Query psy11818
Match_columns 331
No_of_seqs 152 out of 923
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 19:45:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11818.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11818hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2166|consensus 100.0 1.9E-49 4.2E-54 413.0 24.4 243 15-289 476-722 (725)
2 KOG2167|consensus 100.0 1E-48 2.2E-53 389.1 15.2 242 18-287 410-656 (661)
3 COG5647 Cullin, a subunit of E 100.0 1.8E-46 4E-51 380.1 22.1 259 4-286 483-766 (773)
4 KOG2284|consensus 100.0 3.4E-41 7.3E-46 324.6 14.1 211 48-286 511-721 (728)
5 KOG2285|consensus 100.0 4.3E-30 9.4E-35 249.9 15.5 250 17-289 502-772 (777)
6 PF00888 Cullin: Cullin family 99.9 3.2E-24 7E-29 220.4 13.9 151 17-193 428-588 (588)
7 PF10557 Cullin_Nedd8: Cullin 99.8 1.1E-21 2.4E-26 148.2 3.8 68 221-288 1-68 (68)
8 KOG2165|consensus 99.6 8.3E-15 1.8E-19 149.6 13.7 127 37-192 537-664 (765)
9 smart00182 CULLIN Cullin. 99.3 3.6E-12 7.7E-17 109.1 8.4 75 16-91 62-142 (142)
10 KOG2284|consensus 98.0 4.2E-06 9.1E-11 82.5 4.1 43 286-328 439-481 (728)
11 COG5647 Cullin, a subunit of E 97.9 9E-06 1.9E-10 84.7 4.0 43 287-329 454-496 (773)
12 KOG2166|consensus 97.7 8.7E-05 1.9E-09 79.0 8.0 95 226-328 361-456 (725)
13 KOG2167|consensus 97.4 7.6E-05 1.7E-09 76.4 2.9 41 287-327 346-386 (661)
14 PF00888 Cullin: Cullin family 95.8 0.0097 2.1E-07 61.6 4.6 41 287-327 365-405 (588)
15 PF09339 HTH_IclR: IclR helix- 95.5 0.023 4.9E-07 40.1 4.2 46 126-175 6-52 (52)
16 TIGR01610 phage_O_Nterm phage 95.3 0.072 1.6E-06 42.6 7.0 65 119-193 21-93 (95)
17 PF13412 HTH_24: Winged helix- 95.1 0.057 1.2E-06 37.2 5.0 44 122-165 2-45 (48)
18 KOG2285|consensus 94.8 0.11 2.4E-06 52.5 7.9 45 287-331 438-482 (777)
19 PF02082 Rrf2: Transcriptional 94.8 0.14 3.1E-06 39.5 7.0 60 124-192 11-71 (83)
20 PF12802 MarR_2: MarR family; 94.6 0.064 1.4E-06 38.5 4.4 51 121-175 3-55 (62)
21 PF08220 HTH_DeoR: DeoR-like h 94.2 0.1 2.2E-06 37.7 4.7 46 125-174 2-47 (57)
22 PF13463 HTH_27: Winged helix 94.1 0.13 2.8E-06 37.6 5.3 51 121-175 1-52 (68)
23 PF01047 MarR: MarR family; I 93.4 0.087 1.9E-06 37.6 3.1 50 122-175 2-51 (59)
24 TIGR02337 HpaR homoprotocatech 92.8 0.27 5.8E-06 40.3 5.7 53 119-175 24-76 (118)
25 smart00346 HTH_ICLR helix_turn 92.5 0.41 9E-06 36.9 6.1 56 126-191 8-64 (91)
26 PF12840 HTH_20: Helix-turn-he 92.2 0.29 6.3E-06 35.5 4.5 49 122-174 9-57 (61)
27 smart00550 Zalpha Z-DNA-bindin 91.6 0.42 9.1E-06 35.8 5.0 47 124-174 7-55 (68)
28 PRK15090 DNA-binding transcrip 91.6 0.53 1.1E-05 43.9 6.7 58 124-191 15-72 (257)
29 PRK11512 DNA-binding transcrip 91.5 0.49 1.1E-05 40.1 5.9 53 119-175 36-88 (144)
30 PF13601 HTH_34: Winged helix 91.5 0.24 5.2E-06 38.3 3.6 45 125-173 2-46 (80)
31 PF01022 HTH_5: Bacterial regu 91.1 0.69 1.5E-05 31.8 5.2 40 125-165 4-43 (47)
32 smart00347 HTH_MARR helix_turn 90.5 0.8 1.7E-05 35.3 5.8 52 119-174 6-57 (101)
33 smart00420 HTH_DEOR helix_turn 90.3 0.82 1.8E-05 31.1 5.2 45 126-174 3-47 (53)
34 PF08279 HTH_11: HTH domain; 90.1 0.65 1.4E-05 32.6 4.6 39 127-165 4-43 (55)
35 PF01978 TrmB: Sugar-specific 90.0 0.33 7.3E-06 35.8 3.1 51 121-175 6-56 (68)
36 PF04492 Phage_rep_O: Bacterio 90.0 1.3 2.9E-05 35.8 6.8 62 119-192 28-97 (100)
37 TIGR01889 Staph_reg_Sar staphy 89.4 1 2.2E-05 36.5 5.8 53 119-175 21-77 (109)
38 PF05732 RepL: Firmicute plasm 88.3 1.2 2.5E-05 39.4 5.8 49 137-196 75-123 (165)
39 cd00090 HTH_ARSR Arsenical Res 88.1 1.8 3.8E-05 31.1 5.9 48 122-174 6-53 (78)
40 PRK10163 DNA-binding transcrip 87.8 1.5 3.3E-05 41.3 6.7 50 122-175 24-74 (271)
41 PRK11569 transcriptional repre 87.3 1.6 3.4E-05 41.3 6.4 53 119-175 24-77 (274)
42 COG3355 Predicted transcriptio 87.3 2 4.3E-05 36.4 6.3 39 133-175 38-76 (126)
43 COG1414 IclR Transcriptional r 86.9 1.8 4E-05 40.4 6.5 55 126-190 7-62 (246)
44 PRK10857 DNA-binding transcrip 86.6 2.7 5.8E-05 37.0 7.1 58 125-191 12-70 (164)
45 PRK13777 transcriptional regul 86.5 1.8 4E-05 38.9 6.1 53 119-175 41-93 (185)
46 smart00419 HTH_CRP helix_turn_ 86.3 2.3 5E-05 28.4 5.2 34 137-174 8-41 (48)
47 TIGR02431 pcaR_pcaU beta-ketoa 86.2 2.2 4.7E-05 39.5 6.6 46 125-174 11-57 (248)
48 PRK09834 DNA-binding transcrip 86.1 2 4.3E-05 40.3 6.4 47 125-175 13-60 (263)
49 PRK03573 transcriptional regul 85.9 1.8 3.8E-05 36.6 5.4 53 119-175 27-80 (144)
50 PHA00738 putative HTH transcri 85.3 2.6 5.5E-05 34.7 5.7 67 118-192 7-73 (108)
51 PF09012 FeoC: FeoC like trans 85.2 0.18 4E-06 37.6 -0.9 48 232-287 4-51 (69)
52 PRK11920 rirA iron-responsive 85.2 3.5 7.7E-05 35.7 7.0 56 127-191 14-69 (153)
53 TIGR02010 IscR iron-sulfur clu 84.6 3.8 8.2E-05 34.5 6.8 44 126-173 13-57 (135)
54 PF13730 HTH_36: Helix-turn-he 84.2 2.9 6.2E-05 29.3 5.0 27 139-165 27-53 (55)
55 smart00345 HTH_GNTR helix_turn 84.2 2.7 6E-05 29.2 5.0 40 132-175 14-54 (60)
56 PF08784 RPA_C: Replication pr 84.1 2 4.4E-05 34.3 4.7 46 120-165 44-93 (102)
57 smart00344 HTH_ASNC helix_turn 83.9 1.8 4E-05 34.5 4.4 44 125-172 5-48 (108)
58 TIGR01884 cas_HTH CRISPR locus 83.9 2.4 5.2E-05 38.2 5.6 53 119-175 139-191 (203)
59 cd00092 HTH_CRP helix_turn_hel 83.3 4 8.6E-05 29.3 5.6 36 135-174 23-58 (67)
60 PF08280 HTH_Mga: M protein tr 83.0 1.6 3.6E-05 31.5 3.4 38 125-162 7-44 (59)
61 TIGR02698 CopY_TcrY copper tra 82.8 9.9 0.00022 32.0 8.6 76 230-309 6-86 (130)
62 PRK10870 transcriptional repre 82.6 4 8.6E-05 36.1 6.4 53 119-175 51-105 (176)
63 TIGR00738 rrf2_super rrf2 fami 82.4 4.3 9.2E-05 33.6 6.2 46 125-174 12-58 (132)
64 smart00418 HTH_ARSR helix_turn 80.9 4.4 9.4E-05 28.1 5.0 36 135-174 8-43 (66)
65 PF05584 Sulfolobus_pRN: Sulfo 80.8 5.2 0.00011 30.6 5.5 34 137-174 18-51 (72)
66 PRK04172 pheS phenylalanyl-tRN 80.7 25 0.00055 36.2 12.4 50 120-173 3-52 (489)
67 TIGR02944 suf_reg_Xantho FeS a 80.3 5.3 0.00011 33.2 6.0 37 134-174 22-58 (130)
68 PF08221 HTH_9: RNA polymerase 80.0 2.9 6.3E-05 30.7 3.8 32 134-165 24-55 (62)
69 COG1846 MarR Transcriptional r 79.8 4.7 0.0001 31.9 5.4 51 121-175 20-70 (126)
70 PRK10141 DNA-binding transcrip 79.4 5.7 0.00012 33.1 5.9 60 123-190 16-75 (117)
71 PF04703 FaeA: FaeA-like prote 78.9 3.1 6.7E-05 30.8 3.7 44 128-175 5-49 (62)
72 PF13404 HTH_AsnC-type: AsnC-t 77.5 4 8.6E-05 27.7 3.6 35 127-161 7-41 (42)
73 PF11994 DUF3489: Protein of u 77.1 11 0.00025 28.8 6.3 51 121-171 8-58 (72)
74 PF01325 Fe_dep_repress: Iron 76.4 7.6 0.00016 28.3 5.1 45 127-175 12-56 (60)
75 PF09012 FeoC: FeoC like trans 76.0 3.9 8.4E-05 30.4 3.6 37 129-165 6-42 (69)
76 COG2345 Predicted transcriptio 75.6 5.1 0.00011 37.1 4.9 44 126-173 14-57 (218)
77 TIGR03879 near_KaiC_dom probab 75.3 2.5 5.4E-05 32.4 2.4 33 133-165 28-60 (73)
78 PRK10434 srlR DNA-bindng trans 74.8 4.9 0.00011 37.7 4.8 47 124-174 6-52 (256)
79 PRK11014 transcriptional repre 74.6 12 0.00026 31.7 6.7 40 132-175 20-59 (141)
80 COG3682 Predicted transcriptio 74.5 6.9 0.00015 33.0 5.0 78 228-309 6-97 (123)
81 PF02002 TFIIE_alpha: TFIIE al 74.0 3.4 7.5E-05 33.2 3.1 45 125-173 15-59 (105)
82 COG1959 Predicted transcriptio 73.2 12 0.00026 32.4 6.4 58 125-191 12-70 (150)
83 PRK11169 leucine-responsive tr 73.2 6.8 0.00015 34.1 5.0 49 120-172 11-59 (164)
84 PRK13509 transcriptional repre 72.6 8 0.00017 36.1 5.6 48 124-175 6-53 (251)
85 cd07377 WHTH_GntR Winged helix 72.5 9.3 0.0002 27.0 4.8 37 134-174 21-58 (66)
86 TIGR02702 SufR_cyano iron-sulf 72.2 12 0.00027 33.6 6.6 44 127-174 5-48 (203)
87 PF05158 RNA_pol_Rpc34: RNA po 72.0 6.6 0.00014 38.4 5.1 149 119-286 80-260 (327)
88 PRK11179 DNA-binding transcrip 71.6 8.2 0.00018 33.1 5.1 49 120-172 6-54 (153)
89 PF04545 Sigma70_r4: Sigma-70, 71.6 11 0.00025 25.7 4.9 35 125-161 10-44 (50)
90 PF01726 LexA_DNA_bind: LexA D 70.8 8.1 0.00018 28.7 4.2 51 121-175 4-60 (65)
91 COG1349 GlpR Transcriptional r 70.2 7.9 0.00017 36.3 5.0 47 124-174 6-52 (253)
92 PRK06266 transcription initiat 70.1 8.4 0.00018 34.4 4.9 45 125-173 24-68 (178)
93 TIGR00373 conserved hypothetic 68.7 12 0.00026 32.7 5.5 44 126-173 17-60 (158)
94 PRK00215 LexA repressor; Valid 68.1 15 0.00031 32.9 6.1 51 121-175 2-58 (205)
95 PF10771 DUF2582: Protein of u 67.4 12 0.00026 28.0 4.4 39 127-165 12-50 (65)
96 PRK10906 DNA-binding transcrip 67.4 10 0.00022 35.5 5.1 48 124-175 6-53 (252)
97 COG1522 Lrp Transcriptional re 66.5 10 0.00022 31.9 4.6 49 121-173 6-54 (154)
98 PRK09802 DNA-binding transcrip 65.9 11 0.00024 35.7 5.1 50 122-175 16-65 (269)
99 PRK10411 DNA-binding transcrip 65.8 13 0.00028 34.6 5.4 47 124-174 5-51 (240)
100 COG4189 Predicted transcriptio 65.5 12 0.00025 35.2 4.9 51 120-174 20-70 (308)
101 PF03965 Penicillinase_R: Peni 65.4 25 0.00055 28.5 6.5 74 230-307 5-83 (115)
102 PRK04424 fatty acid biosynthes 65.0 6.3 0.00014 35.2 3.1 47 123-173 7-53 (185)
103 PF00325 Crp: Bacterial regula 64.0 12 0.00026 24.0 3.4 28 138-165 3-30 (32)
104 smart00421 HTH_LUXR helix_turn 63.9 17 0.00037 24.5 4.6 39 122-162 5-43 (58)
105 cd06170 LuxR_C_like C-terminal 63.4 18 0.00038 24.5 4.6 37 124-162 4-40 (57)
106 PF14394 DUF4423: Domain of un 62.9 27 0.00058 30.9 6.7 56 116-175 17-75 (171)
107 PF01638 HxlR: HxlR-like helix 62.0 18 0.0004 28.1 4.9 44 126-174 8-52 (90)
108 PF02796 HTH_7: Helix-turn-hel 61.4 14 0.0003 25.1 3.6 31 127-159 13-43 (45)
109 PF01853 MOZ_SAS: MOZ/SAS fami 61.2 7.5 0.00016 35.1 2.8 26 136-161 149-174 (188)
110 TIGR02844 spore_III_D sporulat 59.7 15 0.00032 28.6 3.9 35 124-159 7-41 (80)
111 PF08220 HTH_DeoR: DeoR-like h 59.2 9.1 0.0002 27.4 2.5 47 231-285 3-49 (57)
112 PF08281 Sigma70_r4_2: Sigma-7 59.1 22 0.00048 24.5 4.4 24 136-159 25-48 (54)
113 PRK10430 DNA-binding transcrip 58.6 33 0.00072 31.0 6.7 48 121-172 159-209 (239)
114 PF01399 PCI: PCI domain; Int 58.4 19 0.00042 27.7 4.5 43 123-165 46-88 (105)
115 PF14947 HTH_45: Winged helix- 58.0 41 0.00088 25.5 6.1 43 126-173 9-51 (77)
116 smart00420 HTH_DEOR helix_turn 58.0 14 0.00031 24.6 3.3 45 232-284 4-48 (53)
117 COG1654 BirA Biotin operon rep 57.4 39 0.00085 26.2 5.9 41 130-172 12-52 (79)
118 smart00344 HTH_ASNC helix_turn 57.3 16 0.00034 29.0 3.8 47 229-283 4-50 (108)
119 PF06163 DUF977: Bacterial pro 56.4 30 0.00065 29.3 5.4 44 122-165 11-54 (127)
120 TIGR00498 lexA SOS regulatory 56.3 15 0.00034 32.6 4.0 51 121-175 4-60 (199)
121 KOG2747|consensus 56.1 15 0.00033 36.8 4.2 25 138-162 330-354 (396)
122 PF01726 LexA_DNA_bind: LexA D 55.7 22 0.00048 26.4 4.1 57 223-286 5-62 (65)
123 PF13545 HTH_Crp_2: Crp-like h 55.2 35 0.00077 25.0 5.3 34 137-174 28-61 (76)
124 PF06784 UPF0240: Uncharacteri 55.2 18 0.0004 32.3 4.3 45 120-164 117-163 (179)
125 PRK10681 DNA-binding transcrip 55.0 19 0.00041 33.6 4.6 39 124-162 8-46 (252)
126 PF00392 GntR: Bacterial regul 54.5 22 0.00048 25.6 4.0 38 134-175 20-58 (64)
127 PF00165 HTH_AraC: Bacterial r 54.4 17 0.00037 23.9 3.1 28 135-162 6-33 (42)
128 PRK11050 manganese transport r 53.6 37 0.00079 29.2 5.8 44 127-174 41-84 (152)
129 PRK03902 manganese transport t 53.3 32 0.00069 29.0 5.3 44 126-173 11-54 (142)
130 smart00753 PAM PCI/PINT associ 52.4 33 0.00073 26.0 4.9 32 134-165 21-52 (88)
131 smart00088 PINT motif in prote 52.4 33 0.00073 26.0 4.9 32 134-165 21-52 (88)
132 smart00550 Zalpha Z-DNA-bindin 51.7 21 0.00045 26.5 3.4 51 229-287 7-59 (68)
133 PF04967 HTH_10: HTH DNA bindi 50.9 46 0.00099 23.8 4.9 29 132-160 18-46 (53)
134 PLN03238 probable histone acet 49.3 27 0.00059 33.6 4.6 36 126-161 211-247 (290)
135 COG4565 CitB Response regulato 49.1 32 0.00069 31.9 4.8 51 119-173 155-205 (224)
136 PF09904 HTH_43: Winged helix- 49.0 45 0.00097 26.6 5.0 37 128-165 13-49 (90)
137 PHA02943 hypothetical protein; 48.9 44 0.00096 29.4 5.4 38 127-165 15-52 (165)
138 TIGR00122 birA_repr_reg BirA b 48.2 80 0.0017 23.0 6.2 29 137-165 13-41 (69)
139 PF13384 HTH_23: Homeodomain-l 47.9 17 0.00038 24.6 2.4 35 128-164 10-44 (50)
140 PF09681 Phage_rep_org_N: N-te 47.8 34 0.00075 28.6 4.5 51 120-174 26-86 (121)
141 cd07153 Fur_like Ferric uptake 47.5 23 0.00049 28.5 3.4 51 232-285 5-56 (116)
142 PF13542 HTH_Tnp_ISL3: Helix-t 47.5 46 0.001 22.6 4.5 41 118-161 11-51 (52)
143 smart00346 HTH_ICLR helix_turn 46.7 41 0.0009 25.5 4.6 54 233-294 10-65 (91)
144 cd07153 Fur_like Ferric uptake 46.7 59 0.0013 26.0 5.7 58 126-190 4-67 (116)
145 PF12324 HTH_15: Helix-turn-he 46.0 51 0.0011 25.6 4.8 39 124-162 25-63 (77)
146 PRK06474 hypothetical protein; 45.4 57 0.0012 28.9 5.8 53 118-174 6-60 (178)
147 PF01978 TrmB: Sugar-specific 44.7 9.9 0.00022 27.8 0.7 53 229-289 9-61 (68)
148 COG4742 Predicted transcriptio 44.2 45 0.00097 31.7 5.2 43 127-174 17-59 (260)
149 PRK14165 winged helix-turn-hel 43.8 53 0.0011 30.3 5.5 46 125-174 9-54 (217)
150 cd06171 Sigma70_r4 Sigma70, re 43.4 51 0.0011 21.4 4.2 39 122-161 12-50 (55)
151 PF00196 GerE: Bacterial regul 43.3 50 0.0011 23.2 4.3 40 122-163 5-44 (58)
152 PF04182 B-block_TFIIIC: B-blo 43.1 54 0.0012 24.7 4.6 48 123-174 2-51 (75)
153 PF02270 TFIIF_beta: Transcrip 43.1 46 0.001 31.6 5.2 59 122-192 215-273 (275)
154 TIGR02698 CopY_TcrY copper tra 42.6 83 0.0018 26.3 6.2 50 121-174 2-55 (130)
155 PHA02591 hypothetical protein; 42.4 29 0.00062 27.1 2.9 25 136-160 58-82 (83)
156 PLN00104 MYST -like histone ac 42.3 37 0.00081 34.7 4.6 30 132-161 369-398 (450)
157 COG4190 Predicted transcriptio 42.2 86 0.0019 26.9 6.0 63 127-193 68-133 (144)
158 COG1522 Lrp Transcriptional re 41.8 28 0.00062 29.2 3.2 51 227-285 7-57 (154)
159 smart00531 TFIIE Transcription 41.6 35 0.00077 29.2 3.8 31 135-165 13-43 (147)
160 PF08784 RPA_C: Replication pr 41.4 22 0.00047 28.2 2.3 48 226-281 45-96 (102)
161 PF09107 SelB-wing_3: Elongati 40.9 79 0.0017 22.3 4.8 42 129-174 2-43 (50)
162 COG1733 Predicted transcriptio 40.5 1.2E+02 0.0025 25.3 6.6 44 126-174 26-70 (120)
163 TIGR02716 C20_methyl_CrtF C-20 39.8 49 0.0011 31.4 4.9 36 135-174 21-56 (306)
164 PRK04214 rbn ribonuclease BN/u 39.8 97 0.0021 31.1 7.2 39 132-174 305-343 (412)
165 PF10007 DUF2250: Uncharacteri 39.1 76 0.0016 25.3 5.0 53 119-175 3-55 (92)
166 PF04760 IF2_N: Translation in 39.1 20 0.00044 25.1 1.6 22 137-158 3-24 (54)
167 PF03444 HrcA_DNA-bdg: Winged 38.9 97 0.0021 24.1 5.4 47 123-173 9-55 (78)
168 PF14493 HTH_40: Helix-turn-he 38.9 70 0.0015 24.8 4.8 36 128-165 6-41 (91)
169 PRK09647 RNA polymerase sigma 38.7 47 0.001 29.7 4.3 25 135-159 152-176 (203)
170 PF13551 HTH_29: Winged helix- 38.3 70 0.0015 24.9 4.9 38 127-165 3-40 (112)
171 TIGR01714 phage_rep_org_N phag 38.2 53 0.0012 27.5 4.2 50 121-174 27-84 (119)
172 PRK08301 sporulation sigma fac 38.2 59 0.0013 29.5 5.0 25 134-158 195-219 (234)
173 COG0735 Fur Fe2+/Zn2+ uptake r 37.9 66 0.0014 27.5 4.9 52 119-174 17-74 (145)
174 COG1510 Predicted transcriptio 37.2 30 0.00066 30.9 2.7 41 124-165 29-69 (177)
175 smart00347 HTH_MARR helix_turn 37.0 43 0.00093 25.3 3.3 49 229-285 11-59 (101)
176 PF02631 RecX: RecX family; I 36.5 82 0.0018 25.6 5.1 52 263-331 7-58 (121)
177 PRK13239 alkylmercury lyase; P 36.5 67 0.0015 29.5 4.9 40 123-162 22-61 (206)
178 PRK10046 dpiA two-component re 36.4 67 0.0015 28.7 5.0 39 127-165 166-205 (225)
179 PRK11179 DNA-binding transcrip 35.3 51 0.0011 28.1 3.8 48 228-283 9-56 (153)
180 smart00345 HTH_GNTR helix_turn 34.7 17 0.00038 24.9 0.7 31 255-285 25-55 (60)
181 TIGR00721 tfx DNA-binding prot 34.6 76 0.0016 27.2 4.7 40 120-161 6-45 (137)
182 TIGR02835 spore_sigmaE RNA pol 34.2 74 0.0016 29.0 4.9 24 135-158 196-219 (234)
183 COG1321 TroR Mn-dependent tran 34.1 89 0.0019 27.2 5.1 46 126-175 13-58 (154)
184 PRK09954 putative kinase; Prov 34.1 57 0.0012 31.6 4.4 39 127-165 7-45 (362)
185 PRK11169 leucine-responsive tr 33.7 56 0.0012 28.3 3.9 47 228-282 14-60 (164)
186 PF04539 Sigma70_r3: Sigma-70 33.4 41 0.00088 25.0 2.6 26 136-161 19-44 (78)
187 PRK09047 RNA polymerase factor 33.1 65 0.0014 26.9 4.1 24 136-159 121-144 (161)
188 PF08766 DEK_C: DEK C terminal 33.0 1.2E+02 0.0025 21.3 4.8 47 227-277 3-51 (54)
189 PF07106 TBPIP: Tat binding pr 33.0 1.1E+02 0.0023 26.7 5.5 59 125-191 3-64 (169)
190 PF14394 DUF4423: Domain of un 32.9 49 0.0011 29.2 3.4 47 261-307 52-109 (171)
191 TIGR02989 Sig-70_gvs1 RNA poly 32.9 64 0.0014 26.9 4.0 37 121-159 112-149 (159)
192 PRK12525 RNA polymerase sigma 32.9 75 0.0016 27.1 4.5 25 135-159 132-156 (168)
193 PLN03239 histone acetyltransfe 32.8 66 0.0014 31.9 4.5 26 136-161 283-308 (351)
194 PRK12522 RNA polymerase sigma 32.7 69 0.0015 27.4 4.3 24 136-159 134-157 (173)
195 PHA03103 double-strand RNA-bin 32.5 95 0.002 28.0 5.1 39 127-165 17-55 (183)
196 TIGR02983 SigE-fam_strep RNA p 32.4 60 0.0013 27.2 3.8 27 135-161 124-150 (162)
197 TIGR02392 rpoH_proteo alternat 32.3 82 0.0018 29.5 5.0 34 125-158 223-257 (270)
198 PF00356 LacI: Bacterial regul 32.3 46 0.00099 23.0 2.4 21 139-159 1-21 (46)
199 PF10668 Phage_terminase: Phag 31.9 61 0.0013 23.9 3.1 25 132-156 17-41 (60)
200 PF07638 Sigma70_ECF: ECF sigm 31.3 56 0.0012 28.7 3.5 26 136-161 150-175 (185)
201 PRK06759 RNA polymerase factor 31.2 83 0.0018 26.1 4.4 25 136-160 121-145 (154)
202 TIGR02394 rpoS_proteo RNA poly 31.1 78 0.0017 29.9 4.7 27 133-159 238-264 (285)
203 PRK11886 bifunctional biotin-- 31.1 1.5E+02 0.0032 28.5 6.6 39 127-165 8-46 (319)
204 PF13936 HTH_38: Helix-turn-he 30.9 87 0.0019 21.0 3.7 24 136-159 19-42 (44)
205 PRK12514 RNA polymerase sigma 30.9 62 0.0013 27.8 3.7 24 136-159 144-167 (179)
206 PRK11534 DNA-binding transcrip 30.9 92 0.002 27.9 5.0 41 131-175 24-64 (224)
207 PRK12529 RNA polymerase sigma 30.7 59 0.0013 28.1 3.5 24 136-159 142-165 (178)
208 PF13518 HTH_28: Helix-turn-he 30.4 1.4E+02 0.003 19.9 4.7 27 139-165 14-40 (52)
209 PRK11753 DNA-binding transcrip 30.2 1.2E+02 0.0025 26.6 5.4 34 137-174 168-201 (211)
210 KOG2593|consensus 29.7 75 0.0016 32.3 4.4 66 121-190 27-98 (436)
211 TIGR03338 phnR_burk phosphonat 29.6 89 0.0019 27.7 4.6 40 132-175 29-68 (212)
212 KOG2905|consensus 29.6 78 0.0017 29.8 4.2 58 124-193 187-244 (254)
213 PRK03975 tfx putative transcri 29.5 94 0.002 26.8 4.4 38 120-159 6-43 (141)
214 TIGR02404 trehalos_R_Bsub treh 29.3 20 0.00044 32.5 0.4 37 255-291 29-66 (233)
215 TIGR02997 Sig70-cyanoRpoD RNA 29.3 89 0.0019 29.8 4.8 27 133-159 265-291 (298)
216 TIGR02147 Fsuc_second hypothet 29.2 1.7E+02 0.0038 27.8 6.6 55 117-175 116-173 (271)
217 PRK12520 RNA polymerase sigma 28.7 85 0.0019 27.3 4.2 24 136-159 146-169 (191)
218 TIGR02787 codY_Gpos GTP-sensin 28.7 1.2E+02 0.0025 28.7 5.2 44 128-175 188-232 (251)
219 TIGR02859 spore_sigH RNA polym 28.5 95 0.0021 26.9 4.5 27 135-161 163-189 (198)
220 smart00342 HTH_ARAC helix_turn 28.5 83 0.0018 22.6 3.6 25 138-162 2-26 (84)
221 PRK07037 extracytoplasmic-func 28.4 99 0.0021 25.9 4.5 24 136-159 124-147 (163)
222 COG3413 Predicted DNA binding 28.4 1E+02 0.0023 27.8 4.9 40 120-159 155-200 (215)
223 TIGR02999 Sig-70_X6 RNA polyme 28.3 62 0.0014 27.8 3.3 24 136-159 149-172 (183)
224 TIGR01764 excise DNA binding d 28.3 76 0.0016 20.6 3.0 21 138-158 2-22 (49)
225 COG2771 CsgD DNA-binding HTH d 28.2 1.7E+02 0.0036 20.2 5.0 41 120-162 4-44 (65)
226 PRK10079 phosphonate metabolis 28.2 40 0.00087 30.8 2.1 50 226-282 18-67 (241)
227 PF01418 HTH_6: Helix-turn-hel 28.1 55 0.0012 24.6 2.5 31 132-162 29-59 (77)
228 PRK09639 RNA polymerase sigma 27.9 1E+02 0.0023 25.8 4.5 24 136-159 126-149 (166)
229 PRK09642 RNA polymerase sigma 27.7 64 0.0014 27.1 3.1 24 136-159 121-144 (160)
230 TIGR02393 RpoD_Cterm RNA polym 27.6 1E+02 0.0022 28.1 4.7 38 122-159 178-218 (238)
231 PRK12527 RNA polymerase sigma 27.2 90 0.0019 26.2 4.0 24 135-158 119-142 (159)
232 PRK11414 colanic acid/biofilm 27.2 1E+02 0.0023 27.6 4.6 42 130-175 27-68 (221)
233 PRK08295 RNA polymerase factor 27.2 83 0.0018 27.6 3.9 37 121-159 156-192 (208)
234 PRK10906 DNA-binding transcrip 27.2 45 0.00098 31.2 2.3 46 230-283 7-52 (252)
235 PRK12534 RNA polymerase sigma 27.1 95 0.0021 26.8 4.2 26 135-160 151-176 (187)
236 PRK12547 RNA polymerase sigma 26.9 96 0.0021 26.3 4.1 25 136-160 127-151 (164)
237 COG3398 Uncharacterized protei 26.9 1.3E+02 0.0029 28.1 5.1 58 127-192 178-235 (240)
238 TIGR02325 C_P_lyase_phnF phosp 26.9 40 0.00086 30.5 1.8 37 256-292 38-75 (238)
239 smart00529 HTH_DTXR Helix-turn 26.8 1E+02 0.0022 23.6 3.9 32 140-175 2-33 (96)
240 PF14502 HTH_41: Helix-turn-he 26.8 1.3E+02 0.0027 21.3 3.8 28 138-165 7-34 (48)
241 PF05043 Mga: Mga helix-turn-h 26.8 77 0.0017 24.1 3.2 29 134-162 27-55 (87)
242 PRK12536 RNA polymerase sigma 26.7 87 0.0019 27.1 3.9 26 135-160 143-168 (181)
243 COG1378 Predicted transcriptio 26.6 1.1E+02 0.0024 28.6 4.8 47 119-165 12-58 (247)
244 PF09114 MotA_activ: Transcrip 26.5 1.4E+02 0.0031 23.9 4.6 45 127-175 20-66 (96)
245 PRK04984 fatty acid metabolism 26.4 1.2E+02 0.0025 27.5 4.8 40 132-175 25-65 (239)
246 COG2996 Predicted RNA-bindinin 26.4 86 0.0019 30.1 3.9 51 115-165 218-274 (287)
247 PRK12423 LexA repressor; Provi 26.2 1.3E+02 0.0029 26.9 5.1 51 122-176 5-61 (202)
248 cd00569 HTH_Hin_like Helix-tur 26.1 1.3E+02 0.0027 17.2 3.6 30 125-156 11-40 (42)
249 PRK12530 RNA polymerase sigma 26.0 1.1E+02 0.0024 26.8 4.4 24 136-159 149-172 (189)
