Query 028526
Match_columns 208
No_of_seqs 253 out of 1340
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 12:53:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028526.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028526hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0489 Transcription factor z 99.8 1.4E-19 3E-24 158.3 3.7 65 143-207 156-220 (261)
2 KOG0842 Transcription factor t 99.7 1.7E-18 3.7E-23 153.8 7.4 65 143-207 150-214 (307)
3 KOG0488 Transcription factor B 99.7 1.1E-18 2.5E-23 155.9 4.3 63 144-206 170-232 (309)
4 KOG0484 Transcription factor P 99.7 5.9E-19 1.3E-23 134.0 1.3 66 142-207 13-78 (125)
5 KOG0850 Transcription factor D 99.7 3.1E-18 6.7E-23 145.7 5.3 64 143-206 119-182 (245)
6 KOG0485 Transcription factor N 99.7 3.9E-18 8.5E-23 144.2 5.1 65 141-205 99-163 (268)
7 KOG0487 Transcription factor A 99.7 2.1E-18 4.4E-23 153.3 3.3 63 144-206 233-295 (308)
8 KOG0843 Transcription factor E 99.7 1.1E-17 2.5E-22 137.8 4.1 63 145-207 101-163 (197)
9 KOG0494 Transcription factor C 99.7 3.3E-17 7.2E-22 141.7 4.9 62 146-207 140-202 (332)
10 PF00046 Homeobox: Homeobox do 99.7 5.3E-17 1.1E-21 110.0 4.6 57 147-203 1-57 (57)
11 KOG0492 Transcription factor M 99.7 6.4E-17 1.4E-21 136.1 4.1 64 143-206 141-204 (246)
12 KOG2251 Homeobox transcription 99.6 1.7E-16 3.6E-21 134.5 4.4 65 143-207 34-98 (228)
13 KOG0493 Transcription factor E 99.6 8.5E-16 1.8E-20 133.2 7.7 59 146-204 246-304 (342)
14 KOG0848 Transcription factor C 99.6 1.1E-16 2.5E-21 138.8 2.1 62 146-207 199-260 (317)
15 KOG0483 Transcription factor H 99.6 3.2E-16 7E-21 132.0 4.0 62 146-207 50-111 (198)
16 KOG0844 Transcription factor E 99.6 7.5E-16 1.6E-20 135.9 2.2 65 142-206 177-241 (408)
17 smart00389 HOX Homeodomain. DN 99.6 5.3E-15 1.2E-19 99.3 5.3 56 147-202 1-56 (56)
18 cd00086 homeodomain Homeodomai 99.6 6.4E-15 1.4E-19 99.5 5.4 57 148-204 2-58 (59)
19 KOG0491 Transcription factor B 99.5 9.5E-16 2.1E-20 125.0 0.6 62 146-207 100-161 (194)
20 TIGR01565 homeo_ZF_HD homeobox 99.5 1.6E-14 3.4E-19 99.6 4.9 53 146-198 1-57 (58)
21 KOG0486 Transcription factor P 99.5 1.3E-14 2.8E-19 128.4 5.2 62 145-206 111-172 (351)
22 COG5576 Homeodomain-containing 99.5 3.1E-14 6.8E-19 116.1 5.9 66 141-206 46-111 (156)
23 KOG3802 Transcription factor O 99.5 4.2E-14 9E-19 128.7 4.6 62 144-205 292-353 (398)
24 KOG4577 Transcription factor L 99.4 6.9E-14 1.5E-18 122.8 4.4 68 141-208 162-229 (383)
25 KOG0847 Transcription factor, 99.4 1.3E-13 2.9E-18 117.1 2.3 65 141-205 162-226 (288)
26 KOG0490 Transcription factor, 99.3 1.8E-12 4E-17 109.2 2.9 62 144-205 58-119 (235)
27 KOG1168 Transcription factor A 99.1 4.5E-11 9.8E-16 105.3 1.9 64 143-206 306-369 (385)
28 KOG0849 Transcription factor P 99.1 1.3E-10 2.8E-15 106.0 4.4 64 142-205 172-235 (354)
29 KOG0775 Transcription factor S 98.9 1.7E-09 3.8E-14 94.6 4.5 53 153-205 183-235 (304)
30 PF05920 Homeobox_KN: Homeobox 98.5 7.1E-08 1.5E-12 61.7 1.9 34 167-200 7-40 (40)
31 KOG0774 Transcription factor P 98.4 1.2E-07 2.7E-12 82.8 3.2 59 146-204 188-249 (334)
32 KOG2252 CCAAT displacement pro 98.3 6.5E-07 1.4E-11 84.9 5.7 62 140-201 414-475 (558)
33 KOG0490 Transcription factor, 98.1 2E-06 4.4E-11 72.3 3.8 62 143-204 150-211 (235)
34 KOG1146 Homeobox protein [Gene 97.8 1.5E-05 3.2E-10 82.0 3.8 60 146-205 903-962 (1406)
35 PF11569 Homez: Homeodomain le 97.2 0.00017 3.8E-09 49.3 1.9 42 158-199 10-51 (56)
36 KOG0773 Transcription factor M 96.9 0.00074 1.6E-08 60.9 3.2 58 146-203 239-299 (342)
37 KOG3623 Homeobox transcription 95.7 0.011 2.3E-07 58.6 3.9 48 158-205 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 93.6 0.16 3.4E-06 34.0 4.4 47 147-198 1-47 (53)
39 PF04618 HD-ZIP_N: HD-ZIP prot 93.3 0.4 8.7E-06 37.2 6.8 17 95-112 88-104 (111)
40 PF04545 Sigma70_r4: Sigma-70, 77.6 2.6 5.7E-05 27.0 2.7 46 152-202 4-49 (50)
41 cd06171 Sigma70_r4 Sigma70, re 73.6 3.3 7.2E-05 25.5 2.3 44 153-201 11-54 (55)
42 KOG1146 Homeobox protein [Gene 68.9 5.9 0.00013 42.2 4.1 60 146-205 705-764 (1406)
43 PF01527 HTH_Tnp_1: Transposas 68.6 2.7 5.9E-05 29.0 1.1 46 148-197 2-47 (76)
44 PF08281 Sigma70_r4_2: Sigma-7 66.9 8.2 0.00018 24.9 3.2 43 153-200 11-53 (54)
45 cd00569 HTH_Hin_like Helix-tur 66.5 13 0.00028 20.2 3.7 37 153-194 6-42 (42)
46 KOG3623 Homeobox transcription 63.6 6.3 0.00014 39.9 2.9 59 146-204 626-684 (1007)
47 PF04967 HTH_10: HTH DNA bindi 63.1 9.4 0.0002 25.7 2.9 40 153-192 1-42 (53)
48 PRK03975 tfx putative transcri 61.5 12 0.00026 30.1 3.8 49 150-204 4-52 (141)
49 PF09607 BrkDBD: Brinker DNA-b 61.0 13 0.00028 25.7 3.3 44 150-195 3-47 (58)
50 PRK09413 IS2 repressor TnpA; R 56.7 23 0.00049 27.2 4.5 45 148-196 8-52 (121)
51 PF10668 Phage_terminase: Phag 56.0 6.2 0.00013 27.3 1.1 20 176-195 25-44 (60)
52 PHA03308 transcriptional regul 53.2 10 0.00022 38.6 2.4 17 144-160 1292-1308(1463)
53 PRK06759 RNA polymerase factor 52.7 18 0.00039 27.9 3.4 47 152-203 106-152 (154)
54 PRK09646 RNA polymerase sigma 50.2 20 0.00044 29.1 3.5 48 152-204 142-189 (194)
55 PRK12526 RNA polymerase sigma 48.3 20 0.00044 29.6 3.2 47 153-204 154-200 (206)
56 PF00424 REV: REV protein (ant 48.2 12 0.00026 28.1 1.6 36 158-207 14-49 (91)
57 PF00196 GerE: Bacterial regul 46.9 26 0.00056 23.0 3.0 45 152-202 3-47 (58)
58 PRK09652 RNA polymerase sigma 46.4 23 0.00049 27.7 3.1 47 152-203 128-174 (182)
59 COG3413 Predicted DNA binding 46.3 24 0.00051 29.7 3.4 49 152-202 155-205 (215)
60 KOG0773 Transcription factor M 43.9 22 0.00048 31.9 3.0 40 165-204 116-155 (342)
61 PF13518 HTH_28: Helix-turn-he 43.7 15 0.00033 23.1 1.4 24 176-199 15-38 (52)
62 PRK12512 RNA polymerase sigma 43.5 28 0.00061 27.8 3.3 47 153-204 132-178 (184)
63 cd04761 HTH_MerR-SF Helix-Turn 43.3 14 0.0003 23.0 1.1 22 176-197 3-24 (49)
64 smart00421 HTH_LUXR helix_turn 42.8 43 0.00093 20.7 3.5 43 153-201 4-46 (58)
65 PRK12514 RNA polymerase sigma 42.7 33 0.00072 27.2 3.6 47 153-204 130-176 (179)
66 COG4367 Uncharacterized protei 42.5 27 0.00059 26.2 2.7 40 153-192 3-42 (97)
67 TIGR03879 near_KaiC_dom probab 41.9 8.1 0.00017 27.8 -0.1 34 164-197 23-56 (73)
68 TIGR02937 sigma70-ECF RNA poly 41.7 32 0.00069 25.4 3.2 46 153-203 111-156 (158)
69 PRK04217 hypothetical protein; 41.5 34 0.00073 26.4 3.3 48 151-203 41-88 (110)
70 TIGR02989 Sig-70_gvs1 RNA poly 41.3 35 0.00076 26.3 3.5 47 152-203 111-157 (159)
71 PRK09642 RNA polymerase sigma 41.3 31 0.00068 26.8 3.2 47 153-204 107-153 (160)
72 PRK11924 RNA polymerase sigma 41.3 31 0.00067 26.9 3.2 46 153-203 126-171 (179)
73 PRK12519 RNA polymerase sigma 40.4 26 0.00057 28.2 2.7 46 153-203 142-187 (194)
74 PF13443 HTH_26: Cro/C1-type H 40.0 16 0.00034 24.1 1.1 27 175-201 12-38 (63)
75 PRK10072 putative transcriptio 39.5 16 0.00035 27.4 1.2 41 152-199 32-72 (96)
76 PRK00118 putative DNA-binding 38.3 42 0.00091 25.6 3.3 46 153-203 18-63 (104)
77 TIGR02999 Sig-70_X6 RNA polyme 38.1 38 0.00082 26.9 3.2 46 153-203 135-180 (183)
78 PRK09648 RNA polymerase sigma 37.4 39 0.00084 27.2 3.2 48 152-204 139-186 (189)
79 TIGR02985 Sig70_bacteroi1 RNA 37.4 42 0.00092 25.5 3.3 46 153-203 114-159 (161)
80 PF13384 HTH_23: Homeodomain-l 36.7 20 0.00043 22.6 1.1 23 174-196 18-40 (50)
81 TIGR02948 SigW_bacill RNA poly 36.7 35 0.00076 27.1 2.8 48 152-204 136-183 (187)
82 PRK09639 RNA polymerase sigma 36.7 52 0.0011 25.6 3.8 45 153-203 113-157 (166)
83 PRK05602 RNA polymerase sigma 36.5 36 0.00079 27.2 2.9 47 153-204 129-175 (186)
84 PF08280 HTH_Mga: M protein tr 36.5 37 0.00081 22.6 2.5 36 156-195 6-41 (59)
