Query 019947
Match_columns 333
No_of_seqs 290 out of 1097
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 05:48:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019947.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019947hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0774 Transcription factor P 100.0 2E-33 4.3E-38 262.7 18.0 206 69-319 27-249 (334)
2 KOG0773 Transcription factor M 99.9 1.6E-28 3.5E-33 238.2 0.3 247 67-321 46-302 (342)
3 PF03791 KNOX2: KNOX2 domain ; 99.9 1.8E-23 4E-28 153.1 6.9 50 126-179 3-52 (52)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 1.3E-20 2.7E-25 134.1 3.0 43 71-113 1-43 (45)
5 PF05920 Homeobox_KN: Homeobox 99.7 4.9E-17 1.1E-21 113.5 4.2 40 276-315 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.5 3.4E-14 7.4E-19 103.4 6.9 57 260-319 2-58 (59)
7 PF03792 PBC: PBC domain; Int 99.5 2E-13 4.3E-18 123.7 13.0 147 69-257 25-190 (191)
8 PF00046 Homeobox: Homeobox do 99.5 4.9E-14 1.1E-18 103.1 5.6 57 259-318 1-57 (57)
9 smart00389 HOX Homeodomain. DN 99.5 7.5E-14 1.6E-18 101.1 6.5 55 260-317 2-56 (56)
10 KOG0775 Transcription factor S 99.3 1.4E-12 3.1E-17 123.6 4.6 50 265-317 183-232 (304)
11 TIGR01565 homeo_ZF_HD homeobox 98.9 1.4E-09 3.1E-14 81.8 5.1 53 258-313 1-57 (58)
12 KOG0843 Transcription factor E 98.9 1.1E-09 2.4E-14 98.9 4.3 60 257-319 101-160 (197)
13 KOG0487 Transcription factor A 98.9 7.7E-10 1.7E-14 107.3 3.1 59 259-320 236-294 (308)
14 KOG0489 Transcription factor z 98.9 1.4E-09 3E-14 103.5 3.8 63 258-323 159-221 (261)
15 KOG0493 Transcription factor E 98.8 4.7E-09 1E-13 99.5 5.0 61 258-321 246-306 (342)
16 KOG0485 Transcription factor N 98.8 8.3E-09 1.8E-13 95.7 6.4 59 258-319 104-162 (268)
17 KOG0842 Transcription factor t 98.8 3.9E-09 8.5E-14 102.5 3.2 59 258-319 153-211 (307)
18 KOG0488 Transcription factor B 98.8 6.5E-09 1.4E-13 101.3 4.6 58 259-319 173-230 (309)
19 KOG0483 Transcription factor H 98.7 1E-08 2.2E-13 94.2 4.1 59 258-319 50-108 (198)
20 KOG0850 Transcription factor D 98.7 1.1E-08 2.3E-13 95.5 4.1 57 260-319 124-180 (245)
21 KOG3802 Transcription factor O 98.7 9.7E-09 2.1E-13 102.1 3.9 65 254-321 290-354 (398)
22 COG5576 Homeodomain-containing 98.6 2.6E-08 5.6E-13 88.5 4.3 62 257-321 50-111 (156)
23 KOG0491 Transcription factor B 98.6 2.2E-08 4.8E-13 89.5 3.0 59 257-318 99-157 (194)
24 KOG0492 Transcription factor M 98.5 7.5E-08 1.6E-12 88.9 3.2 65 251-318 137-201 (246)
25 KOG0494 Transcription factor C 98.4 1.7E-07 3.7E-12 89.0 4.2 56 262-320 145-200 (332)
26 KOG0484 Transcription factor P 98.4 2.7E-07 5.9E-12 77.1 4.3 59 258-319 17-75 (125)
27 KOG2251 Homeobox transcription 98.4 3.4E-07 7.3E-12 85.2 4.3 59 258-319 37-95 (228)
28 KOG0848 Transcription factor C 98.3 1.9E-07 4.2E-12 89.0 1.2 56 262-320 203-258 (317)
29 KOG0486 Transcription factor P 98.3 4.7E-07 1E-11 88.0 2.7 59 259-320 113-171 (351)
30 KOG4577 Transcription factor L 98.2 1E-06 2.3E-11 84.9 3.1 63 254-319 163-225 (383)
31 KOG0847 Transcription factor, 98.1 2.2E-06 4.7E-11 80.0 2.7 61 258-321 167-227 (288)
32 KOG2252 CCAAT displacement pro 98.0 7.1E-06 1.5E-10 84.7 5.4 56 259-317 421-476 (558)
33 KOG0844 Transcription factor E 97.8 9.5E-06 2.1E-10 78.9 1.7 55 262-319 185-239 (408)
34 KOG1168 Transcription factor A 97.8 6.7E-06 1.5E-10 79.4 0.7 65 256-323 307-371 (385)
35 KOG0490 Transcription factor, 97.8 1.1E-05 2.4E-10 73.3 1.9 62 256-320 58-119 (235)
36 KOG0849 Transcription factor P 97.7 2.6E-05 5.6E-10 77.5 3.7 59 259-320 177-235 (354)
37 KOG0773 Transcription factor M 97.5 6.6E-05 1.4E-09 73.4 2.7 64 258-322 95-158 (342)
38 PF03789 ELK: ELK domain ; In 97.2 0.00026 5.6E-09 43.7 2.3 22 236-257 1-22 (22)
39 PF11569 Homez: Homeodomain le 97.2 0.00041 8.9E-09 52.1 3.3 43 270-315 10-52 (56)
40 KOG0490 Transcription factor, 95.4 0.011 2.5E-07 53.5 2.9 61 258-321 153-213 (235)
41 KOG1146 Homeobox protein [Gene 91.9 0.13 2.8E-06 58.6 3.5 60 257-319 902-961 (1406)
42 KOG3623 Homeobox transcription 88.5 0.87 1.9E-05 49.6 5.9 52 270-324 568-619 (1007)
43 PF04218 CENP-B_N: CENP-B N-te 86.8 1.2 2.7E-05 32.5 4.2 47 259-313 1-47 (53)
44 PF01527 HTH_Tnp_1: Transposas 73.8 4.8 0.0001 30.2 3.7 47 260-313 2-48 (76)
45 cd00569 HTH_Hin_like Helix-tur 70.0 14 0.00029 22.0 4.6 39 263-309 4-42 (42)
46 cd06171 Sigma70_r4 Sigma70, re 67.6 9.1 0.0002 25.5 3.7 46 264-317 10-55 (55)
47 PF08281 Sigma70_r4_2: Sigma-7 61.9 14 0.00031 26.0 3.9 44 264-315 10-53 (54)
48 PRK06759 RNA polymerase factor 57.5 13 0.00029 31.1 3.6 47 264-318 106-152 (154)
49 PF04545 Sigma70_r4: Sigma-70, 57.1 15 0.00033 25.7 3.3 47 264-318 4-50 (50)
50 PRK09646 RNA polymerase sigma 50.6 17 0.00037 32.2 3.3 50 264-321 142-191 (194)
51 PF13443 HTH_26: Cro/C1-type H 50.2 13 0.00028 26.9 2.1 24 290-313 12-35 (63)
52 PRK09642 RNA polymerase sigma 48.5 22 0.00047 30.2 3.5 48 264-319 106-153 (160)
53 TIGR02937 sigma70-ECF RNA poly 46.4 31 0.00067 27.7 4.0 47 264-318 110-156 (158)
54 PRK09644 RNA polymerase sigma 43.7 27 0.00059 29.9 3.4 50 263-320 107-156 (165)
55 PF13518 HTH_28: Helix-turn-he 43.6 24 0.00053 24.3 2.6 24 291-314 15-38 (52)
56 TIGR02985 Sig70_bacteroi1 RNA 42.7 43 0.00093 27.7 4.4 47 264-318 113-159 (161)
57 PRK11924 RNA polymerase sigma 42.4 26 0.00057 29.7 3.1 48 264-319 125-172 (179)
58 KOG4445 Uncharacterized conser 41.8 55 0.0012 32.8 5.5 46 132-179 134-179 (368)
59 PRK03975 tfx putative transcri 41.7 31 0.00066 30.5 3.4 48 262-318 4-51 (141)
60 PF06729 CENP-R: Kinetochore c 41.5 2.5E+02 0.0054 25.0 8.9 33 130-171 54-86 (139)
61 PRK09652 RNA polymerase sigma 41.4 29 0.00064 29.5 3.3 48 264-319 128-175 (182)
62 KOG2070 Guanine nucleotide exc 40.8 53 0.0012 35.0 5.5 25 130-154 183-214 (661)
63 smart00421 HTH_LUXR helix_turn 40.3 60 0.0013 21.9 4.2 47 264-319 3-49 (58)
64 PRK12514 RNA polymerase sigma 40.3 31 0.00067 29.9 3.3 48 264-319 129-176 (179)
65 PRK00118 putative DNA-binding 40.0 36 0.00079 28.5 3.5 47 264-318 17-63 (104)
66 TIGR02939 RpoE_Sigma70 RNA pol 39.7 25 0.00054 30.5 2.6 49 264-320 138-186 (190)
67 PRK12547 RNA polymerase sigma 39.3 33 0.00072 29.5 3.3 48 264-319 112-159 (164)
68 PRK12541 RNA polymerase sigma 38.8 35 0.00075 29.0 3.3 49 263-319 111-159 (161)
69 TIGR02989 Sig-70_gvs1 RNA poly 38.6 38 0.00082 28.5 3.5 47 264-318 111-157 (159)
70 PRK06811 RNA polymerase factor 38.4 37 0.00079 30.0 3.5 48 264-319 131-178 (189)
71 TIGR02999 Sig-70_X6 RNA polyme 37.6 39 0.00084 29.3 3.5 48 264-319 134-181 (183)
72 TIGR02983 SigE-fam_strep RNA p 37.0 38 0.00083 28.7 3.3 50 264-321 110-159 (162)
73 PF13097 CENP-U: CENP-A nucleo 36.1 93 0.002 28.6 5.7 46 130-178 102-148 (175)
74 PF05190 MutS_IV: MutS family 36.0 62 0.0013 24.8 4.1 26 129-154 1-26 (92)
75 PRK12526 RNA polymerase sigma 35.3 42 0.00092 30.2 3.4 49 264-320 153-201 (206)
76 PF10668 Phage_terminase: Phag 35.0 31 0.00067 26.3 2.1 21 290-310 24-44 (60)
77 PF11288 DUF3089: Protein of u 34.5 10 0.00022 35.5 -0.7 38 58-101 100-137 (207)
78 PF01381 HTH_3: Helix-turn-hel 33.5 32 0.00069 24.1 1.9 21 292-312 13-33 (55)
79 PRK12523 RNA polymerase sigma 32.7 52 0.0011 28.4 3.5 48 264-319 119-166 (172)
80 PF12022 DUF3510: Domain of un 32.7 2E+02 0.0042 24.5 6.9 20 160-179 79-98 (125)
81 PRK09648 RNA polymerase sigma 32.6 51 0.0011 28.8 3.4 48 264-319 139-186 (189)
82 PRK05602 RNA polymerase sigma 31.6 47 0.001 29.0 3.0 50 264-321 128-177 (186)
83 PRK12546 RNA polymerase sigma 31.4 48 0.001 29.6 3.1 49 264-320 113-161 (188)
84 PRK12512 RNA polymerase sigma 31.3 53 0.0012 28.5 3.3 49 264-320 131-179 (184)
85 PRK09047 RNA polymerase factor 31.0 63 0.0014 27.2 3.6 48 264-319 106-153 (161)
86 PF00196 GerE: Bacterial regul 31.0 69 0.0015 23.0 3.4 48 264-320 3-50 (58)
87 PRK12532 RNA polymerase sigma 30.4 55 0.0012 28.8 3.3 49 264-320 136-184 (195)
88 cd00131 PAX Paired Box domain 30.2 1.6E+02 0.0035 25.1 6.0 46 264-312 75-127 (128)
89 PRK09649 RNA polymerase sigma 30.0 62 0.0013 28.5 3.5 48 264-319 130-177 (185)
90 KOG4040 NADH:ubiquinone oxidor 29.7 32 0.0007 31.4 1.6 40 265-304 21-61 (186)
91 PF07425 Pardaxin: Pardaxin; 29.7 35 0.00077 22.6 1.4 22 73-94 5-26 (33)
92 TIGR02954 Sig70_famx3 RNA poly 29.6 60 0.0013 27.8 3.3 48 264-319 119-166 (169)
93 PRK15369 two component system 29.5 1.2E+02 0.0027 25.1 5.2 48 264-320 149-196 (211)
