Query 048741
Match_columns 314
No_of_seqs 260 out of 1183
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 12:36:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048741.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048741hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04770 ZF-HD_dimer: ZF-HD pr 100.0 4.7E-39 1E-43 240.7 2.3 58 80-137 2-60 (60)
2 TIGR01566 ZF_HD_prot_N ZF-HD h 100.0 5E-39 1.1E-43 233.6 1.8 52 83-134 1-53 (53)
3 TIGR01565 homeo_ZF_HD homeobox 99.8 2E-21 4.3E-26 145.6 6.5 58 241-298 1-58 (58)
4 KOG0843 Transcription factor E 99.7 1.4E-17 3E-22 149.4 3.5 65 239-307 100-164 (197)
5 KOG2251 Homeobox transcription 99.7 4.7E-17 1E-21 149.5 4.4 67 237-307 33-99 (228)
6 KOG0484 Transcription factor P 99.7 8.3E-18 1.8E-22 140.0 -0.7 64 238-305 14-77 (125)
7 KOG0485 Transcription factor N 99.6 1.3E-16 2.9E-21 146.9 4.9 66 237-306 100-165 (268)
8 KOG0494 Transcription factor C 99.6 2.2E-16 4.8E-21 148.5 5.5 69 240-312 140-208 (332)
9 KOG0489 Transcription factor z 99.6 7.9E-17 1.7E-21 150.8 1.2 66 239-308 157-222 (261)
10 KOG0488 Transcription factor B 99.6 8.9E-16 1.9E-20 147.4 4.6 63 238-304 169-231 (309)
11 KOG0844 Transcription factor E 99.6 1.7E-15 3.7E-20 145.2 4.3 65 237-305 177-241 (408)
12 PF00046 Homeobox: Homeobox do 99.6 1E-15 2.2E-20 110.7 1.8 57 242-302 1-57 (57)
13 KOG0493 Transcription factor E 99.5 3.4E-15 7.4E-20 140.7 2.8 60 242-305 247-306 (342)
14 KOG0842 Transcription factor t 99.5 1.9E-14 4.1E-19 138.2 7.7 65 238-306 150-214 (307)
15 KOG0850 Transcription factor D 99.5 6E-15 1.3E-19 136.5 3.6 63 240-306 121-183 (245)
16 KOG0487 Transcription factor A 99.5 2.5E-14 5.5E-19 137.4 4.3 64 240-307 234-297 (308)
17 KOG0492 Transcription factor M 99.4 1.2E-13 2.5E-18 126.8 3.1 61 241-305 144-204 (246)
18 KOG3802 Transcription factor O 99.4 5.6E-13 1.2E-17 131.2 7.5 64 238-305 291-354 (398)
19 KOG0486 Transcription factor P 99.4 2.8E-13 6E-18 130.2 4.6 63 240-306 111-173 (351)
20 KOG4577 Transcription factor L 99.4 1.8E-13 3.9E-18 130.6 3.0 62 240-305 166-227 (383)
21 smart00389 HOX Homeodomain. DN 99.4 3.3E-13 7.1E-18 96.5 3.0 56 242-301 1-56 (56)
22 cd00086 homeodomain Homeodomai 99.4 3.6E-13 7.8E-18 96.6 2.8 58 242-303 1-58 (59)
23 KOG0848 Transcription factor C 99.3 2.4E-13 5.2E-18 128.5 -0.4 61 239-303 197-257 (317)
24 KOG0490 Transcription factor, 99.3 1.5E-12 3.4E-17 115.7 3.5 63 239-305 58-120 (235)
25 COG5576 Homeodomain-containing 99.2 6.6E-12 1.4E-16 110.6 4.0 64 239-306 49-112 (156)
26 KOG0847 Transcription factor, 99.2 2.5E-12 5.5E-17 119.1 1.3 70 239-312 165-234 (288)
27 KOG0491 Transcription factor B 99.2 9.4E-13 2E-17 117.3 -1.7 65 240-308 99-163 (194)
28 KOG0483 Transcription factor H 99.2 7E-12 1.5E-16 114.3 2.2 56 246-305 55-110 (198)
29 KOG1168 Transcription factor A 99.0 7.7E-11 1.7E-15 112.9 2.5 68 239-310 307-374 (385)
30 KOG0849 Transcription factor P 99.0 1.4E-10 3E-15 113.4 2.3 63 239-305 174-236 (354)
31 KOG0490 Transcription factor, 98.2 5.5E-07 1.2E-11 80.2 2.2 64 238-305 150-213 (235)
32 KOG1146 Homeobox protein [Gene 98.1 2E-06 4.3E-11 95.2 4.0 64 238-305 900-963 (1406)
33 KOG2252 CCAAT displacement pro 98.0 2.9E-06 6.3E-11 87.2 3.2 57 240-300 419-475 (558)
34 KOG0775 Transcription factor S 97.7 2E-05 4.4E-10 75.5 3.4 48 252-303 187-234 (304)
35 KOG0774 Transcription factor P 97.6 6.2E-05 1.3E-09 72.0 3.8 62 242-304 189-250 (334)
36 PF05920 Homeobox_KN: Homeobox 97.3 3E-05 6.4E-10 54.2 -1.1 35 265-299 6-40 (40)
37 PF04218 CENP-B_N: CENP-B N-te 95.4 0.011 2.4E-07 43.3 2.3 47 242-297 1-47 (53)
38 KOG3623 Homeobox transcription 94.4 0.027 5.9E-07 60.6 2.7 52 248-304 564-615 (1007)
39 KOG0773 Transcription factor M 94.1 0.041 8.8E-07 53.2 3.2 61 240-302 238-299 (342)
40 PF11569 Homez: Homeodomain le 92.9 0.028 6.1E-07 42.4 -0.1 41 253-297 10-50 (56)
41 PF01527 HTH_Tnp_1: Transposas 90.4 0.11 2.3E-06 39.0 0.7 44 243-294 2-45 (76)
42 cd00569 HTH_Hin_like Helix-tur 78.8 1.9 4.1E-05 25.6 2.1 38 247-293 5-42 (42)
43 PF04967 HTH_10: HTH DNA bindi 78.0 1.7 3.6E-05 32.3 2.0 41 248-290 1-41 (53)
44 PRK03975 tfx putative transcri 74.3 1.1 2.3E-05 39.5 0.1 48 246-303 5-52 (141)
45 cd06171 Sigma70_r4 Sigma70, re 71.3 1.4 3E-05 29.3 0.1 44 247-299 10-53 (55)
46 COG2963 Transposase and inacti 64.1 7.1 0.00015 31.8 3.0 42 245-294 5-47 (116)
47 PRK12512 RNA polymerase sigma 62.2 3.7 7.9E-05 35.4 1.0 53 247-308 131-183 (184)
48 PF13936 HTH_38: Helix-turn-he 61.7 0.75 1.6E-05 32.2 -2.8 39 246-293 3-41 (44)
49 PF08281 Sigma70_r4_2: Sigma-7 60.9 1.4 2.9E-05 31.2 -1.6 41 248-297 11-51 (54)
50 PF02796 HTH_7: Helix-turn-hel 60.7 2.4 5.3E-05 29.6 -0.3 38 247-293 5-42 (45)
51 PF09607 BrkDBD: Brinker DNA-b 60.6 4.8 0.0001 30.7 1.2 45 245-294 3-47 (58)
52 PHA02893 hypothetical protein; 60.4 3.3 7.1E-05 33.9 0.3 10 115-124 67-76 (88)
53 PF06056 Terminase_5: Putative 58.8 4 8.7E-05 30.6 0.6 37 256-303 6-42 (58)
54 smart00421 HTH_LUXR helix_turn 57.3 2.8 6.1E-05 28.5 -0.5 45 247-301 3-47 (58)
55 PRK09413 IS2 repressor TnpA; R 57.2 5.8 0.00013 33.1 1.3 42 245-294 10-51 (121)
56 PF00196 GerE: Bacterial regul 56.1 2.1 4.4E-05 31.0 -1.4 45 247-301 3-47 (58)
57 KOG3623 Homeobox transcription 56.0 9.6 0.00021 42.0 3.0 62 239-304 624-685 (1007)
58 PRK09646 RNA polymerase sigma 55.7 2 4.3E-05 37.7 -1.8 49 247-304 142-190 (194)
59 PRK06424 transcription factor; 54.7 12 0.00027 32.9 3.0 24 275-298 100-123 (144)
60 PF04545 Sigma70_r4: Sigma-70, 54.5 3 6.5E-05 29.2 -0.7 46 247-301 4-49 (50)
61 PRK10072 putative transcriptio 53.4 5.5 0.00012 32.8 0.6 40 248-298 33-72 (96)
62 KOG1146 Homeobox protein [Gene 53.0 8.6 0.00019 44.5 2.2 62 240-305 443-504 (1406)
63 PRK09652 RNA polymerase sigma 52.7 5.2 0.00011 33.6 0.3 48 247-303 128-175 (182)
64 PRK06759 RNA polymerase factor 52.6 5.6 0.00012 33.0 0.5 48 247-303 106-153 (154)
65 TIGR02989 Sig-70_gvs1 RNA poly 51.9 3.8 8.3E-05 34.1 -0.6 47 247-302 111-157 (159)
66 PRK12519 RNA polymerase sigma 51.8 2.7 5.9E-05 36.5 -1.5 32 272-303 157-188 (194)
67 PRK02220 4-oxalocrotonate taut 50.4 30 0.00064 24.9 4.0 34 249-296 13-46 (61)
68 PRK12526 RNA polymerase sigma 50.0 6.5 0.00014 35.0 0.5 49 247-304 153-201 (206)
69 PRK04217 hypothetical protein; 49.7 6.7 0.00014 33.2 0.5 47 247-302 42-88 (110)
70 TIGR02939 RpoE_Sigma70 RNA pol 49.7 2.8 6.1E-05 36.0 -1.8 32 273-304 155-186 (190)
71 PRK00118 putative DNA-binding 49.0 7.1 0.00015 32.7 0.6 47 247-302 17-63 (104)
72 PF13384 HTH_23: Homeodomain-l 48.8 4.3 9.3E-05 28.1 -0.7 22 274-295 19-40 (50)
73 COG3413 Predicted DNA binding 48.6 12 0.00027 33.9 2.1 41 247-289 155-195 (215)
74 TIGR02937 sigma70-ECF RNA poly 48.4 5.9 0.00013 31.4 0.0 47 247-302 110-156 (158)
75 TIGR03879 near_KaiC_dom probab 48.2 3.3 7.1E-05 32.8 -1.4 27 271-297 31-57 (73)
76 PF13698 DUF4156: Domain of un 48.1 6.6 0.00014 31.9 0.3 18 85-102 51-68 (93)
77 PRK09639 RNA polymerase sigma 47.1 6.7 0.00014 33.0 0.1 47 247-303 112-158 (166)
78 PRK09642 RNA polymerase sigma 46.7 8.4 0.00018 32.3 0.7 48 247-303 106-153 (160)
79 PRK09648 RNA polymerase sigma 46.5 2.9 6.3E-05 36.3 -2.2 49 246-303 138-186 (189)
80 PRK09644 RNA polymerase sigma 46.3 3.2 7E-05 35.2 -1.9 48 247-304 108-156 (165)
81 PRK12514 RNA polymerase sigma 45.9 9.7 0.00021 32.6 0.9 30 274-303 147-176 (179)
82 PRK12541 RNA polymerase sigma 45.7 3 6.5E-05 35.1 -2.2 49 247-304 112-160 (161)
83 PRK10100 DNA-binding transcrip 45.6 4.7 0.0001 36.9 -1.1 47 247-303 155-201 (216)
84 PRK05602 RNA polymerase sigma 45.4 7.3 0.00016 33.7 0.1 37 274-310 146-182 (186)
85 COG2944 Predicted transcriptio 44.1 9.5 0.00021 32.2 0.6 40 248-298 44-83 (104)
86 PRK12537 RNA polymerase sigma 44.0 11 0.00025 32.5 1.1 48 247-303 133-180 (182)
87 PRK12546 RNA polymerase sigma 43.1 4.2 9E-05 36.0 -1.8 32 273-304 130-161 (188)
88 PRK12530 RNA polymerase sigma 42.9 3.6 7.7E-05 36.1 -2.2 48 247-303 134-181 (189)
89 TIGR02999 Sig-70_X6 RNA polyme 42.8 9.9 0.00021 32.5 0.5 47 248-303 135-181 (183)
90 TIGR02959 SigZ RNA polymerase 42.4 10 0.00022 32.6 0.5 48 247-303 100-147 (170)
91 smart00109 C1 Protein kinase C 42.3 15 0.00033 24.7 1.3 29 99-133 13-41 (49)
92 TIGR02948 SigW_bacill RNA poly 41.8 4.6 0.0001 34.5 -1.7 48 247-303 136-183 (187)
93 TIGR02985 Sig70_bacteroi1 RNA 41.4 6.8 0.00015 32.1 -0.7 29 274-302 131-159 (161)
94 PRK12513 RNA polymerase sigma 40.7 3.4 7.4E-05 36.0 -2.7 37 270-306 153-189 (194)
95 PRK10403 transcriptional regul 40.4 5.9 0.00013 33.0 -1.2 48 246-303 152-199 (215)
96 cd00029 C1 Protein kinase C co 40.3 13 0.00029 25.3 0.8 30 99-133 13-42 (50)
97 PF01381 HTH_3: Helix-turn-hel 40.3 11 0.00023 26.4 0.3 22 276-297 13-34 (55)
98 TIGR02983 SigE-fam_strep RNA p 40.1 11 0.00024 31.5 0.4 49 247-304 110-158 (162)
99 TIGR02950 SigM_subfam RNA poly 39.9 9.5 0.00021 31.5 -0.0 34 269-302 118-151 (154)
100 PRK06811 RNA polymerase factor 39.5 5.1 0.00011 35.0 -1.8 49 247-304 131-179 (189)
101 PRK12539 RNA polymerase sigma 39.4 6 0.00013 34.3 -1.3 49 247-304 131-179 (184)
102 cd04762 HTH_MerR-trunc Helix-T 39.4 7.7 0.00017 25.6 -0.5 25 275-299 3-27 (49)
103 PRK09047 RNA polymerase factor 39.0 13 0.00028 31.0 0.6 48 247-303 106-153 (161)
104 PRK02289 4-oxalocrotonate taut 38.9 68 0.0015 23.4 4.4 33 249-295 13-45 (60)
105 PF06163 DUF977: Bacterial pro 38.7 11 0.00024 32.9 0.2 44 247-294 4-48 (127)
106 PRK12516 RNA polymerase sigma 38.3 5.3 0.00011 35.2 -1.9 30 274-303 134-163 (187)
107 PRK12547 RNA polymerase sigma 38.2 4.5 9.8E-05 34.4 -2.3 48 247-303 112-159 (164)
108 TIGR03070 couple_hipB transcri 38.1 14 0.0003 25.5 0.6 35 255-297 6-40 (58)
109 PRK09726 antitoxin HipB; Provi 38.1 20 0.00043 28.1 1.6 21 276-296 29-49 (88)
110 PRK11924 RNA polymerase sigma 38.0 13 0.00029 31.0 0.6 30 274-303 143-172 (179)
111 TIGR02947 SigH_actino RNA poly 37.9 5.1 0.00011 35.0 -2.1 35 269-303 144-178 (193)
112 PRK12536 RNA polymerase sigma 37.7 13 0.00029 32.1 0.5 31 273-303 146-176 (181)
113 TIGR00721 tfx DNA-binding prot 37.0 11 0.00024 33.0 -0.0 48 245-302 4-51 (137)
114 TIGR00270 conserved hypothetic 36.7 8.8 0.00019 34.0 -0.7 23 275-297 85-107 (154)
115 PHA02535 P terminase ATPase su 36.7 22 0.00047 38.1 2.0 42 246-296 1-42 (581)
116 PRK09649 RNA polymerase sigma 36.5 5.4 0.00012 34.9 -2.1 29 274-302 148-176 (185)
117 TIGR02954 Sig70_famx3 RNA poly 35.9 14 0.00031 31.3 0.5 48 247-303 119-166 (169)
118 PF10668 Phage_terminase: Phag 35.9 8.8 0.00019 29.4 -0.7 21 274-294 24-44 (60)
119 PRK07037 extracytoplasmic-func 35.8 14 0.0003 31.0 0.4 30 274-303 127-156 (163)
120 PRK12520 RNA polymerase sigma 35.7 3.9 8.6E-05 35.6 -3.1 48 247-303 131-178 (191)
121 TIGR02952 Sig70_famx2 RNA poly 35.3 13 0.00028 31.2 0.0 47 247-302 122-168 (170)
