=-0.026 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
..+||..+ |++...|..|..+++
T Consensus 18 q~~lA~~~----gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLA----GVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHh----CCCHHHHHHHHCCCC
Confidence 56788888 999999999997653
No 195
>PRK10403 transcriptional regulator NarP; Provisional
Probab=23.21 E-value=1.4e+02 Score=21.64 Aligned_cols=43 Identities=21% Similarity=0.242 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHH
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k 79 (162)
.+|..+..+|+-+.+. ...++||..+ +++++.|++...|=+.|
T Consensus 153 ~Lt~~e~~vl~~~~~g-------~s~~~ia~~l----~~s~~tv~~~~~~i~~k 195 (215)
T PRK10403 153 VLTERELDVLHELAQG-------LSNKQIASVL----NISEQTVKVHIRNLLRK 195 (215)
T ss_pred cCCHHHHHHHHHHHCC-------CCHHHHHHHc----CCCHHHHHHHHHHHHHH
Confidence 5889888888765432 1357889999 99999999988765544
No 196
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=23.09 E-value=1.6e+02 Score=24.07 Aligned_cols=47 Identities=26% Similarity=0.206 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHH
Q 031304 24 RWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 81 (162)
Q Consensus 24 Rt~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~k 81 (162)
...+|+.+..+|.-.. .. + .-.+||..| ++++..|+.+.+|=+.|..
T Consensus 188 ~~~LT~RE~evl~l~a-~G-~-----s~~eIA~~L----~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 188 AGLITAREAEILAWVR-DG-K-----TNEEIAAIL----GISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred ccCCCHHHHHHHHHHH-CC-C-----CHHHHHHHH----CcCHHHHHHHHHHHHHHhC
Confidence 4478999999999654 32 2 467789999 9999999999987665543
No 197
>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=23.09 E-value=54 Score=18.51 Aligned_cols=23 Identities=17% Similarity=0.407 Sum_probs=18.2
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
..++|..| |++...|..|.++.+
T Consensus 4 ~~e~a~~l----gis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYL----GVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHH----CCCHHHHHHHHHcCC
Confidence 45677778 999999999986544
No 198
>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=22.92 E-value=51 Score=18.25 Aligned_cols=22 Identities=9% Similarity=0.265 Sum_probs=18.2
Q ss_pred HHHHHHHHHHhcCCCccchhhhhhhh
Q 031304 51 IQDMTAELAKHGQISETNVYNWFQNR 76 (162)
Q Consensus 51 r~~LA~~l~~~~~ls~~~V~iWFqNR 76 (162)
..++|..+ |+++..|..|..+.
T Consensus 15 ~~~~a~~~----~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKL----GVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHH----CCCHHHHHHHHcCC
Confidence 45688888 99999999998765
No 199
>cd00131 PAX Paired Box domain
Probab=22.87 E-value=3e+02 Score=19.87 Aligned_cols=46 Identities=17% Similarity=0.206 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCC-------Cccchhhhhhhh
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQI-------SETNVYNWFQNR 76 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~l-------s~~~V~iWFqNR 76 (162)
..+..+...++.+...+| ..+..+. +..|... |+ +...|-.||+++
T Consensus 75 ~~~~~~~~~i~~~v~~~p-~~Tl~El---~~~L~~~-gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQENP-GMFAWEI---RDRLLQE-GVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHCC-CCCHHHH---HHHHHHc-CCcccCCCCCHHHHHHHHHhc
Confidence 446666666777667765 3544444 4344322 44 777887777653
No 200
>PRK13558 bacterio-opsin activator; Provisional
Probab=22.33 E-value=82 Score=28.63 Aligned_cols=41 Identities=22% Similarity=0.294 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCC---CCHHHHHHHHHHHHHhcCCCccchhh
Q 031304 25 WTPTPAQLQILEHVYDECKGT---PRKQKIQDMTAELAKHGQISETNVYN 71 (162)
Q Consensus 25 t~ft~~ql~~Le~~F~~~~~y---p~~~~r~~LA~~l~~~~~ls~~~V~i 71 (162)
..+|..|...|+.+|+.. | |-...-++||..| |++...+..
T Consensus 606 ~~lt~~q~e~l~~a~~~g--yf~~pr~~~~~e~a~~l----~is~~t~~~ 649 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSG--YFEWPRRVEGEELAESM----GISRSTFHQ 649 (665)
T ss_pred hhCCHHHHHHHHHHHHcC--CCCCCccCCHHHHHHHh----CCCHHHHHH
Confidence 479999999999999886 4 7777789999999 999876543
No 201
>PHA02955 hypothetical protein; Provisional
Probab=22.11 E-value=1.1e+02 Score=24.69 Aligned_cols=44 Identities=11% Similarity=0.099 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhh
Q 031304 29 PAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNR 76 (162)
Q Consensus 29 ~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNR 76 (162)
..++..|-+.|...-.-.+..++.++|++| |+....|..||.+.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~l----gI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADI----GINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHh----CCChhhccCcccch
Confidence 356666666666551247788999999999 99998788999774
No 202
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=21.90 E-value=1.3e+02 Score=21.49 Aligned_cols=39 Identities=18% Similarity=0.321 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhH
Q 031304 27 PTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 77 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR 77 (162)
+++.++..+.+.+.-. ....|.-| |++...|+.|=|+|+
T Consensus 44 ls~~eIk~iRe~~~lS--------Q~vFA~~L----~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 44 LSPTEIKAIREKLGLS--------QPVFARYL----GVSVSTVRKWEQGRK 82 (104)
T ss_pred CCHHHHHHHHHHhCCC--------HHHHHHHH----CCCHHHHHHHHcCCc
Confidence 6666677776655443 23456666 999999999999876
No 203
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=21.79 E-value=1.5e+02 Score=23.71 Aligned_cols=32 Identities=28% Similarity=0.289 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhcCCCccchhhhhhhhHHHHHHhhc
Q 031304 50 KIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQS 85 (162)
Q Consensus 50 ~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr~~~ 85 (162)
.-.+||..| |+++..|+.+...-|.+-|....