250 PRK05803 sporulation sigma fac 26.0 1.2E+02 0.0025 27.6 4.7 24 135-158 193-216 (233)
251 PRK09646 RNA polymerase sigma 25.9 1E+02 0.0022 27.0 4.2 24 136-159 157-180 (194)
252 TIGR03697 NtcA_cyano global ni 25.9 1.7E+02 0.0036 25.1 5.6 34 137-174 143-176 (193)
253 PF11784 DUF3320: Protein of u 25.9 1.2E+02 0.0026 21.3 3.8 35 223-257 7-41 (52)
254 PF05225 HTH_psq: helix-turn-h 25.8 1.7E+02 0.0038 19.8 4.4 35 124-160 5-39 (45)
255 PRK12543 RNA polymerase sigma 25.7 71 0.0015 27.6 3.1 23 136-158 132-154 (179)
256 PRK04217 hypothetical protein; 25.7 95 0.0021 25.6 3.6 40 120-160 42-81 (110)
257 PF01475 FUR: Ferric uptake re 25.6 97 0.0021 25.0 3.8 65 119-190 4-74 (120)
258 PRK11402 DNA-binding transcrip 25.6 26 0.00057 32.0 0.4 29 254-282 37-65 (241)
259 cd04762 HTH_MerR-trunc Helix-T 25.6 90 0.002 20.1 3.0 20 138-157 1-20 (49)
260 PF12728 HTH_17: Helix-turn-he 25.6 87 0.0019 21.2 3.0 20 138-157 2-21 (51)
261 TIGR03209 P21_Cbot clostridium 25.5 65 0.0014 26.5 2.7 20 136-155 122-141 (142)
262 PRK09649 RNA polymerase sigma 25.5 1.1E+02 0.0023 26.7 4.3 24 136-159 145-168 (185)
263 COG1802 GntR Transcriptional r 25.4 1.1E+02 0.0023 27.8 4.3 44 128-175 30-73 (230)
264 PRK09651 RNA polymerase sigma 25.4 87 0.0019 26.9 3.6 25 135-159 133-157 (172)
265 PRK00117 recX recombination re 25.3 2.2E+02 0.0048 24.2 6.1 33 261-302 39-71 (157)
266 PRK09462 fur ferric uptake reg 25.1 1.6E+02 0.0035 24.9 5.2 52 119-174 13-71 (148)
267 PRK14999 histidine utilization 24.9 1.1E+02 0.0024 27.9 4.4 38 134-175 32-70 (241)
268 COG2378 Predicted transcriptio 24.8 2E+02 0.0044 27.7 6.4 61 125-193 10-70 (311)
269 PRK11161 fumarate/nitrate redu 24.7 1.6E+02 0.0034 26.3 5.4 34 137-174 184-217 (235)
270 PHA02701 ORF020 dsRNA-binding 24.7 1.6E+02 0.0035 26.6 5.2 40 126-165 7-47 (183)
271 PRK12524 RNA polymerase sigma 24.7 1.2E+02 0.0025 26.7 4.4 24 136-159 151-174 (196)
272 PRK12531 RNA polymerase sigma 24.7 1.2E+02 0.0026 26.5 4.4 25 136-160 156-180 (194)
273 TIGR03001 Sig-70_gmx1 RNA poly 24.7 1.1E+02 0.0025 28.3 4.5 24 136-159 176-199 (244)
274 TIGR02950 SigM_subfam RNA poly 24.7 80 0.0017 26.1 3.2 25 136-160 120-144 (154)
275 PF00538 Linker_histone: linke 24.6 66 0.0014 24.3 2.4 56 228-284 8-65 (77)
276 PRK12537 RNA polymerase sigma 24.6 87 0.0019 27.1 3.5 25 135-159 147-171 (182)
277 PRK05949 RNA polymerase sigma 24.4 1.2E+02 0.0026 29.6 4.7 38 121-158 267-307 (327)
278 TIGR03433 padR_acidobact trans 24.4 1E+02 0.0022 24.4 3.6 54 229-283 5-58 (100)
279 KOG1466|consensus 24.3 96 0.0021 29.8 3.8 70 262-331 90-183 (313)
280 PRK12528 RNA polymerase sigma 24.3 1.3E+02 0.0028 25.2 4.5 24 136-159 128-151 (161)
281 PRK12539 RNA polymerase sigma 24.3 1.2E+02 0.0025 26.3 4.3 24 136-159 146-169 (184)
282 PRK09415 RNA polymerase factor 24.2 1.1E+02 0.0025 26.3 4.2 24 136-159 142-165 (179)
283 PRK13919 putative RNA polymera 24.1 1.1E+02 0.0024 26.3 4.1 25 135-159 149-173 (186)
284 PRK07500 rpoH2 RNA polymerase 24.1 1.2E+02 0.0027 28.7 4.7 39 121-159 228-267 (289)
285 PF03849 Tfb2: Transcription f 24.0 1.1E+02 0.0025 30.3 4.6 45 115-159 306-361 (366)
286 PRK06986 fliA flagellar biosyn 23.9 1.2E+02 0.0026 27.6 4.4 25 135-159 198-222 (236)
287 PRK09464 pdhR transcriptional 23.9 1.3E+02 0.0028 27.5 4.7 40 132-175 28-68 (254)
288 PRK12545 RNA polymerase sigma 23.8 1.2E+02 0.0026 26.8 4.4 24 135-158 153-176 (201)
289 PRK07405 RNA polymerase sigma 23.8 1.3E+02 0.0027 29.2 4.7 32 127-158 264-297 (317)
290 PRK13918 CRP/FNR family transc 23.8 1.7E+02 0.0036 25.4 5.2 33 137-173 149-181 (202)
291 TIGR02939 RpoE_Sigma70 RNA pol 23.7 1E+02 0.0022 26.5 3.7 24 136-159 153-176 (190)
292 COG2512 Predicted membrane-ass 23.6 1.4E+02 0.0031 28.2 4.9 49 123-175 196-244 (258)
293 PRK10402 DNA-binding transcrip 23.4 2.3E+02 0.0049 25.4 6.1 34 137-174 169-202 (226)
294 PRK12541 RNA polymerase sigma 23.0 1.1E+02 0.0024 25.7 3.8 24 136-159 127-150 (161)
295 PRK00118 putative DNA-binding 23.0 97 0.0021 25.3 3.2 25 136-160 32-56 (104)
296 TIGR02846 spore_sigmaK RNA pol 22.8 1.5E+02 0.0032 26.8 4.8 24 135-158 192-215 (227)
297 PRK12523 RNA polymerase sigma 22.8 91 0.002 26.6 3.2 24 136-159 134-157 (172)
298 PRK09645 RNA polymerase sigma 22.7 89 0.0019 26.5 3.2 23 136-158 133-155 (173)
299 PRK12518 RNA polymerase sigma 22.7 88 0.0019 26.6 3.1 24 136-159 135-158 (175)
300 PTZ00064 histone acetyltransfe 22.7 80 0.0017 32.9 3.2 41 138-191 472-512 (552)
301 PRK05602 RNA polymerase sigma 22.7 1.3E+02 0.0028 26.0 4.2 24 136-159 143-166 (186)
302 PRK12540 RNA polymerase sigma 22.7 1.3E+02 0.0029 26.2 4.3 24 136-159 126-149 (182)
303 PRK08558 adenine phosphoribosy 22.5 73 0.0016 29.6 2.7 25 135-159 21-45 (238)
304 PF03428 RP-C: Replication pro 22.5 1.3E+02 0.0028 26.8 4.2 32 139-174 72-104 (177)
305 PTZ00326 phenylalanyl-tRNA syn 22.5 1.9E+02 0.0041 30.1 5.9 44 122-165 5-49 (494)
306 TIGR02404 trehalos_R_Bsub treh 22.4 1.2E+02 0.0025 27.5 4.0 34 138-175 25-58 (233)
307 TIGR02947 SigH_actino RNA poly 22.3 91 0.002 27.2 3.2 25 135-159 145-169 (193)
308 PRK12533 RNA polymerase sigma 22.3 1.1E+02 0.0024 27.7 3.9 24 136-159 149-172 (216)
309 PRK09483 response regulator; P 22.2 1.7E+02 0.0037 25.0 5.0 42 120-163 148-189 (217)
310 PRK09652 RNA polymerase sigma 22.2 1.4E+02 0.0031 25.0 4.4 24 136-159 143-166 (182)
311 PRK00135 scpB segregation and 22.2 1.3E+02 0.0028 27.1 4.2 34 130-163 12-46 (188)
312 PF04157 EAP30: EAP30/Vps36 fa 22.2 1.5E+02 0.0034 27.0 4.8 44 122-165 173-218 (223)
313 TIGR02943 Sig70_famx1 RNA poly 22.2 1.3E+02 0.0029 26.2 4.3 24 136-159 146-169 (188)
314 TIGR02325 C_P_lyase_phnF phosp 22.1 1.2E+02 0.0025 27.4 4.0 37 135-175 29-66 (238)
315 TIGR02952 Sig70_famx2 RNA poly 22.1 1.3E+02 0.0027 25.3 4.0 25 136-160 137-161 (170)
316 PF04801 Sin_N: Sin-like prote 22.1 1.1E+02 0.0024 30.7 4.2 37 127-163 341-377 (421)
317 PF12395 DUF3658: Protein of u 21.9 1.3E+02 0.0028 24.5 3.7 60 228-290 48-107 (111)
318 KOG3471|consensus 21.9 2E+02 0.0043 29.3 5.6 49 115-163 315-374 (465)
319 TIGR03882 cyclo_dehyd_2 bacter 21.7 99 0.0021 27.7 3.3 47 230-284 32-78 (193)
320 TIGR02985 Sig70_bacteroi1 RNA 21.7 1E+02 0.0022 25.4 3.2 25 136-160 128-152 (161)
321 PRK06704 RNA polymerase factor 21.6 1.2E+02 0.0025 28.1 3.9 24 136-159 131-154 (228)
322 COG1595 RpoE DNA-directed RNA 21.6 99 0.0021 26.8 3.3 25 135-159 141-165 (182)
323 PF08221 HTH_9: RNA polymerase 21.6 1.8E+02 0.004 21.1 4.2 52 222-281 7-58 (62)
324 cd04761 HTH_MerR-SF Helix-Turn 21.6 1.2E+02 0.0025 20.0 2.9 24 138-165 1-24 (49)
325 COG2197 CitB Response regulato 21.6 1.7E+02 0.0037 26.3 4.9 42 120-163 148-189 (211)
326 TIGR00625 tfb2 Transcription f 21.5 1.7E+02 0.0037 30.1 5.2 60 82-164 291-361 (448)
327 PLN02853 Probable phenylalanyl 21.5 1.9E+02 0.0041 30.1 5.6 42 124-165 4-46 (492)
328 COG4519 Uncharacterized protei 21.5 1.7E+02 0.0036 23.1 4.0 38 128-165 13-50 (95)
329 PRK03837 transcriptional regul 21.5 1.7E+02 0.0038 26.3 5.0 39 133-175 32-71 (241)
330 TIGR01889 Staph_reg_Sar staphy 21.4 51 0.0011 26.4 1.3 39 239-285 40-78 (109)
331 TIGR02954 Sig70_famx3 RNA poly 21.4 1.5E+02 0.0032 25.1 4.3 24 136-159 134-157 (169)
332 PRK06811 RNA polymerase factor 21.3 1.3E+02 0.0029 26.1 4.0 23 136-158 146-168 (189)
333 PF12793 SgrR_N: Sugar transpo 21.3 1.5E+02 0.0032 24.5 4.0 36 136-175 18-53 (115)
334 smart00342 HTH_ARAC helix_turn 21.2 2.7E+02 0.0057 19.8 5.1 26 137-162 50-76 (84)
335 PRK10225 DNA-binding transcrip 21.2 1.8E+02 0.0039 26.7 5.1 41 131-175 26-67 (257)
336 PF10078 DUF2316: Uncharacteri 21.2 99 0.0021 24.6 2.8 24 136-159 22-45 (89)
337 PF12108 SF3a60_bindingd: Spli 21.1 67 0.0014 20.1 1.4 15 289-303 3-17 (28)
338 PF13411 MerR_1: MerR HTH fami 21.0 91 0.002 22.3 2.5 20 138-157 1-20 (69)
339 PRK12513 RNA polymerase sigma 21.0 96 0.0021 27.0 3.1 24 135-158 153-176 (194)
340 cd07977 TFIIE_beta_winged_heli 21.0 90 0.002 23.8 2.5 26 228-253 9-36 (75)
341 PRK12511 RNA polymerase sigma 21.0 1.5E+02 0.0033 25.8 4.3 24 136-159 126-149 (182)
342 PRK12427 flagellar biosynthesi 20.7 1.6E+02 0.0035 26.9 4.6 36 125-162 189-224 (231)
343 PRK12516 RNA polymerase sigma 20.7 1.3E+02 0.0029 26.3 3.9 24 136-159 131-154 (187)
344 PRK09764 DNA-binding transcrip 20.7 1.6E+02 0.0035 26.8 4.6 38 134-175 25-63 (240)
345 PRK09391 fixK transcriptional 20.5 1.4E+02 0.0031 26.9 4.2 33 137-173 179-211 (230)
346 TIGR02812 fadR_gamma fatty aci 20.4 1.8E+02 0.0039 26.2 4.8 40 132-175 24-64 (235)
347 PRK13719 conjugal transfer tra 20.3 2E+02 0.0043 26.7 5.0 44 118-163 141-184 (217)
348 PRK09648 RNA polymerase sigma 20.3 1.7E+02 0.0036 25.4 4.4 23 136-158 154-176 (189)
349 PRK05472 redox-sensing transcr 20.2 1.5E+02 0.0033 26.6 4.3 43 122-164 15-59 (213)
350 PRK12538 RNA polymerase sigma 20.2 1.3E+02 0.0029 27.5 4.0 25 135-159 185-209 (233)
351 PRK12542 RNA polymerase sigma 20.1 1.1E+02 0.0024 26.5 3.2 24 136-159 137-160 (185)
352 TIGR02937 sigma70-ECF RNA poly 20.1 1.6E+02 0.0034 23.4 4.0 40 121-161 111-150 (158)
No 1
>KOG2166|consensus
Probab=100.00 E-value=1.9e-49 Score=413.00 Aligned_cols=243 Identities=43% Similarity=0.604 Sum_probs=217.7
Q ss_pred HHhhHHHHHHHhhcCCCCcccc---cccCCCCCC-CCCCCCCHHHHHHHHhhhHhhhcccCCCCeEEeecCCceEEEEEE
Q psy11818 15 RLENDLFKFYLAKHSGRQLTLQ---PQMGSADLN-AVFFGPRREEVHIFSIYPLRFYLAKHSGRQLTLQPQMGSADLNAV 90 (331)
Q Consensus 15 ~~~~~~f~~~~~~~~~~~~~~~---~~~~swp~~-~~~~~lP~~L~~~~~~F~~~fY~~k~~~RkL~W~~~Lg~~~l~~~ 90 (331)
+..+..|+++...+....++|. +|.|+||.+ ..+|.+|++|..+++.| ..||..+|+||+|+|+|+||.|+|.++
T Consensus 476 ~~l~~~F~~~~~~~~~~~~df~v~VLt~g~WP~~~~~~~~LP~el~~~~e~F-~~~Y~~kh~gR~L~w~~~l~~~ei~~~ 554 (725)
T KOG2166|consen 476 RELQTAFADYANYSANLGIDFTVTVLTTGFWPSYKSTDINLPSEMSDCVEMF-KGFYATKHNGRRLTWIYSLGTGEINGK 554 (725)
T ss_pred HHHHHHHHhhhchhccCCCceeEEEeecCCcCCccCCCCCCChhHHHHHHHH-HHHHhhccCCCeeeeeeccCceEEEEE
Confidence 3456778877222233357775 589999986 46899999999999999 999999999999999999999999999
Q ss_pred EcCCCcCCCCCCCCCCCCCCCCCCCcEEEEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccc
Q psy11818 91 FFGPRREEGEGKDGASSSTSPPAPRKHIIQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRI 170 (331)
Q Consensus 91 f~~~~k~~~~~~~~~~~~~~~~~~~~~~l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~I 170 (331)
|. +++|+|+|||+|||||++||+.+.+|+++|.++|+|+.+++.++|+||...| +.+
T Consensus 555 ~~---------------------~~~~~l~vst~Qm~VLlLFN~~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K--~~v 611 (725)
T KOG2166|consen 555 FD---------------------KKTVELQVSTYQMAVLLLFNNTEKLTYEEILEQTNLGHEDLARLLQSLSCLK--YKI 611 (725)
T ss_pred ec---------------------CceEEEEEEhHHHHHHHHccchhhccHHHHHHHhCCCHHHHHHHHHHHHHHh--Hhh
Confidence 97 3589999999999999999999999999999999999999999999997666 456
Q ss_pred eeecCCCCCCCCCCeEEEecCCCCCceeEEEeccccCCCChhHHHHhhhhhHHhhhhhHHHHHHHhhhcccCCChHHHHH
Q psy11818 171 LIRYPKTKEIEPNHVFFVNDSFTSKLHRVKIQTVAAKGESEPERRETRSKVDEDRKHEIEAAVVRIMKARKRMQHNTLIT 250 (331)
Q Consensus 171 L~~~~~~~~i~~~~~f~lN~~F~~k~~ki~i~~~~~k~e~~~e~~~~~~~v~edR~~~IqAaIVRIMK~~K~l~~~~Li~ 250 (331)
+.. |.+.. ++++.|.+|.+|+++..|++++.++++ |.+.+++.+++||++.|+||||||||+||.|.|.+|+.
T Consensus 612 ~~~-~~s~~-~~~~~~~~N~~f~sk~~Rv~i~~~~~~-----e~~~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~ 684 (725)
T KOG2166|consen 612 LLK-PMSRT-SPNDEFAFNSKFTSKMRRVKIPLPPMD-----ERKKVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVS 684 (725)
T ss_pred ccC-ccccC-CCCcEEEeeccccCcceeeccCCCCch-----hHHHHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHH
Confidence 666 66666 889999999999999999999977554 67789999999999999999999999999999999999
Q ss_pred HHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCccccc
Q psy11818 251 EVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDRFL 289 (331)
Q Consensus 251 ~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~~i 289 (331)
+|.+|+++||.|++.+||+|||.||+||||+|| +|+++
T Consensus 685 Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~-~~~~~ 722 (725)
T KOG2166|consen 685 EVVEQLSERFKPDIKMIKKRIEDLIEREYLERD-ENPNI 722 (725)
T ss_pred HHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc-CCCCc
Confidence 999999999999999999999999999999999 87765
No 2
>KOG2167|consensus
Probab=100.00 E-value=1e-48 Score=389.07 Aligned_cols=242 Identities=45% Similarity=0.611 Sum_probs=221.1
Q ss_pred hHHHHHHHhhc--CCCC-cccc-cccCCCCCCC-CCCCCCHHHHHHHHhhhHhhhcccCCCCeEEeecCCceEEEEEEEc
Q psy11818 18 NDLFKFYLAKH--SGRQ-LTLQ-PQMGSADLNA-VFFGPRREEVHIFSIYPLRFYLAKHSGRQLTLQPQMGSADLNAVFF 92 (331)
Q Consensus 18 ~~~f~~~~~~~--~~~~-~~~~-~~~~swp~~~-~~~~lP~~L~~~~~~F~~~fY~~k~~~RkL~W~~~Lg~~~l~~~f~ 92 (331)
+..|+++..+. ...+ +..+ +|.++||-.. .++.+|++|..+++.| ..||..+|+||+|+|++.||+|+|++.|.
T Consensus 410 ~~~f~~~~~~~~~~~~~l~~v~vlt~~yWpty~~~ev~Lp~em~~~~e~F-~~fyl~k~sgrklqW~~~lg~~v~ka~f~ 488 (661)
T KOG2167|consen 410 NRAFKQSKGANNRLEGNLLTVNVLTMGYWPTYPPMEVLLPKEMRDCQEIF-KKFYLGKHSGRKLQWQDSLGHCVLKAEFK 488 (661)
T ss_pred HHHHHHHHHhhccCcCCceEEEeecccccCCCCchhccCCHHHHHHHHHH-HHhccccccCcceeeecCCcchhhhhhcc
Confidence 45688884333 2234 4444 7899999875 5999999999999999 99999999999999999999999999998
Q ss_pred CCCcCCCCCCCCCCCCCCCCCCCcEEEEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCccccee
Q psy11818 93 GPRREEGEGKDGASSSTSPPAPRKHIIQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILI 172 (331)
Q Consensus 93 ~~~k~~~~~~~~~~~~~~~~~~~~~~l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~ 172 (331)
.| +.+|.||++|++||++||+.+.||++||.++|||.+.+|.+.|++|..++. ++|.
T Consensus 489 ~g---------------------kkel~~slfq~~vll~fn~~~~~s~~ei~~~t~i~d~el~rtlqsl~cgr~--rvl~ 545 (661)
T KOG2167|consen 489 EG---------------------KKELQVSLFQTLVLLMFNEGEGLSYEEIKESTGIEDIELRRTLQSLACGRA--RVLQ 545 (661)
T ss_pred CC---------------------chHHHHHHHHHhHhhccCCCCcccHHHHHHhccccHHHHHHHHHHHhcccc--eeee
Confidence 44 557999999999999999999999999999999999999999999999884 6999
Q ss_pred ecCCCCCCCCCCeEEEecCCCCCceeEEEeccccCCCChhHHHHhhhhhHHhhhhhHHHHHHHhhhcccCCChHHHHHHH
Q psy11818 173 RYPKTKEIEPNHVFFVNDSFTSKLHRVKIQTVAAKGESEPERRETRSKVDEDRKHEIEAAVVRIMKARKRMQHNTLITEV 252 (331)
Q Consensus 173 ~~~~~~~i~~~~~f~lN~~F~~k~~ki~i~~~~~k~e~~~e~~~~~~~v~edR~~~IqAaIVRIMK~~K~l~~~~Li~~V 252 (331)
+.|.|+.+.+++.|.+|..|+++..||+|+.+.+| |+.+|+++|.++|.+||++.||||||||||+||+|+|+.|+.++
T Consensus 546 ~~pkg~~~~~~~~f~~n~~f~~kl~rikinqi~~k-e~~ee~~~~~e~v~~drqy~idaaivrimk~rk~l~h~~l~~el 624 (661)
T KOG2167|consen 546 KVPKGKEVEDGDKFIVNDKFTHKLYRIKINQIQMK-ETVEENKSTTERVFQDRQYQIDAAIVRIMKMRKTLSHNLLVTEL 624 (661)
T ss_pred eCCCCCCCCCCCEEEechhhcchhheehHhhhhHH-HHHHhhhhhHHHHHhhhhHHHHHHHHHHHHHHHhhchhHHHHHH
Confidence 99999999999999999999999999999999888 77888999999999999999999999999999999999999999
Q ss_pred HHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCccc
Q psy11818 253 TEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDR 287 (331)
Q Consensus 253 ~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~ 287 (331)
.+|++ |+..+ ++|+|||+||+|||++||++|.
T Consensus 625 ~~qlk--fpv~~-d~kkriesli~rey~erd~n~~ 656 (661)
T KOG2167|consen 625 FNQLK--FPVKP-DLKKRIESLIDREYLERDDNNI 656 (661)
T ss_pred HHhcC--CCCCh-hHHHHHHHHHhHHHhccccccc
Confidence 99996 98888 9999999999999999995543
No 3
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.8e-46 Score=380.12 Aligned_cols=259 Identities=37% Similarity=0.559 Sum_probs=226.0
Q ss_pred ccccchhHHHHHHhhHHHHHHHh----hcC----------------CCCcccc---cccCCCCCCC--CCCCCCHHHHHH
Q psy11818 4 AENNVNFGLVLRLENDLFKFYLA----KHS----------------GRQLTLQ---PQMGSADLNA--VFFGPRREEVHI 58 (331)
Q Consensus 4 ~~~~~~~~~~~~~~~~~f~~~~~----~~~----------------~~~~~~~---~~~~swp~~~--~~~~lP~~L~~~ 58 (331)
++|...++.+++..+..|-.++. +.+ ...+||. ++..+||+++ +.+.+|++|.+.
T Consensus 483 ~~E~~mis~LKk~~g~~fT~Kle~Mf~DIsLS~e~~~af~~s~~s~~~~~Dl~v~VLt~a~WP~sp~~~~~~lP~~l~p~ 562 (773)
T COG5647 483 QAELKMISMLKKVCGQEFTSKLEGMFRDISLSSEFTEAFQHSPQSYNKYLDLFVWVLTQAYWPLSPEEVSIRLPKELVPI 562 (773)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHhcchhHHHHHHHhhCchhhccccchhHHHHHHhcCCCCccccccCCChHHHHH
Confidence 45677889999998888876651 111 1134554 6799999874 699999999999
Q ss_pred HHhhhHhhhcccCCCCeEEeecCCceEEEEEEEcCCCcCCCCCCCCCCCCCCCCCCCcEEEEEchHHHHHHHHhcCCCCC
Q psy11818 59 FSIYPLRFYLAKHSGRQLTLQPQMGSADLNAVFFGPRREEGEGKDGASSSTSPPAPRKHIIQVSTYQMCVLLLFNNREKL 138 (331)
Q Consensus 59 ~~~F~~~fY~~k~~~RkL~W~~~Lg~~~l~~~f~~~~k~~~~~~~~~~~~~~~~~~~~~~l~vs~~Qa~ILllFN~~~~l 138 (331)
++.| ++||..+|+||+|.|.|+||+|+|++.|..+.+ .....+++++|+.|+++||+++++
T Consensus 563 le~f-~~~Y~sKhngRkL~W~~hLg~~evkarf~~~~~------------------~~~is~~s~~q~~vfll~n~~e~l 623 (773)
T COG5647 563 LEGF-KKFYSSKHNGRKLKWYWHLGSGEVKARFNEGQK------------------YLEISTFSVYQLLVFLLFNDHEEL 623 (773)
T ss_pred HHHH-HHHHHHhccCceEEeeeccccEEEEeeccCCcc------------------ceehhHHHHHHHHHHHHhcCccce
Confidence 9999 999999999999999999999999999985421 234455899999999999999999
Q ss_pred CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCCCCCceeEEEeccccCCCChhHHHHhh
Q psy11818 139 TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSFTSKLHRVKIQTVAAKGESEPERRETR 218 (331)
Q Consensus 139 t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F~~k~~ki~i~~~~~k~e~~~e~~~~~ 218 (331)
|++||.+.|+|+.++++++|++|++.+ +...-++++.++|++.|.+|++|++++.+|+++.+... +..++...++
T Consensus 624 t~eei~e~T~l~~~dl~~~L~sl~~ak----~~~l~~~~~~~~p~~~fy~ne~f~~~~~rIki~~~~~~-~~~q~~~~~h 698 (773)
T COG5647 624 TFEEILELTKLSTDDLKRVLQSLSCAK----LVVLLKDDKLVSPNTKFYVNENFSSKLERIKINYIAES-ECMQDNLDTH 698 (773)
T ss_pred eHHHHHhhcCCChhhHHHHHHHHHhhh----eeeeccccccCCCCceEEEccccccccceeeecccccc-hhhccchhhH
Confidence 999999999999999999999999998 55555557789999999999999999999999988543 3344666788
Q ss_pred hhhHHhhhhhHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCcc
Q psy11818 219 SKVDEDRKHEIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPED 286 (331)
Q Consensus 219 ~~v~edR~~~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d 286 (331)
+++++||+..+|||||||||++|+|+|.+|+++|+.++++||.|++.+||++|+.|||||||+|.++|
T Consensus 699 ~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~dd 766 (773)
T COG5647 699 ETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQADD 766 (773)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999887
No 4
>KOG2284|consensus
Probab=100.00 E-value=3.4e-41 Score=324.56 Aligned_cols=211 Identities=31% Similarity=0.493 Sum_probs=197.2
Q ss_pred CCCCCHHHHHHHHhhhHhhhcccCCCCeEEeecCCceEEEEEEEcCCCcCCCCCCCCCCCCCCCCCCCcEEEEEchHHHH
Q psy11818 48 FFGPRREEVHIFSIYPLRFYLAKHSGRQLTLQPQMGSADLNAVFFGPRREEGEGKDGASSSTSPPAPRKHIIQVSTYQMC 127 (331)
Q Consensus 48 ~~~lP~~L~~~~~~F~~~fY~~k~~~RkL~W~~~Lg~~~l~~~f~~~~k~~~~~~~~~~~~~~~~~~~~~~l~vs~~Qa~ 127 (331)
+|.+|.+|+..++.| +.||..+|+||+|+|++.++.++++++|. ++.|.-.|++|||+
T Consensus 511 nf~~pq~l~~~iq~f-e~fyt~~~~grkltwl~~~~~g~v~~~yl---------------------~k~yva~~~~yqma 568 (728)
T KOG2284|consen 511 NFHLPQILQPVIQEF-EKFYTGKHNGRKLTWLFNMSQGDVRLTYL---------------------DKQYVAQMYVYQMA 568 (728)
T ss_pred hccchHHHHHHHHHH-HHHhccccCCceehhhhhhcccceeeeec---------------------CchHHHHHHHHHHH
Confidence 899999999999999 99999999999999999999999999997 56888899999999
Q ss_pred HHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCCCCCceeEEEeccccC
Q psy11818 128 VLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSFTSKLHRVKIQTVAAK 207 (331)
Q Consensus 128 ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F~~k~~ki~i~~~~~k 207 (331)
+||+||..+.+++.||.+.+|++.+.|.+.+.++++.+ +|..+ +.++..++.|.+|.+|+++..++++..++..
T Consensus 569 ~ll~f~~~~~i~~k~i~~~~~~~~~~l~kti~tildv~----~~~~d--~~~~~a~s~~~lnm~~tskr~kf~~~~p~~~ 642 (728)
T KOG2284|consen 569 ALLCFERRDAILVKDIGEEIGVSGDYLLKTIRTILDVT----LLTCD--DQNLTADSLVRLNMSMTSKRMKFRLQAPQVN 642 (728)
T ss_pred HHHHhcccccchHHhhhhhhCccHHHHHHHHHHHHhce----eeccc--ccccChhhhhhccccccccceeeEecchhhc
Confidence 99999999999999999999999999999999999987 77654 3578888999999999999999999987654
Q ss_pred CCChhHHHHhhhhhHHhhhhhHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCcc
Q psy11818 208 GESEPERRETRSKVDEDRKHEIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPED 286 (331)
Q Consensus 208 ~e~~~e~~~~~~~v~edR~~~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d 286 (331)
..+.+|...+...|.+||++.++||||||||+||.+.|+.|+.+|++|.++||.|++++||+|||.||++.||+|...+
T Consensus 643 k~~~~e~e~~~~~v~~drk~y~~~aivrimk~rkvl~hnalv~ei~~qt~~rf~p~v~~ikk~ie~li~k~yi~rt~~~ 721 (728)
T KOG2284|consen 643 KAVEKEQEAVANTVSQDRKYYMECAIVRIMKTRKVLKHNALVTEIMDQTKGRFSPDVPFIKKSIEDLIEKMYIQRTDQN 721 (728)
T ss_pred cccHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHHHhhcccc
Confidence 3666778888999999999999999999999999999999999999999999999999999999999999999997653
No 5
>KOG2285|consensus
Probab=99.97 E-value=4.3e-30 Score=249.92 Aligned_cols=250 Identities=28% Similarity=0.411 Sum_probs=209.5
Q ss_pred hhHHHHHHHhhcCCC----Ccccc-cccCCCCCCC--CCCCCCHHHHHHHHhhhHhhhcccCCCCeEEeecCCceEEEEE
Q psy11818 17 ENDLFKFYLAKHSGR----QLTLQ-PQMGSADLNA--VFFGPRREEVHIFSIYPLRFYLAKHSGRQLTLQPQMGSADLNA 89 (331)
Q Consensus 17 ~~~~f~~~~~~~~~~----~~~~~-~~~~swp~~~--~~~~lP~~L~~~~~~F~~~fY~~k~~~RkL~W~~~Lg~~~l~~ 89 (331)
.|..|+.-+..++-. .++.- +.+|.|--.. +.+.+|.+|...+-.. ++||+.+|+||+|+|.|+++.++|..