122 PRK13919 putative RNA polymera 34.9 17 0.00037 31.2 0.8 48 247-303 135-182 (186)
123 PRK05657 RNA polymerase sigma 34.7 13 0.00028 36.3 -0.0 52 247-303 262-313 (325)
124 PRK12524 RNA polymerase sigma 34.6 6.2 0.00013 34.6 -2.0 48 247-303 136-183 (196)
125 PRK08301 sporulation sigma fac 34.6 12 0.00026 33.9 -0.3 52 247-303 178-229 (234)
126 PRK08295 RNA polymerase factor 34.4 10 0.00022 33.1 -0.7 47 247-303 155-201 (208)
127 cd04761 HTH_MerR-SF Helix-Turn 34.2 9.6 0.00021 25.9 -0.7 24 275-298 3-26 (49)
128 PRK12538 RNA polymerase sigma 34.0 6 0.00013 36.5 -2.3 31 273-303 188-218 (233)
129 PRK12523 RNA polymerase sigma 33.9 6.8 0.00015 33.5 -1.9 52 247-307 119-170 (172)
130 PRK12545 RNA polymerase sigma 33.9 7 0.00015 34.7 -1.9 31 273-303 156-186 (201)
131 PRK12543 RNA polymerase sigma 33.8 6.8 0.00015 33.8 -1.9 31 273-303 134-164 (179)
132 PRK12515 RNA polymerase sigma 33.7 5.9 0.00013 34.4 -2.3 48 246-303 130-178 (189)
133 PF13518 HTH_28: Helix-turn-he 33.4 12 0.00025 25.8 -0.4 24 274-297 14-37 (52)
134 PF13551 HTH_29: Winged helix- 33.1 38 0.00083 26.4 2.5 20 243-262 53-72 (112)
135 PF13443 HTH_26: Cro/C1-type H 32.8 9.8 0.00021 27.4 -0.9 25 274-298 12-36 (63)
136 PRK12532 RNA polymerase sigma 32.7 7.1 0.00015 34.1 -2.0 31 273-303 153-183 (195)
137 PF01710 HTH_Tnp_IS630: Transp 32.6 25 0.00054 29.3 1.4 39 247-294 2-40 (119)
138 PRK01271 4-oxalocrotonate taut 32.6 92 0.002 24.6 4.5 34 249-296 14-47 (76)
139 cd06170 LuxR_C_like C-terminal 32.6 12 0.00025 25.6 -0.5 22 274-295 17-38 (57)
140 PRK12533 RNA polymerase sigma 32.5 7.5 0.00016 35.5 -1.9 31 273-303 151-181 (216)
141 PRK12535 RNA polymerase sigma 32.5 7.9 0.00017 34.4 -1.7 35 273-307 150-184 (196)
142 PF01361 Tautomerase: Tautomer 32.4 85 0.0018 22.5 4.0 33 249-295 12-44 (60)
143 PRK09645 RNA polymerase sigma 32.2 7.7 0.00017 33.0 -1.8 48 247-303 118-165 (173)
144 PRK06930 positive control sigm 32.1 12 0.00025 33.4 -0.7 48 247-303 114-161 (170)
145 PRK06986 fliA flagellar biosyn 31.7 9.6 0.00021 34.7 -1.3 31 273-303 201-231 (236)
146 PRK09637 RNA polymerase sigma 31.6 8.7 0.00019 33.6 -1.6 31 273-303 123-153 (181)
147 cd00093 HTH_XRE Helix-turn-hel 31.2 19 0.00041 23.2 0.4 20 277-296 17-36 (58)
148 PRK12518 RNA polymerase sigma 30.8 5.5 0.00012 33.8 -2.9 36 269-304 133-168 (175)
149 PRK12522 RNA polymerase sigma 30.7 8.7 0.00019 32.8 -1.7 31 273-303 136-166 (173)
150 PF05077 DUF678: Protein of un 30.6 20 0.00043 28.7 0.4 9 116-124 56-64 (74)
151 PRK09638 RNA polymerase sigma 30.6 8.2 0.00018 32.8 -1.9 33 271-303 141-173 (176)
152 PLN03207 stomagen; Provisional 30.5 41 0.00088 28.6 2.3 57 52-127 52-113 (113)
153 TIGR03541 reg_near_HchA LuxR f 30.4 14 0.0003 33.9 -0.5 50 245-304 169-218 (232)
154 PRK10360 DNA-binding transcrip 30.3 12 0.00026 31.3 -1.0 47 247-303 137-183 (196)
155 PRK12511 RNA polymerase sigma 30.0 8.8 0.00019 33.7 -1.9 49 247-304 111-159 (182)
156 TIGR03020 EpsA transcriptional 29.5 13 0.00028 35.2 -0.9 50 245-304 188-237 (247)
157 PRK09390 fixJ response regulat 29.4 13 0.00029 30.3 -0.8 47 248-304 142-188 (202)
158 PRK12531 RNA polymerase sigma 29.3 23 0.00051 31.0 0.7 49 247-304 141-189 (194)
159 PRK09651 RNA polymerase sigma 29.2 10 0.00023 32.5 -1.5 45 247-300 119-163 (172)
160 PRK00745 4-oxalocrotonate taut 29.2 1E+02 0.0022 22.1 4.0 34 249-296 13-46 (62)
161 PRK01964 4-oxalocrotonate taut 29.1 1E+02 0.0022 22.5 4.0 34 249-296 13-46 (64)
162 PRK09647 RNA polymerase sigma 28.9 18 0.00039 32.4 -0.1 31 274-304 156-186 (203)
163 PRK12542 RNA polymerase sigma 28.9 8.4 0.00018 33.3 -2.2 47 247-303 122-169 (185)
164 cd00491 4Oxalocrotonate_Tautom 28.7 1.3E+02 0.0027 21.1 4.3 35 249-297 12-46 (58)
165 PRK09641 RNA polymerase sigma 28.6 8.5 0.00018 32.9 -2.1 31 273-303 153-183 (187)
166 PRK15369 two component system 28.6 15 0.00033 30.1 -0.5 45 247-301 149-193 (211)
167 PRK11923 algU RNA polymerase s 28.4 9.5 0.00021 33.1 -1.9 32 272-303 154-185 (193)
168 PHA01976 helix-turn-helix prot 28.4 25 0.00053 25.6 0.6 18 277-294 20-37 (67)
169 PRK10651 transcriptional regul 28.2 14 0.00031 30.8 -0.8 46 247-302 155-200 (216)
170 PF12824 MRP-L20: Mitochondria 27.5 85 0.0018 28.3 3.9 44 244-293 82-125 (164)
171 TIGR02607 antidote_HigA addict 27.5 25 0.00053 26.2 0.5 18 277-294 23-40 (78)
172 PRK12540 RNA polymerase sigma 27.4 9.5 0.00021 33.4 -2.1 33 273-305 128-160 (182)
173 TIGR02957 SigX4 RNA polymerase 27.3 14 0.00031 34.7 -1.1 50 247-305 108-157 (281)
174 PRK12529 RNA polymerase sigma 27.3 8.8 0.00019 33.2 -2.3 48 247-303 127-174 (178)
175 TIGR02859 spore_sigH RNA polym 27.3 17 0.00037 31.4 -0.5 30 273-302 166-195 (198)
176 PRK09636 RNA polymerase sigma 26.9 12 0.00026 35.2 -1.6 50 247-305 115-164 (293)
177 KOG3755 SATB1 matrix attachmen 26.8 8.2 0.00018 41.6 -3.0 60 241-304 691-758 (769)
178 KOG2767 Translation initiation 26.6 20 0.00043 36.4 -0.2 17 116-132 117-133 (400)
179 PRK13558 bacterio-opsin activa 26.2 43 0.00092 34.7 2.1 40 246-289 606-647 (665)
180 PF13411 MerR_1: MerR HTH fami 26.2 15 0.00033 26.8 -0.9 22 275-296 3-24 (69)
181 TIGR02943 Sig70_famx1 RNA poly 26.0 27 0.00059 30.6 0.5 48 247-303 131-178 (188)
182 PTZ00397 macrophage migration 25.7 1.4E+02 0.003 24.4 4.6 36 249-298 70-105 (116)
183 TIGR02479 FliA_WhiG RNA polyme 25.2 27 0.00058 31.5 0.3 48 247-303 175-222 (224)
184 PF06252 DUF1018: Protein of u 25.0 75 0.0016 26.4 3.0 26 244-269 18-43 (119)
185 PF00440 TetR_N: Bacterial reg 25.0 26 0.00056 24.3 0.2 37 255-296 4-40 (47)
186 TIGR03001 Sig-70_gmx1 RNA poly 25.0 10 0.00022 35.4 -2.5 30 274-303 179-208 (244)
187 TIGR00013 taut 4-oxalocrotonat 24.7 1.6E+02 0.0035 21.1 4.3 34 249-296 13-46 (63)
188 PF11516 DUF3220: Protein of u 24.7 12 0.00026 30.8 -1.8 9 288-296 32-40 (106)
189 KOG0705 GTPase-activating prot 24.5 34 0.00073 37.0 0.9 36 97-133 514-550 (749)
190 PRK11511 DNA-binding transcrip 24.4 30 0.00066 28.8 0.5 42 250-296 8-49 (127)
191 PF12844 HTH_19: Helix-turn-he 24.0 25 0.00055 25.3 -0.0 23 275-297 15-37 (64)
192 PRK15008 HTH-type transcriptio 23.5 64 0.0014 28.6 2.4 36 258-298 29-64 (212)
193 PRK09935 transcriptional regul 23.4 21 0.00046 29.8 -0.6 46 246-301 148-193 (210)
194 PRK11922 RNA polymerase sigma 23.2 14 0.0003 33.6 -2.0 35 270-304 163-197 (231)
195 PF00130 C1_1: Phorbol esters/ 23.0 50 0.0011 23.1 1.4 30 99-133 13-42 (53)
196 PRK12544 RNA polymerase sigma 22.9 34 0.00074 30.7 0.5 30 274-303 166-195 (206)
197 PF07750 GcrA: GcrA cell cycle 22.8 97 0.0021 27.7 3.4 34 247-289 2-36 (162)
198 PRK09480 slmA division inhibit 22.7 51 0.0011 28.0 1.6 30 267-297 26-55 (194)
199 TIGR02846 spore_sigmaK RNA pol 22.7 22 0.00048 32.2 -0.7 53 246-303 173-225 (227)
200 PLN03162 golden-2 like transcr 22.5 74 0.0016 32.9 2.8 61 240-302 232-292 (526)
201 PRK09975 DNA-binding transcrip 22.2 31 0.00068 30.0 0.2 28 271-298 30-57 (213)
202 TIGR02394 rpoS_proteo RNA poly 22.0 30 0.00064 32.7 -0.0 52 247-303 222-273 (285)
203 PRK08583 RNA polymerase sigma 22.0 15 0.00033 33.8 -2.0 48 247-303 205-252 (257)
204 TIGR02960 SigX5 RNA polymerase 21.2 15 0.00032 34.6 -2.2 32 274-305 160-191 (324)
205 TIGR02980 SigBFG RNA polymeras 21.0 38 0.00083 30.4 0.5 47 247-302 178-224 (227)
206 TIGR01764 excise DNA binding d 21.0 25 0.00055 23.3 -0.5 23 275-297 4-26 (49)
207 PRK09415 RNA polymerase factor 21.0 14 0.00031 31.9 -2.2 29 274-302 145-173 (179)
208 PRK12534 RNA polymerase sigma 20.9 50 0.0011 28.4 1.2 47 247-302 137-183 (187)
209 cd04763 HTH_MlrA-like Helix-Tu 20.9 23 0.0005 26.1 -0.8 21 275-295 3-23 (68)
210 PRK12527 RNA polymerase sigma 20.8 13 0.00029 31.1 -2.4 30 274-303 123-152 (159)
211 PRK09640 RNA polymerase sigma 20.3 28 0.00061 30.2 -0.5 31 273-303 151-181 (188)
212 PRK00432 30S ribosomal protein 20.3 49 0.0011 24.2 0.8 18 103-124 26-44 (50)
213 PRK06704 RNA polymerase factor 20.2 15 0.00033 34.1 -2.3 31 274-304 134-164 (228)
214 PF13309 HTH_22: HTH domain 20.0 87 0.0019 23.6 2.2 40 246-289 19-59 (64)
No 1
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=100.00 E-value=4.7e-39 Score=240.74 Aligned_cols=58 Identities=78% Similarity=1.471 Sum_probs=55.1
Q ss_pred ceeeeHHhhhhhcccCCCcccccccccccC-CCCCCcccccccccccccchhhhhhhcc
Q 048741 80 KMVKYKECLKNHAAGMGGNATDGCGEFMPS-GEEGTIEALTCSACNCHRNFHRKEIEGE 137 (314)
Q Consensus 80 ~~v~Y~eClkNhaa~~Gg~a~DGCgEFm~~-~~~gt~~~l~CaaCgCHRnFHr~e~~~~ 137 (314)
.+|+||||||||||+||||||||||||||+ +++||+++|+||||||||||||||++++
T Consensus 2 ~~v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~~~al~CaACgCHRnFHRre~~~e 60 (60)
T PF04770_consen 2 KVVRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGTPEALKCAACGCHRNFHRREVEGE 60 (60)
T ss_pred CceeHHHHHhhHhHhhCCcccccccccccCCCCCCCcccceecccCcchhcccCCcCCC
Confidence 478999999999999999999999999999 8999999999999999999999998753
No 2
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=100.00 E-value=5e-39 Score=233.65 Aligned_cols=52 Identities=79% Similarity=1.421 Sum_probs=50.1
Q ss_pred eeHHhhhhhcccCCCccccccccccc-CCCCCCcccccccccccccchhhhhh
Q 048741 83 KYKECLKNHAAGMGGNATDGCGEFMP-SGEEGTIEALTCSACNCHRNFHRKEI 134 (314)
Q Consensus 83 ~Y~eClkNhaa~~Gg~a~DGCgEFm~-~~~~gt~~~l~CaaCgCHRnFHr~e~ 134 (314)
+||||||||||+|||||||||||||| +++++|+++|+||||||||||||||+
T Consensus 1 ~Y~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~~~al~CaACgCHRnFHRre~ 53 (53)
T TIGR01566 1 LYKECLKNHAASIGGHALDGCGEFMPSSGEEGDPESLTCAACGCHRNFHRKEP 53 (53)
T ss_pred CHHHHHHhhHHHhCCcccccccccccCCCCCCCCcceeeeecCcccccccCCC
Confidence 69999999999999999999999999 68899999999999999999999985
No 3
>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=99.84 E-value=2e-21 Score=145.57 Aligned_cols=58 Identities=66% Similarity=1.116 Sum_probs=56.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccc
Q 048741 241 KKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKH 298 (314)
Q Consensus 241 kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRa 298 (314)
+||+||+||.+|+++|+.+|+++|||++.+|..+|++||.+|||++.||||||||+|.
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~ 58 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK 58 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence 5899999999999999999999999999999999999999999999999999999974
No 4
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.68 E-value=1.4e-17 Score=149.37 Aligned_cols=65 Identities=26% Similarity=0.333 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCC
Q 048741 239 LVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNIN 307 (314)
Q Consensus 239 ~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~ 307 (314)
.+.||.||.||.+|+.+||..|+. ++|....+|++||+.|+|++.||||||||||.|.||++...