94 PRK12536 RNA polymerase sigma 29.4 62 0.0013 28.2 3.4 48 264-319 129-176 (181)
95 PRK09413 IS2 repressor TnpA; R 29.4 78 0.0017 26.5 3.9 48 260-314 8-55 (121)
96 PRK11511 DNA-binding transcrip 29.3 1.5E+02 0.0032 24.9 5.6 41 268-312 9-49 (127)
97 PRK12516 RNA polymerase sigma 29.2 59 0.0013 28.9 3.3 49 264-320 116-164 (187)
98 TIGR03070 couple_hipB transcri 29.2 38 0.00083 23.4 1.7 22 292-313 19-40 (58)
99 PRK12520 RNA polymerase sigma 28.7 66 0.0014 28.3 3.5 48 264-319 131-178 (191)
100 PRK12519 RNA polymerase sigma 28.6 48 0.001 29.1 2.6 47 264-318 141-187 (194)
101 PRK13919 putative RNA polymera 28.4 65 0.0014 28.0 3.4 48 264-319 135-182 (186)
102 PRK12530 RNA polymerase sigma 28.4 63 0.0014 28.6 3.3 48 264-319 134-181 (189)
103 PRK12535 RNA polymerase sigma 28.2 65 0.0014 28.9 3.4 52 264-323 133-184 (196)
104 PRK12542 RNA polymerase sigma 28.1 65 0.0014 28.1 3.3 48 264-319 122-169 (185)
105 cd01392 HTH_LacI Helix-turn-he 28.0 33 0.00071 23.8 1.1 20 293-312 2-21 (52)
106 PRK12537 RNA polymerase sigma 27.7 67 0.0014 28.0 3.3 48 264-319 133-180 (182)
107 PRK12531 RNA polymerase sigma 27.6 60 0.0013 28.7 3.1 51 263-321 140-190 (194)
108 PF13384 HTH_23: Homeodomain-l 27.5 51 0.0011 22.7 2.1 23 291-313 20-42 (50)
109 TIGR02959 SigZ RNA polymerase 27.5 71 0.0015 27.7 3.4 48 264-319 100-147 (170)
110 cd00093 HTH_XRE Helix-turn-hel 27.4 49 0.0011 21.4 1.9 21 292-312 16-36 (58)
111 PRK12524 RNA polymerase sigma 27.3 67 0.0014 28.5 3.3 50 264-321 136-185 (196)
112 PF15500 Toxin_39: Putative RN 27.2 1.4E+02 0.003 24.7 4.8 39 128-173 44-82 (96)
113 PRK09639 RNA polymerase sigma 27.0 72 0.0016 27.0 3.3 47 264-319 112-158 (166)
114 PF13551 HTH_29: Winged helix- 26.8 3.1E+02 0.0067 21.4 7.1 46 265-310 58-109 (112)
115 PRK12533 RNA polymerase sigma 26.7 64 0.0014 29.7 3.1 49 264-320 134-182 (216)
116 PRK10072 putative transcriptio 26.7 42 0.00091 27.7 1.7 23 291-313 49-71 (96)
117 PRK12529 RNA polymerase sigma 26.2 88 0.0019 27.3 3.8 50 264-321 127-176 (178)
118 PF07037 DUF1323: Putative tra 26.1 68 0.0015 27.9 2.9 32 292-326 4-35 (122)
119 PF12362 DUF3646: DNA polymera 25.9 51 0.0011 28.1 2.2 26 65-90 83-108 (117)
120 PRK08583 RNA polymerase sigma 25.7 87 0.0019 29.1 3.9 48 264-319 205-252 (257)
121 PRK06986 fliA flagellar biosyn 25.4 66 0.0014 29.5 3.0 48 264-319 184-231 (236)
122 PF13411 MerR_1: MerR HTH fami 25.1 53 0.0011 24.0 1.9 18 292-309 4-21 (69)
123 PRK09645 RNA polymerase sigma 25.0 82 0.0018 27.0 3.3 49 264-320 118-166 (173)
124 PRK09636 RNA polymerase sigma 24.9 94 0.002 29.6 4.0 51 264-322 115-165 (293)
125 PRK12515 RNA polymerase sigma 24.9 85 0.0018 27.5 3.5 48 264-319 131-178 (189)
126 TIGR02947 SigH_actino RNA poly 24.6 38 0.00082 29.8 1.2 48 264-319 131-178 (193)
127 cd06170 LuxR_C_like C-terminal 24.2 1.4E+02 0.0031 20.1 3.9 30 290-319 17-46 (57)
128 PRK09415 RNA polymerase factor 24.1 73 0.0016 27.8 2.9 47 264-318 127-173 (179)
129 PRK08241 RNA polymerase factor 24.1 87 0.0019 30.2 3.7 50 264-321 153-202 (339)
130 smart00530 HTH_XRE Helix-turn- 23.8 62 0.0013 20.7 1.9 22 291-312 13-34 (56)
131 PRK12539 RNA polymerase sigma 23.7 84 0.0018 27.4 3.2 48 264-319 131-178 (184)
132 PF11348 DUF3150: Protein of u 23.6 5E+02 0.011 24.9 8.7 21 131-151 98-118 (257)
133 PRK07037 extracytoplasmic-func 23.6 90 0.0019 26.4 3.3 48 264-319 109-156 (163)
134 PRK12543 RNA polymerase sigma 23.5 94 0.002 27.0 3.5 47 264-318 117-163 (179)
135 COG2979 Uncharacterized protei 23.4 2.2E+02 0.0048 27.2 5.9 30 128-169 142-171 (225)
136 TIGR02941 Sigma_B RNA polymera 23.0 99 0.0021 28.7 3.7 47 264-318 205-251 (255)
137 PRK12528 RNA polymerase sigma 22.9 1.1E+02 0.0024 25.9 3.7 46 264-317 113-158 (161)
138 TIGR03001 Sig-70_gmx1 RNA poly 22.7 89 0.0019 29.4 3.4 48 264-319 161-208 (244)
139 TIGR02948 SigW_bacill RNA poly 22.7 88 0.0019 26.9 3.1 48 264-319 136-183 (187)
140 PF04967 HTH_10: HTH DNA bindi 22.3 2E+02 0.0043 21.3 4.4 47 265-312 1-47 (53)
141 PRK12513 RNA polymerase sigma 22.2 42 0.0009 29.5 1.0 48 264-319 139-186 (194)
142 PF14978 MRP-63: Mitochondrial 22.2 2.3E+02 0.0049 23.3 5.2 57 258-315 8-70 (91)
143 PF13865 FoP_duplication: C-te 22.1 85 0.0018 24.5 2.6 6 133-138 48-53 (74)
144 PRK04053 rps13p 30S ribosomal 22.0 76 0.0016 28.3 2.5 31 256-286 47-77 (149)
145 TIGR02943 Sig70_famx1 RNA poly 21.9 1E+02 0.0023 27.2 3.5 48 264-319 131-178 (188)
146 PHA01976 helix-turn-helix prot 21.8 65 0.0014 23.5 1.8 22 292-313 19-40 (67)
147 PRK12545 RNA polymerase sigma 21.7 98 0.0021 27.7 3.3 49 264-320 139-187 (201)
148 cd04761 HTH_MerR-SF Helix-Turn 21.7 78 0.0017 21.4 2.1 20 292-311 4-23 (49)
149 PRK04217 hypothetical protein; 21.4 1.7E+02 0.0036 24.8 4.4 49 263-319 41-89 (110)
150 PRK12540 RNA polymerase sigma 21.2 1E+02 0.0022 27.2 3.2 50 264-321 111-160 (182)
151 PRK09647 RNA polymerase sigma 21.1 1E+02 0.0023 27.8 3.4 48 264-319 138-185 (203)
152 PRK12538 RNA polymerase sigma 21.1 84 0.0018 29.2 2.8 48 264-319 171-218 (233)
153 TIGR03629 arch_S13P archaeal r 21.0 86 0.0019 27.7 2.7 31 256-287 43-73 (144)
154 TIGR02607 antidote_HigA addict 20.9 66 0.0014 24.1 1.7 22 292-313 22-43 (78)
155 PRK12511 RNA polymerase sigma 20.8 1E+02 0.0023 27.2 3.2 48 264-319 111-158 (182)
156 PRK12534 RNA polymerase sigma 20.6 1.1E+02 0.0023 26.7 3.2 47 264-318 137-183 (187)
157 PRK07670 RNA polymerase sigma 20.5 1.1E+02 0.0023 28.5 3.4 47 264-318 201-247 (251)
158 PF13730 HTH_36: Helix-turn-he 20.2 2.9E+02 0.0064 19.2 4.9 48 264-314 2-51 (55)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=100.00 E-value=2e-33 Score=262.65 Aligned_cols=206 Identities=24% Similarity=0.384 Sum_probs=178.4
Q ss_pred hhHHHHHHHhhCCChHHHHHHHHhh-----hcccCCCcchhhHHHHHhhHHHHHHhhhhccCC---------CCCCChHH
Q 019947 69 ETVKCKAEIVGHPLYEQLLSAHVSC-----LRIATPVDQLPKIDAQLSRSRDVLAKYSAVANG---------RVLDDKEL 134 (333)
Q Consensus 69 e~~~iKakI~sHPlYp~Ll~A~idC-----~KVGaP~e~~~~ld~~l~~~~~~~~~~~~~~~~---------~~g~dpEL 134 (333)
|+++.|.+|.|||+||+|++++|+. +.|....|.-|. |.+++++++|+.+++++|+. ..|+..++
T Consensus 27 eaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~-dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsdY 105 (334)
T KOG0774|consen 27 EAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPP-DPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSDY 105 (334)
T ss_pred hHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCC-ChHHHHHHHHHHHhcccCccccchhhhhccCCChHHH
Confidence 5568999999999999999999996 444444443222 56777788888888888764 24567888
Q ss_pred HHHHHHHHHHHHHHHHHHhhHHhhhhHHHHHHHHHHHHHhhhhhCCCCCCCCCCCCCCccccccCCCCCcCCCCCCCCCC
Q 019947 135 DQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGVSPGESTGATMSDDDEDQVDSDTNFFDGSLDGPDS 214 (333)
Q Consensus 135 DqFMe~Yc~vL~kykEEL~kP~~~~~~EA~~fc~~iEsQL~sL~~~s~~~~~~~~~S~dede~~~s~~~~~~g~~~~~d~ 214 (333)
.+-+.+ +.+.|++||++ +..+|+++.+.+.+|.. ++
T Consensus 106 R~kL~q---iR~iy~~Elek--------yeqaCneftthV~nlL~---------------------------------eQ 141 (334)
T KOG0774|consen 106 RAKLLQ---IRQIYHNELEK--------YEQACNEFTTHVMNLLR---------------------------------EQ 141 (334)
T ss_pred HHHHHH---HHHHHHHHHHH--------HHHHHHHHHHHHHHHHH---------------------------------Hh
Confidence 887776 99999999988 67789999999999985 34
Q ss_pred CCCCCCCCChhhhh--hHHHHHHHHHHHHHHhHHHHHHHHHHHHhh-hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHH
Q 019947 215 MGFGPLVPTESERS--LMERVRHELKHELKQGYKEKIVDIREEILR-KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDK 291 (333)
Q Consensus 215 ~~f~p~~~~~~e~~--~~~~~~~eLK~~l~~~y~~~i~~lr~e~~k-krkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK 291 (333)
+.|+||.|.++|+. .|++.|.-++.+|++..|+.+..||.++.. +|||++|+|.++.+|.+||..|..||||++++|
T Consensus 142 sr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K 221 (334)
T KOG0774|consen 142 SRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAK 221 (334)
T ss_pred cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHH
Confidence 56999999999985 488999999999999999999999999885 567889999999999999999999999999999
Q ss_pred HHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 292 ARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 292 ~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
++||++||++..||+|||.|+|.|.||.