85 PF02796 HTH_7: Helix-turn-hel 36.2 48 0.001 20.8 2.9 37 153-194 6-42 (45)
86 PRK12515 RNA polymerase sigma 36.2 42 0.00091 27.0 3.3 48 152-204 131-178 (189)
87 PRK09644 RNA polymerase sigma 35.8 41 0.00089 26.3 3.1 46 153-203 109-154 (165)
88 TIGR02939 RpoE_Sigma70 RNA pol 35.7 32 0.00069 27.4 2.5 30 175-204 156-185 (190)
89 TIGR02959 SigZ RNA polymerase 35.4 45 0.00098 26.5 3.3 47 152-203 100-146 (170)
90 PRK12541 RNA polymerase sigma 35.3 42 0.00091 26.1 3.1 47 153-204 113-159 (161)
91 PRK12537 RNA polymerase sigma 35.2 51 0.0011 26.4 3.6 46 153-203 134-179 (182)
92 PRK06811 RNA polymerase factor 35.0 49 0.0011 26.7 3.5 49 152-205 131-179 (189)
93 PF11167 DUF2953: Protein of u 34.8 4.1 8.9E-05 26.8 -2.4 19 1-19 3-21 (53)
94 PF06056 Terminase_5: Putative 33.7 26 0.00057 23.8 1.4 26 175-202 15-40 (58)
95 PF13411 MerR_1: MerR HTH fami 33.7 24 0.00052 23.6 1.2 21 176-196 3-23 (69)
96 PF13936 HTH_38: Helix-turn-he 33.7 35 0.00077 21.5 1.9 40 151-195 3-42 (44)
97 TIGR02954 Sig70_famx3 RNA poly 33.3 52 0.0011 25.8 3.3 47 153-204 120-166 (169)
98 smart00027 EH Eps15 homology d 33.3 76 0.0016 22.9 4.0 43 153-195 4-51 (96)
99 PRK09047 RNA polymerase factor 32.7 53 0.0011 25.3 3.2 46 153-203 107-152 (161)
100 PRK12530 RNA polymerase sigma 32.5 51 0.0011 26.7 3.2 47 153-204 135-181 (189)
101 PHA02955 hypothetical protein; 32.4 58 0.0013 28.1 3.6 44 155-198 60-104 (213)
102 PRK12546 RNA polymerase sigma 32.1 48 0.001 27.1 3.0 46 153-203 114-159 (188)
103 cd01392 HTH_LacI Helix-turn-he 31.0 20 0.00042 22.7 0.4 21 178-198 2-22 (52)
104 TIGR02983 SigE-fam_strep RNA p 30.8 56 0.0012 25.3 3.1 47 153-204 111-157 (162)
105 cd06170 LuxR_C_like C-terminal 30.6 76 0.0016 19.6 3.2 41 154-200 2-42 (57)
106 PRK13919 putative RNA polymera 30.6 63 0.0014 25.7 3.4 47 153-204 136-182 (186)
107 cd04762 HTH_MerR-trunc Helix-T 30.1 29 0.00062 20.9 1.1 24 176-199 3-26 (49)
108 PRK09637 RNA polymerase sigma 29.9 60 0.0013 26.2 3.2 46 153-203 107-152 (181)
109 COG2963 Transposase and inacti 29.7 1.1E+02 0.0023 22.9 4.3 44 150-197 5-49 (116)
110 PRK06930 positive control sigm 29.6 60 0.0013 26.6 3.1 47 153-204 115-161 (170)
111 PRK12536 RNA polymerase sigma 29.2 64 0.0014 25.8 3.2 30 175-204 147-176 (181)
112 PRK07037 extracytoplasmic-func 29.2 67 0.0014 24.9 3.3 46 153-203 110-155 (163)
113 PRK06986 fliA flagellar biosyn 28.7 57 0.0012 27.5 3.0 47 153-204 185-231 (236)
114 PRK15369 two component system 28.5 85 0.0018 24.0 3.8 45 152-202 149-193 (211)
115 PRK12524 RNA polymerase sigma 28.5 65 0.0014 26.1 3.2 46 153-203 137-182 (196)
116 PRK12547 RNA polymerase sigma 28.5 68 0.0015 25.2 3.2 46 153-203 113-158 (164)
117 PF01381 HTH_3: Helix-turn-hel 27.9 32 0.0007 21.8 1.1 23 176-198 12-34 (55)
118 PRK12532 RNA polymerase sigma 27.4 69 0.0015 25.8 3.2 47 153-204 137-183 (195)
119 PRK12538 RNA polymerase sigma 27.3 57 0.0012 27.8 2.7 29 176-204 190-218 (233)
120 PRK12518 RNA polymerase sigma 27.3 33 0.00073 27.0 1.2 30 175-204 138-167 (175)
121 TIGR02952 Sig70_famx2 RNA poly 27.2 75 0.0016 24.6 3.3 47 152-203 122-168 (170)
122 PRK12529 RNA polymerase sigma 27.2 76 0.0017 25.3 3.3 47 153-204 128-174 (178)
123 PF00376 MerR: MerR family reg 27.1 36 0.00077 21.0 1.1 20 176-195 2-21 (38)
124 PRK05657 RNA polymerase sigma 26.9 68 0.0015 28.9 3.3 52 152-204 262-313 (325)
125 PRK12533 RNA polymerase sigma 26.8 64 0.0014 27.1 2.9 47 153-204 135-181 (216)
126 cd04764 HTH_MlrA-like_sg1 Heli 26.8 37 0.0008 22.8 1.2 21 176-196 3-23 (67)
127 cd04763 HTH_MlrA-like Helix-Tu 26.8 36 0.00078 23.0 1.2 21 176-196 3-23 (68)
128 PRK12543 RNA polymerase sigma 26.3 79 0.0017 25.2 3.3 46 153-203 118-163 (179)
129 PRK10403 transcriptional regul 26.0 61 0.0013 25.2 2.5 45 152-202 153-197 (215)
130 PRK09649 RNA polymerase sigma 25.8 76 0.0017 25.6 3.1 46 153-203 131-176 (185)
131 PRK08301 sporulation sigma fac 24.7 64 0.0014 27.0 2.6 51 153-204 179-229 (234)
132 TIGR02479 FliA_WhiG RNA polyme 24.7 82 0.0018 26.2 3.2 47 152-203 175-221 (224)
133 PF13551 HTH_29: Winged helix- 24.4 2.2E+02 0.0047 20.3 5.1 47 149-195 54-109 (112)
134 PRK09480 slmA division inhibit 24.4 81 0.0018 24.9 3.0 36 163-199 21-56 (194)
135 TIGR00721 tfx DNA-binding prot 24.3 1.2E+02 0.0026 24.2 3.9 48 150-203 4-51 (137)
136 PRK12545 RNA polymerase sigma 23.9 90 0.0019 25.5 3.2 47 153-204 140-186 (201)
137 TIGR02950 SigM_subfam RNA poly 23.8 42 0.00092 25.7 1.2 32 172-203 120-151 (154)
138 PRK09645 RNA polymerase sigma 23.7 1E+02 0.0022 24.1 3.4 47 153-204 119-165 (173)
139 PRK12516 RNA polymerase sigma 23.6 93 0.002 25.2 3.3 46 153-203 117-162 (187)
140 cd00093 HTH_XRE Helix-turn-hel 23.4 48 0.001 19.6 1.2 23 176-198 15-37 (58)
141 PRK12539 RNA polymerase sigma 23.3 99 0.0022 24.7 3.4 46 153-203 132-177 (184)
142 TIGR03070 couple_hipB transcri 23.2 47 0.001 20.8 1.2 23 176-198 18-40 (58)
143 TIGR02947 SigH_actino RNA poly 23.0 46 0.00099 26.9 1.3 30 175-204 149-178 (193)
144 COG1905 NuoE NADH:ubiquinone o 23.0 1.2E+02 0.0025 25.1 3.6 36 155-190 25-60 (160)
145 PRK10360 DNA-binding transcrip 22.9 78 0.0017 24.5 2.6 44 152-201 137-180 (196)
146 PRK12523 RNA polymerase sigma 22.8 1E+02 0.0022 24.2 3.3 46 153-203 120-165 (172)
147 PRK12542 RNA polymerase sigma 22.7 95 0.0021 24.8 3.1 46 153-203 123-168 (185)
148 TIGR02859 spore_sigH RNA polym 22.7 46 0.00099 26.7 1.2 30 174-203 166-195 (198)
149 TIGR02943 Sig70_famx1 RNA poly 22.6 99 0.0021 25.0 3.2 47 153-204 132-178 (188)
150 PRK12531 RNA polymerase sigma 22.4 1E+02 0.0022 24.9 3.3 47 153-204 142-188 (194)
151 PRK12544 RNA polymerase sigma 22.3 98 0.0021 25.6 3.2 47 153-204 149-195 (206)
152 PRK08583 RNA polymerase sigma 22.2 96 0.0021 26.4 3.2 48 152-204 205-252 (257)
153 PRK09651 RNA polymerase sigma 22.1 74 0.0016 25.2 2.3 46 153-203 120-165 (172)
154 TIGR02980 SigBFG RNA polymeras 22.1 1E+02 0.0022 25.6 3.2 47 152-203 178-224 (227)
155 TIGR03001 Sig-70_gmx1 RNA poly 21.8 98 0.0021 26.6 3.2 29 176-204 180-208 (244)
156 PRK12520 RNA polymerase sigma 21.8 1.1E+02 0.0023 24.6 3.2 47 153-204 132-178 (191)
157 PRK12511 RNA polymerase sigma 21.7 1.1E+02 0.0023 24.8 3.3 46 153-203 112-157 (182)
158 cd01104 HTH_MlrA-CarA Helix-Tu 21.5 52 0.0011 21.8 1.2 21 176-196 3-23 (68)
159 cd00131 PAX Paired Box domain 21.4 2.8E+02 0.006 21.5 5.4 46 152-197 75-127 (128)
160 PRK09647 RNA polymerase sigma 21.2 1.1E+02 0.0024 25.3 3.3 28 176-203 157-184 (203)
161 PRK12535 RNA polymerase sigma 21.1 1.1E+02 0.0023 25.1 3.2 47 153-204 134-180 (196)
162 PRK09641 RNA polymerase sigma 21.0 1E+02 0.0023 24.3 3.0 47 153-204 137-183 (187)
163 TIGR02941 Sigma_B RNA polymera 20.9 1E+02 0.0022 26.2 3.1 47 152-203 205-251 (255)
164 PRK12513 RNA polymerase sigma 20.9 51 0.0011 26.5 1.2 30 175-204 157-186 (194)
165 PRK07670 RNA polymerase sigma 20.8 1.1E+02 0.0023 26.2 3.2 46 153-203 202-247 (251)
166 PRK12522 RNA polymerase sigma 20.7 1.2E+02 0.0026 23.9 3.3 28 176-203 138-165 (173)
167 COG2944 Predicted transcriptio 20.6 97 0.0021 23.8 2.6 40 153-199 44-83 (104)
168 TIGR01764 excise DNA binding d 20.4 57 0.0012 19.7 1.1 23 176-198 4-26 (49)
169 PRK10651 transcriptional regul 20.4 1.4E+02 0.0029 23.2 3.5 45 152-202 155-199 (216)
No 1
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.77 E-value=1.4e-19 Score=158.27 Aligned_cols=65 Identities=31% Similarity=0.519 Sum_probs=61.0
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 143 ~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
.++.||.||.||..|+.+||+.|..|+|+++..|.+||..|+|+++||||||||||+||||..+.