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~----~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEG----NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhc----CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 377999999999999999999999 99999999999999999999999999999999999887653
No 5
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.66 E-value=4.7e-17 Score=149.53 Aligned_cols=67 Identities=18% Similarity=0.313 Sum_probs=63.1
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCC
Q 048741 237 AQLVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNIN 307 (314)
Q Consensus 237 ~~~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~ 307 (314)
+.++.||.||.||.+|++.||++|++ .+|||...|++||.+|+|.+.+|||||+|||+|+|+++++.
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~k----TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAK----TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHh----hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 35678999999999999999999999 99999999999999999999999999999999999888763
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.66 E-value=8.3e-18 Score=139.97 Aligned_cols=64 Identities=17% Similarity=0.346 Sum_probs=60.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 238 QLVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 238 ~~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
.++.||-||.||..|+.+|+..|.. ..|||+..|+|||.+|.|++..|||||||||+|++|+++
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~E----THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAE----THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHh----hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 3467889999999999999999999 999999999999999999999999999999999999874
No 7
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.64 E-value=1.3e-16 Score=146.87 Aligned_cols=66 Identities=15% Similarity=0.228 Sum_probs=62.0
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCC
Q 048741 237 AQLVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNI 306 (314)
Q Consensus 237 ~~~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~ 306 (314)
+..+|||.||.|+..|+..||..||. .+|.+..+|..||++|.|++.||||||||||.|||||...
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~----krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFEL----KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHH----HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 34589999999999999999999999 8999999999999999999999999999999999998643
No 8
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.63 E-value=2.2e-16 Score=148.50 Aligned_cols=69 Identities=19% Similarity=0.266 Sum_probs=62.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCCCCCCC
Q 048741 240 VKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNINPPSTT 312 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~p~s~~ 312 (314)
++|++||.||..|+++||..|.. -.|||...|+-|+.++.|.+.+|+|||||||+||||+++.-..++.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFke----aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~ 208 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKE----AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTI 208 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhh----ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchh
Confidence 34456999999999999999999 9999999999999999999999999999999999999987666553
No 9
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.62 E-value=7.9e-17 Score=150.79 Aligned_cols=66 Identities=21% Similarity=0.248 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCCC
Q 048741 239 LVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNINP 308 (314)
Q Consensus 239 ~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~p 308 (314)
...||.||.||..|+.+||..|.. |+|.....|.|+|..|.|+|++|||||||||+||||.++...
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhf----N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHF----NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhcc----ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 457899999999999999999999 999999999999999999999999999999999998775443
No 10
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.58 E-value=8.9e-16 Score=147.41 Aligned_cols=63 Identities=16% Similarity=0.273 Sum_probs=59.4
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 238 QLVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 238 ~~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
..++|+.||.||..|+.+||.-|++ ..|....+|.+||+.|||+..|||+||||||+||||+.
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~----QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEK----QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHH----hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 3566778999999999999999999 89999999999999999999999999999999999875
No 11
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.56 E-value=1.7e-15 Score=145.18 Aligned_cols=65 Identities=18% Similarity=0.281 Sum_probs=59.6
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 237 AQLVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 237 ~~~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
....-||.||.||.||+.+||..|-| -.|.+...|.|||.+|+|++.+|||||||||+|.|||.-
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyr----ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYR----ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHH----hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 34456899999999999999988888 799999999999999999999999999999999999864
No 12
>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=99.56 E-value=1e-15 Score=110.74 Aligned_cols=57 Identities=26% Similarity=0.475 Sum_probs=55.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 242 KRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 242 KR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
||.|+.||.+|+..|+++|+. ++||+..++++||.++||+..+|++||+|+|.++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE----NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH----SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH----hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 688999999999999999999 999999999999999999999999999999999986
No 13
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.52 E-value=3.4e-15 Score=140.71 Aligned_cols=60 Identities=28% Similarity=0.464 Sum_probs=57.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 242 KRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 242 KR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
||.||.||.|||++|++.|.. ++|..+..|++|+.||||.+.+|||||||+|+|.||-..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~e----nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQE----NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred cCccccccHHHHHHHHHHHhh----hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 678999999999999999999 999999999999999999999999999999999998753
No 14
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.52 E-value=1.9e-14 Score=138.20 Aligned_cols=65 Identities=12% Similarity=0.218 Sum_probs=60.4
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCC
Q 048741 238 QLVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNI 306 (314)
Q Consensus 238 ~~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~ 306 (314)
..+|||.|-.||+.|..+||+-|.. .+|.+..||++||..|.|++.||||||||||-|.||++..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrq----QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQ----QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred cccccccccccchhHHHHHHHHHHh----hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence 4467778889999999999999999 9999999999999999999999999999999999998754
No 15
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.51 E-value=6e-15 Score=136.53 Aligned_cols=63 Identities=14% Similarity=0.261 Sum_probs=58.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCC
Q 048741 240 VKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNI 306 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~ 306 (314)
+.|+.||.|+.-||..|..-|++ .+|.-..+|.|||..|||+..+|||||||||.|+||..+.
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQk----TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQ----TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhh----cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence 34567999999999999999999 9999999999999999999999999999999999987763
No 16
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.47 E-value=2.5e-14 Score=137.40 Aligned_cols=64 Identities=16% Similarity=0.198 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCC
Q 048741 240 VKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNIN 307 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~ 307 (314)
+-|++|.-+|..|+.+||..|-. |.|+..+.|.||++.|+|+++||||||||||+|+||..+.+
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlf----N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLF----NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHH----HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 44667889999999999999999 99999999999999999999999999999999999987533
No 17
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.40 E-value=1.2e-13 Score=126.82 Aligned_cols=61 Identities=16% Similarity=0.267 Sum_probs=57.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 241 KKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 241 kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
.|+.||-||..||..||.-|.. .+|.++.+|.||+..|.|++.+|||||||||+|.||.+.
T Consensus 144 nRkPRtPFTtqQLlaLErkfre----kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFRE----KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhH----hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 4668999999999999999988 899999999999999999999999999999999998764
No 18
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.39 E-value=5.6e-13 Score=131.25 Aligned_cols=64 Identities=16% Similarity=0.287 Sum_probs=61.1
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 238 QLVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 238 ~~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
..+|||+||.|....+..||.+|.+ |++|+..++.+||.+|+|.+.||+|||.|||+|+||-.+
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~----npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLK----NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3478899999999999999999999 999999999999999999999999999999999999876
No 19
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.38 E-value=2.8e-13 Score=130.25 Aligned_cols=63 Identities=17% Similarity=0.297 Sum_probs=60.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCC
Q 048741 240 VKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNI 306 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~ 306 (314)
++||.||.||..|+++||..|.+ ++|||...|+|+|.-++|++..|+|||+|||+||+|+++.
T Consensus 111 KqrrQrthFtSqqlqele~tF~r----NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN 173 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQR----NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN 173 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhh----ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence 56789999999999999999999 9999999999999999999999999999999999999864
No 20
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.37 E-value=1.8e-13 Score=130.61 Aligned_cols=62 Identities=27% Similarity=0.398 Sum_probs=58.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 240 VKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
..||.||.+|..|++-|+..|.. ..+|...+|++|+.++||..+||||||||||+|+||.++
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~----SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNT----SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcC----CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 46899999999999999999999 999999999999999999999999999999999987653
No 21
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.36 E-value=3.3e-13 Score=96.52 Aligned_cols=56 Identities=27% Similarity=0.433 Sum_probs=52.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhh
Q 048741 242 KRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLA 301 (314)
Q Consensus 242 KR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~K 301 (314)
++.|+.|+.+|+..|+++|++ +.||+..++++|+.++||+..+|+.||+|+|.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~----~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQK----NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 467889999999999999999 99999999999999999999999999999998764
No 22
>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=99.35 E-value=3.6e-13 Score=96.63 Aligned_cols=58 Identities=29% Similarity=0.509 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 242 KRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 242 KR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
++.|+.|+.+|+..|+++|+. ++||+..++++||.++||+..+|++||+|+|.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~----~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK----NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 457889999999999999999 9999999999999999999999999999999998875
No 23
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.31 E-value=2.4e-13 Score=128.51 Aligned_cols=61 Identities=16% Similarity=0.325 Sum_probs=56.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 239 LVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 239 ~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
+.|-+.|-.+|..|+-+||..|.- .+|+.+..+.||+..|||+|+||||||||||+|+||.
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~----SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~ 257 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHT----SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKD 257 (317)
T ss_pred ecccceeEEecchhhhhhhhhhcc----ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHH
Confidence 345567889999999999999999 9999999999999999999999999999999998754
No 24
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.29 E-value=1.5e-12 Score=115.68 Aligned_cols=63 Identities=19% Similarity=0.217 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 239 LVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 239 ~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
.++||.||.|+..|++.|+..|++ .+|||...|+.++..+++++..|||||||+|+||+|++.
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~----~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEK----VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcC----CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 467999999999999999999999 899999999999999999999999999999999999874
No 25
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.22 E-value=6.6e-12 Score=110.56 Aligned_cols=64 Identities=16% Similarity=0.121 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCC
Q 048741 239 LVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNI 306 (314)
Q Consensus 239 ~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~ 306 (314)
...|++|++-|.+|+..|+..|+. +++|+...|.+|+..|+|+++.|||||||+|++.|++...
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i----~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEI----NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhcc----CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 345777888899999999999999 9999999999999999999999999999999999987643
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.22 E-value=2.5e-12 Score=119.13 Aligned_cols=70 Identities=23% Similarity=0.276 Sum_probs=65.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCCCCCCC
Q 048741 239 LVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNINPPSTT 312 (314)
Q Consensus 239 ~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~p~s~~ 312 (314)
+++|-.|..|+-.|+..|+.-||. .+|+-..+|.++|..+|+.+.+|||||||||.|||||...+..+.+
T Consensus 165 G~rk~srPTf~g~qi~~le~~feq----tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasak 234 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQ----TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAK 234 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhh----hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhcc
Confidence 356778899999999999999999 9999999999999999999999999999999999999988887765
No 27
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.21 E-value=9.4e-13 Score=117.34 Aligned_cols=65 Identities=17% Similarity=0.283 Sum_probs=60.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCCC
Q 048741 240 VKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNINP 308 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~p 308 (314)
++++.||.|+..|+..|++-||+ .+|.+..+|.||+..|+|++.+||.||||||+|.||+++.+.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~----QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFER----QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HhhhhcccccCccccccHHHHhh----hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 45678999999999999999999 899999999999999999999999999999999998876554
No 28
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.18 E-value=7e-12 Score=114.26 Aligned_cols=56 Identities=23% Similarity=0.368 Sum_probs=52.8
Q ss_pred CCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 246 TKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 246 T~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
-+||.+|...|+.-|+. ..+.....+..||++|||..+||+|||||||++||.|+-
T Consensus 55 ~Rlt~eQ~~~LE~~F~~----~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 55 RRLTSEQVKFLEKSFES----EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred ccccHHHHHHhHHhhcc----ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 35899999999999999 899999999999999999999999999999999998864
No 29
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.04 E-value=7.7e-11 Score=112.90 Aligned_cols=68 Identities=16% Similarity=0.314 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCCCCC
Q 048741 239 LVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNINPPS 310 (314)
Q Consensus 239 ~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~p~s 310 (314)
..|||+||.+-...|+.||+||.. .++|+.+.+..+|++|.|++.||+|||.|+|+|.||.+..-...
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFav----QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa~~~ 374 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAV----QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSATAV 374 (385)
T ss_pred cccccccccccCcccccHHHHhcc----CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhhcee
Confidence 468999999999999999999999 89999999999999999999999999999999999876544433
No 30
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.99 E-value=1.4e-10 Score=113.38 Aligned_cols=63 Identities=17% Similarity=0.308 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 239 LVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 239 ~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
.+.+|.||+|+.+|++.|++.|++ ++||+...|++|+.++++++..|+|||+|+|++++|...
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~r----t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQR----TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccccchHHHHHHHhcC----CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 456778999999999999999999 999999999999999999999999999999999999883
No 31
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.22 E-value=5.5e-07 Score=80.18 Aligned_cols=64 Identities=28% Similarity=0.459 Sum_probs=59.3
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 238 QLVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 238 ~~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
..+.++.||.|+..|++.|...|.. ..+|+...+++|+..+|+.+.+|+|||||+|.+.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRA----TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccC----CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3467889999999999999999999 999999999999999999999999999999999998654
No 32
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=98.10 E-value=2e-06 Score=95.19 Aligned_cols=64 Identities=19% Similarity=0.310 Sum_probs=58.8
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 238 QLVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 238 ~~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
...+|+.||.|+.+|+..|+.+|+. ..++...+.|.|-.++++..++|+|||||.|+|.+|..-
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~----q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEA----QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhh----ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 3467889999999999999999999 888999999999999999999999999999999987753
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.03 E-value=2.9e-06 Score=87.16 Aligned_cols=57 Identities=14% Similarity=0.218 Sum_probs=53.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchh
Q 048741 240 VKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNL 300 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~ 300 (314)
..||.|..||+.|++.|.++|+. +++|+....+.|+.+|+|...+|..||.|-|.+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke----~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE----NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc----CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 45778999999999999999999 9999999999999999999999999999987763
No 34
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=97.74 E-value=2e-05 Score=75.49 Aligned_cols=48 Identities=6% Similarity=0.158 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 252 QKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 252 Qk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
-...|+++|.+ ++||...++.+||+.+||+..||-.||+|||++.|-.
T Consensus 187 SR~~LrewY~~----~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 187 SRSLLREWYLQ----NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred hHHHHHHHHhc----CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence 35678899998 9999999999999999999999999999999999843
No 35
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.56 E-value=6.2e-05 Score=72.04 Aligned_cols=62 Identities=13% Similarity=0.256 Sum_probs=55.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 242 KRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 242 KR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
||+|-.|+..--+.|.++|-. .-.++||++.++++||++.+++..+|--||.|.|-++||.-
T Consensus 189 rRKRRNFsK~aTeiLneyF~~-h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYS-HLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHhhcccchhHHHHHHHHHHH-hcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 677889999999999999864 34588999999999999999999999999999999998753
No 36
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=97.33 E-value=3e-05 Score=54.24 Aligned_cols=35 Identities=11% Similarity=0.353 Sum_probs=29.2
Q ss_pred cccCCCCHHHHHHHHHHhCCCCCeeeeecccccch
Q 048741 265 WKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHN 299 (314)
Q Consensus 265 Wr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK 299 (314)
+.++||+..++++||.++|++..+|..||-|.|.+
T Consensus 6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 45899999999999999999999999999998853
No 37
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.43 E-value=0.011 Score=43.29 Aligned_cols=47 Identities=26% Similarity=0.368 Sum_probs=36.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeeccccc
Q 048741 242 KRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 242 KR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRR 297 (314)
||.|..+|-+|+..+...++. .. ...++|.++||+..+|.-|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~----g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE----GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC----TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc----CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 678999999999999999998 43 577899999999999999998753
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.36 E-value=0.027 Score=60.61 Aligned_cols=52 Identities=13% Similarity=0.282 Sum_probs=46.6
Q ss_pred CCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 248 FTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 248 FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
|+.. ...|+++|.. |..|...+...|+.++||+..+||+||++++++....+
T Consensus 564 ~~~p-~sllkayyal----n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYAL----NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred cCCc-HHHHHHHHHh----cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 4444 6778899999 99999999999999999999999999999999988766
No 39
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.12 E-value=0.041 Score=53.15 Aligned_cols=61 Identities=16% Similarity=0.194 Sum_probs=50.1
Q ss_pred CCCCCCCCCCHHHHHHHHHH-HHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 240 VKKRFRTKFTQEQKEKMFNF-AEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~-FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.++|.+..|..+....|++. |+-+- .+||.+.++..|+.++||+..+|..||-|.|-+..|
T Consensus 238 ~~~r~~~~lP~~a~~ilr~Wl~~h~~--~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 238 SKWRPQRGLPKEAVSILRAWLFEHLL--HPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHhcc--CCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 35666779999999999844 55322 579999999999999999999999999999987654
No 40
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=92.87 E-value=0.028 Score=42.45 Aligned_cols=41 Identities=10% Similarity=0.316 Sum_probs=30.3
Q ss_pred HHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeeccccc
Q 048741 253 KEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 253 k~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRR 297 (314)
...|+++|.+ .....+...++||.+.+|+..+|+.||--++
T Consensus 10 ~~pL~~Yy~~----h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLK----HKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHH----T----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHH----cCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 3459999999 8888889999999999999999999996554
No 41
>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=90.38 E-value=0.11 Score=39.01 Aligned_cols=44 Identities=20% Similarity=0.307 Sum_probs=31.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecc
Q 048741 243 RFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMH 294 (314)
Q Consensus 243 R~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQ 294 (314)
+.|..||.+++..+...+.. ....+.++|.++||+..+|.-|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~--------~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE--------SGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHH--------HHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH--------CCCceEeeecccccccccccHHHH
Confidence 45778999999999877743 124778999999999999999875
No 42
>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=78.80 E-value=1.9 Score=25.60 Aligned_cols=38 Identities=29% Similarity=0.414 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeec
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWM 293 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWF 293 (314)
.++.+++..+...++. || ...+++.++|++..+|..|+
T Consensus 5 ~~~~~~~~~i~~~~~~-~~--------s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA-GE--------SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc-CC--------CHHHHHHHHCCCHHHHHHhC
Confidence 4678888877777654 22 45688999999998887774
No 43
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=77.97 E-value=1.7 Score=32.34 Aligned_cols=41 Identities=17% Similarity=0.323 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeee
Q 048741 248 FTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLK 290 (314)
Q Consensus 248 FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVK 290 (314)
+|..|.+.|...++. |+=. +|.....++||.++||+..+|-
T Consensus 1 LT~~Q~e~L~~A~~~-GYfd-~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYEL-GYFD-VPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHc-CCCC-CCCcCCHHHHHHHhCCCHHHHH
Confidence 588999999999987 3211 2556677899999999998753
No 44
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=74.28 E-value=1.1 Score=39.48 Aligned_cols=48 Identities=21% Similarity=0.278 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 246 TKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 246 T~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
+.+|..|++.|.. +.+ ||. .+++|..+|+++.+|+.|.++-+.|+++.
