Query 010353
Match_columns 512
No_of_seqs 130 out of 269
Neff 8.0
Searched_HMMs 46136
Date Thu Mar 28 23:32:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010353.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010353hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2587 RNA polymerase III (C) 100.0 8.9E-79 1.9E-83 611.3 40.0 485 2-512 1-551 (551)
2 PF05645 RNA_pol_Rpc82: RNA po 99.8 4.6E-20 1E-24 181.9 9.9 163 152-326 1-176 (258)
3 PF08221 HTH_9: RNA polymerase 99.8 6.8E-20 1.5E-24 139.2 6.6 61 8-68 1-61 (62)
4 PF02002 TFIIE_alpha: TFIIE al 99.5 1.4E-14 3.1E-19 122.9 4.2 103 359-463 2-104 (105)
5 TIGR00373 conserved hypothetic 99.0 4.5E-09 9.8E-14 95.5 11.7 106 359-466 3-108 (158)
6 PRK06266 transcription initiat 98.9 1.5E-08 3.3E-13 93.7 11.6 109 356-466 6-116 (178)
7 COG1675 TFA1 Transcription ini 98.7 1.5E-07 3.2E-12 85.9 11.3 104 359-467 10-113 (176)
8 smart00531 TFIIE Transcription 98.4 4.2E-07 9.1E-12 81.8 6.9 93 373-466 4-98 (147)
9 PF02002 TFIIE_alpha: TFIIE al 98.1 5.9E-06 1.3E-10 70.0 6.0 89 8-100 1-89 (105)
10 PF08221 HTH_9: RNA polymerase 97.4 0.00032 6.9E-09 53.3 5.5 60 359-419 2-61 (62)
11 TIGR00373 conserved hypothetic 97.3 0.0013 2.8E-08 59.9 9.2 88 9-100 3-90 (158)
12 PRK06266 transcription initiat 96.7 0.011 2.4E-07 54.8 9.5 83 13-99 13-97 (178)
13 PHA02943 hypothetical protein; 95.9 0.055 1.2E-06 47.9 8.9 73 375-457 16-88 (165)
14 smart00550 Zalpha Z-DNA-bindin 95.9 0.011 2.4E-07 45.7 4.0 44 373-417 9-54 (68)
15 PF01978 TrmB: Sugar-specific 95.7 0.029 6.3E-07 43.2 5.7 46 20-65 8-53 (68)
16 KOG2593 Transcription initiati 95.3 0.08 1.7E-06 54.6 8.9 141 359-504 18-198 (436)
17 PF13412 HTH_24: Winged helix- 95.1 0.034 7.3E-07 39.6 4.1 44 372-416 5-48 (48)
18 PF04337 DUF480: Protein of un 95.1 0.45 9.8E-06 42.0 11.7 123 20-168 3-144 (148)
19 smart00531 TFIIE Transcription 95.0 0.061 1.3E-06 48.4 6.4 74 24-100 5-80 (147)
20 PF13601 HTH_34: Winged helix 94.9 0.11 2.4E-06 41.5 6.9 75 24-107 4-78 (80)
21 KOG2587 RNA polymerase III (C) 94.6 0.15 3.3E-06 53.6 8.7 91 6-98 383-474 (551)
22 smart00550 Zalpha Z-DNA-bindin 94.6 0.1 2.2E-06 40.4 5.7 45 21-65 7-53 (68)
23 PF04703 FaeA: FaeA-like prote 94.5 0.058 1.3E-06 40.8 4.2 56 375-436 5-61 (62)
24 PHA02943 hypothetical protein; 94.2 1.2 2.6E-05 39.6 12.1 102 23-158 14-118 (165)
25 TIGR02702 SufR_cyano iron-sulf 93.5 1.7 3.7E-05 41.1 13.1 66 22-92 3-68 (203)
26 PF01978 TrmB: Sugar-specific 93.4 0.1 2.3E-06 40.1 3.8 47 372-419 10-56 (68)
27 PF13412 HTH_24: Winged helix- 93.2 0.25 5.4E-06 35.1 5.3 43 22-64 5-47 (48)
28 PF09339 HTH_IclR: IclR helix- 93.1 0.15 3.2E-06 37.0 4.1 44 22-65 5-49 (52)
29 PRK10141 DNA-binding transcrip 93.1 0.96 2.1E-05 38.9 9.7 64 17-90 12-76 (117)
30 COG3355 Predicted transcriptio 93.1 0.67 1.5E-05 40.2 8.5 61 10-70 15-78 (126)
31 PF09339 HTH_IclR: IclR helix- 92.7 0.098 2.1E-06 38.0 2.6 46 371-416 4-49 (52)
32 PRK11239 hypothetical protein; 92.2 2.8 6E-05 39.6 12.0 125 17-168 4-154 (215)
33 COG3355 Predicted transcriptio 92.1 1.9 4.2E-05 37.4 10.1 82 374-458 31-117 (126)
34 COG1510 Predicted transcriptio 92.0 0.32 6.9E-06 44.2 5.4 57 10-66 7-73 (177)
35 smart00418 HTH_ARSR helix_turn 91.8 0.71 1.5E-05 34.0 6.6 56 25-91 2-57 (66)
36 KOG2593 Transcription initiati 91.8 0.53 1.1E-05 48.8 7.4 101 7-109 16-116 (436)
37 PF03962 Mnd1: Mnd1 family; I 91.2 2.3 5.1E-05 39.8 10.6 87 376-468 2-94 (188)
38 smart00347 HTH_MARR helix_turn 90.9 2.2 4.7E-05 34.7 9.2 68 18-92 8-75 (101)
39 COG3132 Uncharacterized protei 90.8 3.7 8E-05 37.4 10.8 122 18-167 5-151 (215)
40 cd00090 HTH_ARSR Arsenical Res 90.8 1.4 3E-05 33.5 7.5 48 20-68 7-54 (78)
41 smart00420 HTH_DEOR helix_turn 90.4 0.76 1.7E-05 32.6 5.3 42 24-65 4-45 (53)
42 PF09012 FeoC: FeoC like trans 90.3 0.52 1.1E-05 36.4 4.5 46 24-69 4-49 (69)
43 COG1675 TFA1 Transcription ini 90.3 2 4.4E-05 39.6 9.0 80 13-96 10-90 (176)
44 PF10771 DUF2582: Protein of u 90.3 0.44 9.6E-06 36.4 4.0 51 15-65 3-53 (65)
45 PF03965 Penicillinase_R: Peni 90.3 3.5 7.6E-05 35.1 10.1 100 19-131 2-106 (115)
46 COG2345 Predicted transcriptio 90.1 2 4.2E-05 41.1 9.0 67 369-438 10-76 (218)
47 COG2345 Predicted transcriptio 89.9 5.8 0.00013 37.9 12.0 93 17-124 8-100 (218)
48 TIGR02698 CopY_TcrY copper tra 89.8 4.9 0.00011 35.2 10.8 99 20-131 4-107 (130)
49 PF01022 HTH_5: Bacterial regu 89.5 0.92 2E-05 32.1 4.9 42 23-65 5-46 (47)
50 COG5647 Cullin, a subunit of E 88.9 2.8 6E-05 46.4 10.1 139 23-167 611-764 (773)
51 smart00344 HTH_ASNC helix_turn 88.7 2.3 4.9E-05 35.6 7.7 63 373-436 6-72 (108)
52 PF04703 FaeA: FaeA-like prote 88.6 1.8 4E-05 32.7 6.1 42 24-65 4-46 (62)
53 COG1378 Predicted transcriptio 88.5 3.7 8E-05 40.2 10.0 48 18-65 14-61 (247)
54 PF12840 HTH_20: Helix-turn-he 88.4 1.4 3E-05 33.0 5.5 46 20-65 10-55 (61)
55 smart00346 HTH_ICLR helix_turn 88.2 1.3 2.9E-05 35.7 5.8 44 22-65 7-51 (91)
56 PF12840 HTH_20: Helix-turn-he 88.2 1 2.2E-05 33.7 4.7 50 370-420 10-59 (61)
57 PF08220 HTH_DeoR: DeoR-like h 88.0 1.3 2.7E-05 32.9 4.9 43 23-65 3-45 (57)
58 PRK00135 scpB segregation and 86.5 15 0.00033 34.4 12.4 121 21-167 5-135 (188)
59 PF10557 Cullin_Nedd8: Cullin 86.2 2 4.4E-05 33.0 5.4 57 111-167 8-64 (68)
60 smart00344 HTH_ASNC helix_turn 86.2 1.5 3.3E-05 36.7 5.2 43 23-65 6-48 (108)
61 PF12802 MarR_2: MarR family; 85.9 2 4.4E-05 31.8 5.2 46 20-65 5-52 (62)
62 PF14947 HTH_45: Winged helix- 85.4 6.5 0.00014 31.0 8.1 70 20-104 6-75 (77)
63 PF06163 DUF977: Bacterial pro 85.4 2.2 4.8E-05 36.8 5.6 46 20-65 12-57 (127)
64 TIGR02702 SufR_cyano iron-sulf 85.3 3.8 8.3E-05 38.8 8.0 63 373-438 4-66 (203)
65 PF02082 Rrf2: Transcriptional 84.6 3.6 7.9E-05 32.8 6.4 42 24-65 12-56 (83)
66 PHA02701 ORF020 dsRNA-binding 84.6 1.3 2.9E-05 40.8 4.2 47 371-418 5-52 (183)
67 PRK11169 leucine-responsive tr 84.3 2.6 5.5E-05 38.5 6.1 43 373-416 17-59 (164)
68 PF01638 HxlR: HxlR-like helix 83.8 12 0.00025 30.4 9.2 63 22-92 7-70 (90)
69 PF01047 MarR: MarR family; I 83.4 2.2 4.7E-05 31.4 4.4 50 372-422 5-54 (59)
70 COG3682 Predicted transcriptio 83.1 3.3 7.1E-05 35.8 5.7 54 109-166 4-57 (123)
71 PF13463 HTH_27: Winged helix 82.6 5.9 0.00013 29.8 6.7 45 25-69 8-53 (68)
72 COG3388 Predicted transcriptio 82.5 2 4.3E-05 34.9 3.9 42 24-65 18-59 (101)
73 PF10771 DUF2582: Protein of u 82.4 1.8 3.8E-05 33.1 3.4 55 366-421 4-58 (65)
74 PF01022 HTH_5: Bacterial regu 82.1 1.6 3.5E-05 30.8 3.0 42 373-416 5-46 (47)
75 PRK11179 DNA-binding transcrip 81.8 5.2 0.00011 36.0 7.0 47 370-417 9-55 (153)
76 PF12802 MarR_2: MarR family; 81.6 3.2 7E-05 30.7 4.7 52 370-422 5-58 (62)
77 smart00346 HTH_ICLR helix_turn 81.3 2.3 5E-05 34.2 4.1 45 371-416 6-51 (91)
78 PF01047 MarR: MarR family; I 80.6 3.7 8.1E-05 30.1 4.7 45 24-68 7-51 (59)
79 PHA00738 putative HTH transcri 79.6 6.9 0.00015 33.0 6.3 60 23-92 15-74 (108)
80 TIGR02337 HpaR homoprotocatech 79.6 34 0.00073 29.0 11.1 66 19-91 27-92 (118)
81 PRK15090 DNA-binding transcrip 79.6 4.2 9.2E-05 39.9 6.1 42 24-65 18-59 (257)
82 cd00092 HTH_CRP helix_turn_hel 78.8 5.6 0.00012 29.8 5.3 35 31-65 22-56 (67)
83 COG1378 Predicted transcriptio 78.7 15 0.00033 35.9 9.6 73 370-450 16-88 (247)
84 smart00420 HTH_DEOR helix_turn 78.2 3.7 8.1E-05 28.9 4.0 43 374-417 4-46 (53)
85 PF03965 Penicillinase_R: Peni 78.2 4.7 0.0001 34.3 5.2 53 110-166 2-54 (115)
86 TIGR01889 Staph_reg_Sar staphy 78.1 40 0.00086 28.3 11.2 90 357-450 10-106 (109)
87 PF02295 z-alpha: Adenosine de 77.6 2.3 5E-05 32.6 2.8 44 373-417 7-52 (66)
88 PF08220 HTH_DeoR: DeoR-like h 77.1 3.8 8.3E-05 30.3 3.8 41 374-415 4-44 (57)
89 COG3682 Predicted transcriptio 76.8 36 0.00078 29.5 10.1 101 18-130 4-108 (123)
90 PF13463 HTH_27: Winged helix 76.3 4.8 0.0001 30.4 4.3 50 372-422 5-55 (68)
91 PF02082 Rrf2: Transcriptional 76.2 3.8 8.2E-05 32.7 3.8 47 370-416 8-56 (83)
92 COG1414 IclR Transcriptional r 76.1 6.5 0.00014 38.4 6.2 42 24-65 8-50 (246)
93 TIGR01610 phage_O_Nterm phage 76.0 5.8 0.00013 32.7 5.0 49 17-65 19-78 (95)
94 PRK06474 hypothetical protein; 76.0 8.1 0.00018 35.8 6.5 69 20-93 11-81 (178)
95 COG1522 Lrp Transcriptional re 76.0 3.7 8E-05 36.6 4.2 69 368-437 6-78 (154)
96 PF08784 RPA_C: Replication pr 75.5 8 0.00017 32.1 5.8 53 17-70 44-100 (102)
97 PF13404 HTH_AsnC-type: AsnC-t 75.5 7.8 0.00017 26.8 4.7 36 23-58 6-41 (42)
98 smart00418 HTH_ARSR helix_turn 75.2 4.1 8.9E-05 29.8 3.6 42 374-417 1-42 (66)
99 PF05645 RNA_pol_Rpc82: RNA po 75.1 4.5 9.8E-05 39.8 4.9 49 82-130 101-149 (258)
100 PRK03902 manganese transport t 74.0 8 0.00017 34.3 5.8 45 21-65 9-53 (142)
101 smart00347 HTH_MARR helix_turn 73.8 23 0.0005 28.4 8.2 49 369-418 9-57 (101)
102 PRK11169 leucine-responsive tr 73.3 6.7 0.00014 35.8 5.2 49 20-68 14-62 (164)
103 TIGR02787 codY_Gpos GTP-sensin 72.3 12 0.00025 36.3 6.6 59 7-65 170-229 (251)
104 TIGR02337 HpaR homoprotocatech 72.2 59 0.0013 27.5 11.0 80 369-455 27-106 (118)
105 PF09824 ArsR: ArsR transcript 72.0 24 0.00053 31.7 8.1 115 16-135 12-131 (160)
106 PF05402 PqqD: Coenzyme PQQ sy 72.0 6.2 0.00013 29.9 4.0 55 108-164 14-68 (68)
107 PF06163 DUF977: Bacterial pro 71.7 11 0.00024 32.6 5.7 49 111-167 12-60 (127)
108 PRK11512 DNA-binding transcrip 70.9 41 0.00089 29.6 9.6 42 24-65 44-85 (144)
109 PF08279 HTH_11: HTH domain; 70.6 10 0.00023 27.3 4.8 48 373-421 3-50 (55)
110 cd07377 WHTH_GntR Winged helix 70.1 8.1 0.00017 28.6 4.2 47 19-65 4-56 (66)
111 PRK11179 DNA-binding transcrip 69.9 10 0.00022 34.0 5.6 48 20-67 9-56 (153)
112 PRK10163 DNA-binding transcrip 69.9 19 0.00042 35.6 8.0 42 24-65 29-71 (271)
113 PRK11512 DNA-binding transcrip 69.4 25 0.00054 31.0 7.9 62 371-436 41-102 (144)
114 smart00419 HTH_CRP helix_turn_ 69.4 8 0.00017 26.7 3.8 32 34-65 8-39 (48)
115 PRK15431 ferrous iron transpor 69.4 13 0.00028 29.4 5.2 45 24-68 6-50 (78)
116 PRK15090 DNA-binding transcrip 69.1 5.4 0.00012 39.2 3.9 44 371-415 15-58 (257)
117 COG3398 Uncharacterized protei 68.4 67 0.0014 30.8 10.5 121 18-164 98-219 (240)
118 COG5625 Predicted transcriptio 68.0 5.7 0.00012 32.8 3.0 48 18-65 19-67 (113)
119 PF08679 DsrD: Dissimilatory s 67.8 14 0.00031 28.1 4.9 34 37-70 22-56 (67)
120 TIGR01610 phage_O_Nterm phage 67.5 9.2 0.0002 31.5 4.3 36 382-418 45-80 (95)
121 PF08280 HTH_Mga: M protein tr 67.3 13 0.00027 27.7 4.6 36 24-59 9-44 (59)
122 PRK09834 DNA-binding transcrip 67.3 14 0.0003 36.4 6.4 43 23-65 14-57 (263)
123 PF13730 HTH_36: Helix-turn-he 67.2 8.5 0.00018 27.8 3.7 29 36-64 27-55 (55)
124 TIGR02010 IscR iron-sulfur clu 67.1 9.8 0.00021 33.4 4.7 75 369-452 7-83 (135)
125 TIGR02698 CopY_TcrY copper tra 66.9 15 0.00033 32.1 5.8 53 110-166 3-55 (130)
126 PF09904 HTH_43: Winged helix- 66.2 12 0.00026 30.4 4.5 62 26-93 13-74 (90)
127 PHA03103 double-strand RNA-bin 66.1 6.4 0.00014 36.5 3.4 44 374-418 17-60 (183)
128 cd00090 HTH_ARSR Arsenical Res 66.1 10 0.00022 28.5 4.2 45 371-417 8-52 (78)
129 PF01325 Fe_dep_repress: Iron 65.6 18 0.00039 27.0 5.2 45 22-66 10-54 (60)
130 TIGR02944 suf_reg_Xantho FeS a 65.6 8.5 0.00018 33.4 4.0 51 367-417 6-57 (130)
131 COG4190 Predicted transcriptio 65.4 26 0.00056 30.6 6.6 52 18-70 62-113 (144)
132 PF08784 RPA_C: Replication pr 65.4 7.7 0.00017 32.2 3.5 48 368-416 45-96 (102)
133 PRK10163 DNA-binding transcrip 65.2 8 0.00017 38.3 4.2 46 371-416 26-71 (271)
134 PRK13777 transcriptional regul 65.2 1.2E+02 0.0026 28.3 13.8 62 372-437 47-108 (185)
135 smart00419 HTH_CRP helix_turn_ 65.1 6.8 0.00015 27.1 2.7 32 387-418 10-41 (48)
136 TIGR01889 Staph_reg_Sar staphy 64.8 28 0.00061 29.2 6.9 52 14-65 17-74 (109)
137 PRK11569 transcriptional repre 64.8 8.2 0.00018 38.4 4.2 46 371-416 29-74 (274)
138 cd07153 Fur_like Ferric uptake 64.6 18 0.00039 30.5 5.8 50 115-167 5-55 (116)
139 PF13601 HTH_34: Winged helix 64.5 17 0.00036 29.0 5.1 48 373-421 3-50 (80)
140 PRK11569 transcriptional repre 64.4 16 0.00035 36.2 6.2 41 25-65 33-74 (274)
141 PF00392 GntR: Bacterial regul 64.0 9 0.0002 28.8 3.4 32 34-65 23-55 (64)
142 PRK09834 DNA-binding transcrip 63.8 8.9 0.00019 37.8 4.2 45 371-416 12-57 (263)
143 TIGR02431 pcaR_pcaU beta-ketoa 63.7 8.3 0.00018 37.6 3.9 46 371-416 10-55 (248)
144 TIGR02844 spore_III_D sporulat 63.6 13 0.00028 29.7 4.2 34 21-55 7-40 (80)
145 PF01325 Fe_dep_repress: Iron 63.6 12 0.00026 28.0 3.9 43 375-418 13-55 (60)
146 TIGR02431 pcaR_pcaU beta-ketoa 63.6 12 0.00027 36.4 5.1 41 25-65 14-55 (248)
147 PF09012 FeoC: FeoC like trans 63.1 14 0.0003 28.3 4.3 48 374-422 4-51 (69)
148 COG1414 IclR Transcriptional r 63.0 9.5 0.0002 37.3 4.2 91 371-468 5-97 (246)
149 PHA02701 ORF020 dsRNA-binding 62.6 18 0.00038 33.6 5.5 46 20-65 4-50 (183)
150 PF01726 LexA_DNA_bind: LexA D 62.4 22 0.00049 27.0 5.2 46 20-65 10-57 (65)
151 smart00345 HTH_GNTR helix_turn 62.3 12 0.00026 27.0 3.7 33 33-65 18-51 (60)
152 cd00092 HTH_CRP helix_turn_hel 61.2 18 0.00038 27.0 4.6 56 97-167 4-59 (67)
153 COG2512 Predicted membrane-ass 61.0 12 0.00025 37.0 4.3 50 375-424 200-249 (258)
154 TIGR00738 rrf2_super rrf2 fami 60.7 13 0.00027 32.3 4.2 46 371-416 9-56 (132)
155 TIGR02944 suf_reg_Xantho FeS a 60.3 21 0.00046 30.9 5.5 34 33-66 24-57 (130)
156 TIGR01884 cas_HTH CRISPR locus 60.2 17 0.00037 34.3 5.3 48 18-65 141-188 (203)
157 PRK03573 transcriptional regul 59.6 1.2E+02 0.0026 26.5 11.9 63 370-436 31-94 (144)
158 TIGR02010 IscR iron-sulfur clu 58.8 28 0.00062 30.5 6.1 33 33-65 24-56 (135)
159 TIGR00738 rrf2_super rrf2 fami 58.2 33 0.00071 29.6 6.4 33 33-65 24-56 (132)
160 PRK11050 manganese transport r 57.3 25 0.00055 31.5 5.6 42 24-65 41-82 (152)
161 PHA03103 double-strand RNA-bin 57.1 25 0.00053 32.7 5.5 47 19-65 12-58 (183)
162 PF04079 DUF387: Putative tran 57.0 61 0.0013 29.5 8.0 117 24-167 2-127 (159)
163 PRK09462 fur ferric uptake reg 56.8 27 0.0006 31.1 5.8 54 111-167 17-72 (148)
164 COG1733 Predicted transcriptio 56.8 48 0.001 28.6 7.0 62 19-88 22-84 (120)
165 cd07153 Fur_like Ferric uptake 56.2 44 0.00095 28.1 6.7 46 24-69 5-56 (116)
166 TIGR01884 cas_HTH CRISPR locus 56.2 16 0.00035 34.5 4.4 50 368-418 141-190 (203)
167 PF12793 SgrR_N: Sugar transpo 56.0 99 0.0022 26.4 8.8 55 34-93 19-73 (115)
168 TIGR02787 codY_Gpos GTP-sensin 56.0 21 0.00045 34.6 5.0 48 373-421 186-234 (251)
169 TIGR00122 birA_repr_reg BirA b 55.6 23 0.00051 26.9 4.5 41 24-65 4-44 (69)
170 PF07848 PaaX: PaaX-like prote 55.5 34 0.00074 26.5 5.3 33 33-65 19-54 (70)
171 PF00392 GntR: Bacterial regul 55.4 23 0.0005 26.5 4.3 36 383-418 21-57 (64)
172 COG1522 Lrp Transcriptional re 54.9 27 0.00059 30.9 5.5 49 21-69 9-57 (154)
173 COG0735 Fur Fe2+/Zn2+ uptake r 54.7 32 0.00068 30.7 5.7 54 111-167 21-75 (145)
174 PRK00135 scpB segregation and 54.4 1.2E+02 0.0026 28.4 9.8 46 367-416 87-132 (188)
175 PRK10870 transcriptional repre 52.4 1.2E+02 0.0027 27.8 9.5 49 17-65 50-102 (176)
176 PF08279 HTH_11: HTH domain; 52.0 41 0.00089 24.1 5.1 39 24-62 4-43 (55)
177 PF04337 DUF480: Protein of un 52.0 35 0.00076 30.4 5.3 49 17-65 85-140 (148)
178 COG1802 GntR Transcriptional r 51.9 1.6E+02 0.0036 28.0 10.8 54 382-442 36-89 (230)
179 PF04079 DUF387: Putative tran 51.5 1.1E+02 0.0023 27.9 8.7 59 367-431 79-137 (159)
180 PRK03573 transcriptional regul 51.4 1.7E+02 0.0036 25.6 12.0 41 25-65 36-77 (144)
181 PRK11014 transcriptional repre 51.3 22 0.00048 31.4 4.2 48 371-418 9-58 (141)
182 PRK10344 DNA-binding transcrip 51.3 33 0.00071 27.9 4.6 34 22-56 10-43 (92)
183 COG1510 Predicted transcriptio 50.9 54 0.0012 30.1 6.5 66 356-421 8-77 (177)
184 PRK13777 transcriptional regul 50.6 2.1E+02 0.0046 26.6 12.5 47 23-70 48-94 (185)
185 PF02796 HTH_7: Helix-turn-hel 50.6 28 0.00062 24.1 3.8 31 23-55 12-42 (45)
186 PF07381 DUF1495: Winged helix 50.6 62 0.0013 26.4 6.2 60 23-91 12-83 (90)
187 PF04492 Phage_rep_O: Bacterio 50.2 26 0.00055 29.3 4.1 50 358-416 36-85 (100)
188 PF10007 DUF2250: Uncharacteri 50.2 28 0.00061 28.6 4.2 46 370-416 7-52 (92)
189 PF01726 LexA_DNA_bind: LexA D 49.9 55 0.0012 24.9 5.5 49 113-168 12-61 (65)
190 PF09681 Phage_rep_org_N: N-te 49.7 46 0.00099 28.8 5.7 48 33-92 52-99 (121)
191 PF05584 Sulfolobus_pRN: Sulfo 49.5 58 0.0013 25.4 5.6 41 24-65 9-49 (72)
192 PRK04424 fatty acid biosynthes 49.5 24 0.00051 32.9 4.2 44 22-65 9-52 (185)
193 PRK09775 putative DNA-binding 49.1 36 0.00078 36.4 6.0 42 25-68 4-45 (442)
194 PRK10434 srlR DNA-bindng trans 49.0 29 0.00063 34.1 5.0 44 22-65 7-50 (256)
195 PF11994 DUF3489: Protein of u 48.5 79 0.0017 24.7 6.2 44 22-65 12-57 (72)
196 PRK11014 transcriptional repre 48.3 30 0.00064 30.6 4.5 32 34-65 25-56 (141)
197 PF01638 HxlR: HxlR-like helix 48.0 29 0.00062 28.1 4.0 47 113-167 7-53 (90)
198 COG5625 Predicted transcriptio 47.9 63 0.0014 26.9 5.8 91 366-460 15-108 (113)
199 COG1846 MarR Transcriptional r 47.8 1.6E+02 0.0034 24.2 9.7 51 18-68 20-70 (126)
200 PRK09954 putative kinase; Prov 47.7 20 0.00044 37.0 3.9 43 373-416 6-48 (362)
201 PRK10906 DNA-binding transcrip 47.5 32 0.00069 33.7 5.0 43 23-65 8-50 (252)
202 TIGR03859 PQQ_PqqD coenzyme PQ 46.3 46 0.001 26.4 4.9 52 110-164 30-81 (81)
203 PF13404 HTH_AsnC-type: AsnC-t 45.7 34 0.00073 23.6 3.5 36 373-409 6-41 (42)
204 PRK09462 fur ferric uptake reg 45.3 80 0.0017 28.0 6.9 50 20-69 17-73 (148)
205 TIGR03879 near_KaiC_dom probab 45.2 36 0.00079 26.6 3.9 45 20-64 18-62 (73)
206 PF09756 DDRGK: DDRGK domain; 45.1 18 0.0004 33.8 2.7 85 21-136 100-184 (188)
207 COG1959 Predicted transcriptio 44.9 35 0.00076 30.6 4.5 57 367-423 5-63 (150)
208 COG4738 Predicted transcriptio 44.5 2E+02 0.0044 24.5 9.9 105 7-122 14-118 (124)
209 PRK10857 DNA-binding transcrip 44.4 30 0.00065 31.6 4.0 50 369-418 7-58 (164)
210 PF04492 Phage_rep_O: Bacterio 44.2 84 0.0018 26.2 6.3 33 33-65 53-85 (100)
211 PF10007 DUF2250: Uncharacteri 44.1 78 0.0017 26.0 5.9 50 20-69 7-56 (92)
212 PF04182 B-block_TFIIIC: B-blo 43.7 1.1E+02 0.0024 23.7 6.7 49 387-435 20-70 (75)
213 PF14947 HTH_45: Winged helix- 43.5 29 0.00062 27.3 3.3 40 374-415 10-49 (77)
214 PLN02853 Probable phenylalanyl 43.4 3.4E+02 0.0074 29.4 12.1 112 22-166 5-117 (492)
215 cd07377 WHTH_GntR Winged helix 43.3 19 0.00041 26.5 2.2 31 387-417 27-57 (66)
216 COG3423 Nlp Predicted transcri 42.9 50 0.0011 26.0 4.3 33 23-56 11-43 (82)
217 COG1321 TroR Mn-dependent tran 42.9 33 0.00071 31.0 4.0 43 375-418 15-57 (154)
218 PF13730 HTH_36: Helix-turn-he 42.8 20 0.00044 25.7 2.2 29 387-415 27-55 (55)
219 PF13545 HTH_Crp_2: Crp-like h 42.0 27 0.00058 26.8 2.9 33 385-418 29-61 (76)
220 COG4189 Predicted transcriptio 41.9 64 0.0014 31.1 5.8 51 373-424 26-76 (308)
221 PF12793 SgrR_N: Sugar transpo 41.6 90 0.002 26.7 6.3 61 386-448 20-80 (115)
222 PRK11534 DNA-binding transcrip 41.4 45 0.00098 31.7 5.0 49 17-65 12-61 (224)
223 COG0735 Fur Fe2+/Zn2+ uptake r 41.3 93 0.002 27.7 6.6 48 23-70 24-77 (145)
224 PRK09802 DNA-binding transcrip 41.0 46 0.001 33.0 5.1 45 21-65 18-62 (269)
225 TIGR03879 near_KaiC_dom probab 40.6 25 0.00055 27.5 2.4 44 371-415 19-62 (73)
226 TIGR03338 phnR_burk phosphonat 40.4 1.6E+02 0.0034 27.5 8.5 33 34-66 34-66 (212)
227 smart00345 HTH_GNTR helix_turn 40.4 28 0.0006 25.0 2.6 30 387-416 22-51 (60)
228 COG1959 Predicted transcriptio 40.2 91 0.002 28.0 6.4 48 19-66 7-57 (150)
229 PF13814 Replic_Relax: Replica 40.0 56 0.0012 30.1 5.2 62 377-439 2-66 (191)
230 PF10415 FumaraseC_C: Fumarase 39.5 56 0.0012 24.0 4.0 41 14-55 5-47 (55)
231 TIGR01714 phage_rep_org_N phag 39.5 72 0.0016 27.5 5.3 47 33-91 50-96 (119)
232 PRK11534 DNA-binding transcrip 39.3 48 0.001 31.5 4.8 59 106-168 5-65 (224)
233 PRK11050 manganese transport r 39.2 1E+02 0.0022 27.6 6.6 41 375-416 42-82 (152)
234 COG1349 GlpR Transcriptional r 38.9 46 0.001 32.6 4.6 47 113-167 7-53 (253)
235 PF01475 FUR: Ferric uptake re 38.8 64 0.0014 27.4 5.0 53 113-168 10-63 (120)
236 PF05158 RNA_pol_Rpc34: RNA po 38.7 31 0.00067 35.3 3.4 45 24-68 88-134 (327)
237 PRK04172 pheS phenylalanyl-tRN 38.1 3.9E+02 0.0084 29.0 12.0 113 21-165 7-119 (489)
238 PRK11920 rirA iron-responsive 37.8 1E+02 0.0022 27.7 6.3 34 33-66 23-56 (153)
239 PRK12423 LexA repressor; Provi 37.8 76 0.0017 29.9 5.8 45 21-65 11-57 (202)
240 PRK03902 manganese transport t 37.7 43 0.00092 29.5 3.8 41 375-416 13-53 (142)
241 PRK10857 DNA-binding transcrip 37.2 61 0.0013 29.6 4.8 33 33-65 24-56 (164)
242 PF02295 z-alpha: Adenosine de 37.2 37 0.0008 25.9 2.9 46 20-65 4-51 (66)
243 PF13693 HTH_35: Winged helix- 37.1 32 0.0007 27.3 2.6 32 23-55 5-36 (78)
244 PRK11414 colanic acid/biofilm 37.0 1.7E+02 0.0036 27.7 8.2 32 34-65 34-65 (221)
245 PF09397 Ftsk_gamma: Ftsk gamm 36.6 1.1E+02 0.0025 23.3 5.4 48 19-66 5-52 (65)
246 PF09743 DUF2042: Uncharacteri 36.3 1.8E+02 0.0039 28.9 8.3 53 13-65 109-161 (272)
247 PRK11920 rirA iron-responsive 36.2 45 0.00097 30.0 3.7 54 368-421 6-60 (153)
248 PF14394 DUF4423: Domain of un 36.0 91 0.002 28.7 5.8 50 16-65 19-72 (171)
249 PRK06474 hypothetical protein; 35.9 98 0.0021 28.6 6.1 49 373-422 14-64 (178)
250 COG4189 Predicted transcriptio 35.9 63 0.0014 31.2 4.7 43 23-65 26-68 (308)
251 PF00325 Crp: Bacterial regula 35.7 59 0.0013 21.1 3.2 30 35-64 3-32 (32)
252 PF09202 Rio2_N: Rio2, N-termi 35.3 57 0.0012 26.1 3.8 36 31-66 21-56 (82)
253 PF09105 SelB-wing_1: Elongati 35.3 1E+02 0.0022 21.9 4.5 37 384-421 17-53 (61)
254 PRK13509 transcriptional repre 35.1 74 0.0016 31.1 5.4 44 22-65 7-50 (251)
255 PRK09464 pdhR transcriptional 35.1 2.2E+02 0.0049 27.4 8.9 36 383-418 31-67 (254)
256 KOG4562 Uncharacterized conser 34.9 37 0.00079 34.7 3.2 68 373-447 223-293 (329)
257 PF10668 Phage_terminase: Phag 34.8 54 0.0012 24.6 3.3 25 29-53 17-41 (60)
258 COG1349 GlpR Transcriptional r 34.8 62 0.0013 31.7 4.8 43 23-65 8-50 (253)
259 COG3888 Predicted transcriptio 34.6 79 0.0017 31.1 5.2 42 374-415 8-50 (321)
260 PRK10870 transcriptional repre 34.4 2.1E+02 0.0046 26.2 8.1 63 366-432 49-115 (176)
261 PHA02591 hypothetical protein; 34.1 98 0.0021 24.5 4.7 35 20-55 46-80 (83)
262 PRK10402 DNA-binding transcrip 33.7 1.2E+02 0.0026 28.8 6.5 58 8-65 138-200 (226)
263 PRK13509 transcriptional repre 33.6 49 0.0011 32.4 3.9 43 373-416 8-50 (251)
264 PF14502 HTH_41: Helix-turn-he 33.6 68 0.0015 23.0 3.4 30 36-65 8-37 (48)
265 COG2512 Predicted membrane-ass 33.2 72 0.0016 31.5 4.9 54 15-68 190-244 (258)
266 PRK11639 zinc uptake transcrip 32.8 90 0.002 28.5 5.3 54 111-167 26-80 (169)
267 PF09202 Rio2_N: Rio2, N-termi 32.7 46 0.001 26.6 2.9 48 370-417 6-56 (82)
268 TIGR03882 cyclo_dehyd_2 bacter 32.2 97 0.0021 29.0 5.5 48 111-166 30-77 (193)
269 COG2238 RPS19A Ribosomal prote 32.1 1.3E+02 0.0029 26.6 5.7 56 112-167 54-115 (147)
270 TIGR03338 phnR_burk phosphonat 32.0 4.2E+02 0.0091 24.6 12.0 36 383-418 32-67 (212)
271 COG1733 Predicted transcriptio 31.2 1.6E+02 0.0035 25.3 6.2 52 109-168 20-72 (120)
272 KOG2165 Anaphase-promoting com 30.8 7.6E+02 0.016 28.0 12.4 142 22-166 604-757 (765)
273 PF03551 PadR: Transcriptional 30.6 1E+02 0.0022 23.7 4.6 48 120-167 4-51 (75)
274 PRK09990 DNA-binding transcrip 30.4 2.8E+02 0.006 26.7 8.6 37 382-418 27-64 (251)
275 PF07278 DUF1441: Protein of u 30.4 1E+02 0.0022 27.8 5.0 45 14-63 95-150 (152)
276 PRK11239 hypothetical protein; 30.1 1.1E+02 0.0024 29.1 5.3 46 17-62 94-144 (215)
277 KOG2166 Cullins [Cell cycle co 29.7 2E+02 0.0043 32.9 8.2 127 32-166 578-717 (725)
278 PRK10906 DNA-binding transcrip 28.5 64 0.0014 31.6 3.7 42 373-415 8-49 (252)
279 TIGR02147 Fsuc_second hypothet 28.2 1.3E+02 0.0027 30.0 5.7 49 17-65 118-170 (271)
280 PF05584 Sulfolobus_pRN: Sulfo 27.7 1E+02 0.0022 24.1 3.9 57 375-436 10-66 (72)
281 PRK10411 DNA-binding transcrip 27.5 1.2E+02 0.0026 29.4 5.4 43 23-65 7-49 (240)
282 cd06571 Bac_DnaA_C C-terminal 27.4 1.9E+02 0.0041 23.3 5.7 37 21-57 30-68 (90)
283 COG5124 Protein predicted to b 27.3 4.1E+02 0.0089 24.6 8.2 39 395-439 38-76 (209)
284 PF10330 Stb3: Putative Sin3 b 27.2 1.1E+02 0.0023 25.1 4.0 35 25-59 11-53 (92)
285 PRK09954 putative kinase; Prov 27.1 1.2E+02 0.0025 31.2 5.6 99 23-125 6-108 (362)
286 PRK03837 transcriptional regul 27.0 1E+02 0.0022 29.5 4.9 33 34-66 36-69 (241)
287 PF09382 RQC: RQC domain; Int 26.8 2.4E+02 0.0052 23.1 6.5 56 111-166 4-75 (106)
288 PF04157 EAP30: EAP30/Vps36 fa 26.8 85 0.0018 30.1 4.2 48 18-65 172-221 (223)
289 TIGR00122 birA_repr_reg BirA b 26.8 1E+02 0.0022 23.3 3.8 42 373-416 3-44 (69)
290 PRK00082 hrcA heat-inducible t 26.7 1.7E+02 0.0037 30.1 6.6 93 28-136 19-113 (339)
291 PF01399 PCI: PCI domain; Int 26.5 99 0.0021 24.9 4.0 37 30-66 56-92 (105)
292 PF03428 RP-C: Replication pro 26.2 5.3E+02 0.011 23.9 10.4 78 387-469 72-156 (177)
293 TIGR03882 cyclo_dehyd_2 bacter 26.1 1.5E+02 0.0032 27.8 5.6 45 19-65 29-75 (193)
294 PRK10141 DNA-binding transcrip 26.0 4.2E+02 0.0091 22.7 10.2 63 368-438 13-76 (117)
295 COG1846 MarR Transcriptional r 25.9 1E+02 0.0022 25.4 4.2 65 368-436 20-84 (126)
296 smart00753 PAM PCI/PINT associ 25.7 1.3E+02 0.0029 23.6 4.6 40 27-66 17-56 (88)
297 smart00088 PINT motif in prote 25.7 1.3E+02 0.0029 23.6 4.6 40 27-66 17-56 (88)
298 TIGR00498 lexA SOS regulatory 25.6 96 0.0021 28.9 4.2 31 35-65 26-57 (199)
299 PRK03837 transcriptional regul 25.5 1.1E+02 0.0024 29.2 4.8 36 383-418 34-70 (241)
300 TIGR00281 segregation and cond 25.5 5.6E+02 0.012 23.9 11.5 121 22-167 3-132 (186)
301 PRK14165 winged helix-turn-hel 25.5 2.3E+02 0.005 27.2 6.8 64 383-456 20-83 (217)
302 COG3398 Uncharacterized protei 25.4 2.4E+02 0.0052 27.1 6.6 64 16-89 170-233 (240)
303 PRK10402 DNA-binding transcrip 25.4 2.4E+02 0.0052 26.7 7.1 32 387-418 171-202 (226)
304 TIGR03697 NtcA_cyano global ni 25.2 2.6E+02 0.0056 25.3 7.1 51 15-65 109-174 (193)
305 PF04255 DUF433: Protein of un 25.2 1.6E+02 0.0034 21.5 4.4 33 22-56 21-54 (56)
306 PF00888 Cullin: Cullin family 24.9 66 0.0014 35.4 3.4 39 29-67 529-567 (588)
307 PF00356 LacI: Bacterial regul 24.9 84 0.0018 22.1 2.8 20 36-55 1-20 (46)
308 PF12324 HTH_15: Helix-turn-he 24.7 2.6E+02 0.0056 22.2 5.7 55 4-58 4-62 (77)
309 PRK15431 ferrous iron transpor 24.3 2.2E+02 0.0048 22.6 5.3 43 117-167 8-50 (78)
310 PF10264 Stork_head: Winged he 23.7 2.5E+02 0.0054 22.4 5.5 44 123-166 27-70 (80)
311 smart00843 Ftsk_gamma This dom 23.7 2.4E+02 0.0052 21.4 5.2 48 19-66 4-51 (63)
312 TIGR02404 trehalos_R_Bsub treh 23.5 91 0.002 29.8 3.7 30 36-65 26-55 (233)
313 COG4860 Uncharacterized protei 23.3 4.8E+02 0.01 23.2 7.6 109 17-133 20-136 (170)
314 PF08281 Sigma70_r4_2: Sigma-7 23.1 1.9E+02 0.0042 20.3 4.6 30 28-57 20-49 (54)
315 COG4742 Predicted transcriptio 23.1 5.5E+02 0.012 25.4 8.9 79 13-105 5-83 (260)
316 COG1802 GntR Transcriptional r 23.0 4.4E+02 0.0095 25.0 8.4 40 30-70 34-74 (230)
317 PF05732 RepL: Firmicute plasm 22.9 2.2E+02 0.0047 26.0 5.8 48 368-415 53-105 (165)
318 COG1777 Predicted transcriptio 22.9 2.9E+02 0.0063 26.3 6.6 55 15-70 9-64 (217)
319 PRK00215 LexA repressor; Valid 22.8 1.9E+02 0.0042 27.0 5.7 43 23-65 11-55 (205)
320 PRK05638 threonine synthase; V 22.8 2.5E+02 0.0054 29.9 7.2 65 18-92 369-435 (442)
321 PF03551 PadR: Transcriptional 22.7 2.5E+02 0.0054 21.5 5.4 56 31-91 6-69 (75)
322 PRK04214 rbn ribonuclease BN/u 22.7 1.1E+02 0.0024 32.4 4.4 67 374-451 296-365 (412)
323 PF13518 HTH_28: Helix-turn-he 22.7 2.3E+02 0.005 19.5 4.9 38 25-64 5-42 (52)
324 PRK11753 DNA-binding transcrip 22.4 2.3E+02 0.005 26.1 6.2 53 13-65 133-199 (211)
325 PF05732 RepL: Firmicute plasm 22.4 1.4E+02 0.003 27.3 4.4 65 16-93 51-121 (165)
326 PF13542 HTH_Tnp_ISL3: Helix-t 22.2 2E+02 0.0044 20.0 4.5 31 24-56 19-49 (52)
327 PRK10225 DNA-binding transcrip 21.8 1.3E+02 0.0028 29.2 4.5 36 383-418 30-66 (257)
328 TIGR02812 fadR_gamma fatty aci 21.7 1.5E+02 0.0032 28.3 4.9 37 382-418 26-63 (235)
329 PRK10434 srlR DNA-bindng trans 21.7 1E+02 0.0022 30.3 3.7 42 373-415 8-49 (256)
330 COG1321 TroR Mn-dependent tran 21.7 5.9E+02 0.013 22.9 9.4 45 25-70 15-59 (154)
331 PRK09990 DNA-binding transcrip 21.5 1.1E+02 0.0025 29.5 4.0 32 34-65 30-62 (251)
332 PHA00738 putative HTH transcri 21.5 2.1E+02 0.0046 24.2 4.9 46 113-166 14-59 (108)
333 PRK09333 30S ribosomal protein 21.4 1.6E+02 0.0036 26.4 4.5 45 21-65 54-112 (150)
334 PRK11886 bifunctional biotin-- 21.2 1.7E+02 0.0036 29.7 5.2 43 23-65 7-49 (319)
335 PF06056 Terminase_5: Putative 21.1 1.9E+02 0.0041 21.4 4.2 30 23-53 3-32 (58)
336 PRK10421 DNA-binding transcrip 20.9 1.5E+02 0.0032 28.7 4.7 36 383-418 23-59 (253)
337 PF13936 HTH_38: Helix-turn-he 20.9 1.7E+02 0.0036 20.1 3.6 29 26-55 13-41 (44)
338 TIGR02812 fadR_gamma fatty aci 20.9 1.2E+02 0.0026 29.0 4.0 32 34-65 29-61 (235)
339 PF08280 HTH_Mga: M protein tr 20.6 1.5E+02 0.0031 21.9 3.5 38 373-411 8-45 (59)
340 PF08100 Dimerisation: Dimeris 20.4 1.6E+02 0.0036 21.2 3.6 21 25-45 11-33 (51)
341 PF01454 MAGE: MAGE family; I 20.4 1.5E+02 0.0033 27.5 4.4 58 375-438 126-185 (195)
No 1
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=100.00 E-value=8.9e-79 Score=611.27 Aligned_cols=485 Identities=26% Similarity=0.415 Sum_probs=368.8
Q ss_pred ccHHHHHHHHHHHHhhhchhHHHHHHHHHhcCCCc-HHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCC
Q 010353 2 LTEYGTKHAVHVITNHFGDLVAKVCECLLRKGPLT-RQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPK 80 (512)
Q Consensus 2 ~s~~~~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~lt-l~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~ 80 (512)
||+|+++||..||++|||++|++|+.+|+++|++| +.-+...++++..+||++|++|||||||.|+..... .+
T Consensus 1 msq~eielc~~lie~~FGeivakV~~~Llr~G~lss~~~~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~------~g 74 (551)
T KOG2587|consen 1 MSQYEIELCSILIEEHFGEIVAKVGEHLLRTGRLSSLRVIAKDTGISLDKVKKALVSLIQHNCVSYQVHTRN------SG 74 (551)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcchhHHHHhhcCCChHHHHHHHHHHHHhcceEEEEecCC------CC
Confidence 79999999999999999999999999999999999 777788899999999999999999999998776532 24
Q ss_pred CccEEEechhhHHHHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccC-----HHHHHHHHH
Q 010353 81 ANTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVD-----LDSLRETLV 155 (512)
Q Consensus 81 ~~~~Y~~~~~~il~rlR~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~-----~~~l~~~f~ 155 (512)
.+|+|++.+++|+++||||+|+..++++||+.|+.|+++|+.+|++|++++++++..+.......+ ...|.+.|.