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~ 220 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA 220 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence 35578999999999999999999999999999999999999999999999999999999987653
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.75 E-value=1.7e-18 Score=153.77 Aligned_cols=65 Identities=31% Similarity=0.520 Sum_probs=59.8
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 143 ~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
..++||.|..|+..|..+||+.|++++|++..||+.||..|.|+++||||||||||-|.||++++
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence 34456667779999999999999999999999999999999999999999999999999998875
No 3
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.74 E-value=1.1e-18 Score=155.86 Aligned_cols=63 Identities=27% Similarity=0.422 Sum_probs=59.5
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccccc
Q 028526 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQD 206 (208)
Q Consensus 144 ~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~ 206 (208)
+++|+.||.||..|+..||+.|++.+|++..+|++||+.|||+..||++||||||+||||+..
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 556777999999999999999999999999999999999999999999999999999999754
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.73 E-value=5.9e-19 Score=133.99 Aligned_cols=66 Identities=29% Similarity=0.432 Sum_probs=61.4
Q ss_pred ccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 142 ~~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
+..++||-||.|+..|+.+||+.|...+||++..|++||.++.|++..|||||||||+|.||+++-
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 345678889999999999999999999999999999999999999999999999999999998753
No 5
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.73 E-value=3.1e-18 Score=145.71 Aligned_cols=64 Identities=30% Similarity=0.447 Sum_probs=59.2
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccccc
Q 028526 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQD 206 (208)
Q Consensus 143 ~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~ 206 (208)
.+|.|+.||.|+.-||..|.+.|++++|+-..||.+||..|||+.+||||||||||.|.||..+
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3445667999999999999999999999999999999999999999999999999999999665
No 6
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.72 E-value=3.9e-18 Score=144.24 Aligned_cols=65 Identities=28% Similarity=0.449 Sum_probs=60.7
Q ss_pred CccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 141 ~~~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
-.+.++||.||+|+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.||||+.
T Consensus 99 ~g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 99 LGDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 34556788899999999999999999999999999999999999999999999999999999974
No 7
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.72 E-value=2.1e-18 Score=153.30 Aligned_cols=63 Identities=33% Similarity=0.493 Sum_probs=59.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccccc
Q 028526 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQD 206 (208)
Q Consensus 144 ~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~ 206 (208)
+..||||..+|+.|+.+||+.|..|.|++.+.|.+|++.|+|++|||||||||||+|+||..+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 557888999999999999999999999999999999999999999999999999999999654
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.69 E-value=1.1e-17 Score=137.79 Aligned_cols=63 Identities=33% Similarity=0.496 Sum_probs=60.3
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 145 VNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 145 ~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
+.||.||.|+.+|+..||..|+.++|....+|+.||+.|+|++.||+|||||||.|.||.+.+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 578889999999999999999999999999999999999999999999999999999998765
No 9
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.67 E-value=3.3e-17 Score=141.73 Aligned_cols=62 Identities=29% Similarity=0.463 Sum_probs=57.9
Q ss_pred CCCC-CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 146 NARK-KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 146 ~rr~-Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
+||. ||.||..|+..||+.|+..+||+...|+.||.++.|.+..|+|||||||+||||.+++
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 4444 8999999999999999999999999999999999999999999999999999998764
No 10
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.67 E-value=5.3e-17 Score=109.99 Aligned_cols=57 Identities=42% Similarity=0.642 Sum_probs=55.0
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 147 rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
||+|+.|+.+|+.+|+..|..++||+..+++.||..+||+..+|++||+|||+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578899999999999999999999999999999999999999999999999999986
No 11
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.65 E-value=6.4e-17 Score=136.07 Aligned_cols=64 Identities=31% Similarity=0.511 Sum_probs=59.9
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccccc
Q 028526 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQD 206 (208)
Q Consensus 143 ~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~ 206 (208)
....|+.|+.|+.+|+..||+.|+..+|+++.+|.+++..|.|++.||+|||||||+|.||.|.
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 4446788999999999999999999999999999999999999999999999999999999664
No 12
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.63 E-value=1.7e-16 Score=134.50 Aligned_cols=65 Identities=31% Similarity=0.456 Sum_probs=61.1
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 143 ~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
.++.||.||.|+-.|+.+||..|.+.+||+...|++||.+|+|.+.+|||||.|||+|+|+++..
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 35578899999999999999999999999999999999999999999999999999999997753
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.62 E-value=8.5e-16 Score=133.17 Aligned_cols=59 Identities=32% Similarity=0.565 Sum_probs=56.7
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.||.||.|+.+||..|+..|+.++|++...|++||.+|+|.+.||+|||||+|+|.||-
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 47889999999999999999999999999999999999999999999999999999984
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.62 E-value=1.1e-16 Score=138.81 Aligned_cols=62 Identities=34% Similarity=0.485 Sum_probs=57.3
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
+-|.|.+++..|..+||+.|..++|.++..+.+||..|+|++|||||||||||+|+||..++
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 45568889999999999999999999999999999999999999999999999999985543
No 15
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.61 E-value=3.2e-16 Score=132.01 Aligned_cols=62 Identities=50% Similarity=0.766 Sum_probs=58.1
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
..+++.+|+.+|...||..|+.+.++.+.++..||+.|||.+|||.|||||||||||.+|++
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 45566689999999999999999999999999999999999999999999999999999876
No 16
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.56 E-value=7.5e-16 Score=135.94 Aligned_cols=65 Identities=32% Similarity=0.424 Sum_probs=61.3
Q ss_pred ccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccccc
Q 028526 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQD 206 (208)
Q Consensus 142 ~~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~ 206 (208)
.+.+-||.||.|+.+|+..||+.|-+..|.++..|.+||..|+|++..|||||||||+|+||+..
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 45567999999999999999999999999999999999999999999999999999999999864
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.56 E-value=5.3e-15 Score=99.26 Aligned_cols=56 Identities=41% Similarity=0.665 Sum_probs=52.6
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhc
Q 028526 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFH 202 (208)
Q Consensus 147 rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~K 202 (208)
++.|+.|+.+|+.+|+..|..++||+..++..||..+||+..+|+.||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35677899999999999999999999999999999999999999999999999865
No 18
>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=99.55 E-value=6.4e-15 Score=99.45 Aligned_cols=57 Identities=40% Similarity=0.662 Sum_probs=54.2
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 148 RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 148 r~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+.|..|+..|+.+|+..|..++||+..+++.||..+||+..+|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567789999999999999999999999999999999999999999999999998874
No 19
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.54 E-value=9.5e-16 Score=124.98 Aligned_cols=62 Identities=31% Similarity=0.475 Sum_probs=58.6
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
+++-|++|+..|+..|++.|+..+|++..+|.+||..|+|++.||+.||||||+|-||+++.
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 56679999999999999999999999999999999999999999999999999999998754
No 20
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.51 E-value=1.6e-14 Score=99.58 Aligned_cols=53 Identities=13% Similarity=0.360 Sum_probs=50.9
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCccchhhhhchhh
Q 028526 146 NARKKLRLTKEQSALLEESFKQHST----LNPKQKQALARQLNLRPRQVEVWFQNRR 198 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~~~~y----Ps~~~r~~LA~~lgLs~rqVqvWFQNRR 198 (208)
+||.||.|+.+|+..|+..|..++| |+..++++||..+||++++|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3788999999999999999999999 9999999999999999999999999975
No 21
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.51 E-value=1.3e-14 Score=128.40 Aligned_cols=62 Identities=27% Similarity=0.450 Sum_probs=59.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccccc
Q 028526 145 VNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQD 206 (208)
Q Consensus 145 ~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~ 206 (208)
++||.|+.|+.+|+.+||..|++++||+...|++||...+|++..|+|||.|||+||||++.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 56778999999999999999999999999999999999999999999999999999999864
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.49 E-value=3.1e-14 Score=116.06 Aligned_cols=66 Identities=30% Similarity=0.451 Sum_probs=60.3
Q ss_pred CccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccccc
Q 028526 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQD 206 (208)
Q Consensus 141 ~~~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~ 206 (208)
+.....+++|++.+..|+.+|++.|..++||+...|..|+..++|+++-|||||||||++.|+...