T Consensus 5 ~~Lt~rqreVL~l-r~~-GlT--------q~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 5 SFLTERQIEVLRL-RER-GLT--------QQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred cCCCHHHHHHHHH-HHc-CCC--------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5689999999876 333 444 45899999999999999999887777654
No 45
>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=71.27 E-value=1.4 Score=29.32 Aligned_cols=44 Identities=14% Similarity=0.327 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccch
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHN 299 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK 299 (314)
.++.++.+.+..+|.. | ....++|.++|++..+|+.|.+.-|.+
T Consensus 10 ~l~~~~~~~~~~~~~~-~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGE-G--------LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhc-C--------CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4677888777766633 1 245678999999999999998765544
No 46
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=64.12 E-value=7.1 Score=31.79 Aligned_cols=42 Identities=21% Similarity=0.325 Sum_probs=35.2
Q ss_pred CCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCC-CCCeeeeecc
Q 048741 245 RTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGV-KRRVLKVWMH 294 (314)
Q Consensus 245 RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv-~~~vVKVWFQ 294 (314)
|.+||.|.|..+-+++.+ ..+ .+.++|+++|| ...++..|..
T Consensus 5 ~r~~s~EfK~~iv~~~~~----~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLR----GGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHh----cCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 789999999999887776 332 67899999996 9999998876
No 47
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=62.17 E-value=3.7 Score=35.40 Aligned_cols=53 Identities=13% Similarity=0.273 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCCC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNINP 308 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~p 308 (314)
.++..+++.+...|-. ....+++|..+|++..+|+++++.-|.+++++-..+|
T Consensus 131 ~L~~~~r~v~~l~~~~---------g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~~~ 183 (184)
T PRK12512 131 TLPPRQRDVVQSISVE---------GASIKETAAKLSMSEGAVRVALHRGLAALAAKFRSEP 183 (184)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCC
Confidence 4566666666644322 2356799999999999999999998888887765554
No 48
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=61.73 E-value=0.75 Score=32.24 Aligned_cols=39 Identities=15% Similarity=0.377 Sum_probs=19.5
Q ss_pred CCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeec
Q 048741 246 TKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWM 293 (314)
Q Consensus 246 T~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWF 293 (314)
..||.+|+..++.+.+. | ....++|..+|+++.+|.-|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~-G--------~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ-G--------MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS------------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHc-C--------CCHHHHHHHHCcCcHHHHHHH
Confidence 46899999999877654 3 245589999999999886554
No 49
>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=60.92 E-value=1.4 Score=31.19 Aligned_cols=41 Identities=10% Similarity=0.192 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeeccccc
Q 048741 248 FTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 248 FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRR 297 (314)
++..|.+.+...| .+.....++|..+|++..+|++|.+.-|
T Consensus 11 L~~~~r~i~~l~~---------~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRY---------FQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHH---------TS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH---------HHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4566666665433 3345677999999999999999997443
No 50
>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=60.68 E-value=2.4 Score=29.62 Aligned_cols=38 Identities=18% Similarity=0.360 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeec
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWM 293 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWF 293 (314)
+++.+|.+.+.++++. - ..+.++|+++||++.+|.=|+
T Consensus 5 ~~~~~~~~~i~~l~~~----G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAE----G-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHT----T-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHC----C-----CCHHHHHHHHCcCHHHHHHHH
Confidence 5777788888877776 1 357799999999999876444
No 51
>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=60.58 E-value=4.8 Score=30.73 Aligned_cols=45 Identities=27% Similarity=0.416 Sum_probs=29.6
Q ss_pred CCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecc
Q 048741 245 RTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMH 294 (314)
Q Consensus 245 RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQ 294 (314)
|-.||.+.+.+..++|++ ...-....|. .+++.||.++.|+-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~----~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK----DNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-----TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHH----ccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 557999999999899988 4443334444 49999999999999975
No 52
>PHA02893 hypothetical protein; Provisional
Probab=60.45 E-value=3.3 Score=33.92 Aligned_cols=10 Identities=30% Similarity=0.800 Sum_probs=8.5
Q ss_pred cccccccccc
Q 048741 115 IEALTCSACN 124 (314)
Q Consensus 115 ~~~l~CaaCg 124 (314)
...|+|+|||
T Consensus 67 ~~tL~CaACG 76 (88)
T PHA02893 67 NSNIKCIACG 76 (88)
T ss_pred CCceeehhhc
Confidence 3579999998
No 53
>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=58.81 E-value=4 Score=30.58 Aligned_cols=37 Identities=22% Similarity=0.527 Sum_probs=27.1
Q ss_pred HHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 256 MFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 256 Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
-..+|.+ ||+.. ++|.+|||++.+|.-|-+ |.+|...
T Consensus 6 A~~LY~~-G~~~~--------eIA~~Lg~~~~TV~~W~~--r~~W~~~ 42 (58)
T PF06056_consen 6 ARSLYLQ-GWSIK--------EIAEELGVPRSTVYSWKD--RYKWDEL 42 (58)
T ss_pred HHHHHHc-CCCHH--------HHHHHHCCChHHHHHHHH--hhCcccc
Confidence 3455665 77654 899999999999999975 5555443
No 54
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=57.34 E-value=2.8 Score=28.47 Aligned_cols=45 Identities=18% Similarity=0.385 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLA 301 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~K 301 (314)
.++..|++.+..++ . |+ ...++|..+|+++.+|+.|.+.-+.|++
T Consensus 3 ~l~~~e~~i~~~~~-~-g~--------s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVLRLLA-E-GL--------TNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHHHHHH-c-CC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 46788888665433 2 22 4578999999999999999875544443
No 55
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=57.17 E-value=5.8 Score=33.09 Aligned_cols=42 Identities=19% Similarity=0.246 Sum_probs=31.1
Q ss_pred CCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecc
Q 048741 245 RTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMH 294 (314)
Q Consensus 245 RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQ 294 (314)
|.+||.+++..+....-. . ...+.++|.++||+..+|.-|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~----~----g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE----P----GMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHc----C----CCCHHHHHHHHCcCHHHHHHHHH
Confidence 456899998776654443 1 12456889999999999999965
No 56
>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=56.10 E-value=2.1 Score=30.99 Aligned_cols=45 Identities=16% Similarity=0.261 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLA 301 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~K 301 (314)
.||..+++.|..+++- ....++|.+++++..+|+.+..|=+.|++
T Consensus 3 ~LT~~E~~vl~~l~~G----------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG----------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT----------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc----------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 5889999988776664 25678999999999999999887666654
No 57
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=56.02 E-value=9.6 Score=41.98 Aligned_cols=62 Identities=11% Similarity=0.169 Sum_probs=45.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 239 LVKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 239 ~~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
..+-|.|+-...++-..|...++. ...+...+....+.++...+.|+.||||+|+.+-++-.
T Consensus 624 ~~p~kv~sp~k~~dq~ql~~a~el----q~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p 685 (1007)
T KOG3623|consen 624 ERPVKVRSPIKEEDQQQLKQAYEL----QASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP 685 (1007)
T ss_pred CCCccccCCCCccchhhhHhhhhc----ccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence 345567788888888888888887 44444444445566678889999999999998876544
No 58
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=55.67 E-value=2 Score=37.68 Aligned_cols=49 Identities=14% Similarity=0.083 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
.++..|++.+...|-. ....+++|..+|++..+|++|++.-|.++|+.-
T Consensus 142 ~L~~~~r~vl~l~~~~---------~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYG---------GLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 4667777776543322 235669999999999999999987777777653
No 59
>PRK06424 transcription factor; Provisional
Probab=54.68 E-value=12 Score=32.89 Aligned_cols=24 Identities=8% Similarity=0.079 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCCCeeeeecccccc
Q 048741 275 VQQFCQEIGVKRRVLKVWMHNNKH 298 (314)
Q Consensus 275 reeLa~eiGv~~~vVKVWFQNRRa 298 (314)
.++||..+|++...|.-|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999987764
No 60
>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=54.48 E-value=3 Score=29.22 Aligned_cols=46 Identities=9% Similarity=0.205 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLA 301 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~K 301 (314)
.++++|.+.|...|.. ....+++|..+|+++.+|+.+...-..|+|
T Consensus 4 ~L~~~er~vi~~~y~~---------~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE---------GLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS---------T-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC---------CCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 4678888888866633 235678999999999999887765444444
No 61
>PRK10072 putative transcriptional regulator; Provisional
Probab=53.39 E-value=5.5 Score=32.78 Aligned_cols=40 Identities=20% Similarity=0.418 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccc
Q 048741 248 FTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKH 298 (314)
Q Consensus 248 FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRa 298 (314)
.+...+..| .+++||. +.+||..+||+..+|.-|.+.+|.
T Consensus 33 ~~~~eik~L---R~~~glT--------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQL---RKGTGLK--------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHH---HHHcCCC--------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 345444444 4566665 458999999999999999987764
No 62
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=53.00 E-value=8.6 Score=44.48 Aligned_cols=62 Identities=10% Similarity=0.033 Sum_probs=53.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 240 VKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
..+-.|++++.-|...|..+|+. ..++.-.++..++.-|+|-.+++-+||++++.++.+...
T Consensus 443 e~~~~s~r~~~~~t~~L~S~~kt----~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~ 504 (1406)
T KOG1146|consen 443 EPLLESKRSLEGQTVVLHSFFKT----LKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHP 504 (1406)
T ss_pred hhhhhhhcccccceeeeeccccc----ccCCccchhhhhHHHhhhcccccccccchhHhHhccccc
Confidence 44567999999999999999977 788999999999999999999988899887777765543
No 63
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=52.70 E-value=5.2 Score=33.61 Aligned_cols=48 Identities=8% Similarity=0.127 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.+++.|++.+...|-. .....++|..+|+++.+|+.|++.-|.++++.
T Consensus 128 ~L~~~~r~vl~l~~~~---------~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIE---------GLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4667777776644322 12456899999999999999999767666654
No 64
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=52.64 E-value=5.6 Score=32.98 Aligned_cols=48 Identities=6% Similarity=0.044 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+...|-. ....+++|..+|++..+|++|.+.-|.++|+.
T Consensus 106 ~L~~~~r~ii~l~~~~---------~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 106 VLDEKEKYIIFERFFV---------GKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred hCCHHHHHHHHHHHhc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 4556666665433322 23567999999999999999998777766653
No 65
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=51.94 E-value=3.8 Score=34.09 Aligned_cols=47 Identities=11% Similarity=0.146 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.++..|++.+...|-. ....+++|..+|++..+|+++.+.-|.++++
T Consensus 111 ~L~~~~r~v~~l~~~~---------g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQR---------GVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhc---------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 5677777776652221 2356689999999999999998866666654
No 66
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=51.85 E-value=2.7 Score=36.49 Aligned_cols=32 Identities=9% Similarity=0.131 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 272 ESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 272 ~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.....++|..+|++..+|++|++.-|.++++.
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34667999999999999999998777777653
No 67
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=50.37 E-value=30 Score=24.85 Aligned_cols=34 Identities=15% Similarity=0.209 Sum_probs=26.5
Q ss_pred CHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccc
Q 048741 249 TQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 249 T~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNR 296 (314)
|.+||++|.+.+.. .++..+|++..-|.|+|...
T Consensus 13 s~eqk~~l~~~it~--------------~l~~~~~~p~~~v~V~i~e~ 46 (61)
T PRK02220 13 TEEQLKALVKDVTA--------------AVSKNTGAPAEHIHVIINEM 46 (61)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcChhhEEEEEEEe
Confidence 79999998755444 78999999888888777654
No 68
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=49.98 E-value=6.5 Score=35.02 Aligned_cols=49 Identities=16% Similarity=0.127 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
.++..|.+.+...|-. ....+++|.++|++..+|+++++.-|.++++.-
T Consensus 153 ~L~~~~r~vl~l~~~~---------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQ---------ELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4566666666532221 235679999999999999999988777777653
No 69
>PRK04217 hypothetical protein; Provisional
Probab=49.74 E-value=6.7 Score=33.15 Aligned_cols=47 Identities=15% Similarity=0.102 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
+++.+|++.+...+.. . ...+++|+.+||++.+|+..++.-|.+++.
T Consensus 42 ~Lt~eereai~l~~~e----G-----lS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 42 FMTYEEFEALRLVDYE----G-----LTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred cCCHHHHHHHHHHHHc----C-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4688888777655533 1 267789999999999999998876666654
No 70
>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=49.72 E-value=2.8 Score=35.96 Aligned_cols=32 Identities=3% Similarity=0.081 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
...+++|..+|++..+|+++...-|.++|+.-
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 45679999999999999999987777777653
No 71
>PRK00118 putative DNA-binding protein; Validated
Probab=49.03 E-value=7.1 Score=32.70 Aligned_cols=47 Identities=15% Similarity=0.202 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.++..|++.+...|.. .....++|..+|+++.+|+.|+..-|.+.++
T Consensus 17 ~L~ekqRevl~L~y~e---------g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLD---------DYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3466777777654443 2356789999999999999999866666554
No 72
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=48.78 E-value=4.3 Score=28.14 Aligned_cols=22 Identities=18% Similarity=0.628 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCCCeeeeeccc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHN 295 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQN 295 (314)
...++|+.+||++.+|.-|.+.
