Query 019231
Match_columns 344
No_of_seqs 288 out of 1080
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:46:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019231hhsearch_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 3.9E-33 8.4E-38 262.1 17.6 207 68-319 26-249 (334)
2 KOG0773 Transcription factor M 99.9 1.8E-28 4E-33 238.6 0.9 249 66-322 45-303 (342)
3 PF03791 KNOX2: KNOX2 domain ; 99.9 1.9E-23 4.2E-28 153.9 6.8 50 126-179 3-52 (52)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 2E-20 4.4E-25 133.9 2.9 43 71-113 1-43 (45)
5 PF05920 Homeobox_KN: Homeobox 99.6 9.8E-17 2.1E-21 112.6 4.1 40 276-315 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.5 3.6E-14 7.9E-19 103.7 6.8 57 260-319 2-58 (59)
7 smart00389 HOX Homeodomain. DN 99.5 7.5E-14 1.6E-18 101.5 6.5 55 260-317 2-56 (56)
8 PF00046 Homeobox: Homeobox do 99.5 5.1E-14 1.1E-18 103.4 5.5 57 259-318 1-57 (57)
9 PF03792 PBC: PBC domain; Int 99.5 4.1E-13 8.9E-18 122.3 12.5 148 68-257 24-190 (191)
10 KOG0775 Transcription factor S 99.3 2.2E-12 4.8E-17 123.0 6.0 50 265-317 183-232 (304)
11 TIGR01565 homeo_ZF_HD homeobox 99.0 9.8E-10 2.1E-14 83.1 5.2 53 258-313 1-57 (58)
12 KOG0843 Transcription factor E 98.9 6.2E-10 1.3E-14 101.1 4.3 61 257-320 101-161 (197)
13 KOG0487 Transcription factor A 98.9 4.3E-10 9.3E-15 109.7 3.1 59 259-320 236-294 (308)
14 KOG0489 Transcription factor z 98.9 5.8E-10 1.3E-14 106.4 3.7 66 258-326 159-224 (261)
15 KOG0485 Transcription factor N 98.8 5E-09 1.1E-13 97.8 6.3 59 258-319 104-162 (268)
16 KOG0493 Transcription factor E 98.8 5.8E-09 1.2E-13 99.5 5.2 61 258-321 246-306 (342)
17 KOG0488 Transcription factor B 98.8 4.4E-09 9.5E-14 102.9 4.5 60 258-320 172-231 (309)
18 KOG0850 Transcription factor D 98.8 5.5E-09 1.2E-13 98.0 4.0 60 259-321 123-182 (245)
19 KOG0842 Transcription factor t 98.7 4.9E-09 1.1E-13 102.3 3.2 59 258-319 153-211 (307)
20 KOG3802 Transcription factor O 98.7 6.6E-09 1.4E-13 103.8 4.0 67 252-321 288-354 (398)
21 KOG0483 Transcription factor H 98.7 1.1E-08 2.3E-13 94.6 4.1 59 258-319 50-108 (198)
22 COG5576 Homeodomain-containing 98.7 2.4E-08 5.2E-13 89.2 5.0 62 258-322 51-112 (156)
23 KOG0491 Transcription factor B 98.6 2E-08 4.2E-13 90.4 3.0 58 258-318 100-157 (194)
24 KOG0492 Transcription factor M 98.6 3.6E-08 7.9E-13 91.5 3.2 65 251-318 137-201 (246)
25 KOG0484 Transcription factor P 98.5 5.2E-08 1.1E-12 81.9 3.3 64 253-319 12-75 (125)
26 KOG2251 Homeobox transcription 98.4 2E-07 4.3E-12 87.2 4.4 59 258-319 37-95 (228)
27 KOG0494 Transcription factor C 98.4 2E-07 4.3E-12 89.2 4.2 55 262-319 145-199 (332)
28 KOG0848 Transcription factor C 98.3 1.3E-07 2.7E-12 90.7 1.0 56 263-321 204-259 (317)
29 KOG4577 Transcription factor L 98.3 3.5E-07 7.5E-12 88.6 3.0 69 252-323 161-229 (383)
30 KOG0486 Transcription factor P 98.3 3.6E-07 7.8E-12 89.2 2.8 60 258-320 112-171 (351)
31 KOG0847 Transcription factor, 98.1 2.3E-06 5E-11 80.3 2.9 61 258-321 167-227 (288)
32 KOG2252 CCAAT displacement pro 98.0 8.8E-06 1.9E-10 84.5 5.4 57 258-317 420-476 (558)
33 KOG0844 Transcription factor E 97.9 4.6E-06 9.9E-11 81.5 1.7 56 262-320 185-240 (408)
34 KOG1168 Transcription factor A 97.9 3.3E-06 7.2E-11 82.0 0.7 68 257-327 308-375 (385)
35 KOG0490 Transcription factor, 97.8 7.2E-06 1.6E-10 74.7 1.9 62 256-320 58-119 (235)
36 KOG0849 Transcription factor P 97.8 1.5E-05 3.2E-10 79.6 3.6 60 258-320 176-235 (354)
37 KOG0773 Transcription factor M 97.5 6.7E-05 1.5E-09 73.6 2.6 66 258-324 95-160 (342)
38 PF03789 ELK: ELK domain ; In 97.1 0.0004 8.6E-09 43.2 2.1 22 236-257 1-22 (22)
39 PF11569 Homez: Homeodomain le 97.0 0.0006 1.3E-08 51.5 3.2 43 270-315 10-52 (56)
40 KOG0490 Transcription factor, 95.5 0.0093 2E-07 54.3 2.8 61 258-321 153-213 (235)
41 KOG1146 Homeobox protein [Gene 91.7 0.14 3.1E-06 58.6 3.5 62 257-321 902-963 (1406)
42 KOG3623 Homeobox transcription 88.3 0.9 2E-05 49.8 5.9 52 270-324 568-619 (1007)
43 PF04218 CENP-B_N: CENP-B N-te 87.2 1.1 2.3E-05 33.1 4.1 47 259-313 1-47 (53)
44 PF01527 HTH_Tnp_1: Transposas 75.9 3.9 8.5E-05 30.9 3.7 47 260-313 2-48 (76)
45 cd00569 HTH_Hin_like Helix-tur 70.0 13 0.00029 22.1 4.5 39 263-309 4-42 (42)
46 cd06171 Sigma70_r4 Sigma70, re 68.2 8.3 0.00018 25.8 3.6 46 264-317 10-55 (55)
47 PF08281 Sigma70_r4_2: Sigma-7 61.2 14 0.00031 26.2 3.8 44 264-315 10-53 (54)
48 PF04545 Sigma70_r4: Sigma-70, 57.7 14 0.00031 26.0 3.3 47 264-318 4-50 (50)
49 PRK06759 RNA polymerase factor 56.3 14 0.0003 31.2 3.6 47 264-318 106-152 (154)
50 KOG2070 Guanine nucleotide exc 50.3 31 0.00067 36.9 5.5 26 129-154 182-214 (661)
51 PRK09646 RNA polymerase sigma 49.7 17 0.00038 32.3 3.3 50 264-321 142-191 (194)
52 PRK09642 RNA polymerase sigma 48.5 21 0.00045 30.5 3.4 48 264-319 106-153 (160)
53 PF13443 HTH_26: Cro/C1-type H 47.5 15 0.00033 26.7 2.1 23 290-312 12-34 (63)
54 PF11288 DUF3089: Protein of u 46.1 5.7 0.00012 37.4 -0.5 38 58-101 100-137 (207)
55 TIGR02937 sigma70-ECF RNA poly 45.6 31 0.00068 27.8 3.9 47 264-318 110-156 (158)
56 PRK03975 tfx putative transcri 44.0 26 0.00057 31.1 3.4 49 262-319 4-52 (141)
57 PRK09644 RNA polymerase sigma 43.9 26 0.00056 30.2 3.3 50 263-320 107-156 (165)
58 TIGR02985 Sig70_bacteroi1 RNA 42.0 44 0.00094 27.8 4.4 47 264-318 113-159 (161)
59 PRK11924 RNA polymerase sigma 41.5 27 0.00058 29.8 3.0 48 264-319 125-172 (179)
60 PRK09652 RNA polymerase sigma 41.3 29 0.00062 29.7 3.2 48 264-319 128-175 (182)
61 TIGR02983 SigE-fam_strep RNA p 41.0 31 0.00068 29.4 3.4 50 264-321 110-159 (162)
62 PRK12514 RNA polymerase sigma 40.6 48 0.0011 28.8 4.6 48 264-319 129-176 (179)
63 smart00421 HTH_LUXR helix_turn 40.5 60 0.0013 22.0 4.2 47 264-319 3-49 (58)
64 PF13518 HTH_28: Helix-turn-he 39.9 29 0.00063 24.0 2.5 24 291-314 15-38 (52)
65 TIGR02939 RpoE_Sigma70 RNA pol 39.2 25 0.00054 30.7 2.5 49 264-320 138-186 (190)
66 PRK12541 RNA polymerase sigma 39.1 33 0.00072 29.3 3.2 48 263-318 111-158 (161)
67 KOG4445 Uncharacterized conser 39.0 61 0.0013 32.7 5.4 47 132-180 134-180 (368)
68 TIGR02999 Sig-70_X6 RNA polyme 38.8 35 0.00076 29.7 3.4 48 264-319 134-181 (183)
69 PRK12547 RNA polymerase sigma 38.5 33 0.00072 29.6 3.2 48 264-319 112-159 (164)
70 PRK06811 RNA polymerase factor 37.6 37 0.00081 30.1 3.4 49 264-320 131-179 (189)
71 TIGR02989 Sig-70_gvs1 RNA poly 37.4 39 0.00084 28.5 3.4 47 264-318 111-157 (159)
72 PRK00118 putative DNA-binding 36.7 44 0.00094 28.2 3.5 47 264-318 17-63 (104)
73 PRK12526 RNA polymerase sigma 35.9 38 0.00082 30.6 3.2 49 264-320 153-201 (206)
74 PF10668 Phage_terminase: Phag 34.0 32 0.0007 26.4 2.1 21 290-310 24-44 (60)
75 PRK12533 RNA polymerase sigma 33.2 42 0.00092 31.0 3.2 50 264-321 134-183 (216)
76 PF05190 MutS_IV: MutS family 32.5 77 0.0017 24.4 4.1 26 129-154 1-26 (92)
77 PRK12523 RNA polymerase sigma 32.4 52 0.0011 28.5 3.4 48 264-319 119-166 (172)
78 PF01381 HTH_3: Helix-turn-hel 32.1 35 0.00077 23.9 1.9 21 292-312 13-33 (55)
79 PRK09648 RNA polymerase sigma 31.6 52 0.0011 28.9 3.4 48 264-319 139-186 (189)
80 PRK12546 RNA polymerase sigma 31.6 46 0.00099 29.9 3.0 49 264-320 113-161 (188)
81 PRK05602 RNA polymerase sigma 31.4 46 0.00099 29.2 2.9 50 264-321 128-177 (186)
82 PF13097 CENP-U: CENP-A nucleo 31.4 1.2E+02 0.0025 28.2 5.6 45 131-178 103-148 (175)
83 PRK09047 RNA polymerase factor 31.0 60 0.0013 27.4 3.5 48 264-319 106-153 (161)
84 PF00196 GerE: Bacterial regul 30.7 67 0.0015 23.2 3.3 48 264-320 3-50 (58)
85 PRK09413 IS2 repressor TnpA; R 30.5 70 0.0015 26.9 3.8 48 260-314 8-55 (121)
86 PRK12512 RNA polymerase sigma 30.4 54 0.0012 28.6 3.2 49 264-320 131-179 (184)
87 PRK12532 RNA polymerase sigma 30.4 54 0.0012 29.1 3.2 49 264-320 136-184 (195)
88 PRK09649 RNA polymerase sigma 30.1 55 0.0012 29.0 3.2 48 264-319 130-177 (185)
89 PRK12516 RNA polymerase sigma 29.9 45 0.00098 29.8 2.7 50 264-321 116-165 (187)
90 PF12022 DUF3510: Domain of un 29.6 2.2E+02 0.0047 24.4 6.7 42 131-180 57-99 (125)
91 PRK15369 two component system 29.2 1.2E+02 0.0027 25.2 5.1 48 264-320 149-196 (211)
92 PRK11511 DNA-binding transcrip 29.2 1.4E+02 0.0031 25.1 5.5 42 267-312 8-49 (127)