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 344557888999999999999999999999999999999999999999999999999999998643
No 23
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.46 E-value=4.2e-14 Score=128.69 Aligned_cols=62 Identities=23% Similarity=0.374 Sum_probs=58.9
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 144 ~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
+++||+||.|.......||..|.+|+.|+.+|+..||.+|+|.+.+|+|||||||+|+||-.
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 46788999999999999999999999999999999999999999999999999999999853
No 24
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.44 E-value=6.9e-14 Score=122.81 Aligned_cols=68 Identities=29% Similarity=0.466 Sum_probs=62.9
Q ss_pred CccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccccccC
Q 028526 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDKA 208 (208)
Q Consensus 141 ~~~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~a 208 (208)
+.++..||.||.++..|++.|+..|+..+.|-+..|++|+.++||..|.|||||||||||+||-++.|
T Consensus 162 ~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 162 EGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred ccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 34566899999999999999999999999999999999999999999999999999999999977654
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.38 E-value=1.3e-13 Score=117.07 Aligned_cols=65 Identities=32% Similarity=0.508 Sum_probs=60.4
Q ss_pred CccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 141 ~~~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
+.+++++..|..|+-.|+..||..|+..+|+-..+|.+||..+|+++.||+|||||||.||||+-
T Consensus 162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 45677777788899999999999999999999999999999999999999999999999999864
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.27 E-value=1.8e-12 Score=109.18 Aligned_cols=62 Identities=27% Similarity=0.243 Sum_probs=59.1
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 144 ~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
.++|+.|+.|+..|+.+|++.|...+||+...++.||..+++++..|+|||||||+||++++
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 45788999999999999999999999999999999999999999999999999999999876
No 27
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.06 E-value=4.5e-11 Score=105.29 Aligned_cols=64 Identities=25% Similarity=0.422 Sum_probs=59.9
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccccc
Q 028526 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQD 206 (208)
Q Consensus 143 ~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~ 206 (208)
.+.+||+||.+.....+.||.+|...+.|+.+.+..||.+|+|.+..|+|||||+|+|.||.+.
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 4558899999999999999999999999999999999999999999999999999999998754
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.05 E-value=1.3e-10 Score=105.99 Aligned_cols=64 Identities=28% Similarity=0.437 Sum_probs=59.7
Q ss_pred ccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 142 ~~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
.+.+.+|.|+.|+..|+..|++.|+.++||....|+.||.++++++..|+|||+|||++++|..
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3455677799999999999999999999999999999999999999999999999999999976
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.87 E-value=1.7e-09 Score=94.60 Aligned_cols=53 Identities=30% Similarity=0.464 Sum_probs=49.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
|...-..+|.++|..++||++.++.+||+.+||+..||-.||.|||+|+|-.+
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence 66677889999999999999999999999999999999999999999999543
No 30
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.47 E-value=7.1e-08 Score=61.69 Aligned_cols=34 Identities=29% Similarity=0.524 Sum_probs=29.1
Q ss_pred hCCCCCHHHHHHHHHHhCCCccchhhhhchhhhh
Q 028526 167 QHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAS 200 (208)
Q Consensus 167 ~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (208)
.++||+.++++.||.++||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999999975
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.44 E-value=1.2e-07 Score=82.77 Aligned_cols=59 Identities=29% Similarity=0.477 Sum_probs=54.9
Q ss_pred CCCCCccCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 146 NARKKLRLTKEQSALLEESFK---QHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~---~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.+|+|..|++....+|..+|. .++||+.+.+++||++++++..||-.||-|.|-++||-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 577888999999999999997 48899999999999999999999999999999999873
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.34 E-value=6.5e-07 Score=84.86 Aligned_cols=62 Identities=24% Similarity=0.317 Sum_probs=56.9
Q ss_pred CCccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhh
Q 028526 140 EDEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASF 201 (208)
Q Consensus 140 ~~~~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~ 201 (208)
.+...+.||.|.+|+..|.+.|..+|+.+++|+.+..+.|+.+|+|....|..||-|-|.|.
T Consensus 414 ~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 414 DDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 44555678889999999999999999999999999999999999999999999999988874
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.13 E-value=2e-06 Score=72.34 Aligned_cols=62 Identities=29% Similarity=0.504 Sum_probs=57.7
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 143 ~~~~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
..+.++.|+.+...|+..|...|....+|....++.|+..++++.+.|++||||+|++.++.
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 34567788999999999999999999999999999999999999999999999999999875
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.81 E-value=1.5e-05 Score=82.02 Aligned_cols=60 Identities=20% Similarity=0.342 Sum_probs=57.1
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
+|++|++++..|+.++..+|....||...+.+.|...+++..+.|++||||.|+|.|+..
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 677899999999999999999999999999999999999999999999999999998854
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.24 E-value=0.00017 Score=49.30 Aligned_cols=42 Identities=24% Similarity=0.422 Sum_probs=31.5
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhh
Q 028526 158 SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA 199 (208)
Q Consensus 158 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRa 199 (208)
+..|+++|..++++...+...|+.+.+|+..||+.||--|+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999999999999999999999999999999976654
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.89 E-value=0.00074 Score=60.91 Aligned_cols=58 Identities=29% Similarity=0.359 Sum_probs=49.0
Q ss_pred CCCCCccCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 146 NARKKLRLTKEQSALLEESFKQ---HSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~~---~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
..|.+..+......+|+.+... .+||+..++..||.++||+..||..||-|.|.|..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 4445557999999999988443 579999999999999999999999999999987654
No 37
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=95.69 E-value=0.011 Score=58.59 Aligned_cols=48 Identities=19% Similarity=0.345 Sum_probs=44.6
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 158 SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 158 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
+.+|..+|..+..|+.++...+|.+.||+.+.|+.||+++++....-+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 778999999999999999999999999999999999999999887644
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.63 E-value=0.16 Score=34.02 Aligned_cols=47 Identities=21% Similarity=0.350 Sum_probs=34.5
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhh
Q 028526 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (208)
Q Consensus 147 rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRR 198 (208)
+|+|..+|-++...+-..++... ....||..+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46788899988777777777655 477899999999999999998854
No 39
>PF04618 HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR006712 Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events []. This domain is the N-terminal of plant homeobox-leucine zipper proteins. Its function is unknown.; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=93.27 E-value=0.4 Score=37.20 Aligned_cols=17 Identities=35% Similarity=0.331 Sum_probs=11.1
Q ss_pred hcCCCCCCCCCCCCCCCC
Q 028526 95 ILNRQASPHSAVSNSFSS 112 (208)
Q Consensus 95 ~l~~~sSp~S~~S~s~ss 112 (208)
+....+||.|++| +.|.
T Consensus 88 Ee~gvSSPNStiS-S~sg 104 (111)
T PF04618_consen 88 EEAGVSSPNSTIS-SVSG 104 (111)
T ss_pred ccccccCCCccce-eccc
Confidence 3356788888887 4443
No 40
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=77.60 E-value=2.6 Score=27.05 Aligned_cols=46 Identities=9% Similarity=0.182 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFH 202 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~K 202 (208)
.+++.+..+|...|... ....++|..+|++...|+.+...-..|.|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 46788889999888322 23678899999999999998876555544
No 41
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=73.63 E-value=3.3 Score=25.46 Aligned_cols=44 Identities=11% Similarity=0.173 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhh
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASF 201 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~ 201 (208)
++..+..++...|... .....+|..+|++...|..|....+.+.
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 5677777777776422 2356789999999999999997665543
No 42
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=68.89 E-value=5.9 Score=42.20 Aligned_cols=60 Identities=18% Similarity=0.265 Sum_probs=54.2
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
.++-|...-.++...|-++|-.+.-|+.+.+..|......+.+++++||+|-|.|.++.+
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 455566777799999999999999999999999999999999999999999999998865
No 43
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=68.58 E-value=2.7 Score=28.98 Aligned_cols=46 Identities=17% Similarity=0.313 Sum_probs=29.0
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchh
Q 028526 148 RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNR 197 (208)
Q Consensus 148 r~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNR 197 (208)
++|..|+.++...+-..+.. .......+|.++||+..+|..|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHHH
Confidence 45677999887766655522 12457789999999999999997543
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=66.89 E-value=8.2 Score=24.88 Aligned_cols=43 Identities=14% Similarity=0.182 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhh
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAS 200 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (208)
+++.+..++...|- ......++|..+|++...|+.|.+.-|.+
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 45556666655543 33456789999999999999999865543
No 45
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=66.46 E-value=13 Score=20.18 Aligned_cols=37 Identities=19% Similarity=0.223 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhh
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWF 194 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWF 194 (208)
++..+...+...|.. .+ ....+|..++++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 566666666666653 22 45678899999998888874
No 46
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=63.60 E-value=6.3 Score=39.85 Aligned_cols=59 Identities=17% Similarity=0.318 Sum_probs=46.1
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 146 ~rr~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+-+.++....++-..|...|..+..++-.+-..++.+|...+..|++||++|+..-+..
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~ 684 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPM 684 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCC
Confidence 34445667777778888888887777777766777778888899999999999877654
No 47
>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=63.09 E-value=9.4 Score=25.66 Aligned_cols=40 Identities=20% Similarity=0.245 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhCCCccchhh
Q 028526 153 LTKEQSALLEESFKQHST--LNPKQKQALARQLNLRPRQVEV 192 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~y--Ps~~~r~~LA~~lgLs~rqVqv 192 (208)
+|..|..+|...|...-| |-.....+||..+|++..-|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 578899999999987554 6566678999999999876554
No 48
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=61.47 E-value=12 Score=30.09 Aligned_cols=49 Identities=18% Similarity=0.091 Sum_probs=37.8
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 150 KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 150 Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
...+++.|..+|...+ .. ....++|..+|++...|+.|.++.+.+.|+.
T Consensus 4 ~~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred ccCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4568899999997732 22 2356899999999999999999877776653
No 49
>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=61.04 E-value=13 Score=25.67 Aligned_cols=44 Identities=30% Similarity=0.388 Sum_probs=22.5
Q ss_pred CccCCHHH-HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 028526 150 KLRLTKEQ-SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (208)
Q Consensus 150 Rt~fs~~Q-l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQ 195 (208)
|..|+... +.+++..+..+. --..+| ..|.++|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNN-CKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TT-TTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccc-hhhhHH-HHHHHhCccHHHHHHHHH
Confidence 44566655 444444443322 111223 349999999999999986
No 50
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=56.69 E-value=23 Score=27.17 Aligned_cols=45 Identities=18% Similarity=0.240 Sum_probs=30.1
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhch
Q 028526 148 RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQN 196 (208)
Q Consensus 148 r~Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQN 196 (208)
++|.+|+.++....-..+..+.+ ...++|.++|++..+|..|.+-
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 34556888875544333333333 3567899999999999999753
No 51
>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=55.98 E-value=6.2 Score=27.33 Aligned_cols=20 Identities=15% Similarity=0.408 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCccchhhhhc
Q 028526 176 KQALARQLNLRPRQVEVWFQ 195 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQ 195 (208)
...||.+||+++.+|+.|=.