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4458999999999999999864
No 73
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=48.57 E-value=12 Score=33.87 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCee
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVL 289 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vV 289 (314)
.+|..|++.|...|+. |+=. +|......+||+++|++..++
T Consensus 155 ~LTdrQ~~vL~~A~~~-GYFd-~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKM-GYFD-YPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHc-CCCC-CCccCCHHHHHHHhCCCHHHH
Confidence 7999999999999986 3211 355667789999999999874
No 74
>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=48.40 E-value=5.9 Score=31.38 Aligned_cols=47 Identities=13% Similarity=0.256 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.++..|++.+...|-. | ....++|.++|+++.+|+.|.+.-+.|.|+
T Consensus 110 ~L~~~~~~ii~~~~~~-g--------~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-G--------LSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc-C--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4567777666544322 2 245589999999999999998876666654
No 75
>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=48.21 E-value=3.3 Score=32.78 Aligned_cols=27 Identities=7% Similarity=0.295 Sum_probs=22.2
Q ss_pred CHHHHHHHHHHhCCCCCeeeeeccccc
Q 048741 271 EESVVQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 271 d~~~reeLa~eiGv~~~vVKVWFQNRR 297 (314)
......++|..+|+++.+|++|+.+..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 334667999999999999999998643
No 76
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=48.12 E-value=6.6 Score=31.91 Aligned_cols=18 Identities=39% Similarity=0.521 Sum_probs=14.9
Q ss_pred HHhhhhhcccCCCccccc
Q 048741 85 KECLKNHAAGMGGNATDG 102 (314)
Q Consensus 85 ~eClkNhaa~~Gg~a~DG 102 (314)
.-=|||.||.|||.+|-.
T Consensus 51 ~NdlrNeAa~lGgntV~~ 68 (93)
T PF13698_consen 51 RNDLRNEAAKLGGNTVVL 68 (93)
T ss_pred HHHHHHHHHHhCCCEEEE
Confidence 345899999999998853
No 77
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=47.13 E-value=6.7 Score=32.96 Aligned_cols=47 Identities=15% Similarity=0.312 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|.+.|.-.| . || ..+++|..+|++..+|+.+.+.-|.++|+.
T Consensus 112 ~L~~~~r~il~l~~-~-g~--------s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF-S-GY--------SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH-c-CC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46677776666555 2 33 456899999999999999998777776653
No 78
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=46.65 E-value=8.4 Score=32.30 Aligned_cols=48 Identities=6% Similarity=0.167 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
+++..|.+.+...|-. ....+++|..+|++..+|+++++.-|.++|+.
T Consensus 106 ~Lp~~~r~v~~l~~~~---------g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLE---------EKSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHh---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4566666666533322 12456899999999999999999777777665
No 79
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=46.48 E-value=2.9 Score=36.27 Aligned_cols=49 Identities=12% Similarity=0.163 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 246 TKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 246 T~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..++..|++.+...|-. ....+++|..+|++..+|+++.+.-|.++|+.
T Consensus 138 ~~L~~~~r~i~~l~~~~---------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 138 DTLPEKQREILILRVVV---------GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HhCCHHHHHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35667777776643222 23567999999999999999998777776654
No 80
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=46.27 E-value=3.2 Score=35.20 Aligned_cols=48 Identities=6% Similarity=0.087 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHH-HHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 247 KFTQEQKEKMFNF-AEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 247 ~FT~eQk~~Le~~-FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
.++..|++.+... ++. ...+++|..+|++..+|++|++--|.++++.-
T Consensus 108 ~L~~~~r~v~~l~~~~g----------~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE----------LTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred hCCHHHHHHHHhHHHhc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4566666666532 332 35679999999999999999997777777653
No 81
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=45.87 E-value=9.7 Score=32.63 Aligned_cols=30 Identities=10% Similarity=0.306 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..+++|..+|++..+|+++++.-|.++|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 567999999999999999999777777764
No 82
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=45.72 E-value=3 Score=35.15 Aligned_cols=49 Identities=8% Similarity=0.119 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
.++..|++.+.-.|- .....+++|..+|++..+|+++.+.-|.++++.+
T Consensus 112 ~L~~~~r~v~~l~~~---------~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~~ 160 (161)
T PRK12541 112 SLPLERRNVLLLRDY---------YGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161)
T ss_pred HCCHHHHHHhhhHHh---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence 466666666653322 2235679999999999999999987777777653
No 83
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=45.58 E-value=4.7 Score=36.89 Aligned_cols=47 Identities=17% Similarity=0.196 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.+|..|++.|+-.++ ||.+ .++|+++++++++||.+..|=..|+.-+
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s~--------~eIA~~L~iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 155 LLTHREKEILNKLRI--GASN--------NEIARSLFISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred CCCHHHHHHHHHHHc--CCCH--------HHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 489999999987766 5554 4899999999999999998876666543
No 84
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=45.40 E-value=7.3 Score=33.68 Aligned_cols=37 Identities=11% Similarity=0.075 Sum_probs=29.9
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhcCCCCCCC
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNINPPS 310 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~p~s 310 (314)
..+++|..+|++..+|+++.+.-|.++++.-...+++
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~ 182 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLADLPGS 182 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 5678999999999999999998888888765544443
No 85
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=44.12 E-value=9.5 Score=32.21 Aligned_cols=40 Identities=13% Similarity=0.251 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccc
Q 048741 248 FTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKH 298 (314)
Q Consensus 248 FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRa 298 (314)
++..+++.|.+-+.- .+.+||+.+|++..+|+-|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~l-----------SQ~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGL-----------SQPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCC-----------CHHHHHHHHCCCHHHHHHHHcCCcC
Confidence 788888888766554 5678999999999999999998864
No 86
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=44.04 E-value=11 Score=32.50 Aligned_cols=48 Identities=10% Similarity=0.274 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+...|- .....+++|..+|++..+|++|.+.-|.++|+.
T Consensus 133 ~L~~~~r~i~~l~~~---------~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYV---------DGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 455566665443222 123567899999999999999998766666653
No 87
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=43.09 E-value=4.2 Score=36.03 Aligned_cols=32 Identities=16% Similarity=0.101 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
...+++|..+|++..+|+++++--|.++|+.-
T Consensus 130 ~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 130 FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35679999999999999999998777777643
No 88
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=42.92 E-value=3.6 Score=36.12 Aligned_cols=48 Identities=19% Similarity=0.214 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+.-.|-. ....+++|..+|+++.+||+++.--|.++|+.
T Consensus 134 ~Lp~~~R~v~~L~~~~---------g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 134 HLPAQQARVFMMREYL---------ELSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred hCCHHHHHHHhHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4566666666543322 23467999999999999999998777666653
No 89
>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=42.77 E-value=9.9 Score=32.52 Aligned_cols=47 Identities=17% Similarity=0.057 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 248 FTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 248 FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
++..|++.+...|.. ....+++|..+|++..+|++.++.-|.++++.
T Consensus 135 Lp~~~r~v~~l~~~~---------g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFA---------GLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHc---------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 556666665543322 23566899999999999999998777777653
No 90
>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=42.45 E-value=10 Score=32.62 Aligned_cols=48 Identities=13% Similarity=0.163 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
+++..|++.+...|-. ....+++|.++|++..+|+++.+--|.++++.
T Consensus 100 ~L~~~~r~v~~l~~~~---------g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 100 ELPDEYREAIRLTELE---------GLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5667776666644432 12566899999999999999998766666643
No 91
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=42.29 E-value=15 Score=24.67 Aligned_cols=29 Identities=24% Similarity=0.358 Sum_probs=21.0
Q ss_pred ccccccccccCCCCCCcccccccccccccchhhhh
Q 048741 99 ATDGCGEFMPSGEEGTIEALTCSACNCHRNFHRKE 133 (314)
Q Consensus 99 a~DGCgEFm~~~~~gt~~~l~CaaCgCHRnFHr~e 133 (314)
.=+.|+++|.... .+++|+.| ....|.+=
T Consensus 13 ~C~~C~~~i~~~~----~~~~C~~C--~~~~H~~C 41 (49)
T smart00109 13 KCCVCRKSIWGSF----QGLRCSWC--KVKCHKKC 41 (49)
T ss_pred CccccccccCcCC----CCcCCCCC--CchHHHHH
Confidence 4588999998643 47999877 56666654
No 92
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=41.83 E-value=4.6 Score=34.52 Aligned_cols=48 Identities=10% Similarity=0.183 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|.+.+... |......+++|..+|+++.+|+++++.-|.++++.
T Consensus 136 ~L~~~~r~v~~l~---------~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLK---------YMEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhH---------HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555565555432 22224567999999999999999998777777654
No 93
>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=41.41 E-value=6.8 Score=32.10 Aligned_cols=29 Identities=14% Similarity=0.359 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
...++|..+|+++.+|+.+.+.-|.|+|+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 56689999999999999998866666654
No 94
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=40.74 E-value=3.4 Score=35.98 Aligned_cols=37 Identities=11% Similarity=0.136 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCC
Q 048741 270 QEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNI 306 (314)
Q Consensus 270 pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~ 306 (314)
......+++|.++|++..+|++++..-|.++|+.-..
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 189 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAE 189 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3445677999999999999999999888888876443
No 95
>PRK10403 transcriptional regulator NarP; Provisional
Probab=40.40 E-value=5.9 Score=32.98 Aligned_cols=48 Identities=15% Similarity=0.266 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 246 TKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 246 T~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..+|..+++.|..+++. ..++++++.+++++++|++..+|=|.|...+
T Consensus 152 ~~Lt~~e~~vl~~~~~g----------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 152 SVLTERELDVLHELAQG----------LSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred ccCCHHHHHHHHHHHCC----------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 36899999888755443 3567899999999999999998777666544
No 96
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=40.32 E-value=13 Score=25.33 Aligned_cols=30 Identities=27% Similarity=0.355 Sum_probs=21.9
Q ss_pred ccccccccccCCCCCCcccccccccccccchhhhh
Q 048741 99 ATDGCGEFMPSGEEGTIEALTCSACNCHRNFHRKE 133 (314)
Q Consensus 99 a~DGCgEFm~~~~~gt~~~l~CaaCgCHRnFHr~e 133 (314)
.=+-|+++|... ...+|+|..| ..+.|++=
T Consensus 13 ~C~~C~~~i~~~---~~~~~~C~~C--~~~~H~~C 42 (50)
T cd00029 13 FCDVCRKSIWGL---FKQGLRCSWC--KVKCHKKC 42 (50)
T ss_pred Chhhcchhhhcc---ccceeEcCCC--CCchhhhh
Confidence 457799999864 3478999887 56777664
No 97
>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=40.25 E-value=11 Score=26.37 Aligned_cols=22 Identities=9% Similarity=0.424 Sum_probs=16.8
Q ss_pred HHHHHHhCCCCCeeeeeccccc
Q 048741 276 QQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 276 eeLa~eiGv~~~vVKVWFQNRR 297 (314)
.+||+.+|+++.+|.-|..+++
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHhCCCcchhHHHhcCCC
Confidence 5788888888888888887754
No 98
>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=40.13 E-value=11 Score=31.54 Aligned_cols=49 Identities=10% Similarity=0.101 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
.++..|++.+...|-. ....+++|..+|++..+|+++...-|.++++.-
T Consensus 110 ~L~~~~r~i~~l~~~~---------g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE---------DLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHh---------cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3455666665533322 224568999999999999999998888877654
No 99
>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=39.86 E-value=9.5 Score=31.53 Aligned_cols=34 Identities=12% Similarity=0.167 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 269 KQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 269 ~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
+......+++|..+|++..+|+++++--|.++++
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3445567899999999999999999866666654
No 100
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=39.53 E-value=5.1 Score=35.00 Aligned_cols=49 Identities=10% Similarity=0.264 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
.++.+|++.+.-.|-. ....+++|..+|++..+|++..+--|.++|++.
T Consensus 131 ~L~~~~r~i~~l~~~~---------g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLL---------GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHc---------cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 4666666666533321 235679999999999999999987787777765
No 101
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=39.40 E-value=6 Score=34.31 Aligned_cols=49 Identities=16% Similarity=0.183 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
.++..|++.+.-.| ......+++|..+|++..+|+.++..-|.++|+.-
T Consensus 131 ~L~~~~r~v~~l~~---------~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVK---------LEGLSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHH---------HcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45566665555322 22245679999999999999999987777777653
No 102
>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=39.37 E-value=7.7 Score=25.61 Aligned_cols=25 Identities=20% Similarity=0.489 Sum_probs=21.2
Q ss_pred HHHHHHHhCCCCCeeeeecccccch
Q 048741 275 VQQFCQEIGVKRRVLKVWMHNNKHN 299 (314)
Q Consensus 275 reeLa~eiGv~~~vVKVWFQNRRaK 299 (314)
..++|..+||++.+|.-|.++.+-.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 4688999999999999999877644
No 103
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=39.03 E-value=13 Score=30.98 Aligned_cols=48 Identities=21% Similarity=0.233 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
+++..|++.+.-.|-. ....+++|..+|++..+|+++++--|.++|+.
T Consensus 106 ~Lp~~~r~v~~l~~~~---------g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYWE---------DMDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHHh---------cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4666666666643322 12456999999999999999998777666654
No 104
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=38.91 E-value=68 Score=23.41 Aligned_cols=33 Identities=15% Similarity=0.273 Sum_probs=26.9
Q ss_pred CHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeeccc
Q 048741 249 TQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHN 295 (314)
Q Consensus 249 T~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQN 295 (314)
|.|||++|-+..-+ .+++.+|+++..|.|.|..
T Consensus 13 s~EqK~~L~~~it~--------------a~~~~~~~p~~~v~V~i~e 45 (60)
T PRK02289 13 SQEQKNALAREVTE--------------VVSRIAKAPKEAIHVFIND 45 (60)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcCcceEEEEEEE
Confidence 79999999654444 6788899999999998865
No 105
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=38.66 E-value=11 Score=32.94 Aligned_cols=44 Identities=20% Similarity=0.448 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHH-HHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecc
Q 048741 247 KFTQEQKEKMFN-FAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMH 294 (314)
Q Consensus 247 ~FT~eQk~~Le~-~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQ 294 (314)
.||++|.++|.. .-|. .+........++...+|+++.++++.|.
T Consensus 4 ~~T~eer~eLk~rIvEl----VRe~GRiTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 4 VFTPEEREELKARIVEL----VREHGRITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred cCCHHHHHHHHHHHHHH----HHHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 589999999983 3333 3333445677889999999998876664
No 106
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=38.29 E-value=5.3 Score=35.20 Aligned_cols=30 Identities=10% Similarity=0.169 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..+++|..+|++..+||+++..-|.++++.
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~ 163 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEI 163 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 556899999999999999999888777754
No 107
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=38.23 E-value=4.5 Score=34.42 Aligned_cols=48 Identities=10% Similarity=0.147 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+.-.+. +....+++|..+|++..+|+++.+--|.+.|+.
T Consensus 112 ~L~~~~r~v~~l~~~---------~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGA---------SGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 455666665553322 223567999999999999999998666666654
No 108
>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=38.11 E-value=14 Score=25.47 Aligned_cols=35 Identities=11% Similarity=0.108 Sum_probs=24.8
Q ss_pred HHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeeccccc
Q 048741 255 KMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 255 ~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRR 297 (314)
.|..+-++.||. .++||..+|++..+|.-|...++
T Consensus 6 ~l~~~r~~~glt--------q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 6 LVRARRKALGLT--------QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHHcCCC--------HHHHHHHhCCCHHHHHHHHCCCC
Confidence 344555555554 45889999999999988886654
No 109
>PRK09726 antitoxin HipB; Provisional
Probab=38.09 E-value=20 Score=28.14 Aligned_cols=21 Identities=19% Similarity=0.498 Sum_probs=13.4
Q ss_pred HHHHHHhCCCCCeeeeecccc
Q 048741 276 QQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 276 eeLa~eiGv~~~vVKVWFQNR 296 (314)
++||..+||+..+|.-|..++
T Consensus 29 ~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 29 SELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHCcCHHHHHHHHCCC
Confidence 466666676666666666543
No 110
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=37.98 E-value=13 Score=31.00 Aligned_cols=30 Identities=13% Similarity=0.216 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..+++|..+|+++.+|+.|.+--|.++|+.
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457999999999999999998766666543
No 111
>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=37.88 E-value=5.1 Score=34.95 Aligned_cols=35 Identities=14% Similarity=0.251 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 269 KQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 269 ~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
|......+++|..+|++..+|+++++--|.++|+.
