Query psy3400
Match_columns 417
No_of_seqs 350 out of 1645
Neff 5.0
Searched_HMMs 46136
Date Sat Aug 17 00:03:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3400.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3400hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3802|consensus 100.0 5.8E-58 1.3E-62 460.1 17.2 166 199-364 194-361 (398)
2 KOG1168|consensus 100.0 8.8E-41 1.9E-45 323.8 10.0 154 206-359 212-371 (385)
3 PF00157 Pou: Pou domain - N-t 99.9 1.2E-28 2.7E-33 198.2 3.6 75 205-279 1-75 (75)
4 smart00352 POU Found in Pit-Oc 99.9 1.4E-22 3E-27 163.2 5.4 75 205-279 1-75 (75)
5 KOG2252|consensus 99.8 6E-18 1.3E-22 176.8 15.7 146 200-352 319-475 (558)
6 KOG0489|consensus 99.7 1.5E-18 3.2E-23 169.6 4.3 68 295-362 157-224 (261)
7 KOG0487|consensus 99.7 3.6E-18 7.8E-23 169.6 1.7 66 294-359 232-297 (308)
8 KOG0848|consensus 99.7 1.3E-17 2.8E-22 161.5 5.0 89 266-359 173-261 (317)
9 KOG0488|consensus 99.7 1.3E-17 2.9E-22 166.5 2.8 64 295-358 170-233 (309)
10 KOG0842|consensus 99.7 1.9E-17 4.1E-22 164.5 3.4 69 294-362 150-218 (307)
11 KOG0850|consensus 99.7 3E-17 6.4E-22 156.2 3.2 70 291-360 116-185 (245)
12 KOG0484|consensus 99.6 1.5E-16 3.3E-21 135.3 3.0 66 293-358 13-78 (125)
13 KOG2251|consensus 99.6 2.2E-16 4.8E-21 149.6 3.2 67 293-359 33-99 (228)
14 KOG0843|consensus 99.6 3.2E-16 7E-21 144.5 3.3 64 296-359 101-164 (197)
15 KOG0485|consensus 99.6 1.8E-16 3.9E-21 149.8 1.4 66 294-359 101-166 (268)
16 PF00046 Homeobox: Homeobox do 99.6 5.8E-16 1.3E-20 116.8 1.8 57 298-354 1-57 (57)
17 KOG0492|consensus 99.6 1.2E-15 2.5E-20 143.6 2.6 68 292-359 139-206 (246)
18 KOG0494|consensus 99.5 2.8E-15 6E-20 144.9 3.4 65 295-359 138-203 (332)
19 KOG4577|consensus 99.5 3.8E-15 8.2E-20 145.7 3.0 67 294-360 164-230 (383)
20 TIGR01565 homeo_ZF_HD homeobox 99.4 4.3E-14 9.4E-19 109.3 3.2 53 297-349 1-57 (58)
21 KOG0844|consensus 99.4 1.5E-14 3.3E-19 142.4 0.7 66 295-360 179-244 (408)
22 smart00389 HOX Homeodomain. DN 99.4 4.9E-14 1.1E-18 105.3 3.2 56 298-353 1-56 (56)
23 cd00086 homeodomain Homeodomai 99.4 5.6E-14 1.2E-18 105.5 3.5 58 298-355 1-58 (59)
24 COG5576 Homeodomain-containing 99.4 8.7E-14 1.9E-18 127.0 5.3 67 293-359 47-113 (156)
25 KOG0491|consensus 99.4 5.6E-14 1.2E-18 128.2 2.1 65 296-360 99-163 (194)
26 KOG0775|consensus 99.4 4.1E-13 8.9E-18 130.8 8.2 108 253-360 121-239 (304)
27 KOG0493|consensus 99.4 1.4E-13 3E-18 133.4 3.0 63 297-359 246-308 (342)
28 KOG0486|consensus 99.4 2E-13 4.3E-18 135.1 2.0 65 295-359 110-174 (351)
29 KOG0483|consensus 99.3 2.2E-12 4.8E-17 121.8 2.9 60 300-359 53-112 (198)
30 KOG0847|consensus 99.2 3.5E-12 7.6E-17 121.2 1.3 67 293-359 163-229 (288)
31 KOG0490|consensus 99.1 3.5E-11 7.6E-16 112.9 4.9 64 294-357 57-120 (235)
32 KOG0849|consensus 98.9 5.2E-10 1.1E-14 114.1 3.5 66 293-358 172-237 (354)
33 KOG0774|consensus 98.5 1.2E-07 2.5E-12 92.7 5.5 62 298-359 189-253 (334)
34 KOG0490|consensus 98.3 4.3E-07 9.2E-12 85.3 4.5 65 293-357 149-213 (235)
35 PF05920 Homeobox_KN: Homeobox 98.3 3.1E-07 6.7E-12 66.1 1.1 34 318-351 7-40 (40)
36 KOG1146|consensus 97.9 8.2E-06 1.8E-10 93.6 3.7 64 296-359 902-965 (1406)
37 KOG0773|consensus 96.1 0.0026 5.6E-08 64.4 1.7 60 297-356 239-301 (342)
38 PF11569 Homez: Homeodomain le 95.7 0.0028 6E-08 49.1 -0.1 44 309-352 10-53 (56)
39 KOG3623|consensus 95.3 0.01 2.2E-07 65.6 2.5 49 309-357 568-616 (1007)
40 PF04218 CENP-B_N: CENP-B N-te 94.2 0.044 9.5E-07 41.5 2.8 47 298-349 1-47 (53)
41 COG3620 Predicted transcriptio 93.6 0.061 1.3E-06 50.3 3.1 56 217-280 7-62 (187)
42 PF13560 HTH_31: Helix-turn-he 92.5 0.072 1.6E-06 40.9 1.7 40 215-260 1-40 (64)
43 KOG3623|consensus 91.3 0.11 2.3E-06 57.9 1.9 90 269-358 598-687 (1007)
44 TIGR03070 couple_hipB transcri 90.1 0.25 5.5E-06 36.0 2.5 38 215-258 2-39 (58)
45 PHA01976 helix-turn-helix prot 88.5 0.41 9E-06 36.7 2.7 38 215-258 2-39 (67)
46 TIGR00270 conserved hypothetic 85.6 0.85 1.8E-05 42.0 3.5 52 211-268 65-118 (154)
47 PRK06424 transcription factor; 85.2 0.93 2E-05 41.3 3.5 44 211-260 80-123 (144)
48 PRK10856 cytoskeletal protein 84.5 1.3 2.9E-05 45.4 4.7 45 209-259 8-52 (331)
49 PRK09726 antitoxin HipB; Provi 82.2 1.3 2.8E-05 36.4 2.9 40 213-258 10-49 (88)
50 TIGR03830 CxxCG_CxxCG_HTH puta 82.1 1.2 2.7E-05 38.1 2.9 36 218-259 68-103 (127)
51 TIGR01321 TrpR trp operon repr 80.2 2.6 5.7E-05 36.0 4.1 60 206-277 31-92 (94)
52 PF13744 HTH_37: Helix-turn-he 80.0 1.4 3.1E-05 35.6 2.4 41 213-259 16-56 (80)
53 PRK09943 DNA-binding transcrip 79.9 1.6 3.5E-05 40.3 3.0 43 211-259 3-45 (185)
54 PF04545 Sigma70_r4: Sigma-70, 77.8 1.2 2.6E-05 32.6 1.2 47 303-354 4-50 (50)
55 PRK08359 transcription factor; 75.2 2.5 5.3E-05 40.0 2.8 58 209-272 79-138 (176)
56 PRK09706 transcriptional repre 74.6 2.8 6E-05 36.9 2.9 40 214-259 4-43 (135)
57 PF01527 HTH_Tnp_1: Transposas 74.1 0.98 2.1E-05 35.3 -0.1 46 299-348 2-47 (76)
58 PF01381 HTH_3: Helix-turn-hel 73.9 2.3 5.1E-05 31.1 1.9 33 220-258 1-33 (55)
59 PF12844 HTH_19: Helix-turn-he 68.5 2.9 6.2E-05 31.6 1.4 36 218-259 2-37 (64)
60 cd06171 Sigma70_r4 Sigma70, re 68.0 2.5 5.4E-05 29.4 0.9 44 304-352 11-54 (55)
61 PRK10072 putative transcriptio 66.4 3.5 7.5E-05 35.2 1.6 37 217-259 35-71 (96)
62 PRK08154 anaerobic benzoate ca 65.8 4.4 9.4E-05 40.8 2.4 52 211-268 24-77 (309)
63 KOG3755|consensus 65.3 1.9 4E-05 47.6 -0.3 50 309-358 704-760 (769)
64 cd00569 HTH_Hin_like Helix-tur 64.9 5.7 0.00012 24.6 2.1 37 304-345 6-42 (42)
65 cd00131 PAX Paired Box domain 64.7 13 0.00028 32.9 4.9 45 304-348 76-127 (128)
66 KOG1146|consensus 64.4 3.8 8.2E-05 48.8 1.9 65 298-362 445-509 (1406)
67 PF13551 HTH_29: Winged helix- 64.3 12 0.00027 30.6 4.5 71 271-346 29-109 (112)
68 KOG0773|consensus 63.7 8.7 0.00019 39.0 4.2 43 317-359 117-159 (342)
69 PF13565 HTH_32: Homeodomain-l 61.5 20 0.00044 27.9 5.1 40 305-344 32-76 (77)
70 PHA00542 putative Cro-like pro 61.2 7.5 0.00016 31.7 2.6 39 222-266 25-66 (82)
71 PF08281 Sigma70_r4_2: Sigma-7 59.4 6.8 0.00015 28.7 1.9 43 304-351 11-53 (54)
72 PF04967 HTH_10: HTH DNA bindi 58.7 6.4 0.00014 30.1 1.7 40 304-343 1-42 (53)
73 TIGR02612 mob_myst_A mobile my 58.6 6.2 0.00013 36.2 1.8 42 219-266 29-74 (150)
74 PRK03975 tfx putative transcri 57.4 8.8 0.00019 35.0 2.6 50 301-356 4-53 (141)
75 PRK13890 conjugal transfer pro 57.2 11 0.00023 33.1 3.0 47 214-266 4-52 (120)
76 PF04814 HNF-1_N: Hepatocyte n 56.5 12 0.00026 35.6 3.4 53 218-278 121-173 (180)
77 COG1476 Predicted transcriptio 55.2 6.5 0.00014 31.8 1.2 33 219-257 5-37 (68)
78 PRK06759 RNA polymerase factor 53.4 11 0.00024 32.9 2.5 48 303-355 106-153 (154)
79 PRK09646 RNA polymerase sigma 52.1 8.9 0.00019 35.3 1.8 50 303-357 142-191 (194)
80 COG4974 XerD Site-specific rec 51.1 45 0.00099 34.1 6.7 99 210-320 31-131 (300)
81 PF00196 GerE: Bacterial regul 50.4 9.3 0.0002 28.6 1.4 46 303-354 3-48 (58)
82 PF06056 Terminase_5: Putative 48.7 8.7 0.00019 29.7 1.0 30 325-356 14-43 (58)
83 PRK10072 putative transcriptio 48.4 13 0.00028 31.7 2.1 40 304-350 33-72 (96)
84 smart00351 PAX Paired Box doma 47.5 50 0.0011 28.9 5.7 43 303-345 75-124 (125)
85 TIGR02937 sigma70-ECF RNA poly 47.2 9.6 0.00021 31.9 1.1 48 303-355 110-157 (158)
86 PF13936 HTH_38: Helix-turn-he 45.4 10 0.00022 27.5 0.8 40 302-346 3-42 (44)
87 smart00421 HTH_LUXR helix_turn 45.2 16 0.00034 25.9 1.8 44 304-353 4-47 (58)
88 PF10668 Phage_terminase: Phag 44.4 10 0.00022 30.0 0.7 20 326-345 24-43 (60)
89 PF01371 Trp_repressor: Trp re 44.4 13 0.00028 31.2 1.5 44 205-254 24-69 (87)
90 PRK04217 hypothetical protein; 43.8 14 0.00031 32.3 1.6 52 302-358 41-92 (110)
91 COG1709 Predicted transcriptio 43.2 22 0.00047 35.1 3.0 55 215-275 27-81 (241)
92 PRK01381 Trp operon repressor; 43.2 42 0.00091 29.1 4.4 59 206-277 31-92 (99)
93 PRK09480 slmA division inhibit 43.2 16 0.00034 32.8 1.9 40 309-349 16-55 (194)
94 COG3413 Predicted DNA binding 41.2 16 0.00035 34.6 1.8 40 303-342 155-196 (215)
95 TIGR02607 antidote_HigA addict 41.0 24 0.00051 27.5 2.4 34 219-258 8-42 (78)
96 PRK09413 IS2 repressor TnpA; R 40.0 18 0.00039 31.5 1.7 42 301-346 10-51 (121)
97 PRK10403 transcriptional regul 39.8 19 0.00041 31.7 1.9 49 302-356 152-200 (215)
98 PRK12514 RNA polymerase sigma 39.6 14 0.00031 33.2 1.1 30 326-355 147-176 (179)
99 cd00093 HTH_XRE Helix-turn-hel 39.5 25 0.00054 23.8 2.1 33 219-257 3-35 (58)
100 PRK11924 RNA polymerase sigma 39.1 14 0.00031 32.4 1.0 33 325-357 142-174 (179)
101 PF02376 CUT: CUT domain; Int 39.0 8.1 0.00018 32.3 -0.6 25 212-236 10-34 (87)
102 TIGR02948 SigW_bacill RNA poly 38.5 13 0.00028 33.4 0.6 49 303-356 136-184 (187)
103 PRK12526 RNA polymerase sigma 38.4 17 0.00038 33.8 1.5 49 304-357 154-202 (206)
104 PF09607 BrkDBD: Brinker DNA-b 38.2 16 0.00035 28.7 1.0 45 301-346 3-47 (58)
105 PRK04140 hypothetical protein; 37.9 24 0.00053 36.2 2.5 48 217-270 128-177 (317)
106 PRK09652 RNA polymerase sigma 37.3 15 0.00032 32.5 0.8 49 303-356 128-176 (182)
107 PRK15369 two component system 35.8 35 0.00076 29.6 2.9 46 302-353 148-193 (211)
108 PRK13355 bifunctional HTH-doma 35.7 30 0.00065 37.0 2.9 45 214-259 2-46 (517)
109 PRK09648 RNA polymerase sigma 35.5 19 0.00041 32.8 1.2 48 303-355 139-186 (189)
110 cd04762 HTH_MerR-trunc Helix-T 35.5 15 0.00033 25.2 0.5 25 327-351 3-27 (49)
111 PRK00118 putative DNA-binding 35.0 18 0.00039 31.3 0.9 48 304-356 18-65 (104)
112 PRK12512 RNA polymerase sigma 34.9 19 0.00042 32.5 1.1 50 304-358 132-181 (184)
113 cd04761 HTH_MerR-SF Helix-Turn 34.4 15 0.00033 25.9 0.3 22 327-348 3-24 (49)
114 TIGR03879 near_KaiC_dom probab 34.0 6.3 0.00014 32.2 -1.9 28 321-348 29-56 (73)
115 TIGR02939 RpoE_Sigma70 RNA pol 33.7 20 0.00043 32.3 1.0 35 322-356 152-186 (190)
116 PF13384 HTH_23: Homeodomain-l 33.0 16 0.00035 26.3 0.2 23 325-347 18-40 (50)
117 PRK06811 RNA polymerase factor 32.8 33 0.00072 31.3 2.4 55 303-362 131-185 (189)
118 PRK12541 RNA polymerase sigma 32.3 28 0.00061 30.7 1.8 48 304-356 113-160 (161)
119 cd06170 LuxR_C_like C-terminal 32.1 36 0.00078 24.1 2.0 26 326-351 17-42 (57)
120 PHA02591 hypothetical protein; 30.8 34 0.00074 28.6 1.8 28 209-240 44-71 (83)
121 COG1426 Predicted transcriptio 30.8 35 0.00077 34.3 2.4 26 215-240 3-28 (284)
122 PRK12515 RNA polymerase sigma 30.4 28 0.00061 31.7 1.5 51 303-358 131-181 (189)
123 PRK10360 DNA-binding transcrip 30.2 29 0.00063 30.5 1.5 45 303-353 137-181 (196)
124 PRK06986 fliA flagellar biosyn 30.2 31 0.00068 32.8 1.8 49 304-357 185-233 (236)
125 PF13518 HTH_28: Helix-turn-he 30.2 26 0.00057 25.0 1.0 25 326-350 14-38 (52)
126 TIGR00721 tfx DNA-binding prot 29.9 45 0.00098 30.3 2.7 48 301-354 4-51 (137)
127 TIGR02999 Sig-70_X6 RNA polyme 29.6 32 0.00069 30.9 1.7 47 304-355 135-181 (183)
128 TIGR02983 SigE-fam_strep RNA p 29.4 26 0.00056 30.8 1.0 33 325-357 127-159 (162)
129 PF13443 HTH_26: Cro/C1-type H 29.3 20 0.00043 26.9 0.2 24 326-349 12-35 (63)
130 TIGR02989 Sig-70_gvs1 RNA poly 29.0 47 0.001 28.9 2.6 47 303-354 111-157 (159)
131 TIGR02985 Sig70_bacteroi1 RNA 29.0 25 0.00055 30.2 0.9 46 304-354 114-159 (161)
132 PRK09935 transcriptional regul 28.9 34 0.00074 30.1 1.7 46 302-353 148-193 (210)
133 PRK09642 RNA polymerase sigma 28.9 21 0.00046 31.4 0.3 50 304-358 107-156 (160)
134 PRK12518 RNA polymerase sigma 28.8 22 0.00048 31.7 0.4 37 322-358 134-170 (175)
135 PRK12537 RNA polymerase sigma 28.4 42 0.00092 30.4 2.3 30 326-355 151-180 (182)
136 PRK05602 RNA polymerase sigma 28.3 33 0.00071 31.1 1.5 35 325-359 145-179 (186)
137 COG2973 TrpR Trp operon repres 28.2 1.1E+02 0.0025 26.6 4.6 56 210-278 40-98 (103)
138 PRK09639 RNA polymerase sigma 28.1 38 0.00083 29.8 1.9 48 304-357 113-160 (166)
139 PRK00283 xerD site-specific ty 27.8 1.2E+02 0.0025 28.7 5.2 21 297-317 107-127 (299)
140 TIGR02959 SigZ RNA polymerase 27.4 37 0.0008 30.5 1.7 50 303-357 100-149 (170)
141 PRK12519 RNA polymerase sigma 27.2 30 0.00065 31.5 1.1 32 324-355 157-188 (194)
142 PF13411 MerR_1: MerR HTH fami 27.2 27 0.00058 26.6 0.6 20 327-346 3-22 (69)
143 TIGR02952 Sig70_famx2 RNA poly 26.8 35 0.00076 30.0 1.4 47 303-354 122-168 (170)
144 PRK10651 transcriptional regul 25.7 53 0.0011 28.9 2.3 46 303-354 155-200 (216)
145 PRK09390 fixJ response regulat 25.2 52 0.0011 28.4 2.2 47 304-356 142-188 (202)
146 COG2963 Transposase and inacti 25.2 58 0.0013 27.6 2.4 42 301-346 5-47 (116)
147 PRK08301 sporulation sigma fac 24.9 44 0.00095 31.7 1.8 53 303-356 178-230 (234)
148 PRK12530 RNA polymerase sigma 24.7 43 0.00093 30.7 1.6 48 304-356 135-182 (189)