T Consensus 25 lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHHHCCCHHHHHHHhh
Confidence 56789999999999999953
No 52
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=53.17 E-value=10 Score=38.58 Aligned_cols=17 Identities=24% Similarity=0.317 Sum_probs=12.9
Q ss_pred CCCCCCCccCCHHHHHH
Q 028526 144 GVNARKKLRLTKEQSAL 160 (208)
Q Consensus 144 ~~~rr~Rt~fs~~Ql~~ 160 (208)
+.+||-|.++..+|...
T Consensus 1292 ~~KKRGRK~LPpe~Ka~ 1308 (1463)
T PHA03308 1292 GGKRRGRQRLPIRDRVY 1308 (1463)
T ss_pred CccccCCCCCChHHhhh
Confidence 34677788899988776
No 53
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=52.66 E-value=18 Score=27.87 Aligned_cols=47 Identities=15% Similarity=0.133 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.+++.+..++...|-.. ....+||..+|++...|+.|...-|.+.|+
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 35666666666554332 236789999999999999999866666654
No 54
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=50.17 E-value=20 Score=29.13 Aligned_cols=48 Identities=13% Similarity=0.090 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.++..+..+|...|-.. ....+||..+|++...|++|...-|.+.|+.
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 36677777776554322 2357899999999999999998777777654
No 55
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=48.29 E-value=20 Score=29.57 Aligned_cols=47 Identities=21% Similarity=0.258 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..+..+|...|-. ....++||..+|++...|+++...-|.+.|+.
T Consensus 154 L~~~~r~vl~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 154 LPEAQQTVVKGVYFQ-----ELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455555555543321 12357899999999999999998777776664
No 56
>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=48.25 E-value=12 Score=28.09 Aligned_cols=36 Identities=17% Similarity=0.292 Sum_probs=19.4
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccccc
Q 028526 158 SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQDK 207 (208)
Q Consensus 158 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q~~ 207 (208)
+.+.+-.|+.++||...--.. | =.|||.+||+++.+
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~Q 49 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHH
Confidence 445556688899997442111 1 14889999887653
No 57
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=46.93 E-value=26 Score=22.99 Aligned_cols=45 Identities=13% Similarity=0.166 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFH 202 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~K 202 (208)
.||+.+..+|.-...- ....++|..+++++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 4788888888766542 23678999999999999999988776654
No 58
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=46.38 E-value=23 Score=27.73 Aligned_cols=47 Identities=11% Similarity=0.033 Sum_probs=34.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.+++.+..+|...|-.. ....++|..+|++...|+.|...-+.+.|+
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36777777776654322 235688999999999999999866666665
No 59
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=46.30 E-value=24 Score=29.66 Aligned_cols=49 Identities=22% Similarity=0.194 Sum_probs=37.3
Q ss_pred cCCHHHHHHHHHHHhhCC--CCCHHHHHHHHHHhCCCccchhhhhchhhhhhc
Q 028526 152 RLTKEQSALLEESFKQHS--TLNPKQKQALARQLNLRPRQVEVWFQNRRASFH 202 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~--yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~K 202 (208)
.+|..|+.+|...|...- ||-.....+||+++|+++..+ |..=|||..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~--~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL--SEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH--HHHHHHHHHH
Confidence 699999999999998655 366677789999999998654 4444555443
No 60
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=43.89 E-value=22 Score=31.93 Aligned_cols=40 Identities=25% Similarity=0.273 Sum_probs=34.9
Q ss_pred HhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 165 FKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 165 F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
-..+.|++..+...++....++..+|.+||-|.|.+.+..
T Consensus 116 ~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 116 HRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 3458899999999999999999999999999998876653
No 61
>PF13518 HTH_28: Helix-turn-helix domain
Probab=43.65 E-value=15 Score=23.12 Aligned_cols=24 Identities=21% Similarity=0.472 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCccchhhhhchhhh
Q 028526 176 KQALARQLNLRPRQVEVWFQNRRA 199 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRRa 199 (208)
..++|.++|++..+|..|.+.-+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 556899999999999999975443
No 62
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=43.52 E-value=28 Score=27.79 Aligned_cols=47 Identities=15% Similarity=0.121 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++...|-.. ..-.+||..+|++...|+.++..-|.+.|+.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5666666666654332 2357899999999999999998888777654
No 63
>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=43.25 E-value=14 Score=23.00 Aligned_cols=22 Identities=14% Similarity=0.176 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCccchhhhhchh
Q 028526 176 KQALARQLNLRPRQVEVWFQNR 197 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNR 197 (208)
..++|+.+|++...|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997654
No 64
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.78 E-value=43 Score=20.68 Aligned_cols=43 Identities=16% Similarity=0.257 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhh
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASF 201 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~ 201 (208)
++..+..++...+. .+ ...++|..++++...|..|.+.-+.+.
T Consensus 4 l~~~e~~i~~~~~~--g~----s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 4 LTPREREVLRLLAE--GL----TNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCHHHHHHHHHHHc--CC----CHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 56777777755332 22 457889999999999999987554443
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=42.73 E-value=33 Score=27.23 Aligned_cols=47 Identities=13% Similarity=0.293 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++...|-. . ...++||..+|++...|+++.+.-|.+.|+.
T Consensus 130 L~~~~r~i~~l~~~~-g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 130 LEKDRAAAVRRAYLE-G----LSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHHHHHc-C----CCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 455555555555421 1 2367899999999999999998777776654
No 66
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.52 E-value=27 Score=26.21 Aligned_cols=40 Identities=23% Similarity=0.300 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhh
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEV 192 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqv 192 (208)
++++|...-...|+.+.-++.-..+++|..|++++..|+.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lek 42 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEK 42 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHH
Confidence 5678888888888888877778889999999998765543
No 67
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=41.87 E-value=8.1 Score=27.78 Aligned_cols=34 Identities=12% Similarity=0.094 Sum_probs=24.6
Q ss_pred HHhhCCCCCHHHHHHHHHHhCCCccchhhhhchh
Q 028526 164 SFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNR 197 (208)
Q Consensus 164 ~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNR 197 (208)
.|...+|.......+||..+|++...|+.|+.+.
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 3444443333456789999999999999999753
No 68
>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=41.73 E-value=32 Score=25.39 Aligned_cols=46 Identities=13% Similarity=0.190 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++...|-. . ....+||..+|++...|..|...-+.+.|+
T Consensus 111 L~~~~~~ii~~~~~~-g----~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLE-G----LSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhc-C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 556666666554432 2 245689999999999999999877666654
No 69
>PRK04217 hypothetical protein; Provisional
Probab=41.47 E-value=34 Score=26.38 Aligned_cols=48 Identities=10% Similarity=0.022 Sum_probs=36.2
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 151 LRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 151 t~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
..++.+|..++...|.... ...+||+.+|++...|...+..-+.+.|.
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3477888877776664332 46779999999999999999877766654
No 70
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=41.34 E-value=35 Score=26.27 Aligned_cols=47 Identities=23% Similarity=0.214 Sum_probs=32.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.+++.+..++...|- ......+||..+|++...|+++...-|.+.|.
T Consensus 111 ~L~~~~r~v~~l~~~-----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-----RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 366666666665442 22246789999999999999998766665543
No 71
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=41.33 E-value=31 Score=26.77 Aligned_cols=47 Identities=15% Similarity=0.150 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++...|-... ...+||..+|++...|++++..-|.+.|+.
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK-----SYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 55555555554432221 246899999999999999998777776654
No 72
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=41.31 E-value=31 Score=26.86 Aligned_cols=46 Identities=13% Similarity=0.130 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++...|-. .....+||..+|++...|..|...-|.+.|+
T Consensus 126 L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 455555555554432 1234789999999999999999877777665
No 73
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=40.35 E-value=26 Score=28.23 Aligned_cols=46 Identities=15% Similarity=0.216 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++...| .......+||..+|++...|+.|+..-|.+.|+
T Consensus 142 L~~~~~~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAY-----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4444555554433 222345789999999999999999877766665
No 74
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=40.02 E-value=16 Score=24.13 Aligned_cols=27 Identities=11% Similarity=0.214 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCccchhhhhchhhhhh
Q 028526 175 QKQALARQLNLRPRQVEVWFQNRRASF 201 (208)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQNRRaK~ 201 (208)
....||+.+|++..+|..|+.++....
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 356789999999999999999874443
No 75
>PRK10072 putative transcriptional regulator; Provisional
Probab=39.54 E-value=16 Score=27.40 Aligned_cols=41 Identities=20% Similarity=0.218 Sum_probs=29.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhh
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA 199 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRa 199 (208)
+.+...+..|..... . ...+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~g----l---TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTG----L---KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcC----C---CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 346666666644322 2 2678999999999999999988764
No 76
>PRK00118 putative DNA-binding protein; Validated
Probab=38.26 E-value=42 Score=25.59 Aligned_cols=46 Identities=15% Similarity=0.147 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
++..|..++...|.... ...+||..+|++...|..|....|.+.|.
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45566666655544322 35679999999999999999876666554
No 77
>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=38.05 E-value=38 Score=26.88 Aligned_cols=46 Identities=22% Similarity=0.177 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|-.. ....++|..+|++...|++..+.-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4555555555443322 134689999999999999999877766655
No 78
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=37.38 E-value=39 Score=27.16 Aligned_cols=48 Identities=17% Similarity=0.084 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.+++.|..++...|-.. ...++||..+|++...|+.+...-|.+.|+.
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 36666667776654432 2367899999999999999997666665543
No 79
>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=37.36 E-value=42 Score=25.49 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
++..+..+|...|-. .+ ...+||..+|++...|+.+...-|.+.|+
T Consensus 114 L~~~~r~il~l~~~~-~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRFE-GK----SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 455555666554421 22 35678999999999999998866666554
No 80
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=36.73 E-value=20 Score=22.63 Aligned_cols=23 Identities=17% Similarity=0.380 Sum_probs=17.3
Q ss_pred HHHHHHHHHhCCCccchhhhhch
Q 028526 174 KQKQALARQLNLRPRQVEVWFQN 196 (208)
Q Consensus 174 ~~r~~LA~~lgLs~rqVqvWFQN 196 (208)
....++|+.+|++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 34678999999999999999853
No 81
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=36.69 E-value=35 Score=27.08 Aligned_cols=48 Identities=10% Similarity=0.145 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.+++.+..++...|-. ....+++|..+|++...|+++++.-|.+.|..