T Consensus 502 lN~~Fk~~~~~~~~~~~aDsiNiKiLNaGAW~R~SErv~vSLP~ELED~iPdv-eEfykk~hsgrkl~w~h~msNG~itf 580 (777)
T KOG2285|consen 502 LNSSFKKALTGTNNNSIADSINIKILNAGAWGRGSERVRVSLPRELEDFIPDV-EEFYKKKHSGRKLQWYHHMSNGTITF 580 (777)
T ss_pred HHHHHHHHHhCCCCCCcccceeeeeecccccccccceEEEeCchhHHHhCccH-HHHHhcccCccchhhhhhccCCeeEe
Confidence 578898887666332 24443 6799997553 6999999999999999 99999999999999999999999964
Q ss_pred EEcCCCcCCCCCCCCCCCCCCCCCCCcEEEEEchHHHHHHHHhcC--CCCCCHHHHHHhcCCCHHHHHHHHHHHHcc-cC
Q psy11818 90 VFFGPRREEGEGKDGASSSTSPPAPRKHIIQVSTYQMCVLLLFNN--REKLTYEEIQSETDIPERDLIRALQSLAMG-KA 166 (331)
Q Consensus 90 ~f~~~~k~~~~~~~~~~~~~~~~~~~~~~l~vs~~Qa~ILllFN~--~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~-k~ 166 (331)
.-. -+.|++.|+|+||+||.+||+ ++.++++.|.-+|.+|+.+|.+.|.||+.. |.
T Consensus 581 ~n~---------------------~GryDLevTTFQmAVLFawNqR~hdKIS~EnLrLATELPDaELrRTLwSLVAfPK~ 639 (777)
T KOG2285|consen 581 VNN---------------------FGRYDLEVTTFQMAVLFAWNQRAHDKISLENLRLATELPDAELRRTLWSLVAFPKM 639 (777)
T ss_pred ecc---------------------cccceeeeehhhHHHHHHhccccccccchHhhhhhhcCCCHHHHHHHHHHHhhhhh
Confidence 422 248999999999999999997 578999999999999999999999999754 55
Q ss_pred cccceeecCC----CCCCCCCCeEEEecCCCC-----CceeEEEeccccCC--CChhHHHHhhhhhHHhhhhhHHHHHHH
Q psy11818 167 SQRILIRYPK----TKEIEPNHVFFVNDSFTS-----KLHRVKIQTVAAKG--ESEPERRETRSKVDEDRKHEIEAAVVR 235 (331)
Q Consensus 167 ~~~IL~~~~~----~~~i~~~~~f~lN~~F~~-----k~~ki~i~~~~~k~--e~~~e~~~~~~~v~edR~~~IqAaIVR 235 (331)
.++||..+|. ++++.+++.|.+|.+|.- ...|.+++.+ ++- .++....+.++.+.+-|....|-+||+
T Consensus 640 k~QiLL~ep~~~~spkDFte~T~F~iNqeF~vvKNgKsQ~RGKvNLI-GRLQLstEr~~eeenesIVqLRiLRtQEaIik 718 (777)
T KOG2285|consen 640 KYQILLCEPPTTVSPKDFTESTKFLINQEFNVVKNGKSQQRGKVNLI-GRLQLSTERNAEEENESIVQLRILRTQEAIIK 718 (777)
T ss_pred hhheeeecCcccCCcccccccceEEeechhhhhhccchhhcccceee-eeeeehhhhhhhhhcchhHHHHHHHHHHHHHH
Confidence 6788888773 467889999999999973 1245666655 231 122223345678889999999999999
Q ss_pred hhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCccccc
Q psy11818 236 IMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDRFL 289 (331)
Q Consensus 236 IMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~~i 289 (331)
|||.||+++..+|-.++.+-++..|.|+..+||+.||.||+..|++||++|.++
T Consensus 719 ImK~RK~~~nAqLq~ELveILKnmFlP~kKmIKEQieWLIEnKYmrRd~dDINt 772 (777)
T KOG2285|consen 719 IMKTRKTYTNAQLQMELVEILKNMFLPNKKMIKEQIEWLIENKYMRRDADDINT 772 (777)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHccCCcHHHHHHHHHHHHhhhhhccchhhccc
Confidence 999999999999999999999999999999999999999999999999998775
No 6
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=99.91 E-value=3.2e-24 Score=220.40 Aligned_cols=151 Identities=34% Similarity=0.459 Sum_probs=119.1
Q ss_pred hhHHHHHHHhhcCCC---Ccccc---cccCCCCCCC-CC-CCCCHHHHHHHHhhhHhhhcccCCCCeEEeecCCceEEEE
Q psy11818 17 ENDLFKFYLAKHSGR---QLTLQ---PQMGSADLNA-VF-FGPRREEVHIFSIYPLRFYLAKHSGRQLTLQPQMGSADLN 88 (331)
Q Consensus 17 ~~~~f~~~~~~~~~~---~~~~~---~~~~swp~~~-~~-~~lP~~L~~~~~~F~~~fY~~k~~~RkL~W~~~Lg~~~l~ 88 (331)
.+..|+++....... .++|. ++.++||... .+ +.+|++|+.+++.| +.||..+|+||+|+|++.+|+|+|+
T Consensus 428 ~~~~f~~~~~~~~~~~~~~~~~~~~vls~~~Wp~~~~~~~~~lP~~l~~~~~~f-~~~Y~~~~~~R~L~w~~~l~~~~i~ 506 (588)
T PF00888_consen 428 LNEEFKQKQSQNNIQLIPPFDFNVKVLSKGYWPKYPSENNIKLPPELQQALDSF-EKFYKEKHKGRKLTWLPSLSSVEIE 506 (588)
T ss_dssp HHHHHHHHHHTTT-SS--CCEEEEEEEETTTS-S-S-SS-----HHHHHHHHHH-HHHHHTTSTTEEEEEEGGGEEEEEE
T ss_pred HHHHHHHHhhhccccccCCCceEEEEecCCCCCCCCCCccccCCHHHHHHHHHH-HHHHHhcCCCcEEEEecccCcEEEE
Confidence 466788876655332 45554 5899999875 34 99999999999999 9999999999999999999999999
Q ss_pred EEEcCCCcCCCCCCCCCCCCCCCCCCCcEEEEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcc
Q psy11818 89 AVFFGPRREEGEGKDGASSSTSPPAPRKHIIQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQ 168 (331)
Q Consensus 89 ~~f~~~~k~~~~~~~~~~~~~~~~~~~~~~l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~ 168 (331)
++|. ++.++++||++||+||++||+.+++|++||++.||++.++++++|.+|+..|
T Consensus 507 ~~~~---------------------~~~~~l~~s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~--- 562 (588)
T PF00888_consen 507 FNFN---------------------NGKYELTVSTLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLVKSK--- 562 (588)
T ss_dssp EESS---------------------SSEEEEEEEHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTT---
T ss_pred EEec---------------------CCceeEEeeHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCC---
Confidence 9987 3579999999999999999999999999999999999999999999999988
Q ss_pred ccee--ecCCCCCCCCCCeEEEecCCC
Q psy11818 169 RILI--RYPKTKEIEPNHVFFVNDSFT 193 (331)
Q Consensus 169 ~IL~--~~~~~~~i~~~~~f~lN~~F~ 193 (331)
+|. ..+++.++++++.|.+|.+|+
T Consensus 563 -~l~~~~~~~~~~~~~~~~f~~N~~F~ 588 (588)
T PF00888_consen 563 -ILILLKEPNSKSFSDNDEFSVNENFT 588 (588)
T ss_dssp -TCSEEETTTSSS--TT-EEEE-TT--
T ss_pred -cceeecCCccCCCCCCCEEEeCCCCC
Confidence 666 556778899999999999996
No 7
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=99.84 E-value=1.1e-21 Score=148.24 Aligned_cols=68 Identities=56% Similarity=0.843 Sum_probs=62.8
Q ss_pred hHHhhhhhHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCcccc
Q psy11818 221 VDEDRKHEIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDRF 288 (331)
Q Consensus 221 v~edR~~~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~~ 288 (331)
++++|.+.|+||||||||++|+|+|++|+.+|.++++.+|.|+..+||++||+||++|||+||++|+|
T Consensus 1 i~~~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~n 68 (68)
T PF10557_consen 1 IEQDRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDPN 68 (68)
T ss_dssp CHHHHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSECT
T ss_pred CcchhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCCC
Confidence 46799999999999999999999999999999999999999999999999999999999999999986
No 8
>KOG2165|consensus
Probab=99.60 E-value=8.3e-15 Score=149.57 Aligned_cols=127 Identities=20% Similarity=0.192 Sum_probs=117.1
Q ss_pred cccCCCCCC-CCCCCCCHHHHHHHHhhhHhhhcccCCCCeEEeecCCceEEEEEEEcCCCcCCCCCCCCCCCCCCCCCCC
Q psy11818 37 PQMGSADLN-AVFFGPRREEVHIFSIYPLRFYLAKHSGRQLTLQPQMGSADLNAVFFGPRREEGEGKDGASSSTSPPAPR 115 (331)
Q Consensus 37 ~~~~swp~~-~~~~~lP~~L~~~~~~F~~~fY~~k~~~RkL~W~~~Lg~~~l~~~f~~~~k~~~~~~~~~~~~~~~~~~~ 115 (331)
++..+||.. ...|-+|.+|+..++.| .+-|...+.+|+|.|.+++|.|+|++.|. ++
T Consensus 537 lS~~fWP~~~~~~~~lP~pl~~el~~Y-~~~Y~~~K~~RkL~w~~~lG~Veieie~~---------------------DR 594 (765)
T KOG2165|consen 537 LSSLFWPPLCDEAFHLPGPLEAELDKY-AEIYEQLKRGRKLQWLKNLGKVEIEIEFE---------------------DR 594 (765)
T ss_pred hhhhcCCccccccccCChhHHHHHHHH-HHHHHHhccCCeeeeecccCeEEEEEEEc---------------------Ce
Confidence 469999975 57999999999999999 99999999999999999999999999997 68
Q ss_pred cEEEEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCC
Q psy11818 116 KHIIQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSF 192 (331)
Q Consensus 116 ~~~l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F 192 (331)
...++||+.||+|+++|.+.++||++|+++.+|||...+.+.|..|++.| +|..++.. ++..+|+++++=
T Consensus 595 tl~~tVsp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~G----vL~e~~~~---s~tgt~T~iEse 664 (765)
T KOG2165|consen 595 TLVLTVSPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKG----VLREEPII---SDTGTLTVIESE 664 (765)
T ss_pred EEEEeeCHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcC----eeecCCCC---CCCceeeecccc
Confidence 99999999999999999999999999999999999999999999999998 99887632 567889999853
No 9
>smart00182 CULLIN Cullin.
Probab=99.33 E-value=3.6e-12 Score=109.13 Aligned_cols=75 Identities=31% Similarity=0.363 Sum_probs=62.5
Q ss_pred HhhHHHHHHHhhcC-CCCcccc---cccCCCCCCC--CCCCCCHHHHHHHHhhhHhhhcccCCCCeEEeecCCceEEEEE
Q psy11818 16 LENDLFKFYLAKHS-GRQLTLQ---PQMGSADLNA--VFFGPRREEVHIFSIYPLRFYLAKHSGRQLTLQPQMGSADLNA 89 (331)
Q Consensus 16 ~~~~~f~~~~~~~~-~~~~~~~---~~~~swp~~~--~~~~lP~~L~~~~~~F~~~fY~~k~~~RkL~W~~~Lg~~~l~~ 89 (331)
-.+.+|+++++..+ ...++|. ++.++||... .++.+|++|+.+++.| +.||..+|+||+|+|+|+||+|+|++
T Consensus 62 ~l~~~f~~~~~~~~~~~~~~~~~~VLs~~~WP~~~~~~~~~lP~~l~~~~~~f-~~~Y~~~~~~RkL~W~~~lg~~~l~~ 140 (142)
T smart00182 62 DLNQSFKDMLENNSNKPIIDLNVRVLTSGYWPTSSTEVEINLPQELEDALEEF-EEFYLAKHSGRKLTWLHSLGRGEVKA 140 (142)
T ss_pred HHHHHHHHHHHhccCCCCCceEEEECCCCCCCCCCCCCceECCHHHHHHHHHH-HHHHHhCCCCCeEEEEcCCceEEEEE
Confidence 34667888876532 2235554 6899999763 5999999999999999 99999999999999999999999998
Q ss_pred EE
Q psy11818 90 VF 91 (331)
Q Consensus 90 ~f 91 (331)
+|
T Consensus 141 ~~ 142 (142)
T smart00182 141 NF 142 (142)
T ss_pred EC
Confidence 75
No 10
>KOG2284|consensus
Probab=98.02 E-value=4.2e-06 Score=82.48 Aligned_cols=43 Identities=42% Similarity=0.743 Sum_probs=40.9
Q ss_pred cccccchHHHHHHHHHHHHhhhhCCCCCCchHHHHHHHHhhhc
Q psy11818 286 DRFLQEKDVFERYYKQHLAKRLLLDKSVSDDSEKNMISKLKVR 328 (331)
Q Consensus 286 d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 (331)
-++|+||||||.||.++||+||.++-+-++|+|.+|+++|||.
T Consensus 439 f~yi~dkdifqkfys~mla~rli~~~s~smd~ee~minklkqa 481 (728)
T KOG2284|consen 439 FRYIEDKDIFQKFYSKMLANRLIASTSISMDAEELMINKLKQA 481 (728)
T ss_pred eeecccHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHH
Confidence 4789999999999999999999999999999999999999984
No 11
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.89 E-value=9e-06 Score=84.71 Aligned_cols=43 Identities=56% Similarity=0.785 Sum_probs=40.3
Q ss_pred ccccchHHHHHHHHHHHHhhhhCCCCCCchHHHHHHHHhhhcc
Q psy11818 287 RFLQEKDVFERYYKQHLAKRLLLDKSVSDDSEKNMISKLKVRN 329 (331)
Q Consensus 287 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 329 (331)
+++.+||||++||+.+|||||+++||++-+.|.+|+.+||+.+
T Consensus 454 ryv~~KDvFe~~Yk~~laKRLL~g~S~s~~~E~~mis~LKk~~ 496 (773)
T COG5647 454 RYVEEKDVFEKYYKKLLAKRLLNGRSASAQAELKMISMLKKVC 496 (773)
T ss_pred HHhhhhHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHh
Confidence 5688999999999999999999999999999999999999763
No 12
>KOG2166|consensus
Probab=97.71 E-value=8.7e-05 Score=79.01 Aligned_cols=95 Identities=34% Similarity=0.476 Sum_probs=64.9
Q ss_pred hhhHHHHHHHhhhcccCCChHHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHHHHHHhCCccccccchHHHHHHHHHHHH
Q psy11818 226 KHEIEAAVVRIMKARKRMQHNTLITEVTEQLKSR-FLPSPVIIKKRIESLIEREYLARTPEDRFLQEKDVFERYYKQHLA 304 (331)
Q Consensus 226 ~~~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~-F~ps~~~IKk~IE~LIereyI~Rd~~d~~i~~~~~~~~~~~~~~~ 304 (331)
...++++.+...+.....+.+-|..-+-+.++.. =.|+...|+..++.+ ----.++.|||||+.||++++|
T Consensus 361 ~~~ld~a~~~fin~n~~~~~E~la~y~D~~lkk~~k~~~e~~ie~~l~~v--------~~l~~yisdKdvF~~~Ykk~la 432 (725)
T KOG2166|consen 361 KKALDAAFEEFINKNVATSAELLATYCDDILKKGSKKLSDEAIEDTLEKV--------VKLLKYISDKDVFAEFYKKVLA 432 (725)
T ss_pred HHHHHHHHHHHHcccCCCcHHHHHHHhHHHhcccccCCchhHHHhHhhcc--------eeeeeeccHHHHHHHHHHHHHH
Confidence 4557777777776665555344444444444321 223344343333322 1234678899999999999999
Q ss_pred hhhhCCCCCCchHHHHHHHHhhhc
Q psy11818 305 KRLLLDKSVSDDSEKNMISKLKVR 328 (331)
Q Consensus 305 ~~~~~~~~~~~~~~~~~~~~~~~~ 328 (331)
+||+++||+++|+|++|+.++++.
T Consensus 433 kRLl~~~S~sdd~E~~mIsklk~~ 456 (725)
T KOG2166|consen 433 RRLLFDRSASDDHEKSLITKLKNL 456 (725)
T ss_pred HHHhhcCccchHHHHHHHHHHHHH
Confidence 999999999999999999999875
No 13
>KOG2167|consensus
Probab=97.44 E-value=7.6e-05 Score=76.41 Aligned_cols=41 Identities=66% Similarity=0.978 Sum_probs=38.9
Q ss_pred ccccchHHHHHHHHHHHHhhhhCCCCCCchHHHHHHHHhhh
Q psy11818 287 RFLQEKDVFERYYKQHLAKRLLLDKSVSDDSEKNMISKLKV 327 (331)
Q Consensus 287 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 327 (331)
++|..||||++||+..+|+||+.+||++-|.|++|+.+++.
T Consensus 346 r~i~gkdvfeA~ykkdLakrLLl~kSAsvdae~~ml~~lk~ 386 (661)
T KOG2167|consen 346 RFIHGKDVFEAFYKKDLAKRLLLGKSASVDAEKSMLSKLKL 386 (661)
T ss_pred HHHhccHHHHHHHHHHHHHHHHhccchhhcchhHHHHHhhh
Confidence 57889999999999999999999999999999999998874
No 14
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=95.83 E-value=0.0097 Score=61.55 Aligned_cols=41 Identities=63% Similarity=0.961 Sum_probs=36.7
Q ss_pred ccccchHHHHHHHHHHHHhhhhCCCCCCchHHHHHHHHhhh
Q psy11818 287 RFLQEKDVFERYYKQHLAKRLLLDKSVSDDSEKNMISKLKV 327 (331)
Q Consensus 287 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 327 (331)
.++.+||+|+.+|.++||+||+..++.+.+.|+.++.+|+.
T Consensus 365 ~~l~~Kd~F~~~Y~~~L~~RLl~~~~~~~~~E~~~i~~Lk~ 405 (588)
T PF00888_consen 365 SYLSDKDVFEKYYKKLLAKRLLSNKSFSEDAEKSMIEKLKK 405 (588)
T ss_dssp TTSSTHHHHHHHHHHHHHHHHHTT-BS-HHHHHHHHHHHHH
T ss_pred eecchhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhc
Confidence 46789999999999999999999999999999999999886
No 15
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=95.54 E-value=0.023 Score=40.15 Aligned_cols=46 Identities=26% Similarity=0.351 Sum_probs=38.5
Q ss_pred HHHHHHhcCCC-CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 126 MCVLLLFNNRE-KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 126 a~ILllFN~~~-~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.||.+|...+ .+|+.||++.+|++...+.+.|..|...+ ++.++|
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g----~v~~dp 52 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEG----YVERDP 52 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTT----SEEECS
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCc----CeecCc
Confidence 46788887764 48999999999999999999999999988 887653
No 16
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=95.33 E-value=0.072 Score=42.56 Aligned_cols=65 Identities=23% Similarity=0.275 Sum_probs=53.7
Q ss_pred EEEchHHHHHHHHhc--------CCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEec
Q psy11818 119 IQVSTYQMCVLLLFN--------NREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVND 190 (331)
Q Consensus 119 l~vs~~Qa~ILllFN--------~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~ 190 (331)
..++.-|+.+|+..- ..+.+|-.||++.+|++...+.++|..|...+ ++.+.. .-..|.+|.
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~G----lI~r~~------~~~~~~~n~ 90 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRR----IIFRQG------MMGIVGVNT 90 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCC----Ceeeec------CCceeecCC
Confidence 567888999888654 46789999999999999999999999999988 887642 236799998
Q ss_pred CCC
Q psy11818 191 SFT 193 (331)
Q Consensus 191 ~F~ 193 (331)
+++
T Consensus 91 ~~~ 93 (95)
T TIGR01610 91 PLS 93 (95)
T ss_pred Ccc
Confidence 764
No 17
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=95.06 E-value=0.057 Score=37.19 Aligned_cols=44 Identities=18% Similarity=0.223 Sum_probs=37.1
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
+..+..||....+++.+|..||++.+|++...+.++|..|...|
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g 45 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKG 45 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCc
Confidence 34577888888888899999999999999999999999999877
No 18
>KOG2285|consensus
Probab=94.76 E-value=0.11 Score=52.48 Aligned_cols=45 Identities=38% Similarity=0.728 Sum_probs=42.1
Q ss_pred ccccchHHHHHHHHHHHHhhhhCCCCCCchHHHHHHHHhhhccCC
Q psy11818 287 RFLQEKDVFERYYKQHLAKRLLLDKSVSDDSEKNMISKLKVRNLP 331 (331)
Q Consensus 287 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 331 (331)
.|++.||||-+||++++.+||.+.-++-.+.|.+||..|+..|.|
T Consensus 438 KYV~NKDVFMRyHkaHLtRRLIL~~SADsEkEE~mVewLREvGMP 482 (777)
T KOG2285|consen 438 KYVENKDVFMRYHKAHLTRRLILEMSADSEKEEMMVEWLREVGMP 482 (777)
T ss_pred HhhcccHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHcCCc
Confidence 467789999999999999999998899999999999999999987
No 19
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=94.75 E-value=0.14 Score=39.54 Aligned_cols=60 Identities=13% Similarity=0.102 Sum_probs=43.3
Q ss_pred HHHHHHHHhcCCC-CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCC
Q psy11818 124 YQMCVLLLFNNRE-KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSF 192 (331)
Q Consensus 124 ~Qa~ILllFN~~~-~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F 192 (331)
+++.+.+..+..+ .+|.+||++.+|++...+.+.|..|.+.+ ++...+. ++.-|.++.+.
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~G----li~s~~G-----~~GGy~L~~~~ 71 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAG----LIESSRG-----RGGGYRLARPP 71 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTT----SEEEETS-----TTSEEEESS-C
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCC----eeEecCC-----CCCceeecCCH
Confidence 4445555545444 49999999999999999999999999988 8875432 35668877654
No 20
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=94.60 E-value=0.064 Score=38.55 Aligned_cols=51 Identities=20% Similarity=0.263 Sum_probs=43.3
Q ss_pred EchHHHHHHHHhcCCCC--CCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 121 VSTYQMCVLLLFNNREK--LTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 121 vs~~Qa~ILllFN~~~~--lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+|..|+.||......+. +|..||++.+|++...+.+.+..|...+ ++.+.+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G----lv~r~~ 55 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG----LVERER 55 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT----SEEEEE
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEeC
Confidence 46788899987776665 9999999999999999999999999988 887654
No 21
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=94.19 E-value=0.1 Score=37.68 Aligned_cols=46 Identities=24% Similarity=0.360 Sum_probs=40.8
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
|..|+.+.+.++.+|++||++.+|++...+++-|..|...+ ++.+.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g----~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQG----LIKRT 47 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEE
Confidence 45678888889999999999999999999999999999887 67654
No 22
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=94.14 E-value=0.13 Score=37.58 Aligned_cols=51 Identities=14% Similarity=0.180 Sum_probs=40.3
Q ss_pred EchHHHHHHHHhc-CCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 121 VSTYQMCVLLLFN-NREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 121 vs~~Qa~ILllFN-~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+|..|..||.... ..+.++..+|++.++++...+-+.|+.|+..+ ++.+.+
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~g----lv~~~~ 52 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKG----LVEKER 52 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTT----SEEEEE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEecC
Confidence 3667889998888 78899999999999999999999999999988 886643
No 23
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=93.40 E-value=0.087 Score=37.60 Aligned_cols=50 Identities=16% Similarity=0.254 Sum_probs=43.7
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
|..|+.+|......+.++..+|++.++++...+.+.+..|.+.+ ++.+.+
T Consensus 2 t~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g----~I~r~~ 51 (59)
T PF01047_consen 2 TPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKG----LIERER 51 (59)
T ss_dssp THHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTT----SEEEEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCC----CEEecc
Confidence 67789999888888889999999999999999999999999988 877654
No 24
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=92.83 E-value=0.27 Score=40.26 Aligned_cols=53 Identities=13% Similarity=0.236 Sum_probs=47.2
Q ss_pred EEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 119 IQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
..++..|+.||......+.+|..||++.+|++...+-+.+..|...+ ++.+.+
T Consensus 24 ~~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~G----lI~r~~ 76 (118)
T TIGR02337 24 HGLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDG----LVTRLK 76 (118)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCC----CEEecc
Confidence 35689999999988888899999999999999999999999999987 777653
No 25
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.54 E-value=0.41 Score=36.90 Aligned_cols=56 Identities=16% Similarity=0.160 Sum_probs=43.8
Q ss_pred HHHHHHhcCC-CCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecC
Q psy11818 126 MCVLLLFNNR-EKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDS 191 (331)
Q Consensus 126 a~ILllFN~~-~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~ 191 (331)
..||..+... +.+|+.||++.+|++...+.+.|..|...+ ++...+ .+..|.+...
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g----~l~~~~------~~~~y~l~~~ 64 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELG----YVEQDG------QNGRYRLGPK 64 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC----CeeecC------CCCceeecHH
Confidence 4566667665 689999999999999999999999999887 887653 2345666543
No 26
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=92.17 E-value=0.29 Score=35.49 Aligned_cols=49 Identities=16% Similarity=0.226 Sum_probs=41.7
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
++.-..||.++...+.+|+.||++.+|++...+..+|..|...+ ++...
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aG----li~~~ 57 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAG----LIEVE 57 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTT----SEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----CeEEe
Confidence 45667788888778899999999999999999999999999988 77654
No 27
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.65 E-value=0.42 Score=35.76 Aligned_cols=47 Identities=17% Similarity=0.244 Sum_probs=39.6
Q ss_pred HHHHHHHHhcCCCC--CCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 124 YQMCVLLLFNNREK--LTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 124 ~Qa~ILllFN~~~~--lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
..-.||.++...+. +|..||++.+|++...+.++|..|...+ ++...
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G----~V~~~ 55 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG----KVCKQ 55 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEec
Confidence 34567777777655 9999999999999999999999999887 77664
No 28
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=91.61 E-value=0.53 Score=43.94 Aligned_cols=58 Identities=9% Similarity=0.126 Sum_probs=47.1
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecC
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDS 191 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~ 191 (331)
-=+.||.+|.....+|+.||++.+|++...+.+.|..|+..+ .|.+++. +..|.+...
T Consensus 15 r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G----~l~~~~~------~~~Y~lG~~ 72 (257)
T PRK15090 15 KVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLG----YVAQEGE------SEKYSLTLK 72 (257)
T ss_pred HHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEcCC------CCcEEecHH
Confidence 346788889887789999999999999999999999999988 8877542 345666543
No 29
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=91.53 E-value=0.49 Score=40.13 Aligned_cols=53 Identities=21% Similarity=0.220 Sum_probs=46.5
Q ss_pred EEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 119 IQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.+|..|+.||......+.+|..||++.+|++...+-+.+..|.+.+ ++.+.+
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~G----lI~R~~ 88 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKG----WVERLP 88 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEecc
Confidence 46788899999877667889999999999999999999999999988 777654
No 30
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=91.50 E-value=0.24 Score=38.34 Aligned_cols=45 Identities=20% Similarity=0.383 Sum_probs=36.8
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
+..||.+.+..+.+++.+|.+.+|++...+-++|..|...+ .+..
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~G----yV~~ 46 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAG----YVEV 46 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTT----SEEE
T ss_pred HHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCC----CEEE
Confidence 45677777778899999999999999999999999999887 6544
No 31
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=91.07 E-value=0.69 Score=31.81 Aligned_cols=40 Identities=20% Similarity=0.325 Sum_probs=33.2
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
..-|+.+.-+ +..++.||++.+|++...+.++|..|...|
T Consensus 4 R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~g 43 (47)
T PF01022_consen 4 RLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAG 43 (47)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCc
Confidence 4456666555 789999999999999999999999999887
No 32
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=90.50 E-value=0.8 Score=35.30 Aligned_cols=52 Identities=17% Similarity=0.300 Sum_probs=46.3
Q ss_pred EEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 119 IQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
..++..+..||......+.++..+|++.++++...+.+.|..|...+ ++...
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g----~v~~~ 57 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKG----LIRRL 57 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCC----CeEec
Confidence 56788899999888877889999999999999999999999999987 77653
No 33
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=90.35 E-value=0.82 Score=31.07 Aligned_cols=45 Identities=24% Similarity=0.328 Sum_probs=36.9
Q ss_pred HHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 126 MCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 126 a~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
-.|+..+.....++..+|++.+|++...+.+.|..|...+ ++...
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g----~i~~~ 47 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQG----LLTRV 47 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEe
Confidence 3456666666789999999999999999999999999887 66543
No 34
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=90.13 E-value=0.65 Score=32.64 Aligned_cols=39 Identities=23% Similarity=0.372 Sum_probs=31.1
Q ss_pred HHHHHh-cCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 127 CVLLLF-NNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 127 ~ILllF-N~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
-||.++ +..+.+|.++|++.+|++...+.+.|..|-..+
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 445444 666679999999999999999999999996654
No 35
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=90.02 E-value=0.33 Score=35.83 Aligned_cols=51 Identities=29% Similarity=0.276 Sum_probs=42.0
Q ss_pred EchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 121 VSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 121 vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.|-.++-|+..+-..+..|..||++.+|++...+.++|..|...| ++.+.+
T Consensus 6 Ls~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~G----lV~~~~ 56 (68)
T PF01978_consen 6 LSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKG----LVEREE 56 (68)
T ss_dssp HHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTT----SEEEEE
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEEc
Confidence 345566666655577889999999999999999999999999988 776653
No 36
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=90.01 E-value=1.3 Score=35.85 Aligned_cols=62 Identities=23% Similarity=0.348 Sum_probs=49.8
Q ss_pred EEEchHHHHHHHH-------hcC-CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEec
Q psy11818 119 IQVSTYQMCVLLL-------FNN-REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVND 190 (331)
Q Consensus 119 l~vs~~Qa~ILll-------FN~-~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~ 190 (331)
..++.-|..|++. ||. .+.+|..++++.||++...+.++++.|+..+ +|..+ +..+-+|.
T Consensus 28 ~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~----vI~~~--------g~~~G~N~ 95 (100)
T PF04492_consen 28 ADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRG----VIIRD--------GKRIGVNK 95 (100)
T ss_pred ccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEeC--------CcEEeeec
Confidence 3567777777766 665 4689999999999999999999999999988 88764 45666666
Q ss_pred CC
Q psy11818 191 SF 192 (331)
Q Consensus 191 ~F 192 (331)
++
T Consensus 96 ~i 97 (100)
T PF04492_consen 96 NI 97 (100)
T ss_pred cc
Confidence 54
No 37
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=89.40 E-value=1 Score=36.50 Aligned_cols=53 Identities=25% Similarity=0.337 Sum_probs=45.0
Q ss_pred EEEchHHHHHHHHhc----CCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 119 IQVSTYQMCVLLLFN----NREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 119 l~vs~~Qa~ILllFN----~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.+|..|..||.... ..+.+|..+|++.++++...+-+.+..|.+.+ ++.+.+
T Consensus 21 ~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg----~I~r~~ 77 (109)
T TIGR01889 21 FNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKG----YLSKER 77 (109)
T ss_pred cCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCC----CEeccC
Confidence 356888888886655 55789999999999999999999999999988 887654
No 38
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=88.33 E-value=1.2 Score=39.39 Aligned_cols=49 Identities=24% Similarity=0.325 Sum_probs=42.2
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCCCCCc
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSFTSKL 196 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F~~k~ 196 (331)
-+|..+|++.+|++...+.+++..|...+ ||.+.. ...|.||++|..+.
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~----iI~k~~-------~G~Y~iNP~~~~kG 123 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEKN----IIKKIR-------NGAYMINPNFFFKG 123 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhCC----cEEEcc-------CCeEEECcHHheeC
Confidence 47999999999999999999999999988 998753 45899999976543
No 39
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=88.13 E-value=1.8 Score=31.07 Aligned_cols=48 Identities=17% Similarity=0.243 Sum_probs=39.9
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+..+..|+..+...+ ++..||++.+|++...+.+.|..|...+ ++...
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g----~i~~~ 53 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAG----LVESR 53 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCC----CeEEE
Confidence 455777787766666 9999999999999999999999998876 77654
No 40
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=87.83 E-value=1.5 Score=41.30 Aligned_cols=50 Identities=14% Similarity=0.230 Sum_probs=42.3
Q ss_pred chHHHHHHHHhcCC-CCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 122 STYQMCVLLLFNNR-EKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 122 s~~Qa~ILllFN~~-~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
---=+.||.+|... ..+|+.||++.+|++...+.+.|.+|+..+ .|.+++
T Consensus 24 l~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G----~l~~~~ 74 (271)
T PRK10163 24 LERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAAD----FVYQDS 74 (271)
T ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEcC
Confidence 33446788889764 579999999999999999999999999988 887754
No 41
>PRK11569 transcriptional repressor IclR; Provisional
Probab=87.32 E-value=1.6 Score=41.27 Aligned_cols=53 Identities=13% Similarity=0.205 Sum_probs=43.3
Q ss_pred EEEchHHHHHHHHhcC-CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 119 IQVSTYQMCVLLLFNN-REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~-~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+..-.-=+.||.+|.. ...+++.||++.+|++...+.+.|.+|+..+ .|.+++
T Consensus 24 v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G----~l~~~~ 77 (274)
T PRK11569 24 VQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQG----FVRQVG 77 (274)
T ss_pred ccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEcC
Confidence 3333344677888986 4569999999999999999999999999998 887754
No 42
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=87.28 E-value=2 Score=36.40 Aligned_cols=39 Identities=21% Similarity=0.255 Sum_probs=35.3
Q ss_pred cCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 133 NNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 133 N~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.++.+|++||++.++.+...+.++|+.|+..| ++.+..