T Consensus 222 ~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 222 EELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHHHcCceehhhccccccceeehhhh
Confidence 9999999999999999999999999974
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.94 E-value=1.6e-28 Score=238.16 Aligned_cols=247 Identities=23% Similarity=0.303 Sum_probs=173.5
Q ss_pred hhhhHHHHHHHhhCCChHHHHHHHHhhhcccCCCcchhhHHHHHhhHHHHHHhhhhccC-----CCCCCChHHHHHHHHH
Q 019947 67 DWETVKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRSRDVLAKYSAVAN-----GRVLDDKELDQFMTHY 141 (333)
Q Consensus 67 ~~e~~~iKakI~sHPlYp~Ll~A~idC~KVGaP~e~~~~ld~~l~~~~~~~~~~~~~~~-----~~~g~dpELDqFMe~Y 141 (333)
.+...-+|..+.+||+|..++.||++|+++++|.+.+.+.+..+.........++..+. ...+..++++.||..|
T Consensus 46 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k~ 125 (342)
T KOG0773|consen 46 MVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSKL 125 (342)
T ss_pred ccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchHH
Confidence 44556789999999999999999999999999999888865544332222222222111 1355889999999999
Q ss_pred HHHHHHHHHHHhhHHhhhhHHHHHHHHHHHHHhhhhhCCCCCCCCCCCCCCcccccc---CCCCCcCCCCCCCCCCCCCC
Q 019947 142 VLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGVSPGESTGATMSDDDEDQV---DSDTNFFDGSLDGPDSMGFG 218 (333)
Q Consensus 142 c~vL~kykEEL~kP~~~~~~EA~~fc~~iEsQL~sL~~~s~~~~~~~~~S~dede~~---~s~~~~~~g~~~~~d~~~f~ 218 (333)
+.+|..+.+.|+..+. .++|+.++++++..+...++..+....+.+...+.++.. .+..... .+..+++
T Consensus 126 ~~~ll~~~~~~~~~~~--~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~------~~~~~~~ 197 (342)
T KOG0773|consen 126 EKILLAVITKLTLTQV--STWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSS------EELLGES 197 (342)
T ss_pred HHHHHHHHHHhhhhhH--HHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccc------ccccccc
Confidence 9999999999999863 389999999999999999876554433332222111110 0000000 0111111
Q ss_pred CCCCChhhhhhH--HHHHHHHHHHHHHhHHHHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 019947 219 PLVPTESERSLM--ERVRHELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQ 296 (333)
Q Consensus 219 p~~~~~~e~~~~--~~~~~eLK~~l~~~y~~~i~~lr~e~~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~ 296 (333)
+......+...+ ......++..+.+.+..++.....+..++|+++.||+.++.+|+.||.+|+.||||++.+|..||+
T Consensus 198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~ 277 (342)
T KOG0773|consen 198 EQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAK 277 (342)
T ss_pred cccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccch
Confidence 111111111000 112344555666665555556566677888889999999999999999999999999999999999
Q ss_pred HhCCChhhhhhhhhhhhhhcccCCC
Q 019947 297 ETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 297 ~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
+|||+..||+|||||+|+|.|++..
T Consensus 278 ~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 278 QTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred hcCCCcccCCchhhhcccccCCchH
Confidence 9999999999999999999999876
No 3
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.89 E-value=1.8e-23 Score=153.13 Aligned_cols=50 Identities=46% Similarity=0.698 Sum_probs=47.4
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHhhHHhhhhHHHHHHHHHHHHHhhhhhC
Q 019947 126 GRVLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTG 179 (333)
Q Consensus 126 ~~~g~dpELDqFMe~Yc~vL~kykEEL~kP~~~~~~EA~~fc~~iEsQL~sL~~ 179 (333)
.++|+||||||||++||.||++|||||++||+ ||++|||+||+||++||+
T Consensus 3 ~~~~~dpELDqFMeaYc~~L~kykeeL~~p~~----EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 3 SSIGADPELDQFMEAYCDMLVKYKEELQRPFQ----EAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHhC
Confidence 46899999999999999999999999999984 999999999999999985
No 4
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.80 E-value=1.3e-20 Score=134.11 Aligned_cols=43 Identities=35% Similarity=0.691 Sum_probs=40.0
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhhcccCCCcchhhHHHHHhhH
Q 019947 71 VKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRS 113 (333)
Q Consensus 71 ~~iKakI~sHPlYp~Ll~A~idC~KVGaP~e~~~~ld~~l~~~ 113 (333)
+.|||+|++||+||+||+|||+|+|||||||++++||++..+.
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~ 43 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAES 43 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 4699999999999999999999999999999999999987654
No 5
>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=99.67 E-value=4.9e-17 Score=113.48 Aligned_cols=40 Identities=55% Similarity=1.074 Sum_probs=36.5
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019947 276 WWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (333)
Q Consensus 276 Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR 315 (333)
||.+|..|||||.+||..||..|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 9999999999999999999999999999999999999998
No 6
>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=99.51 E-value=3.4e-14 Score=103.43 Aligned_cols=57 Identities=26% Similarity=0.520 Sum_probs=53.8
Q ss_pred cCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 260 rkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
+++..|++.+..+|+.||.. +|||+.+++..||..|||+..||.+||.|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 56679999999999999999 8999999999999999999999999999999998864
No 7
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=99.51 E-value=2e-13 Score=123.66 Aligned_cols=147 Identities=21% Similarity=0.303 Sum_probs=115.4
Q ss_pred hhHHHHHHHhhCCChHHHHHHHHhh-----hcccCCCcchhhHHHHHhhHHHHHHhhhhccCCCCCC----------C--
Q 019947 69 ETVKCKAEIVGHPLYEQLLSAHVSC-----LRIATPVDQLPKIDAQLSRSRDVLAKYSAVANGRVLD----------D-- 131 (333)
Q Consensus 69 e~~~iKakI~sHPlYp~Ll~A~idC-----~KVGaP~e~~~~ld~~l~~~~~~~~~~~~~~~~~~g~----------d-- 131 (333)
|++++|.+|.+||+||+|++++|+. +++..+.+..+. |+++.++++|+.+.++.|+...|. |
T Consensus 25 eaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~-dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~~ 103 (191)
T PF03792_consen 25 EAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPP-DPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADNS 103 (191)
T ss_pred HHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCC-chhhhhhhcchhhhcCcCCCCcccchhhhhccCcccc
Confidence 6689999999999999999999996 444444433222 677778899999999888753221 1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhHHhhhhHHHHHHHHHHHHHhhhhhCCCCCCCCCCCCCCccccccCCCCCcCCCCCCC
Q 019947 132 KELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGVSPGESTGATMSDDDEDQVDSDTNFFDGSLDG 211 (333)
Q Consensus 132 pELDqFMe~Yc~vL~kykEEL~kP~~~~~~EA~~fc~~iEsQL~sL~~~s~~~~~~~~~S~dede~~~s~~~~~~g~~~~ 211 (333)
-|-+.|-...-++...|++||++ +...|+++...+.+|..
T Consensus 104 ~d~~dYr~kL~~ir~~y~~el~k--------ye~ac~eF~~hV~~lLr-------------------------------- 143 (191)
T PF03792_consen 104 IDHSDYRAKLSQIRQIYHSELEK--------YEQACNEFTEHVMNLLR-------------------------------- 143 (191)
T ss_pred cchHHHHHHHHHHHHHHHHHHHH--------HHHHhhhhHHHHHHHHH--------------------------------
Confidence 13344555555699999999987 56689999999999985
Q ss_pred CCCCCCCCCCCChhhhh--hHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Q 019947 212 PDSMGFGPLVPTESERS--LMERVRHELKHELKQGYKEKIVDIREEIL 257 (333)
Q Consensus 212 ~d~~~f~p~~~~~~e~~--~~~~~~~eLK~~l~~~y~~~i~~lr~e~~ 257 (333)
+++.|+||.|.++|+. .+++.|.-+..+||++.|+.+..||..|.
T Consensus 144 -eQs~~RPIs~keiE~m~~~i~~Kf~~iq~qLKQstCEaVm~LRsRfl 190 (191)
T PF03792_consen 144 -EQSEFRPISPKEIERMVNIIHRKFSKIQMQLKQSTCEAVMILRSRFL 190 (191)
T ss_pred -HhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 2346999999999985 48899999999999999999999998775
No 8
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.48 E-value=4.9e-14 Score=103.08 Aligned_cols=57 Identities=30% Similarity=0.704 Sum_probs=54.0
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 259 krkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
||++..|+.++..+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.+.|+
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 467889999999999999999 899999999999999999999999999999999874
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=7.5e-14 Score=101.11 Aligned_cols=55 Identities=25% Similarity=0.497 Sum_probs=51.4
Q ss_pred cCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019947 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (333)
Q Consensus 260 rkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~k 317 (333)
+.+..|++++..+|+.||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 45667999999999999999 79999999999999999999999999999999864
No 10
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.31 E-value=1.4e-12 Score=123.64 Aligned_cols=50 Identities=40% Similarity=0.883 Sum_probs=47.1
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019947 265 LPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (333)
Q Consensus 265 lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~k 317 (333)
|...++..|++||.. +|||++++|++||+.|||+..||.|||.|+|.|.+
T Consensus 183 FKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 345789999999997 89999999999999999999999999999999998
No 11
>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=98.93 E-value=1.4e-09 Score=81.76 Aligned_cols=53 Identities=19% Similarity=0.401 Sum_probs=50.2
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPY----PTEEDKARLVQETGLQLKQINNWFINQR 313 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PY----Ps~~eK~~LA~~tgLs~kQV~NWF~N~R 313 (333)
+||.|+.|+.+++..|+..|.. ++| |+..++..||..+||+..+|.+||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4778899999999999999999 899 9999999999999999999999999964
No 12
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.90 E-value=1.1e-09 Score=98.91 Aligned_cols=60 Identities=20% Similarity=0.277 Sum_probs=56.5
Q ss_pred hhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 257 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 257 ~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
..||.|+.|+.+++..|+..|.. +.|-.-.||..||+.++|+..||..||+|+|.|+|+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~ 160 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRM 160 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHH
Confidence 35677889999999999999999 8999999999999999999999999999999999975
No 13
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.89 E-value=7.7e-10 Score=107.35 Aligned_cols=59 Identities=24% Similarity=0.339 Sum_probs=54.8
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 259 krkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
+|||..++|.|+..|+.-|.- |-|.|++-|.+|++.++||..||+.||||+|+|.||-+
T Consensus 236 RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred ccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 445668999999999999888 79999999999999999999999999999999999976
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.86 E-value=1.4e-09 Score=103.46 Aligned_cols=63 Identities=22% Similarity=0.258 Sum_probs=58.2
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSS 323 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~s~ 323 (333)
.||.|+.|+..++..|+.-|.- |.|.|...|.++|..+.|++.||.+||+|+|+|+||.+...
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 6778889999999999999988 89999999999999999999999999999999999876533
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.80 E-value=4.7e-09 Score=99.54 Aligned_cols=61 Identities=31% Similarity=0.408 Sum_probs=57.2
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
.||.|+-|+.++.+-|+.-|.+ |-|.|+.-|+.||.++||.+.||..||+|+|.+.||...
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred hcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 4677889999999999999999 899999999999999999999999999999999999654
No 16
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.80 E-value=8.3e-09 Score=95.74 Aligned_cols=59 Identities=19% Similarity=0.261 Sum_probs=56.0
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
|||.|+.|+..|+..|+.-|.. .-|.+..||..||+.+.|++.||+.||||+|.|+|+.
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 6778899999999999999999 7999999999999999999999999999999999875
No 17
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.76 E-value=3.9e-09 Score=102.45 Aligned_cols=59 Identities=17% Similarity=0.294 Sum_probs=54.3
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
|||+|--|++.|+-.|+.-|.+ .-|.|.-||+.||..++||.+||+.||||+|.|-|+.
T Consensus 153 kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~ 211 (307)
T KOG0842|consen 153 KRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQ 211 (307)
T ss_pred ccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhh
Confidence 4455558999999999999999 7999999999999999999999999999999998864
No 18
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.76 E-value=6.5e-09 Score=101.28 Aligned_cols=58 Identities=19% Similarity=0.309 Sum_probs=53.7
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 259 krkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
+|.|+-|+..++..|+.-|.. --|.+..||..||+..||+-.||..||+|||+|+|+.
T Consensus 173 RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq 230 (309)
T KOG0488|consen 173 RKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQ 230 (309)
T ss_pred ccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHH
Confidence 344668999999999999999 7999999999999999999999999999999999974
No 19
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.71 E-value=1e-08 Score=94.24 Aligned_cols=59 Identities=29% Similarity=0.389 Sum_probs=54.0
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.++|+.+|+.+++..|+.-|.. +-|..+++|..||+++||.+.||..||+|+|+|.|.+
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 4556678999999999999999 6889999999999999999999999999999999864
No 20
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.70 E-value=1.1e-08 Score=95.52 Aligned_cols=57 Identities=19% Similarity=0.266 Sum_probs=53.4
Q ss_pred cCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 260 rkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
|.|+.++.-+.+.|..-|++ .-|.--.||.+||..+||+.+||+.||+|+|-|.||.