93 TIGR03070 couple_hipB transcri 29.2 39 0.00085 23.5 1.7 22 292-313 19-40 (58)
94 PRK12520 RNA polymerase sigma 29.2 62 0.0013 28.6 3.4 48 264-319 131-178 (191)
95 PRK12536 RNA polymerase sigma 29.1 61 0.0013 28.4 3.3 48 264-319 129-176 (181)
96 TIGR02954 Sig70_famx3 RNA poly 29.1 61 0.0013 27.9 3.3 48 264-319 119-166 (169)
97 PRK12530 RNA polymerase sigma 29.0 59 0.0013 28.9 3.2 48 264-319 134-181 (189)
98 cd00131 PAX Paired Box domain 29.0 1.7E+02 0.0037 25.1 6.0 46 264-312 75-127 (128)
99 PRK13919 putative RNA polymera 28.9 62 0.0013 28.3 3.3 49 264-320 135-183 (186)
100 PRK12519 RNA polymerase sigma 28.8 45 0.00098 29.4 2.5 47 264-318 141-187 (194)
101 PRK12531 RNA polymerase sigma 28.3 62 0.0013 28.8 3.3 50 263-320 140-189 (194)
102 PF15500 Toxin_39: Putative RN 28.3 1.3E+02 0.0028 25.1 4.8 39 128-173 44-82 (96)
103 PRK12542 RNA polymerase sigma 27.7 64 0.0014 28.3 3.2 48 264-319 122-169 (185)
104 PRK12524 RNA polymerase sigma 27.6 63 0.0014 28.8 3.2 49 264-320 136-184 (196)
105 PF13551 HTH_29: Winged helix- 27.4 3.1E+02 0.0066 21.5 6.9 46 265-310 58-109 (112)
106 cd01392 HTH_LacI Helix-turn-he 27.4 35 0.00075 23.8 1.2 20 293-312 2-21 (52)
107 PRK12537 RNA polymerase sigma 27.1 67 0.0015 28.2 3.2 47 264-318 133-179 (182)
108 TIGR02959 SigZ RNA polymerase 27.1 70 0.0015 27.8 3.4 50 264-321 100-149 (170)
109 PRK10072 putative transcriptio 26.5 46 0.001 27.6 1.9 23 291-313 49-71 (96)
110 cd00093 HTH_XRE Helix-turn-hel 26.3 54 0.0012 21.3 2.0 21 292-312 16-36 (58)
111 PF07425 Pardaxin: Pardaxin; 26.2 44 0.00095 22.4 1.4 22 73-94 5-26 (33)
112 PRK09636 RNA polymerase sigma 26.2 86 0.0019 30.0 4.0 51 264-322 115-165 (293)
113 KOG4040 NADH:ubiquinone oxidor 26.1 36 0.00078 31.3 1.3 40 265-304 21-61 (186)
114 PRK12535 RNA polymerase sigma 26.0 81 0.0018 28.4 3.6 51 264-322 133-183 (196)
115 PRK08583 RNA polymerase sigma 25.9 83 0.0018 29.4 3.8 48 264-319 205-252 (257)
116 PRK09639 RNA polymerase sigma 25.4 82 0.0018 26.8 3.4 47 264-319 112-158 (166)
117 PRK09645 RNA polymerase sigma 25.2 78 0.0017 27.2 3.3 49 264-320 118-166 (173)
118 PRK06986 fliA flagellar biosyn 25.1 65 0.0014 29.7 2.9 48 264-319 184-231 (236)
119 PF12362 DUF3646: DNA polymera 25.1 45 0.00098 28.7 1.7 27 64-90 82-108 (117)
120 PRK12515 RNA polymerase sigma 24.9 82 0.0018 27.7 3.4 48 264-319 131-178 (189)
121 PRK12529 RNA polymerase sigma 24.8 90 0.0019 27.4 3.6 48 264-319 127-174 (178)
122 PF13384 HTH_23: Homeodomain-l 24.8 61 0.0013 22.5 2.1 23 291-313 20-42 (50)
123 TIGR02947 SigH_actino RNA poly 24.7 36 0.00079 30.1 1.1 49 264-320 131-179 (193)
124 cd06170 LuxR_C_like C-terminal 24.4 1.4E+02 0.003 20.4 3.8 45 266-319 2-46 (57)
125 PF14978 MRP-63: Mitochondrial 24.4 2E+02 0.0043 23.8 5.2 58 258-316 8-71 (91)
126 TIGR02948 SigW_bacill RNA poly 24.4 67 0.0014 27.9 2.7 48 264-319 136-183 (187)
127 PRK07037 extracytoplasmic-func 24.1 83 0.0018 26.7 3.2 48 264-319 109-156 (163)
128 PF04967 HTH_10: HTH DNA bindi 23.7 1.7E+02 0.0037 21.8 4.3 47 265-312 1-47 (53)
129 PRK09415 RNA polymerase factor 23.7 73 0.0016 27.9 2.8 47 264-318 127-173 (179)
130 PRK12543 RNA polymerase sigma 23.6 91 0.002 27.3 3.4 48 264-319 117-164 (179)
131 smart00530 HTH_XRE Helix-turn- 23.3 66 0.0014 20.7 1.9 22 291-312 13-34 (56)
132 PRK08241 RNA polymerase factor 23.2 94 0.002 30.2 3.7 50 264-321 153-202 (339)
133 TIGR03001 Sig-70_gmx1 RNA poly 23.2 83 0.0018 29.7 3.3 48 264-319 161-208 (244)
134 PRK12511 RNA polymerase sigma 23.0 99 0.0021 27.5 3.6 53 264-324 111-163 (182)
135 PRK12539 RNA polymerase sigma 23.0 86 0.0019 27.5 3.1 48 264-319 131-178 (184)
136 PF13411 MerR_1: MerR HTH fami 23.0 61 0.0013 23.9 1.9 18 292-309 4-21 (69)
137 TIGR02941 Sigma_B RNA polymera 22.8 97 0.0021 28.9 3.6 48 264-319 205-252 (255)
138 PRK12528 RNA polymerase sigma 22.7 1E+02 0.0022 26.3 3.5 46 264-317 113-158 (161)
139 PF13865 FoP_duplication: C-te 22.6 78 0.0017 24.9 2.5 8 131-138 46-53 (74)
140 PRK12513 RNA polymerase sigma 22.3 40 0.00086 29.8 0.9 49 264-320 139-187 (194)
141 PF10782 DUF2602: Protein of u 22.2 80 0.0017 24.3 2.3 40 132-177 8-53 (58)
142 PRK12545 RNA polymerase sigma 21.8 94 0.002 27.9 3.2 49 264-320 139-187 (201)
143 PHA01976 helix-turn-helix prot 21.6 72 0.0016 23.4 2.0 22 292-313 19-40 (67)
144 PRK12540 RNA polymerase sigma 21.4 96 0.0021 27.5 3.1 51 264-322 111-161 (182)
145 PRK12538 RNA polymerase sigma 21.2 80 0.0017 29.5 2.7 48 264-319 171-218 (233)
146 PRK04217 hypothetical protein; 21.2 1.6E+02 0.0035 25.0 4.3 50 263-320 41-90 (110)
147 PRK09647 RNA polymerase sigma 21.1 1E+02 0.0022 28.0 3.3 48 264-319 138-185 (203)
148 TIGR02943 Sig70_famx1 RNA poly 20.7 1.2E+02 0.0025 27.0 3.6 48 264-319 131-178 (188)
149 PF13730 HTH_36: Helix-turn-he 20.6 2.7E+02 0.0059 19.5 4.9 48 264-314 2-51 (55)
150 PRK07670 RNA polymerase sigma 20.5 1E+02 0.0022 28.8 3.3 47 264-318 201-247 (251)
151 TIGR02607 antidote_HigA addict 20.4 70 0.0015 24.1 1.8 23 291-313 21-43 (78)
152 TIGR02479 FliA_WhiG RNA polyme 20.4 1.3E+02 0.0028 27.5 3.8 47 264-318 175-221 (224)
153 PRK12534 RNA polymerase sigma 20.2 1.1E+02 0.0023 26.8 3.2 47 264-318 137-183 (187)
154 TIGR02957 SigX4 RNA polymerase 20.1 1.3E+02 0.0028 28.8 3.9 51 264-322 108-158 (281)
155 TIGR02980 SigBFG RNA polymeras 20.1 1.2E+02 0.0026 27.6 3.6 47 264-318 178-224 (227)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=100.00 E-value=3.9e-33 Score=262.09 Aligned_cols=207 Identities=24% Similarity=0.372 Sum_probs=182.3
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHhh-----hcccCCCcchhhHHHHHHhHHHHHHhhhhccCC---------CCCCChH
Q 019231 68 WETVKCKAEIVGHPLYEQLLSAHVSC-----LRIATPVDQLPKIDAQLSRSRDVLAKYSAVANG---------RVLDDKE 133 (344)
Q Consensus 68 ~e~~~lKa~I~sHPlYp~Ll~A~idC-----~KVgaP~e~~~~ld~~l~~~~~~~~k~~~~~~~---------~~g~dpE 133 (344)
+|+++.|.+|.|||+||+|++++|+. +.|....|.-|. |++++++++|+...+++|+. .-|+..+
T Consensus 26 Deaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~-dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsd 104 (334)
T KOG0774|consen 26 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPP-DPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSD 104 (334)
T ss_pred chHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCC-ChHHHHHHHHHHHhcccCccccchhhhhccCCChHH
Confidence 56668999999999999999999995 666666654444 67888899999999988864 2345688
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHhhhhhHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCccccccCCCCccCCCCCCCCC
Q 019231 134 LDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGVSPGESTGATMSDDDEDQVDSDTNFFDGSLDGPD 213 (344)
Q Consensus 134 LDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~~s~~~~~~~~~S~de~~~~~s~~~~~~g~~~~~d 213 (344)
+++-+.+ +...|++||++ +..+|+++.+.+.+|.. +
T Consensus 105 YR~kL~q---iR~iy~~Elek--------yeqaCneftthV~nlL~---------------------------------e 140 (334)
T KOG0774|consen 105 YRAKLLQ---IRQIYHNELEK--------YEQACNEFTTHVMNLLR---------------------------------E 140 (334)
T ss_pred HHHHHHH---HHHHHHHHHHH--------HHHHHHHHHHHHHHHHH---------------------------------H
Confidence 8888877 99999999988 66789999999999995 3
Q ss_pred CCCCCCCCCChhhHhh--HHHHHHHHHHHHhhhhhhHHHHHHHHHhh-hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHH
Q 019231 214 SMGFGPLVPTESERSL--MERVRHELKHELKQGYKEKIVDIREEILR-KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEED 290 (344)
Q Consensus 214 ~~~f~p~~~~~~e~~~--~~~~~~eLk~~L~~ky~~~i~~lr~e~~k-kRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~e 290 (344)
++.|+||.|.++|+.+ |.+.|.-++..|++..|..+..||.++.. +|||++|+|.++.+|..||+.|..||||++++
T Consensus 141 Qsr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~ 220 (334)
T KOG0774|consen 141 QSRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEA 220 (334)
T ss_pred hcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHH
Confidence 3569999999999864 78889999999999999999999999986 56788999999999999999999999999999
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 291 KARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 291 K~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
|++||++||++..||+|||.|+|.|.||.