T Consensus 38 ~~~~~~tvdelae~lnr~rStv~rsl~~L~~~G----lV~Rek 76 (126)
T COG3355 38 EENGPLTVDELAEILNRSRSTVYRSLQNLLEAG----LVEREK 76 (126)
T ss_pred hhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcC----Ceeeee
Confidence 368899999999999999999999999999998 887753
No 43
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=86.88 E-value=1.8 Score=40.37 Aligned_cols=55 Identities=18% Similarity=0.298 Sum_probs=44.9
Q ss_pred HHHHHHhcCCCC-CCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEec
Q psy11818 126 MCVLLLFNNREK-LTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVND 190 (331)
Q Consensus 126 a~ILllFN~~~~-lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~ 190 (331)
+.||.+|..... +++.||++.+|++...+.+.|..|+..+ ++.+++. +..|.+-.
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G----~v~~d~~------~g~Y~Lg~ 62 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELG----YVEQDPE------DGRYRLGP 62 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCC----CEEEcCC------CCcEeehH
Confidence 468888887554 7899999999999999999999999998 9988752 33566654
No 44
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=86.63 E-value=2.7 Score=37.00 Aligned_cols=58 Identities=10% Similarity=0.161 Sum_probs=42.8
Q ss_pred HHHHHHHhcC-CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecC
Q psy11818 125 QMCVLLLFNN-REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDS 191 (331)
Q Consensus 125 Qa~ILllFN~-~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~ 191 (331)
.+.+.+.|+. ...+|.++|++.+|+|...+.+.|..|...+ |+..... +++-|.+..+
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aG----Lv~s~rG-----~~GGy~Lar~ 70 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNG----LVSSVRG-----PGGGYLLGKD 70 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEeCCC-----CCCCeeccCC
Confidence 3444455665 4579999999999999999999999999998 8875321 2334666544
No 45
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=86.52 E-value=1.8 Score=38.89 Aligned_cols=53 Identities=9% Similarity=-0.013 Sum_probs=47.3
Q ss_pred EEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 119 IQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.+|..|..||......+.+|..+|++.++++...+.+.+..|...+ ++.+.+
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kG----lI~R~~ 93 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERG----YLTFSK 93 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCC----CEEecC
Confidence 56889999999999888899999999999999999999999999887 777653
No 46
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=86.26 E-value=2.3 Score=28.38 Aligned_cols=34 Identities=24% Similarity=0.298 Sum_probs=30.5
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.++..||++.+|++...+.+.|..|...+ ++...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g----~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEG----LISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEe
Confidence 47899999999999999999999999987 88654
No 47
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=86.18 E-value=2.2 Score=39.53 Aligned_cols=46 Identities=20% Similarity=0.237 Sum_probs=40.0
Q ss_pred HHHHHHHhcC-CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 125 QMCVLLLFNN-REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 125 Qa~ILllFN~-~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
-+.||.+|.. ...+++.||++.+|++...+.+.|..|...+ .|.++
T Consensus 11 al~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G----~l~~~ 57 (248)
T TIGR02431 11 GLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELG----YVTSD 57 (248)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEeC
Confidence 3578888986 5679999999999999999999999999988 77653
No 48
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=86.08 E-value=2 Score=40.28 Aligned_cols=47 Identities=19% Similarity=0.167 Sum_probs=40.3
Q ss_pred HHHHHHHhcCCC-CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 125 QMCVLLLFNNRE-KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 125 Qa~ILllFN~~~-~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
=+.||.+|...+ .+|..||++.+|++...+.+.|..|...+ +|.+++
T Consensus 13 al~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g----~v~~~~ 60 (263)
T PRK09834 13 GLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEG----YVRRSA 60 (263)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEec
Confidence 356778886654 59999999999999999999999999988 888764
No 49
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=85.94 E-value=1.8 Score=36.56 Aligned_cols=53 Identities=13% Similarity=0.230 Sum_probs=45.2
Q ss_pred EEEchHHHHHHHHhcC-CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 119 IQVSTYQMCVLLLFNN-REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~-~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.+|..|..||..... .+.+|..||++.+|++...+.+.+..|.+.+ ++.+.+
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~G----lV~r~~ 80 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKG----LISRQT 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCC----CEeeec
Confidence 4678889888877765 3578999999999999999999999999988 877654
No 50
>PHA00738 putative HTH transcription regulator
Probab=85.28 E-value=2.6 Score=34.75 Aligned_cols=67 Identities=13% Similarity=0.099 Sum_probs=54.0
Q ss_pred EEEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCC
Q psy11818 118 IIQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSF 192 (331)
Q Consensus 118 ~l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F 192 (331)
++...+.--.||.++.+.+.+++.||++.++|+...+-++|..|-..+ |+.....|. ...|.+|.+.
T Consensus 7 ~~~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAG----LV~srK~Gr----~vyY~Ln~~~ 73 (108)
T PHA00738 7 EIRAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQG----YIELYKEGR----TLYAKIRENS 73 (108)
T ss_pred cccCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCC----ceEEEEECC----EEEEEECCCc
Confidence 466777777888877777789999999999999999999999999998 887655432 3457777764
No 51
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=85.20 E-value=0.18 Score=37.63 Aligned_cols=48 Identities=21% Similarity=0.371 Sum_probs=35.7
Q ss_pred HHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCccc
Q psy11818 232 AVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDR 287 (331)
Q Consensus 232 aIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~ 287 (331)
.|-.+|+.++.++..+|- .+|..+++.+...|+.|+.+|||++.+...
T Consensus 4 ~i~~~l~~~~~~S~~eLa--------~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELA--------REFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHHHS-SEEHHHHH--------HHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHHHcCCcCHHHHH--------HHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 356678889998888553 347789999999999999999999876543
No 52
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=85.19 E-value=3.5 Score=35.71 Aligned_cols=56 Identities=16% Similarity=0.080 Sum_probs=41.5
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecC
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDS 191 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~ 191 (331)
.+.|..+..+.++..+|++..|+|...|.+.|..|.+.+ |+..... ++.-|.|...
T Consensus 14 L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aG----lv~S~rG-----~~GGy~La~~ 69 (153)
T PRK11920 14 LMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAG----LVETVRG-----RNGGVRLGRP 69 (153)
T ss_pred HHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEeecC-----CCCCeeecCC
Confidence 334444555668999999999999999999999999988 8875432 2334665543
No 53
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=84.61 E-value=3.8 Score=34.53 Aligned_cols=44 Identities=16% Similarity=0.163 Sum_probs=35.9
Q ss_pred HHHHHHhcCC-CCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 126 MCVLLLFNNR-EKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 126 a~ILllFN~~-~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
+.+.+.++.. ..+|..+|++.+++|...+.+.|..|.+.+ ++..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~g----lv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAG----LVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC----ceEE
Confidence 3444555543 469999999999999999999999999988 8764
No 54
>PF13730 HTH_36: Helix-turn-helix domain
Probab=84.21 E-value=2.9 Score=29.26 Aligned_cols=27 Identities=19% Similarity=0.340 Sum_probs=25.5
Q ss_pred CHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 139 TYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 139 t~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
|.+.|++.+|++...+.+++..|...|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G 53 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKG 53 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCc
Confidence 899999999999999999999998876
No 55
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=84.16 E-value=2.7 Score=29.17 Aligned_cols=40 Identities=20% Similarity=0.350 Sum_probs=33.6
Q ss_pred hcCCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 132 FNNREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 132 FN~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+...+.+ |..+|++.+|++...+.++|..|...+ ++...+
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g----~i~~~~ 54 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLEAEG----LVQRRP 54 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEec
Confidence 4445567 999999999999999999999999887 776543
No 56
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=84.08 E-value=2 Score=34.28 Aligned_cols=46 Identities=24% Similarity=0.292 Sum_probs=39.7
Q ss_pred EEchHHHHHHHHhcC----CCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 120 QVSTYQMCVLLLFNN----REKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~----~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
.++..|-.||-.+.. .+.+++++|++.++++..+++.+|..|+..+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG 93 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEG 93 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTT
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 688999999998876 5679999999999999999999999999887
No 57
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=83.86 E-value=1.8 Score=34.52 Aligned_cols=44 Identities=7% Similarity=0.188 Sum_probs=38.9
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCccccee
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILI 172 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~ 172 (331)
...||..+..+..+|+.+|++.+|++...+.+.+..|...+ ++.
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g----~i~ 48 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEG----VIK 48 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC----Cee
Confidence 45677777777889999999999999999999999999887 776
No 58
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=83.85 E-value=2.4 Score=38.22 Aligned_cols=53 Identities=13% Similarity=0.134 Sum_probs=47.0
Q ss_pred EEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 119 IQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
...+..|+.||..+.+++.++..||++.+|++...+.+.|..|...+ ++.+.+
T Consensus 139 ~~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~G----lI~r~~ 191 (203)
T TIGR01884 139 AGLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKG----LVEQKG 191 (203)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEEc
Confidence 35688899999999887889999999999999999999999999887 887753
No 59
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=83.27 E-value=4 Score=29.28 Aligned_cols=36 Identities=22% Similarity=0.279 Sum_probs=32.3
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
...+|..||++.+|++...+.+.|..|...+ ++...
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g----~i~~~ 58 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEG----LISRR 58 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEec
Confidence 3569999999999999999999999999987 88764
No 60
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=82.98 E-value=1.6 Score=31.53 Aligned_cols=38 Identities=24% Similarity=0.380 Sum_probs=30.4
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
|.-+|.++-+.+.+|+.||++.+|++...++..+.-|-
T Consensus 7 q~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 7 QLKLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55666555448899999999999999999999888774
No 61
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=82.79 E-value=9.9 Score=32.01 Aligned_cols=76 Identities=22% Similarity=0.220 Sum_probs=49.8
Q ss_pred HHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCccc-cc----cchHHHHHHHHHHHH
Q psy11818 230 EAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDR-FL----QEKDVFERYYKQHLA 304 (331)
Q Consensus 230 qAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~-~i----~~~~~~~~~~~~~~~ 304 (331)
+..|++++-..+.++..+++.. +.........-|...|..|.++|||.|..+.+ ++ .+++=|.....+.+.
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~----l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr~~~Y~p~vs~ee~~~~~~~~~~ 81 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRI----LAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGRKFIYTALVSEDEAVENAAQELF 81 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHH----HhhccCCcHHHHHHHHHHHHHCCceeeecCCCcEEEEecCCHHHHHHHHHHHHH
Confidence 4567888877788877755544 44445678889999999999999999874433 22 334444444445554
Q ss_pred hhhhC
Q psy11818 305 KRLLL 309 (331)
Q Consensus 305 ~~~~~ 309 (331)
.++..
T Consensus 82 ~~~f~ 86 (130)
T TIGR02698 82 SRICS 86 (130)
T ss_pred HHHHC
Confidence 44433
No 62
>PRK10870 transcriptional repressor MprA; Provisional
Probab=82.61 E-value=4 Score=36.11 Aligned_cols=53 Identities=9% Similarity=0.115 Sum_probs=44.0
Q ss_pred EEEchHHHHHHHHhcC--CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 119 IQVSTYQMCVLLLFNN--REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~--~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.+|..|..||..... ...+|..||++.+|++...+.+.+..|.+.| ++.+.+
T Consensus 51 ~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kG----lV~R~~ 105 (176)
T PRK10870 51 QGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRG----WIERRE 105 (176)
T ss_pred CCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEecC
Confidence 3466778888877653 4679999999999999999999999999988 887754
No 63
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=82.42 E-value=4.3 Score=33.59 Aligned_cols=46 Identities=17% Similarity=0.212 Sum_probs=35.9
Q ss_pred HHHHHHHhcC-CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 125 QMCVLLLFNN-REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 125 Qa~ILllFN~-~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
++.+.+.-+. ...+|.++|++.+|++...+.+.|..|...+ ++...
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~g----li~~~ 58 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAG----LVESV 58 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC----cEEec
Confidence 3334444333 3479999999999999999999999999987 77653
No 64
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=80.88 E-value=4.4 Score=28.09 Aligned_cols=36 Identities=11% Similarity=0.127 Sum_probs=31.8
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.+..|..+|++.+|++...+.+.|..|...+ ++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g----~i~~~ 43 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAG----LVESR 43 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCC----Ceeee
Confidence 5678999999999999999999999999887 77543
No 65
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=80.79 E-value=5.2 Score=30.60 Aligned_cols=34 Identities=32% Similarity=0.354 Sum_probs=31.2
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+.|++||.+.||++...|.-+|.-|.+.+ |+.+.
T Consensus 18 c~TLeeL~ekTgi~k~~LlV~LsrL~k~G----iI~Rk 51 (72)
T PF05584_consen 18 CCTLEELEEKTGISKNTLLVYLSRLAKRG----IIERK 51 (72)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCC----Ceeee
Confidence 89999999999999999999999999987 77653
No 66
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=80.71 E-value=25 Score=36.17 Aligned_cols=50 Identities=18% Similarity=0.253 Sum_probs=45.0
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
.+|..|..||......+.+|..+|++.+|++...+.+++..|...+ ++..
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kG----lV~~ 52 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKG----LVKV 52 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCC----CEEE
Confidence 4688999999999988899999999999999999999999998876 6654
No 67
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=80.25 E-value=5.3 Score=33.19 Aligned_cols=37 Identities=16% Similarity=0.300 Sum_probs=32.7
Q ss_pred CCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 134 NREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 134 ~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
..+.+++.||++.+|++...+.+.|..|...+ ++...
T Consensus 22 ~~~~~s~~eia~~l~is~~~v~~~l~~L~~~G----li~~~ 58 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLNAPTVSKILKQLSLAG----IVTSK 58 (130)
T ss_pred CCCCccHHHHHHHHCcCHHHHHHHHHHHHHCC----cEEec
Confidence 34679999999999999999999999999988 88643
No 68
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=79.95 E-value=2.9 Score=30.72 Aligned_cols=32 Identities=28% Similarity=0.392 Sum_probs=27.2
Q ss_pred CCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 134 NREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 134 ~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
.++..|+.+|...|+++.+.++.+|..|++.+
T Consensus 24 ~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~ 55 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLSPKQVKKALVVLIQHN 55 (62)
T ss_dssp HC-SEEHHHHHHHHT--HHHHHHHHHHHHHTT
T ss_pred HcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence 46789999999999999999999999999987
No 69
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=79.84 E-value=4.7 Score=31.91 Aligned_cols=51 Identities=20% Similarity=0.253 Sum_probs=44.4
Q ss_pred EchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 121 VSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 121 vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.+..|+.||......+..+..+|++.++++...+.+.+..|...+ ++.+.+
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~g----lv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKG----LIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCC----CeeecC
Confidence 788999999888877776669999999999999999999999988 777654
No 70
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=79.36 E-value=5.7 Score=33.10 Aligned_cols=60 Identities=15% Similarity=0.212 Sum_probs=44.3
Q ss_pred hHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEec
Q psy11818 123 TYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVND 190 (331)
Q Consensus 123 ~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~ 190 (331)
+.-..||.+.-+.+.+++.||++.+|++...+-++|.-|...+ ++.....|. .-.|.+|.
T Consensus 16 ptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AG----LV~~~r~Gr----~~~Y~l~~ 75 (117)
T PRK10141 16 ETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESG----LLLDRKQGK----WVHYRLSP 75 (117)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC----ceEEEEEcC----EEEEEECc
Confidence 4445566555455679999999999999999999999999998 887554321 23466654
No 71
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=78.88 E-value=3.1 Score=30.84 Aligned_cols=44 Identities=18% Similarity=0.162 Sum_probs=35.0
Q ss_pred HHHHhcC-CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 128 VLLLFNN-REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 128 ILllFN~-~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
||..++. +..++-.||++++|++....+..|..|.+.+ .+...|
T Consensus 5 Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG----~V~~~~ 49 (62)
T PF04703_consen 5 ILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEG----KVERSP 49 (62)
T ss_dssp HHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCT----SEEEES
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC----CEEEec
Confidence 4555565 6789999999999999999999999999887 666554
No 72
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=77.45 E-value=4 Score=27.66 Aligned_cols=35 Identities=23% Similarity=0.433 Sum_probs=26.5
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
.||..+......++.+|++.+|++...+.+-+.-|
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 46666666788999999999999999998877654
No 73
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=77.13 E-value=11 Score=28.75 Aligned_cols=51 Identities=24% Similarity=0.163 Sum_probs=44.0
Q ss_pred EchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccce
Q psy11818 121 VSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRIL 171 (331)
Q Consensus 121 vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL 171 (331)
-.+=|+.++.++-..+.-|+++|+++||--...++-+|.-+++.+.++.|.
T Consensus 8 ~~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i~ 58 (72)
T PF11994_consen 8 EGTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTIT 58 (72)
T ss_pred cccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEEE
Confidence 367799999999999999999999999999999999999998777544443
No 74
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=76.36 E-value=7.6 Score=28.28 Aligned_cols=45 Identities=13% Similarity=0.178 Sum_probs=37.3
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+|..+-.+...++..+|++.+|++...+...+.-|...+ ++...+
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~G----lV~~~~ 56 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKG----LVEYEP 56 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTT----SEEEET
T ss_pred HHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCC----CEEecC
Confidence 444455578899999999999999999999999999888 887654
No 75
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=75.97 E-value=3.9 Score=30.38 Aligned_cols=37 Identities=16% Similarity=0.195 Sum_probs=29.7
Q ss_pred HHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 129 LLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 129 LllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
.-...++..+|+.||+..++++.+.+...|..|+..+
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG 42 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKG 42 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCT
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 3344567889999999999999999999999999887
No 76
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=75.63 E-value=5.1 Score=37.07 Aligned_cols=44 Identities=18% Similarity=0.234 Sum_probs=38.1
Q ss_pred HHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 126 MCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 126 a~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
..||.+.+..+.+|.+||++.+||+...++++|..|...+ ++..
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~G----lv~~ 57 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEG----LVEV 57 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCc----ceee
Confidence 3566667888999999999999999999999999999887 6653
No 77
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=75.29 E-value=2.5 Score=32.39 Aligned_cols=33 Identities=18% Similarity=0.126 Sum_probs=27.8
Q ss_pred cCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 133 NNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 133 N~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
...+.+|+.||++.+|++...++..+..+...+
T Consensus 28 R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~ 60 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTEQTVRNHLKGETKAG 60 (73)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccc
Confidence 334679999999999999999999988776655
No 78
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=74.82 E-value=4.9 Score=37.70 Aligned_cols=47 Identities=21% Similarity=0.239 Sum_probs=42.4
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
-|..|+.+.+.++.+++.||++.+|++...+++-|..|-..+ +|.+.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g----~l~r~ 52 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAG----TVIRT 52 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEE
Confidence 477899999999999999999999999999999999998877 77664
No 79
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=74.56 E-value=12 Score=31.68 Aligned_cols=40 Identities=5% Similarity=0.166 Sum_probs=34.4
Q ss_pred hcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 132 FNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 132 FN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.....++..+|++.+|++...+.++|..|...+ ++...+
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~G----lv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAG----YVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCC----EEEEec
Confidence 4445578999999999999999999999999988 887654
No 80
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=74.52 E-value=6.9 Score=33.00 Aligned_cols=78 Identities=19% Similarity=0.230 Sum_probs=60.3
Q ss_pred hHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCccc--------------cccchH
Q psy11818 228 EIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDR--------------FLQEKD 293 (331)
Q Consensus 228 ~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~--------------~i~~~~ 293 (331)
..++.|++||=.++..+.+|++.++.+. +.++..-|+--|..|..||+|.|..+++ .....+
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~----~ews~sTV~TLl~RL~KKg~l~~~kdgr~~~y~pL~~~~~~~~~~~~~ 81 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD----REWSYSTVKTLLNRLVKKGLLTRKKDGRAFRYSPLLTRDQYVAGESQD 81 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc----ccccHHHHHHHHHHHHhccchhhhhcCCeeeeecccCHHHHHHHHHHH
Confidence 4678899999999999999777766554 7788999999999999999999976543 233456
Q ss_pred HHHHHHHHHHHhhhhC
Q psy11818 294 VFERYYKQHLAKRLLL 309 (331)
Q Consensus 294 ~~~~~~~~~~~~~~~~ 309 (331)
+-+++|...++.-+.|
T Consensus 82 ~l~k~~d~~~~~lv~~ 97 (123)
T COG3682 82 LLDKICDGGLASLVAH 97 (123)
T ss_pred HHHHHHcccchHHHHH
Confidence 6677777766554444
No 81
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=73.97 E-value=3.4 Score=33.15 Aligned_cols=45 Identities=13% Similarity=0.200 Sum_probs=32.1
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
.+.|+..+..++.++-++|++.+|++..++++.|..|...+ ++..
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~----lv~~ 59 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDG----LVSY 59 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHS----S-EE
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC----CeEE
Confidence 34566566556789999999999999999999999999887 7643
No 82
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=73.21 E-value=12 Score=32.36 Aligned_cols=58 Identities=12% Similarity=0.098 Sum_probs=42.0
Q ss_pred HHHHHHHhcCCC-CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecC
Q psy11818 125 QMCVLLLFNNRE-KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDS 191 (331)
Q Consensus 125 Qa~ILllFN~~~-~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~ 191 (331)
.+.+.|.-+..+ ..|+++|++..|++...|.+.|..|.+.+ ++..... ++.-|.|+..
T Consensus 12 ~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaG----lV~S~rG-----~~GGy~Lar~ 70 (150)
T COG1959 12 RALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAG----LVKSVRG-----KGGGYRLARP 70 (150)
T ss_pred HHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcC----CEEeecC-----CCCCccCCCC
Confidence 344444444444 68899999999999999999999999998 8865432 2344666654
No 83
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=73.18 E-value=6.8 Score=34.08 Aligned_cols=49 Identities=6% Similarity=0.154 Sum_probs=44.0
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCccccee
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILI 172 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~ 172 (331)
.+.-.-..||..+..+..+|+.||++.+|++...+.+.++.|...| ++.
T Consensus 11 ~lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G----vI~ 59 (164)
T PRK11169 11 DLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQG----FIQ 59 (164)
T ss_pred hHHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC----CeE
Confidence 3566778899899999999999999999999999999999999988 775
No 84
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=72.56 E-value=8 Score=36.13 Aligned_cols=48 Identities=17% Similarity=0.128 Sum_probs=42.3
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
-|..|+..++.++.+++.||++.+|++...+++-|..|-..+ ++.+..
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g----~i~r~~ 53 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESG----KLKKVR 53 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEec
Confidence 466788899999999999999999999999999999998876 776644
No 85
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=72.49 E-value=9.3 Score=26.96 Aligned_cols=37 Identities=19% Similarity=0.302 Sum_probs=30.9
Q ss_pred CCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 134 NREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 134 ~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
....+ |..+|++.+|++...+.++|..|...+ ++...
T Consensus 21 ~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G----~i~~~ 58 (66)
T cd07377 21 PGDRLPSERELAEELGVSRTTVREALRELEAEG----LVERR 58 (66)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEec
Confidence 33444 499999999999999999999999987 77654
No 86
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=72.16 E-value=12 Score=33.55 Aligned_cols=44 Identities=14% Similarity=0.141 Sum_probs=36.7
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.||......+.+|..||++.+|++...+.++|..|...+ ++.+.
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~G----lV~r~ 48 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEG----LIEYE 48 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC----CeEEe
Confidence 455555455679999999999999999999999999987 77654
No 87
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=72.01 E-value=6.6 Score=38.44 Aligned_cols=149 Identities=13% Similarity=0.127 Sum_probs=42.1
Q ss_pred EEEchHHHHHHHHhcC--CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCCCCCc
Q psy11818 119 IQVSTYQMCVLLLFNN--REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSFTSKL 196 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~--~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F~~k~ 196 (331)
-.++..+..|.-+-.+ +..+-..+|...|||+...+.+.|..|...+ ++..-. +..+++
T Consensus 80 ~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~----lIK~vk---------------sv~~~~ 140 (327)
T PF05158_consen 80 KGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKK----LIKSVK---------------SVKNPN 140 (327)
T ss_dssp -SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTT----SEEEE-----------------SS-SS
T ss_pred cCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCC----CEEEec---------------CcCCCC
Confidence 4567777777766553 5678889999999999999999999998876 665422 233334
Q ss_pred eeEEEeccccCCCC-hhHHHHhhhhhHHhhhhhHHHHHHHhhhcccC-----------------------------CChH
Q psy11818 197 HRVKIQTVAAKGES-EPERRETRSKVDEDRKHEIEAAVVRIMKARKR-----------------------------MQHN 246 (331)
Q Consensus 197 ~ki~i~~~~~k~e~-~~e~~~~~~~v~edR~~~IqAaIVRIMK~~K~-----------------------------l~~~ 246 (331)
+|+.+-.--..++. ....=-+.++.+.+--..|...|.+++..+.. .+.+
T Consensus 141 rK~Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~ 220 (327)
T PF05158_consen 141 RKVYMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLE 220 (327)
T ss_dssp --EEEESSS-----------------------------------------------------------------------
T ss_pred eEEEEEccCCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccccccCCCCCHH
Confidence 44444322100000 00000112233333444555556666665544 4445
Q ss_pred HHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCcc
Q psy11818 247 TLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPED 286 (331)
Q Consensus 247 ~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d 286 (331)
++...+.+.=-..-..+.++|...|+-|+=-|-|++-...
T Consensus 221 eI~~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~ 260 (327)
T PF05158_consen 221 EIAEFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSG 260 (327)
T ss_dssp ----------------------------------------
T ss_pred HHHHHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEecc
Confidence 5555444322123456889999999999999999987665
No 88
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=71.58 E-value=8.2 Score=33.13 Aligned_cols=49 Identities=10% Similarity=0.232 Sum_probs=43.2
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCccccee
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILI 172 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~ 172 (331)
.+...-..||..+..+...++.+|++.+|++...+.+.++.|...| ++.
T Consensus 6 ~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G----vI~ 54 (153)
T PRK11179 6 QIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAG----IIT 54 (153)
T ss_pred ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC----Cee
Confidence 3456677888888888999999999999999999999999999988 775
No 89
>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=71.55 E-value=11 Score=25.74 Aligned_cols=35 Identities=29% Similarity=0.339 Sum_probs=25.6
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
+..|-+.| ...+|++||++.+|++...+.+.+..-
T Consensus 10 r~vi~~~y--~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 10 REVIRLRY--FEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp HHHHHHHH--TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred HHHHHHHh--cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 34445666 567999999999999998887766543
No 90
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=70.79 E-value=8.1 Score=28.70 Aligned_cols=51 Identities=22% Similarity=0.209 Sum_probs=36.4
Q ss_pred EchHHHHHHHHhcC-----CCCCCHHHHHHhcCCC-HHHHHHHHHHHHcccCcccceeecC
Q psy11818 121 VSTYQMCVLLLFNN-----REKLTYEEIQSETDIP-ERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 121 vs~~Qa~ILllFN~-----~~~lt~~eL~~~tgi~-~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.|.-|.-||...-+ .-.-|+.||++.+|+. ...+..+|..|...+ .|.+.+
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG----~I~r~~ 60 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKG----YIRRDP 60 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTT----SEEEGC
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCc----CccCCC
Confidence 45566666655322 3357999999999997 889999999999887 888765
No 91
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=70.21 E-value=7.9 Score=36.28 Aligned_cols=47 Identities=23% Similarity=0.343 Sum_probs=42.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
-|-.|+.+.+.++.++++||++.+|+++.++++=|..|-..+ +|.+.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g----~l~R~ 52 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQG----LLLRV 52 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCC----cEEEE
Confidence 356788889999999999999999999999999999999887 77764
No 92
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=70.13 E-value=8.4 Score=34.39 Aligned_cols=45 Identities=22% Similarity=0.183 Sum_probs=37.8
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
...||...-.++.+|-+||++.+||+...++++|..|...+ ++..
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~g----Lv~~ 68 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDAR----LADY 68 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC----CeEE
Confidence 34566656667789999999999999999999999999887 7763
No 93
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=68.66 E-value=12 Score=32.67 Aligned_cols=44 Identities=25% Similarity=0.184 Sum_probs=36.1
Q ss_pred HHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 126 MCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 126 a~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
+.|+...=.++.+|-+||+..+||+..++++.|..|...+ ++.+
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~----Lv~~ 60 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAG----LADY 60 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----Ccee
Confidence 4455444455689999999999999999999999999987 7753
No 94
>PRK00215 LexA repressor; Validated
Probab=68.14 E-value=15 Score=32.95 Aligned_cols=51 Identities=16% Similarity=0.174 Sum_probs=41.5
Q ss_pred EchHHHHHHHHhc-----CCCCCCHHHHHHhcCC-CHHHHHHHHHHHHcccCcccceeecC
Q psy11818 121 VSTYQMCVLLLFN-----NREKLTYEEIQSETDI-PERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 121 vs~~Qa~ILllFN-----~~~~lt~~eL~~~tgi-~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+|.-|..||.... ....+|+.||++.+|+ +...+.+.|..|...+ ++.+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g----~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKG----FIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCC----CEEeCC
Confidence 3566888886554 2456899999999999 9999999999999887 887765
No 95
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=67.41 E-value=12 Score=28.02 Aligned_cols=39 Identities=21% Similarity=0.309 Sum_probs=33.1
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
.|--+.++...+|+.+|++.+|+++.++..+|.=|..-+
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~ 50 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAREN 50 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTT
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccC
Confidence 455667888999999999999999999999999887664
No 96
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=67.37 E-value=10 Score=35.55 Aligned_cols=48 Identities=17% Similarity=0.256 Sum_probs=42.3
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
-|..|+.+.+.++.+++.||++.++++...+++-|..|-..+ +|.+.-
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g----~l~r~~ 53 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQN----KILRHH 53 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCC----CEEEec
Confidence 466788888999999999999999999999999999999887 776653
No 97
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=66.50 E-value=10 Score=31.92 Aligned_cols=49 Identities=10% Similarity=0.284 Sum_probs=42.2
Q ss_pred EchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 121 VSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 121 vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
+.-.-.-||..+......++.+|++.+|++...+.+.+.-|...| |+..
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~G----iI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEG----VIKG 54 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----ceee
Confidence 345566788888888889999999999999999999999999988 7765
No 98
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=65.92 E-value=11 Score=35.66 Aligned_cols=50 Identities=10% Similarity=0.107 Sum_probs=43.9
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.--|..|+.+.+.++.+++.||++.+|++...++|-|..|-..+ ++.+..
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G----~l~r~~ 65 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQG----IAVRAY 65 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCC----CeEEEe
Confidence 45788999999999999999999999999999999999998776 666543
No 99
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=65.83 E-value=13 Score=34.60 Aligned_cols=47 Identities=21% Similarity=0.321 Sum_probs=40.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
-|..|+..++.++.++.+||++.+|++...+++-|..|...+ .|.+.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~----~l~r~ 51 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQG----KILRN 51 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEe
Confidence 456788888888999999999999999999999999998765 55543
No 100
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=65.50 E-value=12 Score=35.23 Aligned_cols=51 Identities=16% Similarity=0.301 Sum_probs=44.8
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
-.|.....||-+...++.+.+.||++++|+|...+..+++.|.+.+ ++..+
T Consensus 20 laS~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aG----lirT~ 70 (308)
T COG4189 20 LASKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAG----LIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcC----ceeee
Confidence 3466677899999999999999999999999999999999999988 77643
No 101
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=65.43 E-value=25 Score=28.54 Aligned_cols=74 Identities=14% Similarity=0.208 Sum_probs=48.4
Q ss_pred HHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCcc-cc----ccchHHHHHHHHHHHH
Q psy11818 230 EAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPED-RF----LQEKDVFERYYKQHLA 304 (331)
Q Consensus 230 qAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d-~~----i~~~~~~~~~~~~~~~ 304 (331)
+..|++++=..+.++..+++. .+.....+...-|...+..|.+||||.|.... .+ +..++-|..--.+.+.