T Consensus 75 ~vt~Y~~~~~ei~hilry~r~~~i~~~~~~q~~~sIv~~Lls~GrLTv~e~i~rv~~~~~~~~~ss~~~ql~~lv~q~F~ 154 (551)
T KOG2587|consen 75 KVTTYEAQCSEILHILRYPRYIYITKTLYSQTAESIVEELLSNGRLTVSEVIKRVADRLTTTMESSKTMQLCALVSQTFV 154 (551)
T ss_pred ceEEEEehhhHHHHHHhcccceeeHHHHhhhHHHHHHHHHHhcCceeHHHHHHHHHhcccccchhhHHHHHHHHHHHHHH
Confidence 579999999999999999999999999999999999999999999999999999987644322111 134667777
Q ss_pred HHHhc---ccccccCCCCCCCCCCCccCCcccccCCCCCcccCCchhhHHHHHHhhCchhhhhhhhhccccccccccccC
Q 010353 156 KLVTA---HYVERCPASEPLLMPISEEEGPARKKGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVGEKEKN 232 (512)
Q Consensus 156 ~Lv~~---~fi~rv~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~a~~~~~~r~~~~~~~~~~~~~~~~~ 232 (512)
.++.. ||..++|.+.+. .+.+.++++.++-+........++..++..++.+....+.+. +
T Consensus 155 ~~~~~~ekH~~~r~~e~~~~-------------~~~~a~~~~~e~~~~~~~~~q~lt~~pkis~~~~~~~~s~s~----~ 217 (551)
T KOG2587|consen 155 ELADPLEKHFVNRCPESVPT-------------VENSAAGPPPEAPTLVINEKQILTLVPKISLPGKGKRRSSSD----E 217 (551)
T ss_pred HhhCchhhHhhccCCCcccc-------------cccccCCCCcccccchhhhccccccccccccCCCCCcccccc----c
Confidence 77777 777776542111 112222222222122222222223333344332221111111 1
Q ss_pred CCCCCCCCcccCCcccccccCCCCCCccEEEecHHHHHHHHHHHHHHHHHHhhcChhHHHHHHHHHhccccc-cc-ccc-
Q 010353 233 SNNVTPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSA-EK-KVK- 309 (512)
Q Consensus 233 ~~~~~~~~Krk~~~~~~d~~~~~~~~~v~wrvN~~rf~~~lR~~~iv~~v~~r~g~~a~~v~~~~L~~~~~~-~~-~~~- 309 (512)
.+...++.++|.- ..|.+...++.+++||+|++||+.++||++|+++|..|.|++++.|+++||...... +. .+.
T Consensus 218 ~d~~~~~~~~k~l--~~D~~~~~~d~ga~wr~N~~rf~~~lRd~~~v~~v~~r~~e~ts~v~~a~Lt~~tie~~r~~~~~ 295 (551)
T KOG2587|consen 218 DDRGEKKAKRKKL--TTDNKTPDPDDGAYWRINLDRFHQHLRDQAIVSAVANRMDEGTSEVLRAMLTRMTIELTRHSPAP 295 (551)
T ss_pred ccccCcccccccc--ccccCCCCCCCceeEehhhHHhhHHhhhHHHHHHHHhcccchhHHHHHHHHHhhhhhhccCCchh
Confidence 1223333333321 112223345678999999999999999999999999999999999999999443211 11 110
Q ss_pred ---------ccCCCcc------ChHHHHHHhhh-----hhcCCCCcHHHHHHHHhhc---------------------CH
Q 010353 310 ---------TKNSVPL------SLSSIYEEVIK-----SEAGRNMTLDHVRASLVQL---------------------DF 348 (512)
Q Consensus 310 ---------~~~s~pi------s~~~i~~~l~~-----~~~~~~~~~~~i~~~L~~l---------------------~~ 348 (512)
...|.++ +...+-..+.. ++++.+...+.++.+|..| ||
T Consensus 296 l~~e~si~~~~~s~n~~s~~~~~~esl~~~~~l~Er~~~ee~~nl~~~~~~~ac~~l~d~slk~l~klges~~G~yiV~y 375 (551)
T KOG2587|consen 296 LDTELSINEIFRSLNVGSNGSISMESLDQYLTLLERGDTEEEENLDADTEDPACASLADDSLKFLGKLGESGGGMYIVNY 375 (551)
T ss_pred hhchhhhhhhccCcccccchHHHHHhhhhHHHHHhhccchhhccccccchhhHHHHhhcchHHHHHHhccCCCCEEEEEH
Confidence 0111111 11111111111 1233344444444444432 99
Q ss_pred HHHHHHHHHHHHHHHHHHHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--CC
Q 010353 349 EKIIEIAQNEEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--AR 426 (512)
Q Consensus 349 ~~~~~~lr~~~le~~v~~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~--~~ 426 (512)
++++..++..++|++|.++||..|.|+||+|..+|++ |||||++.|||+.||+|..||+|+++|||++||||||+ +|
T Consensus 376 ~k~i~vl~~~~~E~vI~~rfG~rAiRl~R~l~~k~~v-eekqv~~~Alm~~Kd~r~~L~~m~~~g~v~lQeVprTaD~~p 454 (551)
T KOG2587|consen 376 HKAIAVLATATYESVIQERFGSRAIRLFRLLLQKKHV-EEKQVEDFALMPAKDARDMLYKMLEEGYVELQEVPRTADRAP 454 (551)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccc-hHHHHHHhhccccccHHHHHHHHHHcCceeeeecCCCCCCCC
Confidence 9999999999999999999999999999999999876 99999999999999999999999999999999999998 99
Q ss_pred CceEEEEEEehHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccccCC-----------hhHHHHHHHHHHHHHHH
Q 010353 427 QSQFLLWKVNRQILWKHVLDEMFHAALNLSLRVSYELDREKELLNLPADKRT-----------GPLQDRYNRIRKVRILL 495 (512)
Q Consensus 427 ~~t~~lw~v~~~~~~~~~l~~~~k~~~nl~~R~~~e~~~~k~ll~k~~~~~~-----------~~e~~~l~~~~~~~~~L 495 (512)
+||||||+||+.++++++++++||++.||+.|++||+.+++.||+|.++-+. +.+..+++++...+-.+
T Consensus 455 srtF~L~~v~~~~a~~~lld~ly~~iaNL~~R~~~eraEn~~LL~Ka~rve~~Ik~~e~~~~k~~qlael~~~~~~ql~l 534 (551)
T KOG2587|consen 455 SRTFYLYTVNILRAYRMLLDELYKSIANLIERLRHERAENKRLLEKAQRVEAIIKGREATGAKEAQLAELEEMYTAQLNL 534 (551)
T ss_pred cceEEEEEeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccHhhhhhHHhhhhHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999765541 67888889999999999
Q ss_pred HHHHhhhhhhhhccccC
Q 010353 496 ESSQMKLDDAILLFHDF 512 (512)
Q Consensus 496 ~~~~~rlD~~l~ll~d~ 512 (512)
+....|+|+++++|++|
T Consensus 535 f~r~s~l~~~~~vf~~~ 551 (551)
T KOG2587|consen 535 FKRASQLDETILVFESY 551 (551)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999999999987
No 2
>PF05645 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; InterPro: IPR008806 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 entry describes the C-terminal region of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2XV4_S 2XUB_A.
Probab=99.81 E-value=4.6e-20 Score=181.89 Aligned_cols=163 Identities=24% Similarity=0.321 Sum_probs=68.8
Q ss_pred HHHHHHHhcccccccCCCCCCCCCCCccCCcccc-cCCCCCcccCCchhhHHHHHHhhCchhhhhhhhhcccccccc---
Q 010353 152 ETLVKLVTAHYVERCPASEPLLMPISEEEGPARK-KGSKSAKKIGEPETIEQQVVEAALPMEAMRFSVVTNVESDVG--- 227 (512)
Q Consensus 152 ~~f~~Lv~~~fi~rv~~~~~~~~~~~~~~~~~~~-~g~~~~~~~~~~~~~~~~~~~~a~~~~~~r~~~~~~~~~~~~--- 227 (512)
.+|.+|+++|||+|||+ .+|.|+.|.+...+. ...+.|++-..+ ..+...+++......+....+......
T Consensus 1 ~~f~~Lv~~~fl~rv~~--~~f~~~~D~~~~~~~~~~~~~p~~~~~~---~~k~~~e~~~~~~~~~~~~~~~~~~~~~~~ 75 (258)
T PF05645_consen 1 KTFVKLVEAGFLERVPP--AHFQPPPDLWNELEEEEKKKIPRSSTVS---EIKKKAEAKEKAKEKFRDLREEPESLKIGL 75 (258)
T ss_dssp HHHHHHHHTTSEEE------------------------------------------------------------------
T ss_pred ChHHHHHhCCCEEEcCc--cccccccchhhHHHHHHhhcCCCCCCCC---CcchHHHHHHHHHHhHHHHHhCcccccccc
Confidence 47999999999999975 578888776543221 111111110000 011111111111222222222211111
Q ss_pred -ccccCCCCCCCCCcccCCcccccccCCCCCCccEEEecHHHHHHHHHHHHHHHHHHhhcChhHHHHHHHHHhccccccc
Q 010353 228 -EKEKNSNNVTPGEKRKHDVLELDECGVADEQSVVYRANFEGFIRRLRHKGCIDHVRAHLDDGAANVLSAMLQATSSAEK 306 (512)
Q Consensus 228 -~~~~~~~~~~~~~Krk~~~~~~d~~~~~~~~~v~wrvN~~rf~~~lR~~~iv~~v~~r~g~~a~~v~~~~L~~~~~~~~ 306 (512)
++.........+.||+.+.. ..+++++|||||+||+++|||++|+++|++|+|..||.||++||++++..++
T Consensus 76 ~~~~~~~~~~~~~~Kr~~~~~-------~~d~~v~~rvN~erF~~~lRn~~lv~~a~~r~g~~ta~Vy~~~L~~~e~~~~ 148 (258)
T PF05645_consen 76 KRSLADSTDPGTSRKRKKDES-------PLDPDVVWRVNYERFLVHLRNQRLVDLAERRIGSVTAEVYRAMLKLSESKTP 148 (258)
T ss_dssp -------------------------------TTTSEEE-HHHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHCTTTTS-
T ss_pred ccccccccCCCccccccccCC-------CCCCCeEEEEEHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHhhccccCC
Confidence 00001123445555554322 2357899999999999999999999999999999999999999999987664
Q ss_pred ccccc--------CCCccChHHHHHHhh
Q 010353 307 KVKTK--------NSVPLSLSSIYEEVI 326 (512)
Q Consensus 307 ~~~~~--------~s~pis~~~i~~~l~ 326 (512)
....+ .|.|+|+.+|.+.|.
T Consensus 149 ~~~~~~~~~~~~~~s~~is~~dI~~~l~ 176 (258)
T PF05645_consen 149 SCRDPPSGEEEKQPSVPISANDIARHLP 176 (258)
T ss_dssp TT-SB------------EEHHHHHHTS-
T ss_pred cccccccccccccCCceecHHHHHHHCc
Confidence 44444 689999999999984
No 3
>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=99.80 E-value=6.8e-20 Score=139.22 Aligned_cols=61 Identities=51% Similarity=0.695 Sum_probs=56.4
Q ss_pred HHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceec
Q 010353 8 KHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (512)
Q Consensus 8 ~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~ 68 (512)
+||+.|++++||++|++|+++|+++|++|+++|++.|++|+++||+||++|||||||.|+.
T Consensus 1 ~L~~~ii~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~~ 61 (62)
T PF08221_consen 1 ELCTLIIEEHFGEIVAKVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQYFE 61 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHHHHHHHHcChHHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeeeec
Confidence 6999999999999999999999999999999999999999999999999999999999765
No 4
>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=99.49 E-value=1.4e-14 Score=122.92 Aligned_cols=103 Identities=23% Similarity=0.401 Sum_probs=60.8
Q ss_pred HHHHHHHHHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehH
Q 010353 359 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 438 (512)
Q Consensus 359 ~le~~v~~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~ 438 (512)
.+..+++..||..|.+|+++|..+|.+ ++++|++.++|+.+++|++||+|.++|||..+..... .++++.|+|++|.+
T Consensus 2 L~~~v~r~~yg~~~~~Il~~L~~~~~l-~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~-~~~~~~~yw~i~~~ 79 (105)
T PF02002_consen 2 LLKEVVRAFYGEEAVRILDALLRKGEL-TDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDD-ERGWTRYYWYIDYD 79 (105)
T ss_dssp ----HHHTTS-STTHHHHHHHHHH--B--HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE---------EEEEE-THH
T ss_pred hHHHHHHHHcCchHHHHHHHHHHcCCc-CHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcC-CCcEEEEEEEEcHH
Confidence 467899999999999999999999998 9999999999999999999999999999988876443 57899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 010353 439 ILWKHVLDEMFHAALNLSLRVSYEL 463 (512)
Q Consensus 439 ~~~~~~l~~~~k~~~nl~~R~~~e~ 463 (512)
.+...+...++++..++..|+++|.
T Consensus 80 ~~~~~ik~r~~~~~~~l~~~l~~e~ 104 (105)
T PF02002_consen 80 QIIDVIKYRIYKMREKLKKRLEFEE 104 (105)
T ss_dssp HH------------------SSS--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999999999999999999988775
No 5
>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=98.99 E-value=4.5e-09 Score=95.50 Aligned_cols=106 Identities=16% Similarity=0.188 Sum_probs=93.6
Q ss_pred HHHHHHHHHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehH
Q 010353 359 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 438 (512)
Q Consensus 359 ~le~~v~~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~ 438 (512)
.+..++..-+|..+..|+..|..+|.+ .+++||+...|+.+++|++||+|.+.|+|. ..-.+....+|..|+|++|.+
T Consensus 3 ~~~~~~~~~~g~~~v~Vl~aL~~~~~~-tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~-~~r~r~~~~gw~~Y~w~i~~~ 80 (158)
T TIGR00373 3 LLNEVVGRAAEEEVGLVLFSLGIKGEF-TDEEISLELGIKLNEVRKALYALYDAGLAD-YKRRKDDETGWYEYTWRINYE 80 (158)
T ss_pred HHHHHHHHHcChhHHHHHHHHhccCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCce-eeeeeecCCCcEEEEEEeCHH
Confidence 456689999999999999999999888 999999999999999999999999999997 332222256889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 010353 439 ILWKHVLDEMFHAALNLSLRVSYELDRE 466 (512)
Q Consensus 439 ~~~~~~l~~~~k~~~nl~~R~~~e~~~~ 466 (512)
.+...+..++.+.+.++..++++|.++.
T Consensus 81 ~i~d~Ik~~~~~~~~~lk~~l~~e~~~~ 108 (158)
T TIGR00373 81 KALDVLKRKLEETAKKLREKLEFETNNM 108 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCC
Confidence 9999999999999999999999876554
No 6
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=98.89 E-value=1.5e-08 Score=93.70 Aligned_cols=109 Identities=17% Similarity=0.238 Sum_probs=93.2
Q ss_pred HHHHHHHHHHHHh--CchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEE
Q 010353 356 QNEEVESVVSKRY--GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLW 433 (512)
Q Consensus 356 r~~~le~~v~~~~--G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw 433 (512)
....+.+++.+-. |..+.+|+..|..+|.+ ++++|++...|+.+++|++||+|.++|+|....+... ..+|..|+|
T Consensus 6 ~~~~v~~~l~~~~~~~~~~~~Vl~~L~~~g~~-tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~-~~Gr~~y~w 83 (178)
T PRK06266 6 NNPLVQKVLFEIMEGDEEGFEVLKALIKKGEV-TDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDE-ETNWYTYTW 83 (178)
T ss_pred cCHHHHHHHHHHhcCCccHhHHHHHHHHcCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeecc-CCCcEEEEE
Confidence 3344445555555 77799999999999888 9999999999999999999999999999986543332 468999999
Q ss_pred EEehHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 010353 434 KVNRQILWKHVLDEMFHAALNLSLRVSYELDRE 466 (512)
Q Consensus 434 ~v~~~~~~~~~l~~~~k~~~nl~~R~~~e~~~~ 466 (512)
++|.+++...+..++++...++..|+++|.+..
T Consensus 84 ~l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~~ 116 (178)
T PRK06266 84 KPELEKLPEIIKKKKMEELKKLKEQLEEEENNM 116 (178)
T ss_pred EeCHHHHHHHHHHHHHHHHHHHHHHhhhccCCC
Confidence 999999999999999999999999999987753
No 7
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=98.70 E-value=1.5e-07 Score=85.90 Aligned_cols=104 Identities=18% Similarity=0.296 Sum_probs=90.9
Q ss_pred HHHHHHHHHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehH
Q 010353 359 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 438 (512)
Q Consensus 359 ~le~~v~~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~ 438 (512)
.+.+++. |+.|.+|+..+.++|.+ ++++|++...|..+++|.+||.|++.|+|..--.... -+++..|+|++|.+
T Consensus 10 ~~~~i~~---g~~~~~v~~~l~~kge~-tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~-~~~~~~y~w~~~~~ 84 (176)
T COG1675 10 LLKSIVR---GDEAVLVVDALLEKGEL-TDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDE-ESGWEEYTWYINYE 84 (176)
T ss_pred HHHHHcc---CchhhHHHHHHHhcCCc-ChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeeccc-CCCcEEEEEEechH
Confidence 3344444 99999999999999877 9999999999999999999999999999965532222 56799999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 010353 439 ILWKHVLDEMFHAALNLSLRVSYELDREK 467 (512)
Q Consensus 439 ~~~~~~l~~~~k~~~nl~~R~~~e~~~~k 467 (512)
.+...+.....+.+-+|..++++|.++.-
T Consensus 85 ~v~~~l~~~~~~~le~Lk~~le~~~~~~~ 113 (176)
T COG1675 85 KVLEVLKGKKRKILEKLKRKLEKETENNY 113 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccCCc
Confidence 99999999999999999999999888764
No 8
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=98.44 E-value=4.2e-07 Score=81.83 Aligned_cols=93 Identities=15% Similarity=0.254 Sum_probs=77.6
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--CCCceEEEEEEehHHHHHHHHHHHHH
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQFLLWKVNRQILWKHVLDEMFH 450 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~--~~~~t~~lw~v~~~~~~~~~l~~~~k 450 (512)
.-|+..|..+|.+ .+++|++...|+.|++|++||+|.+++++...-....+ +.+++.|+|++|.+.+...+...+++
T Consensus 4 ~~v~d~L~~~~~~-~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~ 82 (147)
T smart00531 4 FLVLDALMRNGCV-TEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDK 82 (147)
T ss_pred EeehHHHHhcCCc-CHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHH
Confidence 4567778888887 99999999999999999999999998876444333222 33489999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhh
Q 010353 451 AALNLSLRVSYELDRE 466 (512)
Q Consensus 451 ~~~nl~~R~~~e~~~~ 466 (512)
...++-.|+++|.++.
T Consensus 83 ~~~~L~~~l~~e~~~~ 98 (147)
T smart00531 83 MRKRLEDKLEDETNNA 98 (147)
T ss_pred HHHHHHHHHhcccCCc
Confidence 9999999998876643
No 9
>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=98.10 E-value=5.9e-06 Score=70.01 Aligned_cols=89 Identities=18% Similarity=0.348 Sum_probs=56.4
Q ss_pred HHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEe
Q 010353 8 KHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVV 87 (512)
Q Consensus 8 ~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~ 87 (512)
+|...+++..||+-+..|..+|+.+|.++=.+|+..++++++.||..|..|.+.++|.+....+++ +....++|.+
T Consensus 1 ~L~~~v~r~~yg~~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~----~~~~~~yw~i 76 (105)
T PF02002_consen 1 ELLKEVVRAFYGEEAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDE----RGWTRYYWYI 76 (105)
T ss_dssp -----HHHTTS-STTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE------------EEEEE-
T ss_pred ChHHHHHHHHcCchHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCC----CcEEEEEEEE
Confidence 366789999999999999999999999999999999999999999999999999999866543321 1344688999
Q ss_pred chhhHHHHhchhh
Q 010353 88 LFDNILHRVRFAK 100 (512)
Q Consensus 88 ~~~~il~rlR~pr 100 (512)
|++.+...+.+-.
T Consensus 77 ~~~~~~~~ik~r~ 89 (105)
T PF02002_consen 77 DYDQIIDVIKYRI 89 (105)
T ss_dssp THHHH--------
T ss_pred cHHHHHHHHHHHH
Confidence 9998887776543
No 10
>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=97.43 E-value=0.00032 Score=53.30 Aligned_cols=60 Identities=18% Similarity=0.218 Sum_probs=52.9
Q ss_pred HHHHHHHHHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEE
Q 010353 359 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEK 419 (512)
Q Consensus 359 ~le~~v~~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QE 419 (512)
....+|++-||+.+.+|+..|..+|.+ .-.+|.+.+.+|.+.+|+.|..|.+.|+|+..+
T Consensus 2 L~~~ii~~~fG~~~~~V~~~Ll~~G~l-tl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~~ 61 (62)
T PF08221_consen 2 LCTLIIEEHFGEIVAKVGEVLLSRGRL-TLREIVRRTGLSPKQVKKALVVLIQHNLVQYFE 61 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHC-SE-EHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcChHHHHHHHHHHHcCCc-CHHHHHHHhCCCHHHHHHHHHHHHHcCCeeeec
Confidence 345789999999999999999999999 999999999999999999999999999998754
No 11
>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=97.33 E-value=0.0013 Score=59.92 Aligned_cols=88 Identities=14% Similarity=0.097 Sum_probs=71.5
Q ss_pred HHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEec
Q 010353 9 HAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVL 88 (512)
Q Consensus 9 Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~ 88 (512)
|.-..+.+.+|+..-.|..+|+.+|.+|--+|+..+|++.+.||.+|-.|.-.|+|.|-....+++ +....+|.++
T Consensus 3 ~~~~~~~~~~g~~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~----gw~~Y~w~i~ 78 (158)
T TIGR00373 3 LLNEVVGRAAEEEVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDET----GWYEYTWRIN 78 (158)
T ss_pred HHHHHHHHHcChhHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCC----CcEEEEEEeC
Confidence 455678889999999999999999999999999999999999999999999999998554322221 2334556799
Q ss_pred hhhHHHHhchhh
Q 010353 89 FDNILHRVRFAK 100 (512)
Q Consensus 89 ~~~il~rlR~pr 100 (512)
.+.++..+++-.
T Consensus 79 ~~~i~d~Ik~~~ 90 (158)
T TIGR00373 79 YEKALDVLKRKL 90 (158)
T ss_pred HHHHHHHHHHHH
Confidence 999887776653
No 12
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=96.69 E-value=0.011 Score=54.84 Aligned_cols=83 Identities=12% Similarity=0.152 Sum_probs=63.9
Q ss_pred HHHhhh--chhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechh
Q 010353 13 VITNHF--GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD 90 (512)
Q Consensus 13 iv~~~F--G~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~ 90 (512)
++.+.. |+..-.|...|..+|.+|-.+|+..+|++...||+.|..|...|+|.|.....++. ++...+|.++.+
T Consensus 13 ~l~~~~~~~~~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~----Gr~~y~w~l~~~ 88 (178)
T PRK06266 13 VLFEIMEGDEEGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEET----NWYTYTWKPELE 88 (178)
T ss_pred HHHHHhcCCccHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCC----CcEEEEEEeCHH
Confidence 344444 77789999999999999999999999999999999999999999999544322121 244556777777
Q ss_pred hHHHHhchh
Q 010353 91 NILHRVRFA 99 (512)
Q Consensus 91 ~il~rlR~p 99 (512)
.+...+.+-
T Consensus 89 ~i~d~ik~~ 97 (178)
T PRK06266 89 KLPEIIKKK 97 (178)
T ss_pred HHHHHHHHH
Confidence 776665543
No 13
>PHA02943 hypothetical protein; Provisional
Probab=95.94 E-value=0.055 Score=47.93 Aligned_cols=73 Identities=23% Similarity=0.355 Sum_probs=60.7
Q ss_pred HHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHHHHHHHHHHHHHHHH
Q 010353 375 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALN 454 (512)
Q Consensus 375 i~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~~k~~~n 454 (512)
|+++| +.|.- ...+|++...++-.+|+-.||.|.++|.| ++|+++. +=+|.++.+ .+..++.++++.+..
T Consensus 16 ILE~L-k~G~~-TtseIAkaLGlS~~qa~~~LyvLErEG~V--krV~~G~-----~tyw~l~~d-ay~~~v~~~~Relwr 85 (165)
T PHA02943 16 TLRLL-ADGCK-TTSRIANKLGVSHSMARNALYQLAKEGMV--LKVEIGR-----AAIWCLDED-AYTNLVFEIKRELWR 85 (165)
T ss_pred HHHHH-hcCCc-cHHHHHHHHCCCHHHHHHHHHHHHHcCce--EEEeecc-----eEEEEEChH-HHHHHHHHHHHHHHH
Confidence 67777 66777 99999999999999999999999999998 4577774 568999975 566668888888877
Q ss_pred HHH
Q 010353 455 LSL 457 (512)
Q Consensus 455 l~~ 457 (512)
++.
T Consensus 86 lv~ 88 (165)
T PHA02943 86 LVC 88 (165)
T ss_pred HHH
Confidence 654
No 14
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=95.88 E-value=0.011 Score=45.74 Aligned_cols=44 Identities=25% Similarity=0.382 Sum_probs=40.5
Q ss_pred HHHHHHHHhcCC--CcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 010353 373 YRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 417 (512)
Q Consensus 373 ~Ri~r~l~~~~~--l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~ 417 (512)
-+|+.+|...|. + ..++|++...|+.+.++..||+|.++|||.-
T Consensus 9 ~~IL~~L~~~g~~~~-ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 9 EKILEFLENSGDETS-TALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHHHCCCCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 478999998877 7 9999999999999999999999999999944
No 15
>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=95.68 E-value=0.029 Score=43.20 Aligned_cols=46 Identities=30% Similarity=0.361 Sum_probs=44.4
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+.=++|..+|+.+|+.|..+|++.+++|.+.|..+|-.|.+.|+|.
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~ 53 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVE 53 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 6778999999999999999999999999999999999999999997
No 16
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=95.33 E-value=0.08 Score=54.62 Aligned_cols=141 Identities=14% Similarity=0.183 Sum_probs=99.9
Q ss_pred HHHHHHHHHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCce---EEEEEE
Q 010353 359 EVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQ---FLLWKV 435 (512)
Q Consensus 359 ~le~~v~~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t---~~lw~v 435 (512)
.+.-+|+-.||..++=|+..|+.++.+ -|+++++..-++.|++|.++..|-.+.||.++-..-++..+++ .-+|++
T Consensus 18 l~k~vvr~fy~~~~~lild~llr~~~v-~Eedl~~llk~~~KqLR~li~~LredKlI~~~~r~E~~~nGr~~~~~~YyyI 96 (436)
T KOG2593|consen 18 LLKKVVRGFYGGEHVLILDALLRRQCV-REEDLKELLKFNKKQLRKLIASLREDKLIKIRTRTETAENGRAVDKHTYYYI 96 (436)
T ss_pred HHHHHHHhcccchhHHHHHHHHHhhhc-chHHHHHHhcccHHHHHHHHHHhhhhhhhhhhhhhhcCCCCcceeeeEEEEe
Confidence 344577888999999999999999888 9999999999999999999999999999987754333322333 357889
Q ss_pred ehHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh--------------------ccc---------------ccccCChh
Q 010353 436 NRQILWKHVLDEMFHAALNLSLRVSYELDREKEL--------------------LNL---------------PADKRTGP 480 (512)
Q Consensus 436 ~~~~~~~~~l~~~~k~~~nl~~R~~~e~~~~k~l--------------------l~k---------------~~~~~~~~ 480 (512)
|+.+++..+-=.+- .+.+|++.+....... ++- .+++..|+
T Consensus 97 nY~~~idvVKyKlh----~m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~~~ 172 (436)
T KOG2593|consen 97 NYAQVIDVVKYKLH----QMRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKLPS 172 (436)
T ss_pred ehHHHHHHHHHHHH----HHHHHHHHHhhhccccccccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccCch
Confidence 99987776654444 5555665554433221 110 00111133
Q ss_pred HH--HHHHHHHHHHHHHHHHHhhhhh
Q 010353 481 LQ--DRYNRIRKVRILLESSQMKLDD 504 (512)
Q Consensus 481 e~--~~l~~~~~~~~~L~~~~~rlD~ 504 (512)
+. ..|.++....+-|...+.++|.
T Consensus 173 ~e~~~~l~~~~~Q~~pi~d~Lk~~e~ 198 (436)
T KOG2593|consen 173 KESRTALNRLMEQLEPIIDLLKELEG 198 (436)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 33 3488888888888888888887
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=95.13 E-value=0.034 Score=39.62 Aligned_cols=44 Identities=16% Similarity=0.312 Sum_probs=39.2
Q ss_pred HHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 372 AYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 372 ~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
-.+|+..|.+++.+ +.++|++...++...+...|.+|.+.|+|+
T Consensus 5 ~~~Il~~l~~~~~~-t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRI-TQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 36899999999888 999999999999999999999999999984
No 18
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=95.12 E-value=0.45 Score=42.01 Aligned_cols=123 Identities=25% Similarity=0.326 Sum_probs=83.9
Q ss_pred hhHHHHHHHHHhc-------CCCcHHHHHHhc----------CCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCc
Q 010353 20 DLVAKVCECLLRK-------GPLTRQNVKRYT----------ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKAN 82 (512)
Q Consensus 20 ~~v~~V~~~Ll~~-------G~ltl~~I~~~t----------~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~ 82 (512)
+.-++|..||+.+ =++||..|...+ +++...|..+|=.|...++|.- ... + .+ +
T Consensus 3 ~~E~RVLG~LiEK~~TTPd~YPLtLNaL~~aCNQKsnR~PVm~l~e~eV~~ald~L~~~~Lv~~-~~~--g-----sR-v 73 (148)
T PF04337_consen 3 PVEARVLGCLIEKEVTTPDQYPLTLNALTTACNQKSNREPVMNLSESEVQAALDELRAKGLVRE-SGF--G-----SR-V 73 (148)
T ss_dssp HHHHHHHHHHHHHHHH-GGG-SEEHHHHHHHHT-SSS-SS-----HHHHHHHHHHHHHTTSEEE--E---------SS--
T ss_pred hhHhhHHHhhheecccCCCcCcchHHHHHHHhccccccCccccCCHHHHHHHHHHHHHCcCeee-cCC--C-----cc-h
Confidence 3456778888765 478899997654 3778999999999999999973 222 1 12 5
Q ss_pred cEEEechhhHHHHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcc-
Q 010353 83 TQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAH- 161 (512)
Q Consensus 83 ~~Y~~~~~~il~rlR~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~- 161 (512)
..|+-+..+.+ .+......|+-.||..|--|+.++-.+..- +- +..+.++++..+..|++.+
T Consensus 74 ~ky~Hr~~~~l--------------~l~~~e~All~~LlLRGpQT~GELR~Rs~R-l~--~F~d~~~Ve~~L~~L~~r~~ 136 (148)
T PF04337_consen 74 AKYEHRFCNTL--------------QLSPQELALLCLLLLRGPQTPGELRTRSER-LH--EFADVAEVEAVLERLAEREP 136 (148)
T ss_dssp -EEEE-HHHHH--------------T--HHHHHHHHHHHHH-SB-HHHHHHHHTT-TS----SSHHHHHHHHHHHHHTT-
T ss_pred HHHHhhhhhhc--------------CCCHHHHHHHHHHHHcCCCchhHHHhhhcc-cc--CCCCHHHHHHHHHHHHhccc
Confidence 78988877762 345677889999999999999999887532 21 2447889999999999999
Q ss_pred -cccccCC
Q 010353 162 -YVERCPA 168 (512)
Q Consensus 162 -fi~rv~~ 168 (512)
++.+.|.