T Consensus 124 KPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 124 KPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred CCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 44678999999999999999 8999999999999999999999999999999998875
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.70 E-value=9.7e-09 Score=102.11 Aligned_cols=65 Identities=17% Similarity=0.417 Sum_probs=60.2
Q ss_pred HHHhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 254 EEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 254 ~e~~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
..-.|||||+.+...++..|+..|.. ||-||.+|.-.||+.++|.+..|++||+|||.|.|+.++
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 33356777889999999999999999 899999999999999999999999999999999999887
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.64 E-value=2.6e-08 Score=88.53 Aligned_cols=62 Identities=18% Similarity=0.318 Sum_probs=57.2
Q ss_pred hhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 257 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 257 ~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
..+++|.+.+..++.+|+.-|.. +|||+...|..|+..+||+++-|+.||+|+|.+.|+...
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 35667788999999999999999 899999999999999999999999999999999997654
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.61 E-value=2.2e-08 Score=89.50 Aligned_cols=59 Identities=19% Similarity=0.317 Sum_probs=54.4
Q ss_pred hhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 257 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 257 ~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.++|.|..|+..+...|+.-|+. --|.+..|+.+||..++|+++||..||+|+|+++||
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred HhhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 35556779999999999999998 689999999999999999999999999999999986
No 24
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.49 E-value=7.5e-08 Score=88.93 Aligned_cols=65 Identities=15% Similarity=0.252 Sum_probs=58.6
Q ss_pred HHHHHHhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 251 DIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 251 ~lr~e~~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||+-...++.|+.|+..+...|++-|.+ ..|.+.+|+.+++..+.|+..||..||||+|.|-|+
T Consensus 137 ~LrKhk~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 137 TLRKHKPNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred hhcccCCCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 45555556677889999999999999999 799999999999999999999999999999999885
No 25
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.43 E-value=1.7e-07 Score=89.04 Aligned_cols=56 Identities=20% Similarity=0.261 Sum_probs=53.0
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 262 r~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
|+.|+..+...|++-|.+ --||..-.|+.||..|+|.+..|.+||+|+|.|++|..
T Consensus 145 RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred cchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 678999999999999999 79999999999999999999999999999999998764
No 26
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.40 E-value=2.7e-07 Score=77.14 Aligned_cols=59 Identities=15% Similarity=0.281 Sum_probs=53.9
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.+|-|+.|+..+...|+..|.+ ..||..-.|++||-...|+...|++||+|+|.+.+|.
T Consensus 17 QRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 17 QRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred hhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 3445679999999999999999 7999999999999999999999999999999998863
No 27
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.36 E-value=3.4e-07 Score=85.17 Aligned_cols=59 Identities=19% Similarity=0.345 Sum_probs=54.5
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.+|-|+.|+..+..+|+.-|.+ .-||+...+++||.+++|.+.+|.+||.|+|++.++.
T Consensus 37 qRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred cccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 3456789999999999999999 8999999999999999999999999999999988754
No 28
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.30 E-value=1.9e-07 Score=88.96 Aligned_cols=56 Identities=23% Similarity=0.306 Sum_probs=51.1
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 262 r~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
|-.++..++-.|+.-|-- .+|.|..-|.+||..+||++.||+.||+|+|.|.+|-|
T Consensus 203 RvVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred eEEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 346899999999988888 89999999999999999999999999999999988743
No 29
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.25 E-value=4.7e-07 Score=87.97 Aligned_cols=59 Identities=19% Similarity=0.318 Sum_probs=54.6
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 259 krkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
+|.|..|+..+.+.|+.||.. |-||+.+.|+++|--|+|+...|.+||.|+|.+++|..
T Consensus 113 rrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 113 RRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 344668999999999999999 89999999999999999999999999999999998864
No 30
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.17 E-value=1e-06 Score=84.87 Aligned_cols=63 Identities=24% Similarity=0.422 Sum_probs=57.8
Q ss_pred HHHhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 254 EEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 254 ~e~~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
-+-..||.|+.++..+...|+.-|.. .|-|-.--|++|+.+|||+...|++||+|+|.+.|+-
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL 225 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL 225 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence 45567899999999999999999888 8999999999999999999999999999999988753
No 31
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.06 E-value=2.2e-06 Score=80.05 Aligned_cols=61 Identities=25% Similarity=0.380 Sum_probs=55.0
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
||..+..|+..++..|+.-|.+ ..||--.++.+||...|++..||.+||+|+|.+++|+-.
T Consensus 167 rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 4445667999999999999999 799999999999999999999999999999999988744
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.00 E-value=7.1e-06 Score=84.72 Aligned_cols=56 Identities=23% Similarity=0.339 Sum_probs=52.4
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019947 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (333)
Q Consensus 259 krkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~k 317 (333)
||.|-.|+..+++.|...|.+ ++||+.+.-+.|+.++||...-|.|||-|+|+|.+
T Consensus 421 KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 421 KKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred CCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 556678999999999999999 89999999999999999999999999999999943
No 33
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.77 E-value=9.5e-06 Score=78.87 Aligned_cols=55 Identities=16% Similarity=0.279 Sum_probs=49.6
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 262 r~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
|+-|+.+|+.-|+.-|+. --|-+.--|.+||..++|.+..|++||||+|+|.|+.
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 467999999999877777 5799999999999999999999999999999999874
No 34
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.77 E-value=6.7e-06 Score=79.42 Aligned_cols=65 Identities=23% Similarity=0.399 Sum_probs=57.9
Q ss_pred HhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCC
Q 019947 256 ILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSS 323 (333)
Q Consensus 256 ~~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~s~ 323 (333)
--|||||+.+-..-++-|+.+|.. -|-|+.+-...+|+++.|.+..|.+||+|+|.+.|+...|.
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred cccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 347888888888888999999999 79999999999999999999999999999999999865443
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.76 E-value=1.1e-05 Score=73.27 Aligned_cols=62 Identities=13% Similarity=0.109 Sum_probs=56.7
Q ss_pred HhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 256 ILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 256 ~~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
+.++|.|..|+..+.+.|+.-|.. .+||....++.||..+++++..|.+||+|+|+++++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 446777889999999999999999 69999999999999999999999999999999988754
No 36
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.70 E-value=2.6e-05 Score=77.53 Aligned_cols=59 Identities=24% Similarity=0.444 Sum_probs=54.2
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 259 krkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
+|.|..|+..+...|..+|.. +|||....++.||.++||+...|..||.|+|.|.++-.
T Consensus 177 rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 344678999999999999999 78999999999999999999999999999999888765
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.46 E-value=6.6e-05 Score=73.37 Aligned_cols=64 Identities=33% Similarity=0.533 Sum_probs=58.7
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~s 322 (333)
..+++++++.+. ..|+.|...|..+|||++-++..|+-.++++..||++||+|.|+|.++.+..
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 445667899999 9999999999999999999999999999999999999999999999987664
No 38
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=97.22 E-value=0.00026 Score=43.69 Aligned_cols=22 Identities=41% Similarity=0.622 Sum_probs=20.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHh
Q 019947 236 ELKHELKQGYKEKIVDIREEIL 257 (333)
Q Consensus 236 eLK~~l~~~y~~~i~~lr~e~~ 257 (333)
|||++|+++|+++|++||+||+
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 6899999999999999999984
No 39
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.15 E-value=0.00041 Score=52.06 Aligned_cols=43 Identities=21% Similarity=0.477 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019947 270 TSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (333)
Q Consensus 270 ~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR 315 (333)
.+.|+++|.. +.++.+.+-..|+.++||+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4669999999 599999999999999999999999999877543
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=95.41 E-value=0.011 Score=53.53 Aligned_cols=61 Identities=25% Similarity=0.468 Sum_probs=52.6
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
.++.+..+...+...|..-|.. .+||....+..|+..+|++...|.+||+|+|.+.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3444567788888888888887 899999999999999999999999999999999987543
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.93 E-value=0.13 Score=58.61 Aligned_cols=60 Identities=23% Similarity=0.294 Sum_probs=55.0
Q ss_pred hhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 257 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 257 ~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.+++.|..++..+..+++..|.. .-||+.++-+.|....+|.+..|..||+|.|.+.++.
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~ 961 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA 961 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence 35566778999999999999999 7999999999999999999999999999999999876
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=88.51 E-value=0.87 Score=49.63 Aligned_cols=52 Identities=31% Similarity=0.562 Sum_probs=46.7
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCC
Q 019947 270 TSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSS 324 (333)
Q Consensus 270 ~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~s~s 324 (333)
+.+|+.+|.. |+.|++++...+|.+.||...-|..||.+.+......+.+++
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 7888999999 899999999999999999999999999999998887664444
No 43
>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=86.82 E-value=1.2 Score=32.53 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=31.9
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019947 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQR 313 (333)
Q Consensus 259 krkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R 313 (333)
||+|..|+-+..-.+-.-+.. .+ -...||+.+|++..+|.+|..|+.
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 456677888776655555555 23 478999999999999999999954
No 44
>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=73.80 E-value=4.8 Score=30.24 Aligned_cols=47 Identities=17% Similarity=0.283 Sum_probs=30.3
Q ss_pred cCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019947 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQR 313 (333)
Q Consensus 260 rkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~R 313 (333)
++++.||.+.+..+-.-+.. .......+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~-------~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE-------SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH-------HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH-------CCCceEeeecccccccccccHHHHHHh
Confidence 34567888886655444322 236678999999999999999987776
No 45
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=69.96 E-value=14 Score=21.96 Aligned_cols=39 Identities=10% Similarity=0.157 Sum_probs=27.6
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 019947 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWF 309 (333)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF 309 (333)
..++.+....+...+.. .+ ....+|+.+|++...|.+|.
T Consensus 4 ~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 45666666666666543 33 34578899999999999985
No 46
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=67.62 E-value=9.1 Score=25.53 Aligned_cols=46 Identities=11% Similarity=0.145 Sum_probs=35.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~k 317 (333)
.++...+.++...+... + .-..+|..+|++...|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~----~----~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG----L----SYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46777888887776542 2 2457899999999999999988877653
No 47
>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=61.86 E-value=14 Score=26.03 Aligned_cols=44 Identities=14% Similarity=0.277 Sum_probs=32.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR 315 (333)
.||+..+.++.-.|... -.-.++|+.+|++...|.+|....|++
T Consensus 10 ~L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 57888888887665553 234589999999999999999998876
No 48
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=57.47 E-value=13 Score=31.14 Aligned_cols=47 Identities=9% Similarity=0.071 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||+..+.++.-.|... .+ -.++|+.+|++...|.+|....|++.++
T Consensus 106 ~L~~~~r~ii~l~~~~~--~s------~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG--KT------MGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 68888999886655552 22 4589999999999999999999998875
No 49
>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=57.11 E-value=15 Score=25.67 Aligned_cols=47 Identities=9% Similarity=0.225 Sum_probs=36.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||+..+.+|...|.. ++ .-.++|+..|++...|..+...+..+.|+
T Consensus 4 ~L~~~er~vi~~~y~~----~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----GL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----CC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 5888899999888744 32 24579999999999999999988887653
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=50.58 E-value=17 Score=32.24 Aligned_cols=50 Identities=6% Similarity=0.016 Sum_probs=40.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
.||+..+.+|.-.+... .+ -.++|+.+|++...|.+++...|++.++...
T Consensus 142 ~L~~~~r~vl~l~~~~~--~s------~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--LT------YREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 48899999997665553 22 3579999999999999999999999887653
No 51
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=50.18 E-value=13 Score=26.92 Aligned_cols=24 Identities=13% Similarity=0.279 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhh
Q 019947 290 DKARLVQETGLQLKQINNWFINQR 313 (333)
Q Consensus 290 eK~~LA~~tgLs~kQV~NWF~N~R 313 (333)
....||+.+|++..+|+.|+.+..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 356899999999999999999763
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=48.46 E-value=22 Score=30.21 Aligned_cols=48 Identities=17% Similarity=0.280 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.+... .+| .++|+.+|++...|.+.+.-+|++.++.