T Consensus 5 E~~IM~~lW~~~~~t~~eI~~----~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~is~~e~~~~~~~~~l 80 (115)
T PF03965_consen 5 ELEIMEILWESGEATVREIHE----ALPEERSWAYSTVQTLLNRLVEKGFLTREKIGRAYVYSPLISREEYLAQELRQFL 80 (115)
T ss_dssp HHHHHHHHHHHSSEEHHHHHH----HHCTTSS--HHHHHHHHHHHHHTTSEEEEEETTCEEEEESSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCCCHHHHHH----HHHhccccchhHHHHHHHHHHhCCceeEeecCCceEEEeCCcHHHHHHHHHHHHH
Confidence 566778887788888775554 45545677899999999999999999998643 33 3334444444444444
Q ss_pred hhh
Q psy11818 305 KRL 307 (331)
Q Consensus 305 ~~~ 307 (331)
.+.
T Consensus 81 ~~~ 83 (115)
T PF03965_consen 81 DRL 83 (115)
T ss_dssp HHH
T ss_pred HHH
Confidence 443
No 102
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=64.97 E-value=6.3 Score=35.21 Aligned_cols=47 Identities=15% Similarity=0.134 Sum_probs=42.1
Q ss_pred hHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 123 TYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 123 ~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
.-+..|+.+.+.++.+++.+|++.+|++...+++-|..|...+ ++.+
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g----~~~r 53 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPE----LRER 53 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcch----HHHH
Confidence 4677889999999999999999999999999999999999887 6654
No 103
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=64.00 E-value=12 Score=24.01 Aligned_cols=28 Identities=18% Similarity=0.260 Sum_probs=23.0
Q ss_pred CCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 138 LTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
+|-+||++.+|++.+.+-+.|.-|-..|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~g 30 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQG 30 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcC
Confidence 6789999999999999999999987765
No 104
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=63.94 E-value=17 Score=24.47 Aligned_cols=39 Identities=28% Similarity=0.342 Sum_probs=29.2
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
+.-+..|+.++- ..++..+|++.+|++...+...+.-+.
T Consensus 5 ~~~e~~i~~~~~--~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 5 TPREREVLRLLA--EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 444555555553 458999999999999999988877654
No 105
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=63.38 E-value=18 Score=24.54 Aligned_cols=37 Identities=27% Similarity=0.278 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
.|.-++.++- +.++..+|++.+|++...+...+.-+.
T Consensus 4 ~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 4 REREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444444332 468999999999999998888877654
No 106
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=62.90 E-value=27 Score=30.88 Aligned_cols=56 Identities=14% Similarity=0.023 Sum_probs=45.9
Q ss_pred cEEEEEchHHHHHHHHhcCCCCC-CHHHHHHhc--CCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 116 KHIIQVSTYQMCVLLLFNNREKL-TYEEIQSET--DIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 116 ~~~l~vs~~Qa~ILllFN~~~~l-t~~eL~~~t--gi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.+.+--+.+..+|+.+..-.+.- +..+|+..+ +|+.++++.+|..|.+.| +|.++.
T Consensus 17 ~~~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~g----li~k~~ 75 (171)
T PF14394_consen 17 EFEYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLG----LIKKDG 75 (171)
T ss_pred HHHHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCC----CeEECC
Confidence 44556677777888777655443 999999999 999999999999999998 998863
No 107
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=61.96 E-value=18 Score=28.09 Aligned_cols=44 Identities=18% Similarity=0.289 Sum_probs=36.2
Q ss_pred HHHHHHhcCCCCCCHHHHHHhc-CCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 126 MCVLLLFNNREKLTYEEIQSET-DIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 126 a~ILllFN~~~~lt~~eL~~~t-gi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+.||..... +...+.||.+.+ |++...|.+.|..|...+ ++.+.
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~G----Lv~r~ 52 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAG----LVERR 52 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTT----SEEEE
T ss_pred HHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcc----hhhcc
Confidence 456655555 789999999999 999999999999999988 88764
No 108
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=61.43 E-value=14 Score=25.09 Aligned_cols=31 Identities=16% Similarity=0.288 Sum_probs=21.5
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
-|+-++.+. +|+.+|++.+|++...+.+.|.
T Consensus 13 ~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 13 EIKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 344445543 9999999999999999988774
No 109
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=61.23 E-value=7.5 Score=35.12 Aligned_cols=26 Identities=35% Similarity=0.580 Sum_probs=22.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
..+|+++|++.|||..+++..+|+.|
T Consensus 149 ~~isi~~is~~Tgi~~~DIi~tL~~l 174 (188)
T PF01853_consen 149 KSISIKDISQETGIRPEDIISTLQQL 174 (188)
T ss_dssp --EEHHHHHHHH-BTHHHHHHHHHHT
T ss_pred CeEEHHHHHHHHCCCHHHHHHHHHHC
Confidence 47999999999999999999999887
No 110
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=59.69 E-value=15 Score=28.63 Aligned_cols=35 Identities=9% Similarity=0.038 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
-|+.|+..... +.+|+.+|++.+|++...+.+.|.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 57788888888 999999999999999999988663
No 111
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=59.21 E-value=9.1 Score=27.41 Aligned_cols=47 Identities=17% Similarity=0.351 Sum_probs=38.9
Q ss_pred HHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCc
Q psy11818 231 AAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPE 285 (331)
Q Consensus 231 AaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~ 285 (331)
..|+.+++.++.++..+|.+ .|..|..-|.+=+..|-+.|+|.|.-+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~--------~~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAE--------EFGVSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHH--------HHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 46788899999999887655 367889999999999999999988543
No 112
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=59.06 E-value=22 Score=24.51 Aligned_cols=24 Identities=29% Similarity=0.466 Sum_probs=17.3
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|+.||++.+|++...+...+.
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHH
Confidence 468999999999999998887664
No 113
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=58.60 E-value=33 Score=30.96 Aligned_cols=48 Identities=15% Similarity=0.160 Sum_probs=37.7
Q ss_pred EchHHHHHHHH---hcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCccccee
Q psy11818 121 VSTYQMCVLLL---FNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILI 172 (331)
Q Consensus 121 vs~~Qa~ILll---FN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~ 172 (331)
.+.-+.-+++. -+....+|.++|++.+|++...++.++..|++.+ +|.
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~----~~~ 209 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCH----ILF 209 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCC----EEE
Confidence 45555444433 2446789999999999999999999999999987 773
No 114
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=58.35 E-value=19 Score=27.73 Aligned_cols=43 Identities=14% Similarity=0.125 Sum_probs=35.5
Q ss_pred hHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 123 TYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 123 ~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
....++.-++.....+++++|++.++++.+++...+..++..|
T Consensus 46 i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~ 88 (105)
T PF01399_consen 46 IRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNG 88 (105)
T ss_dssp HHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCC
Confidence 4445555556678899999999999999999999999999887
No 115
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=58.00 E-value=41 Score=25.47 Aligned_cols=43 Identities=14% Similarity=0.222 Sum_probs=31.7
Q ss_pred HHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 126 MCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 126 a~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
+-||.... .+..+..+|+..+|++...+.+.|..|...+ ++..
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~g----LI~~ 51 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKG----LIKK 51 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTT----SEEE
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCc----CeeC
Confidence 45666555 6788999999999999999999999999987 6643
No 116
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=57.98 E-value=14 Score=24.63 Aligned_cols=45 Identities=16% Similarity=0.291 Sum_probs=34.0
Q ss_pred HHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCC
Q psy11818 232 AVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTP 284 (331)
Q Consensus 232 aIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~ 284 (331)
.|.++|.....++..+|...+ ..+..-+.+.|..|.++|+|.+..
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l--------~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 4 QILELLAQQGKVSVEELAELL--------GVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEEee
Confidence 355566666677777666553 568888999999999999998754
No 117
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=57.37 E-value=39 Score=26.21 Aligned_cols=41 Identities=20% Similarity=0.184 Sum_probs=33.5
Q ss_pred HHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCccccee
Q psy11818 130 LLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILI 172 (331)
Q Consensus 130 llFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~ 172 (331)
+.-.+.+..|.++|++.+|++...+-++++.|=..+ +.|..
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G--~~I~s 52 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEG--VDIES 52 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhC--CceEe
Confidence 334566789999999999999999999999997766 44554
No 118
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=57.30 E-value=16 Score=29.02 Aligned_cols=47 Identities=19% Similarity=0.301 Sum_probs=38.9
Q ss_pred HHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhC
Q psy11818 229 IEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLART 283 (331)
Q Consensus 229 IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd 283 (331)
+|-.|++.+.....++..+|...+ ..+.+.+.++|..|.++|+|.|.
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l--------~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKV--------GLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeece
Confidence 466788999998889988766554 56788899999999999999964
No 119
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=56.41 E-value=30 Score=29.33 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=39.6
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
..+.+-|+.+--.++.+|+.|+...||++-..+.+++.-|+..|
T Consensus 11 ~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G 54 (127)
T PF06163_consen 11 EELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARG 54 (127)
T ss_pred HHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence 34667788888889999999999999999999999999999887
No 120
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=56.30 E-value=15 Score=32.61 Aligned_cols=51 Identities=20% Similarity=0.154 Sum_probs=41.4
Q ss_pred EchHHHHHHHHhcC-----CCCCCHHHHHHhcCCC-HHHHHHHHHHHHcccCcccceeecC
Q psy11818 121 VSTYQMCVLLLFNN-----REKLTYEEIQSETDIP-ERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 121 vs~~Qa~ILllFN~-----~~~lt~~eL~~~tgi~-~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
++..|..||....+ .-..|+.||++.+|++ ...+.++|..|.+.+ +|.+.+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g----~i~~~~ 60 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKG----YIERDP 60 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCC----CEecCC
Confidence 46778888866552 2348899999999998 999999999999988 887653
No 121
>KOG2747|consensus
Probab=56.08 E-value=15 Score=36.81 Aligned_cols=25 Identities=44% Similarity=0.610 Sum_probs=23.6
Q ss_pred CCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 138 LTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
+|++||+..|||..+++...|.+|-
T Consensus 330 isI~~iS~~Tgi~~~DIisTL~~L~ 354 (396)
T KOG2747|consen 330 ISIKEISKETGIRPDDIISTLQSLN 354 (396)
T ss_pred ccHHHHHHhhCCCHHHHHHHHHhhC
Confidence 9999999999999999999999883
No 122
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=55.72 E-value=22 Score=26.36 Aligned_cols=57 Identities=18% Similarity=0.362 Sum_probs=38.9
Q ss_pred HhhhhhHHHHHHHhhhcccC-CChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCcc
Q psy11818 223 EDRKHEIEAAVVRIMKARKR-MQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPED 286 (331)
Q Consensus 223 edR~~~IqAaIVRIMK~~K~-l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d 286 (331)
.+|+..|=.+|...+...+. -+.. ++.+.+. +. |..-+..-|+.|.++|||+|++.-
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~Pt~r----EIa~~~g--~~-S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 5 TERQKEVLEFIREYIEENGYPPTVR----EIAEALG--LK-STSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp -HHHHHHHHHHHHHHHHHSS---HH----HHHHHHT--SS-SHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCHH----HHHHHhC--CC-ChHHHHHHHHHHHHCcCccCCCCC
Confidence 35666677777777777653 4444 4444442 22 678889999999999999998764
No 123
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=55.24 E-value=35 Score=24.98 Aligned_cols=34 Identities=26% Similarity=0.244 Sum_probs=30.5
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.+|.++|++.+|++...+.+.|.-|.+.+ ++...
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g----~I~~~ 61 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEG----IIEVK 61 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTT----SEEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEc
Confidence 37999999999999999999999999887 87654
No 124
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=55.20 E-value=18 Score=32.32 Aligned_cols=45 Identities=24% Similarity=0.205 Sum_probs=37.8
Q ss_pred EEchHHHHHHHHhcC--CCCCCHHHHHHhcCCCHHHHHHHHHHHHcc
Q psy11818 120 QVSTYQMCVLLLFNN--REKLTYEEIQSETDIPERDLIRALQSLAMG 164 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~--~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~ 164 (331)
.||+.||.-|+.-.. -..||.+.|++..+|+.+++...|..+.-.
T Consensus 117 kltl~qal~lL~~Hq~~P~~WtaekIA~eY~L~~~dv~~iL~yF~~F 163 (179)
T PF06784_consen 117 KLTLRQALELLNNHQLDPETWTAEKIAQEYKLDEKDVKNILKYFKPF 163 (179)
T ss_pred ceeHHHHHHHHHHhccCccccCHHHHHHHhCCCHHHHHHHHHhcCCc
Confidence 588999998887543 357999999999999999999988887544
No 125
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=55.01 E-value=19 Score=33.60 Aligned_cols=39 Identities=15% Similarity=0.182 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
-|..|+.+.+.++.+++.||++.+|+++..+++=|..|-
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le 46 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHS 46 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhh
Confidence 578899999999999999999999999999999999876
No 126
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=54.52 E-value=22 Score=25.63 Aligned_cols=38 Identities=18% Similarity=0.332 Sum_probs=31.7
Q ss_pred CCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 134 NREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 134 ~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
..+.+ |..+|++.+|++...+.++|..|...+ ++...+
T Consensus 20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g----~i~~~~ 58 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVSRTTVREALRRLEAEG----LIERRP 58 (64)
T ss_dssp TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTT----SEEEET
T ss_pred CCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCC----cEEEEC
Confidence 45778 999999999999999999999999987 887654
No 127
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=54.40 E-value=17 Score=23.91 Aligned_cols=28 Identities=21% Similarity=0.342 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
...|+++||++..|++...+.+.++...
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5679999999999999999998887654
No 128
>PRK11050 manganese transport regulator MntR; Provisional
Probab=53.60 E-value=37 Score=29.22 Aligned_cols=44 Identities=11% Similarity=0.130 Sum_probs=36.4
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.|+.++...+.++..||++.+|++...+.+.|..|...+ ++.+.
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~G----lI~r~ 84 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDG----LVEMR 84 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEe
Confidence 344466667889999999999999999999999998876 66543
No 129
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=53.31 E-value=32 Score=28.96 Aligned_cols=44 Identities=16% Similarity=0.241 Sum_probs=36.5
Q ss_pred HHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 126 MCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 126 a~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
-.|..+.+..+..++.+|++.+|++...+.+.|..|...+ ++.+
T Consensus 11 ~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~G----li~~ 54 (142)
T PRK03902 11 EQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDE----YLIY 54 (142)
T ss_pred HHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCC----CEEE
Confidence 3445555677889999999999999999999999999887 6654
No 130
>smart00753 PAM PCI/PINT associated module.
Probab=52.38 E-value=33 Score=26.01 Aligned_cols=32 Identities=0% Similarity=0.050 Sum_probs=29.1
Q ss_pred CCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 134 NREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 134 ~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
....+++++|++.++++.+++...+..++..+
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~ 52 (88)
T smart00753 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDG 52 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCC
Confidence 46789999999999999999999999998877
No 131
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=52.38 E-value=33 Score=26.01 Aligned_cols=32 Identities=0% Similarity=0.050 Sum_probs=29.1
Q ss_pred CCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 134 NREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 134 ~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
....+++++|++.++++.+++...+..++..+
T Consensus 21 ~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~ 52 (88)
T smart00088 21 PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDG 52 (88)
T ss_pred HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCC
Confidence 46789999999999999999999999998877
No 132
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=51.74 E-value=21 Score=26.49 Aligned_cols=51 Identities=8% Similarity=0.099 Sum_probs=38.9
Q ss_pred HHHHHHHhhhcccC--CChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCccc
Q psy11818 229 IEAAVVRIMKARKR--MQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDR 287 (331)
Q Consensus 229 IqAaIVRIMK~~K~--l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~ 287 (331)
.+..|..+|+.++. ++-.+|-.++ ..+...+.+.+..|.++|||.++++.|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~l--------gl~~~~v~r~L~~L~~~G~V~~~~~~~ 59 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNL--------GLPKKEVNRVLYSLEKKGKVCKQGGTP 59 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 34568889999877 8877655443 245567999999999999999987653
No 133
>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=50.88 E-value=46 Score=23.80 Aligned_cols=29 Identities=24% Similarity=0.429 Sum_probs=23.7
Q ss_pred hcCCCCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 132 FNNREKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 132 FN~~~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
|+.--..|++||++.+||+...+-.+|..
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 55556899999999999998877776654
No 134
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=49.25 E-value=27 Score=33.62 Aligned_cols=36 Identities=22% Similarity=0.378 Sum_probs=28.6
Q ss_pred HHHHHHh-cCCCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 126 MCVLLLF-NNREKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 126 a~ILllF-N~~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
..|+-.+ +....+|+++|+..|||..+++..+|+.|
T Consensus 211 ~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l 247 (290)
T PLN03238 211 RVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL 247 (290)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 3444333 44578999999999999999999999876
No 135
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=49.14 E-value=32 Score=31.90 Aligned_cols=51 Identities=25% Similarity=0.173 Sum_probs=41.9
Q ss_pred EEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 119 IQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
|.-.|+|...-..=.....+|.+|+++++|++-...++.|.-|++.+ +|..
T Consensus 155 i~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~----~l~a 205 (224)
T COG4565 155 LDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNG----ILEA 205 (224)
T ss_pred cCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcC----eeeE
Confidence 67788887655443345789999999999999999999999999887 7753
No 136
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=49.04 E-value=45 Score=26.63 Aligned_cols=37 Identities=16% Similarity=0.327 Sum_probs=25.4
Q ss_pred HHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 128 VLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 128 ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
+..+..+.+. ++..|.+.||||...++..|.+|-..+
T Consensus 13 la~li~~~~~-nvp~L~~~TGmPrRT~Qd~i~aL~~~~ 49 (90)
T PF09904_consen 13 LAYLIDSGER-NVPALMEATGMPRRTIQDTIKALPELG 49 (90)
T ss_dssp HHHHHHHS-B--HHHHHHHH---HHHHHHHHHGGGGGT
T ss_pred HHHHHhcCCc-cHHHHHHHhCCCHhHHHHHHHHhhcCC
Confidence 3344445555 999999999999999999999998665
No 137
>PHA02943 hypothetical protein; Provisional
Probab=48.92 E-value=44 Score=29.37 Aligned_cols=38 Identities=21% Similarity=0.090 Sum_probs=32.2
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
-||.++ ..+..|..||++++|++-....-+|..|-..|
T Consensus 15 eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG 52 (165)
T PHA02943 15 KTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEG 52 (165)
T ss_pred HHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence 355555 66788999999999999999999999887776
No 138
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=48.19 E-value=80 Score=22.97 Aligned_cols=29 Identities=10% Similarity=0.134 Sum_probs=26.4
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
..+..+|++.+|++...+.+++..|-..+
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L~~~g 41 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTLREWG 41 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 47899999999999999999999997765
No 139
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=47.86 E-value=17 Score=24.60 Aligned_cols=35 Identities=11% Similarity=0.227 Sum_probs=21.4
Q ss_pred HHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcc
Q psy11818 128 VLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMG 164 (331)
Q Consensus 128 ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~ 164 (331)
++.++.+ .+|..+|++.+|++...+.+-+.-+-..
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~~~ 44 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYREE 44 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT-----
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHcccc
Confidence 4444443 8999999999999999998877766443
No 140
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=47.85 E-value=34 Score=28.61 Aligned_cols=51 Identities=18% Similarity=0.073 Sum_probs=39.5
Q ss_pred EEchHHHHHHHH----------hcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 120 QVSTYQMCVLLL----------FNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 120 ~vs~~Qa~ILll----------FN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
-+-.++-.+++. |+..-.+|.++||..++-+.+.++.+|..|.+.+ ++...
T Consensus 26 ~~~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~AL~~f~k~g----lIe~~ 86 (121)
T PF09681_consen 26 YTVIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEFDRPVDTVRLALAVFQKLG----LIEID 86 (121)
T ss_pred eHHHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEe
Confidence 344555555555 3445689999999999999999999999999887 77554
No 141
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=47.52 E-value=23 Score=28.45 Aligned_cols=51 Identities=10% Similarity=0.105 Sum_probs=40.9
Q ss_pred HHHHhhhc-ccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCc
Q psy11818 232 AVVRIMKA-RKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPE 285 (331)
Q Consensus 232 aIVRIMK~-~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~ 285 (331)
+|..+|.. .+.++.++|...+.++. ..++..-|=+.|+.|.+.|+|.+-..
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 45666655 56799999998887664 46788999999999999999998643
No 142
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=47.47 E-value=46 Score=22.62 Aligned_cols=41 Identities=15% Similarity=0.179 Sum_probs=30.1
Q ss_pred EEEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 118 IIQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 118 ~l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
-++-.+-|+++-++.+. .|+.+++..+|++...+.+.+...
T Consensus 11 r~T~~~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 11 RITKRLEQYILKLLRES---RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cHHHHHHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34555555555555443 799999999999999999987643
No 143
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=46.70 E-value=41 Score=25.45 Aligned_cols=54 Identities=17% Similarity=0.225 Sum_probs=38.2
Q ss_pred HHHhhhcc-cCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCC-ccccccchHH
Q psy11818 233 VVRIMKAR-KRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTP-EDRFLQEKDV 294 (331)
Q Consensus 233 IVRIMK~~-K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~-~d~~i~~~~~ 294 (331)
|...+... +.++..+|..++ ..+...+.+.+..|.+.|||.+++ +..+.-...+
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l--------~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~ 65 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERL--------GLSKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKV 65 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCeeecCCCCceeecHHH
Confidence 44555554 678888877766 346777899999999999999975 3344444433
No 144
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=46.67 E-value=59 Score=25.97 Aligned_cols=58 Identities=19% Similarity=0.213 Sum_probs=41.5
Q ss_pred HHHHHHhcC-CCCCCHHHHHHhc-----CCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEec
Q psy11818 126 MCVLLLFNN-REKLTYEEIQSET-----DIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVND 190 (331)
Q Consensus 126 a~ILllFN~-~~~lt~~eL~~~t-----gi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~ 190 (331)
..||..+.. ...+|.+||.+.+ +++...+-++|..|...+ ++.+...+. ....|.++.
T Consensus 4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~G----li~~~~~~~---~~~~y~~~~ 67 (116)
T cd07153 4 LAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAG----LVREIELGD---GKARYELNT 67 (116)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCC----CEEEEEeCC---CceEEEeCC
Confidence 345655544 5679999999998 688999999999999998 887643211 124566654
No 145
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=46.00 E-value=51 Score=25.57 Aligned_cols=39 Identities=18% Similarity=0.267 Sum_probs=28.1
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
+...+|-+.-....+|..+|+.++|.+.+++..+|..+-
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 344566666778899999999999999999999998763
No 146
>PRK06474 hypothetical protein; Provisional
Probab=45.42 E-value=57 Score=28.92 Aligned_cols=53 Identities=25% Similarity=0.258 Sum_probs=43.1
Q ss_pred EEEEchHHHHHHHHhcCCC-CCCHHHHHHhc-CCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 118 IIQVSTYQMCVLLLFNNRE-KLTYEEIQSET-DIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 118 ~l~vs~~Qa~ILllFN~~~-~lt~~eL~~~t-gi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
++-.+.....||..+-..+ .+|..+|++.+ +++...+-++|..|...| ++...
T Consensus 6 ~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~G----LI~~~ 60 (178)
T PRK06474 6 EILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSG----ILHVV 60 (178)
T ss_pred HhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCC----CEEEe
Confidence 4556777788886665544 49999999999 799999999999999998 88754
No 147
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=44.73 E-value=9.9 Score=27.79 Aligned_cols=53 Identities=17% Similarity=0.119 Sum_probs=39.1
Q ss_pred HHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCccccc
Q psy11818 229 IEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDRFL 289 (331)
Q Consensus 229 IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~~i 289 (331)
.++.|...|-..+.++..+|...+ ..+.+.+-+.++.|.++|+|+|.+.++.+
T Consensus 9 ~E~~vy~~Ll~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~~~~~ 61 (68)
T PF01978_consen 9 NEAKVYLALLKNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEGRPKV 61 (68)
T ss_dssp HHHHHHHHHHHHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEECCEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcCceEE
Confidence 345555555577788888655544 24677789999999999999999877654
No 148
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=44.23 E-value=45 Score=31.73 Aligned_cols=43 Identities=21% Similarity=0.371 Sum_probs=36.0
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.||++.-+ +..|++||.+.++++...+..+|+-|.+.+ ++.++
T Consensus 17 ~lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~~~~----LV~~~ 59 (260)
T COG4742 17 DLLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLKDKG----LVVQE 59 (260)
T ss_pred HHHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHhhCC----CEEec
Confidence 45555544 789999999999999999999999999887 77764
No 149
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=43.81 E-value=53 Score=30.33 Aligned_cols=46 Identities=22% Similarity=0.280 Sum_probs=37.7
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+.+.+-.-++...+|..||++.+|++...+.+.|..|...+ ++.+.
T Consensus 9 ~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~G----lI~R~ 54 (217)
T PRK14165 9 KLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEG----YITRT 54 (217)
T ss_pred HHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEE
Confidence 34444445566679999999999999999999999999887 87764
No 150
>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=43.42 E-value=51 Score=21.44 Aligned_cols=39 Identities=28% Similarity=0.294 Sum_probs=27.2
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
+..+..++.++- .+.++..+|++.+|++...+.+.+...
T Consensus 12 ~~~~~~~~~~~~-~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 12 PEREREVILLRF-GEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 344444443332 256899999999999999988877654
No 151
>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=43.26 E-value=50 Score=23.20 Aligned_cols=40 Identities=20% Similarity=0.292 Sum_probs=30.9
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHc
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAM 163 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~ 163 (331)
|.-+..||.++-. ..+..||++.+|++...+..++..+..
T Consensus 5 T~~E~~vl~~l~~--G~~~~eIA~~l~is~~tV~~~~~~i~~ 44 (58)
T PF00196_consen 5 TERELEVLRLLAQ--GMSNKEIAEELGISEKTVKSHRRRIMK 44 (58)
T ss_dssp -HHHHHHHHHHHT--TS-HHHHHHHHTSHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHh--cCCcchhHHhcCcchhhHHHHHHHHHH
Confidence 4556677766654 579999999999999999999888764
No 152
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=43.14 E-value=54 Score=24.67 Aligned_cols=48 Identities=17% Similarity=0.306 Sum_probs=39.6
Q ss_pred hHHHHHHHHhcC--CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 123 TYQMCVLLLFNN--REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 123 ~~Qa~ILllFN~--~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
..|.++|..--. ...++-.||+..+|++...+-..++.|...+ ++.+.
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~g----LI~k~ 51 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKG----LIVKQ 51 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCC----CEEEE
Confidence 457777777653 4678999999999999999999999999887 77664
No 153
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=43.06 E-value=46 Score=31.59 Aligned_cols=59 Identities=15% Similarity=0.302 Sum_probs=33.4
Q ss_pred chHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCC
Q psy11818 122 STYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSF 192 (331)
Q Consensus 122 s~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F 192 (331)
.-+--.|.-+|..+..|++.+|.+.|+-|+..|+.+|..++ +|.+.+. -...|.|=++|
T Consensus 215 ~eL~d~lF~~Fe~~~ywslK~L~~~t~QP~~yLKeiL~eIa-------~~~k~g~-----~~~~w~LKpey 273 (275)
T PF02270_consen 215 NELLDLLFKLFEKHQYWSLKDLRQRTQQPEAYLKEILEEIA-------VLNKRGP-----HKNMWELKPEY 273 (275)
T ss_dssp HHHHHHHHHHHHH-S-B-HHHHHHH--S-HHHHHHHHHHH---------EE--TT--------EE----SS
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH-------HHhccCC-----cCCcEecchHH
Confidence 44556677889999999999999999999999999999875 5655421 12456665555
No 154
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=42.65 E-value=83 Score=26.35 Aligned_cols=50 Identities=16% Similarity=0.058 Sum_probs=39.3
Q ss_pred EchHHHHHHHHhcCCCCCCHHHHHHhc----CCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 121 VSTYQMCVLLLFNNREKLTYEEIQSET----DIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 121 vs~~Qa~ILllFN~~~~lt~~eL~~~t----gi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+|..++.|+..+=+.+..|..||.+.+ |++...+...|.-|...| ++.+.
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG----~v~~~ 55 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKG----CLTTE 55 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCC----ceeee
Confidence 456778888776566789999966665 788899999999999877 77653
No 155
>PHA02591 hypothetical protein; Provisional
Probab=42.42 E-value=29 Score=27.06 Aligned_cols=25 Identities=32% Similarity=0.360 Sum_probs=22.6
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
-.+|.++|++.+|++.+.+.+.|.+
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 4799999999999999999998865
No 156
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=42.34 E-value=37 Score=34.73 Aligned_cols=30 Identities=27% Similarity=0.459 Sum_probs=26.6
Q ss_pred hcCCCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 132 FNNREKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 132 FN~~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
.+....+|+++|+..|||..+++..+|+.|
T Consensus 369 ~~~~~~~si~~is~~T~i~~~Dii~tL~~l 398 (450)
T PLN00104 369 KKHKGNISIKELSDMTAIKAEDIVSTLQSL 398 (450)
T ss_pred HhcCCCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 345578999999999999999999999987
No 157
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=42.24 E-value=86 Score=26.95 Aligned_cols=63 Identities=16% Similarity=0.203 Sum_probs=45.5
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCC---CCeEEEecCCC
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEP---NHVFFVNDSFT 193 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~---~~~f~lN~~F~ 193 (331)
.+|-+.-..+..|+.|+++.+|=+...+-+.|..|...+ ++..+.++....+ -+.|.++-.|.
T Consensus 68 eLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~G----lI~fe~~gq~k~P~~~y~~l~I~lpf~ 133 (144)
T COG4190 68 ELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLG----LIFFEEDGQRKQPVVWYDELVIDLPFD 133 (144)
T ss_pred HHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcC----eEEEecCCcccCceeeccccEEeeecC
Confidence 344455678899999999999999999999999999988 7776544433222 23445555554
No 158
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=41.81 E-value=28 Score=29.18 Aligned_cols=51 Identities=22% Similarity=0.399 Sum_probs=42.8
Q ss_pred hhHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCc
Q psy11818 227 HEIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPE 285 (331)
Q Consensus 227 ~~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~ 285 (331)
-.+|..|.+++.....+++.+|-+.|- .+.+.+..+|+.|.++|.|++..-
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg--------lS~~~v~~Ri~~L~~~GiI~~~~~ 57 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG--------LSPSTVLRRIKRLEEEGVIKGYTA 57 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC--------CCHHHHHHHHHHHHHCCceeeEEE
Confidence 357788999999999999997776663 577889999999999999999644
No 159
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=41.57 E-value=35 Score=29.21 Aligned_cols=31 Identities=23% Similarity=0.185 Sum_probs=28.6
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
++.+|-+||++.+||+...+++.|..|...+
T Consensus 13 ~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~ 43 (147)
T smart00531 13 NGCVTEEDLAELLGIKQKQLRKILYLLYDEK 43 (147)
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHhhh
Confidence 4579999999999999999999999998866
No 160
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=41.40 E-value=22 Score=28.23 Aligned_cols=48 Identities=10% Similarity=0.170 Sum_probs=32.5
Q ss_pred hhhHHHHHHHhhhc----ccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHH
Q psy11818 226 KHEIEAAVVRIMKA----RKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLA 281 (331)
Q Consensus 226 ~~~IqAaIVRIMK~----~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~ 281 (331)
..-++..|..++|. .--++.++|.+.+ ..+...|+++|+.|++.|+|=
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--------~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--------GMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHS--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--------CcCHHHHHHHHHHHHhCCeEe
Confidence 34455666777777 3457777555444 347889999999999999764
No 161
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=40.94 E-value=79 Score=22.26 Aligned_cols=42 Identities=19% Similarity=0.177 Sum_probs=34.4
Q ss_pred HHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 129 LLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 129 LllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
-.+|..++.+|+.++.+.+|++-+.....|.-|=..+ +..+.
T Consensus 2 ~~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g----~T~R~ 43 (50)
T PF09107_consen 2 RELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLDREG----ITRRV 43 (50)
T ss_dssp HHHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTT----SEEEE
T ss_pred hHHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHhccC----CEEEe
Confidence 3467788999999999999999999999999887666 66654
No 162
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=40.45 E-value=1.2e+02 Score=25.29 Aligned_cols=44 Identities=18% Similarity=0.268 Sum_probs=35.9
Q ss_pred HHHHHHhcCCCCCCHHHHHHhcC-CCHHHHHHHHHHHHcccCcccceeec
Q psy11818 126 MCVLLLFNNREKLTYEEIQSETD-IPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 126 a~ILllFN~~~~lt~~eL~~~tg-i~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+.||....+ +..-+.||...++ |+...|.+.|+.|...+ ++.+.
T Consensus 26 ~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~G----lv~R~ 70 (120)
T COG1733 26 LLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEEDG----LVERV 70 (120)
T ss_pred HHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHCC----CEEee
Confidence 345543333 7889999999998 99999999999999988 88764
No 163
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=39.82 E-value=49 Score=31.40 Aligned_cols=36 Identities=11% Similarity=0.057 Sum_probs=32.5
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
....|.+||++.+|+++..+.+-|..|+..+ +|.+.