T Consensus 221 K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 221 KEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHHHHcCceehhhccccccceeehhhh
Confidence 99999999999999999999999999974
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.94 E-value=1.8e-28 Score=238.62 Aligned_cols=249 Identities=23% Similarity=0.302 Sum_probs=175.8
Q ss_pred chhhhHHHHHHHhhCCChHHHHHHHHhhhcccCCCcchhhHHHHHHhHHHHHHhhhhccC-----CCCCCChHHHHHHHH
Q 019231 66 EDWETVKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRSRDVLAKYSAVAN-----GRVLDDKELDQFMTH 140 (344)
Q Consensus 66 ~~~e~~~lKa~I~sHPlYp~Ll~A~idC~KVgaP~e~~~~ld~~l~~~~~~~~k~~~~~~-----~~~g~dpELDqFMea 140 (344)
......-+|..+.+||+|..++.||++|+++++|.+.+.+.++...........+..++. ...+..++|+.||..
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k 124 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSK 124 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchH
Confidence 345666789999999999999999999999999999888865543322222222222111 134568999999999
Q ss_pred HHHHHHHHHHHHhHHhhhhhHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCccccccC---CCCccCCCCCCCCCCCCC
Q 019231 141 YVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGVSPGESTGATMSDDDEDQVD---SDTNFFDGSLDGPDSMGF 217 (344)
Q Consensus 141 Yc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~~s~~~~~~~~~S~de~~~~~---s~~~~~~g~~~~~d~~~f 217 (344)
|+.+|..+.+.|+..+. -++++.++++++..+.+.+..++......+...+.++... +...... +..++
T Consensus 125 ~~~~ll~~~~~~~~~~~--~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~------~~~~~ 196 (342)
T KOG0773|consen 125 LEKILLAVITKLTLTQV--STWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSE------ELLGE 196 (342)
T ss_pred HHHHHHHHHHHhhhhhH--HHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcccccccccccc------ccccc
Confidence 99999999999999863 3899999999999999999876654443322222111100 0000000 11111
Q ss_pred CCCCCChhhHhhH--HHHHHHHHHHHhhhhhhHHHHHHHHHhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 019231 218 GPLVPTESERSLM--ERVRHELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLV 295 (344)
Q Consensus 218 ~p~~~~~~e~~~~--~~~~~eLk~~L~~ky~~~i~~lr~e~~kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA 295 (344)
++......+..-+ ......++..+.+.+..++.....+..++|+++.||+.++.+|+.||.+|+.||||++.+|..||
T Consensus 197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La 276 (342)
T KOG0773|consen 197 SEQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLA 276 (342)
T ss_pred ccccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccc
Confidence 1111111111000 11234555666666665556666667788888999999999999999999999999999999999
Q ss_pred HHhCCChhhhhhhhhhhhhhccccCCC
Q 019231 296 QETGLQLKQINNWFINQRKRNWHANPS 322 (344)
Q Consensus 296 ~~tgLs~kQV~nWF~N~R~R~kk~~~s 322 (344)
.+|||+..||+|||||+|+|.|++...
T Consensus 277 ~~TGLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 277 KQTGLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred hhcCCCcccCCchhhhcccccCCchHH
Confidence 999999999999999999999999863
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=1.9e-23 Score=153.93 Aligned_cols=50 Identities=46% Similarity=0.698 Sum_probs=47.4
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHhHHhhhhhHHHHHHHHHHHHHhhhhcC
Q 019231 126 GRVLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTG 179 (344)
Q Consensus 126 ~~~g~dpELDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~ 179 (344)
.++|+||||||||++||.||++|||||++||+ ||++|||+||+||++||+
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 46899999999999999999999999999985 999999999999999995
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=2e-20 Score=133.91 Aligned_cols=43 Identities=35% Similarity=0.691 Sum_probs=39.9
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhhcccCCCcchhhHHHHHHhH
Q 019231 71 VKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRS 113 (344)
Q Consensus 71 ~~lKa~I~sHPlYp~Ll~A~idC~KVgaP~e~~~~ld~~l~~~ 113 (344)
+.|||+|++||+||+||+|||+|+|||||||++++||+++.+.
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 3699999999999999999999999999999999999987654
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=99.65 E-value=9.8e-17 Score=112.62 Aligned_cols=40 Identities=55% Similarity=1.074 Sum_probs=36.5
Q ss_pred HHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019231 276 WWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (344)
Q Consensus 276 Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R 315 (344)
||.+|..|||||.+||..||..|||+.+||+|||+|+|+|
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=3.6e-14 Score=103.68 Aligned_cols=57 Identities=26% Similarity=0.520 Sum_probs=53.9
Q ss_pred cCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 260 Rkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
+++..|++.+..+|+.||.. +|||+.+++..||..|||+..||.+||.|+|.+.++.
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 56779999999999999999 8999999999999999999999999999999998864
No 7
>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=101.53 Aligned_cols=55 Identities=25% Similarity=0.497 Sum_probs=51.5
Q ss_pred cCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019231 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (344)
Q Consensus 260 Rkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~k 317 (344)
+.++.|++++..+|+.||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
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 45678999999999999999 79999999999999999999999999999999864
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=5.1e-14 Score=103.44 Aligned_cols=57 Identities=30% Similarity=0.704 Sum_probs=54.1
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 259 kRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
||+|..|++++..+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.+.|+
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
>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=99.48 E-value=4.1e-13 Score=122.30 Aligned_cols=148 Identities=21% Similarity=0.296 Sum_probs=116.1
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHhh-----hcccCCCcchhhHHHHHHhHHHHHHhhhhccCCCCCC----------Ch
Q 019231 68 WETVKCKAEIVGHPLYEQLLSAHVSC-----LRIATPVDQLPKIDAQLSRSRDVLAKYSAVANGRVLD----------DK 132 (344)
Q Consensus 68 ~e~~~lKa~I~sHPlYp~Ll~A~idC-----~KVgaP~e~~~~ld~~l~~~~~~~~k~~~~~~~~~g~----------dp 132 (344)
+|++++|.+|.+||+||.|++++|+- +++..+.+..+. |+++.++++|+.+.++.|+...|. |-
T Consensus 24 Deaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~-dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~ 102 (191)
T PF03792_consen 24 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPP-DPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADN 102 (191)
T ss_pred hHHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCC-chhhhhhhcchhhhcCcCCCCcccchhhhhccCccc
Confidence 56689999999999999999999995 566665544333 678888999999999888753221 10
Q ss_pred --HHHHHHHHHHHHHHHHHHHHhHHhhhhhHHHHHHHHHHHHHhhhhcCCCCCCCCCCCCCCccccccCCCCccCCCCCC
Q 019231 133 --ELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGVSPGESTGATMSDDDEDQVDSDTNFFDGSLD 210 (344)
Q Consensus 133 --ELDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~~s~~~~~~~~~S~de~~~~~s~~~~~~g~~~ 210 (344)
|-+.|-...-.+...|++||++ +...|+++...+.+|..
T Consensus 103 ~~d~~dYr~kL~~ir~~y~~el~k--------ye~ac~eF~~hV~~lLr------------------------------- 143 (191)
T PF03792_consen 103 SIDHSDYRAKLSQIRQIYHSELEK--------YEQACNEFTEHVMNLLR------------------------------- 143 (191)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHH--------HHHHhhhhHHHHHHHHH-------------------------------
Confidence 2233444444588899999987 55679999999999985
Q ss_pred CCCCCCCCCCCCChhhHh--hHHHHHHHHHHHHhhhhhhHHHHHHHHHh
Q 019231 211 GPDSMGFGPLVPTESERS--LMERVRHELKHELKQGYKEKIVDIREEIL 257 (344)
Q Consensus 211 ~~d~~~f~p~~~~~~e~~--~~~~~~~eLk~~L~~ky~~~i~~lr~e~~ 257 (344)
+++.|+||.|.++|+. .+.+.+.-+..+||++.|+.+..||.+|+
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 2345999999999995 47899999999999999999999998875
No 10
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.31 E-value=2.2e-12 Score=123.02 Aligned_cols=50 Identities=40% Similarity=0.883 Sum_probs=47.3
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019231 265 LPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (344)
Q Consensus 265 lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~k 317 (344)
|....+.+|++||.. +|||++++|++||+.|||+..||.|||.|+|.|.+
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 445789999999997 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=98.96 E-value=9.8e-10 Score=83.15 Aligned_cols=53 Identities=19% Similarity=0.401 Sum_probs=50.2
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPY----PTEEDKARLVQETGLQLKQINNWFINQR 313 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PY----Ps~~eK~~LA~~tgLs~kQV~nWF~N~R 313 (344)
+||.|+.|+.+++..|+..|.. ++| |+..++..||..+||+..+|.+||+|-+
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 4788999999999999999999 899 9999999999999999999999999954
No 12
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.94 E-value=6.2e-10 Score=101.06 Aligned_cols=61 Identities=20% Similarity=0.277 Sum_probs=57.0
Q ss_pred hhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 257 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 257 ~kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
..||.|+.|+.++...|+..|.. +-|-.-.||..||+.++|++.||++||+|+|.|+|+.-
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence 35677899999999999999999 89999999999999999999999999999999999753
No 13
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.93 E-value=4.3e-10 Score=109.66 Aligned_cols=59 Identities=24% Similarity=0.339 Sum_probs=54.9
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 259 kRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
+|||..++|.|+..|+.-|.- |-|.|++-|.+|++.++||..||+.||||||+|.||-+
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 445668999999999999998 79999999999999999999999999999999999976
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.93 E-value=5.8e-10 Score=106.44 Aligned_cols=66 Identities=23% Similarity=0.264 Sum_probs=60.5
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCCcc
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSSTA 326 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s~~t~ 326 (344)
.||.|+.|+..|+..|+.-|.- |.|.|+..|.+||..+.|++.||++||||||+|+||.+...+..
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 6778899999999999999999 89999999999999999999999999999999999877655444
No 15
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.84 E-value=5e-09 Score=97.76 Aligned_cols=59 Identities=19% Similarity=0.261 Sum_probs=55.9
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
|||.|+.|+..|+..|+.-|.. -.|.+..+|..||..+.|++.||+.||||+|.|.|+.