149 PRK09637 RNA polymerase sigma 24.6 47 0.001 30.3 1.9 49 304-357 107-155 (181)
150 TIGR03541 reg_near_HchA LuxR f 24.6 36 0.00077 32.7 1.1 51 301-357 169-219 (232)
151 PF02796 HTH_7: Helix-turn-hel 24.6 44 0.00095 24.1 1.3 37 304-345 6-42 (45)
152 TIGR02954 Sig70_famx3 RNA poly 24.5 43 0.00094 29.7 1.5 31 325-355 136-166 (169)
153 PF00376 MerR: MerR family reg 24.3 30 0.00064 24.5 0.4 19 327-345 2-20 (38)
154 PRK07037 extracytoplasmic-func 24.3 46 0.00099 29.3 1.6 49 303-356 109-157 (163)
155 TIGR02479 FliA_WhiG RNA polyme 24.1 48 0.001 31.3 1.8 48 303-355 175-222 (224)
156 PRK12513 RNA polymerase sigma 24.1 36 0.00078 31.0 1.0 36 322-357 153-188 (194)
157 PRK06930 positive control sigm 24.0 43 0.00094 31.1 1.5 50 303-357 114-163 (170)
158 cd01392 HTH_LacI Helix-turn-he 24.0 22 0.00048 25.5 -0.4 21 329-349 2-22 (52)
159 PRK12546 RNA polymerase sigma 23.9 46 0.001 30.7 1.7 33 326-358 131-163 (188)
160 PRK09047 RNA polymerase factor 23.8 52 0.0011 28.7 1.9 50 303-357 106-155 (161)
161 PRK12547 RNA polymerase sigma 23.8 46 0.001 29.6 1.6 48 304-356 113-160 (164)
162 PRK08583 RNA polymerase sigma 23.7 36 0.00079 32.8 1.0 50 303-357 205-254 (257)
163 TIGR03020 EpsA transcriptional 23.4 56 0.0012 32.3 2.2 50 301-356 188-237 (247)
164 PRK12539 RNA polymerase sigma 23.2 53 0.0012 29.8 1.9 50 303-357 131-180 (184)
165 PF07900 DUF1670: Protein of u 23.2 49 0.0011 32.5 1.7 43 301-343 172-216 (220)
166 PRK12538 RNA polymerase sigma 23.1 44 0.00095 32.2 1.4 33 325-357 188-220 (233)
167 TIGR02941 Sigma_B RNA polymera 23.0 51 0.0011 31.7 1.9 48 303-355 205-252 (255)
168 PRK08295 RNA polymerase factor 22.9 63 0.0014 29.6 2.4 33 325-357 171-203 (208)
169 PRK12524 RNA polymerase sigma 22.7 48 0.001 30.4 1.5 50 304-358 137-186 (196)
170 PF01316 Arg_repressor: Argini 22.6 67 0.0014 25.9 2.1 34 216-253 10-43 (70)
171 PRK07670 RNA polymerase sigma 22.5 40 0.00087 32.5 1.0 47 304-355 202-248 (251)
172 PRK09645 RNA polymerase sigma 22.4 57 0.0012 29.0 1.9 49 304-357 119-167 (173)
173 PRK09644 RNA polymerase sigma 22.0 40 0.00087 29.9 0.8 51 303-358 108-158 (165)
174 PRK09975 DNA-binding transcrip 21.9 40 0.00086 30.9 0.8 41 309-350 17-57 (213)
175 COG0568 RpoD DNA-directed RNA 21.8 33 0.00072 35.7 0.3 49 304-353 280-328 (342)
176 KOG3755|consensus 21.8 44 0.00095 37.4 1.2 66 294-359 644-713 (769)
177 PRK12529 RNA polymerase sigma 21.3 64 0.0014 29.2 2.0 48 303-355 127-174 (178)
178 PRK07408 RNA polymerase sigma 21.3 42 0.0009 32.7 0.9 50 304-358 204-253 (256)
179 PRK05657 RNA polymerase sigma 21.2 57 0.0012 33.2 1.8 55 303-358 262-316 (325)
180 PF13413 HTH_25: Helix-turn-he 20.9 42 0.00091 26.1 0.6 36 219-260 1-36 (62)
181 PRK09638 RNA polymerase sigma 20.6 51 0.0011 29.3 1.2 34 323-356 141-174 (176)
182 TIGR03764 ICE_PFGI_1_parB inte 20.4 82 0.0018 31.6 2.7 49 207-256 112-163 (258)
183 TIGR02950 SigM_subfam RNA poly 20.4 44 0.00094 28.9 0.7 35 321-355 118-152 (154)
184 TIGR02947 SigH_actino RNA poly 20.3 47 0.001 30.3 1.0 36 322-357 145-180 (193)
185 PF13730 HTH_36: Helix-turn-he 20.0 63 0.0014 23.5 1.4 23 325-347 26-48 (55)
186 PRK12523 RNA polymerase sigma 20.0 48 0.001 29.7 0.9 51 303-358 119-169 (172)
No 1
>KOG3802|consensus
Probab=100.00 E-value=5.8e-58 Score=460.15 Aligned_cols=166 Identities=79% Similarity=1.206 Sum_probs=156.8
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCChhhhhhcchhHHHHHHhh
Q psy3400 199 APSGSEEDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEA 278 (417)
Q Consensus 199 ~~s~~~~d~~~~~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWLeEa 278 (417)
..+.++||..++||||+|||+||+|||+|||||+|||++||++||++||||||||||+|+|||||||||||+|+|||+|+
T Consensus 194 ~~~~~~ed~~~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEA 273 (398)
T KOG3802|consen 194 ATEPSDEDTPDLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEA 273 (398)
T ss_pred CCCCCcccccCHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHH
Confidence 45567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hc--CCCCCCchhHHhhcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 279 DS--TTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 279 e~--~~~s~~s~~~~~~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
|. +.+..++++++..+.|||||||+|+...+..||+.|.+|++|+.+||..||++|+|+++||||||||||+|+||.+
T Consensus 274 es~~~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 274 ESRESTGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred hcccccCCCCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 98 6677889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCC
Q psy3400 357 PPNTLGGP 364 (417)
Q Consensus 357 ~~~~~g~p 364 (417)
+....+.|
T Consensus 354 ~~~~~~~P 361 (398)
T KOG3802|consen 354 PFPSAGSP 361 (398)
T ss_pred CCccCCCC
Confidence 84434433
No 2
>KOG1168|consensus
Probab=100.00 E-value=8.8e-41 Score=323.78 Aligned_cols=154 Identities=53% Similarity=0.831 Sum_probs=138.3
Q ss_pred CCCChHHHHHHHHHHHhhhhhhccchhhhhhhhhcccc---cccccccccchhcccCChhhhhhcchhHHHHHHhhhcCC
Q psy3400 206 DAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYG---NVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEADSTT 282 (417)
Q Consensus 206 d~~~~~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g---~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWLeEae~~~ 282 (417)
-..|.+|||.||+.||||||+||+||+|||.+|..|.. ..+||+||||||+|.||..||..|||+|+.||||+|..-
T Consensus 212 ~dtDPReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE~a~ 291 (385)
T KOG1168|consen 212 MDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEAAM 291 (385)
T ss_pred cCCCHHHHHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHHHHH
Confidence 34579999999999999999999999999999999985 458999999999999999999999999999999998654
Q ss_pred CC---CCchhHHhhcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 283 GS---PTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 283 ~s---~~s~~~~~~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
.+ ...+.++.....||||||.|-.-+++.||++|..+++|+.+.|..||++|.|.+.+|||||||.|+|.||++...
T Consensus 292 keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 292 KEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred HhhccCCchhhccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 33 334446656667788999999999999999999999999999999999999999999999999999999976553
No 3
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=99.95 E-value=1.2e-28 Score=198.21 Aligned_cols=75 Identities=81% Similarity=1.287 Sum_probs=69.5
Q ss_pred CCCCChHHHHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCChhhhhhcchhHHHHHHhhh
Q psy3400 205 EDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEAD 279 (417)
Q Consensus 205 ~d~~~~~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWLeEae 279 (417)
||.++++||++||++||+|||+|||||+|||.+|+.+||..|||+||||||+++||++|||||+|+|++||+|+|
T Consensus 1 ~~~~~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~eaE 75 (75)
T PF00157_consen 1 EDTPDLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 75 (75)
T ss_dssp --CHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred CCccCHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhcC
Confidence 467789999999999999999999999999999999999999999999999999999999999999999999986
No 4
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=99.86 E-value=1.4e-22 Score=163.23 Aligned_cols=75 Identities=81% Similarity=1.271 Sum_probs=72.9
Q ss_pred CCCCChHHHHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCChhhhhhcchhHHHHHHhhh
Q psy3400 205 EDAPTSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEAD 279 (417)
Q Consensus 205 ~d~~~~~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWLeEae 279 (417)
+|.++++|||.|++.||++|+.+||||+||+.+++++||..++|+||||||+++|||+|||||+|+|++||+++|
T Consensus 1 ~~~~~~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~e 75 (75)
T smart00352 1 DEDTDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 75 (75)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhcC
Confidence 578899999999999999999999999999999999999999999999999999999999999999999999875
No 5
>KOG2252|consensus
Probab=99.77 E-value=6e-18 Score=176.76 Aligned_cols=146 Identities=22% Similarity=0.313 Sum_probs=125.0
Q ss_pred CCCCCCCCCChHHHHHHHHHHHhhhhhhc-cchhhhhhhhhcccccccccccccchhcccCChhhhhhcchhHHHHHHhh
Q psy3400 200 PSGSEEDAPTSDDLEAFAKQFKQRRIKLG-FTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEA 278 (417)
Q Consensus 200 ~s~~~~d~~~~~ele~Fak~fK~rRI~lG-~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWLeEa 278 (417)
.++.+|++.|.+-..++..+||++-|... |.|..+|+..|+|.+.+...+.|.+++..+.+|.+|++ ||++.
T Consensus 319 ~~~d~eeldTkeia~rI~~eLk~~sIpQaiFAervLcRSQGTLSDLLrnPKPW~klKsGRetFrRM~~-------WL~eP 391 (558)
T KOG2252|consen 319 ESGDDEELDTKEIAQRIKAELKRYSIPQAIFAERVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMAN-------WLEEP 391 (558)
T ss_pred hcCCcceecHHHHHHHHHHHHhhcCCcHHHHHHHHhhcccchHHHHhhCCCchhhhccccHHHHHHHH-------HhcCH
Confidence 46677888889999999999999999998 99999999999999999999999999999999999999 88876
Q ss_pred hcCC-CCCCchhHH---------hhcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchh
Q psy3400 279 DSTT-GSPTSIDKI---------AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNR 348 (417)
Q Consensus 279 e~~~-~s~~s~~~~---------~~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNR 348 (417)
+... ...+.+..+ .+.-+.||.|++||..|++.|..+|+.+++|+.++++.|+.+|+|+.++|.+||.|.
T Consensus 392 ~~~r~m~~L~~~a~kRke~ep~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNa 471 (558)
T KOG2252|consen 392 EFQRLMSALRKKACKRKEQEPTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNA 471 (558)
T ss_pred HHHHHHHHHHHHHhhhcccCCCccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhh
Confidence 6443 222221111 112345778999999999999999999999999999999999999999999999999
Q ss_pred hhhh
Q psy3400 349 RQKE 352 (417)
Q Consensus 349 R~K~ 352 (417)
|.|.
T Consensus 472 RRRs 475 (558)
T KOG2252|consen 472 RRRS 475 (558)
T ss_pred hhhc
Confidence 9885
No 6
>KOG0489|consensus
Probab=99.73 E-value=1.5e-18 Score=169.62 Aligned_cols=68 Identities=25% Similarity=0.414 Sum_probs=63.3
Q ss_pred CCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCCCCC
Q psy3400 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNTLG 362 (417)
Q Consensus 295 ~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~~~g 362 (417)
++.||.||.||..|+.+||++|..|+|.++.+|.|||..|.|+|+||||||||||+||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 45678999999999999999999999999999999999999999999999999999999988876443
No 7
>KOG0487|consensus
Probab=99.69 E-value=3.6e-18 Score=169.60 Aligned_cols=66 Identities=32% Similarity=0.433 Sum_probs=62.3
Q ss_pred cCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 294 ~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
-++-||||.-+|+.|+.+||++|..|.|.++++|.||++.|+|+++||+|||||||+|+||+.+.+
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 367788999999999999999999999999999999999999999999999999999999998643
No 8
>KOG0848|consensus
Probab=99.69 E-value=1.3e-17 Score=161.53 Aligned_cols=89 Identities=24% Similarity=0.356 Sum_probs=73.5
Q ss_pred hcchhHHHHHHhhhcCCCCCCchhHHhhcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhccc
Q psy3400 266 KLKPLLQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWF 345 (417)
Q Consensus 266 kLkPlLqkWLeEae~~~~s~~s~~~~~~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWF 345 (417)
+-|+....|+...-.... ....+-|.|.|-|.+||+.|+.+||++|..++|.+++++.|||..|+|+||||||||
T Consensus 173 ~~R~s~~dwmrkpa~~~~-----g~~~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWF 247 (317)
T KOG0848|consen 173 KSRRSPYDWMRKPAQPGT-----GQNVKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWF 247 (317)
T ss_pred cCCCChhhhhhcccccCC-----CCCceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhh
Confidence 345566668876543321 122234567788999999999999999999999999999999999999999999999
Q ss_pred chhhhhhhccCCCC
Q psy3400 346 CNRRQKEKRMTPPN 359 (417)
Q Consensus 346 QNRR~K~KR~~~~~ 359 (417)
||||+|+||+++++
T Consensus 248 QNRRAKERK~nKKk 261 (317)
T KOG0848|consen 248 QNRRAKERKDNKKK 261 (317)
T ss_pred hhhhHHHHHHHHHH
Confidence 99999999998886
No 9
>KOG0488|consensus
Probab=99.67 E-value=1.3e-17 Score=166.54 Aligned_cols=64 Identities=39% Similarity=0.462 Sum_probs=62.0
Q ss_pred CCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 295 ~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
+|+||.||.||..|+..||+.|++.+|.+..+|.+||..|||+..||++||||||+||||.+..