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lg----ll~~~ 56 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLRQMR----VINLE 56 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHHhCC----CeEec
Confidence 3579999999999999999999999999888 88764
No 164
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=39.82 E-value=97 Score=31.09 Aligned_cols=39 Identities=23% Similarity=0.129 Sum_probs=34.9
Q ss_pred hcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 132 FNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 132 FN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+.....+|.++|++.++++.+.+.+.|..|.+.+ ++.+.
T Consensus 305 ~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~ag----LI~~~ 343 (412)
T PRK04214 305 RKHGKALDVDEIRRLEPMGYDELGELLCELARIG----LLRRG 343 (412)
T ss_pred HhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCC----CeEec
Confidence 5667789999999999999999999999999988 88753
No 165
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=39.10 E-value=76 Score=25.35 Aligned_cols=53 Identities=17% Similarity=0.193 Sum_probs=45.0
Q ss_pred EEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 119 IQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+..+....-||..+...+.=...-|+..++++.+++...|..|...| +|.+..
T Consensus 3 l~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~G----Ller~~ 55 (92)
T PF10007_consen 3 LILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMG----LLERVE 55 (92)
T ss_pred cccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCC----CeEEec
Confidence 45566778899888877777888899999999999999999999988 888753
No 166
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=39.09 E-value=20 Score=25.10 Aligned_cols=22 Identities=27% Similarity=0.652 Sum_probs=19.1
Q ss_pred CCCHHHHHHhcCCCHHHHHHHH
Q psy11818 137 KLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L 158 (331)
.+++.||++.+|++..++.+.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5789999999999999988887
No 167
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=38.91 E-value=97 Score=24.07 Aligned_cols=47 Identities=13% Similarity=0.094 Sum_probs=38.7
Q ss_pred hHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 123 TYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 123 ~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
.+++.|=+.-.....+...+|++.++++...++..|..|-.-+ +|..
T Consensus 9 IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lG----lve~ 55 (78)
T PF03444_consen 9 ILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELG----LVES 55 (78)
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCC----CccC
Confidence 3455555555677889999999999999999999999998877 7764
No 168
>PF14493 HTH_40: Helix-turn-helix domain
Probab=38.85 E-value=70 Score=24.84 Aligned_cols=36 Identities=25% Similarity=0.299 Sum_probs=30.9
Q ss_pred HHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 128 VLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 128 ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
.+.+|++ ++|++||++.-|+....+..+|..++..+
T Consensus 6 T~~l~~~--G~si~eIA~~R~L~~sTI~~HL~~~~~~g 41 (91)
T PF14493_consen 6 TYELFQK--GLSIEEIAKIRGLKESTIYGHLAELIESG 41 (91)
T ss_pred HHHHHHc--CCCHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence 3456664 69999999999999999999999998765
No 169
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=38.75 E-value=47 Score=29.71 Aligned_cols=25 Identities=24% Similarity=0.341 Sum_probs=20.4
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
-+.++++||++.+|++...++..|.
T Consensus 152 ~~g~s~~EIA~~Lgis~~tV~~~l~ 176 (203)
T PRK09647 152 IEGLSYEEIAATLGVKLGTVRSRIH 176 (203)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3579999999999999987666554
No 170
>PF13551 HTH_29: Winged helix-turn helix
Probab=38.26 E-value=70 Score=24.93 Aligned_cols=38 Identities=29% Similarity=0.357 Sum_probs=29.3
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
.+++++.+... |..+++..+|++...+.+.+.-+-..+
T Consensus 3 ~~l~l~~~g~~-~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 3 QILLLLAEGVS-TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred HHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 34555554333 799999999999999999998887655
No 171
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=38.22 E-value=53 Score=27.48 Aligned_cols=50 Identities=16% Similarity=0.122 Sum_probs=38.3
Q ss_pred EchHHHHHHHHhcC--------CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 121 VSTYQMCVLLLFNN--------REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 121 vs~~Qa~ILllFN~--------~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+..+.-..|+..|+ .-.+|.++|+..++-+.+.++.+|..|.+.+ ++...
T Consensus 27 ~~I~lkLll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~k~g----lIe~~ 84 (119)
T TIGR01714 27 TIIWLKLLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESLG----LIEKK 84 (119)
T ss_pred HHHHHHHHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEe
Confidence 34445555555554 4579999999999999999999999999887 66543
No 172
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=38.21 E-value=59 Score=29.48 Aligned_cols=25 Identities=20% Similarity=0.171 Sum_probs=21.1
Q ss_pred CCCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 134 NREKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 134 ~~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
..+.+|++||++.+|++...++..+
T Consensus 195 ~~eg~s~~EIA~~lgis~~tVk~~~ 219 (234)
T PRK08301 195 GGEEKTQKEVADMLGISQSYISRLE 219 (234)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 3578999999999999998876654
No 173
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=37.92 E-value=66 Score=27.51 Aligned_cols=52 Identities=23% Similarity=0.337 Sum_probs=43.3
Q ss_pred EEEchHHHHHHHHhcC-CCCCCHHHHHHhc-----CCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 119 IQVSTYQMCVLLLFNN-REKLTYEEIQSET-----DIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~-~~~lt~~eL~~~t-----gi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+.+|..+.+||.++.+ .+.+|.++|-..+ +++...+-++|..|...| ++.+.
T Consensus 17 lr~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~G----lv~~~ 74 (145)
T COG0735 17 LRLTPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAG----LVHRL 74 (145)
T ss_pred CCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCC----CEEEE
Confidence 6789999999977764 4669999998776 478899999999999998 87754
No 174
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=37.21 E-value=30 Score=30.89 Aligned_cols=41 Identities=22% Similarity=0.295 Sum_probs=31.3
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
.|..=+|.+ +.+.+|++||+++||++...+-..+.-|..-+
T Consensus 29 G~iYgilyl-s~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~ 69 (177)
T COG1510 29 GQIYGILYL-SRKPLTLDEIAEALGMSKSNVSMGLKKLQDWN 69 (177)
T ss_pred HHHhhhhee-cCCCccHHHHHHHHCCCcchHHHHHHHHHhcc
Confidence 333333433 46789999999999999998888888887665
No 175
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=37.00 E-value=43 Score=25.33 Aligned_cols=49 Identities=18% Similarity=0.320 Sum_probs=36.8
Q ss_pred HHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCc
Q psy11818 229 IEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPE 285 (331)
Q Consensus 229 IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~ 285 (331)
.+..|...+...+.++..+|...+ ..+...|.+.|..|.++|+|.+..+
T Consensus 11 ~~~~il~~l~~~~~~~~~~la~~~--------~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 11 TQFLVLRILYEEGPLSVSELAKRL--------GVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHH--------CCCchhHHHHHHHHHHCCCeEecCC
Confidence 455677777777778887765543 4567778999999999999987644
No 176
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=36.55 E-value=82 Score=25.64 Aligned_cols=52 Identities=25% Similarity=0.351 Sum_probs=29.6
Q ss_pred CHHHHHHHHHHHHHHHHHHhCCccccccchHHHHHHHHHHHHhhhhCCCCCCchHHHHHHHHhhhccCC
Q psy11818 263 SPVIIKKRIESLIEREYLARTPEDRFLQEKDVFERYYKQHLAKRLLLDKSVSDDSEKNMISKLKVRNLP 331 (331)
Q Consensus 263 s~~~IKk~IE~LIereyI~Rd~~d~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 331 (331)
+.+.|...|+.|.+.||| .|...+++|-++.+. ..+. .+..+..+|+++|++
T Consensus 7 ~~e~I~~vi~~l~~~gyi---------dD~~ya~~~v~~~~~-~~~~-------G~~~I~~~L~~kGi~ 58 (121)
T PF02631_consen 7 SEEAIEEVIDRLKELGYI---------DDERYAESYVRSRLR-RKGK-------GPRRIRQKLKQKGID 58 (121)
T ss_dssp -HHHHHHHHHHHHHTTSS----------HHHHHHHHHHHHHH-HTT---------HHHHHHHHHHTT--
T ss_pred CHHHHHHHHHHHHHcCCC---------CHHHHHHHHHHHhcc-cccc-------cHHHHHHHHHHHCCC
Confidence 667789999999999987 255555555554443 1111 234455566666653
No 177
>PRK13239 alkylmercury lyase; Provisional
Probab=36.48 E-value=67 Score=29.49 Aligned_cols=40 Identities=13% Similarity=0.238 Sum_probs=34.6
Q ss_pred hHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 123 TYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 123 ~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
.+...||.++-+....|+.+|++.+|.+.+.+.+.|..|-
T Consensus 22 ~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 22 TLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 3566677777788899999999999999999999999874
No 178
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=36.43 E-value=67 Score=28.67 Aligned_cols=39 Identities=23% Similarity=0.182 Sum_probs=32.4
Q ss_pred HHHHHhcCC-CCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 127 CVLLLFNNR-EKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 127 ~ILllFN~~-~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
-|+.++-.. ...|.+||++.+||+...++.++..|...+
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~ 205 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRH 205 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCC
Confidence 466555432 368999999999999999999999999887
No 179
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=35.28 E-value=51 Score=28.15 Aligned_cols=48 Identities=17% Similarity=0.264 Sum_probs=40.1
Q ss_pred hHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhC
Q psy11818 228 EIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLART 283 (331)
Q Consensus 228 ~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd 283 (331)
.+|-.|.+.|.....+++.+|-+++ ..+.+.+..+|+.|.+.|+|++.
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l--------glS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF--------GVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeeeE
Confidence 3567889999999999999776655 35788899999999999999863
No 180
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=34.72 E-value=17 Score=24.94 Aligned_cols=31 Identities=16% Similarity=0.296 Sum_probs=25.2
Q ss_pred HhccCCCCCHHHHHHHHHHHHHHHHHHhCCc
Q psy11818 255 QLKSRFLPSPVIIKKRIESLIEREYLARTPE 285 (331)
Q Consensus 255 ~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~ 285 (331)
++...|..+...+.+.+..|.+.|+|.+..+
T Consensus 25 ~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 25 ELAAQLGVSRTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3444567889999999999999999987654
No 181
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=34.58 E-value=76 Score=27.22 Aligned_cols=40 Identities=20% Similarity=0.167 Sum_probs=31.8
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
..|.-|..|+.++ ...+|.+||++.+|++...+...+...
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 4577788888876 478999999999999998877555443
No 182
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=34.22 E-value=74 Score=29.02 Aligned_cols=24 Identities=17% Similarity=0.122 Sum_probs=20.9
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
.+.+|++||++.+|++...+...+
T Consensus 196 ~eg~s~~EIA~~Lgis~~tV~~~l 219 (234)
T TIGR02835 196 GTEKTQKEVADMLGISQSYISRLE 219 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHH
Confidence 468999999999999998887665
No 183
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=34.08 E-value=89 Score=27.16 Aligned_cols=46 Identities=11% Similarity=0.140 Sum_probs=38.3
Q ss_pred HHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 126 MCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 126 a~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
-+|..++.+.......+|++.++++...+...++-|...| ++.+.+
T Consensus 13 ~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~G----lV~~~~ 58 (154)
T COG1321 13 ETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLG----LVEYEP 58 (154)
T ss_pred HHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCC----CeEEec
Confidence 3455566678889999999999999999999999999887 776653
No 184
>PRK09954 putative kinase; Provisional
Probab=34.07 E-value=57 Score=31.65 Aligned_cols=39 Identities=13% Similarity=0.159 Sum_probs=35.1
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
-||..+.++..+|..||++.+|++...+.+.|..|...+
T Consensus 7 ~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g 45 (362)
T PRK09954 7 EILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKG 45 (362)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 477777788899999999999999999999999998866
No 185
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=33.71 E-value=56 Score=28.30 Aligned_cols=47 Identities=17% Similarity=0.280 Sum_probs=40.3
Q ss_pred hHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHh
Q psy11818 228 EIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLAR 282 (331)
Q Consensus 228 ~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~R 282 (331)
.+|-.|.+++.....+++.+|-+.| ..+.+-+.+||..|.+.|.|++
T Consensus 14 ~~D~~IL~~Lq~d~R~s~~eiA~~l--------glS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 14 RIDRNILNELQKDGRISNVELSKRV--------GLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHHHHHhccCCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEE
Confidence 4788899999999999998766655 3577889999999999999986
No 186
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=33.42 E-value=41 Score=24.99 Aligned_cols=26 Identities=31% Similarity=0.290 Sum_probs=20.4
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
-.-|.+||++.+||+.+.+...|...
T Consensus 19 r~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 19 REPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp S--BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHcccHHHHHHHHHhC
Confidence 35799999999999999999988753
No 187
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=33.09 E-value=65 Score=26.92 Aligned_cols=24 Identities=13% Similarity=0.127 Sum_probs=20.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..+.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHH
Confidence 579999999999999988765543
No 188
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=32.97 E-value=1.2e+02 Score=21.34 Aligned_cols=47 Identities=32% Similarity=0.422 Sum_probs=28.6
Q ss_pred hhHHHHHHHhhhccc--CCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHH
Q psy11818 227 HEIEAAVVRIMKARK--RMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIER 277 (331)
Q Consensus 227 ~~IqAaIVRIMK~~K--~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIer 277 (331)
..|.++|..||+... +++.. .|.+++..+|..+...-|..|..+|..
T Consensus 3 ~~i~~~i~~iL~~~dl~~vT~k----~vr~~Le~~~~~dL~~~K~~I~~~I~~ 51 (54)
T PF08766_consen 3 EEIREAIREILREADLDTVTKK----QVREQLEERFGVDLSSRKKFIKELIDE 51 (54)
T ss_dssp HHHHHHHHHHHTTS-GGG--HH----HHHHHHHHH-SS--SHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCHhHhhHH----HHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 357889999999873 45555 455555556666666777777777764
No 189
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=32.96 E-value=1.1e+02 Score=26.69 Aligned_cols=59 Identities=15% Similarity=0.305 Sum_probs=43.5
Q ss_pred HHHHHHHhcCC-CCCCHHHHHHhc--CCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecC
Q psy11818 125 QMCVLLLFNNR-EKLTYEEIQSET--DIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDS 191 (331)
Q Consensus 125 Qa~ILllFN~~-~~lt~~eL~~~t--gi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~ 191 (331)
...|+-.|... -.++..+|...+ +++...+.++|..|+..| .|..+. +....+|..|.+
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g---~i~~K~-----~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEG---KIVEKE-----YGKQKIYFANQD 64 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCC---Ceeeee-----ecceEEEeeCcc
Confidence 35677777754 569999999999 488899999999999887 365543 234456666654
No 190
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=32.95 E-value=49 Score=29.21 Aligned_cols=47 Identities=17% Similarity=0.246 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhCCccccccch-----------HHHHHHHHHHHHhhh
Q psy11818 261 LPSPVIIKKRIESLIEREYLARTPEDRFLQEK-----------DVFERYYKQHLAKRL 307 (331)
Q Consensus 261 ~ps~~~IKk~IE~LIereyI~Rd~~d~~i~~~-----------~~~~~~~~~~~~~~~ 307 (331)
..+..+++++|+.|.+-|+|+++++..+.... ..-.+|+++++-.++
T Consensus 52 ~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~~~lA~ 109 (171)
T PF14394_consen 52 KISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEAVRSYHKQMLELAQ 109 (171)
T ss_pred CCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHHHHHHHHHHHHHHH
Confidence 45899999999999999999999986655443 344667666655444
No 191
>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=32.86 E-value=64 Score=26.87 Aligned_cols=37 Identities=14% Similarity=0.228 Sum_probs=27.7
Q ss_pred EchHHHHHHHH-hcCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 121 VSTYQMCVLLL-FNNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 121 vs~~Qa~ILll-FN~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
++.-|..|+.+ | -+.++++||++.+|++...+...+.
T Consensus 112 L~~~~r~v~~l~~--~~g~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 112 LPERQRELLQLRY--QRGVSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CCHHHHHHHHHHH--hcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 55556666655 3 3579999999999999988776654
No 192
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=32.85 E-value=75 Score=27.08 Aligned_cols=25 Identities=24% Similarity=0.270 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
.+.+|++||++.+|++...++..|.
T Consensus 132 ~eg~s~~EIA~~l~is~~tV~~~l~ 156 (168)
T PRK12525 132 LEGLTYVEIGERLGVSLSRIHQYMV 156 (168)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3568999999999999987665553
No 193
>PLN03239 histone acetyltransferase; Provisional
Probab=32.79 E-value=66 Score=31.91 Aligned_cols=26 Identities=31% Similarity=0.445 Sum_probs=24.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
..+|+++|+..|||..+++..+|..|
T Consensus 283 ~~~si~dis~~Tgi~~~DIi~tL~~l 308 (351)
T PLN03239 283 SSLSIMDIAKKTSIMAEDIVFALNQL 308 (351)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHC
Confidence 46999999999999999999999876
No 194
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=32.72 E-value=69 Score=27.37 Aligned_cols=24 Identities=25% Similarity=0.420 Sum_probs=20.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.++++||++.+|++...++..|.
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 468999999999999987766654
No 195
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=32.51 E-value=95 Score=28.00 Aligned_cols=39 Identities=18% Similarity=0.124 Sum_probs=34.4
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
-++.-.+.++..|..+|+..+||+..++.++|-.|...+
T Consensus 17 ~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~ 55 (183)
T PHA03103 17 KEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREG 55 (183)
T ss_pred HHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcC
Confidence 455666778899999999999999999999999998887
No 196
>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=32.44 E-value=60 Score=27.25 Aligned_cols=27 Identities=15% Similarity=0.149 Sum_probs=21.9
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
-+.+|.+||++.+|++...++..+.-.
T Consensus 124 ~~g~s~~eIA~~lgis~~tV~~~l~ra 150 (162)
T TIGR02983 124 YEDLSEAQVAEALGISVGTVKSRLSRA 150 (162)
T ss_pred HhcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 357999999999999998877765543
No 197
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. 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 RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=32.34 E-value=82 Score=29.50 Aligned_cols=34 Identities=15% Similarity=0.260 Sum_probs=24.3
Q ss_pred HHHHH-HHhcCCCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 125 QMCVL-LLFNNREKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 125 Qa~IL-llFN~~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
|-.|| +.|-..+.+|+.||++.+|++...+.+..
T Consensus 223 er~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~ 257 (270)
T TIGR02392 223 SRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIE 257 (270)
T ss_pred HHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence 33344 44533457999999999999998877544
No 198
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=32.25 E-value=46 Score=22.97 Aligned_cols=21 Identities=24% Similarity=0.439 Sum_probs=18.6
Q ss_pred CHHHHHHhcCCCHHHHHHHHH
Q psy11818 139 TYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 139 t~~eL~~~tgi~~~~l~~~L~ 159 (331)
|+.||++..|++...+-++|+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHh
Confidence 789999999999998888775
No 199
>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=31.86 E-value=61 Score=23.88 Aligned_cols=25 Identities=12% Similarity=0.295 Sum_probs=20.5
Q ss_pred hcCCCCCCHHHHHHhcCCCHHHHHH
Q psy11818 132 FNNREKLTYEEIQSETDIPERDLIR 156 (331)
Q Consensus 132 FN~~~~lt~~eL~~~tgi~~~~l~~ 156 (331)
....+.++..||++.+|+++..+..
T Consensus 17 ~~~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 17 KESNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred HHhCCCccHHHHHHHHCCCHHHHHH
Confidence 3456789999999999999977653
No 200
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=31.33 E-value=56 Score=28.71 Aligned_cols=26 Identities=38% Similarity=0.483 Sum_probs=22.8
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
+++|.+||++.+|+++..+.+.|...
T Consensus 150 ~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 150 EGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999998887654
No 201
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=31.24 E-value=83 Score=26.08 Aligned_cols=25 Identities=20% Similarity=0.112 Sum_probs=21.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
+.+|++||++.+|++...+...+.-
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4689999999999999888776653
No 202
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=31.15 E-value=78 Score=29.86 Aligned_cols=27 Identities=19% Similarity=0.190 Sum_probs=22.0
Q ss_pred cCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 133 NNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 133 N~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
...+.+|+.||++.+|++...++..+.
T Consensus 238 ~~~e~~s~~EIA~~Lgis~~tVk~~l~ 264 (285)
T TIGR02394 238 LGYEPATLEEVAAEVGLTRERVRQIQV 264 (285)
T ss_pred CCCCCccHHHHHHHHCCCHHHHHHHHH
Confidence 456789999999999999987766544
No 203
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=31.10 E-value=1.5e+02 Score=28.52 Aligned_cols=39 Identities=18% Similarity=0.204 Sum_probs=33.9
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
.||.+..+....+.++|++.+|++...+.++|..|...+
T Consensus 8 ~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G 46 (319)
T PRK11886 8 QLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWG 46 (319)
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 455556667789999999999999999999999999876
No 204
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=30.94 E-value=87 Score=21.04 Aligned_cols=24 Identities=17% Similarity=0.275 Sum_probs=16.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
..+|+.+|+..+|.+...+-+.|.
T Consensus 19 ~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 19 QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp S---HHHHHHHTT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 459999999999999988877653
No 205
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=30.91 E-value=62 Score=27.77 Aligned_cols=24 Identities=29% Similarity=0.535 Sum_probs=20.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHH
Confidence 569999999999999988766553
No 206
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=30.88 E-value=92 Score=27.94 Aligned_cols=41 Identities=22% Similarity=0.215 Sum_probs=35.4
Q ss_pred HhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 131 LFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 131 lFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.|...+.++..+|++.+|++-..++.+|.-|...| ++...|
T Consensus 24 ~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eG----lv~~~~ 64 (224)
T PRK11534 24 NFQPDEKLRMSLLTSRYALGVGPLREALSQLVAER----LVTVVN 64 (224)
T ss_pred CCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCC----CEEEeC
Confidence 35557889999999999999999999999999887 887654
No 207
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=30.66 E-value=59 Score=28.13 Aligned_cols=24 Identities=13% Similarity=0.264 Sum_probs=20.5
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+++|++||++.+|++...++..|.
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 579999999999999988766654
No 208
>PF13518 HTH_28: Helix-turn-helix domain
Probab=30.44 E-value=1.4e+02 Score=19.90 Aligned_cols=27 Identities=22% Similarity=0.289 Sum_probs=22.8
Q ss_pred CHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 139 TYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 139 t~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
|+.+++..+||+...+.+-+.-+-..+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 999999999999988888777665544
No 209
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=30.17 E-value=1.2e+02 Score=26.55 Aligned_cols=34 Identities=21% Similarity=0.153 Sum_probs=30.7
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.+|-++|++.+|++...+-+.|..|.+.+ ++...
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~g----ii~~~ 201 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQG----LISAH 201 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCC----CEEec
Confidence 58889999999999999999999999887 88764
No 210
>KOG2593|consensus
Probab=29.68 E-value=75 Score=32.32 Aligned_cols=66 Identities=12% Similarity=0.233 Sum_probs=48.1
Q ss_pred EchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec------CCCCCCCCCCeEEEec
Q psy11818 121 VSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY------PKTKEIEPNHVFFVND 190 (331)
Q Consensus 121 vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~------~~~~~i~~~~~f~lN~ 190 (331)
.+...+.||...-.+..+.-++|++.++++.+.|+..|..|=..| ++... ++|+.+.....|+||+
T Consensus 27 y~~~~~lild~llr~~~v~Eedl~~llk~~~KqLR~li~~LredK----lI~~~~r~E~~~nGr~~~~~~YyyInY 98 (436)
T KOG2593|consen 27 YGGEHVLILDALLRRQCVREEDLKELLKFNKKQLRKLIASLREDK----LIKIRTRTETAENGRAVDKHTYYYINY 98 (436)
T ss_pred ccchhHHHHHHHHHhhhcchHHHHHHhcccHHHHHHHHHHhhhhh----hhhhhhhhhcCCCCcceeeeEEEEeeh
Confidence 355667777666666789999999999999999999999997776 66432 2244443356677775
No 211
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=29.62 E-value=89 Score=27.67 Aligned_cols=40 Identities=13% Similarity=0.175 Sum_probs=35.0
Q ss_pred hcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 132 FNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 132 FN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
|--.+.++..+|++.+|++-..++.+|..|...| ++...|
T Consensus 29 l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eG----lv~~~~ 68 (212)
T TIGR03338 29 LPPGAKLNESDIAARLGVSRGPVREAFRALEEAG----LVRNEK 68 (212)
T ss_pred CCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCC----CEEEec
Confidence 4456789999999999999999999999999887 887654
No 212
>KOG2905|consensus
Probab=29.61 E-value=78 Score=29.82 Aligned_cols=58 Identities=14% Similarity=0.192 Sum_probs=43.2
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCCC
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSFT 193 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F~ 193 (331)
+-..+.-+|.....||+.+|.+.|+=|+..|+..|..++ +|..-+ .-...|.|-++|.
T Consensus 187 vld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~ic-------v~NkKg-----~~k~tyeLKPEYK 244 (254)
T KOG2905|consen 187 VLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDIC-------VLNKKG-----PYKNTYELKPEYK 244 (254)
T ss_pred HHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHH-------HHhccC-----cccCceecCHHHh
Confidence 334556778899999999999999999999999999886 554321 0134577777764
No 213
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=29.54 E-value=94 Score=26.78 Aligned_cols=38 Identities=21% Similarity=0.149 Sum_probs=30.0
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
..|.-|..||.++ ...+|.+||++.+|++...+...+.
T Consensus 6 ~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie~ 43 (141)
T PRK03975 6 FLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIEK 43 (141)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4578888888776 4679999999999999866555544
No 214
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=29.32 E-value=20 Score=32.53 Aligned_cols=37 Identities=16% Similarity=0.337 Sum_probs=29.5
Q ss_pred HhccCCCCCHHHHHHHHHHHHHHHHHHhCC-ccccccc
Q psy11818 255 QLKSRFLPSPVIIKKRIESLIEREYLARTP-EDRFLQE 291 (331)
Q Consensus 255 ~l~~~F~ps~~~IKk~IE~LIereyI~Rd~-~d~~i~~ 291 (331)
+|..+|..+..-|.++|+.|++.|+|.|.. ...++.+
T Consensus 29 eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G~GTfV~~ 66 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNLLTEAGYIQKIQGKGSIVLN 66 (233)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCceEEEec
Confidence 455568899999999999999999999964 4455533
No 215
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=29.26 E-value=89 Score=29.76 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=22.7
Q ss_pred cCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 133 NNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 133 N~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
++.+.+|++||++.+|++.+.+++.+.
T Consensus 265 ~~~~~~Tl~EIa~~lgiS~erVrq~~~ 291 (298)
T TIGR02997 265 DGGEPLTLAEIGRRLNLSRERVRQIEA 291 (298)
T ss_pred CCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 345789999999999999998877654
No 216
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=29.15 E-value=1.7e+02 Score=27.82 Aligned_cols=55 Identities=13% Similarity=0.012 Sum_probs=42.0
Q ss_pred EEEEEchHHHHHHHHhcCC-CCCCHHHHHHhcC--CCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 117 HIIQVSTYQMCVLLLFNNR-EKLTYEEIQSETD--IPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 117 ~~l~vs~~Qa~ILllFN~~-~~lt~~eL~~~tg--i~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.+--+-+..+|..+..-. ...+.++|++.++ |+.++++.+|..|.+.| +|.++.
T Consensus 116 ~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~g----likk~~ 173 (271)
T TIGR02147 116 FEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERLG----LIKKNE 173 (271)
T ss_pred HHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCC----CeeECC
Confidence 3344456666666665543 3458999999999 89999999999999998 998763
No 217
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=28.74 E-value=85 Score=27.30 Aligned_cols=24 Identities=29% Similarity=0.207 Sum_probs=19.9
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~ 169 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLY 169 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 469999999999999988766543
No 218
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=28.69 E-value=1.2e+02 Score=28.74 Aligned_cols=44 Identities=14% Similarity=0.220 Sum_probs=35.9
Q ss_pred HHHHhcC-CCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 128 VLLLFNN-REKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 128 ILllFN~-~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
||-.++. ...++..+|++.+|++...+.+++..|...+ ++...+
T Consensus 188 IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aG----vIe~r~ 232 (251)
T TIGR02787 188 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAG----VIESRS 232 (251)
T ss_pred HHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEecc
Confidence 3444455 3689999999999999999999999999988 776543
No 219
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=28.54 E-value=95 Score=26.93 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=22.3
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
-+.+|++||++.+|++...+...|.-.
T Consensus 163 ~~~~s~~eIA~~l~~s~~tV~~~l~r~ 189 (198)
T TIGR02859 163 LDGKSYQEIACDLNRHVKSIDNALQRV 189 (198)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 368999999999999998887766543
No 220
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=28.53 E-value=83 Score=22.56 Aligned_cols=25 Identities=24% Similarity=0.387 Sum_probs=22.0
Q ss_pred CCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 138 LTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
+|+++|++.+|++...+.+.+....
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 7999999999999999988887654
No 221
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.43 E-value=99 Score=25.94 Aligned_cols=24 Identities=13% Similarity=0.077 Sum_probs=19.8
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
..+|.+||++.+|++...++..|.
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 478999999999999987766543
No 222
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=28.39 E-value=1e+02 Score=27.77 Aligned_cols=40 Identities=23% Similarity=0.410 Sum_probs=31.0
Q ss_pred EEchHHHHHHHH------hcCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 120 QVSTYQMCVLLL------FNNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 120 ~vs~~Qa~ILll------FN~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
..|.-|+.||.. |+.--..++.||++.+||+...+..+|.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHH
Confidence 678889988854 4555679999999999999766555544
No 223
>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=28.33 E-value=62 Score=27.76 Aligned_cols=24 Identities=29% Similarity=0.309 Sum_probs=20.6
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Confidence 579999999999999988776654
No 224
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=28.32 E-value=76 Score=20.64 Aligned_cols=21 Identities=24% Similarity=0.314 Sum_probs=17.6
Q ss_pred CCHHHHHHhcCCCHHHHHHHH
Q psy11818 138 LTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~L 158 (331)
+|++|+++.+|++...+.+.+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~ 22 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLI 22 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 689999999999998776643
No 225
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=28.22 E-value=1.7e+02 Score=20.25 Aligned_cols=41 Identities=17% Similarity=0.201 Sum_probs=34.4
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
..|.-+..++.++-.. .+..||+..+|++...+..++..+.
T Consensus 4 ~Lt~rE~~v~~l~~~G--~s~~eia~~l~is~~tV~~h~~~i~ 44 (65)
T COG2771 4 DLTPREREILRLVAQG--KSNKEIARILGISEETVKTHLRNIY 44 (65)
T ss_pred cCCHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4567788888777765 8999999999999999999888764
No 226
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=28.15 E-value=40 Score=30.84 Aligned_cols=50 Identities=16% Similarity=0.387 Sum_probs=0.0
Q ss_pred hhhHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHh
Q psy11818 226 KHEIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLAR 282 (331)
Q Consensus 226 ~~~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~R 282 (331)
...|...|...++....|.-+ .+|...|..+..-|+++|+.|++.|||.|
T Consensus 18 ~~~L~~~I~~~~~~G~~LPsE-------~eLa~~~~VSR~TVR~Al~~L~~eGli~r 67 (241)
T PRK10079 18 AAKLEQELRQHYRCGDYLPAE-------QQLAARYEVNRHTLRRAIDQLVEKGWVQR 67 (241)
T ss_pred HHHHHHHHhcccCCCCcCCCH-------HHHHHHHCCCHHHHHHHHHHHHHCCCEEE
No 227
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=28.14 E-value=55 Score=24.65 Aligned_cols=31 Identities=10% Similarity=0.232 Sum_probs=22.5
Q ss_pred hcCCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 132 FNNREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 132 FN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
..+-..+|+.||++.+|++...+.|-.+.|=
T Consensus 29 ~~~~~~~si~elA~~~~vS~sti~Rf~kkLG 59 (77)
T PF01418_consen 29 PDEIAFMSISELAEKAGVSPSTIVRFCKKLG 59 (77)
T ss_dssp HHHHCT--HHHHHHHCTS-HHHHHHHHHHCT
T ss_pred HHHHHHccHHHHHHHcCCCHHHHHHHHHHhC
Confidence 3344679999999999999999988777663
No 228
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=27.90 E-value=1e+02 Score=25.81 Aligned_cols=24 Identities=25% Similarity=0.346 Sum_probs=20.2
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
..++++||++.+|++...++..+.
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ 149 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLA 149 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 579999999999999987766553
No 229
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.72 E-value=64 Score=27.09 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=20.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHH
Confidence 469999999999999988765543
No 230
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=27.59 E-value=1e+02 Score=28.13 Aligned_cols=38 Identities=16% Similarity=0.210 Sum_probs=26.5
Q ss_pred chHHHHHH-HHh--cCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 122 STYQMCVL-LLF--NNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 122 s~~Qa~IL-llF--N~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.-|-.|| +.| ++.+.+|++||++.+|++...+.+...