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3566666666554322 23457899999999999999998777776653
No 82
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=36.68 E-value=52 Score=25.57 Aligned_cols=45 Identities=16% Similarity=0.262 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
++..+..+|.-.| ..+ ...+||..+|++...|+.+...-|.+.|+
T Consensus 113 L~~~~r~il~l~~--~g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 113 MTERDRTVLLLRF--SGY----SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666667776666 232 35789999999999999999776666655
No 83
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=36.49 E-value=36 Score=27.23 Aligned_cols=47 Identities=13% Similarity=0.140 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++...|-. .....+||..+|++...|+.+...-|.+.|+.
T Consensus 129 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 129 LPERQREAIVLQYYQ-----GLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred CCHHHHHHhhHHHhc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 455555555554322 12356889999999999999998777777664
No 84
>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=36.48 E-value=37 Score=22.65 Aligned_cols=36 Identities=31% Similarity=0.356 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 028526 156 EQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (208)
Q Consensus 156 ~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQ 195 (208)
.|+..|+-.|. +...+.. +||..++++.+.|+.-..
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 57788888888 6666544 899999999999876543
No 85
>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=36.24 E-value=48 Score=20.83 Aligned_cols=37 Identities=22% Similarity=0.323 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhh
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWF 194 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWF 194 (208)
++.++...+...+... ....+||+.+|++...|..|+
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 5666666666666644 237789999999999888776
No 86
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=36.22 E-value=42 Score=26.99 Aligned_cols=48 Identities=10% Similarity=0.217 Sum_probs=34.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.+++.+..+|...|-.. ....++|..+|++...|++.+..-|.+.|+.
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 36666666666554322 2356889999999999999998777777653
No 87
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=35.79 E-value=41 Score=26.35 Aligned_cols=46 Identities=11% Similarity=0.018 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|- .....++||..+|++...|++|.+.-|.+.|+
T Consensus 109 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 109 LPVIEAQAILLCDV-----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CCHHHHHHHHhHHH-----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45555555544322 12235789999999999999999877776665
No 88
>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=35.68 E-value=32 Score=27.38 Aligned_cols=30 Identities=13% Similarity=0.129 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 175 QKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.-.+||..+|++...|+++...-|.+.|+.
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999998766666653
No 89
>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=35.40 E-value=45 Score=26.47 Aligned_cols=47 Identities=17% Similarity=0.142 Sum_probs=33.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.+++.+..+|.-.|-.. ....+||..+|++...|+++.+.-|.+.|+
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666666554322 235789999999999999998766666655
No 90
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=35.31 E-value=42 Score=26.13 Aligned_cols=47 Identities=15% Similarity=0.060 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..|..+|.-.|-.. ....++|..+|++...|+++...-|.+.|+.
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5555656555543221 2356899999999999999998666666543
No 91
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=35.24 E-value=51 Score=26.37 Aligned_cols=46 Identities=11% Similarity=0.226 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++...|-.. ....+||..+|++...|++|...-|.+.|+
T Consensus 134 L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 134 LEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 5555555555444221 235789999999999999999877766654
No 92
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=34.98 E-value=49 Score=26.69 Aligned_cols=49 Identities=12% Similarity=0.219 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcccc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFLQ 205 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~q 205 (208)
.+++.+..++.-.|-.. ....+||..+|++...|+...+.-|.+.|++.
T Consensus 131 ~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 36666666666544321 23578999999999999999887777776654
No 93
>PF11167 DUF2953: Protein of unknown function (DUF2953); InterPro: IPR021338 This family of proteins has no known function.
Probab=34.79 E-value=4.1 Score=26.83 Aligned_cols=19 Identities=37% Similarity=0.758 Sum_probs=15.4
Q ss_pred CCCCCCCCCcceeeccccc
Q 028526 1 MGFDDGCNTGLVLGLGFAS 19 (208)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~ 19 (208)
+|++|.+.||+..|+--+.
T Consensus 3 ~G~~Daa~Tgi~~G~l~~~ 21 (53)
T PF11167_consen 3 IGLGDAADTGILYGLLWAI 21 (53)
T ss_pred eeccCHHHHHHHHHHHHHH
Confidence 5899999999988876553
No 94
>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=33.68 E-value=26 Score=23.76 Aligned_cols=26 Identities=19% Similarity=0.376 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCCccchhhhhchhhhhhc
Q 028526 175 QKQALARQLNLRPRQVEVWFQNRRASFH 202 (208)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQNRRaK~K 202 (208)
...+||..||++...|..|-+ |-+|.
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 356899999999999999975 44443
No 95
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=33.68 E-value=24 Score=23.62 Aligned_cols=21 Identities=14% Similarity=0.347 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCccchhhhhch
Q 028526 176 KQALARQLNLRPRQVEVWFQN 196 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQN 196 (208)
..++|+.+|++...|+.|=..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999643
No 96
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=33.68 E-value=35 Score=21.49 Aligned_cols=40 Identities=20% Similarity=0.216 Sum_probs=20.4
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhc
Q 028526 151 LRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (208)
Q Consensus 151 t~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQ 195 (208)
..++.++...++..+... .-..+||..+|.+...|..|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 457888888888776533 3456799999999998887764
No 97
>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=33.34 E-value=52 Score=25.80 Aligned_cols=47 Identities=9% Similarity=0.112 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..+..++...|-.. ....++|..+|++...|+++...-|.+.|+.
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5555556665544322 2357899999999999999988777666654
No 98
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=33.27 E-value=76 Score=22.85 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHHhCCCccchhhhhc
Q 028526 153 LTKEQSALLEESFKQ-----HSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~-----~~yPs~~~r~~LA~~lgLs~rqVqvWFQ 195 (208)
++.+|+..|...|.. ..+.+..+...+...++++...|..+|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 577888888888874 3468888888877778888888887774
No 99
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=32.69 E-value=53 Score=25.31 Aligned_cols=46 Identities=9% Similarity=0.034 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|-... ...+||..+|++...|+++...-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 107 LPARQREAFLLRYWEDM-----DVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666655443221 25789999999999999998866666655
No 100
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=32.47 E-value=51 Score=26.69 Aligned_cols=47 Identities=9% Similarity=0.137 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..+..++.-.|-.. ....+||..+|+++..|+++...-|.+.|+.
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555555555554321 2357899999999999999998767666653
No 101
>PHA02955 hypothetical protein; Provisional
Probab=32.37 E-value=58 Score=28.11 Aligned_cols=44 Identities=11% Similarity=0.175 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHhhC-CCCCHHHHHHHHHHhCCCccchhhhhchhh
Q 028526 155 KEQSALLEESFKQH-STLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (208)
Q Consensus 155 ~~Ql~~Le~~F~~~-~yPs~~~r~~LA~~lgLs~rqVqvWFQNRR 198 (208)
..|+..|-+.|... .-++.++|.++++++|+....|..||.+--
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 35667777777654 568889999999999999887899998753
No 102
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=32.05 E-value=48 Score=27.09 Aligned_cols=46 Identities=17% Similarity=-0.002 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..+|.-.|- ......++|..+|++...|+++++.-|.+.|+
T Consensus 114 Lp~~~r~v~~L~~~-----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 114 LPDEQREALILVGA-----SGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred CCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45555555554432 11235689999999999999999877776665
No 103
>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=31.02 E-value=20 Score=22.69 Aligned_cols=21 Identities=14% Similarity=0.188 Sum_probs=19.0
Q ss_pred HHHHHhCCCccchhhhhchhh
Q 028526 178 ALARQLNLRPRQVEVWFQNRR 198 (208)
Q Consensus 178 ~LA~~lgLs~rqVqvWFQNRR 198 (208)
+||..+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999874
No 104
>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=30.83 E-value=56 Score=25.31 Aligned_cols=47 Identities=17% Similarity=0.193 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..+..++...|-. . ...+++|..+|++...|+.+...-|.+.|+.
T Consensus 111 L~~~~r~i~~l~~~~-g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 111 LPARQRAVVVLRYYE-D----LSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CCHHHHHHhhhHHHh-c----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 455566666554422 1 2356789999999999999998877777764
No 105
>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=30.59 E-value=76 Score=19.64 Aligned_cols=41 Identities=17% Similarity=0.228 Sum_probs=26.9
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhh
Q 028526 154 TKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAS 200 (208)
Q Consensus 154 s~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (208)
+..+..++...+ .. ....++|..++++...|+.|...-+.+
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~~~~~~ 42 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLRNIMRK 42 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 344555554433 22 245778999999999999998643433
No 106
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.55 E-value=63 Score=25.69 Aligned_cols=47 Identities=15% Similarity=0.162 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..+..+|.-.|-. ...-++||..+|++...|+.+.+.-|.+.|..
T Consensus 136 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 136 LSPEERRVIEVLYYQ-----GYTHREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 555666666544321 12356889999999999999988766666654
No 107
>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=30.07 E-value=29 Score=20.92 Aligned_cols=24 Identities=17% Similarity=0.451 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCccchhhhhchhhh
Q 028526 176 KQALARQLNLRPRQVEVWFQNRRA 199 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRRa 199 (208)
..++|..+|++...|..|.++.+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999876553
No 108
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=29.94 E-value=60 Score=26.15 Aligned_cols=46 Identities=15% Similarity=0.135 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..+|...|- ......+||..+|++...|+.++..-|.+.|+
T Consensus 107 L~~~~r~i~~l~~~-----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 107 LPEKYAEALRLTEL-----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 55555555554432 12235789999999999999999866666554
No 109
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.72 E-value=1.1e+02 Score=22.87 Aligned_cols=44 Identities=11% Similarity=0.165 Sum_probs=33.5
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-Cccchhhhhchh
Q 028526 150 KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNL-RPRQVEVWFQNR 197 (208)
Q Consensus 150 Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgL-s~rqVqvWFQNR 197 (208)
|.+|+.+....+-+.+....+ ....+|+.+|+ ...++..|-..-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~ 49 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQL 49 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHHH
Confidence 677999987777666655554 57789999996 999999887533
No 110
>PRK06930 positive control sigma-like factor; Validated
Probab=29.63 E-value=60 Score=26.58 Aligned_cols=47 Identities=13% Similarity=0.089 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++.-.|-.. ....++|..+|++...|+.+...-|.+.++.