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s~------~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KSY------QEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48999999987665552 232 4799999999999999999999988764
No 53
>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=46.37 E-value=31 Score=27.69 Aligned_cols=47 Identities=17% Similarity=0.284 Sum_probs=36.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||+..+.++.-.+.. .|+ -..+|+.+|+++..|.+|....+++.++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~s----~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GLS----YKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4677787887544333 332 3489999999999999999999988775
No 54
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=43.68 E-value=27 Score=29.89 Aligned_cols=50 Identities=14% Similarity=0.040 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
..||+..++++.-++..+ .+ -.++|..+|++...|.+|..-.|++.++..
T Consensus 107 ~~L~~~~r~v~~l~~~~g--~s------~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE--LT------YEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 358888999998776664 33 358999999999999999999999988753
No 55
>PF13518 HTH_28: Helix-turn-helix domain
Probab=43.60 E-value=24 Score=24.28 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhh
Q 019947 291 KARLVQETGLQLKQINNWFINQRK 314 (333)
Q Consensus 291 K~~LA~~tgLs~kQV~NWF~N~Rr 314 (333)
...+|..+|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 346999999999999999987775
No 56
>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=42.71 E-value=43 Score=27.73 Aligned_cols=47 Identities=15% Similarity=0.203 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||...+.++.-.+.. .++- .++|+.+|++...|.++....|++.++
T Consensus 113 ~L~~~~r~il~l~~~~----~~~~----~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GKSY----KEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHc----CCCH----HHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5788888888765544 3332 358999999999999999999998875
No 57
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=42.40 E-value=26 Score=29.68 Aligned_cols=48 Identities=8% Similarity=0.160 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.+.. .+ .-..+|+..|++...|.+|..-.|++.++.
T Consensus 125 ~L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4778888888665544 22 235899999999999999999999998764
No 58
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=41.78 E-value=55 Score=32.80 Aligned_cols=46 Identities=11% Similarity=0.179 Sum_probs=37.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhHHhhhhHHHHHHHHHHHHHhhhhhC
Q 019947 132 KELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTG 179 (333)
Q Consensus 132 pELDqFMe~Yc~vL~kykEEL~kP~~~~~~EA~~fc~~iEsQL~sL~~ 179 (333)
-+-|.||--|| |.+|-.+|.+=+|-.++++..-+..+-.|+..+|.
T Consensus 134 T~C~Hy~H~~C--laRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcp 179 (368)
T KOG4445|consen 134 TACDHYMHFAC--LARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCP 179 (368)
T ss_pred ehhHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Confidence 36899999999 45677777766666777888888899999999985
No 59
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=41.74 E-value=31 Score=30.49 Aligned_cols=48 Identities=8% Similarity=0.022 Sum_probs=38.1
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 262 r~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
...|++.++++|.- +.. .+ .-.++|+.+|++...|.+|..+++++.++
T Consensus 4 ~~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999976 333 32 23489999999999999999999988765
No 60
>PF06729 CENP-R: Kinetochore component, CENP-R; InterPro: IPR009601 This family consists of mammalian nuclear receptor co-activator NRIF3 proteins. NRIF3 exhibits a distinct receptor specificity in interacting with and potentiating the activity of only TRs and RXRs but not other examined nuclear receptors. NRIF3 as a coregulator that possesses both transactivation and transrepression domains and/or functions. Collectively, the NRIF3 family of coregulators may play dual roles in mediating both positive and negative regulatory effects on gene expression [].
Probab=41.52 E-value=2.5e+02 Score=24.96 Aligned_cols=33 Identities=27% Similarity=0.329 Sum_probs=21.0
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHhhHHhhhhHHHHHHHHHHH
Q 019947 130 DDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLE 171 (333)
Q Consensus 130 ~dpELDqFMe~Yc~vL~kykEEL~kP~~~~~~EA~~fc~~iE 171 (333)
...+.|.||.- |-+-+.-+.+ |+|++.-+..|.
T Consensus 54 p~t~dD~fm~L----~SkvekS~ee-----ime~~qnL~slQ 86 (139)
T PF06729_consen 54 PQTEDDEFMVL----LSKVEKSLEE-----IMEIRQNLSSLQ 86 (139)
T ss_pred CCcchhHHHHH----HHHHHHHHHH-----HHHHHHHHHHHH
Confidence 45677999964 5555555554 567776665554
No 61
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=41.41 E-value=29 Score=29.46 Aligned_cols=48 Identities=8% Similarity=0.141 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.|... .+ -..+|+.+|++...|.+|....|++.++.
T Consensus 128 ~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG--LS------YEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888887654442 23 24789999999999999999999988764
No 62
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=40.76 E-value=53 Score=34.97 Aligned_cols=25 Identities=12% Similarity=0.271 Sum_probs=13.7
Q ss_pred CChHHHHHHHHHH-------HHHHHHHHHHhh
Q 019947 130 DDKELDQFMTHYV-------LLLYSFKEQLQQ 154 (333)
Q Consensus 130 ~dpELDqFMe~Yc-------~vL~kykEEL~k 154 (333)
.-|++.-..-+|| .||.+|.+||++
T Consensus 183 ~ap~mkt~~~aYcanHP~AV~VL~k~~dELek 214 (661)
T KOG2070|consen 183 LAPQMKTLYLAYCANHPSAVNVLTKHSDELEK 214 (661)
T ss_pred hhHHHHHHHHHHHhcCchhhhHHHHhHHHHHH
Confidence 4455555555555 355555555554
No 63
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.32 E-value=60 Score=21.91 Aligned_cols=47 Identities=11% Similarity=0.147 Sum_probs=34.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.|+.....++.-+ .. .+ ....+|+.+|++...|..|....+.+..-.
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 4777777777543 32 22 346889999999999999999888776543
No 64
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=40.32 E-value=31 Score=29.90 Aligned_cols=48 Identities=13% Similarity=0.270 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.|.. .++ -.++|+.+|++...|.+++...|++.++.
T Consensus 129 ~L~~~~r~i~~l~~~~----g~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE----GLS----YKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 4788888888877765 222 35799999999999999999999998764
No 65
>PRK00118 putative DNA-binding protein; Validated
Probab=40.05 E-value=36 Score=28.52 Aligned_cols=47 Identities=11% Similarity=0.193 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||..++.++.-++... + .-..+|+.+|++..-|.+|....|++.++
T Consensus 17 ~L~ekqRevl~L~y~eg----~----S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD----Y----SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57888999997776663 2 23469999999999999999999888765
No 66
>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=39.72 E-value=25 Score=30.50 Aligned_cols=49 Identities=10% Similarity=0.062 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.||+..++++.-.|..+ + .-.++|+.+|++...|.++.-..|++.++..
T Consensus 138 ~L~~~~r~v~~l~~~~~----~----s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG----L----SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 46778888886555442 2 2357999999999999999999999988754
No 67
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=39.29 E-value=33 Score=29.46 Aligned_cols=48 Identities=15% Similarity=0.021 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..++++.-.+...+ + -.++|+.+|++...|.++..-.|++.+..
T Consensus 112 ~L~~~~r~v~~l~~~~g~--s------~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGASGF--S------YEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHHcCC--C------HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 588999998887666632 2 34799999999999999999999988754
No 68
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=38.83 E-value=35 Score=29.03 Aligned_cols=49 Identities=20% Similarity=0.249 Sum_probs=39.4
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
..||..++.++.-.+... .+| .++|..+|++...|..+....|++.++.
T Consensus 111 ~~L~~~~r~v~~l~~~~~--~s~------~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG--FSY------KEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHCCHHHHHHhhhHHhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 368999999988766553 232 4799999999999999999999988753
No 69
>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=38.58 E-value=38 Score=28.47 Aligned_cols=47 Identities=19% Similarity=0.233 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||+..+.++.-.|.. .++ -.++|+.+|++...|.++..-.|++.+.
T Consensus 111 ~L~~~~r~v~~l~~~~----g~~----~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQR----GVS----LTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHhc----CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 5888888888875554 222 2478999999999999999999988765
No 70
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=38.42 E-value=37 Score=29.96 Aligned_cols=48 Identities=17% Similarity=0.163 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.|... .+ -.++|+.+|++...|.+...-.|++.++.
T Consensus 131 ~L~~~~r~i~~l~~~~g--~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--EK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred hCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 68999999998665552 33 24799999999999999999999998875
No 71
>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=37.61 E-value=39 Score=29.26 Aligned_cols=48 Identities=4% Similarity=0.100 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+.++.++.-.+... .+ -.++|+.+|++...|.+.+...|++.++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG--LT------VEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 48899999988776663 22 24799999999999999999999988763
No 72
>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=36.96 E-value=38 Score=28.66 Aligned_cols=50 Identities=10% Similarity=0.229 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
.||+..+.++.-.|... ++ -.++|..+|++...|.++....|++.++...
T Consensus 110 ~L~~~~r~i~~l~~~~g----~s----~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 110 RLPARQRAVVVLRYYED----LS----EAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred hCCHHHHHHhhhHHHhc----CC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 58888888887665552 22 2478999999999999999999999887544
No 73
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=36.12 E-value=93 Score=28.63 Aligned_cols=46 Identities=15% Similarity=0.252 Sum_probs=37.1
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHhhHHhhhhHHH-HHHHHHHHHHhhhhh
Q 019947 130 DDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEA-VMACWDLEQSLQSLT 178 (333)
Q Consensus 130 ~dpELDqFMe~Yc~vL~kykEEL~kP~~~~~~EA-~~fc~~iEsQL~sL~ 178 (333)
+=-|||-.+.++-.++..|++.++-.+= .+| ..||..|..||-.+.
T Consensus 102 DItELDVvL~~FEk~~~eYkq~ieS~~c---r~AI~~F~~~~keqL~~~i 148 (175)
T PF13097_consen 102 DITELDVVLSAFEKTALEYKQSIESKIC---RKAINKFYSNFKEQLIEMI 148 (175)
T ss_pred cchHHHHHHHHHHHHHHHHHHhhccHHH---HHHHHHHHHHHHHHHHHHH
Confidence 4489999999999999999999976552 233 358889999998765
No 74
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=35.96 E-value=62 Score=24.78 Aligned_cols=26 Identities=27% Similarity=0.319 Sum_probs=21.1
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHhh
Q 019947 129 LDDKELDQFMTHYVLLLYSFKEQLQQ 154 (333)
Q Consensus 129 g~dpELDqFMe~Yc~vL~kykEEL~k 154 (333)
|-||+||.....|..+.....+.+.+
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~~~ 26 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELLEE 26 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56999999999999888777666643
No 75
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=35.25 E-value=42 Score=30.15 Aligned_cols=49 Identities=14% Similarity=0.207 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.||+..+.++.-.+... .. -.++|+.+|++...|.+++..+|++.++-.
T Consensus 153 ~L~~~~r~vl~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--LS------QEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888989987655542 22 357999999999999999999999887643
No 76
>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=34.96 E-value=31 Score=26.33 Aligned_cols=21 Identities=14% Similarity=0.355 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCChhhhhhhhh
Q 019947 290 DKARLVQETGLQLKQINNWFI 310 (333)
Q Consensus 290 eK~~LA~~tgLs~kQV~NWF~ 310 (333)
.-..||+++|++..||..|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 356899999999999999943
No 77
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=34.49 E-value=10 Score=35.47 Aligned_cols=38 Identities=34% Similarity=0.468 Sum_probs=30.3
Q ss_pred CCCCCcchhhhhhHHHHHHHhhCCChHHHHHHHHhhhcccCCCc
Q 019947 58 ASNDNGRAEDWETVKCKAEIVGHPLYEQLLSAHVSCLRIATPVD 101 (333)
Q Consensus 58 ~~~~~~~~~~~e~~~iKakI~sHPlYp~Ll~A~idC~KVGaP~e 101 (333)
+|||-|...- ...||..|..||++.+||.||+ ||.|.-
T Consensus 100 aGHSQGs~~l--~~LL~e~~~~~pl~~rLVAAYl----iG~~v~ 137 (207)
T PF11288_consen 100 AGHSQGSMHL--LRLLKEEIAGDPLRKRLVAAYL----IGYPVT 137 (207)
T ss_pred EEeChHHHHH--HHHHHHHhcCchHHhhhheeee----cCcccc
Confidence 5666665553 4589999999999999999999 887754
No 78
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=33.48 E-value=32 Score=24.05 Aligned_cols=21 Identities=14% Similarity=0.189 Sum_probs=18.3
Q ss_pred HHHHHHhCCChhhhhhhhhhh
Q 019947 292 ARLVQETGLQLKQINNWFINQ 312 (333)
Q Consensus 292 ~~LA~~tgLs~kQV~NWF~N~ 312 (333)
..||+.+|+++..|..|..+.