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 6999999999999999999999999999999999874
No 16
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.79 E-value=5.8e-09 Score=99.54 Aligned_cols=61 Identities=31% Similarity=0.408 Sum_probs=57.2
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.||.|+-|+.++.+.|+.-|.. |-|.|+.-|+.||.++||.+.||+.||+|+|.+.||..-
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 899999999999999999999999999999999998653
No 17
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.79 E-value=4.4e-09 Score=102.95 Aligned_cols=60 Identities=20% Similarity=0.328 Sum_probs=54.8
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
++|.|+-|+..++..|+.-|.. -.|.+..+|..||...||+..||.+||+|||+|.|+..
T Consensus 172 ~RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 172 RRKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred cccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 3445678999999999999999 79999999999999999999999999999999999754
No 18
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.76 E-value=5.5e-09 Score=98.00 Aligned_cols=60 Identities=18% Similarity=0.269 Sum_probs=55.1
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 259 kRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
+|.|+.++.-+.+.|..-|++ .-|.-..||.+||..+|||.+||+.||+|+|-|.||...
T Consensus 123 RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 345778999999999999999 899999999999999999999999999999999997644
No 19
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.74 E-value=4.9e-09 Score=102.27 Aligned_cols=59 Identities=17% Similarity=0.294 Sum_probs=54.0
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
|||+|--|++.|+-.|+.-|.+ ..|.|.-||+.||..++||.+||+.||||+|-|-|+.
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 4444558999999999999999 7999999999999999999999999999999999864
No 20
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.73 E-value=6.6e-09 Score=103.80 Aligned_cols=67 Identities=18% Similarity=0.420 Sum_probs=61.1
Q ss_pred HHHHHhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 252 IREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 252 lr~e~~kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
+-..-.|||||+.+.-.++..|+..|.. ||-||.+|.-.||+.++|.+..|++||+|||.|.|+.++
T Consensus 288 i~a~~RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 288 IGAQSRKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred hhccccccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3333456777889999999999999999 899999999999999999999999999999999999988
No 21
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.70 E-value=1.1e-08 Score=94.61 Aligned_cols=59 Identities=29% Similarity=0.389 Sum_probs=53.8
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.++|+.+|+.+++..|+.-|.. +-|..++.|..||+++||++.||.+||||+|+|.|.+
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 3456678999999999999999 5888999999999999999999999999999999854
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.67 E-value=2.4e-08 Score=89.18 Aligned_cols=62 Identities=18% Similarity=0.333 Sum_probs=57.5
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s 322 (344)
.+++|.+.+..++.+|+..|.. +|||+..+|..|+..++|+++-|+.||+|+|.+.|+....
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 5667788999999999999999 8999999999999999999999999999999999987654
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.62 E-value=2e-08 Score=90.39 Aligned_cols=58 Identities=19% Similarity=0.335 Sum_probs=54.0
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
++|.|+.|+..+...|+.-|+. -.|.+-.|+.+||..++|+++||++||+|+|+++||
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred hhhhcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 4556779999999999999998 689999999999999999999999999999999996
No 24
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.56 E-value=3.6e-08 Score=91.48 Aligned_cols=65 Identities=15% Similarity=0.252 Sum_probs=59.0
Q ss_pred HHHHHHhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 251 DIREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 251 ~lr~e~~kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+....++.|+.|+..+...|++-|.+ ..|.+.+|+.+++..+.|+..||+.||||+|.|.|+
T Consensus 137 ~LrKhk~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 137 TLRKHKPNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred hhcccCCCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 35555566777889999999999999999 799999999999999999999999999999999885
No 25
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.54 E-value=5.2e-08 Score=81.95 Aligned_cols=64 Identities=16% Similarity=0.260 Sum_probs=57.1
Q ss_pred HHHHhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 253 REEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 253 r~e~~kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.+..+.+|-|+.|+..+...|+..|.+ .-||..-.|++||-+..|++..|++||+|+|.+.+|.
T Consensus 12 ~ekrKQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 12 TEKRKQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred hHHHHhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 344445566789999999999999999 7999999999999999999999999999999999864
No 26
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.42 E-value=2e-07 Score=87.17 Aligned_cols=59 Identities=19% Similarity=0.345 Sum_probs=54.6
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.+|-|+.|+..+..+|+.-|.+ .-||+...+++||.+++|.+.+|.+||.|+|++.++.
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 8999999999999999999999999999999988753
No 27
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.41 E-value=2e-07 Score=89.15 Aligned_cols=55 Identities=20% Similarity=0.261 Sum_probs=52.3
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 262 r~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
|+.|+..+...|+.-|.+ --||+.-.|+.||..|+|.+..|.+||+|+|.+.+|.
T Consensus 145 RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred cchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 679999999999999999 7999999999999999999999999999999998874
No 28
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.34 E-value=1.3e-07 Score=90.74 Aligned_cols=56 Identities=23% Similarity=0.306 Sum_probs=51.7
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
-.++..++-.|+.-|.- .+|.|..-|.+||..+||++.||+.||+|||.|.+|-|.
T Consensus 204 vVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 204 VVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred EEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 46789999999999988 899999999999999999999999999999999987653
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.30 E-value=3.5e-07 Score=88.59 Aligned_cols=69 Identities=22% Similarity=0.409 Sum_probs=61.4
Q ss_pred HHHHHhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCC
Q 019231 252 IREEILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSS 323 (344)
Q Consensus 252 lr~e~~kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s~ 323 (344)
|-.+-..||.|++++..+...|++-|.. .|-|.+--|++|+.+|||+...|++||+|+|.+.|+-....
T Consensus 161 l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 161 LEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred cccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 3345668999999999999999999988 89999999999999999999999999999999988754443
No 30
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.29 E-value=3.6e-07 Score=89.24 Aligned_cols=60 Identities=18% Similarity=0.321 Sum_probs=55.0
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
++|.|+.|+..+.+.|+.||.. |-||+.+.|++||--|+|++..|.+||.|+|.+.+|..
T Consensus 112 qrrQrthFtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 3445678999999999999999 89999999999999999999999999999999988753
No 31
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.06 E-value=2.3e-06 Score=80.35 Aligned_cols=61 Identities=25% Similarity=0.380 Sum_probs=55.2
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
+|..|.+|+..++..|+.-|.+ ..||--.++.+||...|+++.||.+||+|+|.+.+|...
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 4445668999999999999999 799999999999999999999999999999999888643
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.96 E-value=8.8e-06 Score=84.48 Aligned_cols=57 Identities=23% Similarity=0.332 Sum_probs=53.0
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~k 317 (344)
.||.|-.|+..+++.|...|.+ +|||+.+.-+.|+.++||...-|.|||-|+|+|.+
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 3566778999999999999999 89999999999999999999999999999999943
No 33
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.89 E-value=4.6e-06 Score=81.48 Aligned_cols=56 Identities=16% Similarity=0.276 Sum_probs=50.8
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 262 r~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
|+-|+.+|+-.|+.-|+. --|-++-.|.+||..++|.+..|++||||+|+|.|+..
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 467999999999888887 58999999999999999999999999999999999743
No 34
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.89 E-value=3.3e-06 Score=81.98 Aligned_cols=68 Identities=22% Similarity=0.408 Sum_probs=60.1
Q ss_pred hhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCCccc
Q 019231 257 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSSTAS 327 (344)
Q Consensus 257 ~kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s~~t~~ 327 (344)
-|||||+.+-..-++-|+.+|.. -|-|+.+-...+|+++.|.+..|.+||+|+|.+.|+..-|...++
T Consensus 308 ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa~~~m 375 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSATAVM 375 (385)
T ss_pred ccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhhceee
Confidence 47888888888889999999999 799999999999999999999999999999999998655555444
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.83 E-value=7.2e-06 Score=74.73 Aligned_cols=62 Identities=13% Similarity=0.109 Sum_probs=56.7
Q ss_pred HhhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 256 ILRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 256 ~~kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
+.++|.|..|+..+...|+.-|.. .+||....++.||..+++++..|.+||+|+|+++++..
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 346777889999999999999999 69999999999999999999999999999999988654
No 36
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.80 E-value=1.5e-05 Score=79.63 Aligned_cols=60 Identities=23% Similarity=0.431 Sum_probs=54.9
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.+|.|+.|+..+...|+.+|.. +|||....++.||.++||+...|..||.|+|.|.++-.
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3445678999999999999999 78999999999999999999999999999999888765
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.45 E-value=6.7e-05 Score=73.63 Aligned_cols=66 Identities=32% Similarity=0.508 Sum_probs=59.6
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCC
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSS 324 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s~~ 324 (344)
..+++++++.+. ..|+.|...|..+|||++.++..|+..++++..||++||+|.|+|.++.+..+.
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~ 160 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTW 160 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCC
Confidence 445667899999 999999999999999999999999999999999999999999999998765533
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=97.07 E-value=0.0004 Score=43.19 Aligned_cols=22 Identities=41% Similarity=0.622 Sum_probs=20.6
Q ss_pred HHHHHHhhhhhhHHHHHHHHHh
Q 019231 236 ELKHELKQGYKEKIVDIREEIL 257 (344)
Q Consensus 236 eLk~~L~~ky~~~i~~lr~e~~ 257 (344)
|||.+|+++|+++|++||+||+
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=97.03 E-value=0.0006 Score=51.51 Aligned_cols=43 Identities=21% Similarity=0.477 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019231 270 TSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (344)
Q Consensus 270 ~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R 315 (344)
++.|+++|.. +.++.+.+...|+.++||+..||.+||.-++.+
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=95.54 E-value=0.0093 Score=54.32 Aligned_cols=61 Identities=25% Similarity=0.468 Sum_probs=53.5
Q ss_pred hhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.++.+..+...+...|..-|.. .+||....+..|+..+|++...|.+||+|+|.+.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3445667888888888888888 899999999999999999999999999999999997655
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.67 E-value=0.14 Score=58.58 Aligned_cols=62 Identities=23% Similarity=0.277 Sum_probs=56.0
Q ss_pred hhhcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 257 LRKRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 257 ~kkRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.+++.|..++..+..+|+..|.. --||+.++-+.|.+..+|....|..||+|.|.+.++.-.
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 35566778999999999999999 799999999999999999999999999999999998744
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=88.34 E-value=0.9 Score=49.81 Aligned_cols=52 Identities=31% Similarity=0.562 Sum_probs=46.8
Q ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCC
Q 019231 270 TSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSS 324 (344)
Q Consensus 270 ~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s~~ 324 (344)
+.+|+.+|.. |+.|+.++...+|...||...-|+.||.+.+......+.+++
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 6788999998 899999999999999999999999999999998887665444
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=87.25 E-value=1.1 Score=33.05 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=32.6
Q ss_pred hcCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019231 259 KRRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQR 313 (344)
Q Consensus 259 kRkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R 313 (344)
||+|..|+-+.+-.+-.-+.. .+ -...||+.+|++..+|.+|..|+.
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 466778888886666555665 23 578999999999999999999854
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=75.88 E-value=3.9 Score=30.91 Aligned_cols=47 Identities=17% Similarity=0.283 Sum_probs=30.8
Q ss_pred cCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 019231 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQR 313 (344)
Q Consensus 260 Rkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R 313 (344)
++++.||++.+..+-.-+.. .......+|...|+++.+|.+|-.-.+
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 34568898886665444433 236778999999999999999987776
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=70.00 E-value=13 Score=22.10 Aligned_cols=39 Identities=10% Similarity=0.157 Sum_probs=27.8
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 019231 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWF 309 (344)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF 309 (344)
..++.+.+..+..++.. .+ ....+|+.+|++...|.+|.