T Consensus 137 plV~~LpR 144 (148)
T PF04337_consen 137 PLVVKLPR 144 (148)
T ss_dssp -SEEEE--
T ss_pred hhheecCC
Confidence 8887763
No 19
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=95.03 E-value=0.061 Score=48.36 Aligned_cols=74 Identities=16% Similarity=0.349 Sum_probs=53.3
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccc--cceecccCCCCCCCCCCCccEEEechhhHHHHhchhh
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNC--VQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAK 100 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~--V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~pr 100 (512)
.|...|+.+|.+|=.+|+..++++.++||..|..|-.+++ +.|-..-.+++ .....++|.+|.+.++..+++-.
T Consensus 5 ~v~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~---~~~~~~yw~i~y~~~~~vik~r~ 80 (147)
T smart00531 5 LVLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPET---KTWYRYYWYINYDTLLDVVKYKL 80 (147)
T ss_pred eehHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCC---ceEEEEEEEecHHHHHHHHHHHH
Confidence 4778899999999999999999999999999999999554 54322221111 01234566788877776666543
No 20
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=94.91 E-value=0.11 Score=41.50 Aligned_cols=75 Identities=17% Similarity=0.199 Sum_probs=56.8
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhchhhHHH
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLT 103 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~pr~l~ 103 (512)
.|..+|...+.+++.+|...++++...+..-|-.|...|+|...... .+ .++.++|++-..+ +-.|.+|+.
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~-~~-----~~p~t~~~lT~~G---r~~~~~~~~ 74 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEF-EG-----RRPRTWYSLTDKG---REAFERYVA 74 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE--SS-----S--EEEEEE-HHH---HHHHHHHHH
T ss_pred HHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEec-cC-----CCCeEEEEECHHH---HHHHHHHHH
Confidence 47889999999999999999999999999999999999999954332 22 2447899999887 456777776
Q ss_pred HHHH
Q 010353 104 ILSQ 107 (512)
Q Consensus 104 ~i~~ 107 (512)
..++
T Consensus 75 ~L~~ 78 (80)
T PF13601_consen 75 ALRE 78 (80)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6654
No 21
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=94.61 E-value=0.15 Score=53.62 Aligned_cols=91 Identities=15% Similarity=0.242 Sum_probs=76.1
Q ss_pred HHHHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCC-CCCCCCccE
Q 010353 6 GTKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGF-ADGPKANTQ 84 (512)
Q Consensus 6 ~~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~-~~~~~~~~~ 84 (512)
..--|..+|.+.||+-|-+++++|.++|-+.=.+|....=++.+..|.-|..|+.-|.|. .++- +..+ ++|.+++..
T Consensus 383 ~~~~~E~vI~~rfG~rAiRl~R~l~~k~~veekqv~~~Alm~~Kd~r~~L~~m~~~g~v~-lQeV-prTaD~~psrtF~L 460 (551)
T KOG2587|consen 383 ATATYESVIQERFGSRAIRLFRLLLQKKHVEEKQVEDFALMPAKDARDMLYKMLEEGYVE-LQEV-PRTADRAPSRTFYL 460 (551)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHhcccchHHHHHHhhccccccHHHHHHHHHHcCcee-eeec-CCCCCCCCcceEEE
Confidence 344678899999999999999999999999999999888899999999999999999996 4433 2333 466777889
Q ss_pred EEechhhHHHHhch
Q 010353 85 YVVLFDNILHRVRF 98 (512)
Q Consensus 85 Y~~~~~~il~rlR~ 98 (512)
|.+|...++..|+-
T Consensus 461 ~~v~~~~a~~~lld 474 (551)
T KOG2587|consen 461 YTVNILRAYRMLLD 474 (551)
T ss_pred EEeccHHHHHHHHH
Confidence 99999888876653
No 22
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=94.58 E-value=0.1 Score=40.37 Aligned_cols=45 Identities=24% Similarity=0.261 Sum_probs=42.4
Q ss_pred hHHHHHHHHHhcCC--CcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 21 LVAKVCECLLRKGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 21 ~v~~V~~~Ll~~G~--ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.-.+|..+|..+|. +|..+|++.++++.+.|+..|..|..+|+|.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 45689999999998 9999999999999999999999999999997
No 23
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.55 E-value=0.058 Score=40.82 Aligned_cols=56 Identities=25% Similarity=0.326 Sum_probs=41.0
Q ss_pred HHHHHHh-cCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEe
Q 010353 375 IFRLLSK-SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 436 (512)
Q Consensus 375 i~r~l~~-~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~ 436 (512)
|+.+|.. ++-+ ...+||+.+.|+...||..|..|.++|.|+-.++.|+. + . +|+++
T Consensus 5 Il~~i~~~~~p~-~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~--~--~-~W~l~ 61 (62)
T PF04703_consen 5 ILEYIKEQNGPL-KTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGK--S--T-YWRLN 61 (62)
T ss_dssp HHHHHHHHTS-E-EHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSS--S----EEEES
T ss_pred HHHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCc--c--e-eeeec
Confidence 5556655 5555 99999999999999999999999999998544444443 2 2 59886
No 24
>PHA02943 hypothetical protein; Provisional
Probab=94.17 E-value=1.2 Score=39.64 Aligned_cols=102 Identities=17% Similarity=0.138 Sum_probs=69.5
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhchhhHH
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFL 102 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~pr~l 102 (512)
..|.++| ..|..|..+|++.+|+|..+++..|.+|-.-|+|.- ... +..++|.++.++..+.
T Consensus 14 ~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vkr--V~~--------G~~tyw~l~~day~~~------- 75 (165)
T PHA02943 14 IKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLK--VEI--------GRAAIWCLDEDAYTNL------- 75 (165)
T ss_pred HHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEE--Eee--------cceEEEEEChHHHHHH-------
Confidence 3566677 889999999999999999999999999999999983 221 2268999998765544
Q ss_pred HHHHHHhhhhHHHHHHHHHHccc---CCHHHHHHHHhhcccCCCccCHHHHHHHHHHHH
Q 010353 103 TILSQEFDQQCVELVQGLLEHGR---LTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLV 158 (512)
Q Consensus 103 ~~i~~~~G~~a~~Iv~~lL~~G~---l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv 158 (512)
+.+-+-+. ..++.+-+ ++++++..-+..+ .+.++.|.++|
T Consensus 76 --v~~~~Rel-----wrlv~s~~~kfi~p~~l~~li~kd---------~~a~~~~ak~v 118 (165)
T PHA02943 76 --VFEIKREL-----WRLVCNSRLKFITPSRLLRLIAKD---------TEAHNIFAKYV 118 (165)
T ss_pred --HHHHHHHH-----HHHHHhccccccChHHHHHHHHhC---------HHHHHHHHHhc
Confidence 22222221 22333444 4577777766543 23566666553
No 25
>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=93.48 E-value=1.7 Score=41.12 Aligned_cols=66 Identities=15% Similarity=0.144 Sum_probs=51.4
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhH
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (512)
-..|...|..+|++|..+|...+++++..|+..|-.|.+.|+|......... ++....|.+...+.
T Consensus 3 r~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~-----gRp~~~y~LT~~G~ 68 (203)
T TIGR02702 3 KEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGM-----GRPQYHYQLSRQGR 68 (203)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCC-----CCCceEEEECcchh
Confidence 4578889999999999999999999999999999999999999833221111 23346777776653
No 26
>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=93.43 E-value=0.1 Score=40.06 Aligned_cols=47 Identities=17% Similarity=0.275 Sum_probs=43.0
Q ss_pred HHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEE
Q 010353 372 AYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEK 419 (512)
Q Consensus 372 ~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QE 419 (512)
=.+|+..|+.+|.. +.++|++...+|...+...|.+|.+.|+|...+
T Consensus 10 E~~vy~~Ll~~~~~-t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 10 EAKVYLALLKNGPA-TAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHCHE-EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 36899999988888 999999999999999999999999999996654
No 27
>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=93.21 E-value=0.25 Score=35.06 Aligned_cols=43 Identities=16% Similarity=0.190 Sum_probs=38.4
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhcccc
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V 64 (512)
-.+|..+|..+|+.|..+|++.++++...|...|--|...|+|
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 4578899999999999999999999999999999999999987
No 28
>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=93.14 E-value=0.15 Score=37.02 Aligned_cols=44 Identities=25% Similarity=0.382 Sum_probs=38.0
Q ss_pred HHHHHHHHHhcCC-CcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 22 VAKVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 22 v~~V~~~Ll~~G~-ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+-.|.++|...+. +|+.+|++.+++|.+.+..-|..|.++|+|.
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 4467777777765 7999999999999999999999999999996
No 29
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=93.14 E-value=0.96 Score=38.93 Aligned_cols=64 Identities=13% Similarity=0.080 Sum_probs=51.5
Q ss_pred hhc-hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechh
Q 010353 17 HFG-DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD 90 (512)
Q Consensus 17 ~FG-~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~ 90 (512)
.+| |.=-+|...|...|..+..+|+..++++++.|-+=|-+|.+-|+|...... + ..+|.+|.+
T Consensus 12 aLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~G---------r-~~~Y~l~~~ 76 (117)
T PRK10141 12 ILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQG---------K-WVHYRLSPH 76 (117)
T ss_pred HhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEc---------C-EEEEEECch
Confidence 344 334478888888899999999999999999999999999999999732221 1 579999865
No 30
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=93.06 E-value=0.67 Score=40.23 Aligned_cols=61 Identities=25% Similarity=0.356 Sum_probs=52.3
Q ss_pred HHHHHHhhhc--hhHHHHHHHHH-hcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceeccc
Q 010353 10 AVHVITNHFG--DLVAKVCECLL-RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (512)
Q Consensus 10 c~~iv~~~FG--~~v~~V~~~Ll-~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~ 70 (512)
|..+++=.|| +.=-.|...|+ .+|++|.-+|+...+.+.+.|..||--|+.-|+|.--..+
T Consensus 15 ~~dvl~c~~GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~ 78 (126)
T COG3355 15 CEDVLKCVYGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVN 78 (126)
T ss_pred HHHHHHHHhCCcHHHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeec
Confidence 5567777788 55667889999 7999999999999999999999999999999999843433
No 31
>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=92.75 E-value=0.098 Score=37.97 Aligned_cols=46 Identities=28% Similarity=0.416 Sum_probs=40.8
Q ss_pred hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 371 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+.+|+++|...+.-+.-.+|++...+|...+..+|..|.+.|||+
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 5788999998877645999999999999999999999999999995
No 32
>PRK11239 hypothetical protein; Provisional
Probab=92.22 E-value=2.8 Score=39.59 Aligned_cols=125 Identities=26% Similarity=0.383 Sum_probs=90.2
Q ss_pred hhchhHHHHHHHHHhcC-------CCcHHHHHHhc----------CCCHHHHHHHHHHHHhccccceecccCCCCCCCCC
Q 010353 17 HFGDLVAKVCECLLRKG-------PLTRQNVKRYT----------ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGP 79 (512)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G-------~ltl~~I~~~t----------~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~ 79 (512)
.+-+.-++|..||+.+. ++||..|...+ +++..+|..||=.|...++|.-.... + .
T Consensus 4 ~Ls~~EaRVlG~LiEKe~TTPd~YPLSLNaL~~aCNQKsnRePVm~lsE~eV~~ald~L~~~~Lv~~~~~~--g-----s 76 (215)
T PRK11239 4 QLTALEARVIGCLLEKQVTTPEQYPLSVNGVVTACNQKTNREPVMNLSESEVQEQLDNLVKRHYLRTVSGF--G-----N 76 (215)
T ss_pred ccCHHHHHHHHHhhhhcccCCCcCcchHHHHHHHhccccccCccccCCHHHHHHHHHHHHhCcCeeeecCC--C-----c
Confidence 35677789999999874 68888887554 37889999999999999999622211 1 1
Q ss_pred CCccEEEechhhHHHHhchhhHHHHH-HHHh-----hhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHH
Q 010353 80 KANTQYVVLFDNILHRVRFAKFLTIL-SQEF-----DQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRET 153 (512)
Q Consensus 80 ~~~~~Y~~~~~~il~rlR~pr~l~~i-~~~~-----G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~ 153 (512)
|.+||-+.. .++| ......|+-.||..|--|+.++-.+..- +- +..+.++++..
T Consensus 77 -----------------Rv~Ky~Hr~~~~ef~~l~l~~~~~All~~LlLRGPQT~gELRtRs~R-l~--~F~dv~~Ve~~ 136 (215)
T PRK11239 77 -----------------RVTKYEQRFCNSEFGDLKLSAAEVALITTLLLRGAQTPGELRSRAAR-MY--EFSDMAEVEST 136 (215)
T ss_pred -----------------chHHHHHhcccccccccCCCHHHHHHHHHHHhcCCCChHHHHHhHhc-CC--cCCCHHHHHHH
Confidence 334443322 2333 3668889999999999999999877532 21 23468899999
Q ss_pred HHHHHhcc---cccccCC
Q 010353 154 LVKLVTAH---YVERCPA 168 (512)
Q Consensus 154 f~~Lv~~~---fi~rv~~ 168 (512)
+..|+... ++.+.|.
T Consensus 137 L~~L~~r~~~plV~~LpR 154 (215)
T PRK11239 137 LEQLANREDGPFVVRLAR 154 (215)
T ss_pred HHHHHhccCCceeeecCC
Confidence 99999874 7777753
No 33
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=92.07 E-value=1.9 Score=37.40 Aligned_cols=82 Identities=17% Similarity=0.318 Sum_probs=62.0
Q ss_pred HHHHHHH-hcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEE-EEehHHHHHHHHH---HH
Q 010353 374 RIFRLLS-KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLW-KVNRQILWKHVLD---EM 448 (512)
Q Consensus 374 Ri~r~l~-~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw-~v~~~~~~~~~l~---~~ 448 (512)
.++-.|+ ..|.+ +.++||+..-.+...+-+.|.+|...|+|+=.-++- -.++..|+| -+|++.+...++. ++
T Consensus 31 ~v~~~LL~~~~~~-tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~--~~Ggy~yiY~~i~~ee~k~~i~~~l~~w 107 (126)
T COG3355 31 EVYKALLEENGPL-TVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL--KGGGYYYLYKPIDPEEIKKKILKDLDEW 107 (126)
T ss_pred HHHHHHHhhcCCc-CHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc--CCCceeEEEecCCHHHHHHHHHHHHHHH
Confidence 4566677 57788 999999999999999999999999999995433332 346778888 8999998876655 44
Q ss_pred HHHHHHHHHH
Q 010353 449 FHAALNLSLR 458 (512)
Q Consensus 449 ~k~~~nl~~R 458 (512)
|..+..+++.
T Consensus 108 ~~~~~~~i~~ 117 (126)
T COG3355 108 YDKMKQLIEE 117 (126)
T ss_pred HHHHHHHHHH
Confidence 5444444443
No 34
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=92.01 E-value=0.32 Score=44.23 Aligned_cols=57 Identities=25% Similarity=0.340 Sum_probs=48.0
Q ss_pred HHHHHHhhhch---------hHHHHHHHHHh-cCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 10 AVHVITNHFGD---------LVAKVCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 10 c~~iv~~~FG~---------~v~~V~~~Ll~-~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
+..++=++||+ .|+.|..+|.- ++++|+.+|...+|+|.+.|-.+|-.|.--|+|..
T Consensus 7 ak~~~Ie~fae~m~r~G~nrtVG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~ 73 (177)
T COG1510 7 AKDIFIEHFAETMSRWGINRTVGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKK 73 (177)
T ss_pred HHHHHHHHHHHHHHHhCCcchHHHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHh
Confidence 34455556655 57788887766 89999999999999999999999999999999984
No 35
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=91.83 E-value=0.71 Score=34.04 Aligned_cols=56 Identities=20% Similarity=0.203 Sum_probs=44.1
Q ss_pred HHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhh
Q 010353 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDN 91 (512)
Q Consensus 25 V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~ 91 (512)
|..+|. .+++|+.+|.+.+++++..+...|-.|.+.|++...... + ..+|.++.+.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~---------~-~~~~~~~~~~ 57 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREG---------K-RVYYSLTDEK 57 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecC---------C-EEEEEEchHH
Confidence 456666 889999999999999999999999999999999732211 1 3567777653
No 36
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=91.81 E-value=0.53 Score=48.76 Aligned_cols=101 Identities=13% Similarity=0.293 Sum_probs=78.9
Q ss_pred HHHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEE
Q 010353 7 TKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYV 86 (512)
Q Consensus 7 ~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~ 86 (512)
.+|.-..|+..||..+.-|..+|++++++.=-+|....+++.+++|.-+..|--..+|...+......+|.....++||.
T Consensus 16 ~~l~k~vvr~fy~~~~~lild~llr~~~v~Eedl~~llk~~~KqLR~li~~LredKlI~~~~r~E~~~nGr~~~~~~Yyy 95 (436)
T KOG2593|consen 16 NDLLKKVVRGFYGGEHVLILDALLRRQCVREEDLKELLKFNKKQLRKLIASLREDKLIKIRTRTETAENGRAVDKHTYYY 95 (436)
T ss_pred HHHHHHHHHhcccchhHHHHHHHHHhhhcchHHHHHHhcccHHHHHHHHHHhhhhhhhhhhhhhhcCCCCcceeeeEEEE
Confidence 36777889999999999999999999999999999999999999999999998888887443321111111111158999
Q ss_pred echhhHHHHhchhhHHHHHHHHh
Q 010353 87 VLFDNILHRVRFAKFLTILSQEF 109 (512)
Q Consensus 87 ~~~~~il~rlR~pr~l~~i~~~~ 109 (512)
+|+-.++-.+||- |+++++++
T Consensus 96 InY~~~idvVKyK--lh~m~krl 116 (436)
T KOG2593|consen 96 INYAQVIDVVKYK--LHQMRKRL 116 (436)
T ss_pred eehHHHHHHHHHH--HHHHHHHH
Confidence 9999999999885 45555554
No 37
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=91.18 E-value=2.3 Score=39.82 Aligned_cols=87 Identities=14% Similarity=0.214 Sum_probs=53.4
Q ss_pred HHHHHhcCCCcchhhh----hhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHH--HHHHHHHHH
Q 010353 376 FRLLSKSGRLLETDKI----SDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQIL--WKHVLDEMF 449 (512)
Q Consensus 376 ~r~l~~~~~l~eek~i----~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~--~~~~l~~~~ 449 (512)
+.++...+....-|+| .+.+.|....++++|..|..+|.|..- --+.+.|+|...-... ...-++.+-
T Consensus 2 l~~f~e~~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~E------KiGssn~YWsFps~~~~~~~~~~~~l~ 75 (188)
T PF03962_consen 2 LEIFHESKDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVE------KIGSSNYYWSFPSQAKQKRQNKLEKLQ 75 (188)
T ss_pred hHHHhhcCCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhh------hccCeeEEEecChHHHHHHHHHHHHHH
Confidence 3445554444455555 444899999999999999999999433 2344678887764433 244444555
Q ss_pred HHHHHHHHHHHHHHHhhhh
Q 010353 450 HAALNLSLRVSYELDREKE 468 (512)
Q Consensus 450 k~~~nl~~R~~~e~~~~k~ 468 (512)
+.+.++..++....+....
T Consensus 76 ~~~~~~~~~i~~l~~~i~~ 94 (188)
T PF03962_consen 76 KEIEELEKKIEELEEKIEE 94 (188)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5555555555444444333
No 38
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=90.94 E-value=2.2 Score=34.68 Aligned_cols=68 Identities=13% Similarity=0.159 Sum_probs=53.0
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhH
Q 010353 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (512)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (512)
....--.|..+|..+|..+..+|.+.+++++..|...|-.|.+.|+|....... ++...+|.+...+.
T Consensus 8 l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~-------~~r~~~~~lT~~g~ 75 (101)
T smart00347 8 LTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPE-------DRRSVLVSLTEEGR 75 (101)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCC-------CCCeEEEEECHhHH
Confidence 445667788899899999999999999999999999999999999998443221 12245777765543
No 39
>COG3132 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.82 E-value=3.7 Score=37.45 Aligned_cols=122 Identities=29% Similarity=0.368 Sum_probs=88.7
Q ss_pred hchhHHHHHHHHHhcC-------CCcHHHHHHhc----------CCCHHHHHHHHHHHHhccccceecccCCCCCCCCCC
Q 010353 18 FGDLVAKVCECLLRKG-------PLTRQNVKRYT----------ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPK 80 (512)
Q Consensus 18 FG~~v~~V~~~Ll~~G-------~ltl~~I~~~t----------~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~ 80 (512)
.-++=++|..||+.+- ++|+.-++-.+ +|+..+|..+|--|++.|+|. +.. + ++
T Consensus 5 l~a~eARViGcLlEKqvtTPe~YPLtlN~l~~AcNQKT~RdPVmnLse~eVq~~l~~L~~r~lvr--~~s--g-----sR 75 (215)
T COG3132 5 LTALEARVIGCLLEKQVTTPEQYPLTLNGLVTACNQKTNRDPVMNLSESEVQEQLDNLEKRHLVR--TVS--G-----SR 75 (215)
T ss_pred CchHHHHHHHHhhhcccCCcccccchHHHHHHHHhccccccchhcCCHHHHHHHHHHHHHhhhHH--Hhh--c-----ch
Confidence 3467789999999764 67788886543 488999999999999999997 322 1 12
Q ss_pred CccEEEechhhHHHHhchhhHHHHHHHHhhh-----hHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHH
Q 010353 81 ANTQYVVLFDNILHRVRFAKFLTILSQEFDQ-----QCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLV 155 (512)
Q Consensus 81 ~~~~Y~~~~~~il~rlR~pr~l~~i~~~~G~-----~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~ 155 (512)
++.|+- .+...+||+ .-..++-.||..|--|+.++..+..--.+ ..+..+++..+.
T Consensus 76 -v~kyeh---------------rfcnsefgdlkl~~~evali~lLlLRGaQTpgELrtRanRm~~---Fsdv~e~e~~Le 136 (215)
T COG3132 76 -VTKYEH---------------RFCNSEFGDLKLSAAEVALITLLLLRGAQTPGELRTRANRMYE---FSDVAEVEHTLE 136 (215)
T ss_pred -HHHHHH---------------HHhhccccceeechHHHHHHHHHHHcCCCChhHHHHHHHhhhc---cchHHHHHHHHH
Confidence 334431 234556773 35568889999999999999987543211 235788999999
Q ss_pred HHHhcc---cccccC
Q 010353 156 KLVTAH---YVERCP 167 (512)
Q Consensus 156 ~Lv~~~---fi~rv~ 167 (512)
.|+..+ |+++.|
T Consensus 137 ~La~R~~gplvv~l~ 151 (215)
T COG3132 137 RLANREDGPLVVRLA 151 (215)
T ss_pred HHhcCCCCceeeecC
Confidence 999998 888875
No 40
>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=90.77 E-value=1.4 Score=33.47 Aligned_cols=48 Identities=21% Similarity=0.156 Sum_probs=41.8
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceec
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~ 68 (512)
+....|..++...+ .+..+|.+.++++...+...|-.|.++|++....
T Consensus 7 ~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 7 PTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred hHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEE
Confidence 45677888887777 8999999999999999999999999999998433
No 41
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=90.38 E-value=0.76 Score=32.63 Aligned_cols=42 Identities=17% Similarity=0.294 Sum_probs=38.7
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|..+|..+|..+..+|.+..++++..|+..|-.|.+.|+|.
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 467777888999999999999999999999999999999987
No 42
>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=90.34 E-value=0.52 Score=36.39 Aligned_cols=46 Identities=20% Similarity=0.311 Sum_probs=38.7
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecc
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~ 69 (512)
.|-.+|-.+|+.|+.+|++..++++..|+.-|-.|++-|-|.-...
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 5778899999999999999999999999999999999999884433
No 43
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=90.34 E-value=2 Score=39.59 Aligned_cols=80 Identities=16% Similarity=0.328 Sum_probs=60.9
Q ss_pred HHHhhh-chhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhh
Q 010353 13 VITNHF-GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDN 91 (512)
Q Consensus 13 iv~~~F-G~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~ 91 (512)
++.+.+ |+-+-.|+.+|+.+|-.|=.+|+..+++....||..|..|---|++.|-..-.+.. +-...+|.++.+.
T Consensus 10 ~~~~i~~g~~~~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~----~~~~y~w~~~~~~ 85 (176)
T COG1675 10 LLKSIVRGDEAVLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEES----GWEEYTWYINYEK 85 (176)
T ss_pred HHHHHccCchhhHHHHHHHhcCCcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCC----CcEEEEEEechHH
Confidence 334444 99999999999999999999999999999999999999999999998543322111 2334566677666
Q ss_pred HHHHh
Q 010353 92 ILHRV 96 (512)
Q Consensus 92 il~rl 96 (512)
+...+
T Consensus 86 v~~~l 90 (176)
T COG1675 86 VLEVL 90 (176)
T ss_pred HHHHH
Confidence 65444
No 44
>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=90.33 E-value=0.44 Score=36.38 Aligned_cols=51 Identities=27% Similarity=0.353 Sum_probs=47.0
Q ss_pred HhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 15 TNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 15 ~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++..|..++.|.+.|..+|.+|+.+|.+.++++...+-.|+==|.+-|=|.
T Consensus 3 ~~~IG~nAG~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~ 53 (65)
T PF10771_consen 3 KENIGENAGKVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIE 53 (65)
T ss_dssp HHHHHHHHHHHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEE
T ss_pred hhHHHHHHHHHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCcee
Confidence 356899999999999999999999999999999999999999999999886
No 45
>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=90.26 E-value=3.5 Score=35.15 Aligned_cols=100 Identities=19% Similarity=0.250 Sum_probs=70.5
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHHhc----CCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechh-hHH
Q 010353 19 GDLVAKVCECLLRKGPLTRQNVKRYT----ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD-NIL 93 (512)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~I~~~t----~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~-~il 93 (512)
|+.=..|-.+|=.+|++|..+|.... +.+++.|+..|-.|.+-|+|...... + ..+|++... +-+
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g---------r-~~~Y~p~is~~e~ 71 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIG---------R-AYVYSPLISREEY 71 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEET---------T-CEEEEESSSHHHH
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecC---------C-ceEEEeCCcHHHH
Confidence 44456788999999999999998774 47799999999999999999854332 2 345665543 333
Q ss_pred HHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHH
Q 010353 94 HRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQM 131 (512)
Q Consensus 94 ~rlR~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~l 131 (512)
..-. .-.++...||.....++..|+....++.+++
T Consensus 72 ~~~~---~~~~l~~~~~gs~~~l~~~l~~~~~ls~~el 106 (115)
T PF03965_consen 72 LAQE---LRQFLDRLFDGSIPQLVAALVESEELSPEEL 106 (115)
T ss_dssp HHHH---HHHHHHHHSTTHHHHHHHHHHHCT-S-HHHH
T ss_pred HHHH---HHHHHHHHhCCCHHHHHHHHHhcCCCCHHHH
Confidence 3222 3345566788889999999999998887765
No 46
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=90.07 E-value=2 Score=41.12 Aligned_cols=67 Identities=22% Similarity=0.331 Sum_probs=55.3
Q ss_pred CchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehH
Q 010353 369 GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 438 (512)
Q Consensus 369 G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~ 438 (512)
|.---+|..+|.+.|-. .-.+|++...|+..-+|.-|-.|..+|+|+.+..+.. .+|..++|+.-..
T Consensus 10 ~~tr~~il~lL~~~g~~-sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g--~GRP~~~y~Lt~~ 76 (218)
T COG2345 10 GSTRERILELLKKSGPV-SADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGG--RGRPAKLYRLTEK 76 (218)
T ss_pred ccHHHHHHHHHhccCCc-cHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCC--CCCCceeeeeccc
Confidence 33445788888888888 9999999999999999999999999999999965554 4777777776543
No 47
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=89.87 E-value=5.8 Score=37.94 Aligned_cols=93 Identities=17% Similarity=0.244 Sum_probs=65.1
Q ss_pred hhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHh
Q 010353 17 HFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRV 96 (512)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rl 96 (512)
.=|..-.+|-..|..+|+.|+.+|+...++++-.||.=|-.|.--|+|.+.... +|-| ++...|.+--.+.=
T Consensus 8 ~~~~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~--~g~G---RP~~~y~Lt~~g~~--- 79 (218)
T COG2345 8 PSGSTRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQ--GGRG---RPAKLYRLTEKGRE--- 79 (218)
T ss_pred CCccHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeecc--CCCC---CCceeeeecccchh---
Confidence 446777889999999999999999999999999999999999999999965332 2222 33345665543321
Q ss_pred chhhHHHHHHHHhhhhHHHHHHHHHHcc
Q 010353 97 RFAKFLTILSQEFDQQCVELVQGLLEHG 124 (512)
Q Consensus 97 R~pr~l~~i~~~~G~~a~~Iv~~lL~~G 124 (512)
.....||+.+..++..|=..|
T Consensus 80 -------~f~~~y~~l~~~~l~~l~~~~ 100 (218)
T COG2345 80 -------QFPKRYGELALALLDALEETG 100 (218)
T ss_pred -------hcchhhHHHHHHHHHHHHHhc
Confidence 333455555555555554444
No 48
>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=89.80 E-value=4.9 Score=35.20 Aligned_cols=99 Identities=18% Similarity=0.290 Sum_probs=69.9
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHh----cCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechh-hHHH
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRY----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD-NILH 94 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~----t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~-~il~ 94 (512)
+.=-.|-.+|-..|+.|..+|... .++++..|...|-.|.+.|+|.. ... ++ ...|++.+. +-+.
T Consensus 4 ~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~-~k~--------gr-~~~Y~p~vs~ee~~ 73 (130)
T TIGR02698 4 DAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTT-EKE--------GR-KFIYTALVSEDEAV 73 (130)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceee-ecC--------CC-cEEEEecCCHHHHH
Confidence 333467788889999999997665 36899999999999999999973 322 12 346775433 3222
Q ss_pred HhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHH
Q 010353 95 RVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQM 131 (512)
Q Consensus 95 rlR~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~l 131 (512)
.-... .+++..||.....++..|+....++.+++
T Consensus 74 ~~~~~---~~~~~~f~gs~~~ll~~l~~~~~ls~eel 107 (130)
T TIGR02698 74 ENAAQ---ELFSRICSRKVGAVIADLIEESPLSQTDI 107 (130)
T ss_pred HHHHH---HHHHHHHCCCHHHHHHHHHhcCCCCHHHH
Confidence 22222 34455788888889999999888887664
No 49
>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=89.46 E-value=0.92 Score=32.07 Aligned_cols=42 Identities=26% Similarity=0.322 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+|...|.. |+++..+|+..++++.+.|.+=|-.|...|+|.
T Consensus 5 ~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 5 LRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 356666665 999999999999999999999999999999986
No 50
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.92 E-value=2.8 Score=46.39 Aligned_cols=139 Identities=17% Similarity=0.222 Sum_probs=97.6
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEec--hhhHHHHhchhh
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVL--FDNILHRVRFAK 100 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~--~~~il~rlR~pr 100 (512)
-.|+.....+..+|+.+|...|+++...++..|..|+--+++. -..+ +....| .+.|.+| ......|++++-
T Consensus 611 ~~vfll~n~~e~lt~eei~e~T~l~~~dl~~~L~sl~~ak~~~-l~~~--~~~~~p---~~~fy~ne~f~~~~~rIki~~ 684 (773)
T COG5647 611 LLVFLLFNDHEELTFEEILELTKLSTDDLKRVLQSLSCAKLVV-LLKD--DKLVSP---NTKFYVNENFSSKLERIKINY 684 (773)
T ss_pred HHHHHHhcCccceeHHHHHhhcCCChhhHHHHHHHHHhhheee-eccc--cccCCC---CceEEEccccccccceeeecc
Confidence 3444555556799999999999999999999999999999886 2322 111111 2455566 446777777776
Q ss_pred HHHHHHHH--------hh-----hhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 101 FLTILSQE--------FD-----QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 101 ~l~~i~~~--------~G-----~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
...-.... +. ..-++|+--.=..++++-.++++.+......--..+++.++.++..|++.+||+|..
T Consensus 685 ~~~~~~~q~~~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKeYLeR~~ 764 (773)
T COG5647 685 IAESECMQDNLDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKEYLERQA 764 (773)
T ss_pred cccchhhccchhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 64332222 11 235778888888999999999888765322111247899999999999999999974
No 51
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=88.65 E-value=2.3 Score=35.64 Aligned_cols=63 Identities=11% Similarity=0.187 Sum_probs=50.5
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce-EEEEec-CC--CCCceEEEEEEe
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL-MEKLVV-TG--ARQSQFLLWKVN 436 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~-~QEvpk-~~--~~~~t~~lw~v~ 436 (512)
.+|++.|..++.. .-.+|++...++...+++.+.+|.+.|+|. ..-+.. .. .+...+..|.++
T Consensus 6 ~~il~~L~~~~~~-~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~ 72 (108)
T smart00344 6 RKILEELQKDARI-SLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLE 72 (108)
T ss_pred HHHHHHHHHhCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEEC
Confidence 6899999998888 999999999999999999999999999997 332222 11 344566677777
No 52
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=88.55 E-value=1.8 Score=32.71 Aligned_cols=42 Identities=26% Similarity=0.293 Sum_probs=35.8
Q ss_pred HHHHHHHh-cCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~-~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|..+|-. +++++-.+|+..++++..++|.=|..|.+.|.|.
T Consensus 4 ~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 4 KILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp CHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 35556666 8999999999999999999999999999999997
No 53
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=88.53 E-value=3.7 Score=40.23 Aligned_cols=48 Identities=23% Similarity=0.269 Sum_probs=45.9
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|++-=++|..+|+.+|+.|-.+|++.+++|..+|-..|-.|..-|+|.
T Consensus 14 lt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~ 61 (247)
T COG1378 14 LTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGLVE 61 (247)
T ss_pred CCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEE
Confidence 447889999999999999999999999999999999999999999998
No 54
>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=88.39 E-value=1.4 Score=33.02 Aligned_cols=46 Identities=17% Similarity=0.227 Sum_probs=42.3
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|.--+|...|...|++|..+|++.++++++.+..-|-.|...|+|.
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 6677888999899999999999999999999999999999999997
No 55
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=88.24 E-value=1.3 Score=35.65 Aligned_cols=44 Identities=23% Similarity=0.192 Sum_probs=40.0
Q ss_pred HHHHHHHHHhc-CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 22 VAKVCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 22 v~~V~~~Ll~~-G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+-.|..+|..+ |++|+.+|++.++++.+.|...|-.|.++|++.
T Consensus 7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 45677778777 899999999999999999999999999999997
No 56
>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=88.24 E-value=1 Score=33.69 Aligned_cols=50 Identities=22% Similarity=0.352 Sum_probs=43.2
Q ss_pred chHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEE
Q 010353 370 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKL 420 (512)
Q Consensus 370 ~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEv 420 (512)
+.-.+|++.|...+.+ .-.+|++...+|...+..-|..|.+.|+|.....
T Consensus 10 p~R~~Il~~L~~~~~~-t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 10 PTRLRILRLLASNGPM-TVSELAEELGISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HHHHHHHHHHHHCSTB-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHHhcCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence 4457899999777788 9999999999999999999999999999987654
No 57
>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=87.96 E-value=1.3 Score=32.87 Aligned_cols=43 Identities=19% Similarity=0.274 Sum_probs=40.6
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
..|..+|-.+|.+++.+|+...+.+...||.=|..|.+.|++.
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~ 45 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIK 45 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4678899999999999999999999999999999999999986
No 58
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=86.48 E-value=15 Score=34.37 Aligned_cols=121 Identities=14% Similarity=0.200 Sum_probs=81.5
Q ss_pred hHHHHHHHHHhcCC--CcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhch
Q 010353 21 LVAKVCECLLRKGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRF 98 (512)
Q Consensus 21 ~v~~V~~~Ll~~G~--ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~ 98 (512)
..+.|=.+|+..|. +|+.+|.+.++.+...|+.+|--|.++ |.... .| .--....+-|.+.--
T Consensus 5 ~~~~iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~-----y~~~~-~g---------i~i~~~~~~y~l~tk 69 (188)
T PRK00135 5 YKSIIEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEK-----YEGDD-RG---------LKLIEFNDVYKLVTK 69 (188)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH-----HhhCC-CC---------EEEEEECCEEEEEEc
Confidence 34567778888883 899999999999999999999999775 11110 00 001111222222233
Q ss_pred hhHHHHHHH--------HhhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 99 AKFLTILSQ--------EFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 99 pr~l~~i~~--------~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
|.|-.+++. .+...+-.++..+..+|-+|-.+|.+.-.. + ....+.+|++.|+|..+.
T Consensus 70 ~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv--------~---~~~ii~~L~~~gLI~e~g 135 (188)
T PRK00135 70 EENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGV--------N---SDGALQTLLAKGLIKEVG 135 (188)
T ss_pred HHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCC--------C---HHHHHHHHHHCCCeEEcC
Confidence 333333333 466779999999999999999998765321 1 267899999999998764
No 59
>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=86.21 E-value=2 Score=33.03 Aligned_cols=57 Identities=14% Similarity=0.251 Sum_probs=46.0
Q ss_pred hhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 111 QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 111 ~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
..-+.||..+=..+.++..+|+..+.+.....-..+...++.++..|++.+||.|-+
T Consensus 8 ~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~ 64 (68)
T PF10557_consen 8 QIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDE 64 (68)
T ss_dssp HHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEES
T ss_pred hhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCC
Confidence 446788999999999999999999887654333457889999999999999999975
No 60
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=86.21 E-value=1.5 Score=36.68 Aligned_cols=43 Identities=19% Similarity=0.268 Sum_probs=40.8
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+|...|...|+.|..+|++.+++++..|+..+-.|.+.|++.
T Consensus 6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 4788899999999999999999999999999999999999987
No 61
>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=85.95 E-value=2 Score=31.83 Aligned_cols=46 Identities=20% Similarity=0.169 Sum_probs=40.8
Q ss_pred hhHHHHHHHHHhcCC--CcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 20 DLVAKVCECLLRKGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~--ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+.-..|..+|..+|. +|..+|++.+++++..|-..+--|++.|+|.
T Consensus 5 ~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 5 PSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp HHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 444567888889988 9999999999999999999999999999998
No 62
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=85.43 E-value=6.5 Score=30.96 Aligned_cols=70 Identities=11% Similarity=0.193 Sum_probs=47.1
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhchh
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFA 99 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p 99 (512)
+++..|-..+. .|+.+..+|+..++++++.+...|--|++.|+|. . . ...|.+-..+--.+-.+-
T Consensus 6 ~Ii~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~-~--~-----------~~~Y~lTekG~~~l~~l~ 70 (77)
T PF14947_consen 6 EIIFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIK-K--K-----------DGKYRLTEKGKEFLEELE 70 (77)
T ss_dssp HHHHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEE-E--E-----------TTEEEE-HHHHHHHHHHH
T ss_pred HHHHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCee-C--C-----------CCEEEECccHHHHHHHHH
Confidence 45556666665 7999999999999999999999999999999994 1 1 136777776655555555
Q ss_pred hHHHH
Q 010353 100 KFLTI 104 (512)
Q Consensus 100 r~l~~ 104 (512)
++..+
T Consensus 71 ~~~~~ 75 (77)
T PF14947_consen 71 ELIEL 75 (77)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 54443
No 63
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=85.36 E-value=2.2 Score=36.80 Aligned_cols=46 Identities=24% Similarity=0.275 Sum_probs=43.4
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++.++|.+.+=.+|+.|+.++...||++...++.-+-.|+-.|-|+
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~ 57 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLY 57 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeE
Confidence 5778899999999999999999999999999999999999999886
No 64
>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=85.29 E-value=3.8 Score=38.75 Aligned_cols=63 Identities=17% Similarity=0.251 Sum_probs=51.2
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehH
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 438 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~ 438 (512)
.+|+..|..+|.+ ...+|++...++...++..|..|.+.|+|.-...+.+ .+|..++|++...