T Consensus 13 ~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHHHhCCCcchhHHHhcCC
Confidence 689999999999999999883
No 79
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=32.74 E-value=52 Score=28.38 Aligned_cols=48 Identities=13% Similarity=0.222 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+.++.++.-.+... .+| .++|+.+|++..-|.++...++++.+..
T Consensus 119 ~Lp~~~r~v~~L~~~~g--~s~------~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG--MGH------AEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887665553 333 4799999999999999999999988654
No 80
>PF12022 DUF3510: Domain of unknown function (DUF3510); InterPro: IPR024603 The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function []. This uncharacterised domain is found in the C-terminal of COG complex subunit 2 proteins.
Probab=32.69 E-value=2e+02 Score=24.53 Aligned_cols=20 Identities=30% Similarity=0.342 Sum_probs=15.4
Q ss_pred hHHHHHHHHHHHHHhhhhhC
Q 019947 160 AMEAVMACWDLEQSLQSLTG 179 (333)
Q Consensus 160 ~~EA~~fc~~iEsQL~sL~~ 179 (333)
+.|...-.+++|..|+-|-.
T Consensus 79 ~~evL~sv~KtEeSL~rlkk 98 (125)
T PF12022_consen 79 ASEVLTSVRKTEESLKRLKK 98 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34666777899999998865
No 81
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=32.59 E-value=51 Score=28.84 Aligned_cols=48 Identities=10% Similarity=0.014 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.--|... + .-.++|+.+|++...|.++....|++.++.
T Consensus 139 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVVG----L----SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887765552 2 245899999999999999999999988764
No 82
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=31.63 E-value=47 Score=29.01 Aligned_cols=50 Identities=6% Similarity=0.092 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
.||+..+.++.-.|... .+ -.++|+.+|++...|.++...+|++.++...
T Consensus 128 ~L~~~~r~i~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 128 ALPERQREAIVLQYYQG--LS------NIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred hCCHHHHHHhhHHHhcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 36788888886554442 22 2479999999999999999999999987644
No 83
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=31.42 E-value=48 Score=29.60 Aligned_cols=49 Identities=14% Similarity=0.111 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.||+..++++.-.+... ++ -.++|+.+|++...|.+++.-.|++.++..
T Consensus 113 ~Lp~~~r~v~~L~~~~g----~s----~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGASG----FS----YEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999999997776552 22 247899999999999999999999988753
No 84
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=31.30 E-value=53 Score=28.54 Aligned_cols=49 Identities=4% Similarity=-0.086 Sum_probs=39.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.||+..+.++.-.+... .+ -.++|+.+|++...|.+++...|++.+...
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s------~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--AS------IKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58888999998866553 22 357999999999999999999999988653
No 85
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=31.00 E-value=63 Score=27.17 Aligned_cols=48 Identities=13% Similarity=0.080 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.+... .+ -.++|+.+|++...|.+...-.|++.++.
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYWED--MD------VAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHHhc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58899999987765552 23 35799999999999999999999988764
No 86
>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=30.97 E-value=69 Score=23.00 Aligned_cols=48 Identities=15% Similarity=0.121 Sum_probs=35.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.|++...++|.-+..- + .-.++|...|++++.|..+..+.++|..-++
T Consensus 3 ~LT~~E~~vl~~l~~G-----~----~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG-----M----SNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHHTT-----S-----HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHHhc-----C----CcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 4677777777655443 2 3457899999999999999999999876543
No 87
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=30.37 E-value=55 Score=28.84 Aligned_cols=49 Identities=12% Similarity=0.178 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.||+..+.++.-.+... + .-.++|+.+|++...|.++...+|++.++..
T Consensus 136 ~L~~~~r~i~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILG----F----SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888888887655552 2 1357999999999999999999999988753
No 88
>cd00131 PAX Paired Box domain
Probab=30.24 E-value=1.6e+02 Score=25.09 Aligned_cols=46 Identities=11% Similarity=0.082 Sum_probs=32.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCC-------Chhhhhhhhhhh
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGL-------QLKQINNWFINQ 312 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgL-------s~kQV~NWF~N~ 312 (333)
.++......+..+..+ +|..|..|-..+-...|+ +..+|+.||.++
T Consensus 75 ~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3455555666667676 798888887666335577 999999998764
No 89
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=30.03 E-value=62 Score=28.52 Aligned_cols=48 Identities=17% Similarity=0.047 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+.++.++.-.+... .+ -.++|+.+|+++..|.++..-.|++.++-
T Consensus 130 ~Lp~~~r~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 177 (185)
T PRK09649 130 DLTTDQREALLLTQLLG--LS------YADAAAVCGCPVGTIRSRVARARDALLAD 177 (185)
T ss_pred hCCHHHhHHhhhHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 58888999887666553 22 24799999999999999999999999874
No 90
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=29.65 E-value=32 Score=31.36 Aligned_cols=40 Identities=25% Similarity=0.536 Sum_probs=31.1
Q ss_pred CChhHHHHHHHHHHHhcCCCCCC-HHHHHHHHHHhCCChhh
Q 019947 265 LPGDTTSLLKAWWLSHAKWPYPT-EEDKARLVQETGLQLKQ 304 (333)
Q Consensus 265 lpk~~~~iL~~Wf~~H~~~PYPs-~~eK~~LA~~tgLs~kQ 304 (333)
.........-.|...|.-.|||+ ++||..-|++.||-+..
T Consensus 21 v~~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 21 VMPRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred ccccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 33445566778999999999995 67888889999987653
No 91
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=29.65 E-value=35 Score=22.60 Aligned_cols=22 Identities=41% Similarity=0.563 Sum_probs=17.5
Q ss_pred HHHHHhhCCChHHHHHHHHhhh
Q 019947 73 CKAEIVGHPLYEQLLSAHVSCL 94 (333)
Q Consensus 73 iKakI~sHPlYp~Ll~A~idC~ 94 (333)
+-.+|++.|||.-||+|--..+
T Consensus 5 lipkiissplfktllsavgsal 26 (33)
T PF07425_consen 5 LIPKIISSPLFKTLLSAVGSAL 26 (33)
T ss_dssp CHHHHCCTTTCHHHHHHHHHHC
T ss_pred hhhHHHccHHHHHHHHHHHHHH
Confidence 3468999999999999865544
No 92
>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=29.63 E-value=60 Score=27.77 Aligned_cols=48 Identities=4% Similarity=0.028 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||...++++.--|... .+ -.++|+.+|++...|.++..-.|++.++.
T Consensus 119 ~L~~~~r~i~~l~~~~g--~s------~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--LT------IKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888886655552 22 24789999999999999999999887753
No 93
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=29.54 E-value=1.2e+02 Score=25.10 Aligned_cols=48 Identities=13% Similarity=0.185 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.|++..+++|.-+ ..+ |. ...+|+..+++.+.|.++..|.|++..-.+
T Consensus 149 ~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~ 196 (211)
T PRK15369 149 LLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHK 196 (211)
T ss_pred CCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 5888889998874 442 32 468889999999999999999999987544
No 94
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=29.42 E-value=62 Score=28.22 Aligned_cols=48 Identities=19% Similarity=0.028 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.+..+ .+ -.++|+.+|++...|.+.+...|++.++.
T Consensus 129 ~L~~~~r~v~~l~~~~g--~s------~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG--LS------VAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46888888776555553 22 35799999999999999999999998864
No 95
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=29.39 E-value=78 Score=26.48 Aligned_cols=48 Identities=6% Similarity=0.060 Sum_probs=32.4
Q ss_pred cCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhh
Q 019947 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 314 (333)
Q Consensus 260 rkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~Rr 314 (333)
+++++++.+-+...-..... +.+ -...+|+..|++..+|.+|..-.+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~---~g~----sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE---PGM----TVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc---CCC----CHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 34567888775544333333 232 2457899999999999999776654
No 96
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=29.27 E-value=1.5e+02 Score=24.90 Aligned_cols=41 Identities=12% Similarity=0.229 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 019947 268 DTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQ 312 (333)
Q Consensus 268 ~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~ 312 (333)
.....+..|...|...| ++. ..||+.+|+++.++..+|...
T Consensus 9 ~~i~~~~~~I~~~~~~~-~sl---~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 9 ITIHSILDWIEDNLESP-LSL---EKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHhcCCC-CCH---HHHHHHHCcCHHHHHHHHHHH
Confidence 44567788888987766 554 568888999999998888754
No 97
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=29.19 E-value=59 Score=28.86 Aligned_cols=49 Identities=18% Similarity=0.190 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.||...+.++.-.+... .+| .++|+.+|++...|.++....|++.++..
T Consensus 116 ~Lp~~~r~i~~L~~~~g--~s~------~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGASG--FAY------EEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888887765552 333 37899999999999999999999988643
No 98
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=29.16 E-value=38 Score=23.36 Aligned_cols=22 Identities=23% Similarity=0.223 Sum_probs=19.0
Q ss_pred HHHHHHhCCChhhhhhhhhhhh
Q 019947 292 ARLVQETGLQLKQINNWFINQR 313 (333)
Q Consensus 292 ~~LA~~tgLs~kQV~NWF~N~R 313 (333)
..||..+|+++..|..|....+
T Consensus 19 ~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 19 ADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHhCCCHHHHHHHHCCCC
Confidence 5799999999999999986653
No 99
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=28.71 E-value=66 Score=28.26 Aligned_cols=48 Identities=15% Similarity=0.085 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+.++.++.-.+... .+| .++|+.+|++..-|.+.....|++.++-
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s~------~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LET------EEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887665552 333 5799999999999999999999988764
No 100
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.56 E-value=48 Score=29.11 Aligned_cols=47 Identities=11% Similarity=0.196 Sum_probs=36.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||+..+.++.--+... .+ -.++|+.+|++...|.+|+..+|++.++
T Consensus 141 ~L~~~~~~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 141 QLPESQRQVLELAYYEG--LS------QSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hCCHHHhhhhhhhhhcC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 57888888886554442 22 3579999999999999999999998775
No 101
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=28.42 E-value=65 Score=27.98 Aligned_cols=48 Identities=13% Similarity=0.159 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.+|.-.+... .. -.++|+.+|++...|.++....|++.++.
T Consensus 135 ~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG--YT------HREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 48888999997665552 22 35799999999999999999999988764
No 102
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.40 E-value=63 Score=28.56 Aligned_cols=48 Identities=10% Similarity=0.149 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||...+.++.-.+... .+ -.++|..+|+++..|.++..-+|++.++.
T Consensus 134 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--LS------SEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred hCCHHHHHHHhHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888988887766552 22 35799999999999999999999988753
No 103
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=28.22 E-value=65 Score=28.90 Aligned_cols=52 Identities=12% Similarity=0.099 Sum_probs=41.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSS 323 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~s~ 323 (333)
.||+..+.++.--+... .+ -.++|+.+|++...|.++....|++.++..+..
T Consensus 133 ~Lp~~~r~v~~l~~~~g--~s------~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 133 ALPPERREALILTQVLG--YT------YEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred cCCHHHHHHhhhHHHhC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 48888888886666553 22 358999999999999999999999998876543
No 104
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=28.06 E-value=65 Score=28.13 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=37.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.+... .+ -.++|+.+|++...|.+.....|++.++.
T Consensus 122 ~L~~~~r~i~~l~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN--LT------YQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888989887654442 22 24799999999999999999999988764
No 105
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=27.98 E-value=33 Score=23.76 Aligned_cols=20 Identities=5% Similarity=0.293 Sum_probs=18.5
Q ss_pred HHHHHhCCChhhhhhhhhhh
Q 019947 293 RLVQETGLQLKQINNWFINQ 312 (333)
Q Consensus 293 ~LA~~tgLs~kQV~NWF~N~ 312 (333)
.||+.+|++...|+.|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 58999999999999999887
No 106
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=27.67 E-value=67 Score=28.04 Aligned_cols=48 Identities=15% Similarity=0.230 Sum_probs=37.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.--|... .+ -.++|+.+|++...|.+|...+|++.++.
T Consensus 133 ~L~~~~r~i~~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYVDG--CS------HAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 57888888776555442 23 35799999999999999999999987753
No 107
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=27.56 E-value=60 Score=28.69 Aligned_cols=51 Identities=16% Similarity=0.271 Sum_probs=40.0
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
..||+..+.++.-.+... .+| .++|+.+|++...|.+-+...|++.++...