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 34578899999999999984
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=68.24 E-value=8.3 Score=25.85 Aligned_cols=46 Identities=11% Similarity=0.125 Sum_probs=35.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~k 317 (344)
.++...+.++...+... -.-..+|+.+|++..+|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46777888887776542 12457899999999999999988877653
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=61.19 E-value=14 Score=26.18 Aligned_cols=44 Identities=14% Similarity=0.277 Sum_probs=32.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 315 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R 315 (344)
.||+..+.++.-.|... -.-.++|+.+|++...|.+|....|++
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 58888888887665553 234589999999999999999998876
No 48
>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=57.72 E-value=14 Score=26.00 Aligned_cols=47 Identities=9% Similarity=0.225 Sum_probs=36.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.+|...|.. ++ .-.++|+..|++...|..+...+..+.|+
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 22 24579999999999999999988887653
No 49
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=56.32 E-value=14 Score=31.19 Aligned_cols=47 Identities=9% Similarity=0.071 Sum_probs=37.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.++..-|... .+ -.++|+.+|++...|.+|....|++.++
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 58888999886655542 22 4579999999999999999999998875
No 50
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=50.28 E-value=31 Score=36.87 Aligned_cols=26 Identities=12% Similarity=0.245 Sum_probs=16.1
Q ss_pred CCChHHHHHHHHHHH-------HHHHHHHHHhH
Q 019231 129 LDDKELDQFMTHYVL-------LLYSFKEQLQQ 154 (344)
Q Consensus 129 g~dpELDqFMeaYc~-------vL~kykEEL~k 154 (344)
..-|++.-..-+||. ||.+|++||++
T Consensus 182 n~ap~mkt~~~aYcanHP~AV~VL~k~~dELek 214 (661)
T KOG2070|consen 182 NLAPQMKTLYLAYCANHPSAVNVLTKHSDELEK 214 (661)
T ss_pred hhhHHHHHHHHHHHhcCchhhhHHHHhHHHHHH
Confidence 445666666666664 66666666655
No 51
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=49.67 E-value=17 Score=32.31 Aligned_cols=50 Identities=6% Similarity=0.016 Sum_probs=40.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.||+..+.+|.-.+... .+ -.++|+.+|++...|.+++...|++.++...
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 48999999987665553 22 3579999999999999999999999887653
No 52
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=48.52 E-value=21 Score=30.45 Aligned_cols=48 Identities=17% Similarity=0.280 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.+... .+| .++|+.+|++...|.+.+.-+|++.++.
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 48999999987666552 222 4799999999999999999999988764
No 53
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=47.47 E-value=15 Score=26.67 Aligned_cols=23 Identities=13% Similarity=0.304 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChhhhhhhhhhh
Q 019231 290 DKARLVQETGLQLKQINNWFINQ 312 (344)
Q Consensus 290 eK~~LA~~tgLs~kQV~nWF~N~ 312 (344)
....||+.+|++..+|+.|+.+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 45689999999999999999976
No 54
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=46.14 E-value=5.7 Score=37.40 Aligned_cols=38 Identities=34% Similarity=0.474 Sum_probs=30.7
Q ss_pred CCCCCcccchhhhHHHHHHHhhCCChHHHHHHHHhhhcccCCCc
Q 019231 58 ASNDNGRAEDWETVKCKAEIVGHPLYEQLLSAHVSCLRIATPVD 101 (344)
Q Consensus 58 ~~~~~~~~~~~e~~~lKa~I~sHPlYp~Ll~A~idC~KVgaP~e 101 (344)
++||-|...-- ..||.+|..||++.+||.||+ ||.|.-
T Consensus 100 aGHSQGs~~l~--~LL~e~~~~~pl~~rLVAAYl----iG~~v~ 137 (207)
T PF11288_consen 100 AGHSQGSMHLL--RLLKEEIAGDPLRKRLVAAYL----IGYPVT 137 (207)
T ss_pred EEeChHHHHHH--HHHHHHhcCchHHhhhheeee----cCcccc
Confidence 56777766444 479999999999999999999 787744
No 55
>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=45.58 E-value=31 Score=27.77 Aligned_cols=47 Identities=17% Similarity=0.285 Sum_probs=35.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.++..-+.. .+ .-..+|+.+|++...|.+|....+.+.++
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4677787777544333 33 23489999999999999999999988775
No 56
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=44.00 E-value=26 Score=31.12 Aligned_cols=49 Identities=10% Similarity=0.038 Sum_probs=38.7
Q ss_pred CCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 262 AGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 262 r~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
...|++.++++|.- +.+ .+ .-.++|+.+|++...|++|....+++.++.
T Consensus 4 ~~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 4 ESFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred ccCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45789999999977 333 22 234899999999999999999999887753
No 57
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=43.94 E-value=26 Score=30.17 Aligned_cols=50 Identities=14% Similarity=0.040 Sum_probs=40.8
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
..||+..++++.-++..+ .+ -.++|..+|++...|.+|..-.|++.++..
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 358889999998776664 33 358999999999999999999999988743
No 58
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=41.96 E-value=44 Score=27.83 Aligned_cols=47 Identities=15% Similarity=0.202 Sum_probs=36.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||...+.++.-.+.. .++ -.++|+.+|++...|.++....|++.++
T Consensus 113 ~L~~~~r~il~l~~~~----~~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GKS----YKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4788888888775544 332 2358999999999999999999998875
No 59
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=41.46 E-value=27 Score=29.76 Aligned_cols=48 Identities=8% Similarity=0.160 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.+.. .+ .-..+|+.+|++...|.+|..-.|++.++.
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 3778888887665544 22 235899999999999999999999998764
No 60
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=41.34 E-value=29 Score=29.67 Aligned_cols=48 Identities=8% Similarity=0.141 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.|... .+ -..+|+.+|++...|.+|....|++.++.
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 47888888886654442 22 24789999999999999999999988864
No 61
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=40.96 E-value=31 Score=29.36 Aligned_cols=50 Identities=10% Similarity=0.229 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.||+..+.++.-.|... ++ -.++|+.+|++...|.++....|++.++...
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 58888888886665552 22 2478999999999999999999999887554
No 62
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=40.58 E-value=48 Score=28.80 Aligned_cols=48 Identities=13% Similarity=0.270 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.|.. .++ -.++|+.+|++...|.+++...|++.++.
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 63
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=40.53 E-value=60 Score=22.03 Aligned_cols=47 Identities=11% Similarity=0.147 Sum_probs=34.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.|+.....++..+ .. .+ ....+|+.+|++...|..|....+.+..-.
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 346889999999999999999887776543
No 64
>PF13518 HTH_28: Helix-turn-helix domain
Probab=39.93 E-value=29 Score=24.03 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhh
Q 019231 291 KARLVQETGLQLKQINNWFINQRK 314 (344)
Q Consensus 291 K~~LA~~tgLs~kQV~nWF~N~R~ 314 (344)
...+|..+|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 446999999999999999987775
No 65
>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=39.22 E-value=25 Score=30.65 Aligned_cols=49 Identities=10% Similarity=0.043 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.-.|..+ -.-.++|+.+|++...|.++....|++.++..
T Consensus 138 ~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG--------LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 46778888886554442 22357999999999999999999999988754
No 66
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=39.06 E-value=33 Score=29.31 Aligned_cols=48 Identities=19% Similarity=0.191 Sum_probs=38.8
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
..||+.++.++.-.+... .+ -.++|..+|++...|..+....|++.++
T Consensus 111 ~~L~~~~r~v~~l~~~~~--~s------~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYG--FS------YKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 358999999987766553 22 2479999999999999999999998875
No 67
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=39.03 E-value=61 Score=32.67 Aligned_cols=47 Identities=13% Similarity=0.200 Sum_probs=36.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhHHhhhhhHHHHHHHHHHHHHhhhhcCC
Q 019231 132 KELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGV 180 (344)
Q Consensus 132 pELDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~~ 180 (344)
-+-|.||--||. .+|-.+|.+-+|-.++++..-+..+-.|+..+|.+
T Consensus 134 T~C~Hy~H~~Cl--aRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV 180 (368)
T KOG4445|consen 134 TACDHYMHFACL--ARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV 180 (368)
T ss_pred ehhHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH
Confidence 478999999994 45666666655556678888888999999999853
No 68
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=38.76 E-value=35 Score=29.67 Aligned_cols=48 Identities=4% Similarity=0.100 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+.++.++.-.+... .+ -.++|+.+|++...|.+.+...|++.++.
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 48999999988776663 22 24799999999999999999999988763
No 69
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=38.54 E-value=33 Score=29.58 Aligned_cols=48 Identities=15% Similarity=0.021 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..++++.-.+...+ . -.++|+.+|++...|.++..-.|++.+..
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 589999998877666632 1 34799999999999999999999988754
No 70
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=37.59 E-value=37 Score=30.06 Aligned_cols=49 Identities=16% Similarity=0.165 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.-.|... .+ -.++|+.+|++...|.+...-.|++.++.-
T Consensus 131 ~L~~~~r~i~~l~~~~g--~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--EK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 68999999998665552 33 347999999999999999999999988753
No 71
>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=37.44 E-value=39 Score=28.52 Aligned_cols=47 Identities=19% Similarity=0.233 Sum_probs=37.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.++.--|.. .++ -..+|+.+|++...|.++..-.|++.+.
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 5888898988875554 222 2478999999999999999999988765
No 72
>PRK00118 putative DNA-binding protein; Validated
Probab=36.71 E-value=44 Score=28.24 Aligned_cols=47 Identities=11% Similarity=0.193 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||..++.++.-++... + .-..+|+.+|++..-|.+|....|++.++
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 57888999997777663 2 23469999999999999999999888775
No 73
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=35.94 E-value=38 Score=30.65 Aligned_cols=49 Identities=14% Similarity=0.208 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.--+... . .-.++|+.+|++...|.+++...|++.++-.
T Consensus 153 ~L~~~~r~vl~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--L------SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888999987655542 1 2357999999999999999999999887643
No 74
>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=34.02 E-value=32 Score=26.42 Aligned_cols=21 Identities=14% Similarity=0.355 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCChhhhhhhhh
Q 019231 290 DKARLVQETGLQLKQINNWFI 310 (344)
Q Consensus 290 eK~~LA~~tgLs~kQV~nWF~ 310 (344)
.-..||+++|++..||..|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456899999999999999943
No 75
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=33.22 E-value=42 Score=31.03 Aligned_cols=50 Identities=16% Similarity=0.164 Sum_probs=41.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.||+..+.++.-.|..+ .+| .++|+.+|++...|.++....|++.++...