T Consensus 4 ~~IL~~L~~~~~~-t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~--~gRp~~~y~LT~~ 66 (203)
T TIGR02702 4 EDILSYLLKQGQA-TAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQG--MGRPQYHYQLSRQ 66 (203)
T ss_pred HHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccC--CCCCceEEEECcc
Confidence 4688889888887 9999999999999999999999999999975544333 3555677777743
No 65
>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=84.62 E-value=3.6 Score=32.83 Aligned_cols=42 Identities=14% Similarity=0.277 Sum_probs=33.9
Q ss_pred HHHHHHHhcC---CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRKG---PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~G---~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++.-+|..++ ++|..+|+..+++|++.+++.|-.|.++|+|.
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIE 56 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeE
Confidence 3444444444 38999999999999999999999999999997
No 66
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=84.55 E-value=1.3 Score=40.83 Aligned_cols=47 Identities=32% Similarity=0.439 Sum_probs=42.5
Q ss_pred hHHHHHHHHHhcC-CCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 371 DAYRIFRLLSKSG-RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 371 ~~~Ri~r~l~~~~-~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
-+.||.-+|..+| +. .-.+|++...|...++-+.||+|++.|.|..-
T Consensus 5 ~~~~i~~~l~~~~~~~-~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 5 CASLILTLLSSSGDKL-PAKRIAKELGISKHEANRCLYRLLESDAVSCE 52 (183)
T ss_pred HHHHHHHHHHhcCCCC-cHHHHHHHhCccHHHHHHHHHHHhhcCcEecC
Confidence 3578999999998 66 99999999999999999999999999999654
No 67
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=84.27 E-value=2.6 Score=38.53 Aligned_cols=43 Identities=19% Similarity=0.310 Sum_probs=41.2
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+|++.|.+.|.. .-.+|++...++...++.-+.+|.+.|+|.
T Consensus 17 ~~IL~~Lq~d~R~-s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 17 RNILNELQKDGRI-SNVELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHhccCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 6799999999999 999999999999999999999999999996
No 68
>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=83.77 E-value=12 Score=30.38 Aligned_cols=63 Identities=14% Similarity=0.210 Sum_probs=45.7
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhc-CCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhH
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYT-ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t-~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (512)
...|...|.. |+..+.+|.+.. +++++.+-..|-.|..+|+|.- .... . .+..+.|.+-..+.
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r-~~~~-~-----~p~~v~Y~LT~~G~ 70 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVER-RVYP-E-----VPPRVEYSLTEKGK 70 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEE-EEES-S-----SSSEEEEEE-HHHH
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhc-cccc-C-----CCCCCccCCCcCHH
Confidence 4456667766 999999999998 8999999999999999999973 2221 1 12246788875543
No 69
>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=83.42 E-value=2.2 Score=31.39 Aligned_cols=50 Identities=20% Similarity=0.400 Sum_probs=43.9
Q ss_pred HHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEec
Q 010353 372 AYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 422 (512)
Q Consensus 372 ~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk 422 (512)
-+.++.+|..+|.+ ...+|++...++...+-.++.+|.+.|||.-+.-|.
T Consensus 5 q~~iL~~l~~~~~~-~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~ 54 (59)
T PF01047_consen 5 QFRILRILYENGGI-TQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPD 54 (59)
T ss_dssp HHHHHHHHHHHSSE-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred HHHHHHHHHHcCCC-CHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCC
Confidence 35788888888888 999999999999999999999999999998877665
No 70
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=83.10 E-value=3.3 Score=35.83 Aligned_cols=54 Identities=15% Similarity=0.249 Sum_probs=47.7
Q ss_pred hhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccccc
Q 010353 109 FDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 109 ~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
.|+.-..||+.+=.+|.+|.+++++.+..+.+. +.+.|+.-+.+|+..|+|.+.
T Consensus 4 Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ew----s~sTV~TLl~RL~KKg~l~~~ 57 (123)
T COG3682 4 ISAAEWEVMEILWSRGPATVREIIEELPADREW----SYSTVKTLLNRLVKKGLLTRK 57 (123)
T ss_pred ccHHHHHHHHHHHHcCCccHHHHHHHHhhcccc----cHHHHHHHHHHHHhccchhhh
Confidence 577788999999999999999999999876443 678899999999999999776
No 71
>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=82.62 E-value=5.9 Score=29.83 Aligned_cols=45 Identities=20% Similarity=0.290 Sum_probs=34.7
Q ss_pred HHHHHH-hcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecc
Q 010353 25 VCECLL-RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (512)
Q Consensus 25 V~~~Ll-~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~ 69 (512)
|-.+|. ..|++|..+|+..++++...|...+-.|+..|+|.-...
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~ 53 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERD 53 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC
Confidence 444555 789999999999999999999999999999999973333
No 72
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=82.51 E-value=2 Score=34.93 Aligned_cols=42 Identities=24% Similarity=0.370 Sum_probs=40.0
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|..+++..++.-+..|++-||+|.-.||.+|-||-|-|++.
T Consensus 18 ~Vl~~v~eeqPiGI~klS~~TGmp~HKVRYSLRVLEq~~iI~ 59 (101)
T COG3388 18 SVLKVVLEEQPIGIIKLSDETGMPEHKVRYSLRVLEQENIIS 59 (101)
T ss_pred HHHHHHHHhCCceeEeechhcCCchhhhhhhhhhhhhcCccC
Confidence 578899999999999999999999999999999999999996
No 73
>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=82.41 E-value=1.8 Score=33.13 Aligned_cols=55 Identities=16% Similarity=0.267 Sum_probs=48.9
Q ss_pred HHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 010353 366 KRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 421 (512)
Q Consensus 366 ~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvp 421 (512)
+..|..|..||++|..+|.+ +-++|.+.+.++.+++--.+-=|.++|=|.+.+..
T Consensus 4 ~~IG~nAG~Vw~~L~~~~~~-s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~ 58 (65)
T PF10771_consen 4 ENIGENAGKVWQLLNENGEW-SVSELKKATGLSDKEVYLAIGWLARENKIEFEEKN 58 (65)
T ss_dssp HHHHHHHHHHHHHHCCSSSE-EHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEET
T ss_pred hHHHHHHHHHHHHHhhCCCc-CHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeC
Confidence 45899999999999998787 99999999999999999999999999999887543
No 74
>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=82.10 E-value=1.6 Score=30.77 Aligned_cols=42 Identities=26% Similarity=0.419 Sum_probs=37.4
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+|+..|.+ |.+ .-.+|++...++...+..-|..|.+.|+|+
T Consensus 5 ~~Il~~L~~-~~~-~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 5 LRILKLLSE-GPL-TVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHTT-SSE-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHh-CCC-chhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 578888877 788 999999999999999999999999999985
No 75
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=81.83 E-value=5.2 Score=36.00 Aligned_cols=47 Identities=13% Similarity=0.039 Sum_probs=43.3
Q ss_pred chHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 010353 370 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 417 (512)
Q Consensus 370 ~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~ 417 (512)
..=.+|++.|...|.. .-.+|++...++...++.-+-+|.+.|+|.-
T Consensus 9 ~~D~~Il~~Lq~d~R~-s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENART-PYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 3456899999999999 9999999999999999999999999999974
No 76
>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=81.64 E-value=3.2 Score=30.70 Aligned_cols=52 Identities=17% Similarity=0.275 Sum_probs=43.7
Q ss_pred chHHHHHHHHHhcCC--CcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEec
Q 010353 370 RDAYRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 422 (512)
Q Consensus 370 ~~~~Ri~r~l~~~~~--l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk 422 (512)
..-++|+..|...+. + ...+|++...++...+-.++.+|.+.|||.-..-|.
T Consensus 5 ~~q~~vL~~l~~~~~~~~-t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~ 58 (62)
T PF12802_consen 5 PSQFRVLMALARHPGEEL-TQSELAERLGISKSTVSRIVKRLEKKGLVERERDPG 58 (62)
T ss_dssp HHHHHHHHHHHHSTTSGE-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SS
T ss_pred HHHHHHHHHHHHCCCCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCC
Confidence 345788889988877 7 999999999999999999999999999997775543
No 77
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=81.28 E-value=2.3 Score=34.21 Aligned_cols=45 Identities=22% Similarity=0.375 Sum_probs=40.6
Q ss_pred hHHHHHHHHHhc-CCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 371 DAYRIFRLLSKS-GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 371 ~~~Ri~r~l~~~-~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+.+|+.+|... +.+ .-.+|++...+|...++..|..|.+.|||.
T Consensus 6 r~~~Il~~l~~~~~~~-t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 6 RGLAVLRALAEEPGGL-TLAELAERLGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHHHHHhCCCCc-CHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 467888988876 566 999999999999999999999999999994
No 78
>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=80.56 E-value=3.7 Score=30.10 Aligned_cols=45 Identities=13% Similarity=0.218 Sum_probs=38.8
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceec
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~ 68 (512)
.|-.+|-.+|++|..+|++..+++++.+-..+--|++.|+|.-..
T Consensus 7 ~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 7 RILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 355667789999999999999999999999999999999998433
No 79
>PHA00738 putative HTH transcription regulator
Probab=79.62 E-value=6.9 Score=32.97 Aligned_cols=60 Identities=17% Similarity=0.071 Sum_probs=48.9
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhH
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (512)
-+|...|...+.++..+|+...+++.+.|-+=|-+|-+-|+|.. ... +...+|+++.+.-
T Consensus 15 r~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~s-rK~---------Gr~vyY~Ln~~~~ 74 (108)
T PHA00738 15 RKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIEL-YKE---------GRTLYAKIRENSK 74 (108)
T ss_pred HHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEE-EEE---------CCEEEEEECCCcc
Confidence 45777777767899999999999999999999999999999983 322 1257999997753
No 80
>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=79.62 E-value=34 Score=29.00 Aligned_cols=66 Identities=9% Similarity=0.109 Sum_probs=50.0
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhh
Q 010353 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDN 91 (512)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~ 91 (512)
++.--.|..+|..+|.+|..+|++.++++...|-..+-.|...|+|.-...+. + .+ ...|.+...+
T Consensus 27 t~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~-D-----~R-~~~v~LT~~G 92 (118)
T TIGR02337 27 TEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASN-D-----QR-RVYISLTPKG 92 (118)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCC-C-----CC-eeEEEECHhH
Confidence 34444688888899999999999999999999999999999999998333332 1 12 3456666544
No 81
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=79.57 E-value=4.2 Score=39.93 Aligned_cols=42 Identities=12% Similarity=0.096 Sum_probs=37.7
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|-++|...+++|+.+|++.+++|.+.+..-|-.|.++|+|.
T Consensus 18 ~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~ 59 (257)
T PRK15090 18 GILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVA 59 (257)
T ss_pred HHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 455566677889999999999999999999999999999997
No 82
>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=78.82 E-value=5.6 Score=29.77 Aligned_cols=35 Identities=31% Similarity=0.436 Sum_probs=33.4
Q ss_pred hcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 31 RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 31 ~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
..+++|..+|+..++++...|...|-.|.+.|+|.
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~ 56 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEEGLIS 56 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 56889999999999999999999999999999997
No 83
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=78.67 E-value=15 Score=35.92 Aligned_cols=73 Identities=16% Similarity=0.158 Sum_probs=57.5
Q ss_pred chHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHHHHHHHHHHH
Q 010353 370 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMF 449 (512)
Q Consensus 370 ~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~~ 449 (512)
.-=++++.-|...|.. +-++|++.+.+|..-+=++|-.|-..|||..| +++.-.+--++++.+.....+++-
T Consensus 16 ~yEa~vY~aLl~~g~~-tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~-------~g~P~~y~av~p~~~i~~~~~~~~ 87 (247)
T COG1378 16 EYEAKVYLALLCLGEA-TAKEISEASGVPRPKVYDVLRSLEKKGLVEVI-------EGRPKKYRAVPPEELIERIKEELQ 87 (247)
T ss_pred HHHHHHHHHHHHhCCc-cHHHHHHHcCCCchhHHHHHHHHHHCCCEEee-------CCCCceEEeCCHHHHHHHHHHHHH
Confidence 3447888899999999 99999999999999999999999999999777 344455666777765555444444
Q ss_pred H
Q 010353 450 H 450 (512)
Q Consensus 450 k 450 (512)
.
T Consensus 88 ~ 88 (247)
T COG1378 88 E 88 (247)
T ss_pred H
Confidence 3
No 84
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=78.25 E-value=3.7 Score=28.91 Aligned_cols=43 Identities=23% Similarity=0.377 Sum_probs=37.7
Q ss_pred HHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 010353 374 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 417 (512)
Q Consensus 374 Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~ 417 (512)
.|++.|..++.+ ...+|++..-++...++..|..|.+.|+|.-
T Consensus 4 ~il~~l~~~~~~-s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 4 QILELLAQQGKV-SVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHHHHHcCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 466777777776 9999999999999999999999999999853
No 85
>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=78.17 E-value=4.7 Score=34.35 Aligned_cols=53 Identities=17% Similarity=0.304 Sum_probs=43.6
Q ss_pred hhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccccc
Q 010353 110 DQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 110 G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
|+.-..||+.|-.+|.++..++.+.+....+ .+...+...+..|++.|||.+-
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~----~~~sTv~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERS----WAYSTVQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS------HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccc----cchhHHHHHHHHHHhCCceeEe
Confidence 5566789999999999999999999865422 3678899999999999999876
No 86
>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=78.14 E-value=40 Score=28.28 Aligned_cols=90 Identities=19% Similarity=0.291 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHhCch--HHHHHHHHH----hcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceE
Q 010353 357 NEEVESVVSKRYGRD--AYRIFRLLS----KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQF 430 (512)
Q Consensus 357 ~~~le~~v~~~~G~~--~~Ri~r~l~----~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~ 430 (512)
-..+.+.+...||-. -++|+.+|. ..|.+ ..++|++...++...+=..+.+|.+.|||.=+.-| ...|.+
T Consensus 10 ~~~~~~~l~~~~~ls~~q~~vL~~l~~~~~~~~~~-t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~---~D~R~~ 85 (109)
T TIGR01889 10 IKSLKRYLKKEFNLSLEELLILYYLGKLENNEGKL-TLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSE---DDERKV 85 (109)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHhhhccCCcC-cHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCc---ccCCeE
Confidence 345556666656543 356777777 44567 99999999999999999999999999999322111 445665
Q ss_pred EEEEEehH-HHHHHHHHHHHH
Q 010353 431 LLWKVNRQ-ILWKHVLDEMFH 450 (512)
Q Consensus 431 ~lw~v~~~-~~~~~~l~~~~k 450 (512)
++.--..- .....+...+++
T Consensus 86 ~i~lT~~G~~~~~~~~~~~~~ 106 (109)
T TIGR01889 86 IISINKEQRSKIESLISEIEQ 106 (109)
T ss_pred EEEECHHHHHHHHHHHHHHHH
Confidence 55433322 233444444443
No 87
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=77.57 E-value=2.3 Score=32.61 Aligned_cols=44 Identities=25% Similarity=0.390 Sum_probs=34.5
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCC--CcccHHHHHHHHhhcccceE
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFV--EKKDAPKILYKLWKDGYLLM 417 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami--~~k~~r~~Ly~L~~~g~v~~ 417 (512)
-+|..+|...|.. .-..++....+ |.|++-..||+|.+.|.|.-
T Consensus 7 e~Il~~L~~~g~~-~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k 52 (66)
T PF02295_consen 7 EKILDFLKELGGS-TATAIAKALGLSVPKKEVNRVLYRLEKQGKVCK 52 (66)
T ss_dssp HHHHHHHHHHTSS-EEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHhcCCc-cHHHHHHHhCcchhHHHHHHHHHHHHHCCCEee
Confidence 4688888888755 66667666665 48999999999999999953
No 88
>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=77.12 E-value=3.8 Score=30.26 Aligned_cols=41 Identities=24% Similarity=0.400 Sum_probs=38.5
Q ss_pred HHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 010353 374 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 415 (512)
Q Consensus 374 Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v 415 (512)
.|+.+|.++|.+ .-+++++.--++...+|.-|..|.+.|+|
T Consensus 4 ~Il~~l~~~~~~-s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 4 QILELLKEKGKV-SVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHcCCE-EHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 588889888888 99999999999999999999999999996
No 89
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=76.82 E-value=36 Score=29.51 Aligned_cols=101 Identities=21% Similarity=0.199 Sum_probs=69.0
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHHh----cCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHH
Q 010353 18 FGDLVAKVCECLLRKGPLTRQNVKRY----TELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNIL 93 (512)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~I~~~----t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il 93 (512)
-|+.=..|-.+|=.+|+.|..+|... ...+++.|+.-|--|..-|+|...... + ...|++..+.--
T Consensus 4 Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdg---------r-~~~y~pL~~~~~ 73 (123)
T COG3682 4 ISAAEWEVMEILWSRGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDG---------R-AFRYSPLLTRDQ 73 (123)
T ss_pred ccHHHHHHHHHHHHcCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhcC---------C-eeeeecccCHHH
Confidence 47777899999999999999999866 458899999999999999999833322 1 357777766543
Q ss_pred HHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHH
Q 010353 94 HRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQ 130 (512)
Q Consensus 94 ~rlR~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~ 130 (512)
++ .+.--.++.+-|+.....++.++..+-.++..+
T Consensus 74 ~~--~~~~~~~l~k~~d~~~~~lv~~F~~~~~l~~~e 108 (123)
T COG3682 74 YV--AGESQDLLDKICDGGLASLVAHFAEKEKLTADE 108 (123)
T ss_pred HH--HHHHHHHHHHHHcccchHHHHHHHHhccCCHHH
Confidence 32 222233344445444555566666655555444
No 90
>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=76.28 E-value=4.8 Score=30.36 Aligned_cols=50 Identities=18% Similarity=0.340 Sum_probs=39.2
Q ss_pred HHHHHHHHH-hcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEec
Q 010353 372 AYRIFRLLS-KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 422 (512)
Q Consensus 372 ~~Ri~r~l~-~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk 422 (512)
-+.|++.|. .++.+ ...+|++...++...+...+.+|.+.|||+-+.-|.
T Consensus 5 q~~vL~~l~~~~~~~-t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~ 55 (68)
T PF13463_consen 5 QWQVLRALAHSDGPM-TQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPH 55 (68)
T ss_dssp HHHHHHHHT--TS-B-EHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred HHHHHHHHHccCCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 356777777 66677 999999999999999999999999999997666554
No 91
>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=76.23 E-value=3.8 Score=32.72 Aligned_cols=47 Identities=26% Similarity=0.272 Sum_probs=38.6
Q ss_pred chHHHHHHHHHhcCC--CcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 370 RDAYRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 370 ~~~~Ri~r~l~~~~~--l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
+-|.|++-.|...+. .+.-++|++..-+|..-+++++.+|.+.|+|.
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIE 56 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeE
Confidence 457888888875543 24999999999999999999999999999983
No 92
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=76.07 E-value=6.5 Score=38.44 Aligned_cols=42 Identities=17% Similarity=0.208 Sum_probs=36.2
Q ss_pred HHHHHHHhcCC-CcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~G~-ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|-.+|...+. +++.+|++.+++|++.+..-|..|+++|+|.
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~ 50 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVE 50 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEE
Confidence 45566665444 5799999999999999999999999999998
No 93
>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=75.99 E-value=5.8 Score=32.66 Aligned_cols=49 Identities=22% Similarity=0.282 Sum_probs=40.8
Q ss_pred hhchhHHHHHHHHH-----------hcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 17 HFGDLVAKVCECLL-----------RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 17 ~FG~~v~~V~~~Ll-----------~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|-++.++++.+|+ ...++|-.+|+..+++++..|..+|-.|.+.|+|.
T Consensus 19 ~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 19 PGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred HhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 35566666666555 35688999999999999999999999999999997
No 94
>PRK06474 hypothetical protein; Provisional
Probab=75.98 E-value=8.1 Score=35.83 Aligned_cols=69 Identities=12% Similarity=0.277 Sum_probs=51.4
Q ss_pred hhHHHHHHHHHhcCC-CcHHHHHHhc-CCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHH
Q 010353 20 DLVAKVCECLLRKGP-LTRQNVKRYT-ELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNIL 93 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~-ltl~~I~~~t-~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il 93 (512)
+.=-+|..+|..+|. +|..+|.... +++...|-.-|-.|..+|+|.......-+| ...-+|.++.+.+-
T Consensus 11 p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~-----~~ek~y~~~~~~~~ 81 (178)
T PRK06474 11 PVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRS-----VSEKYYAINEEDAK 81 (178)
T ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccC-----ceeEEEEeccceee
Confidence 334578888988876 9999999887 799999999999999999998444332111 12357888876643
No 95
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=75.95 E-value=3.7 Score=36.64 Aligned_cols=69 Identities=17% Similarity=0.250 Sum_probs=54.0
Q ss_pred hCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--C--CCceEEEEEEeh
Q 010353 368 YGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--A--RQSQFLLWKVNR 437 (512)
Q Consensus 368 ~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~--~--~~~t~~lw~v~~ 437 (512)
....-.||+++|.+.+.. ...+|++...++...++..+.+|.+.|+|.--.+--.. . +-..|..+.+..
T Consensus 6 lD~~D~~IL~~L~~d~r~-~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~~ 78 (154)
T COG1522 6 LDDIDRRILRLLQEDARI-SNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLER 78 (154)
T ss_pred ccHHHHHHHHHHHHhCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEecC
Confidence 344567899999999998 99999999999999999999999999999666542221 1 112666777665
No 96
>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=75.52 E-value=8 Score=32.10 Aligned_cols=53 Identities=17% Similarity=0.234 Sum_probs=43.5
Q ss_pred hhchhHHHHHHHHHh----cCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceeccc
Q 010353 17 HFGDLVAKVCECLLR----KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (512)
Q Consensus 17 ~FG~~v~~V~~~Ll~----~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~ 70 (512)
.++++-.+|..+|-. .-.+++.+|.+.++++..+||.+|--|+-.|.|+ .+.+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY-sTiD 100 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY-STID 100 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE-ESSS
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe-cccC
Confidence 567888999999987 3357999999999999999999999999999995 5544
No 97
>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=75.50 E-value=7.8 Score=26.76 Aligned_cols=36 Identities=19% Similarity=0.231 Sum_probs=28.3
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHH
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVL 58 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vL 58 (512)
.+|...|...|+.|+.+|.+.+|+++..|..-+--|
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 467888999999999999999999999998766543
No 98
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=75.16 E-value=4.1 Score=29.77 Aligned_cols=42 Identities=21% Similarity=0.329 Sum_probs=36.2
Q ss_pred HHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 010353 374 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 417 (512)
Q Consensus 374 Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~ 417 (512)
+|+++|. .+.. ...+|++...++...++..|.+|.+.|+|..
T Consensus 1 ~il~~l~-~~~~-~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 1 KILKLLA-EGEL-CVCELAEILGLSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred CHHHHhh-cCCc-cHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence 3666766 5566 8899999999999999999999999999963
No 99
>PF05645 RNA_pol_Rpc82: RNA polymerase III subunit RPC82; InterPro: IPR008806 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 entry describes the C-terminal region of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2XV4_S 2XUB_A.
Probab=75.10 E-value=4.5 Score=39.83 Aligned_cols=49 Identities=10% Similarity=0.255 Sum_probs=42.1
Q ss_pred ccEEEechhhHHHHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHH
Q 010353 82 NTQYVVLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQ 130 (512)
Q Consensus 82 ~~~Y~~~~~~il~rlR~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~ 130 (512)
.+++.+|++.....+|--.++.+++.+||..++.|++.+|.....+...
T Consensus 101 ~v~~rvN~erF~~~lRn~~lv~~a~~r~g~~ta~Vy~~~L~~~e~~~~~ 149 (258)
T PF05645_consen 101 DVVWRVNYERFLVHLRNQRLVDLAERRIGSVTAEVYRAMLKLSESKTPS 149 (258)
T ss_dssp TTSEEE-HHHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHCTTTTS-T
T ss_pred CeEEEEEHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHHHhhccccCCc
Confidence 4579999999999999999999999999999999999999998776443
No 100
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=74.04 E-value=8 Score=34.26 Aligned_cols=45 Identities=9% Similarity=0.114 Sum_probs=41.1
Q ss_pred hHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
....|...+-..|..++.+|++..+++++.|...|-.|.+.|+|.
T Consensus 9 yL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 9 YIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 456677778888999999999999999999999999999999997
No 101
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=73.78 E-value=23 Score=28.42 Aligned_cols=49 Identities=18% Similarity=0.309 Sum_probs=42.9
Q ss_pred CchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 369 GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 369 G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
.....+|+.+|...+.+ ..++|++...++...+...+.+|.+.|+|...
T Consensus 9 ~~~~~~il~~l~~~~~~-~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 9 TPTQFLVLRILYEEGPL-SVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred CHHHHHHHHHHHHcCCc-CHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 34457889999888777 99999999999999999999999999999654
No 102
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=73.29 E-value=6.7 Score=35.77 Aligned_cols=49 Identities=16% Similarity=0.251 Sum_probs=43.9
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceec
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~ 68 (512)
++=.+|...|...||.|..+|++.+|++.+.|+.=+--|.+.|++.-|+
T Consensus 14 ~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~ 62 (164)
T PRK11169 14 RIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYT 62 (164)
T ss_pred HHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 3446788999999999999999999999999999999999999997343
No 103
>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=72.34 E-value=12 Score=36.33 Aligned_cols=59 Identities=17% Similarity=0.201 Sum_probs=49.2
Q ss_pred HHHHHHHHHhhhchhHHHHHHHHHh-cCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 7 TKHAVHVITNHFGDLVAKVCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 7 ~~Lc~~iv~~~FG~~v~~V~~~Ll~-~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+++|..-+...==+.+.+|.+.|-. .|+++-.+|+...|++++.|++++-.|.+-|++.
T Consensus 170 Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe 229 (251)
T TIGR02787 170 VQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIE 229 (251)
T ss_pred HHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444444433333778999999999 5999999999999999999999999999999998
No 104
>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=72.20 E-value=59 Score=27.46 Aligned_cols=80 Identities=16% Similarity=0.272 Sum_probs=54.5
Q ss_pred CchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHHHHHHHHHH
Q 010353 369 GRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEM 448 (512)
Q Consensus 369 G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~ 448 (512)
+..-.+|+..|..++.+ ...+|++...++...+-..+.+|.+.|||.-+.-|. ..|. ..+++.. --..+++.+
T Consensus 27 t~~q~~iL~~l~~~~~~-t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~---D~R~-~~v~LT~--~G~~~~~~~ 99 (118)
T TIGR02337 27 TEQQWRILRILAEQGSM-EFTQLANQACILRPSLTGILARLERDGLVTRLKASN---DQRR-VYISLTP--KGQALYASL 99 (118)
T ss_pred CHHHHHHHHHHHHcCCc-CHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCC---CCCe-eEEEECH--hHHHHHHHh
Confidence 44556788888888887 999999999999999999999999999995443222 2343 3344443 233444444
Q ss_pred HHHHHHH
Q 010353 449 FHAALNL 455 (512)
Q Consensus 449 ~k~~~nl 455 (512)
...+...
T Consensus 100 ~~~~~~~ 106 (118)
T TIGR02337 100 SPQIEEI 106 (118)
T ss_pred hHHHHHH
Confidence 4444333
No 105
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=72.02 E-value=24 Score=31.74 Aligned_cols=115 Identities=16% Similarity=0.204 Sum_probs=64.7
Q ss_pred hhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc-eecccCCCC-CC-CCCCCccEEEechhhH
Q 010353 16 NHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ-AFTTEQPDG-FA-DGPKANTQYVVLFDNI 92 (512)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~-~~~~~~~~~-~~-~~~~~~~~Y~~~~~~i 92 (512)
..||.-+-+=.--++..|.+|..+|....|-.. +.||.+|=+-|++. -|..+.+|+ |. ++..+.+...+|..--
T Consensus 12 ~~f~s~~~kkV~~~Ls~~W~T~~El~e~~G~d~---~~~L~~LkK~gLiE~qWrmP~pG~kPeKEYhtsYs~vqaNFqcs 88 (160)
T PF09824_consen 12 QTFNSEVYKKVYDELSKGWMTEEELEEKYGKDV---RESLLILKKGGLIESQWRMPEPGEKPEKEYHTSYSKVQANFQCS 88 (160)
T ss_pred HHhCCHHHHHHHHHHHhccCCHHHHHHHHCcCH---HHHHHHHHHcCchhhccccCCCCCCchHHHHhhHhheeeeeEee
Confidence 467855554444455799999999999887655 89999999999997 244443321 11 1111112222332211
Q ss_pred HHHhchhhHHHHHHHHhh--hhHHHHHHHHHHcccCCHHHHHHHH
Q 010353 93 LHRVRFAKFLTILSQEFD--QQCVELVQGLLEHGRLTLKQMFDRA 135 (512)
Q Consensus 93 l~rlR~pr~l~~i~~~~G--~~a~~Iv~~lL~~G~l~~~~li~~~ 135 (512)
+- =.+.+|..+-.-+. .+.+.-++..+..|..++.++.+.+
T Consensus 89 ~~--DLsdii~i~f~~deel~~~~e~i~~~v~~Gn~Sl~~lsr~l 131 (160)
T PF09824_consen 89 ME--DLSDIIYIAFMSDEELRDYVEKIEKEVEAGNTSLSDLSRKL 131 (160)
T ss_pred HH--HHHHHHheeecCHHHHHHHHHHHHHHHHcCCCcHHHHHHHh
Confidence 11 12333333322222 2233344555566999999987765
No 106
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=72.00 E-value=6.2 Score=29.92 Aligned_cols=55 Identities=15% Similarity=0.154 Sum_probs=35.1
Q ss_pred HhhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccc
Q 010353 108 EFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVE 164 (512)
Q Consensus 108 ~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~ 164 (512)
...+.|..|.+.+ .|..|++++++.+.+..+........++..-+.+|.+.|+|+
T Consensus 14 ~Ln~~a~~Iw~~~--~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 14 TLNETAAFIWELL--DGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp ---THHHHHHHH----SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred cccHHHHHHHHHc--cCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCcC
Confidence 4556677777776 689999999999887654322234678999999999999884
No 107
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=71.66 E-value=11 Score=32.57 Aligned_cols=49 Identities=24% Similarity=0.369 Sum_probs=42.1
Q ss_pred hhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 111 QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 111 ~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
...+.|++-+=+||++|+.|+...... +...++..|.+||..|-|.+..
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGa--------sR~Tvk~~lreLVa~G~l~~~G 60 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGA--------SRNTVKRYLRELVARGDLYRHG 60 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCC--------CHHHHHHHHHHHHHcCCeEeCC
Confidence 447889999999999999999877532 6788999999999999998864
No 108
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=70.92 E-value=41 Score=29.65 Aligned_cols=42 Identities=17% Similarity=0.116 Sum_probs=38.0
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|...|...|++|..+|+...+++++.|-..+-.|.+.|+|.
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~ 85 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVE 85 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 455666678999999999999999999999999999999998
No 109
>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=70.63 E-value=10 Score=27.29 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=37.1
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 421 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvp 421 (512)
.+|+.+|...+..+.-++|++...++...++.-+..|-+.| +.+.-.|
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~-~~I~~~~ 50 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG-IPIESKR 50 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT--EEEEET
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC-CeEEeeC
Confidence 36788886655545999999999999999999999999888 5444433
No 110
>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=70.13 E-value=8.1 Score=28.59 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=35.9
Q ss_pred chhHHHHHHHHHh----cCC--CcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 19 GDLVAKVCECLLR----KGP--LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 19 G~~v~~V~~~Ll~----~G~--ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.++...+...+.. .|. .|..+|++..+++...|+++|..|.+-|+|.
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444555555443 232 3488999999999999999999999999986
No 111
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=69.90 E-value=10 Score=34.04 Aligned_cols=48 Identities=10% Similarity=0.117 Sum_probs=43.8
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhcccccee
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAF 67 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~ 67 (512)
++=.+|...|...||.|..+|++.+|+++..|+.-+-.|...|++.-|
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 455688999999999999999999999999999999999999999744
No 112
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=69.90 E-value=19 Score=35.60 Aligned_cols=42 Identities=17% Similarity=0.166 Sum_probs=36.3
Q ss_pred HHHHHHHhc-CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~-G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|.+++-.. +.+|+.+|++.+++|.+.+..-|..|+++|+|.
T Consensus 29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY 71 (271)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 455555554 568999999999999999999999999999997
No 113
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=69.41 E-value=25 Score=31.04 Aligned_cols=62 Identities=8% Similarity=0.097 Sum_probs=47.6
Q ss_pred hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEe
Q 010353 371 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 436 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~ 436 (512)
.-++|+..|...+.+ .+++|++...+++..+=.++.+|.+.|||.-+.-| ...|..+++--+
T Consensus 41 ~q~~vL~~l~~~~~~-t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~---~DrR~~~l~LT~ 102 (144)
T PRK11512 41 AQFKVLCSIRCAACI-TPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP---NDKRGVLVKLTT 102 (144)
T ss_pred HHHHHHHHHHHcCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc---ccCCeeEeEECh
Confidence 445677777666777 99999999999999999999999999999332222 456766665544
No 114
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=69.38 E-value=8 Score=26.71 Aligned_cols=32 Identities=31% Similarity=0.451 Sum_probs=30.3
Q ss_pred CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 34 ~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+.|..+|++.++++...|...|-.|.++|++.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 56899999999999999999999999999997
No 115
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=69.36 E-value=13 Score=29.43 Aligned_cols=45 Identities=11% Similarity=0.130 Sum_probs=41.4
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceec
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~ 68 (512)
.|-++|-.+|+.++.+|.+..+.|+.-|+.=|-.|+.-|-|....
T Consensus 6 qlRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 6 QVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 577899999999999999999999999999999999999998443
No 116
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=69.13 E-value=5.4 Score=39.15 Aligned_cols=44 Identities=16% Similarity=0.349 Sum_probs=39.8
Q ss_pred hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 010353 371 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 415 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v 415 (512)
.+++|+++|...+.+ .-.+|++...||...+..+|+.|.+.|||
T Consensus 15 r~l~IL~~l~~~~~l-~l~eia~~lgl~kstv~Rll~tL~~~G~l 58 (257)
T PRK15090 15 KVFGILQALGEEREI-GITELSQRVMMSKSTVYRFLQTMKTLGYV 58 (257)
T ss_pred HHHHHHHHhhcCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 467888888776666 99999999999999999999999999998
No 117
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=68.39 E-value=67 Score=30.78 Aligned_cols=121 Identities=7% Similarity=0.003 Sum_probs=88.7
Q ss_pred hc-hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHh
Q 010353 18 FG-DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRV 96 (512)
Q Consensus 18 FG-~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rl 96 (512)
|+ ..=..|.++...+++.++.|+....+++.+..|-=|-+|-.|+.+..+... + . ..||-+|.+-
T Consensus 98 ~~ns~R~~Iy~~i~~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~--g------~-~~yfpa~~t~----- 163 (240)
T COG3398 98 FLNSKRDGIYNYIKPNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVG--G------A-LRYFPADMTY----- 163 (240)
T ss_pred HhhhhHHHHHHHhccCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccC--C------c-eEEccCCCCc-----
Confidence 44 334578999999999999999999999999999999999999999854433 1 1 2233333210
Q ss_pred chhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccc
Q 010353 97 RFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVE 164 (512)
Q Consensus 97 R~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~ 164 (512)
.+ .-+-..=|.....|+.++..++..+...+-.... .+.+.+.=...+|-+-|+|.
T Consensus 164 -~~---~e~~~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l~--------ls~aTV~~~lk~l~~~Gii~ 219 (240)
T COG3398 164 -GE---AEVLSLKNETSKAIIYEIQENKCNTNLLIAYELN--------LSVATVAYHLKKLEELGIIP 219 (240)
T ss_pred -cc---chHHHhhchhHHHHHHHHhcCCcchHHHHHHHcC--------ccHHHHHHHHHHHHHcCCCc
Confidence 00 0022334677899999999999999888766542 36777888889999999873
No 118
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=67.95 E-value=5.7 Score=32.77 Aligned_cols=48 Identities=19% Similarity=0.366 Sum_probs=41.2
Q ss_pred hchhHHHHHHHHHhcCC-CcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 18 FGDLVAKVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 18 FG~~v~~V~~~Ll~~G~-ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|-+---.|.+.|+.+|+ .-+++|.+..+++...|+.++.+|...|++.
T Consensus 19 lk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~ 67 (113)
T COG5625 19 LKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLA 67 (113)
T ss_pred CCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHH
Confidence 33333578999999987 8999999999999999999999999888875
No 119
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=67.79 E-value=14 Score=28.13 Aligned_cols=34 Identities=9% Similarity=0.267 Sum_probs=28.7
Q ss_pred HHHHHH-hcCCCHHHHHHHHHHHHhccccceeccc
Q 010353 37 RQNVKR-YTELSDEQVKNALLVLIQQNCVQAFTTE 70 (512)
Q Consensus 37 l~~I~~-~t~l~~~~Vr~aL~vLIQhn~V~~~~~~ 70 (512)
+.++.. .....++.|++++-.||+-+.+.||...
T Consensus 22 fkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~yWSSG 56 (67)
T PF08679_consen 22 FKDFYKAFPDAKPREVKKIVNELVNEGKLEYWSSG 56 (67)
T ss_dssp HHHHHHH-TTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHCCCcCHHHHHHHHHHHHhhCeEEEEcCC
Confidence 778877 5789999999999999999999988865
No 120
>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=67.51 E-value=9.2 Score=31.47 Aligned_cols=36 Identities=11% Similarity=0.201 Sum_probs=32.1
Q ss_pred cCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 382 SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 382 ~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
...+ .+.+|++.+.++...+.+.|.+|.+.|+|..+
T Consensus 45 ~~~i-s~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 45 QDRV-TATVIAELTGLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred CCcc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence 3456 99999999999999999999999999999643
No 121
>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=67.35 E-value=13 Score=27.67 Aligned_cols=36 Identities=25% Similarity=0.326 Sum_probs=31.1
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHH
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLI 59 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLI 59 (512)
.+...|+..+..|+.+|+..++++.+.|++-+--|-
T Consensus 9 ~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 9 KLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 577889999999999999999999999999887653
No 122
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=67.29 E-value=14 Score=36.43 Aligned_cols=43 Identities=23% Similarity=0.166 Sum_probs=37.4
Q ss_pred HHHHHHHHhcC-CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G-~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
-.|..+|..++ ++++.+|.+.++++.+.+...|-.|.++|+|.