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 7788999999999999999999999999999999999999999999999999999999998776
No 10
>KOG0842|consensus
Probab=99.67 E-value=1.9e-17 Score=164.46 Aligned_cols=69 Identities=38% Similarity=0.491 Sum_probs=64.4
Q ss_pred cCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCCCCC
Q psy3400 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNTLG 362 (417)
Q Consensus 294 ~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~~~g 362 (417)
.++|||+|..|+..|..+||+.|.+++|.+..||+.||..|+|+++||||||||||-|+||..+.+...
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 357788899999999999999999999999999999999999999999999999999999998887544
No 11
>KOG0850|consensus
Probab=99.66 E-value=3e-17 Score=156.21 Aligned_cols=70 Identities=30% Similarity=0.389 Sum_probs=65.2
Q ss_pred HhhcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCCC
Q psy3400 291 IAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNT 360 (417)
Q Consensus 291 ~~~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~~ 360 (417)
..+.+|.||.||.|+..||..|++.|++++|....||.+||.+|||+.+||||||||||.|.||+.+...
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~ 185 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGS 185 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCC
Confidence 3456788899999999999999999999999999999999999999999999999999999999998543
No 12
>KOG0484|consensus
Probab=99.62 E-value=1.5e-16 Score=135.33 Aligned_cols=66 Identities=26% Similarity=0.396 Sum_probs=61.9
Q ss_pred hcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 293 AQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 293 ~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
..+|.||-||+||..|+.+||+.|..+.||++..|++||.++.|++..|||||||||+|.||+.+.
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 346778899999999999999999999999999999999999999999999999999999998654
No 13
>KOG2251|consensus
Probab=99.61 E-value=2.2e-16 Score=149.56 Aligned_cols=67 Identities=31% Similarity=0.432 Sum_probs=63.6
Q ss_pred hcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 293 AQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 293 ~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
..+|.||.||+|+..|+.+||+.|.++.||+...|++||.+|+|.+.+|+|||.|||+|+|++.+..
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 4578899999999999999999999999999999999999999999999999999999999988764
No 14
>KOG0843|consensus
Probab=99.60 E-value=3.2e-16 Score=144.54 Aligned_cols=64 Identities=36% Similarity=0.483 Sum_probs=60.9
Q ss_pred CCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 296 kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
|.||.||.|+.+|+..||..|+.|.|....||+.||+.|+|++.||+|||||||.|.||+....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 6778999999999999999999999999999999999999999999999999999999987663
No 15
>KOG0485|consensus
Probab=99.60 E-value=1.8e-16 Score=149.84 Aligned_cols=66 Identities=38% Similarity=0.473 Sum_probs=62.3
Q ss_pred cCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 294 ~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
+.||||.||+|+..|+..||..|+..+|.+..||.-||++|.|+++||||||||||.||||+....
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 457888999999999999999999999999999999999999999999999999999999987653
No 16
>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=99.57 E-value=5.8e-16 Score=116.84 Aligned_cols=57 Identities=40% Similarity=0.628 Sum_probs=55.3
Q ss_pred CCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhc
Q psy3400 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354 (417)
Q Consensus 298 RRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR 354 (417)
||+|+.||.+|+.+|+.+|..++||+..+++.||..|+|+..+|++||+|||+|+||
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 578999999999999999999999999999999999999999999999999999986
No 17
>KOG0492|consensus
Probab=99.56 E-value=1.2e-15 Score=143.56 Aligned_cols=68 Identities=32% Similarity=0.474 Sum_probs=63.1
Q ss_pred hhcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 292 AAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 292 ~~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
.+.+..||.||-||..|+..||+.|.+.+|.++.||.+++..|.|+++||+|||||||+|.||....+
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae 206 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE 206 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence 45566789999999999999999999999999999999999999999999999999999999986543
No 18
>KOG0494|consensus
Probab=99.54 E-value=2.8e-15 Score=144.92 Aligned_cols=65 Identities=29% Similarity=0.426 Sum_probs=59.8
Q ss_pred CCCCCC-CceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 295 GRKRKK-RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 295 ~kkRRk-RT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
++|||. ||.||..|+.+||+.|++..||+...|+.||.++.|.+++|+|||||||+||||..+.-
T Consensus 138 k~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred ccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 334444 99999999999999999999999999999999999999999999999999999987764
No 19
>KOG4577|consensus
Probab=99.52 E-value=3.8e-15 Score=145.74 Aligned_cols=67 Identities=31% Similarity=0.548 Sum_probs=62.4
Q ss_pred cCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCCC
Q psy3400 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNT 360 (417)
Q Consensus 294 ~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~~ 360 (417)
....||.||+||..|++.|...|...++|.+..|+.|+.++||+-++|||||||||+|+||.++...
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 3456789999999999999999999999999999999999999999999999999999999987753
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=99.45 E-value=4.3e-14 Score=109.26 Aligned_cols=53 Identities=19% Similarity=0.429 Sum_probs=51.0
Q ss_pred CCCCCceechhhHHHHhhhccCCCC----CCHHHHHHHHHHcCCCCCchhcccchhh
Q psy3400 297 KRKKRTSIEVTVKGALETHFHKQPK----PSAQEITTLADSLQLEKEVVRVWFCNRR 349 (417)
Q Consensus 297 kRRkRT~fT~~Ql~~LE~~F~~n~y----PS~~er~eLA~~LgLs~~qVqVWFQNRR 349 (417)
+||.||.||.+|+..||..|..+.| |+..++++||..|||++++|+|||||-+
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 4789999999999999999999999 9999999999999999999999999975
No 21
>KOG0844|consensus
Probab=99.44 E-value=1.5e-14 Score=142.42 Aligned_cols=66 Identities=30% Similarity=0.435 Sum_probs=61.5
Q ss_pred CCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCCC
Q psy3400 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNT 360 (417)
Q Consensus 295 ~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~~ 360 (417)
..-||-||.||.+|+..||++|-+..|.++..|.|||..|+|.+.+|||||||||+|+||+.-...
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlama 244 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMA 244 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhcc
Confidence 446789999999999999999999999999999999999999999999999999999999876543
No 22
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.44 E-value=4.9e-14 Score=105.30 Aligned_cols=56 Identities=46% Similarity=0.650 Sum_probs=53.0
Q ss_pred CCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhh
Q psy3400 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353 (417)
Q Consensus 298 RRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~K 353 (417)
++.|+.|+..++..|+..|..++||+..++..||..|||+..+|++||+|||.+.|
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 35788899999999999999999999999999999999999999999999999865
No 23
>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=99.44 E-value=5.6e-14 Score=105.53 Aligned_cols=58 Identities=43% Similarity=0.638 Sum_probs=55.0
Q ss_pred CCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 298 RRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
+++|+.|+..++..|++.|..++||+..++..||.++||++++|++||+|||.+.|+.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 3578899999999999999999999999999999999999999999999999998874
No 24
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.44 E-value=8.7e-14 Score=127.01 Aligned_cols=67 Identities=27% Similarity=0.392 Sum_probs=61.7
Q ss_pred hcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 293 AQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 293 ~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
..+..+++|++.|..|+.+|++.|..|+||+..+|.+|+..|+|+++.|||||||||++.|+.....
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 3456677889999999999999999999999999999999999999999999999999999887764
No 25
>KOG0491|consensus
Probab=99.41 E-value=5.6e-14 Score=128.24 Aligned_cols=65 Identities=37% Similarity=0.522 Sum_probs=61.7
Q ss_pred CCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCCC
Q psy3400 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNT 360 (417)
Q Consensus 296 kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~~ 360 (417)
++||.||+|+..|+..||+.|+..+|.+.++|.|||..|+|++.||+.||||||+|.||..+.+.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 46789999999999999999999999999999999999999999999999999999999887764
No 26
>KOG0775|consensus
Probab=99.41 E-value=4.1e-13 Score=130.83 Aligned_cols=108 Identities=28% Similarity=0.419 Sum_probs=88.9
Q ss_pred chhcccCChhhhhhcch-hHHHHHHhhhcCCCCCC-chhHHhhcCCCCCCCc---------eechhhHHHHhhhccCCCC
Q psy3400 253 RFEALQLSFKNMCKLKP-LLQKWLEEADSTTGSPT-SIDKIAAQGRKRKKRT---------SIEVTVKGALETHFHKQPK 321 (417)
Q Consensus 253 RFE~lqLS~knm~kLkP-lLqkWLeEae~~~~s~~-s~~~~~~~~kkRRkRT---------~fT~~Ql~~LE~~F~~n~y 321 (417)
-+|.-.++..+..+|.- +|+..+.|+|...+.++ .++++..++|.--+|| +|...-+..|..+|.+|+|
T Consensus 121 iLE~h~Fs~~~h~~LQ~lWl~AhY~EAek~RGR~LgaV~KYRvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~Y 200 (304)
T KOG0775|consen 121 ILENHKFSPHNHPKLQALWLKAHYKEAEKLRGRPLGAVDKYRVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPY 200 (304)
T ss_pred HHHhccCChhhhHHHHHHHHHHHHHHHHHhcCCcCCccccceeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCC
Confidence 34666777778777765 56667889998888765 6777777666666787 6777788999999999999
Q ss_pred CCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCCC
Q psy3400 322 PSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNT 360 (417)
Q Consensus 322 PS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~~ 360 (417)
|+..++.+||+.+||+..||.+||.|||+|+|-...+..
T Consensus 201 Psp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ak~~ 239 (304)
T KOG0775|consen 201 PSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAAKNS 239 (304)
T ss_pred CChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcccccc
Confidence 999999999999999999999999999999996555543
No 27
>KOG0493|consensus
Probab=99.38 E-value=1.4e-13 Score=133.37 Aligned_cols=63 Identities=25% Similarity=0.447 Sum_probs=59.6
Q ss_pred CCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 297 KRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 297 kRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
.||.||.||.+||..|..+|..|+|.+.+.|.+||.+|+|.+.||+|||||+|+|.||-+..+
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCC
Confidence 467899999999999999999999999999999999999999999999999999999976654
No 28
>KOG0486|consensus
Probab=99.35 E-value=2e-13 Score=135.11 Aligned_cols=65 Identities=28% Similarity=0.427 Sum_probs=61.3
Q ss_pred CCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 295 GRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 295 ~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
+|+||.||.||..|+.+||..|.+|+||+-..|++||...+|++.+|+|||.|||+||||++.-.
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 47889999999999999999999999999999999999999999999999999999999986543
No 29
>KOG0483|consensus
Probab=99.26 E-value=2.2e-12 Score=121.80 Aligned_cols=60 Identities=28% Similarity=0.381 Sum_probs=55.4
Q ss_pred CCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 300 KRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 300 kRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
++.+|+.+|+..||+.|..+.+....++..||++|||..+||.|||||||+|||......
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence 344599999999999999999999999999999999999999999999999999876654
No 30
>KOG0847|consensus
Probab=99.20 E-value=3.5e-12 Score=121.19 Aligned_cols=67 Identities=24% Similarity=0.424 Sum_probs=61.3
Q ss_pred hcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 293 AQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 293 ~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
+.++++..|.+|+-.|+..||+.|++.+|+-..+|.+||..+|+++.+|+|||||||.||||+...+
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence 3456677899999999999999999999999999999999999999999999999999999976543
No 31
>KOG0490|consensus
Probab=99.14 E-value=3.5e-11 Score=112.88 Aligned_cols=64 Identities=30% Similarity=0.340 Sum_probs=60.8
Q ss_pred cCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 294 QGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 294 ~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
..++||.||.|+..|+.+||+.|.++.||+...++.||..+++++..|+|||||||+||++...
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4577889999999999999999999999999999999999999999999999999999998874
No 32
>KOG0849|consensus
Probab=98.92 E-value=5.2e-10 Score=114.14 Aligned_cols=66 Identities=36% Similarity=0.471 Sum_probs=61.8
Q ss_pred hcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 293 AQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 293 ~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
..++.||+||+|+..|+..||+.|..++||++..|++||.++++.+..|+|||+|||+|++|....
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 346777889999999999999999999999999999999999999999999999999999998844
No 33
>KOG0774|consensus
Probab=98.51 E-value=1.2e-07 Score=92.67 Aligned_cols=62 Identities=27% Similarity=0.418 Sum_probs=56.2
Q ss_pred CCCCceechhhHHHHhhhc---cCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 298 RKKRTSIEVTVKGALETHF---HKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 298 RRkRT~fT~~Ql~~LE~~F---~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
||||..|++...++|..+| ..|+||+.+++++||++++++..||.+||.|+|-+.||...+.
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 4667789999999999999 4789999999999999999999999999999999998876554
No 34
>KOG0490|consensus
Probab=98.34 E-value=4.3e-07 Score=85.31 Aligned_cols=65 Identities=34% Similarity=0.569 Sum_probs=60.6
Q ss_pred hcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 293 AQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 293 ~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
...+.++.|+.+...|+..|+..|..+.+|+...++.|+..+++++++|+|||+|+|.+.|+...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34677788999999999999999999999999999999999999999999999999999998765
No 35
>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=98.25 E-value=3.1e-07 Score=66.12 Aligned_cols=34 Identities=32% Similarity=0.623 Sum_probs=29.4
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCchhcccchhhhh
Q psy3400 318 KQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351 (417)
Q Consensus 318 ~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K 351 (417)
.+|||+.+++++||.++||+..||.+||-|.|.|
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 5799999999999999999999999999999975
No 36
>KOG1146|consensus
Probab=97.88 E-value=8.2e-06 Score=93.57 Aligned_cols=64 Identities=28% Similarity=0.432 Sum_probs=59.7
Q ss_pred CCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 296 RKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 296 kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
.+|++||.++..|++.|..+|....||.-++++.|-..+++.+++|+|||||.|+|.||.....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 4677899999999999999999999999999999999999999999999999999999876643
No 37
>KOG0773|consensus
Probab=96.10 E-value=0.0026 Score=64.39 Aligned_cols=60 Identities=23% Similarity=0.323 Sum_probs=48.5
Q ss_pred CCCCCceechhhHHHHhhhcc---CCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 297 KRKKRTSIEVTVKGALETHFH---KQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 297 kRRkRT~fT~~Ql~~LE~~F~---~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
+.|++..+......+|+.+.. ..+||+..++..||.++||+..+|.+||-|.|.|..+-.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 334455777888888887733 358999999999999999999999999999998766543
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.69 E-value=0.0028 Score=49.08 Aligned_cols=44 Identities=27% Similarity=0.487 Sum_probs=32.3
Q ss_pred HHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhh
Q psy3400 309 KGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKE 352 (417)
Q Consensus 309 l~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~ 352 (417)
+..|+.+|....++...++..|+.+.+|+..+|+.||-.|+.+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e~ 53 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQEE 53 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--S
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcccc
Confidence 45699999999999999999999999999999999998776543
No 39
>KOG3623|consensus
Probab=95.29 E-value=0.01 Score=65.63 Aligned_cols=49 Identities=22% Similarity=0.432 Sum_probs=46.1
Q ss_pred HHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 309 KGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 309 l~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
+..|..+|..|..|+..+...||.+.||..++|++||.++|++..+...