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s~------~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LPH------QQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CCH------HHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 368888999997655442 333 479999999999999999999998886543
No 108
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.53 E-value=51 Score=22.74 Aligned_cols=23 Identities=13% Similarity=0.379 Sum_probs=16.9
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 019947 291 KARLVQETGLQLKQINNWFINQR 313 (333)
Q Consensus 291 K~~LA~~tgLs~kQV~NWF~N~R 313 (333)
...+|+.+|++...|.+|....+
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHHCcCHHHHHHHHHHcc
Confidence 45899999999999999976544
No 109
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=27.49 E-value=71 Score=27.66 Aligned_cols=48 Identities=17% Similarity=0.227 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.+|.-.+... |+ -.++|+.+|++...|.++..-.|++.++-
T Consensus 100 ~L~~~~r~v~~l~~~~g----~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG----LS----QQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888888766653 22 34799999999999999999999888764
No 110
>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=27.44 E-value=49 Score=21.39 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=18.7
Q ss_pred HHHHHHhCCChhhhhhhhhhh
Q 019947 292 ARLVQETGLQLKQINNWFINQ 312 (333)
Q Consensus 292 ~~LA~~tgLs~kQV~NWF~N~ 312 (333)
..+|..+|++...|.+|..+.
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCC
Confidence 488999999999999998875
No 111
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=27.28 E-value=67 Score=28.46 Aligned_cols=50 Identities=4% Similarity=0.060 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
.||+..+.++.-.+.. .|+ -.++|+.+|++...|.+++.-+|++.++...
T Consensus 136 ~L~~~~r~i~~L~~~~----g~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GLS----NPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 5888888888665444 222 3479999999999999999999999887543
No 112
>PF15500 Toxin_39: Putative RNase-like toxin
Probab=27.24 E-value=1.4e+02 Score=24.73 Aligned_cols=39 Identities=21% Similarity=0.162 Sum_probs=27.1
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHhhHHhhhhHHHHHHHHHHHHH
Q 019947 128 VLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQS 173 (333)
Q Consensus 128 ~g~dpELDqFMe~Yc~vL~kykEEL~kP~~~~~~EA~~fc~~iEsQ 173 (333)
++++|+|.+.|+. ++-+++.--++ .++||...+..+|.-
T Consensus 44 l~a~p~lk~wne~-vq~~Rk~dp~~------aAdeaakLi~alE~a 82 (96)
T PF15500_consen 44 LAADPALKAWNET-VQAKRKLDPKF------AADEAAKLIQALETA 82 (96)
T ss_pred hccCHHHHHHHHH-HHHHHhhchhh------hHHHHHHHHHHHHHH
Confidence 6799999999998 34445554444 357888776666643
No 113
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=26.99 E-value=72 Score=27.02 Aligned_cols=47 Identities=13% Similarity=0.249 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||...+.+|.-.+ . .+ .-.++|..+|++...|.++....|++.++-
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 47888888887666 4 22 235799999999999999999999988763
No 114
>PF13551 HTH_29: Winged helix-turn helix
Probab=26.77 E-value=3.1e+02 Score=21.38 Aligned_cols=46 Identities=17% Similarity=0.052 Sum_probs=30.0
Q ss_pred CChhHHHHHHHHHHHhcCCC--CCCHHHHHH-H-HHHh--CCChhhhhhhhh
Q 019947 265 LPGDTTSLLKAWWLSHAKWP--YPTEEDKAR-L-VQET--GLQLKQINNWFI 310 (333)
Q Consensus 265 lpk~~~~iL~~Wf~~H~~~P--YPs~~eK~~-L-A~~t--gLs~kQV~NWF~ 310 (333)
++.+....|.+++.++.... ..+...-.. | .+.+ .++...|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 89999999999999952211 234444443 4 3333 477778888864
No 115
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=26.74 E-value=64 Score=29.70 Aligned_cols=49 Identities=16% Similarity=0.178 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.||...+.++.-.|..+ .+| .++|+.+|++...|.++....|++.++..
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s~------~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MSY------REIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 68888999998877764 232 47899999999999999999999988754
No 116
>PRK10072 putative transcriptional regulator; Provisional
Probab=26.74 E-value=42 Score=27.66 Aligned_cols=23 Identities=9% Similarity=0.289 Sum_probs=20.3
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 019947 291 KARLVQETGLQLKQINNWFINQR 313 (333)
Q Consensus 291 K~~LA~~tgLs~kQV~NWF~N~R 313 (333)
...||+.+|++...|.+|...+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45899999999999999998765
No 117
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=26.21 E-value=88 Score=27.29 Aligned_cols=50 Identities=10% Similarity=0.055 Sum_probs=39.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
.||+.++.++.-.+... .+| .++|+.+|++..-|.+.+..++++.....+
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~s~------~EIA~~lgis~~tVk~~l~rAl~~~~~~~~ 176 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--MKQ------KDIAQALDIALPTVKKYIHQAYVTCLSLMP 176 (178)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence 58999999887766653 232 479999999999999999998888765533
No 118
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=26.06 E-value=68 Score=27.86 Aligned_cols=32 Identities=31% Similarity=0.703 Sum_probs=26.0
Q ss_pred HHHHHHhCCChhhhhhhhhhhhhhcccCCCCCCcc
Q 019947 292 ARLVQETGLQLKQINNWFINQRKRNWHANPSSSTA 326 (333)
Q Consensus 292 ~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~s~st~ 326 (333)
++||..||++..-||-|. |+..|+..|-|+-.
T Consensus 4 eELA~~tG~srQTINrWv---RkegW~T~p~pGVk 35 (122)
T PF07037_consen 4 EELAELTGYSRQTINRWV---RKEGWKTEPKPGVK 35 (122)
T ss_pred HHHHHHhCccHHHHHHHH---HhcCceeccCCccc
Confidence 579999999999999995 77788876665543
No 119
>PF12362 DUF3646: DNA polymerase III gamma and tau subunits C terminal; InterPro: IPR022107 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00004 from PFAM. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=25.88 E-value=51 Score=28.13 Aligned_cols=26 Identities=27% Similarity=0.317 Sum_probs=21.2
Q ss_pred hhhhhhHHHHHHHhhCCChHHHHHHH
Q 019947 65 AEDWETVKCKAEIVGHPLYEQLLSAH 90 (333)
Q Consensus 65 ~~~~e~~~iKakI~sHPlYp~Ll~A~ 90 (333)
....+.+..++.+..||++...|.+|
T Consensus 83 ~~~~~~~~~~~~a~~~P~V~avL~~F 108 (117)
T PF12362_consen 83 QEAAAKEARRAAARAHPLVKAVLAAF 108 (117)
T ss_pred HHHHHHHHHHHHHHhCcHHHHHHHHC
Confidence 33445567899999999999999887
No 120
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=25.65 E-value=87 Score=29.13 Aligned_cols=48 Identities=10% Similarity=0.159 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.+|.-.|... .+ -.++|+.+|++...|.+|....+++.++.
T Consensus 205 ~L~~~~r~vl~l~~~~g--~s------~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN--LS------QKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48888999998766552 22 26899999999999999999999988754
No 121
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=25.36 E-value=66 Score=29.55 Aligned_cols=48 Identities=13% Similarity=0.175 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.--|... + .-.++|+.+|++...|.++...+|++.++.
T Consensus 184 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE----L----NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhccC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888887665542 2 245899999999999999999999998764
No 122
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.14 E-value=53 Score=24.05 Aligned_cols=18 Identities=6% Similarity=0.143 Sum_probs=16.2
Q ss_pred HHHHHHhCCChhhhhhhh
Q 019947 292 ARLVQETGLQLKQINNWF 309 (333)
Q Consensus 292 ~~LA~~tgLs~kQV~NWF 309 (333)
.++|+.+|++..+|..|-
T Consensus 4 ~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 478999999999999993
No 123
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.03 E-value=82 Score=26.99 Aligned_cols=49 Identities=12% Similarity=0.223 Sum_probs=39.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.||+..+.+|.--+... .+ -.++|+.+|++...|.+...-.|++.++..
T Consensus 118 ~L~~~~r~vl~L~~~~g--~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRG--WS------TAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48899999987765552 22 347999999999999999999999888753
No 124
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=24.88 E-value=94 Score=29.58 Aligned_cols=51 Identities=14% Similarity=0.095 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~s 322 (333)
.||+.++.++.-.+... .+| .++|+.+|++..-|.+.+..+|++.++..+.
T Consensus 115 ~L~~~~R~v~~L~~~~g--~s~------~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~ 165 (293)
T PRK09636 115 RLSPLERAAFLLHDVFG--VPF------DEIASTLGRSPAACRQLASRARKHVRAARPR 165 (293)
T ss_pred hCCHHHHHHHHHHHHhC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 48888888876554442 343 4799999999999999999999999987653
No 125
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.87 E-value=85 Score=27.50 Aligned_cols=48 Identities=10% Similarity=0.131 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.+|.--+... .+ -.++|+.+|++...|.+-+...|++.++.
T Consensus 131 ~L~~~~r~vl~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE--KS------VEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 58888999986655442 22 35799999999999999999999988764
No 126
>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=24.62 E-value=38 Score=29.84 Aligned_cols=48 Identities=10% Similarity=0.098 Sum_probs=36.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.+... .+ -.++|+.+|++...|.++..-.|++.++.
T Consensus 131 ~Lp~~~r~i~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEG--FA------YKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred hCCHHHhhheeehhhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57777877775544442 22 35799999999999999999999988764
No 127
>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=24.19 E-value=1.4e+02 Score=20.12 Aligned_cols=30 Identities=10% Similarity=0.113 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 290 DKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 290 eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.-..+|+.+|++...|..|..-.+++..-.
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 346789999999999999998776665543
No 128
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=24.14 E-value=73 Score=27.76 Aligned_cols=47 Identities=9% Similarity=0.175 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
+||+..+.++.-.+... .+ -.++|+.+|++...|.++..-.|++.++
T Consensus 127 ~L~~~~r~v~~l~~~~g--~s------~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE--LS------IKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 58888989886655553 23 2479999999999999999999988875
No 129
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=24.12 E-value=87 Score=30.24 Aligned_cols=50 Identities=16% Similarity=0.213 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
.||...+.++.-.+... .+ -.++|+.+|++...|.+...-.|++.++..+
T Consensus 153 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~ 202 (339)
T PRK08241 153 HLPPRQRAVLILRDVLG--WS------AAEVAELLDTSVAAVNSALQRARATLAERGP 202 (339)
T ss_pred hCCHHHhhhhhhHHhhC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHhhcCC
Confidence 57888888887665553 22 2479999999999999999999999998543
No 130
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=23.78 E-value=62 Score=20.71 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChhhhhhhhhhh
Q 019947 291 KARLVQETGLQLKQINNWFINQ 312 (333)
Q Consensus 291 K~~LA~~tgLs~kQV~NWF~N~ 312 (333)
...||+.+|++..+|..|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 3488999999999999997654
No 131
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=23.71 E-value=84 Score=27.45 Aligned_cols=48 Identities=15% Similarity=0.065 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.+... .+ -.++|+.+|++...|.++....|++.++.
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--LS------VAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred hCCHHHHHHHHHHHHcC--Cc------HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 58999999998655543 22 34799999999999999999999988764
No 132
>PF11348 DUF3150: Protein of unknown function (DUF3150); InterPro: IPR021496 This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=23.65 E-value=5e+02 Score=24.93 Aligned_cols=21 Identities=14% Similarity=0.433 Sum_probs=14.3
Q ss_pred ChHHHHHHHHHHHHHHHHHHH
Q 019947 131 DKELDQFMTHYVLLLYSFKEQ 151 (333)
Q Consensus 131 dpELDqFMe~Yc~vL~kykEE 151 (333)
+.+-++|+..|=+.+..+..+
T Consensus 98 ~~~k~~Fl~~Yd~~i~~w~~~ 118 (257)
T PF11348_consen 98 EQEKQDFLANYDQAIEEWIDR 118 (257)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 456677777777777666665
No 133
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=23.55 E-value=90 Score=26.40 Aligned_cols=48 Identities=15% Similarity=0.179 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.|... .+ -.++|+.+|++...|.....-+|++.++.