T Consensus 178 ~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~ 218 (238)
T TIGR02393 178 TERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIES 218 (238)
T ss_pred CHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHH
Confidence 33344444 444 345789999999999999988766544
No 231
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=27.22 E-value=90 Score=26.17 Aligned_cols=24 Identities=17% Similarity=0.205 Sum_probs=19.8
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
.+.+|++||++.+|++...++..|
T Consensus 119 ~~~~s~~eIA~~lgis~~tv~~~l 142 (159)
T PRK12527 119 LEGLSHQQIAEHLGISRSLVEKHI 142 (159)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 467999999999999987765554
No 232
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=27.22 E-value=1e+02 Score=27.56 Aligned_cols=42 Identities=14% Similarity=0.110 Sum_probs=35.7
Q ss_pred HHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 130 LLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 130 llFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
-.|...+.++..+|++.+|++-..++.+|..|...| ++...|
T Consensus 27 g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eG----LV~~~~ 68 (221)
T PRK11414 27 GALKPGARLITKNLAEQLGMSITPVREALLRLVSVN----ALSVAP 68 (221)
T ss_pred CCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCC----CEEecC
Confidence 335557889999999999999999999999999887 887654
No 233
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=27.19 E-value=83 Score=27.60 Aligned_cols=37 Identities=30% Similarity=0.375 Sum_probs=26.1
Q ss_pred EchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 121 VSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 121 vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
++..+-.|+.++ -+.+|++||++.+|++...++..|.
T Consensus 156 L~~~~r~vl~l~--~e~~s~~EIA~~lgis~~tV~~~l~ 192 (208)
T PRK08295 156 LSELEKEVLELY--LDGKSYQEIAEELNRHVKSIDNALQ 192 (208)
T ss_pred CCHHHHHHHHHH--HccCCHHHHHHHHCCCHHHHHHHHH
Confidence 344444455443 3579999999999999988766554
No 234
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=27.17 E-value=45 Score=31.17 Aligned_cols=46 Identities=22% Similarity=0.452 Sum_probs=39.5
Q ss_pred HHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhC
Q psy11818 230 EAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLART 283 (331)
Q Consensus 230 qAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd 283 (331)
+..|+.+++.++.++..+|.+ +|..+..-|.+-|+.|-++|+|.|.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~--------~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVE--------HFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHcCCEeHHHHHH--------HhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 356788889999999987766 4678999999999999999999995
No 235
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=27.08 E-value=95 Score=26.81 Aligned_cols=26 Identities=31% Similarity=0.439 Sum_probs=21.4
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
-+.++++||++.+|++...+...|.-
T Consensus 151 ~~g~s~~eIA~~lgis~~~v~~~l~R 176 (187)
T PRK12534 151 FEGITYEELAARTDTPIGTVKSWIRR 176 (187)
T ss_pred HcCCCHHHHHHHhCCChhHHHHHHHH
Confidence 36799999999999999887766543
No 236
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=26.92 E-value=96 Score=26.30 Aligned_cols=25 Identities=8% Similarity=0.158 Sum_probs=21.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
++++++||++.+|++...++..|.-
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~R 151 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSR 151 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5799999999999999887766543
No 237
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.89 E-value=1.3e+02 Score=28.07 Aligned_cols=58 Identities=14% Similarity=0.109 Sum_probs=45.0
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCC
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSF 192 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F 192 (331)
.|+....+.++.|.-+|+...|++.+.+.-++..|-..+ +...+..| ..-.|.+|+.+
T Consensus 178 ~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~G----ii~~~~~G----r~iiy~in~s~ 235 (240)
T COG3398 178 AIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEELG----IIPEDREG----RSIIYSINPSI 235 (240)
T ss_pred HHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcC----CCcccccC----ceEEEEeCHHH
Confidence 455556667889999999999999999999999998877 76654322 23568888765
No 238
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=26.88 E-value=40 Score=30.51 Aligned_cols=37 Identities=24% Similarity=0.424 Sum_probs=28.9
Q ss_pred hccCCCCCHHHHHHHHHHHHHHHHHHhC-Cccccccch
Q psy11818 256 LKSRFLPSPVIIKKRIESLIEREYLART-PEDRFLQEK 292 (331)
Q Consensus 256 l~~~F~ps~~~IKk~IE~LIereyI~Rd-~~d~~i~~~ 292 (331)
|..+|..+..-+.++|+.|.+.|||.|. +...++..+
T Consensus 38 La~~~~VSR~TvR~Al~~L~~eGli~r~~G~GtfV~~~ 75 (238)
T TIGR02325 38 LAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFVAAR 75 (238)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEecCCEEEECCC
Confidence 4446888999999999999999999995 455566443
No 239
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=26.85 E-value=1e+02 Score=23.63 Aligned_cols=32 Identities=16% Similarity=0.247 Sum_probs=28.1
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 140 YEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 140 ~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+.+|++.+|++...+.+.|..|...+ ++.+.+
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~g----lI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDG----LVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCC----CEEEcC
Confidence 46899999999999999999999887 887753
No 240
>PF14502 HTH_41: Helix-turn-helix domain
Probab=26.81 E-value=1.3e+02 Score=21.28 Aligned_cols=28 Identities=18% Similarity=0.152 Sum_probs=26.2
Q ss_pred CCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 138 LTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
-|++|+++..+++...+..+|..|-..+
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~g 34 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENG 34 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCC
Confidence 5899999999999999999999998877
No 241
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=26.80 E-value=77 Score=24.08 Aligned_cols=29 Identities=24% Similarity=0.395 Sum_probs=22.5
Q ss_pred CCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 134 NREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 134 ~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
..+..|++++++.++++...+.+.+..+-
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~ 55 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLN 55 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45678999999999999999988887764
No 242
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=26.71 E-value=87 Score=27.06 Aligned_cols=26 Identities=19% Similarity=0.204 Sum_probs=21.8
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
-+.+|++||++.+|++...++..|.-
T Consensus 143 ~~g~s~~EIA~~l~is~~tV~~~l~r 168 (181)
T PRK12536 143 LEGLSVAETAQLTGLSESAVKVGIHR 168 (181)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35799999999999999888777654
No 243
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=26.61 E-value=1.1e+02 Score=28.61 Aligned_cols=47 Identities=21% Similarity=0.301 Sum_probs=39.9
Q ss_pred EEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 119 IQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
|-.|-++|-+-+..=..+..|..||++.+|+|..-+-.+|.+|...|
T Consensus 12 lGlt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG 58 (247)
T COG1378 12 LGLTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKG 58 (247)
T ss_pred cCCCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCC
Confidence 45667777776666667889999999999999999999999999877
No 244
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=26.55 E-value=1.4e+02 Score=23.87 Aligned_cols=45 Identities=9% Similarity=0.181 Sum_probs=33.5
Q ss_pred HHHHHhcCCCCCCHHHHHHhc--CCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 127 CVLLLFNNREKLTYEEIQSET--DIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~t--gi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.|+-..-.++.+|..++.+.+ .+....+...+.-|++.+ ++.+++
T Consensus 20 ~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKkg----lIEKSG 66 (96)
T PF09114_consen 20 NILIQVAKKNFITASEVREALATEMNKASVNSNIGVLIKKG----LIEKSG 66 (96)
T ss_dssp HHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHHHTT----SEEEET
T ss_pred HHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHHHcC----cccccC
Confidence 444444567789999999977 788899999999999987 887764
No 245
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=26.36 E-value=1.2e+02 Score=27.54 Aligned_cols=40 Identities=23% Similarity=0.170 Sum_probs=35.1
Q ss_pred hcCCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 132 FNNREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 132 FN~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
|...+.+ |..+|++.+|++-..++.+|.-|...| ++...+
T Consensus 25 l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eG----lv~~~~ 65 (239)
T PRK04984 25 FPPGSILPAERELSELIGVTRTTLREVLQRLARDG----WLTIQH 65 (239)
T ss_pred CCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEeC
Confidence 4556789 899999999999999999999999888 887665
No 246
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=26.36 E-value=86 Score=30.10 Aligned_cols=51 Identities=25% Similarity=0.289 Sum_probs=36.8
Q ss_pred CcEEEEEchHHHHHHHHhcC------CCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 115 RKHIIQVSTYQMCVLLLFNN------REKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 115 ~~~~l~vs~~Qa~ILllFN~------~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
..++-.....|+..-.+-.. .|.=+-++|.+..||+...++++|..|++.+
T Consensus 218 ~~~E~l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g 274 (287)
T COG2996 218 RAHEMLDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAG 274 (287)
T ss_pred ccHHhhhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 34444455566655444221 2345889999999999999999999999987
No 247
>PRK12423 LexA repressor; Provisional
Probab=26.21 E-value=1.3e+02 Score=26.93 Aligned_cols=51 Identities=14% Similarity=0.202 Sum_probs=39.7
Q ss_pred chHHHHHHHHhcC---CCC--CCHHHHHHhcCC-CHHHHHHHHHHHHcccCcccceeecCC
Q psy11818 122 STYQMCVLLLFNN---REK--LTYEEIQSETDI-PERDLIRALQSLAMGKASQRILIRYPK 176 (331)
Q Consensus 122 s~~Qa~ILllFN~---~~~--lt~~eL~~~tgi-~~~~l~~~L~sL~~~k~~~~IL~~~~~ 176 (331)
|.-|-.||...-+ ... -|+.||++.+|+ +...+..+|..|...+ +|...+.
T Consensus 5 t~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G----~l~~~~~ 61 (202)
T PRK12423 5 TPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAG----LIEVVPN 61 (202)
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCC----CEEecCC
Confidence 5667777765543 233 499999999995 7888999999999987 8887653
No 248
>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=26.09 E-value=1.3e+02 Score=17.19 Aligned_cols=30 Identities=17% Similarity=0.100 Sum_probs=21.4
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHH
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIR 156 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~ 156 (331)
...|+..+.+ .++..++++.+|++...+..
T Consensus 11 ~~~i~~~~~~--~~s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 11 IEEARRLLAA--GESVAEIARRLGVSRSTLYR 40 (42)
T ss_pred HHHHHHHHHc--CCCHHHHHHHHCCCHHHHHH
Confidence 3445555553 46999999999998876654
No 249
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=26.03 E-value=1.1e+02 Score=26.76 Aligned_cols=24 Identities=33% Similarity=0.336 Sum_probs=20.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 149 LELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 479999999999999988765543
No 250
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=26.02 E-value=1.2e+02 Score=27.65 Aligned_cols=24 Identities=21% Similarity=0.137 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
.+.+|++||++.+|++...+...+
T Consensus 193 ~e~~S~~EIA~~lgis~~tV~~~~ 216 (233)
T PRK05803 193 GKEKTQREIAKALGISRSYVSRIE 216 (233)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHH
Confidence 478999999999999998876664
No 251
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=25.91 E-value=1e+02 Score=27.04 Aligned_cols=24 Identities=21% Similarity=0.396 Sum_probs=20.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 157 ~~~s~~EIA~~Lgis~~tVk~~l~ 180 (194)
T PRK09646 157 GGLTYREVAERLAVPLGTVKTRMR 180 (194)
T ss_pred cCCCHHHHHHHhCCChHhHHHHHH
Confidence 469999999999999988766553
No 252
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=25.89 E-value=1.7e+02 Score=25.07 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=30.5
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.+|-+||++.+|++.+.+-+.|.-|...+ ++...
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g----~I~~~ 176 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKK----LISIH 176 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCC----CEEec
Confidence 47999999999999999999999999887 77653
No 253
>PF11784 DUF3320: Protein of unknown function (DUF3320); InterPro: IPR021754 This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins.
Probab=25.88 E-value=1.2e+02 Score=21.31 Aligned_cols=35 Identities=6% Similarity=0.238 Sum_probs=30.7
Q ss_pred HhhhhhHHHHHHHhhhcccCCChHHHHHHHHHHhc
Q psy11818 223 EDRKHEIEAAVVRIMKARKRMQHNTLITEVTEQLK 257 (331)
Q Consensus 223 edR~~~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~ 257 (331)
......|...|..|+..++.++.+.|+..+...+.
T Consensus 7 ~~~~~~L~~~i~~Iv~~EgPI~~~~L~~Ri~~a~G 41 (52)
T PF11784_consen 7 PEYRPQLARMIRQIVEVEGPIHEDELARRIARAWG 41 (52)
T ss_pred hhHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHcC
Confidence 34567789999999999999999999999998774
No 254
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=25.81 E-value=1.7e+02 Score=19.82 Aligned_cols=35 Identities=17% Similarity=0.311 Sum_probs=23.7
Q ss_pred HHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 124 YQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 124 ~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
+|.+|-..-|.. +|+.+.+...|||...|.+.+..
T Consensus 5 l~~Ai~~v~~g~--~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 5 LQKAIEAVKNGK--MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHTTS--S-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHhCC--CCHHHHHHHHCcCHHHHHHHHcC
Confidence 455665554433 99999999999999999887664
No 255
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=25.73 E-value=71 Score=27.57 Aligned_cols=23 Identities=22% Similarity=0.267 Sum_probs=19.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
+.+|++||++.+|++...++..|
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l 154 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRI 154 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHH
Confidence 46899999999999988755544
No 256
>PRK04217 hypothetical protein; Provisional
Probab=25.66 E-value=95 Score=25.58 Aligned_cols=40 Identities=28% Similarity=0.264 Sum_probs=26.5
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
..+.-|..++.+. ..+.+|++||++.+|++...+...|..
T Consensus 42 ~Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 42 FMTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred cCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444444443322 234679999999999999887776654
No 257
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=25.62 E-value=97 Score=25.03 Aligned_cols=65 Identities=18% Similarity=0.287 Sum_probs=46.0
Q ss_pred EEEchHHHHHHHHhcC-CCCCCHHHHHHhc-----CCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEec
Q psy11818 119 IQVSTYQMCVLLLFNN-REKLTYEEIQSET-----DIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVND 190 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~-~~~lt~~eL~~~t-----gi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~ 190 (331)
+.+|....+||..+.+ ...+|.+||...+ +++...+-++|..|...| ++.+...+ .....|.++.
T Consensus 4 lr~T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~G----li~~~~~~---~~~~~Y~~~~ 74 (120)
T PF01475_consen 4 LRLTPQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAG----LIRKIEFG---DGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTT----SEEEEEET---TSEEEEEESS
T ss_pred CCCCHHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCC----eEEEEEcC---CCcceEeecC
Confidence 4567777888877765 4589999999887 577889999999999998 88764311 1234566655
No 258
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=25.60 E-value=26 Score=32.05 Aligned_cols=29 Identities=28% Similarity=0.434 Sum_probs=0.0
Q ss_pred HHhccCCCCCHHHHHHHHHHHHHHHHHHh
Q psy11818 254 EQLKSRFLPSPVIIKKRIESLIEREYLAR 282 (331)
Q Consensus 254 ~~l~~~F~ps~~~IKk~IE~LIereyI~R 282 (331)
.+|...|..+..-++++|+.|++.|+|.|
T Consensus 37 ~eLa~~~~VSR~TvR~Al~~L~~eGli~r 65 (241)
T PRK11402 37 NELCTQYNVSRITIRKAISDLVADGVLIR 65 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEE
No 259
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=25.59 E-value=90 Score=20.07 Aligned_cols=20 Identities=25% Similarity=0.170 Sum_probs=16.8
Q ss_pred CCHHHHHHhcCCCHHHHHHH
Q psy11818 138 LTYEEIQSETDIPERDLIRA 157 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~ 157 (331)
+|..|+++.+|++...+.+-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~ 20 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRW 20 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 57899999999999777653
No 260
>PF12728 HTH_17: Helix-turn-helix domain
Probab=25.55 E-value=87 Score=21.20 Aligned_cols=20 Identities=25% Similarity=0.205 Sum_probs=17.0
Q ss_pred CCHHHHHHhcCCCHHHHHHH
Q psy11818 138 LTYEEIQSETDIPERDLIRA 157 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~ 157 (331)
+|.+|+++.+|++...+.+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~ 21 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRW 21 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHH
Confidence 68999999999999776653
No 261
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=25.50 E-value=65 Score=26.55 Aligned_cols=20 Identities=15% Similarity=0.275 Sum_probs=17.4
Q ss_pred CCCCHHHHHHhcCCCHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLI 155 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~ 155 (331)
+.+|++||++.+|++...++
T Consensus 122 ~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 122 EDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred cCCCHHHHHHHHCcCHHhhc
Confidence 46899999999999987764
No 262
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=25.47 E-value=1.1e+02 Score=26.69 Aligned_cols=24 Identities=13% Similarity=0.206 Sum_probs=20.5
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
..+|++||++.+|++...++..|.
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~ 168 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 579999999999999988776654
No 263
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=25.38 E-value=1.1e+02 Score=27.77 Aligned_cols=44 Identities=20% Similarity=0.230 Sum_probs=37.3
Q ss_pred HHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 128 VLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 128 ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
+-..|.-.+.++..+|++.+|++-.-++.+|.-|...| ++...|
T Consensus 30 l~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eG----lv~~~p 73 (230)
T COG1802 30 LSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEG----LVEIEP 73 (230)
T ss_pred HhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCC----CeEecC
Confidence 33445567899999999999999999999999999888 887665
No 264
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=25.38 E-value=87 Score=26.85 Aligned_cols=25 Identities=20% Similarity=0.332 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
-+.+|++||++.+|++...++..|.
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK09651 133 LDGLTYSEIAHKLGVSVSSVKKYVA 157 (172)
T ss_pred ccCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4679999999999999887665543
No 265
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=25.31 E-value=2.2e+02 Score=24.16 Aligned_cols=33 Identities=18% Similarity=0.255 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhCCccccccchHHHHHHHHHH
Q psy11818 261 LPSPVIIKKRIESLIEREYLARTPEDRFLQEKDVFERYYKQH 302 (331)
Q Consensus 261 ~ps~~~IKk~IE~LIereyI~Rd~~d~~i~~~~~~~~~~~~~ 302 (331)
..+...|..+|+.|.+.||| .|...+++|-+..
T Consensus 39 g~~~~~i~~vl~~l~~~~~l---------dD~~~a~~~~~~~ 71 (157)
T PRK00117 39 GFSEEVIEAVLDRLKEEGLL---------DDERFAESFVRSR 71 (157)
T ss_pred CCCHHHHHHHHHHHHHcCCC---------CHHHHHHHHHHHH
Confidence 45678899999999998888 3556666665554
No 266
>PRK09462 fur ferric uptake regulator; Provisional
Probab=25.12 E-value=1.6e+02 Score=24.90 Aligned_cols=52 Identities=15% Similarity=0.279 Sum_probs=42.9
Q ss_pred EEEchHHHHHHHHhcC--CCCCCHHHHHHhc-----CCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 119 IQVSTYQMCVLLLFNN--REKLTYEEIQSET-----DIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 119 l~vs~~Qa~ILllFN~--~~~lt~~eL~~~t-----gi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
+.+|.-..+||..+-. .+.+|.+||.+.+ +++...+-++|..|...+ ++.+.
T Consensus 13 lr~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~G----li~~~ 71 (148)
T PRK09462 13 LKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAG----IVTRH 71 (148)
T ss_pred CCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCC----CEEEE
Confidence 5688888999977754 3689999998876 467899999999999998 88654
No 267
>PRK14999 histidine utilization repressor; Provisional
Probab=24.85 E-value=1.1e+02 Score=27.87 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=33.2
Q ss_pred CCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 134 NREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 134 ~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
..+.+ |-.||++..|++-..++++|..|...| +|.+.+
T Consensus 32 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eG----li~r~~ 70 (241)
T PRK14999 32 PHDRIPSEAELVAQYGFSRMTINRALRELTDEG----WLVRLQ 70 (241)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEec
Confidence 35566 999999999999999999999999998 887654
No 268
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=24.83 E-value=2e+02 Score=27.73 Aligned_cols=61 Identities=15% Similarity=0.300 Sum_probs=46.4
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecCCC
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDSFT 193 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~F~ 193 (331)
...|+..++....+|..+|++.+|++...+.+=+..|-..+ +-+.... ..+..|.+...|.
T Consensus 10 L~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RDi~~L~~~g----vPI~~e~----G~~~gy~~~~~~~ 70 (311)
T COG2378 10 LLQIIQILRAKETVTAAELADEFEVSVRTIYRDIATLRAAG----VPIEGER----GKGGGYRLRPGFK 70 (311)
T ss_pred HHHHHHHHHhCccchHHHHHHhcCCCHHHHHHHHHHHHHCC----CCeEeec----CCCccEEEccCCC
Confidence 45677777877779999999999999999999999998776 3332211 1246688888884
No 269
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=24.74 E-value=1.6e+02 Score=26.31 Aligned_cols=34 Identities=15% Similarity=0.154 Sum_probs=30.1
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.+|-++|++.+|++...+-+.|..|-+.+ ++...
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g----~I~~~ 217 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSG----MLAVK 217 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCC----CEEec
Confidence 37889999999999999999999999887 77654
No 270
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=24.73 E-value=1.6e+02 Score=26.55 Aligned_cols=40 Identities=25% Similarity=0.307 Sum_probs=32.7
Q ss_pred HHHHHHhcCCC-CCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 126 MCVLLLFNNRE-KLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 126 a~ILllFN~~~-~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
..||.++-..+ .+|..+|+..+||+...+.++|-.|...+
T Consensus 7 ~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~ 47 (183)
T PHA02701 7 SLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESD 47 (183)
T ss_pred HHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcC
Confidence 34555554444 69999999999999999999999998887
No 271
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=24.71 E-value=1.2e+02 Score=26.67 Aligned_cols=24 Identities=21% Similarity=0.151 Sum_probs=19.7
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.++++||++.+|++...++..|.
T Consensus 151 ~g~s~~eIA~~lgis~~tV~~~l~ 174 (196)
T PRK12524 151 EGLSNPEIAEVMEIGVEAVESLTA 174 (196)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 579999999999999877665543
No 272
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=24.68 E-value=1.2e+02 Score=26.54 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=20.9
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
+.+|++||++.+|++...++..|.-
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~r 180 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRL 180 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHH
Confidence 5799999999999999887766543
No 273
>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=24.67 E-value=1.1e+02 Score=28.25 Aligned_cols=24 Identities=13% Similarity=0.224 Sum_probs=20.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~ 199 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVA 199 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999887765543
No 274
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=24.65 E-value=80 Score=26.13 Aligned_cols=25 Identities=16% Similarity=0.286 Sum_probs=21.2
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
+.++++||++.+|++...+...+.-
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~R 144 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFR 144 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHH
Confidence 5799999999999999888776643
No 275
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=24.64 E-value=66 Score=24.28 Aligned_cols=56 Identities=18% Similarity=0.247 Sum_probs=39.9
Q ss_pred hHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCC--CHHHHHHHHHHHHHHHHHHhCC
Q psy11818 228 EIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLP--SPVIIKKRIESLIEREYLARTP 284 (331)
Q Consensus 228 ~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~p--s~~~IKk~IE~LIereyI~Rd~ 284 (331)
.|..|| .-|+.++..+...|...+.+.-.-...+ -...++++|..++++|-|.+..
T Consensus 8 mI~eAI-~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 8 MILEAI-KALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHH-HHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred HHHHHH-HHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 455554 6788888999998888887755322222 2467899999999999877754
No 276
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=24.61 E-value=87 Score=27.08 Aligned_cols=25 Identities=12% Similarity=0.096 Sum_probs=20.8
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
-+.++++||++.+|++...++..+.
T Consensus 147 ~~~~s~~eIA~~lgis~~tV~~~l~ 171 (182)
T PRK12537 147 VDGCSHAEIAQRLGAPLGTVKAWIK 171 (182)
T ss_pred HcCCCHHHHHHHHCCChhhHHHHHH
Confidence 3579999999999999988776654
No 277
>PRK05949 RNA polymerase sigma factor; Validated
Probab=24.38 E-value=1.2e+02 Score=29.55 Aligned_cols=38 Identities=16% Similarity=0.276 Sum_probs=26.8
Q ss_pred EchHHHHHH-HHh--cCCCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 121 VSTYQMCVL-LLF--NNREKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 121 vs~~Qa~IL-llF--N~~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
.+.-+-.|+ +.| .+.+.+|++||++.+|++.+.+++.+
T Consensus 267 L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~ 307 (327)
T PRK05949 267 LTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLE 307 (327)
T ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 344444444 444 45678999999999999988776654
No 278
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=24.36 E-value=1e+02 Score=24.37 Aligned_cols=54 Identities=6% Similarity=0.136 Sum_probs=44.7
Q ss_pred HHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhC
Q psy11818 229 IEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLART 283 (331)
Q Consensus 229 IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd 283 (331)
++-+|..++. .+.++=-+|.+.+.+.....+.++...|=..+..|-++|+|++.
T Consensus 5 l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~ 58 (100)
T TIGR03433 5 LDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAE 58 (100)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEE
Confidence 4556777776 56789999999998776556788899999999999999999983
No 279
>KOG1466|consensus
Probab=24.35 E-value=96 Score=29.76 Aligned_cols=70 Identities=23% Similarity=0.246 Sum_probs=50.4
Q ss_pred CCHHHHHHHHHHHHHHH--HHHhCCccccccc-------------------hHHHHHHHHHHHHhhhhC---CCCCCchH
Q psy11818 262 PSPVIIKKRIESLIERE--YLARTPEDRFLQE-------------------KDVFERYYKQHLAKRLLL---DKSVSDDS 317 (331)
Q Consensus 262 ps~~~IKk~IE~LIere--yI~Rd~~d~~i~~-------------------~~~~~~~~~~~~~~~~~~---~~~~~~~~ 317 (331)
-+.+++.+|-..|++|| |++|.-..++..+ +-||+-+-.++-.+-+.+ +-+-|...
T Consensus 90 ld~~Df~~ck~~l~erg~~F~~~~~~sR~~IA~l~~~Fi~dg~~ILtHg~SRvVl~~L~~Aa~~~~~F~V~vTEsrPd~s 169 (313)
T KOG1466|consen 90 LDYEDFEQCKQHLLERGELFIERARKSRQKIAMLAQDFITDGCTILTHGYSRVVLEVLLTAAQNKKRFRVYVTESRPDGS 169 (313)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHhhCCCEEEEcchhHHHHHHHHHHHhcCceEEEEEecCCCCCc
Confidence 35678899999999998 8888665555443 235555555554444444 44778899
Q ss_pred HHHHHHHhhhccCC
Q psy11818 318 EKNMISKLKVRNLP 331 (331)
Q Consensus 318 ~~~~~~~~~~~~~~ 331 (331)
++.|..-|++.|+|
T Consensus 170 G~lm~~~L~~~~IP 183 (313)
T KOG1466|consen 170 GKLMAKELKKLGIP 183 (313)
T ss_pred hhHHHHHHHhcCCC
Confidence 99999999999987
No 280
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=24.28 E-value=1.3e+02 Score=25.20 Aligned_cols=24 Identities=33% Similarity=0.428 Sum_probs=20.5
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
++++++||++.+|++...++..|.
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ 151 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLN 151 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 579999999999999988776654
No 281
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=24.28 E-value=1.2e+02 Score=26.30 Aligned_cols=24 Identities=17% Similarity=0.290 Sum_probs=20.3
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.++++||++.+|++...++..|.
T Consensus 146 ~g~s~~eIA~~lgis~~tV~~~l~ 169 (184)
T PRK12539 146 EGLSVAEAATRSGMSESAVKVSVH 169 (184)
T ss_pred cCCcHHHHHHHHCcCHHHHHHHHH
Confidence 479999999999999988776654
No 282
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=24.20 E-value=1.1e+02 Score=26.26 Aligned_cols=24 Identities=29% Similarity=0.412 Sum_probs=20.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..+.
T Consensus 142 ~g~s~~EIA~~l~is~~tv~~~l~ 165 (179)
T PRK09415 142 EELSIKEIAEVTGVNENTVKTRLK 165 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 468999999999999988766554
No 283
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=24.14 E-value=1.1e+02 Score=26.32 Aligned_cols=25 Identities=16% Similarity=0.086 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
-+.++++||++.+|++...++..|.
T Consensus 149 ~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 149 YQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3579999999999999988775543
No 284
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=24.10 E-value=1.2e+02 Score=28.75 Aligned_cols=39 Identities=10% Similarity=0.106 Sum_probs=27.2
Q ss_pred EchHHHHHHHH-hcCCCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 121 VSTYQMCVLLL-FNNREKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 121 vs~~Qa~ILll-FN~~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
.+.-|-.|+.+ |-..+.+|++||++.+|++.+.+.+.+.
T Consensus 228 L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~ 267 (289)
T PRK07500 228 LNERELRIIRERRLREDGATLEALGEELGISKERVRQIEA 267 (289)
T ss_pred CCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45555555543 4334689999999999999887765543
No 285
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=24.00 E-value=1.1e+02 Score=30.28 Aligned_cols=45 Identities=24% Similarity=0.327 Sum_probs=34.9
Q ss_pred CcEEEEEchHHHHHHHHhcC---------CCCCCHHHHHHhc--CCCHHHHHHHHH
Q psy11818 115 RKHIIQVSTYQMCVLLLFNN---------REKLTYEEIQSET--DIPERDLIRALQ 159 (331)
Q Consensus 115 ~~~~l~vs~~Qa~ILllFN~---------~~~lt~~eL~~~t--gi~~~~l~~~L~ 159 (331)
+.|--+-|++|.+||.+|-+ -+.+|-+-+.+++ ||..+.+...|.
T Consensus 306 rvYAYT~s~l~iaiL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~ 361 (366)
T PF03849_consen 306 RVYAYTNSPLQIAILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLR 361 (366)
T ss_pred eEEEecCCHHHHHHHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHH
Confidence 36777889999999999975 2467888887776 788877776665
No 286
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.92 E-value=1.2e+02 Score=27.55 Aligned_cols=25 Identities=20% Similarity=0.298 Sum_probs=20.6
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
.+.+|++||++.+|++...++..+.
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3678999999999999988775543
No 287
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=23.89 E-value=1.3e+02 Score=27.54 Aligned_cols=40 Identities=28% Similarity=0.385 Sum_probs=34.8
Q ss_pred hcCCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 132 FNNREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 132 FN~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
|...+.+ +..+|++.+|++-..++.+|.-|...| ++...|
T Consensus 28 l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eG----lv~~~~ 68 (254)
T PRK09464 28 LRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKG----LLLRRQ 68 (254)
T ss_pred CCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCC----CEEEec
Confidence 4456788 899999999999999999999999887 887665
No 288
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=23.84 E-value=1.2e+02 Score=26.77 Aligned_cols=24 Identities=13% Similarity=0.108 Sum_probs=19.9
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
-+.++++||++.+|++...++..|
T Consensus 153 ~eg~s~~EIA~~lgis~~tVk~~l 176 (201)
T PRK12545 153 FLDFEIDDICTELTLTANHCSVLL 176 (201)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 357999999999999998876543
No 289
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=23.81 E-value=1.3e+02 Score=29.18 Aligned_cols=32 Identities=19% Similarity=0.296 Sum_probs=24.1
Q ss_pred HHHHHh--cCCCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 127 CVLLLF--NNREKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 127 ~ILllF--N~~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
.|.+.| ++.+.+|++||++.+|++.+.+++.+
T Consensus 264 Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~ 297 (317)
T PRK07405 264 VIALRFGLEDGQPLTLAKIGERLNISRERVRQIE 297 (317)
T ss_pred HHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence 334455 35577999999999999998876654
No 290
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=23.76 E-value=1.7e+02 Score=25.40 Aligned_cols=33 Identities=9% Similarity=0.116 Sum_probs=29.7
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
.+|-++|++.+|++.+.+-+.|..|.+.+ ++..
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g----~I~~ 181 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREG----YIRS 181 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCC----CEEc
Confidence 47899999999999999999999999887 7764
No 291
>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=23.73 E-value=1e+02 Score=26.52 Aligned_cols=24 Identities=29% Similarity=0.411 Sum_probs=20.3
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.++++||++.+|++...++..|.
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~ 176 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIF 176 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHH
Confidence 679999999999999887766554
No 292
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=23.57 E-value=1.4e+02 Score=28.20 Aligned_cols=49 Identities=12% Similarity=0.175 Sum_probs=40.4
Q ss_pred hHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 123 TYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 123 ~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.-|..+-+.-+..+.++-.||.+++|+|...+-+.|..|-+.| +..+..
T Consensus 196 ~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~G----lIe~~K 244 (258)
T COG2512 196 DEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRG----LIEKEK 244 (258)
T ss_pred HHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCC----ceEEEE
Confidence 3455555666677889999999999999999999999999887 877654
No 293
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=23.40 E-value=2.3e+02 Score=25.38 Aligned_cols=34 Identities=12% Similarity=0.088 Sum_probs=30.1
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
.+|-++|++.+|++.+.+-+.|..|.+.| ++...