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence 7789999999999999999999999999999999999999999888763
No 40
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.16 E-value=0.044 Score=41.53 Aligned_cols=47 Identities=15% Similarity=0.253 Sum_probs=36.6
Q ss_pred CCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhh
Q psy3400 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRR 349 (417)
Q Consensus 298 RRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR 349 (417)
||+|..+|-+++..+-..++... ....||.++|+...+|..|..|+.
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 56889999999998888887776 467899999999999999999864
No 41
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=93.57 E-value=0.061 Score=50.26 Aligned_cols=56 Identities=36% Similarity=0.523 Sum_probs=42.2
Q ss_pred HHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCChhhhhhcchhHHHHHHhhhc
Q psy3400 217 AKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEADS 280 (417)
Q Consensus 217 ak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWLeEae~ 280 (417)
..++|.+|-.||+||.++.+.-|. ||..|.|+|+..+.+ ...+++.+|+ .|+|++.
T Consensus 7 pedlrk~Rk~LGitQ~dLA~~aGV------SQ~~IArlE~G~vdP-rlSt~k~Il~-aL~e~e~ 62 (187)
T COG3620 7 PEDLRKRRKELGITQKDLARRAGV------SQPYIARLEAGKVDP-RLSTVKRILE-ALEEAEK 62 (187)
T ss_pred HHHHHHHHHHcCCCHHHHHHHcCc------cHHHHHHHhcCCCCc-cHHHHHHHHH-HHHHhhc
Confidence 456799999999999999976544 999999999998875 3445555554 4566554
No 42
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=92.53 E-value=0.072 Score=40.93 Aligned_cols=40 Identities=28% Similarity=0.456 Sum_probs=33.2
Q ss_pred HHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCC
Q psy3400 215 AFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLS 260 (417)
Q Consensus 215 ~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS 260 (417)
+|...++..|...|+||.+|+..+| +++++++++|+-...
T Consensus 1 ~lg~~lr~~R~~~gls~~~lA~~~g------~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 1 QLGRRLRRLRERAGLSQAQLADRLG------VSQSTVSRIERGRRP 40 (64)
T ss_dssp HHHHHHHHHHHCHTS-HHHHHHHHT------S-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHC------cCHHHHHHHHCCCCC
Confidence 5888999999999999999999886 588899999887753
No 43
>KOG3623|consensus
Probab=91.30 E-value=0.11 Score=57.92 Aligned_cols=90 Identities=23% Similarity=0.337 Sum_probs=65.3
Q ss_pred hhHHHHHHhhhcCCCCCCchhHHhhcCCCCCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchh
Q psy3400 269 PLLQKWLEEADSTTGSPTSIDKIAAQGRKRKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNR 348 (417)
Q Consensus 269 PlLqkWLeEae~~~~s~~s~~~~~~~~kkRRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNR 348 (417)
-+.++|+++.+....+...........++-|-|+.+..++-..|...+..+-.++..+...++..|...+.+|.|||++|
T Consensus 598 ~vvk~wfE~~~a~e~sv~rsps~psg~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsr 677 (1007)
T KOG3623|consen 598 AVVKAWFEDEEAEEMSVERSPSQPSGERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSR 677 (1007)
T ss_pred HHHHHHHHhhhhhhhhhccCccCCCCCCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCC
Confidence 35678998876443322222222333344456677777788888899988888888888888888999999999999999
Q ss_pred hhhhhccCCC
Q psy3400 349 RQKEKRMTPP 358 (417)
Q Consensus 349 R~K~KR~~~~ 358 (417)
+...+.+...
T Consensus 678 sstpsp~pl~ 687 (1007)
T KOG3623|consen 678 SSTPSPMPLF 687 (1007)
T ss_pred CCCCCCCccc
Confidence 9988876544
No 44
>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=90.13 E-value=0.25 Score=36.01 Aligned_cols=38 Identities=29% Similarity=0.297 Sum_probs=32.5
Q ss_pred HHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhccc
Q psy3400 215 AFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ 258 (417)
Q Consensus 215 ~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lq 258 (417)
.|...++..|...|+||.+++..++ .++++++++|+..
T Consensus 2 ~~~~~l~~~r~~~gltq~~lA~~~g------vs~~~vs~~e~g~ 39 (58)
T TIGR03070 2 QIGMLVRARRKALGLTQADLADLAG------VGLRFIRDVENGK 39 (58)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHCCC
Confidence 4778889999999999999998876 4788999998765
No 45
>PHA01976 helix-turn-helix protein
Probab=88.46 E-value=0.41 Score=36.66 Aligned_cols=38 Identities=24% Similarity=0.346 Sum_probs=32.6
Q ss_pred HHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhccc
Q psy3400 215 AFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ 258 (417)
Q Consensus 215 ~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lq 258 (417)
.|.+.+|+.|...|+||.+++..++. ++++|+++|+-.
T Consensus 2 ~~~~rl~~~R~~~glt~~~lA~~~gv------s~~~v~~~e~g~ 39 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRAGV------RHSLIYDFEADK 39 (67)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCC
Confidence 37889999999999999999998764 678899988764
No 46
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=85.60 E-value=0.85 Score=41.97 Aligned_cols=52 Identities=19% Similarity=0.289 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCC--hhhhhhcc
Q psy3400 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLS--FKNMCKLK 268 (417)
Q Consensus 211 ~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS--~knm~kLk 268 (417)
+-++.|.+.+|+.|...|+||.+++..++ +++++|+++|+-... ...+.+|-
T Consensus 65 ~l~~~~g~~Ir~~Re~~glSqeeLA~~lg------vs~s~IsriE~G~~~Ps~~~l~kLa 118 (154)
T TIGR00270 65 ELVEDYGIIIRREREKRGWSQEQLAKKIQ------EKESLIKKIENAEIEPEPKVVEKLE 118 (154)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHCCCCCCCHHHHHHHH
Confidence 44567999999999999999999998875 478999999986643 34444433
No 47
>PRK06424 transcription factor; Provisional
Probab=85.16 E-value=0.93 Score=41.35 Aligned_cols=44 Identities=27% Similarity=0.344 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCC
Q psy3400 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLS 260 (417)
Q Consensus 211 ~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS 260 (417)
+.++.|+..++..|...|+||.+++..++. ++++|.++|+....
T Consensus 80 ~~~~~~g~~Ir~lRe~~GLSQ~eLA~~iGv------s~stIskiE~G~~~ 123 (144)
T PRK06424 80 DIVEDYAELVKNARERLSMSQADLAAKIFE------RKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHCCCCC
Confidence 446889999999999999999999988764 78899999887653
No 48
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=84.48 E-value=1.3 Score=45.38 Aligned_cols=45 Identities=22% Similarity=0.265 Sum_probs=35.9
Q ss_pred ChHHHHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccC
Q psy3400 209 TSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL 259 (417)
Q Consensus 209 ~~~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL 259 (417)
+..+...|-+.||+.|..+|+||.+|...|+. ++.+|.++|.-+.
T Consensus 8 ~~~~~~~~G~~Lr~aRe~~GlSq~~vA~~l~l------~~~~I~~iE~g~~ 52 (331)
T PRK10856 8 DQNEALTTGERLRQAREQLGLTQQAVAERLCL------KVSTVRDIEEDKA 52 (331)
T ss_pred chhHHHHHHHHHHHHHHHcCCCHHHHHHHHCC------CHHHHHHHHCCCC
Confidence 44444567888999999999999999988763 6778888887765
No 49
>PRK09726 antitoxin HipB; Provisional
Probab=82.19 E-value=1.3 Score=36.41 Aligned_cols=40 Identities=30% Similarity=0.419 Sum_probs=33.6
Q ss_pred HHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhccc
Q psy3400 213 LEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ 258 (417)
Q Consensus 213 le~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lq 258 (417)
.++|...+|..|...|+||.+++..+|. ++.+|.++|+..
T Consensus 10 ~~~l~~~lk~~R~~~gltq~elA~~~gv------s~~tis~~e~g~ 49 (88)
T PRK09726 10 PTQLANAMKLVRQQNGWTQSELAKKIGI------KQATISNFENNP 49 (88)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCc------CHHHHHHHHCCC
Confidence 5578888999999999999999998764 688888887753
No 50
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=82.09 E-value=1.2 Score=38.12 Aligned_cols=36 Identities=25% Similarity=0.443 Sum_probs=29.4
Q ss_pred HHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccC
Q psy3400 218 KQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL 259 (417)
Q Consensus 218 k~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL 259 (417)
.++|..|..+|+||.+++..+|. ++.||.++|+...
T Consensus 68 ~~i~~~r~~~gltq~~lA~~lg~------~~~tis~~e~g~~ 103 (127)
T TIGR03830 68 PEIRRIRKKLGLSQREAAELLGG------GVNAFSRYERGEV 103 (127)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHCCCC
Confidence 35677788889999999987754 6789999988776
No 51
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=80.16 E-value=2.6 Score=36.01 Aligned_cols=60 Identities=18% Similarity=0.248 Sum_probs=43.5
Q ss_pred CCCChHHHHHHHHHHHhhh--hhhccchhhhhhhhhcccccccccccccchhcccCChhhhhhcchhHHHHHHh
Q psy3400 206 DAPTSDDLEAFAKQFKQRR--IKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEE 277 (417)
Q Consensus 206 d~~~~~ele~Fak~fK~rR--I~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWLeE 277 (417)
+..|.+|++.++..++--+ +.-++||.+|...+|. |++||+|-++.- ....|-+..||+.
T Consensus 31 ~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGi------S~atIsR~sn~l------k~~~~~~~~~l~~ 92 (94)
T TIGR01321 31 LILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGV------SIATITRGSNNL------KTMDPNFKQFLRK 92 (94)
T ss_pred HhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCC------ChhhhhHHHhhc------ccCCHHHHHHHHh
Confidence 5567888888887777766 2346999999998876 889999975322 1244677778864
No 52
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=80.02 E-value=1.4 Score=35.64 Aligned_cols=41 Identities=27% Similarity=0.394 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccC
Q psy3400 213 LEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL 259 (417)
Q Consensus 213 le~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL 259 (417)
-..++..+++.|-..|+||.++...+|. +|++|+++++...
T Consensus 16 k~~l~~~i~~~~~~~~ltQ~e~A~~lgi------sq~~vS~l~~g~~ 56 (80)
T PF13744_consen 16 KAQLMAAIRELREERGLTQAELAERLGI------SQPRVSRLENGKI 56 (80)
T ss_dssp HHHHHHHHHHHHHCCT--HHHHHHHHTS-------HHHHHHHHTT-G
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCC------ChhHHHHHHcCcc
Confidence 3457777888888899999999998876 8999999986543
No 53
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=79.86 E-value=1.6 Score=40.33 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccC
Q psy3400 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL 259 (417)
Q Consensus 211 ~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL 259 (417)
|+...+.+.+|..|...|+||.+++..++. ++++|+++|+...
T Consensus 3 ~~~~~~g~~l~~~R~~~glt~~elA~~~gi------s~~~is~~E~g~~ 45 (185)
T PRK09943 3 DEGLAPGKRLSEIRQQQGLSQRRAAELSGL------THSAISTIEQDKV 45 (185)
T ss_pred chhhHHHHHHHHHHHHcCCCHHHHHHHHCC------CHHHHHHHHcCCC
Confidence 344568899999999999999999988764 7889999987654
No 54
>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=77.78 E-value=1.2 Score=32.56 Aligned_cols=47 Identities=11% Similarity=0.244 Sum_probs=35.5
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR 354 (417)
.+++.++.+|...|... ....+||+.+|++...|+.+...-..|-|+
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 36778888999888322 346789999999999999998777666553
No 55
>PRK08359 transcription factor; Validated
Probab=75.17 E-value=2.5 Score=39.96 Aligned_cols=58 Identities=21% Similarity=0.297 Sum_probs=45.0
Q ss_pred ChHHHHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccC--ChhhhhhcchhHH
Q psy3400 209 TSDDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL--SFKNMCKLKPLLQ 272 (417)
Q Consensus 209 ~~~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL--S~knm~kLkPlLq 272 (417)
..+-++.|+..+|+-|...|+||.+++..++. ++++|.++|+-.. ++..+.+|--+|.
T Consensus 79 ~~elv~dy~~rIkeaRe~kglSQeeLA~~lgv------s~stI~~iE~G~~~Ps~~~l~kLak~l~ 138 (176)
T PRK08359 79 TEDIVEDYAERVYEAIQKSGLSYEELSHEVGL------SVNDLRRIAHGEYEPTIKEAKKLERYFK 138 (176)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHCCCcCCCHHHHHHHHHHhC
Confidence 45667789999999999999999999988754 7889999987765 4455555544443
No 56
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=74.59 E-value=2.8 Score=36.95 Aligned_cols=40 Identities=20% Similarity=0.334 Sum_probs=33.7
Q ss_pred HHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccC
Q psy3400 214 EAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL 259 (417)
Q Consensus 214 e~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL 259 (417)
..|.+.+|..|...|+||.+++..+|. ++++|+++|+...
T Consensus 4 ~~~g~rlk~~R~~~gltq~~lA~~~gv------s~~~is~~E~g~~ 43 (135)
T PRK09706 4 LTLGQRIRYRRKQLKLSQRSLAKAVKV------SHVSISQWERDET 43 (135)
T ss_pred hhHHHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCC
Confidence 457888999999999999999998865 6788888887653
No 57
>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=74.05 E-value=0.98 Score=35.30 Aligned_cols=46 Identities=13% Similarity=0.190 Sum_probs=30.8
Q ss_pred CCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchh
Q psy3400 299 KKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNR 348 (417)
Q Consensus 299 RkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNR 348 (417)
++|..|+.+++..+-..+. -....+.+||.++||+..+|..|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHHHH
Confidence 4678899998887777662 234678899999999999999995433
No 58
>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=73.91 E-value=2.3 Score=31.06 Aligned_cols=33 Identities=33% Similarity=0.481 Sum_probs=25.7
Q ss_pred HHhhhhhhccchhhhhhhhhcccccccccccccchhccc
Q psy3400 220 FKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ 258 (417)
Q Consensus 220 fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lq 258 (417)
+|+.|...|+||.+++..+|. ++++|.++|+..
T Consensus 1 ik~~r~~~gls~~~la~~~gi------s~~~i~~~~~g~ 33 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLGI------SRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHTS-------HHHHHHHHTTS
T ss_pred CHHHHHHcCCCHHHHHHHhCC------CcchhHHHhcCC
Confidence 577888999999999998863 778888888764
No 59
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=68.46 E-value=2.9 Score=31.64 Aligned_cols=36 Identities=33% Similarity=0.458 Sum_probs=26.7
Q ss_pred HHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccC
Q psy3400 218 KQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL 259 (417)
Q Consensus 218 k~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL 259 (417)
+.||+.|...|+||.+|+..++. +.++++++|+-+.
T Consensus 2 ~~lk~~r~~~~lt~~~~a~~~~i------~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 2 ERLKELREEKGLTQKDLAEKLGI------SRSTISKIENGKR 37 (64)
T ss_dssp HHHHHHHHHCT--HHHHHHHHTS-------HHHHHHHHTTSS
T ss_pred HHHHHHHHHcCCCHHHHHHHHCc------CHHHHHHHHCCCc
Confidence 45799999999999999998765 5778888876654
No 60
>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=67.97 E-value=2.5 Score=29.42 Aligned_cols=44 Identities=14% Similarity=0.178 Sum_probs=31.9
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhh
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKE 352 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~ 352 (417)
++..++..++..|... ....+||..++++..+|+.|....|.+.
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 4566677776665322 3466789999999999999987666553
No 61
>PRK10072 putative transcriptional regulator; Provisional
Probab=66.39 E-value=3.5 Score=35.17 Aligned_cols=37 Identities=24% Similarity=0.357 Sum_probs=29.4
Q ss_pred HHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccC
Q psy3400 217 AKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL 259 (417)
Q Consensus 217 ak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL 259 (417)
..+||..|..+|+||.+++..+|. +++||+++|....