T Consensus 115 L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 115 LTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 6666666666544222 1356789999999999999998887777654
No 111
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=29.24 E-value=64 Score=25.77 Aligned_cols=30 Identities=13% Similarity=0.026 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 175 QKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
..+++|..+|++...|++....-|.+.|+.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999998777777653
No 112
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=29.19 E-value=67 Score=24.91 Aligned_cols=46 Identities=15% Similarity=0.188 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|-.. ....++|..+|++...|+.+...-|.+.|+
T Consensus 110 L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 110 LPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5556666665544322 125789999999999999987766666655
No 113
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=28.71 E-value=57 Score=27.47 Aligned_cols=47 Identities=9% Similarity=0.130 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++...|... ....+||..+|++...|+.+...-|.+.|+.
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5566666666655322 2357899999999999999998888877764
No 114
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=28.55 E-value=85 Score=24.04 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFH 202 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~K 202 (208)
.++..+..+|.- +..+ + ...++|..++++.+.|+.|.+|=+.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876 3322 2 2578899999999999999998777653
No 115
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.52 E-value=65 Score=26.12 Aligned_cols=46 Identities=11% Similarity=0.108 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|-. . ..-++||..+|++...|+.++..-|.+.|+
T Consensus 137 L~~~~r~i~~L~~~~-g----~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 137 LPERQRQAVVLRHIE-G----LSNPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred CCHHHHHHHHHHHHc-C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 455555555444321 1 225688999999999999999877766665
No 116
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=28.49 E-value=68 Score=25.16 Aligned_cols=46 Identities=9% Similarity=-0.056 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|-.. ....+||..+|++...|+++...-|.+.|.
T Consensus 113 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 113 LSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5555666555543321 235789999999999999999866666554
No 117
>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=27.94 E-value=32 Score=21.85 Aligned_cols=23 Identities=17% Similarity=0.310 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCccchhhhhchhh
Q 028526 176 KQALARQLNLRPRQVEVWFQNRR 198 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRR 198 (208)
..+||..+|++...|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 36899999999999999998855
No 118
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=27.35 E-value=69 Score=25.84 Aligned_cols=47 Identities=6% Similarity=0.053 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..+..++.-.|-.. ....+||..+|++...|+.+...-|.+.|+.
T Consensus 137 L~~~~r~i~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 137 LPENTARVFTLKEILG-----FSSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555555555433211 2257899999999999999998777776653
No 119
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=27.28 E-value=57 Score=27.76 Aligned_cols=29 Identities=17% Similarity=0.228 Sum_probs=24.5
Q ss_pred HHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 176 KQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.++||..+|++...|+++.+.-|.+.|+.
T Consensus 190 ~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 190 NGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999998777776653
No 120
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=27.27 E-value=33 Score=26.98 Aligned_cols=30 Identities=17% Similarity=0.206 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 175 QKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.-+++|..+|++...|++.+..-|++.|+.
T Consensus 138 s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 138 PQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999998777777664
No 121
>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=27.19 E-value=75 Score=24.61 Aligned_cols=47 Identities=19% Similarity=0.128 Sum_probs=31.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.+++.+..+|.-.|-.. ....+||..+|++...|+....--|.+.|+
T Consensus 122 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666666544322 235689999999999999988655555544
No 122
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=27.18 E-value=76 Score=25.33 Aligned_cols=47 Identities=11% Similarity=0.118 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.|..++.-.|-.. ...++||..+|+++..|+.....-+.+.+.+
T Consensus 128 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 128 LRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 6666666666544322 1356899999999999999998777766543
No 123
>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=27.12 E-value=36 Score=21.01 Aligned_cols=20 Identities=20% Similarity=0.389 Sum_probs=15.8
Q ss_pred HHHHHHHhCCCccchhhhhc
Q 028526 176 KQALARQLNLRPRQVEVWFQ 195 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQ 195 (208)
+.++|+.+|++.+.|+.|=+
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 35789999999999999953
No 124
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=26.88 E-value=68 Score=28.90 Aligned_cols=52 Identities=15% Similarity=0.194 Sum_probs=39.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.++..|..+|...|....+ .....++||..+|++...|+.+...-+.+.|+.
T Consensus 262 ~L~~~~R~vl~lrygL~~~-e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGY-EAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred cCCHHHHHHHHHHhccCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4788888888887743322 233467899999999999999998777777664
No 125
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=26.84 E-value=64 Score=27.15 Aligned_cols=47 Identities=15% Similarity=0.067 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..+..+|...|-. .+ ..++||..+|++...|+++...-|.+.|+.
T Consensus 135 Lp~~~R~v~~L~y~e-g~----s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 135 LPVEYREVLVLRELE-DM----SYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred CCHHHHhHhhhHHhc-CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455555555554432 22 256889999999999999998777777664
No 126
>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=26.81 E-value=37 Score=22.79 Aligned_cols=21 Identities=5% Similarity=0.325 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCccchhhhhch
Q 028526 176 KQALARQLNLRPRQVEVWFQN 196 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQN 196 (208)
..++|+.+|++.+.|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999764
No 127
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=26.79 E-value=36 Score=22.99 Aligned_cols=21 Identities=14% Similarity=0.376 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCccchhhhhch
Q 028526 176 KQALARQLNLRPRQVEVWFQN 196 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQN 196 (208)
..++|+.+|++...|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999864
No 128
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=26.28 E-value=79 Score=25.17 Aligned_cols=46 Identities=9% Similarity=0.110 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|-.. ....+||..+|++...|++....-|.+.|+
T Consensus 118 Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 118 LPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555555555443222 235688999999999999999888777766
No 129
>PRK10403 transcriptional regulator NarP; Provisional
Probab=26.02 E-value=61 Score=25.17 Aligned_cols=45 Identities=22% Similarity=0.285 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFH 202 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~K 202 (208)
.++..+..+|...... ..+.+||..++++++.|+++.+|=|.|..
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 4888888888765432 23578899999999999999988777654
No 130
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=25.83 E-value=76 Score=25.55 Aligned_cols=46 Identities=13% Similarity=-0.034 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.|..++.-.|-.. ....+||..+|++...|+++...-|.+.|+
T Consensus 131 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 131 LTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CCHHHhHHhhhHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4455555554433211 225689999999999999999766666654
No 131
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=24.74 E-value=64 Score=27.01 Aligned_cols=51 Identities=12% Similarity=0.131 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++.-.|.... .......++|..+|++...|+.+...-|.+.|+.
T Consensus 179 Lp~~~R~v~~L~y~l~~-~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 179 LSDREKQIMELRFGLNG-GEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CCHHHHHHHHHHhccCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 66667777766652111 1222367889999999999999988777776654
No 132
>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=24.73 E-value=82 Score=26.22 Aligned_cols=47 Identities=11% Similarity=0.154 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.++..+..+|...|-... ...++|..+|++...|+.+...-+.+.|+
T Consensus 175 ~L~~~~r~il~l~y~~~~-----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEEL-----NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 367777777777763322 35789999999999999998766666554
No 133
>PF13551 HTH_29: Winged helix-turn helix
Probab=24.45 E-value=2.2e+02 Score=20.32 Aligned_cols=47 Identities=19% Similarity=0.352 Sum_probs=31.0
Q ss_pred CCccCCHHHHHHHHHHHhhCC-----CCCHHHHHH-H-HHHh--CCCccchhhhhc
Q 028526 149 KKLRLTKEQSALLEESFKQHS-----TLNPKQKQA-L-ARQL--NLRPRQVEVWFQ 195 (208)
Q Consensus 149 ~Rt~fs~~Ql~~Le~~F~~~~-----yPs~~~r~~-L-A~~l--gLs~rqVqvWFQ 195 (208)
.+..++.++...|.+.+..++ ..+...... | .... .++...|..|++
T Consensus 54 ~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 54 PRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 333489999999999998765 344444444 4 3333 467777887774
No 134
>PRK09480 slmA division inhibitor protein; Provisional
Probab=24.37 E-value=81 Score=24.90 Aligned_cols=36 Identities=8% Similarity=0.137 Sum_probs=29.0
Q ss_pred HHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhh
Q 028526 163 ESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA 199 (208)
Q Consensus 163 ~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRa 199 (208)
..|..++. .......||++.|++...+-.+|.|+-.
T Consensus 21 ~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 21 QMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 33544545 7778899999999999999999999753
No 135
>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=24.33 E-value=1.2e+02 Score=24.25 Aligned_cols=48 Identities=19% Similarity=0.150 Sum_probs=36.3
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 150 KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 150 Rt~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.+.++..|..+|.-.+ ..+ ..+++|..+|++...|..|-..-|.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~Gl----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KGL----SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cCC----CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4568888999987742 222 46789999999999999998876666654
No 136
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=23.93 E-value=90 Score=25.55 Aligned_cols=47 Identities=11% Similarity=0.107 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++.-.|-.. ....+||..+|++...|++....-|.+.|+.
T Consensus 140 Lp~~~r~v~~L~~~eg-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 140 LPEQIGRVFMMREFLD-----FEIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4555555555443211 2356889999999999999988777766653
No 137
>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=23.78 E-value=42 Score=25.66 Aligned_cols=32 Identities=19% Similarity=0.145 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 172 NPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 172 s~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.....++||..+|++...|+++..--|.+.|+
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33446789999999999999999866666554
No 138
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=23.65 E-value=1e+02 Score=24.15 Aligned_cols=47 Identities=17% Similarity=0.237 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..+|.-.|-.. ...++||..+|++...|+.+...-|.+.|+.