T Consensus 169 ~~t~~~lA~~lG~sretvsR~L~~L~~~G----~I~~~ 202 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYVLAQFIQDG----YLKKS 202 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHHHHHHHHCC----CEEee
Confidence 36889999999999999999999999887 77653
No 294
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=23.02 E-value=1.1e+02 Score=25.67 Aligned_cols=24 Identities=21% Similarity=0.275 Sum_probs=20.3
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.++++||++.+|++...++..+.
T Consensus 127 ~~~s~~eIA~~lgis~~tv~~~l~ 150 (161)
T PRK12541 127 YGFSYKEIAEMTGLSLAKVKIELH 150 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 468999999999999988776654
No 295
>PRK00118 putative DNA-binding protein; Validated
Probab=22.99 E-value=97 Score=25.28 Aligned_cols=25 Identities=12% Similarity=0.332 Sum_probs=21.2
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
+.+|+.||++.+|++...+.+.+.-
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3789999999999999888777654
No 296
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=22.84 E-value=1.5e+02 Score=26.84 Aligned_cols=24 Identities=21% Similarity=0.109 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
.+.+|++||++.+|++...+...+
T Consensus 192 ~e~~S~~EIAe~lgis~~tV~~~~ 215 (227)
T TIGR02846 192 GRRKTQREIAKILGISRSYVSRIE 215 (227)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHH
Confidence 478999999999999998876553
No 297
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=22.76 E-value=91 Score=26.61 Aligned_cols=24 Identities=13% Similarity=0.162 Sum_probs=20.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+++.||++.+|++...++..|.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLA 157 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 579999999999999987766553
No 298
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=22.74 E-value=89 Score=26.54 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=19.2
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
+.+|++||++.+|++...++..|
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHH
Confidence 47999999999999988775443
No 299
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=22.73 E-value=88 Score=26.59 Aligned_cols=24 Identities=29% Similarity=0.314 Sum_probs=19.8
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+++|++||++.+|++...++..+.
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~ 158 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLF 158 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 689999999999999877655543
No 300
>PTZ00064 histone acetyltransferase; Provisional
Probab=22.73 E-value=80 Score=32.87 Aligned_cols=41 Identities=24% Similarity=0.360 Sum_probs=31.3
Q ss_pred CCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecCCCCCCCCCCeEEEecC
Q psy11818 138 LTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYPKTKEIEPNHVFFVNDS 191 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~~~~~i~~~~~f~lN~~ 191 (331)
+|+++|++.|||..+++..+|+.| + +|.... ....+.++.+
T Consensus 472 iSI~dIS~~TgI~~eDII~TLq~L---~----llky~k------gq~~I~~~~~ 512 (552)
T PTZ00064 472 KFIDNVVRSTGIRREDVIRILEEN---G----IMRNIK------DQHYIFCNQE 512 (552)
T ss_pred ccHHHHHHHhCCCHHHHHHHHHHC---C----cEEEeC------CCEEEEECHH
Confidence 899999999999999999999987 2 666532 2445555544
No 301
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=22.72 E-value=1.3e+02 Score=25.99 Aligned_cols=24 Identities=25% Similarity=0.189 Sum_probs=20.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..+.
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHH
Confidence 579999999999999887665543
No 302
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=22.67 E-value=1.3e+02 Score=26.16 Aligned_cols=24 Identities=8% Similarity=0.174 Sum_probs=19.8
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~ 149 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVN 149 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 679999999999999877655543
No 303
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=22.52 E-value=73 Score=29.65 Aligned_cols=25 Identities=40% Similarity=0.583 Sum_probs=20.8
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
++.+|++||++.||+|+..|-|+.+
T Consensus 21 k~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 21 KKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred hcccCHHHHHHHHCCCHHHHHHHHc
Confidence 4568999999999999988777643
No 304
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=22.51 E-value=1.3e+02 Score=26.84 Aligned_cols=32 Identities=22% Similarity=0.389 Sum_probs=28.3
Q ss_pred CHHHHHHhc-CCCHHHHHHHHHHHHcccCcccceeec
Q psy11818 139 TYEEIQSET-DIPERDLIRALQSLAMGKASQRILIRY 174 (331)
Q Consensus 139 t~~eL~~~t-gi~~~~l~~~L~sL~~~k~~~~IL~~~ 174 (331)
|-..|++.+ ||++..+.++|..|+..| ++.+.
T Consensus 72 SN~~La~r~~G~s~~tlrR~l~~LveaG----LI~rr 104 (177)
T PF03428_consen 72 SNAQLAERLNGMSERTLRRHLARLVEAG----LIVRR 104 (177)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHCC----Ceeec
Confidence 557899999 999999999999999998 77653
No 305
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=22.48 E-value=1.9e+02 Score=30.12 Aligned_cols=44 Identities=14% Similarity=0.211 Sum_probs=38.1
Q ss_pred chHHHHHHHHhcC-CCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 122 STYQMCVLLLFNN-REKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 122 s~~Qa~ILllFN~-~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
...|..||..+.+ .+.++..+|++.+|++.+.+..++.+|-..+
T Consensus 5 ~~~e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg 49 (494)
T PTZ00326 5 ELEENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESAN 49 (494)
T ss_pred hHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCC
Confidence 4567888888887 6779999999999999999999999997765
No 306
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=22.45 E-value=1.2e+02 Score=27.51 Aligned_cols=34 Identities=12% Similarity=0.141 Sum_probs=30.6
Q ss_pred CCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 138 LTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
-|-.||++..|++-..++++|..|+..| +|.+..
T Consensus 25 PsE~eLa~~~gVSR~TVR~Al~~L~~eG----li~r~~ 58 (233)
T TIGR02404 25 PSEHELMDQYGASRETVRKALNLLTEAG----YIQKIQ 58 (233)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEeC
Confidence 3889999999999999999999999998 887654
No 307
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=22.29 E-value=91 Score=27.19 Aligned_cols=25 Identities=24% Similarity=0.381 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
-+.+|++||++.+|++...++..|.
T Consensus 145 ~~g~s~~EIA~~lgis~~tVk~~l~ 169 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTPIGTVMSRLH 169 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3579999999999999887665543
No 308
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=22.27 E-value=1.1e+02 Score=27.68 Aligned_cols=24 Identities=29% Similarity=0.595 Sum_probs=20.5
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+||+...++..|.
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~ 172 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLA 172 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 579999999999999988766654
No 309
>PRK09483 response regulator; Provisional
Probab=22.23 E-value=1.7e+02 Score=24.99 Aligned_cols=42 Identities=10% Similarity=0.197 Sum_probs=35.4
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHc
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAM 163 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~ 163 (331)
..|.-+.-||.++. .++|.++|++.++++...++.++..+..
T Consensus 148 ~Lt~rE~~vl~~~~--~G~~~~~Ia~~l~is~~TV~~~~~~i~~ 189 (217)
T PRK09483 148 SLSERELQIMLMIT--KGQKVNEISEQLNLSPKTVNSYRYRMFS 189 (217)
T ss_pred ccCHHHHHHHHHHH--CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46888888887765 4589999999999999999999988764
No 310
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=22.22 E-value=1.4e+02 Score=25.04 Aligned_cols=24 Identities=29% Similarity=0.354 Sum_probs=20.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|.+||++.+|++...+...+.
T Consensus 143 ~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 143 EGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 578999999999999988766554
No 311
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=22.21 E-value=1.3e+02 Score=27.09 Aligned_cols=34 Identities=24% Similarity=0.413 Sum_probs=29.2
Q ss_pred HHhcCCCC-CCHHHHHHhcCCCHHHHHHHHHHHHc
Q psy11818 130 LLFNNREK-LTYEEIQSETDIPERDLIRALQSLAM 163 (331)
Q Consensus 130 llFN~~~~-lt~~eL~~~tgi~~~~l~~~L~sL~~ 163 (331)
++|-..+. +|+++|++.+|++...+..+|..|..
T Consensus 12 ~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~ 46 (188)
T PRK00135 12 LLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQE 46 (188)
T ss_pred HHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56777775 99999999999999889999988854
No 312
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=22.19 E-value=1.5e+02 Score=26.95 Aligned_cols=44 Identities=23% Similarity=0.136 Sum_probs=37.1
Q ss_pred chHHHHHHHHh--cCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 122 STYQMCVLLLF--NNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 122 s~~Qa~ILllF--N~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
+..|..|+-.- .....+|..+|++.+|++....+..|..+...+
T Consensus 173 ~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G 218 (223)
T PF04157_consen 173 SKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREG 218 (223)
T ss_dssp -HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTT
T ss_pred hHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCC
Confidence 46678888777 667889999999999999999999999998877
No 313
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=22.16 E-value=1.3e+02 Score=26.18 Aligned_cols=24 Identities=21% Similarity=0.153 Sum_probs=20.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.++++||++.+|++...++..|.
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~ 169 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLY 169 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHH
Confidence 468999999999999988766654
No 314
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=22.12 E-value=1.2e+02 Score=27.40 Aligned_cols=37 Identities=14% Similarity=0.152 Sum_probs=32.0
Q ss_pred CCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 135 REKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 135 ~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.+.+ |-.||++..|++-..++++|..|...| +|.+..
T Consensus 29 G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eG----li~r~~ 66 (238)
T TIGR02325 29 GDYLPAEMQLAERFGVNRHTVRRAIAALVERG----LLRAEQ 66 (238)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEec
Confidence 3444 889999999999999999999999998 887654
No 315
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=22.10 E-value=1.3e+02 Score=25.30 Aligned_cols=25 Identities=12% Similarity=0.007 Sum_probs=21.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
+.++++||++.+|++...++..|.-
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~r 161 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFR 161 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999888776643
No 316
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=22.08 E-value=1.1e+02 Score=30.66 Aligned_cols=37 Identities=30% Similarity=0.538 Sum_probs=33.6
Q ss_pred HHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHc
Q psy11818 127 CVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAM 163 (331)
Q Consensus 127 ~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~ 163 (331)
.||.+|.....++-.+|...++++.++++..|..+..
T Consensus 341 ~iL~~F~~~~~v~r~~l~~~~~l~~~~~~eiL~~~a~ 377 (421)
T PF04801_consen 341 YILLLFTKSRYVKRKELMSATKLPPEDVKEILKEIAV 377 (421)
T ss_pred HHHHHhcCCCceeHHHhhhhcCCCHHHHHHHHHHHhh
Confidence 4788999989999999999999999999999998864
No 317
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=21.90 E-value=1.3e+02 Score=24.52 Aligned_cols=60 Identities=13% Similarity=0.103 Sum_probs=42.1
Q ss_pred hHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCcccccc
Q psy11818 228 EIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPEDRFLQ 290 (331)
Q Consensus 228 ~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~d~~i~ 290 (331)
.+|+.|.+- ....-.....++.+|+.+.. ..++...+--||+.||+.|.++-.++-..++
T Consensus 48 ~yD~~Il~~-~~~~~~~~arvIg~vl~~~~--~~i~D~f~~~Ri~~Li~~G~le~~g~~~~mr 107 (111)
T PF12395_consen 48 YYDDFILEQ-APDEFQKAARVIGEVLGHSD--QGIGDWFLEYRIRELISQGVLEIKGDPKDMR 107 (111)
T ss_pred HhhHHHHhc-CCccccHHHHHHHHHHHhcC--cCCChHHHHHHHHHHHHCCCEEEecCCCccc
Confidence 456666661 12333556678888888763 3478889999999999999988776655443
No 318
>KOG3471|consensus
Probab=21.86 E-value=2e+02 Score=29.33 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=34.9
Q ss_pred CcEEEEEchHHHHHHHHhcC---------CCCCCHHHHHHhc--CCCHHHHHHHHHHHHc
Q psy11818 115 RKHIIQVSTYQMCVLLLFNN---------REKLTYEEIQSET--DIPERDLIRALQSLAM 163 (331)
Q Consensus 115 ~~~~l~vs~~Qa~ILllFN~---------~~~lt~~eL~~~t--gi~~~~l~~~L~sL~~ 163 (331)
+-|--+-|.+|.+|+-+|-+ .+.+|-+-+..++ ||..+.++..|..=..
T Consensus 315 riYAYT~S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ah 374 (465)
T KOG3471|consen 315 RIYAYTNSPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAH 374 (465)
T ss_pred EEEEecCCHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccC
Confidence 47888999999999999964 2456666666554 6777666666654443
No 319
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=21.73 E-value=99 Score=27.72 Aligned_cols=47 Identities=15% Similarity=0.293 Sum_probs=34.4
Q ss_pred HHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCC
Q psy11818 230 EAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTP 284 (331)
Q Consensus 230 qAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~ 284 (331)
-+.+++.|-. ..+.++|+..+... |+ ..+|...|+.|.++|||..+.
T Consensus 32 ~~~L~~lLdG--~rt~~eI~~~l~~~----~p--~~~v~~~L~~L~~~G~l~~~~ 78 (193)
T TIGR03882 32 YCQLAPLLDG--RRTLDEIIAALAGR----FP--AEEVLYALDRLERRGYLVEDA 78 (193)
T ss_pred HHHHHHHHcC--CCCHHHHHHHhhcc----CC--HHHHHHHHHHHHHCCCEeccC
Confidence 4566777755 56777777666553 43 777999999999999999654
No 320
>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=21.70 E-value=1e+02 Score=25.35 Aligned_cols=25 Identities=24% Similarity=0.344 Sum_probs=21.4
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQS 160 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~s 160 (331)
+.+|+.||++.+|++...+...+.-
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~r 152 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISK 152 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4789999999999999888776654
No 321
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=21.64 E-value=1.2e+02 Score=28.07 Aligned_cols=24 Identities=13% Similarity=0.148 Sum_probs=19.9
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 131 eg~S~~EIAe~LgiS~~tVksrL~ 154 (228)
T PRK06704 131 FQYSIADIAKVCSVSEGAVKASLF 154 (228)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHH
Confidence 469999999999999987766544
No 322
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=21.61 E-value=99 Score=26.75 Aligned_cols=25 Identities=32% Similarity=0.355 Sum_probs=20.7
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
-+.+|++||++.+|++...++..|.
T Consensus 141 ~~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 141 LEGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4689999999999999887766543
No 323
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=21.59 E-value=1.8e+02 Score=21.06 Aligned_cols=52 Identities=25% Similarity=0.331 Sum_probs=39.2
Q ss_pred HHhhhhhHHHHHHHhhhcccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHH
Q psy11818 222 DEDRKHEIEAAVVRIMKARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLA 281 (331)
Q Consensus 222 ~edR~~~IqAaIVRIMK~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~ 281 (331)
.++.-=.+-|.|...+-.++.++..+|...+- -+...||+++-.||+.+++.
T Consensus 7 i~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t~--------l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 7 IEEHFGEIVAKVGEVLLSRGRLTLREIVRRTG--------LSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHC-SEEHHHHHHHHT----------HHHHHHHHHHHHHTTSEE
T ss_pred HHHHcChHHHHHHHHHHHcCCcCHHHHHHHhC--------CCHHHHHHHHHHHHHcCCee
Confidence 34445557788999999999999998887664 35778999999999987653
No 324
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.59 E-value=1.2e+02 Score=20.03 Aligned_cols=24 Identities=17% Similarity=0.036 Sum_probs=18.9
Q ss_pred CCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 138 LTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
+|+.|+++.+|++...|.. |.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~----~~~~g 24 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRY----YERIG 24 (49)
T ss_pred CcHHHHHHHHCcCHHHHHH----HHHCC
Confidence 5789999999999976664 55555
No 325
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=21.57 E-value=1.7e+02 Score=26.35 Aligned_cols=42 Identities=19% Similarity=0.324 Sum_probs=36.7
Q ss_pred EEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHc
Q psy11818 120 QVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAM 163 (331)
Q Consensus 120 ~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~ 163 (331)
..|.-|..||.++-. .+|-+||++.+++++.+++.+...+..
T Consensus 148 ~LT~RE~eVL~lla~--G~snkeIA~~L~iS~~TVk~h~~~i~~ 189 (211)
T COG2197 148 LLTPRELEVLRLLAE--GLSNKEIAEELNLSEKTVKTHVSNILR 189 (211)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHHCCCHhHHHHHHHHHHH
Confidence 478889999887765 689999999999999999999988764
No 326
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.54 E-value=1.7e+02 Score=30.08 Aligned_cols=60 Identities=22% Similarity=0.311 Sum_probs=46.3
Q ss_pred CceEEEEEEEcCCCcCCCCCCCCCCCCCCCCCCCcEEEEEchHHHHHHHHhcC---------CCCCCHHHHHHhc--CCC
Q psy11818 82 MGSADLNAVFFGPRREEGEGKDGASSSTSPPAPRKHIIQVSTYQMCVLLLFNN---------REKLTYEEIQSET--DIP 150 (331)
Q Consensus 82 Lg~~~l~~~f~~~~k~~~~~~~~~~~~~~~~~~~~~~l~vs~~Qa~ILllFN~---------~~~lt~~eL~~~t--gi~ 150 (331)
-|.+.|++|| +-|-.+-|.+|.+||.+|-+ .+.+|-+-+.+++ ||.
T Consensus 291 ~g~iivEtNf-----------------------rvYaYt~s~l~~~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIT 347 (448)
T TIGR00625 291 LGFIIVETNY-----------------------RLYAYTESPLQIALIALFSELLARFPNMVVGQITRESIRRALANGIT 347 (448)
T ss_pred CceEEEEecc-----------------------eEEEecCCHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHcCCC
Confidence 4777888887 37888999999999999975 2468888887776 788
Q ss_pred HHHHHHHHHHHHcc
Q psy11818 151 ERDLIRALQSLAMG 164 (331)
Q Consensus 151 ~~~l~~~L~sL~~~ 164 (331)
.+.++..|.+=...
T Consensus 348 a~qIi~fl~~~ahp 361 (448)
T TIGR00625 348 AQQIIHYLRTHAHP 361 (448)
T ss_pred HHHHHHHHHhcCCh
Confidence 88877777655443
No 327
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=21.54 E-value=1.9e+02 Score=30.12 Aligned_cols=42 Identities=12% Similarity=0.177 Sum_probs=36.6
Q ss_pred HHHHHHHHhcCCCC-CCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 124 YQMCVLLLFNNREK-LTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 124 ~Qa~ILllFN~~~~-lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
.|..||..+.+.+. ++.++|++.+|++...+..++.+|-..+
T Consensus 4 ~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg 46 (492)
T PLN02853 4 AEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFR 46 (492)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCC
Confidence 56788888887774 8999999999999999999999997765
No 328
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.53 E-value=1.7e+02 Score=23.07 Aligned_cols=38 Identities=18% Similarity=0.234 Sum_probs=30.9
Q ss_pred HHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHccc
Q psy11818 128 VLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAMGK 165 (331)
Q Consensus 128 ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k 165 (331)
+.++..+.+..++-+|.++||.|-..+...+..|-.-+
T Consensus 13 la~Li~S~e~~nVP~lm~~TGwPRRT~QDvikAlpglg 50 (95)
T COG4519 13 LAYLIDSGETANVPELMAATGWPRRTAQDVIKALPGLG 50 (95)
T ss_pred HHHHHhccccCChHHHHHHcCCchhHHHHHHHhCcCCC
Confidence 34556777889999999999999999999888875443
No 329
>PRK03837 transcriptional regulator NanR; Provisional
Probab=21.49 E-value=1.7e+02 Score=26.30 Aligned_cols=39 Identities=15% Similarity=0.123 Sum_probs=33.9
Q ss_pred cCCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 133 NNREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 133 N~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
-..+.+ +..+|++.+|++-..++.+|.-|...| ++...+
T Consensus 32 ~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eG----lv~~~~ 71 (241)
T PRK03837 32 GPGDQLPSERELMAFFGVGRPAVREALQALKRKG----LVQISH 71 (241)
T ss_pred CCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC----CEEEec
Confidence 346778 999999999999999999999999887 887654
No 330
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=21.38 E-value=51 Score=26.42 Aligned_cols=39 Identities=21% Similarity=0.357 Sum_probs=27.6
Q ss_pred cccCCChHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHhCCc
Q psy11818 239 ARKRMQHNTLITEVTEQLKSRFLPSPVIIKKRIESLIEREYLARTPE 285 (331)
Q Consensus 239 ~~K~l~~~~Li~~V~~~l~~~F~ps~~~IKk~IE~LIereyI~Rd~~ 285 (331)
..+.++..+|... ...+.+.+-+.|..|.++|||.|..+
T Consensus 40 ~~~~~t~~eL~~~--------l~~~~stvs~~i~~Le~kg~I~r~~~ 78 (109)
T TIGR01889 40 NEGKLTLKEIIKE--------ILIKQSALVKIIKKLSKKGYLSKERS 78 (109)
T ss_pred cCCcCcHHHHHHH--------HCCCHHHHHHHHHHHHHCCCEeccCC
Confidence 3455666655443 33466778999999999999998544
No 331
>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=21.36 E-value=1.5e+02 Score=25.10 Aligned_cols=24 Identities=29% Similarity=0.360 Sum_probs=20.1
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..+.
T Consensus 134 ~g~s~~eiA~~lgis~~tv~~~l~ 157 (169)
T TIGR02954 134 HDLTIKEIAEVMNKPEGTVKTYLH 157 (169)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 469999999999999988766554
No 332
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.34 E-value=1.3e+02 Score=26.13 Aligned_cols=23 Identities=17% Similarity=0.137 Sum_probs=18.8
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
+.+|++||++.+|++...+...+
T Consensus 146 ~g~s~~EIAe~lgis~~~V~~~l 168 (189)
T PRK06811 146 LGEKIEEIAKKLGLTRSAIDNRL 168 (189)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHH
Confidence 46999999999999987655443
No 333
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=21.28 E-value=1.5e+02 Score=24.48 Aligned_cols=36 Identities=14% Similarity=0.138 Sum_probs=32.5
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
-.+|++||++.+..+....+..|+.|...+ .|...|
T Consensus 18 ~~vtl~elA~~l~cS~Rn~r~lLkkm~~~g----Wi~W~p 53 (115)
T PF12793_consen 18 VEVTLDELAELLFCSRRNARTLLKKMQEEG----WITWQP 53 (115)
T ss_pred cceeHHHHHHHhCCCHHHHHHHHHHHHHCC----CeeeeC
Confidence 468999999999999999999999999887 887765
No 334
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=21.24 E-value=2.7e+02 Score=19.75 Aligned_cols=26 Identities=23% Similarity=0.300 Sum_probs=22.7
Q ss_pred CCCHHHHHHhcCC-CHHHHHHHHHHHH
Q psy11818 137 KLTYEEIQSETDI-PERDLIRALQSLA 162 (331)
Q Consensus 137 ~lt~~eL~~~tgi-~~~~l~~~L~sL~ 162 (331)
.+++++|+...|+ +...+.+......
T Consensus 50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 50 DLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 7999999999999 8888888877654
No 335
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=21.22 E-value=1.8e+02 Score=26.71 Aligned_cols=41 Identities=22% Similarity=0.219 Sum_probs=35.5
Q ss_pred HhcCCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 131 LFNNREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 131 lFN~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
.|--.+.+ |..+|++.+|++-..++.+|.-|...| ++...+
T Consensus 26 ~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eG----lV~~~~ 67 (257)
T PRK10225 26 PYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKG----LVEVRR 67 (257)
T ss_pred CCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCC----CEEEec
Confidence 35567889 799999999999999999999999887 887655
No 336
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=21.18 E-value=99 Score=24.62 Aligned_cols=24 Identities=21% Similarity=0.335 Sum_probs=21.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
..+|.++|+..+|++.+.|.++|+
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 479999999999999999888765
No 337
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=21.08 E-value=67 Score=20.07 Aligned_cols=15 Identities=20% Similarity=0.516 Sum_probs=9.3
Q ss_pred ccchHHHHHHHHHHH
Q psy11818 289 LQEKDVFERYYKQHL 303 (331)
Q Consensus 289 i~~~~~~~~~~~~~~ 303 (331)
+...|+|..||.+.-
T Consensus 3 is~~d~f~eFY~rlk 17 (28)
T PF12108_consen 3 ISGGDPFSEFYERLK 17 (28)
T ss_dssp --S--HHHHHHHHHH
T ss_pred CCCCChHHHHHHHHH
Confidence 457899999998754
No 338
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=21.04 E-value=91 Score=22.33 Aligned_cols=20 Identities=15% Similarity=0.102 Sum_probs=16.8
Q ss_pred CCHHHHHHhcCCCHHHHHHH
Q psy11818 138 LTYEEIQSETDIPERDLIRA 157 (331)
Q Consensus 138 lt~~eL~~~tgi~~~~l~~~ 157 (331)
+|+.|+++.+|++...|+..
T Consensus 1 yti~eva~~~gvs~~tlr~y 20 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYY 20 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHH
T ss_pred CcHHHHHHHHCcCHHHHHHH
Confidence 47899999999999777654
No 339
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=21.02 E-value=96 Score=26.99 Aligned_cols=24 Identities=33% Similarity=0.457 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
-+.+|++||++.+|++...++..|
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l 176 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRL 176 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHH
Confidence 367999999999999998876544
No 340
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=21.01 E-value=90 Score=23.81 Aligned_cols=26 Identities=19% Similarity=0.302 Sum_probs=21.1
Q ss_pred hHHHHHHHhhhccc--CCChHHHHHHHH
Q psy11818 228 EIEAAVVRIMKARK--RMQHNTLITEVT 253 (331)
Q Consensus 228 ~IqAaIVRIMK~~K--~l~~~~Li~~V~ 253 (331)
..=|.||..||.+. .++++||+.++.
T Consensus 9 t~l~~aV~ymK~r~~~Plt~~EIl~~ls 36 (75)
T cd07977 9 TQLAKIVDYMKKRHQHPLTLDEILDYLS 36 (75)
T ss_pred hhHHHHHHHHHhcCCCCccHHHHHHHHh
Confidence 34578999999986 799998888775
No 341
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=21.01 E-value=1.5e+02 Score=25.82 Aligned_cols=24 Identities=29% Similarity=0.466 Sum_probs=20.2
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..|.
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~ 149 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIG 149 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHH
Confidence 579999999999999987766553
No 342
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=20.72 E-value=1.6e+02 Score=26.93 Aligned_cols=36 Identities=19% Similarity=0.373 Sum_probs=26.2
Q ss_pred HHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHH
Q psy11818 125 QMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLA 162 (331)
Q Consensus 125 Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~ 162 (331)
+..+.+.| .+.+|++||++.+|++...+.+....+.
T Consensus 189 r~vi~l~~--~~~~t~~EIA~~lgis~~~V~q~~~~~~ 224 (231)
T PRK12427 189 QLILHLYY--QHEMSLKEIALVLDLTEARICQLNKKIA 224 (231)
T ss_pred HHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 33444445 3579999999999999998877665543
No 343
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=20.69 E-value=1.3e+02 Score=26.28 Aligned_cols=24 Identities=13% Similarity=0.162 Sum_probs=20.3
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.++++||++.+|++...++..|.
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~ 154 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVN 154 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 579999999999999887766554
No 344
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=20.67 E-value=1.6e+02 Score=26.81 Aligned_cols=38 Identities=24% Similarity=0.270 Sum_probs=33.1
Q ss_pred CCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 134 NREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 134 ~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
..+.+ |-.||++..|++-..++++|.-|...| +|.+..
T Consensus 25 ~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eG----li~r~~ 63 (240)
T PRK09764 25 PGDALPTESALQTEFGVSRVTVRQALRQLVEQQ----ILESIQ 63 (240)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCC----CEEEec
Confidence 35567 899999999999999999999999988 887654
No 345
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=20.47 E-value=1.4e+02 Score=26.92 Aligned_cols=33 Identities=15% Similarity=0.154 Sum_probs=29.7
Q ss_pred CCCHHHHHHhcCCCHHHHHHHHHHHHcccCcccceee
Q psy11818 137 KLTYEEIQSETDIPERDLIRALQSLAMGKASQRILIR 173 (331)
Q Consensus 137 ~lt~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~ 173 (331)
.+|-++|++.+|++.+.+-+.|+.|.+.+ ++..
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~~~G----lI~~ 211 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQDRG----LIGL 211 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCC----cEEe
Confidence 37889999999999999999999999887 7765
No 346
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=20.39 E-value=1.8e+02 Score=26.22 Aligned_cols=40 Identities=23% Similarity=0.170 Sum_probs=35.0
Q ss_pred hcCCCCC-CHHHHHHhcCCCHHHHHHHHHHHHcccCcccceeecC
Q psy11818 132 FNNREKL-TYEEIQSETDIPERDLIRALQSLAMGKASQRILIRYP 175 (331)
Q Consensus 132 FN~~~~l-t~~eL~~~tgi~~~~l~~~L~sL~~~k~~~~IL~~~~ 175 (331)
|.-.+.+ +..+|++.+|++-..++.+|.-|...| ++...|
T Consensus 24 l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eG----lV~~~~ 64 (235)
T TIGR02812 24 FPPGSILPAERELSELIGVTRTTLREVLQRLARDG----WLTIQH 64 (235)
T ss_pred CCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCC----CEEEeC
Confidence 4456789 899999999999999999999999887 887654
No 347
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=20.32 E-value=2e+02 Score=26.67 Aligned_cols=44 Identities=18% Similarity=0.197 Sum_probs=37.5
Q ss_pred EEEEchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHHHc
Q psy11818 118 IIQVSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSLAM 163 (331)
Q Consensus 118 ~l~vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL~~ 163 (331)
.-..|..+..||.+.-. ++|.+||++.++++...++.++..+..
T Consensus 141 ~~~LS~RE~eVL~Lia~--G~SnkEIA~~L~IS~~TVk~hvs~I~~ 184 (217)
T PRK13719 141 KNKVTKYQNDVFILYSF--GFSHEYIAQLLNITVGSSKNKISEILK 184 (217)
T ss_pred cCCCCHHHHHHHHHHHC--CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34578889999988765 589999999999999999999887764
No 348
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=20.32 E-value=1.7e+02 Score=25.36 Aligned_cols=23 Identities=17% Similarity=0.027 Sum_probs=19.2
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRAL 158 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L 158 (331)
+.+|++||++.+|++...++..+
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l 176 (189)
T PRK09648 154 VGLSAEETAEAVGSTPGAVRVAQ 176 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHH
Confidence 36899999999999988766554
No 349
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=20.24 E-value=1.5e+02 Score=26.61 Aligned_cols=43 Identities=7% Similarity=0.072 Sum_probs=36.0
Q ss_pred chHHHHHHHHhcCCC--CCCHHHHHHhcCCCHHHHHHHHHHHHcc
Q psy11818 122 STYQMCVLLLFNNRE--KLTYEEIQSETDIPERDLIRALQSLAMG 164 (331)
Q Consensus 122 s~~Qa~ILllFN~~~--~lt~~eL~~~tgi~~~~l~~~L~sL~~~ 164 (331)
..-+..||..++..+ .++..||++..|++...+++-|..|-..
T Consensus 15 ~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~ 59 (213)
T PRK05472 15 LPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEF 59 (213)
T ss_pred hHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhc
Confidence 455677888888877 8999999999999999999988887444
No 350
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.19 E-value=1.3e+02 Score=27.49 Aligned_cols=25 Identities=20% Similarity=0.226 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 135 REKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 135 ~~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
-+.+|++||++.+|++...++..|.
T Consensus 185 ~eg~s~~EIA~~Lgis~~tVk~~l~ 209 (233)
T PRK12538 185 HENMSNGEIAEVMDTTVAAVESLLK 209 (233)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3579999999999999887665543
No 351
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=20.07 E-value=1.1e+02 Score=26.46 Aligned_cols=24 Identities=33% Similarity=0.509 Sum_probs=20.0
Q ss_pred CCCCHHHHHHhcCCCHHHHHHHHH
Q psy11818 136 EKLTYEEIQSETDIPERDLIRALQ 159 (331)
Q Consensus 136 ~~lt~~eL~~~tgi~~~~l~~~L~ 159 (331)
+.+|++||++.+|++...++..+.
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~ 160 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFE 160 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 469999999999999988766543
No 352
>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=20.07 E-value=1.6e+02 Score=23.43 Aligned_cols=40 Identities=28% Similarity=0.283 Sum_probs=28.1
Q ss_pred EchHHHHHHHHhcCCCCCCHHHHHHhcCCCHHHHHHHHHHH
Q psy11818 121 VSTYQMCVLLLFNNREKLTYEEIQSETDIPERDLIRALQSL 161 (331)
Q Consensus 121 vs~~Qa~ILllFN~~~~lt~~eL~~~tgi~~~~l~~~L~sL 161 (331)
++.-|..|+.++- ..+++..||++.+|++...+...+...
T Consensus 111 L~~~~~~ii~~~~-~~g~s~~eIA~~l~~s~~~v~~~~~~~ 150 (158)
T TIGR02937 111 LPEREREVLVLRY-LEGLSYKEIAEILGISVGTVKRRLKRA 150 (158)
T ss_pred CCHHHHHHHhhHH-hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4455555543321 136899999999999999888877654
Done!