T Consensus 109 ~L~~~~r~v~~l~~~~~--~s------~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG--ET------QKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 58888989987655442 22 35799999999999999998888887764
No 134
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=23.54 E-value=94 Score=27.01 Aligned_cols=47 Identities=13% Similarity=0.222 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||+..+.++.--+..+ .+ -.++|+.+|++...|.+.....|++.++
T Consensus 117 ~Lp~~~r~i~~l~~~e~--~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--YS------QEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred hCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 58888888887755553 12 3479999999999999999999998875
No 135
>COG2979 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.41 E-value=2.2e+02 Score=27.18 Aligned_cols=30 Identities=23% Similarity=0.261 Sum_probs=23.6
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHhhHHhhhhHHHHHHHHH
Q 019947 128 VLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWD 169 (333)
Q Consensus 128 ~g~dpELDqFMe~Yc~vL~kykEEL~kP~~~~~~EA~~fc~~ 169 (333)
.|.|||..+|+|+ ||++|++ ..|-..+.++
T Consensus 142 sG~d~e~~~~le~----------El~~PlD--~~~ia~~a~~ 171 (225)
T COG2979 142 SGVDPEAQAFLEQ----------ELEQPLD--PDEIAAAARN 171 (225)
T ss_pred cCCCHHHHHHHHH----------HHhCCCC--HHHHHHHhcC
Confidence 6789999999987 8899985 4565666665
No 136
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=22.98 E-value=99 Score=28.73 Aligned_cols=47 Identities=6% Similarity=0.055 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||...+.++.-.|... .. -.++|+.+|++...|..+...++++.++
T Consensus 205 ~L~~~~r~ii~l~~~~g--~s------~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN--LS------QKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 58888999987776553 22 2589999999999999999999988775
No 137
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.95 E-value=1.1e+02 Score=25.91 Aligned_cols=46 Identities=15% Similarity=0.254 Sum_probs=36.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~k 317 (333)
.||+.++.++.-.+... .+| .++|..+|++...|.++....+++..
T Consensus 113 ~L~~~~r~v~~L~~~~g--~s~------~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDG--LGY------GEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 58888989886665552 333 47999999999999999998887754
No 138
>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=22.71 E-value=89 Score=29.38 Aligned_cols=48 Identities=15% Similarity=0.270 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||...+.++.-.+... .+ -.++|..+|++...|.++...+|++.++.
T Consensus 161 ~Lp~~~R~v~~L~~~eg--~S------~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~ 208 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG--LS------MDRIGAMYQVHRSTVSRWVAQARERLLER 208 (244)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 58888888887766663 22 24799999999999999999999987753
No 139
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.68 E-value=88 Score=26.95 Aligned_cols=48 Identities=8% Similarity=0.111 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.|.. .++ -.++|+.+|++...|.+++...|++.++.
T Consensus 136 ~L~~~~r~v~~l~~~~----g~s----~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DLS----LKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4888888888664444 222 35789999999999999999999987753
No 140
>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=22.26 E-value=2e+02 Score=21.27 Aligned_cols=47 Identities=17% Similarity=0.236 Sum_probs=35.2
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 019947 265 LPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQ 312 (333)
Q Consensus 265 lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~ 312 (333)
|+..++.+|..-+..=+ .-+|-...-..||+..|++..-+..=+.+.
T Consensus 1 LT~~Q~e~L~~A~~~GY-fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 1 LTDRQREILKAAYELGY-FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHHHHHHcCC-CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56778888887766633 234788888999999999999887655443
No 141
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=22.18 E-value=42 Score=29.55 Aligned_cols=48 Identities=8% Similarity=0.095 Sum_probs=36.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.|.. .|+ -.++|+.+|++...|.++...+|++.++.
T Consensus 139 ~L~~~~r~i~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 139 TLPDEQREVFLLREHG----DLE----LEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hCCHhHhhheeeehcc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4777777777654433 222 24789999999999999999999998864
No 142
>PF14978 MRP-63: Mitochondrial ribosome protein 63
Probab=22.15 E-value=2.3e+02 Score=23.32 Aligned_cols=57 Identities=18% Similarity=0.225 Sum_probs=37.0
Q ss_pred hhcCCCCCChhHHHHHHHHHHH------hcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019947 258 RKRRAGKLPGDTTSLLKAWWLS------HAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (333)
Q Consensus 258 kkrkr~~lpk~~~~iL~~Wf~~------H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR 315 (333)
|-|+-+.++...++.+..-|.. ...+||.|.++=.-.|...+- .++...|+.-++.+
T Consensus 8 KhR~~r~vt~~~k~~~~~~le~E~eN~~~Ls~PYLT~EQE~gh~~e~r~-~k~~~~~~~~~~~~ 70 (91)
T PF14978_consen 8 KHRRPRKVTWQMKENMIRRLEIEEENMYWLSRPYLTAEQEYGHAKERRK-EKAFFEWIKEKKRS 70 (91)
T ss_pred cCCCcCCCCHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHcchHHHHhH-HHHHHHHHHHHHHc
Confidence 4455556777666666443332 234799999998888888776 56666676665533
No 143
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=22.07 E-value=85 Score=24.53 Aligned_cols=6 Identities=67% Similarity=1.193 Sum_probs=2.2
Q ss_pred HHHHHH
Q 019947 133 ELDQFM 138 (333)
Q Consensus 133 ELDqFM 138 (333)
|||+||
T Consensus 48 ELD~Ym 53 (74)
T PF13865_consen 48 ELDAYM 53 (74)
T ss_pred HHHHHH
Confidence 333333
No 144
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=22.03 E-value=76 Score=28.32 Aligned_cols=31 Identities=13% Similarity=0.106 Sum_probs=25.7
Q ss_pred HhhhcCCCCCChhHHHHHHHHHHHhcCCCCC
Q 019947 256 ILRKRRAGKLPGDTTSLLKAWWLSHAKWPYP 286 (333)
Q Consensus 256 ~~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYP 286 (333)
+....+-+.|+.++...|..++...+..++|
T Consensus 47 i~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP 77 (149)
T PRK04053 47 LDPNAKLGYLSDEEIEKIEEALEDPAEEGIP 77 (149)
T ss_pred cCCCCccCcCCHHHHHHHHHHHHhhccccCc
Confidence 4456677899999999999999887777777
No 145
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.92 E-value=1e+02 Score=27.19 Aligned_cols=48 Identities=13% Similarity=0.129 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.|... .+ -.++|+.+|++..-|.+...-.|++.++.
T Consensus 131 ~L~~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--FE------SDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887766553 22 35899999999999999999999988764
No 146
>PHA01976 helix-turn-helix protein
Probab=21.78 E-value=65 Score=23.47 Aligned_cols=22 Identities=18% Similarity=0.377 Sum_probs=18.7
Q ss_pred HHHHHHhCCChhhhhhhhhhhh
Q 019947 292 ARLVQETGLQLKQINNWFINQR 313 (333)
Q Consensus 292 ~~LA~~tgLs~kQV~NWF~N~R 313 (333)
..||+.+|++...|.+|....+
T Consensus 19 ~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 19 PELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHhCCCHHHHHHHHcCCC
Confidence 4799999999999999986543
No 147
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=21.74 E-value=98 Score=27.68 Aligned_cols=49 Identities=12% Similarity=0.121 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~ 320 (333)
.||+..+.++.-.+... .+| .++|+.+|++...|.+....+|++.++..
T Consensus 139 ~Lp~~~r~v~~L~~~eg--~s~------~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD--FEI------DDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 58888988887665552 232 47899999999999999999999988743
No 148
>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=21.69 E-value=78 Score=21.37 Aligned_cols=20 Identities=15% Similarity=0.157 Sum_probs=17.0
Q ss_pred HHHHHHhCCChhhhhhhhhh
Q 019947 292 ARLVQETGLQLKQINNWFIN 311 (333)
Q Consensus 292 ~~LA~~tgLs~kQV~NWF~N 311 (333)
.++|+.+|+++..|..|...
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 47899999999999999543
No 149
>PRK04217 hypothetical protein; Provisional
Probab=21.43 E-value=1.7e+02 Score=24.83 Aligned_cols=49 Identities=8% Similarity=-0.034 Sum_probs=38.6
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
..|+.+.+.++..++.+. + .-.++|+.+|++...|.+.+...|++.+..
T Consensus 41 ~~Lt~eereai~l~~~eG----l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG----L----TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467888888887776552 2 345799999999999999999998887653
No 150
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.18 E-value=1e+02 Score=27.23 Aligned_cols=50 Identities=18% Similarity=0.058 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~~~ 321 (333)
.||+..+.++.-.+... .+ -.++|+.+|++...|.....-+|++.++...
T Consensus 111 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 111 KLPQDQREALILVGASG--FS------YEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred hCCHHHHHHhhHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47888989887766553 12 3479999999999999999999999887544
No 151
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.15 E-value=1e+02 Score=27.81 Aligned_cols=48 Identities=15% Similarity=0.225 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.--|... .+| .++|+.+|++...|.++..-.|++.++.
T Consensus 138 ~L~~~~r~v~~L~~~~g--~s~------~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG--LSY------EEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57777878765554442 343 4799999999999999999999998864
No 152
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=21.11 E-value=84 Score=29.21 Aligned_cols=48 Identities=6% Similarity=0.133 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||...+.++.-.|... .+ -.++|+.+|++...|.++....|++.++.
T Consensus 171 ~Lp~~~R~v~~L~~~eg--~s------~~EIA~~Lgis~~tVk~~l~RAr~kLr~~ 218 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN--MS------NGEIAEVMDTTVAAVESLLKRGRQQLRDL 218 (233)
T ss_pred hCCHHHHHHhhhHHhcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 47888888876555442 23 25799999999999999999999998864
No 153
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=20.96 E-value=86 Score=27.75 Aligned_cols=31 Identities=13% Similarity=0.162 Sum_probs=23.7
Q ss_pred HhhhcCCCCCChhHHHHHHHHHHHhcCCCCCC
Q 019947 256 ILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPT 287 (333)
Q Consensus 256 ~~kkrkr~~lpk~~~~iL~~Wf~~H~~~PYPs 287 (333)
+....+-+-|+.++...|..++.. ...++|.
T Consensus 43 i~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~ 73 (144)
T TIGR03629 43 VDPNAKLGYLDDEEIEKLEEAVEN-YEYGIPS 73 (144)
T ss_pred cCCCCCcccCCHHHHHHHHHHHHh-ccccCCH
Confidence 445667789999999999999876 5555554
No 154
>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=20.90 E-value=66 Score=24.06 Aligned_cols=22 Identities=14% Similarity=0.240 Sum_probs=19.3
Q ss_pred HHHHHHhCCChhhhhhhhhhhh
Q 019947 292 ARLVQETGLQLKQINNWFINQR 313 (333)
Q Consensus 292 ~~LA~~tgLs~kQV~NWF~N~R 313 (333)
..||+.+|++...|..|+.+.|
T Consensus 22 ~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 22 RALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHhCCCHHHHHHHHcCCC
Confidence 5799999999999999997654
No 155
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=20.80 E-value=1e+02 Score=27.20 Aligned_cols=48 Identities=10% Similarity=0.066 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk~ 319 (333)
.||+..+.++.-.+... .+ -.++|+.+|++..-|.++..-.|++.++-
T Consensus 111 ~Lp~~~R~v~~L~~~eg--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG--LS------YQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 58999999998766652 22 24799999999999999999999888764
No 156
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=20.57 E-value=1.1e+02 Score=26.66 Aligned_cols=47 Identities=11% Similarity=0.202 Sum_probs=37.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||+..+.++...|... .+ -.++|..+|++...|.+-...+|++.++
T Consensus 137 ~L~~~~r~i~~l~~~~g--~s------~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 137 ELEPPRSELIRTAFFEG--IT------YEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 57888888887666542 22 2479999999999999999999988775
No 157
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=20.50 E-value=1.1e+02 Score=28.54 Aligned_cols=47 Identities=9% Similarity=0.071 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019947 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~RrR~kk 318 (333)
.||+..+.++.-.|... + .-.++|..+|++...|.+++...|++.++
T Consensus 201 ~L~~~~r~vl~l~~~~~----~----s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLFYKEE----L----TLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHHHhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 48888889988766542 2 24689999999999999999999998875
No 158
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.20 E-value=2.9e+02 Score=19.18 Aligned_cols=48 Identities=8% Similarity=0.109 Sum_probs=31.1
Q ss_pred CCChhHHHHHHHHHHH--hcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhh
Q 019947 264 KLPGDTTSLLKAWWLS--HAKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 314 (333)
Q Consensus 264 ~lpk~~~~iL~~Wf~~--H~~~PYPs~~eK~~LA~~tgLs~kQV~NWF~N~Rr 314 (333)
.|+..++.++-.-+.. .....||| ...||+.+|++...|..+...-..
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3556665555322222 22347887 557999999999999998765443
Done!