T Consensus 134 S~~EIAe~L----giS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 134 SIADIAKVC----SVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred CHHHHHHHH----CcCHHHHHHHHHHHHHHHHHHHH
Confidence 356677888 99999999998877766665443
No 204
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=21.46 E-value=98 Score=24.28 Aligned_cols=40 Identities=10% Similarity=0.137 Sum_probs=32.1
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHH
Q 031304 34 ILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARL 80 (162)
Q Consensus 34 ~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~ 80 (162)
.-...|.... |- ....+||+.. |++...|..+|.+|..=.
T Consensus 21 aA~~lF~~~G-y~--~s~~~IA~~A----Gvsk~tiy~~F~sKe~L~ 60 (225)
T PRK11552 21 AALAQFGEYG-LH--ATTRDIAAQA----GQNIAAITYYFGSKEDLY 60 (225)
T ss_pred HHHHHHHHhC-cc--CCHHHHHHHh----CCCHHHHHHHcCCHHHHH
Confidence 3344588885 66 6788899999 999999999999987754
No 205
>PF13730 HTH_36: Helix-turn-helix domain
Probab=21.39 E-value=1.7e+02 Score=17.21 Aligned_cols=43 Identities=12% Similarity=0.123 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHhhc--CCCCCHHHHHHHHHHHHHhcCCCccchhhhhh
Q 031304 27 PTPAQLQILEHVYDEC--KGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 74 (162)
Q Consensus 27 ft~~ql~~Le~~F~~~--~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFq 74 (162)
+++.++.++-..+... ... ..+....||..+ |++.+.|+.+..
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~----g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDL----GVSRRTVQRAIK 47 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHH----CcCHHHHHHHHH
Confidence 4555555554443221 112 334577888899 999999988764
No 206
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=21.37 E-value=85 Score=23.84 Aligned_cols=39 Identities=10% Similarity=0.226 Sum_probs=30.2
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHH
Q 031304 34 ILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 78 (162)
Q Consensus 34 ~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~ 78 (162)
.....|.... .......+||+.. |++...+..+|.+|-.
T Consensus 19 aa~~lf~~~G--~~~~ti~~Ia~~a----gvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 19 TAIAQFALRG--VSNTTLNDIADAA----NVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHcC--cccCCHHHHHHHc----CCCHHHHHHHcCCHHH
Confidence 3444577764 4556678889999 9999999999999876
No 207
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=20.59 E-value=1.2e+02 Score=22.34 Aligned_cols=34 Identities=15% Similarity=0.186 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHHHHH
Q 031304 45 TPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82 (162)
Q Consensus 45 yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k~kr 82 (162)
|......++||..+ |++...|+.+...=|.+.++
T Consensus 139 ~~~g~s~~eIA~~l----~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 139 HYYGYTYEEIAKML----NIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hhcCCCHHHHHHHH----CCChhHHHHHHHHHHHHHHH
Confidence 33444567788888 99999999988766666554
No 208
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=20.53 E-value=87 Score=23.55 Aligned_cols=38 Identities=13% Similarity=0.253 Sum_probs=29.5
Q ss_pred HHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHHH
Q 031304 36 EHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79 (162)
Q Consensus 36 e~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~k 79 (162)
...|.+.. .......+||+.. |++...+...|.|+-.=
T Consensus 18 ~~lf~e~G--~~~~s~~~IA~~a----gvs~~~lY~hF~sKe~L 55 (202)
T TIGR03613 18 LDTFSRFG--FHGTSLEQIAELA----GVSKTNLLYYFPSKDAL 55 (202)
T ss_pred HHHHHHhC--cccCCHHHHHHHh----CCCHHHHHHHcCCHHHH
Confidence 33477773 5566677889999 99999999999997543
No 209
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=20.06 E-value=1.4e+02 Score=22.33 Aligned_cols=39 Identities=13% Similarity=0.097 Sum_probs=30.5
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhhhHH
Q 031304 34 ILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRA 78 (162)
Q Consensus 34 ~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqNRR~ 78 (162)
.-...|.+.. | ......+||+.. |++...+..+|.||..
T Consensus 16 aA~~lf~e~G-~-~~tSi~~Ia~~a----Gvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 16 AAMRVALAEG-F-AAMTVRRIASEA----QVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHhcC-h-hhccHHHHHHHh----CCCcHHHHHHcCCHHH
Confidence 3344577774 5 556678889999 9999999999999766
No 210
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=20.05 E-value=1.5e+02 Score=23.06 Aligned_cols=39 Identities=10% Similarity=0.101 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHhcCCCccchhhhhhh
Q 031304 26 TPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQN 75 (162)
Q Consensus 26 ~ft~~ql~~Le~~F~~~~~yp~~~~r~~LA~~l~~~~~ls~~~V~iWFqN 75 (162)
.+|+.++++|.-+-+-. .-.++|.+| +++++.|+.-..|
T Consensus 137 ~LT~RE~eVL~lla~G~-------snkeIA~~L----~iS~~TVk~h~~~ 175 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQ-------GTIQISDQM----NIKAKTVSSHKGN 175 (207)
T ss_pred cCCHHHHHHHHHHHcCC-------CHHHHHHHc----CCCHHHHHHHHHH
Confidence 49999999997665433 247789999 9999999987754
Done!