T Consensus 134 ~Lp~~~R~v~~L~y~eg--~s~------~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 134 KLPVEYREVLVLRELED--MSY------REIAAIADVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred cCCHHHHhHhhhHHhcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 58888999998877764 222 478999999999999999999999997543
No 76
>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=32.49 E-value=77 Score=24.38 Aligned_cols=26 Identities=27% Similarity=0.319 Sum_probs=20.8
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHhH
Q 019231 129 LDDKELDQFMTHYVLLLYSFKEQLQQ 154 (344)
Q Consensus 129 g~dpELDqFMeaYc~vL~kykEEL~k 154 (344)
|-||+||.....|..+.....+.+.+
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 56899999999999888777666643
No 77
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=32.45 E-value=52 Score=28.53 Aligned_cols=48 Identities=13% Similarity=0.222 Sum_probs=38.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+.++.++.-.+... .+| .++|+.+|++..-|.++....+++.+..
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 58888989887665552 333 4799999999999999999999988653
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=32.09 E-value=35 Score=23.95 Aligned_cols=21 Identities=14% Similarity=0.189 Sum_probs=18.3
Q ss_pred HHHHHHhCCChhhhhhhhhhh
Q 019231 292 ARLVQETGLQLKQINNWFINQ 312 (344)
Q Consensus 292 ~~LA~~tgLs~kQV~nWF~N~ 312 (344)
..||+.+|++...|..|..+.
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
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=31.65 E-value=52 Score=28.92 Aligned_cols=48 Identities=10% Similarity=0.014 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.--|... + .-.++|+.+|++...|.++....|++.++.
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 58888888887755552 2 245899999999999999999999988764
No 80
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=31.62 E-value=46 Score=29.89 Aligned_cols=49 Identities=14% Similarity=0.111 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.-.+... ++ -.++|+.+|++...|.+++.-.|++.++..
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 58999999997776652 22 247899999999999999999999998754
No 81
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=31.42 E-value=46 Score=29.21 Aligned_cols=50 Identities=6% Similarity=0.092 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.||+..+.++.--|... .+ -.++|+.+|++...|.++....|++.++...
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 36888888886554442 22 3479999999999999999999999987543
No 82
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=31.40 E-value=1.2e+02 Score=28.18 Aligned_cols=45 Identities=13% Similarity=0.223 Sum_probs=36.5
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHhHHhhhhhHHH-HHHHHHHHHHhhhhc
Q 019231 131 DKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEA-VMACWDLEQSLQSLT 178 (344)
Q Consensus 131 dpELDqFMeaYc~vL~kykEEL~kP~~~~~~EA-~~fc~~iE~QL~sL~ 178 (344)
=-|||-.+.++-.++..|++.++-.+= .+| ..||..|..||-.+.
T Consensus 103 ItELDVvL~~FEk~~~eYkq~ieS~~c---r~AI~~F~~~~keqL~~~i 148 (175)
T PF13097_consen 103 ITELDVVLSAFEKTALEYKQSIESKIC---RKAINKFYSNFKEQLIEMI 148 (175)
T ss_pred chHHHHHHHHHHHHHHHHHHhhccHHH---HHHHHHHHHHHHHHHHHHH
Confidence 379999999999999999999976552 233 358889999997776
No 83
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=31.03 E-value=60 Score=27.41 Aligned_cols=48 Identities=13% Similarity=0.080 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.+... .+ -.++|+.+|++...|.+...-.|++.++.
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 58999999987765552 22 35799999999999999999999988764
No 84
>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=30.73 E-value=67 Score=23.23 Aligned_cols=48 Identities=15% Similarity=0.108 Sum_probs=35.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.|++....+|.-+..- ..-.++|...|++++.|..+..+.++|..-++
T Consensus 3 ~LT~~E~~vl~~l~~G---------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG---------MSNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHHTT---------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHHhc---------CCcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 4677777877665444 23457899999999999999999999876543
No 85
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=30.50 E-value=70 Score=26.93 Aligned_cols=48 Identities=6% Similarity=0.060 Sum_probs=32.3
Q ss_pred cCCCCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhh
Q 019231 260 RRAGKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 314 (344)
Q Consensus 260 Rkr~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~ 314 (344)
+++++++.+-+...-..... ..+ ....+|+..|++..+|.+|..-.+.
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 34567888875544333333 232 3457899999999999999766654
No 86
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=30.41 E-value=54 Score=28.62 Aligned_cols=49 Identities=4% Similarity=-0.086 Sum_probs=39.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.-.+... . .-.++|+.+|++...|.+++...|++.+...
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--A------SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 58888999998765552 2 2357999999999999999999999988654
No 87
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=30.36 E-value=54 Score=29.07 Aligned_cols=49 Identities=12% Similarity=0.178 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.-.+... + .-.++|+.+|++...|.++...+|++.++..
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 48888888887655552 2 2357999999999999999999999988754
No 88
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=30.08 E-value=55 Score=29.01 Aligned_cols=48 Identities=17% Similarity=0.047 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+.++.++.-.+... .+ -.++|+.+|++...|.++..-.|++.++-
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 58889999987666553 22 34799999999999999999999999873
No 89
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=29.90 E-value=45 Score=29.78 Aligned_cols=50 Identities=18% Similarity=0.185 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.||+..+.++.-.+... .+| .++|+.+|++...|.++....|++.++...
T Consensus 116 ~Lp~~~r~i~~L~~~~g--~s~------~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGASG--FAY------EEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 47888888887765552 232 378999999999999999999999987654
No 90
>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=29.60 E-value=2.2e+02 Score=24.41 Aligned_cols=42 Identities=17% Similarity=0.267 Sum_probs=24.7
Q ss_pred ChHHHHHHHHHHH-HHHHHHHHHhHHhhhhhHHHHHHHHHHHHHhhhhcCC
Q 019231 131 DKELDQFMTHYVL-LLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGV 180 (344)
Q Consensus 131 dpELDqFMeaYc~-vL~kykEEL~kP~~~~~~EA~~fc~~iE~QL~sL~~~ 180 (344)
+....+++...+. +...|.+. +.|...-.+++|..|+-|=..
T Consensus 57 ~~~~~~~~~~v~~~v~~~y~~~--------~~evL~sv~KtEeSL~rlkk~ 99 (125)
T PF12022_consen 57 PEIIEEWLQKVITEVTERYYEI--------ASEVLTSVRKTEESLKRLKKR 99 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHh
Confidence 4455555554332 33344443 346666778999999988653
No 91
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=29.24 E-value=1.2e+02 Score=25.25 Aligned_cols=48 Identities=13% Similarity=0.185 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.|++..+++|.-+ ..+ |. ...+|+..+++.+.|.++..+.|++..-.+
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 5899889998874 442 22 468899999999999999999999987544
No 92
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=29.24 E-value=1.4e+02 Score=25.12 Aligned_cols=42 Identities=12% Similarity=0.227 Sum_probs=31.5
Q ss_pred hhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 019231 267 GDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQ 312 (344)
Q Consensus 267 k~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~ 312 (344)
......+..|...|...| ++. ..||+.+|+++.++..+|...
T Consensus 8 ~~~i~~~~~~I~~~~~~~-~sl---~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNLESP-LSL---EKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhcCCC-CCH---HHHHHHHCcCHHHHHHHHHHH
Confidence 344567788889987666 454 568888999999998888754
No 93
>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=29.17 E-value=39 Score=23.45 Aligned_cols=22 Identities=23% Similarity=0.223 Sum_probs=19.1
Q ss_pred HHHHHHhCCChhhhhhhhhhhh
Q 019231 292 ARLVQETGLQLKQINNWFINQR 313 (344)
Q Consensus 292 ~~LA~~tgLs~kQV~nWF~N~R 313 (344)
..||+.+|+++..|..|..+++
T Consensus 19 ~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 19 ADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHhCCCHHHHHHHHCCCC
Confidence 5799999999999999987653
No 94
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=29.16 E-value=62 Score=28.58 Aligned_cols=48 Identities=15% Similarity=0.099 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+.++.++.-.+... .+ -.++|+.+|++..-|.+.....|++.++-
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48888888887665552 23 25799999999999999999999998764
No 95
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=29.11 E-value=61 Score=28.40 Aligned_cols=48 Identities=19% Similarity=0.028 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.+..+ . .-.++|+.+|++...|.+.+...|++.++.
T Consensus 129 ~L~~~~r~v~~l~~~~g--~------s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG--L------SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HCCHHHHHHHHHHHHcC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888776555553 2 235799999999999999999999998864
No 96
>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=29.07 E-value=61 Score=27.90 Aligned_cols=48 Identities=4% Similarity=0.028 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||...++++.--|... .+ -..+|+.+|++...|.++..-.|++.++.
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 47888888886665552 22 34789999999999999999999887753
No 97
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.98 E-value=59 Score=28.91 Aligned_cols=48 Identities=10% Similarity=0.149 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.+... .+ -.++|+.+|++...|.++..-+|++.++.
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 58888989887766552 22 35799999999999999999999988763
No 98
>cd00131 PAX Paired Box domain
Probab=28.96 E-value=1.7e+02 Score=25.09 Aligned_cols=46 Identities=11% Similarity=0.082 Sum_probs=32.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCC-------Chhhhhhhhhhh
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGL-------QLKQINNWFINQ 312 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgL-------s~kQV~nWF~N~ 312 (344)
.++......+..+... +|.-|..|-..+-...|+ +..+|+.||.++
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 4455566666667777 798888887666335577 999999998764
No 99
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=28.88 E-value=62 Score=28.26 Aligned_cols=49 Identities=12% Similarity=0.135 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.+|.-.+... . .-.++|+.+|++...|.++....|++.++..
T Consensus 135 ~L~~~~r~vl~l~~~~~--~------s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG--Y------THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 48889999997665552 2 2357999999999999999999999887643
No 100
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.76 E-value=45 Score=29.38 Aligned_cols=47 Identities=11% Similarity=0.197 Sum_probs=36.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.++.--+... . .-.++|+.+|++...|.+|+...|++.++
T Consensus 141 ~L~~~~~~v~~l~~~~g--~------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 141 QLPESQRQVLELAYYEG--L------SQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hCCHHHhhhhhhhhhcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 57888888886654442 2 23579999999999999999999998875
No 101
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=28.31 E-value=62 Score=28.76 Aligned_cols=50 Identities=16% Similarity=0.281 Sum_probs=39.3
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
..||+..+.++.-.+... .+| .++|+.+|++...|.+.+...|++.++..
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s~------~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LPH------QQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CCH------HHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 358888999987655442 333 47999999999999999999999888644
No 102
>PF15500 Toxin_39: Putative RNase-like toxin
Probab=28.28 E-value=1.3e+02 Score=25.09 Aligned_cols=39 Identities=21% Similarity=0.162 Sum_probs=27.3
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHhHHhhhhhHHHHHHHHHHHHH
Q 019231 128 VLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQS 173 (344)
Q Consensus 128 ~g~dpELDqFMeaYc~vL~kykEEL~kP~~~~~~EA~~fc~~iE~Q 173 (344)
++++|+|.+.|+. ++-+++.--++ .++||...+..+|.-
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 6789999999998 34445544444 357888777776643
No 103
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=27.66 E-value=64 Score=28.30 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=37.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.+... .+ -.++|+.+|++...|.+.....|++.++.
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 48888999987654442 22 24799999999999999999999988764
No 104
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=27.59 E-value=63 Score=28.75 Aligned_cols=49 Identities=4% Similarity=0.059 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.-.+.. .|+ -.++|+.+|++...|.+++.-+|++.++..