T Consensus 35 ~~eik~LR~~~glTQ~elA~~lGv------S~~TVs~WE~G~r 71 (96)
T PRK10072 35 FTEFEQLRKGTGLKIDDFARVLGV------SVAMVKEWESRRV 71 (96)
T ss_pred hHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCC
Confidence 355788899999999999998874 6778888776543
No 62
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=65.83 E-value=4.4 Score=40.75 Aligned_cols=52 Identities=19% Similarity=0.278 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhccc--CChhhhhhcc
Q psy3400 211 DDLEAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSFKNMCKLK 268 (417)
Q Consensus 211 ~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lq--LS~knm~kLk 268 (417)
+=+..|.+.+|..|...|+||.+++..+|. ++++|.++|+.. .++.+..++-
T Consensus 24 ~~~~~~g~rl~~~R~~~gltq~~lA~~~gv------s~~~i~~~E~g~~~ps~~~l~~ia 77 (309)
T PRK08154 24 PFLAALGERVRTLRARRGMSRKVLAQASGV------SERYLAQLESGQGNVSILLLRRVA 77 (309)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHCc------CHHHHHHHHCCCCCCCHHHHHHHH
Confidence 334668888999999999999999987764 677888887664 3444444433
No 63
>KOG3755|consensus
Probab=65.29 E-value=1.9 Score=47.58 Aligned_cols=50 Identities=22% Similarity=0.282 Sum_probs=37.5
Q ss_pred HHHHhhhccCCCCCCHHHHHHHHHHcC-------CCCCchhcccchhhhhhhccCCC
Q psy3400 309 KGALETHFHKQPKPSAQEITTLADSLQ-------LEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 309 l~~LE~~F~~n~yPS~~er~eLA~~Lg-------Ls~~qVqVWFQNRR~K~KR~~~~ 358 (417)
..+-+.+|.++..++...+.+.-+.+. .+...|+.||.|||.++||.+-.
T Consensus 704 ~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 704 YEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred eecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 334466788888888887777666554 34567999999999999997654
No 64
>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=64.86 E-value=5.7 Score=24.62 Aligned_cols=37 Identities=5% Similarity=0.137 Sum_probs=25.2
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhccc
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWF 345 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWF 345 (417)
++..++..+...|... + ...++|+.++++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 4555555555555432 2 45678999999999998884
No 65
>cd00131 PAX Paired Box domain
Probab=64.67 E-value=13 Score=32.93 Aligned_cols=45 Identities=16% Similarity=0.029 Sum_probs=28.4
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCC-------CCCchhcccchh
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQL-------EKEVVRVWFCNR 348 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgL-------s~~qVqVWFQNR 348 (417)
.+..+...++.....++..+..|+.++...-++ +..+|-.||+++
T Consensus 76 ~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 76 ATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 345555666666678888888877654223355 677777776653
No 66
>KOG1146|consensus
Probab=64.41 E-value=3.8 Score=48.78 Aligned_cols=65 Identities=14% Similarity=-0.002 Sum_probs=57.0
Q ss_pred CCCCceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCCCCC
Q psy3400 298 RKKRTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNTLG 362 (417)
Q Consensus 298 RRkRT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~~~g 362 (417)
+-.|+.++..+...|...|+...+|...+...+++.|++--+.+-.||+++++++.+.......+
T Consensus 445 ~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg 509 (1406)
T KOG1146|consen 445 LLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARG 509 (1406)
T ss_pred hhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhcccccccccc
Confidence 34577888999999999999999999999999999999999999999999999888776665543
No 67
>PF13551 HTH_29: Winged helix-turn helix
Probab=64.28 E-value=12 Score=30.63 Aligned_cols=71 Identities=14% Similarity=0.330 Sum_probs=41.8
Q ss_pred HHHHHHhhhcCCCCCCchhHHhh-cCCCCCCCceechhhHHHHhhhccCCC-----CCCHHHHHH-H-HHHc--CCCCCc
Q psy3400 271 LQKWLEEADSTTGSPTSIDKIAA-QGRKRKKRTSIEVTVKGALETHFHKQP-----KPSAQEITT-L-ADSL--QLEKEV 340 (417)
Q Consensus 271 LqkWLeEae~~~~s~~s~~~~~~-~~kkRRkRT~fT~~Ql~~LE~~F~~n~-----yPS~~er~e-L-A~~L--gLs~~q 340 (417)
+.+|+..-+... ++.+.. ..+..+.+..++.++...|.+.+..++ ..+..++.+ | .+.. .++.++
T Consensus 29 v~r~~~~~~~~G-----~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~t 103 (112)
T PF13551_consen 29 VYRWLKRYREGG-----IEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPST 103 (112)
T ss_pred HHHHHHHHHccc-----HHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHH
Confidence 344666554322 333433 222334444489999999999998876 355565554 4 3333 467777
Q ss_pred hhcccc
Q psy3400 341 VRVWFC 346 (417)
Q Consensus 341 VqVWFQ 346 (417)
|+.|+.
T Consensus 104 i~r~L~ 109 (112)
T PF13551_consen 104 IRRILK 109 (112)
T ss_pred HHHHHH
Confidence 877764
No 68
>KOG0773|consensus
Probab=63.71 E-value=8.7 Score=38.96 Aligned_cols=43 Identities=30% Similarity=0.377 Sum_probs=37.6
Q ss_pred cCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 317 HKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 317 ~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
..++|++..+...++....|+..+|.+||-|.|.+.++..+..
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~ 159 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMT 159 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCC
Confidence 4689999999999999999999999999999999877765553
No 69
>PF13565 HTH_32: Homeodomain-like domain
Probab=61.50 E-value=20 Score=27.86 Aligned_cols=40 Identities=13% Similarity=0.264 Sum_probs=29.4
Q ss_pred chhhHHHHhhhccCCCCCCHHHHHH-HHHHcCC----CCCchhcc
Q psy3400 305 EVTVKGALETHFHKQPKPSAQEITT-LADSLQL----EKEVVRVW 344 (417)
Q Consensus 305 T~~Ql~~LE~~F~~n~yPS~~er~e-LA~~LgL----s~~qVqVW 344 (417)
+.++...|.+.+..++..+..++.. |.+++|+ +.++|..|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 6777788899999998888888865 6666664 55555544
No 70
>PHA00542 putative Cro-like protein
Probab=61.24 E-value=7.5 Score=31.73 Aligned_cols=39 Identities=28% Similarity=0.371 Sum_probs=28.5
Q ss_pred hhhhhhccchhhhhhhhhcccccccccccccchhcccC---Chhhhhh
Q psy3400 222 QRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL---SFKNMCK 266 (417)
Q Consensus 222 ~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL---S~knm~k 266 (417)
..+...|+||.+++..+|. ++.+|++++.... ++..+.+
T Consensus 25 ~~l~~~glTq~elA~~lgI------s~~tIsr~e~g~~~~p~~~~l~k 66 (82)
T PHA00542 25 CALIRAGWSQEQIADATDV------SQPTICRIYSGRHKDPRYSVVEK 66 (82)
T ss_pred HHHHHCCCCHHHHHHHHCc------CHHHHHHHHcCCCCCCCHHHHHH
Confidence 3345668999999998876 8889999987663 3444444
No 71
>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=59.38 E-value=6.8 Score=28.69 Aligned_cols=43 Identities=12% Similarity=0.228 Sum_probs=28.7
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhh
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQK 351 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K 351 (417)
+++.+..++...|.. .....+||+.+|+++..|++|.+.-|.|
T Consensus 11 L~~~~r~i~~l~~~~-----g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQ-----GMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-----CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 455666666655433 3457899999999999999999866654
No 72
>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=58.74 E-value=6.4 Score=30.14 Aligned_cols=40 Identities=18% Similarity=0.265 Sum_probs=31.2
Q ss_pred echhhHHHHhhhccCC--CCCCHHHHHHHHHHcCCCCCchhc
Q psy3400 304 IEVTVKGALETHFHKQ--PKPSAQEITTLADSLQLEKEVVRV 343 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n--~yPS~~er~eLA~~LgLs~~qVqV 343 (417)
+|..|+.+|...|..- .+|-.....+||+.||+++..|..
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 4778899999887655 346666678999999999987654
No 73
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=58.59 E-value=6.2 Score=36.25 Aligned_cols=42 Identities=19% Similarity=0.305 Sum_probs=33.0
Q ss_pred HHHhhhhhhccchhhhhhhhhcccccccccccccchhccc----CChhhhhh
Q psy3400 219 QFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ----LSFKNMCK 266 (417)
Q Consensus 219 ~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lq----LS~knm~k 266 (417)
.+|..|..+|+||.+++..+|. ++.+|+++|+-. .++.++.+
T Consensus 29 ~Ir~~R~~lGmTq~eLAerlGV------S~~tIs~iE~G~~~~~psl~~L~k 74 (150)
T TIGR02612 29 WVRAIRKALGMSGAQLAGRLGV------TPQRVEALEKSELSGTVTLKTLRA 74 (150)
T ss_pred HHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCCCHHHHHH
Confidence 4688899999999999988764 788999999875 35444444
No 74
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=57.36 E-value=8.8 Score=35.00 Aligned_cols=50 Identities=12% Similarity=0.043 Sum_probs=38.6
Q ss_pred CceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 301 RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 301 RT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
...+++.|+.+|+..+ + .....+||+.||++...|+.|..+.|.|.|+..
T Consensus 4 ~~~Lt~rqreVL~lr~-~-----GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-R-----GLTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred ccCCCHHHHHHHHHHH-c-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567888999987743 1 133568999999999999999998888776643
No 75
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=57.20 E-value=11 Score=33.13 Aligned_cols=47 Identities=15% Similarity=0.057 Sum_probs=35.5
Q ss_pred HHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhccc--CChhhhhh
Q psy3400 214 EAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSFKNMCK 266 (417)
Q Consensus 214 e~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lq--LS~knm~k 266 (417)
+-|...+++.|...|+||.+|+..+|. ++++|.++|+-. .++..+.+
T Consensus 4 ~i~~~~l~~ll~~~Glsq~eLA~~~Gi------s~~~is~iE~g~~~ps~~~l~k 52 (120)
T PRK13890 4 YIFFTNVLRLLDERHMTKKELSERSGV------SISFLSDLTTGKANPSLKVMEA 52 (120)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCc------CHHHHHHHHcCCCCCCHHHHHH
Confidence 347778888899999999999988764 678888888754 34444444
No 76
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=56.49 E-value=12 Score=35.62 Aligned_cols=53 Identities=17% Similarity=0.211 Sum_probs=28.9
Q ss_pred HHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCChhhhhhcchhHHHHHHhh
Q psy3400 218 KQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEA 278 (417)
Q Consensus 218 k~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWLeEa 278 (417)
+++|.+--.-.|+|+.|...-|. ||+.|+.|=...+.+++.. |-.|..|+.-.
T Consensus 121 eeIK~fl~~h~IsQ~~V~q~TGi------sQS~lSq~L~kGt~Mk~qK--R~alY~Wy~~~ 173 (180)
T PF04814_consen 121 EEIKAFLQQHNISQREVVQVTGI------SQSHLSQHLNKGTPMKEQK--RRALYRWYVRK 173 (180)
T ss_dssp HHHHHHHHHCT--CHHHHHHHT--------HHHHHHHHCTB----HHH--HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCcHHHHHHHhhh------hHHHHHHHHHcCCCccHHH--HHHHHHHHHHH
Confidence 33333333334599999987654 8999998844444444433 47888998643
No 77
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=55.17 E-value=6.5 Score=31.75 Aligned_cols=33 Identities=33% Similarity=0.481 Sum_probs=25.8
Q ss_pred HHHhhhhhhccchhhhhhhhhcccccccccccccchhcc
Q psy3400 219 QFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEAL 257 (417)
Q Consensus 219 ~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~l 257 (417)
.+|+.|..+|+||.+++..+|. +-.||..+|+-
T Consensus 5 k~k~~R~~~~ltQ~elA~~vgV------sRQTi~~iEkg 37 (68)
T COG1476 5 KLKELRAELGLTQEELAKLVGV------SRQTIIAIEKG 37 (68)
T ss_pred HHHHHHHHhCcCHHHHHHHcCc------CHHHHHHHHcC
Confidence 6789999999999999998876 44466666544
No 78
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=53.38 E-value=11 Score=32.86 Aligned_cols=48 Identities=13% Similarity=0.090 Sum_probs=35.5
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
.++..++.++...|-.. ....+||+.||++..+|++|...-|.|.|+.
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 45566677666554332 3477999999999999999998777777653
No 79
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=52.15 E-value=8.9 Score=35.26 Aligned_cols=50 Identities=8% Similarity=0.076 Sum_probs=37.5
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
.++..++.+|...|... ....+||+.||++..+|+++....|++.|+...
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 35666666665544222 346789999999999999999988888887654
No 80
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=51.12 E-value=45 Score=34.12 Aligned_cols=99 Identities=23% Similarity=0.268 Sum_probs=62.0
Q ss_pred hHHHHHHHHHHHhhhh-hhc-cchhhhhhhhhcccccccccccccchhcccCChhhhhhcchhHHHHHHhhhcCCCCCCc
Q psy3400 210 SDDLEAFAKQFKQRRI-KLG-FTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWLEEADSTTGSPTS 287 (417)
Q Consensus 210 ~~ele~Fak~fK~rRI-~lG-~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWLeEae~~~~s~~s 287 (417)
.+||+.|++-+.++-| .+. ++-.++...|..+....|+-+++.|. +..+|-+.+ |+....-....+.
T Consensus 31 rrDL~~f~~~L~~~~~~~l~~~~~~di~~yl~~l~~~g~s~~S~aR~---------lsalR~fy~-fl~~E~~~~~dP~- 99 (300)
T COG4974 31 RRDLEDFREWLEERGITDLADATEADIREYLTELAEQGLSATSIARA---------LSALRSFYQ-FLIREGLREDDPT- 99 (300)
T ss_pred HHHHHHHHHHHHhcCCCChhhcCHHHHHHHHHHHHhCCcChhhHHHH---------HHHHHHHHH-HHHHCCCcccCch-
Confidence 6899999999999977 564 88888888888888888888888773 233333333 4332222222222
Q ss_pred hhHHhhcCCCCCCCceechhhHHHHhhhccCCC
Q psy3400 288 IDKIAAQGRKRKKRTSIEVTVKGALETHFHKQP 320 (417)
Q Consensus 288 ~~~~~~~~kkRRkRT~fT~~Ql~~LE~~F~~n~ 320 (417)
..+...+..|+--..++.+|...|-..-..+.
T Consensus 100 -~~l~~PK~~~~LPk~Ls~~eve~Ll~~~~~~~ 131 (300)
T COG4974 100 -RLLDSPKLPKRLPKFLSEEEVEALLEAPDEDT 131 (300)
T ss_pred -hhhcCCCCCCcCCcccCHHHHHHHHhCCCCCC
Confidence 12233344444556788888888877444443
No 81
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=50.42 E-value=9.3 Score=28.64 Aligned_cols=46 Identities=13% Similarity=0.031 Sum_probs=33.8
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR 354 (417)
.||..++.+|.-...- ....+||..+++++++|+.+..|-+.|.+-
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 4677777777665432 346789999999999999999988887653
No 82
>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=48.71 E-value=8.7 Score=29.75 Aligned_cols=30 Identities=23% Similarity=0.328 Sum_probs=23.3
Q ss_pred HHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 325 QEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 325 ~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
-...+||+.||++.++|+.|-+ |.+|....
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~--r~~W~~~~ 43 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD--RYKWDELL 43 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH--hhCccccC
Confidence 3467899999999999999965 55655543
No 83
>PRK10072 putative transcriptional regulator; Provisional
Probab=48.43 E-value=13 Score=31.70 Aligned_cols=40 Identities=20% Similarity=0.218 Sum_probs=29.3
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhh
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQ 350 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~ 350 (417)
.+...+..|...-..+ ..+||+.+|++..+|+.|.+.+|.
T Consensus 33 ~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3556666665443222 668999999999999999987764
No 84
>smart00351 PAX Paired Box domain.
Probab=47.51 E-value=50 Score=28.95 Aligned_cols=43 Identities=14% Similarity=-0.018 Sum_probs=26.0
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCC-------CCCchhccc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQL-------EKEVVRVWF 345 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgL-------s~~qVqVWF 345 (417)
..+..+...++....+++..+..++.++-...|+ +..+|-.||
T Consensus 75 ~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 75 VATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred ccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 3444555566666778888888887553334444 445555554
No 85
>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=47.24 E-value=9.6 Score=31.86 Aligned_cols=48 Identities=13% Similarity=0.197 Sum_probs=34.6
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
.++..++..+...|.. .....+||+.+|+++..|+.|...-+.|.|+.