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34445677999999999999999999777777654
No 112
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=37.70 E-value=13 Score=32.07 Aligned_cols=31 Identities=29% Similarity=0.315 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|+++.+|++.+..-|.++|+.
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999999999888887765
No 113
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=37.01 E-value=11 Score=32.97 Aligned_cols=48 Identities=21% Similarity=0.228 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 245 RTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 245 RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.+.+|..|++.+..+ .+ || ..+++|..+|+++.+|+.|-+.-|.|+++
T Consensus 4 ~~~Lte~qr~VL~Lr-~~-Gl--------Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EK-GL--------SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHH-Hc-CC--------CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 467899999988764 32 44 45699999999999999998877777765
No 114
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=36.72 E-value=8.8 Score=34.04 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCCCeeeeeccccc
Q 048741 275 VQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 275 reeLa~eiGv~~~vVKVWFQNRR 297 (314)
+++||..+|++..+|.-|-.+.+
T Consensus 85 qeeLA~~lgvs~s~IsriE~G~~ 107 (154)
T TIGR00270 85 QEQLAKKIQEKESLIKKIENAEI 107 (154)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56899999999999988887654
No 115
>PHA02535 P terminase ATPase subunit; Provisional
Probab=36.68 E-value=22 Score=38.07 Aligned_cols=42 Identities=19% Similarity=0.544 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccc
Q 048741 246 TKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 246 T~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNR 296 (314)
+.||.|-+.+-..+|.+ ||+.. ++|++|||+.++|.-|-+.-
T Consensus 1 ~~yt~EfK~~Av~Ly~~-G~sv~--------eIA~~LGv~~~Tl~~W~kr~ 42 (581)
T PHA02535 1 TAYDDDVRRAAKFLYWQ-GWTVA--------EIAEELGLKSRTIYSWKERD 42 (581)
T ss_pred CCCCHHHHHHHHHHHHc-CCCHH--------HHHHHhCCChhHHHHHhccc
Confidence 36899988888888887 88764 89999999999999997754
No 116
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=36.47 E-value=5.4 Score=34.87 Aligned_cols=29 Identities=7% Similarity=0.066 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
..+|+|..+|++..+|+++++--|.++|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 56799999999999999999866655555
No 117
>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=35.93 E-value=14 Score=31.27 Aligned_cols=48 Identities=8% Similarity=0.223 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+...|-. ....+++|+.+|++..+|+++..--|.++++.
T Consensus 119 ~L~~~~r~i~~l~~~~---------g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYH---------DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4566666666533322 12456899999999999999988666666653
No 118
>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=35.91 E-value=8.8 Score=29.36 Aligned_cols=21 Identities=14% Similarity=0.578 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCCCCeeeeecc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMH 294 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQ 294 (314)
...+||.+|||+..+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 445789999999999999953
No 119
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=35.83 E-value=14 Score=30.97 Aligned_cols=30 Identities=13% Similarity=0.259 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..+++|.++|++..+|+++++--|.++++.
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456999999999999999887666666654
No 120
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=35.65 E-value=3.9 Score=35.58 Aligned_cols=48 Identities=13% Similarity=0.136 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+.-.|- .....+++|..+|+++.+|++.++.-|.++++.
T Consensus 131 ~Lp~~~r~v~~l~~~---------~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 131 RLPPRTGRVFMMREW---------LELETEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455556655553322 223567999999999999999998877777654
No 121
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=35.33 E-value=13 Score=31.20 Aligned_cols=47 Identities=13% Similarity=0.156 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.++..|++.+.-.|-. ....+++|..+|++..+|++...--|.++|+
T Consensus 122 ~L~~~~r~vl~l~~~~---------g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQ---------NLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4566666666543222 2345689999999999999988755555554
No 122
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=34.90 E-value=17 Score=31.19 Aligned_cols=48 Identities=13% Similarity=0.108 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+...|-. ....+++|..+|++..+|+++.+.-|.++++.
T Consensus 135 ~L~~~~r~vl~l~~~~---------~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 135 ALSPEERRVIEVLYYQ---------GYTHREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4566666666533221 23456899999999999999998666666654
No 123
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=34.72 E-value=13 Score=36.29 Aligned_cols=52 Identities=15% Similarity=0.204 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|+..|...|-. .+......+++|..+||++.+|+++.+.-+.|+|+.
T Consensus 262 ~L~~~~R~vl~lrygL-----~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 262 ELNDKQREVLARRFGL-----LGYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred cCCHHHHHHHHHHhcc-----CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5667777776655532 233445678999999999999999999888887765
No 124
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=34.62 E-value=6.2 Score=34.65 Aligned_cols=48 Identities=8% Similarity=0.076 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+.-.|-. ....+++|..+|++..+|+++++--|.++|+.
T Consensus 136 ~L~~~~r~i~~L~~~~---------g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 136 ALPERQRQAVVLRHIE---------GLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4566666655533222 23466899999999999999999777777654
No 125
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=34.59 E-value=12 Score=33.88 Aligned_cols=52 Identities=15% Similarity=0.159 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+...|.. .+......+++|..+|++..+|+++.+.-|.++|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l-----~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGL-----NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhcc-----CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4566666666544410 112334567899999999999999998777777664
No 126
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=34.38 E-value=10 Score=33.13 Aligned_cols=47 Identities=15% Similarity=0.204 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..+++.+..+|+. ...+++|..+|++..+|++.++.-|.++++.
T Consensus 155 ~L~~~~r~vl~l~~e~----------~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 155 LLSELEKEVLELYLDG----------KSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred hCCHHHHHHHHHHHcc----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4455555555443332 3556899999999999999888777777664
No 127
>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=34.18 E-value=9.6 Score=25.86 Aligned_cols=24 Identities=13% Similarity=0.214 Sum_probs=20.3
Q ss_pred HHHHHHHhCCCCCeeeeecccccc
Q 048741 275 VQQFCQEIGVKRRVLKVWMHNNKH 298 (314)
Q Consensus 275 reeLa~eiGv~~~vVKVWFQNRRa 298 (314)
..++|+.+||+..+|+.|.++..-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~l 26 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGLL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCC
Confidence 468899999999999999876653
No 128
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=33.96 E-value=6 Score=36.49 Aligned_cols=31 Identities=3% Similarity=0.103 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|++..+|+++.+.-|.++|+.
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3557999999999999999999888877764
No 129
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=33.91 E-value=6.8 Score=33.52 Aligned_cols=52 Identities=6% Similarity=0.067 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCCCC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNIN 307 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~ 307 (314)
.++..|++.+.-.+- .....+++|..+|++..+|+++...-+.+.+..-..+
T Consensus 119 ~Lp~~~r~v~~L~~~---------~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~~ 170 (172)
T PRK12523 119 KLSSKARAAFLYNRL---------DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYGE 170 (172)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcCC
Confidence 455666665553322 2235679999999999999999987777666544433
No 130
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=33.85 E-value=7 Score=34.70 Aligned_cols=31 Identities=13% Similarity=0.248 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
....++|..+|+++.+||+.++.-|.++|+.
T Consensus 156 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 156 FEIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999999998777777653
No 131
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=33.80 E-value=6.8 Score=33.83 Aligned_cols=31 Identities=16% Similarity=0.206 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|++..+|++.++.-|.++|+.
T Consensus 134 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 134 YSQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999999888887753
No 132
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=33.66 E-value=5.9 Score=34.43 Aligned_cols=48 Identities=17% Similarity=0.299 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHH-HHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 246 TKFTQEQKEKMFN-FAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 246 T~FT~eQk~~Le~-~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..++.+|.+.|.. +|+. ...+++|..+|++..+|++.++.-|.++++.
T Consensus 130 ~~L~~~~r~vl~l~~~~~----------~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHE----------KSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred HhCCHHHHHHHHHHHHcC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3567777777753 3333 3567899999999999999998888777765
No 133
>PF13518 HTH_28: Helix-turn-helix domain
Probab=33.41 E-value=12 Score=25.78 Aligned_cols=24 Identities=21% Similarity=0.613 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCCCeeeeeccccc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRR 297 (314)
...++|.++||+..+|.-|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 456799999999999999997543
No 134
>PF13551 HTH_29: Winged helix-turn helix
Probab=33.06 E-value=38 Score=26.38 Aligned_cols=20 Identities=20% Similarity=0.521 Sum_probs=16.6
Q ss_pred CCCCCCCHHHHHHHHHHHHH
Q 048741 243 RFRTKFTQEQKEKMFNFAEK 262 (314)
Q Consensus 243 R~RT~FT~eQk~~Le~~Fer 262 (314)
|.++.++.+|.+.|.+++..
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~ 72 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRE 72 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHH
Confidence 34444999999999999998
No 135
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=32.76 E-value=9.8 Score=27.38 Aligned_cols=25 Identities=12% Similarity=0.328 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCCCCeeeeecccccc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKH 298 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRa 298 (314)
.+.+||+++|+++.+|.-|+.++..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~ 36 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPS 36 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT--
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccc
Confidence 4668999999999999999987743
No 136
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=32.69 E-value=7.1 Score=34.09 Aligned_cols=31 Identities=16% Similarity=0.200 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|++..+|+++++.-|.++|+.
T Consensus 153 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 153 FSSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999999998777666643
No 137
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=32.59 E-value=25 Score=29.25 Aligned_cols=39 Identities=15% Similarity=0.510 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMH 294 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQ 294 (314)
.+|.+-.+++.++++. . ....+.|...+|+..+|.-||+
T Consensus 2 aYS~DlR~rVl~~~~~----g-----~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 2 AYSLDLRQRVLAYIEK----G-----KSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCCHHHHHHHHHHHHc----c-----chHHHHHHHhCcHHHHHHHHHH
Confidence 3677778888888877 2 1456789999999999999998
No 138
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=32.59 E-value=92 Score=24.60 Aligned_cols=34 Identities=12% Similarity=0.145 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccc
Q 048741 249 TQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 249 T~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNR 296 (314)
|.||+++|-+.+-+ .+++.+|.++..|.|.|+.=
T Consensus 14 s~EqK~~La~~iT~--------------a~~~~lg~~~e~v~V~I~ev 47 (76)
T PRK01271 14 DEEQKAALAADITD--------------VIIRHLNSKDSSISIALQQI 47 (76)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcCcceEEEEEEEc
Confidence 79999998755554 67889999999999999753
No 139
>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=32.58 E-value=12 Score=25.55 Aligned_cols=22 Identities=14% Similarity=0.422 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCCCCeeeeeccc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHN 295 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQN 295 (314)
...++|..+++++.+|+.|...
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4568899999999999999863
No 140
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=32.53 E-value=7.5 Score=35.48 Aligned_cols=31 Identities=10% Similarity=0.053 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|+++.+|+++.+.-|.++++.
T Consensus 151 ~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 151 MSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567999999999999999999777777764
No 141
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=32.47 E-value=7.9 Score=34.42 Aligned_cols=35 Identities=6% Similarity=0.098 Sum_probs=28.5
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhcCCCC
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNNIN 307 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~~~ 307 (314)
...+++|..+|++..+|+++.+.-|.++|+.-...
T Consensus 150 ~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 150 YTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 35679999999999999999988777777665443
No 142
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=32.40 E-value=85 Score=22.47 Aligned_cols=33 Identities=18% Similarity=0.291 Sum_probs=24.5
Q ss_pred CHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeeccc
Q 048741 249 TQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHN 295 (314)
Q Consensus 249 T~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQN 295 (314)
|.+||++|-+..-. .+.+.+|+++..|.|.|+.
T Consensus 12 ~~e~K~~l~~~it~--------------~~~~~lg~~~~~i~V~i~E 44 (60)
T PF01361_consen 12 TAEQKRELAEAITD--------------AVVEVLGIPPERISVVIEE 44 (60)
T ss_dssp -HHHHHHHHHHHHH--------------HHHHHHTS-GGGEEEEEEE
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcCCCeEEEEEEE
Confidence 78998888644443 6788899999999998875
No 143
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=32.18 E-value=7.7 Score=32.96 Aligned_cols=48 Identities=13% Similarity=0.211 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|.+.|...|-. ....+++|..+|+++.+|++++..-|.++|+.
T Consensus 118 ~L~~~~r~vl~L~~~~---------g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 118 QLSPEHRAVLVRSYYR---------GWSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4566666666543221 13467999999999999999998777666654
No 144
>PRK06930 positive control sigma-like factor; Validated
Probab=32.14 E-value=12 Score=33.44 Aligned_cols=48 Identities=10% Similarity=0.227 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..+++.+...|.. .....++|..+|++..+|++++..-|.|+++.
T Consensus 114 ~L~~rer~V~~L~~~e---------g~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 114 VLTEREKEVYLMHRGY---------GLSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5677777776643322 13566899999999999999999888777764
No 145
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=31.74 E-value=9.6 Score=34.66 Aligned_cols=31 Identities=10% Similarity=0.117 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|++..+|+.+++.-+.++|+.
T Consensus 201 ~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 201 LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999999999888887764
No 146
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=31.55 E-value=8.7 Score=33.59 Aligned_cols=31 Identities=10% Similarity=0.171 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|++..+|+.+++.-|.++++.
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999998666666643
No 147
>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=31.24 E-value=19 Score=23.16 Aligned_cols=20 Identities=15% Similarity=0.401 Sum_probs=13.5
Q ss_pred HHHHHhCCCCCeeeeecccc
Q 048741 277 QFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 277 eLa~eiGv~~~vVKVWFQNR 296 (314)
+||..+|+++.+|.-|+.++
T Consensus 17 ~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 17 ELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHCCCHHHHHHHHcCC
Confidence 66677777777666666654
No 148
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=30.79 E-value=5.5 Score=33.84 Aligned_cols=36 Identities=11% Similarity=0.131 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 269 KQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 269 ~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
|.+....+++|..+|++..+|++.++.-|.+.++.-
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 334446779999999999999999988887777653
No 149
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=30.73 E-value=8.7 Score=32.82 Aligned_cols=31 Identities=6% Similarity=0.167 Sum_probs=25.3
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|++..+|++++..-|.++++.
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 136 YSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3556999999999999999998777666653
No 150
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=30.59 E-value=20 Score=28.68 Aligned_cols=9 Identities=56% Similarity=1.294 Sum_probs=8.0
Q ss_pred ccccccccc
Q 048741 116 EALTCSACN 124 (314)
Q Consensus 116 ~~l~CaaCg 124 (314)
..|.|||||
T Consensus 56 ~tLsCsACG 64 (74)
T PF05077_consen 56 NTLSCSACG 64 (74)
T ss_pred CeEeehhcc
Confidence 579999998
No 151
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=30.58 E-value=8.2 Score=32.83 Aligned_cols=33 Identities=12% Similarity=0.220 Sum_probs=27.1
Q ss_pred CHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 271 EESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 271 d~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.....+++|..+|++...|+++...-|.+++++
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 344667999999999999999998777777664
No 152
>PLN03207 stomagen; Provisional
Probab=30.52 E-value=41 Score=28.61 Aligned_cols=57 Identities=32% Similarity=0.571 Sum_probs=36.5
Q ss_pred CCCCCCCCCCCCCCcccccCCcccccccceeeeHHhhhhhcccCCCccccccc-----ccccCCCCCCcccccccccccc
Q 048741 52 ISPINGPPIPISTNLEDQQNGSTINVNKKMVKYKECLKNHAAGMGGNATDGCG-----EFMPSGEEGTIEALTCSACNCH 126 (314)
Q Consensus 52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~Y~eClkNhaa~~Gg~a~DGCg-----EFm~~~~~gt~~~l~CaaCgCH 126 (314)
+.-.||.. .+.+-++.-.|+.+ ....|.||. ||. |-+|-...+...+-.=-.|-||
T Consensus 52 ~~~l~g~~--~~k~srr~~igs~a----ptctynecr-------------gcr~kc~~eqvpv~~~dp~nsayhy~cvch 112 (113)
T PLN03207 52 VKLLNGGH--LSKSSRRLMIGSTA----PTCTYNECR-------------GCRYKCRAEQVPVEGNDPINSAYHYKCVCH 112 (113)
T ss_pred cccccccc--cchhhhhhhhcCcC----Ccccccccc-------------CccccccceeccccCCCCCccccccccCCC
Confidence 34566666 55677888888877 477899995 553 5556433333444444567788
Q ss_pred c
Q 048741 127 R 127 (314)
Q Consensus 127 R 127 (314)
|
T Consensus 113 R 113 (113)
T PLN03207 113 R 113 (113)
T ss_pred C
Confidence 7
No 153
>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=30.35 E-value=14 Score=33.91 Aligned_cols=50 Identities=12% Similarity=0.227 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 245 RTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 245 RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
...+|..|++.|.-.++ | ..-.++|..+||++++|+.+++|=+.|++-+.