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 34556666665 59999999999999999999999999999997
No 123
>PF13730 HTH_36: Helix-turn-helix domain
Probab=67.22 E-value=8.5 Score=27.79 Aligned_cols=29 Identities=14% Similarity=0.248 Sum_probs=27.2
Q ss_pred cHHHHHHhcCCCHHHHHHHHHHHHhcccc
Q 010353 36 TRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (512)
Q Consensus 36 tl~~I~~~t~l~~~~Vr~aL~vLIQhn~V 64 (512)
+...|+..++++.+.|+.++-.|.++|++
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 68999999999999999999999999975
No 124
>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=67.09 E-value=9.8 Score=33.42 Aligned_cols=75 Identities=15% Similarity=0.039 Sum_probs=52.6
Q ss_pred CchHHHHHHHHHhc--CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHHHHHHHH
Q 010353 369 GRDAYRIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLD 446 (512)
Q Consensus 369 G~~~~Ri~r~l~~~--~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~~~~~l~ 446 (512)
..-|+|++-.|..+ +..+.-++|++..-+|..-++++|.+|.+.|+|..+ ++... -|.+.-+++. .-+.
T Consensus 7 ~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~---~G~~G---gy~l~~~~~~---Itl~ 77 (135)
T TIGR02010 7 GRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSV---RGPGG---GYQLGRPAED---ISVA 77 (135)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE---eCCCC---CEeccCCHHH---CcHH
Confidence 34578888888743 334599999999999999999999999999999542 22211 2555555543 3344
Q ss_pred HHHHHH
Q 010353 447 EMFHAA 452 (512)
Q Consensus 447 ~~~k~~ 452 (512)
+++.++
T Consensus 78 dv~~a~ 83 (135)
T TIGR02010 78 DIIDAV 83 (135)
T ss_pred HHHHHh
Confidence 555554
No 125
>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=66.91 E-value=15 Score=32.12 Aligned_cols=53 Identities=11% Similarity=0.114 Sum_probs=42.9
Q ss_pred hhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccccc
Q 010353 110 DQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 110 G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
++.-..||..|-.+|.+++.++.+.+....+ .+...+...+..|.+.|||.+.
T Consensus 3 t~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~----~~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 3 SDAEWEVMRVVWTLGETTSRDIIRILAEKKD----WSDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred CHHHHHHHHHHHcCCCCCHHHHHHHHhhccC----CcHHHHHHHHHHHHHCCceeee
Confidence 4455678888889999999999988764322 2577899999999999999765
No 126
>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=66.25 E-value=12 Score=30.39 Aligned_cols=62 Identities=10% Similarity=0.098 Sum_probs=39.4
Q ss_pred HHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHH
Q 010353 26 CECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNIL 93 (512)
Q Consensus 26 ~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il 93 (512)
...|+.+|.-+++.|...||+|.+.++.+|..|--.++.--|..+... ...-||.+.-=+++
T Consensus 13 la~li~~~~~nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~~Fvq~G~R------~~~GyY~i~~WG~i 74 (90)
T PF09904_consen 13 LAYLIDSGERNVPALMEATGMPRRTIQDTIKALPELGIECEFVQDGER------NNAGYYRISDWGPI 74 (90)
T ss_dssp HHHHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS-------S--EEEEEE-TTB
T ss_pred HHHHHhcCCccHHHHHHHhCCCHhHHHHHHHHhhcCCeEEEEEecCcc------CCCCcEEeeecCCC
Confidence 356888888899999999999999999999999999987766653211 11348888744444
No 127
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=66.10 E-value=6.4 Score=36.53 Aligned_cols=44 Identities=27% Similarity=0.385 Sum_probs=37.2
Q ss_pred HHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 374 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 374 Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
++...|...++. .-.+|++...|+.+++-..||+|++.|.|..-
T Consensus 17 ~~~~~l~~~~~~-~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~ 60 (183)
T PHA03103 17 KEVKNLGLGEGI-TAIEISRKLNIEKSEVNKQLYKLQREGMVYMS 60 (183)
T ss_pred HHHHHhccCCCc-cHHHHHHHhCCCHHHHHHHHHHHHhcCceecC
Confidence 355566665666 99999999999999999999999999999543
No 128
>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=66.05 E-value=10 Score=28.49 Aligned_cols=45 Identities=22% Similarity=0.303 Sum_probs=38.6
Q ss_pred hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 010353 371 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 417 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~ 417 (512)
....|+..+...+ . ..++|++...++...++..|..|...|+|.-
T Consensus 8 ~~~~il~~l~~~~-~-~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 8 TRLRILRLLLEGP-L-TVSELAERLGLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred HHHHHHHHHHHCC-c-CHHHHHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence 4466777777765 5 9999999999999999999999999999953
No 129
>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=65.63 E-value=18 Score=27.02 Aligned_cols=45 Identities=18% Similarity=0.248 Sum_probs=38.3
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
...|+..--..+..+..+|++..+++++.|-..|-.|...|+|.|
T Consensus 10 L~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~ 54 (60)
T PF01325_consen 10 LKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEY 54 (60)
T ss_dssp HHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEe
Confidence 345566666778999999999999999999999999999999984
No 130
>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=65.62 E-value=8.5 Score=33.44 Aligned_cols=51 Identities=18% Similarity=0.200 Sum_probs=43.0
Q ss_pred HhCchHHHHHHHHHhc-CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 010353 367 RYGRDAYRIFRLLSKS-GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 417 (512)
Q Consensus 367 ~~G~~~~Ri~r~l~~~-~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~ 417 (512)
+..+-|.|++..|... +..+.-++|++...+|..-++++|..|.+.|+|.-
T Consensus 6 ~~~~yal~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 6 KLTDYATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred hHHhHHHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 3456788999998764 34449999999999999999999999999999944
No 131
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=65.39 E-value=26 Score=30.64 Aligned_cols=52 Identities=12% Similarity=0.174 Sum_probs=44.9
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceeccc
Q 010353 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (512)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~ 70 (512)
.-|-.-.....+..+++.++.++++.++=..+.|...|..|+..|+|. |..+
T Consensus 62 Lsp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~-fe~~ 113 (144)
T COG4190 62 LSPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIF-FEED 113 (144)
T ss_pred hChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEE-EecC
Confidence 344455667788889999999999999999999999999999999998 6653
No 132
>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=65.37 E-value=7.7 Score=32.22 Aligned_cols=48 Identities=13% Similarity=0.213 Sum_probs=36.3
Q ss_pred hCchHHHHHHHHHh----cCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 368 YGRDAYRIFRLLSK----SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 368 ~G~~~~Ri~r~l~~----~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+...-+||++|.. ...+ .-++|++..-++.+++|+.|..|..+|+|.
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv-~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGV-HVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTE-EHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHhcCCCCCcc-cHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 34445567777766 2234 778899999999999999999999999984
No 133
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=65.24 E-value=8 Score=38.34 Aligned_cols=46 Identities=20% Similarity=0.182 Sum_probs=39.8
Q ss_pred hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 371 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+.+|+++|...+.-+.-.+|++...||...+..+|..|.+.|||.
T Consensus 26 r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 26 RGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY 71 (271)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4567888887665434999999999999999999999999999993
No 134
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=65.21 E-value=1.2e+02 Score=28.30 Aligned_cols=62 Identities=15% Similarity=0.105 Sum_probs=48.4
Q ss_pred HHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEeh
Q 010353 372 AYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNR 437 (512)
Q Consensus 372 ~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~ 437 (512)
-++|+-+|..++.+ .+++|++...++...+-.++.+|-+.|||.-+.-| ...|..+++--+.
T Consensus 47 q~~iL~~L~~~~~i-tq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~---~DrR~~~I~LTek 108 (185)
T PRK13777 47 EHHILWIAYHLKGA-SISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKE---DDKRNTYIELTEK 108 (185)
T ss_pred HHHHHHHHHhCCCc-CHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCC---CCCCeeEEEECHH
Confidence 34778778777777 99999999999999999999999999999432222 4567777766553
No 135
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=65.15 E-value=6.8 Score=27.08 Aligned_cols=32 Identities=19% Similarity=0.308 Sum_probs=29.9
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 387 ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 387 eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
..++|++...++...+.+.|.+|.+.|+|..+
T Consensus 10 s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 10 TRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 78899999999999999999999999999654
No 136
>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=64.82 E-value=28 Score=29.18 Aligned_cols=52 Identities=12% Similarity=0.162 Sum_probs=42.2
Q ss_pred HHhhhchhHH--HHHHHHH----hcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 14 ITNHFGDLVA--KVCECLL----RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 14 v~~~FG~~v~--~V~~~Ll----~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++..||-... .|..+|. ..|++|..+|+..++++++.|-..+-.|.+.|+|.
T Consensus 17 l~~~~~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 17 LKKEFNLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred HHHHcCCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence 4445564443 4566666 55889999999999999999999999999999997
No 137
>PRK11569 transcriptional repressor IclR; Provisional
Probab=64.76 E-value=8.2 Score=38.35 Aligned_cols=46 Identities=7% Similarity=0.270 Sum_probs=39.8
Q ss_pred hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 371 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+++|+++|.+.+.-+.-.+|++...+|...+..+|..|.+.|||.
T Consensus 29 ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 29 RGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4677888887654434999999999999999999999999999994
No 138
>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=64.58 E-value=18 Score=30.51 Aligned_cols=50 Identities=26% Similarity=0.407 Sum_probs=40.3
Q ss_pred HHHHHHHH-cccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 115 ELVQGLLE-HGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 115 ~Iv~~lL~-~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
.|++.|.. .++++++++.+.+....+ ..+...+-.++..|++.|+|.++.
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~---~i~~~TVYR~L~~L~~~Gli~~~~ 55 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGP---SISLATVYRTLELLEEAGLVREIE 55 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCC---CCCHHHHHHHHHHHHhCCCEEEEE
Confidence 46777776 468999999999865422 347888999999999999999985
No 139
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=64.45 E-value=17 Score=28.95 Aligned_cols=48 Identities=23% Similarity=0.255 Sum_probs=39.5
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 421 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvp 421 (512)
..|+-+|...+.+ +-++|.+...++.......|..|.++|||+.....
T Consensus 3 l~Il~~L~~~~~~-~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~ 50 (80)
T PF13601_consen 3 LAILALLYANEEA-TFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEF 50 (80)
T ss_dssp HHHHHHHHHHSEE-EHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-
T ss_pred HHHHHHHhhcCCC-CHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEec
Confidence 3577788887788 99999999999999999999999999999876543
No 140
>PRK11569 transcriptional repressor IclR; Provisional
Probab=64.38 E-value=16 Score=36.23 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=35.4
Q ss_pred HHHHHHh-cCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 25 VCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 25 V~~~Ll~-~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|-++|.. .+++|+.+|++.+++|.+.|..-|..|.++|+|.
T Consensus 33 IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 33 LLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3344444 4679999999999999999999999999999997
No 141
>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=64.01 E-value=9 Score=28.76 Aligned_cols=32 Identities=19% Similarity=0.252 Sum_probs=28.5
Q ss_pred CC-cHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 34 PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 34 ~l-tl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++ +..+|++..+++...|+.||-.|.+-|+|.
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 56 789999999999999999999999999997
No 142
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=63.78 E-value=8.9 Score=37.80 Aligned_cols=45 Identities=16% Similarity=0.307 Sum_probs=40.6
Q ss_pred hHHHHHHHHHhcCC-CcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 371 DAYRIFRLLSKSGR-LLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~-l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+.+|+++|..++. + ...+|++...+|...+..+|..|.+.|||.
T Consensus 12 ral~iL~~l~~~~~~l-s~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 12 RGLMVLRALNRLDGGA-TVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHHHHhcCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 57889999977655 6 999999999999999999999999999994
No 143
>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=63.67 E-value=8.3 Score=37.61 Aligned_cols=46 Identities=15% Similarity=0.258 Sum_probs=39.9
Q ss_pred hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 371 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+.+|++++...+.-+.-.+|++...+|...+..+|..|.+.|||.
T Consensus 10 ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 10 RGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 5778888887644333999999999999999999999999999995
No 144
>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=63.63 E-value=13 Score=29.69 Aligned_cols=34 Identities=12% Similarity=0.171 Sum_probs=31.0
Q ss_pred hHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHH
Q 010353 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (512)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL 55 (512)
-...|...|.. |..|+.+|++.+|++...|+.+|
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 45678899999 99999999999999999999966
No 145
>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=63.60 E-value=12 Score=28.02 Aligned_cols=43 Identities=23% Similarity=0.342 Sum_probs=36.2
Q ss_pred HHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 375 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 375 i~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
||++-. .+..+..++|++..-+++..+-+.+.+|.+.|||..+
T Consensus 13 Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 13 IYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence 666665 4555599999999999999999999999999999765
No 146
>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=63.59 E-value=12 Score=36.40 Aligned_cols=41 Identities=27% Similarity=0.305 Sum_probs=35.3
Q ss_pred HHHHHHh-cCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 25 VCECLLR-KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 25 V~~~Ll~-~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|-+++.. .+++++.+|++.+++|.+.+..-|..|.++|+|.
T Consensus 14 IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 14 VIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3344443 5679999999999999999999999999999996
No 147
>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=63.09 E-value=14 Score=28.34 Aligned_cols=48 Identities=17% Similarity=0.288 Sum_probs=39.1
Q ss_pred HHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEec
Q 010353 374 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVV 422 (512)
Q Consensus 374 Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk 422 (512)
.|..+|..+|.. +-.+|+...-+++..++..|-.|.+.|+|.-.+.+.
T Consensus 4 ~i~~~l~~~~~~-S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 4 EIRDYLRERGRV-SLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHHHS-SE-EHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 466778888777 999999999999999999999999999998776655
No 148
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=62.98 E-value=9.5 Score=37.32 Aligned_cols=91 Identities=18% Similarity=0.146 Sum_probs=61.8
Q ss_pred hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHHHHHHHHH--H
Q 010353 371 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDE--M 448 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~~~~~l~~--~ 448 (512)
+|++|+.+|........-.+|++...+|...++.+|..|.+.|||.- +..+.+|+|.--- -.+-...+.. +
T Consensus 5 ral~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~------d~~~g~Y~Lg~~~-~~lg~~~l~~~~l 77 (246)
T COG1414 5 RALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQ------DPEDGRYRLGPRL-LELGAAALSSLDL 77 (246)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEE------cCCCCcEeehHHH-HHHHHHHHhcCCH
Confidence 57889999987544237999999999999999999999999999922 1112334443222 2233444443 7
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q 010353 449 FHAALNLSLRVSYELDREKE 468 (512)
Q Consensus 449 ~k~~~nl~~R~~~e~~~~k~ 468 (512)
.+.+.-.+.++..+......
T Consensus 78 ~~~a~p~l~~L~~~tgetv~ 97 (246)
T COG1414 78 VSLARPLLEELAEETGETVH 97 (246)
T ss_pred HHHhHHHHHHHHHHhCCcEE
Confidence 77777777777776664443
No 149
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=62.61 E-value=18 Score=33.57 Aligned_cols=46 Identities=17% Similarity=0.308 Sum_probs=42.8
Q ss_pred hhHHHHHHHHHhcC-CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 20 DLVAKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G-~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+..++|+.+|-++| ++|..+|.+..+++.+.|=..|.-|.+-+.|.
T Consensus 4 ~~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~ 50 (183)
T PHA02701 4 DCASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESDAVS 50 (183)
T ss_pred hHHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEe
Confidence 34678999999999 89999999999999999999999999999996
No 150
>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=62.39 E-value=22 Score=27.04 Aligned_cols=46 Identities=17% Similarity=0.301 Sum_probs=38.1
Q ss_pred hhHHHHHHHHHhcC-CCcHHHHHHhcCCC-HHHHHHHHHHHHhccccc
Q 010353 20 DLVAKVCECLLRKG-PLTRQNVKRYTELS-DEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G-~ltl~~I~~~t~l~-~~~Vr~aL~vLIQhn~V~ 65 (512)
++-..|..+...+| +-|+.+|++..+++ ++.|..-|-.|..-|++.
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 45566778888888 45799999999997 999999999999999997
No 151
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=62.34 E-value=12 Score=27.03 Aligned_cols=33 Identities=24% Similarity=0.259 Sum_probs=30.4
Q ss_pred CCC-cHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 33 GPL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 33 G~l-tl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+++ |..+|++..+++...|+.+|-.|.+.|+|.
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 356 799999999999999999999999999986
No 152
>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=61.24 E-value=18 Score=26.97 Aligned_cols=56 Identities=27% Similarity=0.285 Sum_probs=40.0
Q ss_pred chhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 97 RFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 97 R~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
|...|+...-+.+|. ....++.++..++.+.+.- +...+...+..|.+.|+|...+
T Consensus 4 ria~~l~~l~~~~~~-------~~~~~~~~s~~ela~~~g~--------s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 4 RLASFLLNLSLRYGA-------GDLVQLPLTRQEIADYLGL--------TRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHHHHHHHHHHHcCC-------CccccCCcCHHHHHHHHCC--------CHHHHHHHHHHHHHCCCEEecC
Confidence 334455544455664 2335788898888877642 6778999999999999998874
No 153
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=61.00 E-value=12 Score=37.00 Aligned_cols=50 Identities=24% Similarity=0.296 Sum_probs=43.7
Q ss_pred HHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC
Q 010353 375 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG 424 (512)
Q Consensus 375 i~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~ 424 (512)
|+.++..+|.-+.|.+|.+...+|...+-.+|.+|-+.|+|+.+..-+++
T Consensus 200 il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n 249 (258)
T COG2512 200 ILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTN 249 (258)
T ss_pred HHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCee
Confidence 66677788876699999999999999999999999999999888665554
No 154
>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=60.66 E-value=13 Score=32.32 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=38.6
Q ss_pred hHHHHHHHHHhc--CCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 371 DAYRIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 371 ~~~Ri~r~l~~~--~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.|.+++-.|... +..+.-++|++..-+|...++++|..|.+.|+|.
T Consensus 9 ~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~ 56 (132)
T TIGR00738 9 YALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVE 56 (132)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 467777777653 2245999999999999999999999999999984
No 155
>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=60.25 E-value=21 Score=30.94 Aligned_cols=34 Identities=21% Similarity=0.232 Sum_probs=32.0
Q ss_pred CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 33 G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
++.+..+|++..++|++.|.+.|-.|.+.|+|..
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 5789999999999999999999999999999973
No 156
>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=60.24 E-value=17 Score=34.31 Aligned_cols=48 Identities=21% Similarity=0.173 Sum_probs=43.2
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
..+.-..|...|..+|..++.+|++.++++++.+.+-|-.|.+.|+|.
T Consensus 141 ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~ 188 (203)
T TIGR01884 141 LSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVE 188 (203)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 345556888888888999999999999999999999999999999998
No 157
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=59.62 E-value=1.2e+02 Score=26.48 Aligned_cols=63 Identities=6% Similarity=0.055 Sum_probs=46.0
Q ss_pred chHHHHHHHHHhcC-CCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEe
Q 010353 370 RDAYRIFRLLSKSG-RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 436 (512)
Q Consensus 370 ~~~~Ri~r~l~~~~-~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~ 436 (512)
..-+.++..|...+ .. .+.+|++...++...+-.++.+|.+.|||+-..-| ...|..+++--+
T Consensus 31 ~~q~~vL~~l~~~~~~~-t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~---~DrR~~~l~LT~ 94 (144)
T PRK03573 31 QTHWVTLHNIHQLPPEQ-SQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCA---SDRRAKRIKLTE 94 (144)
T ss_pred HHHHHHHHHHHHcCCCC-CHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCC---CCcCeeeeEECh
Confidence 33445677776544 46 89999999999999999999999999999433222 446666655444
No 158
>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=58.75 E-value=28 Score=30.45 Aligned_cols=33 Identities=18% Similarity=0.275 Sum_probs=31.4
Q ss_pred CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 33 G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++.|..+|+..+++|+.-+++.|-.|.+.|+|.
T Consensus 24 ~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~ 56 (135)
T TIGR02010 24 GPVTLADISERQGISLSYLEQLFAKLRKAGLVK 56 (135)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceE
Confidence 468999999999999999999999999999997
No 159
>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=58.17 E-value=33 Score=29.64 Aligned_cols=33 Identities=18% Similarity=0.338 Sum_probs=31.6
Q ss_pred CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 33 G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++.|..+|+..+++|++.|++.|-.|.+.|+|.
T Consensus 24 ~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~ 56 (132)
T TIGR00738 24 GPVSVKEIAERQGISRSYLEKILRTLRRAGLVE 56 (132)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 489999999999999999999999999999997
No 160
>PRK11050 manganese transport regulator MntR; Provisional
Probab=57.26 E-value=25 Score=31.55 Aligned_cols=42 Identities=14% Similarity=0.201 Sum_probs=37.7
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|...+...|..+..+|++.++++++.|...|-.|.+.|+|.
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~ 82 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVE 82 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 455566677999999999999999999999999999999886
No 161
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=57.07 E-value=25 Score=32.74 Aligned_cols=47 Identities=21% Similarity=0.203 Sum_probs=44.1
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
=++|-+++..|-..|..|..+|.+..+++.+.|=..|..|.+-+.|.
T Consensus 12 ~~lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~ 58 (183)
T PHA03103 12 YELVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVY 58 (183)
T ss_pred HHHHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCcee
Confidence 36788999999999999999999999999999999999999999996
No 162
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=57.02 E-value=61 Score=29.49 Aligned_cols=117 Identities=14% Similarity=0.162 Sum_probs=73.6
Q ss_pred HHHHHHHhcC-CCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhchhhHH
Q 010353 24 KVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFL 102 (512)
Q Consensus 24 ~V~~~Ll~~G-~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~pr~l 102 (512)
.|=..|+..| ++++.+|.+.++ +...|+.+|--|.+.- .... . ..--....+-+.+.--|.|-
T Consensus 2 ~iEAlLF~s~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y-----~~~~-~---------gl~l~~~~~~y~l~tk~~~~ 65 (159)
T PF04079_consen 2 IIEALLFASGEPVSIEELAEILG-SEDEVEEALEELQEEY-----NEED-R---------GLELVEVGGGYRLQTKPEYA 65 (159)
T ss_dssp HHHHHHHH-SS-B-HHHHHHHCT--HHHHHHHHHHHHHHH-----HHCT-----------SEEEEEETTEEEEEE-GGGH
T ss_pred hhHhhHHHcCCCCCHHHHHHHhC-CHHHHHHHHHHHHHHh-----ccCC-C---------CEEEEEECCEEEEEEhHHHH
Confidence 3445677775 899999999999 9999999999998753 2111 1 12223334444444556666
Q ss_pred HHHHHHhh--------hhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 103 TILSQEFD--------QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 103 ~~i~~~~G--------~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
.++++.++ ..+-+++..+..++=+|-.+|-+-= .. .-...+.+|.+.|||..+.
T Consensus 66 ~~v~~~~~~~~~~~LS~aalEtLAiIAY~QPiTr~eIe~IR-Gv----------~s~~~i~~L~e~glI~~~g 127 (159)
T PF04079_consen 66 EYVEKLFKKPKPPKLSQAALETLAIIAYKQPITRAEIEEIR-GV----------NSDSVIKTLLERGLIEEVG 127 (159)
T ss_dssp HHHHHHHCTCCCHHHHHHHHHHHHHHHHH-SEEHHHHHHHH-TS------------HCHHHHHHHTTSEEEEE
T ss_pred HHHHHHhccCccCCCCHHHHHHHHHHHhcCCcCHHHHHHHc-CC----------ChHHHHHHHHHCCCEEecC
Confidence 66665555 4577777778888888877764331 10 1456789999999998885
No 163
>PRK09462 fur ferric uptake regulator; Provisional
Probab=56.80 E-value=27 Score=31.06 Aligned_cols=54 Identities=15% Similarity=0.212 Sum_probs=43.1
Q ss_pred hhHHHHHHHHHHc--ccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 111 QQCVELVQGLLEH--GRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 111 ~~a~~Iv~~lL~~--G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
..=..|++.|..+ +++++.+|.+.+....+ ..+...|-.++..|++.|+|.++.
T Consensus 17 ~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~---~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGE---EIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHCCCEEEEE
Confidence 4456677777763 69999999999865433 347888999999999999999875
No 164
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=56.76 E-value=48 Score=28.58 Aligned_cols=62 Identities=16% Similarity=0.224 Sum_probs=47.0
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHHhcC-CCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEec
Q 010353 19 GDLVAKVCECLLRKGPLTRQNVKRYTE-LSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVL 88 (512)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~I~~~t~-l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~ 88 (512)
|.-..-|...|.. |..-+.+|.+..+ ++++-+-+.|-.|.++|+|.- ...++ .+..++|++-
T Consensus 22 ~kW~~lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R-~~~~~------~PprveY~LT 84 (120)
T COG1733 22 GKWTLLILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVER-VVYPE------EPPRVEYRLT 84 (120)
T ss_pred CccHHHHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEe-eecCC------CCceeEEEEh
Confidence 3555667777776 9999999999977 999999999999999999982 22211 1225788775
No 165
>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=56.22 E-value=44 Score=28.08 Aligned_cols=46 Identities=24% Similarity=0.278 Sum_probs=37.8
Q ss_pred HHHHHHHhc-CCCcHHHHHHhc-----CCCHHHHHHHHHHHHhccccceecc
Q 010353 24 KVCECLLRK-GPLTRQNVKRYT-----ELSDEQVKNALLVLIQQNCVQAFTT 69 (512)
Q Consensus 24 ~V~~~Ll~~-G~ltl~~I~~~t-----~l~~~~Vr~aL~vLIQhn~V~~~~~ 69 (512)
.|..+|... +.+|..+|.... +++...|-.+|-.|.+.|+|.-...
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 577777764 579999998775 6899999999999999999985443
No 166
>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=56.15 E-value=16 Score=34.45 Aligned_cols=50 Identities=16% Similarity=0.245 Sum_probs=42.9
Q ss_pred hCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 368 YGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 368 ~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
......+|+..|..+|.. ..++|++...++...++..|.+|.+.|+|.-.
T Consensus 141 ls~~~~~IL~~l~~~g~~-s~~eia~~l~is~stv~r~L~~Le~~GlI~r~ 190 (203)
T TIGR01884 141 LSREELKVLEVLKAEGEK-SVKNIAKKLGKSLSTISRHLRELEKKGLVEQK 190 (203)
T ss_pred CCHHHHHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 344456788888877787 99999999999999999999999999999754
No 167
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=56.05 E-value=99 Score=26.42 Aligned_cols=55 Identities=9% Similarity=0.194 Sum_probs=44.1
Q ss_pred CCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHH
Q 010353 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNIL 93 (512)
Q Consensus 34 ~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il 93 (512)
..||.+|+....-+.+.+|.-|--|.+.|.+. |++....| +++......+++.++
T Consensus 19 ~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~-W~pg~GRG----~~S~L~~l~~~~~~~ 73 (115)
T PF12793_consen 19 EVTLDELAELLFCSRRNARTLLKKMQEEGWIT-WQPGRGRG----NRSQLTFLKSPEELL 73 (115)
T ss_pred ceeHHHHHHHhCCCHHHHHHHHHHHHHCCCee-eeCCCCCC----CCCeeEEeeCHHHHH
Confidence 56999999999999999999999999999998 78765444 455556666666544
No 168
>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=56.04 E-value=21 Score=34.65 Aligned_cols=48 Identities=27% Similarity=0.250 Sum_probs=42.6
Q ss_pred HHHHHHHHh-cCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 010353 373 YRIFRLLSK-SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 421 (512)
Q Consensus 373 ~Ri~r~l~~-~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvp 421 (512)
-+|++.|.. .|.+ .+.+|++...++..-+|+.+-+|-..|+|+.+..-
T Consensus 186 ~~IL~~L~~~egrl-se~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG 234 (251)
T TIGR02787 186 EHIFEELDGNEGLL-VASKIADRVGITRSVIVNALRKLESAGVIESRSLG 234 (251)
T ss_pred HHHHHHhccccccc-cHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence 568899987 4788 99999999999999999999999999999776533
No 169
>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=55.62 E-value=23 Score=26.88 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=35.6
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++... +..|..+..+|+...+++.+.|++.+..|-+.|+..
T Consensus 4 ~il~~-L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 4 RLLAL-LADNPFSGEKLGEALGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred HHHHH-HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 45555 457788999999999999999999999999999875
No 170
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=55.46 E-value=34 Score=26.50 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=26.8
Q ss_pred CCCcHHHHHHh---cCCCHHHHHHHHHHHHhccccc
Q 010353 33 GPLTRQNVKRY---TELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 33 G~ltl~~I~~~---t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|.++...|+.. .+++...||.||.-|.+.|.+.
T Consensus 19 ~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~ 54 (70)
T PF07848_consen 19 GWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLE 54 (70)
T ss_dssp S-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEE
T ss_pred CceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCcee
Confidence 57788888776 6799999999999999999997
No 171
>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=55.36 E-value=23 Score=26.50 Aligned_cols=36 Identities=17% Similarity=0.248 Sum_probs=30.5
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 383 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 383 ~~l~-eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
|..+ .+.+|++.-.++...+|+.|..|..+|+|+..
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence 5555 99999999999999999999999999999654
No 172
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=54.94 E-value=27 Score=30.94 Aligned_cols=49 Identities=12% Similarity=0.231 Sum_probs=43.9
Q ss_pred hHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecc
Q 010353 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (512)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~ 69 (512)
+=.+|-..|...|+.|+.+|++..++|++.|+.=+--|...|++.-|+.
T Consensus 9 ~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~ 57 (154)
T COG1522 9 IDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTA 57 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEE
Confidence 3457888999999999999999999999999999999999998885554
No 173
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=54.66 E-value=32 Score=30.72 Aligned_cols=54 Identities=24% Similarity=0.351 Sum_probs=43.9
Q ss_pred hhHHHHHHHHHHc-ccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 111 QQCVELVQGLLEH-GRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 111 ~~a~~Iv~~lL~~-G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
+.=..|++.|..+ |++++.++.+.+....+ ..+.+.|-+++..|.+.|+|.++.
T Consensus 21 ~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p---~islaTVYr~L~~l~e~Glv~~~~ 75 (145)
T COG0735 21 PQRLAVLELLLEADGHLSAEELYEELREEGP---GISLATVYRTLKLLEEAGLVHRLE 75 (145)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhCC---CCCHhHHHHHHHHHHHCCCEEEEE
Confidence 4456788888866 77999999999876433 357889999999999999999974
No 174
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=54.41 E-value=1.2e+02 Score=28.36 Aligned_cols=46 Identities=13% Similarity=0.201 Sum_probs=41.4
Q ss_pred HhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 367 RYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 367 ~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
++...++.++.++.-++-. +..+|++.-.++. -.++.+|.+.|+|.
T Consensus 87 ~LS~aaLEtLaiIay~qPi-Tr~eI~~irGv~~---~~ii~~L~~~gLI~ 132 (188)
T PRK00135 87 SLSQAALEVLAIIAYKQPI-TRIEIDEIRGVNS---DGALQTLLAKGLIK 132 (188)
T ss_pred CCCHHHHHHHHHHHHcCCc-CHHHHHHHHCCCH---HHHHHHHHHCCCeE
Confidence 6888899999999998777 9999999999885 78999999999994
No 175
>PRK10870 transcriptional repressor MprA; Provisional
Probab=52.36 E-value=1.2e+02 Score=27.75 Aligned_cols=49 Identities=8% Similarity=-0.067 Sum_probs=38.6
Q ss_pred hhchhHH--HHHHHHHh--cCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 17 HFGDLVA--KVCECLLR--KGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 17 ~FG~~v~--~V~~~Ll~--~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+|-..+ .|...|.. .|++|..+|++..++++..|-..+-.|.+.|+|.
T Consensus 50 ~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~ 102 (176)
T PRK10870 50 AQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIE 102 (176)
T ss_pred HCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4553333 34444443 3568999999999999999999999999999998
No 176
>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=52.04 E-value=41 Score=24.08 Aligned_cols=39 Identities=18% Similarity=0.296 Sum_probs=33.3
Q ss_pred HHHHHHH-hcCCCcHHHHHHhcCCCHHHHHHHHHHHHhcc
Q 010353 24 KVCECLL-RKGPLTRQNVKRYTELSDEQVKNALLVLIQQN 62 (512)
Q Consensus 24 ~V~~~Ll-~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn 62 (512)
+|...|+ ..++.|..+|+..++++.+.|++-|-.|-..+
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 5677784 55679999999999999999999999998888
No 177
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=52.04 E-value=35 Score=30.39 Aligned_cols=49 Identities=22% Similarity=0.263 Sum_probs=37.2
Q ss_pred hhchhHHHHHHHHHhcCCCcHHHHHHhcC-C----CHHHHHHHHHHHHhcc--ccc
Q 010353 17 HFGDLVAKVCECLLRKGPLTRQNVKRYTE-L----SDEQVKNALLVLIQQN--CVQ 65 (512)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~-l----~~~~Vr~aL~vLIQhn--~V~ 65 (512)
.|.+--..|...|+-||++|..+|..+++ | +...|...|--|++++ +|.
T Consensus 85 ~l~~~e~All~~LlLRGpQT~GELR~Rs~Rl~~F~d~~~Ve~~L~~L~~r~~plV~ 140 (148)
T PF04337_consen 85 QLSPQELALLCLLLLRGPQTPGELRTRSERLHEFADVAEVEAVLERLAEREPPLVV 140 (148)
T ss_dssp T--HHHHHHHHHHHHH-SB-HHHHHHHHTTTS--SSHHHHHHHHHHHHHTT--SEE
T ss_pred CCCHHHHHHHHHHHHcCCCchhHHHhhhccccCCCCHHHHHHHHHHHHhccchhhe
Confidence 45566677888899999999999976654 2 6789999999999999 664
No 178
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=51.87 E-value=1.6e+02 Score=27.96 Aligned_cols=54 Identities=13% Similarity=0.181 Sum_probs=42.8
Q ss_pred cCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHHHH
Q 010353 382 SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWK 442 (512)
Q Consensus 382 ~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~~~ 442 (512)
-|.-+.|.+|++.-.++..=+|+.|.+|..+|+|... |.+-++.=.++...+..
T Consensus 36 pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~-------p~rG~~V~~~~~~~~~e 89 (230)
T COG1802 36 PGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIE-------PNRGAFVAPLSLAEARE 89 (230)
T ss_pred CCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEec-------CCCCCeeCCCCHHHHHH
Confidence 3544499999999999999999999999999999665 44456666666665554
No 179
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=51.52 E-value=1.1e+02 Score=27.91 Aligned_cols=59 Identities=10% Similarity=0.204 Sum_probs=41.1
Q ss_pred HhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEE
Q 010353 367 RYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFL 431 (512)
Q Consensus 367 ~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~ 431 (512)
++...++.++-++.-+.-. +..+|.+.=..+ +...+.+|.+.|+|. ++.+...|+|.+.
T Consensus 79 ~LS~aalEtLAiIAY~QPi-Tr~eIe~IRGv~---s~~~i~~L~e~glI~--~~gr~~~~Grp~l 137 (159)
T PF04079_consen 79 KLSQAALETLAIIAYKQPI-TRAEIEEIRGVN---SDSVIKTLLERGLIE--EVGRKDTPGRPIL 137 (159)
T ss_dssp HHHHHHHHHHHHHHHH-SE-EHHHHHHHHTS-----HCHHHHHHHTTSEE--EEEE-TTTT--EE
T ss_pred CCCHHHHHHHHHHHhcCCc-CHHHHHHHcCCC---hHHHHHHHHHCCCEE--ecCcCCCCCCCeE
Confidence 6667788888888877555 999999888776 778899999999993 3344435777654
No 180
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=51.36 E-value=1.7e+02 Score=25.58 Aligned_cols=41 Identities=5% Similarity=0.050 Sum_probs=36.0
Q ss_pred HHHHHHhc-CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 25 VCECLLRK-GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 25 V~~~Ll~~-G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|-..|... +.+|..+|++.++++++.|-..+-.|.+.|+|.
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~ 77 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLIS 77 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEe
Confidence 45556555 468999999999999999999999999999998
No 181
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=51.35 E-value=22 Score=31.40 Aligned_cols=48 Identities=19% Similarity=0.350 Sum_probs=37.7
Q ss_pred hHHHHHHHHHh--cCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 371 DAYRIFRLLSK--SGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 371 ~~~Ri~r~l~~--~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
-|.|..=.+.. .|..+.+++|++...+|..-+|++|.+|.++|+|...
T Consensus 9 YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~ 58 (141)
T PRK11014 9 YGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAV 58 (141)
T ss_pred HHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEe
Confidence 34555544432 3455699999999999999999999999999999444
No 182
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=51.32 E-value=33 Score=27.94 Aligned_cols=34 Identities=29% Similarity=0.315 Sum_probs=29.4
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHH
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALL 56 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~ 56 (512)
.+.|...|-.+|- ||..|.+..|++.+.+++||.
T Consensus 10 ~adI~AaL~KrG~-sLa~lsr~~Gls~~TL~nAL~ 43 (92)
T PRK10344 10 PADIIAGLRKKGT-SMAAESRRNGLSSSTLANALS 43 (92)
T ss_pred HHHHHHHHHHcCC-cHHHHHHHcCCChHHHHHHHc
Confidence 3567788888886 999999999999999999874
No 183
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=50.86 E-value=54 Score=30.11 Aligned_cols=66 Identities=20% Similarity=0.155 Sum_probs=48.5
Q ss_pred HHHHHHHHHH--HHhCc--hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 010353 356 QNEEVESVVS--KRYGR--DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 421 (512)
Q Consensus 356 r~~~le~~v~--~~~G~--~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvp 421 (512)
++..++.+-+ .+||. -..+|+-+|.-..+-+.-++|++...|+..-+=..+-+|...|+|+.+-.|
T Consensus 8 k~~~Ie~fae~m~r~G~nrtVG~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~ 77 (177)
T COG1510 8 KDIFIEHFAETMSRWGINRTVGQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEK 77 (177)
T ss_pred HHHHHHHHHHHHHHhCCcchHHHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhcc
Confidence 3334444333 45554 345677777654444499999999999999999999999999999777666
No 184
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=50.61 E-value=2.1e+02 Score=26.62 Aligned_cols=47 Identities=6% Similarity=0.041 Sum_probs=41.5
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceeccc
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~ 70 (512)
..|-.+|..+|.+|..+|++.+.++.+.|-..|-.|...|+|. ...+
T Consensus 48 ~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~-R~~~ 94 (185)
T PRK13777 48 HHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLT-FSKK 94 (185)
T ss_pred HHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEE-ecCC
Confidence 3677888888999999999999999999999999999999998 4433
No 185
>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=50.58 E-value=28 Score=24.14 Aligned_cols=31 Identities=19% Similarity=0.291 Sum_probs=22.3
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHH
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL 55 (512)
..|.. |+..| .|+.+|++.++++...|...|
T Consensus 12 ~~i~~-l~~~G-~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 12 EEIKE-LYAEG-MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp HHHHH-HHHTT---HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHH-HHHCC-CCHHHHHHHHCcCHHHHHHHH
Confidence 34444 77888 899999999999999988754
No 186
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=50.56 E-value=62 Score=26.45 Aligned_cols=60 Identities=20% Similarity=0.117 Sum_probs=45.5
Q ss_pred HHHHHHHHhc--CCCcHHHHHHhcCCCHHHHHHHHH----------HHHhccccceecccCCCCCCCCCCCccEEEechh
Q 010353 23 AKVCECLLRK--GPLTRQNVKRYTELSDEQVKNALL----------VLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFD 90 (512)
Q Consensus 23 ~~V~~~Ll~~--G~ltl~~I~~~t~l~~~~Vr~aL~----------vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~ 90 (512)
.+|..+|... .+.++.+|++.++.+++.|+-||. .|+..|+|...... .+ ..+|.+...