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 3456666666554322 23566899999999999999998888777653
No 86
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=45.40 E-value=10 Score=27.45 Aligned_cols=40 Identities=13% Similarity=0.153 Sum_probs=20.6
Q ss_pred ceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccc
Q psy3400 302 TSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFC 346 (417)
Q Consensus 302 T~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQ 346 (417)
..+|.+++..++..+.+. ....+||+.||.++.+|..|..
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 457778888888776533 4466799999999999987754
No 87
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=45.20 E-value=16 Score=25.87 Aligned_cols=44 Identities=14% Similarity=0.142 Sum_probs=30.4
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhh
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~K 353 (417)
++..++..+...+.. ....+||+.++++...|+.|...-+.|.+
T Consensus 4 l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 4 LTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 556666666553321 24578999999999999999876555443
No 88
>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=44.42 E-value=10 Score=29.95 Aligned_cols=20 Identities=20% Similarity=0.592 Sum_probs=17.5
Q ss_pred HHHHHHHHcCCCCCchhccc
Q psy3400 326 EITTLADSLQLEKEVVRVWF 345 (417)
Q Consensus 326 er~eLA~~LgLs~~qVqVWF 345 (417)
...+||++||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 35689999999999999994
No 89
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=44.42 E-value=13 Score=31.25 Aligned_cols=44 Identities=32% Similarity=0.462 Sum_probs=35.7
Q ss_pred CCCCChHHHHHHHHHHHhhh--hhhccchhhhhhhhhcccccccccccccch
Q psy3400 205 EDAPTSDDLEAFAKQFKQRR--IKLGFTQADVGLALGTLYGNVFSQTTICRF 254 (417)
Q Consensus 205 ~d~~~~~ele~Fak~fK~rR--I~lG~TQ~dVg~aLg~l~g~~~SQtTI~RF 254 (417)
+|..|.+|++.+++.++--+ +.-|.||.++...+|. |-.||+|-
T Consensus 24 ~dL~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgv------S~aTItRv 69 (87)
T PF01371_consen 24 EDLCTPDELEALAQRWQVAKELLDEGKSYREIAEETGV------SIATITRV 69 (87)
T ss_dssp HHHSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTS------THHHHHHH
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCC------CHHHHHHH
Confidence 35678999999999888766 5568999999988766 67788885
No 90
>PRK04217 hypothetical protein; Provisional
Probab=43.75 E-value=14 Score=32.31 Aligned_cols=52 Identities=12% Similarity=-0.017 Sum_probs=39.4
Q ss_pred ceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 302 TSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 302 T~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
..++.+++.++...|...- ...+||+.+++++.+|+..+...|.+.|.....
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~ 92 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLVE 92 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 3567777777776654332 567899999999999999999888887765443
No 91
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=43.24 E-value=22 Score=35.05 Aligned_cols=55 Identities=15% Similarity=0.263 Sum_probs=42.2
Q ss_pred HHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCChhhhhhcchhHHHHH
Q psy3400 215 AFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLQKWL 275 (417)
Q Consensus 215 ~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~kLkPlLqkWL 275 (417)
.+.+.+|.+|.-++++|.++.+.|+. |++-|+.+|..+-.+....-+|-+.+.-+
T Consensus 27 ~pge~lrKWR~~F~vSQ~elA~~l~v------SpSVISDYE~GRRk~Pg~~~vkk~V~ALI 81 (241)
T COG1709 27 DPGETLRKWREIFNVSQTELARELGV------SPSVISDYESGRRKSPGIAFVKKFVEALI 81 (241)
T ss_pred ChhHHHHHHHHHhCccHHHHHHHhCC------CcceeehhhccCccCccHHHHHHHHHHHH
Confidence 35577999999999999999998866 88899999988776555555555555433
No 92
>PRK01381 Trp operon repressor; Provisional
Probab=43.24 E-value=42 Score=29.06 Aligned_cols=59 Identities=29% Similarity=0.391 Sum_probs=40.6
Q ss_pred CCCChHHHHHHHHHHHhhhh-hhc-cchhhhhhhhhcccccccccccccchhcccCChhhhhh-cchhHHHHHHh
Q psy3400 206 DAPTSDDLEAFAKQFKQRRI-KLG-FTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCK-LKPLLQKWLEE 277 (417)
Q Consensus 206 d~~~~~ele~Fak~fK~rRI-~lG-~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~k-LkPlLqkWLeE 277 (417)
+..|.+|++.++..++--+. --| .||.++...+|. |-+||.|- +|+.| ..+-++.||+.
T Consensus 31 ~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGv------SiaTITRg-------sn~Lk~~~~~~k~~l~~ 92 (99)
T PRK01381 31 LLLTPDEREALGTRVRIVEELLRGELSQREIKQELGV------GIATITRG-------SNSLKTAPPEFKEWLEQ 92 (99)
T ss_pred HhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCC------ceeeehhh-------HHHhccCCHHHHHHHHH
Confidence 45778888888777766653 234 999999998876 66788874 24444 33566778765
No 93
>PRK09480 slmA division inhibitor protein; Provisional
Probab=43.21 E-value=16 Score=32.83 Aligned_cols=40 Identities=15% Similarity=0.190 Sum_probs=32.4
Q ss_pred HHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhh
Q psy3400 309 KGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRR 349 (417)
Q Consensus 309 l~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR 349 (417)
+......|..++. ....+..||++.|+++..+..+|.|+.
T Consensus 16 l~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 16 LQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 3444455666656 778899999999999999999999986
No 94
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=41.17 E-value=16 Score=34.60 Aligned_cols=40 Identities=15% Similarity=0.211 Sum_probs=34.4
Q ss_pred eechhhHHHHhhhccCC--CCCCHHHHHHHHHHcCCCCCchh
Q psy3400 303 SIEVTVKGALETHFHKQ--PKPSAQEITTLADSLQLEKEVVR 342 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n--~yPS~~er~eLA~~LgLs~~qVq 342 (417)
.+|..|+++|...|..- -+|-.....+||++||+++..+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 69999999999998766 56777788899999999997754
No 95
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=40.95 E-value=24 Score=27.49 Aligned_cols=34 Identities=24% Similarity=0.310 Sum_probs=26.1
Q ss_pred HHH-hhhhhhccchhhhhhhhhcccccccccccccchhccc
Q psy3400 219 QFK-QRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ 258 (417)
Q Consensus 219 ~fK-~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lq 258 (417)
.++ ..|...|+||.+++..+|. ++++|.++++..
T Consensus 8 ~i~~~~~~~~~~t~~~lA~~~gi------s~~tis~~~~g~ 42 (78)
T TIGR02607 8 ILREEFLEPLGLSIRALAKALGV------SRSTLSRIVNGR 42 (78)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCC
Confidence 356 5677889999999998864 677888887654
No 96
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=40.01 E-value=18 Score=31.45 Aligned_cols=42 Identities=12% Similarity=0.092 Sum_probs=28.9
Q ss_pred CceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccc
Q psy3400 301 RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFC 346 (417)
Q Consensus 301 RT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQ 346 (417)
|..|+.+++...-.....+.+ ...+||..+|++..+|..|..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 445777776655444433332 356789999999999999944
No 97
>PRK10403 transcriptional regulator NarP; Provisional
Probab=39.84 E-value=19 Score=31.66 Aligned_cols=49 Identities=14% Similarity=0.112 Sum_probs=37.6
Q ss_pred ceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 302 TSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 302 T~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
..+|..++..|+..... ....+||+.+++++++|++..+|-|.|-...+
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 35788888888765433 33568899999999999999999888865443
No 98
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=39.62 E-value=14 Score=33.17 Aligned_cols=30 Identities=17% Similarity=0.298 Sum_probs=26.2
Q ss_pred HHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 326 EITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 326 er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
..++||+.||+++..|+++...-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999888887765
No 99
>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=39.52 E-value=25 Score=23.77 Aligned_cols=33 Identities=36% Similarity=0.511 Sum_probs=22.7
Q ss_pred HHHhhhhhhccchhhhhhhhhcccccccccccccchhcc
Q psy3400 219 QFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEAL 257 (417)
Q Consensus 219 ~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~l 257 (417)
.++..|...++++.+++..++. ++.++++++..
T Consensus 3 ~l~~~~~~~~~s~~~~a~~~~~------~~~~v~~~~~g 35 (58)
T cd00093 3 RLKELRKEKGLTQEELAEKLGV------SRSTISRIENG 35 (58)
T ss_pred HHHHHHHHcCCCHHHHHHHHCC------CHHHHHHHHcC
Confidence 4566677778999999988764 44555555544
No 100
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=39.11 E-value=14 Score=32.44 Aligned_cols=33 Identities=15% Similarity=0.117 Sum_probs=27.4
Q ss_pred HHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 325 QEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 325 ~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
....+||+.+|+++.+|+.|..--|.|.|+...
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 345789999999999999999988888776543
No 101
>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.
Probab=38.97 E-value=8.1 Score=32.33 Aligned_cols=25 Identities=16% Similarity=0.169 Sum_probs=13.8
Q ss_pred HHHHHHHHHHhhhhhhccchhhhhh
Q psy3400 212 DLEAFAKQFKQRRIKLGFTQADVGL 236 (417)
Q Consensus 212 ele~Fak~fK~rRI~lG~TQ~dVg~ 236 (417)
|-..+|.++|+..-..+++|..++.
T Consensus 10 dT~~I~~~ik~~L~~~~IsQ~~Fa~ 34 (87)
T PF02376_consen 10 DTKEIARRIKEWLKRNNISQRVFAK 34 (87)
T ss_dssp -HHHHHHHHHHHHHHTT--HHHHHH
T ss_pred CHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 3445566666666666677877664
No 102
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=38.50 E-value=13 Score=33.41 Aligned_cols=49 Identities=8% Similarity=0.177 Sum_probs=35.4
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
.++..++.+++..|. .....++||+.||++..+|+++++..|.|.|+..
T Consensus 136 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 345555555554332 2345678999999999999999998888877653
No 103
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=38.42 E-value=17 Score=33.85 Aligned_cols=49 Identities=12% Similarity=0.032 Sum_probs=34.9
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
++..++.+|...| .......+||+.||++..+|+++....|.+.|+...
T Consensus 154 L~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 154 LPEAQQTVVKGVY-----FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4444555554332 222346789999999999999999988888887654
No 104
>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=38.17 E-value=16 Score=28.66 Aligned_cols=45 Identities=18% Similarity=0.180 Sum_probs=24.5
Q ss_pred CceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccc
Q psy3400 301 RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFC 346 (417)
Q Consensus 301 RT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQ 346 (417)
|..|+...+...-.+|.....--...|. .|.++++++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4567776665555555444332223333 49999999999999965
No 105
>PRK04140 hypothetical protein; Provisional
Probab=37.89 E-value=24 Score=36.21 Aligned_cols=48 Identities=25% Similarity=0.423 Sum_probs=35.9
Q ss_pred HHHHHhhhhhhccchhhhhhhhhcccccccccccccchhccc--CChhhhhhcchh
Q psy3400 217 AKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSFKNMCKLKPL 270 (417)
Q Consensus 217 ak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lq--LS~knm~kLkPl 270 (417)
.+.+|+.|...|+||.+++..+|. ++.+++++|... .+...+.++--+
T Consensus 128 GerLk~lRe~~GlSq~eLA~~lGV------Sr~tIskyE~G~~~Ps~e~~~kLa~~ 177 (317)
T PRK04140 128 GDVLREAREELGLSLGELASELGV------SRRTISKYENGGMNASIEVAIKLEEI 177 (317)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 466788999999999999998865 788999998743 344555554433
No 106
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.34 E-value=15 Score=32.46 Aligned_cols=49 Identities=12% Similarity=0.102 Sum_probs=35.7
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
.+++.++.+|...|.. .....+||..||++..+|+.|...-|.|.|+..
T Consensus 128 ~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4566667777655422 234568999999999999999987777777643
No 107
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=35.76 E-value=35 Score=29.58 Aligned_cols=46 Identities=13% Similarity=0.088 Sum_probs=35.1
Q ss_pred ceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhh
Q psy3400 302 TSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353 (417)
Q Consensus 302 T~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~K 353 (417)
..+|..++..|+- +..+. ...+||+.+++++++|+++.+|-|.|..
T Consensus 148 ~~lt~~e~~vl~l-~~~g~-----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKL-ITEGY-----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHH-HHCCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3478888887766 33332 2578899999999999999999888765
No 108
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=35.73 E-value=30 Score=37.01 Aligned_cols=45 Identities=22% Similarity=0.290 Sum_probs=36.4
Q ss_pred HHHHHHHHhhhhhhccchhhhhhhhhcccccccccccccchhcccC
Q psy3400 214 EAFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQL 259 (417)
Q Consensus 214 e~Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqL 259 (417)
+.|.+.+|+.|...|++|.++...++. .|..+++++|+++|+-..
T Consensus 2 ~~~~~rL~~~r~~~g~tq~~la~~~~~-~g~~vs~~~is~~e~g~~ 46 (517)
T PRK13355 2 TTFAERLKQAMKARGLKQEDLVHAAEA-RGVKLGKSHISQYVSGKT 46 (517)
T ss_pred chHHHHHHHHHHHCCCCHHHHHHHHHh-ccCCcCHHHHHHHHCCCC
Confidence 468889999999999999999988654 344578889999987653
No 109
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=35.54 E-value=19 Score=32.76 Aligned_cols=48 Identities=10% Similarity=0.004 Sum_probs=35.6
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
.++..++.++...|-. ....++||+.||++..+|+++....|.|.|+.
T Consensus 139 ~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4556666666654433 24477999999999999999998777777764
No 110
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=35.47 E-value=15 Score=25.24 Aligned_cols=25 Identities=20% Similarity=0.348 Sum_probs=20.8
Q ss_pred HHHHHHHcCCCCCchhcccchhhhh
Q psy3400 327 ITTLADSLQLEKEVVRVWFCNRRQK 351 (417)
Q Consensus 327 r~eLA~~LgLs~~qVqVWFQNRR~K 351 (417)
..++|+.|++++++|+.|..+.+..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 4688999999999999998765543
No 111
>PRK00118 putative DNA-binding protein; Validated
Probab=35.03 E-value=18 Score=31.34 Aligned_cols=48 Identities=6% Similarity=0.115 Sum_probs=34.7
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
++..|+.++...|... ....+||+.+|+++.+|+.|....|.+.|+..
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3455666665554332 34678999999999999999988887776643
No 112
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=34.87 E-value=19 Score=32.48 Aligned_cols=50 Identities=12% Similarity=0.077 Sum_probs=35.8
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
++..++.+|...|.. .....+||..||++..+|++++..-|.|.|+....
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 132 LPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 444555555554322 23467899999999999999999888888876543
No 113
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.44 E-value=15 Score=25.91 Aligned_cols=22 Identities=18% Similarity=0.101 Sum_probs=18.6
Q ss_pred HHHHHHHcCCCCCchhcccchh
Q psy3400 327 ITTLADSLQLEKEVVRVWFCNR 348 (417)
Q Consensus 327 r~eLA~~LgLs~~qVqVWFQNR 348 (417)
+.++|+.+|++.++|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4688999999999999996543
No 114
>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=34.02 E-value=6.3 Score=32.20 Aligned_cols=28 Identities=14% Similarity=0.253 Sum_probs=22.3
Q ss_pred CCCHHHHHHHHHHcCCCCCchhcccchh
Q psy3400 321 KPSAQEITTLADSLQLEKEVVRVWFCNR 348 (417)
Q Consensus 321 yPS~~er~eLA~~LgLs~~qVqVWFQNR 348 (417)
|-......+||+.|++++..|++|+.+.
T Consensus 29 ~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 29 EEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 3344457899999999999999998753
No 115
>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=33.67 E-value=20 Score=32.29 Aligned_cols=35 Identities=11% Similarity=0.016 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 322 PSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 322 PS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
.......+||+.||+++.+|+++....|.+.|+..
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34445679999999999999999988888877654
No 116
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=33.01 E-value=16 Score=26.26 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=17.3
Q ss_pred HHHHHHHHHcCCCCCchhcccch
Q psy3400 325 QEITTLADSLQLEKEVVRVWFCN 347 (417)
Q Consensus 325 ~er~eLA~~LgLs~~qVqVWFQN 347 (417)
....+||+.||++..+|..|.+.