T Consensus 169 ~~~Lt~re~evl~~~a~--G--------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~ 218 (232)
T TIGR03541 169 AGVLSEREREVLAWTAL--G--------RRQADIAAILGISERTVENHLRSARRKLGVAT 218 (232)
T ss_pred hccCCHHHHHHHHHHHC--C--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCC
Confidence 44789999999876532 2 24568999999999999999998888776443
No 154
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=30.27 E-value=12 Score=31.27 Aligned_cols=47 Identities=17% Similarity=0.290 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.+|..+.+.|.-+++- ..++++++++++++++|++..+|=|.|+..+
T Consensus 137 ~Lt~~E~~il~~l~~g----------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~ 183 (196)
T PRK10360 137 PLTKRERQVAEKLAQG----------MAVKEIAAELGLSPKTVHVHRANLMEKLGVS 183 (196)
T ss_pred CCCHHHHHHHHHHHCC----------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 5888888888776654 2577899999999999999888776666533
No 155
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=29.98 E-value=8.8 Score=33.73 Aligned_cols=49 Identities=16% Similarity=0.161 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
.++..|.+.+.-.|- .....+++|..+|++..+|+++.+--|.++++..
T Consensus 111 ~Lp~~~R~v~~L~~~---------eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAI---------EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 456666666653222 2235679999999999999999987676666543
No 156
>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=29.54 E-value=13 Score=35.22 Aligned_cols=50 Identities=12% Similarity=0.147 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 245 RTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 245 RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
...+|..+++.|.-.++- ....++|..+++++.+||.+++|=+.|++-+.
T Consensus 188 ~~~LT~RE~evl~l~a~G----------~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG----------KTNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHHHHHCC----------CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 347899999999865432 24568999999999999999998877766544
No 157
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=29.37 E-value=13 Score=30.34 Aligned_cols=47 Identities=9% Similarity=0.240 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 248 FTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 248 FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
++..+.+.|..+++. + .-++++.++|++..+|+++.++=|.|+++..
T Consensus 142 l~~~e~~vl~~~~~~--~--------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~ 188 (202)
T PRK09390 142 LSERERQVMDGLVAG--L--------SNKVIARDLDISPRTVEVYRANVMTKMQAGS 188 (202)
T ss_pred hhhhHHHHHHHHHcc--C--------chHHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence 556666665543332 1 2456889999999999999988777766543
No 158
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=29.28 E-value=23 Score=30.96 Aligned_cols=49 Identities=12% Similarity=0.115 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
.++.+|++.+...|-. ....+++|..+|++..+|++.++.-|.++|+.-
T Consensus 141 ~Lp~~~r~v~~l~~~e---------g~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 141 RLPKAQRDVLQAVYLE---------ELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 4555666665532222 235669999999999999999987777776653
No 159
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=29.23 E-value=10 Score=32.51 Aligned_cols=45 Identities=9% Similarity=0.234 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNL 300 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~ 300 (314)
.++.+|++.+.. .|......+++|..+|++..+|++++..-+.+.
T Consensus 119 ~L~~~~r~i~~l---------~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 119 GLNGKTREAFLL---------SQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163 (172)
T ss_pred hCCHHHhHHhhh---------hhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 455555555442 223334567999999999999999987544443
No 160
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=29.19 E-value=1e+02 Score=22.11 Aligned_cols=34 Identities=18% Similarity=0.264 Sum_probs=26.9
Q ss_pred CHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccc
Q 048741 249 TQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 249 T~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNR 296 (314)
|.+|++.|-+..-. .+++.+|++..-|.|.|..-
T Consensus 13 s~eqk~~l~~~it~--------------~l~~~~~~p~~~v~V~i~e~ 46 (62)
T PRK00745 13 TVEQKRKLVEEITR--------------VTVETLGCPPESVDIIITDV 46 (62)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHcCCChhHEEEEEEEc
Confidence 78999888644443 68889999999999988754
No 161
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=29.12 E-value=1e+02 Score=22.46 Aligned_cols=34 Identities=9% Similarity=0.229 Sum_probs=26.6
Q ss_pred CHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccc
Q 048741 249 TQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 249 T~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNR 296 (314)
|.+|+++|-+...+ .++..+|++...|.|.|...
T Consensus 13 t~eqk~~l~~~it~--------------~l~~~lg~p~~~v~V~i~e~ 46 (64)
T PRK01964 13 PEEKIKNLIREVTE--------------AISATLDVPKERVRVIVNEV 46 (64)
T ss_pred CHHHHHHHHHHHHH--------------HHHHHhCcChhhEEEEEEEc
Confidence 78999888644443 68889999999999887654
No 162
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=28.91 E-value=18 Score=32.44 Aligned_cols=31 Identities=16% Similarity=0.331 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
..+++|..+|++..+|+++++--|.++++.-
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999998777777654
No 163
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=28.85 E-value=8.4 Score=33.34 Aligned_cols=47 Identities=4% Similarity=0.137 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHH-HHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFN-FAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~-~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+.. +|+. ...+++|..+|++..+|++..+.-|.++++.
T Consensus 122 ~L~~~~r~i~~l~~~~g----------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN----------LTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred hCCHHHHHHHHHHHHcC----------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456666666653 3332 3567999999999999999998777776654
No 164
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=28.65 E-value=1.3e+02 Score=21.09 Aligned_cols=35 Identities=17% Similarity=0.279 Sum_probs=26.5
Q ss_pred CHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeeccccc
Q 048741 249 TQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 249 T~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRR 297 (314)
|.+||++|-+..- +.++..+|+++..|-|.|....
T Consensus 12 t~eqk~~l~~~i~--------------~~l~~~~g~~~~~v~V~i~e~~ 46 (58)
T cd00491 12 TDEQKRELIERVT--------------EAVSEILGAPEATIVVIIDEMP 46 (58)
T ss_pred CHHHHHHHHHHHH--------------HHHHHHhCcCcccEEEEEEEeC
Confidence 5889888864433 3678889999999999887643
No 165
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=28.61 E-value=8.5 Score=32.88 Aligned_cols=31 Identities=13% Similarity=0.288 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|++..+|+++.+.-|.++++.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999999988777777653
No 166
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=28.57 E-value=15 Score=30.09 Aligned_cols=45 Identities=7% Similarity=0.108 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLA 301 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~K 301 (314)
.+|..+++.|.-+ .. . + ...++|+++++++++|+.|.+|=+.|+.
T Consensus 149 ~lt~~e~~vl~l~-~~----g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKLI-TE----G-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHHH-HC----C-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5888888887754 33 1 1 3568899999999999999987666554
No 167
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=28.42 E-value=9.5 Score=33.09 Aligned_cols=32 Identities=3% Similarity=0.083 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 272 ESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 272 ~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
....+++|..+|++..+|++.++.-|.++|+.
T Consensus 154 g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 154 GLSYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567999999999999999998777777754
No 168
>PHA01976 helix-turn-helix protein
Probab=28.41 E-value=25 Score=25.57 Aligned_cols=18 Identities=11% Similarity=0.342 Sum_probs=8.8
Q ss_pred HHHHHhCCCCCeeeeecc
Q 048741 277 QFCQEIGVKRRVLKVWMH 294 (314)
Q Consensus 277 eLa~eiGv~~~vVKVWFQ 294 (314)
+||..+||+..+|.-|..
T Consensus 20 ~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 20 ELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHHHhCCCHHHHHHHHc
Confidence 445555555554444443
No 169
>PRK10651 transcriptional regulator NarL; Provisional
Probab=28.24 E-value=14 Score=30.77 Aligned_cols=46 Identities=9% Similarity=0.177 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.+|..+++.|+.+++- ...++++++++++..+|++..+|=|.|+.-
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 4999999888765542 135578999999999999998877766643
No 170
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=27.54 E-value=85 Score=28.27 Aligned_cols=44 Identities=7% Similarity=0.128 Sum_probs=35.8
Q ss_pred CCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeec
Q 048741 244 FRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWM 293 (314)
Q Consensus 244 ~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWF 293 (314)
+...+|.|++++|..+-.. .|..-.|..||++.||+..-|.+=.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~------DP~~wTr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAE------DPEKWTRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred ccccCCHHHHHHHHHHHHc------CchHhhHHHHHHHhCCCHHHHHHhc
Confidence 3468999999999887665 6777899999999999987766443
No 171
>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=27.47 E-value=25 Score=26.21 Aligned_cols=18 Identities=22% Similarity=0.451 Sum_probs=8.4
Q ss_pred HHHHHhCCCCCeeeeecc
Q 048741 277 QFCQEIGVKRRVLKVWMH 294 (314)
Q Consensus 277 eLa~eiGv~~~vVKVWFQ 294 (314)
+||+.+|+++.+|.-|+.
T Consensus 23 ~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 23 ALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHHHhCCCHHHHHHHHc
Confidence 444444444444444443
No 172
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=27.39 E-value=9.5 Score=33.45 Aligned_cols=33 Identities=9% Similarity=0.031 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
...+++|..+|+++.+|++.++--|.++++.-.
T Consensus 128 ~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 128 FSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356799999999999999999877777766543
No 173
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=27.34 E-value=14 Score=34.73 Aligned_cols=50 Identities=4% Similarity=0.086 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
.+++.|++.+.-.+-. ....+|+|..+|+++.+|+.+++.-|.++++..+
T Consensus 108 ~L~~~~R~v~~L~~~~---------g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 108 RLSPLERAVFVLREVF---------DYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 4566666665532221 1245689999999999999999988888776543
No 174
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=27.27 E-value=8.8 Score=33.23 Aligned_cols=48 Identities=8% Similarity=0.101 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++.+|++.+.-.|-. ....+|+|..+|+++.+||+.+..-+.+.+..
T Consensus 127 ~Lp~~~R~v~~L~~~~---------g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLD---------GMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHc---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 4667777666542222 23567999999999999999998665555443
No 175
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=27.26 E-value=17 Score=31.39 Aligned_cols=30 Identities=13% Similarity=0.192 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
...+++|..+|++..+|+++++--|.++|+
T Consensus 166 ~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 166 KSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 355699999999999999998866666654
No 176
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=26.88 E-value=12 Score=35.20 Aligned_cols=50 Identities=2% Similarity=0.078 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
.++..|++.+.-.+-. ....+|+|..+|+++.+||..++.-|.++++..+
T Consensus 115 ~L~~~~R~v~~L~~~~---------g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 115 RLSPLERAAFLLHDVF---------GVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred hCCHHHHHHHHHHHHh---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 4566666665532221 1245699999999999999999987777776543
No 177
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=26.76 E-value=8.2 Score=41.55 Aligned_cols=60 Identities=15% Similarity=0.180 Sum_probs=0.0
Q ss_pred CCCCCCCCCHHHHHHHH-HHHHHcCcccCCCCHHHHHHHHHHhCCCCCe-------eeeecccccchhhhcC
Q 048741 241 KKRFRTKFTQEQKEKMF-NFAEKVGWKIQKQEESVVQQFCQEIGVKRRV-------LKVWMHNNKHNLAKKN 304 (314)
Q Consensus 241 kKR~RT~FT~eQk~~Le-~~FerlGWr~~~pd~~~reeLa~eiGv~~~v-------VKVWFQNRRaK~KKk~ 304 (314)
.||.|.+|-.+|...+. ..|-+ +..+....+.+.-.+..+.... |+.||.|||.+.++.+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k----~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLK----TRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheec----ccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
No 178
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=26.56 E-value=20 Score=36.40 Aligned_cols=17 Identities=24% Similarity=0.642 Sum_probs=12.8
Q ss_pred ccccccccccccchhhh
Q 048741 116 EALTCSACNCHRNFHRK 132 (314)
Q Consensus 116 ~~l~CaaCgCHRnFHr~ 132 (314)
-+++|+||||+-+---|
T Consensus 117 i~~~CkACG~r~~~d~r 133 (400)
T KOG2767|consen 117 ISLKCKACGFRSDMDLR 133 (400)
T ss_pred hhhHHHHcCCcccccch
Confidence 37899999998765433
No 179
>PRK13558 bacterio-opsin activator; Provisional
Probab=26.23 E-value=43 Score=34.73 Aligned_cols=40 Identities=10% Similarity=0.111 Sum_probs=33.9
Q ss_pred CCCCHHHHHHHHHHHHHcCcccCC--CCHHHHHHHHHHhCCCCCee
Q 048741 246 TKFTQEQKEKMFNFAEKVGWKIQK--QEESVVQQFCQEIGVKRRVL 289 (314)
Q Consensus 246 T~FT~eQk~~Le~~FerlGWr~~~--pd~~~reeLa~eiGv~~~vV 289 (314)
..+|..|.+.|+..|+. -.| |....-++||.++|++..+|
T Consensus 606 ~~lt~~q~e~l~~a~~~----gyf~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 606 NDLTDRQLTALQKAYVS----GYFEWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhCCHHHHHHHHHHHHc----CCCCCCccCCHHHHHHHhCCCHHHH
Confidence 47999999999999997 443 66677889999999999875
No 180
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=26.21 E-value=15 Score=26.78 Aligned_cols=22 Identities=14% Similarity=0.410 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCCCeeeeecccc
Q 048741 275 VQQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 275 reeLa~eiGv~~~vVKVWFQNR 296 (314)
..++|+.+||+..+|+.|-+..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHHhc
Confidence 4689999999999999997644
No 181
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=26.01 E-value=27 Score=30.60 Aligned_cols=48 Identities=10% Similarity=0.136 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.+...|- +....+++|..+|++..+|+++..--|.++++.
T Consensus 131 ~L~~~~r~v~~l~~~---------~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMREV---------LGFESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHHHH---------hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 455556665553322 223567999999999999999988777776654
No 182
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=25.70 E-value=1.4e+02 Score=24.40 Aligned_cols=36 Identities=6% Similarity=0.108 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccc
Q 048741 249 TQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKH 298 (314)
Q Consensus 249 T~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRa 298 (314)
+.+|+++|-+.. -+.|.+.+|++...|-|.|++...