T Consensus 136 ~L~~~~r~i~~L~~~~----g~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIE----GLS----NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHc----CCC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5888888888665444 222 347999999999999999999999998754
No 105
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.39 E-value=3.1e+02 Score=21.53 Aligned_cols=46 Identities=17% Similarity=0.052 Sum_probs=29.7
Q ss_pred CChhHHHHHHHHHHHhcCCC--CCCHHHHHH-H-HHHh--CCChhhhhhhhh
Q 019231 265 LPGDTTSLLKAWWLSHAKWP--YPTEEDKAR-L-VQET--GLQLKQINNWFI 310 (344)
Q Consensus 265 lpk~~~~iL~~Wf~~H~~~P--YPs~~eK~~-L-A~~t--gLs~kQV~nWF~ 310 (344)
++.+....|.+++.++.... ..+...-.. | .+.+ .++...|..|+.
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 234444433 4 3333 377777888764
No 106
>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=27.38 E-value=35 Score=23.77 Aligned_cols=20 Identities=5% Similarity=0.293 Sum_probs=18.5
Q ss_pred HHHHHhCCChhhhhhhhhhh
Q 019231 293 RLVQETGLQLKQINNWFINQ 312 (344)
Q Consensus 293 ~LA~~tgLs~kQV~nWF~N~ 312 (344)
.||+.+|++...|+.|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 58999999999999999887
No 107
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=27.12 E-value=67 Score=28.17 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=36.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.++.--|... .+ -..+|+.+|++...|.+|...+|++.++
T Consensus 133 ~L~~~~r~i~~l~~~~~--~s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 133 QLEPARRNCILHAYVDG--CS------HAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 57888888766555442 22 3579999999999999999999988775
No 108
>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=27.10 E-value=70 Score=27.83 Aligned_cols=50 Identities=16% Similarity=0.195 Sum_probs=40.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.||+..+.+|.-.+... |+ -.++|+.+|++...|.++..-.|++.++-..
T Consensus 100 ~L~~~~r~v~~l~~~~g----~s----~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG----LS----QQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 58888888887766653 22 3479999999999999999999999887554
No 109
>PRK10072 putative transcriptional regulator; Provisional
Probab=26.55 E-value=46 Score=27.61 Aligned_cols=23 Identities=9% Similarity=0.289 Sum_probs=20.4
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 019231 291 KARLVQETGLQLKQINNWFINQR 313 (344)
Q Consensus 291 K~~LA~~tgLs~kQV~nWF~N~R 313 (344)
...||+.+|++...|.+|...+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999998765
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=26.31 E-value=54 Score=21.30 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=18.7
Q ss_pred HHHHHHhCCChhhhhhhhhhh
Q 019231 292 ARLVQETGLQLKQINNWFINQ 312 (344)
Q Consensus 292 ~~LA~~tgLs~kQV~nWF~N~ 312 (344)
..+|+.+|++...|..|..+.
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCC
Confidence 488999999999999998875
No 111
>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=26.22 E-value=44 Score=22.37 Aligned_cols=22 Identities=41% Similarity=0.563 Sum_probs=17.4
Q ss_pred HHHHHhhCCChHHHHHHHHhhh
Q 019231 73 CKAEIVGHPLYEQLLSAHVSCL 94 (344)
Q Consensus 73 lKa~I~sHPlYp~Ll~A~idC~ 94 (344)
+-.+|++.|||.-||+|--..+
T Consensus 5 lipkiissplfktllsavgsal 26 (33)
T PF07425_consen 5 LIPKIISSPLFKTLLSAVGSAL 26 (33)
T ss_dssp CHHHHCCTTTCHHHHHHHHHHC
T ss_pred hhhHHHccHHHHHHHHHHHHHH
Confidence 3468999999999999865444
No 112
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=26.18 E-value=86 Score=29.99 Aligned_cols=51 Identities=14% Similarity=0.095 Sum_probs=40.2
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s 322 (344)
.||+.++.++.--+... .+| .++|+.+|++..-|.+.+...|++.++..+.
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 333 4789999999999999999999999987654
No 113
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=26.10 E-value=36 Score=31.28 Aligned_cols=40 Identities=25% Similarity=0.536 Sum_probs=30.9
Q ss_pred CChhHHHHHHHHHHHhcCCCCCC-HHHHHHHHHHhCCChhh
Q 019231 265 LPGDTTSLLKAWWLSHAKWPYPT-EEDKARLVQETGLQLKQ 304 (344)
Q Consensus 265 lpk~~~~iL~~Wf~~H~~~PYPs-~~eK~~LA~~tgLs~kQ 304 (344)
......+..-.|...|.-.|||+ ++||..-|++.||-+..
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 77888889999986654
No 114
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=25.97 E-value=81 Score=28.41 Aligned_cols=51 Identities=12% Similarity=0.098 Sum_probs=40.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s 322 (344)
.||+..+.++.--+... .+ -.++|+.+|++...|.++....|++.++....
T Consensus 133 ~Lp~~~r~v~~l~~~~g--~s------~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 133 ALPPERREALILTQVLG--YT------YEEAAKIADVRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred cCCHHHHHHhhhHHHhC--CC------HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 48888888886666553 22 35899999999999999999999999876543
No 115
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=25.87 E-value=83 Score=29.42 Aligned_cols=48 Identities=10% Similarity=0.159 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.+|.-.|... .+ -.++|+.+|++...|.+|....+++.++.
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 116
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=25.45 E-value=82 Score=26.80 Aligned_cols=47 Identities=13% Similarity=0.249 Sum_probs=37.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.+|.-.+ . .+ .-..+|..+|++...|.++....|++.++-
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 5 22 235799999999999999999999988763
No 117
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.20 E-value=78 Score=27.25 Aligned_cols=49 Identities=12% Similarity=0.223 Sum_probs=39.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.+|.--+... .+ -.++|+.+|++...|.+...-.|++.++..
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 347999999999999999999999888643
No 118
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=25.08 E-value=65 Score=29.74 Aligned_cols=48 Identities=13% Similarity=0.175 Sum_probs=38.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++..-|... + .-.++|+.+|++...|.++....|++.++.
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 346899999999999999999999998764
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=25.05 E-value=45 Score=28.65 Aligned_cols=27 Identities=26% Similarity=0.310 Sum_probs=22.1
Q ss_pred ccchhhhHHHHHHHhhCCChHHHHHHH
Q 019231 64 RAEDWETVKCKAEIVGHPLYEQLLSAH 90 (344)
Q Consensus 64 ~~~~~e~~~lKa~I~sHPlYp~Ll~A~ 90 (344)
+....+.+..++.+..||++...|.+|
T Consensus 82 E~~~~~~~~~~~~a~~~P~V~avL~~F 108 (117)
T PF12362_consen 82 EQEAAAKEARRAAARAHPLVKAVLAAF 108 (117)
T ss_pred HHHHHHHHHHHHHHHhCcHHHHHHHHC
Confidence 444456677899999999999999887
No 120
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.86 E-value=82 Score=27.73 Aligned_cols=48 Identities=10% Similarity=0.132 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.+|.--+... . .-.++|+.+|++...|.+-+...|++.++.
T Consensus 131 ~L~~~~r~vl~l~~~~~--~------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE--K------SVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 48888999986655442 2 235799999999999999999999988864
No 121
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.80 E-value=90 Score=27.38 Aligned_cols=48 Identities=8% Similarity=0.042 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+.++.++.-.+... .+ -.++|+.+|++..-|.+.+..++.+....
T Consensus 127 ~Lp~~~R~v~~L~~~~g--~s------~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG--MK------QKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 58999999887766653 22 24799999999999999999888887654
No 122
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.77 E-value=61 Score=22.46 Aligned_cols=23 Identities=13% Similarity=0.379 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 019231 291 KARLVQETGLQLKQINNWFINQR 313 (344)
Q Consensus 291 K~~LA~~tgLs~kQV~nWF~N~R 313 (344)
...+|+.+|++...|.+|....+
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 123
>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=24.75 E-value=36 Score=30.09 Aligned_cols=49 Identities=10% Similarity=0.081 Sum_probs=37.4
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.-.+... + .-.++|+.+|++...|.++..-.|++.++..
T Consensus 131 ~Lp~~~r~i~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEG----F----AYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888775544442 2 2357999999999999999999999988643
No 124
>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=24.42 E-value=1.4e+02 Score=20.37 Aligned_cols=45 Identities=9% Similarity=0.076 Sum_probs=30.5
Q ss_pred ChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 266 PGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 266 pk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
+.....++.-+ .. .+ .-..+|+.+|++...|..|..-.+++..-+
T Consensus 2 ~~~e~~i~~~~-~~----~~----s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 2 TPREREVLRLL-AE----GK----TNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 45556666443 22 22 346788999999999999998766665543
No 125
>PF14978 MRP-63: Mitochondrial ribosome protein 63
Probab=24.39 E-value=2e+02 Score=23.84 Aligned_cols=58 Identities=17% Similarity=0.226 Sum_probs=38.3
Q ss_pred hhcCCCCCChhHHHHHHHHHHH------hcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 019231 258 RKRRAGKLPGDTTSLLKAWWLS------HAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRN 316 (344)
Q Consensus 258 kkRkr~~lpk~~~~iL~~Wf~~------H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~ 316 (344)
|-|+-+.++...++.+.+-|.. .+..||.|.++=...|...+- .++...|+.-++.+.
T Consensus 8 KhR~~r~vt~~~k~~~~~~le~E~eN~~~Ls~PYLT~EQE~gh~~e~r~-~k~~~~~~~~~~~~k 71 (91)
T PF14978_consen 8 KHRRPRKVTWQMKENMIRRLEIEEENMYWLSRPYLTAEQEYGHAKERRK-EKAFFEWIKEKKRSK 71 (91)
T ss_pred cCCCcCCCCHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHcchHHHHhH-HHHHHHHHHHHHHcc
Confidence 4455556777666665443332 244799999998888888877 666777776665443
No 126
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.37 E-value=67 Score=27.86 Aligned_cols=48 Identities=8% Similarity=0.111 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.--|.. .+ .-.++|+.+|++...|.+++...|++.++.
T Consensus 136 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4888888888664443 22 235789999999999999999999988764
No 127
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=24.08 E-value=83 Score=26.72 Aligned_cols=48 Identities=15% Similarity=0.179 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.--|... .+ -.++|+.+|++...|.....-.|++.++.
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 58888999987655442 22 35799999999999999998888887764
No 128
>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=23.71 E-value=1.7e+02 Score=21.78 Aligned_cols=47 Identities=17% Similarity=0.187 Sum_probs=35.8
Q ss_pred CChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 019231 265 LPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQ 312 (344)
Q Consensus 265 lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~ 312 (344)
|++.++.+|..-+..=+. -+|-...-..||+..|++..-+..-+.+.