T Consensus 12 ~~vl~~L~~~yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~-~g--------~k~Y~lT~~ 82 (90)
T PF07381_consen 12 KKVLEYLCSIYPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEK-GG--------FKYYRLTEK 82 (90)
T ss_pred HHHHHHHHHcCCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeec-CC--------eeEEEeChh
Confidence 5678888887 355688999999999999999996 69999999422322 11 358888765
Q ss_pred h
Q 010353 91 N 91 (512)
Q Consensus 91 ~ 91 (512)
+
T Consensus 83 G 83 (90)
T PF07381_consen 83 G 83 (90)
T ss_pred h
Confidence 4
No 187
>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=50.18 E-value=26 Score=29.28 Aligned_cols=50 Identities=20% Similarity=0.387 Sum_probs=43.9
Q ss_pred HHHHHHHHHHhCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 358 EEVESVVSKRYGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 358 ~~le~~v~~~~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.++..+++..||-. ++...+...|+++.+.++...+.+.+..|.+.|+|.
T Consensus 36 ki~~ai~RkTyG~n---------Kk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~ 85 (100)
T PF04492_consen 36 KILLAIIRKTYGWN---------KKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVII 85 (100)
T ss_pred HHHHHHHHHccCCC---------CccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 56778888888876 555666999999999999999999999999999993
No 188
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=50.16 E-value=28 Score=28.57 Aligned_cols=46 Identities=22% Similarity=0.190 Sum_probs=39.4
Q ss_pred chHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 370 RDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 370 ~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
+....|+..|.+-|-= -.+.|+....+|..+++..|-+|.+.|+|+
T Consensus 7 ~l~~~IL~hl~~~~~D-y~k~ia~~l~~~~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 7 PLDLKILQHLKKAGPD-YAKSIARRLKIPLEEVREALEKLEEMGLLE 52 (92)
T ss_pred hhHHHHHHHHHHHCCC-cHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 4567788888776655 778899999999999999999999999994
No 189
>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=49.90 E-value=55 Score=24.91 Aligned_cols=49 Identities=14% Similarity=0.196 Sum_probs=35.5
Q ss_pred HHHHHHHHHHcccCC-HHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccCC
Q 010353 113 CVELVQGLLEHGRLT-LKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 168 (512)
Q Consensus 113 a~~Iv~~lL~~G~l~-~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~~ 168 (512)
-..|.+.+-.+|... ..+|.+.+.- .|...+...+..|.+.|||.+.|.
T Consensus 12 L~~I~~~~~~~G~~Pt~rEIa~~~g~-------~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 12 LEFIREYIEENGYPPTVREIAEALGL-------KSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp HHHHHHHHHHHSS---HHHHHHHHTS-------SSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCC-------CChHHHHHHHHHHHHCcCccCCCC
Confidence 345666677788775 5677666532 268889999999999999999863
No 190
>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=49.72 E-value=46 Score=28.82 Aligned_cols=48 Identities=15% Similarity=0.196 Sum_probs=38.5
Q ss_pred CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhH
Q 010353 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (512)
Q Consensus 33 G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (512)
.+-|..+|+..++-+...|+.||.+|.+.|++. ...+ .++|-.++.+.
T Consensus 52 ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe-~~ed-----------~~i~i~~~~~~ 99 (121)
T PF09681_consen 52 IPYTAEMLALEFDRPVDTVRLALAVFQKLGLIE-IDED-----------GVIYIPNWEKH 99 (121)
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EecC-----------CeEEeecHHHH
Confidence 366778888999999999999999999999998 4333 25777777654
No 191
>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=49.49 E-value=58 Score=25.42 Aligned_cols=41 Identities=20% Similarity=0.166 Sum_probs=35.5
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|-.+| +++.+|+.+|...|+++.+.+--.|.-|...|++.
T Consensus 9 ~IL~~l-s~~c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~ 49 (72)
T PF05584_consen 9 KILIIL-SKRCCTLEELEEKTGISKNTLLVYLSRLAKRGIIE 49 (72)
T ss_pred HHHHHH-HhccCCHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 444444 45599999999999999999999999999999997
No 192
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=49.45 E-value=24 Score=32.93 Aligned_cols=44 Identities=9% Similarity=-0.006 Sum_probs=41.0
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
=..|...|..+|..++.+|++..+.|...||.=|..|-+.|.|.
T Consensus 9 ~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~ 52 (185)
T PRK04424 9 QKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRE 52 (185)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHH
Confidence 35788899999999999999999999999999999999999887
No 193
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=49.13 E-value=36 Score=36.36 Aligned_cols=42 Identities=24% Similarity=0.339 Sum_probs=37.1
Q ss_pred HHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceec
Q 010353 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (512)
Q Consensus 25 V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~ 68 (512)
...+++..|+.|..+|+..++++...|-+-|.+| .++|....
T Consensus 4 ~~~~~L~~g~~~~~eL~~~l~~sq~~~s~~L~~L--~~~V~~~~ 45 (442)
T PRK09775 4 LLTTLLLQGPLSAAELAARLGVSQATLSRLLAAL--GDQVVRFG 45 (442)
T ss_pred HHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHHh--hcceeEec
Confidence 4567888999999999999999999999999999 88887433
No 194
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=48.99 E-value=29 Score=34.11 Aligned_cols=44 Identities=18% Similarity=0.372 Sum_probs=41.1
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
=.+|...|-.+|+.++.+|++.++.+...||.=|-.|-+.|+|.
T Consensus 7 ~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~ 50 (256)
T PRK10434 7 QAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVI 50 (256)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 35788999999999999999999999999999999999999886
No 195
>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=48.49 E-value=79 Score=24.69 Aligned_cols=44 Identities=20% Similarity=0.086 Sum_probs=38.3
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHH--Hhccccc
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVL--IQQNCVQ 65 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vL--IQhn~V~ 65 (512)
=+.|...|...+.-|+.+|+..|+-.+-.||-+|.-+ =+.|+..
T Consensus 12 qa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i 57 (72)
T PF11994_consen 12 QAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTI 57 (72)
T ss_pred HHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEE
Confidence 3678889999999999999999999999999999999 5556554
No 196
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.32 E-value=30 Score=30.58 Aligned_cols=32 Identities=13% Similarity=0.079 Sum_probs=30.5
Q ss_pred CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 34 ~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
..+..+|+...++|+.-|+++|..|.++|+|.
T Consensus 25 ~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~ 56 (141)
T PRK11014 25 MTSISEVTEVYGVSRNHMVKIINQLSRAGYVT 56 (141)
T ss_pred ccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEE
Confidence 56889999999999999999999999999998
No 197
>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=48.04 E-value=29 Score=28.07 Aligned_cols=47 Identities=21% Similarity=0.345 Sum_probs=37.9
Q ss_pred HHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 113 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 113 a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
...|+..|.. |..+.+++.+.+.. .+...+.+.+..|.++|+|.+..
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l~~-------is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRLPG-------ISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHSTT-------S-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHh-CCCcHHHHHHhcch-------hHHHHHHHHHHHHHHcchhhccc
Confidence 4566777776 99999999888643 26778999999999999999974
No 198
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=47.92 E-value=63 Score=26.87 Aligned_cols=91 Identities=15% Similarity=0.210 Sum_probs=64.1
Q ss_pred HHhCchH--HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEE-ehHHHHH
Q 010353 366 KRYGRDA--YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKV-NRQILWK 442 (512)
Q Consensus 366 ~~~G~~~--~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v-~~~~~~~ 442 (512)
+..|-+. .||+++|..++.-+--.+|+-.-.|+.-.+|..+..|++.||+.=.=| ..+|--|.|.- .++....
T Consensus 15 ~~~glk~~eI~IY~lLve~~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relv----qkgWvGYiya~~~P~k~le 90 (113)
T COG5625 15 EAIGLKKNEIRIYSLLVEKGRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELV----QKGWVGYIYATTPPPKPLE 90 (113)
T ss_pred HHcCCCcchhhhhhHHHHhcCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHH----hccceeeEecCCCCchHHH
Confidence 3456666 899999998876338899999999999999999999999999931111 45666666654 4555556
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 010353 443 HVLDEMFHAALNLSLRVS 460 (512)
Q Consensus 443 ~~l~~~~k~~~nl~~R~~ 460 (512)
.+-+++.+++..+-.-.+
T Consensus 91 ei~~~i~keiEelEk~~k 108 (113)
T COG5625 91 EIEEEIMKEIEELEKEFK 108 (113)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 665566555554443333
No 199
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=47.83 E-value=1.6e+02 Score=24.25 Aligned_cols=51 Identities=16% Similarity=0.155 Sum_probs=42.9
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceec
Q 010353 18 FGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (512)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~ 68 (512)
+++.-..|..+|...|..+..+|....+++++.|-..+-.|.+.|+|.-..
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~ 70 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLR 70 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence 445566677777888887779999999999999999999999999998333
No 200
>PRK09954 putative kinase; Provisional
Probab=47.74 E-value=20 Score=36.96 Aligned_cols=43 Identities=14% Similarity=0.325 Sum_probs=39.6
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+|+++|.+.+.. ...+|++..-++...+++.+.+|.++|+|.
T Consensus 6 ~~il~~l~~~~~~-s~~~la~~l~~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 6 KEILAILRRNPLI-QQNEIADILQISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHHCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence 3689999988777 999999999999999999999999999984
No 201
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=47.47 E-value=32 Score=33.74 Aligned_cols=43 Identities=16% Similarity=0.239 Sum_probs=40.7
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+|...|-.+|.+++.+|++..+++...||.=|..|-+.|++.
T Consensus 8 ~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~ 50 (252)
T PRK10906 8 DAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 5788899999999999999999999999999999999999986
No 202
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=46.31 E-value=46 Score=26.40 Aligned_cols=52 Identities=13% Similarity=0.151 Sum_probs=40.4
Q ss_pred hhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccc
Q 010353 110 DQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVE 164 (512)
Q Consensus 110 G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~ 164 (512)
.+.|..|.+.+ .|.-|+++|+..+.+..+. ......++.+-+.+|.+.|+|.
T Consensus 30 n~~g~~Iw~ll--dg~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~L~~~gli~ 81 (81)
T TIGR03859 30 NDSAGEILELC--DGKRSLAEIIQELAQRFPA-AEEIEDDVIAFLAVARAKHWLE 81 (81)
T ss_pred ChHHHHHHHHc--cCCCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHHHHHCcCcC
Confidence 46677777765 7788999999998887665 3345678888899999999873
No 203
>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=45.71 E-value=34 Score=23.57 Aligned_cols=36 Identities=19% Similarity=0.374 Sum_probs=30.0
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHH
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKL 409 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L 409 (512)
.+|++.|...+.. .-.+|++...++...++.-+.+|
T Consensus 6 ~~Il~~Lq~d~r~-s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRR-SYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCc-cHHHHHHHHCcCHHHHHHHHHHh
Confidence 5799999999999 99999999999999999888776
No 204
>PRK09462 fur ferric uptake regulator; Provisional
Probab=45.28 E-value=80 Score=28.04 Aligned_cols=50 Identities=14% Similarity=0.062 Sum_probs=40.3
Q ss_pred hhHHHHHHHHHhc--CCCcHHHHHHh-----cCCCHHHHHHHHHHHHhccccceecc
Q 010353 20 DLVAKVCECLLRK--GPLTRQNVKRY-----TELSDEQVKNALLVLIQQNCVQAFTT 69 (512)
Q Consensus 20 ~~v~~V~~~Ll~~--G~ltl~~I~~~-----t~l~~~~Vr~aL~vLIQhn~V~~~~~ 69 (512)
+-=..|..+|... +.+|..+|... .++++..|-.+|-.|.+.|+|.-+..
T Consensus 17 ~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~ 73 (148)
T PRK09462 17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNF 73 (148)
T ss_pred HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEc
Confidence 4445788899863 69999999765 35889999999999999999975543
No 205
>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=45.16 E-value=36 Score=26.63 Aligned_cols=45 Identities=11% Similarity=0.070 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhcccc
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V 64 (512)
+.+..++...-....+|..+|++.+++|++.|+.-+..+.+.+.+
T Consensus 18 ~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 18 SLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 445555555544477899999999999999999999888877754
No 206
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=45.07 E-value=18 Score=33.80 Aligned_cols=85 Identities=13% Similarity=0.246 Sum_probs=39.9
Q ss_pred hHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhchhh
Q 010353 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAK 100 (512)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~pr 100 (512)
+......++-.+--++|.+|+...+|+...+.+-+-.|...|.+.=...+ . |+
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~Dd--r-------------------------Gk 152 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDD--R-------------------------GK 152 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-T--T---------------------------
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcC--C-------------------------CC
Confidence 67778889999999999999999999999999999999999988622211 1 44
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHh
Q 010353 101 FLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAK 136 (512)
Q Consensus 101 ~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~ 136 (512)
||++-.+.+ ..|...+-+.||+++++|...+.
T Consensus 153 fIyIs~eE~----~~va~fi~~rGRvsi~el~~~~N 184 (188)
T PF09756_consen 153 FIYISEEEM----EAVAKFIKQRGRVSISELAQESN 184 (188)
T ss_dssp EEE---------------------------------
T ss_pred eEEecHHHH----HHHHHHHHHcCCccHHHHHHHHH
Confidence 555555555 34556677899999999887653
No 207
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=44.90 E-value=35 Score=30.64 Aligned_cols=57 Identities=21% Similarity=0.131 Sum_probs=46.8
Q ss_pred HhCchHHHHHHHHHhcCC--CcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecC
Q 010353 367 RYGRDAYRIFRLLSKSGR--LLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVT 423 (512)
Q Consensus 367 ~~G~~~~Ri~r~l~~~~~--l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~ 423 (512)
..|.-|.+++=.|..+.. .+.-++|++.-.+|+.=.++++.+|-+.|+|+-..=|++
T Consensus 5 ~~~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~G 63 (150)
T COG1959 5 SKGEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGG 63 (150)
T ss_pred hhHhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCC
Confidence 346678888888876543 668999999999999999999999999999977654443
No 208
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=44.53 E-value=2e+02 Score=24.55 Aligned_cols=105 Identities=13% Similarity=0.173 Sum_probs=78.3
Q ss_pred HHHHHHHHHhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEE
Q 010353 7 TKHAVHVITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYV 86 (512)
Q Consensus 7 ~~Lc~~iv~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~ 86 (512)
-++...+=.-...--+|....||...+-.+=.+|-+.+||-.+.|--|+--|-..|-|.--..-..|. +++.-.|.
T Consensus 14 ~~~ie~L~~lgi~R~vA~tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gWV~~R~eKKkGK----GRPik~Y~ 89 (124)
T COG4738 14 YEIIELLRILGIPRNVATTLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENGWVDEREEKKKGK----GRPIKLYR 89 (124)
T ss_pred HHHHHHHHHcCCCchHHHHHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccccchHHhcccCC----CCCceEEE
Confidence 34455554445567788889999999999999999999999999999999999999998433322222 34456787
Q ss_pred echhhHHHHhchhhHHHHHHHHhhhhHHHHHHHHHH
Q 010353 87 VLFDNILHRVRFAKFLTILSQEFDQQCVELVQGLLE 122 (512)
Q Consensus 87 ~~~~~il~rlR~pr~l~~i~~~~G~~a~~Iv~~lL~ 122 (512)
+-. -|+.++..+.+.+-.+...|+.++=.
T Consensus 90 Lt~-------~~~eIvs~iee~~~ke~k~i~~~ier 118 (124)
T COG4738 90 LTV-------PFDEIVSEIEEEIIKESKEIIYNIER 118 (124)
T ss_pred ecC-------cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 663 36778888888888888777776644
No 209
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=44.43 E-value=30 Score=31.59 Aligned_cols=50 Identities=16% Similarity=0.145 Sum_probs=41.1
Q ss_pred CchHHHHHHHHHhc--CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 369 GRDAYRIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 369 G~~~~Ri~r~l~~~--~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
..-|+|++-.|..+ +..+.-++|++...+|.+-++++|.+|.+.|+|.-+
T Consensus 7 ~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 7 GRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 34577888777633 335599999999999999999999999999999643
No 210
>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=44.19 E-value=84 Score=26.18 Aligned_cols=33 Identities=24% Similarity=0.380 Sum_probs=30.9
Q ss_pred CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 33 G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+.|..++...|++++..|..++-.|+.-|++.
T Consensus 53 d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~ 85 (100)
T PF04492_consen 53 DRISNSQIAEMTGLSRDHVSKALNELIRRGVII 85 (100)
T ss_pred ceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 378999999999999999999999999999995
No 211
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=44.07 E-value=78 Score=26.00 Aligned_cols=50 Identities=22% Similarity=0.270 Sum_probs=43.7
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecc
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTT 69 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~ 69 (512)
|+.-.|...|-..|+=.-.-|++.++++...|+..|--|.+-|+|..+..
T Consensus 7 ~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 7 PLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred hhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 45567888888889888889999999999999999999999999996654
No 212
>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=43.69 E-value=1.1e+02 Score=23.71 Aligned_cols=49 Identities=16% Similarity=0.155 Sum_probs=39.2
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC--CCCceEEEEEE
Q 010353 387 ETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG--ARQSQFLLWKV 435 (512)
Q Consensus 387 eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~--~~~~t~~lw~v 435 (512)
.+.++++...++++.+-..+-.|.+.|+|.=|.++... ...+|..+|.-
T Consensus 20 ~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~~~~~~~~~~~t~ll~l~ 70 (75)
T PF04182_consen 20 TQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSVISSSNSKGTRTNLLHLK 70 (75)
T ss_pred ehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEeccccCCCceEEEEEEEe
Confidence 88899999999999999999999999999999995322 44555555543
No 213
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=43.51 E-value=29 Score=27.26 Aligned_cols=40 Identities=23% Similarity=0.311 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 010353 374 RIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 415 (512)
Q Consensus 374 Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v 415 (512)
.|+..+. +|.. .-.+|+..+-++.+.+.+.|..|.+.|+|
T Consensus 10 ~IL~~l~-~~~~-~~t~i~~~~~L~~~~~~~yL~~L~~~gLI 49 (77)
T PF14947_consen 10 DILKILS-KGGA-KKTEIMYKANLNYSTLKKYLKELEEKGLI 49 (77)
T ss_dssp HHHHHH--TT-B--HHHHHTTST--HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHH-cCCC-CHHHHHHHhCcCHHHHHHHHHHHHHCcCe
Confidence 4555554 5677 88999999999999999999999999999
No 214
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=43.38 E-value=3.4e+02 Score=29.45 Aligned_cols=112 Identities=10% Similarity=0.083 Sum_probs=78.2
Q ss_pred HHHHHHHHHhcCC-CcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhchhh
Q 010353 22 VAKVCECLLRKGP-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAK 100 (512)
Q Consensus 22 v~~V~~~Ll~~G~-ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~pr 100 (512)
-.+|-..|...|. .+..+|+..++++...|..++..|-..|+|.. .... ...|.+..++--
T Consensus 5 e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~-~~~~----------~~~~~LT~eG~~------- 66 (492)
T PLN02853 5 EEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDA-QDIK----------RETWVLTEEGKK------- 66 (492)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE-EEEE----------EEEEEECHHHHH-------
Confidence 4567777877785 89999999999999999999999999999983 3321 467888766521
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccccc
Q 010353 101 FLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 101 ~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
+++ =|.--+.|+..|-..|.+.++++...+. ...+.-+|-.+.+.|||..-
T Consensus 67 ---~l~--~G~PE~rl~~~l~~~~~~~~~eL~~~l~----------~~~~~i~~g~a~k~gwi~i~ 117 (492)
T PLN02853 67 ---YAA--EGSPEVQLFAAVPAEGSISKDELQKKLD----------PAVFDIGFKQAMKNKWLEMG 117 (492)
T ss_pred ---HHH--cCCHHHHHHHHHhhcCCccHHHHHHhhC----------chhHHHHHHHHHHCCcEEEC
Confidence 111 2434455555555557778888765431 12466788888889988663
No 215
>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=43.31 E-value=19 Score=26.49 Aligned_cols=31 Identities=13% Similarity=0.177 Sum_probs=28.7
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 010353 387 ETDKISDTTFVEKKDAPKILYKLWKDGYLLM 417 (512)
Q Consensus 387 eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~ 417 (512)
...+|++...++...+++.|.+|.+.|+|..
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 4889999999999999999999999999853
No 216
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=42.92 E-value=50 Score=25.99 Aligned_cols=33 Identities=30% Similarity=0.374 Sum_probs=28.4
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHH
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALL 56 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~ 56 (512)
+.|...|-.+|. ||..|.+..|++++.++++|.
T Consensus 11 adI~A~Lkk~G~-Sl~~LS~~agls~~tL~n~L~ 43 (82)
T COG3423 11 ADIIAALKKKGT-SLAALSREAGLSSSTLANALD 43 (82)
T ss_pred HHHHHHHHHccc-cHHHHHHHcCCCHHHHHHHHc
Confidence 556777877787 999999999999999999874
No 217
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=42.85 E-value=33 Score=31.01 Aligned_cols=43 Identities=26% Similarity=0.365 Sum_probs=36.9
Q ss_pred HHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 375 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 375 i~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
|+.+...+|.. -.++||+..-+++..+.+.+.+|.+.|||...
T Consensus 15 Iy~l~~~~~~~-~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~ 57 (154)
T COG1321 15 IYELLEEKGFA-RTKDIAERLKVSPPSVTEMLKRLERLGLVEYE 57 (154)
T ss_pred HHHHHhccCcc-cHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEe
Confidence 55566666666 99999999999999999999999999999553
No 218
>PF13730 HTH_36: Helix-turn-helix domain
Probab=42.82 E-value=20 Score=25.72 Aligned_cols=29 Identities=10% Similarity=0.282 Sum_probs=27.8
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccc
Q 010353 387 ETDKISDTTFVEKKDAPKILYKLWKDGYL 415 (512)
Q Consensus 387 eek~i~~~ami~~k~~r~~Ly~L~~~g~v 415 (512)
+.++|++.+.++.+.+++.+..|.+.|||
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 78999999999999999999999999986
No 219
>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=42.01 E-value=27 Score=26.84 Aligned_cols=33 Identities=24% Similarity=0.427 Sum_probs=30.7
Q ss_pred CcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 385 LLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 385 l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
+ ..++||+.+.++...+-.+|.+|.++|+|+.+
T Consensus 29 l-t~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 29 L-TQEEIADMLGVSRETVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp S-SHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred C-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEc
Confidence 5 89999999999999999999999999999743
No 220
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=41.95 E-value=64 Score=31.12 Aligned_cols=51 Identities=20% Similarity=0.279 Sum_probs=46.7
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCC
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTG 424 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~ 424 (512)
.+|+.+|..||-+ .-.+|++...+|...+-.-+..|-+.|+|+..-+|-..
T Consensus 26 v~Il~lL~~k~pl-NvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~kark 76 (308)
T COG4189 26 VAILQLLHRKGPL-NVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVKARK 76 (308)
T ss_pred HHHHHHHHHhCCC-CHHHHHHHhCCchhhhhhhHHHHHhcCceeeeeecccc
Confidence 6789999999889 99999999999999999999999999999998887654
No 221
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=41.65 E-value=90 Score=26.68 Aligned_cols=61 Identities=15% Similarity=0.282 Sum_probs=47.9
Q ss_pred cchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHHHHHHHHHH
Q 010353 386 LETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEM 448 (512)
Q Consensus 386 ~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~ 448 (512)
+.-.+||+..--+.+-||.+|-+|.+.|.|.-|.=+- =.+++..-|.++++.+....+.++
T Consensus 20 vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg~G--RG~~S~L~~l~~~~~~~~~~~~~~ 80 (115)
T PF12793_consen 20 VTLDELAELLFCSRRNARTLLKKMQEEGWITWQPGRG--RGNRSQLTFLKSPEELLEQQAEEL 80 (115)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCCCC--CCCCCeeEEeeCHHHHHHHHHHHH
Confidence 3778999999999999999999999999997763222 246778888899887765555443
No 222
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=41.41 E-value=45 Score=31.69 Aligned_cols=49 Identities=14% Similarity=0.115 Sum_probs=37.9
Q ss_pred hhchhHHHHHHHHHhcC-CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 17 HFGDLVAKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G-~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.|..+-..|.+-=+.-| ++|-.+|+...|+|..-||.||..|.+-|+|.
T Consensus 12 vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~ 61 (224)
T PRK11534 12 GYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVT 61 (224)
T ss_pred HHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 33344444444434445 77889999999999999999999999999998
No 223
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=41.31 E-value=93 Score=27.70 Aligned_cols=48 Identities=25% Similarity=0.252 Sum_probs=38.4
Q ss_pred HHHHHHHHhc-CCCcHHHHHHh-----cCCCHHHHHHHHHHHHhccccceeccc
Q 010353 23 AKVCECLLRK-GPLTRQNVKRY-----TELSDEQVKNALLVLIQQNCVQAFTTE 70 (512)
Q Consensus 23 ~~V~~~Ll~~-G~ltl~~I~~~-----t~l~~~~Vr~aL~vLIQhn~V~~~~~~ 70 (512)
..|.++|... +++|..+|.+. .++++..|-++|=.|...|+|.-+...
T Consensus 24 ~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~ 77 (145)
T COG0735 24 LAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFE 77 (145)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeC
Confidence 3577888855 67888888655 468999999999999999999855544
No 224
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=40.96 E-value=46 Score=32.97 Aligned_cols=45 Identities=16% Similarity=0.221 Sum_probs=42.0
Q ss_pred hHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
--.+|...|-.+|+.++.+|++.++.+...||.=|..|-+.|++.
T Consensus 18 R~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 18 RREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 356788999999999999999999999999999999999999887
No 225
>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=40.63 E-value=25 Score=27.51 Aligned_cols=44 Identities=16% Similarity=-0.008 Sum_probs=35.6
Q ss_pred hHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 010353 371 DAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 415 (512)
Q Consensus 371 ~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v 415 (512)
....+|-+.+....+ +.++|++...+|.+.++..+..+..+|.+
T Consensus 19 ~~r~af~L~R~~eGl-S~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 19 LAEAAAALAREEAGK-TASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 344456555554678 99999999999999999999999988764
No 226
>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=40.43 E-value=1.6e+02 Score=27.54 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=30.5
Q ss_pred CCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 34 ~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
++|-.+|+...++|...||.||..|.+.|+|..
T Consensus 34 ~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~ 66 (212)
T TIGR03338 34 KLNESDIAARLGVSRGPVREAFRALEEAGLVRN 66 (212)
T ss_pred EecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE
Confidence 667789999999999999999999999999983
No 227
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=40.40 E-value=28 Score=24.97 Aligned_cols=30 Identities=13% Similarity=0.199 Sum_probs=28.5
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 387 ETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 387 eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
++.+|++...++...+++.|.+|.++|+|.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 788999999999999999999999999985
No 228
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=40.18 E-value=91 Score=27.95 Aligned_cols=48 Identities=15% Similarity=0.202 Sum_probs=39.0
Q ss_pred chhHHHHHHHHHhcC---CCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 19 GDLVAKVCECLLRKG---PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 19 G~~v~~V~~~Ll~~G---~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
|+.+=.+--+|..++ ..|+.+|+...++|+.-+++.|.-|-+.|+|..
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S 57 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKS 57 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEe
Confidence 444445555666543 578999999999999999999999999999983
No 229
>PF13814 Replic_Relax: Replication-relaxation
Probab=39.96 E-value=56 Score=30.07 Aligned_cols=62 Identities=26% Similarity=0.221 Sum_probs=47.4
Q ss_pred HHHHhcCCCcchhhhhhhcCCCcc---cHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHH
Q 010353 377 RLLSKSGRLLETDKISDTTFVEKK---DAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQI 439 (512)
Q Consensus 377 r~l~~~~~l~eek~i~~~ami~~k---~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~ 439 (512)
++|-+.+.+ +.+||+...-.+.+ -++..|.+|.+.|+|.--..+.+......-+.|++...-
T Consensus 2 ~~L~~~r~l-t~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G 66 (191)
T PF13814_consen 2 RLLARHRFL-TTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAG 66 (191)
T ss_pred hhHHHhcCc-CHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHH
Confidence 456666667 99999999999998 799999999999999777665322334455788887553
No 230
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=39.50 E-value=56 Score=23.97 Aligned_cols=41 Identities=20% Similarity=0.329 Sum_probs=31.5
Q ss_pred HHhhhc-hhHHHHHHHHHhcCCCcHHHHHHhcC-CCHHHHHHHH
Q 010353 14 ITNHFG-DLVAKVCECLLRKGPLTRQNVKRYTE-LSDEQVKNAL 55 (512)
Q Consensus 14 v~~~FG-~~v~~V~~~Ll~~G~ltl~~I~~~t~-l~~~~Vr~aL 55 (512)
+.-++| +.+++|+..=+..|+ |+++++...+ |+..++...|
T Consensus 5 L~p~iGYe~aa~iAk~A~~~g~-svre~v~~~g~lt~ee~d~ll 47 (55)
T PF10415_consen 5 LNPYIGYEKAAEIAKEALAEGR-SVREVVLEEGLLTEEELDELL 47 (55)
T ss_dssp GHHHHHHHHHHHHHHHHHHHT---HHHHHHHTTSS-HHHHHHHT
T ss_pred ccchhccHHHHHHHHHHHHcCC-CHHHHHHHcCCCCHHHHHHHc
Confidence 456778 889999999999999 9999998877 7888877654
No 231
>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=39.47 E-value=72 Score=27.52 Aligned_cols=47 Identities=6% Similarity=0.133 Sum_probs=36.5
Q ss_pred CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhh
Q 010353 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDN 91 (512)
Q Consensus 33 G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~ 91 (512)
.+-|...|+..++-+...|+.||.++.+.|++. ...+ ..+|-.|++.
T Consensus 50 ipy~~e~LA~~~~~~~~~V~~Al~~f~k~glIe-~~d~-----------g~i~i~~~~~ 96 (119)
T TIGR01714 50 APYNAEMLATMFNRNVGDIRITLQTLESLGLIE-KKNN-----------GDIFLENWEK 96 (119)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE-EecC-----------CcEEehhHHH
Confidence 355667788888999999999999999999998 4432 1467777664
No 232
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=39.33 E-value=48 Score=31.52 Aligned_cols=59 Identities=17% Similarity=0.160 Sum_probs=42.3
Q ss_pred HHHhhhhHHHHHHHHHHcccCCHHHHHHH--HhhcccCCCccCHHHHHHHHHHHHhcccccccCC
Q 010353 106 SQEFDQQCVELVQGLLEHGRLTLKQMFDR--AKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 168 (512)
Q Consensus 106 ~~~~G~~a~~Iv~~lL~~G~l~~~~li~~--~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~~ 168 (512)
+...++.+..-+..-+..|.+.+++-+.. +++... .|+.-|++++..|...|+|...|.
T Consensus 5 ~~~~~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lg----VSRtpVREAL~~L~~eGlv~~~~~ 65 (224)
T PRK11534 5 MQITALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYA----LGVGPLREALSQLVAERLVTVVNQ 65 (224)
T ss_pred HHhhhHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHC----CChHHHHHHHHHHHHCCCEEEeCC
Confidence 44566777777778888888876655422 222222 377889999999999999998864
No 233
>PRK11050 manganese transport regulator MntR; Provisional
Probab=39.22 E-value=1e+02 Score=27.56 Aligned_cols=41 Identities=24% Similarity=0.327 Sum_probs=36.3
Q ss_pred HHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 375 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 375 i~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
|++++...+.. ...+|++...++...+...+.+|.+.|+|.
T Consensus 42 I~~~l~~~~~~-t~~eLA~~l~is~stVsr~l~~Le~~GlI~ 82 (152)
T PRK11050 42 IADLIAEVGEA-RQVDIAARLGVSQPTVAKMLKRLARDGLVE 82 (152)
T ss_pred HHHHHHhcCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 66677666666 999999999999999999999999999984
No 234
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=38.90 E-value=46 Score=32.63 Aligned_cols=47 Identities=17% Similarity=0.249 Sum_probs=41.8
Q ss_pred HHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 113 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 113 a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
...|++.|-++|.++++++.+.+. .|...++.=+..|.+.|+|.|+.
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~--------VS~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFG--------VSEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhC--------CCHHHHHHhHHHHHHCCcEEEEe
Confidence 468999999999999999998874 36778999999999999999974
No 235
>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=38.78 E-value=64 Score=27.36 Aligned_cols=53 Identities=19% Similarity=0.276 Sum_probs=40.7
Q ss_pred HHHHHHHHHHc-ccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccCC
Q 010353 113 CVELVQGLLEH-GRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 168 (512)
Q Consensus 113 a~~Iv~~lL~~-G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~~ 168 (512)
-..|++.|..+ +++|+.++.+.+.... ...+.+.|-.++..|.+.|+|.+++.
T Consensus 10 R~~Il~~l~~~~~~~ta~ei~~~l~~~~---~~is~~TVYR~L~~L~e~Gli~~~~~ 63 (120)
T PF01475_consen 10 RLAILELLKESPEHLTAEEIYDKLRKKG---PRISLATVYRTLDLLEEAGLIRKIEF 63 (120)
T ss_dssp HHHHHHHHHHHSSSEEHHHHHHHHHHTT---TT--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHhhhcc---CCcCHHHHHHHHHHHHHCCeEEEEEc
Confidence 35677777775 5999999999886532 23578899999999999999999853
No 236
>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=38.70 E-value=31 Score=35.33 Aligned_cols=45 Identities=18% Similarity=0.279 Sum_probs=33.3
Q ss_pred HHHHHHHhcC--CCcHHHHHHhcCCCHHHHHHHHHHHHhccccceec
Q 010353 24 KVCECLLRKG--PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (512)
Q Consensus 24 ~V~~~Ll~~G--~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~ 68 (512)
.|.++.-.-| ..-..+|...|+|+..+|.++|-.|.+.+++....
T Consensus 88 lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vk 134 (327)
T PF05158_consen 88 LVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVK 134 (327)
T ss_dssp HHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE-
T ss_pred HHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEec
Confidence 4555555544 45689999999999999999999999999998543
No 237
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=38.06 E-value=3.9e+02 Score=28.95 Aligned_cols=113 Identities=16% Similarity=0.110 Sum_probs=77.4
Q ss_pred hHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhchhh
Q 010353 21 LVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAK 100 (512)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~pr 100 (512)
.-..|-..|-.+|.++..+|++.+++++..|-.++-.|-..|+|.. ... + ...|++-.++-
T Consensus 7 ~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~-~~~---------~-~~~i~LTeeG~-------- 67 (489)
T PRK04172 7 NEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKV-EER---------V-EEVYVLTEEGK-------- 67 (489)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEE-Eee---------e-EEEEEECHHHH--------
Confidence 3456777888889999999999999999999999999999999983 321 1 24555554431
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccc
Q 010353 101 FLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVER 165 (512)
Q Consensus 101 ~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~r 165 (512)
.+++ =|.-...+++.+...|-.+++++...+ .+ .......+..|.+.||+..
T Consensus 68 --~~~~--~g~pE~rl~~~l~~~~g~~~~el~~~a---L~------~~~~~i~~~~l~k~g~i~i 119 (489)
T PRK04172 68 --KYAE--EGLPERRLLNALKDGGEVSLDELKEAL---LD------KKEVGIALGNLARKGWAKI 119 (489)
T ss_pred --HHHH--hcCHHHHHHHhhHhcCCcCHHHHHHhh---cc------chhHHHHHHHHHHCCCeec
Confidence 1111 122345566666655667888776542 11 1245677888889999876
No 238
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=37.82 E-value=1e+02 Score=27.71 Aligned_cols=34 Identities=15% Similarity=0.088 Sum_probs=31.3
Q ss_pred CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 33 G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
+..|..+|+...++|+.-+++.|..|.+.|+|..
T Consensus 23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S 56 (153)
T PRK11920 23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVET 56 (153)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 3468999999999999999999999999999983
No 239
>PRK12423 LexA repressor; Provisional
Probab=37.78 E-value=76 Score=29.86 Aligned_cols=45 Identities=13% Similarity=0.251 Sum_probs=37.0
Q ss_pred hHHHHHHHHHhcC-CCcHHHHHHhcCC-CHHHHHHHHHHHHhccccc
Q 010353 21 LVAKVCECLLRKG-PLTRQNVKRYTEL-SDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 21 ~v~~V~~~Ll~~G-~ltl~~I~~~t~l-~~~~Vr~aL~vLIQhn~V~ 65 (512)
+...+.+.+..+| +-|..+|++.+++ ++..|+..|-+|.+-|++.
T Consensus 11 il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~ 57 (202)
T PRK12423 11 ILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIE 57 (202)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 3455566666666 3589999999996 8999999999999999997
No 240
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=37.73 E-value=43 Score=29.54 Aligned_cols=41 Identities=29% Similarity=0.472 Sum_probs=36.0
Q ss_pred HHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 375 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 375 i~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
|++++..+|.. ..++|++...+++..+...+.+|.+.|||.
T Consensus 13 I~~l~~~~~~~-~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 13 IYLLIEEKGYA-RVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred HHHHHhcCCCc-CHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 56666666666 999999999999999999999999999995
No 241
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=37.19 E-value=61 Score=29.60 Aligned_cols=33 Identities=15% Similarity=0.235 Sum_probs=31.7
Q ss_pred CCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 33 GPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 33 G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++.|..+|+...++|+.-+.+.|-.|-+.|+|.
T Consensus 24 ~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~ 56 (164)
T PRK10857 24 GPVPLADISERQGISLSYLEQLFSRLRKNGLVS 56 (164)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 478999999999999999999999999999998
No 242
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=37.19 E-value=37 Score=25.95 Aligned_cols=46 Identities=28% Similarity=0.289 Sum_probs=40.0
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCC--HHHHHHHHHHHHhccccc
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELS--DEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~--~~~Vr~aL~vLIQhn~V~ 65 (512)
+.-.+|+.+|...|..|...|....+|+ .+.|=..|..|...|.|.
T Consensus 4 ~~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~ 51 (66)
T PF02295_consen 4 DLEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVC 51 (66)
T ss_dssp HHHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred hHHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEe
Confidence 3457899999999998999888876654 899999999999999996
No 243
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=37.06 E-value=32 Score=27.30 Aligned_cols=32 Identities=28% Similarity=0.435 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHH
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL 55 (512)
+.|...|-.+|- ||..|.+..|++++.++++|
T Consensus 5 adI~AaL~krG~-sL~~lsr~~Gl~~~tl~nal 36 (78)
T PF13693_consen 5 ADIKAALRKRGT-SLAALSREAGLSSSTLRNAL 36 (78)
T ss_dssp HHHHHHHCTTS---HHHHHHHHSS-HHHHHHTT
T ss_pred HHHHHHHHHcCC-CHHHHHHHcCCCHHHHHHHH
Confidence 456667777774 99999999999999999886
No 244
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=36.97 E-value=1.7e+02 Score=27.67 Aligned_cols=32 Identities=28% Similarity=0.355 Sum_probs=30.5
Q ss_pred CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 34 PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 34 ~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++|-.+|+...|+|...||.||..|.+-|+|.