T Consensus 70 ~~e~k~~l~~~i--------------~~~l~~~lgi~~~rv~I~f~~~~~ 105 (116)
T PTZ00397 70 SRSNNSSIAAAI--------------TKILASHLKVKSERVYIEFKDCSA 105 (116)
T ss_pred CHHHHHHHHHHH--------------HHHHHHHhCcCcccEEEEEEECCh
Confidence 578888775333 336889999999999999988654
No 183
>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=25.17 E-value=27 Score=31.45 Aligned_cols=48 Identities=8% Similarity=0.130 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.|...|.. ....+++|..+|++..+|+.|.+.-+.++|++
T Consensus 175 ~L~~~~r~il~l~y~~---------~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYE---------ELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhC---------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4566666666654432 22567999999999999999998777666653
No 184
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=25.02 E-value=75 Score=26.40 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=21.5
Q ss_pred CCCCCCHHHHHHHHHHHHHcCcccCC
Q 048741 244 FRTKFTQEQKEKMFNFAEKVGWKIQK 269 (314)
Q Consensus 244 ~RT~FT~eQk~~Le~~FerlGWr~~~ 269 (314)
.-+.+|..|+..+.+.|+++||+.++
T Consensus 18 S~k~lt~~el~~vl~~l~~~G~k~~~ 43 (119)
T PF06252_consen 18 SSKDLTEAELEKVLDELKRLGFKPPK 43 (119)
T ss_pred hHHHCCHHHHHHHHHHHHHccCcCcc
Confidence 33468999999999999999997544
No 185
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=25.02 E-value=26 Score=24.27 Aligned_cols=37 Identities=8% Similarity=0.296 Sum_probs=27.6
Q ss_pred HHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccc
Q 048741 255 KMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 255 ~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNR 296 (314)
.-.+.|.+.||+.- ...++|+++|+++..|--.|.|+
T Consensus 4 aa~~l~~~~G~~~~-----s~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 4 AALELFAEKGYEAV-----SIRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp HHHHHHHHHHTTTS-----SHHHHHHHHTSCHHHHHHHCSSH
T ss_pred HHHHHHHHhCHHhC-----CHHHHHHHHccchhhHHHHcCCH
Confidence 33455666666654 67789999999999988877765
No 186
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=25.01 E-value=10 Score=35.36 Aligned_cols=30 Identities=13% Similarity=0.357 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..+|+|..+|++..+||++++.-|.+++++
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~ 208 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLER 208 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 466999999999999999999877776654
No 187
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=24.71 E-value=1.6e+02 Score=21.05 Aligned_cols=34 Identities=18% Similarity=0.308 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccc
Q 048741 249 TQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 249 T~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNR 296 (314)
|.+|++.|-+..- +.++..+|++...+-|.+...
T Consensus 13 t~eqK~~l~~~it--------------~~l~~~lg~~~~~v~V~i~e~ 46 (63)
T TIGR00013 13 TDEQKRQLIEGVT--------------EAMAETLGANLESIVVIIDEM 46 (63)
T ss_pred CHHHHHHHHHHHH--------------HHHHHHhCCCcccEEEEEEEc
Confidence 7899988864333 368889999999998887654
No 188
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=24.71 E-value=12 Score=30.77 Aligned_cols=9 Identities=56% Similarity=0.962 Sum_probs=7.1
Q ss_pred eeeeecccc
Q 048741 288 VLKVWMHNN 296 (314)
Q Consensus 288 vVKVWFQNR 296 (314)
-|||||||-
T Consensus 32 dvkvwmqnl 40 (106)
T PF11516_consen 32 DVKVWMQNL 40 (106)
T ss_dssp HHHHHHHHH
T ss_pred cHHHHHHHH
Confidence 379999983
No 189
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=24.50 E-value=34 Score=37.03 Aligned_cols=36 Identities=28% Similarity=0.533 Sum_probs=25.4
Q ss_pred CcccccccccccCCCCCCccccccccc-ccccchhhhh
Q 048741 97 GNATDGCGEFMPSGEEGTIEALTCSAC-NCHRNFHRKE 133 (314)
Q Consensus 97 g~a~DGCgEFm~~~~~gt~~~l~CaaC-gCHRnFHr~e 133 (314)
++.|| |+---|.-..-.+.+|.|--| |||||++...
T Consensus 514 ~~c~d-c~~~n~~wAslnlg~l~cieCsgihr~lgt~l 550 (749)
T KOG0705|consen 514 SHCVD-CGTPNPKWASLNLGVLMCIECSGIHRNLGTHL 550 (749)
T ss_pred ceeee-cCCCCcccccccCCeEEEEEchhhhhhhhhhh
Confidence 35666 765544333345689999999 8999999765
No 190
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=24.41 E-value=30 Score=28.85 Aligned_cols=42 Identities=7% Similarity=0.181 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccc
Q 048741 250 QEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNN 296 (314)
Q Consensus 250 ~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNR 296 (314)
..-++++.++.+. .+.+...+++||..+|+++++++-||+..
T Consensus 8 ~~~i~~~~~~I~~-----~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIED-----NLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHH-----hcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3344556666665 34445678899999999999998888753
No 191
>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=24.04 E-value=25 Score=25.25 Aligned_cols=23 Identities=9% Similarity=0.377 Sum_probs=13.3
Q ss_pred HHHHHHHhCCCCCeeeeeccccc
Q 048741 275 VQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 275 reeLa~eiGv~~~vVKVWFQNRR 297 (314)
..+||..+|+++.+|.-|-.+++
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHHCcCHHHHHHHHCCCc
Confidence 34566666666666666665544
No 192
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=23.47 E-value=64 Score=28.56 Aligned_cols=36 Identities=14% Similarity=0.270 Sum_probs=27.0
Q ss_pred HHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccc
Q 048741 258 NFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKH 298 (314)
Q Consensus 258 ~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRa 298 (314)
..|.+.||.. ....++|++.||+...|-..|.|+..
T Consensus 29 ~lf~e~Gy~~-----~s~~dIA~~aGvs~gtiY~hF~sKe~ 64 (212)
T PRK15008 29 DTFSQFGFHG-----TRLEQIAELAGVSKTNLLYYFPSKEA 64 (212)
T ss_pred HHHHHhCccc-----CCHHHHHHHhCcCHHHHHHHCCCHHH
Confidence 3455544433 36778999999999999999988754
No 193
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=23.36 E-value=21 Score=29.79 Aligned_cols=46 Identities=7% Similarity=0.077 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhh
Q 048741 246 TKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLA 301 (314)
Q Consensus 246 T~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~K 301 (314)
..+|..+.+.|..+++- ..+++++.+++++.++|+++..+=|.|+.
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 35788888887654443 36789999999999999999987776654
No 194
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.18 E-value=14 Score=33.62 Aligned_cols=35 Identities=23% Similarity=0.344 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 270 QEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 270 pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
......+++|..+|++..+|++..+.-|.++|+.-
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 33446679999999999999999987787777654
No 195
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.04 E-value=50 Score=23.13 Aligned_cols=30 Identities=30% Similarity=0.479 Sum_probs=19.4
Q ss_pred ccccccccccCCCCCCcccccccccccccchhhhh
Q 048741 99 ATDGCGEFMPSGEEGTIEALTCSACNCHRNFHRKE 133 (314)
Q Consensus 99 a~DGCgEFm~~~~~gt~~~l~CaaCgCHRnFHr~e 133 (314)
-=|-|+++|.+ ....+++|+.|+ ...|++=
T Consensus 13 ~C~~C~~~i~g---~~~~g~~C~~C~--~~~H~~C 42 (53)
T PF00130_consen 13 YCDVCGKFIWG---LGKQGYRCSWCG--LVCHKKC 42 (53)
T ss_dssp B-TTSSSBECS---SSSCEEEETTTT---EEETTG
T ss_pred CCcccCcccCC---CCCCeEEECCCC--ChHhhhh
Confidence 34779999954 234689999765 5666554
No 196
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.87 E-value=34 Score=30.75 Aligned_cols=30 Identities=13% Similarity=0.289 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..+++|..+|++..+|+++.+--|.++|+.
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999998777777764
No 197
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=22.85 E-value=97 Score=27.66 Aligned_cols=34 Identities=24% Similarity=0.483 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhC-CCCCee
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIG-VKRRVL 289 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiG-v~~~vV 289 (314)
.+|.|+++.|.+++.. |+ ...++|.+|| |++..|
T Consensus 2 ~Wtde~~~~L~~lw~~-G~--------SasqIA~~lg~vsRnAV 36 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GL--------SASQIARQLGGVSRNAV 36 (162)
T ss_pred CCCHHHHHHHHHHHHc-CC--------CHHHHHHHhCCcchhhh
Confidence 4789999999988876 32 3457899999 888854
No 198
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.69 E-value=51 Score=28.02 Aligned_cols=30 Identities=13% Similarity=0.183 Sum_probs=26.2
Q ss_pred cCCCCHHHHHHHHHHhCCCCCeeeeeccccc
Q 048741 267 IQKQEESVVQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 267 ~~~pd~~~reeLa~eiGv~~~vVKVWFQNRR 297 (314)
... .....+++|.+.||++.+|=-+|.|+.
T Consensus 26 ~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 26 PPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred cCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 345 777899999999999999999999865
No 199
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=22.65 E-value=22 Score=32.21 Aligned_cols=53 Identities=9% Similarity=0.064 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 246 TKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 246 T~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..++..|++.+...|-. . .......+++|..+|++..+|+++.+.-|.+++++
T Consensus 173 ~~L~~~~r~il~l~y~~----~-~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 173 SVLDGREREVIEMRYGL----G-DGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred HhCCHHHHHHHHHHHcC----C-CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35677777777654410 0 01223567999999999999998877556666553
No 200
>PLN03162 golden-2 like transcription factor; Provisional
Probab=22.55 E-value=74 Score=32.86 Aligned_cols=61 Identities=15% Similarity=0.212 Sum_probs=45.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 240 VKKRFRTKFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 240 ~kKR~RT~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.+||.|-++|.+--++.....++||- .+-.-..+-++...-||++..||--.|--|...|+
T Consensus 232 g~KKpRLrWTpELH~rFVeAV~qLG~--dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~ 292 (526)
T PLN03162 232 GKKKAKVDWTPELHRRFVHAVEQLGV--EKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRH 292 (526)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHhCc--CccchHHHHHHcCCCCcCHHHHHHHHHHHHHhccc
Confidence 46778999999999999999999993 33444555666666688888888888766655443
No 201
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=22.24 E-value=31 Score=30.04 Aligned_cols=28 Identities=11% Similarity=0.246 Sum_probs=23.8
Q ss_pred CHHHHHHHHHHhCCCCCeeeeecccccc
Q 048741 271 EESVVQQFCQEIGVKRRVLKVWMHNNKH 298 (314)
Q Consensus 271 d~~~reeLa~eiGv~~~vVKVWFQNRRa 298 (314)
+....+++|++.||++.+|-.+|.|+..
T Consensus 30 ~~~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 30 SNTTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred ccCCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 3457789999999999999999988754
No 202
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=22.05 E-value=30 Score=32.66 Aligned_cols=52 Identities=13% Similarity=0.202 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|+..|...|-. .+.......++|..+|++..+|+.+...-+.++|+.
T Consensus 222 ~Lp~~~R~Vl~l~ygL-----~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~ 273 (285)
T TIGR02394 222 ELNERQREVLARRFGL-----LGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRI 273 (285)
T ss_pred cCCHHHHHHHHHHhCC-----CCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5666666666654411 223334677999999999999999998777777654
No 203
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=21.97 E-value=15 Score=33.82 Aligned_cols=48 Identities=6% Similarity=0.063 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
.++..|++.|...|-. .....++|..+||++.+|+.|...-+.++|+.
T Consensus 205 ~L~~~~r~vl~l~~~~---------g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIE---------NLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhC---------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4566666666543322 22457999999999999999998777776654
No 204
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.22 E-value=15 Score=34.61 Aligned_cols=32 Identities=6% Similarity=0.123 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhcCC
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKKNN 305 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~~ 305 (314)
..+++|..+|++..+||..++--|.++|+.-.
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 45699999999999999999877777776543
No 205
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=20.99 E-value=38 Score=30.35 Aligned_cols=47 Identities=4% Similarity=0.171 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.++..|++.+...|.. .....++|..+|++..+|+.|...-+.++++
T Consensus 178 ~L~~~~r~vl~l~y~~---------~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFE---------DKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhc---------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5777777777654432 2356799999999999999998765555554
No 206
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=20.98 E-value=25 Score=23.27 Aligned_cols=23 Identities=17% Similarity=0.397 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCCCeeeeeccccc
Q 048741 275 VQQFCQEIGVKRRVLKVWMHNNK 297 (314)
Q Consensus 275 reeLa~eiGv~~~vVKVWFQNRR 297 (314)
.+++|+.+||++.+|.-|.++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 46788889999999888887665
No 207
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=20.96 E-value=14 Score=31.89 Aligned_cols=29 Identities=21% Similarity=0.371 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
..+++|..+|++..+|+.+.+--|.++++
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56799999999999999998866666654
No 208
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=20.95 E-value=50 Score=28.43 Aligned_cols=47 Identities=11% Similarity=0.154 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHHcCcccCCCCHHHHHHHHHHhCCCCCeeeeecccccchhhh
Q 048741 247 KFTQEQKEKMFNFAEKVGWKIQKQEESVVQQFCQEIGVKRRVLKVWMHNNKHNLAK 302 (314)
Q Consensus 247 ~FT~eQk~~Le~~FerlGWr~~~pd~~~reeLa~eiGv~~~vVKVWFQNRRaK~KK 302 (314)
.++..|.+.+...|. .....+++|..+|++..+|++..+.-|.++|+
T Consensus 137 ~L~~~~r~i~~l~~~---------~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 137 ELEPPRSELIRTAFF---------EGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred hCCHHHHHHHHHHHH---------cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 455555555543332 22356789999999999999988766666654
No 209
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=20.87 E-value=23 Score=26.13 Aligned_cols=21 Identities=24% Similarity=0.571 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCCeeeeeccc
Q 048741 275 VQQFCQEIGVKRRVLKVWMHN 295 (314)
Q Consensus 275 reeLa~eiGv~~~vVKVWFQN 295 (314)
..++|+.+||+.++|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 468899999999999999764
No 210
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=20.80 E-value=13 Score=31.12 Aligned_cols=30 Identities=17% Similarity=0.320 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
..+++|.++|+++.+|++.+..-|.++++.
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 556999999999999999988666666654
No 211
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=20.30 E-value=28 Score=30.21 Aligned_cols=31 Identities=13% Similarity=0.096 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCCCCeeeeecccccchhhhc
Q 048741 273 SVVQQFCQEIGVKRRVLKVWMHNNKHNLAKK 303 (314)
Q Consensus 273 ~~reeLa~eiGv~~~vVKVWFQNRRaK~KKk 303 (314)
...+++|..+|++..+|++|...-|.++|+.
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999999998777777654
No 212
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.25 E-value=49 Score=24.19 Aligned_cols=18 Identities=33% Similarity=0.933 Sum_probs=14.4
Q ss_pred ccc-cccCCCCCCcccccccccc
Q 048741 103 CGE-FMPSGEEGTIEALTCSACN 124 (314)
Q Consensus 103 CgE-Fm~~~~~gt~~~l~CaaCg 124 (314)
||. ||...+ +.+.|..||
T Consensus 26 Cg~~~m~~~~----~r~~C~~Cg 44 (50)
T PRK00432 26 CGSGFMAEHL----DRWHCGKCG 44 (50)
T ss_pred CCcchheccC----CcEECCCcC
Confidence 777 998655 589999997
No 213
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=20.23 E-value=15 Score=34.14 Aligned_cols=31 Identities=10% Similarity=0.206 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCCCeeeeecccccchhhhcC
Q 048741 274 VVQQFCQEIGVKRRVLKVWMHNNKHNLAKKN 304 (314)
Q Consensus 274 ~reeLa~eiGv~~~vVKVWFQNRRaK~KKk~ 304 (314)
..+|+|+.+|+++.+||++.+--|.++++.-
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999998887777654
No 214
>PF13309 HTH_22: HTH domain
Probab=20.02 E-value=87 Score=23.59 Aligned_cols=40 Identities=18% Similarity=0.360 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHH-HHHHHcCcccCCCCHHHHHHHHHHhCCCCCee
Q 048741 246 TKFTQEQKEKMF-NFAEKVGWKIQKQEESVVQQFCQEIGVKRRVL 289 (314)
Q Consensus 246 T~FT~eQk~~Le-~~FerlGWr~~~pd~~~reeLa~eiGv~~~vV 289 (314)
..++.+++..+- .++++ --+.-...++.+|+.||+++.+|
T Consensus 19 ~~l~~~~k~~iV~~L~~~----G~F~lKgav~~vA~~L~iS~~TV 59 (64)
T PF13309_consen 19 SRLSKEEKKEIVRQLYEK----GIFLLKGAVEYVAEKLGISRATV 59 (64)
T ss_pred hhCCHHHHHHHHHHHHHC----CCcccCcHHHHHHHHHCCCHHHH
Confidence 345666666555 44555 45666678899999999998765
Done!