T Consensus 119 L~~~~r~vl~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG-----WSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5566666666554321 1257899999999999999987666666553
No 139
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=23.63 E-value=93 Score=25.23 Aligned_cols=46 Identities=9% Similarity=-0.043 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
++..+..++.-.|-.. ..-.+||..+|++...|+++...-|.+.|+
T Consensus 117 Lp~~~r~i~~L~~~~g-----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~ 162 (187)
T PRK12516 117 LPDDQREAIILVGASG-----FAYEEAAEICGCAVGTIKSRVNRARQRLQE 162 (187)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455555554433211 124688999999999999999877776665
No 140
>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=23.37 E-value=48 Score=19.61 Aligned_cols=23 Identities=17% Similarity=0.299 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCccchhhhhchhh
Q 028526 176 KQALARQLNLRPRQVEVWFQNRR 198 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRR 198 (208)
...+|..++++...|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35789999999999999998764
No 141
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=23.32 E-value=99 Score=24.70 Aligned_cols=46 Identities=9% Similarity=0.021 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|-. .....+||..+|++...|+.+...-|.+.|+
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 132 LPEKMRLAIQAVKLE-----GLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 566666666654322 2235789999999999999999877766665
No 142
>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=23.15 E-value=47 Score=20.84 Aligned_cols=23 Identities=13% Similarity=0.036 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCccchhhhhchhh
Q 028526 176 KQALARQLNLRPRQVEVWFQNRR 198 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRR 198 (208)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999997764
No 143
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=22.97 E-value=46 Score=26.87 Aligned_cols=30 Identities=10% Similarity=0.045 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 175 QKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
...+||..+|++...|+++...-|.+.|+.
T Consensus 149 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 149 AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999998777776653
No 144
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=22.96 E-value=1.2e+02 Score=25.09 Aligned_cols=36 Identities=22% Similarity=0.250 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccch
Q 028526 155 KEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQV 190 (208)
Q Consensus 155 ~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqV 190 (208)
..-+..|...++...|........+|..|+++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 456788999999999999999999999999997754
No 145
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=22.94 E-value=78 Score=24.55 Aligned_cols=44 Identities=25% Similarity=0.311 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhh
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASF 201 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~ 201 (208)
.+++.+..+|+-...- + .+++||..++++.+.|++..++=|.|.
T Consensus 137 ~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4788888888766542 2 577889999999999999998877764
No 146
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=22.85 E-value=1e+02 Score=24.25 Aligned_cols=46 Identities=11% Similarity=0.097 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|-.. ..-.+||..+|++...|+++...-+.+.+.
T Consensus 120 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 120 LSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455555555443211 234688999999999999999877777654
No 147
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.70 E-value=95 Score=24.77 Aligned_cols=46 Identities=11% Similarity=0.155 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.|-.. ...++||..+|++...|++....-|.+.|+
T Consensus 123 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 123 LNESNRQVFKYKVFYN-----LTYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5556666665443222 235689999999999999998776666655
No 148
>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=22.69 E-value=46 Score=26.70 Aligned_cols=30 Identities=20% Similarity=0.218 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 174 KQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 174 ~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
....+||..+|++...|++++..-|.+.|+
T Consensus 166 ~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 166 KSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999998766666554
No 149
>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=22.56 E-value=99 Score=24.99 Aligned_cols=47 Identities=11% Similarity=0.145 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++.-.|-.. ...++||..+|++...|+++...-|.+.|+.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 132 LPEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5556666665554322 2357899999999999999988766666653
No 150
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=22.35 E-value=1e+02 Score=24.90 Aligned_cols=47 Identities=15% Similarity=0.205 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..+..++.-.|-.. ..-+++|..+|++...|++....-|.+.|+.
T Consensus 142 Lp~~~r~v~~l~~~eg-----~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 142 LPKAQRDVLQAVYLEE-----LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 5555666665443322 2356889999999999999887777666653
No 151
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.31 E-value=98 Score=25.63 Aligned_cols=47 Identities=9% Similarity=0.081 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.|..++.-.|-... ...+||..+|++...|+++.+.-|.+.|+.
T Consensus 149 L~~~~r~v~~L~~~~g~-----s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 149 LPAKYARVFMMREFIEL-----ETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 55555555555443221 246899999999999999998777777664
No 152
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=22.18 E-value=96 Score=26.41 Aligned_cols=48 Identities=8% Similarity=0.169 Sum_probs=34.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.+++.+..+|...|-... ...+||..+|++...|+.|...-+.+.|+.
T Consensus 205 ~L~~~~r~vl~l~~~~g~-----s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIENL-----SQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 366777777776653221 347899999999999999998766666553
No 153
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=22.14 E-value=74 Score=25.20 Aligned_cols=46 Identities=13% Similarity=0.127 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++.-.| .......+||..+|++...|+++...-+.+.+.
T Consensus 120 L~~~~r~i~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 120 LNGKTREAFLLSQ-----LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CCHHHhHHhhhhh-----ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4455555544332 222236789999999999999999766666554
No 154
>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=22.06 E-value=1e+02 Score=25.62 Aligned_cols=47 Identities=15% Similarity=0.224 Sum_probs=34.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.+++.+..++...|-.. ....+||..+|++...|..|...-+.+.|+
T Consensus 178 ~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 47777777777766422 246789999999999999998766665554
No 155
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=21.84 E-value=98 Score=26.60 Aligned_cols=29 Identities=10% Similarity=0.196 Sum_probs=24.8
Q ss_pred HHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 176 KQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
.++||..+|++...|+++...-|.+.|+.
T Consensus 180 ~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~ 208 (244)
T TIGR03001 180 MDRIGAMYQVHRSTVSRWVAQARERLLER 208 (244)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56899999999999999998877766653
No 156
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=21.77 E-value=1.1e+02 Score=24.63 Aligned_cols=47 Identities=9% Similarity=0.075 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.|..++.-.|-.. ....+||..+|++...|++....-|.+.|+.
T Consensus 132 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 132 LPPRTGRVFMMREWLE-----LETEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5555555555543222 2256899999999999999998777766653
No 157
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=21.74 E-value=1.1e+02 Score=24.79 Aligned_cols=46 Identities=22% Similarity=0.124 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
++..+..++.-.|-. . ....+||..+|++...|+++...-|.+.|+
T Consensus 112 Lp~~~R~v~~L~~~e-g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 112 LPEEQRAALHLVAIE-G----LSYQEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred CCHHHHHHHHHHHHc-C----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 556666666554432 1 235689999999999999998766666554
No 158
>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=21.49 E-value=52 Score=21.84 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCccchhhhhch
Q 028526 176 KQALARQLNLRPRQVEVWFQN 196 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQN 196 (208)
..++|+.+|++...++.|-+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999863
No 159
>cd00131 PAX Paired Box domain
Probab=21.41 E-value=2.8e+02 Score=21.49 Aligned_cols=46 Identities=11% Similarity=0.013 Sum_probs=30.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-------Cccchhhhhchh
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNL-------RPRQVEVWFQNR 197 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgL-------s~rqVqvWFQNR 197 (208)
..+..+...++.....++..+..+..++...-++ +...|-.||+++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3456666667766777888877777654334455 777888887653
No 160
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.25 E-value=1.1e+02 Score=25.30 Aligned_cols=28 Identities=14% Similarity=0.210 Sum_probs=23.5
Q ss_pred HHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 176 KQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
..+||..+|++...|+++...-|.+.|+
T Consensus 157 ~~EIA~~Lgis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 157 YEEIAATLGVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5688999999999999999866666655
No 161
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=21.11 E-value=1.1e+02 Score=25.12 Aligned_cols=47 Identities=15% Similarity=0.063 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
+++.+..++.-.|-.. ..-.+||..+|++...|+++...-|.+.|+.
T Consensus 134 Lp~~~r~v~~l~~~~g-----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 134 LPPERREALILTQVLG-----YTYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4555555554443222 2356899999999999999998777766653
No 162
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=21.03 E-value=1e+02 Score=24.26 Aligned_cols=47 Identities=11% Similarity=0.164 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
++..+..+|...|- ....-+++|..+|++...|+.+...-|.+.|+.
T Consensus 137 L~~~~r~il~l~~~-----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 137 LPEKYRTVIVLKYI-----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHhhhHHh-----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44445555543332 223457899999999999999988777766653
No 163
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=20.90 E-value=1e+02 Score=26.20 Aligned_cols=47 Identities=9% Similarity=0.208 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
.+++.+..++...|.... ...+||..+|++...|+.+...-+.+.|+
T Consensus 205 ~L~~~~r~ii~l~~~~g~-----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL-----SQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 366777777777764322 34789999999999999999876666655
No 164
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=20.89 E-value=51 Score=26.54 Aligned_cols=30 Identities=10% Similarity=0.103 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCccchhhhhchhhhhhccc
Q 028526 175 QKQALARQLNLRPRQVEVWFQNRRASFHFL 204 (208)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk~ 204 (208)
...+||..+|++...|+.+...-|.+.|+.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 157 ELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999988777776653
No 165
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=20.81 E-value=1.1e+02 Score=26.16 Aligned_cols=46 Identities=11% Similarity=0.180 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
+++.+..++...|.. .....+||..+|++...|+.++..-|.+.|+
T Consensus 202 L~~~~r~vl~l~~~~-----~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYKE-----ELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 566666666665532 2235789999999999999999877776655
No 166
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=20.73 E-value=1.2e+02 Score=23.86 Aligned_cols=28 Identities=11% Similarity=0.137 Sum_probs=23.3
Q ss_pred HHHHHHHhCCCccchhhhhchhhhhhcc
Q 028526 176 KQALARQLNLRPRQVEVWFQNRRASFHF 203 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRRaK~Kk 203 (208)
-+++|..+|++...|+++...-|.+.|+
T Consensus 138 ~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 138 YKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4689999999999999998866666654
No 167
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=20.60 E-value=97 Score=23.76 Aligned_cols=40 Identities=23% Similarity=0.371 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhh
Q 028526 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA 199 (208)
Q Consensus 153 fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRa 199 (208)
++..++..+.+.+... ....|..||++...|+.|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 7888888888776533 356799999999999999999864
No 168
>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=20.44 E-value=57 Score=19.69 Aligned_cols=23 Identities=13% Similarity=0.082 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhchhh
Q 028526 176 KQALARQLNLRPRQVEVWFQNRR 198 (208)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRR 198 (208)
..++|+.+|++...|..|.++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 45788999999999999986654
No 169
>PRK10651 transcriptional regulator NarL; Provisional
Probab=20.43 E-value=1.4e+02 Score=23.23 Aligned_cols=45 Identities=18% Similarity=0.295 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccchhhhhchhhhhhc
Q 028526 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRASFH 202 (208)
Q Consensus 152 ~fs~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~rqVqvWFQNRRaK~K 202 (208)
.+++.+..+|+-..+ .+ ...++|.+++++.+.|++..+|=|.|..
T Consensus 155 ~Lt~rE~~vl~~l~~--g~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQ--GL----PNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHc--CC----CHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 389999988876542 12 2567789999999999999998877754
Done!