T Consensus 34 ~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~ 65 (221)
T PRK11414 34 RLITKNLAEQLGMSITPVREALLRLVSVNALS 65 (221)
T ss_pred ccCHHHHHHHHCCCchhHHHHHHHHHHCCCEE
Confidence 67888999999999999999999999999998
No 245
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=36.56 E-value=1.1e+02 Score=23.29 Aligned_cols=48 Identities=13% Similarity=0.176 Sum_probs=41.6
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
.|+-..+..+++..|..+...|.|..++....--..+=.|-+.|+|..
T Consensus 5 D~ly~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~ 52 (65)
T PF09397_consen 5 DPLYEEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSP 52 (65)
T ss_dssp STTHHHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE-
T ss_pred cHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCC
Confidence 467778888999999999999999999999999999999999999973
No 246
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=36.34 E-value=1.8e+02 Score=28.93 Aligned_cols=53 Identities=15% Similarity=0.256 Sum_probs=43.6
Q ss_pred HHHhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 13 VITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 13 iv~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|=++++-.++..|-..|-.+|..++.+|++..+||..-++..++.-.-...+.
T Consensus 109 it~~Yld~l~~Eine~Lqe~G~vsi~eLa~~~~Lp~efl~~~li~~~lg~~I~ 161 (272)
T PF09743_consen 109 ITDSYLDSLAEEINEKLQESGQVSISELAKQYDLPSEFLKEELISKRLGKIIK 161 (272)
T ss_pred ccHHHHHHHHHHHHHHHHHcCeEeHHHHHHhcCCcHHHHHHHHhhhhcCccee
Confidence 44567888999999999999999999999999999998887766664444443
No 247
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=36.20 E-value=45 Score=30.04 Aligned_cols=54 Identities=20% Similarity=0.111 Sum_probs=43.7
Q ss_pred hCchHHHHHHHHHhc-CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 010353 368 YGRDAYRIFRLLSKS-GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 421 (512)
Q Consensus 368 ~G~~~~Ri~r~l~~~-~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvp 421 (512)
..+-|+|++-.|... +..+.-++|++.-.+|.+=.+++|..|.+.|+|.-..=+
T Consensus 6 ~~~YAlr~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~ 60 (153)
T PRK11920 6 QTNYAIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGR 60 (153)
T ss_pred HHhHHHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCC
Confidence 445688888888643 444588999999999999999999999999999655433
No 248
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=36.03 E-value=91 Score=28.66 Aligned_cols=50 Identities=14% Similarity=0.147 Sum_probs=39.8
Q ss_pred hhhchhHHHHHHHHHhc--CCCcHHHHHHhc--CCCHHHHHHHHHHHHhccccc
Q 010353 16 NHFGDLVAKVCECLLRK--GPLTRQNVKRYT--ELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~--G~ltl~~I~~~t--~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++|....--|...|+.- |.-+...|++.+ +++..+|++||-.|.+.|++.
T Consensus 19 ~~~~~W~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~ 72 (171)
T PF14394_consen 19 EYYSSWYHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIK 72 (171)
T ss_pred HHHhhhHHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeE
Confidence 35555555655556554 333899999998 999999999999999999997
No 249
>PRK06474 hypothetical protein; Provisional
Probab=35.93 E-value=98 Score=28.60 Aligned_cols=49 Identities=16% Similarity=0.139 Sum_probs=40.0
Q ss_pred HHHHHHHHhcCC-Ccchhhhhhhc-CCCcccHHHHHHHHhhcccceEEEEec
Q 010353 373 YRIFRLLSKSGR-LLETDKISDTT-FVEKKDAPKILYKLWKDGYLLMEKLVV 422 (512)
Q Consensus 373 ~Ri~r~l~~~~~-l~eek~i~~~a-mi~~k~~r~~Ly~L~~~g~v~~QEvpk 422 (512)
.+|++.|...+. + +-.+|++.. -+|...+-..|..|.+.|+|..-+.++
T Consensus 14 ~~Il~~L~~~~~~~-ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~ 64 (178)
T PRK06474 14 MKICQVLMRNKEGL-TPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKK 64 (178)
T ss_pred HHHHHHHHhCCCCC-CHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeeccc
Confidence 578888887665 7 999998887 688888999999999999997655444
No 250
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=35.90 E-value=63 Score=31.17 Aligned_cols=43 Identities=21% Similarity=0.353 Sum_probs=40.0
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
-+|.+.|-++|++.+.+|+...+||.+.+-..+-+|..-|++.
T Consensus 26 v~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlir 68 (308)
T COG4189 26 VAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIR 68 (308)
T ss_pred HHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCcee
Confidence 3577888889999999999999999999999999999999998
No 251
>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=35.71 E-value=59 Score=21.10 Aligned_cols=30 Identities=33% Similarity=0.473 Sum_probs=24.0
Q ss_pred CcHHHHHHhcCCCHHHHHHHHHHHHhcccc
Q 010353 35 LTRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (512)
Q Consensus 35 ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V 64 (512)
+|-.+|+..+++++..|-..|-.|-+.|++
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 577899999999999999999999888763
No 252
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=35.33 E-value=57 Score=26.13 Aligned_cols=36 Identities=17% Similarity=0.227 Sum_probs=30.4
Q ss_pred hcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 31 RKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 31 ~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
.+--.|+..|.+.++++...+...|-.|+.|++|.+
T Consensus 21 ~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~ 56 (82)
T PF09202_consen 21 NHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR 56 (82)
T ss_dssp T-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred CCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc
Confidence 345679999999999999999999999999999996
No 253
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 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 1". 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 []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=35.30 E-value=1e+02 Score=21.88 Aligned_cols=37 Identities=11% Similarity=0.188 Sum_probs=30.2
Q ss_pred CCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEe
Q 010353 384 RLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLV 421 (512)
Q Consensus 384 ~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvp 421 (512)
.+ |=.+-+..|-++..++|++|..|...|-|.+-.|.
T Consensus 17 gl-dwqeaatraslsleetrkllqsmaaagqvtllrve 53 (61)
T PF09105_consen 17 GL-DWQEAATRASLSLEETRKLLQSMAAAGQVTLLRVE 53 (61)
T ss_dssp -E-EHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred cC-cHHHHHHHhhccHHHHHHHHHHHHhcCceEEEEec
Confidence 45 88888999999999999999999999999876654
No 254
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=35.12 E-value=74 Score=31.12 Aligned_cols=44 Identities=16% Similarity=0.107 Sum_probs=41.0
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
-.+|...|..+|..++.+|++..+.+...||.=|-.|-+.|++.
T Consensus 7 ~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 7 HQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 35688899999999999999999999999999999999999986
No 255
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=35.08 E-value=2.2e+02 Score=27.43 Aligned_cols=36 Identities=19% Similarity=0.264 Sum_probs=32.4
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 383 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 383 ~~l~-eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
|.-+ .|.+|++...++..-+|+.|..|..+|+|++.
T Consensus 31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~ 67 (254)
T PRK09464 31 GEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRR 67 (254)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 5544 89999999999999999999999999999764
No 256
>KOG4562 consensus Uncharacterized conserved protein (tumor-rejection antigen MAGE in humans) [Function unknown]
Probab=34.91 E-value=37 Score=34.67 Aligned_cols=68 Identities=19% Similarity=0.240 Sum_probs=42.7
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHH-HHHhhcccceEEEEecCCCCCceEEEEEE--ehHHHHHHHHHH
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKIL-YKLWKDGYLLMEKLVVTGARQSQFLLWKV--NRQILWKHVLDE 447 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~L-y~L~~~g~v~~QEvpk~~~~~~t~~lw~v--~~~~~~~~~l~~ 447 (512)
.-||.+|..-|-. +.+.-. ---+.|+++ ..|.+++|++.++||.++ |.+..|||-- ..+.....|++-
T Consensus 223 e~iWe~L~~lGv~-~g~~H~-----ifGeprkLiT~dlVqq~YLeYr~Vp~sd-P~~YEFlWGpRA~~EtskmKVLeF 293 (329)
T KOG4562|consen 223 EEIWEVLRRLGVY-DGREHS-----IFGEPRKLLTQDLVQEKYLEYRQVPDSD-PPRYEFLWGPRAHAETSKMKVLEF 293 (329)
T ss_pred HHHHHHHHHhcCC-CCcccc-----ccCChHHHHHHHHHHhhceeeeecCCCC-CCceEEeecccchhhHHHHHHHHH
Confidence 3466666655544 332211 124556655 678899999999999996 9999999963 333333444433
No 257
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=34.78 E-value=54 Score=24.63 Aligned_cols=25 Identities=8% Similarity=0.248 Sum_probs=21.9
Q ss_pred HHhcCCCcHHHHHHhcCCCHHHHHH
Q 010353 29 LLRKGPLTRQNVKRYTELSDEQVKN 53 (512)
Q Consensus 29 Ll~~G~ltl~~I~~~t~l~~~~Vr~ 53 (512)
+-..|..++.+|+...++++++|+.
T Consensus 17 ~~~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 17 KESNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred HHhCCCccHHHHHHHHCCCHHHHHH
Confidence 4457899999999999999999984
No 258
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=34.78 E-value=62 Score=31.75 Aligned_cols=43 Identities=21% Similarity=0.275 Sum_probs=41.2
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+|.+.|-.+|..++.+|+...+.+...||.=|..|-+.|.+.
T Consensus 8 ~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~ 50 (253)
T COG1349 8 QKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLL 50 (253)
T ss_pred HHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence 5788999999999999999999999999999999999999987
No 259
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=34.60 E-value=79 Score=31.12 Aligned_cols=42 Identities=21% Similarity=0.359 Sum_probs=37.2
Q ss_pred HHHHHHHhcCC-CcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 010353 374 RIFRLLSKSGR-LLETDKISDTTFVEKKDAPKILYKLWKDGYL 415 (512)
Q Consensus 374 Ri~r~l~~~~~-l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v 415 (512)
.+.|.|...|. -++|-+|.+...++...+-+.|..|-+.|.|
T Consensus 8 klir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv 50 (321)
T COG3888 8 KLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIV 50 (321)
T ss_pred HHHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCee
Confidence 57788877765 2499999999999999999999999999999
No 260
>PRK10870 transcriptional repressor MprA; Provisional
Probab=34.44 E-value=2.1e+02 Score=26.21 Aligned_cols=63 Identities=16% Similarity=0.148 Sum_probs=44.8
Q ss_pred HHhCchHH--HHHHHHHhc--CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEE
Q 010353 366 KRYGRDAY--RIFRLLSKS--GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLL 432 (512)
Q Consensus 366 ~~~G~~~~--Ri~r~l~~~--~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~l 432 (512)
..+|-... .|+..|... +.+ ...+|++...++...+-.++.+|.+.|||.-+.-| ...|..++
T Consensus 49 ~~~gLt~~q~~iL~~L~~~~~~~i-t~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~---~DrR~~~v 115 (176)
T PRK10870 49 KAQGINETLFMALITLESQENHSI-QPSELSCALGSSRTNATRIADELEKRGWIERRESD---NDRRCLHL 115 (176)
T ss_pred HHCCCCHHHHHHHHHHhcCCCCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCC---CCCCeeEE
Confidence 34665444 566666543 345 88999999999999999999999999999443322 33455544
No 261
>PHA02591 hypothetical protein; Provisional
Probab=34.11 E-value=98 Score=24.49 Aligned_cols=35 Identities=29% Similarity=0.289 Sum_probs=30.1
Q ss_pred hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHH
Q 010353 20 DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (512)
Q Consensus 20 ~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL 55 (512)
+..-.|+.-|...|- |..+|++.++++...|++-|
T Consensus 46 dd~~~vA~eL~eqGl-SqeqIA~~LGVsqetVrKYL 80 (83)
T PHA02591 46 DDLISVTHELARKGF-TVEKIASLLGVSVRKVRRYL 80 (83)
T ss_pred chHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHH
Confidence 345568889999987 99999999999999999865
No 262
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=33.69 E-value=1.2e+02 Score=28.82 Aligned_cols=58 Identities=16% Similarity=0.193 Sum_probs=46.3
Q ss_pred HHHHHHHHhhhchhHHHHHHHHHhc---C--CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 8 KHAVHVITNHFGDLVAKVCECLLRK---G--PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 8 ~Lc~~iv~~~FG~~v~~V~~~Ll~~---G--~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+...+......++-++|+.+|+.. | +.|-.+|+...|+++..|-..|--|.+.|++.
T Consensus 138 ~~~~~~~~~~~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~ 200 (226)
T PRK10402 138 RNIVSLTQNQSFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLK 200 (226)
T ss_pred HHHHHHHHhccChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEE
Confidence 3344445555557889999999853 2 35779999999999999999999999999997
No 263
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=33.64 E-value=49 Score=32.38 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=39.1
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+|.++|.++|.. ..++|++...++...+|.-|..|.+.|.+.
T Consensus 8 ~~Il~~l~~~~~~-~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 8 QILLELLAQLGFV-TVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred HHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4588888888788 999999999999999999999999999983
No 264
>PF14502 HTH_41: Helix-turn-helix domain
Probab=33.56 E-value=68 Score=22.95 Aligned_cols=30 Identities=20% Similarity=0.228 Sum_probs=28.5
Q ss_pred cHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 36 TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 36 tl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|+.++....+++...|.+||-.|-..++|.
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 788999999999999999999999999997
No 265
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=33.25 E-value=72 Score=31.49 Aligned_cols=54 Identities=15% Similarity=0.228 Sum_probs=47.7
Q ss_pred HhhhchhHHHHHHHHHhcC-CCcHHHHHHhcCCCHHHHHHHHHHHHhccccceec
Q 010353 15 TNHFGDLVAKVCECLLRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFT 68 (512)
Q Consensus 15 ~~~FG~~v~~V~~~Ll~~G-~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~ 68 (512)
+..|-+.=..|..++..+| +.+-.+|.+.+++|...|-..|.-|-+-|+|.-+.
T Consensus 190 ~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 190 EYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEK 244 (258)
T ss_pred cCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEE
Confidence 4567777788999999996 59999999999999999999999999999998444
No 266
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=32.76 E-value=90 Score=28.54 Aligned_cols=54 Identities=15% Similarity=0.222 Sum_probs=41.9
Q ss_pred hhHHHHHHHHHH-cccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 111 QQCVELVQGLLE-HGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 111 ~~a~~Iv~~lL~-~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
..=..|++.|.. .+++++.+|.+.+.+..+ ..+...|-.++..|++.|+|.++.
T Consensus 26 ~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~---~is~aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 26 PQRLEVLRLMSLQPGAISAYDLLDLLREAEP---QAKPPTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHhhCC---CCCcchHHHHHHHHHHCCCEEEEe
Confidence 344566666664 479999999999865433 346788999999999999999985
No 267
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=32.71 E-value=46 Score=26.65 Aligned_cols=48 Identities=17% Similarity=0.260 Sum_probs=36.9
Q ss_pred chHHHHHHHHH---hcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceE
Q 010353 370 RDAYRIFRLLS---KSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLM 417 (512)
Q Consensus 370 ~~~~Ri~r~l~---~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~ 417 (512)
..-.||++.+. ++..++-.+.|.+.+-++..++...|.+|.+.++|.-
T Consensus 6 ~~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~ 56 (82)
T PF09202_consen 6 KEDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR 56 (82)
T ss_dssp HHHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc
Confidence 34566666663 3456779999999999999999999999999999955
No 268
>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=32.22 E-value=97 Score=29.04 Aligned_cols=48 Identities=19% Similarity=0.190 Sum_probs=36.8
Q ss_pred hhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccccc
Q 010353 111 QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 111 ~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
.....|+. +..|+-|.++|++.+.... ...++.+++.+|.+.|||+..
T Consensus 30 ~~~~~L~~--lLdG~rt~~eI~~~l~~~~------p~~~v~~~L~~L~~~G~l~~~ 77 (193)
T TIGR03882 30 ALYCQLAP--LLDGRRTLDEIIAALAGRF------PAEEVLYALDRLERRGYLVED 77 (193)
T ss_pred hhHHHHHH--HHcCCCCHHHHHHHhhccC------CHHHHHHHHHHHHHCCCEecc
Confidence 33444444 5688999999999886532 467799999999999999754
No 269
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=32.05 E-value=1.3e+02 Score=26.60 Aligned_cols=56 Identities=16% Similarity=0.285 Sum_probs=41.2
Q ss_pred hHHHHHHHHHHcccCCHHHHHHHHhhcccCCC------ccCHHHHHHHHHHHHhcccccccC
Q 010353 112 QCVELVQGLLEHGRLTLKQMFDRAKSSEKEGN------LVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 112 ~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~------~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
-|+.|+-.+..+|-+..+-+-...-.+..-|. .-+.+-++.+|.+|-+.|||+..|
T Consensus 54 RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~ 115 (147)
T COG2238 54 RAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP 115 (147)
T ss_pred HHHHHHHHHHhcCchhHHHHHHHHCccccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC
Confidence 37888888888888887777666544322221 125677899999999999999986
No 270
>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=32.04 E-value=4.2e+02 Score=24.60 Aligned_cols=36 Identities=19% Similarity=0.186 Sum_probs=31.9
Q ss_pred CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 383 GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 383 ~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
|.-+.|.+|++.-.++..-+|+.|..|..+|+|+.+
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNE 67 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEe
Confidence 543489999999999999999999999999999653
No 271
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=31.16 E-value=1.6e+02 Score=25.35 Aligned_cols=52 Identities=15% Similarity=0.235 Sum_probs=39.1
Q ss_pred hhhh-HHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccCC
Q 010353 109 FDQQ-CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCPA 168 (512)
Q Consensus 109 ~G~~-a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~~ 168 (512)
.|.- ...|+-.|.. |..+.+++-..+.. .+...+.+.+..|.++|+|.|...
T Consensus 20 ig~kW~~lIl~~L~~-g~~RF~eL~r~i~~-------Is~k~Ls~~Lk~Le~~Glv~R~~~ 72 (120)
T COG1733 20 IGGKWTLLILRDLFD-GPKRFNELRRSIGG-------ISPKMLSRRLKELEEDGLVERVVY 72 (120)
T ss_pred HcCccHHHHHHHHhc-CCCcHHHHHHHccc-------cCHHHHHHHHHHHHHCCCEEeeec
Confidence 3444 4445555555 99999999887542 367789999999999999999854
No 272
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=30.82 E-value=7.6e+02 Score=27.98 Aligned_cols=142 Identities=16% Similarity=0.149 Sum_probs=82.4
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCC----------CCCCCCCccEEEechhh
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDG----------FADGPKANTQYVVLFDN 91 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~----------~~~~~~~~~~Y~~~~~~ 91 (512)
-|.|...-......|+.+++..+++|+..+++=|-..||||++.--+...+.| ... ......-++.-++
T Consensus 604 qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~~s~tgt~T~iEse~d~~q-~~~~~~~e~eee~ 682 (765)
T KOG2165|consen 604 QAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEPIISDTGTLTVIESEMDFDQ-AEGTVLLEAEEEN 682 (765)
T ss_pred HHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCCCCCCCceeeeccccccccc-cCCCccccccccc
Confidence 34455555566789999999999999999999999999999986222110000 000 0000111111111
Q ss_pred HHHHhchhhHHHHHHHHhhhhHHHHHHHHHHcccCCHHHHHHHHhhccc-CCC-ccCHHHHHHHHHHHHhccccccc
Q 010353 92 ILHRVRFAKFLTILSQEFDQQCVELVQGLLEHGRLTLKQMFDRAKSSEK-EGN-LVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 92 il~rlR~pr~l~~i~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~-~~~-~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
+=.+-.-++..-+++++-.-.-|+--|-..|.+.++-+-..+.=-.+ .+. ..+..+++.-+..+|..|-++-.
T Consensus 683 --~e~~~as~vdqle~el~~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~kV~e~kL~f~ 757 (765)
T KOG2165|consen 683 --YESHNASEVDQLEEELTLFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQRKVREGKLEFI 757 (765)
T ss_pred --chhhhhhHHHHHHHHHHHHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHHHhhccceEEe
Confidence 11223344555566666444445444444499987665443211111 222 24788999999999999887543
No 273
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=30.58 E-value=1e+02 Score=23.67 Aligned_cols=48 Identities=17% Similarity=0.075 Sum_probs=33.7
Q ss_pred HHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 120 LLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 120 lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
+|..|-++.-+|.+.+......--..+...|-.++.+|.++|||....
T Consensus 4 ~L~~~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~ 51 (75)
T PF03551_consen 4 LLSEGPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRW 51 (75)
T ss_dssp HHHHS-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEE
T ss_pred hhccCCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEee
Confidence 445577787888877765421111347889999999999999998763
No 274
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=30.43 E-value=2.8e+02 Score=26.74 Aligned_cols=37 Identities=14% Similarity=0.144 Sum_probs=33.0
Q ss_pred cCCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 382 SGRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 382 ~~~l~-eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
-|.-+ .|.+|++.-.++..-+|+.|-.|..+|+|++.
T Consensus 27 pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~ 64 (251)
T PRK09990 27 VGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETA 64 (251)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 35555 89999999999999999999999999999665
No 275
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=30.42 E-value=1e+02 Score=27.78 Aligned_cols=45 Identities=22% Similarity=0.395 Sum_probs=35.1
Q ss_pred HHhhhchhHHHHHHHHHhcCCCcHHHHHHh-cCCCHHH----------HHHHHHHHHhccc
Q 010353 14 ITNHFGDLVAKVCECLLRKGPLTRQNVKRY-TELSDEQ----------VKNALLVLIQQNC 63 (512)
Q Consensus 14 v~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~-t~l~~~~----------Vr~aL~vLIQhn~ 63 (512)
|.++|+.++..|...|- |++++... .+|++.+ +|..|..-|++-|
T Consensus 95 V~~~~s~~~Kav~q~Le-----tlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~~ 150 (152)
T PF07278_consen 95 VRREMSEMAKAVVQVLE-----TLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEAC 150 (152)
T ss_pred HHHHHHHHHHHHHHHHH-----HhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 67889999999999997 99999765 9999976 4555555555544
No 276
>PRK11239 hypothetical protein; Provisional
Probab=30.09 E-value=1.1e+02 Score=29.12 Aligned_cols=46 Identities=15% Similarity=0.227 Sum_probs=37.8
Q ss_pred hhchhHHHHHHHHHhcCCCcHHHHHHhcC----C-CHHHHHHHHHHHHhcc
Q 010353 17 HFGDLVAKVCECLLRKGPLTRQNVKRYTE----L-SDEQVKNALLVLIQQN 62 (512)
Q Consensus 17 ~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~----l-~~~~Vr~aL~vLIQhn 62 (512)
.|.+--..|...|+-||++|..+|-.+++ + +...|.+.|--|+++.
T Consensus 94 ~l~~~~~All~~LlLRGPQT~gELRtRs~Rl~~F~dv~~Ve~~L~~L~~r~ 144 (215)
T PRK11239 94 KLSAAEVALITTLLLRGAQTPGELRSRAARMYEFSDMAEVESTLEQLANRE 144 (215)
T ss_pred CCCHHHHHHHHHHHhcCCCChHHHHHhHhcCCcCCCHHHHHHHHHHHHhcc
Confidence 34566677888899999999999976654 3 6789999999999995
No 277
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=29.65 E-value=2e+02 Score=32.87 Aligned_cols=127 Identities=16% Similarity=0.212 Sum_probs=80.7
Q ss_pred cCCCcHHHHHHhcCCCHHHHHHHHHHH--HhccccceecccCCCCCCCCCCCccEEEechh--hHHHHhchh----hHHH
Q 010353 32 KGPLTRQNVKRYTELSDEQVKNALLVL--IQQNCVQAFTTEQPDGFADGPKANTQYVVLFD--NILHRVRFA----KFLT 103 (512)
Q Consensus 32 ~G~ltl~~I~~~t~l~~~~Vr~aL~vL--IQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~--~il~rlR~p----r~l~ 103 (512)
+-++|+.+|...|+++.+.+..+|-+| +...+.. . +.+.. .+...+++|.+ .-..|+.-| +--.
T Consensus 578 ~d~lt~~eI~~~t~i~~~~l~~~L~Sl~~~K~~v~~--~-~~s~~-----~~~~~~~~N~~f~sk~~Rv~i~~~~~~e~~ 649 (725)
T KOG2166|consen 578 TEKLTYEEILEQTNLGHEDLARLLQSLSCLKYKILL--K-PMSRT-----SPNDEFAFNSKFTSKMRRVKIPLPPMDERK 649 (725)
T ss_pred hhhccHHHHHHHhCCCHHHHHHHHHHHHHHhHhhcc--C-ccccC-----CCCcEEEeeccccCcceeeccCCCCchhHH
Confidence 468999999999999999999999999 5522221 1 11100 11234555543 444444444 2223
Q ss_pred HHHHHhh-----hhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccccc
Q 010353 104 ILSQEFD-----QQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 104 ~i~~~~G-----~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
.+.+..+ ..-|+||--.=..+++.-.+++..+.+.....=..++..|+.++..|++.+||+|-
T Consensus 650 ~~~~~ve~dRk~~i~AaIVRIMK~rK~l~h~~Lv~Ev~~ql~~RF~p~v~~IKk~Ie~LIEkeYleR~ 717 (725)
T KOG2166|consen 650 KVVEDVDKDRKYAIDAAIVRIMKSRKVLGHQQLVSEVVEQLSERFKPDIKMIKKRIEDLIEREYLERD 717 (725)
T ss_pred HHHhhhhhHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcc
Confidence 3333444 23677887777888888777777665422111112678999999999999999995
No 278
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=28.50 E-value=64 Score=31.63 Aligned_cols=42 Identities=17% Similarity=0.243 Sum_probs=38.7
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 415 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v 415 (512)
.+|..+|.++|.+ ..++|++.--++...+|.-|..|.+.|++
T Consensus 8 ~~Il~~l~~~~~~-~~~ela~~l~vS~~TiRRdL~~Le~~g~l 49 (252)
T PRK10906 8 DAIIELVKQQGYV-STEELVEHFSVSPQTIRRDLNDLAEQNKI 49 (252)
T ss_pred HHHHHHHHHcCCE-eHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 4578888888888 99999999999999999999999999997
No 279
>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=28.15 E-value=1.3e+02 Score=30.00 Aligned_cols=49 Identities=20% Similarity=0.152 Sum_probs=41.6
Q ss_pred hhchhHHHHHHHHHhc--CCCcHHHHHHhcC--CCHHHHHHHHHHHHhccccc
Q 010353 17 HFGDLVAKVCECLLRK--GPLTRQNVKRYTE--LSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 17 ~FG~~v~~V~~~Ll~~--G~ltl~~I~~~t~--l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+|....--|...|+.- |.-+...|++.++ ++..+|+.||-.|.+.|++.
T Consensus 118 y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glik 170 (271)
T TIGR02147 118 YYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIK 170 (271)
T ss_pred HHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCee
Confidence 5667777788888854 6667888999987 89999999999999999997
No 280
>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=27.67 E-value=1e+02 Score=24.06 Aligned_cols=57 Identities=18% Similarity=0.151 Sum_probs=41.7
Q ss_pred HHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEe
Q 010353 375 IFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 436 (512)
Q Consensus 375 i~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~ 436 (512)
|+-.+.. +.. .-+++.+...++.++.--.|.+|.+.|.|.=.... -+++.+=.|.+.
T Consensus 10 IL~~ls~-~c~-TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~---~~gkk~R~YclK 66 (72)
T PF05584_consen 10 ILIILSK-RCC-TLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRK---FGGKKYREYCLK 66 (72)
T ss_pred HHHHHHh-ccC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEE---ecCeEEEEEEec
Confidence 4444444 477 99999999999999999999999999999433221 345556556654
No 281
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=27.53 E-value=1.2e+02 Score=29.41 Aligned_cols=43 Identities=21% Similarity=0.282 Sum_probs=39.6
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+|...|..+|..+..+|++..+++...||.=|-.|...|.+.
T Consensus 7 ~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 7 QAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4578889999999999999999999999999999999988776
No 282
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=27.37 E-value=1.9e+02 Score=23.26 Aligned_cols=37 Identities=19% Similarity=0.176 Sum_probs=24.7
Q ss_pred hHHHHHHHHHhc-CCCcHHHHHHhcC-CCHHHHHHHHHH
Q 010353 21 LVAKVCECLLRK-GPLTRQNVKRYTE-LSDEQVKNALLV 57 (512)
Q Consensus 21 ~v~~V~~~Ll~~-G~ltl~~I~~~t~-l~~~~Vr~aL~v 57 (512)
.+..|+-+|+.+ ..+|+.+|.+..+ -+.+.|-+++-.
T Consensus 30 ~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~r 68 (90)
T cd06571 30 LARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRK 68 (90)
T ss_pred hHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHH
Confidence 455566677766 3777777777776 777766666543
No 283
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=27.32 E-value=4.1e+02 Score=24.57 Aligned_cols=39 Identities=21% Similarity=0.326 Sum_probs=28.7
Q ss_pred cCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHH
Q 010353 395 TFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQI 439 (512)
Q Consensus 395 ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~ 439 (512)
-.|-...++.+|.+|..+|+|...-+ +++.|+|...-+.
T Consensus 38 K~IVl~tVKd~lQqlVDDgvV~~EK~------GtsN~YWsF~s~~ 76 (209)
T COG5124 38 KQIVLMTVKDLLQQLVDDGVVSVEKC------GTSNIYWSFKSQT 76 (209)
T ss_pred cccHHHHHHHHHHHHhhcCceeeeee------ccceeEEecchHH
Confidence 34445789999999999999965543 4457889887553
No 284
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=27.18 E-value=1.1e+02 Score=25.06 Aligned_cols=35 Identities=26% Similarity=0.528 Sum_probs=24.8
Q ss_pred HHHHHHhcCCCcHHHHHHhc--------CCCHHHHHHHHHHHH
Q 010353 25 VCECLLRKGPLTRQNVKRYT--------ELSDEQVKNALLVLI 59 (512)
Q Consensus 25 V~~~Ll~~G~ltl~~I~~~t--------~l~~~~Vr~aL~vLI 59 (512)
+-+.|+.+|+++++.|..+. ++|+++-|.-++.-+
T Consensus 11 Lp~iLl~~GPLaIRhI~~~Lt~~vPgF~~ls~sKqRRLi~~AL 53 (92)
T PF10330_consen 11 LPEILLNHGPLAIRHITGYLTTSVPGFSDLSPSKQRRLIMAAL 53 (92)
T ss_pred hHHHHHhcCcHHHHHHHHHHhccCCCcccCCHHHHHHHHHHHH
Confidence 34599999999999998762 467766655444433
No 285
>PRK09954 putative kinase; Provisional
Probab=27.10 E-value=1.2e+02 Score=31.25 Aligned_cols=99 Identities=10% Similarity=0.076 Sum_probs=65.1
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHh-chhhH
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRV-RFAKF 101 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rl-R~pr~ 101 (512)
.+|.+.|..+++.|..+|.+..+++.+.|+.-|--|.+-|++.-+...-.. +......=.+++|-++..- ++|.-
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~----~~~v~viG~~~vD~~~~~~~~~p~~ 81 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTE----QEYCVVVGAINMDIRGMADIRYPQA 81 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcC----CccEEEEEEEEEEEEEeeCCcCcCC
Confidence 468899999999999999999999999999999999999988633321100 0111233445555443211 23321
Q ss_pred ---HHHHHHHhhhhHHHHHHHHHHccc
Q 010353 102 ---LTILSQEFDQQCVELVQGLLEHGR 125 (512)
Q Consensus 102 ---l~~i~~~~G~~a~~Iv~~lL~~G~ 125 (512)
...+....|-.+.-+...+-..|.
T Consensus 82 ~~~~~~~~~~~GG~~~NvA~~larLG~ 108 (362)
T PRK09954 82 ASHPGTIHCSAGGVGRNIAHNLALLGR 108 (362)
T ss_pred CCCCceEEEecCcHHHHHHHHHHHcCC
Confidence 222344467777777777777775
No 286
>PRK03837 transcriptional regulator NanR; Provisional
Probab=26.96 E-value=1e+02 Score=29.46 Aligned_cols=33 Identities=21% Similarity=0.327 Sum_probs=30.6
Q ss_pred CC-cHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 34 PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 34 ~l-tl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
++ +-.+|+...+++...||.||..|-+.|+|..
T Consensus 36 ~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~ 69 (241)
T PRK03837 36 QLPSERELMAFFGVGRPAVREALQALKRKGLVQI 69 (241)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 56 6889999999999999999999999999983
No 287
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=26.81 E-value=2.4e+02 Score=23.09 Aligned_cols=56 Identities=16% Similarity=0.265 Sum_probs=37.8
Q ss_pred hhHHHHHHHHHHc-ccCCHHHHHHHHhhcc---------------cCCCccCHHHHHHHHHHHHhccccccc
Q 010353 111 QQCVELVQGLLEH-GRLTLKQMFDRAKSSE---------------KEGNLVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 111 ~~a~~Iv~~lL~~-G~l~~~~li~~~~~~~---------------~~~~~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
++|..|+..+-.. |+.+...++.-+.... ..++..+...++..+.+|+..|||...
T Consensus 4 ~~a~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~ 75 (106)
T PF09382_consen 4 EEAKKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSED 75 (106)
T ss_dssp HHHHHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceec
Confidence 5677777777775 6678777777654321 112345789999999999999999554
No 288
>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=26.80 E-value=85 Score=30.10 Aligned_cols=48 Identities=19% Similarity=0.138 Sum_probs=42.3
Q ss_pred hchhHHHHHHHH--HhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 18 FGDLVAKVCECL--LRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 18 FG~~v~~V~~~L--l~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+....+|...+ -..|..|..+|....+.++...+..|-.+++.|+|+
T Consensus 172 ~~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 172 LSKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLW 221 (223)
T ss_dssp H-HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred hhHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence 356778888888 888999999999999999999999999999999986
No 289
>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=26.79 E-value=1e+02 Score=23.29 Aligned_cols=42 Identities=17% Similarity=0.259 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccce
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLL 416 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~ 416 (512)
.+|+++|. .+.. .-++|++...++...++..+..|.+.|+.-
T Consensus 3 ~~il~~L~-~~~~-~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 3 LRLLALLA-DNPF-SGEKLGEALGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred HHHHHHHH-cCCc-CHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 46888876 4577 799999999999999999999999999963
No 290
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=26.70 E-value=1.7e+02 Score=30.05 Aligned_cols=93 Identities=11% Similarity=0.195 Sum_probs=57.8
Q ss_pred HHHhcCCCcHHHHHHh--cCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhchhhHHHHH
Q 010353 28 CLLRKGPLTRQNVKRY--TELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFAKFLTIL 105 (512)
Q Consensus 28 ~Ll~~G~ltl~~I~~~--t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~pr~l~~i 105 (512)
++-..++.+..+|++. .++++..||+-|..|-+.|++..-+. .+++-|...-..|+++ +. +...
T Consensus 19 yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~h~---sagrIPT~kGYR~YVd--~L---~~~~------ 84 (339)
T PRK00082 19 YIATGEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKPHT---SSGRIPTDKGYRYFVD--HL---LEVK------ 84 (339)
T ss_pred HHhcCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCCcC---CCCCCcCHHHHHHHHH--Hh---CCCC------
Confidence 5667789999999966 88999999999999999999872221 2222222111223333 21 1110
Q ss_pred HHHhhhhHHHHHHHHHHcccCCHHHHHHHHh
Q 010353 106 SQEFDQQCVELVQGLLEHGRLTLKQMFDRAK 136 (512)
Q Consensus 106 ~~~~G~~a~~Iv~~lL~~G~l~~~~li~~~~ 136 (512)
.+.+.-...+...+......++++++.++
T Consensus 85 --~~~~~~~~~i~~~~~~~~~~~~~~l~~aa 113 (339)
T PRK00082 85 --PLSEEERRAIEKFLDERGVSLEDVLQEAA 113 (339)
T ss_pred --CCCHHHHHHHHHHHHhccCCHHHHHHHHH
Confidence 13444445566666666678888887643
No 291
>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=26.47 E-value=99 Score=24.91 Aligned_cols=37 Identities=22% Similarity=0.361 Sum_probs=33.8
Q ss_pred HhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 30 LRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 30 l~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
..+.++++.+|++..+++...|..-|+-+|..|.+..
T Consensus 56 ~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~ 92 (105)
T PF01399_consen 56 KPYSSISISEIAKALQLSEEEVESILIDLISNGLIKA 92 (105)
T ss_dssp HC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEE
T ss_pred HHhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEE
Confidence 3778999999999999999999999999999999984
No 292
>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=26.16 E-value=5.3e+02 Score=23.87 Aligned_cols=78 Identities=9% Similarity=0.046 Sum_probs=55.6
Q ss_pred chhhhhhhc-CCCcccHHHHHHHHhhcccceEEEEecCC------CCCceEEEEEEehHHHHHHHHHHHHHHHHHHHHHH
Q 010353 387 ETDKISDTT-FVEKKDAPKILYKLWKDGYLLMEKLVVTG------ARQSQFLLWKVNRQILWKHVLDEMFHAALNLSLRV 459 (512)
Q Consensus 387 eek~i~~~a-mi~~k~~r~~Ly~L~~~g~v~~QEvpk~~------~~~~t~~lw~v~~~~~~~~~l~~~~k~~~nl~~R~ 459 (512)
+-.+|+..+ .|+...+|..|-.|.+.|+|..+.-|... ..+.-..-|-+|+.-+....-+ +..+-++.
T Consensus 72 SN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~NgkRy~~R~~~G~I~~A~GfdLsPL~~R~~E-----l~~~a~~~ 146 (177)
T PF03428_consen 72 SNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSPNGKRYARRDRGGRIVEAFGFDLSPLIARAEE-----LAALAEAA 146 (177)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCCCCCccCccCCCCCEEeEeCcCHHHHHHHHHH-----HHHHHHHH
Confidence 667899999 99999999999999999999888777754 3346677888898876655432 22333444
Q ss_pred HHHHHhhhhh
Q 010353 460 SYELDREKEL 469 (512)
Q Consensus 460 ~~e~~~~k~l 469 (512)
..|....+.+
T Consensus 147 ~~~~~~~r~l 156 (177)
T PF03428_consen 147 RAERRALRRL 156 (177)
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 293
>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=26.11 E-value=1.5e+02 Score=27.79 Aligned_cols=45 Identities=22% Similarity=0.232 Sum_probs=37.7
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHHhc--CCCHHHHHHHHHHHHhccccc
Q 010353 19 GDLVAKVCECLLRKGPLTRQNVKRYT--ELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~I~~~t--~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|+.+..+...| .|+.|+.+|.... .+++..|.++|..|.+.|++.