T Consensus 1 LT~~Q~e~L~~A~~~GYf-d~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF-DVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHHHHHHcCCC-CCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 567788899887776332 34788889999999999999887655443
No 129
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=23.66 E-value=73 Score=27.90 Aligned_cols=47 Identities=9% Similarity=0.175 Sum_probs=37.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
+||+..+.++.-.+... .+ -.++|+.+|++...|.++..-.|++.++
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 58888989986655553 22 2479999999999999999999988875
No 130
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=23.59 E-value=91 Score=27.26 Aligned_cols=48 Identities=13% Similarity=0.215 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.--+..+ . .-.++|+.+|++...|.+.....|++.++-
T Consensus 117 ~Lp~~~r~i~~l~~~e~--~------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD--Y------SQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred hCCHHHHHHHHHHHHcc--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 48888888887755553 1 234799999999999999999999988763
No 131
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=23.31 E-value=66 Score=20.70 Aligned_cols=22 Identities=9% Similarity=0.176 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChhhhhhhhhhh
Q 019231 291 KARLVQETGLQLKQINNWFINQ 312 (344)
Q Consensus 291 K~~LA~~tgLs~kQV~nWF~N~ 312 (344)
...||+.+|++...|..|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4488999999999999997654
No 132
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=23.24 E-value=94 Score=30.18 Aligned_cols=50 Identities=16% Similarity=0.213 Sum_probs=39.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANP 321 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~ 321 (344)
.||+..+.++.-.+... .+ -.++|+.+|++...|.+...-.|++.++..+
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 47888888887665553 22 2479999999999999999999999998544
No 133
>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=23.20 E-value=83 Score=29.74 Aligned_cols=48 Identities=15% Similarity=0.270 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.+... .+ -.++|..+|++...|.++....|++.++.
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 58888888887776663 22 34799999999999999999999988764
No 134
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=23.04 E-value=99 Score=27.50 Aligned_cols=53 Identities=9% Similarity=0.077 Sum_probs=41.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCCCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPSSS 324 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s~~ 324 (344)
.||+..+.++.-.+... .+ -.++|+.+|++..-|.++..-.|++.++-...-.
T Consensus 111 ~Lp~~~R~v~~L~~~eg--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~~ 163 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG--LS------YQEAAAVLGIPIGTLMSRIGRARAALRAFEEGTG 163 (182)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 58999999998766652 22 3479999999999999999999999887554433
No 135
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=22.96 E-value=86 Score=27.53 Aligned_cols=48 Identities=15% Similarity=0.065 Sum_probs=38.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.+... .+ -.++|+.+|++...|.++....|++.++.
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 48999999998655543 22 34799999999999999999999988864
No 136
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.96 E-value=61 Score=23.85 Aligned_cols=18 Identities=6% Similarity=0.143 Sum_probs=16.2
Q ss_pred HHHHHHhCCChhhhhhhh
Q 019231 292 ARLVQETGLQLKQINNWF 309 (344)
Q Consensus 292 ~~LA~~tgLs~kQV~nWF 309 (344)
.++|+.+|++..+|..|-
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 137
>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=22.84 E-value=97 Score=28.95 Aligned_cols=48 Identities=8% Similarity=0.076 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.|... + .-.++|+.+|++...|..+....+++.++.
T Consensus 205 ~L~~~~r~ii~l~~~~g----~----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN----L----SQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 58888999987776553 2 225899999999999999999999888753
No 138
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.67 E-value=1e+02 Score=26.26 Aligned_cols=46 Identities=15% Similarity=0.254 Sum_probs=35.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 317 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~k 317 (344)
.||+.++.++.-.+... .+| .++|+.+|++...|.++....+++..
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 48888999886665552 232 47899999999999999998887653
No 139
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=22.61 E-value=78 Score=24.91 Aligned_cols=8 Identities=63% Similarity=1.074 Sum_probs=3.7
Q ss_pred ChHHHHHH
Q 019231 131 DKELDQFM 138 (344)
Q Consensus 131 dpELDqFM 138 (344)
|.|||+||
T Consensus 46 DaELD~Ym 53 (74)
T PF13865_consen 46 DAELDAYM 53 (74)
T ss_pred HHHHHHHH
Confidence 34444444
No 140
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=22.35 E-value=40 Score=29.82 Aligned_cols=49 Identities=8% Similarity=0.073 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.-.|.. .|+ -.++|+.+|++...|.++....|++.++..
T Consensus 139 ~L~~~~r~i~~l~~~~----g~s----~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHG----DLE----LEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehcc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4777777777654433 222 347899999999999999999999988643
No 141
>PF10782 DUF2602: Protein of unknown function (DUF2602); InterPro: IPR019718 This bacterial family of proteins that has no known function.
Probab=22.16 E-value=80 Score=24.27 Aligned_cols=40 Identities=20% Similarity=0.365 Sum_probs=27.3
Q ss_pred hHHHHHHHHHHH---HHHHHHHHHhHHhhhhhHHHHHHHHH---HHHHhhhh
Q 019231 132 KELDQFMTHYVL---LLYSFKEQLQQHVRVHAMEAVMACWD---LEQSLQSL 177 (344)
Q Consensus 132 pELDqFMeaYc~---vL~kykEEL~kP~~~~~~EA~~fc~~---iE~QL~sL 177 (344)
-|+|+.|++||. +-..++.+..+. -|..||.+ |=.||..|
T Consensus 8 ~~I~~L~dtyC~gC~lk~~~rk~~gk~------~ah~fCI~~CtVGkqik~l 53 (58)
T PF10782_consen 8 IEIDDLQDTYCKGCFLKKHFRKEKGKT------YAHSFCINQCTVGKQIKQL 53 (58)
T ss_pred HHHHHHHHHHhcCCchHHHhHHHhccc------ccchHHHHhCcHhHHHHHH
Confidence 478999999998 335667777774 48888863 33444443
No 142
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=21.84 E-value=94 Score=27.94 Aligned_cols=49 Identities=12% Similarity=0.112 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
.||+..+.++.--+... .+ -.++|+.+|++...|.+....+|++.++..
T Consensus 139 ~Lp~~~r~v~~L~~~eg--~s------~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD--FE------IDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48888988887665552 22 247899999999999999999999988643
No 143
>PHA01976 helix-turn-helix protein
Probab=21.57 E-value=72 Score=23.37 Aligned_cols=22 Identities=18% Similarity=0.377 Sum_probs=18.8
Q ss_pred HHHHHHhCCChhhhhhhhhhhh
Q 019231 292 ARLVQETGLQLKQINNWFINQR 313 (344)
Q Consensus 292 ~~LA~~tgLs~kQV~nWF~N~R 313 (344)
..||+.+|++...|.+|....+
T Consensus 19 ~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 19 PELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHhCCCHHHHHHHHcCCC
Confidence 5799999999999999986543
No 144
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.39 E-value=96 Score=27.52 Aligned_cols=51 Identities=18% Similarity=0.060 Sum_probs=40.7
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s 322 (344)
.||+..+.++.-.+... + .-.++|+.+|++...|.....-.|++.++....
T Consensus 111 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~ 161 (182)
T PRK12540 111 KLPQDQREALILVGASG----F----SYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (182)
T ss_pred hCCHHHHHHhhHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 47888989987766553 2 134799999999999999999999999876554
No 145
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=21.24 E-value=80 Score=29.50 Aligned_cols=48 Identities=6% Similarity=0.133 Sum_probs=37.6
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||..++.++.-.|... .+ -.++|+.+|++...|.++....|++.++.
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 22 35799999999999999999999998864
No 146
>PRK04217 hypothetical protein; Provisional
Probab=21.19 E-value=1.6e+02 Score=25.04 Aligned_cols=50 Identities=8% Similarity=-0.053 Sum_probs=39.6
Q ss_pred CCCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccC
Q 019231 263 GKLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHAN 320 (344)
Q Consensus 263 ~~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~ 320 (344)
..|+.+.+.++..++... + .-.++|+.+|++...|.+.+...|++.+...
T Consensus 41 ~~Lt~eereai~l~~~eG----l----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEG----L----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 467888888887776552 2 3457999999999999999999998887643
No 147
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.06 E-value=1e+02 Score=28.04 Aligned_cols=48 Identities=15% Similarity=0.225 Sum_probs=37.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.--+... .+| .++|+.+|++...|.++..-.|++.++.
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 47888888765554442 333 4799999999999999999999998864
No 148
>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=20.71 E-value=1.2e+02 Score=27.00 Aligned_cols=48 Identities=13% Similarity=0.151 Sum_probs=38.9
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHA 319 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~ 319 (344)
.||+..+.++.-.|... . .-.++|+.+|++..-|.+...-.|++.++.
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--F------ESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 58888888887766553 2 235899999999999999999999998764
No 149
>PF13730 HTH_36: Helix-turn-helix domain
Probab=20.62 E-value=2.7e+02 Score=19.50 Aligned_cols=48 Identities=8% Similarity=0.109 Sum_probs=31.4
Q ss_pred CCChhHHHHHHHHHHH--hcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhh
Q 019231 264 KLPGDTTSLLKAWWLS--HAKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 314 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~--H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~ 314 (344)
.|++.++.++-.-+.. .....||+ ...||+.+|++...|..+...-..
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 4566665555332222 22347887 557999999999999988765443
No 150
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=20.52 E-value=1e+02 Score=28.78 Aligned_cols=47 Identities=9% Similarity=0.071 Sum_probs=38.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.++.-.|... + .-..+|..+|++...|.+++...|++.++
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 48888999987766542 2 24689999999999999999999998875
No 151
>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=20.38 E-value=70 Score=24.06 Aligned_cols=23 Identities=13% Similarity=0.199 Sum_probs=19.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhhh
Q 019231 291 KARLVQETGLQLKQINNWFINQR 313 (344)
Q Consensus 291 K~~LA~~tgLs~kQV~nWF~N~R 313 (344)
...||+.+|++...|..|+.+.|
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 35799999999999999997654
No 152
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=20.38 E-value=1.3e+02 Score=27.50 Aligned_cols=47 Identities=11% Similarity=0.158 Sum_probs=38.8
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.+|...|... + .-..+|+.+|++...|..+....+++.++
T Consensus 175 ~L~~~~r~il~l~y~~~----~----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE----L----NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 48999999998877652 2 23689999999999999999999988775
No 153
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=20.21 E-value=1.1e+02 Score=26.81 Aligned_cols=47 Identities=11% Similarity=0.210 Sum_probs=37.1
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.++...|... ++ -.++|..+|++...|.+-....|++.++
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 47888888887666542 22 2479999999999999999999998875
No 154
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=20.08 E-value=1.3e+02 Score=28.77 Aligned_cols=51 Identities=12% Similarity=0.152 Sum_probs=39.3
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccccCCC
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHANPS 322 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk~~~s 322 (344)
.||+.++.++.--+... .+| .++|+.+|++...|.+.+...|++.+...+.
T Consensus 108 ~L~~~~R~v~~L~~~~g--~s~------~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~ 158 (281)
T TIGR02957 108 RLSPLERAVFVLREVFD--YPY------EEIASIVGKSEANCRQLVSRARRHLDARRPR 158 (281)
T ss_pred hCCHHHHHHHHHHHHcC--CCH------HHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 57888888875543331 232 4789999999999999999999999886553
No 155
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=20.08 E-value=1.2e+02 Score=27.60 Aligned_cols=47 Identities=11% Similarity=0.227 Sum_probs=38.5
Q ss_pred CCChhHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 019231 264 KLPGDTTSLLKAWWLSHAKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 318 (344)
Q Consensus 264 ~lpk~~~~iL~~Wf~~H~~~PYPs~~eK~~LA~~tgLs~kQV~nWF~N~R~R~kk 318 (344)
.||+..+.++...|.. .+ .-.++|+.+|++...|..|....+++.++
T Consensus 178 ~L~~~~r~vl~l~y~~----~~----s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFE----DK----TQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhc----CC----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5899999999877654 21 34689999999999999999999988775
Done!