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 45678999999999999999653
No 117
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=32.79 E-value=33 Score=31.30 Aligned_cols=55 Identities=16% Similarity=0.250 Sum_probs=38.4
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCCCCCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPNTLG 362 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~~~g 362 (417)
.++..++.++.-.|-. .....+||+.||++...|++..+..|.+.|+..-.-..+
T Consensus 131 ~L~~~~r~i~~l~~~~-----g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~~~~~~ 185 (189)
T PRK06811 131 DLEKLDREIFIRRYLL-----GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLNISLG 185 (189)
T ss_pred hCCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcccCcccC
Confidence 3555666666544322 234678999999999999999988888888766544333
No 118
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=32.31 E-value=28 Score=30.68 Aligned_cols=48 Identities=13% Similarity=0.118 Sum_probs=34.1
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
++..|+.+|.-.|.. .....+||..+|++...|+++....|.|.|+.+
T Consensus 113 L~~~~r~v~~l~~~~-----~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 113 LPLERRNVLLLRDYY-----GFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred CCHHHHHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 455555555544322 234678999999999999999988888777653
No 119
>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=32.08 E-value=36 Score=24.12 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=20.7
Q ss_pred HHHHHHHHcCCCCCchhcccchhhhh
Q psy3400 326 EITTLADSLQLEKEVVRVWFCNRRQK 351 (417)
Q Consensus 326 er~eLA~~LgLs~~qVqVWFQNRR~K 351 (417)
...+||+.++++.++|+.|...-+.+
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~~~ 42 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIMRK 42 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45788999999999999998744443
No 120
>PHA02591 hypothetical protein; Provisional
Probab=30.85 E-value=34 Score=28.61 Aligned_cols=28 Identities=29% Similarity=0.528 Sum_probs=21.7
Q ss_pred ChHHHHHHHHHHHhhhhhhccchhhhhhhhhc
Q psy3400 209 TSDDLEAFAKQFKQRRIKLGFTQADVGLALGT 240 (417)
Q Consensus 209 ~~~ele~Fak~fK~rRI~lG~TQ~dVg~aLg~ 240 (417)
..||+...|++| .++||||.+++..||.
T Consensus 44 ~~dd~~~vA~eL----~eqGlSqeqIA~~LGV 71 (83)
T PHA02591 44 SEDDLISVTHEL----ARKGFTVEKIASLLGV 71 (83)
T ss_pred ccchHHHHHHHH----HHcCCCHHHHHHHhCC
Confidence 456777777766 4679999999998876
No 121
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=30.83 E-value=35 Score=34.33 Aligned_cols=26 Identities=19% Similarity=0.335 Sum_probs=21.1
Q ss_pred HHHHHHHhhhhhhccchhhhhhhhhc
Q psy3400 215 AFAKQFKQRRIKLGFTQADVGLALGT 240 (417)
Q Consensus 215 ~Fak~fK~rRI~lG~TQ~dVg~aLg~ 240 (417)
.+-..||+.|..+|+|+.||...+..
T Consensus 3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I 28 (284)
T COG1426 3 TLGERLRQAREEKGLSLEDVAARTKI 28 (284)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHhCc
Confidence 45577999999999999999865543
No 122
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=30.36 E-value=28 Score=31.66 Aligned_cols=51 Identities=6% Similarity=0.199 Sum_probs=37.4
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
.++..++.+|+..|.. .....+||..+|++..+|++-+..-|.+.|+....
T Consensus 131 ~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (189)
T PRK12515 131 KLSPAHREIIDLVYYH-----EKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKA 181 (189)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666666554322 23467899999999999999999889888876554
No 123
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=30.22 E-value=29 Score=30.51 Aligned_cols=45 Identities=18% Similarity=0.145 Sum_probs=35.4
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhh
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~K 353 (417)
.+|..+...|+-.+.- ..+++||+.+++++++|++..++=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5777788777765543 25778999999999999999998887754
No 124
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=30.20 E-value=31 Score=32.83 Aligned_cols=49 Identities=6% Similarity=0.073 Sum_probs=36.8
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
++..++.++...|... ....+||..+|++...|+++...-|.|.|+...
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 233 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4556666666655322 346789999999999999999988888877543
No 125
>PF13518 HTH_28: Helix-turn-helix domain
Probab=30.16 E-value=26 Score=25.01 Aligned_cols=25 Identities=16% Similarity=0.426 Sum_probs=20.4
Q ss_pred HHHHHHHHcCCCCCchhcccchhhh
Q psy3400 326 EITTLADSLQLEKEVVRVWFCNRRQ 350 (417)
Q Consensus 326 er~eLA~~LgLs~~qVqVWFQNRR~ 350 (417)
...++|.++|++..+|..|.+.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3557999999999999999875544
No 126
>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=29.85 E-value=45 Score=30.28 Aligned_cols=48 Identities=15% Similarity=0.064 Sum_probs=37.6
Q ss_pred CceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhc
Q psy3400 301 RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354 (417)
Q Consensus 301 RT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR 354 (417)
.+.++..|+.+|+..+ + .....+||+.||+++..|+.|-..-|.|.|+
T Consensus 4 ~~~Lte~qr~VL~Lr~-~-----GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-K-----GLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-c-----CCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678888898887742 1 1246789999999999999998887777775
No 127
>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=29.57 E-value=32 Score=30.87 Aligned_cols=47 Identities=13% Similarity=0.087 Sum_probs=33.5
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
++..++.++...|-.. ....+||+.||+++.+|++....-|.+.|+.
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4455555555443222 3367899999999999999999888887764
No 128
>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=29.40 E-value=26 Score=30.81 Aligned_cols=33 Identities=9% Similarity=0.153 Sum_probs=27.6
Q ss_pred HHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 325 QEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 325 ~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
....+||..+|++..+|+++-...|.+.|+...
T Consensus 127 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 127 LSEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 346789999999999999999988888877543
No 129
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=29.33 E-value=20 Score=26.87 Aligned_cols=24 Identities=8% Similarity=0.115 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCCCCchhcccchhh
Q psy3400 326 EITTLADSLQLEKEVVRVWFCNRR 349 (417)
Q Consensus 326 er~eLA~~LgLs~~qVqVWFQNRR 349 (417)
.+.+||+.+|+++.+|..||.+++
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 356899999999999999999874
No 130
>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=29.01 E-value=47 Score=28.89 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=33.4
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR 354 (417)
.++..++.++...|. ......+||+.+|++..+|+++...-|.|.|.
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 456666666665432 23457789999999999999998766666554
No 131
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=29.00 E-value=25 Score=30.24 Aligned_cols=46 Identities=7% Similarity=0.127 Sum_probs=32.5
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhc
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR 354 (417)
++..+...|...|. ......+||+.+|+++..|+++....|.|.|+
T Consensus 114 L~~~~r~il~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRF-----EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 44555555555432 22346679999999999999998877777765
No 132
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=28.92 E-value=34 Score=30.14 Aligned_cols=46 Identities=20% Similarity=0.058 Sum_probs=35.4
Q ss_pred ceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhh
Q psy3400 302 TSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353 (417)
Q Consensus 302 T~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~K 353 (417)
..+|..+...|...+.. ..+++||+.|+++.++|+++.++-|.|..
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 35777777777644333 55778999999999999999998887754
No 133
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=28.87 E-value=21 Score=31.38 Aligned_cols=50 Identities=12% Similarity=0.165 Sum_probs=35.5
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
++..++.++...|... ....+||+.||++..+|++.+...|.+.|+..+.
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 4455555555443222 2356899999999999999999888888876543
No 134
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=28.78 E-value=22 Score=31.69 Aligned_cols=37 Identities=11% Similarity=0.156 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 322 PSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 322 PS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
......++||+.+|++...|++.+..-|.|.|+..+.
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~ 170 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3444577999999999999999999999988886553
No 135
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.40 E-value=42 Score=30.37 Aligned_cols=30 Identities=13% Similarity=0.222 Sum_probs=25.5
Q ss_pred HHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 326 EITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 326 er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
...+||+.+|++...|++|...-|.+.|+.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 467899999999999999998777777654
No 136
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.27 E-value=33 Score=31.10 Aligned_cols=35 Identities=6% Similarity=0.045 Sum_probs=29.1
Q ss_pred HHHHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 325 QEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 325 ~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
....+||+.||++..+|+++....|.+.|+.....
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (186)
T PRK05602 145 LSNIEAAAVMDISVDALESLLARGRRALRAQLADL 179 (186)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 34678999999999999999998888888766543
No 137
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=28.17 E-value=1.1e+02 Score=26.57 Aligned_cols=56 Identities=32% Similarity=0.501 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHHhhhhhh-c-cchhhhhhhhhcccccccccccccchhcccCChhhhhh-cchhHHHHHHhh
Q psy3400 210 SDDLEAFAKQFKQRRIKL-G-FTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCK-LKPLLQKWLEEA 278 (417)
Q Consensus 210 ~~ele~Fak~fK~rRI~l-G-~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS~knm~k-LkPlLqkWLeEa 278 (417)
.+|.+..+..++-.+-=| | ++|.+|...||. +-.||.|= .|+.| +.|-++.||++.
T Consensus 40 pdEReal~~Rv~Iv~eLL~ge~sQREi~~~Lgv------siAtITRG-------SN~LK~~~~~~k~~L~~~ 98 (103)
T COG2973 40 PDEREALGTRVRIVEELLRGELSQREIAQKLGV------SIATITRG-------SNSLKTADPEFKQWLEKV 98 (103)
T ss_pred HhHHHHHHHHHHHHHHHHhccccHHHHHHHhCc------chhhhccc-------hhhhccCCHHHHHHHHHH
Confidence 344454444333332222 3 788888877765 44556552 35555 557888898763
No 138
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=28.07 E-value=38 Score=29.78 Aligned_cols=48 Identities=13% Similarity=0.221 Sum_probs=36.3
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
++..+..+|...| . .....+||..||++...|+++...-|.+.|+...
T Consensus 113 L~~~~r~il~l~~-~-----g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 113 MTERDRTVLLLRF-S-----GYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CCHHHHHHHHHHH-c-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5566666666665 2 2346789999999999999999888888777543
No 139
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=27.82 E-value=1.2e+02 Score=28.74 Aligned_cols=21 Identities=14% Similarity=0.042 Sum_probs=13.8
Q ss_pred CCCCCceechhhHHHHhhhcc
Q psy3400 297 KRKKRTSIEVTVKGALETHFH 317 (417)
Q Consensus 297 kRRkRT~fT~~Ql~~LE~~F~ 317 (417)
+++.+..++.+++..|.....
T Consensus 107 ~~~~~~~l~~ee~~~l~~~~~ 127 (299)
T PRK00283 107 PRRLPKTLSEAQVEALLDAPD 127 (299)
T ss_pred CCcCCCCCCHHHHHHHHhcCC
Confidence 334455688888887766653
No 140
>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=27.39 E-value=37 Score=30.52 Aligned_cols=50 Identities=14% Similarity=0.094 Sum_probs=37.3
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
.++..++.+|...|... ....+||..||++..+|+++...-|.+.|+...
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666654332 346789999999999999999888888777654
No 141
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=27.21 E-value=30 Score=31.48 Aligned_cols=32 Identities=13% Similarity=0.094 Sum_probs=27.0
Q ss_pred HHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 324 AQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 324 ~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
.....+||+.+|++...|++|+...|.|.|+.
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999998888877764
No 142
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=27.17 E-value=27 Score=26.59 Aligned_cols=20 Identities=20% Similarity=0.245 Sum_probs=17.5
Q ss_pred HHHHHHHcCCCCCchhcccc
Q psy3400 327 ITTLADSLQLEKEVVRVWFC 346 (417)
Q Consensus 327 r~eLA~~LgLs~~qVqVWFQ 346 (417)
+.++|+.+|++.++|+.|=.
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999943
No 143
>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=26.77 E-value=35 Score=29.99 Aligned_cols=47 Identities=15% Similarity=0.143 Sum_probs=32.7
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR 354 (417)
.++..++.+|...|- ......+||+.||+++.+|++...--|.|.|+
T Consensus 122 ~L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFG-----QNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345555666655432 22346789999999999999998766666665
No 144
>PRK10651 transcriptional regulator NarL; Provisional
Probab=25.71 E-value=53 Score=28.91 Aligned_cols=46 Identities=15% Similarity=0.117 Sum_probs=35.8
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKR 354 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR 354 (417)
.+|..+.++|+-...- ....+||++|++++++|++..+|-|.|..-
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 4888888888765421 235678999999999999999998888654
No 145
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=25.23 E-value=52 Score=28.37 Aligned_cols=47 Identities=13% Similarity=0.139 Sum_probs=33.5
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
++..+...|+..+... .-.+||+.+++++.+|+++-++-|.|.++.+
T Consensus 142 l~~~e~~vl~~~~~~~------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~ 188 (202)
T PRK09390 142 LSERERQVMDGLVAGL------SNKVIARDLDISPRTVEVYRANVMTKMQAGS 188 (202)
T ss_pred hhhhHHHHHHHHHccC------chHHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence 5566666666433322 2566899999999999999998888876543
No 146
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.19 E-value=58 Score=27.60 Aligned_cols=42 Identities=10% Similarity=0.157 Sum_probs=33.1
Q ss_pred CceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCC-CCCchhcccc
Q psy3400 301 RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQL-EKEVVRVWFC 346 (417)
Q Consensus 301 RT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgL-s~~qVqVWFQ 346 (417)
|..|+.+.+..+-+.+....+ ...+||.++|+ ...++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 677999888777776655554 57789999996 9999999944
No 147
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=24.94 E-value=44 Score=31.68 Aligned_cols=53 Identities=13% Similarity=0.082 Sum_probs=36.7
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
.++..++.++...|.. .+-......+||+.||++..+|+++...-|.|.|+..
T Consensus 178 ~Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3556666666665521 0122234678999999999999999888888877653
No 148
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.71 E-value=43 Score=30.72 Aligned_cols=48 Identities=4% Similarity=0.001 Sum_probs=34.4
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
++..++.++...|.. .....+||..||+++.+|+++...-|.+.|+..
T Consensus 135 Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 135 LPAQQARVFMMREYL-----ELSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred CCHHHHHHHhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 455556555554422 233678999999999999999988888777654
No 149
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=24.65 E-value=47 Score=30.31 Aligned_cols=49 Identities=16% Similarity=0.070 Sum_probs=34.8
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
++..++.+|...| .......+||..+|+++..|++.+..-|.+.|+...
T Consensus 107 L~~~~r~i~~l~~-----~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 107 LPEKYAEALRLTE-----LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CCHHHHHHHHHHH-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4455555554433 223447789999999999999999888887776544
No 150
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=24.60 E-value=36 Score=32.70 Aligned_cols=51 Identities=14% Similarity=0.082 Sum_probs=39.7
Q ss_pred CceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 301 RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 301 RT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
...+|..++++|.-.. ....-.+||..|++++++|+.+..|-|.|.+..++
T Consensus 169 ~~~Lt~re~evl~~~a------~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 169 AGVLSEREREVLAWTA------LGRRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hccCCHHHHHHHHHHH------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 3468888888887643 22446788999999999999999999988775543
No 151
>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=24.56 E-value=44 Score=24.06 Aligned_cols=37 Identities=8% Similarity=0.223 Sum_probs=23.8
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhccc
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWF 345 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWF 345 (417)
++.++...+.+.+..- ..+.+||+.+|++..+|.-++
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 5555555555555443 347789999999999987765
No 152
>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=24.47 E-value=43 Score=29.73 Aligned_cols=31 Identities=16% Similarity=0.270 Sum_probs=26.2
Q ss_pred HHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 325 QEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 325 ~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
....+||+.||++..+|+++..-.|.+.|+.
T Consensus 136 ~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 136 LTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999998888877764
No 153
>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=24.27 E-value=30 Score=24.47 Aligned_cols=19 Identities=21% Similarity=0.279 Sum_probs=15.7
Q ss_pred HHHHHHHcCCCCCchhccc
Q psy3400 327 ITTLADSLQLEKEVVRVWF 345 (417)
Q Consensus 327 r~eLA~~LgLs~~qVqVWF 345 (417)
+.++|+.+|++.++|+.|=
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 4678999999999999993
No 154
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=24.26 E-value=46 Score=29.25 Aligned_cols=49 Identities=10% Similarity=0.085 Sum_probs=34.0
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
.+++.++.+|...|... ....+||+.+|++..+|+....-.|.+.|+..