T Consensus 29 ~~~~~~L~~lL--dG~rt~~eI~~~l~~~~p~~~v~~~L~~L~~~G~l~ 75 (193)
T TIGR03882 29 GALYCQLAPLL--DGRRTLDEIIAALAGRFPAEEVLYALDRLERRGYLV 75 (193)
T ss_pred chhHHHHHHHH--cCCCCHHHHHHHhhccCCHHHHHHHHHHHHHCCCEe
Confidence 66777777755 6888999998774 478999999999999999887
No 294
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=25.97 E-value=4.2e+02 Score=22.67 Aligned_cols=63 Identities=19% Similarity=0.258 Sum_probs=47.4
Q ss_pred hCchH-HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehH
Q 010353 368 YGRDA-YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQ 438 (512)
Q Consensus 368 ~G~~~-~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~ 438 (512)
+|+.. .+|+++|...|.+ .-.+|++..-+++..+=.-|-.|.+.|+|..... ++ .-+|++|.+
T Consensus 13 LadptRl~IL~~L~~~~~~-~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~------Gr-~~~Y~l~~~ 76 (117)
T PRK10141 13 LSDETRLGIVLLLRESGEL-CVCDLCTALDQSQPKISRHLALLRESGLLLDRKQ------GK-WVHYRLSPH 76 (117)
T ss_pred hCCHHHHHHHHHHHHcCCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEE------cC-EEEEEECch
Confidence 34443 4788888876677 8889999999999999999999999999954422 22 234666754
No 295
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=25.92 E-value=1e+02 Score=25.43 Aligned_cols=65 Identities=11% Similarity=0.225 Sum_probs=47.7
Q ss_pred hCchHHHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEe
Q 010353 368 YGRDAYRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVN 436 (512)
Q Consensus 368 ~G~~~~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~ 436 (512)
++..-.+++.+|...+.. ...+|++...++...+-..+.+|.+.|||.-+..| ...|..++.--+
T Consensus 20 lt~~q~~~L~~l~~~~~~-~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~---~DrR~~~l~lT~ 84 (126)
T COG1846 20 LTPPQYQVLLALYEAGGI-TVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDP---EDRRAVLVRLTE 84 (126)
T ss_pred CCHHHHHHHHHHHHhCCC-cHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc---cccceeeEEECc
Confidence 556667778788777665 33999999999999999999999999999433222 234555554444
No 296
>smart00753 PAM PCI/PINT associated module.
Probab=25.72 E-value=1.3e+02 Score=23.62 Aligned_cols=40 Identities=13% Similarity=0.124 Sum_probs=35.3
Q ss_pred HHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 27 ECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 27 ~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
++.-.+..+++.+|.+..+++...|-..++-+|..|.+..
T Consensus 17 ~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00753 17 QLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEE
Confidence 3334578999999999999999999999999999999974
No 297
>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=25.72 E-value=1.3e+02 Score=23.62 Aligned_cols=40 Identities=13% Similarity=0.124 Sum_probs=35.3
Q ss_pred HHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 27 ECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 27 ~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
++.-.+..+++.+|.+..+++...|-..++-+|..|.+..
T Consensus 17 ~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00088 17 QLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEE
Confidence 3334578999999999999999999999999999999974
No 298
>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=25.58 E-value=96 Score=28.91 Aligned_cols=31 Identities=13% Similarity=0.207 Sum_probs=29.5
Q ss_pred CcHHHHHHhcCCC-HHHHHHHHHHHHhccccc
Q 010353 35 LTRQNVKRYTELS-DEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 35 ltl~~I~~~t~l~-~~~Vr~aL~vLIQhn~V~ 65 (512)
.|+.+|++.++++ ++.|...|-.|.+.|++.
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~ 57 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALERKGYIE 57 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEe
Confidence 6789999999998 999999999999999997
No 299
>PRK03837 transcriptional regulator NanR; Provisional
Probab=25.54 E-value=1.1e+02 Score=29.21 Aligned_cols=36 Identities=17% Similarity=0.190 Sum_probs=32.9
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 383 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 383 ~~l~-eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
|.-+ .|.+|++.-.++..-+|+.|..|..+|+|++.
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 6555 89999999999999999999999999999774
No 300
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=25.54 E-value=5.6e+02 Score=23.92 Aligned_cols=121 Identities=15% Similarity=0.181 Sum_probs=71.0
Q ss_pred HHHHHHHHHhcC-C-CcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhHHHHhchh
Q 010353 22 VAKVCECLLRKG-P-LTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNILHRVRFA 99 (512)
Q Consensus 22 v~~V~~~Ll~~G-~-ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~il~rlR~p 99 (512)
.+.|=.+|+..| + +|+.+|+..++.+......+++-+++.. |..+. .| .--....+-|.+.--|
T Consensus 3 ~~~iEAlLF~sg~pgls~~~La~il~~~~~~~~~~~l~~l~~~----~~~~~-~g---------l~l~~~~~~y~l~tk~ 68 (186)
T TIGR00281 3 KAIIEALLFVSGEPGVTLAELVRILGKEKAEKLNAIMELLEDY----LSRDT-AG---------IEIIKFGQSYSLVTKP 68 (186)
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHhCCCchHHHHHHHHHHHHH----HhcCC-CC---------EEEEEECCEEEEEEhH
Confidence 456667888887 3 9999999999998554444444444332 11110 00 0011112222222333
Q ss_pred hHHHHHHHH-------hhhhHHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 100 KFLTILSQE-------FDQQCVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 100 r~l~~i~~~-------~G~~a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
.|-.+++.. +...+-..+..+..++=+|-.+|-+-= .. .-..++.+|++.|||..+.
T Consensus 69 e~~~~i~~~~~~~~~~LS~aaLEtLAIIAY~QPITr~eIe~IR-Gv----------~s~~~l~~L~ergLI~~~G 132 (186)
T TIGR00281 69 AFADYIHRFLPAKLKNLNSASLEVLAIIAYKQPITRARINEIR-GV----------KSYQIVDDLVEKGLVVELG 132 (186)
T ss_pred HHHHHHHHHhccccccCCHHHHHHHHHHHHcCCcCHHHHHHHc-CC----------CHHHHHHHHHHCCCeEecC
Confidence 333333333 445777888888888888887765431 10 1367899999999998874
No 301
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=25.53 E-value=2.3e+02 Score=27.17 Aligned_cols=64 Identities=17% Similarity=0.205 Sum_probs=47.1
Q ss_pred CCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHHHHHHHHHHHHHHHHHH
Q 010353 383 GRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFHAALNLS 456 (512)
Q Consensus 383 ~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~~k~~~nl~ 456 (512)
.++ ...+|++...++...+-..|-+|-+.|||.-+..|+. +.|++... -..+++..|....+++
T Consensus 20 ~~I-S~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~-------~~v~LTek--G~~ll~~~~~d~~~if 83 (217)
T PRK14165 20 VKI-SSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRG-------QLITITEK--GLDVLYNEYADYSRIF 83 (217)
T ss_pred CCc-CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCc-------eEEEECHH--HHHHHHHHHHHHHHHh
Confidence 345 8999999999999999999999999999966554422 45666533 2445566666665555
No 302
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.41 E-value=2.4e+02 Score=27.13 Aligned_cols=64 Identities=13% Similarity=-0.024 Sum_probs=52.5
Q ss_pred hhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEech
Q 010353 16 NHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLF 89 (512)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~ 89 (512)
.-=|+....|+..+...++.|...|.+..+++...|.-.+--|---|++. -+.. | + .+.|++|.
T Consensus 170 ~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~-~~~~--G------r-~iiy~in~ 233 (240)
T COG3398 170 SLKNETSKAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEELGIIP-EDRE--G------R-SIIYSINP 233 (240)
T ss_pred HhhchhHHHHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcCCCc-cccc--C------c-eEEEEeCH
Confidence 33466778999999999999999999999999999999999999999986 2211 1 2 57888985
No 303
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=25.36 E-value=2.4e+02 Score=26.66 Aligned_cols=32 Identities=19% Similarity=0.251 Sum_probs=29.8
Q ss_pred chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 387 ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 387 eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
..++||+...++...+-..|.+|.++|+|+.+
T Consensus 171 t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 171 KHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred hHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence 78999999999999999999999999999654
No 304
>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=25.23 E-value=2.6e+02 Score=25.31 Aligned_cols=51 Identities=18% Similarity=0.181 Sum_probs=43.1
Q ss_pred HhhhchhHHHHHHHHHhc----C-----------CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 15 TNHFGDLVAKVCECLLRK----G-----------PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 15 ~~~FG~~v~~V~~~Ll~~----G-----------~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.-.+.+.-++|+.+|+.. | ++|-.+|+...|+++..|-.+|--|-+.|++.
T Consensus 109 ~l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 174 (193)
T TIGR03697 109 TLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLIS 174 (193)
T ss_pred HHHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEE
Confidence 345678888999988641 1 46889999999999999999999999999997
No 305
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=25.21 E-value=1.6e+02 Score=21.51 Aligned_cols=33 Identities=21% Similarity=0.335 Sum_probs=22.7
Q ss_pred HHHHHHHHHhcCCCcHHHHHHhcC-CCHHHHHHHHH
Q 010353 22 VAKVCECLLRKGPLTRQNVKRYTE-LSDEQVKNALL 56 (512)
Q Consensus 22 v~~V~~~Ll~~G~ltl~~I~~~t~-l~~~~Vr~aL~ 56 (512)
|..|...+ ..|- |..+|..... |+..+|+.||.
T Consensus 21 v~~i~~~~-~~G~-s~eeI~~~yp~Lt~~~i~aAl~ 54 (56)
T PF04255_consen 21 VRDILDLL-AAGE-SPEEIAEDYPSLTLEDIRAALA 54 (56)
T ss_dssp HHHHHHHH-HTT---HHHHHHHSTT--HHHHHHHHH
T ss_pred HHHHHHHH-HcCC-CHHHHHHHCCCCCHHHHHHHHH
Confidence 56677777 5555 9999988765 99999999985
No 306
>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=24.87 E-value=66 Score=35.42 Aligned_cols=39 Identities=23% Similarity=0.353 Sum_probs=31.5
Q ss_pred HHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhcccccee
Q 010353 29 LLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAF 67 (512)
Q Consensus 29 Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~ 67 (512)
....+.+|+.+|...|+++...++.+|..|++++++...
T Consensus 529 Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~~~l~~~ 567 (588)
T PF00888_consen 529 FNDNDSLTVEEISEKTGISEEELKRALKSLVKSKILILL 567 (588)
T ss_dssp GGSSSEEEHHHHHHHC---HHHHHHHHHCCCTTTTCSEE
T ss_pred HccCCCccHHHHHHHHCcCHHHHHHHHHHHHhCCcceee
Confidence 344678899999999999999999999999999998743
No 307
>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=24.86 E-value=84 Score=22.10 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=14.9
Q ss_pred cHHHHHHhcCCCHHHHHHHH
Q 010353 36 TRQNVKRYTELSDEQVKNAL 55 (512)
Q Consensus 36 tl~~I~~~t~l~~~~Vr~aL 55 (512)
||.+|++..|++...|-.+|
T Consensus 1 Ti~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 67788888888877776654
No 308
>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=24.69 E-value=2.6e+02 Score=22.16 Aligned_cols=55 Identities=20% Similarity=0.213 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHhhhc----hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHH
Q 010353 4 EYGTKHAVHVITNHFG----DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVL 58 (512)
Q Consensus 4 ~~~~~Lc~~iv~~~FG----~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vL 58 (512)
++..+|...+-.-.-+ .+-..+.+.|..-.+.|..+|+..++.+..+|+.+|..+
T Consensus 4 ~l~~~l~~~L~~~~~~~~~~~L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 4 ELATRLAERLTSGNRPGGFAWLLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp TTHHHHHHHHHHHHSSTTHHHHHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred HHHHHHHHHhcCCCCCCccHHHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 4444555555544323 233344455555568999999999999999999999766
No 309
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=24.33 E-value=2.2e+02 Score=22.59 Aligned_cols=43 Identities=16% Similarity=0.117 Sum_probs=36.6
Q ss_pred HHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhcccccccC
Q 010353 117 VQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERCP 167 (512)
Q Consensus 117 v~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv~ 167 (512)
=..|-.||++...+|-..+.. +..-|+.-+..|+..|=|++++
T Consensus 8 Rd~l~~~gr~s~~~Ls~~~~~--------p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 8 RDLLALRGRMEAAQISQTLNT--------PQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHcCcccHHHHHHHHCc--------CHHHHHHHHHHHHHCCCeEeec
Confidence 346778999999999888753 4677999999999999999996
No 310
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=23.71 E-value=2.5e+02 Score=22.43 Aligned_cols=44 Identities=11% Similarity=0.057 Sum_probs=33.2
Q ss_pred cccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccccc
Q 010353 123 HGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 123 ~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
...++.+.|.+.+....++-...+.+.+.+++..|++++.|-..
T Consensus 27 ~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY~t 70 (80)
T PF10264_consen 27 GQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIYHT 70 (80)
T ss_pred CCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCceeeC
Confidence 34456777777776665554455889999999999999998655
No 311
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=23.71 E-value=2.4e+02 Score=21.40 Aligned_cols=48 Identities=10% Similarity=0.144 Sum_probs=43.2
Q ss_pred chhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccce
Q 010353 19 GDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQA 66 (512)
Q Consensus 19 G~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~ 66 (512)
-|+-..++.+.+..|..+..-|.|..++....--..+=.|-+.|+|..
T Consensus 4 D~ly~~a~~~V~~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p 51 (63)
T smart00843 4 DELYDEAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGP 51 (63)
T ss_pred cHHHHHHHHHHHHhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCC
Confidence 356678888999999999999999999999999999999999999973
No 312
>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=23.53 E-value=91 Score=29.81 Aligned_cols=30 Identities=23% Similarity=0.298 Sum_probs=28.4
Q ss_pred cHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 36 TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 36 tl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
|=.+|+...+.+...||+||-.|++.|+|.
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~ 55 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQ 55 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 478999999999999999999999999997
No 313
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.32 E-value=4.8e+02 Score=23.21 Aligned_cols=109 Identities=18% Similarity=0.270 Sum_probs=59.5
Q ss_pred hhc-hhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc-eecccCCCCCCCCCCC-ccEE---Eechh
Q 010353 17 HFG-DLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ-AFTTEQPDGFADGPKA-NTQY---VVLFD 90 (512)
Q Consensus 17 ~FG-~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~-~~~~~~~~~~~~~~~~-~~~Y---~~~~~ 90 (512)
.|| ++-.+++..| +.|..|+++|-+.-|-.. +.||.+|-.-+++. -|-.+. +| +.|.+. +++| ++|..
T Consensus 20 ~~~set~rKl~~aL-stgW~T~~eiee~iG~eg---~RaL~iLkkagmlEtqWr~p~-~G-~kPeKeYHtsYt~VqiNf~ 93 (170)
T COG4860 20 AADSETKRKLLLAL-STGWITLPEIEEKIGKEG---RRALLILKKAGMLETQWRTPS-NG-QKPEKEYHTSYTNVQINFM 93 (170)
T ss_pred HcccHHHHHHHHHH-hhcceeHHHHHHHhchhh---HHHHHHHHhhcchhheeeccC-CC-CCchhhhhhheeeEEEEEE
Confidence 344 4455666666 589999999988766433 34999999999986 233332 22 122222 2333 33433
Q ss_pred hHHHHhchhhHHHHHHHHhh--hhHHHHHHHHHHcccCCHHHHHH
Q 010353 91 NILHRVRFAKFLTILSQEFD--QQCVELVQGLLEHGRLTLKQMFD 133 (512)
Q Consensus 91 ~il~rlR~pr~l~~i~~~~G--~~a~~Iv~~lL~~G~l~~~~li~ 133 (512)
.-+.=| ..+|..+---+. .++..=+..++..|...+.++-.
T Consensus 94 ~Sl~dL--~dii~~~f~sdeev~ey~~ei~~l~e~g~ts~~~vt~ 136 (170)
T COG4860 94 GSLSDL--ADIIYAAFLSDEEVKEYEDEIKALMEEGNTSFLDVTD 136 (170)
T ss_pred EeHHHH--HHHHHHHhCCHHHHHHHHHHHHHHHHcCCceEeehhh
Confidence 322222 233333322222 34555566677777777665443
No 314
>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=23.14 E-value=1.9e+02 Score=20.34 Aligned_cols=30 Identities=17% Similarity=0.114 Sum_probs=20.6
Q ss_pred HHHhcCCCcHHHHHHhcCCCHHHHHHHHHH
Q 010353 28 CLLRKGPLTRQNVKRYTELSDEQVKNALLV 57 (512)
Q Consensus 28 ~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~v 57 (512)
.|..-...|..+|+..++++++.|+..+.-
T Consensus 20 ~l~~~~g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 20 LLRYFQGMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp HHHHTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 344456669999999999999999987653
No 315
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=23.10 E-value=5.5e+02 Score=25.39 Aligned_cols=79 Identities=18% Similarity=0.168 Sum_probs=60.4
Q ss_pred HHHhhhchhHHHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhH
Q 010353 13 VITNHFGDLVAKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (512)
Q Consensus 13 iv~~~FG~~v~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (512)
++.-.|..-..+=.=.|+..|+.|+.+|....+.++..|-.-|-.|.-.|+|. ... -.|++-.-+-
T Consensus 5 ll~~if~SekRk~lLllL~egPkti~EI~~~l~vs~~ai~pqiKkL~~~~LV~--~~~------------~~Y~LS~~G~ 70 (260)
T COG4742 5 LLDLLFLSEKRKDLLLLLKEGPKTIEEIKNELNVSSSAILPQIKKLKDKGLVV--QEG------------DRYSLSSLGK 70 (260)
T ss_pred HHHHHHccHHHHHHHHHHHhCCCCHHHHHHHhCCCcHHHHHHHHHHhhCCCEE--ecC------------CEEEecchHH
Confidence 45556666666666677888999999999999999999999999999999997 222 2688887766
Q ss_pred HHHhchhhHHHHH
Q 010353 93 LHRVRFAKFLTIL 105 (512)
Q Consensus 93 l~rlR~pr~l~~i 105 (512)
+.......++..+
T Consensus 71 iiv~km~~ll~tl 83 (260)
T COG4742 71 IIVEKMEPLLDTL 83 (260)
T ss_pred HHHHHHHHHHHHH
Confidence 6665555555443
No 316
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=22.99 E-value=4.4e+02 Score=24.96 Aligned_cols=40 Identities=23% Similarity=0.296 Sum_probs=34.0
Q ss_pred HhcC-CCcHHHHHHhcCCCHHHHHHHHHHHHhccccceeccc
Q 010353 30 LRKG-PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (512)
Q Consensus 30 l~~G-~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~ 70 (512)
+.-| +++-.+|+...++|..-||.||..|-+-|+|. ..+.
T Consensus 34 l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~-~~p~ 74 (230)
T COG1802 34 LAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVE-IEPN 74 (230)
T ss_pred CCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeE-ecCC
Confidence 3344 78899999999999999999999999999998 4433
No 317
>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=22.91 E-value=2.2e+02 Score=26.04 Aligned_cols=48 Identities=13% Similarity=0.261 Sum_probs=41.7
Q ss_pred hCchHHHHHHHHHhcC-----CCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 010353 368 YGRDAYRIFRLLSKSG-----RLLETDKISDTTFVEKKDAPKILYKLWKDGYL 415 (512)
Q Consensus 368 ~G~~~~Ri~r~l~~~~-----~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v 415 (512)
.|.++.+|+-+|+++- -..++++|++...++...+...+-.|.+.|||
T Consensus 53 ~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI 105 (165)
T PF05732_consen 53 IGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNII 105 (165)
T ss_pred hchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcE
Confidence 5778899999998751 13488999999999999999999999999999
No 318
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=22.88 E-value=2.9e+02 Score=26.33 Aligned_cols=55 Identities=16% Similarity=0.243 Sum_probs=42.2
Q ss_pred HhhhchhHH-HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceeccc
Q 010353 15 TNHFGDLVA-KVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (512)
Q Consensus 15 ~~~FG~~v~-~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~ 70 (512)
-+..|.-.. +|.+.| .+-++-..+|++..|++++.|=.=|-.|-+-|+|..+-..
T Consensus 9 ldvLGNetRR~Il~lL-t~~p~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~ie~ 64 (217)
T COG1777 9 LDVLGNETRRRILQLL-TRRPCYVSEISRELGVSQKAVLKHLRILERAGLVESRIEK 64 (217)
T ss_pred HHHHcCcHHHHHHHHH-hcCchHHHHHHhhcCcCHHHHHHHHHHHHHcCCchhhccc
Confidence 355664444 455555 4555899999999999999999999999999999964433
No 319
>PRK00215 LexA repressor; Validated
Probab=22.79 E-value=1.9e+02 Score=26.99 Aligned_cols=43 Identities=19% Similarity=0.295 Sum_probs=35.4
Q ss_pred HHHHHHHHhcC-CCcHHHHHHhcCC-CHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKG-PLTRQNVKRYTEL-SDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G-~ltl~~I~~~t~l-~~~~Vr~aL~vLIQhn~V~ 65 (512)
..+..+...+| +.|+.+|++.+++ +.+.|..-|-.|.+.|++.
T Consensus 11 ~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~ 55 (205)
T PRK00215 11 DFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIR 55 (205)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 33444444555 4789999999999 9999999999999999997
No 320
>PRK05638 threonine synthase; Validated
Probab=22.78 E-value=2.5e+02 Score=29.92 Aligned_cols=65 Identities=9% Similarity=0.076 Sum_probs=49.4
Q ss_pred hchhHHHHHHHHHhcCCCcHHHHHHhcC--CCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhhH
Q 010353 18 FGDLVAKVCECLLRKGPLTRQNVKRYTE--LSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDNI 92 (512)
Q Consensus 18 FG~~v~~V~~~Ll~~G~ltl~~I~~~t~--l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~i 92 (512)
-|+.--.|...| .+|.++..+|.+..+ ++...|...|-.|-+.|+|...... + + ..+|++....-
T Consensus 369 ~~~~r~~IL~~L-~~~~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~--g------~-~~~Y~Lt~~g~ 435 (442)
T PRK05638 369 IGGTKLEILKIL-SEREMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYRK--G------R-RVYYKLTEKGR 435 (442)
T ss_pred ccchHHHHHHHH-hhCCccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeecC--C------C-cEEEEECcHHH
Confidence 356666677765 477899999999987 8999999999999999999732111 1 1 46899986653
No 321
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=22.74 E-value=2.5e+02 Score=21.48 Aligned_cols=56 Identities=16% Similarity=0.221 Sum_probs=38.1
Q ss_pred hcCCCcHHHHHHh--------cCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEechhh
Q 010353 31 RKGPLTRQNVKRY--------TELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLFDN 91 (512)
Q Consensus 31 ~~G~ltl~~I~~~--------t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~~~ 91 (512)
..|+.+=.+|.+. ..+++..|-.+|-.|.+.|+|........+ ++...+|++...+
T Consensus 6 ~~~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~-----~~~rk~Y~iT~~G 69 (75)
T PF03551_consen 6 SEGPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEGN-----GRPRKYYRITEKG 69 (75)
T ss_dssp HHS-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEETT-----SSEEEEEEESHHH
T ss_pred ccCCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccCC-----CCCCEEEEECHHH
Confidence 3466676666544 347899999999999999999855444222 2335688887543
No 322
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=22.70 E-value=1.1e+02 Score=32.35 Aligned_cols=67 Identities=19% Similarity=0.237 Sum_probs=45.8
Q ss_pred HHHHHH---HhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccceEEEEecCCCCCceEEEEEEehHHHHHHHHHHHHH
Q 010353 374 RIFRLL---SKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYLLMEKLVVTGARQSQFLLWKVNRQILWKHVLDEMFH 450 (512)
Q Consensus 374 Ri~r~l---~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~QEvpk~~~~~~t~~lw~v~~~~~~~~~l~~~~k 450 (512)
.|+..+ .++|+-++.+++++..-+|...++++|.+|.+.|+|. ++... -|....|+++ .-+.++|+
T Consensus 296 ~iL~~l~~~~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~-----~~~~g---~~~l~rd~~~---itL~dv~~ 364 (412)
T PRK04214 296 RLLGRLDQARKHGKALDVDEIRRLEPMGYDELGELLCELARIGLLR-----RGERG---QWVLARDLDS---VPLAELYE 364 (412)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeE-----ecCCC---ceEecCCHHh---CcHHHHHH
Confidence 344444 2345555999999999999999999999999999995 23211 2555555554 34455555
Q ss_pred H
Q 010353 451 A 451 (512)
Q Consensus 451 ~ 451 (512)
+
T Consensus 365 ~ 365 (412)
T PRK04214 365 L 365 (412)
T ss_pred h
Confidence 4
No 323
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.69 E-value=2.3e+02 Score=19.51 Aligned_cols=38 Identities=16% Similarity=0.155 Sum_probs=30.3
Q ss_pred HHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhcccc
Q 010353 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCV 64 (512)
Q Consensus 25 V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V 64 (512)
|+...+ .|. |+.++++..+++.++|..-+-..-.+|..
T Consensus 5 iv~~~~-~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~~ 42 (52)
T PF13518_consen 5 IVELYL-EGE-SVREIAREFGISRSTVYRWIKRYREGGIE 42 (52)
T ss_pred HHHHHH-cCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCHH
Confidence 344444 677 99999999999999998888877777754
No 324
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=22.42 E-value=2.3e+02 Score=26.14 Aligned_cols=53 Identities=30% Similarity=0.372 Sum_probs=42.0
Q ss_pred HHHhhhchhHHHHHHHHHhc-----------C---CCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 13 VITNHFGDLVAKVCECLLRK-----------G---PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 13 iv~~~FG~~v~~V~~~Ll~~-----------G---~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
+..-.+=+..++|+.+|+.. | ++|-.+|+..+|+++..|-.+|--|-+.|++.
T Consensus 133 ~~~~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~ 199 (211)
T PRK11753 133 VGDLAFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQGLIS 199 (211)
T ss_pred HHHHHhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 33344556777888776531 1 67779999999999999999999999999997
No 325
>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=22.37 E-value=1.4e+02 Score=27.33 Aligned_cols=65 Identities=17% Similarity=0.241 Sum_probs=50.0
Q ss_pred hhhchhHHHHHHHHHhcC------CCcHHHHHHhcCCCHHHHHHHHHHHHhccccceecccCCCCCCCCCCCccEEEech
Q 010353 16 NHFGDLVAKVCECLLRKG------PLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTEQPDGFADGPKANTQYVVLF 89 (512)
Q Consensus 16 ~~FG~~v~~V~~~Ll~~G------~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~~~~~~~~~~~~~~~Y~~~~ 89 (512)
+..|.-..+|..+|+.+= -.|..+|+..++++...|..++-.|...+++. ... .-.|.+|+
T Consensus 51 ~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~--k~~-----------~G~Y~iNP 117 (165)
T PF05732_consen 51 DLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIK--KIR-----------NGAYMINP 117 (165)
T ss_pred hhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEE--Ecc-----------CCeEEECc
Confidence 345666778888888652 35788999999999999999999999999886 211 12689998
Q ss_pred hhHH
Q 010353 90 DNIL 93 (512)
Q Consensus 90 ~~il 93 (512)
+-+.
T Consensus 118 ~~~~ 121 (165)
T PF05732_consen 118 NFFF 121 (165)
T ss_pred HHhe
Confidence 7654
No 326
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.16 E-value=2e+02 Score=20.02 Aligned_cols=31 Identities=16% Similarity=0.075 Sum_probs=23.2
Q ss_pred HHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHH
Q 010353 24 KVCECLLRKGPLTRQNVKRYTELSDEQVKNALL 56 (512)
Q Consensus 24 ~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~ 56 (512)
.|...|... .|+.++++.++++...|+..+-
T Consensus 19 ~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 19 YILKLLRES--RSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHH
Confidence 444444333 6999999999999999987653
No 327
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=21.76 E-value=1.3e+02 Score=29.24 Aligned_cols=36 Identities=19% Similarity=0.195 Sum_probs=32.0
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 383 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 383 ~~l~-eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
|.-+ .|.+|++.-.++..-+|+.|..|..+|+|+..
T Consensus 30 G~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~ 66 (257)
T PRK10225 30 GERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVR 66 (257)
T ss_pred CCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 5444 69999999999999999999999999999654
No 328
>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=21.74 E-value=1.5e+02 Score=28.30 Aligned_cols=37 Identities=24% Similarity=0.485 Sum_probs=32.8
Q ss_pred cCCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 382 SGRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 382 ~~~l~-eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
-|.-+ .|.+|++.-.++..-+|+.|..|..+|+|++.
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~ 63 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ 63 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 36555 79999999999999999999999999999654
No 329
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=21.72 E-value=1e+02 Score=30.25 Aligned_cols=42 Identities=19% Similarity=0.188 Sum_probs=39.1
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhhcccc
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWKDGYL 415 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~~g~v 415 (512)
.+|+.+|.++|.+ .-++|++.--++...+|.-|-.|.+.|+|
T Consensus 8 ~~Il~~L~~~~~v-~v~eLa~~l~VS~~TIRRDL~~Le~~g~l 49 (256)
T PRK10434 8 AAILEYLQKQGKT-SVEELAQYFDTTGTTIRKDLVILEHAGTV 49 (256)
T ss_pred HHHHHHHHHcCCE-EHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 4688889888888 99999999999999999999999999987
No 330
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=21.69 E-value=5.9e+02 Score=22.86 Aligned_cols=45 Identities=20% Similarity=0.222 Sum_probs=38.4
Q ss_pred HHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccceeccc
Q 010353 25 VCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQAFTTE 70 (512)
Q Consensus 25 V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~~~~~~ 70 (512)
|....-..|.....+|++..+++|+.|...|--|..-|+|. |.+.
T Consensus 15 Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~-~~~y 59 (154)
T COG1321 15 IYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVE-YEPY 59 (154)
T ss_pred HHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeE-EecC
Confidence 33344478999999999999999999999999999999999 4433
No 331
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=21.50 E-value=1.1e+02 Score=29.46 Aligned_cols=32 Identities=16% Similarity=0.265 Sum_probs=30.0
Q ss_pred CC-cHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 34 PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 34 ~l-tl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++ +-.+|+...+++...||.||..|.+.|+|.
T Consensus 30 ~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~ 62 (251)
T PRK09990 30 ALPSERRLCEKLGFSRSALREGLTVLRGRGIIE 62 (251)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 57 578999999999999999999999999998
No 332
>PHA00738 putative HTH transcription regulator
Probab=21.47 E-value=2.1e+02 Score=24.18 Aligned_cols=46 Identities=13% Similarity=0.103 Sum_probs=36.2
Q ss_pred HHHHHHHHHHcccCCHHHHHHHHhhcccCCCccCHHHHHHHHHHHHhccccccc
Q 010353 113 CVELVQGLLEHGRLTLKQMFDRAKSSEKEGNLVDLDSLRETLVKLVTAHYVERC 166 (512)
Q Consensus 113 a~~Iv~~lL~~G~l~~~~li~~~~~~~~~~~~~~~~~l~~~f~~Lv~~~fi~rv 166 (512)
=..|++.|...|.+++.++.+.+. .+...+...+..|-++|+|..-
T Consensus 14 Rr~IL~lL~~~e~~~V~eLae~l~--------lSQptVS~HLKvLreAGLV~sr 59 (108)
T PHA00738 14 RRKILELIAENYILSASLISHTLL--------LSYTTVLRHLKILNEQGYIELY 59 (108)
T ss_pred HHHHHHHHHHcCCccHHHHHHhhC--------CCHHHHHHHHHHHHHCCceEEE
Confidence 345677777666899999877752 3677899999999999999764
No 333
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=21.42 E-value=1.6e+02 Score=26.41 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=39.4
Q ss_pred hHHHHHHHHHhcCCCcHHHHHHhcCC--------------CHHHHHHHHHHHHhccccc
Q 010353 21 LVAKVCECLLRKGPLTRQNVKRYTEL--------------SDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 21 ~v~~V~~~Ll~~G~ltl~~I~~~t~l--------------~~~~Vr~aL~vLIQhn~V~ 65 (512)
-++.|.+.+--+|+..+..|.+..|. +.+.||.+|-.|-+-++|.
T Consensus 54 R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVe 112 (150)
T PRK09333 54 RAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVE 112 (150)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCee
Confidence 37889999999999999999988765 3356999999999999998
No 334
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=21.17 E-value=1.7e+02 Score=29.68 Aligned_cols=43 Identities=7% Similarity=-0.044 Sum_probs=38.7
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
.+|-..|....+.+..+|++..+++.+.|++.|-.|.+.|++.
T Consensus 7 ~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i 49 (319)
T PRK11886 7 LQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDI 49 (319)
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 4677778777789999999999999999999999999999965
No 335
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=21.12 E-value=1.9e+02 Score=21.41 Aligned_cols=30 Identities=10% Similarity=0.106 Sum_probs=23.8
Q ss_pred HHHHHHHHhcCCCcHHHHHHhcCCCHHHHHH
Q 010353 23 AKVCECLLRKGPLTRQNVKRYTELSDEQVKN 53 (512)
Q Consensus 23 ~~V~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~ 53 (512)
...+..|.-.|- +..+|++.++++.+.|.+
T Consensus 3 k~~A~~LY~~G~-~~~eIA~~Lg~~~~TV~~ 32 (58)
T PF06056_consen 3 KEQARSLYLQGW-SIKEIAEELGVPRSTVYS 32 (58)
T ss_pred HHHHHHHHHcCC-CHHHHHHHHCCChHHHHH
Confidence 345677777766 999999999999888764
No 336
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=20.90 E-value=1.5e+02 Score=28.74 Aligned_cols=36 Identities=25% Similarity=0.278 Sum_probs=32.3
Q ss_pred CCCc-chhhhhhhcCCCcccHHHHHHHHhhcccceEE
Q 010353 383 GRLL-ETDKISDTTFVEKKDAPKILYKLWKDGYLLME 418 (512)
Q Consensus 383 ~~l~-eek~i~~~ami~~k~~r~~Ly~L~~~g~v~~Q 418 (512)
|..+ .|.+|++.-.++..-+|+.|..|..+|+|.+.
T Consensus 23 G~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~ 59 (253)
T PRK10421 23 GMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSR 59 (253)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 5444 69999999999999999999999999999765
No 337
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=20.89 E-value=1.7e+02 Score=20.15 Aligned_cols=29 Identities=24% Similarity=0.381 Sum_probs=19.3
Q ss_pred HHHHHhcCCCcHHHHHHhcCCCHHHHHHHH
Q 010353 26 CECLLRKGPLTRQNVKRYTELSDEQVKNAL 55 (512)
Q Consensus 26 ~~~Ll~~G~ltl~~I~~~t~l~~~~Vr~aL 55 (512)
...|...| .|..+|++..+.+++.|..-|
T Consensus 13 I~~l~~~G-~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 13 IEALLEQG-MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp HHHHHCS----HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHcC-CCHHHHHHHHCcCcHHHHHHH
Confidence 44566677 699999999999999987754
No 338
>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=20.88 E-value=1.2e+02 Score=28.95 Aligned_cols=32 Identities=9% Similarity=0.224 Sum_probs=30.0
Q ss_pred CC-cHHHHHHhcCCCHHHHHHHHHHHHhccccc
Q 010353 34 PL-TRQNVKRYTELSDEQVKNALLVLIQQNCVQ 65 (512)
Q Consensus 34 ~l-tl~~I~~~t~l~~~~Vr~aL~vLIQhn~V~ 65 (512)
++ +-.+|+...|+|..-||.||..|.+-|+|.
T Consensus 29 ~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~ 61 (235)
T TIGR02812 29 ILPAERELSELIGVTRTTLREVLQRLARDGWLT 61 (235)
T ss_pred cCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 67 588999999999999999999999999998
No 339
>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=20.60 E-value=1.5e+02 Score=21.85 Aligned_cols=38 Identities=11% Similarity=0.225 Sum_probs=32.9
Q ss_pred HHHHHHHHhcCCCcchhhhhhhcCCCcccHHHHHHHHhh
Q 010353 373 YRIFRLLSKSGRLLETDKISDTTFVEKKDAPKILYKLWK 411 (512)
Q Consensus 373 ~Ri~r~l~~~~~l~eek~i~~~ami~~k~~r~~Ly~L~~ 411 (512)
.+|+.+|.+++.+ .-++|++...++.+.+|.-+..|-.
T Consensus 8 ~~Ll~~L~~~~~~-~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 8 LKLLELLLKNKWI-TLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHHHHTSB-BHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCC-cHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5688899888788 9999999999999999999988863
No 340
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=20.43 E-value=1.6e+02 Score=21.18 Aligned_cols=21 Identities=14% Similarity=0.311 Sum_probs=17.1
Q ss_pred HHHHHHhcC--CCcHHHHHHhcC
Q 010353 25 VCECLLRKG--PLTRQNVKRYTE 45 (512)
Q Consensus 25 V~~~Ll~~G--~ltl~~I~~~t~ 45 (512)
|++++.++| ++|+.||+..+.
T Consensus 11 I~dii~~~g~~~ls~~eia~~l~ 33 (51)
T PF08100_consen 11 IPDIIHNAGGGPLSLSEIAARLP 33 (51)
T ss_dssp HHHHHHHHTTS-BEHHHHHHTST
T ss_pred cHHHHHHcCCCCCCHHHHHHHcC
Confidence 678888887 999999998766
No 341
>PF01454 MAGE: MAGE family; InterPro: IPR002190 The first mammalian members of the MAGE (melanoma-associated antigen) gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors. However, other members of the family were recently found to be expressed in normal cells, indicating that the family is larger and more disparate than initially expected. MAGE-like genes have also been identified in non-mammalian species, including Drosophila melanogaster (Fruit fly) and Danio rerio (Zebrafish). Although no MAGE homologous sequences have been identified in Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast) or Schizosaccharomyces pombe (Fission yeast), MAGE sequences have been found in several vegetal species, including Arabidopsis thaliana (Mouse-ear cress) []. The only region of homology shared by all of the members of the family is a stretch of about 200 amino acids which has been named the MAGE conserved domain. The MAGE conserved domain is usually located close to the C-terminal, although it can also be found in a more central position in some proteins. The MAGE conserved domain is generally present as a single copy but it is duplicated in some proteins. It has been proposed that the MAGE conserved domain of MAGE-D proteins might interact with p75 neurotrophin or related receptors [].; PDB: 3NW0_B 2WA0_A 1I4F_C.
Probab=20.38 E-value=1.5e+02 Score=27.51 Aligned_cols=58 Identities=16% Similarity=0.375 Sum_probs=25.6
Q ss_pred HHHHHHhcCCCcchhhhhhhcCCCcccHHHHH-HHHhhcccc-eEEEEecCCCCCceEEEEEEehH
Q 010353 375 IFRLLSKSGRLLETDKISDTTFVEKKDAPKIL-YKLWKDGYL-LMEKLVVTGARQSQFLLWKVNRQ 438 (512)
Q Consensus 375 i~r~l~~~~~l~eek~i~~~ami~~k~~r~~L-y~L~~~g~v-~~QEvpk~~~~~~t~~lw~v~~~ 438 (512)
+|+.|..-| + +++. ....... +.++++ ..|.+.||+ ...++|.++ |....|.|.+-+.
T Consensus 126 L~~~L~~lg-i-~~~~--~~~~~g~-~~~~~i~~~~vkq~YL~~~k~~~~~~-~~~~~~~y~~G~R 185 (195)
T PF01454_consen 126 LWKFLRRLG-I-DEDE--KHPILGM-DIKKLILKEFVKQGYLVRYKQVPNSD-PEEYEFSYSWGPR 185 (195)
T ss_dssp HHHHHHHTT----TTS---BTTTB---HHHHHHCHHHHCTSE-EEE-----------EEEE---HH
T ss_pred HHHHHHhcC-C-Cccc--cCccCCC-CHHHHHHHHHHHhcCHHheeecCCCC-CCceEEEeCCcCc
Confidence 555555432 2 3332 3333332 455555 999999999 777788775 5567777987754
Done!