T Consensus 109 ~L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34555666665544222 23678999999999999999777777766654
No 155
>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=24.14 E-value=48 Score=31.27 Aligned_cols=48 Identities=13% Similarity=0.132 Sum_probs=37.0
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
.++..++.+|...|... ....+||..+|++...|+.+....+.|.|+.
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 46777788887776332 2467899999999999999988888777754
No 156
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=24.06 E-value=36 Score=31.04 Aligned_cols=36 Identities=17% Similarity=0.190 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 322 PSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 322 PS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
.......+||+.||++..+|+++....|.+.|+...
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 334457789999999999999999888888877543
No 157
>PRK06930 positive control sigma-like factor; Validated
Probab=23.97 E-value=43 Score=31.08 Aligned_cols=50 Identities=18% Similarity=0.131 Sum_probs=36.9
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
.++..++.++...|... ....+||..||++..+|+++....|.|.++...
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46666677666644222 236789999999999999999988888876543
No 158
>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=23.97 E-value=22 Score=25.53 Aligned_cols=21 Identities=10% Similarity=0.083 Sum_probs=19.2
Q ss_pred HHHHHcCCCCCchhcccchhh
Q psy3400 329 TLADSLQLEKEVVRVWFCNRR 349 (417)
Q Consensus 329 eLA~~LgLs~~qVqVWFQNRR 349 (417)
+||+.+|++..+|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999884
No 159
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.91 E-value=46 Score=30.74 Aligned_cols=33 Identities=9% Similarity=0.014 Sum_probs=28.2
Q ss_pred HHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 326 EITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 326 er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
...+||..||++...|++++..-|.+.|+....
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 467899999999999999999888888776554
No 160
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=23.81 E-value=52 Score=28.71 Aligned_cols=50 Identities=6% Similarity=0.129 Sum_probs=35.5
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
.++..++.++.-.|-.. ....+||+.||++...|++.....|.+.|+...
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 106 KLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35566666666543222 236789999999999999998888877776543
No 161
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.76 E-value=46 Score=29.59 Aligned_cols=48 Identities=8% Similarity=0.005 Sum_probs=34.1
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
++..++.++...|. .....++||..||++..+|+++...-|.+.|+..
T Consensus 113 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 113 LSADQREAIILIGA-----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 44455555544332 2234678999999999999999998888877654
No 162
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=23.66 E-value=36 Score=32.83 Aligned_cols=50 Identities=10% Similarity=0.040 Sum_probs=37.0
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
.++..++.+|...|-. .....+||..||++..+|+.|...-|.|.|+...
T Consensus 205 ~L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~ 254 (257)
T PRK08583 205 VLSDREKSIIQCTFIE-----NLSQKETGERLGISQMHVSRLQRQAIKKLREAAF 254 (257)
T ss_pred hCCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 3566677777665532 2235789999999999999999888888776543
No 163
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=23.44 E-value=56 Score=32.28 Aligned_cols=50 Identities=12% Similarity=-0.033 Sum_probs=38.8
Q ss_pred CceechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 301 RTSIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 301 RT~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
...+|..++++|.-... .....+||+.|++++++|+.+..|-+.|.+..+
T Consensus 188 ~~~LT~RE~evl~l~a~------G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILAWVRD------GKTNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHHHHHC------CCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 34688888888886432 234568899999999999999999988876544
No 164
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=23.16 E-value=53 Score=29.77 Aligned_cols=50 Identities=8% Similarity=0.041 Sum_probs=35.7
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
.++..++.+++-.|- ......+||+.||++..+|+.+....|.+.|+...
T Consensus 131 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12539 131 RLPEKMRLAIQAVKL-----EGLSVAEAATRSGMSESAVKVSVHRGLKALAALIG 180 (184)
T ss_pred hCCHHHHHHHHHHHH-----cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHh
Confidence 355556656654332 23456789999999999999999888888776543
No 165
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=23.16 E-value=49 Score=32.48 Aligned_cols=43 Identities=12% Similarity=0.056 Sum_probs=26.4
Q ss_pred CceechhhHHHHhhhccCCCCC--CHHHHHHHHHHcCCCCCchhc
Q psy3400 301 RTSIEVTVKGALETHFHKQPKP--SAQEITTLADSLQLEKEVVRV 343 (417)
Q Consensus 301 RT~fT~~Ql~~LE~~F~~n~yP--S~~er~eLA~~LgLs~~qVqV 343 (417)
||.-|.+....--+.|.+-.+. .....++||..+|++++.|+-
T Consensus 172 ~t~HS~~av~rYi~~F~rV~~l~~~~~~~~eia~~tg~S~~Lv~e 216 (220)
T PF07900_consen 172 RTNHSPEAVDRYIKDFKRVLMLYEKGMSPEEIAFITGMSERLVKE 216 (220)
T ss_pred HhccCHHHHHHHHHhhHHhHHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 4555555555555556555443 334456788888888887764
No 166
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=23.14 E-value=44 Score=32.20 Aligned_cols=33 Identities=12% Similarity=0.128 Sum_probs=28.0
Q ss_pred HHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 325 QEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 325 ~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
....+||+.||++...|++.....|.|.|+...
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999988888887654
No 167
>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=22.97 E-value=51 Score=31.75 Aligned_cols=48 Identities=13% Similarity=0.075 Sum_probs=36.2
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
.++..++.++...|... ....+||..+|++...|+.+...-+.|.|+.
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45666777776665433 2357899999999999999998888877753
No 168
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.87 E-value=63 Score=29.57 Aligned_cols=33 Identities=9% Similarity=0.121 Sum_probs=27.4
Q ss_pred HHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 325 QEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 325 ~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
....+||+.||++..+|++.+...|.|.|+...
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~ 203 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKYLE 203 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999998888888777543
No 169
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=22.69 E-value=48 Score=30.42 Aligned_cols=50 Identities=8% Similarity=0.079 Sum_probs=35.0
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
++..++.++.-.|. .....++||+.||++..+|++++.-.|.+.|+....
T Consensus 137 L~~~~r~i~~L~~~-----~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 186 (196)
T PRK12524 137 LPERQRQAVVLRHI-----EGLSNPEIAEVMEIGVEAVESLTARGKRALAALLAG 186 (196)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 44555544444332 123366899999999999999999888888876543
No 170
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=22.61 E-value=67 Score=25.92 Aligned_cols=34 Identities=24% Similarity=0.247 Sum_probs=20.7
Q ss_pred HHHHHHhhhhhhccchhhhhhhhhcccccccccccccc
Q psy3400 216 FAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICR 253 (417)
Q Consensus 216 Fak~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~R 253 (417)
+.+-++.+.| .||.++...|... |-..+|+||+|
T Consensus 10 I~~li~~~~i---~sQ~eL~~~L~~~-Gi~vTQaTiSR 43 (70)
T PF01316_consen 10 IKELISEHEI---SSQEELVELLEEE-GIEVTQATISR 43 (70)
T ss_dssp HHHHHHHS------SHHHHHHHHHHT-T-T--HHHHHH
T ss_pred HHHHHHHCCc---CCHHHHHHHHHHc-CCCcchhHHHH
Confidence 3344455555 4999999888774 77789999988
No 171
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=22.55 E-value=40 Score=32.53 Aligned_cols=47 Identities=11% Similarity=0.158 Sum_probs=34.4
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
+...++.++...|. ......+||..||++...|++++..-|.+.|+.
T Consensus 202 L~~~~r~vl~l~~~-----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 202 LSEKEQLVISLFYK-----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45555666655442 223467899999999999999998888887764
No 172
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=22.43 E-value=57 Score=29.01 Aligned_cols=49 Identities=8% Similarity=0.107 Sum_probs=34.6
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
++..++.+|...|-. ....++||+.||+++..|++.....|.+.|+...
T Consensus 119 L~~~~r~vl~L~~~~-----g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 119 LSPEHRAVLVRSYYR-----GWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 445555555554322 2236789999999999999998888888777654
No 173
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.04 E-value=40 Score=29.88 Aligned_cols=51 Identities=14% Similarity=0.087 Sum_probs=36.0
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
.++..++.++...| ......++||..||++..+|++|...-|.|.|+....
T Consensus 108 ~L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 108 TLPVIEAQAILLCD-----VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred hCCHHHHHHHHhHH-----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 34555555554332 2223467899999999999999999888888876543
No 174
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=21.89 E-value=40 Score=30.91 Aligned_cols=41 Identities=15% Similarity=0.231 Sum_probs=30.7
Q ss_pred HHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhh
Q psy3400 309 KGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQ 350 (417)
Q Consensus 309 l~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~ 350 (417)
+....+.|.+..|-... ..+||+..|+++..+..+|.|+..
T Consensus 17 l~aa~~lf~~~G~~~~t-i~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 17 IETAIAQFALRGVSNTT-LNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHHcCcccCC-HHHHHHHcCCCHHHHHHHcCCHHH
Confidence 34444556666654443 678999999999999999999865
No 175
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=21.81 E-value=33 Score=35.67 Aligned_cols=49 Identities=12% Similarity=0.209 Sum_probs=41.3
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhh
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEK 353 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~K 353 (417)
+|..+..+|...|... --.....++|+..+++++++|+.+=++.=.|.|
T Consensus 280 Lt~rE~~Vi~~R~gl~-~~~~~TLeevg~~~~isrERvRQIE~kAl~KLr 328 (342)
T COG0568 280 LTERERRVIRLRFGLD-DGEPKTLEELGEEFGISRERVRQIEAKALRKLR 328 (342)
T ss_pred CCHHHHHHHHHHhccC-CCCcchHHHHHHHhCCcHHHHHHHHHHHHHHHH
Confidence 8899999999999886 233667889999999999999999887766666
No 176
>KOG3755|consensus
Probab=21.75 E-value=44 Score=37.38 Aligned_cols=66 Identities=27% Similarity=0.334 Sum_probs=53.9
Q ss_pred cCCCCCCCceechhhHHHHhhhccC-CCCCCHHH---HHHHHHHcCCCCCchhcccchhhhhhhccCCCC
Q psy3400 294 QGRKRKKRTSIEVTVKGALETHFHK-QPKPSAQE---ITTLADSLQLEKEVVRVWFCNRRQKEKRMTPPN 359 (417)
Q Consensus 294 ~~kkRRkRT~fT~~Ql~~LE~~F~~-n~yPS~~e---r~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~~ 359 (417)
...+.++|+.+..+-+..|...-.. --||+... +..|+..+++.++.+...|+|.|...|+..+.+
T Consensus 644 n~~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~~w~~k 713 (769)
T KOG3755|consen 644 NWHKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKHHWKLK 713 (769)
T ss_pred hccCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecchhheec
Confidence 4557788999999999888776433 35888888 889999999999999999999999877665554
No 177
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=21.35 E-value=64 Score=29.20 Aligned_cols=48 Identities=13% Similarity=0.122 Sum_probs=35.8
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
.++..|+.++.-.|... ...++||..||+++.+|++.....+.+++..
T Consensus 127 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 45666776666644322 2467899999999999999999888887665
No 178
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=21.32 E-value=42 Score=32.72 Aligned_cols=50 Identities=18% Similarity=0.186 Sum_probs=36.8
Q ss_pred echhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 304 IEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 304 fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
++..++.+|...|.. .....+||..+|++..+|+.+..--+.|.|+....
T Consensus 204 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~ 253 (256)
T PRK07408 204 LEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQP 253 (256)
T ss_pred CCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhc
Confidence 455555666555532 34567899999999999999999888888776543
No 179
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.23 E-value=57 Score=33.25 Aligned_cols=55 Identities=15% Similarity=0.176 Sum_probs=40.8
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
.++..++.+|+..|-.. +-.....++||..||++..+|+.+....|.|.|+....
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~ 316 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQT 316 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 56777777887666221 12334567899999999999999999888888876543
No 180
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=20.91 E-value=42 Score=26.13 Aligned_cols=36 Identities=17% Similarity=0.195 Sum_probs=22.6
Q ss_pred HHHhhhhhhccchhhhhhhhhcccccccccccccchhcccCC
Q psy3400 219 QFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLS 260 (417)
Q Consensus 219 ~fK~rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~lqLS 260 (417)
.||+.|...|+|..+|...+.. +...|..+|.-++.
T Consensus 1 ~Lr~~R~~~glsl~~va~~t~I------~~~~l~aiE~~~~~ 36 (62)
T PF13413_consen 1 RLREAREAKGLSLEDVAEETKI------SVSYLEAIENGDFD 36 (62)
T ss_dssp -HHHHHHCTT--HHHHHHHCS--------HHHHHHHHCT-GC
T ss_pred ChHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHCcChh
Confidence 3789999999999999976533 44566666666544
No 181
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=20.57 E-value=51 Score=29.31 Aligned_cols=34 Identities=9% Similarity=0.079 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHcCCCCCchhcccchhhhhhhccC
Q psy3400 323 SAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMT 356 (417)
Q Consensus 323 S~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~ 356 (417)
.....++||..||++...|+++....|.+.|+..
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l 174 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEW 174 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHHh
Confidence 3455778999999999999999988888877643
No 182
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=20.41 E-value=82 Score=31.62 Aligned_cols=49 Identities=16% Similarity=0.158 Sum_probs=32.3
Q ss_pred CCChHHHHHHHHHHHh---hhhhhccchhhhhhhhhcccccccccccccchhc
Q psy3400 207 APTSDDLEAFAKQFKQ---RRIKLGFTQADVGLALGTLYGNVFSQTTICRFEA 256 (417)
Q Consensus 207 ~~~~~ele~Fak~fK~---rRI~lG~TQ~dVg~aLg~l~g~~~SQtTI~RFE~ 256 (417)
.-+..|...+.+.+++ +-...++||.++...|+. .|...++++|+++..
T Consensus 112 dLsfIE~A~~~~~l~~l~e~~~g~~ltq~ela~~lgk-~g~~isrs~Isn~lr 163 (258)
T TIGR03764 112 DLTFIEKALGVQKARALYEKELGESLSQRELARRLSA-DGYPISQSHISRMGD 163 (258)
T ss_pred CCCHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHhcc-cCCCCCHHHHHHHHH
Confidence 3344555555555553 333367999999999877 455568888888643
No 183
>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=20.39 E-value=44 Score=28.95 Aligned_cols=35 Identities=17% Similarity=0.202 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHcCCCCCchhcccchhhhhhhcc
Q psy3400 321 KPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRM 355 (417)
Q Consensus 321 yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~ 355 (417)
|.......+||..||+++.+|+++..-.|.|.|+.
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34445678999999999999999998777776653
No 184
>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=20.33 E-value=47 Score=30.28 Aligned_cols=36 Identities=8% Similarity=0.040 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCC
Q psy3400 322 PSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTP 357 (417)
Q Consensus 322 PS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~ 357 (417)
.......+||..||++...|+++...-|.+.|+...
T Consensus 145 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 334457799999999999999999988888887654
No 185
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.03 E-value=63 Score=23.54 Aligned_cols=23 Identities=22% Similarity=0.211 Sum_probs=18.8
Q ss_pred HHHHHHHHHcCCCCCchhcccch
Q psy3400 325 QEITTLADSLQLEKEVVRVWFCN 347 (417)
Q Consensus 325 ~er~eLA~~LgLs~~qVqVWFQN 347 (417)
.-.+.||+.+|+++++|+.+...
T Consensus 26 pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHH
Confidence 34678999999999999888653
No 186
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.01 E-value=48 Score=29.68 Aligned_cols=51 Identities=10% Similarity=0.051 Sum_probs=36.5
Q ss_pred eechhhHHHHhhhccCCCCCCHHHHHHHHHHcCCCCCchhcccchhhhhhhccCCC
Q psy3400 303 SIEVTVKGALETHFHKQPKPSAQEITTLADSLQLEKEVVRVWFCNRRQKEKRMTPP 358 (417)
Q Consensus 303 ~fT~~Ql~~LE~~F~~n~yPS~~er~eLA~~LgLs~~qVqVWFQNRR~K~KR~~~~ 358 (417)
.++..++.++.-.|-. .....+||+.||++...|+++...-|.++++....
T Consensus 119 ~Lp~~~r~v~~L~~~~-----g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 119 KLSSKARAAFLYNRLD-----GMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 3455566665554322 23467899999999999999999888888876543
Done!